Query         gi|254780945|ref|YP_003065358.1| ATP-dependent DNA helicase RecG [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 700
No_of_seqs    269 out of 3258
Neff          6.5 
Searched_HMMs 39220
Date          Mon May 30 03:32:44 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254780945.hhm -d /home/congqian_1/database/cdd/Cdd.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 COG1200 RecG RecG-like helicas 100.0       0       0 1842.9  62.4  660    1-671     1-663 (677)
  2 PRK10917 ATP-dependent DNA hel 100.0       0       0 1836.0  65.2  659    5-675     2-661 (677)
  3 TIGR00643 recG ATP-dependent D 100.0       0       0 1832.2  50.4  627   36-663     1-721 (721)
  4 TIGR00580 mfd transcription-re 100.0       0       0 1068.2  31.2  412  240-664   476-899 (997)
  5 PRK10689 transcription-repair  100.0       0       0 1045.4  40.2  414  240-664   568-987 (1148)
  6 COG1197 Mfd Transcription-repa 100.0       0       0  981.7  35.7  415  240-665   562-982 (1139)
  7 PRK05580 primosome assembly pr 100.0 1.5E-35 3.9E-40  298.4  30.3  376  268-666   164-627 (699)
  8 COG1198 PriA Primosomal protei 100.0 1.1E-32 2.9E-37  275.9  30.4  393  269-683   195-682 (730)
  9 PRK11192 ATP-dependent RNA hel 100.0 1.6E-26 4.1E-31  227.6  30.6  332  256-614     9-365 (417)
 10 PRK01172 ski2-like helicase; P  99.9 3.2E-24 8.2E-29  209.5  27.3  319  260-599    10-378 (674)
 11 PRK11776 ATP-dependent RNA hel  99.9 1.5E-23 3.9E-28  204.2  29.9  332  256-615    10-361 (459)
 12 PRK11634 ATP-dependent RNA hel  99.9 7.2E-23 1.8E-27  199.0  30.7  331  257-615    13-364 (629)
 13 PRK02362 ski2-like helicase; P  99.9   1E-23 2.6E-28  205.6  25.8  320  261-599    11-397 (736)
 14 PRK10590 ATP-dependent RNA hel  99.9 1.7E-22 4.3E-27  196.0  30.4  320  257-599     8-352 (457)
 15 PTZ00110 helicase; Provisional  99.9 3.9E-22 9.9E-27  193.2  31.0  347  262-631   193-567 (602)
 16 PRK04837 ATP-dependent RNA hel  99.9 2.9E-22 7.5E-27  194.1  29.9  331  255-614    14-374 (423)
 17 TIGR00595 priA primosomal prot  99.9 2.6E-23 6.6E-28  202.4  24.0  318  297-624     1-417 (524)
 18 PRK00254 ski2-like helicase; P  99.9   6E-23 1.5E-27  199.5  24.9  322  260-599    10-387 (717)
 19 PRK13766 Hef nuclease; Provisi  99.9 2.2E-23 5.5E-28  203.0  20.9  312  272-601    15-481 (764)
 20 PRK04537 ATP-dependent RNA hel  99.9   1E-21 2.6E-26  190.0  29.3  317  257-598    16-363 (574)
 21 PRK01297 ATP-dependent RNA hel  99.9   4E-22   1E-26  193.1  26.8  318  258-599    92-439 (472)
 22 COG0513 SrmB Superfamily II DN  99.9   9E-21 2.3E-25  182.5  29.2  320  257-599    36-380 (513)
 23 KOG0344 consensus               99.9 9.9E-25 2.5E-29  213.5   7.9  350  267-640   152-534 (593)
 24 COG4098 comFA Superfamily II D  99.9 4.4E-20 1.1E-24  177.1  24.1  299  271-598    96-416 (441)
 25 PRK11057 ATP-dependent DNA hel  99.9 1.6E-18 4.1E-23  164.8  29.0  309  265-599    17-343 (607)
 26 COG1204 Superfamily II helicas  99.9 6.8E-19 1.7E-23  167.7  24.2  319  258-591    16-398 (766)
 27 COG1111 MPH1 ERCC4-like helica  99.9 2.6E-18 6.7E-23  163.1  25.1  334  274-622    17-509 (542)
 28 PRK13767 ATP-dependent helicas  99.9 4.2E-18 1.1E-22  161.6  26.0  312  265-598    26-397 (878)
 29 COG1061 SSL2 DNA or RNA helica  99.9 2.5E-18 6.3E-23  163.4  24.1  294  267-592    31-383 (442)
 30 COG1203 CRISPR-associated heli  99.8 1.8E-17 4.7E-22  156.6  24.2  324  260-599   183-550 (733)
 31 COG1205 Distinct helicase fami  99.8 1.3E-16 3.4E-21  149.8  25.9  326  256-599    54-422 (851)
 32 KOG0354 consensus               99.8 1.5E-17 3.9E-22  157.1  19.0  329  264-610    54-539 (746)
 33 KOG0952 consensus               99.8 7.4E-16 1.9E-20  144.0  24.1  316  267-598   104-490 (1230)
 34 TIGR03158 cas3_cyano CRISPR-as  99.8 8.2E-17 2.1E-21  151.4  18.7  283  277-584     2-357 (357)
 35 KOG0331 consensus               99.8 5.5E-16 1.4E-20  145.0  21.9  336  272-630   113-482 (519)
 36 pfam00270 DEAD DEAD/DEAH box h  99.8 1.8E-17 4.7E-22  156.5  13.3  151  274-435     1-164 (167)
 37 PRK05298 excinuclease ABC subu  99.8 5.1E-15 1.3E-19  137.4  24.2  309  268-602     9-559 (657)
 38 COG1201 Lhr Lhr-like helicases  99.7 5.4E-15 1.4E-19  137.2  23.9  319  260-597    10-360 (814)
 39 KOG0335 consensus               99.7 8.6E-15 2.2E-19  135.6  23.6  330  272-616    96-461 (482)
 40 KOG0350 consensus               99.7 1.4E-15 3.6E-20  141.8  18.7  332  275-616   162-554 (620)
 41 COG0514 RecQ Superfamily II DN  99.7   1E-14 2.6E-19  135.0  22.9  305  272-600    17-338 (590)
 42 KOG0344 consensus               99.7 8.4E-20 2.1E-24  174.9  -3.9  448   34-573   121-593 (593)
 43 smart00487 DEXDc DEAD-like hel  99.7 3.2E-16 8.2E-21  146.8  13.5  155  268-431     4-171 (201)
 44 cd00079 HELICc Helicase superf  99.7 2.9E-16 7.3E-21  147.2  13.1  129  457-595     1-131 (131)
 45 KOG0348 consensus               99.7 6.7E-15 1.7E-19  136.5  19.0  350  258-626   144-575 (708)
 46 KOG0342 consensus               99.7 8.9E-15 2.3E-19  135.5  19.3  314  261-598    92-436 (543)
 47 KOG0333 consensus               99.7 4.7E-14 1.2E-18  129.8  22.4  321  259-602   254-627 (673)
 48 KOG0345 consensus               99.7 1.3E-13 3.2E-18  126.4  24.2  316  260-598    15-363 (567)
 49 PRK09751 putative ATP-dependen  99.7 4.1E-14 1.1E-18  130.2  21.3  278  302-596     5-382 (1490)
 50 COG1202 Superfamily II helicas  99.7 1.6E-14 4.2E-19  133.4  16.9  315  262-598   205-552 (830)
 51 PRK09694 hypothetical protein;  99.7 2.5E-13 6.4E-18  124.1  22.2  311  270-597   286-682 (878)
 52 cd00046 DEXDc DEAD-like helica  99.6 3.1E-15 7.8E-20  139.1  11.8  131  295-430     2-144 (144)
 53 COG0556 UvrB Helicase subunit   99.6 7.1E-13 1.8E-17  120.6  22.3  195  392-601   329-558 (663)
 54 KOG0343 consensus               99.6 2.7E-13 6.8E-18  123.9  19.7  297  272-599    91-422 (758)
 55 PRK09401 reverse gyrase; Revie  99.6 6.3E-13 1.6E-17  121.0  20.4  283  261-565    67-403 (1176)
 56 PRK11664 ATP-dependent RNA hel  99.6 2.4E-12 6.1E-17  116.4  22.9  293  279-598     8-338 (812)
 57 KOG0334 consensus               99.6 1.2E-11   3E-16  111.0  25.9  372  260-677   375-799 (997)
 58 KOG4284 consensus               99.6 1.2E-13   3E-18  126.7  14.2  321  272-611    47-388 (980)
 59 KOG0339 consensus               99.6 5.6E-12 1.4E-16  113.5  22.7  332  258-615   231-591 (731)
 60 KOG0328 consensus               99.6 7.1E-13 1.8E-17  120.6  16.5  305  260-597    37-371 (400)
 61 KOG0330 consensus               99.6 3.1E-12   8E-17  115.5  19.7  323  255-611    66-418 (476)
 62 KOG0338 consensus               99.5 7.5E-12 1.9E-16  112.5  21.4  322  265-616   195-546 (691)
 63 COG4581 Superfamily II RNA hel  99.5 1.6E-12 4.1E-17  117.8  17.6  318  262-601   109-539 (1041)
 64 COG1110 Reverse gyrase [DNA re  99.5 6.4E-12 1.6E-16  113.1  20.6  281  260-566    70-412 (1187)
 65 TIGR00631 uvrb excinuclease AB  99.5 6.8E-12 1.7E-16  112.9  19.8  305  270-602     7-560 (667)
 66 KOG0951 consensus               99.5 1.4E-12 3.5E-17  118.3  15.3  305  277-597   306-700 (1674)
 67 KOG0347 consensus               99.5 1.9E-12 4.9E-17  117.2  15.7  371  263-670   193-642 (731)
 68 KOG0326 consensus               99.5 4.1E-12 1.1E-16  114.6  17.1  293  267-596   114-426 (459)
 69 KOG0336 consensus               99.5 2.5E-11 6.5E-16  108.4  18.8  292  297-615   254-588 (629)
 70 KOG0332 consensus               99.5 4.3E-11 1.1E-15  106.6  19.5  313  274-612   114-453 (477)
 71 cd00268 DEADc DEAD-box helicas  99.5 7.7E-12   2E-16  112.4  15.5  167  256-433     5-187 (203)
 72 TIGR01587 cas3_core CRISPR-ass  99.4 2.6E-12 6.7E-17  116.1  12.1  288  297-599     3-393 (424)
 73 KOG0340 consensus               99.4 4.1E-10   1E-14   98.9  22.7  319  260-613    16-371 (442)
 74 cd04488 RecG_wedge_OBF RecG_we  99.4 3.5E-12 8.9E-17  115.1  11.7   74   71-145     1-74  (75)
 75 KOG0327 consensus               99.4 7.4E-11 1.9E-15  104.7  18.3  293  269-596    44-367 (397)
 76 KOG0351 consensus               99.4 6.3E-10 1.6E-14   97.4  21.8  319  273-622   265-612 (941)
 77 TIGR01054 rgy reverse gyrase;   99.3 6.3E-10 1.6E-14   97.4  19.2  281  260-561    72-436 (1843)
 78 KOG0346 consensus               99.3 8.1E-10 2.1E-14   96.6  18.8  322  264-611    32-421 (569)
 79 PRK11131 ATP-dependent RNA hel  99.3 5.6E-09 1.4E-13   90.0  21.8  288  282-598    80-410 (1295)
 80 PRK04914 ATP-dependent helicas  99.3 2.1E-10 5.4E-15  101.1  14.4  318  272-618   151-629 (955)
 81 KOG0337 consensus               99.3   5E-10 1.3E-14   98.2  16.1  315  256-596    27-365 (529)
 82 KOG0950 consensus               99.3 4.2E-10 1.1E-14   98.8  14.6  314  275-599   215-611 (1008)
 83 PRK11448 hsdR type I restricti  99.2 2.9E-09 7.3E-14   92.3  17.9  299  270-598   414-816 (1126)
 84 KOG0341 consensus               99.2 1.7E-10 4.4E-15  101.8  10.7  284  301-611   215-540 (610)
 85 KOG0352 consensus               99.2 1.8E-08 4.6E-13   86.0  20.0  313  274-632    22-383 (641)
 86 pfam04851 ResIII Type III rest  99.2 1.2E-10 3.2E-15  103.0   8.6  100  271-431     2-102 (103)
 87 PRK12903 secA preprotein trans  99.2 4.8E-09 1.2E-13   90.5  16.4  279  301-599    99-539 (885)
 88 smart00490 HELICc helicase sup  99.2   1E-10 2.7E-15  103.6   7.9   79  507-587     4-82  (82)
 89 pfam00271 Helicase_C Helicase   99.1 1.6E-10 4.1E-15  102.1   7.6   73  514-587     6-78  (78)
 90 KOG0947 consensus               99.1 4.7E-08 1.2E-12   82.7  20.2  357  260-639   285-780 (1248)
 91 PRK12906 secA preprotein trans  99.1 7.4E-09 1.9E-13   89.0  13.8  280  301-597   101-580 (823)
 92 KOG0948 consensus               99.1 1.8E-09 4.6E-14   93.8  10.5  328  266-622   123-564 (1041)
 93 PRK12326 preprotein translocas  99.1 1.6E-08 4.1E-13   86.4  15.2  287  296-599   100-558 (775)
 94 PRK09200 preprotein translocas  99.1   5E-08 1.3E-12   82.5  17.4  278  301-598    99-544 (799)
 95 PRK12904 preprotein translocas  99.1 2.9E-08 7.5E-13   84.3  16.2  281  301-598   102-571 (833)
 96 COG1643 HrpA HrpA-like helicas  99.1 2.1E-07 5.3E-12   77.7  20.2  306  261-598    41-386 (845)
 97 CHL00122 secA preprotein trans  99.0   7E-08 1.8E-12   81.4  17.3  242  301-557    97-490 (891)
 98 PRK13103 secA preprotein trans  99.0 6.2E-08 1.6E-12   81.8  15.1   96  301-402   103-210 (913)
 99 PRK08074 bifunctional ATP-depe  99.0 4.6E-06 1.2E-10   67.2  24.4  134  270-406   256-468 (932)
100 PRK12898 secA preprotein trans  99.0 8.8E-08 2.2E-12   80.6  15.6  280  301-598   139-600 (673)
101 TIGR00614 recQ_fam ATP-depende  98.9 3.1E-06   8E-11   68.4  22.1  317  274-617    13-364 (497)
102 PRK13104 secA preprotein trans  98.9 2.8E-07 7.2E-12   76.6  16.6   96  301-402   103-210 (896)
103 PRK12902 secA preprotein trans  98.9 1.2E-07 3.2E-12   79.4  13.9   96  301-402   106-213 (946)
104 PRK12900 secA preprotein trans  98.9 6.1E-07 1.6E-11   74.0  16.9  163  421-598   490-666 (983)
105 PRK12899 secA preprotein trans  98.8 8.6E-07 2.2E-11   72.9  15.6   79  301-385   115-193 (969)
106 TIGR01389 recQ ATP-dependent D  98.8   3E-07 7.6E-12   76.4  13.1  300  274-599    15-333 (607)
107 PRK13107 preprotein translocas  98.7 1.8E-06 4.7E-11   70.2  16.1   96  301-402   103-210 (908)
108 PRK12901 secA preprotein trans  98.7   3E-06 7.8E-11   68.5  16.2   96  301-402   192-300 (1111)
109 KOG0920 consensus               98.7 3.1E-07   8E-12   76.3  10.2  309  260-598   163-543 (924)
110 COG4096 HsdR Type I site-speci  98.6 4.8E-06 1.2E-10   67.0  15.8  295  272-585   165-524 (875)
111 KOG0922 consensus               98.6   1E-05 2.7E-10   64.3  17.0  300  267-598    48-389 (674)
112 KOG0349 consensus               98.6 1.5E-06 3.9E-11   70.9  12.1  302  314-652   279-696 (725)
113 pfam00176 SNF2_N SNF2 family N  98.6 1.8E-06 4.6E-11   70.3  12.0  145  295-445    18-171 (295)
114 PRK10917 ATP-dependent DNA hel  98.6 7.8E-07   2E-11   73.2  10.2  120  309-431   455-586 (677)
115 COG4889 Predicted helicase [Ge  98.5 2.2E-05 5.6E-10   61.8  16.7  352  269-636   158-636 (1518)
116 COG0653 SecA Preprotein transl  98.5   2E-05 5.1E-10   62.1  14.9  110  281-402    87-208 (822)
117 KOG0953 consensus               98.4 5.4E-05 1.4E-09   58.8  16.2  276  266-587   158-462 (700)
118 PRK07246 bifunctional ATP-depe  98.4 0.00044 1.1E-08   51.6  23.4  137  268-407   241-449 (820)
119 COG1200 RecG RecG-like helicas  98.4 3.4E-06 8.6E-11   68.2   9.2  116  313-431   465-592 (677)
120 KOG0385 consensus               98.4 0.00033 8.5E-09   52.5  19.3  361  273-643   168-659 (971)
121 pfam07517 SecA_DEAD SecA DEAD-  98.3   3E-06 7.8E-11   68.5   7.7  102  295-402    92-205 (381)
122 PRK13480 3'-5' exoribonuclease  98.2 3.8E-05 9.6E-10   60.0  12.0   88   59-147     3-91  (314)
123 KOG0387 consensus               98.2 1.6E-05 4.1E-10   62.9   9.6  318  275-603   208-663 (923)
124 TIGR00643 recG ATP-dependent D  98.2 1.1E-05 2.9E-10   64.1   8.8  122  471-600   345-473 (721)
125 KOG0353 consensus               98.2 0.00044 1.1E-08   51.6  16.7  366  275-669    97-556 (695)
126 KOG0329 consensus               98.2 1.7E-05 4.2E-10   62.8   9.4  282  270-625    61-375 (387)
127 pfam01336 tRNA_anti OB-fold nu  98.2 3.6E-05 9.2E-10   60.1  10.3   73   70-145     1-74  (75)
128 PRK11747 dinG ATP-dependent DN  98.1 9.5E-05 2.4E-09   56.8  12.0   84  468-563   520-607 (697)
129 KOG0951 consensus               98.1  0.0013 3.2E-08   48.0  17.1  280  295-599  1161-1494(1674)
130 TIGR01970 DEAH_box_HrpB ATP-de  98.1 0.00031 7.9E-09   52.8  13.9  322  281-648     7-386 (858)
131 pfam07652 Flavi_DEAD Flaviviru  98.0 5.9E-05 1.5E-09   58.5   8.6  119  297-430     6-134 (146)
132 PRK10689 transcription-repair   97.9 0.00012   3E-09   56.1   9.6  107  467-581   634-744 (1148)
133 KOG0924 consensus               97.9  0.0021 5.4E-08   46.3  16.0  271  296-598   374-696 (1042)
134 TIGR00963 secA preprotein tran  97.9   5E-05 1.3E-09   59.0   7.4  138  297-451    72-253 (904)
135 KOG0923 consensus               97.9 0.00087 2.2E-08   49.3  13.5  346  296-674   283-674 (902)
136 TIGR01054 rgy reverse gyrase;   97.9 2.7E-05 6.9E-10   61.1   5.6  308  256-579   309-685 (1843)
137 KOG0390 consensus               97.9  0.0046 1.2E-07   43.6  22.2  330  270-607   236-716 (776)
138 TIGR01407 dinG_rel DnaQ family  97.8 0.00058 1.5E-08   50.6  11.2  155  253-407   229-475 (944)
139 COG0610 Type I site-specific r  97.7  0.0072 1.8E-07   42.1  21.1  330  276-615   252-667 (962)
140 PRK12366 replication factor A;  97.7 0.00068 1.7E-08   50.1   9.9   99   43-142    48-155 (649)
141 PRK07373 DNA polymerase III su  97.7   0.001 2.6E-08   48.8  10.5   93  424-526   247-342 (447)
142 KOG0389 consensus               97.7 0.00042 1.1E-08   51.8   8.6  330  270-608   397-897 (941)
143 COG1197 Mfd Transcription-repa  97.6 0.00069 1.8E-08   50.1   9.2  120  466-600   627-753 (1139)
144 smart00489 DEXDc3 DEAD-like he  97.6   0.002 5.2E-08   46.4  11.6   76  268-345     4-85  (289)
145 smart00488 DEXDc2 DEAD-like he  97.6   0.002 5.2E-08   46.4  11.6   76  268-345     4-85  (289)
146 PRK07279 dnaE DNA polymerase I  97.6  0.0016   4E-08   47.3  10.8   61  508-579   696-758 (1033)
147 PRK07012 consensus              97.6  0.0014 3.6E-08   47.6  10.5   67  508-580   767-843 (1173)
148 PRK05580 primosome assembly pr  97.6  0.0004   1E-08   51.9   7.6   72  327-401   455-528 (699)
149 KOG0925 consensus               97.6  0.0081 2.1E-07   41.7  14.3  278  288-599    59-387 (699)
150 PRK07374 dnaE DNA polymerase I  97.6  0.0014 3.7E-08   47.6  10.3   81  508-594   775-867 (1171)
151 TIGR00580 mfd transcription-re  97.6 0.00051 1.3E-08   51.1   7.9  117  469-600   544-671 (997)
152 PRK07892 consensus              97.5   0.003 7.7E-08   45.0  11.3   83  508-596   794-888 (1180)
153 PRK06826 dnaE DNA polymerase I  97.5  0.0072 1.8E-07   42.1  13.1   82  508-595   769-862 (1157)
154 PRK05673 dnaE DNA polymerase I  97.4  0.0072 1.8E-07   42.1  12.6   67  508-580   763-832 (1143)
155 PRK05672 dnaE2 error-prone DNA  97.4  0.0036 9.1E-08   44.5  10.6  106  508-620   751-872 (1050)
156 PRK06658 consensus              97.3  0.0061 1.5E-07   42.7  10.9  127  508-640   762-919 (1145)
157 TIGR03117 cas_csf4 CRISPR-asso  97.3  0.0046 1.2E-07   43.6  10.0  165  469-668   456-634 (636)
158 PRK09401 reverse gyrase; Revie  97.3 0.00075 1.9E-08   49.8   6.0  106  258-385   280-385 (1176)
159 KOG1803 consensus               97.2   0.022 5.6E-07   38.3  13.1   68  262-334   175-242 (649)
160 COG1110 Reverse gyrase [DNA re  97.2  0.0012 3.1E-08   48.1   6.3  370  258-679   289-753 (1187)
161 pfam09848 DUF2075 Uncharacteri  97.2  0.0013 3.4E-08   47.8   6.5   85  296-406     4-91  (348)
162 COG1198 PriA Primosomal protei  97.2  0.0021 5.4E-08   46.2   7.5  111  332-445   491-618 (730)
163 PRK09074 consensus              97.2  0.0076 1.9E-07   41.9  10.3  134  508-648   771-935 (1149)
164 PRK06637 consensus              97.2   0.011 2.8E-07   40.6  11.0   39  508-546   771-812 (1182)
165 PRK06920 dnaE DNA polymerase I  97.2  0.0069 1.8E-07   42.2   9.9   68  508-581   742-812 (1107)
166 PRK07211 replication factor A;  97.2  0.0042 1.1E-07   43.9   8.7   91   54-144    49-148 (473)
167 cd04492 YhaM_OBF_like YhaM_OBF  97.1  0.0069 1.8E-07   42.2   9.2   70   78-148     8-78  (83)
168 PRK08957 consensus              97.1  0.0078   2E-07   41.8   9.3   68  508-581   772-843 (1159)
169 PRK06461 single-stranded DNA-b  97.0  0.0081 2.1E-07   41.7   9.3  103   57-163     3-119 (130)
170 cd04485 DnaE_OBF DnaE_OBF: A s  97.0    0.01 2.6E-07   40.9   9.5   72   71-142     1-73  (84)
171 PRK06326 consensus              97.0   0.025 6.3E-07   37.9  11.3   81  508-594   810-902 (1240)
172 cd00079 HELICc Helicase superf  97.0  0.0059 1.5E-07   42.8   8.0   85  315-404    22-106 (131)
173 TIGR00348 hsdR type I site-spe  96.9  0.0036 9.1E-08   44.5   6.8  194  240-446   268-506 (813)
174 KOG0384 consensus               96.9   0.042 1.1E-06   36.1  11.9  324  272-606   370-819 (1373)
175 PRK11192 ATP-dependent RNA hel  96.9  0.0052 1.3E-07   43.2   7.1   87  309-400   235-321 (417)
176 PRK09183 transposase/IS protei  96.9  0.0041   1E-07   44.0   6.6  129  193-335    11-143 (258)
177 PRK08181 transposase; Validate  96.9   0.014 3.4E-07   39.9   9.1  131  192-335    14-148 (269)
178 KOG0386 consensus               96.8  0.0039   1E-07   44.1   6.3  291  295-599   415-839 (1157)
179 PRK04537 ATP-dependent RNA hel  96.8   0.011 2.9E-07   40.5   8.4   78  318-400   254-331 (574)
180 PRK04837 ATP-dependent RNA hel  96.8  0.0089 2.3E-07   41.4   7.7   77  319-400   254-330 (423)
181 smart00490 HELICc helicase sup  96.7  0.0028 7.1E-08   45.3   4.9   63  340-403     2-64  (82)
182 PRK10590 ATP-dependent RNA hel  96.7   0.015 3.7E-07   39.7   8.2   84  312-400   236-319 (457)
183 pfam00271 Helicase_C Helicase   96.6  0.0046 1.2E-07   43.6   5.3   59  344-403     2-60  (78)
184 PRK06526 transposase; Provisio  96.6   0.031   8E-07   37.1   9.5  130  192-335     7-140 (254)
185 PRK08116 hypothetical protein;  96.6  0.0067 1.7E-07   42.3   6.1   65  271-335    81-150 (262)
186 PRK11634 ATP-dependent RNA hel  96.6   0.011 2.9E-07   40.5   7.2   98  308-411   233-338 (629)
187 cd04478 RPA2_DBD_D RPA2_DBD_D:  96.5   0.027 6.9E-07   37.6   8.8   69   70-142     2-73  (95)
188 COG1199 DinG Rad3-related DNA   96.5   0.012 2.9E-07   40.5   6.7  170  420-601   403-619 (654)
189 PRK05298 excinuclease ABC subu  96.5   0.016   4E-07   39.4   7.4   89  314-407   439-527 (657)
190 cd00009 AAA The AAA+ (ATPases   96.5   0.014 3.5E-07   39.9   7.0   54  276-329     2-55  (151)
191 PRK08512 consensus              96.4   0.047 1.2E-06   35.7   9.5   81  508-594   788-883 (1185)
192 KOG1123 consensus               96.4   0.014 3.6E-07   39.8   6.8  339  273-662   303-707 (776)
193 PTZ00110 helicase; Provisional  96.4   0.031 7.9E-07   37.1   8.6   68  409-492   297-370 (602)
194 cd03524 RPA2_OBF_family RPA2_O  96.4   0.052 1.3E-06   35.4   9.6   68   72-140     2-70  (75)
195 PRK08533 flagellar accessory p  96.4  0.0082 2.1E-07   41.6   5.4   48  282-329    11-60  (230)
196 cd04489 ExoVII_LU_OBF ExoVII_L  96.4   0.031 7.8E-07   37.1   8.3   70   70-142     2-73  (78)
197 pfam02562 PhoH PhoH-like prote  96.4    0.12 3.1E-06   32.5  12.6  139  272-426     4-152 (205)
198 PRK11776 ATP-dependent RNA hel  96.4   0.036 9.2E-07   36.6   8.5   95  312-411   233-335 (459)
199 COG1107 Archaea-specific RecJ-  96.3   0.084 2.1E-06   33.7  10.3  103   56-182   203-307 (715)
200 KOG0392 consensus               96.3    0.13 3.2E-06   32.3  14.9  311  290-611   991-1469(1549)
201 PRK00286 xseA exodeoxyribonucl  96.3   0.044 1.1E-06   35.9   8.8  160   37-210     4-189 (443)
202 PRK01216 DNA polymerase IV; Va  96.3  0.0028   7E-08   45.4   2.6   65  279-357   123-187 (351)
203 PRK00448 polC DNA polymerase I  96.2    0.12   3E-06   32.6  10.6   86   54-139   220-311 (1436)
204 cd04484 polC_OBF polC_OBF: A s  96.2   0.083 2.1E-06   33.8   9.8   66   69-134     1-68  (82)
205 KOG0949 consensus               96.2   0.013 3.3E-07   40.1   5.6   81  517-597   964-1046(1330)
206 COG1570 XseA Exonuclease VII,   96.2   0.045 1.2E-06   35.8   8.3   73   68-143    24-98  (440)
207 PRK08744 consensus              96.2    0.09 2.3E-06   33.5   9.8  127  508-640   787-945 (1195)
208 COG0513 SrmB Superfamily II DN  96.2   0.035   9E-07   36.7   7.7   72  323-399   275-346 (513)
209 smart00382 AAA ATPases associa  96.2    0.03 7.6E-07   37.2   7.3  117  295-436     4-135 (148)
210 PRK07211 replication factor A;  96.1   0.059 1.5E-06   34.9   8.7  107   58-165   162-279 (473)
211 COG0553 HepA Superfamily II DN  96.1  0.0062 1.6E-07   42.6   3.6  317  271-594   337-815 (866)
212 cd04474 RPA1_DBD_A RPA1_DBD_A:  96.1   0.045 1.1E-06   35.8   7.8   84   60-144     1-93  (104)
213 cd04491 SoSSB_OBF SoSSB_OBF: A  96.1   0.059 1.5E-06   34.9   8.4   67   71-140     1-73  (82)
214 COG0556 UvrB Helicase subunit   96.0   0.039   1E-06   36.3   7.3  127  270-407   398-527 (663)
215 PRK12366 replication factor A;  96.0   0.097 2.5E-06   33.2   9.1   87   57-146   174-267 (649)
216 PRK07952 DNA replication prote  96.0   0.038 9.8E-07   36.4   7.0   97  272-410    73-172 (242)
217 cd01700 Pol_V Pol V was discov  95.9  0.0062 1.6E-07   42.6   2.8   18  276-293   137-154 (344)
218 COG4098 comFA Superfamily II D  95.9   0.048 1.2E-06   35.6   7.4   93  317-416   301-393 (441)
219 PRK01297 ATP-dependent RNA hel  95.9   0.025 6.3E-07   37.9   5.9   75  321-400   332-406 (472)
220 TIGR01448 recD_rel helicase, R  95.9   0.059 1.5E-06   34.9   7.8  116  261-410   339-468 (769)
221 PRK03348 DNA polymerase IV; Pr  95.9  0.0057 1.5E-07   42.9   2.5   17  518-534   336-352 (456)
222 KOG1000 consensus               95.9   0.054 1.4E-06   35.2   7.5  326  267-617   198-626 (689)
223 PRK02406 DNA polymerase IV; Va  95.8  0.0068 1.7E-07   42.3   2.8   40  301-352   145-184 (355)
224 KOG1802 consensus               95.8   0.036 9.1E-07   36.6   6.4   80  268-358   407-487 (935)
225 cd04483 hOBFC1_like hOBFC1_lik  95.8    0.11 2.8E-06   32.8   8.9   67   72-142     2-88  (92)
226 cd01701 Pol_zeta Pol_zeta, a m  95.8  0.0064 1.6E-07   42.5   2.5   15  403-417   261-275 (405)
227 PRK06835 DNA replication prote  95.7   0.042 1.1E-06   36.1   6.3   48  287-335   178-225 (330)
228 PRK06921 hypothetical protein;  95.7   0.061 1.6E-06   34.8   7.1   53  283-335   103-159 (265)
229 COG3267 ExeA Type II secretory  95.6   0.027 6.9E-07   37.6   5.2   54  273-329    32-86  (269)
230 KOG4150 consensus               95.6   0.088 2.2E-06   33.6   7.8  286  302-598   310-639 (1034)
231 TIGR02621 cas3_GSU0051 CRISPR-  95.6   0.013 3.4E-07   40.0   3.6  282  302-597    41-432 (975)
232 PRK04036 DNA polymerase II sma  95.6    0.18 4.5E-06   31.2   9.3  103   38-143   106-224 (497)
233 TIGR00631 uvrb excinuclease AB  95.6   0.019 4.9E-07   38.7   4.3   81  314-399   440-520 (667)
234 cd01124 KaiC KaiC is a circadi  95.6   0.052 1.3E-06   35.4   6.5   48  296-344     2-49  (187)
235 KOG1805 consensus               95.5    0.26 6.6E-06   29.9  10.9   51   92-144   127-184 (1100)
236 COG5235 RFA2 Single-stranded D  95.5   0.083 2.1E-06   33.8   7.4   72   68-144    67-141 (258)
237 PRK03103 DNA polymerase IV; Re  95.5   0.011 2.8E-07   40.6   2.8   15  574-588   372-386 (410)
238 PRK00440 rfc replication facto  95.5    0.19 4.9E-06   30.9   9.1  204  276-541    20-241 (318)
239 COG2176 PolC DNA polymerase II  95.5    0.27 6.8E-06   29.8   9.8   94   49-142   220-319 (1444)
240 PRK02794 DNA polymerase IV; Pr  95.5   0.011 2.8E-07   40.6   2.7   14  341-354   202-215 (417)
241 TIGR00150 TIGR00150 conserved   95.5   0.031   8E-07   37.1   5.0   60  274-336     6-68  (147)
242 PRK13767 ATP-dependent helicas  95.4    0.14 3.6E-06   32.0   8.3   87  313-400   276-364 (878)
243 TIGR00617 rpa1 replication fac  95.4   0.045 1.1E-06   35.9   5.7  120   49-171   205-333 (671)
244 pfam01695 IstB IstB-like ATP b  95.4   0.034 8.6E-07   36.8   4.9   61  272-335    29-89  (178)
245 PRK08939 primosomal protein Dn  95.3    0.17 4.4E-06   31.2   8.5   71  271-346   130-205 (306)
246 PRK03352 DNA polymerase IV; Va  95.3   0.014 3.5E-07   39.9   2.8   17  403-419   213-231 (345)
247 cd04490 PolII_SU_OBF PolII_SU_  95.3    0.19 4.8E-06   31.0   8.6   71   69-142     1-76  (79)
248 KOG0333 consensus               95.3   0.081 2.1E-06   33.8   6.6   89  322-411   493-610 (673)
249 PRK03858 DNA polymerase IV; Va  95.2   0.014 3.6E-07   39.8   2.6   12  576-587   367-378 (398)
250 PRK11773 uvrD DNA-dependent he  95.1   0.099 2.5E-06   33.2   6.6   49  605-660   595-645 (722)
251 PRK12377 putative replication   95.0    0.11 2.9E-06   32.7   6.7   62  273-335    79-143 (248)
252 COG4085 Predicted RNA-binding   95.0    0.29 7.5E-06   29.4   8.7   73   65-139    49-126 (204)
253 COG1061 SSL2 DNA or RNA helica  94.9   0.096 2.4E-06   33.3   6.2   76  320-401   282-357 (442)
254 PRK13342 recombination factor   94.9    0.13 3.4E-06   32.1   6.9  108  276-429    17-127 (417)
255 KOG0391 consensus               94.8    0.22 5.6E-06   30.4   7.8  120  515-636  1300-1429(1958)
256 cd03586 Pol_IV_kappa Pol_IV_ka  94.8   0.023 5.9E-07   38.1   2.8   11  341-351   165-175 (337)
257 TIGR03015 pepcterm_ATPase puta  94.8   0.081 2.1E-06   33.8   5.5  177  272-482    23-208 (269)
258 pfam03796 DnaB_C DnaB-like hel  94.8   0.096 2.5E-06   33.2   5.9   84  280-367     8-92  (186)
259 COG1484 DnaC DNA replication p  94.7    0.17 4.4E-06   31.3   6.9   61  272-334    86-146 (254)
260 pfam04466 Terminase_3 Phage te  94.6    0.44 1.1E-05   28.0   9.0  131  295-433     4-141 (387)
261 pfam00580 UvrD-helicase UvrD/R  94.6     0.1 2.6E-06   33.0   5.7   21  395-415   213-233 (494)
262 COG3587 Restriction endonuclea  94.6   0.053 1.4E-06   35.3   4.2   15  430-444   593-607 (985)
263 PRK09361 radB DNA repair and r  94.6    0.24 6.2E-06   30.1   7.5   48  283-331    11-60  (224)
264 cd01702 Pol_eta Pol eta is mem  94.5   0.029 7.4E-07   37.3   2.8   18  340-357   174-191 (358)
265 PRK00652 lpxK tetraacyldisacch  94.5    0.47 1.2E-05   27.8  11.0  205  303-549    61-291 (334)
266 COG3973 Superfamily I DNA and   94.4   0.085 2.2E-06   33.7   4.9  368  282-669   218-653 (747)
267 PRK03609 umuC DNA polymerase V  94.3   0.026 6.6E-07   37.7   2.1   10  507-516   377-386 (422)
268 PRK12727 flagellar biosynthesi  94.3    0.52 1.3E-05   27.5  13.9  223  255-513   302-543 (557)
269 PRK07135 dnaE DNA polymerase I  94.3    0.53 1.3E-05   27.4   9.0   66  508-579   695-763 (987)
270 KOG3108 consensus               94.3    0.39   1E-05   28.5   8.0   88   69-161    70-161 (265)
271 COG0587 DnaE DNA polymerase II  94.3    0.53 1.4E-05   27.4   9.3  129  508-642   762-919 (1139)
272 PRK07217 replication factor A;  94.3    0.53 1.4E-05   27.4   8.9   82   54-139    67-150 (311)
273 cd00424 Pol_Y Y-family of DNA   94.2   0.037 9.4E-07   36.5   2.7   19  403-421   210-229 (341)
274 PRK06067 flagellar accessory p  94.1   0.095 2.4E-06   33.3   4.6   57  283-340    20-78  (241)
275 TIGR00595 priA primosomal prot  94.0    0.26 6.5E-06   29.9   6.6  126  323-451   273-416 (524)
276 PRK09694 hypothetical protein;  93.9    0.53 1.4E-05   27.4   8.1   99  311-413   551-664 (878)
277 PRK08402 replication factor A;  93.8    0.49 1.2E-05   27.7   7.8  108   16-138    34-153 (357)
278 TIGR03117 cas_csf4 CRISPR-asso  93.7    0.66 1.7E-05   26.7   8.8   80  277-358     2-86  (636)
279 smart00487 DEXDc DEAD-like hel  93.6    0.69 1.8E-05   26.6  10.3  115  474-600    44-171 (201)
280 PRK06386 replication factor A;  93.3    0.76 1.9E-05   26.2   8.9   77   58-139     2-84  (358)
281 PRK00484 lysS lysyl-tRNA synth  93.3    0.77   2E-05   26.2  12.6   97   46-147    23-134 (491)
282 COG5271 MDN1 AAA ATPase contai  93.2     0.7 1.8E-05   26.5   7.7   37  271-309  1830-1866(4600)
283 PRK04328 hypothetical protein;  93.2    0.19 4.9E-06   30.9   4.9   54  289-343    18-73  (250)
284 pfam00270 DEAD DEAD/DEAH box h  93.1    0.45 1.2E-05   28.0   6.7   80  481-572    44-132 (167)
285 PRK05159 aspC aspartyl-tRNA sy  93.0    0.83 2.1E-05   25.9  10.6   86   57-147     6-99  (434)
286 COG1444 Predicted P-loop ATPas  93.0     0.6 1.5E-05   27.0   7.2  272  272-589   211-513 (758)
287 pfam03354 Terminase_1 Phage Te  92.9    0.27 6.9E-06   29.8   5.3  140  297-440    26-174 (473)
288 TIGR02928 TIGR02928 orc1/cdc6   92.9     0.2 5.2E-06   30.7   4.7  143  275-448    23-182 (383)
289 PRK11057 ATP-dependent DNA hel  92.9    0.87 2.2E-05   25.7  11.0   76  319-399   234-309 (607)
290 cd01122 GP4d_helicase GP4d_hel  92.9    0.55 1.4E-05   27.3   6.8   62  281-345    20-82  (271)
291 COG0389 DinP Nucleotidyltransf  92.8   0.073 1.9E-06   34.2   2.2   69  267-346   155-223 (354)
292 KOG0388 consensus               92.7    0.88 2.2E-05   25.7   7.7  155  272-437   567-740 (1185)
293 cd00268 DEADc DEAD-box helicas  92.7    0.68 1.7E-05   26.6   7.1  111  480-603    67-187 (203)
294 pfam05970 DUF889 PIF1 helicase  92.7    0.13 3.2E-06   32.3   3.3   19   89-107    74-92  (418)
295 PRK06731 flhF flagellar biosyn  92.6    0.93 2.4E-05   25.5   7.8  185  291-509    73-265 (270)
296 COG0017 AsnS Aspartyl/asparagi  92.5    0.97 2.5E-05   25.4  10.3   84   60-147     9-98  (435)
297 PRK08074 bifunctional ATP-depe  92.4    0.99 2.5E-05   25.3   8.3   85  469-562   742-829 (932)
298 cd04487 RecJ_OBF2_like RecJ_OB  92.3       1 2.6E-05   25.2   7.6   67   70-142     1-69  (73)
299 pfam03237 Terminase_6 Terminas  92.2       1 2.6E-05   25.2   7.7  136  297-440     1-144 (380)
300 cd04497 hPOT1_OB1_like hPOT1_O  92.2       1 2.7E-05   25.1   9.2   83   58-141     3-94  (138)
301 PRK00476 aspS aspartyl-tRNA sy  92.2       1 2.7E-05   25.1  10.7   69   58-131     8-79  (587)
302 COG0378 HypB Ni2+-binding GTPa  92.1     1.1 2.7E-05   25.0   9.3  171  291-479    10-200 (202)
303 TIGR02237 recomb_radB DNA repa  92.1    0.16 4.2E-06   31.4   3.3   47  298-348    17-64  (223)
304 PRK05898 dnaE DNA polymerase I  92.1     1.1 2.7E-05   25.0   8.9   82  508-596   690-785 (971)
305 TIGR01405 polC_Gram_pos DNA po  92.0     1.1 2.8E-05   25.0   9.3   78   65-143     5-91  (1264)
306 COG4626 Phage terminase-like p  92.0    0.46 1.2E-05   28.0   5.5  134  267-415    56-204 (546)
307 PRK10919 ATP-dependent DNA hel  91.9    0.54 1.4E-05   27.4   5.8   75  569-653   550-637 (672)
308 TIGR02903 spore_lon_C ATP-depe  91.9    0.24 6.2E-06   30.1   4.0   47  270-316   153-199 (616)
309 PRK08840 replicative DNA helic  91.9    0.84 2.1E-05   25.9   6.8   73  296-370   220-293 (464)
310 pfam11731 Cdd1 Pathogenicity l  91.8    0.12 3.2E-06   32.4   2.5   39   11-55     12-50  (92)
311 pfam05707 Zot Zonular occluden  91.8    0.24 6.2E-06   30.1   3.9   35  294-328     1-36  (183)
312 PRK10536 hypothetical protein;  91.8    0.36 9.2E-06   28.8   4.8  142  271-426    58-209 (262)
313 pfam05496 RuvB_N Holliday junc  91.8     1.2   3E-05   24.7   7.7   20  397-416   104-123 (234)
314 cd01120 RecA-like_NTPases RecA  91.7    0.72 1.8E-05   26.4   6.3   46  296-342     2-47  (165)
315 PRK04195 replication factor C   91.6     1.2   3E-05   24.7   8.3   17  296-312    43-59  (403)
316 TIGR02236 recomb_radA DNA repa  91.6    0.11 2.8E-06   32.7   2.0  101   12-121     1-120 (333)
317 PRK02983 lysS lysyl-tRNA synth  91.5     1.2 3.2E-05   24.5  12.0  117   21-148   618-740 (1099)
318 pfam04076 BOF Bacterial OB fol  91.3     1.3 3.3E-05   24.4   7.5   73   59-145    49-121 (126)
319 COG3743 Uncharacterized conser  91.2    0.17 4.4E-06   31.3   2.7   29   11-45     67-95  (133)
320 smart00483 POLXc DNA polymeras  91.2    0.19 4.9E-06   30.9   2.9   10  372-381   179-188 (334)
321 PRK10416 cell division protein  91.0     1.4 3.5E-05   24.2   7.1  170  288-489   290-474 (499)
322 COG0467 RAD55 RecA-superfamily  90.7    0.51 1.3E-05   27.6   4.7   59  281-343    12-72  (260)
323 KOG0952 consensus               90.7    0.28 7.2E-06   29.6   3.3   31  354-384   401-431 (1230)
324 COG1203 CRISPR-associated heli  90.6       1 2.6E-05   25.3   6.2   95  314-415   433-538 (733)
325 pfam06745 KaiC KaiC. This fami  90.6     0.5 1.3E-05   27.6   4.6   56  288-344    12-70  (231)
326 KOG0921 consensus               90.5   0.066 1.7E-06   34.6  -0.1  332  263-636   371-813 (1282)
327 PTZ00205 DNA polymerase kappa;  90.5    0.22 5.7E-06   30.4   2.7   18  164-181    54-71  (571)
328 TIGR02782 TrbB_P P-type conjug  90.4    0.32 8.2E-06   29.2   3.5   39  272-315   123-161 (315)
329 pfam10391 DNA_pol_lambd_f Fing  90.4    0.25 6.5E-06   29.9   2.9   28   13-46      4-31  (52)
330 PRK08506 replicative DNA helic  90.3     1.5 3.9E-05   23.8   7.1   73  297-371   197-269 (473)
331 TIGR02538 type_IV_pilB type IV  90.3    0.28   7E-06   29.7   3.0  133  169-319   193-351 (577)
332 cd03769 SR_IS607_transposase_l  90.2     1.6 4.1E-05   23.7   8.2   93  275-371    17-112 (134)
333 cd00141 NT_POLXc Nucleotidyltr  90.1    0.27 6.9E-06   29.7   2.9   29  602-631   254-282 (307)
334 cd01394 radB RadB. The archaea  90.1     1.6 4.1E-05   23.6   8.5   49  282-331     6-56  (218)
335 PRK12278 50S ribosomal protein  89.8    0.27 6.8E-06   29.8   2.6   29  165-193   160-188 (216)
336 cd04317 EcAspRS_like_N EcAspRS  89.7     1.7 4.4E-05   23.4  10.9   65   62-131     9-76  (135)
337 PRK06995 flhF flagellar biosyn  89.5     1.8 4.5E-05   23.3  13.7  244  258-538   131-391 (404)
338 PRK00076 recR recombination pr  89.5    0.17 4.4E-06   31.3   1.5   29    1-29      1-29  (197)
339 pfam02367 UPF0079 Uncharacteri  89.4    0.35 8.9E-06   28.9   3.0   51  282-337     6-56  (123)
340 PHA00012 assembly protein       89.3    0.85 2.2E-05   25.8   4.9   82  296-403     4-90  (361)
341 pfam06431 Polyoma_lg_T_C Polyo  89.2     1.9 4.8E-05   23.2   7.0  109  223-334    81-194 (417)
342 PRK12445 lysyl-tRNA synthetase  89.2     1.9 4.8E-05   23.1  11.9   97   47-147    35-147 (505)
343 KOG1808 consensus               89.1    0.74 1.9E-05   26.3   4.5   40  271-312   419-459 (1856)
344 PRK07218 replication factor A;  89.0     1.9 4.9E-05   23.0   8.4   84   50-139    46-141 (430)
345 pfam11798 IMS_HHH IMS family H  88.9    0.25 6.5E-06   30.0   2.0   26    3-30      6-31  (33)
346 PRK12726 flagellar biosynthesi  88.6     1.7 4.4E-05   23.4   6.1  162  296-490   209-377 (407)
347 PRK10867 signal recognition pa  88.5       2 5.2E-05   22.8   9.5  217  288-541    95-327 (453)
348 COG0802 Predicted ATPase or ki  88.5    0.47 1.2E-05   27.9   3.1   57  276-337     9-66  (149)
349 PRK13889 conjugal transfer rel  88.4     1.6 4.1E-05   23.7   5.8  140  269-413   343-508 (992)
350 pfam00158 Sigma54_activat Sigm  88.4    0.55 1.4E-05   27.3   3.4   23  291-313    20-42  (168)
351 PRK08769 DNA polymerase III su  88.4    0.91 2.3E-05   25.6   4.5   50  272-321     4-54  (319)
352 PRK00313 lpxK tetraacyldisacch  88.3     2.1 5.4E-05   22.7   6.5  120  303-430    63-204 (332)
353 TIGR00603 rad25 DNA repair hel  88.3    0.74 1.9E-05   26.3   4.0  329  273-666   270-688 (756)
354 PRK03932 asnC asparaginyl-tRNA  88.3     2.1 5.4E-05   22.7  11.6   77   66-146    16-99  (462)
355 PRK04301 radA DNA repair and r  88.2    0.35 8.9E-06   28.9   2.3  142   11-175     7-158 (318)
356 cd04316 ND_PkAspRS_like_N ND_P  88.1     2.2 5.5E-05   22.6  10.9   83   61-148     6-96  (108)
357 PRK08903 hypothetical protein;  88.0     1.5 3.9E-05   23.8   5.5  116  279-450    27-148 (227)
358 pfam04994 TfoX_C TfoX C-termin  88.0    0.46 1.2E-05   27.9   2.8   31   13-49      1-31  (77)
359 COG3390 Uncharacterized protei  88.0     2.2 5.6E-05   22.6   7.9   75   68-144    46-127 (196)
360 pfam00154 RecA recA bacterial   88.0     2.2 5.7E-05   22.6   7.6   82  290-379    47-134 (322)
361 cd04496 SSB_OBF SSB_OBF: A sub  87.7     2.3 5.8E-05   22.5   7.2   38   96-133    41-78  (100)
362 KOG0949 consensus               87.7     0.6 1.5E-05   27.0   3.3  153  271-435   510-676 (1330)
363 PRK10646 putative ATPase; Prov  87.5    0.37 9.4E-06   28.7   2.1   42  293-337    28-69  (153)
364 COG2247 LytB Putative cell wal  87.4     1.2 3.1E-05   24.6   4.7   67  500-573   112-186 (337)
365 KOG2383 consensus               87.3    0.42 1.1E-05   28.2   2.3   42  290-343   111-154 (467)
366 PRK08006 replicative DNA helic  87.2     2.4 6.2E-05   22.3   7.4   71  297-369   228-299 (471)
367 PRK09302 circadian clock prote  87.2    0.81 2.1E-05   26.0   3.7   36  294-329   267-302 (501)
368 PRK13341 recombination factor   87.2     2.2 5.6E-05   22.6   5.9  152    1-181    22-183 (726)
369 cd04482 RPA2_OBF_like RPA2_OBF  87.1     2.5 6.3E-05   22.2   9.7   61   71-133     2-64  (91)
370 pfam03969 AFG1_ATPase AFG1-lik  87.0       2 5.1E-05   22.9   5.6   43  293-346    61-103 (361)
371 COG0541 Ffh Signal recognition  86.9     2.5 6.5E-05   22.1   9.5  122  288-429    95-223 (451)
372 PRK08609 hypothetical protein;  86.7    0.65 1.6E-05   26.8   3.0   30   12-46     89-118 (570)
373 PRK05703 flhF flagellar biosyn  86.7     2.6 6.6E-05   22.0  15.2  159  297-489   214-379 (412)
374 PRK13844 recombination protein  86.6    0.32 8.1E-06   29.2   1.4   29    1-29      5-33  (200)
375 COG1571 Predicted DNA-binding   86.5     2.6 6.7E-05   22.0   6.9  104   15-133   217-332 (421)
376 TIGR00455 apsK adenylylsulfate  86.5    0.59 1.5E-05   27.1   2.6  104  296-492    22-130 (187)
377 TIGR02759 TraD_Ftype type IV c  86.4    0.78   2E-05   26.1   3.3   37  295-332   210-246 (613)
378 COG2874 FlaH Predicted ATPases  86.4     1.6   4E-05   23.8   4.8   50  282-332    15-66  (235)
379 pfam10236 DAP3 Mitochondrial r  86.4     1.3 3.3E-05   24.4   4.4   38  291-329    21-58  (274)
380 PRK11608 pspF phage shock prot  86.3    0.84 2.1E-05   25.9   3.4   33  279-313    17-49  (325)
381 PRK10875 recD exonuclease V su  86.3       2   5E-05   23.0   5.3   88  255-349   128-222 (607)
382 KOG0987 consensus               86.3     1.8 4.7E-05   23.2   5.1   72  262-334   107-178 (540)
383 PRK06696 uridine kinase; Valid  85.8     2.1 5.2E-05   22.8   5.2   60  277-336     7-75  (227)
384 PRK06893 DNA replication initi  85.8     2.8 7.3E-05   21.7   9.0   34  296-329    42-75  (229)
385 pfam02606 LpxK Tetraacyldisacc  85.7    0.46 1.2E-05   27.9   1.8  204  303-548    47-279 (318)
386 PRK06904 replicative DNA helic  85.6     2.7 6.8E-05   21.9   5.7   70  297-369   225-297 (472)
387 PRK05022 anaerobic nitric oxid  85.6    0.62 1.6E-05   26.9   2.4   38  276-313   190-229 (510)
388 PRK12820 bifunctional aspartyl  85.4       3 7.5E-05   21.6  10.2   92   53-148     4-109 (706)
389 PRK07004 replicative DNA helic  85.3       3 7.6E-05   21.5   6.9   72  296-369   216-288 (460)
390 cd00984 DnaB_C DnaB helicase C  85.2     2.6 6.8E-05   22.0   5.5   72  295-368    15-87  (242)
391 TIGR03600 phage_DnaB phage rep  84.9     3.1 7.9E-05   21.4   6.1   71  296-369   197-269 (421)
392 PRK13609 diacylglycerol glucos  84.9     3.1 7.9E-05   21.4  10.4  159  365-552    94-288 (388)
393 PRK05642 DNA replication initi  84.8     3.1   8E-05   21.4   8.8   33  297-329    49-81  (234)
394 PRK12374 putative dithiobiotin  84.8     0.9 2.3E-05   25.6   2.9   33  297-329     6-39  (231)
395 COG0132 BioD Dethiobiotin synt  84.7    0.87 2.2E-05   25.7   2.8   30  300-329    10-39  (223)
396 PRK07263 consensus              84.5     3.2 8.2E-05   21.3   8.0   86  280-369   192-278 (453)
397 cd03468 Pol_Y_like Pol_Y_like:  84.4    0.97 2.5E-05   25.4   2.9   49  277-333   114-162 (330)
398 PRK08084 DNA replication initi  84.3     3.3 8.4E-05   21.2   6.2   36  296-332    48-83  (235)
399 TIGR00615 recR recombination p  84.3    0.41   1E-05   28.3   1.0  136    3-166     4-157 (205)
400 cd00983 recA RecA is a  bacter  84.3     3.3 8.4E-05   21.2   7.0   83  290-380    50-138 (325)
401 COG0210 UvrD Superfamily I DNA  84.2     3.3 8.5E-05   21.2   6.6   34  605-643   597-632 (655)
402 KOG3416 consensus               84.1     3.3 8.5E-05   21.2   8.0  102   58-167     4-109 (134)
403 PRK12402 replication factor C   84.1     1.5 3.8E-05   23.9   3.8   42  276-317    19-60  (337)
404 PRK05480 uridine kinase; Provi  84.1       2   5E-05   23.0   4.4   25  288-312     1-25  (209)
405 PRK07459 single-stranded DNA-b  84.0     3.4 8.6E-05   21.2   8.4   63   69-131     5-76  (121)
406 PRK08760 replicative DNA helic  84.0       2 5.1E-05   22.9   4.4   72  297-370   233-305 (476)
407 PRK00090 bioD dithiobiotin syn  84.0       1 2.6E-05   25.3   2.9   32  298-329     4-36  (223)
408 COG3111 Periplasmic protein wi  83.9     3.4 8.7E-05   21.1   7.6   71   59-138    49-119 (128)
409 PRK11388 DNA-binding transcrip  83.8     1.3 3.2E-05   24.5   3.3  160  275-481   332-515 (639)
410 PRK08763 single-stranded DNA-b  83.8     3.4 8.7E-05   21.1   7.7   64   68-131     6-84  (160)
411 PRK08727 hypothetical protein;  83.7     3.1 7.9E-05   21.4   5.3   36  296-332    44-79  (233)
412 PRK05636 replicative DNA helic  83.6     3.5 8.9E-05   21.0   6.7   72  297-370   271-343 (507)
413 cd02028 UMPK_like Uridine mono  83.6     1.3 3.4E-05   24.3   3.4   31  297-327     3-33  (179)
414 PRK07471 DNA polymerase III su  83.5     1.8 4.6E-05   23.3   4.0   41  275-315    20-61  (363)
415 pfam05876 Terminase_GpA Phage   83.5     3.5 8.9E-05   21.0   5.8  130  272-407    16-147 (552)
416 COG1663 LpxK Tetraacyldisaccha  83.3     1.5 3.7E-05   24.0   3.5   95  303-408    59-173 (336)
417 COG3421 Uncharacterized protei  83.3    0.68 1.7E-05   26.6   1.8   60  264-328   408-468 (812)
418 TIGR01447 recD exodeoxyribonuc  83.1     3.6 9.3E-05   20.9   7.3  142  263-426   211-366 (753)
419 cd01127 TrwB Bacterial conjuga  83.0     2.3 5.8E-05   22.5   4.4  111  441-561   254-371 (410)
420 PRK12373 NADH dehydrogenase su  83.0    0.78   2E-05   26.1   2.0   12  151-162    21-32  (403)
421 pfam00485 PRK Phosphoribulokin  83.0     1.7 4.3E-05   23.5   3.7   27  297-323     3-29  (196)
422 PRK06674 DNA polymerase III su  82.8     3.7 9.5E-05   20.8   8.1   19   89-107   119-137 (563)
423 PRK08486 single-stranded DNA-b  82.6     3.8 9.7E-05   20.7   7.7   63   69-131     4-81  (180)
424 COG3972 Superfamily I DNA and   82.2     1.9 4.9E-05   23.0   3.8  142  259-408   150-309 (660)
425 PHA00350 putative assembly pro  82.2     1.3 3.3E-05   24.4   2.9   18  475-492   364-382 (402)
426 cd02025 PanK Pantothenate kina  82.0     1.4 3.5E-05   24.2   2.9   30  298-327     4-35  (220)
427 PRK10053 hypothetical protein;  82.0       4  0.0001   20.6   7.3   64   61-133    55-118 (130)
428 PRK10365 transcriptional regul  81.9     2.1 5.4E-05   22.7   3.9   35  277-313   148-182 (441)
429 pfam06068 TIP49 TIP49 C-termin  81.9     2.5 6.3E-05   22.2   4.2  132  276-428    28-182 (395)
430 TIGR00101 ureG urease accessor  81.9     2.2 5.5E-05   22.7   3.9   61  297-360     5-67  (199)
431 COG2256 MGS1 ATPase related to  81.8     3.1   8E-05   21.4   4.7  101  284-429    39-139 (436)
432 COG0593 DnaA ATPase involved i  81.6     1.8 4.5E-05   23.3   3.4   98  297-437   117-224 (408)
433 PRK06751 single-stranded DNA-b  81.3     4.2 0.00011   20.4   7.7   63   69-131     3-78  (172)
434 COG1485 Predicted ATPase [Gene  81.0     1.5 3.9E-05   23.8   2.9   72  297-404    69-140 (367)
435 PRK08694 consensus              80.9     4.3 0.00011   20.3   6.9   73  296-370   221-294 (468)
436 KOG3928 consensus               80.9     2.4 6.2E-05   22.3   3.9   38  291-329   176-214 (461)
437 cd03115 SRP The signal recogni  80.8     4.3 0.00011   20.3   5.8  156  297-477     4-164 (173)
438 cd01983 Fer4_NifH The Fer4_Nif  80.8     1.4 3.6E-05   24.1   2.6   30  299-328     5-34  (99)
439 COG3911 Predicted ATPase [Gene  80.7       2 5.1E-05   22.9   3.4   44  292-339     4-51  (183)
440 TIGR03420 DnaA_homol_Hda DnaA   80.6     4.4 0.00011   20.2   8.4   92  297-437    42-139 (226)
441 PRK10820 DNA-binding transcrip  80.6       2 5.1E-05   22.9   3.4  100  292-432   226-342 (513)
442 PRK10246 exonuclease subunit S  80.5     1.3 3.2E-05   24.5   2.3   13  370-382   499-511 (1047)
443 TIGR00963 secA preprotein tran  80.5     0.6 1.5E-05   27.0   0.7   81  578-695   645-728 (904)
444 PRK06863 single-stranded DNA-b  80.5     4.4 0.00011   20.2   5.4   65   68-132     5-85  (168)
445 PRK11361 acetoacetate metaboli  80.3     2.7   7E-05   21.9   4.0   36  276-313   151-186 (457)
446 KOG0701 consensus               80.2    0.61 1.6E-05   27.0   0.6   66  529-596   709-786 (1606)
447 TIGR00382 clpX ATP-dependent C  80.2    0.95 2.4E-05   25.5   1.6   19  292-310   151-169 (452)
448 PRK07275 single-stranded DNA-b  80.1     4.5 0.00012   20.1   7.6   63   69-131     4-79  (163)
449 pfam07015 VirC1 VirC1 protein.  79.9     1.7 4.2E-05   23.6   2.8   31  298-328     7-37  (231)
450 PRK13765 ATP-dependent proteas  79.9     4.6 0.00012   20.1   5.5  102  380-484   209-336 (637)
451 PRK07220 DNA topoisomerase I;   79.7     1.7 4.4E-05   23.4   2.8   13  391-403   415-427 (740)
452 cd02023 UMPK Uridine monophosp  79.6     3.6 9.2E-05   20.9   4.4   29  297-327     3-31  (198)
453 pfam06309 Torsin Torsin. This   79.6     4.3 0.00011   20.3   4.8   54  271-324    28-84  (127)
454 pfam03808 Glyco_tran_WecB Glyc  79.5     4.7 0.00012   20.0   7.1   98  472-591    38-137 (172)
455 cd01393 recA_like RecA is a  b  79.4     3.2 8.2E-05   21.3   4.1   40  283-322     7-48  (226)
456 COG0353 RecR Recombinational D  79.2    0.89 2.3E-05   25.7   1.2   29    1-29      2-30  (198)
457 KOG1942 consensus               79.2       2   5E-05   23.0   3.0   57  276-333    42-103 (456)
458 COG1221 PspF Transcriptional r  79.1       4  0.0001   20.6   4.5  201  276-539    86-312 (403)
459 KOG2093 consensus               79.1     1.7 4.3E-05   23.5   2.6  195  160-361   418-660 (1016)
460 PRK10923 glnG nitrogen regulat  79.1     2.4 6.1E-05   22.3   3.4   33  279-311   145-179 (469)
461 pfam05729 NACHT NACHT domain.   78.9     1.7 4.2E-05   23.6   2.5   25  296-320     3-27  (165)
462 pfam00493 MCM MCM2/3/5 family.  78.8     3.4 8.5E-05   21.2   4.1   86  294-416    58-143 (327)
463 PRK07274 single-stranded DNA-b  78.6       5 0.00013   19.8   7.9   80   69-148     4-104 (131)
464 cd01294 DHOase Dihydroorotase   78.6     1.5 3.9E-05   23.8   2.2   25  360-384   219-244 (335)
465 PRK12311 rpsB 30S ribosomal pr  78.5     1.5 3.9E-05   23.9   2.2   15  113-127    59-73  (332)
466 COG3640 CooC CO dehydrogenase   78.5       3 7.7E-05   21.5   3.7   35  294-328     1-36  (255)
467 PRK09354 recA recombinase A; P  78.4     5.1 0.00013   19.7   6.6   85  290-381    55-144 (350)
468 pfam10412 TrwB_AAD_bind Type I  78.4     4.8 0.00012   19.9   4.7  125  421-555   204-338 (386)
469 TIGR03491 RecB family nuclease  78.3     2.8 7.1E-05   21.8   3.5   41  114-154    60-102 (457)
470 PRK08058 DNA polymerase III su  78.3     5.1 0.00013   19.7   6.6  143  272-439     6-157 (329)
471 PRK09112 DNA polymerase III su  78.2     2.6 6.6E-05   22.0   3.3   44  275-318    26-70  (352)
472 PRK06958 single-stranded DNA-b  78.2     5.1 0.00013   19.7   7.3   64   68-131     5-84  (181)
473 TIGR03167 tRNA_sel_U_synt tRNA  78.1     3.3 8.5E-05   21.2   3.9   77  260-348    89-171 (311)
474 TIGR01292 TRX_reduct thioredox  78.1     4.4 0.00011   20.3   4.5   81  478-568   147-231 (321)
475 COG2251 Predicted nuclease (Re  78.1     2.1 5.3E-05   22.8   2.8   34  427-464   232-265 (474)
476 pfam02399 Herpes_ori_bp Origin  78.0     4.9 0.00012   19.9   4.7   25  529-553   588-612 (829)
477 PRK13732 single-stranded DNA-b  78.0     5.2 0.00013   19.7   7.8   65   68-132     7-87  (175)
478 cd04486 YhcR_OBF_like YhcR_OBF  78.0     5.2 0.00013   19.6   6.2   68   71-145     1-74  (78)
479 COG1341 Predicted GTPase or GT  77.9     5.2 0.00013   19.6   5.6   65  270-334    45-125 (398)
480 pfam02765 Telo_bind Telomeric   77.9     5.3 0.00013   19.6   9.9   80   61-140     6-94  (141)
481 KOG0554 consensus               77.8     5.3 0.00013   19.6   6.1   99   64-174    17-118 (446)
482 cd03109 DTBS Dethiobiotin synt  77.3     2.6 6.7E-05   22.0   3.1   34  298-331     4-37  (134)
483 cd04323 AsnRS_cyto_like_N AsnR  77.3     5.4 0.00014   19.5  10.3   62   69-134     1-64  (84)
484 COG1224 TIP49 DNA helicase TIP  77.2     3.4 8.7E-05   21.1   3.7  173  276-469    43-247 (450)
485 pfam07728 AAA_5 AAA domain (dy  76.8     1.7 4.4E-05   23.4   2.1   18  296-313     2-19  (139)
486 PRK05201 hslU ATP-dependent pr  76.8     1.5 3.9E-05   23.8   1.8   22  292-313    49-70  (442)
487 PRK05733 single-stranded DNA-b  76.7     5.6 0.00014   19.4   7.9   66   68-133     6-87  (172)
488 PTZ00301 uridine kinase; Provi  76.7       3 7.5E-05   21.6   3.3   14  297-310     7-20  (210)
489 PRK13849 putative crown gall t  76.6     2.4 6.1E-05   22.3   2.8   31  298-328     7-37  (231)
490 COG4962 CpaF Flp pilus assembl  76.5     5.4 0.00014   19.5   4.6   60  272-337   157-216 (355)
491 PRK05748 replicative DNA helic  76.5     5.7 0.00015   19.4   6.3   73  296-370   206-279 (448)
492 PRK05973 replicative DNA helic  76.4     5.7 0.00015   19.3   6.4   58  283-343    56-113 (237)
493 TIGR01967 DEAH_box_HrpA ATP-de  76.3     1.6   4E-05   23.7   1.8  271  276-599    71-423 (1320)
494 PTZ00150 phosphoglucomutase; P  76.2     2.7 6.9E-05   21.9   3.0   20  522-541   472-491 (593)
495 cd04480 RPA1_DBD_A_like RPA1_D  76.2     5.8 0.00015   19.3   9.6   74   72-145     2-78  (86)
496 pfam00436 SSB Single-strand bi  75.7     5.9 0.00015   19.2   8.0   64   69-132     3-81  (104)
497 pfam00308 Bac_DnaA Bacterial d  75.7     5.9 0.00015   19.2   6.7   48  280-329    22-72  (219)
498 pfam00448 SRP54 SRP54-type pro  75.7       6 0.00015   19.2   6.6   87  293-380     1-88  (196)
499 PHA02518 ParA-like protein; Pr  75.6     2.6 6.7E-05   22.0   2.8   25  303-327    11-35  (211)
500 PRK07276 DNA polymerase III su  75.5       4  0.0001   20.6   3.7   46  272-317     2-48  (290)

No 1  
>COG1200 RecG RecG-like helicase [DNA replication, recombination, and repair / Transcription]
Probab=100.00  E-value=0  Score=1842.93  Aligned_cols=660  Identities=47%  Similarity=0.780  Sum_probs=644.1

Q ss_pred             CCCCHHCHHCCCHHHCCCCCHHHHHHHHHHCCCCCCCCCCHHHHHHHCCCCCCCCCCCCCHHHCCCCCEEEEEEEEEEEE
Q ss_conf             97102021017721367858899999887401246885548987870897401344446478889987899999998975
Q gi|254780945|r    1 MRPSFLNPLFAPLSTFRGVGKKYSLFLSKIINCGNANETRFIDLLFYHPSSFIDRHYRPKISEISEERIVTITGYISQHS   80 (700)
Q Consensus         1 mrp~~l~~L~~pI~~LkGVGpk~a~~L~kl~~l~~~GI~ti~DLL~~~PrrYeDr~~~~~I~~l~~g~~vti~g~V~~~~   80 (700)
                      |++..+++ +.|+++|+||||+++++|+++      ||+|+.|||+|||++|+||+....|.++.+|+.+|++|+|.++.
T Consensus         1 ~~~~~~~~-~~~l~~l~gig~~~a~~l~~L------gi~tv~DLL~~~P~~YeD~~~~~~i~~~~~g~~vti~g~V~~~~   73 (677)
T COG1200           1 MMLSLLDP-FVPLSTLKGIGPKTAEKLKKL------GIHTVQDLLLYLPRRYEDRTLLPGIAEARPGEIVTIEGTVLSHE   73 (677)
T ss_pred             CCCCCCCC-CCCHHHHCCCCHHHHHHHHHC------CCCCHHHHHHHCCCCHHHCCCCCCHHHCCCCCEEEEEEEEEEEE
T ss_conf             97331356-543255238687789999871------98759999986862142146567843537786699999997640


Q ss_pred             EECCCCCCEEEEEEECCCCEEEEEEECCCHHHHHHHCCCCCEEEEEEEEEECCCEEEEECCEEEECCCCCCCCCCCCCCC
Q ss_conf             42158983389999818936999995188789987328988899998997318779997786896264334444411000
Q gi|254780945|r   81 SFQLQKRRPYKILLNDGTGEITLLFFYRKTEMLKNVFFEGRKITVTGKIKKLKNRIIMVHPHYIFHNSQDVNFPLIEAVY  160 (700)
Q Consensus        81 ~~~~~~r~~~~v~v~D~tg~i~lvfFn~~~~yl~k~lk~G~~v~vsGKv~~~~~~~qi~hPe~~~~~~~~~~~~~I~PIY  160 (700)
                      ..+.++++++++.+.|++|.+.++|||++ +|+++.|++|+++++|||++.+++.+||+||+|....+.....+.++|||
T Consensus        74 ~~~~~~~~~l~v~~~d~~~~l~l~fFn~~-~~l~~~~~~G~~v~v~Gk~~~~~~~~~~~hpe~~~~~~~~~~~~~i~PvY  152 (677)
T COG1200          74 KFPFGKRKLLKVTLSDGTGVLTLVFFNFP-AYLKKKLKVGERVIVYGKVKRFKGGLQITHPEYIVNDDGSELEERLTPVY  152 (677)
T ss_pred             CCCCCCCCEEEEEEECCCEEEEEEEECCC-HHHHHHCCCCCEEEEEEEEEECCCCEEEECCEEEECCCCCCCCCCEEEEE
T ss_conf             25778873499999629689999997866-88884187998899999895036835887666783278765556235511


Q ss_pred             CCCHHHHHHHHHHHHHHHHHHHC-CCCCCCCHHHHHCCCCCCHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             00000004543001345787404-68433897786205699988999862045896565667999999987666666677
Q gi|254780945|r  161 SLPTGLSVDLFKKIIVEALSRLP-VLPEWIEKDLLQKKSFPSIAEAFNIIHNPRKAKDFEWTSPARERLAYDELLAGQIA  239 (700)
Q Consensus       161 plt~GLsqk~irk~I~~aL~~~~-~i~E~LP~~ll~k~~L~s~~eAL~~IH~P~~~~dle~~~~ArkRLafeELl~~QL~  239 (700)
                      |+|+||+|+.+|++|.+||+.++ .++||+|..++++|+++++.+|++.||+|++..+++   .+++||+|||+|++|++
T Consensus       153 ~~t~gl~~~~lrk~i~~aL~~~~~~l~e~lp~~l~~k~~l~~~~~al~~lH~P~~~~~~~---~~~rRL~f~Ell~~ql~  229 (677)
T COG1200         153 PLTEGLKQKTLRKLIQQALEVLPSELEELLPEELLEKYGLPSLDEALRTLHFPKDEEDLK---RARRRLAFEELLALQLS  229 (677)
T ss_pred             ECCCCCCHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHCCCCCCHHHHH---HHHHHHHHHHHHHHHHH
T ss_conf             101354879999999999985154303347788986306854999998655999777899---99876789999999999


Q ss_pred             HHHHHHHHHHCCCCCCCCCCHHHHHHHHHCCCCCCHHHHHHHHHHHHHHCCCCCCEEEEEECCCCCHHHHHHHHHHHHHH
Q ss_conf             77655554320357678775789999863024679889999999998410013430788621442236999999733444
Q gi|254780945|r  240 LLLMRKQFKKEIGIPINVEGKIAQKILRNIPFSPTKSQESAIKDILQDMSQKNRMLRILQGDVGSGKTLVALIAMAAAVE  319 (700)
Q Consensus       240 l~~~r~~~~~~~~~~~~~~~~~~~~f~~~LPF~LT~~Q~~ai~eI~~Dl~~~~pM~RLLQGDVGSGKTiVA~~A~l~~~~  319 (700)
                      |+.+|.+.++..+.++..++.+.++|+++|||+||++|++|++||..||+++.|||||||||||||||+||++||+++++
T Consensus       230 l~~~r~~~~~~~~~~~~~~~~l~~~~~~~LPF~LT~aQ~~vi~EI~~Dl~~~~~M~RLlQGDVGSGKTvVA~laml~ai~  309 (677)
T COG1200         230 LLLRRAKRQKRSGIPLPANGELLAKFLAALPFKLTNAQKRVIKEILADLASPVPMNRLLQGDVGSGKTVVALLAMLAAIE  309 (677)
T ss_pred             HHHHHHHHHHCCCCCCCCCHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHCCCHHHHHHHCCCCCCCHHHHHHHHHHHHHH
T ss_conf             99999987522688888647999999985899767899999999986644866667875267677789999999999987


Q ss_pred             HHCCEEEEEHHHHHHHHHHHHHHHHCCCCCCEEEEEECCCCHHHHHHHHHHHCCCCCEEEEECHHHCCCCCCCCCCCEEE
Q ss_conf             30545886127999999998621101457865899624642256676877621347548641112013345544441788
Q gi|254780945|r  320 AGGQAVIMAPIGILAQQHYEFIKKYTQNTQIIVEIITGNMPQAHRRKALERIAHGQAHIIIGTHALFQDSIQYYKLILVI  399 (700)
Q Consensus       320 ~G~Q~alMaPTEILA~QH~~~~~~~~~~~~i~v~lLtg~~~~~er~~i~~~i~~G~~~iiIGTHAL~q~~v~F~~LgLvV  399 (700)
                      +|||||+||||||||+|||+++++||+++|++|+|||||+++++|+++++.|++|+++|||||||||||+|.|+||||||
T Consensus       310 ~G~Q~ALMAPTEILA~QH~~~~~~~l~~~~i~V~lLtG~~kgk~r~~~l~~l~~G~~~ivVGTHALiQd~V~F~~LgLVI  389 (677)
T COG1200         310 AGYQAALMAPTEILAEQHYESLRKWLEPLGIRVALLTGSLKGKARKEILEQLASGEIDIVVGTHALIQDKVEFHNLGLVI  389 (677)
T ss_pred             CCCEEEEECCHHHHHHHHHHHHHHHHHHCCCEEEEEECCCCHHHHHHHHHHHHCCCCCEEEECCHHHHCCEEECCEEEEE
T ss_conf             28816886637999999999999876651974898644665067999999874799897997221220450442023899


Q ss_pred             ECCCCCCCHHHHHHHHHCCC-CCCCEEECHHHHHHHHHHHHHHCCCHHHHCCCCCCCCCCEEEEEECCCHHHHHHHHHHH
Q ss_conf             52101335688998740256-77610101013227899997520101111023557666207999702002689999763
Q gi|254780945|r  400 VDEQHRFGVQQRLKLTQKAT-APHVLLMTATPIPRTLVLTSLGDIDISKITEKPAGRKPIKTVIIPINRIDEVIERLKVV  478 (700)
Q Consensus       400 iDEQHRFGV~QR~~L~~Kg~-~ph~L~MtATPIPRTLal~~ygdldvS~i~e~P~gR~~I~T~~~~~~~~~~~~~~i~~~  478 (700)
                      |||||||||+||..|.+||. +||+|+|||||||||||||.|||||+|+|||+|+||+||+|+|++.+++++++++|+++
T Consensus       390 iDEQHRFGV~QR~~L~~KG~~~Ph~LvMTATPIPRTLAlt~fgDldvS~IdElP~GRkpI~T~~i~~~~~~~v~e~i~~e  469 (677)
T COG1200         390 IDEQHRFGVHQRLALREKGEQNPHVLVMTATPIPRTLALTAFGDLDVSIIDELPPGRKPITTVVIPHERRPEVYERIREE  469 (677)
T ss_pred             EECCCCCCHHHHHHHHHHCCCCCCEEEEECCCCHHHHHHHHHCCCCCHHHCCCCCCCCCEEEEEECCCCHHHHHHHHHHH
T ss_conf             72521022999999997378999679995798507889888614630111257989974089996444479999999999


Q ss_pred             HCCCCEEEEEECCCCCCCCCCCCHHHHHHHHHHHHCCC-CEECCCCCCCHHHHHHHHHHHHCCCEEEEEECHHHHCCCCC
Q ss_conf             10387389997120122111210146666666866371-03120146998999999999755986999980034104688
Q gi|254780945|r  479 LSEGKKAYWICPQIEEKKESNFRSVVERFNSLHEHFTS-SIAIIHGRMSDIDKESVMDSFKNGTCKLLIATTVIEVGIDV  557 (700)
Q Consensus       479 l~~g~q~y~VcPlIeese~~~~~~~~~~~~~l~~~~~~-~v~~lHGkm~~~ek~~~m~~F~~g~~~iLvaTtviEVGvdv  557 (700)
                      +.+|+|||||||||||||++++++|+++|++|+..||. +||++||||+++|||+||.+|++||++||||||||||||||
T Consensus       470 i~~GrQaY~VcPLIeeSE~l~l~~a~~~~~~L~~~~~~~~vgL~HGrm~~~eKd~vM~~Fk~~e~~ILVaTTVIEVGVdV  549 (677)
T COG1200         470 IAKGRQAYVVCPLIEESEKLELQAAEELYEELKSFLPELKVGLVHGRMKPAEKDAVMEAFKEGEIDILVATTVIEVGVDV  549 (677)
T ss_pred             HHCCCEEEEEECCCCCCCCCHHHHHHHHHHHHHHHCCCCEEEEEECCCCHHHHHHHHHHHHCCCCCEEEEEEEEEECCCC
T ss_conf             97499799995253543311365499999999987054636777568986779999999980887689981389952357


Q ss_pred             CCCCEEEEECHHHCCHHHHHHHHHCCCCCCCCEEEEEEECCCCCHHHHHHHHHHHHHCHHHHHHHHHHHHCCCCCCCCCH
Q ss_conf             87658998585254746887730116678983599997088899879999999984142589999998520630002600
Q gi|254780945|r  558 VDASIIIIENAEHFGLAQLHQLRGRVGRGEEISSCILLYHPPLSKNSYTRLSVLKNTEDGFLIAEEDLKQRKEGEILGIK  637 (700)
Q Consensus       558 pna~~mvI~~aerfGLsqLHQLRGRVGRg~~~s~c~l~~~~~~~~~~~~Rl~~l~~~~dGf~iAe~Dl~lRG~G~~~G~~  637 (700)
                      ||||+||||||||||||||||||||||||+.+|||+|+|+++.++.+++||++|++|+|||+|||+||++|||||+||++
T Consensus       550 PnATvMVIe~AERFGLaQLHQLRGRVGRG~~qSyC~Ll~~~~~~~~a~~RL~im~~t~DGF~IAE~DLklRGpGe~lG~r  629 (677)
T COG1200         550 PNATVMVIENAERFGLAQLHQLRGRVGRGDLQSYCVLLYKPPLSEVAKQRLKIMRETTDGFVIAEEDLKLRGPGELLGTR  629 (677)
T ss_pred             CCCEEEEEECHHHHHHHHHHHHCCCCCCCCCCEEEEEEECCCCCHHHHHHHHHHHHCCCCCEEHHHHHHCCCCCCCCCCC
T ss_conf             88707999654330378888752655788754489999679877568999998874487601046567413886546875


Q ss_pred             HCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHCC
Q ss_conf             0698744000388759999999999999998484
Q gi|254780945|r  638 QSGMPKFLIAQPELHDSLLEIARKDAKHILTQDP  671 (700)
Q Consensus       638 QsG~~~~~~~d~~~d~~ll~~a~~~a~~~~~~d~  671 (700)
                      |||.|+|++||+++|+++|+.||++|..++.+||
T Consensus       630 QSG~~~f~~Adl~~D~~ile~ar~~a~~~~~~~~  663 (677)
T COG1200         630 QSGLPEFRVADLVRDYDILEEARKDAAKLLSRDP  663 (677)
T ss_pred             CCCCCCEEEEEHHHHHHHHHHHHHHHHHHHHHCC
T ss_conf             5688654773087569999999999999976184


No 2  
>PRK10917 ATP-dependent DNA helicase RecG; Provisional
Probab=100.00  E-value=0  Score=1836.02  Aligned_cols=659  Identities=45%  Similarity=0.746  Sum_probs=640.3

Q ss_pred             HHCHHCCCHHHCCCCCHHHHHHHHHHCCCCCCCCCCHHHHHHHCCCCCCCCCCCCCHHHCCCCCEEEEEEEEEEEEEECC
Q ss_conf             20210177213678588999998874012468855489878708974013444464788899878999999989754215
Q gi|254780945|r    5 FLNPLFAPLSTFRGVGKKYSLFLSKIINCGNANETRFIDLLFYHPSSFIDRHYRPKISEISEERIVTITGYISQHSSFQL   84 (700)
Q Consensus         5 ~l~~L~~pI~~LkGVGpk~a~~L~kl~~l~~~GI~ti~DLL~~~PrrYeDr~~~~~I~~l~~g~~vti~g~V~~~~~~~~   84 (700)
                      .+..|++||++|||||||+++.|+|+      ||+|+.|||+|||+||+||+.+++|+++.+|+.+++.|+|.++.. .+
T Consensus         2 ~~~~L~~pI~~LKGVGpK~a~~L~kL------GI~TV~DLL~~fPrrYeDRt~i~~I~el~~Ge~vtI~g~V~~~~~-~~   74 (677)
T PRK10917          2 MLLLLDAPLTSLKGVGPKTAEKLAKL------GIHTVQDLLLHLPRRYEDRTRLKPIAELRPGEKVTVEGTVLSAEV-YF   74 (677)
T ss_pred             CCHHHCCCHHHCCCCCHHHHHHHHHC------CCCCHHHHHHCCCCCEEECCCCCCHHHCCCCCEEEEEEEEEEEEC-CC
T ss_conf             21032488755799789999999976------999499998519985187686777789799987999999999843-77


Q ss_pred             CCCCEEEEEEECCCCEEEEEEECCCHHHHHHHCCCCCEEEEEEEEEECCCEEEEECCEEEECCCCCCCCCCCCCCCCCCH
Q ss_conf             89833899998189369999951887899873289888999989973187799977868962643344444110000000
Q gi|254780945|r   85 QKRRPYKILLNDGTGEITLLFFYRKTEMLKNVFFEGRKITVTGKIKKLKNRIIMVHPHYIFHNSQDVNFPLIEAVYSLPT  164 (700)
Q Consensus        85 ~~r~~~~v~v~D~tg~i~lvfFn~~~~yl~k~lk~G~~v~vsGKv~~~~~~~qi~hPe~~~~~~~~~~~~~I~PIYplt~  164 (700)
                      ++|+++++.+.|++|.+.++|||. .+|+++.|++|++++||||++.|++.+||+||+|+..+++ ...+.|+||||+|+
T Consensus        75 ~~r~~l~v~v~D~tG~I~lvfFn~-~pyl~k~l~~G~~v~VsGKV~~~~~~lQm~hPe~e~~~~~-~~~~~I~PVYplT~  152 (677)
T PRK10917         75 GPRRRLRVTLSDGTGVLTLVFFNN-QPYLKKQLKVGKRVAVYGKVKRGKYGLEIVHPEYEVLGEE-TSIGRLTPVYPLTE  152 (677)
T ss_pred             CCCCEEEEEEEECCEEEEEEEECC-CHHHHHHCCCCCEEEEEEEEEEECCEEEEECCEEEECCCC-CCCCCEEEECCCCC
T ss_conf             897249999998987999999898-4789963899998999999985599899978989813875-45685455350776


Q ss_pred             HHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHCCCCCCHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             00045430013457874046843389778620569998899986204589656566799999998766666667777655
Q gi|254780945|r  165 GLSVDLFKKIIVEALSRLPVLPEWIEKDLLQKKSFPSIAEAFNIIHNPRKAKDFEWTSPARERLAYDELLAGQIALLLMR  244 (700)
Q Consensus       165 GLsqk~irk~I~~aL~~~~~i~E~LP~~ll~k~~L~s~~eAL~~IH~P~~~~dle~~~~ArkRLafeELl~~QL~l~~~r  244 (700)
                      ||+|++||++|.++|+.++.++||+|.+++++|+|+++.+||++||||++.+++   .+||+||+|||||++|+++..+|
T Consensus       153 GLsqk~irklI~~aL~~~~~l~E~LP~~ll~k~~L~s~~~AL~~IHfP~s~edl---~~ArrRLaFEELf~~QL~l~~~r  229 (677)
T PRK10917        153 GLKQKTLRKLIKQALERLPALPELLPEELLEKYGLLSLAEALRAIHFPPSDEDL---HPARRRLKFEELFALQLSLLLLR  229 (677)
T ss_pred             CCCHHHHHHHHHHHHHHHHCCCCCCCHHHHHHCCCCCHHHHHHHHHCCCCHHHH---HHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             678699999999999874314333998889663899899999997589976789---99999999999999999999999


Q ss_pred             HHHHHCCCCCCCCCCHHHHHHHHHCCCCCCHHHHHHHHHHHHHHCCCCCCEEEEEECCCCCHHHHHHHHHHHHHHHHCCE
Q ss_conf             55432035767877578999986302467988999999999841001343078862144223699999973344430545
Q gi|254780945|r  245 KQFKKEIGIPINVEGKIAQKILRNIPFSPTKSQESAIKDILQDMSQKNRMLRILQGDVGSGKTLVALIAMAAAVEAGGQA  324 (700)
Q Consensus       245 ~~~~~~~~~~~~~~~~~~~~f~~~LPF~LT~~Q~~ai~eI~~Dl~~~~pM~RLLQGDVGSGKTiVA~~A~l~~~~~G~Q~  324 (700)
                      ++.++.++.++..++.+.+.|+++|||+||++|++|++||.+||+++.||+||||||||||||+||++||+.|++|||||
T Consensus       230 ~~~~~~~~~~~~~~~~~~~~~~~~LPF~LT~~Q~~~~~ei~~dl~~~~~m~rllqGDVGsGKT~va~~a~~~~~~~g~q~  309 (677)
T PRK10917        230 AERRKLAAPPLPADGELLKKFLASLPFELTGAQKRVVAEILADLASPKPMNRLLQGDVGSGKTVVAALAALAAIEAGYQA  309 (677)
T ss_pred             HHHHHCCCCCCCCCHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHCCCCCCHHHHCCCCCCCHHHHHHHHHHHHHHHCCEE
T ss_conf             99873268777887699999998099988988999999999876599542777328767888999999999999819948


Q ss_pred             EEEEHHHHHHHHHHHHHHHHCCCCCCEEEEEECCCCHHHHHHHHHHHCCCCCEEEEECHHHCCCCCCCCCCCEEEECCCC
Q ss_conf             88612799999999862110145786589962464225667687762134754864111201334554444178852101
Q gi|254780945|r  325 VIMAPIGILAQQHYEFIKKYTQNTQIIVEIITGNMPQAHRRKALERIAHGQAHIIIGTHALFQDSIQYYKLILVIVDEQH  404 (700)
Q Consensus       325 alMaPTEILA~QH~~~~~~~~~~~~i~v~lLtg~~~~~er~~i~~~i~~G~~~iiIGTHAL~q~~v~F~~LgLvViDEQH  404 (700)
                      |+||||||||+|||++|+++|++++++|+||||++++++|+++++++++|+++||||||||||++|.|+|||||||||||
T Consensus       310 a~maPTeiLa~Qh~~~~~~~~~~~~i~v~lltg~~~~~~~~~~~~~~~~g~~~i~iGTHal~~~~v~f~~LglvviDEQH  389 (677)
T PRK10917        310 ALMAPTEILAEQHYRNLKKWLEPLGIRVALLTGSLKGKERREILEALASGEADIVIGTHALIQDDVEFHNLGLVIIDEQH  389 (677)
T ss_pred             EEECCCHHHHHHHHHHHHHHHHHCCCEEEEEECCCHHHHHHHHHHHHHCCCCCEEEEHHHHHHCCCCCCCCCEEEECHHH
T ss_conf             99876799999999999987763498899840774177899999998579977897307877355644666569953057


Q ss_pred             CCCHHHHHHHHHCCCCCCCEEECHHHHHHHHHHHHHHCCCHHHHCCCCCCCCCCEEEEEECCCHHHHHHHHHHHHCCCCE
Q ss_conf             33568899874025677610101013227899997520101111023557666207999702002689999763103873
Q gi|254780945|r  405 RFGVQQRLKLTQKATAPHVLLMTATPIPRTLVLTSLGDIDISKITEKPAGRKPIKTVIIPINRIDEVIERLKVVLSEGKK  484 (700)
Q Consensus       405 RFGV~QR~~L~~Kg~~ph~L~MtATPIPRTLal~~ygdldvS~i~e~P~gR~~I~T~~~~~~~~~~~~~~i~~~l~~g~q  484 (700)
                      ||||+||.+|.+||.+||+|+|||||||||||||+|||||+|+|+|+|+||+||+|++++.++++++|++|++++++|+|
T Consensus       390 rFGV~QR~~l~~k~~~~~~L~mtATPIPRtla~~~~g~~d~s~i~~~P~~r~~i~T~~~~~~~~~~~~~~i~~~~~~g~q  469 (677)
T PRK10917        390 RFGVHQRLALREKGENPHVLVMTATPIPRTLAMTAYGDLDVSVIDELPPGRKPITTVVIPDSRRDEVYERIREEIAKGRQ  469 (677)
T ss_pred             HHHHHHHHHHHHCCCCCEEEEEECCCCHHHHHHHHHCCCCEEECCCCCCCCCCCEEEEECHHHHHHHHHHHHHHHHCCCE
T ss_conf             76399999998439997299983688438899987357666666779999987269997625689999999999975992


Q ss_pred             EEEEECCCCCCCCCCCCHHHHHHHHHHHHCCC-CEECCCCCCCHHHHHHHHHHHHCCCEEEEEECHHHHCCCCCCCCCEE
Q ss_conf             89997120122111210146666666866371-03120146998999999999755986999980034104688876589
Q gi|254780945|r  485 AYWICPQIEEKKESNFRSVVERFNSLHEHFTS-SIAIIHGRMSDIDKESVMDSFKNGTCKLLIATTVIEVGIDVVDASII  563 (700)
Q Consensus       485 ~y~VcPlIeese~~~~~~~~~~~~~l~~~~~~-~v~~lHGkm~~~ek~~~m~~F~~g~~~iLvaTtviEVGvdvpna~~m  563 (700)
                      ||||||+|||||++|+.|+++.|+.|++.||+ +|+++||||+++||+++|++|++|++|||||||||||||||||||+|
T Consensus       470 ~y~v~p~ieese~~~~~~~~~~~~~l~~~~~~~~v~~~hG~m~~~ek~~~m~~F~~g~~~iLvsTtviEvGvdvpna~~m  549 (677)
T PRK10917        470 AYVVCPLIEESEKLDLQSAEETYEELQKALPELRVGLLHGRMKPAEKDAVMAAFKAGEIDILVATTVIEVGVDVPNATVM  549 (677)
T ss_pred             EEEEECCCCCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCCCHHHHHHHHHHHHCCCCCEEEECCEEECCCCCCCCCEE
T ss_conf             89994131123320177799999999844899759983078987899999999983999999989897558678888589


Q ss_pred             EEECHHHCCHHHHHHHHHCCCCCCCCEEEEEEECCCCCHHHHHHHHHHHHHCHHHHHHHHHHHHCCCCCCCCCHHCCCCC
Q ss_conf             98585254746887730116678983599997088899879999999984142589999998520630002600069874
Q gi|254780945|r  564 IIENAEHFGLAQLHQLRGRVGRGEEISSCILLYHPPLSKNSYTRLSVLKNTEDGFLIAEEDLKQRKEGEILGIKQSGMPK  643 (700)
Q Consensus       564 vI~~aerfGLsqLHQLRGRVGRg~~~s~c~l~~~~~~~~~~~~Rl~~l~~~~dGf~iAe~Dl~lRG~G~~~G~~QsG~~~  643 (700)
                      ||+||||||||||||||||||||+.+|||||+++++.++.+++||++|++|+|||+|||+||++|||||+||++|||.|+
T Consensus       550 vi~~aerfGlsqLhQLRGRVgRg~~~~~c~l~~~~~~~~~~~~Rl~~~~~~~dGf~iae~Dl~lRg~G~~~G~~QsG~~~  629 (677)
T PRK10917        550 VIENAERFGLAQLHQLRGRVGRGAAQSYCVLLYKDPLSETARERLKIMRETNDGFEIAEKDLELRGPGELLGTRQSGLPE  629 (677)
T ss_pred             EEECCCCCCHHHHHHHCCCCCCCCCCEEEEEEECCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHCCCCCCCCCCCCCCCC
T ss_conf             99770105367887742743678884589998389999789999999998587499999999615885668876669887


Q ss_pred             CCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCC
Q ss_conf             40003887599999999999999984846366
Q gi|254780945|r  644 FLIAQPELHDSLLEIARKDAKHILTQDPDLTS  675 (700)
Q Consensus       644 ~~~~d~~~d~~ll~~a~~~a~~~~~~d~~l~~  675 (700)
                      |++||+.+|.+||+.||++|+.++++||+|..
T Consensus       630 f~~adl~~D~~il~~Ar~~A~~il~~dp~l~~  661 (677)
T PRK10917        630 FKVADLVRDQELLEEARKEARELLERDPELAE  661 (677)
T ss_pred             CEEEEHHHHHHHHHHHHHHHHHHHHHCHHHHH
T ss_conf             44740887799999999999999987979899


No 3  
>TIGR00643 recG ATP-dependent DNA helicase RecG; InterPro: IPR004609 The ATP-dependent DNA helicase RecG 3.6.1 from EC plays a critical role in recombination and DNA repair. It helps to process Holliday junction intermediates to mature products by catalysing branch migration. RecG has DNA unwinding activity characteristic of a DNA helicase with 3' to 5' polarity.; GO: 0004003 ATP-dependent DNA helicase activity, 0006281 DNA repair, 0006310 DNA recombination.
Probab=100.00  E-value=0  Score=1832.22  Aligned_cols=627  Identities=42%  Similarity=0.670  Sum_probs=595.4

Q ss_pred             CCCCCHHHHHHHCCCCCCCCC----------CCCCHHHCCCCC--EEEEEEEEE-----------EEE----EECCCCCC
Q ss_conf             885548987870897401344----------446478889987--899999998-----------975----42158983
Q gi|254780945|r   36 ANETRFIDLLFYHPSSFIDRH----------YRPKISEISEER--IVTITGYIS-----------QHS----SFQLQKRR   88 (700)
Q Consensus        36 ~GI~ti~DLL~~~PrrYeDr~----------~~~~I~~l~~g~--~vti~g~V~-----------~~~----~~~~~~r~   88 (700)
                      +||+||.|||+|||++|+|++          ....|.++.+|+  .+++.++|.           ++.    ....++++
T Consensus         1 lgi~tv~DLL~yfP~~Y~D~~naqvdiedGq~~~~~~~~~~~~g~~~~~~~~V~~~~~~~~~~~~~~~Pedl~~~~~~~~   80 (721)
T TIGR00643         1 LGIHTVQDLLFYFPRRYEDRTNAQVDIEDGQQLQTIGELLSGEGVRVTVVGEVLEVIVSTEPKGRSLKPEDLIFGFKRRK   80 (721)
T ss_pred             CCCCHHHHHHHHCCCCEECCCCCCCCHHCCHHHEEHHHCCCCCCEEEEEEEEEEEEEEECCCCCCCCCCHHHHHCCCCCC
T ss_conf             96001789996488750000234010002401100211122474599999999999997267888667212110146775


Q ss_pred             EEEEEEEC--CCCEEEEEEEC--CCHHHHHHHCCCCCEEEEEEEEEECCC----------EEEEECCEEEECCCC-C--C
Q ss_conf             38999981--89369999951--887899873289888999989973187----------799977868962643-3--4
Q gi|254780945|r   89 PYKILLND--GTGEITLLFFY--RKTEMLKNVFFEGRKITVTGKIKKLKN----------RIIMVHPHYIFHNSQ-D--V  151 (700)
Q Consensus        89 ~~~v~v~D--~tg~i~lvfFn--~~~~yl~k~lk~G~~v~vsGKv~~~~~----------~~qi~hPe~~~~~~~-~--~  151 (700)
                      .+++.+.|  +...+.++|||  + .+|+++.|++|++++||||++.+++          .-.|.||++...... +  .
T Consensus        81 ~l~~~~~~~~~~~~~~~~ffnrGf-~~~~~~~f~~G~~v~~yG~~k~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e  159 (721)
T TIGR00643        81 VLKLRLKDGKGEKVLELRFFNRGF-RAFLKKKFKVGSKVVVYGKVKSSKFEDQLEMRRYLKALLSHPEVKSEKDSVDEFE  159 (721)
T ss_pred             EEEEEEEECCCEEEEEEEEECCCH-HHHHHHHCCCCCEEEEEEEEEECCHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCH
T ss_conf             368999971414789999616661-5899975266979999987761320210001355467650775200212377401


Q ss_pred             CCCCCCCCCCCCHH-----HHHHHHHHHHHHHHHHHCC-----CCCCCCHHHHHCCCCCCHHHHHHHHC-CCCCHHH--H
Q ss_conf             44441100000000-----0045430013457874046-----84338977862056999889998620-4589656--5
Q gi|254780945|r  152 NFPLIEAVYSLPTG-----LSVDLFKKIIVEALSRLPV-----LPEWIEKDLLQKKSFPSIAEAFNIIH-NPRKAKD--F  218 (700)
Q Consensus       152 ~~~~I~PIYplt~G-----Lsqk~irk~I~~aL~~~~~-----i~E~LP~~ll~k~~L~s~~eAL~~IH-~P~~~~d--l  218 (700)
                      ..++|.||||+++|     |+|+.+++.|.+||+.+..     ++|.||++++++|+|+++.+||+.|| +|++.++  +
T Consensus       160 ~~~~i~PvY~~~~gGelqe~~~~~l~k~i~~AL~~l~~~~yry~~~~lP~~l~~ky~l~~~~~al~~~H~~P~~~~~~~L  239 (721)
T TIGR00643       160 LEGKILPVYPLTEGGELQELKQKKLRKLIKQALDQLDKSLYRYLEDPLPEELREKYGLLSLEDALRAIHRFPKTLELEAL  239 (721)
T ss_pred             HCCCEEEEEECCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHCCCCCCCCCHHHH
T ss_conf             05721223423557421103877888999999999987776530333674678640578879999843889986116877


Q ss_pred             H-HHHHHHHHHHHHHHHHHHHHHHHHHHH----------HH-HCCCCCCCCCC-HHHHHHHH-HCCCCCCHHHHHHHHHH
Q ss_conf             6-679999999876666666777765555----------43-20357678775-78999986-30246798899999999
Q gi|254780945|r  219 E-WTSPARERLAYDELLAGQIALLLMRKQ----------FK-KEIGIPINVEG-KIAQKILR-NIPFSPTKSQESAIKDI  284 (700)
Q Consensus       219 e-~~~~ArkRLafeELl~~QL~l~~~r~~----------~~-~~~~~~~~~~~-~~~~~f~~-~LPF~LT~~Q~~ai~eI  284 (700)
                      + ..+.||+||+|||+|++|+++..+|.+          .+ +..+.+...+. ++.++|++ +|||+||+||++||+||
T Consensus       240 ~~g~~~A~~rLif~E~f~lQl~~~~~~~~~~~~~~l~~~~~~~~~a~~~~~~~~~~l~k~~~~~LPF~LT~aQ~r~v~EI  319 (721)
T TIGR00643       240 ESGLELARRRLIFDELFLLQLAMLARRLEKLIEKDLLREEKQQFSAPPLNVSENELLEKFLAKSLPFELTRAQKRVVKEI  319 (721)
T ss_pred             HHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEEEECHHHHHHHHHHHCCCCCCCHHHHHHHHHH
T ss_conf             76543143011699999999999988875431145565454305665110020579999998528887767789999999


Q ss_pred             HHHHCCCCCCEEEEEECCCCCHHHHHHHHHHHHHHHHCCEEEEEHHHHHHHHHHHHHHHHCCCCCCEEEEEECCCCHHHH
Q ss_conf             98410013430788621442236999999733444305458861279999999986211014578658996246422566
Q gi|254780945|r  285 LQDMSQKNRMLRILQGDVGSGKTLVALIAMAAAVEAGGQAVIMAPIGILAQQHYEFIKKYTQNTQIIVEIITGNMPQAHR  364 (700)
Q Consensus       285 ~~Dl~~~~pM~RLLQGDVGSGKTiVA~~A~l~~~~~G~Q~alMaPTEILA~QH~~~~~~~~~~~~i~v~lLtg~~~~~er  364 (700)
                      ..||+++.|||||||||||||||+||++||+.++++||||||||||||||+|||+++.+||++++++|+|||||+++++|
T Consensus       320 ~~DL~~~~pMnRLlQGDVGSGKT~VA~la~l~~i~~GYQ~ALMAPTEiLA~QHy~~~~~~l~p~~~~vaLLTGs~k~~~r  399 (721)
T TIGR00643       320 LQDLKSDVPMNRLLQGDVGSGKTLVAALAMLAAIESGYQVALMAPTEILAEQHYDSLRNLLAPLGIEVALLTGSLKGKQR  399 (721)
T ss_pred             HHHHCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCEEEEECCHHHHHHHHHHHHHHHHCCCCCEEEEEECCCCHHHH
T ss_conf             98614787532221101066389999999999984698099917768999999999999623548578886156678789


Q ss_pred             HHHHHHHCCCCCEEEEECHHHCCCCCCCCCCCEEEECCCCCCCHHHHHHHHHCCC-------CCCCEEECHHHHHHHHHH
Q ss_conf             7687762134754864111201334554444178852101335688998740256-------776101010132278999
Q gi|254780945|r  365 RKALERIAHGQAHIIIGTHALFQDSIQYYKLILVIVDEQHRFGVQQRLKLTQKAT-------APHVLLMTATPIPRTLVL  437 (700)
Q Consensus       365 ~~i~~~i~~G~~~iiIGTHAL~q~~v~F~~LgLvViDEQHRFGV~QR~~L~~Kg~-------~ph~L~MtATPIPRTLal  437 (700)
                      +++++.|++|++++||||||||||.|+|++||||||||||||||.||.+|.+||.       +||+|+||||||||||||
T Consensus       400 ~~~~e~i~~G~~~~~vGTHALiqe~vef~~L~lVIiDEQHRFGV~QR~~L~~KG~~~~~~G~~PH~L~MtATPIPRTLAL  479 (721)
T TIGR00643       400 KELLETIASGEIHLVVGTHALIQEKVEFKRLGLVIIDEQHRFGVEQRKKLREKGQEGSMIGFAPHVLVMTATPIPRTLAL  479 (721)
T ss_pred             HHHHHHHHCCCCEEEEHHHHHHHHHHHHHCCCEEEEECCCCCHHHHHHHHHHHHHCCCCCCCCCCEEEEECCCCHHHHHH
T ss_conf             99999986395205733135545214431477489932335607899999986220688677777646637881478997


Q ss_pred             HHHHCCCHHHHCCCCCCCCCCEEEEEECCCH----HHHHHHHHHHHCCCCEEEEEECCCCCCCCC-CCCHHHHHHHHHHH
Q ss_conf             9752010111102355766620799970200----268999976310387389997120122111-21014666666686
Q gi|254780945|r  438 TSLGDIDISKITEKPAGRKPIKTVIIPINRI----DEVIERLKVVLSEGKKAYWICPQIEEKKES-NFRSVVERFNSLHE  512 (700)
Q Consensus       438 ~~ygdldvS~i~e~P~gR~~I~T~~~~~~~~----~~~~~~i~~~l~~g~q~y~VcPlIeese~~-~~~~~~~~~~~l~~  512 (700)
                      |+|||||+|+|||||+||+||+|+|+..++.    ++||+++.+||++|+|||||||+|||||++ |+++|++.|+.|++
T Consensus       480 t~yGDld~S~I~elP~GR~pi~T~~~~~~~~~aW~~~v~~~~~~E~~~GrQaYvv~PlI~ESE~lp~lk~A~~~~~~l~~  559 (721)
T TIGR00643       480 TVYGDLDVSIIDELPPGRKPITTYLIKHKEKGAWIDIVYEFIEEEIAKGRQAYVVYPLIEESEKLPDLKAAEALYERLKK  559 (721)
T ss_pred             HHHHCCEEEEECCCCCCCCEEEEEEEECCCCCCCHHHHHHHHHHHHHCCCCEEEEECCCCCCCCCCHHHHHHHHHHHHHH
T ss_conf             76500003343168545933899888427887756899999999983289089996440320047168999999999888


Q ss_pred             HC-CC-CEECCCCCCCHHHHHHHHHHHHCCCEEEEEECHHHHCCCCCCCCCEEEEECHHHCCHHHHHHHHHCCCCCCCCE
Q ss_conf             63-71-03120146998999999999755986999980034104688876589985852547468877301166789835
Q gi|254780945|r  513 HF-TS-SIAIIHGRMSDIDKESVMDSFKNGTCKLLIATTVIEVGIDVVDASIIIIENAEHFGLAQLHQLRGRVGRGEEIS  590 (700)
Q Consensus       513 ~~-~~-~v~~lHGkm~~~ek~~~m~~F~~g~~~iLvaTtviEVGvdvpna~~mvI~~aerfGLsqLHQLRGRVGRg~~~s  590 (700)
                      .| |. +|+|+||||+++|||+||++|++|++||||||||||||||||||||||||||||||||||||||||||||+++|
T Consensus       560 ~f~~~~~v~LlHGrm~~~eK~~vm~~F~~~~~~ILVsTTVIEVGVDVPnAtvMVIe~AeRFGLSQLHQLRGRVGRG~~~S  639 (721)
T TIGR00643       560 AFLPKYNVGLLHGRMKSDEKEAVMEEFREGEVDILVSTTVIEVGVDVPNATVMVIEDAERFGLSQLHQLRGRVGRGDHQS  639 (721)
T ss_pred             HHCCCCEEEEECCCCCHHHHHHHHHHHHHCCCEEEEEEEEEEEEEECCCCCEEEEECCCHHHHHHHHHHCEEECCCCCCC
T ss_conf             61221001133068984789999998521583699997689998617977278886655103688876350012689750


Q ss_pred             EEEEEEC----CCCCHHHHHHHHHHHHHCHHHHHHHHHHHHCCCCCCCC---CHHCC-CCCCCCCCHHH-HHHHHHHHHH
Q ss_conf             9999708----88998799999999841425899999985206300026---00069-87440003887-5999999999
Q gi|254780945|r  591 SCILLYH----PPLSKNSYTRLSVLKNTEDGFLIAEEDLKQRKEGEILG---IKQSG-MPKFLIAQPEL-HDSLLEIARK  661 (700)
Q Consensus       591 ~c~l~~~----~~~~~~~~~Rl~~l~~~~dGf~iAe~Dl~lRG~G~~~G---~~QsG-~~~~~~~d~~~-d~~ll~~a~~  661 (700)
                      ||+|+++    +|.++.+++||++|.+|+|||.|||+||++|||||+||   ++||| +++|++|||++ |.++|..||+
T Consensus       640 yC~L~~kdei~~p~~~~~~~RL~~~~~~~DGF~iAE~DL~lRGPGd~lGtk~~~QSG~~~~F~vA~l~~qD~~~l~~ar~  719 (721)
T TIGR00643       640 YCLLVYKDEIKNPKSESAKKRLRVMAETLDGFVIAEEDLKLRGPGDLLGTKGTKQSGKLPEFRVADLVRQDREILQEARE  719 (721)
T ss_pred             EEEEECCCCCCCCCCHHHHHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHH
T ss_conf             79981253257888646899999985155606778875532588242358884021556674213767722899999998


Q ss_pred             HH
Q ss_conf             99
Q gi|254780945|r  662 DA  663 (700)
Q Consensus       662 ~a  663 (700)
                      +|
T Consensus       720 ~a  721 (721)
T TIGR00643       720 AA  721 (721)
T ss_pred             HC
T ss_conf             39


No 4  
>TIGR00580 mfd transcription-repair coupling factor; InterPro: IPR004576 All proteins in this family for which functions are known are DNA-dependent ATPases that function in the process of transcription-coupled DNA repair in which the repair of the transcribed strand of actively transcribed genes is repaired at a higher rate than the repair of non-transcribed regions of the genome and than the non-transcribed strand of the same gene. A lesion in the template strand blocks the RNA polymerase complex (RNAP). The RNAP-DNA-RNA complex is specifically recognised by TcrF, which releases RNAP and the truncated transcript. The TcrF may replace RNAP at the lesion site and then recruit the UvrA/B/C repair system.; GO: 0003684 damaged DNA binding, 0005524 ATP binding, 0006281 DNA repair.
Probab=100.00  E-value=0  Score=1068.19  Aligned_cols=412  Identities=37%  Similarity=0.561  Sum_probs=389.1

Q ss_pred             HHHHHHHHHHCCCCCCCCCCHHHHHHHHHCCCCCCHHHHHHHHHHHHHHCCCCCCEEEEEECCCCCHHHHHHHHHHHHHH
Q ss_conf             77655554320357678775789999863024679889999999998410013430788621442236999999733444
Q gi|254780945|r  240 LLLMRKQFKKEIGIPINVEGKIAQKILRNIPFSPTKSQESAIKDILQDMSQKNRMLRILQGDVGSGKTLVALIAMAAAVE  319 (700)
Q Consensus       240 l~~~r~~~~~~~~~~~~~~~~~~~~f~~~LPF~LT~~Q~~ai~eI~~Dl~~~~pM~RLLQGDVGSGKTiVA~~A~l~~~~  319 (700)
                      |..+..+++...|.+++.+.++...|-+++||+-|+||.+||+||.+||.++.||-|||+||||-|||.|||.|++.|+.
T Consensus       476 Li~lyA~R~~~~G~af~~D~e~~~~Fe~~FPfeeT~DQ~~AI~eik~Dm~~~~~MDRL~CGDVGfGKTEVAmRAaFkAv~  555 (997)
T TIGR00580       476 LIELYAKRKASKGHAFPPDDEWQAEFEDSFPFEETPDQLKAIEEIKADMESPRPMDRLVCGDVGFGKTEVAMRAAFKAVL  555 (997)
T ss_pred             HHHHHHHHHHCCCCCCCCCHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHCCCCCCCEEEECCCCCCHHHHHHHHHHHHHC
T ss_conf             99999987515898898880899999983878897789999999999740689873465245488536888878887633


Q ss_pred             HH----CCEEEEEHHHHHHHHHHHHHHHHCCCCCCEEEEEECCCCHHHHHHHHHHHCCCCCEEEEECHHHCCCCCCCCCC
Q ss_conf             30----54588612799999999862110145786589962464225667687762134754864111201334554444
Q gi|254780945|r  320 AG----GQAVIMAPIGILAQQHYEFIKKYTQNTQIIVEIITGNMPQAHRRKALERIAHGQAHIIIGTHALFQDSIQYYKL  395 (700)
Q Consensus       320 ~G----~Q~alMaPTEILA~QH~~~~~~~~~~~~i~v~lLtg~~~~~er~~i~~~i~~G~~~iiIGTHAL~q~~v~F~~L  395 (700)
                      +|    +|||+||||.|||+|||+||++.|.++||+|++|.+=.+++|.++|+.++++|+||||||||+|+|.+|.|+||
T Consensus       556 ~gneylKQVavLVPTT~LA~QHf~tf~~RF~~fPv~I~~LSRF~~~~E~~~iL~~la~G~iDI~IGTH~lL~k~v~FKdL  635 (997)
T TIGR00580       556 DGNEYLKQVAVLVPTTILAQQHFETFKERFANFPVTIELLSRFRSAKEKKEILKELASGKIDILIGTHKLLQKDVKFKDL  635 (997)
T ss_pred             CCCCEECEEEEECCHHHHHHHHHHHHHHHHCCCCEEEEECCCCCCCHHHHHHHHHHHCCCEEEEECCHHHHCCCEEEECC
T ss_conf             87822011689627044277788999997378981687527756737899999997559422663010412785468638


Q ss_pred             CEEEECCCCCCCHHHHHHHHHCCCCCCCEEECHHHHHHHHHHHHHHCCCHHHHCCCCCCCCCCEEEEEECCCHHHHHHHH
Q ss_conf             17885210133568899874025677610101013227899997520101111023557666207999702002689999
Q gi|254780945|r  396 ILVIVDEQHRFGVQQRLKLTQKATAPHVLLMTATPIPRTLVLTSLGDIDISKITEKPAGRKPIKTVIIPINRIDEVIERL  475 (700)
Q Consensus       396 gLvViDEQHRFGV~QR~~L~~Kg~~ph~L~MtATPIPRTLal~~ygdldvS~i~e~P~gR~~I~T~~~~~~~~~~~~~~i  475 (700)
                      ||+||||+|||||+|.++|.+=-.+.|+|.||||||||||-|++-|=-|+|+|.++|.+|.||.|++.+.+. .-|=++|
T Consensus       636 GLlIiDEEQRFGV~~KE~lK~~~~~VDvLtlsATPIPRTL~MSl~g~RdlS~I~TPP~~R~pv~T~v~~~~~-~~~~~AI  714 (997)
T TIGR00580       636 GLLIIDEEQRFGVKQKEKLKELKTSVDVLTLSATPIPRTLHMSLSGIRDLSIIATPPEDRLPVRTFVMEYDD-ELVREAI  714 (997)
T ss_pred             CCEEEECCCCCCCCHHHHHCCCCCCCCEEEEECCCCHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCH-HHHHHHH
T ss_conf             646983143488311555300156765676337896055899987553322105788877424887742786-8999999


Q ss_pred             HHHHCCCCEEEEEECCCCCCCCCCCCHHHHHHHHHHHHCCC-CEECCCCCCCHHHHHHHHHHHHCCCEEEEEECHHHHCC
Q ss_conf             76310387389997120122111210146666666866371-03120146998999999999755986999980034104
Q gi|254780945|r  476 KVVLSEGKKAYWICPQIEEKKESNFRSVVERFNSLHEHFTS-SIAIIHGRMSDIDKESVMDSFKNGTCKLLIATTVIEVG  554 (700)
Q Consensus       476 ~~~l~~g~q~y~VcPlIeese~~~~~~~~~~~~~l~~~~~~-~v~~lHGkm~~~ek~~~m~~F~~g~~~iLvaTtviEVG  554 (700)
                      ++||.+|+|||+|+|.||        |.+..-..|++..|+ +|++.||||..+|-|.||.+|..|+.|||||||+||-|
T Consensus       715 ~rEL~RgGQvFyv~Nrie--------~i~~~~~~l~~LVP~arIaiaHGqM~e~eLE~~m~~F~~~~~~vLvcTTIIE~G  786 (997)
T TIGR00580       715 RRELLRGGQVFYVHNRIE--------SIEKLKTQLRELVPEARIAIAHGQMTENELEEVMLEFYKGEFDVLVCTTIIESG  786 (997)
T ss_pred             HHHHCCCCEEEEEECCCC--------CHHHHHHHHHHCCCCEEEEEEECCCCHHHHHHHHHHHHCCCCCEEEEHHHHHCC
T ss_conf             975313981899808813--------578999999850843267888335684568999998626843301322146505


Q ss_pred             CCCCCCCEEEEECHHHCCHHHHHHHHHCCCCCCCCEEEEEEECC--CCCHHHHHHHHHHHHHCH---HHHHHHHHHHHCC
Q ss_conf             68887658998585254746887730116678983599997088--899879999999984142---5899999985206
Q gi|254780945|r  555 IDVVDASIIIIENAEHFGLAQLHQLRGRVGRGEEISSCILLYHP--PLSKNSYTRLSVLKNTED---GFLIAEEDLKQRK  629 (700)
Q Consensus       555 vdvpna~~mvI~~aerfGLsqLHQLRGRVGRg~~~s~c~l~~~~--~~~~~~~~Rl~~l~~~~d---Gf~iAe~Dl~lRG  629 (700)
                      |||||||+|||++||.||||||||||||||||.+++||||+|.+  ++|+.|.+||++|.+.++   ||.||-+||++||
T Consensus       787 IDIPnANTiIi~~AD~FGLaQLYQLRGRVGRs~~~AYAYlL~~~~~~Lt~~A~~RL~ai~~f~eLGaGf~iA~hDlEIRG  866 (997)
T TIGR00580       787 IDIPNANTIIIDRADKFGLAQLYQLRGRVGRSKKKAYAYLLYPHQKALTEDALKRLEAIQEFSELGAGFKIALHDLEIRG  866 (997)
T ss_pred             CCHHHHHHHHHHHHCCCCHHHHHHCCCEECCCCCEEEEEECCCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHCCCCCC
T ss_conf             64100126868752114703474536312058712689833477400145899999999730113521678863110035


Q ss_pred             CCCCCCCHHCCCCCCCCCCHHHHH--HHHHHHHHHHH
Q ss_conf             300026000698744000388759--99999999999
Q gi|254780945|r  630 EGEILGIKQSGMPKFLIAQPELHD--SLLEIARKDAK  664 (700)
Q Consensus       630 ~G~~~G~~QsG~~~~~~~d~~~d~--~ll~~a~~~a~  664 (700)
                      .|++||..|||    .+..+-.|.  .+|++|=+.-+
T Consensus       867 aGNLLG~eQSG----~I~~vGfdLY~~lL~eAi~~~~  899 (997)
T TIGR00580       867 AGNLLGEEQSG----HIESVGFDLYVELLEEAIEELK  899 (997)
T ss_pred             CHHHCCCCCCC----HHHHHHHHHHHHHHHHHHHHHH
T ss_conf             50012601264----0656778999999999999987


No 5  
>PRK10689 transcription-repair coupling factor; Provisional
Probab=100.00  E-value=0  Score=1045.40  Aligned_cols=414  Identities=36%  Similarity=0.526  Sum_probs=388.0

Q ss_pred             HHHHHHHHHHCCCCCCCCCCHHHHHHHHHCCCCCCHHHHHHHHHHHHHHCCCCCCEEEEEECCCCCHHHHHHHHHHHHHH
Q ss_conf             77655554320357678775789999863024679889999999998410013430788621442236999999733444
Q gi|254780945|r  240 LLLMRKQFKKEIGIPINVEGKIAQKILRNIPFSPTKSQESAIKDILQDMSQKNRMLRILQGDVGSGKTLVALIAMAAAVE  319 (700)
Q Consensus       240 l~~~r~~~~~~~~~~~~~~~~~~~~f~~~LPF~LT~~Q~~ai~eI~~Dl~~~~pM~RLLQGDVGSGKTiVA~~A~l~~~~  319 (700)
                      |.....+++..+|+++..+..+..+|-+++||+.|.||.+||+||.+||.+++||.|||+||||.|||.||+.|++.|+.
T Consensus       568 Ll~lYA~R~~~~G~af~~d~~~~~eFe~~FpyeET~DQl~AI~eV~~DMes~~PMDRLiCGDVGfGKTEVA~RAAFkav~  647 (1148)
T PRK10689        568 LLDIYAQRAAKEGFAFKHDREQYQLFCDSFPFETTPDQAQAINAVLSDMCQPLAMDRLVCGDVGFGKTEVAMRAAFLAVE  647 (1148)
T ss_pred             HHHHHHHHHCCCCCCCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHCCCCCCEEEECCCCCCHHHHHHHHHHHHHH
T ss_conf             99999987205688678984999999960999787689999999987763886774156768888779999999999996


Q ss_pred             HHCCEEEEEHHHHHHHHHHHHHHHHCCCCCCEEEEEECCCCHHHHHHHHHHHCCCCCEEEEECHHHCCCCCCCCCCCEEE
Q ss_conf             30545886127999999998621101457865899624642256676877621347548641112013345544441788
Q gi|254780945|r  320 AGGQAVIMAPIGILAQQHYEFIKKYTQNTQIIVEIITGNMPQAHRRKALERIAHGQAHIIIGTHALFQDSIQYYKLILVI  399 (700)
Q Consensus       320 ~G~Q~alMaPTEILA~QH~~~~~~~~~~~~i~v~lLtg~~~~~er~~i~~~i~~G~~~iiIGTHAL~q~~v~F~~LgLvV  399 (700)
                      +|+|||+||||+|||+|||++|++.|.+++|+|++|+.-.++||++++++++++|++|||||||+|+|++|.|+||||+|
T Consensus       648 ~gkQVavlvPTTiLA~QH~~tF~~Rf~~~pv~i~~LsRf~s~ke~~~i~~~l~~G~idIvIGTH~ll~~dv~f~~LGLlI  727 (1148)
T PRK10689        648 NHKQVAVLVPTTLLAQQHYDNFRDRFANWPVRIEMLSRFRSAKEQTQILAEAAEGKIDILIGTHKLLQSDVKWKDLGLLI  727 (1148)
T ss_pred             CCCEEEEEECCCCCHHHHHHHHHHHHHCCCCEEEEECCCCCHHHHHHHHHHHHCCCCCEEEHHHHHHCCCCCCCCCCEEE
T ss_conf             39808998366223799999999876415733775038888999999999986699877620488866986546664378


Q ss_pred             ECCCCCCCHHHHHHHHHCCCCCCCEEECHHHHHHHHHHHHHHCCCHHHHCCCCCCCCCCEEEEEECCCHHHHHHHHHHHH
Q ss_conf             52101335688998740256776101010132278999975201011110235576662079997020026899997631
Q gi|254780945|r  400 VDEQHRFGVQQRLKLTQKATAPHVLLMTATPIPRTLVLTSLGDIDISKITEKPAGRKPIKTVIIPINRIDEVIERLKVVL  479 (700)
Q Consensus       400 iDEQHRFGV~QR~~L~~Kg~~ph~L~MtATPIPRTLal~~ygdldvS~i~e~P~gR~~I~T~~~~~~~~~~~~~~i~~~l  479 (700)
                      |||+|||||.|+++|.+...++|+|+||||||||||.|++.|..|+|+|.+.|.+|.||+|++...+.. -+-++|.+|+
T Consensus       728 iDEEqrFGV~~KE~lk~l~~~vdvLtltATPIPRTL~msl~G~rdlS~i~tpP~~R~~v~T~v~~~~~~-~i~eai~re~  806 (1148)
T PRK10689        728 VDEEHRFGVRHKERIKAMRADVDILTLTATPIPRTLNMAMSGMRDLSIIATPPARRLAVKTFVREYDSL-VVREAILREI  806 (1148)
T ss_pred             ECCCHHCCHHHHHHHHHCCCCCCEEEEECCCCHHHHHHHHCCCCCEEEECCCCCCCCCCEEEEECCCHH-HHHHHHHHHH
T ss_conf             601021379999999722899878976255644699998807733022136999898708998358729-9999999999


Q ss_pred             CCCCEEEEEECCCCCCCCCCCCHHHHHHHHHHHHCCC-CEECCCCCCCHHHHHHHHHHHHCCCEEEEEECHHHHCCCCCC
Q ss_conf             0387389997120122111210146666666866371-031201469989999999997559869999800341046888
Q gi|254780945|r  480 SEGKKAYWICPQIEEKKESNFRSVVERFNSLHEHFTS-SIAIIHGRMSDIDKESVMDSFKNGTCKLLIATTVIEVGIDVV  558 (700)
Q Consensus       480 ~~g~q~y~VcPlIeese~~~~~~~~~~~~~l~~~~~~-~v~~lHGkm~~~ek~~~m~~F~~g~~~iLvaTtviEVGvdvp  558 (700)
                      .+|+|||||||.|+        ++++..+.|++.+|+ +|++.||+|+..|.|++|.+|.+|++|||||||+||+|||||
T Consensus       807 ~rggq~~~~~~~~~--------~i~~~~~~~~~~~p~~~~~~~hg~m~~~~~e~~m~~f~~~~~~~l~~ttiie~g~dip  878 (1148)
T PRK10689        807 LRGGQVYYLYNDVE--------NIQKAAERLAELVPEARIAIGHGQMRERELERVMNDFHHQRFNVLVCTTIIETGIDIP  878 (1148)
T ss_pred             HHCCEEEEEECCHH--------HHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHHHHHHCCCCCEEEECCEEECCCCCC
T ss_conf             81880899953254--------1999999999748777189998999989999999999759988999897876586677


Q ss_pred             CCCEEEEECHHHCCHHHHHHHHHCCCCCCCCEEEEEEECC--CCCHHHHHHHHHHHHHCH---HHHHHHHHHHHCCCCCC
Q ss_conf             7658998585254746887730116678983599997088--899879999999984142---58999999852063000
Q gi|254780945|r  559 DASIIIIENAEHFGLAQLHQLRGRVGRGEEISSCILLYHP--PLSKNSYTRLSVLKNTED---GFLIAEEDLKQRKEGEI  633 (700)
Q Consensus       559 na~~mvI~~aerfGLsqLHQLRGRVGRg~~~s~c~l~~~~--~~~~~~~~Rl~~l~~~~d---Gf~iAe~Dl~lRG~G~~  633 (700)
                      |||+|||++||+||||||||||||||||++++||||++++  .+++.|++||+++.+.++   ||.||..||++||+|++
T Consensus       879 ~ant~ii~~a~~~gl~ql~qlrgrvgr~~~~ayaYll~~~~~~lt~~A~kRL~ai~~~~~lGsGf~iA~~DLeIRGaG~l  958 (1148)
T PRK10689        879 TANTIIIERADHFGLAQLHQLRGRVGRSHHQAYAWLLTPHPKAMTTDAQKRLEAIASLEDLGAGFALATHDLEIRGAGEL  958 (1148)
T ss_pred             CCCEEEEECHHHCCHHHHHHHCCCCCCCCCEEEEEEEECCCCCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCC
T ss_conf             88479997532145577775436557788707999986787778989999999999706776439999987722778567


Q ss_pred             CCCHHCCCCCCCCCCHHHHHHHHHHHHHHHH
Q ss_conf             2600069874400038875999999999999
Q gi|254780945|r  634 LGIKQSGMPKFLIAQPELHDSLLEIARKDAK  664 (700)
Q Consensus       634 ~G~~QsG~~~~~~~d~~~d~~ll~~a~~~a~  664 (700)
                      ||..|||.-.=.=.|++  .++|++|-...+
T Consensus       959 LG~~QsG~i~~vG~~lY--~~mL~~av~~lk  987 (1148)
T PRK10689        959 LGEEQSGSMETIGFSLY--MELLENAVDALK  987 (1148)
T ss_pred             CCCCCCCCHHHCCHHHH--HHHHHHHHHHHH
T ss_conf             88645631555069999--999999999986


No 6  
>COG1197 Mfd Transcription-repair coupling factor (superfamily II helicase) [DNA replication, recombination, and repair / Transcription]
Probab=100.00  E-value=0  Score=981.72  Aligned_cols=415  Identities=34%  Similarity=0.528  Sum_probs=389.4

Q ss_pred             HHHHHHHHHHCCCCCCCCCCHHHHHHHHHCCCCCCHHHHHHHHHHHHHHCCCCCCEEEEEECCCCCHHHHHHHHHHHHHH
Q ss_conf             77655554320357678775789999863024679889999999998410013430788621442236999999733444
Q gi|254780945|r  240 LLLMRKQFKKEIGIPINVEGKIAQKILRNIPFSPTKSQESAIKDILQDMSQKNRMLRILQGDVGSGKTLVALIAMAAAVE  319 (700)
Q Consensus       240 l~~~r~~~~~~~~~~~~~~~~~~~~f~~~LPF~LT~~Q~~ai~eI~~Dl~~~~pM~RLLQGDVGSGKTiVA~~A~l~~~~  319 (700)
                      |.....+++..+|+++..+..+.++|.+++||+.|.||.+||+||.+||.+++||.||++||||-|||.||+.|++.|+.
T Consensus       562 Li~lyA~R~~~~G~af~~d~~~q~~F~~~FPyeET~DQl~AI~eVk~DM~~~kpMDRLiCGDVGFGKTEVAmRAAFkAV~  641 (1139)
T COG1197         562 LIKLYAKRQAKKGFAFPPDTEWQEEFEASFPYEETPDQLKAIEEVKRDMESGKPMDRLICGDVGFGKTEVAMRAAFKAVM  641 (1139)
T ss_pred             HHHHHHHHHHCCCCCCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHCCCCCCHHEEECCCCCCHHHHHHHHHHHHHC
T ss_conf             99999987305687879985899999854998578789999999998860698661025657687599999999999863


Q ss_pred             HHCCEEEEEHHHHHHHHHHHHHHHHCCCCCCEEEEEECCCCHHHHHHHHHHHCCCCCEEEEECHHHCCCCCCCCCCCEEE
Q ss_conf             30545886127999999998621101457865899624642256676877621347548641112013345544441788
Q gi|254780945|r  320 AGGQAVIMAPIGILAQQHYEFIKKYTQNTQIIVEIITGNMPQAHRRKALERIAHGQAHIIIGTHALFQDSIQYYKLILVI  399 (700)
Q Consensus       320 ~G~Q~alMaPTEILA~QH~~~~~~~~~~~~i~v~lLtg~~~~~er~~i~~~i~~G~~~iiIGTHAL~q~~v~F~~LgLvV  399 (700)
                      +|+|||+||||.|||+|||+||++.|.+++|+|++|..-.++||.+++++++++|++|||||||+|+|++|+|+||||+|
T Consensus       642 ~GKQVAvLVPTTlLA~QHy~tFkeRF~~fPV~I~~LSRF~s~kE~~~il~~la~G~vDIvIGTHrLL~kdv~FkdLGLlI  721 (1139)
T COG1197         642 DGKQVAVLVPTTLLAQQHYETFKERFAGFPVRIEVLSRFRSAKEQKEILKGLAEGKVDIVIGTHRLLSKDVKFKDLGLLI  721 (1139)
T ss_pred             CCCEEEEECCCHHHHHHHHHHHHHHHCCCCEEEEEECCCCCHHHHHHHHHHHHCCCCCEEEECHHHHCCCCEEECCCEEE
T ss_conf             79749999260786899899999873389825888605578899999999985698458996317647896770476489


Q ss_pred             ECCCCCCCHHHHHHHHHCCCCCCCEEECHHHHHHHHHHHHHHCCCHHHHCCCCCCCCCCEEEEEECCCHHHHHHHHHHHH
Q ss_conf             52101335688998740256776101010132278999975201011110235576662079997020026899997631
Q gi|254780945|r  400 VDEQHRFGVQQRLKLTQKATAPHVLLMTATPIPRTLVLTSLGDIDISKITEKPAGRKPIKTVIIPINRIDEVIERLKVVL  479 (700)
Q Consensus       400 iDEQHRFGV~QR~~L~~Kg~~ph~L~MtATPIPRTLal~~ygdldvS~i~e~P~gR~~I~T~~~~~~~~~~~~~~i~~~l  479 (700)
                      |||+|||||.|+++|.+--.+.|+|.||||||||||-|++-|--|+|+|.+.|.+|.||.|++.+.+. .-+-+.|.+|+
T Consensus       722 IDEEqRFGVk~KEkLK~Lr~~VDvLTLSATPIPRTL~Msm~GiRdlSvI~TPP~~R~pV~T~V~~~d~-~~ireAI~REl  800 (1139)
T COG1197         722 IDEEQRFGVKHKEKLKELRANVDVLTLSATPIPRTLNMSLSGIRDLSVIATPPEDRLPVKTFVSEYDD-LLIREAILREL  800 (1139)
T ss_pred             EECHHHCCCCHHHHHHHHHCCCCEEEEECCCCCCHHHHHHHCCHHHHHCCCCCCCCCCEEEEEECCCH-HHHHHHHHHHH
T ss_conf             74435327117899987750572897417887544777774430331114799877212888715882-89999999987


Q ss_pred             CCCCEEEEEECCCCCCCCCCCCHHHHHHHHHHHHCCC-CEECCCCCCCHHHHHHHHHHHHCCCEEEEEECHHHHCCCCCC
Q ss_conf             0387389997120122111210146666666866371-031201469989999999997559869999800341046888
Q gi|254780945|r  480 SEGKKAYWICPQIEEKKESNFRSVVERFNSLHEHFTS-SIAIIHGRMSDIDKESVMDSFKNGTCKLLIATTVIEVGIDVV  558 (700)
Q Consensus       480 ~~g~q~y~VcPlIeese~~~~~~~~~~~~~l~~~~~~-~v~~lHGkm~~~ek~~~m~~F~~g~~~iLvaTtviEVGvdvp  558 (700)
                      .+|+|||+|||.|+        +.++..+.|++..|+ +|++.||+|...|-|++|.+|.+|+.|||||||+||-|||||
T Consensus       801 ~RgGQvfYv~NrV~--------~Ie~~~~~L~~LVPEarI~vaHGQM~e~eLE~vM~~F~~g~~dVLv~TTIIEtGIDIP  872 (1139)
T COG1197         801 LRGGQVFYVHNRVE--------SIEKKAERLRELVPEARIAVAHGQMRERELEEVMLDFYNGEYDVLVCTTIIETGIDIP  872 (1139)
T ss_pred             HCCCEEEEEECCCC--------CHHHHHHHHHHHCCCEEEEEEECCCCHHHHHHHHHHHHCCCCCEEEEEEEEECCCCCC
T ss_conf             15987999943331--------2999999999859846888852588889999999999728888898823430476777


Q ss_pred             CCCEEEEECHHHCCHHHHHHHHHCCCCCCCCEEEEEEECC--CCCHHHHHHHHHHHHHCH---HHHHHHHHHHHCCCCCC
Q ss_conf             7658998585254746887730116678983599997088--899879999999984142---58999999852063000
Q gi|254780945|r  559 DASIIIIENAEHFGLAQLHQLRGRVGRGEEISSCILLYHP--PLSKNSYTRLSVLKNTED---GFLIAEEDLKQRKEGEI  633 (700)
Q Consensus       559 na~~mvI~~aerfGLsqLHQLRGRVGRg~~~s~c~l~~~~--~~~~~~~~Rl~~l~~~~d---Gf~iAe~Dl~lRG~G~~  633 (700)
                      |||+|+|++||+|||||||||||||||+++++||||+|++  .+++.|.+||+++.+.++   ||.||.+||++||.|++
T Consensus       873 nANTiIIe~AD~fGLsQLyQLRGRVGRS~~~AYAYfl~p~~k~lT~~A~kRL~aI~~~~~LGaGf~lA~~DLeIRGaGNl  952 (1139)
T COG1197         873 NANTIIIERADKFGLAQLYQLRGRVGRSNKQAYAYFLYPPQKALTEDAEKRLEAIASFTELGAGFKLAMHDLEIRGAGNL  952 (1139)
T ss_pred             CCCEEEEECCCCCCHHHHHHHCCCCCCCCCEEEEEEEECCCCCCCHHHHHHHHHHHHHHHCCCHHHHHHCCHHCCCCCCC
T ss_conf             87558896543345788887516547767628999962675545878999999997233237517887520100454134


Q ss_pred             CCCHHCCCCCCCCCCHHHHHHHHHHHHHHHHH
Q ss_conf             26000698744000388759999999999999
Q gi|254780945|r  634 LGIKQSGMPKFLIAQPELHDSLLEIARKDAKH  665 (700)
Q Consensus       634 ~G~~QsG~~~~~~~d~~~d~~ll~~a~~~a~~  665 (700)
                      ||..|||.-.=.=+||+  .++|++|-..-+.
T Consensus       953 LG~eQSG~I~~VGf~LY--~~mLeeAI~~lk~  982 (1139)
T COG1197         953 LGEEQSGHIESVGFDLY--MEMLEEAIAALKG  982 (1139)
T ss_pred             CCCCCCCCHHEECHHHH--HHHHHHHHHHHHC
T ss_conf             67545676101229999--9999999998736


No 7  
>PRK05580 primosome assembly protein PriA; Validated
Probab=100.00  E-value=1.5e-35  Score=298.36  Aligned_cols=376  Identities=24%  Similarity=0.337  Sum_probs=285.9

Q ss_pred             HCCCCCCHHHHHHHHHHHHHHCCCCCCEEEEEECCCCCHHHHHHHHHHHHHHHHCCEEEEEHHHH-HHHHHHHHHHHHCC
Q ss_conf             30246798899999999984100134307886214422369999997334443054588612799-99999986211014
Q gi|254780945|r  268 NIPFSPTKSQESAIKDILQDMSQKNRMLRILQGDVGSGKTLVALIAMAAAVEAGGQAVIMAPIGI-LAQQHYEFIKKYTQ  346 (700)
Q Consensus       268 ~LPF~LT~~Q~~ai~eI~~Dl~~~~pM~RLLQGDVGSGKTiVA~~A~l~~~~~G~Q~alMaPTEI-LA~QH~~~~~~~~~  346 (700)
                      .-+..||++|+.|+++|.+. ....  .-||+|..|||||.|++-++..++..|.||.+|+| || |+.|-.+.|++.|+
T Consensus       164 ~~~~~L~~eQ~~a~~~i~~~-~~~~--~~LL~GvTGSGKTevYl~li~~~l~~GkqvLiLvP-EI~lt~q~~~rl~~~fg  239 (699)
T PRK05580        164 TEPPTLNEEQAAALAAIRAA-GGFS--AFLLDGVTGSGKTEVYLQAIAEALAQGKQALVLVP-EIALTPQLLARFRARFG  239 (699)
T ss_pred             CCCCCCCHHHHHHHHHHHHC-CCCC--CEEEECCCCCHHHHHHHHHHHHHHHCCCCEEEEEC-CHHHHHHHHHHHHHHHC
T ss_conf             67878899999999999855-8887--17874789860799999999999973997899917-67878999999998709


Q ss_pred             CCCCEEEEEECCCCHHHHHHHHHHHCCCCCEEEEEC-HHHCCCCCCCCCCCEEEECCCC----------CCCHHHHHHHH
Q ss_conf             578658996246422566768776213475486411-1201334554444178852101----------33568899874
Q gi|254780945|r  347 NTQIIVEIITGNMPQAHRRKALERIAHGQAHIIIGT-HALFQDSIQYYKLILVIVDEQH----------RFGVQQRLKLT  415 (700)
Q Consensus       347 ~~~i~v~lLtg~~~~~er~~i~~~i~~G~~~iiIGT-HAL~q~~v~F~~LgLvViDEQH----------RFGV~QR~~L~  415 (700)
                         .++++++++++.++|.+.|.++.+|+++||||| .|+|   ..|+||||+||||+|          ||-+..=+.++
T Consensus       240 ---~~v~v~HS~ls~~eR~~~w~~i~~G~~~IVIGtRSAvF---aP~~nLgLIIVDEEhd~SYKq~~~Pry~ARdvA~~R  313 (699)
T PRK05580        240 ---ARVAVLHSGLSDGERYRAWLAALRGEARVVIGTRSALF---APFKNLGLIIVDEEHDDSYKQQDGPRYHARDVAVLR  313 (699)
T ss_pred             ---CCEEEECCCCCHHHHHHHHHHHHCCCCEEEEECCCEEE---CCCCCCCEEEEECCCCHHHCCCCCCCCCHHHHHHHH
T ss_conf             ---95799648898579999999997699719997360110---657898489997365454446668761199999999


Q ss_pred             HCCCCCCCEEECHHHHHHHHHHHHHHCCCHHHHCCCCCCCCCCEEEEEECCC--------H-HHHHHHHHHHHCCCCEEE
Q ss_conf             0256776101010132278999975201011110235576662079997020--------0-268999976310387389
Q gi|254780945|r  416 QKATAPHVLLMTATPIPRTLVLTSLGDIDISKITEKPAGRKPIKTVIIPINR--------I-DEVIERLKVVLSEGKKAY  486 (700)
Q Consensus       416 ~Kg~~ph~L~MtATPIPRTLal~~ygdldvS~i~e~P~gR~~I~T~~~~~~~--------~-~~~~~~i~~~l~~g~q~y  486 (700)
                      .+-.+..++..||||==.|...+.-|......+++...+...-.-.++...+        + ..+++.|++.|++|+||.
T Consensus       314 a~~~~~~liLgSaTPSlEs~~~~~~g~~~~~~l~~r~~~~~~P~v~ivDm~~~~~~~~~~ls~~l~~~i~~~L~~g~qvl  393 (699)
T PRK05580        314 AKQEGCPVVLGSATPSLESLANAESGKYHLLRLTRRAGAAALPRVEIIDMREEPLERGAGLSPPLLEAIREALERGEQVL  393 (699)
T ss_pred             HHHHCCCEEECCCCCCHHHHHHHHCCCCEEECCCCCCCCCCCCEEEECCCCCCCCCCCCCCCHHHHHHHHHHHHCCCEEE
T ss_conf             99849988961689999999999759976644653223478983793354214100257546999999999997388479


Q ss_pred             EEECCCC-------------------------C-------------------------CCCCC--CCHHHHHHHHHHHHC
Q ss_conf             9971201-------------------------2-------------------------21112--101466666668663
Q gi|254780945|r  487 WICPQIE-------------------------E-------------------------KKESN--FRSVVERFNSLHEHF  514 (700)
Q Consensus       487 ~VcPlIe-------------------------e-------------------------se~~~--~~~~~~~~~~l~~~~  514 (700)
                      +.-|.=.                         .                         |.+..  -...+...++|++.|
T Consensus       394 l~lnRrGya~~~~C~~Cg~~~~C~~C~~~L~~h~~~~~l~Ch~Cg~~~~~~~~Cp~Cgs~~l~~~g~Gteri~eel~~~F  473 (699)
T PRK05580        394 LFLNRRGYAPFLLCRDCGWVARCPHCDGPLTLHRAGRRLRCHHCGYQEPIPRACPECGSTDLRAVGVGTERTEEELARLF  473 (699)
T ss_pred             EEECCCCCCCEEECHHCCCEEECCCCCCEEEECCCCCCEECCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHC
T ss_conf             99547752251474531994565678986342068983322646883657554656799752411168599999999778


Q ss_pred             CC-CEECCCCCC--CHHHHHHHHHHHHCCCEEEEEECHHHHCCCCCCCCCEEEEECHHHC-----------CHHHHHHHH
Q ss_conf             71-031201469--9899999999975598699998003410468887658998585254-----------746887730
Q gi|254780945|r  515 TS-SIAIIHGRM--SDIDKESVMDSFKNGTCKLLIATTVIEVGIDVVDASIIIIENAEHF-----------GLAQLHQLR  580 (700)
Q Consensus       515 ~~-~v~~lHGkm--~~~ek~~~m~~F~~g~~~iLvaTtviEVGvdvpna~~mvI~~aerf-----------GLsqLHQLR  580 (700)
                      |+ +|..+.+--  +...-+.++++|.+|++||||.|..|--|.|.||.++.+|.|||..           -...|+|.=
T Consensus       474 P~~~i~r~d~d~~~~~~~~~~~~~~~~~~~~dIlvGTqmiakG~df~~v~lv~vldaD~~l~~pd~ra~E~~~qll~qva  553 (699)
T PRK05580        474 PGARVLRIDRDTTRRKGALEQLLEDFARGEADILVGTQMLAKGHDFPNVTLVGVLDADTGLFSPDFRAAERTFQLLTQVA  553 (699)
T ss_pred             CCCCEEEECCCCCCCCCCHHHHHHHHHCCCCCEEECCCCCCCCCCCCCEEEEEEECHHHHCCCCCCCHHHHHHHHHHHHH
T ss_conf             99988998475567863168899997468987897773345567777626998732265354888347999999999998


Q ss_pred             HCCCCCCCCEEEEEEECCCCCHHHHHHHHHHHHHCHHHHHHHHHHHHCCCCCCCCCHHCCCCCCC-CCCHHHHHHHHHHH
Q ss_conf             11667898359999708889987999999998414258999999852063000260006987440-00388759999999
Q gi|254780945|r  581 GRVGRGEEISSCILLYHPPLSKNSYTRLSVLKNTEDGFLIAEEDLKQRKEGEILGIKQSGMPKFL-IAQPELHDSLLEIA  659 (700)
Q Consensus       581 GRVGRg~~~s~c~l~~~~~~~~~~~~Rl~~l~~~~dGf~iAe~Dl~lRG~G~~~G~~QsG~~~~~-~~d~~~d~~ll~~a  659 (700)
                      ||+||+.++|..++-+..+.+..    ++.+.+ .|-...++..|+.|        ++.++|.|. ++-+.-...-.+.+
T Consensus       554 gragr~~~~g~viiQt~~p~~~~----~~~l~~-~d~~~f~~~el~~R--------~~~~~PPf~~l~~i~~~~~~~~~~  620 (699)
T PRK05580        554 GRAGRAEKPGEVLIQTYEPEHPL----LQALLR-WDYDAFAEAELAER--------REAGLPPFVRLALVRGSAKAVAKA  620 (699)
T ss_pred             HHHCCCCCCCEEEEEECCCCCHH----HHHHHH-CCHHHHHHHHHHHH--------HHCCCCCHHHHHEEEEECCCHHHH
T ss_conf             76556788987999937999899----999996-89999999999999--------970999868751789953999999


Q ss_pred             HHHHHHH
Q ss_conf             9999999
Q gi|254780945|r  660 RKDAKHI  666 (700)
Q Consensus       660 ~~~a~~~  666 (700)
                      .+.+..+
T Consensus       621 ~~~~~~~  627 (699)
T PRK05580        621 LKFAQQL  627 (699)
T ss_pred             HHHHHHH
T ss_conf             9999999


No 8  
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=100.00  E-value=1.1e-32  Score=275.86  Aligned_cols=393  Identities=24%  Similarity=0.349  Sum_probs=292.7

Q ss_pred             CCCCCCHHHHHHHHHHHHHHCCCCCCEEEEEECCCCCHHHHHHHHHHHHHHHHCCEEEEEHHHH-HHHHHHHHHHHHCCC
Q ss_conf             0246798899999999984100134307886214422369999997334443054588612799-999999862110145
Q gi|254780945|r  269 IPFSPTKSQESAIKDILQDMSQKNRMLRILQGDVGSGKTLVALIAMAAAVEAGGQAVIMAPIGI-LAQQHYEFIKKYTQN  347 (700)
Q Consensus       269 LPF~LT~~Q~~ai~eI~~Dl~~~~pM~RLLQGDVGSGKTiVA~~A~l~~~~~G~Q~alMaPTEI-LA~QH~~~~~~~~~~  347 (700)
                      -+..|+..|+.|++.|...+....  .-||+|..|||||.|.+-++..++..|+||.+|+| || |..|-.+.|+.+|+ 
T Consensus       195 ~~~~Ln~~Q~~a~~~i~~~~~~~~--~~Ll~GvTGSGKTEvYl~~i~~~L~~GkqvLvLVP-EI~Ltpq~~~rf~~rFg-  270 (730)
T COG1198         195 EWLALNQEQQAAVEAILSSLGGFA--PFLLDGVTGSGKTEVYLEAIAKVLAQGKQVLVLVP-EIALTPQLLARFKARFG-  270 (730)
T ss_pred             CCCCCCHHHHHHHHHHHHHCCCCC--CEEEECCCCCCHHHHHHHHHHHHHHCCCEEEEEEC-CCCCHHHHHHHHHHHHC-
T ss_conf             311038899999999997505666--53676777885899999999999975987999956-53456999999999867-


Q ss_pred             CCCEEEEEECCCCHHHHHHHHHHHCCCCCEEEEEC-HHHCCCCCCCCCCCEEEECCCCCCCHHH----------HHHHHH
Q ss_conf             78658996246422566768776213475486411-1201334554444178852101335688----------998740
Q gi|254780945|r  348 TQIIVEIITGNMPQAHRRKALERIAHGQAHIIIGT-HALFQDSIQYYKLILVIVDEQHRFGVQQ----------RLKLTQ  416 (700)
Q Consensus       348 ~~i~v~lLtg~~~~~er~~i~~~i~~G~~~iiIGT-HAL~q~~v~F~~LgLvViDEQHRFGV~Q----------R~~L~~  416 (700)
                        .+|+.++++++.++|.+.|.++.+|++.||||| .|||   ..|+||||+||||+|--.-.|          =+.++.
T Consensus       271 --~~v~vlHS~Ls~~er~~~W~~~~~G~~~vVIGtRSAlF---~Pf~~LGLIIvDEEHD~sYKq~~~prYhARdvA~~Ra  345 (730)
T COG1198         271 --AKVAVLHSGLSPGERYRVWRRARRGEARVVIGTRSALF---LPFKNLGLIIVDEEHDSSYKQEDGPRYHARDVAVLRA  345 (730)
T ss_pred             --CCHHHHCCCCCHHHHHHHHHHHHCCCCEEEEEECHHHC---CCHHHCCEEEEECCCCCCCCCCCCCCCCHHHHHHHHH
T ss_conf             --87453146579278999999985597159997122330---7231257699702456432477777767899999998


Q ss_pred             CCCCCCCEEECHHHHHHHHHHHHHHCCCHHHHCCCCCCCCCCEEEEEECCC----H-----HHHHHHHHHHHCCCCEEEE
Q ss_conf             256776101010132278999975201011110235576662079997020----0-----2689999763103873899
Q gi|254780945|r  417 KATAPHVLLMTATPIPRTLVLTSLGDIDISKITEKPAGRKPIKTVIIPINR----I-----DEVIERLKVVLSEGKKAYW  487 (700)
Q Consensus       417 Kg~~ph~L~MtATPIPRTLal~~ygdldvS~i~e~P~gR~~I~T~~~~~~~----~-----~~~~~~i~~~l~~g~q~y~  487 (700)
                      +-.+.-++.=||||==-|.+...-|.-....+.....+-.+..-.++...+    .     ..+++.|++.+++|+|+-+
T Consensus       346 ~~~~~pvvLgSATPSLES~~~~~~g~y~~~~L~~R~~~a~~p~v~iiDmr~e~~~~~~~lS~~Ll~~i~~~l~~geQ~ll  425 (730)
T COG1198         346 KKENAPVVLGSATPSLESYANAESGKYKLLRLTNRAGRARLPRVEIIDMRKEPLETGRSLSPALLEAIRKTLERGEQVLL  425 (730)
T ss_pred             HHCCCCEEEECCCCCHHHHHHHHCCCEEEEECCCCCCCCCCCCCEEEECCCCCCCCCCCCCHHHHHHHHHHHHCCCEEEE
T ss_conf             86099889826887789998665385589970354555678762587356665546775799999999999842986899


Q ss_pred             EECC--------------------CC------------------------------CCCCCC--CCHHHHHHHHHHHHCC
Q ss_conf             9712--------------------01------------------------------221112--1014666666686637
Q gi|254780945|r  488 ICPQ--------------------IE------------------------------EKKESN--FRSVVERFNSLHEHFT  515 (700)
Q Consensus       488 VcPl--------------------Ie------------------------------ese~~~--~~~~~~~~~~l~~~~~  515 (700)
                      .-|.                    -+                              .|+.+-  -...+...++|++.||
T Consensus       426 flnRRGys~~l~C~~Cg~v~~Cp~Cd~~lt~H~~~~~L~CH~Cg~~~~~p~~Cp~Cgs~~L~~~G~GterieeeL~~~FP  505 (730)
T COG1198         426 FLNRRGYAPLLLCRDCGYIAECPNCDSPLTLHKATGQLRCHYCGYQEPIPQSCPECGSEHLRAVGPGTERIEEELKRLFP  505 (730)
T ss_pred             EECCCCCCCEEECCCCCCCCCCCCCCCCEEEECCCCEEEECCCCCCCCCCCCCCCCCCCEEEEECCCHHHHHHHHHHHCC
T ss_conf             97167765400425689802489999512786479806707799989988779899997369964619999999998789


Q ss_pred             C-CEECCCCCCCH--HHHHHHHHHHHCCCEEEEEECHHHHCCCCCCCCCEEEEECHHH-C----------CHHHHHHHHH
Q ss_conf             1-03120146998--9999999997559869999800341046888765899858525-4----------7468877301
Q gi|254780945|r  516 S-SIAIIHGRMSD--IDKESVMDSFKNGTCKLLIATTVIEVGIDVVDASIIIIENAEH-F----------GLAQLHQLRG  581 (700)
Q Consensus       516 ~-~v~~lHGkm~~--~ek~~~m~~F~~g~~~iLvaTtviEVGvdvpna~~mvI~~aer-f----------GLsqLHQLRG  581 (700)
                      + +|.-+-+-...  ..-+..+++|.+||+||||.|..|--|.|.||.|+..|.|||- +          ....|.|.=|
T Consensus       506 ~~rv~r~d~Dtt~~k~~~~~~l~~~~~ge~dILiGTQmiaKG~~fp~vtLVgvl~aD~~L~~~DfRAsEr~fqll~QvaG  585 (730)
T COG1198         506 GARIIRIDSDTTRRKGALEDLLDQFANGEADILIGTQMIAKGHDFPNVTLVGVLDADTGLGSPDFRASERTFQLLMQVAG  585 (730)
T ss_pred             CCCEEEECCCCCCCHHHHHHHHHHHHCCCCCEEECCHHHHCCCCCCCCEEEEEEECHHHHCCCCCCHHHHHHHHHHHHHH
T ss_conf             99479984666664356899999975799886634166642788666318999963143158884357899999999975


Q ss_pred             CCCCCCCCEEEEEEECCCCCHHHHHHHHHHHHHCHHHHHHHHHHHHCCCCCCCCCHHCCCCCCCCC-CHH----HHHHHH
Q ss_conf             166789835999970888998799999999841425899999985206300026000698744000-388----759999
Q gi|254780945|r  582 RVGRGEEISSCILLYHPPLSKNSYTRLSVLKNTEDGFLIAEEDLKQRKEGEILGIKQSGMPKFLIA-QPE----LHDSLL  656 (700)
Q Consensus       582 RVGRg~~~s~c~l~~~~~~~~~~~~Rl~~l~~~~dGf~iAe~Dl~lRG~G~~~G~~QsG~~~~~~~-d~~----~d~~ll  656 (700)
                      |.||++++|--++-+-.+ +..+.+  .++.+-.++|  +|.-|+.|        ++-|+|.|... -+.    .....+
T Consensus       586 RAgR~~~~G~VvIQT~~P-~hp~i~--~~~~~dy~~F--~~~El~~R--------k~~~~PPf~~l~~v~~~~~~~~~~~  652 (730)
T COG1198         586 RAGRAGKPGEVVIQTYNP-DHPAIQ--ALKRGDYEAF--YEQELAER--------KELGLPPFSRLAAVIASAKNEEKAL  652 (730)
T ss_pred             HHCCCCCCCEEEEEECCC-CCHHHH--HHHHCCHHHH--HHHHHHHH--------HHCCCCCHHHHEEEEECCCCHHHHH
T ss_conf             532678898699996799-857999--9986699999--99999988--------8618997065446673378989999


Q ss_pred             HHHHHHH---HHHHHHCCCCCCCCCHHHHH
Q ss_conf             9999999---99998484636655648899
Q gi|254780945|r  657 EIARKDA---KHILTQDPDLTSVRGQSIRI  683 (700)
Q Consensus       657 ~~a~~~a---~~~~~~d~~l~~~~~~~l~~  683 (700)
                      +.++..+   +.....|..+-.|-...+..
T Consensus       653 ~~~~~~~~~l~~~~~~~~~vLGP~~a~~~r  682 (730)
T COG1198         653 EFARALRELLKEALPVDVEVLGPAPAPLAK  682 (730)
T ss_pred             HHHHHHHHHHHHCCCCCCEEECCCCCHHHH
T ss_conf             999999999986275565046887562677


No 9  
>PRK11192 ATP-dependent RNA helicase SrmB; Provisional
Probab=99.97  E-value=1.6e-26  Score=227.60  Aligned_cols=332  Identities=19%  Similarity=0.256  Sum_probs=238.0

Q ss_pred             CCCCHHHHHHHHHCCC-CCCHHHHHHHHHHHHHHCCCCCCEEEEEECCCCCHHHHHHHHHHHHHH-------HHCCEEEE
Q ss_conf             8775789999863024-679889999999998410013430788621442236999999733444-------30545886
Q gi|254780945|r  256 NVEGKIAQKILRNIPF-SPTKSQESAIKDILQDMSQKNRMLRILQGDVGSGKTLVALIAMAAAVE-------AGGQAVIM  327 (700)
Q Consensus       256 ~~~~~~~~~f~~~LPF-~LT~~Q~~ai~eI~~Dl~~~~pM~RLLQGDVGSGKTiVA~~A~l~~~~-------~G~Q~alM  327 (700)
                      ..+..+.+.+ +.+.| ++|.=|..||-.|.+.      -+-+++.-.|||||+.+++.++.-+.       ++-++.++
T Consensus         9 ~L~~~l~~~L-~~~g~~~pT~IQ~~aIp~il~g------~dvl~~A~TGSGKTlaylLPil~~l~~~~~~~~~~~~~LIl   81 (417)
T PRK11192          9 DLDPSLLEAL-QDKGYTRPTAIQAEAIPPALDG------RDVLGSAPTGTGKTAAFLLPALQHLLDFPRRKSGPPRILIL   81 (417)
T ss_pred             CCCHHHHHHH-HHCCCCCCCHHHHHHHHHHHCC------CCEEEECCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEEE
T ss_conf             9899999999-9779999999999999999779------98899899986799999999999987521036899649999


Q ss_pred             EHHHHHHHHHHHHHHHHCCCCCCEEEEEECCCCHHHHHHHHHHHCCCCCEEEEECHH-----HCCCCCCCCCCCEEEECC
Q ss_conf             127999999998621101457865899624642256676877621347548641112-----013345544441788521
Q gi|254780945|r  328 APIGILAQQHYEFIKKYTQNTQIIVEIITGNMPQAHRRKALERIAHGQAHIIIGTHA-----LFQDSIQYYKLILVIVDE  402 (700)
Q Consensus       328 aPTEILA~QH~~~~~~~~~~~~i~v~lLtg~~~~~er~~i~~~i~~G~~~iiIGTHA-----L~q~~v~F~~LgLvViDE  402 (700)
                      +||--||.|.++.++.+....++++.+++|+++..+..+.+.    ..++|+|||-.     +-+..+.++++.++|+||
T Consensus        82 ~PTrELa~Qi~~~~~~l~~~~~i~~~~i~Gg~~~~~q~~~l~----~~~dIlV~TPgRL~~~l~~~~~~l~~l~~lVlDE  157 (417)
T PRK11192         82 TPTRELAMQVADQARELAKHTHLDIATITGGVAYMNHAEVFS----ENQDIVVATPGRLLQYIKEENFDCRAVETLILDE  157 (417)
T ss_pred             ECHHHHHHHHHHHHHHHHCCCCCCEEEEECCCCHHHHHHHHH----CCCCEEEECCCHHHHHHHHCCCCCCCCCEEEEEC
T ss_conf             471999999999999864005730599856878799999983----6999899786077778863670104574899967


Q ss_pred             CCCCCH----HHHHHHHHC-CCCCCCEEECHHHH---HHHHHHHHHHCCCHHHHCCCCCCC--CCCEEEEEECCCHHHHH
Q ss_conf             013356----889987402-56776101010132---278999975201011110235576--66207999702002689
Q gi|254780945|r  403 QHRFGV----QQRLKLTQK-ATAPHVLLMTATPI---PRTLVLTSLGDIDISKITEKPAGR--KPIKTVIIPINRIDEVI  472 (700)
Q Consensus       403 QHRFGV----~QR~~L~~K-g~~ph~L~MtATPI---PRTLal~~ygdldvS~i~e~P~gR--~~I~T~~~~~~~~~~~~  472 (700)
                      -||.=-    .+=..+... ......+.+|||-=   -+.++-.+..+  -..|...|+++  ..|.-.++..++.+.-+
T Consensus       158 AD~mld~gF~~~i~~I~~~~~~~~Q~llfSATl~~~~v~~l~~~~l~~--p~~i~~~~~~~~~~~i~q~~~~~~~~~~k~  235 (417)
T PRK11192        158 ADRMLDMGFAQDVEHIAAETRWRKQTLLFSATLEGDGVQDFAERLLND--PVEVDAEPSRRERKKIHQWYYRADDLEHKT  235 (417)
T ss_pred             CCCCCCCCCHHHHHHHHHHCCCCCEEEEEEEECCHHHHHHHHHHHCCC--CEEEEECCCCCCCCCEEEEEEEECCHHHHH
T ss_conf             552111354789999986476772389997326847899999983679--889996467666674369999937689999


Q ss_pred             HHHHHHHCC--CCEEEEEECCCCCCCCCCCCHHHHHHHHHHHHCCCCEECCCCCCCHHHHHHHHHHHHCCCEEEEEECHH
Q ss_conf             999763103--873899971201221112101466666668663710312014699899999999975598699998003
Q gi|254780945|r  473 ERLKVVLSE--GKKAYWICPQIEEKKESNFRSVVERFNSLHEHFTSSIAIIHGRMSDIDKESVMDSFKNGTCKLLIATTV  550 (700)
Q Consensus       473 ~~i~~~l~~--g~q~y~VcPlIeese~~~~~~~~~~~~~l~~~~~~~v~~lHGkm~~~ek~~~m~~F~~g~~~iLvaTtv  550 (700)
                      ..+..-+..  ..|+.|-|...        ..++..++.|.+. +-++..+||.|+.++++++|++|++|+++|||||-|
T Consensus       236 ~~L~~ll~~~~~~k~iIF~~t~--------~~~~~l~~~L~~~-g~~~~~lhg~l~q~~R~~~l~~F~~g~~~vLVaTDv  306 (417)
T PRK11192        236 ALLCHLLKQEEVTRSIVFVRTR--------ERVHELAGWLRKA-GINCCYLEGEMVQKKRNEAIKRLTDGRVNVLVATDV  306 (417)
T ss_pred             HHHHHHHHCCCCCCCEEEECCH--------HHHHHHHHHHHCC-CCCEEEECCCCCHHHHHHHHHHHHCCCCCEEEECCH
T ss_conf             9999998534766521531124--------6676898865314-883575400179999999999997699989998124


Q ss_pred             HHCCCCCCCCCEEEEECHHHCCHHHHHHHHHCCCCCCCCEEEEEEECCCCCHHHHHHHHHHHHH
Q ss_conf             4104688876589985852547468877301166789835999970888998799999999841
Q gi|254780945|r  551 IEVGIDVVDASIIIIENAEHFGLAQLHQLRGRVGRGEEISSCILLYHPPLSKNSYTRLSVLKNT  614 (700)
Q Consensus       551 iEVGvdvpna~~mvI~~aerfGLsqLHQLRGRVGRg~~~s~c~l~~~~~~~~~~~~Rl~~l~~~  614 (700)
                      ..-|+|+|+.+..|-+|.=+---+=+|. =||.||.+..|.|+-++.+.    -...|+.+++.
T Consensus       307 aaRGiDi~~V~~VInyd~P~~~~~YvHR-iGRTGR~G~~G~ait~v~~~----d~~~~~~ie~~  365 (417)
T PRK11192        307 AARGIDIDDISHVINFDMPRSADTYLHR-IGRTGRAGKKGTAISLVEAH----DHLLLGKIERY  365 (417)
T ss_pred             HHCCCCCCCCCEEEEECCCCCHHHHHHH-CCHHHCCCCCEEEEEEECHH----HHHHHHHHHHH
T ss_conf             3467770469889997999988892330-67723489954899987489----99999999999


No 10 
>PRK01172 ski2-like helicase; Provisional
Probab=99.95  E-value=3.2e-24  Score=209.52  Aligned_cols=319  Identities=19%  Similarity=0.285  Sum_probs=235.0

Q ss_pred             HHHHHHHHHCCCCCCHHHHHHHHHHHHHHCCCCCCEEEEEECCCCCHHHHHHHHHHHHHHHHCCEEEEEHHHHHHHHHHH
Q ss_conf             78999986302467988999999999841001343078862144223699999973344430545886127999999998
Q gi|254780945|r  260 KIAQKILRNIPFSPTKSQESAIKDILQDMSQKNRMLRILQGDVGSGKTLVALIAMAAAVEAGGQAVIMAPIGILAQQHYE  339 (700)
Q Consensus       260 ~~~~~f~~~LPF~LT~~Q~~ai~eI~~Dl~~~~pM~RLLQGDVGSGKTiVA~~A~l~~~~~G~Q~alMaPTEILA~QH~~  339 (700)
                      +.+.+|.++-.|+|-+-|..|++.+.    .++  |-++.--.|||||+||.+||+.++..|..+.+++|+--||+|-|+
T Consensus        10 ~~~~~~~~~~g~~l~p~Q~ea~~~~~----~gk--NllvsaPTgsGKTlvAe~ai~~~l~~~~k~iyi~P~kAL~~EK~~   83 (674)
T PRK01172         10 DEFLNLFTGNDFELYDHQRMAIEQLR----KGE--NVIVSVPTAAGKTLIAYSAIYETFLAGLKSIYIVPLRSLAMEKYE   83 (674)
T ss_pred             HHHHHHHHHCCCCCCHHHHHHHHHHH----CCC--CEEEECCCCCCHHHHHHHHHHHHHHHCCCEEEECCHHHHHHHHHH
T ss_conf             79999999679988989999999997----799--599978999869999999999999858979998778999999999


Q ss_pred             HHHHHCCCCCCEEEEEECCCCHHHHHHHHHHHCCCCCEEEEEC----HHHCCCC-CCCCCCCEEEECCCCCCCHHHHHHH
Q ss_conf             6211014578658996246422566768776213475486411----1201334-5544441788521013356889987
Q gi|254780945|r  340 FIKKYTQNTQIIVEIITGNMPQAHRRKALERIAHGQAHIIIGT----HALFQDS-IQYYKLILVIVDEQHRFGVQQRLKL  414 (700)
Q Consensus       340 ~~~~~~~~~~i~v~lLtg~~~~~er~~i~~~i~~G~~~iiIGT----HAL~q~~-v~F~~LgLvViDEQHRFGV~QR~~L  414 (700)
                      .|+++ .++|++|...||.......       ..+..+|+|-|    ++|+..+ -.++++|+|||||=|=.|=..|-..
T Consensus        84 ~~~~~-~~~g~~v~~~tGd~~~~~~-------~~~~~~I~V~T~Ek~~sl~~~~~~~l~~v~~vViDEiH~i~d~~RG~~  155 (674)
T PRK01172         84 ELSRL-RSLGMRVKISIGDYDDPPD-------FIKRYDVVILTSEKADSLIHHDPYIINDVGLIVADEIHIIGDEDRGPT  155 (674)
T ss_pred             HHHHH-HCCCCEEEEEECCCCCCCC-------CCCCCCEEEECHHHHHHHHHCCCHHHCCCCEEEEECCEECCCCCCHHH
T ss_conf             99988-7379827788538889801-------025589999878999999864950221369899826525068772499


Q ss_pred             HH--------CCCCCCCEEECHHHHHHH--HHHHHHHCCCHHHHCCCCCCCCCCEEEEEECCC---------HHHHHHHH
Q ss_conf             40--------256776101010132278--999975201011110235576662079997020---------02689999
Q gi|254780945|r  415 TQ--------KATAPHVLLMTATPIPRT--LVLTSLGDIDISKITEKPAGRKPIKTVIIPINR---------IDEVIERL  475 (700)
Q Consensus       415 ~~--------Kg~~ph~L~MtATPIPRT--Lal~~ygdldvS~i~e~P~gR~~I~T~~~~~~~---------~~~~~~~i  475 (700)
                      .+        -+..+.++.|||| ||-.  +|-=+-+++-.|  +..|   .|....++..++         ...+...+
T Consensus       156 lE~~l~kl~~l~~~~qiIgLSAT-i~N~~~la~WL~a~~~~~--~~RP---VpL~~~v~~~~~~~~~~~~~~~~~~~~l~  229 (674)
T PRK01172        156 LETVLSSARYVNPDARILALSAT-VSNANELAQWLNASLIKS--NFRP---VPLKLGILYRKRLILDGYERSQVDINSLI  229 (674)
T ss_pred             HHHHHHHHHHCCCCEEEEEECCC-CCCHHHHHHHHCCCEEEC--CCCC---CCCEEEEEECCCCCCCCHHHCCCCHHHHH
T ss_conf             99999999853866079971578-689999998838855647--9998---66089888346011470432345399999


Q ss_pred             HHHHCCCCEEEEEECCCCCCCCC------------C--CCH--HHHHHHHHHHHCCCCEECCCCCCCHHHHHHHHHHHHC
Q ss_conf             76310387389997120122111------------2--101--4666666686637103120146998999999999755
Q gi|254780945|r  476 KVVLSEGKKAYWICPQIEEKKES------------N--FRS--VVERFNSLHEHFTSSIAIIHGRMSDIDKESVMDSFKN  539 (700)
Q Consensus       476 ~~~l~~g~q~y~VcPlIeese~~------------~--~~~--~~~~~~~l~~~~~~~v~~lHGkm~~~ek~~~m~~F~~  539 (700)
                      .+.+.+|+||.|-||.=...|+.            +  +.+  ..-.-+.|.+..+..|+.-|+-|..+|++.|=+.|++
T Consensus       230 ~~~~~~~~~~LVF~~sR~~~e~~A~~l~~~~~~~~~~~~~~~~~~~~~~~L~~~l~~GVafHHaGL~~~eR~lVE~~f~~  309 (674)
T PRK01172        230 KETVNDGGQVLVFVSSRKNAEDYAEMLIQHFPEFNDFKVSSENNNVYDDSLNEMLPHGVAFHHAGLSNEQRRFIEEMFRN  309 (674)
T ss_pred             HHHHHCCCCEEEEEECHHHHHHHHHHHHHHHHHCCCHHCCHHHHHCCCHHHHHHHHCCEEEECCCCCHHHHHHHHHHHHC
T ss_conf             99996699479995075889999999998532101001031543112099999996282830689998999999999986


Q ss_pred             CCEEEEEECHHHHCCCCCCCCCEEEEECHHHC--------CHHHHHHHHHCCCCCC--CCEEEEEEECCC
Q ss_conf             98699998003410468887658998585254--------7468877301166789--835999970888
Q gi|254780945|r  540 GTCKLLIATTVIEVGIDVVDASIIIIENAEHF--------GLAQLHQLRGRVGRGE--EISSCILLYHPP  599 (700)
Q Consensus       540 g~~~iLvaTtviEVGvdvpna~~mvI~~aerf--------GLsqLHQLRGRVGRg~--~~s~c~l~~~~~  599 (700)
                      |.+++||||+-.-.|||.|.-+|+ |.+-.||        .-++.+|.-||-||-+  ..|+|+++...+
T Consensus       310 g~i~vl~aT~TLAaGVNlPAr~VI-i~~~~r~~~~~~~~l~~~e~~QM~GRAGR~g~D~~G~~ii~~~~~  378 (674)
T PRK01172        310 RYIKVIVATPTLAAGVNLPARLVI-VRDITRYGNGGIRYLSNMEIKQMIGRAGRPGYDQYGIGYIYAASP  378 (674)
T ss_pred             CCCEEEEECCHHHHHCCCCEEEEE-EEEEEEECCCCEEECCHHHHHHHCCCCCCCCCCCCCCEEEEECCC
T ss_conf             996499714467654478605999-930078179971577789899861358999999887089997282


No 11 
>PRK11776 ATP-dependent RNA helicase DbpA; Provisional
Probab=99.95  E-value=1.5e-23  Score=204.25  Aligned_cols=332  Identities=21%  Similarity=0.334  Sum_probs=232.0

Q ss_pred             CCCCHHHHHHHHHCCC-CCCHHHHHHHHHHHHHHCCCCCCEEEEEECCCCCHHHHHHHHHHHHHHH---HCCEEEEEHHH
Q ss_conf             8775789999863024-6798899999999984100134307886214422369999997334443---05458861279
Q gi|254780945|r  256 NVEGKIAQKILRNIPF-SPTKSQESAIKDILQDMSQKNRMLRILQGDVGSGKTLVALIAMAAAVEA---GGQAVIMAPIG  331 (700)
Q Consensus       256 ~~~~~~~~~f~~~LPF-~LT~~Q~~ai~eI~~Dl~~~~pM~RLLQGDVGSGKTiVA~~A~l~~~~~---G~Q~alMaPTE  331 (700)
                      ..+..+.+. ++.+.| ++|.=|+.||..|.+.    +  +-+.|.-.|||||+.+++.++.-++.   +-|+.+++||-
T Consensus        10 ~L~~~ll~a-L~~~G~~~pTpIQ~~aIP~il~G----~--Dvi~~A~TGSGKTlAfllPil~~l~~~~~~~qaLIL~PTR   82 (459)
T PRK11776         10 PLPPALLAN-LDELGYTEMTPIQAQSLPAILAG----K--DVIAQAKTGSGKTAAFGLGLLQKLDVKRFRVQALVLCPTR   82 (459)
T ss_pred             CCCHHHHHH-HHHCCCCCCCHHHHHHHHHHHCC----C--CEEEECCCCCHHHHHHHHHHHHHCCCCCCCCCEEEEECHH
T ss_conf             979999999-99779999998999999999779----9--8899889985899999999998411367898599996759


Q ss_pred             HHHHHHHHHHHHHCCCC-CCEEEEEECCCCHHHHHHHHHHHCCCCCEEEEECHH-----HCCCCCCCCCCCEEEECCCCC
Q ss_conf             99999998621101457-865899624642256676877621347548641112-----013345544441788521013
Q gi|254780945|r  332 ILAQQHYEFIKKYTQNT-QIIVEIITGNMPQAHRRKALERIAHGQAHIIIGTHA-----LFQDSIQYYKLILVIVDEQHR  405 (700)
Q Consensus       332 ILA~QH~~~~~~~~~~~-~i~v~lLtg~~~~~er~~i~~~i~~G~~~iiIGTHA-----L~q~~v~F~~LgLvViDEQHR  405 (700)
                      =||.|-++.++++-... ++++..++|+.+..+.   ...++.| ++|||||-.     +-+..+.++++.++|+||-++
T Consensus        83 ELa~QV~~~~~~l~~~~~~ikv~~l~GG~~~~~q---~~~L~~~-~~IvV~TPGRl~d~l~~~~l~l~~v~~lVlDEAD~  158 (459)
T PRK11776         83 ELADQVAKEIRRLARFIPNIKVLTLCGGVPMGPQ---IGSLEHG-AHIIVGTPGRILDHLRKGTLDLDALNTLVLDEADR  158 (459)
T ss_pred             HHHHHHHHHHHHHHHHCCCCEEEEEECCCCHHHH---HHHHHCC-CCEEEECCHHHHHHHHCCCCCCCCEEEEEEECCHH
T ss_conf             9999999999999850588259999899327999---9997469-99999895899988751663223103899706245


Q ss_pred             C---CH-HHHHHHHHC-CCCCCCEEECHHHHHHH--HHHHHHHC-CCHHHHCCCCCCCCCCEEEEEECC--CHHHHHHHH
Q ss_conf             3---56-889987402-56776101010132278--99997520-101111023557666207999702--002689999
Q gi|254780945|r  406 F---GV-QQRLKLTQK-ATAPHVLLMTATPIPRT--LVLTSLGD-IDISKITEKPAGRKPIKTVIIPIN--RIDEVIERL  475 (700)
Q Consensus       406 F---GV-~QR~~L~~K-g~~ph~L~MtATPIPRT--Lal~~ygd-ldvS~i~e~P~gR~~I~T~~~~~~--~~~~~~~~i  475 (700)
                      .   |- ++=..+.+. ......+.+|||=-+..  ++-.+..+ .-+. +.... ....|.-+++..+  ++..+...+
T Consensus       159 mLd~gF~~~i~~Il~~~p~~rQ~~lfSAT~p~~i~~l~~~~l~~p~~i~-v~~~~-~~~~I~q~~~~v~~~~K~~~L~~l  236 (459)
T PRK11776        159 MLDMGFQDAIDAIIRQAPARRQTLLFSATYPEGIAAISARFQRDPVEVK-VESTH-DDSTIEQRFYEVDPDERLPALQRL  236 (459)
T ss_pred             HHCCCCHHHHHHHHHHCCCCCEEEEEECCCCHHHHHHHHHHCCCCEEEE-ECCCC-CCCCCEEEEEEECHHHHHHHHHHH
T ss_conf             4327866889999986881302688845689899999999778989999-67877-798637999997718789999999


Q ss_pred             HHHHCCCCEEEEEECCCCCCCCCCCCHHHHHHHHHHHHCCCCEECCCCCCCHHHHHHHHHHHHCCCEEEEEECHHHHCCC
Q ss_conf             76310387389997120122111210146666666866371031201469989999999997559869999800341046
Q gi|254780945|r  476 KVVLSEGKKAYWICPQIEEKKESNFRSVVERFNSLHEHFTSSIAIIHGRMSDIDKESVMDSFKNGTCKLLIATTVIEVGI  555 (700)
Q Consensus       476 ~~~l~~g~q~y~VcPlIeese~~~~~~~~~~~~~l~~~~~~~v~~lHGkm~~~ek~~~m~~F~~g~~~iLvaTtviEVGv  555 (700)
                      -... +..++.|-|...        ..+++.++.|++. +-.+..+||.|+..+++++|++|++|+++|||||.|..=|+
T Consensus       237 l~~~-~~~~~IIFcntk--------~~v~~l~~~L~~~-g~~~~~lHg~m~q~~R~~~l~~F~~g~~~iLVaTDvaaRGI  306 (459)
T PRK11776        237 LLHY-RPESCVVFCNTK--------KECQEVADALNAQ-GFSALALHGDLEQRDRDQVLVRFANRSCSVLVATDVAARGL  306 (459)
T ss_pred             HHHC-CCCCEEEEECCH--------HHHHHHHHHHHHC-CCCEEEEECCCCHHHHHHHHHHHHCCCCCEEEEHHHHHCCC
T ss_conf             9736-876603761748--------9999999999867-99689987999999999999999779997998810434767


Q ss_pred             CCCCCCEEEEECHHHCCHHHHHHHHHCCCCCCCCEEEEEEECCCCCHHHHHHHHHHHHHC
Q ss_conf             888765899858525474688773011667898359999708889987999999998414
Q gi|254780945|r  556 DVVDASIIIIENAEHFGLAQLHQLRGRVGRGEEISSCILLYHPPLSKNSYTRLSVLKNTE  615 (700)
Q Consensus       556 dvpna~~mvI~~aerfGLsqLHQLRGRVGRg~~~s~c~l~~~~~~~~~~~~Rl~~l~~~~  615 (700)
                      |+|+.+..|-+|.-.-=-+=+|- =||.||.++.|.||.+..+    .-..+|+.+++..
T Consensus       307 Di~~V~~VInyDlP~~~e~YvHR-iGRTGRaG~~G~ait~vt~----~e~~~l~~ie~~~  361 (459)
T PRK11776        307 DIKSLEAVINYELARDPEVHVHR-IGRTGRAGSKGLALSLVAP----EEMQRAAAIEDYL  361 (459)
T ss_pred             CCCCCCEEEEECCCCCHHHHHHC-CCHHHCCCCCEEEEEEECH----HHHHHHHHHHHHH
T ss_conf             71359889997898974552020-5251378996579999868----9999999999997


No 12 
>PRK11634 ATP-dependent RNA helicase DeaD; Provisional
Probab=99.94  E-value=7.2e-23  Score=198.95  Aligned_cols=331  Identities=20%  Similarity=0.282  Sum_probs=232.7

Q ss_pred             CCCHHHHHHHHHCCC-CCCHHHHHHHHHHHHHHCCCCCCEEEEEECCCCCHHHHHHHHHHHHHHH---HCCEEEEEHHHH
Q ss_conf             775789999863024-6798899999999984100134307886214422369999997334443---054588612799
Q gi|254780945|r  257 VEGKIAQKILRNIPF-SPTKSQESAIKDILQDMSQKNRMLRILQGDVGSGKTLVALIAMAAAVEA---GGQAVIMAPIGI  332 (700)
Q Consensus       257 ~~~~~~~~f~~~LPF-~LT~~Q~~ai~eI~~Dl~~~~pM~RLLQGDVGSGKTiVA~~A~l~~~~~---G~Q~alMaPTEI  332 (700)
                      .+..+++. ++.+.| ++|.=|++||--|...      -+-+.|--.|||||+-.++.++..++.   +-|+.++|||-=
T Consensus        13 L~~~ll~a-L~~~Gf~~PTpIQ~~aIP~iL~G------kDvi~~AqTGSGKTlAFlLPiL~~l~~~~~~pqaLIL~PTRE   85 (629)
T PRK11634         13 LKAPILEA-LNDLGYEKPSPIQAECIPHLLNG------RDVLGMAQTGSGKTAAFSLPLLHNLDPELKAPQILVLAPTRE   85 (629)
T ss_pred             CCHHHHHH-HHHCCCCCCCHHHHHHHHHHHCC------CCEEEECCCCCHHHHHHHHHHHHHHHHCCCCCCEEEECCCHH
T ss_conf             89999999-99879999999999999999679------988997888478999999999998662368986899789989


Q ss_pred             HHHHHHHHHHHHCCCC-CCEEEEEECCCCHHHHHHHHHHHCCCCCEEEEECHH-H----CCCCCCCCCCCEEEECCCCC-
Q ss_conf             9999998621101457-865899624642256676877621347548641112-0----13345544441788521013-
Q gi|254780945|r  333 LAQQHYEFIKKYTQNT-QIIVEIITGNMPQAHRRKALERIAHGQAHIIIGTHA-L----FQDSIQYYKLILVIVDEQHR-  405 (700)
Q Consensus       333 LA~QH~~~~~~~~~~~-~i~v~lLtg~~~~~er~~i~~~i~~G~~~iiIGTHA-L----~q~~v~F~~LgLvViDEQHR-  405 (700)
                      ||.|-++.++.+...+ ++++..+.|+.+..   ..+..++.| ++|||||-. |    -...+.++++-.+|+||=.+ 
T Consensus        86 LA~QV~~~~~~l~~~~~~i~v~~l~GG~~~~---~q~~~L~~g-~~IVVgTPGRL~d~l~~~~l~L~~l~~lVLDEAD~m  161 (629)
T PRK11634         86 LAVQVAEAMTDFSKHMRGVNVVALYGGQRYD---VQLRALRQG-PQIVVGTPGRLLDHLKRGTLDLSKLSGLVLDEADEM  161 (629)
T ss_pred             HHHHHHHHHHHHHHCCCCCEEEEEECCCCHH---HHHHHHCCC-CCEEEECHHHHHHHHHCCCCCHHHCCEEEEECHHHH
T ss_conf             9999999999997217997799998997789---999986279-999996989999999729641200767898671553


Q ss_pred             ----CCHHHHHHHHHC-CCCCCCEEECHHHHH--HHHHHHHHHCCCHHHHCCCCCCCCCCEEEEEEC--C-CHHHHHHHH
Q ss_conf             ----356889987402-567761010101322--789999752010111102355766620799970--2-002689999
Q gi|254780945|r  406 ----FGVQQRLKLTQK-ATAPHVLLMTATPIP--RTLVLTSLGDIDISKITEKPAGRKPIKTVIIPI--N-RIDEVIERL  475 (700)
Q Consensus       406 ----FGV~QR~~L~~K-g~~ph~L~MtATPIP--RTLal~~ygdldvS~i~e~P~gR~~I~T~~~~~--~-~~~~~~~~i  475 (700)
                          |- ++=..+.+. ......++.|||-=+  +.++-.+..+-..-.+......+..|.-.++..  . +.+.+...+
T Consensus       162 L~~gF~-~di~~Il~~lp~~~Qt~LfSATmp~~i~~la~~~l~~P~~i~i~~~~~t~~~i~q~~~~v~~~~K~~aL~~~L  240 (629)
T PRK11634        162 LRMGFI-EDVETIMAQIPEGHQTALFSATMPEAIRRITRRFMKEPQEVRIQSSVTTRPDISQSYWTVWGMRKNEALVRFL  240 (629)
T ss_pred             CCCCCH-HHHHHHHHHCCCCCEEEEEECCCCHHHHHHHHHHCCCCEEEEECCCCCCCCCCEEEEEEECCHHHHHHHHHHH
T ss_conf             363659-9999999867403144666314659999999987569879740455555776305999965245799999998


Q ss_pred             HHHHCCCCEEEEEECCCCCCCCCCCCHHHHHHHHHHHHCCCCEECCCCCCCHHHHHHHHHHHHCCCEEEEEECHHHHCCC
Q ss_conf             76310387389997120122111210146666666866371031201469989999999997559869999800341046
Q gi|254780945|r  476 KVVLSEGKKAYWICPQIEEKKESNFRSVVERFNSLHEHFTSSIAIIHGRMSDIDKESVMDSFKNGTCKLLIATTVIEVGI  555 (700)
Q Consensus       476 ~~~l~~g~q~y~VcPlIeese~~~~~~~~~~~~~l~~~~~~~v~~lHGkm~~~ek~~~m~~F~~g~~~iLvaTtviEVGv  555 (700)
                      ..  ..-.++.|-|...        ..+.+.++.|.+ .+.++..+||.|+..+++.+|++|++|+++|||||-|.-=|+
T Consensus       241 ~~--~~~~~~IIF~~Tk--------~~~~~l~~~L~~-~g~~~~~LHgdm~q~~R~~~l~~Fr~g~~~ILVaTDvaARGL  309 (629)
T PRK11634        241 EA--EDFDAAIIFVRTK--------NATLEVAEALER-NGYNSAALNGDMNQALREQTLERLKDGRLDILIATDVAARGL  309 (629)
T ss_pred             HH--CCCCEEEEEEECH--------HHHHHHHHHHHH-CCCCEEEEECCCCHHHHHHHHHHHHCCCCCEEEECCCCCCCC
T ss_conf             61--5888489998227--------889999999997-699657656899999999999999759998898786210557


Q ss_pred             CCCCCCEEEEECHHHCCHHHHHHHHHCCCCCCCCEEEEEEECCCCCHHHHHHHHHHHHHC
Q ss_conf             888765899858525474688773011667898359999708889987999999998414
Q gi|254780945|r  556 DVVDASIIIIENAEHFGLAQLHQLRGRVGRGEEISSCILLYHPPLSKNSYTRLSVLKNTE  615 (700)
Q Consensus       556 dvpna~~mvI~~aerfGLsqLHQLRGRVGRg~~~s~c~l~~~~~~~~~~~~Rl~~l~~~~  615 (700)
                      |||+.+..|-+|.=.---+=+|- =||.||.+.+|.|+++..+.    -+..|+.++...
T Consensus       310 Di~~V~~VINyDlP~d~e~YVHR-iGRTGRaGr~G~Aitfv~~~----e~~~l~~ier~~  364 (629)
T PRK11634        310 DVERISLVVNYDIPMDSESYVHR-IGRTGRAGRAGRALLFVENR----ERRLLRNIERTM  364 (629)
T ss_pred             CCCCCCEEEEECCCCCHHHCCCC-CCCCCCCCCCEEEEEEECHH----HHHHHHHHHHHH
T ss_conf             72568889996898974340102-58331689964699988889----999999999997


No 13 
>PRK02362 ski2-like helicase; Provisional
Probab=99.94  E-value=1e-23  Score=205.60  Aligned_cols=320  Identities=20%  Similarity=0.292  Sum_probs=232.3

Q ss_pred             HHHHHHHHCCC-CCCHHHHHHHHHHHHHHCCCCCCEEEEEECCCCCHHHHHHHHHHHHHHHHCCEEEEEHHHHHHHHHHH
Q ss_conf             89999863024-67988999999999841001343078862144223699999973344430545886127999999998
Q gi|254780945|r  261 IAQKILRNIPF-SPTKSQESAIKDILQDMSQKNRMLRILQGDVGSGKTLVALIAMAAAVEAGGQAVIMAPIGILAQQHYE  339 (700)
Q Consensus       261 ~~~~f~~~LPF-~LT~~Q~~ai~eI~~Dl~~~~pM~RLLQGDVGSGKTiVA~~A~l~~~~~G~Q~alMaPTEILA~QH~~  339 (700)
                      .+.++++...+ +|-+-|..|++.   .+-.++  |=++.-=.|||||+||-+||+.++..|..+.+++|+--||+|-|.
T Consensus        11 ~~~~~~~~~gI~~Lyp~Q~eal~~---gl~~g~--NlvvsaPTgsGKTlvAElail~~l~~g~k~vYi~P~kALa~EK~~   85 (736)
T PRK02362         11 GVIDFYEGSGIEELYPPQAEAVEA---GLLEGK--NLLAAIPTASGKTLLAELAMLKAIAEGGKALYIVPLRALASEKFE   85 (736)
T ss_pred             HHHHHHHHCCCCCCCHHHHHHHHH---HHCCCC--CEEEECCCCCCHHHHHHHHHHHHHHHCCEEEEECCHHHHHHHHHH
T ss_conf             999999976997578999999986---435698--189979999858999999999999839979998587999999999


Q ss_pred             HHHHHCCCCCCEEEEEECCCCHHHHHHHHHHHCCCCCEEEEEC----HHHCCCCC-CCCCCCEEEECCCCCCCHHHHHHH
Q ss_conf             6211014578658996246422566768776213475486411----12013345-544441788521013356889987
Q gi|254780945|r  340 FIKKYTQNTQIIVEIITGNMPQAHRRKALERIAHGQAHIIIGT----HALFQDSI-QYYKLILVIVDEQHRFGVQQRLKL  414 (700)
Q Consensus       340 ~~~~~~~~~~i~v~lLtg~~~~~er~~i~~~i~~G~~~iiIGT----HAL~q~~v-~F~~LgLvViDEQHRFGV~QR~~L  414 (700)
                      .|++ |.++|++|.++||......+     .  -+..+|+|-|    .+|+.... -+.++|+|||||=|=.|=..|-..
T Consensus        86 ~~~~-~~~~gi~V~~~tGd~~~~~~-----~--l~~~dIiV~T~EK~dsl~r~~~~~l~~v~lVViDEiHli~d~~RG~~  157 (736)
T PRK02362         86 EFSE-FSELGLRVGISTGDYDRRDE-----Y--LGRNDIIVATSEKTDSLLRNGAPWIDDISCVVADEVHLIDSPNRGPT  157 (736)
T ss_pred             HHHH-HHCCCCEEEEEECCCCCCHH-----H--CCCCCEEEECHHHHHHHHHCCCHHHHCCCEEEEECCEEECCCCCHHH
T ss_conf             9998-74579989998089887831-----4--36899999997999999844816765089899817678668872499


Q ss_pred             HH--------CCCCCCCEEECHH-HHHHHHHHHHHHCCCHHHHCCCCCCCCCCEEEEE--------------ECCCHHHH
Q ss_conf             40--------2567761010101-3227899997520101111023557666207999--------------70200268
Q gi|254780945|r  415 TQ--------KATAPHVLLMTAT-PIPRTLVLTSLGDIDISKITEKPAGRKPIKTVII--------------PINRIDEV  471 (700)
Q Consensus       415 ~~--------Kg~~ph~L~MtAT-PIPRTLal~~ygdldvS~i~e~P~gR~~I~T~~~--------------~~~~~~~~  471 (700)
                      .+        .+.++.++.|||| |=|.-+|--+-+++=.|  +-.|.   |....++              .....+..
T Consensus       158 lE~~lskl~~~~~~iqiIgLSATl~N~~~la~WL~a~~~~s--~~RPV---~L~~~v~~~~~~~~~~~~~~~~~~~~~~~  232 (736)
T PRK02362        158 LEVTLAKLRRLNPDMQVIALSATIGNADELAAWLDAELVDS--EWRPV---DLREGVFYGGAIHFKDTERELEVPSKDED  232 (736)
T ss_pred             HHHHHHHHHHCCCCCEEEEEECCCCCHHHHHHHHCCCCCCC--CCCCC---CCEEEEEECCEECCCCCCCHHCCCCCCHH
T ss_conf             99999999733877438986245589999999838862158--98886---75565650770103510030002564058


Q ss_pred             HHHHHHHHCCCCEEEEEECCCCCCCCCC------------------CCHH---------HHHHHHHHHHCCCCEECCCCC
Q ss_conf             9999763103873899971201221112------------------1014---------666666686637103120146
Q gi|254780945|r  472 IERLKVVLSEGKKAYWICPQIEEKKESN------------------FRSV---------VERFNSLHEHFTSSIAIIHGR  524 (700)
Q Consensus       472 ~~~i~~~l~~g~q~y~VcPlIeese~~~------------------~~~~---------~~~~~~l~~~~~~~v~~lHGk  524 (700)
                      ...+.+.+.+|+||.|-||-=...|+.-                  +...         ++..+.|++..+..|+.-|.-
T Consensus       233 ~~l~~~~~~~~~~~LVF~~SR~~~e~~A~~la~~~~~~~~~~~~~~l~~~~~~i~~~~~~~~~~~L~~~l~~GVafHHAG  312 (736)
T PRK02362        233 LNLVLDTLDEGGQCLVFVSSRRNAEAFAKRAASALKKALSAEEREALAGIAEEIREVSETDTSKVLADCVRSGAAFHHAG  312 (736)
T ss_pred             HHHHHHHHHCCCCEEEEEECHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHCCEEEECCC
T ss_conf             99999999739906999824999999999998752421575668899999999973444203599999996094851599


Q ss_pred             CCHHHHHHHHHHHHCCCEEEEEECHHHHCCCCCCCCCEEEEECHHHC---------CHHHHHHHHHCCCCC--CCCEEEE
Q ss_conf             99899999999975598699998003410468887658998585254---------746887730116678--9835999
Q gi|254780945|r  525 MSDIDKESVMDSFKNGTCKLLIATTVIEVGIDVVDASIIIIENAEHF---------GLAQLHQLRGRVGRG--EEISSCI  593 (700)
Q Consensus       525 m~~~ek~~~m~~F~~g~~~iLvaTtviEVGvdvpna~~mvI~~aerf---------GLsqLHQLRGRVGRg--~~~s~c~  593 (700)
                      |..++|+.|-+.|++|.++||+||+-.-.|||.|--+|+ |-+-.||         ..++.+|.-||-||-  +..|+|+
T Consensus       313 L~~~~R~lVE~~Fr~g~Ikvl~aTsTLA~GVNLPAr~VI-i~~~~~~~~~~g~~~l~~~e~~QM~GRAGRpg~D~~G~ai  391 (736)
T PRK02362        313 LSREHRELVEEGFRDGLIKVISSTPTLAAGLNLPARRVI-IRDYRRYDSGAGMQPIPVLEYHQMAGRAGRPRLDPYGEAV  391 (736)
T ss_pred             CCHHHHHHHHHHHHCCCCCEEEECCHHHCCCCCCEEEEE-EECCEEECCCCCCEECCHHHHHHHHHHCCCCCCCCCCEEE
T ss_conf             998999999999987998389725166505578526999-8043673698883368899999998524899889886299


Q ss_pred             EEECCC
Q ss_conf             970888
Q gi|254780945|r  594 LLYHPP  599 (700)
Q Consensus       594 l~~~~~  599 (700)
                      +++++.
T Consensus       392 li~~~~  397 (736)
T PRK02362        392 LLAKSY  397 (736)
T ss_pred             EEECCH
T ss_conf             996782


No 14 
>PRK10590 ATP-dependent RNA helicase RhlE; Provisional
Probab=99.94  E-value=1.7e-22  Score=196.03  Aligned_cols=320  Identities=18%  Similarity=0.271  Sum_probs=227.4

Q ss_pred             CCCHHHHHHHHHCCC-CCCHHHHHHHHHHHHHHCCCCCCEEEEEECCCCCHHHHHHHHHHHHHHHH---------CCEEE
Q ss_conf             775789999863024-67988999999999841001343078862144223699999973344430---------54588
Q gi|254780945|r  257 VEGKIAQKILRNIPF-SPTKSQESAIKDILQDMSQKNRMLRILQGDVGSGKTLVALIAMAAAVEAG---------GQAVI  326 (700)
Q Consensus       257 ~~~~~~~~f~~~LPF-~LT~~Q~~ai~eI~~Dl~~~~pM~RLLQGDVGSGKTiVA~~A~l~~~~~G---------~Q~al  326 (700)
                      .+..+++.+ +.+.| ++|.=|.+||-.|.+.      -+-+.+--.|||||+.+++.++.-+...         .|+.+
T Consensus         8 L~~~ll~aL-~~~G~~~PTpIQ~~aIP~iL~G------rDvl~~A~TGSGKTlAflLPil~~l~~~~~~~~~~~~~~aLI   80 (457)
T PRK10590          8 LSPDILRAV-AEQGYREPTPIQQQAIPAVLEG------RDLMASAQTGTGKTAGFTLPLLQHLITRQPHAKGRRPVRALI   80 (457)
T ss_pred             CCHHHHHHH-HHCCCCCCCHHHHHHHHHHHCC------CCEEEECCCCHHHHHHHHHHHHHHHHHCCCCCCCCCCCEEEE
T ss_conf             899999999-9779999999999999999779------988998898118999999999999863676544568824999


Q ss_pred             EEHHHHHHHHHHHHHHHHCCCCCCEEEEEECCCCHHHHHHHHHHHCCCCCEEEEECH-----HHCCCCCCCCCCCEEEEC
Q ss_conf             612799999999862110145786589962464225667687762134754864111-----201334554444178852
Q gi|254780945|r  327 MAPIGILAQQHYEFIKKYTQNTQIIVEIITGNMPQAHRRKALERIAHGQAHIIIGTH-----ALFQDSIQYYKLILVIVD  401 (700)
Q Consensus       327 MaPTEILA~QH~~~~~~~~~~~~i~v~lLtg~~~~~er~~i~~~i~~G~~~iiIGTH-----AL~q~~v~F~~LgLvViD  401 (700)
                      ++||-=||.|-++.++.+-..+++++.++.|+.+....   ...+.. .++|||||=     -+-+..+.++++-++|+|
T Consensus        81 L~PTRELA~Qi~~~~~~l~~~~~~~~~~~~Gg~~~~~q---~~~l~~-~~dIlVaTPGRLldl~~~~~~~l~~v~~lVlD  156 (457)
T PRK10590         81 LTPTRELAAQIGENVRDYSKYLNIRSLVVFGGVSINPQ---MMKLRG-GVDVLVATPGRLLDLEHQNAVKLDQVEILVLD  156 (457)
T ss_pred             ECCHHHHHHHHHHHHHHHCCCCCCEEEEEECCCCHHHH---HHHHCC-CCCEEEECCHHHHHHHHCCCCCCCCCEEEEEE
T ss_conf             76879999999999997425589459999799777599---998618-99989989288898886267765752399983


Q ss_pred             CCCCC---C-HHHHHHHHHC-CCCCCCEEECHHHHH--HHHHHHHHHC-CCHHHHCCCCCCCCCCEEEEEE--CCCHHHH
Q ss_conf             10133---5-6889987402-567761010101322--7899997520-1011110235576662079997--0200268
Q gi|254780945|r  402 EQHRF---G-VQQRLKLTQK-ATAPHVLLMTATPIP--RTLVLTSLGD-IDISKITEKPAGRKPIKTVIIP--INRIDEV  471 (700)
Q Consensus       402 EQHRF---G-V~QR~~L~~K-g~~ph~L~MtATPIP--RTLal~~ygd-ldvS~i~e~P~gR~~I~T~~~~--~~~~~~~  471 (700)
                      |=+|.   | .++=..+..+ ......+..|||==+  +.++-.+..+ ..+++-..-.. -..|.-++.-  .++...+
T Consensus       157 EAD~mLd~gF~~di~~Il~~lp~~rQ~llfSAT~~~~v~~l~~~~l~~p~~i~v~~~~~~-~~~i~q~~~~v~~~~k~~~  235 (457)
T PRK10590        157 EADRMLDMGFIHDIRRVLAKLPAKRQNLLFSATFSDDIKALAEKLLHNPLEIEVARRNTA-SEQVTQHVHFVDKKRKREL  235 (457)
T ss_pred             CCHHHHCCCCHHHHHHHHHHCCCCCEEEEEECCCCHHHHHHHHHHCCCCEEEEECCCCCC-CCCEEEEEEEECHHHHHHH
T ss_conf             705651566536689998638765268999504888999999997689889996367665-6130489999566789999


Q ss_pred             HHHHHHHHCCCCEEEEEECCCCCCCCCCCCHHHHHHHHHHHHCCCCEECCCCCCCHHHHHHHHHHHHCCCEEEEEECHHH
Q ss_conf             99997631038738999712012211121014666666686637103120146998999999999755986999980034
Q gi|254780945|r  472 IERLKVVLSEGKKAYWICPQIEEKKESNFRSVVERFNSLHEHFTSSIAIIHGRMSDIDKESVMDSFKNGTCKLLIATTVI  551 (700)
Q Consensus       472 ~~~i~~~l~~g~q~y~VcPlIeese~~~~~~~~~~~~~l~~~~~~~v~~lHGkm~~~ek~~~m~~F~~g~~~iLvaTtvi  551 (700)
                      +..+-... ...|+.|-|...        ..++..++.|.+. +-.+..+||.|+..+++.+|++|++|+++|||||-|.
T Consensus       236 L~~ll~~~-~~~~~iIF~~tk--------~~a~~l~~~L~~~-g~~~~~lHg~~sq~~R~~~l~~F~~g~~~vLVaTDva  305 (457)
T PRK10590        236 LSQMIGKG-NWQQVLVFTRTK--------HGANHLAEQLNKD-GIRSAAIHGNKSQGARTRALADFKSGDIRVLVATDIA  305 (457)
T ss_pred             HHHHHHHC-CCCCEEEEECHH--------HHHHHHHHHHHHC-CCCCEEEECCCCHHHHHHHHHHHHCCCCCEEEECCCC
T ss_conf             99998615-866335884119--------9999999998556-9982323247899999999999986998299957701


Q ss_pred             HCCCCCCCCCEEEEECHHHCCHHHHHHHHHCCCCCCCCEEEEEEECCC
Q ss_conf             104688876589985852547468877301166789835999970888
Q gi|254780945|r  552 EVGIDVVDASIIIIENAEHFGLAQLHQLRGRVGRGEEISSCILLYHPP  599 (700)
Q Consensus       552 EVGvdvpna~~mvI~~aerfGLsqLHQLRGRVGRg~~~s~c~l~~~~~  599 (700)
                      .=|||+|+.+..|=+|.=+---+=+|- =||.||.+..|.|+-++.++
T Consensus       306 aRGiDi~~V~~VInyD~P~~~e~YvHR-iGRTGRaG~~G~ait~v~~~  352 (457)
T PRK10590        306 ARGLDIEELPHVVNYELPNVPEDYVHR-IGRTGRAAATGEALSLVCVD  352 (457)
T ss_pred             CCCCCCCCCCEEEEECCCCCHHHEECC-CCCCCCCCCCEEEEEEECHH
T ss_conf             155663568879993899974450022-67060589953699986689


No 15 
>PTZ00110 helicase; Provisional
Probab=99.94  E-value=3.9e-22  Score=193.20  Aligned_cols=347  Identities=20%  Similarity=0.268  Sum_probs=243.0

Q ss_pred             HHHHHHHCCC-CCCHHHHHHHHHHHHHHCCCCCCEEEEEECCCCCHHHHHHHHHHHHHH--------HHCCEEEEEHHHH
Q ss_conf             9999863024-679889999999998410013430788621442236999999733444--------3054588612799
Q gi|254780945|r  262 AQKILRNIPF-SPTKSQESAIKDILQDMSQKNRMLRILQGDVGSGKTLVALIAMAAAVE--------AGGQAVIMAPIGI  332 (700)
Q Consensus       262 ~~~f~~~LPF-~LT~~Q~~ai~eI~~Dl~~~~pM~RLLQGDVGSGKTiVA~~A~l~~~~--------~G~Q~alMaPTEI  332 (700)
                      +-+-+++..| ++|.=|.++|--+++    ++-|  +-+--.|||||+-.++-++.-+.        .|-+|.+||||-=
T Consensus       193 il~~i~~~GF~~PTPIQ~qaIPiaLs----GrDv--IgiAqTGSGKTLAFlLP~l~hi~~q~~~~~~~gP~aLILaPTRE  266 (602)
T PTZ00110        193 ILKSIEAAGFTEPTPIQVQGWPIALS----GRDM--IGIAETGSGKTLAFLLPAIVHINAQPLLRPGDGPIVLVLAPTRE  266 (602)
T ss_pred             HHHHHHHCCCCCCCHHHHHHHHHHHC----CCCE--EEECCCCCHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEECCHHH
T ss_conf             99999976999999899999879856----9867--99878978899999999999985163436789976999738399


Q ss_pred             HHHHHHHHHHHHCCCCCCEEEEEECCCCHHHHHHHHHHHCCCCCEEEEECH-----HHCCCCCCCCCCCEEEECCCCC--
Q ss_conf             999999862110145786589962464225667687762134754864111-----2013345544441788521013--
Q gi|254780945|r  333 LAQQHYEFIKKYTQNTQIIVEIITGNMPQAHRRKALERIAHGQAHIIIGTH-----ALFQDSIQYYKLILVIVDEQHR--  405 (700)
Q Consensus       333 LA~QH~~~~~~~~~~~~i~v~lLtg~~~~~er~~i~~~i~~G~~~iiIGTH-----AL~q~~v~F~~LgLvViDEQHR--  405 (700)
                      ||.|-++.+.++-...+++++++.|+.+.++   ....|+.| ++|||||-     -|=...+.++++.++|+||=-|  
T Consensus       267 LA~QI~~e~~~~~~~~~ir~~~i~GG~~~~~---Q~~~L~~G-~dIvVATPGRLiDlL~~~~~~L~~v~yLVLDEADRML  342 (602)
T PTZ00110        267 LAEQIREQALQFGRSSKLKNSVAYGGVPKRF---QTYALRRG-VEILIACPGRLIDFLESNVTNLRRVTYLVLDEADRML  342 (602)
T ss_pred             HHHHHHHHHHHHHCCCCCEEEEEECCCCHHH---HHHHHCCC-CCEEEECCHHHHHHHHCCCCCCCCEEEEEEECHHHHH
T ss_conf             9999999999971547854999979968799---99987169-9999979238999996499874310289987577663


Q ss_pred             ---CCHHHHHHHHHCCCCCCCEEECHHHHHHH--HHHHHHHC----CCHHHHCCCCCCCCCCEEEEE--E-CCCHHHHHH
Q ss_conf             ---35688998740256776101010132278--99997520----101111023557666207999--7-020026899
Q gi|254780945|r  406 ---FGVQQRLKLTQKATAPHVLLMTATPIPRT--LVLTSLGD----IDISKITEKPAGRKPIKTVII--P-INRIDEVIE  473 (700)
Q Consensus       406 ---FGV~QR~~L~~Kg~~ph~L~MtATPIPRT--Lal~~ygd----ldvS~i~e~P~gR~~I~T~~~--~-~~~~~~~~~  473 (700)
                         |--.=|.-+..-...--.|++|||-=+.-  ||-.+..+    +++..++....  ..|.-.++  . .++...+..
T Consensus       343 DmGFe~qI~~Il~~i~pdRQTlLFSAT~p~~V~~LA~~~L~~~Pv~I~Vg~~~~~a~--~~I~Q~v~vv~~~eK~~~L~~  420 (602)
T PTZ00110        343 DMGFEPQIRKIVSQIRPDRQTLMWSATWPKEVQSLARDLCKEEPVHVNVGSLDLTTC--HNIKQEVFVIEEHEKRAKLKE  420 (602)
T ss_pred             CCCCHHHHHHHHHHCCCCCEEEEEECCCCHHHHHHHHHHHCCCCEEEEECCCCCCCC--CCCEEEEEEECHHHHHHHHHH
T ss_conf             546299999999858978779999558998999999998206988999368887777--870589999651889999999


Q ss_pred             HHHHHHCCCCEEEEEECCCCCCCCCCCCHHHHHHHHHHHHCCCCEECCCCCCCHHHHHHHHHHHHCCCEEEEEECHHHHC
Q ss_conf             99763103873899971201221112101466666668663710312014699899999999975598699998003410
Q gi|254780945|r  474 RLKVVLSEGKKAYWICPQIEEKKESNFRSVVERFNSLHEHFTSSIAIIHGRMSDIDKESVMDSFKNGTCKLLIATTVIEV  553 (700)
Q Consensus       474 ~i~~~l~~g~q~y~VcPlIeese~~~~~~~~~~~~~l~~~~~~~v~~lHGkm~~~ek~~~m~~F~~g~~~iLvaTtviEV  553 (700)
                      .+++. ..+.++.|-|-..        ..++..+..|+. .+-.+..+||.|+..|.+.+|++|++|+++|||||-|.-=
T Consensus       421 lL~~~-~~~~kvIIFvnTK--------~~ad~L~~~L~~-~G~~a~~LHGd~~Q~eR~~~L~~Fr~G~~~ILVATDVAAR  490 (602)
T PTZ00110        421 LLGQI-MDGGKILIFSETK--------KGADTLTKELRL-DGWPALCIHGDKKQEERTWVLNEFKTGKHPIMIATDVASR  490 (602)
T ss_pred             HHHHC-CCCCCEEEEECCH--------HHHHHHHHHHHH-CCCCEEEEECCCCHHHHHHHHHHHHCCCCCEEEECCHHHC
T ss_conf             99852-7899689992973--------899999999986-7995798208899999999999997699988988222331


Q ss_pred             CCCCCCCCEEEEECHHHCCHHHHHHHHHCCCCCCCCEEEEEEECCCCCHHHHHHHHHHHHHCHHHHHHHHHHHHCCCC
Q ss_conf             468887658998585254746887730116678983599997088899879999999984142589999998520630
Q gi|254780945|r  554 GIDVVDASIIIIENAEHFGLAQLHQLRGRVGRGEEISSCILLYHPPLSKNSYTRLSVLKNTEDGFLIAEEDLKQRKEG  631 (700)
Q Consensus       554 Gvdvpna~~mvI~~aerfGLsqLHQLRGRVGRg~~~s~c~l~~~~~~~~~~~~Rl~~l~~~~dGf~iAe~Dl~lRG~G  631 (700)
                      |+|||+.+..|=+|.-+=-=.=.|-. ||.||.+..|..+-...+.....+++=.++|++.+-----.-+.|..+.++
T Consensus       491 GLDI~dV~~VINYD~P~~~edYVHRI-GRTGRAG~kG~A~TF~Tpd~~~~a~~Lv~~L~ea~q~vp~~L~~la~~~~~  567 (602)
T PTZ00110        491 GLDVRDVKYVINFDFPNQIEDYVHRI-GRTGRAGAKGASYTFLTPDKYRSARELVKLMREAKQEIPPELEKLANERSY  567 (602)
T ss_pred             CCCCCCCCEEEEECCCCCCCCCCCCC-CCCCCCCCCEEEEEEECCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHCCCC
T ss_conf             55515798799958979802210135-615068993169999777707789999999998389999899998735688


No 16 
>PRK04837 ATP-dependent RNA helicase RhlB; Provisional
Probab=99.93  E-value=2.9e-22  Score=194.14  Aligned_cols=331  Identities=20%  Similarity=0.232  Sum_probs=226.1

Q ss_pred             CCCCCHHHHHHHHHCCC-CCCHHHHHHHHHHHHHHCCCCCCEEEEEECCCCCHHHHHHHHHHHHHH----------HHCC
Q ss_conf             78775789999863024-679889999999998410013430788621442236999999733444----------3054
Q gi|254780945|r  255 INVEGKIAQKILRNIPF-SPTKSQESAIKDILQDMSQKNRMLRILQGDVGSGKTLVALIAMAAAVE----------AGGQ  323 (700)
Q Consensus       255 ~~~~~~~~~~f~~~LPF-~LT~~Q~~ai~eI~~Dl~~~~pM~RLLQGDVGSGKTiVA~~A~l~~~~----------~G~Q  323 (700)
                      +..+..+++.+ +.+.| .+|.=|..||--|.+.      -+-+.|--.|||||+..++.++..+-          ++-+
T Consensus        14 lgL~~~ll~~L-~~~g~~~pTpIQ~~aIP~il~G------~Dvi~~A~TGSGKTlAfllPil~~ll~~~~~~~~~~~~p~   86 (423)
T PRK04837         14 FALHPKVVEAL-EKKGFEYCTPIQALALPLTLAG------RDVAGQAQTGTGKTMAFLTATFHHLLSHPAPEGRKVNQPR   86 (423)
T ss_pred             CCCCHHHHHHH-HHCCCCCCCHHHHHHHHHHHCC------CCEEEECCCCCHHHHHHHHHHHHHHHHCCCCCCCCCCCCE
T ss_conf             79699999999-9779999999999999999679------9889989998749999999999999837453345567861


Q ss_pred             EEEEEHHHHHHHHHHHHHHHHCCCCCCEEEEEECCCCHHHHHHHHHHHCCCCCEEEEECHH-----HCCCCCCCCCCCEE
Q ss_conf             5886127999999998621101457865899624642256676877621347548641112-----01334554444178
Q gi|254780945|r  324 AVIMAPIGILAQQHYEFIKKYTQNTQIIVEIITGNMPQAHRRKALERIAHGQAHIIIGTHA-----LFQDSIQYYKLILV  398 (700)
Q Consensus       324 ~alMaPTEILA~QH~~~~~~~~~~~~i~v~lLtg~~~~~er~~i~~~i~~G~~~iiIGTHA-----L~q~~v~F~~LgLv  398 (700)
                      +.+||||-=||.|-++.++.+....++++.++.|+.+..+...   .+.+| ++|||||-.     +-+..+.++++-.+
T Consensus        87 aLIL~PTRELa~Qi~~~~~~l~~~~~l~~~~~~GG~~~~~q~~---~l~~~-~dIlV~TPgRL~d~~~~~~~~l~~i~~l  162 (423)
T PRK04837         87 ALIMAPTRELAVQIHADAEPLAQATGLKLGLAYGGEGYDKQLK---VLESG-VDILIGTTGRLIDYAKQNHINLGAIQVV  162 (423)
T ss_pred             EEEEECCHHHHHHHHHHHHHHHCCCCCEEEEEECCCCHHHHHH---HHHCC-CCEEEECHHHHHHHHHHCCCCCCCCEEE
T ss_conf             8999388999999999999974325845999989988799999---87179-9989989189999986422123664289


Q ss_pred             EECCCCC-----CCHHHHHHHHHCCCCC-C--CEEECHHHHHHHHHHHHHHCC-CHHHHCCCCCCC--CCCEEEEEECC-
Q ss_conf             8521013-----3568899874025677-6--101010132278999975201-011110235576--66207999702-
Q gi|254780945|r  399 IVDEQHR-----FGVQQRLKLTQKATAP-H--VLLMTATPIPRTLVLTSLGDI-DISKITEKPAGR--KPIKTVIIPIN-  466 (700)
Q Consensus       399 ViDEQHR-----FGV~QR~~L~~Kg~~p-h--~L~MtATPIPRTLal~~ygdl-dvS~i~e~P~gR--~~I~T~~~~~~-  466 (700)
                      |+||=+|     |.=.-+ .+..+-..+ .  .+..|||==++.-.+ .+-.| +-..|.-.|...  ..|.-.++-.+ 
T Consensus       163 VlDEAD~lld~gF~~~i~-~i~~~~p~~~~r~~~lfSATl~~~v~~l-a~~~l~~p~~i~v~~~~~~~~~i~~~~~~~~~  240 (423)
T PRK04837        163 VLDEADRMFDLGFIKDIR-WLFRRMPPANQRLNMLFSATLSYRVREL-AFEHMNNPEYVEVEPEQKTGHRIKEELFYPSN  240 (423)
T ss_pred             EEECHHHHHHCCCHHHHH-HHHHHCCCCHHEEEEEEECCCCHHHHHH-HHHHCCCCEEEEECCCCCCCCCEEEEEEEECH
T ss_conf             963446543026399999-9999689622108999703688899999-99977898799965776566542699999172


Q ss_pred             --CHHHHHHHHHHHHCCCCEEEEEECCCCCCCCCCCCHHHHHHHHHHHHCCCCEECCCCCCCHHHHHHHHHHHHCCCEEE
Q ss_conf             --002689999763103873899971201221112101466666668663710312014699899999999975598699
Q gi|254780945|r  467 --RIDEVIERLKVVLSEGKKAYWICPQIEEKKESNFRSVVERFNSLHEHFTSSIAIIHGRMSDIDKESVMDSFKNGTCKL  544 (700)
Q Consensus       467 --~~~~~~~~i~~~l~~g~q~y~VcPlIeese~~~~~~~~~~~~~l~~~~~~~v~~lHGkm~~~ek~~~m~~F~~g~~~i  544 (700)
                        +..-++..+++.  ...|+.|-|...        ..++..++.|.+ .+.+++.+||.|+..++..+|++|++|+++|
T Consensus       241 ~~K~~~L~~ll~~~--~~~k~iIF~nt~--------~~~~~l~~~L~~-~g~~~~~lhg~~~q~~R~~~l~~F~~g~~~v  309 (423)
T PRK04837        241 EEKMRLLQTLIEEE--WPDRAIIFANTK--------HRCEEIWGHLAA-DGHRVGLLTGDVPQKKRLRILEQFTRGDLDI  309 (423)
T ss_pred             HHHHHHHHHHHHHH--CCCCEEEECCHH--------HHHHHHHHHHHH-CCCCEEEECCCCCHHHHHHHHHHHHCCCCCE
T ss_conf             77999999999840--887468861628--------889999999976-5981787225457999999999997699989


Q ss_pred             EEECHHHHCCCCCCCCCEEEEECHHHCCHHHHHHHHHCCCCCCCCEEEEEEECCCCCHHHHHHHHHHHHH
Q ss_conf             9980034104688876589985852547468877301166789835999970888998799999999841
Q gi|254780945|r  545 LIATTVIEVGIDVVDASIIIIENAEHFGLAQLHQLRGRVGRGEEISSCILLYHPPLSKNSYTRLSVLKNT  614 (700)
Q Consensus       545 LvaTtviEVGvdvpna~~mvI~~aerfGLsqLHQLRGRVGRg~~~s~c~l~~~~~~~~~~~~Rl~~l~~~  614 (700)
                      ||||-|.-=|+|+|+.+..|-+|.-.=--.=+|- =||.||.+..|.|+-++.    +.-...|..+++.
T Consensus       310 LVaTDvaaRGLDi~~V~~VInyD~P~~~~~YiHR-iGRTgRaG~~G~aitf~~----~~~~~~l~~ie~~  374 (423)
T PRK04837        310 LVATDVAARGLHIPDVTHVFNYDLPDDCEDYVHR-IGRTGRAGASGHSISFAC----EEYALNLPAIETY  374 (423)
T ss_pred             EEEHHHHHCCCCCCCCCEEEEECCCCCHHHEECC-CCHHHCCCCCEEEEEEEC----HHHHHHHHHHHHH
T ss_conf             9870043277772679889996998974551004-654127899468999873----9999999999999


No 17 
>TIGR00595 priA primosomal protein N'; InterPro: IPR005259    All proteins in this family for which functions are known are components of the primosome which is involved in replication, repair, and recombination.; GO: 0003677 DNA binding, 0006260 DNA replication.
Probab=99.93  E-value=2.6e-23  Score=202.42  Aligned_cols=318  Identities=25%  Similarity=0.377  Sum_probs=257.1

Q ss_pred             EEEECCCCCHHHHHHHHHHHHHHHHCCEEEEEHHHH-HHHHHHHHHHHHCCCCCCEEEEEECC-CCHHHHHHHHHHHCCC
Q ss_conf             886214422369999997334443054588612799-99999986211014578658996246-4225667687762134
Q gi|254780945|r  297 ILQGDVGSGKTLVALIAMAAAVEAGGQAVIMAPIGI-LAQQHYEFIKKYTQNTQIIVEIITGN-MPQAHRRKALERIAHG  374 (700)
Q Consensus       297 LLQGDVGSGKTiVA~~A~l~~~~~G~Q~alMaPTEI-LA~QH~~~~~~~~~~~~i~v~lLtg~-~~~~er~~i~~~i~~G  374 (700)
                      ||.|+.|||||.|.+-++..+...|.|+.+|+| || |+.|--..|+..|..   .++++.++ ++..+|...|.++..|
T Consensus         1 ll~G~tGsGkte~y~~~~~~~l~~g~~~~~l~P-ei~l~~q~~~~~~~~fg~---~~~~~h~~~l~~~~~~~~w~~~~~g   76 (524)
T TIGR00595         1 LLFGVTGSGKTEVYLQAIEKVLALGKSALVLVP-EIALTPQTLQRFKGRFGS---QVAVLHSGKLSDSEKLDAWRKVKLG   76 (524)
T ss_pred             CCCCCCCCCHHHHHHHHHHHHHHCCCEEEEEEC-CHHHHHHHHHHHHHHHCC---CHHHHCCCCCCCHHHHHHHHHHHCC
T ss_conf             954567886168889999999733771789704-211016789999997187---2010100136734568899998518


Q ss_pred             CCEEEEEC-HHHCCCCCCCCCCCEEEECCCCCCCHHHHHH-H----------HHCCCCCCCEEECHHHHHHHHHHHHHHC
Q ss_conf             75486411-1201334554444178852101335688998-7----------4025677610101013227899997520
Q gi|254780945|r  375 QAHIIIGT-HALFQDSIQYYKLILVIVDEQHRFGVQQRLK-L----------TQKATAPHVLLMTATPIPRTLVLTSLGD  442 (700)
Q Consensus       375 ~~~iiIGT-HAL~q~~v~F~~LgLvViDEQHRFGV~QR~~-L----------~~Kg~~ph~L~MtATPIPRTLal~~ygd  442 (700)
                      ++.+|||| .|+|   ..|+||||+|+||+|-+.-+|-.. -          ..+..+.-+++-||||---|..-..-|-
T Consensus        77 ~~~~v~G~rsa~f---~P~~~lglii~deehd~~yk~~~~~p~y~ar~~~~~~~~~~~~p~~lgsatP~le~~~~~~~~~  153 (524)
T TIGR00595        77 EALVVIGTRSALF---LPLKNLGLIIVDEEHDSSYKQEELPPRYHARDVAVYRAKLFNCPVVLGSATPSLESYHNAKRGK  153 (524)
T ss_pred             CCEEEECCCHHHH---CCCCCCCEEEEECCCCCCCCCCCCCCCCCHHHHHHHHHHHCCCCEEECCCCCCHHHHHHHHCCC
T ss_conf             6005640303432---4621145478734645210013688552067889887640488578805672278999987166


Q ss_pred             CC----HHHHCCCCCCCCCCEEEEEECCCH----------HHHHHHHHHHHCCCCEEEEEE-------------------
Q ss_conf             10----111102355766620799970200----------268999976310387389997-------------------
Q gi|254780945|r  443 ID----ISKITEKPAGRKPIKTVIIPINRI----------DEVIERLKVVLSEGKKAYWIC-------------------  489 (700)
Q Consensus       443 ld----vS~i~e~P~gR~~I~T~~~~~~~~----------~~~~~~i~~~l~~g~q~y~Vc-------------------  489 (700)
                      .+    ...+...-.++.+-.-.++..+..          ..++..+++.+++|+|+.+-.                   
T Consensus       154 ~~p~~~~~~l~~r~~~~~~p~~~~~d~~~~~~~~~~~~~~~~l~~~~~~~~~~~~q~~~f~n~rg~~~~~~c~~cg~~~~  233 (524)
T TIGR00595       154 YRPQRHLLVLPRRVGGRKPPEVKLIDLRKEPRQGNRSFLSPELLTALEETLAAGEQAILFLNRRGYSPNLLCRSCGYVLE  233 (524)
T ss_pred             CCCHHHHHHHHHHHCCCCCCEEEEEECCCCCCCCCCCCCCHHHHHHHHHHHHCCCCEEEEEECCCCCCCEEECCCCCCEE
T ss_conf             56203211101320577575156762210002132102258999999988741670689861556653000002675010


Q ss_pred             -CCCCC----------------------------------CCC-CC--CCHHHHHHHHHHHHCCC-CEECCCCCCCHHHH
Q ss_conf             -12012----------------------------------211-12--10146666666866371-03120146998999
Q gi|254780945|r  490 -PQIEE----------------------------------KKE-SN--FRSVVERFNSLHEHFTS-SIAIIHGRMSDIDK  530 (700)
Q Consensus       490 -PlIee----------------------------------se~-~~--~~~~~~~~~~l~~~~~~-~v~~lHGkm~~~ek  530 (700)
                       |.-+-                                  |+. +.  -...+...+.+.+.||. ++..+-.--...++
T Consensus       234 cp~c~~~~~~h~~~~~g~p~l~ch~c~~~~~~p~~cp~c~~~~~~~~~g~G~~~~~~~l~~~~p~~~~~~~d~d~~~~~~  313 (524)
T TIGR00595       234 CPNCDVSLTYHKKEGNGQPKLRCHYCGYQEPVPKTCPACGSEDTLKYKGLGTEKVEEELAKLFPGARIARLDSDTTSRKG  313 (524)
T ss_pred             CCCCCEEEEEEEECCCCCCEEEEECCCCCCCCCCCCCCCCCCCCEEECCCCHHHHHHHHHHHCCCCCEEEEECCCCCCCH
T ss_conf             56653023553213688620122105766777543644466430120354278999999985588736764122123514


Q ss_pred             --HHHHHHHHCCCEEEEEECHHHHCCCCCCCCCEEEEECHHH-----------CCHHHHHHHHHCCCCCCCCEEEEEEEC
Q ss_conf             --9999997559869999800341046888765899858525-----------474688773011667898359999708
Q gi|254780945|r  531 --ESVMDSFKNGTCKLLIATTVIEVGIDVVDASIIIIENAEH-----------FGLAQLHQLRGRVGRGEEISSCILLYH  597 (700)
Q Consensus       531 --~~~m~~F~~g~~~iLvaTtviEVGvdvpna~~mvI~~aer-----------fGLsqLHQLRGRVGRg~~~s~c~l~~~  597 (700)
                        +..+++|.+|++|||+.|.+|--|.|.|+.++..|.++|-           -+.+-|+|.-||-||+..+|..++-+.
T Consensus       314 ~~~~~~~~f~~g~~d~l~Gtq~~~kG~~fp~~~l~g~~~~d~~l~~~d~r~~e~~~~l~~q~~Gr~gr~~~~g~v~iqt~  393 (524)
T TIGR00595       314 AHEALLNQFANGKADILIGTQMIAKGHDFPNVTLVGVLDADSGLHSPDFRAAERGFQLLTQVAGRAGRAEDPGEVIIQTY  393 (524)
T ss_pred             HHHHHHHHHHCCCCEEEECHHHHHCCCCCCCEEEEEEEECCCCCCCCCHHHHHHHHHHHHHHHHHCCCCCCCCEEEEEEE
T ss_conf             68999999750784067500344315774420367787312002554213467788888876410023468874799730


Q ss_pred             CCCCHHHHHHHHHHHHHCHHHHHHHHH
Q ss_conf             889987999999998414258999999
Q gi|254780945|r  598 PPLSKNSYTRLSVLKNTEDGFLIAEED  624 (700)
Q Consensus       598 ~~~~~~~~~Rl~~l~~~~dGf~iAe~D  624 (700)
                      .+ +..+.  .....+..++|+--|.+
T Consensus       394 ~P-~~~~~--~~~~~~~~~~f~~~~~~  417 (524)
T TIGR00595       394 NP-GHPAI--QAALTGDYEAFYEQELA  417 (524)
T ss_pred             CC-CHHHH--HHHHHCCCHHHHHHHHH
T ss_conf             77-51688--98760681678999887


No 18 
>PRK00254 ski2-like helicase; Provisional
Probab=99.93  E-value=6e-23  Score=199.54  Aligned_cols=322  Identities=21%  Similarity=0.315  Sum_probs=231.2

Q ss_pred             HHHHHHHHHCCC-CCCHHHHHHHHHHHHHHCCCCCCEEEEEECCCCCHHHHHHHHHHH-HHHHHCCEEEEEHHHHHHHHH
Q ss_conf             789999863024-679889999999998410013430788621442236999999733-444305458861279999999
Q gi|254780945|r  260 KIAQKILRNIPF-SPTKSQESAIKDILQDMSQKNRMLRILQGDVGSGKTLVALIAMAA-AVEAGGQAVIMAPIGILAQQH  337 (700)
Q Consensus       260 ~~~~~f~~~LPF-~LT~~Q~~ai~eI~~Dl~~~~pM~RLLQGDVGSGKTiVA~~A~l~-~~~~G~Q~alMaPTEILA~QH  337 (700)
                      +.+.++++.-.. +|-+-|..|++.   .+-.++  |=++.-=.|||||+||-+||+. +...|..+.+++|+--||+|-
T Consensus        10 ~~~~~~~~~~gI~~l~p~Q~e~l~~---g~~~g~--NllvsaPT~sGKTlvAElail~~~l~~~~k~iyi~P~kALa~EK   84 (717)
T PRK00254         10 ERIKEILKERGIEELYPPQAEALTS---GVLEGK--NLLIAIPTASGKTLIAEIAMVNKLLREGGKAVYLVPLKALAEEK   84 (717)
T ss_pred             HHHHHHHHHCCCCCCCHHHHHHHHH---HHCCCC--CEEEECCCCCCHHHHHHHHHHHHHHHCCCEEEEECCHHHHHHHH
T ss_conf             8999999976987268999999874---233698--18998998874899999999999985299299992679999999


Q ss_pred             HHHHHHHCCCCCCEEEEEECCCCHHHHHHHHHHHCCCCCEEEEEC----HHHCCCCC-CCCCCCEEEECCCCCCCHHHHH
Q ss_conf             986211014578658996246422566768776213475486411----12013345-5444417885210133568899
Q gi|254780945|r  338 YEFIKKYTQNTQIIVEIITGNMPQAHRRKALERIAHGQAHIIIGT----HALFQDSI-QYYKLILVIVDEQHRFGVQQRL  412 (700)
Q Consensus       338 ~~~~~~~~~~~~i~v~lLtg~~~~~er~~i~~~i~~G~~~iiIGT----HAL~q~~v-~F~~LgLvViDEQHRFGV~QR~  412 (700)
                      |..|++ |..+|++|..+||......+       .-++.+|+|-|    ++|+.... -+.++|+|||||=|=.|=..|-
T Consensus        85 ~~~f~~-~~~~g~~V~~~tGd~~~~~~-------~l~~~dIiV~T~Ek~dsl~r~~~~~l~~i~lvViDEiH~igD~~RG  156 (717)
T PRK00254         85 FREFKD-WEVLGLRVAMATGDYDSKDE-------WLGKYDIIIATAEKFDSLLRHGSSWIKDVKLLVADEIHLIGSRDRG  156 (717)
T ss_pred             HHHHHH-HHHCCCEEEEEECCCCCCCC-------CCCCCCEEEECHHHHHHHHHCCHHHHHCCCEEEEECEEECCCCCCH
T ss_conf             999987-77449889897489888701-------0468999998889999999716256532698999760788898740


Q ss_pred             HHHH----C-CCCCCCEEECHH-HHHHHHHHHHHHCCCHHHHCCCCCCCCCCEEEEEEC----------CCHHHHHHHHH
Q ss_conf             8740----2-567761010101-322789999752010111102355766620799970----------20026899997
Q gi|254780945|r  413 KLTQ----K-ATAPHVLLMTAT-PIPRTLVLTSLGDIDISKITEKPAGRKPIKTVIIPI----------NRIDEVIERLK  476 (700)
Q Consensus       413 ~L~~----K-g~~ph~L~MtAT-PIPRTLal~~ygdldvS~i~e~P~gR~~I~T~~~~~----------~~~~~~~~~i~  476 (700)
                      ...+    | -..+.++.|||| |=|.-+|--+-+++  -.=+..|   .|....+...          ++....-+.+.
T Consensus       157 ~~lE~~l~~l~~~~qiIgLSATi~N~~~la~WL~a~~--~~~~~RP---VpL~~~v~~~~~~~~~~~~~~~~~~~~~l~~  231 (717)
T PRK00254        157 ATLEFILTHMLGRAQIIGLSATIGNPEELAEWLNAEL--IVSDWRP---VKLRKGVFYQGFVFWEDGKIDRYNSWEELVY  231 (717)
T ss_pred             HHHHHHHHHHHCCCEEEEEEEECCCHHHHHHHHCCCC--CCCCCCC---CCEEEEEEECCEEEECCCCCHHHHHHHHHHH
T ss_conf             9999999951003669999633499899999828852--1568857---7527644206601104562054430789999


Q ss_pred             HHHCCCCEEEEEECCCCCCCCC--CCC-------------HHHHH---------HHHHHHHCCCCEECCCCCCCHHHHHH
Q ss_conf             6310387389997120122111--210-------------14666---------66668663710312014699899999
Q gi|254780945|r  477 VVLSEGKKAYWICPQIEEKKES--NFR-------------SVVER---------FNSLHEHFTSSIAIIHGRMSDIDKES  532 (700)
Q Consensus       477 ~~l~~g~q~y~VcPlIeese~~--~~~-------------~~~~~---------~~~l~~~~~~~v~~lHGkm~~~ek~~  532 (700)
                      +.+.+|+||-|-||.=...|+.  ++.             ...+.         .+.|.+.+...|+.-|+-|..++++.
T Consensus       232 ~~~~~~~~~LVF~~tR~~~e~~A~~la~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~L~~~l~~GVafHHAGL~~~~R~l  311 (717)
T PRK00254        232 DAVKRGKGALIFVNMRRKAEKTALELAKKIKNLLTKPELRELKELADSLEENPTNEKLAKALRGGVAFHHAGLGRDERVL  311 (717)
T ss_pred             HHHHCCCCCEEEEECHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHCCCCHHHHHHHHHCHHHHCCCCCHHHHHH
T ss_conf             99974998189995579999999999998876307688999999999987376518999999708312158999889999


Q ss_pred             HHHHHHCCCEEEEEECHHHHCCCCCCCCCEEEEE-------CHHHCCHHHHHHHHHCCCCC--CCCEEEEEEECCC
Q ss_conf             9999755986999980034104688876589985-------85254746887730116678--9835999970888
Q gi|254780945|r  533 VMDSFKNGTCKLLIATTVIEVGIDVVDASIIIIE-------NAEHFGLAQLHQLRGRVGRG--EEISSCILLYHPP  599 (700)
Q Consensus       533 ~m~~F~~g~~~iLvaTtviEVGvdvpna~~mvI~-------~aerfGLsqLHQLRGRVGRg--~~~s~c~l~~~~~  599 (700)
                      |=..|++|.++||+||+-.-.|||.|.-+|+|-.       +-+....++.+|.-||-||-  +..|+|++++..+
T Consensus       312 VE~~Fr~g~Ikvl~aTsTLA~GVNLPAr~VIi~~~~~~~~~g~~~i~~~e~~QM~GRAGR~G~D~~G~~iii~~~~  387 (717)
T PRK00254        312 VEDNFRKGLIKVVVATPTLSAGINTPAFRVIIRDTWRYSEFGMERIPVLEIQQMMGRAGRPKYDEVGEAIIVSTTE  387 (717)
T ss_pred             HHHHHHCCCCEEEEECCHHHCCCCCCCEEEEEECCEEECCCCCEECCHHHHHHHHHHCCCCCCCCCCEEEEEECCC
T ss_conf             9999987995899816446504577605999926567079972378753688862506999878885089995485


No 19 
>PRK13766 Hef nuclease; Provisional
Probab=99.93  E-value=2.2e-23  Score=203.02  Aligned_cols=312  Identities=24%  Similarity=0.359  Sum_probs=195.4

Q ss_pred             CCCHHHHHHHHHHHHHHCCCCCCEEEEEECCCCCHHHHHHHHHHHHHH-HHCCEEEEEHHHHHHHHHHHHHHHHCCCCCC
Q ss_conf             679889999999998410013430788621442236999999733444-3054588612799999999862110145786
Q gi|254780945|r  272 SPTKSQESAIKDILQDMSQKNRMLRILQGDVGSGKTLVALIAMAAAVE-AGGQAVIMAPIGILAQQHYEFIKKYTQNTQI  350 (700)
Q Consensus       272 ~LT~~Q~~ai~eI~~Dl~~~~pM~RLLQGDVGSGKTiVA~~A~l~~~~-~G~Q~alMaPTEILA~QH~~~~~~~~~~~~i  350 (700)
                      +.=.-|...++.-..   .    |-|+.=+.|||||.||++.|..... .+..+.|||||--|+.||++.|++++.--+.
T Consensus        15 e~R~YQ~el~~~Al~---~----NtiVvLPTG~GKT~IA~lvi~~~l~~~~gKilFLaPT~pLV~Qq~~~~~~~l~i~~~   87 (764)
T PRK13766         15 EARLYQQLLAAKALK---G----NTLVVLPTGLGKTAIALLVIAERLQKYGGKVLILAPTKPLVEQHAEFFRKFLNIDPE   87 (764)
T ss_pred             CCCHHHHHHHHHHHH---C----CEEEEECCCCCHHHHHHHHHHHHHHHCCCEEEEECCCHHHHHHHHHHHHHHCCCCCC
T ss_conf             653879999999985---8----989995998668999999999999748988999858888999999999997099955


Q ss_pred             EEEEEECCCCHHHHHHHHHHHCCCCCEEEEECH-----HHCCCCCCCCCCCEEEECCCCCC-C------HHHHHHHHHCC
Q ss_conf             589962464225667687762134754864111-----20133455444417885210133-5------68899874025
Q gi|254780945|r  351 IVEIITGNMPQAHRRKALERIAHGQAHIIIGTH-----ALFQDSIQYYKLILVIVDEQHRF-G------VQQRLKLTQKA  418 (700)
Q Consensus       351 ~v~lLtg~~~~~er~~i~~~i~~G~~~iiIGTH-----AL~q~~v~F~~LgLvViDEQHRF-G------V~QR~~L~~Kg  418 (700)
                      ++..+||.++..+|.++|+     +.+|+|.|-     +|....+..+++.|+|+||=||- |      +.++  +....
T Consensus        88 ~i~~ltG~~~~~~r~~~w~-----~~~Viv~TPQvl~ndL~~g~i~l~dv~lLVfDEaHha~Gnh~Y~~I~~~--y~~~~  160 (764)
T PRK13766         88 KIVVLTGEISPEKRAALWE-----KAKVIVATPQVIENDLLAGRISLEDVSLLIFDEAHRAVGNYAYVFIAER--YHEDA  160 (764)
T ss_pred             EEEEEECCCCHHHHHHHHC-----CCCEEEECCHHHHHHHHHCCCCHHHCCEEEEECCCCCCCCCCHHHHHHH--HHHCC
T ss_conf             2899988878276899860-----7999999908999999829867888228999746666677628999999--98537


Q ss_pred             CCCCCEEECHHHHHHHHH--HHHHHCCCHHHHCCCCC---------CCCCCEEEEEEC-CCHHHHHHHHH----HHHCCC
Q ss_conf             677610101013227899--99752010111102355---------766620799970-20026899997----631038
Q gi|254780945|r  419 TAPHVLLMTATPIPRTLV--LTSLGDIDISKITEKPA---------GRKPIKTVIIPI-NRIDEVIERLK----VVLSEG  482 (700)
Q Consensus       419 ~~ph~L~MtATPIPRTLa--l~~ygdldvS~i~e~P~---------gR~~I~T~~~~~-~~~~~~~~~i~----~~l~~g  482 (700)
                      .+|++|-|||||-= ...  ..+-..|.++.+.-...         .++.+....+.. +...++.+.+.    ..+..-
T Consensus       161 ~~PrILGLTASPGs-~~e~I~ev~~nL~i~~ie~rte~d~dv~~yv~~~~ie~i~V~l~~~~~~i~~~l~~~l~~~l~~L  239 (764)
T PRK13766        161 KNPLVLGLTASPGS-DEEKIKEVCENLGIEHVEVKTEDDPDVRPYVHKVKVEWIRVELPEELKEIRDLLNEALKDRLKKL  239 (764)
T ss_pred             CCCEEEEECCCCCC-CHHHHHHHHHHCCCCEEEEECCCCHHHHHHCCCCCEEEEEECCCHHHHHHHHHHHHHHHHHHHHH
T ss_conf             78558850368876-44899999986598728961444434454335673279980797899999999999999999999


Q ss_pred             CEEEEEECC---C-----------------------------------------------------------CCCCCC--
Q ss_conf             738999712---0-----------------------------------------------------------122111--
Q gi|254780945|r  483 KKAYWICPQ---I-----------------------------------------------------------EEKKES--  498 (700)
Q Consensus       483 ~q~y~VcPl---I-----------------------------------------------------------eese~~--  498 (700)
                      ....+.++.   +                                                           ++....  
T Consensus       240 ~~~~~~~~~~~~~sk~~l~~~~~~~~~~i~~~~~~~~~~~~~~a~~~kl~~a~ell~tqg~~~~~~yl~~l~~~~~~~~~  319 (764)
T PRK13766        240 KELGVIVSISPDVSKKELLGLQKRIQQEIARGDPEGYEAISIHAEAMKLRHAVELLETQGVEALRRYLERLREEARSSGS  319 (764)
T ss_pred             HHCCCEECCCCCCCHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCC
T ss_conf             96697004555468999999999999988646879999999999999999999999985189999999999973013332


Q ss_pred             -----------------------------------------------------CCCHHHHHHHHHHHHCCCCEECCCC--
Q ss_conf             -----------------------------------------------------2101466666668663710312014--
Q gi|254780945|r  499 -----------------------------------------------------NFRSVVERFNSLHEHFTSSIAIIHG--  523 (700)
Q Consensus       499 -----------------------------------------------------~~~~~~~~~~~l~~~~~~~v~~lHG--  523 (700)
                                                                           .-.+|...++.|.+. +-+...+.|  
T Consensus       320 k~~k~l~~d~~~~~~~~~~~~~~~~hPKl~kL~eiL~~~~~~~~~sRvIIFv~~R~Ta~~L~~~L~~~-~ik~~~fVGq~  398 (764)
T PRK13766        320 KASKRLVEDPRFKKAVRLLKELDIEHPKLEKLLEIVKEQLGKKPDSRIIVFTQYRDTAEKIVDLLNKN-GIKAIRFVGQA  398 (764)
T ss_pred             HHHHHHHHCHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHCCCCCCEEEEEECCHHHHHHHHHHHHHC-CCCCEEEEECC
T ss_conf             67899875877899999876446789379999999999972699980899927679999999998658-99722898368


Q ss_pred             ------CCCHHHHHHHHHHHHCCCEEEEEECHHHHCCCCCCCCCEEEEECHHHCCHHHHHHHHHCCCCCCCCEEE-EEEE
Q ss_conf             ------699899999999975598699998003410468887658998585254746887730116678983599-9970
Q gi|254780945|r  524 ------RMSDIDKESVMDSFKNGTCKLLIATTVIEVGIDVVDASIIIIENAEHFGLAQLHQLRGRVGRGEEISSC-ILLY  596 (700)
Q Consensus       524 ------km~~~ek~~~m~~F~~g~~~iLvaTtviEVGvdvpna~~mvI~~aerfGLsqLHQLRGRVGRg~~~s~c-~l~~  596 (700)
                            -|+..+..+++++|++|++++||||+|-|=|+|||..++.|-+++.-=-+-+ =|=|||-||... |.| +|++
T Consensus       399 s~~~~kGmsqkeQ~evL~~FR~Ge~NvLVATSV~EEGLDIP~cdLVI~Yd~v~S~IR~-IQR~GRTGR~r~-G~v~vLi~  476 (764)
T PRK13766        399 SRDGDKGMSQKEQIETLDRFRAGEYNVLVATSVAEEGLDIPSVDLVIFYEPVPSEIRS-IQRKGRTGRQRG-GRVVVLIA  476 (764)
T ss_pred             CCCCCCCCCHHHHHHHHHHHHCCCCCEEEECCHHHCCCCCCCCCEEEEECCCCCHHHH-HHHCCCCCCCCC-CEEEEEEE
T ss_conf             9878889898999999999857998889876766448888778889993799619999-997466567789-74999995


Q ss_pred             CCCCC
Q ss_conf             88899
Q gi|254780945|r  597 HPPLS  601 (700)
Q Consensus       597 ~~~~~  601 (700)
                      .....
T Consensus       477 ~gt~d  481 (764)
T PRK13766        477 KGTRD  481 (764)
T ss_pred             CCCHH
T ss_conf             68626


No 20 
>PRK04537 ATP-dependent RNA helicase RhlB; Provisional
Probab=99.93  E-value=1e-21  Score=189.96  Aligned_cols=317  Identities=21%  Similarity=0.260  Sum_probs=223.4

Q ss_pred             CCCHHHHHHHHHCCC-CCCHHHHHHHHHHHHHHCCCCCCEEEEEECCCCCHHHHHHHHHHHHHH----------HHCCEE
Q ss_conf             775789999863024-679889999999998410013430788621442236999999733444----------305458
Q gi|254780945|r  257 VEGKIAQKILRNIPF-SPTKSQESAIKDILQDMSQKNRMLRILQGDVGSGKTLVALIAMAAAVE----------AGGQAV  325 (700)
Q Consensus       257 ~~~~~~~~f~~~LPF-~LT~~Q~~ai~eI~~Dl~~~~pM~RLLQGDVGSGKTiVA~~A~l~~~~----------~G~Q~a  325 (700)
                      .+..+++. ++.+.| .+|.=|++||--|.+.    +  +-+.|--.|||||+-+++.++..+.          .+-|+.
T Consensus        16 L~~~Ll~a-L~~~Gf~~PTpIQ~~aIP~iL~G----k--Dvi~~A~TGSGKTLAYlLPiL~~Ll~~~~l~~~~~~~p~aL   88 (574)
T PRK04537         16 LHPALVAG-LESAGFTRCTPIQALTLPVALPG----G--DVAGQAQTGTGKTLAFLVAVMNRLLSRPALADRKPEDPRAL   88 (574)
T ss_pred             CCHHHHHH-HHHCCCCCCCHHHHHHHHHHHCC----C--CEEEECCCCCHHHHHHHHHHHHHHHHCCCCCCCCCCCCEEE
T ss_conf             89999999-99779998999999999999579----9--88998489888999999999999983744345778996199


Q ss_pred             EEEHHHHHHHHHHHHHHHHCCCCCCEEEEEECCCCHHHHHHHHHHHCCCCCEEEEECH-HHC----CCC-CCCCCCCEEE
Q ss_conf             8612799999999862110145786589962464225667687762134754864111-201----334-5544441788
Q gi|254780945|r  326 IMAPIGILAQQHYEFIKKYTQNTQIIVEIITGNMPQAHRRKALERIAHGQAHIIIGTH-ALF----QDS-IQYYKLILVI  399 (700)
Q Consensus       326 lMaPTEILA~QH~~~~~~~~~~~~i~v~lLtg~~~~~er~~i~~~i~~G~~~iiIGTH-AL~----q~~-v~F~~LgLvV  399 (700)
                      +++||-=||.|-++.+.++...+++++.++.|+.+..+..+.   +.. .++|||||= .|+    +.+ +.++++-++|
T Consensus        89 ILvPTRELA~QI~~~~~~l~~~~~lr~~~l~GG~~~~~q~~~---L~~-g~dIVVaTPGRLld~L~~~~~~~L~~vk~LV  164 (574)
T PRK04537         89 ILAPTRELAIQIHKDAVKFGADLGLRFALVYGGVDYDKQREL---LQQ-GVDVIIATPGRLIDYVKQHKVVSLHACEICV  164 (574)
T ss_pred             EECCCHHHHHHHHHHHHHHHCCCCCEEEEEECCCCHHHHHHH---HCC-CCCEEEECHHHHHHHHHHCCCCCCCCEEEEE
T ss_conf             977989999999999999864589779999799668899998---735-9998998989999999817986533315899


Q ss_pred             ECCCCC-----CCHHHHHHHHHCC--CCCCCEEECHHHHHHHHHHH--HHHCCCHHHHC--CCCCCCCCCEEEEEE--CC
Q ss_conf             521013-----3568899874025--67761010101322789999--75201011110--235576662079997--02
Q gi|254780945|r  400 VDEQHR-----FGVQQRLKLTQKA--TAPHVLLMTATPIPRTLVLT--SLGDIDISKIT--EKPAGRKPIKTVIIP--IN  466 (700)
Q Consensus       400 iDEQHR-----FGV~QR~~L~~Kg--~~ph~L~MtATPIPRTLal~--~ygdldvS~i~--e~P~gR~~I~T~~~~--~~  466 (700)
                      +||=.+     |--.-+.-|..-.  .....++.|||==++-..++  ...+-..-.+.  +...  ..|.-.++-  .+
T Consensus       165 LDEAD~LLd~gF~~di~~IL~~lP~~~~rQ~iLfSATl~~~V~~la~~~l~~P~~i~v~~~~~~~--~~I~Q~~~~~~~~  242 (574)
T PRK04537        165 LDEADRMFDLGFIKDIRFLLRRMPERGTRQTLLFSATLSHRVLELAYEHMNEPEKLVVETETITA--ARVRQRIYFPSDE  242 (574)
T ss_pred             ECCCHHHHCCCCHHHHHHHHHHCCCCCCCEEEEEEECCCHHHHHHHHHHCCCCEEEEECCCCCCC--CCEEEEEEECCHH
T ss_conf             62732654287799999999966655685589998327779999999977998699965665457--7603899977778


Q ss_pred             -CHHHHHHHHHHHHCCCCEEEEEECCCCCCCCCCCCHHHHHHHHHHHHCCCCEECCCCCCCHHHHHHHHHHHHCCCEEEE
Q ss_conf             -0026899997631038738999712012211121014666666686637103120146998999999999755986999
Q gi|254780945|r  467 -RIDEVIERLKVVLSEGKKAYWICPQIEEKKESNFRSVVERFNSLHEHFTSSIAIIHGRMSDIDKESVMDSFKNGTCKLL  545 (700)
Q Consensus       467 -~~~~~~~~i~~~l~~g~q~y~VcPlIeese~~~~~~~~~~~~~l~~~~~~~v~~lHGkm~~~ek~~~m~~F~~g~~~iL  545 (700)
                       +...++..+.+  ..+.|+.|-|...        ..++..++.|++. +.++..+||.|+..+++.+|++|++|+++||
T Consensus       243 ~K~~~L~~LL~~--~~~~k~IIF~nT~--------~~ve~l~~~L~~~-g~~v~~LHG~lsQ~eR~~~L~~Fk~G~~~VL  311 (574)
T PRK04537        243 EKQTLLLGLLSR--SEGARTMVFVNTK--------AFVERVARTLERH-GYRVGVLSGDVPQKKRESLLNRFQKGQLEIL  311 (574)
T ss_pred             HHHHHHHHHHHH--CCCCCCEEECCHH--------HHHHHHHHHHHHC-CCCEEEEECCCCHHHHHHHHHHHHCCCCCEE
T ss_conf             999999999972--6776511533418--------9999999999977-9968997099999999999999976999799


Q ss_pred             EECHHHHCCCCCCCCCEEEEECHHHCCHHHHHHHHHCCCCCCCCEEEEEEECC
Q ss_conf             98003410468887658998585254746887730116678983599997088
Q gi|254780945|r  546 IATTVIEVGIDVVDASIIIIENAEHFGLAQLHQLRGRVGRGEEISSCILLYHP  598 (700)
Q Consensus       546 vaTtviEVGvdvpna~~mvI~~aerfGLsqLHQLRGRVGRg~~~s~c~l~~~~  598 (700)
                      |||-|.-=|+|+|+.+..|=+|.=.---+=+|- =||.||.+.+|.|+-+..+
T Consensus       312 VaTDVAARGIDIp~V~~VINYDlP~~~e~YVHR-IGRTGRaGr~G~AITfv~~  363 (574)
T PRK04537        312 VATDVAARGLHIDGVKYVYNYDLPFDAEDYVHR-IGRTARLGEEGDAISFACE  363 (574)
T ss_pred             EECCCCCCCCCCCCCCEEEEECCCCCHHHHHCC-CCHHHCCCCCEEEEEEECH
T ss_conf             773500233571469979995796982141124-5350378993359998777


No 21 
>PRK01297 ATP-dependent RNA helicase RhlB; Provisional
Probab=99.93  E-value=4e-22  Score=193.12  Aligned_cols=318  Identities=19%  Similarity=0.207  Sum_probs=224.0

Q ss_pred             CCHHHHHHHHHCCC-CCCHHHHHHHHHHHHHHCCCCCCEEEEEECCCCCHHHHHHHHHHHHHHH----------HCCEEE
Q ss_conf             75789999863024-6798899999999984100134307886214422369999997334443----------054588
Q gi|254780945|r  258 EGKIAQKILRNIPF-SPTKSQESAIKDILQDMSQKNRMLRILQGDVGSGKTLVALIAMAAAVEA----------GGQAVI  326 (700)
Q Consensus       258 ~~~~~~~f~~~LPF-~LT~~Q~~ai~eI~~Dl~~~~pM~RLLQGDVGSGKTiVA~~A~l~~~~~----------G~Q~al  326 (700)
                      ...+++ -++.+.| .+|.=|.+||-.|.+-    +  +-+++--.|||||+.+++.++.-+.+          +-|+.+
T Consensus        92 ~~~ll~-aL~~~Gf~~PTpIQ~~aIP~iL~G----k--Dvi~~A~TGSGKTlAyLLPil~~ll~~~~~~~~~~~~p~aLI  164 (472)
T PRK01297         92 APELMH-AIHDLGFPYCTPIQAQVLGYTLAG----H--DAIGRAQTGTGKTAAFLISIINQLLQTPPPKERYMGEPRALI  164 (472)
T ss_pred             CHHHHH-HHHHCCCCCCCHHHHHHHHHHHCC----C--CEEEECCCCCHHHHHHHHHHHHHHHHCCCCHHCCCCCCEEEE
T ss_conf             999999-999779999999999999999769----9--889989998679999999999999717751011368952999


Q ss_pred             EEHHHHHHHHHHHHHHHHCCCCCCEEEEEECCCCHHHHHHHHHHHCCCCCEEEEECHH-----HCCCCCCCCCCCEEEEC
Q ss_conf             6127999999998621101457865899624642256676877621347548641112-----01334554444178852
Q gi|254780945|r  327 MAPIGILAQQHYEFIKKYTQNTQIIVEIITGNMPQAHRRKALERIAHGQAHIIIGTHA-----LFQDSIQYYKLILVIVD  401 (700)
Q Consensus       327 MaPTEILA~QH~~~~~~~~~~~~i~v~lLtg~~~~~er~~i~~~i~~G~~~iiIGTHA-----L~q~~v~F~~LgLvViD  401 (700)
                      +|||-=||.|-++.++.+....++++.+++|++...   +....+.+..++|||||=.     +-+..+.++++-++|+|
T Consensus       165 L~PTRELa~QI~~~~~~L~~~~~l~v~~~~GG~~~~---~q~~~l~~~~~dIvVaTPGRL~~l~~~~~~~l~~v~~lVlD  241 (472)
T PRK01297        165 IAPTRELVVQIAKDAAALTKYTGLNVMTFVGGMDFD---KQLKQLEARFCDILVATPGRLLDFNQRGEVHLDMVEVMVLD  241 (472)
T ss_pred             ECCCHHHHHHHHHHHHHHHCCCCCEEEEEECCCCHH---HHHHHHHCCCCCEEEECHHHHHHHHCCCCEECCCCEEEEEE
T ss_conf             879999999999999997462797699997898879---99999855899889979799998743482542552299998


Q ss_pred             CCCCC-----CHHHHHHHHH--CCCCCCCEEECHHHHHHHHHHH--HHHCCCHHHHCCCCCCC--CCCEEEEEECCC---
Q ss_conf             10133-----5688998740--2567761010101322789999--75201011110235576--662079997020---
Q gi|254780945|r  402 EQHRF-----GVQQRLKLTQ--KATAPHVLLMTATPIPRTLVLT--SLGDIDISKITEKPAGR--KPIKTVIIPINR---  467 (700)
Q Consensus       402 EQHRF-----GV~QR~~L~~--Kg~~ph~L~MtATPIPRTLal~--~ygdldvS~i~e~P~gR--~~I~T~~~~~~~---  467 (700)
                      |=+|.     .-.-+.-+..  +...--.++.|||--+-...+.  +..+  -..+.--+.+.  ..|.-+++....   
T Consensus       242 EAD~LLd~gf~~~v~~Il~~~p~~~~rQ~~lfSATl~~~v~~l~~~~~~~--p~~v~i~~~~~~~~~v~q~~~~~~~~dk  319 (472)
T PRK01297        242 EADRMLDMGFIPQVRQIIRQTPRKEERQTLLFSATFTDDVMNLAKQWTTD--PAIVEIEPENVASDTVEQHVYAVAGSDK  319 (472)
T ss_pred             CHHHHHCCCCHHHHHHHHHHCCCCCCCEEEEEECCCCHHHHHHHHHHCCC--CEEEEECCCCCCCCCEEEEEEECCHHHH
T ss_conf             73121025759999999996898557169998525778999999997799--8899965776677760289998188899


Q ss_pred             HHHHHHHHHHHHCCCCEEEEEECCCCCCCCCCCCHHHHHHHHHHHHCCCCEECCCCCCCHHHHHHHHHHHHCCCEEEEEE
Q ss_conf             02689999763103873899971201221112101466666668663710312014699899999999975598699998
Q gi|254780945|r  468 IDEVIERLKVVLSEGKKAYWICPQIEEKKESNFRSVVERFNSLHEHFTSSIAIIHGRMSDIDKESVMDSFKNGTCKLLIA  547 (700)
Q Consensus       468 ~~~~~~~i~~~l~~g~q~y~VcPlIeese~~~~~~~~~~~~~l~~~~~~~v~~lHGkm~~~ek~~~m~~F~~g~~~iLva  547 (700)
                      ..-+++.++..  .-.|+.|-|...+        .++..++.|.+ .+-++..+||.|+..++..+|++|++|++.||||
T Consensus       320 ~~~L~~ll~~~--~~~k~IIF~nt~~--------~~~~l~~~L~~-~g~~~~~lhg~l~q~~R~~~l~~F~~g~~~iLVa  388 (472)
T PRK01297        320 YKLLYNLVTQN--PWERVMVFANRKD--------EVRRIEERLVK-DGINAAQLSGDVPQHKRIKTLEGFREGKIRVLVA  388 (472)
T ss_pred             HHHHHHHHHHC--CCCCEEEECCCHH--------HHHHHHHHHHH-CCCCEEEEECCCCHHHHHHHHHHHHCCCCCEEEE
T ss_conf             99999999847--9873689617499--------99999987654-4961686437789999999999997699969988


Q ss_pred             CHHHHCCCCCCCCCEEEEECHHHCCHHHHHHHHHCCCCCCCCEEEEEEECCC
Q ss_conf             0034104688876589985852547468877301166789835999970888
Q gi|254780945|r  548 TTVIEVGIDVVDASIIIIENAEHFGLAQLHQLRGRVGRGEEISSCILLYHPP  599 (700)
Q Consensus       548 TtviEVGvdvpna~~mvI~~aerfGLsqLHQLRGRVGRg~~~s~c~l~~~~~  599 (700)
                      |-|..=|+|+|+.+..|-+|.=+---+=+|- =||.||.+..|.|+.++.+.
T Consensus       389 TDvaaRGLDi~~V~~VInyD~P~~~~~YIHR-iGRTGRaG~~G~aisfv~~~  439 (472)
T PRK01297        389 TDVAGRGIHIDGISHVINFTLPEDPDDYVHR-IGRTGRAGASGVSISFAGED  439 (472)
T ss_pred             CCHHHCCCCCCCCCEEEEECCCCCHHHHHHC-CCHHHCCCCCEEEEEEECHH
T ss_conf             6613366775788889996898976760102-65312689963799986388


No 22 
>COG0513 SrmB Superfamily II DNA and RNA helicases [DNA replication, recombination, and repair / Transcription / Translation, ribosomal structure and biogenesis]
Probab=99.91  E-value=9e-21  Score=182.48  Aligned_cols=320  Identities=24%  Similarity=0.314  Sum_probs=227.4

Q ss_pred             CCCHHHHHHHHHCCC-CCCHHHHHHHHHHHHHHCCCCCCEEEEEECCCCCHHHHHHHHHHHHHHH----HCC-EEEEEHH
Q ss_conf             775789999863024-6798899999999984100134307886214422369999997334443----054-5886127
Q gi|254780945|r  257 VEGKIAQKILRNIPF-SPTKSQESAIKDILQDMSQKNRMLRILQGDVGSGKTLVALIAMAAAVEA----GGQ-AVIMAPI  330 (700)
Q Consensus       257 ~~~~~~~~f~~~LPF-~LT~~Q~~ai~eI~~Dl~~~~pM~RLLQGDVGSGKTiVA~~A~l~~~~~----G~Q-~alMaPT  330 (700)
                      .+..+.+.+.+ +.| ++|.=|.++|-.+..-      -.-+.|.-.|||||.-..+.++..+..    .++ +.+++||
T Consensus        36 l~~~ll~~l~~-~gf~~pt~IQ~~~iP~~l~g------~Dvi~~A~TGsGKT~Af~lP~l~~i~~~~~~~~~~aLil~PT  108 (513)
T COG0513          36 LSPELLQALKD-LGFEEPTPIQLAAIPLILAG------RDVLGQAQTGTGKTAAFLLPLLQKILKSVERKYVSALILAPT  108 (513)
T ss_pred             CCHHHHHHHHH-CCCCCCCHHHHHHCHHHHCC------CCEEEECCCCCHHHHHHHHHHHHHHHHCCCCCCCCEEEECCC
T ss_conf             99999999996-59899898999658776369------997998689871789999999999740045577756997799


Q ss_pred             HHHHHHHHHHHHHHCCCC-CCEEEEEECCCCHHHHHHHHHHHCCCCCEEEEECHH----HCC-CCCCCCCCCEEEECCCC
Q ss_conf             999999998621101457-865899624642256676877621347548641112----013-34554444178852101
Q gi|254780945|r  331 GILAQQHYEFIKKYTQNT-QIIVEIITGNMPQAHRRKALERIAHGQAHIIIGTHA----LFQ-DSIQYYKLILVIVDEQH  404 (700)
Q Consensus       331 EILA~QH~~~~~~~~~~~-~i~v~lLtg~~~~~er~~i~~~i~~G~~~iiIGTHA----L~q-~~v~F~~LgLvViDEQH  404 (700)
                      -=||.|-++.+.++-... ++++++++|+++.....   ..++.| ++|||||..    +++ ..+.++++..+|+||--
T Consensus       109 RELA~Qi~~~~~~~~~~~~~~~~~~i~GG~~~~~q~---~~l~~g-~~ivVaTPGRllD~i~~~~l~l~~v~~lVlDEAD  184 (513)
T COG0513         109 RELAVQIAEELRKLGKNLGGLRVAVVYGGVSIRKQI---EALKRG-VDIVVATPGRLLDLIKRGKLDLSGVETLVLDEAD  184 (513)
T ss_pred             HHHHHHHHHHHHHHHHHCCCCEEEEEECCCCHHHHH---HHHHCC-CCEEEECCCHHHHHHHCCCCCCCCEEEEEECCHH
T ss_conf             999999999999998624584299998998989999---987249-9899979608999986488554650189967617


Q ss_pred             CC---CHHHH-HHHHHC-CCCCCCEEECHHHHHHHHHHHHHHCC-CHHHHCCCCCC----CCCCEEEEEECCCHH---HH
Q ss_conf             33---56889-987402-56776101010132278999975201-01111023557----666207999702002---68
Q gi|254780945|r  405 RF---GVQQR-LKLTQK-ATAPHVLLMTATPIPRTLVLTSLGDI-DISKITEKPAG----RKPIKTVIIPINRID---EV  471 (700)
Q Consensus       405 RF---GV~QR-~~L~~K-g~~ph~L~MtATPIPRTLal~~ygdl-dvS~i~e~P~g----R~~I~T~~~~~~~~~---~~  471 (700)
                      |.   |...= ..+... .....+|..|||-=+....++ ..-| +-..|.--|..    -..|.-.++.....+   .+
T Consensus       185 rmld~gf~~~i~~I~~~~p~~~qtllfSAT~~~~i~~l~-~~~l~~p~~i~v~~~~~~~~~~~i~q~~~~v~~~~~k~~~  263 (513)
T COG0513         185 RMLDMGFIDDIEKILKALPPDRQTLLFSATMPDDIRELA-RRYLNDPVEIEVSVEKLERTLKKIKQFYLEVESEEEKLEL  263 (513)
T ss_pred             HHCCCCCHHHHHHHHHHCCCCCEEEEEEECCCHHHHHHH-HHHCCCCCEEEECCCCCCCCCCCCEEEEEEECCHHHHHHH
T ss_conf             663887689999999738977489999824898999999-9973688079964322335300470799980856779999


Q ss_pred             HHHHHHHHCCCCEEEEEECCCCCCCCCCCCHHHHHHHHHHHHCCCCEECCCCCCCHHHHHHHHHHHHCCCEEEEEECHHH
Q ss_conf             99997631038738999712012211121014666666686637103120146998999999999755986999980034
Q gi|254780945|r  472 IERLKVVLSEGKKAYWICPQIEEKKESNFRSVVERFNSLHEHFTSSIAIIHGRMSDIDKESVMDSFKNGTCKLLIATTVI  551 (700)
Q Consensus       472 ~~~i~~~l~~g~q~y~VcPlIeese~~~~~~~~~~~~~l~~~~~~~v~~lHGkm~~~ek~~~m~~F~~g~~~iLvaTtvi  551 (700)
                      ...+-+....+ |++|.|...        ..+...+..|... +-++..+||.|+.++.++++++|++|+.+|||||-|.
T Consensus       264 L~~ll~~~~~~-~~IVF~~tk--------~~~~~l~~~l~~~-g~~~~~lhG~l~q~~R~~~l~~F~~g~~~iLVaTDva  333 (513)
T COG0513         264 LLKLLKDEDEG-RVIVFVRTK--------RLVEELAESLRKR-GFKVAALHGDLPQEERDRALEKFKDGELRVLVATDVA  333 (513)
T ss_pred             HHHHHHCCCCC-EEEEEECCH--------HHHHHHHHHHHHC-CCEEEEEECCCCHHHHHHHHHHHHCCCCCEEEEECHH
T ss_conf             99998278888-399995767--------7699999999978-9659997388998899999999975998989980654


Q ss_pred             HCCCCCCCCCEEEEECHHHCCHHHHHHHHHCCCCCCCCEEEEEEECCC
Q ss_conf             104688876589985852547468877301166789835999970888
Q gi|254780945|r  552 EVGIDVVDASIIIIENAEHFGLAQLHQLRGRVGRGEEISSCILLYHPP  599 (700)
Q Consensus       552 EVGvdvpna~~mvI~~aerfGLsqLHQLRGRVGRg~~~s~c~l~~~~~  599 (700)
                      --|+|+|+.+..|=+|...=-=.-+|- -||.||.+..|.++.+..+.
T Consensus       334 aRGiDi~~v~~VinyD~p~~~e~yvHR-iGRTgRaG~~G~ai~fv~~~  380 (513)
T COG0513         334 ARGLDIPDVSHVINYDLPLDPEDYVHR-IGRTGRAGRKGVAISFVTEE  380 (513)
T ss_pred             HCCCCCCCCCEEEECCCCCCCCCCCCC-CCCCCCCCCCCEEEEEECCH
T ss_conf             468996667479978799980413173-45343489987279985562


No 23 
>KOG0344 consensus
Probab=99.91  E-value=9.9e-25  Score=213.52  Aligned_cols=350  Identities=21%  Similarity=0.310  Sum_probs=253.3

Q ss_pred             HHCCC-CCCHHHHHHHHHHHHHHCCCCCCEEEEEECCCCCHHHHHHHHHHHHH--------HHHCCEEEEEHHHHHHHHH
Q ss_conf             63024-67988999999999841001343078862144223699999973344--------4305458861279999999
Q gi|254780945|r  267 RNIPF-SPTKSQESAIKDILQDMSQKNRMLRILQGDVGSGKTLVALIAMAAAV--------EAGGQAVIMAPIGILAQQH  337 (700)
Q Consensus       267 ~~LPF-~LT~~Q~~ai~eI~~Dl~~~~pM~RLLQGDVGSGKTiVA~~A~l~~~--------~~G~Q~alMaPTEILA~QH  337 (700)
                      ..++| +.|..|.+|+--...      --+-|-++-.|||||+-..+-++.-+        ..|.++++++||+-||.|-
T Consensus       152 ~~~~F~~Pt~iq~~aipvfl~------~r~~lAcapTGsgKtlaf~~Pil~~L~~~~~~~~~~gl~a~Il~ptreLa~Qi  225 (593)
T KOG0344         152 QELGFDEPTPIQKQAIPVFLE------KRDVLACAPTGSGKTLAFNLPILQHLKDLSQEKHKVGLRALILSPTRELAAQI  225 (593)
T ss_pred             HHCCCCCCCCCCCHHHHHHHC------CCCEEEECCCCCCCHHHHHHHHHHHHHHHHCCCCCCCEEEEEECCHHHHHHHH
T ss_conf             627888877310011566641------33058863578862056556999999875203576542788844449999999


Q ss_pred             HHHHHHHC--CCCCCEEEEEECCCCHHHHHHHHHHHCCCCCEEEEECHH----HCCCC---CCCCCCCEEEECCCCC---
Q ss_conf             98621101--457865899624642256676877621347548641112----01334---5544441788521013---
Q gi|254780945|r  338 YEFIKKYT--QNTQIIVEIITGNMPQAHRRKALERIAHGQAHIIIGTHA----LFQDS---IQYYKLILVIVDEQHR---  405 (700)
Q Consensus       338 ~~~~~~~~--~~~~i~v~lLtg~~~~~er~~i~~~i~~G~~~iiIGTHA----L~q~~---v~F~~LgLvViDEQHR---  405 (700)
                      |....++-  +..+.+++.++....+++|..-+..   -..+++|+|-+    +++-+   +.+.+.--.|+||+-|   
T Consensus       226 ~re~~k~~~~~~t~~~a~~~~~~~~~~qk~a~~~~---~k~dili~TP~ri~~~~~~~~~~idl~~V~~lV~dEaD~lfe  302 (593)
T KOG0344         226 YREMRKYSIDEGTSLRAAQFSKPAYPSQKPAFLSD---EKYDILISTPMRIVGLLGLGKLNIDLSKVEWLVVDEADLLFE  302 (593)
T ss_pred             HHHHHHCCCCCCCCHHHHHCCCCCCHHHCCCHHHH---HHHHHHHCCHHHHHHHHCCCCCCCHHHEEEEEEECHHHHHHC
T ss_conf             99998557777875345516666531103324677---788788618799999855897532012035676646876508


Q ss_pred             --CCHHHHHHHHHCCCCCCCEE--ECHHHHHHHHHHHHHHCCCHHHHCCCCCCCCCCEEEEEE-----CCCHHHHHHHHH
Q ss_conf             --35688998740256776101--010132278999975201011110235576662079997-----020026899997
Q gi|254780945|r  406 --FGVQQRLKLTQKATAPHVLL--MTATPIPRTLVLTSLGDIDISKITEKPAGRKPIKTVIIP-----INRIDEVIERLK  476 (700)
Q Consensus       406 --FGV~QR~~L~~Kg~~ph~L~--MtATPIPRTLal~~ygdldvS~i~e~P~gR~~I~T~~~~-----~~~~~~~~~~i~  476 (700)
                        |=++|=..+.+--.+||+.+  .|||= |--  -.-|..+-.|.+.-.+-|.++-.+-.+.     --+...-+-.++
T Consensus       303 ~~~f~~Qla~I~sac~s~~i~~a~FSat~-~~~--VEE~~~~i~~~~~~vivg~~~sa~~~V~QelvF~gse~~K~lA~r  379 (593)
T KOG0344         303 PEFFVEQLADIYSACQSPDIRVALFSATI-SVY--VEEWAELIKSDLKRVIVGLRNSANETVDQELVFCGSEKGKLLALR  379 (593)
T ss_pred             HHHHHHHHHHHHHHHCCCCHHHHHHHCCC-CHH--HHHHHHHHHCCCEEEEEECCHHHHHHHHHHHEEEECCHHHHHHHH
T ss_conf             15699999999998528522256632146-077--999999865053368984252576554555121104345778899


Q ss_pred             HHHCCCCEEEEEECCCCCCCCCCCCHHHHHHHHHHHHCCC-CEECCCCCCCHHHHHHHHHHHHCCCEEEEEECHHHHCCC
Q ss_conf             6310387389997120122111210146666666866371-031201469989999999997559869999800341046
Q gi|254780945|r  477 VVLSEGKKAYWICPQIEEKKESNFRSVVERFNSLHEHFTS-SIAIIHGRMSDIDKESVMDSFKNGTCKLLIATTVIEVGI  555 (700)
Q Consensus       477 ~~l~~g~q~y~VcPlIeese~~~~~~~~~~~~~l~~~~~~-~v~~lHGkm~~~ek~~~m~~F~~g~~~iLvaTtviEVGv  555 (700)
                      +-++.|-+-=++-+.      .+..-+.+.|+.|. .|++ +|+.+||..++.+.+++|++|+.|+|.+|+||-|++-|+
T Consensus       380 q~v~~g~~PP~lIfV------Qs~eRak~L~~~L~-~~~~i~v~vIh~e~~~~qrde~~~~FR~g~IwvLicTdll~RGi  452 (593)
T KOG0344         380 QLVASGFKPPVLIFV------QSKERAKQLFEELE-IYDNINVDVIHGERSQKQRDETMERFRIGKIWVLICTDLLARGI  452 (593)
T ss_pred             HHHHCCCCCCEEEEE------ECHHHHHHHHHHHH-HCCCCCEEEEECCCCHHHHHHHHHHHHCCCEEEEEEHHHHHCCC
T ss_conf             998615899748988------53888999999864-23576634676366666778999998506706888504665455


Q ss_pred             CCCCCCEEEEECHHHCCHHHHHHHHHCCCCCCCCEEEEEEECCCCCHHHHHHHHHHHHHC--HHHHHHHHHHHHCCCCCC
Q ss_conf             888765899858525474688773011667898359999708889987999999998414--258999999852063000
Q gi|254780945|r  556 DVVDASIIIIENAEHFGLAQLHQLRGRVGRGEEISSCILLYHPPLSKNSYTRLSVLKNTE--DGFLIAEEDLKQRKEGEI  633 (700)
Q Consensus       556 dvpna~~mvI~~aerfGLsqLHQLRGRVGRg~~~s~c~l~~~~~~~~~~~~Rl~~l~~~~--dGf~iAe~Dl~lRG~G~~  633 (700)
                      |.-|++++|.+|---+++|++|++ ||+||.+..|..|..|.+    .+..|+++++++-  .||+++|.++.+++.++.
T Consensus       453 Df~gvn~VInyD~p~s~~syihrI-GRtgRag~~g~Aitfytd----~d~~~ir~iae~~~~sG~evpe~~m~~~k~~~~  527 (593)
T KOG0344         453 DFKGVNLVINYDFPQSDLSYIHRI-GRTGRAGRSGKAITFYTD----QDMPRIRSIAEVMEQSGCEVPEKIMGIKKLSRL  527 (593)
T ss_pred             CCCCCCEEEECCCCCHHHHHHHHH-HCCCCCCCCCCEEEEECC----CCCHHHHHHHHHHHHCCCCCHHHHHHHHHHHHH
T ss_conf             645763689537872247888873-025788988616998632----553455568999997188633999865666655


Q ss_pred             CCCHHCC
Q ss_conf             2600069
Q gi|254780945|r  634 LGIKQSG  640 (700)
Q Consensus       634 ~G~~QsG  640 (700)
                      .+..+.-
T Consensus       528 ~kk~~~k  534 (593)
T KOG0344         528 KKKKLLK  534 (593)
T ss_pred             HHHHHHH
T ss_conf             5555431


No 24 
>COG4098 comFA Superfamily II DNA/RNA helicase required for DNA uptake (late competence protein) [DNA replication, recombination, and repair]
Probab=99.89  E-value=4.4e-20  Score=177.10  Aligned_cols=299  Identities=24%  Similarity=0.394  Sum_probs=228.0

Q ss_pred             CCCCHHHHHHHHHHHHHHCCCCCCEEEEEECCCCCHHHHHHHHHHHHHHHHCCEEEEEHHHHHHHHHHHHHHHHCCCCCC
Q ss_conf             46798899999999984100134307886214422369999997334443054588612799999999862110145786
Q gi|254780945|r  271 FSPTKSQESAIKDILQDMSQKNRMLRILQGDVGSGKTLVALIAMAAAVEAGGQAVIMAPIGILAQQHYEFIKKYTQNTQI  350 (700)
Q Consensus       271 F~LT~~Q~~ai~eI~~Dl~~~~pM~RLLQGDVGSGKTiVA~~A~l~~~~~G~Q~alMaPTEILA~QH~~~~~~~~~~~~i  350 (700)
                      =+||..|++|-+....-+++..+|  |++.-.|||||..-+-++..++.+|.-+++-.|--=.+--.|..++.-|.+  +
T Consensus        96 G~Ls~~Q~~as~~l~q~i~~k~~~--lv~AV~GaGKTEMif~~i~~al~~G~~vciASPRvDVclEl~~Rlk~aF~~--~  171 (441)
T COG4098          96 GTLSPGQKKASNQLVQYIKQKEDT--LVWAVTGAGKTEMIFQGIEQALNQGGRVCIASPRVDVCLELYPRLKQAFSN--C  171 (441)
T ss_pred             CCCCHHHHHHHHHHHHHHHHCCCE--EEEEECCCCCHHHHHHHHHHHHHCCCEEEEECCCCCCHHHHHHHHHHHHCC--C
T ss_conf             532724789999999998715768--999742798510169999999965986998468610117778999976214--9


Q ss_pred             EEEEEECCCCHHHHHHHHHHHCCCCCEEEEEC-HHHCCCCCCCCCCCEEEECCCCCCCHH--HHHHHHHC-C--CCCCCE
Q ss_conf             58996246422566768776213475486411-120133455444417885210133568--89987402-5--677610
Q gi|254780945|r  351 IVEIITGNMPQAHRRKALERIAHGQAHIIIGT-HALFQDSIQYYKLILVIVDEQHRFGVQ--QRLKLTQK-A--TAPHVL  424 (700)
Q Consensus       351 ~v~lLtg~~~~~er~~i~~~i~~G~~~iiIGT-HAL~q~~v~F~~LgLvViDEQHRFGV~--QR~~L~~K-g--~~ph~L  424 (700)
                      .+.+|.|..+..-           ...+||-| |-|+-=+=.|   -++||||=--|--.  |-...+-+ .  .....+
T Consensus       172 ~I~~Lyg~S~~~f-----------r~plvVaTtHQLlrFk~aF---D~liIDEVDAFP~~~d~~L~~Av~~ark~~g~~I  237 (441)
T COG4098         172 DIDLLYGDSDSYF-----------RAPLVVATTHQLLRFKQAF---DLLIIDEVDAFPFSDDQSLQYAVKKARKKEGATI  237 (441)
T ss_pred             CEEEEECCCCHHC-----------CCCEEEEEHHHHHHHHHHC---CEEEEECCCCCCCCCCHHHHHHHHHHHCCCCCEE
T ss_conf             8666725871313-----------3447997668888888643---3899830245656678889999997512367369


Q ss_pred             EECHHHHHHHHH-HHHHHCCCHHHHCCCCCCCC-CC-EEEEEECCC-------H-HHHHHHHHHHHCCCCEEEEEECCCC
Q ss_conf             101013227899-99752010111102355766-62-079997020-------0-2689999763103873899971201
Q gi|254780945|r  425 LMTATPIPRTLV-LTSLGDIDISKITEKPAGRK-PI-KTVIIPINR-------I-DEVIERLKVVLSEGKKAYWICPQIE  493 (700)
Q Consensus       425 ~MtATPIPRTLa-l~~ygdldvS~i~e~P~gR~-~I-~T~~~~~~~-------~-~~~~~~i~~~l~~g~q~y~VcPlIe  493 (700)
                      +||||| |++|- -..-|.+-.-.|...=.|+. || ++.|++.-+       + .+++..++++...|.-+++-.|-|+
T Consensus       238 ylTATp-~k~l~r~~~~g~~~~~klp~RfH~~pLpvPkf~w~~~~~k~l~r~kl~~kl~~~lekq~~~~~P~liF~p~I~  316 (441)
T COG4098         238 YLTATP-TKKLERKILKGNLRILKLPARFHGKPLPVPKFVWIGNWNKKLQRNKLPLKLKRWLEKQRKTGRPVLIFFPEIE  316 (441)
T ss_pred             EEECCC-HHHHHHHHHHCCEEEEECCHHHCCCCCCCCCEEEECCHHHHHHHCCCCHHHHHHHHHHHHCCCCEEEEECCHH
T ss_conf             996488-0788887540775676344654389989874288644777766444778999999998743882899925058


Q ss_pred             CCCCCCCCHHHHHHHHHHHHCCC-CEECCCCCCCHHHHHHHHHHHHCCCEEEEEECHHHHCCCCCCCCCEEEEECHHH-C
Q ss_conf             22111210146666666866371-031201469989999999997559869999800341046888765899858525-4
Q gi|254780945|r  494 EKKESNFRSVVERFNSLHEHFTS-SIAIIHGRMSDIDKESVMDSFKNGTCKLLIATTVIEVGIDVVDASIIIIENAEH-F  571 (700)
Q Consensus       494 ese~~~~~~~~~~~~~l~~~~~~-~v~~lHGkm~~~ek~~~m~~F~~g~~~iLvaTtviEVGvdvpna~~mvI~~aer-f  571 (700)
                              ..++..+-|++.+|. +++.+|..  +..+-+..++|++|+++||++||+.|-||.+||..+-|+..-.| |
T Consensus       317 --------~~eq~a~~lk~~~~~~~i~~Vhs~--d~~R~EkV~~fR~G~~~lLiTTTILERGVTfp~vdV~Vlgaeh~vf  386 (441)
T COG4098         317 --------TMEQVAAALKKKLPKETIASVHSE--DQHRKEKVEAFRDGKITLLITTTILERGVTFPNVDVFVLGAEHRVF  386 (441)
T ss_pred             --------HHHHHHHHHHHHCCCCCEEEEECC--CCCHHHHHHHHHCCCEEEEEEEEHHHCCCCCCCCEEEEECCCCCCC
T ss_conf             --------899999999861886421565336--7017899999875863899984403326643562399954776420


Q ss_pred             CHHHHHHHHHCCCCCCCC---EEEEEEECC
Q ss_conf             746887730116678983---599997088
Q gi|254780945|r  572 GLAQLHQLRGRVGRGEEI---SSCILLYHP  598 (700)
Q Consensus       572 GLsqLHQLRGRVGRg~~~---s~c~l~~~~  598 (700)
                      -=|-|-|.-|||||+-..   -.||+.+..
T Consensus       387 TesaLVQIaGRvGRs~~~PtGdv~FFH~G~  416 (441)
T COG4098         387 TESALVQIAGRVGRSLERPTGDVLFFHYGK  416 (441)
T ss_pred             CHHHHHHHHHHCCCCCCCCCCCEEEEECCC
T ss_conf             188999975231678768987589996463


No 25 
>PRK11057 ATP-dependent DNA helicase RecQ; Provisional
Probab=99.88  E-value=1.6e-18  Score=164.81  Aligned_cols=309  Identities=18%  Similarity=0.285  Sum_probs=226.3

Q ss_pred             HHHHCCC-CCCHHHHHHHHHHHHHHCCCCCCEEEEEECCCCCHHHHHHHHHHHHHHHHCCEEEEEHHHHHHHHHHHHHHH
Q ss_conf             9863024-679889999999998410013430788621442236999999733444305458861279999999986211
Q gi|254780945|r  265 ILRNIPF-SPTKSQESAIKDILQDMSQKNRMLRILQGDVGSGKTLVALIAMAAAVEAGGQAVIMAPIGILAQQHYEFIKK  343 (700)
Q Consensus       265 f~~~LPF-~LT~~Q~~ai~eI~~Dl~~~~pM~RLLQGDVGSGKTiVA~~A~l~~~~~G~Q~alMaPTEILA~QH~~~~~~  343 (700)
                      +.+.+.| ++-..|..+|+.|.+-  .+    -|..==.|+||++.+-+.++.  . +.-+.+..|+==|.......+..
T Consensus        17 L~~~FG~~~Fr~~Q~e~i~~~l~g--~D----~l~~mpTG~GKSlcyQlPal~--~-~g~tiVisPLisLm~DQv~~L~~   87 (607)
T PRK11057         17 LQETFGYQQFRPGQEEIIDTVLSG--RD----CLVVMPTGGGKSLCYQIPALV--L-DGLTLVVSPLISLMKDQVDQLLA   87 (607)
T ss_pred             HHHHCCCCCCCHHHHHHHHHHHCC--CC----EEEECCCCCHHHHHHHHHHHH--C-CCCEEEECCHHHHHHHHHHHHHH
T ss_conf             998669843457699999999869--98----899878995597999999987--7-99889986879999999999997


Q ss_pred             HCCCCCCEEEEEECCCCHHHHHHHHHHHCCCCCEEEEECH-HH----CCCCCCCCCCCEEEECCCCC---CCHHHHHH--
Q ss_conf             0145786589962464225667687762134754864111-20----13345544441788521013---35688998--
Q gi|254780945|r  344 YTQNTQIIVEIITGNMPQAHRRKALERIAHGQAHIIIGTH-AL----FQDSIQYYKLILVIVDEQHR---FGVQQRLK--  413 (700)
Q Consensus       344 ~~~~~~i~v~lLtg~~~~~er~~i~~~i~~G~~~iiIGTH-AL----~q~~v~F~~LgLvViDEQHR---FGV~QR~~--  413 (700)
                      .    ||+.+.|+|+++..++.+++.++.+|+++++.-|- -|    |.+.+.-.+++++||||=|.   .|=.-|-.  
T Consensus        88 ~----gi~a~~l~s~~~~~e~~~~~~~~~~g~~~llyvtPErl~~~~~~~~l~~~~i~~~viDEAHcvs~WGhdFRp~Y~  163 (607)
T PRK11057         88 N----GVAAACLNSTQTREQQLEVMAGCRTGQIKLLYIAPERLMMDNFLEHLAHWNPVLLAVDEAHCISQWGHDFRPEYA  163 (607)
T ss_pred             C----CCCEEEECCCCCHHHHHHHHHHHHCCCCCEEEECHHHHCCHHHHHHHHHCCCCEEEEEHHHHHHHCCCCCHHHHH
T ss_conf             8----992999569999999999999997599879998855856978999997188664885306667541550038899


Q ss_pred             ----HHHCCCCCCCEEECHHHHHHHHHHHH--HHCCCHHHHCCCCCCCCCCEEEEEEC-CCHHHHHHHHHHHHCCCCEEE
Q ss_conf             ----74025677610101013227899997--52010111102355766620799970-200268999976310387389
Q gi|254780945|r  414 ----LTQKATAPHVLLMTATPIPRTLVLTS--LGDIDISKITEKPAGRKPIKTVIIPI-NRIDEVIERLKVVLSEGKKAY  486 (700)
Q Consensus       414 ----L~~Kg~~ph~L~MtATPIPRTLal~~--ygdldvS~i~e~P~gR~~I~T~~~~~-~~~~~~~~~i~~~l~~g~q~y  486 (700)
                          |.++=..+-++.+|||--|++-.-..  .+--+--+.. --..|..+.-.++.. +..+.++++++.+  .|....
T Consensus       164 ~l~~l~~~~~~~p~~AlTATAt~~v~~di~~~L~l~~~~~~~-~~f~RpNl~~~v~~~~~~~~~~~~~~~~~--~~~sgI  240 (607)
T PRK11057        164 ALGQLRQRFPTLPFMALTATADDTTRQDIVRLLGLNDPLIQI-SSFDRPNIRYMLMEKFKPLDQLMRYVQEQ--RGKSGI  240 (607)
T ss_pred             HHHHHHHHCCCCCEEEEEECCCHHHHHHHHHHHCCCCCCEEE-CCCCCCCCEEEEEECCCHHHHHHHHHHHC--CCCCEE
T ss_conf             999999976999748999636878999999970899980782-57788874145554477399999998706--899779


Q ss_pred             EEECCCCCCCCCCCCHHHHHHHHHHHHCCCCEECCCCCCCHHHHHHHHHHHHCCCEEEEEECHHHHCCCCCCCCCEEEEE
Q ss_conf             99712012211121014666666686637103120146998999999999755986999980034104688876589985
Q gi|254780945|r  487 WICPQIEEKKESNFRSVVERFNSLHEHFTSSIAIIHGRMSDIDKESVMDSFKNGTCKLLIATTVIEVGIDVVDASIIIIE  566 (700)
Q Consensus       487 ~VcPlIeese~~~~~~~~~~~~~l~~~~~~~v~~lHGkm~~~ek~~~m~~F~~g~~~iLvaTtviEVGvdvpna~~mvI~  566 (700)
                      |-|+..        +.+++.++.|++. +-++..-||.|++++++.+.++|.+|+++|+|||.---.|||-||....|=.
T Consensus       241 IYc~tr--------k~~e~la~~L~~~-G~~~~~YHagl~~~~R~~~q~~f~~~~~~vivAT~AFGMGIdk~dVR~ViH~  311 (607)
T PRK11057        241 IYCNSR--------AKVEDTAARLQSR-GISAAAYHAGLDNDVRADVQEAFQRDDLQIVVATVAFGMGINKPNVRFVVHF  311 (607)
T ss_pred             EEECCH--------HHHHHHHHHHHHC-CCCEEECCCCCCHHHHHHHHHHHHCCCCCEEEEEHHHHCCCCCCCCCEEEEC
T ss_conf             996928--------9999999999857-9754530589997899999998756887589975011057677776679977


Q ss_pred             CHHHCCHHHHHHHHHCCCCCCCCEEEEEEECCC
Q ss_conf             852547468877301166789835999970888
Q gi|254780945|r  567 NAEHFGLAQLHQLRGRVGRGEEISSCILLYHPP  599 (700)
Q Consensus       567 ~aerfGLsqLHQLRGRVGRg~~~s~c~l~~~~~  599 (700)
                      +.- -.+....|==||-||-+.+|.|+|+|+..
T Consensus       312 ~~P-~s~e~yyQE~GRAGRDG~~a~c~l~y~~~  343 (607)
T PRK11057        312 DIP-RNIESYYQETGRAGRDGLPAEAMLFYDPA  343 (607)
T ss_pred             CCC-CCHHHHHHHHHHCCCCCCCCEEEEEECHH
T ss_conf             899-99999999886352589854189985687


No 26 
>COG1204 Superfamily II helicase [General function prediction only]
Probab=99.87  E-value=6.8e-19  Score=167.74  Aligned_cols=319  Identities=21%  Similarity=0.288  Sum_probs=233.0

Q ss_pred             CCHHHHHHHHHCCC-CCCHHHHHHHHHHHHHHCCCCCCEEEEEECCCCCHHHHHHHHHHHHHHH-HCCEEEEEHHHHHHH
Q ss_conf             75789999863024-6798899999999984100134307886214422369999997334443-054588612799999
Q gi|254780945|r  258 EGKIAQKILRNIPF-SPTKSQESAIKDILQDMSQKNRMLRILQGDVGSGKTLVALIAMAAAVEA-GGQAVIMAPIGILAQ  335 (700)
Q Consensus       258 ~~~~~~~f~~~LPF-~LT~~Q~~ai~eI~~Dl~~~~pM~RLLQGDVGSGKTiVA~~A~l~~~~~-G~Q~alMaPTEILA~  335 (700)
                      ....+.++.+.-++ +|=+.|+.++....-+   +.  |=|+.-=.|||||.||++|++..+.. |.-+.+.|||--||+
T Consensus        16 ~~~~v~~i~~~~~~~el~~~qq~av~~~~~~---~~--N~li~aPTgsGKTlIA~lai~~~l~~~~~k~vYivPlkALa~   90 (766)
T COG1204          16 LDDRVLEILKGDGIDELFNPQQEAVEKGLLS---DE--NVLISAPTGSGKTLIALLAILSTLLEGGGKVVYIVPLKALAE   90 (766)
T ss_pred             CCHHHHHHHCCCCHHHHHHHHHHHHHCCCCC---CC--CEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECHHHHHH
T ss_conf             2078998860488477557899874111257---98--679976788866999999999999855983899907599999


Q ss_pred             HHHHHHHHHCCCCCCEEEEEECCCCHHHHHHHHHHHCCCCCEEEEECH----HHC-CCCCCCCCCCEEEECCCCCCCHHH
Q ss_conf             999862110145786589962464225667687762134754864111----201-334554444178852101335688
Q gi|254780945|r  336 QHYEFIKKYTQNTQIIVEIITGNMPQAHRRKALERIAHGQAHIIIGTH----ALF-QDSIQYYKLILVIVDEQHRFGVQQ  410 (700)
Q Consensus       336 QH~~~~~~~~~~~~i~v~lLtg~~~~~er~~i~~~i~~G~~~iiIGTH----AL~-q~~v~F~~LgLvViDEQHRFGV~Q  410 (700)
                      |-|++|+ +|+.+|++|..+||......       -.-+..+|||.|-    ++. ....-..+.+||||||=|--|=.-
T Consensus        91 Ek~~~~~-~~~~~GirV~~~TgD~~~~~-------~~l~~~~ViVtT~EK~Dsl~R~~~~~~~~V~lvViDEiH~l~d~~  162 (766)
T COG1204          91 EKYEEFS-RLEELGIRVGISTGDYDLDD-------ERLARYDVIVTTPEKLDSLTRKRPSWIEEVDLVVIDEIHLLGDRT  162 (766)
T ss_pred             HHHHHHH-HHHHCCCEEEEECCCCCCCH-------HHHCCCCEEEECHHHHHHHHHCCCCHHHCCCEEEEEEEEECCCCC
T ss_conf             9999866-68865977999648865553-------341458879974678667650675333401689994210148756


Q ss_pred             HHHHHH----C----CCCCCCEEECHHHHHH--HHHHHHHHCCCHHHHCCCCCCCCCCEEE-EEECC---------CHHH
Q ss_conf             998740----2----5677610101013227--8999975201011110235576662079-99702---------0026
Q gi|254780945|r  411 RLKLTQ----K----ATAPHVLLMTATPIPR--TLVLTSLGDIDISKITEKPAGRKPIKTV-IIPIN---------RIDE  470 (700)
Q Consensus       411 R~~L~~----K----g~~ph~L~MtATPIPR--TLal~~ygdldvS~i~e~P~gR~~I~T~-~~~~~---------~~~~  470 (700)
                      |-.-.+    +    +...-++-.||| +|.  .+|--+-+.+..|.-.--|--|+-..+. +....         ..+.
T Consensus       163 RG~~lE~iv~r~~~~~~~~rivgLSAT-lpN~~evA~wL~a~~~~~~~rp~~l~~~v~~~~~~~~~~~~~k~~~~~~~~~  241 (766)
T COG1204         163 RGPVLESIVARMRRLNELIRIVGLSAT-LPNAEEVADWLNAKLVESDWRPVPLRRGVPYVGAFLGADGKKKTWPLLIDNL  241 (766)
T ss_pred             CCCEEHHHHHHHHHHCCCEEEEEEEEE-CCCHHHHHHHHCCCCCCCCCCCCCCCCCCCCCEEEEEECCCCCCCCCCCHHH
T ss_conf             586402279888852755179887311-6888999998588355567788620157765317987147643454210579


Q ss_pred             HHHHHHHHHCCCCEEEEEECCCCCCCC------------------C--C--------CCHHHHHHHHHHHHCCCCEECCC
Q ss_conf             899997631038738999712012211------------------1--2--------10146666666866371031201
Q gi|254780945|r  471 VIERLKVVLSEGKKAYWICPQIEEKKE------------------S--N--------FRSVVERFNSLHEHFTSSIAIIH  522 (700)
Q Consensus       471 ~~~~i~~~l~~g~q~y~VcPlIeese~------------------~--~--------~~~~~~~~~~l~~~~~~~v~~lH  522 (700)
                      +++.+.+.++.|+||-+-||.=.+.+.                  .  +        ..+-....+.|.+.++..|++=|
T Consensus       242 ~~~~v~~~~~~~~qvLvFv~sR~~a~~~A~~l~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~l~e~v~~GvafHh  321 (766)
T COG1204         242 ALELVLESLAEGGQVLVFVHSRKEAEKTAKKLRIKMSATLSDDEKIVLDEGASPILIPETPTSEDEELAELVLRGVAFHH  321 (766)
T ss_pred             HHHHHHHHHHCCCEEEEEEECCCHHHHHHHHHHHHHHHCCCHHHHHHCCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCCC
T ss_conf             99999999856986999974572599999999998751277165430122344211235543221789999972754112


Q ss_pred             CCCCHHHHHHHHHHHHCCCEEEEEECHHHHCCCCCCCCCEEEEECHHHCC---------HHHHHHHHHCCCCCCCCEE
Q ss_conf             46998999999999755986999980034104688876589985852547---------4688773011667898359
Q gi|254780945|r  523 GRMSDIDKESVMDSFKNGTCKLLIATTVIEVGIDVVDASIIIIENAEHFG---------LAQLHQLRGRVGRGEEISS  591 (700)
Q Consensus       523 Gkm~~~ek~~~m~~F~~g~~~iLvaTtviEVGvdvpna~~mvI~~aerfG---------LsqLHQLRGRVGRg~~~s~  591 (700)
                      .-|..++++.+=+.|++|.++|||||.-.-.|||.|-= .-||-+..||.         ..--.|+=||-||-+...|
T Consensus       322 AGL~~~~R~~vE~~Fr~g~ikVlv~TpTLA~GVNLPA~-~VIIk~~~~y~~~~g~~~i~~~dv~QM~GRAGRPg~d~~  398 (766)
T COG1204         322 AGLPREDRQLVEDAFRKGKIKVLVSTPTLAAGVNLPAR-TVIIKDTRRYDPKGGIVDIPVLDVLQMAGRAGRPGYDDY  398 (766)
T ss_pred             CCCCHHHHHHHHHHHHCCCCEEEEECHHHHHHCCCCCE-EEEEEEEEEECCCCCEEECCHHHHHHCCCCCCCCCCCCC
T ss_conf             68978899999999866985499954577621688632-899910387757788477764148655676799875777


No 27 
>COG1111 MPH1 ERCC4-like helicases [DNA replication, recombination, and repair]
Probab=99.86  E-value=2.6e-18  Score=163.15  Aligned_cols=334  Identities=22%  Similarity=0.282  Sum_probs=216.1

Q ss_pred             CHHHHHHHHHHHHHHCCCCCCEEEEEECCCCCHHHHHHHHHHHHH-HHHCCEEEEEHHHHHHHHHHHHHHHHCCCCCCEE
Q ss_conf             988999999999841001343078862144223699999973344-4305458861279999999986211014578658
Q gi|254780945|r  274 TKSQESAIKDILQDMSQKNRMLRILQGDVGSGKTLVALIAMAAAV-EAGGQAVIMAPIGILAQQHYEFIKKYTQNTQIIV  352 (700)
Q Consensus       274 T~~Q~~ai~eI~~Dl~~~~pM~RLLQGDVGSGKTiVA~~A~l~~~-~~G~Q~alMaPTEILA~QH~~~~~~~~~~~~i~v  352 (700)
                      -.-|.........-       |-|+-=-.|=|||+||++-|+.-. ..+..+.|||||--|..||++.+++.+.--.-.+
T Consensus        17 R~YQ~~i~a~al~~-------NtLvvlPTGLGKT~IA~~V~~~~l~~~~~kvlfLAPTKPLV~Qh~~~~~~v~~ip~~~i   89 (542)
T COG1111          17 RLYQLNIAAKALFK-------NTLVVLPTGLGKTFIAAMVIANRLRWFGGKVLFLAPTKPLVLQHAEFCRKVTGIPEDEI   89 (542)
T ss_pred             HHHHHHHHHHHHHC-------CEEEEECCCCCHHHHHHHHHHHHHHHCCCEEEEECCCCHHHHHHHHHHHHHHCCCHHHE
T ss_conf             89999999998644-------83899528750799999999999874588489965895179999999999858984332


Q ss_pred             EEEECCCCHHHHHHHHHHHCCCCCEEEEECHHHCCC-----CCCCCCCCEEEECCCCCCCHHHH-----HHHHHCCCCCC
Q ss_conf             996246422566768776213475486411120133-----45544441788521013356889-----98740256776
Q gi|254780945|r  353 EIITGNMPQAHRRKALERIAHGQAHIIIGTHALFQD-----SIQYYKLILVIVDEQHRFGVQQR-----LKLTQKATAPH  422 (700)
Q Consensus       353 ~lLtg~~~~~er~~i~~~i~~G~~~iiIGTHAL~q~-----~v~F~~LgLvViDEQHRFGV~QR-----~~L~~Kg~~ph  422 (700)
                      +-|||..+..+|+..|.     +.+|+|-|--.++.     .+.-.+.-++|+||-||===+--     .....-..+|+
T Consensus        90 ~~ltGev~p~~R~~~w~-----~~kVfvaTPQvveNDl~~Grid~~dv~~lifDEAHRAvGnyAYv~Va~~y~~~~k~~~  164 (542)
T COG1111          90 AALTGEVRPEEREELWA-----KKKVFVATPQVVENDLKAGRIDLDDVSLLIFDEAHRAVGNYAYVFVAKEYLRSAKNPL  164 (542)
T ss_pred             EEECCCCCHHHHHHHHH-----HCCEEEECCHHHHHHHHCCCCCHHHCEEEEECHHHHCCCCCHHHHHHHHHHHHCCCCE
T ss_conf             31117778688999875-----1778995638777687617667678058986235541376069999999998256843


Q ss_pred             CEEECHHHHHHHH-HHHHHHCCCHHHHCCCCCC-------CCCCEEEEEEC---CCHHHH-------HHHHHHHHCCCCE
Q ss_conf             1010101322789-9997520101111023557-------66620799970---200268-------9999763103873
Q gi|254780945|r  423 VLLMTATPIPRTL-VLTSLGDIDISKITEKPAG-------RKPIKTVIIPI---NRIDEV-------IERLKVVLSEGKK  484 (700)
Q Consensus       423 ~L~MtATPIPRTL-al~~ygdldvS~i~e~P~g-------R~~I~T~~~~~---~~~~~~-------~~~i~~~l~~g~q  484 (700)
                      +|-|||||=--.= -+.+--.|.+|.|--+--+       =++++-.|+.-   +.++++       ++-.-+.|+..+=
T Consensus       165 ilgLTASPGs~~ekI~eV~~nLgIe~vevrTE~d~DV~~Yv~~~kve~ikV~lp~e~~~ir~~l~~~l~~~Lk~L~~~g~  244 (542)
T COG1111         165 ILGLTASPGSDLEKIQEVVENLGIEKVEVRTEEDPDVRPYVKKIKVEWIKVDLPEEIKEIRDLLRDALKPRLKPLKELGV  244 (542)
T ss_pred             EEEEECCCCCCHHHHHHHHHHCCCCEEEEECCCCCCHHHHHCCCEEEEEECCCCHHHHHHHHHHHHHHHHHHHHHHHCCC
T ss_conf             79872389998799999998379542898457885177751404248996368589999999999999999999997695


Q ss_pred             EEEEECCCC------------------CCCCC-------------------C----------------------------
Q ss_conf             899971201------------------22111-------------------2----------------------------
Q gi|254780945|r  485 AYWICPQIE------------------EKKES-------------------N----------------------------  499 (700)
Q Consensus       485 ~y~VcPlIe------------------ese~~-------------------~----------------------------  499 (700)
                      .--.|| +.                  ++++-                   +                            
T Consensus       245 ~~~~~~-~~~kdl~~~~~~~~~~a~~~~~~~~~~l~~~a~~~kl~~a~elletqGi~~~~~Yl~~l~e~~~~~~sk~a~~  323 (542)
T COG1111         245 IESSSP-VSKKDLLELRQIRLIMAKNEDSDKFRLLSVLAEAIKLAHALELLETQGIRPFYQYLEKLEEEATKGGSKAAKS  323 (542)
T ss_pred             EECCCC-CCHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHCCCCHHHHHH
T ss_conf             323573-1076899999989986357617888999999999888899999985086999999999998750352077898


Q ss_pred             ----------------------------------------------------CCHHHHHHHHHHHHCCCCEECCCC----
Q ss_conf             ----------------------------------------------------101466666668663710312014----
Q gi|254780945|r  500 ----------------------------------------------------FRSVVERFNSLHEHFTSSIAIIHG----  523 (700)
Q Consensus       500 ----------------------------------------------------~~~~~~~~~~l~~~~~~~v~~lHG----  523 (700)
                                                                          ..+|+...+.|++.++......-|    
T Consensus       324 l~~d~~~~~al~~~~~~~~~~v~HPKl~~l~eilke~~~k~~~~RvIVFT~yRdTae~i~~~L~~~~~~~~~rFiGQa~r  403 (542)
T COG1111         324 LLADPYFKRALRLLIRADESGVEHPKLEKLREILKEQLEKNGDSRVIVFTEYRDTAEEIVNFLKKIGIKARVRFIGQASR  403 (542)
T ss_pred             HHCCHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHCCCCCEEEEEEHHHHHHHHHHHHHHHCCCCCEEEEEECCCC
T ss_conf             75382047999999974003688961899999999997238985599996147589999999985287520688611454


Q ss_pred             ----CCCHHHHHHHHHHHHCCCEEEEEECHHHHCCCCCCCCCEEEEECHHHCCHHHHHHHHHCCCCCCCCEEE-EEEECC
Q ss_conf             ----699899999999975598699998003410468887658998585254746887730116678983599-997088
Q gi|254780945|r  524 ----RMSDIDKESVMDSFKNGTCKLLIATTVIEVGIDVVDASIIIIENAEHFGLAQLHQLRGRVGRGEEISSC-ILLYHP  598 (700)
Q Consensus       524 ----km~~~ek~~~m~~F~~g~~~iLvaTtviEVGvdvpna~~mvI~~aerfGLsqLHQLRGRVGRg~~~s~c-~l~~~~  598 (700)
                          -|+..|..+++++|++|+.++||||+|=|=|+|+|...++|-+.|--=-. ---|=+||-||+ ..|+. +|++.+
T Consensus       404 ~~~~GMsQkeQ~eiI~~Fr~Ge~nVLVaTSVgEEGLDIp~vDlVifYEpvpSeI-R~IQR~GRTGR~-r~Grv~vLvt~g  481 (542)
T COG1111         404 EGDKGMSQKEQKEIIDQFRKGEYNVLVATSVGEEGLDIPEVDLVIFYEPVPSEI-RSIQRKGRTGRK-RKGRVVVLVTEG  481 (542)
T ss_pred             CCCCCCCHHHHHHHHHHHHCCCCEEEEECCCCCCCCCCCCCCEEEEECCCCHHH-HHHHHHCCCCCC-CCCEEEEEEECC
T ss_conf             556665888999999998657851899812322467887656799956885788-999860744557-797499999658


Q ss_pred             CCC----HHHHHHHHHHHHHCHHHHHHH
Q ss_conf             899----879999999984142589999
Q gi|254780945|r  599 PLS----KNSYTRLSVLKNTEDGFLIAE  622 (700)
Q Consensus       599 ~~~----~~~~~Rl~~l~~~~dGf~iAe  622 (700)
                      ...    ..|++|.+-|.++--|...+.
T Consensus       482 trdeayy~~s~rke~~m~e~i~~~~~~~  509 (542)
T COG1111         482 TRDEAYYYSSRRKEQKMIESIRGLSLEL  509 (542)
T ss_pred             CHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             6278999999999999999999888762


No 28 
>PRK13767 ATP-dependent helicase; Provisional
Probab=99.86  E-value=4.2e-18  Score=161.57  Aligned_cols=312  Identities=21%  Similarity=0.283  Sum_probs=227.1

Q ss_pred             HHHHCCCCCCHHHHHHHHHHHHHHCCCCCCEEEEEECCCCCHHHHHHHHHHHHH---------HHHCCEEEEEHHHHHHH
Q ss_conf             986302467988999999999841001343078862144223699999973344---------43054588612799999
Q gi|254780945|r  265 ILRNIPFSPTKSQESAIKDILQDMSQKNRMLRILQGDVGSGKTLVALIAMAAAV---------EAGGQAVIMAPIGILAQ  335 (700)
Q Consensus       265 f~~~LPF~LT~~Q~~ai~eI~~Dl~~~~pM~RLLQGDVGSGKTiVA~~A~l~~~---------~~G~Q~alMaPTEILA~  335 (700)
                      |.+.. -++|.-|+.|+..|.+.    +  |-|+.--.|||||.-|++.++..+         ..|-++.++.|+--||+
T Consensus        26 f~~~~-~~p~~~Q~~a~~~i~~G----~--~~Li~ApTGsGKTlAaflp~l~~l~~~~~~~~~~~~~~~LyIsPLkAL~~   98 (878)
T PRK13767         26 FKRKF-GTFTPPQRYAIPLIHEG----K--NVLISSPTGSGKTLAAFLGIIDELFRLAEEGELEDSVYCIYVSPLRALNN   98 (878)
T ss_pred             HHHCC-CCCCHHHHHHHHHHHCC----C--CEEEECCCCCHHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEECCHHHHHH
T ss_conf             98537-99998999999999679----9--88998999813999999999999985000367788728999684798899


Q ss_pred             HHHHHHHHHCCC------------CCCEEEEEECCCCHHHHHHHHHHHCCCCCEEEEEC----HHHCCC---CCCCCCCC
Q ss_conf             999862110145------------78658996246422566768776213475486411----120133---45544441
Q gi|254780945|r  336 QHYEFIKKYTQN------------TQIIVEIITGNMPQAHRRKALERIAHGQAHIIIGT----HALFQD---SIQYYKLI  396 (700)
Q Consensus       336 QH~~~~~~~~~~------------~~i~v~lLtg~~~~~er~~i~~~i~~G~~~iiIGT----HAL~q~---~v~F~~Lg  396 (700)
                      ..+.++..-+..            .+|+|+.-||.|+.++|++...    ..++|+|-|    |.|+..   .-.|++|-
T Consensus        99 D~~r~L~~pl~~i~~~~~~~g~~~~~i~v~vr~GDT~~~er~r~~~----~pp~ILiTTPEsL~lll~~~~~~~~l~~l~  174 (878)
T PRK13767         99 DIHRNLEEPLEEIREIAKERGIELPEIRHAVRTGDTSSYEKQKMLR----KPPHILITTPETLAILLNSPKFREKLRTVK  174 (878)
T ss_pred             HHHHHHHHHHHHHHHHHHHCCCCCCCCEEEEECCCCCHHHHHHHHH----CCCCEEECCHHHHHHHHCCHHHHHHHCCCC
T ss_conf             9999888699999999875278877744776369999999999974----899879879899999954967999855899


Q ss_pred             EEEECCCCC-----CCHHHHHHHHHC----CCCCCCEEECHHHH-HHHHHHHHHH------CCCHHHHCCCCCCCCCCEE
Q ss_conf             788521013-----356889987402----56776101010132-2789999752------0101111023557666207
Q gi|254780945|r  397 LVIVDEQHR-----FGVQQRLKLTQK----ATAPHVLLMTATPI-PRTLVLTSLG------DIDISKITEKPAGRKPIKT  460 (700)
Q Consensus       397 LvViDEQHR-----FGV~QR~~L~~K----g~~ph~L~MtATPI-PRTLal~~yg------dldvS~i~e~P~gR~~I~T  460 (700)
                      .|||||=|-     +|+.=...|..-    +..+-.+-+|||-= |...|-.+.|      .-++.+++...  .+++.-
T Consensus       175 ~VIvDE~H~l~~~kRG~~l~l~L~RL~~~~~~~~~riglSATv~~~~~~a~~L~g~~~~g~~r~~~iv~~~~--~k~~~~  252 (878)
T PRK13767        175 WVIVDEIHSLAENKRGVHLSLSLERLEELVGGEFVRIGLSATIEPLEEVAKFLVGYNDDGEPRDCEIVDTRF--AKPIDI  252 (878)
T ss_pred             EEEECCCHHHHCCCCHHHHHHHHHHHHHHCCCCCEEEEEECCCCCHHHHHHHHCCCCCCCCCCCEEEECCCC--CCCCEE
T ss_conf             999817167524774589999999999866899879999646489999999851556679998528954687--787426


Q ss_pred             EEEEC-C-----C----HHHHHHHHHHHHCCCCEEEEEECCCCCCCCCCCCHHHHHHHHHHHHCCC-----CEECCCCCC
Q ss_conf             99970-2-----0----0268999976310387389997120122111210146666666866371-----031201469
Q gi|254780945|r  461 VIIPI-N-----R----IDEVIERLKVVLSEGKKAYWICPQIEEKKESNFRSVVERFNSLHEHFTS-----SIAIIHGRM  525 (700)
Q Consensus       461 ~~~~~-~-----~----~~~~~~~i~~~l~~g~q~y~VcPlIeese~~~~~~~~~~~~~l~~~~~~-----~v~~lHGkm  525 (700)
                      .++.. .     .    -..+++.+.+.++++..+-+-|-        .-..+|..+..|++.+++     +|++-||-|
T Consensus       253 ~~~~p~~~~~~~~~~~~~~~~~~~l~~~i~~~~~tLvF~N--------tR~~aE~~~~~L~~~~~~~~~~~~i~~HHgSl  324 (878)
T PRK13767        253 KVLCPVDDLIHTPAEEISEALYETLDELIQEHRTTLIFTN--------TRSGAERVVYKLRKRYPEEYDEDNIGAHHSSL  324 (878)
T ss_pred             EEECCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCEEEEEC--------CHHHHHHHHHHHHHHHHHCCCCCCEEEECCCC
T ss_conf             8844562124588556899999999999983897799915--------58999999999998534306754322201778


Q ss_pred             CHHHHHHHHHHHHCCCEEEEEECHHHHCCCCCCCCCEEEEECHHHCCHHHHHHHHHCCCCC-CCCEEEEEEECC
Q ss_conf             9899999999975598699998003410468887658998585254746887730116678-983599997088
Q gi|254780945|r  526 SDIDKESVMDSFKNGTCKLLIATTVIEVGIDVVDASIIIIENAEHFGLAQLHQLRGRVGRG-EEISSCILLYHP  598 (700)
Q Consensus       526 ~~~ek~~~m~~F~~g~~~iLvaTtviEVGvdvpna~~mvI~~aerfGLsqLHQLRGRVGRg-~~~s~c~l~~~~  598 (700)
                      +.++..++-++|++|+++.+|||+-.|-|||+.+....|=.++-+ +.|-|-|==||-|.. +..|..+++..+
T Consensus       325 s~e~R~~vE~~lk~G~l~~vV~TsSLELGIDiG~Vd~Viq~gsP~-svarllQR~GRsGH~~g~~s~g~~vp~~  397 (878)
T PRK13767        325 SREVRLEVEEKLKRGELKVVVSSTSLELGIDIGYIDLVVLLGSPK-SVSRLLQRIGRAGHRLGEVSKGRIIVVD  397 (878)
T ss_pred             CHHHHHHHHHHHHCCCCCEEEEECHHHCCCCCCCCCEEEECCCCH-HHHHHHHHHCCCCCCCCCEEEEEEEECC
T ss_conf             999999999998579986899827365077777525899758961-1899999833578999980469999798


No 29 
>COG1061 SSL2 DNA or RNA helicases of superfamily II [Transcription / DNA replication, recombination, and repair]
Probab=99.85  E-value=2.5e-18  Score=163.36  Aligned_cols=294  Identities=23%  Similarity=0.309  Sum_probs=193.9

Q ss_pred             HHCCCCCCHHHHHHHHHHHHHHCCCCCCEEEEEECCCCCHHHHHHHHHHHHHHHHCCEEEEEHHHHHHHHHHHHHHHHCC
Q ss_conf             63024679889999999998410013430788621442236999999733444305458861279999999986211014
Q gi|254780945|r  267 RNIPFSPTKSQESAIKDILQDMSQKNRMLRILQGDVGSGKTLVALIAMAAAVEAGGQAVIMAPIGILAQQHYEFIKKYTQ  346 (700)
Q Consensus       267 ~~LPF~LT~~Q~~ai~eI~~Dl~~~~pM~RLLQGDVGSGKTiVA~~A~l~~~~~G~Q~alMaPTEILA~QH~~~~~~~~~  346 (700)
                      ....|+|-.-|+.|++.+.+...+  .+.-++.-=.|||||+||+.++..+-.+   +.++|||+.|+.|-++.+.+.+.
T Consensus        31 ~~~~~~lr~yQ~~al~a~~~~~~~--~~~gvivlpTGaGKT~va~~~~~~~~~~---~Lvlv~~~~L~~Qw~~~~~~~~~  105 (442)
T COG1061          31 VAFEFELRPYQEEALDALVKNRRT--ERRGVIVLPTGAGKTVVAAEAIAELKRS---TLVLVPTKELLDQWAEALKKFLL  105 (442)
T ss_pred             CCCCCCCHHHHHHHHHHHHHHCCC--CCCEEEEECCCCCHHHHHHHHHHHHCCC---EEEEECCHHHHHHHHHHHHHHCC
T ss_conf             235788859999999999962225--7867999679998899999999982698---89997829999999999997348


Q ss_pred             CCCCEEEEEECCCCHHHHHHHHHHHCCCCCEEEEEC-HHHCC----CCCCCCCCCEEEECCCCCCCHHHHHHHHHCCCCC
Q ss_conf             578658996246422566768776213475486411-12013----3455444417885210133568899874025677
Q gi|254780945|r  347 NTQIIVEIITGNMPQAHRRKALERIAHGQAHIIIGT-HALFQ----DSIQYYKLILVIVDEQHRFGVQQRLKLTQKATAP  421 (700)
Q Consensus       347 ~~~i~v~lLtg~~~~~er~~i~~~i~~G~~~iiIGT-HAL~q----~~v~F~~LgLvViDEQHRFGV~QR~~L~~Kg~~p  421 (700)
                      .. ..+..+.|..+.-+          + ..|.|+| .++..    +...-..-+|+|+||=|..+-.==..+.+--.++
T Consensus       106 ~~-~~~g~~~~~~~~~~----------~-~~i~vat~qtl~~~~~l~~~~~~~~~liI~DE~Hh~~a~~~~~~~~~~~~~  173 (442)
T COG1061         106 LN-DEIGIYGGGEKELE----------P-AKVTVATVQTLARRQLLDEFLGNEFGLIIFDEVHHLPAPSYRRILELLSAA  173 (442)
T ss_pred             CC-CCCCEECCCCCCCC----------C-CCEEEEEEHHHHHHHHHHHHCCCCCCEEEEECCCCCCCHHHHHHHHHHHCC
T ss_conf             86-76603368723357----------7-748999838976415555403566675999752457847799999975103


Q ss_pred             C-CEEECHHHHHHHHH-H--HHHHCC-----CHHHHCCCCCCCC-CCEEEEEEC--C-CHH-------------------
Q ss_conf             6-10101013227899-9--975201-----0111102355766-620799970--2-002-------------------
Q gi|254780945|r  422 H-VLLMTATPIPRTLV-L--TSLGDI-----DISKITEKPAGRK-PIKTVIIPI--N-RID-------------------  469 (700)
Q Consensus       422 h-~L~MtATPIPRTLa-l--~~ygdl-----dvS~i~e~P~gR~-~I~T~~~~~--~-~~~-------------------  469 (700)
                      - +|-+||||. |+-. .  -+|.-+     +++.-+..=.|-. |..-..+..  . ...                   
T Consensus       174 ~~~LGLTATp~-R~D~~~~~~l~~~~g~~vy~~~~~~li~~g~Lap~~~~~i~~~~t~~~~~~~~~~~~~~~~~~~~~~~  252 (442)
T COG1061         174 YPRLGLTATPE-REDGGRIGDLFDLIGPIVYEVSLKELIDEGYLAPYKYVEIKVTLTEDEEREYAKESARFRELLRARGT  252 (442)
T ss_pred             CEEEEEECCCC-CCCCCCHHHHHHHCCCEEEECCHHHHHHCCCCCCEEEEEEEECCCHHHHHHCCHHHHHHHHHHHHHCC
T ss_conf             10467714872-44877524877405755673358998337875774999986236628777403155555555543100


Q ss_pred             ---------------HHHHHHHHHHC---CCCEEEEEECCCCCCCCCCCCHHHHHHHHHHHHCCC--CEECCCCCCCHHH
Q ss_conf             ---------------68999976310---387389997120122111210146666666866371--0312014699899
Q gi|254780945|r  470 ---------------EVIERLKVVLS---EGKKAYWICPQIEEKKESNFRSVVERFNSLHEHFTS--SIAIIHGRMSDID  529 (700)
Q Consensus       470 ---------------~~~~~i~~~l~---~g~q~y~VcPlIeese~~~~~~~~~~~~~l~~~~~~--~v~~lHGkm~~~e  529 (700)
                                     .-+..++..+.   +|..+-+.|..++.+            ..+.+.|..  -+..+.|+.+.+|
T Consensus       253 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lif~~~~~~a------------~~i~~~~~~~~~~~~it~~t~~~e  320 (442)
T COG1061         253 LRAENEARRIAIASERKIAAVRGLLLKHARGDKTLIFASDVEHA------------YEIAKLFLAPGIVEAITGETPKEE  320 (442)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEEEEECCHHHH------------HHHHHHHCCCCCEEEEECCCCHHH
T ss_conf             13456777776642899999999987532688669997577999------------999998626774246657899889


Q ss_pred             HHHHHHHHHCCCEEEEEECHHHHCCCCCCCCCEEEEECHHHCC-HHHHHHHHHCCCC-CCCCEEE
Q ss_conf             9999999755986999980034104688876589985852547-4688773011667-8983599
Q gi|254780945|r  530 KESVMDSFKNGTCKLLIATTVIEVGIDVVDASIIIIENAEHFG-LAQLHQLRGRVGR-GEEISSC  592 (700)
Q Consensus       530 k~~~m~~F~~g~~~iLvaTtviEVGvdvpna~~mvI~~aerfG-LsqLHQLRGRVGR-g~~~s~c  592 (700)
                      .++++++|+.|++++||++.|..-|||+|+|++.|+..+  .| -.|.-|-.||+=| ...+++|
T Consensus       321 R~~il~~fr~g~~~~lv~~~vl~EGvDiP~~~~~i~~~~--t~S~~~~~Q~lGR~LR~~~~k~~~  383 (442)
T COG1061         321 REAILERFRTGGIKVLVTVKVLDEGVDIPDADVLIILRP--TGSRRLFIQRLGRGLRPAEGKEDT  383 (442)
T ss_pred             HHHHHHHHHCCCCEEEEEEEEECCCCCCCCCCEEEEECC--CCCHHHHHHHHHHHHCCCCCCCCE
T ss_conf             999999987089529999614126657888757999779--987999999961663478899965


No 30 
>COG1203 CRISPR-associated helicase Cas3 [Defense mechanisms]
Probab=99.83  E-value=1.8e-17  Score=156.55  Aligned_cols=324  Identities=23%  Similarity=0.266  Sum_probs=219.1

Q ss_pred             HHHHHHHHHCCCCCCHHHHHHHHHHHHHHCCCCCCEEEEEECCCCCHHHHHHHHHHHHHHH----HCCEEEEEHHHHHHH
Q ss_conf             7899998630246798899999999984100134307886214422369999997334443----054588612799999
Q gi|254780945|r  260 KIAQKILRNIPFSPTKSQESAIKDILQDMSQKNRMLRILQGDVGSGKTLVALIAMAAAVEA----GGQAVIMAPIGILAQ  335 (700)
Q Consensus       260 ~~~~~f~~~LPF~LT~~Q~~ai~eI~~Dl~~~~pM~RLLQGDVGSGKTiVA~~A~l~~~~~----G~Q~alMaPTEILA~  335 (700)
                      ...+.+.+..+......|..+++++..-...+.  .-.|+.-.|+|||.+++.-++....+    .-.+-..-|+-.+.+
T Consensus       183 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~vl~aPTG~GKT~asl~~a~~~~~~~~~~~~r~i~vlP~~t~ie  260 (733)
T COG1203         183 ARINKFKSFIEHEGYELQEKALELILRLEKRSL--LVVLEAPTGYGKTEASLILALALLDEKIKLKSRVIYVLPFRTIIE  260 (733)
T ss_pred             HHHHHHHCCCCCCHHHHHHHHHHHHHHCCCCCC--EEEEEECCCCCHHHHHHHHHHHHHHCCCCCCCEEEEECCHHHHHH
T ss_conf             776543311455113556799999873225575--189991688871999999999975311354562899655899999


Q ss_pred             HHHHHHHHHCCCCCCEEEEEECCCCHHH-HHH-----HH----HHHCC-CCCEEEEECHHHCC--C-CCCCC-----CCC
Q ss_conf             9998621101457865899624642256-676-----87----76213-47548641112013--3-45544-----441
Q gi|254780945|r  336 QHYEFIKKYTQNTQIIVEIITGNMPQAH-RRK-----AL----ERIAH-GQAHIIIGTHALFQ--D-SIQYY-----KLI  396 (700)
Q Consensus       336 QH~~~~~~~~~~~~i~v~lLtg~~~~~e-r~~-----i~----~~i~~-G~~~iiIGTHAL~q--~-~v~F~-----~Lg  396 (700)
                      |-|+.+++++...++....+.|+....- ...     ..    ..-+. .-.-+++.|+-.+-  - ...|.     -.+
T Consensus       261 ~~~~r~~~~~~~~~~~~~~~h~~~~~~~~~~~~~~~~~~~~~~ds~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~S  340 (733)
T COG1203         261 DMYRRAKEIFGLFSVIGKSLHSSSKEPLLLEPDQDILLTLTTNDSYKKLLLALIVVTPIQILIFSVKGFKFEFLALLLTS  340 (733)
T ss_pred             HHHHHHHHHHCCCCCCCCCCCCCCHHHHHHCCCCCCCEEEEECCCCCCCCCCCEEECHHHHHHHHHCCCCCHHHHHHHHC
T ss_conf             99999987512355433100131025565170100225888124223620452220699985574046672577887646


Q ss_pred             EEEECCCCCCCHH--HHHHH----HHCCCCCCCEEECHHHHHHHHH---HHHHHCC-CHHHH-CCCCCCCCCCEEEEEEC
Q ss_conf             7885210133568--89987----4025677610101013227899---9975201-01111-02355766620799970
Q gi|254780945|r  397 LVIVDEQHRFGVQ--QRLKL----TQKATAPHVLLMTATPIPRTLV---LTSLGDI-DISKI-TEKPAGRKPIKTVIIPI  465 (700)
Q Consensus       397 LvViDEQHRFGV~--QR~~L----~~Kg~~ph~L~MtATPIPRTLa---l~~ygdl-dvS~i-~e~P~gR~~I~T~~~~~  465 (700)
                      ++|.||=|-+.=+  =+..+    ..+-...-+++||||+ |-.+-   ...++.- .++.. ...|....+........
T Consensus       341 ~vIlDE~h~~~~~~~~~~l~~~i~~l~~~g~~ill~SATl-P~~~~~~l~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~  419 (733)
T COG1203         341 LVILDEVHLYADETMLAALLALLEALAEAGVPVLLMSATL-PPFLKEKLKKALGKGREVVENAKFCPKEDEPGLKRKERV  419 (733)
T ss_pred             CEEEECHHHCCCCCHHHHHHHHHHHHHHCCCCEEEEECCC-CHHHHHHHHHHHCCCCEECCCCCCCCCCCCCCCCEECCH
T ss_conf             7787427541654308999999999996899789992789-979999999985037612134432334554330000011


Q ss_pred             CCHH----HHHHHHHHHHCCCCEEEEEECCCCCCCCCCCCHHHHHHHHHHHHCCCCEECCCCCCCHHHHHHHHHHH----
Q ss_conf             2002----68999976310387389997120122111210146666666866371031201469989999999997----
Q gi|254780945|r  466 NRID----EVIERLKVVLSEGKKAYWICPQIEEKKESNFRSVVERFNSLHEHFTSSIAIIHGRMSDIDKESVMDSF----  537 (700)
Q Consensus       466 ~~~~----~~~~~i~~~l~~g~q~y~VcPlIeese~~~~~~~~~~~~~l~~~~~~~v~~lHGkm~~~ek~~~m~~F----  537 (700)
                      +-.+    ...+.+..++.+|.++.|||-.|        ..|.+.|+.|++.-+ .+.++|+||....+++.++..    
T Consensus       420 ~~~~~~~~~~~~~~~~~~~~~~kvlvI~NTV--------~~Aie~Y~~Lk~~~~-~v~LlHSRf~~~dR~~ke~~l~~~~  490 (733)
T COG1203         420 DVEDGPQEELIELISEEVKEGKKVLVIVNTV--------DRAIELYEKLKEKGP-KVLLLHSRFTLKDREEKERELKKLF  490 (733)
T ss_pred             HHHCCCHHHHHHHHHHHHCCCCCEEEEEECH--------HHHHHHHHHHHCCCC-CEEEEECCCCHHHHHHHHHHHHHHH
T ss_conf             1320303776655677642588289999278--------999999999855589-5799886355766999999998887


Q ss_pred             HCCCEEEEEECHHHHCCCCCCCCCEEEEECHHHCCHHHHHHHHHCCCCCC--CCEEEEEEECCC
Q ss_conf             55986999980034104688876589985852547468877301166789--835999970888
Q gi|254780945|r  538 KNGTCKLLIATTVIEVGIDVVDASIIIIENAEHFGLAQLHQLRGRVGRGE--EISSCILLYHPP  599 (700)
Q Consensus       538 ~~g~~~iLvaTtviEVGvdvpna~~mvI~~aerfGLsqLHQLRGRVGRg~--~~s~c~l~~~~~  599 (700)
                      ..++..|+|||.|||||||+- ..+|+-+-|   .+.-|=|.=|||.|-+  ..++-+.....+
T Consensus       491 ~~~~~~IvVaTQVIEagvDid-fd~mITe~a---PidSLIQR~GRv~R~g~~~~~~~~v~~~~~  550 (733)
T COG1203         491 KQNEGFIVVATQVIEAGVDID-FDVLITELA---PIDSLIQRAGRVNRHGKKENGKIYVYNDEE  550 (733)
T ss_pred             HCCCCEEEEECCEEEEEECCC-CCEEEECCC---CHHHHHHHHHHHHHCCCCCCCCEEEEECCC
T ss_conf             537862999834599886266-684663478---756799987777415666687169983466


No 31 
>COG1205 Distinct helicase family with a unique C-terminal domain including a metal-binding cysteine cluster [General function prediction only]
Probab=99.82  E-value=1.3e-16  Score=149.76  Aligned_cols=326  Identities=18%  Similarity=0.217  Sum_probs=249.6

Q ss_pred             CCCCHHHHHHHHHCCCCCCHHHHHHHHHHHHHHCCCCCCEEEEEECCCCCHHHHHHHHHHHHHHHHCCE--EEEEHHHHH
Q ss_conf             877578999986302467988999999999841001343078862144223699999973344430545--886127999
Q gi|254780945|r  256 NVEGKIAQKILRNIPFSPTKSQESAIKDILQDMSQKNRMLRILQGDVGSGKTLVALIAMAAAVEAGGQA--VIMAPIGIL  333 (700)
Q Consensus       256 ~~~~~~~~~f~~~LPF~LT~~Q~~ai~eI~~Dl~~~~pM~RLLQGDVGSGKTiVA~~A~l~~~~~G~Q~--alMaPTEIL  333 (700)
                      ..++.+...+.+.+++.|=.-|..|++-|.+.      .|-++.--.|||||.-.+++++..+..+-++  .++=||--|
T Consensus        54 ~~~~~l~~~l~~~g~~~lY~HQ~~A~~~~~~G------~~vvVtTgTgSGKTe~FllPIld~~l~~~~a~AL~lYPtnAL  127 (851)
T COG1205          54 LRDESLKSALVKAGIERLYSHQVDALRLIREG------RNVVVTTGTGSGKTESFLLPILDHLLRDPSARALLLYPTNAL  127 (851)
T ss_pred             HCCHHHHHHHHHHCCCCCCHHHHHHHHHHHCC------CCEEEECCCCCCHHHHHHHHHHHHHHCCCCCEEEEEECHHHH
T ss_conf             20037889999743442007799999999779------988997899885458989999999830866508998043776


Q ss_pred             HHHHHHHHHHHCCCCC--CEEEEEECCCCHHHHHHHHHHHCCCCCEEEEEC----HH-HC----CCCCCCCCCCEEEECC
Q ss_conf             9999986211014578--658996246422566768776213475486411----12-01----3345544441788521
Q gi|254780945|r  334 AQQHYEFIKKYTQNTQ--IIVEIITGNMPQAHRRKALERIAHGQAHIIIGT----HA-LF----QDSIQYYKLILVIVDE  402 (700)
Q Consensus       334 A~QH~~~~~~~~~~~~--i~v~lLtg~~~~~er~~i~~~i~~G~~~iiIGT----HA-L~----q~~v~F~~LgLvViDE  402 (700)
                      |+-..+.|+++...++  +.+...||.++..+|+.+++    +.++|++-+    |- |+    +....|++|-++|+||
T Consensus       128 a~DQ~~rl~~~~~~~~~~v~~~~y~Gdt~~~~r~~~~~----~pp~IllTNpdMLh~~llr~~~~~~~~~~~Lk~lVvDE  203 (851)
T COG1205         128 ANDQAERLRELISDLPGKVTFGRYTGDTPPEERRAIIR----NPPDILLTNPDMLHYLLLRNHDAWLWLLRNLKYLVVDE  203 (851)
T ss_pred             HHHHHHHHHHHHHHCCCCEEEEEECCCCCHHHHHHHHH----CCCCEEEECHHHHHHHHHCCCCCHHHHHHCCCEEEEEC
T ss_conf             76699999999984787513544348896788899873----89978983889998986368822788873275899844


Q ss_pred             CC----CCCHHH-----HHHHHH--CCCCCCCEEECHHH-HHHHHHHHHHHCCCHHHHCCCCCCCCCCEEEEEEC-----
Q ss_conf             01----335688-----998740--25677610101013-22789999752010111102355766620799970-----
Q gi|254780945|r  403 QH----RFGVQQ-----RLKLTQ--KATAPHVLLMTATP-IPRTLVLTSLGDIDISKITEKPAGRKPIKTVIIPI-----  465 (700)
Q Consensus       403 QH----RFGV~Q-----R~~L~~--Kg~~ph~L~MtATP-IPRTLal~~ygdldvS~i~e~P~gR~~I~T~~~~~-----  465 (700)
                      =|    .||-+=     |....-  -|.+|.++.+|||= =|--.+..++|..-...+++-...+-++...+...     
T Consensus       204 lHtYrGv~GS~vA~llRRL~~~~~~~~~~~q~i~~SAT~~np~e~~~~l~~~~f~~~v~~~g~~~~~~~~~~~~p~~~~~  283 (851)
T COG1205         204 LHTYRGVQGSEVALLLRRLLRRLRRYGSPLQIICTSATLANPGEFAEELFGRDFEVPVDEDGSPRGLRYFVRREPPIREL  283 (851)
T ss_pred             CEECCCCHHHHHHHHHHHHHHHHHCCCCCCEEEEEECCCCCHHHHHHHHCCCCCEEECCCCCCCCCCEEEEEECCCCHHH
T ss_conf             41215603788999999999997245899628998312468288999862872146314788887874899856851133


Q ss_pred             ------CCHHHHHHHHHHHHCCCCEEEEEECCCCCCCCCCCCHHHHHHHHHHH-------HCCCCEECCCCCCCHHHHHH
Q ss_conf             ------20026899997631038738999712012211121014666666686-------63710312014699899999
Q gi|254780945|r  466 ------NRIDEVIERLKVVLSEGKKAYWICPQIEEKKESNFRSVVERFNSLHE-------HFTSSIAIIHGRMSDIDKES  532 (700)
Q Consensus       466 ------~~~~~~~~~i~~~l~~g~q~y~VcPlIeese~~~~~~~~~~~~~l~~-------~~~~~v~~lHGkm~~~ek~~  532 (700)
                            +....+-.++...+.+|-|.-|-|--    .    +-++..+....+       .+...|..-||-|..+|...
T Consensus       284 ~~~~r~s~~~~~~~~~~~~~~~~~~tL~F~~s----r----~~~e~~~~~~~~~~~~~~~~l~~~v~~~~~~~~~~er~~  355 (851)
T COG1205         284 AESIRRSALAELATLAALLVRNGIQTLVFFRS----R----KQVELLYLSPRRRLVREGGKLLDAVSTYRAGLHREERRR  355 (851)
T ss_pred             HHHCCCCHHHHHHHHHHHHHHCCCEEEEEEEH----H----HHHHHHHHHHHHHHHHCCCCHHHHEEECCCCCCHHHHHH
T ss_conf             22112345779999999998769659999835----7----567887541578875406010331342336699999999


Q ss_pred             HHHHHHCCCEEEEEECHHHHCCCCCCCCCEEEEECHHHCCHHHHHHHHHCCCCCCCCEEEEEEECCC
Q ss_conf             9999755986999980034104688876589985852547468877301166789835999970888
Q gi|254780945|r  533 VMDSFKNGTCKLLIATTVIEVGIDVVDASIIIIENAEHFGLAQLHQLRGRVGRGEEISSCILLYHPP  599 (700)
Q Consensus       533 ~m~~F~~g~~~iLvaTtviEVGvdvpna~~mvI~~aerfGLsqLHQLRGRVGRg~~~s~c~l~~~~~  599 (700)
                      +-.+|++|++..++||.-.|+|||+-....+|...==--+.+.+.|-.||.||-...+.-+.+....
T Consensus       356 ie~~~~~g~~~~~~st~AlelgidiG~ldavi~~g~P~~s~~~~~Q~~GRaGR~~~~~l~~~v~~~~  422 (851)
T COG1205         356 IEAEFKEGELLGVIATNALELGIDIGSLDAVIAYGYPGVSVLSFRQRAGRAGRRGQESLVLVVLRSD  422 (851)
T ss_pred             HHHHHHCCCCCEEEECHHHCCCEEECCEEEEEECCCCCCHHHHHHHHHCCCCCCCCCCEEEEEECCC
T ss_conf             9999746884178612101226567021145304889702888988611035887875379983788


No 32 
>KOG0354 consensus
Probab=99.80  E-value=1.5e-17  Score=157.15  Aligned_cols=329  Identities=21%  Similarity=0.325  Sum_probs=210.2

Q ss_pred             HHHHHCCCCCCHHHHHHHHHHHHHHCCCCCCEEEEEECCCCCHHHHHHHHHHHHHHH--HCCEEEEEHHHHHHHHHHHHH
Q ss_conf             998630246798899999999984100134307886214422369999997334443--054588612799999999862
Q gi|254780945|r  264 KILRNIPFSPTKSQESAIKDILQDMSQKNRMLRILQGDVGSGKTLVALIAMAAAVEA--GGQAVIMAPIGILAQQHYEFI  341 (700)
Q Consensus       264 ~f~~~LPF~LT~~Q~~ai~eI~~Dl~~~~pM~RLLQGDVGSGKTiVA~~A~l~~~~~--G~Q~alMaPTEILA~QH~~~~  341 (700)
                      .+.=-=+|+|-+-|...+.   ..|.+    |-|+---.|||||.||+..|+.-.+.  ...++|||||--|-.|+...|
T Consensus        54 ~~~~p~~~~lR~YQ~eivq---~ALgk----Ntii~lPTG~GKTfIAa~Vm~nh~rw~p~~KiVF~aP~~pLv~QQ~a~~  126 (746)
T KOG0354          54 RWIYPTNLELRNYQEELVQ---PALGK----NTIIALPTGSGKTFIAAVIMKNHFEWRPKGKVVFLAPTRPLVNQQIACF  126 (746)
T ss_pred             CCCCCCCCCCCHHHHHHHH---HHHCC----CEEEEEECCCCCCCHHHHHHHHHHHCCCCCEEEEEECCCHHHHHHHHHH
T ss_conf             4104676656078999867---86268----7699953599861047999999972377643899607711788889887


Q ss_pred             HHHCCCCCCEEEEEECCCCHHHHHHHHHHHCCCCCEEEEECHHHCCCCC------CCCCCCEEEECCCCCC------CHH
Q ss_conf             1101457865899624642256676877621347548641112013345------5444417885210133------568
Q gi|254780945|r  342 KKYTQNTQIIVEIITGNMPQAHRRKALERIAHGQAHIIIGTHALFQDSI------QYYKLILVIVDEQHRF------GVQ  409 (700)
Q Consensus       342 ~~~~~~~~i~v~lLtg~~~~~er~~i~~~i~~G~~~iiIGTHAL~q~~v------~F~~LgLvViDEQHRF------GV~  409 (700)
                      +.++.+.. ..+.++|-.+...|..++.     ..+++|-|--+++.++      .|+..-++||||=||=      -+-
T Consensus       127 ~~~~~~~~-~T~~l~~~~~~~~r~~i~~-----s~~vff~TpQil~ndL~~~~~~~ls~fs~iv~DE~Hra~kn~~Y~~V  200 (746)
T KOG0354         127 SIYLIPYS-VTGQLGDTVPRSNRGEIVA-----SKRVFFRTPQILENDLKSGLHDELSDFSLIVFDECHRTSKNHPYNNI  200 (746)
T ss_pred             HHCCCCCC-CEEECCCCCCCCCHHHHHC-----CCCEEEECHHHHHHHCCCCCCCCCCEEEEEEECCCCCCCCCCCHHHH
T ss_conf             62067601-0455057568876245310-----26358967276343325433454551799997222445556617999


Q ss_pred             HHHHHHHCCCCCCCEEECHHHHHHHHHHH-----HHHCCCHHHHCCC----CCCCCCCEEEEEE----CCC----HHHHH
Q ss_conf             89987402567761010101322789999-----7520101111023----5576662079997----020----02689
Q gi|254780945|r  410 QRLKLTQKATAPHVLLMTATPIPRTLVLT-----SLGDIDISKITEK----PAGRKPIKTVIIP----INR----IDEVI  472 (700)
Q Consensus       410 QR~~L~~Kg~~ph~L~MtATPIPRTLal~-----~ygdldvS~i~e~----P~gR~~I~T~~~~----~~~----~~~~~  472 (700)
                      =|.-|..|...+-+|-+||||=--+.++-     ++..||+..+...    +.- +.+....+.    ...    ...++
T Consensus       201 mr~~l~~k~~~~qILgLTASpG~~~~~v~~~I~~L~asldvr~~ssi~~~y~~l-r~~~~i~v~~~~~~~~~~~~f~~~i  279 (746)
T KOG0354         201 MREYLDLKNQGNQILGLTASPGSKLEQVQNVIDNLCASLDVRTESSIKSNYEEL-REHVQIPVDLSLCERDIEDPFGMII  279 (746)
T ss_pred             HHHHHHHHHCCCCEEEEECCCCCCHHHHHHHHHHHHEECCCCHHHHHHHHHHHH-HCCCCCCCCHHHHHHHHHHHHHHHH
T ss_conf             999998651466179985588845899999998520332555044565418987-2467524758876411343699999


Q ss_pred             HHHHHHHC--------CCCEEE--EEE-------CCCCCCCC--------------------------------------
Q ss_conf             99976310--------387389--997-------12012211--------------------------------------
Q gi|254780945|r  473 ERLKVVLS--------EGKKAY--WIC-------PQIEEKKE--------------------------------------  497 (700)
Q Consensus       473 ~~i~~~l~--------~g~q~y--~Vc-------PlIeese~--------------------------------------  497 (700)
                      +.+-..+.        ...+.|  ||.       |-..+.++                                      
T Consensus       280 ~p~l~~l~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~q~~~f~~~~~~~~~~~ll~~~gir~~~~l~~~~~f~~e~~  359 (746)
T KOG0354         280 EPLLQQLQEEGLIEISDKSTSYEQWVVQAEKAAAPNGPENQRNCFYALHLRKYNLALLISDGIRFVDALDYLEDFYEEVA  359 (746)
T ss_pred             HHHHHHHHHCCCCCCCCCCCCCCCHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHCCCCC
T ss_conf             99999998638541024333444404330022236887432036789999987888876323403777765554300000


Q ss_pred             -------------------------------------C-----------------------C-CCHHHHHHHHHHHHC-C
Q ss_conf             -------------------------------------1-----------------------2-101466666668663-7
Q gi|254780945|r  498 -------------------------------------S-----------------------N-FRSVVERFNSLHEHF-T  515 (700)
Q Consensus       498 -------------------------------------~-----------------------~-~~~~~~~~~~l~~~~-~  515 (700)
                                                           +                       + -.+|......|.+.. +
T Consensus       360 ~~k~~~~~~e~~~~~~~~~~m~~~~~l~~~~~~~npkle~l~~~l~e~f~~~~dsR~IIFve~R~sa~~l~~~l~~~~~~  439 (746)
T KOG0354         360 LKKYLKLELEARLIRNFTENMNELEHLSLDPPKENPKLEKLVEILVEQFEQNPDSRTIIFVETRESALALKKWLLQLHEL  439 (746)
T ss_pred             HHHHHHHHHCCHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHCCCCCCEEEEEEHHHHHHHHHHHHHHHHHC
T ss_conf             46788987422106778898876443202787668469999999999860598850799973288999999999754013


Q ss_pred             C-C----EECCCC----CCCHHHHHHHHHHHHCCCEEEEEECHHHHCCCCCCCCCEEEEECHHHCCHHHHHHHHHCCCCC
Q ss_conf             1-0----312014----699899999999975598699998003410468887658998585254746887730116678
Q gi|254780945|r  516 S-S----IAIIHG----RMSDIDKESVMDSFKNGTCKLLIATTVIEVGIDVVDASIIIIENAEHFGLAQLHQLRGRVGRG  586 (700)
Q Consensus       516 ~-~----v~~lHG----km~~~ek~~~m~~F~~g~~~iLvaTtviEVGvdvpna~~mvI~~aerfGLsqLHQLRGRVGRg  586 (700)
                      . +    ||--+|    .|+..+..++|++|++|++.+||||+|-|=|+|||..+++|-+|+--= --+.-|=||| || 
T Consensus       440 ~ir~~~fiGq~~s~~~~gmtqk~Q~evl~~Fr~G~~NvLVATSV~EEGLDI~ec~lVIcYd~~sn-pIrmIQrrGR-gR-  516 (746)
T KOG0354         440 GIKAEIFIGQGKSTQSTGMTQKEQKEVLDKFRDGEINVLVATSVAEEGLDIGECNLVICYDYSSN-PIRMVQRRGR-GR-  516 (746)
T ss_pred             CCCCCEEEECCCCCCCCCCCHHHHHHHHHHHHCCCCCEEEEECCHHCCCCCCCCCEEEEECCCCC-HHHHHHHHCC-CC-
T ss_conf             54402156035445444457899999999985798027998101004677421128999657766-8899998631-01-


Q ss_pred             CCCEEEEEEECCCCCHHHHHHHHH
Q ss_conf             983599997088899879999999
Q gi|254780945|r  587 EEISSCILLYHPPLSKNSYTRLSV  610 (700)
Q Consensus       587 ~~~s~c~l~~~~~~~~~~~~Rl~~  610 (700)
                      .+.|+|+|++. .....-.+|-+.
T Consensus       517 a~ns~~vll~t-~~~~~~~E~~~~  539 (746)
T KOG0354         517 ARNSKCVLLTT-GSEVIEFERNNL  539 (746)
T ss_pred             CCCCEEEEEEC-CHHHHHHHHHHH
T ss_conf             01876999972-516889988887


No 33 
>KOG0952 consensus
Probab=99.78  E-value=7.4e-16  Score=143.96  Aligned_cols=316  Identities=24%  Similarity=0.358  Sum_probs=223.0

Q ss_pred             HHCCCC-CCHHHHHHHHHHHHHHCCCCCCEEEEEECCCCCHHHHHHHHHHHHHH----------HHCCEEEEEHHHHHHH
Q ss_conf             630246-79889999999998410013430788621442236999999733444----------3054588612799999
Q gi|254780945|r  267 RNIPFS-PTKSQESAIKDILQDMSQKNRMLRILQGDVGSGKTLVALIAMAAAVE----------AGGQAVIMAPIGILAQ  335 (700)
Q Consensus       267 ~~LPF~-LT~~Q~~ai~eI~~Dl~~~~pM~RLLQGDVGSGKTiVA~~A~l~~~~----------~G~Q~alMaPTEILA~  335 (700)
                      .-++|+ |..=|..|..-+..   ++.-|  |+..-.|||||.||+++++..+.          +++..++.||+--||.
T Consensus       104 ~~f~f~~fN~iQS~vFp~aY~---SneNM--LIcAPTGsGKT~la~L~ILr~ik~~~~~~~i~k~~fKiVYIaPmKALa~  178 (1230)
T KOG0952         104 GFFSFEEFNRIQSEVFPVAYK---SNENM--LICAPTGSGKTVLAELCILRTIKEHEEQGDIAKDDFKIVYIAPMKALAA  178 (1230)
T ss_pred             HCCCHHHHHHHHHHHHHHHHC---CCCCE--EEECCCCCCCHHHHHHHHHHHHHHHCCCCCCCCCCCEEEEEECHHHHHH
T ss_conf             006688887778774146514---78877--9977789971678999999999850145543468713999925688999


Q ss_pred             HHHHHHHHHCCCCCCEEEEEECCCCHHHHHHHHHHHCCCCCEEEEECHHHC----C----CCCCCCCCCEEEECCCCCCC
Q ss_conf             999862110145786589962464225667687762134754864111201----3----34554444178852101335
Q gi|254780945|r  336 QHYEFIKKYTQNTQIIVEIITGNMPQAHRRKALERIAHGQAHIIIGTHALF----Q----DSIQYYKLILVIVDEQHRFG  407 (700)
Q Consensus       336 QH~~~~~~~~~~~~i~v~lLtg~~~~~er~~i~~~i~~G~~~iiIGTHAL~----q----~~v~F~~LgLvViDEQHRFG  407 (700)
                      --+++|.+-|.++|++|.-|||.+...+-+ +.      ..+|||-|--=+    -    +..-|...+||||||=|=--
T Consensus       179 Em~~~~~kkl~~~gi~v~ELTGD~ql~~te-i~------~tqiiVTTPEKwDvvTRk~~~d~~l~~~V~LviIDEVHlLh  251 (1230)
T KOG0952         179 EMVDKFSKKLAPLGISVRELTGDTQLTKTE-IA------DTQIIVTTPEKWDVVTRKSVGDSALFSLVRLVIIDEVHLLH  251 (1230)
T ss_pred             HHHHHHHHHCCCCCCEEEEECCCCHHHHHH-HH------HCCEEEECCCCEEEEEEEECCCHHHHHHEEEEEEEEEHHHC
T ss_conf             999998664242462588841754566778-77------43779706340004665412626555542048853001215


Q ss_pred             -----HHH----H-HHHHHCC-CCCCCEEECHHHHHHHHHHHHHHCCC-----HHH-HCCCCCCCCCCEEEEEECCC---
Q ss_conf             -----688----9-9874025-67761010101322789999752010-----111-10235576662079997020---
Q gi|254780945|r  408 -----VQQ----R-LKLTQKA-TAPHVLLMTATPIPRTLVLTSLGDID-----ISK-ITEKPAGRKPIKTVIIPINR---  467 (700)
Q Consensus       408 -----V~Q----R-~~L~~Kg-~~ph~L~MtATPIPRTLal~~ygdld-----vS~-i~e~P~gR~~I~T~~~~~~~---  467 (700)
                           |--    | ..+.+-+ ...-++-.||| +|--+-++.|=-..     .|. ..-.|   .|.+..+++.+.   
T Consensus       252 d~RGpvlEtiVaRtlr~vessqs~IRivgLSAT-lPN~eDvA~fL~vn~~~glfsFd~~yRP---vpL~~~~iG~k~~~~  327 (1230)
T KOG0952         252 DDRGPVLETIVARTLRLVESSQSMIRIVGLSAT-LPNYEDVARFLRVNPYAGLFSFDQRYRP---VPLTQGFIGIKGKKN  327 (1230)
T ss_pred             CCCCCHHHHHHHHHHHHHHHHHHHEEEEEEECC-CCCHHHHHHHHCCCCCCCEEEECCCCCC---CCEEEEEEEEECCCC
T ss_conf             766406999999999998854200578886245-7877999998667875662652023203---431116874212442


Q ss_pred             ------HHH-HHHHHHHHHCCCCEEEEEECCCCCCC--------------CCCCCHHHHHHHHHHHHCCCCEECCCCCCC
Q ss_conf             ------026-89999763103873899971201221--------------112101466666668663710312014699
Q gi|254780945|r  468 ------IDE-VIERLKVVLSEGKKAYWICPQIEEKK--------------ESNFRSVVERFNSLHEHFTSSIAIIHGRMS  526 (700)
Q Consensus       468 ------~~~-~~~~i~~~l~~g~q~y~VcPlIeese--------------~~~~~~~~~~~~~l~~~~~~~v~~lHGkm~  526 (700)
                            +++ .|+.+.+-+++|+||.+.|+.=.+.-              ..++-.-..+-+.|++.|...+|+=|.-|.
T Consensus       328 ~~~~~~~d~~~~~kv~e~~~~g~qVlvFvhsR~~Ti~tA~~l~~~a~~~g~~~~f~~~~~~k~l~elf~~g~~iHhAGm~  407 (1230)
T KOG0952         328 RQQKKNIDEVCYDKVVEFLQEGHQVLVFVHSRNETIRTAKKLRERAETNGEKDLFLPSPRNKQLKELFQQGMGIHHAGML  407 (1230)
T ss_pred             HHHHHHHHHHHHHHHHHHHHCCCEEEEEEECCHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCC
T ss_conf             00246677789999999997498599999657489999999999988628656567883667899998740102025643


Q ss_pred             HHHHHHHHHHHHCCCEEEEEECHHHHCCCCCCCCCEEE----EECHHH-----CCHHHHHHHHHCCCCC--CCCEEEEEE
Q ss_conf             89999999997559869999800341046888765899----858525-----4746887730116678--983599997
Q gi|254780945|r  527 DIDKESVMDSFKNGTCKLLIATTVIEVGIDVVDASIII----IENAEH-----FGLAQLHQLRGRVGRG--EEISSCILL  595 (700)
Q Consensus       527 ~~ek~~~m~~F~~g~~~iLvaTtviEVGvdvpna~~mv----I~~aer-----fGLsqLHQLRGRVGRg--~~~s~c~l~  595 (700)
                      -.++.-+=+-|..|-+.||+||.-.-+||+.|.--++|    +++|..     .|..-.-|+=||-||-  +..|..+++
T Consensus       408 r~DR~l~E~~F~~G~i~vL~cTaTLAwGVNLPA~aViIKGT~~ydsskg~f~dlgilDVlQifGRAGRPqFd~~G~giIi  487 (1230)
T KOG0952         408 RSDRQLVEKEFKEGHIKVLCCTATLAWGVNLPAYAVIIKGTQVYDSSKGSFVDLGILDVLQIFGRAGRPQFDSSGEGIII  487 (1230)
T ss_pred             HHHHHHHHHHHHCCCCEEEEECCEEEECCCCCCEEEEECCCCCCCCCCCCEEEEHHHHHHHHHHCCCCCCCCCCCEEEEE
T ss_conf             14689999998559822899612133125776418986487411356684354028888998720689987777628999


Q ss_pred             ECC
Q ss_conf             088
Q gi|254780945|r  596 YHP  598 (700)
Q Consensus       596 ~~~  598 (700)
                      +..
T Consensus       488 Tt~  490 (1230)
T KOG0952         488 TTR  490 (1230)
T ss_pred             ECC
T ss_conf             665


No 34 
>TIGR03158 cas3_cyano CRISPR-associated helicase, Cyano-type. subtype of CRISPR/Cas locus, found in several species of Cyanobacteria and several archaeal species. It contains helicase motifs and appears to represent the Cas3 protein of the Cyano subtype of CRISPR/Cas system.
Probab=99.78  E-value=8.2e-17  Score=151.44  Aligned_cols=283  Identities=20%  Similarity=0.302  Sum_probs=174.4

Q ss_pred             HHHHHHHHHHHHCCCCCCEEEEEECCCCCHHHHHHHHHHHHHHHHCCEEEEEHHHHHHHHHHHHHHHHCCCCC----CEE
Q ss_conf             9999999998410013430788621442236999999733444305458861279999999986211014578----658
Q gi|254780945|r  277 QESAIKDILQDMSQKNRMLRILQGDVGSGKTLVALIAMAAAVEAGGQAVIMAPIGILAQQHYEFIKKYTQNTQ----IIV  352 (700)
Q Consensus       277 Q~~ai~eI~~Dl~~~~pM~RLLQGDVGSGKTiVA~~A~l~~~~~G~Q~alMaPTEILA~QH~~~~~~~~~~~~----i~v  352 (700)
                      |-.+++.|.+-   +.+ --++.--.|||||.-|++.++   .++..+.+..||--||++.+++++++++.++    +++
T Consensus         2 q~~~~~~~~~~---~~~-~ivitAPTgsGKT~Aa~lp~l---~~~~~~lyi~P~kAL~~Dq~~~l~~~~~~~~~~~~~~~   74 (357)
T TIGR03158         2 QVATFEALQSK---DAD-IIFNTAPTGAGKTLAWLTPLL---HGENDTIALYPTNALIEDQTEAIKEFVDVFKPERDVNL   74 (357)
T ss_pred             HHHHHHHHHCC---CCC-EEEEECCCCCCHHHHHHHHHH---HCCCCEEEECCHHHHHHHHHHHHHHHHHHHCCCCCCCE
T ss_conf             68999999768---998-699989998569999999997---38987999777899999999999999987442346440


Q ss_pred             EEEECCCCH-----------HHHHHH-----HHHHCCCCCEEEEEC----HHHCCC---------CCCCCCCCEEEECCC
Q ss_conf             996246422-----------566768-----776213475486411----120133---------455444417885210
Q gi|254780945|r  353 EIITGNMPQ-----------AHRRKA-----LERIAHGQAHIIIGT----HALFQD---------SIQYYKLILVIVDEQ  403 (700)
Q Consensus       353 ~lLtg~~~~-----------~er~~i-----~~~i~~G~~~iiIGT----HAL~q~---------~v~F~~LgLvViDEQ  403 (700)
                      .-++|.+..           ..+.+.     ...+.....+|++-|    |-++..         .--|.+|.+|||||=
T Consensus        75 ~~~~~~~~~~~~~~~~d~~~~~~g~~~~~~~r~~~~~~~p~ILlTtPd~l~~~l~~~~~~~~~~~~~~~~~l~~VViDEi  154 (357)
T TIGR03158        75 LHVSKATLKDIKEYANDKVGSSKGEKLYNLLRNPIGTSTPIILLTNPDIFVYLTRFAYIDRGDIAAGFYTKFSTVIFDEF  154 (357)
T ss_pred             EECCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCCEEEEECHHHHHHHHHHHCCCCCHHHHHHHHCCCEEEEEEE
T ss_conf             21146432334446555534344541025665430258990999288999999762013651039999851674775620


Q ss_pred             CCCCHHHHHH----------HHHCCCCCCCEEECHHHHHHHHH-HHHHHC--CCHHHHC---------------CCCCCC
Q ss_conf             1335688998----------74025677610101013227899-997520--1011110---------------235576
Q gi|254780945|r  404 HRFGVQQRLK----------LTQKATAPHVLLMTATPIPRTLV-LTSLGD--IDISKIT---------------EKPAGR  455 (700)
Q Consensus       404 HRFGV~QR~~----------L~~Kg~~ph~L~MtATPIPRTLa-l~~ygd--ldvS~i~---------------e~P~gR  455 (700)
                      |-|.-.++..          ...+...+.++.|||||-|--.. +...+.  -+++.++               +.|.+.
T Consensus       155 H~y~~~~~~~~~~~l~~~~~~~~~~~~~~~i~lSAT~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  234 (357)
T TIGR03158       155 HLYDAKQLVGMLFLLAYMQLIRFFECRRKFVFLSATPDPALILRLQNAKQAGVKIAPIDGEKYQFPDNPELEADNKTQSF  234 (357)
T ss_pred             HCCCCCCHHHHHHHHHHHHHHHHCCCCCEEEEECCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
T ss_conf             00067620899999999999863368980899827998035789863234576434565444456787433345543455


Q ss_pred             C----CCEEEEEECC-----CHHHHHHHHHHHHC--CCCEEEEEECCCCCCCCCCCCHHHHHHHHHHHHC-CCCEECCCC
Q ss_conf             6----6207999702-----00268999976310--3873899971201221112101466666668663-710312014
Q gi|254780945|r  456 K----PIKTVIIPIN-----RIDEVIERLKVVLS--EGKKAYWICPQIEEKKESNFRSVVERFNSLHEHF-TSSIAIIHG  523 (700)
Q Consensus       456 ~----~I~T~~~~~~-----~~~~~~~~i~~~l~--~g~q~y~VcPlIeese~~~~~~~~~~~~~l~~~~-~~~v~~lHG  523 (700)
                      .    ||........     ...+..+.+.+.+.  .|.++-++|-.+        ..+...++.|++.. +.+++-+||
T Consensus       235 ~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~v~~~s~--------~~~~~l~~~l~~~~~~~~~~~~~~  306 (357)
T TIGR03158       235 RPVLPPVELELIPAPDFKEEELSELAEEVIERFRQLPGERGAIILDSL--------DEVNRLSDLLQQQGLGDDIGRITG  306 (357)
T ss_pred             CCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCEEEEECCH--------HHHHHHHHHHHHCCCCCHHHHHCC
T ss_conf             444675011234663044679999999999999985267179995589--------999999999986336411455425


Q ss_pred             CCCHHHHHHHHHHHHCCCEEEEEECHHHHCCCCCCCCCEEEEECHHHCCHHHHHHHHHCCC
Q ss_conf             6998999999999755986999980034104688876589985852547468877301166
Q gi|254780945|r  524 RMSDIDKESVMDSFKNGTCKLLIATTVIEVGIDVVDASIIIIENAEHFGLAQLHQLRGRVG  584 (700)
Q Consensus       524 km~~~ek~~~m~~F~~g~~~iLvaTtviEVGvdvpna~~mvI~~aerfGLsqLHQLRGRVG  584 (700)
                      -...++++      +.++.+++|||+++|+|||+ +..++|.+-   +..|.|-|==||+|
T Consensus       307 ~~~~~~re------k~~~~~~vVaTsaLElGIDi-~~d~~i~~~---~~v~sl~QR~GRaG  357 (357)
T TIGR03158       307 FAPKKDRE------RAMQFDILLGTSTVDVGVDF-KRDWLIFSA---RDAAAFWQRLGRLG  357 (357)
T ss_pred             CCHHHHHH------CCCCCCEEEECCCCEEEEEC-CCCEEEECC---CCHHHHHHCCCCCC
T ss_conf             56188985------04899999987701035611-789899589---87888997266799


No 35 
>KOG0331 consensus
Probab=99.77  E-value=5.5e-16  Score=144.98  Aligned_cols=336  Identities=22%  Similarity=0.327  Sum_probs=230.2

Q ss_pred             CCCHHHHHHHHHHHHHHCCCCCCEEEEEECCCCCHHHHHHHHHHHHHHH---------HCCEEEEEHHHHHHHHHHHHHH
Q ss_conf             6798899999999984100134307886214422369999997334443---------0545886127999999998621
Q gi|254780945|r  272 SPTKSQESAIKDILQDMSQKNRMLRILQGDVGSGKTLVALIAMAAAVEA---------GGQAVIMAPIGILAQQHYEFIK  342 (700)
Q Consensus       272 ~LT~~Q~~ai~eI~~Dl~~~~pM~RLLQGDVGSGKTiVA~~A~l~~~~~---------G~Q~alMaPTEILA~QH~~~~~  342 (700)
                      .+|.=|.+++--...    +.-|  ...-..|||||+=.++.++.-+.+         |-++.++|||-=||.|-.+.+.
T Consensus       113 ~PtpIQaq~wp~~l~----GrD~--v~iA~TGSGKTLay~lP~i~~l~~~~~~~~~~~~P~vLVL~PTRELA~QV~~~~~  186 (519)
T KOG0331         113 KPTPIQAQGWPIALS----GRDL--VGIARTGSGKTLAYLLPAIVHLNNEQGKLSRGDGPIVLVLAPTRELAVQVQAEAR  186 (519)
T ss_pred             CCCHHHHCCCCEECC----CCCE--EEEECCCCCCHHHHHHHHHHHHHHCCCCCCCCCCCEEEEECCCHHHHHHHHHHHH
T ss_conf             885344144651126----8865--7782357862055555799998700444347999869997685999999999999


Q ss_pred             HHCCCCCCEEEEEECCCCHHHHHHHHHHHCCCCCEEEEECHHHC-----CCCCCCCCCCEEEECCCCC-----CCHHHHH
Q ss_conf             10145786589962464225667687762134754864111201-----3345544441788521013-----3568899
Q gi|254780945|r  343 KYTQNTQIIVEIITGNMPQAHRRKALERIAHGQAHIIIGTHALF-----QDSIQYYKLILVIVDEQHR-----FGVQQRL  412 (700)
Q Consensus       343 ~~~~~~~i~v~lLtg~~~~~er~~i~~~i~~G~~~iiIGTHAL~-----q~~v~F~~LgLvViDEQHR-----FGV~QR~  412 (700)
                      ++-..+++++.+++|..+..   ....++..| ++|+|||---+     +..+.++++.++|.||=-|     |.= |=.
T Consensus       187 ~~~~~~~~~~~cvyGG~~~~---~Q~~~l~~g-vdiviaTPGRl~d~le~g~~~l~~v~ylVLDEADrMldmGFe~-qI~  261 (519)
T KOG0331         187 EFGKSLRLRSTCVYGGAPKG---PQLRDLERG-VDVVIATPGRLIDLLEEGSLNLSRVTYLVLDEADRMLDMGFEP-QIR  261 (519)
T ss_pred             HHCCCCCCCEEEEECCCCCC---HHHHHHHCC-CCEEEECCHHHHHHHHCCCCCCCCEEEEEECCHHHHHCCCCHH-HHH
T ss_conf             97077774079986898863---788987559-8189807717899997488564530399963477663135379-999


Q ss_pred             HHHHCCCCCC-CEEE-CHHHHHH---HHHHHHHHC-CCHHHH--CCCCCCCCCCEEEEEEC---CCHHHHHHHHHHHH-C
Q ss_conf             8740256776-1010-1013227---899997520-101111--02355766620799970---20026899997631-0
Q gi|254780945|r  413 KLTQKATAPH-VLLM-TATPIPR---TLVLTSLGD-IDISKI--TEKPAGRKPIKTVIIPI---NRIDEVIERLKVVL-S  480 (700)
Q Consensus       413 ~L~~Kg~~ph-~L~M-tATPIPR---TLal~~ygd-ldvS~i--~e~P~gR~~I~T~~~~~---~~~~~~~~~i~~~l-~  480 (700)
                      ++.++-..|+ +.+| ||| .|.   -||-.+-++ ..+.+.  +++=. +..|.-.+..-   .+..++...+.+.. .
T Consensus       262 ~Il~~i~~~~rQtlm~saT-wp~~v~~lA~~fl~~~~~i~ig~~~~~~a-~~~i~qive~~~~~~K~~~l~~lL~~~~~~  339 (519)
T KOG0331         262 KILSQIPRPDRQTLMFSAT-WPKEVRQLAEDFLNNPIQINVGNKKELKA-NHNIRQIVEVCDETAKLRKLGKLLEDISSD  339 (519)
T ss_pred             HHHHHCCCCCCCEEEEEEE-CCHHHHHHHHHHHCCCEEEEECCHHHHHH-HCCHHHHHHHCCHHHHHHHHHHHHHHHHCC
T ss_conf             9987558975227888654-64889999999845964899612145544-333146511268788988799999997356


Q ss_pred             CCCEEEEEECCCCCCCCCCCCHHHHHHHHHHHHCCCCEECCCCCCCHHHHHHHHHHHHCCCEEEEEECHHHHCCCCCCCC
Q ss_conf             38738999712012211121014666666686637103120146998999999999755986999980034104688876
Q gi|254780945|r  481 EGKKAYWICPQIEEKKESNFRSVVERFNSLHEHFTSSIAIIHGRMSDIDKESVMDSFKNGTCKLLIATTVIEVGIDVVDA  560 (700)
Q Consensus       481 ~g~q~y~VcPlIeese~~~~~~~~~~~~~l~~~~~~~v~~lHGkm~~~ek~~~m~~F~~g~~~iLvaTtviEVGvdvpna  560 (700)
                      .++++.|-|-..        ..+++....++.. +-+...+||..+..|.+.+|+.|++|+..|||||-|--=|+|||+.
T Consensus       340 ~~~KvIIFc~tk--------r~~~~l~~~l~~~-~~~a~~iHGd~sQ~eR~~~L~~FreG~~~vLVATdVAaRGLDi~dV  410 (519)
T KOG0331         340 SEGKVIIFCETK--------RTCDELARNLRRK-GWPAVAIHGDKSQSERDWVLKGFREGKSPVLVATDVAARGLDVPDV  410 (519)
T ss_pred             CCCCEEEEECCH--------HHHHHHHHHHHHC-CCCEEEECCCCCHHHHHHHHHHCCCCCCCEEEECCCCCCCCCCCCC
T ss_conf             898689996433--------6499999887751-7661550066648899999975026885469881531256887666


Q ss_pred             CEEEEECHHHCCHHHHHHHHHCCCCCCCCEEEEEEECCCCCHHHHHHHHHHHHHC---HHHHHHHHHHHHCCC
Q ss_conf             5899858525474688773011667898359999708889987999999998414---258999999852063
Q gi|254780945|r  561 SIIIIENAEHFGLAQLHQLRGRVGRGEEISSCILLYHPPLSKNSYTRLSVLKNTE---DGFLIAEEDLKQRKE  630 (700)
Q Consensus       561 ~~mvI~~aerfGLsqLHQLRGRVGRg~~~s~c~l~~~~~~~~~~~~Rl~~l~~~~---dGf~iAe~Dl~lRG~  630 (700)
                      .+.|=++--+===.=.|. =||-||.+..|..+.++.......+.+=.+++.+-+   ........+-..=|+
T Consensus       411 ~lVInydfP~~vEdYVHR-iGRTGRa~~~G~A~tfft~~~~~~a~~l~~~l~e~~q~v~~~l~~~~~~~~~~~  482 (519)
T KOG0331         411 DLVINYDFPNNVEDYVHR-IGRTGRAGKKGTAITFFTSDNAKLARELIKVLREAGQTVPPDLLEYARVSGSGG  482 (519)
T ss_pred             CEEEECCCCCCHHHHHHH-CCCCCCCCCCCEEEEEEEHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCC
T ss_conf             479967899998998865-376545788824899972788777899999999706878747888876204687


No 36 
>pfam00270 DEAD DEAD/DEAH box helicase. Members of this family include the DEAD and DEAH box helicases. Helicases are involved in unwinding nucleic acids. The DEAD box helicases are involved in various aspects of RNA metabolism, including nuclear transcription, pre mRNA splicing, ribosome biogenesis, nucleocytoplasmic transport, translation, RNA decay and organellar gene expression.
Probab=99.76  E-value=1.8e-17  Score=156.53  Aligned_cols=151  Identities=31%  Similarity=0.412  Sum_probs=121.1

Q ss_pred             CHHHHHHHHHHHHHHCCCCCCEEEEEECCCCCHHHHHHHHHHHHHH---HHCCEEEEEHHHHHHHHHHHHHHHHCCCCCC
Q ss_conf             9889999999998410013430788621442236999999733444---3054588612799999999862110145786
Q gi|254780945|r  274 TKSQESAIKDILQDMSQKNRMLRILQGDVGSGKTLVALIAMAAAVE---AGGQAVIMAPIGILAQQHYEFIKKYTQNTQI  350 (700)
Q Consensus       274 T~~Q~~ai~eI~~Dl~~~~pM~RLLQGDVGSGKTiVA~~A~l~~~~---~G~Q~alMaPTEILA~QH~~~~~~~~~~~~i  350 (700)
                      |.-|++|++.+.+      -.+-++++..|||||.+|+++++..+.   +|.++.+++||.-|++|+++.+++++...++
T Consensus         1 ~~~Q~~~i~~~~~------g~~~iv~~pTGsGKT~~~~~~~l~~~~~~~~~~~~v~l~Pt~aL~~q~~~~~~~~~~~~~~   74 (167)
T pfam00270         1 TPIQAEAIPAILE------GKDVLVQAPTGSGKTLAFLLPALQALLKNPDGPQALVLAPTRELAEQIYEELKKLGKYLGL   74 (167)
T ss_pred             CHHHHHHHHHHHC------CCCEEEECCCCCCHHHHHHHHHHHHHHHCCCCCEEEEECCHHHHHHHHHHHHHHHHHCCCC
T ss_conf             9459999999976------9978998899975899999999999874778987999906088888999886432102676


Q ss_pred             EEEEEECCCCHHHHHHHHHHHCCCCCEEEEECHH-----HCCCCCCCCCCCEEEECCCCCCCH-----HHHHHHHHCCCC
Q ss_conf             5899624642256676877621347548641112-----013345544441788521013356-----889987402567
Q gi|254780945|r  351 IVEIITGNMPQAHRRKALERIAHGQAHIIIGTHA-----LFQDSIQYYKLILVIVDEQHRFGV-----QQRLKLTQKATA  420 (700)
Q Consensus       351 ~v~lLtg~~~~~er~~i~~~i~~G~~~iiIGTHA-----L~q~~v~F~~LgLvViDEQHRFGV-----~QR~~L~~Kg~~  420 (700)
                      ++..++|..+..++...+.    ..++|+|+|+.     +....+.|++++++|+||-|+++=     .-+.-+.....+
T Consensus        75 ~~~~~~g~~~~~~~~~~~~----~~~~Ilv~Tp~~l~~~l~~~~~~~~~~~~lIvDE~H~~~~~~~g~~~~~il~~l~~~  150 (167)
T pfam00270        75 KVALLYGGDSPKEQLRKLK----KGPDILVGTPGRLLDLLERGGLLLKNLKLLVLDEAHRLLDQGFGDDLEEILRRLPPK  150 (167)
T ss_pred             CEEEECCCCCHHHHHHHHC----CCCCEEEECHHHHHHHHHHCCCCCCCEEEEEEECHHHHHCCCHHHHHHHHHHHCCCC
T ss_conf             4046417861788987640----577079947899999998033121100389988088673358299999999857999


Q ss_pred             CCCEEECHHHHHHHH
Q ss_conf             761010101322789
Q gi|254780945|r  421 PHVLLMTATPIPRTL  435 (700)
Q Consensus       421 ph~L~MtATPIPRTL  435 (700)
                      +.++.||||+ |+.+
T Consensus       151 ~q~v~~SAT~-~~~~  164 (167)
T pfam00270       151 RQILLLSATL-PRNV  164 (167)
T ss_pred             CCEEEEECCC-CHHH
T ss_conf             9789997269-9778


No 37 
>PRK05298 excinuclease ABC subunit B; Provisional
Probab=99.75  E-value=5.1e-15  Score=137.36  Aligned_cols=309  Identities=22%  Similarity=0.354  Sum_probs=216.5

Q ss_pred             HCCCCCCHHHHHHHHHHHHHHCCCCCCEEEEEECCCCCHHHHHHHHHHHHHHH-HCCEEEEEHHHHHHHHHHHHHHHHCC
Q ss_conf             30246798899999999984100134307886214422369999997334443-05458861279999999986211014
Q gi|254780945|r  268 NIPFSPTKSQESAIKDILQDMSQKNRMLRILQGDVGSGKTLVALIAMAAAVEA-GGQAVIMAPIGILAQQHYEFIKKYTQ  346 (700)
Q Consensus       268 ~LPF~LT~~Q~~ai~eI~~Dl~~~~pM~RLLQGDVGSGKTiVA~~A~l~~~~~-G~Q~alMaPTEILA~QH~~~~~~~~~  346 (700)
                      .=||+++.||-+||+++.+.+.++.+-. .|.|-.|||||-.    |++++++ +.-+.+|||.-.||-|.|..|+.+|+
T Consensus         9 ~s~~~P~GDQP~AI~~L~~gi~~g~~~Q-~LlGvTGSGKTfT----mAnvI~~~~rPtLVlahNKTLAAQLy~Efk~fFP   83 (657)
T PRK05298          9 VSPYKPAGDQPQAIAELVEGIESGEKHQ-TLLGVTGSGKTFT----MANVIARVQRPTLVLAHNKTLAAQLYGEFKEFFP   83 (657)
T ss_pred             CCCCCCCCCCHHHHHHHHHHHHCCCCEE-EEECCCCCCHHHH----HHHHHHHHCCCEEEECCCHHHHHHHHHHHHHHCC
T ss_conf             8889999987999999998997499636-9970367856689----9999998689759976658899999999997688


Q ss_pred             CCCCEEEEEECC-------------CC------------HH---------------------------------------
Q ss_conf             578658996246-------------42------------25---------------------------------------
Q gi|254780945|r  347 NTQIIVEIITGN-------------MP------------QA---------------------------------------  362 (700)
Q Consensus       347 ~~~i~v~lLtg~-------------~~------------~~---------------------------------------  362 (700)
                      +.  .|+.-.|-             .+            .+                                       
T Consensus        84 ~N--aVEYFVSYyDYYQPEAYip~tDtYIEKdssIN~eId~lR~sAT~SLl~RrDVIVVASVSCIYGLGsPe~Y~~~~l~  161 (657)
T PRK05298         84 EN--AVEYFVSYYDYYQPEAYVPSSDTYIEKDSSINEEIERLRLSATKSLLERRDVIVVASVSCIYGLGSPEEYLKMVLH  161 (657)
T ss_pred             CC--CEEEEECCCCCCCCCCCCCCCCCEEECCCHHHHHHHHHHHHHHHHHHCCCCEEEEEEHHHCCCCCCHHHHHHCEEE
T ss_conf             87--1799851445669711147888524236346699999999999988547986999736761689997999734377


Q ss_pred             -------HHHHHHHHH----------------------------------------------------------------
Q ss_conf             -------667687762----------------------------------------------------------------
Q gi|254780945|r  363 -------HRRKALERI----------------------------------------------------------------  371 (700)
Q Consensus       363 -------er~~i~~~i----------------------------------------------------------------  371 (700)
                             .|++++.++                                                                
T Consensus       162 l~~G~~i~r~~ll~~LV~~qY~RnD~~~~RG~FRVrGDvVdI~Pa~~ed~aiRIeffgDeIE~I~~~Dpltg~~i~~~~~  241 (657)
T PRK05298        162 LRVGQEIDRRELLRRLVELQYERNDIDFQRGTFRVRGDVIDIFPAEYEDRAIRIEFFGDEIERISEFDPLTGEVLGELDR  241 (657)
T ss_pred             EECCCEECHHHHHHHHHHHCCCCCCCCCCCCEEEEECCEEEEECCCCCCEEEEEEEECCCEEEEEEECCCCCCCCCCCCE
T ss_conf             75897717999999999828776765116855577366478833777761699999578062899982778835243334


Q ss_pred             ----------------------------------------------------------CCCCCEE-----------EEEC
Q ss_conf             ----------------------------------------------------------1347548-----------6411
Q gi|254780945|r  372 ----------------------------------------------------------AHGQAHI-----------IIGT  382 (700)
Q Consensus       372 ----------------------------------------------------------~~G~~~i-----------iIGT  382 (700)
                                                                                ..|-+.=           --|.
T Consensus       242 ~~IfPAshyVt~~e~l~~Ai~~I~~EL~eRl~~f~~~gKllEAqRL~qRT~yDlEMl~E~GyCsGIENYSRhl~gR~pGe  321 (657)
T PRK05298        242 VTIYPASHYVTPRERLERAIESIKEELEERLKELEKEGKLLEAQRLEQRTRYDLEMLRELGYCSGIENYSRHLSGRAPGE  321 (657)
T ss_pred             EEEECCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCCCCC
T ss_conf             99817867689979999999999999999999999767779888999998879999998287756012156506999887


Q ss_pred             --HHHCCCCCCCCCCCEEEECCCCCCCHHHH-----------HHHHHCC-------------------CCCCCEEECHHH
Q ss_conf             --12013345544441788521013356889-----------9874025-------------------677610101013
Q gi|254780945|r  383 --HALFQDSIQYYKLILVIVDEQHRFGVQQR-----------LKLTQKA-------------------TAPHVLLMTATP  430 (700)
Q Consensus       383 --HAL~q~~v~F~~LgLvViDEQHRFGV~QR-----------~~L~~Kg-------------------~~ph~L~MtATP  430 (700)
                        ..||-   -|..=-|.||||-|= -|-|=           ..|.+-|                   ..|.+++.||||
T Consensus       322 ~P~tLlD---Yfp~DfLl~iDESHv-tvPQi~gMy~GDrsRK~~LVe~GFRLPSAlDNRPL~feEFe~~~~q~iyVSATP  397 (657)
T PRK05298        322 PPPTLLD---YFPDDFLLFIDESHV-TVPQIGGMYNGDRSRKETLVEYGFRLPSALDNRPLKFEEFEAKVPQTIYVSATP  397 (657)
T ss_pred             CCCHHHH---HCCCCEEEEECCCCC-CCHHHHHHHCCCHHHHHHHHHHCCCCCCCCCCCCCCHHHHHHHCCCEEEEECCC
T ss_conf             8944887---577565999832112-408788786231577888987057787233489978899997448779995698


Q ss_pred             HHHHHHHHHHHCCCHHHHCCCCCCCC-CCEEEEEECCCHHHHHHHHHHHHCCCCEEEEEECCCCCCCCCCCCHHHHHHHH
Q ss_conf             22789999752010111102355766-62079997020026899997631038738999712012211121014666666
Q gi|254780945|r  431 IPRTLVLTSLGDIDISKITEKPAGRK-PIKTVIIPINRIDEVIERLKVVLSEGKKAYWICPQIEEKKESNFRSVVERFNS  509 (700)
Q Consensus       431 IPRTLal~~ygdldvS~i~e~P~gR~-~I~T~~~~~~~~~~~~~~i~~~l~~g~q~y~VcPlIeese~~~~~~~~~~~~~  509 (700)
                      =|--|..+  |..---+  =.|-|=. |++..--..++.+.++..|++.+++|+.+.|. .       +.-+-+++..+.
T Consensus       398 g~yEl~~s--~~vvEQi--IRPTGLlDP~ievrp~~~Qiddl~~ei~~~~~~~er~Lvt-t-------lTkkmaEdLt~y  465 (657)
T PRK05298        398 GDYELEKS--GQVVEQI--IRPTGLLDPEIEVRPTKGQVDDLLSEIRKRVAKGERVLVT-T-------LTKRMAEDLTDY  465 (657)
T ss_pred             CHHHHHHC--CCEEEEE--ECCCCCCCCCEEEECCCCCHHHHHHHHHHHHHCCCEEEEE-E-------CHHHHHHHHHHH
T ss_conf             58988736--6734577--7788787984599648787999999999996369769999-5-------459899999999


Q ss_pred             HHHHCCCCEECCCCCCCHHHHHHHHHHHHCCCEEEEEECHHHHCCCCCCCCCEEEEECHHHCCH----HHHHHHHHCCCC
Q ss_conf             6866371031201469989999999997559869999800341046888765899858525474----688773011667
Q gi|254780945|r  510 LHEHFTSSIAIIHGRMSDIDKESVMDSFKNGTCKLLIATTVIEVGIDVVDASIIIIENAEHFGL----AQLHQLRGRVGR  585 (700)
Q Consensus       510 l~~~~~~~v~~lHGkm~~~ek~~~m~~F~~g~~~iLvaTtviEVGvdvpna~~mvI~~aerfGL----sqLHQLRGRVGR  585 (700)
                      |.+. +-++..+|.-.+.-|.-+++.+++.|++|+||.-...-=|+|+|..++..|.|||.=|.    ..|-|-=||..|
T Consensus       466 l~~~-~ik~~YlHs~i~t~eR~eIl~~LR~G~~DVlVGINLLREGLDlPEVSLVaILDADKeGFLRs~~SLiQtiGRAAR  544 (657)
T PRK05298        466 LKEL-GIKVRYLHSDIDTLERVEIIRDLRLGEFDVLVGINLLREGLDIPEVSLVAILDADKEGFLRSERSLIQTIGRAAR  544 (657)
T ss_pred             HHHC-CCEEEEEECCCCHHHHHHHHHHHHCCCCCEEEEECHHHCCCCCCCEEEEEEEECCCCCCCCCCCHHHHHHHHHHH
T ss_conf             9967-980799626661889999999985888758975002204578761357988706852210352059999878862


Q ss_pred             CCCCEEEEEEECCCCCH
Q ss_conf             89835999970888998
Q gi|254780945|r  586 GEEISSCILLYHPPLSK  602 (700)
Q Consensus       586 g~~~s~c~l~~~~~~~~  602 (700)
                      + ..|.|+|.. +++++
T Consensus       545 N-~~G~vIlYA-D~iT~  559 (657)
T PRK05298        545 N-VNGKVILYA-DKITD  559 (657)
T ss_pred             C-CCCEEEEEE-CCCCH
T ss_conf             5-797499981-54509


No 38 
>COG1201 Lhr Lhr-like helicases [General function prediction only]
Probab=99.75  E-value=5.4e-15  Score=137.16  Aligned_cols=319  Identities=22%  Similarity=0.257  Sum_probs=243.6

Q ss_pred             HHHHHHHHHCCCCCCHHHHHHHHHHHHHHCCCCCCEEEEEECCCCCHHHHHHHHHHHHHHH--------HCCEEEEEHHH
Q ss_conf             7899998630246798899999999984100134307886214422369999997334443--------05458861279
Q gi|254780945|r  260 KIAQKILRNIPFSPTKSQESAIKDILQDMSQKNRMLRILQGDVGSGKTLVALIAMAAAVEA--------GGQAVIMAPIG  331 (700)
Q Consensus       260 ~~~~~f~~~LPF~LT~~Q~~ai~eI~~Dl~~~~pM~RLLQGDVGSGKTiVA~~A~l~~~~~--------G~Q~alMaPTE  331 (700)
                      ..+.++.+.-==+||.-|..|+.+|.+.-      |-|+--=.|||||.-|+++++..+-.        |-.|.+..|=-
T Consensus        10 ~~v~~~~~~~~~~~t~~Q~~a~~~i~~G~------nvLiiAPTGsGKTeAAfLpil~~l~~~~~~~~~~~i~~lYIsPLk   83 (814)
T COG1201          10 PRVREWFKRKFTSLTPPQRYAIPEIHSGE------NVLIIAPTGSGKTEAAFLPVINELLSLGKGKLEDGIYALYISPLK   83 (814)
T ss_pred             HHHHHHHHHHCCCCCHHHHHHHHHHHCCC------CEEEECCCCCCHHHHHHHHHHHHHHHCCCCCCCCCEEEEEECCHH
T ss_conf             99999999850899878999999985898------469986899973799999999999860688888856999957078


Q ss_pred             HHHHHHHHHHHHHCCCCCCEEEEEECCCCHHHHHHHHHHHCCCCCEEEEEC----HHHCCC---CCCCCCCCEEEECCCC
Q ss_conf             999999986211014578658996246422566768776213475486411----120133---4554444178852101
Q gi|254780945|r  332 ILAQQHYEFIKKYTQNTQIIVEIITGNMPQAHRRKALERIAHGQAHIIIGT----HALFQD---SIQYYKLILVIVDEQH  404 (700)
Q Consensus       332 ILA~QH~~~~~~~~~~~~i~v~lLtg~~~~~er~~i~~~i~~G~~~iiIGT----HAL~q~---~v~F~~LgLvViDEQH  404 (700)
                      -|++--..++..|...+|++|+.-||-|+.++|.....    .-++|+|-|    .+++..   .=.|.|+-.|||||=|
T Consensus        84 ALn~Di~~rL~~~~~~~G~~v~vRhGDT~~~er~r~~~----~PPdILiTTPEsL~lll~~~~~r~~l~~vr~VIVDEiH  159 (814)
T COG1201          84 ALNNDIRRRLEEPLRELGIEVAVRHGDTPQSEKQKMLK----NPPHILITTPESLAILLNSPKFRELLRDVRYVIVDEIH  159 (814)
T ss_pred             HHHHHHHHHHHHHHHHCCCCCCEECCCCCHHHHHHCCC----CCCCEEEECHHHHHHHHCCHHHHHHHCCCCEEEEEHHH
T ss_conf             88789999999999975984444228788677630469----99968995834899983688899986078099951254


Q ss_pred             CCCHHHHHHHHHCC--------CCCCCEEECHHHHHHHH-HHHHHHCCCHHHHCCCCCCCCCCEEEEEECCC-------H
Q ss_conf             33568899874025--------67761010101322789-99975201011110235576662079997020-------0
Q gi|254780945|r  405 RFGVQQRLKLTQKA--------TAPHVLLMTATPIPRTL-VLTSLGDIDISKITEKPAGRKPIKTVIIPINR-------I  468 (700)
Q Consensus       405 RFGV~QR~~L~~Kg--------~~ph~L~MtATPIPRTL-al~~ygdldvS~i~e~P~gR~~I~T~~~~~~~-------~  468 (700)
                      -+--+-|-....-+        ..+--.-.|||==|=.. |--+.|+=+...|-+.+.++++=...+.+...       .
T Consensus       160 el~~sKRG~~Lsl~LeRL~~l~~~~qRIGLSATV~~~~~varfL~g~~~~~~Iv~~~~~k~~~i~v~~p~~~~~~~~~~~  239 (814)
T COG1201         160 ALAESKRGVQLALSLERLRELAGDFQRIGLSATVGPPEEVAKFLVGFGDPCEIVDVSAAKKLEIKVISPVEDLIYDEELW  239 (814)
T ss_pred             HHHCCCCCHHHHHHHHHHHHHCCCCEEEEEHHCCCCHHHHHHHHCCCCCCEEEEECCCCCCCEEEEEECCCCCCCCCCHH
T ss_conf             54345653134332999985175537975402158889999985478984299974567753179980477500026246


Q ss_pred             HHHHHHHHHHHCCCCEEEEEECCCCCCCCCCCCHHHHHHHHHHHHCCCCEECCCCCCCHHHHHHHHHHHHCCCEEEEEEC
Q ss_conf             26899997631038738999712012211121014666666686637103120146998999999999755986999980
Q gi|254780945|r  469 DEVIERLKVVLSEGKKAYWICPQIEEKKESNFRSVVERFNSLHEHFTSSIAIIHGRMSDIDKESVMDSFKNGTCKLLIAT  548 (700)
Q Consensus       469 ~~~~~~i~~~l~~g~q~y~VcPlIeese~~~~~~~~~~~~~l~~~~~~~v~~lHGkm~~~ek~~~m~~F~~g~~~iLvaT  548 (700)
                      ..+++.|.+.+++-.-+-|...        .-..+|..+.+|++.++..|..-||-++.+++..+=++|++|+.+.+|||
T Consensus       240 ~~~~~~i~~~v~~~~ttLIF~N--------TR~~aE~l~~~L~~~~~~~i~~HHgSlSre~R~~vE~~lk~G~lravV~T  311 (814)
T COG1201         240 AALYERIAELVKKHRTTLIFTN--------TRSGAERLAFRLKKLGPDIIEVHHGSLSRELRLEVEERLKEGELKAVVAT  311 (814)
T ss_pred             HHHHHHHHHHHHHCCCEEEEEE--------CHHHHHHHHHHHHHHCCCCEEEECCCCCHHHHHHHHHHHHCCCCEEEEEC
T ss_conf             7899999999961685899972--------72789999999987268755653166657789999999866886299980


Q ss_pred             HHHHCCCCCCCCCEEEEECHHHCCHHHHHHHHHCCCCCCC-CEEEEEEEC
Q ss_conf             0341046888765899858525474688773011667898-359999708
Q gi|254780945|r  549 TVIEVGIDVVDASIIIIENAEHFGLAQLHQLRGRVGRGEE-ISSCILLYH  597 (700)
Q Consensus       549 tviEVGvdvpna~~mvI~~aerfGLsqLHQLRGRVGRg~~-~s~c~l~~~  597 (700)
                      |=.|-|||+-.....|=.++-| +.|-+-|==||.|+.-. .|--+++..
T Consensus       312 SSLELGIDiG~vdlVIq~~SP~-sV~r~lQRiGRsgHr~~~~Skg~ii~~  360 (814)
T COG1201         312 SSLELGIDIGDIDLVIQLGSPK-SVNRFLQRIGRAGHRLGEVSKGIIIAE  360 (814)
T ss_pred             CCHHHCCCCCCCEEEEEECCCH-HHHHHHHHCCCCCCCCCCCCCEEEEEC
T ss_conf             6422050247742999817938-888886850314665688642799816


No 39 
>KOG0335 consensus
Probab=99.74  E-value=8.6e-15  Score=135.59  Aligned_cols=330  Identities=20%  Similarity=0.268  Sum_probs=239.4

Q ss_pred             CCCHHHHHHHHHHHHHHCCCCCCEEEEEECCCCCHHHHHHHHHHHHHHH-------------HCCEEEEEHHHHHHHHHH
Q ss_conf             6798899999999984100134307886214422369999997334443-------------054588612799999999
Q gi|254780945|r  272 SPTKSQESAIKDILQDMSQKNRMLRILQGDVGSGKTLVALIAMAAAVEA-------------GGQAVIMAPIGILAQQHY  338 (700)
Q Consensus       272 ~LT~~Q~~ai~eI~~Dl~~~~pM~RLLQGDVGSGKTiVA~~A~l~~~~~-------------G~Q~alMaPTEILA~QH~  338 (700)
                      .+|.=|+-+|.-|..--.-      +..+-.|||||.-.++-++..+-.             +-++.+||||-=||.|-|
T Consensus        96 ~ptpvQk~sip~i~~Grdl------macAqTGsGKT~aFLiPii~~~~~~~~~~~~~~~~~~~P~~lIlapTReL~~Qi~  169 (482)
T KOG0335          96 KPTPVQKYSIPIISGGRDL------MACAQTGSGKTAAFLIPIISYLLDEGPEDRGESGGGVYPRALILAPTRELVDQIY  169 (482)
T ss_pred             CCCCCEECCCCEEECCCCE------EEECCCCCCCHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCEEEEECCHHHHHHHH
T ss_conf             8986156042244258842------7882578851378888899999864865666567788972599817378766788


Q ss_pred             HHHHHHCCCCCCEEEEEECCCCHHHHHHHHHHHCCCCCEEEEEC----HHHC-CCCCCCCCCCEEEECCCCC------CC
Q ss_conf             86211014578658996246422566768776213475486411----1201-3345544441788521013------35
Q gi|254780945|r  339 EFIKKYTQNTQIIVEIITGNMPQAHRRKALERIAHGQAHIIIGT----HALF-QDSIQYYKLILVIVDEQHR------FG  407 (700)
Q Consensus       339 ~~~~~~~~~~~i~v~lLtg~~~~~er~~i~~~i~~G~~~iiIGT----HAL~-q~~v~F~~LgLvViDEQHR------FG  407 (700)
                      +..+++....++++...-|.++..   .....+..| ++|+|.|    -+++ ..+|...+++++|+||--|      ||
T Consensus       170 nea~k~~~~s~~~~~~~ygg~~~~---~q~~~~~~g-cdIlvaTpGrL~d~~e~g~i~l~~~k~~vLDEADrMlD~mgF~  245 (482)
T KOG0335         170 NEARKFSYLSGMKSVVVYGGTDLG---AQLRFIKRG-CDILVATPGRLKDLIERGKISLDNCKFLVLDEADRMLDEMGFE  245 (482)
T ss_pred             HHHHHHCCCCCCEEEEEECCCCHH---HHHHHHCCC-CCEEEECCCHHHHHHHCCEEEHHHCCEEEECCHHHHHHHCCCC
T ss_conf             888764022122033005784454---422333257-5578855750564554151126238589952367766632666


Q ss_pred             HHHHHHHHHCCC----CCCCEEECHH---HHHHHHHHHHHH---CCCHHHHCCCCCCCCCCEEEEEECCCHHHHHHHHHH
Q ss_conf             688998740256----7761010101---322789999752---010111102355766620799970200268999976
Q gi|254780945|r  408 VQQRLKLTQKAT----APHVLLMTAT---PIPRTLVLTSLG---DIDISKITEKPAGRKPIKTVIIPINRIDEVIERLKV  477 (700)
Q Consensus       408 V~QR~~L~~Kg~----~ph~L~MtAT---PIPRTLal~~yg---dldvS~i~e~P~gR~~I~T~~~~~~~~~~~~~~i~~  477 (700)
                      -.=|..+...+.    +-..++.|||   =|+|..+..+.-   -+.|..+..-+.+=+.=.+.+...++++++++.+..
T Consensus       246 p~Ir~Iv~~~~~~~~~~~qt~mFSAtfp~~iq~l~~~fl~~~yi~laV~rvg~~~~ni~q~i~~V~~~~kr~~Lldll~~  325 (482)
T KOG0335         246 PQIRKIVEQLGMPPKNNRQTLLFSATFPKEIQRLAADFLKDNYIFLAVGRVGSTSENITQKILFVNEMEKRSKLLDLLNK  325 (482)
T ss_pred             HHHHHHHCCCCCCCCCCEEEEEEECCCCHHHHHHHHHHHHHCCEEEEEEEECCCCCCCEEEEEEECCHHHHHHHHHHHHC
T ss_conf             20799962558887466137887355775666447887641513888753046665634676642111357899988613


Q ss_pred             HHCC--CCEEEEEECCCCCCCCCCCCHHHHHHHHHHHHCCCCEECCCCCCCHHHHHHHHHHHHCCCEEEEEECHHHHCCC
Q ss_conf             3103--87389997120122111210146666666866371031201469989999999997559869999800341046
Q gi|254780945|r  478 VLSE--GKKAYWICPQIEEKKESNFRSVVERFNSLHEHFTSSIAIIHGRMSDIDKESVMDSFKNGTCKLLIATTVIEVGI  555 (700)
Q Consensus       478 ~l~~--g~q~y~VcPlIeese~~~~~~~~~~~~~l~~~~~~~v~~lHGkm~~~ek~~~m~~F~~g~~~iLvaTtviEVGv  555 (700)
                      .-..  -.-+||=--+|--+-+   +-+.+....|... +...--+||--+..|.++.++.|++|.+++||||.|-.-|+
T Consensus       326 ~~~~~~~~~~~~e~tlvFvEt~---~~~d~l~~~l~~~-~~~~~sIhg~~tq~er~~al~~Fr~g~~pvlVaT~VaaRGl  401 (482)
T KOG0335         326 DDGPPSDGEPKWEKTLVFVETK---RGADELAAFLSSN-GYPAKSIHGDRTQIEREQALNDFRNGKAPVLVATNVAARGL  401 (482)
T ss_pred             CCCCCCCCCCCCCEEEEEEECC---HHHHHHHHHHHCC-CCCCEEECCHHHHHHHHHHHHHHHCCCCCEEEEEHHHHCCC
T ss_conf             4678665776431389996130---0326999998617-98745603325563799998776469866798703665478


Q ss_pred             CCCCCCEEEEECHHHCCHHHHHHHHHCCCCCCCCEEEEEEECCCCCHHHHHHHHHHHHHCH
Q ss_conf             8887658998585254746887730116678983599997088899879999999984142
Q gi|254780945|r  556 DVVDASIIIIENAEHFGLAQLHQLRGRVGRGEEISSCILLYHPPLSKNSYTRLSVLKNTED  616 (700)
Q Consensus       556 dvpna~~mvI~~aerfGLsqLHQLRGRVGRg~~~s~c~l~~~~~~~~~~~~Rl~~l~~~~d  616 (700)
                      |+||.+..|.++=---+=.-+|-. ||+||++.-|...-+++.+....+..=.++|.+++-
T Consensus       402 Di~~V~hVInyDmP~d~d~YvHRI-GRTGR~Gn~G~atsf~n~~~~~i~~~L~~~l~ea~q  461 (482)
T KOG0335         402 DIPNVKHVINYDMPADIDDYVHRI-GRTGRVGNGGRATSFFNEKNQNIAKALVEILTEANQ  461 (482)
T ss_pred             CCCCCCEEEEEECCCCHHHHHHHC-CCCCCCCCCCEEEEEECCCCCHHHHHHHHHHHHHCC
T ss_conf             876874358863675246677741-543557777326887647430068999999998426


No 40 
>KOG0350 consensus
Probab=99.73  E-value=1.4e-15  Score=141.77  Aligned_cols=332  Identities=19%  Similarity=0.264  Sum_probs=212.8

Q ss_pred             HHHHHHHHHHHHHHCCCCCCE---EEEEECCCCCHHHHHHHHHHHHHHHH----CCEEEEEHHHHHHHHHHHHHHHHCCC
Q ss_conf             889999999998410013430---78862144223699999973344430----54588612799999999862110145
Q gi|254780945|r  275 KSQESAIKDILQDMSQKNRML---RILQGDVGSGKTLVALIAMAAAVEAG----GQAVIMAPIGILAQQHYEFIKKYTQN  347 (700)
Q Consensus       275 ~~Q~~ai~eI~~Dl~~~~pM~---RLLQGDVGSGKTiVA~~A~l~~~~~G----~Q~alMaPTEILA~QH~~~~~~~~~~  347 (700)
                      .=|..++--|+.+..++-|..   -.+-.-.|||||+-+.+-+.+++.+-    -+|.+.+||--||-|-|.+|++|.++
T Consensus       162 PVQ~aVlp~ll~~~~~p~~~r~rDIcV~ApTGSGKTLaY~iPIVQ~L~~R~v~~LRavVivPtr~L~~QV~~~f~~~~~~  241 (620)
T KOG0350         162 PVQYAVLPSLLEEIRSPPPSRPRDICVNAPTGSGKTLAYVIPIVQLLSSRPVKRLRAVVIVPTRELALQVYDTFKRLNSG  241 (620)
T ss_pred             CHHHHHHHHHHHHHCCCCCCCCCCEEEECCCCCCCEEEEHHHHHHHHCCCCCCCEEEEEEEEHHHHHHHHHHHHHHHCCC
T ss_conf             05888888999861479998877547755789884566513789997038734057999954799999999999985668


Q ss_pred             CCCEEEEEECCCCHHHHHHHHH-HHCCCCCEEEEECHHHC------CCCCCCCCCCEEEECCCCCCCHHHHHHHHH----
Q ss_conf             7865899624642256676877-62134754864111201------334554444178852101335688998740----
Q gi|254780945|r  348 TQIIVEIITGNMPQAHRRKALE-RIAHGQAHIIIGTHALF------QDSIQYYKLILVIVDEQHRFGVQQRLKLTQ----  416 (700)
Q Consensus       348 ~~i~v~lLtg~~~~~er~~i~~-~i~~G~~~iiIGTHAL~------q~~v~F~~LgLvViDEQHRFGV~QR~~L~~----  416 (700)
                      .|+.|+.++|.-+-+.-...+. .-....+||+|.|-+=+      -+.+..++|.+.||||--|.+=.-+..-..    
T Consensus       242 tgL~V~~~sgq~sl~~E~~qL~~~~~~~~~DIlVaTPGRLVDHl~~~k~f~Lk~LrfLVIDEADRll~qsfQ~Wl~~v~~  321 (620)
T KOG0350         242 TGLAVCSLSGQNSLEDEARQLASDPPECRIDILVATPGRLVDHLNNTKSFDLKHLRFLVIDEADRLLDQSFQEWLDTVMS  321 (620)
T ss_pred             CCEEEEECCCCCCHHHHHHHHHCCCCCCCCCEEECCCHHHHHHCCCCCCCCHHHCEEEEECHHHHHHHHHHHHHHHHHHH
T ss_conf             86598860145405789999725997654366973726888860489875644535777525778999999988999999


Q ss_pred             --CCC-----CCCCEEECHHHHHHHHHHHHHHCCCHHHHCCCCCCCCCCEEEEEE--CCCHHHHHHHHHH--HHCC-CCE
Q ss_conf             --256-----776101010132278999975201011110235576662079997--0200268999976--3103-873
Q gi|254780945|r  417 --KAT-----APHVLLMTATPIPRTLVLTSLGDIDISKITEKPAGRKPIKTVIIP--INRIDEVIERLKV--VLSE-GKK  484 (700)
Q Consensus       417 --Kg~-----~ph~L~MtATPIPRTLal~~ygdldvS~i~e~P~gR~~I~T~~~~--~~~~~~~~~~i~~--~l~~-g~q  484 (700)
                        |+.     .-+++-|.--|-|     +.|++++-+..+.-|+--+=+.+..+.  .++..++--++-+  ...+ -.-
T Consensus       322 ~~~~~k~~~~~~nii~~~~~~~p-----t~~~e~~t~~~~~~~~l~kL~~satLsqdP~Kl~~l~l~~Prl~~v~~~~~~  396 (620)
T KOG0350         322 LCKTMKRVACLDNIIRQRQAPQP-----TVLSELLTKLGKLYPPLWKLVFSATLSQDPSKLKDLTLHIPRLFHVSKPLIG  396 (620)
T ss_pred             HHCCCHHHCCHHHHHHHCCCCCC-----HHHHHHHHHCCCCCCHHHHHHCCHHHHCCHHHHHHHHCCCCCEEEEECCCCE
T ss_conf             83774010471544410146774-----0058777412776752676530133304968876533279835886225432


Q ss_pred             EEEEECCCCCC--------------------CC-------CCCCHHHHHHHHHHHHCCC---CEECCCCCCCHHHHHHHH
Q ss_conf             89997120122--------------------11-------1210146666666866371---031201469989999999
Q gi|254780945|r  485 AYWICPQIEEK--------------------KE-------SNFRSVVERFNSLHEHFTS---SIAIIHGRMSDIDKESVM  534 (700)
Q Consensus       485 ~y~VcPlIees--------------------e~-------~~~~~~~~~~~~l~~~~~~---~v~~lHGkm~~~ek~~~m  534 (700)
                      .|-+|+-++++                    +-       ....++.....-|+-.|..   ++.-..|.+..+...+.+
T Consensus       397 ryslp~~l~~~~vv~~~~~kpl~~~~lI~~~k~~r~lcf~~S~~sa~Rl~~~L~v~~~~~~~~~s~~t~~l~~k~r~k~l  476 (620)
T KOG0350         397 RYSLPSSLSHRLVVTEPKFKPLAVYALITSNKLNRTLCFVNSVSSANRLAHVLKVEFCSDNFKVSEFTGQLNGKRRYKML  476 (620)
T ss_pred             EEECCHHHHHCEEECCCCCCHHHHHHHHHHHHCCEEEEEECCHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHH
T ss_conf             66157554213342023554376999997740104899952468899999999998626440255652344388999999


Q ss_pred             HHHHCCCEEEEEECHHHHCCCCCCCCCEEEEECHHHCCHHHHHHHHHCCCCCCCCEEEEEEECCCCCHHHHHHH-HHHHH
Q ss_conf             99755986999980034104688876589985852547468877301166789835999970888998799999-99984
Q gi|254780945|r  535 DSFKNGTCKLLIATTVIEVGIDVVDASIIIIENAEHFGLAQLHQLRGRVGRGEEISSCILLYHPPLSKNSYTRL-SVLKN  613 (700)
Q Consensus       535 ~~F~~g~~~iLvaTtviEVGvdvpna~~mvI~~aerfGLsqLHQLRGRVGRg~~~s~c~l~~~~~~~~~~~~Rl-~~l~~  613 (700)
                      ++|..|++.+|||+-+.--||||.+.++.|=+|.-++-=.=.|- -||-+|-+..||||-+....   . ..+. +.+.+
T Consensus       477 ~~f~~g~i~vLIcSD~laRGiDv~~v~~VINYd~P~~~ktyVHR-~GRTARAgq~G~a~tll~~~---~-~r~F~klL~~  551 (620)
T KOG0350         477 EKFAKGDINVLICSDALARGIDVNDVDNVINYDPPASDKTYVHR-AGRTARAGQDGYAITLLDKH---E-KRLFSKLLKK  551 (620)
T ss_pred             HHHHCCCCEEEEEHHHHHCCCCCCCCCEEEECCCCCHHHHHHHH-HCCCCCCCCCCEEEEEECCC---C-CHHHHHHHHH
T ss_conf             98753895299852365547760246047635898126578776-02210056774478963155---4-0379999987


Q ss_pred             HCH
Q ss_conf             142
Q gi|254780945|r  614 TED  616 (700)
Q Consensus       614 ~~d  616 (700)
                      +++
T Consensus       552 ~~~  554 (620)
T KOG0350         552 TNL  554 (620)
T ss_pred             HCC
T ss_conf             435


No 41 
>COG0514 RecQ Superfamily II DNA helicase [DNA replication, recombination, and repair]
Probab=99.73  E-value=1e-14  Score=134.99  Aligned_cols=305  Identities=23%  Similarity=0.312  Sum_probs=219.6

Q ss_pred             CCCHHHHHHHHHHHHHHCCCCCCEEEEEECCCCCHHHHHHHHHHHHHHHHCCEEEEEHHHHHHHHHHHHHHHHCCCCCCE
Q ss_conf             67988999999999841001343078862144223699999973344430545886127999999998621101457865
Q gi|254780945|r  272 SPTKSQESAIKDILQDMSQKNRMLRILQGDVGSGKTLVALIAMAAAVEAGGQAVIMAPIGILAQQHYEFIKKYTQNTQII  351 (700)
Q Consensus       272 ~LT~~Q~~ai~eI~~Dl~~~~pM~RLLQGDVGSGKTiVA~~A~l~~~~~G~Q~alMaPTEILA~QH~~~~~~~~~~~~i~  351 (700)
                      .+-.+|+.+|+.+.+-      ++-|.-==.|+||.+.+-+.++.-  .| =+.+..|===|=+-.-..+..    .|++
T Consensus        17 ~FR~gQ~evI~~~l~g------~d~lvvmPTGgGKSlCyQiPAll~--~G-~TLVVSPLiSLM~DQV~~l~~----~Gi~   83 (590)
T COG0514          17 SFRPGQQEIIDALLSG------KDTLVVMPTGGGKSLCYQIPALLL--EG-LTLVVSPLISLMKDQVDQLEA----AGIR   83 (590)
T ss_pred             CCCCCHHHHHHHHHCC------CCEEEECCCCCCCCHHHHHHHHHC--CC-CEEEECCHHHHHHHHHHHHHH----CCCE
T ss_conf             0388889999999658------867998538987106743678865--99-789978568889999999997----5965


Q ss_pred             EEEEECCCCHHHHHHHHHHHCCCCCEEEEECHH-----HCCCCCCCCCCCEEEECCCC---CCCHHHHHHHH------HC
Q ss_conf             899624642256676877621347548641112-----01334554444178852101---33568899874------02
Q gi|254780945|r  352 VEIITGNMPQAHRRKALERIAHGQAHIIIGTHA-----LFQDSIQYYKLILVIVDEQH---RFGVQQRLKLT------QK  417 (700)
Q Consensus       352 v~lLtg~~~~~er~~i~~~i~~G~~~iiIGTHA-----L~q~~v~F~~LgLvViDEQH---RFGV~QR~~L~------~K  417 (700)
                      ++.|.|+++..|+..++..+.+|.++++-=+-.     -|.+-+.=-.++|+||||=|   .+|=.=|-...      ..
T Consensus        84 A~~lnS~l~~~e~~~v~~~l~~g~~klLyisPErl~~~~f~~~L~~~~i~l~vIDEAHCiSqWGhdFRP~Y~~lg~l~~~  163 (590)
T COG0514          84 AAYLNSTLSREERQQVLNQLKSGQLKLLYISPERLMSPRFLELLKRLPISLVAIDEAHCISQWGHDFRPDYRRLGRLRAG  163 (590)
T ss_pred             EEHHHCCCCHHHHHHHHHHHHCCCEEEEEECCHHHCCHHHHHHHHHCCCCEEEECHHHHHHHCCCCCCHHHHHHHHHHHH
T ss_conf             20442436787799999998649645999881363176899999708875699621777764177437768999999851


Q ss_pred             CCCCCCEEECHHHHHHHHHHH--HHHCCCHHHHCCCCCCCCCCEEEEEECC-CHHHHHHHHHHHHCCCCEEEEEECCCCC
Q ss_conf             567761010101322789999--7520101111023557666207999702-0026899997631038738999712012
Q gi|254780945|r  418 ATAPHVLLMTATPIPRTLVLT--SLGDIDISKITEKPAGRKPIKTVIIPIN-RIDEVIERLKVVLSEGKKAYWICPQIEE  494 (700)
Q Consensus       418 g~~ph~L~MtATPIPRTLal~--~ygdldvS~i~e~P~gR~~I~T~~~~~~-~~~~~~~~i~~~l~~g~q~y~VcPlIee  494 (700)
                      =.+|-++..|||-=|++-.-.  ..+.=+-.++.. -..|..|.-.++... -+.+.. |+.+....+.+.=+||-+   
T Consensus       164 ~~~~p~~AlTATA~~~v~~DI~~~L~l~~~~~~~~-sfdRpNi~~~v~~~~~~~~q~~-fi~~~~~~~~~~GIIYc~---  238 (590)
T COG0514         164 LPNPPVLALTATATPRVRDDIREQLGLQDANIFRG-SFDRPNLALKVVEKGEPSDQLA-FLATVLPQLSKSGIIYCL---  238 (590)
T ss_pred             CCCCCEEEEECCCCHHHHHHHHHHHCCCCCCEEEE-CCCCCHHHHHHHHCCCHHHHHH-HHHHHCCCCCCCEEEEEE---
T ss_conf             79997799737898678999999846788664871-5898523455642564788899-987413246897289993---


Q ss_pred             CCCCCCCHHHHHHHHHHHHCCCCEECCCCCCCHHHHHHHHHHHHCCCEEEEEECHHHHCCCCCCCCCEEEEECHHHCCHH
Q ss_conf             21112101466666668663710312014699899999999975598699998003410468887658998585254746
Q gi|254780945|r  495 KKESNFRSVVERFNSLHEHFTSSIAIIHGRMSDIDKESVMDSFKNGTCKLLIATTVIEVGIDVVDASIIIIENAEHFGLA  574 (700)
Q Consensus       495 se~~~~~~~~~~~~~l~~~~~~~v~~lHGkm~~~ek~~~m~~F~~g~~~iLvaTtviEVGvdvpna~~mvI~~aerfGLs  574 (700)
                          .-..+++.+++|.+. +-+++.-||-|+++|++.+=++|.+++++|+|||.---.|||-||....|=+|.-+ -+.
T Consensus       239 ----sRk~~E~ia~~L~~~-g~~a~~YHaGl~~~eR~~~q~~f~~~~~~iiVAT~AFGMGIdKpdVRfViH~~lP~-s~E  312 (590)
T COG0514         239 ----TRKKVEELAEWLRKN-GISAGAYHAGLSNEERERVQQAFLNDEIKVMVATNAFGMGIDKPDVRFVIHYDLPG-SIE  312 (590)
T ss_pred             ----EHHHHHHHHHHHHHC-CCCEEEECCCCCHHHHHHHHHHHHCCCCCEEEEECCCCCCCCCCCCEEEEEECCCC-CHH
T ss_conf             ----377599999999977-97257751898899999999997169986899964624776788840799806998-989


Q ss_pred             HHHHHHHCCCCCCCCEEEEEEECCCC
Q ss_conf             88773011667898359999708889
Q gi|254780945|r  575 QLHQLRGRVGRGEEISSCILLYHPPL  600 (700)
Q Consensus       575 qLHQLRGRVGRg~~~s~c~l~~~~~~  600 (700)
                      -.-|==||-||.+.+|.|+|+|++..
T Consensus       313 sYyQE~GRAGRDG~~a~aill~~~~D  338 (590)
T COG0514         313 SYYQETGRAGRDGLPAEAILLYSPED  338 (590)
T ss_pred             HHHHHHHHCCCCCCCCEEEEEECCCC
T ss_conf             99999713567877021788606300


No 42 
>KOG0344 consensus
Probab=99.72  E-value=8.4e-20  Score=174.88  Aligned_cols=448  Identities=17%  Similarity=0.176  Sum_probs=277.7

Q ss_pred             CCCCCCCHHHHHHHCCCCCCCCCCCCCHHHCCC---CCEEEEEEEEEEEEEEC-CCCCCEEEEEEECCCCEEEEEEECCC
Q ss_conf             468855489878708974013444464788899---87899999998975421-58983389999818936999995188
Q gi|254780945|r   34 GNANETRFIDLLFYHPSSFIDRHYRPKISEISE---ERIVTITGYISQHSSFQ-LQKRRPYKILLNDGTGEITLLFFYRK  109 (700)
Q Consensus        34 ~~~GI~ti~DLL~~~PrrYeDr~~~~~I~~l~~---g~~vti~g~V~~~~~~~-~~~r~~~~v~v~D~tg~i~lvfFn~~  109 (700)
                      +..|.++..-++.|.|..|.+--.-.-+.++..   .+...++-     ...+ +..++-..+-.--++|.  ..=||..
T Consensus       121 ~v~G~~~~~~l~~f~~lt~~~~~~~~ll~nl~~~~F~~Pt~iq~-----~aipvfl~~r~~lAcapTGsgK--tlaf~~P  193 (593)
T KOG0344         121 NVDGFHLPPPLLSFSDLTYDYSMNKRLLENLQELGFDEPTPIQK-----QAIPVFLEKRDVLACAPTGSGK--TLAFNLP  193 (593)
T ss_pred             ECCCCCCCCCCCCCCCCCHHHHHCHHHHHHHHHCCCCCCCCCCC-----HHHHHHHCCCCEEEECCCCCCC--HHHHHHH
T ss_conf             14477788743453211104321489997676278888773100-----1156664133058863578862--0565569


Q ss_pred             -HHHHHHHC----CCCCEEEEEEEEEECCCEEEEECCEEEECCCCCCC-CCCCCCCCCCCHHHHHHHHHHHHHHHHHHHC
Q ss_conf             -78998732----89888999989973187799977868962643344-4441100000000004543001345787404
Q gi|254780945|r  110 -TEMLKNVF----FEGRKITVTGKIKKLKNRIIMVHPHYIFHNSQDVN-FPLIEAVYSLPTGLSVDLFKKIIVEALSRLP  183 (700)
Q Consensus       110 -~~yl~k~l----k~G~~v~vsGKv~~~~~~~qi~hPe~~~~~~~~~~-~~~I~PIYplt~GLsqk~irk~I~~aL~~~~  183 (700)
                       ...++...    +.|-..+|.+..+....+.-..--+|......... ...-.|.||.-   .++........+|    
T Consensus       194 il~~L~~~~~~~~~~gl~a~Il~ptreLa~Qi~re~~k~~~~~~t~~~a~~~~~~~~~~q---k~a~~~~~k~dil----  266 (593)
T KOG0344         194 ILQHLKDLSQEKHKVGLRALILSPTRELAAQIYREMRKYSIDEGTSLRAAQFSKPAYPSQ---KPAFLSDEKYDIL----  266 (593)
T ss_pred             HHHHHHHHHCCCCCCCEEEEEECCHHHHHHHHHHHHHHCCCCCCCCHHHHHCCCCCCHHH---CCCHHHHHHHHHH----
T ss_conf             999998752035765427888444499999999999855777787534551666653110---3324677788788----


Q ss_pred             CCCCCCCHHHHHCCCCCCHHHHHHHHCCCCCHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHC-C---CCCCCCC
Q ss_conf             684338977862056999889998620458965656679999999876-6666667777655554320-3---5767877
Q gi|254780945|r  184 VLPEWIEKDLLQKKSFPSIAEAFNIIHNPRKAKDFEWTSPARERLAYD-ELLAGQIALLLMRKQFKKE-I---GIPINVE  258 (700)
Q Consensus       184 ~i~E~LP~~ll~k~~L~s~~eAL~~IH~P~~~~dle~~~~ArkRLafe-ELl~~QL~l~~~r~~~~~~-~---~~~~~~~  258 (700)
                         =-.|..+..-.++.+...++..+|++-.. +-+   .     .|+ |.|..|++-.+.-...... .   +..++..
T Consensus       267 ---i~TP~ri~~~~~~~~~~idl~~V~~lV~d-EaD---~-----lfe~~~f~~Qla~I~sac~s~~i~~a~FSat~~~~  334 (593)
T KOG0344         267 ---ISTPMRIVGLLGLGKLNIDLSKVEWLVVD-EAD---L-----LFEPEFFVEQLADIYSACQSPDIRVALFSATISVY  334 (593)
T ss_pred             ---HCCHHHHHHHHCCCCCCCHHHEEEEEEEC-HHH---H-----HHCHHHHHHHHHHHHHHHCCCCHHHHHHHCCCCHH
T ss_conf             ---61879999985589753201203567664-687---6-----50815699999999998528522256632146077


Q ss_pred             ----CHHHHHHHHHCCCCCCHHHHHHHHHHHHHHCCCCCCEEEEEECCCCCHHHHHHHHHHHHHHHHCCEEEEEHHHHHH
Q ss_conf             ----5789999863024679889999999998410013430788621442236999999733444305458861279999
Q gi|254780945|r  259 ----GKIAQKILRNIPFSPTKSQESAIKDILQDMSQKNRMLRILQGDVGSGKTLVALIAMAAAVEAGGQAVIMAPIGILA  334 (700)
Q Consensus       259 ----~~~~~~f~~~LPF~LT~~Q~~ai~eI~~Dl~~~~pM~RLLQGDVGSGKTiVA~~A~l~~~~~G~Q~alMaPTEILA  334 (700)
                          ...+..+..+++..++++|                |+++.|++|+|||+.++++|+...+.+|     |.|+++++
T Consensus       335 VEE~~~~i~~~~~~vivg~~~sa----------------~~~V~QelvF~gse~~K~lA~rq~v~~g-----~~PP~lIf  393 (593)
T KOG0344         335 VEEWAELIKSDLKRVIVGLRNSA----------------NETVDQELVFCGSEKGKLLALRQLVASG-----FKPPVLIF  393 (593)
T ss_pred             HHHHHHHHHCCCEEEEEECCHHH----------------HHHHHHHHEEEECCHHHHHHHHHHHHCC-----CCCCEEEE
T ss_conf             99999986505336898425257----------------6554555121104345778899998615-----89974898


Q ss_pred             HHHHHHHHHHCCCC----CCEEEEEECCCCHHHHHHHHHHHCCCCCEEEEECHHHCCCCCCCCCCCEEEECCCCCCCHHH
Q ss_conf             99998621101457----86589962464225667687762134754864111201334554444178852101335688
Q gi|254780945|r  335 QQHYEFIKKYTQNT----QIIVEIITGNMPQAHRRKALERIAHGQAHIIIGTHALFQDSIQYYKLILVIVDEQHRFGVQQ  410 (700)
Q Consensus       335 ~QH~~~~~~~~~~~----~i~v~lLtg~~~~~er~~i~~~i~~G~~~iiIGTHAL~q~~v~F~~LgLvViDEQHRFGV~Q  410 (700)
                      -||++.-+.+|..+    +|.|...+|..+.++|++.+++...|++.++|-|- |++.++.|++..+||.+.=..+++.+
T Consensus       394 VQs~eRak~L~~~L~~~~~i~v~vIh~e~~~~qrde~~~~FR~g~IwvLicTd-ll~RGiDf~gvn~VInyD~p~s~~sy  472 (593)
T KOG0344         394 VQSKERAKQLFEELEIYDNINVDVIHGERSQKQRDETMERFRIGKIWVLICTD-LLARGIDFKGVNLVINYDFPQSDLSY  472 (593)
T ss_pred             EECHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHHHHHHCCCEEEEEEHH-HHHCCCCCCCCCEEEECCCCCHHHHH
T ss_conf             85388899999986423576634676366666778999998506706888504-66545564576368953787224788


Q ss_pred             HHHHHHCCCCCCCEEECHHHHHHHHHHHHHHCCCHHHHCCCCCCCCCCEEEEEECCCHHHHHHHHHH--HHCCCCEEEEE
Q ss_conf             9987402567761010101322789999752010111102355766620799970200268999976--31038738999
Q gi|254780945|r  411 RLKLTQKATAPHVLLMTATPIPRTLVLTSLGDIDISKITEKPAGRKPIKTVIIPINRIDEVIERLKV--VLSEGKKAYWI  488 (700)
Q Consensus       411 R~~L~~Kg~~ph~L~MtATPIPRTLal~~ygdldvS~i~e~P~gR~~I~T~~~~~~~~~~~~~~i~~--~l~~g~q~y~V  488 (700)
                                .|-+-||++|+|+..|.|+|+|      ..+|..|.++.|.-.+.....+-.-.++.  .+.++      
T Consensus       473 ----------ihrIGRtgRag~~g~Aitfytd------~d~~~ir~iae~~~~sG~evpe~~m~~~k~~~~~kk------  530 (593)
T KOG0344         473 ----------IHRIGRTGRAGRSGKAITFYTD------QDMPRIRSIAEVMEQSGCEVPEKIMGIKKLSRLKKK------  530 (593)
T ss_pred             ----------HHHHHCCCCCCCCCCEEEEECC------CCCHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHH------
T ss_conf             ----------8873025788988616998632------553455568999997188633999865666655555------


Q ss_pred             ECCCCCCCCCCCCHHHHHHHHHHHHCCCCEECCCCCCCHHHHHHHHHHHHCCCEEEEEECHHHHCCCCCCCCCEEEEECH
Q ss_conf             71201221112101466666668663710312014699899999999975598699998003410468887658998585
Q gi|254780945|r  489 CPQIEEKKESNFRSVVERFNSLHEHFTSSIAIIHGRMSDIDKESVMDSFKNGTCKLLIATTVIEVGIDVVDASIIIIENA  568 (700)
Q Consensus       489 cPlIeese~~~~~~~~~~~~~l~~~~~~~v~~lHGkm~~~ek~~~m~~F~~g~~~iLvaTtviEVGvdvpna~~mvI~~a  568 (700)
                               .-+.++.++.+.-...||.           .-|+...++|++++.+++  +|++|.|++.+.+.-|..+++
T Consensus       531 ---------~~~k~~~~r~~I~t~~~p~-----------~~~k~~~~k~~~~ek~~~--~~~~~~~~k~~~~~~~~~~~~  588 (593)
T KOG0344         531 ---------KLLKAASKREEISTKKFPK-----------YKKKEALEKAKSQEKKIL--KQETEIAVKKEGKIKKKVENK  588 (593)
T ss_pred             ---------HHHHCCCCCCCEEEECCCC-----------CHHHHHHHHHHHHHHHHH--HHHHHHCCCCCHHHHHHHHHH
T ss_conf             ---------5431554210014412455-----------306788888776778888--887664025520257788866


Q ss_pred             HHCCH
Q ss_conf             25474
Q gi|254780945|r  569 EHFGL  573 (700)
Q Consensus       569 erfGL  573 (700)
                      ++||.
T Consensus       589 ~~~~~  593 (593)
T KOG0344         589 ENFGI  593 (593)
T ss_pred             HHCCC
T ss_conf             51279


No 43 
>smart00487 DEXDc DEAD-like helicases superfamily.
Probab=99.71  E-value=3.2e-16  Score=146.76  Aligned_cols=155  Identities=29%  Similarity=0.364  Sum_probs=126.7

Q ss_pred             HCCCCCCHHHHHHHHHHHHHHCCCCCCEEEEEECCCCCHHHHHHHHHHHHHHHH--CCEEEEEHHHHHHHHHHHHHHHHC
Q ss_conf             302467988999999999841001343078862144223699999973344430--545886127999999998621101
Q gi|254780945|r  268 NIPFSPTKSQESAIKDILQDMSQKNRMLRILQGDVGSGKTLVALIAMAAAVEAG--GQAVIMAPIGILAQQHYEFIKKYT  345 (700)
Q Consensus       268 ~LPF~LT~~Q~~ai~eI~~Dl~~~~pM~RLLQGDVGSGKTiVA~~A~l~~~~~G--~Q~alMaPTEILA~QH~~~~~~~~  345 (700)
                      ...+.+++.|..+++.+....     ...++++..|||||.++++.++....++  .++.+++||..|+.|.++.+.+++
T Consensus         4 ~~~~~~~~~Q~~~~~~~~~~~-----~~~~i~~~tGsGKT~~~~~~~~~~~~~~~~~~~li~~P~~~l~~q~~~~~~~~~   78 (201)
T smart00487        4 FGFEPLRPYQKEAIEALLSGL-----RDVILAAPTGSGKTLAALLPALEALKRGKGKRVLVLVPTRELAEQWAEELKKLG   78 (201)
T ss_pred             CCCCCCCHHHHHHHHHHHCCC-----CCEEEECCCCCCHHHHHHHHHHHHHHCCCCCEEEEEECCHHHHHHHHHHHHHCC
T ss_conf             379999988999999998389-----988998999960999999999998633899759999085999999998860102


Q ss_pred             CCCC-CEEEEEECCCCHHHHHHHHHHHCCCCCEEEEEC-----HHHCCCCCCCCCCCEEEECCCCCCCH-HHHHHHHHC-
Q ss_conf             4578-658996246422566768776213475486411-----12013345544441788521013356-889987402-
Q gi|254780945|r  346 QNTQ-IIVEIITGNMPQAHRRKALERIAHGQAHIIIGT-----HALFQDSIQYYKLILVIVDEQHRFGV-QQRLKLTQK-  417 (700)
Q Consensus       346 ~~~~-i~v~lLtg~~~~~er~~i~~~i~~G~~~iiIGT-----HAL~q~~v~F~~LgLvViDEQHRFGV-~QR~~L~~K-  417 (700)
                      +... ..+..++|...    ...++.+.++..+|+|+|     +.+......+.+.+++|+||-|.+.- .++..+... 
T Consensus        79 ~~~~~~~~~~~~~~~~----~~~~~~~~~~~~~i~i~t~~~l~~~~~~~~~~~~~~~~vIiDE~H~~~~~~~~~~~~~~~  154 (201)
T smart00487       79 PSLGLKVVGLYGGDSK----REQLRKLESGKTDILVTTPGRLLDLLENDLLELSNVDLVILDEAHRLLDGGFGDQLEKLL  154 (201)
T ss_pred             CCCEEEEEEEECCCCH----HHHHHHHHCCCCCEEEECHHHHHHHHHHCCCCCCCCEEEEEECHHHHHCCCCHHHHHHHH
T ss_conf             1020445565247737----999999975999899955899999997275452543199998967751257099999999


Q ss_pred             ---CCCCCCEEECHHHH
Q ss_conf             ---56776101010132
Q gi|254780945|r  418 ---ATAPHVLLMTATPI  431 (700)
Q Consensus       418 ---g~~ph~L~MtATPI  431 (700)
                         ..+++++.|||||+
T Consensus       155 ~~~~~~~~~i~lSAT~~  171 (201)
T smart00487      155 KLLPKNVQLLLLSATPP  171 (201)
T ss_pred             HHCCCCCCEEEECCCCC
T ss_conf             96799997899924898


No 44 
>cd00079 HELICc Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may not be an autonomously folding unit, but an integral part of the helicase; 4 helicase superfamilies at present according to the organization of their signature motifs; all helicases share the ability to unwind nucleic acid duplexes with a distinct directional polarity; they utilize the free energy from nucleoside triphosphate hydrolysis to fuel their translocation along DNA, unwinding the duplex in the process
Probab=99.71  E-value=2.9e-16  Score=147.16  Aligned_cols=129  Identities=31%  Similarity=0.505  Sum_probs=110.4

Q ss_pred             CCEEEEEE--CCCHHHHHHHHHHHHCCCCEEEEEECCCCCCCCCCCCHHHHHHHHHHHHCCCCEECCCCCCCHHHHHHHH
Q ss_conf             62079997--0200268999976310387389997120122111210146666666866371031201469989999999
Q gi|254780945|r  457 PIKTVIIP--INRIDEVIERLKVVLSEGKKAYWICPQIEEKKESNFRSVVERFNSLHEHFTSSIAIIHGRMSDIDKESVM  534 (700)
Q Consensus       457 ~I~T~~~~--~~~~~~~~~~i~~~l~~g~q~y~VcPlIeese~~~~~~~~~~~~~l~~~~~~~v~~lHGkm~~~ek~~~m  534 (700)
                      |+.++.+.  +++.+.+++.+++.+.+|+++.|.|+.++        .++..++.|++ .+.++..+||.|+.+|++.+|
T Consensus         1 ~~~~~~~~~~~~K~~~l~~~i~~~~~~~~kviIF~~~~~--------~~~~l~~~L~~-~~~~~~~~~~~~~~~~R~~~~   71 (131)
T cd00079           1 PIKQYVLPVEDEKLEALLELLKEHLKKGGKVLIFCPSKK--------MLDELAELLRK-PGIKVAALHGDGSQEEREEVL   71 (131)
T ss_pred             CCEEEEEECCHHHHHHHHHHHHHHHHCCCEEEEEECCHH--------HHHHHHHHHHH-CCCCEEEEECCCCHHHHHHHH
T ss_conf             922899938669999999999999978990999978899--------99999999955-899899998999999999999


Q ss_pred             HHHHCCCEEEEEECHHHHCCCCCCCCCEEEEECHHHCCHHHHHHHHHCCCCCCCCEEEEEE
Q ss_conf             9975598699998003410468887658998585254746887730116678983599997
Q gi|254780945|r  535 DSFKNGTCKLLIATTVIEVGIDVVDASIIIIENAEHFGLAQLHQLRGRVGRGEEISSCILL  595 (700)
Q Consensus       535 ~~F~~g~~~iLvaTtviEVGvdvpna~~mvI~~aerfGLsqLHQLRGRVGRg~~~s~c~l~  595 (700)
                      ++|++|+.+|||||++.+.|+|+|+|+++|+.+.. +..++++|-.||+||.+.+|+|+++
T Consensus        72 ~~F~~~~~~ilv~t~~~~~Gldl~~~~~vI~~~~~-~s~~~~~Q~~GR~~R~gq~~~~~~~  131 (131)
T cd00079          72 KDFREGEIVVLVATDVIARGIDLPNVSVVINYDLP-WSPSSYLQRIGRAGRAGQKGTAILL  131 (131)
T ss_pred             HHHHHHCEEEEEEEECCEECCCCCCCCEEEEECCC-CCHHHHHHHHHCCCCCCCCEEEEEC
T ss_conf             99775401048875112003661028799997899-6989999897216708996379979


No 45 
>KOG0348 consensus
Probab=99.70  E-value=6.7e-15  Score=136.45  Aligned_cols=350  Identities=23%  Similarity=0.371  Sum_probs=215.8

Q ss_pred             CCHHHHHHHHHCCC-CCCHHHHHHHHHHHHHHCCCCCCEEEEEECCCCCHHHHHHHHHHHHHH---------HHCCEEEE
Q ss_conf             75789999863024-679889999999998410013430788621442236999999733444---------30545886
Q gi|254780945|r  258 EGKIAQKILRNIPF-SPTKSQESAIKDILQDMSQKNRMLRILQGDVGSGKTLVALIAMAAAVE---------AGGQAVIM  327 (700)
Q Consensus       258 ~~~~~~~f~~~LPF-~LT~~Q~~ai~eI~~Dl~~~~pM~RLLQGDVGSGKTiVA~~A~l~~~~---------~G~Q~alM  327 (700)
                      +..++..+-..+.+ ++|.=|+++|-+|..+  +    .-|+.--.|||||+-+++-+...+.         .|-=+.+|
T Consensus       144 ~~~lv~~L~~~m~i~~pTsVQkq~IP~lL~g--r----D~lV~aQTGSGKTLAYllPiVq~Lq~m~~ki~Rs~G~~ALVi  217 (708)
T KOG0348         144 HPHLVSHLNTKMKISAPTSVQKQAIPVLLEG--R----DALVRAQTGSGKTLAYLLPIVQSLQAMEPKIQRSDGPYALVI  217 (708)
T ss_pred             CHHHHHHHHHHHCCCCCCHHHHCCHHHHHCC--C----CEEEECCCCCCCCHHHHHHHHHHHHHCCCCCCCCCCCEEEEE
T ss_conf             7799999988745576406765020355258--6----347885778862179999999999726865555688348998


Q ss_pred             EHHHHHHHHHHHHHHHHCCCCC--CEEEEEECCCCHHHHHHHHHHHCCCCCEEEEEC------HHHCCCCCCCCCCCEEE
Q ss_conf             1279999999986211014578--658996246422566768776213475486411------12013345544441788
Q gi|254780945|r  328 APIGILAQQHYEFIKKYTQNTQ--IIVEIITGNMPQAHRRKALERIAHGQAHIIIGT------HALFQDSIQYYKLILVI  399 (700)
Q Consensus       328 aPTEILA~QH~~~~~~~~~~~~--i~v~lLtg~~~~~er~~i~~~i~~G~~~iiIGT------HAL~q~~v~F~~LgLvV  399 (700)
                      |||-=||.|-|+++.+++.++.  |++.|+-|--+++||..+..    | |+|+|||      |-.=-+.+.|++|..+|
T Consensus       218 vPTREL~~Q~y~~~qKLl~~~hWIVPg~lmGGEkkKSEKARLRK----G-iNILIgTPGRLvDHLknT~~i~~s~LRwlV  292 (708)
T KOG0348         218 VPTRELALQIYETVQKLLKPFHWIVPGVLMGGEKKKSEKARLRK----G-INILIGTPGRLVDHLKNTKSIKFSRLRWLV  292 (708)
T ss_pred             ECHHHHHHHHHHHHHHHHCCCEEEEECEEECCCCCCCHHHHHHC----C-CEEEECCCHHHHHHHHCCCHHEEEEEEEEE
T ss_conf             04199999999999987257437730212236331017888754----8-548975842788987430022100356898


Q ss_pred             ECCCCCC-----C--HHHHHHHHHCCC--------CCCC---EEECHHHHH---HHHHHHH----HHCCCHHHHCCC---
Q ss_conf             5210133-----5--688998740256--------7761---010101322---7899997----520101111023---
Q gi|254780945|r  400 VDEQHRF-----G--VQQRLKLTQKAT--------APHV---LLMTATPIP---RTLVLTS----LGDIDISKITEK---  451 (700)
Q Consensus       400 iDEQHRF-----G--V~QR~~L~~Kg~--------~ph~---L~MtATPIP---RTLal~~----ygdldvS~i~e~---  451 (700)
                      .||--|-     +  +.|=.+...++.        -||.   +..|||=--   |---+++    |=++|-|--...   
T Consensus       293 lDEaDrlleLGfekdit~Il~~v~~~~~~e~~~~~lp~q~q~mLlSATLtd~V~rLa~~sLkDpv~I~ld~s~~~~~p~~  372 (708)
T KOG0348         293 LDEADRLLELGFEKDITQILKAVHSIQNAECKDPKLPHQLQNMLLSATLTDGVNRLADLSLKDPVYISLDKSHSQLNPKD  372 (708)
T ss_pred             ECCHHHHHHCCCHHHHHHHHHHHHHCCCHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCEEEECCCHHHHCCCCH
T ss_conf             53436787624300399999987500200102556637877676665567778887633156855640430122038631


Q ss_pred             ---------CCCCCCCEEE-----------EEECC-CHHHHHHHHHHHHCCC-CE---EEEEEC-CCCC-----CCCCCC
Q ss_conf             ---------5576662079-----------99702-0026899997631038-73---899971-2012-----211121
Q gi|254780945|r  452 ---------PAGRKPIKTV-----------IIPIN-RIDEVIERLKVVLSEG-KK---AYWICP-QIEE-----KKESNF  500 (700)
Q Consensus       452 ---------P~gR~~I~T~-----------~~~~~-~~~~~~~~i~~~l~~g-~q---~y~VcP-lIee-----se~~~~  500 (700)
                               |.|- +....           +++.+ +.--+..++.+.++.- .|   ||+-|- ++|-     ++.+.-
T Consensus       373 ~a~~ev~~~~~~~-~l~~~~iPeqL~qry~vVPpKLRLV~Laa~L~~~~k~~~~qk~iVF~S~~d~VeFHy~lf~~~l~~  451 (708)
T KOG0348         373 KAVQEVDDGPAGD-KLDSFAIPEQLLQRYTVVPPKLRLVALAALLLNKVKFEEKQKMIVFFSCSDSVEFHYSLFSEALLS  451 (708)
T ss_pred             HHHHHCCCCCCCC-CCCCCCCCHHHHHCEEECCCCHHHHHHHHHHHHHHHHHHHCEEEEEEECHHHHHHHHHHHHHHHHC
T ss_conf             4566337753456-320123868765006852874108999999999865444230699996325789999999865402


Q ss_pred             ----CHHHHHHHHHHHHCCC-CEECCCCCCCHHHHHHHHHHHHCCCEEEEEECHHHHCCCCCCCCCEEEEECHHHCCHHH
Q ss_conf             ----0146666666866371-03120146998999999999755986999980034104688876589985852547468
Q gi|254780945|r  501 ----RSVVERFNSLHEHFTS-SIAIIHGRMSDIDKESVMDSFKNGTCKLLIATTVIEVGIDVVDASIIIIENAEHFGLAQ  575 (700)
Q Consensus       501 ----~~~~~~~~~l~~~~~~-~v~~lHGkm~~~ek~~~m~~F~~g~~~iLvaTtviEVGvdvpna~~mvI~~aerfGLsq  575 (700)
                          .+....-+-+...|-+ ++--|||-|..+|...+...|+.-+--||.||-|.--|+|+|+.+++|=+||--=----
T Consensus       452 ~~e~~s~~~~s~g~~~l~~~~k~~rLHGsm~QeeRts~f~~Fs~~~~~VLLcTDVAaRGLDlP~V~~vVQYd~P~s~ady  531 (708)
T KOG0348         452 HLEGSSGAPDSEGLPPLFMDLKFYRLHGSMEQEERTSVFQEFSHSRRAVLLCTDVAARGLDLPHVGLVVQYDPPFSTADY  531 (708)
T ss_pred             CCCCCCCCCCCCCCHHHHHCCEEEEECCCHHHHHHHHHHHHHCCCCCEEEEEHHHHHCCCCCCCCCEEEEECCCCCHHHH
T ss_conf             32366678666798103314637884274348899999875303544278850345426888776769982799988999


Q ss_pred             HHHHHHCCCCCCCCEEEEEEECCCCCHHHHHHHHHHHHHCHHHHHHHHHHH
Q ss_conf             877301166789835999970888998799999999841425899999985
Q gi|254780945|r  576 LHQLRGRVGRGEEISSCILLYHPPLSKNSYTRLSVLKNTEDGFLIAEEDLK  626 (700)
Q Consensus       576 LHQLRGRVGRg~~~s~c~l~~~~~~~~~~~~Rl~~l~~~~dGf~iAe~Dl~  626 (700)
                      +|- =||-.|-+..|-.+|..-+.  |.  +=++.+..+..-  +-|.|+.
T Consensus       532 lHR-vGRTARaG~kG~alLfL~P~--Ea--ey~~~l~~~~~~--l~q~~~~  575 (708)
T KOG0348         532 LHR-VGRTARAGEKGEALLFLLPS--EA--EYVNYLKKHHIM--LLQFDME  575 (708)
T ss_pred             HHH-HHHHHHCCCCCCEEEEECCC--HH--HHHHHHHHHCCH--HHCCCHH
T ss_conf             998-40454346777157886651--79--999988750223--4326366


No 46 
>KOG0342 consensus
Probab=99.70  E-value=8.9e-15  Score=135.47  Aligned_cols=314  Identities=21%  Similarity=0.304  Sum_probs=228.1

Q ss_pred             HHHHHHHHCCC-CCCHHHHHHHHHHHHHHCCCCCCEEEEEECCCCCHHHHHHHHHHHHH-------HHHCCEEEEEHHHH
Q ss_conf             89999863024-67988999999999841001343078862144223699999973344-------43054588612799
Q gi|254780945|r  261 IAQKILRNIPF-SPTKSQESAIKDILQDMSQKNRMLRILQGDVGSGKTLVALIAMAAAV-------EAGGQAVIMAPIGI  332 (700)
Q Consensus       261 ~~~~f~~~LPF-~LT~~Q~~ai~eI~~Dl~~~~pM~RLLQGDVGSGKTiVA~~A~l~~~-------~~G~Q~alMaPTEI  332 (700)
                      ...+-++...| .+|.=|++++.+|..-    +  .-|.+--.|||||+-.++.+...+       .+|--|.+.+||-.
T Consensus        92 ~t~kAi~~~GF~~MT~VQ~~ti~pll~g----k--Dvl~~AKTGtGKTlAFLiPaie~l~k~~~~~r~~~~vlIi~PTRE  165 (543)
T KOG0342          92 LTLKAIKEMGFETMTPVQQKTIPPLLEG----K--DVLAAAKTGTGKTLAFLLPAIELLRKLKFKPRNGTGVLIICPTRE  165 (543)
T ss_pred             HHHHHHHHCCCCCCHHHHHHHCCCCCCC----C--CCEEEECCCCCCEEEEHHHHHHHHHHCCCCCCCCEEEEEECCCHH
T ss_conf             8887887358530028887426766798----4--312451268874101046899999853657778714899656289


Q ss_pred             HHHHHHHHHHHHCCCC-CCEEEEEECCCCHHHHHHHHHHHCCCCCEEEEECHHHC----C--CCCCCCCCCEEEECCCCC
Q ss_conf             9999998621101457-86589962464225667687762134754864111201----3--345544441788521013
Q gi|254780945|r  333 LAQQHYEFIKKYTQNT-QIIVEIITGNMPQAHRRKALERIAHGQAHIIIGTHALF----Q--DSIQYYKLILVIVDEQHR  405 (700)
Q Consensus       333 LA~QH~~~~~~~~~~~-~i~v~lLtg~~~~~er~~i~~~i~~G~~~iiIGTHAL~----q--~~v~F~~LgLvViDEQHR  405 (700)
                      ||-|-|...++++... ++.|.++-|++..   ..--+++.. -++|+|.|--=+    |  ....|+++-.-|+||--|
T Consensus       166 LA~Q~~~eak~Ll~~h~~~~v~~viGG~~~---~~e~~kl~k-~~niliATPGRLlDHlqNt~~f~~r~~k~lvlDEADr  241 (543)
T KOG0342         166 LAMQIFAEAKELLKYHESITVGIVIGGNNF---SVEADKLVK-GCNILIATPGRLLDHLQNTSGFLFRNLKCLVLDEADR  241 (543)
T ss_pred             HHHHHHHHHHHHHHHCCCCCEEEEECCCCC---HHHHHHHHC-CCCEEEECCCHHHHHHHCCCCCHHHCCCEEEEECCHH
T ss_conf             999899999999972767734787677410---589997515-5527886784177676557841221220357502035


Q ss_pred             C-------CHHHHHHHHHCCCCCCCEEECHHHHHH--HHHHHHHHCCCHHHHCCCCCCCCCCE-----EEEEECCC--HH
Q ss_conf             3-------568899874025677610101013227--89999752010111102355766620-----79997020--02
Q gi|254780945|r  406 F-------GVQQRLKLTQKATAPHVLLMTATPIPR--TLVLTSLGDIDISKITEKPAGRKPIK-----TVIIPINR--ID  469 (700)
Q Consensus       406 F-------GV~QR~~L~~Kg~~ph~L~MtATPIPR--TLal~~ygdldvS~i~e~P~gR~~I~-----T~~~~~~~--~~  469 (700)
                      -       +++|=.++.-  ..--.+..|||-=|.  -||....+- |-..|+....|..+-.     -+++....  .-
T Consensus       242 lLd~GF~~di~~Ii~~lp--k~rqt~LFSAT~~~kV~~l~~~~L~~-d~~~v~~~d~~~~~The~l~Qgyvv~~~~~~f~  318 (543)
T KOG0342         242 LLDIGFEEDVEQIIKILP--KQRQTLLFSATQPSKVKDLARGALKR-DPVFVNVDDGGERETHERLEQGYVVAPSDSRFS  318 (543)
T ss_pred             HHHCCCHHHHHHHHHHCC--CCCCEEEEECCCCHHHHHHHHHHHCC-CCEEEECCCCCCCCHHHCCCCEEEECCCCCHHH
T ss_conf             665251888999987523--55304676478968899999876337-746862478997302324664079626541179


Q ss_pred             HHHHHHHHHHCCCCEEEEEECCCCCCCCCCCCHHHHHHHHHHHHCCCCEECCCCCCCHHHHHHHHHHHHCCCEEEEEECH
Q ss_conf             68999976310387389997120122111210146666666866371031201469989999999997559869999800
Q gi|254780945|r  470 EVIERLKVVLSEGKKAYWICPQIEEKKESNFRSVVERFNSLHEHFTSSIAIIHGRMSDIDKESVMDSFKNGTCKLLIATT  549 (700)
Q Consensus       470 ~~~~~i~~~l~~g~q~y~VcPlIeese~~~~~~~~~~~~~l~~~~~~~v~~lHGkm~~~ek~~~m~~F~~g~~~iLvaTt  549 (700)
                      -+|.++++.+.+ -.+.|-||.+         ..+..+..|-++..-.|-.+|||++....-.+..+|++-+.-|||||-
T Consensus       319 ll~~~LKk~~~~-~KiiVF~sT~---------~~vk~~~~lL~~~dlpv~eiHgk~~Q~kRT~~~~~F~kaesgIL~cTD  388 (543)
T KOG0342         319 LLYTFLKKNIKR-YKIIVFFSTC---------MSVKFHAELLNYIDLPVLEIHGKQKQNKRTSTFFEFCKAESGILVCTD  388 (543)
T ss_pred             HHHHHHHHHCCC-CEEEEEECHH---------HHHHHHHHHHHHCCCCHHHHHCCCCCCCCCHHHHHHHHCCCCEEEECC
T ss_conf             999999973477-2499993302---------679999999850687532442578532202389988610664399603


Q ss_pred             HHHCCCCCCCCCEEEEECHHHCCHHHHHHHHHCCCCCCCCEEEEEEECC
Q ss_conf             3410468887658998585254746887730116678983599997088
Q gi|254780945|r  550 VIEVGIDVVDASIIIIENAEHFGLAQLHQLRGRVGRGEEISSCILLYHP  598 (700)
Q Consensus       550 viEVGvdvpna~~mvI~~aerfGLsqLHQLRGRVGRg~~~s~c~l~~~~  598 (700)
                      |.--|+|+||.+.+|=++.--=-=--.|-+ ||-||.++.|..+|+.-+
T Consensus       389 VaARGlD~P~V~~VvQ~~~P~d~~~YIHRv-GRTaR~gk~G~alL~l~p  436 (543)
T KOG0342         389 VAARGLDIPDVDWVVQYDPPSDPEQYIHRV-GRTAREGKEGKALLLLAP  436 (543)
T ss_pred             HHHCCCCCCCCEEEEEECCCCCHHHHHHHH-CCCCCCCCCCEEEEEECH
T ss_conf             221368888840799858999989989873-212236898638999676


No 47 
>KOG0333 consensus
Probab=99.69  E-value=4.7e-14  Score=129.81  Aligned_cols=321  Identities=23%  Similarity=0.299  Sum_probs=210.1

Q ss_pred             CHHHHHHHHHCCC-CCCHHHHHHHHHHHHHHCCCCCCEEEEEECCCCCHHHHHHHHHHHHH------------HHHCCEE
Q ss_conf             5789999863024-67988999999999841001343078862144223699999973344------------4305458
Q gi|254780945|r  259 GKIAQKILRNIPF-SPTKSQESAIKDILQDMSQKNRMLRILQGDVGSGKTLVALIAMAAAV------------EAGGQAV  325 (700)
Q Consensus       259 ~~~~~~f~~~LPF-~LT~~Q~~ai~eI~~Dl~~~~pM~RLLQGDVGSGKTiVA~~A~l~~~------------~~G~Q~a  325 (700)
                      .+++. .+....| +.|.=|..||--..  -..    +-|.--..|||||.-.++-++..+            .-|--+.
T Consensus       254 ~e~l~-~I~~~~y~eptpIqR~aipl~l--Q~r----D~igvaETgsGktaaf~ipLl~~IsslP~~~~~en~~~gpyai  326 (673)
T KOG0333         254 LELLS-VIKKPGYKEPTPIQRQAIPLGL--QNR----DPIGVAETGSGKTAAFLIPLLIWISSLPPMARLENNIEGPYAI  326 (673)
T ss_pred             HHHHH-HHHHCCCCCCCHHHHHHCCCHH--CCC----CEEEEEECCCCCCCCCHHHHHHHHHCCCCCCHHHHCCCCCEEE
T ss_conf             89999-9973489998467886311010--147----7236873167753200015889987089841444234686001


Q ss_pred             EEEHHHHHHHHHHHHHHHHCCCCCCEEEEEECCCCHHHHHHHHHHHCCCCCEEEEECH-----HHCCCCCCCCCCCEEEE
Q ss_conf             8612799999999862110145786589962464225667687762134754864111-----20133455444417885
Q gi|254780945|r  326 IMAPIGILAQQHYEFIKKYTQNTQIIVEIITGNMPQAHRRKALERIAHGQAHIIIGTH-----ALFQDSIQYYKLILVIV  400 (700)
Q Consensus       326 lMaPTEILA~QH~~~~~~~~~~~~i~v~lLtg~~~~~er~~i~~~i~~G~~~iiIGTH-----AL~q~~v~F~~LgLvVi  400 (700)
                      +||||-=||+|.++.-.++..++|+++.-+.|..+--|.   --.+..| +.|+|||-     .|=+-.+..+.-.+||-
T Consensus       327 ilaptReLaqqIeeEt~kf~~~lg~r~vsvigg~s~EEq---~fqls~g-ceiviatPgrLid~Lenr~lvl~qctyvvl  402 (673)
T KOG0333         327 ILAPTRELAQQIEEETNKFGKPLGIRTVSVIGGLSFEEQ---GFQLSMG-CEIVIATPGRLIDSLENRYLVLNQCTYVVL  402 (673)
T ss_pred             EECHHHHHHHHHHHHHHHHCCCCCCEEEEEECCCCHHHH---HHHHHCC-CEEEECCCHHHHHHHHHHHHHHCCCCEEEC
T ss_conf             203379999999999987503014328998546336653---0246415-414424740788877778887505846762


Q ss_pred             CCCCCC---CH-HHHHHHHHC--------------C------------CCCCCEEECHHHHHHH--HHHHHHHCCCHHHH
Q ss_conf             210133---56-889987402--------------5------------6776101010132278--99997520101111
Q gi|254780945|r  401 DEQHRF---GV-QQRLKLTQK--------------A------------TAPHVLLMTATPIPRT--LVLTSLGDIDISKI  448 (700)
Q Consensus       401 DEQHRF---GV-~QR~~L~~K--------------g------------~~ph~L~MtATPIPRT--Lal~~ygdldvS~i  448 (700)
                      ||--|-   |- .|=.+.++.              |            ..--.++.|||==|+-  ||-+++-+--+-.|
T Consensus       403 deadrmiDmgfE~dv~~iL~~mPssn~k~~tde~~~~~~~~~~~~~~k~yrqT~mftatm~p~verlar~ylr~pv~vti  482 (673)
T KOG0333         403 DEADRMIDMGFEPDVQKILEQMPSSNAKPDTDEKEGEERVRKNFSSSKKYRQTVMFTATMPPAVERLARSYLRRPVVVTI  482 (673)
T ss_pred             CCHHHHHCCCCCHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHCCCCCCEEEEEEEECCCCHHHHHHHHHHHHCCEEEEE
T ss_conf             40666542466677888998387634588863102188887510312102578998447876799999998527769995


Q ss_pred             C--CCCCCCCCCEEEEEECCCHHHHHHHHHHHHCCCCE-EEEEECCCCCCCCCCCCHHHHHHHHHHHHCCCCEECCCCCC
Q ss_conf             0--23557666207999702002689999763103873-89997120122111210146666666866371031201469
Q gi|254780945|r  449 T--EKPAGRKPIKTVIIPINRIDEVIERLKVVLSEGKK-AYWICPQIEEKKESNFRSVVERFNSLHEHFTSSIAIIHGRM  525 (700)
Q Consensus       449 ~--e~P~gR~~I~T~~~~~~~~~~~~~~i~~~l~~g~q-~y~VcPlIeese~~~~~~~~~~~~~l~~~~~~~v~~lHGkm  525 (700)
                      .  .+|.-|.  .-+|+....-++ +..+.+.++++.+ -.+|.-       ...++++...+.|.+. +.++-.|||--
T Consensus       483 g~~gk~~~rv--eQ~v~m~~ed~k-~kkL~eil~~~~~ppiIIFv-------N~kk~~d~lAk~LeK~-g~~~~tlHg~k  551 (673)
T KOG0333         483 GSAGKPTPRV--EQKVEMVSEDEK-RKKLIEILESNFDPPIIIFV-------NTKKGADALAKILEKA-GYKVTTLHGGK  551 (673)
T ss_pred             CCCCCCCCCH--HEEEEEECCHHH-HHHHHHHHHHCCCCCEEEEE-------ECHHHHHHHHHHHHHC-CCEEEEEECCC
T ss_conf             4678986021--117888155688-99999999847999879998-------3132489999998644-32479961785


Q ss_pred             CHHHHHHHHHHHHCCCEEEEEECHHHHCCCCCCCCCEEEEECHHHCCHHHHHHHHHCCCCCCCCEEEEEEECCCCCH
Q ss_conf             98999999999755986999980034104688876589985852547468877301166789835999970888998
Q gi|254780945|r  526 SDIDKESVMDSFKNGTCKLLIATTVIEVGIDVVDASIIIIENAEHFGLAQLHQLRGRVGRGEEISSCILLYHPPLSK  602 (700)
Q Consensus       526 ~~~ek~~~m~~F~~g~~~iLvaTtviEVGvdvpna~~mvI~~aerfGLsqLHQLRGRVGRg~~~s~c~l~~~~~~~~  602 (700)
                      +.++.+.++++|++|..+|||||.|.--||||||.++.|=++--.==--=+|-. ||-||-++.|..+-.+.+..++
T Consensus       552 ~qeQRe~aL~~fr~~t~dIlVaTDvAgRGIDIpnVSlVinydmaksieDYtHRI-GRTgRAGk~GtaiSflt~~dt~  627 (673)
T KOG0333         552 SQEQRENALADFREGTGDILVATDVAGRGIDIPNVSLVINYDMAKSIEDYTHRI-GRTGRAGKSGTAISFLTPADTA  627 (673)
T ss_pred             CHHHHHHHHHHHHHCCCCEEEEECCCCCCCCCCCCCEEEECCHHHHHHHHHHHH-CCCCCCCCCCEEEEEECCCHHH
T ss_conf             277899999998715787799832212577777612146220556589998874-2344466675368986401117


No 48 
>KOG0345 consensus
Probab=99.69  E-value=1.3e-13  Score=126.43  Aligned_cols=316  Identities=21%  Similarity=0.328  Sum_probs=209.3

Q ss_pred             HHHHHHHHHCCC-CCCHHHHHHHHHHHHHHCCCCCCEEEEEECCCCCHHHHHHHHHHHHH--H----HH--CCEEEEEHH
Q ss_conf             789999863024-67988999999999841001343078862144223699999973344--4----30--545886127
Q gi|254780945|r  260 KIAQKILRNIPF-SPTKSQESAIKDILQDMSQKNRMLRILQGDVGSGKTLVALIAMAAAV--E----AG--GQAVIMAPI  330 (700)
Q Consensus       260 ~~~~~f~~~LPF-~LT~~Q~~ai~eI~~Dl~~~~pM~RLLQGDVGSGKTiVA~~A~l~~~--~----~G--~Q~alMaPT  330 (700)
                      .++.+-+....| ..|+-|..+|-...+    .+-  -.++--.|||||+-.++-|+-.+  .    ..  .-+.+.+||
T Consensus        15 ~~l~~~l~~~GF~~mTpVQa~tIPlll~----~KD--VvveavTGSGKTlAFllP~le~i~rr~~~~~~~~vgalIIsPT   88 (567)
T KOG0345          15 PWLLEALDESGFEKMTPVQAATIPLLLK----NKD--VVVEAVTGSGKTLAFLLPMLEIIYRREAKTPPGQVGALIISPT   88 (567)
T ss_pred             HHHHHHHHHCCCCCCCHHHHHHHHHHHC----CCC--EEEECCCCCCCCHHHHHHHHHHHHHHCCCCCCCCEEEEEECCC
T ss_conf             8999999862886368778746678852----785--6898567887106689999999986115789651247996571


Q ss_pred             HHHHHHHHHHHHHHCCC-CCCEEEEEECCCCHHHHHHHHHHHCCCCCEEEEECH----HHCC---CCCCCCCCCEEEECC
Q ss_conf             99999999862110145-786589962464225667687762134754864111----2013---345544441788521
Q gi|254780945|r  331 GILAQQHYEFIKKYTQN-TQIIVEIITGNMPQAHRRKALERIAHGQAHIIIGTH----ALFQ---DSIQYYKLILVIVDE  402 (700)
Q Consensus       331 EILA~QH~~~~~~~~~~-~~i~v~lLtg~~~~~er~~i~~~i~~G~~~iiIGTH----AL~q---~~v~F~~LgLvViDE  402 (700)
                      -=||.|.++-...++.. .++++.|++|+.+..   +-+..++.-.++|+|||-    -++|   +.+.|++|.+.|+||
T Consensus        89 RELa~QI~~V~~~F~~~l~~l~~~l~vGG~~v~---~Di~~fkee~~nIlVgTPGRL~di~~~~~~~l~~rsLe~LVLDE  165 (567)
T KOG0345          89 RELARQIREVAQPFLEHLPNLNCELLVGGRSVE---EDIKTFKEEGPNILVGTPGRLLDILQREAEKLSFRSLEILVLDE  165 (567)
T ss_pred             HHHHHHHHHHHHHHHHHCCCCCEEEEECCCCHH---HHHHHHHHHCCCEEEECCHHHHHHHHCHHHCCCCCCCCEEEECC
T ss_conf             999999999999999850365459997686477---79999997099589947624999984530003613311577514


Q ss_pred             CCCC---C----HHHHHHHHHCCCCCCCEEECHHHHHHHHHHHHHHCC---CHHHHC-C---CCCCCCCCEEEEEEC-CC
Q ss_conf             0133---5----688998740256776101010132278999975201---011110-2---355766620799970-20
Q gi|254780945|r  403 QHRF---G----VQQRLKLTQKATAPHVLLMTATPIPRTLVLTSLGDI---DISKIT-E---KPAGRKPIKTVIIPI-NR  467 (700)
Q Consensus       403 QHRF---G----V~QR~~L~~Kg~~ph~L~MtATPIPRTLal~~ygdl---dvS~i~-e---~P~gR~~I~T~~~~~-~~  467 (700)
                      --|+   |    |++=....-|....  =..|||-----=-|...|--   .||+=. .   .|. +....-.+++. .+
T Consensus       166 ADrLldmgFe~~~n~ILs~LPKQRRT--GLFSATq~~~v~dL~raGLRNpv~V~V~~k~~~~tPS-~L~~~Y~v~~a~eK  242 (567)
T KOG0345         166 ADRLLDMGFEASVNTILSFLPKQRRT--GLFSATQTQEVEDLARAGLRNPVRVSVKEKSKSATPS-SLALEYLVCEADEK  242 (567)
T ss_pred             HHHHHCCCHHHHHHHHHHHCCCCCCC--CCCEEHHHHHHHHHHHHHCCCCEEEEECCCCCCCCCH-HHHHEEEEECHHHH
T ss_conf             67674432799999999866210002--4430021466889998535686365412344555842-31112567577888


Q ss_pred             HHHHHHHHHHHHCCCCEEEEEECCCCCCCCCCCCHHHHHHHHHHHHCCC-CEECCCCCCCHHHHHHHHHHHHCCCEEEEE
Q ss_conf             0268999976310387389997120122111210146666666866371-031201469989999999997559869999
Q gi|254780945|r  468 IDEVIERLKVVLSEGKKAYWICPQIEEKKESNFRSVVERFNSLHEHFTS-SIAIIHGRMSDIDKESVMDSFKNGTCKLLI  546 (700)
Q Consensus       468 ~~~~~~~i~~~l~~g~q~y~VcPlIeese~~~~~~~~~~~~~l~~~~~~-~v~~lHGkm~~~ek~~~m~~F~~g~~~iLv  546 (700)
                      ...+++++...-.  ..+.|-.|.        -.+|+=.+..+....+. .+--+||||+..+.+.++++|++-.-.+|.
T Consensus       243 ~~~lv~~L~~~~~--kK~iVFF~T--------CasVeYf~~~~~~~l~~~~i~~iHGK~~q~~R~k~~~~F~~~~~~vl~  312 (567)
T KOG0345         243 LSQLVHLLNNNKD--KKCIVFFPT--------CASVEYFGKLFSRLLKKREIFSIHGKMSQKARAKVLEAFRKLSNGVLF  312 (567)
T ss_pred             HHHHHHHHHCCCC--CCEEEEECC--------CCHHHHHHHHHHHHHCCCCEEEECCHHCCHHHHHHHHHHHHCCCCEEE
T ss_conf             9999999962454--627999347--------540999998888760787479862201234688999998715686188


Q ss_pred             ECHHHHCCCCCCCCCEEEEECHHHCCHHHHHHHHHCCCCCCCCEEEEEEECC
Q ss_conf             8003410468887658998585254746887730116678983599997088
Q gi|254780945|r  547 ATTVIEVGIDVVDASIIIIENAEHFGLAQLHQLRGRVGRGEEISSCILLYHP  598 (700)
Q Consensus       547 aTtviEVGvdvpna~~mvI~~aerfGLsqLHQLRGRVGRg~~~s~c~l~~~~  598 (700)
                      ||-|---|+|+|+....|=.|.-.=-=+=.|- -||-||.+.+|..+....+
T Consensus       313 ~TDVaARGlDip~iD~VvQ~DpP~~~~~FvHR-~GRTaR~gr~G~Aivfl~p  363 (567)
T KOG0345         313 CTDVAARGLDIPGIDLVVQFDPPKDPSSFVHR-CGRTARAGREGNAIVFLNP  363 (567)
T ss_pred             EEHHHHCCCCCCCCEEEEECCCCCCHHHHHHH-CCHHHHCCCCCCEEEEECC
T ss_conf             60455536898897079970799981477774-1214435676634899766


No 49 
>PRK09751 putative ATP-dependent helicase Lhr; Provisional
Probab=99.68  E-value=4.1e-14  Score=130.24  Aligned_cols=278  Identities=22%  Similarity=0.300  Sum_probs=192.7

Q ss_pred             CCCCHHHHHHHHHHHHHH-------------HHCCEEEEEHHHHHHHHHHHHHHHHCC------------CCCCEEEEEE
Q ss_conf             442236999999733444-------------305458861279999999986211014------------5786589962
Q gi|254780945|r  302 VGSGKTLVALIAMAAAVE-------------AGGQAVIMAPIGILAQQHYEFIKKYTQ------------NTQIIVEIIT  356 (700)
Q Consensus       302 VGSGKTiVA~~A~l~~~~-------------~G~Q~alMaPTEILA~QH~~~~~~~~~------------~~~i~v~lLt  356 (700)
                      .|||||.-|++.++..+-             .+.++.+..|+--||.--..|+..-+.            ..+|+|+.=|
T Consensus         5 TGSGKTLAAFL~aLd~L~~~~~~~~~~~~~~~~~~VLYISPLKALa~Dv~rNL~~PL~gI~~~~~~~g~~~~~i~V~vRt   84 (1490)
T PRK09751          5 TGSGKTLAAFLYALDRLFREGGEDTREAHKRKTSRILYISPIKALGTDVQRNLQIPLKGIADERRRRGETEVNLRVGIRT   84 (1490)
T ss_pred             CCCCHHHHHHHHHHHHHHHHCCCCCCCCCCCCCEEEEEECCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCEEEEEC
T ss_conf             87439899999999999961455555567889738999592788899999999879988899998625678997586379


Q ss_pred             CCCCHHHHHHHHHHHCCCCCEEEEEC----HHHCCC--CCCCCCCCEEEECCCC-----CCCHHHHHHHHHC----CCCC
Q ss_conf             46422566768776213475486411----120133--4554444178852101-----3356889987402----5677
Q gi|254780945|r  357 GNMPQAHRRKALERIAHGQAHIIIGT----HALFQD--SIQYYKLILVIVDEQH-----RFGVQQRLKLTQK----ATAP  421 (700)
Q Consensus       357 g~~~~~er~~i~~~i~~G~~~iiIGT----HAL~q~--~v~F~~LgLvViDEQH-----RFGV~QR~~L~~K----g~~p  421 (700)
                      |.|+.+||++...    .-++|+|-|    |.++..  .=.|++|-.|||||=|     |+|++==..|..-    +..+
T Consensus        85 GDT~~~eR~r~~r----~PPdILITTPESL~LlLtsk~r~~L~~v~~VIVDEiHalagsKRGahLaLsLeRL~~l~~~~~  160 (1490)
T PRK09751         85 GDTPAQERSKLTR----NPPDILITTPESLYLMLTSRARETLRGVETVIIDEVHAVAGSKRGAHLALSLERLDALLHTSA  160 (1490)
T ss_pred             CCCCHHHHHHHHH----CCCCEEEECHHHHHHHHHHHHHHHHCCCCEEEECCCHHHHCCCCHHHHHHHHHHHHHHCCCCC
T ss_conf             9999999999850----899839848899999873569999779989996286442058839999999999998658999


Q ss_pred             CCEEECHHHHHHHHHHHHHHC-CCHHHHCCCCCCCCCCEEEEEECCCH-----------------------HHHHHHHHH
Q ss_conf             610101013227899997520-10111102355766620799970200-----------------------268999976
Q gi|254780945|r  422 HVLLMTATPIPRTLVLTSLGD-IDISKITEKPAGRKPIKTVIIPINRI-----------------------DEVIERLKV  477 (700)
Q Consensus       422 h~L~MtATPIPRTLal~~ygd-ldvS~i~e~P~gR~~I~T~~~~~~~~-----------------------~~~~~~i~~  477 (700)
                      -..-+|||=-|-..+....|. -.+.+++ .|..++.-...+++..++                       ..++..+.+
T Consensus       161 qRIGLSATv~p~e~vA~fLgg~rpv~IV~-~~~~k~~~l~v~vPv~d~~~~~~~~~~~g~~~~~~~~~siw~~v~~~i~~  239 (1490)
T PRK09751        161 QRIGLSATVRSASDVAAFLGGDRPVTVVN-PPAMRHPQIRIVVPVANMDDVSSVASGTGEDSHAGREGSIWPYIETGILD  239 (1490)
T ss_pred             CEEEEECCCCCHHHHHHHHCCCCCEEEEC-CCCCCCCEEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHH
T ss_conf             68999776689999998737999837868-88888752799704665333332356776322355545316788999999


Q ss_pred             HHCCCCEEEEEECCCCCCCCCCCCHHHHHHHHHHHHCCCC------E--------------------------ECCCCCC
Q ss_conf             3103873899971201221112101466666668663710------3--------------------------1201469
Q gi|254780945|r  478 VLSEGKKAYWICPQIEEKKESNFRSVVERFNSLHEHFTSS------I--------------------------AIIHGRM  525 (700)
Q Consensus       478 ~l~~g~q~y~VcPlIeese~~~~~~~~~~~~~l~~~~~~~------v--------------------------~~lHGkm  525 (700)
                      .+.+++-..|-+-        .-..+|.....|++.+..+      +                          ..=||-|
T Consensus       240 ~i~~hrsTLVF~N--------TR~~AErl~~~L~el~~erl~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~ia~aHHGSl  311 (1490)
T PRK09751        240 EVLRHRSTIVFTN--------SRGLAEKLTARLNELYAARLQRSPSIAVDAAHFESTSGATSNRVQSSDVFIARSHHGSV  311 (1490)
T ss_pred             HHHHCCCEEEEEC--------CHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
T ss_conf             9972687699978--------87999999999999999873246432211000011122221123566543344555768


Q ss_pred             CHHHHHHHHHHHHCCCEEEEEECHHHHCCCCCCCCCEEEEECHHHCCHHHHHHHHHCCCCCCC----CEEEEEEE
Q ss_conf             989999999997559869999800341046888765899858525474688773011667898----35999970
Q gi|254780945|r  526 SDIDKESVMDSFKNGTCKLLIATTVIEVGIDVVDASIIIIENAEHFGLAQLHQLRGRVGRGEE----ISSCILLY  596 (700)
Q Consensus       526 ~~~ek~~~m~~F~~g~~~iLvaTtviEVGvdvpna~~mvI~~aerfGLsqLHQLRGRVGRg~~----~s~c~l~~  596 (700)
                      +.++...+=+++++|+.+.+|||+=.|-|||+-.....|-.++-+ +.|-+-|   ||||.++    .|..+++.
T Consensus       312 Ske~R~~vE~~LK~G~LraVVaTSSLELGIDiG~VDlVVQvgsP~-sVAs~lQ---RvGRAGH~vg~~S~g~~~p  382 (1490)
T PRK09751        312 SKEQRAITEQALKSGELRCVVATSSLELGIDMGAVDLVIQVATPL-SVASGLQ---RIGRAGHQVGGVSKGLFFP  382 (1490)
T ss_pred             CHHHHHHHHHHHHCCCCCEEEECCCHHHCCCCCCCCEEEEECCCH-HHHHHHH---HHCCCCCCCCCCCCEEEEC
T ss_conf             999999999998679977899778054077644655799806966-7889999---7101257889844079962


No 50 
>COG1202 Superfamily II helicase, archaea-specific [General function prediction only]
Probab=99.66  E-value=1.6e-14  Score=133.37  Aligned_cols=315  Identities=21%  Similarity=0.267  Sum_probs=224.2

Q ss_pred             HHHHHHHCC-CCCCHHHHHHHHHHHHHHCCCCCCEEEEEECCCCCHHHHHHHHHHHHHHH-HCCEEEEEHHHHHHHHHHH
Q ss_conf             999986302-46798899999999984100134307886214422369999997334443-0545886127999999998
Q gi|254780945|r  262 AQKILRNIP-FSPTKSQESAIKDILQDMSQKNRMLRILQGDVGSGKTLVALIAMAAAVEA-GGQAVIMAPIGILAQQHYE  339 (700)
Q Consensus       262 ~~~f~~~LP-F~LT~~Q~~ai~eI~~Dl~~~~pM~RLLQGDVGSGKTiVA~~A~l~~~~~-G~Q~alMaPTEILA~QH~~  339 (700)
                      .+..++.-. =+|+.-|-.|++.   -|-.+.  |-|+---.+||||+|+-+|-+.-+-+ |..-.+++|---||.|-|+
T Consensus       205 fk~~lk~~G~~eLlPVQ~laVe~---GLLeG~--nllVVSaTasGKTLIgElAGi~~~l~~g~KmlfLvPLVALANQKy~  279 (830)
T COG1202         205 FKRMLKREGIEELLPVQVLAVEA---GLLEGE--NLLVVSATASGKTLIGELAGIPRLLSGGKKMLFLVPLVALANQKYE  279 (830)
T ss_pred             HHHHHHHCCCCEECCHHHHHHHH---CCCCCC--CEEEEECCCCCCCHHHHHHCCHHHHHCCCEEEEEEHHHHHHCCHHH
T ss_conf             99999863864430234655661---440577--3499940577751477763738788378728997316876311189


Q ss_pred             HHHHHCCCCCCEEEEEECCCCHHHHHHHHHHHCCCCCEEEEEC-----HHHCCCCCCCCCCCEEEECCCCCCCHHHH---
Q ss_conf             6211014578658996246422566768776213475486411-----12013345544441788521013356889---
Q gi|254780945|r  340 FIKKYTQNTQIIVEIITGNMPQAHRRKALERIAHGQAHIIIGT-----HALFQDSIQYYKLILVIVDEQHRFGVQQR---  411 (700)
Q Consensus       340 ~~~~~~~~~~i~v~lLtg~~~~~er~~i~~~i~~G~~~iiIGT-----HAL~q~~v~F~~LgLvViDEQHRFGV~QR---  411 (700)
                      .|+..+.++|+++++-.|...-+.+.+--..-.+-.+||||||     |.|=. .....+.|-|||||=|-.--+.|   
T Consensus       280 dF~~rYs~LglkvairVG~srIk~~~~pv~~~t~~dADIIVGTYEGiD~lLRt-g~~lgdiGtVVIDEiHtL~deERG~R  358 (830)
T COG1202         280 DFKERYSKLGLKVAIRVGMSRIKTREEPVVVDTSPDADIIVGTYEGIDYLLRT-GKDLGDIGTVVIDEIHTLEDEERGPR  358 (830)
T ss_pred             HHHHHHHCCCCEEEEEECHHHHCCCCCCCCCCCCCCCCEEEEECHHHHHHHHC-CCCCCCCCEEEEEEEEECCCHHCCCC
T ss_conf             99998650166278884234522467753568998776798611107899870-78555443599650120440101632


Q ss_pred             -------HHHHHCCCCCCCEEECHHH-HHHHHHHHHHHCCCHHHHCCCCCCCCCCEEEEEECCCHHHHHHHH----HHHH
Q ss_conf             -------9874025677610101013-227899997520101111023557666207999702002689999----7631
Q gi|254780945|r  412 -------LKLTQKATAPHVLLMTATP-IPRTLVLTSLGDIDISKITEKPAGRKPIKTVIIPINRIDEVIERL----KVVL  479 (700)
Q Consensus       412 -------~~L~~Kg~~ph~L~MtATP-IPRTLal~~ygdldvS~i~e~P~gR~~I~T~~~~~~~~~~~~~~i----~~~l  479 (700)
                             ..-.-  ..+.++.+|||- =|--||-  +=++....-++.|   .|+.-+++-..+..+-|+.|    +.+-
T Consensus       359 LdGLI~RLr~l~--~~AQ~i~LSATVgNp~elA~--~l~a~lV~y~~RP---VplErHlvf~~~e~eK~~ii~~L~k~E~  431 (830)
T COG1202         359 LDGLIGRLRYLF--PGAQFIYLSATVGNPEELAK--KLGAKLVLYDERP---VPLERHLVFARNESEKWDIIARLVKREF  431 (830)
T ss_pred             HHHHHHHHHHHC--CCCEEEEEEEECCCHHHHHH--HHCCEEEEECCCC---CCHHHEEEEECCCHHHHHHHHHHHHHHH
T ss_conf             352899999867--77749998743388699998--8387258655887---8736706640481677789999999997


Q ss_pred             C----CC--CEEEEEECCCCCCCCCCCCHHHHHHHHHHHHCCCCEECCCCCCCHHHHHHHHHHHHCCCEEEEEECHHHHC
Q ss_conf             0----38--73899971201221112101466666668663710312014699899999999975598699998003410
Q gi|254780945|r  480 S----EG--KKAYWICPQIEEKKESNFRSVVERFNSLHEHFTSSIAIIHGRMSDIDKESVMDSFKNGTCKLLIATTVIEV  553 (700)
Q Consensus       480 ~----~g--~q~y~VcPlIeese~~~~~~~~~~~~~l~~~~~~~v~~lHGkm~~~ek~~~m~~F~~g~~~iLvaTtviEV  553 (700)
                      .    +|  +|+.|- .       ..-+........|... +-+..--|+-|+..|...+=.+|.+++++..|.|.-.-.
T Consensus       432 ~~~sskg~rGQtIVF-T-------~SRrr~h~lA~~L~~k-G~~a~pYHaGL~y~eRk~vE~~F~~q~l~~VVTTAAL~A  502 (830)
T COG1202         432 STESSKGYRGQTIVF-T-------YSRRRCHELADALTGK-GLKAAPYHAGLPYKERKSVERAFAAQELAAVVTTAALAA  502 (830)
T ss_pred             HHHHCCCCCCCEEEE-E-------CCHHHHHHHHHHHHCC-CCCCCCCCCCCCHHHHHHHHHHHHCCCCCEEEEHHHHHC
T ss_conf             544113767736999-4-------2166699999886107-866654437986788888999976087555764245644


Q ss_pred             CCCCCCCCEEE---EECHHHCCHHHHHHHHHCCCCCCC--CEEEEEEECC
Q ss_conf             46888765899---858525474688773011667898--3599997088
Q gi|254780945|r  554 GIDVVDASIII---IENAEHFGLAQLHQLRGRVGRGEE--ISSCILLYHP  598 (700)
Q Consensus       554 Gvdvpna~~mv---I~~aerfGLsqLHQLRGRVGRg~~--~s~c~l~~~~  598 (700)
                      |||.|.-.+|.   -++.+-.-..-.||.-||-||-+.  .|..||+..+
T Consensus       503 GVDFPASQVIFEsLaMG~~WLs~~EF~QM~GRAGRp~yHdrGkVyllvep  552 (830)
T COG1202         503 GVDFPASQVIFESLAMGIEWLSVREFQQMLGRAGRPDYHDRGKVYLLVEP  552 (830)
T ss_pred             CCCCCHHHHHHHHHHCCCCCCCHHHHHHHHCCCCCCCCCCCCEEEEEECC
T ss_conf             78875189999998710432789999998504699872337339999557


No 51 
>PRK09694 hypothetical protein; Provisional
Probab=99.65  E-value=2.5e-13  Score=124.09  Aligned_cols=311  Identities=21%  Similarity=0.276  Sum_probs=198.6

Q ss_pred             CCCCCHHHHHHHHHHHHHHCCCCCCEEEEEECCCCCHHHHHHHHHHHHH-HHHCCEEE-EEHHHHHHHHHHHHHHHHCCC
Q ss_conf             2467988999999999841001343078862144223699999973344-43054588-612799999999862110145
Q gi|254780945|r  270 PFSPTKSQESAIKDILQDMSQKNRMLRILQGDVGSGKTLVALIAMAAAV-EAGGQAVI-MAPIGILAQQHYEFIKKYTQN  347 (700)
Q Consensus       270 PF~LT~~Q~~ai~eI~~Dl~~~~pM~RLLQGDVGSGKTiVA~~A~l~~~-~~G~Q~al-MaPTEILA~QH~~~~~~~~~~  347 (700)
                      .|+.|.-|+.+ .++    . ..|-.-+|--..|||||.-|++++..-. ..|....+ -.||--=|++.|..+.+++..
T Consensus       286 ~~~PrplQ~~~-~~l----~-~~PgL~IiEAptG~GKTEAAL~~A~~L~~~~~~~Gl~faLPT~ATaNaMf~Rv~~~~~~  359 (878)
T PRK09694        286 GYQPRQLQTLV-DAL----P-LAPGLTVIEAPTGSGKTETALAYAWKLIDQQLADSVIFALPTQATANAMLSRMEAAASK  359 (878)
T ss_pred             CCCCCHHHHHH-HHC----C-CCCCEEEEECCCCCCHHHHHHHHHHHHHHHCCCCCEEEECCHHHHHHHHHHHHHHHHHH
T ss_conf             99996799999-845----6-79987999758999758999999999997348983699774798899999999999997


Q ss_pred             C--CCEEEEEECCCCHHHHHHH------------------HHHHCCC-----CCEEEEEC--HHHCCC-CCCCCCC----
Q ss_conf             7--8658996246422566768------------------7762134-----75486411--120133-4554444----
Q gi|254780945|r  348 T--QIIVEIITGNMPQAHRRKA------------------LERIAHG-----QAHIIIGT--HALFQD-SIQYYKL----  395 (700)
Q Consensus       348 ~--~i~v~lLtg~~~~~er~~i------------------~~~i~~G-----~~~iiIGT--HAL~q~-~v~F~~L----  395 (700)
                      .  .-++.|++|+-.-.+...-                  -+-+..|     -..+.|||  +||+.- .+.+..|    
T Consensus       360 ~~~~~~v~LaHg~a~l~~~~~~l~~~~~~~~~~~~~~~~~~~W~~~~~Kr~LLap~~VGTiDQaLla~L~~kH~~LR~~g  439 (878)
T PRK09694        360 LFPSPNLILAHGNSRFNHLFQSIKSRAITEQGQEEAWVQCCQWLSQSNKRVFLGQIGVCTIDQVLISVLPVKHRFIRGLG  439 (878)
T ss_pred             HCCCCCEEEECCHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHCCCHHHHHCCCCEECCHHHHHHHHHCCCHHHHHHHH
T ss_conf             36899769744736550566651013676544543015777664111022313771546799999987461489999998


Q ss_pred             ---CEEEECCCCCCCHHHHHHHHH-----CCCCCCCEEECHHHHHHHH---HHHHHHCCCH----------------HHH
Q ss_conf             ---178852101335688998740-----2567761010101322789---9997520101----------------111
Q gi|254780945|r  396 ---ILVIVDEQHRFGVQQRLKLTQ-----KATAPHVLLMTATPIPRTL---VLTSLGDIDI----------------SKI  448 (700)
Q Consensus       396 ---gLvViDEQHRFGV~QR~~L~~-----Kg~~ph~L~MtATPIPRTL---al~~ygdldv----------------S~i  448 (700)
                         ..|||||=|=+-+-...-|..     ......+++||||= |..+   -+..||.-..                .-.
T Consensus       440 La~kvvIiDEVHAYD~Ym~~lL~~lL~wl~~~g~~viLLSATL-P~~~R~~L~~ay~~~~~~~~~~~~YP~it~~~~~~~  518 (878)
T PRK09694        440 IGRSVLIVDEVHAYDAYMNGLLEAVLKAQAQVGGSVILLSATL-PMTQKQKLLDTYGLHTDPVENNSAYPLINWRGVNGA  518 (878)
T ss_pred             HCCCEEEEECCCCCCHHHHHHHHHHHHHHHHCCCCEEEEECCC-CHHHHHHHHHHHCCCCCCCCCCCCCCEEEECCCCCC
T ss_conf             6287489725333458899999999999998399889992789-899999999975568876666778861363155666


Q ss_pred             CC------CCCCCCCCEEEEEECCC---HHHHHHHHHHHHCCCCEEEEEECCCCCCCCCCCCHHHHHHHHHHHHCCC--C
Q ss_conf             02------35576662079997020---0268999976310387389997120122111210146666666866371--0
Q gi|254780945|r  449 TE------KPAGRKPIKTVIIPINR---IDEVIERLKVVLSEGKKAYWICPQIEEKKESNFRSVVERFNSLHEHFTS--S  517 (700)
Q Consensus       449 ~e------~P~gR~~I~T~~~~~~~---~~~~~~~i~~~l~~g~q~y~VcPlIeese~~~~~~~~~~~~~l~~~~~~--~  517 (700)
                      .+      ..+.|+.|.-..+..+.   -..+.+.+.+.+++|..|-|||-.|+        .|.+.|+.|++.++.  .
T Consensus       519 ~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~l~~~~~~G~~v~vI~NTV~--------rAq~~y~~L~~~~~~~~~  590 (878)
T PRK09694        519 QRFDLLAHQLPPRFSIQPEPICLADMLPDLTMLERMIAAANAGAQVCVICNLVD--------DAQVCYQRLKELNNTQVD  590 (878)
T ss_pred             CCCCCCCCCCCCCCEEEEEEEECCCCCCCHHHHHHHHHHHHCCCEEEEEECCHH--------HHHHHHHHHHHHCCCCCC
T ss_conf             753446555677723788876314447648999999999978995999938899--------999999999985289987


Q ss_pred             EECCCCCCCHHHH----HHHHHHHHCCC----EEEEEECHHHHCCCCCCCCCEEEEECH------HHCCHHHHHHHHHCC
Q ss_conf             3120146998999----99999975598----699998003410468887658998585------254746887730116
Q gi|254780945|r  518 IAIIHGRMSDIDK----ESVMDSFKNGT----CKLLIATTVIEVGIDVVDASIIIIENA------EHFGLAQLHQLRGRV  583 (700)
Q Consensus       518 v~~lHGkm~~~ek----~~~m~~F~~g~----~~iLvaTtviEVGvdvpna~~mvI~~a------erfGLsqLHQLRGRV  583 (700)
                      |.++|+|....++    +++++.|-.+.    -.|||||.|||+-.|+ ++.+||-+-|      .|+|=-+=|+=+.| 
T Consensus       591 v~L~HsRF~~~DR~~~E~~vl~~~Gk~~~r~~g~IlVaTQVvEQSLDi-DfD~liTDLAPiDlLlQR~GRLhRH~R~~R-  668 (878)
T PRK09694        591 IDLFHARFTFNDRREKENRVISNFGKNGKRNVGRILVATQVVEQSLDL-DFDWLITQHCPADLLFQRMGRLHRHHRKYR-  668 (878)
T ss_pred             EEEEECCCCHHHHHHHHHHHHHHHCCCCCCCCCEEEEECCEEEEEECC-CCCHHHCCCCCHHHHHHHHHHHHCCCCCCC-
T ss_conf             799868887766999999999986889889998699977333243033-533011046869999987423205899888-


Q ss_pred             CCCCCCEEEEEEEC
Q ss_conf             67898359999708
Q gi|254780945|r  584 GRGEEISSCILLYH  597 (700)
Q Consensus       584 GRg~~~s~c~l~~~  597 (700)
                      ..|-..-.|+.+.+
T Consensus       669 P~g~~~P~~~Vl~P  682 (878)
T PRK09694        669 PAGFEIPVATILLP  682 (878)
T ss_pred             CCCCCCCEEEEECC
T ss_conf             87777876999788


No 52 
>cd00046 DEXDc DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Probab=99.65  E-value=3.1e-15  Score=139.11  Aligned_cols=131  Identities=33%  Similarity=0.493  Sum_probs=107.7

Q ss_pred             EEEEEECCCCCHHHHHHHHHHHHHH--HHCCEEEEEHHHHHHHHHHHHHHHHCCCCCCEEEEEECCCCHHHHHHHHHHHC
Q ss_conf             0788621442236999999733444--30545886127999999998621101457865899624642256676877621
Q gi|254780945|r  295 LRILQGDVGSGKTLVALIAMAAAVE--AGGQAVIMAPIGILAQQHYEFIKKYTQNTQIIVEIITGNMPQAHRRKALERIA  372 (700)
Q Consensus       295 ~RLLQGDVGSGKTiVA~~A~l~~~~--~G~Q~alMaPTEILA~QH~~~~~~~~~~~~i~v~lLtg~~~~~er~~i~~~i~  372 (700)
                      +-++++.+|||||.+|+++++..+.  .+.++.+|+||..|+.|.++.++++++. +..+...+|..+..++.    ...
T Consensus         2 ~~lv~~ptGsGKT~~~~~~~~~~~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~-~~~~~~~~~~~~~~~~~----~~~   76 (144)
T cd00046           2 DVLLAAPTGSGKTLAALLPILELLDSLKGGQVLVLAPTRELANQVAERLKELFGE-GIKVGYLIGGTSIKQQE----KLL   76 (144)
T ss_pred             CEEEECCCCCHHHHHHHHHHHHHHHHCCCCEEEEECCHHHHHHHHHHHHHHHCCC-CCEEEEEECCCCHHHHH----HHH
T ss_conf             9999889971799999999999997568976999746799999999999997488-71799996136367789----874


Q ss_pred             CCCCEEEEECHHHC-----CCCCCCCCCCEEEECCCCC-----CCHHHHHHHHHCCCCCCCEEECHHH
Q ss_conf             34754864111201-----3345544441788521013-----3568899874025677610101013
Q gi|254780945|r  373 HGQAHIIIGTHALF-----QDSIQYYKLILVIVDEQHR-----FGVQQRLKLTQKATAPHVLLMTATP  430 (700)
Q Consensus       373 ~G~~~iiIGTHAL~-----q~~v~F~~LgLvViDEQHR-----FGV~QR~~L~~Kg~~ph~L~MtATP  430 (700)
                      .+..+|+|+|..-+     ...+.+++++++|+||-|+     ||..+...+.....+++++.|||||
T Consensus        77 ~~~~~ilv~T~~~l~~~~~~~~~~~~~~~~vViDEaH~~~~~~~~~~~~~~~~~~~~~~~~l~lSATp  144 (144)
T cd00046          77 SGKTDIVVGTPGRLLDELERLKLSLKKLDLLILDEAHRLLNQGFGLLGLKILLKLPKDRQVLLLSATP  144 (144)
T ss_pred             CCCCCEEECCHHHHHHHHHCCCCCCCCCCEEEEECHHHHHCCCCHHHHHHHHHHCCCCCCEEEECCCC
T ss_conf             58984998288999999973876555100999988887643796999999999679999489982899


No 53 
>COG0556 UvrB Helicase subunit of the DNA excision repair complex [DNA replication, recombination, and repair]
Probab=99.63  E-value=7.1e-13  Score=120.57  Aligned_cols=195  Identities=19%  Similarity=0.351  Sum_probs=142.7

Q ss_pred             CCCCCEEEECCCCCCCHHHH-----------HHHHHCC-------------------CCCCCEEECHHHHHHHHHHHHHH
Q ss_conf             44441788521013356889-----------9874025-------------------67761010101322789999752
Q gi|254780945|r  392 YYKLILVIVDEQHRFGVQQR-----------LKLTQKA-------------------TAPHVLLMTATPIPRTLVLTSLG  441 (700)
Q Consensus       392 F~~LgLvViDEQHRFGV~QR-----------~~L~~Kg-------------------~~ph~L~MtATPIPRTLal~~yg  441 (700)
                      |..=.|+||||-|- -|-|=           ..|.+-|                   ..+.+++.||||=|--+..+- |
T Consensus       329 fp~d~Ll~IDESHv-TvPQi~gMynGDrsRK~~LVeyGFRLPSAlDNRPL~feEf~~~~~q~i~VSATPg~~E~e~s~-~  406 (663)
T COG0556         329 FPDDFLLFIDESHV-TVPQIGGMYNGDRSRKQTLVEYGFRLPSALDNRPLKFEEFEAKIPQTIYVSATPGDYELEQSG-G  406 (663)
T ss_pred             CCCCEEEEEECCCC-CHHHHHCHHCCCHHHHHHHHHHCCCCCCCCCCCCCCHHHHHHHCCCEEEEECCCCHHHHHHCC-C
T ss_conf             88413899824446-507653201333788888987157686111379977799997459779997899748777455-8


Q ss_pred             CCCHHHHCCCCCCCC-CCEEEEEECCCHHHHHHHHHHHHCCCCEEEEEECCCCCCCCCCCCHHHHHHHHHHHHCCCCEEC
Q ss_conf             010111102355766-6207999702002689999763103873899971201221112101466666668663710312
Q gi|254780945|r  442 DIDISKITEKPAGRK-PIKTVIIPINRIDEVIERLKVVLSEGKKAYWICPQIEEKKESNFRSVVERFNSLHEHFTSSIAI  520 (700)
Q Consensus       442 dldvS~i~e~P~gR~-~I~T~~~~~~~~~~~~~~i~~~l~~g~q~y~VcPlIeese~~~~~~~~~~~~~l~~~~~~~v~~  520 (700)
                      .+---+|  .|-|=. |+...--...+.+.+++-|++.+++|.++.|..        +.-+-|++..+.|++. +-+|..
T Consensus       407 ~vveQiI--RPTGLlDP~ievRp~~~QvdDL~~EI~~r~~~~eRvLVTt--------LTKkmAEdLT~Yl~e~-gikv~Y  475 (663)
T COG0556         407 NVVEQII--RPTGLLDPEIEVRPTKGQVDDLLSEIRKRVAKNERVLVTT--------LTKKMAEDLTEYLKEL-GIKVRY  475 (663)
T ss_pred             CEEEEEE--CCCCCCCCCEEEECCCCCHHHHHHHHHHHHHCCCEEEEEE--------EHHHHHHHHHHHHHHC-CCEEEE
T ss_conf             4268872--4778889852651487747899999999996497299984--------3688899999999866-964786


Q ss_pred             CCCCCCHHHHHHHHHHHHCCCEEEEEECHHHHCCCCCCCCCEEEEECHHHCCH----HHHHHHHHCCCCCCCCEEEEEEE
Q ss_conf             01469989999999997559869999800341046888765899858525474----68877301166789835999970
Q gi|254780945|r  521 IHGRMSDIDKESVMDSFKNGTCKLLIATTVIEVGIDVVDASIIIIENAEHFGL----AQLHQLRGRVGRGEEISSCILLY  596 (700)
Q Consensus       521 lHGkm~~~ek~~~m~~F~~g~~~iLvaTtviEVGvdvpna~~mvI~~aerfGL----sqLHQLRGRVGRg~~~s~c~l~~  596 (700)
                      +|.-.+.-|.-+++.+.+.|++|+||.-...-=|+|+|..++..|.+||.=|.    ..|-|-=||-.|+. .|..+| |
T Consensus       476 lHSdidTlER~eIirdLR~G~~DvLVGINLLREGLDiPEVsLVAIlDADKeGFLRse~SLIQtIGRAARN~-~GkvIl-Y  553 (663)
T COG0556         476 LHSDIDTLERVEIIRDLRLGEFDVLVGINLLREGLDLPEVSLVAILDADKEGFLRSERSLIQTIGRAARNV-NGKVIL-Y  553 (663)
T ss_pred             EECCCHHHHHHHHHHHHHCCCCCEEEEEHHHHCCCCCCCEEEEEEEECCCCCCCCCCCHHHHHHHHHHHCC-CCEEEE-E
T ss_conf             42440389999999997577874898501331347886455798860685444345325999987886357-973999-7


Q ss_pred             CCCCC
Q ss_conf             88899
Q gi|254780945|r  597 HPPLS  601 (700)
Q Consensus       597 ~~~~~  601 (700)
                      .++++
T Consensus       554 AD~iT  558 (663)
T COG0556         554 ADKIT  558 (663)
T ss_pred             CCHHH
T ss_conf             10114


No 54 
>KOG0343 consensus
Probab=99.62  E-value=2.7e-13  Score=123.89  Aligned_cols=297  Identities=24%  Similarity=0.342  Sum_probs=198.9

Q ss_pred             CCCHHHHHHHHHHHHHHCCCCCCEEEEEE-------CCCCCHHHHHHHHHHHHH-------HHHCCEEEEEHHHHHHHHH
Q ss_conf             67988999999999841001343078862-------144223699999973344-------4305458861279999999
Q gi|254780945|r  272 SPTKSQESAIKDILQDMSQKNRMLRILQG-------DVGSGKTLVALIAMAAAV-------EAGGQAVIMAPIGILAQQH  337 (700)
Q Consensus       272 ~LT~~Q~~ai~eI~~Dl~~~~pM~RLLQG-------DVGSGKTiVA~~A~l~~~-------~~G~Q~alMaPTEILA~QH  337 (700)
                      .+|+=|+.+|           ||.  |||       -.|||||+-.+...+.++       .-|--|.+..||-=||-|.
T Consensus        91 ~~teiQ~~~I-----------p~a--L~G~DvlGAAkTGSGKTLAFlvPvlE~L~r~kWs~~DGlGalIISPTRELA~Qt  157 (758)
T KOG0343          91 KMTEIQRDTI-----------PMA--LQGHDVLGAAKTGSGKTLAFLVPVLEALYRLKWSPTDGLGALIISPTRELALQT  157 (758)
T ss_pred             CHHHHHHHHC-----------CHH--CCCCCCCCCCCCCCCCEEEEHHHHHHHHHHCCCCCCCCCEEEEECCHHHHHHHH
T ss_conf             6999987641-----------422--057500010235888446543999999997177887883269956529999999


Q ss_pred             HHHHHHHCCCCCCEEEEEECCCCHHHHHHHHHHHCCCCCEEEEEC-HHHCC---CCCCCC--CCCEEEECCCCCC---CH
Q ss_conf             986211014578658996246422566768776213475486411-12013---345544--4417885210133---56
Q gi|254780945|r  338 YEFIKKYTQNTQIIVEIITGNMPQAHRRKALERIAHGQAHIIIGT-HALFQ---DSIQYY--KLILVIVDEQHRF---GV  408 (700)
Q Consensus       338 ~~~~~~~~~~~~i~v~lLtg~~~~~er~~i~~~i~~G~~~iiIGT-HAL~q---~~v~F~--~LgLvViDEQHRF---GV  408 (700)
                      |+.+.+.-...++++.|+-|+.-.+     .+...-..++|+|+| --|+|   +.+.|+  +|-+.|.||--|-   |-
T Consensus       158 FevL~kvgk~h~fSaGLiiGG~~~k-----~E~eRi~~mNILVCTPGRLLQHmde~~~f~t~~lQmLvLDEADR~LDMGF  232 (758)
T KOG0343         158 FEVLNKVGKHHDFSAGLIIGGKDVK-----FELERISQMNILVCTPGRLLQHMDENPNFSTSNLQMLVLDEADRMLDMGF  232 (758)
T ss_pred             HHHHHHHHHCCCCCCCEEECCCHHH-----HHHHHHHCCCEEEECHHHHHHHHHHCCCCCCCCCEEEEECCHHHHHHHHH
T ss_conf             9999987520564311366571268-----89976625776996617899875416787877604787320888987767


Q ss_pred             -HHHHHHHHC-CCCCCCEEECHHHHHHHHHHHHH--HCCCHHHHCC-----CCCCCCCCEEE-EEE-CCCHHHHHHHHHH
Q ss_conf             -889987402-56776101010132278999975--2010111102-----35576662079-997-0200268999976
Q gi|254780945|r  409 -QQRLKLTQK-ATAPHVLLMTATPIPRTLVLTSL--GDIDISKITE-----KPAGRKPIKTV-IIP-INRIDEVIERLKV  477 (700)
Q Consensus       409 -~QR~~L~~K-g~~ph~L~MtATPIPRTLal~~y--gdldvS~i~e-----~P~gR~~I~T~-~~~-~~~~~~~~~~i~~  477 (700)
                       .|=..+.+- ...-..|..||||---+--|+-.  -|-.+-.+.+     -|..=.  .++ +++ .++++-+|.||+.
T Consensus       233 k~tL~~Ii~~lP~~RQTLLFSATqt~svkdLaRLsL~dP~~vsvhe~a~~atP~~L~--Q~y~~v~l~~Ki~~L~sFI~s  310 (758)
T KOG0343         233 KKTLNAIIENLPKKRQTLLFSATQTKSVKDLARLSLKDPVYVSVHENAVAATPSNLQ--QSYVIVPLEDKIDMLWSFIKS  310 (758)
T ss_pred             HHHHHHHHHHCCHHHEEEEEECCCCHHHHHHHHHHCCCCCEEEEECCCCCCCHHHHH--HEEEEEEHHHHHHHHHHHHHH
T ss_conf             888999987377233046663255113999997534798579972353336836453--327997601478999999984


Q ss_pred             HHCCCCEEEEEECCCCCCCCCCCCHHHHHHHHHHHHCCC-CEECCCCCCCHHHHHHHHHHHHCCCEEEEEECHHHHCCCC
Q ss_conf             310387389997120122111210146666666866371-0312014699899999999975598699998003410468
Q gi|254780945|r  478 VLSEGKKAYWICPQIEEKKESNFRSVVERFNSLHEHFTS-SIAIIHGRMSDIDKESVMDSFKNGTCKLLIATTVIEVGID  556 (700)
Q Consensus       478 ~l~~g~q~y~VcPlIeese~~~~~~~~~~~~~l~~~~~~-~v~~lHGkm~~~ek~~~m~~F~~g~~~iLvaTtviEVGvd  556 (700)
                      ++....-||+-       -.-+++-+.+.   +++.-|. .+-.|||+|+....-++.++|....--||.||-|.--|+|
T Consensus       311 hlk~K~iVF~S-------scKqvkf~~e~---F~rlrpg~~l~~L~G~~~Q~~R~ev~~~F~~~~~~vLF~TDv~aRGLD  380 (758)
T KOG0343         311 HLKKKSIVFLS-------SCKQVKFLYEA---FCRLRPGIPLLALHGTMSQKKRIEVYKKFVRKRAVVLFCTDVAARGLD  380 (758)
T ss_pred             CCCCCEEEEEE-------HHHHHHHHHHH---HHHCCCCCCEEEECCCHHHHHHHHHHHHHHHHCCEEEEEEHHHHCCCC
T ss_conf             52543699986-------00689999999---985089983254216313778899999998755558986025543689


Q ss_pred             CCCCCEEEEECHHHCCHHHHHHHHHCCCCCCCCEEEEEEECCC
Q ss_conf             8876589985852547468877301166789835999970888
Q gi|254780945|r  557 VVDASIIIIENAEHFGLAQLHQLRGRVGRGEEISSCILLYHPP  599 (700)
Q Consensus       557 vpna~~mvI~~aerfGLsqLHQLRGRVGRg~~~s~c~l~~~~~  599 (700)
                      .|..+..|=.++--= .++---=-||-.|-...|-|+|+..+.
T Consensus       381 FpaVdwViQ~DCPed-v~tYIHRvGRtAR~~~~G~sll~L~ps  422 (758)
T KOG0343         381 FPAVDWVIQVDCPED-VDTYIHRVGRTARYKERGESLLMLTPS  422 (758)
T ss_pred             CCCCCEEEEECCCHH-HHHHHHHHHHHHCCCCCCCEEEEECCH
T ss_conf             864336998068205-889998721221136778568997631


No 55 
>PRK09401 reverse gyrase; Reviewed
Probab=99.61  E-value=6.3e-13  Score=120.97  Aligned_cols=283  Identities=18%  Similarity=0.282  Sum_probs=199.3

Q ss_pred             HHHHHHHHCCCCCCHHHHHHHHHHHHHHCCCCCCEEEEEECCCCCHHHHHHHHHHHHHHHHCCEEEEEHHHHHHHHHHHH
Q ss_conf             89999863024679889999999998410013430788621442236999999733444305458861279999999986
Q gi|254780945|r  261 IAQKILRNIPFSPTKSQESAIKDILQDMSQKNRMLRILQGDVGSGKTLVALIAMAAAVEAGGQAVIMAPIGILAQQHYEF  340 (700)
Q Consensus       261 ~~~~f~~~LPF~LT~~Q~~ai~eI~~Dl~~~~pM~RLLQGDVGSGKTiVA~~A~l~~~~~G~Q~alMaPTEILA~QH~~~  340 (700)
                      +.+-|.+...|++.+.|+.=.+-+...    ...  -+---.|.|||--.+.+++..+..|..+.+..||..|+.|-++.
T Consensus        67 f~~fF~~~~G~~~w~~Qr~WakR~~~g----~SF--aiiAPTG~GKTtfgl~~sly~a~kgkks~~i~PT~~Lv~Q~~~k  140 (1176)
T PRK09401         67 FEEFFKKKVGSEPWSLQRTWAKRLLLG----ESF--AIIAPTGVGKTTFGLVMALYLAKKGKKSYIIFPTRLLVEQVVEK  140 (1176)
T ss_pred             HHHHHHHHHCCCCCHHHHHHHHHHHCC----CCE--EEECCCCCCHHHHHHHHHHHHHHCCCEEEEEECCHHHHHHHHHH
T ss_conf             999999986899848899999998668----974--89888998888999999999986598399996888999999999


Q ss_pred             HHHHCCCCC--CEEEEEECCCCHHHHHHHHHHHCCCCCEEEEECHHHCCCCC---CCCCCCEEEECCCCCC---------
Q ss_conf             211014578--65899624642256676877621347548641112013345---5444417885210133---------
Q gi|254780945|r  341 IKKYTQNTQ--IIVEIITGNMPQAHRRKALERIAHGQAHIIIGTHALFQDSI---QYYKLILVIVDEQHRF---------  406 (700)
Q Consensus       341 ~~~~~~~~~--i~v~lLtg~~~~~er~~i~~~i~~G~~~iiIGTHAL~q~~v---~F~~LgLvViDEQHRF---------  406 (700)
                      +.++-...|  +++...+|++++++|++.++.+++|+-+|+|.|.+-+..+.   .=.+-.+|.||-=--|         
T Consensus       141 l~~~~~~~~~~~~~~~y~~~~~~~~kee~~~~~~~gdfdIlitT~~fl~kn~~~l~~~~f~fifvDDVDs~LKssKnid~  220 (1176)
T PRK09401        141 LRKLAEKVGVKVRLLYYHSSLKKKEKEEFLERLEEGDFDILVTTSQFLSKNFDELPKDRFDFVFVDDVDAVLKSSKNIDK  220 (1176)
T ss_pred             HHHHHHHHCCCCEEEEEECCCCHHHHHHHHHHHHCCCCCEEEEEHHHHHHHHHHCCCCCCCEEEEECHHHHHHHHHHHHH
T ss_conf             99999970998408998567766678999988655998689985676765487603568888999341877752340999


Q ss_pred             -----CHHH-------------------------HHHHH---HCCCCCCCEEECHHHHHHHHHHHHHHCC---CHHHHCC
Q ss_conf             -----5688-------------------------99874---0256776101010132278999975201---0111102
Q gi|254780945|r  407 -----GVQQ-------------------------RLKLT---QKATAPHVLLMTATPIPRTLVLTSLGDI---DISKITE  450 (700)
Q Consensus       407 -----GV~Q-------------------------R~~L~---~Kg~~ph~L~MtATPIPRTLal~~ygdl---dvS~i~e  450 (700)
                           |..+                         +..+.   .+....-+.+.|||-=||+.-.-+|-+|   |++... 
T Consensus       221 ~l~llGf~~e~i~~a~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~livsSAT~~prg~r~~lfreLlgFevg~~~-  299 (1176)
T PRK09401        221 LLKLLGFSEEDIEKAMELIKLKRKTEELKEEIEELEEKIREIRKKKKGVLVVSSATGRPRGIRIKLFRELLGFEVGRPR-  299 (1176)
T ss_pred             HHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCEEEEEECCCCCCCCCHHHHHHHHHCCCCCCCC-
T ss_conf             9998399999999999999975234344456778899999874368749999757778888538999998298678864-


Q ss_pred             CCCCCCCCEEEEEECCCHHHHHHHHHHHHCCCCEEEEEECCCCCCCCCCCCHHHHHHHHHHHHCCCCEECCCCCCCHHHH
Q ss_conf             35576662079997020026899997631038738999712012211121014666666686637103120146998999
Q gi|254780945|r  451 KPAGRKPIKTVIIPINRIDEVIERLKVVLSEGKKAYWICPQIEEKKESNFRSVVERFNSLHEHFTSSIAIIHGRMSDIDK  530 (700)
Q Consensus       451 ~P~gR~~I~T~~~~~~~~~~~~~~i~~~l~~g~q~y~VcPlIeese~~~~~~~~~~~~~l~~~~~~~v~~lHGkm~~~ek  530 (700)
                       ..-|--+-++....+..+.+.+.+ +.+..|+-+|+=       ......-+++..+.|++. +-+++..|..-     
T Consensus       300 -~~lRni~D~y~~~~~~~~~~~e~v-~~lG~GgLifv~-------~~~g~e~~~~~~~~l~~~-g~~a~~~~~~~-----  364 (1176)
T PRK09401        300 -FYLRNIVDVYIEPEDLVEKLVELV-KRLGDGGLVFVP-------TDYGKEYAEELKEYLESH-GIKAEAYSGRK-----  364 (1176)
T ss_pred             -CCEEEEEEEECCCCCHHHHHHHHH-HHHCCCEEEEEE-------CCCCHHHHHHHHHHHHHC-CCEEEEEECCC-----
T ss_conf             -230212577605766889999999-984895499976-------765889999999999976-96699960588-----


Q ss_pred             HHHHHHHHCCCEEEEEEC----HHHHCCCCCCCCCEEEE
Q ss_conf             999999755986999980----03410468887658998
Q gi|254780945|r  531 ESVMDSFKNGTCKLLIAT----TVIEVGIDVVDASIIII  565 (700)
Q Consensus       531 ~~~m~~F~~g~~~iLvaT----tviEVGvdvpna~~mvI  565 (700)
                      ...+++|.+|++|+||..    .++=-|+|.|..-=-+|
T Consensus       365 ~~~le~f~~Ge~dvLvG~asyyg~lvRGiDlP~~irYai  403 (1176)
T PRK09401        365 KEFLEKFEEGEIDVLIGVASYYGVLVRGIDLPERIRYAI  403 (1176)
T ss_pred             HHHHHHHHCCCCCEEEEECCCCCCCCCCCCCCCEEEEEE
T ss_conf             668889757886489997012452101577641168999


No 56 
>PRK11664 ATP-dependent RNA helicase HrpB; Provisional
Probab=99.60  E-value=2.4e-12  Score=116.42  Aligned_cols=293  Identities=19%  Similarity=0.262  Sum_probs=194.8

Q ss_pred             HHHHHHHHHHCCCCCCEEEEEECCCCCHHHHHHHHHHHHHHHHCCEEEEEHHHHHHHHHHHHHHHHCC-CCCCEEEEEEC
Q ss_conf             99999998410013430788621442236999999733444305458861279999999986211014-57865899624
Q gi|254780945|r  279 SAIKDILQDMSQKNRMLRILQGDVGSGKTLVALIAMAAAVEAGGQAVIMAPIGILAQQHYEFIKKYTQ-NTQIIVEIITG  357 (700)
Q Consensus       279 ~ai~eI~~Dl~~~~pM~RLLQGDVGSGKTiVA~~A~l~~~~~G~Q~alMaPTEILA~QH~~~~~~~~~-~~~i~v~lLtg  357 (700)
                      ....+|.+-+..+..  -+|+|+.|||||-.-=..++..-......++.-|--|-|.--++.+...+. +.|-.|..-..
T Consensus         8 ~~~~~i~~~l~~~~~--~vl~a~tGsGKtTqvP~~ll~~~~~~g~I~~~qPRR~AA~s~A~RvA~e~~e~~G~~VGY~vR   85 (812)
T PRK11664          8 AVLPELLTALKTAPQ--VLLKAPTGAGKSTWLPLQLLQQGGINGKIIMLEPRRLAARNVAQRLAEQLGEKPGETVGYRMR   85 (812)
T ss_pred             HHHHHHHHHHHHCCE--EEEEECCCCCHHHHHHHHHHHCCCCCCCEEEECCHHHHHHHHHHHHHHHHCCCCCCEEEEEEC
T ss_conf             899999999997997--999908999989999999996468899389938839999999999999729999986757825


Q ss_pred             CCCHHHHHHHHHHHCCCCCEEEEECHHHC----CCCCCCCCCCEEEECCCCCCCHHHHHHH--H---HCC--CCCCCEEE
Q ss_conf             64225667687762134754864111201----3345544441788521013356889987--4---025--67761010
Q gi|254780945|r  358 NMPQAHRRKALERIAHGQAHIIIGTHALF----QDSIQYYKLILVIVDEQHRFGVQQRLKL--T---QKA--TAPHVLLM  426 (700)
Q Consensus       358 ~~~~~er~~i~~~i~~G~~~iiIGTHAL~----q~~v~F~~LgLvViDEQHRFGV~QR~~L--~---~Kg--~~ph~L~M  426 (700)
                      ..+          -.+....|.+=|-.++    +.+-...+.+.||+||=|-=.++-=..|  .   .+.  ..-.+++|
T Consensus        86 ~e~----------~~s~~Tri~~~T~GiLlr~l~~dp~L~~~~~vI~DE~HER~l~~Dl~l~l~~~~~~~~r~dLklvvM  155 (812)
T PRK11664         86 AES----------KVGPNTRLEVVTEGILTRMIQRDPELSGVGLVILDEFHERSLQADLALALLLDVQQGLRDDLKLLIM  155 (812)
T ss_pred             CCC----------CCCCCCEEEEECHHHHHHHHHHCCCCCCCCEEEEECCCCCCHHHHHHHHHHHHHHHHHCCCCEEEEE
T ss_conf             677----------8899857999755899999724977677888999575468751899999999999861898289998


Q ss_pred             CHHHHHHHHHHHHHHCCCHHHHCCCCCCCC-CCEEEEEECCCHHHHHHH----HHHHHCC-CCEEEEEECCCCCCCCCCC
Q ss_conf             101322789999752010111102355766-620799970200268999----9763103-8738999712012211121
Q gi|254780945|r  427 TATPIPRTLVLTSLGDIDISKITEKPAGRK-PIKTVIIPINRIDEVIER----LKVVLSE-GKKAYWICPQIEEKKESNF  500 (700)
Q Consensus       427 tATPIPRTLal~~ygdldvS~i~e~P~gR~-~I~T~~~~~~~~~~~~~~----i~~~l~~-g~q~y~VcPlIeese~~~~  500 (700)
                      |||.=.-.++- ++|+-.+-.+    +||. ||.++..+....+.+.+.    ++..+.. .+-+-|--|=++       
T Consensus       156 SATld~~~~~~-~~~~~~~i~~----~gr~fpV~~~y~~~~~~~~~~~~~~~~i~~~~~~~~G~iLvFLPG~~-------  223 (812)
T PRK11664        156 SATLDNDRLQQ-LLPDAPYIES----EGRSFPVERRYQPLPAHQRFDEAVAVATAELLRQESGSLLLFLPGVG-------  223 (812)
T ss_pred             CCCCCHHHHHH-HCCCCCEEEE----CCCCCCEEEEECCCCCCCHHHHHHHHHHHHHHHCCCCCEEEECCCHH-------
T ss_conf             47888488997-5899988987----87433115785468852069999999999997358998899769989-------


Q ss_pred             CHHHHHHHHHHHHCCC--CEECCCCCCCHHHHHHHHHHHHCCCEEEEEECHHHHCCCCCCCCCEEEE--------ECHHH
Q ss_conf             0146666666866371--0312014699899999999975598699998003410468887658998--------58525
Q gi|254780945|r  501 RSVVERFNSLHEHFTS--SIAIIHGRMSDIDKESVMDSFKNGTCKLLIATTVIEVGIDVVDASIIII--------ENAEH  570 (700)
Q Consensus       501 ~~~~~~~~~l~~~~~~--~v~~lHGkm~~~ek~~~m~~F~~g~~~iLvaTtviEVGvdvpna~~mvI--------~~aer  570 (700)
                       .+....+.|.+.++.  .|--|||.|+.+|.++++..-..|.-+|.+||.|-|..|.||+.++.|=        +|+. 
T Consensus       224 -EI~~~~~~L~~~~~~~~~i~pL~g~l~~~~Q~~~~~~~~~g~rKvIlaTnIAEtSlTI~gV~~VIDsG~~r~~~~d~~-  301 (812)
T PRK11664        224 -EIQRVQEQLASRVGSDVLLCPLYGALSLAEQQKAILPAPAGMRKVVLATNIAETSLTIEGIRLVVDSGLERVARFDPK-  301 (812)
T ss_pred             -HHHHHHHHHHHHCCCCEEEEECCCCCCHHHHHHHHCCCCCCCEEEEEECCCHHCEEEECCEEEEEECHHHHHHEECCC-
T ss_conf             -999999998633557808996447899889877606799995379995020002020178148974022344323435-


Q ss_pred             CCH----------HHHHHHHHCCCCCCCCEEEEEEECC
Q ss_conf             474----------6887730116678983599997088
Q gi|254780945|r  571 FGL----------AQLHQLRGRVGRGEEISSCILLYHP  598 (700)
Q Consensus       571 fGL----------sqLHQLRGRVGRg~~~s~c~l~~~~  598 (700)
                      -|+          |+--|=+||.||- .+|.||=+|+.
T Consensus       302 ~g~~~L~~~~iSkasa~QRaGRAGR~-~pG~cyRL~s~  338 (812)
T PRK11664        302 TGLTRLETQRISQASMTQRAGRAGRL-EPGICLHLYAK  338 (812)
T ss_pred             CCCCEEEEEECCHHHHHCCCCCCCCC-CCCEEEEEECH
T ss_conf             79756767704544353136767888-99707873359


No 57 
>KOG0334 consensus
Probab=99.59  E-value=1.2e-11  Score=110.96  Aligned_cols=372  Identities=23%  Similarity=0.322  Sum_probs=228.6

Q ss_pred             HHHHHHHHHCCC-CCCHHHHHHHHHHHHHHCCCCCCEEEEEECCCCCHHHHHHHHHHHHHH--------HHCCEEEEEHH
Q ss_conf             789999863024-679889999999998410013430788621442236999999733444--------30545886127
Q gi|254780945|r  260 KIAQKILRNIPF-SPTKSQESAIKDILQDMSQKNRMLRILQGDVGSGKTLVALIAMAAAVE--------AGGQAVIMAPI  330 (700)
Q Consensus       260 ~~~~~f~~~LPF-~LT~~Q~~ai~eI~~Dl~~~~pM~RLLQGDVGSGKTiVA~~A~l~~~~--------~G~Q~alMaPT  330 (700)
                      .++. -+++|.| ..|.=|.+||-.|..    ++-  -+-++-.|||||+=.++-|+-.+.        -|==+.+||||
T Consensus       375 ~il~-tlkkl~y~k~~~IQ~qAiP~Ims----Grd--vIgvakTgSGKT~af~LPmirhi~dQr~~~~gdGPi~li~aPt  447 (997)
T KOG0334         375 KILE-TLKKLGYEKPTPIQAQAIPAIMS----GRD--VIGVAKTGSGKTLAFLLPMIRHIKDQRPLEEGDGPIALILAPT  447 (997)
T ss_pred             HHHH-HHHHHCCCCCCCHHHHHCCHHCC----CCC--EEEEECCCCCCCHHHHHHHHHHHCCCCCHHCCCCCEEEEECCC
T ss_conf             8999-99970689987556643012225----774--5877326886203442115554204797110788647997377


Q ss_pred             HHHHHHHHHHHHHHCCCCCCEEEEEECCCCHHHHHHHHHHHCCCCCEEEEECHHHCC-----CCCCCCCCC---EEEECC
Q ss_conf             999999998621101457865899624642256676877621347548641112013-----345544441---788521
Q gi|254780945|r  331 GILAQQHYEFIKKYTQNTQIIVEIITGNMPQAHRRKALERIAHGQAHIIIGTHALFQ-----DSIQYYKLI---LVIVDE  402 (700)
Q Consensus       331 EILA~QH~~~~~~~~~~~~i~v~lLtg~~~~~er~~i~~~i~~G~~~iiIGTHAL~q-----~~v~F~~Lg---LvViDE  402 (700)
                      -=||.|.++.+++|...+++++++..|..   .+.+...+++.| ..|+|+|-.-+-     ..-.--||-   .+|-||
T Consensus       448 rela~QI~r~~~kf~k~l~ir~v~vygg~---~~~~qiaelkRg-~eIvV~tpGRmiD~l~~n~grvtnlrR~t~lv~de  523 (997)
T KOG0334         448 RELAMQIHREVRKFLKLLGIRVVCVYGGS---GISQQIAELKRG-AEIVVCTPGRMIDILCANSGRVTNLRRVTYLVLDE  523 (997)
T ss_pred             HHHHHHHHHHHHHHHHHCCCEEEEECCCC---CHHHHHHHHHCC-CCEEEECCCHHHHHHHHCCCCCCCCCCCCEEEECH
T ss_conf             78999999999998774176279842785---188789998678-96599645032336661577623310110355411


Q ss_pred             CCCCCHHHHHHHHHCCCCC-----------C-CEEECHHHHHHHHHHHHHHCCCHHHHCCCCCCCCCCEEEEEE------
Q ss_conf             0133568899874025677-----------6-101010132278999975201011110235576662079997------
Q gi|254780945|r  403 QHRFGVQQRLKLTQKATAP-----------H-VLLMTATPIPRTLVLTSLGDIDISKITEKPAGRKPIKTVIIP------  464 (700)
Q Consensus       403 QHRFGV~QR~~L~~Kg~~p-----------h-~L~MtATPIPRTLal~~ygdldvS~i~e~P~gR~~I~T~~~~------  464 (700)
                      --|      ..  .+|..|           + +.+|++---||.+--  .   +.-+++      +||. .++.      
T Consensus       524 aDr------mf--dmgfePq~~~Ii~nlrpdrQtvlfSatfpr~m~~--l---a~~vl~------~Pve-iiv~~~svV~  583 (997)
T KOG0334         524 ADR------MF--DMGFEPQITRILQNLRPDRQTVLFSATFPRSMEA--L---ARKVLK------KPVE-IIVGGRSVVC  583 (997)
T ss_pred             HHH------HH--HCCCCCCCEEHHHHCCHHHHHHHHHHHHHHHHHH--H---HHHHHC------CCEE-EEECCCEEEE
T ss_conf             235------44--0045754040976466035434566220699999--9---988615------8808-9974630574


Q ss_pred             -------------CCCHHHHHHHHHHHHCCCCEEEEEECCCCCCCCCCCCHHHHHHHHHHHHCCCCEECCCCCCCHHHHH
Q ss_conf             -------------0200268999976310387389997120122111210146666666866371031201469989999
Q gi|254780945|r  465 -------------INRIDEVIERLKVVLSEGKKAYWICPQIEEKKESNFRSVVERFNSLHEHFTSSIAIIHGRMSDIDKE  531 (700)
Q Consensus       465 -------------~~~~~~~~~~i~~~l~~g~q~y~VcPlIeese~~~~~~~~~~~~~l~~~~~~~v~~lHGkm~~~ek~  531 (700)
                                   .+++.++.+.+...-..|.-+.+| -   .+     ..+-...+.|.+ -+...-.|||--+..+.+
T Consensus       584 k~V~q~v~V~~~e~eKf~kL~eLl~e~~e~~~tiiFv-~---~q-----e~~d~l~~~L~~-ag~~~~slHGgv~q~dR~  653 (997)
T KOG0334         584 KEVTQVVRVCAIENEKFLKLLELLGERYEDGKTIIFV-D---KQ-----EKADALLRDLQK-AGYNCDSLHGGVDQHDRS  653 (997)
T ss_pred             CCEEEEEEEECCCHHHHHHHHHHHHHHHHCCCEEEEE-C---CC-----HHHHHHHHHHHH-CCCCHHHHCCCCCHHHHH
T ss_conf             2404899981483677999999999886248879998-4---71-----478899999985-686054305787567788


Q ss_pred             HHHHHHHCCCEEEEEECHHHHCCCCCCCCCEEEEECHHHCCHHHHHHHHHCCCCCCCCEEEEEEECCCCCHHHHHHHHHH
Q ss_conf             99999755986999980034104688876589985852547468877301166789835999970888998799999999
Q gi|254780945|r  532 SVMDSFKNGTCKLLIATTVIEVGIDVVDASIIIIENAEHFGLAQLHQLRGRVGRGEEISSCILLYHPPLSKNSYTRLSVL  611 (700)
Q Consensus       532 ~~m~~F~~g~~~iLvaTtviEVGvdvpna~~mvI~~aerfGLsqLHQLRGRVGRg~~~s~c~l~~~~~~~~~~~~Rl~~l  611 (700)
                      .++++|++|...+||+|.|+--|+||++.-+.|.+++-. +-.++--==||-||.+..|+|+-...+...+.+..=-+.|
T Consensus       654 sti~dfK~~~~~LLvaTsvvarGLdv~~l~Lvvnyd~pn-h~edyvhR~gRTgragrkg~AvtFi~p~q~~~a~dl~~al  732 (997)
T KOG0334         654 STIEDFKNGVVNLLVATSVVARGLDVKELILVVNYDFPN-HYEDYVHRVGRTGRAGRKGAAVTFITPDQLKYAGDLCKAL  732 (997)
T ss_pred             HHHHHHHCCCCEEEEEHHHHHCCCCCCCEEEEEECCCCH-HHHHHHHHHCCCCCCCCCCEEEEEECHHHHHHHHHHHHHH
T ss_conf             589997456742898514542676665405899736631-2799999851356677763379985778864378899999


Q ss_pred             HHHC--HH---HHHHHHHHHHCCCCCCCCCHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCC
Q ss_conf             8414--25---899999985206300026000698744000388759999999999999998484636655
Q gi|254780945|r  612 KNTE--DG---FLIAEEDLKQRKEGEILGIKQSGMPKFLIAQPELHDSLLEIARKDAKHILTQDPDLTSVR  677 (700)
Q Consensus       612 ~~~~--dG---f~iAe~Dl~lRG~G~~~G~~QsG~~~~~~~d~~~d~~ll~~a~~~a~~~~~~d~~l~~~~  677 (700)
                      ..+.  .-   =.+++.=+.---.| --+..++|  .|.-..+..| +..++++...++....++++....
T Consensus       733 ~~~~~~~P~~l~~l~~~f~~~~~~~-~s~~~~~G--g~~G~g~~~~-~~~~~~~~~~ke~q~~~~g~~~~d  799 (997)
T KOG0334         733 ELSKQPVPKLLQALSERFKAKQKAG-GSQVHGGG--GFGGKGLKFD-EVEEELRQERKEAQRKDLGLKEGD  799 (997)
T ss_pred             HHCCCCCCHHHHHHHHHHHHHHHCC-CCCCCCCC--CCCCCCCCCC-HHHHHHHHHHHHCCCCCCCCCCCC
T ss_conf             8615899567899999988652300-45466667--5467766631-789999988862244567877677


No 58 
>KOG4284 consensus
Probab=99.58  E-value=1.2e-13  Score=126.68  Aligned_cols=321  Identities=21%  Similarity=0.288  Sum_probs=215.9

Q ss_pred             CCCHHHHHHHHHHHHHHCCCCCCEEEEEECCCCCHHHHHHHHHHHHH---HHHCCEEEEEHHHHHHHHHHHHHHHHCCCC
Q ss_conf             67988999999999841001343078862144223699999973344---430545886127999999998621101457
Q gi|254780945|r  272 SPTKSQESAIKDILQDMSQKNRMLRILQGDVGSGKTLVALIAMAAAV---EAGGQAVIMAPIGILAQQHYEFIKKYTQNT  348 (700)
Q Consensus       272 ~LT~~Q~~ai~eI~~Dl~~~~pM~RLLQGDVGSGKTiVA~~A~l~~~---~~G~Q~alMaPTEILA~QH~~~~~~~~~~~  348 (700)
                      ..|.=|..||--|..-      |.-++|.--|.|||+|...+++...   .+.-|..+++||-=+|-|..++|.++.+.+
T Consensus        47 ~ptkiQaaAIP~~~~k------mDliVQaKSGTGKTlVfsv~av~sl~~~~~~~q~~Iv~PTREiaVQI~~tv~~v~~sf  120 (980)
T KOG4284          47 LPTKIQAAAIPAIFSK------MDLIVQAKSGTGKTLVFSVLAVESLDSRSSHIQKVIVTPTREIAVQIKETVRKVAPSF  120 (980)
T ss_pred             CCCCHHHHHHHHHHCC------CCEEEEECCCCCCEEEEEEEEEHHCCCCCCCCEEEEEECCHHHHHHHHHHHHHHCCCC
T ss_conf             7870134321144315------5358981378885589985430222756676206997143566457999999865244


Q ss_pred             -CCEEEEEECCCCHHHHHHHHHHHCCCCCEEEEECHH----HC-CCCCCCCCCCEEEECCCCCC---CHHHH--HHHHHC
Q ss_conf             -865899624642256676877621347548641112----01-33455444417885210133---56889--987402
Q gi|254780945|r  349 -QIIVEIITGNMPQAHRRKALERIAHGQAHIIIGTHA----LF-QDSIQYYKLILVIVDEQHRF---GVQQR--LKLTQK  417 (700)
Q Consensus       349 -~i~v~lLtg~~~~~er~~i~~~i~~G~~~iiIGTHA----L~-q~~v~F~~LgLvViDEQHRF---GV~QR--~~L~~K  417 (700)
                       |.+|....|++..+.-+.-+     .+..|+|||-.    |+ -+-....++.|-|.||--+.   |+-|-  ..+.+-
T Consensus       121 ~g~~csvfIGGT~~~~d~~rl-----k~~rIvIGtPGRi~qL~el~~~n~s~vrlfVLDEADkL~~t~sfq~~In~ii~s  195 (980)
T KOG4284         121 TGARCSVFIGGTAHKLDLIRL-----KQTRIVIGTPGRIAQLVELGAMNMSHVRLFVLDEADKLMDTESFQDDINIIINS  195 (980)
T ss_pred             CCCCEEEEECCCHHHHHHHHH-----HHCEEEECCCHHHHHHHHHCCCCCCCEEEEEECCHHHHHCHHHHHHHHHHHHHH
T ss_conf             576058996685435556665-----402378438358899987067771102688843177663202478889999974


Q ss_pred             -CCCCCCEEECHHHHHHHHHHHHHHCCCHH---HHCCCCCCCCCCEEEEEECCCHHHHHHHHHHHHCCCCEEEEEECCCC
Q ss_conf             -56776101010132278999975201011---11023557666207999702002689999763103873899971201
Q gi|254780945|r  418 -ATAPHVLLMTATPIPRTLVLTSLGDIDIS---KITEKPAGRKPIKTVIIPINRIDEVIERLKVVLSEGKKAYWICPQIE  493 (700)
Q Consensus       418 -g~~ph~L~MtATPIPRTLal~~ygdldvS---~i~e~P~gR~~I~T~~~~~~~~~~~~~~i~~~l~~g~q~y~VcPlIe  493 (700)
                       -.+-.+++.||| -||-|+-.+---|+=-   ...+--+-=--|+-+++....-+...+-++..++.=.|+|=--|...
T Consensus       196 lP~~rQv~a~SAT-Yp~nLdn~Lsk~mrdp~lVr~n~~d~~L~GikQyv~~~~s~nnsveemrlklq~L~~vf~~ipy~Q  274 (980)
T KOG4284         196 LPQIRQVAAFSAT-YPRNLDNLLSKFMRDPALVRFNADDVQLFGIKQYVVAKCSPNNSVEEMRLKLQKLTHVFKSIPYVQ  274 (980)
T ss_pred             CCHHHEEEEEECC-CCHHHHHHHHHHHCCCCEEECCCCCCEEECHHHEEEECCCCCCHHHHHHHHHHHHHHHHHHCCHHH
T ss_conf             5000025677335-735689999987046222432667742530102035226886358999999999999986072677


Q ss_pred             CCCCCCCCHHHHHHHHHHHHCC---CCEECCCCCCCHHHHHHHHHHHHCCCEEEEEECHHHHCCCCCCCCCEEEEECHHH
Q ss_conf             2211121014666666686637---1031201469989999999997559869999800341046888765899858525
Q gi|254780945|r  494 EKKESNFRSVVERFNSLHEHFT---SSIAIIHGRMSDIDKESVMDSFKNGTCKLLIATTVIEVGIDVVDASIIIIENAEH  570 (700)
Q Consensus       494 ese~~~~~~~~~~~~~l~~~~~---~~v~~lHGkm~~~ek~~~m~~F~~g~~~iLvaTtviEVGvdvpna~~mvI~~aer  570 (700)
                         .+-..+...+.+.++.++.   -.+.++.|-|+..++--+|+..++-...|||||-.---|||-||+|+.|=.+|--
T Consensus       275 ---AlVF~~~~sra~~~a~~L~ssG~d~~~ISgaM~Q~~Rl~a~~~lr~f~~rILVsTDLtaRGIDa~~vNLVVNiD~p~  351 (980)
T KOG4284         275 ---ALVFCDQISRAEPIATHLKSSGLDVTFISGAMSQKDRLLAVDQLRAFRVRILVSTDLTARGIDADNVNLVVNIDAPA  351 (980)
T ss_pred             ---HHHHHHHHHHHHHHHHHHHCCCCCEEEECCCCCHHHHHHHHHHHHHCEEEEEEECCHHHCCCCCCCCCEEEECCCCC
T ss_conf             ---77654134210478877511698717741411235788999874201689998523122267865553698358773


Q ss_pred             CCHHHHHHHHHCCCCCCCCEEEEEEECCCCCHHHHHHHHHH
Q ss_conf             47468877301166789835999970888998799999999
Q gi|254780945|r  571 FGLAQLHQLRGRVGRGEEISSCILLYHPPLSKNSYTRLSVL  611 (700)
Q Consensus       571 fGLsqLHQLRGRVGRg~~~s~c~l~~~~~~~~~~~~Rl~~l  611 (700)
                      =--.-+|-. ||-||=+..|-.+-+...+   ...+|...|
T Consensus       352 d~eTY~HRI-GRAgRFG~~G~aVT~~~~~---~e~~~f~~m  388 (980)
T KOG4284         352 DEETYFHRI-GRAGRFGAHGAAVTLLEDE---RELKGFTAM  388 (980)
T ss_pred             CHHHHHHHH-HHCCCCCCCCEEEEEECCC---HHHHHHHHH
T ss_conf             067899884-0000145565068886060---443036999


No 59 
>KOG0339 consensus
Probab=99.58  E-value=5.6e-12  Score=113.54  Aligned_cols=332  Identities=22%  Similarity=0.281  Sum_probs=215.6

Q ss_pred             CCHHHHHHHHHCCCCCCHHHHHHHHHHHHHHCCCCCCEEEEE--ECCCCCHHHHHHHHHHHHH--------HHHCCEEEE
Q ss_conf             757899998630246798899999999984100134307886--2144223699999973344--------430545886
Q gi|254780945|r  258 EGKIAQKILRNIPFSPTKSQESAIKDILQDMSQKNRMLRILQ--GDVGSGKTLVALIAMAAAV--------EAGGQAVIM  327 (700)
Q Consensus       258 ~~~~~~~f~~~LPF~LT~~Q~~ai~eI~~Dl~~~~pM~RLLQ--GDVGSGKTiVA~~A~l~~~--------~~G~Q~alM  327 (700)
                      +..+.....+.==-+.|..|..++.--        -|-|=+-  .-.|||||.-.+.-|+.-+        .+|-=++++
T Consensus       231 DkqLm~airk~Ey~kptpiq~qalpta--------lsgrdvigIAktgSgktaAfi~pm~~himdq~eL~~g~gPi~vil  302 (731)
T KOG0339         231 DKQLMTAIRKSEYEKPTPIQCQALPTA--------LSGRDVIGIAKTGSGKTAAFIWPMIVHIMDQPELKPGEGPIGVIL  302 (731)
T ss_pred             HHHHHHHHHHHHCCCCCCCCCCCCCCC--------CCCCCCHHEEECCCCCHHHHHHHHHHHHCCHHHHCCCCCCEEEEE
T ss_conf             399999986420046775233435522--------466521111211575056777777777414052068999769998


Q ss_pred             EHHHHHHHHHHHHHHHHCCCCCCEEEEEECCCCHHHHHHHHHHHCCCCCEEEEECH-HHC----CCCCCCCCCCEEEECC
Q ss_conf             12799999999862110145786589962464225667687762134754864111-201----3345544441788521
Q gi|254780945|r  328 APIGILAQQHYEFIKKYTQNTQIIVEIITGNMPQAHRRKALERIAHGQAHIIIGTH-ALF----QDSIQYYKLILVIVDE  402 (700)
Q Consensus       328 aPTEILA~QH~~~~~~~~~~~~i~v~lLtg~~~~~er~~i~~~i~~G~~~iiIGTH-AL~----q~~v~F~~LgLvViDE  402 (700)
                      |||.=||.|.|...+++-+.+|+++..+.|+.+.-|.   ...|+. .+-|||-|- -||    -+.+.+.+..+.|+||
T Consensus       303 vPTrela~Qi~~eaKkf~K~ygl~~v~~ygGgsk~eQ---~k~Lk~-g~EivVaTPgRlid~VkmKatn~~rvS~LV~DE  378 (731)
T KOG0339         303 VPTRELASQIFSEAKKFGKAYGLRVVAVYGGGSKWEQ---SKELKE-GAEIVVATPGRLIDMVKMKATNLSRVSYLVLDE  378 (731)
T ss_pred             ECCHHHHHHHHHHHHHHHHHCCCEEEEEECCCCHHHH---HHHHHC-CCEEEEECHHHHHHHHHHHCCCCEEEEEEEEEC
T ss_conf             0638999999999998631126427886368748887---776502-772899662888999886033310035788711


Q ss_pred             CCCC---CHH-HHHHHHHCCCCC--CCEEECHHHHHHH--HHHHHHHCC-CHHHHCCCCCCCCCCEEEEE--EC--CCHH
Q ss_conf             0133---568-899874025677--6101010132278--999975201-01111023557666207999--70--2002
Q gi|254780945|r  403 QHRF---GVQ-QRLKLTQKATAP--HVLLMTATPIPRT--LVLTSLGDI-DISKITEKPAGRKPIKTVII--PI--NRID  469 (700)
Q Consensus       403 QHRF---GV~-QR~~L~~Kg~~p--h~L~MtATPIPRT--Lal~~ygdl-dvS~i~e~P~gR~~I~T~~~--~~--~~~~  469 (700)
                      --|.   |-+ |=..+.+ ...|  ..|+.|||==-+-  ||-.+.+|= .+..- +.-.--..|+-.+.  +.  .+..
T Consensus       379 adrmfdmGfe~qVrSI~~-hirpdrQtllFsaTf~~kIe~lard~L~dpVrvVqg-~vgean~dITQ~V~V~~s~~~Kl~  456 (731)
T KOG0339         379 ADRMFDMGFEPQVRSIKQ-HIRPDRQTLLFSATFKKKIEKLARDILSDPVRVVQG-EVGEANEDITQTVSVCPSEEKKLN  456 (731)
T ss_pred             HHHHHCCCCHHHHHHHHH-HCCCCCEEEEEECCCHHHHHHHHHHHHCCCEEEEEE-EHHCCCCCHHHEEEECCCCHHHHH
T ss_conf             111312654798999986-448864279860310688999999973597267874-010256652424652368178889


Q ss_pred             HHHHHHHHHHCCCCEEEEEECCCCCCCCCCCCHHHHHHHHHHHHCCCCEECCCCCCCHHHHHHHHHHHHCCCEEEEEECH
Q ss_conf             68999976310387389997120122111210146666666866371031201469989999999997559869999800
Q gi|254780945|r  470 EVIERLKVVLSEGKKAYWICPQIEEKKESNFRSVVERFNSLHEHFTSSIAIIHGRMSDIDKESVMDSFKNGTCKLLIATT  549 (700)
Q Consensus       470 ~~~~~i~~~l~~g~q~y~VcPlIeese~~~~~~~~~~~~~l~~~~~~~v~~lHGkm~~~ek~~~m~~F~~g~~~iLvaTt  549 (700)
                      .+...+-.-...|.-.|+|.      .+   .++++..+.|+-. +.+|.++||-|...|+++++.+|+.++.+|||+|-
T Consensus       457 wl~~~L~~f~S~gkvlifVT------Kk---~~~e~i~a~Lklk-~~~v~llhgdkdqa~rn~~ls~fKkk~~~VlvatD  526 (731)
T KOG0339         457 WLLRHLVEFSSEGKVLIFVT------KK---ADAEEIAANLKLK-GFNVSLLHGDKDQAERNEVLSKFKKKRKPVLVATD  526 (731)
T ss_pred             HHHHHHHHHCCCCCEEEEEE------CC---CCHHHHHHHHCCC-CCEEEEECCCHHHHHHHHHHHHHHHCCCCEEEEEE
T ss_conf             99997550136784799994------22---7899999873205-63256522745667777799987624775488840


Q ss_pred             HHHCCCCCCCCCEEEEECHHHCCHHHHH-HHHHCCCCCCCCEEEEEEECCCCCHHHHHHHHHHHHHC
Q ss_conf             3410468887658998585254746887-73011667898359999708889987999999998414
Q gi|254780945|r  550 VIEVGIDVVDASIIIIENAEHFGLAQLH-QLRGRVGRGEEISSCILLYHPPLSKNSYTRLSVLKNTE  615 (700)
Q Consensus       550 viEVGvdvpna~~mvI~~aerfGLsqLH-QLRGRVGRg~~~s~c~l~~~~~~~~~~~~Rl~~l~~~~  615 (700)
                      |---|.|||.-.+  |.|-|-|-=--.| |-=||-||-+..|..|-+..++..+-+-.=.+.|+...
T Consensus       527 vaargldI~~ikT--VvnyD~ardIdththrigrtgRag~kGvayTlvTeKDa~fAG~LVnnLe~ag  591 (731)
T KOG0339         527 VAARGLDIPSIKT--VVNYDFARDIDTHTHRIGRTGRAGEKGVAYTLVTEKDAEFAGHLVNNLEGAG  591 (731)
T ss_pred             HHHCCCCCCCCCE--EECCCCCCHHHHHHHHHHHCCCCCCCCEEEEEECHHHHHHHHHHHHHHHHCC
T ss_conf             7651787522010--2343222106778877510233555651368733556777668998876236


No 60 
>KOG0328 consensus
Probab=99.55  E-value=7.1e-13  Score=120.57  Aligned_cols=305  Identities=24%  Similarity=0.348  Sum_probs=213.2

Q ss_pred             HHHHHHHHHCCCC-CCHHHHHHHHHHHHHHCCCCCCEEEEEECCCCCHHHHHHHHHHHHHHHH---CCEEEEEHHHHHHH
Q ss_conf             7899998630246-7988999999999841001343078862144223699999973344430---54588612799999
Q gi|254780945|r  260 KIAQKILRNIPFS-PTKSQESAIKDILQDMSQKNRMLRILQGDVGSGKTLVALIAMAAAVEAG---GQAVIMAPIGILAQ  335 (700)
Q Consensus       260 ~~~~~f~~~LPF~-LT~~Q~~ai~eI~~Dl~~~~pM~RLLQGDVGSGKTiVA~~A~l~~~~~G---~Q~alMaPTEILA~  335 (700)
                      ++...+++ -.|+ +..=|++||-.|.+-    +  +-..|.--|.|||+-..+..+.+++-+   -||.++.||-=||.
T Consensus        37 dlLrgiY~-yGfekPS~IQqrAi~~IlkG----r--dViaQaqSGTGKTa~~si~vlq~~d~~~r~tQ~lilsPTRELa~  109 (400)
T KOG0328          37 DLLRGIYA-YGFEKPSAIQQRAIPQILKG----R--DVIAQAQSGTGKTATFSISVLQSLDISVRETQALILSPTRELAV  109 (400)
T ss_pred             HHHHHHHH-HCCCCCHHHHHHHHHHHHCC----C--CEEEEECCCCCCEEEEEEEEEEECCCCCCEEEEEEECCHHHHHH
T ss_conf             99999997-22578167776102456336----6--14787047888447898663140343420035789547089999


Q ss_pred             HHHHHHHHHCCCCCCEEEEEECCCCHHHHHHHHHHHCCCCCEEEEECHHH-C----CCCCCCCCCCEEEECCCCCCCHHH
Q ss_conf             99986211014578658996246422566768776213475486411120-1----334554444178852101335688
Q gi|254780945|r  336 QHYEFIKKYTQNTQIIVEIITGNMPQAHRRKALERIAHGQAHIIIGTHAL-F----QDSIQYYKLILVIVDEQHRFGVQQ  410 (700)
Q Consensus       336 QH~~~~~~~~~~~~i~v~lLtg~~~~~er~~i~~~i~~G~~~iiIGTHAL-~----q~~v~F~~LgLvViDEQHRFGV~Q  410 (700)
                      |.-+.+..+-++.+|+|.--.|+.+-.|--+.++   -| .++|.||-.- +    -..+..++.-+.|.||-.      
T Consensus       110 Qi~~vi~alg~~mnvq~hacigg~n~gedikkld---~G-~hvVsGtPGrv~dmikr~~L~tr~vkmlVLDEaD------  179 (400)
T KOG0328         110 QIQKVILALGDYMNVQCHACIGGKNLGEDIKKLD---YG-QHVVSGTPGRVLDMIKRRSLRTRAVKMLVLDEAD------  179 (400)
T ss_pred             HHHHHHHHHCCCCCCEEEEEECCCCCCHHHHHHC---CC-CEEEECCCCHHHHHHHHCCCCCCCEEEEEECCHH------
T ss_conf             9999999832423644898735775103456532---56-1475079815999998623101142689854589------


Q ss_pred             HHHHHHCC-------------CCCCCEEECHHHHHHHHHHHHHHCCCHHHHCCCCCCC--CCCEEEEEECCCHH---HHH
Q ss_conf             99874025-------------6776101010132278999975201011110235576--66207999702002---689
Q gi|254780945|r  411 RLKLTQKA-------------TAPHVLLMTATPIPRTLVLTSLGDIDISKITEKPAGR--KPIKTVIIPINRID---EVI  472 (700)
Q Consensus       411 R~~L~~Kg-------------~~ph~L~MtATPIPRTLal~~ygdldvS~i~e~P~gR--~~I~T~~~~~~~~~---~~~  472 (700)
                        .|.+||             ....+.+.|||-=---|-||-.=--|--.|-.++-+-  --|+-+.+.-++.+   ...
T Consensus       180 --emL~kgfk~Qiydiyr~lp~~~Qvv~~SATlp~eilemt~kfmtdpvrilvkrdeltlEgIKqf~v~ve~EewKfdtL  257 (400)
T KOG0328         180 --EMLNKGFKEQIYDIYRYLPPGAQVVLVSATLPHEILEMTEKFMTDPVRILVKRDELTLEGIKQFFVAVEKEEWKFDTL  257 (400)
T ss_pred             --HHHHHHHHHHHHHHHHHCCCCCEEEEEECCCCHHHHHHHHHHCCCCEEEEEECCCCCHHHHHHHEEEECHHHHHHHHH
T ss_conf             --998756778899999847998669999645869999999874488526887057776666555424413225537689


Q ss_pred             HHHHHHHCCCCEEEEEECCCCCCCCCCCCHHHHHHHHHHHHCCC---CEECCCCCCCHHHHHHHHHHHHCCCEEEEEECH
Q ss_conf             99976310387389997120122111210146666666866371---031201469989999999997559869999800
Q gi|254780945|r  473 ERLKVVLSEGKKAYWICPQIEEKKESNFRSVVERFNSLHEHFTS---SIAIIHGRMSDIDKESVMDSFKNGTCKLLIATT  549 (700)
Q Consensus       473 ~~i~~~l~~g~q~y~VcPlIeese~~~~~~~~~~~~~l~~~~~~---~v~~lHGkm~~~ek~~~m~~F~~g~~~iLvaTt  549 (700)
                      --+.+.|. =.|+.+-|..            ....++|.+..-+   .|..+||-|..+|+|++|++|++|+..||++|-
T Consensus       258 cdLYd~Lt-ItQavIFcnT------------k~kVdwLtekm~~~nftVssmHGDm~qkERd~im~dFRsg~SrvLitTD  324 (400)
T KOG0328         258 CDLYDTLT-ITQAVIFCNT------------KRKVDWLTEKMREANFTVSSMHGDMEQKERDKIMNDFRSGKSRVLITTD  324 (400)
T ss_pred             HHHHHHHE-HHEEEEEECC------------CCHHHHHHHHHHHHCCEEEECCCCCCHHHHHHHHHHHHCCCCEEEEEEC
T ss_conf             88864306-1147999626------------4043688999886173366305776456799999876547834999710


Q ss_pred             HHHCCCCCCCCCEEEEECHHHCCHHHHHHHHHCCCCCCCCEEEEEEEC
Q ss_conf             341046888765899858525474688773011667898359999708
Q gi|254780945|r  550 VIEVGIDVVDASIIIIENAEHFGLAQLHQLRGRVGRGEEISSCILLYH  597 (700)
Q Consensus       550 viEVGvdvpna~~mvI~~aerfGLsqLHQLRGRVGRg~~~s~c~l~~~  597 (700)
                      |---|+|||..|++|=++--..-=--.|- =||-||=+..|..+=...
T Consensus       325 VwaRGiDv~qVslviNYDLP~nre~YIHR-IGRSGRFGRkGvainFVk  371 (400)
T KOG0328         325 VWARGIDVQQVSLVINYDLPNNRELYIHR-IGRSGRFGRKGVAINFVK  371 (400)
T ss_pred             HHHCCCCCCEEEEEEECCCCCCHHHHHHH-HCCCCCCCCCCEEEEEEC
T ss_conf             44425875005789943788548787665-013565677606998751


No 61 
>KOG0330 consensus
Probab=99.55  E-value=3.1e-12  Score=115.49  Aligned_cols=323  Identities=20%  Similarity=0.258  Sum_probs=205.4

Q ss_pred             CCCCCHHHHHHHHHCCCCCCHHHHHHHHHHHHHHCCCCCCEEEEEECCCCCHHHHHHHHHHHHHHH---HCCEEEEEHHH
Q ss_conf             787757899998630246798899999999984100134307886214422369999997334443---05458861279
Q gi|254780945|r  255 INVEGKIAQKILRNIPFSPTKSQESAIKDILQDMSQKNRMLRILQGDVGSGKTLVALIAMAAAVEA---GGQAVIMAPIG  331 (700)
Q Consensus       255 ~~~~~~~~~~f~~~LPF~LT~~Q~~ai~eI~~Dl~~~~pM~RLLQGDVGSGKTiVA~~A~l~~~~~---G~Q~alMaPTE  331 (700)
                      +.....+++......==.+|.=|+++|--...    +..  -+---..|||||.-.++-++..+-.   -+-|.+++||-
T Consensus        66 Lgv~~~L~~ac~~l~~~~PT~IQ~~aiP~~L~----g~d--vIglAeTGSGKT~afaLPIl~~LL~~p~~~~~lVLtPtR  139 (476)
T KOG0330          66 LGVHPELLEACQELGWKKPTKIQSEAIPVALG----GRD--VIGLAETGSGKTGAFALPILQRLLQEPKLFFALVLTPTR  139 (476)
T ss_pred             CCCCHHHHHHHHHHCCCCCCHHHHHHCCHHHC----CCC--EEEEECCCCCCHHHHHHHHHHHHHCCCCCCEEEEECCCH
T ss_conf             37689999999984767874444520655437----985--799943588840231799999997198774489964828


Q ss_pred             HHHHHHHHHHHHHCCCCCCEEEEEECCCCHHHHHHHHHHHCCCCCEEEEECHHHC------CCCCCCCCCCEEEECCCCC
Q ss_conf             9999999862110145786589962464225667687762134754864111201------3345544441788521013
Q gi|254780945|r  332 ILAQQHYEFIKKYTQNTQIIVEIITGNMPQAHRRKALERIAHGQAHIIIGTHALF------QDSIQYYKLILVIVDEQHR  405 (700)
Q Consensus       332 ILA~QH~~~~~~~~~~~~i~v~lLtg~~~~~er~~i~~~i~~G~~~iiIGTHAL~------q~~v~F~~LgLvViDEQHR  405 (700)
                      =||.|..+.|..+=...|++|+.|.|++..-.-...    .+-+++|+|+|---+      ......++|...|.||--|
T Consensus       140 ELA~QI~e~fe~Lg~~iglr~~~lvGG~~m~~q~~~----L~kkPhilVaTPGrL~dhl~~Tkgf~le~lk~LVlDEADr  215 (476)
T KOG0330         140 ELAQQIAEQFEALGSGIGLRVAVLVGGMDMMLQANQ----LSKKPHILVATPGRLWDHLENTKGFSLEQLKFLVLDEADR  215 (476)
T ss_pred             HHHHHHHHHHHHHCCCCCEEEEEEECCCHHHHHHHH----HHCCCCEEEECCHHHHHHHHHCCCCCHHHHHHHHHCHHHH
T ss_conf             999999999987535667279998658329999887----6248987983707899998743684088757876331776


Q ss_pred             C-----CHHHHHHHHHCCCCCCCEEECHHHHHHHHHHHHHHCCCHHHHCCCCCCCCCCE---------------EE-EEE
Q ss_conf             3-----56889987402567761010101322789999752010111102355766620---------------79-997
Q gi|254780945|r  406 F-----GVQQRLKLTQKATAPHVLLMTATPIPRTLVLTSLGDIDISKITEKPAGRKPIK---------------TV-IIP  464 (700)
Q Consensus       406 F-----GV~QR~~L~~Kg~~ph~L~MtATPIPRTLal~~ygdldvS~i~e~P~gR~~I~---------------T~-~~~  464 (700)
                      +     ++.=-.-|..--...-.+..|||=---+      +-|..+.++.      |++               |+ .++
T Consensus       216 lLd~dF~~~ld~ILk~ip~erqt~LfsATMt~kv------~kL~rasl~~------p~~v~~s~ky~tv~~lkQ~ylfv~  283 (476)
T KOG0330         216 LLDMDFEEELDYILKVIPRERQTFLFSATMTKKV------RKLQRASLDN------PVKVAVSSKYQTVDHLKQTYLFVP  283 (476)
T ss_pred             HHHHHHHHHHHHHHHHCCCCCEEEEEEEECCHHH------HHHHHHCCCC------CEEEECCCHHCCHHHHHHHEEECC
T ss_conf             6211568999999874674414899986444136------7787641589------717860430111677664557632


Q ss_pred             CCCHHHHHHHHHHHHCCCCEEEEEECCCCCCCCCCCCHHHHHHHHHHHHCCCCEECCCCCCCHHHHHHHHHHHHCCCEEE
Q ss_conf             02002689999763103873899971201221112101466666668663710312014699899999999975598699
Q gi|254780945|r  465 INRIDEVIERLKVVLSEGKKAYWICPQIEEKKESNFRSVVERFNSLHEHFTSSIAIIHGRMSDIDKESVMDSFKNGTCKL  544 (700)
Q Consensus       465 ~~~~~~~~~~i~~~l~~g~q~y~VcPlIeese~~~~~~~~~~~~~l~~~~~~~v~~lHGkm~~~ek~~~m~~F~~g~~~i  544 (700)
                      .+..+--.-.+-++.. |+-+.|-|-.         .+-++....+-...+-..--|||+|+...+-.+|++|++|..+|
T Consensus       284 ~k~K~~yLV~ll~e~~-g~s~iVF~~t---------~~tt~~la~~L~~lg~~a~~LhGqmsq~~Rlg~l~~Fk~~~r~i  353 (476)
T KOG0330         284 GKDKDTYLVYLLNELA-GNSVIVFCNT---------CNTTRFLALLLRNLGFQAIPLHGQMSQSKRLGALNKFKAGARSI  353 (476)
T ss_pred             CCCCCHHHHHHHHHHC-CCCEEEEEEC---------CCHHHHHHHHHHHCCCCEECCCCHHHHHHHHHHHHHHHCCCCCE
T ss_conf             6666523899887635-9847999834---------64089999999862764320566035778877899875147767


Q ss_pred             EEECHHHHCCCCCCCCCEEEEECHHHCCHHHHHHHHHCCCCCCCCEEEEEEECCCCCHHHHHHHHHH
Q ss_conf             9980034104688876589985852547468877301166789835999970888998799999999
Q gi|254780945|r  545 LIATTVIEVGIDVVDASIIIIENAEHFGLAQLHQLRGRVGRGEEISSCILLYHPPLSKNSYTRLSVL  611 (700)
Q Consensus       545 LvaTtviEVGvdvpna~~mvI~~aerfGLsqLHQLRGRVGRg~~~s~c~l~~~~~~~~~~~~Rl~~l  611 (700)
                      ||||-|---|.|+|.+.+.|=+|----+=.-.|- =||+||-+..|..+-+...- .-+-.+|++..
T Consensus       354 Lv~TDVaSRGLDip~Vd~VVNyDiP~~skDYIHR-vGRtaRaGrsG~~ItlVtqy-Dve~~qrIE~~  418 (476)
T KOG0330         354 LVCTDVASRGLDIPHVDVVVNYDIPTHSKDYIHR-VGRTARAGRSGKAITLVTQY-DVELVQRIEHA  418 (476)
T ss_pred             EEECCHHCCCCCCCCCEEEEECCCCCCHHHHHHH-CCCCCCCCCCCCEEEEEEHH-HHHHHHHHHHH
T ss_conf             9861301046898771079953789837888887-04300167775148987445-56999999999


No 62 
>KOG0338 consensus
Probab=99.55  E-value=7.5e-12  Score=112.54  Aligned_cols=322  Identities=19%  Similarity=0.269  Sum_probs=207.0

Q ss_pred             HHHHCCC-CCCHHHHHHHH--HHHHHHCCCCCCEEEEEECCCCCHHHHHHHHHHHHH------HHHCCEEEEEHHHHHHH
Q ss_conf             9863024-67988999999--999841001343078862144223699999973344------43054588612799999
Q gi|254780945|r  265 ILRNIPF-SPTKSQESAIK--DILQDMSQKNRMLRILQGDVGSGKTLVALIAMAAAV------EAGGQAVIMAPIGILAQ  335 (700)
Q Consensus       265 f~~~LPF-~LT~~Q~~ai~--eI~~Dl~~~~pM~RLLQGDVGSGKTiVA~~A~l~~~------~~G~Q~alMaPTEILA~  335 (700)
                      -+..|.| .+|.=|...|-  -.-.|+...        .-.|||||.-.++..+--+      -.--.|.+++||-=||-
T Consensus       195 a~~~lGy~~PTpIQ~a~IPvallgkDIca~--------A~TGsGKTAAF~lPiLERLlYrPk~~~~TRVLVL~PTRELai  266 (691)
T KOG0338         195 ACSTLGYKKPTPIQVATIPVALLGKDICAC--------AATGSGKTAAFALPILERLLYRPKKVAATRVLVLVPTRELAI  266 (691)
T ss_pred             HHHHCCCCCCCCHHHHCCCHHHHCCHHHHE--------ECCCCCCHHHHHHHHHHHHHCCCCCCCCEEEEEEECCHHHHH
T ss_conf             887438788874033101277522225640--------114687114567889999852735676126999835089999


Q ss_pred             HHHHHHHHHCCCCCCEEEEEECCCCHHHHHHHHHHHCCCCCEEEEECHH------HCCCCCCCCCCCEEEECCCCCCCH-
Q ss_conf             9998621101457865899624642256676877621347548641112------013345544441788521013356-
Q gi|254780945|r  336 QHYEFIKKYTQNTQIIVEIITGNMPQAHRRKALERIAHGQAHIIIGTHA------LFQDSIQYYKLILVIVDEQHRFGV-  408 (700)
Q Consensus       336 QH~~~~~~~~~~~~i~v~lLtg~~~~~er~~i~~~i~~G~~~iiIGTHA------L~q~~v~F~~LgLvViDEQHRFGV-  408 (700)
                      |-|.-++++..-..|.|+|-.|++.-+..+..|.    ..+||||.|--      ==+..+...++...|.||--|.=- 
T Consensus       267 Qv~sV~~qlaqFt~I~~~L~vGGL~lk~QE~~LR----s~PDIVIATPGRlIDHlrNs~sf~ldsiEVLvlDEADRMLee  342 (691)
T KOG0338         267 QVHSVTKQLAQFTDITVGLAVGGLDLKAQEAVLR----SRPDIVIATPGRLIDHLRNSPSFNLDSIEVLVLDEADRMLEE  342 (691)
T ss_pred             HHHHHHHHHHHHCCCEEEEEECCCCHHHHHHHHH----HCCCEEEECCHHHHHHHCCCCCCCCCCEEEEEECHHHHHHHH
T ss_conf             9999999987660402444524745788999983----089879946505888751588765343257773338889999


Q ss_pred             ---HHHHHHHH-CCCCCCCEEECHHHHHHHHHHHHHHCC-CHHHHCCCCCCCCCCEEEEEECCCHHHH--HHHHHHH-HC
Q ss_conf             ---88998740-256776101010132278999975201-0111102355766620799970200268--9999763-10
Q gi|254780945|r  409 ---QQRLKLTQ-KATAPHVLLMTATPIPRTLVLTSLGDI-DISKITEKPAGRKPIKTVIIPINRIDEV--IERLKVV-LS  480 (700)
Q Consensus       409 ---~QR~~L~~-Kg~~ph~L~MtATPIPRTLal~~ygdl-dvS~i~e~P~gR~~I~T~~~~~~~~~~~--~~~i~~~-l~  480 (700)
                         .|=..+.. -..+-..+..|||=----      -|| .+|.       .+||.-.+=++.+...-  -+||+-. -.
T Consensus       343 gFademnEii~lcpk~RQTmLFSATMteeV------kdL~slSL-------~kPvrifvd~~~~~a~~LtQEFiRIR~~r  409 (691)
T KOG0338         343 GFADEMNEIIRLCPKNRQTMLFSATMTEEV------KDLASLSL-------NKPVRIFVDPNKDTAPKLTQEFIRIRPKR  409 (691)
T ss_pred             HHHHHHHHHHHHCCCCCCCEEEHHHHHHHH------HHHHHHHC-------CCCEEEEECCCCCCCHHHHHHHHEECCCC
T ss_conf             999999999985510230012112257889------99997551-------79858985786544404447781005564


Q ss_pred             CCCEEEEEECCCCCCCCC---CCCHHHHHHHHHHHHC---CCCEECCCCCCCHHHHHHHHHHHHCCCEEEEEECHHHHCC
Q ss_conf             387389997120122111---2101466666668663---7103120146998999999999755986999980034104
Q gi|254780945|r  481 EGKKAYWICPQIEEKKES---NFRSVVERFNSLHEHF---TSSIAIIHGRMSDIDKESVMDSFKNGTCKLLIATTVIEVG  554 (700)
Q Consensus       481 ~g~q~y~VcPlIeese~~---~~~~~~~~~~~l~~~~---~~~v~~lHGkm~~~ek~~~m~~F~~g~~~iLvaTtviEVG  554 (700)
                      .|-+-.+|..||-..-.-   -.-.-.....+|+=.|   +-++|-|||-++.++.=+.+++|+++++|+||||-|---|
T Consensus       410 e~dRea~l~~l~~rtf~~~~ivFv~tKk~AHRl~IllGLlgl~agElHGsLtQ~QRlesL~kFk~~eidvLiaTDvAsRG  489 (691)
T KOG0338         410 EGDREAMLASLITRTFQDRTIVFVRTKKQAHRLRILLGLLGLKAGELHGSLTQEQRLESLEKFKKEEIDVLIATDVASRG  489 (691)
T ss_pred             CCCCHHHHHHHHHHHCCCCEEEEEEHHHHHHHHHHHHHHHHCHHHHHCCCCCHHHHHHHHHHHHHCCCCEEEEECHHHCC
T ss_conf             44417899999987604336999720877889999998730106655054108889999998774568779872044446


Q ss_pred             CCCCCCCEEEEECHHHCCHHHHHHHHHCCCCCCCCEEEEEEECCCCCHHHHHHHHHHHHHCH
Q ss_conf             68887658998585254746887730116678983599997088899879999999984142
Q gi|254780945|r  555 IDVVDASIIIIENAEHFGLAQLHQLRGRVGRGEEISSCILLYHPPLSKNSYTRLSVLKNTED  616 (700)
Q Consensus       555 vdvpna~~mvI~~aerfGLsqLHQLRGRVGRg~~~s~c~l~~~~~~~~~~~~Rl~~l~~~~d  616 (700)
                      +|++..-+.|=++.-+===.-||-. ||-.|-+..|+.+-+..    +..++=|+.+.+++.
T Consensus       490 LDI~gV~tVINy~mP~t~e~Y~HRV-GRTARAGRaGrsVtlvg----E~dRkllK~iik~~~  546 (691)
T KOG0338         490 LDIEGVQTVINYAMPKTIEHYLHRV-GRTARAGRAGRSVTLVG----ESDRKLLKEIIKSST  546 (691)
T ss_pred             CCCCCEEEEEECCCCHHHHHHHHHH-HHHHHCCCCCCEEEEEC----CCCHHHHHHHHHHHH
T ss_conf             7765516888426752689999874-00332456764378744----540889999985103


No 63 
>COG4581 Superfamily II RNA helicase [DNA replication, recombination, and repair]
Probab=99.54  E-value=1.6e-12  Score=117.77  Aligned_cols=318  Identities=21%  Similarity=0.304  Sum_probs=209.0

Q ss_pred             HHHHHHHCCCCCCHHHHHHHHHHHHHHCCCCCCEEEEEECCCCCHHHHHHHHHHHHHHHHCCEEEEEHHHHHHHHHHHHH
Q ss_conf             99998630246798899999999984100134307886214422369999997334443054588612799999999862
Q gi|254780945|r  262 AQKILRNIPFSPTKSQESAIKDILQDMSQKNRMLRILQGDVGSGKTLVALIAMAAAVEAGGQAVIMAPIGILAQQHYEFI  341 (700)
Q Consensus       262 ~~~f~~~LPF~LT~~Q~~ai~eI~~Dl~~~~pM~RLLQGDVGSGKTiVA~~A~l~~~~~G~Q~alMaPTEILA~QH~~~~  341 (700)
                      ...+...+||+|-+-|++|+.-|..|=      .+|+.--.|||||+||..|+..+..+|.-+-+-+|+--|..|-|.-|
T Consensus       109 ~~~~~~~~~F~LD~fQ~~a~~~Ler~e------sVlV~ApTssGKTvVaeyAi~~al~~~qrviYTsPIKALsNQKyrdl  182 (1041)
T COG4581         109 LAPPAREYPFELDPFQQEAIAILERGE------SVLVCAPTSSGKTVVAEYAIALALRDGQRVIYTSPIKALSNQKYRDL  182 (1041)
T ss_pred             CCCHHHHCCCCCCHHHHHHHHHHHCCC------CEEEECCCCCCCCHHHHHHHHHHHHCCCCEEECCCHHHHHHHHHHHH
T ss_conf             683787489896789999999984799------57997337898555999999999871894486163066420679999


Q ss_pred             HHHCCCCCCEEEEEECCCCHHHHHHHHHHHCCCCCEEEEECHHHC-----CCCCCCCCCCEEEECCCCCCCHHHHHHHHH
Q ss_conf             110145786589962464225667687762134754864111201-----334554444178852101335688998740
Q gi|254780945|r  342 KKYTQNTQIIVEIITGNMPQAHRRKALERIAHGQAHIIIGTHALF-----QDSIQYYKLILVIVDEQHRFGVQQRLKLTQ  416 (700)
Q Consensus       342 ~~~~~~~~i~v~lLtg~~~~~er~~i~~~i~~G~~~iiIGTHAL~-----q~~v~F~~LgLvViDEQHRFGV~QR~~L~~  416 (700)
                      ...|.+..-.|.|+||..+-           ++.+.++|=|.-++     +..-.-..+.-||-||+|=-|=..|..-++
T Consensus       183 ~~~fgdv~~~vGL~TGDv~I-----------N~~A~clvMTTEILRnMlyrg~~~~~~i~~ViFDEvHyi~D~eRG~VWE  251 (1041)
T COG4581         183 LAKFGDVADMVGLMTGDVSI-----------NPDAPCLVMTTEILRNMLYRGSESLRDIEWVVFDEVHYIGDRERGVVWE  251 (1041)
T ss_pred             HHHHHHHHHHCCCEECCEEE-----------CCCCCEEEEEHHHHHHHHCCCCCCCCCCCEEEEEEEEECCCCCCCHHHH
T ss_conf             99860056540401054342-----------7999668860999999862586101353068887666504632212578


Q ss_pred             C-----CCCCCCEEECHHHHHHHHHHHHHHCCCHHHHCCCCC------CCC-CCEEEEEECCC--------HH---H---
Q ss_conf             2-----567761010101322789999752010111102355------766-62079997020--------02---6---
Q gi|254780945|r  417 K-----ATAPHVLLMTATPIPRTLVLTSLGDIDISKITEKPA------GRK-PIKTVIIPINR--------ID---E---  470 (700)
Q Consensus       417 K-----g~~ph~L~MtATPIPRTLal~~ygdldvS~i~e~P~------gR~-~I~T~~~~~~~--------~~---~---  470 (700)
                      -     -...++..|||| ||-+.-.+.+    +|.++..|.      -|. |-.-++....+        .+   .   
T Consensus       252 E~Ii~lP~~v~~v~LSAT-v~N~~EF~~W----i~~~~~~~~~vv~t~~RpvPL~~~~~~~~~l~~lvde~~~~~~~~~~  326 (1041)
T COG4581         252 EVIILLPDHVRFVFLSAT-VPNAEEFAEW----IQRVHSQPIHVVSTEHRPVPLEHFVYVGKGLFDLVDEKKKFNAENFP  326 (1041)
T ss_pred             HHHHHCCCCCCEEEEECC-CCCHHHHHHH----HHHCCCCCEEEEEECCCCCCEEEEEECCCCEEEEECCCCCCHHHCCH
T ss_conf             999866777768999678-8987999999----97403787489950688897179886587514535456530111343


Q ss_pred             -HHHHHH------HHHCCCCEEEE------------E----------------ECCCCCC-------------CCCCCCH
Q ss_conf             -899997------63103873899------------9----------------7120122-------------1112101
Q gi|254780945|r  471 -VIERLK------VVLSEGKKAYW------------I----------------CPQIEEK-------------KESNFRS  502 (700)
Q Consensus       471 -~~~~i~------~~l~~g~q~y~------------V----------------cPlIees-------------e~~~~~~  502 (700)
                       +-..+.      .+-+.|.+.|.            +                -|.|.-+             ..+|+.+
T Consensus       327 ~a~~~l~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~iv~~l~~~~~lP~I~F~FSr~~Ce~~a~~~~~ldl~~  406 (1041)
T COG4581         327 SANRSLSCFSEKVRETDDGDVGRYARRTKALRGSAKGPAGRPEIVNKLDKDNLLPAIVFSFSRRGCEEAAQILSTLDLVL  406 (1041)
T ss_pred             HHHHHHHCCCHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCEEEEEECHHHHHHHHHHHCCCCCCC
T ss_conf             34334302200013567654321233334567766565530577766544037852899973651899998750364215


Q ss_pred             HHH-------------------------HHHHHHHHCCCCEECCCCCCCHHHHHHHHHHHHCCCEEEEEECHHHHCCCCC
Q ss_conf             466-------------------------6666686637103120146998999999999755986999980034104688
Q gi|254780945|r  503 VVE-------------------------RFNSLHEHFTSSIAIIHGRMSDIDKESVMDSFKNGTCKLLIATTVIEVGIDV  557 (700)
Q Consensus       503 ~~~-------------------------~~~~l~~~~~~~v~~lHGkm~~~ek~~~m~~F~~g~~~iLvaTtviEVGvdv  557 (700)
                      .++                         .+..+.+.+...+|+=|+.|=+..|+.+=.-|..|-++++.||-+--.|+|+
T Consensus       407 ~~~~e~~i~~ii~~~i~~L~~ed~~lp~~~~~~~~~L~RGiavHH~GlLP~~K~~vE~Lfq~GLvkvvFaTeT~s~GiNm  486 (1041)
T COG4581         407 TEEKERAIREIIDHAIGDLAEEDRELPLQILEISALLLRGIAVHHAGLLPAIKELVEELFQEGLVKVVFATETFAIGINM  486 (1041)
T ss_pred             CCCHHHHHHHHHHHHHHHCCHHHHCCCCCHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHCCCEEEEEEHHHHHHHCCC
T ss_conf             88278889999999985347202127500999999876034540245036899999999860430577533346401578


Q ss_pred             CCCCEEEE----EC--HHHC-CHHHHHHHHHCCCCCCC--CEEEEEEECCCCC
Q ss_conf             87658998----58--5254-74688773011667898--3599997088899
Q gi|254780945|r  558 VDASIIII----EN--AEHF-GLAQLHQLRGRVGRGEE--ISSCILLYHPPLS  601 (700)
Q Consensus       558 pna~~mvI----~~--aerf-GLsqLHQLRGRVGRg~~--~s~c~l~~~~~~~  601 (700)
                      |-=|+..=    .+  +.|+ -=...||+-||+||-+.  .|.-+.+-.+..+
T Consensus       487 Partvv~~~l~K~dG~~~r~L~~gEy~QmsGRAGRRGlD~~G~vI~~~~~~~~  539 (1041)
T COG4581         487 PARTVVFTSLSKFDGNGHRWLSPGEYTQMSGRAGRRGLDVLGTVIVIEPPFES  539 (1041)
T ss_pred             CCCCEEEEEEEEECCCCEEECCHHHHHHHHHHHCCCCCCCCCEEEEECCCCCC
T ss_conf             40013546557754885356581577775444301556546549995578878


No 64 
>COG1110 Reverse gyrase [DNA replication, recombination, and repair]
Probab=99.54  E-value=6.4e-12  Score=113.07  Aligned_cols=281  Identities=21%  Similarity=0.348  Sum_probs=197.8

Q ss_pred             HHHHHHHHHCCCCCCHHHHHHHHHHHHHHCCCCCCEEEEEECCCCCHHHHHHHHHHHHHHHHCCEEEEEHHHHHHHHHHH
Q ss_conf             78999986302467988999999999841001343078862144223699999973344430545886127999999998
Q gi|254780945|r  260 KIAQKILRNIPFSPTKSQESAIKDILQDMSQKNRMLRILQGDVGSGKTLVALIAMAAAVEAGGQAVIMAPIGILAQQHYE  339 (700)
Q Consensus       260 ~~~~~f~~~LPF~LT~~Q~~ai~eI~~Dl~~~~pM~RLLQGDVGSGKTiVA~~A~l~~~~~G~Q~alMaPTEILA~QH~~  339 (700)
                      ...+-|.+...|++..+|+.=.+-+..--  +..    +---.|.|||---++.++..+..|..+.+..||..|++|-++
T Consensus        70 ~~~~fF~k~~G~~~ws~QR~WakR~~rg~--SFa----iiAPTGvGKTTfg~~~sl~~a~kgkr~yii~PT~~Lv~Q~~~  143 (1187)
T COG1110          70 EFEEFFKKATGFRPWSAQRVWAKRLVRGK--SFA----IIAPTGVGKTTFGLLMSLYLAKKGKRVYIIVPTTTLVRQVYE  143 (1187)
T ss_pred             HHHHHHHHHHCCCCHHHHHHHHHHHHCCC--CEE----EECCCCCCHHHHHHHHHHHHHHCCCEEEEEECCHHHHHHHHH
T ss_conf             99999998638986078899999987378--448----982788765479999999987558749999667899999999


Q ss_pred             HHHHHCCCCC-CEEEE-EECCCCHHHHHHHHHHHCCCCCEEEEECHHHCCCC------CCCCCCCEEEECCCCCC-----
Q ss_conf             6211014578-65899-62464225667687762134754864111201334------55444417885210133-----
Q gi|254780945|r  340 FIKKYTQNTQ-IIVEI-ITGNMPQAHRRKALERIAHGQAHIIIGTHALFQDS------IQYYKLILVIVDEQHRF-----  406 (700)
Q Consensus       340 ~~~~~~~~~~-i~v~l-Ltg~~~~~er~~i~~~i~~G~~~iiIGTHAL~q~~------v~F~~LgLvViDEQHRF-----  406 (700)
                      .+.++-+..+ ..+-+ .+|.++.++|++++++|.+|..||+|.|.+-+...      ..|+   +|.||.=--|     
T Consensus       144 kl~~~~e~~~~~~~~~~yh~~l~~~ekee~le~i~~gdfdIlitTs~FL~k~~e~L~~~kFd---fifVDDVDA~Lkask  220 (1187)
T COG1110         144 RLKKFAEDAGSLDVLVVYHSALPTKEKEEALERIESGDFDILITTSQFLSKRFEELSKLKFD---FIFVDDVDAILKASK  220 (1187)
T ss_pred             HHHHHHHHCCCCCEEEEECCCCCHHHHHHHHHHHHCCCCCEEEEEHHHHHHHHHHHCCCCCC---EEEECCHHHHHHCCC
T ss_conf             99998865378524665312366577999999986599639997478788669984045777---899804788986344


Q ss_pred             ---------CHHH------------HHHHH---------------------HCCCCCCCEEECHHHHHHHHHHHHHHCC-
Q ss_conf             ---------5688------------99874---------------------0256776101010132278999975201-
Q gi|254780945|r  407 ---------GVQQ------------RLKLT---------------------QKATAPHVLLMTATPIPRTLVLTSLGDI-  443 (700)
Q Consensus       407 ---------GV~Q------------R~~L~---------------------~Kg~~ph~L~MtATPIPRTLal~~ygdl-  443 (700)
                               |..|            |..+.                     .+....-+.++|||-=||---.-+|-+| 
T Consensus       221 NvDriL~LlGf~eE~i~~a~~~~~lr~~~~~~~~~~~~~e~~~~~e~~~~~~r~k~g~LvvsSATg~~rg~R~~LfReLl  300 (1187)
T COG1110         221 NVDRLLRLLGFSEEVIESAYELIKLRRKLYGEKRAERVREELREVEREREKKRRKLGILVVSSATGKPRGSRLKLFRELL  300 (1187)
T ss_pred             CHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEEEEEECCCCCCCCHHHHHHHHH
T ss_conf             48889998088878888889999999986322367789999998888887750477369996055787774388999983


Q ss_pred             --CHHHHCCCCCCCCCCEEEEEECCCHHHHHHHHHHHHCCCCEEEEEECCCCCCCCCCCCHHHHHHHHHHHHCCCCEECC
Q ss_conf             --011110235576662079997020026899997631038738999712012211121014666666686637103120
Q gi|254780945|r  444 --DISKITEKPAGRKPIKTVIIPINRIDEVIERLKVVLSEGKKAYWICPQIEEKKESNFRSVVERFNSLHEHFTSSIAII  521 (700)
Q Consensus       444 --dvS~i~e~P~gR~~I~T~~~~~~~~~~~~~~i~~~l~~g~q~y~VcPlIeese~~~~~~~~~~~~~l~~~~~~~v~~l  521 (700)
                        ++.-..+.  =|--+.+++.+ ...+++.+.+ +.+..|+-+|+=       ......-|++.+++|+.+ +-++++.
T Consensus       301 gFevG~~~~~--LRNIvD~y~~~-~~~e~~~elv-k~lG~GgLIfV~-------~d~G~e~aeel~e~Lr~~-Gi~a~~~  368 (1187)
T COG1110         301 GFEVGSGGEG--LRNIVDIYVES-ESLEKVVELV-KKLGDGGLIFVP-------IDYGREKAEELAEYLRSH-GINAELI  368 (1187)
T ss_pred             CCCCCCCCHH--HHHEEEEECCC-CCHHHHHHHH-HHHCCCEEEEEE-------CHHHHHHHHHHHHHHHHC-CCEEEEE
T ss_conf             9856764031--30004420368-6378899999-984897499997-------177389999999999866-9607986


Q ss_pred             CCCCCHHHHHHHHHHHHCCCEEEEEEC----HHHHCCCCCCCCCEEEEE
Q ss_conf             146998999999999755986999980----034104688876589985
Q gi|254780945|r  522 HGRMSDIDKESVMDSFKNGTCKLLIAT----TVIEVGIDVVDASIIIIE  566 (700)
Q Consensus       522 HGkm~~~ek~~~m~~F~~g~~~iLvaT----tviEVGvdvpna~~mvI~  566 (700)
                      |.     ++++.++.|..||+|+||..    -|+=-|+|.|..-=-+|.
T Consensus       369 ~a-----~~~~~le~F~~GeidvLVGvAsyYG~lVRGlDLP~rirYaIF  412 (1187)
T COG1110         369 HA-----EKEEALEDFEEGEVDVLVGVASYYGVLVRGLDLPHRIRYAVF  412 (1187)
T ss_pred             EC-----CCHHHHHHHCCCCEEEEEEECCCCCCEEECCCCHHHEEEEEE
T ss_conf             23-----202245665067601799850213430224774345457899


No 65 
>TIGR00631 uvrb excinuclease ABC, B subunit; InterPro: IPR004807 All proteins in this family for which functions are known are DNA helicases that function in the nucleotide excision repair and are endonucleases that make the 3' incision next to DNA damage. They are part of a pathway requiring UvrA, UvrB, UvrC, and UvrD homologs.; GO: 0009381 excinuclease ABC activity, 0006289 nucleotide-excision repair, 0005737 cytoplasm, 0009380 excinuclease repair complex.
Probab=99.53  E-value=6.8e-12  Score=112.85  Aligned_cols=305  Identities=21%  Similarity=0.391  Sum_probs=217.5

Q ss_pred             CCCCCHHHHHHHHHHHHHHCCCCCCEEEEEECCCCCHHHHHHHHHHHHHHH-HCCEEEEEHHHHHHHHHHHHHHHHCCCC
Q ss_conf             246798899999999984100134307886214422369999997334443-0545886127999999998621101457
Q gi|254780945|r  270 PFSPTKSQESAIKDILQDMSQKNRMLRILQGDVGSGKTLVALIAMAAAVEA-GGQAVIMAPIGILAQQHYEFIKKYTQNT  348 (700)
Q Consensus       270 PF~LT~~Q~~ai~eI~~Dl~~~~pM~RLLQGDVGSGKTiVA~~A~l~~~~~-G~Q~alMaPTEILA~QH~~~~~~~~~~~  348 (700)
                      ||.+++||=+||+++.+-+..+.+-. -|-|-.|||||--    |++++.. +.=+.+|||-=.||-|-|+.||.|||+.
T Consensus         7 ~f~P~GDQP~AI~~L~~~l~~G~~~Q-tLLGvTGsGKTFT----~AnVIa~~~rPTLV~aHNKTLAAQLY~EfKefFPeN   81 (667)
T TIGR00631         7 PFQPAGDQPKAIAKLVEGLEAGEKEQ-TLLGVTGSGKTFT----MANVIAQVQRPTLVLAHNKTLAAQLYNEFKEFFPEN   81 (667)
T ss_pred             CCCCCCCHHHHHHHHHHHHHCCCCCE-EEEEEECCCHHHH----HHHHHHHHCCCEEEECCCHHHHHHHHHHHHHHCCCC
T ss_conf             88567881899999999985688714-7853214862788----989999847984998577767999999998638677


Q ss_pred             C-----------------------------------------------------------------------CEEEEEEC
Q ss_conf             8-----------------------------------------------------------------------65899624
Q gi|254780945|r  349 Q-----------------------------------------------------------------------IIVEIITG  357 (700)
Q Consensus       349 ~-----------------------------------------------------------------------i~v~lLtg  357 (700)
                      -                                                                       ..+.|-.|
T Consensus        82 AVEYFvSYYDYYQPEAYvP~~DtyIEKdaSINdeIerlR~SAT~SLl~RrDVIVVASVScIYGLG~P~~Y~~~~~~l~vG  161 (667)
T TIGR00631        82 AVEYFVSYYDYYQPEAYVPSKDTYIEKDASINDEIERLRLSATKSLLERRDVIVVASVSCIYGLGSPEEYLKMVLHLEVG  161 (667)
T ss_pred             CEEEEEECCCCCCCCCCCCCCCCEEECCCCHHHHHHHHHHHHHHHHCCCCCEEEEEEEEEECCCCCCHHHHCCEEEEEEC
T ss_conf             24525520323787321479884130455300467677889888642378789998755206888825564227865407


Q ss_pred             CCCHHHHHHHHHHH------------------------------------------------------------------
Q ss_conf             64225667687762------------------------------------------------------------------
Q gi|254780945|r  358 NMPQAHRRKALERI------------------------------------------------------------------  371 (700)
Q Consensus       358 ~~~~~er~~i~~~i------------------------------------------------------------------  371 (700)
                      ..  -++++++.+|                                                                  
T Consensus       162 ~~--~~~~~ll~~LV~lqY~RNd~~f~RG~FRvrGDVvEIfP~~~~~~~~~RiEfF~DEie~I~~~dpLtg~~~~~~~~~  239 (667)
T TIGR00631       162 KE--IDRRELLRRLVELQYERNDVDFQRGTFRVRGDVVEIFPAAYEDEFAVRIEFFGDEIERISLVDPLTGEVLRELDSF  239 (667)
T ss_pred             CC--CCHHHHHHHHHHHCEEECCEECCCCCEEEEEEEEEEECCCCCCCCEEEEEEECCEEEEHHHHCCCCCCHHHHCCCE
T ss_conf             85--5889999886340305712340577125763189863477677724899852554320212051105111005615


Q ss_pred             ---------------------------------------------------------CCCCC-------EEEE----EC-
Q ss_conf             ---------------------------------------------------------13475-------4864----11-
Q gi|254780945|r  372 ---------------------------------------------------------AHGQA-------HIII----GT-  382 (700)
Q Consensus       372 ---------------------------------------------------------~~G~~-------~iiI----GT-  382 (700)
                                                                               +-|-|       .-+=    |. 
T Consensus       240 ~ifPA~HyV~p~e~~~~Ai~~I~~EL~eRl~~f~~~~kllEaQRL~qRT~yDLEMl~e~G~C~GIENYSRhl~GR~~GEp  319 (667)
T TIGR00631       240 TIFPASHYVTPEERLERAIKEIEKELEERLKYFEEQGKLLEAQRLKQRTEYDLEMLREMGYCSGIENYSRHLSGRKPGEP  319 (667)
T ss_pred             EEECCCEECCCCHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHCCCCCCCCCCCC
T ss_conf             86054000258047999999999999999999987795178888988688778887506733770000002167776315


Q ss_pred             -HHHCCCCC-CCCCCCEEEECCCCCCCHHH-----H------HHHHHCC-------------------CCCCCEEECHHH
Q ss_conf             -12013345-54444178852101335688-----9------9874025-------------------677610101013
Q gi|254780945|r  383 -HALFQDSI-QYYKLILVIVDEQHRFGVQQ-----R------LKLTQKA-------------------TAPHVLLMTATP  430 (700)
Q Consensus       383 -HAL~q~~v-~F~~LgLvViDEQHRFGV~Q-----R------~~L~~Kg-------------------~~ph~L~MtATP  430 (700)
                       +.|| |=+ -|..=.|+||||=| --|=|     +      ..|.+=|                   ..+-+.+.||||
T Consensus       320 P~tLl-DYF~gfP~DfLlviDESH-VT~PQ~~GMY~GD~SRK~~LVeYGFRLPSAlDNRPLkfeEF~~~~~Q~vyVSATP  397 (667)
T TIGR00631       320 PYTLL-DYFIGFPEDFLLVIDESH-VTLPQIGGMYNGDRSRKQTLVEYGFRLPSALDNRPLKFEEFEERINQVVYVSATP  397 (667)
T ss_pred             CCCHH-HHCCCCCCCEEEEEEECC-CCHHHHHHHHHCCHHHHHHHHHCCCCCCHHCCCCCCCHHHHHHHCCCEEEEECCC
T ss_conf             96477-650468865089884025-7502213441304676543320277530013587898799998559889996388


Q ss_pred             HHHHHHHHHHHCCCHHHHCC--CCCCCCCCEEEEEE-CCCHHHHHHHHHHHHCCCCEEEEEECCCCCCCCCCCCHHHHHH
Q ss_conf             22789999752010111102--35576662079997-0200268999976310387389997120122111210146666
Q gi|254780945|r  431 IPRTLVLTSLGDIDISKITE--KPAGRKPIKTVIIP-INRIDEVIERLKVVLSEGKKAYWICPQIEEKKESNFRSVVERF  507 (700)
Q Consensus       431 IPRTLal~~ygdldvS~i~e--~P~gR~~I~T~~~~-~~~~~~~~~~i~~~l~~g~q~y~VcPlIeese~~~~~~~~~~~  507 (700)
                      =|==+..|--     .++.+  .|-|=..-.=.|-+ ..+.+.+++-|++..++|++|.|.        .+.-+=|    
T Consensus       398 G~~E~e~S~~-----~vvEQiiRPTGLlDP~i~VRP~~gQvdDL~~EI~~R~~~~ERvLVT--------TLTKkMA----  460 (667)
T TIGR00631       398 GDYELEQSGG-----NVVEQIIRPTGLLDPEIEVRPTDGQVDDLLSEIRQRVARNERVLVT--------TLTKKMA----  460 (667)
T ss_pred             CHHHHHHHCC-----CEEEEEECCCCCCCCEEEEECCCCHHHHHHHHHHHHHHCCCCEEEE--------EHHHHHH----
T ss_conf             5899973269-----1589987377864883688358515888899999999728948998--------2016778----


Q ss_pred             HHHHHHCC---CCEECCCCCCCHHHHHHHHHHHHCCCEEEEEECHHHHCCCCCCCCCEEEEECHHHCCH----HHHHHHH
Q ss_conf             66686637---1031201469989999999997559869999800341046888765899858525474----6887730
Q gi|254780945|r  508 NSLHEHFT---SSIAIIHGRMSDIDKESVMDSFKNGTCKLLIATTVIEVGIDVVDASIIIIENAEHFGL----AQLHQLR  580 (700)
Q Consensus       508 ~~l~~~~~---~~v~~lHGkm~~~ek~~~m~~F~~g~~~iLvaTtviEVGvdvpna~~mvI~~aerfGL----sqLHQLR  580 (700)
                      |.|.++|.   -+|-.||.-.+.-|.-+++.+.+.|++||||.=.-.==|+|+|..|+.=|.|||.=|.    .-|=|-=
T Consensus       461 EdLTdYl~E~Gikv~YLHSeIdt~ER~eiirdLR~G~fDVLVGINLLREGLDlPEVSLVAILDADKEGFLRSerSLIQTI  540 (667)
T TIGR00631       461 EDLTDYLKELGIKVRYLHSEIDTLERVEIIRDLRLGEFDVLVGINLLREGLDLPEVSLVAILDADKEGFLRSERSLIQTI  540 (667)
T ss_pred             HHHHHHHHCCCCEEEEECCHHHHHHHHHHHHHHCCCCCEEEEECCHHHCCCCCHHHHHHHHHCCCCCCCCCCCCHHHHHH
T ss_conf             89999970588379871455789999999998447884088600020024651148899763278889986630278898


Q ss_pred             HCCCCCCCCEEEEEEECCCCCH
Q ss_conf             1166789835999970888998
Q gi|254780945|r  581 GRVGRGEEISSCILLYHPPLSK  602 (700)
Q Consensus       581 GRVGRg~~~s~c~l~~~~~~~~  602 (700)
                      ||-.|+. .|..+| |-+++|+
T Consensus       541 GRAARN~-~G~Vil-YAD~iT~  560 (667)
T TIGR00631       541 GRAARNV-NGKVIL-YADKITD  560 (667)
T ss_pred             HHHHHCC-CCEEEE-ECCCCCH
T ss_conf             8875257-965999-7287007


No 66 
>KOG0951 consensus
Probab=99.51  E-value=1.4e-12  Score=118.29  Aligned_cols=305  Identities=22%  Similarity=0.311  Sum_probs=206.5

Q ss_pred             HHHHHHHHHHHH---CCCCCCEEEEEECCCCCHHHHHHHHHHHHHHHHCC-----------EEEEEHHHHHHHHHHHHHH
Q ss_conf             999999999841---00134307886214422369999997334443054-----------5886127999999998621
Q gi|254780945|r  277 QESAIKDILQDM---SQKNRMLRILQGDVGSGKTLVALIAMAAAVEAGGQ-----------AVIMAPIGILAQQHYEFIK  342 (700)
Q Consensus       277 Q~~ai~eI~~Dl---~~~~pM~RLLQGDVGSGKTiVA~~A~l~~~~~G~Q-----------~alMaPTEILA~QH~~~~~  342 (700)
                      |.+.++.|..-+   +-..--|-||.|-.|+|||-||++.|+..+.+++-           ....||+--|++---.+|+
T Consensus       306 g~~sLNrIQS~V~daAl~~~EnmLlCAPTGaGKTNVAvLtiLqel~~h~r~dgs~nl~~fKIVYIAPmKaLVqE~VgsfS  385 (1674)
T KOG0951         306 GKQSLNRIQSKVYDAALRGDENMLLCAPTGAGKTNVAVLTILQELGNHLREDGSVNLAPFKIVYIAPMKALVQEMVGSFS  385 (1674)
T ss_pred             CCHHHHHHHHHHHHHHHCCCCCEEEECCCCCCCHHHHHHHHHHHHHCCCCCCCCEECCCCEEEEEEEHHHHHHHHHHHHH
T ss_conf             40456678877778875576737874267888237999999999853545445410256137998428999999998888


Q ss_pred             HHCCCCCCEEEEEECCCCHHHHHHHHHHHCCCCCEEEEECHH---HCCCC---CCCCC-CCEEEECCCCCCC-----H--
Q ss_conf             101457865899624642256676877621347548641112---01334---55444-4178852101335-----6--
Q gi|254780945|r  343 KYTQNTQIIVEIITGNMPQAHRRKALERIAHGQAHIIIGTHA---LFQDS---IQYYK-LILVIVDEQHRFG-----V--  408 (700)
Q Consensus       343 ~~~~~~~i~v~lLtg~~~~~er~~i~~~i~~G~~~iiIGTHA---L~q~~---v~F~~-LgLvViDEQHRFG-----V--  408 (700)
                      +++.++||+|.=+||...-. ++++-      +.+++|||--   .+.++   -.+.+ ..|+||||=|=-+     |  
T Consensus       386 kRla~~GItV~ElTgD~~l~-~~qie------eTQVIVtTPEKwDiITRk~gdraY~qlvRLlIIDEIHLLhDdRGpVLE  458 (1674)
T KOG0951         386 KRLAPLGITVLELTGDSQLG-KEQIE------ETQVIVTTPEKWDIITRKSGDRAYEQLVRLLIIDEIHLLHDDRGPVLE  458 (1674)
T ss_pred             HHCCCCCCEEEEECCCCCCH-HHHHH------CCEEEEECCCHHHHHHCCCCCHHHHHHHHHHHHHHHHHCCCCCCHHHH
T ss_conf             64235671798732654100-44321------220287064222211104674238888888765444321556640788


Q ss_pred             --HHHHHHHHC--CCCCCCEEECHHHHHHHHHHHHHHCCCHHHHCCCC--------CCCC-CCEEEEEECCCH-------
Q ss_conf             --889987402--56776101010132278999975201011110235--------5766-620799970200-------
Q gi|254780945|r  409 --QQRLKLTQK--ATAPHVLLMTATPIPRTLVLTSLGDIDISKITEKP--------AGRK-PIKTVIIPINRI-------  468 (700)
Q Consensus       409 --~QR~~L~~K--g~~ph~L~MtATPIPRTLal~~ygdldvS~i~e~P--------~gR~-~I~T~~~~~~~~-------  468 (700)
                        -+|..-..+  -+.+.+.-+|||= |      -|-|.. +.|.-.|        .-|+ |+.-.+++-..+       
T Consensus       459 SIVaRt~r~ses~~e~~RlVGLSATL-P------Ny~DV~-~Fl~v~~~glf~fd~syRpvPL~qq~Igitek~~~~~~q  530 (1674)
T KOG0951         459 SIVARTFRRSESTEEGSRLVGLSATL-P------NYEDVA-SFLRVDPEGLFYFDSSYRPVPLKQQYIGITEKKPLKRFQ  530 (1674)
T ss_pred             HHHHHHHHHHHHCCCCCEEEEECCCC-C------CHHHHH-HHHCCCCCCCCCCCCCCCCCCCCCEEECCCCCCCHHHHH
T ss_conf             99999999865124574364101557-8------616557-775558532413575557677641476330378067777


Q ss_pred             ---HHHHHHHHHHHCCCCEEEE-EECCCCCCCCCC---------------------------CCHHHHHHHHHHHHCCCC
Q ss_conf             ---2689999763103873899-971201221112---------------------------101466666668663710
Q gi|254780945|r  469 ---DEVIERLKVVLSEGKKAYW-ICPQIEEKKESN---------------------------FRSVVERFNSLHEHFTSS  517 (700)
Q Consensus       469 ---~~~~~~i~~~l~~g~q~y~-VcPlIeese~~~---------------------------~~~~~~~~~~l~~~~~~~  517 (700)
                         +-+|+.|-+...+ +||.| |..+-|.++...                           ..+....-..|++.+|..
T Consensus       531 amNe~~yeKVme~agk-~qVLVFVHsRKET~ktA~aIRd~~le~dtls~fmre~s~s~eilrtea~~~kn~dLkdLLpyg  609 (1674)
T KOG0951         531 AMNEACYEKVLEHAGK-NQVLVFVHSRKETAKTARAIRDKALEEDTLSRFMREDSASREILRTEAGQAKNPDLKDLLPYG  609 (1674)
T ss_pred             HHHHHHHHHHHHHCCC-CCEEEEEEECHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHCCCCHHHHHHHHCC
T ss_conf             7789999999973787-858999983357889999999988645379998763441145655444201583078773135


Q ss_pred             EECCCCCCCHHHHHHHHHHHHCCCEEEEEECHHHHCCCCCCCCCEEE----EECHHHCC---HHHH--HHHHHCCCCCCC
Q ss_conf             31201469989999999997559869999800341046888765899----85852547---4688--773011667898
Q gi|254780945|r  518 IAIIHGRMSDIDKESVMDSFKNGTCKLLIATTVIEVGIDVVDASIII----IENAEHFG---LAQL--HQLRGRVGRGEE  588 (700)
Q Consensus       518 v~~lHGkm~~~ek~~~m~~F~~g~~~iLvaTtviEVGvdvpna~~mv----I~~aerfG---LsqL--HQLRGRVGRg~~  588 (700)
                      +++-|.-|+..+++.+=+-|++|++++||||--.+-||+.|.-|+|+    ++|+|+=-   |+++  -|.=||-||...
T Consensus       610 faIHhAGl~R~dR~~~EdLf~~g~iqvlvstatlawgvnlpahtViikgtqvy~pekg~w~elsp~dv~qmlgragrp~~  689 (1674)
T KOG0951         610 FAIHHAGLNRKDRELVEDLFADGHIQVLVSTATLAWGVNLPAHTVIIKGTQVYDPEKGRWTELSPLDVMQMLGRAGRPQY  689 (1674)
T ss_pred             CEEECCCCCCCHHHHHHHHHHCCCEEEEEEEHHHHHHCCCCCCEEEECCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCCC
T ss_conf             13311677862377899987448626887502456424777626896076215834576662787999999754489764


Q ss_pred             CEEE--EEEEC
Q ss_conf             3599--99708
Q gi|254780945|r  589 ISSC--ILLYH  597 (700)
Q Consensus       589 ~s~c--~l~~~  597 (700)
                      ..+-  +.+++
T Consensus       690 D~~gegiiit~  700 (1674)
T KOG0951         690 DTCGEGIIITD  700 (1674)
T ss_pred             CCCCCEEECCC
T ss_conf             76786455047


No 67 
>KOG0347 consensus
Probab=99.51  E-value=1.9e-12  Score=117.20  Aligned_cols=371  Identities=23%  Similarity=0.322  Sum_probs=238.3

Q ss_pred             HHHHHHCCC-CCCHHHHHHHHHHHHHHCCCCCCEEEEEECCCCCHHHHHHHHHHH--------------HHHHHCC--EE
Q ss_conf             999863024-679889999999998410013430788621442236999999733--------------4443054--58
Q gi|254780945|r  263 QKILRNIPF-SPTKSQESAIKDILQDMSQKNRMLRILQGDVGSGKTLVALIAMAA--------------AVEAGGQ--AV  325 (700)
Q Consensus       263 ~~f~~~LPF-~LT~~Q~~ai~eI~~Dl~~~~pM~RLLQGDVGSGKTiVA~~A~l~--------------~~~~G~Q--~a  325 (700)
                      -+-+..+.| .+|+=|..++-++..|=.     .-|=-.+.|||||+-..+-|+.              +...+-|  +.
T Consensus       193 L~aL~~~gFs~Pt~IQsl~lp~ai~gk~-----DIlGaAeTGSGKTLAFGIPiv~~l~~~s~~s~e~~~~~~k~~k~~~L  267 (731)
T KOG0347         193 LRALSNLGFSRPTEIQSLVLPAAIRGKV-----DILGAAETGSGKTLAFGIPIVERLLESSDDSQELSNTSAKYVKPIAL  267 (731)
T ss_pred             HHHHHHCCCCCCCCCHHHCCCHHHCCCH-----HCCCCCCCCCCCEEEECCHHHHHHHHCCCHHHHHHHHHHCCCCCEEE
T ss_conf             9999864789986104411667654630-----00033346887424412325454330365376544677605764038


Q ss_pred             EEEHHHHHHHHHHHHHHHHCCCCCCEEEEEECCCCHHHHHHHHHHHCCCCCEEEEEC----HHHCCCCC----CCCCCCE
Q ss_conf             861279999999986211014578658996246422566768776213475486411----12013345----5444417
Q gi|254780945|r  326 IMAPIGILAQQHYEFIKKYTQNTQIIVEIITGNMPQAHRRKALERIAHGQAHIIIGT----HALFQDSI----QYYKLIL  397 (700)
Q Consensus       326 lMaPTEILA~QH~~~~~~~~~~~~i~v~lLtg~~~~~er~~i~~~i~~G~~~iiIGT----HAL~q~~v----~F~~LgL  397 (700)
                      +++||-=||-|--+-|....+..+|+++-+||++.......++..    .++|||.|    -+|++++=    .|+++.-
T Consensus       268 V~tPTRELa~QV~~Hl~ai~~~t~i~v~si~GGLavqKQqRlL~~----~p~IVVATPGRlweli~e~n~~l~~~k~vkc  343 (731)
T KOG0347         268 VVTPTRELAHQVKQHLKAIAEKTQIRVASITGGLAVQKQQRLLNQ----RPDIVVATPGRLWELIEEDNTHLGNFKKVKC  343 (731)
T ss_pred             EECCHHHHHHHHHHHHHHHCCCCCEEEEEEECHHHHHHHHHHHHC----CCCEEEECCHHHHHHHHHHHHHHHHHHHCEE
T ss_conf             963709999999999998613467278875230579999999852----9987993662899999751066642332407


Q ss_pred             EEECCCCCCCHHHH------HHHHH------CCCCCCCEEECHHHHHHHHHHHHHHCCCHHHHC----------------
Q ss_conf             88521013356889------98740------256776101010132278999975201011110----------------
Q gi|254780945|r  398 VIVDEQHRFGVQQR------LKLTQ------KATAPHVLLMTATPIPRTLVLTSLGDIDISKIT----------------  449 (700)
Q Consensus       398 vViDEQHRFGV~QR------~~L~~------Kg~~ph~L~MtATPIPRTLal~~ygdldvS~i~----------------  449 (700)
                      .|+||--|.=  |.      .+|..      +...-..|+.|||=     .+...-  +++.-.                
T Consensus       344 LVlDEaDRmv--ekghF~Els~lL~~L~e~~~~~qrQTlVFSATl-----t~~~~~--~~~~~~k~~~k~~~~~~kiq~L  414 (731)
T KOG0347         344 LVLDEADRMV--EKGHFEELSKLLKHLNEEQKNRQRQTLVFSATL-----TLVLQQ--PLSSSRKKKDKEDELNAKIQHL  414 (731)
T ss_pred             EEECCHHHHH--HHCCHHHHHHHHHHHHHHHCCCCCCEEEEEEEE-----EHHHCC--HHHHHHHCCCHHHHHHHHHHHH
T ss_conf             8873477775--511099999999986031105101258998776-----333217--0577654221145566799999


Q ss_pred             --CCCCCCCCCEEEEEECCCHHHHHHHHHHHHCCCCEEEEEECCCCCC------------CCCCCCHHHHHHHHHHHHCC
Q ss_conf             --2355766620799970200268999976310387389997120122------------11121014666666686637
Q gi|254780945|r  450 --EKPAGRKPIKTVIIPINRIDEVIERLKVVLSEGKKAYWICPQIEEK------------KESNFRSVVERFNSLHEHFT  515 (700)
Q Consensus       450 --e~P~gR~~I~T~~~~~~~~~~~~~~i~~~l~~g~q~y~VcPlIees------------e~~~~~~~~~~~~~l~~~~~  515 (700)
                        +.-..-+|   .++..+.-..+-..+.+.       -+-||.-|..            ..+-..+..+-.++|.-.+.
T Consensus       415 mk~ig~~~kp---kiiD~t~q~~ta~~l~Es-------~I~C~~~eKD~ylyYfl~ryPGrTlVF~NsId~vKRLt~~L~  484 (731)
T KOG0347         415 MKKIGFRGKP---KIIDLTPQSATASTLTES-------LIECPPLEKDLYLYYFLTRYPGRTLVFCNSIDCVKRLTVLLN  484 (731)
T ss_pred             HHHHCCCCCC---EEEECCCCHHHHHHHHHH-------HHCCCCCCCCEEEEEEEEECCCCEEEEECHHHHHHHHHHHHH
T ss_conf             9984756898---267668204478888877-------635885445406899886369835998411889999999974


Q ss_pred             C-CE--ECCCCCCCHHHHHHHHHHHHCCCEEEEEECHHHHCCCCCCCCCEEEEECHHHCCHHHHHHHHHCCCCCCCCEEE
Q ss_conf             1-03--12014699899999999975598699998003410468887658998585254746887730116678983599
Q gi|254780945|r  516 S-SI--AIIHGRMSDIDKESVMDSFKNGTCKLLIATTVIEVGIDVVDASIIIIENAEHFGLAQLHQLRGRVGRGEEISSC  592 (700)
Q Consensus       516 ~-~v--~~lHGkm~~~ek~~~m~~F~~g~~~iLvaTtviEVGvdvpna~~mvI~~aerfGLsqLHQLRGRVGRg~~~s~c  592 (700)
                      . +|  -.||..|.....=+-+++|++...-+|+||-|---|+|+|+....|-++--|=-=--.|- -||-.|-+..|.-
T Consensus       485 ~L~i~p~~LHA~M~QKqRLknLEkF~~~~~~VLiaTDVAARGLDIp~V~HVIHYqVPrtseiYVHR-SGRTARA~~~Gvs  563 (731)
T KOG0347         485 NLDIPPLPLHASMIQKQRLKNLEKFKQSPSGVLIATDVAARGLDIPGVQHVIHYQVPRTSEIYVHR-SGRTARANSEGVS  563 (731)
T ss_pred             HCCCCCCHHHHHHHHHHHHHHHHHHHCCCCEEEEEEHHHHCCCCCCCCCEEEEEECCCCCCEEEEC-CCCCCCCCCCCEE
T ss_conf             169997102577889999876998744888179962344425888786367896068753246762-6653225678837


Q ss_pred             EEEECCCCCHHHHHHH-HHHHHHCHH--HHHHHHHH------HHCCCCCCCCCHHCCCCCCCCCCHHHHHHHHHHHHHHH
Q ss_conf             9970888998799999-999841425--89999998------52063000260006987440003887599999999999
Q gi|254780945|r  593 ILLYHPPLSKNSYTRL-SVLKNTEDG--FLIAEEDL------KQRKEGEILGIKQSGMPKFLIAQPELHDSLLEIARKDA  663 (700)
Q Consensus       593 ~l~~~~~~~~~~~~Rl-~~l~~~~dG--f~iAe~Dl------~lRG~G~~~G~~QsG~~~~~~~d~~~d~~ll~~a~~~a  663 (700)
                      +++++++. -....+| +.|...+|=  |-| +.|+      +.|=++++-      ..+++-..+..+..+++.|..++
T Consensus       564 vml~~P~e-~~~~~KL~ktL~k~~dlpifPv-~~~~m~~lkeRvrLA~ei~------~~e~k~~~v~~~~sWlkkaA~el  635 (731)
T KOG0347         564 VMLCGPQE-VGPLKKLCKTLKKKEDLPIFPV-ETDIMDALKERVRLAREID------KLEIKSKRVRKEESWLKKAADEL  635 (731)
T ss_pred             EEEECHHH-HHHHHHHHHHHHHCCCCCCEEC-CHHHHHHHHHHHHHHHHHH------HHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             99868177-5789999998732367773002-1789999999999999888------76644302321178999999982


Q ss_pred             HHHHHHC
Q ss_conf             9999848
Q gi|254780945|r  664 KHILTQD  670 (700)
Q Consensus       664 ~~~~~~d  670 (700)
                      .-.+.+|
T Consensus       636 ~id~d~d  642 (731)
T KOG0347         636 GIDVDED  642 (731)
T ss_pred             CCCCCCC
T ss_conf             8765555


No 68 
>KOG0326 consensus
Probab=99.50  E-value=4.1e-12  Score=114.56  Aligned_cols=293  Identities=24%  Similarity=0.343  Sum_probs=199.2

Q ss_pred             HHCCCCCCHHHHHHHHHHHHHHCCCCCCEEEEEECCCCCHHHHHHHHHHHHH---HHHCCEEEEEHHHHHHHHHHHHHHH
Q ss_conf             6302467988999999999841001343078862144223699999973344---4305458861279999999986211
Q gi|254780945|r  267 RNIPFSPTKSQESAIKDILQDMSQKNRMLRILQGDVGSGKTLVALIAMAAAV---EAGGQAVIMAPIGILAQQHYEFIKK  343 (700)
Q Consensus       267 ~~LPF~LT~~Q~~ai~eI~~Dl~~~~pM~RLLQGDVGSGKTiVA~~A~l~~~---~~G~Q~alMaPTEILA~QH~~~~~~  343 (700)
                      ++.|-.||.-      +|..            -.--|.|||.-..+.++.-+   .+.-|+.+|+||-=||-|--+..+.
T Consensus       114 esIPiaLtGr------diLa------------RaKNGTGKT~a~~IP~Lekid~~~~~IQ~~ilVPtrelALQtSqvc~~  175 (459)
T KOG0326         114 ESIPIALTGR------DILA------------RAKNGTGKTAAYCIPVLEKIDPKKNVIQAIILVPTRELALQTSQVCKE  175 (459)
T ss_pred             CCCCEEECCH------HHHH------------HCCCCCCCCCCEECHHHHHCCCCCCCEEEEEEEECCHHHHHHHHHHHH
T ss_conf             2354442351------3555------------501898873304412566528221004479996163266788799999


Q ss_pred             HCCCCCCEEEEEECCCCHHHHHHHHHHHCCCCCEEEEECH----HHCCCCC-CCCCCCEEEECCCCC-----CCHHHHHH
Q ss_conf             0145786589962464225667687762134754864111----2013345-544441788521013-----35688998
Q gi|254780945|r  344 YTQNTQIIVEIITGNMPQAHRRKALERIAHGQAHIIIGTH----ALFQDSI-QYYKLILVIVDEQHR-----FGVQQRLK  413 (700)
Q Consensus       344 ~~~~~~i~v~lLtg~~~~~er~~i~~~i~~G~~~iiIGTH----AL~q~~v-~F~~LgLvViDEQHR-----FGV~QR~~  413 (700)
                      +-+.++++|..-||+|+-+  .+|+.  -++.++++|||-    -|..++| .+++-.+.|.||-.+     |+-.- +.
T Consensus       176 lskh~~i~vmvttGGT~lr--DDI~R--l~~~VH~~vgTPGRIlDL~~KgVa~ls~c~~lV~DEADKlLs~~F~~~~-e~  250 (459)
T KOG0326         176 LSKHLGIKVMVTTGGTSLR--DDIMR--LNQTVHLVVGTPGRILDLAKKGVADLSDCVILVMDEADKLLSVDFQPIV-EK  250 (459)
T ss_pred             HHCCCCEEEEEECCCCCCC--CCEEE--ECCCEEEEECCCHHHHHHHHCCCCCCHHCEEEEECHHHHHHCHHHHHHH-HH
T ss_conf             8604684999943886544--32056--1582699972871788888626522001147874105544141456789-99


Q ss_pred             HHHC-CCCCCCEEECHHHHHHHHHHHH----HHCCCHHHHCCCCCCCCCCEEEEEECCCHHH--HHHHHHHHHCCCCEEE
Q ss_conf             7402-5677610101013227899997----5201011110235576662079997020026--8999976310387389
Q gi|254780945|r  414 LTQK-ATAPHVLLMTATPIPRTLVLTS----LGDIDISKITEKPAGRKPIKTVIIPINRIDE--VIERLKVVLSEGKKAY  486 (700)
Q Consensus       414 L~~K-g~~ph~L~MtATPIPRTLal~~----ygdldvS~i~e~P~gR~~I~T~~~~~~~~~~--~~~~i~~~l~~g~q~y  486 (700)
                      |.+. -.+..+|+.||| -|-|.---.    -.-..+-..+|+-.  +-|+-+..--+.+.+  ..+-+-..|+- +|+.
T Consensus       251 li~~lP~~rQillySAT-FP~tVk~Fm~~~l~kPy~INLM~eLtl--~GvtQyYafV~e~qKvhCLntLfskLqI-NQsI  326 (459)
T KOG0326         251 LISFLPKERQILLYSAT-FPLTVKGFMDRHLKKPYEINLMEELTL--KGVTQYYAFVEERQKVHCLNTLFSKLQI-NQSI  326 (459)
T ss_pred             HHHHCCCCCEEEEEECC-CCHHHHHHHHHHCCCCCEEEHHHHHHH--CCHHHHEEEECHHHHHHHHHHHHHHHCC-CCEE
T ss_conf             98757854204676313-640588899986058602204656320--3523210110235555649989887500-4459


Q ss_pred             EEECCCCCCCCCCCCHHHHHHHHHHHHCCCCEECCCCCCCHHHHHHHHHHHHCCCEEEEEECHHHHCCCCCCCCCEEEEE
Q ss_conf             99712012211121014666666686637103120146998999999999755986999980034104688876589985
Q gi|254780945|r  487 WICPQIEEKKESNFRSVVERFNSLHEHFTSSIAIIHGRMSDIDKESVMDSFKNGTCKLLIATTVIEVGIDVVDASIIIIE  566 (700)
Q Consensus       487 ~VcPlIeese~~~~~~~~~~~~~l~~~~~~~v~~lHGkm~~~ek~~~m~~F~~g~~~iLvaTtviEVGvdvpna~~mvI~  566 (700)
                      +-|-.+.        -||-..+.+.+ .+...-.+|.||..+.++.+..+|++|....||||-.+--|||+++.|+.|=.
T Consensus       327 IFCNS~~--------rVELLAkKITe-lGyscyyiHakM~Q~hRNrVFHdFr~G~crnLVctDL~TRGIDiqavNvVINF  397 (459)
T KOG0326         327 IFCNSTN--------RVELLAKKITE-LGYSCYYIHAKMAQEHRNRVFHDFRNGKCRNLVCTDLFTRGIDIQAVNVVINF  397 (459)
T ss_pred             EEECCCH--------HHHHHHHHHHH-CCCHHHHHHHHHHHHHHHHHHHHHHCCCCCEEEEHHHHHCCCCCCEEEEEEEC
T ss_conf             9963631--------76798988886-16436677888877654245565432532012420233046554102599963


Q ss_pred             CHHHCCHHHHHHHHHCCCCCCCCEEEEEEE
Q ss_conf             852547468877301166789835999970
Q gi|254780945|r  567 NAEHFGLAQLHQLRGRVGRGEEISSCILLY  596 (700)
Q Consensus       567 ~aerfGLsqLHQLRGRVGRg~~~s~c~l~~  596 (700)
                      +--+--=+-||-. ||-||=++.|..+=+.
T Consensus       398 Dfpk~aEtYLHRI-GRsGRFGhlGlAInLi  426 (459)
T KOG0326         398 DFPKNAETYLHRI-GRSGRFGHLGLAINLI  426 (459)
T ss_pred             CCCCCHHHHHHHC-CCCCCCCCCCEEEEEE
T ss_conf             7887778999871-6776578762479987


No 69 
>KOG0336 consensus
Probab=99.47  E-value=2.5e-11  Score=108.36  Aligned_cols=292  Identities=26%  Similarity=0.377  Sum_probs=197.8

Q ss_pred             EEEE-------CCCCCHHHHHHHHHHHHHH---------HHCCEEEEEHHHHHHHHHHHHHHHHCCCCCCEEEEEECCCC
Q ss_conf             8862-------1442236999999733444---------30545886127999999998621101457865899624642
Q gi|254780945|r  297 ILQG-------DVGSGKTLVALIAMAAAVE---------AGGQAVIMAPIGILAQQHYEFIKKYTQNTQIIVEIITGNMP  360 (700)
Q Consensus       297 LLQG-------DVGSGKTiVA~~A~l~~~~---------~G~Q~alMaPTEILA~QH~~~~~~~~~~~~i~v~lLtg~~~  360 (700)
                      ||||       -.|+|||+-.++-.+.-++         +|--+.+++||-=||.|.--..+++=-+--..+++..|   
T Consensus       254 ~LQG~DliGVAQTgtgKtL~~L~pg~ihi~aqp~~~~qr~~p~~lvl~ptreLalqie~e~~kysyng~ksvc~ygg---  330 (629)
T KOG0336         254 LLQGIDLIGVAQTGTGKTLAFLLPGFIHIDAQPKRREQRNGPGVLVLTPTRELALQIEGEVKKYSYNGLKSVCVYGG---  330 (629)
T ss_pred             EECCCCEEEEEECCCCCCHHHHCCCEEEEECCCHHHHCCCCCCEEEEECCHHHHHHHHHHHHHHHHCCCCEEEEECC---
T ss_conf             11376447787448984778750540145146111203689854998333888998876776764358432887548---


Q ss_pred             HHHHHHHHHHHCCCCCEEEEECHH----HCCC-CCCCCCCCEEEECCCCC-----CCHHHHHHHHHCCCCCCC-EEE-CH
Q ss_conf             256676877621347548641112----0133-45544441788521013-----356889987402567761-010-10
Q gi|254780945|r  361 QAHRRKALERIAHGQAHIIIGTHA----LFQD-SIQYYKLILVIVDEQHR-----FGVQQRLKLTQKATAPHV-LLM-TA  428 (700)
Q Consensus       361 ~~er~~i~~~i~~G~~~iiIGTHA----L~q~-~v~F~~LgLvViDEQHR-----FGV~QR~~L~~Kg~~ph~-L~M-tA  428 (700)
                       ..|.+..++++.| +.|+|-|--    |+.+ -|..++.-++|+||-.|     |-+.-|.-|.+  ..||- -+| ||
T Consensus       331 -gnR~eqie~lkrg-veiiiatPgrlndL~~~n~i~l~siTYlVlDEADrMLDMgFEpqIrkilld--iRPDRqtvmTSA  406 (629)
T KOG0336         331 -GNRNEQIEDLKRG-VEIIIATPGRLNDLQMDNVINLASITYLVLDEADRMLDMGFEPQIRKILLD--IRPDRQTVMTSA  406 (629)
T ss_pred             -CCCHHHHHHHHCC-CEEEEECCCHHHHHHHCCEEEEEEEEEEEECCHHHHHCCCCCHHHHHHHHH--CCCCCEEEEECC
T ss_conf             -7854689987457-417760785176555317200112588986126666445662888988652--277622553105


Q ss_pred             H--HHHHHHHHHHH--------HCCCHHHHCCCCCCCCCCEEEE-EECCC-HHHHHHHHHHHHCCCCEEEEEECCCCCCC
Q ss_conf             1--32278999975--------2010111102355766620799-97020-02689999763103873899971201221
Q gi|254780945|r  429 T--PIPRTLVLTSL--------GDIDISKITEKPAGRKPIKTVI-IPINR-IDEVIERLKVVLSEGKKAYWICPQIEEKK  496 (700)
Q Consensus       429 T--PIPRTLal~~y--------gdldvS~i~e~P~gR~~I~T~~-~~~~~-~~~~~~~i~~~l~~g~q~y~VcPlIeese  496 (700)
                      |  |=-|-||.++.        |.||+....       .|+-.+ ++.+. .-.+..+.-+.....-++.+-|..     
T Consensus       407 TWP~~VrrLa~sY~Kep~~v~vGsLdL~a~~-------sVkQ~i~v~~d~~k~~~~~~f~~~ms~ndKvIiFv~~-----  474 (629)
T KOG0336         407 TWPEGVRRLAQSYLKEPMIVYVGSLDLVAVK-------SVKQNIIVTTDSEKLEIVQFFVANMSSNDKVIIFVSR-----  474 (629)
T ss_pred             CCCHHHHHHHHHHHHCCEEEEECCCCEEEEE-------EEEEEEEECCCHHHHHHHHHHHHHCCCCCEEEEEEEC-----
T ss_conf             5866899999986408549996143435541-------0102588436189999999999855888618999831-----


Q ss_pred             CCCCCHHHHHHHHHHHHCC--C-CEECCCCCCCHHHHHHHHHHHHCCCEEEEEECHHHHCCCCCCCCCEEEEECHHHCCH
Q ss_conf             1121014666666686637--1-031201469989999999997559869999800341046888765899858525474
Q gi|254780945|r  497 ESNFRSVVERFNSLHEHFT--S-SIAIIHGRMSDIDKESVMDSFKNGTCKLLIATTVIEVGIDVVDASIIIIENAEHFGL  573 (700)
Q Consensus       497 ~~~~~~~~~~~~~l~~~~~--~-~v~~lHGkm~~~ek~~~m~~F~~g~~~iLvaTtviEVGvdvpna~~mvI~~aerfGL  573 (700)
                      +       .....|...|-  . ....|||--...+.|.+++.|++|+++|||||.+.--|+|||+.|...=++--|===
T Consensus       475 K-------~~AD~LSSd~~l~gi~~q~lHG~r~Q~DrE~al~~~ksG~vrILvaTDlaSRGlDv~DiTHV~NyDFP~nIe  547 (629)
T KOG0336         475 K-------VMADHLSSDFCLKGISSQSLHGNREQSDREMALEDFKSGEVRILVATDLASRGLDVPDITHVYNYDFPRNIE  547 (629)
T ss_pred             H-------HHHHHCCCHHHHCCCCHHHCCCCHHHHHHHHHHHHHHCCCEEEEEEECHHHCCCCCHHCCEEECCCCCCCHH
T ss_conf             0-------322102310211461011025872243599999764158169999722343378820020354057875599


Q ss_pred             HHHHHHHHCCCCCCCCEEEEEEECCCCCHHHHHHHHHHHHHC
Q ss_conf             688773011667898359999708889987999999998414
Q gi|254780945|r  574 AQLHQLRGRVGRGEEISSCILLYHPPLSKNSYTRLSVLKNTE  615 (700)
Q Consensus       574 sqLHQLRGRVGRg~~~s~c~l~~~~~~~~~~~~Rl~~l~~~~  615 (700)
                      --.|- =||.||-+.+|..+-..--.....+.+=+++|...+
T Consensus       548 eYVHR-vGrtGRaGr~G~sis~lt~~D~~~a~eLI~ILe~ae  588 (629)
T KOG0336         548 EYVHR-VGRTGRAGRTGTSISFLTRNDWSMAEELIQILERAE  588 (629)
T ss_pred             HHHHH-HCCCCCCCCCCCEEEEEEHHHHHHHHHHHHHHHHHH
T ss_conf             99987-123565777763278886304777999999999865


No 70 
>KOG0332 consensus
Probab=99.46  E-value=4.3e-11  Score=106.55  Aligned_cols=313  Identities=22%  Similarity=0.328  Sum_probs=186.5

Q ss_pred             CHHHHHHHHHHHHHHCCCCCCEEEEEECCCCCHHHHHHHHHHHHHHH---HCCEEEEEHHHHHHHHHHHHHHHHCCCCCC
Q ss_conf             98899999999984100134307886214422369999997334443---054588612799999999862110145786
Q gi|254780945|r  274 TKSQESAIKDILQDMSQKNRMLRILQGDVGSGKTLVALIAMAAAVEA---GGQAVIMAPIGILAQQHYEFIKKYTQNTQI  350 (700)
Q Consensus       274 T~~Q~~ai~eI~~Dl~~~~pM~RLLQGDVGSGKTiVA~~A~l~~~~~---G~Q~alMaPTEILA~QH~~~~~~~~~~~~i  350 (700)
                      +.=|..|+--+..    +-|-|-.-|---|+|||.-..++|+.-++.   -=|+.-+|||-=||.|--+-+.++=+-.++
T Consensus       114 skIQe~aLPlll~----~Pp~nlIaQsqsGtGKTaaFvL~MLsRvd~~~~~PQ~iCLaPtrELA~Q~~eVv~eMGKf~~i  189 (477)
T KOG0332         114 SKIQETALPLLLA----EPPQNLIAQSQSGTGKTAAFVLTMLSRVDPDVVVPQCICLAPTRELAPQTGEVVEEMGKFTEL  189 (477)
T ss_pred             CHHHHHHCCHHHC----CCCHHHHHHHCCCCCHHHHHHHHHHHHCCCCCCCCCCEEECCHHHHHHHHHHHHHHHCCCEEE
T ss_conf             2577752125305----982656655017886058999999873483335877405476177799898999984670114


Q ss_pred             EEEEEECCCCHHHHHHHHHHHCCCCCEEEEECHHHCCC------CCCCCCCCEEEECCC------CCCCHHHHHHHH-HC
Q ss_conf             58996246422566768776213475486411120133------455444417885210------133568899874-02
Q gi|254780945|r  351 IVEIITGNMPQAHRRKALERIAHGQAHIIIGTHALFQD------SIQYYKLILVIVDEQ------HRFGVQQRLKLT-QK  417 (700)
Q Consensus       351 ~v~lLtg~~~~~er~~i~~~i~~G~~~iiIGTHAL~q~------~v~F~~LgLvViDEQ------HRFGV~QR~~L~-~K  417 (700)
                      ++.+..-.-+.+.-..+-       ..|+|||---+-|      -..-...-.-|-||-      +-|+ .|-..+. .-
T Consensus       190 ta~yair~sk~~rG~~l~-------eqIviGTPGtv~Dl~~klk~id~~kikvfVlDEAD~Mi~tqG~~-D~S~rI~~~l  261 (477)
T KOG0332         190 TASYAIRGSKAKRGNKLT-------EQIVIGTPGTVLDLMLKLKCIDLEKIKVFVLDEADVMIDTQGFQ-DQSIRIMRSL  261 (477)
T ss_pred             EEEEEECCCCCCCCCCCH-------HHEEECCCCCHHHHHHHHHHHCHHHCEEEEECCHHHHHHCCCCC-CCCHHHHHHC
T ss_conf             689985376444677332-------22131799428999999874276664388853225554313665-5431044316


Q ss_pred             CCCCCCEEECHHHHHHHHHHHH--HHCCCHHHHCCCCCCCCCCEEEEEECCCHHHHHHHHHH---HHCCCCEEEEEECCC
Q ss_conf             5677610101013227899997--52010111102355766620799970200268999976---310387389997120
Q gi|254780945|r  418 ATAPHVLLMTATPIPRTLVLTS--LGDIDISKITEKPAGRKPIKTVIIPINRIDEVIERLKV---VLSEGKKAYWICPQI  492 (700)
Q Consensus       418 g~~ph~L~MtATPIPRTLal~~--ygdldvS~i~e~P~gR~~I~T~~~~~~~~~~~~~~i~~---~l~~g~q~y~VcPlI  492 (700)
                      ..+..+|..|||---+--+.+.  --|-.+-.|+.---.=-+|+-+.+--..++.-|+.+.+   -+.-| |..+-|-. 
T Consensus       262 P~~~QllLFSATf~e~V~~Fa~kivpn~n~i~Lk~eel~L~~IkQlyv~C~~~~~K~~~l~~lyg~~tig-qsiIFc~t-  339 (477)
T KOG0332         262 PRNQQLLLFSATFVEKVAAFALKIVPNANVIILKREELALDNIKQLYVLCACRDDKYQALVNLYGLLTIG-QSIIFCHT-  339 (477)
T ss_pred             CCCCEEEEEECHHHHHHHHHHHHHCCCCCEEEEEHHHCCCCCHHHHEEECCCHHHHHHHHHHHHHHHHHH-HEEEEEEE-
T ss_conf             8762377640103779999999854898403656343064213431366555166799999987011110-05899962-


Q ss_pred             CCCCCCCCCHHHHHHHHHHHHCCCCEECCCCCCCHHHHHHHHHHHHCCCEEEEEECHHHHCCCCCCCCCEEEEECH----
Q ss_conf             1221112101466666668663710312014699899999999975598699998003410468887658998585----
Q gi|254780945|r  493 EEKKESNFRSVVERFNSLHEHFTSSIAIIHGRMSDIDKESVMDSFKNGTCKLLIATTVIEVGIDVVDASIIIIENA----  568 (700)
Q Consensus       493 eese~~~~~~~~~~~~~l~~~~~~~v~~lHGkm~~~ek~~~m~~F~~g~~~iLvaTtviEVGvdvpna~~mvI~~a----  568 (700)
                             -.+|...|+.+.+. ++.|.+|||-|.-++++.+|++|+.|..++||+|.|+--||||+..|+.|=+|-    
T Consensus       340 -------k~ta~~l~~~m~~~-Gh~V~~l~G~l~~~~R~~ii~~Fr~g~~kVLitTnV~ARGiDv~qVs~VvNydlP~~~  411 (477)
T KOG0332         340 -------KATAMWLYEEMRAE-GHQVSLLHGDLTVEQRAAIIDRFREGKEKVLITTNVCARGIDVAQVSVVVNYDLPVKY  411 (477)
T ss_pred             -------HHHHHHHHHHHHHC-CCEEEEEECCCHHHHHHHHHHHHHCCCCEEEEEECHHHCCCCCCEEEEEEECCCCCCC
T ss_conf             -------02699999999843-7536785065306788999999865760699870111235653137999944776455


Q ss_pred             -HHCC-HHHHHHHHHCCCCCCCCEEEEEEECCCCCHHHHHHHHHHH
Q ss_conf             -2547-4688773011667898359999708889987999999998
Q gi|254780945|r  569 -EHFG-LAQLHQLRGRVGRGEEISSCILLYHPPLSKNSYTRLSVLK  612 (700)
Q Consensus       569 -erfG-LsqLHQLRGRVGRg~~~s~c~l~~~~~~~~~~~~Rl~~l~  612 (700)
                       ++=- =.-||-. ||-||=++.|..|=+.+++.+   ++-|+.+.
T Consensus       412 ~~~pD~etYlHRi-GRtGRFGkkG~a~n~v~~~~s---~~~mn~iq  453 (477)
T KOG0332         412 TGEPDYETYLHRI-GRTGRFGKKGLAINLVDDKDS---MNIMNKIQ  453 (477)
T ss_pred             CCCCCHHHHHHHH-CCCCCCCCCCEEEEEECCCCC---HHHHHHHH
T ss_conf             7898778898870-234656655248986416575---89999999


No 71 
>cd00268 DEADc DEAD-box helicases. A diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker  B motif (motif II). This domain contains the ATP- binding region.
Probab=99.46  E-value=7.7e-12  Score=112.42  Aligned_cols=167  Identities=28%  Similarity=0.356  Sum_probs=123.6

Q ss_pred             CCCCHHHHHHHHHCCCC-CCHHHHHHHHHHHHHHCCCCCCEEEEEECCCCCHHHHHHHHHHHHH-----HHHCCEEEEEH
Q ss_conf             87757899998630246-7988999999999841001343078862144223699999973344-----43054588612
Q gi|254780945|r  256 NVEGKIAQKILRNIPFS-PTKSQESAIKDILQDMSQKNRMLRILQGDVGSGKTLVALIAMAAAV-----EAGGQAVIMAP  329 (700)
Q Consensus       256 ~~~~~~~~~f~~~LPF~-LT~~Q~~ai~eI~~Dl~~~~pM~RLLQGDVGSGKTiVA~~A~l~~~-----~~G~Q~alMaP  329 (700)
                      ..+..+.+.+ ++..|+ +|.=|++|+..|.+.      -+-++|.-.|||||..+++.++..+     .++-|+.+++|
T Consensus         5 ~L~~~ll~~l-~~~g~~~pt~IQ~~~ip~il~g------~dvi~~a~TGSGKTlay~lpil~~l~~~~~~~~~~alil~P   77 (203)
T cd00268           5 GLSPELLRGI-YALGFEKPTPIQARAIPPLLSG------RDVIGQAQTGSGKTAAFLIPILEKLDPSPKKDGPQALILAP   77 (203)
T ss_pred             CCCHHHHHHH-HHCCCCCCCHHHHHHHHHHHCC------CCEEEECCCCCCCHHHHHHHHHHHHHCCCCCCCCEEEEEEC
T ss_conf             6599999999-9879999999999999999779------98899757997222888869999986166768966999968


Q ss_pred             HHHHHHHHHHHHHHHCCCCCCEEEEEECCCCHHHHHHHHHHHCCCCCEEEEEC-----HHHCCCCCCCCCCCEEEECCCC
Q ss_conf             79999999986211014578658996246422566768776213475486411-----1201334554444178852101
Q gi|254780945|r  330 IGILAQQHYEFIKKYTQNTQIIVEIITGNMPQAHRRKALERIAHGQAHIIIGT-----HALFQDSIQYYKLILVIVDEQH  404 (700)
Q Consensus       330 TEILA~QH~~~~~~~~~~~~i~v~lLtg~~~~~er~~i~~~i~~G~~~iiIGT-----HAL~q~~v~F~~LgLvViDEQH  404 (700)
                      |.=||.|-++.+.++....++++.+++|+++.++..+   .++. .++|+|||     +-+-+..+.++++.++|+||=+
T Consensus        78 TrELa~Qi~~~~~~l~~~~~i~~~~~~gg~~~~~~~~---~l~~-~~~IlI~TPgrl~~~l~~~~~~l~~l~~lVlDEAD  153 (203)
T cd00268          78 TRELALQIAEVARKLGKHTNLKVVVIYGGTSIDKQIR---KLKR-GPHIVVATPGRLLDLLERGKLDLSKVKYLVLDEAD  153 (203)
T ss_pred             CHHHHHHHHHHHHHHCCCCCEEEEEEECCCCHHHHHH---HHHC-CCEEEEECCHHHHHHHHCCCCCCCCCCEEEEECHH
T ss_conf             7999999999999850579838999838988799999---9853-87599968189999998488651322489998588


Q ss_pred             CC-----CHHHHHHHHHCCCCCCCEEECHHHHHH
Q ss_conf             33-----568899874025677610101013227
Q gi|254780945|r  405 RF-----GVQQRLKLTQKATAPHVLLMTATPIPR  433 (700)
Q Consensus       405 RF-----GV~QR~~L~~Kg~~ph~L~MtATPIPR  433 (700)
                      +.     +-.-+.-+..-..+...+++|||=-+.
T Consensus       154 ~ll~~gf~~~i~~I~~~l~~~~Q~~lfSAT~~~~  187 (203)
T cd00268         154 RMLDMGFEDQIREILKLLPKDRQTLLFSATMPKE  187 (203)
T ss_pred             HHHHCCCHHHHHHHHHHCCCCCEEEEEEECCCHH
T ss_conf             8874776999999998589677799998049988


No 72 
>TIGR01587 cas3_core CRISPR-associated helicase Cas3; InterPro: IPR006474    This entry represents a highly conserved core region of the Cas3 sequences. The proteins are found in association with CRISPR repeat elements in a broad range of bacteria and Archaea . Cas3 appears to be a helicase, containing a DEAD/DEAH box region and conserved C-terminal domain. Some but not all members have an N-terminal HD domain region (IPR006674 from INTERPRO), these sequences are not included within this group..
Probab=99.44  E-value=2.6e-12  Score=116.12  Aligned_cols=288  Identities=24%  Similarity=0.335  Sum_probs=191.9

Q ss_pred             EEEECCCCCHHHHHHHHHHH---HHHHH--CCEEEEEHHHHHHHHHHHHHHH----HCCCCCCEEEEEEC------CCCH
Q ss_conf             88621442236999999733---44430--5458861279999999986211----01457865899624------6422
Q gi|254780945|r  297 ILQGDVGSGKTLVALIAMAA---AVEAG--GQAVIMAPIGILAQQHYEFIKK----YTQNTQIIVEIITG------NMPQ  361 (700)
Q Consensus       297 LLQGDVGSGKTiVA~~A~l~---~~~~G--~Q~alMaPTEILA~QH~~~~~~----~~~~~~i~v~lLtg------~~~~  361 (700)
                      +|+-=.|+|||..|++=+..   .++++  -.+.+.-||-..++--|+.+++    +|+.=+ .+.++.|      +..-
T Consensus         3 v~~APTG~GKTe~aL~~A~~sah~~k~~~~~~~I~alP~r~~~na~~~r~~~sash~Fg~P~-~~~~~~ssrfnh~~~~i   81 (424)
T TIGR01587         3 VIEAPTGYGKTEAALLWALKSAHLIKKQKADKVIFALPTRVTINAMYRRLKESASHLFGSPE-LVLLLHSSRFNHLASSI   81 (424)
T ss_pred             EEECCCCCCHHHHHHHHHHHHHHHHHHHHHCCEEEECCHHHHHHHHHHHHHHHHHHHCCCCC-CCCCCCCCHHHHHHHHH
T ss_conf             88617899878999999986366642244401012202688899999999986775417854-32334552267899999


Q ss_pred             HHH-----------HHHHHHHCCCCC-----EEEEEC--HHHCCC------CCCCC-------CCCEEEECCCCCCCHHH
Q ss_conf             566-----------768776213475-----486411--120133------45544-------44178852101335688
Q gi|254780945|r  362 AHR-----------RKALERIAHGQA-----HIIIGT--HALFQD------SIQYY-------KLILVIVDEQHRFGVQQ  410 (700)
Q Consensus       362 ~er-----------~~i~~~i~~G~~-----~iiIGT--HAL~q~------~v~F~-------~LgLvViDEQHRFGV~Q  410 (700)
                      +-|           ..++.....+..     .|=|-|  |.+..-      .+.+.       ...++|+||=|=.--.-
T Consensus        82 k~~~~~~~~d~~~~~~~~~~~~~~~~~~~~~pi~~~T~d~~~~~~~~~ssGs~~~~~~~~~~~~~S~~i~DE~h~y~~~~  161 (424)
T TIGR01587        82 KLRKIKEKGDSEELEKLVKLYIHSNKKLFLKPITVCTIDQVLKSVFGESSGSFGHYEITLASIANSLIIFDEVHAYEEYT  161 (424)
T ss_pred             HHHHHHCCCCHHHHHHHHHHHCCCCHHEEECCCCCCCHHHHHEEEECCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             98776304782799999985224212101317885341220000005534452056888877776765625367776425


Q ss_pred             HHH-HH-----HC-CCCCCCEEECHHHHHHH---HHHHHHHCCCHHHHCCCCCCCCCCE---------------------
Q ss_conf             998-74-----02-56776101010132278---9999752010111102355766620---------------------
Q gi|254780945|r  411 RLK-LT-----QK-ATAPHVLLMTATPIPRT---LVLTSLGDIDISKITEKPAGRKPIK---------------------  459 (700)
Q Consensus       411 R~~-L~-----~K-g~~ph~L~MtATPIPRT---Lal~~ygdldvS~i~e~P~gR~~I~---------------------  459 (700)
                      +.. +.     -| -...-+|+|||| +||-   +=...+-+++.-.=.+.|+ ++++.                     
T Consensus       162 ~~~~~l~~L~~~~~~~~~~~~lMsAT-lP~~~~~~l~~~~~~~~~~~~~~~~~-~~~~~GvnGaqrfdllahPe~~~~r~  239 (424)
T TIGR01587       162 LALTILAALEVLKIDNDVKILLMSAT-LPRELKKFLKEYLEKIEYVEENELLD-LKEVEGVNGAQRFDLLAHPEFKEKRF  239 (424)
T ss_pred             HHHHHHHHHHHHHHHCCCCEEEEECC-CCHHHHHHHHHHHHCCCCCCCCCCCC-CCCCCCCCCHHHHHHHCCCHHHHHHH
T ss_conf             55569999999998738988998405-67578999998731047633335578-66435464202333321720210022


Q ss_pred             ---EEEEECC---CHHHHHHHH-HHHHCCCCEEEEEECCCCCCCCCCCCHHHHHHHHHHHHCCC--CEECCCCCCCHH--
Q ss_conf             ---7999702---002689999-76310387389997120122111210146666666866371--031201469989--
Q gi|254780945|r  460 ---TVIIPIN---RIDEVIERL-KVVLSEGKKAYWICPQIEEKKESNFRSVVERFNSLHEHFTS--SIAIIHGRMSDI--  528 (700)
Q Consensus       460 ---T~~~~~~---~~~~~~~~i-~~~l~~g~q~y~VcPlIeese~~~~~~~~~~~~~l~~~~~~--~v~~lHGkm~~~--  528 (700)
                         -.++..+   .--..++.+ -+.+.++.++.|||-.|        ..|.+.|+.+++.-|.  .|-|+|||++..  
T Consensus       240 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ii~NtV--------~~A~~~Y~~~kE~~p~~~~~~L~HsRF~~~DR  311 (424)
T TIGR01587       240 ENHRISLIEKDKVGEISSLERLLLEELKKGGKVLIIVNTV--------DRAQEFYQKLKEKAPELEEVILLHSRFTEKDR  311 (424)
T ss_pred             HCCCCCHHHHHCCCCHHHHHHHHHHHCCCCCCEEEEEECH--------HHHHHHHHHHHHCCCCCCCEEEEECCCCHHHH
T ss_conf             1576421343203313466667787415778669998543--------89999999985126520021244044770036


Q ss_pred             -HHH---HHHHHHHC-----CCEEEEEECHHHHCCCCCCCCCEEEEECHHHCCHHHHHHHHHCCCC-CCCCE-----EEE
Q ss_conf             -999---99999755-----9869999800341046888765899858525474688773011667-89835-----999
Q gi|254780945|r  529 -DKE---SVMDSFKN-----GTCKLLIATTVIEVGIDVVDASIIIIENAEHFGLAQLHQLRGRVGR-GEEIS-----SCI  593 (700)
Q Consensus       529 -ek~---~~m~~F~~-----g~~~iLvaTtviEVGvdvpna~~mvI~~aerfGLsqLHQLRGRVGR-g~~~s-----~c~  593 (700)
                       +||   +.|++|.+     ++--|+|+|.|||||||+ .+.+||=|.|   -+.-|-|==|||-| |.+-+     --|
T Consensus       312 ~~KEde~~~l~e~~~S~~~~~~~~v~V~TQv~E~SlD~-s~D~~iTe~a---P~d~LiQR~GR~~R~~~~~~d~~~~~~y  387 (424)
T TIGR01587       312 AKKEDEAELLKELKKSAWKDNEKFVIVATQVIEVSLDI-SVDVMITELA---PIDSLIQRLGRLNRYGRKIGDIENREVY  387 (424)
T ss_pred             HHHHHHHHHHHHHHCCCCCCCCCEEEEEEEEEEEEEEC-CCCHHHHHCC---CHHHHHHHHHHHCCCCCCCCCCCCCCEE
T ss_conf             67767999999851013544577069987878886420-4441343115---0123355421110113565788987203


Q ss_pred             EEECCC
Q ss_conf             970888
Q gi|254780945|r  594 LLYHPP  599 (700)
Q Consensus       594 l~~~~~  599 (700)
                      .++..+
T Consensus       388 ~~~~~~  393 (424)
T TIGR01587       388 ILTILL  393 (424)
T ss_pred             EEEECC
T ss_conf             785257


No 73 
>KOG0340 consensus
Probab=99.43  E-value=4.1e-10  Score=98.94  Aligned_cols=319  Identities=19%  Similarity=0.277  Sum_probs=200.6

Q ss_pred             HHHHHHHHHCC-CCCCHHHHHHHHHHHHHHCCCCCCEEEEEECCCCCHHHHHHHHHHHHH---HHHCCEEEEEHHHHHHH
Q ss_conf             78999986302-467988999999999841001343078862144223699999973344---43054588612799999
Q gi|254780945|r  260 KIAQKILRNIP-FSPTKSQESAIKDILQDMSQKNRMLRILQGDVGSGKTLVALIAMAAAV---EAGGQAVIMAPIGILAQ  335 (700)
Q Consensus       260 ~~~~~f~~~LP-F~LT~~Q~~ai~eI~~Dl~~~~pM~RLLQGDVGSGKTiVA~~A~l~~~---~~G~Q~alMaPTEILA~  335 (700)
                      .|.-+-++.|. .+.|.=|+.+|-.|++--.      -|=..-.|||||.-.++-++.-.   -+|.=+.++.||-=||-
T Consensus        16 ~Wlve~l~~l~i~~pTpiQ~~cIpkILeGrd------cig~AkTGsGKT~AFaLPil~rLsedP~giFalvlTPTrELA~   89 (442)
T KOG0340          16 PWLVEQLKALGIKKPTPIQQACIPKILEGRD------CIGCAKTGSGKTAAFALPILNRLSEDPYGIFALVLTPTRELAL   89 (442)
T ss_pred             HHHHHHHHHHCCCCCCCHHHHHHHHHHCCCC------CCCCCCCCCCCCHHHHHHHHHHHCCCCCCCEEEEECCHHHHHH
T ss_conf             8999999983588998267652487854663------1031346887411222787776133887606999545288888


Q ss_pred             HHHHHHHHHCCCCCCEEEEEECCCCHHHHHHHHHHHCCCCCEEEEECHHH----CCC-----CCCCCCCCEEEECCCCCC
Q ss_conf             99986211014578658996246422566768776213475486411120----133-----455444417885210133
Q gi|254780945|r  336 QHYEFIKKYTQNTQIIVEIITGNMPQAHRRKALERIAHGQAHIIIGTHAL----FQD-----SIQYYKLILVIVDEQHRF  406 (700)
Q Consensus       336 QH~~~~~~~~~~~~i~v~lLtg~~~~~er~~i~~~i~~G~~~iiIGTHAL----~q~-----~v~F~~LgLvViDEQHRF  406 (700)
                      |..+.|.-+=..++++++...|.+..-.-..    .-+-.+++||-|--=    +..     .-.|+++-..|+||--|-
T Consensus        90 QiaEQF~alGk~l~lK~~vivGG~d~i~qa~----~L~~rPHvVvatPGRlad~l~sn~~~~~~~~~rlkflVlDEADrv  165 (442)
T KOG0340          90 QIAEQFIALGKLLNLKVSVIVGGTDMIMQAA----ILSDRPHVVVATPGRLADHLSSNLGVCSWIFQRLKFLVLDEADRV  165 (442)
T ss_pred             HHHHHHHHHCCCCCCEEEEEECCHHHHHHHH----HCCCCCCEEECCCCCCCCCCCCCCCCCHHHHHCEEEEEECCHHHH
T ss_conf             8889999845645632799975688764544----426698757517633354112687655255530046774130265


Q ss_pred             CHHHHHHHHHC----CCCC-CCEEECHHHHHHHHHHHHHHCCCHHHHCCCCCCCCCCEEEEEECCCHHHHHHHHHHHHCC
Q ss_conf             56889987402----5677-610101013227899997520101111023557666207999702002689999763103
Q gi|254780945|r  407 GVQQRLKLTQK----ATAP-HVLLMTATPIPRTLVLTSLGDIDISKITEKPAGRKPIKTVIIPINRIDEVIERLKVVLSE  481 (700)
Q Consensus       407 GV~QR~~L~~K----g~~p-h~L~MtATPIPRTLal~~ygdldvS~i~e~P~gR~~I~T~~~~~~~~~~~~~~i~~~l~~  481 (700)
                      =-.+=..-.+-    -+.| ..|..||| |--|+          +.+...|. ++++ -+..+...-..    +-+.|. 
T Consensus       166 L~~~f~d~L~~i~e~lP~~RQtLlfSAT-itd~i----------~ql~~~~i-~k~~-a~~~e~~~~vs----tvetL~-  227 (442)
T KOG0340         166 LAGCFPDILEGIEECLPKPRQTLLFSAT-ITDTI----------KQLFGCPI-TKSI-AFELEVIDGVS----TVETLY-  227 (442)
T ss_pred             HCCCHHHHHHHHHCCCCCCCCEEEEEEE-HHHHH----------HHHHCCCC-CCCC-CEEEECCCCCC----CHHHHH-
T ss_conf             4156056776665048876433799866-36579----------98636874-5550-26885269987----254552-


Q ss_pred             CCEEEEEECCC-----------CCCC--CCC---CCHHHHHHHHHHHHCCC---CEECCCCCCCHHHHHHHHHHHHCCCE
Q ss_conf             87389997120-----------1221--112---10146666666866371---03120146998999999999755986
Q gi|254780945|r  482 GKKAYWICPQI-----------EEKK--ESN---FRSVVERFNSLHEHFTS---SIAIIHGRMSDIDKESVMDSFKNGTC  542 (700)
Q Consensus       482 g~q~y~VcPlI-----------eese--~~~---~~~~~~~~~~l~~~~~~---~v~~lHGkm~~~ek~~~m~~F~~g~~  542 (700)
                        |-|+.||-=           ..++  +..   ..+-+..++.|.-.+..   +|+-+|+.|...|.-..+.+|+++.+
T Consensus       228 --q~yI~~~~~vkdaYLv~~Lr~~~~~~~~simIFvnttr~cQ~l~~~l~~le~r~~~lHs~m~Q~eR~~aLsrFrs~~~  305 (442)
T KOG0340         228 --QGYILVSIDVKDAYLVHLLRDFENKENGSIMIFVNTTRECQLLSMTLKNLEVRVVSLHSQMPQKERLAALSRFRSNAA  305 (442)
T ss_pred             --HHEEECCHHHHHHHHHHHHHHHHHCCCCEEEEEEEHHHHHHHHHHHHHHHCEEEEEHHHCCHHHHHHHHHHHHHHCCC
T ss_conf             --022205444567889987752221357608999604689999999996303445431100508889989987762674


Q ss_pred             EEEEECHHHHCCCCCCCCCEEEEECHHHCCHHHHHHHHHCCCCCCCCEEEEEEECCCCCHHHHHHHHHHHH
Q ss_conf             99998003410468887658998585254746887730116678983599997088899879999999984
Q gi|254780945|r  543 KLLIATTVIEVGIDVVDASIIIIENAEHFGLAQLHQLRGRVGRGEEISSCILLYHPPLSKNSYTRLSVLKN  613 (700)
Q Consensus       543 ~iLvaTtviEVGvdvpna~~mvI~~aerfGLsqLHQLRGRVGRg~~~s~c~l~~~~~~~~~~~~Rl~~l~~  613 (700)
                      +||+||-|---|.|+|...+.|=++--|=-=--.|- -||-.|-+..|..+=+.    ++..-+++.++++
T Consensus       306 ~iliaTDVAsRGLDIP~V~LVvN~diPr~P~~yiHR-vGRtARAGR~G~aiSiv----t~rDv~l~~aiE~  371 (442)
T KOG0340         306 RILIATDVASRGLDIPTVELVVNHDIPRDPKDYIHR-VGRTARAGRKGMAISIV----TQRDVELLQAIEE  371 (442)
T ss_pred             CEEEEECHHHCCCCCCCEEEEEECCCCCCHHHHHHH-HCCHHCCCCCCCEEEEE----CHHHHHHHHHHHH
T ss_conf             089973134327898844678706889987888876-03012056776428986----2422799999999


No 74 
>cd04488 RecG_wedge_OBF RecG_wedge_OBF: A subfamily of OB folds corresponding to the OB fold found in the N-terminal (wedge) domain of Escherichia coli RecG. RecG is a branched-DNA-specific helicase, which catalyzes the interconversion of a DNA replication fork to a four-stranded (Holliday) junction in vivo and in vitro. This interconversion provides a route to repair stalled forks. The RecG monomer contains three domains. The N-terminal domain is named for its wedge structure, and may provide the specificity of RecG for binding branched-DNA structures. During the reversal of fork to Holliday junction, the wedge domain is fixed at the junction of the fork where the leading and lagging strand duplex arms meet, and is thought to promote the unwinding of the nascent leading and lagging strands. In order to form the Holliday junction, these nascent strands would be annealed, and the parental strands reannealed. The wedge domain may also be a processivity factor of RecG on these branched cha
Probab=99.42  E-value=3.5e-12  Score=115.13  Aligned_cols=74  Identities=34%  Similarity=0.623  Sum_probs=68.6

Q ss_pred             EEEEEEEEEEEECCCCCCEEEEEEECCCCEEEEEEECCCHHHHHHHCCCCCEEEEEEEEEECCCEEEEECCEEEE
Q ss_conf             999999897542158983389999818936999995188789987328988899998997318779997786896
Q gi|254780945|r   71 TITGYISQHSSFQLQKRRPYKILLNDGTGEITLLFFYRKTEMLKNVFFEGRKITVTGKIKKLKNRIIMVHPHYIF  145 (700)
Q Consensus        71 ti~g~V~~~~~~~~~~r~~~~v~v~D~tg~i~lvfFn~~~~yl~k~lk~G~~v~vsGKv~~~~~~~qi~hPe~~~  145 (700)
                      |+.|+|.++...+.++++++++.+.|++|.++++|||. .+|+++.|++|++++++||++.+++.+||+||+|+.
T Consensus         1 ti~g~I~~~~~~~~~~r~~l~~~v~D~tg~i~l~~Fn~-~~~~~~~~~~G~~v~v~Gkv~~~~~~~q~~hP~~~~   74 (75)
T cd04488           1 TVEGTVVSVEVVPRRGRRRLKVTLSDGTGTLTLVFFNF-QPYLKKQLPPGTRVRVSGKVKRFRGGLQIVHPEYEL   74 (75)
T ss_pred             CEEEEEEEEEEECCCCCEEEEEEEEECCCEEEEEEECC-CHHHHHHCCCCCEEEEEEEEEECCCEEEEECCCEEE
T ss_conf             99999999885458997089999996998899999899-779995388999999999997139999997997996


No 75 
>KOG0327 consensus
Probab=99.42  E-value=7.4e-11  Score=104.71  Aligned_cols=293  Identities=23%  Similarity=0.359  Sum_probs=198.1

Q ss_pred             CCCC-CCHHHHHHHHHHHHHHCCCCCCEEEEEECCCCCHHHHHHHHHHHHH---HHHCCEEEEEHHHHHHHHHHHHHHHH
Q ss_conf             0246-7988999999999841001343078862144223699999973344---43054588612799999999862110
Q gi|254780945|r  269 IPFS-PTKSQESAIKDILQDMSQKNRMLRILQGDVGSGKTLVALIAMAAAV---EAGGQAVIMAPIGILAQQHYEFIKKY  344 (700)
Q Consensus       269 LPF~-LT~~Q~~ai~eI~~Dl~~~~pM~RLLQGDVGSGKTiVA~~A~l~~~---~~G~Q~alMaPTEILA~QH~~~~~~~  344 (700)
                      ..|+ ++.=|++||--|..-      -+-..|-+-|+|||.....+++.-+   ..--||.++|||-.||.|-++....+
T Consensus        44 ~GFekPSaIQqrAI~p~i~G------~dv~~qaqsgTgKt~af~i~ilq~iD~~~ke~qalilaPtreLa~q~~~v~~~l  117 (397)
T KOG0327          44 YGFEKPSAIQQRAILPCIKG------HDVIAQAQSGTGKTAAFLISILQQIDMSVKETQALILAPTRELAQQIQKVVRAL  117 (397)
T ss_pred             HCCCCCHHHHHCCCCCCCCC------CCEEEEEECCCCCHHHHHHHHHHHCCCCHHHHHHHHHCCHHHHHHHHHHHHHHH
T ss_conf             03688227776343553468------744676302544114667888751374167777988613278889899998864


Q ss_pred             CCCCCCEEEEEECCCCHHHHHHHHHHHCCCCCEEEEECH----HHCCCC-CCCCCCCEEEECCC---CCCCH-HHHHHHH
Q ss_conf             145786589962464225667687762134754864111----201334-55444417885210---13356-8899874
Q gi|254780945|r  345 TQNTQIIVEIITGNMPQAHRRKALERIAHGQAHIIIGTH----ALFQDS-IQYYKLILVIVDEQ---HRFGV-QQRLKLT  415 (700)
Q Consensus       345 ~~~~~i~v~lLtg~~~~~er~~i~~~i~~G~~~iiIGTH----AL~q~~-v~F~~LgLvViDEQ---HRFGV-~QR~~L~  415 (700)
                      ....+++|..++|.+.-....   ..++.-.+.|++||-    -.++.. +.-++.-+.|.||-   --+|. +|=..+.
T Consensus       118 g~~~~~~v~~~igg~~~~~~~---~~i~~~~~hivvGTpgrV~dml~~~~l~~~~iKmfvlDEaDEmLs~gfkdqI~~if  194 (397)
T KOG0327         118 GDHMDVSVHACIGGTNVRRED---QALLKDKPHIVVGTPGRVFDMLNRGSLSTDGIKMFVLDEADEMLSRGFKDQIYDIF  194 (397)
T ss_pred             HCCCCEEEEEECCCCCCHHHH---HHHHCCCCEEECCCCHHHHHHHCCCCCCCCCEEEEEECCHHHHHCCCHHHHHHHHH
T ss_conf             112461466531764100345---55520476354378505777641364566654677524367663056489999999


Q ss_pred             -HCCCCCCCEEECHHHHHHHHHHHHHHCCCHHHHCCCCCCCCCCEEEEEEC-----------------CCHHHHHHHHHH
Q ss_conf             -02567761010101322789999752010111102355766620799970-----------------200268999976
Q gi|254780945|r  416 -QKATAPHVLLMTATPIPRTLVLTSLGDIDISKITEKPAGRKPIKTVIIPI-----------------NRIDEVIERLKV  477 (700)
Q Consensus       416 -~Kg~~ph~L~MtATPIPRTLal~~ygdldvS~i~e~P~gR~~I~T~~~~~-----------------~~~~~~~~~i~~  477 (700)
                       .-+.+.-+++.|||=-+--|-.+-            -..|-||.+.+-..                 ++.+-+.++.+ 
T Consensus       195 ~~lp~~vQv~l~SAT~p~~vl~vt~------------~f~~~pv~i~vkk~~ltl~gikq~~i~v~k~~k~~~l~dl~~-  261 (397)
T KOG0327         195 QELPSDVQVVLLSATMPSDVLEVTK------------KFMREPVRILVKKDELTLEGIKQFYINVEKEEKLDTLCDLYR-  261 (397)
T ss_pred             HHCCCCHHHEEECCCCCHHHHHHHH------------HHCCCCEEEEECCHHHHHHHEEEEEEECCCCCCCCHHHHHHH-
T ss_conf             8759432201001368588999988------------740475689952002012220022201054311227999998-


Q ss_pred             HHCCCCEEEEEECCCCCCCCCCCCHHHHHHHHHHHHCCCCEECCCCCCCHHHHHHHHHHHHCCCEEEEEECHHHHCCCCC
Q ss_conf             31038738999712012211121014666666686637103120146998999999999755986999980034104688
Q gi|254780945|r  478 VLSEGKKAYWICPQIEEKKESNFRSVVERFNSLHEHFTSSIAIIHGRMSDIDKESVMDSFKNGTCKLLIATTVIEVGIDV  557 (700)
Q Consensus       478 ~l~~g~q~y~VcPlIeese~~~~~~~~~~~~~l~~~~~~~v~~lHGkm~~~ek~~~m~~F~~g~~~iLvaTtviEVGvdv  557 (700)
                         +-.|+-+.|--.        .-+.+....| ..++-++..+||-|...+.+.+|..|++|+..+|+.|..---|+||
T Consensus       262 ---~~~q~~if~nt~--------r~v~~l~~~L-~~~~~~~s~i~~d~~q~~R~~~~~~f~~g~srvlIttdl~argidv  329 (397)
T KOG0327         262 ---RVTQAVIFCNTR--------RKVDNLTDKL-RAHGFTVSAIHGDMEQNERDTLMREFRSGSSRVLITTDLLARGIDV  329 (397)
T ss_pred             ---HHHCCEEEECCH--------HHHHHHHHHH-HHCCCEEEEEECCCCHHHHHHHHHHHHCCCCEEEEECCCCCCCCCH
T ss_conf             ---643105785104--------5677789998-6277337876346430034689998645872377412212465411


Q ss_pred             CCCCEEEEECHHHCCHHHHHHHHHCCCCCCCCEEEEEEE
Q ss_conf             876589985852547468877301166789835999970
Q gi|254780945|r  558 VDASIIIIENAEHFGLAQLHQLRGRVGRGEEISSCILLY  596 (700)
Q Consensus       558 pna~~mvI~~aerfGLsqLHQLRGRVGRg~~~s~c~l~~  596 (700)
                      -+.+..|-+++-.=--+=.|- -||-||=+.+|..+=+.
T Consensus       330 ~~~slvinydlP~r~~~yihR-~gr~gr~grkg~~in~v  367 (397)
T KOG0327         330 QQVSLVVNYDLPARKENYIHR-IGRAGRFGRKGVAINFV  367 (397)
T ss_pred             HHCCEEEEECCCCCHHHHHHH-CCCCCCCCCCCEEEEEE
T ss_conf             101225650165206666652-55456567771355520


No 76 
>KOG0351 consensus
Probab=99.40  E-value=6.3e-10  Score=97.42  Aligned_cols=319  Identities=24%  Similarity=0.322  Sum_probs=211.7

Q ss_pred             CCHHHHHHHHHHHHHHCCCCCCEEEEEECCCCCHHHHHHHHHHHHHHHHCCEEEEEHHHHHHHHHHHHHHHHCCCCCCEE
Q ss_conf             79889999999998410013430788621442236999999733444305458861279999999986211014578658
Q gi|254780945|r  273 PTKSQESAIKDILQDMSQKNRMLRILQGDVGSGKTLVALIAMAAAVEAGGQAVIMAPIGILAQQHYEFIKKYTQNTQIIV  352 (700)
Q Consensus       273 LT~~Q~~ai~eI~~Dl~~~~pM~RLLQGDVGSGKTiVA~~A~l~~~~~G~Q~alMaPTEILA~QH~~~~~~~~~~~~i~v  352 (700)
                      .-..|.+||.-+..   ....+   +-==.|.||-+-+-+-   |+-.+.=..+..|=+=|-+-.   ...+ .+.+|+.
T Consensus       265 FR~~Q~eaI~~~l~---Gkd~f---vlmpTG~GKSLCYQlP---A~l~~gitvVISPL~SLm~DQ---v~~L-~~~~I~a  331 (941)
T KOG0351         265 FRPNQLEAINATLS---GKDCF---VLMPTGGGKSLCYQLP---ALLLGGVTVVISPLISLMQDQ---VTHL-SKKGIPA  331 (941)
T ss_pred             CCHHHHHHHHHHHC---CCCEE---EEEECCCCEEEEEECC---CCCCCCCEEEECCHHHHHHHH---HHHH-HHCCCCE
T ss_conf             88439999999974---88469---9953488625676666---101389369963389999999---9743-2148541


Q ss_pred             EEEECCCCHHHHHHHHHHHCCC--CCEEEEECH-------HHCCCCCCCCC---CCEEEECCCCC---CCHHHH-----H
Q ss_conf             9962464225667687762134--754864111-------20133455444---41788521013---356889-----9
Q gi|254780945|r  353 EIITGNMPQAHRRKALERIAHG--QAHIIIGTH-------ALFQDSIQYYK---LILVIVDEQHR---FGVQQR-----L  412 (700)
Q Consensus       353 ~lLtg~~~~~er~~i~~~i~~G--~~~iiIGTH-------AL~q~~v~F~~---LgLvViDEQHR---FGV~QR-----~  412 (700)
                      ..|+|.++..++..+++.|++|  .++|+-=|-       .+.+..-.-..   |++.||||-|=   +|=.=|     .
T Consensus       332 ~~L~s~q~~~~~~~i~q~l~~~~~~ikilYvtPE~v~~~~~l~~~~~~L~~~~~lal~vIDEAHCVSqWgHdFRp~Yk~l  411 (941)
T KOG0351         332 CFLSSIQTAAERLAILQKLANGNPIIKILYVTPEKVVASEGLLESLADLYARGLLALFVIDEAHCVSQWGHDFRPSYKRL  411 (941)
T ss_pred             EECCCCCCHHHHHHHHHHHHCCCCEEEEEEECHHHHHCCCCHHHHHHHCCCCCEEEEEEECHHHHHHHHCCCCCHHHHHH
T ss_conf             32356566888999999985788767899967788633321566787506787048887227887664223334778999


Q ss_pred             -HHHHCCCCCCCEEECHHHHHHHH--HHHHHHCCCHHHHCCCCCCCCCCEEEEEECCCHHHHHHHHHH-HHCCCCEEEEE
Q ss_conf             -87402567761010101322789--999752010111102355766620799970200268999976-31038738999
Q gi|254780945|r  413 -KLTQKATAPHVLLMTATPIPRTL--VLTSLGDIDISKITEKPAGRKPIKTVIIPINRIDEVIERLKV-VLSEGKKAYWI  488 (700)
Q Consensus       413 -~L~~Kg~~ph~L~MtATPIPRTL--al~~ygdldvS~i~e~P~gR~~I~T~~~~~~~~~~~~~~i~~-~l~~g~q~y~V  488 (700)
                       .|..+-...-++.+|||-=||+-  .+...|--..-++... ++|....=.|......+.++..... ......|.-||
T Consensus       412 ~~l~~~~~~vP~iALTATAT~~v~~DIi~~L~l~~~~~~~~s-fnR~NL~yeV~~k~~~~~~~~~~~~~~~~~~~~s~II  490 (941)
T KOG0351         412 GLLRIRFPGVPFIALTATATERVREDVIRSLGLRNPELFKSS-FNRPNLKYEVSPKTDKDALLDILEESKLRHPDQSGII  490 (941)
T ss_pred             HHHHHHCCCCCEEEEEHHCCHHHHHHHHHHHCCCCCCEECCC-CCCCCCEEEEEECCCCCCHHHHHHHHHHCCCCCCEEE
T ss_conf             999852789976875300208899999998278886322256-7998855999856675316889887651289998379


Q ss_pred             ECCCCCCCCCCCCHHHHHHHHHHHHCCCCEECCCCCCCHHHHHHHHHHHHCCCEEEEEECHHHHCCCCCCCCCEEEEECH
Q ss_conf             71201221112101466666668663710312014699899999999975598699998003410468887658998585
Q gi|254780945|r  489 CPQIEEKKESNFRSVVERFNSLHEHFTSSIAIIHGRMSDIDKESVMDSFKNGTCKLLIATTVIEVGIDVVDASIIIIENA  568 (700)
Q Consensus       489 cPlIeese~~~~~~~~~~~~~l~~~~~~~v~~lHGkm~~~ek~~~m~~F~~g~~~iLvaTtviEVGvdvpna~~mvI~~a  568 (700)
                      |=+   |    -.+.+.....|++. +-+-+-.|.-|.+.+++.|-.+|..++++|.|||----.|||.|+....+=   
T Consensus       491 YC~---s----r~~ce~vs~~L~~~-~~~a~~YHAGl~~~~R~~Vq~~w~~~~~~VivATVAFGMGIdK~DVR~ViH---  559 (941)
T KOG0351         491 YCL---S----RKECEQVSAVLRSL-GKSAAFYHAGLPPKERETVQKAWMSDKIRVIVATVAFGMGIDKPDVRFVIH---  559 (941)
T ss_pred             EEC---C----CCHHHHHHHHHHHH-CHHHHHHHCCCCHHHHHHHHHHHHCCCCEEEEEEEECCCCCCCCCEEEEEE---
T ss_conf             968---8----23199999999873-520575526788788899999985688708999852247877786359997---


Q ss_pred             HHCCHHH----HHHHHHCCCCCCCCEEEEEEECCCCCHHHHHHHHHHHHHC-HHHHHHH
Q ss_conf             2547468----8773011667898359999708889987999999998414-2589999
Q gi|254780945|r  569 EHFGLAQ----LHQLRGRVGRGEEISSCILLYHPPLSKNSYTRLSVLKNTE-DGFLIAE  622 (700)
Q Consensus       569 erfGLsq----LHQLRGRVGRg~~~s~c~l~~~~~~~~~~~~Rl~~l~~~~-dGf~iAe  622 (700)
                        |+|-.    -+|==||-||-+.+|+|.|+|+..    ...|++-|..+. +++..-+
T Consensus       560 --~~lPks~E~YYQE~GRAGRDG~~s~C~l~y~~~----D~~~l~~ll~s~~~~~~~~~  612 (941)
T KOG0351         560 --YSLPKSFEGYYQEAGRAGRDGLPSSCVLLYGYA----DISELRRLLTSGNRLSGVKK  612 (941)
T ss_pred             --CCCCHHHHHHHHHCCCCCCCCCCCEEEEECCHH----HHHHHHHHHHCCCCCCCHHH
T ss_conf             --778614788887403367678800267742613----78999999872653101121


No 77 
>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=99.34  E-value=6.3e-10  Score=97.42  Aligned_cols=281  Identities=19%  Similarity=0.264  Sum_probs=201.1

Q ss_pred             HHHHHHHHHCCCCCCHHHHHHHHHHHHHHCCCCCCEEEEEECCCCCHHHHHHHHHHHHHHH-HCCEEEEEHHHHHHHHHH
Q ss_conf             7899998630246798899999999984100134307886214422369999997334443-054588612799999999
Q gi|254780945|r  260 KIAQKILRNIPFSPTKSQESAIKDILQDMSQKNRMLRILQGDVGSGKTLVALIAMAAAVEA-GGQAVIMAPIGILAQQHY  338 (700)
Q Consensus       260 ~~~~~f~~~LPF~LT~~Q~~ai~eI~~Dl~~~~pM~RLLQGDVGSGKTiVA~~A~l~~~~~-G~Q~alMaPTEILA~QH~  338 (700)
                      ++.+=|.+.+.++|=..|+.=.+-|...-+  ..    +--=.|=|||---+..++-.+.. |..|-+..||+.||+|-|
T Consensus        72 ~f~~FF~~~~G~~pws~Qk~WAKRv~~~~S--Fa----i~APTGVGKttFG~~mslflA~kKGkR~y~ilPT~lLv~Qv~  145 (1843)
T TIGR01054        72 EFEEFFKKAVGSEPWSIQKSWAKRVLKGDS--FA----IVAPTGVGKTTFGLVMSLFLAKKKGKRSYIILPTTLLVKQVA  145 (1843)
T ss_pred             HHHHHHHHHHCCCCHHHHHHHHHHHHCCCC--EE----EECCCCCCHHHHHHHHHHHHHHHCCCEEEEEECHHHHHHHHH
T ss_conf             999999997188843567999999641796--48----980588767799999999986542987899947078899999


Q ss_pred             HHHHHHCCCCCCEEE----EEECCCCHHHHHHHHHHHCCCCCEEEEECHHHCCCC-------CCCCCCCEEEECCCC---
Q ss_conf             862110145786589----962464225667687762134754864111201334-------554444178852101---
Q gi|254780945|r  339 EFIKKYTQNTQIIVE----IITGNMPQAHRRKALERIAHGQAHIIIGTHALFQDS-------IQYYKLILVIVDEQH---  404 (700)
Q Consensus       339 ~~~~~~~~~~~i~v~----lLtg~~~~~er~~i~~~i~~G~~~iiIGTHAL~q~~-------v~F~~LgLvViDEQH---  404 (700)
                      +.++++-+..|+.+.    ..+|.++.++|+++.++|.+|..+|+|+|.+=+++.       ..|+   ||.||-==   
T Consensus       146 ~kl~~~~~k~g~~~~~l~~~yhS~L~~~~kke~~Eri~~GDfdilitT~~FL~K~~~~L~~~y~F~---liFVDDVDa~L  222 (1843)
T TIGR01054       146 EKLSSLAEKEGVGIVRLLGAYHSKLSTKEKKEVKERIENGDFDILITTSMFLSKNFDKLKNQYKFD---LIFVDDVDALL  222 (1843)
T ss_pred             HHHHHHCCCCCCCCEEEEEEEECCCCHHHHHHHHHHHHCCCEEEEHHHHHHHHHHHHHCCCCCEEE---EEEEECHHHHH
T ss_conf             998752002575000022210112654567889998731891786122468887665178985144---89971536763


Q ss_pred             -----------------------------------------C----CCHHHHHHHHHC---------------CCCCCCE
Q ss_conf             -----------------------------------------3----356889987402---------------5677610
Q gi|254780945|r  405 -----------------------------------------R----FGVQQRLKLTQK---------------ATAPHVL  424 (700)
Q Consensus       405 -----------------------------------------R----FGV~QR~~L~~K---------------g~~ph~L  424 (700)
                                                               |    -=-+||.++.+.               |...-+.
T Consensus       223 k~skNVD~~L~LlGF~eE~i~~a~~~i~L~~k~~k~~~~~~~~~~~~R~E~~~~~LE~~~r~~~~~a~~~~krGr~g~Li  302 (1843)
T TIGR01054       223 KASKNVDKILKLLGFSEELIEKAYELIKLKLKENKLEEDLAREKIVVRLEARKKLLEAKRRLEKLEAEIKKKRGRKGVLI  302 (1843)
T ss_pred             HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEEEE
T ss_conf             16555667775517889999999999999887643577888888864678889999999998987764743248864699


Q ss_pred             EECHHHHHHHHHHHHHHCC-CHHHHCCCCC-CCCCCEEEEEECCCHHHHHHH---HHHHHCCCCEEEEEECCCCCCCCCC
Q ss_conf             1010132278999975201-0111102355-766620799970200268999---9763103873899971201221112
Q gi|254780945|r  425 LMTATPIPRTLVLTSLGDI-DISKITEKPA-GRKPIKTVIIPINRIDEVIER---LKVVLSEGKKAYWICPQIEEKKESN  499 (700)
Q Consensus       425 ~MtATPIPRTLal~~ygdl-dvS~i~e~P~-gR~~I~T~~~~~~~~~~~~~~---i~~~l~~g~q~y~VcPlIeese~~~  499 (700)
                      +-|||==||.-=.-+|=.| +.-+=...-. =|-=|-++.-..+-..+-...   +-+.+-.|+=||+       |-...
T Consensus       303 vsSATG~prG~r~~LFR~LL~FevG~~~~~GLRnvvD~y~~~~d~v~E~~~~sve~v~~LG~GGlVyv-------s~~yG  375 (1843)
T TIGR01054       303 VSSATGKPRGKRVKLFRELLGFEVGKGSDTGLRNVVDVYEEDEDGVKEKLLESVELVKKLGKGGLVYV-------SIDYG  375 (1843)
T ss_pred             EEECCCCCCCCHHHHHHHHCCCCCCCCCCCCCCCEEEEEECCCCCHHHHHHHHHHHHHHHCCCEEEEE-------ECCCC
T ss_conf             98514888761336536552710057642233213885114888446889999999998479439997-------12225


Q ss_pred             CCHHHHHHHHHHHHCCCCEECCCCCCCHHHHHHHHHHHHCCCEEEEEECH----HHHCCCCCCCCC
Q ss_conf             10146666666866371031201469989999999997559869999800----341046888765
Q gi|254780945|r  500 FRSVVERFNSLHEHFTSSIAIIHGRMSDIDKESVMDSFKNGTCKLLIATT----VIEVGIDVVDAS  561 (700)
Q Consensus       500 ~~~~~~~~~~l~~~~~~~v~~lHGkm~~~ek~~~m~~F~~g~~~iLvaTt----viEVGvdvpna~  561 (700)
                      ...|++.++.|+++ +=+...+|-+-    +.+-.++|..||+|+||.+.    ++==|+|.|.-.
T Consensus       376 ~e~a~ei~~~L~~~-Gv~A~~~~~~k----~~~~~~~F~~GE~dVliG~a~yyg~LVRGLDLP~rv  436 (1843)
T TIGR01054       376 KEKAEEIKEFLREH-GVKAVAYHAKK----PKEDLEKFAEGEIDVLIGVASYYGVLVRGLDLPERV  436 (1843)
T ss_pred             HHHHHHHHHHHHHC-CCEEEEEEECC----CCCCHHHHHCCCEEEEEEEECCCCCEEECCCCCCHH
T ss_conf             58999999999857-94799984037----732034663485136877101547635326661010


No 78 
>KOG0346 consensus
Probab=99.32  E-value=8.1e-10  Score=96.58  Aligned_cols=322  Identities=23%  Similarity=0.318  Sum_probs=211.3

Q ss_pred             HHHHHCCCC-CCHHHHHHHHHHHHHHCCCCCCEEEEEECCCCCHHHHHHHHHHHHH---------HHHCCEEEEEHHHHH
Q ss_conf             998630246-7988999999999841001343078862144223699999973344---------430545886127999
Q gi|254780945|r  264 KILRNIPFS-PTKSQESAIKDILQDMSQKNRMLRILQGDVGSGKTLVALIAMAAAV---------EAGGQAVIMAPIGIL  333 (700)
Q Consensus       264 ~f~~~LPF~-LT~~Q~~ai~eI~~Dl~~~~pM~RLLQGDVGSGKTiVA~~A~l~~~---------~~G~Q~alMaPTEIL  333 (700)
                      +-+..|.|+ .|-=|..||-=+.+.   .   +-+-+.-.|||||.-+++.++.-+         +.|--+.++|||-=|
T Consensus        32 kAi~~lG~ekpTlIQs~aIplaLEg---K---DvvarArTGSGKT~AYliPllqkll~~k~t~~~e~~~sa~iLvPTkEL  105 (569)
T KOG0346          32 KAITKLGWEKPTLIQSSAIPLALEG---K---DVVARARTGSGKTAAYLIPLLQKLLAEKKTNDGEQGPSAVILVPTKEL  105 (569)
T ss_pred             HHHHHHCCCCCCHHHHCCCCHHHCC---C---CEEEEECCCCCCHHHHHHHHHHHHHHHHHCCCCCCCCEEEEEECHHHH
T ss_conf             9999717677623443221243248---6---314652268871378899999999976403643246306999250999


Q ss_pred             HHHHHHHHHHHCCCC--CCEEEEEECCCCHHHHHHHHHHHCCCCCEEEEECHH----HCCCCC--CCCCCCEEEECCCC-
Q ss_conf             999998621101457--865899624642256676877621347548641112----013345--54444178852101-
Q gi|254780945|r  334 AQQHYEFIKKYTQNT--QIIVEIITGNMPQAHRRKALERIAHGQAHIIIGTHA----LFQDSI--QYYKLILVIVDEQH-  404 (700)
Q Consensus       334 A~QH~~~~~~~~~~~--~i~v~lLtg~~~~~er~~i~~~i~~G~~~iiIGTHA----L~q~~v--~F~~LgLvViDEQH-  404 (700)
                      |+|-|.-+.++-.-.  .+++.-++++++...-..    .-.+.++|||||-|    .++.++  .-..|.+.|+||-- 
T Consensus       106 ~qQvy~viekL~~~c~k~lr~~nl~s~~sdsv~~~----~L~d~pdIvV~TP~~ll~~~~~~~~~~~~~l~~LVvDEADL  181 (569)
T KOG0346         106 AQQVYKVIEKLVEYCSKDLRAINLASSMSDSVNSV----ALMDLPDIVVATPAKLLRHLAAGVLEYLDSLSFLVVDEADL  181 (569)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHH----HHCCCCCEEEECHHHHHHHHHHCCCHHHHHEEEEEECHHHH
T ss_conf             99999999999998787655542103311677788----87059975871718899998606302120102578503566


Q ss_pred             --CCCHHHHHHH-HHCC-CCCCCEEECHHHHHHHHHHH---HHHCCCHHHH--CCCCCCCCCCEEEEEECCC---HHHHH
Q ss_conf             --3356889987-4025-67761010101322789999---7520101111--0235576662079997020---02689
Q gi|254780945|r  405 --RFGVQQRLKL-TQKA-TAPHVLLMTATPIPRTLVLT---SLGDIDISKI--TEKPAGRKPIKTVIIPINR---IDEVI  472 (700)
Q Consensus       405 --RFGV~QR~~L-~~Kg-~~ph~L~MtATPIPRTLal~---~ygdldvS~i--~e~P~gR~~I~T~~~~~~~---~~~~~  472 (700)
                        -||-+--.+= .+.= .....++||||-=----+|-   +.+-.- -.+  .|+| +--...-+++.-+.   .--+|
T Consensus       182 llsfGYeedlk~l~~~LPr~~Q~~LmSATl~dDv~~LKkL~l~nPvi-Lkl~e~el~-~~dqL~Qy~v~cse~DKfllly  259 (569)
T KOG0346         182 LLSFGYEEDLKKLRSHLPRIYQCFLMSATLSDDVQALKKLFLHNPVI-LKLTEGELP-NPDQLTQYQVKCSEEDKFLLLY  259 (569)
T ss_pred             HHHCCCHHHHHHHHHHCCCHHHHEEEHHHHHHHHHHHHHHHCCCCEE-EEECCCCCC-CCCCCEEEEEEECCCHHHHHHH
T ss_conf             64236088899998748825650200313556799999975169768-983266689-8452258999703530688999


Q ss_pred             HHHHHHHCCCCEEEEEECCCCCCCCCCCCHHHHHH--HHHHHHCCCCEECCCCCCCHHHHHHHHHHHHCCCEEEEEECHH
Q ss_conf             99976310387389997120122111210146666--6668663710312014699899999999975598699998003
Q gi|254780945|r  473 ERLKVVLSEGKKAYWICPQIEEKKESNFRSVVERF--NSLHEHFTSSIAIIHGRMSDIDKESVMDSFKNGTCKLLIATTV  550 (700)
Q Consensus       473 ~~i~~~l~~g~q~y~VcPlIeese~~~~~~~~~~~--~~l~~~~~~~v~~lHGkm~~~ek~~~m~~F~~g~~~iLvaTtv  550 (700)
                      ...+=++-+|.-..+|            .++...|  ..+-+.|+-+--+|.|.|...-.--|+++|..|-.||++||-+
T Consensus       260 allKL~LI~gKsliFV------------NtIdr~YrLkLfLeqFGiksciLNseLP~NSR~Hii~QFNkG~YdivIAtD~  327 (569)
T KOG0346         260 ALLKLRLIRGKSLIFV------------NTIDRCYRLKLFLEQFGIKSCILNSELPANSRCHIIEQFNKGLYDIVIATDD  327 (569)
T ss_pred             HHHHHHHHCCCEEEEE------------ECHHHHHHHHHHHHHHCCHHHHHCCCCCCCCHHHHHHHHHCCCEEEEEECCC
T ss_conf             9999988627549998------------5002468899999980737665256466432122898860761159997067


Q ss_pred             -----------------------------------HHCCCCCCCCCEEEEECHHHCCHHHHHHHHHCCCCCCCCEEEEEE
Q ss_conf             -----------------------------------410468887658998585254746887730116678983599997
Q gi|254780945|r  551 -----------------------------------IEVGIDVVDASIIIIENAEHFGLAQLHQLRGRVGRGEEISSCILL  595 (700)
Q Consensus       551 -----------------------------------iEVGvdvpna~~mvI~~aerfGLsqLHQLRGRVGRg~~~s~c~l~  595 (700)
                                                         +--|||..+.++.+=.|--+=--|-.|- =||-+||+.+|..+=.
T Consensus       328 s~~~~~~eee~kgk~~e~~~kndkkskkK~D~E~GVsRGIDF~~V~~VlNFD~P~t~~sYIHR-vGRTaRg~n~GtalSf  406 (569)
T KOG0346         328 SADGDKLEEEVKGKSDEKNPKNDKKSKKKLDKESGVSRGIDFHHVSNVLNFDFPETVTSYIHR-VGRTARGNNKGTALSF  406 (569)
T ss_pred             CCCHHHHHCCCCCCCCCCCCCCCCCCCCCCCCHHCHHCCCCCHHEEEEEECCCCCCHHHHHHH-CCCCCCCCCCCCEEEE
T ss_conf             641355521112544456887742124445701121216540121145613789854788886-1222347898725999


Q ss_pred             ECCCCCHHHHHHHHHH
Q ss_conf             0888998799999999
Q gi|254780945|r  596 YHPPLSKNSYTRLSVL  611 (700)
Q Consensus       596 ~~~~~~~~~~~Rl~~l  611 (700)
                      ..+. .+.+.+-|+-+
T Consensus       407 v~P~-e~~g~~~le~~  421 (569)
T KOG0346         407 VSPK-EEFGKESLESI  421 (569)
T ss_pred             ECCH-HHHHHHHHHHH
T ss_conf             6646-77606679999


No 79 
>PRK11131 ATP-dependent RNA helicase HrpA; Provisional
Probab=99.30  E-value=5.6e-09  Score=89.98  Aligned_cols=288  Identities=19%  Similarity=0.290  Sum_probs=176.3

Q ss_pred             HHHHHHHCCCCCCEEEEEECCCCCHHHHHHHHHHHHHHHHCCEEE--EEHHHHHHHHHHHHHHHHCC-CCCCEEEEEECC
Q ss_conf             999984100134307886214422369999997334443054588--61279999999986211014-578658996246
Q gi|254780945|r  282 KDILQDMSQKNRMLRILQGDVGSGKTLVALIAMAAAVEAGGQAVI--MAPIGILAQQHYEFIKKYTQ-NTQIIVEIITGN  358 (700)
Q Consensus       282 ~eI~~Dl~~~~pM~RLLQGDVGSGKTiVA~~A~l~~~~~G~Q~al--MaPTEILA~QH~~~~~~~~~-~~~i~v~lLtg~  358 (700)
                      +||.+-+..+.-.  .+.|+.|||||-=-=--++. ...|..+.+  -=|--|-|.--.+-+..-++ .+|-.|..-.. 
T Consensus        80 ~~i~~~i~~nqVv--ii~GeTGsGKTTQiPq~~le-~g~g~~~~I~~TQPRRiAA~svA~RVA~E~~~~lG~~VGY~VR-  155 (1295)
T PRK11131         80 QDILEAIRDHQVV--IVAGETGSGKTTQLPKICLE-LGRGIKGLIGHTQPRRLAARTVANRIAEELETELGGCVGYKVR-  155 (1295)
T ss_pred             HHHHHHHHHCCEE--EEECCCCCCHHHHHHHHHHH-CCCCCCCEEEECCCHHHHHHHHHHHHHHHHCCCCCCEEEEEEC-
T ss_conf             9999999979969--99768999878899999996-2799999899779659999999999999819998998888945-


Q ss_pred             CCHHHHHHHHHHHCCCCCEEEEECHHH----CCCCCCCCCCCEEEECCCCCCCHHHHH------HHHHCCCCCCCEEECH
Q ss_conf             422566768776213475486411120----133455444417885210133568899------8740256776101010
Q gi|254780945|r  359 MPQAHRRKALERIAHGQAHIIIGTHAL----FQDSIQYYKLILVIVDEQHRFGVQQRL------KLTQKATAPHVLLMTA  428 (700)
Q Consensus       359 ~~~~er~~i~~~i~~G~~~iiIGTHAL----~q~~v~F~~LgLvViDEQHRFGV~QR~------~L~~Kg~~ph~L~MtA  428 (700)
                               +++-.+....|.+=|.-+    ++.+-..++-.-|||||=|-=.++-=.      .+..+-..-.+++|||
T Consensus       156 ---------f~~~~s~~t~i~~~TdGiLL~e~~~d~~L~~y~~iIiDEaHERsl~~D~LLg~Lk~ll~~R~dLKvIimSA  226 (1295)
T PRK11131        156 ---------FNDQVSDNTMVKLMTDGILLAEIQQDRLLMQYDTIIIDEAHERSLNIDFILGYLKELLPRRPDLKVIITSA  226 (1295)
T ss_pred             ---------CCCCCCCCCEEEEECCHHHHHHHHHCCCCCCCCEEEEECCCCCCCHHHHHHHHHHHHHHHCCCCEEEEECC
T ss_conf             ---------69887999779997656999986209987887779986855688019999999999983399988999558


Q ss_pred             HHHHHHHHHHHHHCCCHHHHCCCCCCCC-CCEEEEEEC---------CCHHHHHHHHHHHHCCC-CEEEEEECCCCCCCC
Q ss_conf             1322789999752010111102355766-620799970---------20026899997631038-738999712012211
Q gi|254780945|r  429 TPIPRTLVLTSLGDIDISKITEKPAGRK-PIKTVIIPI---------NRIDEVIERLKVVLSEG-KKAYWICPQIEEKKE  497 (700)
Q Consensus       429 TPIPRTLal~~ygdldvS~i~e~P~gR~-~I~T~~~~~---------~~~~~~~~~i~~~l~~g-~q~y~VcPlIeese~  497 (700)
                      |-=+-..+- +||+-.+-.   .| ||. ||.++..+.         +....+++.+.+....| +-+-|-.|-.+    
T Consensus       227 Tid~e~fs~-yF~~apvi~---v~-Gr~~PVev~y~p~~~~~~~~~~d~~~~i~~~v~~~~~~~~GdILVFLpG~~----  297 (1295)
T PRK11131        227 TIDPERFSR-HFNNAPIIE---VS-GRTYPVEVRYRPIVEEADDTERDQLQAIFDAVDELGRESPGDILIFMSGER----  297 (1295)
T ss_pred             CCCHHHHHH-HCCCCCEEE---EC-CCCCCEEEEEECCCCCCCCHHHHHHHHHHHHHHHHHCCCCCCEEEECCCHH----
T ss_conf             689799996-579999898---78-917886757636866544215899999999999985489987798669799----


Q ss_pred             CCCCHHHHHHHHHHHH-CCC-CEECCCCCCCHHHHHHHHHHHHCCCEEEEEECHHHHCCCCCCCCCEEEEEC--------
Q ss_conf             1210146666666866-371-031201469989999999997559869999800341046888765899858--------
Q gi|254780945|r  498 SNFRSVVERFNSLHEH-FTS-SIAIIHGRMSDIDKESVMDSFKNGTCKLLIATTVIEVGIDVVDASIIIIEN--------  567 (700)
Q Consensus       498 ~~~~~~~~~~~~l~~~-~~~-~v~~lHGkm~~~ek~~~m~~F~~g~~~iLvaTtviEVGvdvpna~~mvI~~--------  567 (700)
                          .+.+..+.|.+. +++ .|--|||+++++|...|++  -.|.-+|.+||.|-|..|.||+....|=-+        
T Consensus       298 ----EI~~~~~~L~~~~~~~~~ilPL~s~ls~~eQ~~vF~--p~~~RkIVlaTNIAETSlTIp~I~yVIDsG~~k~~~y~  371 (1295)
T PRK11131        298 ----EIRDTADALNKLNLRHTEILPLYARLSNSEQNRVFQ--SHSGRRIVLATNVAETSLTVPGIKYVIDPGTARISRYS  371 (1295)
T ss_pred             ----HHHHHHHHHHHCCCCCCEEEECCCCCCHHHHHHHHC--CCCCCEEEEECCCCCCCCEECCEEEEEECCCEEEEEEC
T ss_conf             ----999999998614898876986557899999999848--89973389840520001000564899937840100475


Q ss_pred             H---------HHCCHHHHHHHHHCCCCCCCCEEEEEEECC
Q ss_conf             5---------254746887730116678983599997088
Q gi|254780945|r  568 A---------EHFGLAQLHQLRGRVGRGEEISSCILLYHP  598 (700)
Q Consensus       568 a---------erfGLsqLHQLRGRVGRg~~~s~c~l~~~~  598 (700)
                      +         +.---|+-.|=+||-||- .+|.||=+|+.
T Consensus       372 ~~~~~~~L~~~~iSqAsA~QR~GRaGR~-~~G~C~RLyse  410 (1295)
T PRK11131        372 YRTKVQRLPIEPISQASANQRKGRCGRV-SEGICIRLYSE  410 (1295)
T ss_pred             CCCCCCEEEEEEECHHHHHHHHHHHCCC-CCCEEEEEECH
T ss_conf             7778664667870165698750540788-99539998359


No 80 
>PRK04914 ATP-dependent helicase HepA; Validated
Probab=99.29  E-value=2.1e-10  Score=101.13  Aligned_cols=318  Identities=21%  Similarity=0.288  Sum_probs=176.8

Q ss_pred             CCCHHHHHHHHHHHHHHCCCCCCEEEEEECCCCCHHHHHHHHHHHHHHHH--CCEEEEEHHHHHHHHHHHHHHHHCCCCC
Q ss_conf             67988999999999841001343078862144223699999973344430--5458861279999999986211014578
Q gi|254780945|r  272 SPTKSQESAIKDILQDMSQKNRMLRILQGDVGSGKTLVALIAMAAAVEAG--GQAVIMAPIGILAQQHYEFIKKYTQNTQ  349 (700)
Q Consensus       272 ~LT~~Q~~ai~eI~~Dl~~~~pM~RLLQGDVGSGKTiVA~~A~l~~~~~G--~Q~alMaPTEILA~QH~~~~~~~~~~~~  349 (700)
                      .|-.-|.-+..|+.+...    =.-||--|||=||||=|.+-+-.-...|  ..+.+++| +-|..|-...+...|   +
T Consensus       151 ~l~pHQ~~ia~~v~~r~~----PRvLLADEVGLGKTIEAGLIl~ell~rgra~RvLIvvP-~~L~~QW~~EL~~KF---~  222 (955)
T PRK04914        151 GLIPHQLYIAHEVGRRHA----PRVLLADEVGLGKTIEAGLIIHQQLLTGRAERVLIIVP-ETLQHQWLVEMLRRF---N  222 (955)
T ss_pred             CCCCHHHHHHHHHHHCCC----CCEEEECCCCCCHHHHHHHHHHHHHHCCCCCEEEEECC-HHHHHHHHHHHHHHC---C
T ss_conf             656379999999971458----84897058888689999999999997487777999927-799899999999983---9


Q ss_pred             CEEEEEECCCCHHHHHHHHHHHCCC------CCEEEEECHHHC-CCCCCCC-----CCCEEEECCCCCC-----CHHHHH
Q ss_conf             6589962464225667687762134------754864111201-3345544-----4417885210133-----568899
Q gi|254780945|r  350 IIVEIITGNMPQAHRRKALERIAHG------QAHIIIGTHALF-QDSIQYY-----KLILVIVDEQHRF-----GVQQRL  412 (700)
Q Consensus       350 i~v~lLtg~~~~~er~~i~~~i~~G------~~~iiIGTHAL~-q~~v~F~-----~LgLvViDEQHRF-----GV~QR~  412 (700)
                      +...++..+     |   +.....+      .-+++|-..-.+ .++..+.     .--||||||=|+-     +..++-
T Consensus       223 L~f~i~D~~-----r---~~~~~~~~~NpF~~~~~vI~Sld~l~~~~~~~e~l~~a~WDLVIVDEAHhL~~~~~~~s~~y  294 (955)
T PRK04914        223 LRFSLFDEE-----R---CAEAQADADNPFETEQLVICSLDFLRKNKKRLEQALDAEWDLLVVDEAHHLVWSEEAPSREY  294 (955)
T ss_pred             CCCEEECCH-----H---HHHHHCCCCCCCCCCCEEEEEHHHHCCCHHHHHHHHCCCCCEEEEHHHHHHCCCCCCCCHHH
T ss_conf             980995518-----8---88753357997545897998789960396789987338988899713445305887888799


Q ss_pred             HHHHC--CCCCCCEEECHHHHH---HH----HHH---HHHHCCCHHH------------HCCCCCCCC------------
Q ss_conf             87402--567761010101322---78----999---9752010111------------102355766------------
Q gi|254780945|r  413 KLTQK--ATAPHVLLMTATPIP---RT----LVL---TSLGDIDISK------------ITEKPAGRK------------  456 (700)
Q Consensus       413 ~L~~K--g~~ph~L~MtATPIP---RT----Lal---~~ygdldvS~------------i~e~P~gR~------------  456 (700)
                      .+.+.  ...+|+|.+||||.=   .+    |.|   ..|.|++.-.            ++.++.+++            
T Consensus       295 ~lve~La~~~~~lLLLTATP~QlG~e~~Fa~L~LLDPdrF~d~~~F~~e~~~y~~va~~v~~L~~~~~l~~~~~~~l~~~  374 (955)
T PRK04914        295 QVVEQLAEVIPGVLLLTATPEQLGQESHFARLRLLDPDRFHDYEAFVEEEQQYRPVADAVQALLDGEKLSDDALNALGEL  374 (955)
T ss_pred             HHHHHHHHHCCCEEEEECCCCCCCCHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHH
T ss_conf             99999985159769984799889866689885277942115888899888755789999998631566888999999998


Q ss_pred             -----------------------------------------------CCE--------EEEEE-----------------
Q ss_conf             -----------------------------------------------620--------79997-----------------
Q gi|254780945|r  457 -----------------------------------------------PIK--------TVIIP-----------------  464 (700)
Q Consensus       457 -----------------------------------------------~I~--------T~~~~-----------------  464 (700)
                                                                     .|.        +.-++                 
T Consensus       375 l~e~~~~~l~~~~~~~~~~~~~~r~~li~~Lldr~gtgrvlfRntRa~v~gfp~R~l~~~~l~~~~~~~~~~~~~~~~~~  454 (955)
T PRK04914        375 LGEQDIEPLLQAINSDSEDAQAARQELISELLDRHGTGRVLFRNTRAAVKGFPKRELHPYPLPLPEQYQTAIRKSLEARA  454 (955)
T ss_pred             HHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHCCCHHHHHHCCCCCCCHHHHHHHHHHHHHHH
T ss_conf             64411447898752144456999999999998623215777765677743165545310567871567876543232467


Q ss_pred             -----------------------CCCHHHHHHHHHHHHCCCCEEEEEECCCCCCCCCCCCHHHHHHHHHHHHCCCCEECC
Q ss_conf             -----------------------020026899997631038738999712012211121014666666686637103120
Q gi|254780945|r  465 -----------------------INRIDEVIERLKVVLSEGKKAYWICPQIEEKKESNFRSVVERFNSLHEHFTSSIAII  521 (700)
Q Consensus       465 -----------------------~~~~~~~~~~i~~~l~~g~q~y~VcPlIeese~~~~~~~~~~~~~l~~~~~~~v~~l  521 (700)
                                             ..+.+.+.+.++..  .+.++-|+|--.        ..+....+.|+...+-++.+.
T Consensus       455 ~~~l~~E~~~~~~~~~~~~~~~~D~rv~~Li~~Lk~~--~~eKvLVFte~~--------~Ta~~L~~~Lr~~~Gi~~avf  524 (955)
T PRK04914        455 RDMLYPEQIYQEFEGDNATWWNFDPRVEWLIDFLKSH--RSEKVLVICAKA--------ETALQLEQALREREGIRAAVF  524 (955)
T ss_pred             HHHHCHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHC--CCCCEEEEECCH--------HHHHHHHHHHHHHCCCCEEEE
T ss_conf             8751735666545655655421388999999999857--798589996838--------999999999987559956997


Q ss_pred             CCCCCHHHHHHHHHHHHCCC--EEEEEECHHHHCCCCCCCCCEEEEECHHHCCHHHHHHHHHCCCCCCCCEE-EEEEECC
Q ss_conf             14699899999999975598--69999800341046888765899858525474688773011667898359-9997088
Q gi|254780945|r  522 HGRMSDIDKESVMDSFKNGT--CKLLIATTVIEVGIDVVDASIIIIENAEHFGLAQLHQLRGRVGRGEEISS-CILLYHP  598 (700)
Q Consensus       522 HGkm~~~ek~~~m~~F~~g~--~~iLvaTtviEVGvdvpna~~mvI~~aerfGLsqLHQLRGRVGRg~~~s~-c~l~~~~  598 (700)
                      ||.|+..|++++...|.+.+  .+|||||-+-.-|+|.--|+.||-+|= =+--..|.|==|||-|=+...- .|-+  +
T Consensus       525 h~gms~~ERdraaa~Fa~~e~gaqVLI~TEagsEG~NLQF~~~LVnyDL-PWNP~rLEQRIGRlDRiGQ~~dV~Ihv--p  601 (955)
T PRK04914        525 HEGMSIIERDRAAAYFADEEDGAQVLLCSEIGSEGRNFQFASHLVLFDL-PFNPDLLEQRIGRLDRIGQKHDIQIHV--P  601 (955)
T ss_pred             ECCCCHHHHHHHHHHHHCCCCCCEEEEEECCCCCCCCHHHHHHHEECCC-CCCHHHHHHHHHHHHHCCCCCCEEEEE--E
T ss_conf             0999989999999986176778519997252124503777435235258-987658899852065427867507986--2


Q ss_pred             CCCHHHHHH--------HHHHHHHCHHH
Q ss_conf             899879999--------99998414258
Q gi|254780945|r  599 PLSKNSYTR--------LSVLKNTEDGF  618 (700)
Q Consensus       599 ~~~~~~~~R--------l~~l~~~~dGf  618 (700)
                      -....+.+|        |+++++++-+.
T Consensus       602 y~~~s~q~~l~~wy~~gl~af~~~~~~g  629 (955)
T PRK04914        602 YLEGTAQERLFRWYHEGLNAFEHTCPTG  629 (955)
T ss_pred             ECCCCHHHHHHHHHHHHHHHHHCCCCHH
T ss_conf             0289889999999998888975569118


No 81 
>KOG0337 consensus
Probab=99.29  E-value=5e-10  Score=98.25  Aligned_cols=315  Identities=22%  Similarity=0.244  Sum_probs=206.3

Q ss_pred             CCCCHHHHHHHHHCCCCCCHHHHHHHHHHHHHHCCCCCCEEEEEECCCCCHHHHHHHHHHHHHHHHC----CEEEEEHHH
Q ss_conf             8775789999863024679889999999998410013430788621442236999999733444305----458861279
Q gi|254780945|r  256 NVEGKIAQKILRNIPFSPTKSQESAIKDILQDMSQKNRMLRILQGDVGSGKTLVALIAMAAAVEAGG----QAVIMAPIG  331 (700)
Q Consensus       256 ~~~~~~~~~f~~~LPF~LT~~Q~~ai~eI~~Dl~~~~pM~RLLQGDVGSGKTiVA~~A~l~~~~~G~----Q~alMaPTE  331 (700)
                      ..+-.....+.+.-==..|.=|.+.+.-|. ++..-.-|.|     ||||||.-.++-|+..+.++-    .+.++.||-
T Consensus        27 gL~~~v~raI~kkg~~~ptpiqRKTipliL-e~~dvv~mar-----tgsgktaaf~ipm~e~Lk~~s~~g~Ralilsptr  100 (529)
T KOG0337          27 GLDYKVLRAIHKKGFNTPTPIQRKTIPLIL-EGRDVVGMAR-----TGSGKTAAFLIPMIEKLKSHSQTGLRALILSPTR  100 (529)
T ss_pred             CCCHHHHHHHHHHHCCCCCCHHCCCCCCEE-ECCCCCEEEE-----CCCCCHHHHHHHHHHHHHHCCCCCCCEEECCCCH
T ss_conf             878899999998623899841103442003-1452100552-----2786104678899999861364462024326708


Q ss_pred             HHHHHHHHHHHHHCCCCCCEEEEEECCCCHHHHHHHHHHHCCCCCEEEEEC-----HHHCCCCCCCCCCCEEEECCCCC-
Q ss_conf             999999986211014578658996246422566768776213475486411-----12013345544441788521013-
Q gi|254780945|r  332 ILAQQHYEFIKKYTQNTQIIVEIITGNMPQAHRRKALERIAHGQAHIIIGT-----HALFQDSIQYYKLILVIVDEQHR-  405 (700)
Q Consensus       332 ILA~QH~~~~~~~~~~~~i~v~lLtg~~~~~er~~i~~~i~~G~~~iiIGT-----HAL~q~~v~F~~LgLvViDEQHR-  405 (700)
                      =||.|-+.-++.+-...+.++.|++|..+..|.   +..|. +..||||.|     |..-.-++..+..-+||.||--| 
T Consensus       101 eLa~qtlkvvkdlgrgt~lr~s~~~ggD~~eeq---f~~l~-~npDii~ATpgr~~h~~vem~l~l~sveyVVfdEadrl  176 (529)
T KOG0337         101 ELALQTLKVVKDLGRGTKLRQSLLVGGDSIEEQ---FILLN-ENPDIIIATPGRLLHLGVEMTLTLSSVEYVVFDEADRL  176 (529)
T ss_pred             HHHHHHHHHHHHHCCCCCHHHHHHCCCCHHHHH---HHHHC-CCCCEEEECCCEEEEEEHHEECCCCCEEEEEEHHHHHH
T ss_conf             899999999998515421121011263248899---99841-59987982485134200210012132256641013478


Q ss_pred             CCH---HHHHHH-HHCCCCCCCEEECHHHHHHHHHHHHHHCCCHHHHCCCCCCCCCCEEEEEE----------CCCHHHH
Q ss_conf             356---889987-40256776101010132278999975201011110235576662079997----------0200268
Q gi|254780945|r  406 FGV---QQRLKL-TQKATAPHVLLMTATPIPRTLVLTSLGDIDISKITEKPAGRKPIKTVIIP----------INRIDEV  471 (700)
Q Consensus       406 FGV---~QR~~L-~~Kg~~ph~L~MtATPIPRTLal~~ygdldvS~i~e~P~gR~~I~T~~~~----------~~~~~~~  471 (700)
                      |.-   +|=... ..-..+...|.|||| -||+|+=-.-..+.-     .-.-|..|.|.+-.          .++...+
T Consensus       177 femgfqeql~e~l~rl~~~~QTllfSat-lp~~lv~fakaGl~~-----p~lVRldvetkise~lk~~f~~~~~a~K~aa  250 (529)
T KOG0337         177 FEMGFQEQLHEILSRLPESRQTLLFSAT-LPRDLVDFAKAGLVP-----PVLVRLDVETKISELLKVRFFRVRKAEKEAA  250 (529)
T ss_pred             HHHHHHHHHHHHHHHCCCCCEEEEEECC-CCHHHHHHHHCCCCC-----CCEEEEEHHHHCCHHHHHHEEEECCHHHHHH
T ss_conf             7653689999998757776307998523-764467788706888-----7168740142105454514223061788999


Q ss_pred             HHHHHHHHCCCCEEEEEECCCCCCCCCCCCHHHHHHHHHHHHCCCCEECCCCCCCHHHHHHHHHHHHCCCEEEEEECHHH
Q ss_conf             99997631038738999712012211121014666666686637103120146998999999999755986999980034
Q gi|254780945|r  472 IERLKVVLSEGKKAYWICPQIEEKKESNFRSVVERFNSLHEHFTSSIAIIHGRMSDIDKESVMDSFKNGTCKLLIATTVI  551 (700)
Q Consensus       472 ~~~i~~~l~~g~q~y~VcPlIeese~~~~~~~~~~~~~l~~~~~~~v~~lHGkm~~~ek~~~m~~F~~g~~~iLvaTtvi  551 (700)
                      .-.+....-+..|.-+-||.         .-..+....+-..++..+.-+-|.|+.+..-.-..+|..++..+||.|-|-
T Consensus       251 Ll~il~~~~~~~~t~vf~~t---------k~hve~~~~ll~~~g~~~s~iysslD~~aRk~~~~~F~~~k~~~lvvTdva  321 (529)
T KOG0337         251 LLSILGGRIKDKQTIVFVAT---------KHHVEYVRGLLRDFGGEGSDIYSSLDQEARKINGRDFRGRKTSILVVTDVA  321 (529)
T ss_pred             HHHHHHCCCCCCCEEEEECC---------CCHHHHHHHHHHHCCCCCCCCCCCCCHHHHHHCCCCCCCCCCCEEEEEHHH
T ss_conf             99998512566650698315---------304789887898639874411144586766504203467755259984233


Q ss_pred             HCCCCCCCCCEEEEECHHHCCHHHHHHHHHCCCCCCCCEEEEEEE
Q ss_conf             104688876589985852547468877301166789835999970
Q gi|254780945|r  552 EVGIDVVDASIIIIENAEHFGLAQLHQLRGRVGRGEEISSCILLY  596 (700)
Q Consensus       552 EVGvdvpna~~mvI~~aerfGLsqLHQLRGRVGRg~~~s~c~l~~  596 (700)
                      --|+|+|-....|=++---=+=-=+| ==|||.|-+..++.|=+.
T Consensus       322 aRG~diplldnvinyd~p~~~klFvh-RVgr~aragrtg~aYs~V  365 (529)
T KOG0337         322 ARGLDIPLLDNVINYDFPPDDKLFVH-RVGRVARAGRTGRAYSLV  365 (529)
T ss_pred             HCCCCCCCCCCCCCCCCCCCCCEEEE-EECCHHHCCCCCEEEEEE
T ss_conf             33588765446564567998755888-712222145662379997


No 82 
>KOG0950 consensus
Probab=99.26  E-value=4.2e-10  Score=98.83  Aligned_cols=314  Identities=22%  Similarity=0.339  Sum_probs=206.7

Q ss_pred             HHHHHHHHHHHHHHCCCCCCEEEEEE-------CCCCCHHHHHHHHHHH-HHHHHCCEEEEEHHHHHHHHHHHHHHHHCC
Q ss_conf             88999999999841001343078862-------1442236999999733-444305458861279999999986211014
Q gi|254780945|r  275 KSQESAIKDILQDMSQKNRMLRILQG-------DVGSGKTLVALIAMAA-AVEAGGQAVIMAPIGILAQQHYEFIKKYTQ  346 (700)
Q Consensus       275 ~~Q~~ai~eI~~Dl~~~~pM~RLLQG-------DVGSGKTiVA~~A~l~-~~~~G~Q~alMaPTEILA~QH~~~~~~~~~  346 (700)
                      .++.+-+.....-..-..--.|+++|       -.+.|||+||-+-|+. ++.-+.-+++..|-+--++-|-..+..++.
T Consensus       215 ~~~~kgi~~~fewq~ecls~~~~~e~~nliys~Pts~gktlvaeilml~~~l~~rr~~llilp~vsiv~Ek~~~l~~~~~  294 (1008)
T KOG0950         215 YAKDKGILKLFEWQAECLSLPRLLERKNLIYSLPTSAGKTLVAEILMLREVLCRRRNVLLILPYVSIVQEKISALSPFSI  294 (1008)
T ss_pred             HHHHHHHHHHHHHHHHHHCCHHHHCCCCEEEECCCCCCHHHHHHHHHHHHHHHHHHCEEEECCEEEHHHHHHHHHHHHCC
T ss_conf             98764489899999987146534235655885787640679999999999988742116742421025877764002203


Q ss_pred             CCCCEEEEEECCCCHHHHHHHHHHHCCCCCEEEEEC----HHHCC---CCCCCCCCCEEEECCCCCCCHHHHHHHHH---
Q ss_conf             578658996246422566768776213475486411----12013---34554444178852101335688998740---
Q gi|254780945|r  347 NTQIIVEIITGNMPQAHRRKALERIAHGQAHIIIGT----HALFQ---DSIQYYKLILVIVDEQHRFGVQQRLKLTQ---  416 (700)
Q Consensus       347 ~~~i~v~lLtg~~~~~er~~i~~~i~~G~~~iiIGT----HAL~q---~~v~F~~LgLvViDEQHRFGV~QR~~L~~---  416 (700)
                      ++|++|+--.|+.+...+.+-.        .+.|-|    +.|+.   +.=.-.-+|+|||||-|=||=.-|..+.+   
T Consensus       295 ~~G~~ve~y~g~~~p~~~~k~~--------sv~i~tiEkanslin~lie~g~~~~~g~vvVdElhmi~d~~rg~~lE~~l  366 (1008)
T KOG0950         295 DLGFPVEEYAGRFPPEKRRKRE--------SVAIATIEKANSLINSLIEQGRLDFLGMVVVDELHMIGDKGRGAILELLL  366 (1008)
T ss_pred             CCCCCCHHHCCCCCCCCCCCCE--------EEEEEEHHHHHHHHHHHHHCCCCCCCCCEEEEEEEEEECCCCCHHHHHHH
T ss_conf             3588622112668998864410--------45542037667688888761783304728975224640356355899999


Q ss_pred             -C----C--CCCCCEEECHHHHHHHHHHHHHHCCCHHHHCCCCC--------C-------CCCCEEE-------EEECCC
Q ss_conf             -2----5--67761010101322789999752010111102355--------7-------6662079-------997020
Q gi|254780945|r  417 -K----A--TAPHVLLMTATPIPRTLVLTSLGDIDISKITEKPA--------G-------RKPIKTV-------IIPINR  467 (700)
Q Consensus       417 -K----g--~~ph~L~MtATPIPRTLal~~ygdldvS~i~e~P~--------g-------R~~I~T~-------~~~~~~  467 (700)
                       |    +  ...-+.-|||| ||--=.+.-+=|-++-.=+..|.        |       |..+.+-       ....++
T Consensus       367 ~k~~y~~~~~~~~iIGMSAT-i~N~~lL~~~L~A~~y~t~fRPv~L~E~ik~G~~i~~~~r~~~lr~ia~l~~~~~g~~d  445 (1008)
T KOG0950         367 AKILYENLETSVQIIGMSAT-IPNNSLLQDWLDAFVYTTRFRPVPLKEYIKPGSLIYESSRNKVLREIANLYSSNLGDED  445 (1008)
T ss_pred             HHHHHHCCCCCEEEEEEECC-CCCHHHHHHHHHHHHEECCCCCCCCHHCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCC
T ss_conf             99999632563467655241-47748899886432320466764301036777630123056777775432222025679


Q ss_pred             HHHHHHHHHHHHCCCCEEEEEECCCCCCCCC---------------------CCCHHHHHHHH--------HHHHCCCCE
Q ss_conf             0268999976310387389997120122111---------------------21014666666--------686637103
Q gi|254780945|r  468 IDEVIERLKVVLSEGKKAYWICPQIEEKKES---------------------NFRSVVERFNS--------LHEHFTSSI  518 (700)
Q Consensus       468 ~~~~~~~i~~~l~~g~q~y~VcPlIeese~~---------------------~~~~~~~~~~~--------l~~~~~~~v  518 (700)
                      -|.+.....+.+.+|.++.++||--...|+.                     ++.++.+....        |++..|..|
T Consensus       446 pD~~v~L~tet~~e~~~~lvfc~sk~~ce~~a~~~~~~vpk~~~~e~~~~~~~~~s~s~~lr~~~~~ld~Vl~~ti~~Gv  525 (1008)
T KOG0950         446 PDHLVGLCTETAPEGSSVLVFCPSKKNCENVASLIAKKVPKHIKSEKRLGLWELLSISNLLRRIPGILDPVLAKTIPYGV  525 (1008)
T ss_pred             CCCEEEEHHHHHHCCCEEEEECCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHEECCCCC
T ss_conf             75544212546525871799757643347788889887267665566545777888875764077544538760200353


Q ss_pred             ECCCCCCCHHHHHHHHHHHHCCCEEEEEECHHHHCCCCCCCCCEEEEECHHHCCHHH-----HHHHHHCCCCC--CCCEE
Q ss_conf             120146998999999999755986999980034104688876589985852547468-----87730116678--98359
Q gi|254780945|r  519 AIIHGRMSDIDKESVMDSFKNGTCKLLIATTVIEVGIDVVDASIIIIENAEHFGLAQ-----LHQLRGRVGRG--EEISS  591 (700)
Q Consensus       519 ~~lHGkm~~~ek~~~m~~F~~g~~~iLvaTtviEVGvdvpna~~mvI~~aerfGLsq-----LHQLRGRVGRg--~~~s~  591 (700)
                      ..-|--+..+|.+.+=..|++|-+.+++||+-+--||+.|--.++  ..|--||-.|     --|.=||-||-  +-.|-
T Consensus       526 AyHhaGLT~eER~~iE~afr~g~i~vl~aTSTlaaGVNLPArRVI--iraP~~g~~~l~~~~YkQM~GRAGR~gidT~Gd  603 (1008)
T KOG0950         526 AYHHAGLTSEEREIIEAAFREGNIFVLVATSTLAAGVNLPARRVI--IRAPYVGREFLTRLEYKQMVGRAGRTGIDTLGD  603 (1008)
T ss_pred             EECCCCCCCCHHHHHHHHHHHCCEEEEEECCHHHCCCCCCCCEEE--EECCCCCCCHHHHHHHHHHHHHHHHCCCCCCCC
T ss_conf             303444650068889999974676999943446406868751158--747754623000246776530200033465765


Q ss_pred             EEEEECCC
Q ss_conf             99970888
Q gi|254780945|r  592 CILLYHPP  599 (700)
Q Consensus       592 c~l~~~~~  599 (700)
                      |+|+....
T Consensus       604 siLI~k~~  611 (1008)
T KOG0950         604 SILIIKSS  611 (1008)
T ss_pred             EEEEEECC
T ss_conf             58985033


No 83 
>PRK11448 hsdR type I restriction enzyme EcoKI subunit R; Provisional
Probab=99.24  E-value=2.9e-09  Score=92.26  Aligned_cols=299  Identities=20%  Similarity=0.244  Sum_probs=180.6

Q ss_pred             CCCCCHHHHHHHHHHHHHHCCCCCCEEEEEECCCCCHHHHHHHHHHHHHHHH--CCEEEEEHHHHHHHHHHHHHHHHCCC
Q ss_conf             2467988999999999841001343078862144223699999973344430--54588612799999999862110145
Q gi|254780945|r  270 PFSPTKSQESAIKDILQDMSQKNRMLRILQGDVGSGKTLVALIAMAAAVEAG--GQAVIMAPIGILAQQHYEFIKKYTQN  347 (700)
Q Consensus       270 PF~LT~~Q~~ai~eI~~Dl~~~~pM~RLLQGDVGSGKTiVA~~A~l~~~~~G--~Q~alMaPTEILA~QH~~~~~~~~~~  347 (700)
                      .+.|-.-|++||..+...+..+++ .-||+==.|+|||-+|+..+..-+.+|  ..+.|+|=..-|+.|-++.|+..-..
T Consensus       414 ~i~lR~YQ~~AI~~v~~a~~~~~r-raLl~MATGTGKTrtaial~~rLlk~~~~kRILFLvDR~~L~~QA~~~F~~~~~~  492 (1126)
T PRK11448        414 ELGLRYYQEDAIQAVEKALANGQR-EILLAMATGTGKTRTAIALMYRLLKAKRFKRILFLVDRRALGEQALDAFKDTKIE  492 (1126)
T ss_pred             CCCCCHHHHHHHHHHHHHHHCCCC-CEEEEECCCCCHHHHHHHHHHHHHHCCCCCEEEEECCHHHHHHHHHHHHHHCCCC
T ss_conf             777868899999999999980985-4688724888589899999999996587672579856589999999987543454


Q ss_pred             CCC------EEEEEECCCCHHHHHHHHHHHCCCCCEEEEEC-HHHC----CCC----CCCCCCCEEEECCCCC-CCH---
Q ss_conf             786------58996246422566768776213475486411-1201----334----5544441788521013-356---
Q gi|254780945|r  348 TQI------IVEIITGNMPQAHRRKALERIAHGQAHIIIGT-HALF----QDS----IQYYKLILVIVDEQHR-FGV---  408 (700)
Q Consensus       348 ~~i------~v~lLtg~~~~~er~~i~~~i~~G~~~iiIGT-HAL~----q~~----v~F~~LgLvViDEQHR-FGV---  408 (700)
                      -+.      .|..|+.+            -..++..|.|.| .++.    +.+    ..-..--||||||=|| +..   
T Consensus       493 ~~~~~~~~~~v~~l~~~------------~~~~~~rv~isT~q~m~~~i~~~~~~~~~~~~~FDlIIiDEaHRgy~ld~e  560 (1126)
T PRK11448        493 GNQTFASIYDIKGLTDK------------FPEDETKVHVATVQSMVKRILQSDDSEPPPVGQYDCIVVDEAHRGYTLDKE  560 (1126)
T ss_pred             CCCCCCHHHHHHHCCCC------------CCCCCCEEEEECHHHHHHHHHCCCCCCCCCCCCCCEEEEECCCCCCCCCCC
T ss_conf             56664002200102567------------878777199973078998752357677999985137989778788743323


Q ss_pred             ---------H-------HHHHHHHCCCCCCCEEECHHHHHHHHHHHHHHCCCH--H----H-----HCCCCCCCCCCEEE
Q ss_conf             ---------8-------899874025677610101013227899997520101--1----1-----10235576662079
Q gi|254780945|r  409 ---------Q-------QRLKLTQKATAPHVLLMTATPIPRTLVLTSLGDIDI--S----K-----ITEKPAGRKPIKTV  461 (700)
Q Consensus       409 ---------~-------QR~~L~~Kg~~ph~L~MtATPIPRTLal~~ygdldv--S----~-----i~e~P~gR~~I~T~  461 (700)
                               .       =|.-|-  -..+..+-|||||-..|..  +||.--.  |    +     ++..||-  .|.|.
T Consensus       561 m~e~e~~~rd~~s~~skyr~Ild--YFDA~~iGLTATP~~~T~~--~Fg~P~~~Ys~~eAV~DG~LVd~~~P~--~i~T~  634 (1126)
T PRK11448        561 MTEGELQFRDQLDYVSKYRRVLD--YFDAVKIGLTATPALHTTE--IFGEPVYTYSYREAVIDGYLIDHEPPI--RIETK  634 (1126)
T ss_pred             CCCCHHCCCCHHHHHHHHHHHHH--HHHHHHHCCCCCCCCCHHH--HHCCCCEEECHHHHHCCCCCCCCCCCE--EEEEE
T ss_conf             11000102320247778999987--6215540476799955567--709973000588873047556886887--99756


Q ss_pred             EEECC----C---------------------------------------HHHHHHHHHHHHCCCC--EEEEEECCCCCCC
Q ss_conf             99702----0---------------------------------------0268999976310387--3899971201221
Q gi|254780945|r  462 IIPIN----R---------------------------------------IDEVIERLKVVLSEGK--KAYWICPQIEEKK  496 (700)
Q Consensus       462 ~~~~~----~---------------------------------------~~~~~~~i~~~l~~g~--q~y~VcPlIeese  496 (700)
                      +...-    .                                       ...+.+.+.+.+..+.  +..|-|-      
T Consensus       635 l~~~Gi~~~~~e~~~~~~~~~~~~~~~~~~de~~~~~~~fnr~v~~~~~nr~v~~~l~~~~~~~~~gKTiIFA~------  708 (1126)
T PRK11448        635 LAKEGIHFEKGEQVEVINTQTGEIDNDTLEDELDFEVEDFNRRVITESFNRVVCEELAKYLDPTGEGKTLIFCV------  708 (1126)
T ss_pred             EECCCCCCCCCCHHHHCCCHHHHHHCCCCCCCCCCCHHHHCCHHCCHHHHHHHHHHHHHHCCCCCCCCEEEEEC------
T ss_conf             51046035876434420300000202558731337888827320383479999999998458899987699927------


Q ss_pred             CCCCCHHHHHHHHHHHHC----CC----CEECCCCCCCHHHHHHHHHHHHCCCE-EEEEECHHHHCCCCCCCCCEEEEEC
Q ss_conf             112101466666668663----71----03120146998999999999755986-9999800341046888765899858
Q gi|254780945|r  497 ESNFRSVVERFNSLHEHF----TS----SIAIIHGRMSDIDKESVMDSFKNGTC-KLLIATTVIEVGIDVVDASIIIIEN  567 (700)
Q Consensus       497 ~~~~~~~~~~~~~l~~~~----~~----~v~~lHGkm~~~ek~~~m~~F~~g~~-~iLvaTtviEVGvdvpna~~mvI~~  567 (700)
                        +-.-|+...+.|++.|    |.    -+..++|+.+.  -+..+++|++.+. .|-|+--++-.|||||....+|-.-
T Consensus       709 --~~~HAd~Iv~~l~e~F~~~y~~~~~~~~~~It~~~~~--~~~lI~~Fkn~~~P~IAVTVDmL~TGiDVPei~nLVF~R  784 (1126)
T PRK11448        709 --TDAHADMVVRLLKEAFKKKYGQVEDDAIIKITGDADK--VQQLIRRFKNERLPNIVVTVDLLTTGIDVPSICNLVFLR  784 (1126)
T ss_pred             --CHHHHHHHHHHHHHHHHHHCCCCCCCEEEEEECCCCC--HHHHHHHHCCCCCCEEEEEECCCCCCCCCCCCEEEEEEE
T ss_conf             --8699999999999998864787678448997088844--789999725789983899856210476664201688766


Q ss_pred             HHHCCHHHHHHHHHCCCCCCC--CEEEEEEECC
Q ss_conf             525474688773011667898--3599997088
Q gi|254780945|r  568 AEHFGLAQLHQLRGRVGRGEE--ISSCILLYHP  598 (700)
Q Consensus       568 aerfGLsqLHQLRGRVGRg~~--~s~c~l~~~~  598 (700)
                      .=+ --.--.|..||=-|=-.  .-.+|.+++.
T Consensus       785 ~V~-S~i~F~QMiGRGTRlc~~i~K~~F~I~Da  816 (1126)
T PRK11448        785 RVK-SRILYEQMKGRATRLCPDIGKTVFRIFDA  816 (1126)
T ss_pred             ECC-CHHHHHHHHCCCCCCCCCCCCCEEEEEEC
T ss_conf             756-67786654167554376668766999601


No 84 
>KOG0341 consensus
Probab=99.22  E-value=1.7e-10  Score=101.83  Aligned_cols=284  Identities=23%  Similarity=0.321  Sum_probs=179.5

Q ss_pred             CCCCCHHHHHHHHHHHHH-----------HHHCCEEEEEHHHHHHHHHHHHHHHHCCCCC------CEEEEEECCCCHHH
Q ss_conf             144223699999973344-----------4305458861279999999986211014578------65899624642256
Q gi|254780945|r  301 DVGSGKTLVALIAMAAAV-----------EAGGQAVIMAPIGILAQQHYEFIKKYTQNTQ------IIVEIITGNMPQAH  363 (700)
Q Consensus       301 DVGSGKTiVA~~A~l~~~-----------~~G~Q~alMaPTEILA~QH~~~~~~~~~~~~------i~v~lLtg~~~~~e  363 (700)
                      =.|||||+|..+.+...+           ..|--+.+.+|.-=||+|.|.-+..++..+.      ++..|-.|+++-++
T Consensus       215 fTGSGKTlvFvLP~imf~LeqE~~lPf~~~EGP~gLiicPSRELArQt~~iie~~~~~L~e~g~P~lRs~LciGG~~v~e  294 (610)
T KOG0341         215 FTGSGKTLVFVLPVIMFALEQEMMLPFARGEGPYGLIICPSRELARQTHDIIEQYVAALQEAGYPELRSLLCIGGVPVRE  294 (610)
T ss_pred             EECCCCEEEEEHHHHHHHHHHHHCCCCCCCCCCEEEEECCCHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHCCCCHHH
T ss_conf             60688468870999999998885186003789735897370899999999999999998764884665665216853898


Q ss_pred             HHHHHHHHCCCCCEEEEECHHHC----CC-CCCCCCCCEEEECCCCC-----CCHHHHHHHHH-CCCCCCCEEECHHHHH
Q ss_conf             67687762134754864111201----33-45544441788521013-----35688998740-2567761010101322
Q gi|254780945|r  364 RRKALERIAHGQAHIIIGTHALF----QD-SIQYYKLILVIVDEQHR-----FGVQQRLKLTQ-KATAPHVLLMTATPIP  432 (700)
Q Consensus       364 r~~i~~~i~~G~~~iiIGTHAL~----q~-~v~F~~LgLvViDEQHR-----FGV~QR~~L~~-Kg~~ph~L~MtATPIP  432 (700)
                         .++.+..| ++|+|.|-.-+    ++ .+...--.+...||-.|     |--.-|.-+.- ||. -..|..||| .|
T Consensus       295 ---ql~~v~~G-vHivVATPGRL~DmL~KK~~sLd~CRyL~lDEADRmiDmGFEddir~iF~~FK~Q-RQTLLFSAT-MP  368 (610)
T KOG0341         295 ---QLDVVRRG-VHIVVATPGRLMDMLAKKIMSLDACRYLTLDEADRMIDMGFEDDIRTIFSFFKGQ-RQTLLFSAT-MP  368 (610)
T ss_pred             ---HHHHHHCC-EEEEECCCCHHHHHHHHHHCCHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHH-HHEEEEECC-CC
T ss_conf             ---99998637-0699817626899998764048887776531477776056326689999997420-223553124-64


Q ss_pred             HHHHHHHHHCCCHHHHCCCCCCCCCCEEEEE--ECCCHH--HHHHHHHHH---------HCCCC-EEEEEECCCCCCCCC
Q ss_conf             7899997520101111023557666207999--702002--689999763---------10387-389997120122111
Q gi|254780945|r  433 RTLVLTSLGDIDISKITEKPAGRKPIKTVII--PINRID--EVIERLKVV---------LSEGK-KAYWICPQIEEKKES  498 (700)
Q Consensus       433 RTLal~~ygdldvS~i~e~P~gR~~I~T~~~--~~~~~~--~~~~~i~~~---------l~~g~-q~y~VcPlIeese~~  498 (700)
                      +-.-.--     -|-+      -|||+--+=  ...+.+  .-.++++.+         |++-. -|.+-|     ..+ 
T Consensus       369 ~KIQ~FA-----kSAL------VKPvtvNVGRAGAAsldViQevEyVkqEaKiVylLeCLQKT~PpVLIFa-----EkK-  431 (610)
T KOG0341         369 KKIQNFA-----KSAL------VKPVTVNVGRAGAASLDVIQEVEYVKQEAKIVYLLECLQKTSPPVLIFA-----EKK-  431 (610)
T ss_pred             HHHHHHH-----HHHC------CCCEEEECCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCCEEEEE-----CCC-
T ss_conf             8899888-----7640------5645884255542202088999999863012069987612799669984-----145-


Q ss_pred             CCCHHHHHHHHHHHHCCCCEECCCCCCCHHHHHHHHHHHHCCCEEEEEECHHHHCCCCCCCCCEEEEECHHHCCHHHHHH
Q ss_conf             21014666666686637103120146998999999999755986999980034104688876589985852547468877
Q gi|254780945|r  499 NFRSVVERFNSLHEHFTSSIAIIHGRMSDIDKESVMDSFKNGTCKLLIATTVIEVGIDVVDASIIIIENAEHFGLAQLHQ  578 (700)
Q Consensus       499 ~~~~~~~~~~~l~~~~~~~v~~lHGkm~~~ek~~~m~~F~~g~~~iLvaTtviEVGvdvpna~~mvI~~aerfGLsqLHQ  578 (700)
                        .++.+.|++|--. +-...-+||--+.+++...+++|+.|+.|+||||.|---|.|.|+.-..|=++---===.-.|-
T Consensus       432 --~DVD~IhEYLLlK-GVEavaIHGGKDQedR~~ai~afr~gkKDVLVATDVASKGLDFp~iqHVINyDMP~eIENYVHR  508 (610)
T KOG0341         432 --ADVDDIHEYLLLK-GVEAVAIHGGKDQEDRHYAIEAFRAGKKDVLVATDVASKGLDFPDIQHVINYDMPEEIENYVHR  508 (610)
T ss_pred             --CCHHHHHHHHHHC-CCEEEEEECCCCHHHHHHHHHHHHCCCCCEEEEECCHHCCCCCCCCHHHCCCCCHHHHHHHHHH
T ss_conf             --6747899999872-5136874168656678889999865787458873100036897450444047880889999997


Q ss_pred             HHHCCCCCCCCEEEEEEECCCCCHHHHHHHHHH
Q ss_conf             301166789835999970888998799999999
Q gi|254780945|r  579 LRGRVGRGEEISSCILLYHPPLSKNSYTRLSVL  611 (700)
Q Consensus       579 LRGRVGRg~~~s~c~l~~~~~~~~~~~~Rl~~l  611 (700)
                       =||-||++..|..--..+.+.++...--|+.|
T Consensus       509 -IGRTGRsg~~GiATTfINK~~~esvLlDLK~L  540 (610)
T KOG0341         509 -IGRTGRSGKTGIATTFINKNQEESVLLDLKHL  540 (610)
T ss_pred             -HCCCCCCCCCCEEEEEECCCCHHHHHHHHHHH
T ss_conf             -12467788864022211456318889879999


No 85 
>KOG0352 consensus
Probab=99.19  E-value=1.8e-08  Score=85.99  Aligned_cols=313  Identities=21%  Similarity=0.287  Sum_probs=197.8

Q ss_pred             CHHHHHHHHHHHHHHCCCCCCEEEEEECCCCCHHHHHHHHHHHHHHHHCCEEEEEHHHHHHHHHHHHHHHHCCCCCCEEE
Q ss_conf             98899999999984100134307886214422369999997334443054588612799999999862110145786589
Q gi|254780945|r  274 TKSQESAIKDILQDMSQKNRMLRILQGDVGSGKTLVALIAMAAAVEAGGQAVIMAPIGILAQQHYEFIKKYTQNTQIIVE  353 (700)
Q Consensus       274 T~~Q~~ai~eI~~Dl~~~~pM~RLLQGDVGSGKTiVA~~A~l~~~~~G~Q~alMaPTEILA~QH~~~~~~~~~~~~i~v~  353 (700)
                      |.=|++|+.-|..--..-     -+.=-.|+||.+-.-+.++.   ++.=..+..|---|-+-.-.-+.+    +.+++.
T Consensus        22 s~LQE~A~~c~VK~k~DV-----yVsMPTGaGKSLCyQLPaL~---~~gITIV~SPLiALIkDQiDHL~~----LKVp~~   89 (641)
T KOG0352          22 SRLQEQAINCIVKRKCDV-----YVSMPTGAGKSLCYQLPALV---HGGITIVISPLIALIKDQIDHLKR----LKVPCE   89 (641)
T ss_pred             CHHHHHHHHHHHHCCCCE-----EEECCCCCCHHHHHHCHHHH---HCCEEEEECHHHHHHHHHHHHHHH----HCCCHH
T ss_conf             757899899988346737-----99646887601454265877---288189930789999999877874----056166


Q ss_pred             EEECCCCHHHHHHHHHHHCCCCCE--EEEEC---------HHHCCCCCCCCCCCEEEECCCCCCCHHHH-----------
Q ss_conf             962464225667687762134754--86411---------12013345544441788521013356889-----------
Q gi|254780945|r  354 IITGNMPQAHRRKALERIAHGQAH--IIIGT---------HALFQDSIQYYKLILVIVDEQHRFGVQQR-----------  411 (700)
Q Consensus       354 lLtg~~~~~er~~i~~~i~~G~~~--iiIGT---------HAL~q~~v~F~~LgLvViDEQHRFGV~QR-----------  411 (700)
                      -|.++++++||++++.+++.-+++  ++-=|         +-|+|.=+.-+.|.+.|+||-|=  |.|-           
T Consensus        90 SLNSKlSt~ER~ri~~DL~~ekp~~K~LYITPE~AAt~~FQ~lLn~L~~r~~L~Y~vVDEAHC--VSQWGHDFRPDYL~L  167 (641)
T KOG0352          90 SLNSKLSTVERSRIMGDLAKEKPTIKMLYITPEGAATDGFQKLLNGLANRDVLRYIVVDEAHC--VSQWGHDFRPDYLTL  167 (641)
T ss_pred             HHHCHHHHHHHHHHHHHHHHCCCCEEEEEECHHHHHHHHHHHHHHHHHHHCEEEEEEECHHHH--HHHHCCCCCCCHHHH
T ss_conf             640121078899998888743775148997631555666899999887414022477334666--776266668204446


Q ss_pred             HHHHHCCCCCCCEEECHHHHHHHHHHHHHHCCCHHHHCCCCCCCCCCEEEEEE----------------CCCHHHHHHHH
Q ss_conf             98740256776101010132278999975201011110235576662079997----------------02002689999
Q gi|254780945|r  412 LKLTQKATAPHVLLMTATPIPRTLVLTSLGDIDISKITEKPAGRKPIKTVIIP----------------INRIDEVIERL  475 (700)
Q Consensus       412 ~~L~~Kg~~ph~L~MtATPIPRTLal~~ygdldvS~i~e~P~gR~~I~T~~~~----------------~~~~~~~~~~i  475 (700)
                      -.|+++-..+-.+.+|||.-|.---= +|.-|-+         |+||.-.--+                .+....+-+|-
T Consensus       168 G~LRS~~~~vpwvALTATA~~~VqED-i~~qL~L---------~~PVAiFkTP~FR~NLFYD~~~K~~I~D~~~~LaDF~  237 (641)
T KOG0352         168 GSLRSVCPGVPWVALTATANAKVQED-IAFQLKL---------RNPVAIFKTPTFRDNLFYDNHMKSFITDCLTVLADFS  237 (641)
T ss_pred             HHHHHHCCCCCEEEEECCCCHHHHHH-HHHHHHC---------CCCHHHHCCCCHHHHHHHHHHHHHHHCCHHHHHHHHH
T ss_conf             66774469996698543467767799-9999760---------5854440574145444578888876413777899999


Q ss_pred             HHHHCC---------CC-EEEEE-ECCCCCCCCCCCCHHHHHHHHHHHHCCCCEECCCCCCCHHHHHHHHHHHHCCCEEE
Q ss_conf             763103---------87-38999-71201221112101466666668663710312014699899999999975598699
Q gi|254780945|r  476 KVVLSE---------GK-KAYWI-CPQIEEKKESNFRSVVERFNSLHEHFTSSIAIIHGRMSDIDKESVMDSFKNGTCKL  544 (700)
Q Consensus       476 ~~~l~~---------g~-q~y~V-cPlIeese~~~~~~~~~~~~~l~~~~~~~v~~lHGkm~~~ek~~~m~~F~~g~~~i  544 (700)
                      ...|-+         +. -|=+| |-.=|+-|        ...-.|. .-+-.-.--|.-++..|..++-++..+|++.|
T Consensus       238 ~~~LG~~~~~~~~~K~~~GCGIVYCRTR~~cE--------q~AI~l~-~~Gi~A~AYHAGLK~~ERTeVQe~WM~~~~Pv  308 (641)
T KOG0352         238 SSNLGKHEKASQNKKTFTGCGIVYCRTRNECE--------QVAIMLE-IAGIPAMAYHAGLKKKERTEVQEKWMNNEIPV  308 (641)
T ss_pred             HHHCCCCHHHHCCCCCCCCCEEEEECCHHHHH--------HHHHHHH-HCCCCHHHHHHHCCCCHHHHHHHHHHCCCCCE
T ss_conf             98628904441178777773279960288999--------8988753-24762677650014112688999986278877


Q ss_pred             EEECHHHHCCCCCCCCCEEEEECHHHCCHHHHHHHHHCCCCCCCCEEEEEEECCCCCHHHHHHHHHHHHHCHHHHHHHHH
Q ss_conf             99800341046888765899858525474688773011667898359999708889987999999998414258999999
Q gi|254780945|r  545 LIATTVIEVGIDVVDASIIIIENAEHFGLAQLHQLRGRVGRGEEISSCILLYHPPLSKNSYTRLSVLKNTEDGFLIAEED  624 (700)
Q Consensus       545 LvaTtviEVGvdvpna~~mvI~~aerfGLsqLHQLRGRVGRg~~~s~c~l~~~~~~~~~~~~Rl~~l~~~~dGf~iAe~D  624 (700)
                      .+||.---.|||-||....+--| --=-+|--.|=-||-||.+++|||-|.|+.+ ...+   +        -|.|..+-
T Consensus       309 I~AT~SFGMGVDKp~VRFViHW~-~~qn~AgYYQESGRAGRDGk~SyCRLYYsR~-D~~~---i--------~FLi~~e~  375 (641)
T KOG0352         309 IAATVSFGMGVDKPDVRFVIHWS-PSQNLAGYYQESGRAGRDGKRSYCRLYYSRQ-DKNA---L--------NFLVSGEL  375 (641)
T ss_pred             EEEEECCCCCCCCCCEEEEEECC-HHHHHHHHHHHCCCCCCCCCCCCEEEEECCC-CHHH---H--------HHHHHHHH
T ss_conf             99960244466877615999517-0565789988615356677725201333214-0577---7--------79977678


Q ss_pred             HHHCCCCC
Q ss_conf             85206300
Q gi|254780945|r  625 LKQRKEGE  632 (700)
Q Consensus       625 l~lRG~G~  632 (700)
                      -++||-|+
T Consensus       376 aklrek~~  383 (641)
T KOG0352         376 AKLREKAK  383 (641)
T ss_pred             HHHHHHCC
T ss_conf             99876313


No 86 
>pfam04851 ResIII Type III restriction enzyme, res subunit.
Probab=99.18  E-value=1.2e-10  Score=102.96  Aligned_cols=100  Identities=26%  Similarity=0.338  Sum_probs=85.9

Q ss_pred             CCCCHHHHHHHHHHHHHHCCCCCCEEEEEECCCCCHHHHHHHHHHHHHHHHCCEEEEEHHHHHHHHHHHHHHHHCCCCCC
Q ss_conf             46798899999999984100134307886214422369999997334443054588612799999999862110145786
Q gi|254780945|r  271 FSPTKSQESAIKDILQDMSQKNRMLRILQGDVGSGKTLVALIAMAAAVEAGGQAVIMAPIGILAQQHYEFIKKYTQNTQI  350 (700)
Q Consensus       271 F~LT~~Q~~ai~eI~~Dl~~~~pM~RLLQGDVGSGKTiVA~~A~l~~~~~G~Q~alMaPTEILA~QH~~~~~~~~~~~~i  350 (700)
                      |+|-+-|++|++.+.+.      =+-++..-.|||||++++..+......+..+.++|||..|..|..+.|         
T Consensus         2 ~~LR~yQ~~a~~~~~~~------~~~~i~~pTGsGKT~~~~~~i~~~~~~~~~~lvlvp~~~L~~Q~~~~~---------   66 (103)
T pfam04851         2 LELRPYQIEAIRNLLEK------KRGLIVMATGSGKTLTAAKLIARLLKGKKKVLFLVPRKDLLEQALEEF---------   66 (103)
T ss_pred             CCCCHHHHHHHHHHHHC------CCEEEEECCCCCHHHHHHHHHHHHHHCCCCEEEEECCHHHHHHHHHHH---------
T ss_conf             98729999999999963------986999589998799999999999846992999908299999999965---------


Q ss_pred             EEEEEECCCCHHHHHHHHHHHCCCCCEEEEECHHHCCCCCCCCCCCEEEECCCCCCCHHHH-HHHHHCCCCCCCEEECHH
Q ss_conf             5899624642256676877621347548641112013345544441788521013356889-987402567761010101
Q gi|254780945|r  351 IVEIITGNMPQAHRRKALERIAHGQAHIIIGTHALFQDSIQYYKLILVIVDEQHRFGVQQR-LKLTQKATAPHVLLMTAT  429 (700)
Q Consensus       351 ~v~lLtg~~~~~er~~i~~~i~~G~~~iiIGTHAL~q~~v~F~~LgLvViDEQHRFGV~QR-~~L~~Kg~~ph~L~MtAT  429 (700)
                                                                    |||+||-|+.+-.+. ..+.+.-..+-+|-||||
T Consensus        67 ----------------------------------------------lii~DE~H~~~a~~~~~~l~~~~~~~~~lGlTAT  100 (103)
T pfam04851        67 ----------------------------------------------VIIIDEAHHSSAKTKYRKILEYFKPAFLLGLTAT  100 (103)
T ss_pred             ----------------------------------------------HHHHHHHHHCCCHHHHHHHHHHCCCCEEEEEEEC
T ss_conf             ----------------------------------------------6460163523537899999995772608998008


Q ss_pred             HH
Q ss_conf             32
Q gi|254780945|r  430 PI  431 (700)
Q Consensus       430 PI  431 (700)
                      |.
T Consensus       101 P~  102 (103)
T pfam04851       101 PE  102 (103)
T ss_pred             CC
T ss_conf             88


No 87 
>PRK12903 secA preprotein translocase subunit SecA; Reviewed
Probab=99.18  E-value=4.8e-09  Score=90.55  Aligned_cols=279  Identities=20%  Similarity=0.264  Sum_probs=189.8

Q ss_pred             CCCCCHHHHHHHHHHHHHHHHCCEEEEEHHHHHHHHHHHHHHHHCCCCCCEEEEEECCCCHHHHHHHHHHHCCCCCEEEE
Q ss_conf             14422369999997334443054588612799999999862110145786589962464225667687762134754864
Q gi|254780945|r  301 DVGSGKTLVALIAMAAAVEAGGQAVIMAPIGILAQQHYEFIKKYTQNTQIIVEIITGNMPQAHRRKALERIAHGQAHIII  380 (700)
Q Consensus       301 DVGSGKTiVA~~A~l~~~~~G~Q~alMaPTEILA~QH~~~~~~~~~~~~i~v~lLtg~~~~~er~~i~~~i~~G~~~iiI  380 (700)
                      -.|-|||+||.++++..+-+|..|-+....+-||+--++...+++.-+|++|.+.++.++..+|++.|.      +||+-
T Consensus        99 ~TGEGKTL~atlp~ylnal~g~gvhvvTvNdYLA~RDae~m~~~y~~lGltvg~~~~~~~~~~r~~aY~------~ditY  172 (885)
T PRK12903         99 KTGEGKTITSIAPVYLNALEGKGVIVSTVNEYLAERDAEEMGKVFKFLGLSVGINKANMDPNLKREAYN------CDITY  172 (885)
T ss_pred             CCCCCHHHHHHHHHHHHHHCCCCCEEEECCHHHHHHHHHHHHHHHHHHCCEEEECCCCCCHHHHHHHHC------CCCEE
T ss_conf             068857999999999987469980898064565585599999999982965601189999799999856------99679


Q ss_pred             ECHHHCC-----CCC-------CCCCCCEEEECCCC-------------------CCCHHHHH-----------------
Q ss_conf             1112013-----345-------54444178852101-------------------33568899-----------------
Q gi|254780945|r  381 GTHALFQ-----DSI-------QYYKLILVIVDEQH-------------------RFGVQQRL-----------------  412 (700)
Q Consensus       381 GTHAL~q-----~~v-------~F~~LgLvViDEQH-------------------RFGV~QR~-----------------  412 (700)
                      ||+.=|-     |+.       .-..+-.+||||=-                   .-..-+..                 
T Consensus       173 ~tn~e~gFDyLrDnm~~~~~~~vqr~~~~aIvDEvDSiLIDeArtPLiisg~~~~~~~~y~~~~~~~~~l~~~dy~id~~  252 (885)
T PRK12903        173 STHSELGFDYLRDNMVSSYEEKVQRGLNFCLIDEVDSILIDEARTPLIISGGKSNESNLYKAADQFVRTLEEDDYKIDEE  252 (885)
T ss_pred             ECCCCEEECCCCCCCCCCHHHHCCCCCCEEEEECCHHHHHCCCCCCCEEECCCCCCCHHHHHHHHHHHHCCCCCEEEECC
T ss_conf             77865030114001135837725889980366541144330467752576789886469999999865336566886314


Q ss_pred             ----HHHHCC----------------------------------------------------------------------
Q ss_conf             ----874025----------------------------------------------------------------------
Q gi|254780945|r  413 ----KLTQKA----------------------------------------------------------------------  418 (700)
Q Consensus       413 ----~L~~Kg----------------------------------------------------------------------  418 (700)
                          .|.++|                                                                      
T Consensus       253 ~~~v~lte~G~~~~e~~~~~~~l~~~~~~~~~~~i~~al~A~~l~~~d~dYiV~d~~v~ivDe~TGR~m~grr~s~GLhQ  332 (885)
T PRK12903        253 SKAIYLTEKGIKKANKFFKLDNLYAIENSELFHRIQNALRAHKVFKEGVEYIVRDGKIELVDQFTGRIMEGRSYSEGLQQ  332 (885)
T ss_pred             CCCCCCCHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCEEEECCEEEEEECCCCCCCCCCCHHHHHHH
T ss_conf             47764251158999984266444661157999999999999999856970799779289987898862788803036899


Q ss_pred             ---------------------------CCCCCEEECHHHHHHHHH---HHHHHCCCHHHHC-CCCCCCCCCEEEEEEC--
Q ss_conf             ---------------------------677610101013227899---9975201011110-2355766620799970--
Q gi|254780945|r  419 ---------------------------TAPHVLLMTATPIPRTLV---LTSLGDIDISKIT-EKPAGRKPIKTVIIPI--  465 (700)
Q Consensus       419 ---------------------------~~ph~L~MtATPIPRTLa---l~~ygdldvS~i~-e~P~gR~~I~T~~~~~--  465 (700)
                                                 ..+.+=-||-|-  .|-+   ..+|+ |+|..|. .+|.-|+.-...++..  
T Consensus       333 aiEaKE~v~i~~e~~t~a~iT~Qn~Fr~y~kl~GmTGTa--~te~~Ef~~iY~-l~v~~iPtn~p~~R~d~~d~vy~t~~  409 (885)
T PRK12903        333 AIQAKEMVEIEPETKTLATITYQNFFRLFKKLSGMTGTA--KTEEQEFIDIYN-MRVNVVPTNKPVIRKDEPDSIFGTKH  409 (885)
T ss_pred             HHHHHCCCCCCCCCCEEEEEEHHHHHHHCCHHCCCCCCC--HHHHHHHHHHHC-CEEEECCCCCCCEEECCCCHHHCCHH
T ss_conf             999872887798873136630998986460422676777--889999999869-73698189998521428323107899


Q ss_pred             CCHHHHHHHHHHHHCCCCEEEEEECCCCCCCCCCCCHHHHHHHHHHHHCCCCEECCCCCCCHHHHHHHHHHHHCCCEEEE
Q ss_conf             20026899997631038738999712012211121014666666686637103120146998999999999755986999
Q gi|254780945|r  466 NRIDEVIERLKVVLSEGKKAYWICPQIEEKKESNFRSVVERFNSLHEHFTSSIAIIHGRMSDIDKESVMDSFKNGTCKLL  545 (700)
Q Consensus       466 ~~~~~~~~~i~~~l~~g~q~y~VcPlIeese~~~~~~~~~~~~~l~~~~~~~v~~lHGkm~~~ek~~~m~~F~~g~~~iL  545 (700)
                      .+...+.+.|++.-++|+-|-|-+..||.||.+   |     +.|++. +-...+|..|-...|-+-|-++  -..-.|-
T Consensus       410 ~k~~av~~ei~~~~~~gqPvLvgt~sve~Se~l---s-----~~L~~~-~i~h~vLNAk~~~~EA~Iia~A--G~~g~VT  478 (885)
T PRK12903        410 AKWKAVVKEVKRVHEKGQPILIGTAQVEDSEQL---H-----EYLLEA-NIPHTVLNAKQHAREAEIIAKA--GQKGAIT  478 (885)
T ss_pred             HHHHHHHHHHHHHHHCCCCEEEECCCHHHHHHH---H-----HHHHHC-CCCCEEEECCCHHHHHHHHHHC--CCCCCEE
T ss_conf             999999999999985799889956847999999---9-----999856-8770355468658899999954--8999189


Q ss_pred             EECHHHHCCCCC------CCCCEEEEECHHHCCHHHH-HHHHHCCCCCCCCEEEEEEECCC
Q ss_conf             980034104688------8765899858525474688-77301166789835999970888
Q gi|254780945|r  546 IATTVIEVGIDV------VDASIIIIENAEHFGLAQL-HQLRGRVGRGEEISSCILLYHPP  599 (700)
Q Consensus       546 vaTtviEVGvdv------pna~~mvI~~aerfGLsqL-HQLRGRVGRg~~~s~c~l~~~~~  599 (700)
                      |||..---|.|+      ..+--.-|...||.--.-. -|||||-||-+.+|..-+..+-+
T Consensus       479 iATNMAGRGTDI~Lg~~v~~~GGL~VigterhesrRiD~QLrGR~gRQGDpG~s~f~~Sle  539 (885)
T PRK12903        479 IATNMAGRGTDIKLSKGVLELGGLYVLGTEKAESRRIDNQLRGRSGRQGDVGESRFFISLD  539 (885)
T ss_pred             EECCCCCCCCCCCCCHHHHHCCCEEEEECCCCCCHHHHHHHCCCCCCCCCCCCEEEEEECC
T ss_conf             8376678996857416589729858984265620458888607434689997359999726


No 88 
>smart00490 HELICc helicase superfamily c-terminal domain.
Probab=99.18  E-value=1e-10  Score=103.57  Aligned_cols=79  Identities=33%  Similarity=0.530  Sum_probs=71.5

Q ss_pred             HHHHHHHCCCCEECCCCCCCHHHHHHHHHHHHCCCEEEEEECHHHHCCCCCCCCCEEEEECHHHCCHHHHHHHHHCCCCC
Q ss_conf             66668663710312014699899999999975598699998003410468887658998585254746887730116678
Q gi|254780945|r  507 FNSLHEHFTSSIAIIHGRMSDIDKESVMDSFKNGTCKLLIATTVIEVGIDVVDASIIIIENAEHFGLAQLHQLRGRVGRG  586 (700)
Q Consensus       507 ~~~l~~~~~~~v~~lHGkm~~~ek~~~m~~F~~g~~~iLvaTtviEVGvdvpna~~mvI~~aerfGLsqLHQLRGRVGRg  586 (700)
                      .+.|++. +-++..+||+|+.+++++++++|++|+++|||||.+.+.|||+|+++++|+.+. ....+++.|-.||+||-
T Consensus         4 ~~~l~~~-g~~~~~i~g~~~~~~R~~~~~~f~~~~~~ilv~t~~~~~Gidl~~~~~vI~~~~-~~~~~~~~Q~~GR~~R~   81 (82)
T smart00490        4 AELLKEL-GIKVARLHGGLSQEEREEILEKFNNGKIKVLVATDVAERGLDLPGVDLVIIYDL-PWSPASYIQRIGRAGRA   81 (82)
T ss_pred             HHHHHHC-CCCEEEEECCCCHHHHHHHHHHHHCCCCEEEEEEEEEEEECCCCCCCEEEEECC-CCCHHHHHHHHCCCCCC
T ss_conf             9999888-991999989699999999999998799719999502421148988999999789-96989999997258789


Q ss_pred             C
Q ss_conf             9
Q gi|254780945|r  587 E  587 (700)
Q Consensus       587 ~  587 (700)
                      +
T Consensus        82 g   82 (82)
T smart00490       82 G   82 (82)
T ss_pred             C
T ss_conf             9


No 89 
>pfam00271 Helicase_C Helicase conserved C-terminal domain. The Prosite family is restricted to DEAD/H helicases, whereas this domain family is found in a wide variety of helicases and helicase related proteins. It may be that this is not an autonomously folding unit, but an integral part of the helicase.
Probab=99.14  E-value=1.6e-10  Score=102.07  Aligned_cols=73  Identities=33%  Similarity=0.541  Sum_probs=68.4

Q ss_pred             CCCCEECCCCCCCHHHHHHHHHHHHCCCEEEEEECHHHHCCCCCCCCCEEEEECHHHCCHHHHHHHHHCCCCCC
Q ss_conf             37103120146998999999999755986999980034104688876589985852547468877301166789
Q gi|254780945|r  514 FTSSIAIIHGRMSDIDKESVMDSFKNGTCKLLIATTVIEVGIDVVDASIIIIENAEHFGLAQLHQLRGRVGRGE  587 (700)
Q Consensus       514 ~~~~v~~lHGkm~~~ek~~~m~~F~~g~~~iLvaTtviEVGvdvpna~~mvI~~aerfGLsqLHQLRGRVGRg~  587 (700)
                      .+-++..+||+|+.+|+++++++|++|+.+|||||.+.+.|+|+|+++++|+.++. +-.+++.|-.||+||.+
T Consensus         6 ~g~~~~~i~g~~~~~~R~~~~~~f~~~~~~ilv~t~~~~~Gid~~~~~~vi~~~~~-~s~~~~~Q~~GR~~R~g   78 (78)
T pfam00271         6 PGIKVARLHGGLSQEEREEILEDFRNGKSKVLVATDVAGRGIDLPDVNVVINYDLP-WNPASYIQRIGRAGRAG   78 (78)
T ss_pred             CCCCEEEEECCCCHHHHHHHHHHHHCCCCEEEEEECCCCCCCCCCCCCEEEEECCC-CCHHHHHHHHCCCCCCC
T ss_conf             89859998697999999999999987997399992565256778789999997899-69899999972687799


No 90 
>KOG0947 consensus
Probab=99.14  E-value=4.7e-08  Score=82.75  Aligned_cols=357  Identities=22%  Similarity=0.293  Sum_probs=222.4

Q ss_pred             HHHHHHHHHCCCCCCHHHHHHHHHHHHHHCCCCCCEEEEEECCCCCHHHHHHHHHHHHHHHHCCEEEEEHHHHHHHHHHH
Q ss_conf             78999986302467988999999999841001343078862144223699999973344430545886127999999998
Q gi|254780945|r  260 KIAQKILRNIPFSPTKSQESAIKDILQDMSQKNRMLRILQGDVGSGKTLVALIAMAAAVEAGGQAVIMAPIGILAQQHYE  339 (700)
Q Consensus       260 ~~~~~f~~~LPF~LT~~Q~~ai~eI~~Dl~~~~pM~RLLQGDVGSGKTiVA~~A~l~~~~~G~Q~alMaPTEILA~QH~~  339 (700)
                      .++.+.....||+|-+=|+.||.-...-    .  .-.+-.-.-||||+||-.|++.+...+..+.+-+|---|..|-|.
T Consensus       285 ~lVpe~a~~~pFelD~FQk~Ai~~lerg----~--SVFVAAHTSAGKTvVAEYAialaq~h~TR~iYTSPIKALSNQKfR  358 (1248)
T KOG0947         285 QLVPEMALIYPFELDTFQKEAIYHLERG----D--SVFVAAHTSAGKTVVAEYAIALAQKHMTRTIYTSPIKALSNQKFR  358 (1248)
T ss_pred             HHCHHHHHHCCCCCCHHHHHHHHHHHCC----C--EEEEEECCCCCCCHHHHHHHHHHHHHCCCEEECCHHHHHCCCHHH
T ss_conf             8440688618877667899999999727----8--179971377884369999999988635515752634654001578


Q ss_pred             HHHHHCCCCCCEEEEEECCCCHHHHHHHHHHHCCCCCEEEEECHHHC-----CCCCCCCCCCEEEECCCCCCCHHHHHHH
Q ss_conf             62110145786589962464225667687762134754864111201-----3345544441788521013356889987
Q gi|254780945|r  340 FIKKYTQNTQIIVEIITGNMPQAHRRKALERIAHGQAHIIIGTHALF-----QDSIQYYKLILVIVDEQHRFGVQQRLKL  414 (700)
Q Consensus       340 ~~~~~~~~~~i~v~lLtg~~~~~er~~i~~~i~~G~~~iiIGTHAL~-----q~~v~F~~LgLvViDEQHRFGV~QR~~L  414 (700)
                      -|+.-|+.-|    ||||...-           +-++.++|=|.-++     +..=.-.++-.||.||=|=--=.-|-..
T Consensus       359 DFk~tF~Dvg----LlTGDvqi-----------nPeAsCLIMTTEILRsMLYrgadliRDvE~VIFDEVHYiND~eRGvV  423 (1248)
T KOG0947         359 DFKETFGDVG----LLTGDVQI-----------NPEASCLIMTTEILRSMLYRGADLIRDVEFVIFDEVHYINDVERGVV  423 (1248)
T ss_pred             HHHHHCCCCC----EEECCEEE-----------CCCCCEEEEHHHHHHHHHHCCCCHHHCCCEEEEEEEEECCCCCCCCC
T ss_conf             8877426665----45144332-----------77754676569999998751554321133698740354144135622


Q ss_pred             HHC-----CCCCCCEEECHHHHHHHHHHHHH-HCC---CHHHHCCCCCCCCCCEEEEEECC-------------------
Q ss_conf             402-----56776101010132278999975-201---01111023557666207999702-------------------
Q gi|254780945|r  415 TQK-----ATAPHVLLMTATPIPRTLVLTSL-GDI---DISKITEKPAGRKPIKTVIIPIN-------------------  466 (700)
Q Consensus       415 ~~K-----g~~ph~L~MtATPIPRTLal~~y-gdl---dvS~i~e~P~gR~~I~T~~~~~~-------------------  466 (700)
                      ++.     -.+..+..+||| +|-|+-.+-+ |-.   .+-+|.+ +.--.|..-++....                   
T Consensus       424 WEEViIMlP~HV~~IlLSAT-VPN~~EFA~WIGRtK~K~IyViST-~kRPVPLEh~l~t~~~l~kiidq~g~fl~~~~~~  501 (1248)
T KOG0947         424 WEEVIIMLPRHVNFILLSAT-VPNTLEFADWIGRTKQKTIYVIST-SKRPVPLEHYLYTKKSLFKIIDQNGIFLLKGIKD  501 (1248)
T ss_pred             CEEEEEECCCCCEEEEEECC-CCCHHHHHHHHHHCCCCEEEEEEC-CCCCCCEEEEEEECCCEEHHHCCCCHHHHHCCHH
T ss_conf             10122532554159998465-798188888750404853899714-7886430789986663100015441435530101


Q ss_pred             -----------------------------------------------CHH-HHHHHHHHHHCCCCEE---EEEE------
Q ss_conf             -----------------------------------------------002-6899997631038738---9997------
Q gi|254780945|r  467 -----------------------------------------------RID-EVIERLKVVLSEGKKA---YWIC------  489 (700)
Q Consensus       467 -----------------------------------------------~~~-~~~~~i~~~l~~g~q~---y~Vc------  489 (700)
                                                                     +++ ..|-.+-..+.+..|-   .+|.      
T Consensus       502 a~~~~~~~ak~~~~~~~~~~~~rgs~~~ggk~~~~~g~~r~~~~~~nrr~~~~~l~lin~L~k~~lLP~VvFvFSkkrCd  581 (1248)
T KOG0947         502 AKDSLKKEAKFVDVEKSDARGGRGSQKRGGKTNYHNGGSRGSGIGKNRRKQPTWLDLINHLRKKNLLPVVVFVFSKKRCD  581 (1248)
T ss_pred             HHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHCCCCCEEEEEECCCCHH
T ss_conf             11122244443313254454666554667767888887666665432344440999999985224676699997356578


Q ss_pred             ---------CCCCCCCCCCCCHHHH-HHHHHH-------------HHCCCCEECCCCCCCHHHHHHHHHHHHCCCEEEEE
Q ss_conf             ---------1201221112101466-666668-------------66371031201469989999999997559869999
Q gi|254780945|r  490 ---------PQIEEKKESNFRSVVE-RFNSLH-------------EHFTSSIAIIHGRMSDIDKESVMDSFKNGTCKLLI  546 (700)
Q Consensus       490 ---------PlIeese~~~~~~~~~-~~~~l~-------------~~~~~~v~~lHGkm~~~ek~~~m~~F~~g~~~iLv  546 (700)
                               -|-+++|+.+.+=.-+ ...+|+             +..-..++.-||-+=+--|+-|=.=|..|=++||.
T Consensus       582 e~a~~L~~~nL~~~~EKseV~lfl~k~~~rLk~~DR~LPQvl~m~~ll~RGiaVHH~GlLPivKE~VE~LFqrGlVKVLF  661 (1248)
T KOG0947         582 EYADYLTNLNLTDSKEKSEVHLFLSKAVARLKGEDRNLPQVLSMRSLLLRGIAVHHGGLLPIVKEVVELLFQRGLVKVLF  661 (1248)
T ss_pred             HHHHHHHCCCCCCCHHHHHHHHHHHHHHHHCCHHHCCCHHHHHHHHHHHHCCHHHCCCCHHHHHHHHHHHHHCCCEEEEE
T ss_conf             99999755576652127899999999998668543143377889999861403303663078999999997558547886


Q ss_pred             ECHHHHCCCCCCCCCEEEE-----ECHHH--CCHHHHHHHHHCCCCCC--CCEEEEEEECCC-CCHHH------------
Q ss_conf             8003410468887658998-----58525--47468877301166789--835999970888-99879------------
Q gi|254780945|r  547 ATTVIEVGIDVVDASIIII-----ENAEH--FGLAQLHQLRGRVGRGE--EISSCILLYHPP-LSKNS------------  604 (700)
Q Consensus       547 aTtviEVGvdvpna~~mvI-----~~aer--fGLsqLHQLRGRVGRg~--~~s~c~l~~~~~-~~~~~------------  604 (700)
                      ||----.|||.|--|+..=     .+-++  .+=--+-|.-||-||-+  ..|+.++++.+. .+...            
T Consensus       662 ATETFAMGVNMPARtvVF~Sl~KhDG~efR~L~PGEytQMAGRAGRRGlD~tGTVii~~~~~vp~~a~l~~li~G~~~~L  741 (1248)
T KOG0947         662 ATETFAMGVNMPARTVVFSSLRKHDGNEFRELLPGEYTQMAGRAGRRGLDETGTVIIMCKDSVPSAATLKRLIMGGPTRL  741 (1248)
T ss_pred             EHHHHHHHCCCCCEEEEEEEHHHCCCCCEEECCCHHHHHHHCCCCCCCCCCCCEEEEEECCCCCCHHHHHHHHCCCCCHH
T ss_conf             41056511688740677330001368642543870577641102445668676089996688999899865750787200


Q ss_pred             --HHHHH--HHHHHCHHHHHHHHHHHHCCCCCCCCCHHC
Q ss_conf             --99999--998414258999999852063000260006
Q gi|254780945|r  605 --YTRLS--VLKNTEDGFLIAEEDLKQRKEGEILGIKQS  639 (700)
Q Consensus       605 --~~Rl~--~l~~~~dGf~iAe~Dl~lRG~G~~~G~~Qs  639 (700)
                        +-||.  .+-+.--+=.+--+||--|.+|+.-..+-+
T Consensus       742 ~SQFRlTY~MILnLLRve~lrvEdm~krSf~E~~s~~~~  780 (1248)
T KOG0947         742 ESQFRLTYGMILNLLRVEALRVEDMMKRSFSEFVSQRLS  780 (1248)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC
T ss_conf             445445799999998777889999999876310231017


No 91 
>PRK12906 secA preprotein translocase subunit SecA; Reviewed
Probab=99.08  E-value=7.4e-09  Score=89.04  Aligned_cols=280  Identities=20%  Similarity=0.248  Sum_probs=183.6

Q ss_pred             CCCCCHHHHHHHHHHHHHHHHCCEEEEEHHHHHHHHHHHHHHHHCCCCCCEEEEEECCCCHHHHHHHHHHHCCCCCEEEE
Q ss_conf             14422369999997334443054588612799999999862110145786589962464225667687762134754864
Q gi|254780945|r  301 DVGSGKTLVALIAMAAAVEAGGQAVIMAPIGILAQQHYEFIKKYTQNTQIIVEIITGNMPQAHRRKALERIAHGQAHIII  380 (700)
Q Consensus       301 DVGSGKTiVA~~A~l~~~~~G~Q~alMaPTEILA~QH~~~~~~~~~~~~i~v~lLtg~~~~~er~~i~~~i~~G~~~iiI  380 (700)
                      ..|-|||+||.++++..+-+|..|-+....+-||+--++...+.+.-+|++|.+.++.++..+|++.+.      +||+-
T Consensus       101 ~TGEGKTL~atlp~ylnaL~GkgvhvvTvNdYLA~RDae~m~~vy~~lGltvg~i~~~~~~~err~aY~------~DItY  174 (823)
T PRK12906        101 RTGEGKTLTATLPVYLNALEGKGVHVVTVNEYLAKRDATEMGELYRWLGLTVGLNLNDMSPDEKREAYN------CDITY  174 (823)
T ss_pred             CCCCCHHHHHHHHHHHHHHCCCCEEEEECCHHHHHHHHHHHHHHHHHCCCEEEEECCCCCHHHHHHHHC------CCCEE
T ss_conf             068858999999999986469980898054465586799999999980966712089999899999850------78446


Q ss_pred             ECHHHCC-----C-------CCCCCCCCEEEECCCCC-------------------------------------------
Q ss_conf             1112013-----3-------45544441788521013-------------------------------------------
Q gi|254780945|r  381 GTHALFQ-----D-------SIQYYKLILVIVDEQHR-------------------------------------------  405 (700)
Q Consensus       381 GTHAL~q-----~-------~v~F~~LgLvViDEQHR-------------------------------------------  405 (700)
                      ||..=|-     |       +..-..+-.+||||=--                                           
T Consensus       175 ~Tn~e~gFDYLRDnm~~~~~~~vqr~~~~aIvDEvDSiLIDEArtPLIISg~~~~~~~~y~~~~~~v~~l~~~~~~~~~~  254 (823)
T PRK12906        175 STNSELGFDYLRDNMVVYKEQMVQRPLNYAIVDEVDSILIDEARTPLIISGPAEGASDLYIRADRFVKTLTKDEDDDADD  254 (823)
T ss_pred             ECCCCEECCCCCCCCCCCHHHHCCCCCCEEEEECHHHHHHHCCCCCEEEECCCCCCCHHHHHHHHHHHHHHHHHHHCCCC
T ss_conf             25655021113544126888834788855898541465432356762662577555358999999999998634311233


Q ss_pred             ------CCHHHHHH---HHHCC----------------------------------------------------------
Q ss_conf             ------35688998---74025----------------------------------------------------------
Q gi|254780945|r  406 ------FGVQQRLK---LTQKA----------------------------------------------------------  418 (700)
Q Consensus       406 ------FGV~QR~~---L~~Kg----------------------------------------------------------  418 (700)
                            |-|..+.+   |.++|                                                          
T Consensus       255 ~~~~~dy~id~~~~~v~lt~~G~~~~e~~~~~~~ly~~~~~~~~~~i~~aL~A~~lf~~d~dYiV~d~~V~ivDe~TGR~  334 (823)
T PRK12906        255 DEDHGDYKIDEPSKTVSLTEEGIEKAEKLLGLDNLYDPENQALVHHIDQALRANYLMLKDKDYIVQNGEVLIVDEFTGRV  334 (823)
T ss_pred             CCCCCCEEEECCCCEEEEEHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCEEEECCCEEEEECCCCCC
T ss_conf             47777758742546677517799998860488877883110599999999999999857985899889189987888886


Q ss_pred             ---------------------------------------CCCCCEEECHHHHHHHHHHHHHHCCCHHHHC-CCCCCCCCC
Q ss_conf             ---------------------------------------6776101010132278999975201011110-235576662
Q gi|254780945|r  419 ---------------------------------------TAPHVLLMTATPIPRTLVLTSLGDIDISKIT-EKPAGRKPI  458 (700)
Q Consensus       419 ---------------------------------------~~ph~L~MtATPIPRTLal~~ygdldvS~i~-e~P~gR~~I  458 (700)
                                                             ..+.+==||.|--.-.--+.--=+|+|..|. .+|.-|+.-
T Consensus       335 m~gRr~s~GLHQAiEaKE~v~i~~e~~tlA~IT~QnfFr~Y~kLsGMTGTA~te~~Ef~~iY~l~Vv~IPTn~P~~R~d~  414 (823)
T PRK12906        335 MEGRRYSDGLHQAIEAKEGVEIQNENQTLATITYQNYFRLYKKLSGMTGTAKTEEEEFREIYNMDVITIPTNRPVIRVDL  414 (823)
T ss_pred             CCCCCCCHHHHHHHHHHCCCCCCCCCCEEEEEEHHHHHHHCHHHCCCCCCCHHHHHHHHHHHCCCEEECCCCCCCEEEEC
T ss_conf             89992664679999987288778887303676699998646253167677687899999986886187179998511507


Q ss_pred             EEEEEEC--CCHHHHHHHHHHHHCCCCEEEEEECCCCCCCCCCCCHHHHHHHHHHHHCCCCEECCCCCCCHHHHHHHHHH
Q ss_conf             0799970--20026899997631038738999712012211121014666666686637103120146998999999999
Q gi|254780945|r  459 KTVIIPI--NRIDEVIERLKVVLSEGKKAYWICPQIEEKKESNFRSVVERFNSLHEHFTSSIAIIHGRMSDIDKESVMDS  536 (700)
Q Consensus       459 ~T~~~~~--~~~~~~~~~i~~~l~~g~q~y~VcPlIeese~~~~~~~~~~~~~l~~~~~~~v~~lHGkm~~~ek~~~m~~  536 (700)
                      ...+...  ++...+.+.|++.-++|+-|-|-+.-||.||.+        .+.|++. +-...+|+.|-.  ++|+.+=+
T Consensus       415 ~d~iy~t~~~K~~Ai~~ei~~~~~~gqPvLvGT~SVe~SE~l--------s~~L~~~-gi~h~vLNAk~~--~~EA~IIa  483 (823)
T PRK12906        415 PDLLYPTLDSKFNAVVDDIKERHAKGQPVLVGTVSIESSERL--------SQLLDKA-GIPHAVLNAKNH--AKEAEIIA  483 (823)
T ss_pred             CCCCCCCHHHHHHHHHHHHHHHHHCCCCEEEEECCHHHHHHH--------HHHHHHC-CCCHHHHCCCCH--HHHHHHHH
T ss_conf             434647999999999999999986799889971758999999--------9999976-870353068775--78999998


Q ss_pred             HHCCCEEEEEECHHHHCCCCCCC-----------------------------------CCEEEEECHHHCCHHHH-HHHH
Q ss_conf             75598699998003410468887-----------------------------------65899858525474688-7730
Q gi|254780945|r  537 FKNGTCKLLIATTVIEVGIDVVD-----------------------------------ASIIIIENAEHFGLAQL-HQLR  580 (700)
Q Consensus       537 F~~g~~~iLvaTtviEVGvdvpn-----------------------------------a~~mvI~~aerfGLsqL-HQLR  580 (700)
                      =.-..-.|-|||.+---|.|+.=                                   +--.-|...||.--+-. -|||
T Consensus       484 ~AG~~GaVTIATNMAGRGTDI~LGg~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~V~~~GGL~VIgTErheSrRIDnQLr  563 (823)
T PRK12906        484 QAGQRGAVTIATNMAGRGTDIKLGGNPFEDIEAYQEAWIRELPKMKQRCEERRDKVRELGGLAVIGTERHESRRIDNQLR  563 (823)
T ss_pred             HCCCCCEEEEECCCCCCCCCEEECCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHH
T ss_conf             34899938970655689879630897302134332224667888888776556899973893798504440256787872


Q ss_pred             HCCCCCCCCEEEEEEEC
Q ss_conf             11667898359999708
Q gi|254780945|r  581 GRVGRGEEISSCILLYH  597 (700)
Q Consensus       581 GRVGRg~~~s~c~l~~~  597 (700)
                      ||-||-+.+|..-+..+
T Consensus       564 GRaGRQGDPGss~F~lS  580 (823)
T PRK12906        564 GRSGRQGDPGSTRFYLS  580 (823)
T ss_pred             CCCCCCCCCCCCEEEEE
T ss_conf             32134799985237653


No 92 
>KOG0948 consensus
Probab=99.07  E-value=1.8e-09  Score=93.84  Aligned_cols=328  Identities=22%  Similarity=0.345  Sum_probs=214.6

Q ss_pred             HHHCCCCCCHHHHHHHHHHHHHHCCCCCCEEEEEECCCCCHHHHHHHHHHHHHHHHCCEEEEEHHHHHHHHHHHHHHHHC
Q ss_conf             86302467988999999999841001343078862144223699999973344430545886127999999998621101
Q gi|254780945|r  266 LRNIPFSPTKSQESAIKDILQDMSQKNRMLRILQGDVGSGKTLVALIAMAAAVEAGGQAVIMAPIGILAQQHYEFIKKYT  345 (700)
Q Consensus       266 ~~~LPF~LT~~Q~~ai~eI~~Dl~~~~pM~RLLQGDVGSGKTiVA~~A~l~~~~~G~Q~alMaPTEILA~QH~~~~~~~~  345 (700)
                      -+..||+|-.=|..||.-|.++-      .-|+-.-.-+|||+||-.|++.++.+...|.+-.|---|..|-|+.+..-|
T Consensus       123 Ak~YPF~LDpFQ~~aI~Cidr~e------SVLVSAHTSAGKTVVAeYAIA~sLr~kQRVIYTSPIKALSNQKYREl~~EF  196 (1041)
T KOG0948         123 AKTYPFTLDPFQSTAIKCIDRGE------SVLVSAHTSAGKTVVAEYAIAMSLREKQRVIYTSPIKALSNQKYRELLEEF  196 (1041)
T ss_pred             CCCCCCCCCCHHHHHHHHHCCCC------EEEEEEECCCCCCHHHHHHHHHHHHHCCEEEEECHHHHHCCHHHHHHHHHH
T ss_conf             35788434806765453112796------389984057885237999999998764858960731554115489999884


Q ss_pred             CCCCCEEEEEECCCCHHHHHHHHHHHCCCCCEEEEECHHH----C-CCCCCCCCCCEEEECCCCCCCHHHHHHHHHC---
Q ss_conf             4578658996246422566768776213475486411120----1-3345544441788521013356889987402---
Q gi|254780945|r  346 QNTQIIVEIITGNMPQAHRRKALERIAHGQAHIIIGTHAL----F-QDSIQYYKLILVIVDEQHRFGVQQRLKLTQK---  417 (700)
Q Consensus       346 ~~~~i~v~lLtg~~~~~er~~i~~~i~~G~~~iiIGTHAL----~-q~~v~F~~LgLvViDEQHRFGV~QR~~L~~K---  417 (700)
                      .    -|.|.||..+-.           -.+..+|=|.-+    + -..=..+-.+-||.||=|=--=..|-..++.   
T Consensus       197 ~----DVGLMTGDVTIn-----------P~ASCLVMTTEILRsMLYRGSEvmrEVaWVIFDEIHYMRDkERGVVWEETII  261 (1041)
T KOG0948         197 K----DVGLMTGDVTIN-----------PDASCLVMTTEILRSMLYRGSEVMREVAWVIFDEIHYMRDKERGVVWEETII  261 (1041)
T ss_pred             C----CCCEEECCEEEC-----------CCCCEEEEHHHHHHHHHHCCCHHHHEEEEEEEEEEHHCCCCCCCEEEEEEEE
T ss_conf             6----365230544668-----------9875453379999998743316755231488620010013445602356678


Q ss_pred             --CCCCCCEEECHHHHHHHHHHHHHHCCCHHHHCCCCCC------C-CCCEEEEEE-----------CC------CHHHH
Q ss_conf             --5677610101013227899997520101111023557------6-662079997-----------02------00268
Q gi|254780945|r  418 --ATAPHVLLMTATPIPRTLVLTSLGDIDISKITEKPAG------R-KPIKTVIIP-----------IN------RIDEV  471 (700)
Q Consensus       418 --g~~ph~L~MtATPIPRTLal~~ygdldvS~i~e~P~g------R-~~I~T~~~~-----------~~------~~~~~  471 (700)
                        ..+.++..+||| ||--+-.+-+    |+-|..-|..      | .|..-++.+           .+      +..++
T Consensus       262 llP~~vr~VFLSAT-iPNA~qFAeW----I~~ihkQPcHVVYTdyRPTPLQHyifP~ggdGlylvVDek~~FrednF~~a  336 (1041)
T KOG0948         262 LLPDNVRFVFLSAT-IPNARQFAEW----ICHIHKQPCHVVYTDYRPTPLQHYIFPAGGDGLYLVVDEKGKFREDNFQKA  336 (1041)
T ss_pred             ECCCCCEEEEEECC-CCCHHHHHHH----HHHHHCCCCEEEEECCCCCCCEEEEECCCCCEEEEEEECCCCCCHHHHHHH
T ss_conf             53666038999565-8777999999----999755874289505878864144530799806999705664226779999


Q ss_pred             HHHH-----------------------------------HHHHCCCCEEEEEECCC-CCC-------CCCCCC------H
Q ss_conf             9999-----------------------------------76310387389997120-122-------111210------1
Q gi|254780945|r  472 IERL-----------------------------------KVVLSEGKKAYWICPQI-EEK-------KESNFR------S  502 (700)
Q Consensus       472 ~~~i-----------------------------------~~~l~~g~q~y~VcPlI-ees-------e~~~~~------~  502 (700)
                      .+.+                                   +-.+.+.-.--+|...= -|-       .++|+.      .
T Consensus       337 m~~l~~~~~~~~~~~~~~k~~kG~~~~~~~~~s~i~kiVkmi~~~~~~PVIvFSFSkkeCE~~Alqm~kldfN~deEk~~  416 (1041)
T KOG0948         337 MSVLRKAGESDGKKKANKKGRKGGTGGKGPGDSDIYKIVKMIMERNYLPVIVFSFSKKECEAYALQMSKLDFNTDEEKEL  416 (1041)
T ss_pred             HHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHCCCCEEEEEECHHHHHHHHHHHCCCCCCCHHHHHH
T ss_conf             99763257786444555445657767889874319999999996268966999814767999997651576788568889


Q ss_pred             HHHHHHHH--------------HHHCCC---CEECCCCCCCHHHHHHHHHHHHCCCEEEEEECHHHHCCCCCCCCCEEEE
Q ss_conf             46666666--------------866371---0312014699899999999975598699998003410468887658998
Q gi|254780945|r  503 VVERFNSL--------------HEHFTS---SIAIIHGRMSDIDKESVMDSFKNGTCKLLIATTVIEVGIDVVDASIIII  565 (700)
Q Consensus       503 ~~~~~~~l--------------~~~~~~---~v~~lHGkm~~~ek~~~m~~F~~g~~~iLvaTtviEVGvdvpna~~mvI  565 (700)
                      |++.|+.-              ...+|-   .||+-|+-+=+--||-|=--|.+|=+++|-||----.|+|.|.-|+ |-
T Consensus       417 V~~iF~nAi~~LseeDr~LPqie~iLPLL~RGIGIHHsGLLPIlKE~IEILFqEGLvKvLFATETFsiGLNMPAkTV-vF  495 (1041)
T KOG0948         417 VETIFNNAIDQLSEEDRELPQIENILPLLRRGIGIHHSGLLPILKEVIEILFQEGLVKVLFATETFSIGLNMPAKTV-VF  495 (1041)
T ss_pred             HHHHHHHHHHHCCHHHCCCHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHCCHHHHHHHHHHHHHCCCCCCEEE-EE
T ss_conf             99999999985485331551788889998735543445504789999999985027988775412310058864058-87


Q ss_pred             ECHHHCCHHH--------HHHHHHCCCCC--CCCEEEEEEECCCCCHHHHHHHHHHHHHC----HHHHHHH
Q ss_conf             5852547468--------87730116678--98359999708889987999999998414----2589999
Q gi|254780945|r  566 ENAEHFGLAQ--------LHQLRGRVGRG--EEISSCILLYHPPLSKNSYTRLSVLKNTE----DGFLIAE  622 (700)
Q Consensus       566 ~~aerfGLsq--------LHQLRGRVGRg--~~~s~c~l~~~~~~~~~~~~Rl~~l~~~~----dGf~iAe  622 (700)
                      -++-.|-=.+        --|.-||-||-  +..|-|+|+.+.+.++..-++|  +.-+.    .-|.+.-
T Consensus       496 T~~rKfDG~~fRwissGEYIQMSGRAGRRG~DdrGivIlmiDekm~~~~ak~m--~kG~aD~LnSaFhLtY  564 (1041)
T KOG0948         496 TAVRKFDGKKFRWISSGEYIQMSGRAGRRGIDDRGIVILMIDEKMEPQVAKDM--LKGSADPLNSAFHLTY  564 (1041)
T ss_pred             EECCCCCCCCEEEECCCCEEEECCCCCCCCCCCCCEEEEEECCCCCHHHHHHH--HCCCCCCHHHHHHHHH
T ss_conf             40111478640453366357741534556778775299995676797899998--6388741053664579


No 93 
>PRK12326 preprotein translocase subunit SecA; Reviewed
Probab=99.07  E-value=1.6e-08  Score=86.40  Aligned_cols=287  Identities=21%  Similarity=0.282  Sum_probs=178.7

Q ss_pred             EEEEEC-----CCCCHHHHHHHHHHHHHHHHCCEEEEEHHHHHHHHHHHHHHHHCCCCCCEEEEEECCCCHHHHHHHHHH
Q ss_conf             788621-----442236999999733444305458861279999999986211014578658996246422566768776
Q gi|254780945|r  296 RILQGD-----VGSGKTLVALIAMAAAVEAGGQAVIMAPIGILAQQHYEFIKKYTQNTQIIVEIITGNMPQAHRRKALER  370 (700)
Q Consensus       296 RLLQGD-----VGSGKTiVA~~A~l~~~~~G~Q~alMaPTEILA~QH~~~~~~~~~~~~i~v~lLtg~~~~~er~~i~~~  370 (700)
                      .|++|+     .|-|||+||.++++..+-+|..|-+....+-||+--.+...+++.-+|++|.++++.++..+|++.|. 
T Consensus       100 ~L~~G~IaEM~TGEGKTL~atlpaylnAL~GkgVHvVTvNDYLA~RDaewm~piy~fLGLtvg~i~~~~~~~err~aY~-  178 (775)
T PRK12326        100 RLLAGDVVEMATGEGKTLAGAIAAAGYALGGRRVHVITVNDYLARRDAEWMGPLLEAFGLTVGWITEESTAEERRAAYA-  178 (775)
T ss_pred             HHHCCCEEEEECCCCHHHHHHHHHHHHHHCCCCCEEEECCHHHHHHHHHHHHHHHHHHCCEECCCCCCCCHHHHHHHCC-
T ss_conf             9845953676068858999999999996369980898225687887699999999982977653789999799998446-


Q ss_pred             HCCCCCEEEEECHHHCC------------CCCCCCCCCEEEECCCC----------------------------------
Q ss_conf             21347548641112013------------34554444178852101----------------------------------
Q gi|254780945|r  371 IAHGQAHIIIGTHALFQ------------DSIQYYKLILVIVDEQH----------------------------------  404 (700)
Q Consensus       371 i~~G~~~iiIGTHAL~q------------~~v~F~~LgLvViDEQH----------------------------------  404 (700)
                           +||+-||..=|-            ++..-..+-.+||||=-                                  
T Consensus       179 -----~DItY~Tn~E~GFDYLRDnm~~~~~~~vqr~~~faIVDEvDSILIDEArTPLIISG~~~~~~~~~~~~~~v~~L~  253 (775)
T PRK12326        179 -----CDVTYASVNEIGFDVLRDQLVTDVADLVSPNPDVAIIDEADSVLVDEALVPLVLAGTTHRETPRGEIIRLVRELK  253 (775)
T ss_pred             -----CCCCCCCCCCCCCCCCHHHHCCCHHHHCCCCCCEEEEECCCHHHHHCCCCCEEECCCCCCCCHHHHHHHHHHHCC
T ss_conf             -----877311555532445513212698884367787599864200012135777065089877664999999998567


Q ss_pred             --------------------------------------------------------------------------------
Q ss_conf             --------------------------------------------------------------------------------
Q gi|254780945|r  405 --------------------------------------------------------------------------------  404 (700)
Q Consensus       405 --------------------------------------------------------------------------------  404 (700)
                                                                                                      
T Consensus       254 ~~~dy~iDe~~k~v~LTe~G~~~vE~~l~~~~ly~~~~~~~~l~~v~~AL~A~~l~~rDvdYIV~dg~V~IVDe~TGR~m  333 (775)
T PRK12326        254 EGKDYTTDEDRRNVHLTDKGARKVEKALGGIDLYSEEHVGTTLTEVNVALHAHVLLQRDVHYIVRDGAVHLINASRGRIA  333 (775)
T ss_pred             CCCCEEEECCCCEEEECCCHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHCCCCEEEECCEEEEEECCCCCCC
T ss_conf             88887985476644225138999999708876467321789999999999899988579747998786899516778767


Q ss_pred             ---CC--CHHHHHHHHHC------C-------------CCCCCEEECHHHHHHHHHHHHHHCCCHHHHC-CCCCCCCCCE
Q ss_conf             ---33--56889987402------5-------------6776101010132278999975201011110-2355766620
Q gi|254780945|r  405 ---RF--GVQQRLKLTQK------A-------------TAPHVLLMTATPIPRTLVLTSLGDIDISKIT-EKPAGRKPIK  459 (700)
Q Consensus       405 ---RF--GV~QR~~L~~K------g-------------~~ph~L~MtATPIPRTLal~~ygdldvS~i~-e~P~gR~~I~  459 (700)
                         |+  |.+|=..-.+.      +             ..|.+==||-|--.-.--+.-.=+|+|..|. .+|.-|+.-.
T Consensus       334 ~gRrwsdGLHQAiEAKEgv~i~~e~~tlAsIT~Qn~Fr~Y~kLsGMTGTA~t~~~Ef~~iY~L~V~~IPtn~P~~R~D~~  413 (775)
T PRK12326        334 QLQRWPDGLQAAVEAKEGLETTETGEVLDTITVQALINRYPTVCGMTGTALAAGEQLRQFYKLGVSVIPPNKPNIREDEA  413 (775)
T ss_pred             CCCCCCCCHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHCCCEEEECCCCCCEEEECC
T ss_conf             89846730679999964987688873145427999997522753777761669999999748865991799984104588


Q ss_pred             EEEEEC--CCHHHHHHHHHHHHCCCCEEEEEECCCCCCCCCCCCHHHHHHHHHHHHCCCCEECCCCCCCHHHHHHHHHHH
Q ss_conf             799970--200268999976310387389997120122111210146666666866371031201469989999999997
Q gi|254780945|r  460 TVIIPI--NRIDEVIERLKVVLSEGKKAYWICPQIEEKKESNFRSVVERFNSLHEHFTSSIAIIHGRMSDIDKESVMDSF  537 (700)
Q Consensus       460 T~~~~~--~~~~~~~~~i~~~l~~g~q~y~VcPlIeese~~~~~~~~~~~~~l~~~~~~~v~~lHGkm~~~ek~~~m~~F  537 (700)
                      ..++..  ++...+.+.|++.-+.|+-|-|-+.-|++||.+        .+.|++. +-...+|.-|-...|-+-|-++=
T Consensus       414 D~vy~t~~~K~~Avv~ei~~~h~~GqPVLVGT~SVe~SE~l--------s~~L~~~-gi~h~VLNAk~~~~EA~IIA~AG  484 (775)
T PRK12326        414 DRVYATAAEKNDAIVEHIAEVHETGQPVLVGTRDVAESEEL--------AERLVRR-GVPAVVLNAKNDAEEAAVIAEAG  484 (775)
T ss_pred             CEEECCHHHHHHHHHHHHHHHHHCCCCEEEEECCHHHHHHH--------HHHHHHC-CCCCEECCCCCHHHHHHHHHHCC
T ss_conf             81646999999999999999997599889970718989999--------9999876-99830236897276999999459


Q ss_pred             HCCCEEEEEECHHHHCCCCCCC-------------CCEEEEECHHHCCHHHH-HHHHHCCCCCCCCEEEEEEECCC
Q ss_conf             5598699998003410468887-------------65899858525474688-77301166789835999970888
Q gi|254780945|r  538 KNGTCKLLIATTVIEVGIDVVD-------------ASIIIIENAEHFGLAQL-HQLRGRVGRGEEISSCILLYHPP  599 (700)
Q Consensus       538 ~~g~~~iLvaTtviEVGvdvpn-------------a~~mvI~~aerfGLsqL-HQLRGRVGRg~~~s~c~l~~~~~  599 (700)
                      +.|  .|-|||.+---|.|+.=             +--.-|...||.--+-+ -|||||-||-+.+|..-+..+-+
T Consensus       485 ~~G--aVTIATNMAGRGTDIkLGg~~e~~~~~V~elGGL~VIgterheSrRIDnQLrGRaGRQGDPGsS~FflSLE  558 (775)
T PRK12326        485 KYG--AVTVSTQMAGRGTDIRLGGSDEADHDRVVELGGLHVVGTGRHRSQRLDNQLRGRAGRQGDPGSSVFFVSWE  558 (775)
T ss_pred             CCC--CEEEECCCCCCCCCEECCCCCHHHHHHHHHCCCEEEEECCCCHHHHHHHHHHCCCCCCCCCCCCEEEEEEC
T ss_conf             999--87982336789868414897223247898659907852143334677867622312379998615899703


No 94 
>PRK09200 preprotein translocase subunit SecA; Reviewed
Probab=99.06  E-value=5e-08  Score=82.52  Aligned_cols=278  Identities=20%  Similarity=0.247  Sum_probs=181.5

Q ss_pred             CCCCCHHHHHHHHHHHHHHHHCCEEEEEHHHHHHHHHHHHHHHHCCCCCCEEEEEECCC-----CHHHHHHHHHHHCCCC
Q ss_conf             14422369999997334443054588612799999999862110145786589962464-----2256676877621347
Q gi|254780945|r  301 DVGSGKTLVALIAMAAAVEAGGQAVIMAPIGILAQQHYEFIKKYTQNTQIIVEIITGNM-----PQAHRRKALERIAHGQ  375 (700)
Q Consensus       301 DVGSGKTiVA~~A~l~~~~~G~Q~alMaPTEILA~QH~~~~~~~~~~~~i~v~lLtg~~-----~~~er~~i~~~i~~G~  375 (700)
                      -.|-|||+||.++++..+-+|.-|-+....+-||+--++...+++.-+|++|.+..+.+     +..+|++.+.      
T Consensus        99 ~TGEGKTL~a~l~~~l~al~g~~vhvvTvNdYLA~RDa~~m~~iy~~lGl~vg~~~~~~~~~~~~~~~r~~~Y~------  172 (799)
T PRK09200         99 QTGEGKTLTATMPLYLNALEGKGVHLITTNDYLAKRDFEEMGQVYEFLGLTVGLNFSDIDDYEYQAGEKKAIYE------  172 (799)
T ss_pred             CCCCCHHHHHHHHHHHHHHCCCCCEEEECCHHHHHHHHHHHHHHHHHCCCEEEECCCCCCCCCCCHHHHHHHHH------
T ss_conf             17885899999999999746998189800557778879999999998296583336888644379799998874------


Q ss_pred             CEEEEECHHHCC------------CCCCCCCCCEEEECCCC----------------------CCCHHHHH---------
Q ss_conf             548641112013------------34554444178852101----------------------33568899---------
Q gi|254780945|r  376 AHIIIGTHALFQ------------DSIQYYKLILVIVDEQH----------------------RFGVQQRL---------  412 (700)
Q Consensus       376 ~~iiIGTHAL~q------------~~v~F~~LgLvViDEQH----------------------RFGV~QR~---------  412 (700)
                      +||+-||.+=|.            ++..-..+-.+||||=-                      -|....+.         
T Consensus       173 ~di~Y~tn~e~gfDyLrDn~~~~~~~~v~r~~~~aivDEvDsiLiDeArtPliisg~~~~~~~~~~~~~~~~~~l~~~~d  252 (799)
T PRK09200        173 ADIIYTTNSELGFDYLRDNLADSKEDKVLRPLNYAIIDEVDSILLDEAQTPLVISGAPRVQSNLYHIAAEFVKTLEEDVD  252 (799)
T ss_pred             CCCEECCCCCCHHHHHCCCCCCCHHHCCCCCCCEEEEECHHHHHHHCCCCCCEECCCCCCCHHHHHHHHHHHHCCCCCCC
T ss_conf             77222356540034530120156765257789668985326677741356412148987652799999999852677443


Q ss_pred             ----------HHHHCC----------------------------------------------------------------
Q ss_conf             ----------874025----------------------------------------------------------------
Q gi|254780945|r  413 ----------KLTQKA----------------------------------------------------------------  418 (700)
Q Consensus       413 ----------~L~~Kg----------------------------------------------------------------  418 (700)
                                .|.++|                                                                
T Consensus       253 y~~d~~~~~v~lt~~G~~~~e~~~~~~~l~~~~~~~~~~~i~~al~A~~~~~~d~~YiV~~~~v~ivDe~TGR~~~gr~~  332 (799)
T PRK09200        253 YEFDKEKKEVWLTDQGIEKAESYFGIDNLYSEEHQVLVRHIILALRAHYLFERDVDYIVYDGEIVLIDRFTGRVLPGRKL  332 (799)
T ss_pred             EEEEHHCCCCCCCHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCEEEECCCEEEEECCCCCCCCCCCC
T ss_conf             78511006776244579999997099754765577899999999999999845862798668189987898874899826


Q ss_pred             ---------------------------------CCCCCEEECHHHHHHHHHH---HHHHCCCHHHH-CCCCCCCCCCEEE
Q ss_conf             ---------------------------------6776101010132278999---97520101111-0235576662079
Q gi|254780945|r  419 ---------------------------------TAPHVLLMTATPIPRTLVL---TSLGDIDISKI-TEKPAGRKPIKTV  461 (700)
Q Consensus       419 ---------------------------------~~ph~L~MtATPIPRTLal---~~ygdldvS~i-~e~P~gR~~I~T~  461 (700)
                                                       ..+++=-||.|-  .|-+-   .+| +|+|..| ..+|.-|+.-...
T Consensus       333 s~GlhQaiEaKE~v~i~~e~~t~a~it~Qn~Fr~y~kl~GmTGTa--~~~~~Ef~~iY-~l~v~~iPtn~p~~r~d~~d~  409 (799)
T PRK09200        333 QDGLHQAIEAKEGVEVTEENRTMASITIQNLFRMFPKLSGMTGTA--KTEEKEFFEVY-NMEVVQIPTNRPIIRIDYPDK  409 (799)
T ss_pred             CHHHHHHHHHHCCCCCCCCCCCEEEEEHHHHHHHCCHHCCCCCCC--HHHHHHHHHHH-CCCEEECCCCCCCEEEECCCC
T ss_conf             657799999870898788873126644898986472312576760--98999999986-877698899998544547430


Q ss_pred             EEEC--CCHHHHHHHHHHHHCCCCEEEEEECCCCCCCCCCCCHHHHHHHHHHHHCCCCEECCCCCCCHHHHHHHHHHHHC
Q ss_conf             9970--20026899997631038738999712012211121014666666686637103120146998999999999755
Q gi|254780945|r  462 IIPI--NRIDEVIERLKVVLSEGKKAYWICPQIEEKKESNFRSVVERFNSLHEHFTSSIAIIHGRMSDIDKESVMDSFKN  539 (700)
Q Consensus       462 ~~~~--~~~~~~~~~i~~~l~~g~q~y~VcPlIeese~~~~~~~~~~~~~l~~~~~~~v~~lHGkm~~~ek~~~m~~F~~  539 (700)
                      +...  ++...+.+.+++.-++|+-|-|.|..||.||.+   |     +.|++. +-...+|+.|-  .++|+.+=+=.-
T Consensus       410 v~~t~~~k~~av~~~v~~~~~~g~pvLvgt~sv~~Se~~---s-----~~L~~~-~i~h~vLnAk~--~~~Ea~Iia~AG  478 (799)
T PRK09200        410 VFATVDEKYKAVIEEVKERHETGRPVLIGTGSIEQSEYF---S-----KLLFEA-GIPHNLLNAKN--AAQEAQIIAEAG  478 (799)
T ss_pred             CCCCHHHHHHHHHHHHHHHHHCCCCEEEEECCHHHHHHH---H-----HHHHHC-CCCHHHCCCCC--HHHHHHHHHHCC
T ss_conf             108999999999999999985799889983857999999---9-----999865-76433205321--778999998278


Q ss_pred             CCEEEEEECHHHHCCCCCC------CCCEEEEECHHHCCHHH-HHHHHHCCCCCCCCEEEEEEECC
Q ss_conf             9869999800341046888------76589985852547468-87730116678983599997088
Q gi|254780945|r  540 GTCKLLIATTVIEVGIDVV------DASIIIIENAEHFGLAQ-LHQLRGRVGRGEEISSCILLYHP  598 (700)
Q Consensus       540 g~~~iLvaTtviEVGvdvp------na~~mvI~~aerfGLsq-LHQLRGRVGRg~~~s~c~l~~~~  598 (700)
                      ..-.|-|||..---|.|+.      .+--.-|...||.--+- --|||||-||-+.+|..-+..+-
T Consensus       479 ~~g~vTiaTnMAGRGtDI~l~~~v~~~GGL~Vigterhes~Rid~QlrGR~gRQGdpG~s~f~~sl  544 (799)
T PRK09200        479 QKGAVTVATNMAGRGTDIKLGEGVHELGGLAVIGTERMESRRVDLQLRGRSGRQGDPGSSQFFISL  544 (799)
T ss_pred             CCCEEEEECCCCCCCCCCCCCCCHHHCCCEEEEECCCCCHHHHHHHHCCCCCCCCCCCCEEEEEEC
T ss_conf             999489845455898695338453543881774034451466776751653457999854899851


No 95 
>PRK12904 preprotein translocase subunit SecA; Reviewed
Probab=99.06  E-value=2.9e-08  Score=84.33  Aligned_cols=281  Identities=22%  Similarity=0.252  Sum_probs=176.7

Q ss_pred             CCCCCHHHHHHHHHHHHHHHHCCEEEEEHHHHHHHHHHHHHHHHCCCCCCEEEEEECCCCHHHHHHHHHHHCCCCCEEEE
Q ss_conf             14422369999997334443054588612799999999862110145786589962464225667687762134754864
Q gi|254780945|r  301 DVGSGKTLVALIAMAAAVEAGGQAVIMAPIGILAQQHYEFIKKYTQNTQIIVEIITGNMPQAHRRKALERIAHGQAHIII  380 (700)
Q Consensus       301 DVGSGKTiVA~~A~l~~~~~G~Q~alMaPTEILA~QH~~~~~~~~~~~~i~v~lLtg~~~~~er~~i~~~i~~G~~~iiI  380 (700)
                      -.|-|||+||.++++..+-+|.-|-+....+-||+--++...+++.-+|++|.++++.++..+|++.|.      +||+-
T Consensus       102 ~TGEGKTL~atlp~ylnal~g~gvhvvTvNdYLA~RDa~~m~~~~~~lGltvg~i~~~~~~~~r~~aY~------~ditY  175 (833)
T PRK12904        102 KTGEGKTLVATLPAYLNALTGKGVHVVTVNDYLAKRDAEWMGPLYNFLGLSVGVILSGMSPEERREAYA------ADITY  175 (833)
T ss_pred             ECCCCHHHHHHHHHHHHHHCCCCEEEEECCHHHHHHHHHHHHHHHHHHCCEEEEECCCCCHHHHHHHHH------CCEEE
T ss_conf             068858999999999997369981998155577787799999999981978804389998399999863------77134


Q ss_pred             ECHHHCCCC------------CCCCCCCEEEECCCC----------------------CCCHHHHH--------------
Q ss_conf             111201334------------554444178852101----------------------33568899--------------
Q gi|254780945|r  381 GTHALFQDS------------IQYYKLILVIVDEQH----------------------RFGVQQRL--------------  412 (700)
Q Consensus       381 GTHAL~q~~------------v~F~~LgLvViDEQH----------------------RFGV~QR~--------------  412 (700)
                      ||..=|-=|            ..-..+-.+||||=-                      .|...-+.              
T Consensus       176 ~tn~e~gFDyLrDnm~~~~~~~v~r~~~~aivDE~DSiLiDeArtPLiisg~~~~~~~~y~~~~~~~~~l~~~~dy~~d~  255 (833)
T PRK12904        176 GTNNEFGFDYLRDNMVFSLEDRVQRGLNYAIVDEVDSILIDEARTPLIISGPAEDSSELYKRANKFVPTLKKEGDYTVDE  255 (833)
T ss_pred             ECCCCCCCCCCCCCCCCCHHHHHHHCCCEEEEECCHHHEEECCCCCEEEECCCCCCHHHHHHHHHHHHHCCCCCCEEEEC
T ss_conf             12543245412555437889875012572688641132013267773886788777799999999999747878679951


Q ss_pred             -----HHHHCC---------------------------------------------------------------------
Q ss_conf             -----874025---------------------------------------------------------------------
Q gi|254780945|r  413 -----KLTQKA---------------------------------------------------------------------  418 (700)
Q Consensus       413 -----~L~~Kg---------------------------------------------------------------------  418 (700)
                           .|.++|                                                                     
T Consensus       256 ~~~~v~lt~~G~~~~e~~~~~~~ly~~~~~~~~~~i~~al~A~~l~~~d~dYiV~d~~v~ivDe~TGR~m~grr~~~Glh  335 (833)
T PRK12904        256 KSRTVGLTEEGIEKAEKLLGIENLYDPENIALVHHVNQALRAHYLFKRDVDYIVKDGEVVIVDEFTGRLMPGRRYSDGLH  335 (833)
T ss_pred             CCCCCCCCHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHCCCCEEEECCEEEEEECCCCCCCCCCCCCHHHH
T ss_conf             55775314526999998506566578432369998899999999985687079887907998667776267870654779


Q ss_pred             ----------------------------CCCCCEEECHHHHHHHHHHHHHHCCCHHHHC-CCCCCCCCCEEEEEEC--CC
Q ss_conf             ----------------------------6776101010132278999975201011110-2355766620799970--20
Q gi|254780945|r  419 ----------------------------TAPHVLLMTATPIPRTLVLTSLGDIDISKIT-EKPAGRKPIKTVIIPI--NR  467 (700)
Q Consensus       419 ----------------------------~~ph~L~MtATPIPRTLal~~ygdldvS~i~-e~P~gR~~I~T~~~~~--~~  467 (700)
                                                  ..+.+==||.|--.-.--+.-.=+|+|..|. .+|.-|+.-...++..  .+
T Consensus       336 QaiEaKE~v~i~~e~~t~a~iT~Qn~Fr~y~klsGMTGTa~te~~Ef~~iY~l~V~~IPtn~p~~R~d~~d~iy~t~~~K  415 (833)
T PRK12904        336 QAIEAKEGVKIQNENQTLASITFQNYFRMYEKLAGMTGTADTEAEEFREIYNLDVVVIPTNRPMIRIDHPDLIYKTEKEK  415 (833)
T ss_pred             HHHHHHHCCCCCCCCCEEEEEEHHHHHHHCCHHCCCCCCCHHHHHHHHHHHCCCEEECCCCCCCEEEECCCCEECCHHHH
T ss_conf             99999848877888700123029889832755135677867789999998688769858999854360887020799999


Q ss_pred             HHHHHHHHHHHHCCCCEEEEEECCCCCCCCCCCCHHHHHHHHHHHHCCCCEECCCCCCCHHHHHHHHHHHHCCCEEEEEE
Q ss_conf             02689999763103873899971201221112101466666668663710312014699899999999975598699998
Q gi|254780945|r  468 IDEVIERLKVVLSEGKKAYWICPQIEEKKESNFRSVVERFNSLHEHFTSSIAIIHGRMSDIDKESVMDSFKNGTCKLLIA  547 (700)
Q Consensus       468 ~~~~~~~i~~~l~~g~q~y~VcPlIeese~~~~~~~~~~~~~l~~~~~~~v~~lHGkm~~~ek~~~m~~F~~g~~~iLva  547 (700)
                      ...+.+.|.+.-.+|+-|-|-...||.||.+   |     +.|++. +-...+|..|-.  ++|+.+=+=.-..-.|-||
T Consensus       416 ~~ai~~ei~~~~~~gqPvLvGT~sve~SE~l---s-----~~L~~~-~i~h~vLNAk~~--~~EA~Iia~AG~~gaVTiA  484 (833)
T PRK12904        416 FDAVVEDIKERHKKGQPVLVGTTSIEKSELL---S-----KLLKKA-GIPHNVLNAKNH--EREAEIIAQAGRPGAVTIA  484 (833)
T ss_pred             HHHHHHHHHHHHHCCCCEEEECCCHHHHHHH---H-----HHHHHC-CCCHHHCCCCHH--HHHHHHHHHCCCCCCEEEE
T ss_conf             9999999999997699789942747989999---9-----999873-782776177366--6688999955999976874


Q ss_pred             CHHHHCCCCCCC-----------------------------------CCEEEEECHHHCCHHHH-HHHHHCCCCCCCCEE
Q ss_conf             003410468887-----------------------------------65899858525474688-773011667898359
Q gi|254780945|r  548 TTVIEVGIDVVD-----------------------------------ASIIIIENAEHFGLAQL-HQLRGRVGRGEEISS  591 (700)
Q Consensus       548 TtviEVGvdvpn-----------------------------------a~~mvI~~aerfGLsqL-HQLRGRVGRg~~~s~  591 (700)
                      |.+---|.|+.=                                   +--.-|...||.--.-. -|||||-||-+.+|.
T Consensus       485 TNMAGRGTDI~LGGn~e~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~GGL~VigterhesrRiD~QLrGR~GRQGDpG~  564 (833)
T PRK12904        485 TNMAGRGTDIKLGGNPEMLAAGLEDETEEQIAKIKAEWQKEHEEVLEAGGLHVIGTERHESRRIDNQLRGRSGRQGDPGS  564 (833)
T ss_pred             ECCCCCCCCEECCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHCCCCCCCCCCC
T ss_conf             02567886821688633444432001466788888887653377886389279851433346678786122145689985


Q ss_pred             EEEEECC
Q ss_conf             9997088
Q gi|254780945|r  592 CILLYHP  598 (700)
Q Consensus       592 c~l~~~~  598 (700)
                      .-+..+-
T Consensus       565 s~f~lSl  571 (833)
T PRK12904        565 SRFYLSL  571 (833)
T ss_pred             CEEEEEC
T ss_conf             3265412


No 96 
>COG1643 HrpA HrpA-like helicases [DNA replication, recombination, and repair]
Probab=99.05  E-value=2.1e-07  Score=77.68  Aligned_cols=306  Identities=21%  Similarity=0.288  Sum_probs=195.9

Q ss_pred             HHHHHHHHCCCCCCHHHHHHHHHHHHHHCCCCCCEEEEEECCCCCHHHHHHHHHHHHH-HHHCCEEEEEHHHHHHHHHHH
Q ss_conf             8999986302467988999999999841001343078862144223699999973344-430545886127999999998
Q gi|254780945|r  261 IAQKILRNIPFSPTKSQESAIKDILQDMSQKNRMLRILQGDVGSGKTLVALIAMAAAV-EAGGQAVIMAPIGILAQQHYE  339 (700)
Q Consensus       261 ~~~~f~~~LPF~LT~~Q~~ai~eI~~Dl~~~~pM~RLLQGDVGSGKTiVA~~A~l~~~-~~G~Q~alMaPTEILA~QH~~  339 (700)
                      ....+.+.||-.      ....+|.+-+......  +|.|..|||||-=--..++.+- ..+...++.=|-.|=|+=-.+
T Consensus        41 ~~~~~~~~LPv~------~~~~~i~~ai~~~~vv--ii~getGsGKTTqlP~~lle~g~~~~g~I~~tQPRRlAArsvA~  112 (845)
T COG1643          41 DILEYRSGLPVT------AVRDEILKAIEQNQVV--IIVGETGSGKTTQLPQFLLEEGLGIAGKIGCTQPRRLAARSVAE  112 (845)
T ss_pred             HHHHCCCCCCCH------HHHHHHHHHHHHCCEE--EEECCCCCCHHHHHHHHHHHHHCCCCCEEEECCCHHHHHHHHHH
T ss_conf             043222139818------8899999999869789--98679988758788999996001668759965843899999999


Q ss_pred             HHHHHCCC-CCCEEEEEECCCCHHHHHHHHHHHCCCCCEEEEECH----HHCCCCCCCCCCCEEEECCCCCCCHHHHHHH
Q ss_conf             62110145-786589962464225667687762134754864111----2013345544441788521013356889987
Q gi|254780945|r  340 FIKKYTQN-TQIIVEIITGNMPQAHRRKALERIAHGQAHIIIGTH----ALFQDSIQYYKLILVIVDEQHRFGVQQRLKL  414 (700)
Q Consensus       340 ~~~~~~~~-~~i~v~lLtg~~~~~er~~i~~~i~~G~~~iiIGTH----AL~q~~v~F~~LgLvViDEQHRFGV~QR~~L  414 (700)
                      .+.+-+.. .|-.|....-          ++.-.+.+-.|-+=|-    .-+|.+-..+..+.|||||=|-=.++-=..|
T Consensus       113 RvAeel~~~~G~~VGY~iR----------fe~~~s~~Trik~mTdGiLlrei~~D~~Ls~ys~vIiDEaHERSl~tDilL  182 (845)
T COG1643         113 RVAEELGEKLGETVGYSIR----------FESKVSPRTRIKVMTDGILLREIQNDPLLSGYSVVIIDEAHERSLNTDILL  182 (845)
T ss_pred             HHHHHHCCCCCCEEEEEEE----------EECCCCCCCEEEEECCHHHHHHHHHCCCCCCCCEEEEECHHHHHHHHHHHH
T ss_conf             9999838986765437999----------622678771468951479999984380204587799701335568889999


Q ss_pred             --HH---CCCC--CCCEEECHHHHHHHHHHHHHHCCCHHHHCCCCCCCC-CCEEEEEECCCHHH-H----HHHHHHHHCC
Q ss_conf             --40---2567--761010101322789999752010111102355766-62079997020026-8----9999763103
Q gi|254780945|r  415 --TQ---KATA--PHVLLMTATPIPRTLVLTSLGDIDISKITEKPAGRK-PIKTVIIPINRIDE-V----IERLKVVLSE  481 (700)
Q Consensus       415 --~~---Kg~~--ph~L~MtATPIPRTLal~~ygdldvS~i~e~P~gR~-~I~T~~~~~~~~~~-~----~~~i~~~l~~  481 (700)
                        ..   +...  --+++||||==+--++- +|++-.+-.|.    ||. ||.++.......+. +    ...+...+..
T Consensus       183 gllk~~~~~rr~DLKiIimSATld~~rfs~-~f~~apvi~i~----GR~fPVei~Y~~~~~~d~~l~~ai~~~v~~~~~~  257 (845)
T COG1643         183 GLLKDLLARRRDDLKLIIMSATLDAERFSA-YFGNAPVIEIE----GRTYPVEIRYLPEAEADYILLDAIVAAVDIHLRE  257 (845)
T ss_pred             HHHHHHHHHCCCCCEEEEEECCCCHHHHHH-HCCCCCEEEEC----CCCCCEEEEECCCCCCCHHHHHHHHHHHHHHCCC
T ss_conf             999999864688705999725358899997-62899878755----8866447886577775136999999999996368


Q ss_pred             CC-EEEEEECCCCCCCCCCCCHHHHHHHHHHH-HCC-C-CEECCCCCCCHHHHHHHHHHHHCCCEEEEEECHHHHCCCCC
Q ss_conf             87-38999712012211121014666666686-637-1-03120146998999999999755986999980034104688
Q gi|254780945|r  482 GK-KAYWICPQIEEKKESNFRSVVERFNSLHE-HFT-S-SIAIIHGRMSDIDKESVMDSFKNGTCKLLIATTVIEVGIDV  557 (700)
Q Consensus       482 g~-q~y~VcPlIeese~~~~~~~~~~~~~l~~-~~~-~-~v~~lHGkm~~~ek~~~m~~F~~g~~~iLvaTtviEVGvdv  557 (700)
                      +. -+.+--|=.        ..+...++.|.+ .++ + .|--|||.|+.+|.+++.+--..|.-+|.+||.|-|-++.|
T Consensus       258 ~~GdILvFLpG~--------~EI~~~~~~L~~~~l~~~~~i~PLy~~L~~~eQ~rvF~p~~~~~RKVVlATNIAETSLTI  329 (845)
T COG1643         258 GSGSILVFLPGQ--------REIERTAEWLEKAELGDDLEILPLYGALSAEEQVRVFEPAPGGKRKVVLATNIAETSLTI  329 (845)
T ss_pred             CCCCEEEECCCH--------HHHHHHHHHHHHCCCCCCCEEEECCCCCCHHHHHHHCCCCCCCCCEEEEECCEEECCEEE
T ss_conf             999889977868--------999999999973244788389404035998999866287888860499975140013115


Q ss_pred             CCCCEEEEEC-------HHHCCHHHH----------HHHHHCCCCCCCCEEEEEEECC
Q ss_conf             8765899858-------525474688----------7730116678983599997088
Q gi|254780945|r  558 VDASIIIIEN-------AEHFGLAQL----------HQLRGRVGRGEEISSCILLYHP  598 (700)
Q Consensus       558 pna~~mvI~~-------aerfGLsqL----------HQLRGRVGRg~~~s~c~l~~~~  598 (700)
                      |+....|=-+       -.+.|++.|          -|=.||-|| ..+|.||=+|+.
T Consensus       330 ~gIr~VIDsG~ak~~~y~~~~g~~~L~~~~ISqAsA~QRaGRAGR-~~pGicyRLyse  386 (845)
T COG1643         330 PGIRYVIDSGLAKEKRYDPRTGLTRLETEPISKASADQRAGRAGR-TGPGICYRLYSE  386 (845)
T ss_pred             CCEEEEEECCCCCCCCCCCCCCCEEEEEEEECHHHHHHHCCCCCC-CCCCEEEEECCH
T ss_conf             785899848825210035134852666787505323343455457-778528994479


No 97 
>CHL00122 secA preprotein translocase subunit SecA; Validated
Probab=99.04  E-value=7e-08  Score=81.38  Aligned_cols=242  Identities=19%  Similarity=0.257  Sum_probs=161.3

Q ss_pred             CCCCCHHHHHHHHHHHHHHHHCCEEEEEHHHHHHHHHHHHHHHHCCCCCCEEEEEECCCCHHHHHHHHHHHCCCCCEEEE
Q ss_conf             14422369999997334443054588612799999999862110145786589962464225667687762134754864
Q gi|254780945|r  301 DVGSGKTLVALIAMAAAVEAGGQAVIMAPIGILAQQHYEFIKKYTQNTQIIVEIITGNMPQAHRRKALERIAHGQAHIII  380 (700)
Q Consensus       301 DVGSGKTiVA~~A~l~~~~~G~Q~alMaPTEILA~QH~~~~~~~~~~~~i~v~lLtg~~~~~er~~i~~~i~~G~~~iiI  380 (700)
                      -.|-|||+||.++++..+-+|.-|-+....+-||+--++...+.+.-+|++|.++++.++..+|++.|.      +||+-
T Consensus        97 ~TGEGKTL~atlp~ylnal~GkgvhvvTvNdYLA~RDae~m~~vy~~lGlsvg~i~~~~~~~er~~aY~------~DItY  170 (891)
T CHL00122         97 KTGEGKTLVATLPAYLNALTGKGVHIVTVNDYLARRDSEWMGQIYRFLGLSVGLIQEDMSIEERKQNYK------ADITY  170 (891)
T ss_pred             CCCCCHHHHHHHHHHHHHHCCCCEEEEECCHHHHHHHHHHHHHHHHHHCCEEEEECCCCCHHHHHHHHC------CCCEE
T ss_conf             068857999999999997559972998064565686699999999982966702089999799999835------89279


Q ss_pred             ECHHHCC------------CCCCCCCCCEEEECCCC----------------------C----------------CCHHH
Q ss_conf             1112013------------34554444178852101----------------------3----------------35688
Q gi|254780945|r  381 GTHALFQ------------DSIQYYKLILVIVDEQH----------------------R----------------FGVQQ  410 (700)
Q Consensus       381 GTHAL~q------------~~v~F~~LgLvViDEQH----------------------R----------------FGV~Q  410 (700)
                      ||..=|-            ++..-..+-++||||=-                      .                |-|..
T Consensus       171 ~Tn~e~gFDyLRDnm~~~~~~~vqr~~~~aIvDEvDSiLIDEArtPLiIsg~~~~~~~~y~~~~~~~~~l~~~~dy~~d~  250 (891)
T CHL00122        171 VTNSELGFDYLRDNMALSLSEVVQRPFNYCIIDEVDSILIDEARTPLIISGPVETPIDKYIVAAEIANYLEKDVHYEVDE  250 (891)
T ss_pred             ECCCCEECCCCCCCCCCCHHHHHCCCCCEEEEECHHHHHHHCCCCCEEEECCCCCCHHHHHHHHHHHHHCCCCCCEEECH
T ss_conf             78876222566633236878840889973788640455432256885862798774478999999986437766678622


Q ss_pred             HH---HHHHCC---------------------------------------------------------------------
Q ss_conf             99---874025---------------------------------------------------------------------
Q gi|254780945|r  411 RL---KLTQKA---------------------------------------------------------------------  418 (700)
Q Consensus       411 R~---~L~~Kg---------------------------------------------------------------------  418 (700)
                      +.   .|.++|                                                                     
T Consensus       251 ~~~~v~lte~G~~~~e~~l~~~~ly~~~~~~~~~i~~al~A~~lf~~d~dYiV~d~~v~ivDe~TGR~m~grr~s~GLHQ  330 (891)
T CHL00122        251 KNRNIILTDQGILQCEKILKIKDLYDPEDPWIPYILNAIKAKELFIKNVHYIVRNNEIIIVDEFTGRIMPGRRWSDGLHQ  330 (891)
T ss_pred             HHCCCCCCHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHCCCCEEEECCEEEEEECCCCCCCCCCCCCHHHHH
T ss_conf             31578506326999986137534478543399999999999987606974899889899986788887899935647799


Q ss_pred             ---------------------------CCCCCEEECHHHHHHHHHHHHHHCCCHHHHC-CCCCCCCCCEEEEEEC--CCH
Q ss_conf             ---------------------------6776101010132278999975201011110-2355766620799970--200
Q gi|254780945|r  419 ---------------------------TAPHVLLMTATPIPRTLVLTSLGDIDISKIT-EKPAGRKPIKTVIIPI--NRI  468 (700)
Q Consensus       419 ---------------------------~~ph~L~MtATPIPRTLal~~ygdldvS~i~-e~P~gR~~I~T~~~~~--~~~  468 (700)
                                                 ..+.+==||.|-..-.--+.--=+|+|..|. .+|.-|+.-...++..  .+.
T Consensus       331 aiEaKE~v~i~~e~~t~A~IT~Qn~Fr~y~klsGMTGTA~te~~Ef~~iY~l~Vv~IPtn~p~~R~D~~d~vy~t~~~K~  410 (891)
T CHL00122        331 AIEAKENVPIQQETQTLASITYQNFFLLYPKLSGMTGTAKTEEVELEKIYNLEVICIPTHRPMQRKDLPDLVYKTEYSKW  410 (891)
T ss_pred             HHHHHCCCCCCCCCCEEEEEEHHHHHHHCCHHCCCCCCCHHHHHHHHHHHCCCEEECCCCCCCEEEECCCEEECCHHHHH
T ss_conf             99987188778887213666599998545042267567687899999985884798899998500308895778899999


Q ss_pred             HHHHHHHHHHHCCCCEEEEEECCCCCCCCCCCCHHHHHHHHHHHHCCCCEECCCCCCCHHHHHHHHHHHHCCCEEEEEEC
Q ss_conf             26899997631038738999712012211121014666666686637103120146998999999999755986999980
Q gi|254780945|r  469 DEVIERLKVVLSEGKKAYWICPQIEEKKESNFRSVVERFNSLHEHFTSSIAIIHGRMSDIDKESVMDSFKNGTCKLLIAT  548 (700)
Q Consensus       469 ~~~~~~i~~~l~~g~q~y~VcPlIeese~~~~~~~~~~~~~l~~~~~~~v~~lHGkm~~~ek~~~m~~F~~g~~~iLvaT  548 (700)
                      ..+.+.|++.-++|+-|-|-...||.||.+   |     +.|++. +-...+|..|-...++|+.+=+=.--.-.|-|||
T Consensus       411 ~Av~~ei~~~h~~GqPVLvGT~SVe~SE~l---s-----~~L~~~-gi~h~vLNAk~~n~~~EA~IiA~AG~~gaVTIAT  481 (891)
T CHL00122        411 KAIADECFDMHKIGRPILVGTTSVEKSELL---S-----QLLEEY-QLPHNLLNAKPENVKRESEIIAQAGRKGAITIAT  481 (891)
T ss_pred             HHHHHHHHHHHHCCCCEEEECCCHHHHHHH---H-----HHHHHC-CCCCHHHCCCCCCHHHHHHHHHHCCCCCCEEEEC
T ss_conf             999999999996799989834655889999---9-----999974-7862202388430789999999569999389715


Q ss_pred             HHHHCCCCC
Q ss_conf             034104688
Q gi|254780945|r  549 TVIEVGIDV  557 (700)
Q Consensus       549 tviEVGvdv  557 (700)
                      .+---|.|+
T Consensus       482 NMAGRGTDI  490 (891)
T CHL00122        482 NMAGRGTDI  490 (891)
T ss_pred             CCCCCCCCE
T ss_conf             556898784


No 98 
>PRK13103 secA preprotein translocase subunit SecA; Reviewed
Probab=98.98  E-value=6.2e-08  Score=81.81  Aligned_cols=96  Identities=26%  Similarity=0.349  Sum_probs=80.0

Q ss_pred             CCCCCHHHHHHHHHHHHHHHHCCEEEEEHHHHHHHHHHHHHHHHCCCCCCEEEEEECCCCHHHHHHHHHHHCCCCCEEEE
Q ss_conf             14422369999997334443054588612799999999862110145786589962464225667687762134754864
Q gi|254780945|r  301 DVGSGKTLVALIAMAAAVEAGGQAVIMAPIGILAQQHYEFIKKYTQNTQIIVEIITGNMPQAHRRKALERIAHGQAHIII  380 (700)
Q Consensus       301 DVGSGKTiVA~~A~l~~~~~G~Q~alMaPTEILA~QH~~~~~~~~~~~~i~v~lLtg~~~~~er~~i~~~i~~G~~~iiI  380 (700)
                      -.|-|||+||.++++..+-+|.-|-+....+-||+--.+...+++.-+|+.|.+++..++..+|++.|.      +||.-
T Consensus       103 ~TGEGKTL~atlp~ylnal~g~gvhvvTvNdYLA~RDae~m~~~y~~lGltvg~i~~~~~~~~r~~aY~------~DitY  176 (913)
T PRK13103        103 RTGEGKTLVGTLAVYLNALSGKGVHVVTVNDYLARRDANWMRPLYEFLGLSVGIVTPFQPPEEKRAAYA------ADITY  176 (913)
T ss_pred             CCCCCHHHHHHHHHHHHHHCCCCEEEECCCHHHHHHHHHHHHHHHHHHCCEEEECCCCCCHHHHHHHCC------CCCEE
T ss_conf             178855999999999987559970997265365586699999999981976855189999799997466------88644


Q ss_pred             ECHHHCC------------CCCCCCCCCEEEECC
Q ss_conf             1112013------------345544441788521
Q gi|254780945|r  381 GTHALFQ------------DSIQYYKLILVIVDE  402 (700)
Q Consensus       381 GTHAL~q------------~~v~F~~LgLvViDE  402 (700)
                      ||..=|-            ++..-..+.++||||
T Consensus       177 ~tn~e~gFDyLRDnm~~~~~~~vqr~~~~aivDE  210 (913)
T PRK13103        177 GTNNEFGFDYLRDNMAFSLDDKFQRELNFAVIDE  210 (913)
T ss_pred             ECCCCCCCCCCCCCHHCCHHHHCCCCCCEEEEEC
T ss_conf             3576433534573310487884366776478742


No 99 
>PRK08074 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
Probab=98.97  E-value=4.6e-06  Score=67.16  Aligned_cols=134  Identities=23%  Similarity=0.324  Sum_probs=101.4

Q ss_pred             CCCCCHHHHHHHHHHHHHHCCCCCCEEEEEECCCCCHHHHHHHHHH-HHHHHHCCEEEEEHHHHHHHHHHHH----HHHH
Q ss_conf             2467988999999999841001343078862144223699999973-3444305458861279999999986----2110
Q gi|254780945|r  270 PFSPTKSQESAIKDILQDMSQKNRMLRILQGDVGSGKTLVALIAMA-AAVEAGGQAVIMAPIGILAQQHYEF----IKKY  344 (700)
Q Consensus       270 PF~LT~~Q~~ai~eI~~Dl~~~~pM~RLLQGDVGSGKTiVA~~A~l-~~~~~G~Q~alMaPTEILA~QH~~~----~~~~  344 (700)
                      .|+.=.+|.+-.+.|.+-+..+.++  +++--+|+|||+=+++.++ .+..+|.++++-.+|-.|-+|.++.    +.+.
T Consensus       256 ~ye~R~~Q~~ma~~V~~al~~~~~l--~iEApTGtGKTlaYLlPai~~A~~~~~~vvIST~T~~LQ~QL~~kdlp~L~~~  333 (932)
T PRK08074        256 GYEKREGQQEMMKEVYTALRDSRHA--LIEAGTGTGKTLAYLLPAAYFAKKKEEPVIISTYTVQLQQQLLEKDIPLLQKI  333 (932)
T ss_pred             CCCCCHHHHHHHHHHHHHHHCCCCE--EEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEECCHHHHHHHHHHHHHHHHHH
T ss_conf             8875878999999999998538847--99868888713687999999999759909999162889999998689999997


Q ss_pred             CCCCCCEEEEEECCCC-----------------------------------HHHH---------HHHHHHHCC-------
Q ss_conf             1457865899624642-----------------------------------2566---------768776213-------
Q gi|254780945|r  345 TQNTQIIVEIITGNMP-----------------------------------QAHR---------RKALERIAH-------  373 (700)
Q Consensus       345 ~~~~~i~v~lLtg~~~-----------------------------------~~er---------~~i~~~i~~-------  373 (700)
                      + +++++++++.|+..                                   ..++         ..+|+.+.+       
T Consensus       334 l-~~~~~~~llKGr~nYlCl~k~~~~l~~~~~~~~~~~~~~~il~Wl~~T~tGD~del~~~~~~~~~w~~i~~~~~~~~~  412 (932)
T PRK08074        334 F-PFPVKAALLKGRSHYLCLRKFEQALQEEDDNYDVALTKAQLLVWLTETETGDLDELNLPSGGKLLWNRIASDGHSPGG  412 (932)
T ss_pred             H-CCCCCEEEEECCHHCCCHHHHHHHHCCCCCCHHHHHHHHHHHHHHHCCCCCCHHHCCCCCCHHHHHHHHCCCCCCCCC
T ss_conf             1-998608999661412776889998535454155788899999987268886887636996348899884557532023


Q ss_pred             ------------------CCCEEEEECHHHCCCC-----CCCCCCCEEEECCCCCC
Q ss_conf             ------------------4754864111201334-----55444417885210133
Q gi|254780945|r  374 ------------------GQAHIIIGTHALFQDS-----IQYYKLILVIVDEQHRF  406 (700)
Q Consensus       374 ------------------G~~~iiIGTHAL~q~~-----v~F~~LgLvViDEQHRF  406 (700)
                                        -.++|||.-||++-.+     -.+..-..+||||=|.|
T Consensus       413 ~~c~~~~~Cf~~~ar~~a~~AdvvI~NHalL~~d~~~~~~ilp~~~~lViDEAH~L  468 (932)
T PRK08074        413 KQSPWFSRCFYQRAKNKAKFADIVITNHALLLTDFTSEEPLLPSYEHIIIDEAHHF  468 (932)
T ss_pred             CCCCCCCCCHHHHHHHHHHHCCEEEECHHHHHHHHHCCCCCCCCCCEEEEECHHHH
T ss_conf             55887577989999997642999998889985656414776887676997313231


No 100
>PRK12898 secA preprotein translocase subunit SecA; Reviewed
Probab=98.97  E-value=8.8e-08  Score=80.60  Aligned_cols=280  Identities=21%  Similarity=0.256  Sum_probs=183.0

Q ss_pred             CCCCCHHHHHHHHHHHHHHHHCCEEEEEHHHHHHHHHHHHHHHHCCCCCCEEEEEECCCCHHHHHHHHHHHCCCCCEEEE
Q ss_conf             14422369999997334443054588612799999999862110145786589962464225667687762134754864
Q gi|254780945|r  301 DVGSGKTLVALIAMAAAVEAGGQAVIMAPIGILAQQHYEFIKKYTQNTQIIVEIITGNMPQAHRRKALERIAHGQAHIII  380 (700)
Q Consensus       301 DVGSGKTiVA~~A~l~~~~~G~Q~alMaPTEILA~QH~~~~~~~~~~~~i~v~lLtg~~~~~er~~i~~~i~~G~~~iiI  380 (700)
                      -.|-|||+||.++++..+-+|.-|-+....+-||+--.+...+++.-+|++|.++++.++..+|++.|.      +||+-
T Consensus       139 ~TGEGKTL~atlpaylnAL~G~gVHvvTvNDYLA~RDae~mg~iy~fLGLsvg~i~~~~~~~eRr~aY~------~DItY  212 (673)
T PRK12898        139 QTGEGKTLTATLPAGTAALAGRPVHVITVNDYLAERDAEQMRPLYEALGVTVGCVIEDQDPEERRAAYG------ADVTY  212 (673)
T ss_pred             ECCCCHHHHHHHHHHHHHHCCCCEEEEECCHHHHHHHHHHHHHHHHHHCCEEEEECCCCCHHHHHHHHC------CCCEE
T ss_conf             078858999999999997369970898045577787699999999982977845179999799999726------99579


Q ss_pred             ECHHHCC-----CCC--------------------------CCCCCCEEEECCCC-------------------CCC---
Q ss_conf             1112013-----345--------------------------54444178852101-------------------335---
Q gi|254780945|r  381 GTHALFQ-----DSI--------------------------QYYKLILVIVDEQH-------------------RFG---  407 (700)
Q Consensus       381 GTHAL~q-----~~v--------------------------~F~~LgLvViDEQH-------------------RFG---  407 (700)
                      ||..=|-     |+.                          .-..|-++||||=-                   .-.   
T Consensus       213 gTn~E~GFDYLRDnm~~~~~~~~~~~~~~~l~~~~~~~~~~vqR~l~fAIVDEvDSILIDEARTPLIISgp~~~~~~~~~  292 (673)
T PRK12898        213 CTNKELVFDYLRDRIALGQRAGDARLALESLRGGSERSGQLLLRGLHFAIVDEADSVLIDEARTPLIISAPAKEEDGAAV  292 (673)
T ss_pred             ECCHHHHHHHHHHHHHCCCCCCCCCCCCHHHCCCCCCHHHHHCCCCCEEEEECHHHEEECCCCCCCCCCCCCCCCCHHHH
T ss_conf             56523324577641302334321111101101334667775135675378733033121024676101477777640899


Q ss_pred             HHHHHHHHHC---------------------C------------------------------------------------
Q ss_conf             6889987402---------------------5------------------------------------------------
Q gi|254780945|r  408 VQQRLKLTQK---------------------A------------------------------------------------  418 (700)
Q Consensus       408 V~QR~~L~~K---------------------g------------------------------------------------  418 (700)
                      ..+-..+..+                     |                                                
T Consensus       293 y~~a~~~~~~L~~~~dY~iDek~k~v~LTe~G~~~ie~~l~~~~~~~~~~~~~~~~i~~ALrA~~lf~rDvdYIV~dgeV  372 (673)
T PRK12898        293 LRRALALAAELQEGEDYRIDAATKQIELTEAGRARIAALAESLPPAWRGAVRREELVRQALSALHLFRRDEHYIVRDGKV  372 (673)
T ss_pred             HHHHHHHHHHCCCCCCEEEECCCCEEEECHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCEEEECCCE
T ss_conf             99999999856788877986688826578679999999724156556531148999999999999985798389978928


Q ss_pred             -------------------------------------------------CCCCCEEECHHHHHHHHHH-HHHHCCCHHHH
Q ss_conf             -------------------------------------------------6776101010132278999-97520101111
Q gi|254780945|r  419 -------------------------------------------------TAPHVLLMTATPIPRTLVL-TSLGDIDISKI  448 (700)
Q Consensus       419 -------------------------------------------------~~ph~L~MtATPIPRTLal-~~ygdldvS~i  448 (700)
                                                                       ..+.+==||-|--.=.--+ .+| +|+|..|
T Consensus       373 vIVDEfTGR~m~GRrwsdGLHQAIEAKEgV~I~~e~qTlAsIT~QnfFR~Y~kLsGMTGTA~tea~Ef~~iY-~L~Vv~I  451 (673)
T PRK12898        373 VIVDEFTGRVMPDRSWSDGLHQAIEAKEGVELTDPRETLARITFQRFFRRYLRLAGMTGTAREVAGELWSVY-GLPVVRI  451 (673)
T ss_pred             EEEECCCCCCCCCCCCCHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHCCHHCCCCCCCHHHHHHHHHHH-CCCEEEC
T ss_conf             998788885068880663789999985399878312356643499999856174057778575799999975-9976986


Q ss_pred             -CCCCCCCCCCEEEEEEC--CCHHHHHHHHHHHHCCCCEEEEEECCCCCCCCCCCCHHHHHHHHHHHHCCCCEECCCCCC
Q ss_conf             -02355766620799970--200268999976310387389997120122111210146666666866371031201469
Q gi|254780945|r  449 -TEKPAGRKPIKTVIIPI--NRIDEVIERLKVVLSEGKKAYWICPQIEEKKESNFRSVVERFNSLHEHFTSSIAIIHGRM  525 (700)
Q Consensus       449 -~e~P~gR~~I~T~~~~~--~~~~~~~~~i~~~l~~g~q~y~VcPlIeese~~~~~~~~~~~~~l~~~~~~~v~~lHGkm  525 (700)
                       ..+|.-|+.-...++..  ++.+.+++.|++.-++|+-|-|-+..||.||.+   |     +.|++. +-...+|.-|-
T Consensus       452 PTnrP~~R~D~~D~vy~t~~~K~~Aii~ei~~~~~~GqPVLVGT~SVe~SE~l---S-----~~L~~~-gi~h~VLNAk~  522 (673)
T PRK12898        452 PTNRPSQRIVLPTEVFLTLAAKWAAVAARVRELHASGRPVLVGTRSVAASERL---S-----ALLREA-GLPHQVLNAKQ  522 (673)
T ss_pred             CCCCCCCCEECCCEEECCHHHHHHHHHHHHHHHHHCCCCEEEEECCHHHHHHH---H-----HHHHHC-CCCHHHCCCCC
T ss_conf             89997301237985856999999999999999986799889983758999999---9-----999986-99756647866


Q ss_pred             CHHHHHHHHHHHHCCCEEEEEECHHHHCCCCCC------CCCEEEEECHHHCCHHHH-HHHHHCCCCCCCCEEEEEEECC
Q ss_conf             989999999997559869999800341046888------765899858525474688-7730116678983599997088
Q gi|254780945|r  526 SDIDKESVMDSFKNGTCKLLIATTVIEVGIDVV------DASIIIIENAEHFGLAQL-HQLRGRVGRGEEISSCILLYHP  598 (700)
Q Consensus       526 ~~~ek~~~m~~F~~g~~~iLvaTtviEVGvdvp------na~~mvI~~aerfGLsqL-HQLRGRVGRg~~~s~c~l~~~~  598 (700)
                      ...|-+-|-++=+.|  .|-|||.+---|.|+.      .+-=.-|...||--=.-. -|||||-||-+.+|..-+..+-
T Consensus       523 ~~~EA~IIA~AG~~G--aVTIATNMAGRGTDI~Lg~~V~~~GGLhVIgTerheSrRIDnQLrGRsGRQGDPGss~f~lSl  600 (673)
T PRK12898        523 DAEEAAIVARAGQRG--RITVATNMAGRGTDIKLEPEVAARGGLHVILTERHESARIDRQLAGRCGRQGDPGSSEAILSL  600 (673)
T ss_pred             HHHHHHHHHHCCCCC--CEEEECCCCCCCCCCCCCHHHHHCCCCEEEECCCCCHHHHHHHHHCCCCCCCCCCCEEEEEEE
T ss_conf             687999999439999--879702367898684767678862898898437551124565642354468999851489981


No 101
>TIGR00614 recQ_fam ATP-dependent DNA helicase, RecQ family; InterPro: IPR004589   The ATP-dependent DNA helicase RecQ (3.6.1 from EC) is involved in genome maintenance . All homologues tested to date unwind paired DNA, translocating in a 3' to 5' direction and several have a preference for forked or 4-way DNA structures (e.g. Holliday junctions) or for G-quartet DNA. The yeast protein, Sgs1, is present in numerous foci that coincide with sites of de novo synthesis DNA, such as the replication fork, and protein levels peak during S-phase.    A model has been proposed for Sgs1p action in the S-phase checkpoint response, both as a 'sensor' for damage during replication and a 'resolvase' for structures that arise at paused forks, such as the four-way 'chickenfoot' structure. The action of Sgs1p may serve to maintain the proper amount and integrity of ss DNA that is necessary for the binding of RPA (replication protein A, the eukaryotic ss DNA-binding protein)DNA pol complexes. Sgs1p would thus function by detecting (or resolving) aberrant DNA structures, and would thus contribute to the full activation of the DNA-dependent protein kinase, Mec1p and the effector kinase, Rad53p. Its ability to bind both the large subunit of RPA and the RecA-like protein Rad51p, place it in a unique position to resolve inappropriate fork structures that can occur when either the leading or lagging strand synthesis is stalled. Thus, RecQ helicases integrate checkpoint activation and checkpoint response. ; GO: 0008026 ATP-dependent helicase activity, 0006310 DNA recombination.
Probab=98.92  E-value=3.1e-06  Score=68.44  Aligned_cols=317  Identities=19%  Similarity=0.306  Sum_probs=219.1

Q ss_pred             CHHHHHHHHHHHHHHCCCCCCEEEEEECCCCCHHHHHHHHHHHHHHHHCCEEEEEHHHH-HHHHHHHHHHHHCCCCCCEE
Q ss_conf             98899999999984100134307886214422369999997334443054588612799-99999986211014578658
Q gi|254780945|r  274 TKSQESAIKDILQDMSQKNRMLRILQGDVGSGKTLVALIAMAAAVEAGGQAVIMAPIGI-LAQQHYEFIKKYTQNTQIIV  352 (700)
Q Consensus       274 T~~Q~~ai~eI~~Dl~~~~pM~RLLQGDVGSGKTiVA~~A~l~~~~~G~Q~alMaPTEI-LA~QH~~~~~~~~~~~~i~v  352 (700)
                      -..|.++|+..+..-...     |+-==.|-||.+=+=++++   -.+.=..+..| =| |=+=....+    ...||+.
T Consensus        13 rp~Q~e~I~~~L~g~RD~-----~vvMpTG~GKSLCYQ~Pa~---~~~G~t~VIsP-LiSLm~DQV~~L----~~~~i~A   79 (497)
T TIGR00614        13 RPVQLEVINAVLEGRRDC-----LVVMPTGGGKSLCYQLPAL---YSDGLTLVISP-LISLMEDQVLQL----KASGIPA   79 (497)
T ss_pred             CHHHHHHHHHHHCCCCCE-----EEEECCCCCHHHHHHHHHH---HCCCCEEEECC-HHHHHHHHHHHH----HHCCCCE
T ss_conf             514899999875489756-----9981589860367640567---50896499736-365689999998----7448630


Q ss_pred             EEEECCCCHHHHHHHHHHH--CCCCCEEEEEC-------HHHCCC---CCCCCCCCEEEECCCC---CCCHHHHHHHHH-
Q ss_conf             9962464225667687762--13475486411-------120133---4554444178852101---335688998740-
Q gi|254780945|r  353 EIITGNMPQAHRRKALERI--AHGQAHIIIGT-------HALFQD---SIQYYKLILVIVDEQH---RFGVQQRLKLTQ-  416 (700)
Q Consensus       353 ~lLtg~~~~~er~~i~~~i--~~G~~~iiIGT-------HAL~q~---~v~F~~LgLvViDEQH---RFGV~QR~~L~~-  416 (700)
                      ++|+|+.+..+...++.++  ++|++.+|==|       ..|||.   -..-.++.+++|||=|   -.|=.=|..... 
T Consensus        80 ~~L~s~~s~~~~~~v~~~~~~k~g~~kllYvtPE~~~~~~~ll~~Le~~Y~~~~~~~iAvDEAHCiSqWGHDFR~~Y~~L  159 (497)
T TIGR00614        80 TFLNSSQSKEQQKEVLTDLSKKDGKLKLLYVTPEKISKSKSLLQTLEKLYERKGITLIAVDEAHCISQWGHDFRPDYKAL  159 (497)
T ss_pred             ECCCCCCCHHHHHHHHHHHHHHCCCEEEEEECHHHHHCCHHHHHHHHHHHHHCCCEEEEEECEEEECCCCCCCCHHHHHH
T ss_conf             10443257789999999987307975899716346534647899999988644966999832154358888740799996


Q ss_pred             -----CCCCCCCEEECHHHHHHHHHH--HHHHCCCHHHHCCCCCCCCCCEEEEEECC----C-HHHHHHHHH-HHHC---
Q ss_conf             -----256776101010132278999--97520101111023557666207999702----0-026899997-6310---
Q gi|254780945|r  417 -----KATAPHVLLMTATPIPRTLVL--TSLGDIDISKITEKPAGRKPIKTVIIPIN----R-IDEVIERLK-VVLS---  480 (700)
Q Consensus       417 -----Kg~~ph~L~MtATPIPRTLal--~~ygdldvS~i~e~P~gR~~I~T~~~~~~----~-~~~~~~~i~-~~l~---  480 (700)
                           +=++.-+..+|||-=|++..=  ...+ |.--.+...-.+|..+.=.+....    + ...+..||. +.-.   
T Consensus       160 G~Lk~~fP~vP~~ALTATA~~~~~~Di~~~L~-l~~p~~~~~SFdRPNl~y~v~~K~~n~~~~~~dl~~f~~~~~~s~~~  238 (497)
T TIGR00614       160 GSLKQKFPNVPIMALTATASPSVREDILRILN-LKNPQVFITSFDRPNLYYEVRRKTSNTKKILEDLLRFIVKKASSAWE  238 (497)
T ss_pred             HHHHHHCCCCCEEEEECCCCHHHHHHHHHHHC-CCCCCEEEECCCCCCCEEEEECCCCCHHHHHHHHHHHHHHHCCCCCC
T ss_conf             57888548874364340578678999998722-13662464046687630340057897025899999998752035652


Q ss_pred             -CCCEEEEEECCCCCCCCCCCCHHHHHHHHHHHHCCCCEECCCCCCCHHHHHHHHHHHH-CCCEEEEEECHHHHCCCCCC
Q ss_conf             -3873899971201221112101466666668663710312014699899999999975-59869999800341046888
Q gi|254780945|r  481 -EGKKAYWICPQIEEKKESNFRSVVERFNSLHEHFTSSIAIIHGRMSDIDKESVMDSFK-NGTCKLLIATTVIEVGIDVV  558 (700)
Q Consensus       481 -~g~q~y~VcPlIeese~~~~~~~~~~~~~l~~~~~~~v~~lHGkm~~~ek~~~m~~F~-~g~~~iLvaTtviEVGvdvp  558 (700)
                       +|.=-.|=||-=        +.+++....|++. +-..+-=|--|+.+++++|=.+|. ..+++|.|||--=-.|||=|
T Consensus       239 ~~G~sGIIYC~SR--------~~~e~~a~~L~~~-G~~a~aYHAGl~~~~R~~V~~~f~nrD~~QvVvATvAFGMGInKp  309 (497)
T TIGR00614       239 FKGKSGIIYCPSR--------KKSEQVAAELQKL-GIAAGAYHAGLEISARKEVQHKFQNRDEIQVVVATVAFGMGINKP  309 (497)
T ss_pred             CCCCCEEEECCCC--------HHHHHHHHHHHHC-CCEEEHHHCCCCHHHHHHHHHHHHCCCCCEEEEEEEECCCCCCCC
T ss_conf             4588302752872--------3489999999755-861002402688647789999875038857999872126888763


Q ss_pred             CCCEEEEECHHHCCHHHHHHHHHCCCCCCCCEEEEEEECCCCCHHHHHHHHHHHHHCHH
Q ss_conf             76589985852547468877301166789835999970888998799999999841425
Q gi|254780945|r  559 DASIIIIENAEHFGLAQLHQLRGRVGRGEEISSCILLYHPPLSKNSYTRLSVLKNTEDG  617 (700)
Q Consensus       559 na~~mvI~~aerfGLsqLHQLRGRVGRg~~~s~c~l~~~~~~~~~~~~Rl~~l~~~~dG  617 (700)
                      |..-.|=.++-| -+=-=.|=-||-||-+.+|.|+|+|.+.  +..+-|= .+.+..+|
T Consensus       310 dvRfViH~~~Pk-~~EsYYQE~GRAGRDgl~s~c~lfy~~a--D~~~~~~-~l~e~~~~  364 (497)
T TIGR00614       310 DVRFVIHYSLPK-SMESYYQESGRAGRDGLPSECVLFYAPA--DIARLRR-LLVEEPDG  364 (497)
T ss_pred             CCCEEEEECCCC-CCCCCCCCCCCCCCCCCCCCEEEEECHH--HHHHHHH-HHEECCCC
T ss_conf             536788507885-6211013555567897320102330435--6999988-74004577


No 102
>PRK13104 secA preprotein translocase subunit SecA; Reviewed
Probab=98.92  E-value=2.8e-07  Score=76.64  Aligned_cols=96  Identities=27%  Similarity=0.364  Sum_probs=81.8

Q ss_pred             CCCCCHHHHHHHHHHHHHHHHCCEEEEEHHHHHHHHHHHHHHHHCCCCCCEEEEEECCCCHHHHHHHHHHHCCCCCEEEE
Q ss_conf             14422369999997334443054588612799999999862110145786589962464225667687762134754864
Q gi|254780945|r  301 DVGSGKTLVALIAMAAAVEAGGQAVIMAPIGILAQQHYEFIKKYTQNTQIIVEIITGNMPQAHRRKALERIAHGQAHIII  380 (700)
Q Consensus       301 DVGSGKTiVA~~A~l~~~~~G~Q~alMaPTEILA~QH~~~~~~~~~~~~i~v~lLtg~~~~~er~~i~~~i~~G~~~iiI  380 (700)
                      -.|-|||+||.++++..+-+|.-|-+....+-||+--++...+++.-+|++|.++++.++..+|+..|.      +||.-
T Consensus       103 ~TGEGKTL~atlp~ylnal~g~gvhvvTvNdYLA~RDae~m~~~y~~lGltvg~i~~~~~~~~r~~aY~------~DitY  176 (896)
T PRK13104        103 RTGEGKTLVATLPAYLNAISGRGVHIVTVNDYLAKRDSQWMKPIYEFLGLTVGVIYPDMSHKEKQEAYK------ADIVY  176 (896)
T ss_pred             CCCCCHHHHHHHHHHHHHHCCCCEEEECCCHHHHHHHHHHHHHHHHHHCCEEEEECCCCCHHHHHHHHC------CCEEE
T ss_conf             178855999999999987559971997265354464499999999981976734189999799999714------99379


Q ss_pred             ECHHHCC-----C-------CCCCCCCCEEEECC
Q ss_conf             1112013-----3-------45544441788521
Q gi|254780945|r  381 GTHALFQ-----D-------SIQYYKLILVIVDE  402 (700)
Q Consensus       381 GTHAL~q-----~-------~v~F~~LgLvViDE  402 (700)
                      ||..=|-     |       +..-..+.++||||
T Consensus       177 ~Tn~e~gFDyLrDnm~~~~~~~vqr~~~~aivDE  210 (896)
T PRK13104        177 GTNNEYGFDYLRDNMAFSLTDKVQRELNFAIVDE  210 (896)
T ss_pred             ECCCCCCCCCCCCCHHCCHHHHCCCCCCEEEEEC
T ss_conf             6786541523572111384762566776478742


No 103
>PRK12902 secA preprotein translocase subunit SecA; Reviewed
Probab=98.89  E-value=1.2e-07  Score=79.42  Aligned_cols=96  Identities=21%  Similarity=0.296  Sum_probs=82.1

Q ss_pred             CCCCCHHHHHHHHHHHHHHHHCCEEEEEHHHHHHHHHHHHHHHHCCCCCCEEEEEECCCCHHHHHHHHHHHCCCCCEEEE
Q ss_conf             14422369999997334443054588612799999999862110145786589962464225667687762134754864
Q gi|254780945|r  301 DVGSGKTLVALIAMAAAVEAGGQAVIMAPIGILAQQHYEFIKKYTQNTQIIVEIITGNMPQAHRRKALERIAHGQAHIII  380 (700)
Q Consensus       301 DVGSGKTiVA~~A~l~~~~~G~Q~alMaPTEILA~QH~~~~~~~~~~~~i~v~lLtg~~~~~er~~i~~~i~~G~~~iiI  380 (700)
                      -.|-|||+||.++++..+-+|.-|-+....+-||+--.+...+.+.-+|++|.++++.++..+|+..|.      +||.-
T Consensus       106 ~TGEGKTL~atlp~ylnAL~GkgvHvvTvNdYLA~RDae~m~~vy~fLGltvg~i~~~~~~~er~~aY~------~DItY  179 (946)
T PRK12902        106 KTGEGKTLVATLPSYLNALTGKGVHVVTVNDYLARRDAEWMGQVHRFLGLSVGLIQQDMSPEERKKNYA------CDITY  179 (946)
T ss_pred             CCCCCHHHHHHHHHHHHHHCCCCEEEECCCHHHHHHHHHHHHHHHHHHCCEEEEECCCCCHHHHHHHHC------CCCEE
T ss_conf             178847999999999986559970997265265686799999999981977835489989899999858------98279


Q ss_pred             ECHHHCC------------CCCCCCCCCEEEECC
Q ss_conf             1112013------------345544441788521
Q gi|254780945|r  381 GTHALFQ------------DSIQYYKLILVIVDE  402 (700)
Q Consensus       381 GTHAL~q------------~~v~F~~LgLvViDE  402 (700)
                      ||..=|-            ++..-..+-++||||
T Consensus       180 ~Tn~E~gFDYLRDnm~~~~~~~vqr~~~~aIvDE  213 (946)
T PRK12902        180 ATNSELGFDYLRDNMATDISEVVQRPFNYCVIDE  213 (946)
T ss_pred             ECCCCCCCCCCCCCCCCCHHHHHCCCCCEEEEEC
T ss_conf             7888757723530447886884387996589854


No 104
>PRK12900 secA preprotein translocase subunit SecA; Reviewed
Probab=98.87  E-value=6.1e-07  Score=74.01  Aligned_cols=163  Identities=18%  Similarity=0.293  Sum_probs=93.7

Q ss_pred             CCCEEECHHHHHHHHH---HHHHHCCCHHHHC-CCCCCCCCCEEEEEEC--CCHHHHHHHHHHHHCCCCEEEEEECCCCC
Q ss_conf             7610101013227899---9975201011110-2355766620799970--20026899997631038738999712012
Q gi|254780945|r  421 PHVLLMTATPIPRTLV---LTSLGDIDISKIT-EKPAGRKPIKTVIIPI--NRIDEVIERLKVVLSEGKKAYWICPQIEE  494 (700)
Q Consensus       421 ph~L~MtATPIPRTLa---l~~ygdldvS~i~-e~P~gR~~I~T~~~~~--~~~~~~~~~i~~~l~~g~q~y~VcPlIee  494 (700)
                      +.+==||-|-  .|-|   ..+|+ |+|..|. .+|.-|+.-...++..  ++...+.+.|++.-++|+-|-|-+..||.
T Consensus       490 ~kLsGMTGTA--~te~~Ef~~iY~-l~Vv~IPTn~P~~R~D~~D~vy~t~~~K~~Aii~ei~~~~~~gqPVLVGT~SVe~  566 (983)
T PRK12900        490 KKLAGMTGTA--ETEASEFFEIYK-LDVVVIPTNRPIVRKDMDDLVYKTRREKYNAIVLKVEELQKKGQPVLVGTASVEV  566 (983)
T ss_pred             CHHCCCCCCC--HHHHHHHHHHHC-CCEEECCCCCCCEEEECCCCCCCCHHHHHHHHHHHHHHHHHCCCCEEEEECCHHH
T ss_conf             4620475674--889999999868-8669848999840012655041899999999999999997479988998387899


Q ss_pred             CCCCCCCHHHHHHHHHHHH-CCCCEECCCCCCCHHHHHHHHHHHHCCCEEEEEECHHHHCCCC------CCCCCEEEEEC
Q ss_conf             2111210146666666866-3710312014699899999999975598699998003410468------88765899858
Q gi|254780945|r  495 KKESNFRSVVERFNSLHEH-FTSSIAIIHGRMSDIDKESVMDSFKNGTCKLLIATTVIEVGID------VVDASIIIIEN  567 (700)
Q Consensus       495 se~~~~~~~~~~~~~l~~~-~~~~v~~lHGkm~~~ek~~~m~~F~~g~~~iLvaTtviEVGvd------vpna~~mvI~~  567 (700)
                      ||.+   |     +.|++. .+.  .+|.-|-...|-+-|-++=+.  -.|-|||..---|.|      |..+-=.-|..
T Consensus       567 SE~l---S-----~~L~~~gI~h--~VLNAk~h~~EA~IIa~AG~~--GaVTIATNMAGRGTDIkLg~~V~elGGL~VIg  634 (983)
T PRK12900        567 SETL---S-----RMLRAKRIEH--NVLNAKQNEREAEIVAEAGQK--GAVTIATNMAGRGTDIKLGEGVRELGGLFILG  634 (983)
T ss_pred             HHHH---H-----HHHHHCCCCH--HHHCCCCHHHHHHHHHHCCCC--CCEEEECCCCCCCCCCCCCCCHHHCCCEEEEE
T ss_conf             9999---9-----9999859955--651678478899999936999--97798243678985825483446538807751


Q ss_pred             HHHCCHHHH-HHHHHCCCCCCCCEEEEEEECC
Q ss_conf             525474688-7730116678983599997088
Q gi|254780945|r  568 AEHFGLAQL-HQLRGRVGRGEEISSCILLYHP  598 (700)
Q Consensus       568 aerfGLsqL-HQLRGRVGRg~~~s~c~l~~~~  598 (700)
                      .||.--.-. -|||||-||-+.+|..-+..+-
T Consensus       635 TErheSrRIDnQLrGRaGRQGDPG~S~F~lSL  666 (983)
T PRK12900        635 SERHESRRIDRQLRGRAGRQGDPGESVFYVSL  666 (983)
T ss_pred             CCCCHHHHHHHHHHCCCCCCCCCCCEEEEEEC
T ss_conf             14230256787860432457999853999964


No 105
>PRK12899 secA preprotein translocase subunit SecA; Reviewed
Probab=98.79  E-value=8.6e-07  Score=72.86  Aligned_cols=79  Identities=19%  Similarity=0.332  Sum_probs=60.1

Q ss_pred             CCCCCHHHHHHHHHHHHHHHHCCEEEEEHHHHHHHHHHHHHHHHCCCCCCEEEEEECCCCHHHHHHHHHHHCCCCCEEEE
Q ss_conf             14422369999997334443054588612799999999862110145786589962464225667687762134754864
Q gi|254780945|r  301 DVGSGKTLVALIAMAAAVEAGGQAVIMAPIGILAQQHYEFIKKYTQNTQIIVEIITGNMPQAHRRKALERIAHGQAHIII  380 (700)
Q Consensus       301 DVGSGKTiVA~~A~l~~~~~G~Q~alMaPTEILA~QH~~~~~~~~~~~~i~v~lLtg~~~~~er~~i~~~i~~G~~~iiI  380 (700)
                      -.|-|||+||.++++..+-+|.-|-+....+-||+--.+...+.+.-+|++|.++.+.++..+|++.|.      +||.-
T Consensus       115 ~TGEGKTLvAtlpayLnAL~GkgVHVVTVNDYLA~RDaewMg~iy~fLGLtVg~i~~~~~~~eRr~aY~------~DItY  188 (969)
T PRK12899        115 QTGEGKTLTAVMPLYLNALTGKPVHLVTVNDYLAQRDCEWVGSVLRWLGLTTGVLVSGSPLEKRKAIYQ------CDVVY  188 (969)
T ss_pred             CCCCCHHHHHHHHHHHHHHCCCCCEEECCCHHHHHHHHHHHHHHHHHHCCEEEEECCCCCHHHHHHHHC------CCCEE
T ss_conf             178848999999999986459970997264365686699999999980977856389989899999866------99678


Q ss_pred             ECHHH
Q ss_conf             11120
Q gi|254780945|r  381 GTHAL  385 (700)
Q Consensus       381 GTHAL  385 (700)
                      ||..=
T Consensus       189 gTn~E  193 (969)
T PRK12899        189 GTASE  193 (969)
T ss_pred             ECCCC
T ss_conf             78866


No 106
>TIGR01389 recQ ATP-dependent DNA helicase RecQ; InterPro: IPR006293   The ATP-dependent DNA helicase RecQ (3.6.1 from EC) is involved in genome maintenance . All homologues tested to date unwind paired DNA, translocating in a 3' to 5' direction and several have a preference for forked or 4-way DNA structures (e.g. Holliday junctions) or for G-quartet DNA. The yeast protein, Sgs1, is present in numerous foci that coincide with sites of de novo synthesis DNA, such as the replication fork, and protein levels peak during S-phase.    A model has been proposed for Sgs1p action in the S-phase checkpoint response, both as a 'sensor' for damage during replication and a 'resolvase' for structures that arise at paused forks, such as the four-way 'chickenfoot' structure. The action of Sgs1p may serve to maintain the proper amount and integrity of ss DNA that is necessary for the binding of RPA (replication protein A, the eukaryotic ss DNA-binding protein)DNA pol complexes. Sgs1p would thus function by detecting (or resolving) aberrant DNA structures, and would thus contribute to the full activation of the DNA-dependent protein kinase, Mec1p and the effector kinase, Rad53p. Its ability to bind both the large subunit of RPA and the RecA-like protein Rad51p, place it in a unique position to resolve inappropriate fork structures that can occur when either the leading or lagging strand synthesis is stalled. Thus, RecQ helicases integrate checkpoint activation and checkpoint response. ; GO: 0004003 ATP-dependent DNA helicase activity, 0006310 DNA recombination, 0009432 SOS response.
Probab=98.79  E-value=3e-07  Score=76.45  Aligned_cols=300  Identities=20%  Similarity=0.289  Sum_probs=214.5

Q ss_pred             CHHHHHHHHHHHHHHCCCCCCEEEEEECCCCCHHHHHHHHHHHHHHHHCCEEEEEHHHH-HHHHHHHHHHHHCCCCCCEE
Q ss_conf             98899999999984100134307886214422369999997334443054588612799-99999986211014578658
Q gi|254780945|r  274 TKSQESAIKDILQDMSQKNRMLRILQGDVGSGKTLVALIAMAAAVEAGGQAVIMAPIGI-LAQQHYEFIKKYTQNTQIIV  352 (700)
Q Consensus       274 T~~Q~~ai~eI~~Dl~~~~pM~RLLQGDVGSGKTiVA~~A~l~~~~~G~Q~alMaPTEI-LA~QH~~~~~~~~~~~~i~v  352 (700)
                      =..|+..|+++...=+--.-|      =.|=||.+=+=+-+|.-   +.=+.+..| =| |=+=--++++..    ||..
T Consensus        15 R~gQe~II~~vL~g~~~l~vm------PTGGGKSlCYQ~PALll---~Glt~VISP-LIsLMkDQVd~L~~~----Gv~A   80 (607)
T TIGR01389        15 RGGQEEIIEHVLDGRDVLVVM------PTGGGKSLCYQVPALLL---KGLTVVISP-LISLMKDQVDQLRAA----GVAA   80 (607)
T ss_pred             CCHHHHHHHHHHCCCCEEEEC------CCCCCHHHHHHHHHHHH---CCCEEEECC-HHHHHHHHHHHHHHC----CCEE
T ss_conf             731589999984779858973------89985127772178872---898799842-363147799999860----7014


Q ss_pred             EEEECCCCHHHHHHHHHHHCCCCCEEE-EEC----HHHCCCCCCCCCCCEEEECCCCC-------CCHHHHH--HHHHC-
Q ss_conf             996246422566768776213475486-411----12013345544441788521013-------3568899--87402-
Q gi|254780945|r  353 EIITGNMPQAHRRKALERIAHGQAHII-IGT----HALFQDSIQYYKLILVIVDEQHR-------FGVQQRL--KLTQK-  417 (700)
Q Consensus       353 ~lLtg~~~~~er~~i~~~i~~G~~~ii-IGT----HAL~q~~v~F~~LgLvViDEQHR-------FGV~QR~--~L~~K-  417 (700)
                      +.|.|+++.+|..+|+..+.+|+++++ |-.    ..=|.+-+.=-++.|+=|||=|=       |=++=|.  .|.+. 
T Consensus        81 a~lNSt~s~~E~~~i~~~~~~G~~~LLYvAPERL~~~~Fl~~L~~~~i~L~AvDEAHCvSQWGHDFRPeY~~L~~l~~~f  160 (607)
T TIGR01389        81 AYLNSTLSAKEQQEIEKALVNGELKLLYVAPERLEQDYFLNMLKRLTIALLAVDEAHCVSQWGHDFRPEYRRLGELAERF  160 (607)
T ss_pred             EEECCCCCHHHHHHHHHHHHCCCEEEEEECCHHHHHHHHHHHHHCCCCEEEEEECCCCCCCCCCCCCHHHHHHHHHHHHC
T ss_conf             52037788889999999984198157751671321189998873199308998325021668888756589999999867


Q ss_pred             CCCCCCEEECHHHHHHHHHHHHHHCCCHHHHCCC--CCCCCCCEEEEEECC-CHHHHHHHHHHHHCCCCEEEEEECCCCC
Q ss_conf             5677610101013227899997520101111023--557666207999702-0026899997631038738999712012
Q gi|254780945|r  418 ATAPHVLLMTATPIPRTLVLTSLGDIDISKITEK--PAGRKPIKTVIIPIN-RIDEVIERLKVVLSEGKKAYWICPQIEE  494 (700)
Q Consensus       418 g~~ph~L~MtATPIPRTLal~~ygdldvS~i~e~--P~gR~~I~T~~~~~~-~~~~~~~~i~~~l~~g~q~y~VcPlIee  494 (700)
                      -..|=++.+|||-=|+|=.=.. --|+++-=.+-  =..|..|.=.++..+ +.+.+.++|+++-.  +|.=|||-.   
T Consensus       161 p~~P~~iALTATAd~~t~~DI~-~~L~L~~~~~f~~SFdRpNl~~~v~~k~n~~~~l~~yl~~~~~--G~SGIIYa~---  234 (607)
T TIGR01389       161 PQVPTRIALTATADAETRQDIV-ELLRLKDANEFISSFDRPNLRFSVVKKNNKKKFLLEYLKKHRE--GQSGIIYAS---  234 (607)
T ss_pred             CCCCEEEEEECCCCHHHHHHHH-HHCCCCCCCCCCCCCCCHHHHHHHHHHCCCCHHHHHHHHCCCC--CCCEEEECC---
T ss_conf             8986699872489987899999-9708898654125677511433431203781368999750799--953478767---


Q ss_pred             CCCCCCCHHHHHHHHHHHHCCCCEECCCCCCCHHHHHHHHHHHHCCCEEEEEECHHHHCCCCCCCCCEEEEECHHHCCHH
Q ss_conf             21112101466666668663710312014699899999999975598699998003410468887658998585254746
Q gi|254780945|r  495 KKESNFRSVVERFNSLHEHFTSSIAIIHGRMSDIDKESVMDSFKNGTCKLLIATTVIEVGIDVVDASIIIIENAEHFGLA  574 (700)
Q Consensus       495 se~~~~~~~~~~~~~l~~~~~~~v~~lHGkm~~~ek~~~m~~F~~g~~~iLvaTtviEVGvdvpna~~mvI~~aerfGLs  574 (700)
                          --+-||+.++.|... +-+.+.=|+-|+.++.++.-++|..-+..|.|||.-==.|||=||..-.|=.|-=+ -|=
T Consensus       235 ----sR~~VE~~~~~L~s~-G~~A~~YHAGL~~~~R~e~Q~~Fl~d~~~vmVAT~AFGMGIdKpnVRFViH~d~P~-~~E  308 (607)
T TIGR01389       235 ----SRKKVEELAERLESQ-GISALAYHAGLSNKVRAENQEDFLYDDVKVMVATNAFGMGIDKPNVRFVIHADMPK-NIE  308 (607)
T ss_pred             ----CHHHHHHHHHHHHHC-CCCEEECCCCCCHHHHHHHHHHHHHHCCEEEEEEECCCCCCCCCCCCEEEEECCCC-CHH
T ss_conf             ----704589999999747-96204036798776899997544462554888871235874787654888636874-211


Q ss_pred             HHHHHHHCCCCCCCCEEEEEEECCC
Q ss_conf             8877301166789835999970888
Q gi|254780945|r  575 QLHQLRGRVGRGEEISSCILLYHPP  599 (700)
Q Consensus       575 qLHQLRGRVGRg~~~s~c~l~~~~~  599 (700)
                      --.|==||-||-+.+|-|+|+|++.
T Consensus       309 sYYQE~GRAGRDGlpae~~lly~~~  333 (607)
T TIGR01389       309 SYYQEAGRAGRDGLPAEAILLYSLA  333 (607)
T ss_pred             HHHCCCCCCCCCCCHHHHHHHCCHH
T ss_conf             1310355468875267786724777


No 107
>PRK13107 preprotein translocase subunit SecA; Reviewed
Probab=98.75  E-value=1.8e-06  Score=70.24  Aligned_cols=96  Identities=24%  Similarity=0.268  Sum_probs=81.0

Q ss_pred             CCCCCHHHHHHHHHHHHHHHHCCEEEEEHHHHHHHHHHHHHHHHCCCCCCEEEEEECCCCHHHHHHHHHHHCCCCCEEEE
Q ss_conf             14422369999997334443054588612799999999862110145786589962464225667687762134754864
Q gi|254780945|r  301 DVGSGKTLVALIAMAAAVEAGGQAVIMAPIGILAQQHYEFIKKYTQNTQIIVEIITGNMPQAHRRKALERIAHGQAHIII  380 (700)
Q Consensus       301 DVGSGKTiVA~~A~l~~~~~G~Q~alMaPTEILA~QH~~~~~~~~~~~~i~v~lLtg~~~~~er~~i~~~i~~G~~~iiI  380 (700)
                      -.|-|||+||.++++..+-+|.-|-+....+-||+--.+...+.+.-+|++|.+.++.++..+|++.|.      +||+-
T Consensus       103 ~TGEGKTL~atlp~ylnal~g~gvhvvTvNdYLA~RDae~m~~vy~~lGlsvg~i~~~~~~~er~~aY~------~DitY  176 (908)
T PRK13107        103 RTGEGKTLTATLPAYLNALTGKGVHVITVNDYLARRDAENNRPLFEFLGLTVGINVAGLGQQEKKAAYN------ADITY  176 (908)
T ss_pred             CCCCCHHHHHHHHHHHHHHCCCCEEEECCCHHHHHHHHHHHHHHHHHHCCEEEECCCCCCHHHHHHHCC------CCCEE
T ss_conf             178855999999999987559970997265355475499999999981975733179999699998456------88645


Q ss_pred             ECHHHCC-----C-------CCCCCCCCEEEECC
Q ss_conf             1112013-----3-------45544441788521
Q gi|254780945|r  381 GTHALFQ-----D-------SIQYYKLILVIVDE  402 (700)
Q Consensus       381 GTHAL~q-----~-------~v~F~~LgLvViDE  402 (700)
                      ||..=|-     |       +..-..|-++||||
T Consensus       177 ~Tn~e~gFDYLRDnm~~~~~~~vqr~~~~aivDE  210 (908)
T PRK13107        177 GTNNEFGFDYLRDNMAFSPQERVQRPLHYALIDE  210 (908)
T ss_pred             ECCCCCCCCCCCCCCCCCHHHHCCCCCCEEEEEC
T ss_conf             3576423423574301575875356776488742


No 108
>PRK12901 secA preprotein translocase subunit SecA; Reviewed
Probab=98.71  E-value=3e-06  Score=68.54  Aligned_cols=96  Identities=29%  Similarity=0.337  Sum_probs=73.0

Q ss_pred             CCCCCHHHHHHHHHHHHHHHHCCEEEEEHHHHHHHHHHHHHHHHCCCCCCEEEEEECCC-CHHHHHHHHHHHCCCCCEEE
Q ss_conf             14422369999997334443054588612799999999862110145786589962464-22566768776213475486
Q gi|254780945|r  301 DVGSGKTLVALIAMAAAVEAGGQAVIMAPIGILAQQHYEFIKKYTQNTQIIVEIITGNM-PQAHRRKALERIAHGQAHII  379 (700)
Q Consensus       301 DVGSGKTiVA~~A~l~~~~~G~Q~alMaPTEILA~QH~~~~~~~~~~~~i~v~lLtg~~-~~~er~~i~~~i~~G~~~ii  379 (700)
                      -.|-|||+||.++++..+-+|.-|-+....+-||+--++...+++.-+|+.|.++.... ...+|++.|.      +||.
T Consensus       192 ~TGEGKTLvatlp~yLnAL~GkgVHvVTvNDYLA~RDaewmg~iy~fLGltvg~i~~~~~~~~~rr~aY~------~DIt  265 (1111)
T PRK12901        192 ATGEGKTLVATLPVFLNALTGNGVHVVTVNDYLAKRDSEWMGPLYMFHGLSVDCIDKHQPNSDARRKAYE------ADIT  265 (1111)
T ss_pred             ECCCCHHHHHHHHHHHHHHCCCCEEEEECCHHHHHHHHHHHHHHHHHHCCEEEEECCCCCCHHHHHHHHH------CCCE
T ss_conf             0688579999999999973699808983156778875998899999949865232699999799999873------7863


Q ss_pred             EECHHHCC------------CCCCCCCCCEEEECC
Q ss_conf             41112013------------345544441788521
Q gi|254780945|r  380 IGTHALFQ------------DSIQYYKLILVIVDE  402 (700)
Q Consensus       380 IGTHAL~q------------~~v~F~~LgLvViDE  402 (700)
                      -||..=|-            ++..-..+.++||||
T Consensus       266 YgTn~EfGFDYLRDnm~~~~~~~vqr~~~~aIVDE  300 (1111)
T PRK12901        266 YGTNNEFGFDYLRDNMAVSPKDLVQRKHNYAIVDE  300 (1111)
T ss_pred             ECCCCCCCHHHHHHHCCCCHHHHCCCCCCEEEEEC
T ss_conf             41565410243564015787872567776588842


No 109
>KOG0920 consensus
Probab=98.67  E-value=3.1e-07  Score=76.30  Aligned_cols=309  Identities=23%  Similarity=0.334  Sum_probs=172.3

Q ss_pred             HHHHHHHHHCCCCCCHHHHHHHHHHHHHHCCCCCCEEEEEECCCCCHHHHHHHHHHHH-HHHHCCEEEEE--HHHHHHHH
Q ss_conf             7899998630246798899999999984100134307886214422369999997334-44305458861--27999999
Q gi|254780945|r  260 KIAQKILRNIPFSPTKSQESAIKDILQDMSQKNRMLRILQGDVGSGKTLVALIAMAAA-VEAGGQAVIMA--PIGILAQQ  336 (700)
Q Consensus       260 ~~~~~f~~~LPF~LT~~Q~~ai~eI~~Dl~~~~pM~RLLQGDVGSGKTiVA~~A~l~~-~~~G~Q~alMa--PTEILA~Q  336 (700)
                      .....+.++||+--  -+++.++.|.    .+.  ..++-|+.|||||.=.---++.. +++|.-+-+++  |--|=|-=
T Consensus       163 ~~~~~~R~~LPa~~--~r~~Il~~i~----~~q--VvvIsGeTGcGKtTQvpQfiLd~~~~~~~~~~IicTQPRRIsAIs  234 (924)
T KOG0920         163 KEMLRFRESLPAYK--MRDTILDAIE----ENQ--VVVISGETGCGKTTQVPQFILDEAIESGAACNIICTQPRRISAIS  234 (924)
T ss_pred             HHHHHHHHHCCCHH--HHHHHHHHHH----HCC--EEEEECCCCCCCHHHHHHHHHHHHHHCCCCCEEEECCCCHHHHHH
T ss_conf             88887787496277--8999999997----496--699957889871224669999999862899738866775177899


Q ss_pred             HHHHHHH-HCCCCCCEEEEEECCCCHHHHHHHHHHHCCCCCEEEEECHHHC----CCCCCCCCCCEEEECCCCCCCHHHH
Q ss_conf             9986211-0145786589962464225667687762134754864111201----3345544441788521013356889
Q gi|254780945|r  337 HYEFIKK-YTQNTQIIVEIITGNMPQAHRRKALERIAHGQAHIIIGTHALF----QDSIQYYKLILVIVDEQHRFGVQQR  411 (700)
Q Consensus       337 H~~~~~~-~~~~~~i~v~lLtg~~~~~er~~i~~~i~~G~~~iiIGTHAL~----q~~v~F~~LgLvViDEQHRFGV~QR  411 (700)
                      -++.+.. ..+..|-.|.--.+          ++.-.+-+..+..-|..++    |.+-...+..-+|+||=|-=+++--
T Consensus       235 vAeRVa~ER~~~~g~~VGYqvr----------l~~~~s~~t~L~fcTtGvLLr~L~~~~~l~~~thiivDEVHER~i~~D  304 (924)
T KOG0920         235 VAERVAKERGESLGEEVGYQVR----------LESKRSRETRLLFCTTGVLLRRLQSDPTLSGVTHIIVDEVHERSINTD  304 (924)
T ss_pred             HHHHHHHHHCCCCCCEEEEEEE----------EECCCCCCEEEEEECHHHHHHHHCCCCCCCCCCEEEEEEEEECCCCCC
T ss_conf             9999988754666871368986----------201367751689840689998754686214586654422797167752


Q ss_pred             HHHHH-C---CCCCC--CEEECHHHHHHHHHHHHHHCCCHHHHCCCCCCC-CCCEEEEEECCCHHHHHHHHHHHHCCCCE
Q ss_conf             98740-2---56776--101010132278999975201011110235576-66207999702002689999763103873
Q gi|254780945|r  412 LKLTQ-K---ATAPH--VLLMTATPIPRTLVLTSLGDIDISKITEKPAGR-KPIKTVIIPINRIDEVIERLKVVLSEGKK  484 (700)
Q Consensus       412 ~~L~~-K---g~~ph--~L~MtATPIPRTLal~~ygdldvS~i~e~P~gR-~~I~T~~~~~~~~~~~~~~i~~~l~~g~q  484 (700)
                      .-|.- |   ..+||  +..||||== =.+=-.+||...+-.|   | || -||+++.     .+++++.+........+
T Consensus       305 flLi~lk~lL~~~p~LkvILMSAT~d-ae~fs~YF~~~pvi~i---~-grtfpV~~~f-----LEDil~~~~~~~~~~~~  374 (924)
T KOG0920         305 FLLILLKDLLPRNPDLKVILMSATLD-AELFSDYFGGCPVITI---P-GRTFPVKEYF-----LEDILSKTGYVSEDDSA  374 (924)
T ss_pred             CHHHHHHHHHHHCCCCEEEEEEEECC-HHHHHHHHCCCCEEEE---C-CCCCCHHHHH-----HHHHHHHHCCCCCCCCC
T ss_conf             17999998862288856998621126-2888987189935864---6-8786458878-----99999875144445565


Q ss_pred             E-----------------------------EEEECCCCCCCC-----CCCCHHHHHHHHHHHH--CCC----CEECCCCC
Q ss_conf             8-----------------------------999712012211-----1210146666666866--371----03120146
Q gi|254780945|r  485 A-----------------------------YWICPQIEEKKE-----SNFRSVVERFNSLHEH--FTS----SIAIIHGR  524 (700)
Q Consensus       485 ~-----------------------------y~VcPlIeese~-----~~~~~~~~~~~~l~~~--~~~----~v~~lHGk  524 (700)
                      -                             .|||+. ++...     -........++.|...  |.+    -|-.+|+.
T Consensus       375 ~~~~~~~~~~~~~~~~~~~~id~~Li~~li~~I~~~-~~~GaILVFLPG~~eI~~~~~~L~~~~~f~~~~~~~ilplHs~  453 (924)
T KOG0920         375 RSGPERSQLRLARLKLWEPEIDYDLIEDLIEYIDER-EFEGAILVFLPGWEEILQLKELLEVNLPFADSLKFAILPLHSS  453 (924)
T ss_pred             CCCCCCCCCCCCCCHHCCCCCCHHHHHHHHHHCCCC-CCCCEEEEECCCHHHHHHHHHHHHHCCCCCCCCCEEEEECCCC
T ss_conf             555566744322200115421477999998740557-8874289974888999999997541566566662588705100


Q ss_pred             CCHHHHHHHHHHHHCCCEEEEEECHHHHCCCCCCCCCEEEE--------ECHHHCCH---------HHHHHHHHCCCCCC
Q ss_conf             99899999999975598699998003410468887658998--------58525474---------68877301166789
Q gi|254780945|r  525 MSDIDKESVMDSFKNGTCKLLIATTVIEVGIDVVDASIIII--------ENAEHFGL---------AQLHQLRGRVGRGE  587 (700)
Q Consensus       525 m~~~ek~~~m~~F~~g~~~iLvaTtviEVGvdvpna~~mvI--------~~aerfGL---------sqLHQLRGRVGRg~  587 (700)
                      |.+.|+..|.+.--.|.-+|++||.+-|-.|.||+....|-        +|+++=..         |.-.|=|||.|| -
T Consensus       454 ~~~~eQ~~VF~~pp~g~RKIIlaTNIAETSITIdDVvyVIDsG~~Ke~~yD~~~~~s~l~~~wvSkAna~QR~GRAGR-v  532 (924)
T KOG0920         454 IPSEEQQAVFKRPPKGTRKIILATNIAETSITIDDVVYVIDSGLVKEKSYDPERKVSCLLLSWVSKANAKQRRGRAGR-V  532 (924)
T ss_pred             CCHHHHHHHCCCCCCCCCHHHHHHHHHHHCCCCCCEEEEEECCEEEEEEECCCCCCCCCEEEECCCCCHHHHCCCCCC-C
T ss_conf             886889986178999951232220137534523674799864715444405667854000242010036775455556-4


Q ss_pred             CCEEEEEEECC
Q ss_conf             83599997088
Q gi|254780945|r  588 EISSCILLYHP  598 (700)
Q Consensus       588 ~~s~c~l~~~~  598 (700)
                      ..|.||=+|..
T Consensus       533 ~~G~cy~Ly~~  543 (924)
T KOG0920         533 RPGICYHLYTR  543 (924)
T ss_pred             CCCEEEEECCC
T ss_conf             57626884053


No 110
>COG4096 HsdR Type I site-specific restriction-modification system, R (restriction) subunit and related helicases [Defense mechanisms]
Probab=98.65  E-value=4.8e-06  Score=66.97  Aligned_cols=295  Identities=19%  Similarity=0.232  Sum_probs=167.6

Q ss_pred             CCCHHHHHHHHHHHHHHCCCCCCEEEEEECCCCCHHHHHHHHHHHHHHHH--CCEEEEEHHHHHHHHHHHHHHHHCCCCC
Q ss_conf             67988999999999841001343078862144223699999973344430--5458861279999999986211014578
Q gi|254780945|r  272 SPTKSQESAIKDILQDMSQKNRMLRILQGDVGSGKTLVALIAMAAAVEAG--GQAVIMAPIGILAQQHYEFIKKYTQNTQ  349 (700)
Q Consensus       272 ~LT~~Q~~ai~eI~~Dl~~~~pM~RLLQGDVGSGKTiVA~~A~l~~~~~G--~Q~alMaPTEILA~QH~~~~~~~~~~~~  349 (700)
                      .+-.-|+.||+-+.+-.+.+++- -||+=-.|+|||=+|+.-+..-..+|  +.|.|+|-+-+|-.|-++.|..+++.. 
T Consensus       165 ~~RyyQ~~AI~rv~Eaf~~g~~r-aLlvMATGTGKTrTAiaii~rL~r~~~~KRVLFLaDR~~Lv~QA~~af~~~~P~~-  242 (875)
T COG4096         165 GPRYYQIIAIRRVIEAFSKGQNR-ALLVMATGTGKTRTAIAIIDRLIKSGWVKRVLFLADRNALVDQAYGAFEDFLPFG-  242 (875)
T ss_pred             CCHHHHHHHHHHHHHHHHCCCCE-EEEEEECCCCCCEEHHHHHHHHHHCCHHHEEEEEECHHHHHHHHHHHHHHHCCCC-
T ss_conf             62278899999999998668744-8999705888523199999999961414305676126789999999999639886-


Q ss_pred             CEEEEEECCCCHHHHHHHHHHHCCCCCEEEEEC-HHH----CCCCCCCCCC-----CEEEECCCCCCCHHHHHHHHHCCC
Q ss_conf             658996246422566768776213475486411-120----1334554444-----178852101335688998740256
Q gi|254780945|r  350 IIVEIITGNMPQAHRRKALERIAHGQAHIIIGT-HAL----FQDSIQYYKL-----ILVIVDEQHRFGVQQRLKLTQKAT  419 (700)
Q Consensus       350 i~v~lLtg~~~~~er~~i~~~i~~G~~~iiIGT-HAL----~q~~v~F~~L-----gLvViDEQHRFGV~QR~~L~~Kg~  419 (700)
                      -.+-++++..-            ++...|.++| .++    -++.+.+...     -||||||-|| |+.++.+=.-.-.
T Consensus       243 ~~~n~i~~~~~------------~~s~~i~lsTyqt~~~~~~~~~~~~~~f~~g~FDlIvIDEaHR-gi~~~~~~I~dYF  309 (875)
T COG4096         243 TKMNKIEDKKG------------DTSSEIYLSTYQTMTGRIEQKEDEYRRFGPGFFDLIVIDEAHR-GIYSEWSSILDYF  309 (875)
T ss_pred             CCEEEECCCCC------------CCCEEEEEEEHHHHHHHHHCCCCCCCCCCCCCEEEEEECHHHH-HHHHHHHHHHHHH
T ss_conf             40123201467------------8630588760377875640654565567888312899606666-6787667898899


Q ss_pred             CCCCEEECHHHHHHHHHHHHHHCC----------CHHHHCCCCCCCCCCEEEEEE------CCCHHHHHHHHHHHHCCCC
Q ss_conf             776101010132278999975201----------011110235576662079997------0200268999976310387
Q gi|254780945|r  420 APHVLLMTATPIPRTLVLTSLGDI----------DISKITEKPAGRKPIKTVIIP------INRIDEVIERLKVVLSEGK  483 (700)
Q Consensus       420 ~ph~L~MtATPIPRTLal~~ygdl----------dvS~i~e~P~gR~~I~T~~~~------~~~~~~~~~~i~~~l~~g~  483 (700)
                      ..-..-.||||=- |....-||--          +--+.|.-=..-++|...+--      .+...+--+...+.+....
T Consensus       310 dA~~~gLTATP~~-~~d~~T~~~F~g~Pt~~YsleeAV~DG~Lvpy~vi~i~~~~~~~G~~~~~~serek~~g~~i~~dd  388 (875)
T COG4096         310 DAATQGLTATPKE-TIDRSTYGFFNGEPTYAYSLEEAVEDGFLVPYKVIRIDTDFDLDGWKPDAGSEREKLQGEAIDEDD  388 (875)
T ss_pred             HHHHHHHCCCCCC-CCCCCCCCCCCCCCCEEECHHHHHHCCCCCCCCCEEEEEECCCCCCCCCCCCHHHHHHCCCCCCCC
T ss_conf             9988761257621-113231013379702241288885215457886337664315667476755232333134368654


Q ss_pred             EEE--------EEECCCCC------CCC-----------------CCCCHHHHHHHHHHHHCCC---C-EECCCCCCCHH
Q ss_conf             389--------99712012------211-----------------1210146666666866371---0-31201469989
Q gi|254780945|r  484 KAY--------WICPQIEE------KKE-----------------SNFRSVVERFNSLHEHFTS---S-IAIIHGRMSDI  528 (700)
Q Consensus       484 q~y--------~VcPlIee------se~-----------------~~~~~~~~~~~~l~~~~~~---~-v~~lHGkm~~~  528 (700)
                      |+|        .|||-=.+      +|.                 .+..-|+...+.+.+.||+   + +-.+.|  +.+
T Consensus       389 ~~~~~~d~dr~~v~~~~~~~V~r~~~e~l~~~~~g~~~~KTIvFa~n~dHAe~i~~~~~~~ype~~~~~a~~IT~--d~~  466 (875)
T COG4096         389 QNFEARDFDRTLVIPFRTETVARELTEYLKRGATGDEIGKTIVFAKNHDHAERIREALVNEYPEYNGRYAMKITG--DAE  466 (875)
T ss_pred             CCCCCCCCCHHEECCCHHHHHHHHHHHHHCCCCCCCCCCCEEEEEECCHHHHHHHHHHHHHCCCCCCCEEEEEEC--CCH
T ss_conf             463335532000031247899999999842566888668458996270789999999987480106745999844--406


Q ss_pred             HHHHHHHHHHCCCEEEEEECH--HHHCCCCCCCCCEEEEECHHHCCHHHHHHHHHCCCC
Q ss_conf             999999997559869999800--341046888765899858525474688773011667
Q gi|254780945|r  529 DKESVMDSFKNGTCKLLIATT--VIEVGIDVVDASIIIIENAEHFGLAQLHQLRGRVGR  585 (700)
Q Consensus       529 ek~~~m~~F~~g~~~iLvaTt--viEVGvdvpna~~mvI~~aerfGLsqLHQLRGRVGR  585 (700)
                      +-.+-+.+|...+-.==+|||  .+-.|||||..-.+|-. -.=+--.---|.-||=-|
T Consensus       467 ~~q~~Id~f~~ke~~P~IaitvdlL~TGiDvpev~nlVF~-r~V~SktkF~QMvGRGTR  524 (875)
T COG4096         467 QAQALIDNFIDKEKYPRIAITVDLLTTGVDVPEVVNLVFD-RKVRSKTKFKQMVGRGTR  524 (875)
T ss_pred             HHHHHHHHHHHCCCCCCEEEEHHHHHCCCCCHHEEEEEEH-HHHHHHHHHHHHHCCCCC
T ss_conf             5689999887437898358761245427876220456431-444668999998667654


No 111
>KOG0922 consensus
Probab=98.63  E-value=1e-05  Score=64.33  Aligned_cols=300  Identities=20%  Similarity=0.284  Sum_probs=181.2

Q ss_pred             HHCCCCCCHHHHHHHHHHHHHHCCCCCCEEEEEECCCCCHH--HHHHHHHHHHHHHHCCEEEEEHHHHHHHHHHHHHHHH
Q ss_conf             63024679889999999998410013430788621442236--9999997334443054588612799999999862110
Q gi|254780945|r  267 RNIPFSPTKSQESAIKDILQDMSQKNRMLRILQGDVGSGKT--LVALIAMAAAVEAGGQAVIMAPIGILAQQHYEFIKKY  344 (700)
Q Consensus       267 ~~LPF~LT~~Q~~ai~eI~~Dl~~~~pM~RLLQGDVGSGKT--iVA~~A~l~~~~~G~Q~alMaPTEILA~QH~~~~~~~  344 (700)
                      ++||-.      +.-++|..-+.++.-+  .+.|+.|||||  |.-.++-.-....|. .|.--|--|=|.--+.....-
T Consensus        48 ~~LPI~------~~r~~il~~ve~nqvl--IviGeTGsGKSTQipQyL~eaG~~~~g~-I~~TQPRRVAavslA~RVAeE  118 (674)
T KOG0922          48 ESLPIY------KYRDQILYAVEDNQVL--IVIGETGSGKSTQIPQYLAEAGFASSGK-IACTQPRRVAAVSLAKRVAEE  118 (674)
T ss_pred             CCCCHH------HHHHHHHHHHHHCCEE--EEECCCCCCCCCCHHHHHHHCCCCCCCC-EEEECCCHHHHHHHHHHHHHH
T ss_conf             159989------9999999999878779--9984898985332769998626566882-775067167788899999998


Q ss_pred             CC-CCCCEEEEEECCCCHHHHHHHHHHHCCCCCEEEEECHHHCCCCC----CCCCCCEEEECCCCCCCHHHHH------H
Q ss_conf             14-57865899624642256676877621347548641112013345----5444417885210133568899------8
Q gi|254780945|r  345 TQ-NTQIIVEIITGNMPQAHRRKALERIAHGQAHIIIGTHALFQDSI----QYYKLILVIVDEQHRFGVQQRL------K  413 (700)
Q Consensus       345 ~~-~~~i~v~lLtg~~~~~er~~i~~~i~~G~~~iiIGTHAL~q~~v----~F~~LgLvViDEQHRFGV~QR~------~  413 (700)
                      +. .+|-.|.--..          .++-.+.+-.|..=|--++....    ..+.-..||+||-|-=-++--.      +
T Consensus       119 ~~~~lG~~VGY~IR----------Fed~ts~~TrikymTDG~LLRE~l~Dp~LskYsvIIlDEAHERsl~TDiLlGlLKk  188 (674)
T KOG0922         119 MGCQLGEEVGYTIR----------FEDSTSKDTRIKYMTDGMLLREILKDPLLSKYSVIILDEAHERSLHTDILLGLLKK  188 (674)
T ss_pred             HCCCCCCEEEEEEE----------ECCCCCCCEEEEEECCHHHHHHHHCCCCCCCCCEEEEECHHHHHHHHHHHHHHHHH
T ss_conf             58976762226998----------45667873369996135999988508764544489983223101578899999999


Q ss_pred             HHHCCCCCCCEEECHHHHHHHHHHHHHHCCCHHHHCCCCCCCC-CCEEEEEECCCHHHHHHHHHHHH------CCCCEEE
Q ss_conf             7402567761010101322789999752010111102355766-62079997020026899997631------0387389
Q gi|254780945|r  414 LTQKATAPHVLLMTATPIPRTLVLTSLGDIDISKITEKPAGRK-PIKTVIIPINRIDEVIERLKVVL------SEGKKAY  486 (700)
Q Consensus       414 L~~Kg~~ph~L~MtATPIPRTLal~~ygdldvS~i~e~P~gR~-~I~T~~~~~~~~~~~~~~i~~~l------~~g~q~y  486 (700)
                      +..|-..--+++||||==-..++- +|+.-.+   =.- +||. ||...+.....-+.+-+.+...+      ..| -+.
T Consensus       189 i~~~R~~LklIimSATlda~kfS~-yF~~a~i---~~i-~GR~fPVei~y~~~p~~dYv~a~~~tv~~Ih~~E~~G-DIL  262 (674)
T KOG0922         189 ILKKRPDLKLIIMSATLDAEKFSE-YFNNAPI---LTI-PGRTFPVEILYLKEPTADYVDAALITVIQIHLTEPPG-DIL  262 (674)
T ss_pred             HHHCCCCCEEEEEEEEECHHHHHH-HHCCCCE---EEE-CCCCCCEEEEECCCCCHHHHHHHHHHHHHHHCCCCCC-CEE
T ss_conf             873277836999923524899999-8647956---766-6887755688636885046789999999987048998-789


Q ss_pred             EEECCCCCCCCCCCCHHHHHHHHHHHHCCCC----EECCCCCCCHHHHHHHHHHHHCCCEEEEEECHHHHCCCCCCCCCE
Q ss_conf             9971201221112101466666668663710----312014699899999999975598699998003410468887658
Q gi|254780945|r  487 WICPQIEEKKESNFRSVVERFNSLHEHFTSS----IAIIHGRMSDIDKESVMDSFKNGTCKLLIATTVIEVGIDVVDASI  562 (700)
Q Consensus       487 ~VcPlIeese~~~~~~~~~~~~~l~~~~~~~----v~~lHGkm~~~ek~~~m~~F~~g~~~iLvaTtviEVGvdvpna~~  562 (700)
                      |--+=-|     +..++.+...+..+..++.    +--+||.|+++|..+|...--.|.-++.+||.+-|.-|.+|.-.-
T Consensus       263 vFLtGqe-----EIe~~~~~l~e~~~~~~~~~~~~~lply~aL~~e~Q~rvF~p~p~g~RKvIlsTNIAETSlTI~GI~Y  337 (674)
T KOG0922         263 VFLTGQE-----EIEAACELLRERAKSLPEDCPELILPLYGALPSEEQSRVFDPAPPGKRKVILSTNIAETSLTIDGIRY  337 (674)
T ss_pred             EEECCHH-----HHHHHHHHHHHHHHHCCCCCCCEEEEEECCCCHHHHHHHCCCCCCCCCEEEEECCEEEEEEEECCEEE
T ss_conf             9937888-----99999999998765312457742222104588787620026799986248997231210177356289


Q ss_pred             EE--------EECHHHCCHH----------HHHHHHHCCCCCCCCEEEEEEECC
Q ss_conf             99--------8585254746----------887730116678983599997088
Q gi|254780945|r  563 II--------IENAEHFGLA----------QLHQLRGRVGRGEEISSCILLYHP  598 (700)
Q Consensus       563 mv--------I~~aerfGLs----------qLHQLRGRVGRg~~~s~c~l~~~~  598 (700)
                      .|        ++|+ +.|+.          |--|=-||-|| ..+|.||=+|..
T Consensus       338 VVDsG~vK~~~y~p-~~g~~~L~v~~ISkasA~QRaGRAGR-t~pGkcyRLYte  389 (674)
T KOG0922         338 VVDSGFVKQKKYNP-RTGLDSLIVVPISKASANQRAGRAGR-TGPGKCYRLYTE  389 (674)
T ss_pred             EECCCCEEEEEECC-CCCCCCEEEEECHHHHHHHHCCCCCC-CCCCEEEEEEEH
T ss_conf             97387367776356-46744126772129877533245789-889448885008


No 112
>KOG0349 consensus
Probab=98.60  E-value=1.5e-06  Score=70.88  Aligned_cols=302  Identities=22%  Similarity=0.286  Sum_probs=162.6

Q ss_pred             HHHHHHHHCCEEEEEHHHHHHHHHHHH---HHHHCCCCCCEEEEEECCCCHHHHHHHHHHHCCCCCEEEEECHHHCCC--
Q ss_conf             733444305458861279999999986---211014578658996246422566768776213475486411120133--
Q gi|254780945|r  314 MAAAVEAGGQAVIMAPIGILAQQHYEF---IKKYTQNTQIIVEIITGNMPQAHRRKALERIAHGQAHIIIGTHALFQD--  388 (700)
Q Consensus       314 ~l~~~~~G~Q~alMaPTEILA~QH~~~---~~~~~~~~~i~v~lLtg~~~~~er~~i~~~i~~G~~~iiIGTHAL~q~--  388 (700)
                      ....+.|..|+.+|-|.--||+|-|++   |+...++-.++--|+.|+.-   ++..+..+++| .+|||||---+.+  
T Consensus       279 ~~k~~pNap~avivepsrelaEqt~N~i~~Fk~h~~np~~r~lLmiggv~---~r~Q~~ql~~g-~~ivvGtpgRl~~~i  354 (725)
T KOG0349         279 SAKPAPNAPEAVIVEPSRELAEQTHNQIEEFKMHTSNPEVRSLLMIGGVL---KRTQCKQLKDG-THIVVGTPGRLLQPI  354 (725)
T ss_pred             CCCCCCCCCCEEEECCCHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHH---HHHHHHHHHCC-CEEEECCCHHHHHHH
T ss_conf             55669998400685476889999876699887643876564441235577---68888876248-605515841565554


Q ss_pred             ---CCCCCCCCEEEECCCCCCCH-----------HHHHHHHHCCCCCCCEEECHHHHHHHHHHHHHHCCCHHHHCCCCCC
Q ss_conf             ---45544441788521013356-----------8899874025677610101013227899997520101111023557
Q gi|254780945|r  389 ---SIQYYKLILVIVDEQHRFGV-----------QQRLKLTQKATAPHVLLMTATPIPRTLVLTSLGDIDISKITEKPAG  454 (700)
Q Consensus       389 ---~v~F~~LgLvViDEQHRFGV-----------~QR~~L~~Kg~~ph~L~MtATPIPRTLal~~ygdldvS~i~e~P~g  454 (700)
                         .|....-...|.||-.-|=-           .|=-.+.+.|..+...+-|||-               ++.+-+|-+
T Consensus       355 s~g~~~lt~crFlvlDead~lL~qgy~d~I~r~h~qip~~tsdg~rlq~~vCsatl---------------h~feVkk~~  419 (725)
T KOG0349         355 SKGLVTLTHCRFLVLDEADLLLGQGYDDKIYRFHGQIPHMTSDGFRLQSPVCSATL---------------HIFEVKKVG  419 (725)
T ss_pred             HCCCEEEEEEEEEEECCHHHHHHCCCHHHHHHHHCCCHHHHCCCCCCCCCEEEEEE---------------EEEEEEEHH
T ss_conf             20651332347898323366550541789999863341331477612331143377---------------677766633


Q ss_pred             CCC-CEEEEEECCCHHHH------------------HHHHHHHH------------------------------------
Q ss_conf             666-20799970200268------------------99997631------------------------------------
Q gi|254780945|r  455 RKP-IKTVIIPINRIDEV------------------IERLKVVL------------------------------------  479 (700)
Q Consensus       455 R~~-I~T~~~~~~~~~~~------------------~~~i~~~l------------------------------------  479 (700)
                      -+- --..|+..+..+.+                  |..++..|                                    
T Consensus       420 ervmhfptwVdLkgeD~vpetvHhvv~lv~p~~d~sw~~lr~~i~td~vh~kdn~~pg~~Spe~~s~a~kilkgEy~v~a  499 (725)
T KOG0349         420 ERVMHFPTWVDLKGEDLVPETVHHVVKLVCPSVDGSWCDLRQFIETDKVHTKDNLLPGQVSPENPSSATKILKGEYGVVA  499 (725)
T ss_pred             HHHCCCCEEEECCCCCCCCHHHCCCEEECCCCCCCCHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCHHHHH
T ss_conf             34314741575035545643221534422776686088876452147766323324565799984566577547332010


Q ss_pred             ---CCCCEEEEEECCCCCCCCCCCCHHHHHHHHHHHHCCC--CEECCCCCCCHHHHHHHHHHHHCCCEEEEEECHHHHCC
Q ss_conf             ---0387389997120122111210146666666866371--03120146998999999999755986999980034104
Q gi|254780945|r  480 ---SEGKKAYWICPQIEEKKESNFRSVVERFNSLHEHFTS--SIAIIHGRMSDIDKESVMDSFKNGTCKLLIATTVIEVG  554 (700)
Q Consensus       480 ---~~g~q~y~VcPlIeese~~~~~~~~~~~~~l~~~~~~--~v~~lHGkm~~~ek~~~m~~F~~g~~~iLvaTtviEVG  554 (700)
                         -+-.||.+.|-.     +.|-.+.+.   .+.+.=+.  ....|||-.+++|..+-++.|+.+..+.|+||.|---|
T Consensus       500 i~~h~mdkaiifcrt-----k~dcDnLer---~~~qkgg~~~scvclhgDrkP~Erk~nle~Fkk~dvkflictdvaarg  571 (725)
T KOG0349         500 IRRHAMDKAIIFCRT-----KQDCDNLER---MMNQKGGKHYSCVCLHGDRKPDERKANLESFKKFDVKFLICTDVAARG  571 (725)
T ss_pred             HHHHCCCCEEEEEEC-----CCCCHHHHH---HHHHCCCCCCEEEEEECCCCHHHHHHHHHHHHHCCEEEEEEEHHHHCC
T ss_conf             555346745999703-----566167999---998727864036888247882677887876652572799971044356


Q ss_pred             CCCCCCCEEEE-----------------ECHHHCCHHH-----------HH--HHHHCCCCC----CCCEEEEEEECCCC
Q ss_conf             68887658998-----------------5852547468-----------87--730116678----98359999708889
Q gi|254780945|r  555 IDVVDASIIII-----------------ENAEHFGLAQ-----------LH--QLRGRVGRG----EEISSCILLYHPPL  600 (700)
Q Consensus       555 vdvpna~~mvI-----------------~~aerfGLsq-----------LH--QLRGRVGRg----~~~s~c~l~~~~~~  600 (700)
                      +|+...-.||-                 -.|||.|||-           -|  --|||---.    ...|-|+- |+.+ 
T Consensus       572 ldi~g~p~~invtlpd~k~nyvhrigrvgraermglaislvat~~ekvwyh~c~srgr~c~nt~l~e~~gc~iw-yne~-  649 (725)
T KOG0349         572 LDITGLPFMINVTLPDDKTNYVHRIGRVGRAERMGLAISLVATVPEKVWYHWCKSRGRSCNNTNLTEVRGCCIW-YNEP-  649 (725)
T ss_pred             CCCCCCCEEEEEECCCCCCHHHHHHHCCCHHHHCCEEEEEEECCCHHEEEHHHHCCCCCCCCCCCCCCCCEEEE-ECCH-
T ss_conf             65427725999855865411545640201454405047776416502131003036876667765234635897-4766-


Q ss_pred             CHHHHHHHHHHHHHCH--HHHHHHHHHHHCCCCC-CCCCHHCCCCCCCCCCHHHH
Q ss_conf             9879999999984142--5899999985206300-02600069874400038875
Q gi|254780945|r  601 SKNSYTRLSVLKNTED--GFLIAEEDLKQRKEGE-ILGIKQSGMPKFLIAQPELH  652 (700)
Q Consensus       601 ~~~~~~Rl~~l~~~~d--Gf~iAe~Dl~lRG~G~-~~G~~QsG~~~~~~~d~~~d  652 (700)
                              +.+.+..|  --.|.+.|-.+.-|=+ +-|.---|..+++-..-++|
T Consensus       650 --------~llaeve~hln~ti~qv~~~~~vpv~~fdgkv~ygqk~~~~g~~y~~  696 (725)
T KOG0349         650 --------NLLAEVEDHLNITIQQVDKTMDVPVNDFDGKVVYGQKNLRTGSGYED  696 (725)
T ss_pred             --------HHHHHHHHHHCCEEEEECCCCCCCCCCCCCEEEECCCCCCCCCCCCC
T ss_conf             --------68898887515550210777777643567707753212566887200


No 113
>pfam00176 SNF2_N SNF2 family N-terminal domain. This domain is found in proteins involved in a variety of processes including transcription regulation (e.g., SNF2, STH1, brahma, MOT1), DNA repair (e.g., ERCC6, RAD16, RAD5), DNA recombination (e.g., RAD54), and chromatin unwinding (e.g., ISWI) as well as a variety of other proteins with little functional information (e.g., lodestar, ETL1).
Probab=98.58  E-value=1.8e-06  Score=70.34  Aligned_cols=145  Identities=22%  Similarity=0.314  Sum_probs=92.8

Q ss_pred             EEEEEECCCCCHHHHHHHHHHHHHHHH---CCEEEEEHHHHHHHHHHHHHHHHCCCCCCEEEEEECCCCHHHHHHH-HHH
Q ss_conf             078862144223699999973344430---5458861279999999986211014578658996246422566768-776
Q gi|254780945|r  295 LRILQGDVGSGKTLVALIAMAAAVEAG---GQAVIMAPIGILAQQHYEFIKKYTQNTQIIVEIITGNMPQAHRRKA-LER  370 (700)
Q Consensus       295 ~RLLQGDVGSGKTiVA~~A~l~~~~~G---~Q~alMaPTEILA~QH~~~~~~~~~~~~i~v~lLtg~~~~~er~~i-~~~  370 (700)
                      .-+|-=|.|-|||+-++..+......+   .-+.+.||..++. |=.+.+.+|+++..  +....|..  +.|.+. ...
T Consensus        18 ggiLaDeMGLGKTiq~ia~l~~~~~~~~~~~~~LIV~P~sl~~-~W~~Ei~~~~~~~~--~~~~~~~~--~~r~~~~~~~   92 (295)
T pfam00176        18 GGILADEMGLGKTLQTISLLAYLKELKPLAGPHLVVCPLSTLD-NWLNEFEKWAPDLN--IVVYYGDG--DSRSELLRNV   92 (295)
T ss_pred             CEEEECCCCCCHHHHHHHHHHHHHHHCCCCCCEEEEECHHHHH-HHHHHHHHHCCCCC--EEEEEECH--HHHHHHHHHH
T ss_conf             9897227875799999999999998388999889997578887-67889998679970--79998470--7689998867


Q ss_pred             HCCCCCEEEEEC-HHHCCCCCCCCC--CCEEEECCCCCCC--HHHHHHHHHCCCCCCCEEECHHHHHHHHHHHHHHCCCH
Q ss_conf             213475486411-120133455444--4178852101335--68899874025677610101013227899997520101
Q gi|254780945|r  371 IAHGQAHIIIGT-HALFQDSIQYYK--LILVIVDEQHRFG--VQQRLKLTQKATAPHVLLMTATPIPRTLVLTSLGDIDI  445 (700)
Q Consensus       371 i~~G~~~iiIGT-HAL~q~~v~F~~--LgLvViDEQHRFG--V~QR~~L~~Kg~~ph~L~MtATPIPRTLal~~ygdldv  445 (700)
                      ...+..+|+|-| +.+-.+.-.+.+  -..||+||=|++-  -.++.+-...=...+.+.+|+|||.-.+.= +|+=+++
T Consensus        93 ~~~~~~~ivitsY~~~~~~~~~l~~~~w~~vI~DEaH~iKN~~s~~~~a~~~l~~~~r~~LTGTPiqN~l~e-l~~ll~f  171 (295)
T pfam00176        93 LRTGKFDVLITSYEYIRRDKDELHKANWRYVILDEGHRIKNAKSKLSLALKSLKTNNRLLLTGTPIQNNLAE-LWSLLNF  171 (295)
T ss_pred             HHCCCCCEEEECHHHHHHHHHHHHCCCCCEEEEECCCCCCCHHHHHHHHHHHCCCCCEEEEECCCCCCCHHH-HHHHHHH
T ss_conf             741688599930999997599984087658998762012587889999999523581899868745588899-9999999


No 114
>PRK10917 ATP-dependent DNA helicase RecG; Provisional
Probab=98.58  E-value=7.8e-07  Score=73.19  Aligned_cols=120  Identities=18%  Similarity=0.387  Sum_probs=97.3

Q ss_pred             HHHHHHHHHHHHHCCEEEEEHH----HH----HHHHHHHHHHHHCCCCCCEEEEEECCCCHHHHHHHHHHHCCCCCEEEE
Q ss_conf             9999973344430545886127----99----999999862110145786589962464225667687762134754864
Q gi|254780945|r  309 VALIAMAAAVEAGGQAVIMAPI----GI----LAQQHYEFIKKYTQNTQIIVEIITGNMPQAHRRKALERIAHGQAHIII  380 (700)
Q Consensus       309 VA~~A~l~~~~~G~Q~alMaPT----EI----LA~QH~~~~~~~~~~~~i~v~lLtg~~~~~er~~i~~~i~~G~~~iiI  380 (700)
                      -+.-.+...+..|.||-+.+|-    |-    =|++-|+.+++.|++  .+|++++|+++..||+++.++..+|+++|+|
T Consensus       455 ~~~~~i~~~~~~g~q~y~v~p~ieese~~~~~~~~~~~~~l~~~~~~--~~v~~~hG~m~~~ek~~~m~~F~~g~~~iLv  532 (677)
T PRK10917        455 EVYERIREEIAKGRQAYVVCPLIEESEKLDLQSAEETYEELQKALPE--LRVGLLHGRMKPAEKDAVMAAFKAGEIDILV  532 (677)
T ss_pred             HHHHHHHHHHHCCCEEEEEECCCCCCCCCHHHHHHHHHHHHHHHCCC--CEEEEECCCCCHHHHHHHHHHHHCCCCCEEE
T ss_conf             99999999997599289994131123320177799999999844899--7599830789878999999999839999999


Q ss_pred             ECHHHCCCCCCCCCCCEEEECCCCCCCHHHHHHHHHC---C-CCCCCEEECHHHH
Q ss_conf             1112013345544441788521013356889987402---5-6776101010132
Q gi|254780945|r  381 GTHALFQDSIQYYKLILVIVDEQHRFGVQQRLKLTQK---A-TAPHVLLMTATPI  431 (700)
Q Consensus       381 GTHAL~q~~v~F~~LgLvViDEQHRFGV~QR~~L~~K---g-~~ph~L~MtATPI  431 (700)
                      .|. ++.-+|.-.|....||..-+|||..|=..|+..   | ....++.|+..|+
T Consensus       533 sTt-viEvGvdvpna~~mvi~~aerfGlsqLhQLRGRVgRg~~~~~c~l~~~~~~  586 (677)
T PRK10917        533 ATT-VIEVGVDVPNATVMVIENAERFGLAQLHQLRGRVGRGAAQSYCVLLYKDPL  586 (677)
T ss_pred             ECC-EEECCCCCCCCCEEEEECCCCCCHHHHHHHCCCCCCCCCCEEEEEEECCCC
T ss_conf             898-975586788885899977010536788774274367888458999838999


No 115
>COG4889 Predicted helicase [General function prediction only]
Probab=98.54  E-value=2.2e-05  Score=61.83  Aligned_cols=352  Identities=22%  Similarity=0.360  Sum_probs=196.9

Q ss_pred             CCCCCCHHHHHHHHHHHHHHCCCCCCEEEEEECCCCCHHHHHHHHHHHHHHHHCCEEEEEHHHHHHHHHHHHHHHHCCC-
Q ss_conf             0246798899999999984100134307886214422369999997334443054588612799999999862110145-
Q gi|254780945|r  269 IPFSPTKSQESAIKDILQDMSQKNRMLRILQGDVGSGKTLVALIAMAAAVEAGGQAVIMAPIGILAQQHYEFIKKYTQN-  347 (700)
Q Consensus       269 LPF~LT~~Q~~ai~eI~~Dl~~~~pM~RLLQGDVGSGKTiVA~~A~l~~~~~G~Q~alMaPTEILA~QH~~~~~~~~~~-  347 (700)
                      =|.+|-+-|+.|++.-.+-++.+-+= .|+. --|.|||--|+--+-+...  ....++||.--|-.|   +|+.|-.. 
T Consensus       158 ~~kk~R~hQq~Aid~a~~~F~~n~RG-kLIM-AcGTGKTfTsLkisEala~--~~iL~LvPSIsLLsQ---Tlrew~~~~  230 (1518)
T COG4889         158 KPKKPRPHQQTAIDAAKEGFSDNDRG-KLIM-ACGTGKTFTSLKISEALAA--ARILFLVPSISLLSQ---TLREWTAQK  230 (1518)
T ss_pred             CCCCCCHHHHHHHHHHHHHCCCCCCC-CEEE-ECCCCCCCHHHHHHHHHHH--HHEEEECCHHHHHHH---HHHHHHHCC
T ss_conf             87899836789999998625516677-5898-3378862137889999864--023654351899999---999885346


Q ss_pred             -CCCEEEEEECCCCHHH-----------------HHHHHHHH----CCCCCEEEEEC-HHHCC----CCCCCCCCCEEEE
Q ss_conf             -7865899624642256-----------------67687762----13475486411-12013----3455444417885
Q gi|254780945|r  348 -TQIIVEIITGNMPQAH-----------------RRKALERI----AHGQAHIIIGT-HALFQ----DSIQYYKLILVIV  400 (700)
Q Consensus       348 -~~i~v~lLtg~~~~~e-----------------r~~i~~~i----~~G~~~iiIGT-HAL~q----~~v~F~~LgLvVi  400 (700)
                       ++++..-.++..+.+.                 -+.|++..    +....-+|.-| ++|.-    ...-|.-.-|||.
T Consensus       231 ~l~~~a~aVcSD~kvsrs~eDik~sdl~~p~sT~~~~il~~~~~~~k~~~~~vvFsTYQSl~~i~eAQe~G~~~fDliic  310 (1518)
T COG4889         231 ELDFRASAVCSDDKVSRSAEDIKASDLPIPVSTDLEDILSEMEHRQKANGLTVVFSTYQSLPRIKEAQEAGLDEFDLIIC  310 (1518)
T ss_pred             CCCCEEEEEECCCCCCCCCCCCCHHCCCCCCCCCHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHHHCCCCCCCEEEE
T ss_conf             65512578863652344412321204788875749999999987533378389997021148789999749997537974


Q ss_pred             CCCCCC-CHHHHHHHHHCCC-------------CCCCEEECHHHHHHHHHHH---HHHCCCHHHHC-CCCCCC-------
Q ss_conf             210133-5688998740256-------------7761010101322789999---75201011110-235576-------
Q gi|254780945|r  401 DEQHRF-GVQQRLKLTQKAT-------------APHVLLMTATPIPRTLVLT---SLGDIDISKIT-EKPAGR-------  455 (700)
Q Consensus       401 DEQHRF-GV~QR~~L~~Kg~-------------~ph~L~MtATPIPRTLal~---~ygdldvS~i~-e~P~gR-------  455 (700)
                      ||-||= |+    .+..+..             ..--|+|||||=-=+=+.-   --.+..+|..| |.-.|-       
T Consensus       311 DEAHRTtGa----~~a~dd~saFt~vHs~~niKa~kRlYmTATPkiy~eS~K~kAkd~s~~l~SMDDe~~fGeef~rl~F  386 (1518)
T COG4889         311 DEAHRTTGA----TLAGDDKSAFTRVHSDQNIKAAKRLYMTATPKIYSESSKAKAKDHSAELSSMDDELTFGEEFHRLGF  386 (1518)
T ss_pred             CCHHCCCCC----EECCCCCCCCEEECCCCCHHHHHHHHCCCCCHHHCHHHHHHHHHCCCEEECCCHHHHHCHHHHCCCH
T ss_conf             400014462----3225772010453376415888766600686021225453032114301125526554546621226


Q ss_pred             -----CCC----EEEEEECCC--H-----------------H------HHHHHHHHHHC-----CC--------CEEEEE
Q ss_conf             -----662----079997020--0-----------------2------68999976310-----38--------738999
Q gi|254780945|r  456 -----KPI----KTVIIPINR--I-----------------D------EVIERLKVVLS-----EG--------KKAYWI  488 (700)
Q Consensus       456 -----~~I----~T~~~~~~~--~-----------------~------~~~~~i~~~l~-----~g--------~q~y~V  488 (700)
                           ..+    +-.++..++  +                 +      -+|..+.++-.     .|        +++.--
T Consensus       387 geAv~rdlLTDYKVmvlaVd~~~i~~~~~~~~~~~~~~L~~dd~~kIvG~wnGlakr~g~~n~~~~~~~d~ap~~RAIaF  466 (1518)
T COG4889         387 GEAVERDLLTDYKVMVLAVDKEVIAGVLQSVLSGPSKGLALDDVSKIVGCWNGLAKRNGEDNDLKNIKADTAPMQRAIAF  466 (1518)
T ss_pred             HHHHHHHHHCCCEEEEEEECHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCHHHHHHHHH
T ss_conf             77876401005258999831766524565630686434243445677777665665325536543676775078899999


Q ss_pred             ECCCCCCCCC--CCCHHHHHHH-HHHHHCCC-CEE--CCCCCCCHHHHHHHHH---HHHCCCEEEEEECHHHHCCCCCCC
Q ss_conf             7120122111--2101466666-66866371-031--2014699899999999---975598699998003410468887
Q gi|254780945|r  489 CPQIEEKKES--NFRSVVERFN-SLHEHFTS-SIA--IIHGRMSDIDKESVMD---SFKNGTCKLLIATTVIEVGIDVVD  559 (700)
Q Consensus       489 cPlIeese~~--~~~~~~~~~~-~l~~~~~~-~v~--~lHGkm~~~ek~~~m~---~F~~g~~~iLvaTtviEVGvdvpn  559 (700)
                      |--|++|.+.  ...-+.+.|. ++++.|++ .+.  -+.|.|...|+..-..   .|...+++||-----.--|||||-
T Consensus       467 ~k~I~tSK~i~~sFe~Vve~Y~~Elk~d~~nL~iSi~HvDGtmNal~R~~l~~l~~~~~~neckIlSNaRcLSEGVDVPa  546 (1518)
T COG4889         467 AKDIKTSKQIAESFETVVEAYDEELKKDFKNLKISIDHVDGTMNALERLDLLELKNTFEPNECKILSNARCLSEGVDVPA  546 (1518)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEEEEECCCCCCHHHHHHHHHHCCCCCCCCHHEEECCCHHHHCCCCCCC
T ss_conf             87667788788888999999999997326683688751467300888877886158899421011013315423788534


Q ss_pred             CCEEEEECHHHCCHHHHHHHHHCCCC---CCCCEEEEEEECCCCC-------------HHHHHHHHHHHHHCHHHHHHHH
Q ss_conf             65899858525474688773011667---8983599997088899-------------8799999999841425899999
Q gi|254780945|r  560 ASIIIIENAEHFGLAQLHQLRGRVGR---GEEISSCILLYHPPLS-------------KNSYTRLSVLKNTEDGFLIAEE  623 (700)
Q Consensus       560 a~~mvI~~aerfGLsqLHQLRGRVGR---g~~~s~c~l~~~~~~~-------------~~~~~Rl~~l~~~~dGf~iAe~  623 (700)
                      ..-.|-.|+ |=..-..-|--|||=|   |..-||-+|-.--+.+             +...+=|++|+.+.+    |+.
T Consensus       547 LDsViFf~p-r~smVDIVQaVGRVMRKa~gK~yGYIILPIalpegi~p~~~l~~n~nFk~VWqVlnALRShD~----amv  621 (1518)
T COG4889         547 LDSVIFFDP-RSSMVDIVQAVGRVMRKAKGKKYGYIILPIALPEGIKPLDELVNNTNFKNVWQVLKALRSHDE----AMV  621 (1518)
T ss_pred             CCEEEEECC-CHHHHHHHHHHHHHHHHCCCCCCCEEEEEECCCCCCCCHHHHHCCCCHHHHHHHHHHHHHCCH----HHH
T ss_conf             123798668-512889999999998727687665699873158777846777347318999999998873377----764


Q ss_pred             HH--HHCCCCCCCCC
Q ss_conf             98--52063000260
Q gi|254780945|r  624 DL--KQRKEGEILGI  636 (700)
Q Consensus       624 Dl--~lRG~G~~~G~  636 (700)
                      |+  ++-++|--.+.
T Consensus       622 ~~k~k~Ki~g~d~a~  636 (1518)
T COG4889         622 DFKEKIKIFGSDDAS  636 (1518)
T ss_pred             HHHHHHHCCCCCCCC
T ss_conf             149875023667788


No 116
>COG0653 SecA Preprotein translocase subunit SecA (ATPase, RNA helicase) [Intracellular trafficking and secretion]
Probab=98.47  E-value=2e-05  Score=62.13  Aligned_cols=110  Identities=25%  Similarity=0.303  Sum_probs=89.8

Q ss_pred             HHHHHHHHCCCCCCEEEEEECCCCCHHHHHHHHHHHHHHHHCCEEEEEHHHHHHHHHHHHHHHHCCCCCCEEEEEECCCC
Q ss_conf             99999841001343078862144223699999973344430545886127999999998621101457865899624642
Q gi|254780945|r  281 IKDILQDMSQKNRMLRILQGDVGSGKTLVALIAMAAAVEAGGQAVIMAPIGILAQQHYEFIKKYTQNTQIIVEIITGNMP  360 (700)
Q Consensus       281 i~eI~~Dl~~~~pM~RLLQGDVGSGKTiVA~~A~l~~~~~G~Q~alMaPTEILA~QH~~~~~~~~~~~~i~v~lLtg~~~  360 (700)
                      +.-|.-....-.+|.      ||=|||+||.++++...-+|.-|-+.-.-|=||+--.+...+++.-+|..|.+...+++
T Consensus        87 iG~i~lh~g~iaEM~------TGEGKTL~atlp~ylnaL~gkgVhvVTvNdYLA~RDae~m~~l~~~LGLsvG~~~~~m~  160 (822)
T COG0653          87 LGGIVLHLGDIAEMR------TGEGKTLVATLPAYLNALAGKGVHVVTVNDYLARRDAEWMGPLYEFLGLSVGVILAGMS  160 (822)
T ss_pred             HHCHHHCCCCEEEEE------CCCCHHHHHHHHHHHHHCCCCCCEEEEEHHHHHHHCHHHHHHHHHHCCCCEEECCCCCC
T ss_conf             612352378144554------37735999889999972389974895004877442899989999876882322358898


Q ss_pred             HHHHHHHHHHHCCCCCEEEEECHHHCC------------CCCCCCCCCEEEECC
Q ss_conf             256676877621347548641112013------------345544441788521
Q gi|254780945|r  361 QAHRRKALERIAHGQAHIIIGTHALFQ------------DSIQYYKLILVIVDE  402 (700)
Q Consensus       361 ~~er~~i~~~i~~G~~~iiIGTHAL~q------------~~v~F~~LgLvViDE  402 (700)
                      ..+|++++.      +||.-||..=|-            ++..-.++..+||||
T Consensus       161 ~~ek~~aY~------~DItY~TnnElGFDYLRDNm~~~~ee~vqr~~~faIvDE  208 (822)
T COG0653         161 PEEKRAAYA------CDITYGTNNELGFDYLRDNMVTSQEEKVQRGLNFAIVDE  208 (822)
T ss_pred             HHHHHHHHH------CCCEECCCCCCCCCHHHHHHHCCHHHHHHCCCCEEEECC
T ss_conf             678688873------375430550017552221432058775503688388755


No 117
>KOG0953 consensus
Probab=98.42  E-value=5.4e-05  Score=58.76  Aligned_cols=276  Identities=21%  Similarity=0.356  Sum_probs=174.0

Q ss_pred             HHHCCCCCC--HHHHHHHHHHHHHHCCC-------CCCEE---EEEECCCCCHHHHHHHHHHHHHHHHCCEEEEEHHHHH
Q ss_conf             863024679--88999999999841001-------34307---8862144223699999973344430545886127999
Q gi|254780945|r  266 LRNIPFSPT--KSQESAIKDILQDMSQK-------NRMLR---ILQGDVGSGKTLVALIAMAAAVEAGGQAVIMAPIGIL  333 (700)
Q Consensus       266 ~~~LPF~LT--~~Q~~ai~eI~~Dl~~~-------~pM~R---LLQGDVGSGKTiVA~~A~l~~~~~G~Q~alMaPTEIL  333 (700)
                      ...+| ++|  ++|+     ...||..|       ..|.|   +=-|-.-||||-=|+    .-..+-..+.+--|--.|
T Consensus       158 k~~fp-~l~~~Ddl~-----~isDLt~P~~WyP~AR~~~RkIi~H~GPTNSGKTy~AL----qrl~~aksGvycGPLrLL  227 (700)
T KOG0953         158 KQEFP-ELTRMDDLK-----KISDLTNPANWYPEARKIRRKIIMHVGPTNSGKTYRAL----QRLKSAKSGVYCGPLRLL  227 (700)
T ss_pred             HHHHC-CCCCCHHHH-----HHHCCCCCCCCCCHHHHHHHEEEEEECCCCCCHHHHHH----HHHHHHCCCEECCHHHHH
T ss_conf             77712-033602555-----54304798544825675431589875788884257999----987540266002608989


Q ss_pred             HHHHHHHHHHHCCCCCCEEEEEECCCCHHHHHHHHHHHCCCCCEEEEECHHHCCCCCCCCCCCEEEECCCCCCCHHHH--
Q ss_conf             999998621101457865899624642256676877621347548641112013345544441788521013356889--
Q gi|254780945|r  334 AQQHYEFIKKYTQNTQIIVEIITGNMPQAHRRKALERIAHGQAHIIIGTHALFQDSIQYYKLILVIVDEQHRFGVQQR--  411 (700)
Q Consensus       334 A~QH~~~~~~~~~~~~i~v~lLtg~~~~~er~~i~~~i~~G~~~iiIGTHAL~q~~v~F~~LgLvViDEQHRFGV~QR--  411 (700)
                      |.--|+.+..    .||+|.|+||-    ||+-.+.+  ...++.+-+|--...-+-.|.   .+||||=+---=.||  
T Consensus       228 A~EV~~r~na----~gipCdL~TGe----E~~~~~~~--~~~a~hvScTVEM~sv~~~ye---VAViDEIQmm~Dp~RGw  294 (700)
T KOG0953         228 AHEVYDRLNA----LGIPCDLLTGE----ERRFVLDN--GNPAQHVSCTVEMVSVNTPYE---VAVIDEIQMMRDPSRGW  294 (700)
T ss_pred             HHHHHHHHHH----CCCCCCCCCCC----EEEECCCC--CCCCCCEEEEEEEEECCCCEE---EEEEHHHHHHCCCCCCH
T ss_conf             9999987643----28873344461----25405788--886651478999840687057---88766677622765235


Q ss_pred             ----HHHHHCCCCCCCE-EECHHHHHHHHHHHHHHCCCHHHHCCCCCCCC-CCEEEEEECCCHHHHHHHHHHHHCCCCEE
Q ss_conf             ----9874025677610-10101322789999752010111102355766-62079997020026899997631038738
Q gi|254780945|r  412 ----LKLTQKATAPHVL-LMTATPIPRTLVLTSLGDIDISKITEKPAGRK-PIKTVIIPINRIDEVIERLKVVLSEGKKA  485 (700)
Q Consensus       412 ----~~L~~Kg~~ph~L-~MtATPIPRTLal~~ygdldvS~i~e~P~gR~-~I~T~~~~~~~~~~~~~~i~~~l~~g~q~  485 (700)
                          +-|.-.....|+- -=+|-||-|.++-..=-|+.|-.-.     |. |.   ++.    +.+...+ ..+..| -|
T Consensus       295 AWTrALLGl~AdEiHLCGepsvldlV~~i~k~TGd~vev~~Ye-----Rl~pL---~v~----~~~~~sl-~nlk~G-DC  360 (700)
T KOG0953         295 AWTRALLGLAADEIHLCGEPSVLDLVRKILKMTGDDVEVREYE-----RLSPL---VVE----ETALGSL-SNLKPG-DC  360 (700)
T ss_pred             HHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHCCCEEEEEEEC-----CCCCC---EEH----HHHHHHH-CCCCCC-CE
T ss_conf             9999987440556100588048999999986317814897600-----05765---000----4232023-068888-76


Q ss_pred             EEEECCCCCCCCCCCCHHHHHHHHHHHHCCCCEECCCCCCCHHHHHHHHHHHHC--CCEEEEEECHHHHCCCCCCCCCEE
Q ss_conf             999712012211121014666666686637103120146998999999999755--986999980034104688876589
Q gi|254780945|r  486 YWICPQIEEKKESNFRSVVERFNSLHEHFTSSIAIIHGRMSDIDKESVMDSFKN--GTCKLLIATTVIEVGIDVVDASII  563 (700)
Q Consensus       486 y~VcPlIeese~~~~~~~~~~~~~l~~~~~~~v~~lHGkm~~~ek~~~m~~F~~--g~~~iLvaTtviEVGvdvpna~~m  563 (700)
                       +||=    |.    +++-+.-..+.+.-..++.++-|-+.++-|-+.-..|.+  ++.||||||--|-.|.|.---.++
T Consensus       361 -vV~F----Sk----k~I~~~k~kIE~~g~~k~aVIYGsLPPeTr~aQA~~FNd~~~e~dvlVAsDAIGMGLNL~IrRii  431 (700)
T KOG0953         361 -VVAF----SK----KDIFTVKKKIEKAGNHKCAVIYGSLPPETRLAQAALFNDPSNECDVLVASDAIGMGLNLNIRRII  431 (700)
T ss_pred             -EEEE----EH----HHHHHHHHHHHHHCCCCEEEEECCCCCCHHHHHHHHHCCCCCCCCEEEEECCCCCCCCCCEEEEE
T ss_conf             -9994----11----14888899999855855489955899730688898737988762568862321455444311798


Q ss_pred             EE-------ECHHHCCHHHHHHHHHCCCCCC
Q ss_conf             98-------5852547468877301166789
Q gi|254780945|r  564 II-------ENAEHFGLAQLHQLRGRVGRGE  587 (700)
Q Consensus       564 vI-------~~aerfGLsqLHQLRGRVGRg~  587 (700)
                      --       ..-+-.-.||.-|.-||-||=+
T Consensus       432 F~sl~Kysg~e~~~it~sqikQIAGRAGRf~  462 (700)
T KOG0953         432 FYSLIKYSGRETEDITVSQIKQIAGRAGRFG  462 (700)
T ss_pred             EEECCCCCCCCCEECCHHHHHHHHHCCCCCC
T ss_conf             7503567766210256899998851015445


No 118
>PRK07246 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
Probab=98.42  E-value=0.00044  Score=51.60  Aligned_cols=137  Identities=17%  Similarity=0.268  Sum_probs=95.0

Q ss_pred             HCCCCCCHHHHHHHHHHHHHHCCCCCCEEEEEECCCCCHHHHHHHHHHHHHHHHCCEEEEEHHHHHHHHHHHH-HHHHCC
Q ss_conf             3024679889999999998410013430788621442236999999733444305458861279999999986-211014
Q gi|254780945|r  268 NIPFSPTKSQESAIKDILQDMSQKNRMLRILQGDVGSGKTLVALIAMAAAVEAGGQAVIMAPIGILAQQHYEF-IKKYTQ  346 (700)
Q Consensus       268 ~LPF~LT~~Q~~ai~eI~~Dl~~~~pM~RLLQGDVGSGKTiVA~~A~l~~~~~G~Q~alMaPTEILA~QH~~~-~~~~~~  346 (700)
                      -+.|+.=.+|.+-.+.|.+.++.+...  ++.--+|.|||+-+++.++ +..++..+.+=..|-.|-+|-++. +..+-.
T Consensus       241 ~~g~E~R~~Q~~Ma~~V~~al~~~~~l--~IEAgTGtGKTlaYLlPai-a~~~~~~vVIST~T~~LQeQL~~kDlp~L~~  317 (820)
T PRK07246        241 LLGLEERPKQEQFAQLVDEDYHDGVAS--FIEAQTGIGKTYGYLLPLL-AQSDQNQIIVSVPTKLLQDQIMAGEVKAIQE  317 (820)
T ss_pred             CCCCCCCHHHHHHHHHHHHHHCCCCCE--EEECCCCCCHHHHHHHHHH-HHCCCCEEEEEECCHHHHHHHHHHHHHHHHH
T ss_conf             679861889999999999998058838--9988999647999999999-8437983999908699999999978999999


Q ss_pred             CCCCEEEEEECCCC-----------------------------------HHHHH---------HHHHHH-----------
Q ss_conf             57865899624642-----------------------------------25667---------687762-----------
Q gi|254780945|r  347 NTQIIVEIITGNMP-----------------------------------QAHRR---------KALERI-----------  371 (700)
Q Consensus       347 ~~~i~v~lLtg~~~-----------------------------------~~er~---------~i~~~i-----------  371 (700)
                      .+++++.+|-|.-.                                   ..++.         ..+..+           
T Consensus       318 ~l~~~~~~lKGr~nYLcL~~~~~~l~~~d~~~~~~~~~~~ll~Wl~~T~tGD~dEL~~~~~~~~~~~~i~~~~~l~~~~~  397 (820)
T PRK07246        318 QFHIACHSLKGPQNYLKLDSFYDSLQQNDQNRLVNRYKMQLLVWLLETETGDLDEIKQKQRYAAYFDQLKHDGDLKQSSL  397 (820)
T ss_pred             HHCCCCCEEECHHHCCCHHHHHHHHCCCCHHHHHHHHHHHHHHHHHCCCCCCHHHCCCCHHHHHHHHHCCCCCCCCCCCC
T ss_conf             84875033656786164888999860453023545899999999726898897772354103578775065577887898


Q ss_pred             ------------CCCCCEEEEECHHHCCCCC----CCCCCCEEEECCCCCCC
Q ss_conf             ------------1347548641112013345----54444178852101335
Q gi|254780945|r  372 ------------AHGQAHIIIGTHALFQDSI----QYYKLILVIVDEQHRFG  407 (700)
Q Consensus       372 ------------~~G~~~iiIGTHAL~q~~v----~F~~LgLvViDEQHRFG  407 (700)
                                  +.-.++|||--||++-.++    .|..-..+||||=|++=
T Consensus       398 ~~~~cf~~~ar~~a~~AdivI~NHalLl~~~~~~~~~~~~~~lIiDEAH~L~  449 (820)
T PRK07246        398 FYDYDFWKRSYEKAKTARLLITNHAYFLTRVQDDKDFVRNKVLVFDEAQKLM  449 (820)
T ss_pred             CCCCHHHHHHHHHHHHCCEEEECHHHHHHHHHHCCCCCCCCEEEEECCCHHH
T ss_conf             7640599999999861658984679999987414457768879998814279


No 119
>COG1200 RecG RecG-like helicase [DNA replication, recombination, and repair / Transcription]
Probab=98.38  E-value=3.4e-06  Score=68.21  Aligned_cols=116  Identities=20%  Similarity=0.418  Sum_probs=99.1

Q ss_pred             HHHHHHHHHCCEEEEEH----HH----HHHHHHHHHHHHHCCCCCCEEEEEECCCCHHHHHHHHHHHCCCCCEEEEECHH
Q ss_conf             97334443054588612----79----99999998621101457865899624642256676877621347548641112
Q gi|254780945|r  313 AMAAAVEAGGQAVIMAP----IG----ILAQQHYEFIKKYTQNTQIIVEIITGNMPQAHRRKALERIAHGQAHIIIGTHA  384 (700)
Q Consensus       313 A~l~~~~~G~Q~alMaP----TE----ILA~QH~~~~~~~~~~~~i~v~lLtg~~~~~er~~i~~~i~~G~~~iiIGTHA  384 (700)
                      -+...+..|.||-+.+|    .|    --|..-|+.++++|+.+  +|.|++|+++.+||.++.++.++|+++|+|-|. 
T Consensus       465 ~i~~ei~~GrQaY~VcPLIeeSE~l~l~~a~~~~~~L~~~~~~~--~vgL~HGrm~~~eKd~vM~~Fk~~e~~ILVaTT-  541 (677)
T COG1200         465 RIREEIAKGRQAYVVCPLIEESEKLELQAAEELYEELKSFLPEL--KVGLVHGRMKPAEKDAVMEAFKEGEIDILVATT-  541 (677)
T ss_pred             HHHHHHHCCCEEEEEECCCCCCCCCHHHHHHHHHHHHHHHCCCC--EEEEEECCCCHHHHHHHHHHHHCCCCCEEEEEE-
T ss_conf             99999974997999952535433113654999999999870546--367775689867799999999808876899813-


Q ss_pred             HCCCCCCCCCCCEEEECCCCCCCHHHHHHHHHC---CC-CCCCEEECHHHH
Q ss_conf             013345544441788521013356889987402---56-776101010132
Q gi|254780945|r  385 LFQDSIQYYKLILVIVDEQHRFGVQQRLKLTQK---AT-APHVLLMTATPI  431 (700)
Q Consensus       385 L~q~~v~F~~LgLvViDEQHRFGV~QR~~L~~K---g~-~ph~L~MtATPI  431 (700)
                      ++.=+|.-.|..+.||..-.|||..|=..|+..   |. ...++.|+-.|-
T Consensus       542 VIEVGVdVPnATvMVIe~AERFGLaQLHQLRGRVGRG~~qSyC~Ll~~~~~  592 (677)
T COG1200         542 VIEVGVDVPNATVMVIENAERFGLAQLHQLRGRVGRGDLQSYCVLLYKPPL  592 (677)
T ss_pred             EEEECCCCCCCEEEEEECHHHHHHHHHHHHCCCCCCCCCCEEEEEEECCCC
T ss_conf             899523578870799965433037888875265578875448999967987


No 120
>KOG0385 consensus
Probab=98.38  E-value=0.00033  Score=52.54  Aligned_cols=361  Identities=17%  Similarity=0.258  Sum_probs=207.6

Q ss_pred             CCHHHHHHHHHHHHHHCCCCCCEEEEEECCCCCHHH--HHHHHHHHHHHH-HCCEEEEEHHHHHHHHHHHHHHHHCCCCC
Q ss_conf             798899999999984100134307886214422369--999997334443-05458861279999999986211014578
Q gi|254780945|r  273 PTKSQESAIKDILQDMSQKNRMLRILQGDVGSGKTL--VALIAMAAAVEA-GGQAVIMAPIGILAQQHYEFIKKYTQNTQ  349 (700)
Q Consensus       273 LT~~Q~~ai~eI~~Dl~~~~pM~RLLQGDVGSGKTi--VA~~A~l~~~~~-G~Q~alMaPTEILA~QH~~~~~~~~~~~~  349 (700)
                      |..-|.+-++=...=-  ....|-+|--..|=|||+  +|+++-+.-..+ -.--.+.||-..|.. -.+.|++|.+.+ 
T Consensus       168 lr~YQveGlnWLi~l~--engingILaDEMGLGKTlQtIs~l~yl~~~~~~~GPfLVi~P~StL~N-W~~Ef~rf~P~l-  243 (971)
T KOG0385         168 LRDYQLEGLNWLISLY--ENGINGILADEMGLGKTLQTISLLGYLKGRKGIPGPFLVIAPKSTLDN-WMNEFKRFTPSL-  243 (971)
T ss_pred             CCHHHHCCHHHHHHHH--HCCCCCEEEHHCCCCHHHHHHHHHHHHHHHCCCCCCEEEEEEHHHHHH-HHHHHHHHCCCC-
T ss_conf             5433203379999998--657665842310453389999999999985179998499812766789-999999768986-


Q ss_pred             CEEEEEECCCCHHHHHHHHHHHC-CCCCEEEEECH-HHCCCCCCCC--CCCEEEECCCCCCCHHHHHHHHH---CCCCCC
Q ss_conf             65899624642256676877621-34754864111-2013345544--44178852101335688998740---256776
Q gi|254780945|r  350 IIVEIITGNMPQAHRRKALERIA-HGQAHIIIGTH-ALFQDSIQYY--KLILVIVDEQHRFGVQQRLKLTQ---KATAPH  422 (700)
Q Consensus       350 i~v~lLtg~~~~~er~~i~~~i~-~G~~~iiIGTH-AL~q~~v~F~--~LgLvViDEQHRFGV~QR~~L~~---Kg~~ph  422 (700)
                       ++..+.|.-  .+|.....++. .|..+|+|-|- -.+-++-.++  +-.++||||-||--- +.-.|..   .=..++
T Consensus       244 -~~~~~~Gdk--~eR~~~~r~~~~~~~fdV~iTsYEi~i~dk~~lk~~~W~ylvIDEaHRiKN-~~s~L~~~lr~f~~~n  319 (971)
T KOG0385         244 -NVVVYHGDK--EERAALRRDIMLPGRFDVCITSYEIAIKDKSFLKKFNWRYLVIDEAHRIKN-EKSKLSKILREFKTDN  319 (971)
T ss_pred             -CEEEEECCH--HHHHHHHHHHHCCCCCCEEEEHHHHHHHHHHHHHCCCCEEEEECHHHHHCC-HHHHHHHHHHHHCCCC
T ss_conf             -349884799--999999998531578766864078898668898619934999523654146-2448999999856655


Q ss_pred             CEEECHHHHHHHHHH----------HHHHCCC-------H---------------------------HHHCCCCCCCCCC
Q ss_conf             101010132278999----------9752010-------1---------------------------1110235576662
Q gi|254780945|r  423 VLLMTATPIPRTLVL----------TSLGDID-------I---------------------------SKITEKPAGRKPI  458 (700)
Q Consensus       423 ~L~MtATPIPRTLal----------~~ygdld-------v---------------------------S~i~e~P~gR~~I  458 (700)
                      -|..|-||+--.|+=          -+|+|.|       .                           -+...+||  |..
T Consensus       320 rLLlTGTPLQNNL~ELWaLLnFllPdiF~~~e~F~swF~~~~~~~~~e~v~~Lh~vL~pFlLRR~K~dVe~sLpp--KkE  397 (971)
T KOG0385         320 RLLLTGTPLQNNLHELWALLNFLLPDIFNSAEDFDSWFDFTNCEGDQELVSRLHKVLRPFLLRRIKSDVEKSLPP--KKE  397 (971)
T ss_pred             EEEEECCCCCCCHHHHHHHHHHHCHHHCCCHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCC--CCE
T ss_conf             267527854364999999997622142057889999971134335589999999866389999988878741897--532


Q ss_pred             EEEEEECCCHH-HHHHHH-HHHHCCCC----------------------EEEE---EEC---------CCCCCCCCC---
Q ss_conf             07999702002-689999-76310387----------------------3899---971---------201221112---
Q gi|254780945|r  459 KTVIIPINRID-EVIERL-KVVLSEGK----------------------KAYW---ICP---------QIEEKKESN---  499 (700)
Q Consensus       459 ~T~~~~~~~~~-~~~~~i-~~~l~~g~----------------------q~y~---VcP---------lIeese~~~---  499 (700)
                      .+..++..++. +.|..+ .+.|..=+                      .-|.   +-|         +|+.|.++-   
T Consensus       398 ~~iyvgms~mQkk~Y~~iL~kdl~~~n~~~~~~k~kL~NI~mQLRKccnHPYLF~g~ePg~pyttdehLv~nSGKm~vLD  477 (971)
T KOG0385         398 LIIYVGMSSMQKKWYKAILMKDLDALNGEGKGEKTKLQNIMMQLRKCCNHPYLFDGAEPGPPYTTDEHLVTNSGKMLVLD  477 (971)
T ss_pred             EEEEECCHHHHHHHHHHHHHHCCHHHCCCCCCCHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHCCCCEEHHH
T ss_conf             67860650889999999996113754266632037899999999974699641488888999886217875476111699


Q ss_pred             ---------------CCHHHHHHHHHHHHC---CCCEECCCCCCCHHHHHHHHHHHHCCC---EEEEEECHHHHCCCCCC
Q ss_conf             ---------------101466666668663---710312014699899999999975598---69999800341046888
Q gi|254780945|r  500 ---------------FRSVVERFNSLHEHF---TSSIAIIHGRMSDIDKESVMDSFKNGT---CKLLIATTVIEVGIDVV  558 (700)
Q Consensus       500 ---------------~~~~~~~~~~l~~~~---~~~v~~lHGkm~~~ek~~~m~~F~~g~---~~iLvaTtviEVGvdvp  558 (700)
                                     ..-.+.....|..+.   +...--+-|.++.+|....|++|.+-.   .=-|+||--=-+|||..
T Consensus       478 kLL~~Lk~~GhRVLIFSQmt~mLDILeDyc~~R~y~ycRiDGSt~~eeR~~aI~~fn~~~s~~FiFlLSTRAGGLGINL~  557 (971)
T KOG0385         478 KLLPKLKEQGHRVLIFSQMTRMLDILEDYCMLRGYEYCRLDGSTSHEEREDAIEAFNAPPSEKFIFLLSTRAGGLGINLT  557 (971)
T ss_pred             HHHHHHHHCCCEEEEEHHHHHHHHHHHHHHHHCCCEEEEECCCCCCHHHHHHHHHCCCCCCCEEEEEEECCCCCCCCCCC
T ss_conf             88899984897699826988899999999875175268723888707899999863899762589998504666630222


Q ss_pred             CCCEEEEECHHHCCHHHHH--HHHHCCCCCCCCEEEEEEECCCCCHH------HHHHHHHHHHHC--------HH-HHHH
Q ss_conf             7658998585254746887--73011667898359999708889987------999999998414--------25-8999
Q gi|254780945|r  559 DASIIIIENAEHFGLAQLH--QLRGRVGRGEEISSCILLYHPPLSKN------SYTRLSVLKNTE--------DG-FLIA  621 (700)
Q Consensus       559 na~~mvI~~aerfGLsqLH--QLRGRVGRg~~~s~c~l~~~~~~~~~------~~~Rl~~l~~~~--------dG-f~iA  621 (700)
                      .|.+.|++++|-=-=+-|.  +=--|+|--..--..=|++.+.+.+.      ++-||.-|+=-.        +| -.-.
T Consensus       558 aADtVIlyDSDWNPQ~DLQAmDRaHRIGQ~K~V~V~RLitentVEe~IveRA~~KL~Ld~~VIq~g~l~~~~~~~~~k~~  637 (971)
T KOG0385         558 AADTVILYDSDWNPQVDLQAMDRAHRIGQKKPVVVYRLITENTVEEKIVERAAAKLRLDKLVIQQGRLEEQKSNGLGKDE  637 (971)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHHHHCCCCCCEEEEEEECCCHHHHHHHHHHHHHHCHHHHHHCCCCHHHHHCCCCCHHH
T ss_conf             36479996689982143788998886078771599997535518999999999874415530137705532035431777


Q ss_pred             HHHHHHCCCCCCCCCHHCCCCC
Q ss_conf             9998520630002600069874
Q gi|254780945|r  622 EEDLKQRKEGEILGIKQSGMPK  643 (700)
Q Consensus       622 e~Dl~lRG~G~~~G~~QsG~~~  643 (700)
                      -.+|---|++.++-..||+..+
T Consensus       638 ~l~~~r~g~~~~f~~~es~~~d  659 (971)
T KOG0385         638 LLNLLRFGADPVFESKESTISD  659 (971)
T ss_pred             HHHHHHCCCHHHHHCCCCCCCH
T ss_conf             9999873826553103455503


No 121
>pfam07517 SecA_DEAD SecA DEAD-like domain. SecA protein binds to the plasma membrane where it interacts with proOmpA to support translocation of proOmpA through the membrane. SecA protein achieves this translocation, in association with SecY protein, in an ATP dependent manner. This domain represents the N-terminal ATP-dependent helicase domain, which is related to the pfam00270.
Probab=98.31  E-value=3e-06  Score=68.54  Aligned_cols=102  Identities=25%  Similarity=0.307  Sum_probs=88.1

Q ss_pred             EEEEEECCCCCHHHHHHHHHHHHHHHHCCEEEEEHHHHHHHHHHHHHHHHCCCCCCEEEEEECCCCHHHHHHHHHHHCCC
Q ss_conf             07886214422369999997334443054588612799999999862110145786589962464225667687762134
Q gi|254780945|r  295 LRILQGDVGSGKTLVALIAMAAAVEAGGQAVIMAPIGILAQQHYEFIKKYTQNTQIIVEIITGNMPQAHRRKALERIAHG  374 (700)
Q Consensus       295 ~RLLQGDVGSGKTiVA~~A~l~~~~~G~Q~alMaPTEILA~QH~~~~~~~~~~~~i~v~lLtg~~~~~er~~i~~~i~~G  374 (700)
                      -++.|=-.|=|||+||.++++..+-+|..|-+....+-||+--.+.+.++|.-+|++|.+.++.++..+|++.+.     
T Consensus        92 G~IaEM~TGEGKTL~atl~a~l~AL~Gk~VhvvTvNdYLA~RDae~m~~vy~~LGLsvg~i~~~~~~~err~aY~-----  166 (381)
T pfam07517        92 GKIAEMKTGEGKTLTATLPAYLNALSGKGVHVVTVNDYLAKRDAEWMGPLYEFLGLSVGVITSDMSPEERREAYN-----  166 (381)
T ss_pred             CCEEEEECCCCCHHHHHHHHHHHHCCCCCCEEEECCHHHHHHHHHHHHHHHHHHCCEEEECCCCCCHHHHHHHHH-----
T ss_conf             872588769981199999999997379974899758888688999979999984860542278898488898751-----


Q ss_pred             CCEEEEECHHHCCC-----CC-------CCCCCCEEEECC
Q ss_conf             75486411120133-----45-------544441788521
Q gi|254780945|r  375 QAHIIIGTHALFQD-----SI-------QYYKLILVIVDE  402 (700)
Q Consensus       375 ~~~iiIGTHAL~q~-----~v-------~F~~LgLvViDE  402 (700)
                       +||+-||.+=|.=     ..       .-..+..+||||
T Consensus       167 -~DItYgTn~e~gFDYLRDnm~~~~~~~vqR~~~~aIVDE  205 (381)
T pfam07517       167 -CDITYGTNSELGFDYLRDNMALSKEDKVQRGLNFAIVDE  205 (381)
T ss_pred             -CCCEECCHHHHHHHHHHHHHHCCHHHHCCCCCCEEEEEC
T ss_conf             -660550322321445323441582543457777699974


No 122
>PRK13480 3'-5' exoribonuclease YhaM; Provisional
Probab=98.25  E-value=3.8e-05  Score=59.98  Aligned_cols=88  Identities=14%  Similarity=0.177  Sum_probs=71.6

Q ss_pred             CCHHHCCCCCEEEEEEEEEEEEEECCCCCCE-EEEEEECCCCEEEEEEECCCHHHHHHHCCCCCEEEEEEEEEECCCEEE
Q ss_conf             6478889987899999998975421589833-899998189369999951887899873289888999989973187799
Q gi|254780945|r   59 PKISEISEERIVTITGYISQHSSFQLQKRRP-YKILLNDGTGEITLLFFYRKTEMLKNVFFEGRKITVTGKIKKLKNRII  137 (700)
Q Consensus        59 ~~I~~l~~g~~vti~g~V~~~~~~~~~~r~~-~~v~v~D~tg~i~lvfFn~~~~yl~k~lk~G~~v~vsGKv~~~~~~~q  137 (700)
                      +.|+++++|+.+.-..-|.+......+.+++ +.+++.|.||.|+.+.|+.. +.....|.+|+-|.|.|++..|++++|
T Consensus         3 ~~i~~l~~G~~v~~~~lv~~~~~~~tknG~~Yl~l~L~D~tG~I~ak~W~~~-~~~~~~~~~g~~V~v~G~v~~y~g~~Q   81 (314)
T PRK13480          3 KGIENLEVGESVDHFLLIKSATKGVASNGKPFLTLILQDKSGDIEAKLWDVS-KEDEATYVPETIVHVKGDIINYRGRKQ   81 (314)
T ss_pred             CCHHHCCCCCEEEEEEEEEECHHHCCCCCCCEEEEEEECCCCEEEEEECCCC-HHHHHHCCCCCEEEEEEEEEEECCCCC
T ss_conf             5141089998888999998714331899981479999837876889967898-666863789988999999987689862


Q ss_pred             EECCEEEECC
Q ss_conf             9778689626
Q gi|254780945|r  138 MVHPHYIFHN  147 (700)
Q Consensus       138 i~hPe~~~~~  147 (700)
                      +.--.+...+
T Consensus        82 l~i~~i~~~~   91 (314)
T PRK13480         82 LKVNQIRLAT   91 (314)
T ss_pred             EEEEEEEECC
T ss_conf             5888857678


No 123
>KOG0387 consensus
Probab=98.22  E-value=1.6e-05  Score=62.88  Aligned_cols=318  Identities=19%  Similarity=0.276  Sum_probs=183.0

Q ss_pred             HHHHHHH---HHHHHHHCCCCCCEEEEEECCCCCHHH--HHHHHHHHHH-HHHCCEEEEEHHHHHHHHHHHHHHHHCCCC
Q ss_conf             8899999---999984100134307886214422369--9999973344-430545886127999999998621101457
Q gi|254780945|r  275 KSQESAI---KDILQDMSQKNRMLRILQGDVGSGKTL--VALIAMAAAV-EAGGQAVIMAPIGILAQQHYEFIKKYTQNT  348 (700)
Q Consensus       275 ~~Q~~ai---~eI~~Dl~~~~pM~RLLQGDVGSGKTi--VA~~A~l~~~-~~G~Q~alMaPTEILA~QH~~~~~~~~~~~  348 (700)
                      +-|+..+   .+...+-+.+     .|--|-|=||||  ||++|++.-- .--.-|.+.+|+.|++ |--..|..|++++
T Consensus       208 ~yQreGV~WL~~L~~q~~GG-----ILgDeMGLGKTIQiisFLaaL~~S~k~~~paLIVCP~Tii~-qW~~E~~~w~p~~  281 (923)
T KOG0387         208 PYQREGVQWLWELYCQRAGG-----ILGDEMGLGKTIQIISFLAALHHSGKLTKPALIVCPATIIH-QWMKEFQTWWPPF  281 (923)
T ss_pred             HHHHHHHHHHHHHHHCCCCC-----EECCCCCCCCCHHHHHHHHHHHHCCCCCCCEEEECCHHHHH-HHHHHHHHHCCCE
T ss_conf             88898899999997325787-----62012357640158999998750243258659982488999-9999998747653


Q ss_pred             CCEEEEEECCCCH---------HHHHHHHHHHCCCCCEEEEECHHHC---CCCCCCCCCCEEEECCCCCCCH--HHHHHH
Q ss_conf             8658996246422---------5667687762134754864111201---3345544441788521013356--889987
Q gi|254780945|r  349 QIIVEIITGNMPQ---------AHRRKALERIAHGQAHIIIGTHALF---QDSIQYYKLILVIVDEQHRFGV--QQRLKL  414 (700)
Q Consensus       349 ~i~v~lLtg~~~~---------~er~~i~~~i~~G~~~iiIGTHAL~---q~~v~F~~LgLvViDEQHRFGV--~QR~~L  414 (700)
                        +|.+|.|+-+.         ..+..++.....-.-.|+|-|-+.|   ++++.=.+-++||.||-||--=  .|+..-
T Consensus       282 --rv~ilh~t~s~~r~~~~~~~~~~~~~L~r~~~~~~~ilitty~~~r~~~d~l~~~~W~y~ILDEGH~IrNpns~isla  359 (923)
T KOG0387         282 --RVFILHGTGSGARYDASHSSHKKDKLLIRKVATDGGILITTYDGFRIQGDDLLGILWDYVILDEGHRIRNPNSKISLA  359 (923)
T ss_pred             --EEEEEECCCCCCCCCCCHHHHHHHHHHEEEECCCCCEEEEEHHHHCCCCCCCCCCCCCEEEECCCCCCCCCCCHHHHH
T ss_conf             --799971477654444310134431222035304684799742242004752346503479823765046985089999


Q ss_pred             HHCCCCCCCEEECHHHHHHHHHHHHHHCCCHHH---HC------------------------------------------
Q ss_conf             402567761010101322789999752010111---10------------------------------------------
Q gi|254780945|r  415 TQKATAPHVLLMTATPIPRTLVLTSLGDIDISK---IT------------------------------------------  449 (700)
Q Consensus       415 ~~Kg~~ph~L~MtATPIPRTLal~~ygdldvS~---i~------------------------------------------  449 (700)
                      ..|-..+|-..||-|||---|.=-. .-.|.-.   +-                                          
T Consensus       360 ckki~T~~RiILSGTPiQNnL~ELw-sLfDFv~PG~Lgt~~~F~~~f~~pI~~GgyaNAs~~qv~~aykca~~Lr~lI~P  438 (923)
T KOG0387         360 CKKIRTVHRIILSGTPIQNNLTELW-SLFDFVFPGKLGTLPVFQQNFEHPINRGGYANASPRQVQTAYKCAVALRDLISP  438 (923)
T ss_pred             HHHCCCCCEEEEECCCCCCHHHHHH-HHHHHCCCCCCCCHHHHHHHHHHHEECCCCCCCCHHHHHHHHHHHHHHHHHHHH
T ss_conf             9861566648861862101089998-776640677445517787630111003565789879999999999999987679


Q ss_pred             -------------CCCCCCCCCEEEEEECCCHHHHHHH------HHHHHCCCCEEEE-------EE--CCCCCCC-----
Q ss_conf             -------------2355766620799970200268999------9763103873899-------97--1201221-----
Q gi|254780945|r  450 -------------EKPAGRKPIKTVIIPINRIDEVIER------LKVVLSEGKKAYW-------IC--PQIEEKK-----  496 (700)
Q Consensus       450 -------------e~P~gR~~I~T~~~~~~~~~~~~~~------i~~~l~~g~q~y~-------Vc--PlIeese-----  496 (700)
                                   .||. ...+.-.+--...-.++|..      |.+.++...+++.       ||  |.+-+.+     
T Consensus       439 ylLRR~K~dv~~~~Lp~-K~E~VlfC~LT~~QR~~Y~~fl~s~~v~~i~ng~~~~l~Gi~iLrkICnHPdll~~~~~~~~  517 (923)
T KOG0387         439 YLLRRMKSDVKGLKLPK-KEEIVLFCRLTKLQRRLYQRFLNSSEVNKILNGKRNCLSGIDILRKICNHPDLLDRRDEDEK  517 (923)
T ss_pred             HHHHHHHHHHHHCCCCC-CCCEEEEEECCHHHHHHHHHHHHHHHHHHHHCCCCCCEECHHHHHHHCCCCCCCCCCCCCCC
T ss_conf             99999998864421788-65258998566999999999860598999974984412151888864589410267642123


Q ss_pred             -CCCC----------CHHHHHHHHHH-------------------HHC-----CCCEECCCCCCCHHHHHHHHHHHHCCC
Q ss_conf             -1121----------01466666668-------------------663-----710312014699899999999975598
Q gi|254780945|r  497 -ESNF----------RSVVERFNSLH-------------------EHF-----TSSIAIIHGRMSDIDKESVMDSFKNGT  541 (700)
Q Consensus       497 -~~~~----------~~~~~~~~~l~-------------------~~~-----~~~v~~lHGkm~~~ek~~~m~~F~~g~  541 (700)
                       ..|.          .-+......|.                   +.|     +....-+-|.-+.......+++|.+++
T Consensus       518 ~~~D~~g~~k~sGKm~vl~~ll~~W~kqg~rvllFsqs~~mLdilE~fL~~~~~ysylRmDGtT~~~~R~~lVd~Fne~~  597 (923)
T KOG0387         518 QGPDYEGDPKRSGKMKVLAKLLKDWKKQGDRVLLFSQSRQMLDILESFLRRAKGYSYLRMDGTTPAALRQKLVDRFNEDE  597 (923)
T ss_pred             CCCCCCCCHHHCCHHHHHHHHHHHHHHCCCEEEEEHHHHHHHHHHHHHHHHCCCCEEEEECCCCCCCHHHHHHHHHCCCC
T ss_conf             58876789565216999999999986179779984137799999999987347853897158886201057898636787


Q ss_pred             -EEE-EEECHHHHCCCCCCCCCEEEEECHHHCCHHHHHHHHHCCCCC---CCCEEEEEEECCCCCHH
Q ss_conf             -699-998003410468887658998585254746887730116678---98359999708889987
Q gi|254780945|r  542 -CKL-LIATTVIEVGIDVVDASIIIIENAEHFGLAQLHQLRGRVGRG---EEISSCILLYHPPLSKN  603 (700)
Q Consensus       542 -~~i-LvaTtviEVGvdvpna~~mvI~~aerfGLsqLHQLRGRVGRg---~~~s~c~l~~~~~~~~~  603 (700)
                       ++| |+.|-|=-.|++.-.|+=+||.++|- -=|.=-|-|-|.=|=   ..-...=||+...+-|.
T Consensus       598 s~~VFLLTTrvGGLGlNLTgAnRVIIfDPdW-NPStD~QAreRawRiGQkkdV~VYRL~t~gTIEEk  663 (923)
T KOG0387         598 SIFVFLLTTRVGGLGLNLTGANRVIIFDPDW-NPSTDNQARERAWRIGQKKDVVVYRLMTAGTIEEK  663 (923)
T ss_pred             CEEEEEEEECCCCCCCCCCCCCEEEEECCCC-CCCCCHHHHHHHHHHCCCCCEEEEEEECCCCHHHH
T ss_conf             4579999730355411245675589979999-97642578888886357465599997327718999


No 124
>TIGR00643 recG ATP-dependent DNA helicase RecG; InterPro: IPR004609 The ATP-dependent DNA helicase RecG 3.6.1 from EC plays a critical role in recombination and DNA repair. It helps to process Holliday junction intermediates to mature products by catalysing branch migration. RecG has DNA unwinding activity characteristic of a DNA helicase with 3' to 5' polarity.; GO: 0004003 ATP-dependent DNA helicase activity, 0006281 DNA repair, 0006310 DNA recombination.
Probab=98.21  E-value=1.1e-05  Score=64.07  Aligned_cols=122  Identities=16%  Similarity=0.398  Sum_probs=91.8

Q ss_pred             HHHHHHHHHCCCCEEEEEECCCCCCCCCCCCHHHHHHHHHHHHCCC---CEECCCCCCCHHHHHHHHHHHHCCCEEEEEE
Q ss_conf             8999976310387389997120122111210146666666866371---0312014699899999999975598699998
Q gi|254780945|r  471 VIERLKVVLSEGKKAYWICPQIEEKKESNFRSVVERFNSLHEHFTS---SIAIIHGRMSDIDKESVMDSFKNGTCKLLIA  547 (700)
Q Consensus       471 ~~~~i~~~l~~g~q~y~VcPlIeese~~~~~~~~~~~~~l~~~~~~---~v~~lHGkm~~~ek~~~m~~F~~g~~~iLva  547 (700)
                      +.-.+-..+.+|-||-.-.|.    |-+    |++-|+.+.+.|+.   +|++|-|.++.++|.++.++-++|+++++|.
T Consensus       345 A~la~l~~i~~GYQ~ALMAPT----EiL----A~QHy~~~~~~l~p~~~~vaLLTGs~k~~~r~~~~e~i~~G~~~~~vG  416 (721)
T TIGR00643       345 AALAMLAAIESGYQVALMAPT----EIL----AEQHYDSLRNLLAPLGIEVALLTGSLKGKQRKELLETIASGEIHLVVG  416 (721)
T ss_pred             HHHHHHHHHHCCCEEEEECCH----HHH----HHHHHHHHHHHHCCCCCEEEEEECCCCHHHHHHHHHHHHCCCCEEEEH
T ss_conf             999999998469809991776----899----999999999962354857888615667878999999986395205733


Q ss_pred             CH-HHHCCCCCCCCCEEEEECHHHCCHHHHHHHHHCCCCC---CCCEEEEEEECCCC
Q ss_conf             00-3410468887658998585254746887730116678---98359999708889
Q gi|254780945|r  548 TT-VIEVGIDVVDASIIIIENAEHFGLAQLHQLRGRVGRG---EEISSCILLYHPPL  600 (700)
Q Consensus       548 Tt-viEVGvdvpna~~mvI~~aerfGLsqLHQLRGRVGRg---~~~s~c~l~~~~~~  600 (700)
                      |- .|-=.||-.+-.+.||.-=+|||.-|=-|||--=--+   +..=.|+.|+-.|+
T Consensus       417 THALiqe~vef~~L~lVIiDEQHRFGV~QR~~L~~KG~~~~~~G~~PH~L~MtATPI  473 (721)
T TIGR00643       417 THALIQEKVEFKRLGLVIIDEQHRFGVEQRKKLREKGQEGSMIGFAPHVLVMTATPI  473 (721)
T ss_pred             HHHHHHHHHHHHCCCEEEEECCCCCHHHHHHHHHHHHHCCCCCCCCCCEEEEECCCC
T ss_conf             135545214431477489932335607899999986220688677777646637881


No 125
>KOG0353 consensus
Probab=98.20  E-value=0.00044  Score=51.57  Aligned_cols=366  Identities=20%  Similarity=0.249  Sum_probs=209.7

Q ss_pred             HHHHHHHHHHHHHHCCCCCCEEEEEECCCCCHHHHHHHHHHHHHHHHCCEEEEEHHHHHHHHHHHHHHHHCCCCCCEEEE
Q ss_conf             88999999999841001343078862144223699999973344430545886127999999998621101457865899
Q gi|254780945|r  275 KSQESAIKDILQDMSQKNRMLRILQGDVGSGKTLVALIAMAAAVEAGGQAVIMAPIGILAQQHYEFIKKYTQNTQIIVEI  354 (700)
Q Consensus       275 ~~Q~~ai~eI~~Dl~~~~pM~RLLQGDVGSGKTiVA~~A~l~~~~~G~Q~alMaPTEILA~QH~~~~~~~~~~~~i~v~l  354 (700)
                      .-|..+   |..-|+.....   |-=-.|-||.+-+-+.++.+   ..-+.+..|---|-+-..-.++.    +||....
T Consensus        97 plq~~a---in~~ma~ed~~---lil~tgggkslcyqlpal~a---dg~alvi~plislmedqil~lkq----lgi~as~  163 (695)
T KOG0353          97 PLQLAA---INATMAGEDAF---LILPTGGGKSLCYQLPALCA---DGFALVICPLISLMEDQILQLKQ----LGIDASM  163 (695)
T ss_pred             HHHHHH---HHHHHCCCCEE---EEEECCCCCCHHHHHHHHHC---CCCEEEECHHHHHHHHHHHHHHH----HCCCHHH
T ss_conf             037877---55522267469---99837996124522358762---87457610268888999999998----0864443


Q ss_pred             EECCCCHHHHHHHHHHHC--CCCCEEEEECHHHC----------CCCCCCCCCCEEEECCCCC---CCHHHHH------H
Q ss_conf             624642256676877621--34754864111201----------3345544441788521013---3568899------8
Q gi|254780945|r  355 ITGNMPQAHRRKALERIA--HGQAHIIIGTHALF----------QDSIQYYKLILVIVDEQHR---FGVQQRL------K  413 (700)
Q Consensus       355 Ltg~~~~~er~~i~~~i~--~G~~~iiIGTHAL~----------q~~v~F~~LgLvViDEQHR---FGV~QR~------~  413 (700)
                      |..++++.+-+.+...+.  +.+..++--|---+          .+...-..+-++-|||-|-   +|-.=|-      -
T Consensus       164 lnansske~~k~v~~~i~nkdse~kliyvtpekiaksk~~mnkleka~~~~~~~~iaidevhccsqwghdfr~dy~~l~i  243 (695)
T KOG0353         164 LNANSSKEEAKRVEAAITNKDSEFKLIYVTPEKIAKSKKFMNKLEKALEAGFFKLIAIDEVHCCSQWGHDFRPDYKALGI  243 (695)
T ss_pred             CCCCCCHHHHHHHHHHHCCCCCEEEEEEECHHHHHHHHHHHHHHHHHHHCCEEEEEEECCEEEHHHHCCCCCCCHHHHHH
T ss_conf             05755488898999987077761589996489987779999999987642604898531023265437665741688889


Q ss_pred             HHHCCCCCCCEEECHHHHHHHHHHHHHHCCCHHHHC-----CCCCCCCCCEEEEEEC-CCHHHHHHHHHHHHC---CCCE
Q ss_conf             740256776101010132278999975201011110-----2355766620799970-200268999976310---3873
Q gi|254780945|r  414 LTQKATAPHVLLMTATPIPRTLVLTSLGDIDISKIT-----EKPAGRKPIKTVIIPI-NRIDEVIERLKVVLS---EGKK  484 (700)
Q Consensus       414 L~~Kg~~ph~L~MtATPIPRTLal~~ygdldvS~i~-----e~P~gR~~I~T~~~~~-~~~~~~~~~i~~~l~---~g~q  484 (700)
                      |...=.++-++-+|||.----|.=.    -|+--|.     .--.+|....-.+... .+.++.++-|.+.++   +|.-
T Consensus       244 lkrqf~~~~iigltatatn~vl~d~----k~il~ie~~~tf~a~fnr~nl~yev~qkp~n~dd~~edi~k~i~~~f~gqs  319 (695)
T KOG0353         244 LKRQFKGAPIIGLTATATNHVLDDA----KDILCIEAAFTFRAGFNRPNLKYEVRQKPGNEDDCIEDIAKLIKGDFAGQS  319 (695)
T ss_pred             HHHHCCCCCEEEEEHHHHCCHHHHH----HHHHHHHHHHEEECCCCCCCCEEEEEECCCCHHHHHHHHHHHHCCCCCCCC
T ss_conf             9975799965632311000035678----887747865112023688873267451899757789999998544437876


Q ss_pred             EEEEECCCCCCCCCCCCHHHHHHHHHHHHCCCCEECCCCCCCHHHHHHHHHHHHCCCEEEEEECHHHHCCCCCCCCCEEE
Q ss_conf             89997120122111210146666666866371031201469989999999997559869999800341046888765899
Q gi|254780945|r  485 AYWICPQIEEKKESNFRSVVERFNSLHEHFTSSIAIIHGRMSDIDKESVMDSFKNGTCKLLIATTVIEVGIDVVDASIII  564 (700)
Q Consensus       485 ~y~VcPlIeese~~~~~~~~~~~~~l~~~~~~~v~~lHGkm~~~ek~~~m~~F~~g~~~iLvaTtviEVGvdvpna~~mv  564 (700)
                      -.+-|-.-.        +.+.....|+.+ +-.-|--|.-|.+++|..+-..+.+|+|++.|||..--.|||-||.... 
T Consensus       320 giiyc~sq~--------d~ekva~alkn~-gi~a~~yha~lep~dks~~hq~w~a~eiqvivatvafgmgidkpdvrfv-  389 (695)
T KOG0353         320 GIIYCFSQK--------DCEKVAKALKNH-GIHAGAYHANLEPEDKSGAHQGWIAGEIQVIVATVAFGMGIDKPDVRFV-  389 (695)
T ss_pred             CEEEEECCC--------CHHHHHHHHHHC-CCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEEEEEECCCCCCCCEEEE-
T ss_conf             569995346--------589999999855-8352214055685344540003304606899998640256788871699-


Q ss_pred             EECHHHCCHHHHHH-------------------------------------------HHHCCCCCCCCEEEEEEECCC--
Q ss_conf             85852547468877-------------------------------------------301166789835999970888--
Q gi|254780945|r  565 IENAEHFGLAQLHQ-------------------------------------------LRGRVGRGEEISSCILLYHPP--  599 (700)
Q Consensus       565 I~~aerfGLsqLHQ-------------------------------------------LRGRVGRg~~~s~c~l~~~~~--  599 (700)
                      |.|+--=.+---.|                                           --||.||.+.+.-|+|.|.-.  
T Consensus       390 ihhsl~ksienyyqasarillrmtkqknksdtggstqinilevctnfkiffavfsekesgragrd~~~a~cilyy~~~di  469 (695)
T KOG0353         390 IHHSLPKSIENYYQASARILLRMTKQKNKSDTGGSTQINILEVCTNFKIFFAVFSEKESGRAGRDDMKADCILYYGFADI  469 (695)
T ss_pred             EECCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCEEEHHHHHCCCEEEEEEECCHHCCCCCCCCCCCCEEEEECHHHH
T ss_conf             95366166899998878999987652255567875300043340131012222031102555668886647998424778


Q ss_pred             --CC------HHHHHHHHHHHHH------CHHHHHHHHHHHHCCCCCCCCCHHCC----CCCCCCCCHHH-HHHHHHHHH
Q ss_conf             --99------8799999999841------42589999998520630002600069----87440003887-599999999
Q gi|254780945|r  600 --LS------KNSYTRLSVLKNT------EDGFLIAEEDLKQRKEGEILGIKQSG----MPKFLIAQPEL-HDSLLEIAR  660 (700)
Q Consensus       600 --~~------~~~~~Rl~~l~~~------~dGf~iAe~Dl~lRG~G~~~G~~QsG----~~~~~~~d~~~-d~~ll~~a~  660 (700)
                        +|      ..+.+.|--|+..      .--..+||.==+---|--  -.+|-.    ...|.=-++.. -.++++.|+
T Consensus       470 fk~ssmv~~e~~g~q~ly~mv~y~~d~s~crrv~laehfde~w~~~~--c~k~cd~c~~~n~f~~~n~~ey~~dl~e~~k  547 (695)
T KOG0353         470 FKISSMVQMENTGIQKLYEMVRYAADISKCRRVKLAEHFDEAWEPEA--CNKMCDNCCKDNAFEGKNIKEYCRDLIEAAK  547 (695)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHH--HHHHHHHHCCCCCCCCCCHHHHHHHHHHHHH
T ss_conf             76777887886658999999999742687779999988886418898--9887640325764236665888899999999


Q ss_pred             HHHHHHHHH
Q ss_conf             999999984
Q gi|254780945|r  661 KDAKHILTQ  669 (700)
Q Consensus       661 ~~a~~~~~~  669 (700)
                      ..|++|-+.
T Consensus       548 t~~~~i~e~  556 (695)
T KOG0353         548 TQAEEIEEH  556 (695)
T ss_pred             HHHHHHHHH
T ss_conf             899999973


No 126
>KOG0329 consensus
Probab=98.20  E-value=1.7e-05  Score=62.75  Aligned_cols=282  Identities=23%  Similarity=0.355  Sum_probs=165.1

Q ss_pred             CCC-CCHHHHHHHHHHHHHHCCCCCCEEEEEECCCCCHHHHHHHHHHHHHH---HHCCEEEEEHHHHHHHHH---HHHHH
Q ss_conf             246-79889999999998410013430788621442236999999733444---305458861279999999---98621
Q gi|254780945|r  270 PFS-PTKSQESAIKDILQDMSQKNRMLRILQGDVGSGKTLVALIAMAAAVE---AGGQAVIMAPIGILAQQH---YEFIK  342 (700)
Q Consensus       270 PF~-LT~~Q~~ai~eI~~Dl~~~~pM~RLLQGDVGSGKTiVA~~A~l~~~~---~G~Q~alMaPTEILA~QH---~~~~~  342 (700)
                      .|+ ..+-|..+|-.      +-.-|.-|-|.--|-|||.|..+|.++-++   .---+.+|+-|--||-|.   |+.|+
T Consensus        61 gfehpsevqhecipq------ailgmdvlcqaksgmgktavfvl~tlqqiepv~g~vsvlvmchtrelafqi~~ey~rfs  134 (387)
T KOG0329          61 GFEHPSEVQHECIPQ------AILGMDVLCQAKSGMGKTAVFVLATLQQIEPVDGQVSVLVMCHTRELAFQISKEYERFS  134 (387)
T ss_pred             CCCCCHHHHHHHHHH------HHHCCHHHEECCCCCCCEEEEEHHHHHHCCCCCCEEEEEEEECCHHHHHHHHHHHHHHH
T ss_conf             578916764420047------76341120100257884365522235523788980799999621899999889999997


Q ss_pred             HHCCCCCCEEEEEECCCCHHHHHHHHHHHCCCCCEEEEEC----HHHCC-CCCCCCCCCEEEECCCCCCCHHHHHHHHHC
Q ss_conf             1014578658996246422566768776213475486411----12013-345544441788521013356889987402
Q gi|254780945|r  343 KYTQNTQIIVEIITGNMPQAHRRKALERIAHGQAHIIIGT----HALFQ-DSIQYYKLILVIVDEQHRFGVQQRLKLTQK  417 (700)
Q Consensus       343 ~~~~~~~i~v~lLtg~~~~~er~~i~~~i~~G~~~iiIGT----HAL~q-~~v~F~~LgLvViDEQHRFGV~QR~~L~~K  417 (700)
                      ++++.  ++++..-|+++.|.-++.+..    -++|+|||    -||.. ..+..+|.---|+||-.+.= +| ..++..
T Consensus       135 kymP~--vkvaVFfGG~~Ikkdee~lk~----~PhivVgTPGrilALvr~k~l~lk~vkhFvlDEcdkml-e~-lDMrRD  206 (387)
T KOG0329         135 KYMPS--VKVSVFFGGLFIKKDEELLKN----CPHIVVGTPGRILALVRNRSLNLKNVKHFVLDECDKML-EQ-LDMRRD  206 (387)
T ss_pred             HHCCC--CEEEEEECCEECCCCHHHHHC----CCEEEECCCHHHHHHHHHCCCCHHHCCEEEHHHHHHHH-HH-HHHHHH
T ss_conf             54888--458999755310346998827----99089768288999987245753203211233377899-98-788887


Q ss_pred             -----CCCCC---CEEECHHHHHHHHHHHHHHCCCHHHHCCCCCCCCCCEEEEEECCCHHHHHHHHHHHHCCCCEEEEEE
Q ss_conf             -----56776---1010101322789999752010111102355766620799970200268999976310387389997
Q gi|254780945|r  418 -----ATAPH---VLLMTATPIPRTLVLTSLGDIDISKITEKPAGRKPIKTVIIPINRIDEVIERLKVVLSEGKKAYWIC  489 (700)
Q Consensus       418 -----g~~ph---~L~MtATPIPRTLal~~ygdldvS~i~e~P~gR~~I~T~~~~~~~~~~~~~~i~~~l~~g~q~y~Vc  489 (700)
                           -..||   +.++|||-                        .+.|...         .-.|+.+-    --+|+  
T Consensus       207 vQEifr~tp~~KQvmmfsatl------------------------skeiRpv---------C~kFmQdP----mEi~v--  247 (387)
T KOG0329         207 VQEIFRMTPHEKQVMMFSATL------------------------SKEIRPV---------CHKFMQDP----MEIFV--  247 (387)
T ss_pred             HHHHHHCCCCCCEEEEEEEEC------------------------CHHHHHH---------HHHHHCCC----HHHHC--
T ss_conf             999863286532034542013------------------------1566788---------77552181----66502--


Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHC-------------CCCEECCCCCCCHHHHHHHHHHHHCCCEEEEEECHHHHCCCC
Q ss_conf             1201221112101466666668663-------------710312014699899999999975598699998003410468
Q gi|254780945|r  490 PQIEEKKESNFRSVVERFNSLHEHF-------------TSSIAIIHGRMSDIDKESVMDSFKNGTCKLLIATTVIEVGID  556 (700)
Q Consensus       490 PlIeese~~~~~~~~~~~~~l~~~~-------------~~~v~~lHGkm~~~ek~~~m~~F~~g~~~iLvaTtviEVGvd  556 (700)
                         ++.-++.++.....|-.|++.-             .+.|-+.   .++-.+   + .|.   .. ||||.+.--|+|
T Consensus       248 ---DdE~KLtLHGLqQ~YvkLke~eKNrkl~dLLd~LeFNQVvIF---vKsv~R---l-~f~---kr-~vat~lfgrgmd  313 (387)
T KOG0329         248 ---DDEAKLTLHGLQQYYVKLKENEKNRKLNDLLDVLEFNQVVIF---VKSVQR---L-SFQ---KR-LVATDLFGRGMD  313 (387)
T ss_pred             ---CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCEEEE---EEHHHH---H-HHH---HH-HHHHHHHCCCCC
T ss_conf             ---415655333477877766555543566656545441204676---203445---5-566---66-677664046667


Q ss_pred             CCCCCEEEEECHHHCCHHHHHHHHHCCCCCCCCEEEEEEECCCCCHHHHHHHHHHHHHCHHHHHHHHHH
Q ss_conf             887658998585254746887730116678983599997088899879999999984142589999998
Q gi|254780945|r  557 VVDASIIIIENAEHFGLAQLHQLRGRVGRGEEISSCILLYHPPLSKNSYTRLSVLKNTEDGFLIAEEDL  625 (700)
Q Consensus       557 vpna~~mvI~~aerfGLsqLHQLRGRVGRg~~~s~c~l~~~~~~~~~~~~Rl~~l~~~~dGf~iAe~Dl  625 (700)
                      +-..|+.+=++--.=.=+-||-. ||-||-+..|..+-..+.+      +--+++...+|-|++.-.+|
T Consensus       314 iervNi~~NYdmp~~~DtYlHrv-~rAgrfGtkglaitfvs~e------~da~iLn~vqdRf~v~i~eL  375 (387)
T KOG0329         314 IERVNIVFNYDMPEDSDTYLHRV-ARAGRFGTKGLAITFVSDE------NDAKILNPVQDRFEVNIKEL  375 (387)
T ss_pred             CCCCEEEECCCCCCCCHHHHHHH-HHHHCCCCCCCEEEHHCCH------HHHHHHCHHHHHHHCCHHHC
T ss_conf             33220232268988712788876-2430356555201000111------26777431667655008656


No 127
>pfam01336 tRNA_anti OB-fold nucleic acid binding domain. This family contains OB-fold domains that bind to nucleic acids. The family includes the anti-codon binding domain of lysyl, aspartyl, and asparaginyl -tRNA synthetases (See pfam00152). Aminoacyl-tRNA synthetases catalyse the addition of an amino acid to the appropriate tRNA molecule EC:6.1.1.-. This family also includes part of RecG helicase involved in DNA repair. Replication factor A is a heterotrimeric complex, that contains a subunit in this family. This domain is also found at the C-terminus of bacterial DNA polymerase III alpha chain.
Probab=98.15  E-value=3.6e-05  Score=60.12  Aligned_cols=73  Identities=29%  Similarity=0.402  Sum_probs=62.0

Q ss_pred             EEEEEEEEEEEEECCCCCCEEEEEEECCCCEEEEEEECCCHHHHHHHCCCCCEEEEEEEEEECCCE-EEEECCEEEE
Q ss_conf             999999989754215898338999981893699999518878998732898889999899731877-9997786896
Q gi|254780945|r   70 VTITGYISQHSSFQLQKRRPYKILLNDGTGEITLLFFYRKTEMLKNVFFEGRKITVTGKIKKLKNR-IIMVHPHYIF  145 (700)
Q Consensus        70 vti~g~V~~~~~~~~~~r~~~~v~v~D~tg~i~lvfFn~~~~yl~k~lk~G~~v~vsGKv~~~~~~-~qi~hPe~~~  145 (700)
                      +++.|+|.+..   ..+++++.+.+.|++|.++++||+....+..+.+++|+.+.++|+++.+++. +++.++++..
T Consensus         1 v~v~G~V~~~~---~~~~~~~~~~l~D~tg~i~~~~~~~~~~~~~~~l~~g~~v~v~G~v~~~~~~~~~i~~~~i~~   74 (75)
T pfam01336         1 VTVAGRVTSVR---RSGGKVAFLTLRDGTGSIQVVLFKEEAEKLAKKLKEGDVVLVTGKVKKRPGGELELVVEEIEV   74 (75)
T ss_pred             CEEEEEEEEEE---ECCCCEEEEEEEECCEEEEEEEEHHHHHHHHHCCCCCCEEEEEEEEEECCCCCEEEEEEEEEE
T ss_conf             99999999518---879998999999799399999952386888632898989999999999749989999989997


No 128
>PRK11747 dinG ATP-dependent DNA helicase DinG; Provisional
Probab=98.13  E-value=9.5e-05  Score=56.81  Aligned_cols=84  Identities=13%  Similarity=0.249  Sum_probs=56.1

Q ss_pred             HHHHHHHHHHHHCCCCEEEEEECCCCCCCCCCCCHHHHHHHHHHHHCCCCEECCCCCCCHHHHHHHHH----HHHCCCEE
Q ss_conf             02689999763103873899971201221112101466666668663710312014699899999999----97559869
Q gi|254780945|r  468 IDEVIERLKVVLSEGKKAYWICPQIEEKKESNFRSVVERFNSLHEHFTSSIAIIHGRMSDIDKESVMD----SFKNGTCK  543 (700)
Q Consensus       468 ~~~~~~~i~~~l~~g~q~y~VcPlIeese~~~~~~~~~~~~~l~~~~~~~v~~lHGkm~~~ek~~~m~----~F~~g~~~  543 (700)
                      .+.+.+.+.+-+...+.++|.++-.        ...+..|+.|.+..+..+ ++.|..+   +.+.++    +|.+|+-.
T Consensus       520 ~~~~~~~i~~~~~~~~g~LVLFtS~--------~~l~~v~~~l~~~~~~~l-l~Qg~~~---r~~ll~~f~~~~~~~~~s  587 (697)
T PRK11747        520 TAEMAAYLPELLEGHKGSLVLFSSR--------RQMQKVADLLPGDLRLLL-LVQGEQP---RQELLEKHKKRVDEGEGS  587 (697)
T ss_pred             HHHHHHHHHHHHHHCCCEEEEECHH--------HHHHHHHHHHHHHCCCCE-EEECCCC---HHHHHHHHHHHHHCCCCE
T ss_conf             9999999999998569849995019--------999999998766348838-9956865---999999999986168982


Q ss_pred             EEEECHHHHCCCCCCCCCEE
Q ss_conf             99980034104688876589
Q gi|254780945|r  544 LLIATTVIEVGIDVVDASII  563 (700)
Q Consensus       544 iLvaTtviEVGvdvpna~~m  563 (700)
                      ||++|---==|||+|.-++.
T Consensus       588 vLlGt~SFwEGVD~pG~~L~  607 (697)
T PRK11747        588 VLFGLQSFAEGLDLPGDYLT  607 (697)
T ss_pred             EEEECCCCCCCEECCCCCEE
T ss_conf             99967531266136987878


No 129
>KOG0951 consensus
Probab=98.09  E-value=0.0013  Score=48.04  Aligned_cols=280  Identities=21%  Similarity=0.296  Sum_probs=175.1

Q ss_pred             EEEEEECCCCCHHHHHHHHHHHHHHHHCCEEEEEHHHHHHHHHHHHHHHHCCC-CCCEEEEEECCCCHHHHHHHHHHHCC
Q ss_conf             07886214422369999997334443054588612799999999862110145-78658996246422566768776213
Q gi|254780945|r  295 LRILQGDVGSGKTLVALIAMAAAVEAGGQAVIMAPIGILAQQHYEFIKKYTQN-TQIIVEIITGNMPQAHRRKALERIAH  373 (700)
Q Consensus       295 ~RLLQGDVGSGKTiVA~~A~l~~~~~G~Q~alMaPTEILA~QH~~~~~~~~~~-~~i~v~lLtg~~~~~er~~i~~~i~~  373 (700)
                      +-++----|||||++|-+|.+. -.+-..++..+|-|-.|.-.|.-..+-|.+ .|.++..|||-++-.-     .-++ 
T Consensus      1161 ~v~vga~~gsgkt~~ae~a~l~-~~~~~~~vyi~p~~~i~~~~~~~w~~~f~~~~G~~~~~l~ge~s~dl-----kl~~- 1233 (1674)
T KOG0951        1161 NVLVGAPNGSGKTACAELALLR-PDTIGRAVYIAPLEEIADEQYRDWEKKFSKLLGLRIVKLTGETSLDL-----KLLQ- 1233 (1674)
T ss_pred             EEEEECCCCCCHHHHHHHHHCC-CCCCEEEEEECCHHHHHHHHHHHHHHHHCCCCCCEEEECCCCCCCCH-----HHHH-
T ss_conf             1899457887344889998628-86632799843668999999999987531045806885178655256-----7764-


Q ss_pred             CCCEEEEECHH---HCCCCCCCCCCCEEEECCCCCCCHHHHHHHH-------------HCCCCCCCEEECHHHHHHHHHH
Q ss_conf             47548641112---0133455444417885210133568899874-------------0256776101010132278999
Q gi|254780945|r  374 GQAHIIIGTHA---LFQDSIQYYKLILVIVDEQHRFGVQQRLKLT-------------QKATAPHVLLMTATPIPRTLVL  437 (700)
Q Consensus       374 G~~~iiIGTHA---L~q~~v~F~~LgLvViDEQHRFGV~QR~~L~-------------~Kg~~ph~L~MtATPIPRTLal  437 (700)
                       .-+++|-||.   ++|   .-.++.|-|.||=|--| .|-.+..             .|....--|.-|-|-+ |.|  
T Consensus      1234 -~~~vii~tpe~~d~lq---~iQ~v~l~i~d~lh~ig-g~~g~v~evi~S~r~ia~q~~k~ir~v~ls~~lana-~d~-- 1305 (1674)
T KOG0951        1234 -KGQVIISTPEQWDLLQ---SIQQVDLFIVDELHLIG-GVYGAVYEVICSMRYIASQLEKKIRVVALSSSLANA-RDL-- 1305 (1674)
T ss_pred             -HCCEEEECHHHHHHHH---HHHHCCEEEEEHHHHHC-CCCCCEEEEEEEHHHHHHHHHHHEEEEEEEHHHCCC-HHH--
T ss_conf             -2455886635777775---54321168610234414-657734898744799999998650588732223041-222--


Q ss_pred             HHHHCCCHHHHCCCCCCCCCC--EEE--EEECCC--------HHHHHHHHHHHHCCCCEEEEEECCCCC-----------
Q ss_conf             975201011110235576662--079--997020--------026899997631038738999712012-----------
Q gi|254780945|r  438 TSLGDIDISKITEKPAGRKPI--KTV--IIPINR--------IDEVIERLKVVLSEGKKAYWICPQIEE-----------  494 (700)
Q Consensus       438 ~~ygdldvS~i~e~P~gR~~I--~T~--~~~~~~--------~~~~~~~i~~~l~~g~q~y~VcPlIee-----------  494 (700)
                         -.+.-|.+=..||++.|+  ...  .++...        .+-.|..+.+...++.-+++-.|-=..           
T Consensus      1306 ---ig~s~~~v~Nf~p~~R~~Pl~i~i~~~~~~~~~s~~~am~~~~~~ai~~~a~~~k~~~vf~p~rk~~~~~a~~~~~~ 1382 (1674)
T KOG0951        1306 ---IGASSSGVFNFSPSVRPVPLEIHIQSVDISHFESRMLAMTKPTYTAIVRHAGNRKPAIVFLPTRKHARLVAVDLVTF 1382 (1674)
T ss_pred             ---CCCCCCCEEECCCCCCCCCEEEEEEEECCCHHHHHHHHHHHHHHHHHHHHHCCCCCEEEEECCCHHHHHHHHCCCHH
T ss_conf             ---05354553605866688760688887324015788877431279999998548997279803401432222120012


Q ss_pred             ----CCCCCCCHHHHHHHHHHHHCCCCEECCCCCCCHHHHHHHHHHHHCCCEEEEEECHHHHCCCCCCCCCEEEEECH--
Q ss_conf             ----21112101466666668663710312014699899999999975598699998003410468887658998585--
Q gi|254780945|r  495 ----KKESNFRSVVERFNSLHEHFTSSIAIIHGRMSDIDKESVMDSFKNGTCKLLIATTVIEVGIDVVDASIIIIENA--  568 (700)
Q Consensus       495 ----se~~~~~~~~~~~~~l~~~~~~~v~~lHGkm~~~ek~~~m~~F~~g~~~iLvaTtviEVGvdvpna~~mvI~~a--  568 (700)
                          ++..-+..-++.-+.|++.++..||  |--|++.+.+-+-.-|..|.|+++|...= --|.-. -|+..||.+-  
T Consensus      1383 s~~~~~~~l~~~~e~~~~~l~e~l~hgvg--~eg~s~~d~~iv~~l~e~g~i~v~v~s~~-c~~~~~-~~~lVvvmgt~~ 1458 (1674)
T KOG0951        1383 SHADEPDYLLSELEECDETLRESLKHGVG--HEGLSSNDQEIVQQLFEAGAIQVCVMSRD-CYGTKL-KAHLVVVMGTQY 1458 (1674)
T ss_pred             HCCCCHHHHHHHHHCCHHHHHHCCCCCCC--CCCCCCCHHHHHHHHHHCCCEEEEEEECC-CCCCCC-CCEEEEEECCEE
T ss_conf             21573888778774345766310134445--44457351899999974695799999721-025532-132899844146


Q ss_pred             --------HHCCHHHHHHHHHCCCCCCCCEEEEEEECCC
Q ss_conf             --------2547468877301166789835999970888
Q gi|254780945|r  569 --------EHFGLAQLHQLRGRVGRGEEISSCILLYHPP  599 (700)
Q Consensus       569 --------erfGLsqLHQLRGRVGRg~~~s~c~l~~~~~  599 (700)
                              +-+-.|-|-|.+|+-.|   .|.|++++..+
T Consensus      1459 ydg~e~~~~~y~i~~ll~m~G~a~~---~~k~vi~~~~~ 1494 (1674)
T KOG0951        1459 YDGKEHSYEDYPIAELLQMVGLASG---AGKCVIMCHTP 1494 (1674)
T ss_pred             ECCCCCCCCCCCHHHHHHHHHHHCC---CCCEEEEECCC
T ss_conf             4265443346866679988414227---86489994486


No 130
>TIGR01970 DEAH_box_HrpB ATP-dependent helicase HrpB; InterPro: IPR010225   This entry represents HrpB, one of two related predicted DEAH-box ATP-dependent helicases of unknown function found in many proteobacteria, but also in a few species of other lineages. The member from Rhizobium meliloti, designated HelO, has been studied but is not essential for growth and mutants have no obvious phenotype . HrpB is typically about 800 residues in length, while its paralog HrpA (IPR010222 from INTERPRO), also uncharacterised, is about 1300 amino acids long. Related characterised eukaryotic proteins are RNA helicases associated with pre-mRNA processing ..
Probab=98.08  E-value=0.00031  Score=52.80  Aligned_cols=322  Identities=21%  Similarity=0.347  Sum_probs=219.5

Q ss_pred             HHHHHHHHCCCCCCEEEEEECCCCCHHHHHHHHHHHHH-HHHCCEEEEEHHHHHHHHHHHHHHHHCCCC-----CCEEEE
Q ss_conf             99999841001343078862144223699999973344-430545886127999999998621101457-----865899
Q gi|254780945|r  281 IKDILQDMSQKNRMLRILQGDVGSGKTLVALIAMAAAV-EAGGQAVIMAPIGILAQQHYEFIKKYTQNT-----QIIVEI  354 (700)
Q Consensus       281 i~eI~~Dl~~~~pM~RLLQGDVGSGKTiVA~~A~l~~~-~~G~Q~alMaPTEILA~QH~~~~~~~~~~~-----~i~v~l  354 (700)
                      +=++..-|...-..  +|.-=-|.|||=--=+|+|.+- ..|..-.++=|==+=|+--.+.+-+-+..-     |.+|-+
T Consensus         7 LP~Lr~al~~~~~v--vL~APpGAGKsT~~PLaLL~~pW~~~~kIimLEPRRlAAR~~A~rlA~~LgE~VG~tVGyRvR~   84 (858)
T TIGR01970         7 LPALRDALAAHPQV--VLEAPPGAGKSTAVPLALLDAPWLIGGKIIMLEPRRLAARSAAQRLASQLGEEVGDTVGYRVRL   84 (858)
T ss_pred             HHHHHHHHHCCCCE--EEECCCCCCHHHHHHHHHHHHHHHCCCEEEEECCHHHHHHHHHHHHHHHHCCCCCCCCCEEEEC
T ss_conf             69999986117650--6416722471105889976626434880787474478999999999997088988620405771


Q ss_pred             EECCCCHHHHHHHHHHHCCCCCEEEEEC----HHHCCCCCCCCCCCEEEECCCCCCCHHHH--HHHHHCC-----CC--C
Q ss_conf             6246422566768776213475486411----12013345544441788521013356889--9874025-----67--7
Q gi|254780945|r  355 ITGNMPQAHRRKALERIAHGQAHIIIGT----HALFQDSIQYYKLILVIVDEQHRFGVQQR--LKLTQKA-----TA--P  421 (700)
Q Consensus       355 Ltg~~~~~er~~i~~~i~~G~~~iiIGT----HAL~q~~v~F~~LgLvViDEQHRFGV~QR--~~L~~Kg-----~~--p  421 (700)
                      = ++++.+-|             |=|=|    .=-||+|=.-.-.|+||.||=|==...==  .+|.-..     +.  =
T Consensus        85 e-nkVs~~TR-------------lEvVTEGiLTRMlQ~DP~L~GVg~liFDEFHERsL~aDLaLALaLdVQs~LRdDPPL  150 (858)
T TIGR01970        85 E-NKVSARTR-------------LEVVTEGILTRMLQDDPELEGVGLLIFDEFHERSLDADLALALALDVQSALRDDPPL  150 (858)
T ss_pred             C-CCCCCCCC-------------EEEEECCHHHHHCCCCCCCCCCCEEEECHHHHHHHHHHHHHHHHHHHHHHHCCCCCC
T ss_conf             1-32587754-------------578723268774016888453523231102243467889999988533431068640


Q ss_pred             CCEEECHHHHHHHHHHHHHHCCCHHHHCCCC----CCCC-CCEEEEEE-CCCHHHHHHHH----HHHHCC--CC--E-EE
Q ss_conf             6101010132278999975201011110235----5766-62079997-02002689999----763103--87--3-89
Q gi|254780945|r  422 HVLLMTATPIPRTLVLTSLGDIDISKITEKP----AGRK-PIKTVIIP-INRIDEVIERL----KVVLSE--GK--K-AY  486 (700)
Q Consensus       422 h~L~MtATPIPRTLal~~ygdldvS~i~e~P----~gR~-~I~T~~~~-~~~~~~~~~~i----~~~l~~--g~--q-~y  486 (700)
                      -+|+||||         +=|+-=-+.+++=|    .||. ||.+++.+ ....+.+-+.+    .+.++.  |.  | +-
T Consensus       151 kil~MSAT---------Ldg~rLs~LL~~Ap~v~S~GR~fPVe~rY~~P~~~~e~l~~~~~r~v~~~La~~~GSGPqd~L  221 (858)
T TIGR01970       151 KILIMSAT---------LDGERLSSLLPDAPVVESEGRSFPVEIRYLPPLREDERLEDRVSRAVEHALAEESGSGPQDVL  221 (858)
T ss_pred             EEHHCCCC---------CHHHHHHHHCCCCCEEEECCCCCCEECCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCCCCCHH
T ss_conf             00000026---------327999974330264200787876110227678755533478999999999616788633010


Q ss_pred             EEECCCCCCCCCCCCHHHHHHHHHHHHCC--CCEEC--CCCCCCHHHHHHHHHHHHCCCEEEEEECHHHHCCCCCCCCCE
Q ss_conf             99712012211121014666666686637--10312--014699899999999975598699998003410468887658
Q gi|254780945|r  487 WICPQIEEKKESNFRSVVERFNSLHEHFT--SSIAI--IHGRMSDIDKESVMDSFKNGTCKLLIATTVIEVGIDVVDASI  562 (700)
Q Consensus       487 ~VcPlIeese~~~~~~~~~~~~~l~~~~~--~~v~~--lHGkm~~~ek~~~m~~F~~g~~~iLvaTtviEVGvdvpna~~  562 (700)
                      |=-|        .-..+....+.|.+.+.  .+|.|  |||.|+.++.+++|+-=-.|.=+|-.||+|=|-=+.++...+
T Consensus       222 vFLP--------G~aEI~Rv~~~L~e~L~~rs~v~lcPLYG~L~~~aQ~~AI~P~a~GrRKVVLATNiAEtSLTIeGvRv  293 (858)
T TIGR01970       222 VFLP--------GQAEIRRVQEQLAERLDARSEVLLCPLYGELELAAQDRAIKPAAAGRRKVVLATNIAETSLTIEGVRV  293 (858)
T ss_pred             EECC--------CHHHHHHHHHHHHHHHCCCCCCHHCCCCCCCCHHHHHHHCCCCCCCCCEEEEEHHHHHHHEEECCEEE
T ss_conf             0168--------77789999999999751787100057678889789998708774667343420001222100176358


Q ss_pred             EEEECHHH---C----CHHHH----------HHHHHCCCCCCCCEEEEEEECCCCCHHHHHHHHHHHHHCHHHHHHHHHH
Q ss_conf             99858525---4----74688----------7730116678983599997088899879999999984142589999998
Q gi|254780945|r  563 IIIENAEH---F----GLAQL----------HQLRGRVGRGEEISSCILLYHPPLSKNSYTRLSVLKNTEDGFLIAEEDL  625 (700)
Q Consensus       563 mvI~~aer---f----GLsqL----------HQLRGRVGRg~~~s~c~l~~~~~~~~~~~~Rl~~l~~~~dGf~iAe~Dl  625 (700)
                      .|=-.=+|   |    |++=|          -|=+||=|| -.+|.||=+++.    .-.+||....+    =||.+.||
T Consensus       294 ViDsGl~R~arFDP~sG~TRL~~~RisqASA~QRAGRAGR-lepGvc~RLw~~----~q~~~l~~~~~----pEIlqaDL  364 (858)
T TIGR01970       294 VIDSGLARVARFDPKSGITRLETQRISQASATQRAGRAGR-LEPGVCYRLWSE----EQHKRLAAQSE----PEILQADL  364 (858)
T ss_pred             EEECCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCCC-CCCCHHEECCCH----HHHHHHHCCCC----CCCCHHHH
T ss_conf             8715655676347888740244578897337651263322-111411122786----89886320478----76327668


Q ss_pred             HHCCCCCCCCCHHCCCC---CCCCCC
Q ss_conf             52063000260006987---440003
Q gi|254780945|r  626 KQRKEGEILGIKQSGMP---KFLIAQ  648 (700)
Q Consensus       626 ~lRG~G~~~G~~QsG~~---~~~~~d  648 (700)
                      -    |=.+-..|.|-.   ++.+.|
T Consensus       365 ~----~LAleLA~WG~~dPsdL~wLd  386 (858)
T TIGR01970       365 A----GLALELARWGAKDPSDLRWLD  386 (858)
T ss_pred             H----HHHHHHHHCCCCCHHHHHHCC
T ss_conf             8----999999742478868874237


No 131
>pfam07652 Flavi_DEAD Flavivirus DEAD domain.
Probab=97.98  E-value=5.9e-05  Score=58.47  Aligned_cols=119  Identities=21%  Similarity=0.265  Sum_probs=77.8

Q ss_pred             EEEECCCCCHH-HHHHHHHHHHHHHHCCEEEEEHHHHHHHHHHHHHHHHCCCCCCEEEEEECCCCHHHHHHHHHHHCCCC
Q ss_conf             88621442236-99999973344430545886127999999998621101457865899624642256676877621347
Q gi|254780945|r  297 ILQGDVGSGKT-LVALIAMAAAVEAGGQAVIMAPIGILAQQHYEFIKKYTQNTQIIVEIITGNMPQAHRRKALERIAHGQ  375 (700)
Q Consensus       297 LLQGDVGSGKT-iVA~~A~l~~~~~G~Q~alMaPTEILA~QH~~~~~~~~~~~~i~v~lLtg~~~~~er~~i~~~i~~G~  375 (700)
                      .|.=-=||||| -|---..-.+++.+.++.++|||-|.|.--++    .+.+.+++..  |..         ...-.+|.
T Consensus         6 ~ld~HPGaGKTr~vLP~~v~~~i~~~lRtlVLaPTRVV~~Em~e----AL~g~~vr~~--t~a---------~~~~~~~~   70 (146)
T pfam07652         6 VLDLHPGAGKTRKVLPELVRECIDRRLRTLVLAPTRVVLAEMEE----ALRGLPIRYH--TPA---------VSSEHTGR   70 (146)
T ss_pred             EEECCCCCCCCCHHHHHHHHHHHHCCCEEEEECCHHHHHHHHHH----HHCCCCCEEE--CHH---------HHCCCCCC
T ss_conf             98538999970224899999999728618997727999999999----9758994675--234---------31366888


Q ss_pred             CEEEEECHHHC----CCCCCCCCCCEEEECCCCCCCH---HHHHHHHHCCC--CCCCEEECHHH
Q ss_conf             54864111201----3345544441788521013356---88998740256--77610101013
Q gi|254780945|r  376 AHIIIGTHALF----QDSIQYYKLILVIVDEQHRFGV---QQRLKLTQKAT--APHVLLMTATP  430 (700)
Q Consensus       376 ~~iiIGTHAL~----q~~v~F~~LgLvViDEQHRFGV---~QR~~L~~Kg~--~ph~L~MtATP  430 (700)
                      --|-+=+||-|    .....-.|-.++|.||-|=---   .-|-.+..+..  ..-++.|||||
T Consensus        71 ~ivdvmCHAT~t~r~l~~~~~~ny~viIMDE~H~~DP~SIAarG~~~~~~~~g~~a~i~mTATP  134 (146)
T pfam07652        71 EIVDVMCHATFTQRLLSPVRVPNYEVIIMDEAHFTDPASIAARGYISTLVELGEAAAIFMTATP  134 (146)
T ss_pred             CEEEEECHHHHHHHHHCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCEEEEEEECCC
T ss_conf             4188971598888973688856447999851223898999988999988543865799995689


No 132
>PRK10689 transcription-repair coupling factor; Provisional
Probab=97.95  E-value=0.00012  Score=56.12  Aligned_cols=107  Identities=12%  Similarity=0.342  Sum_probs=90.0

Q ss_pred             CHHHHHHHHHHHHCCCCEEEEEECCCCCCCCCCCCHHHHHHHHHHHHC---CCCEECCCCCCCHHHHHHHHHHHHCCCEE
Q ss_conf             002689999763103873899971201221112101466666668663---71031201469989999999997559869
Q gi|254780945|r  467 RIDEVIERLKVVLSEGKKAYWICPQIEEKKESNFRSVVERFNSLHEHF---TSSIAIIHGRMSDIDKESVMDSFKNGTCK  543 (700)
Q Consensus       467 ~~~~~~~~i~~~l~~g~q~y~VcPlIeese~~~~~~~~~~~~~l~~~~---~~~v~~lHGkm~~~ek~~~m~~F~~g~~~  543 (700)
                      +-+-++.+.=+.+..|.||-++||.-        -=|.+-|+.+++.|   |-+|++|..=.++.|+.++++.+++|++|
T Consensus       634 KTEVA~RAAFkav~~gkQVavlvPTT--------iLA~QH~~tF~~Rf~~~pv~i~~LsRf~s~ke~~~i~~~l~~G~id  705 (1148)
T PRK10689        634 KTEVAMRAAFLAVENHKQVAVLVPTT--------LLAQQHYDNFRDRFANWPVRIEMLSRFRSAKEQTQILAEAAEGKID  705 (1148)
T ss_pred             HHHHHHHHHHHHHHCCCEEEEEECCC--------CCHHHHHHHHHHHHHCCCCEEEEECCCCCHHHHHHHHHHHHCCCCC
T ss_conf             79999999999996398089983662--------2379999999987641573377503888899999999998669987


Q ss_pred             EEEECH-HHHCCCCCCCCCEEEEECHHHCCHHHHHHHHH
Q ss_conf             999800-34104688876589985852547468877301
Q gi|254780945|r  544 LLIATT-VIEVGIDVVDASIIIIENAEHFGLAQLHQLRG  581 (700)
Q Consensus       544 iLvaTt-viEVGvdvpna~~mvI~~aerfGLsqLHQLRG  581 (700)
                      |+|.|- .+--.|...|..++||.--.|||..|=..|+-
T Consensus       706 IvIGTH~ll~~dv~f~~LGLlIiDEEqrFGV~~KE~lk~  744 (1148)
T PRK10689        706 ILIGTHKLLQSDVKWKDLGLLIVDEEHRFGVRHKERIKA  744 (1148)
T ss_pred             EEEHHHHHHCCCCCCCCCCEEEECCCHHCCHHHHHHHHH
T ss_conf             762048886698654666437860102137999999972


No 133
>KOG0924 consensus
Probab=97.94  E-value=0.0021  Score=46.25  Aligned_cols=271  Identities=19%  Similarity=0.251  Sum_probs=162.7

Q ss_pred             EEEEECCCCCHHHHHHH-HHHH-HHHHHCCEEEEEHHHHHHHHHHHHHHHHCC-CCC------CEEEEEECCCCHHHHHH
Q ss_conf             78862144223699999-9733-444305458861279999999986211014-578------65899624642256676
Q gi|254780945|r  296 RILQGDVGSGKTLVALI-AMAA-AVEAGGQAVIMAPIGILAQQHYEFIKKYTQ-NTQ------IIVEIITGNMPQAHRRK  366 (700)
Q Consensus       296 RLLQGDVGSGKTiVA~~-A~l~-~~~~G~Q~alMaPTEILA~QH~~~~~~~~~-~~~------i~v~lLtg~~~~~er~~  366 (700)
                      -++-|..|||||---.- -... ..++| -.-.--|--+-|.--+..+..-+. .+|      |+-+=.||-        
T Consensus       374 vvivgETGSGKTTQl~QyL~edGY~~~G-mIGcTQPRRvAAiSVAkrVa~EM~~~lG~~VGYsIRFEdvT~~--------  444 (1042)
T KOG0924         374 VVIVGETGSGKTTQLAQYLYEDGYADNG-MIGCTQPRRVAAISVAKRVAEEMGVTLGDTVGYSIRFEDVTSE--------  444 (1042)
T ss_pred             EEEEECCCCCCHHHHHHHHHHCCCCCCC-EEEECCCHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCC--------
T ss_conf             9999358898501667999862245587-1543572278999999999998587645311248885204787--------


Q ss_pred             HHHHHCCCCCEEEEEC-HHHCCCCCCCC---CCCEEEECCCCCCCHHHH-------HHHHHCCCCCCCEEECHHHHHHHH
Q ss_conf             8776213475486411-12013345544---441788521013356889-------987402567761010101322789
Q gi|254780945|r  367 ALERIAHGQAHIIIGT-HALFQDSIQYY---KLILVIVDEQHRFGVQQR-------LKLTQKATAPHVLLMTATPIPRTL  435 (700)
Q Consensus       367 i~~~i~~G~~~iiIGT-HAL~q~~v~F~---~LgLvViDEQHRFGV~QR-------~~L~~Kg~~ph~L~MtATPIPRTL  435 (700)
                              .-.|=.=| --|++|.+.=.   +-..||.||-|-=.++--       ..+.. -.+--+++||||==---+
T Consensus       445 --------~T~IkymTDGiLLrEsL~d~~L~kYSviImDEAHERslNtDilfGllk~~lar-RrdlKliVtSATm~a~kf  515 (1042)
T KOG0924         445 --------DTKIKYMTDGILLRESLKDRDLDKYSVIIMDEAHERSLNTDILFGLLKKVLAR-RRDLKLIVTSATMDAQKF  515 (1042)
T ss_pred             --------CEEEEEECCCHHHHHHHHHHHHHHEEEEEECHHHHCCCCHHHHHHHHHHHHHH-HCCCEEEEEECCCCHHHH
T ss_conf             --------60578742305779776330044401788511433030058999999999874-226359976220248999


Q ss_pred             HHHHHHCCCHHHHCCCCCCCC-CCEEEEEECCCHHHHHHHHHHHHC----CCCEEEEEECCCCCCCCCCCCHHHHHHHHH
Q ss_conf             999752010111102355766-620799970200268999976310----387389997120122111210146666666
Q gi|254780945|r  436 VLTSLGDIDISKITEKPAGRK-PIKTVIIPINRIDEVIERLKVVLS----EGKKAYWICPQIEEKKESNFRSVVERFNSL  510 (700)
Q Consensus       436 al~~ygdldvS~i~e~P~gR~-~I~T~~~~~~~~~~~~~~i~~~l~----~g~q~y~VcPlIeese~~~~~~~~~~~~~l  510 (700)
                      +- +||.--.=.|    +||. ||.|......-.+.|-..+++.+.    .+.--..|.+.=    .   ..++.++..+
T Consensus       516 ~n-fFgn~p~f~I----pGRTyPV~~~~~k~p~eDYVeaavkq~v~Ihl~~~~GdilIfmtG----q---ediE~t~~~i  583 (1042)
T KOG0924         516 SN-FFGNCPQFTI----PGRTYPVEIMYTKTPVEDYVEAAVKQAVQIHLSGPPGDILIFMTG----Q---EDIECTCDII  583 (1042)
T ss_pred             HH-HHCCCCEEEE----CCCCCCEEEEECCCCHHHHHHHHHHHHEEEECCCCCCCEEEECCC----C---CCHHHHHHHH
T ss_conf             88-7278860101----587642377752685588999987654585446898877995278----7---6326789999


Q ss_pred             HHHC------C--C-CEECCCCCCCHHHHHHHHHHHHCCCEEEEEECHHHHCCCCCCCCCEEE--------EECHHHCCH
Q ss_conf             8663------7--1-031201469989999999997559869999800341046888765899--------858525474
Q gi|254780945|r  511 HEHF------T--S-SIAIIHGRMSDIDKESVMDSFKNGTCKLLIATTVIEVGIDVVDASIII--------IENAEHFGL  573 (700)
Q Consensus       511 ~~~~------~--~-~v~~lHGkm~~~ek~~~m~~F~~g~~~iLvaTtviEVGvdvpna~~mv--------I~~aerfGL  573 (700)
                      ++.+      +  + .|--+-.+|+++-..++...--.|.-++.|||.|-|.-+.||+-...|        ++|. |-|+
T Consensus       584 ~~~l~ql~~~~~~~L~vlpiYSQLp~dlQ~kiFq~a~~~vRK~IvATNIAETSLTi~gI~yVID~Gy~K~kvyn~-~~G~  662 (1042)
T KOG0924         584 KEKLEQLDSAPTTDLAVLPIYSQLPADLQAKIFQKAEGGVRKCIVATNIAETSLTIPGIRYVIDTGYCKLKVYNP-RIGM  662 (1042)
T ss_pred             HHHHHHHHCCCCCCEEEEEEHHHCCHHHHHHHCCCCCCCCEEEEEECCCHHHCEEECCEEEEEECCCEEEEECCC-CCCC
T ss_conf             999975523888862788405528666664330568888126998622112113326648997257245641056-6564


Q ss_pred             ----------HHHHHHHHCCCCCCCCEEEEEEECC
Q ss_conf             ----------6887730116678983599997088
Q gi|254780945|r  574 ----------AQLHQLRGRVGRGEEISSCILLYHP  598 (700)
Q Consensus       574 ----------sqLHQLRGRVGRg~~~s~c~l~~~~  598 (700)
                                |+-.|=-||-|| ..+|.||=+|..
T Consensus       663 D~L~~~pIS~AnA~QRaGRAGR-t~pG~cYRlYTe  696 (1042)
T KOG0924         663 DALQIVPISQANADQRAGRAGR-TGPGTCYRLYTE  696 (1042)
T ss_pred             CEEEEEECHHCCCHHHCCCCCC-CCCCCEEEEHHH
T ss_conf             2257875122131011244578-899626530236


No 134
>TIGR00963 secA preprotein translocase, SecA subunit; InterPro: IPR000185   Secretion across the inner membrane in some Gram-negative bacteria occurs via the preprotein translocase pathway. Proteins are produced in the cytoplasm as precursors, and require a chaperone subunit to direct them to the translocase component. . From there, the mature proteins are either targeted to the outer membrane, or remain as periplasmic proteins. The translocase protein subunits are encoded on the bacterial chromosome.     The translocase itself comprises 7 proteins, including a chaperone protein (SecB), an ATPase (SecA), an integral membrane complex (SecCY, SecE and SecG), and two additional membrane proteins that promote the release of the mature peptide into the periplasm (SecD and SecF) . The chaperone protein SecB  is a highly acidic homotetrameric protein that exists as a "dimer of dimers" in the bacterial cytoplasm. SecB maintains preproteins in an unfolded state after translation, and targets these to the peripheral membrane protein ATPase SecA for secretion .   SecA is a cytoplasmic protein of 800 to 960 amino acid residues. Homologs of secA are also encoded in the chloroplast genome of some algae  as well as in the nuclear genome of plants . It could be involved in the intraorganellar protein transport into thylakoids.; GO: 0005524 ATP binding, 0006605 protein targeting, 0006886 intracellular protein transport.
Probab=97.92  E-value=5e-05  Score=58.99  Aligned_cols=138  Identities=24%  Similarity=0.324  Sum_probs=106.4

Q ss_pred             EEEEC-----CCCCHHHHHHHHHHHHHHHHCCEEEEEHHHHHHHHHHHHHHHHCCCCCCEEEEEECCCCHHHHHHHHHHH
Q ss_conf             88621-----4422369999997334443054588612799999999862110145786589962464225667687762
Q gi|254780945|r  297 ILQGD-----VGSGKTLVALIAMAAAVEAGGQAVIMAPIGILAQQHYEFIKKYTQNTQIIVEIITGNMPQAHRRKALERI  371 (700)
Q Consensus       297 LLQGD-----VGSGKTiVA~~A~l~~~~~G~Q~alMaPTEILA~QH~~~~~~~~~~~~i~v~lLtg~~~~~er~~i~~~i  371 (700)
                      |-+|+     .|=|||+||.++++.-+-+|.=|=+.-=-|=||+==.++..+.|.=+|++|.|.-.+++..+|++.|.  
T Consensus        72 LH~G~IAEMkTGEGKTL~AtLpaYLNAL~GkGVHvVTVNdYLA~RD~e~m~~v~~FLGL~VGl~~~~m~~~eRr~aY~--  149 (904)
T TIGR00963        72 LHKGKIAEMKTGEGKTLVATLPAYLNALTGKGVHVVTVNDYLARRDAEWMGQVYRFLGLSVGLILSSMSPEERREAYA--  149 (904)
T ss_pred             HCCCCEEEECCCCCHHHHHHHHHHHHHHCCCCCEEEEECCHHHHHHHHHHHHHHHHCCCEEEEECCCCCHHHHHHHHC--
T ss_conf             808966783148862899999999876517962799635044488899878999684936888617998589999854--


Q ss_pred             CCCCCEEEEECHHH------------CCCCCCCCCCCEEEECCCCCCCHHHHHHHHHC----------CCCCCCEEE---
Q ss_conf             13475486411120------------13345544441788521013356889987402----------567761010---
Q gi|254780945|r  372 AHGQAHIIIGTHAL------------FQDSIQYYKLILVIVDEQHRFGVQQRLKLTQK----------ATAPHVLLM---  426 (700)
Q Consensus       372 ~~G~~~iiIGTHAL------------~q~~v~F~~LgLvViDEQHRFGV~QR~~L~~K----------g~~ph~L~M---  426 (700)
                          +||.=||=.=            --+++.-+.+-.+||||     |.  --|.+-          .+++--+++   
T Consensus       150 ----cDITY~TNnELGFDYLRDNM~~~~ee~vqR~f~FAIIDE-----VD--SILIDEARTPLIISGpae~~~~~Y~ev~  218 (904)
T TIGR00963       150 ----CDITYGTNNELGFDYLRDNMALSKEEKVQRPFNFAIIDE-----VD--SILIDEARTPLIISGPAEKSTEKYLEVN  218 (904)
T ss_pred             ----CCEEEECCCCCCHHHHHHHHHCCHHHHHCCCCCCEEEEE-----EC--CEEECCCCCCCCCCCCCCCCCCCHHHHH
T ss_conf             ----981653265420246667641150121016722268864-----24--4642333686523576678630100178


Q ss_pred             -------------CHHHHHHHHHHHHHH-CCCHHHHCCC
Q ss_conf             -------------101322789999752-0101111023
Q gi|254780945|r  427 -------------TATPIPRTLVLTSLG-DIDISKITEK  451 (700)
Q Consensus       427 -------------tATPIPRTLal~~yg-dldvS~i~e~  451 (700)
                                   .|--+|.+|.   -. |-|. .+||+
T Consensus       219 ~~~~~l~e~~~~p~a~~~~~~l~---e~W~~dY-~vDeK  253 (904)
T TIGR00963       219 KLVDPLKETDKLPQANEVAKALK---EKWDVDY-EVDEK  253 (904)
T ss_pred             HHHHHHHCCCCCCCHHHHHHHHH---HHCCCCC-EEECC
T ss_conf             78866416655750445689986---3116770-35104


No 135
>KOG0923 consensus
Probab=97.90  E-value=0.00087  Score=49.27  Aligned_cols=346  Identities=18%  Similarity=0.209  Sum_probs=177.6

Q ss_pred             EEEEECCCCCHHHH--HHHHHHHHHHHHCCEEEEEHHHHHHHHHHHHHHHHC-CCCCCEEEEEECCCCHHHHHHHHHHHC
Q ss_conf             78862144223699--999973344430545886127999999998621101-457865899624642256676877621
Q gi|254780945|r  296 RILQGDVGSGKTLV--ALIAMAAAVEAGGQAVIMAPIGILAQQHYEFIKKYT-QNTQIIVEIITGNMPQAHRRKALERIA  372 (700)
Q Consensus       296 RLLQGDVGSGKTiV--A~~A~l~~~~~G~Q~alMaPTEILA~QH~~~~~~~~-~~~~i~v~lLtg~~~~~er~~i~~~i~  372 (700)
                      =++-|+.|||||--  -.+--.-....|.-.+.--|--|-|.--...+.+-+ ..+|-.|..--.          +++--
T Consensus       283 LiI~GeTGSGKTTQiPQyL~EaGytk~gk~IgcTQPRRVAAmSVAaRVA~EMgvkLG~eVGYsIR----------FEdcT  352 (902)
T KOG0923         283 LIIVGETGSGKTTQIPQYLYEAGYTKGGKKIGCTQPRRVAAMSVAARVAEEMGVKLGHEVGYSIR----------FEDCT  352 (902)
T ss_pred             EEEECCCCCCCCCCCCHHHHHCCCCCCCCEEEECCCCHHHHHHHHHHHHHHHCCCCCCCCCEEEE----------ECCCC
T ss_conf             99975788986445628988542135894674068506887779999999857401431444888----------50356


Q ss_pred             CCCCEEEEEC----HHHCCCCCCCCCCCEEEECCCCC--------CCHHHHHHHHHCCCCCCCEEECHHHHHHHHHHHHH
Q ss_conf             3475486411----12013345544441788521013--------35688998740256776101010132278999975
Q gi|254780945|r  373 HGQAHIIIGT----HALFQDSIQYYKLILVIVDEQHR--------FGVQQRLKLTQKATAPHVLLMTATPIPRTLVLTSL  440 (700)
Q Consensus       373 ~G~~~iiIGT----HAL~q~~v~F~~LgLvViDEQHR--------FGV~QR~~L~~Kg~~ph~L~MtATPIPRTLal~~y  440 (700)
                      +.+--|=.=|    +-=|+.+-...+-..+||||-|-        ||.--+.+=..  ..--+|+||||==---.+ +.|
T Consensus       353 SekTvlKYMTDGmLlREfL~epdLasYSViiiDEAHERTL~TDILfgLvKDIar~R--pdLKllIsSAT~DAekFS-~fF  429 (902)
T KOG0923         353 SEKTVLKYMTDGMLLREFLSEPDLASYSVIIVDEAHERTLHTDILFGLVKDIARFR--PDLKLLISSATMDAEKFS-AFF  429 (902)
T ss_pred             CCCEEEEEECCHHHHHHHHCCCCCCCEEEEEEEHHHHHHHHHHHHHHHHHHHHHHC--CCCEEEEECCCCCHHHHH-HHC
T ss_conf             74122432243067998714634223359996024320034567999878887508--760477322226789998-761


Q ss_pred             HCCCHHHHCCCCCCCCCCEEEEEECC---CHHHHHHHHHHH--HCCCCEEEEEECCCCCCCCCCCCHHHHHHHHHHHHCC
Q ss_conf             20101111023557666207999702---002689999763--1038738999712012211121014666666686637
Q gi|254780945|r  441 GDIDISKITEKPAGRKPIKTVIIPIN---RIDEVIERLKVV--LSEGKKAYWICPQIEEKKESNFRSVVERFNSLHEHFT  515 (700)
Q Consensus       441 gdldvS~i~e~P~gR~~I~T~~~~~~---~~~~~~~~i~~~--l~~g~q~y~VcPlIeese~~~~~~~~~~~~~l~~~~~  515 (700)
                      +|   -.|=-.|.-|=||.++.-...   .++-++..|.+.  -+.++-+.|--+.=||     ...+.+....++..++
T Consensus       430 Dd---apIF~iPGRRyPVdi~Yt~~PEAdYldAai~tVlqIH~tqp~GDILVFltGQeE-----IEt~~e~l~~~~~~LG  501 (902)
T KOG0923         430 DD---APIFRIPGRRYPVDIFYTKAPEADYLDAAIVTVLQIHLTQPLGDILVFLTGQEE-----IETVKENLKERCRRLG  501 (902)
T ss_pred             CC---CCEEECCCCCCCEEEECCCCCCHHHHHHHHHHHEEEEECCCCCCEEEEECCHHH-----HHHHHHHHHHHHHHHC
T ss_conf             68---857723686565134304588530799988654046751577657999446789-----9999999999999853


Q ss_pred             CC-----EECCCCCCCHHHHHHHHHHHHCCCEEEEEECHHHHCCCCCCCCCEEEEE-----C--HHHCCHHHHH------
Q ss_conf             10-----3120146998999999999755986999980034104688876589985-----8--5254746887------
Q gi|254780945|r  516 SS-----IAIIHGRMSDIDKESVMDSFKNGTCKLLIATTVIEVGIDVVDASIIIIE-----N--AEHFGLAQLH------  577 (700)
Q Consensus       516 ~~-----v~~lHGkm~~~ek~~~m~~F~~g~~~iLvaTtviEVGvdvpna~~mvI~-----~--aerfGLsqLH------  577 (700)
                      .+     |-=+|.-++++....|.+---.|.-++.+||.+-|.-+.+++..-.|=-     |  -.|=|.-+|+      
T Consensus       502 ski~eliv~PiYaNLPselQakIFePtP~gaRKVVLATNIAETSlTIdgI~yViDpGf~K~nsynprtGmesL~v~piSK  581 (902)
T KOG0923         502 SKIRELIVLPIYANLPSELQAKIFEPTPPGARKVVLATNIAETSLTIDGIKYVIDPGFVKQNSYNPRTGMESLLVTPISK  581 (902)
T ss_pred             CCCCEEEEEECCCCCCHHHHHHHCCCCCCCCEEEEEEECCHHHCEEECCEEEEECCCCCCCCCCCCCCCCEEEEEEEECH
T ss_conf             36550798400046986888763588998850489861101210544675899667621124768776850677763110


Q ss_pred             ----HHHHCCCCCCCCEEEEEEECCCCCHHHHH---HHHHHHHHCHHHHHHHHHHHHCCCCCCCCCHHCCCCCCCCCCHH
Q ss_conf             ----73011667898359999708889987999---99999841425899999985206300026000698744000388
Q gi|254780945|r  578 ----QLRGRVGRGEEISSCILLYHPPLSKNSYT---RLSVLKNTEDGFLIAEEDLKQRKEGEILGIKQSGMPKFLIAQPE  650 (700)
Q Consensus       578 ----QLRGRVGRg~~~s~c~l~~~~~~~~~~~~---Rl~~l~~~~dGf~iAe~Dl~lRG~G~~~G~~QsG~~~~~~~d~~  650 (700)
                          |=-||-||- .+|.||=+|..-.=..-.+   -=+|...+-++-.+.-+-|-+           +-+..|-|.|+-
T Consensus       582 AsA~QRaGRAGRt-gPGKCfRLYt~~aY~~eLE~~t~PEIqRtnL~nvVL~LkSLGI-----------~Dl~~FdFmDpP  649 (902)
T KOG0923         582 ASANQRAGRAGRT-GPGKCFRLYTAWAYEHELEEMTVPEIQRTNLGNVVLLLKSLGI-----------HDLIHFDFLDPP  649 (902)
T ss_pred             HHHHHHCCCCCCC-CCCCEEEEECHHHHHHHHCCCCCCCEEECCCHHHHHHHHHCCC-----------CHHCCCCCCCCC
T ss_conf             0044442345788-9972578500666653420278740342252238898885273-----------030046667999


Q ss_pred             HHHHH-HHHHHHHHHHHHHHCCCCC
Q ss_conf             75999-9999999999998484636
Q gi|254780945|r  651 LHDSL-LEIARKDAKHILTQDPDLT  674 (700)
Q Consensus       651 ~d~~l-l~~a~~~a~~~~~~d~~l~  674 (700)
                      -...| ....+-.|..-++++-+|.
T Consensus       650 p~etL~~aLE~LyaLGALn~~GeLT  674 (902)
T KOG0923         650 PTETLLKALEQLYALGALNHLGELT  674 (902)
T ss_pred             CHHHHHHHHHHHHHHHCCCCCCCHH
T ss_conf             7489999999998744233356211


No 136
>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=97.89  E-value=2.7e-05  Score=61.08  Aligned_cols=308  Identities=16%  Similarity=0.320  Sum_probs=135.7

Q ss_pred             CCCCHHHHHHHHHCCCCCCHHHHHHHHHHHHHHCCCCCCEEEEEECCCCCHHHHHHHHHHHHHHHHCCEEEEEHHHHHHH
Q ss_conf             87757899998630246798899999999984100134307886214422369999997334443054588612799999
Q gi|254780945|r  256 NVEGKIAQKILRNIPFSPTKSQESAIKDILQDMSQKNRMLRILQGDVGSGKTLVALIAMAAAVEAGGQAVIMAPIGILAQ  335 (700)
Q Consensus       256 ~~~~~~~~~f~~~LPF~LT~~Q~~ai~eI~~Dl~~~~pM~RLLQGDVGSGKTiVA~~A~l~~~~~G~Q~alMaPTEILA~  335 (700)
                      ..-+.-..-|.+-|.|+-=.+-..-+..|.+-=..+.        | |=+-|++--.-.....  |.=+.+-+|+.. =.
T Consensus       309 ~prG~r~~LFR~LL~FevG~~~~~GLRnvvD~y~~~~--------d-~v~E~~~~sve~v~~L--G~GGlVyvs~~y-G~  376 (1843)
T TIGR01054       309 KPRGKRVKLFRELLGFEVGKGSDTGLRNVVDVYEEDE--------D-GVKEKLLESVELVKKL--GKGGLVYVSIDY-GK  376 (1843)
T ss_pred             CCCCCHHHHHHHHCCCCCCCCCCCCCCCEEEEEECCC--------C-CHHHHHHHHHHHHHHH--CCCEEEEEECCC-CH
T ss_conf             8876133653655271005764223321388511488--------8-4468899999999984--794399971222-55


Q ss_pred             HHHHHHHHHCCCCCCEEEEEECCCCHHHHHHHHHHHCCCCCEEEEECHHHC---CCCCCCCC-CCEEEEC--CCCCCCHH
Q ss_conf             999862110145786589962464225667687762134754864111201---33455444-4178852--10133568
Q gi|254780945|r  336 QHYEFIKKYTQNTQIIVEIITGNMPQAHRRKALERIAHGQAHIIIGTHALF---QDSIQYYK-LILVIVD--EQHRFGVQ  409 (700)
Q Consensus       336 QH~~~~~~~~~~~~i~v~lLtg~~~~~er~~i~~~i~~G~~~iiIGTHAL~---q~~v~F~~-LgLvViD--EQHRFGV~  409 (700)
                      -..+.+.+.|...||++..++...    .++-++..+.|++|++||+-.--   =.++.... .-++|-=  =.|||+..
T Consensus       377 e~a~ei~~~L~~~Gv~A~~~~~~k----~~~~~~~F~~GE~dVliG~a~yyg~LVRGLDLP~rvRYAvF~G~Pk~k~~~~  452 (1843)
T TIGR01054       377 EKAEEIKEFLREHGVKAVAYHAKK----PKEDLEKFAEGEIDVLIGVASYYGVLVRGLDLPERVRYAVFLGVPKFKVPLK  452 (1843)
T ss_pred             HHHHHHHHHHHHCCCEEEEEEECC----CCCCHHHHHCCCEEEEEEEECCCCCEEECCCCCCHHEEEEECCCCCEEEEEE
T ss_conf             899999999985794799984037----7320346634851368771015476353266610100023438995066412


Q ss_pred             ------HHH-HHHHCCC--CCCCEEECHHHHHHHHHHHHHHCCCHHHHCCCCCC-------CCCCEE----EEEECCC--
Q ss_conf             ------899-8740256--77610101013227899997520101111023557-------666207----9997020--
Q gi|254780945|r  410 ------QRL-KLTQKAT--APHVLLMTATPIPRTLVLTSLGDIDISKITEKPAG-------RKPIKT----VIIPINR--  467 (700)
Q Consensus       410 ------QR~-~L~~Kg~--~ph~L~MtATPIPRTLal~~ygdldvS~i~e~P~g-------R~~I~T----~~~~~~~--  467 (700)
                            .|. +|++=-.  .-+==+=|+.+==|++.+-++=++++|++...=.+       +..|.-    .+-...+  
T Consensus       453 ~~~~~p~~~~~LLSl~~~~~~e~~i~~~~~~~~~~~~~L~r~~~ls~~e~~~~~~~~~~~~~~e~~~Gydr~i~e~~~~~  532 (1843)
T TIGR01054       453 VALSSPRRLLALLSLLALILKEERIESLAEKARKLLGRLKRYIDLSVIERALEEKLEARRARGEVKEGYDRIIEEVLKFL  532 (1843)
T ss_pred             ECCCCHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHH
T ss_conf             03787578999999999851432035789999999999988654443328889999852376502201568999888778


Q ss_pred             -----HHHHHHH-HHH-----HHCCCCEEEEEECCCC----CCCCC--------------CCCHHHHHHHHHHHHCC---
Q ss_conf             -----0268999-976-----3103873899971201----22111--------------21014666666686637---
Q gi|254780945|r  468 -----IDEVIER-LKV-----VLSEGKKAYWICPQIE----EKKES--------------NFRSVVERFNSLHEHFT---  515 (700)
Q Consensus       468 -----~~~~~~~-i~~-----~l~~g~q~y~VcPlIe----ese~~--------------~~~~~~~~~~~l~~~~~---  515 (700)
                           .+.+++. +.+     -..+|+..|+|.|=+.    .|...              =+.+..+.++.|.+...   
T Consensus       533 ~~~L~~e~~~~~G~~~~~~~~~~~~e~~~ylvvpD~~tYiQASGRTSRl~aGGlTkGlS~Vl~dd~~~~~aL~kr~~lyy  612 (1843)
T TIGR01054       533 REALKREDVLEKGIKESEDLSLVAKEGKLYLVVPDVKTYIQASGRTSRLYAGGLTKGLSVVLVDDPEAFEALKKRLKLYY  612 (1843)
T ss_pred             HHHHHHHHHHHCCCCCCCCEEEECCCCEEEEEECCCCCCCCCCCHHHHHHHHHHHHCCEEEEECCHHHHHHHHHHHHHHH
T ss_conf             88775202553265410344786179725999668774424674156655423230534899654789999998886666


Q ss_pred             CCEECCCCCCCHHHHHHHHHHHHCC--CEEEEEECHHHHCCCCCCCCCEEEEECHH-------HCCHHHHHHH
Q ss_conf             1031201469989999999997559--86999980034104688876589985852-------5474688773
Q gi|254780945|r  516 SSIAIIHGRMSDIDKESVMDSFKNG--TCKLLIATTVIEVGIDVVDASIIIIENAE-------HFGLAQLHQL  579 (700)
Q Consensus       516 ~~v~~lHGkm~~~ek~~~m~~F~~g--~~~iLvaTtviEVGvdvpna~~mvI~~ae-------rfGLsqLHQL  579 (700)
                      -.-.+=-=+++.-+-++++..--+-  ++.--+.--++--+.|.=-.++||||.+.       =||==+--.+
T Consensus       613 ~~~ei~fk~i~EVDL~~l~rEIDEdR~k~r~~~~g~~~A~~~dLvKt~L~vVESPnKARTIA~FFGkP~~R~i  685 (1843)
T TIGR01054       613 FTQEIEFKRIDEVDLEKLLREIDEDREKVRRIVEGKVKAKVKDLVKTALLVVESPNKARTIARFFGKPSVRKI  685 (1843)
T ss_pred             HHHCCCCCCCCCCCHHHHHHHHHHCCCCCCEEEECCEEEEEECCCCCEEEEEECCCCHHHHHHHCCCCCCEEC
T ss_conf             5201355445600178887764101012401220762664202424137998278604455343069963551


No 137
>KOG0390 consensus
Probab=97.88  E-value=0.0046  Score=43.62  Aligned_cols=330  Identities=17%  Similarity=0.176  Sum_probs=200.3

Q ss_pred             CCCCCHHHHHHHHHHHHHHCCCC----CCEEEEEECCCCCHHHHHHHHHHHHHHHHCC-------EEEEEHHHHHHHHHH
Q ss_conf             24679889999999998410013----4307886214422369999997334443054-------588612799999999
Q gi|254780945|r  270 PFSPTKSQESAIKDILQDMSQKN----RMLRILQGDVGSGKTLVALIAMAAAVEAGGQ-------AVIMAPIGILAQQHY  338 (700)
Q Consensus       270 PF~LT~~Q~~ai~eI~~Dl~~~~----pM~RLLQGDVGSGKTiVA~~A~l~~~~~G~Q-------~alMaPTEILA~QH~  338 (700)
                      --.|-.-|+..++=+.+.+....    +=-=.+--.-|+|||.-.+.-+...+..+.|       +.+.||-.++ .--+
T Consensus       236 ~~~LrPHQ~EG~~FL~knl~g~~~~~~~~GCImAd~~GlGKTlq~IsflwtlLrq~P~~~~~~~k~lVV~P~sLv-~nWk  314 (776)
T KOG0390         236 KKILRPHQREGFEFLYKNLAGLIRPKNSGGCIMADEPGLGKTLQCISFIWTLLRQFPQAKPLINKPLVVAPSSLV-NNWK  314 (776)
T ss_pred             HHHCCCHHHHHHHHHHHHHHCCCCCCCCCCEEEECCCCCCHHHHHHHHHHHHHHHCCCCCCCCCCCEEECCHHHH-HHHH
T ss_conf             641281578778997864113111588875472078876407888999999998686755444660798458888-7899


Q ss_pred             HHHHHHCCCCCCEEEEEECCCCH--HHHHHHHHH--HCCCCCEEEEECHHHC--CCCCCCCCCCEEEECCCCCCCHHHHH
Q ss_conf             86211014578658996246422--566768776--2134754864111201--33455444417885210133568899
Q gi|254780945|r  339 EFIKKYTQNTQIIVEIITGNMPQ--AHRRKALER--IAHGQAHIIIGTHALF--QDSIQYYKLILVIVDEQHRFGVQQRL  412 (700)
Q Consensus       339 ~~~~~~~~~~~i~v~lLtg~~~~--~er~~i~~~--i~~G~~~iiIGTHAL~--q~~v~F~~LgLvViDEQHRFGV~QR~  412 (700)
                      +.|.+|+.+..+.+.-+.|..+.  -..+.++..  -.-..+-.++++-++-  -+.+.-...||+|-||=||-= ++..
T Consensus       315 kEF~KWl~~~~i~~l~~~~~~~~~w~~~~sil~~~~~~~~~~vli~sye~~~~~~~~il~~~~glLVcDEGHrlk-N~~s  393 (776)
T KOG0390         315 KEFGKWLGNHRINPLDFYSTKKSSWIKLKSILFLGYKQFTTPVLIISYETASDYCRKILLIRPGLLVCDEGHRLK-NSDS  393 (776)
T ss_pred             HHHHHHCCCCCCCEEEEECCCCHHHHHHHHHHHHHHHHEEEEEEECCHHHHHHHHHHHHCCCCCEEEECCCCCCC-CHHH
T ss_conf             999874253555404542345256666678988622112578786369999999999854789869977988856-2245


Q ss_pred             HHH---HCCCCCCCEEECHHHHHHHHHHHHHHCCCHH-------------------------------------------
Q ss_conf             874---0256776101010132278999975201011-------------------------------------------
Q gi|254780945|r  413 KLT---QKATAPHVLLMTATPIPRTLVLTSLGDIDIS-------------------------------------------  446 (700)
Q Consensus       413 ~L~---~Kg~~ph~L~MtATPIPRTLal~~ygdldvS-------------------------------------------  446 (700)
                      .+.   .+=..|+-++.|-|||---+.= +|.-||+.                                           
T Consensus       394 ~~~kaL~~l~t~rRVLLSGTp~QNdl~E-yFnlL~fvrP~~Lgs~~sf~k~~~~~i~~~~~~~~s~e~~~~~~rl~eL~~  472 (776)
T KOG0390         394 LTLKALSSLKTPRRVLLTGTPIQNDLKE-YFNLLDFVRPGFLGSISSFKKKFEIPILRGRDADASEEDREREERLQELRE  472 (776)
T ss_pred             HHHHHHHHCCCCCEEEEECCCCCCCHHH-HHHHHHHCCHHHCCCHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHHHHHH
T ss_conf             8999997468773699607753346999-978885157011255378887751344235677855354525799999999


Q ss_pred             ------------H-HCCCCCCCCCCEEEEEEC-CCHHHHHHHHHHHHCCCCEEEEEECCCC-------------------
Q ss_conf             ------------1-102355766620799970-2002689999763103873899971201-------------------
Q gi|254780945|r  447 ------------K-ITEKPAGRKPIKTVIIPI-NRIDEVIERLKVVLSEGKKAYWICPQIE-------------------  493 (700)
Q Consensus       447 ------------~-i~e~P~gR~~I~T~~~~~-~~~~~~~~~i~~~l~~g~q~y~VcPlIe-------------------  493 (700)
                                  + .+.+|+  +-..|.+++. ..-.++|..+.+.-  -...|-.|+++-                   
T Consensus       473 ~t~~fi~rrt~~il~k~LP~--k~e~vv~~n~t~~Q~~~~~~l~~~~--~~~~~~~~~l~~~~~L~k~cnhP~L~~~~~~  548 (776)
T KOG0390         473 LTNKFILRRTGDILLKYLPG--KYEYVVFCNPTPIQKELYKKLLDSM--KMRTLKGYALELITKLKKLCNHPSLLLLCEK  548 (776)
T ss_pred             HHHHHEEECCCCHHHHHCCC--CEEEEEEECCCHHHHHHHHHHHHHH--HHHHHHCCHHHHHHHHHHHHCCHHHHCCCCC
T ss_conf             99765221112034553888--5469999578089999999998777--7654313225588998987368776313322


Q ss_pred             -CCCCCC------------------------------------------------CCHHHHHHHHHHHHCCCCEECCCCC
Q ss_conf             -221112------------------------------------------------1014666666686637103120146
Q gi|254780945|r  494 -EKKESN------------------------------------------------FRSVVERFNSLHEHFTSSIAIIHGR  524 (700)
Q Consensus       494 -ese~~~------------------------------------------------~~~~~~~~~~l~~~~~~~v~~lHGk  524 (700)
                       ++|+..                                                +.-..+.++.+++.-+..+-.|||+
T Consensus       549 ~~~e~~~~~~~~~~~~~~~~~~~~~~~ks~kl~~L~~ll~~~~ek~~~~~v~Isny~~tldl~e~~~~~~g~~~~rLdG~  628 (776)
T KOG0390         549 TEKEKAFKNPALLLDPGKLKLDAGDGSKSGKLLVLVFLLEVIREKLLVKSVLISNYTQTLDLFEQLCRWRGYEVLRLDGK  628 (776)
T ss_pred             CCCCCCCCCHHHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCEEEEEECCHHHHHHHHHHHHHHCCCEEEEECCC
T ss_conf             34441226857650321246665551156689999999999865223179996228999999999976538448997387


Q ss_pred             CCHHHHHHHHHHHHCCCEE---EEEECHHHHCCCCCCCCCEEEEECHHHCCHHHHHHHHHCCCCCCCCEEEEE---EECC
Q ss_conf             9989999999997559869---999800341046888765899858525474688773011667898359999---7088
Q gi|254780945|r  525 MSDIDKESVMDSFKNGTCK---LLIATTVIEVGIDVVDASIIIIENAEHFGLAQLHQLRGRVGRGEEISSCIL---LYHP  598 (700)
Q Consensus       525 m~~~ek~~~m~~F~~g~~~---iLvaTtviEVGvdvpna~~mvI~~aerfGLsqLHQLRGRVGRg~~~s~c~l---~~~~  598 (700)
                      |+..+++.+|+.|.+-+-+   .|.||+-=-+|++.-.||=.|+.|.| .-=|.=-|==.||=|-+.+=-||.   ++..
T Consensus       629 ~~~~qRq~~vd~FN~p~~~~~vfLlSsKAgg~GinLiGAsRlil~D~d-WNPa~d~QAmaR~~RdGQKk~v~iYrLlatG  707 (776)
T KOG0390         629 TSIKQRQKLVDTFNDPESPSFVFLLSSKAGGEGLNLIGASRLILFDPD-WNPAVDQQAMARAWRDGQKKPVYIYRLLATG  707 (776)
T ss_pred             CCHHHHHHHHHHCCCCCCCCEEEEEECCCCCCCEEECCCCEEEEECCC-CCCHHHHHHHHHHCCCCCCCEEEEEEEECCC
T ss_conf             766888899873359988741899854455576320134038995799-9823678999976457874268999963279


Q ss_pred             CCCHHHHHH
Q ss_conf             899879999
Q gi|254780945|r  599 PLSKNSYTR  607 (700)
Q Consensus       599 ~~~~~~~~R  607 (700)
                      .+-|.-.+|
T Consensus       708 tiEEk~~qr  716 (776)
T KOG0390         708 TIEEKIYQR  716 (776)
T ss_pred             CCHHHHHHH
T ss_conf             813888999


No 138
>TIGR01407 dinG_rel DnaQ family exonuclease/DinG family helicase, putative; InterPro: IPR006310   These are a family of proteins in Gram-positive bacteria. The N-terminal region of about 200 amino acids resembles the epsilon subunit of E. coli DNA polymerase III and the homologous region of the Gram-positive type DNA polymerase III alpha subunit. The epsilon subunit contains an exonuclease domain. The remainder of this protein family resembles a predicted ATP-dependent helicase, the DNA damage-inducible protein DinG of Escherichia coli. .
Probab=97.80  E-value=0.00058  Score=50.65  Aligned_cols=155  Identities=18%  Similarity=0.214  Sum_probs=113.7

Q ss_pred             CCCCCCCHHHHHHHHHCCCC------------CCHHHHHHHHHHHHHHCCCCCCEEEEEECCCCCHHHHHHHHHHHHHH-
Q ss_conf             76787757899998630246------------79889999999998410013430788621442236999999733444-
Q gi|254780945|r  253 IPINVEGKIAQKILRNIPFS------------PTKSQESAIKDILQDMSQKNRMLRILQGDVGSGKTLVALIAMAAAVE-  319 (700)
Q Consensus       253 ~~~~~~~~~~~~f~~~LPF~------------LT~~Q~~ai~eI~~Dl~~~~pM~RLLQGDVGSGKTiVA~~A~l~~~~-  319 (700)
                      ..+........+.++.|.|+            -=..|.+-.+.|...|..+.--.-|++-=.|+|||.=++++|+.... 
T Consensus       229 ~~~~~l~~~fsk~~~~l~l~GGslskaf~~y~~R~~Q~~la~~v~~~l~~Gt~~~~lIEA~tG~GKtlgYLLPal~~~~~  308 (944)
T TIGR01407       229 TEYQTLTSTFSKNIDRLGLEGGSLSKAFLRYEYREEQLKLAELVEDELTHGTEEKSLIEAPTGTGKTLGYLLPALYLAKE  308 (944)
T ss_pred             CCCCCCCHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHEECCCCCCHHHHHHHHHHHHCCC
T ss_conf             32200014677788763167623788877653138899999999998415766113302376643258999999973137


Q ss_pred             HHCCEEEEEHHHHHHHHHHHHHHHHCCC---CCCEEEEEECC-------------------------------------C
Q ss_conf             3054588612799999999862110145---78658996246-------------------------------------4
Q gi|254780945|r  320 AGGQAVIMAPIGILAQQHYEFIKKYTQN---TQIIVEIITGN-------------------------------------M  359 (700)
Q Consensus       320 ~G~Q~alMaPTEILA~QH~~~~~~~~~~---~~i~v~lLtg~-------------------------------------~  359 (700)
                      .+.++++=.+|-||=.|-.+.=-+.+..   +.+++.+|-|.                                     |
T Consensus       309 ~~~~vviST~Tk~LQ~QL~E~d~P~l~~~~~fk~~~~~iKg~~~YlsL~~F~~~L~~~Cet~~~~~~~~KM~~LvWLTET  388 (944)
T TIGR01407       309 EEKPVVISTATKVLQSQLLEKDIPLLNKILNFKLNVALIKGKKNYLSLQKFSQLLKENCETDNKEFELFKMQVLVWLTET  388 (944)
T ss_pred             CCCCEEEEECCHHHHHHHHHHHHHHHHHHCCCCEEEEEEECCCCCCCHHHHHHHHCCCCCCCHHHHHHHHHHHHEEEECC
T ss_conf             88856998363665656568888988865189712788507655436789999960478882489999987543210037


Q ss_pred             CHHHH--------------------------------HHHHHHH--CCCCCEEEEECHHHC-CCCCC----CCCCCEEEE
Q ss_conf             22566--------------------------------7687762--134754864111201-33455----444417885
Q gi|254780945|r  360 PQAHR--------------------------------RKALERI--AHGQAHIIIGTHALF-QDSIQ----YYKLILVIV  400 (700)
Q Consensus       360 ~~~er--------------------------------~~i~~~i--~~G~~~iiIGTHAL~-q~~v~----F~~LgLvVi  400 (700)
                      ...+.                                ..-|..+  +.-+++|+|-=||.+ ++.+.    |..=-..||
T Consensus       389 etGDldEl~l~~~~~~f~~~~~~dG~~~l~~~~~~~~~dF~~~~~~~A~~~~~~itNHA~L~~~~~~~~~~~~~~~~lii  468 (944)
T TIGR01407       389 ETGDLDELNLLTGNKSFFAEVRHDGLGFLSKKDLFYEVDFYKRAQKKAEQAEILITNHAYLITRLVDKPELLPEFRLLII  468 (944)
T ss_pred             CCCCHHHHCCCCCCCHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHCCEEEECHHHHHHHHHHCCCCCCCCCCEEE
T ss_conf             98756752024675035778856056445665521128899999988833634565017887777644777766773252


Q ss_pred             CCCCCCC
Q ss_conf             2101335
Q gi|254780945|r  401 DEQHRFG  407 (700)
Q Consensus       401 DEQHRFG  407 (700)
                      ||=|||-
T Consensus       469 DEAh~l~  475 (944)
T TIGR01407       469 DEAHHLP  475 (944)
T ss_pred             HHHHHHH
T ss_conf             2265379


No 139
>COG0610 Type I site-specific restriction-modification system, R (restriction) subunit and related helicases [Defense mechanisms]
Probab=97.74  E-value=0.0072  Score=42.06  Aligned_cols=330  Identities=19%  Similarity=0.218  Sum_probs=179.2

Q ss_pred             HHHHHHH----HHHHHHCCCCCCEEEEEECCCCCHHHHHHHHHHHHHHH--HCCEEEEEHHHHHHHHHHHHHHHHCCCCC
Q ss_conf             8999999----99984100134307886214422369999997334443--05458861279999999986211014578
Q gi|254780945|r  276 SQESAIK----DILQDMSQKNRMLRILQGDVGSGKTLVALIAMAAAVEA--GGQAVIMAPIGILAQQHYEFIKKYTQNTQ  349 (700)
Q Consensus       276 ~Q~~ai~----eI~~Dl~~~~pM~RLLQGDVGSGKTiVA~~A~l~~~~~--G~Q~alMaPTEILA~QH~~~~~~~~~~~~  349 (700)
                      .|.++++    .+......+..-.-+++---|||||+--+.++-..++.  .-.+.|++=.--|-.|.+++|.++-....
T Consensus       252 ~q~~a~~~~i~~~~~~~~~~~~~~G~IWHtqGSGKTltm~~~A~~l~~~~~~~~v~fvvDR~dLd~Q~~~~f~~~~~~~~  331 (962)
T COG0610         252 AQYRAVQKAIKRILKASNPGDGKGGYIWHTQGSGKTLTMFKLARLLLELPKNPKVLFVVDRKDLDDQTSDEFQSFGKVAF  331 (962)
T ss_pred             HHHHHHHHHHHHHHHHCCCCCCCCEEEEECCCCCHHHHHHHHHHHHHHCCCCCEEEEEECHHHHHHHHHHHHHHHHHHHH
T ss_conf             99999999999999712678777238984069837899999999998365999699996728899999999999887632


Q ss_pred             CEEEEEECCCCHHHHHHHHHHHCCCCCEEEEEC-H---HHCCCC---CCCCCCCEEEECCCCCCCHHHHHHHHHCCC-CC
Q ss_conf             658996246422566768776213475486411-1---201334---554444178852101335688998740256-77
Q gi|254780945|r  350 IIVEIITGNMPQAHRRKALERIAHGQAHIIIGT-H---ALFQDS---IQYYKLILVIVDEQHRFGVQQRLKLTQKAT-AP  421 (700)
Q Consensus       350 i~v~lLtg~~~~~er~~i~~~i~~G~~~iiIGT-H---AL~q~~---v~F~~LgLvViDEQHRFGV~QR~~L~~Kg~-~p  421 (700)
                      ...    .+.+..+-++.++   ++.-.|||-| |   ....+.   ....+==.||+||=||.=-.-..+...++. +.
T Consensus       332 ~~~----~~~s~~~Lk~~l~---~~~~~ii~TTIQKf~~~~~~~~~~~~~~~~ivvI~DEaHRSQ~G~~~~~~~~~~~~a  404 (962)
T COG0610         332 NDP----KAESTSELKELLE---DGKGKIIVTTIQKFNKAVKEDELELLKRKNVVVIIDEAHRSQYGELAKLLKKALKKA  404 (962)
T ss_pred             CCC----CCCCHHHHHHHHH---CCCCCEEEEEECCCCHHHHCCCCCCCCCCCEEEEEECCCCCCCHHHHHHHHHHHCCC
T ss_conf             044----4457999999986---589848999710264333333200047876799986401035607899999870367


Q ss_pred             CCEEECHHHHHHHHHHH---HHHC-CCHHHHCCCCCCCCCCEEE--------E---------------------------
Q ss_conf             61010101322789999---7520-1011110235576662079--------9---------------------------
Q gi|254780945|r  422 HVLLMTATPIPRTLVLT---SLGD-IDISKITEKPAGRKPIKTV--------I---------------------------  462 (700)
Q Consensus       422 h~L~MtATPIPRTLal~---~ygd-ldvS~i~e~P~gR~~I~T~--------~---------------------------  462 (700)
                      ...-.|.|||=-.-+-|   .||+ ++.-+|++-=....-+.+.        +                           
T Consensus       405 ~~~gFTGTPi~~~d~~tt~~~fg~ylh~Y~i~~aI~Dg~vl~i~y~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  484 (962)
T COG0610         405 IFIGFTGTPIFKEDKDTTKDVFGDYLHTYTITDAIRDGAVLPVYYENRVELELIEESIKEEAEELDERIEEITEDILEKI  484 (962)
T ss_pred             EEEEEECCCCCCCCCCCHHHHHCCEEEEEECCHHHCCCCEEEEEECCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             08975178564022420355517447998652232357633258403123453200124566666999842279999999


Q ss_pred             -----------EECCCH----HHHHHHHHHHHCCCCEEEEEECCCC---CC------CCCCCCHHHH---HHHHHHHHCC
Q ss_conf             -----------970200----2689999763103873899971201---22------1112101466---6666686637
Q gi|254780945|r  463 -----------IPINRI----DEVIERLKVVLSEGKKAYWICPQIE---EK------KESNFRSVVE---RFNSLHEHFT  515 (700)
Q Consensus       463 -----------~~~~~~----~~~~~~i~~~l~~g~q~y~VcPlIe---es------e~~~~~~~~~---~~~~l~~~~~  515 (700)
                                 ....+.    ..+++..++....+..+-+||+.-.   ++      ...+..+-+.   ..+.....|.
T Consensus       485 ~k~~~~~~~~~~~~~r~~~~a~~~~~~f~~~~~~~~kam~V~~sr~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~  564 (962)
T COG0610         485 KKKTKNLEFLAMLAVRLIRAAKDIYDHFKKEEVFDLKAMVVASSRKVAVELYEAEIAARLDWHSKESLEGAIKDYNTEFE  564 (962)
T ss_pred             HHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHCCCCCEEEEEEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC
T ss_conf             99875556875144889999999999998611558359999841687877678887751556665300528999861322


Q ss_pred             CCEECC--CCCCCHHHHHHHHHH-HHCCCEEEEEECHHHHCCCCCCCCCEEEEECHHHCCHHHHHHHHHCCCCCC---CC
Q ss_conf             103120--146998999999999-755986999980034104688876589985852547468877301166789---83
Q gi|254780945|r  516 SSIAII--HGRMSDIDKESVMDS-FKNGTCKLLIATTVIEVGIDVVDASIIIIENAEHFGLAQLHQLRGRVGRGE---EI  589 (700)
Q Consensus       516 ~~v~~l--HGkm~~~ek~~~m~~-F~~g~~~iLvaTtviEVGvdvpna~~mvI~~aerfGLsqLHQLRGRVGRg~---~~  589 (700)
                      ..-..-  |.+.+...++..-.. +.+-..+||+-+-.-=.|-|.|..++|=|.-.=+-.  .|-|==-||-|--   +.
T Consensus       565 ~~~~~~~~~~~~~~~~~~~~~r~~~~~d~~kllIV~dMlLTGFDaP~L~TmYvDK~Lk~H--~L~QAisRtNR~~~~~K~  642 (962)
T COG0610         565 TDFDKKQSHAKLKDEKKDLIKRFKLKDDPLDLLIVVDMLLTGFDAPCLNTLYVDKPLKYH--NLIQAISRTNRVFPGKKK  642 (962)
T ss_pred             CCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCEEEEECCCCCCCCCCCCCEEEECCCCCCC--HHHHHHHHHCCCCCCCCC
T ss_conf             320234455777777653323212757787689997762046775420126744554433--189999886458878888


Q ss_pred             EEEEEEECCCCCHHHHHHHHHHHHHC
Q ss_conf             59999708889987999999998414
Q gi|254780945|r  590 SSCILLYHPPLSKNSYTRLSVLKNTE  615 (700)
Q Consensus       590 s~c~l~~~~~~~~~~~~Rl~~l~~~~  615 (700)
                      .=|+.-|-. +-+.-.+=|+...++.
T Consensus       643 ~G~IVDf~g-~~e~~~~Al~~y~~~~  667 (962)
T COG0610         643 FGLIVDFRG-LKEALKKALKLYSNEG  667 (962)
T ss_pred             CCEEEECCC-HHHHHHHHHHHHHHCC
T ss_conf             957997814-6999999999975135


No 140
>PRK12366 replication factor A; Reviewed
Probab=97.67  E-value=0.00068  Score=50.13  Aligned_cols=99  Identities=23%  Similarity=0.296  Sum_probs=76.6

Q ss_pred             HHHHHCCCCCCCCCCCCCHHHCCCCC-EEEEEEEEEEEEEECC-CCC-----CEEEEEEECCCCEEEEEEECCCHHHHHH
Q ss_conf             87870897401344446478889987-8999999989754215-898-----3389999818936999995188789987
Q gi|254780945|r   43 DLLFYHPSSFIDRHYRPKISEISEER-IVTITGYISQHSSFQL-QKR-----RPYKILLNDGTGEITLLFFYRKTEMLKN  115 (700)
Q Consensus        43 DLL~~~PrrYeDr~~~~~I~~l~~g~-~vti~g~V~~~~~~~~-~~r-----~~~~v~v~D~tg~i~lvfFn~~~~yl~k  115 (700)
                      +|-...|....+-....+|+++.+|+ .|.|.|+|++....+. .++     +-..+.+.|+||.+++++|+.....+ +
T Consensus        48 elG~~~~~~~~~e~e~~~I~DIe~g~~~V~~~gkV~~Isd~rtF~r~dGs~GrV~nl~VaDeTG~iRltLWdd~a~li-~  126 (649)
T PRK12366         48 EIGIEITYGQDEEEYIFLISDIEEGQKNVEITGKIIEISNIKEFNRKDGSTGKVASITIGDNTGIIRLTLWNDKTKLI-E  126 (649)
T ss_pred             HHCCCCCCCCCCCCCCCCHHCCCCCCCCEEEEEEEEEEECCCEEECCCCCCCEEEEEEEECCCCCEEEEEECCHHHHH-H
T ss_conf             854455555565322201300665765238999998850561044268985248999997378968999860334576-3


Q ss_pred             HCCCCCEEEEEEE-EEECCCEEEEE-CCE
Q ss_conf             3289888999989-97318779997-786
Q gi|254780945|r  116 VFFEGRKITVTGK-IKKLKNRIIMV-HPH  142 (700)
Q Consensus       116 ~lk~G~~v~vsGK-v~~~~~~~qi~-hPe  142 (700)
                      .+++|+.+.+.|. .+.|++..++. +|+
T Consensus       127 ~le~GdvikI~g~~~r~~~g~~El~~g~~  155 (649)
T PRK12366        127 GLKEGDVIKIENAFSRKWNGDVELNSGSE  155 (649)
T ss_pred             CCCCCCEEEECCCCCCCCCCCEEEEECCC
T ss_conf             56777589984631213588337871688


No 141
>PRK07373 DNA polymerase III subunit alpha; Reviewed
Probab=97.65  E-value=0.001  Score=48.78  Aligned_cols=93  Identities=15%  Similarity=0.266  Sum_probs=44.4

Q ss_pred             EEECHHHHHHHH-HHHHHHCCCHHHHCCCCCCCCCCEEEEEECCCHHHHHHHHHHHH-CCCCEEEEEECCCCCCCCCCCC
Q ss_conf             010101322789-99975201011110235576662079997020026899997631-0387389997120122111210
Q gi|254780945|r  424 LLMTATPIPRTL-VLTSLGDIDISKITEKPAGRKPIKTVIIPINRIDEVIERLKVVL-SEGKKAYWICPQIEEKKESNFR  501 (700)
Q Consensus       424 L~MtATPIPRTL-al~~ygdldvS~i~e~P~gR~~I~T~~~~~~~~~~~~~~i~~~l-~~g~q~y~VcPlIeese~~~~~  501 (700)
                      ++.|.-|+=.=- .+..++..+++.+.+.+.+ +.|....+-.+        ++... ++| +-+-..-+-+++...++.
T Consensus       247 fYlSgHPL~~y~~~~~~~~~~~~~~l~~~~~~-~~V~~~g~I~~--------vr~~~TKkG-~~MAfvtLeD~tG~iEvv  316 (447)
T PRK07373        247 FYVSEHPLKSLQRPAPLLSPINLSQLEEQKER-TKVSAVVMLNG--------VKKIVTKKG-DPMAFLQLEDLSGQSEAV  316 (447)
T ss_pred             EEECCCHHHHHHHHHHHHCCCCHHHHHHCCCC-CEEEEEEEEEE--------EEEEECCCC-CEEEEEEEEECCCCEEEE
T ss_conf             68620737899999888387138996402489-78999999999--------999870489-659999999789748999


Q ss_pred             HHHHHHHHHHHHCC-CCEECCCCCCC
Q ss_conf             14666666686637-10312014699
Q gi|254780945|r  502 SVVERFNSLHEHFT-SSIAIIHGRMS  526 (700)
Q Consensus       502 ~~~~~~~~l~~~~~-~~v~~lHGkm~  526 (700)
                      -=.+.|+..+..+- +.+-++.|+..
T Consensus       317 vFpe~ye~~~~~L~~d~ivlv~Gkv~  342 (447)
T PRK07373        317 VFPKSYERIQELLQEDSRLIIWGKVD  342 (447)
T ss_pred             EEHHHHHHHHHHHCCCCEEEEEEEEE
T ss_conf             80899999988733799899999999


No 142
>KOG0389 consensus
Probab=97.65  E-value=0.00042  Score=51.79  Aligned_cols=330  Identities=21%  Similarity=0.294  Sum_probs=192.8

Q ss_pred             CCCCCHHHHHHHHHHHHHHCCCCCCEEEEEECCCCCHHH--HHHHHHHHHHHHHCCEEEEEHHHHHHHHHHHHHHHHCCC
Q ss_conf             246798899999999984100134307886214422369--999997334443054588612799999999862110145
Q gi|254780945|r  270 PFSPTKSQESAIKDILQDMSQKNRMLRILQGDVGSGKTL--VALIAMAAAVEAGGQAVIMAPIGILAQQHYEFIKKYTQN  347 (700)
Q Consensus       270 PF~LT~~Q~~ai~eI~~Dl~~~~pM~RLLQGDVGSGKTi--VA~~A~l~~~~~G~Q~alMaPTEILA~QH~~~~~~~~~~  347 (700)
                      .++|-.-|.--++=..  |--.+-|+-.|--+-|=|||+  ||++|.+.-..+..--.+.||...|-.= ...|.+|+|.
T Consensus       397 ~i~LkdYQlvGvNWL~--Llyk~~l~gILADEMGLGKTiQvIaFlayLkq~g~~gpHLVVvPsSTleNW-lrEf~kwCPs  473 (941)
T KOG0389         397 GIQLKDYQLVGVNWLL--LLYKKKLNGILADEMGLGKTIQVIAFLAYLKQIGNPGPHLVVVPSSTLENW-LREFAKWCPS  473 (941)
T ss_pred             CCCCCCHHHHHHHHHH--HHHHCCCCCEEHHHCCCCCHHHHHHHHHHHHHCCCCCCCEEEECCHHHHHH-HHHHHHHCCC
T ss_conf             8733422202289999--999742330532220576334899999999972999983799203168889-9999975975


Q ss_pred             CCCEEEEEECCCCHHHHHHHHHHHCCC--CCEEEEECHHHCC---CCCCC---CCCCEEEECCCCCC--CHHHHHHHHHC
Q ss_conf             786589962464225667687762134--7548641112013---34554---44417885210133--56889987402
Q gi|254780945|r  348 TQIIVEIITGNMPQAHRRKALERIAHG--QAHIIIGTHALFQ---DSIQY---YKLILVIVDEQHRF--GVQQRLKLTQK  417 (700)
Q Consensus       348 ~~i~v~lLtg~~~~~er~~i~~~i~~G--~~~iiIGTHAL~q---~~v~F---~~LgLvViDEQHRF--GV~QR~~L~~K  417 (700)
                      +  +|+...||.  .||+++...++++  ..++++-|--|..   ++..|   .++-.||.||-|=.  --.+|-+=.=+
T Consensus       474 l--~Ve~YyGSq--~ER~~lR~~i~~~~~~ydVllTTY~la~~~kdDRsflk~~~~n~viyDEgHmLKN~~SeRy~~LM~  549 (941)
T KOG0389         474 L--KVEPYYGSQ--DERRELRERIKKNKDDYDVLLTTYNLAASSKDDRSFLKNQKFNYVIYDEGHMLKNRTSERYKHLMS  549 (941)
T ss_pred             E--EEEECCCCH--HHHHHHHHHHHCCCCCCCEEEEEEECCCCCHHHHHHHHHCCCCEEEECCHHHHHCCCHHHHHHHCC
T ss_conf             2--877415768--999999999861688852899872110388677899986666679961326542133498887506


Q ss_pred             CCCCCCEEECHHHHHHHHH----H---HH---H----HCCC----------------------H----------------
Q ss_conf             5677610101013227899----9---97---5----2010----------------------1----------------
Q gi|254780945|r  418 ATAPHVLLMTATPIPRTLV----L---TS---L----GDID----------------------I----------------  445 (700)
Q Consensus       418 g~~ph~L~MtATPIPRTLa----l---~~---y----gdld----------------------v----------------  445 (700)
                      =..---|.+|-||.---|-    |   .+   |    -|+|                      |                
T Consensus       550 I~An~RlLLTGTPLQNNL~ELiSLL~FvlP~vF~~~~~dl~~if~~k~~~d~d~e~~~l~qerIsrAK~im~PFILRR~K  629 (941)
T KOG0389         550 INANFRLLLTGTPLQNNLKELISLLAFVLPKVFDSSMEDLDVIFKAKKTSDGDIENALLSQERISRAKTIMKPFILRRLK  629 (941)
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             46553588518742012999999999974575532224799998246776430467788999999999754278899989


Q ss_pred             -HHHCCCCCCCCCCEEEEEECCCHHHHHHHHHHHHC-------CC--CEE-EE--------EECCCCC------------
Q ss_conf             -11102355766620799970200268999976310-------38--738-99--------9712012------------
Q gi|254780945|r  446 -SKITEKPAGRKPIKTVIIPINRIDEVIERLKVVLS-------EG--KKA-YW--------ICPQIEE------------  494 (700)
Q Consensus       446 -S~i~e~P~gR~~I~T~~~~~~~~~~~~~~i~~~l~-------~g--~q~-y~--------VcPlIee------------  494 (700)
                       -+++.+||-- .++-++-..+.-.++|..+-+...       ..  .+- .+        -.||.--            
T Consensus       630 ~qVL~~LPpK~-~~Ie~c~mse~Q~~~Y~~~~~~~~~~~~~~~~ns~~~~~~vlmqlRK~AnHPLL~R~~Y~de~L~~ma  708 (941)
T KOG0389         630 SQVLKQLPPKI-QRIEYCEMSEKQKQLYDELIELYDVKLNEVSKNSELKSGNVLMQLRKAANHPLLFRSIYTDEKLRKMA  708 (941)
T ss_pred             HHHHHHCCCCC-CEEEEEECCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHCCHHHHHHHCCHHHHHHHH
T ss_conf             98987469743-25676424638999999999998511043223310256139999998735725778760388999999


Q ss_pred             -----------------CCCCCCCHHHHHH-------------------------HHHH---------------------
Q ss_conf             -----------------2111210146666-------------------------6668---------------------
Q gi|254780945|r  495 -----------------KKESNFRSVVERF-------------------------NSLH---------------------  511 (700)
Q Consensus       495 -----------------se~~~~~~~~~~~-------------------------~~l~---------------------  511 (700)
                                       .|.+...|--+.+                         ..|+                     
T Consensus       709 k~il~e~ay~~~n~qyIfEDm~~msDfelHqLc~~f~~~~~f~L~d~~~mdSgK~r~L~~LLp~~k~~G~RVLiFSQFTq  788 (941)
T KOG0389         709 KRILNEPAYKKANEQYIFEDMEVMSDFELHQLCCQFRHLSKFQLKDDLWMDSGKCRKLKELLPKIKKKGDRVLIFSQFTQ  788 (941)
T ss_pred             HHHHCCHHHHHCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHCCCEEEEEEHHHH
T ss_conf             99727553320278888998876518999999986578765323884443003276999987887616877999608889


Q ss_pred             ---------HHCCCCEECCCCCCCHHHHHHHHHHHHCCC--EEEEEECHHHHCCCCCCCCCEEEEECHHH--CCHHHHHH
Q ss_conf             ---------663710312014699899999999975598--69999800341046888765899858525--47468877
Q gi|254780945|r  512 ---------EHFTSSIAIIHGRMSDIDKESVMDSFKNGT--CKLLIATTVIEVGIDVVDASIIIIENAEH--FGLAQLHQ  578 (700)
Q Consensus       512 ---------~~~~~~v~~lHGkm~~~ek~~~m~~F~~g~--~~iLvaTtviEVGvdvpna~~mvI~~aer--fGLsqLHQ  578 (700)
                               +..+.+.--|-|.-.-.+++..+.+|...+  .=-|+||--=-+|||..-|++.||.+-+-  |-=-|---
T Consensus       789 mLDILE~~L~~l~~~ylRLDGsTqV~~RQ~lId~Fn~d~difVFLLSTKAGG~GINLt~An~VIihD~dFNP~dD~QAED  868 (941)
T KOG0389         789 MLDILEVVLDTLGYKYLRLDGSTQVNDRQDLIDEFNTDKDIFVFLLSTKAGGFGINLTCANTVIIHDIDFNPYDDKQAED  868 (941)
T ss_pred             HHHHHHHHHHHCCCEEEEECCCCCCHHHHHHHHHHCCCCCEEEEEEEECCCCCEECCCCCCEEEEEECCCCCCCCCHHHH
T ss_conf             99999999986273378614886413899999862667755799986146765021123645899605779755204688


Q ss_pred             HHHCCCCCCCCEEEEEEECCCCCHHHHHHH
Q ss_conf             301166789835999970888998799999
Q gi|254780945|r  579 LRGRVGRGEEISSCILLYHPPLSKNSYTRL  608 (700)
Q Consensus       579 LRGRVGRg~~~s~c~l~~~~~~~~~~~~Rl  608 (700)
                      =--|||--.---..=|++...+ |+.+.||
T Consensus       869 RcHRvGQtkpVtV~rLItk~TI-EE~I~~l  897 (941)
T KOG0389         869 RCHRVGQTKPVTVYRLITKSTI-EEGILRL  897 (941)
T ss_pred             HHHHHCCCCEEEEEEEEECCCH-HHHHHHH
T ss_conf             8876178540699998745718-9999999


No 143
>COG1197 Mfd Transcription-repair coupling factor (superfamily II helicase) [DNA replication, recombination, and repair / Transcription]
Probab=97.61  E-value=0.00069  Score=50.07  Aligned_cols=120  Identities=17%  Similarity=0.396  Sum_probs=99.4

Q ss_pred             CCHHHHHHHHHHHHCCCCEEEEEECCCCCCCCCCCCHHHHHHHHHHHHCC---CCEECCCCCCCHHHHHHHHHHHHCCCE
Q ss_conf             20026899997631038738999712012211121014666666686637---103120146998999999999755986
Q gi|254780945|r  466 NRIDEVIERLKVVLSEGKKAYWICPQIEEKKESNFRSVVERFNSLHEHFT---SSIAIIHGRMSDIDKESVMDSFKNGTC  542 (700)
Q Consensus       466 ~~~~~~~~~i~~~l~~g~q~y~VcPlIeese~~~~~~~~~~~~~l~~~~~---~~v~~lHGkm~~~ek~~~m~~F~~g~~  542 (700)
                      -+-+-++.+.=..+..|-||.|++|.        .-=|++-|+.+++.|.   -+|++|.-=-++.|+.++++..++|++
T Consensus       627 GKTEVAmRAAFkAV~~GKQVAvLVPT--------TlLA~QHy~tFkeRF~~fPV~I~~LSRF~s~kE~~~il~~la~G~v  698 (1139)
T COG1197         627 GKTEVAMRAAFKAVMDGKQVAVLVPT--------TLLAQQHYETFKERFAGFPVRIEVLSRFRSAKEQKEILKGLAEGKV  698 (1139)
T ss_pred             CHHHHHHHHHHHHHCCCCEEEEECCC--------HHHHHHHHHHHHHHHCCCCEEEEEECCCCCHHHHHHHHHHHHCCCC
T ss_conf             59999999999986379749999260--------7868998999998733898258886055788999999999856984


Q ss_pred             EEEEECH-HHHCCCCCCCCCEEEEECHHHCCHHH---HHHHHHCCCCCCCCEEEEEEECCCC
Q ss_conf             9999800-34104688876589985852547468---8773011667898359999708889
Q gi|254780945|r  543 KLLIATT-VIEVGIDVVDASIIIIENAEHFGLAQ---LHQLRGRVGRGEEISSCILLYHPPL  600 (700)
Q Consensus       543 ~iLvaTt-viEVGvdvpna~~mvI~~aerfGLsq---LHQLRGRVGRg~~~s~c~l~~~~~~  600 (700)
                      ||+|.|- ++--+|-..|.-+|||..-.|||..|   |-|||.       .--|.-++..|+
T Consensus       699 DIvIGTHrLL~kdv~FkdLGLlIIDEEqRFGVk~KEkLK~Lr~-------~VDvLTLSATPI  753 (1139)
T COG1197         699 DIVIGTHRLLSKDVKFKDLGLLIIDEEQRFGVKHKEKLKELRA-------NVDVLTLSATPI  753 (1139)
T ss_pred             CEEEECHHHHCCCCEEECCCEEEEECHHHCCCCHHHHHHHHHC-------CCCEEEEECCCC
T ss_conf             5899631764789677047648974435327117899987750-------572897417887


No 144
>smart00489 DEXDc3 DEAD-like helicases superfamily.
Probab=97.61  E-value=0.002  Score=46.38  Aligned_cols=76  Identities=17%  Similarity=0.242  Sum_probs=55.3

Q ss_pred             HCCCCCCHHHHHHHHHHHHHHCCCCCCEEEEEECCCCCHHHHHHHHHHHHHHH------HCCEEEEEHHHHHHHHHHHHH
Q ss_conf             30246798899999999984100134307886214422369999997334443------054588612799999999862
Q gi|254780945|r  268 NIPFSPTKSQESAIKDILQDMSQKNRMLRILQGDVGSGKTLVALIAMAAAVEA------GGQAVIMAPIGILAQQHYEFI  341 (700)
Q Consensus       268 ~LPF~LT~~Q~~ai~eI~~Dl~~~~pM~RLLQGDVGSGKTiVA~~A~l~~~~~------G~Q~alMaPTEILA~QH~~~~  341 (700)
                      .+||+.=+.|...++.|..-+.....  =|++.=.|+|||+-.+.+++..+.+      +..+++..-|.-.-+|..+.+
T Consensus         4 ~FPy~py~~Q~e~m~~v~~~l~~~~~--~llEaPTGtGKTlalL~~al~~~~~~~~~~~~~ki~~~t~t~~~~~~~~~el   81 (289)
T smart00489        4 YFPYEPYPIQYEFMEELKRVLDRGKI--GILESPTGTGKTLSLLCLTLTWLRSFPERIQKIKLIYLSRTVSEIEKRLEEL   81 (289)
T ss_pred             CCCCCCCHHHHHHHHHHHHHHHCCCE--EEEECCCCHHHHHHHHHHHHHHHHHCHHCCCCCEEEEEECCHHHHHHHHHHH
T ss_conf             78999998999999999999974997--9998999651899999999999996701024561687615378899999999


Q ss_pred             HHHC
Q ss_conf             1101
Q gi|254780945|r  342 KKYT  345 (700)
Q Consensus       342 ~~~~  345 (700)
                      ++..
T Consensus        82 r~~~   85 (289)
T smart00489       82 RKLM   85 (289)
T ss_pred             HHHC
T ss_conf             8632


No 145
>smart00488 DEXDc2 DEAD-like helicases superfamily.
Probab=97.61  E-value=0.002  Score=46.38  Aligned_cols=76  Identities=17%  Similarity=0.242  Sum_probs=55.3

Q ss_pred             HCCCCCCHHHHHHHHHHHHHHCCCCCCEEEEEECCCCCHHHHHHHHHHHHHHH------HCCEEEEEHHHHHHHHHHHHH
Q ss_conf             30246798899999999984100134307886214422369999997334443------054588612799999999862
Q gi|254780945|r  268 NIPFSPTKSQESAIKDILQDMSQKNRMLRILQGDVGSGKTLVALIAMAAAVEA------GGQAVIMAPIGILAQQHYEFI  341 (700)
Q Consensus       268 ~LPF~LT~~Q~~ai~eI~~Dl~~~~pM~RLLQGDVGSGKTiVA~~A~l~~~~~------G~Q~alMaPTEILA~QH~~~~  341 (700)
                      .+||+.=+.|...++.|..-+.....  =|++.=.|+|||+-.+.+++..+.+      +..+++..-|.-.-+|..+.+
T Consensus         4 ~FPy~py~~Q~e~m~~v~~~l~~~~~--~llEaPTGtGKTlalL~~al~~~~~~~~~~~~~ki~~~t~t~~~~~~~~~el   81 (289)
T smart00488        4 YFPYEPYPIQYEFMEELKRVLDRGKI--GILESPTGTGKTLSLLCLTLTWLRSFPERIQKIKLIYLSRTVSEIEKRLEEL   81 (289)
T ss_pred             CCCCCCCHHHHHHHHHHHHHHHCCCE--EEEECCCCHHHHHHHHHHHHHHHHHCHHCCCCCEEEEEECCHHHHHHHHHHH
T ss_conf             78999998999999999999974997--9998999651899999999999996701024561687615378899999999


Q ss_pred             HHHC
Q ss_conf             1101
Q gi|254780945|r  342 KKYT  345 (700)
Q Consensus       342 ~~~~  345 (700)
                      ++..
T Consensus        82 r~~~   85 (289)
T smart00488       82 RKLM   85 (289)
T ss_pred             HHHC
T ss_conf             8632


No 146
>PRK07279 dnaE DNA polymerase III DnaE; Reviewed
Probab=97.60  E-value=0.0016  Score=47.29  Aligned_cols=61  Identities=10%  Similarity=0.128  Sum_probs=30.9

Q ss_pred             HHHHHHCCCC--EECCCCCCCHHHHHHHHHHHHCCCEEEEEECHHHHCCCCCCCCCEEEEECHHHCCHHHHHHH
Q ss_conf             6668663710--31201469989999999997559869999800341046888765899858525474688773
Q gi|254780945|r  508 NSLHEHFTSS--IAIIHGRMSDIDKESVMDSFKNGTCKLLIATTVIEVGIDVVDASIIIIENAEHFGLAQLHQL  579 (700)
Q Consensus       508 ~~l~~~~~~~--v~~lHGkm~~~ek~~~m~~F~~g~~~iLvaTtviEVGvdvpna~~mvI~~aerfGLsqLHQL  579 (700)
                      .+||.+||..  .++|..++     ..-+.+-++-.+.||      -.-||-.....-+-.++=||||+..--+
T Consensus       696 AyLKahYP~eF~aalL~~~~-----~~yi~ea~~~gi~vl------pPdIN~S~~~f~~~~~~Ir~GL~aIkgv  758 (1033)
T PRK07279        696 AYFKAHYPAVFYDIMLNYSS-----SDYITDALEFGFEVA------QLSINTIPYHDKIENKKIYLGLKNIKGL  758 (1033)
T ss_pred             HHHHHCCHHHHHHHHHCCCH-----HHHHHHHHHCCCCCC------CCCCCCCCCCCEECCCEEEEHHHHHCCC
T ss_conf             99984488999999845777-----899999998499745------8865336776511388188737866587


No 147
>PRK07012 consensus
Probab=97.58  E-value=0.0014  Score=47.59  Aligned_cols=67  Identities=18%  Similarity=0.205  Sum_probs=46.1

Q ss_pred             HHHHHHCCCC--EECCCCCCCHHHH-HHHHHHHHCCCEEEEEECHHHHCCCCCCCCCEEEEEC-------HHHCCHHHHH
Q ss_conf             6668663710--3120146998999-9999997559869999800341046888765899858-------5254746887
Q gi|254780945|r  508 NSLHEHFTSS--IAIIHGRMSDIDK-ESVMDSFKNGTCKLLIATTVIEVGIDVVDASIIIIEN-------AEHFGLAQLH  577 (700)
Q Consensus       508 ~~l~~~~~~~--v~~lHGkm~~~ek-~~~m~~F~~g~~~iLvaTtviEVGvdvpna~~mvI~~-------aerfGLsqLH  577 (700)
                      .+||.+||..  .++|...|...+| ...+.+-++-.+.||      -.-||-.....-++.+       +=||||+...
T Consensus       767 AyLK~hyP~eF~aAlLs~~~~~~~k~~~~i~ear~~gi~Vl------pPdIN~S~~~f~~~~~~~~~~~~~Ir~GL~aIk  840 (1173)
T PRK07012        767 AWLKAHHPAEFMAANMSLAMDDTDKVKILFDDCLVNGLAVL------PPDINASHYRFEPVAEADGKRSRTIRYGLGAVK  840 (1173)
T ss_pred             HHHHHCCHHHHHHHHHCCCCCCCHHHHHHHHHHHHCCCEEC------CCCCCCCCCEEEECCCCCCCCCCEEEEEHHHHC
T ss_conf             99987389999999837687997589999999998789164------884225577025525766676763898435415


Q ss_pred             HHH
Q ss_conf             730
Q gi|254780945|r  578 QLR  580 (700)
Q Consensus       578 QLR  580 (700)
                      -+.
T Consensus       841 gvg  843 (1173)
T PRK07012        841 GSG  843 (1173)
T ss_pred             CCC
T ss_conf             898


No 148
>PRK05580 primosome assembly protein PriA; Validated
Probab=97.58  E-value=0.0004  Score=51.92  Aligned_cols=72  Identities=21%  Similarity=0.318  Sum_probs=54.4

Q ss_pred             EEHHHHHHHHHHHHHHHHCCCCCCEEEEEECCCC--HHHHHHHHHHHCCCCCEEEEECHHHCCCCCCCCCCCEEEEC
Q ss_conf             6127999999998621101457865899624642--25667687762134754864111201334554444178852
Q gi|254780945|r  327 MAPIGILAQQHYEFIKKYTQNTQIIVEIITGNMP--QAHRRKALERIAHGQAHIIIGTHALFQDSIQYYKLILVIVD  401 (700)
Q Consensus       327 MaPTEILA~QH~~~~~~~~~~~~i~v~lLtg~~~--~~er~~i~~~i~~G~~~iiIGTHAL~q~~v~F~~LgLvViD  401 (700)
                      +.+.-+=+++..+.+++.|++.  +|.-+.+.+.  ...-+.+++++.+|+++|+|||. .+.++..|.+++||+|=
T Consensus       455 l~~~g~Gteri~eel~~~FP~~--~i~r~d~d~~~~~~~~~~~~~~~~~~~~dIlvGTq-miakG~df~~v~lv~vl  528 (699)
T PRK05580        455 LRAVGVGTERTEEELARLFPGA--RVLRIDRDTTRRKGALEQLLEDFARGEADILVGTQ-MLAKGHDFPNVTLVGVL  528 (699)
T ss_pred             CCCCCHHHHHHHHHHHHHCCCC--CEEEECCCCCCCCCCHHHHHHHHHCCCCCEEECCC-CCCCCCCCCCEEEEEEE
T ss_conf             2411168599999999778999--88998475567863168899997468987897773-34556777762699873


No 149
>KOG0925 consensus
Probab=97.58  E-value=0.0081  Score=41.67  Aligned_cols=278  Identities=17%  Similarity=0.285  Sum_probs=157.5

Q ss_pred             HCCCCCCEEEEEECCCCCHHH-HHHHHHHHHHHHHCCEEEEEHHHHHHHHHHHHHHHHCCCCCCEEEEEECCC-C---HH
Q ss_conf             100134307886214422369-999997334443054588612799999999862110145786589962464-2---25
Q gi|254780945|r  288 MSQKNRMLRILQGDVGSGKTL-VALIAMAAAVEAGGQAVIMAPIGILAQQHYEFIKKYTQNTQIIVEIITGNM-P---QA  362 (700)
Q Consensus       288 l~~~~pM~RLLQGDVGSGKTi-VA~~A~l~~~~~G~Q~alMaPTEILA~QH~~~~~~~~~~~~i~v~lLtg~~-~---~~  362 (700)
                      +..+.-+  .+-||.|||||- |--.++..+.....|+|---|--+-|-|-......-++   +.+.-=.|.. +   -.
T Consensus        59 l~~nQ~~--v~vGetgsGKttQiPq~~~~~~~~~~~~v~CTQprrvaamsva~RVadEMD---v~lG~EVGysIrfEdC~  133 (699)
T KOG0925          59 LLNNQII--VLVGETGSGKTTQIPQFVLEYELSHLTGVACTQPRRVAAMSVAQRVADEMD---VTLGEEVGYSIRFEDCT  133 (699)
T ss_pred             HHCCCEE--EEEECCCCCCCCCCCHHHHHHHHHHCCCEEECCCHHHHHHHHHHHHHHHHC---CCCCHHCCCCCCCCCCC
T ss_conf             8648269--999348888645474999999876336613247157889999998888744---31020115321212368


Q ss_pred             HHHHHHHHHCCCCCEEEEECHHHCCCCC---CCCCCCEEEECCCCC--------CCHHHHHHHHHCCCCCCCEEECHHHH
Q ss_conf             6676877621347548641112013345---544441788521013--------35688998740256776101010132
Q gi|254780945|r  363 HRRKALERIAHGQAHIIIGTHALFQDSI---QYYKLILVIVDEQHR--------FGVQQRLKLTQKATAPHVLLMTATPI  431 (700)
Q Consensus       363 er~~i~~~i~~G~~~iiIGTHAL~q~~v---~F~~LgLvViDEQHR--------FGV~QR~~L~~Kg~~ph~L~MtATPI  431 (700)
                      .-+.++.-.-+|         -|++|-.   -..+-|.+|.||-|-        +|+-+...+..  ..--+.+||||--
T Consensus       134 ~~~T~Lky~tDg---------mLlrEams~p~l~~y~viiLDeahERtlATDiLmGllk~v~~~r--pdLk~vvmSatl~  202 (699)
T KOG0925         134 SPNTLLKYCTDG---------MLLREAMSDPLLGRYGVIILDEAHERTLATDILMGLLKEVVRNR--PDLKLVVMSATLD  202 (699)
T ss_pred             CHHHHHHHHCCH---------HHHHHHHCCCCCCCCCEEEECHHHHHHHHHHHHHHHHHHHHHHC--CCCEEEEEECCCC
T ss_conf             715899995332---------89998750855453007995316666678999999999998619--8816999406012


Q ss_pred             HHHHHHHHHHCCCHHHHCCCCCCCCCCEEEEEECCCHHHHHHHHHHHHCC-----CCEEEEEECCCCCCCCCCCCHHHHH
Q ss_conf             27899997520101111023557666207999702002689999763103-----8738999712012211121014666
Q gi|254780945|r  432 PRTLVLTSLGDIDISKITEKPAGRKPIKTVIIPINRIDEVIERLKVVLSE-----GKKAYWICPQIEEKKESNFRSVVER  506 (700)
Q Consensus       432 PRTLal~~ygdldvS~i~e~P~gR~~I~T~~~~~~~~~~~~~~i~~~l~~-----g~q~y~VcPlIeese~~~~~~~~~~  506 (700)
                      ---+- .+|||--+-.+   | |+-|+.-..-++..++.+-..++..++-     -+-+.+--|--|        .+++.
T Consensus       203 a~Kfq-~yf~n~Pll~V---p-g~~PvEi~Yt~e~erDylEaairtV~qih~~ee~GDilvFLtgee--------eIe~a  269 (699)
T KOG0925         203 AEKFQ-RYFGNAPLLAV---P-GTHPVEIFYTPEPERDYLEAAIRTVLQIHMCEEPGDILVFLTGEE--------EIEDA  269 (699)
T ss_pred             HHHHH-HHCCCCCEEEC---C-CCCCEEEEECCCCCHHHHHHHHHHHHHHHHCCCCCCEEEEECCHH--------HHHHH
T ss_conf             59999-87079975645---8-988457883588873689999999999984168887899946778--------99999


Q ss_pred             HHHHHHH-------CCC-CEECCCCCCCHHHHHHHHHHHHC---C--CEEEEEECHHHHCCCCCCCCCEEE--------E
Q ss_conf             6666866-------371-03120146998999999999755---9--869999800341046888765899--------8
Q gi|254780945|r  507 FNSLHEH-------FTS-SIAIIHGRMSDIDKESVMDSFKN---G--TCKLLIATTVIEVGIDVVDASIII--------I  565 (700)
Q Consensus       507 ~~~l~~~-------~~~-~v~~lHGkm~~~ek~~~m~~F~~---g--~~~iLvaTtviEVGvdvpna~~mv--------I  565 (700)
                      ++.+...       .+. +|-=||    +.++..+.+.--.   |  .-++.|||.+-|--+.++..-..|        |
T Consensus       270 C~~i~re~~~L~~~~g~l~v~PLy----P~~qq~iFep~p~~~~~~~~RKvVvstniaetsltidgiv~VIDpGf~kqkV  345 (699)
T KOG0925         270 CRKISREVDNLGPQVGPLKVVPLY----PAQQQRIFEPAPEKRNGAYGRKVVVSTNIAETSLTIDGIVFVIDPGFSKQKV  345 (699)
T ss_pred             HHHHHHHHHHHCCCCCCCEEEECC----CHHHCCCCCCCCCCCCCCCCCEEEEEECCHHEEEEECCEEEEECCCHHHHCC
T ss_conf             999999887525156883688458----1564365678984547876654999814034057506479996676013003


Q ss_pred             ECH----HH-----CCHHHHHHHHHCCCCCCCCEEEEEEECCC
Q ss_conf             585----25-----47468877301166789835999970888
Q gi|254780945|r  566 ENA----EH-----FGLAQLHQLRGRVGRGEEISSCILLYHPP  599 (700)
Q Consensus       566 ~~a----er-----fGLsqLHQLRGRVGRg~~~s~c~l~~~~~  599 (700)
                      +|+    |-     ..=||-+|=+||-|| ..+|.||-+|..+
T Consensus       346 YNPRIRvesllv~PISkasA~qR~gragr-t~pGkcfrLYte~  387 (699)
T KOG0925         346 YNPRIRVESLLVSPISKASAQQRAGRAGR-TRPGKCFRLYTEE  387 (699)
T ss_pred             CCCCEEEEEEEECCCHHHHHHHHHHHCCC-CCCCCEEEEECHH
T ss_conf             47520331013061167679987543078-9998368850077


No 150
>PRK07374 dnaE DNA polymerase III subunit alpha; Validated
Probab=97.57  E-value=0.0014  Score=47.56  Aligned_cols=81  Identities=19%  Similarity=0.220  Sum_probs=57.2

Q ss_pred             HHHHHHCCCC--EECCCCCCCHHHH-HHHHHHHHCCCEEEEEECHHHHCCCCCCCCCEEEEECHHHCCHHHHHHHH----
Q ss_conf             6668663710--3120146998999-99999975598699998003410468887658998585254746887730----
Q gi|254780945|r  508 NSLHEHFTSS--IAIIHGRMSDIDK-ESVMDSFKNGTCKLLIATTVIEVGIDVVDASIIIIENAEHFGLAQLHQLR----  580 (700)
Q Consensus       508 ~~l~~~~~~~--v~~lHGkm~~~ek-~~~m~~F~~g~~~iLvaTtviEVGvdvpna~~mvI~~aerfGLsqLHQLR----  580 (700)
                      .+||.+||..  .+++...|...+| ...+.+-++-.+.|      .-+-||-.++...+-.++=||||+...-+.    
T Consensus       775 AyLK~hyP~eF~aalL~~~~~~~~k~~~~i~ea~~~gi~v------lpPdIN~S~~~f~~~~~~I~~gl~~Ikgvg~~~~  848 (1171)
T PRK07374        775 AYLKAHYPVAYMAALLTVNAGSSDKVQRYISNCNSMGIEV------MPPDINASGIDFTPKGNRILFGLSAVKNLGDGAI  848 (1171)
T ss_pred             HHHHHCCHHHHHHHHHCCCCCCCHHHHHHHHHHHHCCCCE------ECCCEEEECCCEEECCCCEEHHHHHHCCCCHHHH
T ss_conf             9999778999999985058899747999999999879916------2883322178216759822146567437339999


Q ss_pred             -----HCCCCCCCCEEEEE
Q ss_conf             -----11667898359999
Q gi|254780945|r  581 -----GRVGRGEEISSCIL  594 (700)
Q Consensus       581 -----GRVGRg~~~s~c~l  594 (700)
                           .|--.|.-.|..-|
T Consensus       849 ~~Iv~~R~~~Gpf~sl~Df  867 (1171)
T PRK07374        849 RNLIASRDSDGPFKSLADL  867 (1171)
T ss_pred             HHHHHHHHHCCCCCCHHHH
T ss_conf             9999999858597989999


No 151
>TIGR00580 mfd transcription-repair coupling factor; InterPro: IPR004576 All proteins in this family for which functions are known are DNA-dependent ATPases that function in the process of transcription-coupled DNA repair in which the repair of the transcribed strand of actively transcribed genes is repaired at a higher rate than the repair of non-transcribed regions of the genome and than the non-transcribed strand of the same gene. A lesion in the template strand blocks the RNA polymerase complex (RNAP). The RNAP-DNA-RNA complex is specifically recognised by TcrF, which releases RNAP and the truncated transcript. The TcrF may replace RNAP at the lesion site and then recruit the UvrA/B/C repair system.; GO: 0003684 damaged DNA binding, 0005524 ATP binding, 0006281 DNA repair.
Probab=97.56  E-value=0.00051  Score=51.09  Aligned_cols=117  Identities=21%  Similarity=0.437  Sum_probs=98.9

Q ss_pred             HHHHHHHHHHHCCC----CEEEEEECCCCCCCCCCCCHHHHHHHHHHHHCCC---CEECCCCCCCHHHHHHHHHHHHCCC
Q ss_conf             26899997631038----7389997120122111210146666666866371---0312014699899999999975598
Q gi|254780945|r  469 DEVIERLKVVLSEG----KKAYWICPQIEEKKESNFRSVVERFNSLHEHFTS---SIAIIHGRMSDIDKESVMDSFKNGT  541 (700)
Q Consensus       469 ~~~~~~i~~~l~~g----~q~y~VcPlIeese~~~~~~~~~~~~~l~~~~~~---~v~~lHGkm~~~ek~~~m~~F~~g~  541 (700)
                      +-++.++=+.+..|    -||-|+.|.        .-=|.+=|+.+++.|.+   +|++|-+=-++.|+.+++++-++|+
T Consensus       544 EVAmRAaFkAv~~gneylKQVavLVPT--------T~LA~QHf~tf~~RF~~fPv~I~~LSRF~~~~E~~~iL~~la~G~  615 (997)
T TIGR00580       544 EVAMRAAFKAVLDGNEYLKQVAVLVPT--------TILAQQHFETFKERFANFPVTIELLSRFRSAKEKKEILKELASGK  615 (997)
T ss_pred             HHHHHHHHHHHCCCCCEECEEEEECCH--------HHHHHHHHHHHHHHHCCCCEEEEECCCCCCCHHHHHHHHHHHCCC
T ss_conf             888878887633878220116896270--------442777889999973789816875277567378999999975594


Q ss_pred             EEEEEECH-HHHCCCCCCCCCEEEEECHHHCCHHH---HHHHHHCCCCCCCCEEEEEEECCCC
Q ss_conf             69999800-34104688876589985852547468---8773011667898359999708889
Q gi|254780945|r  542 CKLLIATT-VIEVGIDVVDASIIIIENAEHFGLAQ---LHQLRGRVGRGEEISSCILLYHPPL  600 (700)
Q Consensus       542 ~~iLvaTt-viEVGvdvpna~~mvI~~aerfGLsq---LHQLRGRVGRg~~~s~c~l~~~~~~  600 (700)
                      +||||.|- ++--.|-..|--+|||.-=.|||..|   |=|||--|       -|.=|+-.|+
T Consensus       616 iDI~IGTH~lL~k~v~FKdLGLlIiDEEQRFGV~~KE~lK~~~~~V-------DvLtlsATPI  671 (997)
T TIGR00580       616 IDILIGTHKLLQKDVKFKDLGLLIIDEEQRFGVKQKEKLKELKTSV-------DVLTLSATPI  671 (997)
T ss_pred             EEEEECCHHHHCCCEEEECCCCEEEECCCCCCCCHHHHHCCCCCCC-------CEEEEECCCC
T ss_conf             2266301041278546863864698314348831155530015676-------5676337896


No 152
>PRK07892 consensus
Probab=97.50  E-value=0.003  Score=45.03  Aligned_cols=83  Identities=14%  Similarity=0.234  Sum_probs=55.2

Q ss_pred             HHHHHHCCCC--EECCCCCCCHHHHHH-HHHHHHCCCEEEEEECHHHHCCCCCCCCCEEEEECHHHCCHHHHHHHH----
Q ss_conf             6668663710--312014699899999-999975598699998003410468887658998585254746887730----
Q gi|254780945|r  508 NSLHEHFTSS--IAIIHGRMSDIDKES-VMDSFKNGTCKLLIATTVIEVGIDVVDASIIIIENAEHFGLAQLHQLR----  580 (700)
Q Consensus       508 ~~l~~~~~~~--v~~lHGkm~~~ek~~-~m~~F~~g~~~iLvaTtviEVGvdvpna~~mvI~~aerfGLsqLHQLR----  580 (700)
                      .+||.+||..  .++|...+.+.+|-. .+.+-+.-.+.||      -.-||-..+...+..++=||||+...-+.    
T Consensus       794 AyLK~hyP~ef~aa~l~~~~~~~~k~~~~~~e~~~~gi~vl------pPdIN~S~~~f~~~~~~Ir~gL~~Ikgvg~~~~  867 (1180)
T PRK07892        794 AYLKANYPAEYMAALLTSVGDDKDKSAVYLAECRRMGITVL------PPDVNESSLNFTAVGDDIRFGLGAVRNVGANVV  867 (1180)
T ss_pred             HHHHHCCHHHHHHHHHHCCCCCCHHHHHHHHHHHHCCCCEE------CCCCCCCCCCCEECCCEEEECCCCCCCCCHHHH
T ss_conf             99865789999999985486731689999999998799073------687544677655269804706620378888899


Q ss_pred             -----HCCCCCCCCEEEEEEE
Q ss_conf             -----1166789835999970
Q gi|254780945|r  581 -----GRVGRGEEISSCILLY  596 (700)
Q Consensus       581 -----GRVGRg~~~s~c~l~~  596 (700)
                           .|--.|.-.|.--|+.
T Consensus       868 ~~Ii~~R~~~G~f~s~~Df~~  888 (1180)
T PRK07892        868 DSIIAAREEKGKFTDFSDFLD  888 (1180)
T ss_pred             HHHHHHHHHCCCCCCHHHHHH
T ss_conf             999999985799998899998


No 153
>PRK06826 dnaE DNA polymerase III DnaE; Reviewed
Probab=97.50  E-value=0.0072  Score=42.09  Aligned_cols=82  Identities=18%  Similarity=0.229  Sum_probs=57.2

Q ss_pred             HHHHHHCCCC--EECCCCCCCHHHH-HHHHHHHHCCCEEEEEECHHHHCCCCCCCCCEEEEECHHHCCHHHHHHHHHCC-
Q ss_conf             6668663710--3120146998999-99999975598699998003410468887658998585254746887730116-
Q gi|254780945|r  508 NSLHEHFTSS--IAIIHGRMSDIDK-ESVMDSFKNGTCKLLIATTVIEVGIDVVDASIIIIENAEHFGLAQLHQLRGRV-  583 (700)
Q Consensus       508 ~~l~~~~~~~--v~~lHGkm~~~ek-~~~m~~F~~g~~~iLvaTtviEVGvdvpna~~mvI~~aerfGLsqLHQLRGRV-  583 (700)
                      .+||.+||..  .++|..-+.+.+| ...+.+-+.-.+.||      -.-|+-.++..-+-.++=||||+....+...+ 
T Consensus       769 AylK~hyP~ef~aa~l~~~~~~~~k~~~~~~e~~~~gi~vl------pPdIn~S~~~f~~~~~~Ir~gl~~Ikgvg~~~~  842 (1157)
T PRK06826        769 AYLKRYYPVEFMAALLNSVMGNSDKVAFYIEECKRLGIEVL------PPDINESYSKFTVKGNKIRFGLAAVKNVGENAI  842 (1157)
T ss_pred             HHHHHCCHHHHHHHHHHHCCCCCCHHHHHHHHHHHCCCEEE------CCEECCCCCCEEEECCEEEEHHHHHCCCCHHHH
T ss_conf             99986287999999865436895068999999998799597------973311388138879978875566268888899


Q ss_pred             --------CCCCCCEEEEEE
Q ss_conf             --------678983599997
Q gi|254780945|r  584 --------GRGEEISSCILL  595 (700)
Q Consensus       584 --------GRg~~~s~c~l~  595 (700)
                              -+|.-.|.-=|+
T Consensus       843 ~~I~~~R~~~G~f~s~~Df~  862 (1157)
T PRK06826        843 DNIVKAREKKGKFTSLVDFC  862 (1157)
T ss_pred             HHHHHHHHHCCCCCCHHHHH
T ss_conf             99999998779999989999


No 154
>PRK05673 dnaE DNA polymerase III subunit alpha; Validated
Probab=97.44  E-value=0.0072  Score=42.09  Aligned_cols=67  Identities=16%  Similarity=0.320  Sum_probs=48.2

Q ss_pred             HHHHHHCCCC--EECCCCCCCHHHH-HHHHHHHHCCCEEEEEECHHHHCCCCCCCCCEEEEECHHHCCHHHHHHHH
Q ss_conf             6668663710--3120146998999-99999975598699998003410468887658998585254746887730
Q gi|254780945|r  508 NSLHEHFTSS--IAIIHGRMSDIDK-ESVMDSFKNGTCKLLIATTVIEVGIDVVDASIIIIENAEHFGLAQLHQLR  580 (700)
Q Consensus       508 ~~l~~~~~~~--v~~lHGkm~~~ek-~~~m~~F~~g~~~iLvaTtviEVGvdvpna~~mvI~~aerfGLsqLHQLR  580 (700)
                      .+||.+||..  .++|...+...+| ...+.+-+.-.+.||      -+-|+-..+..-+-.++=||||+..--+.
T Consensus       763 AyLKahyP~eF~aalL~~~~~~~~k~~~~i~ea~~~gi~vl------ppdin~S~~~f~~~~~~Ir~gL~~Ikgvg  832 (1143)
T PRK05673        763 AYLKAHYPAEFMAALLTSDMDNTDKVAVYLDECRRMGIKVL------PPDVNESLYRFTVVGGDIRYGLGAIKGVG  832 (1143)
T ss_pred             HHHHHCCHHHHHHHHHHCCCCCCHHHHHHHHHHHHCCCCEE------CCEECCCCCCCEECCCEEEEHHHHHCCCC
T ss_conf             99856586999999974077884679999999998799175------87431356873653998987167506787


No 155
>PRK05672 dnaE2 error-prone DNA polymerase; Validated
Probab=97.40  E-value=0.0036  Score=44.48  Aligned_cols=106  Identities=15%  Similarity=0.128  Sum_probs=55.0

Q ss_pred             HHHHHHCCCC--EECC-CCCCCHHHHHHHHHHHHCCCEEEEEECHHHHCCCCCCCCCEEEE-----ECHHHCCHHHHHHH
Q ss_conf             6668663710--3120-14699899999999975598699998003410468887658998-----58525474688773
Q gi|254780945|r  508 NSLHEHFTSS--IAII-HGRMSDIDKESVMDSFKNGTCKLLIATTVIEVGIDVVDASIIII-----ENAEHFGLAQLHQL  579 (700)
Q Consensus       508 ~~l~~~~~~~--v~~l-HGkm~~~ek~~~m~~F~~g~~~iLvaTtviEVGvdvpna~~mvI-----~~aerfGLsqLHQL  579 (700)
                      .+||.+||..  .++| +..|.....+..+++-+.-.+.||-      +-|+-..+..-+-     .++=||||+...-+
T Consensus       751 AylK~hyP~ef~aalL~~~~~~~~~~~~~~~e~~~~gi~vlp------pdin~S~~~~~~~~~~~~~~~ir~gl~~ikg~  824 (1050)
T PRK05672        751 SWLKCHHPAAFCAALLNSQPMGFYSPQQLVQDARRHGVEVLP------VDVNASGWDATLEPRPGGGPAVRLGLRLVRGL  824 (1050)
T ss_pred             HHHHHCCHHHHHHHHHCCCCCCCCCHHHHHHHHHHCCCCEEC------CEEECCCCCCEEEECCCCCCEEEEHHHHHCCC
T ss_conf             999873999999998567876776689999999985992618------74202577535631478886487457875557


Q ss_pred             HHCC--------CCCCCCEEEEEEECCCCCHHHHHHHHHHHHHCHHHHH
Q ss_conf             0116--------6789835999970888998799999999841425899
Q gi|254780945|r  580 RGRV--------GRGEEISSCILLYHPPLSKNSYTRLSVLKNTEDGFLI  620 (700)
Q Consensus       580 RGRV--------GRg~~~s~c~l~~~~~~~~~~~~Rl~~l~~~~dGf~i  620 (700)
                      +..+        ..|.-.|.-=++....++....+.|- .+-.-|+|..
T Consensus       825 g~~~~~~I~~~R~~g~f~s~~Df~~R~~~~~~~~e~Li-~aGafD~~g~  872 (1050)
T PRK05672        825 GEEAAERIVAARARGPFTSVEDLARRAGLDRRALEALA-DAGALRSLGG  872 (1050)
T ss_pred             HHHHHHHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHH-HCCCCCCCCC
T ss_conf             09999999999716999999999988589999999998-6798400160


No 156
>PRK06658 consensus
Probab=97.31  E-value=0.0061  Score=42.66  Aligned_cols=127  Identities=13%  Similarity=0.126  Sum_probs=75.1

Q ss_pred             HHHHHHCCC--CEECCCCCCCHHHH-HHHHHHHHCCCEEEEEECHHHHCCCCCCCCCEEEEECHHHCCHHHHHHHHH---
Q ss_conf             666866371--03120146998999-999999755986999980034104688876589985852547468877301---
Q gi|254780945|r  508 NSLHEHFTS--SIAIIHGRMSDIDK-ESVMDSFKNGTCKLLIATTVIEVGIDVVDASIIIIENAEHFGLAQLHQLRG---  581 (700)
Q Consensus       508 ~~l~~~~~~--~v~~lHGkm~~~ek-~~~m~~F~~g~~~iLvaTtviEVGvdvpna~~mvI~~aerfGLsqLHQLRG---  581 (700)
                      .+||.+||.  -.++|...+...+| ...+.+-+.-.+.|      .-.-|+-.+...-|-.++=||||+...-+..   
T Consensus       762 AyLK~hyP~ef~aa~l~~~~~~~~k~~~~~~e~~~~gi~v------lppdIn~S~~~f~~~~~~Ir~gl~~Ikgvg~~~~  835 (1145)
T PRK06658        762 AYLKANFPAEFMAANLTNEINSNDKLPYYIAEAEKMGLNI------LKPDVNRSFPYFSVTDGGISYGLLGIKGLGEQVA  835 (1145)
T ss_pred             HHHHHCCHHHHHHHHHCCCCCCCHHHHHHHHHHHHCCCCC------CCCEEECCCCCCEECCCCCEEHHHHCCCCCHHHH
T ss_conf             9970567999999985058898657999999999859946------3872221688636628954233344578778999


Q ss_pred             ------CCCCCCCCEEEEEEECCCCCHHHHHHHHHHHHHC--HHHHH---------------HHHHH--HHCCCCCCCCC
Q ss_conf             ------1667898359999708889987999999998414--25899---------------99998--52063000260
Q gi|254780945|r  582 ------RVGRGEEISSCILLYHPPLSKNSYTRLSVLKNTE--DGFLI---------------AEEDL--KQRKEGEILGI  636 (700)
Q Consensus       582 ------RVGRg~~~s~c~l~~~~~~~~~~~~Rl~~l~~~~--dGf~i---------------Ae~Dl--~lRG~G~~~G~  636 (700)
                            |--.|.-.|+-=++..-......++-++.|...-  |+|..               |+..-  +..|.+++|+.
T Consensus       836 ~~Iv~~R~~~G~f~s~~Df~~Rv~~~~~nk~~le~Li~aGAfD~~g~~R~~ll~~~~~~~~~~~~~~~~~~~gq~~Lf~~  915 (1145)
T PRK06658        836 DLIIDEREKNGKYSSFEDFLRRVDDKVINKKNLESMIKSGCFDSLGQNRKTLFENLDRAIEYVSEKKNNKSLGQNSLFDV  915 (1145)
T ss_pred             HHHHHHHHHHCCCCCHHHHHHHHHHCCCCHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCC
T ss_conf             99999999818999889999872110379999999997797233303599999819999999999736654578777677


Q ss_pred             HHCC
Q ss_conf             0069
Q gi|254780945|r  637 KQSG  640 (700)
Q Consensus       637 ~QsG  640 (700)
                      ..++
T Consensus       916 ~~~~  919 (1145)
T PRK06658        916 LESQ  919 (1145)
T ss_pred             CCCC
T ss_conf             6655


No 157
>TIGR03117 cas_csf4 CRISPR-associated DEAD/DEAH-box helicase Csf4. Members of this family show up near CRISPR repeats in Acidithiobacillus ferrooxidans ATCC 23270, Azoarcus sp. EbN1, and Rhodoferax ferrireducens DSM 15236. In the latter two species, the CRISPR/cas locus is found on a plasmid. This family is one of several characteristic of a type of CRISPR-associated (cas) gene cluster we designate Aferr after A. ferrooxidans, where it is both chromosomal and the only type of cas gene cluster found. The gene is designated csf4 (CRISPR/cas Subtype as in A. ferrooxidans protein 1), as it lies farthest (fourth closest) from the repeats in the A. ferrooxidans genome.
Probab=97.28  E-value=0.0046  Score=43.58  Aligned_cols=165  Identities=18%  Similarity=0.205  Sum_probs=98.6

Q ss_pred             HHHHHHHHHHHC-CCCEEEEEECCCCCCCCCCCCHHHHHHHHHHHHCCCCEECCCCCCC-HHHHHHHHHHHHCCCEEEEE
Q ss_conf             268999976310-3873899971201221112101466666668663710312014699-89999999997559869999
Q gi|254780945|r  469 DEVIERLKVVLS-EGKKAYWICPQIEEKKESNFRSVVERFNSLHEHFTSSIAIIHGRMS-DIDKESVMDSFKNGTCKLLI  546 (700)
Q Consensus       469 ~~~~~~i~~~l~-~g~q~y~VcPlIeese~~~~~~~~~~~~~l~~~~~~~v~~lHGkm~-~~ek~~~m~~F~~g~~~iLv  546 (700)
                      +++.+.+.+-+. .++.+++.|.-        .+.+.+.++.++...+..+-+-++... +.-+++-++.|.+++-.||.
T Consensus       456 ~~l~~~l~~li~~~~Gr~LvLFTS--------~r~~~~~ae~l~~~l~~~~l~Qge~~~~~~l~~~~~~~f~~~~~svLf  527 (636)
T TIGR03117       456 ENVSLSTAAILRKAQGGTLVLTTA--------FSHISAIGQLVELGIPAEIVIQSEKNRLASAEQQFLALYANGIQPVLI  527 (636)
T ss_pred             HHHHHHHHHHHHHCCCCEEEEECC--------HHHHHHHHHHHHHCCCCCEEEECCCCCHHHHHHHHHHHHHCCCCCEEE
T ss_conf             999999999998707988997040--------999999999997227886587457640356899999987278996898


Q ss_pred             ECHHHHCCCCCCCCCE---------EEEECHHHCCHHHHHHHHHCCCCCCCCEEEEEEECCCCCHHHHHHHHHHHHHCHH
Q ss_conf             8003410468887658---------9985852547468877301166789835999970888998799999999841425
Q gi|254780945|r  547 ATTVIEVGIDVVDASI---------IIIENAEHFGLAQLHQLRGRVGRGEEISSCILLYHPPLSKNSYTRLSVLKNTEDG  617 (700)
Q Consensus       547 aTtviEVGvdvpna~~---------mvI~~aerfGLsqLHQLRGRVGRg~~~s~c~l~~~~~~~~~~~~Rl~~l~~~~dG  617 (700)
                      +|.=-==|||||..++         .||..-==|++-                         .+..-..|.+  ...-+.
T Consensus       528 GT~SfWEGVDvpG~~~~~~~Gd~Ls~VII~rLPF~~p-------------------------~~p~~~~r~~--~~~g~~  580 (636)
T TIGR03117       528 AAGGAWTGIDLTHKPVSPDKDNLLTDLIITCAPFGLN-------------------------RSLSMLKRIR--KTSVRP  580 (636)
T ss_pred             ECCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCCCCC-------------------------CCHHHHHHHH--HCCCCH
T ss_conf             6776406625788666788777420665756998999-------------------------8789999997--149987


Q ss_pred             HH-HHHHHHHHC-CCCCCCCCH-HCCCCCCCCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf             89-999998520-630002600-0698744000388759999999999999998
Q gi|254780945|r  618 FL-IAEEDLKQR-KEGEILGIK-QSGMPKFLIAQPELHDSLLEIARKDAKHILT  668 (700)
Q Consensus       618 f~-iAe~Dl~lR-G~G~~~G~~-QsG~~~~~~~d~~~d~~ll~~a~~~a~~~~~  668 (700)
                      |. +.|.=+++| |.|=++-+. ++..-..-+.|..-+..-++--.+-.+.|+.
T Consensus       581 ~~~vp~A~i~lkQG~GRLIRs~d~~D~G~vaiLD~RI~~~~~~~~~~~~~~~~~  634 (636)
T TIGR03117       581 WEIINESLMMLRQGLGRLVRHPDMPQNRRIHMLDGRIHWPYMESWQESVKTILD  634 (636)
T ss_pred             HHHHHHHHHHHHHHCCCEECCCCCCCCEEEEEECCCCCHHHHHHHHHHHHHHCC
T ss_conf             777999999997745730314778896589996475532443146677998604


No 158
>PRK09401 reverse gyrase; Reviewed
Probab=97.28  E-value=0.00075  Score=49.79  Aligned_cols=106  Identities=20%  Similarity=0.377  Sum_probs=66.3

Q ss_pred             CCHHHHHHHHHCCCCCCHHHHHHHHHHHHHHCCCCCCEEEEEECCCCCHHHHHHHHHHHHHHHHCCEEEEEHHHHHHHHH
Q ss_conf             75789999863024679889999999998410013430788621442236999999733444305458861279999999
Q gi|254780945|r  258 EGKIAQKILRNIPFSPTKSQESAIKDILQDMSQKNRMLRILQGDVGSGKTLVALIAMAAAVEAGGQAVIMAPIGILAQQH  337 (700)
Q Consensus       258 ~~~~~~~f~~~LPF~LT~~Q~~ai~eI~~Dl~~~~pM~RLLQGDVGSGKTiVA~~A~l~~~~~G~Q~alMaPTEILA~QH  337 (700)
                      .+.....|..-|.|+.-..+. ++.-|. |+--.       ..|+-  .+++-++--     =|--+.+.+|++- -..-
T Consensus       280 rg~r~~lfreLlgFevg~~~~-~lRni~-D~y~~-------~~~~~--~~~~e~v~~-----lG~GgLifv~~~~-g~e~  342 (1176)
T PRK09401        280 RGIRIKLFRELLGFEVGRPRF-YLRNIV-DVYIE-------PEDLV--EKLVELVKR-----LGDGGLVFVPTDY-GKEY  342 (1176)
T ss_pred             CCCHHHHHHHHHCCCCCCCCC-CEEEEE-EEECC-------CCCHH--HHHHHHHHH-----HCCCEEEEEECCC-CHHH
T ss_conf             885389999982986788642-302125-77605-------76688--999999998-----4895499976765-8899


Q ss_pred             HHHHHHHCCCCCCEEEEEECCCCHHHHHHHHHHHCCCCCEEEEECHHH
Q ss_conf             986211014578658996246422566768776213475486411120
Q gi|254780945|r  338 YEFIKKYTQNTQIIVEIITGNMPQAHRRKALERIAHGQAHIIIGTHAL  385 (700)
Q Consensus       338 ~~~~~~~~~~~~i~v~lLtg~~~~~er~~i~~~i~~G~~~iiIGTHAL  385 (700)
                      .+.+.+++...|+++++.++.     +++.+++.+.|+++++||..+-
T Consensus       343 ~~~~~~~l~~~g~~a~~~~~~-----~~~~le~f~~Ge~dvLvG~asy  385 (1176)
T PRK09401        343 AEELKEYLESHGIKAEAYSGR-----KKEFLEKFEEGEIDVLIGVASY  385 (1176)
T ss_pred             HHHHHHHHHHCCCEEEEEECC-----CHHHHHHHHCCCCCEEEEECCC
T ss_conf             999999999769669996058-----8668889757886489997012


No 159
>KOG1803 consensus
Probab=97.24  E-value=0.022  Score=38.30  Aligned_cols=68  Identities=21%  Similarity=0.300  Sum_probs=54.7

Q ss_pred             HHHHHHHCCCCCCHHHHHHHHHHHHHHCCCCCCEEEEEECCCCCHHHHHHHHHHHHHHHHCCEEEEEHHHHHH
Q ss_conf             9999863024679889999999998410013430788621442236999999733444305458861279999
Q gi|254780945|r  262 AQKILRNIPFSPTKSQESAIKDILQDMSQKNRMLRILQGDVGSGKTLVALIAMAAAVEAGGQAVIMAPIGILA  334 (700)
Q Consensus       262 ~~~f~~~LPF~LT~~Q~~ai~eI~~Dl~~~~pM~RLLQGDVGSGKTiVA~~A~l~~~~~G~Q~alMaPTEILA  334 (700)
                      ...-+.-+|+.|-.+|++|+.-   -++...+|  ++||-=|.|||-.-..-+.+++..|.|+.+.|||-+=-
T Consensus       175 ~~~~~~~~~~~ln~SQk~Av~~---~~~~k~l~--~I~GPPGTGKT~TlvEiI~qlvk~~k~VLVcaPSn~AV  242 (649)
T KOG1803         175 EIKKITFFNKNLNSSQKAAVSF---AINNKDLL--IIHGPPGTGKTRTLVEIISQLVKQKKRVLVCAPSNVAV  242 (649)
T ss_pred             HHCCCCCCCCCCCHHHHHHHHH---HHCCCCCE--EEECCCCCCCEEEHHHHHHHHHHCCCEEEEECCCHHHH
T ss_conf             4400136774323779999999---73568835--75579988840439999999997288599976736789


No 160
>COG1110 Reverse gyrase [DNA replication, recombination, and repair]
Probab=97.20  E-value=0.0012  Score=48.12  Aligned_cols=370  Identities=20%  Similarity=0.301  Sum_probs=171.5

Q ss_pred             CCHHHHHHHHHCCCCCCHHHHHHHHHHHHHHCCCCCCEEEEEECCCCCHHHHHHHHHHHHHHHHCCEEEEEHHHHHHHHH
Q ss_conf             75789999863024679889999999998410013430788621442236999999733444305458861279999999
Q gi|254780945|r  258 EGKIAQKILRNIPFSPTKSQESAIKDILQDMSQKNRMLRILQGDVGSGKTLVALIAMAAAVEAGGQAVIMAPIGILAQQH  337 (700)
Q Consensus       258 ~~~~~~~f~~~LPF~LT~~Q~~ai~eI~~Dl~~~~pM~RLLQGDVGSGKTiVA~~A~l~~~~~G~Q~alMaPTEILA~QH  337 (700)
                      -+.....|..-|.|+.-.++.-.= .|.. ..-..          .|=-+++.++-.     -|.-+.+.+|++- ..+-
T Consensus       289 rg~R~~LfReLlgFevG~~~~~LR-NIvD-~y~~~----------~~~e~~~elvk~-----lG~GgLIfV~~d~-G~e~  350 (1187)
T COG1110         289 RGSRLKLFRELLGFEVGSGGEGLR-NIVD-IYVES----------ESLEKVVELVKK-----LGDGGLIFVPIDY-GREK  350 (1187)
T ss_pred             CCCHHHHHHHHHCCCCCCCCHHHH-HEEE-EECCC----------CCHHHHHHHHHH-----HCCCEEEEEECHH-HHHH
T ss_conf             774388999983985676403130-0044-20368----------637889999998-----4897499997177-3899


Q ss_pred             HHHHHHHCCCCCCEEEEEECCCCHHHHHHHHHHHCCCCCEEEEECHHHCCCCCCCCCCCEEEECCCCC------CCHH-H
Q ss_conf             98621101457865899624642256676877621347548641112013345544441788521013------3568-8
Q gi|254780945|r  338 YEFIKKYTQNTQIIVEIITGNMPQAHRRKALERIAHGQAHIIIGTHALFQDSIQYYKLILVIVDEQHR------FGVQ-Q  410 (700)
Q Consensus       338 ~~~~~~~~~~~~i~v~lLtg~~~~~er~~i~~~i~~G~~~iiIGTHAL~q~~v~F~~LgLvViDEQHR------FGV~-Q  410 (700)
                      .+.+.+++...|+++++.++     ++++.++..+.|+++++||..+-..-=|       ==+|.-||      .||- +
T Consensus       351 aeel~e~Lr~~Gi~a~~~~a-----~~~~~le~F~~GeidvLVGvAsyYG~lV-------RGlDLP~rirYaIF~GvPk~  418 (1187)
T COG1110         351 AEELAEYLRSHGINAELIHA-----EKEEALEDFEEGEVDVLVGVASYYGVLV-------RGLDLPHRIRYAVFYGVPKF  418 (1187)
T ss_pred             HHHHHHHHHHCCCEEEEEEC-----CCHHHHHHHCCCCEEEEEEECCCCCCEE-------ECCCCHHHEEEEEEECCCCE
T ss_conf             99999999866960798623-----2022456650676017998502134302-------24774345457899558740


Q ss_pred             HHHHHHCCCC--CCCEEECHHHHHHHHHHHHHHCC----------------CHHHHCCCCCCCCCCEEEEEECCCHHHHH
Q ss_conf             9987402567--76101010132278999975201----------------01111023557666207999702002689
Q gi|254780945|r  411 RLKLTQKATA--PHVLLMTATPIPRTLVLTSLGDI----------------DISKITEKPAGRKPIKTVIIPINRIDEVI  472 (700)
Q Consensus       411 R~~L~~Kg~~--ph~L~MtATPIPRTLal~~ygdl----------------dvS~i~e~P~gR~~I~T~~~~~~~~~~~~  472 (700)
                      |..|..--.+  -++.+||+-+ |+-.+.-..+.+                ....+..-|    .|.-+.+  +.....+
T Consensus       419 rf~l~~~~~~~~~~l~~ls~~~-~~~~~~~~~~~~~rl~~~ir~~~~~~l~~~~~l~~~~----~~~~~~~--e~v~~~~  491 (1187)
T COG1110         419 RFRLTLEESDPKRLLYLLSALS-DREARSRLEGLAGRLRRIIRRLSPYSLLKLMKLKKRP----DVDRHLA--EEVRTLA  491 (1187)
T ss_pred             EEECCCCCCCHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHCC----CCCHHHH--HHHHHHH
T ss_conf             5640412366277898987510-4654246677789999998631598877489886445----7313679--9999999


Q ss_pred             HHHHHHHC-------------------CCCEEEEEECCC----CCCCCC--------------CCCHHHHHHHHHHHHCC
Q ss_conf             99976310-------------------387389997120----122111--------------21014666666686637
Q gi|254780945|r  473 ERLKVVLS-------------------EGKKAYWICPQI----EEKKES--------------NFRSVVERFNSLHEHFT  515 (700)
Q Consensus       473 ~~i~~~l~-------------------~g~q~y~VcPlI----eese~~--------------~~~~~~~~~~~l~~~~~  515 (700)
                      +++++.+.                   .|.- |++.|=.    ..|...              =+-+..+.++.|.+..-
T Consensus       492 ~~~~e~L~~e~~~k~i~e~~~~vl~~~eg~~-yi~vPD~~TYIQaSGRtSRLyaGglTkGlSvvlvdd~~~f~~L~krm~  570 (1187)
T COG1110         492 EFVRELLKDEERVKKIAESADLVLVYEEGEL-YLEVPDVRTYIQASGRTSRLYAGGLTKGLSVVLVDDPEVFEGLIKRMS  570 (1187)
T ss_pred             HHHHHHHHHHHHHHHHHHCCCEEEEECCCCE-EEEECCHHHHEECCCHHHHHHCCCCCCCEEEEEECCHHHHHHHHHHHH
T ss_conf             9999998778899865404736999427835-999557466310266176654266346228999568899999999998


Q ss_pred             ---CCEECCCCCCCHHHHHH----------HHHHHHCCCEEEEEECHHHHCCCCCCCCCEEEEECHH-------HCCHHH
Q ss_conf             ---10312014699899999----------9999755986999980034104688876589985852-------547468
Q gi|254780945|r  516 ---SSIAIIHGRMSDIDKES----------VMDSFKNGTCKLLIATTVIEVGIDVVDASIIIIENAE-------HFGLAQ  575 (700)
Q Consensus       516 ---~~v~~lHGkm~~~ek~~----------~m~~F~~g~~~iLvaTtviEVGvdvpna~~mvI~~ae-------rfGLsq  575 (700)
                         ..+..-  +++..+-++          -..+-..|+.        +|-+.|.-.-++||||.+.       -||=.+
T Consensus       571 ~~~~e~e~k--~l~evdL~el~reIdEdR~~~r~~~~g~~--------~~~~~dlvkt~L~IVESPnKARTIA~FFgrPS  640 (1187)
T COG1110         571 WKFIEIEFK--EISEVDLEELLREIDEDRERVRRVLEGKL--------KEETKDLVKTALMIVESPNKARTIASFFGRPS  640 (1187)
T ss_pred             HHHCCCCEE--ECCCCCHHHHHHHHHHHHHHHHHHHHCCC--------HHHHHHHHHCEEEEEECCHHHHHHHHHHCCCC
T ss_conf             751234230--52114799999997766899988872431--------12333211015899967718889999848962


Q ss_pred             HHHHHHCCCCCCCCEEEEEEECCCCC-------HHHHHHHHHHHHHCHHHHHHHHHHH--HCCCCCCCCCHHCCCCCCCC
Q ss_conf             87730116678983599997088899-------8799999999841425899999985--20630002600069874400
Q gi|254780945|r  576 LHQLRGRVGRGEEISSCILLYHPPLS-------KNSYTRLSVLKNTEDGFLIAEEDLK--QRKEGEILGIKQSGMPKFLI  646 (700)
Q Consensus       576 LHQLRGRVGRg~~~s~c~l~~~~~~~-------~~~~~Rl~~l~~~~dGf~iAe~Dl~--lRG~G~~~G~~QsG~~~~~~  646 (700)
                      .--+.|.|-=-.--|--+|+.-+..+       +...--    +--.||=++.-.|.-  -|.-|..+-..|-=.|.-.=
T Consensus       641 ~R~~~~~~vYEv~~gD~vL~ItAS~GHv~DLvt~~g~hG----vl~~~~~~vPvY~tIKrC~dcg~q~~~~~~~cP~Cgs  716 (1187)
T COG1110         641 VRRLGGGVVYEVAIGDLVLTITASGGHVFDLVTEPGVHG----VLVKDGKYVPVYDTIKRCRDCGEQFVDSEDKCPRCGS  716 (1187)
T ss_pred             EEEECCEEEEEEECCCEEEEEEECCCEEEEEECCCCCCE----EECCCCCEEEHHHHHHHHHHCCCEECCCCCCCCCCCC
T ss_conf             355479068999618758999953871688631465210----5605870686278888885158440443235988788


Q ss_pred             CCHHHHHHHHHHHHHHHHH----HHHHCCCCCCCCCH
Q ss_conf             0388759999999999999----99848463665564
Q gi|254780945|r  647 AQPELHDSLLEIARKDAKH----ILTQDPDLTSVRGQ  679 (700)
Q Consensus       647 ~d~~~d~~ll~~a~~~a~~----~~~~d~~l~~~~~~  679 (700)
                      .+...-.+.++.-|+.|.+    ++..||+-+.++-.
T Consensus       717 ~~v~d~~~~ve~lRelA~EvDeVlIgTDPDtEGEKIa  753 (1187)
T COG1110         717 RNVEDKTETVEALRELALEVDEILIGTDPDTEGEKIA  753 (1187)
T ss_pred             CCCCCCHHHHHHHHHHHHHCCEEEECCCCCCCCCHHH
T ss_conf             3202407799999998865277998179987644257


No 161
>pfam09848 DUF2075 Uncharacterized conserved protein (DUF2075). This domain, found in various prokaryotic proteins (including putative ATP/GTP binding proteins), has no known function.
Probab=97.20  E-value=0.0013  Score=47.83  Aligned_cols=85  Identities=26%  Similarity=0.305  Sum_probs=50.7

Q ss_pred             EEEEECCCCCHHHHHHHHHHHHH--HHHCCEEEEEHHHHHHHHHHHHHHHHCCCCCCEEEEEECCCCHHHHHHHHHHHCC
Q ss_conf             78862144223699999973344--4305458861279999999986211014578658996246422566768776213
Q gi|254780945|r  296 RILQGDVGSGKTLVALIAMAAAV--EAGGQAVIMAPIGILAQQHYEFIKKYTQNTQIIVEIITGNMPQAHRRKALERIAH  373 (700)
Q Consensus       296 RLLQGDVGSGKTiVA~~A~l~~~--~~G~Q~alMaPTEILA~QH~~~~~~~~~~~~i~v~lLtg~~~~~er~~i~~~i~~  373 (700)
                      -+++|+=|||||+||+-.+....  ..++.+.++.+.-=|..--++.+..-.+..                         
T Consensus         4 ~~V~G~pGtGKTvv~l~l~~~l~~~~~~~~~~~l~~N~~~~~~l~~~l~~~~~~~-------------------------   58 (348)
T pfam09848         4 FLVTGGPGTGKTVVALNLFAELSDSDLGRTAVFLSGNHPLVLVLYEALAGDLKVR-------------------------   58 (348)
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHHCCCCCCEEEEECCHHHHHHHHHHHHHHCCHH-------------------------
T ss_conf             9997779938999999999998644026820899578669999999986041200-------------------------


Q ss_pred             CCCEEEEECHHHCCC-CCCCCCCCEEEECCCCCC
Q ss_conf             475486411120133-455444417885210133
Q gi|254780945|r  374 GQAHIIIGTHALFQD-SIQYYKLILVIVDEQHRF  406 (700)
Q Consensus       374 G~~~iiIGTHAL~q~-~v~F~~LgLvViDEQHRF  406 (700)
                       ...++.+..+.+|. +-...+.-++|+||=||-
T Consensus        59 -~~~~~~~~~~fi~~~~~~~~~~dvvivDEAhRl   91 (348)
T pfam09848        59 -KKKLFRKPTSFINNLHKAPPHEDVVIVDEAHRL   91 (348)
T ss_pred             -HCCCCCCCHHHHCCCCCCCCCCCEEEEEHHHHH
T ss_conf             -102000725231652357986778998317866


No 162
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=97.19  E-value=0.0021  Score=46.24  Aligned_cols=111  Identities=21%  Similarity=0.272  Sum_probs=65.5

Q ss_pred             HHHHHHHHHHHHHCCCCCCEEEEEECCCCHHH--HHHHHHHHCCCCCEEEEECHHHCCCCCCCCCCCEEEE---CCC---
Q ss_conf             99999998621101457865899624642256--6768776213475486411120133455444417885---210---
Q gi|254780945|r  332 ILAQQHYEFIKKYTQNTQIIVEIITGNMPQAH--RRKALERIAHGQAHIIIGTHALFQDSIQYYKLILVIV---DEQ---  403 (700)
Q Consensus       332 ILA~QH~~~~~~~~~~~~i~v~lLtg~~~~~e--r~~i~~~i~~G~~~iiIGTHAL~q~~v~F~~LgLvVi---DEQ---  403 (700)
                      +=+++-.+.++++|++.  ++.-+.+.++...  -+.++..+..|+++|+|||.-+ .++..|.|++||.|   |.=   
T Consensus       491 ~GterieeeL~~~FP~~--rv~r~d~Dtt~~k~~~~~~l~~~~~ge~dILiGTQmi-aKG~~fp~vtLVgvl~aD~~L~~  567 (730)
T COG1198         491 PGTERIEEELKRLFPGA--RIIRIDSDTTRRKGALEDLLDQFANGEADILIGTQMI-AKGHDFPNVTLVGVLDADTGLGS  567 (730)
T ss_pred             CCHHHHHHHHHHHCCCC--CEEEECCCCCCCHHHHHHHHHHHHCCCCCEEECCHHH-HCCCCCCCCEEEEEEECHHHHCC
T ss_conf             61999999999878999--4799846666643568999999757998866341666-42788666318999963143158


Q ss_pred             CCCCHHHH--------HHHHHCC-CCCCCEEECHHHHHHHHHHHHHHCCCH
Q ss_conf             13356889--------9874025-677610101013227899997520101
Q gi|254780945|r  404 HRFGVQQR--------LKLTQKA-TAPHVLLMTATPIPRTLVLTSLGDIDI  445 (700)
Q Consensus       404 HRFGV~QR--------~~L~~Kg-~~ph~L~MtATPIPRTLal~~ygdldv  445 (700)
                      .-|=-.-|        .....-+ ....+++=|+.|===++.....+|.+-
T Consensus       568 ~DfRAsEr~fqll~QvaGRAgR~~~~G~VvIQT~~P~hp~i~~~~~~dy~~  618 (730)
T COG1198         568 PDFRASERTFQLLMQVAGRAGRAGKPGEVVIQTYNPDHPAIQALKRGDYEA  618 (730)
T ss_pred             CCCCHHHHHHHHHHHHHHHHCCCCCCCEEEEEECCCCCHHHHHHHHCCHHH
T ss_conf             884357899999999975532678898699996799857999998669999


No 163
>PRK09074 consensus
Probab=97.19  E-value=0.0076  Score=41.88  Aligned_cols=134  Identities=13%  Similarity=0.158  Sum_probs=75.3

Q ss_pred             HHHHHHCCCC--EECCCCCCCHHHH-HHHHHHHHCCCEEEEEECHHHHCCCCCCCCCEEEEECHHHCCHHHHHHH-----
Q ss_conf             6668663710--3120146998999-9999997559869999800341046888765899858525474688773-----
Q gi|254780945|r  508 NSLHEHFTSS--IAIIHGRMSDIDK-ESVMDSFKNGTCKLLIATTVIEVGIDVVDASIIIIENAEHFGLAQLHQL-----  579 (700)
Q Consensus       508 ~~l~~~~~~~--v~~lHGkm~~~ek-~~~m~~F~~g~~~iLvaTtviEVGvdvpna~~mvI~~aerfGLsqLHQL-----  579 (700)
                      .+||.+||..  .++|...+...+| ...+++-+.-.+.||      -+-|+-.++..-+-.++=||||+..--+     
T Consensus       771 AylK~hyP~ef~aall~~~~~~~~k~~~~~~e~~~~gi~vl------ppdin~S~~~f~~~~~~Ir~gl~~ikgvg~~~~  844 (1149)
T PRK09074        771 AYMKANYPVEFLAASMTLDMSNTDKLADFRQEARRLGIEVV------PPSVNRSGATFEVGDGAIYYALAALKGVGEAAM  844 (1149)
T ss_pred             HHHHHCCHHHHHHHHCCCCCCCCHHHHHHHHHHHHCCCCEE------CCEEECCCCCEEEECCEEEECCHHHCCCCHHHH
T ss_conf             99986284999986433376755589999999998798164------864403478337728878874333266888999


Q ss_pred             ----HHCCCCCCCCEEEEEEE---CCCCCHHHHH--------------HHHHHHHHCHHHHHHHHHHHH--CCCCCCCCC
Q ss_conf             ----01166789835999970---8889987999--------------999998414258999999852--063000260
Q gi|254780945|r  580 ----RGRVGRGEEISSCILLY---HPPLSKNSYT--------------RLSVLKNTEDGFLIAEEDLKQ--RKEGEILGI  636 (700)
Q Consensus       580 ----RGRVGRg~~~s~c~l~~---~~~~~~~~~~--------------Rl~~l~~~~dGf~iAe~Dl~l--RG~G~~~G~  636 (700)
                          ..| ..|.-.|.-=|+.   ....+....+              |-..+..-.+-+.-|+..-+-  .|-.++||.
T Consensus       845 ~~Iv~~R-~~g~f~s~~Df~~Rv~~~~~nk~~le~Li~aGAfD~~~~~R~~l~~~~~~~~~~~~~~~~~~~~gq~~LF~~  923 (1149)
T PRK09074        845 DHIVAAR-GDKPFADLADFAARVDPKIVNKRVLESLARAGAFDCLDPNRARVFAGADALLAYAQRAHENAASGQSDLFGG  923 (1149)
T ss_pred             HHHHHHH-CCCCCCCHHHHHHHHCCCCCCHHHHHHHHHCCCHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCC
T ss_conf             9999754-469999999999871503489999999997487322072799999959999999999879875688665577


Q ss_pred             HHCCCCCCCCCC
Q ss_conf             006987440003
Q gi|254780945|r  637 KQSGMPKFLIAQ  648 (700)
Q Consensus       637 ~QsG~~~~~~~d  648 (700)
                      .-...+...+.+
T Consensus       924 ~~~~~~~~~~~~  935 (1149)
T PRK09074        924 AGADAEPLRLPQ  935 (1149)
T ss_pred             CCCCCCCCCCCC
T ss_conf             766656788889


No 164
>PRK06637 consensus
Probab=97.17  E-value=0.011  Score=40.60  Aligned_cols=39  Identities=15%  Similarity=0.328  Sum_probs=30.2

Q ss_pred             HHHHHHCCCC--EECCCCCCCHHHH-HHHHHHHHCCCEEEEE
Q ss_conf             6668663710--3120146998999-9999997559869999
Q gi|254780945|r  508 NSLHEHFTSS--IAIIHGRMSDIDK-ESVMDSFKNGTCKLLI  546 (700)
Q Consensus       508 ~~l~~~~~~~--v~~lHGkm~~~ek-~~~m~~F~~g~~~iLv  546 (700)
                      .+||.+||..  .++|...|...+| ...+.+-+...+.||-
T Consensus       771 AyLKahYP~eF~aAlL~s~~~~~~k~~~~i~ear~~Gi~Vlp  812 (1182)
T PRK06637        771 AYLKANYPAEFLVACLNLELNNHDKINLFLQEAKDNGIKIIA  812 (1182)
T ss_pred             HHHHHHCHHHHHHHHHCCCCCCCHHHHHHHHHHHHCCCEECC
T ss_conf             999972899999998516878865799999999987895818


No 165
>PRK06920 dnaE DNA polymerase III DnaE; Reviewed
Probab=97.16  E-value=0.0069  Score=42.21  Aligned_cols=68  Identities=15%  Similarity=0.194  Sum_probs=52.6

Q ss_pred             HHHHHHCCC--CEECCCCCCCHHHH-HHHHHHHHCCCEEEEEECHHHHCCCCCCCCCEEEEECHHHCCHHHHHHHHH
Q ss_conf             666866371--03120146998999-999999755986999980034104688876589985852547468877301
Q gi|254780945|r  508 NSLHEHFTS--SIAIIHGRMSDIDK-ESVMDSFKNGTCKLLIATTVIEVGIDVVDASIIIIENAEHFGLAQLHQLRG  581 (700)
Q Consensus       508 ~~l~~~~~~--~v~~lHGkm~~~ek-~~~m~~F~~g~~~iLvaTtviEVGvdvpna~~mvI~~aerfGLsqLHQLRG  581 (700)
                      .+||.+||.  -.++|...+...+| ...+.+.+.-.+.||      -.-|+-.+....+-.++=||||+..-.++-
T Consensus       742 AyLK~hyP~eF~aalL~~~~~~~~k~~~~i~e~~~~gi~vl------ppdin~S~~~f~~~~~~Ir~gl~~ikgvg~  812 (1107)
T PRK06920        742 AYLKANYPLEFMTALLSSAIGNEDKIVQYIRETKRKGFHVL------PPSLQRSGYNFQIEGNAIRYSLLSIRNIGM  812 (1107)
T ss_pred             HHHHHCCHHHHHHHHHHHCCCCCHHHHHHHHHHHHCCCCCC------CCEEEECCCCEEEECCEEEEHHHHHCCCCH
T ss_conf             99987575999999976446885679999999998699514------973442388508878906636556456669


No 166
>PRK07211 replication factor A; Reviewed
Probab=97.15  E-value=0.0042  Score=43.95  Aligned_cols=91  Identities=11%  Similarity=0.190  Sum_probs=70.2

Q ss_pred             CCCCCCCHHHCCCCC-EEEEEEEEEEEEEEC-CCC-------CCEEEEEEECCCCEEEEEEECCCHHHHHHHCCCCCEEE
Q ss_conf             344446478889987-899999998975421-589-------83389999818936999995188789987328988899
Q gi|254780945|r   54 DRHYRPKISEISEER-IVTITGYISQHSSFQ-LQK-------RRPYKILLNDGTGEITLLFFYRKTEMLKNVFFEGRKIT  124 (700)
Q Consensus        54 Dr~~~~~I~~l~~g~-~vti~g~V~~~~~~~-~~~-------r~~~~v~v~D~tg~i~lvfFn~~~~yl~k~lk~G~~v~  124 (700)
                      ++.....|.++.+|. .|.|.|+|+++...+ |.|       .+-..+.+.|+||.|++++|.-...-+...+++|+.+.
T Consensus        49 ~~~ev~~I~dI~~~~~~V~F~akV~~v~d~RtF~R~~~dg~~GrV~ni~VaDeTG~IRvtLWDe~A~a~~~~ievGdVLk  128 (473)
T PRK07211         49 DDGEVNGVADIEPGMDEVKFLAKVTRVGDLRTFERDDEDDDDGRVINVEVADESGDVRVALWDDQAVAADDDLEPGDVLR  128 (473)
T ss_pred             CHHHHCHHHCCCCCCCEEEEEEEEEEECCCEEEECCCCCCCCCEEEEEEEECCCCCEEEEEECCHHHHHHHCCCCCCEEE
T ss_conf             61020202105777634799999815148644441688877633899998647895899985334677762445674899


Q ss_pred             EEEEEEECCCEEEEECCEEE
Q ss_conf             99899731877999778689
Q gi|254780945|r  125 VTGKIKKLKNRIIMVHPHYI  144 (700)
Q Consensus       125 vsGKv~~~~~~~qi~hPe~~  144 (700)
                      |.|+++..++..++.--.++
T Consensus       129 I~Gr~k~G~~G~Evs~~kie  148 (473)
T PRK07211        129 IKGRPKDGYNGLEVSADEVE  148 (473)
T ss_pred             EEECCCCCCCCCEECHHHCC
T ss_conf             94034678666353021133


No 167
>cd04492 YhaM_OBF_like YhaM_OBF_like: A subfamily of OB folds similar to that found in Bacillus subtilis YhaM and Staphylococcus aureus cmp-binding factor-1 (SaCBF1). Both these proteins are 3'-to-5'exoribonucleases. YhaM requires Mn2+ or Co2+ for activity and is inactive in the presence of Mg2+. YhaM also has a Mn2+ dependent 3'-to-5'single-stranded DNA exonuclease activity. SaCBF is also a double-stranded DNA binding protein, binding specifically to cmp, the replication enhancer found in S. aureus plasmid pT181. Proteins in this group combine an N-terminal OB fold with a C-terminal HD domain. The HD domain is found in metal-dependent phosphohydrolases.
Probab=97.08  E-value=0.0069  Score=42.21  Aligned_cols=70  Identities=17%  Similarity=0.252  Sum_probs=54.0

Q ss_pred             EEEEECCCCCC-EEEEEEECCCCEEEEEEECCCHHHHHHHCCCCCEEEEEEEEEECCCEEEEECCEEEECCC
Q ss_conf             97542158983-389999818936999995188789987328988899998997318779997786896264
Q gi|254780945|r   78 QHSSFQLQKRR-PYKILLNDGTGEITLLFFYRKTEMLKNVFFEGRKITVTGKIKKLKNRIIMVHPHYIFHNS  148 (700)
Q Consensus        78 ~~~~~~~~~r~-~~~v~v~D~tg~i~lvfFn~~~~yl~k~lk~G~~v~vsGKv~~~~~~~qi~hPe~~~~~~  148 (700)
                      +......+.++ .+.+++.|.||.|..+.|+.. +.....|..|.-|.|.|++..|++.+|+.--.+...++
T Consensus         8 ~~~~~~tk~G~~Yl~l~L~D~tG~I~ak~W~~~-~~~~~~~~~g~~V~v~G~v~~y~g~~Ql~I~~i~~~~~   78 (83)
T cd04492           8 SKELRTAKNGKPYLALTLQDKTGEIEAKLWDAS-EEDEEKFKPGDIVHVKGRVEEYRGRLQLKIQRIRLVTE   78 (83)
T ss_pred             EHHHHCCCCCCCEEEEEEECCCCEEEEEECCCC-HHHHHCCCCCCEEEEEEEEEEECCCEEEEEEEEEECCC
T ss_conf             801000579991789999878876888885788-67883078999999999998889951089989689983


No 168
>PRK08957 consensus
Probab=97.06  E-value=0.0078  Score=41.83  Aligned_cols=68  Identities=16%  Similarity=0.240  Sum_probs=46.2

Q ss_pred             HHHHHHCCCC--EECCCCCCCHHHH-HHHHHHHHCCCEEEEEECHHHHCCCCCCCCCEEEEEC-HHHCCHHHHHHHHH
Q ss_conf             6668663710--3120146998999-9999997559869999800341046888765899858-52547468877301
Q gi|254780945|r  508 NSLHEHFTSS--IAIIHGRMSDIDK-ESVMDSFKNGTCKLLIATTVIEVGIDVVDASIIIIEN-AEHFGLAQLHQLRG  581 (700)
Q Consensus       508 ~~l~~~~~~~--v~~lHGkm~~~ek-~~~m~~F~~g~~~iLvaTtviEVGvdvpna~~mvI~~-aerfGLsqLHQLRG  581 (700)
                      .+||.+||..  .++|...+...+| ...+.+-+.-.+.||      -.-|+-.++..-|-++ +=||||+-...+.-
T Consensus       772 AyLK~hyP~ef~aa~L~~~~~~~~k~~~~~~e~~~~gi~vl------pPdIN~S~~~f~~~~~~~I~~gL~~Ikgvg~  843 (1159)
T PRK08957        772 LWLKTHYPAEFMAAVMTADMDNTDKIVGLVDECWRMGLKIL------PPDINSGLYHFHVNDDGEIVYGIGAIKGVGE  843 (1159)
T ss_pred             HHHHHHCHHHHHHHHHHHCCCCCHHHHHHHHHHHHCCCCCC------CCCCCCCCCCCEECCCCCEEECHHHHCCCCH
T ss_conf             99997184999999753157982679999999998599524------8850677886467689965247276457878


No 169
>PRK06461 single-stranded DNA-binding protein; Reviewed
Probab=97.04  E-value=0.0081  Score=41.68  Aligned_cols=103  Identities=16%  Similarity=0.199  Sum_probs=70.9

Q ss_pred             CCCCHHHCCCC-CEEEEEEEEEEEEE---ECCCCC--CEEEEEEECCCCEEEEEEECCCHHHHHHHCCCCCEEEE-EEEE
Q ss_conf             44647888998-78999999989754---215898--33899998189369999951887899873289888999-9899
Q gi|254780945|r   57 YRPKISEISEE-RIVTITGYISQHSS---FQLQKR--RPYKILLNDGTGEITLLFFYRKTEMLKNVFFEGRKITV-TGKI  129 (700)
Q Consensus        57 ~~~~I~~l~~g-~~vti~g~V~~~~~---~~~~~r--~~~~v~v~D~tg~i~lvfFn~~~~yl~k~lk~G~~v~v-sGKv  129 (700)
                      .+++|++|.+| ..+++.++|++...   +..++.  +...+.+.|+||.|.++.|+-.   . ..+++|+.+.+ -|.+
T Consensus         3 ~~~KI~dL~pg~~~V~v~~rVl~~~~~r~~~~~~g~~~V~~~~V~DeTG~I~~tlWde~---~-~~i~~GD~V~I~nayv   78 (130)
T PRK06461          3 DITKIKDLKPGMRRVNVTGRVLEVGEPKVIQTKGGPRTISEAVVGDETGRVKLTLWGDQ---A-GTLKEGEVVKIENAWT   78 (130)
T ss_pred             CEEEHHHCCCCCCCEEEEEEEEECCCCCEEECCCCCEEEEEEEEECCCCEEEEEEECCC---C-CCCCCCCEEEEECCEE
T ss_conf             30589888899898269999997689727862899668999999879986999994564---5-6468999999944798


Q ss_pred             EECCCEEEEECCE---EEECCCC----CCCCCCCCCCCCCC
Q ss_conf             7318779997786---8962643----34444411000000
Q gi|254780945|r  130 KKLKNRIIMVHPH---YIFHNSQ----DVNFPLIEAVYSLP  163 (700)
Q Consensus       130 ~~~~~~~qi~hPe---~~~~~~~----~~~~~~I~PIYplt  163 (700)
                      +.|++.+++.-=.   ++...++    ...++-.+|.++-.
T Consensus        79 ~~~~g~l~L~vGk~g~I~~~~d~~~p~~e~i~~~ep~~~~~  119 (130)
T PRK06461         79 TLYRGKVQLNVGRYGSISESDDEEVPEAEEIPEDEPEASYQ  119 (130)
T ss_pred             EEECCEEEEEECCCEEEEECCCCCCCCCCCCCCCCCCCCCC
T ss_conf             88888699986896268976874454245378667575456


No 170
>cd04485 DnaE_OBF DnaE_OBF: A subfamily of OB folds corresponding to the C-terminal OB-fold nucleic acid binding domain of Thermus aquaticus and Escherichia coli type C replicative DNA polymerase III alpha subunit (DnaE). The DNA polymerase holoenzyme of E. coli contains two copies of this replicative polymerase, each of which copies a different DNA strand. This group also contains Bacillus subtilis DnaE. Replication in B. subtilis and Staphylococcus aureus requires two different type C polymerases, polC and DnaE, both of which are thought to be included in the DNA polymerase holoenzyme. At the B. subtilis replication fork, polC appears to be involved in leading strand synthesis and DnaE in lagging strand synthesis.
Probab=97.00  E-value=0.01  Score=40.89  Aligned_cols=72  Identities=21%  Similarity=0.337  Sum_probs=55.7

Q ss_pred             EEEEEEEEEEEECCCCC-CEEEEEEECCCCEEEEEEECCCHHHHHHHCCCCCEEEEEEEEEECCCEEEEECCE
Q ss_conf             99999989754215898-3389999818936999995188789987328988899998997318779997786
Q gi|254780945|r   71 TITGYISQHSSFQLQKR-RPYKILLNDGTGEITLLFFYRKTEMLKNVFFEGRKITVTGKIKKLKNRIIMVHPH  142 (700)
Q Consensus        71 ti~g~V~~~~~~~~~~r-~~~~v~v~D~tg~i~lvfFn~~~~yl~k~lk~G~~v~vsGKv~~~~~~~qi~hPe  142 (700)
                      ++.|.|.+......+++ ++..++++|.+|.+++++|.....-.+..+..|.-+.+.|+++...+.++++--+
T Consensus         1 ~iaG~I~~~k~~~tk~G~~~a~~tleD~~g~~e~~~F~~~~~~~~~~l~~~~~v~i~g~v~~~~~~~~l~~~~   73 (84)
T cd04485           1 TVAGLVTSVRRRRTKKGKRMAFVTLEDLTGSIEVVVFPETYEKYRDLLKEDALLLVEGKVERRDGGLRLIAER   73 (84)
T ss_pred             CEEEEEEEEEEEECCCCCEEEEEEEECCCCCEEEEECHHHHHHHHHHHCCCCEEEEEEEEEEECCEEEEEEEE
T ss_conf             9899999989985579998999999437874999996999999888744698899999999969989999999


No 171
>PRK06326 consensus
Probab=96.98  E-value=0.025  Score=37.86  Aligned_cols=81  Identities=14%  Similarity=0.202  Sum_probs=56.8

Q ss_pred             HHHHHHCCC--CEECCCCCCCHHHH-HHHHHHHHCCCEEEEEECHHHHCCCCCCCCCEEEEECHHHCCHHHHHHHHH---
Q ss_conf             666866371--03120146998999-999999755986999980034104688876589985852547468877301---
Q gi|254780945|r  508 NSLHEHFTS--SIAIIHGRMSDIDK-ESVMDSFKNGTCKLLIATTVIEVGIDVVDASIIIIENAEHFGLAQLHQLRG---  581 (700)
Q Consensus       508 ~~l~~~~~~--~v~~lHGkm~~~ek-~~~m~~F~~g~~~iLvaTtviEVGvdvpna~~mvI~~aerfGLsqLHQLRG---  581 (700)
                      .+||.+||.  -.++|...+...+| ...+.+-++-.+.||      -.-||-......+..++=||||++.--++.   
T Consensus       810 AyLK~~yP~ef~aAlL~s~~~~~~k~~~~i~ear~~Gi~Vl------pPdIN~S~~~f~~~~~~Ir~GL~aIKgvg~~~~  883 (1240)
T PRK06326        810 AYLKANYPKEWLAALLTCDSDDIEKVGKLIREAHSMNIPIL------PPDINESGQDFVATDEGIRFAMGAIKGVGRGLV  883 (1240)
T ss_pred             HHHHHCCHHHHHHHHHCCCCCCCHHHHHHHHHHHHCCCEEE------CCCCCCCCCCCEECCCCEEECHHHHCCCCHHHH
T ss_conf             99986687999999843787996589999999998799684------885366778637708937876365478869999


Q ss_pred             ------CCCCCCCCEEEEE
Q ss_conf             ------1667898359999
Q gi|254780945|r  582 ------RVGRGEEISSCIL  594 (700)
Q Consensus       582 ------RVGRg~~~s~c~l  594 (700)
                            |-.+|.-.|.-=|
T Consensus       884 ~~Iv~~R~~~Gpf~s~~Df  902 (1240)
T PRK06326        884 ESIVEEREKHGPYKSIQDF  902 (1240)
T ss_pred             HHHHHHHHHCCCCCCHHHH
T ss_conf             9999999868698999999


No 172
>cd00079 HELICc Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may not be an autonomously folding unit, but an integral part of the helicase; 4 helicase superfamilies at present according to the organization of their signature motifs; all helicases share the ability to unwind nucleic acid duplexes with a distinct directional polarity; they utilize the free energy from nucleoside triphosphate hydrolysis to fuel their translocation along DNA, unwinding the duplex in the process
Probab=96.96  E-value=0.0059  Score=42.75  Aligned_cols=85  Identities=18%  Similarity=0.347  Sum_probs=70.0

Q ss_pred             HHHHHHHCCEEEEEHHHHHHHHHHHHHHHHCCCCCCEEEEEECCCCHHHHHHHHHHHCCCCCEEEEECHHHCCCCCCCCC
Q ss_conf             33444305458861279999999986211014578658996246422566768776213475486411120133455444
Q gi|254780945|r  315 AAAVEAGGQAVIMAPIGILAQQHYEFIKKYTQNTQIIVEIITGNMPQAHRRKALERIAHGQAHIIIGTHALFQDSIQYYK  394 (700)
Q Consensus       315 l~~~~~G~Q~alMaPTEILA~QH~~~~~~~~~~~~i~v~lLtg~~~~~er~~i~~~i~~G~~~iiIGTHAL~q~~v~F~~  394 (700)
                      -..+++|.++.+.+++.-.++.    +.++|...++++..++|+++..+|+.+.+..++|+.+|++.|.+ +..++.+.+
T Consensus        22 ~~~~~~~~kviIF~~~~~~~~~----l~~~L~~~~~~~~~~~~~~~~~~R~~~~~~F~~~~~~ilv~t~~-~~~Gldl~~   96 (131)
T cd00079          22 KEHLKKGGKVLIFCPSKKMLDE----LAELLRKPGIKVAALHGDGSQEEREEVLKDFREGEIVVLVATDV-IARGIDLPN   96 (131)
T ss_pred             HHHHHCCCEEEEEECCHHHHHH----HHHHHHHCCCCEEEEECCCCHHHHHHHHHHHHHHCEEEEEEEEC-CEECCCCCC
T ss_conf             9999789909999788999999----99999558998999989999999999999977540104887511-200366102


Q ss_pred             CCEEEECCCC
Q ss_conf             4178852101
Q gi|254780945|r  395 LILVIVDEQH  404 (700)
Q Consensus       395 LgLvViDEQH  404 (700)
                      .-.||+-+..
T Consensus        97 ~~~vI~~~~~  106 (131)
T cd00079          97 VSVVINYDLP  106 (131)
T ss_pred             CCEEEEECCC
T ss_conf             8799997899


No 173
>TIGR00348 hsdR type I site-specific deoxyribonuclease, HsdR family; InterPro: IPR004473   There are four classes of restriction endonucleases: types I, II,III and IV. All types of enzymes recognise specific short DNA sequences and carry out the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. They differ in their recognition sequence, subunit composition, cleavage position, and cofactor requirements , , as summarised below:    Type I enzymes (3.1.21.3 from EC) cleave at sites remote from recognition site; require both ATP and S-adenosyl-L-methionine to function; multifunctional protein with both restriction and methylase (2.1.1.72 from EC) activities. Type II enzymes (3.1.21.4 from EC) cleave within or at short specific distances from recognition site; most require magnesium; single function (restriction) enzymes independent of methylase. Type III enzymes (3.1.21.5 from EC) cleave at sites a short distance from recognition site; require ATP (but doesn't hydrolyse it); S-adenosyl-L-methionine stimulates reaction but is not required; exists as part of a complex with a modification methylase methylase (2.1.1.72 from EC). Type IV enzymes target methylated DNA.    Type I restriction endonucleases are components of prokaryotic DNA restriction-modification mechanisms that protects the organism against invading foreign DNA. Type I enzymes have three different subunits subunits - M (modification), S (specificity) and R (restriction) - that form multifunctional enzymes with restriction (3.1.21.3 from EC), methylase (2.1.1.72 from EC) and ATPase activities , . The S subunit is required for both restriction and modification and is responsible for recognition of the DNA sequence specific for the system. The M subunit is necessary for modification, and the R subunit is required for restriction. These enzymes use S-Adenosyl-L-methionine (AdoMet) as the methyl group donor in the methylation reaction, and have a requirement for ATP. They recognize asymmetric DNA sequences split into two domains of specific sequence, one 3-4 bp long and another 4-5 bp long, separated by a nonspecific spacer 6-8 bp in length. Cleavage occurs a considerable distance from the recognition sites, rarely less than 400 bp away and up to 7000 bp away. Adenosyl residues are methylated, one on each strand of the recognition sequence. These enzymes are widespread in eubacteria and archaea. In enteric bacteria they have been subdivide into four families: types IA, IB, IC and ID.   This entry represents the R subunit (HsdR) of type I restriction endonucleases such as EcoRI (3.1.21.3 from EC), which recognises the DNA sequence 5'-GAATTC; the R protein (HsdR) is required for both nuclease and ATPase activity , , , .; GO: 0003677 DNA binding, 0005524 ATP binding, 0009035 Type I site-specific deoxyribonuclease activity, 0009307 DNA restriction-modification system.
Probab=96.94  E-value=0.0036  Score=44.49  Aligned_cols=194  Identities=22%  Similarity=0.215  Sum_probs=117.6

Q ss_pred             HHHHHHHHHHCCCCCCCCCCHHHHHHHHHCCCCCCHHHHHHHHHHHHHHCC---CCCCE-E-EEEECCCCCHHHHHHHHH
Q ss_conf             776555543203576787757899998630246798899999999984100---13430-7-886214422369999997
Q gi|254780945|r  240 LLLMRKQFKKEIGIPINVEGKIAQKILRNIPFSPTKSQESAIKDILQDMSQ---KNRML-R-ILQGDVGSGKTLVALIAM  314 (700)
Q Consensus       240 l~~~r~~~~~~~~~~~~~~~~~~~~f~~~LPF~LT~~Q~~ai~eI~~Dl~~---~~pM~-R-LLQGDVGSGKTiVA~~A~  314 (700)
                      ++....-..-..-+.+--..+.+....+.+|+-   .|.+|++.|..-...   +++-. | |+===-|||||+--+.++
T Consensus       268 llkkE~lLd~i~~f~~f~~~~~~g~~~k~~~~y---~qy~av~ki~~~~~~~~~~k~~~n~G~iWHtQGSGKtlTm~f~A  344 (813)
T TIGR00348       268 LLKKERLLDFIRNFIIFDKEESVGLVTKVIARY---MQYRAVKKIVESILRKEKGKDKRNKGLIWHTQGSGKTLTMLFLA  344 (813)
T ss_pred             CCCCHHHHHHHCCEEEEECCCCCCHHHCCCHHH---HHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEECCCHHHHHHHHH
T ss_conf             677036876331213661451100110100388---99999999999998531378863674489850763788999999


Q ss_pred             HHHH--HHHCC--EEEEEHHHHHHHHHHHHHHHHCCCCCCEEEEEECCCCHHHHHHHHHHHC-------CCCCEEEEEC-
Q ss_conf             3344--43054--5886127999999998621101457865899624642256676877621-------3475486411-
Q gi|254780945|r  315 AAAV--EAGGQ--AVIMAPIGILAQQHYEFIKKYTQNTQIIVEIITGNMPQAHRRKALERIA-------HGQAHIIIGT-  382 (700)
Q Consensus       315 l~~~--~~G~Q--~alMaPTEILA~QH~~~~~~~~~~~~i~v~lLtg~~~~~er~~i~~~i~-------~G~~~iiIGT-  382 (700)
                      ..+.  ..-.+  +.||+==-=|=.|-+..|.++.+.+.   ...-+..+.++=++.|+...       .|+-.|+|-| 
T Consensus       345 ~k~~~~~~~~~p~v~fvvDR~eLd~Ql~~~~~~~~~~~~---~~~~~~eS~~~Lk~~L~~~~~sennPn~~k~g~~~t~I  421 (813)
T TIGR00348       345 RKLRKQKELKNPKVFFVVDRRELDEQLYKEFSSLKDLIK---DCAERIESIAELKELLEKNDESENNPNISKRGIIITTI  421 (813)
T ss_pred             HHHHHHHHHCCCEEEEEEECHHHHHHHHHHHHHHHHHCH---HHHHCCCCHHHHHHHHHHCCCCCCCCCCCCCCEEEEEE
T ss_conf             999874652698499997272778899999987642010---10420678889999875177645675535676799960


Q ss_pred             HHHC-------CC-----C---CCCCCCCEEEECCCCC--CCHHHH-----------HHHHHCCCCCCCEEECHHHHHHH
Q ss_conf             1201-------33-----4---5544441788521013--356889-----------98740256776101010132278
Q gi|254780945|r  383 HALF-------QD-----S---IQYYKLILVIVDEQHR--FGVQQR-----------LKLTQKATAPHVLLMTATPIPRT  434 (700)
Q Consensus       383 HAL~-------q~-----~---v~F~~LgLvViDEQHR--FGV~QR-----------~~L~~Kg~~ph~L~MtATPIPRT  434 (700)
                      |=+=       .|     .   +.+++==+||+||=||  ||-.|+           ..|.+.=.+++.+--|+|||   
T Consensus       422 qKF~~~~~~k~~e~~~~~~~~i~~~r~~vv~i~DEaHRsqyG~tqklhnGkfqtGla~~~~~~lknA~f~gFTGTPI---  498 (813)
T TIGR00348       422 QKFDDELLDKLKEEEEKFPESIIIDRKEVVVIIDEAHRSQYGKTQKLHNGKFQTGLAKALKKALKNASFFGFTGTPI---  498 (813)
T ss_pred             ECCCHHHHHHHHHHHHCCCCEEEEEECCEEEEEECCCCCCCCCCCCCCCCHHHHHHHHHHHHHCHHHHHHCCCCCCC---
T ss_conf             01040344536888743873689871608999706755535341100044135899999987431120101224776---


Q ss_pred             HHHHHHHCCCHH
Q ss_conf             999975201011
Q gi|254780945|r  435 LVLTSLGDIDIS  446 (700)
Q Consensus       435 Lal~~ygdldvS  446 (700)
                          .+-|+|.+
T Consensus       499 ----~~~d~~T~  506 (813)
T TIGR00348       499 ----SKKDRDTF  506 (813)
T ss_pred             ----CHHCCCCC
T ss_conf             ----53247766


No 174
>KOG0384 consensus
Probab=96.89  E-value=0.042  Score=36.05  Aligned_cols=324  Identities=19%  Similarity=0.304  Sum_probs=189.6

Q ss_pred             CCCHHHHHHHHHHHHHHCCCCCCEEEEEECCCCCHHH--HHHHHHHHHHH-HHCCEEEEEHHHHHHHHHHHHHHHHCCCC
Q ss_conf             6798899999999984100134307886214422369--99999733444-30545886127999999998621101457
Q gi|254780945|r  272 SPTKSQESAIKDILQDMSQKNRMLRILQGDVGSGKTL--VALIAMAAAVE-AGGQAVIMAPIGILAQQHYEFIKKYTQNT  348 (700)
Q Consensus       272 ~LT~~Q~~ai~eI~~Dl~~~~pM~RLLQGDVGSGKTi--VA~~A~l~~~~-~G~Q~alMaPTEILA~QH~~~~~~~~~~~  348 (700)
                      +|-+-|..-++=...--...  -|-.|--.-|=||||  |++++-+.-.. -..-..+.||-..++.= -+.|..|.   
T Consensus       370 ~LRDYQLeGlNWLl~~W~k~--~n~ILADEMGLGKTvQtI~FLs~l~~~~~~~GPfLvVvPLSTi~~W-~ref~~Wt---  443 (1373)
T KOG0384         370 ELRDYQLEGLNWLLYSWYKR--NNCILADEMGLGKTVQTITFLSYLFHSLQIHGPFLVVVPLSTITAW-EREFETWT---  443 (1373)
T ss_pred             CHHHHHHCCHHHHHHHHHCC--CCEEEECCCCCCCHHHHHHHHHHHHHHCCCCCCEEEEEECCCCHHH-HHHHHHHH---
T ss_conf             14465631328999988646--8647540025774013459999999845447886999864000789-99999875---


Q ss_pred             CCEEEEEECCCCHHHHHHHHHHHCCC-----CCEEEEECH-HHCCCCCCCCC--CCEEEECCCCCCCHHHHHHHHHCCC-
Q ss_conf             86589962464225667687762134-----754864111-20133455444--4178852101335688998740256-
Q gi|254780945|r  349 QIIVEIITGNMPQAHRRKALERIAHG-----QAHIIIGTH-ALFQDSIQYYK--LILVIVDEQHRFGVQQRLKLTQKAT-  419 (700)
Q Consensus       349 ~i~v~lLtg~~~~~er~~i~~~i~~G-----~~~iiIGTH-AL~q~~v~F~~--LgLvViDEQHRFGV~QR~~L~~Kg~-  419 (700)
                      +++|...+|++...+--..++-.-++     +.+++|-|- -++.+.-..++  -..++|||-||.  .-+..++-++- 
T Consensus       444 dmN~ivY~G~~~SR~~I~qYE~~~~~~~~~~KFn~LlTTyE~vLkDk~~L~~i~W~~~~vDEAHRL--KN~~s~Ly~~L~  521 (1373)
T KOG0384         444 DMNVIVYHGNLESRQLIRQYEFYHSSNTKKLKFNALLTTYEIVLKDKAELSKIPWRYLLVDEAHRL--KNDESKLYESLN  521 (1373)
T ss_pred             HCCEEEEECCHHHHHHHHHHHEEECCCCCEEEEEEEEHHHHHHHCCHHHHCCCCEEEEEECHHHHH--CCCHHHHHHHHH
T ss_conf             146588826656789998765045477751788764001898972688864575278974166550--650448999999


Q ss_pred             ---CCCCEEECHHHHHHHHH----HHHH-------------HCC------CHHHH-----------------CCCCCCCC
Q ss_conf             ---77610101013227899----9975-------------201------01111-----------------02355766
Q gi|254780945|r  420 ---APHVLLMTATPIPRTLV----LTSL-------------GDI------DISKI-----------------TEKPAGRK  456 (700)
Q Consensus       420 ---~ph~L~MtATPIPRTLa----l~~y-------------gdl------dvS~i-----------------~e~P~gR~  456 (700)
                         .-|-|..|-||.--++-    |--|             .+-      +|..+                 +-+|+   
T Consensus       522 ~f~~~hrlLiTGTPLQNsi~EL~sLL~Fl~P~kF~~~~ef~~e~~~~~e~~v~~Lq~~L~P~~LRRlKkDVEKSLp~---  598 (1373)
T KOG0384         522 QFKMNHRLLITGTPLQNSLKELWSLLHFLMPGKFDSWDEFLEEFDEETEEQVRKLQQILKPFLLRRLKKDVEKSLPP---  598 (1373)
T ss_pred             HHHHCCEEEEECCCCCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCC---
T ss_conf             86430757754785403199999998773755578678998873302388999999987689999988877522786---


Q ss_pred             CCEEEE-EECCCH-HHHHHHHH----HHHCCCCE---------------EEEEECCCCCCCC---CCCC---------H-
Q ss_conf             620799-970200-26899997----63103873---------------8999712012211---1210---------1-
Q gi|254780945|r  457 PIKTVI-IPINRI-DEVIERLK----VVLSEGKK---------------AYWICPQIEEKKE---SNFR---------S-  502 (700)
Q Consensus       457 ~I~T~~-~~~~~~-~~~~~~i~----~~l~~g~q---------------~y~VcPlIeese~---~~~~---------~-  502 (700)
                      ++.|.+ +....+ .+-|.+|-    ..|.+|..               |---|-||...|.   .+..         . 
T Consensus       599 K~E~IlrVels~lQk~yYk~ILtkN~~~LtkG~~g~~~~llNimmELkKccNHpyLi~gaee~~~~~~~~~~~d~~l~~l  678 (1373)
T KOG0384         599 KEETILRVELSDLQKQYYKAILTKNFSALTKGAKGSTPSLLNIMMELKKCCNHPYLIKGAEEKILGDFRDKMRDEALQAL  678 (1373)
T ss_pred             CCCEEEEEHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHCCHHHHHHHH
T ss_conf             31225654056789999999998539998366788980299999999986478000485888888765301467999999


Q ss_pred             -----------------------------HHHHHHHHHHHCC---CCEECCCCCCCHHHHHHHHHHHHCCCE---EEEEE
Q ss_conf             -----------------------------4666666686637---103120146998999999999755986---99998
Q gi|254780945|r  503 -----------------------------VVERFNSLHEHFT---SSIAIIHGRMSDIDKESVMDSFKNGTC---KLLIA  547 (700)
Q Consensus       503 -----------------------------~~~~~~~l~~~~~---~~v~~lHGkm~~~ek~~~m~~F~~g~~---~iLva  547 (700)
                                                   .......|.+++-   ....-|-|.++.+-..++|..|.+-..   =-|+|
T Consensus       679 I~sSGKlVLLDKLL~rLk~~GHrVLIFSQMVRmLDIL~eYL~~r~ypfQRLDGsvrgelRq~AiDhFnap~SddFvFLLS  758 (1373)
T KOG0384         679 IQSSGKLVLLDKLLPRLKEGGHRVLIFSQMVRMLDILAEYLSLRGYPFQRLDGSVRGELRQQAIDHFNAPDSDDFVFLLS  758 (1373)
T ss_pred             HHHCCCEEEHHHHHHHHHCCCCEEEEEHHHHHHHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHCCCCCCCCEEEEEE
T ss_conf             97168588698778998618945997199999999999999973886111468761688998887436999886499983


Q ss_pred             CHHHHCCCCCCCCCEEEEECHHHCCHHHHH-HHH-HCCCCCCCCEEEEEEECCCCCHHHHH
Q ss_conf             003410468887658998585254746887-730-11667898359999708889987999
Q gi|254780945|r  548 TTVIEVGIDVVDASIIIIENAEHFGLAQLH-QLR-GRVGRGEEISSCILLYHPPLSKNSYT  606 (700)
Q Consensus       548 TtviEVGvdvpna~~mvI~~aerfGLsqLH-QLR-GRVGRg~~~s~c~l~~~~~~~~~~~~  606 (700)
                      |--=-+|||..-|.+.||.++|-=-=+-|- |-| -|+|-...--.-=||+.+..-++-.+
T Consensus       759 TRAGGLGINLatADTVIIFDSDWNPQNDLQAqARaHRIGQkk~VnVYRLVTk~TvEeEilE  819 (1373)
T KOG0384         759 TRAGGLGINLATADTVIIFDSDWNPQNDLQAQARAHRIGQKKHVNVYRLVTKNTVEEEILE  819 (1373)
T ss_pred             CCCCCCCCCCCCCCEEEEECCCCCCCHHHHHHHHHHHHCCCCEEEEEEEECCCCHHHHHHH
T ss_conf             1567664022446669996899995057899998866066454789997457844899999


No 175
>PRK11192 ATP-dependent RNA helicase SrmB; Provisional
Probab=96.88  E-value=0.0052  Score=43.20  Aligned_cols=87  Identities=17%  Similarity=0.297  Sum_probs=69.2

Q ss_pred             HHHHHHHHHHHHHCCEEEEEHHHHHHHHHHHHHHHHCCCCCCEEEEEECCCCHHHHHHHHHHHCCCCCEEEEECHHHCCC
Q ss_conf             99999733444305458861279999999986211014578658996246422566768776213475486411120133
Q gi|254780945|r  309 VALIAMAAAVEAGGQAVIMAPIGILAQQHYEFIKKYTQNTQIIVEIITGNMPQAHRRKALERIAHGQAHIIIGTHALFQD  388 (700)
Q Consensus       309 VA~~A~l~~~~~G~Q~alMaPTEILA~QH~~~~~~~~~~~~i~v~lLtg~~~~~er~~i~~~i~~G~~~iiIGTHAL~q~  388 (700)
                      .+++.-+..-.+..|+.+-+.|---|..    +.++|...|+++..++|+++..+|.+++++..+|+++|+|.|. ++..
T Consensus       235 ~~~L~~ll~~~~~~k~iIF~~t~~~~~~----l~~~L~~~g~~~~~lhg~l~q~~R~~~l~~F~~g~~~vLVaTD-vaaR  309 (417)
T PRK11192        235 TALLCHLLKQEEVTRSIVFVRTRERVHE----LAGWLRKAGINCCYLEGEMVQKKRNEAIKRLTDGRVNVLVATD-VAAR  309 (417)
T ss_pred             HHHHHHHHHCCCCCCCEEEECCHHHHHH----HHHHHHCCCCCEEEECCCCCHHHHHHHHHHHHCCCCCEEEECC-HHHC
T ss_conf             9999999853476652153112466768----9886531488357540017999999999999769998999812-4346


Q ss_pred             CCCCCCCCEEEE
Q ss_conf             455444417885
Q gi|254780945|r  389 SIQYYKLILVIV  400 (700)
Q Consensus       389 ~v~F~~LgLvVi  400 (700)
                      ++.|.++.+||-
T Consensus       310 GiDi~~V~~VIn  321 (417)
T PRK11192        310 GIDIDDISHVIN  321 (417)
T ss_pred             CCCCCCCCEEEE
T ss_conf             777046988999


No 176
>PRK09183 transposase/IS protein; Provisional
Probab=96.87  E-value=0.0041  Score=44.02  Aligned_cols=129  Identities=16%  Similarity=0.107  Sum_probs=75.0

Q ss_pred             HHHCCCCCCHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH--HH--HHHHHCCCCCCCCCCHHHHHHHHH
Q ss_conf             86205699988999862045896565667999999987666666677776--55--554320357678775789999863
Q gi|254780945|r  193 LLQKKSFPSIAEAFNIIHNPRKAKDFEWTSPARERLAYDELLAGQIALLL--MR--KQFKKEIGIPINVEGKIAQKILRN  268 (700)
Q Consensus       193 ll~k~~L~s~~eAL~~IH~P~~~~dle~~~~ArkRLafeELl~~QL~l~~--~r--~~~~~~~~~~~~~~~~~~~~f~~~  268 (700)
                      .+++.+|+...+++..+        +  ..+....+.|+|+|..-+.-..  ++  +.....+.-.++... -++.|.-.
T Consensus        11 ~l~~LkL~~m~~~~~~~--------~--~~a~~~~~s~~e~L~~Ll~~E~~~R~~rr~~r~lk~A~fp~~k-tle~fDf~   79 (258)
T PRK09183         11 LCGQLQLESLISAAPAL--------A--QQAVDQEWSYMDFLEHLLHEEKLARHQRKQAMYTRMAAFPAVK-TFEEYDFT   79 (258)
T ss_pred             HHHHCCCHHHHHHHHHH--------H--HHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCC-CHHHCCCC
T ss_conf             99987831899999999--------9--9887639999999999999999999999999999977999987-77555654


Q ss_pred             CCCCCCHHHHHHHHHHHHHHCCCCCCEEEEEECCCCCHHHHHHHHHHHHHHHHCCEEEEEHHHHHHH
Q ss_conf             0246798899999999984100134307886214422369999997334443054588612799999
Q gi|254780945|r  269 IPFSPTKSQESAIKDILQDMSQKNRMLRILQGDVGSGKTLVALIAMAAAVEAGGQAVIMAPIGILAQ  335 (700)
Q Consensus       269 LPF~LT~~Q~~ai~eI~~Dl~~~~pM~RLLQGDVGSGKTiVA~~A~l~~~~~G~Q~alMaPTEILA~  335 (700)
                      .+=.+...|...+... .-  -...-|-++.|-+|+|||-.|..-...|+.+||.|.|.-=++++.+
T Consensus        80 ~~~~l~~~~i~~La~~-~f--i~~~~Nvil~G~~GtGKThLA~Alg~~A~~~G~~v~f~~~~~L~~~  143 (258)
T PRK09183         80 FATGAPQKQLQSLRSL-SF--IERNENIVLLGPSGVGKTHLAIALGYEAVRAGIKVRFTTAADLLLQ  143 (258)
T ss_pred             CCCCCCHHHHHHHHCC-CH--HHCCCCEEEECCCCCCHHHHHHHHHHHHHHCCCEEEEEEHHHHHHH
T ss_conf             6886238999988258-16--6558867998999986899999999999987993999789999999


No 177
>PRK08181 transposase; Validated
Probab=96.85  E-value=0.014  Score=39.94  Aligned_cols=131  Identities=17%  Similarity=0.101  Sum_probs=74.1

Q ss_pred             HHHHCCCCCCHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH--HH--HHHHHHCCCCCCCCCCHHHHHHHH
Q ss_conf             78620569998899986204589656566799999998766666667777--65--555432035767877578999986
Q gi|254780945|r  192 DLLQKKSFPSIAEAFNIIHNPRKAKDFEWTSPARERLAYDELLAGQIALL--LM--RKQFKKEIGIPINVEGKIAQKILR  267 (700)
Q Consensus       192 ~ll~k~~L~s~~eAL~~IH~P~~~~dle~~~~ArkRLafeELl~~QL~l~--~~--r~~~~~~~~~~~~~~~~~~~~f~~  267 (700)
                      .++++.+|+...+++..+=        +  ......+-|+|+|..-+.-.  .+  |+..+..+.-.++.. .-++.|.=
T Consensus        14 ~lLk~LkL~~~~~~~~~~~--------~--~a~~~~~s~~e~L~~Lle~E~~~R~~rr~~rrlk~A~fp~~-ktLe~fDf   82 (269)
T PRK08181         14 LLLNELRLPTIKTLWPQFA--------E--QADKEGWPAARFLAAIAEHEIAERARRRIERHLAEAHLPPG-KTLDSFDF   82 (269)
T ss_pred             HHHHHCCCHHHHHHHHHHH--------H--HHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCC-CCHHHCCC
T ss_conf             9999868528999999999--------9--99875999999999999999999999999999986897998-88654785


Q ss_pred             HCCCCCCHHHHHHHHHHHHHHCCCCCCEEEEEECCCCCHHHHHHHHHHHHHHHHCCEEEEEHHHHHHH
Q ss_conf             30246798899999999984100134307886214422369999997334443054588612799999
Q gi|254780945|r  268 NIPFSPTKSQESAIKDILQDMSQKNRMLRILQGDVGSGKTLVALIAMAAAVEAGGQAVIMAPIGILAQ  335 (700)
Q Consensus       268 ~LPF~LT~~Q~~ai~eI~~Dl~~~~pM~RLLQGDVGSGKTiVA~~A~l~~~~~G~Q~alMaPTEILA~  335 (700)
                      ..+=.+...|...+..-..-+  ...-|-++.|-.|+|||-+|..-...|+.+||.|.|.-=++.+.+
T Consensus        83 ~~~p~i~~~~i~~L~~~~~fi--~~~~Nvil~Gp~GtGKThLA~Alg~~A~~~G~~V~f~~~~~L~~~  148 (269)
T PRK08181         83 EAVPMISKAQVMALAAGDSWL--AKGANLLLFGPPGGGKSHLAAAIGLALIENGWRVLFTRTTDLVQK  148 (269)
T ss_pred             CCCCCCCHHHHHHHHCCCHHH--HCCCEEEEECCCCCCHHHHHHHHHHHHHHCCCEEEEEEHHHHHHH
T ss_conf             568998999999996567588--648708998999987889999999999987993999789999999


No 178
>KOG0386 consensus
Probab=96.85  E-value=0.0039  Score=44.14  Aligned_cols=291  Identities=19%  Similarity=0.300  Sum_probs=156.5

Q ss_pred             EEEEEECCCCCHHHHH--HHHHHHHHHHHC-CEEEEEHHHHHHHHHHHHHHHHCCCCCCEEEEEECCCCHHHHHHHHHHH
Q ss_conf             0788621442236999--999733444305-4588612799999999862110145786589962464225667687762
Q gi|254780945|r  295 LRILQGDVGSGKTLVA--LIAMAAAVEAGG-QAVIMAPIGILAQQHYEFIKKYTQNTQIIVEIITGNMPQAHRRKALERI  371 (700)
Q Consensus       295 ~RLLQGDVGSGKTiVA--~~A~l~~~~~G~-Q~alMaPTEILA~QH~~~~~~~~~~~~i~v~lLtg~~~~~er~~i~~~i  371 (700)
                      |-.|--..|=||||=.  +++-+.-...-. --.+.+|+-.|..=- ..|-+|-+    +|....+.-++.+|+.+...+
T Consensus       415 NGILADEMGLGKTIQtIsLitYLmE~K~~~GP~LvivPlstL~NW~-~Ef~kWaP----Sv~~i~YkGtp~~R~~l~~qi  489 (1157)
T KOG0386         415 NGILADEMGLGKTIQTISLITYLMEHKQMQGPFLIIVPLSTLVNWS-SEFPKWAP----SVQKIQYKGTPQQRSGLTKQQ  489 (1157)
T ss_pred             CCCCCHHCCCCHHHHHHHHHHHHHHHCCCCCCEEEECCCCCCCCCH-HHCCCCCC----CEEEEEEECCHHHHHHHHHHH
T ss_conf             4332001044148899999999999705679838954354567712-20243466----513565417888886678988


Q ss_pred             CCCCCEEEEEC-------HHHCCCCCCCCCCCEEEECCCCCCCHHHHH---HHHHCCCCCCCEEECHHHHHHHH----HH
Q ss_conf             13475486411-------120133455444417885210133568899---87402567761010101322789----99
Q gi|254780945|r  372 AHGQAHIIIGT-------HALFQDSIQYYKLILVIVDEQHRFGVQQRL---KLTQKATAPHVLLMTATPIPRTL----VL  437 (700)
Q Consensus       372 ~~G~~~iiIGT-------HAL~q~~v~F~~LgLvViDEQHRFGV~QR~---~L~~Kg~~ph~L~MtATPIPRTL----al  437 (700)
                      ..|+.+|++-|       -||++ ++.++   +.||||+||--=++-.   .|..-+..++-|..|-||+--.|    ||
T Consensus       490 r~gKFnVLlTtyEyiikdk~lLs-KI~W~---yMIIDEGHRmKNa~~KLt~~L~t~y~~q~RLLLTGTPLQN~LpELWaL  565 (1157)
T KOG0386         490 RHGKFNVLLTTYEYIIKDKALLS-KISWK---YMIIDEGHRMKNAICKLTDTLNTHYRAQRRLLLTGTPLQNNLPELWAL  565 (1157)
T ss_pred             HCCCCEEEEEEHHHHCCCHHHHH-CCCCC---CEEECCCCCCCCHHHHHHHHHHCCCCCHHHHHHCCCHHHHCCHHHHHH
T ss_conf             60011034200877537999984-46986---356322222451255788775025521215653288322211778999


Q ss_pred             H--------------------HH---HC-CCHH------HH--------------------CCCCCCCCCCEEEEEECCC
Q ss_conf             9--------------------75---20-1011------11--------------------0235576662079997020
Q gi|254780945|r  438 T--------------------SL---GD-IDIS------KI--------------------TEKPAGRKPIKTVIIPINR  467 (700)
Q Consensus       438 ~--------------------~y---gd-ldvS------~i--------------------~e~P~gR~~I~T~~~~~~~  467 (700)
                      -                    -|   |+ .+++      +|                    .++| +....+-++..+.-
T Consensus       566 LNFlLP~IFnS~~~FeqWFN~PFantGek~eLteEEtlLIIrRLHkVLRPFlLRRlKkeVE~~LP-dKve~viKC~mSal  644 (1157)
T KOG0386         566 LNFLLPNIFNSCKAFEQWFNQPFANTGEKVELTEEETLLIIRRLHKVLRPFLLRRLKKEVEQELP-DKVEDVIKCDMSAL  644 (1157)
T ss_pred             HHHHCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC-HHHHHHHHEEHHHH
T ss_conf             98763521104757989861266643873125522789999998876647888765677766473-45547630202056


Q ss_pred             HHHHHHHHHHHHCCCCEEE---------------------------EEECCCCCCCCC-----CCCHHHHHHHHHH----
Q ss_conf             0268999976310387389---------------------------997120122111-----2101466666668----
Q gi|254780945|r  468 IDEVIERLKVVLSEGKKAY---------------------------WICPQIEEKKES-----NFRSVVERFNSLH----  511 (700)
Q Consensus       468 ~~~~~~~i~~~l~~g~q~y---------------------------~VcPlIeese~~-----~~~~~~~~~~~l~----  511 (700)
                      -..+|..+.    +.++.+                           ++.+-||++=..     |+--+.-.++.|.    
T Consensus       645 Qq~lY~~m~----~~g~l~~d~~~g~~g~k~L~N~imqLRKiCNHP~lf~~ve~~~~~~~~~~dL~R~sGKfELLDRiLP  720 (1157)
T KOG0386         645 QQSLYKQMQ----NKGQLLKDTAKGKKGYKPLFNTIMQLRKLCNHPYLFANVENSYTLHYDIKDLVRVSGKFELLDRILP  720 (1157)
T ss_pred             HHHHHHHHH----HCCCCCCCCHHCCCCCHHHHHHHHHHHHHCCCCHHHHHHCCCCCCCCCHHHHHHHCCHHHHHHHHHH
T ss_conf             676318888----4798876721003464115457699998547721544430342200270578773147999976608


Q ss_pred             -----------------------HHCC--C-CEECCCCCCCHHHHHHHHHHHHCCCEE---EEEECHHHHCCCCCCCCCE
Q ss_conf             -----------------------6637--1-031201469989999999997559869---9998003410468887658
Q gi|254780945|r  512 -----------------------EHFT--S-SIAIIHGRMSDIDKESVMDSFKNGTCK---LLIATTVIEVGIDVVDASI  562 (700)
Q Consensus       512 -----------------------~~~~--~-~v~~lHGkm~~~ek~~~m~~F~~g~~~---iLvaTtviEVGvdvpna~~  562 (700)
                                             .++.  . +.-.+-|.-+.+|.-..++.|..-..+   .|.||--=-.|+|.--|.+
T Consensus       721 KLkatgHRVLlF~qMTrlmdimEdyL~~~~~kYlRLDG~TK~~eRg~ll~~FN~Pds~yf~FllstragglglNlQtadt  800 (1157)
T KOG0386         721 KLKATGHRVLLFSQMTRLMDILEDYLQIREYKYLRLDGQTKVEERGDLLEIFNAPDSPYFIFLLSTRAGGLGLNLQTADT  800 (1157)
T ss_pred             HHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHEEEECCCCCHHHHHHHHHHHCCCCCCEEEEEEEECCCCCCCCHHHCCE
T ss_conf             87732760115777888899999998662421244158766146899999715999862564332102555403211352


Q ss_pred             EEEECHHHCCHH--HHHHHHHCCCCCCCCEEEEEEECCC
Q ss_conf             998585254746--8877301166789835999970888
Q gi|254780945|r  563 IIIENAEHFGLA--QLHQLRGRVGRGEEISSCILLYHPP  599 (700)
Q Consensus       563 mvI~~aerfGLs--qLHQLRGRVGRg~~~s~c~l~~~~~  599 (700)
                      .||.+.|-----  |---+--|+|--...-...|++-.+
T Consensus       801 viifdsdwnp~~d~qaqdrahrigq~~evRv~rl~tv~s  839 (1157)
T KOG0386         801 VIIFDSDWNPHQDLQAQDRAHRIGQKKEVRVLRLITVNS  839 (1157)
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHHCHHHEEEEEEEHHHH
T ss_conf             788658888316799999999750212301123100407


No 179
>PRK04537 ATP-dependent RNA helicase RhlB; Provisional
Probab=96.80  E-value=0.011  Score=40.51  Aligned_cols=78  Identities=17%  Similarity=0.327  Sum_probs=67.0

Q ss_pred             HHHHCCEEEEEHHHHHHHHHHHHHHHHCCCCCCEEEEEECCCCHHHHHHHHHHHCCCCCEEEEECHHHCCCCCCCCCCCE
Q ss_conf             44305458861279999999986211014578658996246422566768776213475486411120133455444417
Q gi|254780945|r  318 VEAGGQAVIMAPIGILAQQHYEFIKKYTQNTQIIVEIITGNMPQAHRRKALERIAHGQAHIIIGTHALFQDSIQYYKLIL  397 (700)
Q Consensus       318 ~~~G~Q~alMaPTEILA~QH~~~~~~~~~~~~i~v~lLtg~~~~~er~~i~~~i~~G~~~iiIGTHAL~q~~v~F~~LgL  397 (700)
                      -..+.|+.+-+.|--.++..++.++    ..++++..|+|.++.++|..++++.++|+++|+|.|- +...++.|.++.+
T Consensus       254 ~~~~~k~IIF~nT~~~ve~l~~~L~----~~g~~v~~LHG~lsQ~eR~~~L~~Fk~G~~~VLVaTD-VAARGIDIp~V~~  328 (574)
T PRK04537        254 RSEGARTMVFVNTKAFVERVARTLE----RHGYRVGVLSGDVPQKKRESLLNRFQKGQLEILVATD-VAARGLHIDGVKY  328 (574)
T ss_pred             HCCCCCCEEECCHHHHHHHHHHHHH----HCCCCEEEEECCCCHHHHHHHHHHHHCCCCCEEEECC-CCCCCCCCCCCCE
T ss_conf             2677651153341899999999999----7799689970999999999999999769997997735-0023357146997


Q ss_pred             EEE
Q ss_conf             885
Q gi|254780945|r  398 VIV  400 (700)
Q Consensus       398 vVi  400 (700)
                      ||-
T Consensus       329 VIN  331 (574)
T PRK04537        329 VYN  331 (574)
T ss_pred             EEE
T ss_conf             999


No 180
>PRK04837 ATP-dependent RNA helicase RhlB; Provisional
Probab=96.78  E-value=0.0089  Score=41.36  Aligned_cols=77  Identities=22%  Similarity=0.277  Sum_probs=64.1

Q ss_pred             HHHCCEEEEEHHHHHHHHHHHHHHHHCCCCCCEEEEEECCCCHHHHHHHHHHHCCCCCEEEEECHHHCCCCCCCCCCCEE
Q ss_conf             43054588612799999999862110145786589962464225667687762134754864111201334554444178
Q gi|254780945|r  319 EAGGQAVIMAPIGILAQQHYEFIKKYTQNTQIIVEIITGNMPQAHRRKALERIAHGQAHIIIGTHALFQDSIQYYKLILV  398 (700)
Q Consensus       319 ~~G~Q~alMaPTEILA~QH~~~~~~~~~~~~i~v~lLtg~~~~~er~~i~~~i~~G~~~iiIGTHAL~q~~v~F~~LgLv  398 (700)
                      ....|+.+-+.|---|+    .+.++|...|+++..|+|.++.++|.+++++.++|+++|+|.|- +...++.|.++.+|
T Consensus       254 ~~~~k~iIF~nt~~~~~----~l~~~L~~~g~~~~~lhg~~~q~~R~~~l~~F~~g~~~vLVaTD-vaaRGLDi~~V~~V  328 (423)
T PRK04837        254 EWPDRAIIFANTKHRCE----EIWGHLAADGHRVGLLTGDVPQKKRLRILEQFTRGDLDILVATD-VAARGLHIPDVTHV  328 (423)
T ss_pred             HCCCCEEEECCHHHHHH----HHHHHHHHCCCCEEEECCCCCHHHHHHHHHHHHCCCCCEEEEHH-HHHCCCCCCCCCEE
T ss_conf             08874688616288899----99999976598178722545799999999999769998998700-43277772679889


Q ss_pred             EE
Q ss_conf             85
Q gi|254780945|r  399 IV  400 (700)
Q Consensus       399 Vi  400 (700)
                      |-
T Consensus       329 In  330 (423)
T PRK04837        329 FN  330 (423)
T ss_pred             EE
T ss_conf             99


No 181
>smart00490 HELICc helicase superfamily c-terminal domain.
Probab=96.75  E-value=0.0028  Score=45.32  Aligned_cols=63  Identities=19%  Similarity=0.355  Sum_probs=54.5

Q ss_pred             HHHHHCCCCCCEEEEEECCCCHHHHHHHHHHHCCCCCEEEEECHHHCCCCCCCCCCCEEEECCC
Q ss_conf             6211014578658996246422566768776213475486411120133455444417885210
Q gi|254780945|r  340 FIKKYTQNTQIIVEIITGNMPQAHRRKALERIAHGQAHIIIGTHALFQDSIQYYKLILVIVDEQ  403 (700)
Q Consensus       340 ~~~~~~~~~~i~v~lLtg~~~~~er~~i~~~i~~G~~~iiIGTHAL~q~~v~F~~LgLvViDEQ  403 (700)
                      .+.++|...|+++..++|.++.++|+++++...+|+++|+|+|- ++.+++.+.+...||+-+-
T Consensus         2 ~l~~~l~~~g~~~~~i~g~~~~~~R~~~~~~f~~~~~~ilv~t~-~~~~Gidl~~~~~vI~~~~   64 (82)
T smart00490        2 ELAELLKELGIKVARLHGGLSQEEREEILEKFNNGKIKVLVATD-VAERGLDLPGVDLVIIYDL   64 (82)
T ss_pred             HHHHHHHHCCCCEEEEECCCCHHHHHHHHHHHHCCCCEEEEEEE-EEEEECCCCCCCEEEEECC
T ss_conf             78999988899199998969999999999999879971999950-2421148988999999789


No 182
>PRK10590 ATP-dependent RNA helicase RhlE; Provisional
Probab=96.68  E-value=0.015  Score=39.66  Aligned_cols=84  Identities=17%  Similarity=0.193  Sum_probs=67.5

Q ss_pred             HHHHHHHHHHCCEEEEEHHHHHHHHHHHHHHHHCCCCCCEEEEEECCCCHHHHHHHHHHHCCCCCEEEEECHHHCCCCCC
Q ss_conf             99733444305458861279999999986211014578658996246422566768776213475486411120133455
Q gi|254780945|r  312 IAMAAAVEAGGQAVIMAPIGILAQQHYEFIKKYTQNTQIIVEIITGNMPQAHRRKALERIAHGQAHIIIGTHALFQDSIQ  391 (700)
Q Consensus       312 ~A~l~~~~~G~Q~alMaPTEILA~QH~~~~~~~~~~~~i~v~lLtg~~~~~er~~i~~~i~~G~~~iiIGTHAL~q~~v~  391 (700)
                      +..+..-.+..|+.+-+.|---|+.-+    ++|...|+++..++|.++..+|..++++.++|+++|+|.|. +...++.
T Consensus       236 L~~ll~~~~~~~~iIF~~tk~~a~~l~----~~L~~~g~~~~~lHg~~sq~~R~~~l~~F~~g~~~vLVaTD-vaaRGiD  310 (457)
T PRK10590        236 LSQMIGKGNWQQVLVFTRTKHGANHLA----EQLNKDGIRSAAIHGNKSQGARTRALADFKSGDIRVLVATD-IAARGLD  310 (457)
T ss_pred             HHHHHHHCCCCCEEEEECHHHHHHHHH----HHHHHCCCCCEEEECCCCHHHHHHHHHHHHCCCCCEEEECC-CCCCCCC
T ss_conf             999986158663358841199999999----99855699823232478999999999999869982999577-0115566


Q ss_pred             CCCCCEEEE
Q ss_conf             444417885
Q gi|254780945|r  392 YYKLILVIV  400 (700)
Q Consensus       392 F~~LgLvVi  400 (700)
                      |.++.+||-
T Consensus       311 i~~V~~VIn  319 (457)
T PRK10590        311 IEELPHVVN  319 (457)
T ss_pred             CCCCCEEEE
T ss_conf             356887999


No 183
>pfam00271 Helicase_C Helicase conserved C-terminal domain. The Prosite family is restricted to DEAD/H helicases, whereas this domain family is found in a wide variety of helicases and helicase related proteins. It may be that this is not an autonomously folding unit, but an integral part of the helicase.
Probab=96.62  E-value=0.0046  Score=43.58  Aligned_cols=59  Identities=20%  Similarity=0.344  Sum_probs=52.5

Q ss_pred             HCCCCCCEEEEEECCCCHHHHHHHHHHHCCCCCEEEEECHHHCCCCCCCCCCCEEEECCC
Q ss_conf             014578658996246422566768776213475486411120133455444417885210
Q gi|254780945|r  344 YTQNTQIIVEIITGNMPQAHRRKALERIAHGQAHIIIGTHALFQDSIQYYKLILVIVDEQ  403 (700)
Q Consensus       344 ~~~~~~i~v~lLtg~~~~~er~~i~~~i~~G~~~iiIGTHAL~q~~v~F~~LgLvViDEQ  403 (700)
                      ++...|+++..++|+++.++|++++++.++|+.+++|.|- .+.+++.+.+.-.||+-.-
T Consensus         2 ~l~~~g~~~~~i~g~~~~~~R~~~~~~f~~~~~~ilv~t~-~~~~Gid~~~~~~vi~~~~   60 (78)
T pfam00271         2 LLRKPGIKVARLHGGLSQEEREEILEDFRNGKSKVLVATD-VAGRGIDLPDVNVVINYDL   60 (78)
T ss_pred             CHHHCCCCEEEEECCCCHHHHHHHHHHHHCCCCEEEEEEC-CCCCCCCCCCCCEEEEECC
T ss_conf             4556898599986979999999999999879973999925-6525677878999999789


No 184
>PRK06526 transposase; Provisional
Probab=96.61  E-value=0.031  Score=37.07  Aligned_cols=130  Identities=15%  Similarity=0.101  Sum_probs=77.5

Q ss_pred             HHHHCCCCCCHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----HHHHHCCCCCCCCCCHHHHHHHH
Q ss_conf             78620569998899986204589656566799999998766666667777655----55432035767877578999986
Q gi|254780945|r  192 DLLQKKSFPSIAEAFNIIHNPRKAKDFEWTSPARERLAYDELLAGQIALLLMR----KQFKKEIGIPINVEGKIAQKILR  267 (700)
Q Consensus       192 ~ll~k~~L~s~~eAL~~IH~P~~~~dle~~~~ArkRLafeELl~~QL~l~~~r----~~~~~~~~~~~~~~~~~~~~f~~  267 (700)
                      .++++.+|+.+.+++..+=.          .+....+-|+|++..-+.-....    +..+..+.-.++.... ++.|.-
T Consensus         7 ~llr~LrL~~ma~~~~~~~~----------~a~~~~~s~~e~L~~Lle~E~~~R~~rr~~rrlk~A~fp~~kt-Le~fd~   75 (254)
T PRK06526          7 YLTRALKAPSLAGAVERLAE----------RARAESWSHEEFLAACLQREVAARESHGGEGRIRAARFPSRKS-LEEFDF   75 (254)
T ss_pred             HHHHHCCHHHHHHHHHHHHH----------HHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCC-HHHCCC
T ss_conf             99998383789999999998----------8876599999999999999999999989999999779799889-876786


Q ss_pred             HCCCCCCHHHHHHHHHHHHHHCCCCCCEEEEEECCCCCHHHHHHHHHHHHHHHHCCEEEEEHHHHHHH
Q ss_conf             30246798899999999984100134307886214422369999997334443054588612799999
Q gi|254780945|r  268 NIPFSPTKSQESAIKDILQDMSQKNRMLRILQGDVGSGKTLVALIAMAAAVEAGGQAVIMAPIGILAQ  335 (700)
Q Consensus       268 ~LPF~LT~~Q~~ai~eI~~Dl~~~~pM~RLLQGDVGSGKTiVA~~A~l~~~~~G~Q~alMaPTEILA~  335 (700)
                      .-.=.+...|..-+.... -  -...-|-++-|..|+|||-+|..-...|+.+||.|.++-=++++.+
T Consensus        76 ~~~~~l~~~~i~~La~~~-f--i~~~~Nvil~G~~GtGKThLA~Alg~~A~~~G~~v~f~~~~~L~~~  140 (254)
T PRK06526         76 DHQRSLKRDTIAHLGTLD-F--VTGKENVVFLGPPGTGKTHLAIGLGIRACQAGHRVLFATAAQWVAR  140 (254)
T ss_pred             CCCCCCCHHHHHHHHCCC-H--HHCCCCEEEECCCCCCHHHHHHHHHHHHHHCCCCEEEEEHHHHHHH
T ss_conf             567898999999986371-7--7658878998999986899999999999986996799877999999


No 185
>PRK08116 hypothetical protein; Validated
Probab=96.61  E-value=0.0067  Score=42.33  Aligned_cols=65  Identities=23%  Similarity=0.287  Sum_probs=47.0

Q ss_pred             CCCCHHHHHHHHHH---HHHHCCCCCCE--EEEEECCCCCHHHHHHHHHHHHHHHHCCEEEEEHHHHHHH
Q ss_conf             46798899999999---98410013430--7886214422369999997334443054588612799999
Q gi|254780945|r  271 FSPTKSQESAIKDI---LQDMSQKNRML--RILQGDVGSGKTLVALIAMAAAVEAGGQAVIMAPIGILAQ  335 (700)
Q Consensus       271 F~LT~~Q~~ai~eI---~~Dl~~~~pM~--RLLQGDVGSGKTiVA~~A~l~~~~~G~Q~alMaPTEILA~  335 (700)
                      |..+++|++|.+--   .++.......+  =+|.|++|+|||-.|...+-.+++.|+.|.++-=.++|.+
T Consensus        81 ~~~~~~~~~a~~~a~~Y~~~f~~~~~~~~GLll~G~~GtGKThLa~aIa~~l~~~g~~V~~~~~~~ll~~  150 (262)
T PRK08116         81 WLFRKGSEKAYKVAVKYVKKFEEMKKESVGLLLWGSPGNGKTYLAAAIANELIEKGVPVVFVNVPELLNR  150 (262)
T ss_pred             CCCCCCHHHHHHHHHHHHHHHHHHCCCCCEEEEECCCCCCHHHHHHHHHHHHHHCCCEEEEEEHHHHHHH
T ss_conf             5689525999999999999898736468618998989998999999999999987993999889999999


No 186
>PRK11634 ATP-dependent RNA helicase DeaD; Provisional
Probab=96.60  E-value=0.011  Score=40.51  Aligned_cols=98  Identities=23%  Similarity=0.323  Sum_probs=73.1

Q ss_pred             HHHHHHHHHHHHHHCCEEEEEHHHHHHHHHHHHHHHHCCCCCCEEEEEECCCCHHHHHHHHHHHCCCCCEEEEECHHHCC
Q ss_conf             99999973344430545886127999999998621101457865899624642256676877621347548641112013
Q gi|254780945|r  308 LVALIAMAAAVEAGGQAVIMAPIGILAQQHYEFIKKYTQNTQIIVEIITGNMPQAHRRKALERIAHGQAHIIIGTHALFQ  387 (700)
Q Consensus       308 iVA~~A~l~~~~~G~Q~alMaPTEILA~QH~~~~~~~~~~~~i~v~lLtg~~~~~er~~i~~~i~~G~~~iiIGTHAL~q  387 (700)
                      .-|++-.+ ......++.+-+.|---+..    +...|...|++++.|+|.++..+|..++++.++|+++|+|.|- +..
T Consensus       233 ~~aL~~~L-~~~~~~~~IIF~~Tk~~~~~----l~~~L~~~g~~~~~LHgdm~q~~R~~~l~~Fr~g~~~ILVaTD-vaA  306 (629)
T PRK11634        233 NEALVRFL-EAEDFDAAIIFVRTKNATLE----VAEALERNGYNSAALNGDMNQALREQTLERLKDGRLDILIATD-VAA  306 (629)
T ss_pred             HHHHHHHH-HHCCCCEEEEEEECHHHHHH----HHHHHHHCCCCEEEEECCCCHHHHHHHHHHHHCCCCCEEEECC-CCC
T ss_conf             99999998-61588848999822788999----9999997699657656899999999999999759998898786-210


Q ss_pred             CCCCCCCCCEEEE--------CCCCCCCHHHH
Q ss_conf             3455444417885--------21013356889
Q gi|254780945|r  388 DSIQYYKLILVIV--------DEQHRFGVQQR  411 (700)
Q Consensus       388 ~~v~F~~LgLvVi--------DEQHRFGV~QR  411 (700)
                      .++.+.++.+||-        +=-||=|=.=|
T Consensus       307 RGLDi~~V~~VINyDlP~d~e~YVHRiGRTGR  338 (629)
T PRK11634        307 RGLDVERISLVVNYDIPMDSESYVHRIGRTGR  338 (629)
T ss_pred             CCCCCCCCCEEEEECCCCCHHHCCCCCCCCCC
T ss_conf             55772568889996898974340102583316


No 187
>cd04478 RPA2_DBD_D RPA2_DBD_D: A subfamily of OB folds corresponding to the OB fold of the central ssDNA-binding domain (DBD)-D of human RPA2 (also called RPA32). RPA2 is a subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). The major DNA binding activity of RPA is associated with RPA1 DBD-A and DBD-B; RPA2 DBD-D is a weak ssDNA-binding domain. RPA2 DBD-D is also involved in trimerization. The ssDNA binding mechanism is believed to be multistep and to involve conformational change. N-terminal to human RPA2 DBD-D is a domain containing all the known phosphorylation sites of RPA. Human RPA2 is phosphorylated in a cell cycle dependent manner in response to DNA dam
Probab=96.54  E-value=0.027  Score=37.56  Aligned_cols=69  Identities=19%  Similarity=0.271  Sum_probs=51.5

Q ss_pred             EEEEEEEEEEEEECCCCCCEEEEEEECCCCEEEEEEE-CCCH--HHHHHHCCCCCEEEEEEEEEECCCEEEEECCE
Q ss_conf             9999999897542158983389999818936999995-1887--89987328988899998997318779997786
Q gi|254780945|r   70 VTITGYISQHSSFQLQKRRPYKILLNDGTGEITLLFF-YRKT--EMLKNVFFEGRKITVTGKIKKLKNRIIMVHPH  142 (700)
Q Consensus        70 vti~g~V~~~~~~~~~~r~~~~v~v~D~tg~i~lvfF-n~~~--~yl~k~lk~G~~v~vsGKv~~~~~~~qi~hPe  142 (700)
                      +++.|.|.++....    ......+.|+||.|.+++| +...  ..-...+++|..+.|+|+++.|++..++.--.
T Consensus         2 V~~VG~V~~v~~~~----t~~~y~idDgTG~i~~~~w~~~~~~~~~~~~~i~~g~YVrV~G~lk~f~~~~~I~~~~   73 (95)
T cd04478           2 VTLVGVVRNVEEQS----TNITYTIDDGTGTIEVRQWLDDDNDDSSEVEPIEEGTYVRVFGNLKSFQGKKSIMAFS   73 (95)
T ss_pred             EEEEEEEEEEEECC----CEEEEEEECCCCCEEEEEECCCCCCCCCCCCCCCCCCEEEEEEEEEEECCEEEEEEEE
T ss_conf             89999999877725----5799999879873999996377876422244332698999999980028913799999


No 188
>COG1199 DinG Rad3-related DNA helicases [Transcription / DNA replication, recombination, and repair]
Probab=96.50  E-value=0.012  Score=40.48  Aligned_cols=170  Identities=18%  Similarity=0.255  Sum_probs=99.1

Q ss_pred             CCCCEEECHHHHHHHHHHHHHHCCCHHHHC-----CCCCCCC-----CCEEEEEEC---CCHHHHHHHHHHHHCC-CCEE
Q ss_conf             776101010132278999975201011110-----2355766-----620799970---2002689999763103-8738
Q gi|254780945|r  420 APHVLLMTATPIPRTLVLTSLGDIDISKIT-----EKPAGRK-----PIKTVIIPI---NRIDEVIERLKVVLSE-GKKA  485 (700)
Q Consensus       420 ~ph~L~MtATPIPRTLal~~ygdldvS~i~-----e~P~gR~-----~I~T~~~~~---~~~~~~~~~i~~~l~~-g~q~  485 (700)
                      ...++.||||==|......+-|-.......     .-|....     -|.|..-..   +...++...+.+.+.. ++.+
T Consensus       403 ~~~~vl~SaTL~~~~~f~~~~~~~~~~~~~~~~~~~spf~~~~~~~~~v~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~  482 (654)
T COG1199         403 VASVVLTSATLSPLDSFSSLLGLLGLEEKLRFLSLPSPFNYEEQGQLYVPTDLPEPREPELLAKLAAYLREILKASPGGV  482 (654)
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHCCCCCCCEEECCCCCCCHHHCCEEECCCCCCCCCCHHHHHHHHHHHHHHHHHCCCCE
T ss_conf             57599982776843559998602565312302147998676553114134445788874799999999999997479988


Q ss_pred             EEEECCCCCCCCCCCCHHHHHHHHHHHHCCCCEECCCCCCCHHHHHHHHHHHHCCCE-EEEEECHHHHCCCCCCCCCE--
Q ss_conf             999712012211121014666666686637103120146998999999999755986-99998003410468887658--
Q gi|254780945|r  486 YWICPQIEEKKESNFRSVVERFNSLHEHFTSSIAIIHGRMSDIDKESVMDSFKNGTC-KLLIATTVIEVGIDVVDASI--  562 (700)
Q Consensus       486 y~VcPlIeese~~~~~~~~~~~~~l~~~~~~~v~~lHGkm~~~ek~~~m~~F~~g~~-~iLvaTtviEVGvdvpna~~--  562 (700)
                      .|.||--+        -....++.++.....   +.+--++..++++.+++|+++.- -+||+|.-.-=|||+|...+  
T Consensus       483 lvlF~Sy~--------~l~~~~~~~~~~~~~---~~v~~q~~~~~~~~l~~f~~~~~~~~lv~~gsf~EGVD~~g~~l~~  551 (654)
T COG1199         483 LVLFPSYE--------YLKRVAERLKDERST---LPVLTQGEDEREELLEKFKASGEGLILVGGGSFWEGVDFPGDALRL  551 (654)
T ss_pred             EEEECCHH--------HHHHHHHHHHHCCCC---CEEECCCCCCHHHHHHHHHHCCCCEEEEEECCEECCEECCCCCEEE
T ss_conf             99917899--------999999986511645---3344568784699999997147864999723310315168876579


Q ss_pred             EEE-----------------ECHHHCC------------HHHHHHHHHCCCCC-CCCEEEEEEECCCCC
Q ss_conf             998-----------------5852547------------46887730116678-983599997088899
Q gi|254780945|r  563 III-----------------ENAEHFG------------LAQLHQLRGRVGRG-EEISSCILLYHPPLS  601 (700)
Q Consensus       563 mvI-----------------~~aerfG------------LsqLHQLRGRVGRg-~~~s~c~l~~~~~~~  601 (700)
                      .||                 +..+++|            +--+-|==|||=|+ +..|+++|+ +.-..
T Consensus       552 vvI~~lPfp~p~dp~~~~r~~~~~~~g~~~f~~~~l~~A~~~l~QavGRlIR~~~D~G~ivll-D~R~~  619 (654)
T COG1199         552 VVIVGLPFPNPDDPLLKARLEFLKRLGGDPFEEFYLPPAVIKLRQAVGRLIRSEDDRGVIVLL-DKRYA  619 (654)
T ss_pred             EEEEECCCCCCCCHHHHHHHHHHHHHCCCCCCEEEHHHHHHHHHHHHCCCCCCCCCCEEEEEE-CCCCC
T ss_conf             999826899899899999999998726997103458999999998743010478871699997-15332


No 189
>PRK05298 excinuclease ABC subunit B; Provisional
Probab=96.49  E-value=0.016  Score=39.39  Aligned_cols=89  Identities=16%  Similarity=0.338  Sum_probs=73.8

Q ss_pred             HHHHHHHHCCEEEEEHHHHHHHHHHHHHHHHCCCCCCEEEEEECCCCHHHHHHHHHHHCCCCCEEEEECHHHCCCCCCCC
Q ss_conf             73344430545886127999999998621101457865899624642256676877621347548641112013345544
Q gi|254780945|r  314 MAAAVEAGGQAVIMAPIGILAQQHYEFIKKYTQNTQIIVEIITGNMPQAHRRKALERIAHGQAHIIIGTHALFQDSIQYY  393 (700)
Q Consensus       314 ~l~~~~~G~Q~alMaPTEILA~QH~~~~~~~~~~~~i~v~lLtg~~~~~er~~i~~~i~~G~~~iiIGTHAL~q~~v~F~  393 (700)
                      +-..++.|..+.+..=|-=.|    +.+..+|...|++|..|++...+-||-+|+.++..|+.|++||-. |+-|++...
T Consensus       439 i~~~~~~~er~LvttlTkkma----EdLt~yl~~~~ik~~YlHs~i~t~eR~eIl~~LR~G~~DVlVGIN-LLREGLDlP  513 (657)
T PRK05298        439 IRKRVAKGERVLVTTLTKRMA----EDLTDYLKELGIKVRYLHSDIDTLERVEIIRDLRLGEFDVLVGIN-LLREGLDIP  513 (657)
T ss_pred             HHHHHHCCCEEEEEECHHHHH----HHHHHHHHHCCCEEEEEECCCCHHHHHHHHHHHHCCCCCEEEEEC-HHHCCCCCC
T ss_conf             999963697699995459899----999999996798079962666188999999998588875897500-220457876


Q ss_pred             CCCEEEECCCCCCC
Q ss_conf             44178852101335
Q gi|254780945|r  394 KLILVIVDEQHRFG  407 (700)
Q Consensus       394 ~LgLvViDEQHRFG  407 (700)
                      -.+||-|=.-.+=|
T Consensus       514 EVSLVaILDADKeG  527 (657)
T PRK05298        514 EVSLVAILDADKEG  527 (657)
T ss_pred             CEEEEEEEECCCCC
T ss_conf             13579887068522


No 190
>cd00009 AAA The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC, RecA-like, VirD4-like, PilT-like, and SF1/2 helicases. Members of the AAA+ ATPases function as molecular chaperons, ATPase subunits of proteases, helicases, or nucleic-acid stimulated ATPases. The AAA+ proteins contain several distinct features in addition to the conserved alpha-beta-alpha core domain structure and the Walker A and B motifs of the P-loop NTPases.
Probab=96.48  E-value=0.014  Score=39.89  Aligned_cols=54  Identities=22%  Similarity=0.276  Sum_probs=38.0

Q ss_pred             HHHHHHHHHHHHHCCCCCCEEEEEECCCCCHHHHHHHHHHHHHHHHCCEEEEEH
Q ss_conf             899999999984100134307886214422369999997334443054588612
Q gi|254780945|r  276 SQESAIKDILQDMSQKNRMLRILQGDVGSGKTLVALIAMAAAVEAGGQAVIMAP  329 (700)
Q Consensus       276 ~Q~~ai~eI~~Dl~~~~pM~RLLQGDVGSGKTiVA~~A~l~~~~~G~Q~alMaP  329 (700)
                      +|.+.+.++...+..+.+-+=||.|-.|+|||.+|-..+-.....++-+...-.
T Consensus         2 ~~~~~~~~l~~~~~~~~~~~ill~GppGtGKT~la~~ia~~~~~~~~~~~~~~~   55 (151)
T cd00009           2 GQEEAIEALREALELPPPKNLLLYGPPGTGKTTLARAIANELFRPGAPFLYLNA   55 (151)
T ss_pred             CCHHHHHHHHHHHHCCCCCEEEEECCCCCCHHHHHHHHHHHHCCCCCCEEEEEH
T ss_conf             857999999999818799808998999988659999999971213798278547


No 191
>PRK08512 consensus
Probab=96.44  E-value=0.047  Score=35.73  Aligned_cols=81  Identities=23%  Similarity=0.273  Sum_probs=50.6

Q ss_pred             HHHHHHCCCC--EECCCCCCCHHHH-HHHHHHHHCCCEEEEEECHHHHCCCCCCCCCEEEEE----CHHHCCHHHHHHHH
Q ss_conf             6668663710--3120146998999-999999755986999980034104688876589985----85254746887730
Q gi|254780945|r  508 NSLHEHFTSS--IAIIHGRMSDIDK-ESVMDSFKNGTCKLLIATTVIEVGIDVVDASIIIIE----NAEHFGLAQLHQLR  580 (700)
Q Consensus       508 ~~l~~~~~~~--v~~lHGkm~~~ek-~~~m~~F~~g~~~iLvaTtviEVGvdvpna~~mvI~----~aerfGLsqLHQLR  580 (700)
                      .+||.+||..  .++|...+.+.+| ...+.+-+.-.+.||-      .-||-.++..-|..    ++=||||+..--+.
T Consensus       788 AyLKahYP~eF~aAlL~s~~~~~~k~~~~i~ear~~GI~Vlp------PdIN~S~~~ftv~~~~~~~~IrfGL~aIkgvg  861 (1185)
T PRK08512        788 AYLKTYYPAEFMAALLTSEENNIDKVAKYIDEVKRLGIKLLP------PSINKSIREFSVAEFDGKDAIIFGLGAIKGVG  861 (1185)
T ss_pred             HHHHHCCHHHHHHHHHCCCCCCCHHHHHHHHHHHHCCCEEEC------CCCCCCCCCCEEECCCCCCEEEECHHHHCCCC
T ss_conf             998767899999998526889962699999999987996848------82046667643543798753773047647898


Q ss_pred             HCC--------CCCCCCEEEEE
Q ss_conf             116--------67898359999
Q gi|254780945|r  581 GRV--------GRGEEISSCIL  594 (700)
Q Consensus       581 GRV--------GRg~~~s~c~l  594 (700)
                      ..+        ..|.-.|.-=|
T Consensus       862 ~~~i~~Iv~~R~~Gpf~sl~Df  883 (1185)
T PRK08512        862 GAAIENIIEAREDGEFKDLEDF  883 (1185)
T ss_pred             HHHHHHHHHHHCCCCCCCHHHH
T ss_conf             9999999985358999999999


No 192
>KOG1123 consensus
Probab=96.44  E-value=0.014  Score=39.83  Aligned_cols=339  Identities=18%  Similarity=0.217  Sum_probs=182.4

Q ss_pred             CCHHHHHHHHHHHHHHCCCCCCEEEEEECCCCCHHHHHHHHHHHHHHHHCCEEEEEHHHHHHHHHHHHHHHHCCCCCCEE
Q ss_conf             79889999999998410013430788621442236999999733444305458861279999999986211014578658
Q gi|254780945|r  273 PTKSQESAIKDILQDMSQKNRMLRILQGDVGSGKTLVALIAMAAAVEAGGQAVIMAPIGILAQQHYEFIKKYTQNTQIIV  352 (700)
Q Consensus       273 LT~~Q~~ai~eI~~Dl~~~~pM~RLLQGDVGSGKTiVA~~A~l~~~~~G~Q~alMaPTEILA~QH~~~~~~~~~~~~i~v  352 (700)
                      +-.-|++++......=   ..-.-.+-=--|+|||+|-+-|+..+   .+.|.+++-.-|=.+|--..|+.|-.--+-.|
T Consensus       303 iRpYQEksL~KMFGNg---RARSGiIVLPCGAGKtLVGvTAa~ti---kK~clvLcts~VSVeQWkqQfk~wsti~d~~i  376 (776)
T KOG1123         303 IRPYQEKSLSKMFGNG---RARSGIIVLPCGAGKTLVGVTAACTI---KKSCLVLCTSAVSVEQWKQQFKQWSTIQDDQI  376 (776)
T ss_pred             CCCHHHHHHHHHHCCC---CCCCCEEEEECCCCCCEEEEEEEEEE---CCCEEEEECCCCCHHHHHHHHHHHHCCCCCCE
T ss_conf             5753787899973788---54476189856998742545555455---14279995575669999999874501685545


Q ss_pred             EEEECCCCHHHHHHHHHHHCCCCCEEEEECHHHCC-------------CCCCCCCCCEEEECCCCCCCHHH-HHHHHHCC
Q ss_conf             99624642256676877621347548641112013-------------34554444178852101335688-99874025
Q gi|254780945|r  353 EIITGNMPQAHRRKALERIAHGQAHIIIGTHALFQ-------------DSIQYYKLILVIVDEQHRFGVQQ-RLKLTQKA  418 (700)
Q Consensus       353 ~lLtg~~~~~er~~i~~~i~~G~~~iiIGTHAL~q-------------~~v~F~~LgLvViDEQHRFGV~Q-R~~L~~Kg  418 (700)
                      +-.|+.-  ||+       ..+.+.++|-|-+.+.             +-+.=.--||.+.||-|---..- |..|.-  
T Consensus       377 ~rFTsd~--Ke~-------~~~~~gvvvsTYsMva~t~kRS~eaek~m~~l~~~EWGllllDEVHvvPA~MFRRVlsi--  445 (776)
T KOG1123         377 CRFTSDA--KER-------FPSGAGVVVTTYSMVAYTGKRSHEAEKIMDFLRGREWGLLLLDEVHVVPAKMFRRVLSI--  445 (776)
T ss_pred             EEEECCC--CCC-------CCCCCCEEEEEEEHHHHCCCCCHHHHHHHHHHHCCEEEEEEEEHHCCCHHHHHHHHHHH--
T ss_conf             7720244--545-------78988579987313110566427799999998437101688421111269999999999--


Q ss_pred             CCCCC-EEECHHHHHHHHHHHHHHCCCHHHHCCCCCCCCCCEEEEEECCCHHHHHHHHHHHHCCCC-----EE-EEEECC
Q ss_conf             67761-010101322789999752010111102355766620799970200268999976310387-----38-999712
Q gi|254780945|r  419 TAPHV-LLMTATPIPRTLVLTSLGDIDISKITEKPAGRKPIKTVIIPINRIDEVIERLKVVLSEGK-----KA-YWICPQ  491 (700)
Q Consensus       419 ~~ph~-L~MtATPIPRTLal~~ygdldvS~i~e~P~gR~~I~T~~~~~~~~~~~~~~i~~~l~~g~-----q~-y~VcPl  491 (700)
                      ...|. |-+|||-.-        -|       +    +..=-..+++    +++|++=.-+|++++     || =|-||+
T Consensus       446 v~aHcKLGLTATLvR--------ED-------d----KI~DLNFLIG----PKlYEAnWmdL~~kGhIA~VqCaEVWCpM  502 (776)
T KOG1123         446 VQAHCKLGLTATLVR--------ED-------D----KITDLNFLIG----PKLYEANWMDLQKKGHIAKVQCAEVWCPM  502 (776)
T ss_pred             HHHHHHCCCEEEEEE--------CC-------C----CCCCCCEEEC----CHHHHCCHHHHHHCCCEEEEEEEEEECCC
T ss_conf             998761265147851--------26-------6----3333300005----43211248989747804677653145577


Q ss_pred             CCCC---------CCCCCCHH-----HHHHHHHHHH----------CCC------------CEECCCCCCCHHHHHHHHH
Q ss_conf             0122---------11121014-----6666666866----------371------------0312014699899999999
Q gi|254780945|r  492 IEEK---------KESNFRSV-----VERFNSLHEH----------FTS------------SIAIIHGRMSDIDKESVMD  535 (700)
Q Consensus       492 Iees---------e~~~~~~~-----~~~~~~l~~~----------~~~------------~v~~lHGkm~~~ek~~~m~  535 (700)
                      --|-         .+--+-.+     -..++.|-++          |.+            +--.+-|--+..|+-+|++
T Consensus       503 t~eFy~eYL~~~t~kr~lLyvMNP~KFraCqfLI~~HE~RgDKiIVFsDnvfALk~YAikl~KpfIYG~Tsq~ERm~ILq  582 (776)
T KOG1123         503 TPEFYREYLRENTRKRMLLYVMNPNKFRACQFLIKFHERRGDKIIVFSDNVFALKEYAIKLGKPFIYGPTSQNERMKILQ  582 (776)
T ss_pred             CHHHHHHHHHHHHHHHHEEEECCCCHHHHHHHHHHHHHHCCCEEEEEECCHHHHHHHHHHCCCCEEECCCCHHHHHHHHH
T ss_conf             88999999853145441224417403378899999998649838998250889999999708963778885558999998


Q ss_pred             HHHCCC-EEEEEECHHHHCCCCCCCCCEEEEECHHHCCHHHHHHHHHCCCCC---CCCEEEEEEECC--CCC-H--HHHH
Q ss_conf             975598-699998003410468887658998585254746887730116678---983599997088--899-8--7999
Q gi|254780945|r  536 SFKNGT-CKLLIATTVIEVGIDVVDASIIIIENAEHFGLAQLHQLRGRVGRG---EEISSCILLYHP--PLS-K--NSYT  606 (700)
Q Consensus       536 ~F~~g~-~~iLvaTtviEVGvdvpna~~mvI~~aerfGLsqLHQLRGRVGRg---~~~s~c~l~~~~--~~~-~--~~~~  606 (700)
                      .|..+. +.-..-.-|=..-+|.|.|||+|-..++-=.=-|=-|==||+=|.   +...|--+.|+-  +.+ |  -|.+
T Consensus       583 nFq~n~~vNTIFlSKVgDtSiDLPEAnvLIQISSH~GSRRQEAQRLGRILRAKk~~de~fnafFYSLVS~DTqEM~YStK  662 (776)
T KOG1123         583 NFQTNPKVNTIFLSKVGDTSIDLPEANVLIQISSHGGSRRQEAQRLGRILRAKKRNDEEFNAFFYSLVSKDTQEMYYSTK  662 (776)
T ss_pred             HCCCCCCCCEEEEEECCCCCCCCCCCCEEEEECCCCCCHHHHHHHHHHHHHHHHCCCCCCCEEEEEEEECCHHHHHHHHH
T ss_conf             53448733348875035765567766089997245662278999988998776337602000244431064188776666


Q ss_pred             HHHHHHHHCHHHHHHHHHHHHCCCCCCCCCHHCCCCCCCCCCHHHHHHHHHHHHHH
Q ss_conf             99999841425899999985206300026000698744000388759999999999
Q gi|254780945|r  607 RLSVLKNTEDGFLIAEEDLKQRKEGEILGIKQSGMPKFLIAQPELHDSLLEIARKD  662 (700)
Q Consensus       607 Rl~~l~~~~dGf~iAe~Dl~lRG~G~~~G~~QsG~~~~~~~d~~~d~~ll~~a~~~  662 (700)
                      |-..|.+--=-|++-         -++-|.  .-.+++.++.-....+||..+-..
T Consensus       663 RQ~FLidQGYsfkVi---------t~L~gm--e~~~~l~y~skeeq~~LLq~Vl~a  707 (776)
T KOG1123         663 RQQFLIDQGYSFKVI---------TNLPGM--ENLEDLAYASKEEQLELLQKVLLA  707 (776)
T ss_pred             HHHHHHHCCCEEEEE---------ECCCCC--CCCCCCCCCCHHHHHHHHHHHHHC
T ss_conf             566554067068986---------058886--767320127889999999999843


No 193
>PTZ00110 helicase; Provisional
Probab=96.43  E-value=0.031  Score=37.10  Aligned_cols=68  Identities=10%  Similarity=0.200  Sum_probs=36.4

Q ss_pred             HHHHHHHHCCCCCCCEEECHHHHHHHHHHHHHHCCCHHHHCCCCCCCCCCEEEEEECCCH------HHHHHHHHHHHCCC
Q ss_conf             889987402567761010101322789999752010111102355766620799970200------26899997631038
Q gi|254780945|r  409 QQRLKLTQKATAPHVLLMTATPIPRTLVLTSLGDIDISKITEKPAGRKPIKTVIIPINRI------DEVIERLKVVLSEG  482 (700)
Q Consensus       409 ~QR~~L~~Kg~~ph~L~MtATPIPRTLal~~ygdldvS~i~e~P~gR~~I~T~~~~~~~~------~~~~~~i~~~l~~g  482 (700)
                      .|...|. +|  ||+++  ||| -|-+-|.--+.+++          ..|+..|+.+.++      ..-+..|-..+...
T Consensus       297 ~Q~~~L~-~G--~dIvV--ATP-GRLiDlL~~~~~~L----------~~v~yLVLDEADRMLDmGFe~qI~~Il~~i~pd  360 (602)
T PTZ00110        297 FQTYALR-RG--VEILI--ACP-GRLIDFLESNVTNL----------RRVTYLVLDEADRMLDMGFEPQIRKIVSQIRPD  360 (602)
T ss_pred             HHHHHHC-CC--CCEEE--ECC-HHHHHHHHCCCCCC----------CCEEEEEEECHHHHHCCCCHHHHHHHHHHCCCC
T ss_conf             9999871-69--99999--792-38999996499874----------310289987577663546299999999858978


Q ss_pred             CEEEEEECCC
Q ss_conf             7389997120
Q gi|254780945|r  483 KKAYWICPQI  492 (700)
Q Consensus       483 ~q~y~VcPlI  492 (700)
                      +|........
T Consensus       361 RQTlLFSAT~  370 (602)
T PTZ00110        361 RQTLMWSATW  370 (602)
T ss_pred             CEEEEEECCC
T ss_conf             7799995589


No 194
>cd03524 RPA2_OBF_family RPA2_OBF_family: A family of oligonucleotide binding (OB) folds with similarity to the OB fold of the single strand (ss) DNA-binding domain (DBD)-D of human RPA2 (also called RPA32). RPA2 is a subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). RPA contains six OB folds, which are involved in ssDNA binding and in trimerization. The ssDNA binding mechanism is believed to be multistep and to involve conformational change. This family also includes OB folds similar to those found in Escherichia coli SSB, the wedge domain of E. coli RecG (a branched-DNA-specific helicase), E. coli ssDNA specific exodeoxyribonuclease VII large subunit, Pyroco
Probab=96.41  E-value=0.052  Score=35.36  Aligned_cols=68  Identities=28%  Similarity=0.503  Sum_probs=54.0

Q ss_pred             EEEEEEEEEEECCCCCCEEEEEEECCC-CEEEEEEECCCHHHHHHHCCCCCEEEEEEEEEECCCEEEEEC
Q ss_conf             999998975421589833899998189-369999951887899873289888999989973187799977
Q gi|254780945|r   72 ITGYISQHSSFQLQKRRPYKILLNDGT-GEITLLFFYRKTEMLKNVFFEGRKITVTGKIKKLKNRIIMVH  140 (700)
Q Consensus        72 i~g~V~~~~~~~~~~r~~~~v~v~D~t-g~i~lvfFn~~~~yl~k~lk~G~~v~vsGKv~~~~~~~qi~h  140 (700)
                      +.|.|........ .+....+.+.|++ +.+.+.+|..........+++|..+.+.|+++.+++..++..
T Consensus         2 i~g~V~~~~~~~~-~~~~~~~~l~D~t~~~i~v~~~~~~~~~~~~~~~~g~~v~i~g~v~~~~~~~~l~~   70 (75)
T cd03524           2 IVGIVVAVEEIRT-EGKVLIFTLTDGTGGTIRVTLFGELAEELENLLKEGQVVYIKGKVKKFRGRLQLIV   70 (75)
T ss_pred             EEEEEEEEEEEEC-CCEEEEEEEECCCCCEEEEEEEEEHHHHHHHHHHCCCEEEEEEEEEECCCEEEEEE
T ss_conf             7899999842003-86499999976999799999998825768778747829999803652366489999


No 195
>PRK08533 flagellar accessory protein FlaH; Reviewed
Probab=96.40  E-value=0.0082  Score=41.65  Aligned_cols=48  Identities=10%  Similarity=0.215  Sum_probs=38.8

Q ss_pred             HHHHHHHCCCCCCE--EEEEECCCCCHHHHHHHHHHHHHHHHCCEEEEEH
Q ss_conf             99998410013430--7886214422369999997334443054588612
Q gi|254780945|r  282 KDILQDMSQKNRML--RILQGDVGSGKTLVALIAMAAAVEAGGQAVIMAP  329 (700)
Q Consensus       282 ~eI~~Dl~~~~pM~--RLLQGDVGSGKTiVA~~A~l~~~~~G~Q~alMaP  329 (700)
                      +|+.+-|..+.|-.  -|+.||.|||||+.+..-++..+.+|..|.++..
T Consensus        11 d~ld~~lggGip~gs~~li~G~~GtGKsi~~~~~~~~~l~~g~~~~yis~   60 (230)
T PRK08533         11 DELHKRLGGGIPFGSIILIEGDESTGKSILSQRLAYGFLQNGYSVSYVSS   60 (230)
T ss_pred             HHHHHHHCCCCCCCCEEEEECCCCCCHHHHHHHHHHHHHHCCCEEEEEEE
T ss_conf             35788717898898489998689987899999999999878986999994


No 196
>cd04489 ExoVII_LU_OBF ExoVII_LU_OBF: A subfamily of OB folds corresponding to the N-terminal OB-fold domain of Escherichia coli exodeoxyribonuclease VII (ExoVII) large subunit. E. coli ExoVII is composed of two non-identical subunits. E. coli ExoVII is a single-strand-specific exonuclease which degrades ssDNA from both 3-prime and 5-prime ends. ExoVII plays a role in methyl-directed mismatch repair in vivo. ExoVII may also guard the genome from mutagenesis by removing excess ssDNA, since the build up of ssDNA would lead to SOS induction and PolIV-dependent mutagenesis.
Probab=96.37  E-value=0.031  Score=37.14  Aligned_cols=70  Identities=19%  Similarity=0.228  Sum_probs=51.9

Q ss_pred             EEEEEEEEEEEEECCCCCCEEEEEEECCCCEEEEEEECCCHHHHHHHCCCCCEEEEEEEEEEC--CCEEEEECCE
Q ss_conf             999999989754215898338999981893699999518878998732898889999899731--8779997786
Q gi|254780945|r   70 VTITGYISQHSSFQLQKRRPYKILLNDGTGEITLLFFYRKTEMLKNVFFEGRKITVTGKIKKL--KNRIIMVHPH  142 (700)
Q Consensus        70 vti~g~V~~~~~~~~~~r~~~~v~v~D~tg~i~lvfFn~~~~yl~k~lk~G~~v~vsGKv~~~--~~~~qi~hPe  142 (700)
                      +-|+|+|.....   .+..-+-..+.|+...+.+++|......+...++.|++|.+.|+++.|  +|++|+.--+
T Consensus         2 vwV~GEIs~~~~---~~sGh~Yf~LkD~~a~i~~v~~~~~~~~~~~~~~~G~~V~v~g~~~~y~~~G~~ql~v~~   73 (78)
T cd04489           2 VWVEGEISNLKR---PSSGHLYFTLKDEDASIRCVMWRSNARRLGFPLEEGMEVLVRGKVSFYEPRGGYQLIVEE   73 (78)
T ss_pred             EEEEEEECCCEE---CCCCEEEEEEECCCEEEEEEEEHHHHHHCCCCCCCCCEEEEEEEEEEECCCCEEEEEEEE
T ss_conf             899999885582---899639999947881999999667883279998899899999999999898409999999


No 197
>pfam02562 PhoH PhoH-like protein. PhoH is a cytoplasmic protein and predicted ATPase that is induced by phosphate starvation.
Probab=96.35  E-value=0.12  Score=32.45  Aligned_cols=139  Identities=19%  Similarity=0.219  Sum_probs=77.6

Q ss_pred             CCCHHHHHHHHHHHHHHCCCCCCEEEEEECCCCCHHHHHHHHHHHHHHHHC--CEEEEEHHHHHHHH-------HHHHHH
Q ss_conf             679889999999998410013430788621442236999999733444305--45886127999999-------998621
Q gi|254780945|r  272 SPTKSQESAIKDILQDMSQKNRMLRILQGDVGSGKTLVALIAMAAAVEAGG--QAVIMAPIGILAQQ-------HYEFIK  342 (700)
Q Consensus       272 ~LT~~Q~~ai~eI~~Dl~~~~pM~RLLQGDVGSGKTiVA~~A~l~~~~~G~--Q~alMaPTEILA~Q-------H~~~~~  342 (700)
                      ..|..|+.+++.|.+     .+ .-.+.|--|||||.+|+.+++..+.+|.  +..+.=|+--..+.       .-+.+.
T Consensus         4 P~~~~Q~~~~~~l~~-----~~-iv~~~GpAGtGKT~la~~~al~~l~~~~~~kiii~Rp~v~~g~~iGfLPG~~~eK~~   77 (205)
T pfam02562         4 PKTLGQKRYVEAIRK-----ND-IVFGIGPAGTGKTYLAVAAAVDALKDGKVKRIILTRPAVEAGEKLGFLPGDLEEKVD   77 (205)
T ss_pred             CCCHHHHHHHHHHHC-----CC-EEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEEECCCCCCCCCCCCCCCHHHHHH
T ss_conf             898889999999717-----98-079989998609999999999999718943799975771257754558897899999


Q ss_pred             HHCCCCCCEEEEEECCCCHHHHHHHHHHHCCCCCEEEEECHHHCCCCCCCCCCCEEEECCCCCCCHHHHHHHH-HCCCCC
Q ss_conf             1014578658996246422566768776213475486411120133455444417885210133568899874-025677
Q gi|254780945|r  343 KYTQNTQIIVEIITGNMPQAHRRKALERIAHGQAHIIIGTHALFQDSIQYYKLILVIVDEQHRFGVQQRLKLT-QKATAP  421 (700)
Q Consensus       343 ~~~~~~~i~v~lLtg~~~~~er~~i~~~i~~G~~~iiIGTHAL~q~~v~F~~LgLvViDEQHRFGV~QR~~L~-~Kg~~p  421 (700)
                      .|+.++--...-+.|      +..+-.-+.+|.+.++  .-+.+ .+..|.| .+||+||=+-+-.+|=..+. .=|.+.
T Consensus        78 p~~~p~~d~l~~~~~------~~~~~~l~~~~~Ie~~--pl~~i-RGrTf~n-~~iIvDEaQN~t~~~lk~ilTRiG~~S  147 (205)
T pfam02562        78 PYLRPLYDALYDMLG------AEKVEKLIERGVIEIA--PLAYM-RGRTLND-AFIILDEAQNTTPEQMKMFLTRIGFNS  147 (205)
T ss_pred             HHHHHHHHHHHHHHC------HHHHHHHHHCCCEEEC--CHHHH-CCCCCCC-CEEEEECHHCCCHHHHHHHHHHCCCCC
T ss_conf             999999999998728------9999999975975661--46765-5476256-889997221399999999984217996


Q ss_pred             CCEEE
Q ss_conf             61010
Q gi|254780945|r  422 HVLLM  426 (700)
Q Consensus       422 h~L~M  426 (700)
                      -+.++
T Consensus       148 K~vi~  152 (205)
T pfam02562       148 KMVVT  152 (205)
T ss_pred             EEEEE
T ss_conf             89994


No 198
>PRK11776 ATP-dependent RNA helicase DbpA; Provisional
Probab=96.35  E-value=0.036  Score=36.59  Aligned_cols=95  Identities=17%  Similarity=0.206  Sum_probs=72.3

Q ss_pred             HHHHHHHHHHCCEEEEEHHHHHHHHHHHHHHHHCCCCCCEEEEEECCCCHHHHHHHHHHHCCCCCEEEEECHHHCCCCCC
Q ss_conf             99733444305458861279999999986211014578658996246422566768776213475486411120133455
Q gi|254780945|r  312 IAMAAAVEAGGQAVIMAPIGILAQQHYEFIKKYTQNTQIIVEIITGNMPQAHRRKALERIAHGQAHIIIGTHALFQDSIQ  391 (700)
Q Consensus       312 ~A~l~~~~~G~Q~alMaPTEILA~QH~~~~~~~~~~~~i~v~lLtg~~~~~er~~i~~~i~~G~~~iiIGTHAL~q~~v~  391 (700)
                      +.-+....+..++.+-+.|---++.    +.++|...|+++..++|.++..+|..++.+.++|+.+|+|.|- +...++.
T Consensus       233 L~~ll~~~~~~~~IIFcntk~~v~~----l~~~L~~~g~~~~~lHg~m~q~~R~~~l~~F~~g~~~iLVaTD-vaaRGID  307 (459)
T PRK11776        233 LQRLLLHYRPESCVVFCNTKKECQE----VADALNAQGFSALALHGDLEQRDRDQVLVRFANRSCSVLVATD-VAARGLD  307 (459)
T ss_pred             HHHHHHHCCCCCEEEEECCHHHHHH----HHHHHHHCCCCEEEEECCCCHHHHHHHHHHHHCCCCCEEEEHH-HHHCCCC
T ss_conf             9999973687660376174899999----9999986799689987999999999999999779997998810-4347677


Q ss_pred             CCCCCEEEEC--------CCCCCCHHHH
Q ss_conf             4444178852--------1013356889
Q gi|254780945|r  392 YYKLILVIVD--------EQHRFGVQQR  411 (700)
Q Consensus       392 F~~LgLvViD--------EQHRFGV~QR  411 (700)
                      |.++.+||-=        ==||=|=.=|
T Consensus       308 i~~V~~VInyDlP~~~e~YvHRiGRTGR  335 (459)
T PRK11776        308 IKSLEAVINYELARDPEVHVHRIGRTGR  335 (459)
T ss_pred             CCCCCEEEEECCCCCHHHHHHCCCHHHC
T ss_conf             1359889997898974552020525137


No 199
>COG1107 Archaea-specific RecJ-like exonuclease, contains DnaJ-type Zn finger domain [DNA replication, recombination, and repair]
Probab=96.33  E-value=0.084  Score=33.70  Aligned_cols=103  Identities=24%  Similarity=0.234  Sum_probs=74.1

Q ss_pred             CCCCCHHHCCCCCEEEEEEEEEEEEEECCCCCCEEEEEEECCCCEEEEEEECCC--HHHHHHHCCCCCEEEEEEEEEECC
Q ss_conf             444647888998789999999897542158983389999818936999995188--789987328988899998997318
Q gi|254780945|r   56 HYRPKISEISEERIVTITGYISQHSSFQLQKRRPYKILLNDGTGEITLLFFYRK--TEMLKNVFFEGRKITVTGKIKKLK  133 (700)
Q Consensus        56 ~~~~~I~~l~~g~~vti~g~V~~~~~~~~~~r~~~~v~v~D~tg~i~lvfFn~~--~~yl~k~lk~G~~v~vsGKv~~~~  133 (700)
                      +.+..|.+ ..|+.|.|.|+|+.+..  +.  -|...++.|+||.+.+.=|-..  ..|  --..+|+.|.+.|+|+.-.
T Consensus       203 ~~i~did~-~ig~tV~I~GeV~qikq--T~--GPTVFtltDetg~i~aAAFe~aGvRAy--P~ievGdiV~ViG~V~~r~  275 (715)
T COG1107         203 TLIDDLDE-MIGKTVRIEGEVTQIKQ--TS--GPTVFTLTDETGAIWAAAFEEAGVRAY--PEIEVGDIVEVIGEVTRRD  275 (715)
T ss_pred             CCHHHHHH-HCCCEEEEEEEEEEEEE--CC--CCEEEEEECCCCCEEHHHHCCCCCCCC--CCCCCCCEEEEEEEEEECC
T ss_conf             10777775-34866999778999997--58--987999806888442666435774348--9987785699987775047


Q ss_pred             CEEEEECCEEEECCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHH
Q ss_conf             7799977868962643344444110000000000454300134578740
Q gi|254780945|r  134 NRIIMVHPHYIFHNSQDVNFPLIEAVYSLPTGLSVDLFKKIIVEALSRL  182 (700)
Q Consensus       134 ~~~qi~hPe~~~~~~~~~~~~~I~PIYplt~GLsqk~irk~I~~aL~~~  182 (700)
                      |++|+---+++.                + .|=...-+|+.|..+|+.-
T Consensus       276 g~lQiE~~~me~----------------L-~G~ea~eVr~rid~ald~~  307 (715)
T COG1107         276 GRLQIEIEAMEK----------------L-TGDEAAEVRKRIDEALDRR  307 (715)
T ss_pred             CCEEEEEHHHHH----------------H-HCCHHHHHHHHHHHHHHHC
T ss_conf             827876243577----------------5-1851899999999998620


No 200
>KOG0392 consensus
Probab=96.32  E-value=0.13  Score=32.33  Aligned_cols=311  Identities=20%  Similarity=0.333  Sum_probs=175.2

Q ss_pred             CCCCCEEEEEECCCCCHHHHHHHHH--HHHHH-------HHCCEEEEEHHHHHHHHHHHHHHHHCCCCCCEEEEEECCCC
Q ss_conf             0134307886214422369999997--33444-------30545886127999999998621101457865899624642
Q gi|254780945|r  290 QKNRMLRILQGDVGSGKTLVALIAM--AAAVE-------AGGQAVIMAPIGILAQQHYEFIKKYTQNTQIIVEIITGNMP  360 (700)
Q Consensus       290 ~~~pM~RLLQGDVGSGKTiVA~~A~--l~~~~-------~G~Q~alMaPTEILA~QH~~~~~~~~~~~~i~v~lLtg~~~  360 (700)
                      ..+..+-.|.-|-|=|||+=++.-.  =.+-.       +-.-+.+.+| --|+----..+.++|+-+  +|.--+|.  
T Consensus       991 nky~LHGILcDDMGLGKTLQticilAsd~y~r~s~~~e~~~~PSLIVCP-sTLtGHW~~E~~kf~pfL--~v~~yvg~-- 1065 (1549)
T KOG0392         991 NKYKLHGILCDDMGLGKTLQTICILASDHYKRRSESSEFNRLPSLIVCP-STLTGHWKSEVKKFFPFL--KVLQYVGP-- 1065 (1549)
T ss_pred             HHHCCCCEEECCCCCCHHHHHHHHHHHHHHHHCCCCHHHCCCCEEEECC-CHHHHHHHHHHHHHCCHH--HHHHHCCC--
T ss_conf             8733354542134632789999999788875024660113587589887-001148999998756301--23431377--


Q ss_pred             HHHHHHHHHHHCCCCCEEEEECHHHCCCCCCC---CCCCEEEECCCCCCCHHHHHHHHH--CC-CCCCCEEECHHHHHHH
Q ss_conf             25667687762134754864111201334554---444178852101335688998740--25-6776101010132278
Q gi|254780945|r  361 QAHRRKALERIAHGQAHIIIGTHALFQDSIQY---YKLILVIVDEQHRFGVQQRLKLTQ--KA-TAPHVLLMTATPIPRT  434 (700)
Q Consensus       361 ~~er~~i~~~i~~G~~~iiIGTHAL~q~~v~F---~~LgLvViDEQHRFGV~QR~~L~~--Kg-~~ph~L~MtATPIPRT  434 (700)
                      ..+|..+....++.  +|+|-.--.+-.++.|   ..--++|.||-|=--= -+.+|..  |. ..-|-|+.|-|||--.
T Consensus      1066 p~~r~~lR~q~~~~--~iiVtSYDv~RnD~d~l~~~~wNYcVLDEGHVikN-~ktkl~kavkqL~a~hRLILSGTPIQNn 1142 (1549)
T KOG0392        1066 PAERRELRDQYKNA--NIIVTSYDVVRNDVDYLIKIDWNYCVLDEGHVIKN-SKTKLTKAVKQLRANHRLILSGTPIQNN 1142 (1549)
T ss_pred             HHHHHHHHHHCCCC--CEEEEEHHHHHHHHHHHHHCCCCEEEECCCCEECC-HHHHHHHHHHHHHHCCEEEEECCCCCCC
T ss_conf             58777777543666--56996589988789999855222699407604211-3889999999976402377408876667


Q ss_pred             H-----------------------------------------------HHHH---------HHCCCHHHHCCCCCCCCCC
Q ss_conf             9-----------------------------------------------9997---------5201011110235576662
Q gi|254780945|r  435 L-----------------------------------------------VLTS---------LGDIDISKITEKPAGRKPI  458 (700)
Q Consensus       435 L-----------------------------------------------al~~---------ygdldvS~i~e~P~gR~~I  458 (700)
                      .                                               ||..         .--|..-++.++||  |-|
T Consensus      1143 vleLWSLFdFLMPGfLGtEKqFqsrf~kpI~asRd~K~Sske~EaG~lAleaLHKqVLPF~LRRlKedVL~DLPp--KII 1220 (1549)
T KOG0392        1143 VLELWSLFDFLMPGFLGTEKQFQSRFGKPILASRDPKSSSKEQEAGVLALEALHKQVLPFLLRRLKEDVLKDLPP--KII 1220 (1549)
T ss_pred             HHHHHHHHHHHCCCCCCCHHHHHHHHCCHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCH--HHH
T ss_conf             999999999846665671888988755504542386556667876488999999988899999988888764885--653


Q ss_pred             EEEEEECCC-HHHHHHHHHHH-------------HCCC------------------CEEEEEECC------C--------
Q ss_conf             079997020-02689999763-------------1038------------------738999712------0--------
Q gi|254780945|r  459 KTVIIPINR-IDEVIERLKVV-------------LSEG------------------KKAYWICPQ------I--------  492 (700)
Q Consensus       459 ~T~~~~~~~-~~~~~~~i~~~-------------l~~g------------------~q~y~VcPl------I--------  492 (700)
                      .-+...... -.++|+.+-+.             ...|                  |-+.|.-|-      |        
T Consensus      1221 QDyyCeLs~lQ~kLY~df~~~~k~~~~~~~d~~~~S~gt~~~HvFqaLqYlrKLcnHpaLvlt~~hp~la~i~~~l~~~~ 1300 (1549)
T KOG0392        1221 QDYYCELSPLQKKLYRDFVKKAKQCVSSQIDGGEESLGTDKTHVFQALQYLRKLCNHPALVLTPVHPDLAAIVSHLAHFN 1300 (1549)
T ss_pred             HHEEECCCHHHHHHHHHHHHHHCCCCCCCCCCCHHCCCCCHHHHHHHHHHHHHHCCCCCEEECCCCCHHHHHHHHHHHHH
T ss_conf             31034067899999999988750352003464321057514889999999998548964442777502999987887740


Q ss_pred             ------C-------------------CC--CC--C------------CCCHHHHHH--HHHHHHCCC-CEECCCCCCCHH
Q ss_conf             ------1-------------------22--11--1------------210146666--666866371-031201469989
Q gi|254780945|r  493 ------E-------------------EK--KE--S------------NFRSVVERF--NSLHEHFTS-SIAIIHGRMSDI  528 (700)
Q Consensus       493 ------e-------------------es--e~--~------------~~~~~~~~~--~~l~~~~~~-~v~~lHGkm~~~  528 (700)
                            +                   +|  |+  .            .+++.-+..  ..+++++|. ..--|-|-..+.
T Consensus      1301 ~~LHdi~hspKl~AL~qLL~eCGig~~~~~~~g~~s~vsqHRiLIFcQlK~mlDlVekDL~k~~mpsVtymRLDGSVpp~ 1380 (1549)
T KOG0392        1301 SSLHDIQHSPKLSALKQLLSECGIGNNSDSEVGTPSDVSQHRILIFCQLKSMLDLVEKDLFKKYMPSVTYMRLDGSVPPG 1380 (1549)
T ss_pred             HHHHHHHHCHHHHHHHHHHHHHCCCCCCCCCCCCCCHHCCCEEEEEEEHHHHHHHHHHHHHHHHCCCEEEEEECCCCCCH
T ss_conf             14777653526789999999817898875333671021155168764077799999999865114751699734888907


Q ss_pred             HHHHHHHHHHCC-CEEEEEECH-HHHCCCCCCCCCEEEEECHHHCCHHHHHHH---HHCCCCCCCCEEEEEEECCCCCHH
Q ss_conf             999999997559-869999800-341046888765899858525474688773---011667898359999708889987
Q gi|254780945|r  529 DKESVMDSFKNG-TCKLLIATT-VIEVGIDVVDASIIIIENAEHFGLAQLHQL---RGRVGRGEEISSCILLYHPPLSKN  603 (700)
Q Consensus       529 ek~~~m~~F~~g-~~~iLvaTt-viEVGvdvpna~~mvI~~aerfGLsqLHQL---RGRVGRg~~~s~c~l~~~~~~~~~  603 (700)
                      .+.++.++|.++ .||+|.=|| |=-+|.|.-.|.+.|-..-|-=-.--| |-   --|+|--.---..=|++...+-|.
T Consensus      1381 ~R~kiV~~FN~DptIDvLlLTThVGGLGLNLTGADTVVFvEHDWNPMrDL-QAMDRAHRIGQKrvVNVyRlItrGTLEEK 1459 (1549)
T KOG0392        1381 DRQKIVERFNEDPTIDVLLLTTHVGGLGLNLTGADTVVFVEHDWNPMRDL-QAMDRAHRIGQKRVVNVYRLITRGTLEEK 1459 (1549)
T ss_pred             HHHHHHHHHCCCCCEEEEEEEEECCCCCCCCCCCCEEEEEECCCCCHHHH-HHHHHHHHHCCCEEEEEEEEHHCCCHHHH
T ss_conf             77999997168985138999620045322467875589972688832457-88778886267315666630230658998


Q ss_pred             --HHHHHHHH
Q ss_conf             --99999999
Q gi|254780945|r  604 --SYTRLSVL  611 (700)
Q Consensus       604 --~~~Rl~~l  611 (700)
                        +.++.+.-
T Consensus      1460 VMgLQkFKmn 1469 (1549)
T KOG0392        1460 VMGLQKFKMN 1469 (1549)
T ss_pred             HHHHHHHHHH
T ss_conf             7657888668


No 201
>PRK00286 xseA exodeoxyribonuclease VII large subunit; Reviewed
Probab=96.31  E-value=0.044  Score=35.94  Aligned_cols=160  Identities=18%  Similarity=0.171  Sum_probs=86.3

Q ss_pred             CCCCHHHHHHHCCCCCCCCCCCCCHHHCCCCCEEEEEEEEEEEEEECCCCCCEEEEEEECCCCEEEEEEECCCHHHHHHH
Q ss_conf             85548987870897401344446478889987899999998975421589833899998189369999951887899873
Q gi|254780945|r   37 NETRFIDLLFYHPSSFIDRHYRPKISEISEERIVTITGYISQHSSFQLQKRRPYKILLNDGTGEITLLFFYRKTEMLKNV  116 (700)
Q Consensus        37 GI~ti~DLL~~~PrrYeDr~~~~~I~~l~~g~~vti~g~V~~~~~~~~~~r~~~~v~v~D~tg~i~lvfFn~~~~yl~k~  116 (700)
                      .+.||-+|..+.=.--+ .       ++   ..+.|.|+|..... + ..+. +-..+.|+...|.+++|......+.-.
T Consensus         4 ~~lsVsel~~~ik~~le-~-------~~---~~v~V~GEIS~~~~-~-~sGH-~YF~LkD~~a~i~~v~~~~~~~~l~~~   69 (443)
T PRK00286          4 NPLSVSELNGYVKSLLE-R-------DL---GQVWVRGEISNFTR-P-SSGH-WYFTLKDEQAQIRCVMFRGSARRLKFK   69 (443)
T ss_pred             CCEEHHHHHHHHHHHHH-H-------HC---CCEEEEEEECCCEE-C-CCCE-EEEEEEECCCEEEEEEECCHHHHCCCC
T ss_conf             86309999999999998-3-------48---98999999646662-8-9964-999998189289999992847528999


Q ss_pred             CCCCCEEEEEEEEEEC--CCEEEEECCEEEECCCC-------------------CCCCCCCCCCCCCCHHH----HHHHH
Q ss_conf             2898889999899731--87799977868962643-------------------34444411000000000----04543
Q gi|254780945|r  117 FFEGRKITVTGKIKKL--KNRIIMVHPHYIFHNSQ-------------------DVNFPLIEAVYSLPTGL----SVDLF  171 (700)
Q Consensus       117 lk~G~~v~vsGKv~~~--~~~~qi~hPe~~~~~~~-------------------~~~~~~I~PIYplt~GL----sqk~i  171 (700)
                      ++.|++|.+.|++..|  +|.+|+.--+++..-..                   +..-.+-.|-||..=|+    +..-+
T Consensus        70 ~~~G~~V~v~g~i~~Y~~~g~~ql~v~~i~~~g~G~L~~~~e~lk~kL~~eGlFd~~~Kk~lP~~P~~IgvITS~tgAa~  149 (443)
T PRK00286         70 PEEGMQVLVRGKVSVYEPRGDYQLIVEDIEPAGIGALAQAFEQLKEKLAAEGLFDPERKKPLPFFPKRIGVITSPTGAAI  149 (443)
T ss_pred             CCCCCEEEEEEEEEEECCCCCEEEEEEEEEECCCCHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCEEEEEECCCHHHH
T ss_conf             98999999999998986886189999781277921899999999999977779687778999878557999836843899


Q ss_pred             HHHHHHHHHHHCCC-CCCCCHHHHHCCCCCCHHHHHHHHC
Q ss_conf             00134578740468-4338977862056999889998620
Q gi|254780945|r  172 KKIIVEALSRLPVL-PEWIEKDLLQKKSFPSIAEAFNIIH  210 (700)
Q Consensus       172 rk~I~~aL~~~~~i-~E~LP~~ll~k~~L~s~~eAL~~IH  210 (700)
                      +-+++.+-+..|.. -...|..+--+.--.+..+||+.+.
T Consensus       150 ~Di~~~~~~R~p~~~i~l~p~~VQG~~A~~~I~~ai~~~~  189 (443)
T PRK00286        150 RDILTVLSRRFPSVEVIIYPTLVQGEGAAASIVEAIERAN  189 (443)
T ss_pred             HHHHHHHHCCCCCEEEEEEECCCCHHHHHHHHHHHHHHHH
T ss_conf             9999998504996599998145626547999999999985


No 202
>PRK01216 DNA polymerase IV; Validated
Probab=96.30  E-value=0.0028  Score=45.36  Aligned_cols=65  Identities=20%  Similarity=0.260  Sum_probs=30.2

Q ss_pred             HHHHHHHHHHCCCCCCEEEEEECCCCCHHHHHHHHHHHHHHHHCCEEEEEHHHHHHHHHHHHHHHHCCCCCCEEEEEEC
Q ss_conf             9999999841001343078862144223699999973344430545886127999999998621101457865899624
Q gi|254780945|r  279 SAIKDILQDMSQKNRMLRILQGDVGSGKTLVALIAMAAAVEAGGQAVIMAPIGILAQQHYEFIKKYTQNTQIIVEIITG  357 (700)
Q Consensus       279 ~ai~eI~~Dl~~~~pM~RLLQGDVGSGKTiVA~~A~l~~~~~G~Q~alMaPTEILA~QH~~~~~~~~~~~~i~v~lLtg  357 (700)
                      ....+|.++........  .---+|+.|+ +|=+|+-.+=-+|.  .++.|.+         +..++.+++++--.=.|
T Consensus       123 ~~a~~ir~~I~~~~glt--~SiGia~nk~-lAKiAs~~~KP~G~--~~v~~~~---------~~~fl~~lpv~~i~GIG  187 (351)
T PRK01216        123 ELARKIKNEILEKEKIT--VTVGIGPNKV-FAKIIADMAKPNGL--GVISPEE---------VKEFLNNLDIDDVPGIG  187 (351)
T ss_pred             HHHHHHHHHHHHHHCCC--EEEEECCCHH-HHHHHHHHCCCCCE--EEECHHH---------HHHHHHCCCCCEECCCC
T ss_conf             99999999999997995--6885665499-99998872399957--9988368---------99987609943854857


No 203
>PRK00448 polC DNA polymerase III PolC; Validated
Probab=96.22  E-value=0.12  Score=32.57  Aligned_cols=86  Identities=24%  Similarity=0.320  Sum_probs=62.3

Q ss_pred             CCCCCCCHHHCCC-CCEEEEEEEEEEEEEECCC-CCCEEEEEEECCCCEEEEEEECCCHH--HHHHHCCCCCEEEEEEEE
Q ss_conf             3444464788899-8789999999897542158-98338999981893699999518878--998732898889999899
Q gi|254780945|r   54 DRHYRPKISEISE-ERIVTITGYISQHSSFQLQ-KRRPYKILLNDGTGEITLLFFYRKTE--MLKNVFFEGRKITVTGKI  129 (700)
Q Consensus        54 Dr~~~~~I~~l~~-g~~vti~g~V~~~~~~~~~-~r~~~~v~v~D~tg~i~lvfFn~~~~--yl~k~lk~G~~v~vsGKv  129 (700)
                      ......++.++.+ ...++|.|.|-+......+ +|..+.+.+.|.|+++.+.+|.....  -....++.|+++.+.|++
T Consensus       220 ~~~~~~~~~~i~~~~~~v~v~G~vf~~e~~~~k~g~~i~~~~itD~t~si~~k~f~~~~~~~~~~~~i~~g~~v~v~g~~  299 (1436)
T PRK00448        220 IKEEITPMIEINEEERRVVVEGYVFKKEIKELKSGRHILTFKITDYTSSITVKKFLRDKEDLKKFDEIKKGDWVKVRGSV  299 (1436)
T ss_pred             CCCCEEEHHHHHCCCCEEEEEEEEEEEEEEECCCCCEEEEEEEEECCCCEEEEEECCCCCHHHHHHHCCCCCEEEEEEEE
T ss_conf             77773458884242581899999986674431579879999998268868999944763327898516799789999998


Q ss_pred             EECC--CEEEEE
Q ss_conf             7318--779997
Q gi|254780945|r  130 KKLK--NRIIMV  139 (700)
Q Consensus       130 ~~~~--~~~qi~  139 (700)
                      ..-.  +.+.|.
T Consensus       300 ~~d~~~~~~~~~  311 (1436)
T PRK00448        300 QNDTFTRDLVMN  311 (1436)
T ss_pred             EECCCCCCEEEE
T ss_conf             512677721787


No 204
>cd04484 polC_OBF polC_OBF: A subfamily of OB folds corresponding to the N-terminal OB-fold nucleic acid binding domain of Bacillus subtilis type C replicative DNA polymerase III alpha subunit (polC). Replication in B. subtilis and Staphylococcus aureus requires two different polymerases, polC and DnaE. The holoenzyme is thought to include the two different polymerases. At the B. subtilis replication fork, polC appears to be involved in leading strand synthesis and DnaE in lagging strand synthesis.
Probab=96.22  E-value=0.083  Score=33.76  Aligned_cols=66  Identities=24%  Similarity=0.248  Sum_probs=49.7

Q ss_pred             EEEEEEEEEEEEEECCCC-CCEEEEEEECCCCEEEEEEECCCHH-HHHHHCCCCCEEEEEEEEEECCC
Q ss_conf             899999998975421589-8338999981893699999518878-99873289888999989973187
Q gi|254780945|r   69 IVTITGYISQHSSFQLQK-RRPYKILLNDGTGEITLLFFYRKTE-MLKNVFFEGRKITVTGKIKKLKN  134 (700)
Q Consensus        69 ~vti~g~V~~~~~~~~~~-r~~~~v~v~D~tg~i~lvfFn~~~~-yl~k~lk~G~~v~vsGKv~~~~~  134 (700)
                      .|++.|.|-.......+. +..+...+.|.|++|.+.+|..... -.....+.|+++.+.|++.+-..
T Consensus         1 nV~i~G~IF~~E~relk~gk~i~~~~iTD~t~Si~~K~F~~~~~~~~~~~~~~G~~v~v~G~v~~D~f   68 (82)
T cd04484           1 NVVVEGEVFDLEIRELKSGRKILTFKVTDYTSSITVKKFLRKDEKDKEELKSKGDWVRVRGKVQYDTF   68 (82)
T ss_pred             CEEEEEEEEEEEEEECCCCCEEEEEEEEECCCCEEEEEEECCCHHHHHHHHCCCCEEEEEEEEEECCC
T ss_conf             98999999978989724898999999980889799999835854445665258979999999963178


No 205
>KOG0949 consensus
Probab=96.19  E-value=0.013  Score=40.06  Aligned_cols=81  Identities=19%  Similarity=0.368  Sum_probs=69.7

Q ss_pred             CEECCCCCCCHHHHHHHHHHHHCCCEEEEEECHHHHCCCCCCCCCEEEEECHHHCCHHHHHHHHHCCCCCC--CCEEEEE
Q ss_conf             03120146998999999999755986999980034104688876589985852547468877301166789--8359999
Q gi|254780945|r  517 SIAIIHGRMSDIDKESVMDSFKNGTCKLLIATTVIEVGIDVVDASIIIIENAEHFGLAQLHQLRGRVGRGE--EISSCIL  594 (700)
Q Consensus       517 ~v~~lHGkm~~~ek~~~m~~F~~g~~~iLvaTtviEVGvdvpna~~mvI~~aerfGLsqLHQLRGRVGRg~--~~s~c~l  594 (700)
                      .+|+-|.-|...++..|=--|+.|...+|.||.-.-.|||.|--|+|---+.=..-----||.-||-||-+  .-|..++
T Consensus       964 GiG~HHaglNr~yR~~VEvLFR~g~L~VlfaT~TLsLGiNMPCrTVvF~gDsLQL~plny~QmaGRAGRRGFD~lGnV~F 1043 (1330)
T KOG0949         964 GIGVHHAGLNRKYRSLVEVLFRQGHLQVLFATETLSLGINMPCRTVVFAGDSLQLDPLNYKQMAGRAGRRGFDTLGNVVF 1043 (1330)
T ss_pred             CCCCCCCCCCHHHHHHHHHHHHCCCEEEEEEEEEHHCCCCCCCEEEEEECCCCCCCCHHHHHHHCCCCCCCCCCCCCEEE
T ss_conf             24411244016888799998644856899982110112688741689703522137145776624033445555565588


Q ss_pred             EEC
Q ss_conf             708
Q gi|254780945|r  595 LYH  597 (700)
Q Consensus       595 ~~~  597 (700)
                      +.=
T Consensus      1044 mgi 1046 (1330)
T KOG0949        1044 MGI 1046 (1330)
T ss_pred             EEC
T ss_conf             727


No 206
>COG1570 XseA Exonuclease VII, large subunit [DNA replication, recombination, and repair]
Probab=96.18  E-value=0.045  Score=35.82  Aligned_cols=73  Identities=25%  Similarity=0.258  Sum_probs=55.7

Q ss_pred             CEEEEEEEEEEEEEECCCCCCEEEEEEECCCCEEEEEEECCCHHHHHHHCCCCCEEEEEEEEEEC--CCEEEEECCEE
Q ss_conf             78999999989754215898338999981893699999518878998732898889999899731--87799977868
Q gi|254780945|r   68 RIVTITGYISQHSSFQLQKRRPYKILLNDGTGEITLLFFYRKTEMLKNVFFEGRKITVTGKIKKL--KNRIIMVHPHY  143 (700)
Q Consensus        68 ~~vti~g~V~~~~~~~~~~r~~~~v~v~D~tg~i~lvfFn~~~~yl~k~lk~G~~v~vsGKv~~~--~~~~qi~hPe~  143 (700)
                      ..|-+.|+|..   ++..+..-+-+.+.|+...|+++.|.....++.-.++.|+.|.+.|+++.|  +|.+|++--+.
T Consensus        24 ~~V~v~GEISn---~t~~~sgH~YFtLKD~~A~i~c~mf~~~~~~l~f~p~eG~~V~v~G~is~Y~~rG~YQi~~~~~   98 (440)
T COG1570          24 GQVWVRGEISN---FTRPASGHLYFTLKDERAQIRCVMFKGNNRRLKFRPEEGMQVLVRGKISLYEPRGDYQIVAESM   98 (440)
T ss_pred             CEEEEEEEECC---CCCCCCCCEEEEECCCCCEEEEEEECCCCCCCCCCCCCCCEEEEEEEEEEECCCCCEEEEEECC
T ss_conf             85999999637---7668886079997167716899997470002687866798899997788876988569998327


No 207
>PRK08744 consensus
Probab=96.17  E-value=0.09  Score=33.47  Aligned_cols=127  Identities=14%  Similarity=0.239  Sum_probs=72.1

Q ss_pred             HHHHHHCCCC--EECCCCCCCHHHH-HHHHHHHHCCCEEEEEECHHHHCCCCCCCCCEEEEE-CHHHCCHHHHHHH----
Q ss_conf             6668663710--3120146998999-999999755986999980034104688876589985-8525474688773----
Q gi|254780945|r  508 NSLHEHFTSS--IAIIHGRMSDIDK-ESVMDSFKNGTCKLLIATTVIEVGIDVVDASIIIIE-NAEHFGLAQLHQL----  579 (700)
Q Consensus       508 ~~l~~~~~~~--v~~lHGkm~~~ek-~~~m~~F~~g~~~iLvaTtviEVGvdvpna~~mvI~-~aerfGLsqLHQL----  579 (700)
                      .+||.+||..  .++|...|...+| ...+.+-++-.+.||      -.-||-.....-++. ++=||||+..--+    
T Consensus       787 AyLKahyP~eFmaA~L~~~~~~~~k~~~~i~ear~~gi~vl------pPdIN~S~~~f~~~~~~~Ir~GL~aIkgvg~~~  860 (1195)
T PRK08744        787 AWLKRHYPAEFMAATLSSDMDNTDKVVGFLDEVRNLGLTVL------PPRVNESAYMFEAASPDTIQYGLGAIKGVGQGA  860 (1195)
T ss_pred             HHHHHCCHHHHHHHHHCCCCCCCHHHHHHHHHHHHCCCEEE------CCCCCCCCCCEEEECCCCEEECCCCCCCCCHHH
T ss_conf             99986589999999844688997589999999998799695------884146788217607995564322113775999


Q ss_pred             -----HHCCCCCCCCEEEEEEEC---CCCCHHHHHHH--------------HHHHHHCHHHHHHHHHHHHC--CCCCCCC
Q ss_conf             -----011667898359999708---88998799999--------------99984142589999998520--6300026
Q gi|254780945|r  580 -----RGRVGRGEEISSCILLYH---PPLSKNSYTRL--------------SVLKNTEDGFLIAEEDLKQR--KEGEILG  635 (700)
Q Consensus       580 -----RGRVGRg~~~s~c~l~~~---~~~~~~~~~Rl--------------~~l~~~~dGf~iAe~Dl~lR--G~G~~~G  635 (700)
                           .-|--.|.-.|..-++..   ...+....+.|              ..|....+-..-|+..-+-+  |-.++||
T Consensus       861 v~~Iv~~R~~~Gpf~sl~Df~~Rv~~~~~nkr~lE~LI~aGAfD~~g~~R~~ll~~~~~~~~~~~~~~~~~~~gq~~LF~  940 (1195)
T PRK08744        861 CEAIVEERLRGGPYTTLLDFCTRVGTAKLNRRTLEAMINAGAMDGLGKNRASLMLQLPEVMKATEQMARERASGQNSLFG  940 (1195)
T ss_pred             HHHHHHHHHHCCCCCCHHHHHHHCCCCCCCHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCC
T ss_conf             99999999848999999999974354569999999998678875768579999998999999999977877558867668


Q ss_pred             CHHCC
Q ss_conf             00069
Q gi|254780945|r  636 IKQSG  640 (700)
Q Consensus       636 ~~QsG  640 (700)
                      ..-..
T Consensus       941 ~~~~~  945 (1195)
T PRK08744        941 GPDPS  945 (1195)
T ss_pred             CCCCC
T ss_conf             88766


No 208
>COG0513 SrmB Superfamily II DNA and RNA helicases [DNA replication, recombination, and repair / Transcription / Translation, ribosomal structure and biogenesis]
Probab=96.17  E-value=0.035  Score=36.68  Aligned_cols=72  Identities=18%  Similarity=0.391  Sum_probs=62.4

Q ss_pred             CEEEEEHHHHHHHHHHHHHHHHCCCCCCEEEEEECCCCHHHHHHHHHHHCCCCCEEEEECHHHCCCCCCCCCCCEEE
Q ss_conf             45886127999999998621101457865899624642256676877621347548641112013345544441788
Q gi|254780945|r  323 QAVIMAPIGILAQQHYEFIKKYTQNTQIIVEIITGNMPQAHRRKALERIAHGQAHIIIGTHALFQDSIQYYKLILVI  399 (700)
Q Consensus       323 Q~alMaPTEILA~QH~~~~~~~~~~~~i~v~lLtg~~~~~er~~i~~~i~~G~~~iiIGTHAL~q~~v~F~~LgLvV  399 (700)
                      |+.+-+.|--.|..    +...+...|+++..|+|+++..+|..+++..++|+.+|+|.|-. ...++.+.++.+||
T Consensus       275 ~~IVF~~tk~~~~~----l~~~l~~~g~~~~~lhG~l~q~~R~~~l~~F~~g~~~iLVaTDv-aaRGiDi~~v~~Vi  346 (513)
T COG0513         275 RVIVFVRTKRLVEE----LAESLRKRGFKVAALHGDLPQEERDRALEKFKDGELRVLVATDV-AARGLDIPDVSHVI  346 (513)
T ss_pred             EEEEEECCHHHHHH----HHHHHHHCCCEEEEEECCCCHHHHHHHHHHHHCCCCCEEEEECH-HHCCCCCCCCCEEE
T ss_conf             39999576776999----99999978965999738899889999999997599898998065-44689966674799


No 209
>smart00382 AAA ATPases associated with a variety of cellular activities. AAA - ATPases associated with a variety of cellular activities. This profile/alignment only detects a fraction of this vast family. The poorly conserved N-terminal helix is missing from the alignment.
Probab=96.16  E-value=0.03  Score=37.24  Aligned_cols=117  Identities=20%  Similarity=0.153  Sum_probs=62.4

Q ss_pred             EEEEEECCCCCHHHHHHHHHHHHHHHHCCEEEEEHHHHHHHHHHHHHHHHCCCCCCEEEEEECCCCHHHHHHHHHHHCCC
Q ss_conf             07886214422369999997334443054588612799999999862110145786589962464225667687762134
Q gi|254780945|r  295 LRILQGDVGSGKTLVALIAMAAAVEAGGQAVIMAPIGILAQQHYEFIKKYTQNTQIIVEIITGNMPQAHRRKALERIAHG  374 (700)
Q Consensus       295 ~RLLQGDVGSGKTiVA~~A~l~~~~~G~Q~alMaPTEILA~QH~~~~~~~~~~~~i~v~lLtg~~~~~er~~i~~~i~~G  374 (700)
                      .-+|.|..|||||..+...+......++.+.+.++......--.........      ...........-+.+.+.++..
T Consensus         4 ~ill~G~~GsGKTtl~~~la~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~~------~~~~~~~~~~~~~~~~~~~~~~   77 (148)
T smart00382        4 VILIVGPPGSGKTTLARALARELGPPGGGVIYIDGEDILEEVLDQLLLIIVG------GKKASGSGELRLRLALALARKL   77 (148)
T ss_pred             EEEEECCCCHHHHHHHHHHHHHHCCCCCCEEEEEHHHHHHHHHHHHHHHHHC------CCCCCCCHHHHHHHHHHHHHHC
T ss_conf             8999999970299999999987266899689987599898889876530001------1221051999999999999844


Q ss_pred             CCEEEEECHHHCCCCCCCCCCCEEEECCCCCCCHHHHHHHHH-----------CCCCCCCEEECHH----HHHHHHH
Q ss_conf             754864111201334554444178852101335688998740-----------2567761010101----3227899
Q gi|254780945|r  375 QAHIIIGTHALFQDSIQYYKLILVIVDEQHRFGVQQRLKLTQ-----------KATAPHVLLMTAT----PIPRTLV  436 (700)
Q Consensus       375 ~~~iiIGTHAL~q~~v~F~~LgLvViDEQHRFGV~QR~~L~~-----------Kg~~ph~L~MtAT----PIPRTLa  436 (700)
                                         ...+++|||=+++.-.....+..           +....-.+++++.    ++|..+.
T Consensus        78 -------------------~~~viiiDei~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vi~~~n~~~~~~~~~~~  135 (148)
T smart00382       78 -------------------KPDVLILDEITSLLDAEQEALLLLLEELRLLLLLKSEKNLTVILTTNDEKDLGPALLR  135 (148)
T ss_pred             -------------------CCCEEEEECCHHHCCCCCHHHHHHHHHHHHHCCCCCCCCEEEEEEECCCCCCCHHHHC
T ss_conf             -------------------9989998275021476207999999999985176578998999956995224987707


No 210
>PRK07211 replication factor A; Reviewed
Probab=96.13  E-value=0.059  Score=34.89  Aligned_cols=107  Identities=12%  Similarity=0.178  Sum_probs=74.4

Q ss_pred             CCCHHHCCCCC-EEEEEEEEEEEEEEC-CCC-----CCEEEEEEECCCCEEEEEEECCCHHHHHHHCCCCCEEEE-EEEE
Q ss_conf             46478889987-899999998975421-589-----833899998189369999951887899873289888999-9899
Q gi|254780945|r   58 RPKISEISEER-IVTITGYISQHSSFQ-LQK-----RRPYKILLNDGTGEITLLFFYRKTEMLKNVFFEGRKITV-TGKI  129 (700)
Q Consensus        58 ~~~I~~l~~g~-~vti~g~V~~~~~~~-~~~-----r~~~~v~v~D~tg~i~lvfFn~~~~yl~k~lk~G~~v~v-sGKv  129 (700)
                      ..+|.++.+|. .+++.|+|++...++ |.|     .+.-.+.+-|+||+|+++.|+.+...+ ..|.+|..|-+ -|-+
T Consensus       162 ~~~I~~l~~g~~dv~l~g~VL~~~~iRtF~R~DGSeGrV~sl~lGDETG~IRvTLWDd~aDl~-~~l~~GdsVeIv~ayv  240 (473)
T PRK07211        162 EYDADDLSLGQSDVTLRGEVLDTDAVRTFDRDDGSEGRVSNLTVGDETGRIRVTLWDDQADRA-DDLDAGASVEIVDGYV  240 (473)
T ss_pred             CCCCCCCCCCCCCCEEEEEEECCCCCCCEECCCCCCCEEEEEEEECCCCEEEEEEECCCCCCC-CCCCCCCEEEEECCEE
T ss_conf             641122667887637999994378874114578986348888985587619999855874100-2589998799932586


Q ss_pred             EECCCEEEEECCEE---EECCCCCCCCCCCCCCCCCCHH
Q ss_conf             73187799977868---9626433444441100000000
Q gi|254780945|r  130 KKLKNRIIMVHPHY---IFHNSQDVNFPLIEAVYSLPTG  165 (700)
Q Consensus       130 ~~~~~~~qi~hPe~---~~~~~~~~~~~~I~PIYplt~G  165 (700)
                      +...+.+++.+-+.   ...+.+-...+.+.||=.+..+
T Consensus       241 REr~g~lEL~vgd~g~I~k~d~~Vey~peftpI~dI~~~  279 (473)
T PRK07211        241 REREGSLELHVGDRGAVDEVDEDVEFVPDTTPIDSVEID  279 (473)
T ss_pred             ECCCCCEEEEECCCCEEEECCCCCCCCCCCCCHHHCCCC
T ss_conf             224785678974631377556540025576527561358


No 211
>COG0553 HepA Superfamily II DNA/RNA helicases, SNF2 family [Transcription / DNA replication, recombination, and repair]
Probab=96.11  E-value=0.0062  Score=42.60  Aligned_cols=317  Identities=19%  Similarity=0.260  Sum_probs=175.2

Q ss_pred             CCCCHHHHHHHHHHHHHHCCCCCCEEEEEECCCCCHHHHHHHHHHHHHHHHC----CEEEEEHHHHHHHHHHHHHHHHCC
Q ss_conf             4679889999999998410013430788621442236999999733444305----458861279999999986211014
Q gi|254780945|r  271 FSPTKSQESAIKDILQDMSQKNRMLRILQGDVGSGKTLVALIAMAAAVEAGG----QAVIMAPIGILAQQHYEFIKKYTQ  346 (700)
Q Consensus       271 F~LT~~Q~~ai~eI~~Dl~~~~pM~RLLQGDVGSGKTiVA~~A~l~~~~~G~----Q~alMaPTEILA~QH~~~~~~~~~  346 (700)
                      -+|-+-|.+.++-... +-....+++.|-.|.|.|||+=++..+......+.    .+.+.+|++++..= -+.+.++.+
T Consensus       337 ~~lr~yq~~g~~wl~~-~l~~~~~~~ilad~mglGKTiq~i~~l~~~~~~~~~~~~~~liv~p~s~~~nw-~~e~~k~~~  414 (866)
T COG0553         337 AELRPYQLEGVNWLSE-LLRSNLLGGILADDMGLGKTVQTIALLLSLLESIKVYLGPALIVVPASLLSNW-KREFEKFAP  414 (866)
T ss_pred             CCCHHHHHHHHHHHHH-HHHHHCCCCEEECCCCCCHHHHHHHHHHHHHHHHCCCCCCEEEECCHHHHHHH-HHHHHHHCC
T ss_conf             1104889986699999-87762368775752334219999999877776401357872687147777679-999986141


Q ss_pred             CCCCEEEEEECCCC-HHHHHHHHHH-HCCC---CCEEEEECHHHCCC----CCCCC--CCCEEEECCCCCCCHHHHHHHH
Q ss_conf             57865899624642-2566768776-2134---75486411120133----45544--4417885210133568899874
Q gi|254780945|r  347 NTQIIVEIITGNMP-QAHRRKALER-IAHG---QAHIIIGTHALFQD----SIQYY--KLILVIVDEQHRFGVQQRLKLT  415 (700)
Q Consensus       347 ~~~i~v~lLtg~~~-~~er~~i~~~-i~~G---~~~iiIGTHAL~q~----~v~F~--~LgLvViDEQHRFGV~QR~~L~  415 (700)
                      .+.. +....|... ...+.+.+.. +..+   ..++++-|-..+..    .-.++  .-+.+|+||-|+  ..=+....
T Consensus       415 ~~~~-~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~v~itty~~l~~~~~~~~~l~~~~~~~~v~DEa~~--ikn~~s~~  491 (866)
T COG0553         415 DLRL-VLVYHGEKSELDKKREALRDLLKLHLVIIFDVVITTYELLRRFLVDHGGLKKIEWDRVVLDEAHR--IKNDQSSE  491 (866)
T ss_pred             HHHH-HHHHCCCCCCCCHHHHHHHHHHHHCCCEEHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHH--HHCHHHHH
T ss_conf             2100-23211531121036999999986213301018999999999750205542236776989978875--40477899


Q ss_pred             H----CCCCCCCEEECHHHHHHHHHH-----------HHHH------------------CC-------------------
Q ss_conf             0----256776101010132278999-----------9752------------------01-------------------
Q gi|254780945|r  416 Q----KATAPHVLLMTATPIPRTLVL-----------TSLG------------------DI-------------------  443 (700)
Q Consensus       416 ~----Kg~~ph~L~MtATPIPRTLal-----------~~yg------------------dl-------------------  443 (700)
                      .    +-...+.+.+|.|||+-.+.=           .++|                  |.                   
T Consensus       492 ~~~l~~~~~~~~~~LtgTPlen~l~eL~sl~~~f~~p~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~  571 (866)
T COG0553         492 GKALQFLKALNRLDLTGTPLENRLGELWSLLQEFLNPGLLGTSFAIFTRLFEKPIQAEEDIGPLEARELGIELLRKLLSP  571 (866)
T ss_pred             HHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHCCHHHHHHHHCHHHHHHHHHHHHHHHHHH
T ss_conf             99999875543322899964560899999989985743266238999998601666543201024567789999864326


Q ss_pred             --------CHHHHCCCCCCCCCCEEEEEECCCHHHHHHHHHH-------HHCC---C-----------CEEEEE------
Q ss_conf             --------0111102355766620799970200268999976-------3103---8-----------738999------
Q gi|254780945|r  444 --------DISKITEKPAGRKPIKTVIIPINRIDEVIERLKV-------VLSE---G-----------KKAYWI------  488 (700)
Q Consensus       444 --------dvS~i~e~P~gR~~I~T~~~~~~~~~~~~~~i~~-------~l~~---g-----------~q~y~V------  488 (700)
                              |+.++.++|+-...+...-... ...++|+....       .+..   .           -+.+++      
T Consensus       572 f~lrr~k~~~~v~~~lp~k~e~~~~~~l~~-~q~~~y~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~lr~  650 (866)
T COG0553         572 FILRRTKEDVEVLKELPPKIEKVLECELSE-EQRELYEALLEGAEKNQQLLEDLEKADSDENRIGDSELNILALLTRLRQ  650 (866)
T ss_pred             HHHHHHHHHHHHHHHCCHHHHEEEECCCCH-HHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
T ss_conf             765400111678874863222001147637-7999999998640337899998875210155554677778788999998


Q ss_pred             -E--C-CCCCC-CC---------------------------CCCCHHHHHH-----------------------HHHHHH
Q ss_conf             -7--1-20122-11---------------------------1210146666-----------------------666866
Q gi|254780945|r  489 -C--P-QIEEK-KE---------------------------SNFRSVVERF-----------------------NSLHEH  513 (700)
Q Consensus       489 -c--P-lIees-e~---------------------------~~~~~~~~~~-----------------------~~l~~~  513 (700)
                       |  | ++++. +.                           .......+..                       ..+...
T Consensus       651 ~~~~p~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~k~~~l~~ll~~~~~~~~~~~kvlifsq~t~~l~il~~~  730 (866)
T COG0553         651 ICNHPALVDEGLEATFDRIVLLLREDKDFDYLKKPLIQLSKGKLQALDELLLDKLLEEGHYHKVLIFSQFTPVLDLLEDY  730 (866)
T ss_pred             HHCCHHHHCCCCCCCCCHHHHHHCCCCCHHHHHHHHHHCCCHHHHHHHHHHHHHHHHCCCCCCEEEEECCCHHHHHHHHH
T ss_conf             72186443043211121244430001102455557886153056899999888998627772348886660599999999


Q ss_pred             CC---CCEECCCCCCCHHHHHHHHHHHHCC--CEEEEEECHHHHCCCCCCCCCEEEEECHHHCCHHHHHHHHHCCCCCCC
Q ss_conf             37---1031201469989999999997559--869999800341046888765899858525474688773011667898
Q gi|254780945|r  514 FT---SSIAIIHGRMSDIDKESVMDSFKNG--TCKLLIATTVIEVGIDVVDASIIIIENAEHFGLAQLHQLRGRVGRGEE  588 (700)
Q Consensus       514 ~~---~~v~~lHGkm~~~ek~~~m~~F~~g--~~~iLvaTtviEVGvdvpna~~mvI~~aerfGLsqLHQLRGRVGRg~~  588 (700)
                      +.   ..+.-++|.++..+++..+++|.++  ..-.|++|-.-.+|++.-.|+..++.+.+.-. ++--|--.|+-|-+.
T Consensus       731 l~~~~~~~~~ldG~~~~~~r~~~i~~f~~~~~~~vflls~kagg~glnLt~a~~vi~~d~~wNp-~~e~Qa~dRa~RigQ  809 (866)
T COG0553         731 LKALGIKYVRLDGSTPAKRRQELIDRFNADEEEKVFLLSLKAGGLGLNLTGADTVILFDPWWNP-AVELQAIDRAHRIGQ  809 (866)
T ss_pred             HHHCCCCEEEEECCCCCCHHHHHHHHHHCCCCCCEEEEEHHCCCCCCCCCCCCEEEECCCCCCH-HHHHHHHHHHHHCCC
T ss_conf             9855875798737875212889999986466775799753005766121456524660776366-799999987876078


Q ss_pred             CEEEEE
Q ss_conf             359999
Q gi|254780945|r  589 ISSCIL  594 (700)
Q Consensus       589 ~s~c~l  594 (700)
                      ..-|..
T Consensus       810 ~~~v~v  815 (866)
T COG0553         810 KRPVKV  815 (866)
T ss_pred             EEEEEE
T ss_conf             015999


No 212
>cd04474 RPA1_DBD_A RPA1_DBD_A: A subfamily of OB folds corresponding to the second OB fold, the ssDNA-binding domain (DBD)-A, of human RPA1 (also called RPA70). RPA1 is the large subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). In addition to DBD-A, RPA1 contains three other OB folds: DBD-B, DBD-C, and RPA1N. The major DNA binding activity of human RPA (hRPA) and Saccharomyces cerevisiae RPA (ScRPA) is associated with DBD-A and DBD-B of RPA1. RPA1 DBD-C is involved in trimerization. The ssDNA-binding mechanism is believed to be multistep and to involve conformational change. Although ScRPA and the hRPA have similar ssDNA-binding properties, they differ funct
Probab=96.07  E-value=0.045  Score=35.84  Aligned_cols=84  Identities=18%  Similarity=0.288  Sum_probs=57.0

Q ss_pred             CHHHCCCC-CEEEEEEEEEEEEEEC-CCC----CCEEEEEEECC-CCEEEEEEECCCHHHHHHHCCCCCEEEEEE-EEEE
Q ss_conf             47888998-7899999998975421-589----83389999818-936999995188789987328988899998-9973
Q gi|254780945|r   60 KISEISEE-RIVTITGYISQHSSFQ-LQK----RRPYKILLNDG-TGEITLLFFYRKTEMLKNVFFEGRKITVTG-KIKK  131 (700)
Q Consensus        60 ~I~~l~~g-~~vti~g~V~~~~~~~-~~~----r~~~~v~v~D~-tg~i~lvfFn~~~~yl~k~lk~G~~v~vsG-Kv~~  131 (700)
                      ||++|.|+ ..-+|.|+|+....++ +..    ++.+.+.+.|+ +|.|.+++|+.--.-....+++|..+.++| +|+.
T Consensus         1 pI~~L~p~~~~w~Ik~RV~~Ks~ir~~~n~~g~gk~f~~~L~De~g~eI~at~f~~~~dkf~~~l~~G~vY~is~g~Vk~   80 (104)
T cd04474           1 PISSLNPYQNKWTIKARVTNKSDIRTWSNARGEGKLFSFDLLDEDGGEIRATFFNDAVDKFYDLLEVGKVYYISKGSVKV   80 (104)
T ss_pred             CCCCCCCCCCCEEEEEEEEECCCCCCEECCCCCCEEEEEEEEECCCCEEEEEEEHHHHHHHHHHCCCCCEEEEECCEEEE
T ss_conf             93014688674599999971577503506899735999999989989899999069999877334328799995659984


Q ss_pred             CCCEE-EEECCEEE
Q ss_conf             18779-99778689
Q gi|254780945|r  132 LKNRI-IMVHPHYI  144 (700)
Q Consensus       132 ~~~~~-qi~hPe~~  144 (700)
                      .+..+ ..-|| |+
T Consensus        81 ank~y~~~~~~-ye   93 (104)
T cd04474          81 ANKKFNTLKND-YE   93 (104)
T ss_pred             CCCCCCCCCCC-EE
T ss_conf             34876689987-89


No 213
>cd04491 SoSSB_OBF SoSSB_OBF: A subfamily of OB folds similar to the OB fold of the crenarchaeote Sulfolobus solfataricus single-stranded (ss) DNA-binding protein (SSoSSB). SSoSSB has a single OB fold, and it physically and functionally interacts with RNA polymerase. In vitro, SSoSSB can substitute for the basal transcription factor TBP, stimulating transcription from promoters under conditions in which TBP is limiting, and supporting transcription when TBP is absent. SSoSSB selectively melts the duplex DNA of promoter sequences. It also relieves transcriptional repression by the chromatin Alba. In addition, SSoSSB activates reverse gyrase activity, which involves DNA binding, DNA cleavage, strand passage and ligation. SSoSSB stimulates all these steps in the presence of the chromatin protein, Sul7d. SSoSSB antagonizes the inhibitory effect of Sul7d on reverse gyrase supercoiling activity. It also physically and functionally interacts with Mini-chromosome Maintenance (MCM), stimulating 
Probab=96.05  E-value=0.059  Score=34.93  Aligned_cols=67  Identities=15%  Similarity=0.274  Sum_probs=49.5

Q ss_pred             EEEEEEEEEEEEC-C----CCCCEEEEEEECCCCEEEEEEECCCHHHHHHHCCCCCEEEEE-EEEEECCCEEEEEC
Q ss_conf             9999998975421-5----898338999981893699999518878998732898889999-89973187799977
Q gi|254780945|r   71 TITGYISQHSSFQ-L----QKRRPYKILLNDGTGEITLLFFYRKTEMLKNVFFEGRKITVT-GKIKKLKNRIIMVH  140 (700)
Q Consensus        71 ti~g~V~~~~~~~-~----~~r~~~~v~v~D~tg~i~lvfFn~~~~yl~k~lk~G~~v~vs-GKv~~~~~~~qi~h  140 (700)
                      ++.|+|++....+ +    ...+...+.+.|+||.+.+++|+..  . ...+++|+.+.+. |.++.|++.+++.-
T Consensus         1 ~v~~~V~~~~~~r~f~~dg~~~~v~~~~i~D~TG~ir~t~W~~~--~-~~~l~~Gd~v~i~~~~v~~~~g~~el~~   73 (82)
T cd04491           1 SVEGKVLSISEPREFTRDGSEGKVQSGLVGDETGTIRFTLWDEK--A-ADDLEPGDVVRIENAYVREFNGRLELSV   73 (82)
T ss_pred             CEEEEEEECCCCEEEEECCCEEEEEEEEEECCCCEEEEEEECCC--C-CCCCCCCCEEEEEEEEEEEECCEEEEEE
T ss_conf             98999998778879973997689999999989987999996874--4-4555899999996899988899799998


No 214
>COG0556 UvrB Helicase subunit of the DNA excision repair complex [DNA replication, recombination, and repair]
Probab=96.01  E-value=0.039  Score=36.30  Aligned_cols=127  Identities=14%  Similarity=0.317  Sum_probs=89.0

Q ss_pred             CCCCCHHHHHHHHHHHHH--HCCCCCCEEEEEECCCCCHHHHHHH-HHHHHHHHHCCEEEEEHHHHHHHHHHHHHHHHCC
Q ss_conf             246798899999999984--1001343078862144223699999-9733444305458861279999999986211014
Q gi|254780945|r  270 PFSPTKSQESAIKDILQD--MSQKNRMLRILQGDVGSGKTLVALI-AMAAAVEAGGQAVIMAPIGILAQQHYEFIKKYTQ  346 (700)
Q Consensus       270 PF~LT~~Q~~ai~eI~~D--l~~~~pM~RLLQGDVGSGKTiVA~~-A~l~~~~~G~Q~alMaPTEILA~QH~~~~~~~~~  346 (700)
                      +|++..+...+++.|..-  |-.|..--|=..|-|-      -++ -+-..+..|..+.+-.=|-=+|+    .+..+|.
T Consensus       398 ~~E~e~s~~~vveQiIRPTGLlDP~ievRp~~~Qvd------DL~~EI~~r~~~~eRvLVTtLTKkmAE----dLT~Yl~  467 (663)
T COG0556         398 DYELEQSGGNVVEQIIRPTGLLDPEIEVRPTKGQVD------DLLSEIRKRVAKNERVLVTTLTKKMAE----DLTEYLK  467 (663)
T ss_pred             HHHHHHCCCCEEEEEECCCCCCCCCEEEECCCCCHH------HHHHHHHHHHHCCCEEEEEEEHHHHHH----HHHHHHH
T ss_conf             487774558426887247788898526514877478------999999999964972999843688899----9999998


Q ss_pred             CCCCEEEEEECCCCHHHHHHHHHHHCCCCCEEEEECHHHCCCCCCCCCCCEEEECCCCCCC
Q ss_conf             5786589962464225667687762134754864111201334554444178852101335
Q gi|254780945|r  347 NTQIIVEIITGNMPQAHRRKALERIAHGQAHIIIGTHALFQDSIQYYKLILVIVDEQHRFG  407 (700)
Q Consensus       347 ~~~i~v~lLtg~~~~~er~~i~~~i~~G~~~iiIGTHAL~q~~v~F~~LgLvViDEQHRFG  407 (700)
                      ..||+|..|++...+-||-+|+.++..|+.|++||-. |+-|++...-.+||-|=.--+=|
T Consensus       468 e~gikv~YlHSdidTlER~eIirdLR~G~~DvLVGIN-LLREGLDiPEVsLVAIlDADKeG  527 (663)
T COG0556         468 ELGIKVRYLHSDIDTLERVEIIRDLRLGEFDVLVGIN-LLREGLDLPEVSLVAILDADKEG  527 (663)
T ss_pred             HCCCEEEEEECCCHHHHHHHHHHHHHCCCCCEEEEEH-HHHCCCCCCCEEEEEEEECCCCC
T ss_conf             6696478642440389999999997577874898501-33134788645579886068544


No 215
>PRK12366 replication factor A; Reviewed
Probab=95.97  E-value=0.097  Score=33.24  Aligned_cols=87  Identities=20%  Similarity=0.261  Sum_probs=63.9

Q ss_pred             CCCCHHHCCCCCEEEEEEEEEEEEEEC-CCC-----CCEEEEEEECCCCEEEEEEECCCHHHHHHHCCCCCEEEEEEEEE
Q ss_conf             446478889987899999998975421-589-----83389999818936999995188789987328988899998997
Q gi|254780945|r   57 YRPKISEISEERIVTITGYISQHSSFQ-LQK-----RRPYKILLNDGTGEITLLFFYRKTEMLKNVFFEGRKITVTGKIK  130 (700)
Q Consensus        57 ~~~~I~~l~~g~~vti~g~V~~~~~~~-~~~-----r~~~~v~v~D~tg~i~lvfFn~~~~yl~k~lk~G~~v~vsGKv~  130 (700)
                      ...+|.++.+|...++.|+|.+...++ |.|     ++--.+.+.|+||+|+++.|+.....   .+..|+.+.|.|=++
T Consensus       174 ~~y~I~el~~~~~~ti~G~V~~~~~irtF~r~DGS~G~v~sl~l~DeTGsIRvTLWdd~ad~---~v~kGD~V~V~Gy~~  250 (649)
T PRK12366        174 DNYKIPELMPNLLKTINGEITKAYPKKEFTKKDGTEGQLKSFIVKDETGSIRVTLWNELTDI---EVKKGDIVEVSGYVK  250 (649)
T ss_pred             CCCCHHHHCCCCCCEEEEEEEECCCCEEEECCCCCCCEEEEEEEECCCCCEEEEEECCCCCC---CCCCCCEEEEEEEEC
T ss_conf             77327782778752699999643686353247898646767899778885899985676654---335798999988872


Q ss_pred             E-CCCEEEEECCEEEEC
Q ss_conf             3-187799977868962
Q gi|254780945|r  131 K-LKNRIIMVHPHYIFH  146 (700)
Q Consensus       131 ~-~~~~~qi~hPe~~~~  146 (700)
                      . |++.+++.--.+.+.
T Consensus       251 egy~g~lel~~~n~~I~  267 (649)
T PRK12366        251 QGYSGNTELSVDNIGIV  267 (649)
T ss_pred             CCCCCCEEEEECCEEEC
T ss_conf             56324048887537850


No 216
>PRK07952 DNA replication protein DnaC; Validated
Probab=95.95  E-value=0.038  Score=36.39  Aligned_cols=97  Identities=21%  Similarity=0.324  Sum_probs=64.4

Q ss_pred             CCCHHHHHHHHHHH---HHHCCCCCCEEEEEECCCCCHHHHHHHHHHHHHHHHCCEEEEEHHHHHHHHHHHHHHHHCCCC
Q ss_conf             67988999999999---841001343078862144223699999973344430545886127999999998621101457
Q gi|254780945|r  272 SPTKSQESAIKDIL---QDMSQKNRMLRILQGDVGSGKTLVALIAMAAAVEAGGQAVIMAPIGILAQQHYEFIKKYTQNT  348 (700)
Q Consensus       272 ~LT~~Q~~ai~eI~---~Dl~~~~pM~RLLQGDVGSGKTiVA~~A~l~~~~~G~Q~alMaPTEILA~QH~~~~~~~~~~~  348 (700)
                      --.++|++|++.-.   +-..++.. .=|..|++|+|||-.|..-+-..++.|+.|.++.=.++|.+     ++.-|..-
T Consensus        73 ~~~~~q~~al~~a~~y~enf~~~~~-gLlF~G~~GTGKThLA~aIan~Li~~G~sVlf~t~~dLl~~-----lr~t~~~~  146 (242)
T PRK07952         73 VECEGQMNALSKARQYVEEFDGNIA-SFIFSGKPGTGKNHLAAAICNELLLRGKSVLIITVADIMSA-----MKDTFRNS  146 (242)
T ss_pred             CCCHHHHHHHHHHHHHHHHHCCCCC-EEEEECCCCCCHHHHHHHHHHHHHHCCCEEEEEEHHHHHHH-----HHHHHHCC
T ss_conf             5877789999999999986543887-17997899997899999999999987994999779999999-----99998068


Q ss_pred             CCEEEEEECCCCHHHHHHHHHHHCCCCCEEEEECHHHCCCCCCCCCCCEEEECCCCCCCHHH
Q ss_conf             86589962464225667687762134754864111201334554444178852101335688
Q gi|254780945|r  349 QIIVEIITGNMPQAHRRKALERIAHGQAHIIIGTHALFQDSIQYYKLILVIVDEQHRFGVQQ  410 (700)
Q Consensus       349 ~i~v~lLtg~~~~~er~~i~~~i~~G~~~iiIGTHAL~q~~v~F~~LgLvViDEQHRFGV~Q  410 (700)
                               ..  .| .+++..                     +.+-.|.||||   +|++.
T Consensus       147 ---------~~--~e-~~~l~~---------------------l~~~dLLIiDd---lG~e~  172 (242)
T PRK07952        147 ---------ET--SE-EQLLND---------------------LSNVDLLVIDE---IGVQT  172 (242)
T ss_pred             ---------CC--CH-HHHHHH---------------------HHCCCEEEEEC---CCCCC
T ss_conf             ---------75--69-999998---------------------63189898730---14665


No 217
>cd01700 Pol_V Pol V was discovered in Escherichia coli as Umuc and UmuD proteins induced by UV. This branch of DNA polymerases is mostly found in bacteria. Pol V enables DNA replication to bypass covalently linked cys-sin T-T photo-dimers and 6-4 T-T or T-C photoproducts, which would otherwise stall the DNA replication fork.
Probab=95.91  E-value=0.0062  Score=42.57  Aligned_cols=18  Identities=6%  Similarity=0.132  Sum_probs=7.8

Q ss_pred             HHHHHHHHHHHHHCCCCC
Q ss_conf             899999999984100134
Q gi|254780945|r  276 SQESAIKDILQDMSQKNR  293 (700)
Q Consensus       276 ~Q~~ai~eI~~Dl~~~~p  293 (700)
                      +-.+.+.-|..|++++.|
T Consensus       137 a~nk~lAKiAs~~~Kp~~  154 (344)
T cd01700         137 GPTKTLAKLANHAAKKWP  154 (344)
T ss_pred             CCCHHHHHHHHHHHCCCC
T ss_conf             431789999788737788


No 218
>COG4098 comFA Superfamily II DNA/RNA helicase required for DNA uptake (late competence protein) [DNA replication, recombination, and repair]
Probab=95.90  E-value=0.048  Score=35.60  Aligned_cols=93  Identities=17%  Similarity=0.283  Sum_probs=74.0

Q ss_pred             HHHHHCCEEEEEHHHHHHHHHHHHHHHHCCCCCCEEEEEECCCCHHHHHHHHHHHCCCCCEEEEECHHHCCCCCCCCCCC
Q ss_conf             44430545886127999999998621101457865899624642256676877621347548641112013345544441
Q gi|254780945|r  317 AVEAGGQAVIMAPIGILAQQHYEFIKKYTQNTQIIVEIITGNMPQAHRRKALERIAHGQAHIIIGTHALFQDSIQYYKLI  396 (700)
Q Consensus       317 ~~~~G~Q~alMaPTEILA~QH~~~~~~~~~~~~i~v~lLtg~~~~~er~~i~~~i~~G~~~iiIGTHAL~q~~v~F~~Lg  396 (700)
                      ...+|+-+.+.+|+=.-.+|-++-+++-++..  +++-.++-+  +.|++.-+...+|+++|+|-|. ++..+|.|.++-
T Consensus       301 q~~~~~P~liF~p~I~~~eq~a~~lk~~~~~~--~i~~Vhs~d--~~R~EkV~~fR~G~~~lLiTTT-ILERGVTfp~vd  375 (441)
T COG4098         301 QRKTGRPVLIFFPEIETMEQVAAALKKKLPKE--TIASVHSED--QHRKEKVEAFRDGKITLLITTT-ILERGVTFPNVD  375 (441)
T ss_pred             HHHCCCCEEEEECCHHHHHHHHHHHHHHCCCC--CEEEEECCC--CCHHHHHHHHHCCCEEEEEEEE-HHHCCCCCCCCE
T ss_conf             87438828999250588999999998618864--215653367--0178999998758638999844-033266435623


Q ss_pred             EEEECCCCCCCHHHHHHHHH
Q ss_conf             78852101335688998740
Q gi|254780945|r  397 LVIVDEQHRFGVQQRLKLTQ  416 (700)
Q Consensus       397 LvViDEQHRFGV~QR~~L~~  416 (700)
                      .+|++-.||-=.  ..+|.+
T Consensus       376 V~Vlgaeh~vfT--esaLVQ  393 (441)
T COG4098         376 VFVLGAEHRVFT--ESALVQ  393 (441)
T ss_pred             EEEECCCCCCCC--HHHHHH
T ss_conf             999547764201--889999


No 219
>PRK01297 ATP-dependent RNA helicase RhlB; Provisional
Probab=95.90  E-value=0.025  Score=37.88  Aligned_cols=75  Identities=20%  Similarity=0.271  Sum_probs=61.6

Q ss_pred             HCCEEEEEHHHHHHHHHHHHHHHHCCCCCCEEEEEECCCCHHHHHHHHHHHCCCCCEEEEECHHHCCCCCCCCCCCEEEE
Q ss_conf             05458861279999999986211014578658996246422566768776213475486411120133455444417885
Q gi|254780945|r  321 GGQAVIMAPIGILAQQHYEFIKKYTQNTQIIVEIITGNMPQAHRRKALERIAHGQAHIIIGTHALFQDSIQYYKLILVIV  400 (700)
Q Consensus       321 G~Q~alMaPTEILA~QH~~~~~~~~~~~~i~v~lLtg~~~~~er~~i~~~i~~G~~~iiIGTHAL~q~~v~F~~LgLvVi  400 (700)
                      ..++.+-+.|---++.    +.+.|...++++..|+|.++..+|..++++.++|+..|+|.|- +...++.|.++.+||-
T Consensus       332 ~~k~IIF~nt~~~~~~----l~~~L~~~g~~~~~lhg~l~q~~R~~~l~~F~~g~~~iLVaTD-vaaRGLDi~~V~~VIn  406 (472)
T PRK01297        332 WERVMVFANRKDEVRR----IEERLVKDGINAAQLSGDVPQHKRIKTLEGFREGKIRVLVATD-VAGRGIHIDGISHVIN  406 (472)
T ss_pred             CCCEEEECCCHHHHHH----HHHHHHHCCCCEEEEECCCCHHHHHHHHHHHHCCCCCEEEECC-HHHCCCCCCCCCEEEE
T ss_conf             8736896174999999----9987654496168643778999999999999769996998866-1336677578888999


No 220
>TIGR01448 recD_rel helicase, RecD/TraA family; InterPro: IPR006345   These sequences represent a family similar to RecD, the exodeoxyribonuclease V alpha chain of IPR006344 from INTERPRO. Members of this family, however, are not found in a context of RecB and RecC and are longer by about 200 amino acids at the amino end. Chlamydia muridarum has both a member of this family and a RecD. .
Probab=95.90  E-value=0.059  Score=34.92  Aligned_cols=116  Identities=24%  Similarity=0.345  Sum_probs=71.8

Q ss_pred             HHHHHHHHCCCCCCHHHHHHHHHHHHHHCCCCCCEEEEEECCCCCHHHH-----HHHHHHHH--------HHHHCCEEEE
Q ss_conf             8999986302467988999999999841001343078862144223699-----99997334--------4430545886
Q gi|254780945|r  261 IAQKILRNIPFSPTKSQESAIKDILQDMSQKNRMLRILQGDVGSGKTLV-----ALIAMAAA--------VEAGGQAVIM  327 (700)
Q Consensus       261 ~~~~f~~~LPF~LT~~Q~~ai~eI~~Dl~~~~pM~RLLQGDVGSGKTiV-----A~~A~l~~--------~~~G~Q~alM  327 (700)
                      .+-+.-+.+-|+|.+.|++|+..+..    .+-|  +|-|==|.|||=|     ++++.+..        +...+.+.|-
T Consensus       339 hi~eve~~~~~~l~~~Qk~AL~~~~~----~Kv~--iLTGGPGTGKtT~t~~i~~~~~~~~gl~l~~~~~vndd~~v~La  412 (769)
T TIGR01448       339 HILEVEKKLRLKLSEEQKEALKTAIQ----DKVV--ILTGGPGTGKTTITKAIIELYEELKGLDLDKDDYVNDDLPVVLA  412 (769)
T ss_pred             HHHHHHHHHCCCHHHHHHHHHHHHHC----CCEE--EEECCCCCCHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCEEEEE
T ss_conf             99986875067706889999999860----9489--98577888616899999999987168775531245677648873


Q ss_pred             EHHHHHHHHHHHHHHHHCCCCCCEEEEEECCCCHHHHHHHHHHHCCCCCEEEEECHH-HCCCCCCCCCCCEEEECCCCCC
Q ss_conf             127999999998621101457865899624642256676877621347548641112-0133455444417885210133
Q gi|254780945|r  328 APIGILAQQHYEFIKKYTQNTQIIVEIITGNMPQAHRRKALERIAHGQAHIIIGTHA-LFQDSIQYYKLILVIVDEQHRF  406 (700)
Q Consensus       328 aPTEILA~QH~~~~~~~~~~~~i~v~lLtg~~~~~er~~i~~~i~~G~~~iiIGTHA-L~q~~v~F~~LgLvViDEQHRF  406 (700)
                      |||-==|+|    +.+.-..--..|.=|-|               -|.-.-.   |. ..++.+...   |+||||   |
T Consensus       413 APTGrAAkR----l~E~TG~~a~TIHRLlG---------------~~~~~~~---~~k~~~~~~~~D---L~IvDE---~  464 (769)
T TIGR01448       413 APTGRAAKR----LAEVTGLEALTIHRLLG---------------YGSDTKS---ENKNLEDPIDAD---LLIVDE---S  464 (769)
T ss_pred             CCCHHHHHH----CCCCCCCHHHHHHHHHC---------------CCCCCCC---CCHHHCCCCCCC---EEEEEC---C
T ss_conf             774378885----11002621234778636---------------8988873---211011347877---699814---6


Q ss_pred             CHHH
Q ss_conf             5688
Q gi|254780945|r  407 GVQQ  410 (700)
Q Consensus       407 GV~Q  410 (700)
                      +---
T Consensus       465 SM~D  468 (769)
T TIGR01448       465 SMVD  468 (769)
T ss_pred             CHHH
T ss_conf             2188


No 221
>PRK03348 DNA polymerase IV; Provisional
Probab=95.87  E-value=0.0057  Score=42.86  Aligned_cols=17  Identities=24%  Similarity=0.485  Sum_probs=9.4

Q ss_pred             EECCCCCCCHHHHHHHH
Q ss_conf             31201469989999999
Q gi|254780945|r  518 IAIIHGRMSDIDKESVM  534 (700)
Q Consensus       518 v~~lHGkm~~~ek~~~m  534 (700)
                      +|+--..+++...+.-.
T Consensus       336 lGV~~s~l~~~~q~~lf  352 (456)
T PRK03348        336 VGVGFSGLSDVRQESLF  352 (456)
T ss_pred             EEEECCCCCHHHHHHHC
T ss_conf             97650675466676525


No 222
>KOG1000 consensus
Probab=95.86  E-value=0.054  Score=35.22  Aligned_cols=326  Identities=20%  Similarity=0.295  Sum_probs=174.1

Q ss_pred             HHCCCCCCHHHHHHHHHHHHHHCCCCCCEEEEEECCCCCHHHHHHHHHHHHHHHHCCEEEEEHHHHHHHHHHHHHHHHCC
Q ss_conf             63024679889999999998410013430788621442236999999733444305458861279999999986211014
Q gi|254780945|r  267 RNIPFSPTKSQESAIKDILQDMSQKNRMLRILQGDVGSGKTLVALIAMAAAVEAGGQAVIMAPIGILAQQHYEFIKKYTQ  346 (700)
Q Consensus       267 ~~LPF~LT~~Q~~ai~eI~~Dl~~~~pM~RLLQGDVGSGKTiVA~~A~l~~~~~G~Q~alMaPTEILA~QH~~~~~~~~~  346 (700)
                      .-|||++-        -..--|.++-.|  ||--|.|=||||-|+ |++.+..+-+--.+.+|..+ -.--.+.+..||+
T Consensus       198 ~LlPFQre--------Gv~faL~RgGR~--llADeMGLGKTiQAl-aIA~yyraEwplliVcPAsv-rftWa~al~r~lp  265 (689)
T KOG1000         198 RLLPFQRE--------GVIFALERGGRI--LLADEMGLGKTIQAL-AIARYYRAEWPLLIVCPASV-RFTWAKALNRFLP  265 (689)
T ss_pred             HHCCHHHH--------HHHHHHHCCCEE--EEECCCCCCHHHHHH-HHHHHHHHCCCEEEEECHHH-HHHHHHHHHHHCC
T ss_conf             61703565--------478898538739--984124541688999-99999860486799922788-6899999998531


Q ss_pred             CCCCEEEEEECCCCHHHHHHHHHHH-CCCCCEEEEECH-HHCCCCCCCCCCCEEEECCCCCCCHHHHHH------HHHCC
Q ss_conf             5786589962464225667687762-134754864111-201334554444178852101335688998------74025
Q gi|254780945|r  347 NTQIIVEIITGNMPQAHRRKALERI-AHGQAHIIIGTH-ALFQDSIQYYKLILVIVDEQHRFGVQQRLK------LTQKA  418 (700)
Q Consensus       347 ~~~i~v~lLtg~~~~~er~~i~~~i-~~G~~~iiIGTH-AL~q~~v~F~~LgLvViDEQHRFGV~QR~~------L~~Kg  418 (700)
                      ... +|.+.-++.-      -+..+ .++++.|+-=-. .+..+-..-..-++||+||-|-.--.|...      +.+  
T Consensus       266 s~~-pi~vv~~~~D------~~~~~~t~~~v~ivSye~ls~l~~~l~~~~~~vvI~DEsH~Lk~sktkr~Ka~~dllk--  336 (689)
T KOG1000         266 SIH-PIFVVDKSSD------PLPDVCTSNTVAIVSYEQLSLLHDILKKEKYRVVIFDESHMLKDSKTKRTKAATDLLK--  336 (689)
T ss_pred             CCC-CEEEEECCCC------CCCCCCCCCEEEEEEHHHHHHHHHHHHCCCCEEEEEECHHHHHCCCHHHHHHHHHHHH--
T ss_conf             026-0478852667------7654566772789878999999998736541189971256541011223666656998--


Q ss_pred             CCCCCEEECHHHH-HHHHHH---------HHHHC-----------------------------------------CCHHH
Q ss_conf             6776101010132-278999---------97520-----------------------------------------10111
Q gi|254780945|r  419 TAPHVLLMTATPI-PRTLVL---------TSLGD-----------------------------------------IDISK  447 (700)
Q Consensus       419 ~~ph~L~MtATPI-PRTLal---------~~ygd-----------------------------------------ldvS~  447 (700)
                      ..-|++.+|-||- -|-.-|         ++|-+                                         +.--+
T Consensus       337 ~akhvILLSGTPavSRP~elytqi~avd~tlfp~f~efa~rYCd~k~vr~~~Dykg~tnl~EL~~lL~k~lMIRRlK~dv  416 (689)
T KOG1000         337 VAKHVILLSGTPAVSRPSELYTQIRAVDHTLFPNFHEFAIRYCDGKQVRFCFDYKGCTNLEELAALLFKRLMIRRLKADV  416 (689)
T ss_pred             HHHHEEEECCCCCCCCCHHHHHHHHHHCCCCCCCHHHHHHHHCCCCCCCEEEECCCCCCHHHHHHHHHHHHHHHHHHHHH
T ss_conf             76444772388556781442135554121004228998777537641102450377877899999999999999999988


Q ss_pred             HCCCCCCCCCCEEEEEECCCHHHHHHHHHHHHCCCCEE----------------------EEEECCCCC--------CCC
Q ss_conf             10235576662079997020026899997631038738----------------------999712012--------211
Q gi|254780945|r  448 ITEKPAGRKPIKTVIIPINRIDEVIERLKVVLSEGKKA----------------------YWICPQIEE--------KKE  497 (700)
Q Consensus       448 i~e~P~gR~~I~T~~~~~~~~~~~~~~i~~~l~~g~q~----------------------y~VcPlIee--------se~  497 (700)
                      +.++|+.|..| +++.........-+.+.+.. ++..+                      --||--|-+        +++
T Consensus       417 L~qLPpKrr~V-v~~~~gr~da~~~~lv~~a~-~~t~~~~~e~~~~~l~l~y~~tgiaK~~av~eyi~~~~~l~d~~~~K  494 (689)
T KOG1000         417 LKQLPPKRREV-VYVSGGRIDARMDDLVKAAA-DYTKVNSMERKHESLLLFYSLTGIAKAAAVCEYILENYFLPDAPPRK  494 (689)
T ss_pred             HHHCCCCCEEE-EEECCCCCCHHHHHHHHHHH-HCCHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHCCCCCCCCCCE
T ss_conf             75388010489-99747862267899998753-20012366665677887898751102088999997474445688735


Q ss_pred             CC-CCHHHHHHHHHHHHCCC-CEEC--CCCCCCHHHHHHHHHHHHCCC-EE-EEEECHHHHCCCCCCCCCEEEEECHHH-
Q ss_conf             12-10146666666866371-0312--014699899999999975598-69-999800341046888765899858525-
Q gi|254780945|r  498 SN-FRSVVERFNSLHEHFTS-SIAI--IHGRMSDIDKESVMDSFKNGT-CK-LLIATTVIEVGIDVVDASIIIIENAEH-  570 (700)
Q Consensus       498 ~~-~~~~~~~~~~l~~~~~~-~v~~--lHGkm~~~ek~~~m~~F~~g~-~~-iLvaTtviEVGvdvpna~~mvI~~aer-  570 (700)
                      .= ..--....+.++..+-+ +||.  +-|.-.+.+++..-+.|...+ +. -++|-|---||++.-.|++.|-  ||- 
T Consensus       495 flVFaHH~~vLd~Iq~~~~~r~vg~IRIDGst~s~~R~ll~qsFQ~seev~VAvlsItA~gvGLt~tAa~~VVF--aEL~  572 (689)
T KOG1000         495 FLVFAHHQIVLDTIQVEVNKRKVGSIRIDGSTPSHRRTLLCQSFQTSEEVRVAVLSITAAGVGLTLTAASVVVF--AELH  572 (689)
T ss_pred             EEEEEHHHHHHHHHHHHHHHCCCCEEEECCCCCCHHHHHHHHHHCCCCCEEEEEEEEEECCCCEEEECCCEEEE--EEEC
T ss_conf             99994148799999999987479758856989843478999873146314799999863144414651325899--9823


Q ss_pred             CCHHHHHHHHHCCCCCCCCEE---EEEEECCCCCH----HHHHHHHHHHHHCHH
Q ss_conf             474688773011667898359---99970888998----799999999841425
Q gi|254780945|r  571 FGLAQLHQLRGRVGRGEEISS---CILLYHPPLSK----NSYTRLSVLKNTEDG  617 (700)
Q Consensus       571 fGLsqLHQLRGRVGRg~~~s~---c~l~~~~~~~~----~~~~Rl~~l~~~~dG  617 (700)
                      |-=+-|-|---|+-|=+..|.   -||+......+    .-.+.|+++.++.+|
T Consensus       573 wnPgvLlQAEDRaHRiGQkssV~v~ylvAKgT~Ddy~Wp~l~~KL~vl~s~gl~  626 (689)
T KOG1000         573 WNPGVLLQAEDRAHRIGQKSSVFVQYLVAKGTADDYMWPMLQQKLDVLGSVGLS  626 (689)
T ss_pred             CCCCEEEECHHHHHHCCCCCEEEEEEEEECCCHHHHHHHHHHHHHHHHHHCCCC
T ss_conf             787547751465664056651138999954845777789999998788662567


No 223
>PRK02406 DNA polymerase IV; Validated
Probab=95.84  E-value=0.0068  Score=42.29  Aligned_cols=40  Identities=23%  Similarity=0.229  Sum_probs=18.0

Q ss_pred             CCCCCHHHHHHHHHHHHHHHHCCEEEEEHHHHHHHHHHHHHHHHCCCCCCEE
Q ss_conf             1442236999999733444305458861279999999986211014578658
Q gi|254780945|r  301 DVGSGKTLVALIAMAAAVEAGGQAVIMAPIGILAQQHYEFIKKYTQNTQIIV  352 (700)
Q Consensus       301 DVGSGKTiVA~~A~l~~~~~G~Q~alMaPTEILA~QH~~~~~~~~~~~~i~v  352 (700)
                      -+|..|++ |=+|.-.+--+| +. ++.|-         .+.+++.+++|+-
T Consensus       145 GIa~nk~l-AK~As~~~KP~G-~~-vv~~~---------~~~~~L~~lpv~~  184 (355)
T PRK02406        145 GVAPNKFL-AKIASDWNKPNG-QF-VITPE---------EVPAFVATLPVEK  184 (355)
T ss_pred             ECCCCHHH-HHHHHHHCCCCC-CE-EECHH---------HHHHHHHHCCCCC
T ss_conf             02567999-999886239876-63-65678---------9999996188740


No 224
>KOG1802 consensus
Probab=95.83  E-value=0.036  Score=36.64  Aligned_cols=80  Identities=29%  Similarity=0.417  Sum_probs=62.2

Q ss_pred             HCCCCCCHHHHHHHHHHHHHHCCCCCCEEEEEECCCCCHHHHHHHHHHHHHH-HHCCEEEEEHHHHHHHHHHHHHHHHCC
Q ss_conf             3024679889999999998410013430788621442236999999733444-305458861279999999986211014
Q gi|254780945|r  268 NIPFSPTKSQESAIKDILQDMSQKNRMLRILQGDVGSGKTLVALIAMAAAVE-AGGQAVIMAPIGILAQQHYEFIKKYTQ  346 (700)
Q Consensus       268 ~LPF~LT~~Q~~ai~eI~~Dl~~~~pM~RLLQGDVGSGKTiVA~~A~l~~~~-~G~Q~alMaPTEILA~QH~~~~~~~~~  346 (700)
                      +|| +|..+|..|++..+.     .|. -|+||--|.|||++...-.++.+. .+.++.+.||.-|-..|..+.+.+-  
T Consensus       407 ~lp-kLN~SQ~~AV~~VL~-----rpl-sLIQGPPGTGKTvtsa~IVyhl~~~~~~~VLvcApSNiAVDqLaeKIh~t--  477 (935)
T KOG1802         407 NLP-KLNASQSNAVKHVLQ-----RPL-SLIQGPPGTGKTVTSATIVYHLARQHAGPVLVCAPSNIAVDQLAEKIHKT--  477 (935)
T ss_pred             CCH-HHCHHHHHHHHHHHC-----CCC-EEEECCCCCCCEEHHHHHHHHHHHHCCCCEEEECCCCHHHHHHHHHHHHC--
T ss_conf             961-224678999999975-----985-15546999883311689999999852895699816500289999999861--


Q ss_pred             CCCCEEEEEECC
Q ss_conf             578658996246
Q gi|254780945|r  347 NTQIIVEIITGN  358 (700)
Q Consensus       347 ~~~i~v~lLtg~  358 (700)
                        |++|.-|+++
T Consensus       478 --gLKVvRl~ak  487 (935)
T KOG1802         478 --GLKVVRLCAK  487 (935)
T ss_pred             --CCEEEEEEHH
T ss_conf             --8547640021


No 225
>cd04483 hOBFC1_like hOBFC1_like: A subfamily of OB folds similar to that found in human OB fold containing protein 1 (hOBFC1). Members of this group belong to the Replication protein A subunit 2 (RPA2) family of OB folds. RPA is a nuclear ssDNA binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). The OB fold domain of RPA2 has dual roles in ssDNA binding and trimerization.
Probab=95.82  E-value=0.11  Score=32.79  Aligned_cols=67  Identities=18%  Similarity=0.254  Sum_probs=51.2

Q ss_pred             EEEEEEEEEEECCCCCCEEEEEEECCCCEEEEEEECCCH-H-------------------HHHHHCCCCCEEEEEEEEEE
Q ss_conf             999998975421589833899998189369999951887-8-------------------99873289888999989973
Q gi|254780945|r   72 ITGYISQHSSFQLQKRRPYKILLNDGTGEITLLFFYRKT-E-------------------MLKNVFFEGRKITVTGKIKK  131 (700)
Q Consensus        72 i~g~V~~~~~~~~~~r~~~~v~v~D~tg~i~lvfFn~~~-~-------------------yl~k~lk~G~~v~vsGKv~~  131 (700)
                      |.|.|++....    ...+...+.|+||-|+++.|-+.. .                   -.+..+.+|+-+.|.|+++.
T Consensus         2 IlG~VVs~~er----e~f~~y~vDDgTGcI~Cv~W~~~~~~~~~s~~~~~~~~~~~~~a~~~~~~l~iG~llRVRG~I~~   77 (92)
T cd04483           2 ILGTVVSRRER----ETFYSFGVDDGTGVVNCVCWKNLSYAEVSSRSDAARILKSALMALKQAKVLEIGDLLRVRGSIRT   77 (92)
T ss_pred             EEEEEEEEEEE----CCEEEEEEECCCCEEEEEEEECCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCCCCEEEEEEEEEE
T ss_conf             37999999760----57169986089866998996045767766667844544445788876115775238999426888


Q ss_pred             CCCEEEEECCE
Q ss_conf             18779997786
Q gi|254780945|r  132 LKNRIIMVHPH  142 (700)
Q Consensus       132 ~~~~~qi~hPe  142 (700)
                      |++..|+.--.
T Consensus        78 yRg~rei~as~   88 (92)
T cd04483          78 YRGEREINASV   88 (92)
T ss_pred             EECEEEEEEEE
T ss_conf             70448996899


No 226
>cd01701 Pol_zeta Pol_zeta, a member of the Y-family of DNA polymerases. Y-family polymerases can transverse normal replication-blocking DNA lesions, such as cyclobutane pyrimidine dimers resulting from UV damage, at higher error rate. The Y-family has no 3'-5' exonuclease activity. Pol zeta has also been named Rev1; this subfamily is mainly present in eukaryotes.
Probab=95.79  E-value=0.0064  Score=42.48  Aligned_cols=15  Identities=33%  Similarity=0.330  Sum_probs=9.1

Q ss_pred             CCCCCHHHHHHHHHC
Q ss_conf             013356889987402
Q gi|254780945|r  403 QHRFGVQQRLKLTQK  417 (700)
Q Consensus       403 QHRFGV~QR~~L~~K  417 (700)
                      +.+||+..=..|...
T Consensus       261 ~~~fG~k~G~~l~~~  275 (405)
T cd01701         261 QKVFGKKTGEKLYNY  275 (405)
T ss_pred             HHHHHHHHHHHHHHH
T ss_conf             999778999999999


No 227
>PRK06835 DNA replication protein DnaC; Validated
Probab=95.68  E-value=0.042  Score=36.07  Aligned_cols=48  Identities=15%  Similarity=0.322  Sum_probs=40.6

Q ss_pred             HHCCCCCCEEEEEECCCCCHHHHHHHHHHHHHHHHCCEEEEEHHHHHHH
Q ss_conf             4100134307886214422369999997334443054588612799999
Q gi|254780945|r  287 DMSQKNRMLRILQGDVGSGKTLVALIAMAAAVEAGGQAVIMAPIGILAQ  335 (700)
Q Consensus       287 Dl~~~~pM~RLLQGDVGSGKTiVA~~A~l~~~~~G~Q~alMaPTEILA~  335 (700)
                      ...++. -|=|+.|+||.|||-.|..-+-..++.|+.|.++..++++..
T Consensus       178 ~F~~~~-~nLlf~G~~G~GKTfLa~~IA~ell~~g~sViy~ta~~L~~~  225 (330)
T PRK06835        178 NFDKNN-ENLLFYGNTGTGKTFLSNCIAKELLDRGKTVIYRTSDELIEN  225 (330)
T ss_pred             HCCCCC-CCEEEECCCCCCHHHHHHHHHHHHHHCCCEEEEEEHHHHHHH
T ss_conf             247888-866988999998899999999999987994999629999999


No 228
>PRK06921 hypothetical protein; Provisional
Probab=95.68  E-value=0.061  Score=34.81  Aligned_cols=53  Identities=19%  Similarity=0.220  Sum_probs=36.5

Q ss_pred             HHHHHHC---CCCCCEEEEEECCCCCHHHHHHHHHHHHHHH-HCCEEEEEHHHHHHH
Q ss_conf             9998410---0134307886214422369999997334443-054588612799999
Q gi|254780945|r  283 DILQDMS---QKNRMLRILQGDVGSGKTLVALIAMAAAVEA-GGQAVIMAPIGILAQ  335 (700)
Q Consensus       283 eI~~Dl~---~~~pM~RLLQGDVGSGKTiVA~~A~l~~~~~-G~Q~alMaPTEILA~  335 (700)
                      +-..+..   ....-+=++.|+||+|||-.|...+-..++. |.+|.+|.=.|++..
T Consensus       103 eY~~~F~~i~~~~~~~l~f~G~~G~GKThLa~aIa~~Ll~~~~~~Vly~~~~~~~~~  159 (265)
T PRK06921        103 EYVKDFEKIQGCRKNSIALLGQPGSGKTHLLTAAANELMRKKGVPVLYFPFVEGFGD  159 (265)
T ss_pred             HHHHHHHHHHCCCCCCEEEECCCCCCHHHHHHHHHHHHHHHCCCEEEEEEHHHHHHH
T ss_conf             999977876077766279972898988999999999999962971999887999999


No 229
>COG3267 ExeA Type II secretory pathway, component ExeA (predicted ATPase) [Intracellular trafficking and secretion]
Probab=95.65  E-value=0.027  Score=37.56  Aligned_cols=54  Identities=20%  Similarity=0.322  Sum_probs=36.9

Q ss_pred             CCHHHHHHHHHHHHHHCCCCCCEEEEEECCCCCHHHHHHHHHHHHHHHHCCEEE-EEH
Q ss_conf             798899999999984100134307886214422369999997334443054588-612
Q gi|254780945|r  273 PTKSQESAIKDILQDMSQKNRMLRILQGDVGSGKTLVALIAMAAAVEAGGQAVI-MAP  329 (700)
Q Consensus       273 LT~~Q~~ai~eI~~Dl~~~~pM~RLLQGDVGSGKTiVA~~A~l~~~~~G~Q~al-MaP  329 (700)
                      .+.+-++++..|..+.+.+.-- -.+-|+||||||++.= |++... ++-|++. +.|
T Consensus        32 ~~a~h~e~l~~l~~~i~d~qg~-~~vtGevGsGKTv~~R-al~~s~-~~d~~~~v~i~   86 (269)
T COG3267          32 WAADHNEALLMLHAAIADGQGI-LAVTGEVGSGKTVLRR-ALLASL-NEDQVAVVVID   86 (269)
T ss_pred             HHHHHHHHHHHHHHHHHCCCCE-EEEEECCCCCHHHHHH-HHHHHC-CCCCEEEEEEC
T ss_conf             3200159999977777517855-9997447776369999-999855-78851799835


No 230
>KOG4150 consensus
Probab=95.64  E-value=0.088  Score=33.56  Aligned_cols=286  Identities=15%  Similarity=0.131  Sum_probs=163.4

Q ss_pred             CCCCHHHHHHHHHHHHHHHHCCEEEEEHHHHH--HHHHHHHHHHHCCCCC----CEEEEEECCCCHHHHHHHHHHHCCCC
Q ss_conf             44223699999973344430545886127999--9999986211014578----65899624642256676877621347
Q gi|254780945|r  302 VGSGKTLVALIAMAAAVEAGGQAVIMAPIGIL--AQQHYEFIKKYTQNTQ----IIVEIITGNMPQAHRRKALERIAHGQ  375 (700)
Q Consensus       302 VGSGKTiVA~~A~l~~~~~G~Q~alMaPTEIL--A~QH~~~~~~~~~~~~----i~v~lLtg~~~~~er~~i~~~i~~G~  375 (700)
                      .-|||..+.-.++.....-..-..+|-|.|.-  |+-.-..++-.++..+    --|+.--|-+-.-++.  +.+   -.
T Consensus       310 ~~~GK~~~~~~~s~~~~~~~~~s~~~~~~~~~~~~~~~~~~~~V~~~~I~~~K~A~V~~~D~~sE~~~~A--~~R---~~  384 (1034)
T KOG4150         310 RQAGKGTCPTSGSRKFQTLCHATNSLLPSEMVEHLRNGSKGQVVHVEVIKARKSAYVEMSDKLSETTKSA--LKR---IG  384 (1034)
T ss_pred             CCCCCCCCCCHHHHHHHHCCCCCCEECCHHHHHHHHCCCCCEEEEEEEHHHHHCCEEECCCCCCCHHHHH--HHH---CC
T ss_conf             1157664645002456532865342214248998634676549998711332112465236777346778--876---27


Q ss_pred             CEEEEECH-----HHCCC----CCCCCCCCEEEECCCCC----CCHHHHHHHH-----HCC----CCCCCEEECHHHHHH
Q ss_conf             54864111-----20133----45544441788521013----3568899874-----025----677610101013227
Q gi|254780945|r  376 AHIIIGTH-----ALFQD----SIQYYKLILVIVDEQHR----FGVQQRLKLT-----QKA----TAPHVLLMTATPIPR  433 (700)
Q Consensus       376 ~~iiIGTH-----AL~q~----~v~F~~LgLvViDEQHR----FGV~QR~~L~-----~Kg----~~ph~L~MtATPIPR  433 (700)
                      .+.+.-..     |.+-.    .+..-.+-++++||-|-    ||-.--..|+     -||    .+-.+.--+||-=-|
T Consensus       385 ~~~~~s~~~~~~s~~L~~~~~~~~~~~~~~~~~~~~~~~Y~~~~~~~~~~~~R~L~~L~~~F~~~~~~~~~~~~~~~K~~  464 (1034)
T KOG4150         385 LNTLYSHQAEAISAALAKSLCYNVPVFEELCKDTNSCALYLFPTKALAQDQLRALSDLIKGFEASINMGVYDGDTPYKDR  464 (1034)
T ss_pred             CCEEECCHHHHHHHHHCCCCCCCHHHHHHHHHHCCEEEEEECCHHHHHHHHHHHHHHHHHHHHHHCCCEEEECCCCCCCH
T ss_conf             52352488899988603333433076887774023001230333668999999999998778860584168478876777


Q ss_pred             HHHHHH-H--HCCCHHHHCCCCCCCCCCEEEEEE----------CCCHHHHHHHHHHHHCCCCEEEEEECCCCCCCCCCC
Q ss_conf             899997-5--201011110235576662079997----------020026899997631038738999712012211121
Q gi|254780945|r  434 TLVLTS-L--GDIDISKITEKPAGRKPIKTVIIP----------INRIDEVIERLKVVLSEGKKAYWICPQIEEKKESNF  500 (700)
Q Consensus       434 TLal~~-y--gdldvS~i~e~P~gR~~I~T~~~~----------~~~~~~~~~~i~~~l~~g~q~y~VcPlIeese~~~~  500 (700)
                      |--|.- +  .++.+-.+|.-|.|-|-.. .|-+          ++...++-....+-+..|-++.--||.-.--|   +
T Consensus       465 ~~~~~~~~~~~E~~Li~~DGSPs~~K~~V-~WNP~~~P~~~~~~~~~i~E~s~~~~~~i~~~~R~IAFC~~R~~CE---L  540 (1034)
T KOG4150         465 TRLRSELANLSELELVTIDGSPSSEKLFV-LWNPSAPPTSKSEKSSKVVEVSHLFAEMVQHGLRCIAFCPSRKLCE---L  540 (1034)
T ss_pred             HHHHHHHCCCCCEEEEEECCCCCCCCEEE-EECCCCCCCCHHHHHHHHHHHHHHHHHHHHCCCCEEEECCHHHHHH---H
T ss_conf             78899855876049997159987741699-9689999830344323899999999999971873899632898999---9


Q ss_pred             CHHHHHHHHHHHHCCC---CEECCCCCCCHHHHHHHHHHHHCCCEEEEEECHHHHCCCCCCCCCEEEEECHHHCCHHHHH
Q ss_conf             0146666666866371---0312014699899999999975598699998003410468887658998585254746887
Q gi|254780945|r  501 RSVVERFNSLHEHFTS---SIAIIHGRMSDIDKESVMDSFKNGTCKLLIATTVIEVGIDVVDASIIIIENAEHFGLAQLH  577 (700)
Q Consensus       501 ~~~~~~~~~l~~~~~~---~v~~lHGkm~~~ek~~~m~~F~~g~~~iLvaTtviEVGvdvpna~~mvI~~aerfGLsqLH  577 (700)
                      - .-..-+.+.+.-++   .|---.|--..+++-++-.+.--|+..-.+||.-.|.|||+-.....+-. .=-..+|-||
T Consensus       541 ~-~~~~R~I~~ET~~~LV~~i~SYRGGY~A~DRRKIE~~~F~G~L~giIaTNALELGIDIG~LDAVl~~-GFP~S~aNl~  618 (1034)
T KOG4150         541 V-LCLTREILAETAPHLVEAITSYRGGYIAEDRRKIESDLFGGKLCGIIATNALELGIDIGHLDAVLHL-GFPGSIANLW  618 (1034)
T ss_pred             H-HHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHCCEEEEEEECCHHHHCCCCCCCCEEEEC-CCCCHHHHHH
T ss_conf             9-9999999987447899999861477535567777888517826899853607444243564368982-6850677899


Q ss_pred             HHHHCCCCCCCCEEEEEEECC
Q ss_conf             730116678983599997088
Q gi|254780945|r  578 QLRGRVGRGEEISSCILLYHP  598 (700)
Q Consensus       578 QLRGRVGRg~~~s~c~l~~~~  598 (700)
                      |--||-||-++.|....+...
T Consensus       619 QQ~GRAGRRNk~SLavyva~~  639 (1034)
T KOG4150         619 QQAGRAGRRNKPSLAVYVAFL  639 (1034)
T ss_pred             HHHHHCCCCCCCCEEEEEEEC
T ss_conf             872110156898448999742


No 231
>TIGR02621 cas3_GSU0051 CRISPR-associated helicase Cas3, Anaes-subtype; InterPro: IPR013444    This entry represents a CRISPR-associated putative DEAH-box helicase, or Cas3, subtype found in Actinomyces naeslundii MG1, Geobacter sulfurreducens PCA, Gemmata obscuriglobus UQM 2246, and Desulfotalea psychrophila. The proteins include both DEAH and HD motifs..
Probab=95.62  E-value=0.013  Score=39.98  Aligned_cols=282  Identities=21%  Similarity=0.256  Sum_probs=164.7

Q ss_pred             CCCCHH-HHHHHHHHHHHHHHCCE-----EEEEHHHHH--------HHHH---HHHHHHHCCCC----------------
Q ss_conf             442236-99999973344430545-----886127999--------9999---98621101457----------------
Q gi|254780945|r  302 VGSGKT-LVALIAMAAAVEAGGQA-----VIMAPIGIL--------AQQH---YEFIKKYTQNT----------------  348 (700)
Q Consensus       302 VGSGKT-iVA~~A~l~~~~~G~Q~-----alMaPTEIL--------A~QH---~~~~~~~~~~~----------------  348 (700)
                      .|+||| .|-+.=.|++..+..|+     .--+|+=+.        -.|-   .+++.+-|...                
T Consensus        41 Tg~GKTlavi~~WlyAl~~~a~~~Grrr~~~~vP~RL~yvVdRR~vVD~~te~a~~i~~aL~~~pe~~Av~~vl~slr~~  120 (975)
T TIGR02621        41 TGLGKTLAVIAVWLYALAIDAEQVGRRRRRRKVPRRLVYVVDRRTVVDQSTEEAEKIREALGEAPELPAVRYVLESLRSA  120 (975)
T ss_pred             CCCHHHHHHHHHHHHHHHHCCCCCCCCCCEEECCCEEEEEEECCEEECCHHHHHHHHHHHCCCCCCHHHHHHHHHHHCCC
T ss_conf             53236899999999998740003673242133683137887142453432789999998546888778999999973236


Q ss_pred             --------CCEEEEEECCCCHHHHHHHHHHHCCCCCEEEEEC-----HHHCCC--CCCCC----------CCCEEEECCC
Q ss_conf             --------8658996246422566768776213475486411-----120133--45544----------4417885210
Q gi|254780945|r  349 --------QIIVEIITGNMPQAHRRKALERIAHGQAHIIIGT-----HALFQD--SIQYY----------KLILVIVDEQ  403 (700)
Q Consensus       349 --------~i~v~lLtg~~~~~er~~i~~~i~~G~~~iiIGT-----HAL~q~--~v~F~----------~LgLvViDEQ  403 (700)
                              .+.|.-|=|......|.-.--...=..+-|||||     .=|+-.  .+-|+          +=+|+|-||=
T Consensus       121 ~~~Pa~a~pl~v~~LRGg~ad~~rDltew~~~P~rPavivgTvDm~gSRLLFrGYg~spk~rpihAal~G~DAl~VlDEA  200 (975)
T TIGR02621       121 FAIPAEAEPLAVSTLRGGFADNDRDLTEWTRDPSRPAVIVGTVDMIGSRLLFRGYGCSPKSRPIHAALLGQDALIVLDEA  200 (975)
T ss_pred             CCCCCCCCCCEEEECCCCCCCHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHHCCCCCCCCCCHHHHHHHCHHHHHHHHH
T ss_conf             78776566523311167553022323345317899669983442023435441345676655112221311066543343


Q ss_pred             CCCCHHHHH-------HHHHCCC-CCCCEEECHHHHHH---HHHHHHHHCCCHHHHC-----------CCCCCCCCCEEE
Q ss_conf             133568899-------8740256-77610101013227---8999975201011110-----------235576662079
Q gi|254780945|r  404 HRFGVQQRL-------KLTQKAT-APHVLLMTATPIPR---TLVLTSLGDIDISKIT-----------EKPAGRKPIKTV  461 (700)
Q Consensus       404 HRFGV~QR~-------~L~~Kg~-~ph~L~MtATPIPR---TLal~~ygdldvS~i~-----------e~P~gR~~I~T~  461 (700)
                      |==---|-.       ..+-+.. .-|+..|||||.-=   ++.+.--+|-.--+.+           .++..-+.+.+.
T Consensus       201 Hl~~~f~e~L~~i~~E~~R~~d~~~~~V~~Ltatp~td~p~~~~~l~~~d~~~~~~~~rL~~kk~~~L~p~~de~~~~~~  280 (975)
T TIGR02621       201 HLSPAFQETLKQIRSEQQRLEDFLPLRVVELTATPRTDTPDTLTLLSAEDYKHPVLKKRLDAKKEVKLDPQSDEKRLSED  280 (975)
T ss_pred             HCCHHHHHHHHHHHHHCCCHHHCCCCEECCEEEECCCCCCCCCCCCCCCCCCCCHHHCCHHHHCCCCCCCCHHHHHHHHH
T ss_conf             05878999999985110470122686203136630147886542235510103133204341202104782689998851


Q ss_pred             EEECC----C-------HHHHHHHHHHHHCCCCEEEEEECCCCCCCCCCCCHHHHHHHHHHHHCCCCEECCCCCCCHHHH
Q ss_conf             99702----0-------026899997631038738999712012211121014666666686637103120146998999
Q gi|254780945|r  462 IIPIN----R-------IDEVIERLKVVLSEGKKAYWICPQIEEKKESNFRSVVERFNSLHEHFTSSIAIIHGRMSDIDK  530 (700)
Q Consensus       462 ~~~~~----~-------~~~~~~~i~~~l~~g~q~y~VcPlIeese~~~~~~~~~~~~~l~~~~~~~v~~lHGkm~~~ek  530 (700)
                      +..-+    +       -+++|++. ++|..|+=+.|+|--+        ..|...+..|++..+. +..+-|++..-||
T Consensus       281 v~~~~~~~~DGkaaaalteqaWsra-kels~g~~~~Vf~~~~--------~~v~~v~a~L~k~~~~-~~~ltG~vr~~~~  350 (975)
T TIGR02621       281 VKELDLKMKDGKAAAALTEQAWSRA-KELSSGEAILVFCNTV--------DEVKKVVAKLPKEARR-LEDLTGTVRGLER  350 (975)
T ss_pred             HHHHHHHHCCHHHHHHHHHHHHHHH-HHHCCCCEEEEEECCC--------CHHHHHHHHCCCCCCC-HHHHCCCCCCCCC
T ss_conf             1355422003056788777776665-5412786699987684--------3068988645774540-7762881043347


Q ss_pred             H------HHHHHHHC-----------CCEEEEEECHHHHCCCCCCCCCEEEEECHHHCCHHHHHHHHHCCCCCCCCEEE-
Q ss_conf             9------99999755-----------98699998003410468887658998585254746887730116678983599-
Q gi|254780945|r  531 E------SVMDSFKN-----------GTCKLLIATTVIEVGIDVVDASIIIIENAEHFGLAQLHQLRGRVGRGEEISSC-  592 (700)
Q Consensus       531 ~------~~m~~F~~-----------g~~~iLvaTtviEVGvdvpna~~mvI~~aerfGLsqLHQLRGRVGRg~~~s~c-  592 (700)
                      +      +++.+|..           -.+=.||||+-+|||+|+ +|+.+|-+++. |+  -|-|==|||-|=+...-| 
T Consensus       351 d~lar~~~~~~~~Lpp~~~~s~g~~~~g~~~vVaTst~EVGadl-dfdhLvt~~~~-~~--sl~QRfGRvnR~G~r~~~~  426 (975)
T TIGR02621       351 DMLARRGEIFNRFLPPYRSGSEGRPQQGTVYVVATSTGEVGADL-DFDHLVTDLAP-FE--SLVQRFGRVNRFGERLDGS  426 (975)
T ss_pred             CCCCCCCCHHHHCCCCCCCCCCCCCCCCCEEEEEECCEEECCCC-CCCHHHHCCCH-HH--HHHHHHHHHCCCCCCCCCE
T ss_conf             85200131453148764567736689987799973242550344-31112211442-45--7865430020002231650


Q ss_pred             -EEEEC
Q ss_conf             -99708
Q gi|254780945|r  593 -ILLYH  597 (700)
Q Consensus       593 -~l~~~  597 (700)
                       -.||.
T Consensus       427 ~~iVh~  432 (975)
T TIGR02621       427 IAIVHS  432 (975)
T ss_pred             EEEEEC
T ss_conf             589856


No 232
>PRK04036 DNA polymerase II small subunit; Validated
Probab=95.61  E-value=0.18  Score=31.18  Aligned_cols=103  Identities=20%  Similarity=0.286  Sum_probs=70.9

Q ss_pred             CCCHHHHHHHCCCCCCC-------CCCCCCHHHC----CCCCEEEEEEEEEEEEEECCCCCCEEEEEEECCCCEEEEEEE
Q ss_conf             55489878708974013-------4444647888----998789999999897542158983389999818936999995
Q gi|254780945|r   38 ETRFIDLLFYHPSSFID-------RHYRPKISEI----SEERIVTITGYISQHSSFQLQKRRPYKILLNDGTGEITLLFF  106 (700)
Q Consensus        38 I~ti~DLL~~~PrrYeD-------r~~~~~I~~l----~~g~~vti~g~V~~~~~~~~~~r~~~~v~v~D~tg~i~lvfF  106 (700)
                      .-++.|..-||=-||+-       |....++.++    ..++.+++.|-|...+.   .++....+.++|.||.+.+.++
T Consensus       106 ~G~v~Dfv~~F~dRy~kL~~ii~~r~~~rpi~~i~~~~~~~~ev~IIGmV~d~r~---tknG~~~~~lED~tG~i~vli~  182 (497)
T PRK04036        106 EGEVEDFVKYFRDRYEKLRRIIRGRVNLRPIESLKKARKGEEEVSIIGMVSDIRS---TKNGHKIVELEDPTGTFSVLIM  182 (497)
T ss_pred             CCCHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCCCEEEEEEECCCEE---CCCCCEEEEEECCCCEEEEEEE
T ss_conf             5768999999999999999999727787875888863168960899999754131---3677479999878983999994


Q ss_pred             CCCHHHH--HHHCCCCCEEEEEEEEEECCCEE---EEECCEE
Q ss_conf             1887899--87328988899998997318779---9977868
Q gi|254780945|r  107 YRKTEML--KNVFFEGRKITVTGKIKKLKNRI---IMVHPHY  143 (700)
Q Consensus       107 n~~~~yl--~k~lk~G~~v~vsGKv~~~~~~~---qi~hPe~  143 (700)
                      ..+...-  ...+-..+-+-|.|++...++.+   .+..|++
T Consensus       183 k~~~~~~~~a~~ll~DeVIgv~G~~s~~g~~~f~~~i~~Pdi  224 (497)
T PRK04036        183 KDREDLGELAEDLLPDEVIGVKGTLSGDGPLMFADEIIRPDV  224 (497)
T ss_pred             CCCHHHHHHHHHCCCCCEEEEEEEECCCCCEEEEEECCCCCC
T ss_conf             783787777762457757899999869987799840477999


No 233
>TIGR00631 uvrb excinuclease ABC, B subunit; InterPro: IPR004807 All proteins in this family for which functions are known are DNA helicases that function in the nucleotide excision repair and are endonucleases that make the 3' incision next to DNA damage. They are part of a pathway requiring UvrA, UvrB, UvrC, and UvrD homologs.; GO: 0009381 excinuclease ABC activity, 0006289 nucleotide-excision repair, 0005737 cytoplasm, 0009380 excinuclease repair complex.
Probab=95.59  E-value=0.019  Score=38.72  Aligned_cols=81  Identities=14%  Similarity=0.306  Sum_probs=63.2

Q ss_pred             HHHHHHHHCCEEEEEHHHHHHHHHHHHHHHHCCCCCCEEEEEECCCCHHHHHHHHHHHCCCCCEEEEECHHHCCCCCCCC
Q ss_conf             73344430545886127999999998621101457865899624642256676877621347548641112013345544
Q gi|254780945|r  314 MAAAVEAGGQAVIMAPIGILAQQHYEFIKKYTQNTQIIVEIITGNMPQAHRRKALERIAHGQAHIIIGTHALFQDSIQYY  393 (700)
Q Consensus       314 ~l~~~~~G~Q~alMaPTEILA~QH~~~~~~~~~~~~i~v~lLtg~~~~~er~~i~~~i~~G~~~iiIGTHAL~q~~v~F~  393 (700)
                      +-..+..|=.|.+..=|==+|+    .++.+|...||+|.-|++-..+-||-+|+.+|..|++|++||== |+=|++.-.
T Consensus       440 I~~R~~~~ERvLVTTLTKkMAE----dLTdYl~E~Gikv~YLHSeIdt~ER~eiirdLR~G~fDVLVGIN-LLREGLDlP  514 (667)
T TIGR00631       440 IRQRVARNERVLVTTLTKKMAE----DLTDYLKELGIKVRYLHSEIDTLERVEIIRDLRLGEFDVLVGIN-LLREGLDLP  514 (667)
T ss_pred             HHHHHHCCCCEEEEEHHHHHHH----HHHHHHHCCCCEEEEECCHHHHHHHHHHHHHHCCCCCEEEEECC-HHHCCCCCH
T ss_conf             9999972894899820167788----99999705883798714557899999999984478840886000-200246511


Q ss_pred             CCCEEE
Q ss_conf             441788
Q gi|254780945|r  394 KLILVI  399 (700)
Q Consensus       394 ~LgLvV  399 (700)
                      =.+||=
T Consensus       515 EVSLVA  520 (667)
T TIGR00631       515 EVSLVA  520 (667)
T ss_pred             HHHHHH
T ss_conf             488997


No 234
>cd01124 KaiC KaiC is a circadian clock protein primarily found in cyanobacteria KaiC is a RecA-like ATPase, having both Walker A and Walker B motifs. A related protein is found in archaea.
Probab=95.59  E-value=0.052  Score=35.37  Aligned_cols=48  Identities=23%  Similarity=0.289  Sum_probs=35.8

Q ss_pred             EEEEECCCCCHHHHHHHHHHHHHHHHCCEEEEEHHHHHHHHHHHHHHHH
Q ss_conf             7886214422369999997334443054588612799999999862110
Q gi|254780945|r  296 RILQGDVGSGKTLVALIAMAAAVEAGGQAVIMAPIGILAQQHYEFIKKY  344 (700)
Q Consensus       296 RLLQGDVGSGKTiVA~~A~l~~~~~G~Q~alMaPTEILA~QH~~~~~~~  344 (700)
                      -|+-|+-|||||+.|+--++..+.+|..|+++.- |--..|..+++..+
T Consensus         2 tLi~G~pGsGKT~~a~qfl~~~a~~ge~~lyis~-eE~~~~l~~~~~~~   49 (187)
T cd01124           2 TLLSGGPGTGKTTFALQFLYAGLARGEPGLYVTL-EESPEELIENAESL   49 (187)
T ss_pred             EEEEECCCCCHHHHHHHHHHHHHHCCCCEEEEEE-CCCHHHHHHHHHHC
T ss_conf             1587689999999999999999876997899995-07999999999983


No 235
>KOG1805 consensus
Probab=95.53  E-value=0.26  Score=29.87  Aligned_cols=51  Identities=18%  Similarity=0.295  Sum_probs=27.1

Q ss_pred             EEEECCCCEEEEEEECCCHHHHHHHCCCCCEEEEEEEEEE-------CCCEEEEECCEEE
Q ss_conf             9998189369999951887899873289888999989973-------1877999778689
Q gi|254780945|r   92 ILLNDGTGEITLLFFYRKTEMLKNVFFEGRKITVTGKIKK-------LKNRIIMVHPHYI  144 (700)
Q Consensus        92 v~v~D~tg~i~lvfFn~~~~yl~k~lk~G~~v~vsGKv~~-------~~~~~qi~hPe~~  144 (700)
                      ..+.|+.|.....++-  .+|-.-.+.+|+.+.+-|....       ..+++-+.||+.-
T Consensus       127 le~~d~~g~~~~~~l~--~~W~~~s~e~Gd~I~lig~~~~d~~~vvD~d~g~lIl~PD~L  184 (1100)
T KOG1805         127 LECGDDEGTTLDVYLR--DEWEEMSMEVGDTINLIGAKDSDKTFVVDDDNGLLILHPDDL  184 (1100)
T ss_pred             HHCCCCCCCEEEEEEE--CCCEEECCCCCCEEEEEECCCCCCCEEEECCCCEEEECCCCC
T ss_conf             1205777714789981--673052045786577630025788688717877599657752


No 236
>COG5235 RFA2 Single-stranded DNA-binding replication protein A (RPA), medium (30 kD) subunit [DNA replication, recombination, and repair]
Probab=95.52  E-value=0.083  Score=33.76  Aligned_cols=72  Identities=18%  Similarity=0.270  Sum_probs=51.4

Q ss_pred             CEEEEEEEEEEEEEECCCCCCEEEEEEECCCCEEEEEEECCCHHHH---HHHCCCCCEEEEEEEEEECCCEEEEECCEEE
Q ss_conf             7899999998975421589833899998189369999951887899---8732898889999899731877999778689
Q gi|254780945|r   68 RIVTITGYISQHSSFQLQKRRPYKILLNDGTGEITLLFFYRKTEML---KNVFFEGRKITVTGKIKKLKNRIIMVHPHYI  144 (700)
Q Consensus        68 ~~vti~g~V~~~~~~~~~~r~~~~v~v~D~tg~i~lvfFn~~~~yl---~k~lk~G~~v~vsGKv~~~~~~~qi~hPe~~  144 (700)
                      ..|++.|.|.....-.    -.....++|+||.|.++||-.. .|.   .+-+..|..+.|+|-++.|+|+..+....+.
T Consensus        67 ~~V~fVGvvrni~~~t----tn~~~~iEDGTG~Ievr~W~~~-~~~~e~~~d~~~~~yvkV~G~lk~F~GK~~I~~~~i~  141 (258)
T COG5235          67 TNVQFVGVVRNIKTST----TNSMFVIEDGTGSIEVRFWPGN-SYEEEQCKDLEEQNYVKVNGSLKTFNGKRSISASHIS  141 (258)
T ss_pred             EEEEEEEEEEEEEECC----CCEEEEEECCCCEEEEEECCCC-CHHHHHCCCCCCCCEEEEECCEEEECCEEEEEHHHEE
T ss_conf             6689999998401034----5418999348742898856887-2377754343326679994211220780577410052


No 237
>PRK03103 DNA polymerase IV; Reviewed
Probab=95.49  E-value=0.011  Score=40.61  Aligned_cols=15  Identities=7%  Similarity=0.164  Sum_probs=8.8

Q ss_pred             HHHHHHHHCCCCCCC
Q ss_conf             688773011667898
Q gi|254780945|r  574 AQLHQLRGRVGRGEE  588 (700)
Q Consensus       574 sqLHQLRGRVGRg~~  588 (700)
                      ..+.++|-|-|++..
T Consensus       372 ~aiD~In~RfG~~~I  386 (410)
T PRK03103        372 YVMDGIKEKYGDTAI  386 (410)
T ss_pred             HHHHHHHHHHCHHHH
T ss_conf             999999986686389


No 238
>PRK00440 rfc replication factor C small subunit; Reviewed
Probab=95.48  E-value=0.19  Score=30.89  Aligned_cols=204  Identities=16%  Similarity=0.209  Sum_probs=96.7

Q ss_pred             HHHHHHHHHHHHHCCCCCCEEEEEECCCCCHHHHHHHHHHHHHHHHCCEEEEEHHHHHHHHHHHHHHHHCCCCCCEEEEE
Q ss_conf             89999999998410013430788621442236999999733444305458861279999999986211014578658996
Q gi|254780945|r  276 SQESAIKDILQDMSQKNRMLRILQGDVGSGKTLVALIAMAAAVEAGGQAVIMAPIGILAQQHYEFIKKYTQNTQIIVEII  355 (700)
Q Consensus       276 ~Q~~ai~eI~~Dl~~~~pM~RLLQGDVGSGKTiVA~~A~l~~~~~G~Q~alMaPTEILA~QH~~~~~~~~~~~~i~v~lL  355 (700)
                      +|+.+++.+.+-+.++..=+=|+.|--|||||-.|.+-+-.....+++.-+                         ++ +
T Consensus        20 g~~~~~~~L~~~i~~~~~phlLf~GppG~GKTt~a~~la~~l~~~~~~~~~-------------------------le-l   73 (318)
T PRK00440         20 GQEEIVERLKSFVKEKNMPHLLFAGPPGTGKTTAALALARELYGEYWRENF-------------------------LE-L   73 (318)
T ss_pred             CCHHHHHHHHHHHHCCCCCEEEEECCCCCCHHHHHHHHHHHHCCCCCCCCE-------------------------EE-E
T ss_conf             969999999999987998669888959988999999999997698643476-------------------------89-5


Q ss_pred             ECCCCH-H--HHHHHHHHHCCCCCEEEEECHHHCCCCCCCCCCCEEEECCCCCCCHHHHHHHHHC---CCCCCCEEECHH
Q ss_conf             246422-5--6676877621347548641112013345544441788521013356889987402---567761010101
Q gi|254780945|r  356 TGNMPQ-A--HRRKALERIAHGQAHIIIGTHALFQDSIQYYKLILVIVDEQHRFGVQQRLKLTQK---ATAPHVLLMTAT  429 (700)
Q Consensus       356 tg~~~~-~--er~~i~~~i~~G~~~iiIGTHAL~q~~v~F~~LgLvViDEQHRFGV~QR~~L~~K---g~~ph~L~MtAT  429 (700)
                      ..|... .  -|..+.+-..         |..+  .+..|+   ++|+||=|++.-..-.+|+.-   -...-...++++
T Consensus        74 nasd~r~id~vr~~i~~~~~---------~~~~--~~~~~k---iiiiDE~d~l~~~aq~aL~~~mE~~~~~~~fil~~n  139 (318)
T PRK00440         74 NASDERGIDVIRNKIKEFAR---------TAPV--GGAPFK---IIFLDEADNLTSDAQQALRRTMEMYSQTTRFILSCN  139 (318)
T ss_pred             CCCCCCCHHHHHHHHHHHHH---------HCCC--CCCCEE---EEEEECCCCCCHHHHHHHHHHHHCCCCCCEEEEECC
T ss_conf             16456671789999999997---------2677--899738---999868553225567888764310566625886348


Q ss_pred             HHHHHHHHHHHHCCCHHHHCCCCCCCCCCEEEE--EECC--CHHHHHHHHHHHHCCCCEEEE----EECCCCCCCCCCCC
Q ss_conf             322789999752010111102355766620799--9702--002689999763103873899----97120122111210
Q gi|254780945|r  430 PIPRTLVLTSLGDIDISKITEKPAGRKPIKTVI--IPIN--RIDEVIERLKVVLSEGKKAYW----ICPQIEEKKESNFR  501 (700)
Q Consensus       430 PIPRTLal~~ygdldvS~i~e~P~gR~~I~T~~--~~~~--~~~~~~~~i~~~l~~g~q~y~----VcPlIeese~~~~~  501 (700)
                      .+.+              |  +|    ||.+++  +...  ..+++.+.++.-+.+-+ +-+    +--+++.| +-|++
T Consensus       140 ~~~k--------------i--i~----~i~SRc~~i~f~~~~~~~i~~~L~~I~~~E~-i~~~~~~l~~i~~~s-~gdlR  197 (318)
T PRK00440        140 YSSK--------------I--ID----PIQSRCAVFRFSPLPKEAVIERLRYIAKNEG-LEITDDALEAIYYVS-EGDMR  197 (318)
T ss_pred             CCCC--------------C--CC----CHHHHHEEEECCCCCHHHHHHHHHHHHHHCC-CCCCHHHHHHHHHHC-CCCHH
T ss_conf             8333--------------7--61----5565510111578999999999999999859-998999999999864-99899


Q ss_pred             HHHHHHHHHHHHCCC----CEECCCCCCCHHHHHHHHHHHHCCC
Q ss_conf             146666666866371----0312014699899999999975598
Q gi|254780945|r  502 SVVERFNSLHEHFTS----SIAIIHGRMSDIDKESVMDSFKNGT  541 (700)
Q Consensus       502 ~~~~~~~~l~~~~~~----~v~~lHGkm~~~ek~~~m~~F~~g~  541 (700)
                      .+.+..+........    .|.-+-|..+.++-+++++...+|+
T Consensus       198 ~ain~Lq~~~~~~~~it~~~v~~~~~~~~~~~i~~ii~~~~~~~  241 (318)
T PRK00440        198 KAINALQAAAATGKEVTEEAVYKITGTARPEEIREMINLALNGD  241 (318)
T ss_pred             HHHHHHHHHHHCCCCCCHHHHHHHHCCCCHHHHHHHHHHHHCCC
T ss_conf             99999999997489878999999976999899999999997089


No 239
>COG2176 PolC DNA polymerase III, alpha subunit (gram-positive type) [DNA replication, recombination, and repair]
Probab=95.47  E-value=0.27  Score=29.80  Aligned_cols=94  Identities=20%  Similarity=0.230  Sum_probs=69.1

Q ss_pred             CCCCCCCCCCCCHHHCCCCCE-EEEEEEEEEEEEECCC-CCCEEEEEEECCCCEEEEEEECCC--HHHHHHHCCCCCEEE
Q ss_conf             974013444464788899878-9999999897542158-983389999818936999995188--789987328988899
Q gi|254780945|r   49 PSSFIDRHYRPKISEISEERI-VTITGYISQHSSFQLQ-KRRPYKILLNDGTGEITLLFFYRK--TEMLKNVFFEGRKIT  124 (700)
Q Consensus        49 PrrYeDr~~~~~I~~l~~g~~-vti~g~V~~~~~~~~~-~r~~~~v~v~D~tg~i~lvfFn~~--~~yl~k~lk~G~~v~  124 (700)
                      ++.-.+...++++.++.+.+. ++|+|.|-+......+ +|..+.+.+.|.+.++.+.||...  -.-....++.|+++.
T Consensus       220 ~~~i~~~~~i~~~~~i~~~~~~v~v~G~IF~~e~~~~ksGr~l~~i~vTD~t~Sl~~k~f~~~~ed~~~~~~ik~g~wvk  299 (1444)
T COG2176         220 GRKIKSTEEIKPLIKINEEETRVKVEGYIFKIEIKELKSGRTLLNIKVTDYTSSLILKKFLRDEEDEKKFDGIKKGMWVK  299 (1444)
T ss_pred             CEECCCCCCEEEHHHCCCCCCCEEEEEEEEEEEEEECCCCCEEEEEEEECCCHHEEEHHHCCCCCCHHHHHHCCCCCEEE
T ss_conf             33235766501546403311105899999887643224686799999862710032021226663188886233384799


Q ss_pred             EEEEEEEC--CCEEEEECCE
Q ss_conf             99899731--8779997786
Q gi|254780945|r  125 VTGKIKKL--KNRIIMVHPH  142 (700)
Q Consensus       125 vsGKv~~~--~~~~qi~hPe  142 (700)
                      +.|.+..-  .+.++|.--+
T Consensus       300 ~~g~v~~d~f~~~l~m~i~~  319 (1444)
T COG2176         300 ARGNVQLDTFTRDLTMIIND  319 (1444)
T ss_pred             EEEEEEECCCCCCEEEEHHH
T ss_conf             99788733555551787533


No 240
>PRK02794 DNA polymerase IV; Provisional
Probab=95.46  E-value=0.011  Score=40.64  Aligned_cols=14  Identities=0%  Similarity=-0.111  Sum_probs=6.5

Q ss_pred             HHHHCCCCCCEEEE
Q ss_conf             21101457865899
Q gi|254780945|r  341 IKKYTQNTQIIVEI  354 (700)
Q Consensus       341 ~~~~~~~~~i~v~l  354 (700)
                      ...++.+++|+--+
T Consensus       202 ~~~~L~~lpv~diw  215 (417)
T PRK02794        202 AAAFLAPKPVGFIW  215 (417)
T ss_pred             HHHHHHCCCHHHHC
T ss_conf             99998538845516


No 241
>TIGR00150 TIGR00150 conserved hypothetical protein TIGR00150; InterPro: IPR003442   This group consists of bacterial proteins, which contain a P-loop. They are probably essential to bacteria as members are found in all genomes so far sequenced and no equivalent genes have been found in the archaea and eukaryotes, suggesting the protein may be involved in cell wall biosynthesis. The sequence of YjeE, from Haemophilus influenzae, has been determined to 1.7-A resolution. The protein has a nucleotide-binding fold with a four-stranded parallel beta-sheet flanked by antiparallel beta-strands on each side. The topology of the beta-sheet is unique among P-loop proteins and has features of different families of enzymes. ADP has been shown to bind to the P-loop in the presence of Mg2+ and ATPase activity has been confirmed by kinetic measurements . .
Probab=95.46  E-value=0.031  Score=37.08  Aligned_cols=60  Identities=22%  Similarity=0.321  Sum_probs=37.2

Q ss_pred             CHHHHHHHHHHHHH---HCCCCCCEEEEEECCCCCHHHHHHHHHHHHHHHHCCEEEEEHHHHHHHH
Q ss_conf             98899999999984---1001343078862144223699999973344430545886127999999
Q gi|254780945|r  274 TKSQESAIKDILQD---MSQKNRMLRILQGDVGSGKTLVALIAMAAAVEAGGQAVIMAPIGILAQQ  336 (700)
Q Consensus       274 T~~Q~~ai~eI~~D---l~~~~pM~RLLQGDVGSGKTiVA~~A~l~~~~~G~Q~alMaPTEILA~Q  336 (700)
                      |++=.+.-+.+..+   +..+....-+|+||+|||||=- .-+++..  =|.|.-+-.||=-|-+.
T Consensus         6 t~a~~~~~~~~a~~llklh~d~~~v~~L~GDlGaGKTtl-~~G~~~~--LG~~~~~~SPTftlv~~   68 (147)
T TIGR00150         6 TKAMDKLGKAFAKPLLKLHLDLGTVVLLKGDLGAGKTTL-VKGLLQG--LGITGNVTSPTFTLVNE   68 (147)
T ss_pred             HHHHHHHHHHHHHHHHHHHCCCCEEEEEECCCCCCHHHH-HHHHHHH--CCCEEEEECCCCCEEEE
T ss_conf             789999999999999985199753899732346665899-9999983--79226885793210100


No 242
>PRK13767 ATP-dependent helicase; Provisional
Probab=95.44  E-value=0.14  Score=31.97  Aligned_cols=87  Identities=11%  Similarity=0.178  Sum_probs=72.9

Q ss_pred             HHHHHHHHHCCEEEEEHHHHHHHHHHHHHHHHCCCC--CCEEEEEECCCCHHHHHHHHHHHCCCCCEEEEECHHHCCCCC
Q ss_conf             973344430545886127999999998621101457--865899624642256676877621347548641112013345
Q gi|254780945|r  313 AMAAAVEAGGQAVIMAPIGILAQQHYEFIKKYTQNT--QIIVEIITGNMPQAHRRKALERIAHGQAHIIIGTHALFQDSI  390 (700)
Q Consensus       313 A~l~~~~~G~Q~alMaPTEILA~QH~~~~~~~~~~~--~i~v~lLtg~~~~~er~~i~~~i~~G~~~iiIGTHAL~q~~v  390 (700)
                      .++..++.+..+.+-+=|-=.|+.-+..++++++..  ..+|+.-+||+++.+|.++-+.+++|+++.||-|.+| .=++
T Consensus       276 ~l~~~i~~~~~tLvF~NtR~~aE~~~~~L~~~~~~~~~~~~i~~HHgSls~e~R~~vE~~lk~G~l~~vV~TsSL-ELGI  354 (878)
T PRK13767        276 TLDELIQEHRTTLIFTNTRSGAERVVYKLRKRYPEEYDEDNIGAHHSSLSREVRLEVEEKLKRGELKVVVSSTSL-ELGI  354 (878)
T ss_pred             HHHHHHHHCCCEEEEECCHHHHHHHHHHHHHHHHHCCCCCCEEEECCCCCHHHHHHHHHHHHCCCCCEEEEECHH-HCCC
T ss_conf             999999838977999155899999999999853430675432220177899999999999857998689982736-5077


Q ss_pred             CCCCCCEEEE
Q ss_conf             5444417885
Q gi|254780945|r  391 QYYKLILVIV  400 (700)
Q Consensus       391 ~F~~LgLvVi  400 (700)
                      .+.++-+||=
T Consensus       355 DiG~Vd~Viq  364 (878)
T PRK13767        355 DIGYIDLVVL  364 (878)
T ss_pred             CCCCCCEEEE
T ss_conf             7775258997


No 243
>TIGR00617 rpa1 replication factor-a protein 1 (rpa1); InterPro: IPR004591 All proteins in this family for which functions are known are part of a multiprotein complex made up of homologs of RPA1, RPA2 and RPA3 that bind single-stranded DNA and function in the recognition of DNA damage for nucleotide excision repair. The complex binds to single-stranded DNA sequences participating in DNA replication in addition to those mediating transcriptional repression and activation, and stimulates the activity of cognate strand exchange protein Sep1. It cooperates with T-AG and DNA topoisomerase I to unwind template DNA containing the Simian virus 40 origin of replication. This family is Replication factor-a protein 1 (RPA1); GO: 0003677 DNA binding, 0006260 DNA replication, 0005634 nucleus.
Probab=95.42  E-value=0.045  Score=35.85  Aligned_cols=120  Identities=19%  Similarity=0.264  Sum_probs=80.6

Q ss_pred             CCCCCCCCCCCCHHHCCCC-CEEEEEEEEEEEEEECCC---C--CCEEEEEEEC-CCCEEEEEEECCCHHHHHHHCCCCC
Q ss_conf             9740134444647888998-789999999897542158---9--8338999981-8936999995188789987328988
Q gi|254780945|r   49 PSSFIDRHYRPKISEISEE-RIVTITGYISQHSSFQLQ---K--RRPYKILLND-GTGEITLLFFYRKTEMLKNVFFEGR  121 (700)
Q Consensus        49 PrrYeDr~~~~~I~~l~~g-~~vti~g~V~~~~~~~~~---~--r~~~~v~v~D-~tg~i~lvfFn~~~~yl~k~lk~G~  121 (700)
                      |+.--.+.++.||..|.|= ..=+|+++|.+...++.-   |  ++.|.+-+.| ++|.|+++=||---.-+-..|.+|.
T Consensus       205 ~~~~~t~~~v~Pi~~LsPYq~~W~IkARVT~K~~irtw~N~RGEGKlFn~~L~D~~sgeIRaTaFNe~ad~FY~~i~~g~  284 (671)
T TIGR00617       205 PNSGSTRERVVPIESLSPYQNKWTIKARVTNKSEIRTWSNARGEGKLFNVELLDSESGEIRATAFNEQADKFYDLIQVGK  284 (671)
T ss_pred             HHHCCCCCCEEEECCCCCCCCCEEEEEEEEEHHCCCCCCCCCCCCEEEEEEEECCCCCEEEEECHHHHHHHHCCEEEECC
T ss_conf             12168977547712258877732898987200013302378888106555747179784677424788753213243367


Q ss_pred             EEEEE-EEEEECCCEEEEECCEEEECCCCCCCCCCCCCCCCCCH-HHHHHHH
Q ss_conf             89999-89973187799977868962643344444110000000-0004543
Q gi|254780945|r  122 KITVT-GKIKKLKNRIIMVHPHYIFHNSQDVNFPLIEAVYSLPT-GLSVDLF  171 (700)
Q Consensus       122 ~v~vs-GKv~~~~~~~qi~hPe~~~~~~~~~~~~~I~PIYplt~-GLsqk~i  171 (700)
                      -|+|| |+++..+.++.-++=+||+-=+.+   ..|.+-|-.+. .|++-.+
T Consensus       285 vYYiSkg~L~~AnKqF~~~~NdYE~tl~~~---t~i~~ced~~~d~~P~~~f  333 (671)
T TIGR00617       285 VYYISKGSLKPANKQFTNVKNDYEMTLDRD---TVIEECEDETADAIPKIQF  333 (671)
T ss_pred             EEEEECCEECCCCCCCCCCCCCEEEECCCC---CEEEECCCCCCCCCCCEEE
T ss_conf             879973784347766677887102505867---4576146888776781464


No 244
>pfam01695 IstB IstB-like ATP binding protein. This protein contains an ATP/GTP binding P-loop motif. It is found associated with IS21 family insertion sequences. The function of this protein is unknown, but it may perform a transposase function.
Probab=95.36  E-value=0.034  Score=36.81  Aligned_cols=61  Identities=18%  Similarity=0.172  Sum_probs=44.9

Q ss_pred             CCCHHHHHHHHHHHHHHCCCCCCEEEEEECCCCCHHHHHHHHHHHHHHHHCCEEEEEHHHHHHH
Q ss_conf             6798899999999984100134307886214422369999997334443054588612799999
Q gi|254780945|r  272 SPTKSQESAIKDILQDMSQKNRMLRILQGDVGSGKTLVALIAMAAAVEAGGQAVIMAPIGILAQ  335 (700)
Q Consensus       272 ~LT~~Q~~ai~eI~~Dl~~~~pM~RLLQGDVGSGKTiVA~~A~l~~~~~G~Q~alMaPTEILA~  335 (700)
                      .+...|..-+... .-+  ....|-+++|.+|+|||=.|...+..++.+||.|.++.=++.+.+
T Consensus        29 ~~~~~~i~~L~~~-~~i--~~~~Nlll~G~~GtGKThLA~Ai~~~~~~~g~~v~f~~~~~L~~~   89 (178)
T pfam01695        29 GLDRRLIAELAGL-DWI--EQAENLLLLGPPGVGKTHLACALGHQACRAGYSVLFTRTPDLVEQ   89 (178)
T ss_pred             CCCHHHHHHHHCC-CCH--HCCCCEEEECCCCCCHHHHHHHHHHHHHHCCCEEEEEECHHHHHH
T ss_conf             9899999988559-742--158768998999987899999999999986985999961679999


No 245
>PRK08939 primosomal protein DnaI; Reviewed
Probab=95.33  E-value=0.17  Score=31.24  Aligned_cols=71  Identities=15%  Similarity=0.186  Sum_probs=47.7

Q ss_pred             CCCCH-HHHHHHHHHHH---HHCCCCCCEE-EEEECCCCCHHHHHHHHHHHHHHHHCCEEEEEHHHHHHHHHHHHHHHHC
Q ss_conf             46798-89999999998---4100134307-8862144223699999973344430545886127999999998621101
Q gi|254780945|r  271 FSPTK-SQESAIKDILQ---DMSQKNRMLR-ILQGDVGSGKTLVALIAMAAAVEAGGQAVIMAPIGILAQQHYEFIKKYT  345 (700)
Q Consensus       271 F~LT~-~Q~~ai~eI~~---Dl~~~~pM~R-LLQGDVGSGKTiVA~~A~l~~~~~G~Q~alMaPTEILA~QH~~~~~~~~  345 (700)
                      |..++ +-..|+.++..   +...+....- +|.|++|+|||-.|...+-..+..|+-++|+-=.+.++     .++.-|
T Consensus       130 ~~~~d~~R~~a~~~a~~F~~~y~~~~~~kGlyl~G~~G~GKTyL~~aian~La~~g~~v~~v~~p~~~~-----~lK~s~  204 (306)
T PRK08939        130 IDLDDLDRLDALMAALDFLEAYKPGEKVKGLYLYGDFGVGKTYLLAAIANELAKKGVSSTLVHFPEFIR-----ELKNAI  204 (306)
T ss_pred             CCCCCHHHHHHHHHHHHHHHHHCCCCCCCEEEEECCCCCCHHHHHHHHHHHHHHCCCEEEEEEHHHHHH-----HHHHHH
T ss_conf             488977899999999999997376988877889899999899999999999998699299987599999-----999986


Q ss_pred             C
Q ss_conf             4
Q gi|254780945|r  346 Q  346 (700)
Q Consensus       346 ~  346 (700)
                      .
T Consensus       205 ~  205 (306)
T PRK08939        205 S  205 (306)
T ss_pred             C
T ss_conf             4


No 246
>PRK03352 DNA polymerase IV; Validated
Probab=95.32  E-value=0.014  Score=39.90  Aligned_cols=17  Identities=29%  Similarity=0.306  Sum_probs=9.0

Q ss_pred             CCCCCHHHHHHHHH--CCC
Q ss_conf             01335688998740--256
Q gi|254780945|r  403 QHRFGVQQRLKLTQ--KAT  419 (700)
Q Consensus       403 QHRFGV~QR~~L~~--Kg~  419 (700)
                      ..+||+..-..|..  .|.
T Consensus       213 ~~~fG~~~g~~l~~~a~G~  231 (345)
T PRK03352        213 TATFGPRTGLWLLLLAKGG  231 (345)
T ss_pred             HHHHCHHHHHHHHHHHCCC
T ss_conf             9997889999999994899


No 247
>cd04490 PolII_SU_OBF PolII_SU_OBF: A subfamily of OB folds corresponding to the OB fold found in Pyrococcus abyssi DNA polymerase II (PolII) small subunit. PolII is a family D DNA polymerase, having a 3-prime to 5-prime exonuclease activity. P. abyssi PolII is heterodimeric. The large subunit appears to be the polymerase, and the small subunit may be the exonuclease. The small subunit contains a calcineurin-like phosphatase superfamily domain C-terminal to this OB-fold domain.
Probab=95.31  E-value=0.19  Score=30.99  Aligned_cols=71  Identities=28%  Similarity=0.374  Sum_probs=49.9

Q ss_pred             EEEEEEEEEEEEEECCCCCCEEEEEEECCCCEEEEEEECCCHHHH--HHHCCCCCEEEEEEEEEECCCEE---EEECCE
Q ss_conf             899999998975421589833899998189369999951887899--87328988899998997318779---997786
Q gi|254780945|r   69 IVTITGYISQHSSFQLQKRRPYKILLNDGTGEITLLFFYRKTEML--KNVFFEGRKITVTGKIKKLKNRI---IMVHPH  142 (700)
Q Consensus        69 ~vti~g~V~~~~~~~~~~r~~~~v~v~D~tg~i~lvfFn~~~~yl--~k~lk~G~~v~vsGKv~~~~~~~---qi~hPe  142 (700)
                      .+++.|-|...+.   .++..+.+.++|.||.+++.+++.+..+.  ...+-+.+-+-|+|++...++.+   .+.+|+
T Consensus         1 ev~iIGmV~d~r~---TknG~~~~~lED~TG~i~vl~~kd~~~~~~~~~~ll~DeVIGV~G~~s~~g~~~f~~~i~~Pd   76 (79)
T cd04490           1 EVSIIGMVNDVRS---TKNGHRIVELEDTTGRITVLLTKDKEELFEEAEDILPDEVIGVSGTVSKDGGLIFADEIFRPD   76 (79)
T ss_pred             CEEEEEEECCCEE---CCCCCEEEEEECCCCEEEEEEECCCHHHHHHHHCCCCCCEEEEEEEECCCCCEEEEECCCCCC
T ss_conf             9699999933276---168878999987999899999689367756675256887899999987899889997124699


No 248
>KOG0333 consensus
Probab=95.25  E-value=0.081  Score=33.84  Aligned_cols=89  Identities=28%  Similarity=0.356  Sum_probs=67.1

Q ss_pred             CCEEEEEH--------HHHHHHH-------------HHHHHHHHCCCCCCEEEEEECCCCHHHHHHHHHHHCCCCCEEEE
Q ss_conf             54588612--------7999999-------------99862110145786589962464225667687762134754864
Q gi|254780945|r  322 GQAVIMAP--------IGILAQQ-------------HYEFIKKYTQNTQIIVEIITGNMPQAHRRKALERIAHGQAHIII  380 (700)
Q Consensus       322 ~Q~alMaP--------TEILA~Q-------------H~~~~~~~~~~~~i~v~lLtg~~~~~er~~i~~~i~~G~~~iiI  380 (700)
                      .|.++|++        -|||+.+             -.+.+.+-|++.|++|.-|+|+-+.-+|+.+++.+.+|..+|+|
T Consensus       493 eQ~v~m~~ed~k~kkL~eil~~~~~ppiIIFvN~kk~~d~lAk~LeK~g~~~~tlHg~k~qeQRe~aL~~fr~~t~dIlV  572 (673)
T KOG0333         493 EQKVEMVSEDEKRKKLIEILESNFDPPIIIFVNTKKGADALAKILEKAGYKVTTLHGGKSQEQRENALADFREGTGDILV  572 (673)
T ss_pred             HEEEEEECCHHHHHHHHHHHHHCCCCCEEEEEECHHHHHHHHHHHHHCCCEEEEEECCCCHHHHHHHHHHHHHCCCCEEE
T ss_conf             11788815568899999999847999879998313248999999864432479961785277899999998715787799


Q ss_pred             ECHHHCCCCCCCCCCCEEE--------ECCCCCCCHHHH
Q ss_conf             1112013345544441788--------521013356889
Q gi|254780945|r  381 GTHALFQDSIQYYKLILVI--------VDEQHRFGVQQR  411 (700)
Q Consensus       381 GTHAL~q~~v~F~~LgLvV--------iDEQHRFGV~QR  411 (700)
                      .|-+.= .++.-.|..|||        .|=-||-|=.-|
T Consensus       573 aTDvAg-RGIDIpnVSlVinydmaksieDYtHRIGRTgR  610 (673)
T KOG0333         573 ATDVAG-RGIDIPNVSLVINYDMAKSIEDYTHRIGRTGR  610 (673)
T ss_pred             EECCCC-CCCCCCCCCEEEECCHHHHHHHHHHHHCCCCC
T ss_conf             832212-57777761214622055658999887423444


No 249
>PRK03858 DNA polymerase IV; Validated
Probab=95.24  E-value=0.014  Score=39.82  Aligned_cols=12  Identities=25%  Similarity=0.623  Sum_probs=4.9

Q ss_pred             HHHHHHCCCCCC
Q ss_conf             877301166789
Q gi|254780945|r  576 LHQLRGRVGRGE  587 (700)
Q Consensus       576 LHQLRGRVGRg~  587 (700)
                      +.++|-|-|++.
T Consensus       367 ~D~In~rfG~~t  378 (398)
T PRK03858        367 IDRVRRRFGNAA  378 (398)
T ss_pred             HHHHHHHHCHHH
T ss_conf             999998758406


No 250
>PRK11773 uvrD DNA-dependent helicase II; Provisional
Probab=95.08  E-value=0.099  Score=33.16  Aligned_cols=49  Identities=20%  Similarity=0.224  Sum_probs=20.7

Q ss_pred             HHHHHHHHHHCHHHHHHHHHHHHCCCC--CCCCCHHCCCCCCCCCCHHHHHHHHHHHH
Q ss_conf             999999984142589999998520630--00260006987440003887599999999
Q gi|254780945|r  605 YTRLSVLKNTEDGFLIAEEDLKQRKEG--EILGIKQSGMPKFLIAQPELHDSLLEIAR  660 (700)
Q Consensus       605 ~~Rl~~l~~~~dGf~iAe~Dl~lRG~G--~~~G~~QsG~~~~~~~d~~~d~~ll~~a~  660 (700)
                      ..||=..     |..=|.+-|-|=-+-  .+.|..+.-.|.=-+.++  +.++++..+
T Consensus       595 ERRLfYV-----aiTRAk~~L~ls~~~~r~~~g~~~~~~pSRFl~ei--p~~~~~~~~  645 (722)
T PRK11773        595 ERRLAYV-----GITRAMQKLTLTYAESRRLYGKEVYHRPSRFIREI--PEECVEEVR  645 (722)
T ss_pred             HHHHHHH-----HHHHHHHHEEEEECCHHHHCCCCCCCCCCCCHHHC--CHHHHHHHH
T ss_conf             9999999-----89887452488551254546777678898146657--899998763


No 251
>PRK12377 putative replication protein; Provisional
Probab=94.98  E-value=0.11  Score=32.67  Aligned_cols=62  Identities=15%  Similarity=0.272  Sum_probs=48.9

Q ss_pred             CCHHHHHHHH---HHHHHHCCCCCCEEEEEECCCCCHHHHHHHHHHHHHHHHCCEEEEEHHHHHHH
Q ss_conf             7988999999---99984100134307886214422369999997334443054588612799999
Q gi|254780945|r  273 PTKSQESAIK---DILQDMSQKNRMLRILQGDVGSGKTLVALIAMAAAVEAGGQAVIMAPIGILAQ  335 (700)
Q Consensus       273 LT~~Q~~ai~---eI~~Dl~~~~pM~RLLQGDVGSGKTiVA~~A~l~~~~~G~Q~alMaPTEILA~  335 (700)
                      -+++|+.|+.   ++...+.+ ..-|-++-|..|.|||=.|..-...++..|+-|.|.-=++++.+
T Consensus        79 ~~~~~~~a~~~a~~~~~~F~~-~~~NlIf~G~pGtGKTHLA~AIg~~a~~~G~sVlF~t~~dLv~~  143 (248)
T PRK12377         79 QNDGQRYALSQAKSIADELMT-GCTNFVFSGKPGTGKNHLAAAIGNRLLAKGRSVIVVTVPDVMSR  143 (248)
T ss_pred             CCHHHHHHHHHHHHHHHHHHC-CCCEEEEECCCCCCHHHHHHHHHHHHHHCCCEEEEEEHHHHHHH
T ss_conf             787899999999999998731-88608998999987889999999999987996999889999999


No 252
>COG4085 Predicted RNA-binding protein, contains TRAM domain [General function prediction only]
Probab=94.95  E-value=0.29  Score=29.44  Aligned_cols=73  Identities=26%  Similarity=0.352  Sum_probs=56.7

Q ss_pred             CCCCEEEEEEEEEEEEEECCCCCCEEEEEEECCCCEEEEEEECCCHHHHH-----HHCCCCCEEEEEEEEEECCCEEEEE
Q ss_conf             99878999999989754215898338999981893699999518878998-----7328988899998997318779997
Q gi|254780945|r   65 SEERIVTITGYISQHSSFQLQKRRPYKILLNDGTGEITLLFFYRKTEMLK-----NVFFEGRKITVTGKIKKLKNRIIMV  139 (700)
Q Consensus        65 ~~g~~vti~g~V~~~~~~~~~~r~~~~v~v~D~tg~i~lvfFn~~~~yl~-----k~lk~G~~v~vsGKv~~~~~~~qi~  139 (700)
                      ...+.++++|.|.+....  -.-....+.+.|++|.++++.|-.....+.     -.+.+|+.+-+-|.++.|+|..++.
T Consensus        49 ~l~e~v~vkg~V~~~~n~--~~~gi~~l~lndgtGti~vva~~~tee~l~~n~~~p~~~eGe~veVtGrv~~yrG~~eVk  126 (204)
T COG4085          49 RLNEEVTVKGEVTADQNA--IGGGIESLVLNDGTGTITVVASRSTEETLELNEGMPVTVEGEIVEVTGRVEEYRGSSEVK  126 (204)
T ss_pred             EEECCCEEEEEEEEEECC--CCCCEEEEEEECCCCCEEEEEECCHHHHHHHCCCCCCCCCCCEEEEEEEEEEECCCCEEE
T ss_conf             120253221489753101--236659999977987489999067367686447887322675899988887717973031


No 253
>COG1061 SSL2 DNA or RNA helicases of superfamily II [Transcription / DNA replication, recombination, and repair]
Probab=94.93  E-value=0.096  Score=33.26  Aligned_cols=76  Identities=25%  Similarity=0.376  Sum_probs=61.0

Q ss_pred             HHCCEEEEEHHHHHHHHHHHHHHHHCCCCCCEEEEEECCCCHHHHHHHHHHHCCCCCEEEEECHHHCCCCCCCCCCCEEE
Q ss_conf             30545886127999999998621101457865899624642256676877621347548641112013345544441788
Q gi|254780945|r  320 AGGQAVIMAPIGILAQQHYEFIKKYTQNTQIIVEIITGNMPQAHRRKALERIAHGQAHIIIGTHALFQDSIQYYKLILVI  399 (700)
Q Consensus       320 ~G~Q~alMaPTEILA~QH~~~~~~~~~~~~i~v~lLtg~~~~~er~~i~~~i~~G~~~iiIGTHAL~q~~v~F~~LgLvV  399 (700)
                      .+-.+.+.+..-    +|...+.+.|..-++ ++.+||+++..||..+++..++|+++++|.+. ++.++|...++..+|
T Consensus       282 ~~~~~lif~~~~----~~a~~i~~~~~~~~~-~~~it~~t~~~eR~~il~~fr~g~~~~lv~~~-vl~EGvDiP~~~~~i  355 (442)
T COG1061         282 RGDKTLIFASDV----EHAYEIAKLFLAPGI-VEAITGETPKEEREAILERFRTGGIKVLVTVK-VLDEGVDIPDADVLI  355 (442)
T ss_pred             CCCCEEEEECCH----HHHHHHHHHHCCCCC-EEEEECCCCHHHHHHHHHHHHCCCCEEEEEEE-EECCCCCCCCCCEEE
T ss_conf             688669997577----999999998626774-24665789988999999998708952999961-412665788875799


Q ss_pred             EC
Q ss_conf             52
Q gi|254780945|r  400 VD  401 (700)
Q Consensus       400 iD  401 (700)
                      +=
T Consensus       356 ~~  357 (442)
T COG1061         356 IL  357 (442)
T ss_pred             EE
T ss_conf             97


No 254
>PRK13342 recombination factor protein RarA; Reviewed
Probab=94.92  E-value=0.13  Score=32.15  Aligned_cols=108  Identities=23%  Similarity=0.282  Sum_probs=59.4

Q ss_pred             HHHHHHHH---HHHHHCCCCCCEEEEEECCCCCHHHHHHHHHHHHHHHHCCEEEEEHHHHHHHHHHHHHHHHCCCCCCEE
Q ss_conf             89999999---998410013430788621442236999999733444305458861279999999986211014578658
Q gi|254780945|r  276 SQESAIKD---ILQDMSQKNRMLRILQGDVGSGKTLVALIAMAAAVEAGGQAVIMAPIGILAQQHYEFIKKYTQNTQIIV  352 (700)
Q Consensus       276 ~Q~~ai~e---I~~Dl~~~~pM~RLLQGDVGSGKTiVA~~A~l~~~~~G~Q~alMaPTEILA~QH~~~~~~~~~~~~i~v  352 (700)
                      +|+..+.+   +.+=+.++..-+-++.|-=|||||-.|-+                    +|.+    ...-|-.+  + 
T Consensus        17 GQ~hllg~~~~L~~~i~~~~~~s~Il~GPPG~GKTTlA~i--------------------iA~~----~~~~f~~l--n-   69 (417)
T PRK13342         17 GQEHLLGPGKPLRRMIEAGRLSSMILWGPPGTGKTTLARI--------------------IAGA----TDAEFEAL--S-   69 (417)
T ss_pred             CCHHHHCCCHHHHHHHHCCCCCEEEEECCCCCCHHHHHHH--------------------HHHH----HCCCEEEE--E-
T ss_conf             9877608971999999769997599889699989999999--------------------9998----68988996--1-


Q ss_pred             EEEECCCCHHHHHHHHHHHCCCCCEEEEECHHHCCCCCCCCCCCEEEECCCCCCCHHHHHHHHHCCCCCCCEEECHH
Q ss_conf             99624642256676877621347548641112013345544441788521013356889987402567761010101
Q gi|254780945|r  353 EIITGNMPQAHRRKALERIAHGQAHIIIGTHALFQDSIQYYKLILVIVDEQHRFGVQQRLKLTQKATAPHVLLMTAT  429 (700)
Q Consensus       353 ~lLtg~~~~~er~~i~~~i~~G~~~iiIGTHAL~q~~v~F~~LgLvViDEQHRFGV~QR~~L~~Kg~~ph~L~MtAT  429 (700)
                         ......++=+++.+..+.-.    -|           ++ -+++|||=|||-=.|-..|..-=++-++...-||
T Consensus        70 ---A~~~gv~dir~ii~~a~~~~----~~-----------~~-tilfiDEIHRfnK~QQD~LLp~vE~g~iiLIgAT  127 (417)
T PRK13342         70 ---AVTSGVKDLREVIEEAKQSR----LG-----------RR-TILFIDEIHRFNKAQQDALLPHVEDGTITLIGAT  127 (417)
T ss_pred             ---CCCCCHHHHHHHHHHHHHHH----CC-----------CC-EEEEEECHHHCCHHHHHHHHHHHHCCCEEEEEEC
T ss_conf             ---41038899999999988631----48-----------96-5999978200588999999875112656999741


No 255
>KOG0391 consensus
Probab=94.82  E-value=0.22  Score=30.42  Aligned_cols=120  Identities=18%  Similarity=0.257  Sum_probs=83.4

Q ss_pred             CCCEECCCCCCCHHHHHHHHHHHHCCC--EEEEEECHHHHCCCCCCCCCEEEEECHHHCC--HHHHHHHHHCCCCCCCCE
Q ss_conf             710312014699899999999975598--6999980034104688876589985852547--468877301166789835
Q gi|254780945|r  515 TSSIAIIHGRMSDIDKESVMDSFKNGT--CKLLIATTVIEVGIDVVDASIIIIENAEHFG--LAQLHQLRGRVGRGEEIS  590 (700)
Q Consensus       515 ~~~v~~lHGkm~~~ek~~~m~~F~~g~--~~iLvaTtviEVGvdvpna~~mvI~~aerfG--LsqLHQLRGRVGRg~~~s  590 (700)
                      +.-.--|.|--+.++++..|++|....  .-..+||--=-||||.-.|.+.|-+|.|-=-  =||-.----|+|+-..-+
T Consensus      1300 gylY~RLDg~t~vEqRQaLmerFNaD~RIfcfILSTrSggvGiNLtgADTVvFYDsDwNPtMDaQaQDrChRIGqtRdVh 1379 (1958)
T KOG0391        1300 GYLYVRLDGNTSVEQRQALMERFNADRRIFCFILSTRSGGVGINLTGADTVVFYDSDWNPTMDAQAQDRCHRIGQTRDVH 1379 (1958)
T ss_pred             CEEEEEECCCCCHHHHHHHHHHHCCCCCEEEEEEECCCCCCCCCCCCCCEEEEECCCCCCHHHHHHHHHHHHHCCCCCEE
T ss_conf             56899844875388999999973678716999985267864201346745898458888013268898888745734137


Q ss_pred             EEEEEECCCCCHH------HHHHHHHHHHHCHHHHHHHHHHHHCCCCCCCCC
Q ss_conf             9999708889987------999999998414258999999852063000260
Q gi|254780945|r  591 SCILLYHPPLSKN------SYTRLSVLKNTEDGFLIAEEDLKQRKEGEILGI  636 (700)
Q Consensus       591 ~c~l~~~~~~~~~------~~~Rl~~l~~~~dGf~iAe~Dl~lRG~G~~~G~  636 (700)
                      -.=|++...+-++      .+.+|.-++--..+|.-|-  ++-|---|+|+.
T Consensus      1380 IYRliSerTIEenILKkanqKr~L~evaiqggdfTtaf--fkQ~tirdLfd~ 1429 (1958)
T KOG0391        1380 IYRLISERTIEENILKKANQKRMLDEVAIQGGDFTTAF--FKQRTIRDLFDV 1429 (1958)
T ss_pred             EEEEECCCHHHHHHHHHHHHHHHHHHHHHCCCCCCHHH--HHHHHHHHHHCC
T ss_conf             88740334078999863227776666642158853888--755359998558


No 256
>cd03586 Pol_IV_kappa Pol_IV_kappa, a member of the Y-family of DNA polymerases. Pol_Y's can transverse replication-blocking DNA lesions, such as cyclobutane pyrimidine dimers resulting from UV damage, at the cost of an elevated error rate. The Y-family has no 3'-5' exonuclease activity. In addition to possessing a topology akin to a right hand, with "thumb", "fingers" and "palm" motifs, like polymerases from the A-, B-, C- and X-families, the Y-family has a unique "little finger" motif. Expression of Y-family polymerases is often induced by DNA damage. These polymerases are phylogenetically unrelated to classical DNA polymerases. Originally called the DinB family, they belong to the recently described Y-family of DNA polymerases. Pol IV is mostly found in bacteria and archaea. Although the structure of Pol IV is similar to that of Pol eta, it shows markedly differenct efficiencies and fidelities in bypassing various DNA lesions. All Pol IV-like polymerases studied to date are able to b
Probab=94.82  E-value=0.023  Score=38.09  Aligned_cols=11  Identities=0%  Similarity=0.036  Sum_probs=5.4

Q ss_pred             HHHHCCCCCCE
Q ss_conf             21101457865
Q gi|254780945|r  341 IKKYTQNTQII  351 (700)
Q Consensus       341 ~~~~~~~~~i~  351 (700)
                      +.+++.++++.
T Consensus       165 ~~~~L~~lpv~  175 (337)
T cd03586         165 VWAFLAPLPVR  175 (337)
T ss_pred             HHHHHCCCCCH
T ss_conf             99986127630


No 257
>TIGR03015 pepcterm_ATPase putative secretion ATPase, PEP-CTERM locus subfamily. Members of this protein are marked as probable ATPases by the nucleotide binding P-loop motif GXXGXGKTT, a motif DEAQ similar to the DEAD/H box of helicases, and extensive homology to ATPases of MSHA-type pilus systems and to GspA proteins associated with type II protein secretion systems.
Probab=94.80  E-value=0.081  Score=33.83  Aligned_cols=177  Identities=18%  Similarity=0.237  Sum_probs=95.5

Q ss_pred             CCCHHHHHHHHHHHHHHCCCCCCEEEEEECCCCCHHHHHHHHHHHHH-HHHCCEEEEEHHHHHHHHHHHHHHHHCCCCCC
Q ss_conf             67988999999999841001343078862144223699999973344-43054588612799999999862110145786
Q gi|254780945|r  272 SPTKSQESAIKDILQDMSQKNRMLRILQGDVGSGKTLVALIAMAAAV-EAGGQAVIMAPIGILAQQHYEFIKKYTQNTQI  350 (700)
Q Consensus       272 ~LT~~Q~~ai~eI~~Dl~~~~pM~RLLQGDVGSGKTiVA~~A~l~~~-~~G~Q~alMaPTEILA~QH~~~~~~~~~~~~i  350 (700)
                      =.+.+.+.|+..+.--+....... +|-|+||||||.+ +.+++..+ .+.+.++++..|.+=...-   ++.+...+|+
T Consensus        23 y~s~~h~~al~~L~~~l~~~~g~~-lltGe~GtGKTtl-lr~l~~~l~~~~~~~~~i~~~~l~~~~l---l~~i~~~lg~   97 (269)
T TIGR03015        23 YPSKGHKRAMAYLEYGLSQREGFI-LITGEVGAGKTTL-IRNLLKRLDQERVVAAKLVNTRVDAEDL---LRMVAADFGL   97 (269)
T ss_pred             CCCHHHHHHHHHHHHHHHCCCCEE-EEECCCCCCHHHH-HHHHHHHCCCCCEEEEEECCCCCCHHHH---HHHHHHHCCC
T ss_conf             478669999999999996489659-9972998988999-9999984593454899976999999999---9999998598


Q ss_pred             EEEEEECCCCHHHHHHHHHHHCCCCCEEEEECHHHCCCCCCCCCCCEEEECCCCCCCHHHHHHHHHC------CCCCCCE
Q ss_conf             5899624642256676877621347548641112013345544441788521013356889987402------5677610
Q gi|254780945|r  351 IVEIITGNMPQAHRRKALERIAHGQAHIIIGTHALFQDSIQYYKLILVIVDEQHRFGVQQRLKLTQK------ATAPHVL  424 (700)
Q Consensus       351 ~v~lLtg~~~~~er~~i~~~i~~G~~~iiIGTHAL~q~~v~F~~LgLvViDEQHRFGV~QR~~L~~K------g~~ph~L  424 (700)
                      ...   +.    .+...+..|..-    +   ..+...+    .--++||||=|....+-=+.|..-      +...=.+
T Consensus        98 ~~~---~~----~~~~~~~~l~~~----L---~~~~~~g----~~~vliIDEAq~L~~~~Le~Lr~L~n~e~~~~~ll~i  159 (269)
T TIGR03015        98 ETE---GR----DKAALLRELEDF----L---IEQFAAG----KRALLVVDEAQNLTPELLEELRMLSNFQTDNAKLLQI  159 (269)
T ss_pred             CCC---CC----CHHHHHHHHHHH----H---HHHHHCC----CCEEEEEECHHHCCHHHHHHHHHHHCCCCCCCCCEEE
T ss_conf             988---98----999999999999----9---9999669----9469997242219999999999997013588870489


Q ss_pred             EECHHH-HHHHHHHHHHHCCCHHHHCCCCCCCCCCEEEE-EECCCHHHHHHHHHHHHCCC
Q ss_conf             101013-22789999752010111102355766620799-97020026899997631038
Q gi|254780945|r  425 LMTATP-IPRTLVLTSLGDIDISKITEKPAGRKPIKTVI-IPINRIDEVIERLKVVLSEG  482 (700)
Q Consensus       425 ~MtATP-IPRTLal~~ygdldvS~i~e~P~gR~~I~T~~-~~~~~~~~~~~~i~~~l~~g  482 (700)
                      ++...| ..++|+...           +++=++.|..++ +..=+.++.-+.|+-+++.-
T Consensus       160 iL~GqpeL~~~L~~~~-----------~~~l~qRI~~~~~L~pl~~eet~~YI~~RL~~A  208 (269)
T TIGR03015       160 FLVGQPEFRETLQSPQ-----------LQQLRQRIIASCHLGPLDREETREYIEHRLERA  208 (269)
T ss_pred             EEECCHHHHHHHCCCC-----------HHHHHHCEEEEEEECCCCHHHHHHHHHHHHHHC
T ss_conf             9957867999872740-----------254555076799847999899999999999866


No 258
>pfam03796 DnaB_C DnaB-like helicase C terminal domain. The hexameric helicase DnaB unwinds the DNA duplex at the Escherichia coli chromosome replication fork. Although the mechanism by which DnaB both couples ATP hydrolysis to translocation along DNA and denatures the duplex is unknown, a change in the quaternary structure of the protein involving dimerization of the N-terminal domain has been observed and may occur during the enzymatic cycle. This C-terminal domain contains an ATP-binding site and is therefore probably the site of ATP hydrolysis.
Probab=94.77  E-value=0.096  Score=33.25  Aligned_cols=84  Identities=14%  Similarity=0.195  Sum_probs=48.7

Q ss_pred             HHHHHHHHHCCCCCCEEEEEECCCCCHHHHHHHHHHHH-HHHHCCEEEEEHHHHHHHHHHHHHHHHCCCCCCEEEEEECC
Q ss_conf             99999984100134307886214422369999997334-44305458861279999999986211014578658996246
Q gi|254780945|r  280 AIKDILQDMSQKNRMLRILQGDVGSGKTLVALIAMAAA-VEAGGQAVIMAPIGILAQQHYEFIKKYTQNTQIIVEIITGN  358 (700)
Q Consensus       280 ai~eI~~Dl~~~~pM~RLLQGDVGSGKTiVA~~A~l~~-~~~G~Q~alMaPTEILA~QH~~~~~~~~~~~~i~v~lLtg~  358 (700)
                      .++++..-+..+.  .-++-|.-|+|||.++.-.++.+ ..+|+.|++..+ |.=.++....+-......+.. .+.+|.
T Consensus         8 ~lD~~~gGl~~G~--l~vi~g~pg~GKS~~~~~~a~~~a~~~g~~Vl~~sl-Em~~~~~~~R~~a~~~~v~~~-~i~~~~   83 (186)
T pfam03796         8 DLDQLTGGLQKGD--LIIIAARPSMGKTAFALNIARNAALKQDKPVLFFSL-EMSAEQLAERLLSSESRISSS-KLRSGQ   83 (186)
T ss_pred             HHHHHHCCCCCCC--EEEEEECCCCCHHHHHHHHHHHHHHHCCCCEEEECC-CCCHHHHHHHHHHHHHCCCHH-HHHCCC
T ss_conf             7886426988881--799996799987999999999999970996687547-552999999999986267655-541251


Q ss_pred             CCHHHHHHH
Q ss_conf             422566768
Q gi|254780945|r  359 MPQAHRRKA  367 (700)
Q Consensus       359 ~~~~er~~i  367 (700)
                      ....+.+++
T Consensus        84 ~~~~~~~~~   92 (186)
T pfam03796        84 LSDEDWERL   92 (186)
T ss_pred             HHHHHHHHH
T ss_conf             216799999


No 259
>COG1484 DnaC DNA replication protein [DNA replication, recombination, and repair]
Probab=94.66  E-value=0.17  Score=31.28  Aligned_cols=61  Identities=18%  Similarity=0.231  Sum_probs=45.5

Q ss_pred             CCCHHHHHHHHHHHHHHCCCCCCEEEEEECCCCCHHHHHHHHHHHHHHHHCCEEEEEHHHHHH
Q ss_conf             679889999999998410013430788621442236999999733444305458861279999
Q gi|254780945|r  272 SPTKSQESAIKDILQDMSQKNRMLRILQGDVGSGKTLVALIAMAAAVEAGGQAVIMAPIGILA  334 (700)
Q Consensus       272 ~LT~~Q~~ai~eI~~Dl~~~~pM~RLLQGDVGSGKTiVA~~A~l~~~~~G~Q~alMaPTEILA  334 (700)
                      ....++...+.++...+.  .+.+=++-|+.|+|||-+|.+.+..++..|.-|.|.-=+|.+.
T Consensus        86 ~~~~~~l~~~~~~~~~~~--~~~nl~l~G~~G~GKthLa~Ai~~~l~~~g~sv~f~~~~el~~  146 (254)
T COG1484          86 GIDKKALEDLASLVEFFE--RGENLVLLGPPGVGKTHLAIAIGNELLKAGISVLFITAPDLLS  146 (254)
T ss_pred             HHHHHHHHHHHHHHHHHC--CCCCEEEECCCCCCHHHHHHHHHHHHHHCCCEEEEEEHHHHHH
T ss_conf             566999999999998732--5882899899998799999999999998398499988599999


No 260
>pfam04466 Terminase_3 Phage terminase large subunit. Initiation of packaging of double-stranded viral DNA involves the specific interaction of the prohead with viral DNA in a process mediated by a phage-encoded terminase protein. The terminase enzymes are usually hetero-oligomers composed of a small and a large subunit. This region is found on the large subunit and possess an endonuclease and ATPase activity that require Mg2+ and a neutral or slightly basic reaction. This region is also found in bacterial sequences.
Probab=94.63  E-value=0.44  Score=28.04  Aligned_cols=131  Identities=13%  Similarity=0.211  Sum_probs=78.1

Q ss_pred             EEEEEECCCCCHHH-HHHHHHHHHHHHHCCEEEEEHHHH-HHHHHHHHHHHHCCCCCCEEEEEECCCCHHHHHHHHHHHC
Q ss_conf             07886214422369-999997334443054588612799-9999998621101457865899624642256676877621
Q gi|254780945|r  295 LRILQGDVGSGKTL-VALIAMAAAVEAGGQAVIMAPIGI-LAQQHYEFIKKYTQNTQIIVEIITGNMPQAHRRKALERIA  372 (700)
Q Consensus       295 ~RLLQGDVGSGKTi-VA~~A~l~~~~~G~Q~alMaPTEI-LA~QH~~~~~~~~~~~~i~v~lLtg~~~~~er~~i~~~i~  372 (700)
                      .+.+.|-.|||||. +|....+.+..+...++++.+|-- |-+=-|+.+++.+..+|+....-.+..+-.    + ....
T Consensus         4 ~~v~~GGrgsgKS~~~a~~~i~~~~~~~~~~l~~r~~~~slr~sv~~~~~~~i~~~~~~~~~~~~~s~~~----i-~~~~   78 (387)
T pfam04466         4 YKVAKGGRGSGKSYHIALKLVLKLLMHPRTNLVIREVKNTIEDSVFTQLQEALSMLGLDHEFKISKSPIE----I-TVKI   78 (387)
T ss_pred             EEEEEECCCCHHHHHHHHHHHHHHHHCCCEEEEEECCHHHHHHHHHHHHHHHHHHCCCCCEEEECCCCEE----E-EECC
T ss_conf             8999908886799999999999998789869999755688999999999999997699734897376148----9-9878


Q ss_pred             CCCCEEEEECHHHCCCCC-CCCCCCEEEECCCCCCCHHHHHHH----HHCCCCCCCEEECHHHHHH
Q ss_conf             347548641112013345-544441788521013356889987----4025677610101013227
Q gi|254780945|r  373 HGQAHIIIGTHALFQDSI-QYYKLILVIVDEQHRFGVQQRLKL----TQKATAPHVLLMTATPIPR  433 (700)
Q Consensus       373 ~G~~~iiIGTHAL~q~~v-~F~~LgLvViDEQHRFGV~QR~~L----~~Kg~~ph~L~MtATPIPR  433 (700)
                      +|..=+.-|.+--  +++ ...++.++.+||=.=|--+.=..|    +..+ ..-.+.||-+|-..
T Consensus        79 ~gs~i~f~G~d~~--~~iks~~~i~~~~~eEa~~~~~~~~~~l~~~~r~~~-~~~~i~~~~NP~~~  141 (387)
T pfam04466        79 NGSKFLFYGMDDP--AKIKSIKDVSDAWIEEAAEFKTEDFDQLIPTIRRPK-PGSEIFMSFNPVNK  141 (387)
T ss_pred             CCCEEEEEECCCH--HHHHCCCCCEEEEEECHHHCCHHHHHHHHHHHCCCC-CCEEEEEECCCCCC
T ss_conf             9969999857896--884163661499994124479989999998853178-87199998289998


No 261
>pfam00580 UvrD-helicase UvrD/REP helicase. The Rep family helicases are composed of four structural domains. The Rep family function as dimers. REP helicases catalyse ATP dependent unwinding of double stranded DNA to single stranded DNA. Bacillus subtilis addA and Escherichia coli exodeoxyribonuclease V beta have large insertions near to the carboxy-terminus relative to other members of the family.
Probab=94.62  E-value=0.1  Score=33.03  Aligned_cols=21  Identities=24%  Similarity=0.167  Sum_probs=14.5

Q ss_pred             CCEEEECCCCCCCHHHHHHHH
Q ss_conf             417885210133568899874
Q gi|254780945|r  395 LILVIVDEQHRFGVQQRLKLT  415 (700)
Q Consensus       395 LgLvViDEQHRFGV~QR~~L~  415 (700)
                      .-.|+|||=|=-...|-.-|.
T Consensus       213 ~~~ilVDEfQDtn~~Q~~il~  233 (494)
T pfam00580       213 FKYILVDEFQDTNPIQYELLK  233 (494)
T ss_pred             CCEEECHHHCCCHHHHHHHHH
T ss_conf             726540343026499999999


No 262
>COG3587 Restriction endonuclease [Defense mechanisms]
Probab=94.59  E-value=0.053  Score=35.26  Aligned_cols=15  Identities=33%  Similarity=0.454  Sum_probs=9.0

Q ss_pred             HHHHHHHHHHHHCCC
Q ss_conf             322789999752010
Q gi|254780945|r  430 PIPRTLVLTSLGDID  444 (700)
Q Consensus       430 PIPRTLal~~ygdld  444 (700)
                      -+|-+++.-+|+|++
T Consensus       593 v~~e~~~~~~f~dl~  607 (985)
T COG3587         593 VLPETLEKLLFGDLI  607 (985)
T ss_pred             CCHHHHHHHHHHHHH
T ss_conf             257788878765410


No 263
>PRK09361 radB DNA repair and recombination protein RadB; Provisional
Probab=94.57  E-value=0.24  Score=30.11  Aligned_cols=48  Identities=17%  Similarity=0.186  Sum_probs=37.1

Q ss_pred             HHHHHHCCCCCCEE--EEEECCCCCHHHHHHHHHHHHHHHHCCEEEEEHHH
Q ss_conf             99984100134307--88621442236999999733444305458861279
Q gi|254780945|r  283 DILQDMSQKNRMLR--ILQGDVGSGKTLVALIAMAAAVEAGGQAVIMAPIG  331 (700)
Q Consensus       283 eI~~Dl~~~~pM~R--LLQGDVGSGKTiVA~~A~l~~~~~G~Q~alMaPTE  331 (700)
                      ++..=|..+.|.-+  ++-|+=|||||-+|+-.+..+..+|+.|+++. ||
T Consensus        11 ~lD~~LgGGi~~G~itei~G~pG~GKTtl~lq~a~~~~~~g~~vlYid-tE   60 (224)
T PRK09361         11 SLDELLGGGIERGTITQIYGPPGSGKTNICIQLAVEAARQGKKVIYID-TE   60 (224)
T ss_pred             HHHHHHCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHCCCCEEEEC-CC
T ss_conf             999862699888879999899998599999999999997499099967-87


No 264
>cd01702 Pol_eta Pol eta is member of the DNA polimerase Y-family. Unlike other Y-family members, Pol eta can efficiently and accurately replicate DNA past UV-induced cis-syn cyclobutane thymine-thumine (T-T) lesions. It synthesizes AA opposite a TT dimer. Pol eta is able to replicate through a variety of other distorting DNA lesion as well.
Probab=94.54  E-value=0.029  Score=37.32  Aligned_cols=18  Identities=11%  Similarity=0.026  Sum_probs=8.8

Q ss_pred             HHHHHCCCCCCEEEEEEC
Q ss_conf             621101457865899624
Q gi|254780945|r  340 FIKKYTQNTQIIVEIITG  357 (700)
Q Consensus       340 ~~~~~~~~~~i~v~lLtg  357 (700)
                      .+.+++.+++|+--.=.|
T Consensus       174 ~~~~~l~~lpI~~i~GvG  191 (358)
T cd01702         174 AVASFLSSLPITKIRGLG  191 (358)
T ss_pred             HHHHHHHCCCCCEECCCC
T ss_conf             999998559976627867


No 265
>PRK00652 lpxK tetraacyldisaccharide 4'-kinase; Reviewed
Probab=94.52  E-value=0.47  Score=27.82  Aligned_cols=205  Identities=18%  Similarity=0.159  Sum_probs=102.9

Q ss_pred             CCCHHHHHHHHHHHHHHHHCCEEEEEHH---------HHHHHHHH-HHHH--H-HCC-CCCCEEEEEECCCCHHHHHHHH
Q ss_conf             4223699999973344430545886127---------99999999-8621--1-014-5786589962464225667687
Q gi|254780945|r  303 GSGKTLVALIAMAAAVEAGGQAVIMAPI---------GILAQQHY-EFIK--K-YTQ-NTQIIVEIITGNMPQAHRRKAL  368 (700)
Q Consensus       303 GSGKTiVA~~A~l~~~~~G~Q~alMaPT---------EILA~QH~-~~~~--~-~~~-~~~i~v~lLtg~~~~~er~~i~  368 (700)
                      |+|||=+...-+-...+.||+++++.=-         .+....|- +..-  . ++. ..+++|.  .|    +.|.+..
T Consensus        61 GtGKTP~v~~la~~l~~~g~~~~IlSRGYg~~~~~~~~v~~~~~~~~~vGDEpllla~~~~~~v~--V~----~~R~~~~  134 (334)
T PRK00652         61 GNGKTPVVIWLAEQLQARGVKVGVVSRGYGGKSKGYPLVLPADTTAAEVGDEPVLIAQRTGAPVA--VS----PDRVKAI  134 (334)
T ss_pred             CCCHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCCCEEEECCCCCHHHCCCHHHHHHHCCCCCEE--EE----CCHHHHH
T ss_conf             87779999999999997699367873466765678727617999835518689998517898399--95----6689999


Q ss_pred             HHHCCCCCEEEEECHHHCCCCCCCCCCCEEEECCCCCCCHHH-------HHHHHHCCCCCCCEEECHHHHHHHHHHHHHH
Q ss_conf             762134754864111201334554444178852101335688-------9987402567761010101322789999752
Q gi|254780945|r  369 ERIAHGQAHIIIGTHALFQDSIQYYKLILVIVDEQHRFGVQQ-------RLKLTQKATAPHVLLMTATPIPRTLVLTSLG  441 (700)
Q Consensus       369 ~~i~~G~~~iiIGTHAL~q~~v~F~~LgLvViDEQHRFGV~Q-------R~~L~~Kg~~ph~L~MtATPIPRTLal~~yg  441 (700)
                      ..+..-.+++||=--+ ||..-.-++|-+|++|.++-||=..       |+-+.. -..+|+++.+-.+-...       
T Consensus       135 ~~l~~~~~dviIlDDG-fQh~~l~rdl~Ivlid~~~~fgn~~llP~GpLREp~~~-l~rAD~ii~~~~~~~~~-------  205 (334)
T PRK00652        135 KALLALGADIIILDDG-LQHYRLHRDFEIVVVDGQRRFGNGWLLPAGPLREPPSR-LKSADAVIVNGGDAQEG-------  205 (334)
T ss_pred             HHHHHCCCCEEEECCC-CCCCCCCCCEEEEEECCCCCCCCCCCCCCCCCCCCHHH-HCCCCEEEEECCCCCCH-------
T ss_conf             9999659999997476-65664468879999747767889867758656589647-61468999938854311-------


Q ss_pred             CCCHHHHCCCCCCCCCCEEEEEECCCHHHHHHHHHHHHCCCCEEEEEECCCCCCCCCCCCHHHHHHHHHHHHCCCC-E--
Q ss_conf             0101111023557666207999702002689999763103873899971201221112101466666668663710-3--
Q gi|254780945|r  442 DIDISKITEKPAGRKPIKTVIIPINRIDEVIERLKVVLSEGKKAYWICPQIEEKKESNFRSVVERFNSLHEHFTSS-I--  518 (700)
Q Consensus       442 dldvS~i~e~P~gR~~I~T~~~~~~~~~~~~~~i~~~l~~g~q~y~VcPlIeese~~~~~~~~~~~~~l~~~~~~~-v--  518 (700)
                      +.....  . +..-+++             .........+|.+++.+|-.         .+-+.-++.|++. +.+ +  
T Consensus       206 ~~~~~~--~-~~~~~~~-------------~~~~~~~~~~~k~v~afsGI---------anP~~F~~~L~~~-g~~i~~~  259 (334)
T PRK00652        206 EIPMRL--A-PGAAVNL-------------RTGESRDVLKGKRVVAFAGI---------GHPPRFFATLRNL-GIEVVGT  259 (334)
T ss_pred             HHHHHH--C-CCCCEEC-------------CCCCCCCCCCCCEEEEEEEC---------CCHHHHHHHHHHC-CCEEEEE
T ss_conf             045553--6-5663676-------------66554633579818999944---------8869999999976-9927342


Q ss_pred             --ECCCCCCCHHHHHHHHHHHHCCCEEEEEECH
Q ss_conf             --1201469989999999997559869999800
Q gi|254780945|r  519 --AIIHGRMSDIDKESVMDSFKNGTCKLLIATT  549 (700)
Q Consensus       519 --~~lHGkm~~~ek~~~m~~F~~g~~~iLvaTt  549 (700)
                        --=|-.-+.++-+.+.+..+.+. +.+|.|-
T Consensus       260 ~~fpDHh~ys~~dl~~i~~~a~~~~-~~iiTTE  291 (334)
T PRK00652        260 VAFPDHQSFTKADLEALVSLAQRQG-LSLLMTE  291 (334)
T ss_pred             EECCCCCCCCHHHHHHHHHHHHHCC-CEEEECC
T ss_conf             5779866689999999999998289-9389855


No 266
>COG3973 Superfamily I DNA and RNA helicases [General function prediction only]
Probab=94.44  E-value=0.085  Score=33.69  Aligned_cols=368  Identities=16%  Similarity=0.152  Sum_probs=180.6

Q ss_pred             HHHHHHHCCCCCCEEEEEECCCCCHHHHHHHHHHHH------HHHHCCEEEEEHHHHHHHHHHHHHHHHCCCCCCE-EEE
Q ss_conf             999984100134307886214422369999997334------4430545886127999999998621101457865-899
Q gi|254780945|r  282 KDILQDMSQKNRMLRILQGDVGSGKTLVALIAMAAA------VEAGGQAVIMAPIGILAQQHYEFIKKYTQNTQII-VEI  354 (700)
Q Consensus       282 ~eI~~Dl~~~~pM~RLLQGDVGSGKTiVA~~A~l~~------~~~G~Q~alMaPTEILA~QH~~~~~~~~~~~~i~-v~l  354 (700)
                      +||..+= ++.+|  .+||--|||||-||+.-.+..      .-++.|+.+++|.-+++.    .++..+|.+|.. |..
T Consensus       218 neIIR~e-k~~il--VVQGaAGSGKTtiALHRvAyLlY~~R~~l~~k~vlvl~PN~vFle----Yis~VLPeLGe~~V~q  290 (747)
T COG3973         218 NEIIRFE-KNKIL--VVQGAAGSGKTTIALHRVAYLLYGYRGPLQAKPVLVLGPNRVFLE----YISRVLPELGEEGVVQ  290 (747)
T ss_pred             HHHHHCC-CCCEE--EEECCCCCCCHHHHHHHHHHHHHCCCCCCCCCCEEEECCCHHHHH----HHHHHCHHHCCCCEEE
T ss_conf             7787555-78748--995588887135889999999853566246686599828389999----9987554416686365


Q ss_pred             EE---------C-CCCHHHHHHHHHHHCCCCCEEEEECH-----HHCCCCCCCCCCCEEEECCCCCCCH---HHHHHHHH
Q ss_conf             62---------4-64225667687762134754864111-----2013345544441788521013356---88998740
Q gi|254780945|r  355 IT---------G-NMPQAHRRKALERIAHGQAHIIIGTH-----ALFQDSIQYYKLILVIVDEQHRFGV---QQRLKLTQ  416 (700)
Q Consensus       355 Lt---------g-~~~~~er~~i~~~i~~G~~~iiIGTH-----AL~q~~v~F~~LgLvViDEQHRFGV---~QR~~L~~  416 (700)
                      =|         | .++..+-...+....-+.-+..+-+-     -+|++   |-++-++=|-+.-.||-   -++..+..
T Consensus       291 ~Tf~e~a~~iLg~~s~d~~lt~~~~e~~~~d~~~~~a~~a~k~~~~~~~---~i~~~v~~is~e~~v~k~i~~~~~~~~s  367 (747)
T COG3973         291 ETFEEWALAILGLKSEDLELTRRTLEKLLMDTDLGIAALAWKRSLLFGD---AIDLDVVRISLEKKVGKDITGAGLQLNS  367 (747)
T ss_pred             CCHHHHHHHHCCCCCCHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             0499988876188971157899987654145077787777630257899---9987765455532267776643477764


Q ss_pred             CCCCC--CCEEECHHHHHHHHHHH---HHHCCCHHHHCCCCCCCCCCEEEEEECCCHHHHHHHHHHHHCCCCEEEEEECC
Q ss_conf             25677--61010101322789999---75201011110235576662079997020026899997631038738999712
Q gi|254780945|r  417 KATAP--HVLLMTATPIPRTLVLT---SLGDIDISKITEKPAGRKPIKTVIIPINRIDEVIERLKVVLSEGKKAYWICPQ  491 (700)
Q Consensus       417 Kg~~p--h~L~MtATPIPRTLal~---~ygdldvS~i~e~P~gR~~I~T~~~~~~~~~~~~~~i~~~l~~g~q~y~VcPl  491 (700)
                      |+.--  -.=.|+--|||+-+--+   ..+++.--.+..    |-.+ +.......+.++|+-.-++++.-    .|.|-
T Consensus       368 k~eir~lF~e~l~~~~l~~r~~~i~~~~~~~ln~l~~~~----~dk~-~~~~~~~~~q~~~ed~v~rlr~~----~~l~e  438 (747)
T COG3973         368 KVEIRGLFTESLSESPLADRLHDIFAQDLLKLNDLSAAI----RDKL-DDLLDIAFRQKVYEDAVKRLRPQ----DVLPE  438 (747)
T ss_pred             HHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCHHHHHHHH----HHHH-HHHHHHHHHHHHHHHHHHHHCCC----CCCCH
T ss_conf             788899999876329577788888631542012456666----5434-46777998888899999863210----35767


Q ss_pred             CCCCCCCCCCHHHHHH---------HHHHHHCCCC---EECCCCCCCHHHHHHHHHHHHCCCEE-EEEE---------CH
Q ss_conf             0122111210146666---------6668663710---31201469989999999997559869-9998---------00
Q gi|254780945|r  492 IEEKKESNFRSVVERF---------NSLHEHFTSS---IAIIHGRMSDIDKESVMDSFKNGTCK-LLIA---------TT  549 (700)
Q Consensus       492 Ieese~~~~~~~~~~~---------~~l~~~~~~~---v~~lHGkm~~~ek~~~m~~F~~g~~~-iLva---------Tt  549 (700)
                      -++++..-.-++....         ..|...|+..   ..+.-|+-+.+++..+=+.|....+| +|.+         --
T Consensus       439 e~~n~~~~~vaa~~y~e~~k~~~l~~~L~r~~~s~~~~~el~~g~~~~e~~r~~ge~~~~~~~d~~l~~dD~a~~lyikd  518 (747)
T COG3973         439 EEENSVRINVAAANYDEAQKSLKLRVLLDRFFASTTPLTELRRGLADAEALRAIGEAKWREQIDKALLSDDVAPRLYIKD  518 (747)
T ss_pred             HHHHHHCCHHHHHHHHHHHCCCCHHHHHHHHHCCCHHHHHHHCCCCCHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHCC
T ss_conf             66655312255534677740400889988653123167898647878899987303544432100000211435665013


Q ss_pred             HHHCCCCCCCCCEEEEECHHH---CCHHHHHHHHHCCCCCCCCEEEEEEECCCCCHHHHHHHHHHHHHCHHHHHHHHHHH
Q ss_conf             341046888765899858525---47468877301166789835999970888998799999999841425899999985
Q gi|254780945|r  550 VIEVGIDVVDASIIIIENAEH---FGLAQLHQLRGRVGRGEEISSCILLYHPPLSKNSYTRLSVLKNTEDGFLIAEEDLK  626 (700)
Q Consensus       550 viEVGvdvpna~~mvI~~aer---fGLsqLHQLRGRVGRg~~~s~c~l~~~~~~~~~~~~Rl~~l~~~~dGf~iAe~Dl~  626 (700)
                      .+|+-=+--+....||..|.-   |-.+-+--|--|-+=--.-.|---+|....--..++|+.++-+.++ |+.---+--
T Consensus       519 ~ldG~k~~~~~kh~vIDeaqdys~~q~~~~r~l~~~as~tivgd~gq~i~~~~~e~~~~e~~~~~fed~~-~e~v~l~~s  597 (747)
T COG3973         519 PLDGIKTERRLKHTVIDEAQDYSRFQFTDNRTLAERASMTIVGDYGQVIYDEAQELSPMERMDVFFEDPS-FEYVGLIAS  597 (747)
T ss_pred             CCCCCCCCCCCCCEEECHHHHCCHHHHHHHHHHHHHCCCEEECCCCCEEHHHHCCCCHHHHHHHHHHCCC-CHHHHHHHH
T ss_conf             2346655420332255134433402458876443203644762478553220122687999888872897-054324565


Q ss_pred             HCCCCCCCCCHHCCCC-CCCCCCHHH------------HHHHHHHHHHHHHHHHHH
Q ss_conf             2063000260006987-440003887------------599999999999999984
Q gi|254780945|r  627 QRKEGEILGIKQSGMP-KFLIAQPEL------------HDSLLEIARKDAKHILTQ  669 (700)
Q Consensus       627 lRG~G~~~G~~QsG~~-~~~~~d~~~------------d~~ll~~a~~~a~~~~~~  669 (700)
                      .|.+-++.-..-|=+| .|++--+.+            +..+.+.+-..+..+-..
T Consensus       598 yrSt~eI~efan~~l~d~~~~~p~~rsge~p~~i~~~~ne~l~qr~~~ii~~mkk~  653 (747)
T COG3973         598 YRSTAEIDEFANSLLPDRFRIHPLTRSGEKPAVIMSVANEELVQRNPDIIPRMKKR  653 (747)
T ss_pred             HCCHHHHHHHHHHHCCCCCCCCHHHCCCCCCEEEECCCHHHHHHHHHHHHHHHHHC
T ss_conf             25858899999986327776661211788762211113398987507788888752


No 267
>PRK03609 umuC DNA polymerase V subunit UmuC; Reviewed
Probab=94.33  E-value=0.026  Score=37.70  Aligned_cols=10  Identities=10%  Similarity=0.222  Sum_probs=3.9

Q ss_pred             HHHHHHHCCC
Q ss_conf             6666866371
Q gi|254780945|r  507 FNSLHEHFTS  516 (700)
Q Consensus       507 ~~~l~~~~~~  516 (700)
                      .+.+++.||.
T Consensus       377 iD~In~rfG~  386 (422)
T PRK03609        377 LDTLNAKEGK  386 (422)
T ss_pred             HHHHHHHHCC
T ss_conf             9999985389


No 268
>PRK12727 flagellar biosynthesis regulator FlhF; Provisional
Probab=94.32  E-value=0.52  Score=27.50  Aligned_cols=223  Identities=15%  Similarity=0.159  Sum_probs=130.8

Q ss_pred             CCCCCHHHHHHHHHCCCCCCHHHHHHHHHHHHHHCCCCCCE----------EEEEECCCCCHH-HHHHHHHHHHHHHHC-
Q ss_conf             78775789999863024679889999999998410013430----------788621442236-999999733444305-
Q gi|254780945|r  255 INVEGKIAQKILRNIPFSPTKSQESAIKDILQDMSQKNRML----------RILQGDVGSGKT-LVALIAMAAAVEAGG-  322 (700)
Q Consensus       255 ~~~~~~~~~~f~~~LPF~LT~~Q~~ai~eI~~Dl~~~~pM~----------RLLQGDVGSGKT-iVA~~A~l~~~~~G~-  322 (700)
                      .-++..+...+...+|-.....  +++..+..-|....|..          --|-|=.|.||| -+|=+|+..+...|- 
T Consensus       302 ~GfS~~Lar~L~~~lP~~~~~~--~a~~~ll~~La~~Lpv~~~d~~~~gGv~AlvGpTGvGKTTT~aKlAa~~~~~~g~~  379 (557)
T PRK12727        302 YGFDAGLTRDVAMQIPADTELH--RGRGLMLGLLSKRLPVAPVDPLERGGVIALVGPTGAGKTTTIAKLAQRFAAQHAPR  379 (557)
T ss_pred             CCCCHHHHHHHHHHCCCCCCHH--HHHHHHHHHHHHHCCCCCCCHHHCCCEEEEECCCCCCCHHHHHHHHHHHHHHCCCC
T ss_conf             6699999999997483327888--99999999999628777775154076478743777673117999999999973998


Q ss_pred             CEEEEEHH--HHHHHHHHHHHHHHCCCCCCEEEEEECCCCHHHHHHHHHHHCCCCCEEEEECHHHCCCCCCCCCCCEEEE
Q ss_conf             45886127--9999999986211014578658996246422566768776213475486411120133455444417885
Q gi|254780945|r  323 QAVIMAPI--GILAQQHYEFIKKYTQNTQIIVEIITGNMPQAHRRKALERIAHGQAHIIIGTHALFQDSIQYYKLILVIV  400 (700)
Q Consensus       323 Q~alMaPT--EILA~QH~~~~~~~~~~~~i~v~lLtg~~~~~er~~i~~~i~~G~~~iiIGTHAL~q~~v~F~~LgLvVi  400 (700)
                      +|||..=-  -|=|.....++.++   +||.|......   .+=...+..+.+-. -|+|-|--.=|.+...        
T Consensus       380 ~valit~DtyRiga~eQL~~y~~i---lgvpv~~~~~~---~~l~~~l~~l~~~~-lvliDTaG~~~rd~~~--------  444 (557)
T PRK12727        380 DVALVTTDTQRVGGREQLHSYGRQ---LGIAVHEADSA---ESLLDLLERLRDYK-LVLIDTAGMGQRDRAL--------  444 (557)
T ss_pred             EEEEEECCCCCHHHHHHHHHHHHH---HCCEEEEECCH---HHHHHHHHHHCCCC-EEEEECCCCCCCCHHH--------
T ss_conf             189997266408799999999998---39757982899---99999999836999-8999499988469999--------


Q ss_pred             CCCCCCCHHHHHHHHHCCCCCCCEEECHHHHHHHHH--HHHHHCCCHHHHCCCCCCCCCCEEEEEECCCHHHHHHHHHHH
Q ss_conf             210133568899874025677610101013227899--997520101111023557666207999702002689999763
Q gi|254780945|r  401 DEQHRFGVQQRLKLTQKATAPHVLLMTATPIPRTLV--LTSLGDIDISKITEKPAGRKPIKTVIIPINRIDEVIERLKVV  478 (700)
Q Consensus       401 DEQHRFGV~QR~~L~~Kg~~ph~L~MtATPIPRTLa--l~~ygdldvS~i~e~P~gR~~I~T~~~~~~~~~~~~~~i~~~  478 (700)
                             .+|-..|..-..--.+|+|+||-=+++|-  +.-|+-+.++         .-|.|++=.......+++.+   
T Consensus       445 -------~~~~~~l~~~~~~~~~Lvl~a~~~~~~l~~~~~~~~~~~~~---------~~i~TKlDE~~~~G~~l~~~---  505 (557)
T PRK12727        445 -------AAQLNWLRAARQVTSLLVLPANAHFSDLDEVVRRFAHAKPQ---------GVVLTKLDETGRFGSALSVV---  505 (557)
T ss_pred             -------HHHHHHHHCCCCCCEEEEEECCCCHHHHHHHHHHHCCCCCC---------EEEEEECCCCCCCCHHHHHH---
T ss_conf             -------99999875147763599996889989999999985379987---------48996143678703999999---


Q ss_pred             HCCCCEEEEEECCCCCCCCC---CCCHHHHHHHHHHHH
Q ss_conf             10387389997120122111---210146666666866
Q gi|254780945|r  479 LSEGKKAYWICPQIEEKKES---NFRSVVERFNSLHEH  513 (700)
Q Consensus       479 l~~g~q~y~VcPlIeese~~---~~~~~~~~~~~l~~~  513 (700)
                      +..+-.+.||.-==.=-|++   +.+....+.+.|.+.
T Consensus       506 ~~~~lp~~y~t~GQ~VPeDi~~a~~~~Lv~Ra~~L~~~  543 (557)
T PRK12727        506 VDHQMPITWVTDGQRVPDDLHRANAASLVLRLEDLRRA  543 (557)
T ss_pred             HHHCCCEEEECCCCCCCCCHHHCCHHHHHHHHHHHHHH
T ss_conf             99689828975898285236438999999999997641


No 269
>PRK07135 dnaE DNA polymerase III DnaE; Validated
Probab=94.28  E-value=0.53  Score=27.45  Aligned_cols=66  Identities=12%  Similarity=0.164  Sum_probs=47.7

Q ss_pred             HHHHHHCCCC--EECCCCCCCHHHH-HHHHHHHHCCCEEEEEECHHHHCCCCCCCCCEEEEECHHHCCHHHHHHH
Q ss_conf             6668663710--3120146998999-9999997559869999800341046888765899858525474688773
Q gi|254780945|r  508 NSLHEHFTSS--IAIIHGRMSDIDK-ESVMDSFKNGTCKLLIATTVIEVGIDVVDASIIIIENAEHFGLAQLHQL  579 (700)
Q Consensus       508 ~~l~~~~~~~--v~~lHGkm~~~ek-~~~m~~F~~g~~~iLvaTtviEVGvdvpna~~mvI~~aerfGLsqLHQL  579 (700)
                      .+||.+||..  .++|...+...+| ...+.+-++-.+.||      -.-|+-......+-.++=||||+..--+
T Consensus       695 AyLK~~yP~eF~aa~L~~~~~~~~k~~~~i~e~~~~gi~vl------pPdiN~S~~~~~~~~~~I~~gl~~Ikgv  763 (987)
T PRK07135        695 AYYKARYPLYFYSVLISNSNGSQEKIKKYVGEAKNNNFKIY------SPDINFSTENAVFDKGKIFLPLLMIKGL  763 (987)
T ss_pred             HHHHHCCHHHHHHHHHCCCCCCCHHHHHHHHHHHHCCCEEE------CCCCCCCCCCCEEECCEEEEHHHHHCCC
T ss_conf             99985488999999845798986449999999998899897------9984468884465799899804743677


No 270
>KOG3108 consensus
Probab=94.27  E-value=0.39  Score=28.46  Aligned_cols=88  Identities=16%  Similarity=0.270  Sum_probs=53.6

Q ss_pred             EEEEEEEEEEEEEECCCCCCEEEEEEECCCCEEEEEEECCCHHHHH---HHCCCCCEEEEEEEEEECCCEEEEECCEEE-
Q ss_conf             8999999989754215898338999981893699999518878998---732898889999899731877999778689-
Q gi|254780945|r   69 IVTITGYISQHSSFQLQKRRPYKILLNDGTGEITLLFFYRKTEMLK---NVFFEGRKITVTGKIKKLKNRIIMVHPHYI-  144 (700)
Q Consensus        69 ~vti~g~V~~~~~~~~~~r~~~~v~v~D~tg~i~lvfFn~~~~yl~---k~lk~G~~v~vsGKv~~~~~~~qi~hPe~~-  144 (700)
                      .|++.|.|.....-    --.....+.|+||.|.++.|+.. .+..   ..+.+|..|.++|.++.|.|...+..-.+- 
T Consensus        70 ~v~~VGivr~~e~~----~t~i~y~I~D~tg~id~r~W~~~-~~~~~e~~~l~~~~yVkv~G~Lk~f~Gk~sl~~fkI~p  144 (265)
T KOG3108          70 AVSIVGIVRNIEKS----ATNITYEIEDGTGQIDVRQWFHD-NAESEEMPALETGTYVKVYGHLKPFQGKKSLQVFKIRP  144 (265)
T ss_pred             EEEEEEEEEECEEC----CCCEEEEEECCCCEEEEEECCCC-CCHHHHCCCCCCCCEEEEECCCCCCCCCEEEEEEEEEE
T ss_conf             88999999702026----76149998268650788870355-30222174124475799640104889952677876555


Q ss_pred             ECCCCCCCCCCCCCCCC
Q ss_conf             62643344444110000
Q gi|254780945|r  145 FHNSQDVNFPLIEAVYS  161 (700)
Q Consensus       145 ~~~~~~~~~~~I~PIYp  161 (700)
                      +.+.++..+-.++++|.
T Consensus       145 v~D~Nevt~h~LE~i~~  161 (265)
T KOG3108         145 VEDFNEVTTHFLEVINA  161 (265)
T ss_pred             EECCCCEEEEEEHHHHH
T ss_conf             40377225773145789


No 271
>COG0587 DnaE DNA polymerase III, alpha subunit [DNA replication, recombination, and repair]
Probab=94.26  E-value=0.53  Score=27.42  Aligned_cols=129  Identities=17%  Similarity=0.222  Sum_probs=76.0

Q ss_pred             HHHHHHCCCC--EECCCCCCCHHHH-HHHHHHHHCCCEEEEEECHHHHCCCCCCCCCEEEEE-CHHHCCHHHHHHHHHCC
Q ss_conf             6668663710--3120146998999-999999755986999980034104688876589985-85254746887730116
Q gi|254780945|r  508 NSLHEHFTSS--IAIIHGRMSDIDK-ESVMDSFKNGTCKLLIATTVIEVGIDVVDASIIIIE-NAEHFGLAQLHQLRGRV  583 (700)
Q Consensus       508 ~~l~~~~~~~--v~~lHGkm~~~ek-~~~m~~F~~g~~~iLvaTtviEVGvdvpna~~mvI~-~aerfGLsqLHQLRGRV  583 (700)
                      .+||.++|..  .+++.-.|.+.+| ...+.+-++..+.|+      .+-||-......+-. ++=||||.+.-=+.-.+
T Consensus       762 AyLKahYP~eF~aall~s~~~n~~k~~~~i~ear~~Gi~Vl------pPdIN~S~~~f~~~~~~~I~~gL~~IKGvg~~~  835 (1139)
T COG0587         762 AYLKAHYPAEFMAALLTSEPMNFDKVAQYIQEARRMGIEVL------PPDINRSGWDFTVEEKKAIRLGLGAIKGVGEDA  835 (1139)
T ss_pred             HHHHHHCCHHHHHHHHHCCCCCCCCHHHHHHHHHHCCCEEE------CCCCCCCCCCCEECCCCCEEEHHHHHCCCCHHH
T ss_conf             99987177999999974477886269999999998597673------785266677646447872787146556876879


Q ss_pred             ------CC-----CCCCEEEEEEECCCCCHH--------------HHHHHHHHHHHCHHHHHHHHHHHHCCCCCCCCCHH
Q ss_conf             ------67-----898359999708889987--------------99999999841425899999985206300026000
Q gi|254780945|r  584 ------GR-----GEEISSCILLYHPPLSKN--------------SYTRLSVLKNTEDGFLIAEEDLKQRKEGEILGIKQ  638 (700)
Q Consensus       584 ------GR-----g~~~s~c~l~~~~~~~~~--------------~~~Rl~~l~~~~dGf~iAe~Dl~lRG~G~~~G~~Q  638 (700)
                            -|     .+..++|-.+-...++..              ...|-.+|..-.+=+.-++.+.+--|.+++||...
T Consensus       836 i~~Iv~~R~~~~~~~~~df~~r~~~~~l~kr~lE~LikaGAfd~~~~~R~~ll~~~~~~~~~~~~~~~~~~q~~lF~~~~  915 (1139)
T COG0587         836 IEEIVEARKEKPFKSLEDFCDRIDRKGLNKRVLESLIKAGAFDSFGKNRAQLLAALDDLLDAASGTAKNSGQLSLFGAAA  915 (1139)
T ss_pred             HHHHHHHHHCCCCCCHHHHHHHHHHCCCCHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHH
T ss_conf             99999976315777676699875240587888999997486421115799999999999988766576316666621121


Q ss_pred             CCCC
Q ss_conf             6987
Q gi|254780945|r  639 SGMP  642 (700)
Q Consensus       639 sG~~  642 (700)
                      ++..
T Consensus       916 ~~~~  919 (1139)
T COG0587         916 AGES  919 (1139)
T ss_pred             CCCC
T ss_conf             2433


No 272
>PRK07217 replication factor A; Reviewed
Probab=94.26  E-value=0.53  Score=27.41  Aligned_cols=82  Identities=17%  Similarity=0.179  Sum_probs=58.6

Q ss_pred             CCCCCCCHHHC-CCCCEEEEEEEEEEEEEECCCCCCEEEEEEECCCCEEEEEEECCCHHHHHHHCCCCCEEEEEEE-EEE
Q ss_conf             34444647888-9987899999998975421589833899998189369999951887899873289888999989-973
Q gi|254780945|r   54 DRHYRPKISEI-SEERIVTITGYISQHSSFQLQKRRPYKILLNDGTGEITLLFFYRKTEMLKNVFFEGRKITVTGK-IKK  131 (700)
Q Consensus        54 Dr~~~~~I~~l-~~g~~vti~g~V~~~~~~~~~~r~~~~v~v~D~tg~i~lvfFn~~~~yl~k~lk~G~~v~vsGK-v~~  131 (700)
                      .-....+|.++ .+|+++++.++|+..-. +....-.-.-.+.|+||.|+.+-|-.  .-+ ..+..|..|.+.-- +..
T Consensus        67 ~~~~~v~i~DI~~p~qWVtv~aKVVqLwe-p~s~sIaQ~GllgDeTG~IkFt~W~k--sd~-P~leeG~~Y~l~nvvvdE  142 (311)
T PRK07217         67 RGNELVNVADIDEPEQWVDVTAKVVQLWE-PSSESIAQVGLIGDETGTIKFTKWAK--SDL-PDLEEGKSYLLKNVVTDE  142 (311)
T ss_pred             CCCCCEEHHHCCCCCCEEEEEEEEEEECC-CCCCCCEEEEEEECCCCEEEEEEECC--CCC-CCCCCCCEEEEEEEEEEE
T ss_conf             87773002220679954899999999507-89964311220004765078887336--898-644378579997888720


Q ss_pred             CCCEEEEE
Q ss_conf             18779997
Q gi|254780945|r  132 LKNRIIMV  139 (700)
Q Consensus       132 ~~~~~qi~  139 (700)
                      |+|.+++.
T Consensus       143 f~G~~sVk  150 (311)
T PRK07217        143 YQGRFSVK  150 (311)
T ss_pred             CCCEEEEE
T ss_conf             28867788


No 273
>cd00424 Pol_Y Y-family of DNA polymerases. Pol_Y's can transverse replication-blocking DNA lesions, such as cyclobutane pyrimidine dimers resulting from UV damage, at the cost of an elevated error rate. The Y-family has no 3'-5' exonuclease activity. In addition to possessing a topology akin to a right hand, with "thumb", "fingers" and "palm" motifs, like polymerases from the A-, B-, C- and X-families, the Y-family has a unique "little finger" motif. Expression of Y-family polymerases is often induced by DNA damage. These polymerases are phylogenetically unrelated to classical DNA polymerases.
Probab=94.22  E-value=0.037  Score=36.52  Aligned_cols=19  Identities=16%  Similarity=-0.020  Sum_probs=8.2

Q ss_pred             CCCCCHH-HHHHHHHCCCCC
Q ss_conf             0133568-899874025677
Q gi|254780945|r  403 QHRFGVQ-QRLKLTQKATAP  421 (700)
Q Consensus       403 QHRFGV~-QR~~L~~Kg~~p  421 (700)
                      +.+||+. ++..-...|...
T Consensus       210 ~~~~~~~g~~l~~~~~G~d~  229 (341)
T cd00424         210 ASLGGKLGERLWSALRGYDG  229 (341)
T ss_pred             HHHCCHHHHHHHHHHCCCCC
T ss_conf             99768899999999659999


No 274
>PRK06067 flagellar accessory protein FlaH; Validated
Probab=94.10  E-value=0.095  Score=33.31  Aligned_cols=57  Identities=12%  Similarity=0.223  Sum_probs=39.8

Q ss_pred             HHHHHHCCCCC--CEEEEEECCCCCHHHHHHHHHHHHHHHHCCEEEEEHHHHHHHHHHHH
Q ss_conf             99984100134--30788621442236999999733444305458861279999999986
Q gi|254780945|r  283 DILQDMSQKNR--MLRILQGDVGSGKTLVALIAMAAAVEAGGQAVIMAPIGILAQQHYEF  340 (700)
Q Consensus       283 eI~~Dl~~~~p--M~RLLQGDVGSGKTiVA~~A~l~~~~~G~Q~alMaPTEILA~QH~~~  340 (700)
                      +..+-|..+.|  -.-|+.|+-|||||+.|+--++.++.+|..|++.+= |--.+|-.++
T Consensus        20 ~lD~~l~GG~p~g~~~li~G~~G~GKt~~~~~f~~~~~~~g~~~~~~~~-ee~~~~~~~~   78 (241)
T PRK06067         20 EIDRKLGGGIPFGSLILIEGENDTGKSVLSQQFVWGALNQGKRGLAITT-ENTSKSYLKQ   78 (241)
T ss_pred             HHHHHCCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHCCCEEEEEEE-CCCHHHHHHH
T ss_conf             5786506997799089998079988799999999999867982999994-2899999999


No 275
>TIGR00595 priA primosomal protein N'; InterPro: IPR005259    All proteins in this family for which functions are known are components of the primosome which is involved in replication, repair, and recombination.; GO: 0003677 DNA binding, 0006260 DNA replication.
Probab=93.97  E-value=0.26  Score=29.91  Aligned_cols=126  Identities=18%  Similarity=0.216  Sum_probs=84.5

Q ss_pred             CEEE-EEHHHHHHHHHHHHHHHHCCCCCCEEEEEECCCCHHHH--HHHHHHHCCCCCEEEEECHHHCCCCCCCCCCCEEE
Q ss_conf             4588-61279999999986211014578658996246422566--76877621347548641112013345544441788
Q gi|254780945|r  323 QAVI-MAPIGILAQQHYEFIKKYTQNTQIIVEIITGNMPQAHR--RKALERIAHGQAHIIIGTHALFQDSIQYYKLILVI  399 (700)
Q Consensus       323 Q~al-MaPTEILA~QH~~~~~~~~~~~~i~v~lLtg~~~~~er--~~i~~~i~~G~~~iiIGTHAL~q~~v~F~~LgLvV  399 (700)
                      ++.. +.|-.+=.++--+.+.++|+..  ++.-+-..++..+.  ...+.+..+|+++|+|||.-+ .++..|.++-|+.
T Consensus       273 ~~~~~~~~~g~G~~~~~~~l~~~~p~~--~~~~~d~d~~~~~~~~~~~~~~f~~g~~d~l~Gtq~~-~kG~~fp~~~l~g  349 (524)
T TIGR00595       273 GSEDTLKYKGLGTEKVEEELAKLFPGA--RIARLDSDTTSRKGAHEALLNQFANGKADILIGTQMI-AKGHDFPNVTLVG  349 (524)
T ss_pred             CCCCCEEECCCCHHHHHHHHHHHCCCC--CEEEEECCCCCCCHHHHHHHHHHHCCCCEEEECHHHH-HCCCCCCCEEEEE
T ss_conf             664301203542789999999855887--3676412212351468999999750784067500344-3157744203677


Q ss_pred             ECCCC------CCCHHHHH-HHHHC--------CCCCCCEEECHHHHHHHHHHHHHHCCCHHHHCCC
Q ss_conf             52101------33568899-87402--------5677610101013227899997520101111023
Q gi|254780945|r  400 VDEQH------RFGVQQRL-KLTQK--------ATAPHVLLMTATPIPRTLVLTSLGDIDISKITEK  451 (700)
Q Consensus       400 iDEQH------RFGV~QR~-~L~~K--------g~~ph~L~MtATPIPRTLal~~ygdldvS~i~e~  451 (700)
                      |=.--      -|--..|. .|...        ...-++++-|-+|---++..+.++|-+--.-.|+
T Consensus       350 ~~~~d~~l~~~d~r~~e~~~~l~~q~~Gr~gr~~~~g~v~iqt~~P~~~~~~~~~~~~~~~f~~~~~  416 (524)
T TIGR00595       350 VLDADSGLHSPDFRAAERGFQLLTQVAGRAGRAEDPGEVIIQTYNPGHPAIQAALTGDYEAFYEQEL  416 (524)
T ss_pred             EEECCCCCCCCCHHHHHHHHHHHHHHHHHCCCCCCCCEEEEEEECCCHHHHHHHHHCCCHHHHHHHH
T ss_conf             8731200255421346778888887641002346887479973077516889876068167899988


No 276
>PRK09694 hypothetical protein; Provisional
Probab=93.90  E-value=0.53  Score=27.43  Aligned_cols=99  Identities=23%  Similarity=0.386  Sum_probs=67.7

Q ss_pred             HHHHHHHHHHHCCEEEEEHHHHHHHHHHHHHHHHCCCCCCEEEEEECCCCHHHHHHHHHHHC-----CCC---CEEEEEC
Q ss_conf             99973344430545886127999999998621101457865899624642256676877621-----347---5486411
Q gi|254780945|r  311 LIAMAAAVEAGGQAVIMAPIGILAQQHYEFIKKYTQNTQIIVEIITGNMPQAHRRKALERIA-----HGQ---AHIIIGT  382 (700)
Q Consensus       311 ~~A~l~~~~~G~Q~alMaPTEILA~QH~~~~~~~~~~~~i~v~lLtg~~~~~er~~i~~~i~-----~G~---~~iiIGT  382 (700)
                      +..+..++.+|.+|++++=|===|++-|+.++..+.. +..|.|+++.-...+|.++-+.+.     +|+   -.|+|||
T Consensus       551 ~~~l~~~~~~G~~v~vI~NTV~rAq~~y~~L~~~~~~-~~~v~L~HsRF~~~DR~~~E~~vl~~~Gk~~~r~~g~IlVaT  629 (878)
T PRK09694        551 LERMIAAANAGAQVCVICNLVDDAQVCYQRLKELNNT-QVDIDLFHARFTFNDRREKENRVISNFGKNGKRNVGRILVAT  629 (878)
T ss_pred             HHHHHHHHHCCCEEEEEECCHHHHHHHHHHHHHHCCC-CCCEEEEECCCCHHHHHHHHHHHHHHHCCCCCCCCCEEEEEC
T ss_conf             9999999978995999938899999999999985289-987799868887766999999999986889889998699977


Q ss_pred             HHHCCC-CCCCCCCCEEEECC------CCCCCHHHHHH
Q ss_conf             120133-45544441788521------01335688998
Q gi|254780945|r  383 HALFQD-SIQYYKLILVIVDE------QHRFGVQQRLK  413 (700)
Q Consensus       383 HAL~q~-~v~F~~LgLvViDE------QHRFGV~QR~~  413 (700)
                      +.+=|. |+.|.   +.|.|=      =+|+|=-+|..
T Consensus       630 QVvEQSLDiDfD---~liTDLAPiDlLlQR~GRLhRH~  664 (878)
T PRK09694        630 QVVEQSLDLDFD---WLITQHCPADLLFQRMGRLHRHH  664 (878)
T ss_pred             CEEEEEECCCCC---HHHCCCCCHHHHHHHHHHHHCCC
T ss_conf             333243033533---01104686999998742320589


No 277
>PRK08402 replication factor A; Reviewed
Probab=93.81  E-value=0.49  Score=27.74  Aligned_cols=108  Identities=19%  Similarity=0.195  Sum_probs=68.6

Q ss_pred             CCCCCHHHHHHHHHHCCCCCCCCCCHHHHHHHCCCCCCCCCCCCCHHHCCCCC---EEEEEEEEEEEEEEC-CCC-----
Q ss_conf             67858899999887401246885548987870897401344446478889987---899999998975421-589-----
Q gi|254780945|r   16 FRGVGKKYSLFLSKIINCGNANETRFIDLLFYHPSSFIDRHYRPKISEISEER---IVTITGYISQHSSFQ-LQK-----   86 (700)
Q Consensus        16 LkGVGpk~a~~L~kl~~l~~~GI~ti~DLL~~~PrrYeDr~~~~~I~~l~~g~---~vti~g~V~~~~~~~-~~~-----   86 (700)
                      -.|||...|..|-.-    ..||.    |    ...++  .....|+++.+|.   .+.|.|+|++.+..+ |.+     
T Consensus        34 e~gISE~gAalllAe----eLGV~----L----~~~ee--e~~~kIkdI~~Gm~~rnVeivgrIi~ky~~REf~kkDGS~   99 (357)
T PRK08402         34 EDGISEHAAALLLAE----RLGVD----L----IKKEE--QSLMKISDLYPGMDPREVNIVGRILKKYPPREYTKKDGST   99 (357)
T ss_pred             HCCCCHHHHHHHHHH----HHCCC----C----CCCCC--CCCCCHHHHHCCCCCCCCEEEEEEEEECCCHHHHHCCCCC
T ss_conf             628776789999999----85886----5----55566--5640577750766756757999873305805530036987


Q ss_pred             CCEEEEEEECCCCEEEEEEECCCH-HHHHHHCCCCCEEEE-EEEEEEC-CCEEEE
Q ss_conf             833899998189369999951887-899873289888999-9899731-877999
Q gi|254780945|r   87 RRPYKILLNDGTGEITLLFFYRKT-EMLKNVFFEGRKITV-TGKIKKL-KNRIIM  138 (700)
Q Consensus        87 r~~~~v~v~D~tg~i~lvfFn~~~-~yl~k~lk~G~~v~v-sGKv~~~-~~~~qi  138 (700)
                      ++...+++.|+||++.++.|-..- .|. +.+.+|+-+.+ -+.|+.. +|..++
T Consensus       100 GkVASL~I~DeTG~aRLvLWD~~v~~yy-~~l~~GDVIKv~~~~Vres~~g~peL  153 (357)
T PRK08402        100 GRVASLIIYDDTGRARVVLWDAKVAEYY-NKLEVGDVIKVLDAQVRESLSGLPEL  153 (357)
T ss_pred             CEEEEEEEECCCCCEEEEEECHHHHHHH-HHCCCCCEEEEECHHHHHHCCCCHHE
T ss_conf             5378999973788389998338789889-75376866998331344311797120


No 278
>TIGR03117 cas_csf4 CRISPR-associated DEAD/DEAH-box helicase Csf4. Members of this family show up near CRISPR repeats in Acidithiobacillus ferrooxidans ATCC 23270, Azoarcus sp. EbN1, and Rhodoferax ferrireducens DSM 15236. In the latter two species, the CRISPR/cas locus is found on a plasmid. This family is one of several characteristic of a type of CRISPR-associated (cas) gene cluster we designate Aferr after A. ferrooxidans, where it is both chromosomal and the only type of cas gene cluster found. The gene is designated csf4 (CRISPR/cas Subtype as in A. ferrooxidans protein 1), as it lies farthest (fourth closest) from the repeats in the A. ferrooxidans genome.
Probab=93.72  E-value=0.66  Score=26.68  Aligned_cols=80  Identities=21%  Similarity=0.292  Sum_probs=56.9

Q ss_pred             HHHHHHHHHHHHCCCCCCEEEEEECCCCCHHHHHHHHHHHHHH--HHCCEEEEEHHHHHHHHHHHHHHHHCC---CCCCE
Q ss_conf             9999999998410013430788621442236999999733444--305458861279999999986211014---57865
Q gi|254780945|r  277 QESAIKDILQDMSQKNRMLRILQGDVGSGKTLVALIAMAAAVE--AGGQAVIMAPIGILAQQHYEFIKKYTQ---NTQII  351 (700)
Q Consensus       277 Q~~ai~eI~~Dl~~~~pM~RLLQGDVGSGKTiVA~~A~l~~~~--~G~Q~alMaPTEILA~QH~~~~~~~~~---~~~i~  351 (700)
                      |.+..=-|..-+......  |+|.-+|.|||.-+++.++..+.  +|.++++=.+|--|=+|-++....++.   +.+++
T Consensus         2 ~~~~~~~~~~a~~~~~v~--lVEAGTGTGKSLAYLvPAl~~a~~~~g~rVVISTaT~aLQeQL~~kd~pl~~~~l~~~~~   79 (636)
T TIGR03117         2 QALFYLNCLTSLRQKRIG--MLEASTGVGKTLAMIMAALTMLKERPDQKIAIAVPTLALMGQLWSELERLTAEGLAGPVQ   79 (636)
T ss_pred             CHHHHHHHHHHHHCCCEE--EEECCCCCCHHHHHHHHHHHHHHHCCCCCEEEECCCHHHHHHHHHHHHHHHHHHCCCCCE
T ss_conf             005999899986038489--998999710889999999999985799988997987999999976656599997599962


Q ss_pred             EEEEECC
Q ss_conf             8996246
Q gi|254780945|r  352 VEIITGN  358 (700)
Q Consensus       352 v~lLtg~  358 (700)
                      +++|-|.
T Consensus        80 ~allKGR   86 (636)
T TIGR03117        80 AGFFPGS   86 (636)
T ss_pred             EEEEECH
T ss_conf             8998772


No 279
>smart00487 DEXDc DEAD-like helicases superfamily.
Probab=93.62  E-value=0.69  Score=26.56  Aligned_cols=115  Identities=17%  Similarity=0.232  Sum_probs=77.9

Q ss_pred             HHHHHHCC--CCEEEEEECCCCCCCCCCCCHHHHHHHHHHHHCCC----CEECCCCCCCHHHHHHHHHHHHCCCEEEEEE
Q ss_conf             99763103--87389997120122111210146666666866371----0312014699899999999975598699998
Q gi|254780945|r  474 RLKVVLSE--GKKAYWICPQIEEKKESNFRSVVERFNSLHEHFTS----SIAIIHGRMSDIDKESVMDSFKNGTCKLLIA  547 (700)
Q Consensus       474 ~i~~~l~~--g~q~y~VcPlIeese~~~~~~~~~~~~~l~~~~~~----~v~~lHGkm~~~ek~~~m~~F~~g~~~iLva  547 (700)
                      .+.+.+.+  +.++.++||..+        -+.+.++.+.+.++.    .+...+|.-.    ....+++.++..+|+|+
T Consensus        44 ~~~~~~~~~~~~~~li~~P~~~--------l~~q~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~~~~~~~i~i~  111 (201)
T smart00487       44 PALEALKRGKGKRVLVLVPTRE--------LAEQWAEELKKLGPSLGLKVVGLYGGDSK----REQLRKLESGKTDILVT  111 (201)
T ss_pred             HHHHHHHCCCCCEEEEEECCHH--------HHHHHHHHHHHCCCCCEEEEEEEECCCCH----HHHHHHHHCCCCCEEEE
T ss_conf             9999863389975999908599--------99999988601021020445565247737----99999997599989995


Q ss_pred             C-----HHHHCC-CCCCCCCEEEEECHHHCCH-HHHHHHHHCCCCCCCCEEEEEEECCCC
Q ss_conf             0-----034104-6888765899858525474-688773011667898359999708889
Q gi|254780945|r  548 T-----TVIEVG-IDVVDASIIIIENAEHFGL-AQLHQLRGRVGRGEEISSCILLYHPPL  600 (700)
Q Consensus       548 T-----tviEVG-vdvpna~~mvI~~aerfGL-sqLHQLRGRVGRg~~~s~c~l~~~~~~  600 (700)
                      |     ..+.-+ .+..+-+++||..|+++.- .....++.-..+-......++++..+.
T Consensus       112 t~~~l~~~~~~~~~~~~~~~~vIiDE~H~~~~~~~~~~~~~~~~~~~~~~~~i~lSAT~~  171 (201)
T smart00487      112 TPGRLLDLLENDLLELSNVDLVILDEAHRLLDGGFGDQLEKLLKLLPKNVQLLLLSATPP  171 (201)
T ss_pred             CHHHHHHHHHHCCCCCCCCEEEEEECHHHHHCCCCHHHHHHHHHHCCCCCCEEEECCCCC
T ss_conf             589999999727545254319999896775125709999999996799997899924898


No 280
>PRK06386 replication factor A; Reviewed
Probab=93.31  E-value=0.76  Score=26.19  Aligned_cols=77  Identities=17%  Similarity=0.177  Sum_probs=57.1

Q ss_pred             CCCHHHCCC-CCEEEEEEEEEEEEEE--CCCCC--CEEEEEEECCCCEEEEEEECCCHHHHHHHCCCCCEEEEEEE-EEE
Q ss_conf             464788899-8789999999897542--15898--33899998189369999951887899873289888999989-973
Q gi|254780945|r   58 RPKISEISE-ERIVTITGYISQHSSF--QLQKR--RPYKILLNDGTGEITLLFFYRKTEMLKNVFFEGRKITVTGK-IKK  131 (700)
Q Consensus        58 ~~~I~~l~~-g~~vti~g~V~~~~~~--~~~~r--~~~~v~v~D~tg~i~lvfFn~~~~yl~k~lk~G~~v~vsGK-v~~  131 (700)
                      +++|+++.+ ++.+++.++|++....  ++.+.  ..+.-.+.|+||.|...+|.+  +   -.+++|+.+.+.+- ++.
T Consensus         2 ~~ki~di~~~~~~v~~k~kVLs~~kr~I~~~~~~~~i~~G~LaDeTG~I~ftsWe~--~---~~~e~GD~v~I~NA~vr~   76 (358)
T PRK06386          2 LSKISDINAARQNVDLKVKVLSLNKRTIKNDRGETIYYYGIIGDETGTVPFTAWEF--P---DAVKSGDVIEIKYCYSKE   76 (358)
T ss_pred             CCCHHHCCCCCCCEEEEEEEEEECCEEEECCCCCEEEEEEEEECCCCEEEEEEECC--C---CCCCCCCEEEECCCEEEE
T ss_conf             53153217677835899999982335663489955999999826876054787338--7---888987889985418856


Q ss_pred             CCCEEEEE
Q ss_conf             18779997
Q gi|254780945|r  132 LKNRIIMV  139 (700)
Q Consensus       132 ~~~~~qi~  139 (700)
                      |++.+++.
T Consensus        77 ~~g~peln   84 (358)
T PRK06386         77 YNGKIRIY   84 (358)
T ss_pred             ECCCEEEE
T ss_conf             48928898


No 281
>PRK00484 lysS lysyl-tRNA synthetase; Reviewed
Probab=93.30  E-value=0.77  Score=26.18  Aligned_cols=97  Identities=18%  Similarity=0.209  Sum_probs=60.1

Q ss_pred             HHCCCCCCCCCCCCCHH---------HCCCCCEEEEEEEEEEEEEECCCCCCEEEEEEECCCCEEEEEEECCC-----HH
Q ss_conf             70897401344446478---------88998789999999897542158983389999818936999995188-----78
Q gi|254780945|r   46 FYHPSSFIDRHYRPKIS---------EISEERIVTITGYISQHSSFQLQKRRPYKILLNDGTGEITLLFFYRK-----TE  111 (700)
Q Consensus        46 ~~~PrrYeDr~~~~~I~---------~l~~g~~vti~g~V~~~~~~~~~~r~~~~v~v~D~tg~i~lvfFn~~-----~~  111 (700)
                      .=||.++..-..+..+.         +...+..|++.|.|.+.+.   .+ +..=+.+.|.+|.|++++-...     ..
T Consensus        23 ~pyp~~~~~~~~~~~~~~~~~~~~~~~~~~~~~V~vaGrv~~~R~---~G-k~~F~~lrD~~g~iQ~~~~~~~~~~~~~~   98 (491)
T PRK00484         23 NPYPNDFERTHTSAELQAKYADLEKEELEALIEVSVAGRVMLKRV---MG-KASFATIQDGSGRIQLYVSKDDVGEEAYE   98 (491)
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHCCCCCCCCCCEEEEEEEEEEEEC---CC-CEEEEEEEECCCCEEEEEECCCCCHHHHH
T ss_conf             999997858666999999875138533467988999987840505---69-81999999699458999966758999999


Q ss_pred             HHHHHCCCCCEEEEEEEEEEC-CCEEEEECCEEEECC
Q ss_conf             998732898889999899731-877999778689626
Q gi|254780945|r  112 MLKNVFFEGRKITVTGKIKKL-KNRIIMVHPHYIFHN  147 (700)
Q Consensus       112 yl~k~lk~G~~v~vsGKv~~~-~~~~qi~hPe~~~~~  147 (700)
                      .+ +.+..|+.+.|.|++... .|.+++.--++.+.+
T Consensus        99 ~~-~~l~~gd~i~v~G~v~~t~~Gel~v~~~~~~iLs  134 (491)
T PRK00484         99 AF-KKLDLGDIIGVEGTLFKTKTGELSVKVTELTLLT  134 (491)
T ss_pred             HH-HCCCCCCEEEEEEEEEECCCCEEEEECCEEEEEC
T ss_conf             99-6068666898787998658851664033179931


No 282
>COG5271 MDN1 AAA ATPase containing von Willebrand factor type A (vWA) domain [General function prediction only]
Probab=93.17  E-value=0.7  Score=26.50  Aligned_cols=37  Identities=30%  Similarity=0.460  Sum_probs=30.2

Q ss_pred             CCCCHHHHHHHHHHHHHHCCCCCCEEEEEECCCCCHHHH
Q ss_conf             467988999999999841001343078862144223699
Q gi|254780945|r  271 FSPTKSQESAIKDILQDMSQKNRMLRILQGDVGSGKTLV  309 (700)
Q Consensus       271 F~LT~~Q~~ai~eI~~Dl~~~~pM~RLLQGDVGSGKTiV  309 (700)
                      |-+-.+|..+++-+..-...+-|.  .|-||.|+|||..
T Consensus      1830 ~~~l~sql~vlEsV~~cIn~nwPl--IlvG~t~~GKt~~ 1866 (4600)
T COG5271        1830 FVLLHSQLQVLESVMRCINMNWPL--ILVGDTGVGKTSL 1866 (4600)
T ss_pred             HHHHHHHHHHHHHHHHHHHCCCCE--EEECCCCCCHHHH
T ss_conf             123554148999999998538977--9976888766899


No 283
>PRK04328 hypothetical protein; Provisional
Probab=93.16  E-value=0.19  Score=30.88  Aligned_cols=54  Identities=15%  Similarity=0.147  Sum_probs=39.6

Q ss_pred             CCCCCCEE--EEEECCCCCHHHHHHHHHHHHHHHHCCEEEEEHHHHHHHHHHHHHHH
Q ss_conf             00134307--88621442236999999733444305458861279999999986211
Q gi|254780945|r  289 SQKNRMLR--ILQGDVGSGKTLVALIAMAAAVEAGGQAVIMAPIGILAQQHYEFIKK  343 (700)
Q Consensus       289 ~~~~pM~R--LLQGDVGSGKTiVA~~A~l~~~~~G~Q~alMaPTEILA~QH~~~~~~  343 (700)
                      ..+.|...  |+.|+-|||||+-|+--++..+.+|..|.+.+= |=-.+|..+++..
T Consensus        18 ~GGlp~gs~~Lv~G~pGtGKT~la~qFl~~g~~~GE~~lyis~-eE~~~~l~~~~~~   73 (250)
T PRK04328         18 YGGIPERNVVLLSGGPGTGKSIFSQQFLWNGLQMGEPGIYVAL-EEHPVQVRRNMAQ   73 (250)
T ss_pred             CCCCCCCEEEEEEECCCCCHHHHHHHHHHHHHHCCCCEEEEEE-ECCHHHHHHHHHH
T ss_conf             5998799699998289999899999999999876997799997-2799999999998


No 284
>pfam00270 DEAD DEAD/DEAH box helicase. Members of this family include the DEAD and DEAH box helicases. Helicases are involved in unwinding nucleic acids. The DEAD box helicases are involved in various aspects of RNA metabolism, including nuclear transcription, pre mRNA splicing, ribosome biogenesis, nucleocytoplasmic transport, translation, RNA decay and organellar gene expression.
Probab=93.14  E-value=0.45  Score=27.98  Aligned_cols=80  Identities=16%  Similarity=0.250  Sum_probs=56.6

Q ss_pred             CCCEEEEEECCCCCCCCCCCCHHHHHHHHHHHHCC---CCEECCCCCCCHHHHHHHHHHHHCCCEEEEEECHHH-----H
Q ss_conf             38738999712012211121014666666686637---103120146998999999999755986999980034-----1
Q gi|254780945|r  481 EGKKAYWICPQIEEKKESNFRSVVERFNSLHEHFT---SSIAIIHGRMSDIDKESVMDSFKNGTCKLLIATTVI-----E  552 (700)
Q Consensus       481 ~g~q~y~VcPlIeese~~~~~~~~~~~~~l~~~~~---~~v~~lHGkm~~~ek~~~m~~F~~g~~~iLvaTtvi-----E  552 (700)
                      .|.++.+++|..+        -+.+.++.+++.+.   -+++.++|-.+..+....+.    +..+|+|+|.-.     .
T Consensus        44 ~~~~~v~l~Pt~a--------L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~----~~~~Ilv~Tp~~l~~~l~  111 (167)
T pfam00270        44 DGPQALVLAPTRE--------LAEQIYEELKKLGKYLGLKVALLYGGDSPKEQLRKLK----KGPDILVGTPGRLLDLLE  111 (167)
T ss_pred             CCCEEEEECCHHH--------HHHHHHHHHHHHHHCCCCCEEEECCCCCHHHHHHHHC----CCCCEEEECHHHHHHHHH
T ss_conf             8987999906088--------8889998864321026764046417861788987640----577079947899999998


Q ss_pred             -CCCCCCCCCEEEEECHHHCC
Q ss_conf             -04688876589985852547
Q gi|254780945|r  553 -VGIDVVDASIIIIENAEHFG  572 (700)
Q Consensus       553 -VGvdvpna~~mvI~~aerfG  572 (700)
                       -.++..+..++|+..|++++
T Consensus       112 ~~~~~~~~~~~lIvDE~H~~~  132 (167)
T pfam00270       112 RGGLLLKNLKLLVLDEAHRLL  132 (167)
T ss_pred             HCCCCCCCEEEEEEECHHHHH
T ss_conf             033121100389988088673


No 285
>PRK05159 aspC aspartyl-tRNA synthetase; Provisional
Probab=93.05  E-value=0.83  Score=25.91  Aligned_cols=86  Identities=21%  Similarity=0.272  Sum_probs=57.7

Q ss_pred             CCCCHHHCCCCCEEEEEEEEEEEEEECCCCCCEEEEEEECCCCEEEEEEECCC-----HHHHHHHCCCCCEEEEEEEEEE
Q ss_conf             44647888998789999999897542158983389999818936999995188-----7899873289888999989973
Q gi|254780945|r   57 YRPKISEISEERIVTITGYISQHSSFQLQKRRPYKILLNDGTGEITLLFFYRK-----TEMLKNVFFEGRKITVTGKIKK  131 (700)
Q Consensus        57 ~~~~I~~l~~g~~vti~g~V~~~~~~~~~~r~~~~v~v~D~tg~i~lvfFn~~-----~~yl~k~lk~G~~v~vsGKv~~  131 (700)
                      .+..|++--.|+.|++.|.|.+.+.   .++ ..=+.+.|++|.+++++=...     ..++ +.+..|+.+.|.|+|..
T Consensus         6 ~~~dl~~~~~g~~V~v~G~v~~~R~---~Gk-l~Fi~LrD~~g~iQ~~~~~~~~~~~~~~~~-~~l~~g~~v~v~G~v~~   80 (434)
T PRK05159          6 YTSEVTPELDGKEVTLAGWVHEIRD---LGG-IKFLLLRDRTGIIQVVVPKKKVDEELFEGI-KKLSRESVVSVTGVVKE   80 (434)
T ss_pred             CCCCCCHHHCCCEEEEEEEEEEEEC---CCC-CEEEEEEECCCCEEEEEECCCCCHHHHHHH-HCCCCCEEEEEEEEEEC
T ss_conf             3154994779999999898872881---798-599999969802899997998998999998-57999629999999985


Q ss_pred             CC---CEEEEECCEEEECC
Q ss_conf             18---77999778689626
Q gi|254780945|r  132 LK---NRIIMVHPHYIFHN  147 (700)
Q Consensus       132 ~~---~~~qi~hPe~~~~~  147 (700)
                      ..   +.+++.-.++.+.+
T Consensus        81 ~~~~~~~~ev~~~~i~ils   99 (434)
T PRK05159         81 SEKAPNGVEVQPEEIEVLN   99 (434)
T ss_pred             CCCCCCCEEEEEEEEEEEE
T ss_conf             8999975899998999983


No 286
>COG1444 Predicted P-loop ATPase fused to an acetyltransferase [General function prediction only]
Probab=93.02  E-value=0.6  Score=27.01  Aligned_cols=272  Identities=20%  Similarity=0.181  Sum_probs=139.6

Q ss_pred             CCCHHHHHHHHHHHHHHCCCCCCEEEEEECCCCCHHHHHHHHHHHHHHHHC--CEEEEEHHHHHHHHHHHHHHHHCCCCC
Q ss_conf             679889999999998410013430788621442236999999733444305--458861279999999986211014578
Q gi|254780945|r  272 SPTKSQESAIKDILQDMSQKNRMLRILQGDVGSGKTLVALIAMAAAVEAGG--QAVIMAPIGILAQQHYEFIKKYTQNTQ  349 (700)
Q Consensus       272 ~LT~~Q~~ai~eI~~Dl~~~~pM~RLLQGDVGSGKTiVA~~A~l~~~~~G~--Q~alMaPTEILA~QH~~~~~~~~~~~~  349 (700)
                      .+|.+|.++++.+..=+..+..| -.|-.|=|=||+.++-+|++.+..-+.  .+.+-|||--=.+.-|+...+-|+.+|
T Consensus       211 ~~T~dQ~~~l~~~~~l~~~~~~~-~vlTAdRGRGKSA~lGi~~~~~~~~~~~~~iiVTAP~~~nv~~Lf~fa~~~l~~lg  289 (758)
T COG1444         211 CLTEDQAEALEILERLLDAPKRA-LVLTADRGRGKSAALGIALAAAARLAGSVRIIVTAPTPANVQTLFEFAGKGLEFLG  289 (758)
T ss_pred             HCCHHHHHHHHHHHHHHCCCCCE-EEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHHHHHHHHC
T ss_conf             03751899999999997089835-99986778747688749999999733772089967977889999999987699827


Q ss_pred             CEEEEEECCCCHHHHHHHHHHHCCCC--CEEEEECHHHCCCCCCCCCCCEEEECCCCCCCHHHHHHHHHCCCCCCCEEEC
Q ss_conf             65899624642256676877621347--5486411120133455444417885210133568899874025677610101
Q gi|254780945|r  350 IIVEIITGNMPQAHRRKALERIAHGQ--AHIIIGTHALFQDSIQYYKLILVIVDEQHRFGVQQRLKLTQKATAPHVLLMT  427 (700)
Q Consensus       350 i~v~lLtg~~~~~er~~i~~~i~~G~--~~iiIGTHAL~q~~v~F~~LgLvViDEQHRFGV~QR~~L~~Kg~~ph~L~Mt  427 (700)
                      .+-..-..+.-     . ........  |..+.=.-|.  +.     =-|+||||--=-+|.==.+|...   -+-++||
T Consensus       290 ~~~~v~~~~~g-----~-~~~~~~~~~~i~y~~P~~a~--~~-----~DllvVDEAAaIplplL~~l~~~---~~rv~~s  353 (758)
T COG1444         290 YKRKVAPDALG-----E-IREVSGDGFRIEYVPPDDAQ--EE-----ADLLVVDEAAAIPLPLLHKLLRR---FPRVLFS  353 (758)
T ss_pred             CCCCCCCCCCC-----C-EEEECCCCEEEEEECCHHHC--CC-----CCEEEEEHHHCCCHHHHHHHHHH---CCCEEEE
T ss_conf             74555634424-----4-00004774257751750012--56-----88899810312886999999864---4816999


Q ss_pred             HHH-----HHHHHHHHHHHCCCHHHHCCCCCCCCC-CEEE-------EEECCCHHHHHHHHHHHHCC-------------
Q ss_conf             013-----227899997520101111023557666-2079-------99702002689999763103-------------
Q gi|254780945|r  428 ATP-----IPRTLVLTSLGDIDISKITEKPAGRKP-IKTV-------IIPINRIDEVIERLKVVLSE-------------  481 (700)
Q Consensus       428 ATP-----IPRTLal~~ygdldvS~i~e~P~gR~~-I~T~-------~~~~~~~~~~~~~i~~~l~~-------------  481 (700)
                      .|=     ==|..        .+-.++.++.-|.- ++-.       +-..+-+++   ++-+.+-=             
T Consensus       354 TTIhGYEGtGRgF--------~lkf~~~l~~~~~~~~~~~~l~ePIRya~gDPiE~---wl~d~LLLdAEp~~~~~~~~~  422 (758)
T COG1444         354 TTIHGYEGTGRGF--------SLKFLARLRKQRDTTLHELELEEPIRYAPGDPIEK---WLYDALLLDAEPAELEPEDLR  422 (758)
T ss_pred             EEECCCCCCCHHH--------HHHHHHHHCCCCCCEEEEEECCCCCCCCCCCCHHH---HHHHHHCCCCCCCCCCCCCCC
T ss_conf             7402446677179--------99999984315653279985468731689996799---998866117876667754345


Q ss_pred             CCEEEEEECCCCCCCCCCCCHHHHHHHHHHHHCCCCEECCCCCCCHHHHHHHHHHHHCCCEEEEEECHHHHCCCCCCCCC
Q ss_conf             87389997120122111210146666666866371031201469989999999997559869999800341046888765
Q gi|254780945|r  482 GKKAYWICPQIEEKKESNFRSVVERFNSLHEHFTSSIAIIHGRMSDIDKESVMDSFKNGTCKLLIATTVIEVGIDVVDAS  561 (700)
Q Consensus       482 g~q~y~VcPlIeese~~~~~~~~~~~~~l~~~~~~~v~~lHGkm~~~ek~~~m~~F~~g~~~iLvaTtviEVGvdvpna~  561 (700)
                      +.++|.-+.      .   ...-.--+.|++.|+- ...-|=|-++.+-.. |.+--..++-+|.+-.      .+|-|.
T Consensus       423 ~~~~~~~~~------~---~~~~~~ee~Lr~~~gl-lV~AHYRnsP~DL~~-L~DaP~h~~~al~~~~------~~~va~  485 (758)
T COG1444         423 GSLEILEVD------Q---RDLLFDEELLRQVYGL-LVSAHYRNSPNDLRR-LLDAPHHHIFALRAPE------GKPVAV  485 (758)
T ss_pred             CCEEEEECC------H---HHHHHCHHHHHHHHHH-HHHHHCCCCHHHHHH-HHCCCCCEEEEEECCC------CCEEEE
T ss_conf             660255236------6---7664298999999877-753334588778998-7218877168887599------956899


Q ss_pred             EEEEECHHH-CCHHHHHHHHHCCCCCCCC
Q ss_conf             899858525-4746887730116678983
Q gi|254780945|r  562 IIIIENAEH-FGLAQLHQLRGRVGRGEEI  589 (700)
Q Consensus       562 ~mvI~~aer-fGLsqLHQLRGRVGRg~~~  589 (700)
                      +-|.+...- =-+.+ -.+|||.-||+.-
T Consensus       486 ~qva~EG~l~~~~i~-~~~~g~r~~GnlI  513 (758)
T COG1444         486 WQVAEEGGLSDELID-IWLGGRRPRGNLI  513 (758)
T ss_pred             EEEECCCCCCHHHHH-HHHCCCCCCCCCC
T ss_conf             986003787288999-9956878887626


No 287
>pfam03354 Terminase_1 Phage Terminase. The majority of the members of this family are bacteriophage proteins, several of which are thought to be terminase large subunit proteins. There are also a number of bacterial proteins of unknown function.
Probab=92.91  E-value=0.27  Score=29.75  Aligned_cols=140  Identities=13%  Similarity=0.144  Sum_probs=70.5

Q ss_pred             EEEECCCCCHHHH-HHHHHHHHH---HHHCCEEEEEHHHHHHHHHHHHHHHHCCCCCCEEEEEECCCCHHHHHHHHHHHC
Q ss_conf             8862144223699-999973344---430545886127999999998621101457865899624642256676877621
Q gi|254780945|r  297 ILQGDVGSGKTLV-ALIAMAAAV---EAGGQAVIMAPIGILAQQHYEFIKKYTQNTQIIVEIITGNMPQAHRRKALERIA  372 (700)
Q Consensus       297 LLQGDVGSGKTiV-A~~A~l~~~---~~G~Q~alMaPTEILA~QH~~~~~~~~~~~~i~v~lLtg~~~~~er~~i~~~i~  372 (700)
                      +|.===|.|||.. |+++.+..+   +.|.|+...|+|+=-|..-|+..+.++...+.--.-.-.......+..+.....
T Consensus        26 ~i~v~RkNGKS~l~a~i~ly~~~~~ge~~~ei~~~A~~~~QA~~~f~~~~~mi~~~p~l~~~~~~~~~~~~~~~i~~~~t  105 (473)
T pfam03354        26 YVSVGRKNGKSYLMAIRVLYELLLGGKSNQEILVAATTFKQAEKLFKYVKNQVKLSPFLSIANENKLLKSQKDGIEMKIN  105 (473)
T ss_pred             EEEEECCCCHHHHHHHHHHHHHHHCCCCCCEEEEEECCHHHHHHHHHHHHHHHHCCHHHHHHHHCCCCCCCCEEEEECCC
T ss_conf             99982686026999999999997099838749999798999999999999999739877755301101310015898078


Q ss_pred             CCCCEEEEECHHHCCCCCCCCCCCEEEECCCCCCCHHHH-HHHHH-CCC--CCCC-EEECHHHHHHHHHHHHH
Q ss_conf             347548641112013345544441788521013356889-98740-256--7761-01010132278999975
Q gi|254780945|r  373 HGQAHIIIGTHALFQDSIQYYKLILVIVDEQHRFGVQQR-LKLTQ-KAT--APHV-LLMTATPIPRTLVLTSL  440 (700)
Q Consensus       373 ~G~~~iiIGTHAL~q~~v~F~~LgLvViDEQHRFGV~QR-~~L~~-Kg~--~ph~-L~MtATPIPRTLal~~y  440 (700)
                      .+.+..+-.-    .+...=.|-.++|+||-|-+.-..= ..|.+ -|.  +|=+ ..-||.|.+-+..-..|
T Consensus       106 ~s~~~~ls~~----~~~~dG~~~~~~i~DE~h~~~~~~~~~~l~sg~~~r~~~l~~~ITTag~~~~~~~~~~~  174 (473)
T pfam03354       106 NNVFKALSNN----GDQYDGGNPSLAIFDEMHEFKDRELVSTIVTGMRKQDNPQTIQITTAGPNRGGPYDEER  174 (473)
T ss_pred             CCEEEEEECC----CCCCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHCCCCCEEEEECCCCCCCCCHHHHHH
T ss_conf             9689998578----98766998728998722304882789999876316888719997677889887189999


No 288
>TIGR02928 TIGR02928 orc1/cdc6 family replication initiation protein; InterPro: IPR014277   This set of DNA binding proteins shows homology to the origin recognition complex subunit 1/cell division control protein 6 family in eukaryotes. The proteins in this entry are found exclusively in the archaea. Several members may be found in a genome and interact with each other..
Probab=92.90  E-value=0.2  Score=30.68  Aligned_cols=143  Identities=18%  Similarity=0.238  Sum_probs=73.8

Q ss_pred             HHHHHHHHHHHHHH-C-CCCCCEEEEEECCCCCHHHHHHHHHHHHHHHHCC-----EE--EEEHHHHHHHHHHHHHHHHC
Q ss_conf             88999999999841-0-0134307886214422369999997334443054-----58--86127999999998621101
Q gi|254780945|r  275 KSQESAIKDILQDM-S-QKNRMLRILQGDVGSGKTLVALIAMAAAVEAGGQ-----AV--IMAPIGILAQQHYEFIKKYT  345 (700)
Q Consensus       275 ~~Q~~ai~eI~~Dl-~-~~~pM~RLLQGDVGSGKTiVA~~A~l~~~~~G~Q-----~a--lMaPTEILA~QH~~~~~~~~  345 (700)
                      ++|...+..++..+ . ...|-|-+|-|-.|+|||.|+-..|=..-+....     +.  ..=+ +.+-. +|..+.++.
T Consensus        23 deqI~~l~~~L~~~l~PG~~P~Ni~iYGkTGtGKT~vt~~v~~~l~~~~~~~d~~D~~~~~~NC-~~~~T-~y~~~~~L~  100 (383)
T TIGR02928        23 DEQIEELAKALRPILRPGSRPSNIFIYGKTGTGKTAVTKYVMKELEEAAEDRDVRDVSTVYINC-QILDT-SYQVLVELA  100 (383)
T ss_pred             HHHHHHHHHHHHHHHCCCCCCCCEEEECCCCCCHHHHHHHHHHHHHHHHHCCCCCCEEEEEECC-CCCCC-HHHHHHHHH
T ss_conf             7899999999887506748987258878889878899999999999986226997158999778-54684-699999999


Q ss_pred             CCC---CCEEEEEECCCCHHHH-HHHHHHHCCCCCEEEEECHHHCCCCCCCCCCCEEEECCCCCCCHHHHHHHHHCCCCC
Q ss_conf             457---8658996246422566-768776213475486411120133455444417885210133568899874025677
Q gi|254780945|r  346 QNT---QIIVEIITGNMPQAHR-RKALERIAHGQAHIIIGTHALFQDSIQYYKLILVIVDEQHRFGVQQRLKLTQKATAP  421 (700)
Q Consensus       346 ~~~---~i~v~lLtg~~~~~er-~~i~~~i~~G~~~iiIGTHAL~q~~v~F~~LgLvViDEQHRFGV~QR~~L~~Kg~~p  421 (700)
                      ..+   +.....-+-+.|.++. +.+|+.|.-                 .+..-=+||.||=        ..|. ++..=
T Consensus       101 ~~ln~~~~~~~vP~tG~s~~~~~~~l~~~l~~-----------------~~~~~~~ivLDEi--------D~Lv-~~~~d  154 (383)
T TIGR02928       101 NQLNRRGSGEEVPTTGLSTSEVFRELYKELNR-----------------ERGDSLIIVLDEI--------DKLV-RKDDD  154 (383)
T ss_pred             HHHCCCCCCCCCCCCCCCHHHHHHHHHHHHHH-----------------HCCCEEEEEECCC--------CHHH-CCCCC
T ss_conf             98515778888988778789999999999832-----------------0188799986231--------0221-58888


Q ss_pred             C----CEEECHHHHHHHHHHHHHHCCCHHHH
Q ss_conf             6----10101013227899997520101111
Q gi|254780945|r  422 H----VLLMTATPIPRTLVLTSLGDIDISKI  448 (700)
Q Consensus       422 h----~L~MtATPIPRTLal~~ygdldvS~i  448 (700)
                      +    -+.|+   +||+=+..-..+-.||+|
T Consensus       155 ~PAyS~~LY~---L~Ra~~~~~~~~~~vgvI  182 (383)
T TIGR02928       155 DPAYSKLLYQ---LSRARENGDLENAKVGVI  182 (383)
T ss_pred             CHHHHHHHHH---HHHHHHCCCCCCCCEEEE
T ss_conf             8078788534---331000357788534899


No 289
>PRK11057 ATP-dependent DNA helicase RecQ; Provisional
Probab=92.88  E-value=0.87  Score=25.74  Aligned_cols=76  Identities=14%  Similarity=0.198  Sum_probs=63.3

Q ss_pred             HHHCCEEEEEHHHHHHHHHHHHHHHHCCCCCCEEEEEECCCCHHHHHHHHHHHCCCCCEEEEECHHHCCCCCCCCCCCEE
Q ss_conf             43054588612799999999862110145786589962464225667687762134754864111201334554444178
Q gi|254780945|r  319 EAGGQAVIMAPIGILAQQHYEFIKKYTQNTQIIVEIITGNMPQAHRRKALERIAHGQAHIIIGTHALFQDSIQYYKLILV  398 (700)
Q Consensus       319 ~~G~Q~alMaPTEILA~QH~~~~~~~~~~~~i~v~lLtg~~~~~er~~i~~~i~~G~~~iiIGTHAL~q~~v~F~~LgLv  398 (700)
                      ..|..+.+-++|-=-+++.++.++    ..|+++...+|+++.++|..+.+...+|+++|+|.|-| |-=++.-.|..+|
T Consensus       234 ~~~~sgIIYc~trk~~e~la~~L~----~~G~~~~~YHagl~~~~R~~~q~~f~~~~~~vivAT~A-FGMGIdk~dVR~V  308 (607)
T PRK11057        234 QRGKSGIIYCNSRAKVEDTAARLQ----SRGISAAAYHAGLDNDVRADVQEAFQRDDLQIVVATVA-FGMGINKPNVRFV  308 (607)
T ss_pred             CCCCCEEEEECCHHHHHHHHHHHH----HCCCCEEECCCCCCHHHHHHHHHHHHCCCCCEEEEEHH-HHCCCCCCCCCEE
T ss_conf             689977999692899999999998----57975453058999789999999875688758997501-1057677776679


Q ss_pred             E
Q ss_conf             8
Q gi|254780945|r  399 I  399 (700)
Q Consensus       399 V  399 (700)
                      |
T Consensus       309 i  309 (607)
T PRK11057        309 V  309 (607)
T ss_pred             E
T ss_conf             9


No 290
>cd01122 GP4d_helicase GP4d_helicase is a homohexameric 5'-3' helicases. Helicases couple NTP hydrolysis to the unwinding of nucleic acid duplexes into their component strands.
Probab=92.88  E-value=0.55  Score=27.30  Aligned_cols=62  Identities=13%  Similarity=0.087  Sum_probs=41.0

Q ss_pred             HHHHHHHHCCCCCCEEEEEECCCCCHHHHHHHHHHHHHH-HHCCEEEEEHHHHHHHHHHHHHHHHC
Q ss_conf             999998410013430788621442236999999733444-30545886127999999998621101
Q gi|254780945|r  281 IKDILQDMSQKNRMLRILQGDVGSGKTLVALIAMAAAVE-AGGQAVIMAPIGILAQQHYEFIKKYT  345 (700)
Q Consensus       281 i~eI~~Dl~~~~pM~RLLQGDVGSGKTiVA~~A~l~~~~-~G~Q~alMaPTEILA~QH~~~~~~~~  345 (700)
                      ++.+..-+..+.  .-++-|..|+|||..+.-.++.++. +|+-|++..+ |.=.+|+...+-...
T Consensus        20 LD~~~~Gl~~Ge--L~viaarpg~GKT~f~~~~a~~~~~~~g~~vl~~Sl-Em~~~~~~~Rlls~~   82 (271)
T cd01122          20 LNKLTKGLRKGE--LIILTAGTGVGKTTFLREYALDLITQHGVRVGTISL-EEPVVRTARRLLGQY   82 (271)
T ss_pred             HHHHHCCCCCCC--EEEEEECCCCCHHHHHHHHHHHHHHHCCCEEEEEEC-CCCHHHHHHHHHHHH
T ss_conf             888737999980--899996899869999999999999976990899970-499999999999998


No 291
>COG0389 DinP Nucleotidyltransferase/DNA polymerase involved in DNA repair [DNA replication, recombination, and repair]
Probab=92.79  E-value=0.073  Score=34.20  Aligned_cols=69  Identities=14%  Similarity=0.053  Sum_probs=38.8

Q ss_pred             HHCCCCCCHHHHHHHHHHHHHHCCCCCCEEEEEECCCCCHHHHHHHHHHHHHHHHCCEEEEEHHHHHHHHHHHHHHHHCC
Q ss_conf             63024679889999999998410013430788621442236999999733444305458861279999999986211014
Q gi|254780945|r  267 RNIPFSPTKSQESAIKDILQDMSQKNRMLRILQGDVGSGKTLVALIAMAAAVEAGGQAVIMAPIGILAQQHYEFIKKYTQ  346 (700)
Q Consensus       267 ~~LPF~LT~~Q~~ai~eI~~Dl~~~~pM~RLLQGDVGSGKTiVA~~A~l~~~~~G~Q~alMaPTEILA~QH~~~~~~~~~  346 (700)
                      .+.|+-.|.-....+.+...+|  +.-+    --.|| ..|...+..+-  +....+.+= .+-+.|+.+-.... .++.
T Consensus       155 ~~kp~gi~~~~~~~~~~~l~~L--pv~~----~~GvG-~~~~~~l~~~G--i~ti~dl~~-~~~~~L~~~~g~~~-~~l~  223 (354)
T COG0389         155 LNKPDGITVIEPEEVPALLWQL--PVLE----FWGVG-KVTAEKLRRLG--ISTIGDLAE-TDLDALKKRFGKLG-ERLY  223 (354)
T ss_pred             CCCCCCEEEECHHHHHHHHHCC--CHHH----HCCCC-HHHHHHHHHCC--CHHHHHHHH-CCHHHHHHHHHHHH-HHHH
T ss_conf             1399885663788899997609--5677----26845-89999999728--488999873-58999999999989-9999


No 292
>KOG0388 consensus
Probab=92.72  E-value=0.88  Score=25.71  Aligned_cols=155  Identities=20%  Similarity=0.285  Sum_probs=90.0

Q ss_pred             CCCHHHHHHHHHHHHHHCCCCCCEEEEEECCCCCHHHHHHHHHHHHHHHH---CCEEEEEHHHHHHHHHHHHHHHHCCCC
Q ss_conf             67988999999999841001343078862144223699999973344430---545886127999999998621101457
Q gi|254780945|r  272 SPTKSQESAIKDILQDMSQKNRMLRILQGDVGSGKTLVALIAMAAAVEAG---GQAVIMAPIGILAQQHYEFIKKYTQNT  348 (700)
Q Consensus       272 ~LT~~Q~~ai~eI~~Dl~~~~pM~RLLQGDVGSGKTiVA~~A~l~~~~~G---~Q~alMaPTEILA~QH~~~~~~~~~~~  348 (700)
                      +|-+-|.+-++=..+=-  ++-.|-.|--+.|-|||+-++..++..++..   .--.+.+|...|-. -.+.+.++++.+
T Consensus       567 tLKEYQlkGLnWLvnlY--dqGiNGILADeMGLGKTVQsisvlAhLaE~~nIwGPFLVVtpaStL~N-WaqEisrFlP~~  643 (1185)
T KOG0388         567 TLKEYQLKGLNWLVNLY--DQGINGILADEMGLGKTVQSISVLAHLAETHNIWGPFLVVTPASTLHN-WAQEISRFLPSF  643 (1185)
T ss_pred             HHHHHHHCCHHHHHHHH--HCCCCCEEHHHHCCCHHHHHHHHHHHHHHHCCCCCCEEEEEHHHHHHH-HHHHHHHHCCCC
T ss_conf             16887650078999998--703441213330453268899999999874458876389602787767-999999858654


Q ss_pred             CCEEEEEECCCCHHHHHHHHHHH-------CCCCCEEEEECHHH-CC-----CCCCCCCCCEEEECCCCCCCHHH--HHH
Q ss_conf             86589962464225667687762-------13475486411120-13-----34554444178852101335688--998
Q gi|254780945|r  349 QIIVEIITGNMPQAHRRKALERI-------AHGQAHIIIGTHAL-FQ-----DSIQYYKLILVIVDEQHRFGVQQ--RLK  413 (700)
Q Consensus       349 ~i~v~lLtg~~~~~er~~i~~~i-------~~G~~~iiIGTHAL-~q-----~~v~F~~LgLvViDEQHRFGV~Q--R~~  413 (700)
                        +|.-.-|+.  ++|+....-.       .+...+++|-+--+ ..     .+|.+.   +.|.||-+----.+  |.+
T Consensus       644 --k~lpywGs~--~eRkiLrKfw~rKnmY~rna~fhVviTSYQlvVtDeky~qkvKWQ---YMILDEAQAIKSSsS~RWK  716 (1185)
T KOG0388         644 --KVLPYWGSP--SERKILRKFWNRKNMYRRNAPFHVVITSYQLVVTDEKYLQKVKWQ---YMILDEAQAIKSSSSSRWK  716 (1185)
T ss_pred             --EEECCCCCH--HHHHHHHHHCCHHHHHCCCCCCEEEEEEEEEEECHHHHHHHHHHH---HEEHHHHHHHHHHHHHHHH
T ss_conf             --243476880--266899974044444304799528997531111159999863345---2005578776432256788


Q ss_pred             -HHHCCCCCCCEEECHHHHHHHHHH
Q ss_conf             -740256776101010132278999
Q gi|254780945|r  414 -LTQKATAPHVLLMTATPIPRTLVL  437 (700)
Q Consensus       414 -L~~Kg~~ph~L~MtATPIPRTLal  437 (700)
                       |.+ =.--+-|.+|-|||--|++=
T Consensus       717 tLLs-F~cRNRLLLTGTPIQNsMqE  740 (1185)
T KOG0388         717 TLLS-FKCRNRLLLTGTPIQNSMQE  740 (1185)
T ss_pred             HHHH-HHCCCEEEECCCCCCHHHHH
T ss_conf             7740-21034045318853017999


No 293
>cd00268 DEADc DEAD-box helicases. A diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker  B motif (motif II). This domain contains the ATP- binding region.
Probab=92.68  E-value=0.68  Score=26.61  Aligned_cols=111  Identities=17%  Similarity=0.305  Sum_probs=71.2

Q ss_pred             CCCCEEEEEECCCCCCCCCCCCHHHHHHHHHHHHCCCCEECCCCCCCHHHHHHHHHHHHCCCEEEEEECH------HHHC
Q ss_conf             0387389997120122111210146666666866371031201469989999999997559869999800------3410
Q gi|254780945|r  480 SEGKKAYWICPQIEEKKESNFRSVVERFNSLHEHFTSSIAIIHGRMSDIDKESVMDSFKNGTCKLLIATT------VIEV  553 (700)
Q Consensus       480 ~~g~q~y~VcPlIeese~~~~~~~~~~~~~l~~~~~~~v~~lHGkm~~~ek~~~m~~F~~g~~~iLvaTt------viEV  553 (700)
                      ..+-|+-|+||.-|=..     -+.+.++.+.+..+-++..++|..+..+..+.+   +. ..+|+|+|.      +-+-
T Consensus        67 ~~~~~alil~PTrELa~-----Qi~~~~~~l~~~~~i~~~~~~gg~~~~~~~~~l---~~-~~~IlI~TPgrl~~~l~~~  137 (203)
T cd00268          67 KDGPQALILAPTRELAL-----QIAEVARKLGKHTNLKVVVIYGGTSIDKQIRKL---KR-GPHIVVATPGRLLDLLERG  137 (203)
T ss_pred             CCCCEEEEEECCHHHHH-----HHHHHHHHHCCCCCEEEEEEECCCCHHHHHHHH---HC-CCEEEEECCHHHHHHHHCC
T ss_conf             68966999968799999-----999999985057983899983898879999998---53-8759996818999999848


Q ss_pred             CCCCCCCCEEEEECHHHC---C-HHHHHHHHHCCCCCCCCEEEEEEECCCCCHH
Q ss_conf             468887658998585254---7-4688773011667898359999708889987
Q gi|254780945|r  554 GIDVVDASIIIIENAEHF---G-LAQLHQLRGRVGRGEEISSCILLYHPPLSKN  603 (700)
Q Consensus       554 Gvdvpna~~mvI~~aerf---G-LsqLHQLRGRVGRg~~~s~c~l~~~~~~~~~  603 (700)
                      .++..+...+|+..||+.   | ..|+..+-.+..+.   --.+ ++++..++.
T Consensus       138 ~~~l~~l~~lVlDEAD~ll~~gf~~~i~~I~~~l~~~---~Q~~-lfSAT~~~~  187 (203)
T cd00268         138 KLDLSKVKYLVLDEADRMLDMGFEDQIREILKLLPKD---RQTL-LFSATMPKE  187 (203)
T ss_pred             CCCCCCCCEEEEECHHHHHHCCCHHHHHHHHHHCCCC---CEEE-EEEECCCHH
T ss_conf             8651322489998588887477699999999858967---7799-998049988


No 294
>pfam05970 DUF889 PIF1 helicase. The PIF1 helicase inhibits telomerase activity and is cell cycle regulated.
Probab=92.67  E-value=0.13  Score=32.33  Aligned_cols=19  Identities=11%  Similarity=0.029  Sum_probs=11.9

Q ss_pred             EEEEEEECCCCEEEEEEEC
Q ss_conf             3899998189369999951
Q gi|254780945|r   89 PYKILLNDGTGEITLLFFY  107 (700)
Q Consensus        89 ~~~v~v~D~tg~i~lvfFn  107 (700)
                      ...+.+-|+-+-+....|-
T Consensus        74 ~~~vLIIDEiSMv~~~lfd   92 (418)
T pfam05970        74 KASLIIWDEAPMTHRHCFE   92 (418)
T ss_pred             HCCEEEEECCCCCCHHHHH
T ss_conf             0879998541135789999


No 295
>PRK06731 flhF flagellar biosynthesis regulator FlhF; Validated
Probab=92.64  E-value=0.93  Score=25.51  Aligned_cols=185  Identities=12%  Similarity=0.086  Sum_probs=93.2

Q ss_pred             CCCCEEEEEECCCCCHHHHHHHHHHHHHHHHCCEEEEEHHHHHHHHHHHHHHHHCCCCCCEEEEEECCCCHHHHHHHHHH
Q ss_conf             13430788621442236999999733444305458861279999999986211014578658996246422566768776
Q gi|254780945|r  291 KNRMLRILQGDVGSGKTLVALIAMAAAVEAGGQAVIMAPIGILAQQHYEFIKKYTQNTQIIVEIITGNMPQAHRRKALER  370 (700)
Q Consensus       291 ~~pM~RLLQGDVGSGKTiVA~~A~l~~~~~G~Q~alMaPTEILA~QH~~~~~~~~~~~~i~v~lLtg~~~~~er~~i~~~  370 (700)
                      ..|-.-++-|=-|||||--++=-++.....|+.+++.+= ..-=.--++.++.|-..+|+++.....  +. +-......
T Consensus        73 ~~~~vI~lvG~~G~GKTTT~AKLA~~~~~~~~kV~lia~-DtyR~aA~eQLk~~a~~l~v~~~~~~~--~~-~~~~~~~~  148 (270)
T PRK06731         73 KEVQTIALIGPTGVGKTTTLAKMAWQFHGKKKTVGFITT-DHSRIGTVQQLQDYVKTIGFEVIAVRD--EA-AMTRALTY  148 (270)
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHHHHHHHCCCEEEEEEE-CCCCHHHHHHHHHHHHHHCCCEECCCC--HH-HHHHHHHH
T ss_conf             998189998889898899999999999867990899983-888888999999999981995354588--78-99999999


Q ss_pred             HCCCCCEEEEECHHHCCCCCCCCCCCEEEECCCCCCCHHHHH--HHH--HCCCCCC--CEEECHHHHHHHHHH--HHHHC
Q ss_conf             213475486411120133455444417885210133568899--874--0256776--101010132278999--97520
Q gi|254780945|r  371 IAHGQAHIIIGTHALFQDSIQYYKLILVIVDEQHRFGVQQRL--KLT--QKATAPH--VLLMTATPIPRTLVL--TSLGD  442 (700)
Q Consensus       371 i~~G~~~iiIGTHAL~q~~v~F~~LgLvViDEQHRFGV~QR~--~L~--~Kg~~ph--~L~MtATPIPRTLal--~~ygd  442 (700)
                      .+               +.   .+.-+|+||---|-..++..  .|.  ....+||  +|+|+||=-...+.-  ..|.+
T Consensus       149 ~~---------------~~---~~~DvilIDTAGR~~~d~~lm~el~~~~~~~~p~~~~Lvldas~~~~~~~~~~~~f~~  210 (270)
T PRK06731        149 FK---------------EE---ARVDYILIDTAGKNYRASETVEEMIETMGQVEPDYICLTLSASMKSKDMIEIITNFKD  210 (270)
T ss_pred             HH---------------HH---CCCCEEEEECCCCCCCCHHHHHHHHHHHCCCCCCEEEEEEECCCCHHHHHHHHHHHCC
T ss_conf             99---------------97---6999999979998714699999999986063898799998687776999999998077


Q ss_pred             CCHHHHCCCCCCCCCCEEEEEECCCHHHHHHHHHHHHCCCCEEEEEECCCCCCCCCCCCHHHHHHHH
Q ss_conf             1011110235576662079997020026899997631038738999712012211121014666666
Q gi|254780945|r  443 IDISKITEKPAGRKPIKTVIIPINRIDEVIERLKVVLSEGKKAYWICPQIEEKKESNFRSVVERFNS  509 (700)
Q Consensus       443 ldvS~i~e~P~gR~~I~T~~~~~~~~~~~~~~i~~~l~~g~q~y~VcPlIeese~~~~~~~~~~~~~  509 (700)
                      +        +.+ .-|.|++=+..+...+++.+.   ..|--+.+++-==.=.|+++..+.+...++
T Consensus       211 ~--------~i~-gvIlTKlD~ta~gG~als~~~---~~~~PI~fig~Ge~VpeDi~~~~~~~la~r  265 (270)
T PRK06731        211 I--------HID-GIVFTKFDETASSGELLKIPA---VSSAPIVLMTDGQDVKKNIHIATAEHLAKQ  265 (270)
T ss_pred             C--------CCC-EEEEECCCCCCCCCHHHHHHH---HHCCCEEEEECCCCCHHHHHCCCHHHHHHH
T ss_conf             9--------998-899965358997729999999---988597999459997021413799999999


No 296
>COG0017 AsnS Aspartyl/asparaginyl-tRNA synthetases [Translation, ribosomal structure and biogenesis]
Probab=92.51  E-value=0.97  Score=25.39  Aligned_cols=84  Identities=17%  Similarity=0.177  Sum_probs=56.2

Q ss_pred             CHHHCCCCCEEEEEEEEEEEEEECCCCCCEEEEEEECCCCEEEEEEECC--CHH-HHHHHCCCCCEEEEEEEEEECC---
Q ss_conf             4788899878999999989754215898338999981893699999518--878-9987328988899998997318---
Q gi|254780945|r   60 KISEISEERIVTITGYISQHSSFQLQKRRPYKILLNDGTGEITLLFFYR--KTE-MLKNVFFEGRKITVTGKIKKLK---  133 (700)
Q Consensus        60 ~I~~l~~g~~vti~g~V~~~~~~~~~~r~~~~v~v~D~tg~i~lvfFn~--~~~-yl~k~lk~G~~v~vsGKv~~~~---  133 (700)
                      .+.+...|+.|++.|=|-+.+.   .+ +..=+.+.|+||.++++..-.  ... +..+.|..++.|.|.|+|....   
T Consensus         9 di~~~~~~~~V~v~GWV~~~R~---~g-~i~Fi~lrDgsg~iQ~v~~~~~~~~~~~~~~~L~~es~v~V~G~v~~~~~a~   84 (435)
T COG0017           9 DIKPHVGGQEVTVRGWVHNKRD---LG-KIIFLVLRDGSGFIQAVVPKNKVYEELFKAKKLTLESSVVVTGIVKASPKAP   84 (435)
T ss_pred             HHHCCCCCCEEEEEEEEEEECC---CC-CEEEEEEECCCCEEEEEEECCCCCHHHHHHHCCCCCCEEEEEEEEECCCCCC
T ss_conf             6504479857999988755001---58-7089999758837999997787717676663178765899999997488999


Q ss_pred             CEEEEECCEEEECC
Q ss_conf             77999778689626
Q gi|254780945|r  134 NRIIMVHPHYIFHN  147 (700)
Q Consensus       134 ~~~qi~hPe~~~~~  147 (700)
                      +++++.--++++..
T Consensus        85 ~g~El~v~~i~Vl~   98 (435)
T COG0017          85 QGFELQVEKIEVLG   98 (435)
T ss_pred             CCEEEEEEEEEEEE
T ss_conf             87799887889940


No 297
>PRK08074 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
Probab=92.42  E-value=0.99  Score=25.31  Aligned_cols=85  Identities=13%  Similarity=0.234  Sum_probs=63.5

Q ss_pred             HHHHHHHHHHHC-CCCEEEEEECCCCCCCCCCCCHHHHHHHHHHHHCCC-CEEC-CCCCCCHHHHHHHHHHHHCCCEEEE
Q ss_conf             268999976310-387389997120122111210146666666866371-0312-0146998999999999755986999
Q gi|254780945|r  469 DEVIERLKVVLS-EGKKAYWICPQIEEKKESNFRSVVERFNSLHEHFTS-SIAI-IHGRMSDIDKESVMDSFKNGTCKLL  545 (700)
Q Consensus       469 ~~~~~~i~~~l~-~g~q~y~VcPlIeese~~~~~~~~~~~~~l~~~~~~-~v~~-lHGkm~~~ek~~~m~~F~~g~~~iL  545 (700)
                      +.+.+.|.+-+. .++++.|.+|--        ...++.|+.++...+. .+.+ .+| |+...+++.+++|++++-.||
T Consensus       742 ~~la~~i~~l~~~~~G~~LVLFtS~--------~~L~~v~~~l~~~~~~~~~~ll~Qg-~~~~sr~~ll~~F~~~~~svL  812 (932)
T PRK08074        742 EEVAAYIAKIAKATKGRMLVLFTSY--------EMLKKTYYNLKNEEELEGYVLLAQG-VTGGSRARLMKKFQQFDKAIL  812 (932)
T ss_pred             HHHHHHHHHHHHHCCCCEEEECCCH--------HHHHHHHHHHHHHCCCCCCEEEEEC-CCCCCHHHHHHHHHHCCCEEE
T ss_conf             9999999999987299999992659--------9999999998643335795599878-987509999999984798499


Q ss_pred             EECHHHHCCCCCCCCCE
Q ss_conf             98003410468887658
Q gi|254780945|r  546 IATTVIEVGIDVVDASI  562 (700)
Q Consensus       546 vaTtviEVGvdvpna~~  562 (700)
                      ++|..-==|||+|.-.+
T Consensus       813 lGt~SFwEGVDlpGd~L  829 (932)
T PRK08074        813 LGTSSFWEGIDIPGDEL  829 (932)
T ss_pred             EECCCCCCCCCCCCCCE
T ss_conf             96566435622799886


No 298
>cd04487 RecJ_OBF2_like RecJ_OBF2_like: A subfamily of OB folds corresponding to the second OB fold (OBF2) of archaeal-specific proteins with similarity to eubacterial RecJ. RecJ is an ssDNA-specific exonuclease. Although the overall sequence similarity of these proteins to eubacterial RecJ proteins is marginal, they appear to carry motifs, which have been shown to be essential for nuclease function in Escherichia coli RecJ. In addition to this OB fold, most proteins in this subfamily contain: i) an N-terminal OB fold belonging to a different domain family (the ribosomal S1-like RNA-binding family); and ii) a domain, C-terminal to OBF2, characteristic of DHH family proteins. DHH family proteins include E. coli RecJ, and are predicted to have a phosphoesterase function.
Probab=92.34  E-value=1  Score=25.25  Aligned_cols=67  Identities=21%  Similarity=0.231  Sum_probs=50.8

Q ss_pred             EEEEEEEEEEEEECCCCCCEEEEEEECCCCEEEEEEECCC--HHHHHHHCCCCCEEEEEEEEEECCCEEEEECCE
Q ss_conf             9999999897542158983389999818936999995188--789987328988899998997318779997786
Q gi|254780945|r   70 VTITGYISQHSSFQLQKRRPYKILLNDGTGEITLLFFYRK--TEMLKNVFFEGRKITVTGKIKKLKNRIIMVHPH  142 (700)
Q Consensus        70 vti~g~V~~~~~~~~~~r~~~~v~v~D~tg~i~lvfFn~~--~~yl~k~lk~G~~v~vsGKv~~~~~~~qi~hPe  142 (700)
                      +.+.|+|.....  +.  -|...++.|++|.+.+-=|.-.  ..|  -....|+.+.+.|+++..+|.+|+---+
T Consensus         1 V~i~GeV~qikQ--T~--GPTIFti~Detg~v~~AAFeeaGvRAy--Pev~~gdiV~v~G~V~~r~g~lQiE~~~   69 (73)
T cd04487           1 VHIEGEVVQIKQ--TS--GPTIFTLRDETGTVWAAAFEEAGVRAY--PEVEVGDIVRVTGEVEPRDGQLQIEVES   69 (73)
T ss_pred             CEEEEEEEEEEE--CC--CCEEEEEECCCCCEEHHHHCCCCCCCC--CCCCCCCEEEEEEEEEEECCEEEEEEEE
T ss_conf             979999999898--89--999999975999698205130674128--8878898899998999708858999730


No 299
>pfam03237 Terminase_6 Terminase-like family. This family represents a group of terminase proteins.
Probab=92.25  E-value=1  Score=25.16  Aligned_cols=136  Identities=13%  Similarity=0.089  Sum_probs=73.9

Q ss_pred             EEEECCCCCHHHHHHHHHH-HHHHHH-CCEEEEEHHHHHHHHHH-HHHHHHCCCCCCEEEEEECCCCHHHHHHHHHHHCC
Q ss_conf             8862144223699999973-344430-54588612799999999-86211014578658996246422566768776213
Q gi|254780945|r  297 ILQGDVGSGKTLVALIAMA-AAVEAG-GQAVIMAPIGILAQQHY-EFIKKYTQNTQIIVEIITGNMPQAHRRKALERIAH  373 (700)
Q Consensus       297 LLQGDVGSGKTiVA~~A~l-~~~~~G-~Q~alMaPTEILA~QH~-~~~~~~~~~~~i~v~lLtg~~~~~er~~i~~~i~~  373 (700)
                      ++.|=.|||||.++...++ .|+.++ ..+++++||.-=|+.-+ ..+.++++.+ ..+.+-..    ++   -.-.+.+
T Consensus         1 ~~~ggr~~GKT~~~~~~~~~~a~~~~~~~~~i~~~t~~~~~~~~~~~~~~~~~~~-~~~~~~~~----~~---~~i~~~n   72 (380)
T pfam03237         1 NILGSRQSGKTFAFAREALRHALGNGPKNQIILSASKAQARLEFKKGIIEIAGDL-LEITFEEK----NG---NPIILPN   72 (380)
T ss_pred             CCCCCCCCCHHHHHHHHHHHHHHHCCCCCEEEEECCHHHHHHHHHHHHHHHHHHH-CCCCEEEC----CC---CEEEECC
T ss_conf             9426452528399999999999858997289997999999999999999966886-38716727----88---7399159


Q ss_pred             CCCEEEEECH-HHCCCCCCCCCCCEEEECC--CCCCCHHHHHHHH--HCCCCCCCEEECHHHHHHHHHHHHH
Q ss_conf             4754864111-2013345544441788521--0133568899874--0256776101010132278999975
Q gi|254780945|r  374 GQAHIIIGTH-ALFQDSIQYYKLILVIVDE--QHRFGVQQRLKLT--QKATAPHVLLMTATPIPRTLVLTSL  440 (700)
Q Consensus       374 G~~~iiIGTH-AL~q~~v~F~~LgLvViDE--QHRFGV~QR~~L~--~Kg~~ph~L~MtATPIPRTLal~~y  440 (700)
                      |..-.+.|+. +-=.+++.=..+.++++||  +++.-...-....  ..+...-.+++|-||=|..-.-.+|
T Consensus        73 Gs~i~~~~~~~~~~~~~~rG~~~~~i~~DE~a~~~~~~~~~~~~~~~~~~~~~~~~~~stp~~~~~~~~~~~  144 (380)
T pfam03237        73 GAKLYFLGLESETTAQGYRGASIAGIYFDEATWLPKFQESELVRRLRATKGKWRKTFFSTPPSPGHWVYDFW  144 (380)
T ss_pred             CCEEEEEECCCCCCHHHCCCCCCCEEEEEEHHHCCCHHHHHHHHHHHCCCCCCCEEEEECCCCCCCCHHHHH
T ss_conf             988999625776643103485455499830453662789999864410479975799988989985198998


No 300
>cd04497 hPOT1_OB1_like hPOT1_OB1_like: A subfamily of OB folds similar to the first OB fold (OB1) of human protection of telomeres 1 protein (hPOT1), the single OB fold of the N-terminal domain of Schizosaccharomyces pombe POT1 (SpPOT1), and the first OB fold of the N-terminal domain of the alpha subunit (OB1Nalpha) of Oxytricha nova telomere end binding protein (OnTEBP). POT1 proteins recognize single-stranded (ss) 3-prime ends of the telomere. A 3-prime ss overhang is conserved in ciliated protozoa, yeast, and mammals. SpPOT1 is essential for telomere maintenance. It binds specifically to the ss G-rich telomeric sequence (GGTTAC) of S. pombe. hPOT1 binds specifically to ss telomeric DNA repeats ending with the sequence GGTTAG. Deletion of the S. pombe pot1+ gene results in a rapid loss of telomere sequences, chromosome mis-segregation and chromosome circularization. hPOT1 is implicated in telomere length regulation. The hPOT1 monomer consists of two closely connected OB folds (OB1-OB
Probab=92.24  E-value=1  Score=25.15  Aligned_cols=83  Identities=16%  Similarity=0.126  Sum_probs=60.3

Q ss_pred             CCCHHHCC--CCCEEEEEEEEEEEEEECCCCCC--EEEEEEECCCC----EEEEEEECCCHHHHHHHCCCCCEEEEEE-E
Q ss_conf             46478889--98789999999897542158983--38999981893----6999995188789987328988899998-9
Q gi|254780945|r   58 RPKISEIS--EERIVTITGYISQHSSFQLQKRR--PYKILLNDGTG----EITLLFFYRKTEMLKNVFFEGRKITVTG-K  128 (700)
Q Consensus        58 ~~~I~~l~--~g~~vti~g~V~~~~~~~~~~r~--~~~v~v~D~tg----~i~lvfFn~~~~yl~k~lk~G~~v~vsG-K  128 (700)
                      ..+|+++.  .|..+.+.|.|+........+++  ...+.+.|.+-    .+.+.+|......|.. .++|+-+.+.. +
T Consensus         3 y~~L~~a~~~~~~~VnvigVV~~~~~p~~s~g~d~~~tl~I~D~S~~~~~~l~v~~F~~~~~~LP~-v~~GDiIll~~~~   81 (138)
T cd04497           3 YTPLSSALKESGGSVNVIGVVVDAGPPVRSKGTDYCCTLTITDPSLANSDGLTVKLFRPNEESLPI-VKVGDIILLRRVK   81 (138)
T ss_pred             EEEHHHHHHHCCCEEEEEEEEEECCCCEECCCCEEEEEEEEECCCCCCCCCEEEEEECCCHHHCCC-CCCCCEEEEEEEE
T ss_conf             150899986349858899999865796446997299999999289999996799998998656989-9999899998889


Q ss_pred             EEECCCEEEEECC
Q ss_conf             9731877999778
Q gi|254780945|r  129 IKKLKNRIIMVHP  141 (700)
Q Consensus       129 v~~~~~~~qi~hP  141 (700)
                      ++.+++..+.+..
T Consensus        82 v~~~~~~~~~~~~   94 (138)
T cd04497          82 IQSYNGKPQGISN   94 (138)
T ss_pred             EEEECCEEEEEEC
T ss_conf             9998890799977


No 301
>PRK00476 aspS aspartyl-tRNA synthetase; Validated
Probab=92.23  E-value=1  Score=25.14  Aligned_cols=69  Identities=20%  Similarity=0.273  Sum_probs=48.3

Q ss_pred             CCCHHHCCCCCEEEEEEEEEEEEEECCCCCCEEEEEEECCCCEEEEEEECCCH---HHHHHHCCCCCEEEEEEEEEE
Q ss_conf             46478889987899999998975421589833899998189369999951887---899873289888999989973
Q gi|254780945|r   58 RPKISEISEERIVTITGYISQHSSFQLQKRRPYKILLNDGTGEITLLFFYRKT---EMLKNVFFEGRKITVTGKIKK  131 (700)
Q Consensus        58 ~~~I~~l~~g~~vti~g~V~~~~~~~~~~r~~~~v~v~D~tg~i~lvfFn~~~---~yl~k~lk~G~~v~vsGKv~~  131 (700)
                      +..|..-..|+.|+|.|.|.+.+.   .++ ..=+.+.|++|.+++++=....   ..+ +.+..|..+.|.|++..
T Consensus         8 ~~~l~~~~~g~~V~v~GwV~~~R~---~Gk-l~F~~LrD~~G~iQiv~~~~~~~~~~~~-~~l~~e~iv~V~G~v~~   79 (587)
T PRK00476          8 CGELRESHVGQTVTLCGWVHRRRD---HGG-VIFIDLRDREGIVQVVFDPDDAEAFAVA-ESLRSEYVIQVTGKVRA   79 (587)
T ss_pred             CCCCCHHHCCCEEEEEEEEEEEEC---CCC-CEEEEEEECCCCEEEEECCCCHHHHHHH-HCCCCCCEEEEEEEEEE
T ss_conf             312884769898999785753664---798-2999998389788999918877899999-66999878999989993


No 302
>COG0378 HypB Ni2+-binding GTPase involved in regulation of expression and maturation of urease and hydrogenase [Posttranslational modification, protein turnover, chaperones / Transcription]
Probab=92.12  E-value=1.1  Score=25.05  Aligned_cols=171  Identities=19%  Similarity=0.247  Sum_probs=105.0

Q ss_pred             CCCCEEE-EEECCCCCHHHHHHHHHHHHHHHHCCEEEEEHHHHHHHHHHHHHHHHCCCCCCE-EEEEECCC---CHHHHH
Q ss_conf             1343078-862144223699999973344430545886127999999998621101457865-89962464---225667
Q gi|254780945|r  291 KNRMLRI-LQGDVGSGKTLVALIAMAAAVEAGGQAVIMAPIGILAQQHYEFIKKYTQNTQII-VEIITGNM---PQAHRR  365 (700)
Q Consensus       291 ~~pM~RL-LQGDVGSGKTiVA~~A~l~~~~~G~Q~alMaPTEILA~QH~~~~~~~~~~~~i~-v~lLtg~~---~~~er~  365 (700)
                      +.||.|+ +-|-||||||.+-...+ ......|..|++.= .++.+--.+.+++.   .+.+ +...||..   .++--.
T Consensus        10 ~~~~~~i~v~Gp~GSGKTaLie~~~-~~L~~~~~~aVI~~-Di~t~~Da~~l~~~---~g~~i~~v~TG~~CH~da~m~~   84 (202)
T COG0378          10 NRPMLRIGVGGPPGSGKTALIEKTL-RALKDEYKIAVITG-DIYTKEDADRLRKL---PGEPIIGVETGKGCHLDASMNL   84 (202)
T ss_pred             CCCEEEEEECCCCCCCHHHHHHHHH-HHHHHHCCEEEEEC-EEECHHHHHHHHHC---CCCEEEEECCCCCCCCCHHHHH
T ss_conf             5864899961799867899999999-99975277689964-04006559999737---7980687403876588678899


Q ss_pred             HHHHHHCCC-C-CEEEEECH-----HHCCCCCCCCCCCEEEECCCCCCCHHHHHHHHHC-CC---CCCCEEECHHHHHHH
Q ss_conf             687762134-7-54864111-----2013345544441788521013356889987402-56---776101010132278
Q gi|254780945|r  366 KALERIAHG-Q-AHIIIGTH-----ALFQDSIQYYKLILVIVDEQHRFGVQQRLKLTQK-AT---APHVLLMTATPIPRT  434 (700)
Q Consensus       366 ~i~~~i~~G-~-~~iiIGTH-----AL~q~~v~F~~LgLvViDEQHRFGV~QR~~L~~K-g~---~ph~L~MtATPIPRT  434 (700)
                      ..++++..- . .++++=-.     +=|+-++. ..++.+|||      |.|=...-.| |+   ..|+++.+-|-    
T Consensus        85 ~ai~~l~~~~~~~Dll~iEs~GNL~~~~sp~L~-d~~~v~Vid------vteGe~~P~K~gP~i~~aDllVInK~D----  153 (202)
T COG0378          85 EAIEELVLDFPDLDLLFIESVGNLVCPFSPDLG-DHLRVVVID------VTEGEDIPRKGGPGIFKADLLVINKTD----  153 (202)
T ss_pred             HHHHHHHHCCCCCCEEEEECCCCEECCCCCCHH-HCEEEEEEE------CCCCCCCCCCCCCCEEEEEEEEEEHHH----
T ss_conf             999998631776778999237643244680413-046999998------788888765579964674189985677----


Q ss_pred             HHHHHHHCCCHHH----HCCCCCCCCCCEEEEEECCCHHHHHHHHHHHH
Q ss_conf             9999752010111----10235576662079997020026899997631
Q gi|254780945|r  435 LVLTSLGDIDISK----ITEKPAGRKPIKTVIIPINRIDEVIERLKVVL  479 (700)
Q Consensus       435 Lal~~ygdldvS~----i~e~P~gR~~I~T~~~~~~~~~~~~~~i~~~l  479 (700)
                        |+-|-+-|+.+    .+++-|++.-|.|.....+..+++++|++...
T Consensus       154 --La~~v~~dlevm~~da~~~np~~~ii~~n~ktg~G~~~~~~~i~~~~  200 (202)
T COG0378         154 --LAPYVGADLEVMARDAKEVNPEAPIIFTNLKTGEGLDEWLRFIEPQA  200 (202)
T ss_pred             --HHHHHCCCHHHHHHHHHHHCCCCCEEEEECCCCCCHHHHHHHHHHHC
T ss_conf             --38772866999999999849999889984787868999999987640


No 303
>TIGR02237 recomb_radB DNA repair and recombination protein RadB; InterPro: IPR011939    This family consists exclusively of archaeal RadB protein, a homolog of bacterial RecA, eukaryotic RAD51 (IPR011941 from INTERPRO) and DMC1 (IPR011940 from INTERPRO), and archaeal RadA (IPR011938 from INTERPRO) ,, .; GO: 0003684 damaged DNA binding, 0005524 ATP binding, 0008094 DNA-dependent ATPase activity, 0006281 DNA repair, 0006310 DNA recombination.
Probab=92.11  E-value=0.16  Score=31.44  Aligned_cols=47  Identities=30%  Similarity=0.379  Sum_probs=37.6

Q ss_pred             EEECCCCCHHHHHHHHHHHHHHHHCCEEEEEHHHH-HHHHHHHHHHHHCCCC
Q ss_conf             86214422369999997334443054588612799-9999998621101457
Q gi|254780945|r  298 LQGDVGSGKTLVALIAMAAAVEAGGQAVIMAPIGI-LAQQHYEFIKKYTQNT  348 (700)
Q Consensus       298 LQGDVGSGKTiVA~~A~l~~~~~G~Q~alMaPTEI-LA~QH~~~~~~~~~~~  348 (700)
                      +-|.=|||||=||+.++..++.+|..|++.= ||= |.   .|-|+.++..-
T Consensus        17 iYGp~G~GKTn~c~~~a~~a~~~Gk~v~YiD-TEGGLS---~ER~~q~~~~~   64 (223)
T TIGR02237        17 IYGPPGSGKTNICLILAVNAARQGKKVVYID-TEGGLS---PERFKQIAEDR   64 (223)
T ss_pred             EECCCCCCHHHHHHHHHHHHHHCCCCEEEEE-CCCCCH---HHHHHHHHHCC
T ss_conf             8758998678999999999986189589996-289832---89999986305


No 304
>PRK05898 dnaE DNA polymerase III DnaE; Validated
Probab=92.09  E-value=1.1  Score=25.02  Aligned_cols=82  Identities=11%  Similarity=0.093  Sum_probs=51.4

Q ss_pred             HHHHHHCCCC--EECCCCCCCHHHH-HHHHHHHHCCCEEEEEECHHHHCCCCCCCCCEEEEE--CHHHCCHHHHHHHH--
Q ss_conf             6668663710--3120146998999-999999755986999980034104688876589985--85254746887730--
Q gi|254780945|r  508 NSLHEHFTSS--IAIIHGRMSDIDK-ESVMDSFKNGTCKLLIATTVIEVGIDVVDASIIIIE--NAEHFGLAQLHQLR--  580 (700)
Q Consensus       508 ~~l~~~~~~~--v~~lHGkm~~~ek-~~~m~~F~~g~~~iLvaTtviEVGvdvpna~~mvI~--~aerfGLsqLHQLR--  580 (700)
                      .+||.+||..  .++|...+.+.+| ...+.+-+.-.+.||      -.-|+-..+...|-.  ++=||||+-.--+.  
T Consensus       690 AyLKahyP~eF~aalL~~~~~~~~k~~~~i~ea~~~gi~vl------pPdIN~S~~~f~~~~~~~~Ir~GL~aIKgvG~~  763 (971)
T PRK05898        690 AYLKHYYPLEFLSILLSHTSASKDKLLSYLNEAKEFNISIK------KPDINYSSNSFVLDTQKQIIRFGFNTIKGFGDE  763 (971)
T ss_pred             HHHHHCCHHHHHHHHHCCCCCCCHHHHHHHHHHHHCCCEEC------CCCCCCCCCCEEEECCCCEEEEEHHHHCCCCHH
T ss_conf             99985478999999846899997579999999998699273------882257778527857998699764760785599


Q ss_pred             -------HCCCCCCCCEEEEEEE
Q ss_conf             -------1166789835999970
Q gi|254780945|r  581 -------GRVGRGEEISSCILLY  596 (700)
Q Consensus       581 -------GRVGRg~~~s~c~l~~  596 (700)
                             -| -.|.-.|++-++.
T Consensus       764 ~~~~Iv~~R-~~g~f~~~~df~~  785 (971)
T PRK05898        764 LLKKIKSAL-QNKTFSDFISYID  785 (971)
T ss_pred             HHHHHHHHH-CCCCCCCHHHHHH
T ss_conf             999999986-6899999999998


No 305
>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=92.02  E-value=1.1  Score=24.97  Aligned_cols=78  Identities=26%  Similarity=0.290  Sum_probs=59.2

Q ss_pred             CCCCEEEEEEEEEEEEEECCC-CCCEEEEEEECCCC--EEEEEEECC----CHHHHHHHCCCCCEEEEEEEEEEC--CCE
Q ss_conf             998789999999897542158-98338999981893--699999518----878998732898889999899731--877
Q gi|254780945|r   65 SEERIVTITGYISQHSSFQLQ-KRRPYKILLNDGTG--EITLLFFYR----KTEMLKNVFFEGRKITVTGKIKKL--KNR  135 (700)
Q Consensus        65 ~~g~~vti~g~V~~~~~~~~~-~r~~~~v~v~D~tg--~i~lvfFn~----~~~yl~k~lk~G~~v~vsGKv~~~--~~~  135 (700)
                      +....+.|.|.|=.......+ +|..+.+.+.|.+.  ++.+.||+.    -...+ ..+++|++|.+.|++..-  .+.
T Consensus         5 ~~e~~~~~~G~iF~~e~~~~ksgr~~~~i~~tD~~~GGSl~~k~F~~~~~eD~~~~-~~~K~~~wv~~~g~~~~~~~~~~   83 (1264)
T TIGR01405         5 EEENRVKVEGVIFKIEIKELKSGRTLLKIKVTDYTDGGSLILKKFLKSEKEDKEKF-DGIKIGKWVRVRGKIELDKFSRD   83 (1264)
T ss_pred             CCCCEEEEEEEEEEEECCCCCCCCEEEEEEEEECCCCCEEEEEEECCCCCCHHHHH-HHHCCCCCEEEEEEEEEECCCCC
T ss_conf             35344899999863302335775279999987317886068876048997205777-34203773599998875221200


Q ss_pred             EEEECCEE
Q ss_conf             99977868
Q gi|254780945|r  136 IIMVHPHY  143 (700)
Q Consensus       136 ~qi~hPe~  143 (700)
                      ++|.=-++
T Consensus        84 ~~~~~~~I   91 (1264)
T TIGR01405        84 LQMIIKDI   91 (1264)
T ss_pred             CEEEEECC
T ss_conf             05877502


No 306
>COG4626 Phage terminase-like protein, large subunit [General function prediction only]
Probab=91.99  E-value=0.46  Score=27.96  Aligned_cols=134  Identities=18%  Similarity=0.200  Sum_probs=86.0

Q ss_pred             HHCCCCCCHHHHHHHHHHHHHHCCCCCCEE----EEEECCCCCHHHHHH-HHHHHHH---HHHCCEEEEEHHHHHHHHHH
Q ss_conf             630246798899999999984100134307----886214422369999-9973344---43054588612799999999
Q gi|254780945|r  267 RNIPFSPTKSQESAIKDILQDMSQKNRMLR----ILQGDVGSGKTLVAL-IAMAAAV---EAGGQAVIMAPIGILAQQHY  338 (700)
Q Consensus       267 ~~LPF~LT~~Q~~ai~eI~~Dl~~~~pM~R----LLQGDVGSGKTiVA~-~A~l~~~---~~G~Q~alMaPTEILA~QH~  338 (700)
                      ...||+|-+=|+=.+.-|..--.+..--+|    ++-=-=|-|||-+|+ ++++..+   .+|++..+.||++=-|.+-|
T Consensus        56 ~~~p~~l~PwQkFiia~l~G~~~k~T~~rrf~e~fI~v~RkngKt~l~A~i~~~~~l~~~~~~~~~~i~A~s~~qa~~~F  135 (546)
T COG4626          56 PGFPESLEPWQKFIVAALFGFYDKQTGIRRFKEAFIFIPRKNGKSTLAAGIMMTALLLNWRSGAGIYILAPSVEQAANSF  135 (546)
T ss_pred             CCCCCCCCCHHHHHHHHHHHEEECCCCEEEEEEEEEEEECCCCHHHHHHHHHHHHHHHHHCCCCEEEEEECCHHHHHHHH
T ss_conf             89863435189999998760350578706888999997457855789999999998765304760899834289998876


Q ss_pred             HHHHHHCCCCCCEEEEEECCCCHHHHHHHHHHHCCCCCEEEEEC-HHHC------CCCCCCCCCCEEEECCCCCCCHHHH
Q ss_conf             86211014578658996246422566768776213475486411-1201------3345544441788521013356889
Q gi|254780945|r  339 EFIKKYTQNTQIIVEIITGNMPQAHRRKALERIAHGQAHIIIGT-HALF------QDSIQYYKLILVIVDEQHRFGVQQR  411 (700)
Q Consensus       339 ~~~~~~~~~~~i~v~lLtg~~~~~er~~i~~~i~~G~~~iiIGT-HAL~------q~~v~F~~LgLvViDEQHRFGV~QR  411 (700)
                      ...+.+....+ ....             +..+......|..+- -|.+      .+.+.=.|-+++|+||=|=||-.| 
T Consensus       136 ~~ar~mv~~~~-~l~~-------------~~~~~~~s~~i~~~~~~s~ik~~aa~~~~~Dg~~~~~~I~DEih~f~~~~-  200 (546)
T COG4626         136 NPARDMVKRDD-DLRD-------------LCNVQTHSRTITHRKTDSTIKAVAADPNTVDGLNSVGAIIDELHLFGKQE-  200 (546)
T ss_pred             HHHHHHHHHCC-CHHH-------------HCCCCCCEEEEEECCCCEEEEEHHCCCCCCCCCCCCEEEEEHHHHHCCHH-
T ss_conf             89999987372-1333-------------20654540489861551113301048875567876548876375416789-


Q ss_pred             HHHH
Q ss_conf             9874
Q gi|254780945|r  412 LKLT  415 (700)
Q Consensus       412 ~~L~  415 (700)
                      ..+.
T Consensus       201 ~~~~  204 (546)
T COG4626         201 DMYS  204 (546)
T ss_pred             HHHH
T ss_conf             9999


No 307
>PRK10919 ATP-dependent DNA helicase Rep; Provisional
Probab=91.94  E-value=0.54  Score=27.36  Aligned_cols=75  Identities=17%  Similarity=0.213  Sum_probs=34.9

Q ss_pred             HHCCHHHHHHHHHCCCCCCCCEEEEEEE------C--CCCC---HHHHHHHHHHHHHCHHHHHHHHHHHHCCCC--CCCC
Q ss_conf             2547468877301166789835999970------8--8899---879999999984142589999998520630--0026
Q gi|254780945|r  569 EHFGLAQLHQLRGRVGRGEEISSCILLY------H--PPLS---KNSYTRLSVLKNTEDGFLIAEEDLKQRKEG--EILG  635 (700)
Q Consensus       569 erfGLsqLHQLRGRVGRg~~~s~c~l~~------~--~~~~---~~~~~Rl~~l~~~~dGf~iAe~Dl~lRG~G--~~~G  635 (700)
                      +.--|.++|+=.|.     .=-++|++.      +  ...+   -+-..||=..     |..=|++-|-|=.+-  ...|
T Consensus       550 ~~V~LmTiH~SKGL-----Ef~~Vfl~gl~eg~~P~~~~~~~~~~eEERRLfYV-----a~TRAk~~L~ls~~~~r~~~g  619 (672)
T PRK10919        550 DQVQLMTLHASKGL-----EFPYVYMVGMEEGFLPHQSSIDEDNIDEERRLAYV-----GITRAQKELTFTLCKERRQYG  619 (672)
T ss_pred             CEEEEEEHHHHHCC-----CCCEEEEECCCCCCCCCCCCCCCCHHHHHHHHHHH-----HHHHHHHHHEEEECCHHHHCC
T ss_conf             90899648862310-----36879996783899987656998608799999999-----999987766550045234388


Q ss_pred             CHHCCCCCCCCCCHHHHH
Q ss_conf             000698744000388759
Q gi|254780945|r  636 IKQSGMPKFLIAQPELHD  653 (700)
Q Consensus       636 ~~QsG~~~~~~~d~~~d~  653 (700)
                      ..++..|.=-+.++-.|.
T Consensus       620 ~~~~~~pSrFl~eip~~~  637 (672)
T PRK10919        620 ELVRPEPSRFLLELPQDD  637 (672)
T ss_pred             CCCCCCCCCCHHHCCHHH
T ss_conf             775899994621378999


No 308
>TIGR02903 spore_lon_C ATP-dependent protease, Lon family; InterPro: IPR014252   This entry shows some relation to the widely distributed ATP-dependent protease La, also called Lon or LonA (IPR004815 from INTERPRO), but is more closely related to LonB (IPR014251 from INTERPRO), a LonA paralog found only in endospore-forming bacteria. Proteins in this entry are unassigned peptidases belonging to the MEROPS peptidase family S16 (lon protease family, clan SJ). They are restricted to a subset of endospore-forming species, and probably participate in the program of endospore formation. We propose the designation LonC..
Probab=91.89  E-value=0.24  Score=30.12  Aligned_cols=47  Identities=36%  Similarity=0.420  Sum_probs=42.2

Q ss_pred             CCCCCHHHHHHHHHHHHHHCCCCCCEEEEEECCCCCHHHHHHHHHHH
Q ss_conf             24679889999999998410013430788621442236999999733
Q gi|254780945|r  270 PFSPTKSQESAIKDILQDMSQKNRMLRILQGDVGSGKTLVALIAMAA  316 (700)
Q Consensus       270 PF~LT~~Q~~ai~eI~~Dl~~~~pM~RLLQGDVGSGKTiVA~~A~l~  316 (700)
                      .|+--=+|.+||+...+-++||+|-+-+|.|==|-|||-+|=+|+=.
T Consensus       153 ~f~EiVGQerAI~aLlaK~aSPfPQHiiLYGPPGVGKTTaARl~LEe  199 (616)
T TIGR02903       153 AFSEIVGQERAIKALLAKLASPFPQHIILYGPPGVGKTTAARLALEE  199 (616)
T ss_pred             CCCCCCCHHHHHHHHHHHHCCCCCCCEEEECCCCCCHHHHHHHHHHH
T ss_conf             67643334689999997631888660785573388478999998762


No 309
>PRK08840 replicative DNA helicase; Provisional
Probab=91.89  E-value=0.84  Score=25.89  Aligned_cols=73  Identities=16%  Similarity=0.142  Sum_probs=45.4

Q ss_pred             EEEEECCCCCHHHHHHHHHHHHH-HHHCCEEEEEHHHHHHHHHHHHHHHHCCCCCCEEEEEECCCCHHHHHHHHHH
Q ss_conf             78862144223699999973344-4305458861279999999986211014578658996246422566768776
Q gi|254780945|r  296 RILQGDVGSGKTLVALIAMAAAV-EAGGQAVIMAPIGILAQQHYEFIKKYTQNTQIIVEIITGNMPQAHRRKALER  370 (700)
Q Consensus       296 RLLQGDVGSGKTiVA~~A~l~~~-~~G~Q~alMaPTEILA~QH~~~~~~~~~~~~i~v~lLtg~~~~~er~~i~~~  370 (700)
                      -.|=|--|+|||..|+--+..++ .+|+.|+|..- |.=++|-...+-......+. -.+-+|.++..+..++...
T Consensus       220 iviaaRPsmGKTalalnia~n~a~~~~~~v~~fSl-EMs~~ql~~Rlls~~s~i~~-~~ir~g~l~~~e~~~i~~a  293 (464)
T PRK08840        220 IIVAARPSMGKTTFAMNLCENAAMDQDKPVLIFSL-EMPAEQLMMRMLASLSRVDQ-TKIRTGQLDDEDWARISST  293 (464)
T ss_pred             EEEEECCCCCHHHHHHHHHHHHHHHCCCCEEEECC-CCCHHHHHHHHHHHHCCCCC-CHHHCCCCCHHHHHHHHHH
T ss_conf             99983798736899999999999965996799767-79989999999998538982-0111488899999999999


No 310
>pfam11731 Cdd1 Pathogenicity locus. Cdd1 is expressed as part of the pathogenicity locus operon in several different orders of bacteria. Many members of the family are annotated as being putative mitomycin resistance proteins but this could not be confirmed.
Probab=91.81  E-value=0.12  Score=32.38  Aligned_cols=39  Identities=18%  Similarity=0.178  Sum_probs=32.9

Q ss_pred             CCHHHCCCCCHHHHHHHHHHCCCCCCCCCCHHHHHHHCCCCCCCC
Q ss_conf             772136785889999988740124688554898787089740134
Q gi|254780945|r   11 APLSTFRGVGKKYSLFLSKIINCGNANETRFIDLLFYHPSSFIDR   55 (700)
Q Consensus        11 ~pI~~LkGVGpk~a~~L~kl~~l~~~GI~ti~DLL~~~PrrYeDr   55 (700)
                      +.++.|+||||++++-|..|      ||+++.||.-.=|..--++
T Consensus        12 ~~L~~lPnIG~a~a~DL~~L------Gi~~~~~L~g~dp~elY~~   50 (92)
T pfam11731        12 KELTDLPNIGKATAKDLRLL------GINSPAQLAGRDPLELYER   50 (92)
T ss_pred             HHHHCCCCCCHHHHHHHHHH------CCCCHHHHHCCCHHHHHHH
T ss_conf             98741897469999999991------8998999917999999999


No 311
>pfam05707 Zot Zonular occludens toxin (Zot). This family consists of bacterial and viral proteins which are very similar to the Zonular occludens toxin (Zot). Zot is elaborated by bacteriophages present in toxigenic strains of Vibrio cholerae. Zot is a single polypeptide chain of 44.8 kDa, with the ability to reversibly alter intestinal epithelial tight junctions, allowing the passage of macromolecules through mucosal barriers
Probab=91.77  E-value=0.24  Score=30.07  Aligned_cols=35  Identities=31%  Similarity=0.518  Sum_probs=28.8

Q ss_pred             CEEEEEECCCCCHHHHHHH-HHHHHHHHHCCEEEEE
Q ss_conf             3078862144223699999-9733444305458861
Q gi|254780945|r  294 MLRILQGDVGSGKTLVALI-AMAAAVEAGGQAVIMA  328 (700)
Q Consensus       294 M~RLLQGDVGSGKTiVA~~-A~l~~~~~G~Q~alMa  328 (700)
                      |--|+.|-=|||||.-|+- .+..++..|..++.=-
T Consensus         1 MI~litG~pGsGKS~~aV~~~i~~al~~GR~V~tNI   36 (183)
T pfam05707         1 MIYLITGKPGSGKTLEAVSYHILPALKKGRKVITNI   36 (183)
T ss_pred             CEEEEECCCCCCCCHHHHHHHHHHHHHCCCEEEECC
T ss_conf             979993599996229999999999987899899878


No 312
>PRK10536 hypothetical protein; Provisional
Probab=91.76  E-value=0.36  Score=28.76  Aligned_cols=142  Identities=18%  Similarity=0.195  Sum_probs=77.2

Q ss_pred             CCCCHHHHHHHHHHHHHHCCCCCCEEEEEECCCCCHHHHHHHHHHHHHHHHC-C-EEEEEHHHHHHH-------HHHHHH
Q ss_conf             4679889999999998410013430788621442236999999733444305-4-588612799999-------999862
Q gi|254780945|r  271 FSPTKSQESAIKDILQDMSQKNRMLRILQGDVGSGKTLVALIAMAAAVEAGG-Q-AVIMAPIGILAQ-------QHYEFI  341 (700)
Q Consensus       271 F~LT~~Q~~ai~eI~~Dl~~~~pM~RLLQGDVGSGKTiVA~~A~l~~~~~G~-Q-~alMaPTEILA~-------QH~~~~  341 (700)
                      +.-|..|++.++.|.+.     . .-...|--|||||.+|+.+++..+..+. . ..+.=|+---.+       -..+.+
T Consensus        58 ~pkt~~Q~~yi~~i~~~-----~-ivf~~GpAGTGKT~lA~a~Al~~l~~~~~~kIIltRP~V~~ge~lGfLPGdl~EK~  131 (262)
T PRK10536         58 LARNEAQLHYLKAIESK-----Q-LIFATGEAGCGKTWISAAKAAEALIHKDVDRIIVTRPVLQADEDLGFLPGDIAEKF  131 (262)
T ss_pred             CCCCHHHHHHHHHHHHC-----C-EEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCCCCCCCCCHHHHH
T ss_conf             78986499999998619-----8-39998999875899999999999985888689996678756766676989879988


Q ss_pred             HHHCCCCCCEEEEEECCCCHHHHHHHHHHHCCCCCEEEEECHHHCCCCCCCCCCCEEEECCCCCCCHHHHHHHH-HCCCC
Q ss_conf             11014578658996246422566768776213475486411120133455444417885210133568899874-02567
Q gi|254780945|r  342 KKYTQNTQIIVEIITGNMPQAHRRKALERIAHGQAHIIIGTHALFQDSIQYYKLILVIVDEQHRFGVQQRLKLT-QKATA  420 (700)
Q Consensus       342 ~~~~~~~~i~v~lLtg~~~~~er~~i~~~i~~G~~~iiIGTHAL~q~~v~F~~LgLvViDEQHRFGV~QR~~L~-~Kg~~  420 (700)
                      ..|+.++--...-+.|.    +..+-+..-..|.+.+  -.-|-+ .+-.|+| ..||+||=+-.-.+|=..+. .-|.+
T Consensus       132 ~Pyl~Pi~D~L~~~lg~----~~~~~~~~~e~G~Iei--~Plafm-RGrTf~n-a~IIvDEaQN~T~~qmk~iLTRiG~~  203 (262)
T PRK10536        132 APYFRPVYDVLVRRLGA----SFMQYCLRPEIGKVEI--APFAYM-RGRTFEN-AVVILDEAQNVTAAQMKMFLTRLGEN  203 (262)
T ss_pred             HHHHHHHHHHHHHHHCH----HHHHHHHHHHCCCEEE--EEHHHH-CCCCCCC-EEEEEEHHHCCCHHHHHHHHHHCCCC
T ss_conf             78887899999999685----9999998730594899--875874-4775144-28998412128999998898542599


Q ss_pred             CCCEEE
Q ss_conf             761010
Q gi|254780945|r  421 PHVLLM  426 (700)
Q Consensus       421 ph~L~M  426 (700)
                      .-+.++
T Consensus       204 SKiVi~  209 (262)
T PRK10536        204 VTVIVN  209 (262)
T ss_pred             CEEEEE
T ss_conf             689996


No 313
>pfam05496 RuvB_N Holliday junction DNA helicase ruvB N-terminus. The RuvB protein makes up part of the RuvABC revolvasome which catalyses the resolution of Holliday junctions that arise during genetic recombination and DNA repair. Branch migration is catalysed by the RuvB protein that is targeted to the Holliday junction by the structure specific RuvA protein. This family contains the N-terminal region of the protein.
Probab=91.75  E-value=1.2  Score=24.75  Aligned_cols=20  Identities=25%  Similarity=0.350  Sum_probs=16.4

Q ss_pred             EEEECCCCCCCHHHHHHHHH
Q ss_conf             78852101335688998740
Q gi|254780945|r  397 LVIVDEQHRFGVQQRLKLTQ  416 (700)
Q Consensus       397 LvViDEQHRFGV~QR~~L~~  416 (700)
                      ++.|||=|||.=.|-..|..
T Consensus       104 ILFIDEIHr~nK~qqd~Llp  123 (234)
T pfam05496       104 VLFIDEIHRLNRAVEEILYP  123 (234)
T ss_pred             EEEEECHHHCCHHHHHHCCC
T ss_conf             89996654358768874455


No 314
>cd01120 RecA-like_NTPases RecA-like NTPases. This family includes the NTP binding domain of F1 and V1 H+ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. This group also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion.
Probab=91.74  E-value=0.72  Score=26.41  Aligned_cols=46  Identities=26%  Similarity=0.268  Sum_probs=35.9

Q ss_pred             EEEEECCCCCHHHHHHHHHHHHHHHHCCEEEEEHHHHHHHHHHHHHH
Q ss_conf             78862144223699999973344430545886127999999998621
Q gi|254780945|r  296 RILQGDVGSGKTLVALIAMAAAVEAGGQAVIMAPIGILAQQHYEFIK  342 (700)
Q Consensus       296 RLLQGDVGSGKTiVA~~A~l~~~~~G~Q~alMaPTEILA~QH~~~~~  342 (700)
                      -|+-|+-|||||..++-.+..+...|..++++.- |--.+|-+..+.
T Consensus         2 ~li~g~~g~GKttl~~~~~~~~~~~~~~~~~~~~-ee~~~q~~~~~~   47 (165)
T cd01120           2 ILVFGPTGSGKTTLALQLALNIATKGGKVVYVDI-EEEIEELTERLI   47 (165)
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHHCCCEEEEEEC-CCCHHHHHHHHH
T ss_conf             8999899998999999999998763997999986-664489999999


No 315
>PRK04195 replication factor C large subunit; Provisional
Probab=91.65  E-value=1.2  Score=24.67  Aligned_cols=17  Identities=41%  Similarity=0.477  Sum_probs=14.7

Q ss_pred             EEEEECCCCCHHHHHHH
Q ss_conf             78862144223699999
Q gi|254780945|r  296 RILQGDVGSGKTLVALI  312 (700)
Q Consensus       296 RLLQGDVGSGKTiVA~~  312 (700)
                      =||.|-=|+|||-.|-+
T Consensus        43 lLL~GPpGvGKTT~a~~   59 (403)
T PRK04195         43 LLLYGPPGVGKTSLAHA   59 (403)
T ss_pred             EEEECCCCCCHHHHHHH
T ss_conf             99889399879999999


No 316
>TIGR02236 recomb_radA DNA repair and recombination protein RadA; InterPro: IPR011938   This family consists exclusively of archaeal RadA protein, a homolog of bacterial RecA, eukaryotic RAD51 (IPR011941 from INTERPRO), and archaeal RadB (IPR011939 from INTERPRO). This protein is involved in DNA repair and recombination. The member from Pyrococcus horikoshii contains an intein .; GO: 0003684 damaged DNA binding, 0005524 ATP binding, 0008094 DNA-dependent ATPase activity, 0006281 DNA repair, 0006310 DNA recombination.
Probab=91.62  E-value=0.11  Score=32.74  Aligned_cols=101  Identities=17%  Similarity=0.114  Sum_probs=52.6

Q ss_pred             CHHHCCCCCHHHHHHHHHHCCCCCCCCCCHHHHHHHCCCCCCCCCCCCCHHHCCCC------CEEEEEEEEEEEEEECCC
Q ss_conf             72136785889999988740124688554898787089740134444647888998------789999999897542158
Q gi|254780945|r   12 PLSTFRGVGKKYSLFLSKIINCGNANETRFIDLLFYHPSSFIDRHYRPKISEISEE------RIVTITGYISQHSSFQLQ   85 (700)
Q Consensus        12 pI~~LkGVGpk~a~~L~kl~~l~~~GI~ti~DLL~~~PrrYeDr~~~~~I~~l~~g------~~vti~g~V~~~~~~~~~   85 (700)
                      .|+.||||||+||++|..-      |-.|+.++=.==|.---+-..+   ++..--      ..+.=.+...+-..+.-+
T Consensus         1 ~ledLPGVGp~TA~KL~Ea------Gy~t~~~iA~A~~~EL~~~~gI---~E~~A~kiI~AAR~a~~~~~F~~a~~vl~r   71 (333)
T TIGR02236         1 DLEDLPGVGPATAEKLREA------GYDTLEAIAVASPKELSEIAGI---GEGTAAKIIQAARKAADLGGFETADDVLER   71 (333)
T ss_pred             CCCCCCCCCHHHHHHHHHH------HHHHHHHHHCCCHHHHHHHCCC---CHHHHHHHHHHHHHHHCCCCCHHHHHHHHH
T ss_conf             9665789757688998861------0788999844585795320378---777899999999998467672148999998


Q ss_pred             CCCEEEEEEE----C-------CCCEEEEEE--ECCCHHHHHHHCCCCC
Q ss_conf             9833899998----1-------893699999--5188789987328988
Q gi|254780945|r   86 KRRPYKILLN----D-------GTGEITLLF--FYRKTEMLKNVFFEGR  121 (700)
Q Consensus        86 ~r~~~~v~v~----D-------~tg~i~lvf--Fn~~~~yl~k~lk~G~  121 (700)
                      |+...+++-.    |       +|..|+=+|  |..+..++.-+|.++-
T Consensus        72 R~~v~kitTgs~~LDeLLGGGiETqaiTE~~GEFGSGKTQ~~HqLAVnV  120 (333)
T TIGR02236        72 RKSVGKITTGSKELDELLGGGIETQAITEVFGEFGSGKTQICHQLAVNV  120 (333)
T ss_pred             HHCCCEEECCCHHHHHHCCCCCCCEEEEEEEEEECCCHHHHHHHHHHHH
T ss_conf             7207504448636765607960000588877100786578766765532


No 317
>PRK02983 lysS lysyl-tRNA synthetase; Provisional
Probab=91.48  E-value=1.2  Score=24.54  Aligned_cols=117  Identities=13%  Similarity=0.092  Sum_probs=74.5

Q ss_pred             HHHHHHHHHHCCCCCCCCCCHHHHHHHCCCCCCCCCCCCCHHHCCCCCEEEEEEEEEEEEEECCCCCCEEEEEEECCCCE
Q ss_conf             89999988740124688554898787089740134444647888998789999999897542158983389999818936
Q gi|254780945|r   21 KKYSLFLSKIINCGNANETRFIDLLFYHPSSFIDRHYRPKISEISEERIVTITGYISQHSSFQLQKRRPYKILLNDGTGE  100 (700)
Q Consensus        21 pk~a~~L~kl~~l~~~GI~ti~DLL~~~PrrYeDr~~~~~I~~l~~g~~vti~g~V~~~~~~~~~~r~~~~v~v~D~tg~  100 (700)
                      +...-.++|+..+-..|+       --||.++.--..+..+.+..+|+.|++.|.|.....    -+...=+.+.|.+|.
T Consensus       618 eq~rvr~~k~~~l~~~g~-------~pypv~~~RTHT~~e~~~~~~G~~VtvaGwV~r~RD----hGgl~FidLRD~~G~  686 (1099)
T PRK02983        618 EQVRVRLAKLDALRESGV-------DAYPVGRPPSHTVAQALAAPDGEEVSVSGRVLRIRD----YGGVLFAQLRDWSGE  686 (1099)
T ss_pred             HHHHHHHHHHHHHHHCCC-------CCCCCCCCCCCCHHHHCCCCCCCEEEEEEEEEEEEC----CCCEEEEEEEECCCC
T ss_conf             999999999999997599-------999999999741666424799998999987999843----788699997418876


Q ss_pred             EEEEEECCC-----HHHHHHHCCCCCEEEEEEEEEE-CCCEEEEECCEEEECCC
Q ss_conf             999995188-----7899873289888999989973-18779997786896264
Q gi|254780945|r  101 ITLLFFYRK-----TEMLKNVFFEGRKITVTGKIKK-LKNRIIMVHPHYIFHNS  148 (700)
Q Consensus       101 i~lvfFn~~-----~~yl~k~lk~G~~v~vsGKv~~-~~~~~qi~hPe~~~~~~  148 (700)
                      +++++=...     ....++.+..|+.+.+.|++.. ..|.+++.--++++...
T Consensus       687 iQvv~~~d~~g~~~~~~~~~~vdlGDvI~V~G~V~~t~tGEisV~a~~~~vlsK  740 (1099)
T PRK02983        687 LQVLLDNSRLGQGRLADFTAAVDLGDLIEATGTMGASRNGTPSLLVTSWRLIGK  740 (1099)
T ss_pred             EEEEEECCCCCHHHHHHHHHHCCCCCEEEEEEEEECCCCCCEEEEEEEEEEEEC
T ss_conf             799997775676899998762577887999858862789845799748998404


No 318
>pfam04076 BOF Bacterial OB fold (BOF) protein. Proteins in this family form an OB-fold. Analysis of the predicted binding site of BOF family proteins implies that they lack nucleic acid-binding properties. They contain an predicted N-terminal signal peptide which indicates that they localize in the periplasm where they may function to bind proteins, small molecules, or other typical OB-fold ligands. As hypothesized for the distantly related OB-fold containing bacterial enterotoxins, the loss of nucleotide-binding function and the rapid evolution of the BOF ligand-binding site may be associated with the presence of BOF proteins in mobile genetic elements and their potential role in bacterial pathogenicity.
Probab=91.28  E-value=1.3  Score=24.40  Aligned_cols=73  Identities=15%  Similarity=0.154  Sum_probs=52.4

Q ss_pred             CCHHHCCCCCEEEEEEEEEEEEEECCCCCCEEEEEEECCCCEEEEEEECCCHHHHHHHCCCCCEEEEEEEEEECCCEEEE
Q ss_conf             64788899878999999989754215898338999981893699999518878998732898889999899731877999
Q gi|254780945|r   59 PKISEISEERIVTITGYISQHSSFQLQKRRPYKILLNDGTGEITLLFFYRKTEMLKNVFFEGRKITVTGKIKKLKNRIIM  138 (700)
Q Consensus        59 ~~I~~l~~g~~vti~g~V~~~~~~~~~~r~~~~v~v~D~tg~i~lvfFn~~~~yl~k~lk~G~~v~vsGKv~~~~~~~qi  138 (700)
                      ....++.++..|++.|.|++.-    +.   =...+.|+||.|.+-.=+.  -|--....+.+.|.++|++....     
T Consensus        49 ~~a~~~~Dd~~V~L~G~Iv~~l----~~---d~Y~F~D~TG~I~VeId~~--~w~G~~v~p~~kVrI~GevDk~~-----  114 (126)
T pfam04076        49 KQAKSAADDAWVSLEGNIVRQI----GD---DEYEFRDASGTIKVDIDDR--VWNGQEVQPKDKVKITGEVDKDL-----  114 (126)
T ss_pred             HHHHHCCCCCCEEEEEEEEEEE----CC---CEEEEECCCCCEEEEECHH--HCCCCCCCCCCEEEEEEEECCCC-----
T ss_conf             9886587999399988999684----89---5389978996399996888--83898179999899999994788-----


Q ss_pred             ECCEEEE
Q ss_conf             7786896
Q gi|254780945|r  139 VHPHYIF  145 (700)
Q Consensus       139 ~hPe~~~  145 (700)
                      ..|++.+
T Consensus       115 ~~~eIdV  121 (126)
T pfam04076       115 NKAEIDV  121 (126)
T ss_pred             CCEEEEE
T ss_conf             8717988


No 319
>COG3743 Uncharacterized conserved protein [Function unknown]
Probab=91.21  E-value=0.17  Score=31.28  Aligned_cols=29  Identities=21%  Similarity=0.405  Sum_probs=25.5

Q ss_pred             CCHHHCCCCCHHHHHHHHHHCCCCCCCCCCHHHHH
Q ss_conf             77213678588999998874012468855489878
Q gi|254780945|r   11 APLSTFRGVGKKYSLFLSKIINCGNANETRFIDLL   45 (700)
Q Consensus        11 ~pI~~LkGVGpk~a~~L~kl~~l~~~GI~ti~DLL   45 (700)
                      ++|+.|+||||+.++.|+.+      ||+|.-++-
T Consensus        67 DDLt~I~GIGPk~e~~Ln~~------GI~tfaQIA   95 (133)
T COG3743          67 DDLTRISGIGPKLEKVLNEL------GIFTFAQIA   95 (133)
T ss_pred             CCCHHHCCCCHHHHHHHHHC------CCCCHHHHH
T ss_conf             54211004378899899874------776399997


No 320
>smart00483 POLXc DNA polymerase X family. includes vertebrate polymerase beta and terminal deoxynucleotidyltransferases
Probab=91.18  E-value=0.19  Score=30.90  Aligned_cols=10  Identities=10%  Similarity=0.199  Sum_probs=5.5

Q ss_pred             CCCCCEEEEE
Q ss_conf             1347548641
Q gi|254780945|r  372 AHGQAHIIIG  381 (700)
Q Consensus       372 ~~G~~~iiIG  381 (700)
                      .+|.+||+|-
T Consensus       179 t~gDIDili~  188 (334)
T smart00483      179 TGHDVDFLIT  188 (334)
T ss_pred             CCCCEEEEEE
T ss_conf             6688128995


No 321
>PRK10416 cell division protein FtsY; Provisional
Probab=90.96  E-value=1.4  Score=24.20  Aligned_cols=170  Identities=17%  Similarity=0.185  Sum_probs=88.0

Q ss_pred             HCCCCCCEEEEEECCCCCHHHHHHHHHHHHHHHHCCEEEEEHHHHHHHHHHHHHHHHCCCCCCEEEEE-ECCCCHHHHHH
Q ss_conf             10013430788621442236999999733444305458861279999999986211014578658996-24642256676
Q gi|254780945|r  288 MSQKNRMLRILQGDVGSGKTLVALIAMAAAVEAGGQAVIMAPIGILAQQHYEFIKKYTQNTQIIVEII-TGNMPQAHRRK  366 (700)
Q Consensus       288 l~~~~pM~RLLQGDVGSGKTiVA~~A~l~~~~~G~Q~alMaPTEILA~QH~~~~~~~~~~~~i~v~lL-tg~~~~~er~~  366 (700)
                      +....|.--|+-|-=|||||--+.--+...-..|+.+.+-|- ..-=---.+.++.|-...++.+.-- +|+.+++--.+
T Consensus       290 ~~~~~P~VIl~vGvNG~GKTTTigKLA~~~~~~gkkVllaA~-DTfRaAAieQL~~w~~r~~v~vi~~~~g~Dpa~V~~d  368 (499)
T PRK10416        290 VEGKTPFVILMVGVNGVGKTTTIGKLARQFEQQGKSVMLAAG-DTFRAAAVEQLQVWGQRNNIPVIAQHTGADSASVIFD  368 (499)
T ss_pred             CCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHCCCCEEEEEE-CCCCHHHHHHHHHHHCCCCCEEEECCCCCCHHHHHHH
T ss_conf             689998799997478787898999999999977995378840-6675689999999842457369836899997999999


Q ss_pred             HHHHHCCCCCEEEEECHHHCCCCCCCCCCCEEEECCCCCCCHHHHH--------HHHHC--CCCCC--CEEECHHHHHHH
Q ss_conf             8776213475486411120133455444417885210133568899--------87402--56776--101010132278
Q gi|254780945|r  367 ALERIAHGQAHIIIGTHALFQDSIQYYKLILVIVDEQHRFGVQQRL--------KLTQK--ATAPH--VLLMTATPIPRT  434 (700)
Q Consensus       367 i~~~i~~G~~~iiIGTHAL~q~~v~F~~LgLvViDEQHRFGV~QR~--------~L~~K--g~~ph--~L~MtATPIPRT  434 (700)
                      .++..++..+|                   ++|||-=-|.-.++..        ....|  ...||  +|++-||-=--.
T Consensus       369 ai~~a~~~~~D-------------------vviiDTAGRl~~~~~LM~EL~ki~rvi~k~~~~aP~e~lLVlDa~tGQna  429 (499)
T PRK10416        369 AIQAAKARNVD-------------------VLIADTAGRLQNKSHLMEELKKIVRVMKKLDVEAPHEVMLTIDASTGQNA  429 (499)
T ss_pred             HHHHHHHCCCC-------------------EEEEECCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCEEEEEEECCCCHHH
T ss_conf             99999972999-------------------89985776432609999999999999972378999748999778767789


Q ss_pred             HHHHH-HHC-CCHHHHCCCCCCCCCCEEEEEECCCHHHHHHHHHHHHCCCCEEEEEE
Q ss_conf             99997-520-10111102355766620799970200268999976310387389997
Q gi|254780945|r  435 LVLTS-LGD-IDISKITEKPAGRKPIKTVIIPINRIDEVIERLKVVLSEGKKAYWIC  489 (700)
Q Consensus       435 Lal~~-ygd-ldvS~i~e~P~gR~~I~T~~~~~~~~~~~~~~i~~~l~~g~q~y~Vc  489 (700)
                      +..+- |.+ ++++         .-|.|++=+..+-. +.-.|...+.  --+++|.
T Consensus       430 ~~qak~F~e~~~lt---------GiIlTKlDGtAKGG-~~lsi~~~~~--~PI~fiG  474 (499)
T PRK10416        430 VSQAKLFHEAVGLT---------GITLTKLDGTAKGG-VIFSVADQFG--IPIRYIG  474 (499)
T ss_pred             HHHHHHHHHCCCCC---------EEEEECCCCCCCCH-HHHHHHHHHC--CCEEEEE
T ss_conf             99999984427997---------59996567788525-9999999988--3959986


No 322
>COG0467 RAD55 RecA-superfamily ATPases implicated in signal transduction [Signal transduction mechanisms]
Probab=90.69  E-value=0.51  Score=27.56  Aligned_cols=59  Identities=19%  Similarity=0.260  Sum_probs=42.0

Q ss_pred             HHHHHHHHCCCCCCEE--EEEECCCCCHHHHHHHHHHHHHHHHCCEEEEEHHHHHHHHHHHHHHH
Q ss_conf             9999984100134307--88621442236999999733444305458861279999999986211
Q gi|254780945|r  281 IKDILQDMSQKNRMLR--ILQGDVGSGKTLVALIAMAAAVEAGGQAVIMAPIGILAQQHYEFIKK  343 (700)
Q Consensus       281 i~eI~~Dl~~~~pM~R--LLQGDVGSGKTiVA~~A~l~~~~~G~Q~alMaPTEILA~QH~~~~~~  343 (700)
                      ++||..   .+.|+.+  |+.|.=|||||+-|+-.+...+.+|.-|.+.+- +-.+..-.+++..
T Consensus        12 lD~~l~---GG~p~g~~~lI~G~pGsGKT~f~~qfl~~~~~~ge~vlyvs~-~e~~~~l~~~~~~   72 (260)
T COG0467          12 LDEILG---GGLPRGSVVLITGPPGTGKTIFALQFLYEGAREGEPVLYVST-EESPEELLENARS   72 (260)
T ss_pred             HHHHHC---CCCCCCCEEEEEECCCCCHHHHHHHHHHHHHHCCCEEEEEEE-ECCHHHHHHHHHH
T ss_conf             888836---898899789999389986899999999977626985899992-0698999999988


No 323
>KOG0952 consensus
Probab=90.66  E-value=0.28  Score=29.60  Aligned_cols=31  Identities=16%  Similarity=0.261  Sum_probs=16.0

Q ss_pred             EEECCCCHHHHHHHHHHHCCCCCEEEEECHH
Q ss_conf             9624642256676877621347548641112
Q gi|254780945|r  354 IITGNMPQAHRRKALERIAHGQAHIIIGTHA  384 (700)
Q Consensus       354 lLtg~~~~~er~~i~~~i~~G~~~iiIGTHA  384 (700)
                      +-..++...+|.-.-...+.|.+.+++-|..
T Consensus       401 iHhAGm~r~DR~l~E~~F~~G~i~vL~cTaT  431 (1230)
T KOG0952         401 IHHAGMLRSDRQLVEKEFKEGHIKVLCCTAT  431 (1230)
T ss_pred             HCCCCCCHHHHHHHHHHHHCCCCEEEEECCE
T ss_conf             2025643146899999985598228996121


No 324
>COG1203 CRISPR-associated helicase Cas3 [Defense mechanisms]
Probab=90.64  E-value=1  Score=25.25  Aligned_cols=95  Identities=16%  Similarity=0.252  Sum_probs=68.9

Q ss_pred             HHHHHHHHCCEEEEEHHHHHHHHHHHHHHHHCCCCCCEEEEEECCCCHHHHHHHHHHHC----CCCCEEEEECHHHCC-C
Q ss_conf             73344430545886127999999998621101457865899624642256676877621----347548641112013-3
Q gi|254780945|r  314 MAAAVEAGGQAVIMAPIGILAQQHYEFIKKYTQNTQIIVEIITGNMPQAHRRKALERIA----HGQAHIIIGTHALFQ-D  388 (700)
Q Consensus       314 ~l~~~~~G~Q~alMaPTEILA~QH~~~~~~~~~~~~i~v~lLtg~~~~~er~~i~~~i~----~G~~~iiIGTHAL~q-~  388 (700)
                      ....+.+|..+++.+=|-=-|.--|+.++..-+    ++.||+|..+.+.|.+..+.+.    .+...|+|+|+.+=+ =
T Consensus       433 ~~~~~~~~~kvlvI~NTV~~Aie~Y~~Lk~~~~----~v~LlHSRf~~~dR~~ke~~l~~~~~~~~~~IvVaTQVIEagv  508 (733)
T COG1203         433 ISEEVKEGKKVLVIVNTVDRAIELYEKLKEKGP----KVLLLHSRFTLKDREEKERELKKLFKQNEGFIVVATQVIEAGV  508 (733)
T ss_pred             HHHHHCCCCCEEEEEECHHHHHHHHHHHHCCCC----CEEEEECCCCHHHHHHHHHHHHHHHHCCCCEEEEECCEEEEEE
T ss_conf             677642588289999278999999999855589----5799886355766999999998887537862999834599886


Q ss_pred             CCCCCCCCEEEECCC------CCCCHHHHHHHH
Q ss_conf             455444417885210------133568899874
Q gi|254780945|r  389 SIQYYKLILVIVDEQ------HRFGVQQRLKLT  415 (700)
Q Consensus       389 ~v~F~~LgLvViDEQ------HRFGV~QR~~L~  415 (700)
                      |+.|.   ++|.|=.      ||||=-+|..-.
T Consensus       509 Didfd---~mITe~aPidSLIQR~GRv~R~g~~  538 (733)
T COG1203         509 DIDFD---VLITELAPIDSLIQRAGRVNRHGKK  538 (733)
T ss_pred             CCCCC---EEEECCCCHHHHHHHHHHHHHCCCC
T ss_conf             26668---4663478756799987777415666


No 325
>pfam06745 KaiC KaiC. This family represents a conserved region within bacterial and archaeal proteins, most of which are hypothetical. More than one copy is sometimes found in each protein. This family includes KaiC, which is one of the Kai proteins among which direct protein-protein association may be a critical process in the generation of circadian rhythms in cyanobacteria.
Probab=90.62  E-value=0.5  Score=27.61  Aligned_cols=56  Identities=21%  Similarity=0.233  Sum_probs=36.6

Q ss_pred             HCCCCCCE--EEEEECCCCCHHHHHHHHHHH-HHHHHCCEEEEEHHHHHHHHHHHHHHHH
Q ss_conf             10013430--788621442236999999733-4443054588612799999999862110
Q gi|254780945|r  288 MSQKNRML--RILQGDVGSGKTLVALIAMAA-AVEAGGQAVIMAPIGILAQQHYEFIKKY  344 (700)
Q Consensus       288 l~~~~pM~--RLLQGDVGSGKTiVA~~A~l~-~~~~G~Q~alMaPTEILA~QH~~~~~~~  344 (700)
                      |..+.|-.  -|+.|+-|||||+-|+--++. +...|..|++..- |-=.+|..+++..+
T Consensus        12 l~GGi~~gs~~LI~G~pGsGKT~la~qfl~~ga~~~ge~~lYis~-ee~~~~l~~~~~~~   70 (231)
T pfam06745        12 LKGGIPEGRVVLITGGPGTGKTIFGLQFLYNGALEYGEPGVYVTL-EEPPEDLRENAKSF   70 (231)
T ss_pred             CCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEEE-CCCHHHHHHHHHHC
T ss_conf             169982996999985897259999999999999865896899981-37999999999982


No 326
>KOG0921 consensus
Probab=90.46  E-value=0.066  Score=34.55  Aligned_cols=332  Identities=22%  Similarity=0.291  Sum_probs=164.9

Q ss_pred             HHHHHHCCCCCCHHHHHHHHHHHHHHCCCCCCEEEEEECCCCCHHHHHHHHHHHHHHHHCCEE-----EEEHHHHHHHHH
Q ss_conf             999863024679889999999998410013430788621442236999999733444305458-----861279999999
Q gi|254780945|r  263 QKILRNIPFSPTKSQESAIKDILQDMSQKNRMLRILQGDVGSGKTLVALIAMAAAVEAGGQAV-----IMAPIGILAQQH  337 (700)
Q Consensus       263 ~~f~~~LPF~LT~~Q~~ai~eI~~Dl~~~~pM~RLLQGDVGSGKTiVA~~A~l~~~~~G~Q~a-----lMaPTEILA~QH  337 (700)
                      -++...||-    +|.+  ++|..-. ..++. -++-|..|||||--..--+|.++..+-|++     .--||.|-|.-.
T Consensus       371 ~a~re~lpv----a~~~--~~i~q~v-~dn~v-~~I~getgcgk~tq~aq~iLe~~~~ns~g~~~na~v~qprrisaisi  442 (1282)
T KOG0921         371 TAQREELPV----AQYR--SEILQAV-AENRV-VIIKGETGCGKSTQVAQFLLESFLENSNGASFNAVVSQPRRISAISL  442 (1282)
T ss_pred             HHHHHHCCH----HHHH--HHHHHHH-HCCCE-EEEEECCCCCCHHHHHHHHHHHHHHCCCCCCCCCEECCCCCCCHHHH
T ss_conf             622431768----8889--9999987-50750-46760236663147889999987622544200210026542111778


Q ss_pred             HHHHHH-HCCCCCC----EEEEEECCCCHHHHHHHHHHHCCCCCEEEEECH-HHC--CCCCCCCCCCEEEECCCCCCCHH
Q ss_conf             986211-0145786----589962464225667687762134754864111-201--33455444417885210133568
Q gi|254780945|r  338 YEFIKK-YTQNTQI----IVEIITGNMPQAHRRKALERIAHGQAHIIIGTH-ALF--QDSIQYYKLILVIVDEQHRFGVQ  409 (700)
Q Consensus       338 ~~~~~~-~~~~~~i----~v~lLtg~~~~~er~~i~~~i~~G~~~iiIGTH-AL~--q~~v~F~~LgLvViDEQHRFGV~  409 (700)
                      .+.+.+ .-+..+-    ++-.. +.++..++            .|..-|- -|+  -+.+-| -..++||||-|-|-|.
T Consensus       443 aerva~er~e~~g~tvgy~vRf~-Sa~prpyg------------~i~fctvgvllr~~e~glr-g~sh~i~deiherdv~  508 (1282)
T KOG0921         443 AERVANERGEEVGETCGYNVRFD-SATPRPYG------------SIMFCTVGVLLRMMENGLR-GISHVIIDEIHERDVD  508 (1282)
T ss_pred             HHHHHHHHHHHHCCCCCCCCCCC-CCCCCCCC------------CEEEECCCHHHHHHHHCCC-CCCCCCCHHHHHHCCC
T ss_conf             89887766776445323332212-24555433------------0232021055555440124-5442342033330230


Q ss_pred             HHHHHHHC------CCCCCCEEECHHHHHHHHHHHHHHCC-CH------------------HHHCCCCCCCCCCEEEEEE
Q ss_conf             89987402------56776101010132278999975201-01------------------1110235576662079997
Q gi|254780945|r  410 QRLKLTQK------ATAPHVLLMTATPIPRTLVLTSLGDI-DI------------------SKITEKPAGRKPIKTVIIP  464 (700)
Q Consensus       410 QR~~L~~K------g~~ph~L~MtATPIPRTLal~~ygdl-dv------------------S~i~e~P~gR~~I~T~~~~  464 (700)
                      --..|.--      ...-|+..|||| |--++-+.+|++. |+                  --+++.|..+-+.+-+...
T Consensus       509 ~dfll~~lr~m~~ty~dl~v~lmsat-IdTd~f~~~f~~~p~~~~~grt~pvq~F~led~~~~~~~vp~~~~~~k~k~~~  587 (1282)
T KOG0921         509 TDFVLIVLREMISTYRDLRVVLMSAT-IDTDLFTNFFSSIPDVTVHGRTFPVQSFFLEDIIQMTQFVPSEPSQKKRKKDD  587 (1282)
T ss_pred             HHHHHHHHHHHHCCCHHHHHHHHHCC-CCHHHHHHHHCCCCCEEECCCCCCHHHHHHHHHHHHHHCCCCCCCCCCHHHCC
T ss_conf             47899998764123114555322212-34045555521464135316655289999998630222057876731011034


Q ss_pred             CCCHHHHHHHHHHHHC-CCCEEEEEE-----CCC-------CC----------------CCCCCC---------CHHHHH
Q ss_conf             0200268999976310-387389997-----120-------12----------------211121---------014666
Q gi|254780945|r  465 INRIDEVIERLKVVLS-EGKKAYWIC-----PQI-------EE----------------KKESNF---------RSVVER  506 (700)
Q Consensus       465 ~~~~~~~~~~i~~~l~-~g~q~y~Vc-----PlI-------ee----------------se~~~~---------~~~~~~  506 (700)
                      .        +.....+ +|+-.=.+|     ..+       +|                |+.++-         .-+...
T Consensus       588 ~--------~~~~~~ddK~~n~n~~~dd~~~~~~~~am~~~se~d~~f~l~Eal~~~i~s~~i~gailvflpgwa~i~~L  659 (1282)
T KOG0921         588 D--------EEDEEVDDKGRNMNILCDPSYNESTRTAMSRLSEKDIPFGLIEALLNDIASRNIDGAVLVFLPGWAEIMTL  659 (1282)
T ss_pred             C--------CCCCHHHHCCCCCCCCCCHHHCCHHHHHHHCCHHHCCHHHHHHHHHHHHCCCCCCCCEEEECCCHHHHHHH
T ss_conf             5--------56750121134445544721051244565222010252578999875430347764023304744776643


Q ss_pred             HHHHH--HHCCC----CEECCCCCCCHHHHHHHHHHHHCCCEEEEEECHHHHCCCCCCCCCEEEE---------------
Q ss_conf             66668--66371----0312014699899999999975598699998003410468887658998---------------
Q gi|254780945|r  507 FNSLH--EHFTS----SIAIIHGRMSDIDKESVMDSFKNGTCKLLIATTVIEVGIDVVDASIIII---------------  565 (700)
Q Consensus       507 ~~~l~--~~~~~----~v~~lHGkm~~~ek~~~m~~F~~g~~~iLvaTtviEVGvdvpna~~mvI---------------  565 (700)
                      ..++.  ..|++    .+--+|.+...+|.-++.+.--.|..||+++|.+.|.-+.+-+.+-+++               
T Consensus       660 ~~~ll~~~~fg~~~~y~ilp~Hsq~~~~eqrkvf~~~p~gv~kii~stniaetsiTidd~v~vid~cka~~~~~~s~nn~  739 (1282)
T KOG0921         660 CNRLLEHQEFGQANKYEILPLHSQLTSQEQRKVFEPVPEGVTKIILSTNIAETSITIDDVVYVIDSCKAKEKLFTSHNNM  739 (1282)
T ss_pred             HHHHHHHHHHCCCHHCCCCCCHHHCCCHHHHHCCCCCCCCCCCCCCCCCEEEEEEEECCEEEEEEEEEEEEEEECCCCCE
T ss_conf             31344433321210034665022014476641367554556540134533667642045068875200111121044320


Q ss_pred             -----ECHHHCCHHHHHHHHHCCCCCCCCEEEEEEECCCCCHHHHHHHHHHHHHCH---------HHHHHHHHHHHCCCC
Q ss_conf             -----585254746887730116678983599997088899879999999984142---------589999998520630
Q gi|254780945|r  566 -----ENAEHFGLAQLHQLRGRVGRGEEISSCILLYHPPLSKNSYTRLSVLKNTED---------GFLIAEEDLKQRKEG  631 (700)
Q Consensus       566 -----~~aerfGLsqLHQLRGRVGRg~~~s~c~l~~~~~~~~~~~~Rl~~l~~~~d---------Gf~iAe~Dl~lRG~G  631 (700)
                           .+|..+-   +-|-+||-|| -.+|+|+-++       ++-|++++...-+         --.+.-+-|.+-.-|
T Consensus       740 ~~~Atvw~sktn---~eqr~gr~gr-vR~G~~f~lc-------s~arF~~l~~~~t~em~r~plhemalTikll~l~SI~  808 (1282)
T KOG0921         740 THYATVWASKTN---LEQRKGRAGR-VRPGFCFHLC-------SRARFEALEDHGTAEMFRTPLHEIALTIKLLRLGSIG  808 (1282)
T ss_pred             EEEEEECCCCCC---HHHHCCCCCE-ECCCCCCCCC-------HHHHHHHHHHCCCHHHHCCCCHHHHHHHHHHHHHHHH
T ss_conf             344552266430---6764266741-3566231210-------7899999876176766257208888667787763488


Q ss_pred             CCCCC
Q ss_conf             00260
Q gi|254780945|r  632 EILGI  636 (700)
Q Consensus       632 ~~~G~  636 (700)
                      .+++.
T Consensus       809 ~fl~k  813 (1282)
T KOG0921         809 EFLGK  813 (1282)
T ss_pred             HHHHH
T ss_conf             99860


No 327
>PTZ00205 DNA polymerase kappa; Provisional
Probab=90.46  E-value=0.22  Score=30.37  Aligned_cols=18  Identities=11%  Similarity=0.102  Sum_probs=11.3

Q ss_pred             HHHHHHHHHHHHHHHHHH
Q ss_conf             000045430013457874
Q gi|254780945|r  164 TGLSVDLFKKIIVEALSR  181 (700)
Q Consensus       164 ~GLsqk~irk~I~~aL~~  181 (700)
                      +|+.+.++.++|.++=+-
T Consensus        54 ~~VDk~Kv~~II~eaSKG   71 (571)
T PTZ00205         54 GNVDKERVEAIIRNVSEG   71 (571)
T ss_pred             CHHHHHHHHHHHHHHCCC
T ss_conf             114399999999985478


No 328
>TIGR02782 TrbB_P P-type conjugative transfer ATPase TrbB; InterPro: IPR014149   This entry represents TrbB, a protein, which is encoded in the trb locus of Agrobacterium Ti plasmids where it is involved in the type IV secretion system for plasmid conjugative transfer . TrbB is a homologue of the vir system VirB11 ATPase , and the Flp pilus system ATPase TadA ..
Probab=90.45  E-value=0.32  Score=29.16  Aligned_cols=39  Identities=28%  Similarity=0.371  Sum_probs=32.0

Q ss_pred             CCCHHHHHHHHHHHHHHCCCCCCEEEEEECCCCCHHHHHHHHHH
Q ss_conf             67988999999999841001343078862144223699999973
Q gi|254780945|r  272 SPTKSQESAIKDILQDMSQKNRMLRILQGDVGSGKTLVALIAMA  315 (700)
Q Consensus       272 ~LT~~Q~~ai~eI~~Dl~~~~pM~RLLQGDVGSGKTiVA~~A~l  315 (700)
                      -+|.+|..++.+-..     ..||-|+-|=.|||||=-|=+-+.
T Consensus       123 imtaaQ~d~l~~Av~-----ar~NIlv~GGTGSGKTTLaNAlla  161 (315)
T TIGR02782       123 IMTAAQRDVLREAVA-----ARKNILVVGGTGSGKTTLANALLA  161 (315)
T ss_pred             CCCHHHHHHHHHHHH-----HCCCEEEECCCCCCHHHHHHHHHH
T ss_conf             455789999999997-----129889981458857999999999


No 329
>pfam10391 DNA_pol_lambd_f Fingers domain of DNA polymerase lambda. DNA polymerases catalyse the addition of dNMPs onto the 3-prime ends of DNA chains. There is a general polymerase fold consisting of three subdomains that have been likened to the fingers, palm, and thumb of a right hand. DNA_pol_lambd_f is the central three-helical region of DNA polymerase lambda referred to as the F and G helices of the fingers domain. Contacts with DNA involve this conserved helix-hairpin-helix motif in the fingers region which interacts with the primer strand. This motif is common to several DNA binding proteins and confers a sequence-independent interaction with the DNA backbone.
Probab=90.36  E-value=0.25  Score=29.94  Aligned_cols=28  Identities=21%  Similarity=0.165  Sum_probs=23.9

Q ss_pred             HHHCCCCCHHHHHHHHHHCCCCCCCCCCHHHHHH
Q ss_conf             2136785889999988740124688554898787
Q gi|254780945|r   13 LSTFRGVGKKYSLFLSKIINCGNANETRFIDLLF   46 (700)
Q Consensus        13 I~~LkGVGpk~a~~L~kl~~l~~~GI~ti~DLL~   46 (700)
                      .+.+-||||++|+.+-..      ||.|+.||--
T Consensus         4 f~~I~GvGp~~A~~~~~~------G~~ti~dL~~   31 (52)
T pfam10391         4 FTNIWGVGPKTARKWYRQ------GIRTLEDLRE   31 (52)
T ss_pred             HHHCCCCCHHHHHHHHHH------CCCCHHHHHH
T ss_conf             663544069999999994------7888999974


No 330
>PRK08506 replicative DNA helicase; Provisional
Probab=90.35  E-value=1.5  Score=23.79  Aligned_cols=73  Identities=15%  Similarity=0.181  Sum_probs=52.5

Q ss_pred             EEEECCCCCHHHHHHHHHHHHHHHHCCEEEEEHHHHHHHHHHHHHHHHCCCCCCEEEEEECCCCHHHHHHHHHHH
Q ss_conf             886214422369999997334443054588612799999999862110145786589962464225667687762
Q gi|254780945|r  297 ILQGDVGSGKTLVALIAMAAAVEAGGQAVIMAPIGILAQQHYEFIKKYTQNTQIIVEIITGNMPQAHRRKALERI  371 (700)
Q Consensus       297 LLQGDVGSGKTiVA~~A~l~~~~~G~Q~alMaPTEILA~QH~~~~~~~~~~~~i~v~lLtg~~~~~er~~i~~~i  371 (700)
                      .|=|=-|.|||..|+--+..++..|+-|+|..- |.=++|....+-......+. -.+-+|.++..+...+....
T Consensus       197 IIAARPsmGKTAfAlniA~~~a~~~~~V~~FSL-EMs~~ql~~Rlls~~s~V~~-~~lr~g~l~~~e~~~~~~a~  269 (473)
T PRK08506        197 IIAARPSMGKTTLVLNMVLKALNQGKGVAFFSL-EMPAEQLMLRMLSAKTSIPL-QNLRTGDLDDDEWENLSDAC  269 (473)
T ss_pred             EEECCCCCCHHHHHHHHHHHHHHCCCCEEEEEC-CCCHHHHHHHHHHHHCCCCC-CCCCCCCCCHHHHHHHHHHH
T ss_conf             995079986789999999999965996589822-47999999999997288783-10006899999999999999


No 331
>TIGR02538 type_IV_pilB type IV-A pilus assembly ATPase PilB; InterPro: IPR013374    This model describes a protein involved in type IV pilus biogenesis designated PilB in Pseudomonas aeruginosa but PilF in Neisseria gonorrhoeae; the more common usage, reflected here, is PilB. This protein is an ATPase involved in protein export for pilin assembly, and is closely related to GspE (IPR013369 from INTERPRO) of type II secretion systems (also referred to as the main terminal branch of the general secretion pathway). Note that type IV pilus systems are often divided into type IV-A and IV-B, with the latter group including bundle-forming pilus, mannose-sensitive hemagglutinin, etc. Members of this family are found in type IV-A systems.; GO: 0005524 ATP binding, 0008565 protein transporter activity, 0009297 pilus biogenesis.
Probab=90.30  E-value=0.28  Score=29.67  Aligned_cols=133  Identities=19%  Similarity=0.310  Sum_probs=68.5

Q ss_pred             HHHHHHHHHHHHH-HCCC-CCCCCHHHHHCCCCCCHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-
Q ss_conf             5430013457874-0468-433897786205699988999862045896565667999999987666666677776555-
Q gi|254780945|r  169 DLFKKIIVEALSR-LPVL-PEWIEKDLLQKKSFPSIAEAFNIIHNPRKAKDFEWTSPARERLAYDELLAGQIALLLMRK-  245 (700)
Q Consensus       169 k~irk~I~~aL~~-~~~i-~E~LP~~ll~k~~L~s~~eAL~~IH~P~~~~dle~~~~ArkRLafeELl~~QL~l~~~r~-  245 (700)
                      |.+.++.-.|+.. ...+ -|+....++-+|.-=..   |+.+=.|+..  +...-.|  |+|-=    -+|=...+|- 
T Consensus       193 KFvN~iL~DAir~GASDIHFEPYE~~yRvRyR~DG~---L~Eva~PP~~--l~~ri~a--RiKvM----S~LDIaEkR~P  261 (577)
T TIGR02538       193 KFVNKILLDAIRKGASDIHFEPYEKKYRVRYRIDGV---LHEVAQPPLK--LANRIAA--RIKVM----SRLDIAEKRIP  261 (577)
T ss_pred             HHHHHHHHHHHHCCCCCCCCCCCCCCCEEEEEECCE---EHHHHCCCHH--HHHHHHH--HHHHH----HCCCCCCCCCC
T ss_conf             338787999984688612113676872067511673---1643258588--9999998--99997----32671224568


Q ss_pred             -------HHHHCCCCCCCCC----------------CHHHHHHHHHCCCCCCHHHHHHHHHHHHHHCCCCCCEEEEEECC
Q ss_conf             -------5432035767877----------------57899998630246798899999999984100134307886214
Q gi|254780945|r  246 -------QFKKEIGIPINVE----------------GKIAQKILRNIPFSPTKSQESAIKDILQDMSQKNRMLRILQGDV  302 (700)
Q Consensus       246 -------~~~~~~~~~~~~~----------------~~~~~~f~~~LPF~LT~~Q~~ai~eI~~Dl~~~~pM~RLLQGDV  302 (700)
                             +..+.++.=|..+                ++-.+-=+..|.|+.  +|++-+-   +-+++|+=|- |+=|=.
T Consensus       262 QDGRiKl~~sk~k~iDFRVStLPTLfGEKvVLRiLDsS~a~Ldi~~LGFeP--~Qk~~fL---~Ai~kPqGMv-LVTGPT  335 (577)
T TIGR02538       262 QDGRIKLKLSKSKAIDFRVSTLPTLFGEKVVLRILDSSAAKLDIDKLGFEP--DQKALFL---EAIHKPQGMV-LVTGPT  335 (577)
T ss_pred             CCCCEEEEECCCEEEEEEECCCCCCCCCEEEEEEECHHHCCCCCHHHCCCH--HHHHHHH---HHHHCCCCCE-EEECCC
T ss_conf             787367753784455125378742024446677655221226742206888--8999999---9970799728-862665


Q ss_pred             CCCHHHHHHHHHHHHHH
Q ss_conf             42236999999733444
Q gi|254780945|r  303 GSGKTLVALIAMAAAVE  319 (700)
Q Consensus       303 GSGKTiVA~~A~l~~~~  319 (700)
                      |||||+ .+.++|+-+.
T Consensus       336 GSGKTV-SLYTaLniLN  351 (577)
T TIGR02538       336 GSGKTV-SLYTALNILN  351 (577)
T ss_pred             CCCHHH-HHHHHHCCCC
T ss_conf             984168-7876311257


No 332
>cd03769 SR_IS607_transposase_like Serine Recombinase (SR) family, IS607-like transposase subfamily, catalytic domain; members contain a DNA binding domain with homology to MerR/SoxR located N-terminal to the catalytic domain. Serine recombinases catalyze site-specific recombination of DNA molecules by a concerted, four-strand cleavage and rejoining mechanism which involves a transient phosphoserine linkage between DNA and the enzyme. They are functionally versatile and include resolvases, invertases, integrases, and transposases. This subfamily is composed of proteins that catalyze the transposition of insertion sequence (IS) elements such as IS607 from Helicobacter and IS1535 from Mycobacterium, and similar proteins from other bacteria and several archaeal species. IS elements are DNA segments that move to new sites in prokaryotic and eukaryotic genomes causing insertion mutations and gene rearrangements.
Probab=90.16  E-value=1.6  Score=23.68  Aligned_cols=93  Identities=16%  Similarity=0.224  Sum_probs=66.6

Q ss_pred             HHHHHHHHHHHHHHCCCCCCEEEEEECCCCCHHHH--HHHHHHHHHHHHC-CEEEEEHHHHHHHHHHHHHHHHCCCCCCE
Q ss_conf             88999999999841001343078862144223699--9999733444305-45886127999999998621101457865
Q gi|254780945|r  275 KSQESAIKDILQDMSQKNRMLRILQGDVGSGKTLV--ALIAMAAAVEAGG-QAVIMAPIGILAQQHYEFIKKYTQNTQII  351 (700)
Q Consensus       275 ~~Q~~ai~eI~~Dl~~~~pM~RLLQGDVGSGKTiV--A~~A~l~~~~~G~-Q~alMaPTEILA~QH~~~~~~~~~~~~i~  351 (700)
                      ..|...+.+-...-  ..  .-=+--|+|||.+.-  .+..++..+.+|. .+.+..--.=|++-+|+-+..+|..+|++
T Consensus        17 ~~Q~~~l~~~~~~~--g~--~~~i~~D~gSG~~~~Rp~l~~Ll~~~~~g~v~~vvV~~~DRL~Rfg~elle~~~~~~gv~   92 (134)
T cd03769          17 ERQIERLEAYATAQ--GW--IVEVIKDIGSGLNEKRKGLLKLLEDVLAGKVERVVITYKDRLARFGFELLEELFKAYGVE   92 (134)
T ss_pred             HHHHHHHHHHHHHC--CC--EEEEEEECCCCCCCCHHHHHHHHHHHHCCCCCEEEEEECCHHHHHHHHHHHHHHHHCCCE
T ss_conf             99999999999955--98--259998567776603589999999997389878999855577876899999999986988


Q ss_pred             EEEEECCCCHHHHHHHHHHH
Q ss_conf             89962464225667687762
Q gi|254780945|r  352 VEIITGNMPQAHRRKALERI  371 (700)
Q Consensus       352 v~lLtg~~~~~er~~i~~~i  371 (700)
                      +..+....+.....+..+++
T Consensus        93 iivin~~~~~~~~~EL~eDl  112 (134)
T cd03769          93 IVVINQEENEELEQELVEDL  112 (134)
T ss_pred             EEEEECCCCCCHHHHHHHHH
T ss_conf             99997998998689999999


No 333
>cd00141 NT_POLXc Nucleotidyltransferase (NT) domain of family X DNA Polymerases. X family polymerases fill in short gaps during DNA repair. They are relatively inaccurate enzymes and play roles in base excision repair, in non-homologous end joining (NHEJ) which acts mainly to repair damage due to ionizing radiation, and in V(D)J recombination. This family includes eukaryotic Pol beta, Pol lambda, Pol mu, and terminal deoxyribonucleotidyl transferase (TdT). Pol beta and Pol lambda are primarily DNA template-dependent polymerases. TdT is a DNA template-independent polymerase. Pol mu has both template dependent and template independent activities. This subgroup belongs to the Pol beta-like NT superfamily. In the majority of enzymes in this superfamily, two carboxylates, Dx[D/E], together with a third more distal carboxylate, coordinate two divalent metal cations involved in a two-metal ion mechanism of nucleotide addition. These three carboxylate residues are fairly well conserved in this
Probab=90.14  E-value=0.27  Score=29.70  Aligned_cols=29  Identities=28%  Similarity=0.316  Sum_probs=13.4

Q ss_pred             HHHHHHHHHHHHHCHHHHHHHHHHHHCCCC
Q ss_conf             879999999984142589999998520630
Q gi|254780945|r  602 KNSYTRLSVLKNTEDGFLIAEEDLKQRKEG  631 (700)
Q Consensus       602 ~~~~~Rl~~l~~~~dGf~iAe~Dl~lRG~G  631 (700)
                      +.=...|+.++. .-|+.+.|.-|.=+..|
T Consensus       254 ~~fn~~lR~~A~-~kG~~Lne~GL~~~~~~  282 (307)
T cd00141         254 KQFNRALRRLAK-EKGLKLNEYGLFDGVDG  282 (307)
T ss_pred             HHHHHHHHHHHH-HCCCCCCCCCCCCCCCC
T ss_conf             999999999999-85996542017458899


No 334
>cd01394 radB RadB. The archaeal protein radB shares similarity radA, the archaeal functional homologue to the bacterial RecA. The precise function of radB is unclear.
Probab=90.09  E-value=1.6  Score=23.64  Aligned_cols=49  Identities=16%  Similarity=0.166  Sum_probs=38.0

Q ss_pred             HHHHHHHCCCCCCEE--EEEECCCCCHHHHHHHHHHHHHHHHCCEEEEEHHH
Q ss_conf             999984100134307--88621442236999999733444305458861279
Q gi|254780945|r  282 KDILQDMSQKNRMLR--ILQGDVGSGKTLVALIAMAAAVEAGGQAVIMAPIG  331 (700)
Q Consensus       282 ~eI~~Dl~~~~pM~R--LLQGDVGSGKTiVA~~A~l~~~~~G~Q~alMaPTE  331 (700)
                      .|+..=|..+.+.-+  ++-|+=|||||-+++-.+..+...|..|++.. ||
T Consensus         6 ~~lD~vLgGGi~~G~it~i~G~pG~GKStl~lq~a~~~~~~g~~v~Yid-tE   56 (218)
T cd01394           6 KGLDELLGGGVERGTVTQVYGPPGTGKTNIAIQLAVETAGQGKKVAYID-TE   56 (218)
T ss_pred             HHHHHHHCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHCCCEEEEEE-CC
T ss_conf             7899985699878879999899998499999999999863698699996-65


No 335
>PRK12278 50S ribosomal protein L21/unknown domain fusion protein; Provisional
Probab=89.76  E-value=0.27  Score=29.78  Aligned_cols=29  Identities=17%  Similarity=0.363  Sum_probs=12.8

Q ss_pred             HHHHHHHHHHHHHHHHHHCCCCCCCCHHH
Q ss_conf             00045430013457874046843389778
Q gi|254780945|r  165 GLSVDLFKKIIVEALSRLPVLPEWIEKDL  193 (700)
Q Consensus       165 GLsqk~irk~I~~aL~~~~~i~E~LP~~l  193 (700)
                      |+..+.=.++...-+..+.++-.|-|.++
T Consensus       160 GIGP~~e~~Ln~~GI~~F~QIA~~t~~di  188 (216)
T PRK12278        160 GVGPALAKKLNEAGITTFAQIAALTDEDI  188 (216)
T ss_pred             CCCHHHHHHHHHHCCCHHHHHHCCCHHHH
T ss_conf             65889999999818723999855999999


No 336
>cd04317 EcAspRS_like_N EcAspRS_like_N: N-terminal, anticodon recognition domain of the type found in Escherichia coli aspartyl-tRNA synthetase (AspRS), the human mitochondrial (mt) AspRS-2, the discriminating (D) Thermus thermophilus AspRS-1, and the nondiscriminating (ND) Helicobacter pylori AspRS.  These homodimeric enzymes are class2b aminoacyl-tRNA synthetases (aaRSs). This domain is a beta-barrel domain (OB fold) involved in binding the tRNA anticodon stem-loop.  aaRSs catalyze the specific attachment of amino acids (AAs) to their cognate tRNAs during protein biosynthesis. This 2-step reaction involves i) the activation of the AA by ATP in the presence of magnesium ions, followed by ii) the transfer of  the activated AA to the terminal ribose of tRNA.  In the case of the class2b aaRSs, the activated AA is attached to the 3'OH of the terminal ribose.  Eukaryotes contain 2 sets of aaRSs, both of which are encoded by the nuclear genome. One set concerns with cytoplasmic synthesis, wh
Probab=89.69  E-value=1.7  Score=23.41  Aligned_cols=65  Identities=23%  Similarity=0.308  Sum_probs=47.0

Q ss_pred             HHCCCCCEEEEEEEEEEEEEECCCCCCEEEEEEECCCCEEEEEEECCCH---HHHHHHCCCCCEEEEEEEEEE
Q ss_conf             8889987899999998975421589833899998189369999951887---899873289888999989973
Q gi|254780945|r   62 SEISEERIVTITGYISQHSSFQLQKRRPYKILLNDGTGEITLLFFYRKT---EMLKNVFFEGRKITVTGKIKK  131 (700)
Q Consensus        62 ~~l~~g~~vti~g~V~~~~~~~~~~r~~~~v~v~D~tg~i~lvfFn~~~---~yl~k~lk~G~~v~vsGKv~~  131 (700)
                      ..-..|+.|++.|.|.+.+.   .+ +..=+.+.|.+|.+++++-....   .++ +.++.+..+.|.|+|..
T Consensus         9 ~~~~~G~~V~v~GwV~~~R~---~g-ki~Fi~LRD~tg~iQ~v~~~~~~~~~~~~-~~l~~EsvV~V~G~V~~   76 (135)
T cd04317           9 RESHVGQEVTLCGWVQRRRD---HG-GLIFIDLRDRYGIVQVVFDPEEAPEFELA-EKLRNESVIQVTGKVRA   76 (135)
T ss_pred             CHHHCCCEEEEEEEEEEEEE---CC-CEEEEEEECCCCEEEEEECCCCCHHHHHH-HHCCCCCEEEEEEEEEE
T ss_conf             95889999999999999971---79-79999985288358899957651678999-71897679999999996


No 337
>PRK06995 flhF flagellar biosynthesis regulator FlhF; Validated
Probab=89.51  E-value=1.8  Score=23.32  Aligned_cols=244  Identities=16%  Similarity=0.149  Sum_probs=128.4

Q ss_pred             CCHHHHHHHHHCCCCCCHHHH--HHHHHHHHHHCC---CCC-CE----EEEEECCCCCHHH-HHHHHHHHHHHHH-CCEE
Q ss_conf             757899998630246798899--999999984100---134-30----7886214422369-9999973344430-5458
Q gi|254780945|r  258 EGKIAQKILRNIPFSPTKSQE--SAIKDILQDMSQ---KNR-ML----RILQGDVGSGKTL-VALIAMAAAVEAG-GQAV  325 (700)
Q Consensus       258 ~~~~~~~f~~~LPF~LT~~Q~--~ai~eI~~Dl~~---~~p-M~----RLLQGDVGSGKTi-VA~~A~l~~~~~G-~Q~a  325 (700)
                      +..+...+++.+|-.....+.  .+...+..-+..   ..+ +.    -.|-|=.|+|||- +|=+|+-.+...| .+++
T Consensus       131 ~~~la~~l~~~l~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~ggV~alVGPTGVGKTTTiAKLAAr~~l~~g~~kVa  210 (404)
T PRK06995        131 SAQLVRMLLENLPAGDDAQAAMDWARSVLASNLPVLGSEDALMERGGVFALVGPTGVGKTTTTAKLAARCVMRHGASKVA  210 (404)
T ss_pred             CHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHCCCCCCCCCHHCCCCEEEEECCCCCCHHHHHHHHHHHHHHHHCCCCEE
T ss_conf             99999999984703389789999999999974666666531011475589866888763758999999999983898379


Q ss_pred             EEEHH--HHHHHHHHHHHHHHCCCCCCEEEEEECCCCHHHHHHHHHHHCCCCCEEEEECHHHCCCCCCCCCCCEEEECCC
Q ss_conf             86127--9999999986211014578658996246422566768776213475486411120133455444417885210
Q gi|254780945|r  326 IMAPI--GILAQQHYEFIKKYTQNTQIIVEIITGNMPQAHRRKALERIAHGQAHIIIGTHALFQDSIQYYKLILVIVDEQ  403 (700)
Q Consensus       326 lMaPT--EILA~QH~~~~~~~~~~~~i~v~lLtg~~~~~er~~i~~~i~~G~~~iiIGTHAL~q~~v~F~~LgLvViDEQ  403 (700)
                      |..=-  -|=|....+++.++   +||++....   +..+-+..++++++.+ -|+|-|--.=     ++       |++
T Consensus       211 LIT~DTYRIgAvEQLktYa~I---lgvPv~vv~---~~~eL~~aL~~l~~~d-lILIDTaGrs-----~r-------D~~  271 (404)
T PRK06995        211 LLTTDSYRIGGHEQLRIYGKI---LGVPVHAVK---DAADLRLALAELRNKH-IVLIDTVGMS-----QR-------DRM  271 (404)
T ss_pred             EEECCCCCHHHHHHHHHHHHH---CCCEEEEEC---CHHHHHHHHHHHCCCC-EEEEECCCCC-----CC-------CHH
T ss_conf             997687547899999999987---595599959---9999999999708999-9998099989-----76-------888


Q ss_pred             CCCCHHHHHHHHHCCC-CCCCEEECHHHHHHHHHHHH--HHCCCHHHHCCCCCCCCCCEEEEEECCCHHHHHHHHHHHHC
Q ss_conf             1335688998740256-77610101013227899997--52010111102355766620799970200268999976310
Q gi|254780945|r  404 HRFGVQQRLKLTQKAT-APHVLLMTATPIPRTLVLTS--LGDIDISKITEKPAGRKPIKTVIIPINRIDEVIERLKVVLS  480 (700)
Q Consensus       404 HRFGV~QR~~L~~Kg~-~ph~L~MtATPIPRTLal~~--ygdldvS~i~e~P~gR~~I~T~~~~~~~~~~~~~~i~~~l~  480 (700)
                      +   ++|...|..-+. .-.+|+||||-=+++|.-++  |+-+++         ..=|-|++=+......+++.+.+   
T Consensus       272 ~---~e~l~~l~~~~~~~~~~LVLsat~~~~dl~~i~~~f~~~~~---------~~~I~TKLDEt~~~G~iln~~~~---  336 (404)
T PRK06995        272 V---SEQIAMLHGAGAPVQRLLLLNATSHGDTLNEVVQAYRGPGL---------AGCILTKLDEAASLGGALDTVIR---  336 (404)
T ss_pred             H---HHHHHHHHHCCCCCEEEEEECCCCCHHHHHHHHHHHCCCCC---------CEEEEECCCCCCCHHHHHHHHHH---
T ss_conf             9---99999997357885289997798999999999998446999---------83998304067972399999999---


Q ss_pred             CCCEEEEEECCCCCCCCCCCCHHHHHHHHHHHHCCCCEECCCCCCCHHHHHHHHHHHH
Q ss_conf             3873899971201221112101466666668663710312014699899999999975
Q gi|254780945|r  481 EGKKAYWICPQIEEKKESNFRSVVERFNSLHEHFTSSIAIIHGRMSDIDKESVMDSFK  538 (700)
Q Consensus       481 ~g~q~y~VcPlIeese~~~~~~~~~~~~~l~~~~~~~v~~lHGkm~~~ek~~~m~~F~  538 (700)
                      .+--+.+|+-==+=-|++...++...   +.+-|...-.--+=.+..+|--.+|..-.
T Consensus       337 ~~lPlsy~T~GQ~VPeDi~~A~~~~L---v~ra~~~~~~~~~~~~~~~~~~~~~~~~~  391 (404)
T PRK06995        337 HKLPLHYVSNGQRVPEDLHVANAKFL---LHRAFCAPREGSPFVPQDDEMPLLLAALA  391 (404)
T ss_pred             HCCCEEEECCCCCCCCCHHCCCHHHH---HHHHHHCCCCCCCCCCCCCHHHHHHHHHH
T ss_conf             78985998189958421210898999---99986264558999988007999998764


No 338
>PRK00076 recR recombination protein RecR; Reviewed
Probab=89.51  E-value=0.17  Score=31.27  Aligned_cols=29  Identities=28%  Similarity=0.406  Sum_probs=26.8

Q ss_pred             CCCCHHCHHCCCHHHCCCCCHHHHHHHHH
Q ss_conf             97102021017721367858899999887
Q gi|254780945|r    1 MRPSFLNPLFAPLSTFRGVGKKYSLFLSK   29 (700)
Q Consensus         1 mrp~~l~~L~~pI~~LkGVGpk~a~~L~k   29 (700)
                      |-|+.++.|-..++.|||||||+|+.++-
T Consensus         1 ~~p~~i~~LI~~l~kLPGIG~KsA~Rla~   29 (197)
T PRK00076          1 MYPPPIEKLIEALRKLPGIGPKSAQRLAF   29 (197)
T ss_pred             CCCHHHHHHHHHHHHCCCCCHHHHHHHHH
T ss_conf             98789999999998789998899999999


No 339
>pfam02367 UPF0079 Uncharacterized P-loop hydrolase UPF0079. This uncharacterized family contains a P-loop.
Probab=89.40  E-value=0.35  Score=28.88  Aligned_cols=51  Identities=25%  Similarity=0.285  Sum_probs=31.5

Q ss_pred             HHHHHHHCCCCCCEEEEEECCCCCHHHHHHHHHHHHHHHHCCEEEEEHHHHHHHHH
Q ss_conf             99998410013430788621442236999999733444305458861279999999
Q gi|254780945|r  282 KDILQDMSQKNRMLRILQGDVGSGKTLVALIAMAAAVEAGGQAVIMAPIGILAQQH  337 (700)
Q Consensus       282 ~eI~~Dl~~~~pM~RLLQGDVGSGKTiVA~~A~l~~~~~G~Q~alMaPTEILA~QH  337 (700)
                      +.|.+.+..+  .--+|+||.|||||.-+=.- +.+.  |....+-.||=.|.+.+
T Consensus         6 ~~ia~~l~~G--~vi~L~G~LGaGKTtfvr~i-~~~l--g~~~~V~SPTF~lv~~Y   56 (123)
T pfam02367         6 KRLAQLLKAG--DVVLLSGDLGAGKTTFVRGL-AKGL--GITGNVTSPTFTLVNVY   56 (123)
T ss_pred             HHHHHHCCCC--CEEEEECCCCCCHHHHHHHH-HHHC--CCCCCCCCCCEEEEEEE
T ss_conf             9999768999--79999888778899999999-9985--99887379955889997


No 340
>PHA00012 assembly protein
Probab=89.27  E-value=0.85  Score=25.84  Aligned_cols=82  Identities=26%  Similarity=0.311  Sum_probs=54.0

Q ss_pred             EEEEECCCCCHHHHHHHHHHHHHHHHCCEEEEEHHHHHHHHHHHHHHHHCCCCC-----CEEEEEECCCCHHHHHHHHHH
Q ss_conf             788621442236999999733444305458861279999999986211014578-----658996246422566768776
Q gi|254780945|r  296 RILQGDVGSGKTLVALIAMAAAVEAGGQAVIMAPIGILAQQHYEFIKKYTQNTQ-----IIVEIITGNMPQAHRRKALER  370 (700)
Q Consensus       296 RLLQGDVGSGKTiVA~~A~l~~~~~G~Q~alMaPTEILA~QH~~~~~~~~~~~~-----i~v~lLtg~~~~~er~~i~~~  370 (700)
                      --+.|.-|||||++|..-+-..+..|.-||-=.+   |-      +.+ |++.+     .++.    ..+.|-.-+-+..
T Consensus         4 Y~vTGKlGsGKsl~av~kiq~~l~~G~~VATNld---l~------le~-mp~~gr~ak~~~v~----RlPDkPt~~DL~a   69 (361)
T PHA00012          4 YVVTGKLGAGKTLVAVSRIQDKLVKGCIVATNLN---LR------LHH-LPQVGRFAKQPRVM----RIPDKPTLEDLEA   69 (361)
T ss_pred             EEEECCCCCCCHHHHHHHHHHHHHCCCEEEECCC---CC------HHH-CCCCCCCCCCCCEE----ECCCCCCHHHHHH
T ss_conf             8996245788602559999999982981441587---67------655-75447655676459----8489998789987


Q ss_pred             HCCCCCEEEEECHHHCCCCCCCCCCCEEEECCC
Q ss_conf             213475486411120133455444417885210
Q gi|254780945|r  371 IAHGQAHIIIGTHALFQDSIQYYKLILVIVDEQ  403 (700)
Q Consensus       371 i~~G~~~iiIGTHAL~q~~v~F~~LgLvViDEQ  403 (700)
                      |..|.            +.-.=++-||+|.||=
T Consensus        70 lG~gn------------~~~dE~knGlLvLDE~   90 (361)
T PHA00012         70 IGRGN------------LSYDESKNGLLVLDEC   90 (361)
T ss_pred             HCCCC------------CCCCCCCCCEEEEEHH
T ss_conf             46898------------7656222764997400


No 341
>pfam06431 Polyoma_lg_T_C Polyomavirus large T antigen C-terminus.
Probab=89.21  E-value=1.9  Score=23.16  Aligned_cols=109  Identities=17%  Similarity=0.193  Sum_probs=61.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCC-CCHHHHHHHHHCC-CC-CCHHHHHHHHHHHHHHCCCCCCEE--E
Q ss_conf             99999987666666677776555543203576787-7578999986302-46-798899999999984100134307--8
Q gi|254780945|r  223 PARERLAYDELLAGQIALLLMRKQFKKEIGIPINV-EGKIAQKILRNIP-FS-PTKSQESAIKDILQDMSQKNRMLR--I  297 (700)
Q Consensus       223 ~ArkRLafeELl~~QL~l~~~r~~~~~~~~~~~~~-~~~~~~~f~~~LP-F~-LT~~Q~~ai~eI~~Dl~~~~pM~R--L  297 (700)
                      -|.||+.--|+-..++.-...+....+..-. +.. ....+..+.+..- |. |-..=..++-+|..-|-.+.|-.|  |
T Consensus        81 lA~rR~~~~~mTR~elL~eRf~~~l~~md~~-~~~~g~~~i~~ymAgvaw~~~L~p~~~~~i~~~lk~~v~N~PKkRy~l  159 (417)
T pfam06431        81 LAKKRVDSLHMTREEMLTERFNDLLDKMDLI-FGAHGNAVLEQYMAGVAWLHCLLPKMDSVIYDFLKCIVYNIPKKRYWL  159 (417)
T ss_pred             HHHHHHHHHHCCHHHHHHHHHHHHHHHHHHH-HCCCCHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHCCCCCCEEEE
T ss_conf             9999888876369999999999999999998-647873899999999999997453327999999999961887411588


Q ss_pred             EEECCCCCHHHHHHHHHHHHHHHHCCEEEEEHHHHHH
Q ss_conf             8621442236999999733444305458861279999
Q gi|254780945|r  298 LQGDVGSGKTLVALIAMAAAVEAGGQAVIMAPIGILA  334 (700)
Q Consensus       298 LQGDVGSGKTiVA~~A~l~~~~~G~Q~alMaPTEILA  334 (700)
                      ..|-|-||||-+|+.  +.-.-.|.---+=.|-|=|+
T Consensus       160 FkGPvNsGKTTlAAA--lldLcgGkaLNIN~P~dkL~  194 (417)
T pfam06431       160 FKGPIDSGKTTLAAA--LLDLCGGKALNVNLPLERLN  194 (417)
T ss_pred             EECCCCCCHHHHHHH--HHHHCCCCEEECCCCHHHCC
T ss_conf             767867774879999--99863686120479856445


No 342
>PRK12445 lysyl-tRNA synthetase; Reviewed
Probab=89.19  E-value=1.9  Score=23.15  Aligned_cols=97  Identities=16%  Similarity=0.148  Sum_probs=59.9

Q ss_pred             HCCCCCCCCCCCCCHHHC----------CCCCEEEEEEEEEEEEEECCCCCCEEEEEEECCCCEEEEEEECCCH---HH-
Q ss_conf             089740134444647888----------9987899999998975421589833899998189369999951887---89-
Q gi|254780945|r   47 YHPSSFIDRHYRPKISEI----------SEERIVTITGYISQHSSFQLQKRRPYKILLNDGTGEITLLFFYRKT---EM-  112 (700)
Q Consensus        47 ~~PrrYeDr~~~~~I~~l----------~~g~~vti~g~V~~~~~~~~~~r~~~~v~v~D~tg~i~lvfFn~~~---~y-  112 (700)
                      -||.+|.--..+..+.+.          ..+..|++.|.|.+.+.   .+ +..=+.+.|.+|.+++++-....   .| 
T Consensus        35 ~yp~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~V~vaGrv~~~R~---~G-k~~F~~LrD~~G~iQ~~~~~~~~~~~~~~  110 (505)
T PRK12445         35 AFPNDFRRDHTSDQLHEEFDAKDNQELESLNIEVSVAGRMMTRRI---MG-KASFVTLQDVGGRIQLYVARDSLPEGVYN  110 (505)
T ss_pred             CCCCCCCCCCCHHHHHHHHCCCCCCCCCCCCCEEEEEEEEEEEEC---CC-CEEEEEEEECCEEEEEEEECCCCCHHHHH
T ss_conf             999989587709999998545684100147988999988987874---79-83999998598439999958868668999


Q ss_pred             -HHHHCCCCCEEEEEEEEEEC-CCEEEEECCEEEECC
Q ss_conf             -98732898889999899731-877999778689626
Q gi|254780945|r  113 -LKNVFFEGRKITVTGKIKKL-KNRIIMVHPHYIFHN  147 (700)
Q Consensus       113 -l~k~lk~G~~v~vsGKv~~~-~~~~qi~hPe~~~~~  147 (700)
                       ..+.+..|+.+-+.|++..- .|.+++.--++.+.+
T Consensus       111 ~~~~~~~~gdii~v~G~~~~t~tGe~~i~~~~~~ils  147 (505)
T PRK12445        111 DQFKKWDLGDIIGARGTLFKTQTGELSIHCTELRLLT  147 (505)
T ss_pred             HHHHHCCCCEEEEEEEEEECCCCCCCCEEEEEEEEEC
T ss_conf             9975121534999963660478776212578999934


No 343
>KOG1808 consensus
Probab=89.14  E-value=0.74  Score=26.29  Aligned_cols=40  Identities=25%  Similarity=0.337  Sum_probs=33.2

Q ss_pred             CCCCHHHHHHHHHHHHHHCCC-CCCEEEEEECCCCCHHHHHHH
Q ss_conf             467988999999999841001-343078862144223699999
Q gi|254780945|r  271 FSPTKSQESAIKDILQDMSQK-NRMLRILQGDVGSGKTLVALI  312 (700)
Q Consensus       271 F~LT~~Q~~ai~eI~~Dl~~~-~pM~RLLQGDVGSGKTiVA~~  312 (700)
                      |-+|..+++.+.++..-..++ .|-  ||||+.|||||-+...
T Consensus       419 ~i~T~~vq~~la~~~~a~~~~~~pi--llqG~tssGKtsii~~  459 (1856)
T KOG1808         419 YIITPRVQKNLADLARAISSGKFPI--LLQGPTSSGKTSIIKE  459 (1856)
T ss_pred             EECCHHHHHHHHHHHHHHHCCCCCE--EEECCCCCCCHHHHHH
T ss_conf             2046899988999999996589986--7754767681159999


No 344
>PRK07218 replication factor A; Provisional
Probab=88.99  E-value=1.9  Score=23.04  Aligned_cols=84  Identities=20%  Similarity=0.264  Sum_probs=59.6

Q ss_pred             CCCCCCCCC------CCHHHCCCC-CEEEEEEEEEEEEEEC--CC--CCCEEEEEEECCCCEEEEEEECCCHHHHHHHCC
Q ss_conf             740134444------647888998-7899999998975421--58--983389999818936999995188789987328
Q gi|254780945|r   50 SSFIDRHYR------PKISEISEE-RIVTITGYISQHSSFQ--LQ--KRRPYKILLNDGTGEITLLFFYRKTEMLKNVFF  118 (700)
Q Consensus        50 rrYeDr~~~------~~I~~l~~g-~~vti~g~V~~~~~~~--~~--~r~~~~v~v~D~tg~i~lvfFn~~~~yl~k~lk  118 (700)
                      |+|-+-+..      ..|+++.++ ..|++.++|+++....  +.  ....+.-.+.|+||.|.-..|-   +|   -+.
T Consensus        46 rky~~~~~~~~~~~~~~i~di~~~~~~V~i~~kVl~~~~rsi~~~g~~~i~~~g~l~d~tg~i~f~~w~---~f---~~e  119 (430)
T PRK07218         46 RKYGDKRKIGSGPSTLDIKDLSTDDKNVTVTARVLTVGERSIRYQGDPSVIYEGELADETGRISYTAWK---EF---PLS  119 (430)
T ss_pred             HHHCCCCCCCCCCCCCCHHHCCCCCCCEEEEEEEEEECCCCEECCCCCCEEEEEEECCCCCCEEEEECC---CC---CCC
T ss_conf             985788765677443557563877682589999987035301026875224432303666624000120---16---889


Q ss_pred             CCCEEEEEEE-EEECCCEEEEE
Q ss_conf             9888999989-97318779997
Q gi|254780945|r  119 EGRKITVTGK-IKKLKNRIIMV  139 (700)
Q Consensus       119 ~G~~v~vsGK-v~~~~~~~qi~  139 (700)
                      +|+.|.+-|- ++.|++..++.
T Consensus       120 ~Gd~v~I~nA~Vre~~g~peLn  141 (430)
T PRK07218        120 PGDTVTIGNAGVREWDGRPELN  141 (430)
T ss_pred             CCCEEEECCCEEEEECCCEEEE
T ss_conf             8878997552851447946786


No 345
>pfam11798 IMS_HHH IMS family HHH motif. These proteins are involved in UV protection, eg.
Probab=88.90  E-value=0.25  Score=29.95  Aligned_cols=26  Identities=42%  Similarity=0.788  Sum_probs=23.3

Q ss_pred             CCHHCHHCCCHHHCCCCCHHHHHHHHHH
Q ss_conf             1020210177213678588999998874
Q gi|254780945|r    3 PSFLNPLFAPLSTFRGVGKKYSLFLSKI   30 (700)
Q Consensus         3 p~~l~~L~~pI~~LkGVGpk~a~~L~kl   30 (700)
                      +++|.+|  ||+.++|||+++++.|+.+
T Consensus         6 ~~~L~~l--pi~~i~GIG~~~~~~L~~~   31 (33)
T pfam11798         6 PEFLWPL--PISKIPGIGRKTAEKLEAL   31 (33)
T ss_pred             HHHHCCC--CCCCCCCCCHHHHHHHHHC
T ss_conf             8886147--6221688666789999982


No 346
>PRK12726 flagellar biosynthesis regulator FlhF; Provisional
Probab=88.61  E-value=1.7  Score=23.42  Aligned_cols=162  Identities=12%  Similarity=0.137  Sum_probs=80.3

Q ss_pred             EEEEECCCCCHHHHHHHHHHHHHHHHCCEEEEEHHHHHHHHHHHHHHHHCCCCCCEEEEEECCCCHHHHHHHHHH-HCCC
Q ss_conf             788621442236999999733444305458861279999999986211014578658996246422566768776-2134
Q gi|254780945|r  296 RILQGDVGSGKTLVALIAMAAAVEAGGQAVIMAPIGILAQQHYEFIKKYTQNTQIIVEIITGNMPQAHRRKALER-IAHG  374 (700)
Q Consensus       296 RLLQGDVGSGKTiVA~~A~l~~~~~G~Q~alMaPTEILA~QH~~~~~~~~~~~~i~v~lLtg~~~~~er~~i~~~-i~~G  374 (700)
                      -+|-|--|||||--++=-+......|+.+++.|- ..-=-=-++.++.|-..++++|.  .++.+..-...+... .+++
T Consensus       209 IaLVGvnGvGKTTTiAKLA~~l~~~gkkV~LVAa-DTFRaAAiEQLk~~g~rlgVpV~--~~~dpa~l~~av~~~a~~~~  285 (407)
T PRK12726        209 ISLIGQTGVGKTTTLVKLGWQLLKQNRTVGFITT-DTFRSGAVEQFQGYADKLDVELI--VATSPAELEEAVQYMTYVNC  285 (407)
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHHCCCCEEEEEC-CCCCHHHHHHHHHHHHHHCCEEE--EECCHHHHHHHHHHHHHCCC
T ss_conf             9998999897899999999999977991799970-66778899999999999796499--81888999999999986289


Q ss_pred             CCEEEEECHHHCCCCCCCCCCCEEEECCCCCCCHHHH--HHHH--HCCCCCCCEE--ECHHHHHHHHHHHHHHCCCHHHH
Q ss_conf             7548641112013345544441788521013356889--9874--0256776101--01013227899997520101111
Q gi|254780945|r  375 QAHIIIGTHALFQDSIQYYKLILVIVDEQHRFGVQQR--LKLT--QKATAPHVLL--MTATPIPRTLVLTSLGDIDISKI  448 (700)
Q Consensus       375 ~~~iiIGTHAL~q~~v~F~~LgLvViDEQHRFGV~QR--~~L~--~Kg~~ph~L~--MtATPIPRTLal~~ygdldvS~i  448 (700)
                                          --+|+||---|--..+.  ..|.  ..-.+||.++  .+|+-=....+- .+..     .
T Consensus       286 --------------------~DvVIIDTAGRl~~d~~Lm~EL~ki~~vi~P~~~lLV~dag~~~~~v~q-a~~~-----~  339 (407)
T PRK12726        286 --------------------VDHILIDTVGRNYLAEESVSEISAYTDVVHPDLTCFTFSSGMKSADVMT-ILPK-----L  339 (407)
T ss_pred             --------------------CCEEEEECCCCCCCCHHHHHHHHHHHHCCCCCEEEEEECCCCCHHHHHH-HHHH-----H
T ss_conf             --------------------9989996999881349999999998733289669999367566999999-9987-----0


Q ss_pred             CCCCCCCCCCEEEEEECCCHHHHHHHHHHHHCCCCEEEEEEC
Q ss_conf             023557666207999702002689999763103873899971
Q gi|254780945|r  449 TEKPAGRKPIKTVIIPINRIDEVIERLKVVLSEGKKAYWICP  490 (700)
Q Consensus       449 ~e~P~gR~~I~T~~~~~~~~~~~~~~i~~~l~~g~q~y~VcP  490 (700)
                      .+.|-. .-|.|++=+..+...+++...+   -|--+.+|+-
T Consensus       340 ~~v~It-GiILTKLDgtAKGG~aLSi~~~---~~lPI~fIG~  377 (407)
T PRK12726        340 AEIPID-GFIITKMDETTRIGDLYTVMQE---TNLPVLYMTD  377 (407)
T ss_pred             CCCCCC-EEEEEECCCCCCCCHHHHHHHH---HCCCEEEEEC
T ss_conf             479998-7999701478985399999999---8889799947


No 347
>PRK10867 signal recognition particle protein; Provisional
Probab=88.55  E-value=2  Score=22.83  Aligned_cols=217  Identities=13%  Similarity=0.124  Sum_probs=103.0

Q ss_pred             HCCCCCCEEEEEECCCCCHHHHHHHHHHHHHHHHCCEEEEEHHHHHHHHHHHHHHHHCCCCCCEEEEE-ECCCCHHHHHH
Q ss_conf             10013430788621442236999999733444305458861279999999986211014578658996-24642256676
Q gi|254780945|r  288 MSQKNRMLRILQGDVGSGKTLVALIAMAAAVEAGGQAVIMAPIGILAQQHYEFIKKYTQNTQIIVEII-TGNMPQAHRRK  366 (700)
Q Consensus       288 l~~~~pM~RLLQGDVGSGKTiVA~~A~l~~~~~G~Q~alMaPTEILA~QH~~~~~~~~~~~~i~v~lL-tg~~~~~er~~  366 (700)
                      +.+..|-.-|+-|==|||||--+.=-+...-..+...+++|...+-=.--++.++.|-...++++.-- +++.+.+--++
T Consensus        95 ~~~~~p~VIm~vGLqGsGKTTT~aKLA~~lk~k~~k~vllvaaDt~RpaA~eQL~~la~~~~v~~~~~~~~~dp~~ia~~  174 (453)
T PRK10867         95 LAAQPPAVVLMAGLQGAGKTTSVGKLGKFLREKHKKKVLVVSADVYRPAAIKQLETLAEQVGVDFFPSDVGQKPVDIVNA  174 (453)
T ss_pred             CCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHCCCCEEEEECCCCCHHHHHHHHHHHHHHCCCCEECCCCCCCHHHHHHH
T ss_conf             37899969999746888518589999999997389837985588770589999999998519804367889988999999


Q ss_pred             HHHHHCCCCCEEEEECHHHCCCCCCCCCCCEEEECCCCCCCHHHHH----HHHHCCCCCC--CEEECHHHHHHHH--HHH
Q ss_conf             8776213475486411120133455444417885210133568899----8740256776--1010101322789--999
Q gi|254780945|r  367 ALERIAHGQAHIIIGTHALFQDSIQYYKLILVIVDEQHRFGVQQRL----KLTQKATAPH--VLLMTATPIPRTL--VLT  438 (700)
Q Consensus       367 i~~~i~~G~~~iiIGTHAL~q~~v~F~~LgLvViDEQHRFGV~QR~----~L~~Kg~~ph--~L~MtATPIPRTL--al~  438 (700)
                      ..+..+....                   -+||||---|--+++-.    +-..+-.+||  +||+-|+-=--..  |-+
T Consensus       175 a~~~ak~~~~-------------------DvvivDTAGRl~~d~~Lm~El~~i~~~~~P~e~llV~Da~~GQ~a~~~a~~  235 (453)
T PRK10867        175 ALKEAKLKFY-------------------DVLLVDTAGRLHVDEAMMDEIKQVHASINPVETLFVVDAMTGQDAANTAKA  235 (453)
T ss_pred             HHHHHHHCCC-------------------CEEEEECCCCHHCCHHHHHHHHHHHHHHCCCCEEEEEECCCCHHHHHHHHH
T ss_conf             9999997799-------------------999997876012108889999999876378713797432235668999999


Q ss_pred             HHHCCCHHHHCCCCCCCCCCEEEEEECCCHHHHHHHHHHHHCCCCEEEEEECCCCCCCCCCCCHHHHHH-HH-HHHHCC-
Q ss_conf             752010111102355766620799970200268999976310387389997120122111210146666-66-686637-
Q gi|254780945|r  439 SLGDIDISKITEKPAGRKPIKTVIIPINRIDEVIERLKVVLSEGKKAYWICPQIEEKKESNFRSVVERF-NS-LHEHFT-  515 (700)
Q Consensus       439 ~ygdldvS~i~e~P~gR~~I~T~~~~~~~~~~~~~~i~~~l~~g~q~y~VcPlIeese~~~~~~~~~~~-~~-l~~~~~-  515 (700)
                      ..        +..|-+ --|.|++=+..+-.-+++...   .-|--+++|+-    .|+.|  +.+.-+ ++ ..+.++ 
T Consensus       236 F~--------~~~~~~-gvIlTKlDgdarGG~alS~~~---~t~~PI~FiG~----GEk~d--dle~F~p~r~asRILGm  297 (453)
T PRK10867        236 FN--------EALPLT-GVVLTKVDGDARGGAALSIRH---ITGKPIKFLGV----GEKTD--ALEPFHPDRIASRILGM  297 (453)
T ss_pred             HH--------HHCCCC-EEEEECCCCCCCCHHHHHHHH---HHCCCCEEEEC----CCCCC--CCCCCCHHHHHHHHCCC
T ss_conf             99--------855987-078750467876138989999---97869678866----99824--58876848999986189


Q ss_pred             -CC---EECCCCCCCHHHHHHHHHHHHCCC
Q ss_conf             -10---312014699899999999975598
Q gi|254780945|r  516 -SS---IAIIHGRMSDIDKESVMDSFKNGT  541 (700)
Q Consensus       516 -~~---v~~lHGkm~~~ek~~~m~~F~~g~  541 (700)
                       +=   +.-+....+.++.++.++++..|+
T Consensus       298 GDi~~Lvek~~~~~d~~~~~~~~~k~~~g~  327 (453)
T PRK10867        298 GDVLSLIEDIESKVDRAQAEKLASKLKKGD  327 (453)
T ss_pred             CCHHHHHHHHHHHHHHHHHHHHHHHHHCCC
T ss_conf             878999999998750889999999987069


No 348
>COG0802 Predicted ATPase or kinase [General function prediction only]
Probab=88.53  E-value=0.47  Score=27.87  Aligned_cols=57  Identities=23%  Similarity=0.390  Sum_probs=32.8

Q ss_pred             HHHHHHHH-HHHHHCCCCCCEEEEEECCCCCHHHHHHHHHHHHHHHHCCEEEEEHHHHHHHHH
Q ss_conf             89999999-998410013430788621442236999999733444305458861279999999
Q gi|254780945|r  276 SQESAIKD-ILQDMSQKNRMLRILQGDVGSGKTLVALIAMAAAVEAGGQAVIMAPIGILAQQH  337 (700)
Q Consensus       276 ~Q~~ai~e-I~~Dl~~~~pM~RLLQGDVGSGKTiVA~~A~l~~~~~G~Q~alMaPTEILA~QH  337 (700)
                      ++...+.+ +...+  +...--+|+||.|+|||--+ -+++.+.  |.+..+-.||=-|.+-+
T Consensus         9 ~~t~~lg~~l~~~l--~~g~Vv~L~GdLGAGKTtf~-rgi~~~L--g~~~~V~SPTFtlv~~Y   66 (149)
T COG0802           9 EATLALGERLAEAL--KAGDVVLLSGDLGAGKTTLV-RGIAKGL--GVDGNVKSPTFTLVEEY   66 (149)
T ss_pred             HHHHHHHHHHHHHC--CCCCEEEEECCCCCCHHHHH-HHHHHHC--CCCCCCCCCCEEEEHHH
T ss_conf             99999999999657--89988999778768859999-9999974--99975249876101211


No 349
>PRK13889 conjugal transfer relaxase TraA; Provisional
Probab=88.41  E-value=1.6  Score=23.67  Aligned_cols=140  Identities=20%  Similarity=0.174  Sum_probs=91.1

Q ss_pred             CCCCCCHHHHHHHHHHHHHHCCCCCCEEEEEECCCCCHHHHHHHHHHHHHHHHCCEEEEEHHHHHHHHHHH-------HH
Q ss_conf             02467988999999999841001343078862144223699999973344430545886127999999998-------62
Q gi|254780945|r  269 IPFSPTKSQESAIKDILQDMSQKNRMLRILQGDVGSGKTLVALIAMAAAVEAGGQAVIMAPIGILAQQHYE-------FI  341 (700)
Q Consensus       269 LPF~LT~~Q~~ai~eI~~Dl~~~~pM~RLLQGDVGSGKTiVA~~A~l~~~~~G~Q~alMaPTEILA~QH~~-------~~  341 (700)
                      =+|.|...|..|+..|..+    .. ..++.|--|+|||-+--.|--+.-.+||.|.=+|||-+=|+..-.       ++
T Consensus       343 ~~~~Ls~EQ~~A~~hiT~~----~~-iavVvG~AGtGKStmL~aAReawEa~GyrV~GaALsGkAAegLe~~sGI~SrTl  417 (992)
T PRK13889        343 RGLVLSGEQADALAHVTDG----RD-LGVVVGYAGTGKSAMLGVAREAWEAAGYEVRGAALSGIAAENLEGGSGIASRTI  417 (992)
T ss_pred             CCCCCCHHHHHHHHHHCCC----CC-EEEEEECCCCCHHHHHHHHHHHHHHCCCEEEEECCCHHHHHHHHHCCCCCCHHH
T ss_conf             2688799999999986478----97-589983388878899999999999779889811500689997653479431679


Q ss_pred             HHHCCCC-------CCE-EEEE--ECCCCHHHHHHHHHHHC-CCCCEEEEECHHHCC---CCCCC----CCCCEEEECCC
Q ss_conf             1101457-------865-8996--24642256676877621-347548641112013---34554----44417885210
Q gi|254780945|r  342 KKYTQNT-------QII-VEII--TGNMPQAHRRKALERIA-HGQAHIIIGTHALFQ---DSIQY----YKLILVIVDEQ  403 (700)
Q Consensus       342 ~~~~~~~-------~i~-v~lL--tg~~~~~er~~i~~~i~-~G~~~iiIGTHAL~q---~~v~F----~~LgLvViDEQ  403 (700)
                      ..|.-..       +-+ |.++  -|=.....-..+++... .|---++||-+.=+|   .+=.|    .+.|.+-++|=
T Consensus       418 As~e~~w~~g~~~L~~~dVlVVDEAGMVgSRqMarll~~Ae~AGAKVVLVGD~~QLq~IeAGaaFral~er~G~aeLteI  497 (992)
T PRK13889        418 ASLEHGWGQGRDLLTARDVLVIDEAGMVGTRQLERVLSHAADAGAKVVLVGDPQQLQAIEAGAAFRSIHERHGGAEIGEV  497 (992)
T ss_pred             HHHHHHHHCCCCCCCCCCEEEEECCCCCCHHHHHHHHHHHHHCCCEEEEECCHHHCCCCCCCHHHHHHHHHCCCEEEEHE
T ss_conf             99999874673347898589996765577499999999999849989994887771886468899999985196751022


Q ss_pred             CCCCH-HHHHH
Q ss_conf             13356-88998
Q gi|254780945|r  404 HRFGV-QQRLK  413 (700)
Q Consensus       404 HRFGV-~QR~~  413 (700)
                      +||-. .||.+
T Consensus       498 rRQr~~w~ReA  508 (992)
T PRK13889        498 RRQREDWQRDA  508 (992)
T ss_pred             ECCCCHHHHHH
T ss_conf             21487999999


No 350
>pfam00158 Sigma54_activat Sigma-54 interaction domain.
Probab=88.37  E-value=0.55  Score=27.30  Aligned_cols=23  Identities=26%  Similarity=0.436  Sum_probs=17.6

Q ss_pred             CCCCEEEEEECCCCCHHHHHHHH
Q ss_conf             13430788621442236999999
Q gi|254780945|r  291 KNRMLRILQGDVGSGKTLVALIA  313 (700)
Q Consensus       291 ~~pM~RLLQGDVGSGKTiVA~~A  313 (700)
                      .....-|++|..|+||+.+|-.-
T Consensus        20 ~~~~pVLI~GE~GtGK~~lAr~I   42 (168)
T pfam00158        20 PTDATVLITGESGTGKELFARAI   42 (168)
T ss_pred             CCCCCEEEECCCCCCHHHHHHHH
T ss_conf             88998899899988889999999


No 351
>PRK08769 DNA polymerase III subunit delta'; Validated
Probab=88.36  E-value=0.91  Score=25.60  Aligned_cols=50  Identities=20%  Similarity=0.228  Sum_probs=35.7

Q ss_pred             CCCHHHHHHHHHHHHHHCCCC-CCEEEEEECCCCCHHHHHHHHHHHHHHHH
Q ss_conf             679889999999998410013-43078862144223699999973344430
Q gi|254780945|r  272 SPTKSQESAIKDILQDMSQKN-RMLRILQGDVGSGKTLVALIAMAAAVEAG  321 (700)
Q Consensus       272 ~LT~~Q~~ai~eI~~Dl~~~~-pM~RLLQGDVGSGKTiVA~~A~l~~~~~G  321 (700)
                      .+|.=|+++++...+-+.+++ |=--|+.|.-|+||+..|..-+-...-++
T Consensus         4 ~~~PWq~~~~~~L~~~i~~~rl~HA~Lf~Gp~G~GK~~~A~~~A~~llc~~   54 (319)
T PRK08769          4 AFSPWQQRAFDQTVAALDAGRLGHGLLICGPEGLGKRAVALALAEHVLASG   54 (319)
T ss_pred             CCCCCCHHHHHHHHHHHHCCCCCCEEEEECCCCCCHHHHHHHHHHHHHCCC
T ss_conf             558776899999999997699420687589998789999999999983799


No 352
>PRK00313 lpxK tetraacyldisaccharide 4'-kinase; Provisional
Probab=88.35  E-value=2.1  Score=22.74  Aligned_cols=120  Identities=18%  Similarity=0.222  Sum_probs=64.1

Q ss_pred             CCCHHHHHHHHHHHHHHHHCCEEEEEH------H----HHHHHHHHHH----HHHHCCCCCCEEEEEECCCCHHHHHHHH
Q ss_conf             422369999997334443054588612------7----9999999986----2110145786589962464225667687
Q gi|254780945|r  303 GSGKTLVALIAMAAAVEAGGQAVIMAP------I----GILAQQHYEF----IKKYTQNTQIIVEIITGNMPQAHRRKAL  368 (700)
Q Consensus       303 GSGKTiVA~~A~l~~~~~G~Q~alMaP------T----EILA~QH~~~----~~~~~~~~~i~v~lLtg~~~~~er~~i~  368 (700)
                      |+|||=+...-+-...+.|++++++.=      +    .|=+....+.    ---+....+++  ...|    ++|.+..
T Consensus        63 GTGKTP~v~~La~~L~~~G~~~~IiSRGYg~~~~~~~~~v~~~~~~~~vGDEpllla~~~~~p--V~V~----~~R~~a~  136 (332)
T PRK00313         63 GTGKTPLILWLIEHCRRRGLRVGVVSRGYGARPPQLPWRVTADQDAAEAGDEPLLIVQRTGVP--LMID----PDRPRAV  136 (332)
T ss_pred             CCCHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCCCCEEECCCCCHHHCCCHHHHHHHCCCCC--EEEC----CCHHHHH
T ss_conf             877779999999999977996589864656766677355457768455585889998506962--9980----7699999


Q ss_pred             H-HHCCCCCEEEEECHHHCCCCCCCCCCCEEEECCCCCCCHHH-------HHHHHHCCCCCCCEEECHHH
Q ss_conf             7-62134754864111201334554444178852101335688-------99874025677610101013
Q gi|254780945|r  369 E-RIAHGQAHIIIGTHALFQDSIQYYKLILVIVDEQHRFGVQQ-------RLKLTQKATAPHVLLMTATP  430 (700)
Q Consensus       369 ~-~i~~G~~~iiIGTHAL~q~~v~F~~LgLvViDEQHRFGV~Q-------R~~L~~Kg~~ph~L~MtATP  430 (700)
                      + .++.+.+++||=--+ ||..-..+++-+|++|.++.||=..       |+-+.. -...|.++.+..+
T Consensus       137 ~~l~~~~~~dviIlDDG-fQh~~l~rDl~Ivvid~~~~fGNg~lLPaGpLREp~~~-l~raD~vi~~g~~  204 (332)
T PRK00313        137 QALLAAEPLDLILSDDG-LQHYRLARDLELVLIDAARGLGNGRCLPAGPLREPAER-LAEVDAVLYNGAA  204 (332)
T ss_pred             HHHHHCCCCCEEEECCC-CCCHHHCCCCEEEEECCCCCCCCCCCCCCCCCCCCHHH-HHCCCEEEECCCC
T ss_conf             99996499988995585-31201048806998456678889888778645588537-6008999997997


No 353
>TIGR00603 rad25 DNA repair helicase rad25; InterPro: IPR001161   Xeroderma pigmentosum (XP)  is a human autosomal recessive disease, characterised by a high incidence of sunlight-induced skin cancer. People's skin cells with this condition are hypersensitive to ultraviolet light, due to defects in the incision step of DNA excision repair. There are a minimum of seven genetic complementation groups involved in this pathway: XP-A to XP-G. XP-G is one of the most rare and phenotypically heterogeneous of XP, showing anything from slight to extreme dysfunction in DNA excision repair , . XP-G can be corrected by a 133 Kd nuclear protein, XPGC . XPGC is an acidic protein that confers normal UV resistance in expressing cells . It is a magnesium-dependent, single-strand DNA endonuclease that makes structure-specific endonucleolytic incisions in a DNA substrate containing a duplex region and single-stranded arms , . XPGC cleaves one strand of the duplex at the border with the single-stranded region .   XPG belongs to a family of proteins that includes RAD2 from Saccharomyces cerevisiae (Baker's yeast) and rad13 from Schizosaccharomyces pombe (Fission yeast), which are single-stranded DNA endonucleases , ; mouse and human FEN-1, a structure-specific endonuclease; RAD2 from fission yeast and RAD27 from budding yeast; fission yeast exo1, a 5'-3' double-stranded DNA exonuclease that may act in a pathway that corrects mismatched base pairs; yeast DHS1, and yeast DIN7. Sequence alignment of this family of proteins reveals that similarities are largely confined to two regions. The first is located at the N-terminal extremity (N-region) and corresponds to the first 95 to 105 amino acids. The second region is internal (I-region) and found towards the C-terminus; it spans about 140 residues and contains a highly conserved core of 27 amino acids that includes a conserved pentapeptide (E-A-[DE]-A-[QS]). It is possible that the conserved acidic residues are involved in the catalytic mechanism of DNA excision repair in XPG. The amino acids linking the N- and I-regions are not conserved.   This entry represents XP group B (XP-B) give rise to both XP and Cockayne syndrome . The DNA/RNA helicase domain IPR001650 from INTERPRO is also present in this group of proteins.; GO: 0003677 DNA binding, 0004003 ATP-dependent DNA helicase activity, 0005524 ATP binding, 0006289 nucleotide-excision repair, 0005634 nucleus.
Probab=88.33  E-value=0.74  Score=26.29  Aligned_cols=329  Identities=19%  Similarity=0.228  Sum_probs=192.7

Q ss_pred             CCHHHHHHHH-HHHHHHCCCCCCEEEEEECCCCCHHHHHHHHHHHHHHHHCCEEEEEHHHHHHHHHHHHHHHHCCCCCCE
Q ss_conf             7988999999-999841001343078862144223699999973344430545886127999999998621101457865
Q gi|254780945|r  273 PTKSQESAIK-DILQDMSQKNRMLRILQGDVGSGKTLVALIAMAAAVEAGGQAVIMAPIGILAQQHYEFIKKYTQNTQII  351 (700)
Q Consensus       273 LT~~Q~~ai~-eI~~Dl~~~~pM~RLLQGDVGSGKTiVA~~A~l~~~~~G~Q~alMaPTEILA~QH~~~~~~~~~~~~i~  351 (700)
                      +=+-|++++. -...   .+..=.=.+====|.|||+|-+-|+..+=   +.+.+++-.-|=-+|=-..|+-|-.--+-.
T Consensus       270 ~RPYQEKSLrsKMFG---NGRARSGiIVLPCGAGKsLVGvTAACTvk---Ks~lVLctS~VSV~QW~~QFk~WSti~d~~  343 (756)
T TIGR00603       270 LRPYQEKSLRSKMFG---NGRARSGIIVLPCGAGKSLVGVTAACTVK---KSVLVLCTSAVSVEQWKQQFKLWSTIDDSQ  343 (756)
T ss_pred             CCCCHHHHCCCCCCC---CCCCCCCCEECCCCCCCCHHHHHHHEEEE---EEEEEEECCCHHHHHHHHHHHHCCCCCCCC
T ss_conf             897511104445667---86110551776778883112254420231---007897267100889998875226887355


Q ss_pred             EEEEECCCCHHHHHHHHHHHCCCCCEEEEECHHHCC-------------CCCCCCCCCEEEECCCCCCCHHH-HHHHHHC
Q ss_conf             899624642256676877621347548641112013-------------34554444178852101335688-9987402
Q gi|254780945|r  352 VEIITGNMPQAHRRKALERIAHGQAHIIIGTHALFQ-------------DSIQYYKLILVIVDEQHRFGVQQ-RLKLTQK  417 (700)
Q Consensus       352 v~lLtg~~~~~er~~i~~~i~~G~~~iiIGTHAL~q-------------~~v~F~~LgLvViDEQHRFGV~Q-R~~L~~K  417 (700)
                      |+--|+..|  ||       -.|++.|+|-|-+.+.             +-+.=.-=||+|.||=|=-=-++ |.-|.- 
T Consensus       344 IcrFTSD~K--e~-------~~~~~gv~vsTYsMva~t~kRS~es~k~m~~l~~rEWGl~~LDEVHvvPA~mFRrVlt~-  413 (756)
T TIGR00603       344 ICRFTSDAK--EK-------FHGEAGVVVSTYSMVAHTGKRSYESEKVMEWLTNREWGLILLDEVHVVPAAMFRRVLTI-  413 (756)
T ss_pred             CCCCCCCCC--CC-------CCCCCCEEEECCCCCCCCCCCHHHHHHHHHHHHCCCCEEEEECCCCCCCCCCCCCHHHH-
T ss_conf             110252135--76-------26653358873300024754318899999997068731798611010350016601014-


Q ss_pred             CCCCCC-EEECHHHHHHHHHHHHHHCCCHHHHCCCCCCCCCCEEEEEECCCH--------HHHHHHHHHHHCCCCEEEEE
Q ss_conf             567761-010101322789999752010111102355766620799970200--------26899997631038738999
Q gi|254780945|r  418 ATAPHV-LLMTATPIPRTLVLTSLGDIDISKITEKPAGRKPIKTVIIPINRI--------DEVIERLKVVLSEGKKAYWI  488 (700)
Q Consensus       418 g~~ph~-L~MtATPIPRTLal~~ygdldvS~i~e~P~gR~~I~T~~~~~~~~--------~~~~~~i~~~l~~g~q~y~V  488 (700)
                       ...|. |=+|||=                               +-+.+++        +++|++=.=+|++++=+-=|
T Consensus       414 -~~aHcKLGLTATL-------------------------------vREDdKI~DLNFLIGPKLYEANWleL~~~GfIA~V  461 (756)
T TIGR00603       414 -VQAHCKLGLTATL-------------------------------VREDDKIQDLNFLIGPKLYEANWLELQKKGFIANV  461 (756)
T ss_pred             -HHHHHCCCCCEEE-------------------------------ECCCCCCCCCCCCCCCHHHHHHHHHHHCCCEEEEE
T ss_conf             -4332001432110-------------------------------01114303122135721345326988208836887


Q ss_pred             ------ECCCCC---------CC-CCC----------------------------------CCHHHHHHHHHHHHCCCCE
Q ss_conf             ------712012---------21-112----------------------------------1014666666686637103
Q gi|254780945|r  489 ------CPQIEE---------KK-ESN----------------------------------FRSVVERFNSLHEHFTSSI  518 (700)
Q Consensus       489 ------cPlIee---------se-~~~----------------------------------~~~~~~~~~~l~~~~~~~v  518 (700)
                            ||+=.|         |. |--                                  +-+..+..-+|.+      
T Consensus       462 qCAEVWCPMt~EFY~EYL~~~~~~Kr~LLY~MNP~KFrACqFLI~fHE~~RgDKIIVFsDNVfAL~~YA~kl~K------  535 (756)
T TIGR00603       462 QCAEVWCPMTPEFYREYLREKSRKKRMLLYVMNPNKFRACQFLIRFHERQRGDKIIVFSDNVFALKEYAIKLGK------  535 (756)
T ss_pred             EECCCCCCCCHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHHHHHHHHCCCCEEEEECCHHHHHHHHHHHCCC------
T ss_conf             41210178877789999855112443031203864435778988885414888589942447899999987389------


Q ss_pred             ECCCCCCCHHHHHHHHHHHHCCCE-EEEEECHHHHCCCCCCCCCEEEEECHHHCCHHHHHHHHHCCCC----------CC
Q ss_conf             120146998999999999755986-9999800341046888765899858525474688773011667----------89
Q gi|254780945|r  519 AIIHGRMSDIDKESVMDSFKNGTC-KLLIATTVIEVGIDVVDASIIIIENAEHFGLAQLHQLRGRVGR----------GE  587 (700)
Q Consensus       519 ~~lHGkm~~~ek~~~m~~F~~g~~-~iLvaTtviEVGvdvpna~~mvI~~aerfGLsqLHQLRGRVGR----------g~  587 (700)
                      -.+-|-=+..|+=+|+++|+-.+. .=.-=.=|=---||+|.|||+|=..++-=-==|==|==|||=|          |+
T Consensus       536 pfIYGpTsq~ER~~IL~nF~~n~~vnTIF~SKVGDtSiDlPEAnvlIQiSSH~GSRRQEAQRLGRILRAK~~~~~r~agg  615 (756)
T TIGR00603       536 PFIYGPTSQQERMQILQNFKHNPKVNTIFLSKVGDTSIDLPEANVLIQISSHYGSRRQEAQRLGRILRAKKKSDARMAGG  615 (756)
T ss_pred             CEEECCCCHHHHHHHHHHCCCCCCCCEEEEEEECCCCCCCCCCCEEEEEEECCCCHHHHHHHCCCCCCCCCCCHHHHCCC
T ss_conf             65407987137999986215588645689843027751422142677653267740368764132016787513331377


Q ss_pred             CCEEEEEEECC--CCC-H--HHHHHHHHHHHHCHHHHHHHHHHHHCCCCCCCCCHHCCCCCCCCCCHHHHHHHHHHHHHH
Q ss_conf             83599997088--899-8--799999999841425899999985206300026000698744000388759999999999
Q gi|254780945|r  588 EISSCILLYHP--PLS-K--NSYTRLSVLKNTEDGFLIAEEDLKQRKEGEILGIKQSGMPKFLIAQPELHDSLLEIARKD  662 (700)
Q Consensus       588 ~~s~c~l~~~~--~~~-~--~~~~Rl~~l~~~~dGf~iAe~Dl~lRG~G~~~G~~QsG~~~~~~~d~~~d~~ll~~a~~~  662 (700)
                      +..|==+-|+-  +.+ |  -|.+|=+-|.+=-=-|++=         -.+-|..+  .+++.++.-..-.+||.++=..
T Consensus       616 kE~YNAFFYSLVS~DTqEmyYStKRQ~FLvDQGYsFKVI---------T~L~G~d~--~~~L~Y~s~~Eq~~LLq~VL~~  684 (756)
T TIGR00603       616 KEEYNAFFYSLVSKDTQEMYYSTKRQRFLVDQGYSFKVI---------THLKGMDE--ESNLAYSSKEEQLELLQKVLAA  684 (756)
T ss_pred             CCCCCEEEEECCCCCCEEEECCHHHHHHHHCCCCCEEEE---------CCCCCCCC--CCCCCCCCHHHHHHHHHHHHHC
T ss_conf             644220121013445146510212355543036503676---------16878887--6333446878999999999632


Q ss_pred             HHHH
Q ss_conf             9999
Q gi|254780945|r  663 AKHI  666 (700)
Q Consensus       663 a~~~  666 (700)
                      .+.-
T Consensus       685 ~d~~  688 (756)
T TIGR00603       685 GDDD  688 (756)
T ss_pred             CCCC
T ss_conf             6311


No 354
>PRK03932 asnC asparaginyl-tRNA synthetase; Validated
Probab=88.29  E-value=2.1  Score=22.71  Aligned_cols=77  Identities=16%  Similarity=0.109  Sum_probs=49.2

Q ss_pred             CCCEEEEEEEEEEEEEECCCCCCEEEEEEECCCCEEEEEEECCC--HHHH--HHHCCCCCEEEEEEEEEECC---CEEEE
Q ss_conf             98789999999897542158983389999818936999995188--7899--87328988899998997318---77999
Q gi|254780945|r   66 EERIVTITGYISQHSSFQLQKRRPYKILLNDGTGEITLLFFYRK--TEML--KNVFFEGRKITVTGKIKKLK---NRIIM  138 (700)
Q Consensus        66 ~g~~vti~g~V~~~~~~~~~~r~~~~v~v~D~tg~i~lvfFn~~--~~yl--~k~lk~G~~v~vsGKv~~~~---~~~qi  138 (700)
                      .|+.|++.|.|.+.+   ..+ +..=+.+.|++|.+++..+...  ..+.  .+.+..|+.|.|.|++....   +.+++
T Consensus        16 ig~~V~v~Grv~~~R---~~G-kl~Fi~LrD~tg~~qiq~~~~~~~~~~~~~~~~l~~gd~V~V~G~v~~t~~~~~~~El   91 (462)
T PRK03932         16 VGQEVTIRGWVRTKR---DSG-KISFLELNDGSCFKQIQVVKNNELPNYGEEVFKLTTGSSVYVTGTVVESPGAGQGYEL   91 (462)
T ss_pred             CCCEEEEEEEEEEEE---CCC-CCEEEEEECCCCCEEEEEEECCCCHHHHHHHHCCCCCEEEEEEEEEEECCCCCCCEEE
T ss_conf             899899989778278---179-8389999828987899999679766799999669995699999999925999977799


Q ss_pred             ECCEEEEC
Q ss_conf             77868962
Q gi|254780945|r  139 VHPHYIFH  146 (700)
Q Consensus       139 ~hPe~~~~  146 (700)
                      .--++.+.
T Consensus        92 ~~~~i~vl   99 (462)
T PRK03932         92 QATKIEVI   99 (462)
T ss_pred             EEEEEEEE
T ss_conf             98389998


No 355
>PRK04301 radA DNA repair and recombination protein RadA; Validated
Probab=88.23  E-value=0.35  Score=28.88  Aligned_cols=142  Identities=15%  Similarity=0.102  Sum_probs=70.2

Q ss_pred             CCHHHCCCCCHHHHHHHHHHCCCCCCCCCCHHHHHHHCCCCCCCCCCCCCHHHCCCCCE------EEEEEEEEEEEEECC
Q ss_conf             77213678588999998874012468855489878708974013444464788899878------999999989754215
Q gi|254780945|r   11 APLSTFRGVGKKYSLFLSKIINCGNANETRFIDLLFYHPSSFIDRHYRPKISEISEERI------VTITGYISQHSSFQL   84 (700)
Q Consensus        11 ~pI~~LkGVGpk~a~~L~kl~~l~~~GI~ti~DLL~~~PrrYeDr~~~~~I~~l~~g~~------vti~g~V~~~~~~~~   84 (700)
                      ..|+.|+||||...++|++-      |++|+.|++..=|....+-.-   |++....+.      ..-.+...+.....-
T Consensus         7 ~~l~~lpGv~~~~~~kL~~a------G~~tv~~l~~~~~~~L~~~~g---is~~~a~ki~~~a~~~~~~~~f~Ta~el~~   77 (318)
T PRK04301          7 KDLEDLPGVGPATAEKLREA------GYDTVEAIAVASPKELSEIAG---ISESTAAKIIEAAREALDIGGFETALEVLE   77 (318)
T ss_pred             CCCCCCCCCCHHHHHHHHHC------CCCCHHHHHCCCHHHHHHHHC---CCHHHHHHHHHHHHHHCCCCCCCCHHHHHH
T ss_conf             77455899899999999986------995499987489999998509---999999999999998536579826999999


Q ss_pred             CCCCEEEEEEECCCCEEEEEEECCCHHHHHHHCCCCCEEEEEEEEEECCCEEEEECCEE---EECCCCCCCCCCCCCCCC
Q ss_conf             89833899998189369999951887899873289888999989973187799977868---962643344444110000
Q gi|254780945|r   85 QKRRPYKILLNDGTGEITLLFFYRKTEMLKNVFFEGRKITVTGKIKKLKNRIIMVHPHY---IFHNSQDVNFPLIEAVYS  161 (700)
Q Consensus        85 ~~r~~~~v~v~D~tg~i~lvfFn~~~~yl~k~lk~G~~v~vsGKv~~~~~~~qi~hPe~---~~~~~~~~~~~~I~PIYp  161 (700)
                      .++..  ..+.-+...++-.        +.--++.|.--=++|.....+  -|+-|---   ....+....-+  .-+|=
T Consensus        78 ~r~~~--~~isTg~~~lD~l--------LgGGi~~g~ITEi~Ge~gsGK--TQlc~qLav~~qlp~~~GGl~g--~vvYI  143 (318)
T PRK04301         78 RRKSI--GKITTGSKELDEL--------LGGGIETQSITEFYGEFGSGK--TQICHQLAVNVQLPEEEGGLEG--KAVYI  143 (318)
T ss_pred             HHHCC--CCCCCCCHHHHHH--------CCCCCCCCEEEEEECCCCCCC--HHHHHHHHHHEECCHHHCCCCC--CEEEE
T ss_conf             86347--8247888788805--------479833670788866887870--3566776765337677789886--37999


Q ss_pred             CCHH-HHHHHHHHHH
Q ss_conf             0000-0045430013
Q gi|254780945|r  162 LPTG-LSVDLFKKII  175 (700)
Q Consensus       162 lt~G-Lsqk~irk~I  175 (700)
                      -|+| .+...++.+.
T Consensus       144 DTEgtF~peRi~qia  158 (318)
T PRK04301        144 DTENTFRPERIEQMA  158 (318)
T ss_pred             ECCCCCCHHHHHHHH
T ss_conf             568986979999999


No 356
>cd04316 ND_PkAspRS_like_N ND_PkAspRS_like_N: N-terminal, anticodon recognition domain of the type found in the homodimeric non-discriminating (ND) Pyrococcus kodakaraensis aspartyl-tRNA synthetase (AspRS).  This domain is a beta-barrel domain (OB fold) involved in binding the tRNA anticodon stem-loop.  P. kodakaraensis AspRS is a class 2b aaRS. aaRSs catalyze the specific attachment of amino acids (AAs) to their cognate tRNAs during protein biosynthesis. This 2-step reaction involves i) the activation the AA by ATP in the presence of magnesium ions, followed by ii) the transfer of  the activated AA to the terminal ribose of tRNA.  In the case of the class2b aaRSs, the activated AA is attached to the 3'OH of the terminal ribose. P. kodakaraensis ND-AspRS can charge both tRNAAsp and tRNAAsn. Some of the enzymes in this group may be discriminating, based on the presence of homologs of asparaginyl-tRNA synthetase (AsnRS) in their completed genomes.
Probab=88.14  E-value=2.2  Score=22.64  Aligned_cols=83  Identities=17%  Similarity=0.211  Sum_probs=56.4

Q ss_pred             HHHCCCCCEEEEEEEEEEEEEECCCCCCEEEEEEECCCCEEEEEEECCCH-----HHHHHHCCCCCEEEEEEEEEECC--
Q ss_conf             78889987899999998975421589833899998189369999951887-----89987328988899998997318--
Q gi|254780945|r   61 ISEISEERIVTITGYISQHSSFQLQKRRPYKILLNDGTGEITLLFFYRKT-----EMLKNVFFEGRKITVTGKIKKLK--  133 (700)
Q Consensus        61 I~~l~~g~~vti~g~V~~~~~~~~~~r~~~~v~v~D~tg~i~lvfFn~~~-----~yl~k~lk~G~~v~vsGKv~~~~--  133 (700)
                      ++.-..|+.|++.|-|.+.+.   .+ +..=+.+.|.+|.+++++-....     .++ +.+..+..+.|.|++....  
T Consensus         6 l~~~~~G~~V~i~Gwv~~~R~---~g-~~~Fi~LRD~~G~vQ~v~~~~~~~~~~~~~~-~~l~~EsvV~V~G~V~~~~~~   80 (108)
T cd04316           6 ITPELDGEEVTVAGWVHEIRD---LG-GIKFVILRDREGIVQVTAPKKKVDKELFKTV-RKLSRESVISVTGTVKAEPKA   80 (108)
T ss_pred             CCHHHCCCEEEEEEEEEEEEC---CC-CEEEEEEECCCEEEEEEEECCCCCHHHHHHH-HCCCCCEEEEEEEEEEECCCC
T ss_conf             983899999999899982321---79-8799999809877999993788898999998-659994499999999948989


Q ss_pred             -CEEEEECCEEEECCC
Q ss_conf             -779997786896264
Q gi|254780945|r  134 -NRIIMVHPHYIFHNS  148 (700)
Q Consensus       134 -~~~qi~hPe~~~~~~  148 (700)
                       +.+++.--++++.+.
T Consensus        81 ~~giEi~v~~i~ils~   96 (108)
T cd04316          81 PNGVEIIPEEIEVLSE   96 (108)
T ss_pred             CCCEEEEEEEEEEEEC
T ss_conf             9967589648999858


No 357
>PRK08903 hypothetical protein; Validated
Probab=88.04  E-value=1.5  Score=23.84  Aligned_cols=116  Identities=21%  Similarity=0.220  Sum_probs=61.3

Q ss_pred             HHHHHHHHHHCCCCCCE-EEEEECCCCCHHHHHHHHHHHHHHHHCCEEEEEHHHHHHHHHHHHHHHHCCCCCCEEEEEEC
Q ss_conf             99999998410013430-78862144223699999973344430545886127999999998621101457865899624
Q gi|254780945|r  279 SAIKDILQDMSQKNRML-RILQGDVGSGKTLVALIAMAAAVEAGGQAVIMAPIGILAQQHYEFIKKYTQNTQIIVEIITG  357 (700)
Q Consensus       279 ~ai~eI~~Dl~~~~pM~-RLLQGDVGSGKTiVA~~A~l~~~~~G~Q~alMaPTEILA~QH~~~~~~~~~~~~i~v~lLtg  357 (700)
                      .++..+..-...+.+.+ =.|.|+.|||||=..-..+-.+...+..+.++-.-+         +...+.           
T Consensus        27 ~~~~~l~~~~~~~~~~~~l~i~G~~G~GKTHLl~a~~~~~~~~~~~~~yl~~~~---------~~~~~~-----------   86 (227)
T PRK08903         27 ELVTRLRELAAGPVADRFFYLWGEAGSGRSHLLQALVAAASEGGKNARYLDPAS---------PLLAFD-----------   86 (227)
T ss_pred             HHHHHHHHHHHCCCCCCEEEEECCCCCCHHHHHHHHHHHHHHCCCCEEEECCCC---------CHHHHH-----------
T ss_conf             999999988743887866999899999888999999999980699749965110---------457774-----------


Q ss_pred             CCCHHHHHHHHHHHCCCCCEEEEECHHHCCCCCCCCCCCEEEECCCCCCCHHHHHHHHH-----CCCCCCCEEECHHHHH
Q ss_conf             64225667687762134754864111201334554444178852101335688998740-----2567761010101322
Q gi|254780945|r  358 NMPQAHRRKALERIAHGQAHIIIGTHALFQDSIQYYKLILVIVDEQHRFGVQQRLKLTQ-----KATAPHVLLMTATPIP  432 (700)
Q Consensus       358 ~~~~~er~~i~~~i~~G~~~iiIGTHAL~q~~v~F~~LgLvViDEQHRFGV~QR~~L~~-----Kg~~ph~L~MtATPIP  432 (700)
                                                       ...+..+++||.=|++.-..-..|-.     +...--+|++|+..=|
T Consensus        87 ---------------------------------~~~~~d~l~iDDi~~i~~~~q~~lF~l~N~~~~~~~~~ll~s~~~~p  133 (227)
T PRK08903         87 ---------------------------------FDPRAELYAVDDVERLDDAQQIALFNLFNRVRAHGKTALLVAGPAAP  133 (227)
T ss_pred             ---------------------------------HHHCCCEEEEECCCCCCCHHHHHHHHHHHHHHHCCCCEEEECCCCCH
T ss_conf             ---------------------------------20018989996411489569999999999999729948997189971


Q ss_pred             HHHHHHHHHCCCHHHHCC
Q ss_conf             789999752010111102
Q gi|254780945|r  433 RTLVLTSLGDIDISKITE  450 (700)
Q Consensus       433 RTLal~~ygdldvS~i~e  450 (700)
                      ..+.+.  .||- |.+.-
T Consensus       134 ~~l~~~--~DL~-SRl~~  148 (227)
T PRK08903        134 LALDVR--EDLR-TRLGW  148 (227)
T ss_pred             HHCCCC--HHHH-HHHHC
T ss_conf             201200--8999-99938


No 358
>pfam04994 TfoX_C TfoX C-terminal domain. TfoX may play a key role in the development of genetic competence by regulating the expression of late competence-specific genes. This family corresponds to the C-terminal presumed domain of TfoX. The domain is found associated with pfam00383 in a cytidine and deoxycytidylate deaminase family protein from Neisseria meningitidis serogroup B. It is also found as an isolated domain in some proteins suggesting this is an autonomous domain.
Probab=88.02  E-value=0.46  Score=27.93  Aligned_cols=31  Identities=23%  Similarity=0.188  Sum_probs=26.3

Q ss_pred             HHHCCCCCHHHHHHHHHHCCCCCCCCCCHHHHHHHCC
Q ss_conf             2136785889999988740124688554898787089
Q gi|254780945|r   13 LSTFRGVGKKYSLFLSKIINCGNANETRFIDLLFYHP   49 (700)
Q Consensus        13 I~~LkGVGpk~a~~L~kl~~l~~~GI~ti~DLL~~~P   49 (700)
                      |..||++||+.+..|++.      ||+|+.||-..=+
T Consensus         1 l~dLpNlg~~~er~L~~v------GI~t~~~L~~~Ga   31 (77)
T pfam04994         1 LKDLPNLGLKLERMLKKA------GIHTVEDLRELGA   31 (77)
T ss_pred             CCCCCCCCHHHHHHHHHC------CCCCHHHHHHHCH
T ss_conf             987889899999999994------9998999998189


No 359
>COG3390 Uncharacterized protein conserved in archaea [Function unknown]
Probab=88.01  E-value=2.2  Score=22.59  Aligned_cols=75  Identities=16%  Similarity=0.282  Sum_probs=53.0

Q ss_pred             CEEEEEEEEEEEEEECCCCCCEEEEEEECCCCEEEEEEECCCHHH---HHHHCCCCCEEEEEEEEEECCCE----EEEEC
Q ss_conf             789999999897542158983389999818936999995188789---98732898889999899731877----99977
Q gi|254780945|r   68 RIVTITGYISQHSSFQLQKRRPYKILLNDGTGEITLLFFYRKTEM---LKNVFFEGRKITVTGKIKKLKNR----IIMVH  140 (700)
Q Consensus        68 ~~vti~g~V~~~~~~~~~~r~~~~v~v~D~tg~i~lvfFn~~~~y---l~k~lk~G~~v~vsGKv~~~~~~----~qi~h  140 (700)
                      ..+-|.|++++...+.. -+-++++.+.|.||.+-+ |=++++|-   ..+....++.+.|-||++.|...    ++.+-
T Consensus        46 nRifivGtltek~~i~e-d~~~~R~rVvDpTGsF~V-yag~yqPEa~a~l~~ve~~~~VaViGKi~~y~~d~g~~~~siR  123 (196)
T COG3390          46 NRIFIVGTLTEKEGIGE-DREYWRIRVVDPTGSFYV-YAGQYQPEAKAFLEDVEVPDLVAVIGKIRTYRTDEGVVLFSIR  123 (196)
T ss_pred             EEEEEEEEEEECCCCCC-CCCEEEEEEECCCCCEEE-ECCCCCHHHHHHHHHCCCCCEEEEECCCCEEECCCCCEEEEEC
T ss_conf             57899998871367677-532789999568861899-8278795789999855677547775132102148883699963


Q ss_pred             CEEE
Q ss_conf             8689
Q gi|254780945|r  141 PHYI  144 (700)
Q Consensus       141 Pe~~  144 (700)
                      ||-+
T Consensus       124 pE~v  127 (196)
T COG3390         124 PELV  127 (196)
T ss_pred             HHHH
T ss_conf             5773


No 360
>pfam00154 RecA recA bacterial DNA recombination protein. RecA is a DNA-dependent ATPase and functions in DNA repair systems. RecA protein catalyses an ATP-dependent DNA strand-exchange reaction that is the central step in the repair of dsDNA breaks by homologous recombination.
Probab=87.95  E-value=2.2  Score=22.56  Aligned_cols=82  Identities=23%  Similarity=0.305  Sum_probs=51.2

Q ss_pred             CCCCCEE--EEEECCCCCHHHHHHHHHHHHHHHHCCEEEEEHHHH-HHHHHHHHHHHHCCCCCCEEE--EEECCCCHHHH
Q ss_conf             0134307--886214422369999997334443054588612799-999999862110145786589--96246422566
Q gi|254780945|r  290 QKNRMLR--ILQGDVGSGKTLVALIAMAAAVEAGGQAVIMAPIGI-LAQQHYEFIKKYTQNTQIIVE--IITGNMPQAHR  364 (700)
Q Consensus       290 ~~~pM~R--LLQGDVGSGKTiVA~~A~l~~~~~G~Q~alMaPTEI-LA~QH~~~~~~~~~~~~i~v~--lLtg~~~~~er  364 (700)
                      .+.|..|  .+-|.=+||||-.|+.++..+-..|..|++.-- |= +-.+       |+..+|+.+.  ++.-..+.-+-
T Consensus        47 GGlP~GRi~ei~G~essGKTtlal~~ia~aQk~gg~~~~iD~-E~a~d~~-------~a~~lGVD~~~l~~~qpd~~Eqa  118 (322)
T pfam00154        47 GGLPKGRIIEIYGPESSGKTTLALHAIAEAQKAGGTAAFIDA-EHALDPV-------YAKKLGVDIDNLLVSQPDTGEQA  118 (322)
T ss_pred             CCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHCCCEEEEEEH-HHHCCHH-------HHHHCCCCHHHEEEECCCHHHHH
T ss_conf             997787089998898777899999999999734993899853-6605988-------99980988025389778839999


Q ss_pred             HHHHHH-HCCCCCEEE
Q ss_conf             768776-213475486
Q gi|254780945|r  365 RKALER-IAHGQAHII  379 (700)
Q Consensus       365 ~~i~~~-i~~G~~~ii  379 (700)
                      -++.+. +.+|.++++
T Consensus       119 l~i~~~li~~~~~~li  134 (322)
T pfam00154       119 LEIADMLVRSGAVDLI  134 (322)
T ss_pred             HHHHHHHHCCCCCCEE
T ss_conf             9999998537997659


No 361
>cd04496 SSB_OBF SSB_OBF: A subfamily of OB folds similar to the OB fold of ssDNA-binding protein (SSB). SSBs bind with high affinity to ssDNA. They bind to and protect ssDNA intermediates during DNA metabolic pathways. All bacterial and eukaryotic SSBs studied to date oligomerize to bring together four OB folds in their active state. The majority (e.g. Escherichia coli SSB) have a single OB fold per monomer, which oligomerize to form a homotetramer. However, Deinococcus and Thermus SSB proteins have two OB folds per monomer, which oligomerize to form a homodimer. Mycobacterium tuberculosis SSB varies in quaternary structure from E. coli SSB. It forms a dimer of dimers having a unique dimer interface, which lends the protein greater stability. Included in this group are OB folds similar to Escherichia coli PriB. E.coli PriB is homodimeric with each monomer having a single OB fold. It does not appear to form higher order oligomers. PriB is an essential protein for the replication restart
Probab=87.75  E-value=2.3  Score=22.47  Aligned_cols=38  Identities=18%  Similarity=0.268  Sum_probs=31.2

Q ss_pred             CCCCEEEEEEECCCHHHHHHHCCCCCEEEEEEEEEECC
Q ss_conf             18936999995188789987328988899998997318
Q gi|254780945|r   96 DGTGEITLLFFYRKTEMLKNVFFEGRKITVTGKIKKLK  133 (700)
Q Consensus        96 D~tg~i~lvfFn~~~~yl~k~lk~G~~v~vsGKv~~~~  133 (700)
                      +++.-+.++.|+.....+.+.+++|+.+.|.|.+....
T Consensus        41 ~~t~~~~v~~wg~~A~~~~~~l~KG~~V~V~G~l~~~~   78 (100)
T cd04496          41 EETDWIRVVAFGKLAENAAKYLKKGDLVYVEGRLRTRS   78 (100)
T ss_pred             CCCEEEEEEEECHHHHHHHHHCCCCCEEEEEEEEECCE
T ss_conf             34199999999708987787537998899999988123


No 362
>KOG0949 consensus
Probab=87.74  E-value=0.6  Score=27.00  Aligned_cols=153  Identities=17%  Similarity=0.221  Sum_probs=93.1

Q ss_pred             CCCCHHHHHHHHHHHHHHCCCCCCEEEEEECCCCCHHHHHHHHHHHHHHH--HCCEEEEEHHHHHHHHHHHHHHHHCCC-
Q ss_conf             46798899999999984100134307886214422369999997334443--054588612799999999862110145-
Q gi|254780945|r  271 FSPTKSQESAIKDILQDMSQKNRMLRILQGDVGSGKTLVALIAMAAAVEA--GGQAVIMAPIGILAQQHYEFIKKYTQN-  347 (700)
Q Consensus       271 F~LT~~Q~~ai~eI~~Dl~~~~pM~RLLQGDVGSGKTiVA~~A~l~~~~~--G~Q~alMaPTEILA~QH~~~~~~~~~~-  347 (700)
                      |..-.=|.+-++-. .-+.|     -++---.-||||-+...||-.+...  ..=+.+.|||.-|-.|--.+...+|.. 
T Consensus       510 F~Pd~WQ~elLDsv-Dr~eS-----avIVAPTSaGKTfisfY~iEKVLResD~~VVIyvaPtKaLVnQvsa~VyaRF~~~  583 (1330)
T KOG0949         510 FCPDEWQRELLDSV-DRNES-----AVIVAPTSAGKTFISFYAIEKVLRESDSDVVIYVAPTKALVNQVSANVYARFDTK  583 (1330)
T ss_pred             CCCCHHHHHHHHHH-HCCCC-----EEEEEECCCCCEECCHHHHHHHHHHCCCCEEEEECCHHHHHHHHHHHHHHHHCCC
T ss_conf             69838888776655-05662-----5998204678610058999999854279879996645877666667788763367


Q ss_pred             CCCEEEEEECCCCHHHHHHHHHHHCCCCCEEEEECHHHC-----CC--CC-CCCCCCEEEECCCCCCCHHHHHHHHHCC-
Q ss_conf             786589962464225667687762134754864111201-----33--45-5444417885210133568899874025-
Q gi|254780945|r  348 TQIIVEIITGNMPQAHRRKALERIAHGQAHIIIGTHALF-----QD--SI-QYYKLILVIVDEQHRFGVQQRLKLTQKA-  418 (700)
Q Consensus       348 ~~i~v~lLtg~~~~~er~~i~~~i~~G~~~iiIGTHAL~-----q~--~v-~F~~LgLvViDEQHRFGV~QR~~L~~Kg-  418 (700)
                      .-.+..-|-|.++.-=+      +.-=.++|+|---..+     +.  .- --++-..||.||=|.-|-.--..+++.- 
T Consensus       584 t~~rg~sl~g~ltqEYs------inp~nCQVLITvPecleslLlspp~~q~~cerIRyiIfDEVH~iG~~ed~l~~Eqll  657 (1330)
T KOG0949         584 TFLRGVSLLGDLTQEYS------INPWNCQVLITVPECLESLLLSPPHHQKFCERIRYIIFDEVHLIGNEEDGLLWEQLL  657 (1330)
T ss_pred             CCCCCHHHHHHHHHHHC------CCCHHCEEEEECHHHHHHHHCCCHHHHHHHHCCEEEEECHHHHCCCCCCCHHHHHHH
T ss_conf             65631346766667735------784113599974678998863856653022400589711233246524341899877


Q ss_pred             --CCCCCEEECHHHHHHHH
Q ss_conf             --67761010101322789
Q gi|254780945|r  419 --TAPHVLLMTATPIPRTL  435 (700)
Q Consensus       419 --~~ph~L~MtATPIPRTL  435 (700)
                        ..+-+|+.|||==|--+
T Consensus       658 ~li~CP~L~LSATigN~~l  676 (1330)
T KOG0949         658 LLIPCPFLVLSATIGNPNL  676 (1330)
T ss_pred             HHCCCCEEEEECCCCCHHH
T ss_conf             7457870687413388889


No 363
>PRK10646 putative ATPase; Provisional
Probab=87.52  E-value=0.37  Score=28.67  Aligned_cols=42  Identities=29%  Similarity=0.361  Sum_probs=28.9

Q ss_pred             CCEEEEEECCCCCHHHHHHHHHHHHHHHHCCEEEEEHHHHHHHHH
Q ss_conf             430788621442236999999733444305458861279999999
Q gi|254780945|r  293 RMLRILQGDVGSGKTLVALIAMAAAVEAGGQAVIMAPIGILAQQH  337 (700)
Q Consensus       293 pM~RLLQGDVGSGKTiVA~~A~l~~~~~G~Q~alMaPTEILA~QH  337 (700)
                      ..--+|+||.|+|||.-+=. ++.+.  |.+..+-.||=.|.+.+
T Consensus        28 g~vi~L~G~LGaGKTtf~r~-i~~~l--g~~~~V~SPTf~lv~~Y   69 (153)
T PRK10646         28 ATVIYLYGDLGAGKTTFSRG-FLQAL--GHQGNVKSPTYTLVEPY   69 (153)
T ss_pred             CCEEEEECCCCCCHHHHHHH-HHHHC--CCCCCCCCCCEEEEEEE
T ss_conf             97999988887899999999-99984--99786269976479973


No 364
>COG2247 LytB Putative cell wall-binding domain [Cell envelope biogenesis, outer membrane]
Probab=87.36  E-value=1.2  Score=24.56  Aligned_cols=67  Identities=15%  Similarity=0.245  Sum_probs=54.8

Q ss_pred             CCHHHHHHHHHHHHCCC-----CEECCCCCCCHHHHHHHHHHHHCCCEEEEEECHHHHCCCCCCCC---CEEEEECHHHC
Q ss_conf             10146666666866371-----03120146998999999999755986999980034104688876---58998585254
Q gi|254780945|r  500 FRSVVERFNSLHEHFTS-----SIAIIHGRMSDIDKESVMDSFKNGTCKLLIATTVIEVGIDVVDA---SIIIIENAEHF  571 (700)
Q Consensus       500 ~~~~~~~~~~l~~~~~~-----~v~~lHGkm~~~ek~~~m~~F~~g~~~iLvaTtviEVGvdvpna---~~mvI~~aerf  571 (700)
                      ...++...+.+++.||.     ++-++||-.-.+   +.|+..++|-+.++++-|+++    +|+-   .+...+.|+++
T Consensus       112 ~ETa~~v~~~~~~~yp~af~n~kvvvv~GwDy~~---~~~e~~k~~~~p~~~~n~~~~----~~~~~~~~l~~s~~a~~~  184 (337)
T COG2247         112 YETAEKVAKFFREDYPNAFKNVKVVVVYGWDYAD---ALMELMKEGIVPVILKNTSIL----VRWSRKLALAESPYAANI  184 (337)
T ss_pred             HHHHHHHHHHHHHHCHHHHCCEEEEEEECCCCHH---HHHHHHHCCCCEEEECCCCCC----CCCCCCEEEEECHHHHHC
T ss_conf             8999999999976442331581799996602277---788887537532674166422----332222113444757854


Q ss_pred             CH
Q ss_conf             74
Q gi|254780945|r  572 GL  573 (700)
Q Consensus       572 GL  573 (700)
                      |-
T Consensus       185 ~~  186 (337)
T COG2247         185 GC  186 (337)
T ss_pred             CC
T ss_conf             88


No 365
>KOG2383 consensus
Probab=87.30  E-value=0.42  Score=28.22  Aligned_cols=42  Identities=31%  Similarity=0.355  Sum_probs=25.2

Q ss_pred             CCCCCEEEEEECCCCCHHHHHHHHHHHHHHHHCCEEEEEHHHHHHHH--HHHHHHH
Q ss_conf             01343078862144223699999973344430545886127999999--9986211
Q gi|254780945|r  290 QKNRMLRILQGDVGSGKTLVALIAMAAAVEAGGQAVIMAPIGILAQQ--HYEFIKK  343 (700)
Q Consensus       290 ~~~pM~RLLQGDVGSGKTiVA~~A~l~~~~~G~Q~alMaPTEILA~Q--H~~~~~~  343 (700)
                      ..-|---.|-||||||||.+    |=...++       .| .|.-+|  ||..|..
T Consensus       111 ~~~PkGlYlYG~VGcGKTmL----MDlFy~~-------~~-~i~rkqRvHFh~fM~  154 (467)
T KOG2383         111 PGPPKGLYLYGSVGCGKTML----MDLFYDA-------LP-PIWRKQRVHFHGFML  154 (467)
T ss_pred             CCCCCEEEEECCCCCCHHHH----HHHHHHC-------CC-CCHHHHHHHHHHHHH
T ss_conf             89984689963567544677----8877632-------78-401344403999999


No 366
>PRK08006 replicative DNA helicase; Provisional
Probab=87.23  E-value=2.4  Score=22.26  Aligned_cols=71  Identities=15%  Similarity=0.113  Sum_probs=44.5

Q ss_pred             EEEECCCCCHHHHHHHHHHHHH-HHHCCEEEEEHHHHHHHHHHHHHHHHCCCCCCEEEEEECCCCHHHHHHHHH
Q ss_conf             8862144223699999973344-430545886127999999998621101457865899624642256676877
Q gi|254780945|r  297 ILQGDVGSGKTLVALIAMAAAV-EAGGQAVIMAPIGILAQQHYEFIKKYTQNTQIIVEIITGNMPQAHRRKALE  369 (700)
Q Consensus       297 LLQGDVGSGKTiVA~~A~l~~~-~~G~Q~alMaPTEILA~QH~~~~~~~~~~~~i~v~lLtg~~~~~er~~i~~  369 (700)
                      .|=|--|.|||..|+--+..++ ..|..|++... |.=++|-+..+-......+. -.+-+|..+..+...+..
T Consensus       228 viaaRPsmGKTalalnia~~~a~~~~~~V~~fSl-EMs~~ql~~Rlla~~s~v~~-~~i~~g~l~~~e~~~l~~  299 (471)
T PRK08006        228 IVAARPSMGKTTFAMNLCENAAMLQDKPVLIFSL-EMPGEQIMMRMLASLSRVDQ-TRIRTGQLDDEDWARISG  299 (471)
T ss_pred             EEEECCCCCHHHHHHHHHHHHHHHCCCCEEEEEC-CCCHHHHHHHHHHHHCCCCC-CCCCCCCCCHHHHHHHHH
T ss_conf             9994699876999999999999866995799816-79999999999997447775-545368879999999999


No 367
>PRK09302 circadian clock protein KaiC; Reviewed
Probab=87.20  E-value=0.81  Score=25.99  Aligned_cols=36  Identities=28%  Similarity=0.431  Sum_probs=31.4

Q ss_pred             CEEEEEECCCCCHHHHHHHHHHHHHHHHCCEEEEEH
Q ss_conf             307886214422369999997334443054588612
Q gi|254780945|r  294 MLRILQGDVGSGKTLVALIAMAAAVEAGGQAVIMAP  329 (700)
Q Consensus       294 M~RLLQGDVGSGKTiVA~~A~l~~~~~G~Q~alMaP  329 (700)
                      -.-|+-|--|||||..|+.-+..++.+|-.|++.+=
T Consensus       267 sstLi~Gp~GtGKTtla~qFl~~~a~~GE~~l~~~F  302 (501)
T PRK09302        267 SIILVSGATGTGKTLLVSKFAEAACRRGERCLLFAF  302 (501)
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHHHHCCCCEEEEEE
T ss_conf             469998899988899999999999865990899999


No 368
>PRK13341 recombination factor protein RarA/unknown domain fusion protein; Reviewed
Probab=87.17  E-value=2.2  Score=22.60  Aligned_cols=152  Identities=17%  Similarity=0.305  Sum_probs=67.4

Q ss_pred             CCCCHHCHHCCCHHHCCCCCHHHHHHHHHHCCCCCCCCCCHHHHHHHCCCCCCCCCCCCCHHHCCCCCEEEEEEEEEEEE
Q ss_conf             97102021017721367858899999887401246885548987870897401344446478889987899999998975
Q gi|254780945|r    1 MRPSFLNPLFAPLSTFRGVGKKYSLFLSKIINCGNANETRFIDLLFYHPSSFIDRHYRPKISEISEERIVTITGYISQHS   80 (700)
Q Consensus         1 mrp~~l~~L~~pI~~LkGVGpk~a~~L~kl~~l~~~GI~ti~DLL~~~PrrYeDr~~~~~I~~l~~g~~vti~g~V~~~~   80 (700)
                      |||..|+.+. .=+.|-|-|.    .|.+++-     =.++.-+++|=|-.-=--|-..-|++-..-..+.+.++...+.
T Consensus        22 mRP~~Lde~v-GQ~hllg~g~----~Lrr~i~-----~~~~~S~Il~GPPGtGKTTLA~iIA~~t~~~F~~lsAv~sgvk   91 (726)
T PRK13341         22 LRPRTLEEFV-GQDHILGEGR----LLRRAIK-----ADRVGSLILYGPPGVGKTTLARIIANHTRAHFSSLNAVLAGVK   91 (726)
T ss_pred             HCCCCHHHHC-CCHHHCCCCC----HHHHHHH-----CCCCCEEEEECCCCCCHHHHHHHHHHHHCCCEEEEECCCCCHH
T ss_conf             2999877735-9575428982----8999997-----6999827888979999999999998874886799856203779


Q ss_pred             EEC-----CCCC-C---EEEEEEECCCCEEEEEEECCCHH-HHHHHCCCCCEEEEEEEEEECCCEEEEECCEEEECCCCC
Q ss_conf             421-----5898-3---38999981893699999518878-998732898889999899731877999778689626433
Q gi|254780945|r   81 SFQ-----LQKR-R---PYKILLNDGTGEITLLFFYRKTE-MLKNVFFEGRKITVTGKIKKLKNRIIMVHPHYIFHNSQD  150 (700)
Q Consensus        81 ~~~-----~~~r-~---~~~v~v~D~tg~i~lvfFn~~~~-yl~k~lk~G~~v~vsGKv~~~~~~~qi~hPe~~~~~~~~  150 (700)
                      .++     .+.+ .   .-++.+-|+     +--||..+. .+-.....|. +++-|--        --||-|++.+.- 
T Consensus        92 dlr~ii~~A~~~~~~~g~~tILFIDE-----IHRfNK~QQD~LLp~vE~G~-i~LIGAT--------TENP~F~vn~AL-  156 (726)
T PRK13341         92 DLRAEVDAAKERLERHGKRTILFIDE-----VHRFNKAQQDALLPWVENGT-VTLIGAT--------TENPYFEVNKAL-  156 (726)
T ss_pred             HHHHHHHHHHHHHHHCCCCEEEEEEC-----HHHCCHHHHHHHHHHHCCCE-EEEEEEC--------CCCCCEEECHHH-
T ss_conf             99999999999987459965999862-----54258878998788860683-8999704--------789743642988-


Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf             4444411000000000045430013457874
Q gi|254780945|r  151 VNFPLIEAVYSLPTGLSVDLFKKIIVEALSR  181 (700)
Q Consensus       151 ~~~~~I~PIYplt~GLsqk~irk~I~~aL~~  181 (700)
                        ..+- -||.+ +.++...+.++++.|++.
T Consensus       157 --lSR~-~vf~L-~~L~~~dl~~il~rAl~d  183 (726)
T PRK13341        157 --VSRS-RLFRL-KSLEDEDLHQLLKRALQD  183 (726)
T ss_pred             --HHHC-EEEEE-CCCCHHHHHHHHHHHHHH
T ss_conf             --8323-46674-389999999999999876


No 369
>cd04482 RPA2_OBF_like RPA2_OBF_like: A subgroup of uncharacterized archaeal OB folds with similarity to the OB fold of the central ssDNA-binding domain (DBD)-D of human RPA2 (also called RPA32). RPA2 is a subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). The major DNA binding activity of RPA is associated with RPA1 DBD-A and DBD-B; RPA2 DBD-D is a weak ssDNA-binding domain. RPA2 DBD-D is also involved in trimerization. The ssDNA binding mechanism is believed to be multistep and to involve conformational change. N-terminal to human RPA2 DBD-D is a domain containing all the known phosphorylation sites of RPA. Human RPA2 is phosphorylated in a cell cycle depende
Probab=87.08  E-value=2.5  Score=22.20  Aligned_cols=61  Identities=20%  Similarity=0.333  Sum_probs=44.3

Q ss_pred             EEEEEEEEEEEECCCCCCEEEEEEECCCCEEEEEEECCCH--HHHHHHCCCCCEEEEEEEEEECC
Q ss_conf             9999998975421589833899998189369999951887--89987328988899998997318
Q gi|254780945|r   71 TITGYISQHSSFQLQKRRPYKILLNDGTGEITLLFFYRKT--EMLKNVFFEGRKITVTGKIKKLK  133 (700)
Q Consensus        71 ti~g~V~~~~~~~~~~r~~~~v~v~D~tg~i~lvfFn~~~--~yl~k~lk~G~~v~vsGKv~~~~  133 (700)
                      .+.|+|.+.... .+++ -..+.+.|+++.+.+..|--..  .-+.+.|.+|+.+.++|-++...
T Consensus         2 ~~~G~V~~~P~~-i~GG-Hv~~~v~~~~~~i~~~afepTg~~r~~~r~L~~GD~I~v~G~v~~~~   64 (91)
T cd04482           2 RVTGKVVEEPRT-IEGG-HVFFKISDGTGEIDCAAYEPTKEFRDVVRLLIPGDEVTVYGSVRPGT   64 (91)
T ss_pred             EEEEEEECCEEE-ECCC-EEEEEEEECCCEEEEEEECCCCHHHHHHHHCCCCCEEEEEEEECCCC
T ss_conf             899999786489-5287-49999993998899999987750889997389999999999987898


No 370
>pfam03969 AFG1_ATPase AFG1-like ATPase. This family of proteins contains a P-loop motif and are predicted to be ATPases.
Probab=87.01  E-value=2  Score=22.89  Aligned_cols=43  Identities=21%  Similarity=0.107  Sum_probs=25.0

Q ss_pred             CCEEEEEECCCCCHHHHHHHHHHHHHHHHCCEEEEEHHHHHHHHHHHHHHHHCC
Q ss_conf             430788621442236999999733444305458861279999999986211014
Q gi|254780945|r  293 RMLRILQGDVGSGKTLVALIAMAAAVEAGGQAVIMAPIGILAQQHYEFIKKYTQ  346 (700)
Q Consensus       293 pM~RLLQGDVGSGKTiVA~~A~l~~~~~G~Q~alMaPTEILA~QH~~~~~~~~~  346 (700)
                      |.-=-|.|+||+|||.+-=+- +.++          |.+-=-+.||..|....-
T Consensus        61 ~kGlYl~G~VGrGKTmLMDlF-y~~l----------p~~~K~R~HFh~FM~~vH  103 (361)
T pfam03969        61 VRGLYLWGGVGRGKTHLMDSF-FESL----------PGERKRRTHFHRFMFRVH  103 (361)
T ss_pred             CCEEEEECCCCCCHHHHHHHH-HHHC----------CCCCCCCCCHHHHHHHHH
T ss_conf             986898899888699999999-9867----------753444566789999999


No 371
>COG0541 Ffh Signal recognition particle GTPase [Intracellular trafficking and secretion]
Probab=86.86  E-value=2.5  Score=22.11  Aligned_cols=122  Identities=21%  Similarity=0.259  Sum_probs=71.2

Q ss_pred             HCCCCCCEEEEEECCCCCHHHHHHHHHHHHHHHHCCEEEEEHHHHHHHHHHHHHHHHCCCCCCEEEEEE-CCCCHHHHHH
Q ss_conf             100134307886214422369999997334443054588612799999999862110145786589962-4642256676
Q gi|254780945|r  288 MSQKNRMLRILQGDVGSGKTLVALIAMAAAVEAGGQAVIMAPIGILAQQHYEFIKKYTQNTQIIVEIIT-GNMPQAHRRK  366 (700)
Q Consensus       288 l~~~~pM~RLLQGDVGSGKTiVA~~A~l~~~~~G~Q~alMaPTEILA~QH~~~~~~~~~~~~i~v~lLt-g~~~~~er~~  366 (700)
                      +....|-.-|+-|==|||||--|.--+...-..|+.+.+.| +.+--.--|+.++.+-...++.+.-.. +..+..--++
T Consensus        95 l~~~~P~vImmvGLQGsGKTTt~~KLA~~lkk~~~kvllVa-aD~~RpAA~eQL~~La~q~~v~~f~~~~~~~Pv~Iak~  173 (451)
T COG0541          95 LAKKPPTVILMVGLQGSGKTTTAGKLAKYLKKKGKKVLLVA-ADTYRPAAIEQLKQLAEQVGVPFFGSGTEKDPVEIAKA  173 (451)
T ss_pred             CCCCCCEEEEEEECCCCCHHHHHHHHHHHHHHCCCCEEEEE-CCCCCHHHHHHHHHHHHHCCCCEECCCCCCCHHHHHHH
T ss_conf             37899858999815679748689999999997499458985-05678689999999998609853167788997999999


Q ss_pred             HHHHHCCCCCEEEEECHHHCCCCCCCCCCCEEEECCCCCCCHHHHH----HHHHCCCCCC--CEEECHH
Q ss_conf             8776213475486411120133455444417885210133568899----8740256776--1010101
Q gi|254780945|r  367 ALERIAHGQAHIIIGTHALFQDSIQYYKLILVIVDEQHRFGVQQRL----KLTQKATAPH--VLLMTAT  429 (700)
Q Consensus       367 i~~~i~~G~~~iiIGTHAL~q~~v~F~~LgLvViDEQHRFGV~QR~----~L~~Kg~~ph--~L~MtAT  429 (700)
                      .++..++...|                   +||||---|-.++...    .-..+-.+||  +||+-|+
T Consensus       174 al~~ak~~~~D-------------------vvIvDTAGRl~ide~Lm~El~~Ik~~~~P~E~llVvDam  223 (451)
T COG0541         174 ALEKAKEEGYD-------------------VVIVDTAGRLHIDEELMDELKEIKEVINPDETLLVVDAM  223 (451)
T ss_pred             HHHHHHHCCCC-------------------EEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEEEECC
T ss_conf             99999974998-------------------899968873303099999999998553987489987644


No 372
>PRK08609 hypothetical protein; Provisional
Probab=86.74  E-value=0.65  Score=26.77  Aligned_cols=30  Identities=27%  Similarity=0.130  Sum_probs=23.7

Q ss_pred             CHHHCCCCCHHHHHHHHHHCCCCCCCCCCHHHHHH
Q ss_conf             72136785889999988740124688554898787
Q gi|254780945|r   12 PLSTFRGVGKKYSLFLSKIINCGNANETRFIDLLF   46 (700)
Q Consensus        12 pI~~LkGVGpk~a~~L~kl~~l~~~GI~ti~DLL~   46 (700)
                      .+..++|||||++..|-+-     .||.|+.||-.
T Consensus        89 eLl~IpGlGPKka~~L~~e-----LGI~sleeL~~  118 (570)
T PRK08609         89 PLLKLPGLGGKKIAKLYKE-----LGVVDKESLKE  118 (570)
T ss_pred             HHHCCCCCCHHHHHHHHHH-----HCCCCHHHHHH
T ss_conf             9977898778999999998-----29999999999


No 373
>PRK05703 flhF flagellar biosynthesis regulator FlhF; Validated
Probab=86.68  E-value=2.6  Score=22.05  Aligned_cols=159  Identities=23%  Similarity=0.241  Sum_probs=94.5

Q ss_pred             EEEECCCCCHHH-HHHHHHHHHHHHHC-CEEEEEH-H-HHHHHHHHHHHHHHCCCCCCEEEEEECCCCHHHHHHHHHHHC
Q ss_conf             886214422369-99999733444305-4588612-7-999999998621101457865899624642256676877621
Q gi|254780945|r  297 ILQGDVGSGKTL-VALIAMAAAVEAGG-QAVIMAP-I-GILAQQHYEFIKKYTQNTQIIVEIITGNMPQAHRRKALERIA  372 (700)
Q Consensus       297 LLQGDVGSGKTi-VA~~A~l~~~~~G~-Q~alMaP-T-EILA~QH~~~~~~~~~~~~i~v~lLtg~~~~~er~~i~~~i~  372 (700)
                      .+-|=.|+|||- +|=+|+..+...|. .++|..= | -|=|....+++.++   +|+++.....   ..+=+++++++.
T Consensus       214 alVGPTGVGKTTTiAKLAA~~~l~~~~~kV~lIT~DtyRigA~eQLk~Ya~i---lgvp~~v~~~---~~~l~~al~~~~  287 (412)
T PRK05703        214 ALVGPTGVGKTTTLAKLAARYALEEGKDKVALITLDTYRIGAVEQLKTYAKI---MGIPVKVAYD---PKELAKALEQLA  287 (412)
T ss_pred             EEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEEEECCCCHHHHHHHHHHHHH---CCCEEEEECC---HHHHHHHHHHHC
T ss_conf             9988888756769999999999972998179998376777799999999997---1973798479---999999998715


Q ss_pred             CCCCEEEEECHHHCCCCCCCCCCCEEEECCCCCCCHHHHHHHHHCCC-CCCCEEECHHHHHHHHHHHH--HHCCCHHHHC
Q ss_conf             34754864111201334554444178852101335688998740256-77610101013227899997--5201011110
Q gi|254780945|r  373 HGQAHIIIGTHALFQDSIQYYKLILVIVDEQHRFGVQQRLKLTQKAT-APHVLLMTATPIPRTLVLTS--LGDIDISKIT  449 (700)
Q Consensus       373 ~G~~~iiIGTHAL~q~~v~F~~LgLvViDEQHRFGV~QR~~L~~Kg~-~ph~L~MtATPIPRTLal~~--ygdldvS~i~  449 (700)
                      +.+ -|+|-|--.=+     +       |+++   +.|=..+..... .--.||||||-=++.|.-++  |+.+.+    
T Consensus       288 ~~d-lILIDTaG~s~-----~-------d~~~---~~eL~~~~~~~~~~~~~LVlsat~~~~dl~~i~~~f~~~~~----  347 (412)
T PRK05703        288 NCD-LILIDTAGRSQ-----R-------DPRL---ISELKALIENSKPIDVYLVLSATTKYRDLKDIVKHFSRLPL----  347 (412)
T ss_pred             CCC-EEEEECCCCCC-----C-------CHHH---HHHHHHHHHHCCCCCEEEEECCCCCHHHHHHHHHHHCCCCC----
T ss_conf             899-79996898897-----8-------9999---99999998624887189997598998999999998467999----


Q ss_pred             CCCCCCCCCEEEEEECCCHHHHHHHHHHHHCCCCEEEEEE
Q ss_conf             2355766620799970200268999976310387389997
Q gi|254780945|r  450 EKPAGRKPIKTVIIPINRIDEVIERLKVVLSEGKKAYWIC  489 (700)
Q Consensus       450 e~P~gR~~I~T~~~~~~~~~~~~~~i~~~l~~g~q~y~Vc  489 (700)
                           ..=|-|++=.......+++.+.+.   +--+.+++
T Consensus       348 -----~~lI~TKlDEt~~~G~il~~~~~~---~lplsy~t  379 (412)
T PRK05703        348 -----DGLILTKLDETSSLGSILSLLIES---GLPISYLT  379 (412)
T ss_pred             -----CEEEEEEECCCCCCCHHHHHHHHH---CCCEEEEE
T ss_conf             -----879997112899862999999998---87969994


No 374
>PRK13844 recombination protein RecR; Provisional
Probab=86.63  E-value=0.32  Score=29.16  Aligned_cols=29  Identities=21%  Similarity=0.260  Sum_probs=25.3

Q ss_pred             CCCCHHCHHCCCHHHCCCCCHHHHHHHHH
Q ss_conf             97102021017721367858899999887
Q gi|254780945|r    1 MRPSFLNPLFAPLSTFRGVGKKYSLFLSK   29 (700)
Q Consensus         1 mrp~~l~~L~~pI~~LkGVGpk~a~~L~k   29 (700)
                      |-|+.+..|-..++.|||||||+|+.++-
T Consensus         5 ~~~~~i~~LI~~l~kLPGIG~KsA~Rla~   33 (200)
T PRK13844          5 IFSPKISAVIESLRKLPTIGKKSSQRLAL   33 (200)
T ss_pred             CCCHHHHHHHHHHHHCCCCCHHHHHHHHH
T ss_conf             58899999999981689987889999999


No 375
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=86.49  E-value=2.6  Score=21.97  Aligned_cols=104  Identities=19%  Similarity=0.196  Sum_probs=65.9

Q ss_pred             HCCCCCHHHHHHHHHHCCCCCCCCCCHHHHHHHCCCCCC-CCCCCC---------CHHHCCCCCEEEEEEEEEEEEEECC
Q ss_conf             367858899999887401246885548987870897401-344446---------4788899878999999989754215
Q gi|254780945|r   15 TFRGVGKKYSLFLSKIINCGNANETRFIDLLFYHPSSFI-DRHYRP---------KISEISEERIVTITGYISQHSSFQL   84 (700)
Q Consensus        15 ~LkGVGpk~a~~L~kl~~l~~~GI~ti~DLL~~~PrrYe-Dr~~~~---------~I~~l~~g~~vti~g~V~~~~~~~~   84 (700)
                      -|.|.-|+....+.++.             ....|-++. ++|+..         +++++.+.....+.|+|......  
T Consensus       217 GIRg~~p~~l~~a~~~i-------------~~e~~e~~~if~TNqatD~hl~~~~~l~d~~~~~~~~v~g~v~~~p~~--  281 (421)
T COG1571         217 GIRGAVPEVLLKAMSLI-------------KRELVERSAIFETNQATDDHLVDKGKLNDIEDYSKYRVVGRVEAEPRA--  281 (421)
T ss_pred             EEECCCHHHHHHHHHHH-------------HCCCCCEEEEEECCCHHHHHCCCCCHHHHHHHCCCEEEEEEEECCCEE--
T ss_conf             98058878999999987-------------315823289984043024330363105455323432899998123189--


Q ss_pred             CCCCEEEEEEECCCCEEEEEEECCCH--HHHHHHCCCCCEEEEEEEEEECC
Q ss_conf             89833899998189369999951887--89987328988899998997318
Q gi|254780945|r   85 QKRRPYKILLNDGTGEITLLFFYRKT--EMLKNVFFEGRKITVTGKIKKLK  133 (700)
Q Consensus        85 ~~r~~~~v~v~D~tg~i~lvfFn~~~--~yl~k~lk~G~~v~vsGKv~~~~  133 (700)
                      ....-..+.+.|++|.|.++.|---.  +-+...+.+|+++.+||.++-..
T Consensus       282 ieGghv~v~i~d~~G~I~~~A~eptk~fr~~a~~L~pGD~i~~~G~~~~~~  332 (421)
T COG1571         282 IEGGHVVVEITDGEGEIGAVAFEPTKEFRELARKLIPGDEITVYGSVKPGT  332 (421)
T ss_pred             EECCEEEEEECCCCCEEEEEEECCCCCCHHHHHHCCCCCEEEEECCCCCCC
T ss_conf             638879999618981699999635552257898568999899805745662


No 376
>TIGR00455 apsK adenylylsulfate kinase; InterPro: IPR002891 Enzyme that catalyses the phosphorylation of adenylylsulphate to 3'-phosphoadenylylsulphate. This domain contains an ATP binding P-loop motif .; GO: 0005524 ATP binding, 0016301 kinase activity, 0016772 transferase activity transferring phosphorus-containing groups, 0000103 sulfate assimilation.
Probab=86.46  E-value=0.59  Score=27.08  Aligned_cols=104  Identities=22%  Similarity=0.299  Sum_probs=66.7

Q ss_pred             EEEEECCCCCHHHHHHHHHHHHHHHHCCEEEEEHHHHHHHHHHHHHHHHCCCCCCEEEEEECCCCHHHHHHHHHHHCCCC
Q ss_conf             78862144223699999973344430545886127999999998621101457865899624642256676877621347
Q gi|254780945|r  296 RILQGDVGSGKTLVALIAMAAAVEAGGQAVIMAPIGILAQQHYEFIKKYTQNTQIIVEIITGNMPQAHRRKALERIAHGQ  375 (700)
Q Consensus       296 RLLQGDVGSGKTiVA~~A~l~~~~~G~Q~alMaPTEILA~QH~~~~~~~~~~~~i~v~lLtg~~~~~er~~i~~~i~~G~  375 (700)
                      ==|-|==|||||.||-+.--.-.+                            .|+++.+|=|--       |.       
T Consensus        22 lWlTGLSGsGKsTiA~Al~~~L~~----------------------------~G~~~~~LDGDn-------vR-------   59 (187)
T TIGR00455        22 LWLTGLSGSGKSTIANALEKKLEK----------------------------KGYRVYVLDGDN-------VR-------   59 (187)
T ss_pred             EEEECCCCCHHHHHHHHHHHHHHH----------------------------CCCEEEEECCCE-------EE-------
T ss_conf             851168856357999999999996----------------------------697499975863-------42-------


Q ss_pred             CEEEEECHHHCCCCCCCCCCCEEEECCCCCCCHHHHH-HHHHCCCCCCCEEECHHHHHHHHHHHHHHCCCHHHHCCCCCC
Q ss_conf             5486411120133455444417885210133568899-874025677610101013227899997520101111023557
Q gi|254780945|r  376 AHIIIGTHALFQDSIQYYKLILVIVDEQHRFGVQQRL-KLTQKATAPHVLLMTATPIPRTLVLTSLGDIDISKITEKPAG  454 (700)
Q Consensus       376 ~~iiIGTHAL~q~~v~F~~LgLvViDEQHRFGV~QR~-~L~~Kg~~ph~L~MtATPIPRTLal~~ygdldvS~i~e~P~g  454 (700)
                             |-|      .++||         |.=+-|. ..+.=|+.+|+|+=+-                          
T Consensus        60 -------~gL------~~dLG---------FS~~DR~eNIRRigEVa~L~~~~G--------------------------   91 (187)
T TIGR00455        60 -------HGL------NKDLG---------FSEEDRKENIRRIGEVAKLLVRNG--------------------------   91 (187)
T ss_pred             -------CCC------CCCCC---------CCHHHHCCCCCEEHHHHHHHHHCC--------------------------
T ss_conf             -------477------88888---------885670568835326467776479--------------------------


Q ss_pred             CCCCEEEEEECCCHHHHHHHHHHHHCCC----CEEEEEECCC
Q ss_conf             6662079997020026899997631038----7389997120
Q gi|254780945|r  455 RKPIKTVIIPINRIDEVIERLKVVLSEG----KKAYWICPQI  492 (700)
Q Consensus       455 R~~I~T~~~~~~~~~~~~~~i~~~l~~g----~q~y~VcPlI  492 (700)
                       .-|.|.+|++-.-++  +.+++.+.+|    -=|||=|||=
T Consensus        92 -~i~ltsfISPyR~~R--~~vR~~~~~~Gl~F~Evfv~~PL~  130 (187)
T TIGR00455        92 -VIVLTSFISPYRADR--QMVRELIEEGGLEFIEVFVKCPLE  130 (187)
T ss_pred             -EEEEEEEECCCHHHH--HHHHHHHHCCCEEEEEEECCCCHH
T ss_conf             -389984217766678--999887540573689972178868


No 377
>TIGR02759 TraD_Ftype type IV conjugative transfer system coupling protein TraD; InterPro: IPR014128   The TraD protein performs an essential coupling function in conjugative type IV secretion systems. This protein sits at the inner membrane in contact with the assembled pilus and its scaffold as well as the relaxosome-plasmid DNA complex (through TraM) , .; GO: 0000746 conjugation.
Probab=86.43  E-value=0.78  Score=26.11  Aligned_cols=37  Identities=30%  Similarity=0.451  Sum_probs=28.0

Q ss_pred             EEEEEECCCCCHHHHHHHHHHHHHHHHCCEEEEEHHHH
Q ss_conf             07886214422369999997334443054588612799
Q gi|254780945|r  295 LRILQGDVGSGKTLVALIAMAAAVEAGGQAVIMAPIGI  332 (700)
Q Consensus       295 ~RLLQGDVGSGKTiVA~~A~l~~~~~G~Q~alMaPTEI  332 (700)
                      +=|+.|-|||||| ||+.-.+..+.+-.+=|+|-=++=
T Consensus       210 h~L~~GTtG~GKs-~~lr~LL~~iR~rGd~AIiYDkgC  246 (613)
T TIGR02759       210 HILIHGTTGSGKS-VALRKLLRWIRQRGDRAIIYDKGC  246 (613)
T ss_pred             CEEEECCCCCHHH-HHHHHHHHHHHHCCCEEEEEECCC
T ss_conf             5266454174389-999999999986398589982574


No 378
>COG2874 FlaH Predicted ATPases involved in biogenesis of archaeal flagella [Cell motility and secretion / Intracellular trafficking and secretion]
Probab=86.40  E-value=1.6  Score=23.76  Aligned_cols=50  Identities=14%  Similarity=0.262  Sum_probs=42.0

Q ss_pred             HHHHHHHCC--CCCCEEEEEECCCCCHHHHHHHHHHHHHHHHCCEEEEEHHHH
Q ss_conf             999984100--134307886214422369999997334443054588612799
Q gi|254780945|r  282 KDILQDMSQ--KNRMLRILQGDVGSGKTLVALIAMAAAVEAGGQAVIMAPIGI  332 (700)
Q Consensus       282 ~eI~~Dl~~--~~pM~RLLQGDVGSGKTiVA~~A~l~~~~~G~Q~alMaPTEI  332 (700)
                      +|+.+-|..  |.+-.-|+-||=|+|||+-...-++-++.+||-+++.+- |-
T Consensus        15 delDkrLGGGiP~GsL~lIEGd~~tGKSvLsqr~~YG~L~~g~~v~yvsT-e~   66 (235)
T COG2874          15 DELDKRLGGGIPVGSLILIEGDNGTGKSVLSQRFAYGFLMNGYRVTYVST-EL   66 (235)
T ss_pred             HHHHHHCCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHCCCEEEEEEE-CH
T ss_conf             77786516997467699998889854889999999988708954899984-03


No 379
>pfam10236 DAP3 Mitochondrial ribosomal death-associated protein 3. This is a family of conserved proteins which were originally described as death-associated-protein-3 (DAP-3). The proteins carry a P-loop DNA-binding motif, and induce apoptosis. DAP3 has been shown to be a pro-apoptotic factor in the mitochondrial matrix and to be crucial for mitochondrial biogenesis and so has also been designated as MRP-S29 (mitochondrial ribosomal protein subunit 29).
Probab=86.38  E-value=1.3  Score=24.36  Aligned_cols=38  Identities=37%  Similarity=0.510  Sum_probs=30.3

Q ss_pred             CCCCEEEEEECCCCCHHHHHHHHHHHHHHHHCCEEEEEH
Q ss_conf             134307886214422369999997334443054588612
Q gi|254780945|r  291 KNRMLRILQGDVGSGKTLVALIAMAAAVEAGGQAVIMAP  329 (700)
Q Consensus       291 ~~pM~RLLQGDVGSGKTiVA~~A~l~~~~~G~Q~alMaP  329 (700)
                      ...-..+|-|.-|||||+.-.-++..|..+|+ .++=+|
T Consensus        21 ~~~~r~vL~G~~GsGKS~~L~q~v~~A~~~~w-iVl~vP   58 (274)
T pfam10236        21 KKVVRFVLTGERGSGKSVLLAQAMAYALTQGW-VVLHVP   58 (274)
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHHHHHHHCCE-EEEECC
T ss_conf             99518998897997799999999999985998-999849


No 380
>PRK11608 pspF phage shock protein operon transcriptional activator; Provisional
Probab=86.34  E-value=0.84  Score=25.86  Aligned_cols=33  Identities=18%  Similarity=0.330  Sum_probs=20.8

Q ss_pred             HHHHHHHHHHCCCCCCEEEEEECCCCCHHHHHHHH
Q ss_conf             99999998410013430788621442236999999
Q gi|254780945|r  279 SAIKDILQDMSQKNRMLRILQGDVGSGKTLVALIA  313 (700)
Q Consensus       279 ~ai~eI~~Dl~~~~pM~RLLQGDVGSGKTiVA~~A  313 (700)
                      ++.+.|..=-.++.|  -|++|..||||+.+|-.-
T Consensus        17 ~v~~~~~~~A~~~~p--VLI~GE~GtGK~~~Ar~I   49 (325)
T PRK11608         17 EVLEQVSHLAPLDKP--VLIIGERGTGKELIASRL   49 (325)
T ss_pred             HHHHHHHHHHCCCCC--EEEECCCCCCHHHHHHHH
T ss_conf             999999999688999--898898983799999999


No 381
>PRK10875 recD exonuclease V subunit alpha; Provisional
Probab=86.29  E-value=2  Score=22.96  Aligned_cols=88  Identities=24%  Similarity=0.374  Sum_probs=57.6

Q ss_pred             CCCCCHHHHHHHHHCCCCC---CHHHHHHHHHHHHHHCCCCCCEEEEEECCCCCHH--HHHHHHHHHHHHH--HCCEEEE
Q ss_conf             7877578999986302467---9889999999998410013430788621442236--9999997334443--0545886
Q gi|254780945|r  255 INVEGKIAQKILRNIPFSP---TKSQESAIKDILQDMSQKNRMLRILQGDVGSGKT--LVALIAMAAAVEA--GGQAVIM  327 (700)
Q Consensus       255 ~~~~~~~~~~f~~~LPF~L---T~~Q~~ai~eI~~Dl~~~~pM~RLLQGDVGSGKT--iVA~~A~l~~~~~--G~Q~alM  327 (700)
                      ...+.......++.| |.-   ++-|+.|+.-   -+.+  +. -++-|-=|+|||  ++.++|++.....  +...++.
T Consensus       128 ~~~~~~~~~~~L~~l-f~~~~~~dwQk~A~a~---Al~~--~~-~vIsGGPGTGKTttV~~lLa~l~~~~~~~~l~I~La  200 (607)
T PRK10875        128 IEVDEALLAQTLDAL-FPPGDEVNWQKVAAAV---ALTR--RI-SVISGGPGTGKTTTVAKLLAALIQLADGERCRIRLA  200 (607)
T ss_pred             CCCCHHHHHHHHHHH-CCCCCCCCHHHHHHHH---HHHC--CE-EEEECCCCCCHHHHHHHHHHHHHHHCCCCCCEEEEE
T ss_conf             889989999999985-7998885189999999---8755--77-899679998778899999999999645899708998


Q ss_pred             EHHHHHHHHHHHHHHHHCCCCC
Q ss_conf             1279999999986211014578
Q gi|254780945|r  328 APIGILAQQHYEFIKKYTQNTQ  349 (700)
Q Consensus       328 aPTEILA~QH~~~~~~~~~~~~  349 (700)
                      |||-==|..--+++.+-+..++
T Consensus       201 APTGKAAaRL~Esi~~~~~~l~  222 (607)
T PRK10875        201 APTGKAAARLTESLGKALRQLP  222 (607)
T ss_pred             CCHHHHHHHHHHHHHHHHHHCC
T ss_conf             8228999999999987875347


No 382
>KOG0987 consensus
Probab=86.28  E-value=1.8  Score=23.21  Aligned_cols=72  Identities=25%  Similarity=0.232  Sum_probs=55.4

Q ss_pred             HHHHHHHCCCCCCHHHHHHHHHHHHHHCCCCCCEEEEEECCCCCHHHHHHHHHHHHHHHHCCEEEEEHHHHHH
Q ss_conf             9999863024679889999999998410013430788621442236999999733444305458861279999
Q gi|254780945|r  262 AQKILRNIPFSPTKSQESAIKDILQDMSQKNRMLRILQGDVGSGKTLVALIAMAAAVEAGGQAVIMAPIGILA  334 (700)
Q Consensus       262 ~~~f~~~LPF~LT~~Q~~ai~eI~~Dl~~~~pM~RLLQGDVGSGKTiVA~~A~l~~~~~G~Q~alMaPTEILA  334 (700)
                      ...--..+|=.||..|+++.++|...+.. ..+....-|.=|+|||.+.-.-+.+.-.-|.+++..|++-+.|
T Consensus       107 ~~~~~~~~~~~l~~eqk~v~d~~~~~v~~-~~g~~ff~g~~gtgKt~l~~t~~~~~~~~g~~~~~v~~s~ia~  178 (540)
T KOG0987         107 LKEKHAELPKKLTPEQKRVYDAILEAVEN-NLGGVFFYGFGGTGKTYLLKTLIAALRSRGKIVLNVASSGIAA  178 (540)
T ss_pred             HHHHHHHHHHHCCHHHHHHHHHHHHHHHC-CCCCEEECCCCCCCCEEEHHHHHHHHHHCCCCEEEEEECCHHH
T ss_conf             55531023665598776379999999854-7876534367886540237889999974587146653301244


No 383
>PRK06696 uridine kinase; Validated
Probab=85.83  E-value=2.1  Score=22.82  Aligned_cols=60  Identities=20%  Similarity=0.229  Sum_probs=39.3

Q ss_pred             HHHHHHHHHHHHCCCCCCEEE---EEECCCCCHHHHHHHHHHHHHHHHCCEE------EEEHHHHHHHH
Q ss_conf             999999999841001343078---8621442236999999733444305458------86127999999
Q gi|254780945|r  277 QESAIKDILQDMSQKNRMLRI---LQGDVGSGKTLVALIAMAAAVEAGGQAV------IMAPIGILAQQ  336 (700)
Q Consensus       277 Q~~ai~eI~~Dl~~~~pM~RL---LQGDVGSGKTiVA~~A~l~~~~~G~Q~a------lMaPTEILA~Q  336 (700)
                      -.+.++||.+-+.+-.|-.++   +-|.-|||||-+|-.-+-..-..|.+|+      |..|-++..++
T Consensus         7 r~~~~~~~~~~i~~~~p~rpl~VgIdG~~gSGKTTlA~~La~~L~~~G~~V~~v~~Ddf~~~~~~r~~~   75 (227)
T PRK06696          7 RKQVVKEIANHILTLNLTRPLRVAIDGITASGKTTFANELAEEIKKRGRPVIRASIDDFHNPKVIRYRR   75 (227)
T ss_pred             HHHHHHHHHHHHHHCCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHCCCCEEEECCCCCCCCHHHHHHH
T ss_conf             878999999999835999868999778998787999999999997469948997154434737777651


No 384
>PRK06893 DNA replication initiation factor; Validated
Probab=85.77  E-value=2.8  Score=21.71  Aligned_cols=34  Identities=15%  Similarity=0.084  Sum_probs=27.4

Q ss_pred             EEEEECCCCCHHHHHHHHHHHHHHHHCCEEEEEH
Q ss_conf             7886214422369999997334443054588612
Q gi|254780945|r  296 RILQGDVGSGKTLVALIAMAAAVEAGGQAVIMAP  329 (700)
Q Consensus       296 RLLQGDVGSGKTiVA~~A~l~~~~~G~Q~alMaP  329 (700)
                      -.|.|+.|||||=..-.++-.+..++..++++--
T Consensus        42 l~i~G~~gsGKTHLLqa~~~~~~~~~~~~~yi~~   75 (229)
T PRK06893         42 FYIWGGKSSGKSHLLKAVSNHYLLNQRTAIYIPL   75 (229)
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHHHCCCEEEEEH
T ss_conf             9998999998899999999999971898599973


No 385
>pfam02606 LpxK Tetraacyldisaccharide-1-P 4'-kinase. This family consists of tetraacyldisaccharide-1-P 4'-kinase also known as Lipid-A 4'-kinase or Lipid A biosynthesis protein LpxK, EC:2.7.1.130. This enzyme catalyses the reaction: ATP + 2,3-bis(3-hydroxytetradecanoyl)-D -glucosaminyl-(beta-D-1,6)-2,3-bis(3-hydroxytetradecanoyl)-D-glu cosam inyl beta-phosphate <= ADP + 2,3,2',3'-tetrakis(3-hydroxytetradecanoyl)-D- glucosaminyl-1,6-beta-D-glucosamine 1,4'-bisphosphate. This enzyme is involved in the synthesis of lipid A portion of the bacterial lipopolysaccharide layer (LPS). The family contains a P-loop motif at the N terminus.
Probab=85.68  E-value=0.46  Score=27.91  Aligned_cols=204  Identities=18%  Similarity=0.209  Sum_probs=101.4

Q ss_pred             CCCHHHHHHHHHHHHHHHHCCEEEEE---------HHHHHHHHHHH-------HHHHHCCCCCCEEEEEECCCCHHHHHH
Q ss_conf             42236999999733444305458861---------27999999998-------621101457865899624642256676
Q gi|254780945|r  303 GSGKTLVALIAMAAAVEAGGQAVIMA---------PIGILAQQHYE-------FIKKYTQNTQIIVEIITGNMPQAHRRK  366 (700)
Q Consensus       303 GSGKTiVA~~A~l~~~~~G~Q~alMa---------PTEILA~QH~~-------~~~~~~~~~~i~v~lLtg~~~~~er~~  366 (700)
                      |+|||=+...-+-...+.|++++++.         |..|=.....+       -+.+.   ++++|.  .|    +.|.+
T Consensus        47 GtGKTP~v~~l~~~l~~~g~~~~ilSRGYg~~~~~~~~v~~~~~~~~~GDEp~lla~~---~~~~v~--V~----~~R~~  117 (318)
T pfam02606        47 GTGKTPLVIALAELLRARGLRPGVLSRGYGGKSKGPVLVDPGSSAAEVGDEPLLLARR---TPVPVV--VG----PDRAA  117 (318)
T ss_pred             CCCHHHHHHHHHHHHHHCCCCEEEECCCCCCCCCCCEEECCCCCHHHCCCHHHHHHHH---CCCCEE--EC----CCHHH
T ss_conf             8785899999999999769944783267676578878971688946739699999875---698599--80----52899


Q ss_pred             HHHH-HCCCCCEEEEECHHHCCCCCCCCCCCEEEECCCCCCCHHH-------HHHHHHCCCCCCCEEECHHHHHHHHHHH
Q ss_conf             8776-2134754864111201334554444178852101335688-------9987402567761010101322789999
Q gi|254780945|r  367 ALER-IAHGQAHIIIGTHALFQDSIQYYKLILVIVDEQHRFGVQQ-------RLKLTQKATAPHVLLMTATPIPRTLVLT  438 (700)
Q Consensus       367 i~~~-i~~G~~~iiIGTHAL~q~~v~F~~LgLvViDEQHRFGV~Q-------R~~L~~Kg~~ph~L~MtATPIPRTLal~  438 (700)
                      ..+. ++...+++||=--+ ||..--.+++-+|++|-+..||=..       |+.+.. -..+|+++.|..|-.....  
T Consensus       118 a~~~l~~~~~~dviIlDDG-fQh~~l~rDl~Ivl~d~~~~fgng~lLPaGpLREp~~~-l~raD~ii~~~~~~~~~~~--  193 (318)
T pfam02606       118 AARALLEAHGADVIILDDG-FQHYRLARDLEIVVVDGARGFGNGRLLPAGPLREPLSR-LKRADAVILNGGEAADPEI--  193 (318)
T ss_pred             HHHHHHHHCCCCEEEECCC-CCCCCCCCCEEEEEECCCCCCCCCCCCCCCCCCCCHHH-HCCCCEEEECCCCCCHHHH--
T ss_conf             9999998489979991486-66730018868999728878879977858135489658-7003999993985321134--


Q ss_pred             HHHCCCHHHHCCCCCCCCCCEEEEEECCCHHHHHHHHHHHHCCCCEEEEEECCCCCCCCCCCCHHHHHHHHHHHHCCCC-
Q ss_conf             7520101111023557666207999702002689999763103873899971201221112101466666668663710-
Q gi|254780945|r  439 SLGDIDISKITEKPAGRKPIKTVIIPINRIDEVIERLKVVLSEGKKAYWICPQIEEKKESNFRSVVERFNSLHEHFTSS-  517 (700)
Q Consensus       439 ~ygdldvS~i~e~P~gR~~I~T~~~~~~~~~~~~~~i~~~l~~g~q~y~VcPlIeese~~~~~~~~~~~~~l~~~~~~~-  517 (700)
                                .+.|.-+    +.+.+... ......-... -+|.++..+|-.         .+-+.-++.|++. +-+ 
T Consensus       194 ----------~~~~~~~----~~~~~~~~-~~~~~~~~~~-l~~~~v~a~sGI---------anP~~F~~~L~~~-g~~i  247 (318)
T pfam02606       194 ----------AEAPVLR----ARLEPSAA-VNLADGERRP-LAGKRVLAFAGI---------GNPQRFFDTLRAL-GLEV  247 (318)
T ss_pred             ----------HHCCHHH----EEEEEEEE-EECCCCCCCC-CCCCEEEEEEEC---------CCHHHHHHHHHHC-CCEE
T ss_conf             ----------4323011----48850044-7427732000-169848999964---------7879999999976-9878


Q ss_pred             ----EECCCCCCCHHHHHHHHHHHHCCCEEEEEEC
Q ss_conf             ----3120146998999999999755986999980
Q gi|254780945|r  518 ----IAIIHGRMSDIDKESVMDSFKNGTCKLLIAT  548 (700)
Q Consensus       518 ----v~~lHGkm~~~ek~~~m~~F~~g~~~iLvaT  548 (700)
                          .--=|-.-+.++-+.+.+..++..   +|.|
T Consensus       248 ~~~~~f~DHh~y~~~dl~~i~~~a~~~~---iitT  279 (318)
T pfam02606       248 VATLAFPDHHPFTAADLAFLEAEAKEPG---LVTT  279 (318)
T ss_pred             EEEEECCCCCCCCHHHHHHHHHHCCCCC---EEEC
T ss_conf             7867778877799999999998656997---5874


No 386
>PRK06904 replicative DNA helicase; Validated
Probab=85.63  E-value=2.7  Score=21.93  Aligned_cols=70  Identities=20%  Similarity=0.168  Sum_probs=39.1

Q ss_pred             EEEECCCCCHHHHHHHHHHHHHHHH-CCEEEEEHHHHHHHHHHHHHHHHCCCCCCEEE-EEECC-CCHHHHHHHHH
Q ss_conf             8862144223699999973344430-54588612799999999862110145786589-96246-42256676877
Q gi|254780945|r  297 ILQGDVGSGKTLVALIAMAAAVEAG-GQAVIMAPIGILAQQHYEFIKKYTQNTQIIVE-IITGN-MPQAHRRKALE  369 (700)
Q Consensus       297 LLQGDVGSGKTiVA~~A~l~~~~~G-~Q~alMaPTEILA~QH~~~~~~~~~~~~i~v~-lLtg~-~~~~er~~i~~  369 (700)
                      +|=|--|+|||..|+--+..++..+ ..|+|.. -|.=++|-+..+-.....  |+.. +-+|. +...+.+++..
T Consensus       225 ViAaRPsmGKTa~alnia~n~A~~~~~~V~~fS-LEM~~~~l~~R~ls~~s~--v~~~~i~~g~~l~~~e~~~~~~  297 (472)
T PRK06904        225 IVAARPSMGKTTFAMNLCENAAMASEKPVLVFS-LEMPAEQIMMRMLASLSR--VDQTKIRTGQNLDQQDWAKISS  297 (472)
T ss_pred             EEEECCCCCHHHHHHHHHHHHHHHCCCCEEEEC-CCCCHHHHHHHHHHHHCC--CCHHHHHCCCCCHHHHHHHHHH
T ss_conf             997379875689999999999995599579977-879999999999998649--9988864688560999999999


No 387
>PRK05022 anaerobic nitric oxide reductase transcription regulator; Provisional
Probab=85.56  E-value=0.62  Score=26.89  Aligned_cols=38  Identities=24%  Similarity=0.462  Sum_probs=27.0

Q ss_pred             HHHHHHHHHHHHHC--CCCCCEEEEEECCCCCHHHHHHHH
Q ss_conf             89999999998410--013430788621442236999999
Q gi|254780945|r  276 SQESAIKDILQDMS--QKNRMLRILQGDVGSGKTLVALIA  313 (700)
Q Consensus       276 ~Q~~ai~eI~~Dl~--~~~pM~RLLQGDVGSGKTiVA~~A  313 (700)
                      +|..++.++.+++.  .+.+.+-|++|..|+||..||-.-
T Consensus       190 G~S~~m~~l~~~i~~vA~sd~pVLI~GEtGTGKelvAr~I  229 (510)
T PRK05022        190 GQSPAMQQLKKEIEVVAASDLNVLITGETGVGKELVARAI  229 (510)
T ss_pred             ECCHHHHHHHHHHHHHHCCCCCEEEECCCCCCHHHHHHHH
T ss_conf             0899999999999999689998898898981399999999


No 388
>PRK12820 bifunctional aspartyl-tRNA synthetase/aspartyl/glutamyl-tRNA amidotransferase subunit C; Provisional
Probab=85.41  E-value=3  Score=21.59  Aligned_cols=92  Identities=17%  Similarity=0.205  Sum_probs=62.0

Q ss_pred             CCCCCCCCHHHCCCCCEEEEEEEEEEEEEECCCCCCEEEEEEECCCCEEEEEEECCCH--H--HHHHHCCCCCEEEEEEE
Q ss_conf             1344446478889987899999998975421589833899998189369999951887--8--99873289888999989
Q gi|254780945|r   53 IDRHYRPKISEISEERIVTITGYISQHSSFQLQKRRPYKILLNDGTGEITLLFFYRKT--E--MLKNVFFEGRKITVTGK  128 (700)
Q Consensus        53 eDr~~~~~I~~l~~g~~vti~g~V~~~~~~~~~~r~~~~v~v~D~tg~i~lvfFn~~~--~--yl~k~lk~G~~v~vsGK  128 (700)
                      -+|..+-.+..-..|+.|++.|-|.+.+.   .+ ...=+.+.|.+|.+++++=....  .  -..+.++.+..+.|.|+
T Consensus         4 ~~~~ycg~l~~~~vG~~V~l~GWV~~~R~---~G-~l~FidLRD~~G~vQvv~~~~~~~~d~~~~~~~l~~E~vI~V~G~   79 (706)
T PRK12820          4 NDRSFCGHLSLDDTGREVCLAGWVDAFRD---HG-ELLFIHLRDRNGFIQAVFSPEAAPADVYELAASLRAEFCVALQGE   79 (706)
T ss_pred             CCCCCCCCCCHHHCCCEEEEEEEEEEEEC---CC-CEEEEEEEECCCCEEEEECCCCCCHHHHHHHHCCCCCCEEEEEEE
T ss_conf             77745134994889998999786878966---89-849999972894589998688688889999853998678999989


Q ss_pred             EEEC----------CCEEEEECCEEEECCC
Q ss_conf             9731----------8779997786896264
Q gi|254780945|r  129 IKKL----------KNRIIMVHPHYIFHNS  148 (700)
Q Consensus       129 v~~~----------~~~~qi~hPe~~~~~~  148 (700)
                      |..-          .|.+++.-.++++.+.
T Consensus        80 V~~r~~~~~n~~~~tGeiEI~v~~l~iLs~  109 (706)
T PRK12820         80 VQKRLEETENPHIETGDIEVFVRELSILAA  109 (706)
T ss_pred             EEECCCCCCCCCCCCCCEEEEEEEEEEEEC
T ss_conf             993476566888988618999769999877


No 389
>PRK07004 replicative DNA helicase; Provisional
Probab=85.28  E-value=3  Score=21.55  Aligned_cols=72  Identities=15%  Similarity=0.086  Sum_probs=45.5

Q ss_pred             EEEEECCCCCHHHHHHHHHHHHH-HHHCCEEEEEHHHHHHHHHHHHHHHHCCCCCCEEEEEECCCCHHHHHHHHH
Q ss_conf             78862144223699999973344-430545886127999999998621101457865899624642256676877
Q gi|254780945|r  296 RILQGDVGSGKTLVALIAMAAAV-EAGGQAVIMAPIGILAQQHYEFIKKYTQNTQIIVEIITGNMPQAHRRKALE  369 (700)
Q Consensus       296 RLLQGDVGSGKTiVA~~A~l~~~-~~G~Q~alMaPTEILA~QH~~~~~~~~~~~~i~v~lLtg~~~~~er~~i~~  369 (700)
                      -.|=|--|.|||..|+--+..++ .+|+-|+|..- |.=++|....+-.-....+ .-.+-+|.++..+..++..
T Consensus       216 iIIAARPsmGKTafAlniA~n~A~~~g~~V~~FSL-EMs~eql~~Rlls~~s~I~-~~~ir~g~l~~~e~~~i~~  288 (460)
T PRK07004        216 IIVAGRPSMGKTAFSMNIGEYVAVEYGLPVAVFSM-EMPGTQLAMRMLGSVGRLD-QHRMRTGRLTDEDWPKLTH  288 (460)
T ss_pred             EEEEECCCCCHHHHHHHHHHHHHHHCCCCEEEECC-CCCHHHHHHHHHHHCCCCC-CCHHHCCCCCHHHHHHHHH
T ss_conf             99973687642699999999998725886699847-7999999999998606988-2110078899999999999


No 390
>cd00984 DnaB_C DnaB helicase C terminal domain. The hexameric helicase DnaB unwinds the DNA duplex at the  chromosome replication fork. Although the mechanism by which DnaB both couples ATP hydrolysis to translocation along DNA and denatures the duplex is unknown, a change in the quaternary structure of the protein involving dimerization of the N-terminal domain has been observed and may occur during the enzymatic cycle. This C-terminal domain contains an ATP-binding site and is therefore probably the site of ATP hydrolysis.
Probab=85.18  E-value=2.6  Score=21.96  Aligned_cols=72  Identities=15%  Similarity=0.190  Sum_probs=46.7

Q ss_pred             EEEEEECCCCCHHHHHHHHHHHH-HHHHCCEEEEEHHHHHHHHHHHHHHHHCCCCCCEEEEEECCCCHHHHHHHH
Q ss_conf             07886214422369999997334-443054588612799999999862110145786589962464225667687
Q gi|254780945|r  295 LRILQGDVGSGKTLVALIAMAAA-VEAGGQAVIMAPIGILAQQHYEFIKKYTQNTQIIVEIITGNMPQAHRRKAL  368 (700)
Q Consensus       295 ~RLLQGDVGSGKTiVA~~A~l~~-~~~G~Q~alMaPTEILA~QH~~~~~~~~~~~~i~v~lLtg~~~~~er~~i~  368 (700)
                      .-++-|.-|+|||..+.-.++.+ ..+|+-|++... |.=.++....+-......+.. .+..+.....+..++.
T Consensus        15 L~vi~a~~g~GKS~~~~~la~~~a~~~g~~V~~~Sl-Em~~~~~~~R~~s~~~~i~~~-~i~~~~~~~~~~~~~~   87 (242)
T cd00984          15 LIIIAARPSMGKTAFALNIAENIAKKQGKPVLFFSL-EMSKEQLLQRLLASESGISLS-KLRTGSLSDEDWERLA   87 (242)
T ss_pred             EEEEEECCCCCHHHHHHHHHHHHHHHCCCCEEEEEC-CCCHHHHHHHHHHHHHCCCHH-HHHCCCCCHHHHHHHH
T ss_conf             899996899999999999999999977995999933-353889999999998297745-5302652279999999


No 391
>TIGR03600 phage_DnaB phage replicative helicase, DnaB family, HK022 subfamily. Members of this family are phage (or prophage-region) homologs of the bacterial homohexameric replicative helicase DnaB. Some phage may rely on host DnaB, while others encode their own verions. This model describes the largest phage-specific clade among the close homologs of DnaB, but there are, or course, other DnaB homologs from phage that fall outside the scope of this model.
Probab=84.92  E-value=3.1  Score=21.43  Aligned_cols=71  Identities=21%  Similarity=0.216  Sum_probs=45.4

Q ss_pred             EEEEECCCCCHHHHHHHHHHH-HHHHHCCEEEEEHHHHHHHHHHHHHHHHCCCCCCEEE-EEECCCCHHHHHHHHH
Q ss_conf             788621442236999999733-4443054588612799999999862110145786589-9624642256676877
Q gi|254780945|r  296 RILQGDVGSGKTLVALIAMAA-AVEAGGQAVIMAPIGILAQQHYEFIKKYTQNTQIIVE-IITGNMPQAHRRKALE  369 (700)
Q Consensus       296 RLLQGDVGSGKTiVA~~A~l~-~~~~G~Q~alMaPTEILA~QH~~~~~~~~~~~~i~v~-lLtg~~~~~er~~i~~  369 (700)
                      -.|-|--|.|||..|+--+.. +..+|+-|++..- |.=++|....+-....+  |+.. +-+|..+..+...+..
T Consensus       197 iIiaARPsmGKTafalnia~n~A~~~g~~Vl~fSL-EMs~eql~~R~la~~s~--i~~~~i~~g~l~~~~~~~~~~  269 (421)
T TIGR03600       197 IVIGARPSMGKTTLALNIAENVALREGKPVLFFSL-EMSAEQLGERLLASKSG--INTGNIRTGRFNDSDFNRLLN  269 (421)
T ss_pred             EEEEEECCCCHHHHHHHHHHHHHHHCCCEEEEEEC-CCCHHHHHHHHHHHHCC--CCHHHHHCCCCCHHHHHHHHH
T ss_conf             99985467874599999999999866983899925-79999999999998548--977666528999899999999


No 392
>PRK13609 diacylglycerol glucosyltransferase; Provisional
Probab=84.89  E-value=3.1  Score=21.42  Aligned_cols=159  Identities=14%  Similarity=0.210  Sum_probs=83.2

Q ss_pred             HHHHHHHCCCCCEEEEECHHHCCC-------CCCCCCCCEEEEC-CCCCCCHH------------HHHHHHHCCCCCCCE
Q ss_conf             768776213475486411120133-------4554444178852-10133568------------899874025677610
Q gi|254780945|r  365 RKALERIAHGQAHIIIGTHALFQD-------SIQYYKLILVIVD-EQHRFGVQ------------QRLKLTQKATAPHVL  424 (700)
Q Consensus       365 ~~i~~~i~~G~~~iiIGTHAL~q~-------~v~F~~LgLvViD-EQHRFGV~------------QR~~L~~Kg~~ph~L  424 (700)
                      +.+.+-|+.-++|+||.||.+..=       +... -+--||.| --|+|=+.            -+..+.++|..++-+
T Consensus        94 ~~l~~li~~~kPDvII~T~P~~~l~~lk~~~~~~i-P~~tViTD~~~H~~Wi~~~~D~y~Vase~~k~~l~~~Gv~~~kI  172 (388)
T PRK13609         94 KRLKLLLQAEKPDIVINTFPIIAVPELKKQTGISI-PVYNVLTDFCVHKIWIHREVDRYFVATDHVKEVMVDIGVPAEQI  172 (388)
T ss_pred             HHHHHHHHHCCCCEEEECCCHHHHHHHHHHCCCCC-CEEEEECCCCCHHHHCCCCCCEEEECCHHHHHHHHHHCCCHHHE
T ss_conf             99999999829599998887899999998459999-88999478520464557899979939899999999809988899


Q ss_pred             EECHHHHHHHHHHHHHHCCCHHHHC---CCCCCCCCCEEEEEEC-C-----CHHHHHHHHHHHHCCCCEEEEEECCCCCC
Q ss_conf             1010132278999975201011110---2355766620799970-2-----00268999976310387389997120122
Q gi|254780945|r  425 LMTATPIPRTLVLTSLGDIDISKIT---EKPAGRKPIKTVIIPI-N-----RIDEVIERLKVVLSEGKKAYWICPQIEEK  495 (700)
Q Consensus       425 ~MtATPIPRTLal~~ygdldvS~i~---e~P~gR~~I~T~~~~~-~-----~~~~~~~~i~~~l~~g~q~y~VcPlIees  495 (700)
                      ..|-.||...-.    ...+-..+.   .+|+.++ +  .++.. .     ...++.+.+..  ..+-|+.|||-.    
T Consensus       173 ~vtGiPVr~~F~----~~~~k~~~r~~lgL~~d~~-~--vLimgGg~G~~g~i~~l~~~L~~--~~~~qiiVVcGr----  239 (388)
T PRK13609        173 VETGIPIRSSFE----LKINPDIIYNKYQLCKNKK-I--LLIVAGAHGVLGNVKELCQSFMS--VPDLQVVVVCGK----  239 (388)
T ss_pred             EEECCCCCHHHC----CCCCHHHHHHHHCCCCCCC-E--EEEECCHHHHHHHHHHHHHHHHC--CCCCEEEEEECC----
T ss_conf             988984387872----7588789999828998784-7--99976601211479999999745--899249999089----


Q ss_pred             CCCCCCHHHHHHHHHHH---HCCCCEECCCCCCCHHHHHHHHHHHHCCCEEEEEE----CHHHH
Q ss_conf             11121014666666686---63710312014699899999999975598699998----00341
Q gi|254780945|r  496 KESNFRSVVERFNSLHE---HFTSSIAIIHGRMSDIDKESVMDSFKNGTCKLLIA----TTVIE  552 (700)
Q Consensus       496 e~~~~~~~~~~~~~l~~---~~~~~v~~lHGkm~~~ek~~~m~~F~~g~~~iLva----TtviE  552 (700)
                            + ++.+++|.+   ..+.+|- +.|=-  ++-.+.|.     ..|++|+    .|+-|
T Consensus       240 ------N-~~L~~~L~~~~~~~~~~v~-vlGf~--~~~~~~~~-----~~d~~i~k~Gg~t~~E  288 (388)
T PRK13609        240 ------N-EALKQDLVGLQETNPDALK-VFGYV--ENIDELFR-----VTSCMITKPGGITLSE  288 (388)
T ss_pred             ------C-HHHHHHHHHHHHCCCCCEE-EEECH--HHHHHHHH-----HCCEEEECCCHHHHHH
T ss_conf             ------9-8999999988750799469-95045--20999998-----5759995786458999


No 393
>PRK05642 DNA replication initiation factor; Validated
Probab=84.84  E-value=3.1  Score=21.40  Aligned_cols=33  Identities=24%  Similarity=0.260  Sum_probs=26.4

Q ss_pred             EEEECCCCCHHHHHHHHHHHHHHHHCCEEEEEH
Q ss_conf             886214422369999997334443054588612
Q gi|254780945|r  297 ILQGDVGSGKTLVALIAMAAAVEAGGQAVIMAP  329 (700)
Q Consensus       297 LLQGDVGSGKTiVA~~A~l~~~~~G~Q~alMaP  329 (700)
                      .|.|.+|||||=..-.++..+.+.|..++++--
T Consensus        49 ~i~G~~G~GKTHLL~A~~~~~~~~~~~~~yl~~   81 (234)
T PRK05642         49 YLWGKDGVGRSHLLQAACLRFEQRGEPAVYLPL   81 (234)
T ss_pred             EEECCCCCCHHHHHHHHHHHHHHCCCCEEEEEH
T ss_conf             998899998899999999999807996799789


No 394
>PRK12374 putative dithiobiotin synthetase; Provisional
Probab=84.78  E-value=0.9  Score=25.64  Aligned_cols=33  Identities=27%  Similarity=0.417  Sum_probs=29.1

Q ss_pred             EEEE-CCCCCHHHHHHHHHHHHHHHHCCEEEEEH
Q ss_conf             8862-14422369999997334443054588612
Q gi|254780945|r  297 ILQG-DVGSGKTLVALIAMAAAVEAGGQAVIMAP  329 (700)
Q Consensus       297 LLQG-DVGSGKTiVA~~A~l~~~~~G~Q~alMaP  329 (700)
                      .+.| |.+.|||+|+..-+......|++++.+=|
T Consensus         6 FITGTDTdVGKT~vsaaL~~~l~~~G~~v~~~KP   39 (231)
T PRK12374          6 FITGTDTSVGKTVVSRALLQALASQGKSVAGYKP   39 (231)
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHHCCCCEEEEEE
T ss_conf             9987899953999999999999978994888856


No 395
>COG0132 BioD Dethiobiotin synthetase [Coenzyme metabolism]
Probab=84.68  E-value=0.87  Score=25.73  Aligned_cols=30  Identities=30%  Similarity=0.337  Sum_probs=27.7

Q ss_pred             ECCCCCHHHHHHHHHHHHHHHHCCEEEEEH
Q ss_conf             214422369999997334443054588612
Q gi|254780945|r  300 GDVGSGKTLVALIAMAAAVEAGGQAVIMAP  329 (700)
Q Consensus       300 GDVGSGKTiVA~~A~l~~~~~G~Q~alMaP  329 (700)
                      =|.|-|||+|+..-+-++..+|++++.+=|
T Consensus        10 TDT~VGKTv~S~aL~~~l~~~g~~~~~~KP   39 (223)
T COG0132          10 TDTGVGKTVVSAALAQALKQQGYSVAGYKP   39 (223)
T ss_pred             CCCCCCHHHHHHHHHHHHHHCCCCEEEECC
T ss_conf             799964999999999999968970598775


No 396
>PRK07263 consensus
Probab=84.49  E-value=3.2  Score=21.29  Aligned_cols=86  Identities=14%  Similarity=0.122  Sum_probs=50.4

Q ss_pred             HHHHHHHHHCCCCCCEEEEEECCCCCHHHHHHHHHHHH-HHHHCCEEEEEHHHHHHHHHHHHHHHHCCCCCCEEEEEECC
Q ss_conf             99999984100134307886214422369999997334-44305458861279999999986211014578658996246
Q gi|254780945|r  280 AIKDILQDMSQKNRMLRILQGDVGSGKTLVALIAMAAA-VEAGGQAVIMAPIGILAQQHYEFIKKYTQNTQIIVEIITGN  358 (700)
Q Consensus       280 ai~eI~~Dl~~~~pM~RLLQGDVGSGKTiVA~~A~l~~-~~~G~Q~alMaPTEILA~QH~~~~~~~~~~~~i~v~lLtg~  358 (700)
                      .++++..-|..+.  .-.|=|--|.|||..|+--+..+ +.+|+-|+|..- |.=++|....+-......+. -.+-+|.
T Consensus       192 ~LD~~t~Gl~~Gd--LiviaaRPsmGKTa~alnia~~iA~~~~~~V~~fSl-EMs~~ql~~R~la~~~~i~~-~~i~~g~  267 (453)
T PRK07263        192 DLDKITTGLHPDQ--LIILAARPAVGKTAFVLNIAQNVGTKQKKTVAIFSL-EMGAESLVDRMLAAEGMVDS-HSLRTGQ  267 (453)
T ss_pred             HHHHHHCCCCCCC--EEEEEECCCCCHHHHHHHHHHHHHHHCCCEEEEEEC-CCCHHHHHHHHHHHHCCCCH-HCCCCCC
T ss_conf             7997732899786--899972788847899999999999855982899924-69989999999998617331-0331365


Q ss_pred             CCHHHHHHHHH
Q ss_conf             42256676877
Q gi|254780945|r  359 MPQAHRRKALE  369 (700)
Q Consensus       359 ~~~~er~~i~~  369 (700)
                      ++..+...+..
T Consensus       268 l~~~e~~~~~~  278 (453)
T PRK07263        268 LTDQDWNNVTI  278 (453)
T ss_pred             CCHHHHHHHHH
T ss_conf             24799999999


No 397
>cd03468 Pol_Y_like Pol_Y_like: a group of putative Y-family DNA polymerases. Y-family polymerases can transverse normal replication-blocking DNA lesions, such as cyclobutane pyrimidine dimers resulting from UV damage, at higher error rate. The Y-family has no 3'-5' exonuclease activity. In addition to possessing a topology akin to a right hand, with "thumb", "fingers" and "palm" motifs, like polymerases from the A-, B-, C- and X-families, the Y-family has a unique "little finger" motif. Expression of Y-family polymerases is often induced by DNA damage. These polymerases are phylogenetically unrelated to classical DNA polymerases.
Probab=84.41  E-value=0.97  Score=25.39  Aligned_cols=49  Identities=16%  Similarity=0.125  Sum_probs=24.9

Q ss_pred             HHHHHHHHHHHHCCCCCCEEEEEECCCCCHHHHHHHHHHHHHHHHCCEEEEEHHHHH
Q ss_conf             999999999841001343078862144223699999973344430545886127999
Q gi|254780945|r  277 QESAIKDILQDMSQKNRMLRILQGDVGSGKTLVALIAMAAAVEAGGQAVIMAPIGIL  333 (700)
Q Consensus       277 Q~~ai~eI~~Dl~~~~pM~RLLQGDVGSGKTiVA~~A~l~~~~~G~Q~alMaPTEIL  333 (700)
                      .....+.|.+-+..-     =+.--||.|-|..++..+.   ..+....+..|.++-
T Consensus       114 ~~~~~~~i~~~l~~~-----gl~~s~Gia~~~~~Aklaa---~~~~~~~~~~~~~~~  162 (330)
T cd03468         114 EAALLERLRAALAAL-----GLTARAALADTPGAAWLLA---RAGAGRVVGAGEALA  162 (330)
T ss_pred             HHHHHHHHHHHHHHH-----CCEEEEEECCCHHHHHHHH---CCCCCCEECCCHHHH
T ss_conf             999999999999983-----9839999899989999984---579998215826788


No 398
>PRK08084 DNA replication initiation factor; Provisional
Probab=84.30  E-value=3.3  Score=21.23  Aligned_cols=36  Identities=22%  Similarity=0.302  Sum_probs=26.1

Q ss_pred             EEEEECCCCCHHHHHHHHHHHHHHHHCCEEEEEHHHH
Q ss_conf             7886214422369999997334443054588612799
Q gi|254780945|r  296 RILQGDVGSGKTLVALIAMAAAVEAGGQAVIMAPIGI  332 (700)
Q Consensus       296 RLLQGDVGSGKTiVA~~A~l~~~~~G~Q~alMaPTEI  332 (700)
                      =.|.|.+|||||=..-.++..+.+.|.++.++ |-+.
T Consensus        48 l~l~G~~G~GKTHLLqA~~~~~~~~~~~~~yl-~~~~   83 (235)
T PRK08084         48 IYLWGREGAGRSHLLHAACAELSQRGDAVGYV-PLDK   83 (235)
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHCCCCCEEEE-EHHH
T ss_conf             99989999888999999999997079857998-7798


No 399
>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=84.26  E-value=0.41  Score=28.34  Aligned_cols=136  Identities=22%  Similarity=0.236  Sum_probs=72.8

Q ss_pred             CCHHCHHCCCHHHCCCCCHHHHHHHHHHCCCCCCCCCCHHHHHHHCCCCCCCCCCCCCHHHCCCC-CEEEEEE--EEEEE
Q ss_conf             10202101772136785889999988740124688554898787089740134444647888998-7899999--99897
Q gi|254780945|r    3 PSFLNPLFAPLSTFRGVGKKYSLFLSKIINCGNANETRFIDLLFYHPSSFIDRHYRPKISEISEE-RIVTITG--YISQH   79 (700)
Q Consensus         3 p~~l~~L~~pI~~LkGVGpk~a~~L~kl~~l~~~GI~ti~DLL~~~PrrYeDr~~~~~I~~l~~g-~~vti~g--~V~~~   79 (700)
                      |..+..|=+.++.|||||||+|++|+=             .||-.=|..-++..+  .+.++..+ ..|...+  .+...
T Consensus         4 ~~~~~~Lie~L~kLPgiG~KsA~RlAf-------------~LL~~~~~~~~~la~--aL~~a~~~~~~C~~C~Cl~~s~~   68 (205)
T TIGR00615         4 PPPISKLIESLKKLPGIGPKSAQRLAF-------------HLLKRDPSEVERLAQ--ALLEAKEELRTCSVCGCLALSDQ   68 (205)
T ss_pred             HHHHHHHHHHHHHCCCCCHHHHHHHHH-------------HHCCCCHHHHHHHHH--HHHHHHHHCCCCCCCCEEECCCC
T ss_conf             668999999864078987147899999-------------860789999999999--99999871474656750211477


Q ss_pred             EE--E--CCCCC-CEEEEEEECCCCEEEEEEECCCHHHHHHHCCCCCEEEEEEEEEECCCEEEEECCEEEECCCCCC---
Q ss_conf             54--2--15898-3389999818936999995188789987328988899998997318779997786896264334---
Q gi|254780945|r   80 SS--F--QLQKR-RPYKILLNDGTGEITLLFFYRKTEMLKNVFFEGRKITVTGKIKKLKNRIIMVHPHYIFHNSQDV---  151 (700)
Q Consensus        80 ~~--~--~~~~r-~~~~v~v~D~tg~i~lvfFn~~~~yl~k~lk~G~~v~vsGKv~~~~~~~qi~hPe~~~~~~~~~---  151 (700)
                      ..  +  -.+|- +....+|++.-...-       ..-++. | .|..+++-|-+.=-    .=+|||=+..+.-..   
T Consensus        69 ~~C~ICsd~~Rde~s~iCvV~~p~Dv~a-------~E~~~~-f-~G~YhVL~G~isPl----~Gigp~~~~i~~L~~riG  135 (205)
T TIGR00615        69 EVCNICSDERRDENSVICVVEDPKDVFA-------LEKTKE-F-RGRYHVLGGLISPL----DGIGPEDLKIAALLKRIG  135 (205)
T ss_pred             CCCCCCCCCCCCCCCEEEEECCHHHHHH-------HHHHHH-H-CCCEEEECCEECCC----CCCCCCCCCHHHHHHHHH
T ss_conf             8777578887344753687447267999-------876542-1-66014315641764----576832214688998860


Q ss_pred             -------CCCCCCCCCCCCHHH
Q ss_conf             -------444411000000000
Q gi|254780945|r  152 -------NFPLIEAVYSLPTGL  166 (700)
Q Consensus       152 -------~~~~I~PIYplt~GL  166 (700)
                             -..-|...=|..+|=
T Consensus       136 eRl~~~~~~EVIlA~nPt~EGe  157 (205)
T TIGR00615       136 ERLQEESVKEVILATNPTVEGE  157 (205)
T ss_pred             CCCCCCCCCEEEEECCCCCHHH
T ss_conf             0000057977886078984134


No 400
>cd00983 recA RecA is a  bacterial enzyme which has roles in homologous recombination, DNA repair, and the induction of the SOS response.  RecA couples ATP hydrolysis to DNA strand exchange.
Probab=84.26  E-value=3.3  Score=21.22  Aligned_cols=83  Identities=23%  Similarity=0.303  Sum_probs=52.6

Q ss_pred             CCCCCEEE--EEECCCCCHHHHHHHHHHHHHHHHCCEEEEEHHHH-HHHHHHHHHHHHCCCCCCEE--EEEECCCCHHHH
Q ss_conf             01343078--86214422369999997334443054588612799-99999986211014578658--996246422566
Q gi|254780945|r  290 QKNRMLRI--LQGDVGSGKTLVALIAMAAAVEAGGQAVIMAPIGI-LAQQHYEFIKKYTQNTQIIV--EIITGNMPQAHR  364 (700)
Q Consensus       290 ~~~pM~RL--LQGDVGSGKTiVA~~A~l~~~~~G~Q~alMaPTEI-LA~QH~~~~~~~~~~~~i~v--~lLtg~~~~~er  364 (700)
                      .+.|..|.  +-|.-+||||-.|+.++..+-..|..||+.-- |= +-       ..|+..+||.+  -++.-..+.-+-
T Consensus        50 GGiP~GRivei~G~essGKTtlal~~ia~aQk~gg~~~~iDa-E~a~d-------~~~a~~lGVD~~~l~~~qp~~~Eq~  121 (325)
T cd00983          50 GGYPKGRIIEIYGPESSGKTTLALHAIAEAQKLGGTVAFIDA-EHALD-------PVYAKKLGVDLDNLLISQPDTGEQA  121 (325)
T ss_pred             CCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHCCCEEEEEEH-HHCCC-------HHHHHHCCCCHHHEEEECCCHHHHH
T ss_conf             996688089998898777999999999998735983999962-54259-------8999980998467589666389999


Q ss_pred             HHHHHH-HCCCCCEEEE
Q ss_conf             768776-2134754864
Q gi|254780945|r  365 RKALER-IAHGQAHIII  380 (700)
Q Consensus       365 ~~i~~~-i~~G~~~iiI  380 (700)
                      -++.+. +++|.++++|
T Consensus       122 l~i~~~li~s~~~dliV  138 (325)
T cd00983         122 LEIADSLVRSGAVDLIV  138 (325)
T ss_pred             HHHHHHHHCCCCCCEEE
T ss_conf             99999975158876799


No 401
>COG0210 UvrD Superfamily I DNA and RNA helicases [DNA replication, recombination, and repair]
Probab=84.16  E-value=3.3  Score=21.19  Aligned_cols=34  Identities=21%  Similarity=0.142  Sum_probs=16.0

Q ss_pred             HHHHHHHHHHCHHHHHHHHHHHHCCCCCC--CCCHHCCCCC
Q ss_conf             99999998414258999999852063000--2600069874
Q gi|254780945|r  605 YTRLSVLKNTEDGFLIAEEDLKQRKEGEI--LGIKQSGMPK  643 (700)
Q Consensus       605 ~~Rl~~l~~~~dGf~iAe~Dl~lRG~G~~--~G~~QsG~~~  643 (700)
                      ..||-...-|.     |++.|-+-.+-.-  .|..+.+.|.
T Consensus       597 ERRL~YVaiTR-----A~~~L~~t~~~~~~~~~~~~~~~~s  632 (655)
T COG0210         597 ERRLLYVAITR-----AKKKLYLTYAASRKLWGKEVEEEPS  632 (655)
T ss_pred             HHHHHHHHHHH-----HHHHHHHHHHHHHHHCCCCCCCCCC
T ss_conf             88899998788-----8765533236555532652344735


No 402
>KOG3416 consensus
Probab=84.13  E-value=3.3  Score=21.18  Aligned_cols=102  Identities=13%  Similarity=0.052  Sum_probs=65.4

Q ss_pred             CCCHHHCCCCCEEEEE-EEEEEEEEE-CCCCC-CEEEEEEECCCCEEEEEEECCCHHHHHHHCCCCCEEEEEEEE-EECC
Q ss_conf             4647888998789999-999897542-15898-338999981893699999518878998732898889999899-7318
Q gi|254780945|r   58 RPKISEISEERIVTIT-GYISQHSSF-QLQKR-RPYKILLNDGTGEITLLFFYRKTEMLKNVFFEGRKITVTGKI-KKLK  133 (700)
Q Consensus        58 ~~~I~~l~~g~~vti~-g~V~~~~~~-~~~~r-~~~~v~v~D~tg~i~lvfFn~~~~yl~k~lk~G~~v~vsGKv-~~~~  133 (700)
                      ..+|.|++||..-... --|+..... +++-+ ..-...+.|+||.|++..||-    .-..|++|+-+.+.|-. +.|+
T Consensus         4 ~i~ikdi~P~~kN~~v~fIvl~~g~~tkTkdg~~v~~~kVaD~TgsI~isvW~e----~~~~~~PGDIirLt~Gy~Si~q   79 (134)
T KOG3416           4 MIFIKDIKPGLKNINVTFIVLEYGRATKTKDGHEVRSCKVADETGSINISVWDE----EGCLIQPGDIIRLTGGYASIFQ   79 (134)
T ss_pred             CHHHHHCCHHHHCCEEEEEEEEECEEEECCCCCEEEEEEEECCCCEEEEEEECC----CCCCCCCCCEEEECCCCHHHHC
T ss_conf             023766682341624899998614030136898888999806655289998347----6764588668996363043403


Q ss_pred             CEEEEECCEEEECCCCCCCCCCCCCCCCCCHHHH
Q ss_conf             7799977868962643344444110000000000
Q gi|254780945|r  134 NRIIMVHPHYIFHNSQDVNFPLIEAVYSLPTGLS  167 (700)
Q Consensus       134 ~~~qi~hPe~~~~~~~~~~~~~I~PIYplt~GLs  167 (700)
                      |.+.+..    -...+-..++.+.-+|..+..++
T Consensus        80 g~LtL~~----GK~Ge~~KiGef~~vf~etpn~S  109 (134)
T KOG3416          80 GCLTLYV----GKGGEVQKIGEFCMVFSETPNIS  109 (134)
T ss_pred             CCEEEEE----CCCCEEEEEEEEEEEEECCCCCC
T ss_conf             8569996----17832767101577653178745


No 403
>PRK12402 replication factor C small subunit 2; Reviewed
Probab=84.08  E-value=1.5  Score=23.90  Aligned_cols=42  Identities=24%  Similarity=0.205  Sum_probs=28.7

Q ss_pred             HHHHHHHHHHHHHCCCCCCEEEEEECCCCCHHHHHHHHHHHH
Q ss_conf             899999999984100134307886214422369999997334
Q gi|254780945|r  276 SQESAIKDILQDMSQKNRMLRILQGDVGSGKTLVALIAMAAA  317 (700)
Q Consensus       276 ~Q~~ai~eI~~Dl~~~~pM~RLLQGDVGSGKTiVA~~A~l~~  317 (700)
                      +|..+++.+.+-+.++..=+=|+.|--|+|||-.|.+-+-..
T Consensus        19 Gq~~i~~~L~~~~~~~~~phlLf~GPpG~GKTt~A~~lA~~l   60 (337)
T PRK12402         19 GQESVVDHLSALAASGNLPHLVVYGPSGSGKTAAVRALAREL   60 (337)
T ss_pred             CCHHHHHHHHHHHHCCCCCEEEEECCCCCCHHHHHHHHHHHH
T ss_conf             979999999999977998769888929848999999999996


No 404
>PRK05480 uridine kinase; Provisional
Probab=84.06  E-value=2  Score=22.99  Aligned_cols=25  Identities=40%  Similarity=0.461  Sum_probs=20.4

Q ss_pred             HCCCCCCEEEEEECCCCCHHHHHHH
Q ss_conf             1001343078862144223699999
Q gi|254780945|r  288 MSQKNRMLRILQGDVGSGKTLVALI  312 (700)
Q Consensus       288 l~~~~pM~RLLQGDVGSGKTiVA~~  312 (700)
                      |...+|+--.+-|+.|||||-+|-.
T Consensus         1 ~~~k~P~iIgIaG~SgSGKTT~a~~   25 (209)
T PRK05480          1 MMMKQPIIIGIAGGSGSGKTTVAST   25 (209)
T ss_pred             CCCCCCEEEEEECCCCCCHHHHHHH
T ss_conf             9988988999989997789999999


No 405
>PRK07459 single-stranded DNA-binding protein; Provisional
Probab=84.04  E-value=3.4  Score=21.15  Aligned_cols=63  Identities=17%  Similarity=0.230  Sum_probs=43.0

Q ss_pred             EEEEEEEEEEEEEECCC-CC-CEEEEEEE-------CCCCEEEEEEECCCHHHHHHHCCCCCEEEEEEEEEE
Q ss_conf             89999999897542158-98-33899998-------189369999951887899873289888999989973
Q gi|254780945|r   69 IVTITGYISQHSSFQLQ-KR-RPYKILLN-------DGTGEITLLFFYRKTEMLKNVFFEGRKITVTGKIKK  131 (700)
Q Consensus        69 ~vti~g~V~~~~~~~~~-~r-~~~~v~v~-------D~tg~i~lvfFn~~~~yl~k~lk~G~~v~vsGKv~~  131 (700)
                      .|++.|.+.+-...++. .+ ......+.       +++.-+.++.|+.....+.+.++.|+.|.|.|++..
T Consensus         5 ~V~LiGrLg~DpElr~t~sG~~v~~fslAv~~~~k~~~t~w~~v~~wgk~Ae~~~~yl~KG~~V~V~G~l~~   76 (121)
T PRK07459          5 SVTLVGRAGRDPEVRYFESGSVVCNLTLAVNRRSRDDEPDWFNLEIWGKTAQVAADYVKKGSLIGITGSLKF   76 (121)
T ss_pred             EEEEEEECCCCCEEEECCCCCEEEEEEEEECCCCCCCCCCEEEEEEECHHHHHHHHHHCCCCEEEEEEEEEC
T ss_conf             899999667696188979997899999984675357787499999989089999887368989999999865


No 406
>PRK08760 replicative DNA helicase; Provisional
Probab=83.99  E-value=2  Score=22.88  Aligned_cols=72  Identities=17%  Similarity=0.117  Sum_probs=42.4

Q ss_pred             EEEECCCCCHHHHHHHHHHHHH-HHHCCEEEEEHHHHHHHHHHHHHHHHCCCCCCEEEEEECCCCHHHHHHHHHH
Q ss_conf             8862144223699999973344-4305458861279999999986211014578658996246422566768776
Q gi|254780945|r  297 ILQGDVGSGKTLVALIAMAAAV-EAGGQAVIMAPIGILAQQHYEFIKKYTQNTQIIVEIITGNMPQAHRRKALER  370 (700)
Q Consensus       297 LLQGDVGSGKTiVA~~A~l~~~-~~G~Q~alMaPTEILA~QH~~~~~~~~~~~~i~v~lLtg~~~~~er~~i~~~  370 (700)
                      .|=|--|.|||..|+--+..++ .+|.-|+|... |.=++|-...+-.-....+. -.+-+|.++..+...+.+.
T Consensus       233 ViaaRPsmGKTalalnia~~~A~~~~~~V~~fSL-EMs~~ql~~Rlls~~s~v~~-~~i~~g~l~~~e~~~~~~a  305 (476)
T PRK08760        233 ILAARPAMGKTTFALNIAEYAAIKSKKGVAVFSM-EMSASQLAMRLISSNGRINA-QRLRTGALEDEDWARVTGA  305 (476)
T ss_pred             EEEECCCCCHHHHHHHHHHHHHHHCCCCEEEEEC-CCCHHHHHHHHHHHHCCCCH-HHHHCCCCCHHHHHHHHHH
T ss_conf             9987788747899999999999837997899703-69999999999998338976-7776489999999999999


No 407
>PRK00090 bioD dithiobiotin synthetase; Reviewed
Probab=83.97  E-value=1  Score=25.27  Aligned_cols=32  Identities=34%  Similarity=0.440  Sum_probs=28.4

Q ss_pred             EEE-CCCCCHHHHHHHHHHHHHHHHCCEEEEEH
Q ss_conf             862-14422369999997334443054588612
Q gi|254780945|r  298 LQG-DVGSGKTLVALIAMAAAVEAGGQAVIMAP  329 (700)
Q Consensus       298 LQG-DVGSGKTiVA~~A~l~~~~~G~Q~alMaP  329 (700)
                      ++| |.|+|||+|++.-+......|+.++.|=|
T Consensus         4 I~GT~T~vGKT~vt~~L~~~l~~~G~~v~~~KP   36 (223)
T PRK00090          4 VTGTDTGVGKTVVTAALAQALREQGYRVAGYKP   36 (223)
T ss_pred             EEECCCCCCHHHHHHHHHHHHHHCCCCEEEECE
T ss_conf             986899976999999999999978994899751


No 408
>COG3111 Periplasmic protein with OB-fold [Function unknown]
Probab=83.87  E-value=3.4  Score=21.10  Aligned_cols=71  Identities=15%  Similarity=0.252  Sum_probs=50.7

Q ss_pred             CCHHHCCCCCEEEEEEEEEEEEEECCCCCCEEEEEEECCCCEEEEEEECCCHHHHHHHCCCCCEEEEEEEEEECCCEEEE
Q ss_conf             64788899878999999989754215898338999981893699999518878998732898889999899731877999
Q gi|254780945|r   59 PKISEISEERIVTITGYISQHSSFQLQKRRPYKILLNDGTGEITLLFFYRKTEMLKNVFFEGRKITVTGKIKKLKNRIIM  138 (700)
Q Consensus        59 ~~I~~l~~g~~vti~g~V~~~~~~~~~~r~~~~v~v~D~tg~i~lvfFn~~~~yl~k~lk~G~~v~vsGKv~~~~~~~qi  138 (700)
                      ..-.++.++..|+++|.|++.-.       -=+..+.|.+|.|++-.=+.  -|.-....+.+.+.++|++...-+..++
T Consensus        49 ~~Ak~~~Dda~V~l~GnIv~qi~-------~D~y~FrD~sGeI~VeIdd~--~w~g~tv~P~dkV~I~GevDk~~~~~eI  119 (128)
T COG3111          49 DQAKTLHDDAWVSLEGNIVRQIG-------DDRYVFRDASGEINVDIDDK--VWNGQTVTPKDKVRIQGEVDKDWNSVEI  119 (128)
T ss_pred             HHHHCCCCCCEEEEEEEEEEEEC-------CCEEEEECCCCCEEEEECCC--CCCCCCCCCCCEEEEEEEECCCCCCCEE
T ss_conf             87533025984999756777607-------83699975896199981601--1389706856689997687378766256


No 409
>PRK11388 DNA-binding transcriptional regulator DhaR; Provisional
Probab=83.81  E-value=1.3  Score=24.47  Aligned_cols=160  Identities=17%  Similarity=0.162  Sum_probs=72.8

Q ss_pred             HHHHHHHHHHHHHHCCCCCCEEEEEECCCCCHHHHHHHHHHHHHH-HHCCEEE---EEHHHHHHHHHHHHHHHHCCCCCC
Q ss_conf             889999999998410013430788621442236999999733444-3054588---612799999999862110145786
Q gi|254780945|r  275 KSQESAIKDILQDMSQKNRMLRILQGDVGSGKTLVALIAMAAAVE-AGGQAVI---MAPIGILAQQHYEFIKKYTQNTQI  350 (700)
Q Consensus       275 ~~Q~~ai~eI~~Dl~~~~pM~RLLQGDVGSGKTiVA~~A~l~~~~-~G~Q~al---MaPTEILA~QH~~~~~~~~~~~~i  350 (700)
                      ..-+++++....-..++.|  -||+|+.|+||+.+|-..-...-. .|-=+++   ..|.|.+....|-.-.        
T Consensus       332 ~~~~~~~~~a~~~a~~~~p--VLI~GE~GtGKe~lAraIH~~S~r~~~pfv~vnC~ai~~~~~e~elfG~~~--------  401 (639)
T PRK11388        332 PQMRRLIHFGRQAAKSSFP--ILLCGEEGVGKALLAQAIHNESERAAGPYIAVNCQLLPDEALAEEFLGSDR--------  401 (639)
T ss_pred             HHHHHHHHHHHHHHCCCCC--EEEECCCCCCHHHHHHHHHHCCCCCCCCEEEEECCCCCHHHHHHHHCCCCC--------
T ss_conf             9999999999999688996--898898981099999999955777899818987898984678998738776--------


Q ss_pred             EEEEEECCCCHHHHHHHHHHHCCCCCEEEEECHHHCCCCCCCCCCCEEEECCCCCCCHHHHHHHHH----C-----C---
Q ss_conf             589962464225667687762134754864111201334554444178852101335688998740----2-----5---
Q gi|254780945|r  351 IVEIITGNMPQAHRRKALERIAHGQAHIIIGTHALFQDSIQYYKLILVIVDEQHRFGVQQRLKLTQ----K-----A---  418 (700)
Q Consensus       351 ~v~lLtg~~~~~er~~i~~~i~~G~~~iiIGTHAL~q~~v~F~~LgLvViDEQHRFGV~QR~~L~~----K-----g---  418 (700)
                            |..+.            |.    .   ..|    +-.+=|-+++||=+-.--....+|..    +     |   
T Consensus       402 ------~~~~~------------g~----~---g~~----e~A~gGTL~LdeI~~lp~~~Q~~LlrvL~~~~~~r~g~~~  452 (639)
T PRK11388        402 ------TDSEN------------GR----L---SKF----ELAHGGTLFLEKVEYLSVELQSALLQVLKTGVITRLDSRR  452 (639)
T ss_pred             ------CCCCC------------CC----C---CHH----HCCCCCEEEECCHHHCCHHHHHHHHHHHHCCCEEECCCCC
T ss_conf             ------76434------------66----8---624----4036982884672649999999999998659378569994


Q ss_pred             -CCCCCEEECHHHHHHHHHH-------HHHHCCCHHHHCCCCCCCCCCEEEEEECCCHHHHHHHHHHHHCC
Q ss_conf             -6776101010132278999-------97520101111023557666207999702002689999763103
Q gi|254780945|r  419 -TAPHVLLMTATPIPRTLVL-------TSLGDIDISKITEKPAGRKPIKTVIIPINRIDEVIERLKVVLSE  481 (700)
Q Consensus       419 -~~ph~L~MtATPIPRTLal-------~~ygdldvS~i~e~P~gR~~I~T~~~~~~~~~~~~~~i~~~l~~  481 (700)
                       ...|+=+++||-.+=.-..       -+|--|....|. +||=|.-       .++++.+++.+-.++..
T Consensus       453 ~~~vdvRiiaat~~~l~~~v~~g~fr~dLyyrl~~~~i~-lPpLReR-------~~Di~~L~~~~l~~~~~  515 (639)
T PRK11388        453 LIPVDVRVIATTTADLAMLVEQNRFSRQLYYALHAFEIT-IPPLRMR-------REDIPALVNNKLRSLEK  515 (639)
T ss_pred             EEEEEEEEEEECCHHHHHHHHCCCCHHHHHHHHHHHHCC-CCCHHHC-------HHHHHHHHHHHHHHHHH
T ss_conf             666427999736450899987498549999876744105-7332325-------34399999999999999


No 410
>PRK08763 single-stranded DNA-binding protein; Provisional
Probab=83.80  E-value=3.4  Score=21.08  Aligned_cols=64  Identities=19%  Similarity=0.258  Sum_probs=42.5

Q ss_pred             CEEEEEEEEEEEEEECCC--CCCEEEEEEE------CC-------CCEEEEEEECCCHHHHHHHCCCCCEEEEEEEEEE
Q ss_conf             789999999897542158--9833899998------18-------9369999951887899873289888999989973
Q gi|254780945|r   68 RIVTITGYISQHSSFQLQ--KRRPYKILLN------DG-------TGEITLLFFYRKTEMLKNVFFEGRKITVTGKIKK  131 (700)
Q Consensus        68 ~~vti~g~V~~~~~~~~~--~r~~~~v~v~------D~-------tg~i~lvfFn~~~~yl~k~lk~G~~v~vsGKv~~  131 (700)
                      ..|++.|.+.+-..+++.  +.....+.+.      |.       +.-+.|+.|+.....+.+.|++|+.|+|.|+++.
T Consensus         6 NkV~LiG~l~~Dpelr~t~sG~~v~~fslA~~~~~~~~~g~~~~~t~w~~vv~~gk~AE~~~~yl~KG~~V~VeGrL~~   84 (160)
T PRK08763          6 NKVILVGNLGNDPDIKYTQSGMTITRISLATTSMRKDREGNTQERTEWHRVKFFGKLGEIAGEYLRKGSQCYIEGEIRY   84 (160)
T ss_pred             CEEEEEEECCCCCEEEECCCCCEEEEEEEEECCCEECCCCCCEECEEEEEEEEEHHHHHHHHHHHHCCCEEEEEEEEEE
T ss_conf             1999987547597587889998799999997787356888825210599999836899999987417998999888888


No 411
>PRK08727 hypothetical protein; Validated
Probab=83.75  E-value=3.1  Score=21.44  Aligned_cols=36  Identities=39%  Similarity=0.530  Sum_probs=29.4

Q ss_pred             EEEEECCCCCHHHHHHHHHHHHHHHHCCEEEEEHHHH
Q ss_conf             7886214422369999997334443054588612799
Q gi|254780945|r  296 RILQGDVGSGKTLVALIAMAAAVEAGGQAVIMAPIGI  332 (700)
Q Consensus       296 RLLQGDVGSGKTiVA~~A~l~~~~~G~Q~alMaPTEI  332 (700)
                      =.|.|..|||||=.+-.++..+...|..++++ |.+-
T Consensus        44 lyl~G~~GsGKTHLl~a~~~~~~~~~~~~~yl-~l~~   79 (233)
T PRK08727         44 LYLSGPAGTGKTHLALSLCAAAEQAGRSSAYL-PLQA   79 (233)
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHHCCCCEEEE-EHHH
T ss_conf             99989999988999999999998279972884-4788


No 412
>PRK05636 replicative DNA helicase; Provisional
Probab=83.61  E-value=3.5  Score=21.03  Aligned_cols=72  Identities=19%  Similarity=0.279  Sum_probs=45.4

Q ss_pred             EEEECCCCCHHHHHHHHHHHH-HHHHCCEEEEEHHHHHHHHHHHHHHHHCCCCCCEEEEEECCCCHHHHHHHHHH
Q ss_conf             886214422369999997334-44305458861279999999986211014578658996246422566768776
Q gi|254780945|r  297 ILQGDVGSGKTLVALIAMAAA-VEAGGQAVIMAPIGILAQQHYEFIKKYTQNTQIIVEIITGNMPQAHRRKALER  370 (700)
Q Consensus       297 LLQGDVGSGKTiVA~~A~l~~-~~~G~Q~alMaPTEILA~QH~~~~~~~~~~~~i~v~lLtg~~~~~er~~i~~~  370 (700)
                      .|=|--|.|||..|+--+..+ +.+|+-|+|... |.=++|-...+-......+.. .+-+|.++..+..++.+.
T Consensus       271 IiAARPsmGKTalAlnia~n~A~~~g~~v~~fSL-EMs~~ql~~Rlla~~s~V~~~-~ir~g~l~~~~~~~l~~a  343 (507)
T PRK05636        271 IVAARPGVGKSTIALDFMRSASIKNNKASVIFSL-EMSKSEIVMRLLSAEAEVRLA-DMRGGKMDEDAWEKLVQR  343 (507)
T ss_pred             EEEECCCCCHHHHHHHHHHHHHHHCCCCEEEEEC-CCCHHHHHHHHHHHHCCCCHH-HHHCCCCCHHHHHHHHHH
T ss_conf             9973787866899999999999876993799715-699899999999984798878-885588788999999999


No 413
>cd02028 UMPK_like Uridine monophosphate kinase_like (UMPK_like) is a family of proteins highly similar to the uridine monophosphate kinase (UMPK, EC 2.7.1.48), also known as uridine kinase or uridine-cytidine kinase (UCK).
Probab=83.60  E-value=1.3  Score=24.30  Aligned_cols=31  Identities=29%  Similarity=0.249  Sum_probs=22.1

Q ss_pred             EEEECCCCCHHHHHHHHHHHHHHHHCCEEEE
Q ss_conf             8862144223699999973344430545886
Q gi|254780945|r  297 ILQGDVGSGKTLVALIAMAAAVEAGGQAVIM  327 (700)
Q Consensus       297 LLQGDVGSGKTiVA~~A~l~~~~~G~Q~alM  327 (700)
                      -+-|+.|||||-+|-.-.-..-.+|.+++++
T Consensus         3 gIaG~SgSGKTT~a~~L~~~l~~~~~~~~vi   33 (179)
T cd02028           3 GIAGPSGSGKTTFAKKLSNQLRVNGIGPVVI   33 (179)
T ss_pred             EEECCCCCCHHHHHHHHHHHHHHCCCCEEEE
T ss_conf             9989897789999999999984648853999


No 414
>PRK07471 DNA polymerase III subunit delta'; Validated
Probab=83.53  E-value=1.8  Score=23.27  Aligned_cols=41  Identities=17%  Similarity=0.197  Sum_probs=31.1

Q ss_pred             HHHHHHHHHHHHHHCCCC-CCEEEEEECCCCCHHHHHHHHHH
Q ss_conf             889999999998410013-43078862144223699999973
Q gi|254780945|r  275 KSQESAIKDILQDMSQKN-RMLRILQGDVGSGKTLVALIAMA  315 (700)
Q Consensus       275 ~~Q~~ai~eI~~Dl~~~~-pM~RLLQGDVGSGKTiVA~~A~l  315 (700)
                      -+|..+.+...+-+.+++ |=--|+.|--|+|||-.|...+-
T Consensus        20 iGqe~~~~~L~~a~~~grl~HA~Lf~Gp~GiGK~tlA~~~A~   61 (363)
T PRK07471         20 FGHAAAEAALLDAYRSGRLHHAWLIGGPQGIGKATLAYRMAR   61 (363)
T ss_pred             CCHHHHHHHHHHHHHCCCCCCEEEEECCCCCCHHHHHHHHHH
T ss_conf             681999999999998599764587679998188999999999


No 415
>pfam05876 Terminase_GpA Phage terminase large subunit (GpA). This family consists of several phage terminase large subunit proteins as well as related sequences from several bacterial species. The DNA packaging enzyme of bacteriophage lambda, terminase, is a heteromultimer composed of a small subunit, gpNu1, and a large subunit, gpA, products of the Nu1 and A genes, respectively. Terminase is involved in the site-specific binding and cutting of the DNA in the initial stages of packaging. It is now known that gpA is actively involved in late stages of packaging, including DNA translocation, and that this enzyme contains separate functional domains for its early and late packaging activities.
Probab=83.53  E-value=3.5  Score=21.00  Aligned_cols=130  Identities=14%  Similarity=0.184  Sum_probs=63.8

Q ss_pred             CCCHHHHHHHHHHHHHHCCCCCCEEEEEECCCCCHHHHHHHHHHHHHHH-HCCEEEEEHHHHHHHHHHH-HHHHHCCCCC
Q ss_conf             6798899999999984100134307886214422369999997334443-0545886127999999998-6211014578
Q gi|254780945|r  272 SPTKSQESAIKDILQDMSQKNRMLRILQGDVGSGKTLVALIAMAAAVEA-GGQAVIMAPIGILAQQHYE-FIKKYTQNTQ  349 (700)
Q Consensus       272 ~LT~~Q~~ai~eI~~Dl~~~~pM~RLLQGDVGSGKTiVA~~A~l~~~~~-G~Q~alMaPTEILA~QH~~-~~~~~~~~~~  349 (700)
                      +.|.-|.    ||.+-|+.+.--.--+++=.-+|||.+....+...++. ---..++-||+-.|+...+ .|..++...+
T Consensus        16 ~~~Py~~----eimd~l~~~~v~~V~~~k~aQ~GkT~~~~n~igy~i~~~P~p~l~v~Pt~~~a~~~s~~rl~Pmi~~sP   91 (552)
T pfam05876        16 DRTPYLR----EIMDALSPPSVERVVFMKSAQVGKTELLLNWIGYFIDHDPAPMLVVQPTDDDAKRFSKDRLDPMIRASP   91 (552)
T ss_pred             CCCCHHH----HHHHHCCCCCCEEEEEEECCCCCHHHHHHHHHHHHHHHCCCCEEEEECCHHHHHHHHHHHHHHHHHCCH
T ss_conf             8880769----999854887844999995787038899999998866308988799941899999999998999986198


Q ss_pred             CEEEEEECCCCHHHHHHHHHHHCCCCCEEEEECHHHCCCCCCCCCCCEEEECCCCCCC
Q ss_conf             6589962464225667687762134754864111201334554444178852101335
Q gi|254780945|r  350 IIVEIITGNMPQAHRRKALERIAHGQAHIIIGTHALFQDSIQYYKLILVIVDEQHRFG  407 (700)
Q Consensus       350 i~v~lLtg~~~~~er~~i~~~i~~G~~~iiIGTHAL~q~~v~F~~LgLvViDEQHRFG  407 (700)
                      .--.+++...+......++.+--.|-.-.++|..+-  .++.=....+++.||=-+|-
T Consensus        92 ~L~~~~~~~~~r~~~nt~~~K~f~gg~l~~~ga~S~--~~L~s~~~r~l~~DEvD~~~  147 (552)
T pfam05876        92 ALRERLAPARSRDSDNTLLSKRFPGGSLLLIGANSP--ANLRSRPVRYVILDEVDAYP  147 (552)
T ss_pred             HHHHHHCCCCCCCCCCCEEEEEECCCEEEEEECCCC--HHHHCCCCCEEEECCHHHCC
T ss_conf             999750755565667741247607837999557996--14304863558851344365


No 416
>COG1663 LpxK Tetraacyldisaccharide-1-P 4'-kinase [Cell envelope biogenesis, outer membrane]
Probab=83.29  E-value=1.5  Score=23.97  Aligned_cols=95  Identities=21%  Similarity=0.212  Sum_probs=54.1

Q ss_pred             CCCHHHHHHHHHHHHH---------HHHCCEEEEEHHHHHHHHH-HHHHH--HH--CCCCCCEEEEEECCCCHHHHHHHH
Q ss_conf             4223699999973344---------4305458861279999999-98621--10--145786589962464225667687
Q gi|254780945|r  303 GSGKTLVALIAMAAAV---------EAGGQAVIMAPIGILAQQH-YEFIK--KY--TQNTQIIVEIITGNMPQAHRRKAL  368 (700)
Q Consensus       303 GSGKTiVA~~A~l~~~---------~~G~Q~alMaPTEILA~QH-~~~~~--~~--~~~~~i~v~lLtg~~~~~er~~i~  368 (700)
                      |+|||=+++.-+-..-         +-||-+-.-++|.+....| .+..-  .+  ....+.++..      ...|.+..
T Consensus        59 GtGKTP~vi~la~~l~~rG~~~gvvSRGYgg~~~~~~~~~~~~~~a~~~GDEPlLlA~~t~~pv~v------~~~R~~~~  132 (336)
T COG1663          59 GTGKTPVVIWLAEALQARGVRVGVVSRGYGGKLKVVPLVDNIHTTAAEVGDEPLLLARRTGAPVAV------SPDRKDAA  132 (336)
T ss_pred             CCCCCHHHHHHHHHHHHCCCEEEEEECCCCCCCCCCCCCCCCCCCHHHCCCHHHHHHHHCCCCEEE------EHHHHHHH
T ss_conf             899688999999999866973679805768887654102567678677284688875533996898------64298999


Q ss_pred             HHHCC--CCCEEEEEC----HHHCCCCCCCCCCCEEEECCCCCCCH
Q ss_conf             76213--475486411----12013345544441788521013356
Q gi|254780945|r  369 ERIAH--GQAHIIIGT----HALFQDSIQYYKLILVIVDEQHRFGV  408 (700)
Q Consensus       369 ~~i~~--G~~~iiIGT----HAL~q~~v~F~~LgLvViDEQHRFGV  408 (700)
                      ..+..  ..++|||=-    |.=++     +++-+||||-|-+||=
T Consensus       133 ~~l~~~~~~~diIi~DDG~Qh~rL~-----rD~eIvvvd~~r~fGn  173 (336)
T COG1663         133 KALLAAHLGCDIIVLDDGLQHYRLH-----RDFEIVVVDGQRGFGN  173 (336)
T ss_pred             HHHHHHCCCCCEEEECCCCHHHHHH-----CCEEEEEEECCCCCCC
T ss_conf             9998517898999976743126764-----3646999736646878


No 417
>COG3421 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=83.29  E-value=0.68  Score=26.61  Aligned_cols=60  Identities=13%  Similarity=0.260  Sum_probs=34.0

Q ss_pred             HHHHHCCCCCCHHHHHHHHHHHHHHCCCCCCEEEEEECCCCCHHHHHHHHHHHHHHH-HCCEEEEE
Q ss_conf             998630246798899999999984100134307886214422369999997334443-05458861
Q gi|254780945|r  264 KILRNIPFSPTKSQESAIKDILQDMSQKNRMLRILQGDVGSGKTLVALIAMAAAVEA-GGQAVIMA  328 (700)
Q Consensus       264 ~f~~~LPF~LT~~Q~~ai~eI~~Dl~~~~pM~RLLQGDVGSGKTiVA~~A~l~~~~~-G~Q~alMa  328 (700)
                      +.+..|-|-=-.+|.+-|.|+.+.+..     -+++--.|.|||+.-.-......++ ||.+++.-
T Consensus       408 r~LE~l~yh~~~~~SkyIseLkn~L~~-----lGl~~~~~~dk~l~k~KLk~~f~~~k~fK~~L~f  468 (812)
T COG3421         408 RILEELFYHTHDEQSKYISELKNELRK-----LGLNPETDADKVLMKFKLKSEFADNKGFKHLLIF  468 (812)
T ss_pred             HHHHHHHHHCCCHHHHHHHHHHHHHHH-----HCCCCCCCCCHHHHHHHHHHHCCCCCCCEEEEEE
T ss_conf             898888766042056469999867888-----4578866631788988864221566673189997


No 418
>TIGR01447 recD exodeoxyribonuclease V, alpha subunit; InterPro: IPR006344   This family describes the exodeoxyribonuclease V alpha subunit, RecD. RecD is part of a RecBCD complex. C-terminal part of the protein matches a domain found in viral RNA helicase, superfamily 1, IPR000606 from INTERPRO. ; GO: 0008854 exodeoxyribonuclease V activity, 0009338 exodeoxyribonuclease V complex.
Probab=83.06  E-value=3.6  Score=20.87  Aligned_cols=142  Identities=19%  Similarity=0.283  Sum_probs=74.8

Q ss_pred             HHHHHHCCCCCCHHHHHH--HHHHHHHHCCCCCCEEEEEECCCCCHH--HHHHHHHHHHHHHH-----CCEEEEEHHHHH
Q ss_conf             999863024679889999--999998410013430788621442236--99999973344430-----545886127999
Q gi|254780945|r  263 QKILRNIPFSPTKSQESA--IKDILQDMSQKNRMLRILQGDVGSGKT--LVALIAMAAAVEAG-----GQAVIMAPIGIL  333 (700)
Q Consensus       263 ~~f~~~LPF~LT~~Q~~a--i~eI~~Dl~~~~pM~RLLQGDVGSGKT--iVA~~A~l~~~~~G-----~Q~alMaPTEIL  333 (700)
                      ..+.+-+|-.-++.++++  ...+...++-..+. -|+-|-=|+|||  |+-+++++..-...     -+.++.|||-==
T Consensus       211 ~~l~~~f~~~~~~~~~~~~D~Q~~a~~~aL~~~f-~li~GGPGTGKTTTv~~LL~al~~~~~~~G~~~~~I~l~APTGKA  289 (753)
T TIGR01447       211 AILENLFPLLNEQNGRKVTDWQKVAVALALKSNF-SLITGGPGTGKTTTVARLLLALIKQSPKQGKPRLRIALAAPTGKA  289 (753)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCE-EEEECCCCCCHHHHHHHHHHHHHHHHHHCCCCCEEEEEECCCHHH
T ss_conf             9999985421045443113799999999860876-899879889778999999999999898649974047886684479


Q ss_pred             HHHHHHHHHHHCCCCCCE-----EEEEECCCCHHHHHHHHHHHCCCCCEEEEECHHHCCCCCCCCCCCEEEECCCCCCCH
Q ss_conf             999998621101457865-----899624642256676877621347548641112013345544441788521013356
Q gi|254780945|r  334 AQQHYEFIKKYTQNTQII-----VEIITGNMPQAHRRKALERIAHGQAHIIIGTHALFQDSIQYYKLILVIVDEQHRFGV  408 (700)
Q Consensus       334 A~QH~~~~~~~~~~~~i~-----v~lLtg~~~~~er~~i~~~i~~G~~~iiIGTHAL~q~~v~F~~LgLvViDEQHRFGV  408 (700)
                      |.--.+++.+-+..+.+.     -+++.+ .+. +- ..+.++- |  ..-|++-..++..=.--++=+.||||      
T Consensus       290 a~RL~esl~~~~~~L~~~~~aid~~~~~~-~~~-~~-~TiHrLL-G--~~~I~~~~fr~h~~N~L~~DVLvvDE------  357 (753)
T TIGR01447       290 AARLAESLRKAVKKLAAENMAIDEDLIAA-LPS-EA-TTIHRLL-G--IKPIDTKRFRHHERNPLPLDVLVVDE------  357 (753)
T ss_pred             HHHHHHHHHHHHHHHHHHCCCCCHHHHCC-CCH-HH-HHHHHHH-C--CCCCCCCCCCCCCCCCCCCCEEEECC------
T ss_conf             99999999988632234236658798548-720-45-6888861-6--61478767767777889855278706------


Q ss_pred             HHHHHHHHCCCCCCCEEE
Q ss_conf             889987402567761010
Q gi|254780945|r  409 QQRLKLTQKATAPHVLLM  426 (700)
Q Consensus       409 ~QR~~L~~Kg~~ph~L~M  426 (700)
                               +.+.|+.+|
T Consensus       358 ---------aSMVdl~lm  366 (753)
T TIGR01447       358 ---------ASMVDLPLM  366 (753)
T ss_pred             ---------CHHCCHHHH
T ss_conf             ---------002267999


No 419
>cd01127 TrwB Bacterial conjugation protein TrwB,  ATP binding domain. TrwB is a homohexamer encoded by conjugative plasmids in Gram-negative bacteria. TrwB also has an all alpha domain which has been hypothesized to be responsible for DNA binding. TrwB is a component of Type IV secretion and is responsible for the horizontal transfer of DNA between bacteria.
Probab=83.05  E-value=2.3  Score=22.50  Aligned_cols=111  Identities=9%  Similarity=0.069  Sum_probs=49.0

Q ss_pred             HCCCHHHHCCCCCCCCCCEEEEEEC-CC---HHHHHHHHHHHHCCCCEEEEEECCCCCCCCCCCCHHHHHH-HHHHH-HC
Q ss_conf             2010111102355766620799970-20---0268999976310387389997120122111210146666-66686-63
Q gi|254780945|r  441 GDIDISKITEKPAGRKPIKTVIIPI-NR---IDEVIERLKVVLSEGKKAYWICPQIEEKKESNFRSVVERF-NSLHE-HF  514 (700)
Q Consensus       441 gdldvS~i~e~P~gR~~I~T~~~~~-~~---~~~~~~~i~~~l~~g~q~y~VcPlIeese~~~~~~~~~~~-~~l~~-~~  514 (700)
                      =++.++.+-.+|+.+.+=.-.++.+ ..   ++.+-+.+..-=..|-.++.++-        ++.-.++.| +...+ .+
T Consensus       254 l~~~~~~ll~~~~~~~~rv~~~lDE~~~l~~l~~~~~~l~~~R~~g~~~~~~~Q--------~~~Ql~~~YG~~~a~~i~  325 (410)
T cd01127         254 LDVAVNTLLGLPENRERRLWFFIDELPSLHKLPDLVDALAEGRKFGGCFVLGIQ--------SYAQLEDIYGKKGAQTLA  325 (410)
T ss_pred             HHHHHHHHHCCCCCCCCCEEEEEECHHCCCCCHHHHHHHHHHHHCCCEEEEEEC--------CHHHHHHHHCHHHHHHHH
T ss_conf             999999985388767860799988700037717799999988517978999917--------889999997873899998


Q ss_pred             CC-CEECCCCCCCHHHHHHHHHHHHCCCEEEEEECHHHHCCCCCCCCC
Q ss_conf             71-031201469989999999997559869999800341046888765
Q gi|254780945|r  515 TS-SIAIIHGRMSDIDKESVMDSFKNGTCKLLIATTVIEVGIDVVDAS  561 (700)
Q Consensus       515 ~~-~v~~lHGkm~~~ek~~~m~~F~~g~~~iLvaTtviEVGvdvpna~  561 (700)
                      .. .+-+.-+ ..+.|-.+-+.+. -|+..|.+.+.-.--|.+--..+
T Consensus       326 ~~~~~~i~~~-~~d~~ta~~~S~~-lG~~~v~~~~~s~s~g~~~~~~~  371 (410)
T cd01127         326 SNLRTRIVLA-APDAKTAEHASDS-LGEQEVREMRENYSYGANNIRDG  371 (410)
T ss_pred             HCCCCEEEEE-CCCHHHHHHHHHH-CCCEEEEEEEEEECCCCCCCCCC
T ss_conf             4277689982-7998899999996-09669988750044787888898


No 420
>PRK12373 NADH dehydrogenase subunit E; Provisional
Probab=83.03  E-value=0.78  Score=26.14  Aligned_cols=12  Identities=8%  Similarity=-0.238  Sum_probs=5.1

Q ss_pred             CCCCCCCCCCCC
Q ss_conf             444441100000
Q gi|254780945|r  151 VNFPLIEAVYSL  162 (700)
Q Consensus       151 ~~~~~I~PIYpl  162 (700)
                      .....++..||.
T Consensus        21 ~~a~~~iakYPe   32 (403)
T PRK12373         21 AWAEKQITKYPE   32 (403)
T ss_pred             HHHHHHHHHCCC
T ss_conf             999999986887


No 421
>pfam00485 PRK Phosphoribulokinase / Uridine kinase family. In Arabidopsis the region carries two binding domains, a phosphoribosylpyrophosphate-binding domain and, at the very C-terminus, a uracil-binding domain.
Probab=83.00  E-value=1.7  Score=23.50  Aligned_cols=27  Identities=30%  Similarity=0.278  Sum_probs=17.3

Q ss_pred             EEEECCCCCHHHHHHHHHHHHHHHHCC
Q ss_conf             886214422369999997334443054
Q gi|254780945|r  297 ILQGDVGSGKTLVALIAMAAAVEAGGQ  323 (700)
Q Consensus       297 LLQGDVGSGKTiVA~~A~l~~~~~G~Q  323 (700)
                      .+-|..|||||-+|-.-.-..-..|.+
T Consensus         3 gIaG~SgSGKTT~a~~L~~~l~~~~~~   29 (196)
T pfam00485         3 GVAGSSGAGKTTVARTFVSIFGREGVP   29 (196)
T ss_pred             EEECCCCCCHHHHHHHHHHHHCCCCCC
T ss_conf             998998571999999999996605877


No 422
>PRK06674 DNA polymerase III subunits gamma and tau; Validated
Probab=82.76  E-value=3.7  Score=20.78  Aligned_cols=19  Identities=21%  Similarity=0.354  Sum_probs=11.4

Q ss_pred             EEEEEEECCCCEEEEEEEC
Q ss_conf             3899998189369999951
Q gi|254780945|r   89 PYKILLNDGTGEITLLFFY  107 (700)
Q Consensus        89 ~~~v~v~D~tg~i~lvfFn  107 (700)
                      .++|.+-|+-..++--=||
T Consensus       119 ~yKV~IIDeah~Lt~~A~N  137 (563)
T PRK06674        119 EYKVYIIDEVHMLSIGAFN  137 (563)
T ss_pred             CEEEEEEECHHHCCHHHHH
T ss_conf             7379998545637999999


No 423
>PRK08486 single-stranded DNA-binding protein; Provisional
Probab=82.56  E-value=3.8  Score=20.73  Aligned_cols=63  Identities=16%  Similarity=0.265  Sum_probs=40.3

Q ss_pred             EEEEEEEEEEEEEECCC-C-CCEEEEE--EE-----------CCCCEEEEEEECCCHHHHHHHCCCCCEEEEEEEEEE
Q ss_conf             89999999897542158-9-8338999--98-----------189369999951887899873289888999989973
Q gi|254780945|r   69 IVTITGYISQHSSFQLQ-K-RRPYKIL--LN-----------DGTGEITLLFFYRKTEMLKNVFFEGRKITVTGKIKK  131 (700)
Q Consensus        69 ~vti~g~V~~~~~~~~~-~-r~~~~v~--v~-----------D~tg~i~lvfFn~~~~yl~k~lk~G~~v~vsGKv~~  131 (700)
                      .|++.|.+.+-..+++. . ....++.  +.           +++.-+.|++|+.....+.+.|++|+.|+|.|++..
T Consensus         4 kViLvGrL~~DpElr~t~~G~~v~~f~lAv~r~~~~~~Ge~~e~t~f~~v~~wgk~AE~~~~yl~KGs~V~VeGrL~~   81 (180)
T PRK08486          4 KVILVGNLTRDVELRYLPSGSAIATIGLATSRRFKKQDGEKGEEVCFIDIRLFGRTAEIANQYLSKGSKVLIEGRLTF   81 (180)
T ss_pred             EEEEEEECCCCCEEEECCCCCEEEEEEEEECCCEECCCCCCCCCCEEEEEEECCHHHHHHHHHCCCCCEEEEEEEEEC
T ss_conf             699988568686388879998899999986686667888780223699998816789888752189999999999884


No 424
>COG3972 Superfamily I DNA and RNA helicases [General function prediction only]
Probab=82.24  E-value=1.9  Score=23.03  Aligned_cols=142  Identities=15%  Similarity=0.053  Sum_probs=73.3

Q ss_pred             CHHHHHHHHHCCCCCCHHHHHHHHHHHHHHCCCCCCEEEEEECCCCCHHHHHHHHHH--HHHHHHCCEEEEEHHHHHHHH
Q ss_conf             578999986302467988999999999841001343078862144223699999973--344430545886127999999
Q gi|254780945|r  259 GKIAQKILRNIPFSPTKSQESAIKDILQDMSQKNRMLRILQGDVGSGKTLVALIAMA--AAVEAGGQAVIMAPIGILAQQ  336 (700)
Q Consensus       259 ~~~~~~f~~~LPF~LT~~Q~~ai~eI~~Dl~~~~pM~RLLQGDVGSGKTiVA~~A~l--~~~~~G~Q~alMaPTEILA~Q  336 (700)
                      +.+++.+.+.. -.+-..|.+|.-++-.    +.+   -++|=-|||||+|-+.-+.  ..-.-..|-|+-.=|-+||.|
T Consensus       150 ~a~l~~ieskI-anfD~~Q~kaa~~~~~----G~q---rIrGLAGSGKT~~La~Kaa~lh~knPd~~I~~Tfftk~L~s~  221 (660)
T COG3972         150 NALLDTIESKI-ANFDTDQTKAAFQSGF----GKQ---RIRGLAGSGKTELLAHKAAELHSKNPDSRIAFTFFTKILAST  221 (660)
T ss_pred             HHHHHHHHHHH-HCCCCHHHEEEEECCC----CHH---HHHCCCCCCCHHHHHHHHHHHHCCCCCCEEEEEEEHHHHHHH
T ss_conf             78999999988-5235042314465477----346---520024787302988777897447998638998666788899


Q ss_pred             HHHHHHHHCCC-------CCC-EEEEEE-CCCCH------HHHHHHHHHHCCCCCEEEEEC-HHHCCCCCCCCCCCEEEE
Q ss_conf             99862110145-------786-589962-46422------566768776213475486411-120133455444417885
Q gi|254780945|r  337 HYEFIKKYTQN-------TQI-IVEIIT-GNMPQ------AHRRKALERIAHGQAHIIIGT-HALFQDSIQYYKLILVIV  400 (700)
Q Consensus       337 H~~~~~~~~~~-------~~i-~v~lLt-g~~~~------~er~~i~~~i~~G~~~iiIGT-HAL~q~~v~F~~LgLvVi  400 (700)
                      .-.-+.++|-.       -+- -++-=- |+++.      .++-.-++.--+|.-.=.=|. .-|+++.-.-+-+-.|.|
T Consensus       222 ~r~lv~~F~f~~~e~~pdW~~~l~~h~wgG~t~~g~y~~~~~~~~~~~~~fsg~g~~F~~aC~eli~~~~~~~~yD~ilI  301 (660)
T COG3972         222 MRTLVPEFFFMRVEKQPDWGTKLFCHNWGGLTKEGFYGMYRYICHYYEIPFSGFGNGFDAACKELIADINNKKAYDYILI  301 (660)
T ss_pred             HHHHHHHHHHHHHHCCCCCCCEEEEECCCCCCCCCCHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCCEEEE
T ss_conf             99999999998862488724268884357878886038899984266545478774067999999986425642317994


Q ss_pred             CCCCCCCH
Q ss_conf             21013356
Q gi|254780945|r  401 DEQHRFGV  408 (700)
Q Consensus       401 DEQHRFGV  408 (700)
                      ||-+-|--
T Consensus       302 DE~QDFP~  309 (660)
T COG3972         302 DESQDFPQ  309 (660)
T ss_pred             CCCCCCCH
T ss_conf             24554778


No 425
>PHA00350 putative assembly protein
Probab=82.17  E-value=1.3  Score=24.40  Aligned_cols=18  Identities=11%  Similarity=-0.045  Sum_probs=7.2

Q ss_pred             HHHHHCCCCEEEE-EECCC
Q ss_conf             9763103873899-97120
Q gi|254780945|r  475 LKVVLSEGKKAYW-ICPQI  492 (700)
Q Consensus       475 i~~~l~~g~q~y~-VcPlI  492 (700)
                      .--+|..|+..+| -|+=.
T Consensus       364 Clv~Lt~~~~~~~VTC~p~  382 (402)
T PHA00350        364 CVYRLTWESNSRVVTCIPR  382 (402)
T ss_pred             EEEEEEECCEEEEEECCCC
T ss_conf             3899877788558965851


No 426
>cd02025 PanK Pantothenate kinase (PanK) catalyzes the phosphorylation of pantothenic acid to form 4'-phosphopantothenic, which is the first of five steps in coenzyme A (CoA) biosynthetic pathway. The reaction carried out by this enzyme is a key regulatory point in CoA biosynthesis.
Probab=82.00  E-value=1.4  Score=24.18  Aligned_cols=30  Identities=17%  Similarity=0.244  Sum_probs=16.6

Q ss_pred             EEECCCCCHHHHHH-HHH-HHHHHHHCCEEEE
Q ss_conf             86214422369999-997-3344430545886
Q gi|254780945|r  298 LQGDVGSGKTLVAL-IAM-AAAVEAGGQAVIM  327 (700)
Q Consensus       298 LQGDVGSGKTiVA~-~A~-l~~~~~G~Q~alM  327 (700)
                      +-|.+|||||-+|- +.. +.....+.+++++
T Consensus         4 IaG~sgSGKST~a~~l~~~l~~~~~~~~v~ii   35 (220)
T cd02025           4 IAGSVAVGKSTTARVLQALLSRWPDHPNVELI   35 (220)
T ss_pred             EECCCCCCHHHHHHHHHHHHHHCCCCCCEEEE
T ss_conf             78899877999999999986002699948999


No 427
>PRK10053 hypothetical protein; Provisional
Probab=81.99  E-value=4  Score=20.58  Aligned_cols=64  Identities=16%  Similarity=0.290  Sum_probs=48.6

Q ss_pred             HHHCCCCCEEEEEEEEEEEEEECCCCCCEEEEEEECCCCEEEEEEECCCHHHHHHHCCCCCEEEEEEEEEECC
Q ss_conf             7888998789999999897542158983389999818936999995188789987328988899998997318
Q gi|254780945|r   61 ISEISEERIVTITGYISQHSSFQLQKRRPYKILLNDGTGEITLLFFYRKTEMLKNVFFEGRKITVTGKIKKLK  133 (700)
Q Consensus        61 I~~l~~g~~vti~g~V~~~~~~~~~~r~~~~v~v~D~tg~i~lvfFn~~~~yl~k~lk~G~~v~vsGKv~~~~  133 (700)
                      -.++.++..|++.|.|++...    .   =...+.|.||.|.+-.=+.  -|--....+.+.|.++|+|..-.
T Consensus        55 Ak~m~Dda~V~L~GnIv~~lg----~---d~Y~FrD~TG~I~VeId~~--~W~G~~VtP~d~V~I~GeVDke~  118 (130)
T PRK10053         55 AKTMHDGATVSLRGNLIDHKG----D---DRYVFRDKSGEINVIIPAA--VFDGREVQPDQMININGSLDKKS  118 (130)
T ss_pred             HHHCCCCCEEEEEEEEEEECC----C---CEEEEECCCCCEEEEECHH--HCCCCCCCCCCEEEEEEEECCCC
T ss_conf             864669984999888886148----8---3489977997599996777--74897859998789988972566


No 428
>PRK10365 transcriptional regulatory protein ZraR; Provisional
Probab=81.92  E-value=2.1  Score=22.71  Aligned_cols=35  Identities=26%  Similarity=0.388  Sum_probs=22.0

Q ss_pred             HHHHHHHHHHHHCCCCCCEEEEEECCCCCHHHHHHHH
Q ss_conf             9999999998410013430788621442236999999
Q gi|254780945|r  277 QESAIKDILQDMSQKNRMLRILQGDVGSGKTLVALIA  313 (700)
Q Consensus       277 Q~~ai~eI~~Dl~~~~pM~RLLQGDVGSGKTiVA~~A  313 (700)
                      =+++.+.|..=  ......-|++|..|+||..+|-.-
T Consensus       148 m~~v~~~i~~~--A~s~~pVLI~GE~GTGK~~~Ar~I  182 (441)
T PRK10365        148 MQHLLSEIALV--APSEATVLIHGDSGTGKELVARAI  182 (441)
T ss_pred             HHHHHHHHHHH--HCCCCCEEEECCCCHHHHHHHHHH
T ss_conf             99999999998--488994899899981099999999


No 429
>pfam06068 TIP49 TIP49 C-terminus. This family consists of the C-terminal region of several eukaryotic and archaeal RuvB-like 1 (Pontin or TIP49a) and RuvB-like 2 (Reptin or TIP49b) proteins. The N-terminal domain contains the pfam00004 domain. In zebrafish, the liebeskummer (lik) mutation, causes development of hyperplastic embryonic hearts. lik encodes Reptin, a component of a DNA-stimulated ATPase complex. Beta-catenin and Pontin, a DNA-stimulated ATPase that is often part of complexes with Reptin, are in the same genetic pathways. The Reptin/Pontin ratio serves to regulate heart growth during development, at least in part via the beta-catenin pathway. TBP-interacting protein 49 (TIP49) was originally identified as a TBP-binding protein, and two related proteins are encoded by individual genes, tip49a and b. Although the function of this gene family has not been elucidated, they are supposed to play a critical role in nuclear events because they interact with various kinds of nuclear
Probab=81.86  E-value=2.5  Score=22.18  Aligned_cols=132  Identities=19%  Similarity=0.337  Sum_probs=64.5

Q ss_pred             HHHHHHHH--HHHHHCCCCCCE-E--EEEECCCCCHHHHHHHHHHHHHHHH----------CCEEEEEHHHHHHHHHHHH
Q ss_conf             89999999--998410013430-7--8862144223699999973344430----------5458861279999999986
Q gi|254780945|r  276 SQESAIKD--ILQDMSQKNRML-R--ILQGDVGSGKTLVALIAMAAAVEAG----------GQAVIMAPIGILAQQHYEF  340 (700)
Q Consensus       276 ~Q~~ai~e--I~~Dl~~~~pM~-R--LLQGDVGSGKTiVA~~A~l~~~~~G----------~Q~alMaPTEILA~QH~~~  340 (700)
                      +|.+|=+.  |.-||-+...|. |  ||-|--|||||..|+. +...+...          -.++=|--||+|.+    .
T Consensus        28 GQ~~AReAagiiv~mIk~~K~aGraiLlaGppGTGKTAlA~a-iakeLG~~vPF~~i~gSEvyS~E~kKTE~L~q----a  102 (395)
T pfam06068        28 GQEKAREAAGVIVEMIKEGKIAGRAVLIAGPPGTGKTALAIA-ISKELGEDTPFCPISGSEVYSLEMKKTEALTQ----A  102 (395)
T ss_pred             CHHHHHHHHHHHHHHHHHCCCCCCEEEEECCCCCCHHHHHHH-HHHHHCCCCCEEEEEHHEEECCCCCHHHHHHH----H
T ss_conf             549999998999999972775773899877999888999999-99974879973450011121256548899999----9


Q ss_pred             HHHHCCCCCCEEEEEECCCCHHHHHHHHHHHCCCCCE-EEE--ECHHH--CCCCCCCCCCCEEEECCCCCCCHHHH--HH
Q ss_conf             2110145786589962464225667687762134754-864--11120--13345544441788521013356889--98
Q gi|254780945|r  341 IKKYTQNTQIIVEIITGNMPQAHRRKALERIAHGQAH-III--GTHAL--FQDSIQYYKLILVIVDEQHRFGVQQR--LK  413 (700)
Q Consensus       341 ~~~~~~~~~i~v~lLtg~~~~~er~~i~~~i~~G~~~-iiI--GTHAL--~q~~v~F~~LgLvViDEQHRFGV~QR--~~  413 (700)
                      |++-   .|+++         +|.+++++    |++- |-+  ..|.+  ......--.++|--.|++-.|-+...  ..
T Consensus       103 fRrs---IGvrI---------kE~~eVyE----GEV~ei~~~~~~~p~~~~~k~~~~~~itLkT~~~~~~l~l~~~i~e~  166 (395)
T pfam06068       103 FRKA---IGVRI---------KEEKEVYE----GEVVELEIEEAENPLSGYGKTIKHGKITLKTTKMEKTLKLGPKIYEQ  166 (395)
T ss_pred             HHHH---HCEEE---------EEEEEEEE----EEEEEEEEEECCCCCCCCCCCCEEEEEEEEECCCCEEEECCHHHHHH
T ss_conf             9887---55686---------78889999----99999997414688898765403799999975881787258899999


Q ss_pred             HHHCCC-CCCCEEECH
Q ss_conf             740256-776101010
Q gi|254780945|r  414 LTQKAT-APHVLLMTA  428 (700)
Q Consensus       414 L~~Kg~-~ph~L~MtA  428 (700)
                      |...+. .-|+.+.-|
T Consensus       167 l~kekV~~GDVI~Id~  182 (395)
T pfam06068       167 LQKEKVQAGDVIYIDK  182 (395)
T ss_pred             HHHCCCCCCCEEEEEC
T ss_conf             9974986687899985


No 430
>TIGR00101 ureG urease accessory protein UreG; InterPro: IPR004400 This is a GTP hydrolase for assembly of the nickel metallocentre of urease. A similar protein, hypB, is an accessory protein for expression of hydrogenase, which also uses nickel. They play a central role in nitrogen metabolism.; GO: 0005524 ATP binding, 0016151 nickel ion binding.
Probab=81.86  E-value=2.2  Score=22.66  Aligned_cols=61  Identities=28%  Similarity=0.418  Sum_probs=42.3

Q ss_pred             EEEECCCCCHHHHHHHHHHHHHHHHCCEEEEEHHHHHHHHHHHHHHHH--CCCCCCEEEEEECCCC
Q ss_conf             886214422369999997334443054588612799999999862110--1457865899624642
Q gi|254780945|r  297 ILQGDVGSGKTLVALIAMAAAVEAGGQAVIMAPIGILAQQHYEFIKKY--TQNTQIIVEIITGNMP  360 (700)
Q Consensus       297 LLQGDVGSGKTiVA~~A~l~~~~~G~Q~alMaPTEILA~QH~~~~~~~--~~~~~i~v~lLtg~~~  360 (700)
                      =+.|-||||||.. +-++...+.+.||.|++.- +|-.+.-.+.+.+-  +++-- -+..=||+-+
T Consensus         5 G~~GPvG~Gktal-~e~l~~~~~~~y~~av~tn-diyt~eda~fl~~~~~l~~~r-i~GvetGGCP   67 (199)
T TIGR00101         5 GVAGPVGSGKTAL-IEALTRELAKKYDLAVITN-DIYTQEDAEFLVKNSVLPPER-ILGVETGGCP   67 (199)
T ss_pred             EEECCCCCCHHHH-HHHHHHHHHHCCCEEEEEC-CHHHHHHHHHHHHHHCCCCCC-EEEEECCCCC
T ss_conf             6504777646899-9999998874066778731-100124688887641266222-6774158987


No 431
>COG2256 MGS1 ATPase related to the helicase subunit of the Holliday junction resolvase [DNA replication, recombination, and repair]
Probab=81.79  E-value=3.1  Score=21.38  Aligned_cols=101  Identities=23%  Similarity=0.304  Sum_probs=53.8

Q ss_pred             HHHHHCCCCCCEEEEEECCCCCHHHHHHHHHHHHHHHHCCEEEEEHHHHHHHHHHHHHHHHCCCCCCEEEEEECCCCHHH
Q ss_conf             99841001343078862144223699999973344430545886127999999998621101457865899624642256
Q gi|254780945|r  284 ILQDMSQKNRMLRILQGDVGSGKTLVALIAMAAAVEAGGQAVIMAPIGILAQQHYEFIKKYTQNTQIIVEIITGNMPQAH  363 (700)
Q Consensus       284 I~~Dl~~~~pM~RLLQGDVGSGKTiVA~~A~l~~~~~G~Q~alMaPTEILA~QH~~~~~~~~~~~~i~v~lLtg~~~~~e  363 (700)
                      |..-+.++..-+=.|-|-=|+|||-+|-+-                    |.    ++..-|..+    .-.++  ..|+
T Consensus        39 lrr~v~~~~l~SmIl~GPPG~GKTTlA~li--------------------A~----~~~~~f~~~----sAv~~--gvkd   88 (436)
T COG2256          39 LRRAVEAGHLHSMILWGPPGTGKTTLARLI--------------------AG----TTNAAFEAL----SAVTS--GVKD   88 (436)
T ss_pred             HHHHHHCCCCCEEEEECCCCCCHHHHHHHH--------------------HH----HHCCCEEEE----CCCCC--CHHH
T ss_conf             899996499860577789998888999999--------------------87----617766995----15234--6799


Q ss_pred             HHHHHHHHCCCCCEEEEECHHHCCCCCCCCCCCEEEECCCCCCCHHHHHHHHHCCCCCCCEEECHH
Q ss_conf             676877621347548641112013345544441788521013356889987402567761010101
Q gi|254780945|r  364 RRKALERIAHGQAHIIIGTHALFQDSIQYYKLILVIVDEQHRFGVQQRLKLTQKATAPHVLLMTAT  429 (700)
Q Consensus       364 r~~i~~~i~~G~~~iiIGTHAL~q~~v~F~~LgLvViDEQHRFGV~QR~~L~~Kg~~ph~L~MtAT  429 (700)
                      =+++.+.-+.-   ..-|            +=-+..|||=|||-=.|-..|..-=++-.++..-||
T Consensus        89 lr~i~e~a~~~---~~~g------------r~tiLflDEIHRfnK~QQD~lLp~vE~G~iilIGAT  139 (436)
T COG2256          89 LREIIEEARKN---RLLG------------RRTILFLDEIHRFNKAQQDALLPHVENGTIILIGAT  139 (436)
T ss_pred             HHHHHHHHHHH---HHCC------------CCEEEEEEHHHHCCHHHHHHHHHHHCCCEEEEEECC
T ss_conf             99999999998---7258------------834998722533374456551033248868999626


No 432
>COG0593 DnaA ATPase involved in DNA replication initiation [DNA replication, recombination, and repair]
Probab=81.57  E-value=1.8  Score=23.35  Aligned_cols=98  Identities=19%  Similarity=0.276  Sum_probs=56.7

Q ss_pred             EEEECCCCCHHHHHHHHHHHHHHHHCCEEEEEHH-HHHHHHHHHHHHHHCCCCCCEEEEEECCCCHHHHHHHHHHHCCCC
Q ss_conf             8862144223699999973344430545886127-999999998621101457865899624642256676877621347
Q gi|254780945|r  297 ILQGDVGSGKTLVALIAMAAAVEAGGQAVIMAPI-GILAQQHYEFIKKYTQNTQIIVEIITGNMPQAHRRKALERIAHGQ  375 (700)
Q Consensus       297 LLQGDVGSGKTiVA~~A~l~~~~~G~Q~alMaPT-EILA~QH~~~~~~~~~~~~i~v~lLtg~~~~~er~~i~~~i~~G~  375 (700)
                      +|.|.||+|||=..-++...+..++..+.++-=| |--.    ..+.                          ..+.++ 
T Consensus       117 fi~G~~GlGKTHLl~Aign~~~~~~~~a~v~y~~se~f~----~~~v--------------------------~a~~~~-  165 (408)
T COG0593         117 FIYGGVGLGKTHLLQAIGNEALANGPNARVVYLTSEDFT----NDFV--------------------------KALRDN-  165 (408)
T ss_pred             EEECCCCCCHHHHHHHHHHHHHHHCCCCEEEECCHHHHH----HHHH--------------------------HHHHHH-
T ss_conf             998799997899999999999862998648850489989----9999--------------------------998850-


Q ss_pred             CEEEEECHHHCCCCCCCCCCCEEEECCCCCCCHH---HHH------HHHHCCCCCCCEEECHHHHHHHHHH
Q ss_conf             5486411120133455444417885210133568---899------8740256776101010132278999
Q gi|254780945|r  376 AHIIIGTHALFQDSIQYYKLILVIVDEQHRFGVQ---QRL------KLTQKATAPHVLLMTATPIPRTLVL  437 (700)
Q Consensus       376 ~~iiIGTHAL~q~~v~F~~LgLvViDEQHRFGV~---QR~------~L~~Kg~~ph~L~MtATPIPRTLal  437 (700)
                            +--=|-+  .| ++-+++||-=|.|+-.   |.+      .|.+.|   ..|++|+-=-|..|..
T Consensus       166 ------~~~~Fk~--~y-~~dlllIDDiq~l~gk~~~qeefFh~FN~l~~~~---kqIvltsdr~P~~l~~  224 (408)
T COG0593         166 ------EMEKFKE--KY-SLDLLLIDDIQFLAGKERTQEEFFHTFNALLENG---KQIVLTSDRPPKELNG  224 (408)
T ss_pred             ------HHHHHHH--HH-CCCEEEECHHHHHCCCHHHHHHHHHHHHHHHHCC---CEEEEECCCCCHHHCC
T ss_conf             ------4888887--64-2673555138675677157999999999888508---8799970788322110


No 433
>PRK06751 single-stranded DNA-binding protein; Provisional
Probab=81.34  E-value=4.2  Score=20.41  Aligned_cols=63  Identities=14%  Similarity=0.286  Sum_probs=41.1

Q ss_pred             EEEEEEEEEEEEEECCC-C-CCEEEEE--EE----C-----CCCEEEEEEECCCHHHHHHHCCCCCEEEEEEEEEE
Q ss_conf             89999999897542158-9-8338999--98----1-----89369999951887899873289888999989973
Q gi|254780945|r   69 IVTITGYISQHSSFQLQ-K-RRPYKIL--LN----D-----GTGEITLLFFYRKTEMLKNVFFEGRKITVTGKIKK  131 (700)
Q Consensus        69 ~vti~g~V~~~~~~~~~-~-r~~~~v~--v~----D-----~tg~i~lvfFn~~~~yl~k~lk~G~~v~vsGKv~~  131 (700)
                      .|++.|.+.+-..+++. . .....+.  +.    |     ++.-+.++.|+.....+.+.+++|+.|+|.|+++.
T Consensus         3 kV~LiGrL~~DPElr~t~~G~~v~~f~lAv~r~~~~~~g~~~td~~~vv~wgk~AE~~~~yl~KG~~V~VeGrl~~   78 (172)
T PRK06751          3 RVILVGRLTKDPDLRYTPNGVAVATFTLAVNRAFANQQGEREADFINCVIWRKQAENVANYLKKGSLAGVDGRLQT   78 (172)
T ss_pred             EEEEEEECCCCCEEEECCCCCEEEEEEEEECCCEECCCCCEEEEEEEEEEECHHHHHHHHHHCCCCEEEEEEEEEC
T ss_conf             7999987687875888899987999999966760267897677899999728889999987578998999998624


No 434
>COG1485 Predicted ATPase [General function prediction only]
Probab=80.99  E-value=1.5  Score=23.82  Aligned_cols=72  Identities=21%  Similarity=0.220  Sum_probs=40.8

Q ss_pred             EEEECCCCCHHHHHHHHHHHHHHHHCCEEEEEHHHHHHHHHHHHHHHHCCCCCCEEEEEECCCCHHHHHHHHHHHCCCCC
Q ss_conf             88621442236999999733444305458861279999999986211014578658996246422566768776213475
Q gi|254780945|r  297 ILQGDVGSGKTLVALIAMAAAVEAGGQAVIMAPIGILAQQHYEFIKKYTQNTQIIVEIITGNMPQAHRRKALERIAHGQA  376 (700)
Q Consensus       297 LLQGDVGSGKTiVA~~A~l~~~~~G~Q~alMaPTEILA~QH~~~~~~~~~~~~i~v~lLtg~~~~~er~~i~~~i~~G~~  376 (700)
                      -|-|+||+|||..    |-...    +   .+|.+---+.||..|....-.   +                +..+. |+.
T Consensus        69 Yl~GgVGrGKT~L----MD~Fy----~---~lp~~~k~R~HFh~FM~~vH~---~----------------l~~l~-g~~  117 (367)
T COG1485          69 YLWGGVGRGKTML----MDLFY----E---SLPGERKRRLHFHRFMARVHQ---R----------------LHTLQ-GQT  117 (367)
T ss_pred             EEECCCCCCHHHH----HHHHH----H---HCCCCCCCCCCHHHHHHHHHH---H----------------HHHHC-CCC
T ss_conf             8889978649999----99998----6---587645665507799999999---9----------------99971-888


Q ss_pred             EEEEECHHHCCCCCCCCCCCEEEECCCC
Q ss_conf             4864111201334554444178852101
Q gi|254780945|r  377 HIIIGTHALFQDSIQYYKLILVIVDEQH  404 (700)
Q Consensus       377 ~iiIGTHAL~q~~v~F~~LgLvViDEQH  404 (700)
                      +.+-..-+=+     +++--+..+||=|
T Consensus       118 dpl~~iA~~~-----~~~~~vLCfDEF~  140 (367)
T COG1485         118 DPLPPIADEL-----AAETRVLCFDEFE  140 (367)
T ss_pred             CCCHHHHHHH-----HHCCCEEEEEEEE
T ss_conf             8657999999-----8417889863036


No 435
>PRK08694 consensus
Probab=80.89  E-value=4.3  Score=20.30  Aligned_cols=73  Identities=15%  Similarity=0.113  Sum_probs=45.2

Q ss_pred             EEEEECCCCCHHHHHHHHHHHHHHHHCC-EEEEEHHHHHHHHHHHHHHHHCCCCCCEEEEEECCCCHHHHHHHHHH
Q ss_conf             7886214422369999997334443054-58861279999999986211014578658996246422566768776
Q gi|254780945|r  296 RILQGDVGSGKTLVALIAMAAAVEAGGQ-AVIMAPIGILAQQHYEFIKKYTQNTQIIVEIITGNMPQAHRRKALER  370 (700)
Q Consensus       296 RLLQGDVGSGKTiVA~~A~l~~~~~G~Q-~alMaPTEILA~QH~~~~~~~~~~~~i~v~lLtg~~~~~er~~i~~~  370 (700)
                      -.+=|--|.|||..|+--+..++..|++ |+|..- |.=++|-+..+-.-....+. -.+-+|.++..+...+...
T Consensus       221 iVIaaRPsmGKTalalnia~~~a~~~~~~V~~fSL-EMs~~~l~~Rlla~~s~v~~-~~i~~g~l~~~e~~~~~~a  294 (468)
T PRK08694        221 IIVAGRPSMGKTAFSINIAEHVAVEGKLPVAVFSM-EMGGAQLVMRMLGSVGRLDQ-SVLKTGRLEDEHWGRLNEA  294 (468)
T ss_pred             EEEEECCCCCHHHHHHHHHHHHHHHCCCCEEEECC-CCCHHHHHHHHHHHHCCCCH-HHCCCCCCCHHHHHHHHHH
T ss_conf             99961786537899999999999847984799778-89999999999997259863-2110489999999999999


No 436
>KOG3928 consensus
Probab=80.85  E-value=2.4  Score=22.27  Aligned_cols=38  Identities=24%  Similarity=0.431  Sum_probs=30.9

Q ss_pred             CCCCEE-EEEECCCCCHHHHHHHHHHHHHHHHCCEEEEEH
Q ss_conf             134307-886214422369999997334443054588612
Q gi|254780945|r  291 KNRMLR-ILQGDVGSGKTLVALIAMAAAVEAGGQAVIMAP  329 (700)
Q Consensus       291 ~~pM~R-LLQGDVGSGKTiVA~~A~l~~~~~G~Q~alMaP  329 (700)
                      ..|-.| +|-|.+||||||--.-|...|+++ .+..+=+|
T Consensus       176 ~~P~~r~vL~Ge~GtGKSiaL~qa~h~a~~~-~wlIlhip  214 (461)
T KOG3928         176 MHPVKRFVLDGEPGTGKSIALAQAVHYAADQ-KWLILHIP  214 (461)
T ss_pred             CCCCEEEEEECCCCCCHHHHHHHHHHHHHCC-CEEEEECC
T ss_conf             6763589985799876205999999987317-85999778


No 437
>cd03115 SRP The signal recognition particle (SRP) mediates the transport to or across the plasma membrane in bacteria and the endoplasmic reticulum in eukaryotes. SRP recognizes N-terminal sighnal sequences of newly synthesized polypeptides at the ribosome. The SRP-polypeptide complex is then targeted to the membrane by an interaction between SRP and its cognated receptor (SR). In mammals, SRP consists of six protein subunits and a 7SL RNA. One of these subunits is a 54 kd protein (SRP54), which is a GTP-binding protein that interacts with the signal sequence when it emerges from the ribosome. SRP54 is a multidomain protein that consists of an N-terminal domain, followed by a central G (GTPase) domain and a C-terminal M domain.
Probab=80.78  E-value=4.3  Score=20.28  Aligned_cols=156  Identities=16%  Similarity=0.090  Sum_probs=73.8

Q ss_pred             EEEECCCCCHHHHHHHHHHHHHHHHCCEEEEEHHHHHHHHHHHHHHHHCCCCCCEEEEEECCCCH-HHHHHHHHHHC-CC
Q ss_conf             88621442236999999733444305458861279999999986211014578658996246422-56676877621-34
Q gi|254780945|r  297 ILQGDVGSGKTLVALIAMAAAVEAGGQAVIMAPIGILAQQHYEFIKKYTQNTQIIVEIITGNMPQ-AHRRKALERIA-HG  374 (700)
Q Consensus       297 LLQGDVGSGKTiVA~~A~l~~~~~G~Q~alMaPTEILA~QH~~~~~~~~~~~~i~v~lLtg~~~~-~er~~i~~~i~-~G  374 (700)
                      ++-|=-|+|||--.+--+.....+|+.+++.+= .-----=.+.++.|-+.+++++.-....... +--++.++.-+ ++
T Consensus         4 ~lvGptGvGKTTTiaKLA~~~~~~~~kV~lit~-Dt~R~gA~eQL~~~a~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~   82 (173)
T cd03115           4 LLVGLQGVGKTTTAAKLALYLKKKGKKVLLVAA-DTYRPAAIEQLRVLGEQVGVPVFEEGEGKDPVSIAKRAIEHAREEN   82 (173)
T ss_pred             EEECCCCCCHHHHHHHHHHHHHHCCCEEEEEEC-CCCCHHHHHHHHHHHHHCCCEEEECCCCCCHHHHHHHHHHHHHHCC
T ss_conf             998999998899999999999976992899974-8875779999999999749859922775587999999999987568


Q ss_pred             CCEEEEECHHHCCCCCCCCCCCEEEECCCCCCCHHHHHHHHH-CCCCCCCEEECHHHHHHHHHH--HHHHCCCHHHHCCC
Q ss_conf             754864111201334554444178852101335688998740-256776101010132278999--97520101111023
Q gi|254780945|r  375 QAHIIIGTHALFQDSIQYYKLILVIVDEQHRFGVQQRLKLTQ-KATAPHVLLMTATPIPRTLVL--TSLGDIDISKITEK  451 (700)
Q Consensus       375 ~~~iiIGTHAL~q~~v~F~~LgLvViDEQHRFGV~QR~~L~~-Kg~~ph~L~MtATPIPRTLal--~~ygdldvS~i~e~  451 (700)
                      .--|+|-|----+.            |+++   .+|=..+.. -.....+|+|+||.=...+..  ..+.        ..
T Consensus        83 ~D~IlIDTaGr~~~------------d~~~---~~el~~l~~~~~p~~~~LVl~a~~~~~~~~~~~~f~~--------~~  139 (173)
T cd03115          83 FDVVIVDTAGRLQI------------DENL---MEELKKIKRVVKPDEVLLVVDAMTGQDAVNQAKAFNE--------AL  139 (173)
T ss_pred             CCEEEEECCCCCCC------------CHHH---HHHHHHHHHHHCCCCCEEECCCCCHHHHHHHHHHHHH--------CC
T ss_conf             99899978887879------------9999---9999999864489721574246550658999999874--------27


Q ss_pred             CCCCCCCEEEEEECCCHHHHHHHHHH
Q ss_conf             55766620799970200268999976
Q gi|254780945|r  452 PAGRKPIKTVIIPINRIDEVIERLKV  477 (700)
Q Consensus       452 P~gR~~I~T~~~~~~~~~~~~~~i~~  477 (700)
                      |.. .=|.|++=+..+...+++.+.+
T Consensus       140 ~~~-~~I~TKlDet~~~G~~ls~~~~  164 (173)
T cd03115         140 GIT-GVILTKLDGDARGGAALSIRAV  164 (173)
T ss_pred             CCC-EEEEEEECCCCCCCHHHHHHHH
T ss_conf             997-8999714389975799999999


No 438
>cd01983 Fer4_NifH The Fer4_NifH superfamily contains a variety of proteins which share a common ATP-binding domain. Functionally, proteins in this superfamily use the energy from hydrolysis of NTP to transfer electron or ion.
Probab=80.77  E-value=1.4  Score=24.15  Aligned_cols=30  Identities=30%  Similarity=0.411  Sum_probs=26.0

Q ss_pred             EECCCCCHHHHHHHHHHHHHHHHCCEEEEE
Q ss_conf             621442236999999733444305458861
Q gi|254780945|r  299 QGDVGSGKTLVALIAMAAAVEAGGQAVIMA  328 (700)
Q Consensus       299 QGDVGSGKTiVA~~A~l~~~~~G~Q~alMa  328 (700)
                      .|=-|+|||-+|..-+....+.|+.+++.-
T Consensus         5 ~~~kGvGKTT~a~~La~~la~~g~~Vl~vD   34 (99)
T cd01983           5 TGKGGVGKTTLAANLAAALAKRGKRVLLID   34 (99)
T ss_pred             ECCCCCCHHHHHHHHHHHHHHCCCEEEEEC
T ss_conf             589977689999999999998899699986


No 439
>COG3911 Predicted ATPase [General function prediction only]
Probab=80.70  E-value=2  Score=22.90  Aligned_cols=44  Identities=36%  Similarity=0.403  Sum_probs=34.7

Q ss_pred             CCCEE----EEEECCCCCHHHHHHHHHHHHHHHHCCEEEEEHHHHHHHHHHH
Q ss_conf             34307----8862144223699999973344430545886127999999998
Q gi|254780945|r  292 NRMLR----ILQGDVGSGKTLVALIAMAAAVEAGGQAVIMAPIGILAQQHYE  339 (700)
Q Consensus       292 ~pM~R----LLQGDVGSGKTiVA~~A~l~~~~~G~Q~alMaPTEILA~QH~~  339 (700)
                      .||||    .|-|--|+|||..    ..+-...|+-+.--+|+.|.+.|-.+
T Consensus         4 ~~~nR~~~fIltGgpGaGKTtL----L~aLa~~Gfatvee~~r~ii~~es~~   51 (183)
T COG3911           4 RPFNRHKRFILTGGPGAGKTTL----LAALARAGFATVEEAGRDIIALESAQ   51 (183)
T ss_pred             CCCCCCEEEEEECCCCCCHHHH----HHHHHHCCCEEECCCHHHHHHHHHHC
T ss_conf             6456533899837999768999----99999758635013416689998754


No 440
>TIGR03420 DnaA_homol_Hda DnaA regulatory inactivator Hda. Members of this protein family are Hda (Homologous to DnaA). These proteins are about half the length of DnaA and homologous over length of Hda. In the model species Escherichia coli, the initiation of DNA replication requires DnaA bound to ATP rather than ADP; Hda helps facilitate the conversion of DnaA-ATP to DnaA-ADP.
Probab=80.63  E-value=4.4  Score=20.24  Aligned_cols=92  Identities=30%  Similarity=0.316  Sum_probs=54.5

Q ss_pred             EEEECCCCCHHHHHHHHHHHHHHHHCCEEEEEHHHHHHHHHHHHHHHHCCCCCCEEEEEECCCCHHHHHHHHHHHCCCCC
Q ss_conf             88621442236999999733444305458861279999999986211014578658996246422566768776213475
Q gi|254780945|r  297 ILQGDVGSGKTLVALIAMAAAVEAGGQAVIMAPIGILAQQHYEFIKKYTQNTQIIVEIITGNMPQAHRRKALERIAHGQA  376 (700)
Q Consensus       297 LLQGDVGSGKTiVA~~A~l~~~~~G~Q~alMaPTEILA~QH~~~~~~~~~~~~i~v~lLtg~~~~~er~~i~~~i~~G~~  376 (700)
                      .|.|..|||||=.+-..+-.+-..|..+.++.. +-+.        .++.+                   +++.      
T Consensus        42 ~i~G~~GsGKTHLl~a~~~~~~~~~~~~~yl~~-~~~~--------~~~~~-------------------~l~~------   87 (226)
T TIGR03420        42 YLWGESGSGKSHLLQAACAAAEERGKSAIYLPL-AELA--------QADPE-------------------VLEG------   87 (226)
T ss_pred             EEECCCCCCHHHHHHHHHHHHHCCCCCEEEECH-HHHH--------HHHHH-------------------HHHH------
T ss_conf             998999998899999999998626995799529-9987--------75399-------------------9972------


Q ss_pred             EEEEECHHHCCCCCCCCCCCEEEECCCCCCCHHHHH--HH---HH-CCCCCCCEEECHHHHHHHHHH
Q ss_conf             486411120133455444417885210133568899--87---40-256776101010132278999
Q gi|254780945|r  377 HIIIGTHALFQDSIQYYKLILVIVDEQHRFGVQQRL--KL---TQ-KATAPHVLLMTATPIPRTLVL  437 (700)
Q Consensus       377 ~iiIGTHAL~q~~v~F~~LgLvViDEQHRFGV~QR~--~L---~~-Kg~~ph~L~MtATPIPRTLal  437 (700)
                                     +++.-+++||.=|.+.-++..  .|   .. --.+-..+++|++.-|+.+..
T Consensus        88 ---------------l~~~d~l~iDDi~~i~~~~~~e~~lF~l~N~~~~~~~~ilits~~~p~~l~~  139 (226)
T TIGR03420        88 ---------------LEQADLVCLDDVEAIAGQPEWQEALFHLYNRVREAGGRLLIAGRAAPAQLPL  139 (226)
T ss_pred             ---------------CCCCCEEEEECHHHHCCCHHHHHHHHHHHHHHHHHCCEEEEECCCCHHHCCC
T ss_conf             ---------------7448999996633343783789999999999986528289867888232032


No 441
>PRK10820 DNA-binding transcriptional regulator TyrR; Provisional
Probab=80.58  E-value=2  Score=22.90  Aligned_cols=100  Identities=20%  Similarity=0.231  Sum_probs=49.9

Q ss_pred             CCCEEEEEECCCCCHHHHHHHHHHHHHHH-HCCEEEEE---HHHHHHHHHHHHHHHHCCCCCCEEEEEECCCCHHHHHHH
Q ss_conf             34307886214422369999997334443-05458861---279999999986211014578658996246422566768
Q gi|254780945|r  292 NRMLRILQGDVGSGKTLVALIAMAAAVEA-GGQAVIMA---PIGILAQQHYEFIKKYTQNTQIIVEIITGNMPQAHRRKA  367 (700)
Q Consensus       292 ~pM~RLLQGDVGSGKTiVA~~A~l~~~~~-G~Q~alMa---PTEILA~QH~~~~~~~~~~~~i~v~lLtg~~~~~er~~i  367 (700)
                      ..+.-|++|..|+||..+|-.--...-.+ +-=+++=+   |.+.+...       +|+..                   
T Consensus       226 ~d~pVLI~GEsGTGKellAraIH~~S~R~~~pFv~vnC~alp~~l~ese-------LFG~a-------------------  279 (513)
T PRK10820        226 LSAPLLITGDTGTGKDLFAYACHLASPRAKKPYLALNCASIPEDAVESE-------LFGHA-------------------  279 (513)
T ss_pred             CCCCEEEECCCCCCHHHHHHHHHHCCCCCCCCCEEEECCCCCHHHHHHH-------HCCCC-------------------
T ss_conf             8998899898982499999999966887899826888998996789998-------63876-------------------


Q ss_pred             HHHHCCCCCEEEEECHHHCCCCCCCCCCCEEEECCCCCCCHHHHHHHHH----C-----C----CCCCCEEECHHHHH
Q ss_conf             7762134754864111201334554444178852101335688998740----2-----5----67761010101322
Q gi|254780945|r  368 LERIAHGQAHIIIGTHALFQDSIQYYKLILVIVDEQHRFGVQQRLKLTQ----K-----A----TAPHVLLMTATPIP  432 (700)
Q Consensus       368 ~~~i~~G~~~iiIGTHAL~q~~v~F~~LgLvViDEQHRFGV~QR~~L~~----K-----g----~~ph~L~MtATPIP  432 (700)
                          ..|+       .-+|    +-.+=|-+..||=+.-....-.+|..    +     |    ...|+=+++||--+
T Consensus       280 ----~~~~-------~G~f----e~A~gGTLfLdEI~~l~~~~Q~kLLr~Lq~~~~~rvG~~~~~~~dvRiIaaT~~d  342 (513)
T PRK10820        280 ----PEGK-------KGFF----EQANGGSVLLDEIGEMSPRMQAKLLRFLNDGTFRRVGEDHEVHVDVRVICATQKN  342 (513)
T ss_pred             ----CCCC-------CCCE----EECCCCEEEEECHHHCCHHHHHHHHHHHHCCEEEECCCCCEEEEEEEEEECCCHH
T ss_conf             ----6688-------9755----7858988999783659999999999998689799659985356778999626530


No 442
>PRK10246 exonuclease subunit SbcC; Provisional
Probab=80.49  E-value=1.3  Score=24.46  Aligned_cols=13  Identities=23%  Similarity=0.483  Sum_probs=10.0

Q ss_pred             HHCCCCCEEEEEC
Q ss_conf             6213475486411
Q gi|254780945|r  370 RIAHGQAHIIIGT  382 (700)
Q Consensus       370 ~i~~G~~~iiIGT  382 (700)
                      .+..|+++-|-|-
T Consensus       499 ~L~~G~pCPVCGS  511 (1047)
T PRK10246        499 QLQAGQPCPLCGS  511 (1047)
T ss_pred             HCCCCCCCCCCCC
T ss_conf             6479998999999


No 443
>TIGR00963 secA preprotein translocase, SecA subunit; InterPro: IPR000185   Secretion across the inner membrane in some Gram-negative bacteria occurs via the preprotein translocase pathway. Proteins are produced in the cytoplasm as precursors, and require a chaperone subunit to direct them to the translocase component. . From there, the mature proteins are either targeted to the outer membrane, or remain as periplasmic proteins. The translocase protein subunits are encoded on the bacterial chromosome.     The translocase itself comprises 7 proteins, including a chaperone protein (SecB), an ATPase (SecA), an integral membrane complex (SecCY, SecE and SecG), and two additional membrane proteins that promote the release of the mature peptide into the periplasm (SecD and SecF) . The chaperone protein SecB  is a highly acidic homotetrameric protein that exists as a "dimer of dimers" in the bacterial cytoplasm. SecB maintains preproteins in an unfolded state after translation, and targets these to the peripheral membrane protein ATPase SecA for secretion .   SecA is a cytoplasmic protein of 800 to 960 amino acid residues. Homologs of secA are also encoded in the chloroplast genome of some algae  as well as in the nuclear genome of plants . It could be involved in the intraorganellar protein transport into thylakoids.; GO: 0005524 ATP binding, 0006605 protein targeting, 0006886 intracellular protein transport.
Probab=80.46  E-value=0.6  Score=27.02  Aligned_cols=81  Identities=28%  Similarity=0.431  Sum_probs=48.5

Q ss_pred             HHHHCCCCCCCCEEE-EEEECCCCCHHHHHHHHHHHHHCHHHHHHHHHHHHCCCCCCCCCHHCC-CCCCCCCC-HHHHHH
Q ss_conf             730116678983599-997088899879999999984142589999998520630002600069-87440003-887599
Q gi|254780945|r  578 QLRGRVGRGEEISSC-ILLYHPPLSKNSYTRLSVLKNTEDGFLIAEEDLKQRKEGEILGIKQSG-MPKFLIAQ-PELHDS  654 (700)
Q Consensus       578 QLRGRVGRg~~~s~c-~l~~~~~~~~~~~~Rl~~l~~~~dGf~iAe~Dl~lRG~G~~~G~~QsG-~~~~~~~d-~~~d~~  654 (700)
                      |||||=||-+.+|-- |++                         |=+|=-||=+|   |.+=.+ +..|.+.| .--...
T Consensus       645 QLRGRsGRQGDPG~SrFfL-------------------------SleD~LmR~Fg---~drl~~~m~~lg~~dd~Pies~  696 (904)
T TIGR00963       645 QLRGRSGRQGDPGSSRFFL-------------------------SLEDNLMRIFG---GDRLKGLMRRLGLEDDEPIESK  696 (904)
T ss_pred             CCCCCCCCCCCCCCCCEEE-------------------------CHHHHHHHHCC---CHHHHHHHHHCCCCCCCCCCCH
T ss_conf             1023243638498731120-------------------------01014776518---7789999986388888966526


Q ss_pred             HHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHH
Q ss_conf             99999999999998484636655648899998512545677
Q gi|254780945|r  655 LLEIARKDAKHILTQDPDLTSVRGQSIRILLYLYQYNEAFQ  695 (700)
Q Consensus       655 ll~~a~~~a~~~~~~d~~l~~~~~~~l~~~~~~~~~~~~~~  695 (700)
                      ++..|=+.||.=++.       .|=.+|+-|  |+||+.+.
T Consensus       697 ~v~r~le~AQKrVE~-------~Nfd~RK~l--leYDdVlN  728 (904)
T TIGR00963       697 MVTRALESAQKRVEA-------RNFDIRKQL--LEYDDVLN  728 (904)
T ss_pred             HHHHHHHHHHHHHHH-------HHHHHHHHH--HHHHHHHH
T ss_conf             788999998889863-------000343113--12679999


No 444
>PRK06863 single-stranded DNA-binding protein; Provisional
Probab=80.46  E-value=4.4  Score=20.20  Aligned_cols=65  Identities=20%  Similarity=0.359  Sum_probs=39.1

Q ss_pred             CEEEEEEEEEEEEEECCC--CCCE--EEEEEE----C-CCC-------EEEEEEECCCHHHHHHHCCCCCEEEEEEEEEE
Q ss_conf             789999999897542158--9833--899998----1-893-------69999951887899873289888999989973
Q gi|254780945|r   68 RIVTITGYISQHSSFQLQ--KRRP--YKILLN----D-GTG-------EITLLFFYRKTEMLKNVFFEGRKITVTGKIKK  131 (700)
Q Consensus        68 ~~vti~g~V~~~~~~~~~--~r~~--~~v~v~----D-~tg-------~i~lvfFn~~~~yl~k~lk~G~~v~vsGKv~~  131 (700)
                      ..|++.|.+.+-..+++.  +...  +.+-+.    | .+|       -+.+++|+.....+.+.|++|+.|+|.|+++.
T Consensus         5 NkV~LiGnlg~DPElr~t~sG~~v~~fslA~~~~~~~~~~ge~~e~t~w~~v~~wgk~AE~~~~yl~KG~~V~VeGrL~~   84 (168)
T PRK06863          5 NKVIIVGHLGNDPEIRTMPNGEAVANISVATSESWTDKNTGERREVTEWHRIVFYRRQAEVAGEYLRKGSQVYVEGRLKT   84 (168)
T ss_pred             CEEEEEEECCCCCEEEECCCCCEEEEEEEEECCCCEECCCCEEEEECHHHHHHHCHHHHHHHHHHHCCCCEEEEEEEEEE
T ss_conf             88999874686854888799987999999961561205887377502032120056899999987568987999888875


Q ss_pred             C
Q ss_conf             1
Q gi|254780945|r  132 L  132 (700)
Q Consensus       132 ~  132 (700)
                      -
T Consensus        85 r   85 (168)
T PRK06863         85 R   85 (168)
T ss_pred             C
T ss_conf             5


No 445
>PRK11361 acetoacetate metabolism regulatory protein AtoC; Provisional
Probab=80.30  E-value=2.7  Score=21.86  Aligned_cols=36  Identities=22%  Similarity=0.369  Sum_probs=23.1

Q ss_pred             HHHHHHHHHHHHHCCCCCCEEEEEECCCCCHHHHHHHH
Q ss_conf             89999999998410013430788621442236999999
Q gi|254780945|r  276 SQESAIKDILQDMSQKNRMLRILQGDVGSGKTLVALIA  313 (700)
Q Consensus       276 ~Q~~ai~eI~~Dl~~~~pM~RLLQGDVGSGKTiVA~~A  313 (700)
                      +-+++.+.|.. + .+.+.+-|++|..|+||.+||-.-
T Consensus       151 ~m~~v~~~i~~-~-A~s~~~VLI~GEsGTGKe~~Ar~I  186 (457)
T PRK11361        151 AMMDICKDTAK-I-ALSQASVLISGESGTGKELIARAI  186 (457)
T ss_pred             HHHHHHHHHHH-H-HCCCCCEEEECCCCCCHHHHHHHH
T ss_conf             99999999999-8-488995899889985789999999


No 446
>KOG0701 consensus
Probab=80.20  E-value=0.61  Score=26.95  Aligned_cols=66  Identities=17%  Similarity=0.115  Sum_probs=35.3

Q ss_pred             HHHHHHHHHHCCCEEEEEECHHHHCCCCCCCCCEEEEE-CHHHCCHHHHHHHHHCC-----------CCCCCCEEEEEEE
Q ss_conf             99999999755986999980034104688876589985-85254746887730116-----------6789835999970
Q gi|254780945|r  529 DKESVMDSFKNGTCKLLIATTVIEVGIDVVDASIIIIE-NAEHFGLAQLHQLRGRV-----------GRGEEISSCILLY  596 (700)
Q Consensus       529 ek~~~m~~F~~g~~~iLvaTtviEVGvdvpna~~mvI~-~aerfGLsqLHQLRGRV-----------GRg~~~s~c~l~~  596 (700)
                      -++..-..|+.+++..+++|.+-+.|-|+-  +++.++ ...+--.--+-|=||||           -||..++--.+..
T Consensus       709 ~rn~~~~~~~~~~v~~~~~pss~~~g~~~~--~~~~v~~~~~~~~i~~~~q~~~~~~~~~s~l~~~~~r~~~~~~~~l~~  786 (1606)
T KOG0701         709 YRNDDQPQFYVAEVLPLLAPSSLFPGLDYE--TFNEVYRFKYALTITSLNQSLLDVDHTSSRLNLLVPRGDNQKGSALPN  786 (1606)
T ss_pred             HHCCCCCCEEEEEEEEECCCHHCCCCCCHH--EEEEEEECCCCCHHHHCCCCCCCCCCCHHHHCCCCCHHHCCCCCEEEC
T ss_conf             424664414654312302631017996621--002356404100122122100355553123202575333146624541


No 447
>TIGR00382 clpX ATP-dependent Clp protease, ATP-binding subunit ClpX; InterPro: IPR004487   ClpX is a member of the HSP (heat-shock protein) 100 family. Gel filtration and electron microscopy showed that ClpX subunits associate to form a six-membered ring that is stabilized by binding of ATP or nonhydrolyzable analogs of ATP . It functions as an ATP-depedent  molecular chaperone and is the regulatory subunit of the ClpXP protease .   ClpXP is involved in DNA damage repair, stationary-phase gene expression, and ssrA-mediated protein quality control. To date more than 50 proteins include transcription factors, metabolic enzymes, and proteins involved in the starvation and oxidative stress responses have been identified as substrates .    The N-terminal domain of ClpX is a C4-type zinc binding domain (ZBD) involved in substrate recognition. ZBD forms a very stable dimer that is essential for promoting the degradation of some typical ClpXP substrates such as lO and MuA .  ; GO: 0005515 protein binding, 0005524 ATP binding, 0016887 ATPase activity, 0015031 protein transport.
Probab=80.15  E-value=0.95  Score=25.47  Aligned_cols=19  Identities=47%  Similarity=0.648  Sum_probs=15.3

Q ss_pred             CCCEEEEEECCCCCHHHHH
Q ss_conf             3430788621442236999
Q gi|254780945|r  292 NRMLRILQGDVGSGKTLVA  310 (700)
Q Consensus       292 ~pM~RLLQGDVGSGKTiVA  310 (700)
                      ..-|-||-|=.|||||+.|
T Consensus       151 ~KSNILLiGPTGSGKTLLA  169 (452)
T TIGR00382       151 SKSNILLIGPTGSGKTLLA  169 (452)
T ss_pred             HCCCEEEECCCCCCHHHHH
T ss_conf             0066245468885268999


No 448
>PRK07275 single-stranded DNA-binding protein; Provisional
Probab=80.13  E-value=4.5  Score=20.12  Aligned_cols=63  Identities=21%  Similarity=0.286  Sum_probs=41.2

Q ss_pred             EEEEEEEEEEEEEECCC--CCCEEEEEEE------C-----CCCEEEEEEECCCHHHHHHHCCCCCEEEEEEEEEE
Q ss_conf             89999999897542158--9833899998------1-----89369999951887899873289888999989973
Q gi|254780945|r   69 IVTITGYISQHSSFQLQ--KRRPYKILLN------D-----GTGEITLLFFYRKTEMLKNVFFEGRKITVTGKIKK  131 (700)
Q Consensus        69 ~vti~g~V~~~~~~~~~--~r~~~~v~v~------D-----~tg~i~lvfFn~~~~yl~k~lk~G~~v~vsGKv~~  131 (700)
                      .|++.|.+.+-..+++.  +....++.+.      |     .+.-+.|+.|+.....+.+.+++|..|+|.|+++.
T Consensus         4 kV~LiGrl~~DpElr~t~~G~~v~~fslAv~r~~k~~~ge~~td~~~~v~wg~~AE~~~~yl~KG~~V~VeGrl~~   79 (163)
T PRK07275          4 NVVLVGRMTRDAELRYTPSNVAVATFTLAVNRTFKSQNGEREADFINCVIWRQQAENLANWAKKGALIGVTGRIQT   79 (163)
T ss_pred             EEEEEEECCCCCEEEECCCCCEEEEEEEEECCCEECCCCCCCCEEEEEEECCHHHHHHHHHHCCCCEEEEEEEEEC
T ss_conf             6999896588863889899988999999847855878895033089999807789999987458999999999721


No 449
>pfam07015 VirC1 VirC1 protein. This family consists of several bacterial VirC1 proteins. In Agrobacterium tumefaciens, a cis-active 24-base-pair sequence adjacent to the right border of the T-DNA, called overdrive, stimulates tumour formation by increasing the level of T-DNA processing. It is thought that the virC operon which enhances T-DNA processing probably does so because the VirC1 protein interacts with overdrive. It has now been shown that the virC1 gene product binds to overdrive but not to the right border of T-DNA.
Probab=79.90  E-value=1.7  Score=23.56  Aligned_cols=31  Identities=19%  Similarity=0.200  Sum_probs=25.6

Q ss_pred             EEECCCCCHHHHHHHHHHHHHHHHCCEEEEE
Q ss_conf             8621442236999999733444305458861
Q gi|254780945|r  298 LQGDVGSGKTLVALIAMAAAVEAGGQAVIMA  328 (700)
Q Consensus       298 LQGDVGSGKTiVA~~A~l~~~~~G~Q~alMa  328 (700)
                      .+.-=|||||-+|+.-+......|+.|+++=
T Consensus         7 ~~~KGG~GKtT~a~~la~~~~~~g~~V~liD   37 (231)
T pfam07015         7 CSFKGGAGKTTALMGLCSALASDGKRVALFE   37 (231)
T ss_pred             EECCCCCCHHHHHHHHHHHHHHCCCEEEEEE
T ss_conf             6179986599999999999996899599996


No 450
>PRK13765 ATP-dependent protease Lon; Provisional
Probab=79.89  E-value=4.6  Score=20.07  Aligned_cols=102  Identities=16%  Similarity=0.315  Sum_probs=50.4

Q ss_pred             EECHH--HC-CCCCCCCCCCEEEECCCCCCCHHHHHHH----HHC-----CCCCC---CEEECHHHHHHHHHHHHHHCCC
Q ss_conf             41112--01-3345544441788521013356889987----402-----56776---1010101322789999752010
Q gi|254780945|r  380 IGTHA--LF-QDSIQYYKLILVIVDEQHRFGVQQRLKL----TQK-----ATAPH---VLLMTATPIPRTLVLTSLGDID  444 (700)
Q Consensus       380 IGTHA--L~-q~~v~F~~LgLvViDEQHRFGV~QR~~L----~~K-----g~~ph---~L~MtATPIPRTLal~~ygdld  444 (700)
                      .||-|  -+ --.+.=.|=|..+|||-.--+..+-..|    .+|     |.++.   -.+ -.-|+|=..-|...|++|
T Consensus       209 lgTPah~Rv~aGAiHkA~gGvL~IDei~~L~~~~q~~Ll~alq~~k~~I~g~~e~SsgA~v-~tepvP~Df~lV~aGn~d  287 (637)
T PRK13765        209 LETPAHERVEAGAIHKAHKGVLFIDEINTLRLESQQSLLTAMQEKKYPITGQSERSSGAMV-RTEPVPCDFIMVAAGNLD  287 (637)
T ss_pred             CCCCCEEEECCCHHHHCCCCEEEEEHHHHCCHHHHHHHHHHHHCCCEECCCCCCCCCCCCC-CCCCCCEEEEEEEECCHH
T ss_conf             8999610002661211358569984456479889999999996591532368866677625-789866136999953727


Q ss_pred             H-HHHCCCCCCCCCCE---EEEE-------ECCCHHHHHHHHHHHHCCCCE
Q ss_conf             1-11102355766620---7999-------702002689999763103873
Q gi|254780945|r  445 I-SKITEKPAGRKPIK---TVII-------PINRIDEVIERLKVVLSEGKK  484 (700)
Q Consensus       445 v-S~i~e~P~gR~~I~---T~~~-------~~~~~~~~~~~i~~~l~~g~q  484 (700)
                      . ..+  .|+-|--|.   -.+.       +.+++.++..||..++++-+.
T Consensus       288 ~~~~m--~palrsri~g~gyev~~~~~m~dt~enr~k~arfiaqev~~dg~  336 (637)
T PRK13765        288 AIENM--HPALRSRIRGYGYEVYMNDTMEDTPENRKKLVRFVAQEVKRDGK  336 (637)
T ss_pred             HHHHC--CHHHHHHHHCCCEEEEECCCCCCCHHHHHHHHHHHHHHHHHCCC
T ss_conf             66643--99888651047749982356778788999999999999974388


No 451
>PRK07220 DNA topoisomerase I; Validated
Probab=79.67  E-value=1.7  Score=23.44  Aligned_cols=13  Identities=0%  Similarity=0.043  Sum_probs=6.3

Q ss_pred             CCCCCCEEEECCC
Q ss_conf             5444417885210
Q gi|254780945|r  391 QYYKLILVIVDEQ  403 (700)
Q Consensus       391 ~F~~LgLvViDEQ  403 (700)
                      .|..=|-+|+++-
T Consensus       415 ~F~a~G~~i~~~G  427 (740)
T PRK07220        415 EFKANGARLLEQG  427 (740)
T ss_pred             EEEEEEEEEEECC
T ss_conf             9998658996376


No 452
>cd02023 UMPK Uridine monophosphate kinase (UMPK, EC 2.7.1.48), also known as uridine kinase or uridine-cytidine kinase (UCK), catalyzes the reversible phosphoryl transfer from ATP to uridine or cytidine to yield UMP or CMP. In the primidine nucleotide-salvage pathway, this enzyme combined with nucleoside diphosphate kinases further phosphorylates UMP and CMP to form UTP and CTP. This kinase also catalyzes the phosphorylation of several cytotoxic ribonucleoside analogs such as 5-flurrouridine and cyclopentenyl-cytidine.
Probab=79.63  E-value=3.6  Score=20.89  Aligned_cols=29  Identities=34%  Similarity=0.333  Sum_probs=18.3

Q ss_pred             EEEECCCCCHHHHHHHHHHHHHHHHCCEEEE
Q ss_conf             8862144223699999973344430545886
Q gi|254780945|r  297 ILQGDVGSGKTLVALIAMAAAVEAGGQAVIM  327 (700)
Q Consensus       297 LLQGDVGSGKTiVA~~A~l~~~~~G~Q~alM  327 (700)
                      .+.|+.|||||-+|-.  +.-.-++..++++
T Consensus         3 gI~G~sgsGKTT~a~~--L~~~l~~~~v~~i   31 (198)
T cd02023           3 GIAGGSGSGKTTVAEE--IIEQLGNPKVVII   31 (198)
T ss_pred             EEECCCCCCHHHHHHH--HHHHHCCCCEEEE
T ss_conf             9889998859999999--9998099985899


No 453
>pfam06309 Torsin Torsin. This family consists of several eukaryotic torsin proteins. Torsion dystonia is an autosomal dominant movement disorder characterized by involuntary, repetitive muscle contractions and twisted postures. The most severe early-onset form of dystonia has been linked to mutations in the human DYT1 (TOR1A) gene encoding a protein termed torsinA. While causative genetic alterations have been identified, the function of torsin proteins and the molecular mechanism underlying dystonia remain unknown. Phylogenetic analysis of the torsin protein family indicates these proteins share distant sequence similarity with the large and diverse family of (pfam00004) proteins. It has been suggested that torsins play a role in effectively managing protein folding and that possible breakdown in a neuroprotective mechanism that is, in part, mediated by torsins may be responsible for the neuronal dysfunction associated with dystonia.
Probab=79.57  E-value=4.3  Score=20.31  Aligned_cols=54  Identities=17%  Similarity=0.294  Sum_probs=38.4

Q ss_pred             CCCCHHHHHHHHHHHHHHCC---CCCCEEEEEECCCCCHHHHHHHHHHHHHHHHCCE
Q ss_conf             46798899999999984100---1343078862144223699999973344430545
Q gi|254780945|r  271 FSPTKSQESAIKDILQDMSQ---KNRMLRILQGDVGSGKTLVALIAMAAAVEAGGQA  324 (700)
Q Consensus       271 F~LT~~Q~~ai~eI~~Dl~~---~~pM~RLLQGDVGSGKTiVA~~A~l~~~~~G~Q~  324 (700)
                      |----+++.+++.|..-+++   .+|+-=-+.|..|+||+-||-+-+-+...+|-..
T Consensus        28 fGQhla~~~v~~al~~~l~~~~p~KpLVlSfHG~tGtGKn~vs~liA~~Ly~~G~~S   84 (127)
T pfam06309        28 FGQHLVKQLVVRSVKGHWENPKPRKPLVLSFHGWTGTGKNFVAEIIADNLYRDGLRS   84 (127)
T ss_pred             CCHHHHHHHHHHHHHHHHCCCCCCCCEEEEECCCCCCCHHHHHHHHHHHHHHCCCCC
T ss_conf             477989999999999997489999974887018999879899999999987543478


No 454
>pfam03808 Glyco_tran_WecB Glycosyl transferase WecB/TagA/CpsF family.
Probab=79.46  E-value=4.7  Score=19.97  Aligned_cols=98  Identities=17%  Similarity=0.207  Sum_probs=66.6

Q ss_pred             HHHHHHHHCCCCEEEEEECCCCCCCCCCCCHHHHHHHHHHHHCCC-C-EECCCCCCCHHHHHHHHHHHHCCCEEEEEECH
Q ss_conf             999976310387389997120122111210146666666866371-0-31201469989999999997559869999800
Q gi|254780945|r  472 IERLKVVLSEGKKAYWICPQIEEKKESNFRSVVERFNSLHEHFTS-S-IAIIHGRMSDIDKESVMDSFKNGTCKLLIATT  549 (700)
Q Consensus       472 ~~~i~~~l~~g~q~y~VcPlIeese~~~~~~~~~~~~~l~~~~~~-~-v~~lHGkm~~~ek~~~m~~F~~g~~~iLvaTt  549 (700)
                      .+.++..-++|..+|++=.    ++    ..+....+.+++.||. + +|..||-++++|.++++++-.+.+.|+++   
T Consensus        38 ~~ll~~~~~~~~~v~llG~----~~----~~~~~~~~~l~~~yP~l~i~g~~~g~f~~~e~~~i~~~I~~~~~div~---  106 (172)
T pfam03808        38 PALLERAAERGKRVFLLGG----KP----GVLEKAAARLRARYPGLRIVGTHDGYFSPEEEEAIIEAINASGPDLLF---  106 (172)
T ss_pred             HHHHHHHHHCCCEEEEEEC----CH----HHHHHHHHHHHHHCCCCEEEEEECCCCCHHHHHHHHHHHHHCCCCEEE---
T ss_conf             9999999864983899808----88----999999999998879955999879999868999999999845999999---


Q ss_pred             HHHCCCCCCCCCEEEEECHHHCCHHHHHHHHHCCCCCCCCEE
Q ss_conf             341046888765899858525474688773011667898359
Q gi|254780945|r  550 VIEVGIDVVDASIIIIENAEHFGLAQLHQLRGRVGRGEEISS  591 (700)
Q Consensus       550 viEVGvdvpna~~mvI~~aerfGLsqLHQLRGRVGRg~~~s~  591 (700)
                         ||+-.|.        -|.|...-.++|...|.=|-..++
T Consensus       107 ---vglG~Pk--------QE~~~~~~~~~~~~~v~~~vGa~~  137 (172)
T pfam03808       107 ---VGLGAPK--------QEKWIARNRARLPVPVFIGVGGSF  137 (172)
T ss_pred             ---EECCCCH--------HHHHHHHHHHHCCCCEEEECCCHH
T ss_conf             ---9569817--------799999999877998798524012


No 455
>cd01393 recA_like RecA is a  bacterial enzyme which has roles in homologous recombination, DNA repair, and the induction of the SOS response.  RecA couples ATP hydrolysis to DNA strand exchange. While prokaryotes have a single RecA protein, eukaryotes have multiple RecA homologs such as Rad51, DMC1 and Rad55/57.  Archaea have the RecA-like homologs radA and radB.
Probab=79.43  E-value=3.2  Score=21.30  Aligned_cols=40  Identities=25%  Similarity=0.223  Sum_probs=31.1

Q ss_pred             HHHHHHCCCCCCEE--EEEECCCCCHHHHHHHHHHHHHHHHC
Q ss_conf             99984100134307--88621442236999999733444305
Q gi|254780945|r  283 DILQDMSQKNRMLR--ILQGDVGSGKTLVALIAMAAAVEAGG  322 (700)
Q Consensus       283 eI~~Dl~~~~pM~R--LLQGDVGSGKTiVA~~A~l~~~~~G~  322 (700)
                      .+..=|..+.|..|  .+.|.=|||||-+|+-.+..+..+|.
T Consensus         7 ~lD~~LgGGip~G~ItEi~G~~gsGKT~l~lqla~~~q~~~~   48 (226)
T cd01393           7 ALDELLGGGIPTGRITEIFGEFGSGKTQLCLQLAVEAQLPGE   48 (226)
T ss_pred             HHHHHHCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHHCCCC
T ss_conf             899885799888839999999999899999999999854221


No 456
>COG0353 RecR Recombinational DNA repair protein (RecF pathway) [DNA replication, recombination, and repair]
Probab=79.23  E-value=0.89  Score=25.68  Aligned_cols=29  Identities=31%  Similarity=0.409  Sum_probs=23.5

Q ss_pred             CCCCHHCHHCCCHHHCCCCCHHHHHHHHH
Q ss_conf             97102021017721367858899999887
Q gi|254780945|r    1 MRPSFLNPLFAPLSTFRGVGKKYSLFLSK   29 (700)
Q Consensus         1 mrp~~l~~L~~pI~~LkGVGpk~a~~L~k   29 (700)
                      |-|..+..|-..+..|||||||+|+.++-
T Consensus         2 ~~~~~i~~LI~~l~kLPGvG~KsA~R~Af   30 (198)
T COG0353           2 MYPPPIEKLIDALKKLPGVGPKSAQRLAF   30 (198)
T ss_pred             CCCHHHHHHHHHHHHCCCCCHHHHHHHHH
T ss_conf             77179999999997689988327999999


No 457
>KOG1942 consensus
Probab=79.19  E-value=2  Score=22.96  Aligned_cols=57  Identities=28%  Similarity=0.388  Sum_probs=39.9

Q ss_pred             HHHHHHH--HHHHHHCCCCCCEE---EEEECCCCCHHHHHHHHHHHHHHHHCCEEEEEHHHHH
Q ss_conf             8999999--99984100134307---8862144223699999973344430545886127999
Q gi|254780945|r  276 SQESAIK--DILQDMSQKNRMLR---ILQGDVGSGKTLVALIAMAAAVEAGGQAVIMAPIGIL  333 (700)
Q Consensus       276 ~Q~~ai~--eI~~Dl~~~~pM~R---LLQGDVGSGKTiVA~~A~l~~~~~G~Q~alMaPTEIL  333 (700)
                      +|..|-+  -|.-||-+.+.|.-   ||-|-+|+|||..|+ |+.+-+.++---+=|+-.|+-
T Consensus        42 GQ~~AReAagiivdlik~KkmaGravLlaGppgtGKTAlAl-aisqELG~kvPFcpmvgSEvy  103 (456)
T KOG1942          42 GQENAREAAGIIVDLIKSKKMAGRAVLLAGPPGTGKTALAL-AISQELGPKVPFCPMVGSEVY  103 (456)
T ss_pred             CCHHHHHHHHHHHHHHHHHHCCCCEEEEECCCCCCHHHHHH-HHHHHHCCCCCCCCCCCHHHH
T ss_conf             52666655108999998663267279973699876568999-999974799985666410555


No 458
>COG1221 PspF Transcriptional regulators containing an AAA-type ATPase domain and a DNA-binding domain [Transcription / Signal transduction mechanisms]
Probab=79.10  E-value=4  Score=20.59  Aligned_cols=201  Identities=18%  Similarity=0.147  Sum_probs=103.8

Q ss_pred             HHHHHHHHHHHHHCCCCCCEEEEEECCCCCHHHHHHHHHHHHHHHH-CCE-------EEEEHHHHHHHHHHHHHHHHCCC
Q ss_conf             8999999999841001343078862144223699999973344430-545-------88612799999999862110145
Q gi|254780945|r  276 SQESAIKDILQDMSQKNRMLRILQGDVGSGKTLVALIAMAAAVEAG-GQA-------VIMAPIGILAQQHYEFIKKYTQN  347 (700)
Q Consensus       276 ~Q~~ai~eI~~Dl~~~~pM~RLLQGDVGSGKTiVA~~A~l~~~~~G-~Q~-------alMaPTEILA~QH~~~~~~~~~~  347 (700)
                      +=+++++.|...=  +.-+.-|+.|+.|.||+.+|-+--  ..++. .++       |.+++.-.+++        +   
T Consensus        86 ~~~~~~eqik~~a--p~~~~vLi~GetGtGKel~A~~iH--~~s~r~~~~PFI~~NCa~~~en~~~~e--------L---  150 (403)
T COG1221          86 SLQELREQIKAYA--PSGLPVLIIGETGTGKELFARLIH--ALSARRAEAPFIAFNCAAYSENLQEAE--------L---  150 (403)
T ss_pred             HHHHHHHHHHHHC--CCCCCEEEECCCCCCHHHHHHHHH--HHHHCCCCCCEEEEEHHHHCCCHHHHH--------H---
T ss_conf             8999999998618--999847986688753889999999--861213589879977777376777777--------7---


Q ss_pred             CCCEEEEEECCCCHHHHHHHHHHHCCCCCEEEEECHHHCCCCCCCCCCCEEEECCCCCCCHHHHHHHH---HCC------
Q ss_conf             78658996246422566768776213475486411120133455444417885210133568899874---025------
Q gi|254780945|r  348 TQIIVEIITGNMPQAHRRKALERIAHGQAHIIIGTHALFQDSIQYYKLILVIVDEQHRFGVQQRLKLT---QKA------  418 (700)
Q Consensus       348 ~~i~v~lLtg~~~~~er~~i~~~i~~G~~~iiIGTHAL~q~~v~F~~LgLvViDEQHRFGV~QR~~L~---~Kg------  418 (700)
                      ||+.-...||....+  .-                  +|    +-.|=|-...||=||+--.+-.+|.   ++|      
T Consensus       151 FG~~kGaftGa~~~k--~G------------------lf----e~A~GGtLfLDEI~~LP~~~Q~kLl~~le~g~~~rvG  206 (403)
T COG1221         151 FGHEKGAFTGAQGGK--AG------------------LF----EQANGGTLFLDEIHRLPPEGQEKLLRVLEEGEYRRVG  206 (403)
T ss_pred             HCCCCCEEECCCCCC--CC------------------HH----EECCCCEEEHHHHHHCCHHHHHHHHHHHHCCCEEECC
T ss_conf             320000002566786--76------------------42----0527977765636537985899999998718657668


Q ss_pred             ----CCCCCEEECHH--HHHHHHHH--HHHHCCCHHHHCCCCCCCCCCEEEEEECCCHHHHHHHHHHHHCCCCEEEEEEC
Q ss_conf             ----67761010101--32278999--97520101111023557666207999702002689999763103873899971
Q gi|254780945|r  419 ----TAPHVLLMTAT--PIPRTLVL--TSLGDIDISKITEKPAGRKPIKTVIIPINRIDEVIERLKVVLSEGKKAYWICP  490 (700)
Q Consensus       419 ----~~ph~L~MtAT--PIPRTLal--~~ygdldvS~i~e~P~gR~~I~T~~~~~~~~~~~~~~i~~~l~~g~q~y~VcP  490 (700)
                          ..+|+.+.+||  .+++.+.-  ++|--+.+-+| ++||=|.    +  ..+...-+--|++....+.+....+- 
T Consensus       207 ~~~~~~~dVRli~AT~~~l~~~~~~g~dl~~rl~~~~I-~LPpLrE----R--~~Di~~L~e~Fl~~~~~~l~~~~~~~-  278 (403)
T COG1221         207 GSQPRPVDVRLICATTEDLEEAVLAGADLTRRLNILTI-TLPPLRE----R--KEDILLLAEHFLKSEARRLGLPLSVD-  278 (403)
T ss_pred             CCCCCCCCCEEEECCCCCHHHHHHHHCCHHHHHCCCEE-CCCCHHH----C--HHHHHHHHHHHHHHHHHHCCCCCCCC-
T ss_conf             88886777404513566879998740525564167543-1897243----5--55599999999999999739998888-


Q ss_pred             CCCCCCCCCCCHHHHHHHHHHH-HCCCCEECCCCCCCHHHHHHHHHHHHC
Q ss_conf             2012211121014666666686-637103120146998999999999755
Q gi|254780945|r  491 QIEEKKESNFRSVVERFNSLHE-HFTSSIAIIHGRMSDIDKESVMDSFKN  539 (700)
Q Consensus       491 lIeese~~~~~~~~~~~~~l~~-~~~~~v~~lHGkm~~~ek~~~m~~F~~  539 (700)
                                 + .+....|.. .||.+|+=|    ++.-+..+...+..
T Consensus       279 -----------~-~~a~~~L~~y~~pGNirEL----kN~Ve~~~~~~~~~  312 (403)
T COG1221         279 -----------S-PEALRALLAYDWPGNIREL----KNLVERAVAQASGE  312 (403)
T ss_pred             -----------C-HHHHHHHHHCCCCCCHHHH----HHHHHHHHHHHCCC
T ss_conf             -----------8-9999999848899839999----99999999973545


No 459
>KOG2093 consensus
Probab=79.09  E-value=1.7  Score=23.51  Aligned_cols=195  Identities=11%  Similarity=0.087  Sum_probs=78.2

Q ss_pred             CCCC-HHHHHHHHHHHHHHHHHHHCCCCCCCCHH-------------HHHCCCC----CCHHHHHHHHCCCCCHHHH--H
Q ss_conf             0000-00004543001345787404684338977-------------8620569----9988999862045896565--6
Q gi|254780945|r  160 YSLP-TGLSVDLFKKIIVEALSRLPVLPEWIEKD-------------LLQKKSF----PSIAEAFNIIHNPRKAKDF--E  219 (700)
Q Consensus       160 Yplt-~GLsqk~irk~I~~aL~~~~~i~E~LP~~-------------ll~k~~L----~s~~eAL~~IH~P~~~~dl--e  219 (700)
                      |+.. .||.+-.+   +.+|++.+|++. .+|.+             .++.|.+    +|..||+-.+--|......  .
T Consensus       418 Y~AR~~GIKNGMf---V~~A~klCPqL~-~lPY~FE~Ykevs~tlYetlasytl~I~aVSCDEa~vd~s~~~~~~~~tp~  493 (1016)
T KOG2093         418 YEARAYGIKNGMF---VRHAKKLCPQLV-ILPYDFEAYKEVSETLYETLASYTLNIEAVSCDEAFVDVSDLSDEENETPA  493 (1016)
T ss_pred             CHHHHHCCCCCEE---HHHHHHHCCCCE-EECCCHHHHHHHHHHHHHHHHHHCCCEEEECCHHHHHHHHHHHHHHCCCHH
T ss_conf             0788738413401---788987493207-616638999999999999998640010231201655211013544316899


Q ss_pred             HHHHHHHHHHHHHH-HH----HHHHHHHHHHHHH-HCCCCCCCCCCHHHHHHHHHCCCCCC-------------------
Q ss_conf             67999999987666-66----6677776555543-20357678775789999863024679-------------------
Q gi|254780945|r  220 WTSPARERLAYDEL-LA----GQIALLLMRKQFK-KEIGIPINVEGKIAQKILRNIPFSPT-------------------  274 (700)
Q Consensus       220 ~~~~ArkRLafeEL-l~----~QL~l~~~r~~~~-~~~~~~~~~~~~~~~~f~~~LPF~LT-------------------  274 (700)
                      .+..+.|--+||-- ..    .--.+++.|-..+ .++.-.+-.+.+.+++|++.++-..-                   
T Consensus       494 ~la~~IRqEI~e~TgC~aS~Gig~t~LLARlATr~AKP~Gq~~l~a~~veeFis~~~v~~LPGVG~sm~~kL~s~~i~tC  573 (1016)
T KOG2093         494 VLAEHIRQEILEKTGCPASAGIGGTMLLARLATRVAKPNGQFYLSAEKVEEFISQLKVDDLPGVGSSMKSKLVSQFIQTC  573 (1016)
T ss_pred             HHHHHHHHHHHHCCCCCEEECCCHHHHHHHHHHHHCCCCCEEEECHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHCCCHH
T ss_conf             99999999998624986231314479999998730588861663588999986105556687742899999998524246


Q ss_pred             -HHHHHHHHHHHHHHCCCCCCEEEEEECCCCCHHHHHHHHHH--HHHHHHCCEEEEEHHHHHHHHHHHHHHHHCCCCCCE
Q ss_conf             -88999999999841001343078862144223699999973--344430545886127999999998621101457865
Q gi|254780945|r  275 -KSQESAIKDILQDMSQKNRMLRILQGDVGSGKTLVALIAMA--AAVEAGGQAVIMAPIGILAQQHYEFIKKYTQNTQII  351 (700)
Q Consensus       275 -~~Q~~ai~eI~~Dl~~~~pM~RLLQGDVGSGKTiVA~~A~l--~~~~~G~Q~alMaPTEILA~QH~~~~~~~~~~~~i~  351 (700)
                       +=|.....+...-+...--|+ +.+|==|.---=++..+.-  ..++=+|---|--|+|+  .|-+..+.+.+..-.+.
T Consensus       574 gdLq~~T~~kl~k~~G~Klgq~-i~~~CrG~Dd~P~~~~~~RKSvS~dIN~GIRFtn~~ev--~~fl~~~~eEl~rkL~e  650 (1016)
T KOG2093         574 GDLQLITLIKLRKVFGPKLGQK-IYRGCRGIDDDPRSIEQVRKSVSADINYGIRFTNIKEV--EQFLCLLSEELRRKLLE  650 (1016)
T ss_pred             HHHHHHHHHHHHHHHCCCHHHH-HHHHCCCCCCCHHHHHHHHCCEEEEEECCEEECCHHHH--HHHHHHHHHHHHHHHHH
T ss_conf             8899999998776535207799-99862787677087765310234310010563557999--99999889999999998


Q ss_pred             EEEEECCCCH
Q ss_conf             8996246422
Q gi|254780945|r  352 VEIITGNMPQ  361 (700)
Q Consensus       352 v~lLtg~~~~  361 (700)
                      +...+++.+-
T Consensus       651 i~k~~~sitL  660 (1016)
T KOG2093         651 ISKTASSITL  660 (1016)
T ss_pred             HHCCCCCHHH
T ss_conf             5401241038


No 460
>PRK10923 glnG nitrogen regulation protein NR(I); Provisional
Probab=79.06  E-value=2.4  Score=22.29  Aligned_cols=33  Identities=27%  Similarity=0.602  Sum_probs=21.0

Q ss_pred             HHHHHHHHHHC--CCCCCEEEEEECCCCCHHHHHH
Q ss_conf             99999998410--0134307886214422369999
Q gi|254780945|r  279 SAIKDILQDMS--QKNRMLRILQGDVGSGKTLVAL  311 (700)
Q Consensus       279 ~ai~eI~~Dl~--~~~pM~RLLQGDVGSGKTiVA~  311 (700)
                      .+++.+..-+.  ......-|++|..|+||+.+|-
T Consensus       145 ~~m~~v~~~i~~~a~~~~pVLI~GE~GTGK~~~Ar  179 (469)
T PRK10923        145 PAMQDVFRIIGRLSRSSISVLINGESGTGKELVAH  179 (469)
T ss_pred             HHHHHHHHHHHHHHCCCCCEEEECCCCCCHHHHHH
T ss_conf             99999999999985889978998989826999999


No 461
>pfam05729 NACHT NACHT domain. This NTPase domain is found in apoptosis proteins as well as those involved in MHC transcription activation. This family is closely related to pfam00931.
Probab=78.90  E-value=1.7  Score=23.57  Aligned_cols=25  Identities=36%  Similarity=0.391  Sum_probs=20.3

Q ss_pred             EEEEECCCCCHHHHHHHHHHHHHHH
Q ss_conf             7886214422369999997334443
Q gi|254780945|r  296 RILQGDVGSGKTLVALIAMAAAVEA  320 (700)
Q Consensus       296 RLLQGDVGSGKTiVA~~A~l~~~~~  320 (700)
                      -+++|+-|+|||..+--.++..++.
T Consensus         3 i~i~G~aG~GKTtll~kl~~~wa~g   27 (165)
T pfam05729         3 VILQGEAGSGKTTLLQKLALLWAQG   27 (165)
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHCC
T ss_conf             9998279898999999999999869


No 462
>pfam00493 MCM MCM2/3/5 family.
Probab=78.85  E-value=3.4  Score=21.16  Aligned_cols=86  Identities=20%  Similarity=0.261  Sum_probs=49.2

Q ss_pred             CEEEEEECCCCCHHHHHHHHHHHHHHHHCCEEEEEHHHHHHHHHHHHHHHHCCCCCCEEEEEECCCCHHHHHHHHHHHCC
Q ss_conf             30788621442236999999733444305458861279999999986211014578658996246422566768776213
Q gi|254780945|r  294 MLRILQGDVGSGKTLVALIAMAAAVEAGGQAVIMAPIGILAQQHYEFIKKYTQNTQIIVEIITGNMPQAHRRKALERIAH  373 (700)
Q Consensus       294 M~RLLQGDVGSGKTiVA~~A~l~~~~~G~Q~alMaPTEILA~QH~~~~~~~~~~~~i~v~lLtg~~~~~er~~i~~~i~~  373 (700)
                      .|-||-||-|.|||-..-.++-           ++|-           ..+....+.+-+=||++... +.       .+
T Consensus        58 ihiLLvGdPG~gKSqlLk~~~~-----------~~pr-----------~~~tsg~~ss~~GLTa~~~~-d~-------~~  107 (327)
T pfam00493        58 INVLLVGDPGTAKSQLLKYVAK-----------LAPR-----------AVYTSGKGSSAAGLTAAVVR-DP-------DT  107 (327)
T ss_pred             CEEEEECCCCCCHHHHHHHHHH-----------HCCC-----------CEEECCCCCCCCCCEEEEEE-EC-------CC
T ss_conf             1189846998156099999998-----------6887-----------08831776656776158998-06-------88


Q ss_pred             CCCEEEEECHHHCCCCCCCCCCCEEEECCCCCCCHHHHHHHHH
Q ss_conf             4754864111201334554444178852101335688998740
Q gi|254780945|r  374 GQAHIIIGTHALFQDSIQYYKLILVIVDEQHRFGVQQRLKLTQ  416 (700)
Q Consensus       374 G~~~iiIGTHAL~q~~v~F~~LgLvViDEQHRFGV~QR~~L~~  416 (700)
                      |+..+-=|  ||     ...+-|.+-|||=.|..-..|.+|.+
T Consensus       108 ~~~~leaG--al-----vlAd~Gv~cIDEfdk~~~~d~saL~E  143 (327)
T pfam00493       108 GEWTLEAG--AL-----VLADGGVCCIDEFDKMNEEDRVAIHE  143 (327)
T ss_pred             CCEEEECC--CE-----EECCCCEEEEECCCCCCHHHHHHHHH
T ss_conf             83698368--47-----75589827850055588767999999


No 463
>PRK07274 single-stranded DNA-binding protein; Provisional
Probab=78.61  E-value=5  Score=19.79  Aligned_cols=80  Identities=14%  Similarity=0.240  Sum_probs=47.3

Q ss_pred             EEEEEEEEEEEEEECCC--CCCEEE--EEEE----CC-----CCEEEEEEECCCHHHHHHHCCCCCEEEEEEEEEECCC-
Q ss_conf             89999999897542158--983389--9998----18-----9369999951887899873289888999989973187-
Q gi|254780945|r   69 IVTITGYISQHSSFQLQ--KRRPYK--ILLN----DG-----TGEITLLFFYRKTEMLKNVFFEGRKITVTGKIKKLKN-  134 (700)
Q Consensus        69 ~vti~g~V~~~~~~~~~--~r~~~~--v~v~----D~-----tg~i~lvfFn~~~~yl~k~lk~G~~v~vsGKv~~~~~-  134 (700)
                      .|++.|.+.+-..+++.  +.....  +-+.    +.     +.-+.++.|+.....+.+.++.|+.+.|.|+++...+ 
T Consensus         4 ~V~LiGrL~~Dpel~~t~~G~~v~~fslAv~r~~k~~~ge~~td~~~vv~wgk~Ae~~~~~~~KG~~V~V~G~L~~~~yd   83 (131)
T PRK07274          4 KVILIGRLTAKPELVKTATDKSVARVTLAVNRRFKNQNGEREADFINVVVWGKLAETLVSYASKGSLISIDGELRTRKYD   83 (131)
T ss_pred             EEEEEEECCCCCEEEECCCCCEEEEEEEEEECCEECCCCCEEEEEEEEEECCHHHHHHHHHCCCCCEEEEEEEEECCCCC
T ss_conf             69999977779769998999889999998713068788978877999998284799998751699999999998874872


Q ss_pred             -------EEEEECCEEEECCC
Q ss_conf             -------79997786896264
Q gi|254780945|r  135 -------RIIMVHPHYIFHNS  148 (700)
Q Consensus       135 -------~~qi~hPe~~~~~~  148 (700)
                             ..+++-.++.++++
T Consensus        84 kdG~~~~~~eI~v~~~~~L~s  104 (131)
T PRK07274         84 KDGQTHYVTEVLCQSFQLLES  104 (131)
T ss_pred             CCCCEEEEEEEEEEEEEECCC
T ss_conf             499799999999978997457


No 464
>cd01294 DHOase Dihydroorotase (DHOase) catalyzes the reversible interconversion of carbamoyl aspartate to dihydroorotate, a key reaction in the pyrimidine biosynthesis. In contrast to the large polyfunctional CAD proteins of higher organisms, this group of DHOases is monofunctional and mainly dimeric.
Probab=78.58  E-value=1.5  Score=23.83  Aligned_cols=25  Identities=16%  Similarity=0.329  Sum_probs=21.7

Q ss_pred             CHHHHHHHHHHHCCCCCEEEEEC-HH
Q ss_conf             22566768776213475486411-12
Q gi|254780945|r  360 PQAHRRKALERIAHGQAHIIIGT-HA  384 (700)
Q Consensus       360 ~~~er~~i~~~i~~G~~~iiIGT-HA  384 (700)
                      +..+|+..++.+.+|.+++.||| ||
T Consensus       219 ~~~Dr~AL~~al~~G~id~~iaTDHA  244 (335)
T cd01294         219 RPEDREALRKAATSGHPKFFLGSDSA  244 (335)
T ss_pred             CHHHHHHHHHHHHCCCCCEEEECCCC
T ss_conf             98999999999974998489847999


No 465
>PRK12311 rpsB 30S ribosomal protein S2; Provisional
Probab=78.54  E-value=1.5  Score=23.86  Aligned_cols=15  Identities=13%  Similarity=0.443  Sum_probs=5.6

Q ss_pred             HHHHCCCCCEEEEEE
Q ss_conf             987328988899998
Q gi|254780945|r  113 LKNVFFEGRKITVTG  127 (700)
Q Consensus       113 l~k~lk~G~~v~vsG  127 (700)
                      +++.-..|..+.|-|
T Consensus        59 v~~ia~~Gg~ILFVG   73 (332)
T PRK12311         59 VSDTVAKGGRVLFVG   73 (332)
T ss_pred             HHHHHHCCCEEEEEE
T ss_conf             999996699799986


No 466
>COG3640 CooC CO dehydrogenase maturation factor [Cell division and chromosome partitioning]
Probab=78.49  E-value=3  Score=21.52  Aligned_cols=35  Identities=23%  Similarity=0.325  Sum_probs=26.4

Q ss_pred             CEEEEEECCCCCHHHHHHH-HHHHHHHHHCCEEEEE
Q ss_conf             3078862144223699999-9733444305458861
Q gi|254780945|r  294 MLRILQGDVGSGKTLVALI-AMAAAVEAGGQAVIMA  328 (700)
Q Consensus       294 M~RLLQGDVGSGKTiVA~~-A~l~~~~~G~Q~alMa  328 (700)
                      |.-.+.|-=|||||-+|++ ++...-..||++...-
T Consensus         1 mkIaI~GKGG~GKTtiaalll~~l~~~~~~~VLvVD   36 (255)
T COG3640           1 MKIAITGKGGVGKTTIAALLLKRLLSKGGYNVLVVD   36 (255)
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHHHHCCCCEEEEEE
T ss_conf             969996599765899999999999864895499994


No 467
>PRK09354 recA recombinase A; Provisional
Probab=78.44  E-value=5.1  Score=19.75  Aligned_cols=85  Identities=22%  Similarity=0.261  Sum_probs=54.1

Q ss_pred             CCCCCEE--EEEECCCCCHHHHHHHHHHHHHHHHCCEEEEEHHHHHHHHHHHHHHHHCCCCCCEEEEEECCC--CHHHHH
Q ss_conf             0134307--886214422369999997334443054588612799999999862110145786589962464--225667
Q gi|254780945|r  290 QKNRMLR--ILQGDVGSGKTLVALIAMAAAVEAGGQAVIMAPIGILAQQHYEFIKKYTQNTQIIVEIITGNM--PQAHRR  365 (700)
Q Consensus       290 ~~~pM~R--LLQGDVGSGKTiVA~~A~l~~~~~G~Q~alMaPTEILA~QH~~~~~~~~~~~~i~v~lLtg~~--~~~er~  365 (700)
                      .+.|..|  -+-|--+||||-.|+.++..+-..|..||+.-----|-.+       |...+|+.+.-|.=+.  +.-+--
T Consensus        55 GG~P~GRivEi~G~esSGKTtlal~~iaeaQk~Gg~~a~iDaE~ald~~-------~a~~lGVd~d~llv~qpd~~Eqal  127 (350)
T PRK09354         55 GGLPKGRIVEIYGPESSGKTTLALHAIAEAQKAGGTAAFIDAEHALDPV-------YAKKLGVDIDNLLVSQPDTGEQAL  127 (350)
T ss_pred             CCCCCCCEEEEECCCCCCHHHHHHHHHHHHHHCCCCEEEEEECCCCCHH-------HHHHCCCCHHHEEEECCCHHHHHH
T ss_conf             9967870899988987779999999999999759947999600027988-------999849771571785686799999


Q ss_pred             HHHHHH-CCCCCEEEEE
Q ss_conf             687762-1347548641
Q gi|254780945|r  366 KALERI-AHGQAHIIIG  381 (700)
Q Consensus       366 ~i~~~i-~~G~~~iiIG  381 (700)
                      ++.+.+ .+|.+++||=
T Consensus       128 ~i~e~Lvrsg~vd~IVv  144 (350)
T PRK09354        128 EIADALVRSGAVDLIVV  144 (350)
T ss_pred             HHHHHHHHCCCCCEEEE
T ss_conf             99999985488418998


No 468
>pfam10412 TrwB_AAD_bind Type IV secretion-system coupling protein DNA-binding domain. The plasmid conjugative coupling protein TrwB forms hexamers from six structurally very similar protomers. This hexamer contains a central channel running from the cytosolic pole (made up by the AADs) to the membrane pole ending at the transmembrane pore shaped by 12 transmembrane helices, rendering an overall mushroom-like structure. The TrwB_AAD (all-alpha domain) domain appears to be the DNA-binding domain of the structure. TrwB, a basic integral inner-membrane nucleoside-triphosphate-binding protein, is the structural prototype for the type IV secretion system coupling proteins, a family of proteins essential for macromolecular transport between cells and export.
Probab=78.37  E-value=4.8  Score=19.92  Aligned_cols=125  Identities=15%  Similarity=0.106  Sum_probs=51.7

Q ss_pred             CCCEEECHHHHHHHHHHH---HHHCCCHHHHCCCCCCCCCCEEEEEEC-CC---HHHHHHHHHHHHCCCCEEEEEECCCC
Q ss_conf             761010101322789999---752010111102355766620799970-20---02689999763103873899971201
Q gi|254780945|r  421 PHVLLMTATPIPRTLVLT---SLGDIDISKITEKPAGRKPIKTVIIPI-NR---IDEVIERLKVVLSEGKKAYWICPQIE  493 (700)
Q Consensus       421 ph~L~MtATPIPRTLal~---~ygdldvS~i~e~P~gR~~I~T~~~~~-~~---~~~~~~~i~~~l~~g~q~y~VcPlIe  493 (700)
                      +..|+.+.+|--++..-.   ++=++-+..+..+|++++.-.-.++.+ ..   ++.+-+.+..--..|-+++.++-   
T Consensus       204 ~~~l~i~~~~~~~~~~~~li~l~~~~~~~~l~~~~~~~~~~v~~~lDEf~~lg~i~~l~~~l~~~Rs~gi~~~l~~Q---  280 (386)
T pfam10412       204 GGWLFITSREDQRAALRPLISLWLDIAIRALLSLPPNRDRRLWFFLDELPSLHKLPSLADALAEGRKFGGCVVLGIQ---  280 (386)
T ss_pred             CEEEEEECCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCEEEEEECHHHCCCCHHHHHHHHHHHCCCCEEEEEEE---
T ss_conf             72999973763589999999999999999997347567874499998711027668899999986407849999983---


Q ss_pred             CCCCCCCCHHHHHH-HHHHHH-CCC-CEECCCCCCCHHHHHHHHHHHHCCCEEEEEECHHHHCCC
Q ss_conf             22111210146666-666866-371-031201469989999999997559869999800341046
Q gi|254780945|r  494 EKKESNFRSVVERF-NSLHEH-FTS-SIAIIHGRMSDIDKESVMDSFKNGTCKLLIATTVIEVGI  555 (700)
Q Consensus       494 ese~~~~~~~~~~~-~~l~~~-~~~-~v~~lHGkm~~~ek~~~m~~F~~g~~~iLvaTtviEVGv  555 (700)
                           ++...++.| +...+. +++ .+-+.- +.++.|-.+-+.+ .-|+..|-+.++=.--|.
T Consensus       281 -----s~~QL~~~YG~~~a~~il~n~~~~i~~-~~~d~eTA~~iS~-~lG~~tv~~~s~s~S~g~  338 (386)
T pfam10412       281 -----SFAQLEEVYGEDGAQTLLGLCNTKLIL-RVSDAETAEWMSE-LLGEQEVERMRESYSYGA  338 (386)
T ss_pred             -----CHHHHHHHHCHHHHHHHHHHCCCEEEE-ECCCHHHHHHHHH-HHCCEEEEEEEEEEECCC
T ss_conf             -----899999987988999999625659998-2799899999999-739749999861055478


No 469
>TIGR03491 RecB family nuclease, putative, TM0106 family. Members of this uncharacterized protein family are found broadly but sporadically among bacteria. The N-terminal region is homologous to the Cas4 protein of CRISPR systems, although this protein family shows no signs of association with CRISPR repeats.
Probab=78.29  E-value=2.8  Score=21.81  Aligned_cols=41  Identities=15%  Similarity=0.232  Sum_probs=23.8

Q ss_pred             HHHCCCCCEEEEEEEEEE--CCCEEEEECCEEEECCCCCCCCC
Q ss_conf             873289888999989973--18779997786896264334444
Q gi|254780945|r  114 KNVFFEGRKITVTGKIKK--LKNRIIMVHPHYIFHNSQDVNFP  154 (700)
Q Consensus       114 ~k~lk~G~~v~vsGKv~~--~~~~~qi~hPe~~~~~~~~~~~~  154 (700)
                      ....+.|..++.-|.+..  +.+..-..||++.+........|
T Consensus        60 ~~am~~G~~~I~~~~L~~~~~~~~~~~g~pdlLvk~~g~S~~G  102 (457)
T TIGR03491        60 LDACAAGADGIYGGRLKHDLPQNLPHVSHPDLLVKDPGRSAWG  102 (457)
T ss_pred             HHHHHCCCCEEEEEEEECCCCCCCCEEEECCEEEECCCCCCCC
T ss_conf             9999738865999998046677884047779899628988878


No 470
>PRK08058 DNA polymerase III subunit delta'; Validated
Probab=78.29  E-value=5.1  Score=19.72  Aligned_cols=143  Identities=13%  Similarity=0.151  Sum_probs=70.9

Q ss_pred             CCCHHHHHHHHHHHHHHCCCCCCEE-EEEECCCCCHHHHHHHH--HHHHHHH-HCCEEEEEHHHHHHHHHHHHHHHHCCC
Q ss_conf             6798899999999984100134307-88621442236999999--7334443-054588612799999999862110145
Q gi|254780945|r  272 SPTKSQESAIKDILQDMSQKNRMLR-ILQGDVGSGKTLVALIA--MAAAVEA-GGQAVIMAPIGILAQQHYEFIKKYTQN  347 (700)
Q Consensus       272 ~LT~~Q~~ai~eI~~Dl~~~~pM~R-LLQGDVGSGKTiVA~~A--~l~~~~~-G~Q~alMaPTEILA~QH~~~~~~~~~~  347 (700)
                      ++..-|..+++-+.+-+.+++--+- |+.|.-|+||+..|..-  ++.|-+. +..++--++.          -+.+-..
T Consensus         6 ~~~~~Q~~i~~~L~~~i~~~rl~HA~Lf~Gp~G~GK~~~A~~~A~~LlC~~~~~~~~Cg~C~~----------C~~~~~~   75 (329)
T PRK08058          6 QLTALQPIVVKMLQNSIAKNRLAHAYLFEGAKGTGKKATALWLAKSLFCLERNGVEPCGTCTN----------CKRIESG   75 (329)
T ss_pred             HHHHHHHHHHHHHHHHHHCCCCCCEEEEECCCCCCHHHHHHHHHHHHCCCCCCCCCCCCCCHH----------HHHHHCC
T ss_conf             888318999999999998599661565578999889999999999973999999998878889----------9998769


Q ss_pred             CCCEEEEEEC---CCCHHHHHHHHHHHCCCCCEEEEECHHHCCCCCCCCCCCEEEECCCCCCCHHHHHHHHHC--CCCCC
Q ss_conf             7865899624---642256676877621347548641112013345544441788521013356889987402--56776
Q gi|254780945|r  348 TQIIVEIITG---NMPQAHRRKALERIAHGQAHIIIGTHALFQDSIQYYKLILVIVDEQHRFGVQQRLKLTQK--ATAPH  422 (700)
Q Consensus       348 ~~i~v~lLtg---~~~~~er~~i~~~i~~G~~~iiIGTHAL~q~~v~F~~LgLvViDEQHRFGV~QR~~L~~K--g~~ph  422 (700)
                      ....+..+..   +.+..+-+++.+.+.-.         +     .. .+--.+||||=|+-..+==++|..-  .+.+|
T Consensus        76 ~HPD~~~i~p~~~~i~idqiR~L~~~~~~~---------p-----~~-g~~KV~II~~Ae~m~~~AaNALLKtLEEPp~~  140 (329)
T PRK08058         76 NHPDVHLVAPDGQSIKKDQIRYLKEEFSKS---------G-----VE-SNKKVYIIEHADKMTASAANSLLKFLEEPSGD  140 (329)
T ss_pred             CCCCEEEECCCCCCCCHHHHHHHHHHHCCC---------C-----CC-CCCEEEEEECHHHHCHHHHHHHHHHHHCCCCC
T ss_conf             999767745661407799999999996438---------7-----57-88679997347762999999999986468978


Q ss_pred             CEEECHHHHHHHHHHHH
Q ss_conf             10101013227899997
Q gi|254780945|r  423 VLLMTATPIPRTLVLTS  439 (700)
Q Consensus       423 ~L~MtATPIPRTLal~~  439 (700)
                      ++..=+|+=|-.+--|+
T Consensus       141 t~fIL~t~~~~~lLpTI  157 (329)
T PRK08058        141 TTAILLTENKHQILPTI  157 (329)
T ss_pred             CEEEEEECCHHHHHHHH
T ss_conf             67998729966643688


No 471
>PRK09112 DNA polymerase III subunit delta'; Validated
Probab=78.24  E-value=2.6  Score=22.04  Aligned_cols=44  Identities=18%  Similarity=0.157  Sum_probs=34.2

Q ss_pred             HHHHHHHHHHHHHHCCCCCCE-EEEEECCCCCHHHHHHHHHHHHH
Q ss_conf             889999999998410013430-78862144223699999973344
Q gi|254780945|r  275 KSQESAIKDILQDMSQKNRML-RILQGDVGSGKTLVALIAMAAAV  318 (700)
Q Consensus       275 ~~Q~~ai~eI~~Dl~~~~pM~-RLLQGDVGSGKTiVA~~A~l~~~  318 (700)
                      -+|..+...+.+-+++++--+ -|+.|--|.|||-.|..-+-...
T Consensus        26 iGq~~~~~~L~~a~~~gRl~HA~Lf~GP~GiGKaTlA~~~A~~Ll   70 (352)
T PRK09112         26 FGHEEARAFLAQAYREGRLHHALLFEGPEGIGKATLAFHLANHIL   70 (352)
T ss_pred             CCHHHHHHHHHHHHHCCCCCCEEEEECCCCCCHHHHHHHHHHHHH
T ss_conf             786999999999998499652465358998089999999999986


No 472
>PRK06958 single-stranded DNA-binding protein; Provisional
Probab=78.20  E-value=5.1  Score=19.70  Aligned_cols=64  Identities=19%  Similarity=0.307  Sum_probs=38.8

Q ss_pred             CEEEEEEEEEEEEEECCC--CCCEEEEEEE--------------CCCCEEEEEEECCCHHHHHHHCCCCCEEEEEEEEEE
Q ss_conf             789999999897542158--9833899998--------------189369999951887899873289888999989973
Q gi|254780945|r   68 RIVTITGYISQHSSFQLQ--KRRPYKILLN--------------DGTGEITLLFFYRKTEMLKNVFFEGRKITVTGKIKK  131 (700)
Q Consensus        68 ~~vti~g~V~~~~~~~~~--~r~~~~v~v~--------------D~tg~i~lvfFn~~~~yl~k~lk~G~~v~vsGKv~~  131 (700)
                      ..|++.|.+.+-..+++.  +.....+.+.              +.|.-+.++.|+..-..+.+.+++|+.|+|.|+++.
T Consensus         5 NkV~LiG~L~~DPelr~t~~G~~va~f~lA~~~~~~d~~~ge~~e~t~w~~v~~~gk~AE~~~~yl~KG~~V~VeGrL~~   84 (181)
T PRK06958          5 NKVILVGNLGADPEVRYLPSGDAVANIRLATTDRYKDKASGEFKEATEWHRVAFFGRLAEIVGEYLKKGSSVYIEGRIRT   84 (181)
T ss_pred             CEEEEEEECCCCCEEEECCCCCEEEEEEEEEECCEEECCCCCEEECCEEEEEECCCHHHHHHHHHCCCCCEEEEEEEEEE
T ss_conf             87999885786965878799977999999986333323788376316377850335699999864479998999757770


No 473
>TIGR03167 tRNA_sel_U_synt tRNA 2-selenouridine synthase. The Escherichia coli YbbB protein was shown to encode a selenophosphate-dependent tRNA 2-selenouridine synthase, essential for modification of some tRNAs to replace a sulfur atom with selenium. This enzyme works with SelD, the selenium donor protein, which also acts in selenocysteine incorporation. Although the members of this protein family show a fairly deep split, sequences from both sides of the split are supported by co-occurence with, and often proximity to, the selD gene.
Probab=78.14  E-value=3.3  Score=21.18  Aligned_cols=77  Identities=25%  Similarity=0.245  Sum_probs=42.3

Q ss_pred             HHHHHHHHHCCCC---CCHHHHHH---HHHHHHHHCCCCCCEEEEEECCCCCHHHHHHHHHHHHHHHHCCEEEEEHHHHH
Q ss_conf             7899998630246---79889999---99999841001343078862144223699999973344430545886127999
Q gi|254780945|r  260 KIAQKILRNIPFS---PTKSQESA---IKDILQDMSQKNRMLRILQGDVGSGKTLVALIAMAAAVEAGGQAVIMAPIGIL  333 (700)
Q Consensus       260 ~~~~~f~~~LPF~---LT~~Q~~a---i~eI~~Dl~~~~pM~RLLQGDVGSGKTiVA~~A~l~~~~~G~Q~alMaPTEIL  333 (700)
                      ..+..+++...|.   |..+=+.=   +-+-...+..+.+. .+|.|=.|||||.+    +-..-.+|+|+.=+   |=|
T Consensus        89 ~s~~~~L~~~G~~v~~l~GGYKayR~~v~~~l~~~~~~~~~-~vl~G~TG~GKT~i----L~~L~~~G~qviDL---Egl  160 (311)
T TIGR03167        89 GSLAWLLAQIGFRVPRLEGGYKAYRRFVIDQLEELPQPFPL-IVLGGMTGSGKTEL----LHALANAGAQVLDL---EGL  160 (311)
T ss_pred             HHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHCCCCCCE-EEEECCCCCCHHHH----HHHHHHCCCCCCCH---HHH
T ss_conf             99999999859984315783899999999999714546876-99878888778999----99999769974258---998


Q ss_pred             HHHHHHHHHHHCCCC
Q ss_conf             999998621101457
Q gi|254780945|r  334 AQQHYEFIKKYTQNT  348 (700)
Q Consensus       334 A~QH~~~~~~~~~~~  348 (700)
                      |.    .--..|...
T Consensus       161 An----HRGS~FG~~  171 (311)
T TIGR03167       161 AN----HRGSSFGAL  171 (311)
T ss_pred             HH----CCCCCCCCC
T ss_conf             63----146534688


No 474
>TIGR01292 TRX_reduct thioredoxin-disulfide reductase; InterPro: IPR005982    Reactive oxygen species (ROS) are known mediators of intracellular signaling cascades. Excessive production of ROS may, however, lead to oxidative stress, loss of cell function, and ultimately apoptosis or necrosis. A balance between oxidant and antioxidant intracellular systems is hence vital for cell function, regulation, and adaptation to diverse growth conditions. Thioredoxin reductase in conjunction with thioredoxin is a ubiquitous oxidoreductase system with antioxidant and redox regulatory roles. Thioredoxin reductase (1.8.1.9 from EC) reduces oxidised thioredoxin in the presence of NADPH. Reduced thioredoxin serves as an electron donor for thioredoxin peroxidase which consequently reduces H_2O_2 to H_2O. In mammals, extracellular forms of Trx also have cytokine-like effects. Mammalian TrxR has a highly reactive active site selenocysteine residue resulting in a profound reductive capacity, reducing several substrates in addition to Trx .; GO: 0004791 thioredoxin-disulfide reductase activity, 0019430 removal of superoxide radicals, 0005737 cytoplasm.
Probab=78.11  E-value=4.4  Score=20.26  Aligned_cols=81  Identities=19%  Similarity=0.197  Sum_probs=62.3

Q ss_pred             HHCCCCEEEEEECCCCCCCCCCCCHHHHHHHHHHHHCCCCEECCCCCCCHHHHHHHHHHHHCC---CEEEEEECHHHHCC
Q ss_conf             310387389997120122111210146666666866371031201469989999999997559---86999980034104
Q gi|254780945|r  478 VLSEGKKAYWICPQIEEKKESNFRSVVERFNSLHEHFTSSIAIIHGRMSDIDKESVMDSFKNG---TCKLLIATTVIEVG  554 (700)
Q Consensus       478 ~l~~g~q~y~VcPlIeese~~~~~~~~~~~~~l~~~~~~~v~~lHGkm~~~ek~~~m~~F~~g---~~~iLvaTtviEVG  554 (700)
                      -+-+|..|.||         =.=.||.+..-+|++ +..+|-++|=|-+---.....+++++.   +|.+|--+||.|+-
T Consensus       147 ~ffk~K~V~Vv---------GGGdsA~eEA~yL~~-~a~kV~lvHRRd~fRA~k~~~~r~~~~~eG~I~~l~n~~v~Ei~  216 (321)
T TIGR01292       147 PFFKNKEVAVV---------GGGDSALEEALYLTR-IAKKVTLVHRRDKFRAEKILLDRLKKNPEGKIEFLWNSTVEEIV  216 (321)
T ss_pred             HHHCCCEEEEE---------CCCCHHHHHHHHHHH-CCCEEEEEECCCCCCCCHHHHHHHHHCCCCCEEEECCCEEEEEE
T ss_conf             12059889998---------798248888899985-38767999779863632899989983789878996486899996


Q ss_pred             CCC-CCCCEEEEECH
Q ss_conf             688-87658998585
Q gi|254780945|r  555 IDV-VDASIIIIENA  568 (700)
Q Consensus       555 vdv-pna~~mvI~~a  568 (700)
                      =|- ...+=.+|.|-
T Consensus       217 G~~~~~V~~v~i~N~  231 (321)
T TIGR01292       217 GDNSKKVESVKIKNT  231 (321)
T ss_pred             CCCCEEEEEEEEEEC
T ss_conf             178315533589962


No 475
>COG2251 Predicted nuclease (RecB family) [General function prediction only]
Probab=78.07  E-value=2.1  Score=22.79  Aligned_cols=34  Identities=21%  Similarity=0.315  Sum_probs=18.0

Q ss_pred             CHHHHHHHHHHHHHHCCCHHHHCCCCCCCCCCEEEEEE
Q ss_conf             10132278999975201011110235576662079997
Q gi|254780945|r  427 TATPIPRTLVLTSLGDIDISKITEKPAGRKPIKTVIIP  464 (700)
Q Consensus       427 tATPIPRTLal~~ygdldvS~i~e~P~gR~~I~T~~~~  464 (700)
                      --||+-++    .|-.+.|.+|+++-.--.||...+.+
T Consensus       232 Gi~~~r~~----~l~~~GI~Ti~~LA~~~~~~~~~~~g  265 (474)
T COG2251         232 GITPSRYD----VLEEVGITTIEDLADASLPILELVAG  265 (474)
T ss_pred             CCCHHHHH----HHHHCCCCHHHHHHHCCCCCHHHHHH
T ss_conf             99878899----99973822399997525540256654


No 476
>pfam02399 Herpes_ori_bp Origin of replication binding protein. This Pfam family represents the herpesvirus origin of replication binding protein, probably involved in DNA replication.
Probab=78.00  E-value=4.9  Score=19.89  Aligned_cols=25  Identities=16%  Similarity=0.215  Sum_probs=9.2

Q ss_pred             HHHHHHHHHHCCCEEEEEECHHHHC
Q ss_conf             9999999975598699998003410
Q gi|254780945|r  529 DKESVMDSFKNGTCKLLIATTVIEV  553 (700)
Q Consensus       529 ek~~~m~~F~~g~~~iLvaTtviEV  553 (700)
                      ....+.+...+|.+.++=.+-+.|.
T Consensus       588 vf~~iy~~Yasg~vP~i~~~G~~e~  612 (829)
T pfam02399       588 VFRRIYDHYASGWVPVLGIAGALET  612 (829)
T ss_pred             HHHHHHHHHCCCCEEEECCCCCEEE
T ss_conf             9999999871684446427887667


No 477
>PRK13732 single-stranded DNA-binding protein; Provisional
Probab=77.97  E-value=5.2  Score=19.65  Aligned_cols=65  Identities=11%  Similarity=0.242  Sum_probs=41.8

Q ss_pred             CEEEEEEEEEEEEEECCC-C-CCE--EEEEEE------------CCCCEEEEEEECCCHHHHHHHCCCCCEEEEEEEEEE
Q ss_conf             789999999897542158-9-833--899998------------189369999951887899873289888999989973
Q gi|254780945|r   68 RIVTITGYISQHSSFQLQ-K-RRP--YKILLN------------DGTGEITLLFFYRKTEMLKNVFFEGRKITVTGKIKK  131 (700)
Q Consensus        68 ~~vti~g~V~~~~~~~~~-~-r~~--~~v~v~------------D~tg~i~lvfFn~~~~yl~k~lk~G~~v~vsGKv~~  131 (700)
                      ..|++.|.+.+-..+++. . ...  +.+.+.            +.+.-+.|+.|+..-..+.+.|++|..|+|-|+++.
T Consensus         7 NkViLiG~Lg~DPElr~t~~G~~va~f~lAt~~~~~d~~~ge~~e~t~w~~vv~~gk~AE~~~~yl~KGs~V~VeGrL~~   86 (175)
T PRK13732          7 NKVILVGRLGKDPEVRYIPNGGAVANLQVATSESWRDKQTGEMREQTEWHRVVLFGKLAEVAGEYLRKGAQVYIEGQLRT   86 (175)
T ss_pred             CEEEEEEECCCCCEEEECCCCCEEEEEEEEEECCCCCCCCCCEECCCCEEEEEEEHHHHHHHHHHHCCCCEEEEEEEEEE
T ss_conf             58999874577961788899987999999983662127788364133548999864899999987279998999998772


Q ss_pred             C
Q ss_conf             1
Q gi|254780945|r  132 L  132 (700)
Q Consensus       132 ~  132 (700)
                      -
T Consensus        87 r   87 (175)
T PRK13732         87 R   87 (175)
T ss_pred             C
T ss_conf             1


No 478
>cd04486 YhcR_OBF_like YhcR_OBF_like: A subfamily of OB-fold domains similar to the OB folds of Bacillus subtilis YhcR. YhcR is a sugar-nonspecific nuclease, which is active in the presence of Ca2+ and Mn2+. It cleaves RNA endonucleolytically, producing 3'-monophosphate nucleosides. YhcR appears to be the major Ca2+ activated nuclease of B. subtilis. YhcR may be localized in the cell wall.
Probab=77.97  E-value=5.2  Score=19.65  Aligned_cols=68  Identities=15%  Similarity=0.122  Sum_probs=40.5

Q ss_pred             EEEEEEEEEEEECCCCCCEEEEEEECC----CC-EEEEEEECCCHHHHHHHCCCCCEEEEEEEEEECCCEEEEECCE-EE
Q ss_conf             999999897542158983389999818----93-6999995188789987328988899998997318779997786-89
Q gi|254780945|r   71 TITGYISQHSSFQLQKRRPYKILLNDG----TG-EITLLFFYRKTEMLKNVFFEGRKITVTGKIKKLKNRIIMVHPH-YI  144 (700)
Q Consensus        71 ti~g~V~~~~~~~~~~r~~~~v~v~D~----tg-~i~lvfFn~~~~yl~k~lk~G~~v~vsGKv~~~~~~~qi~hPe-~~  144 (700)
                      +++|.|.....  .....-  ..++|.    .. .-.-+|-... .  ...+++|++|.+.|++..|++..|+..+. +.
T Consensus         1 tv~GvVTa~~~--~~~~~G--FyiQ~~~~d~~~~tS~gifV~~~-~--~~~~~~Gd~V~vtG~V~Ey~g~TqL~~~~~~~   73 (78)
T cd04486           1 TVEGVVTAVFS--GGGLGG--FYIQDEDGDGDPATSEGIFVYTG-S--GADVAVGDLVRVTGTVTEYYGLTQLTAVSAIE   73 (78)
T ss_pred             CEEEEEEEECC--CCCCCE--EEEECCCCCCCCCCCCEEEEECC-C--CCCCCCCCEEEEEEEEEEECCCEEEECCCCEE
T ss_conf             92899999752--898476--99972789999764237999817-8--88889899999978998624858984451169


Q ss_pred             E
Q ss_conf             6
Q gi|254780945|r  145 F  145 (700)
Q Consensus       145 ~  145 (700)
                      .
T Consensus        74 ~   74 (78)
T cd04486          74 V   74 (78)
T ss_pred             E
T ss_conf             8


No 479
>COG1341 Predicted GTPase or GTP-binding protein [General function prediction only]
Probab=77.95  E-value=5.2  Score=19.65  Aligned_cols=65  Identities=22%  Similarity=0.227  Sum_probs=45.2

Q ss_pred             CCCCCHHHHHHHHHHHH-----HHCCCCCCEEEEEECCCCCHHHHHHHHHHHHHHHHC----------CEEEEEHHHH-H
Q ss_conf             24679889999999998-----410013430788621442236999999733444305----------4588612799-9
Q gi|254780945|r  270 PFSPTKSQESAIKDILQ-----DMSQKNRMLRILQGDVGSGKTLVALIAMAAAVEAGG----------QAVIMAPIGI-L  333 (700)
Q Consensus       270 PF~LT~~Q~~ai~eI~~-----Dl~~~~pM~RLLQGDVGSGKTiVA~~A~l~~~~~G~----------Q~alMaPTEI-L  333 (700)
                      +++-+.+-...+++|..     +.+...+-.-++-|+|+||||=-+.+-+=....-|+          |.-+..|+-| |
T Consensus        45 ~ve~P~d~~~~~e~i~~~~~~~~~~~~~~~~vmvvG~vDSGKSTLt~~LaN~~l~rG~~v~iiDaDvGQ~ei~pPg~ISL  124 (398)
T COG1341          45 LVEVPEDRSEPLEEIADTWESKSESAGKVGVVMVVGPVDSGKSTLTTYLANKLLARGRKVAIIDADVGQSEIGPPGFISL  124 (398)
T ss_pred             CCCCCHHHHHHHHHHHHCCCCCCHHCCCCCEEEEECCCCCCHHHHHHHHHHHHHHCCCEEEEEECCCCCCCCCCCCEEEE
T ss_conf             42281676317899763224420120687389998986767889999999887644741899968999766679746774


Q ss_pred             H
Q ss_conf             9
Q gi|254780945|r  334 A  334 (700)
Q Consensus       334 A  334 (700)
                      |
T Consensus       125 ~  125 (398)
T COG1341         125 A  125 (398)
T ss_pred             E
T ss_conf             1


No 480
>pfam02765 Telo_bind Telomeric single stranded DNA binding POT1/CDC13. This domain binds single stranded telomeric DNA and adopts an OB fold. It includes the proteins POT1 and CDC13 which have been shown to regulate telomere length, replication and capping.
Probab=77.85  E-value=5.3  Score=19.63  Aligned_cols=80  Identities=18%  Similarity=0.213  Sum_probs=57.6

Q ss_pred             HHHCCCCCEEEEEEEEEEEEEECCCCCC--EEEEEEECCC------CEEEEEEECCCHHHHHHHCCCCCEEEEE-EEEEE
Q ss_conf             7888998789999999897542158983--3899998189------3699999518878998732898889999-89973
Q gi|254780945|r   61 ISEISEERIVTITGYISQHSSFQLQKRR--PYKILLNDGT------GEITLLFFYRKTEMLKNVFFEGRKITVT-GKIKK  131 (700)
Q Consensus        61 I~~l~~g~~vti~g~V~~~~~~~~~~r~--~~~v~v~D~t------g~i~lvfFn~~~~yl~k~lk~G~~v~vs-GKv~~  131 (700)
                      ......|..+.+.|.|+........++.  .+...+.|.+      ..+.+.+|......+...-..|+-+++. =+++.
T Consensus         6 ~a~~~~~~~vnv~gVV~~~~~p~~s~g~~~~~t~~i~d~s~~~~~~~~l~v~~F~~~~e~LP~v~~~GDIi~l~r~~v~~   85 (141)
T pfam02765         6 LALLKSGVVVNVIGVVVDAKFPSKSRGSDYDFTLTIVDEDNKGDSNDGLTVKLFSENFEDLPNVQSAGDIIRLHRVKVKL   85 (141)
T ss_pred             HHHHCCCCEEEEEEEEEECCCCEECCCCCEEEEEEEECCCCCCCCCCCCEEEEECCCHHHCCCCCCCCCEEEEEEEEEEE
T ss_conf             23317798899999995635753459985799999990788877899639999899967899867779899997789999


Q ss_pred             CCCEEEEEC
Q ss_conf             187799977
Q gi|254780945|r  132 LKNRIIMVH  140 (700)
Q Consensus       132 ~~~~~qi~h  140 (700)
                      |++..+.+-
T Consensus        86 ~~~~~~~~~   94 (141)
T pfam02765        86 YNGKPQGVA   94 (141)
T ss_pred             ECCEEEEEE
T ss_conf             989678987


No 481
>KOG0554 consensus
Probab=77.82  E-value=5.3  Score=19.62  Aligned_cols=99  Identities=14%  Similarity=0.253  Sum_probs=63.9

Q ss_pred             CCCCCEEEEEEEEEEEEEECCCCCCEEEEEEECCCC--EEEEEEECCCHHHHHHHCCCCCEEEEEEEEEECCCEEEEECC
Q ss_conf             899878999999989754215898338999981893--699999518878998732898889999899731877999778
Q gi|254780945|r   64 ISEERIVTITGYISQHSSFQLQKRRPYKILLNDGTG--EITLLFFYRKTEMLKNVFFEGRKITVTGKIKKLKNRIIMVHP  141 (700)
Q Consensus        64 l~~g~~vti~g~V~~~~~~~~~~r~~~~v~v~D~tg--~i~lvfFn~~~~yl~k~lk~G~~v~vsGKv~~~~~~~qi~hP  141 (700)
                      -..|+..++-|=|.+++.    .++..-+.+.|++.  .++++-=   .+ .-+.+..|+.+.+.|.....++..|-++ 
T Consensus        17 ~~~g~t~~i~GWvKsvr~----~~~~~Fl~i~DGs~~~~lQvVv~---~~-~~q~la~Gt~i~~~g~l~~~~~~~q~ie-   87 (446)
T KOG0554          17 PRAGDTISIGGWVKSVRK----LKKVTFLDINDGSCPSPLQVVVD---SE-QSQLLATGTCISAEGVLKVSKGAKQQIE-   87 (446)
T ss_pred             CCCCCCEEECCHHHHCCC----CCCEEEEEECCCCCCCCEEEEEC---HH-HHHHCCCCCEEEEEEEEEECCCHHEEEE-
T ss_conf             889980463324541314----55428999558988766499956---27-8402056526999756873465010110-


Q ss_pred             EEEECCCCCCCCCCCCCCCCCCHH-HHHHHHHHH
Q ss_conf             689626433444441100000000-004543001
Q gi|254780945|r  142 HYIFHNSQDVNFPLIEAVYSLPTG-LSVDLFKKI  174 (700)
Q Consensus       142 e~~~~~~~~~~~~~I~PIYplt~G-Lsqk~irk~  174 (700)
                         ...+.....|.+.|-||+.+. ++...+|..
T Consensus        88 ---l~~eki~~vG~v~~~ypl~Kk~lt~e~LR~~  118 (446)
T KOG0554          88 ---LNAEKIKVVGTVDESYPLQKKKLTPEMLRDK  118 (446)
T ss_pred             ---EEEEEEEEEEECCCCCCCCCCCCCHHHHHHC
T ss_conf             ---2005789985348998774233898898532


No 482
>cd03109 DTBS Dethiobiotin synthetase (DTBS) is the penultimate enzyme in the biotin biosynthesis pathway in Escherichia coli and other microorganisms. The enzyme catalyzes formation of the ureido ring of dethiobiotin from (7R,8S)-7,8-diaminononanoic acid (DAPA) and carbon dioxide. The enzyme utilizes carbon dioxide instead of hydrogen carbonate as substrate and is dependent on ATP and divalent metal ions as cofactors.
Probab=77.31  E-value=2.6  Score=21.98  Aligned_cols=34  Identities=24%  Similarity=0.295  Sum_probs=29.8

Q ss_pred             EEECCCCCHHHHHHHHHHHHHHHHCCEEEEEHHH
Q ss_conf             8621442236999999733444305458861279
Q gi|254780945|r  298 LQGDVGSGKTLVALIAMAAAVEAGGQAVIMAPIG  331 (700)
Q Consensus       298 LQGDVGSGKTiVA~~A~l~~~~~G~Q~alMaPTE  331 (700)
                      +==|.|-|||+|...-+-...+.|+.++.|=|-+
T Consensus         4 ~GTdT~VGKT~vt~~l~~~l~~~G~~v~~~KPv~   37 (134)
T cd03109           4 FGTGTDIGKTVATAILARALKEKGYRVAPLKPVQ   37 (134)
T ss_pred             EECCCCCCHHHHHHHHHHHHHHCCCCEEEECHHH
T ss_conf             5278887689999999999997799177875667


No 483
>cd04323 AsnRS_cyto_like_N AsnRS_cyto_like_N: N-terminal, anticodon recognition domain of the type found in human and Saccharomyces cerevisiae cytoplasmic asparaginyl-tRNA synthetase (AsnRS), in Brugia malayai AsnRs and, in various putative bacterial AsnRSs.  This domain is a beta-barrel domain (OB fold) involved in binding the tRNA anticodon stem-loop. The enzymes in this group are homodimeric class2b aminoacyl-tRNA synthetases (aaRSs). aaRSs catalyze the specific attachment of amino acids (AAs) to their cognate tRNAs during protein biosynthesis. This 2-step reaction involves i) the activation of the AA by ATP in the presence of magnesium ions, followed by ii) the transfer of  the activated AA to the terminal ribose of tRNA.  In the case of the class2b aaRSs, the activated AA is attached to the 3'OH of the terminal ribose. Eukaryotes contain 2 sets of aaRSs, both of which are encoded by the nuclear genome. One set concerns with cytoplasmic synthesis, whereas the other exclusively with 
Probab=77.28  E-value=5.4  Score=19.51  Aligned_cols=62  Identities=19%  Similarity=0.304  Sum_probs=44.2

Q ss_pred             EEEEEEEEEEEEEECCCCCCEEEEEEECCCCEEEEEEECCCH--HHHHHHCCCCCEEEEEEEEEECCC
Q ss_conf             899999998975421589833899998189369999951887--899873289888999989973187
Q gi|254780945|r   69 IVTITGYISQHSSFQLQKRRPYKILLNDGTGEITLLFFYRKT--EMLKNVFFEGRKITVTGKIKKLKN  134 (700)
Q Consensus        69 ~vti~g~V~~~~~~~~~~r~~~~v~v~D~tg~i~lvfFn~~~--~yl~k~lk~G~~v~vsGKv~~~~~  134 (700)
                      .|++.|-|.+.+.    .+...=+.+.|++|.+++++.....  ....+.+..+..+.+.|++.....
T Consensus         1 kV~l~GWV~~~R~----~g~l~Fi~LRD~~G~iQ~V~~~~~~~~~~~~~~l~~Es~v~V~G~v~~~~~   64 (84)
T cd04323           1 RVKVFGWVHRLRS----QKKLMFLVLRDGTGFLQCVLSKKLVTEFYDAKSLTQESSVEVTGEVKEDPR   64 (84)
T ss_pred             CEEEEEEEEEEEC----CCCCEEEEEEECCEEEEEEECCCCCCHHHHHHHCCCCEEEEEEEEEEECCC
T ss_conf             9999998998623----899289999508879999988865736899973888359999999997897


No 484
>COG1224 TIP49 DNA helicase TIP49, TBP-interacting protein [Transcription]
Probab=77.19  E-value=3.4  Score=21.11  Aligned_cols=173  Identities=17%  Similarity=0.228  Sum_probs=77.3

Q ss_pred             HHHHHHHH--HHHHHCCCCCCE---EEEEECCCCCHHHHHHHHHHHHHHHH----------CCEEEEEHHHHHHHHHHHH
Q ss_conf             89999999--998410013430---78862144223699999973344430----------5458861279999999986
Q gi|254780945|r  276 SQESAIKD--ILQDMSQKNRML---RILQGDVGSGKTLVALIAMAAAVEAG----------GQAVIMAPIGILAQQHYEF  340 (700)
Q Consensus       276 ~Q~~ai~e--I~~Dl~~~~pM~---RLLQGDVGSGKTiVA~~A~l~~~~~G----------~Q~alMaPTEILA~QH~~~  340 (700)
                      +|.+|=+.  |.-+|-+...|.   -|+-|..|||||..|+.-+ .-+..+          --.+=|--||.|-+-    
T Consensus        43 GQ~~AReAaGvIv~mik~gk~aGrgiLi~GppgTGKTAlA~gIa-~eLG~dvPF~~isgsEiYS~E~kKTE~L~qa----  117 (450)
T COG1224          43 GQEEAREAAGVIVKMIKQGKMAGRGILIVGPPGTGKTALAMGIA-RELGEDVPFVAISGSEIYSLEVKKTEALTQA----  117 (450)
T ss_pred             CHHHHHHHHHHHHHHHHHCCCCCCEEEEECCCCCCHHHHHHHHH-HHHCCCCCCEEECCCEEEEECCCHHHHHHHH----
T ss_conf             24988876259999997176666179997899976889999999-9858999821501332233100088999999----


Q ss_pred             HHHHCCCCCCEEEEEECCCCHHHHHHHHHHHCCCCCE---EEEECHHHC--CCCCCCCCCCEEEECCCCCCCHHHH--HH
Q ss_conf             2110145786589962464225667687762134754---864111201--3345544441788521013356889--98
Q gi|254780945|r  341 IKKYTQNTQIIVEIITGNMPQAHRRKALERIAHGQAH---IIIGTHALF--QDSIQYYKLILVIVDEQHRFGVQQR--LK  413 (700)
Q Consensus       341 ~~~~~~~~~i~v~lLtg~~~~~er~~i~~~i~~G~~~---iiIGTHAL~--q~~v~F~~LgLvViDEQHRFGV~QR--~~  413 (700)
                      |++-   .|+++         +|.+++++    |++-   +--.-|-+=  ++-..=-.+.|---||.-.|-+.-.  ..
T Consensus       118 ~Rra---IGvri---------kE~reV~E----GeV~~l~i~~~~~p~~~y~~~~~~~~i~LkT~d~~k~~~lg~~i~~q  181 (450)
T COG1224         118 LRRA---IGVRI---------KETREVYE----GEVVELEIRRARNPLNPYGKVPSGAIITLKTKDEEKTLRLGPEIAEQ  181 (450)
T ss_pred             HHHH---HCEEE---------EEEEEEEE----EEEEEEEEEECCCCCCCCCCCCCCEEEEEEECCCCEEEECCHHHHHH
T ss_conf             9986---45486---------46668887----78999987623579987665545328999963664576259899999


Q ss_pred             HHHCCC-CCCCEEECH-----HHHHHHHHHHH-HHCCCHHHHCCCCCCCC---CCEEEEEECCCHH
Q ss_conf             740256-776101010-----13227899997-52010111102355766---6207999702002
Q gi|254780945|r  414 LTQKAT-APHVLLMTA-----TPIPRTLVLTS-LGDIDISKITEKPAGRK---PIKTVIIPINRID  469 (700)
Q Consensus       414 L~~Kg~-~ph~L~MtA-----TPIPRTLal~~-ygdldvS~i~e~P~gR~---~I~T~~~~~~~~~  469 (700)
                      |..-|. .-|+.+.-|     +-+-|+-+-.- --|+....--++|.|-.   +=.|+.++..+++
T Consensus       182 l~~~~V~~GDVI~Id~etG~V~klGrs~~~~~~~~dl~~~~~V~~P~Gev~K~KEi~~~vTLHDlD  247 (450)
T COG1224         182 LVKEGVEEGDVIYIDAETGRVKKLGRSKARAREDFDLEDTRFVPLPEGEVQKRKEIVQTVTLHDLD  247 (450)
T ss_pred             HHHHCCCCCCEEEEECCCCEEEEEECCCCCCCCCCCCCCEEEEECCCCCEEEEEEEEEEEEEHHHH
T ss_conf             998374458789998256679994224233542233442179877988525667789998700313


No 485
>pfam07728 AAA_5 AAA domain (dynein-related subfamily). This Pfam entry includes some of the AAA proteins not detected by the pfam00004 model.
Probab=76.84  E-value=1.7  Score=23.40  Aligned_cols=18  Identities=33%  Similarity=0.405  Sum_probs=15.0

Q ss_pred             EEEEECCCCCHHHHHHHH
Q ss_conf             788621442236999999
Q gi|254780945|r  296 RILQGDVGSGKTLVALIA  313 (700)
Q Consensus       296 RLLQGDVGSGKTiVA~~A  313 (700)
                      -||+|.-|+|||.+|-.-
T Consensus         2 vll~Gp~G~GKT~la~~l   19 (139)
T pfam07728         2 VLLVGPPGTGKSELAERL   19 (139)
T ss_pred             EEEECCCCCHHHHHHHHH
T ss_conf             899989975699999999


No 486
>PRK05201 hslU ATP-dependent protease ATP-binding subunit; Provisional
Probab=76.83  E-value=1.5  Score=23.83  Aligned_cols=22  Identities=27%  Similarity=0.262  Sum_probs=18.8

Q ss_pred             CCCEEEEEECCCCCHHHHHHHH
Q ss_conf             3430788621442236999999
Q gi|254780945|r  292 NRMLRILQGDVGSGKTLVALIA  313 (700)
Q Consensus       292 ~pM~RLLQGDVGSGKTiVA~~A  313 (700)
                      .|.|-|+-|-.|||||.+|=.-
T Consensus        49 ~pkNILmIGPTGvGKTeIARrL   70 (442)
T PRK05201         49 TPKNILMIGPTGVGKTEIARRL   70 (442)
T ss_pred             CCCCEEEECCCCCCHHHHHHHH
T ss_conf             6431688788886678999999


No 487
>PRK05733 single-stranded DNA-binding protein; Provisional
Probab=76.69  E-value=5.6  Score=19.39  Aligned_cols=66  Identities=14%  Similarity=0.214  Sum_probs=41.7

Q ss_pred             CEEEEEEEEEEEEEECCC-CC-CE--EEEEEE------------CCCCEEEEEEECCCHHHHHHHCCCCCEEEEEEEEEE
Q ss_conf             789999999897542158-98-33--899998------------189369999951887899873289888999989973
Q gi|254780945|r   68 RIVTITGYISQHSSFQLQ-KR-RP--YKILLN------------DGTGEITLLFFYRKTEMLKNVFFEGRKITVTGKIKK  131 (700)
Q Consensus        68 ~~vti~g~V~~~~~~~~~-~r-~~--~~v~v~------------D~tg~i~lvfFn~~~~yl~k~lk~G~~v~vsGKv~~  131 (700)
                      ..|++.|.+.+-..+++. .. ..  +.+-+.            +.|.-+.|+.|...-..+.+.+++|+.|+|.|+++.
T Consensus         6 NkV~LiG~lg~DPElr~t~~G~~v~~fslAt~~~~~~~~~ge~~e~T~w~~v~~wgk~AE~~~~yl~KG~~V~VeGrL~t   85 (172)
T PRK05733          6 NKVILVGTCGQDPEVRYLPNGNAVTNLSLATSEQWTDKQSGQKVERTEWHRVSLFGKVAEIAGEYLRKGSQVYIEGKLQT   85 (172)
T ss_pred             CEEEEEEECCCCCEEEECCCCCEEEEEEEEEECCCCCCCCCCEECCCCEEEEEEECHHHHHHHHHCCCCCEEEEEEEEEE
T ss_conf             28999755577963888899987999999972550016787583123228998734578888865389998999988884


Q ss_pred             CC
Q ss_conf             18
Q gi|254780945|r  132 LK  133 (700)
Q Consensus       132 ~~  133 (700)
                      ..
T Consensus        86 r~   87 (172)
T PRK05733         86 RE   87 (172)
T ss_pred             EC
T ss_conf             04


No 488
>PTZ00301 uridine kinase; Provisional
Probab=76.66  E-value=3  Score=21.58  Aligned_cols=14  Identities=36%  Similarity=0.589  Sum_probs=11.3

Q ss_pred             EEEECCCCCHHHHH
Q ss_conf             88621442236999
Q gi|254780945|r  297 ILQGDVGSGKTLVA  310 (700)
Q Consensus       297 LLQGDVGSGKTiVA  310 (700)
                      -+-|+-|||||-+|
T Consensus         7 gIaGgSgSGKTT~a   20 (210)
T PTZ00301          7 GISGASGSGKSSLS   20 (210)
T ss_pred             EEECCCCCCHHHHH
T ss_conf             99688767899999


No 489
>PRK13849 putative crown gall tumor protein VirC1; Provisional
Probab=76.63  E-value=2.4  Score=22.32  Aligned_cols=31  Identities=23%  Similarity=0.214  Sum_probs=24.9

Q ss_pred             EEECCCCCHHHHHHHHHHHHHHHHCCEEEEE
Q ss_conf             8621442236999999733444305458861
Q gi|254780945|r  298 LQGDVGSGKTLVALIAMAAAVEAGGQAVIMA  328 (700)
Q Consensus       298 LQGDVGSGKTiVA~~A~l~~~~~G~Q~alMa  328 (700)
                      .+.-=|||||-+|+.-+......|+.|+++=
T Consensus         7 ~~~KGG~GKtT~a~~la~~~~~~g~~v~~iD   37 (231)
T PRK13849          7 CSFKGGAGKTTALMGLCAALASDGKRVALFE   37 (231)
T ss_pred             EECCCCCCHHHHHHHHHHHHHHCCCEEEEEE
T ss_conf             6189987699999999999997899599996


No 490
>COG4962 CpaF Flp pilus assembly protein, ATPase CpaF [Intracellular trafficking and secretion]
Probab=76.55  E-value=5.4  Score=19.51  Aligned_cols=60  Identities=18%  Similarity=0.310  Sum_probs=44.1

Q ss_pred             CCCHHHHHHHHHHHHHHCCCCCCEEEEEECCCCCHHHHHHHHHHHHHHHHCCEEEEEHHHHHHHHH
Q ss_conf             679889999999998410013430788621442236999999733444305458861279999999
Q gi|254780945|r  272 SPTKSQESAIKDILQDMSQKNRMLRILQGDVGSGKTLVALIAMAAAVEAGGQAVIMAPIGILAQQH  337 (700)
Q Consensus       272 ~LT~~Q~~ai~eI~~Dl~~~~pM~RLLQGDVGSGKTiVA~~A~l~~~~~G~Q~alMaPTEILA~QH  337 (700)
                      +++.+|...+.-+..-     .+|-|+.|-.|||||-- +-|++..+...-.+..+=-|+-|.-||
T Consensus       157 t~~~~~a~~L~~av~~-----r~NILisGGTGSGKTTl-LNal~~~i~~~eRvItiEDtaELql~~  216 (355)
T COG4962         157 TMIRRAAKFLRRAVGI-----RCNILISGGTGSGKTTL-LNALSGFIDSDERVITIEDTAELQLAH  216 (355)
T ss_pred             CCCHHHHHHHHHHHHH-----CEEEEEECCCCCCHHHH-HHHHHHCCCCCCEEEEEEEHHHHCCCC
T ss_conf             9588999999999862-----01599967878879999-999971579765089981236644699


No 491
>PRK05748 replicative DNA helicase; Provisional
Probab=76.50  E-value=5.7  Score=19.36  Aligned_cols=73  Identities=15%  Similarity=0.073  Sum_probs=42.8

Q ss_pred             EEEEECCCCCHHHHHHHHHHHHH-HHHCCEEEEEHHHHHHHHHHHHHHHHCCCCCCEEEEEECCCCHHHHHHHHHH
Q ss_conf             78862144223699999973344-4305458861279999999986211014578658996246422566768776
Q gi|254780945|r  296 RILQGDVGSGKTLVALIAMAAAV-EAGGQAVIMAPIGILAQQHYEFIKKYTQNTQIIVEIITGNMPQAHRRKALER  370 (700)
Q Consensus       296 RLLQGDVGSGKTiVA~~A~l~~~-~~G~Q~alMaPTEILA~QH~~~~~~~~~~~~i~v~lLtg~~~~~er~~i~~~  370 (700)
                      -.+=|--|.|||..|+--+..++ .+|+-|+|..- |.=++|....+-......+. -.+-.|.++..+...+...
T Consensus       206 iviaaRP~mGKTa~alnia~~~a~~~~~~v~~fSl-EM~~~~l~~R~la~~s~v~~-~~i~~g~l~~~~~~~~~~a  279 (448)
T PRK05748        206 IIVAARPSVGKTAFALNIAQNVATKTDKNVAIFSL-EMGAESLVMRMLCAEGRIDQ-QKLRTGQLTDEDWPKLTIA  279 (448)
T ss_pred             EEEEECCCCCHHHHHHHHHHHHHHHCCCEEEEEEC-CCCHHHHHHHHHHHHHCCCH-HHHHCCCCCHHHHHHHHHH
T ss_conf             99984799876899999999999856980899817-78888999999999746777-7776289999999999999


No 492
>PRK05973 replicative DNA helicase; Provisional
Probab=76.39  E-value=5.7  Score=19.34  Aligned_cols=58  Identities=17%  Similarity=0.344  Sum_probs=40.6

Q ss_pred             HHHHHHCCCCCCEEEEEECCCCCHHHHHHHHHHHHHHHHCCEEEEEHHHHHHHHHHHHHHH
Q ss_conf             9998410013430788621442236999999733444305458861279999999986211
Q gi|254780945|r  283 DILQDMSQKNRMLRILQGDVGSGKTLVALIAMAAAVEAGGQAVIMAPIGILAQQHYEFIKK  343 (700)
Q Consensus       283 eI~~Dl~~~~pM~RLLQGDVGSGKTiVA~~A~l~~~~~G~Q~alMaPTEILA~QH~~~~~~  343 (700)
                      |+..-|.-+- | -+|-|==|=|||.-|+--+..|+.+|+.|+|-.= |-=++|-...+..
T Consensus        56 ~l~~gLqPGD-L-IIlAARPsMGKTafaLnla~~A~k~g~~v~fFSL-EM~~~ql~~RL~~  113 (237)
T PRK05973         56 ELFGQLRPGD-L-VLLGARPGQGKTLLGLELAVEAMKSGRTGVFFTL-EYTEKDVLDRLRA  113 (237)
T ss_pred             HHHCCCCCCC-E-EEEECCCCCCHHHHHHHHHHHHHHHCCCEEEEEE-CCCHHHHHHHHHH
T ss_conf             9856899867-7-9994289887899999999999995996699961-5999999999997


No 493
>TIGR01967 DEAH_box_HrpA ATP-dependent helicase HrpA; InterPro: IPR010222   This entry represents HrpA, one of two related but uncharacterised DEAH-box ATP-dependent helicases in many Proteobacteria and a few high-GC Gram-positive bacteria. HrpA is about 1300 amino acids long, while its paralog HrpB, also uncharacterised, is about 800 amino acids long. Related characterised eukaryotic proteins are RNA helicases associated with pre-mRNA processing.; GO: 0005524 ATP binding, 0008026 ATP-dependent helicase activity.
Probab=76.33  E-value=1.6  Score=23.73  Aligned_cols=271  Identities=21%  Similarity=0.347  Sum_probs=150.2

Q ss_pred             HHHHHHHHHHHHHCCCCCCEEEEEECCCCCHH------------------------HHHHHHHHHHHHH----------H
Q ss_conf             89999999998410013430788621442236------------------------9999997334443----------0
Q gi|254780945|r  276 SQESAIKDILQDMSQKNRMLRILQGDVGSGKT------------------------LVALIAMAAAVEA----------G  321 (700)
Q Consensus       276 ~Q~~ai~eI~~Dl~~~~pM~RLLQGDVGSGKT------------------------iVA~~A~l~~~~~----------G  321 (700)
                      +++|  +||.+-++.+.-.  .+-|..|||||                        =+|+.+.+.-+..          |
T Consensus        71 S~kR--edI~~AI~~nQVv--iiAGETGSGKTTQLPKICLELGrG~~GlIGHTQPRRlAAR~VA~R~AeELgtplGe~VG  146 (1320)
T TIGR01967        71 SAKR--EDIAKAIAENQVV--IIAGETGSGKTTQLPKICLELGRGSRGLIGHTQPRRLAARSVAERVAEELGTPLGELVG  146 (1320)
T ss_pred             HHHH--HHHHHHHHHCCEE--EEECCCCCCCCCCCHHHHHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHCCCCCCCCC
T ss_conf             1118--9999999848989--99724487620232167775427876541247146889999999999983889886132


Q ss_pred             CCEEEEEHHHHHHHHHHHHHHHHCCCCCCEEEEEECCCCHHHHHHHHHHHCCCCCEEEEECHHHCCCCCCCCCCCEEEEC
Q ss_conf             54588612799999999862110145786589962464225667687762134754864111201334554444178852
Q gi|254780945|r  322 GQAVIMAPIGILAQQHYEFIKKYTQNTQIIVEIITGNMPQAHRRKALERIAHGQAHIIIGTHALFQDSIQYYKLILVIVD  401 (700)
Q Consensus       322 ~Q~alMaPTEILA~QH~~~~~~~~~~~~i~v~lLtg~~~~~er~~i~~~i~~G~~~iiIGTHAL~q~~v~F~~LgLvViD  401 (700)
                      |+|=               |..-.++ +--|-|+|-++=       |.++..               |=-...=--+|||
T Consensus       147 YkVR---------------F~D~v~~-~t~VKLmTDGiL-------LAE~Q~---------------DRfL~~YDTIIID  188 (1320)
T TIGR01967       147 YKVR---------------FEDQVSS-NTLVKLMTDGIL-------LAETQQ---------------DRFLERYDTIIID  188 (1320)
T ss_pred             CEEE---------------ECCCCCC-CCEEEEHHHHHH-------HHHHHH---------------HHHHHHCCCEEEC
T ss_conf             0366---------------3142688-543630322358-------998520---------------0222106733651


Q ss_pred             CCCCCCHHHHHHHH-HCC---CCCCC--EEECHHHHHHHHHHHHHHCC--CHHHHCCCCCCCC-CCEEEEEECC------
Q ss_conf             10133568899874-025---67761--01010132278999975201--0111102355766-6207999702------
Q gi|254780945|r  402 EQHRFGVQQRLKLT-QKA---TAPHV--LLMTATPIPRTLVLTSLGDI--DISKITEKPAGRK-PIKTVIIPIN------  466 (700)
Q Consensus       402 EQHRFGV~QR~~L~-~Kg---~~ph~--L~MtATPIPRTLal~~ygdl--dvS~i~e~P~gR~-~I~T~~~~~~------  466 (700)
                      |=|==.-|==--|. -|+   ..||+  +.-|||==|==-|-= |.+=  .-.=|-| =+||+ ||.|+.-+-.      
T Consensus       189 EAHERSLNIDFLLGYLK~lL~rRPDLKiIITSATID~ERFs~H-Fn~AeGkPaPIIE-VSGRTyPVe~RYRPL~~~~~~~  266 (1320)
T TIGR01967       189 EAHERSLNIDFLLGYLKQLLPRRPDLKIIITSATIDPERFSRH-FNNAEGKPAPIIE-VSGRTYPVEVRYRPLVEEQEDD  266 (1320)
T ss_pred             CHHHHHHHHHHHHHHHHHHCCCCCCCCEEEECCCCCHHHHHHH-HCCCCCCCCCEEE-ECCCCCCCCEEECCCCCCCCCC
T ss_conf             1231123388999888763266886525740023574468786-2278889887555-2785466511116876444887


Q ss_pred             ---------CHHHHHHHHHHHHCCCCE-----EEEEECCCCCCCCCCCCHHHHHHHHHHHHCCC--CEECCCCCCCHHHH
Q ss_conf             ---------002689999763103873-----89997120122111210146666666866371--03120146998999
Q gi|254780945|r  467 ---------RIDEVIERLKVVLSEGKK-----AYWICPQIEEKKESNFRSVVERFNSLHEHFTS--SIAIIHGRMSDIDK  530 (700)
Q Consensus       467 ---------~~~~~~~~i~~~l~~g~q-----~y~VcPlIeese~~~~~~~~~~~~~l~~~~~~--~v~~lHGkm~~~ek  530 (700)
                               .++-+++.|.+=.+.|..     -=|.|=+=.|-      .+-+..+.|.+.-..  +|-=|.+|++++|.
T Consensus       267 Gnqi~~d~d~~~ai~~AvdEL~~e~~~eGkGPGDiLIFlpGER------EIRDaAE~L~k~~~rhtEIlPLYARLS~~EQ  340 (1320)
T TIGR01967       267 GNQIVIDLDQLEAILAAVDELVAEGPDEGKGPGDILIFLPGER------EIRDAAEILRKRNLRHTEILPLYARLSNKEQ  340 (1320)
T ss_pred             CCEEEECCCHHHHHHHHHHHHHHCCCCCCCCCCCEEEECCCCC------CHHHHHHHHHCCCCCCEEEECCHHHCCHHHC
T ss_conf             7704101127889999999997427555789972676378886------3689999984468787044055221586447


Q ss_pred             HHHHHHHHCCCEEEEEECHHHHCCCCCCCCCEEEEECH-----------------HHCCHHHHHHHHHCCCCCCCCEEEE
Q ss_conf             99999975598699998003410468887658998585-----------------2547468877301166789835999
Q gi|254780945|r  531 ESVMDSFKNGTCKLLIATTVIEVGIDVVDASIIIIENA-----------------EHFGLAQLHQLRGRVGRGEEISSCI  593 (700)
Q Consensus       531 ~~~m~~F~~g~~~iLvaTtviEVGvdvpna~~mvI~~a-----------------erfGLsqLHQLRGRVGRg~~~s~c~  593 (700)
                      ++|.+.=.  .=.|..||.|=|--..||.---.|==+-                 |+--=|-=-|=.||-||= .+|-|+
T Consensus       341 ~RvF~pHs--GRRIVLaTNVAETSLTVPGI~YVIDtGtARiSRYS~RTKVQRLPIEpISQASANQRkGRCGRV-~~GICI  417 (1320)
T TIGR01967       341 QRVFQPHS--GRRIVLATNVAETSLTVPGIRYVIDTGTARISRYSYRTKVQRLPIEPISQASANQRKGRCGRV-APGICI  417 (1320)
T ss_pred             CCCCCCCC--CCEEEEECCHHHHHCCCCCCCCEECCCCCCCCCCCCCCCCCCCCCCHHHHCCCCCCCCCCCCC-CCCEEE
T ss_conf             44006859--623453301013305788711135688532000100330133676603122320068875414-777047


Q ss_pred             EEECCC
Q ss_conf             970888
Q gi|254780945|r  594 LLYHPP  599 (700)
Q Consensus       594 l~~~~~  599 (700)
                      =+|+..
T Consensus       418 RLYSE~  423 (1320)
T TIGR01967       418 RLYSEE  423 (1320)
T ss_pred             ECCCHH
T ss_conf             557757


No 494
>PTZ00150 phosphoglucomutase; Provisional
Probab=76.25  E-value=2.7  Score=21.91  Aligned_cols=20  Identities=15%  Similarity=0.182  Sum_probs=14.3

Q ss_pred             CCCCCHHHHHHHHHHHHCCC
Q ss_conf             14699899999999975598
Q gi|254780945|r  522 HGRMSDIDKESVMDSFKNGT  541 (700)
Q Consensus       522 HGkm~~~ek~~~m~~F~~g~  541 (700)
                      +...+.++...+|++|+...
T Consensus       472 ~~~~~~~~i~~i~~~~r~~~  491 (593)
T PTZ00150        472 YIVLDPNDIVSIFNDFRGNG  491 (593)
T ss_pred             EEECCHHHHHHHHHHHHCCC
T ss_conf             87279899999999986189


No 495
>cd04480 RPA1_DBD_A_like RPA1_DBD_A_like: A subgroup of uncharacterized plant OB folds with similarity to the second OB fold, the ssDNA-binding domain (DBD)-A, of human RPA1 (also called RPA70). RPA1 is the large subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). In addition to DBD-A, RPA1 contains three other OB folds: DBD-B, DBD-C, and RPA1N. The major DNA binding activity of RPA is associated with DBD-A and DBD-B of RPA1. RPA1 DBD-C is involved in trimerization. The ssDNA-binding mechanism is believed to be multistep and to involve conformational change.
Probab=76.23  E-value=5.8  Score=19.31  Aligned_cols=74  Identities=14%  Similarity=0.104  Sum_probs=50.7

Q ss_pred             EEEEEEEEEEECC-CCCCEEEEEEECCCC-EEEEEEECCCHHHHHHHCCCCCEEEEE-EEEEECCCEEEEECCEEEE
Q ss_conf             9999989754215-898338999981893-699999518878998732898889999-8997318779997786896
Q gi|254780945|r   72 ITGYISQHSSFQL-QKRRPYKILLNDGTG-EITLLFFYRKTEMLKNVFFEGRKITVT-GKIKKLKNRIIMVHPHYIF  145 (700)
Q Consensus        72 i~g~V~~~~~~~~-~~r~~~~v~v~D~tg-~i~lvfFn~~~~yl~k~lk~G~~v~vs-GKv~~~~~~~qi~hPe~~~  145 (700)
                      |.++|.+.-.... .....+..++.|+.| .|.+..+..........|++|..+.++ ++|....+.+-.+...|.+
T Consensus         2 I~Vrv~r~W~~~~~~~~~~~~mvL~De~G~~I~a~i~~~~~~~f~~~L~eg~vy~is~F~V~~~~~~yk~t~~~y~I   78 (86)
T cd04480           2 ICVRVLRLWDVYNNASGESLEMVLVDEKGNRIHATIPKRLAAKFRPLLKEGKWYTISNFEVAPNTGSYRPTDHPYKI   78 (86)
T ss_pred             EEEEEEEEEECCCCCCCCEEEEEEECCCCCEEEEEECHHHHHHHHHHCCCCCEEEECCEEEEECCCCEEEECCCEEE
T ss_conf             89999996866788997178899987899999999948998777755100629998719999689981781996899


No 496
>pfam00436 SSB Single-strand binding protein family. This family includes single stranded binding proteins and also the primosomal replication protein N (PriB). PriB forms a complex with PriA, PriC and ssDNA.
Probab=75.72  E-value=5.9  Score=19.21  Aligned_cols=64  Identities=14%  Similarity=0.320  Sum_probs=42.6

Q ss_pred             EEEEEEEEEEEEEECC-CCCCE---EEEEEE-----------CCCCEEEEEEECCCHHHHHHHCCCCCEEEEEEEEEEC
Q ss_conf             8999999989754215-89833---899998-----------1893699999518878998732898889999899731
Q gi|254780945|r   69 IVTITGYISQHSSFQL-QKRRP---YKILLN-----------DGTGEITLLFFYRKTEMLKNVFFEGRKITVTGKIKKL  132 (700)
Q Consensus        69 ~vti~g~V~~~~~~~~-~~r~~---~~v~v~-----------D~tg~i~lvfFn~~~~yl~k~lk~G~~v~vsGKv~~~  132 (700)
                      .+++.|.+.+-...+. ...++   +.+.+.           +.+.-+.++.|+.....+.+.+++|+.+.|.|+++..
T Consensus         3 ~v~l~G~l~~dpe~r~~~~g~~~~~f~va~~~~~~~~~~~~~~~t~~~~v~~~g~~A~~~~~~l~KG~~V~V~G~l~~~   81 (104)
T pfam00436         3 KVILVGRLTRDPELRYTPNGNAVANFTLAVNRRFKDQNGESDEETDFIRVVVWGKLAENAAEYLKKGSLVYVEGRLRTR   81 (104)
T ss_pred             EEEEEEEECCCCEEEECCCCCEEEEEEEEEEECCCCCCCCCCCCCEEEEEEECCHHHHHHHHCCCCCCEEEEEEEEEEE
T ss_conf             9999999056989999689988999999996021346787024558998773054465431227899799999997811


No 497
>pfam00308 Bac_DnaA Bacterial dnaA protein.
Probab=75.70  E-value=5.9  Score=19.20  Aligned_cols=48  Identities=19%  Similarity=0.159  Sum_probs=27.0

Q ss_pred             HHHHHHHHHCCCCCCE-EEEEECCCCCHHHHHHHHHHHHHHH--HCCEEEEEH
Q ss_conf             9999998410013430-7886214422369999997334443--054588612
Q gi|254780945|r  280 AIKDILQDMSQKNRML-RILQGDVGSGKTLVALIAMAAAVEA--GGQAVIMAP  329 (700)
Q Consensus       280 ai~eI~~Dl~~~~pM~-RLLQGDVGSGKTiVA~~A~l~~~~~--G~Q~alMaP  329 (700)
                      +.+.|.+.-..  ++| =.|.|..|||||=..-.++..+...  +..+.++-+
T Consensus        22 ~~~~i~~~~~~--~~npl~i~G~~G~GKTHLLqA~~~~~~~~~~~~~v~yl~~   72 (219)
T pfam00308        22 AALAVAEAPGK--AYNPLFIYGGVGLGKTHLLHAIGNYALRNFPNLRVVYLTS   72 (219)
T ss_pred             HHHHHHHCCCC--CCCCEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEEEH
T ss_conf             99999967587--6782699889999888999999999998499982888439


No 498
>pfam00448 SRP54 SRP54-type protein, GTPase domain. This family includes relatives of the G-domain of the SRP54 family of proteins.
Probab=75.67  E-value=6  Score=19.20  Aligned_cols=87  Identities=22%  Similarity=0.229  Sum_probs=0.0

Q ss_pred             CCEEEEEECCCCCHHHHHHHHHHHHHHHHCCEEEEEHHHHHHHHHHHHHHHHCCCCCCEEEEE-ECCCCHHHHHHHHHHH
Q ss_conf             430788621442236999999733444305458861279999999986211014578658996-2464225667687762
Q gi|254780945|r  293 RMLRILQGDVGSGKTLVALIAMAAAVEAGGQAVIMAPIGILAQQHYEFIKKYTQNTQIIVEII-TGNMPQAHRRKALERI  371 (700)
Q Consensus       293 pM~RLLQGDVGSGKTiVA~~A~l~~~~~G~Q~alMaPTEILA~QH~~~~~~~~~~~~i~v~lL-tg~~~~~er~~i~~~i  371 (700)
                      |---++-|=-|+|||--++--++.....|+.+++.+= ..----=.+.++.|-+.+++++... +++.+..-.++.++..
T Consensus         1 P~vi~lvGptGvGKTTTiaKLAa~~~~~~~~V~lit~-Dt~R~gA~eQL~~ya~~l~v~~~~~~~~~d~~~~~~~~l~~~   79 (196)
T pfam00448         1 PNVILLVGLQGSGKTTTIAKLAAYLKKQGKKVLLVAA-DTFRAAAIEQLKQLAERLGVPVFGSGTGSDPAAVAFDAVEKA   79 (196)
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHHHHHCCCEEEEEEC-CCCCHHHHHHHHHHHHHCCCEEEECCCCCCHHHHHHHHHHHH
T ss_conf             9699998999998899999999999977992899975-877688999999999863981781487778789999999998


Q ss_pred             CCCCCEEEE
Q ss_conf             134754864
Q gi|254780945|r  372 AHGQAHIII  380 (700)
Q Consensus       372 ~~G~~~iiI  380 (700)
                      +....|+|+
T Consensus        80 ~~~~~D~Il   88 (196)
T pfam00448        80 KAENYDVVL   88 (196)
T ss_pred             HHCCCCEEE
T ss_conf             846899999


No 499
>PHA02518 ParA-like protein; Provisional
Probab=75.57  E-value=2.6  Score=21.99  Aligned_cols=25  Identities=28%  Similarity=0.341  Sum_probs=0.0

Q ss_pred             CCCHHHHHHHHHHHHHHHHCCEEEE
Q ss_conf             4223699999973344430545886
Q gi|254780945|r  303 GSGKTLVALIAMAAAVEAGGQAVIM  327 (700)
Q Consensus       303 GSGKTiVA~~A~l~~~~~G~Q~alM  327 (700)
                      |+|||-+|+.-+......|+.|+++
T Consensus        11 GvGKTT~a~nLA~~la~~G~~Vlli   35 (211)
T PHA02518         11 GAGKTTVATNLASWLHADGHKVLLV   35 (211)
T ss_pred             CCHHHHHHHHHHHHHHHCCCCEEEE
T ss_conf             9749999999999999789948999


No 500
>PRK07276 DNA polymerase III subunit delta'; Validated
Probab=75.50  E-value=4  Score=20.59  Aligned_cols=46  Identities=13%  Similarity=0.077  Sum_probs=0.0

Q ss_pred             CCCHHHHHHHHHHHHHHCCCCCCEE-EEEECCCCCHHHHHHHHHHHH
Q ss_conf             6798899999999984100134307-886214422369999997334
Q gi|254780945|r  272 SPTKSQESAIKDILQDMSQKNRMLR-ILQGDVGSGKTLVALIAMAAA  317 (700)
Q Consensus       272 ~LT~~Q~~ai~eI~~Dl~~~~pM~R-LLQGDVGSGKTiVA~~A~l~~  317 (700)
                      +++.-|-++++...+-+.+++--+- |+.|++|+|++..++..++.|
T Consensus         2 ~~~~~Qp~i~~~l~~~i~~~rl~HAyLf~G~~Gk~~~A~~~A~~l~C   48 (290)
T PRK07276          2 DLAQKQPKLFQRFQTILEQDRLNHAYLFSGDFASFEMALFLAQSLFC   48 (290)
T ss_pred             CHHHHHHHHHHHHHHHHHCCCCCEEEECCCCCCHHHHHHHHHHHHHC
T ss_conf             87787899999999999849965054216986879999999999818


Done!