Query         gi|254780619|ref|YP_003065032.1| primosome assembly protein PriA [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 731
No_of_seqs    228 out of 3255
Neff          7.4 
Searched_HMMs 39220
Date          Sun May 29 23:56:40 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254780619.hhm -d /home/congqian_1/database/cdd/Cdd.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 COG1198 PriA Primosomal protei 100.0       0       0 1597.9  59.3  714   14-730     2-730 (730)
  2 PRK05580 primosome assembly pr 100.0       0       0 1565.1  61.3  694   13-730     3-699 (699)
  3 TIGR00595 priA primosomal prot 100.0       0       0 1025.4  36.8  507  222-728     1-524 (524)
  4 TIGR00643 recG ATP-dependent D 100.0 2.2E-42       0  343.3  24.7  354  195-631   303-683 (721)
  5 TIGR00580 mfd transcription-re 100.0 1.2E-42       0  345.4  22.6  344  195-634   504-870 (997)
  6 PRK10917 ATP-dependent DNA hel 100.0 9.8E-42       0  338.2  25.3  362  195-643   253-635 (677)
  7 PRK10689 transcription-repair  100.0 2.2E-41       0  335.6  24.9  314  194-602   595-916 (1148)
  8 COG1197 Mfd Transcription-repa 100.0 2.1E-38 5.4E-43  312.8  24.2  345  194-633   589-951 (1139)
  9 COG1200 RecG RecG-like helicas 100.0 4.4E-38 1.1E-42  310.3  23.5  356  195-638   258-637 (677)
 10 COG4098 comFA Superfamily II D 100.0 1.4E-26 3.5E-31  222.5  21.4  316  198-607    97-418 (441)
 11 PRK01297 ATP-dependent RNA hel  99.8 2.1E-17 5.2E-22  152.3  23.5  318  157-600    86-434 (472)
 12 PRK11192 ATP-dependent RNA hel  99.8 8.7E-18 2.2E-22  155.1  21.1  349  159-639     7-383 (417)
 13 PRK10590 ATP-dependent RNA hel  99.8 7.7E-17   2E-21  147.9  22.2  348  159-636     5-378 (457)
 14 PRK04537 ATP-dependent RNA hel  99.8 7.3E-17 1.9E-21  148.1  21.3  317  158-600    12-359 (574)
 15 TIGR00631 uvrb excinuclease AB  99.8 8.4E-17 2.1E-21  147.6  19.1  129  495-644   456-586 (667)
 16 PRK11776 ATP-dependent RNA hel  99.8 2.6E-16 6.5E-21  143.9  21.2  378  159-662     8-409 (459)
 17 PRK13766 Hef nuclease; Provisi  99.8 2.7E-17   7E-22  151.3  15.9  153  192-361     9-173 (764)
 18 PRK05298 excinuclease ABC subu  99.8 2.5E-16 6.5E-21  143.9  20.1  410  198-636    13-586 (657)
 19 PRK04837 ATP-dependent RNA hel  99.8 8.9E-16 2.3E-20  139.8  21.7  325  158-600    12-358 (423)
 20 PRK11634 ATP-dependent RNA hel  99.8 3.3E-16 8.5E-21  143.0  18.9  315  158-600     9-347 (629)
 21 PRK01172 ski2-like helicase; P  99.8 1.8E-15 4.5E-20  137.5  22.5  369  160-618     6-392 (674)
 22 PRK02362 ski2-like helicase; P  99.7 1.7E-16 4.4E-21  145.2  16.2  380  159-618     5-412 (736)
 23 PRK00254 ski2-like helicase; P  99.7 8.3E-16 2.1E-20  140.0  18.9  378  159-618     5-401 (717)
 24 COG1204 Superfamily II helicas  99.7 3.7E-16 9.5E-21  142.6  15.8  379  198-629    31-434 (766)
 25 PTZ00110 helicase; Provisional  99.7 4.8E-14 1.2E-18  126.5  23.3  327  158-607   185-536 (602)
 26 COG0556 UvrB Helicase subunit   99.7 4.9E-15 1.2E-19  134.1  17.1  109  495-614   455-565 (663)
 27 PRK11057 ATP-dependent DNA hel  99.7 2.8E-13 7.1E-18  120.7  23.0  319  198-617    25-355 (607)
 28 COG0513 SrmB Superfamily II DN  99.6 8.1E-13 2.1E-17  117.1  22.7  341  159-614    33-390 (513)
 29 PRK13767 ATP-dependent helicas  99.6 6.8E-13 1.7E-17  117.7  21.9  324  198-606    32-399 (878)
 30 COG1111 MPH1 ERCC4-like helica  99.6 3.9E-13   1E-17  119.5  16.7  367  201-604    18-481 (542)
 31 KOG0952 consensus               99.6   1E-12 2.6E-17  116.4  17.2  347  194-605   106-491 (1230)
 32 COG1061 SSL2 DNA or RNA helica  99.5 1.2E-12 3.1E-17  115.7  17.0  335  194-606    32-393 (442)
 33 pfam00270 DEAD DEAD/DEAH box h  99.5 1.5E-13 3.7E-18  122.8  12.1  151  200-365     1-164 (167)
 34 smart00487 DEXDc DEAD-like hel  99.5 4.1E-13   1E-17  119.4  13.8  157  196-361     6-171 (201)
 35 COG1203 CRISPR-associated heli  99.5 1.6E-12 4.2E-17  114.8  16.3  318  198-605   195-550 (733)
 36 COG1205 Distinct helicase fami  99.5 3.1E-11 7.8E-16  105.1  20.5  332  199-616    71-431 (851)
 37 KOG0331 consensus               99.5 5.4E-12 1.4E-16  110.8  16.3  282  223-600   133-443 (519)
 38 COG1201 Lhr Lhr-like helicases  99.4   8E-11   2E-15  101.9  20.3  303  197-593    21-349 (814)
 39 COG0514 RecQ Superfamily II DN  99.4 1.4E-10 3.7E-15   99.9  21.2  316  199-616    18-348 (590)
 40 cd00046 DEXDc DEAD-like helica  99.4 2.1E-12 5.4E-17  113.9  11.3  132  220-360     2-144 (144)
 41 TIGR03158 cas3_cyano CRISPR-as  99.4 2.4E-11 6.2E-16  105.8  16.6  153  203-363     2-194 (357)
 42 KOG0354 consensus               99.4 2.3E-10 5.8E-15   98.4  20.5  380  194-610    58-534 (746)
 43 KOG0330 consensus               99.4 5.7E-11 1.5E-15  103.0  15.4  349  160-637    66-428 (476)
 44 COG1202 Superfamily II helicas  99.3 2.2E-11 5.7E-16  106.1  11.8  294  222-601   236-549 (830)
 45 KOG0345 consensus               99.3 2.6E-10 6.7E-15   97.9  16.9  301  198-601    28-360 (567)
 46 KOG0344 consensus               99.3 3.9E-10 9.9E-15   96.6  16.4  303  219-613   174-503 (593)
 47 PRK09401 reverse gyrase; Revie  99.3 3.2E-09   8E-14   89.7  18.9  269  198-555    78-398 (1176)
 48 PRK09694 hypothetical protein;  99.3 2.1E-09 5.4E-14   91.0  17.9  312  198-595   288-666 (878)
 49 KOG0333 consensus               99.3 5.3E-09 1.3E-13   87.9  19.7  315  220-637   284-647 (673)
 50 KOG0348 consensus               99.2 1.6E-09   4E-14   92.0  15.7  347  198-616   159-565 (708)
 51 KOG0951 consensus               99.2 1.1E-09 2.7E-14   93.3  13.4  352  198-606   309-703 (1674)
 52 COG1110 Reverse gyrase [DNA re  99.2 4.9E-09 1.2E-13   88.2  16.3  118  199-323    83-212 (1187)
 53 PRK09751 putative ATP-dependen  99.2 4.4E-09 1.1E-13   88.6  15.7  312  227-592     5-371 (1490)
 54 PRK11448 hsdR type I restricti  99.1 1.1E-09 2.8E-14   93.2  11.9  170  197-373   415-609 (1126)
 55 cd00268 DEADc DEAD-box helicas  99.1   4E-09   1E-13   88.9  13.9  174  160-368     4-192 (203)
 56 KOG0342 consensus               99.1 5.8E-09 1.5E-13   87.6  14.5  326  198-614   104-446 (543)
 57 KOG0335 consensus               99.0 1.1E-07 2.8E-12   77.9  17.3  326  198-614    96-453 (482)
 58 pfam04851 ResIII Type III rest  99.0 1.6E-09 4.1E-14   91.9   7.7   64  198-266     3-66  (103)
 59 TIGR01587 cas3_core CRISPR-ass  99.0 4.1E-08 1.1E-12   81.1  14.9  328  221-631     2-418 (424)
 60 COG4096 HsdR Type I site-speci  99.0 1.3E-08 3.4E-13   84.9  11.7  323  196-592   163-525 (875)
 61 PRK11664 ATP-dependent RNA hel  99.0 1.1E-07 2.7E-12   78.0  15.7   70  236-305   201-273 (812)
 62 KOG0346 consensus               98.9 8.9E-09 2.3E-13   86.2   9.4  385  158-640    22-440 (569)
 63 KOG0338 consensus               98.9 1.4E-07 3.7E-12   77.0  15.1  290  225-616   225-544 (691)
 64 KOG0343 consensus               98.9 1.7E-07 4.4E-12   76.3  14.8  313  160-600    74-417 (758)
 65 KOG0351 consensus               98.8 3.6E-07 9.2E-12   73.9  14.8  322  199-617   265-604 (941)
 66 COG4581 Superfamily II RNA hel  98.8 1.3E-07 3.3E-12   77.4  12.2  143  196-361   117-271 (1041)
 67 KOG0350 consensus               98.7 1.8E-06 4.6E-11   68.6  16.0  331  199-600   160-535 (620)
 68 KOG0334 consensus               98.7 3.5E-06   9E-11   66.4  17.2  287  200-598   389-713 (997)
 69 TIGR01389 recQ ATP-dependent D  98.7 2.8E-06   7E-11   67.2  16.4  336  199-634    14-362 (607)
 70 KOG0339 consensus               98.7 3.2E-06   8E-11   66.7  16.7  289  226-606   268-574 (731)
 71 KOG4284 consensus               98.7   5E-08 1.3E-12   80.5   7.4  312  200-607    49-379 (980)
 72 KOG0328 consensus               98.7 1.2E-08 2.9E-13   85.4   3.9  323  200-626    51-389 (400)
 73 KOG0327 consensus               98.7 5.8E-07 1.5E-11   72.4  11.5  324  200-626    50-386 (397)
 74 KOG0336 consensus               98.7 1.5E-05 3.9E-10   61.5  18.5  283  220-599   252-566 (629)
 75 KOG0347 consensus               98.6 1.2E-06   3E-11   70.0  12.3  348  160-606   186-570 (731)
 76 cd00079 HELICc Helicase superf  98.6 1.9E-07 4.8E-12   76.1   7.4  116  408-600    15-130 (131)
 77 KOG0352 consensus               98.6 4.8E-06 1.2E-10   65.3  13.7  333  199-619    21-376 (641)
 78 TIGR01054 rgy reverse gyrase;   98.5 7.7E-07   2E-11   71.4   8.1  114  201-322    87-217 (1843)
 79 TIGR00614 recQ_fam ATP-depende  98.4 0.00037 9.5E-09   50.9  20.1  344  199-632    12-377 (497)
 80 KOG0947 consensus               98.4 5.8E-06 1.5E-10   64.7  10.4  138  198-359   297-443 (1248)
 81 KOG0332 consensus               98.4 4.7E-06 1.2E-10   65.4   9.3  285  224-600   135-438 (477)
 82 PRK04914 ATP-dependent helicas  98.3   2E-05 5.2E-10   60.5  11.8  156  198-366   151-323 (955)
 83 KOG0326 consensus               98.3 8.2E-06 2.1E-10   63.5   9.5  279  226-604   130-429 (459)
 84 COG4889 Predicted helicase [Ge  98.3  0.0002   5E-09   53.0  16.0  369  196-606   159-589 (1518)
 85 PRK12904 preprotein translocas  98.2 0.00066 1.7E-08   49.0  17.1   77  226-308   102-181 (833)
 86 KOG0340 consensus               98.2 0.00024 6.2E-09   52.3  14.9  117  198-323    29-162 (442)
 87 COG1643 HrpA HrpA-like helicas  98.2 5.2E-05 1.3E-09   57.4  11.4   59  247-305   260-321 (845)
 88 smart00490 HELICc helicase sup  98.2 1.3E-06 3.3E-11   69.7   3.1   81  496-592     1-81  (82)
 89 pfam07652 Flavi_DEAD Flaviviru  98.1 2.1E-05 5.2E-10   60.5   8.2  123  221-361     5-135 (146)
 90 KOG0337 consensus               98.1 9.3E-05 2.4E-09   55.5  11.4  244  225-562    65-337 (529)
 91 PRK11131 ATP-dependent RNA hel  98.0 0.00086 2.2E-08   48.1  14.8  147  198-369    74-237 (1295)
 92 PRK12906 secA preprotein trans  97.9 0.00036 9.2E-09   51.0  12.1   92  226-323   101-209 (823)
 93 pfam00271 Helicase_C Helicase   97.9 7.4E-06 1.9E-10   63.9   2.9   72  507-592     6-77  (78)
 94 pfam05876 Terminase_GpA Phage   97.9 0.00022 5.7E-09   52.6   9.8  159  198-362    16-181 (552)
 95 KOG0920 consensus               97.8 0.00036 9.2E-09   51.0  10.6  330  200-599   175-538 (924)
 96 PRK10917 ATP-dependent DNA hel  97.8 0.00036 9.2E-09   51.0  10.2   85  237-321   458-552 (677)
 97 TIGR00643 recG ATP-dependent D  97.7 0.00028 7.2E-09   51.8   8.2   87  232-320   514-614 (721)
 98 pfam00176 SNF2_N SNF2 family N  97.6  0.0056 1.4E-07   41.9  13.6  119  203-325     2-130 (295)
 99 COG1200 RecG RecG-like helicas  97.6 0.00067 1.7E-08   48.9   8.7   92  229-321   457-558 (677)
100 PRK11747 dinG ATP-dependent DN  97.4  0.0058 1.5E-07   41.7  11.8   65  200-264    27-94  (697)
101 PRK08074 bifunctional ATP-depe  97.4  0.0048 1.2E-07   42.4  11.4  127  199-326   259-468 (932)
102 pfam09848 DUF2075 Uncharacteri  97.4  0.0012   3E-08   47.0   7.8   83  219-326     2-91  (348)
103 PRK07952 DNA replication prote  97.4  0.0016 4.2E-08   45.9   8.4   93  198-323    73-168 (242)
104 KOG0950 consensus               97.3  0.0033 8.3E-08   43.7   9.6  136  221-367   242-398 (1008)
105 KOG1805 consensus               97.3   0.004   1E-07   43.0   9.6  122  195-324   666-806 (1100)
106 COG1198 PriA Primosomal protei  97.2  0.0085 2.2E-07   40.5  10.4   26  494-521   540-566 (730)
107 PRK10689 transcription-repair   97.2  0.0043 1.1E-07   42.7   9.0   75  488-565   655-732 (1148)
108 cd00079 HELICc Helicase superf  97.2  0.0099 2.5E-07   40.0  10.7   92  228-320    10-102 (131)
109 pfam05707 Zot Zonular occluden  97.2  0.0014 3.5E-08   46.6   6.2  113  219-361     1-117 (183)
110 KOG0341 consensus               97.1  0.0014 3.5E-08   46.5   5.5   96  523-641   458-555 (610)
111 PRK05582 DNA topoisomerase I;   97.0   0.001 2.6E-08   47.6   4.4   40  447-486   622-670 (692)
112 PHA00350 putative assembly pro  97.0  0.0033 8.3E-08   43.7   6.6  125  219-370     2-153 (402)
113 pfam03796 DnaB_C DnaB-like hel  96.9  0.0097 2.5E-07   40.0   8.8   50  219-269    20-70  (186)
114 pfam07517 SecA_DEAD SecA DEAD-  96.9  0.0081 2.1E-07   40.6   8.4  128  222-373    94-238 (381)
115 PRK05580 primosome assembly pr  96.9   0.028 7.1E-07   36.5  11.1   25  217-241   239-264 (699)
116 cd01122 GP4d_helicase GP4d_hel  96.8   0.021 5.4E-07   37.4  10.0  138  219-358    31-189 (271)
117 TIGR03420 DnaA_homol_Hda DnaA   96.8   0.026 6.7E-07   36.8  10.4   37  217-253    37-73  (226)
118 PRK12377 putative replication   96.7   0.027 6.9E-07   36.6   9.9   95  195-323    75-172 (248)
119 pfam02562 PhoH PhoH-like prote  96.7  0.0071 1.8E-07   41.1   6.9  168  197-398     3-189 (205)
120 TIGR00373 TIGR00373 conserved   96.7  0.0019 4.9E-08   45.4   3.9   64  408-504    93-158 (168)
121 PRK08620 DNA topoisomerase III  96.7  0.0012 3.1E-08   47.0   2.7   51  444-494   608-666 (726)
122 PRK08620 DNA topoisomerase III  96.6  0.0014 3.6E-08   46.5   2.7   53  421-476   616-680 (726)
123 PRK05636 replicative DNA helic  96.6   0.077   2E-06   33.2  12.2  131  220-357   269-424 (507)
124 COG1197 Mfd Transcription-repa  96.6   0.018 4.5E-07   38.1   8.2  165  488-662   649-853 (1139)
125 KOG1803 consensus               96.6  0.0054 1.4E-07   42.0   5.5   67  196-267   183-250 (649)
126 KOG0948 consensus               96.6    0.03 7.6E-07   36.3   9.2  369  197-616   128-551 (1041)
127 PRK05642 DNA replication initi  96.6   0.034 8.7E-07   35.9   9.4   48  204-252    30-79  (234)
128 TIGR01074 rep ATP-dependent DN  96.5  0.0041 1.1E-07   42.9   4.6  117  198-350     3-123 (677)
129 COG0610 Type I site-specific r  96.5    0.09 2.3E-06   32.6  11.8  331  219-592   274-636 (962)
130 PRK08938 DNA topoisomerase I;   96.5  0.0044 1.1E-07   42.7   4.5   60  425-486   588-668 (692)
131 PRK10590 ATP-dependent RNA hel  96.5   0.094 2.4E-06   32.5  11.4  123  223-356   224-349 (457)
132 pfam00580 UvrD-helicase UvrD/R  96.5  0.0047 1.2E-07   42.4   4.5   67  199-272     1-71  (494)
133 COG1201 Lhr Lhr-like helicases  96.4   0.018 4.5E-07   38.0   7.4   71  236-306   243-313 (814)
134 cd01120 RecA-like_NTPases RecA  96.4   0.038 9.6E-07   35.5   8.9   45  221-266     2-46  (165)
135 PRK08413 consensus              96.4  0.0043 1.1E-07   42.7   4.1   49  446-494   570-631 (733)
136 PRK07219 DNA topoisomerase I;   96.4  0.0031 7.9E-08   43.8   3.3   39  447-485   672-725 (769)
137 PRK08082 consensus              96.4     0.1 2.7E-06   32.2  12.2  132  219-358   204-362 (453)
138 CHL00122 secA preprotein trans  96.4     0.1 2.6E-06   32.2  11.0   92  226-323    97-205 (891)
139 PRK10919 ATP-dependent DNA hel  96.3  0.0072 1.8E-07   41.1   4.7   25  538-562   551-575 (672)
140 PRK11634 ATP-dependent RNA hel  96.3    0.12   3E-06   31.7  11.8  125  224-361   225-352 (629)
141 PRK11192 ATP-dependent RNA hel  96.2   0.049 1.3E-06   34.7   8.7  119  228-357   231-352 (417)
142 TIGR02237 recomb_radB DNA repa  96.2   0.014 3.6E-07   38.8   5.9  118  220-355    14-154 (223)
143 PRK12326 preprotein translocas  96.2   0.025 6.3E-07   37.0   7.2   92  226-323   110-218 (775)
144 PRK05298 excinuclease ABC subu  96.2   0.059 1.5E-06   34.1   9.1  277  224-572   249-563 (657)
145 PRK12903 secA preprotein trans  96.2   0.052 1.3E-06   34.5   8.6   92  226-323    99-207 (885)
146 PRK13767 ATP-dependent helicas  96.2   0.023 5.8E-07   37.2   6.7   84  237-320   275-364 (878)
147 COG4098 comFA Superfamily II D  96.1   0.047 1.2E-06   34.8   8.2   85  236-324   295-383 (441)
148 PRK13104 secA preprotein trans  96.1   0.097 2.5E-06   32.4   9.5   92  226-323   103-211 (896)
149 PRK07263 consensus              96.1    0.15 3.9E-06   30.9  11.8  132  219-357   204-361 (453)
150 TIGR02928 TIGR02928 orc1/cdc6   96.0   0.057 1.5E-06   34.2   8.2  134  196-346    18-168 (383)
151 TIGR03015 pepcterm_ATPase puta  96.0   0.083 2.1E-06   32.9   9.0   75  198-273    23-98  (269)
152 cd00984 DnaB_C DnaB helicase C  96.0    0.11 2.8E-06   32.0   9.6  136  219-359    14-172 (242)
153 PRK00349 uvrA excinuclease ABC  96.0   0.028 7.2E-07   36.5   6.5   67  409-489   707-773 (944)
154 PRK01297 ATP-dependent RNA hel  96.0   0.088 2.2E-06   32.7   9.0   23  232-255   108-130 (472)
155 PRK09137 DNA topoisomerase I;   96.0   0.015 3.7E-07   38.7   4.9   29  447-475   591-624 (761)
156 KOG0353 consensus               96.0    0.17 4.2E-06   30.6  17.0  298  219-605   111-467 (695)
157 COG3973 Superfamily I DNA and   96.0   0.016 4.1E-07   38.3   5.1   53  198-256   212-270 (747)
158 KOG0953 consensus               95.9   0.018 4.5E-07   38.0   5.3  103  531-638   402-515 (700)
159 PRK08903 hypothetical protein;  95.9    0.17 4.4E-06   30.5  10.3   36  219-254    43-78  (227)
160 PRK11776 ATP-dependent RNA hel  95.9   0.098 2.5E-06   32.4   8.9  126  223-361   221-349 (459)
161 KOG0926 consensus               95.9   0.051 1.3E-06   34.6   7.4  204  196-429   255-489 (1172)
162 PRK13107 preprotein translocas  95.8    0.17 4.2E-06   30.6   9.8   92  226-323   103-211 (908)
163 PRK04537 ATP-dependent RNA hel  95.8     0.1 2.6E-06   32.2   8.6  121  226-357   239-362 (574)
164 smart00382 AAA ATPases associa  95.8   0.063 1.6E-06   33.8   7.4   46  219-264     3-48  (148)
165 PRK08116 hypothetical protein;  95.7   0.094 2.4E-06   32.5   8.3  109  219-367   109-221 (262)
166 TIGR02759 TraD_Ftype type IV c  95.7   0.013 3.4E-07   39.0   4.0  126  219-371   209-348 (613)
167 PRK06835 DNA replication prote  95.7   0.049 1.3E-06   34.6   6.8   60  204-268   166-228 (330)
168 KOG0329 consensus               95.7   0.014 3.7E-07   38.8   4.0  135  221-364    82-231 (387)
169 COG1203 CRISPR-associated heli  95.6   0.067 1.7E-06   33.6   7.2   24  523-546   451-475 (733)
170 KOG0951 consensus               95.6    0.22 5.6E-06   29.7  10.3  195  221-436  1162-1374(1674)
171 PRK13103 secA preprotein trans  95.6    0.13 3.3E-06   31.4   8.6   92  226-323   103-211 (913)
172 smart00489 DEXDc3 DEAD-like he  95.6    0.13 3.3E-06   31.4   8.5   45  200-245    10-54  (289)
173 smart00488 DEXDc2 DEAD-like he  95.6    0.13 3.3E-06   31.4   8.5   45  200-245    10-54  (289)
174 PRK06904 replicative DNA helic  95.6    0.23 5.9E-06   29.5   9.7  132  219-357   222-381 (472)
175 PRK08084 DNA replication initi  95.6    0.21 5.5E-06   29.8   9.6   37  216-253    43-80  (235)
176 PRK11057 ATP-dependent DNA hel  95.5   0.041   1E-06   35.3   5.8   86  245-333   235-325 (607)
177 KOG0987 consensus               95.5   0.029 7.4E-07   36.4   5.1   77  196-273   115-194 (540)
178 PRK09361 radB DNA repair and r  95.5    0.12   3E-06   31.8   8.1   37  219-255    24-60  (224)
179 pfam00308 Bac_DnaA Bacterial d  95.5   0.078   2E-06   33.1   7.1  167  207-421    23-201 (219)
180 COG0468 RecA RecA/RadA recombi  95.5     0.1 2.6E-06   32.2   7.7   88  219-321    61-148 (279)
181 cd01123 Rad51_DMC1_radA Rad51_  95.5    0.19 4.7E-06   30.3   9.0   43  219-261    20-68  (235)
182 cd01393 recA_like RecA is a  b  95.5    0.15 3.7E-06   31.0   8.5   48  219-266    20-73  (226)
183 PRK11054 helD DNA helicase IV;  95.5   0.048 1.2E-06   34.8   6.0   77  196-279   194-277 (684)
184 COG1199 DinG Rad3-related DNA   95.5    0.11 2.7E-06   32.1   7.8   77  526-602   517-615 (654)
185 PRK00149 dnaA chromosomal repl  95.5   0.028 7.2E-07   36.5   4.8  116  205-361   132-252 (447)
186 TIGR00580 mfd transcription-re  95.4     0.1 2.6E-06   32.2   7.5  158  498-662   577-771 (997)
187 PRK08006 replicative DNA helic  95.4    0.26 6.7E-06   29.1  10.6  133  219-358   225-384 (471)
188 COG2888 Predicted Zn-ribbon RN  95.4  0.0074 1.9E-07   41.0   1.6   40  436-483     9-57  (61)
189 COG0593 DnaA ATPase involved i  95.3    0.22 5.6E-06   29.7   9.0   39  210-249   105-144 (408)
190 PRK04837 ATP-dependent RNA hel  95.3    0.17 4.3E-06   30.5   8.3  119  228-357   240-361 (423)
191 TIGR01448 recD_rel helicase, R  95.2   0.058 1.5E-06   34.1   5.8  130  197-363   349-498 (769)
192 pfam04216 FdhE Protein involve  95.2  0.0098 2.5E-07   40.0   1.8   45  446-490   167-219 (283)
193 PRK09137 DNA topoisomerase I;   95.2    0.03 7.7E-07   36.3   4.2   64  423-489   598-693 (761)
194 COG0210 UvrD Superfamily I DNA  95.2   0.068 1.7E-06   33.6   6.0   26  538-563   554-579 (655)
195 PRK04023 DNA polymerase II lar  95.1   0.022 5.6E-07   37.4   3.3   61  413-485   616-679 (1128)
196 PRK03564 formate dehydrogenase  95.1  0.0087 2.2E-07   40.4   1.3   33  461-493   210-243 (307)
197 COG0556 UvrB Helicase subunit   95.1    0.21 5.3E-06   29.9   8.3  118  199-320    13-160 (663)
198 COG1110 Reverse gyrase [DNA re  95.1   0.023 5.9E-07   37.2   3.4   55  244-304   333-390 (1187)
199 PRK10416 cell division protein  95.1    0.29 7.4E-06   28.8   9.0   39  217-255   294-332 (499)
200 TIGR00963 secA preprotein tran  95.1    0.12 3.1E-06   31.7   7.0  265  226-546    81-445 (904)
201 TIGR00631 uvrb excinuclease AB  95.0   0.063 1.6E-06   33.9   5.5  146  199-348    10-190 (667)
202 cd01127 TrwB Bacterial conjuga  95.0   0.078   2E-06   33.1   5.9   69  220-294    44-112 (410)
203 COG3587 Restriction endonuclea  95.0    0.15 3.9E-06   30.9   7.3   31  226-256    82-114 (985)
204 PRK10536 hypothetical protein;  95.0    0.12   3E-06   31.8   6.8   54  196-254    57-112 (262)
205 PRK08760 replicative DNA helic  95.0    0.34 8.8E-06   28.2   9.7  131  219-357   230-386 (476)
206 PRK06526 transposase; Provisio  94.9   0.092 2.3E-06   32.6   6.1  130  197-369    79-209 (254)
207 PRK08506 replicative DNA helic  94.9    0.36 9.1E-06   28.1  11.2  132  219-357   194-350 (473)
208 KOG0922 consensus               94.9    0.23 5.8E-06   29.6   8.0  136  218-370    66-215 (674)
209 PRK08181 transposase; Validate  94.9    0.25 6.3E-06   29.3   8.1  132  197-370    86-218 (269)
210 KOG0952 consensus               94.8   0.068 1.7E-06   33.6   5.2   73  232-304   335-429 (1230)
211 cd01394 radB RadB. The archaea  94.8    0.24 6.1E-06   29.4   8.0   38  219-256    20-57  (218)
212 PRK08074 bifunctional ATP-depe  94.8     0.1 2.7E-06   32.2   6.1   33  525-557   797-829 (932)
213 PRK08727 hypothetical protein;  94.8    0.38 9.7E-06   27.9  10.0   36  217-252    40-75  (233)
214 PRK09694 hypothetical protein;  94.8     0.2   5E-06   30.1   7.5   39  389-430   443-481 (878)
215 KOG0344 consensus               94.8   0.036 9.1E-07   35.7   3.6   83  223-308   273-357 (593)
216 PRK06319 DNA topoisomerase I/S  94.8   0.045 1.2E-06   34.9   4.2   10  358-369   494-503 (864)
217 KOG0924 consensus               94.7    0.39 9.9E-06   27.8   9.7  134  218-369   371-519 (1042)
218 PRK11788 hypothetical protein;  94.6   0.011 2.9E-07   39.5   0.8   32  460-491   351-383 (389)
219 TIGR03600 phage_DnaB phage rep  94.6    0.42 1.1E-05   27.6  10.7  131  219-357   195-351 (421)
220 COG1435 Tdk Thymidine kinase [  94.6     0.3 7.8E-06   28.6   8.1  105  220-356     6-116 (201)
221 KOG1002 consensus               94.6    0.38 9.6E-06   27.9   8.5  120  198-327   184-329 (791)
222 PRK09200 preprotein translocas  94.6    0.42 1.1E-05   27.5  11.3   92  226-323    99-212 (799)
223 KOG0736 consensus               94.6    0.28 7.1E-06   28.9   7.8  109  218-365   431-546 (953)
224 PRK08413 consensus              94.6   0.046 1.2E-06   34.9   3.8   27  433-459   586-627 (733)
225 cd00983 recA RecA is a  bacter  94.5    0.26 6.7E-06   29.1   7.6   79  219-301    56-137 (325)
226 pfam01695 IstB IstB-like ATP b  94.5    0.12 3.1E-06   31.7   5.9   48  216-268    45-92  (178)
227 PRK05595 replicative DNA helic  94.5    0.44 1.1E-05   27.4  11.7  130  219-357   202-358 (444)
228 PRK11773 uvrD DNA-dependent he  94.5   0.021 5.5E-07   37.4   2.0   33  538-574   553-585 (722)
229 PRK09354 recA recombinase A; P  94.5    0.35 8.9E-06   28.2   8.1   90  219-312    61-153 (350)
230 PRK01172 ski2-like helicase; P  94.4    0.23   6E-06   29.5   7.2   84  235-321   225-335 (674)
231 pfam05621 TniB Bacterial TniB   94.4    0.46 1.2E-05   27.2  10.3   68  313-391   144-214 (302)
232 PRK08694 consensus              94.4    0.46 1.2E-05   27.2  10.5  131  219-357   219-377 (468)
233 PRK05582 DNA topoisomerase I;   94.3   0.037 9.5E-07   35.6   2.9   41  446-486   574-630 (692)
234 KOG4439 consensus               94.3     0.1 2.7E-06   32.2   5.1  122  198-325   325-474 (901)
235 PRK06921 hypothetical protein;  94.2     0.2 5.2E-06   30.0   6.5   49  216-269   114-163 (265)
236 TIGR02782 TrbB_P P-type conjug  94.2    0.11 2.8E-06   32.0   5.2   38  193-234   118-155 (315)
237 COG0513 SrmB Superfamily II DN  94.2    0.41 1.1E-05   27.6   8.1  117  230-358   259-379 (513)
238 PRK08840 replicative DNA helic  94.2    0.51 1.3E-05   26.9  10.3  132  219-357   218-376 (464)
239 PTZ00110 helicase; Provisional  94.2    0.51 1.3E-05   26.9  12.9   35  391-428   333-367 (602)
240 PRK09165 replicative DNA helic  94.2    0.51 1.3E-05   26.9  11.6  132  219-357   206-378 (484)
241 TIGR03117 cas_csf4 CRISPR-asso  94.2    0.22 5.5E-06   29.8   6.5  116  494-613   482-625 (636)
242 COG1484 DnaC DNA replication p  94.1    0.26 6.7E-06   29.1   6.9   88  199-322    84-175 (254)
243 PRK12726 flagellar biosynthesi  94.1    0.48 1.2E-05   27.1   8.2   37  219-255   207-243 (407)
244 COG0552 FtsY Signal recognitio  94.1    0.52 1.3E-05   26.9   8.3   39  216-254   137-175 (340)
245 PRK12422 chromosomal replicati  94.1    0.21 5.5E-06   29.8   6.4  105  217-362   140-247 (455)
246 TIGR01970 DEAH_box_HrpB ATP-de  94.1    0.53 1.3E-05   26.8   8.4  290  220-597    19-338 (858)
247 PRK05748 replicative DNA helic  94.0    0.54 1.4E-05   26.7  10.3  130  219-357   204-362 (448)
248 CHL00174 accD acetyl-CoA carbo  94.0   0.024   6E-07   37.1   1.4  121  446-583    49-172 (305)
249 PRK03824 hypA hydrogenase nick  94.0   0.041   1E-06   35.3   2.5   35  452-486    59-117 (135)
250 PRK06893 DNA replication initi  94.0    0.36 9.2E-06   28.1   7.3   33  220-252    41-73  (229)
251 PRK06319 DNA topoisomerase I/S  93.9   0.042 1.1E-06   35.2   2.4   10  448-457   648-657 (864)
252 PRK12902 secA preprotein trans  93.9    0.25 6.5E-06   29.2   6.5   92  226-323   106-214 (946)
253 COG3857 AddB ATP-dependent nuc  93.9    0.13 3.3E-06   31.5   4.9   67  563-632   912-994 (1108)
254 KOG0390 consensus               93.8    0.59 1.5E-05   26.4  10.3  128  198-326   238-388 (776)
255 pfam00154 RecA recA bacterial   93.7    0.59 1.5E-05   26.4   8.1   70  219-292    53-124 (322)
256 PRK07219 DNA topoisomerase I;   93.7    0.09 2.3E-06   32.7   3.9   18  160-177   290-311 (769)
257 PRK12898 secA preprotein trans  93.7     0.3 7.7E-06   28.6   6.6   78  225-308   138-218 (673)
258 pfam10412 TrwB_AAD_bind Type I  93.7    0.12 3.1E-06   31.6   4.6   36  220-255    17-52  (386)
259 TIGR00064 ftsY signal recognit  93.7    0.59 1.5E-05   26.4   8.0   40  214-253    78-117 (284)
260 PRK00411 cdc6 cell division co  93.7    0.62 1.6E-05   26.2  10.2   44  199-242    34-79  (394)
261 TIGR03167 tRNA_sel_U_synt tRNA  93.6    0.13 3.4E-06   31.4   4.6   42  204-250   114-155 (311)
262 PRK07220 DNA topoisomerase I;   93.6   0.056 1.4E-06   34.2   2.6   41  445-485   589-644 (740)
263 PRK02362 ski2-like helicase; P  93.5     0.4   1E-05   27.7   7.0   84  235-321   232-353 (736)
264 pfam06745 KaiC KaiC. This fami  93.5     0.2 5.1E-06   30.0   5.4   49  218-267    19-68  (231)
265 COG0514 RecQ Superfamily II DN  93.5    0.47 1.2E-05   27.1   7.3   73  245-319   229-303 (590)
266 PRK06321 replicative DNA helic  93.5    0.66 1.7E-05   26.0  12.8  132  219-357   227-386 (472)
267 COG3357 Predicted transcriptio  93.5   0.076 1.9E-06   33.2   3.2   50  411-490    40-89  (97)
268 TIGR00614 recQ_fam ATP-depende  93.5    0.39 9.9E-06   27.8   6.8  126  185-333   200-331 (497)
269 PRK13700 conjugal transfer pro  93.4    0.14 3.5E-06   31.2   4.4   37  219-255   186-222 (732)
270 PRK12900 secA preprotein trans  93.4    0.32   8E-06   28.5   6.2   92  226-323   115-223 (983)
271 PRK08939 primosomal protein Dn  93.4    0.46 1.2E-05   27.3   7.0   50  219-273   158-207 (306)
272 cd03115 SRP The signal recogni  93.3     0.7 1.8E-05   25.8   9.2   36  219-254     1-36  (173)
273 PRK12899 secA preprotein trans  93.3    0.37 9.3E-06   28.0   6.4   76  226-307   115-193 (969)
274 KOG0340 consensus               93.3    0.53 1.4E-05   26.7   7.2   74  527-613   295-369 (442)
275 PRK08938 DNA topoisomerase I;   93.3   0.087 2.2E-06   32.8   3.2   45  446-491   578-631 (692)
276 PRK05973 replicative DNA helic  93.3     0.3 7.7E-06   28.6   6.0  113  219-358    65-191 (237)
277 PRK08769 DNA polymerase III su  93.2     0.2   5E-06   30.0   5.0   49  198-246     4-54  (319)
278 cd01126 TraG_VirD4 The TraG/Tr  93.2    0.33 8.4E-06   28.3   6.1   55  221-278     2-56  (384)
279 TIGR02788 VirB11 P-type DNA tr  93.2    0.12   3E-06   31.7   3.8   51   78-128    31-91  (328)
280 PRK07246 bifunctional ATP-depe  93.2    0.52 1.3E-05   26.8   7.1   65  199-265   246-310 (820)
281 TIGR00515 accD acetyl-CoA carb  93.2    0.11 2.7E-06   32.1   3.6   96  443-563    31-136 (292)
282 PRK04023 DNA polymerase II lar  93.1   0.044 1.1E-06   35.0   1.5   35  445-485   633-667 (1128)
283 PRK04328 hypothetical protein;  93.1    0.16 4.1E-06   30.7   4.4   38  218-255    24-61  (250)
284 PRK13342 recombination factor   93.1    0.66 1.7E-05   26.0   7.5   73  494-571   213-289 (417)
285 PRK06696 uridine kinase; Valid  93.0    0.36 9.2E-06   28.0   6.0   32  221-252    29-60  (227)
286 PRK05654 acetyl-CoA carboxylas  92.9    0.13 3.3E-06   31.4   3.7  112  446-582    31-152 (288)
287 COG0846 SIR2 NAD-dependent pro  92.9    0.15 3.9E-06   30.9   4.1   47  476-544   146-192 (250)
288 COG1379 PHP family phosphoeste  92.9     0.5 1.3E-05   27.0   6.6   61  248-314    84-146 (403)
289 cd01124 KaiC KaiC is a circadi  92.8    0.17 4.3E-06   30.5   4.2   47  220-267     1-47  (187)
290 PRK00481 NAD-dependent deacety  92.8    0.12 3.1E-06   31.6   3.4   48  476-546   142-189 (239)
291 TIGR03676 aRF1/eRF1 peptide ch  92.8    0.41   1E-05   27.6   6.1   91  411-521   293-385 (403)
292 cd03223 ABCD_peroxisomal_ALDP   92.8    0.22 5.6E-06   29.7   4.7  119  219-362    28-150 (166)
293 PRK06266 transcription initiat  92.8    0.11 2.8E-06   32.0   3.1   42  447-504   119-160 (178)
294 PRK10246 exonuclease subunit S  92.7    0.11 2.9E-06   31.9   3.2   34   80-113   121-155 (1047)
295 smart00490 HELICc helicase sup  92.7    0.35 8.8E-06   28.2   5.6   58  263-321     4-62  (82)
296 COG1618 Predicted nucleotide k  92.7    0.13 3.2E-06   31.5   3.3   38  220-257     7-45  (179)
297 PRK09401 reverse gyrase; Revie  92.6    0.23   6E-06   29.5   4.7   51  463-518   677-728 (1176)
298 PRK11664 ATP-dependent RNA hel  92.6    0.42 1.1E-05   27.5   6.0  300  207-599    10-333 (812)
299 TIGR02487 NrdD anaerobic ribon  92.6   0.047 1.2E-06   34.8   1.1   39  463-503   590-634 (655)
300 PRK04195 replication factor C   92.6    0.88 2.2E-05   25.1   7.8   17  219-235    41-57  (403)
301 PRK11823 DNA repair protein Ra  92.5   0.057 1.5E-06   34.1   1.5  156  219-401    91-273 (454)
302 PRK00564 hypA hydrogenase nick  92.5   0.086 2.2E-06   32.8   2.3   35  452-486    60-98  (117)
303 KOG0949 consensus               92.5    0.12 3.1E-06   31.6   3.1  142  200-359   513-670 (1330)
304 TIGR00416 sms DNA repair prote  92.5   0.048 1.2E-06   34.7   1.0  171  219-399   104-302 (481)
305 COG3972 Superfamily I DNA and   92.4    0.17 4.4E-06   30.5   3.8  121  218-347   176-320 (660)
306 PRK07111 anaerobic ribonucleos  92.4   0.053 1.3E-06   34.4   1.2   28  413-440   353-388 (703)
307 KOG0949 consensus               92.4    0.36 9.1E-06   28.1   5.3   69  531-611   983-1053(1330)
308 PRK08270 anaerobic ribonucleos  92.3   0.062 1.6E-06   33.9   1.4   78  222-317   180-272 (681)
309 TIGR02642 phage_xxxx uncharact  92.3    0.07 1.8E-06   33.5   1.6   65  411-506   157-222 (270)
310 COG3267 ExeA Type II secretory  92.3    0.71 1.8E-05   25.8   6.8  113  199-335    32-152 (269)
311 PRK06450 threonine synthase; V  92.2   0.087 2.2E-06   32.8   2.1   35  241-277   113-147 (336)
312 PRK04296 thymidine kinase; Pro  92.2    0.83 2.1E-05   25.3   7.0  105  220-356     4-114 (197)
313 KOG1123 consensus               92.2    0.51 1.3E-05   26.9   5.9  113  198-324   302-432 (776)
314 PRK05823 consensus              92.1   0.093 2.4E-06   32.5   2.1   39  447-485   603-659 (691)
315 TIGR01054 rgy reverse gyrase;   92.1    0.05 1.3E-06   34.6   0.7   29  219-250   560-593 (1843)
316 PRK06067 flagellar accessory p  92.1    0.37 9.4E-06   28.0   5.1   49  218-267    32-80  (241)
317 PRK13826 Dtr system oriT relax  92.1       1 2.6E-05   24.6   9.0  103  197-304   380-504 (1102)
318 COG0068 HypF Hydrogenase matur  92.1    0.11 2.7E-06   32.1   2.3   90  262-365   232-334 (750)
319 KOG1802 consensus               91.9    0.45 1.1E-05   27.3   5.4   69  193-267   405-475 (935)
320 cd01130 VirB11-like_ATPase Typ  91.9    0.51 1.3E-05   26.9   5.7   49  198-251     9-57  (186)
321 PRK06731 flhF flagellar biosyn  91.8     1.1 2.7E-05   24.5   7.6   37  218-254    75-111 (270)
322 PRK13889 conjugal transfer rel  91.8     1.1 2.7E-05   24.5  10.6  103  197-304   345-469 (992)
323 pfam08423 Rad51 Rad51. Rad51 i  91.8    0.78   2E-05   25.5   6.5   53  219-271    44-102 (261)
324 KOG0925 consensus               91.8    0.36 9.1E-06   28.1   4.8   34  494-536   505-538 (699)
325 PRK11784 tRNA 2-selenouridine   91.8    0.17 4.4E-06   30.5   3.2   28  219-250   138-165 (333)
326 TIGR01967 DEAH_box_HrpA ATP-de  91.7    0.19 4.9E-06   30.1   3.3  141  198-366    69-229 (1320)
327 TIGR00143 hypF [NiFe] hydrogen  91.7   0.096 2.4E-06   32.5   1.7   86  260-359   231-330 (799)
328 PRK05541 adenylylsulfate kinas  91.7     1.1 2.8E-05   24.3   7.2   62  218-294     7-68  (176)
329 cd00009 AAA The AAA+ (ATPases   91.7     1.1 2.8E-05   24.3   8.1   33  216-248    17-49  (151)
330 pfam07191 DUF1407 Protein of u  91.7   0.081 2.1E-06   33.0   1.4   38  446-485     2-39  (70)
331 PRK06620 hypothetical protein;  91.6     1.1 2.7E-05   24.4   7.1   36  199-234    20-60  (214)
332 COG1675 TFA1 Transcription ini  91.6    0.15 3.8E-06   31.0   2.7   46  447-504   115-160 (176)
333 PRK08665 ribonucleotide-diphos  91.6   0.096 2.5E-06   32.4   1.7   24  295-318   242-265 (733)
334 COG0777 AccD Acetyl-CoA carbox  91.5     0.4   1E-05   27.7   4.8  119  443-586    26-154 (294)
335 pfam10083 DUF2321 Uncharacteri  91.5   0.054 1.4E-06   34.3   0.4   48  436-485    28-77  (158)
336 PRK08533 flagellar accessory p  91.4     1.2   3E-05   24.2   8.6   38  219-256    25-62  (230)
337 TIGR02538 type_IV_pilB type IV  91.4    0.21 5.3E-06   29.9   3.2  197  200-495   311-518 (577)
338 PRK07004 replicative DNA helic  91.4     1.2   3E-05   24.1  10.6  131  219-357   214-371 (460)
339 PRK00254 ski2-like helicase; P  91.4    0.83 2.1E-05   25.3   6.3   83  236-321   227-344 (717)
340 PRK06260 threonine synthase; V  91.4   0.097 2.5E-06   32.4   1.5   12  244-255   139-150 (400)
341 TIGR00354 polC DNA polymerase   91.4   0.082 2.1E-06   33.0   1.1   49   49-97    315-369 (1173)
342 PRK09087 hypothetical protein;  91.4     1.2   3E-05   24.1   8.2   34  201-234    27-60  (226)
343 pfam00271 Helicase_C Helicase   91.2    0.52 1.3E-05   26.8   5.1   53  269-321     5-58  (78)
344 pfam09332 Mcm10 Mcm10 replicat  91.2    0.11 2.8E-06   32.0   1.7   57  435-492   253-320 (346)
345 PRK09001 DNA topoisomerase I;   91.2    0.14 3.5E-06   31.3   2.1   12  165-176   311-322 (869)
346 PRK09183 transposase/IS protei  91.2    0.54 1.4E-05   26.7   5.2  130  197-369    82-213 (258)
347 COG1592 Rubrerythrin [Energy p  91.2     0.1 2.6E-06   32.2   1.5   40  408-485   119-158 (166)
348 pfam01155 HypA Hydrogenase exp  91.1    0.17 4.3E-06   30.6   2.5   55  406-486    38-95  (112)
349 KOG0387 consensus               91.1     1.3 3.2E-05   23.9   8.2  364  198-581   205-643 (923)
350 pfam02146 SIR2 Sir2 family. Th  91.0    0.34 8.7E-06   28.2   4.0   18  528-545   156-173 (177)
351 PRK08579 anaerobic ribonucleos  91.0   0.095 2.4E-06   32.5   1.1   37  279-318   144-180 (623)
352 COG4260 Membrane protease subu  91.0   0.089 2.3E-06   32.7   1.0   38  432-485   302-343 (345)
353 TIGR01384 TFS_arch transcripti  91.0   0.085 2.2E-06   32.8   0.9   30  448-477     3-34  (111)
354 COG1096 Predicted RNA-binding   91.0   0.091 2.3E-06   32.6   1.0   27  446-474   150-176 (188)
355 COG0529 CysC Adenylylsulfate k  90.9     0.9 2.3E-05   25.0   6.1  140  215-392    20-171 (197)
356 COG1439 Predicted nucleic acid  90.8    0.12 3.1E-06   31.7   1.6   74  405-487    82-164 (177)
357 PRK09263 anaerobic ribonucleos  90.8   0.098 2.5E-06   32.4   1.1   18  233-250   202-225 (711)
358 PRK07667 uridine kinase; Provi  90.8    0.35 8.8E-06   28.2   3.9   33  220-252    16-48  (190)
359 cd01409 SIRT4 SIRT4: Eukaryoti  90.7    0.34 8.8E-06   28.2   3.8   17  431-447   113-129 (260)
360 cd03214 ABC_Iron-Siderophores_  90.7    0.98 2.5E-05   24.7   6.1  116  219-358    26-156 (180)
361 PRK13894 conjugal transfer ATP  90.5     1.4 3.6E-05   23.6   8.9   41  198-242   133-173 (320)
362 PRK11827 hypothetical protein;  90.5    0.12 3.2E-06   31.6   1.4   34  444-477     7-40  (60)
363 TIGR00376 TIGR00376 DNA helica  90.5     1.2   3E-05   24.1   6.4   73  197-273   201-275 (709)
364 COG4306 Uncharacterized protei  90.4   0.095 2.4E-06   32.5   0.8   45  438-486    30-78  (160)
365 PRK00133 metG methionyl-tRNA s  90.4    0.89 2.3E-05   25.0   5.7   14  164-177   104-117 (666)
366 cd01410 SIRT7 SIRT7: Eukaryoti  90.4    0.23 5.9E-06   29.5   2.7   47  475-546   119-167 (206)
367 PRK12901 secA preprotein trans  90.4     1.2 3.1E-05   24.0   6.4   92  226-323   192-301 (1111)
368 PRK03846 adenylylsulfate kinas  90.4     1.4 3.6E-05   23.5   8.4   67  214-294    20-86  (198)
369 KOG0923 consensus               90.3    0.44 1.1E-05   27.4   4.1  138  218-366   280-426 (902)
370 TIGR01407 dinG_rel DnaQ family  90.3     1.4 3.7E-05   23.4   7.2   67  200-266   262-330 (944)
371 PRK09194 prolyl-tRNA synthetas  90.3    0.42 1.1E-05   27.6   4.0   18  488-505   440-457 (570)
372 TIGR03346 chaperone_ClpB ATP-d  90.2    0.74 1.9E-05   25.7   5.1  174  463-660   580-775 (852)
373 PRK03681 hypA hydrogenase nick  90.1    0.21 5.3E-06   29.9   2.3   35  452-486    59-97  (114)
374 COG1571 Predicted DNA-binding   90.1    0.13 3.3E-06   31.4   1.3   35  444-479   349-383 (421)
375 cd01675 RNR_III Class III ribo  90.0    0.13 3.4E-06   31.3   1.2   35  282-319   130-164 (555)
376 PRK04011 peptide chain release  89.9     1.5 3.9E-05   23.2   7.1   89  411-520   300-390 (409)
377 KOG4150 consensus               89.9    0.89 2.3E-05   25.0   5.3   68  526-605   573-641 (1034)
378 pfam10236 DAP3 Mitochondrial r  89.8     1.2 3.1E-05   24.0   6.0   38  218-256    23-60  (274)
379 COG2835 Uncharacterized conser  89.7    0.18 4.7E-06   30.3   1.8   34  444-477     7-40  (60)
380 PRK05333 NAD-dependent deacety  89.7    0.45 1.1E-05   27.3   3.7   17  431-447   123-139 (285)
381 PRK12380 hydrogenase nickel in  89.7    0.25 6.3E-06   29.3   2.4   35  452-486    59-96  (113)
382 cd01129 PulE-GspE PulE/GspE Th  89.7     1.3 3.2E-05   23.9   6.0   51  199-252    64-114 (264)
383 PRK09302 circadian clock prote  89.7     0.7 1.8E-05   25.8   4.7  167  218-403    24-218 (501)
384 TIGR02773 addB_Gpos ATP-depend  89.6     0.6 1.5E-05   26.4   4.3  146  561-729   967-1143(1192)
385 PRK11169 leucine-responsive tr  89.6     1.4 3.6E-05   23.5   6.2   97  133-229    11-112 (164)
386 PRK09001 DNA topoisomerase I;   89.6    0.31 7.9E-06   28.6   2.8   12  479-490   716-727 (869)
387 KOG2324 consensus               89.5    0.41 1.1E-05   27.6   3.4  158  328-514   145-322 (457)
388 PRK07418 acetolactate synthase  89.5    0.46 1.2E-05   27.2   3.7   10  296-305   291-300 (615)
389 COG2956 Predicted N-acetylgluc  89.5    0.15 3.7E-06   31.0   1.1   31  460-490   351-382 (389)
390 TIGR01073 pcrA ATP-dependent D  89.5    0.31   8E-06   28.5   2.8   64  198-272     4-75  (811)
391 pfam00448 SRP54 SRP54-type pro  89.4     1.7 4.3E-05   22.9   9.2   36  219-254     2-37  (196)
392 PRK10220 hypothetical protein;  89.3    0.19 4.8E-06   30.2   1.5   30  444-474     2-31  (111)
393 pfam12340 DUF3638 Protein of u  89.3    0.62 1.6E-05   26.3   4.2  109  198-310    23-143 (229)
394 KOG2041 consensus               89.3    0.22 5.6E-06   29.7   1.9   25  488-512   862-886 (1189)
395 pfam09862 DUF2089 Protein of u  89.3    0.28 7.1E-06   28.9   2.4   58  448-510     1-67  (113)
396 TIGR00150 TIGR00150 conserved   89.3     1.1 2.7E-05   24.4   5.4   52  218-280    28-80  (147)
397 PRK00762 hypA hydrogenase nick  89.2     0.3 7.6E-06   28.7   2.5   33  453-486    60-102 (124)
398 TIGR02012 tigrfam_recA protein  89.2     1.7 4.4E-05   22.8   7.3   92  219-314    56-150 (322)
399 cd01413 SIR2_Af2 SIR2_Af2: Arc  89.1     0.4   1E-05   27.7   3.1   74  431-546   108-183 (222)
400 TIGR00603 rad25 DNA repair hel  89.1     0.6 1.5E-05   26.4   4.0  111  198-324   269-400 (756)
401 PRK06749 replicative DNA helic  89.0     1.8 4.5E-05   22.7  11.8  131  219-357   187-347 (428)
402 cd01675 RNR_III Class III ribo  89.0    0.51 1.3E-05   26.9   3.6   25  337-362   398-422 (555)
403 PRK00889 adenylylsulfate kinas  88.9     1.8 4.6E-05   22.7   7.9  106  216-358     3-108 (175)
404 cd01412 SIRT5_Af1_CobB SIRT5_A  88.9    0.41   1E-05   27.6   3.0   39  431-490   104-142 (224)
405 pfam00437 GSPII_E Type II/IV s  88.8     1.8 4.7E-05   22.6   9.4   49  199-252   124-173 (283)
406 smart00492 HELICc3 helicase su  88.8     1.2 3.1E-05   24.0   5.4   79  523-601    34-135 (141)
407 COG0419 SbcC ATPase involved i  88.7    0.44 1.1E-05   27.4   3.1   67   40-109    70-137 (908)
408 COG0484 DnaJ DnaJ-class molecu  88.7    0.29 7.4E-06   28.8   2.1   54  433-486   139-207 (371)
409 PRK00420 hypothetical protein;  88.6    0.23 5.8E-06   29.6   1.6   24  446-470    20-43  (107)
410 PRK07246 bifunctional ATP-depe  88.6    0.84 2.1E-05   25.2   4.5   78  523-601   681-780 (820)
411 cd01372 KISc_KIF4 Kinesin moto  88.6    0.37 9.5E-06   27.9   2.6   35  199-233    50-89  (341)
412 PRK00091 miaA tRNA delta(2)-is  88.6    0.54 1.4E-05   26.7   3.5   25  218-242     4-28  (304)
413 cd01364 KISc_BimC_Eg5 Kinesin   88.5    0.39   1E-05   27.8   2.7   34  199-232    58-96  (352)
414 COG3421 Uncharacterized protei  88.5    0.36 9.2E-06   28.0   2.5   21  258-278   288-308 (812)
415 cd01366 KISc_C_terminal Kinesi  88.4    0.28 7.2E-06   28.9   1.9   34  199-232    55-92  (329)
416 PRK10434 srlR DNA-bindng trans  88.2       2 5.1E-05   22.4  13.4  114  135-255     4-122 (256)
417 TIGR00354 polC DNA polymerase   88.2     0.2 5.1E-06   30.0   1.1   46  435-486   678-726 (1173)
418 COG0429 Predicted hydrolase of  88.2       2 5.1E-05   22.3   6.8   75  217-304    75-155 (345)
419 cd00106 KISc Kinesin motor dom  88.1    0.45 1.2E-05   27.3   2.8   34  199-232    55-93  (328)
420 pfam01583 APS_kinase Adenylyls  88.1       2 5.2E-05   22.3   6.4   61  220-294     4-64  (157)
421 PRK11032 hypothetical protein;  88.1     0.2 5.1E-06   30.0   1.0   12  477-489   143-154 (160)
422 cd01365 KISc_KIF1A_KIF1B Kines  88.0    0.45 1.1E-05   27.3   2.8   32  201-232    67-103 (356)
423 KOG1808 consensus               88.0     2.1 5.2E-05   22.3   6.3   86  158-243   372-465 (1856)
424 COG2816 NPY1 NTP pyrophosphohy  88.0    0.23 5.9E-06   29.5   1.3   34  447-481   113-146 (279)
425 TIGR01143 murF UDP-N-acetylmur  87.9    0.86 2.2E-05   25.2   4.1   85  163-248    22-111 (462)
426 cd03221 ABCF_EF-3 ABCF_EF-3  E  87.8     2.1 5.4E-05   22.2   7.5   71  219-323    27-97  (144)
427 PRK07591 threonine synthase; V  87.8    0.26 6.7E-06   29.1   1.4   12  244-255   160-171 (422)
428 TIGR00382 clpX ATP-dependent C  87.8    0.35 8.9E-06   28.1   2.1   89  219-342   153-243 (452)
429 PRK00241 nudC NADH pyrophospha  87.7    0.25 6.3E-06   29.3   1.3   35  447-482   102-136 (257)
430 cd01373 KISc_KLP2_like Kinesin  87.6    0.49 1.2E-05   27.0   2.8   34  199-232    51-89  (337)
431 cd01408 SIRT1 SIRT1: Eukaryoti  87.6    0.47 1.2E-05   27.2   2.6   20  527-546   168-187 (235)
432 cd01367 KISc_KIF2_like Kinesin  87.6    0.51 1.3E-05   26.9   2.8   34  199-232    61-99  (322)
433 cd01371 KISc_KIF3 Kinesin moto  87.5    0.47 1.2E-05   27.1   2.6   34  199-232    58-96  (333)
434 TIGR01562 FdhE formate dehydro  87.4    0.26 6.6E-06   29.2   1.2   53  438-493   190-245 (312)
435 COG2805 PilT Tfp pilus assembl  87.4     2.2 5.7E-05   22.0   6.3   39  214-253   121-159 (353)
436 cd01368 KISc_KIF23_like Kinesi  87.3    0.51 1.3E-05   26.9   2.7   35  199-233    65-104 (345)
437 CHL00095 clpC Clp protease ATP  87.3     1.1 2.7E-05   24.4   4.4  234  462-727   523-805 (823)
438 COG1998 RPS31 Ribosomal protei  87.3    0.19 4.7E-06   30.2   0.5   27  446-474    20-48  (51)
439 PRK00652 lpxK tetraacyldisacch  87.2     2.3 5.8E-05   21.9   7.3   28  226-253    59-86  (334)
440 COG0467 RAD55 RecA-superfamily  87.1     1.8 4.5E-05   22.8   5.4   39  218-256    23-61  (260)
441 pfam03237 Terminase_6 Terminas  87.0     1.2   3E-05   24.2   4.4  132  223-366     2-140 (380)
442 TIGR00041 DTMP_kinase thymidyl  86.9    0.99 2.5E-05   24.7   4.0   39  221-260     5-44  (211)
443 cd00296 SIR2 SIR2 superfamily   86.9     0.9 2.3E-05   25.0   3.8   71  432-546   109-181 (222)
444 COG5257 GCD11 Translation init  86.9    0.34 8.7E-06   28.2   1.6   15   38-52     11-25  (415)
445 PRK10906 DNA-binding transcrip  86.7     2.4 6.1E-05   21.8  13.8  187  135-352     4-200 (252)
446 COG4962 CpaF Flp pilus assembl  86.7     2.2 5.6E-05   22.0   5.7   50  198-252   157-206 (355)
447 PRK04301 radA DNA repair and r  86.7     2.4 6.1E-05   21.7   6.8   53  219-271   104-162 (318)
448 TIGR01046 S10_Arc_S20_Euk ribo  86.6    0.85 2.2E-05   25.2   3.5   42  641-683     3-44  (99)
449 cd01374 KISc_CENP_E Kinesin mo  86.6    0.56 1.4E-05   26.6   2.6   34  199-232    50-88  (321)
450 KOG0247 consensus               86.5    0.57 1.5E-05   26.5   2.6   33  200-233    92-130 (809)
451 pfam07282 Transposase_35 Putat  86.4    0.95 2.4E-05   24.8   3.7   27  418-447    13-39  (69)
452 COG0542 clpA ATP-binding subun  86.4     1.5 3.8E-05   23.3   4.7  218  483-727   522-776 (786)
453 COG1645 Uncharacterized Zn-fin  86.4    0.28 7.2E-06   28.9   1.0   27  446-474    29-55  (131)
454 pfam03266 DUF265 Protein of un  86.3    0.79   2E-05   25.5   3.2   36  221-256     2-38  (168)
455 smart00129 KISc Kinesin motor,  86.3    0.63 1.6E-05   26.2   2.7   33  200-232    57-94  (335)
456 COG4031 Predicted metal-bindin  86.2    0.25 6.3E-06   29.3   0.6   33  464-498     1-33  (227)
457 PRK00133 metG methionyl-tRNA s  86.2    0.31 7.8E-06   28.6   1.1   11  140-150   105-115 (666)
458 PRK12496 hypothetical protein;  86.2     0.2 5.2E-06   29.9   0.2   25  463-487   129-156 (166)
459 pfam09538 FYDLN_acid Protein o  86.1    0.35 8.9E-06   28.1   1.3   32  442-474     6-37  (104)
460 TIGR03345 VI_ClpV1 type VI sec  86.1     2.5 6.3E-05   21.7   5.7  184  464-671   582-794 (852)
461 PRK11889 flhF flagellar biosyn  86.0     2.6 6.6E-05   21.5  12.4  134  205-370   218-372 (436)
462 PRK13900 type IV secretion sys  86.0       2 5.2E-05   22.3   5.2   32  219-251   161-192 (332)
463 PRK07220 DNA topoisomerase I;   86.0    0.73 1.9E-05   25.7   2.9   36  449-484   617-665 (740)
464 cd01407 SIR2-fam SIR2 family o  86.0    0.75 1.9E-05   25.6   3.0   18  529-546   162-179 (218)
465 cd01369 KISc_KHC_KIF5 Kinesin   85.9    0.66 1.7E-05   26.1   2.7   34  199-232    53-91  (325)
466 PRK03918 chromosome segregatio  85.9    0.76 1.9E-05   25.5   3.0   10   40-49     67-76  (882)
467 pfam01745 IPT Isopentenyl tran  85.9    0.76   2E-05   25.5   3.0   24  219-242     2-25  (232)
468 PRK10865 protein disaggregatio  85.8     2.1 5.3E-05   22.3   5.2  174  464-660   584-778 (857)
469 COG1592 Rubrerythrin [Energy p  85.8    0.65 1.7E-05   26.1   2.6   16  439-455   144-159 (166)
470 cd01370 KISc_KIP3_like Kinesin  85.5    0.66 1.7E-05   26.0   2.5   34  199-232    64-102 (338)
471 cd02027 APSK Adenosine 5'-phos  85.5     2.7   7E-05   21.3   6.3   59  222-294     3-61  (149)
472 LOAD_sir2 consensus             85.5    0.59 1.5E-05   26.4   2.3   15  474-490   141-155 (217)
473 PRK13833 conjugal transfer pro  85.4     2.8   7E-05   21.3   9.4   41  198-243   128-168 (323)
474 PRK05823 consensus              85.4    0.57 1.5E-05   26.5   2.1   14  617-630   549-562 (691)
475 pfam09567 RE_MamI MamI restric  85.4    0.26 6.6E-06   29.1   0.4   47  426-490    69-115 (350)
476 PRK09519 recA recombinase A; R  85.4     2.8 7.1E-05   21.3   7.4   88  220-311    62-152 (790)
477 pfam00225 Kinesin Kinesin moto  85.3    0.81 2.1E-05   25.3   2.9   34  199-232    50-88  (321)
478 PRK00440 rfc replication facto  85.3     2.3 5.9E-05   21.9   5.2   42  203-244    21-63  (318)
479 TIGR01278 DPOR_BchB light-inde  85.1    0.67 1.7E-05   26.0   2.4   49  496-554   348-400 (562)
480 cd03279 ABC_sbcCD SbcCD and ot  85.1    0.97 2.5E-05   24.7   3.2   25  219-244    29-53  (213)
481 pfam01443 Viral_helicase1 Vira  85.1    0.94 2.4E-05   24.9   3.1   28  222-255     2-29  (226)
482 pfam01935 DUF87 Domain of unkn  85.0     1.6 4.2E-05   23.0   4.3   34  221-254    26-60  (218)
483 cd01375 KISc_KIF9_like Kinesin  85.0    0.69 1.8E-05   25.9   2.4   32  201-232    59-95  (334)
484 PRK09521 exosome complex RNA-b  84.9    0.36 9.1E-06   28.1   0.9   33  440-474   144-177 (187)
485 KOG0732 consensus               84.8     2.9 7.4E-05   21.1   6.3  158  218-420   299-472 (1080)
486 PRK06450 threonine synthase; V  84.8    0.46 1.2E-05   27.2   1.4   61  227-288    75-135 (336)
487 PRK13341 recombination factor   84.8     2.9 7.5E-05   21.1   7.4   28  574-607   580-607 (726)
488 PRK12402 replication factor C   84.8     2.2 5.7E-05   22.0   4.9   41  203-243    20-61  (337)
489 TIGR00618 sbcc exonuclease Sbc  84.7    0.88 2.2E-05   25.1   2.8   21  236-256   289-309 (1063)
490 COG1474 CDC6 Cdc6-related prot  84.6       3 7.6E-05   21.0   9.1   72  200-271    22-98  (366)
491 COG1656 Uncharacterized conser  84.5    0.59 1.5E-05   26.4   1.9   58  444-506    96-157 (165)
492 TIGR02639 ClpA ATP-dependent C  84.5     1.4 3.7E-05   23.4   3.9  163  465-664   514-708 (774)
493 PRK11512 DNA-binding transcrip  84.5     1.8 4.5E-05   22.8   4.3   75  131-212    35-113 (144)
494 COG1503 eRF1 Peptide chain rel  84.5    0.58 1.5E-05   26.4   1.8   92  406-518   295-388 (411)
495 PRK00423 tfb transcription ini  84.3    0.51 1.3E-05   26.9   1.5   31  443-473     9-40  (310)
496 pfam03215 Rad17 Rad17 cell cyc  84.2     3.1 7.9E-05   20.9   8.3  154  219-394    46-205 (490)
497 pfam01580 FtsK_SpoIIIE FtsK/Sp  84.0    0.98 2.5E-05   24.7   2.8   27  220-246    40-66  (202)
498 TIGR02349 DnaJ_bact chaperone   83.9    0.91 2.3E-05   25.0   2.6   55  433-487   168-239 (386)
499 PRK05638 threonine synthase; V  83.9    0.53 1.4E-05   26.7   1.5   39  237-277   127-165 (443)
500 smart00242 MYSc Myosin. Large   83.9     2.8 7.1E-05   21.2   5.1   43  204-248    80-122 (677)

No 1  
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=100.00  E-value=0  Score=1597.93  Aligned_cols=714  Identities=45%  Similarity=0.731  Sum_probs=659.8

Q ss_pred             EEEEEECCCCCCCCCCCCCCCCCCC-CCCCEEEEECCCCEEEEEEEEECCCCCCCCCHHCCCHHHHCCC-CCCCHHHHHH
Q ss_conf             6777631778786616378888884-8875899618996899999982488767880111418884066-8999899999
Q gi|254780619|r   14 SRVIILLLQAVSGPYIYSVPSAMKV-ELGSIVRVPLRSRTVLGIVWYNSEEKYKIDSLKLRPIEYVFDC-PPLSRQMCEF   91 (731)
Q Consensus        14 ~rV~Vllp~pL~~~FtY~vP~~l~i-~iG~RV~VPFg~r~~~GiVv~~~~~~~~~~~~kLK~I~~VlD~-~~L~~~ll~L   91 (731)
                      ..+.|++|+|+.++|||.+|+++.. ++|+||.||||++.++||||+...++. .+..|||+|.+++|. +++++++++|
T Consensus         2 ~~~~V~v~vp~~~~fdY~~p~~l~~~~~G~rV~VPfg~~~~~GiV~~~~~~~~-~~~~klk~i~~v~d~~p~l~~~~~~L   80 (730)
T COG1198           2 RYAEVAVPVPLLRPFDYLIPEGLEPDQPGSRVRVPFGGRLVVGIVVELSSESD-VDGRKLKEIERVLDTEPVLTPELLRL   80 (730)
T ss_pred             CEEEEEECCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCEEEEEEEEECCCCC-CCHHHHHHHHHHHCCCCCCCHHHHHH
T ss_conf             36999953776765234588666778986489997699248999998336787-65665331676506777889899999


Q ss_pred             HHHHHHHCCCCHHHHHHHHCCCCCCCCCCCCCHH-----CC----CCCC-CCCCHHHHHHHHHHHCCCCCCHHHHHHHHC
Q ss_conf             9999853088788999985753223333200000-----13----3334-458688999999988098878788887709
Q gi|254780619|r   92 VKWVADYTFSPMGLVARMVVSALSETEKMEEKIQ-----FT----GIFP-RINTVARLRVLDKIKDGKIWEKRDLIRASQ  161 (731)
Q Consensus        92 ~~wiA~yY~~plG~vLk~aLP~~~k~~~~~~~~~-----~~----~~~~-~~~~~~~~~~l~~l~~~~~~~~~el~~~~~  161 (731)
                      +.|+|+||++|+|+++++++|+.++.........     ..    ...+ ...++++.++++.+..+..+....+....+
T Consensus        81 ~~w~s~yy~~~~g~vl~~~lP~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~kq~~~l~~l~~~~~~~~~~l~~~~~  160 (730)
T COG1198          81 IEWAADYYLSPLGDVLRLALPVLLRQGYAKPSLPVLFYRLTERGRAALPDLKRAKKQARVLEALLQGGEWTRSALAHAAG  160 (730)
T ss_pred             HHHHHHHHCCCHHHHHHHHCCHHHCCCCCCCCCHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHCCCCCCHHHHHHHCC
T ss_conf             99999764576889999867634305655555403778763010110433112356999999987077322145543213


Q ss_pred             CCHHHHHHHHHCCHHHHHHHHHCCCCCCCCCCC-CCCCCCHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHHHHHH
Q ss_conf             998999752455722344554102356654344-6666883789999999875204896199844753157999999999
Q gi|254780619|r  162 VSSHVIDGLKAQGVIKQIFEVISPVVDSPNLYF-SLPILDKNQQDVVEQVVPLCTKGFAVSLISGVTGSGKTEVYLEIVA  240 (731)
Q Consensus       162 ~s~~~i~~L~~kglI~~~~~~~~~~~~~~~~~~-~~~~Lt~eQ~~a~~~i~~~~~~~f~~~LL~GvTGSGKTEVYl~li~  240 (731)
                      +|.++++.|.++|+++.......+......... ..+.||.+|+.|++.|.... .+|.++||+|||||||||||+++|+
T Consensus       161 ~s~~~~~~l~~~g~~~~~~~~~~~~~~~~~~~~~~~~~Ln~~Q~~a~~~i~~~~-~~~~~~Ll~GvTGSGKTEvYl~~i~  239 (730)
T COG1198         161 VSLSVLKGLEKKGLIEIIELEPPLVVAPPDPSLSEWLALNQEQQAAVEAILSSL-GGFAPFLLDGVTGSGKTEVYLEAIA  239 (730)
T ss_pred             HHHHHHHHHHHCCCEEEECCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHC-CCCCCEEEECCCCCCHHHHHHHHHH
T ss_conf             038989888765735653036777522346565431103889999999999750-5666536767778858999999999


Q ss_pred             HHHHCCCCEEEEECCCHHHHHHHHHHHCCCCCEEEEEECCCCCHHHHHHHHHHHCCCCEEEEECCHHHHHHHCCCEEEEE
Q ss_conf             98514684799715210013445554303897689962355723566789999719973999400121100100013677
Q gi|254780619|r  241 AVLHLGKQVLILLPEISLTSAILERFQKRFGVKPAEWHSSLSTSMREKIWRQVARGAISVIVGVRSALFLPFKKLGLIVI  320 (731)
Q Consensus       241 ~~L~~GkqvLiLvPEI~Lt~Q~~~rl~~rF~~~v~v~HS~ls~~eR~~~w~~i~~G~~~IVIGtRSAif~P~~nLglIIv  320 (731)
                      ++|++|||||+|||||+||||+.+||+.|||.+|++|||+||+++|+++|.++++|+++||||||||+|+||+|||||||
T Consensus       240 ~~L~~GkqvLvLVPEI~Ltpq~~~rf~~rFg~~v~vlHS~Ls~~er~~~W~~~~~G~~~vVIGtRSAlF~Pf~~LGLIIv  319 (730)
T COG1198         240 KVLAQGKQVLVLVPEIALTPQLLARFKARFGAKVAVLHSGLSPGERYRVWRRARRGEARVVIGTRSALFLPFKNLGLIIV  319 (730)
T ss_pred             HHHHCCCEEEEEECCCCCHHHHHHHHHHHHCCCHHHHCCCCCHHHHHHHHHHHHCCCCEEEEEECHHHCCCHHHCCEEEE
T ss_conf             99975987999956534569999999998678745314657927899999998559715999712233072312576997


Q ss_pred             EECCCCCCHHCCCCCCCHHHHHHHHHHHCCCCEECCCCCCCHHHHHHHHHHHHHHHCCCCCCCCCCCCCCEECCCCCCCC
Q ss_conf             40553210000244322489999975110321000024543246775321234441243223676543321102222332
Q gi|254780619|r  321 DEEHDISYKQEEGILYNARDMSIVRGKIESFPVVLVSATPSIESRVNGISRRYHSVHLSTRYRNSALPHLQVIDMRGQTI  400 (731)
Q Consensus       321 DEEHd~sykq~~~pry~aRdvA~~Ra~~~~~~lilgSATPSles~~~~~~g~~~~~~l~~R~~~~~~P~i~ivDm~~~~~  400 (731)
                      |||||+||||+++|||||||||++||+.++||+||||||||+|||+++++|+|.++.|++|++++.+|++++||||++..
T Consensus       320 DEEHD~sYKq~~~prYhARdvA~~Ra~~~~~pvvLgSATPSLES~~~~~~g~y~~~~L~~R~~~a~~p~v~iiDmr~e~~  399 (730)
T COG1198         320 DEEHDSSYKQEDGPRYHARDVAVLRAKKENAPVVLGSATPSLESYANAESGKYKLLRLTNRAGRARLPRVEIIDMRKEPL  399 (730)
T ss_pred             ECCCCCCCCCCCCCCCCHHHHHHHHHHHCCCCEEEECCCCCHHHHHHHHCCCEEEEECCCCCCCCCCCCCEEEECCCCCC
T ss_conf             02456432477777767899999998860998898268877899986653855899703545556787625873566655


Q ss_pred             CCCCCCCHHHHHHHHHHHCCCCEEEEEECCCCEEHHCCCCCCCCCCCCCCCCCEEEEECCCCCCEECHHHCCCCCCCCCC
Q ss_conf             22454798999999886226551799742220000002356543431014652012113578320000210244655566
Q gi|254780619|r  401 AQGKSLSPEMIDGIRHTLARNEQTLLFLNRRGYAPLTLCQVCGNRLKCLHCSCWLVEHRSKKKLYCHQCGHSAIYSQSCV  480 (731)
Q Consensus       401 ~~~~~lS~~l~~~i~~~l~~g~qvll~lnRrGya~~~~C~~Cg~~~~C~~C~~~l~~h~~~~~l~Ch~Cg~~~~~~~~Cp  480 (731)
                      ..|.+||+.|+++|+++|++|+|||||+|||||||+++|++|||+++|||||++||||+..+.|.|||||++.+.|..||
T Consensus       400 ~~~~~lS~~Ll~~i~~~l~~geQ~llflnRRGys~~l~C~~Cg~v~~Cp~Cd~~lt~H~~~~~L~CH~Cg~~~~~p~~Cp  479 (730)
T COG1198         400 ETGRSLSPALLEAIRKTLERGEQVLLFLNRRGYAPLLLCRDCGYIAECPNCDSPLTLHKATGQLRCHYCGYQEPIPQSCP  479 (730)
T ss_pred             CCCCCCCHHHHHHHHHHHHCCCEEEEEECCCCCCCEEECCCCCCCCCCCCCCCCEEEECCCCEEEECCCCCCCCCCCCCC
T ss_conf             46775799999999999842986899971677654004256898024899995127864798067077999899887798


Q ss_pred             CCCCCCEECCCCCCHHHHHHHHHHCCCCCHHHHCCCCCCCCHHHHHHHHHHHCCCCCCEEEEEHHHCCCCCCCCCCHHHH
Q ss_conf             67874110013542899888852048520001023211358678999998621257657987044302311345201233
Q gi|254780619|r  481 VCGSSGKMIACGFGIERIAEEVCEYFPLARISILSSDLEGGGGRLQLQLSAIAKGEIDIIIGTQLVAKGHNFPRMSLVGV  560 (731)
Q Consensus       481 ~Cg~~~~l~~~G~Gte~~~e~l~~~fp~~~v~~~d~d~~~~~~~~~~~~~~~~~~~~~ilvgTq~i~kg~~fp~v~lv~i  560 (731)
                      +|||. .++++|.||||+||||+++||+++|+|||+|+|+++++++.++..|.+||+|||||||||||||||||||||||
T Consensus       480 ~Cgs~-~L~~~G~GterieeeL~~~FP~~rv~r~d~Dtt~~k~~~~~~l~~~~~ge~dILiGTQmiaKG~~fp~vtLVgv  558 (730)
T COG1198         480 ECGSE-HLRAVGPGTERIEEELKRLFPGARIIRIDSDTTRRKGALEDLLDQFANGEADILIGTQMIAKGHDFPNVTLVGV  558 (730)
T ss_pred             CCCCC-EEEEECCCHHHHHHHHHHHCCCCCEEEECCCCCCCHHHHHHHHHHHHCCCCCEEECCHHHHCCCCCCCCEEEEE
T ss_conf             99997-36996461999999999878999479984666664356899999975799886634166642788666318999


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEECCCCCHHHHHHHHCCHHHHHHHHHHHHHHCCCCCCHHE
Q ss_conf             00034431024557899999875431102566788689999329864888999958979999999999998188880118
Q gi|254780619|r  561 VDGDLGLTNADLRSSERTFQLLSQVTGRAGRFGLKSLGLIQAYQPTHPVMQALVSGDADSFYESEIRARESVNLPPFGRL  640 (731)
Q Consensus       561 l~aD~~l~~pd~ra~E~~~qll~qv~gRagr~~~~g~v~iQt~~p~~~~~~~~~~~d~~~f~~~el~~R~~~~~PPf~~~  640 (731)
                      +|||.+|+.|||||+||+||||+||+|||||++++|+|+||||+||||+++++.++||++||++||++|++++||||+++
T Consensus       559 l~aD~~L~~~DfRAsEr~fqll~QvaGRAgR~~~~G~VvIQT~~P~hp~i~~~~~~dy~~F~~~El~~Rk~~~~PPf~~l  638 (730)
T COG1198         559 LDADTGLGSPDFRASERTFQLLMQVAGRAGRAGKPGEVVIQTYNPDHPAIQALKRGDYEAFYEQELAERKELGLPPFSRL  638 (730)
T ss_pred             EECHHHHCCCCCCHHHHHHHHHHHHHHHHCCCCCCCEEEEEECCCCCHHHHHHHHCCHHHHHHHHHHHHHHCCCCCHHHH
T ss_conf             96314315888435789999999997553267889869999679985799999866999999999998886189970654


Q ss_pred             EEEEEECCCHHHHHHHHHHHHHHCC--CCCCCEEECCCCCHHHHHCCEEEEEEEEECCCHHHHHHHHHHHHHHHHHCCCC
Q ss_conf             9998845998999999999998573--43884998176752688588237999998099389999999999864210378
Q gi|254780619|r  641 AAVIISGTKYQEVENYAYNLKEHAP--RSSDIVVFGPAESPLFMVRGRYRFRLLIHGKRNSNLQGFFSQMYDNTIKRSNA  718 (731)
Q Consensus       641 ~~i~~~~~~~~~~~~~~~~~~~~~~--~~~~~~v~GP~~~~~~k~~~~~r~~~~ik~~~~~~l~~~l~~~~~~~~~~~~~  718 (731)
                      +.+++++++++.+.++++.+.+.+.  ...+++++||+|+++.|++|+|||||+++++++..|++.++.++......+++
T Consensus       639 ~~v~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~vLGP~~a~~~r~~g~yR~qiLl~~~~~~~L~~~l~~~~~~~~~~~~~  718 (730)
T COG1198         639 AAVIASAKNEEKALEFARALRELLKEALPVDVEVLGPAPAPLAKLAGRYRYQILLKSPSRADLQKLLRAWLAVLPKRSGK  718 (730)
T ss_pred             EEEEECCCCHHHHHHHHHHHHHHHHHCCCCCCEEECCCCCHHHHHCCCEEEEEEEECCCHHHHHHHHHHHHHHHCCCCCC
T ss_conf             46673378989999999999999986275565046887562677378558999981685778999999999863034675


Q ss_pred             CEEEEEECCHHH
Q ss_conf             689997068021
Q gi|254780619|r  719 LRVQFDIDPQNF  730 (731)
Q Consensus       719 ~~~~iDvDP~~~  730 (731)
                      ++|.|||||++|
T Consensus       719 v~~~iDiDP~~~  730 (730)
T COG1198         719 VRVSIDIDPQSF  730 (730)
T ss_pred             EEEEEECCCCCC
T ss_conf             169994489879


No 2  
>PRK05580 primosome assembly protein PriA; Validated
Probab=100.00  E-value=0  Score=1565.14  Aligned_cols=694  Identities=41%  Similarity=0.679  Sum_probs=652.7

Q ss_pred             EEEEEEECCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCEEEEEEEEECCCCCCCCCHHCCCHHHHCCCC-CCCHHHHHH
Q ss_conf             3677763177878661637888888488758996189968999999824887678801114188840668-999899999
Q gi|254780619|r   13 CSRVIILLLQAVSGPYIYSVPSAMKVELGSIVRVPLRSRTVLGIVWYNSEEKYKIDSLKLRPIEYVFDCP-PLSRQMCEF   91 (731)
Q Consensus        13 ~~rV~Vllp~pL~~~FtY~vP~~l~i~iG~RV~VPFg~r~~~GiVv~~~~~~~~~~~~kLK~I~~VlD~~-~L~~~ll~L   91 (731)
                      +..+.|++|+|++++|||.+|+++++++|+||+||||+|.++|+||+..+.+ +.+..+||+|.+|+|.. .+++++++|
T Consensus         3 m~ia~V~l~~pl~~~FtY~vp~~l~~~~G~rV~VpFg~r~~~GiV~~~~~~~-~~~~~~lK~I~~vld~~p~l~~~~l~l   81 (699)
T PRK05580          3 MPVARVLLPVPLPHPFDYLVPEGLEAQPGVRVRVPFGGRLVDGVVVERRDES-DVPLGKLKPIEEVLDPEPVLTPELLRL   81 (699)
T ss_pred             CCEEEEEECCCCCCCCCCCCCCCCCCCCCEEEEEECCCEEEEEEEEEECCCC-CCCHHCCEEHHHHCCCCCCCCHHHHHH
T ss_conf             7359999889999798169998788999708999618917999999825789-997320677665249998889999999


Q ss_pred             HHHHHHHCCCCHHHHHHHHCCCCCCCCCCCCCHHCCCCCCCCCCHHHHHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHH
Q ss_conf             99998530887889999857532233332000001333344586889999999880988787888877099989997524
Q gi|254780619|r   92 VKWVADYTFSPMGLVARMVVSALSETEKMEEKIQFTGIFPRINTVARLRVLDKIKDGKIWEKRDLIRASQVSSHVIDGLK  171 (731)
Q Consensus        92 ~~wiA~yY~~plG~vLk~aLP~~~k~~~~~~~~~~~~~~~~~~~~~~~~~l~~l~~~~~~~~~el~~~~~~s~~~i~~L~  171 (731)
                      ++|+|+||+||+|+++++++|+..+                 .+++|.++++.+.   .....+.....+.|.++++.|.
T Consensus        82 ~~wia~yY~~~~g~vl~~~lP~~~~-----------------~~~kq~~~l~~l~---~~~~~~~~~~~~~s~~~l~~l~  141 (699)
T PRK05580         82 ADWVADYYLGPLGDVLRLALPPRLR-----------------RAPKQQRLLAALG---GAWTAALLEKAGVSASVLKGLA  141 (699)
T ss_pred             HHHHHHHHCCCHHHHHHHHCCCCCC-----------------CCHHHHHHHHHHC---CCCHHHHHHHCCCCHHHHHHHH
T ss_conf             9999985787799999996898632-----------------4777999998632---3242678876289889999999


Q ss_pred             HCCHHHHHHHHHCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHHHHHHHHHHCCCCEEE
Q ss_conf             55722344554102356654344666688378999999987520489619984475315799999999998514684799
Q gi|254780619|r  172 AQGVIKQIFEVISPVVDSPNLYFSLPILDKNQQDVVEQVVPLCTKGFAVSLISGVTGSGKTEVYLEIVAAVLHLGKQVLI  251 (731)
Q Consensus       172 ~kglI~~~~~~~~~~~~~~~~~~~~~~Lt~eQ~~a~~~i~~~~~~~f~~~LL~GvTGSGKTEVYl~li~~~L~~GkqvLi  251 (731)
                      ++|+++.......+...........+.||++|+.+++.|..  ..+|.++||||||||||||||+++|+++|++|+|||+
T Consensus       142 ~~g~~~~~~~~~~~~~~~~~~~~~~~~L~~eQ~~a~~~i~~--~~~~~~~LL~GvTGSGKTevYl~li~~~l~~GkqvLi  219 (699)
T PRK05580        142 KKGLIEIVERPPLRLRDPPDPDTEPPTLNEEQAAALAAIRA--AGGFSAFLLDGVTGSGKTEVYLQAIAEALAQGKQALV  219 (699)
T ss_pred             HCCCEEEEEECCCCCCCCCCCCCCCCCCCHHHHHHHHHHHH--CCCCCCEEEECCCCCHHHHHHHHHHHHHHHCCCCEEE
T ss_conf             78971675321456543344456787889999999999985--5888717874789860799999999999973997899


Q ss_pred             EECCCHHHHHHHHHHHCCCCCEEEEEECCCCCHHHHHHHHHHHCCCCEEEEECCHHHHHHHCCCEEEEEEECCCCCCHHC
Q ss_conf             71521001344555430389768996235572356678999971997399940012110010001367740553210000
Q gi|254780619|r  252 LLPEISLTSAILERFQKRFGVKPAEWHSSLSTSMREKIWRQVARGAISVIVGVRSALFLPFKKLGLIVIDEEHDISYKQE  331 (731)
Q Consensus       252 LvPEI~Lt~Q~~~rl~~rF~~~v~v~HS~ls~~eR~~~w~~i~~G~~~IVIGtRSAif~P~~nLglIIvDEEHd~sykq~  331 (731)
                      |||||+||+|+++||+++||++|++|||++|+++|+++|+++++|+++||||||||+|+||+||||||||||||+||||+
T Consensus       220 LvPEI~lt~q~~~rl~~~fg~~v~v~HS~ls~~eR~~~w~~i~~G~~~IVIGtRSAvFaP~~nLgLIIVDEEhd~SYKq~  299 (699)
T PRK05580        220 LVPEIALTPQLLARFRARFGARVAVLHSGLSDGERYRAWLAALRGEARVVIGTRSALFAPFKNLGLIIVDEEHDDSYKQQ  299 (699)
T ss_pred             EECCHHHHHHHHHHHHHHHCCCEEEECCCCCHHHHHHHHHHHHCCCCEEEEECCCEEECCCCCCCEEEEECCCCHHHCCC
T ss_conf             91767878999999998709957996488985799999999976997199973601106578984899973654544466


Q ss_pred             CCCCCCHHHHHHHHHHHCCCCEECCCCCCCHHHHHHHHHHHHHHHCCCCCCCCCCCCCCEECCCCCCCCCCCCCCCHHHH
Q ss_conf             24432248999997511032100002454324677532123444124322367654332110222233222454798999
Q gi|254780619|r  332 EGILYNARDMSIVRGKIESFPVVLVSATPSIESRVNGISRRYHSVHLSTRYRNSALPHLQVIDMRGQTIAQGKSLSPEMI  411 (731)
Q Consensus       332 ~~pry~aRdvA~~Ra~~~~~~lilgSATPSles~~~~~~g~~~~~~l~~R~~~~~~P~i~ivDm~~~~~~~~~~lS~~l~  411 (731)
                      ++|||||||||++||+.+||++||||||||+|+||++++|+|.+++|++|+.++.+|+|++|||+++....+..||+.|+
T Consensus       300 ~~Pry~ARdvA~~Ra~~~~~~liLgSaTPSlEs~~~~~~g~~~~~~l~~r~~~~~~P~v~ivDm~~~~~~~~~~ls~~l~  379 (699)
T PRK05580        300 DGPRYHARDVAVLRAKQEGCPVVLGSATPSLESLANAESGKYHLLRLTRRAGAAALPRVEIIDMREEPLERGAGLSPPLL  379 (699)
T ss_pred             CCCCCCHHHHHHHHHHHHCCCEEECCCCCCHHHHHHHHCCCCEEECCCCCCCCCCCCEEEECCCCCCCCCCCCCCCHHHH
T ss_conf             68761199999999998499889616899999999997599766446532234789837933542141002575469999


Q ss_pred             HHHHHHHCCCCEEEEEECCCCEEHHCCCCCCCCCCCCCCCCCEEEEECCCCCCEECHHHCCCCCCCCCCCCCCCCEECCC
Q ss_conf             99988622655179974222000000235654343101465201211357832000021024465556667874110013
Q gi|254780619|r  412 DGIRHTLARNEQTLLFLNRRGYAPLTLCQVCGNRLKCLHCSCWLVEHRSKKKLYCHQCGHSAIYSQSCVVCGSSGKMIAC  491 (731)
Q Consensus       412 ~~i~~~l~~g~qvll~lnRrGya~~~~C~~Cg~~~~C~~C~~~l~~h~~~~~l~Ch~Cg~~~~~~~~Cp~Cg~~~~l~~~  491 (731)
                      ++|+++|++|+|||||+|||||||+++|++|||+++||+||++||||+..+.|.|||||++.+.|+.||+|||. .+..+
T Consensus       380 ~~i~~~L~~g~qvll~lnRrGya~~~~C~~Cg~~~~C~~C~~~L~~h~~~~~l~Ch~Cg~~~~~~~~Cp~Cgs~-~l~~~  458 (699)
T PRK05580        380 EAIREALERGEQVLLFLNRRGYAPFLLCRDCGWVARCPHCDGPLTLHRAGRRLRCHHCGYQEPIPRACPECGST-DLRAV  458 (699)
T ss_pred             HHHHHHHHCCCEEEEEECCCCCCCEEECHHCCCEEECCCCCCEEEECCCCCCEECCCCCCCCCCCCCCCCCCCC-CCCCC
T ss_conf             99999997388479995477522514745319945656789863420689833226468836575546567997-52411


Q ss_pred             CCCHHHHHHHHHHCCCCCHHHHCCCCCCCCHHHHHHHHHHHCCCCCCEEEEEHHHCCCCCCCCCCHHHHHHHHHHHHHHH
Q ss_conf             54289988885204852000102321135867899999862125765798704430231134520123300034431024
Q gi|254780619|r  492 GFGIERIAEEVCEYFPLARISILSSDLEGGGGRLQLQLSAIAKGEIDIIIGTQLVAKGHNFPRMSLVGVVDGDLGLTNAD  571 (731)
Q Consensus       492 G~Gte~~~e~l~~~fp~~~v~~~d~d~~~~~~~~~~~~~~~~~~~~~ilvgTq~i~kg~~fp~v~lv~il~aD~~l~~pd  571 (731)
                      |.||||++|||+++||+++|+|+|+|++++++++++++++|.+|++|||||||||+||||||+|+||||+|||.+|+.||
T Consensus       459 g~Gteri~eel~~~FP~~~i~r~d~d~~~~~~~~~~~~~~~~~~~~dIlvGTqmiakG~df~~v~lv~vldaD~~l~~pd  538 (699)
T PRK05580        459 GVGTERTEEELARLFPGARVLRIDRDTTRRKGALEQLLEDFARGEADILVGTQMLAKGHDFPNVTLVGVLDADTGLFSPD  538 (699)
T ss_pred             CHHHHHHHHHHHHHCCCCCEEEECCCCCCCCCCHHHHHHHHHCCCCCEEECCCCCCCCCCCCCEEEEEEECHHHHCCCCC
T ss_conf             16859999999977899988998475567863168899997468987897773345567777626998732265354888


Q ss_pred             HHHHHHHHHHHHHHHHCCCCCCCCCEEEEEECCCCCHHHHHHHHCCHHHHHHHHHHHHHHCCCCCCHHEEEEEEECCCHH
Q ss_conf             55789999987543110256678868999932986488899995897999999999999818888011899988459989
Q gi|254780619|r  572 LRSSERTFQLLSQVTGRAGRFGLKSLGLIQAYQPTHPVMQALVSGDADSFYESEIRARESVNLPPFGRLAAVIISGTKYQ  651 (731)
Q Consensus       572 ~ra~E~~~qll~qv~gRagr~~~~g~v~iQt~~p~~~~~~~~~~~d~~~f~~~el~~R~~~~~PPf~~~~~i~~~~~~~~  651 (731)
                      |||.||+||||+||+|||||+.++|+|+|||++|||++++++.++||+.||++||++|+.++||||++++.|++++++++
T Consensus       539 ~ra~E~~~qll~qvagragr~~~~g~viiQt~~p~~~~~~~l~~~d~~~f~~~el~~R~~~~~PPf~~l~~i~~~~~~~~  618 (699)
T PRK05580        539 FRAAERTFQLLTQVAGRAGRAEKPGEVLIQTYEPEHPLLQALLRWDYDAFAEAELAERREAGLPPFVRLALVRGSAKAVA  618 (699)
T ss_pred             CCHHHHHHHHHHHHHHHHCCCCCCCEEEEEECCCCCHHHHHHHHCCHHHHHHHHHHHHHHCCCCCHHHHHEEEEECCCHH
T ss_conf             34799999999999876556788987999937999899999996899999999999999709998687517899539999


Q ss_pred             HHHHHHHHHHHHCCC--CCCCEEECCCCCHHHHHCCEEEEEEEEECCCHHHHHHHHHHHHHHHHHCCCCCEEEEEECCHH
Q ss_conf             999999999985734--388499817675268858823799999809938999999999986421037868999706802
Q gi|254780619|r  652 EVENYAYNLKEHAPR--SSDIVVFGPAESPLFMVRGRYRFRLLIHGKRNSNLQGFFSQMYDNTIKRSNALRVQFDIDPQN  729 (731)
Q Consensus       652 ~~~~~~~~~~~~~~~--~~~~~v~GP~~~~~~k~~~~~r~~~~ik~~~~~~l~~~l~~~~~~~~~~~~~~~~~iDvDP~~  729 (731)
                      .+.+.+..+.+.++.  ..+++|+||+|++++|++|+|||+|+||++++..|++.++.++....+.+++++|.|||||+|
T Consensus       619 ~~~~~~~~~~~~~~~~~~~~~~vlGP~~~~i~k~~~~yr~~ilik~~~~~~l~~~l~~~~~~~~~~~~~v~~~idvDP~~  698 (699)
T PRK05580        619 KALKFAQQLALLLKPPLGEGVEVLGPVPAPIARIAGRYRWQILLRSPRRAALQAALRAWLALLSALRRKVRLSIDIDPLD  698 (699)
T ss_pred             HHHHHHHHHHHHHHHCCCCCEEEECCCCCCHHHHCCEEEEEEEEECCCHHHHHHHHHHHHHHHHCCCCCCEEEEECCCCC
T ss_conf             99999999999876314799099898676537878906999999879779999999999998742788866999718989


Q ss_pred             H
Q ss_conf             1
Q gi|254780619|r  730 F  730 (731)
Q Consensus       730 ~  730 (731)
                      |
T Consensus       699 f  699 (699)
T PRK05580        699 F  699 (699)
T ss_pred             C
T ss_conf             8


No 3  
>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=100.00  E-value=0  Score=1025.39  Aligned_cols=507  Identities=44%  Similarity=0.747  Sum_probs=490.2

Q ss_pred             EEECCCCHHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHCCCCCEEEEEECC-CCCHHHHHHHHHHHCCCCEE
Q ss_conf             98447531579999999999851468479971521001344555430389768996235-57235667899997199739
Q gi|254780619|r  222 LISGVTGSGKTEVYLEIVAAVLHLGKQVLILLPEISLTSAILERFQKRFGVKPAEWHSS-LSTSMREKIWRQVARGAISV  300 (731)
Q Consensus       222 LL~GvTGSGKTEVYl~li~~~L~~GkqvLiLvPEI~Lt~Q~~~rl~~rF~~~v~v~HS~-ls~~eR~~~w~~i~~G~~~I  300 (731)
                      ||+|||||||||||++++++++.+|+|+|+|||||+||+|+..||+.+||..+++|||+ ++.++|+..|.++.+|+..|
T Consensus         1 ll~G~tGsGkte~y~~~~~~~l~~g~~~~~l~Pei~l~~q~~~~~~~~fg~~~~~~h~~~l~~~~~~~~w~~~~~g~~~~   80 (524)
T TIGR00595         1 LLFGVTGSGKTEVYLQAIEKVLALGKSALVLVPEIALTPQTLQRFKGRFGSQVAVLHSGKLSDSEKLDAWRKVKLGEALV   80 (524)
T ss_pred             CCCCCCCCCHHHHHHHHHHHHHHCCCEEEEEECCHHHHHHHHHHHHHHHCCCHHHHCCCCCCCHHHHHHHHHHHCCCCEE
T ss_conf             95456788616888999999973377178970421101678999999718720101001367345688999985186005


Q ss_pred             EEECCHHHHHHHCCCEEEEEEECCCCCCHHCCC-CCCCHHHHHHHHHHHCCCCEECCCCCCCHHHHHHHHHHHHH----H
Q ss_conf             994001211001000136774055321000024-43224899999751103210000245432467753212344----4
Q gi|254780619|r  301 IVGVRSALFLPFKKLGLIVIDEEHDISYKQEEG-ILYNARDMSIVRGKIESFPVVLVSATPSIESRVNGISRRYH----S  375 (731)
Q Consensus       301 VIGtRSAif~P~~nLglIIvDEEHd~sykq~~~-pry~aRdvA~~Ra~~~~~~lilgSATPSles~~~~~~g~~~----~  375 (731)
                      |||+|||+|+|++|||+||+|||||+||||++. |+|||||+|++|++.+++|+||||||||+|+|++++++.|.    +
T Consensus        81 v~G~rsa~f~P~~~lglii~deehd~~yk~~~~~p~y~ar~~~~~~~~~~~~p~~lgsatP~le~~~~~~~~~~~p~~~~  160 (524)
T TIGR00595        81 VIGTRSALFLPLKNLGLIIVDEEHDSSYKQEELPPRYHARDVAVYRAKLFNCPVVLGSATPSLESYHNAKRGKYRPQRHL  160 (524)
T ss_pred             EECCCHHHHCCCCCCCEEEEECCCCCCCCCCCCCCCCCHHHHHHHHHHHCCCCEEECCCCCCHHHHHHHHCCCCCCHHHH
T ss_conf             64030343246211454787346452100136885520678898876404885788056722789999871665620321


Q ss_pred             HCCCCCCCCCCCCCCEECCCCCCCCCCC-CCCCHHHHHHHHHHHCCCCEEEEEECCCCEEHHCCCCCCCCCCCCCCCCCE
Q ss_conf             1243223676543321102222332224-547989999998862265517997422200000023565434310146520
Q gi|254780619|r  376 VHLSTRYRNSALPHLQVIDMRGQTIAQG-KSLSPEMIDGIRHTLARNEQTLLFLNRRGYAPLTLCQVCGNRLKCLHCSCW  454 (731)
Q Consensus       376 ~~l~~R~~~~~~P~i~ivDm~~~~~~~~-~~lS~~l~~~i~~~l~~g~qvll~lnRrGya~~~~C~~Cg~~~~C~~C~~~  454 (731)
                      +.|++|+.++.+|.++++||+++...++ .++|..|++++++++++|+|+++|+|||||++.+.|++|||++.||+|+.+
T Consensus       161 ~~l~~r~~~~~~p~~~~~d~~~~~~~~~~~~~~~~l~~~~~~~~~~~~q~~~f~n~rg~~~~~~c~~cg~~~~cp~c~~~  240 (524)
T TIGR00595       161 LVLPRRVGGRKPPEVKLIDLRKEPRQGNRSFLSPELLTALEETLAAGEQAILFLNRRGYSPNLLCRSCGYVLECPNCDVS  240 (524)
T ss_pred             HHHHHHHCCCCCCEEEEEECCCCCCCCCCCCCCHHHHHHHHHHHHCCCCEEEEEECCCCCCCEEECCCCCCEECCCCCEE
T ss_conf             11013205775751567622100021321022589999999887416706898615566530000026750105665302


Q ss_pred             EEEECCCC----CCEECHHHCCCCCCCCCCCCCCCCEECCCCCCHHHHHHHHHHCCCCCHHHHCCCCCCCCHHHHHHHHH
Q ss_conf             12113578----32000021024465556667874110013542899888852048520001023211358678999998
Q gi|254780619|r  455 LVEHRSKK----KLYCHQCGHSAIYSQSCVVCGSSGKMIACGFGIERIAEEVCEYFPLARISILSSDLEGGGGRLQLQLS  530 (731)
Q Consensus       455 l~~h~~~~----~l~Ch~Cg~~~~~~~~Cp~Cg~~~~l~~~G~Gte~~~e~l~~~fp~~~v~~~d~d~~~~~~~~~~~~~  530 (731)
                      |+||+..+    .|.|||||++.+.|..||.|++...+.++|.|||++++++...||++++.|+|+|+++.++.++.+++
T Consensus       241 ~~~h~~~~~g~p~l~ch~c~~~~~~p~~cp~c~~~~~~~~~g~G~~~~~~~l~~~~p~~~~~~~d~d~~~~~~~~~~~~~  320 (524)
T TIGR00595       241 LTYHKKEGNGQPKLRCHYCGYQEPVPKTCPACGSEDTLKYKGLGTEKVEEELAKLFPGARIARLDSDTTSRKGAHEALLN  320 (524)
T ss_pred             EEEEEECCCCCCEEEEECCCCCCCCCCCCCCCCCCCCEEECCCCHHHHHHHHHHHCCCCCEEEEECCCCCCCHHHHHHHH
T ss_conf             35532136886201221057667775436444664301203542789999999855887367641221235146899999


Q ss_pred             HHCCCCCCEEEEEHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEECCCCCHHH
Q ss_conf             62125765798704430231134520123300034431024557899999875431102566788689999329864888
Q gi|254780619|r  531 AIAKGEIDIIIGTQLVAKGHNFPRMSLVGVVDGDLGLTNADLRSSERTFQLLSQVTGRAGRFGLKSLGLIQAYQPTHPVM  610 (731)
Q Consensus       531 ~~~~~~~~ilvgTq~i~kg~~fp~v~lv~il~aD~~l~~pd~ra~E~~~qll~qv~gRagr~~~~g~v~iQt~~p~~~~~  610 (731)
                      +|..|++|||||||||+||||||+++||||+++|.+|+.|||||.||.||+++||+|||||+..+|+|+|||++|.|+.+
T Consensus       321 ~f~~g~~d~l~Gtq~~~kG~~fp~~~l~g~~~~d~~l~~~d~r~~e~~~~l~~q~~Gr~gr~~~~g~v~iqt~~P~~~~~  400 (524)
T TIGR00595       321 QFANGKADILIGTQMIAKGHDFPNVTLVGVLDADSGLHSPDFRAAERGFQLLTQVAGRAGRAEDPGEVIIQTYNPGHPAI  400 (524)
T ss_pred             HHHCCCCEEEECHHHHHCCCCCCCEEEEEEEECCCCCCCCCHHHHHHHHHHHHHHHHHCCCCCCCCEEEEEEECCCHHHH
T ss_conf             97507840675003443157744203677873120025542134677888888764100234688747997307751688


Q ss_pred             HHHHHCCHHHHHHHHHHHHHHCCCCCCHHEEEEEEECCCHHHHHHHHHHHHHHCC-C--CCCCEEECCCCCHHHHHCCEE
Q ss_conf             9999589799999999999981888801189998845998999999999998573-4--388499817675268858823
Q gi|254780619|r  611 QALVSGDADSFYESEIRARESVNLPPFGRLAAVIISGTKYQEVENYAYNLKEHAP-R--SSDIVVFGPAESPLFMVRGRY  687 (731)
Q Consensus       611 ~~~~~~d~~~f~~~el~~R~~~~~PPf~~~~~i~~~~~~~~~~~~~~~~~~~~~~-~--~~~~~v~GP~~~~~~k~~~~~  687 (731)
                      +.+..+||+.||++|+.+|+.++||||++++.+++.++++..+...++.+...+. .  ..+.+++||+|+++.|++++|
T Consensus       401 ~~~~~~~~~~f~~~~~~~r~~~~~PP~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lgp~~~~~~~~~~~~  480 (524)
T TIGR00595       401 QAALTGDYEAFYEQELAQRRALNYPPFGRLILLVFLGKNEEKAKKTAQALAELLKSALLGEGLDVLGPSPAPIAKIAGRY  480 (524)
T ss_pred             HHHHHCCCHHHHHHHHHHHHHHHCCCCCCEEEEEEECCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHCCC
T ss_conf             98760681678999887778762698310799987076335689999999975101104655311143212366651231


Q ss_pred             EEEEEEECCCHHHHHHHHHHHHH---HHHHCCCCCEEEEEECCH
Q ss_conf             79999980993899999999998---642103786899970680
Q gi|254780619|r  688 RFRLLIHGKRNSNLQGFFSQMYD---NTIKRSNALRVQFDIDPQ  728 (731)
Q Consensus       688 r~~~~ik~~~~~~l~~~l~~~~~---~~~~~~~~~~~~iDvDP~  728 (731)
                      ||++++++++...+...++.++.   .....+.++++.+|+||+
T Consensus       481 r~~~l~~~~~~~~~~~~~~~~l~~~~~~~~~~~~v~~~~d~dP~  524 (524)
T TIGR00595       481 RYQILLKSPSFLKLQKLVNKTLAHLLKEIPPSPGVYVEVDVDPV  524 (524)
T ss_pred             EEEEEEECCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEEECCCC
T ss_conf             02455423541467888999999888740678862588604679


No 4  
>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=2.2e-42  Score=343.27  Aligned_cols=354  Identities=23%  Similarity=0.346  Sum_probs=277.4

Q ss_pred             CCC-CCCHHHHHHHHHHHHHHCCC-CCEEEEECCCCHHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHCCCC-
Q ss_conf             666-68837899999998752048-961998447531579999999999851468479971521001344555430389-
Q gi|254780619|r  195 SLP-ILDKNQQDVVEQVVPLCTKG-FAVSLISGVTGSGKTEVYLEIVAAVLHLGKQVLILLPEISLTSAILERFQKRFG-  271 (731)
Q Consensus       195 ~~~-~Lt~eQ~~a~~~i~~~~~~~-f~~~LL~GvTGSGKTEVYl~li~~~L~~GkqvLiLvPEI~Lt~Q~~~rl~~rF~-  271 (731)
                      .+| .||..|+.++.+|..++.+. .+..||+|+.|||||-|.+=++-.++.+|+||++|+|+=-|+.|+++.|++-|+ 
T Consensus       303 ~LPF~LT~aQ~r~v~EI~~DL~~~~pMnRLlQGDVGSGKT~VA~la~l~~i~~GYQ~ALMAPTEiLA~QHy~~~~~~l~p  382 (721)
T TIGR00643       303 SLPFELTRAQKRVVKEILQDLKSDVPMNRLLQGDVGSGKTLVAALAMLAAIESGYQVALMAPTEILAEQHYDSLRNLLAP  382 (721)
T ss_pred             CCCCCCCHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCEEEEECCHHHHHHHHHHHHHHHHCC
T ss_conf             28887767789999999986147875322211010663899999999999846980999177689999999999996235


Q ss_pred             --CEEEEEECCCCCHHHHHHHHHHHCCCCEEEEECCHHHH---HHHCCCEEEEEEECCCCCCHHCCCCCC--CHHHHHHH
Q ss_conf             --76899623557235667899997199739994001211---001000136774055321000024432--24899999
Q gi|254780619|r  272 --VKPAEWHSSLSTSMREKIWRQVARGAISVIVGVRSALF---LPFKKLGLIVIDEEHDISYKQEEGILY--NARDMSIV  344 (731)
Q Consensus       272 --~~v~v~HS~ls~~eR~~~w~~i~~G~~~IVIGtRSAif---~P~~nLglIIvDEEHd~sykq~~~pry--~aRdvA~~  344 (731)
                        .+|++|.++++.++|......|++|++.+||||+ |+|   .-|++||||||||.|          ||  +-|+....
T Consensus       383 ~~~~vaLLTGs~k~~~r~~~~e~i~~G~~~~~vGTH-ALiqe~vef~~L~lVIiDEQH----------RFGV~QR~~L~~  451 (721)
T TIGR00643       383 LGIEVALLTGSLKGKQRKELLETIASGEIHLVVGTH-ALIQEKVEFKRLGLVIIDEQH----------RFGVEQRKKLRE  451 (721)
T ss_pred             CCCEEEEEECCCCHHHHHHHHHHHHCCCCEEEEHHH-HHHHHHHHHHCCCEEEEECCC----------CCHHHHHHHHHH
T ss_conf             485788861566787899999998639520573313-554521443147748993233----------560789999998


Q ss_pred             HHHHC----CCC-EECCCCCCCHHHHHHHHHHHHHHHCCCCCCCCCCCCCCEECCCCCCCCCCCCCCCHHHHHHHHHHHC
Q ss_conf             75110----321-0000245432467753212344412432236765433211022223322245479899999988622
Q gi|254780619|r  345 RGKIE----SFP-VVLVSATPSIESRVNGISRRYHSVHLSTRYRNSALPHLQVIDMRGQTIAQGKSLSPEMIDGIRHTLA  419 (731)
Q Consensus       345 Ra~~~----~~~-lilgSATPSles~~~~~~g~~~~~~l~~R~~~~~~P~i~ivDm~~~~~~~~~~lS~~l~~~i~~~l~  419 (731)
                      .++..    ..| +++-||||.+.|++.+..|.+..-.+.+=+.|+..-...++  +.+  ..+.| -+...+.+++.++
T Consensus       452 KG~~~~~~G~~PH~L~MtATPIPRTLALt~yGDld~S~I~elP~GR~pi~T~~~--~~~--~~~aW-~~~v~~~~~~E~~  526 (721)
T TIGR00643       452 KGQEGSMIGFAPHVLVMTATPIPRTLALTVYGDLDVSIIDELPPGRKPITTYLI--KHK--EKGAW-IDIVYEFIEEEIA  526 (721)
T ss_pred             HHHCCCCCCCCCCEEEEECCCCHHHHHHHHHHCCEEEEECCCCCCCCEEEEEEE--ECC--CCCCC-HHHHHHHHHHHHH
T ss_conf             622068867777764663788147899776500003343168545933899888--427--88775-6899999999983


Q ss_pred             CCCEEEEEECCCCEEHHCCCCCCCCCCCCCCCCCEEEEECCCCCCEECHHHCCCCCCCCCCCCCCCCEE-CCCCCCHHHH
Q ss_conf             655179974222000000235654343101465201211357832000021024465556667874110-0135428998
Q gi|254780619|r  420 RNEQTLLFLNRRGYAPLTLCQVCGNRLKCLHCSCWLVEHRSKKKLYCHQCGHSAIYSQSCVVCGSSGKM-IACGFGIERI  498 (731)
Q Consensus       420 ~g~qvll~lnRrGya~~~~C~~Cg~~~~C~~C~~~l~~h~~~~~l~Ch~Cg~~~~~~~~Cp~Cg~~~~l-~~~G~Gte~~  498 (731)
                      +|+||.|.-                         ||.                          ..+..+ ...  -.+.+
T Consensus       527 ~GrQaYvv~-------------------------PlI--------------------------~ESE~lp~lk--~A~~~  553 (721)
T TIGR00643       527 KGRQAYVVY-------------------------PLI--------------------------EESEKLPDLK--AAEAL  553 (721)
T ss_pred             CCCCEEEEE-------------------------CCC--------------------------CCCCCCCHHH--HHHHH
T ss_conf             289089996-------------------------440--------------------------3200471689--99999


Q ss_pred             HHHHHHCC-CCCHHHHCCCCCCCCHHHHHHHHHHHCCCCCCEEEEEHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             88852048-52000102321135867899999862125765798704430231134520123300034431024557899
Q gi|254780619|r  499 AEEVCEYF-PLARISILSSDLEGGGGRLQLQLSAIAKGEIDIIIGTQLVAKGHNFPRMSLVGVVDGDLGLTNADLRSSER  577 (731)
Q Consensus       499 ~e~l~~~f-p~~~v~~~d~d~~~~~~~~~~~~~~~~~~~~~ilvgTq~i~kg~~fp~v~lv~il~aD~~l~~pd~ra~E~  577 (731)
                      .++|++.| |..+|.-+.+-. ..++ -+.+++.|++++.||||.|+.|.-|-|.||.|+++|.|||            |
T Consensus       554 ~~~l~~~f~~~~~v~LlHGrm-~~~e-K~~vm~~F~~~~~~ILVsTTVIEVGVDVPnAtvMVIe~Ae------------R  619 (721)
T TIGR00643       554 YERLKKAFLPKYNVGLLHGRM-KSDE-KEAVMEEFREGEVDILVSTTVIEVGVDVPNATVMVIEDAE------------R  619 (721)
T ss_pred             HHHHHHHHCCCCEEEEECCCC-CHHH-HHHHHHHHHHCCCEEEEEEEEEEEEEECCCCCEEEEECCC------------H
T ss_conf             999888612210011330689-8478-9999998521583699997689998617977278886655------------1


Q ss_pred             H-HHHHHHHHHCCCCCCCCCEEEEEEC----CCCC-HHHHHH--H--HCCHHHHHHHHHHHHHH
Q ss_conf             9-9987543110256678868999932----9864-888999--9--58979999999999998
Q gi|254780619|r  578 T-FQLLSQVTGRAGRFGLKSLGLIQAY----QPTH-PVMQAL--V--SGDADSFYESEIRARES  631 (731)
Q Consensus       578 ~-~qll~qv~gRagr~~~~g~v~iQt~----~p~~-~~~~~~--~--~~d~~~f~~~el~~R~~  631 (731)
                      + .+.|+|+.||+|||..++-.++-+-    +|-+ ..-+.|  .  ..|=...++..|+.|..
T Consensus       620 FGLSQLHQLRGRVGRG~~~SyC~L~~kdei~~p~~~~~~~RL~~~~~~~DGF~iAE~DL~lRGP  683 (721)
T TIGR00643       620 FGLSQLHQLRGRVGRGDHQSYCLLVYKDEIKNPKSESAKKRLRVMAETLDGFVIAEEDLKLRGP  683 (721)
T ss_pred             HHHHHHHHHCEEECCCCCCCEEEEECCCCCCCCCCHHHHHHHHHHHCCCCHHHHHHHHHHHCCC
T ss_conf             0368887635001268975079981253257888646899999985155606778875532588


No 5  
>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=1.2e-42  Score=345.37  Aligned_cols=344  Identities=26%  Similarity=0.345  Sum_probs=268.7

Q ss_pred             CCC-CCCHHHHHHHHHHHHHHCCC-CCEEEEECCCCHHHHHHHHHHHHHHHHCC----CCEEEEECCCHHHHHHHHHHHC
Q ss_conf             666-68837899999998752048-96199844753157999999999985146----8479971521001344555430
Q gi|254780619|r  195 SLP-ILDKNQQDVVEQVVPLCTKG-FAVSLISGVTGSGKTEVYLEIVAAVLHLG----KQVLILLPEISLTSAILERFQK  268 (731)
Q Consensus       195 ~~~-~Lt~eQ~~a~~~i~~~~~~~-f~~~LL~GvTGSGKTEVYl~li~~~L~~G----kqvLiLvPEI~Lt~Q~~~rl~~  268 (731)
                      ..| .-|++|..|+++|.++|.+. .+=.|+.|+.|-|||||.|+|+=+++..|    |||+||||+.-|+.|++.+|++
T Consensus       504 ~FPfeeT~DQ~~AI~eik~Dm~~~~~MDRL~CGDVGfGKTEVAmRAaFkAv~~gneylKQVavLVPTT~LA~QHf~tf~~  583 (997)
T TIGR00580       504 SFPFEETPDQLKAIEEIKADMESPRPMDRLVCGDVGFGKTEVAMRAAFKAVLDGNEYLKQVAVLVPTTILAQQHFETFKE  583 (997)
T ss_pred             HCCCCCCHHHHHHHHHHHHHHCCCCCCCEEEECCCCCCHHHHHHHHHHHHHCCCCCEECEEEEECCHHHHHHHHHHHHHH
T ss_conf             38788977899999999997406898734652454885368888788876338782201168962704427778899999


Q ss_pred             CC---CCEEEEEECCCCCHHHHHHHHHHHCCCCEEEEECCHHHH---HHHCCCEEEEEEECCCCCCHHCCCCCCCHHHHH
Q ss_conf             38---976899623557235667899997199739994001211---001000136774055321000024432248999
Q gi|254780619|r  269 RF---GVKPAEWHSSLSTSMREKIWRQVARGAISVIVGVRSALF---LPFKKLGLIVIDEEHDISYKQEEGILYNARDMS  342 (731)
Q Consensus       269 rF---~~~v~v~HS~ls~~eR~~~w~~i~~G~~~IVIGtRSAif---~P~~nLglIIvDEEHd~sykq~~~pry~aRdvA  342 (731)
                      ||   |.+|..+.+-.+.+|..++...+++|+++|||||+ +++   +-|+||||+||||||-=.=||-|.         
T Consensus       584 RF~~fPv~I~~LSRF~~~~E~~~iL~~la~G~iDI~IGTH-~lL~k~v~FKdLGLlIiDEEQRFGV~~KE~---------  653 (997)
T TIGR00580       584 RFANFPVTIELLSRFRSAKEKKEILKELASGKIDILIGTH-KLLQKDVKFKDLGLLIIDEEQRFGVKQKEK---------  653 (997)
T ss_pred             HHCCCCEEEEECCCCCCCHHHHHHHHHHHCCCEEEEECCH-HHHCCCEEEECCCCEEEECCCCCCCCHHHH---------
T ss_conf             7378981687527756737899999997559422663010-412785468638646983143488311555---------


Q ss_pred             HHHHHHCCCCEECCCCCCCHHHHHHHHHHHHHHHCCCCCCCCCCCCCCEECCCCCCCCCCCCCCCH-HHHHHHHHHHCCC
Q ss_conf             997511032100002454324677532123444124322367654332110222233222454798-9999998862265
Q gi|254780619|r  343 IVRGKIESFPVVLVSATPSIESRVNGISRRYHSVHLSTRYRNSALPHLQVIDMRGQTIAQGKSLSP-EMIDGIRHTLARN  421 (731)
Q Consensus       343 ~~Ra~~~~~~lilgSATPSles~~~~~~g~~~~~~l~~R~~~~~~P~i~ivDm~~~~~~~~~~lS~-~l~~~i~~~l~~g  421 (731)
                       +-.-..++-++=-||||-+.|+|....|-=.+-.+..-+.++ +|--..|          ...++ .+.+||+..|.||
T Consensus       654 -lK~~~~~VDvLtlsATPIPRTL~MSl~g~RdlS~I~TPP~~R-~pv~T~v----------~~~~~~~~~~AI~rEL~Rg  721 (997)
T TIGR00580       654 -LKELKTSVDVLTLSATPIPRTLHMSLSGIRDLSIIATPPEDR-LPVRTFV----------MEYDDELVREAIRRELLRG  721 (997)
T ss_pred             -HCCCCCCCCEEEEECCCCHHHHHHHHHHHHHHHHCCCCCCCC-CCEEEEE----------ECCCHHHHHHHHHHHHCCC
T ss_conf             -300156765676337896055899987553322105788877-4248877----------4278689999999753139


Q ss_pred             CEEEEEECCCCEEHHCCCCCCCCCCCCCCCCCEEEEECCCCCCEECHHHCCCCCCCCCCCCCCCCEECCCCCCHHHHHHH
Q ss_conf             51799742220000002356543431014652012113578320000210244655566678741100135428998888
Q gi|254780619|r  422 EQTLLFLNRRGYAPLTLCQVCGNRLKCLHCSCWLVEHRSKKKLYCHQCGHSAIYSQSCVVCGSSGKMIACGFGIERIAEE  501 (731)
Q Consensus       422 ~qvll~lnRrGya~~~~C~~Cg~~~~C~~C~~~l~~h~~~~~l~Ch~Cg~~~~~~~~Cp~Cg~~~~l~~~G~Gte~~~e~  501 (731)
                      +||+.+.||                                                         +.    .++++++.
T Consensus       722 GQvFyv~Nr---------------------------------------------------------ie----~i~~~~~~  740 (997)
T TIGR00580       722 GQVFYVHNR---------------------------------------------------------IE----SIEKLKTQ  740 (997)
T ss_pred             CEEEEEECC---------------------------------------------------------CC----CHHHHHHH
T ss_conf             818998088---------------------------------------------------------13----57899999


Q ss_pred             HHHCCCCCHHHHCCCCCCCCHHHHHHHHHHHCCCCCCEEEEEHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             52048520001023211358678999998621257657987044302311345201233000344310245578999998
Q gi|254780619|r  502 VCEYFPLARISILSSDLEGGGGRLQLQLSAIAKGEIDIIIGTQLVAKGHNFPRMSLVGVVDGDLGLTNADLRSSERTFQL  581 (731)
Q Consensus       502 l~~~fp~~~v~~~d~d~~~~~~~~~~~~~~~~~~~~~ilvgTq~i~kg~~fp~v~lv~il~aD~~l~~pd~ra~E~~~ql  581 (731)
                      |+.+-|.++|....+-.+  .+.+|.++.+|..++.||||.|.+|.-|.|.||++.++|=+||.+--           +.
T Consensus       741 l~~LVP~arIaiaHGqM~--e~eLE~~m~~F~~~~~~vLvcTTIIE~GIDIPnANTiIi~~AD~FGL-----------aQ  807 (997)
T TIGR00580       741 LRELVPEARIAIAHGQMT--ENELEEVMLEFYKGEFDVLVCTTIIESGIDIPNANTIIIDRADKFGL-----------AQ  807 (997)
T ss_pred             HHHCCCCEEEEEEECCCC--HHHHHHHHHHHHCCCCCEEEEHHHHHCCCCHHHHHHHHHHHHCCCCH-----------HH
T ss_conf             985084326788833568--45689999986268433013221465056410012686875211470-----------34


Q ss_pred             HHHHHHCCCCCCCCCEEEEEECCCC---CHHH---HHHHHC----CHHHHHHHHHHHHHHCCC
Q ss_conf             7543110256678868999932986---4888---999958----979999999999998188
Q gi|254780619|r  582 LSQVTGRAGRFGLKSLGLIQAYQPT---HPVM---QALVSG----DADSFYESEIRARESVNL  634 (731)
Q Consensus       582 l~qv~gRagr~~~~g~v~iQt~~p~---~~~~---~~~~~~----d~~~f~~~el~~R~~~~~  634 (731)
                      |+|+-||+||+++.|=.++-..+..   ....   +++.+.    -=...+-+.|+.|=.-|+
T Consensus       808 LYQLRGRVGRs~~~AYAYlL~~~~~~Lt~~A~~RL~ai~~f~eLGaGf~iA~hDlEIRGaGNL  870 (997)
T TIGR00580       808 LYQLRGRVGRSKKKAYAYLLYPHQKALTEDALKRLEAIQEFSELGAGFKIALHDLEIRGAGNL  870 (997)
T ss_pred             HHHCCCEECCCCCEEEEEECCCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHCCCCCCCHHH
T ss_conf             745363120587126898334774001458999999997301135216788631100355001


No 6  
>PRK10917 ATP-dependent DNA helicase RecG; Provisional
Probab=100.00  E-value=9.8e-42  Score=338.25  Aligned_cols=362  Identities=24%  Similarity=0.331  Sum_probs=285.1

Q ss_pred             CCC-CCCHHHHHHHHHHHHHHCCCC-CEEEEECCCCHHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHCCCC-
Q ss_conf             666-688378999999987520489-61998447531579999999999851468479971521001344555430389-
Q gi|254780619|r  195 SLP-ILDKNQQDVVEQVVPLCTKGF-AVSLISGVTGSGKTEVYLEIVAAVLHLGKQVLILLPEISLTSAILERFQKRFG-  271 (731)
Q Consensus       195 ~~~-~Lt~eQ~~a~~~i~~~~~~~f-~~~LL~GvTGSGKTEVYl~li~~~L~~GkqvLiLvPEI~Lt~Q~~~rl~~rF~-  271 (731)
                      .+| .||++|+.|+++|..++.++. +..||+|+.|||||+|.+.++-.++..|.||.+|+|.--|+.|++..|+++|+ 
T Consensus       253 ~LPF~LT~~Q~~~~~ei~~dl~~~~~m~rllqGDVGsGKT~va~~a~~~~~~~g~q~a~maPTeiLa~Qh~~~~~~~~~~  332 (677)
T PRK10917        253 SLPFELTGAQKRVVAEILADLASPKPMNRLLQGDVGSGKTVVAALAALAAIEAGYQAALMAPTEILAEQHYRNLKKWLEP  332 (677)
T ss_pred             HCCCCCCHHHHHHHHHHHHHHCCCCCCHHHHCCCCCCCHHHHHHHHHHHHHHHCCEEEEECCCHHHHHHHHHHHHHHHHH
T ss_conf             09998898899999999987659954277732876788899999999999981994899876799999999999987763


Q ss_pred             --CEEEEEECCCCCHHHHHHHHHHHCCCCEEEEECCHHHH---HHHCCCEEEEEEECCCCCCHHCCCCCCCHHHHHHHHH
Q ss_conf             --76899623557235667899997199739994001211---0010001367740553210000244322489999975
Q gi|254780619|r  272 --VKPAEWHSSLSTSMREKIWRQVARGAISVIVGVRSALF---LPFKKLGLIVIDEEHDISYKQEEGILYNARDMSIVRG  346 (731)
Q Consensus       272 --~~v~v~HS~ls~~eR~~~w~~i~~G~~~IVIGtRSAif---~P~~nLglIIvDEEHd~sykq~~~pry~aRdvA~~Ra  346 (731)
                        .+|+++.++++.++|.++...+.+|+++|||||+ |+|   +.|+||||+||||+|          ||-+..=..++.
T Consensus       333 ~~i~v~lltg~~~~~~~~~~~~~~~~g~~~i~iGTH-al~~~~v~f~~LglvviDEQH----------rFGV~QR~~l~~  401 (677)
T PRK10917        333 LGIRVALLTGSLKGKERREILEALASGEADIVIGTH-ALIQDDVEFHNLGLVIIDEQH----------RFGVHQRLALRE  401 (677)
T ss_pred             CCCEEEEEECCCHHHHHHHHHHHHHCCCCCEEEEHH-HHHHCCCCCCCCCEEEECHHH----------HHHHHHHHHHHH
T ss_conf             498899840774177899999998579977897307-877355644666569953057----------763999999984


Q ss_pred             HHCCCCEECCCCCCCHHHHHHHHHHHHHHHCCCCCCCCCCCCCCEECCCCCCCCCCCCCCCHHHHHHHHHHHCCCCEEEE
Q ss_conf             11032100002454324677532123444124322367654332110222233222454798999999886226551799
Q gi|254780619|r  347 KIESFPVVLVSATPSIESRVNGISRRYHSVHLSTRYRNSALPHLQVIDMRGQTIAQGKSLSPEMIDGIRHTLARNEQTLL  426 (731)
Q Consensus       347 ~~~~~~lilgSATPSles~~~~~~g~~~~~~l~~R~~~~~~P~i~ivDm~~~~~~~~~~lS~~l~~~i~~~l~~g~qvll  426 (731)
                      +-.+.-++..||||-..|+..+..|......+.+.+.++..-...++.-.         --..+.+.|++.+++|+||.+
T Consensus       402 k~~~~~~L~mtATPIPRtla~~~~g~~d~s~i~~~P~~r~~i~T~~~~~~---------~~~~~~~~i~~~~~~g~q~y~  472 (677)
T PRK10917        402 KGENPHVLVMTATPIPRTLAMTAYGDLDVSVIDELPPGRKPITTVVIPDS---------RRDEVYERIREEIAKGRQAYV  472 (677)
T ss_pred             CCCCCEEEEEECCCCHHHHHHHHHCCCCEEECCCCCCCCCCCEEEEECHH---------HHHHHHHHHHHHHHCCCEEEE
T ss_conf             39997299983688438899987357666666779999987269997625---------689999999999975992899


Q ss_pred             EECCCCEEHHCCCCCCCCCCCCCCCCCEEEEECCCCCCEECHHHCCCCCCCCCCCCCCCCEECCCCCCHHHHHHHHHHCC
Q ss_conf             74222000000235654343101465201211357832000021024465556667874110013542899888852048
Q gi|254780619|r  427 FLNRRGYAPLTLCQVCGNRLKCLHCSCWLVEHRSKKKLYCHQCGHSAIYSQSCVVCGSSGKMIACGFGIERIAEEVCEYF  506 (731)
Q Consensus       427 ~lnRrGya~~~~C~~Cg~~~~C~~C~~~l~~h~~~~~l~Ch~Cg~~~~~~~~Cp~Cg~~~~l~~~G~Gte~~~e~l~~~f  506 (731)
                      .-                         |+.-.                         |. .+.  ....+...+.|++.|
T Consensus       473 v~-------------------------p~iee-------------------------se-~~~--~~~~~~~~~~l~~~~  499 (677)
T PRK10917        473 VC-------------------------PLIEE-------------------------SE-KLD--LQSAEETYEELQKAL  499 (677)
T ss_pred             EE-------------------------CCCCC-------------------------CC-CCH--HHHHHHHHHHHHHHC
T ss_conf             94-------------------------13112-------------------------33-201--777999999998448


Q ss_pred             CCCHHHHCCCCCCCCHHHHHHHHHHHCCCCCCEEEEEHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             52000102321135867899999862125765798704430231134520123300034431024557899999875431
Q gi|254780619|r  507 PLARISILSSDLEGGGGRLQLQLSAIAKGEIDIIIGTQLVAKGHNFPRMSLVGVVDGDLGLTNADLRSSERTFQLLSQVT  586 (731)
Q Consensus       507 p~~~v~~~d~d~~~~~~~~~~~~~~~~~~~~~ilvgTq~i~kg~~fp~v~lv~il~aD~~l~~pd~ra~E~~~qll~qv~  586 (731)
                      |+.+|..+..-.  +....+.++++|.+|++||||.|.+|.-|.|.||.++++|.|||..-           .++|+|+.
T Consensus       500 ~~~~v~~~hG~m--~~~ek~~~m~~F~~g~~~iLvsTtviEvGvdvpna~~mvi~~aerfG-----------lsqLhQLR  566 (677)
T PRK10917        500 PELRVGLLHGRM--KPAEKDAVMAAFKAGEIDILVATTVIEVGVDVPNATVMVIENAERFG-----------LAQLHQLR  566 (677)
T ss_pred             CCCEEEEECCCC--CHHHHHHHHHHHHCCCCCEEEECCEEECCCCCCCCCEEEEECCCCCC-----------HHHHHHHC
T ss_conf             997599830789--87899999999983999999989897558678888589997701053-----------67887742


Q ss_pred             HCCCCCCCCCEEEEEECCCCCH-H---HHHHH-HCCHHHHHHHHHHHH--------HHCCCCCCHHEEEE
Q ss_conf             1025667886899993298648-8---89999-589799999999999--------98188880118999
Q gi|254780619|r  587 GRAGRFGLKSLGLIQAYQPTHP-V---MQALV-SGDADSFYESEIRAR--------ESVNLPPFGRLAAV  643 (731)
Q Consensus       587 gRagr~~~~g~v~iQt~~p~~~-~---~~~~~-~~d~~~f~~~el~~R--------~~~~~PPf~~~~~i  643 (731)
                      ||+||+..+|-.++-+..+-+. .   ++.+. ..|-...++..|+.|        ++.|+|.| +++-+
T Consensus       567 GRVgRg~~~~~c~l~~~~~~~~~~~~Rl~~~~~~~dGf~iae~Dl~lRg~G~~~G~~QsG~~~f-~~adl  635 (677)
T PRK10917        567 GRVGRGAAQSYCVLLYKDPLSETARERLKIMRETNDGFEIAEKDLELRGPGELLGTRQSGLPEF-KVADL  635 (677)
T ss_pred             CCCCCCCCCEEEEEEECCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHCCCCCCCCCCCCCCCCC-EEEEH
T ss_conf             7436788845899983899997899999999985874999999996158856688766698874-47408


No 7  
>PRK10689 transcription-repair coupling factor; Provisional
Probab=100.00  E-value=2.2e-41  Score=335.59  Aligned_cols=314  Identities=22%  Similarity=0.311  Sum_probs=259.3

Q ss_pred             CCCC-CCCHHHHHHHHHHHHHHCCC-CCEEEEECCCCHHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHCCC-
Q ss_conf             4666-68837899999998752048-96199844753157999999999985146847997152100134455543038-
Q gi|254780619|r  194 FSLP-ILDKNQQDVVEQVVPLCTKG-FAVSLISGVTGSGKTEVYLEIVAAVLHLGKQVLILLPEISLTSAILERFQKRF-  270 (731)
Q Consensus       194 ~~~~-~Lt~eQ~~a~~~i~~~~~~~-f~~~LL~GvTGSGKTEVYl~li~~~L~~GkqvLiLvPEI~Lt~Q~~~rl~~rF-  270 (731)
                      ...| ..|++|..|++++..++.++ .+-.|+.|+.|.|||||.|+++-.++..||||.||||+.-|+.|+++.|++|| 
T Consensus       595 ~~FpyeET~DQl~AI~eV~~DMes~~PMDRLiCGDVGfGKTEVA~RAAFkav~~gkQVavlvPTTiLA~QH~~tF~~Rf~  674 (1148)
T PRK10689        595 DSFPFETTPDQAQAINAVLSDMCQPLAMDRLVCGDVGFGKTEVAMRAAFLAVENHKQVAVLVPTTLLAQQHYDNFRDRFA  674 (1148)
T ss_pred             HCCCCCCCHHHHHHHHHHHHHHHCCCCCCEEEECCCCCCHHHHHHHHHHHHHHCCCEEEEEECCCCCHHHHHHHHHHHHH
T ss_conf             60999787689999999987763886774156768888779999999999996398089983662237999999998764


Q ss_pred             --CCEEEEEECCCCCHHHHHHHHHHHCCCCEEEEECCHHHH---HHHCCCEEEEEEECCCCCCHHCCCCCCCHHHHHHHH
Q ss_conf             --976899623557235667899997199739994001211---001000136774055321000024432248999997
Q gi|254780619|r  271 --GVKPAEWHSSLSTSMREKIWRQVARGAISVIVGVRSALF---LPFKKLGLIVIDEEHDISYKQEEGILYNARDMSIVR  345 (731)
Q Consensus       271 --~~~v~v~HS~ls~~eR~~~w~~i~~G~~~IVIGtRSAif---~P~~nLglIIvDEEHd~sykq~~~pry~aRdvA~~R  345 (731)
                        +.+|.++.--.|++|+.++...+++|+++|||||+ +++   .-|+||||+||||||          ||-++.=-.++
T Consensus       675 ~~pv~i~~LsRf~s~ke~~~i~~~l~~G~idIvIGTH-~ll~~dv~f~~LGLlIiDEEq----------rFGV~~KE~lk  743 (1148)
T PRK10689        675 NWPVRIEMLSRFRSAKEQTQILAEAAEGKIDILIGTH-KLLQSDVKWKDLGLLIVDEEH----------RFGVRHKERIK  743 (1148)
T ss_pred             CCCCEEEEECCCCCHHHHHHHHHHHHCCCCCEEEHHH-HHHCCCCCCCCCCEEEECCCH----------HCCHHHHHHHH
T ss_conf             1573377503888899999999998669987762048-886698654666437860102----------13799999997


Q ss_pred             HHHCCCCEECCCCCCCHHHHHHHHHHHHHHHCCCCCCCCCCCCCCEECCCCCCCCCCCCCCCHHHHHHHHHHHCCCCEEE
Q ss_conf             51103210000245432467753212344412432236765433211022223322245479899999988622655179
Q gi|254780619|r  346 GKIESFPVVLVSATPSIESRVNGISRRYHSVHLSTRYRNSALPHLQVIDMRGQTIAQGKSLSPEMIDGIRHTLARNEQTL  425 (731)
Q Consensus       346 a~~~~~~lilgSATPSles~~~~~~g~~~~~~l~~R~~~~~~P~i~ivDm~~~~~~~~~~lS~~l~~~i~~~l~~g~qvl  425 (731)
                      ....++.++--||||-..|++.+..|--.+..+.+-+.++ +|--+.|      .   .+=.....++|...+.+|.||.
T Consensus       744 ~l~~~vdvLtltATPIPRTL~msl~G~rdlS~i~tpP~~R-~~v~T~v------~---~~~~~~i~eai~re~~rggq~~  813 (1148)
T PRK10689        744 AMRADVDILTLTATPIPRTLNMAMSGMRDLSIIATPPARR-LAVKTFV------R---EYDSLVVREAILREILRGGQVY  813 (1148)
T ss_pred             HCCCCCCEEEEECCCCHHHHHHHHCCCCCEEEECCCCCCC-CCCEEEE------E---CCCHHHHHHHHHHHHHHCCEEE
T ss_conf             2289987897625564469999880773302213699989-8708998------3---5872999999999998188089


Q ss_pred             EEECCCCEEHHCCCCCCCCCCCCCCCCCEEEEECCCCCCEECHHHCCCCCCCCCCCCCCCCEECCCCCCHHHHHHHHHHC
Q ss_conf             97422200000023565434310146520121135783200002102446555666787411001354289988885204
Q gi|254780619|r  426 LFLNRRGYAPLTLCQVCGNRLKCLHCSCWLVEHRSKKKLYCHQCGHSAIYSQSCVVCGSSGKMIACGFGIERIAEEVCEY  505 (731)
Q Consensus       426 l~lnRrGya~~~~C~~Cg~~~~C~~C~~~l~~h~~~~~l~Ch~Cg~~~~~~~~Cp~Cg~~~~l~~~G~Gte~~~e~l~~~  505 (731)
                      ++.||--                                                             +++++++.|+++
T Consensus       814 ~~~~~~~-------------------------------------------------------------~i~~~~~~~~~~  832 (1148)
T PRK10689        814 YLYNDVE-------------------------------------------------------------NIQKAAERLAEL  832 (1148)
T ss_pred             EEECCHH-------------------------------------------------------------HHHHHHHHHHHH
T ss_conf             9953254-------------------------------------------------------------199999999974


Q ss_pred             CCCCHHHHCCCCCCCCHHHHHHHHHHHCCCCCCEEEEEHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             85200010232113586789999986212576579870443023113452012330003443102455789999987543
Q gi|254780619|r  506 FPLARISILSSDLEGGGGRLQLQLSAIAKGEIDIIIGTQLVAKGHNFPRMSLVGVVDGDLGLTNADLRSSERTFQLLSQV  585 (731)
Q Consensus       506 fp~~~v~~~d~d~~~~~~~~~~~~~~~~~~~~~ilvgTq~i~kg~~fp~v~lv~il~aD~~l~~pd~ra~E~~~qll~qv  585 (731)
                      +|+++|.......  +...+++.+.+|..|+.||||.|.+|.-|+|.||++.++|-+||.+-.           +.|+|+
T Consensus       833 ~p~~~~~~~hg~m--~~~~~e~~m~~f~~~~~~~l~~ttiie~g~dip~ant~ii~~a~~~gl-----------~ql~ql  899 (1148)
T PRK10689        833 VPEARIAIGHGQM--RERELERVMNDFHHQRFNVLVCTTIIETGIDIPTANTIIIERADHFGL-----------AQLHQL  899 (1148)
T ss_pred             CCCCCEEEEECCC--CHHHHHHHHHHHHCCCCCEEEECCEEECCCCCCCCCEEEEECHHHCCH-----------HHHHHH
T ss_conf             8777189998999--989999999999759988999897876586677884799975321455-----------777754


Q ss_pred             HHCCCCCCCCCEEEEEE
Q ss_conf             11025667886899993
Q gi|254780619|r  586 TGRAGRFGLKSLGLIQA  602 (731)
Q Consensus       586 ~gRagr~~~~g~v~iQt  602 (731)
                      .||+||+.+.+-.++-+
T Consensus       900 rgrvgr~~~~ayaYll~  916 (1148)
T PRK10689        900 RGRVGRSHHQAYAWLLT  916 (1148)
T ss_pred             CCCCCCCCCEEEEEEEE
T ss_conf             36557788707999986


No 8  
>COG1197 Mfd Transcription-repair coupling factor (superfamily II helicase) [DNA replication, recombination, and repair / Transcription]
Probab=100.00  E-value=2.1e-38  Score=312.75  Aligned_cols=345  Identities=25%  Similarity=0.324  Sum_probs=264.1

Q ss_pred             CCCC-CCCHHHHHHHHHHHHHHCCC-CCEEEEECCCCHHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHCCC-
Q ss_conf             4666-68837899999998752048-96199844753157999999999985146847997152100134455543038-
Q gi|254780619|r  194 FSLP-ILDKNQQDVVEQVVPLCTKG-FAVSLISGVTGSGKTEVYLEIVAAVLHLGKQVLILLPEISLTSAILERFQKRF-  270 (731)
Q Consensus       194 ~~~~-~Lt~eQ~~a~~~i~~~~~~~-f~~~LL~GvTGSGKTEVYl~li~~~L~~GkqvLiLvPEI~Lt~Q~~~rl~~rF-  270 (731)
                      ...| ..|++|..|++++..++.++ .+-.|+.|+.|-|||||.|+++-.++..||||.||||..-|+.|+++.|++|| 
T Consensus       589 ~~FPyeET~DQl~AI~eVk~DM~~~kpMDRLiCGDVGFGKTEVAmRAAFkAV~~GKQVAvLVPTTlLA~QHy~tFkeRF~  668 (1139)
T COG1197         589 ASFPYEETPDQLKAIEEVKRDMESGKPMDRLICGDVGFGKTEVAMRAAFKAVMDGKQVAVLVPTTLLAQQHYETFKERFA  668 (1139)
T ss_pred             HCCCCCCCHHHHHHHHHHHHHHCCCCCCHHEEECCCCCCHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHHHHHC
T ss_conf             54998578789999999998860698661025657687599999999999863797499992607868998999998733


Q ss_pred             --CCEEEEEECCCCCHHHHHHHHHHHCCCCEEEEECCHHHH--HHHCCCEEEEEEECCCCCCHHCCCCCCCHHHHHHHHH
Q ss_conf             --976899623557235667899997199739994001211--0010001367740553210000244322489999975
Q gi|254780619|r  271 --GVKPAEWHSSLSTSMREKIWRQVARGAISVIVGVRSALF--LPFKKLGLIVIDEEHDISYKQEEGILYNARDMSIVRG  346 (731)
Q Consensus       271 --~~~v~v~HS~ls~~eR~~~w~~i~~G~~~IVIGtRSAif--~P~~nLglIIvDEEHd~sykq~~~pry~aRdvA~~Ra  346 (731)
                        +.+|.++..-.|.+|...+...+++|+++|||||+.-+-  .-|+||||+||||||          ||-++.=-....
T Consensus       669 ~fPV~I~~LSRF~s~kE~~~il~~la~G~vDIvIGTHrLL~kdv~FkdLGLlIIDEEq----------RFGVk~KEkLK~  738 (1139)
T COG1197         669 GFPVRIEVLSRFRSAKEQKEILKGLAEGKVDIVIGTHRLLSKDVKFKDLGLLIIDEEQ----------RFGVKHKEKLKE  738 (1139)
T ss_pred             CCCEEEEEECCCCCHHHHHHHHHHHHCCCCCEEEECHHHHCCCCEEECCCEEEEECHH----------HCCCCHHHHHHH
T ss_conf             8982588860557889999999998569845899631764789677047648974435----------327117899987


Q ss_pred             HHCCCCEECCCCCCCHHHHHHHHHHHHHHHCCCCCCCCCCCCCCEECCCCCCCCCCCCCCCHHHHHHHHHHHCCCCEEEE
Q ss_conf             11032100002454324677532123444124322367654332110222233222454798999999886226551799
Q gi|254780619|r  347 KIESFPVVLVSATPSIESRVNGISRRYHSVHLSTRYRNSALPHLQVIDMRGQTIAQGKSLSPEMIDGIRHTLARNEQTLL  426 (731)
Q Consensus       347 ~~~~~~lilgSATPSles~~~~~~g~~~~~~l~~R~~~~~~P~i~ivDm~~~~~~~~~~lS~~l~~~i~~~l~~g~qvll  426 (731)
                      -..++.++--||||...|++.+..|-=.+..+..-+.+ .+|--..|      .+.+   +..+.++|...|.+|.||+.
T Consensus       739 Lr~~VDvLTLSATPIPRTL~Msm~GiRdlSvI~TPP~~-R~pV~T~V------~~~d---~~~ireAI~REl~RgGQvfY  808 (1139)
T COG1197         739 LRANVDVLTLSATPIPRTLNMSLSGIRDLSVIATPPED-RLPVKTFV------SEYD---DLLIREAILRELLRGGQVFY  808 (1139)
T ss_pred             HHCCCCEEEEECCCCCCHHHHHHHCCHHHHHCCCCCCC-CCCEEEEE------ECCC---HHHHHHHHHHHHHCCCEEEE
T ss_conf             75057289741788754477777443033111479987-72128887------1588---28999999998715987999


Q ss_pred             EECCCCEEHHCCCCCCCCCCCCCCCCCEEEEECCCCCCEECHHHCCCCCCCCCCCCCCCCEECCCCCCHHHHHHHHHHCC
Q ss_conf             74222000000235654343101465201211357832000021024465556667874110013542899888852048
Q gi|254780619|r  427 FLNRRGYAPLTLCQVCGNRLKCLHCSCWLVEHRSKKKLYCHQCGHSAIYSQSCVVCGSSGKMIACGFGIERIAEEVCEYF  506 (731)
Q Consensus       427 ~lnRrGya~~~~C~~Cg~~~~C~~C~~~l~~h~~~~~l~Ch~Cg~~~~~~~~Cp~Cg~~~~l~~~G~Gte~~~e~l~~~f  506 (731)
                      +.||                                                         .    -.+|++.++|++++
T Consensus       809 v~Nr---------------------------------------------------------V----~~Ie~~~~~L~~LV  827 (1139)
T COG1197         809 VHNR---------------------------------------------------------V----ESIEKKAERLRELV  827 (1139)
T ss_pred             EECC---------------------------------------------------------C----CCHHHHHHHHHHHC
T ss_conf             9433---------------------------------------------------------3----12999999999859


Q ss_pred             CCCHHHHCCCCCCCCHHHHHHHHHHHCCCCCCEEEEEHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             52000102321135867899999862125765798704430231134520123300034431024557899999875431
Q gi|254780619|r  507 PLARISILSSDLEGGGGRLQLQLSAIAKGEIDIIIGTQLVAKGHNFPRMSLVGVVDGDLGLTNADLRSSERTFQLLSQVT  586 (731)
Q Consensus       507 p~~~v~~~d~d~~~~~~~~~~~~~~~~~~~~~ilvgTq~i~kg~~fp~v~lv~il~aD~~l~~pd~ra~E~~~qll~qv~  586 (731)
                      |+++|.......  +...+|+++.+|.+|+.||||.|.+|.-|.|.||++.+.|=+||.+-.           ++|+|+.
T Consensus       828 PEarI~vaHGQM--~e~eLE~vM~~F~~g~~dVLv~TTIIEtGIDIPnANTiIIe~AD~fGL-----------sQLyQLR  894 (1139)
T COG1197         828 PEARIAVAHGQM--RERELEEVMLDFYNGEYDVLVCTTIIETGIDIPNANTIIIERADKFGL-----------AQLYQLR  894 (1139)
T ss_pred             CCEEEEEEECCC--CHHHHHHHHHHHHCCCCCEEEEEEEEECCCCCCCCCEEEEECCCCCCH-----------HHHHHHC
T ss_conf             846888852588--889999999999728888898823430476777875588965433457-----------8888751


Q ss_pred             HCCCCCCCCCEEEEEECCCCCH-------HHHHHHHC----CHHHHHHHHHHHHHHCC
Q ss_conf             1025667886899993298648-------88999958----97999999999999818
Q gi|254780619|r  587 GRAGRFGLKSLGLIQAYQPTHP-------VMQALVSG----DADSFYESEIRARESVN  633 (731)
Q Consensus       587 gRagr~~~~g~v~iQt~~p~~~-------~~~~~~~~----d~~~f~~~el~~R~~~~  633 (731)
                      ||+||+.+.+=.+.-+ .|+..       =++++.+.    .-...+.+.|+.|-.-+
T Consensus       895 GRVGRS~~~AYAYfl~-p~~k~lT~~A~kRL~aI~~~~~LGaGf~lA~~DLeIRGaGN  951 (1139)
T COG1197         895 GRVGRSNKQAYAYFLY-PPQKALTEDAEKRLEAIASFTELGAGFKLAMHDLEIRGAGN  951 (1139)
T ss_pred             CCCCCCCCEEEEEEEE-CCCCCCCHHHHHHHHHHHHHHHCCCHHHHHHCCHHCCCCCC
T ss_conf             6547767628999962-67554587899999999723323751788752010045413


No 9  
>COG1200 RecG RecG-like helicase [DNA replication, recombination, and repair / Transcription]
Probab=100.00  E-value=4.4e-38  Score=310.31  Aligned_cols=356  Identities=27%  Similarity=0.400  Sum_probs=277.3

Q ss_pred             CCC-CCCHHHHHHHHHHHHHHCCCC-CEEEEECCCCHHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHCCC--
Q ss_conf             666-688378999999987520489-6199844753157999999999985146847997152100134455543038--
Q gi|254780619|r  195 SLP-ILDKNQQDVVEQVVPLCTKGF-AVSLISGVTGSGKTEVYLEIVAAVLHLGKQVLILLPEISLTSAILERFQKRF--  270 (731)
Q Consensus       195 ~~~-~Lt~eQ~~a~~~i~~~~~~~f-~~~LL~GvTGSGKTEVYl~li~~~L~~GkqvLiLvPEI~Lt~Q~~~rl~~rF--  270 (731)
                      .+| .||..|+.++++|..++.++. +..||+|+.|||||-|.+-++-.++.+|+|+.+|+|.--|+.|++..|.+.|  
T Consensus       258 ~LPF~LT~aQ~~vi~EI~~Dl~~~~~M~RLlQGDVGSGKTvVA~laml~ai~~G~Q~ALMAPTEILA~QH~~~~~~~l~~  337 (677)
T COG1200         258 ALPFKLTNAQKRVIKEILADLASPVPMNRLLQGDVGSGKTVVALLAMLAAIEAGYQAALMAPTEILAEQHYESLRKWLEP  337 (677)
T ss_pred             HCCCCCCHHHHHHHHHHHHHHCCCHHHHHHHCCCCCCCHHHHHHHHHHHHHHCCCEEEEECCHHHHHHHHHHHHHHHHHH
T ss_conf             58997678999999999866448666678752676777899999999999872881688663799999999999987665


Q ss_pred             -CCEEEEEECCCCCHHHHHHHHHHHCCCCEEEEECCHHHH---HHHCCCEEEEEEECCCCCCHHCCCCCC--CHHHHHHH
Q ss_conf             -976899623557235667899997199739994001211---001000136774055321000024432--24899999
Q gi|254780619|r  271 -GVKPAEWHSSLSTSMREKIWRQVARGAISVIVGVRSALF---LPFKKLGLIVIDEEHDISYKQEEGILY--NARDMSIV  344 (731)
Q Consensus       271 -~~~v~v~HS~ls~~eR~~~w~~i~~G~~~IVIGtRSAif---~P~~nLglIIvDEEHd~sykq~~~pry--~aRdvA~~  344 (731)
                       |-+|+.+.++++.++|.....++.+|+++|||||+ |+|   .-|.||||+||||.|          ||  |-|..  +
T Consensus       338 ~~i~V~lLtG~~kgk~r~~~l~~l~~G~~~ivVGTH-ALiQd~V~F~~LgLVIiDEQH----------RFGV~QR~~--L  404 (677)
T COG1200         338 LGIRVALLTGSLKGKARKEILEQLASGEIDIVVGTH-ALIQDKVEFHNLGLVIIDEQH----------RFGVHQRLA--L  404 (677)
T ss_pred             CCCEEEEEECCCCHHHHHHHHHHHHCCCCCEEEECC-HHHHCCEEECCEEEEEEECCC----------CCCHHHHHH--H
T ss_conf             197489864466506799999987479989799722-122045044202389972521----------022999999--9


Q ss_pred             HHHHC-CCCEECCCCCCCHHHHHHHHHHHHHHHCCCCCCCCCCCCCCEECCCCCCCCCCCCCCCHHHHHHHHHHHCCCCE
Q ss_conf             75110-32100002454324677532123444124322367654332110222233222454798999999886226551
Q gi|254780619|r  345 RGKIE-SFPVVLVSATPSIESRVNGISRRYHSVHLSTRYRNSALPHLQVIDMRGQTIAQGKSLSPEMIDGIRHTLARNEQ  423 (731)
Q Consensus       345 Ra~~~-~~~lilgSATPSles~~~~~~g~~~~~~l~~R~~~~~~P~i~ivDm~~~~~~~~~~lS~~l~~~i~~~l~~g~q  423 (731)
                      |.+-. +--+++-||||...|+..+..|.+....+.+-+.+++.-...+|  ..+.       -+..++.|++.+.+|+|
T Consensus       405 ~~KG~~~Ph~LvMTATPIPRTLAlt~fgDldvS~IdElP~GRkpI~T~~i--~~~~-------~~~v~e~i~~ei~~GrQ  475 (677)
T COG1200         405 REKGEQNPHVLVMTATPIPRTLALTAFGDLDVSIIDELPPGRKPITTVVI--PHER-------RPEVYERIREEIAKGRQ  475 (677)
T ss_pred             HHHCCCCCCEEEEECCCCHHHHHHHHHCCCCCHHHCCCCCCCCCEEEEEE--CCCC-------HHHHHHHHHHHHHCCCE
T ss_conf             97378999679995798507889888614630111257989974089996--4444-------79999999999974997


Q ss_pred             EEEEECCCCEEHHCCCCCCCCCCCCCCCCCEEEEECCCCCCEECHHHCCCCCCCCCCCCCCCCEECCCCCCHHHHHHHHH
Q ss_conf             79974222000000235654343101465201211357832000021024465556667874110013542899888852
Q gi|254780619|r  424 TLLFLNRRGYAPLTLCQVCGNRLKCLHCSCWLVEHRSKKKLYCHQCGHSAIYSQSCVVCGSSGKMIACGFGIERIAEEVC  503 (731)
Q Consensus       424 vll~lnRrGya~~~~C~~Cg~~~~C~~C~~~l~~h~~~~~l~Ch~Cg~~~~~~~~Cp~Cg~~~~l~~~G~Gte~~~e~l~  503 (731)
                      |.|.                    |     ||.-                          .+.++..  ...+.+.++|+
T Consensus       476 aY~V--------------------c-----PLIe--------------------------eSE~l~l--~~a~~~~~~L~  502 (677)
T COG1200         476 AYVV--------------------C-----PLIE--------------------------ESEKLEL--QAAEELYEELK  502 (677)
T ss_pred             EEEE--------------------E-----CCCC--------------------------CCCCCHH--HHHHHHHHHHH
T ss_conf             9999--------------------5-----2535--------------------------4331136--54999999999


Q ss_pred             HCCCCCHHHHCCCCCCCCHHHHHHHHHHHCCCCCCEEEEEHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             04852000102321135867899999862125765798704430231134520123300034431024557899999875
Q gi|254780619|r  504 EYFPLARISILSSDLEGGGGRLQLQLSAIAKGEIDIIIGTQLVAKGHNFPRMSLVGVVDGDLGLTNADLRSSERTFQLLS  583 (731)
Q Consensus       504 ~~fp~~~v~~~d~d~~~~~~~~~~~~~~~~~~~~~ilvgTq~i~kg~~fp~v~lv~il~aD~~l~~pd~ra~E~~~qll~  583 (731)
                      ..||+.+|..+..-. +. ..-+.+...|.+||.||||.|..|.-|.|.||.|+++|.|||..-           .+.|+
T Consensus       503 ~~~~~~~vgL~HGrm-~~-~eKd~vM~~Fk~~e~~ILVaTTVIEVGVdVPnATvMVIe~AERFG-----------LaQLH  569 (677)
T COG1200         503 SFLPELKVGLVHGRM-KP-AEKDAVMEAFKEGEIDILVATTVIEVGVDVPNATVMVIENAERFG-----------LAQLH  569 (677)
T ss_pred             HHCCCCEEEEEECCC-CH-HHHHHHHHHHHCCCCCEEEEEEEEEECCCCCCCEEEEEECHHHHH-----------HHHHH
T ss_conf             870546367775689-86-779999999980887689981389952357887079996543303-----------78888


Q ss_pred             HHHHCCCCCCCCCEEEEEECCCCCHH-HHHH--H--HCCHHHHHHHHHHHHH--------HCCCCCCH
Q ss_conf             43110256678868999932986488-8999--9--5897999999999999--------81888801
Q gi|254780619|r  584 QVTGRAGRFGLKSLGLIQAYQPTHPV-MQAL--V--SGDADSFYESEIRARE--------SVNLPPFG  638 (731)
Q Consensus       584 qv~gRagr~~~~g~v~iQt~~p~~~~-~~~~--~--~~d~~~f~~~el~~R~--------~~~~PPf~  638 (731)
                      |+.||+|||..++-.++-+..|.... -+.+  .  ..|-...++..|+.|.        +.|+|-|-
T Consensus       570 QLRGRVGRG~~qSyC~Ll~~~~~~~~a~~RL~im~~t~DGF~IAE~DLklRGpGe~lG~rQSG~~~f~  637 (677)
T COG1200         570 QLRGRVGRGDLQSYCVLLYKPPLSEVAKQRLKIMRETTDGFVIAEEDLKLRGPGELLGTRQSGLPEFR  637 (677)
T ss_pred             HHCCCCCCCCCCEEEEEEECCCCCHHHHHHHHHHHHCCCCCEEHHHHHHCCCCCCCCCCCCCCCCCEE
T ss_conf             75265578875448999967987756899999887448760104656741388654687556886547


No 10 
>COG4098 comFA Superfamily II DNA/RNA helicase required for DNA uptake (late competence protein) [DNA replication, recombination, and repair]
Probab=99.96  E-value=1.4e-26  Score=222.47  Aligned_cols=316  Identities=19%  Similarity=0.314  Sum_probs=249.7

Q ss_pred             CCCHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHCCCC-CEEEE
Q ss_conf             68837899999998752048961998447531579999999999851468479971521001344555430389-76899
Q gi|254780619|r  198 ILDKNQQDVVEQVVPLCTKGFAVSLISGVTGSGKTEVYLEIVAAVLHLGKQVLILLPEISLTSAILERFQKRFG-VKPAE  276 (731)
Q Consensus       198 ~Lt~eQ~~a~~~i~~~~~~~f~~~LL~GvTGSGKTEVYl~li~~~L~~GkqvLiLvPEI~Lt~Q~~~rl~~rF~-~~v~v  276 (731)
                      .|++.|+.|.+.....+.+. ...|+|.||||||||.-++.|+.++.+|.-|.+--|-|...-.++.||++.|. ..|..
T Consensus        97 ~Ls~~Q~~as~~l~q~i~~k-~~~lv~AV~GaGKTEMif~~i~~al~~G~~vciASPRvDVclEl~~Rlk~aF~~~~I~~  175 (441)
T COG4098          97 TLSPGQKKASNQLVQYIKQK-EDTLVWAVTGAGKTEMIFQGIEQALNQGGRVCIASPRVDVCLELYPRLKQAFSNCDIDL  175 (441)
T ss_pred             CCCHHHHHHHHHHHHHHHHC-CCEEEEEECCCCCHHHHHHHHHHHHHCCCEEEEECCCCCCHHHHHHHHHHHHCCCCEEE
T ss_conf             32724789999999998715-76899974279851016999999996598699846861011777899997621498666


Q ss_pred             EECCCCCHHHHHHHHHHHCCCCEEEEECCHHHHHHHCCCEEEEEEECCCCC-CHHCCCCCCCHHHHHHHHHHHCCCCEEC
Q ss_conf             623557235667899997199739994001211001000136774055321-0000244322489999975110321000
Q gi|254780619|r  277 WHSSLSTSMREKIWRQVARGAISVIVGVRSALFLPFKKLGLIVIDEEHDIS-YKQEEGILYNARDMSIVRGKIESFPVVL  355 (731)
Q Consensus       277 ~HS~ls~~eR~~~w~~i~~G~~~IVIGtRSAif~P~~nLglIIvDEEHd~s-ykq~~~pry~aRdvA~~Ra~~~~~~lil  355 (731)
                      +|.+-.+.-           ++.+||.|-.-++-=-+-..++||||- |.. |--+.     .-..|+.-|...+.+.|+
T Consensus       176 Lyg~S~~~f-----------r~plvVaTtHQLlrFk~aFD~liIDEV-DAFP~~~d~-----~L~~Av~~ark~~g~~Iy  238 (441)
T COG4098         176 LYGDSDSYF-----------RAPLVVATTHQLLRFKQAFDLLIIDEV-DAFPFSDDQ-----SLQYAVKKARKKEGATIY  238 (441)
T ss_pred             EECCCCHHC-----------CCCEEEEEHHHHHHHHHHCCEEEEECC-CCCCCCCCH-----HHHHHHHHHHCCCCCEEE
T ss_conf             725871313-----------344799766888888864338998302-456566788-----899999975123673699


Q ss_pred             CCCCCCHHHHHHHHHHHHHHHCCCCCCCCCCCCCCEECCCCC--CCCCCCCCCCHHHHHHHHHHHCCCCEEEEEECCCCE
Q ss_conf             024543246775321234441243223676543321102222--332224547989999998862265517997422200
Q gi|254780619|r  356 VSATPSIESRVNGISRRYHSVHLSTRYRNSALPHLQVIDMRG--QTIAQGKSLSPEMIDGIRHTLARNEQTLLFLNRRGY  433 (731)
Q Consensus       356 gSATPSles~~~~~~g~~~~~~l~~R~~~~~~P~i~ivDm~~--~~~~~~~~lS~~l~~~i~~~l~~g~qvll~lnRrGy  433 (731)
                      -||||+-+.-..+.+|+...++++.|+++.++|..+.+-...  .....| .|+..|.+-|++....|.++|+|.|    
T Consensus       239 lTATp~k~l~r~~~~g~~~~~klp~RfH~~pLpvPkf~w~~~~~k~l~r~-kl~~kl~~~lekq~~~~~P~liF~p----  313 (441)
T COG4098         239 LTATPTKKLERKILKGNLRILKLPARFHGKPLPVPKFVWIGNWNKKLQRN-KLPLKLKRWLEKQRKTGRPVLIFFP----  313 (441)
T ss_pred             EECCCHHHHHHHHHHCCEEEEECCHHHCCCCCCCCCEEEECCHHHHHHHC-CCCHHHHHHHHHHHHCCCCEEEEEC----
T ss_conf             96488078888754077567634465438998987428864477776644-4778999999998743882899925----


Q ss_pred             EHHCCCCCCCCCCCCCCCCCEEEEECCCCCCEECHHHCCCCCCCCCCCCCCCCEECCCCCCHHHHHHHHHHCCCCCHHHH
Q ss_conf             00002356543431014652012113578320000210244655566678741100135428998888520485200010
Q gi|254780619|r  434 APLTLCQVCGNRLKCLHCSCWLVEHRSKKKLYCHQCGHSAIYSQSCVVCGSSGKMIACGFGIERIAEEVCEYFPLARISI  513 (731)
Q Consensus       434 a~~~~C~~Cg~~~~C~~C~~~l~~h~~~~~l~Ch~Cg~~~~~~~~Cp~Cg~~~~l~~~G~Gte~~~e~l~~~fp~~~v~~  513 (731)
                                                                        +   +..    .|++.+.|++.||..++.-
T Consensus       314 --------------------------------------------------~---I~~----~eq~a~~lk~~~~~~~i~~  336 (441)
T COG4098         314 --------------------------------------------------E---IET----MEQVAAALKKKLPKETIAS  336 (441)
T ss_pred             --------------------------------------------------C---HHH----HHHHHHHHHHHCCCCCEEE
T ss_conf             --------------------------------------------------0---588----9999999986188642156


Q ss_pred             CCCCCCCCHHHHHHHHHHHCCCCCCEEEEEHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCC
Q ss_conf             23211358678999998621257657987044302311345201233000344310245578999998754311025667
Q gi|254780619|r  514 LSSDLEGGGGRLQLQLSAIAKGEIDIIIGTQLVAKGHNFPRMSLVGVVDGDLGLTNADLRSSERTFQLLSQVTGRAGRFG  593 (731)
Q Consensus       514 ~d~d~~~~~~~~~~~~~~~~~~~~~ilvgTq~i~kg~~fp~v~lv~il~aD~~l~~pd~ra~E~~~qll~qv~gRagr~~  593 (731)
                      +.|.+..++    +.++.|++|+.+|||.|.++..|..||+|. |+|++|.+..+         +-+-|.|.|||+||..
T Consensus       337 Vhs~d~~R~----EkV~~fR~G~~~lLiTTTILERGVTfp~vd-V~Vlgaeh~vf---------TesaLVQIaGRvGRs~  402 (441)
T COG4098         337 VHSEDQHRK----EKVEAFRDGKITLLITTTILERGVTFPNVD-VFVLGAEHRVF---------TESALVQIAGRVGRSL  402 (441)
T ss_pred             EECCCCCHH----HHHHHHHCCCEEEEEEEEHHHCCCCCCCCE-EEEECCCCCCC---------CHHHHHHHHHHCCCCC
T ss_conf             533670178----999998758638999844033266435623-99954776420---------1889999752316787


Q ss_pred             C--CCEEEEEECCCCC
Q ss_conf             8--8689999329864
Q gi|254780619|r  594 L--KSLGLIQAYQPTH  607 (731)
Q Consensus       594 ~--~g~v~iQt~~p~~  607 (731)
                      .  .|.|+.=-|...-
T Consensus       403 ~~PtGdv~FFH~G~sk  418 (441)
T COG4098         403 ERPTGDVLFFHYGKSK  418 (441)
T ss_pred             CCCCCCEEEEECCCHH
T ss_conf             6898758999646338


No 11 
>PRK01297 ATP-dependent RNA helicase RhlB; Provisional
Probab=99.83  E-value=2.1e-17  Score=152.27  Aligned_cols=318  Identities=17%  Similarity=0.256  Sum_probs=189.1

Q ss_pred             HHHHCCCHHHHHHHHHCCHHHHHHHHHCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHH
Q ss_conf             87709998999752455722344554102356654344666688378999999987520489619984475315799999
Q gi|254780619|r  157 IRASQVSSHVIDGLKAQGVIKQIFEVISPVVDSPNLYFSLPILDKNQQDVVEQVVPLCTKGFAVSLISGVTGSGKTEVYL  236 (731)
Q Consensus       157 ~~~~~~s~~~i~~L~~kglI~~~~~~~~~~~~~~~~~~~~~~Lt~eQ~~a~~~i~~~~~~~f~~~LL~GvTGSGKTEVYl  236 (731)
                      ....+++..++++|.+.|+-.                     .|+=|+.++-.+...     .-.+...-||||||.-|+
T Consensus        86 F~dl~L~~~ll~aL~~~Gf~~---------------------PTpIQ~~aIP~iL~G-----kDvi~~A~TGSGKTlAyL  139 (472)
T PRK01297         86 FHDFNLAPELMHAIHDLGFPY---------------------CTPIQAQVLGYTLAG-----HDAIGRAQTGTGKTAAFL  139 (472)
T ss_pred             HHHCCCCHHHHHHHHHCCCCC---------------------CCHHHHHHHHHHHCC-----CCEEEECCCCCHHHHHHH
T ss_conf             864788999999999779999---------------------999999999999769-----988998999867999999


Q ss_pred             H-HHHHHHHC---------CCCEEEEECCCHHHHHHHHH---HHCCCCCEEEEEECCCCCHHHHHHHHHHHCCCCEEEEE
Q ss_conf             9-99998514---------68479971521001344555---43038976899623557235667899997199739994
Q gi|254780619|r  237 E-IVAAVLHL---------GKQVLILLPEISLTSAILER---FQKRFGVKPAEWHSSLSTSMREKIWRQVARGAISVIVG  303 (731)
Q Consensus       237 ~-li~~~L~~---------GkqvLiLvPEI~Lt~Q~~~r---l~~rF~~~v~v~HS~ls~~eR~~~w~~i~~G~~~IVIG  303 (731)
                      = ++...++.         +-++|||+|.--|+.|+.+.   |.+..+.++..+.++.+-.+..   ..+....++||||
T Consensus       140 LPil~~ll~~~~~~~~~~~~p~aLIL~PTRELa~QI~~~~~~L~~~~~l~v~~~~GG~~~~~q~---~~l~~~~~dIvVa  216 (472)
T PRK01297        140 ISIINQLLQTPPPKERYMGEPRALIIAPTRELVVQIAKDAAALTKYTGLNVMTFVGGMDFDKQL---KQLEARFCDILVA  216 (472)
T ss_pred             HHHHHHHHHCCCCHHCCCCCCEEEEECCCHHHHHHHHHHHHHHHCCCCCEEEEEECCCCHHHHH---HHHHCCCCCEEEE
T ss_conf             9999999717751011368952999879999999999999997462797699997898879999---9985589988997


Q ss_pred             CCHHHH-------HHHCCCEEEEEEECCCCCCHHCCCCCCCHHHHHHHHHHHCCCCEECCCCCCCHHHHHHHHHHHHHHH
Q ss_conf             001211-------0010001367740553210000244322489999975110321000024543246775321234441
Q gi|254780619|r  304 VRSALF-------LPFKKLGLIVIDEEHDISYKQEEGILYNARDMSIVRGKIESFPVVLVSATPSIESRVNGISRRYHSV  376 (731)
Q Consensus       304 tRSAif-------~P~~nLglIIvDEEHd~sykq~~~pry~aRdvA~~Ra~~~~~~lilgSATPSles~~~~~~g~~~~~  376 (731)
                      |-.-+.       .-+.++..+|+||-+ --+  +.++.=+.+.+.-......+-..+|-|||-+-+....+..-    +
T Consensus       217 TPGRL~~l~~~~~~~l~~v~~lVlDEAD-~LL--d~gf~~~v~~Il~~~p~~~~rQ~~lfSATl~~~v~~l~~~~----~  289 (472)
T PRK01297        217 TPGRLLDFNQRGEVHLDMVEVMVLDEAD-RML--DMGFIPQVRQIIRQTPRKEERQTLLFSATFTDDVMNLAKQW----T  289 (472)
T ss_pred             CHHHHHHHHCCCCEECCCCEEEEEECHH-HHH--CCCCHHHHHHHHHHCCCCCCCEEEEEECCCCHHHHHHHHHH----C
T ss_conf             9799998743482542552299998731-210--25759999999996898557169998525778999999997----7


Q ss_pred             CCCCCCCCCCCCCCEECCCCCCC-----CCCC-CCCC-----HHHHHHHHHHHCCCCEEEEEECCCCEEHHCCCCCCCCC
Q ss_conf             24322367654332110222233-----2224-5479-----89999998862265517997422200000023565434
Q gi|254780619|r  377 HLSTRYRNSALPHLQVIDMRGQT-----IAQG-KSLS-----PEMIDGIRHTLARNEQTLLFLNRRGYAPLTLCQVCGNR  445 (731)
Q Consensus       377 ~l~~R~~~~~~P~i~ivDm~~~~-----~~~~-~~lS-----~~l~~~i~~~l~~g~qvll~lnRrGya~~~~C~~Cg~~  445 (731)
                        .+       |.  +|....+.     .... ....     ..|.+.+++.  ...++|||.|++--+           
T Consensus       290 --~~-------p~--~v~i~~~~~~~~~v~q~~~~~~~~dk~~~L~~ll~~~--~~~k~IIF~nt~~~~-----------  345 (472)
T PRK01297        290 --TD-------PA--IVEIEPENVASDTVEQHVYAVAGSDKYKLLYNLVTQN--PWERVMVFANRKDEV-----------  345 (472)
T ss_pred             --CC-------CE--EEEECCCCCCCCCEEEEEEECCHHHHHHHHHHHHHHC--CCCCEEEECCCHHHH-----------
T ss_conf             --99-------88--9996577667776028999818889999999999847--987368961749999-----------


Q ss_pred             CCCCCCCCEEEEECCCCCCEECHHHCCCCCCCCCCCCCCCCEECCCCCCHHHHHHHHHHCCCCCHHHHCCCCCCCCHHHH
Q ss_conf             31014652012113578320000210244655566678741100135428998888520485200010232113586789
Q gi|254780619|r  446 LKCLHCSCWLVEHRSKKKLYCHQCGHSAIYSQSCVVCGSSGKMIACGFGIERIAEEVCEYFPLARISILSSDLEGGGGRL  525 (731)
Q Consensus       446 ~~C~~C~~~l~~h~~~~~l~Ch~Cg~~~~~~~~Cp~Cg~~~~l~~~G~Gte~~~e~l~~~fp~~~v~~~d~d~~~~~~~~  525 (731)
                                                                        +++.+.|.+.  +.++..+.+|..  ....
T Consensus       346 --------------------------------------------------~~l~~~L~~~--g~~~~~lhg~l~--q~~R  371 (472)
T PRK01297        346 --------------------------------------------------RRIEERLVKD--GINAAQLSGDVP--QHKR  371 (472)
T ss_pred             --------------------------------------------------HHHHHHHHHC--CCCEEEEECCCC--HHHH
T ss_conf             --------------------------------------------------9999876544--961686437789--9999


Q ss_pred             HHHHHHHCCCCCCEEEEEHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCEEEE
Q ss_conf             999986212576579870443023113452012330003443102455789999987543110256678868999
Q gi|254780619|r  526 QLQLSAIAKGEIDIIIGTQLVAKGHNFPRMSLVGVVDGDLGLTNADLRSSERTFQLLSQVTGRAGRFGLKSLGLI  600 (731)
Q Consensus       526 ~~~~~~~~~~~~~ilvgTq~i~kg~~fp~v~lv~il~aD~~l~~pd~ra~E~~~qll~qv~gRagr~~~~g~v~i  600 (731)
                      ...+++|.+|+..|||.|-+.+.|+|||+|++|+-.|.      |.      ...-+.+=+||+||+.+.|.++.
T Consensus       372 ~~~l~~F~~g~~~iLVaTDvaaRGLDi~~V~~VInyD~------P~------~~~~YIHRiGRTGRaG~~G~ais  434 (472)
T PRK01297        372 IKTLEGFREGKIRVLVATDVAGRGIHIDGISHVINFTL------PE------DPDDYVHRIGRTGRAGASGVSIS  434 (472)
T ss_pred             HHHHHHHHCCCCCEEEECCHHHCCCCCCCCCEEEEECC------CC------CHHHHHHCCCHHHCCCCCEEEEE
T ss_conf             99999997699969988661336677578888999689------89------76760102653126899637999


No 12 
>PRK11192 ATP-dependent RNA helicase SrmB; Provisional
Probab=99.82  E-value=8.7e-18  Score=155.11  Aligned_cols=349  Identities=16%  Similarity=0.221  Sum_probs=204.4

Q ss_pred             HHCCCHHHHHHHHHCCHHHHHHHHHCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHHHH
Q ss_conf             70999899975245572234455410235665434466668837899999998752048961998447531579999999
Q gi|254780619|r  159 ASQVSSHVIDGLKAQGVIKQIFEVISPVVDSPNLYFSLPILDKNQQDVVEQVVPLCTKGFAVSLISGVTGSGKTEVYLEI  238 (731)
Q Consensus       159 ~~~~s~~~i~~L~~kglI~~~~~~~~~~~~~~~~~~~~~~Lt~eQ~~a~~~i~~~~~~~f~~~LL~GvTGSGKTEVYl~l  238 (731)
                      .++++..++++|.+.|+-                     .+|+=|+.++-.+...     .-.++..-||||||..|+=-
T Consensus         7 ~l~L~~~l~~~L~~~g~~---------------------~pT~IQ~~aIp~il~g-----~dvl~~A~TGSGKTlaylLP   60 (417)
T PRK11192          7 ELDLDPSLLEALQDKGYT---------------------RPTAIQAEAIPPALDG-----RDVLGSAPTGTGKTAAFLLP   60 (417)
T ss_pred             HCCCCHHHHHHHHHCCCC---------------------CCCHHHHHHHHHHHCC-----CCEEEECCCCCHHHHHHHHH
T ss_conf             779899999999977999---------------------9999999999999779-----98899899986799999999


Q ss_pred             HH-HHHH------CCCCEEEEECCCHHHHHHHHHHHCC---CCCEEEEEECCCCCHHHHHHHHHHHCCCCEEEEECCHHH
Q ss_conf             99-9851------4684799715210013445554303---897689962355723566789999719973999400121
Q gi|254780619|r  239 VA-AVLH------LGKQVLILLPEISLTSAILERFQKR---FGVKPAEWHSSLSTSMREKIWRQVARGAISVIVGVRSAL  308 (731)
Q Consensus       239 i~-~~L~------~GkqvLiLvPEI~Lt~Q~~~rl~~r---F~~~v~v~HS~ls~~eR~~~w~~i~~G~~~IVIGtRSAi  308 (731)
                      +- ..+.      .+-++|||+|.-.|+.|+.+.++..   .+..++.+.++.+..+..+    .....++|||||-.-+
T Consensus        61 il~~l~~~~~~~~~~~~~LIl~PTrELa~Qi~~~~~~l~~~~~i~~~~i~Gg~~~~~q~~----~l~~~~dIlV~TPgRL  136 (417)
T PRK11192         61 ALQHLLDFPRRKSGPPRILILTPTRELAMQVADQARELAKHTHLDIATITGGVAYMNHAE----VFSENQDIVVATPGRL  136 (417)
T ss_pred             HHHHHHHHHCCCCCCCEEEEEECHHHHHHHHHHHHHHHHCCCCCCEEEEECCCCHHHHHH----HHHCCCCEEEECCCHH
T ss_conf             999987521036899649999471999999999999864005730599856878799999----9836999899786077


Q ss_pred             H-------HHHCCCEEEEEEECCCCCCHHCCCCCCCHHHHHHHHHHHCCCCEECCCCCCC---HHHHHHHHHHHHHHHCC
Q ss_conf             1-------0010001367740553210000244322489999975110321000024543---24677532123444124
Q gi|254780619|r  309 F-------LPFKKLGLIVIDEEHDISYKQEEGILYNARDMSIVRGKIESFPVVLVSATPS---IESRVNGISRRYHSVHL  378 (731)
Q Consensus       309 f-------~P~~nLglIIvDEEHd~sykq~~~pry~aRdvA~~Ra~~~~~~lilgSATPS---les~~~~~~g~~~~~~l  378 (731)
                      .       .-+.++..+|+||-|.-.   +.+..-+.+.+...  ....-..+|-|||-.   ++.+..-      ++  
T Consensus       137 ~~~l~~~~~~l~~l~~lVlDEAD~ml---d~gF~~~i~~I~~~--~~~~~Q~llfSATl~~~~v~~l~~~------~l--  203 (417)
T PRK11192        137 LQYIKEENFDCRAVETLILDEADRML---DMGFAQDVEHIAAE--TRWRKQTLLFSATLEGDGVQDFAER------LL--  203 (417)
T ss_pred             HHHHHHCCCCCCCCCEEEEECCCCCC---CCCCHHHHHHHHHH--CCCCCEEEEEEEECCHHHHHHHHHH------HC--
T ss_conf             77886367010457489996755211---13547899999864--7677238999732684789999998------36--


Q ss_pred             CCCCCCCCCCC-CEECCCCCCCCCCCC---CCC--HHHHHHHHHHHCC--CCEEEEEECCCCEEHHCCCCCCCCCCCCCC
Q ss_conf             32236765433-211022223322245---479--8999999886226--551799742220000002356543431014
Q gi|254780619|r  379 STRYRNSALPH-LQVIDMRGQTIAQGK---SLS--PEMIDGIRHTLAR--NEQTLLFLNRRGYAPLTLCQVCGNRLKCLH  450 (731)
Q Consensus       379 ~~R~~~~~~P~-i~ivDm~~~~~~~~~---~lS--~~l~~~i~~~l~~--g~qvll~lnRrGya~~~~C~~Cg~~~~C~~  450 (731)
                      .+       |. +.+-..+.+...-..   ..+  +.-...+..-+..  .+++|+|.|.+                   
T Consensus       204 ~~-------p~~i~~~~~~~~~~~i~q~~~~~~~~~~k~~~L~~ll~~~~~~k~iIF~~t~-------------------  257 (417)
T PRK11192        204 ND-------PVEVDAEPSRRERKKIHQWYYRADDLEHKTALLCHLLKQEEVTRSIVFVRTR-------------------  257 (417)
T ss_pred             CC-------CEEEEECCCCCCCCCEEEEEEEECCHHHHHHHHHHHHHCCCCCCCEEEECCH-------------------
T ss_conf             79-------8899964676666743699999376899999999998534766521531124-------------------


Q ss_pred             CCCEEEEECCCCCCEECHHHCCCCCCCCCCCCCCCCEECCCCCCHHHHHHHHHHCCCCCHHHHCCCCCCCCHHHHHHHHH
Q ss_conf             65201211357832000021024465556667874110013542899888852048520001023211358678999998
Q gi|254780619|r  451 CSCWLVEHRSKKKLYCHQCGHSAIYSQSCVVCGSSGKMIACGFGIERIAEEVCEYFPLARISILSSDLEGGGGRLQLQLS  530 (731)
Q Consensus       451 C~~~l~~h~~~~~l~Ch~Cg~~~~~~~~Cp~Cg~~~~l~~~G~Gte~~~e~l~~~fp~~~v~~~d~d~~~~~~~~~~~~~  530 (731)
                                                                ..++.+.+.|.+.  +.++..+.+|..  ......+++
T Consensus       258 ------------------------------------------~~~~~l~~~L~~~--g~~~~~lhg~l~--q~~R~~~l~  291 (417)
T PRK11192        258 ------------------------------------------ERVHELAGWLRKA--GINCCYLEGEMV--QKKRNEAIK  291 (417)
T ss_pred             ------------------------------------------HHHHHHHHHHHCC--CCCEEEECCCCC--HHHHHHHHH
T ss_conf             ------------------------------------------6676898865314--883575400179--999999999


Q ss_pred             HHCCCCCCEEEEEHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEECCCCCHHH
Q ss_conf             62125765798704430231134520123300034431024557899999875431102566788689999329864888
Q gi|254780619|r  531 AIAKGEIDIIIGTQLVAKGHNFPRMSLVGVVDGDLGLTNADLRSSERTFQLLSQVTGRAGRFGLKSLGLIQAYQPTHPVM  610 (731)
Q Consensus       531 ~~~~~~~~ilvgTq~i~kg~~fp~v~lv~il~aD~~l~~pd~ra~E~~~qll~qv~gRagr~~~~g~v~iQt~~p~~~~~  610 (731)
                      +|.+|+.+|||+|-+.+.|+|||+|+.|+-.|.      |  +    ...-+.+=+||+||+.+.|.+|----.-|...+
T Consensus       292 ~F~~g~~~vLVaTDvaaRGiDi~~V~~VInyd~------P--~----~~~~YvHRiGRTGR~G~~G~ait~v~~~d~~~~  359 (417)
T PRK11192        292 RLTDGRVNVLVATDVAARGIDIDDISHVINFDM------P--R----SADTYLHRIGRTGRAGKKGTAISLVEAHDHLLL  359 (417)
T ss_pred             HHHCCCCCEEEECCHHHCCCCCCCCCEEEEECC------C--C----CHHHHHHHCCHHHCCCCCEEEEEEECHHHHHHH
T ss_conf             997699989998124346777046988999799------9--9----888923306772348995489998748999999


Q ss_pred             HHHHHCCHHHHHHHHHHHHHHCCCCCCHH
Q ss_conf             99995897999999999999818888011
Q gi|254780619|r  611 QALVSGDADSFYESEIRARESVNLPPFGR  639 (731)
Q Consensus       611 ~~~~~~d~~~f~~~el~~R~~~~~PPf~~  639 (731)
                      +     +.+.+.++.|+.|..-+|.|=..
T Consensus       360 ~-----~ie~~~~~~~~~~~~~~~~~~~~  383 (417)
T PRK11192        360 G-----KIERYIEEPLKRRVIDELRPKTK  383 (417)
T ss_pred             H-----HHHHHHCCCCCCCCCCCCCCCCC
T ss_conf             9-----99999779887312688688988


No 13 
>PRK10590 ATP-dependent RNA helicase RhlE; Provisional
Probab=99.80  E-value=7.7e-17  Score=147.86  Aligned_cols=348  Identities=18%  Similarity=0.250  Sum_probs=200.1

Q ss_pred             HHCCCHHHHHHHHHCCHHHHHHHHHCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHHHH
Q ss_conf             70999899975245572234455410235665434466668837899999998752048961998447531579999999
Q gi|254780619|r  159 ASQVSSHVIDGLKAQGVIKQIFEVISPVVDSPNLYFSLPILDKNQQDVVEQVVPLCTKGFAVSLISGVTGSGKTEVYLEI  238 (731)
Q Consensus       159 ~~~~s~~~i~~L~~kglI~~~~~~~~~~~~~~~~~~~~~~Lt~eQ~~a~~~i~~~~~~~f~~~LL~GvTGSGKTEVYl~l  238 (731)
                      .++++..++++|.+.|+.+                     .|+=|+.++-.+...     .-.+..--||||||.-|+=-
T Consensus         5 ~lgL~~~ll~aL~~~G~~~---------------------PTpIQ~~aIP~iL~G-----rDvl~~A~TGSGKTlAflLP   58 (457)
T PRK10590          5 SLGLSPDILRAVAEQGYRE---------------------PTPIQQQAIPAVLEG-----RDLMASAQTGTGKTAGFTLP   58 (457)
T ss_pred             HCCCCHHHHHHHHHCCCCC---------------------CCHHHHHHHHHHHCC-----CCEEEECCCCHHHHHHHHHH
T ss_conf             3498999999999779999---------------------999999999999779-----98899889811899999999


Q ss_pred             HHHHHHCC---------CCEEEEECCCHHHHHHHHHHH---CCCCCEEEEEECCCCCHHHHHHHHHHHCCCCEEEEECCH
Q ss_conf             99985146---------847997152100134455543---038976899623557235667899997199739994001
Q gi|254780619|r  239 VAAVLHLG---------KQVLILLPEISLTSAILERFQ---KRFGVKPAEWHSSLSTSMREKIWRQVARGAISVIVGVRS  306 (731)
Q Consensus       239 i~~~L~~G---------kqvLiLvPEI~Lt~Q~~~rl~---~rF~~~v~v~HS~ls~~eR~~~w~~i~~G~~~IVIGtRS  306 (731)
                      +-+.|...         -++|||+|.--|+.|+.+.++   ..++..+.++.++.+-...   ...+. +.++|||||-.
T Consensus        59 il~~l~~~~~~~~~~~~~~aLIL~PTRELA~Qi~~~~~~l~~~~~~~~~~~~Gg~~~~~q---~~~l~-~~~dIlVaTPG  134 (457)
T PRK10590         59 LLQHLITRQPHAKGRRPVRALILTPTRELAAQIGENVRDYSKYLNIRSLVVFGGVSINPQ---MMKLR-GGVDVLVATPG  134 (457)
T ss_pred             HHHHHHHCCCCCCCCCCCEEEEECCHHHHHHHHHHHHHHHCCCCCCEEEEEECCCCHHHH---HHHHC-CCCCEEEECCH
T ss_conf             999986367654456882499976879999999999997425589459999799777599---99861-89998998928


Q ss_pred             HHH-------HHHCCCEEEEEEECCCCCCHHCCCCCCCHHHHHHHHHHHCCCCEECCCCCCCHHHHHHHHHHHHHHHCCC
Q ss_conf             211-------0010001367740553210000244322489999975110321000024543246775321234441243
Q gi|254780619|r  307 ALF-------LPFKKLGLIVIDEEHDISYKQEEGILYNARDMSIVRGKIESFPVVLVSATPSIESRVNGISRRYHSVHLS  379 (731)
Q Consensus       307 Aif-------~P~~nLglIIvDEEHd~sykq~~~pry~aRdvA~~Ra~~~~~~lilgSATPSles~~~~~~g~~~~~~l~  379 (731)
                      -++       .-+.++..+|+||-+.-.   +.++.-+.+.+.-..  -.....+|-|||-+-+....+..    ++.-+
T Consensus       135 RLldl~~~~~~~l~~v~~lVlDEAD~mL---d~gF~~di~~Il~~l--p~~rQ~llfSAT~~~~v~~l~~~----~l~~p  205 (457)
T PRK10590        135 RLLDLEHQNAVKLDQVEILVLDEADRML---DMGFIHDIRRVLAKL--PAKRQNLLFSATFSDDIKALAEK----LLHNP  205 (457)
T ss_pred             HHHHHHHCCCCCCCCCEEEEEECCHHHH---CCCCHHHHHHHHHHC--CCCCEEEEEECCCCHHHHHHHHH----HCCCC
T ss_conf             8898886267765752399983705651---566536689998638--76526899950488899999999----76898


Q ss_pred             CCCCCCCCCCCEECCCCC--CCCCCC-CCCC-HHHHHHHHHHHCC--CCEEEEEECCCCEEHHCCCCCCCCCCCCCCCCC
Q ss_conf             223676543321102222--332224-5479-8999999886226--551799742220000002356543431014652
Q gi|254780619|r  380 TRYRNSALPHLQVIDMRG--QTIAQG-KSLS-PEMIDGIRHTLAR--NEQTLLFLNRRGYAPLTLCQVCGNRLKCLHCSC  453 (731)
Q Consensus       380 ~R~~~~~~P~i~ivDm~~--~~~~~~-~~lS-~~l~~~i~~~l~~--g~qvll~lnRrGya~~~~C~~Cg~~~~C~~C~~  453 (731)
                      .        .|.+..-..  +..... .... ..-.+.+..-+.+  ..|+|||.|.+                      
T Consensus       206 ~--------~i~v~~~~~~~~~i~q~~~~v~~~~k~~~L~~ll~~~~~~~~iIF~~tk----------------------  255 (457)
T PRK10590        206 L--------EIEVARRNTASEQVTQHVHFVDKKRKRELLSQMIGKGNWQQVLVFTRTK----------------------  255 (457)
T ss_pred             E--------EEEECCCCCCCCCEEEEEEEECHHHHHHHHHHHHHHCCCCCEEEEECHH----------------------
T ss_conf             8--------9996367665613048999956678999999998615866335884119----------------------


Q ss_pred             EEEEECCCCCCEECHHHCCCCCCCCCCCCCCCCEECCCCCCHHHHHHHHHHCCCCCHHHHCCCCCCCCHHHHHHHHHHHC
Q ss_conf             01211357832000021024465556667874110013542899888852048520001023211358678999998621
Q gi|254780619|r  454 WLVEHRSKKKLYCHQCGHSAIYSQSCVVCGSSGKMIACGFGIERIAEEVCEYFPLARISILSSDLEGGGGRLQLQLSAIA  533 (731)
Q Consensus       454 ~l~~h~~~~~l~Ch~Cg~~~~~~~~Cp~Cg~~~~l~~~G~Gte~~~e~l~~~fp~~~v~~~d~d~~~~~~~~~~~~~~~~  533 (731)
                                                             .+++++.+.|.+.  +.++..+.+|..  ....+..+++|.
T Consensus       256 ---------------------------------------~~a~~l~~~L~~~--g~~~~~lHg~~s--q~~R~~~l~~F~  292 (457)
T PRK10590        256 ---------------------------------------HGANHLAEQLNKD--GIRSAAIHGNKS--QGARTRALADFK  292 (457)
T ss_pred             ---------------------------------------HHHHHHHHHHHHC--CCCCEEEECCCC--HHHHHHHHHHHH
T ss_conf             ---------------------------------------9999999998556--998232324789--999999999998


Q ss_pred             CCCCCEEEEEHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEECCCC-CHHHHH
Q ss_conf             2576579870443023113452012330003443102455789999987543110256678868999932986-488899
Q gi|254780619|r  534 KGEIDIIIGTQLVAKGHNFPRMSLVGVVDGDLGLTNADLRSSERTFQLLSQVTGRAGRFGLKSLGLIQAYQPT-HPVMQA  612 (731)
Q Consensus       534 ~~~~~ilvgTq~i~kg~~fp~v~lv~il~aD~~l~~pd~ra~E~~~qll~qv~gRagr~~~~g~v~iQt~~p~-~~~~~~  612 (731)
                      +|+..|||+|-+.|.|+|||+|++|+-.|.      |+      ...-+..=+||+||+.+.|.+|-- ..|+ ...++ 
T Consensus       293 ~g~~~vLVaTDvaaRGiDi~~V~~VInyD~------P~------~~e~YvHRiGRTGRaG~~G~ait~-v~~~e~~~~~-  358 (457)
T PRK10590        293 SGDIRVLVATDIAARGLDIEELPHVVNYEL------PN------VPEDYVHRIGRTGRAAATGEALSL-VCVDEHKLLR-  358 (457)
T ss_pred             CCCCCEEEECCCCCCCCCCCCCCEEEEECC------CC------CHHHEECCCCCCCCCCCCEEEEEE-ECHHHHHHHH-
T ss_conf             699829995770115566356887999389------99------744500226706058995369998-6689999999-


Q ss_pred             HHHCCHHHHHHHHHHHHHHCCCCC
Q ss_conf             995897999999999999818888
Q gi|254780619|r  613 LVSGDADSFYESEIRARESVNLPP  636 (731)
Q Consensus       613 ~~~~d~~~f~~~el~~R~~~~~PP  636 (731)
                          +.+.+...++.....-+|-|
T Consensus       359 ----~ie~~~~~~~~~~~~~~~~~  378 (457)
T PRK10590        359 ----DIEKLLKKEIPRIAIPGYEP  378 (457)
T ss_pred             ----HHHHHHCCCCCCCCCCCCCC
T ss_conf             ----99999779887403788787


No 14 
>PRK04537 ATP-dependent RNA helicase RhlB; Provisional
Probab=99.80  E-value=7.3e-17  Score=148.07  Aligned_cols=317  Identities=20%  Similarity=0.247  Sum_probs=186.1

Q ss_pred             HHHCCCHHHHHHHHHCCHHHHHHHHHCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHHH
Q ss_conf             77099989997524557223445541023566543446666883789999999875204896199844753157999999
Q gi|254780619|r  158 RASQVSSHVIDGLKAQGVIKQIFEVISPVVDSPNLYFSLPILDKNQQDVVEQVVPLCTKGFAVSLISGVTGSGKTEVYLE  237 (731)
Q Consensus       158 ~~~~~s~~~i~~L~~kglI~~~~~~~~~~~~~~~~~~~~~~Lt~eQ~~a~~~i~~~~~~~f~~~LL~GvTGSGKTEVYl~  237 (731)
                      ..++++..++++|.+.|+..                     .|+=|+.++-.+...     .-.+..--||||||.-|+=
T Consensus        12 ~~LgL~~~Ll~aL~~~Gf~~---------------------PTpIQ~~aIP~iL~G-----kDvi~~A~TGSGKTLAYlL   65 (574)
T PRK04537         12 SSFDLHPALVAGLESAGFTR---------------------CTPIQALTLPVALPG-----GDVAGQAQTGTGKTLAFLV   65 (574)
T ss_pred             HHCCCCHHHHHHHHHCCCCC---------------------CCHHHHHHHHHHHCC-----CCEEEECCCCCHHHHHHHH
T ss_conf             66698999999999779998---------------------999999999999579-----9889984898889999999


Q ss_pred             HHHH-HHH---------CCCCEEEEECCCHHHHHHHHHHH---CCCCCEEEEEECCCCCHHHHHHHHHHHCCCCEEEEEC
Q ss_conf             9999-851---------46847997152100134455543---0389768996235572356678999971997399940
Q gi|254780619|r  238 IVAA-VLH---------LGKQVLILLPEISLTSAILERFQ---KRFGVKPAEWHSSLSTSMREKIWRQVARGAISVIVGV  304 (731)
Q Consensus       238 li~~-~L~---------~GkqvLiLvPEI~Lt~Q~~~rl~---~rF~~~v~v~HS~ls~~eR~~~w~~i~~G~~~IVIGt  304 (731)
                      -+-+ .+.         .+-++|||+|.--|+.|+.+.+.   ..++.++.++.++.+-.+.    .......++|||||
T Consensus        66 PiL~~Ll~~~~l~~~~~~~p~aLILvPTRELA~QI~~~~~~l~~~~~lr~~~l~GG~~~~~q----~~~L~~g~dIVVaT  141 (574)
T PRK04537         66 AVMNRLLSRPALADRKPEDPRALILAPTRELAIQIHKDAVKFGADLGLRFALVYGGVDYDKQ----RELLQQGVDVIIAT  141 (574)
T ss_pred             HHHHHHHHCCCCCCCCCCCCEEEEECCCHHHHHHHHHHHHHHHCCCCCEEEEEECCCCHHHH----HHHHCCCCCEEEEC
T ss_conf             99999983744345778996199977989999999999999864589779999799668899----99873599989989


Q ss_pred             CHHHH--------HHHCCCEEEEEEECC---CCCCHHCCCCCCCHHHHHHHHHHHCCCCEECCCCCCCHHHHHHHHHHHH
Q ss_conf             01211--------001000136774055---3210000244322489999975110321000024543246775321234
Q gi|254780619|r  305 RSALF--------LPFKKLGLIVIDEEH---DISYKQEEGILYNARDMSIVRGKIESFPVVLVSATPSIESRVNGISRRY  373 (731)
Q Consensus       305 RSAif--------~P~~nLglIIvDEEH---d~sykq~~~pry~aRdvA~~Ra~~~~~~lilgSATPSles~~~~~~g~~  373 (731)
                      -.-++        ..+.++.++|+||-.   |.+|.+      +.+.+.-..-+..+...+|-|||-+-+....+..   
T Consensus       142 PGRLld~L~~~~~~~L~~vk~LVLDEAD~LLd~gF~~------di~~IL~~lP~~~~rQ~iLfSATl~~~V~~la~~---  212 (574)
T PRK04537        142 PGRLIDYVKQHKVVSLHACEICVLDEADRMFDLGFIK------DIRFLLRRMPERGTRQTLLFSATLSHRVLELAYE---  212 (574)
T ss_pred             HHHHHHHHHHCCCCCCCCEEEEEECCCHHHHCCCCHH------HHHHHHHHCCCCCCCEEEEEEECCCHHHHHHHHH---
T ss_conf             8999999981798653331589962732654287799------9999999666556855899983277799999999---


Q ss_pred             HHHCCCCCCCCCCCCCCEECCCCC---CCCCCCC-CCCH-HHHHHHHHHH--CCCCEEEEEECCCCEEHHCCCCCCCCCC
Q ss_conf             441243223676543321102222---3322245-4798-9999998862--2655179974222000000235654343
Q gi|254780619|r  374 HSVHLSTRYRNSALPHLQVIDMRG---QTIAQGK-SLSP-EMIDGIRHTL--ARNEQTLLFLNRRGYAPLTLCQVCGNRL  446 (731)
Q Consensus       374 ~~~~l~~R~~~~~~P~i~ivDm~~---~~~~~~~-~lS~-~l~~~i~~~l--~~g~qvll~lnRrGya~~~~C~~Cg~~~  446 (731)
                       ++.-         |..-+++...   ....... ..++ .-...+..-|  ....|+|||.|.+               
T Consensus       213 -~l~~---------P~~i~v~~~~~~~~~I~Q~~~~~~~~~K~~~L~~LL~~~~~~k~IIF~nT~---------------  267 (574)
T PRK04537        213 -HMNE---------PEKLVVETETITAARVRQRIYFPSDEEKQTLLLGLLSRSEGARTMVFVNTK---------------  267 (574)
T ss_pred             -HCCC---------CEEEEECCCCCCCCCEEEEEEECCHHHHHHHHHHHHHHCCCCCCEEECCHH---------------
T ss_conf             -7799---------869996566545776038999777789999999999726776511533418---------------


Q ss_pred             CCCCCCCEEEEECCCCCCEECHHHCCCCCCCCCCCCCCCCEECCCCCCHHHHHHHHHHCCCCCHHHHCCCCCCCCHHHHH
Q ss_conf             10146520121135783200002102446555666787411001354289988885204852000102321135867899
Q gi|254780619|r  447 KCLHCSCWLVEHRSKKKLYCHQCGHSAIYSQSCVVCGSSGKMIACGFGIERIAEEVCEYFPLARISILSSDLEGGGGRLQ  526 (731)
Q Consensus       447 ~C~~C~~~l~~h~~~~~l~Ch~Cg~~~~~~~~Cp~Cg~~~~l~~~G~Gte~~~e~l~~~fp~~~v~~~d~d~~~~~~~~~  526 (731)
                                                                    ..++++.+.|++.  +.++..+.+|..  ....+
T Consensus       268 ----------------------------------------------~~ve~l~~~L~~~--g~~v~~LHG~ls--Q~eR~  297 (574)
T PRK04537        268 ----------------------------------------------AFVERVARTLERH--GYRVGVLSGDVP--QKKRE  297 (574)
T ss_pred             ----------------------------------------------HHHHHHHHHHHHC--CCCEEEEECCCC--HHHHH
T ss_conf             ----------------------------------------------9999999999977--996899709999--99999


Q ss_pred             HHHHHHCCCCCCEEEEEHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCEEEE
Q ss_conf             99986212576579870443023113452012330003443102455789999987543110256678868999
Q gi|254780619|r  527 LQLSAIAKGEIDIIIGTQLVAKGHNFPRMSLVGVVDGDLGLTNADLRSSERTFQLLSQVTGRAGRFGLKSLGLI  600 (731)
Q Consensus       527 ~~~~~~~~~~~~ilvgTq~i~kg~~fp~v~lv~il~aD~~l~~pd~ra~E~~~qll~qv~gRagr~~~~g~v~i  600 (731)
                      ..+++|.+++..|||.|-+.|.|+|||+|++|+-.|.      |.      ...-+..=+||+||+.+.|.+|-
T Consensus       298 ~~L~~Fk~G~~~VLVaTDVAARGIDIp~V~~VINYDl------P~------~~e~YVHRIGRTGRaGr~G~AIT  359 (574)
T PRK04537        298 SLLNRFQKGQLEILVATDVAARGLHIDGVKYVYNYDL------PF------DAEDYVHRIGRTARLGEEGDAIS  359 (574)
T ss_pred             HHHHHHHCCCCCEEEECCCCCCCCCCCCCCEEEEECC------CC------CHHHHHCCCCHHHCCCCCEEEEE
T ss_conf             9999997699979977350023357146997999579------69------82141124535037899335999


No 15 
>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=99.78  E-value=8.4e-17  Score=147.60  Aligned_cols=129  Identities=24%  Similarity=0.367  Sum_probs=90.2

Q ss_pred             HHHHHHHHHHCCC--CCHHHHCCCCCCCCHHHHHHHHHHHCCCCCCEEEEEHHHCCCCCCCCCCHHHHHHHHHHHHHHHH
Q ss_conf             8998888520485--20001023211358678999998621257657987044302311345201233000344310245
Q gi|254780619|r  495 IERIAEEVCEYFP--LARISILSSDLEGGGGRLQLQLSAIAKGEIDIIIGTQLVAKGHNFPRMSLVGVVDGDLGLTNADL  572 (731)
Q Consensus       495 te~~~e~l~~~fp--~~~v~~~d~d~~~~~~~~~~~~~~~~~~~~~ilvgTq~i~kg~~fp~v~lv~il~aD~~l~~pd~  572 (731)
                      |-|.+|+|...|-  +++|--|.||-- +-. .-.++.+.+.|+.|+|||==++=-|+|.|.|.||+|||||.--+.   
T Consensus       456 TKkMAEdLTdYl~E~Gikv~YLHSeId-t~E-R~eiirdLR~G~fDVLVGINLLREGLDlPEVSLVAILDADKEGFL---  530 (667)
T TIGR00631       456 TKKMAEDLTDYLKELGIKVRYLHSEID-TLE-RVEIIRDLRLGEFDVLVGINLLREGLDLPEVSLVAILDADKEGFL---  530 (667)
T ss_pred             HHHHHHHHHHHHHCCCCEEEEECCHHH-HHH-HHHHHHHHCCCCCEEEEECCHHHCCCCCHHHHHHHHHCCCCCCCC---
T ss_conf             167788999997058837987145578-999-999999844788408860002002465114889976327888998---


Q ss_pred             HHHHHHHHHHHHHHHCCCCCCCCCEEEEEECCCCCHHHHHHHHCCHHHHHHHHHHHHHHCCCCCCHHEEEEE
Q ss_conf             578999998754311025667886899993298648889999589799999999999981888801189998
Q gi|254780619|r  573 RSSERTFQLLSQVTGRAGRFGLKSLGLIQAYQPTHPVMQALVSGDADSFYESEIRARESVNLPPFGRLAAVI  644 (731)
Q Consensus       573 ra~E~~~qll~qv~gRagr~~~~g~v~iQt~~p~~~~~~~~~~~d~~~f~~~el~~R~~~~~PPf~~~~~i~  644 (731)
                      ||    -.-|.|..|||.|... |+||+---.-. ..++.++.         |-+.|++... =|+.---|+
T Consensus       531 RS----erSLIQTIGRAARN~~-G~VilYAD~iT-~sM~~AI~---------ET~RRR~~Q~-~YNe~HgIt  586 (667)
T TIGR00631       531 RS----ERSLIQTIGRAARNVN-GKVILYADKIT-DSMQKAIE---------ETERRRKIQI-AYNEEHGIT  586 (667)
T ss_pred             CC----CCHHHHHHHHHHHCCC-CEEEEECCCCC-HHHHHHHH---------HHHHHHHHHH-HHHHHCCCC
T ss_conf             66----3027889888752579-65999728700-78999999---------8788899999-999753897


No 16 
>PRK11776 ATP-dependent RNA helicase DbpA; Provisional
Probab=99.78  E-value=2.6e-16  Score=143.88  Aligned_cols=378  Identities=17%  Similarity=0.220  Sum_probs=210.7

Q ss_pred             HHCCCHHHHHHHHHCCHHHHHHHHHCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHHHH
Q ss_conf             70999899975245572234455410235665434466668837899999998752048961998447531579999999
Q gi|254780619|r  159 ASQVSSHVIDGLKAQGVIKQIFEVISPVVDSPNLYFSLPILDKNQQDVVEQVVPLCTKGFAVSLISGVTGSGKTEVYLEI  238 (731)
Q Consensus       159 ~~~~s~~~i~~L~~kglI~~~~~~~~~~~~~~~~~~~~~~Lt~eQ~~a~~~i~~~~~~~f~~~LL~GvTGSGKTEVYl~l  238 (731)
                      ..+.+...+++|.+.|+-                     .+|+=|+.++-.+...     .-.+...-||||||.-|+=-
T Consensus         8 ~l~L~~~ll~aL~~~G~~---------------------~pTpIQ~~aIP~il~G-----~Dvi~~A~TGSGKTlAfllP   61 (459)
T PRK11776          8 TLPLPPALLANLDELGYT---------------------EMTPIQAQSLPAILAG-----KDVIAQAKTGSGKTAAFGLG   61 (459)
T ss_pred             HCCCCHHHHHHHHHCCCC---------------------CCCHHHHHHHHHHHCC-----CCEEEECCCCCHHHHHHHHH
T ss_conf             489799999999977999---------------------9998999999999779-----98899889985899999999


Q ss_pred             HHHHHHC---CCCEEEEECCCHHHHHHHHHHHCC---C-CCEEEEEECCCCCHHHHHHHHHHHCCCCEEEEECCHHHH--
Q ss_conf             9998514---684799715210013445554303---8-976899623557235667899997199739994001211--
Q gi|254780619|r  239 VAAVLHL---GKQVLILLPEISLTSAILERFQKR---F-GVKPAEWHSSLSTSMREKIWRQVARGAISVIVGVRSALF--  309 (731)
Q Consensus       239 i~~~L~~---GkqvLiLvPEI~Lt~Q~~~rl~~r---F-~~~v~v~HS~ls~~eR~~~w~~i~~G~~~IVIGtRSAif--  309 (731)
                      +-+-+..   +-|+|||+|.-.|+.|..+.++..   . +.++..+.++.+-.+..   ..+.+ .+.|||||-.-+.  
T Consensus        62 il~~l~~~~~~~qaLIL~PTRELa~QV~~~~~~l~~~~~~ikv~~l~GG~~~~~q~---~~L~~-~~~IvV~TPGRl~d~  137 (459)
T PRK11776         62 LLQKLDVKRFRVQALVLCPTRELADQVAKEIRRLARFIPNIKVLTLCGGVPMGPQI---GSLEH-GAHIIVGTPGRILDH  137 (459)
T ss_pred             HHHHCCCCCCCCCEEEEECHHHHHHHHHHHHHHHHHHCCCCEEEEEECCCCHHHHH---HHHHC-CCCEEEECCHHHHHH
T ss_conf             99841136789859999675999999999999998505882599998993279999---99746-999999895899988


Q ss_pred             -----HHHCCCEEEEEEECCCCCCHHCCCCCCCHHHHHHH-HHHHCCCCEECCCCCCCHHHHHHHHHHHHHHHCCCCCCC
Q ss_conf             -----00100013677405532100002443224899999-751103210000245432467753212344412432236
Q gi|254780619|r  310 -----LPFKKLGLIVIDEEHDISYKQEEGILYNARDMSIV-RGKIESFPVVLVSATPSIESRVNGISRRYHSVHLSTRYR  383 (731)
Q Consensus       310 -----~P~~nLglIIvDEEHd~sykq~~~pry~aRdvA~~-Ra~~~~~~lilgSATPSles~~~~~~g~~~~~~l~~R~~  383 (731)
                           +.+.++..+|+||-+.- .  +.++.   .|+... ..--.....+|-|||-+-+....+..  |  ++-+.   
T Consensus       138 l~~~~l~l~~v~~lVlDEAD~m-L--d~gF~---~~i~~Il~~~p~~rQ~~lfSAT~p~~i~~l~~~--~--l~~p~---  204 (459)
T PRK11776        138 LRKGTLDLDALNTLVLDEADRM-L--DMGFQ---DAIDAIIRQAPARRQTLLFSATYPEGIAAISAR--F--QRDPV---  204 (459)
T ss_pred             HHCCCCCCCCEEEEEEECCHHH-H--CCCCH---HHHHHHHHHCCCCCEEEEEECCCCHHHHHHHHH--H--CCCCE---
T ss_conf             7516632231038997062454-3--27866---889999986881302688845689899999999--7--78989---


Q ss_pred             CCCCCCCEECCCCCCCCCCCCCCCHHHHHHHHHHHCCCCEEEEEECCCCEEHHCCCCCCCCCCCCCCCCCEEEEECCCCC
Q ss_conf             76543321102222332224547989999998862265517997422200000023565434310146520121135783
Q gi|254780619|r  384 NSALPHLQVIDMRGQTIAQGKSLSPEMIDGIRHTLARNEQTLLFLNRRGYAPLTLCQVCGNRLKCLHCSCWLVEHRSKKK  463 (731)
Q Consensus       384 ~~~~P~i~ivDm~~~~~~~~~~lS~~l~~~i~~~l~~g~qvll~lnRrGya~~~~C~~Cg~~~~C~~C~~~l~~h~~~~~  463 (731)
                           .|.+ +  ...  ..   +         .+   +|.++.++...                            +-.
T Consensus       205 -----~i~v-~--~~~--~~---~---------~I---~q~~~~v~~~~----------------------------K~~  231 (459)
T PRK11776        205 -----EVKV-E--STH--DD---S---------TI---EQRFYEVDPDE----------------------------RLP  231 (459)
T ss_pred             -----EEEE-C--CCC--CC---C---------CC---EEEEEEECHHH----------------------------HHH
T ss_conf             -----9996-7--877--79---8---------63---79999977187----------------------------899


Q ss_pred             CEECHHHCCCCCCCCCCCCCCCCEECCCCCCHHHHHHHHHHCCCCCHHHHCCCCCCCCHHHHHHHHHHHCCCCCCEEEEE
Q ss_conf             20000210244655566678741100135428998888520485200010232113586789999986212576579870
Q gi|254780619|r  464 LYCHQCGHSAIYSQSCVVCGSSGKMIACGFGIERIAEEVCEYFPLARISILSSDLEGGGGRLQLQLSAIAKGEIDIIIGT  543 (731)
Q Consensus       464 l~Ch~Cg~~~~~~~~Cp~Cg~~~~l~~~G~Gte~~~e~l~~~fp~~~v~~~d~d~~~~~~~~~~~~~~~~~~~~~ilvgT  543 (731)
                      ..|+......+ ...-=-|.+.       -.++.+.+.|...  +.++..+.+|..  ....+..++.|.+|+.+|||+|
T Consensus       232 ~L~~ll~~~~~-~~~IIFcntk-------~~v~~l~~~L~~~--g~~~~~lHg~m~--q~~R~~~l~~F~~g~~~iLVaT  299 (459)
T PRK11776        232 ALQRLLLHYRP-ESCVVFCNTK-------KECQEVADALNAQ--GFSALALHGDLE--QRDRDQVLVRFANRSCSVLVAT  299 (459)
T ss_pred             HHHHHHHHCCC-CCEEEEECCH-------HHHHHHHHHHHHC--CCCEEEEECCCC--HHHHHHHHHHHHCCCCCEEEEH
T ss_conf             99999973687-6603761748-------9999999999867--996899879999--9999999999977999799881


Q ss_pred             HHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEECCCC-CHHHHHHHHCCHHHHH
Q ss_conf             443023113452012330003443102455789999987543110256678868999932986-4888999958979999
Q gi|254780619|r  544 QLVAKGHNFPRMSLVGVVDGDLGLTNADLRSSERTFQLLSQVTGRAGRFGLKSLGLIQAYQPT-HPVMQALVSGDADSFY  622 (731)
Q Consensus       544 q~i~kg~~fp~v~lv~il~aD~~l~~pd~ra~E~~~qll~qv~gRagr~~~~g~v~iQt~~p~-~~~~~~~~~~d~~~f~  622 (731)
                      -+.|.|+|||+|++|+-.|.=.            ...-+.+=+||+||+.+.|..+.- ..|+ ...++.+     +.+.
T Consensus       300 DvaaRGIDi~~V~~VInyDlP~------------~~e~YvHRiGRTGRaG~~G~ait~-vt~~e~~~l~~i-----e~~~  361 (459)
T PRK11776        300 DVAARGLDIKSLEAVINYELAR------------DPEVHVHRIGRTGRAGSKGLALSL-VAPEEMQRAAAI-----EDYL  361 (459)
T ss_pred             HHHHCCCCCCCCCEEEEECCCC------------CHHHHHHCCCHHHCCCCCEEEEEE-ECHHHHHHHHHH-----HHHH
T ss_conf             0434767713598899978989------------745520205251378996579999-868999999999-----9997


Q ss_pred             HHHHHH------HHHCCCCCCHHEEEEEEECCCHHHH--HHHHHHHHH
Q ss_conf             999999------9981888801189998845998999--999999998
Q gi|254780619|r  623 ESEIRA------RESVNLPPFGRLAAVIISGTKYQEV--ENYAYNLKE  662 (731)
Q Consensus       623 ~~el~~------R~~~~~PPf~~~~~i~~~~~~~~~~--~~~~~~~~~  662 (731)
                      ..++..      ......|+-..+..+.+++-..+.+  .++...+..
T Consensus       362 ~~~i~~~~~p~~~~~~~~~~~~~~~~l~i~~G~k~k~~~~divg~~~~  409 (459)
T PRK11776        362 GRKLNWEPLPSLSPLSGVPLLPPMVTLCIDGGKKDKLRPGDILGALTG  409 (459)
T ss_pred             CCCCCCCCCCCCCCCCCCCCCCCEEEEEEECCCCCCCCHHHHHHHHCC
T ss_conf             899864169996755678889985999993753148777888998617


No 17 
>PRK13766 Hef nuclease; Provisional
Probab=99.77  E-value=2.7e-17  Score=151.30  Aligned_cols=153  Identities=25%  Similarity=0.294  Sum_probs=114.5

Q ss_pred             CCCCCCCCCHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHHHHHHHHHHC-CCCEEEEECCCHHHHHHHHHHHCCC
Q ss_conf             344666688378999999987520489619984475315799999999998514-6847997152100134455543038
Q gi|254780619|r  192 LYFSLPILDKNQQDVVEQVVPLCTKGFAVSLISGVTGSGKTEVYLEIVAAVLHL-GKQVLILLPEISLTSAILERFQKRF  270 (731)
Q Consensus       192 ~~~~~~~Lt~eQ~~a~~~i~~~~~~~f~~~LL~GvTGSGKTEVYl~li~~~L~~-GkqvLiLvPEI~Lt~Q~~~rl~~rF  270 (731)
                      +..+....-+-|..+++.....      ..|+.=-||||||.|.+-+|.+.+.. ++.+++|+|...|..|..+.|++.+
T Consensus         9 ~~p~~ie~R~YQ~el~~~Al~~------NtiVvLPTG~GKT~IA~lvi~~~l~~~~gKilFLaPT~pLV~Qq~~~~~~~l   82 (764)
T PRK13766          9 IKPNTIEARLYQQLLAAKALKG------NTLVVLPTGLGKTAIALLVIAERLQKYGGKVLILAPTKPLVEQHAEFFRKFL   82 (764)
T ss_pred             CCCCCCCCCHHHHHHHHHHHHC------CEEEEECCCCCHHHHHHHHHHHHHHHCCCEEEEECCCHHHHHHHHHHHHHHC
T ss_conf             5868776538799999999858------9899959986689999999999997489889998588889999999999970


Q ss_pred             C---CEEEEEECCCCCHHHHHHHHHHHCCCCEEEEECCHHH-------HHHHCCCEEEEEEECCCCCCHHCCCCCCCHHH
Q ss_conf             9---7689962355723566789999719973999400121-------10010001367740553210000244322489
Q gi|254780619|r  271 G---VKPAEWHSSLSTSMREKIWRQVARGAISVIVGVRSAL-------FLPFKKLGLIVIDEEHDISYKQEEGILYNARD  340 (731)
Q Consensus       271 ~---~~v~v~HS~ls~~eR~~~w~~i~~G~~~IVIGtRSAi-------f~P~~nLglIIvDEEHd~sykq~~~pry~aRd  340 (731)
                      +   ..++.+++..++.+|.+.|.     +.+|||.|---+       +.++.++.+||+||-|...   .+.| |  ..
T Consensus        83 ~i~~~~i~~ltG~~~~~~r~~~w~-----~~~Viv~TPQvl~ndL~~g~i~l~dv~lLVfDEaHha~---Gnh~-Y--~~  151 (764)
T PRK13766         83 NIDPEKIVVLTGEISPEKRAALWE-----KAKVIVATPQVIENDLLAGRISLEDVSLLIFDEAHRAV---GNYA-Y--VF  151 (764)
T ss_pred             CCCCCEEEEEECCCCHHHHHHHHC-----CCCEEEECCHHHHHHHHHCCCCHHHCCEEEEECCCCCC---CCCC-H--HH
T ss_conf             999552899988878276899860-----79999999089999998298678882289997466666---7762-8--99


Q ss_pred             HHHHHHHHCCCCEECC-CCCCC
Q ss_conf             9999751103210000-24543
Q gi|254780619|r  341 MSIVRGKIESFPVVLV-SATPS  361 (731)
Q Consensus       341 vA~~Ra~~~~~~lilg-SATPS  361 (731)
                      ++...-....-|.||| ||||.
T Consensus       152 I~~~y~~~~~~PrILGLTASPG  173 (764)
T PRK13766        152 IAERYHEDAKNPLVLGLTASPG  173 (764)
T ss_pred             HHHHHHHCCCCCEEEEECCCCC
T ss_conf             9999985377855885036887


No 18 
>PRK05298 excinuclease ABC subunit B; Provisional
Probab=99.77  E-value=2.5e-16  Score=143.91  Aligned_cols=410  Identities=22%  Similarity=0.293  Sum_probs=212.8

Q ss_pred             CCCHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHCCCCCEEEEE
Q ss_conf             68837899999998752048961998447531579999999999851468479971521001344555430389768996
Q gi|254780619|r  198 ILDKNQQDVVEQVVPLCTKGFAVSLISGVTGSGKTEVYLEIVAAVLHLGKQVLILLPEISLTSAILERFQKRFGVKPAEW  277 (731)
Q Consensus       198 ~Lt~eQ~~a~~~i~~~~~~~f~~~LL~GvTGSGKTEVYl~li~~~L~~GkqvLiLvPEI~Lt~Q~~~rl~~rF~~~v~v~  277 (731)
                      .-+.+|-.|++++.....++..--.|-||||||||=.-...|+++   +|-+|||.|.--|+.|++.-|++.|+++-+.|
T Consensus        13 ~P~GDQP~AI~~L~~gi~~g~~~Q~LlGvTGSGKTfTmAnvI~~~---~rPtLVlahNKTLAAQLy~Efk~fFP~NaVEY   89 (657)
T PRK05298         13 KPAGDQPQAIAELVEGIESGEKHQTLLGVTGSGKTFTMANVIARV---QRPTLVLAHNKTLAAQLYGEFKEFFPENAVEY   89 (657)
T ss_pred             CCCCCCHHHHHHHHHHHHCCCCEEEEECCCCCCHHHHHHHHHHHH---CCCEEEECCCHHHHHHHHHHHHHHCCCCCEEE
T ss_conf             999987999999998997499636997036785668999999986---89759976658899999999997688871799


Q ss_pred             E-CC----CC---------------------CHHHHHHHHHHHCCCCEEEEECCHHHH---HHHCCCEEEEE---EECCC
Q ss_conf             2-35----57---------------------235667899997199739994001211---00100013677---40553
Q gi|254780619|r  278 H-SS----LS---------------------TSMREKIWRQVARGAISVIVGVRSALF---LPFKKLGLIVI---DEEHD  325 (731)
Q Consensus       278 H-S~----ls---------------------~~eR~~~w~~i~~G~~~IVIGtRSAif---~P~~nLglIIv---DEEHd  325 (731)
                      - |.    ..                     ++-|...-.++.+-+--|||.+=|+++   .|-.-..+++.   .++.+
T Consensus        90 FVSYyDYYQPEAYip~tDtYIEKdssIN~eId~lR~sAT~SLl~RrDVIVVASVSCIYGLGsPe~Y~~~~l~l~~G~~i~  169 (657)
T PRK05298         90 FVSYYDYYQPEAYVPSSDTYIEKDSSINEEIERLRLSATKSLLERRDVIVVASVSCIYGLGSPEEYLKMVLHLRVGQEID  169 (657)
T ss_pred             EECCCCCCCCCCCCCCCCCEEECCCHHHHHHHHHHHHHHHHHHCCCCEEEEEEHHHCCCCCCHHHHHHCEEEEECCCEEC
T ss_conf             85144566971114788852423634669999999999998854798699973676168999799973437775897717


Q ss_pred             CC--CHHCCCCCCCHHHHHHHHHHH--------------CCCC--E-ECC----------------------------C-
Q ss_conf             21--000024432248999997511--------------0321--0-000----------------------------2-
Q gi|254780619|r  326 IS--YKQEEGILYNARDMSIVRGKI--------------ESFP--V-VLV----------------------------S-  357 (731)
Q Consensus       326 ~s--ykq~~~pry~aRdvA~~Ra~~--------------~~~~--l-ilg----------------------------S-  357 (731)
                      -.  -++--...|.--|+...|+..              ++..  + .+|                            | 
T Consensus       170 r~~ll~~LV~~qY~RnD~~~~RG~FRVrGDvVdI~Pa~~ed~aiRIeffgDeIE~I~~~Dpltg~~i~~~~~~~IfPAsh  249 (657)
T PRK05298        170 RRELLRRLVELQYERNDIDFQRGTFRVRGDVIDIFPAEYEDRAIRIEFFGDEIERISEFDPLTGEVLGELDRVTIYPASH  249 (657)
T ss_pred             HHHHHHHHHHHCCCCCCCCCCCCEEEEECCEEEEECCCCCCEEEEEEEECCCEEEEEEECCCCCCCCCCCCEEEEECCCC
T ss_conf             99999999982877676511685557736647883377776169999957806289998277883524333499817867


Q ss_pred             -CCCCHHHHHHH----------------HHHH------------HHH----------------HCCCCCCCCCCCCC---
Q ss_conf             -45432467753----------------2123------------444----------------12432236765433---
Q gi|254780619|r  358 -ATPSIESRVNG----------------ISRR------------YHS----------------VHLSTRYRNSALPH---  389 (731)
Q Consensus       358 -ATPSles~~~~----------------~~g~------------~~~----------------~~l~~R~~~~~~P~---  389 (731)
                       .||. +....|                .+|+            |.+                -.|..|..|.+++.   
T Consensus       250 yVt~~-e~l~~Ai~~I~~EL~eRl~~f~~~gKllEAqRL~qRT~yDlEMl~E~GyCsGIENYSRhl~gR~pGe~P~tLlD  328 (657)
T PRK05298        250 YVTPR-ERLERAIESIKEELEERLKELEKEGKLLEAQRLEQRTRYDLEMLRELGYCSGIENYSRHLSGRAPGEPPPTLLD  328 (657)
T ss_pred             CCCCH-HHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCCCCCCCCHHHH
T ss_conf             68997-99999999999999999999997677798889999988799999982877560121565069998878944887


Q ss_pred             ------CEECC-----------C------CCC-CCCCCCCCCHHHHH---HHHHHHCCCCEEEEEECCCCEEHHCCCCCC
Q ss_conf             ------21102-----------2------223-32224547989999---998862265517997422200000023565
Q gi|254780619|r  390 ------LQVID-----------M------RGQ-TIAQGKSLSPEMID---GIRHTLARNEQTLLFLNRRGYAPLTLCQVC  442 (731)
Q Consensus       390 ------i~ivD-----------m------~~~-~~~~~~~lS~~l~~---~i~~~l~~g~qvll~lnRrGya~~~~C~~C  442 (731)
                            +-+||           |      |++ ....|..|++++-+   ...+-.+.-.|++..-..=|---.-.   |
T Consensus       329 Yfp~DfLl~iDESHvtvPQi~gMy~GDrsRK~~LVe~GFRLPSAlDNRPL~feEFe~~~~q~iyVSATPg~yEl~~---s  405 (657)
T PRK05298        329 YFPDDFLLFIDESHVTVPQIGGMYNGDRSRKETLVEYGFRLPSALDNRPLKFEEFEAKVPQTIYVSATPGDYELEK---S  405 (657)
T ss_pred             HCCCCEEEEECCCCCCCHHHHHHHCCCHHHHHHHHHHCCCCCCCCCCCCCCHHHHHHHCCCEEEEECCCCHHHHHH---C
T ss_conf             5775659998321124087887862315778889870577872334899788999974487799956985898873---6


Q ss_pred             CCCCCCCC-----CCCEEEEECCCCCC--EECHHHCCCCCCCCCCCCCCCCEECCCCCCHHHHHHHHHHCCCC--CHHHH
Q ss_conf             43431014-----65201211357832--00002102446555666787411001354289988885204852--00010
Q gi|254780619|r  443 GNRLKCLH-----CSCWLVEHRSKKKL--YCHQCGHSAIYSQSCVVCGSSGKMIACGFGIERIAEEVCEYFPL--ARISI  513 (731)
Q Consensus       443 g~~~~C~~-----C~~~l~~h~~~~~l--~Ch~Cg~~~~~~~~Cp~Cg~~~~l~~~G~Gte~~~e~l~~~fp~--~~v~~  513 (731)
                      |.++..--     .|-........|+.  ...-|.       .|-.-|.. .|.  -.=|-|..|+|...|-+  +++--
T Consensus       406 ~~vvEQiIRPTGLlDP~ievrp~~~Qiddl~~ei~-------~~~~~~er-~Lv--ttlTkkmaEdLt~yl~~~~ik~~Y  475 (657)
T PRK05298        406 GQVVEQIIRPTGLLDPEIEVRPTKGQVDDLLSEIR-------KRVAKGER-VLV--TTLTKRMAEDLTDYLKELGIKVRY  475 (657)
T ss_pred             CCEEEEEECCCCCCCCCEEEECCCCCHHHHHHHHH-------HHHHCCCE-EEE--EECHHHHHHHHHHHHHHCCCEEEE
T ss_conf             67345777788787984599648787999999999-------99636976-999--954598999999999967980799


Q ss_pred             CCCCCCCCHHHHHHHHHHHCCCCCCEEEEEHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCC
Q ss_conf             23211358678999998621257657987044302311345201233000344310245578999998754311025667
Q gi|254780619|r  514 LSSDLEGGGGRLQLQLSAIAKGEIDIIIGTQLVAKGHNFPRMSLVGVVDGDLGLTNADLRSSERTFQLLSQVTGRAGRFG  593 (731)
Q Consensus       514 ~d~d~~~~~~~~~~~~~~~~~~~~~ilvgTq~i~kg~~fp~v~lv~il~aD~~l~~pd~ra~E~~~qll~qv~gRagr~~  593 (731)
                      +.||...  -..-+++.+++.|+.|+|||-.++--|+|.|.|+||+|||||..-+.   |+    -.-|.|.+|||.|..
T Consensus       476 lHs~i~t--~eR~eIl~~LR~G~~DVlVGINLLREGLDlPEVSLVaILDADKeGFL---Rs----~~SLiQtiGRAARN~  546 (657)
T PRK05298        476 LHSDIDT--LERVEIIRDLRLGEFDVLVGINLLREGLDIPEVSLVAILDADKEGFL---RS----ERSLIQTIGRAARNV  546 (657)
T ss_pred             EECCCCH--HHHHHHHHHHHCCCCCEEEEECHHHCCCCCCCEEEEEEEECCCCCCC---CC----CCHHHHHHHHHHHCC
T ss_conf             6266618--89999999985888758975002204578761357988706852210---35----205999987886257


Q ss_pred             CCCEEEEEECCCCCHHHHHHHHCCHHHHHHHHHHHHHHCCCCC
Q ss_conf             8868999932986488899995897999999999999818888
Q gi|254780619|r  594 LKSLGLIQAYQPTHPVMQALVSGDADSFYESEIRARESVNLPP  636 (731)
Q Consensus       594 ~~g~v~iQt~~p~~~~~~~~~~~d~~~f~~~el~~R~~~~~PP  636 (731)
                       .|+||+-...- ...++.++.. -..==+..++.-++.|--|
T Consensus       547 -~G~vIlYAD~i-T~SM~~ai~E-T~rRR~iQ~~yN~~h~ItP  586 (657)
T PRK05298        547 -NGKVILYADKI-TDSMQKAIDE-TERRREIQIAYNEEHGITP  586 (657)
T ss_pred             -CCEEEEEECCC-CHHHHHHHHH-HHHHHHHHHHHHHHCCCCC
T ss_conf             -97499981545-0999999999-9989999999999569986


No 19 
>PRK04837 ATP-dependent RNA helicase RhlB; Provisional
Probab=99.76  E-value=8.9e-16  Score=139.76  Aligned_cols=325  Identities=18%  Similarity=0.227  Sum_probs=179.6

Q ss_pred             HHHCCCHHHHHHHHHCCHHHHHHHHHCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHHH
Q ss_conf             77099989997524557223445541023566543446666883789999999875204896199844753157999999
Q gi|254780619|r  158 RASQVSSHVIDGLKAQGVIKQIFEVISPVVDSPNLYFSLPILDKNQQDVVEQVVPLCTKGFAVSLISGVTGSGKTEVYLE  237 (731)
Q Consensus       158 ~~~~~s~~~i~~L~~kglI~~~~~~~~~~~~~~~~~~~~~~Lt~eQ~~a~~~i~~~~~~~f~~~LL~GvTGSGKTEVYl~  237 (731)
                      ..++++..++++|.+.|+.                     ..|+=|+.++-.+...     .-.+...-||||||.-|+=
T Consensus        12 ~~lgL~~~ll~~L~~~g~~---------------------~pTpIQ~~aIP~il~G-----~Dvi~~A~TGSGKTlAfll   65 (423)
T PRK04837         12 SDFALHPKVVEALEKKGFE---------------------YCTPIQALALPLTLAG-----RDVAGQAQTGTGKTMAFLT   65 (423)
T ss_pred             HHCCCCHHHHHHHHHCCCC---------------------CCCHHHHHHHHHHHCC-----CCEEEECCCCCHHHHHHHH
T ss_conf             2479699999999977999---------------------9999999999999679-----9889989998749999999


Q ss_pred             HHHH-HHH----CC-----CCEEEEECCCHHHHHHHHHHH---CCCCCEEEEEECCCCCHHHHHHHHHHHCCCCEEEEEC
Q ss_conf             9999-851----46-----847997152100134455543---0389768996235572356678999971997399940
Q gi|254780619|r  238 IVAA-VLH----LG-----KQVLILLPEISLTSAILERFQ---KRFGVKPAEWHSSLSTSMREKIWRQVARGAISVIVGV  304 (731)
Q Consensus       238 li~~-~L~----~G-----kqvLiLvPEI~Lt~Q~~~rl~---~rF~~~v~v~HS~ls~~eR~~~w~~i~~G~~~IVIGt  304 (731)
                      -+-+ .+.    .+     -++|||+|.--|+.|+.+.++   +..+.++.+..++.+-.+..    ......++|||||
T Consensus        66 Pil~~ll~~~~~~~~~~~~p~aLIL~PTRELa~Qi~~~~~~l~~~~~l~~~~~~GG~~~~~q~----~~l~~~~dIlV~T  141 (423)
T PRK04837         66 ATFHHLLSHPAPEGRKVNQPRALIMAPTRELAVQIHADAEPLAQATGLKLGLAYGGEGYDKQL----KVLESGVDILIGT  141 (423)
T ss_pred             HHHHHHHHCCCCCCCCCCCCEEEEEECCHHHHHHHHHHHHHHHCCCCCEEEEEECCCCHHHHH----HHHHCCCCEEEEC
T ss_conf             999999837453345567861899938899999999999997432584599998998879999----9871799989989


Q ss_pred             CHHHH-------HHHCCCEEEEEEECCCCCCHHCCCCCCCHHHHHHHHHHHCCCCEECCCCCCCHHHHHHHHHHHHHHHC
Q ss_conf             01211-------00100013677405532100002443224899999751103210000245432467753212344412
Q gi|254780619|r  305 RSALF-------LPFKKLGLIVIDEEHDISYKQEEGILYNARDMSIVRGKIESFPVVLVSATPSIESRVNGISRRYHSVH  377 (731)
Q Consensus       305 RSAif-------~P~~nLglIIvDEEHd~sykq~~~pry~aRdvA~~Ra~~~~~~lilgSATPSles~~~~~~g~~~~~~  377 (731)
                      -.-+.       ..+.++..+|+||-+ --+  +.++.=+.+.+.-..-....-..+|-|||-|-+....+..    .+.
T Consensus       142 PgRL~d~~~~~~~~l~~i~~lVlDEAD-~ll--d~gF~~~i~~i~~~~p~~~~r~~~lfSATl~~~v~~la~~----~l~  214 (423)
T PRK04837        142 TGRLIDYAKQNHINLGAIQVVVLDEAD-RMF--DLGFIKDIRWLFRRMPPANQRLNMLFSATLSYRVRELAFE----HMN  214 (423)
T ss_pred             HHHHHHHHHHCCCCCCCCEEEEEECHH-HHH--HCCCHHHHHHHHHHCCCCHHEEEEEEECCCCHHHHHHHHH----HCC
T ss_conf             189999986422123664289963446-543--0263999999999689622108999703688899999999----778


Q ss_pred             CCCCCCCCCCCCCEEC-CCCCCCCC-CCCCCCHHHHHHHHHHHCCCCEEEEEECCCCEEHHCCCCCCCCCCCCCCCCCEE
Q ss_conf             4322367654332110-22223322-245479899999988622655179974222000000235654343101465201
Q gi|254780619|r  378 LSTRYRNSALPHLQVI-DMRGQTIA-QGKSLSPEMIDGIRHTLARNEQTLLFLNRRGYAPLTLCQVCGNRLKCLHCSCWL  455 (731)
Q Consensus       378 l~~R~~~~~~P~i~iv-Dm~~~~~~-~~~~lS~~l~~~i~~~l~~g~qvll~lnRrGya~~~~C~~Cg~~~~C~~C~~~l  455 (731)
                      -+..+...  |.-... .++..... .+..--..|...+++.  ..+++|+|.|.+-                       
T Consensus       215 ~p~~i~v~--~~~~~~~~i~~~~~~~~~~~K~~~L~~ll~~~--~~~k~iIF~nt~~-----------------------  267 (423)
T PRK04837        215 NPEYVEVE--PEQKTGHRIKEELFYPSNEEKMRLLQTLIEEE--WPDRAIIFANTKH-----------------------  267 (423)
T ss_pred             CCEEEEEC--CCCCCCCCEEEEEEEECHHHHHHHHHHHHHHH--CCCCEEEECCHHH-----------------------
T ss_conf             98799965--77656654269999917277999999999840--8874688616288-----------------------


Q ss_pred             EEECCCCCCEECHHHCCCCCCCCCCCCCCCCEECCCCCCHHHHHHHHHHCCCCCHHHHCCCCCCCCHHHHHHHHHHHCCC
Q ss_conf             21135783200002102446555666787411001354289988885204852000102321135867899999862125
Q gi|254780619|r  456 VEHRSKKKLYCHQCGHSAIYSQSCVVCGSSGKMIACGFGIERIAEEVCEYFPLARISILSSDLEGGGGRLQLQLSAIAKG  535 (731)
Q Consensus       456 ~~h~~~~~l~Ch~Cg~~~~~~~~Cp~Cg~~~~l~~~G~Gte~~~e~l~~~fp~~~v~~~d~d~~~~~~~~~~~~~~~~~~  535 (731)
                                                            ..+++...|...  +.++..+.+|..  .......+++|.+|
T Consensus       268 --------------------------------------~~~~l~~~L~~~--g~~~~~lhg~~~--q~~R~~~l~~F~~g  305 (423)
T PRK04837        268 --------------------------------------RCEEIWGHLAAD--GHRVGLLTGDVP--QKKRLRILEQFTRG  305 (423)
T ss_pred             --------------------------------------HHHHHHHHHHHC--CCCEEEECCCCC--HHHHHHHHHHHHCC
T ss_conf             --------------------------------------899999999765--981787225457--99999999999769


Q ss_pred             CCCEEEEEHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCEEEE
Q ss_conf             76579870443023113452012330003443102455789999987543110256678868999
Q gi|254780619|r  536 EIDIIIGTQLVAKGHNFPRMSLVGVVDGDLGLTNADLRSSERTFQLLSQVTGRAGRFGLKSLGLI  600 (731)
Q Consensus       536 ~~~ilvgTq~i~kg~~fp~v~lv~il~aD~~l~~pd~ra~E~~~qll~qv~gRagr~~~~g~v~i  600 (731)
                      +.+|||+|-+.|.|+|||+|++|+-.|.      |+      ...-+..=+||+||+.+.|.++-
T Consensus       306 ~~~vLVaTDvaaRGLDi~~V~~VInyD~------P~------~~~~YiHRiGRTgRaG~~G~ait  358 (423)
T PRK04837        306 DLDILVATDVAARGLHIPDVTHVFNYDL------PD------DCEDYVHRIGRTGRAGASGHSIS  358 (423)
T ss_pred             CCCEEEEHHHHHCCCCCCCCCEEEEECC------CC------CHHHEECCCCHHHCCCCCEEEEE
T ss_conf             9989987004327777267988999699------89------74551004654127899468999


No 20 
>PRK11634 ATP-dependent RNA helicase DeaD; Provisional
Probab=99.76  E-value=3.3e-16  Score=143.03  Aligned_cols=315  Identities=20%  Similarity=0.249  Sum_probs=183.5

Q ss_pred             HHHCCCHHHHHHHHHCCHHHHHHHHHCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHHH
Q ss_conf             77099989997524557223445541023566543446666883789999999875204896199844753157999999
Q gi|254780619|r  158 RASQVSSHVIDGLKAQGVIKQIFEVISPVVDSPNLYFSLPILDKNQQDVVEQVVPLCTKGFAVSLISGVTGSGKTEVYLE  237 (731)
Q Consensus       158 ~~~~~s~~~i~~L~~kglI~~~~~~~~~~~~~~~~~~~~~~Lt~eQ~~a~~~i~~~~~~~f~~~LL~GvTGSGKTEVYl~  237 (731)
                      ..++++..++++|.+.|+-                     ..|+=|+.++-.+...     .-.+..--||||||--|+=
T Consensus         9 ~~lgL~~~ll~aL~~~Gf~---------------------~PTpIQ~~aIP~iL~G-----kDvi~~AqTGSGKTlAFlL   62 (629)
T PRK11634          9 ADLGLKAPILEALNDLGYE---------------------KPSPIQAECIPHLLNG-----RDVLGMAQTGSGKTAAFSL   62 (629)
T ss_pred             HHCCCCHHHHHHHHHCCCC---------------------CCCHHHHHHHHHHHCC-----CCEEEECCCCCHHHHHHHH
T ss_conf             7679899999999987999---------------------9999999999999679-----9889978884789999999


Q ss_pred             HHHHHHHC---CCCEEEEECCCHHHHHHHHHHHCC---C-CCEEEEEECCCCCHHHHHHHHHHHCCCCEEEEECCHHHH-
Q ss_conf             99998514---684799715210013445554303---8-976899623557235667899997199739994001211-
Q gi|254780619|r  238 IVAAVLHL---GKQVLILLPEISLTSAILERFQKR---F-GVKPAEWHSSLSTSMREKIWRQVARGAISVIVGVRSALF-  309 (731)
Q Consensus       238 li~~~L~~---GkqvLiLvPEI~Lt~Q~~~rl~~r---F-~~~v~v~HS~ls~~eR~~~w~~i~~G~~~IVIGtRSAif-  309 (731)
                      -+-+.+..   +-|+|||+|.--|+.|+.+.++..   + +..+..+.++.+    ++.-.+.....++|||||-.-++ 
T Consensus        63 PiL~~l~~~~~~pqaLIL~PTRELA~QV~~~~~~l~~~~~~i~v~~l~GG~~----~~~q~~~L~~g~~IVVgTPGRL~d  138 (629)
T PRK11634         63 PLLHNLDPELKAPQILVLAPTRELAVQVAEAMTDFSKHMRGVNVVALYGGQR----YDVQLRALRQGPQIVVGTPGRLLD  138 (629)
T ss_pred             HHHHHHHHCCCCCCEEEECCCHHHHHHHHHHHHHHHHCCCCCEEEEEECCCC----HHHHHHHHCCCCCEEEECHHHHHH
T ss_conf             9999866236898689978998999999999999972179977999989977----899999862799999969899999


Q ss_pred             ------HHHCCCEEEEEEECCCCCCHHCCCCCCCHHHHHHHHHH-HCCCCEECCCCCCCHHHHHHHHHHHHHHHCCCCCC
Q ss_conf             ------00100013677405532100002443224899999751-10321000024543246775321234441243223
Q gi|254780619|r  310 ------LPFKKLGLIVIDEEHDISYKQEEGILYNARDMSIVRGK-IESFPVVLVSATPSIESRVNGISRRYHSVHLSTRY  382 (731)
Q Consensus       310 ------~P~~nLglIIvDEEHd~sykq~~~pry~aRdvA~~Ra~-~~~~~lilgSATPSles~~~~~~g~~~~~~l~~R~  382 (731)
                            +.+.++..+|+||-. .-.  +.+..   .|+-..... -.....+|-|||-+-+....+..  |  +.-+.  
T Consensus       139 ~l~~~~l~L~~l~~lVLDEAD-~mL--~~gF~---~di~~Il~~lp~~~Qt~LfSATmp~~i~~la~~--~--l~~P~--  206 (629)
T PRK11634        139 HLKRGTLDLSKLSGLVLDEAD-EML--RMGFI---EDVETIMAQIPEGHQTALFSATMPEAIRRITRR--F--MKEPQ--  206 (629)
T ss_pred             HHHCCCCCHHHCCEEEEECHH-HHC--CCCCH---HHHHHHHHHCCCCCEEEEEECCCCHHHHHHHHH--H--CCCCE--
T ss_conf             997296412007678986715-533--63659---999999986740314466631465999999998--7--56987--


Q ss_pred             CCCCCCCCEECCCCCCCC-----CCCCC-C-CHHHHHHHHHHHC--CCCEEEEEECCCCEEHHCCCCCCCCCCCCCCCCC
Q ss_conf             676543321102222332-----22454-7-9899999988622--6551799742220000002356543431014652
Q gi|254780619|r  383 RNSALPHLQVIDMRGQTI-----AQGKS-L-SPEMIDGIRHTLA--RNEQTLLFLNRRGYAPLTLCQVCGNRLKCLHCSC  453 (731)
Q Consensus       383 ~~~~~P~i~ivDm~~~~~-----~~~~~-l-S~~l~~~i~~~l~--~g~qvll~lnRrGya~~~~C~~Cg~~~~C~~C~~  453 (731)
                            .|.+   .....     ....+ + +..-.+++.+.|.  .-.++|||.|                        
T Consensus       207 ------~i~i---~~~~~t~~~i~q~~~~v~~~~K~~aL~~~L~~~~~~~~IIF~~------------------------  253 (629)
T PRK11634        207 ------EVRI---QSSVTTRPDISQSYWTVWGMRKNEALVRFLEAEDFDAAIIFVR------------------------  253 (629)
T ss_pred             ------EEEE---CCCCCCCCCCEEEEEEECCHHHHHHHHHHHHHCCCCEEEEEEE------------------------
T ss_conf             ------9740---4555557763059999652457999999986158884899982------------------------


Q ss_pred             EEEEECCCCCCEECHHHCCCCCCCCCCCCCCCCEECCCCCCHHHHHHHHHHCCCCCHHHHCCCCCCCCHHHHHHHHHHHC
Q ss_conf             01211357832000021024465556667874110013542899888852048520001023211358678999998621
Q gi|254780619|r  454 WLVEHRSKKKLYCHQCGHSAIYSQSCVVCGSSGKMIACGFGIERIAEEVCEYFPLARISILSSDLEGGGGRLQLQLSAIA  533 (731)
Q Consensus       454 ~l~~h~~~~~l~Ch~Cg~~~~~~~~Cp~Cg~~~~l~~~G~Gte~~~e~l~~~fp~~~v~~~d~d~~~~~~~~~~~~~~~~  533 (731)
                                                 .+          -.++.+.+.|.+.  +.++..+.+|..  ....+..++.|.
T Consensus       254 ---------------------------Tk----------~~~~~l~~~L~~~--g~~~~~LHgdm~--q~~R~~~l~~Fr  292 (629)
T PRK11634        254 ---------------------------TK----------NATLEVAEALERN--GYNSAALNGDMN--QALREQTLERLK  292 (629)
T ss_pred             ---------------------------CH----------HHHHHHHHHHHHC--CCCEEEEECCCC--HHHHHHHHHHHH
T ss_conf             ---------------------------27----------8899999999976--996576568999--999999999997


Q ss_pred             CCCCCEEEEEHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCEEEE
Q ss_conf             2576579870443023113452012330003443102455789999987543110256678868999
Q gi|254780619|r  534 KGEIDIIIGTQLVAKGHNFPRMSLVGVVDGDLGLTNADLRSSERTFQLLSQVTGRAGRFGLKSLGLI  600 (731)
Q Consensus       534 ~~~~~ilvgTq~i~kg~~fp~v~lv~il~aD~~l~~pd~ra~E~~~qll~qv~gRagr~~~~g~v~i  600 (731)
                      +|+.+|||+|-+.|.|+|||+|++|+-.|.      |.      ...-++.=+||+||+.+.|..|.
T Consensus       293 ~g~~~ILVaTDvaARGLDi~~V~~VINyDl------P~------d~e~YVHRiGRTGRaGr~G~Ait  347 (629)
T PRK11634        293 DGRLDILIATDVAARGLDVERISLVVNYDI------PM------DSESYVHRIGRTGRAGRAGRALL  347 (629)
T ss_pred             CCCCCEEEECCCCCCCCCCCCCCEEEEECC------CC------CHHHCCCCCCCCCCCCCCEEEEE
T ss_conf             599988987862105577256888999689------89------74340102583316899646999


No 21 
>PRK01172 ski2-like helicase; Provisional
Probab=99.76  E-value=1.8e-15  Score=137.48  Aligned_cols=369  Identities=20%  Similarity=0.231  Sum_probs=203.8

Q ss_pred             HCCCHHHHHHHHHCCHHHHHHHHHCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHHHHH
Q ss_conf             09998999752455722344554102356654344666688378999999987520489619984475315799999999
Q gi|254780619|r  160 SQVSSHVIDGLKAQGVIKQIFEVISPVVDSPNLYFSLPILDKNQQDVVEQVVPLCTKGFAVSLISGVTGSGKTEVYLEIV  239 (731)
Q Consensus       160 ~~~s~~~i~~L~~kglI~~~~~~~~~~~~~~~~~~~~~~Lt~eQ~~a~~~i~~~~~~~f~~~LL~GvTGSGKTEVYl~li  239 (731)
                      .+.+...++-+.++||                      .|-+.|..+++.+..    + ...|+--=||||||-|..-+|
T Consensus         6 ~~~~~~~~~~~~~~g~----------------------~l~p~Q~ea~~~~~~----g-kNllvsaPTgsGKTlvAe~ai   58 (674)
T PRK01172          6 LGYDDEFLNLFTGNDF----------------------ELYDHQRMAIEQLRK----G-ENVIVSVPTAAGKTLIAYSAI   58 (674)
T ss_pred             CCCCHHHHHHHHHCCC----------------------CCCHHHHHHHHHHHC----C-CCEEEECCCCCCHHHHHHHHH
T ss_conf             2999799999996799----------------------889899999999977----9-959997899986999999999


Q ss_pred             HHHHHCCCCEEEEECCCHHHHHHHHHHHC--CCCCEEEEEECCCCCHHHHHHHHHHHCCCCEEEEEC----CHHHH-HH-
Q ss_conf             99851468479971521001344555430--389768996235572356678999971997399940----01211-00-
Q gi|254780619|r  240 AAVLHLGKQVLILLPEISLTSAILERFQK--RFGVKPAEWHSSLSTSMREKIWRQVARGAISVIVGV----RSALF-LP-  311 (731)
Q Consensus       240 ~~~L~~GkqvLiLvPEI~Lt~Q~~~rl~~--rF~~~v~v~HS~ls~~eR~~~w~~i~~G~~~IVIGt----RSAif-~P-  311 (731)
                      .+.+..|+.+++++|-.+|+.|-+..|+.  .+|.+|....+........       .++.+|+|-|    .|.+. -| 
T Consensus        59 ~~~l~~~~k~iyi~P~kAL~~EK~~~~~~~~~~g~~v~~~tGd~~~~~~~-------~~~~~I~V~T~Ek~~sl~~~~~~  131 (674)
T PRK01172         59 YETFLAGLKSIYIVPLRSLAMEKYEELSRLRSLGMRVKISIGDYDDPPDF-------IKRYDVVILTSEKADSLIHHDPY  131 (674)
T ss_pred             HHHHHHCCCEEEECCHHHHHHHHHHHHHHHHCCCCEEEEEECCCCCCCCC-------CCCCCEEEECHHHHHHHHHCCCH
T ss_conf             99998589799987789999999999998873798277885388898010-------25589999878999999864950


Q ss_pred             -HCCCEEEEEEECCCCCCHHCCCCCCCHHHHHHHHH--HHCCCCEECCCCC-CCHHHHHHHHHHHHHHHCCCCCCCCCCC
Q ss_conf             -10001367740553210000244322489999975--1103210000245-4324677532123444124322367654
Q gi|254780619|r  312 -FKKLGLIVIDEEHDISYKQEEGILYNARDMSIVRG--KIESFPVVLVSAT-PSIESRVNGISRRYHSVHLSTRYRNSAL  387 (731)
Q Consensus       312 -~~nLglIIvDEEHd~sykq~~~pry~aRdvA~~Ra--~~~~~~lilgSAT-PSles~~~~~~g~~~~~~l~~R~~~~~~  387 (731)
                       +.++|+|||||=|--+= .+.||.+   ++.+.+.  ...++.+|.-||| |-.+.+.......  ++.-.-|+  .++
T Consensus       132 ~l~~v~~vViDEiH~i~d-~~RG~~l---E~~l~kl~~l~~~~qiIgLSATi~N~~~la~WL~a~--~~~~~~RP--VpL  203 (674)
T PRK01172        132 IINDVGLIVADEIHIIGD-EDRGPTL---ETVLSSARYVNPDARILALSATVSNANELAQWLNAS--LIKSNFRP--VPL  203 (674)
T ss_pred             HHCCCCEEEEECCEECCC-CCCHHHH---HHHHHHHHHCCCCEEEEEECCCCCCHHHHHHHHCCC--EEECCCCC--CCC
T ss_conf             221369899826525068-7724999---999999985386607997157868999999883885--56479998--660


Q ss_pred             CCCEECCCCCCCCCCC-CCCCHHHHHHHHHHHCCCCEEEEEECCCCEEHHCCCCCCCCCCCCCCCCCEEEEECCCCCCEE
Q ss_conf             3321102222332224-547989999998862265517997422200000023565434310146520121135783200
Q gi|254780619|r  388 PHLQVIDMRGQTIAQG-KSLSPEMIDGIRHTLARNEQTLLFLNRRGYAPLTLCQVCGNRLKCLHCSCWLVEHRSKKKLYC  466 (731)
Q Consensus       388 P~i~ivDm~~~~~~~~-~~lS~~l~~~i~~~l~~g~qvll~lnRrGya~~~~C~~Cg~~~~C~~C~~~l~~h~~~~~l~C  466 (731)
                       +..++- ++.....+ ..........+.+++.+|.|+|+|.+.|--        |...+      ..|.-|        
T Consensus       204 -~~~v~~-~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~LVF~~sR~~--------~e~~A------~~l~~~--------  259 (674)
T PRK01172        204 -KLGILY-RKRLILDGYERSQVDINSLIKETVNDGGQVLVFVSSRKN--------AEDYA------EMLIQH--------  259 (674)
T ss_pred             -EEEEEE-CCCCCCCCHHHCCCCHHHHHHHHHHCCCCEEEEEECHHH--------HHHHH------HHHHHH--------
T ss_conf             -898883-460114704323453999999999669947999507588--------99999------999985--------


Q ss_pred             CHHHCCCCCCCCCCCCCCCCEECCCCCCHHHHHHHHHHCCCCCHHHHCCCCCCCCHHHHHHHHHHHCCCCCCEEEEEHHH
Q ss_conf             00210244655566678741100135428998888520485200010232113586789999986212576579870443
Q gi|254780619|r  467 HQCGHSAIYSQSCVVCGSSGKMIACGFGIERIAEEVCEYFPLARISILSSDLEGGGGRLQLQLSAIAKGEIDIIIGTQLV  546 (731)
Q Consensus       467 h~Cg~~~~~~~~Cp~Cg~~~~l~~~G~Gte~~~e~l~~~fp~~~v~~~d~d~~~~~~~~~~~~~~~~~~~~~ilvgTq~i  546 (731)
                        ++..... .......       .+.. +.+.+-+..     .|..-.+.-+  ....+.+-+.|.+|.+.+|++|.-+
T Consensus       260 --~~~~~~~-~~~~~~~-------~~~~-~~L~~~l~~-----GVafHHaGL~--~~eR~lVE~~f~~g~i~vl~aT~TL  321 (674)
T PRK01172        260 --FPEFNDF-KVSSENN-------NVYD-DSLNEMLPH-----GVAFHHAGLS--NEQRRFIEEMFRNRYIKVIVATPTL  321 (674)
T ss_pred             --HHHCCCH-HCCHHHH-------HCCC-HHHHHHHHC-----CEEEECCCCC--HHHHHHHHHHHHCCCCEEEEECCHH
T ss_conf             --3210100-1031543-------1120-999999962-----8283068999--8999999999986996499714467


Q ss_pred             CCCCCCCCCCHHHHHHHHHHH--HHHHHHHHHHHHHHHHHHHHCCCCCC--CCCEEEEEECCCC-CHHHHHHHHCCH
Q ss_conf             023113452012330003443--10245578999998754311025667--8868999932986-488899995897
Q gi|254780619|r  547 AKGHNFPRMSLVGVVDGDLGL--TNADLRSSERTFQLLSQVTGRAGRFG--LKSLGLIQAYQPT-HPVMQALVSGDA  618 (731)
Q Consensus       547 ~kg~~fp~v~lv~il~aD~~l--~~pd~ra~E~~~qll~qv~gRagr~~--~~g~v~iQt~~p~-~~~~~~~~~~d~  618 (731)
                      |-|.|+|. ..|+|-+....-  ..-.+     ...-+.|.+|||||-.  ..|+.+|-..+++ ...++.++.++.
T Consensus       322 AaGVNlPA-r~VIi~~~~r~~~~~~~~l-----~~~e~~QM~GRAGR~g~D~~G~~ii~~~~~~~~~~~~~~l~~~~  392 (674)
T PRK01172        322 AAGVNLPA-RLVIVRDITRYGNGGIRYL-----SNMEIKQMIGRAGRPGYDQYGIGYIYAASPASYDAAKKYLSGEP  392 (674)
T ss_pred             HHHCCCCE-EEEEEEEEEEECCCCEEEC-----CHHHHHHHCCCCCCCCCCCCCCEEEEECCCHHHHHHHHHHCCCC
T ss_conf             65447860-5999930078179971577-----78989986135899999988708999728228999999852898


No 22 
>PRK02362 ski2-like helicase; Provisional
Probab=99.75  E-value=1.7e-16  Score=145.18  Aligned_cols=380  Identities=21%  Similarity=0.203  Sum_probs=207.9

Q ss_pred             HHCCCHHHHHHHHHCCHHHHHHHHHCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHHHH
Q ss_conf             70999899975245572234455410235665434466668837899999998752048961998447531579999999
Q gi|254780619|r  159 ASQVSSHVIDGLKAQGVIKQIFEVISPVVDSPNLYFSLPILDKNQQDVVEQVVPLCTKGFAVSLISGVTGSGKTEVYLEI  238 (731)
Q Consensus       159 ~~~~s~~~i~~L~~kglI~~~~~~~~~~~~~~~~~~~~~~Lt~eQ~~a~~~i~~~~~~~f~~~LL~GvTGSGKTEVYl~l  238 (731)
                      ..+.+..+++.+.++|+-                     .|.+.|..++..-   ...+ ...++--=||||||.|.--+
T Consensus         5 ~l~LP~~~~~~~~~~gI~---------------------~Lyp~Q~eal~~g---l~~g-~NlvvsaPTgsGKTlvAEla   59 (736)
T PRK02362          5 DLPLPDGVIDFYEGSGIE---------------------ELYPPQAEAVEAG---LLEG-KNLLAAIPTASGKTLLAELA   59 (736)
T ss_pred             HCCCCHHHHHHHHHCCCC---------------------CCCHHHHHHHHHH---HCCC-CCEEEECCCCCCHHHHHHHH
T ss_conf             239998999999976997---------------------5789999999864---3569-81899799998589999999


Q ss_pred             HHHHHHCCCCEEEEECCCHHHHHHHHHHHCC--CCCEEEEEECCCCCHHHHHHHHHHHCCCCEEEEECC----HHHH--H
Q ss_conf             9998514684799715210013445554303--897689962355723566789999719973999400----1211--0
Q gi|254780619|r  239 VAAVLHLGKQVLILLPEISLTSAILERFQKR--FGVKPAEWHSSLSTSMREKIWRQVARGAISVIVGVR----SALF--L  310 (731)
Q Consensus       239 i~~~L~~GkqvLiLvPEI~Lt~Q~~~rl~~r--F~~~v~v~HS~ls~~eR~~~w~~i~~G~~~IVIGtR----SAif--~  310 (731)
                      |.+.+.+|+-|++++|-.+|+.|-+..|++.  +|.+|.++++..+...+   |    -++.+|+|-|-    |-+-  .
T Consensus        60 il~~l~~g~k~vYi~P~kALa~EK~~~~~~~~~~gi~V~~~tGd~~~~~~---~----l~~~dIiV~T~EK~dsl~r~~~  132 (736)
T PRK02362         60 MLKAIAEGGKALYIVPLRALASEKFEEFSEFSELGLRVGISTGDYDRRDE---Y----LGRNDIIVATSEKTDSLLRNGA  132 (736)
T ss_pred             HHHHHHHCCEEEEECCHHHHHHHHHHHHHHHHCCCCEEEEEECCCCCCHH---H----CCCCCEEEECHHHHHHHHHCCC
T ss_conf             99999839979998587999999999999874579989998089887831---4----3689999999799999984481


Q ss_pred             H-HCCCEEEEEEECCCCCCHHCCCCCCCHHHHHHHHH--HHCCCCEECCCCC-CCHHHHHHHHHHHHHHHCCCCCCCCCC
Q ss_conf             0-10001367740553210000244322489999975--1103210000245-432467753212344412432236765
Q gi|254780619|r  311 P-FKKLGLIVIDEEHDISYKQEEGILYNARDMSIVRG--KIESFPVVLVSAT-PSIESRVNGISRRYHSVHLSTRYRNSA  386 (731)
Q Consensus       311 P-~~nLglIIvDEEHd~sykq~~~pry~aRdvA~~Ra--~~~~~~lilgSAT-PSles~~~~~~g~~~~~~l~~R~~~~~  386 (731)
                      + +.++++|||||=|--.- .+.++.+   ++.+-|-  .-.++.+|.-||| |-.+.+.......  ++.-.-|+  .+
T Consensus       133 ~~l~~v~lVViDEiHli~d-~~RG~~l---E~~lskl~~~~~~iqiIgLSATl~N~~~la~WL~a~--~~~s~~RP--V~  204 (736)
T PRK02362        133 PWIDDISCVVADEVHLIDS-PNRGPTL---EVTLAKLRRLNPDMQVIALSATIGNADELAAWLDAE--LVDSEWRP--VD  204 (736)
T ss_pred             HHHHCCCEEEEECCEEECC-CCCHHHH---HHHHHHHHHCCCCCEEEEEECCCCCHHHHHHHHCCC--CCCCCCCC--CC
T ss_conf             6765089899817678668-8724999---999999973387743898624558999999983886--21589888--67


Q ss_pred             CC-------CCEECCCCCCCCCCCCCCCHHHHHHHHHHHCCCCEEEEEECCCCEEHHCCCCCCCCCCC--CCCCCCEEEE
Q ss_conf             43-------32110222233222454798999999886226551799742220000002356543431--0146520121
Q gi|254780619|r  387 LP-------HLQVIDMRGQTIAQGKSLSPEMIDGIRHTLARNEQTLLFLNRRGYAPLTLCQVCGNRLK--CLHCSCWLVE  457 (731)
Q Consensus       387 ~P-------~i~ivDm~~~~~~~~~~lS~~l~~~i~~~l~~g~qvll~lnRrGya~~~~C~~Cg~~~~--C~~C~~~l~~  457 (731)
                      +-       .+..-|..++.   ...-.......+.+++.+|.|+|+|.+-|-.+        ...++  +....-.+..
T Consensus       205 L~~~v~~~~~~~~~~~~~~~---~~~~~~~~~~l~~~~~~~~~~~LVF~~SR~~~--------e~~A~~la~~~~~~~~~  273 (736)
T PRK02362        205 LREGVFYGGAIHFKDTEREL---EVPSKDEDLNLVLDTLDEGGQCLVFVSSRRNA--------EAFAKRAASALKKALSA  273 (736)
T ss_pred             CEEEEEECCEECCCCCCCHH---CCCCCCHHHHHHHHHHHCCCCEEEEEECHHHH--------HHHHHHHHHHHHHCCCH
T ss_conf             55656507701035100300---02564058999999997399069998249999--------99999998752421575


Q ss_pred             ECCCCCCEECHHHCCCCCCCCCCCCCCCCEECCCCCCHHHHHHHHHHCCCCCHHHHCCCCCCCCHHHHHHHHHHHCCCCC
Q ss_conf             13578320000210244655566678741100135428998888520485200010232113586789999986212576
Q gi|254780619|r  458 HRSKKKLYCHQCGHSAIYSQSCVVCGSSGKMIACGFGIERIAEEVCEYFPLARISILSSDLEGGGGRLQLQLSAIAKGEI  537 (731)
Q Consensus       458 h~~~~~l~Ch~Cg~~~~~~~~Cp~Cg~~~~l~~~G~Gte~~~e~l~~~fp~~~v~~~d~d~~~~~~~~~~~~~~~~~~~~  537 (731)
                       .....+    .+....+.. +.+.         +.+ +.+.+-+..     .|..-.+.-+  ....+.+=+.|.+|.+
T Consensus       274 -~~~~~l----~~~~~~i~~-~~~~---------~~~-~~L~~~l~~-----GVafHHAGL~--~~~R~lVE~~Fr~g~I  330 (736)
T PRK02362        274 -EEREAL----AGIAEEIRE-VSET---------DTS-KVLADCVRS-----GAAFHHAGLS--REHRELVEEGFRDGLI  330 (736)
T ss_pred             -HHHHHH----HHHHHHHHH-CCCC---------CHH-HHHHHHHHC-----CEEEECCCCC--HHHHHHHHHHHHCCCC
T ss_conf             -668899----999999973-4442---------035-999999960-----9485159999--8999999999987998


Q ss_pred             CEEEEEHHHCCCCCCCCCCHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHCCCCCC--CCCEEEEEECCCCC--HHH
Q ss_conf             579870443023113452012330003---44310245578999998754311025667--88689999329864--888
Q gi|254780619|r  538 DIIIGTQLVAKGHNFPRMSLVGVVDGD---LGLTNADLRSSERTFQLLSQVTGRAGRFG--LKSLGLIQAYQPTH--PVM  610 (731)
Q Consensus       538 ~ilvgTq~i~kg~~fp~v~lv~il~aD---~~l~~pd~ra~E~~~qll~qv~gRagr~~--~~g~v~iQt~~p~~--~~~  610 (731)
                      .||+.|.-+|-|.|+|.- .|+|-+.-   .....-++.     ..-+.|.+|||||-+  ..|+.+|-+.+.+.  .++
T Consensus       331 kvl~aTsTLA~GVNLPAr-~VIi~~~~~~~~~~g~~~l~-----~~e~~QM~GRAGRpg~D~~G~aili~~~~~~~~~l~  404 (736)
T PRK02362        331 KVISSTPTLAAGLNLPAR-RVIIRDYRRYDSGAGMQPIP-----VLEYHQMAGRAGRPRLDPYGEAVLLAKSYDEVDELF  404 (736)
T ss_pred             CEEEECCHHHCCCCCCEE-EEEEECCEEECCCCCCEECC-----HHHHHHHHHHCCCCCCCCCCEEEEEECCHHHHHHHH
T ss_conf             389725166505578526-99980436736988833688-----999999985248998898862999967827899999


Q ss_pred             HHHHHCCH
Q ss_conf             99995897
Q gi|254780619|r  611 QALVSGDA  618 (731)
Q Consensus       611 ~~~~~~d~  618 (731)
                      +..+.++.
T Consensus       405 ~~~i~~~~  412 (736)
T PRK02362        405 ERYIEADA  412 (736)
T ss_pred             HHHHCCCC
T ss_conf             99843897


No 23 
>PRK00254 ski2-like helicase; Provisional
Probab=99.74  E-value=8.3e-16  Score=139.97  Aligned_cols=378  Identities=20%  Similarity=0.216  Sum_probs=205.8

Q ss_pred             HHCCCHHHHHHHHHCCHHHHHHHHHCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHHHH
Q ss_conf             70999899975245572234455410235665434466668837899999998752048961998447531579999999
Q gi|254780619|r  159 ASQVSSHVIDGLKAQGVIKQIFEVISPVVDSPNLYFSLPILDKNQQDVVEQVVPLCTKGFAVSLISGVTGSGKTEVYLEI  238 (731)
Q Consensus       159 ~~~~s~~~i~~L~~kglI~~~~~~~~~~~~~~~~~~~~~~Lt~eQ~~a~~~i~~~~~~~f~~~LL~GvTGSGKTEVYl~l  238 (731)
                      .++++..+.+-+.++|+-                     .|.+.|.++++.-  .. ++ ...|+--=||||||.|.--+
T Consensus         5 ~l~~~~~~~~~~~~~gI~---------------------~l~p~Q~e~l~~g--~~-~g-~NllvsaPT~sGKTlvAEla   59 (717)
T PRK00254          5 ELRVDERIKEILKERGIE---------------------ELYPPQAEALTSG--VL-EG-KNLLIAIPTASGKTLIAEIA   59 (717)
T ss_pred             HCCCCHHHHHHHHHCCCC---------------------CCCHHHHHHHHHH--HC-CC-CCEEEECCCCCCHHHHHHHH
T ss_conf             439998999999976987---------------------2689999998742--33-69-81899899887489999999


Q ss_pred             H-HHHHHCCCCEEEEECCCHHHHHHHHHHHC--CCCCEEEEEECCCCCHHHHHHHHHHHCCCCEEEEEC----CHHHHH-
Q ss_conf             9-99851468479971521001344555430--389768996235572356678999971997399940----012110-
Q gi|254780619|r  239 V-AAVLHLGKQVLILLPEISLTSAILERFQK--RFGVKPAEWHSSLSTSMREKIWRQVARGAISVIVGV----RSALFL-  310 (731)
Q Consensus       239 i-~~~L~~GkqvLiLvPEI~Lt~Q~~~rl~~--rF~~~v~v~HS~ls~~eR~~~w~~i~~G~~~IVIGt----RSAif~-  310 (731)
                      | ..++..|+.+++++|-.+|+.|-+..|++  .+|.+|+.+++......+   |.    ++.+|+|.|    +|-+-- 
T Consensus        60 il~~~l~~~~k~iyi~P~kALa~EK~~~f~~~~~~g~~V~~~tGd~~~~~~---~l----~~~dIiV~T~Ek~dsl~r~~  132 (717)
T PRK00254         60 MVNKLLREGGKAVYLVPLKALAEEKFREFKDWEVLGLRVAMATGDYDSKDE---WL----GKYDIIIATAEKFDSLLRHG  132 (717)
T ss_pred             HHHHHHHCCCEEEEECCHHHHHHHHHHHHHHHHHCCCEEEEEECCCCCCCC---CC----CCCCEEEECHHHHHHHHHCC
T ss_conf             999998529929999267999999999998777449889897489888701---04----68999998889999999716


Q ss_pred             H--HCCCEEEEEEECCCCCCHHCCCCCCCHHHHHHHHHHHCCCCEECCCCC-CCHHHHHHHHHHHHHHHCCCCCCCCCCC
Q ss_conf             0--100013677405532100002443224899999751103210000245-4324677532123444124322367654
Q gi|254780619|r  311 P--FKKLGLIVIDEEHDISYKQEEGILYNARDMSIVRGKIESFPVVLVSAT-PSIESRVNGISRRYHSVHLSTRYRNSAL  387 (731)
Q Consensus       311 P--~~nLglIIvDEEHd~sykq~~~pry~aRdvA~~Ra~~~~~~lilgSAT-PSles~~~~~~g~~~~~~l~~R~~~~~~  387 (731)
                      +  +.++|+|||||=|--.= .+.||.+   ++.+.+.. ..+.+|.-||| |-.+.+.......  ++.-..|+  .++
T Consensus       133 ~~~l~~i~lvViDEiH~igD-~~RG~~l---E~~l~~l~-~~~qiIgLSATi~N~~~la~WL~a~--~~~~~~RP--VpL  203 (717)
T PRK00254        133 SSWIKDVKLLVADEIHLIGS-RDRGATL---EFILTHML-GRAQIIGLSATIGNPEELAEWLNAE--LIVSDWRP--VKL  203 (717)
T ss_pred             HHHHHCCCEEEEECEEECCC-CCCHHHH---HHHHHHHH-CCCEEEEEEEECCCHHHHHHHHCCC--CCCCCCCC--CCE
T ss_conf             25653269899976078889-8740999---99999510-0366999963349989999982885--21568857--752


Q ss_pred             CC-CEECCCCCCCCCCCC--CCCHHHHHHHHHHHCCCCEEEEEECCCCEEHHCCCCCCCCCCCCCCCCCEEEEECCCCCC
Q ss_conf             33-211022223322245--479899999988622655179974222000000235654343101465201211357832
Q gi|254780619|r  388 PH-LQVIDMRGQTIAQGK--SLSPEMIDGIRHTLARNEQTLLFLNRRGYAPLTLCQVCGNRLKCLHCSCWLVEHRSKKKL  464 (731)
Q Consensus       388 P~-i~ivDm~~~~~~~~~--~lS~~l~~~i~~~l~~g~qvll~lnRrGya~~~~C~~Cg~~~~C~~C~~~l~~h~~~~~l  464 (731)
                      -+ +..-+.  -....+.  .+ ....+.+.+++.+|+|+|+|.|.|--+-.+..    ..  +.++...++- .....+
T Consensus       204 ~~~v~~~~~--~~~~~~~~~~~-~~~~~l~~~~~~~~~~~LVF~~tR~~~e~~A~----~l--a~~~~~~~~~-~~~~~l  273 (717)
T PRK00254        204 RKGVFYQGF--VFWEDGKIDRY-NSWEELVYDAVKRGKGALIFVNMRRKAEKTAL----EL--AKKIKNLLTK-PELREL  273 (717)
T ss_pred             EEEEEECCE--EEECCCCCHHH-HHHHHHHHHHHHCCCCCEEEEECHHHHHHHHH----HH--HHHHHHHCCH-HHHHHH
T ss_conf             764420660--11045620544-30789999999749981899955799999999----99--9988763076-889999


Q ss_pred             EECHHHCCCCCCCCCCCCCCCCEECCCCCCHHHHHHHHHH--CCCCCHHHHCCCCCCCCHHHHHHHHHHHCCCCCCEEEE
Q ss_conf             0000210244655566678741100135428998888520--48520001023211358678999998621257657987
Q gi|254780619|r  465 YCHQCGHSAIYSQSCVVCGSSGKMIACGFGIERIAEEVCE--YFPLARISILSSDLEGGGGRLQLQLSAIAKGEIDIIIG  542 (731)
Q Consensus       465 ~Ch~Cg~~~~~~~~Cp~Cg~~~~l~~~G~Gte~~~e~l~~--~fp~~~v~~~d~d~~~~~~~~~~~~~~~~~~~~~ilvg  542 (731)
                      ..        .......+.         . .+.+.+-+..  .|-++...         ....+.+-..|.+|.+.||+.
T Consensus       274 ~~--------~~~~~~~~~---------~-~~~L~~~l~~GVafHHAGL~---------~~~R~lVE~~Fr~g~Ikvl~a  326 (717)
T PRK00254        274 KE--------LADSLEENP---------T-NEKLAKALRGGVAFHHAGLG---------RDERVLVEDNFRKGLIKVVVA  326 (717)
T ss_pred             HH--------HHHHHHHCC---------C-CHHHHHHHHHCHHHHCCCCC---------HHHHHHHHHHHHCCCCEEEEE
T ss_conf             99--------999987376---------5-18999999708312158999---------889999999998799589981


Q ss_pred             EHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCC--CCCEEEEEECCCC-CHHHHHHHHCCH
Q ss_conf             044302311345201233000344310245578999998754311025667--8868999932986-488899995897
Q gi|254780619|r  543 TQLVAKGHNFPRMSLVGVVDGDLGLTNADLRSSERTFQLLSQVTGRAGRFG--LKSLGLIQAYQPT-HPVMQALVSGDA  618 (731)
Q Consensus       543 Tq~i~kg~~fp~v~lv~il~aD~~l~~pd~ra~E~~~qll~qv~gRagr~~--~~g~v~iQt~~p~-~~~~~~~~~~d~  618 (731)
                      |.-+|-|.|+|.-+ |+|-+....   .++.-..-.-.-+.|.+|||||-.  ..|+.+|-+...+ ..++.....++.
T Consensus       327 TsTLA~GVNLPAr~-VIi~~~~~~---~~~g~~~i~~~e~~QM~GRAGR~G~D~~G~~iii~~~~~~~~~~~~~~~~~~  401 (717)
T PRK00254        327 TPTLSAGINTPAFR-VIIRDTWRY---SEFGMERIPVLEIQQMMGRAGRPKYDEVGEAIIVSTTEDPSKVMDRYIFGKP  401 (717)
T ss_pred             CCHHHCCCCCCCEE-EEEECCEEE---CCCCCEECCHHHHHHHHHHCCCCCCCCCCEEEEEECCCCHHHHHHHHHCCCC
T ss_conf             64465045776059-999265670---7997237875368886250699987888508999548578999999861896


No 24 
>COG1204 Superfamily II helicase [General function prediction only]
Probab=99.73  E-value=3.7e-16  Score=142.64  Aligned_cols=379  Identities=23%  Similarity=0.213  Sum_probs=220.3

Q ss_pred             CCCHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHHHHHHHHHHCC-CCEEEEECCCHHHHHHHHHHH--CCCCCEE
Q ss_conf             6883789999999875204896199844753157999999999985146-847997152100134455543--0389768
Q gi|254780619|r  198 ILDKNQQDVVEQVVPLCTKGFAVSLISGVTGSGKTEVYLEIVAAVLHLG-KQVLILLPEISLTSAILERFQ--KRFGVKP  274 (731)
Q Consensus       198 ~Lt~eQ~~a~~~i~~~~~~~f~~~LL~GvTGSGKTEVYl~li~~~L~~G-kqvLiLvPEI~Lt~Q~~~rl~--~rF~~~v  274 (731)
                      .+.+.||.++...... .   ...|+--=||||||-|.+-+|...+.+| .-++++||--+|+.|.+..|+  +.||.+|
T Consensus        31 el~~~qq~av~~~~~~-~---~N~li~aPTgsGKTlIA~lai~~~l~~~~~k~vYivPlkALa~Ek~~~~~~~~~~GirV  106 (766)
T COG1204          31 ELFNPQQEAVEKGLLS-D---ENVLISAPTGSGKTLIALLAILSTLLEGGGKVVYIVPLKALAEEKYEEFSRLEELGIRV  106 (766)
T ss_pred             HHHHHHHHHHHCCCCC-C---CCEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECHHHHHHHHHHHHHHHHHCCCEE
T ss_conf             7557899874111257-9---86799767888669999999999998559838999075999999999866688659779


Q ss_pred             EEEECCCCCH-HHHHHHHHHHCCCCEEEEECCHHHH-------HHHCCCEEEEEEECCCCCCHHCCCCCCCHHHHHHHHH
Q ss_conf             9962355723-5667899997199739994001211-------0010001367740553210000244322489999975
Q gi|254780619|r  275 AEWHSSLSTS-MREKIWRQVARGAISVIVGVRSALF-------LPFKKLGLIVIDEEHDISYKQEEGILYNARDMSIVRG  346 (731)
Q Consensus       275 ~v~HS~ls~~-eR~~~w~~i~~G~~~IVIGtRSAif-------~P~~nLglIIvDEEHd~sykq~~~pry~aRdvA~~Ra  346 (731)
                      +++++..-.. ++.        .+.+|||.|-=-++       ..+.+.+++||||=|=-.- ...+|..-+ .++.+|.
T Consensus       107 ~~~TgD~~~~~~~l--------~~~~ViVtT~EK~Dsl~R~~~~~~~~V~lvViDEiH~l~d-~~RG~~lE~-iv~r~~~  176 (766)
T COG1204         107 GISTGDYDLDDERL--------ARYDVIVTTPEKLDSLTRKRPSWIEEVDLVVIDEIHLLGD-RTRGPVLES-IVARMRR  176 (766)
T ss_pred             EEECCCCCCCHHHH--------CCCCEEEECHHHHHHHHHCCCCHHHCCCEEEEEEEEECCC-CCCCCEEHH-HHHHHHH
T ss_conf             99648865553341--------4588799746786676506753334016899942101487-565864022-7988885


Q ss_pred             HHCCCCEECCCCC-CCHHHHHHHHHHHHHHHCCCCCCCC--CCCCCCEECC-CCCCCCCCCCCCCHHHHHHHHHHHCCCC
Q ss_conf             1103210000245-4324677532123444124322367--6543321102-2223322245479899999988622655
Q gi|254780619|r  347 KIESFPVVLVSAT-PSIESRVNGISRRYHSVHLSTRYRN--SALPHLQVID-MRGQTIAQGKSLSPEMIDGIRHTLARNE  422 (731)
Q Consensus       347 ~~~~~~lilgSAT-PSles~~~~~~g~~~~~~l~~R~~~--~~~P~i~ivD-m~~~~~~~~~~lS~~l~~~i~~~l~~g~  422 (731)
                      ....+.++=-||| |-.+......+++..  ...=|+..  +.-|...-+. ............-...+..+.++++.|+
T Consensus       177 ~~~~~rivgLSATlpN~~evA~wL~a~~~--~~~~rp~~l~~~v~~~~~~~~~~~~~k~~~~~~~~~~~~~v~~~~~~~~  254 (766)
T COG1204         177 LNELIRIVGLSATLPNAEEVADWLNAKLV--ESDWRPVPLRRGVPYVGAFLGADGKKKTWPLLIDNLALELVLESLAEGG  254 (766)
T ss_pred             HCCCEEEEEEEEECCCHHHHHHHHCCCCC--CCCCCCCCCCCCCCCCEEEEEECCCCCCCCCCCHHHHHHHHHHHHHCCC
T ss_conf             27551798873116888999998588355--5677886201577653179871476434542105799999999985698


Q ss_pred             EEEEEECCCCEEHHCCCCCCCCCCCCCCCCCEEEEECCCCCCEECHHHCCCCCCCCCCCCCCCCEECC---CCCCHHHHH
Q ss_conf             17997422200000023565434310146520121135783200002102446555666787411001---354289988
Q gi|254780619|r  423 QTLLFLNRRGYAPLTLCQVCGNRLKCLHCSCWLVEHRSKKKLYCHQCGHSAIYSQSCVVCGSSGKMIA---CGFGIERIA  499 (731)
Q Consensus       423 qvll~lnRrGya~~~~C~~Cg~~~~C~~C~~~l~~h~~~~~l~Ch~Cg~~~~~~~~Cp~Cg~~~~l~~---~G~Gte~~~  499 (731)
                      |||+|+|-|..+-...        +=-.=-..-+.  .....             .|-.=++. .+..   .-.+.+.++
T Consensus       255 qvLvFv~sR~~a~~~A--------~~l~~~~~~~~--~~~~~-------------~~~~~~a~-~~~~~~~~~~~~~~l~  310 (766)
T COG1204         255 QVLVFVHSRKEAEKTA--------KKLRIKMSATL--SDDEK-------------IVLDEGAS-PILIPETPTSEDEELA  310 (766)
T ss_pred             EEEEEEECCCHHHHHH--------HHHHHHHHHCC--CHHHH-------------HHCCCCCC-CCCCCCCCCCCHHHHH
T ss_conf             6999974572599999--------99999875127--71654-------------30122344-2112355432217899


Q ss_pred             HHHHH--CCCCCHHHHCCCCCCCCHHHHHHHHHHHCCCCCCEEEEEHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             88520--4852000102321135867899999862125765798704430231134520123300034431024557899
Q gi|254780619|r  500 EEVCE--YFPLARISILSSDLEGGGGRLQLQLSAIAKGEIDIIIGTQLVAKGHNFPRMSLVGVVDGDLGLTNADLRSSER  577 (731)
Q Consensus       500 e~l~~--~fp~~~v~~~d~d~~~~~~~~~~~~~~~~~~~~~ilvgTq~i~kg~~fp~v~lv~il~aD~~l~~pd~ra~E~  577 (731)
                      +-+..  .|-++-+.+.++         +-+=..|+.|++.||+.|.-+|.|-+.|.-+ |+|=|.  ..+.| +...+.
T Consensus       311 e~v~~GvafHhAGL~~~~R---------~~vE~~Fr~g~ikVlv~TpTLA~GVNLPA~~-VIIk~~--~~y~~-~~g~~~  377 (766)
T COG1204         311 ELVLRGVAFHHAGLPREDR---------QLVEDAFRKGKIKVLVSTPTLAAGVNLPART-VIIKDT--RRYDP-KGGIVD  377 (766)
T ss_pred             HHHHHCCCCCCCCCCHHHH---------HHHHHHHHCCCCEEEEECHHHHHHCCCCCEE-EEEEEE--EEECC-CCCEEE
T ss_conf             9997275411268978899---------9999998669854999545776216886328-999103--87757-788477


Q ss_pred             H-HHHHHHHHHCCCCCC--CCCEEEEEECCC--CCHHHHHHHHCCHHHHHHHHHHHH
Q ss_conf             9-998754311025667--886899993298--648889999589799999999999
Q gi|254780619|r  578 T-FQLLSQVTGRAGRFG--LKSLGLIQAYQP--THPVMQALVSGDADSFYESEIRAR  629 (731)
Q Consensus       578 ~-~qll~qv~gRagr~~--~~g~v~iQt~~p--~~~~~~~~~~~d~~~f~~~el~~R  629 (731)
                      . -.=..|.+|||||-.  .-|..+|-++.-  ++........++.+.+..+-..++
T Consensus       378 i~~~dv~QM~GRAGRPg~d~~G~~~i~~~~~~~~~~~~~~~~~~~~e~~~s~l~~~~  434 (766)
T COG1204         378 IPVLDVLQMAGRAGRPGYDDYGEAIILATSHDELEYLAELYIQSEPEPIESKLGDEL  434 (766)
T ss_pred             CCHHHHHHCCCCCCCCCCCCCCCEEEEECCCCCHHHHHHHHHCCCCCHHHHHHCCCC
T ss_conf             764148655676799875777827999358631558998752158626887652021


No 25 
>PTZ00110 helicase; Provisional
Probab=99.70  E-value=4.8e-14  Score=126.48  Aligned_cols=327  Identities=17%  Similarity=0.197  Sum_probs=185.5

Q ss_pred             HHHCCCHHHHHHHHHCCHHHHHHHHHCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHHH
Q ss_conf             77099989997524557223445541023566543446666883789999999875204896199844753157999999
Q gi|254780619|r  158 RASQVSSHVIDGLKAQGVIKQIFEVISPVVDSPNLYFSLPILDKNQQDVVEQVVPLCTKGFAVSLISGVTGSGKTEVYLE  237 (731)
Q Consensus       158 ~~~~~s~~~i~~L~~kglI~~~~~~~~~~~~~~~~~~~~~~Lt~eQ~~a~~~i~~~~~~~f~~~LL~GvTGSGKTEVYl~  237 (731)
                      ...+++..+++.+.+.|+-+                     .|+=|.+++=.+..    + .-.+-..-||||||.-|+-
T Consensus       185 ~~~~fp~~il~~i~~~GF~~---------------------PTPIQ~qaIPiaLs----G-rDvIgiAqTGSGKTLAFlL  238 (602)
T PTZ00110        185 EYTSFPDYILKSIEAAGFTE---------------------PTPIQVQGWPIALS----G-RDMIGIAETGSGKTLAFLL  238 (602)
T ss_pred             HHCCCCHHHHHHHHHCCCCC---------------------CCHHHHHHHHHHHC----C-CCEEEECCCCCHHHHHHHH
T ss_conf             01599999999999769999---------------------99899999879856----9-8679987897889999999


Q ss_pred             -HHHHHHHC-------CCCEEEEECCCHHHHHHHHHHHC---CCCCEEEEEECCCCCHHHHHHHHHHHCCCCEEEEECCH
Q ss_conf             -99998514-------68479971521001344555430---38976899623557235667899997199739994001
Q gi|254780619|r  238 -IVAAVLHL-------GKQVLILLPEISLTSAILERFQK---RFGVKPAEWHSSLSTSMREKIWRQVARGAISVIVGVRS  306 (731)
Q Consensus       238 -li~~~L~~-------GkqvLiLvPEI~Lt~Q~~~rl~~---rF~~~v~v~HS~ls~~eR~~~w~~i~~G~~~IVIGtRS  306 (731)
                       ++.+.+.+       |-.||||+|.=-|+.|+.+-+..   ..+.+++..-++.+.++   +...++.| +.|||||-.
T Consensus       239 P~l~hi~~q~~~~~~~gP~aLILaPTRELA~QI~~e~~~~~~~~~ir~~~i~GG~~~~~---Q~~~L~~G-~dIvVATPG  314 (602)
T PTZ00110        239 PAIVHINAQPLLRPGDGPIVLVLAPTRELAEQIREQALQFGRSSKLKNSVAYGGVPKRF---QTYALRRG-VEILIACPG  314 (602)
T ss_pred             HHHHHHHHCCCCCCCCCCEEEEECCHHHHHHHHHHHHHHHHCCCCCEEEEEECCCCHHH---HHHHHCCC-CCEEEECCH
T ss_conf             99999851634367899769997383999999999999971547854999979968799---99987169-999997923


Q ss_pred             HHH-------HHHCCCEEEEEEECCCCCCHHCCCCCCCHHHHHHHHHHHCCCCEECCCCCCCHHHHHHHHHH--H-HHHH
Q ss_conf             211-------00100013677405532100002443224899999751103210000245432467753212--3-4441
Q gi|254780619|r  307 ALF-------LPFKKLGLIVIDEEHDISYKQEEGILYNARDMSIVRGKIESFPVVLVSATPSIESRVNGISR--R-YHSV  376 (731)
Q Consensus       307 Aif-------~P~~nLglIIvDEEHd~sykq~~~pry~aRdvA~~Ra~~~~~~lilgSATPSles~~~~~~g--~-~~~~  376 (731)
                      =+.       +-+.++..+|+||. |--+  ++++.-+.+.+.-.  -..+-..+|-|||-+-+.-..+..-  . ...+
T Consensus       315 RLiDlL~~~~~~L~~v~yLVLDEA-DRML--DmGFe~qI~~Il~~--i~pdRQTlLFSAT~p~~V~~LA~~~L~~~Pv~I  389 (602)
T PTZ00110        315 RLIDFLESNVTNLRRVTYLVLDEA-DRML--DMGFEPQIRKIVSQ--IRPDRQTLMWSATWPKEVQSLARDLCKEEPVHV  389 (602)
T ss_pred             HHHHHHHCCCCCCCCEEEEEEECH-HHHH--CCCCHHHHHHHHHH--CCCCCEEEEEECCCCHHHHHHHHHHHCCCCEEE
T ss_conf             899999649987431028998757-7663--54629999999985--897877999955899899999999820698899


Q ss_pred             CCCCCCCCCCCC----CCEECCCCCCCCCCCCCCCHHHHHHHHHHHCCCCEEEEEECCCCEEHHCCCCCCCCCCCCCCCC
Q ss_conf             243223676543----3211022223322245479899999988622655179974222000000235654343101465
Q gi|254780619|r  377 HLSTRYRNSALP----HLQVIDMRGQTIAQGKSLSPEMIDGIRHTLARNEQTLLFLNRRGYAPLTLCQVCGNRLKCLHCS  452 (731)
Q Consensus       377 ~l~~R~~~~~~P----~i~ivDm~~~~~~~~~~lS~~l~~~i~~~l~~g~qvll~lnRrGya~~~~C~~Cg~~~~C~~C~  452 (731)
                      ..... ......    .+.+++   +..     --..|...+.+.. .+.++|||.|.+-                    
T Consensus       390 ~Vg~~-~~~a~~~I~Q~v~vv~---~~e-----K~~~L~~lL~~~~-~~~kvIIFvnTK~--------------------  439 (602)
T PTZ00110        390 NVGSL-DLTTCHNIKQEVFVIE---EHE-----KRAKLKELLGQIM-DGGKILIFSETKK--------------------  439 (602)
T ss_pred             EECCC-CCCCCCCCEEEEEEEC---HHH-----HHHHHHHHHHHCC-CCCCEEEEECCHH--------------------
T ss_conf             93688-8777787058999965---188-----9999999998527-8996899929738--------------------


Q ss_pred             CEEEEECCCCCCEECHHHCCCCCCCCCCCCCCCCEECCCCCCHHHHHHHHHHCCCCCHHHHCCCCCCCCHHHHHHHHHHH
Q ss_conf             20121135783200002102446555666787411001354289988885204852000102321135867899999862
Q gi|254780619|r  453 CWLVEHRSKKKLYCHQCGHSAIYSQSCVVCGSSGKMIACGFGIERIAEEVCEYFPLARISILSSDLEGGGGRLQLQLSAI  532 (731)
Q Consensus       453 ~~l~~h~~~~~l~Ch~Cg~~~~~~~~Cp~Cg~~~~l~~~G~Gte~~~e~l~~~fp~~~v~~~d~d~~~~~~~~~~~~~~~  532 (731)
                                                               .++++...|...  +.++.-+..|..  ....+..+++|
T Consensus       440 -----------------------------------------~ad~L~~~L~~~--G~~a~~LHGd~~--Q~eR~~~L~~F  474 (602)
T PTZ00110        440 -----------------------------------------GADTLTKELRLD--GWPALCIHGDKK--QEERTWVLNEF  474 (602)
T ss_pred             -----------------------------------------HHHHHHHHHHHC--CCCEEEEECCCC--HHHHHHHHHHH
T ss_conf             -----------------------------------------999999999867--995798208899--99999999999


Q ss_pred             CCCCCCEEEEEHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEECCCCC
Q ss_conf             125765798704430231134520123300034431024557899999875431102566788689999329864
Q gi|254780619|r  533 AKGEIDIIIGTQLVAKGHNFPRMSLVGVVDGDLGLTNADLRSSERTFQLLSQVTGRAGRFGLKSLGLIQAYQPTH  607 (731)
Q Consensus       533 ~~~~~~ilvgTq~i~kg~~fp~v~lv~il~aD~~l~~pd~ra~E~~~qll~qv~gRagr~~~~g~v~iQt~~p~~  607 (731)
                      .+|+..|||+|-+.|.|+|+|+|++|+-.|.=  -..-|          .+-=.||.||+.+.|..+- -+.||+
T Consensus       475 r~G~~~ILVATDVAARGLDI~dV~~VINYD~P--~~~ed----------YVHRIGRTGRAG~kG~A~T-F~Tpd~  536 (602)
T PTZ00110        475 KTGKHPIMIATDVASRGLDVRDVKYVINFDFP--NQIED----------YVHRIGRTGRAGAKGASYT-FLTPDK  536 (602)
T ss_pred             HCCCCCEEEECCHHHCCCCCCCCCEEEEECCC--CCCCC----------CCCCCCCCCCCCCCEEEEE-EECCCC
T ss_conf             76999889882223315551579879995897--98022----------1013561506899316999-977770


No 26 
>COG0556 UvrB Helicase subunit of the DNA excision repair complex [DNA replication, recombination, and repair]
Probab=99.69  E-value=4.9e-15  Score=134.10  Aligned_cols=109  Identities=28%  Similarity=0.406  Sum_probs=75.5

Q ss_pred             HHHHHHHHHHCCC--CCHHHHCCCCCCCCHHHHHHHHHHHCCCCCCEEEEEHHHCCCCCCCCCCHHHHHHHHHHHHHHHH
Q ss_conf             8998888520485--20001023211358678999998621257657987044302311345201233000344310245
Q gi|254780619|r  495 IERIAEEVCEYFP--LARISILSSDLEGGGGRLQLQLSAIAKGEIDIIIGTQLVAKGHNFPRMSLVGVVDGDLGLTNADL  572 (731)
Q Consensus       495 te~~~e~l~~~fp--~~~v~~~d~d~~~~~~~~~~~~~~~~~~~~~ilvgTq~i~kg~~fp~v~lv~il~aD~~l~~pd~  572 (731)
                      |-|.+|+|...|-  +++|--|.||.- +-. .-+++.+.+.|+.|+|||--++--|+|.|.|+||+|+|||..-+.   
T Consensus       455 TKkmAEdLT~Yl~e~gikv~YlHSdid-TlE-R~eIirdLR~G~~DvLVGINLLREGLDiPEVsLVAIlDADKeGFL---  529 (663)
T COG0556         455 TKKMAEDLTEYLKELGIKVRYLHSDID-TLE-RVEIIRDLRLGEFDVLVGINLLREGLDLPEVSLVAILDADKEGFL---  529 (663)
T ss_pred             HHHHHHHHHHHHHHCCCEEEEEECCCH-HHH-HHHHHHHHHCCCCCEEEEEHHHHCCCCCCCEEEEEEEECCCCCCC---
T ss_conf             688899999999866964786424403-899-999999975778748985013313478864557988606854443---


Q ss_pred             HHHHHHHHHHHHHHHCCCCCCCCCEEEEEECCCCCHHHHHHH
Q ss_conf             578999998754311025667886899993298648889999
Q gi|254780619|r  573 RSSERTFQLLSQVTGRAGRFGLKSLGLIQAYQPTHPVMQALV  614 (731)
Q Consensus       573 ra~E~~~qll~qv~gRagr~~~~g~v~iQt~~p~~~~~~~~~  614 (731)
                      |+ |   .-|.|..|||.|.. .|+||+-...- ...++.++
T Consensus       530 Rs-e---~SLIQtIGRAARN~-~GkvIlYAD~i-T~sM~~Ai  565 (663)
T COG0556         530 RS-E---RSLIQTIGRAARNV-NGKVILYADKI-TDSMQKAI  565 (663)
T ss_pred             CC-C---CHHHHHHHHHHHCC-CCEEEEECCHH-HHHHHHHH
T ss_conf             45-3---25999987886357-97399971011-49999999


No 27 
>PRK11057 ATP-dependent DNA helicase RecQ; Provisional
Probab=99.66  E-value=2.8e-13  Score=120.66  Aligned_cols=319  Identities=21%  Similarity=0.289  Sum_probs=203.5

Q ss_pred             CCCHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHCCCCCEEEEE
Q ss_conf             68837899999998752048961998447531579999999999851468479971521001344555430389768996
Q gi|254780619|r  198 ILDKNQQDVVEQVVPLCTKGFAVSLISGVTGSGKTEVYLEIVAAVLHLGKQVLILLPEISLTSAILERFQKRFGVKPAEW  277 (731)
Q Consensus       198 ~Lt~eQ~~a~~~i~~~~~~~f~~~LL~GvTGSGKTEVYl~li~~~L~~GkqvLiLvPEI~Lt~Q~~~rl~~rF~~~v~v~  277 (731)
                      ..-+.|.++++.+....    . .|.-==||+||+..|. +  -++-.++-+||+-|-|+|-..-+..+... |...+.+
T Consensus        25 ~Fr~~Q~e~i~~~l~g~----D-~l~~mpTG~GKSlcyQ-l--Pal~~~g~tiVisPLisLm~DQv~~L~~~-gi~a~~l   95 (607)
T PRK11057         25 QFRPGQEEIIDTVLSGR----D-CLVVMPTGGGKSLCYQ-I--PALVLDGLTLVVSPLISLMKDQVDQLLAN-GVAAACL   95 (607)
T ss_pred             CCCHHHHHHHHHHHCCC----C-EEEECCCCCHHHHHHH-H--HHHHCCCCEEEECCHHHHHHHHHHHHHHC-CCCEEEE
T ss_conf             34576999999998699----8-8998789955979999-9--99877998899868799999999999978-9929995


Q ss_pred             ECCCCCHHHHHHHHHHHCCCCEEEEECCHHH-------HHHHCCCEEEEEEECCCCC-CHHCCCCCCCHHHHHHHHHHHC
Q ss_conf             2355723566789999719973999400121-------1001000136774055321-0000244322489999975110
Q gi|254780619|r  278 HSSLSTSMREKIWRQVARGAISVIVGVRSAL-------FLPFKKLGLIVIDEEHDIS-YKQEEGILYNARDMSIVRGKIE  349 (731)
Q Consensus       278 HS~ls~~eR~~~w~~i~~G~~~IVIGtRSAi-------f~P~~nLglIIvDEEHd~s-ykq~~~pry~aRdvA~~Ra~~~  349 (731)
                      +|.++..|+.++|.++.+|+.+++.-|.--+       ++.-.++++|+|||-|=-| |-.+-.|  +-+.++.+|..+-
T Consensus        96 ~s~~~~~e~~~~~~~~~~g~~~llyvtPErl~~~~~~~~l~~~~i~~~viDEAHcvs~WGhdFRp--~Y~~l~~l~~~~~  173 (607)
T PRK11057         96 NSTQTREQQLEVMAGCRTGQIKLLYIAPERLMMDNFLEHLAHWNPVLLAVDEAHCISQWGHDFRP--EYAALGQLRQRFP  173 (607)
T ss_pred             CCCCCHHHHHHHHHHHHCCCCCEEEECHHHHCCHHHHHHHHHCCCCEEEEEHHHHHHHCCCCCHH--HHHHHHHHHHHCC
T ss_conf             69999999999999997599879998855856978999997188664885306667541550038--8999999999769


Q ss_pred             CCCEECCCCCCCHHHHHHHHHHHHHHHCCCCC---CCCCCCCCCEECCCCCCCCCCCCCCCHHHHHHHHHHHCCCCEEEE
Q ss_conf             32100002454324677532123444124322---367654332110222233222454798999999886226551799
Q gi|254780619|r  350 SFPVVLVSATPSIESRVNGISRRYHSVHLSTR---YRNSALPHLQVIDMRGQTIAQGKSLSPEMIDGIRHTLARNEQTLL  426 (731)
Q Consensus       350 ~~~lilgSATPSles~~~~~~g~~~~~~l~~R---~~~~~~P~i~ivDm~~~~~~~~~~lS~~l~~~i~~~l~~g~qvll  426 (731)
                      +.|++--|||-+.++..-+    ...+.|.+.   ..+...|++.. ++...    .... +.+.+.+...         
T Consensus       174 ~~p~~AlTATAt~~v~~di----~~~L~l~~~~~~~~~f~RpNl~~-~v~~~----~~~~-~~~~~~~~~~---------  234 (607)
T PRK11057        174 TLPFMALTATADDTTRQDI----VRLLGLNDPLIQISSFDRPNIRY-MLMEK----FKPL-DQLMRYVQEQ---------  234 (607)
T ss_pred             CCCEEEEEECCCHHHHHHH----HHHHCCCCCCEEECCCCCCCCEE-EEEEC----CCHH-HHHHHHHHHC---------
T ss_conf             9974899963687899999----99708999807825778887414-55544----7739-9999998706---------


Q ss_pred             EECCCCEEHHCCCCCCCCCCCCCCCCCEEEEECCCCCCEECHHHCCCCCCCCCCCCCCCCEECCCCCCHHHHHHHHHHCC
Q ss_conf             74222000000235654343101465201211357832000021024465556667874110013542899888852048
Q gi|254780619|r  427 FLNRRGYAPLTLCQVCGNRLKCLHCSCWLVEHRSKKKLYCHQCGHSAIYSQSCVVCGSSGKMIACGFGIERIAEEVCEYF  506 (731)
Q Consensus       427 ~lnRrGya~~~~C~~Cg~~~~C~~C~~~l~~h~~~~~l~Ch~Cg~~~~~~~~Cp~Cg~~~~l~~~G~Gte~~~e~l~~~f  506 (731)
                          +|-++.++                                           |.+.       ..+|.+.+.|++. 
T Consensus       235 ----~~~sgIIY-------------------------------------------c~tr-------k~~e~la~~L~~~-  259 (607)
T PRK11057        235 ----RGKSGIIY-------------------------------------------CNSR-------AKVEDTAARLQSR-  259 (607)
T ss_pred             ----CCCCEEEE-------------------------------------------ECCH-------HHHHHHHHHHHHC-
T ss_conf             ----89977999-------------------------------------------6928-------9999999999857-


Q ss_pred             CCCHHHHCCCCCCCCHHHHHHHHHHHCCCCCCEEEEEHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             52000102321135867899999862125765798704430231134520123300034431024557899999875431
Q gi|254780619|r  507 PLARISILSSDLEGGGGRLQLQLSAIAKGEIDIIIGTQLVAKGHNFPRMSLVGVVDGDLGLTNADLRSSERTFQLLSQVT  586 (731)
Q Consensus       507 p~~~v~~~d~d~~~~~~~~~~~~~~~~~~~~~ilvgTq~i~kg~~fp~v~lv~il~aD~~l~~pd~ra~E~~~qll~qv~  586 (731)
                       +.++....++.  .....+...+.|..++.+|+|+|-.-.=|.|.|||.+|+-.+.=        .+-|.    +.|=+
T Consensus       260 -G~~~~~YHagl--~~~~R~~~q~~f~~~~~~vivAT~AFGMGIdk~dVR~ViH~~~P--------~s~e~----yyQE~  324 (607)
T PRK11057        260 -GISAAAYHAGL--DNDVRADVQEAFQRDDLQIVVATVAFGMGINKPNVRFVVHFDIP--------RNIES----YYQET  324 (607)
T ss_pred             -CCCEEECCCCC--CHHHHHHHHHHHHCCCCCEEEEEHHHHCCCCCCCCCEEEECCCC--------CCHHH----HHHHH
T ss_conf             -97545305899--97899999998756887589975011057677776679977899--------99999----99988


Q ss_pred             HCCCCCCCCCEEEEEECCCCC-HHHHHHHHCC
Q ss_conf             102566788689999329864-8889999589
Q gi|254780619|r  587 GRAGRFGLKSLGLIQAYQPTH-PVMQALVSGD  617 (731)
Q Consensus       587 gRagr~~~~g~v~iQt~~p~~-~~~~~~~~~d  617 (731)
                      |||||...+.+.++- |++.. ..++.++...
T Consensus       325 GRAGRDG~~a~c~l~-y~~~D~~~~~~~i~~~  355 (607)
T PRK11057        325 GRAGRDGLPAEAMLF-YDPADMAWLRRCLEEK  355 (607)
T ss_pred             HHCCCCCCCCEEEEE-ECHHHHHHHHHHHHCC
T ss_conf             635258985418998-5687899999998548


No 28 
>COG0513 SrmB Superfamily II DNA and RNA helicases [DNA replication, recombination, and repair / Transcription / Translation, ribosomal structure and biogenesis]
Probab=99.63  E-value=8.1e-13  Score=117.11  Aligned_cols=341  Identities=21%  Similarity=0.253  Sum_probs=186.4

Q ss_pred             HHCCCHHHHHHHHHCCHHHHHHHHHCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHHHH
Q ss_conf             70999899975245572234455410235665434466668837899999998752048961998447531579999999
Q gi|254780619|r  159 ASQVSSHVIDGLKAQGVIKQIFEVISPVVDSPNLYFSLPILDKNQQDVVEQVVPLCTKGFAVSLISGVTGSGKTEVYLEI  238 (731)
Q Consensus       159 ~~~~s~~~i~~L~~kglI~~~~~~~~~~~~~~~~~~~~~~Lt~eQ~~a~~~i~~~~~~~f~~~LL~GvTGSGKTEVYl~l  238 (731)
                      .++.+...+++|.+.|+..                     .|+=|+.++-.+...     .-.+...-||||||.-|+--
T Consensus        33 ~l~l~~~ll~~l~~~gf~~---------------------pt~IQ~~~iP~~l~g-----~Dvi~~A~TGsGKT~Af~lP   86 (513)
T COG0513          33 SLGLSPELLQALKDLGFEE---------------------PTPIQLAAIPLILAG-----RDVLGQAQTGTGKTAAFLLP   86 (513)
T ss_pred             HCCCCHHHHHHHHHCCCCC---------------------CCHHHHHHCHHHHCC-----CCEEEECCCCCHHHHHHHHH
T ss_conf             6599999999999659899---------------------898999658776369-----99799868987178999999


Q ss_pred             HHHHHH---CC-CC-EEEEECCCHHHHHHHHHHHCC---C-CCEEEEEECCCCCHHHHHHHHHHHCCCCEEEEECCHHHH
Q ss_conf             999851---46-84-799715210013445554303---8-976899623557235667899997199739994001211
Q gi|254780619|r  239 VAAVLH---LG-KQ-VLILLPEISLTSAILERFQKR---F-GVKPAEWHSSLSTSMREKIWRQVARGAISVIVGVRSALF  309 (731)
Q Consensus       239 i~~~L~---~G-kq-vLiLvPEI~Lt~Q~~~rl~~r---F-~~~v~v~HS~ls~~eR~~~w~~i~~G~~~IVIGtRSAif  309 (731)
                      +-+.+.   .. .+ +|||+|.=-|+-|+.+.+...   . +..++.+.++.+.....   .+++.| ++|||||-.=++
T Consensus        87 ~l~~i~~~~~~~~~~aLil~PTRELA~Qi~~~~~~~~~~~~~~~~~~i~GG~~~~~q~---~~l~~g-~~ivVaTPGRll  162 (513)
T COG0513          87 LLQKILKSVERKYVSALILAPTRELAVQIAEELRKLGKNLGGLRVAVVYGGVSIRKQI---EALKRG-VDIVVATPGRLL  162 (513)
T ss_pred             HHHHHHHCCCCCCCCEEEECCCHHHHHHHHHHHHHHHHHCCCCEEEEEECCCCHHHHH---HHHHCC-CCEEEECCCHHH
T ss_conf             9999740045577756997799999999999999998624584299998998989999---987249-989997960899


Q ss_pred             -------HHHCCCEEEEEEECCCCCCHHCCCCCCCHHHHHHHHHHHCCCCEECCCCCCCHHHHHHHHHHHHHHHCCCCCC
Q ss_conf             -------0010001367740553210000244322489999975110321000024543246775321234441243223
Q gi|254780619|r  310 -------LPFKKLGLIVIDEEHDISYKQEEGILYNARDMSIVRGKIESFPVVLVSATPSIESRVNGISRRYHSVHLSTRY  382 (731)
Q Consensus       310 -------~P~~nLglIIvDEEHd~sykq~~~pry~aRdvA~~Ra~~~~~~lilgSATPSles~~~~~~g~~~~~~l~~R~  382 (731)
                             +.+.++..+|+||. |-=.  +.++.=....+.-..  -.+...+|-|||-+-+....+..  |  +.-+.  
T Consensus       163 D~i~~~~l~l~~v~~lVlDEA-Drml--d~gf~~~i~~I~~~~--p~~~qtllfSAT~~~~i~~l~~~--~--l~~p~--  231 (513)
T COG0513         163 DLIKRGKLDLSGVETLVLDEA-DRML--DMGFIDDIEKILKAL--PPDRQTLLFSATMPDDIRELARR--Y--LNDPV--  231 (513)
T ss_pred             HHHHCCCCCCCCEEEEEECCH-HHHC--CCCCHHHHHHHHHHC--CCCCEEEEEEECCCHHHHHHHHH--H--CCCCC--
T ss_conf             998648855465018996761-7663--887689999999738--97748999982489899999999--7--36880--


Q ss_pred             CCCCCCCCEECCCCCCCCCCCCCCCHHHHHHHHHHHCCCCEEEEEECCCCEEHHCCCCCCCCCCCCCCCCCEEEEECCCC
Q ss_conf             67654332110222233222454798999999886226551799742220000002356543431014652012113578
Q gi|254780619|r  383 RNSALPHLQVIDMRGQTIAQGKSLSPEMIDGIRHTLARNEQTLLFLNRRGYAPLTLCQVCGNRLKCLHCSCWLVEHRSKK  462 (731)
Q Consensus       383 ~~~~~P~i~ivDm~~~~~~~~~~lS~~l~~~i~~~l~~g~qvll~lnRrGya~~~~C~~Cg~~~~C~~C~~~l~~h~~~~  462 (731)
                            .+.+ +....                ..+..+=+|.++.+..+=                           ...
T Consensus       232 ------~i~v-~~~~~----------------~~~~~~i~q~~~~v~~~~---------------------------~k~  261 (513)
T COG0513         232 ------EIEV-SVEKL----------------ERTLKKIKQFYLEVESEE---------------------------EKL  261 (513)
T ss_pred             ------EEEE-CCCCC----------------CCCCCCCEEEEEEECCHH---------------------------HHH
T ss_conf             ------7996-43223----------------353004707999808567---------------------------799


Q ss_pred             CCEECHHHCCCCCCCCCCCCCCCCEECCCCCCHHHHHHHHHHCCCCCHHHHCCCCCCCCHHHHHHHHHHHCCCCCCEEEE
Q ss_conf             32000021024465556667874110013542899888852048520001023211358678999998621257657987
Q gi|254780619|r  463 KLYCHQCGHSAIYSQSCVVCGSSGKMIACGFGIERIAEEVCEYFPLARISILSSDLEGGGGRLQLQLSAIAKGEIDIIIG  542 (731)
Q Consensus       463 ~l~Ch~Cg~~~~~~~~Cp~Cg~~~~l~~~G~Gte~~~e~l~~~fp~~~v~~~d~d~~~~~~~~~~~~~~~~~~~~~ilvg  542 (731)
                      .+.++.|.....  ..   |   --|......++++.+.|.+.  +.++.-+..|.+  ....++.++.|.+|+.+|||+
T Consensus       262 ~~L~~ll~~~~~--~~---~---IVF~~tk~~~~~l~~~l~~~--g~~~~~lhG~l~--q~~R~~~l~~F~~g~~~iLVa  329 (513)
T COG0513         262 ELLLKLLKDEDE--GR---V---IVFVRTKRLVEELAESLRKR--GFKVAALHGDLP--QEERDRALEKFKDGELRVLVA  329 (513)
T ss_pred             HHHHHHHHCCCC--CE---E---EEEECCHHHHHHHHHHHHHC--CCEEEEEECCCC--HHHHHHHHHHHHCCCCCEEEE
T ss_conf             999999827888--83---9---99957677699999999978--965999738899--889999999997599898998


Q ss_pred             EHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCEEEEE-ECCCCCHHHHHHH
Q ss_conf             04430231134520123300034431024557899999875431102566788689999-3298648889999
Q gi|254780619|r  543 TQLVAKGHNFPRMSLVGVVDGDLGLTNADLRSSERTFQLLSQVTGRAGRFGLKSLGLIQ-AYQPTHPVMQALV  614 (731)
Q Consensus       543 Tq~i~kg~~fp~v~lv~il~aD~~l~~pd~ra~E~~~qll~qv~gRagr~~~~g~v~iQ-t~~p~~~~~~~~~  614 (731)
                      |-..|.|+|+|+|+.|+  |-|.-...-+|          ..=.||+||+.+.|..+.= +-..|...+..+.
T Consensus       330 TDvaaRGiDi~~v~~Vi--nyD~p~~~e~y----------vHRiGRTgRaG~~G~ai~fv~~~~e~~~l~~i~  390 (513)
T COG0513         330 TDVAARGLDIPDVSHVI--NYDLPLDPEDY----------VHRIGRTGRAGRKGVAISFVTEEEEVKKLKRIE  390 (513)
T ss_pred             ECHHHCCCCCCCCCEEE--ECCCCCCCCCC----------CCCCCCCCCCCCCCEEEEEECCHHHHHHHHHHH
T ss_conf             06544689966674799--78799980413----------173453434899872799855623499999999


No 29 
>PRK13767 ATP-dependent helicase; Provisional
Probab=99.62  E-value=6.8e-13  Score=117.73  Aligned_cols=324  Identities=16%  Similarity=0.183  Sum_probs=181.1

Q ss_pred             CCCHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHHH-HHHHHH--------HCCCCEEEEECCCHHHHHHHHHHHC
Q ss_conf             6883789999999875204896199844753157999999-999985--------1468479971521001344555430
Q gi|254780619|r  198 ILDKNQQDVVEQVVPLCTKGFAVSLISGVTGSGKTEVYLE-IVAAVL--------HLGKQVLILLPEISLTSAILERFQK  268 (731)
Q Consensus       198 ~Lt~eQ~~a~~~i~~~~~~~f~~~LL~GvTGSGKTEVYl~-li~~~L--------~~GkqvLiLvPEI~Lt~Q~~~rl~~  268 (731)
                      .+++-|..|+..|...     ...||.-=|||||||-++- .+.+.+        ..|-++|++.|-.+|...+.+++..
T Consensus        32 ~p~~~Q~~a~~~i~~G-----~~~Li~ApTGsGKTlAaflp~l~~l~~~~~~~~~~~~~~~LyIsPLkAL~~D~~r~L~~  106 (878)
T PRK13767         32 TFTPPQRYAIPLIHEG-----KNVLISSPTGSGKTLAAFLGIIDELFRLAEEGELEDSVYCIYVSPLRALNNDIHRNLEE  106 (878)
T ss_pred             CCCHHHHHHHHHHHCC-----CCEEEECCCCCHHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEECCHHHHHHHHHHHHHH
T ss_conf             9998999999999679-----98899899981399999999999998500036778872899968479889999998886


Q ss_pred             ----------C-----CCCEEEEEECCCCCHHHHHHHHHHHCCCCEEEEECCHHHH--------H-HHCCCEEEEEEECC
Q ss_conf             ----------3-----8976899623557235667899997199739994001211--------0-01000136774055
Q gi|254780619|r  269 ----------R-----FGVKPAEWHSSLSTSMREKIWRQVARGAISVIVGVRSALF--------L-PFKKLGLIVIDEEH  324 (731)
Q Consensus       269 ----------r-----F~~~v~v~HS~ls~~eR~~~w~~i~~G~~~IVIGtRSAif--------~-P~~nLglIIvDEEH  324 (731)
                                .     .+.+|.++|+..+.++|.+    ....-+.|+|.|-=.+.        . =|.||..|||||=|
T Consensus       107 pl~~i~~~~~~~g~~~~~i~v~vr~GDT~~~er~r----~~~~pp~ILiTTPEsL~lll~~~~~~~~l~~l~~VIvDE~H  182 (878)
T PRK13767        107 PLEEIREIAKERGIELPEIRHAVRTGDTSSYEKQK----MLRKPPHILITTPETLAILLNSPKFREKLRTVKWVIVDEIH  182 (878)
T ss_pred             HHHHHHHHHHHCCCCCCCCEEEEECCCCCHHHHHH----HHHCCCCEEECCHHHHHHHHCCHHHHHHHCCCCEEEECCCH
T ss_conf             99999999875278877744776369999999999----97489987987989999995496799985589999981716


Q ss_pred             CCCCHHCCCCC-CC-HHHHHHHHHHHC-CCCEECCCCCCC-HHHHHHHHHHHHH-----HHCCCCCCCCCCCCCCEECCC
Q ss_conf             32100002443-22-489999975110-321000024543-2467753212344-----412432236765433211022
Q gi|254780619|r  325 DISYKQEEGIL-YN-ARDMSIVRGKIE-SFPVVLVSATPS-IESRVNGISRRYH-----SVHLSTRYRNSALPHLQVIDM  395 (731)
Q Consensus       325 d~sykq~~~pr-y~-aRdvA~~Ra~~~-~~~lilgSATPS-les~~~~~~g~~~-----~~~l~~R~~~~~~P~i~ivDm  395 (731)
                      +-.  .  +-| -| +-.++.+++-.. +...|--|||-. +|......-|.-.     -..+. +........+.++--
T Consensus       183 ~l~--~--~kRG~~l~l~L~RL~~~~~~~~~riglSATv~~~~~~a~~L~g~~~~g~~r~~~iv-~~~~~k~~~~~~~~p  257 (878)
T PRK13767        183 SLA--E--NKRGVHLSLSLERLEELVGGEFVRIGLSATIEPLEEVAKFLVGYNDDGEPRDCEIV-DTRFAKPIDIKVLCP  257 (878)
T ss_pred             HHH--C--CCCHHHHHHHHHHHHHHCCCCCEEEEEECCCCCHHHHHHHHCCCCCCCCCCCEEEE-CCCCCCCCEEEEECC
T ss_conf             752--4--77458999999999986689987999964648999999985155667999852895-468778742688445


Q ss_pred             -CCCCCCCCCCCCHHHHHHHHHHHCCCCEEEEEECCCCEEHHCCCCCCCCCCCCCCCCCEEEEECCCCCCEECHHHCCCC
Q ss_conf             -2233222454798999999886226551799742220000002356543431014652012113578320000210244
Q gi|254780619|r  396 -RGQTIAQGKSLSPEMIDGIRHTLARNEQTLLFLNRRGYAPLTLCQVCGNRLKCLHCSCWLVEHRSKKKLYCHQCGHSAI  474 (731)
Q Consensus       396 -~~~~~~~~~~lS~~l~~~i~~~l~~g~qvll~lnRrGya~~~~C~~Cg~~~~C~~C~~~l~~h~~~~~l~Ch~Cg~~~~  474 (731)
                       ..........++..+.+.+.+.++++..+|+|.|.|.-+-.+.= ...  ..|+....       .....|||      
T Consensus       258 ~~~~~~~~~~~~~~~~~~~l~~~i~~~~~tLvF~NtR~~aE~~~~-~L~--~~~~~~~~-------~~~i~~HH------  321 (878)
T PRK13767        258 VDDLIHTPAEEISEALYETLDELIQEHRTTLIFTNTRSGAERVVY-KLR--KRYPEEYD-------EDNIGAHH------  321 (878)
T ss_pred             CCCCCCCCHHHHHHHHHHHHHHHHHHCCCEEEEECCHHHHHHHHH-HHH--HHHHHCCC-------CCCEEEEC------
T ss_conf             621245885568999999999999838977999155899999999-999--85343067-------54322201------


Q ss_pred             CCCCCCCCCCCCEECCCCCCHHHHHHHHHHCCCCCHHHHCCCCCCCCHHHHHHHHHHHCCCCCCEEEEEHHHCCCCCCCC
Q ss_conf             65556667874110013542899888852048520001023211358678999998621257657987044302311345
Q gi|254780619|r  475 YSQSCVVCGSSGKMIACGFGIERIAEEVCEYFPLARISILSSDLEGGGGRLQLQLSAIAKGEIDIIIGTQLVAKGHNFPR  554 (731)
Q Consensus       475 ~~~~Cp~Cg~~~~l~~~G~Gte~~~e~l~~~fp~~~v~~~d~d~~~~~~~~~~~~~~~~~~~~~ilvgTq~i~kg~~fp~  554 (731)
                              ||   +                                .+...+++-+.|.+|+.+.+|.|.-+.=|.|+..
T Consensus       322 --------gS---l--------------------------------s~e~R~~vE~~lk~G~l~~vV~TsSLELGIDiG~  358 (878)
T PRK13767        322 --------SS---L--------------------------------SREVRLEVEEKLKRGELKVVVSSTSLELGIDIGY  358 (878)
T ss_pred             --------CC---C--------------------------------CHHHHHHHHHHHHCCCCCEEEEECHHHCCCCCCC
T ss_conf             --------77---8--------------------------------9999999999985799868998273650777775


Q ss_pred             CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCC-CCEEEEEECCCC
Q ss_conf             2012330003443102455789999987543110256678-868999932986
Q gi|254780619|r  555 MSLVGVVDGDLGLTNADLRSSERTFQLLSQVTGRAGRFGL-KSLGLIQAYQPT  606 (731)
Q Consensus       555 v~lv~il~aD~~l~~pd~ra~E~~~qll~qv~gRagr~~~-~g~v~iQt~~p~  606 (731)
                      |.+|+-+++=            +...-+.|=+||||..-. ..+.++-+.+.+
T Consensus       359 Vd~Viq~gsP------------~svarllQR~GRsGH~~g~~s~g~~vp~~~~  399 (878)
T PRK13767        359 IDLVVLLGSP------------KSVSRLLQRIGRAGHRLGEVSKGRIIVVDRD  399 (878)
T ss_pred             CCEEEECCCC------------HHHHHHHHHHCCCCCCCCCEEEEEEEECCCH
T ss_conf             2589975896------------1189999983357899998046999979816


No 30 
>COG1111 MPH1 ERCC4-like helicases [DNA replication, recombination, and repair]
Probab=99.57  E-value=3.9e-13  Score=119.51  Aligned_cols=367  Identities=19%  Similarity=0.174  Sum_probs=208.0

Q ss_pred             HHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHHHHHHHHHHC-CCCEEEEECCCHHHHHHHHHHHCCCC---CEEEE
Q ss_conf             378999999987520489619984475315799999999998514-68479971521001344555430389---76899
Q gi|254780619|r  201 KNQQDVVEQVVPLCTKGFAVSLISGVTGSGKTEVYLEIVAAVLHL-GKQVLILLPEISLTSAILERFQKRFG---VKPAE  276 (731)
Q Consensus       201 ~eQ~~a~~~i~~~~~~~f~~~LL~GvTGSGKTEVYl~li~~~L~~-GkqvLiLvPEI~Lt~Q~~~rl~~rF~---~~v~v  276 (731)
                      .-|..++....      |...|+-==||=|||-|.+-.|+.-|.. |+-+|+|.|.--|.-|+...|++.+|   +.++.
T Consensus        18 ~YQ~~i~a~al------~~NtLvvlPTGLGKT~IA~~V~~~~l~~~~~kvlfLAPTKPLV~Qh~~~~~~v~~ip~~~i~~   91 (542)
T COG1111          18 LYQLNIAAKAL------FKNTLVVLPTGLGKTFIAAMVIANRLRWFGGKVLFLAPTKPLVLQHAEFCRKVTGIPEDEIAA   91 (542)
T ss_pred             HHHHHHHHHHH------HCCEEEEECCCCCHHHHHHHHHHHHHHHCCCEEEEECCCCHHHHHHHHHHHHHHCCCHHHEEE
T ss_conf             99999999986------448389952875079999999999987458848996589517999999999985898433231


Q ss_pred             EECCCCCHHHHHHHHHHHCCCCEEEEECCHHHH-------HHHCCCEEEEEEECCCCCCHHCCCCCCCHHHHHHHHHHHC
Q ss_conf             623557235667899997199739994001211-------0010001367740553210000244322489999975110
Q gi|254780619|r  277 WHSSLSTSMREKIWRQVARGAISVIVGVRSALF-------LPFKKLGLIVIDEEHDISYKQEEGILYNARDMSIVRGKIE  349 (731)
Q Consensus       277 ~HS~ls~~eR~~~w~~i~~G~~~IVIGtRSAif-------~P~~nLglIIvDEEHd~sykq~~~pry~aRdvA~~Ra~~~  349 (731)
                      +.+..++.+|...|.     ..+|++.|.-.+.       ....+..+||.||-|-..      =.|---+||...-+..
T Consensus        92 ltGev~p~~R~~~w~-----~~kVfvaTPQvveNDl~~Grid~~dv~~lifDEAHRAv------GnyAYv~Va~~y~~~~  160 (542)
T COG1111          92 LTGEVRPEEREELWA-----KKKVFVATPQVVENDLKAGRIDLDDVSLLIFDEAHRAV------GNYAYVFVAKEYLRSA  160 (542)
T ss_pred             ECCCCCHHHHHHHHH-----HCCEEEECCHHHHHHHHCCCCCHHHCEEEEECHHHHCC------CCCHHHHHHHHHHHHC
T ss_conf             117778688999875-----17789956387776876176676780589862355413------7606999999999825


Q ss_pred             CCCEECC-CCCC--CHHHHHHHHHH-HHHHHCCC-CC-CCCC---CCCCCEECC--CCCC------------------CC
Q ss_conf             3210000-2454--32467753212-34441243-22-3676---543321102--2223------------------32
Q gi|254780619|r  350 SFPVVLV-SATP--SIESRVNGISR-RYHSVHLS-TR-YRNS---ALPHLQVID--MRGQ------------------TI  400 (731)
Q Consensus       350 ~~~lilg-SATP--Sles~~~~~~g-~~~~~~l~-~R-~~~~---~~P~i~ivD--m~~~------------------~~  400 (731)
                      .-|+||| ||||  +.|....+-.+ .+..+... +. ..-.   ..-+++.|+  +-.+                  ..
T Consensus       161 k~~~ilgLTASPGs~~ekI~eV~~nLgIe~vevrTE~d~DV~~Yv~~~kve~ikV~lp~e~~~ir~~l~~~l~~~Lk~L~  240 (542)
T COG1111         161 KNPLILGLTASPGSDLEKIQEVVENLGIEKVEVRTEEDPDVRPYVKKIKVEWIKVDLPEEIKEIRDLLRDALKPRLKPLK  240 (542)
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHHHCCCCEEEEECCCCCCHHHHHCCCEEEEEECCCCHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             68437987238999879999999837954289845788517775140424899636858999999999999999999999


Q ss_pred             CCCCC-----CCH-HHHHHHHHHHC--CCCEEEEEECCC---CEEHHCCCCCCCCCCCCCCCCCEEEEECCCCCC-----
Q ss_conf             22454-----798-99999988622--655179974222---000000235654343101465201211357832-----
Q gi|254780619|r  401 AQGKS-----LSP-EMIDGIRHTLA--RNEQTLLFLNRR---GYAPLTLCQVCGNRLKCLHCSCWLVEHRSKKKL-----  464 (731)
Q Consensus       401 ~~~~~-----lS~-~l~~~i~~~l~--~g~qvll~lnRr---Gya~~~~C~~Cg~~~~C~~C~~~l~~h~~~~~l-----  464 (731)
                      ..|..     +|. .++......+.  +++      ++-   ..+-+..|-+|.|...--.|.+-=++++.-.++     
T Consensus       241 ~~g~~~~~~~~~~kdl~~~~~~~~~~a~~~------~~~~~~~l~~~a~~~kl~~a~elletqGi~~~~~Yl~~l~e~~~  314 (542)
T COG1111         241 ELGVIESSSPVSKKDLLELRQIRLIMAKNE------DSDKFRLLSVLAEAIKLAHALELLETQGIRPFYQYLEKLEEEAT  314 (542)
T ss_pred             HCCCEECCCCCCHHHHHHHHHHHHHHCCCC------CHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHC
T ss_conf             769532357310768999999899863576------17888999999999888899999985086999999999998750


Q ss_pred             ------------------E---E---CHHHCCCCCCC----CCC-----CCCCC-CEECCCCCCHHHHHHHHHHCCCCCH
Q ss_conf             ------------------0---0---00210244655----566-----67874-1100135428998888520485200
Q gi|254780619|r  465 ------------------Y---C---HQCGHSAIYSQ----SCV-----VCGSS-GKMIACGFGIERIAEEVCEYFPLAR  510 (731)
Q Consensus       465 ------------------~---C---h~Cg~~~~~~~----~Cp-----~Cg~~-~~l~~~G~Gte~~~e~l~~~fp~~~  510 (731)
                                        .   |   --||..-|--.    .|.     +-++. .-|..+.--.|.|.++|++.+|.++
T Consensus       315 ~~~sk~a~~l~~d~~~~~al~~~~~~~~~~v~HPKl~~l~eilke~~~k~~~~RvIVFT~yRdTae~i~~~L~~~~~~~~  394 (542)
T COG1111         315 KGGSKAAKSLLADPYFKRALRLLIRADESGVEHPKLEKLREILKEQLEKNGDSRVIVFTEYRDTAEEIVNFLKKIGIKAR  394 (542)
T ss_pred             CCCHHHHHHHHCCHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHCCCCCEEEEEEHHHHHHHHHHHHHHHCCCCCE
T ss_conf             35207789875382047999999974003688961899999999997238985599996147589999999985287520


Q ss_pred             HHHC----CCCCCC--CHHHHHHHHHHHCCCCCCEEEEEHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             0102----321135--8678999998621257657987044302311345201233000344310245578999998754
Q gi|254780619|r  511 ISIL----SSDLEG--GGGRLQLQLSAIAKGEIDIIIGTQLVAKGHNFPRMSLVGVVDGDLGLTNADLRSSERTFQLLSQ  584 (731)
Q Consensus       511 v~~~----d~d~~~--~~~~~~~~~~~~~~~~~~ilvgTq~i~kg~~fp~v~lv~il~aD~~l~~pd~ra~E~~~qll~q  584 (731)
                       .|+    |++...  +.....++++.|..|+.++||.|.+-.-|+|.|.|++|+.-++-.        |.-|+    .|
T Consensus       395 -~rFiGQa~r~~~~GMsQkeQ~eiI~~Fr~Ge~nVLVaTSVgEEGLDIp~vDlVifYEpvp--------SeIR~----IQ  461 (542)
T COG1111         395 -VRFIGQASREGDKGMSQKEQKEIIDQFRKGEYNVLVATSVGEEGLDIPEVDLVIFYEPVP--------SEIRS----IQ  461 (542)
T ss_pred             -EEEEECCCCCCCCCCCHHHHHHHHHHHHCCCCEEEEECCCCCCCCCCCCCCEEEEECCCC--------HHHHH----HH
T ss_conf             -688611454556665888999999998657851899812322467887656799956885--------78899----98


Q ss_pred             HHHCCCCCCCCCEEEEE-ECC
Q ss_conf             31102566788689999-329
Q gi|254780619|r  585 VTGRAGRFGLKSLGLIQ-AYQ  604 (731)
Q Consensus       585 v~gRagr~~~~g~v~iQ-t~~  604 (731)
                      =-||.||. ++|+|++- |.+
T Consensus       462 R~GRTGR~-r~Grv~vLvt~g  481 (542)
T COG1111         462 RKGRTGRK-RKGRVVVLVTEG  481 (542)
T ss_pred             HHCCCCCC-CCCEEEEEEECC
T ss_conf             60744557-797499999658


No 31 
>KOG0952 consensus
Probab=99.55  E-value=1e-12  Score=116.35  Aligned_cols=347  Identities=22%  Similarity=0.274  Sum_probs=212.0

Q ss_pred             CCCCCCCHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHHHHHHHHHHC----------CCCEEEEECCCHHHHHHH
Q ss_conf             4666688378999999987520489619984475315799999999998514----------684799715210013445
Q gi|254780619|r  194 FSLPILDKNQQDVVEQVVPLCTKGFAVSLISGVTGSGKTEVYLEIVAAVLHL----------GKQVLILLPEISLTSAIL  263 (731)
Q Consensus       194 ~~~~~Lt~eQ~~a~~~i~~~~~~~f~~~LL~GvTGSGKTEVYl~li~~~L~~----------GkqvLiLvPEI~Lt~Q~~  263 (731)
                      ++...+|.=|..++..+-....    ..|+-.=||||||-|++-.|-+++++          +--+++.+|--+|+..++
T Consensus       106 f~f~~fN~iQS~vFp~aY~Sne----NMLIcAPTGsGKT~la~L~ILr~ik~~~~~~~i~k~~fKiVYIaPmKALa~Em~  181 (1230)
T KOG0952         106 FSFEEFNRIQSEVFPVAYKSNE----NMLICAPTGSGKTVLAELCILRTIKEHEEQGDIAKDDFKIVYIAPMKALAAEMV  181 (1230)
T ss_pred             CCHHHHHHHHHHHHHHHHCCCC----CEEEECCCCCCCHHHHHHHHHHHHHHHCCCCCCCCCCCEEEEEECHHHHHHHHH
T ss_conf             6688887778774146514788----779977789971678999999999850145543468713999925688999999


Q ss_pred             HHHHCCCC---CEEEEEECCCCCHHHHHHHHHHHCCCCEEEEEC--------CHHH--HHHHCCCEEEEEEECCCCCCHH
Q ss_conf             55430389---768996235572356678999971997399940--------0121--1001000136774055321000
Q gi|254780619|r  264 ERFQKRFG---VKPAEWHSSLSTSMREKIWRQVARGAISVIVGV--------RSAL--FLPFKKLGLIVIDEEHDISYKQ  330 (731)
Q Consensus       264 ~rl~~rF~---~~v~v~HS~ls~~eR~~~w~~i~~G~~~IVIGt--------RSAi--f~P~~nLglIIvDEEHd~sykq  330 (731)
                      +.|.++|+   -.|..|.+.+.-.+-     .++  +.+|+|.|        |-++  -.=+...+|+||||=|=  .+.
T Consensus       182 ~~~~kkl~~~gi~v~ELTGD~ql~~t-----ei~--~tqiiVTTPEKwDvvTRk~~~d~~l~~~V~LviIDEVHl--Lhd  252 (1230)
T KOG0952         182 DKFSKKLAPLGISVRELTGDTQLTKT-----EIA--DTQIIVTTPEKWDVVTRKSVGDSALFSLVRLVIIDEVHL--LHD  252 (1230)
T ss_pred             HHHHHHCCCCCCEEEEECCCCHHHHH-----HHH--HCCEEEECCCCEEEEEEEECCCHHHHHHEEEEEEEEEHH--HCC
T ss_conf             99866424246258884175456677-----877--437797063400046654126265555420488530012--157


Q ss_pred             CCCCCC---CHHHHHHHHHHHCCCCEECCCCC-CCHHHHHHHHHHH--HHHHCCCCCCCCCCCCCCEECCCCCCC-CCCC
Q ss_conf             024432---24899999751103210000245-4324677532123--444124322367654332110222233-2224
Q gi|254780619|r  331 EEGILY---NARDMSIVRGKIESFPVVLVSAT-PSIESRVNGISRR--YHSVHLSTRYRNSALPHLQVIDMRGQT-IAQG  403 (731)
Q Consensus       331 ~~~pry---~aRdvA~~Ra~~~~~~lilgSAT-PSles~~~~~~g~--~~~~~l~~R~~~~~~P~i~ivDm~~~~-~~~~  403 (731)
                      +.||--   =||-.-..-..+..+.+|=-||| |-.|.......=.  ..++....|++.-++ .-.++-++... ....
T Consensus       253 ~RGpvlEtiVaRtlr~vessqs~IRivgLSATlPN~eDvA~fL~vn~~~glfsFd~~yRPvpL-~~~~iG~k~~~~~~~~  331 (1230)
T KOG0952         253 DRGPVLETIVARTLRLVESSQSMIRIVGLSATLPNYEDVARFLRVNPYAGLFSFDQRYRPVPL-TQGFIGIKGKKNRQQK  331 (1230)
T ss_pred             CCCCHHHHHHHHHHHHHHHHHHHEEEEEEECCCCCHHHHHHHHCCCCCCCEEEECCCCCCCCE-EEEEEEEECCCCHHHH
T ss_conf             664069999999999988542005788862457877999998667875662652023203431-1168742124420024


Q ss_pred             CCCCHHHHHHHHHHHCCCCEEEEEECCCCEEHHCCCCCCCCCCCCCCCCCEEEEECCCCCCEECHHHCCCCCCCCCCCCC
Q ss_conf             54798999999886226551799742220000002356543431014652012113578320000210244655566678
Q gi|254780619|r  404 KSLSPEMIDGIRHTLARNEQTLLFLNRRGYAPLTLCQVCGNRLKCLHCSCWLVEHRSKKKLYCHQCGHSAIYSQSCVVCG  483 (731)
Q Consensus       404 ~~lS~~l~~~i~~~l~~g~qvll~lnRrGya~~~~C~~Cg~~~~C~~C~~~l~~h~~~~~l~Ch~Cg~~~~~~~~Cp~Cg  483 (731)
                      ..+.....+++.+-+.+|.||++|+.-|+-.--..=.=         |+-..                         .||
T Consensus       332 ~~~d~~~~~kv~e~~~~g~qVlvFvhsR~~Ti~tA~~l---------~~~a~-------------------------~~g  377 (1230)
T KOG0952         332 KNIDEVCYDKVVEFLQEGHQVLVFVHSRNETIRTAKKL---------RERAE-------------------------TNG  377 (1230)
T ss_pred             HHHHHHHHHHHHHHHHCCCEEEEEEECCHHHHHHHHHH---------HHHHH-------------------------HCC
T ss_conf             66777899999999974985999996574899999999---------99988-------------------------628


Q ss_pred             CCCEECCCCCCHHHHHHHHHHC--CCCCHHHHCCCCCCCCHHHHHHHHHHHCCCCCCEEEEEHHHCCCCCCCCCCHHHHH
Q ss_conf             7411001354289988885204--85200010232113586789999986212576579870443023113452012330
Q gi|254780619|r  484 SSGKMIACGFGIERIAEEVCEY--FPLARISILSSDLEGGGGRLQLQLSAIAKGEIDIIIGTQLVAKGHNFPRMSLVGVV  561 (731)
Q Consensus       484 ~~~~l~~~G~Gte~~~e~l~~~--fp~~~v~~~d~d~~~~~~~~~~~~~~~~~~~~~ilvgTq~i~kg~~fp~v~lv~il  561 (731)
                      ..+-+.+ +.--+.+.|..+.-  +-+|.+.|-|+-         -.-..|..|-+.||+.|--+|=|-+.|... |+|=
T Consensus       378 ~~~~f~~-~~~~k~l~elf~~g~~iHhAGm~r~DR~---------l~E~~F~~G~i~vL~cTaTLAwGVNLPA~a-ViIK  446 (1230)
T KOG0952         378 EKDLFLP-SPRNKQLKELFQQGMGIHHAGMLRSDRQ---------LVEKEFKEGHIKVLCCTATLAWGVNLPAYA-VIIK  446 (1230)
T ss_pred             CCCCCCC-CHHHHHHHHHHHHHHHHCCCCCCHHHHH---------HHHHHHHCCCCEEEEECCEEEECCCCCCEE-EEEC
T ss_conf             6565678-8366789999874010202564314689---------999998559822899612133125776418-9864


Q ss_pred             HHHHHHHHHHHHHHHHH-----HHHHHHHHHCCCC--CCCCCEEEEEECCC
Q ss_conf             00344310245578999-----9987543110256--67886899993298
Q gi|254780619|r  562 DGDLGLTNADLRSSERT-----FQLLSQVTGRAGR--FGLKSLGLIQAYQP  605 (731)
Q Consensus       562 ~aD~~l~~pd~ra~E~~-----~qll~qv~gRagr--~~~~g~v~iQt~~p  605 (731)
                      .      .+-|.|++--     .--..|.-|||||  ++..|.++|=|..-
T Consensus       447 G------T~~ydsskg~f~dlgilDVlQifGRAGRPqFd~~G~giIiTt~d  491 (1230)
T KOG0952         447 G------TQVYDSSKGSFVDLGILDVLQIFGRAGRPQFDSSGEGIIITTRD  491 (1230)
T ss_pred             C------CCCCCCCCCCEEEEHHHHHHHHHHCCCCCCCCCCCEEEEEECCC
T ss_conf             8------74113566843540288889987206899877776289996650


No 32 
>COG1061 SSL2 DNA or RNA helicases of superfamily II [Transcription / DNA replication, recombination, and repair]
Probab=99.54  E-value=1.2e-12  Score=115.74  Aligned_cols=335  Identities=19%  Similarity=0.177  Sum_probs=180.7

Q ss_pred             CCCCCCCHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHCCCCC-
Q ss_conf             4666688378999999987520489619984475315799999999998514684799715210013445554303897-
Q gi|254780619|r  194 FSLPILDKNQQDVVEQVVPLCTKGFAVSLISGVTGSGKTEVYLEIVAAVLHLGKQVLILLPEISLTSAILERFQKRFGV-  272 (731)
Q Consensus       194 ~~~~~Lt~eQ~~a~~~i~~~~~~~f~~~LL~GvTGSGKTEVYl~li~~~L~~GkqvLiLvPEI~Lt~Q~~~rl~~rF~~-  272 (731)
                      .....|.+.|+.|++.+.....+ .+..++.-=||||||-+.+++|...-..   +|||||..-|..|+.+++...++. 
T Consensus        32 ~~~~~lr~yQ~~al~a~~~~~~~-~~~gvivlpTGaGKT~va~~~~~~~~~~---~Lvlv~~~~L~~Qw~~~~~~~~~~~  107 (442)
T COG1061          32 AFEFELRPYQEEALDALVKNRRT-ERRGVIVLPTGAGKTVVAAEAIAELKRS---TLVLVPTKELLDQWAEALKKFLLLN  107 (442)
T ss_pred             CCCCCCHHHHHHHHHHHHHHCCC-CCCEEEEECCCCCHHHHHHHHHHHHCCC---EEEEECCHHHHHHHHHHHHHHCCCC
T ss_conf             35788859999999999962225-7867999679998899999999982698---8999782999999999999734886


Q ss_pred             -EEEEEECCCCCHHHHHHHHHHHCCCCEEEEECCHHHHH-----HHC--CCEEEEEEECCCCCCHHCCCCCCCHHHHHHH
Q ss_conf             -68996235572356678999971997399940012110-----010--0013677405532100002443224899999
Q gi|254780619|r  273 -KPAEWHSSLSTSMREKIWRQVARGAISVIVGVRSALFL-----PFK--KLGLIVIDEEHDISYKQEEGILYNARDMSIV  344 (731)
Q Consensus       273 -~v~v~HS~ls~~eR~~~w~~i~~G~~~IVIGtRSAif~-----P~~--nLglIIvDEEHd~sykq~~~pry~aRdvA~~  344 (731)
                       .+.++.++...-+.           ..|+|+|-..+..     .+.  .-+|||+||-|..+     .+  ..|.++-.
T Consensus       108 ~~~g~~~~~~~~~~~-----------~~i~vat~qtl~~~~~l~~~~~~~~~liI~DE~Hh~~-----a~--~~~~~~~~  169 (442)
T COG1061         108 DEIGIYGGGEKELEP-----------AKVTVATVQTLARRQLLDEFLGNEFGLIIFDEVHHLP-----AP--SYRRILEL  169 (442)
T ss_pred             CCCCEECCCCCCCCC-----------CCEEEEEEHHHHHHHHHHHHCCCCCCEEEEECCCCCC-----CH--HHHHHHHH
T ss_conf             766033687233577-----------7489998389764155554035666759997524578-----47--79999997


Q ss_pred             HHHHCCCCE-ECC-CCCCCHHHHHHHHHHHHHHHCCC----------CCCCCCCCCCCEECCCCCCCCCCCCCCCHHHHH
Q ss_conf             751103210-000-24543246775321234441243----------223676543321102222332224547989999
Q gi|254780619|r  345 RGKIESFPV-VLV-SATPSIESRVNGISRRYHSVHLS----------TRYRNSALPHLQVIDMRGQTIAQGKSLSPEMID  412 (731)
Q Consensus       345 Ra~~~~~~l-ilg-SATPSles~~~~~~g~~~~~~l~----------~R~~~~~~P~i~ivDm~~~~~~~~~~lS~~l~~  412 (731)
                          ...+. +|| ||||--+.-.    +...+..+.          +-...--+.+.+++..+................
T Consensus       170 ----~~~~~~~LGLTATp~R~D~~----~~~~l~~~~g~~vy~~~~~~li~~g~Lap~~~~~i~~~~t~~~~~~~~~~~~  241 (442)
T COG1061         170 ----LSAAYPRLGLTATPEREDGG----RIGDLFDLIGPIVYEVSLKELIDEGYLAPYKYVEIKVTLTEDEEREYAKESA  241 (442)
T ss_pred             ----HHCCCEEEEEECCCCCCCCC----CHHHHHHHCCCEEEECCHHHHHHCCCCCCEEEEEEEECCCHHHHHHCCHHHH
T ss_conf             ----51031046771487244877----5248774057556733589983378757749999862366287774031555


Q ss_pred             HHHHHHCCCCEEEEEECCCCEEHHCCCCCCCCCCCCCCCCCEEEEECCCCCC--EECHHHCCCCCCCCCCCCCCCCEECC
Q ss_conf             9988622655179974222000000235654343101465201211357832--00002102446555666787411001
Q gi|254780619|r  413 GIRHTLARNEQTLLFLNRRGYAPLTLCQVCGNRLKCLHCSCWLVEHRSKKKL--YCHQCGHSAIYSQSCVVCGSSGKMIA  490 (731)
Q Consensus       413 ~i~~~l~~g~qvll~lnRrGya~~~~C~~Cg~~~~C~~C~~~l~~h~~~~~l--~Ch~Cg~~~~~~~~Cp~Cg~~~~l~~  490 (731)
                      ...+ ..+..+.                     ..-.+|.-...++...+..  .+++.-+.         ++..  ..-
T Consensus       242 ~~~~-~~~~~~~---------------------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---------~~~~--~li  288 (442)
T COG1061         242 RFRE-LLRARGT---------------------LRAENEARRIAIASERKIAAVRGLLLKHA---------RGDK--TLI  288 (442)
T ss_pred             HHHH-HHHHHCC---------------------HHHHHHHHHHHHHHHHHHHHHHHHHHHHC---------CCCC--EEE
T ss_conf             5555-5543100---------------------13456777776642899999999987532---------6886--699


Q ss_pred             CCCCHHHHHHHHHHCCCCCH-HHHCCCCCCCCHHHHHHHHHHHCCCCCCEEEEEHHHCCCCCCCCCCHHHHHHHHHHHHH
Q ss_conf             35428998888520485200-01023211358678999998621257657987044302311345201233000344310
Q gi|254780619|r  491 CGFGIERIAEEVCEYFPLAR-ISILSSDLEGGGGRLQLQLSAIAKGEIDIIIGTQLVAKGHNFPRMSLVGVVDGDLGLTN  569 (731)
Q Consensus       491 ~G~Gte~~~e~l~~~fp~~~-v~~~d~d~~~~~~~~~~~~~~~~~~~~~ilvgTq~i~kg~~fp~v~lv~il~aD~~l~~  569 (731)
                      ++.=++.. +++.+.|..-. +..++.+|  .+...+.+++.|+.|+.++||.+.|+.-|.|+|++..++++....    
T Consensus       289 f~~~~~~a-~~i~~~~~~~~~~~~it~~t--~~~eR~~il~~fr~g~~~~lv~~~vl~EGvDiP~~~~~i~~~~t~----  361 (442)
T COG1061         289 FASDVEHA-YEIAKLFLAPGIVEAITGET--PKEEREAILERFRTGGIKVLVTVKVLDEGVDIPDADVLIILRPTG----  361 (442)
T ss_pred             EECCHHHH-HHHHHHHCCCCCEEEEECCC--CHHHHHHHHHHHHCCCCEEEEEEEEECCCCCCCCCCEEEEECCCC----
T ss_conf             97577999-99999862677424665789--988999999998708952999961412665788875799977998----


Q ss_pred             HHHHHHHHHHHHHHHHHHCCCCCCC-CCE--EEEEECCCC
Q ss_conf             2455789999987543110256678-868--999932986
Q gi|254780619|r  570 ADLRSSERTFQLLSQVTGRAGRFGL-KSL--GLIQAYQPT  606 (731)
Q Consensus       570 pd~ra~E~~~qll~qv~gRagr~~~-~g~--v~iQt~~p~  606 (731)
                              ...++.|-.||.=|... ++.  ++.-+..++
T Consensus       362 --------S~~~~~Q~lGR~LR~~~~k~~~~~~~~~~~~~  393 (442)
T COG1061         362 --------SRRLFIQRLGRGLRPAEGKEDTLALDYSLVPD  393 (442)
T ss_pred             --------CHHHHHHHHHHHHCCCCCCCCEEEEEEECCCC
T ss_conf             --------79999999616634788999659999964567


No 33 
>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=99.54  E-value=1.5e-13  Score=122.80  Aligned_cols=151  Identities=26%  Similarity=0.304  Sum_probs=113.0

Q ss_pred             CHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHHHHHHHHHH---CCCCEEEEECCCHHHHHHHHHHHCCCCC---E
Q ss_conf             837899999998752048961998447531579999999999851---4684799715210013445554303897---6
Q gi|254780619|r  200 DKNQQDVVEQVVPLCTKGFAVSLISGVTGSGKTEVYLEIVAAVLH---LGKQVLILLPEISLTSAILERFQKRFGV---K  273 (731)
Q Consensus       200 t~eQ~~a~~~i~~~~~~~f~~~LL~GvTGSGKTEVYl~li~~~L~---~GkqvLiLvPEI~Lt~Q~~~rl~~rF~~---~  273 (731)
                      ++-|+.+++.+..     ....++.+-||||||++|+-.+...+.   .|.++++++|..+|..|+.++|++.++.   +
T Consensus         1 ~~~Q~~~i~~~~~-----g~~~iv~~pTGsGKT~~~~~~~l~~~~~~~~~~~~v~l~Pt~aL~~q~~~~~~~~~~~~~~~   75 (167)
T pfam00270         1 TPIQAEAIPAILE-----GKDVLVQAPTGSGKTLAFLLPALQALLKNPDGPQALVLAPTRELAEQIYEELKKLGKYLGLK   75 (167)
T ss_pred             CHHHHHHHHHHHC-----CCCEEEECCCCCCHHHHHHHHHHHHHHHCCCCCEEEEECCHHHHHHHHHHHHHHHHHCCCCC
T ss_conf             9459999999976-----99789988999758999999999998747789879999060888889998864321026764


Q ss_pred             EEEEECCCCCHHHHHHHHHHHCCCCEEEEECCHHHH-------HHHCCCEEEEEEECCCCCCHHCCCCCCCHHHHHHHHH
Q ss_conf             899623557235667899997199739994001211-------0010001367740553210000244322489999975
Q gi|254780619|r  274 PAEWHSSLSTSMREKIWRQVARGAISVIVGVRSALF-------LPFKKLGLIVIDEEHDISYKQEEGILYNARDMSIVRG  346 (731)
Q Consensus       274 v~v~HS~ls~~eR~~~w~~i~~G~~~IVIGtRSAif-------~P~~nLglIIvDEEHd~sykq~~~pry~aRdvA~~Ra  346 (731)
                      +..++++.+..++...|.    +..+|+|+|...+.       .-+.+++++|+||-|.-+   +.+.+.+.+++  .+.
T Consensus        76 ~~~~~g~~~~~~~~~~~~----~~~~Ilv~Tp~~l~~~l~~~~~~~~~~~~lIvDE~H~~~---~~~~g~~~~~i--l~~  146 (167)
T pfam00270        76 VALLYGGDSPKEQLRKLK----KGPDILVGTPGRLLDLLERGGLLLKNLKLLVLDEAHRLL---DQGFGDDLEEI--LRR  146 (167)
T ss_pred             EEEECCCCCHHHHHHHHC----CCCCEEEECHHHHHHHHHHCCCCCCCEEEEEEECHHHHH---CCCHHHHHHHH--HHH
T ss_conf             046417861788987640----577079947899999998033121100389988088673---35829999999--985


Q ss_pred             HHCCCCEECCCCCCCHHHH
Q ss_conf             1103210000245432467
Q gi|254780619|r  347 KIESFPVVLVSATPSIESR  365 (731)
Q Consensus       347 ~~~~~~lilgSATPSles~  365 (731)
                      ...++++++.|||++ +..
T Consensus       147 l~~~~q~v~~SAT~~-~~~  164 (167)
T pfam00270       147 LPPKRQILLLSATLP-RNV  164 (167)
T ss_pred             CCCCCCEEEEECCCC-HHH
T ss_conf             799997899972699-778


No 34 
>smart00487 DEXDc DEAD-like helicases superfamily.
Probab=99.53  E-value=4.1e-13  Score=119.38  Aligned_cols=157  Identities=22%  Similarity=0.280  Sum_probs=115.2

Q ss_pred             CCCCCHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHHHHHHHHHHCC--CCEEEEECCCHHHHHHHHHHHCCCCCE
Q ss_conf             666883789999999875204896199844753157999999999985146--847997152100134455543038976
Q gi|254780619|r  196 LPILDKNQQDVVEQVVPLCTKGFAVSLISGVTGSGKTEVYLEIVAAVLHLG--KQVLILLPEISLTSAILERFQKRFGVK  273 (731)
Q Consensus       196 ~~~Lt~eQ~~a~~~i~~~~~~~f~~~LL~GvTGSGKTEVYl~li~~~L~~G--kqvLiLvPEI~Lt~Q~~~rl~~rF~~~  273 (731)
                      ...+++.|..++..+....    ...++.+-||||||++++..+.+.+..+  .++|+++|..+|+.|+.++|.+.++..
T Consensus         6 ~~~~~~~Q~~~~~~~~~~~----~~~~i~~~tGsGKT~~~~~~~~~~~~~~~~~~~li~~P~~~l~~q~~~~~~~~~~~~   81 (201)
T smart00487        6 FEPLRPYQKEAIEALLSGL----RDVILAAPTGSGKTLAALLPALEALKRGKGKRVLVLVPTRELAEQWAEELKKLGPSL   81 (201)
T ss_pred             CCCCCHHHHHHHHHHHCCC----CCEEEECCCCCCHHHHHHHHHHHHHHCCCCCEEEEEECCHHHHHHHHHHHHHCCCCC
T ss_conf             9999988999999998389----988998999960999999999998633899759999085999999998860102102


Q ss_pred             EEEEECCCCCHHHHHHHHHHHCCCCEEEEECCHHHHH-------HHCCCEEEEEEECCCCCCHHCCCCCCCHHHHHHHHH
Q ss_conf             8996235572356678999971997399940012110-------010001367740553210000244322489999975
Q gi|254780619|r  274 PAEWHSSLSTSMREKIWRQVARGAISVIVGVRSALFL-------PFKKLGLIVIDEEHDISYKQEEGILYNARDMSIVRG  346 (731)
Q Consensus       274 v~v~HS~ls~~eR~~~w~~i~~G~~~IVIGtRSAif~-------P~~nLglIIvDEEHd~sykq~~~pry~aRdvA~~Ra  346 (731)
                      -....+..+...+...|.+..++...|+|+|-..+..       -+.+.++||+||-|.....   ..+...+.+...+ 
T Consensus        82 ~~~~~~~~~~~~~~~~~~~~~~~~~~i~i~t~~~l~~~~~~~~~~~~~~~~vIiDE~H~~~~~---~~~~~~~~~~~~~-  157 (201)
T smart00487       82 GLKVVGLYGGDSKREQLRKLESGKTDILVTTPGRLLDLLENDLLELSNVDLVILDEAHRLLDG---GFGDQLEKLLKLL-  157 (201)
T ss_pred             EEEEEEEECCCCHHHHHHHHHCCCCCEEEECHHHHHHHHHHCCCCCCCCEEEEEECHHHHHCC---CCHHHHHHHHHHC-
T ss_conf             044556524773799999997599989995589999999727545254319999896775125---7099999999967-


Q ss_pred             HHCCCCEECCCCCCC
Q ss_conf             110321000024543
Q gi|254780619|r  347 KIESFPVVLVSATPS  361 (731)
Q Consensus       347 ~~~~~~lilgSATPS  361 (731)
                       ..+..+++-||||.
T Consensus       158 -~~~~~~i~lSAT~~  171 (201)
T smart00487      158 -PKNVQLLLLSATPP  171 (201)
T ss_pred             -CCCCCEEEECCCCC
T ss_conf             -99997899924898


No 35 
>COG1203 CRISPR-associated helicase Cas3 [Defense mechanisms]
Probab=99.52  E-value=1.6e-12  Score=114.78  Aligned_cols=318  Identities=21%  Similarity=0.194  Sum_probs=171.4

Q ss_pred             CCCHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHHHHHHHHHHC----CCCEEEEECCCHHHHHHHHHHHCCCCCE
Q ss_conf             688378999999987520489619984475315799999999998514----6847997152100134455543038976
Q gi|254780619|r  198 ILDKNQQDVVEQVVPLCTKGFAVSLISGVTGSGKTEVYLEIVAAVLHL----GKQVLILLPEISLTSAILERFQKRFGVK  273 (731)
Q Consensus       198 ~Lt~eQ~~a~~~i~~~~~~~f~~~LL~GvTGSGKTEVYl~li~~~L~~----GkqvLiLvPEI~Lt~Q~~~rl~~rF~~~  273 (731)
                      ...+.|+.+++.+......++ .+.|..-||+||||+-+..+-..+..    ...++.++|-.++..++..|++..|+..
T Consensus       195 ~~~~~~~~~~~~~~~~~~~~~-~~vl~aPTG~GKT~asl~~a~~~~~~~~~~~~r~i~vlP~~t~ie~~~~r~~~~~~~~  273 (733)
T COG1203         195 EGYELQEKALELILRLEKRSL-LVVLEAPTGYGKTEASLILALALLDEKIKLKSRVIYVLPFRTIIEDMYRRAKEIFGLF  273 (733)
T ss_pred             CHHHHHHHHHHHHHHCCCCCC-EEEEEECCCCCHHHHHHHHHHHHHHCCCCCCCEEEEECCHHHHHHHHHHHHHHHHCCC
T ss_conf             113556799999873225575-1899916888719999999999753113545628996558999999999998751235


Q ss_pred             E--EE-EECCCC-CHHHHHHH---------HHH-HCCCCEEEEECCHHHH---HHH-----CCC--EEEEEEECCCCCCH
Q ss_conf             8--99-623557-23566789---------999-7199739994001211---001-----000--13677405532100
Q gi|254780619|r  274 P--AE-WHSSLS-TSMREKIW---------RQV-ARGAISVIVGVRSALF---LPF-----KKL--GLIVIDEEHDISYK  329 (731)
Q Consensus       274 v--~v-~HS~ls-~~eR~~~w---------~~i-~~G~~~IVIGtRSAif---~P~-----~nL--glIIvDEEHd~syk  329 (731)
                      .  .. +||... +......+         ..- ...-+.+++.+-.-+.   -++     ..+  .++|.||-|.-   
T Consensus       274 ~~~~~~~h~~~~~~~~~~~~~~~~~~~~~~ds~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~S~vIlDE~h~~---  350 (733)
T COG1203         274 SVIGKSLHSSSKEPLLLEPDQDILLTLTTNDSYKKLLLALIVVTPIQILIFSVKGFKFEFLALLLTSLVILDEVHLY---  350 (733)
T ss_pred             CCCCCCCCCCCHHHHHHCCCCCCCEEEEECCCCCCCCCCCEEECHHHHHHHHHCCCCCHHHHHHHHCCEEEECHHHC---
T ss_conf             54331001310255651701002258881242236204522206999855740466725778876467787427541---


Q ss_pred             HCC-CCCCCHHHHHHHHHHHCCCCEECCCCCCCHHHHHHHHHHHHHHHCCCCCCCCCCCCCCEECC-CCCCCCCCCCCCC
Q ss_conf             002-44322489999975110321000024543246775321234441243223676543321102-2223322245479
Q gi|254780619|r  330 QEE-GILYNARDMSIVRGKIESFPVVLVSATPSIESRVNGISRRYHSVHLSTRYRNSALPHLQVID-MRGQTIAQGKSLS  407 (731)
Q Consensus       330 q~~-~pry~aRdvA~~Ra~~~~~~lilgSATPSles~~~~~~g~~~~~~l~~R~~~~~~P~i~ivD-m~~~~~~~~~~lS  407 (731)
                      +++ .++.-.+  ++......|+++|+.|||++.-- .......+.    ..+......+-...+| .............
T Consensus       351 ~~~~~~~~l~~--~i~~l~~~g~~ill~SATlP~~~-~~~l~~~~~----~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~  423 (733)
T COG1203         351 ADETMLAALLA--LLEALAEAGVPVLLMSATLPPFL-KEKLKKALG----KGREVVENAKFCPKEDEPGLKRKERVDVED  423 (733)
T ss_pred             CCCCHHHHHHH--HHHHHHHCCCCEEEEECCCCHHH-HHHHHHHHC----CCCEECCCCCCCCCCCCCCCCEECCHHHHC
T ss_conf             65430899999--99999968997899927899799-999999850----376121344323345543300000111320


Q ss_pred             ---HHHHHHHHHHHCCCCEEEEEECCCCEEHHCCCCCCCCCCCCCCCCCEEEEECCCCCCEECHHHCCCCCCCCCC-CC-
Q ss_conf             ---8999999886226551799742220000002356543431014652012113578320000210244655566-67-
Q gi|254780619|r  408 ---PEMIDGIRHTLARNEQTLLFLNRRGYAPLTLCQVCGNRLKCLHCSCWLVEHRSKKKLYCHQCGHSAIYSQSCV-VC-  482 (731)
Q Consensus       408 ---~~l~~~i~~~l~~g~qvll~lnRrGya~~~~C~~Cg~~~~C~~C~~~l~~h~~~~~l~Ch~Cg~~~~~~~~Cp-~C-  482 (731)
                         ......+...++.|..|++..|...=|--++     ...            +                 ..|+ .| 
T Consensus       424 ~~~~~~~~~~~~~~~~~~kvlvI~NTV~~Aie~Y-----~~L------------k-----------------~~~~~v~L  469 (733)
T COG1203         424 GPQEELIELISEEVKEGKKVLVIVNTVDRAIELY-----EKL------------K-----------------EKGPKVLL  469 (733)
T ss_pred             CCHHHHHHHHHHHHCCCCCEEEEEECHHHHHHHH-----HHH------------H-----------------CCCCCEEE
T ss_conf             3037766556776425882899992789999999-----998------------5-----------------55895799


Q ss_pred             -CCCCEECCCCCCHHHHHHHHHHCCCCCHHHHCCCCCCCCHHHHHHHHHHHCCCCCCEEEEEHHHCCCCCCCCCCHHHHH
Q ss_conf             -8741100135428998888520485200010232113586789999986212576579870443023113452012330
Q gi|254780619|r  483 -GSSGKMIACGFGIERIAEEVCEYFPLARISILSSDLEGGGGRLQLQLSAIAKGEIDIIIGTQLVAKGHNFPRMSLVGVV  561 (731)
Q Consensus       483 -g~~~~l~~~G~Gte~~~e~l~~~fp~~~v~~~d~d~~~~~~~~~~~~~~~~~~~~~ilvgTq~i~kg~~fp~v~lv~il  561 (731)
                       +|.  +...  ==++.+++|.+.|                          ..++..|+||||.|.-|.|+         
T Consensus       470 lHSR--f~~~--dR~~ke~~l~~~~--------------------------~~~~~~IvVaTQVIEagvDi---------  510 (733)
T COG1203         470 LHSR--FTLK--DREEKERELKKLF--------------------------KQNEGFIVVATQVIEAGVDI---------  510 (733)
T ss_pred             EECC--CCHH--HHHHHHHHHHHHH--------------------------HCCCCEEEEECCEEEEEECC---------
T ss_conf             8863--5576--6999999998887--------------------------53786299983459988626---------


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCC--CCCEEEEEECCC
Q ss_conf             00344310245578999998754311025667--886899993298
Q gi|254780619|r  562 DGDLGLTNADLRSSERTFQLLSQVTGRAGRFG--LKSLGLIQAYQP  605 (731)
Q Consensus       562 ~aD~~l~~pd~ra~E~~~qll~qv~gRagr~~--~~g~v~iQt~~p  605 (731)
                      |.|.+..  |+-    ..-.|.|-+||..|..  .+|.+++-...+
T Consensus       511 dfd~mIT--e~a----PidSLIQR~GRv~R~g~~~~~~~~v~~~~~  550 (733)
T COG1203         511 DFDVLIT--ELA----PIDSLIQRAGRVNRHGKKENGKIYVYNDEE  550 (733)
T ss_pred             CCCEEEE--CCC----CHHHHHHHHHHHHHCCCCCCCCEEEEECCC
T ss_conf             6684663--478----756799987777415666687169983466


No 36 
>COG1205 Distinct helicase family with a unique C-terminal domain including a metal-binding cysteine cluster [General function prediction only]
Probab=99.49  E-value=3.1e-11  Score=105.06  Aligned_cols=332  Identities=19%  Similarity=0.207  Sum_probs=186.8

Q ss_pred             CCHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHHHHHHHHHHCCCCE--EEEECCCHHHHHHHHHHHCC---CC--
Q ss_conf             883789999999875204896199844753157999999999985146847--99715210013445554303---89--
Q gi|254780619|r  199 LDKNQQDVVEQVVPLCTKGFAVSLISGVTGSGKTEVYLEIVAAVLHLGKQV--LILLPEISLTSAILERFQKR---FG--  271 (731)
Q Consensus       199 Lt~eQ~~a~~~i~~~~~~~f~~~LL~GvTGSGKTEVYl~li~~~L~~Gkqv--LiLvPEI~Lt~Q~~~rl~~r---F~--  271 (731)
                      |-.-|.+|+..+...     +..++---|||||||.|+=.|-+.+-++.++  |+|-|.-+|+..-.+||++.   ++  
T Consensus        71 lY~HQ~~A~~~~~~G-----~~vvVtTgTgSGKTe~FllPIld~~l~~~~a~AL~lYPtnALa~DQ~~rl~~~~~~~~~~  145 (851)
T COG1205          71 LYSHQVDALRLIREG-----RNVVVTTGTGSGKTESFLLPILDHLLRDPSARALLLYPTNALANDQAERLRELISDLPGK  145 (851)
T ss_pred             CCHHHHHHHHHHHCC-----CCEEEECCCCCCHHHHHHHHHHHHHHCCCCCEEEEEECHHHHHHHHHHHHHHHHHHCCCC
T ss_conf             007799999999779-----988997899885458989999999830866508998043776766999999999847875


Q ss_pred             CEEEEEECCCCCHHHHHHHHHHHCCCCEEEEECCHHHH-----------HHHCCCEEEEEEECCCCCCH--HCCCCCCCH
Q ss_conf             76899623557235667899997199739994001211-----------00100013677405532100--002443224
Q gi|254780619|r  272 VKPAEWHSSLSTSMREKIWRQVARGAISVIVGVRSALF-----------LPFKKLGLIVIDEEHDISYK--QEEGILYNA  338 (731)
Q Consensus       272 ~~v~v~HS~ls~~eR~~~w~~i~~G~~~IVIGtRSAif-----------~P~~nLglIIvDEEHd~syk--q~~~pry~a  338 (731)
                      ..+..|++...+.+|.    .+..+.++|++.+..=+-           -=+.+|..|||||-|  +|.  |-...-|=.
T Consensus       146 v~~~~y~Gdt~~~~r~----~~~~~pp~IllTNpdMLh~~llr~~~~~~~~~~~Lk~lVvDElH--tYrGv~GS~vA~ll  219 (851)
T COG1205         146 VTFGRYTGDTPPEERR----AIIRNPPDILLTNPDMLHYLLLRNHDAWLWLLRNLKYLVVDELH--TYRGVQGSEVALLL  219 (851)
T ss_pred             EEEEEECCCCCHHHHH----HHHHCCCCEEEECHHHHHHHHHCCCCCHHHHHHCCCEEEEECCE--ECCCCHHHHHHHHH
T ss_conf             1354434889678889----98738997898388999898636882278887327589984441--21560378899999


Q ss_pred             HHHHHHHHHHCC--CCEECCCCCCCHHHHHHHHHHHHHHHCC-CCCCCCCCCCCCEECCCCCCCC---CCC--CCCCHHH
Q ss_conf             899999751103--2100002454324677532123444124-3223676543321102222332---224--5479899
Q gi|254780619|r  339 RDMSIVRGKIES--FPVVLVSATPSIESRVNGISRRYHSVHL-STRYRNSALPHLQVIDMRGQTI---AQG--KSLSPEM  410 (731)
Q Consensus       339 RdvA~~Ra~~~~--~~lilgSATPSles~~~~~~g~~~~~~l-~~R~~~~~~P~i~ivDm~~~~~---~~~--~~lS~~l  410 (731)
                      |.+-.+ ++..+  -.+|..|||=+-..-....-.. ..... ... .+++....+++ +...+.   ..+  ......+
T Consensus       220 RRL~~~-~~~~~~~~q~i~~SAT~~np~e~~~~l~~-~~f~~~v~~-~g~~~~~~~~~-~~~p~~~~~~~~~r~s~~~~~  295 (851)
T COG1205         220 RRLLRR-LRRYGSPLQIICTSATLANPGEFAEELFG-RDFEVPVDE-DGSPRGLRYFV-RREPPIRELAESIRRSALAEL  295 (851)
T ss_pred             HHHHHH-HHCCCCCCEEEEEECCCCCHHHHHHHHCC-CCCEEECCC-CCCCCCCEEEE-EECCCCHHHHHHCCCCHHHHH
T ss_conf             999999-72458996289983124682889998628-721463147-88887874899-856851133221123457799


Q ss_pred             HHHHHHHHCCCCEEEEEECCCCEEHHCCCCCCCCCCCCCCCCCEEEEECCCCCCEECHHHCCCCCCCCCCCCCCCCEECC
Q ss_conf             99998862265517997422200000023565434310146520121135783200002102446555666787411001
Q gi|254780619|r  411 IDGIRHTLARNEQTLLFLNRRGYAPLTLCQVCGNRLKCLHCSCWLVEHRSKKKLYCHQCGHSAIYSQSCVVCGSSGKMIA  490 (731)
Q Consensus       411 ~~~i~~~l~~g~qvll~lnRrGya~~~~C~~Cg~~~~C~~C~~~l~~h~~~~~l~Ch~Cg~~~~~~~~Cp~Cg~~~~l~~  490 (731)
                      -..+...+.+|-|+|+|..=|..+..+.=                                         .+..  .+..
T Consensus       296 ~~~~~~~~~~~~~tL~F~~sr~~~e~~~~-----------------------------------------~~~~--~~~~  332 (851)
T COG1205         296 ATLAALLVRNGIQTLVFFRSRKQVELLYL-----------------------------------------SPRR--RLVR  332 (851)
T ss_pred             HHHHHHHHHCCCEEEEEEEHHHHHHHHHH-----------------------------------------HHHH--HHHH
T ss_conf             99999998769659999835756788754-----------------------------------------1578--8754


Q ss_pred             CC-CCHHHHHHHHHHCCCCCHHHHCCCCCCCCHHHHHHHHHHHCCCCCCEEEEEHHHCCCCCCCCCCHHHHHHHHHHHHH
Q ss_conf             35-42899888852048520001023211358678999998621257657987044302311345201233000344310
Q gi|254780619|r  491 CG-FGIERIAEEVCEYFPLARISILSSDLEGGGGRLQLQLSAIAKGEIDIIIGTQLVAKGHNFPRMSLVGVVDGDLGLTN  569 (731)
Q Consensus       491 ~G-~Gte~~~e~l~~~fp~~~v~~~d~d~~~~~~~~~~~~~~~~~~~~~ilvgTq~i~kg~~fp~v~lv~il~aD~~l~~  569 (731)
                      .| .+..++.-.-.               ...+....++..+|..|+...++.|-++.=|.|.-.+..|      ..-..
T Consensus       333 ~~~~l~~~v~~~~~---------------~~~~~er~~ie~~~~~g~~~~~~st~AlelgidiG~ldav------i~~g~  391 (851)
T COG1205         333 EGGKLLDAVSTYRA---------------GLHREERRRIEAEFKEGELLGVIATNALELGIDIGSLDAV------IAYGY  391 (851)
T ss_pred             CCCCHHHHEEECCC---------------CCCHHHHHHHHHHHHCCCCCEEEECHHHCCCEEECCEEEE------EECCC
T ss_conf             06010331342336---------------6999999999999746884178612101226567021145------30488


Q ss_pred             HHHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEECCCCCHHHHHHHHC
Q ss_conf             24557899999875431102566788689999329864888999958
Q gi|254780619|r  570 ADLRSSERTFQLLSQVTGRAGRFGLKSLGLIQAYQPTHPVMQALVSG  616 (731)
Q Consensus       570 pd~ra~E~~~qll~qv~gRagr~~~~g~v~iQt~~p~~~~~~~~~~~  616 (731)
                      |.-     .+..+.|-+|||||....+.+++.-.  ++++-++...+
T Consensus       392 P~~-----s~~~~~Q~~GRaGR~~~~~l~~~v~~--~~~~d~yy~~~  431 (851)
T COG1205         392 PGV-----SVLSFRQRAGRAGRRGQESLVLVVLR--SDPLDSYYLRH  431 (851)
T ss_pred             CCC-----HHHHHHHHHCCCCCCCCCCEEEEEEC--CCCCCHHHHHC
T ss_conf             970-----28889886110358878753799837--88400445508


No 37 
>KOG0331 consensus
Probab=99.48  E-value=5.4e-12  Score=110.81  Aligned_cols=282  Identities=20%  Similarity=0.266  Sum_probs=156.1

Q ss_pred             EECCCCHHHHHHHHH-HHHHHHHC--------CCCEEEEECCCHHHHHHHHHHHCC---CCCEEEEEECCCCCHHHHHHH
Q ss_conf             844753157999999-99998514--------684799715210013445554303---897689962355723566789
Q gi|254780619|r  223 ISGVTGSGKTEVYLE-IVAAVLHL--------GKQVLILLPEISLTSAILERFQKR---FGVKPAEWHSSLSTSMREKIW  290 (731)
Q Consensus       223 L~GvTGSGKTEVYl~-li~~~L~~--------GkqvLiLvPEI~Lt~Q~~~rl~~r---F~~~v~v~HS~ls~~eR~~~w  290 (731)
                      .---||||||.=|+- +|.+....        |-+||||+|.=-|+.|+.+-+.+.   ++-+...+.++.+...   +-
T Consensus       133 ~iA~TGSGKTLay~lP~i~~l~~~~~~~~~~~~P~vLVL~PTRELA~QV~~~~~~~~~~~~~~~~cvyGG~~~~~---Q~  209 (519)
T KOG0331         133 GIARTGSGKTLAYLLPAIVHLNNEQGKLSRGDGPIVLVLAPTRELAVQVQAEAREFGKSLRLRSTCVYGGAPKGP---QL  209 (519)
T ss_pred             EEECCCCCCHHHHHHHHHHHHHHCCCCCCCCCCCEEEEECCCHHHHHHHHHHHHHHCCCCCCCEEEEECCCCCCH---HH
T ss_conf             782357862055555799998700444347999869997685999999999999970777740799868988637---88


Q ss_pred             HHHHCCCCEEEEECCHHHH-------HHHCCCEEEEEEECCCCCCHHCCCCCCCHHHHHHHHHHHC--CCCEECCCCCCC
Q ss_conf             9997199739994001211-------0010001367740553210000244322489999975110--321000024543
Q gi|254780619|r  291 RQVARGAISVIVGVRSALF-------LPFKKLGLIVIDEEHDISYKQEEGILYNARDMSIVRGKIE--SFPVVLVSATPS  361 (731)
Q Consensus       291 ~~i~~G~~~IVIGtRSAif-------~P~~nLglIIvDEEHd~sykq~~~pry~aRdvA~~Ra~~~--~~~lilgSATPS  361 (731)
                      ..+.+| ++|||||.-=+.       +++.++...|+||- |-..  ++++.=..|.+.   .+..  ....+|-|||=+
T Consensus       210 ~~l~~g-vdiviaTPGRl~d~le~g~~~l~~v~ylVLDEA-DrMl--dmGFe~qI~~Il---~~i~~~~rQtlm~saTwp  282 (519)
T KOG0331         210 RDLERG-VDVVIATPGRLIDLLEEGSLNLSRVTYLVLDEA-DRML--DMGFEPQIRKIL---SQIPRPDRQTLMFSATWP  282 (519)
T ss_pred             HHHHCC-CCEEEECCHHHHHHHHCCCCCCCCEEEEEECCH-HHHH--CCCCHHHHHHHH---HHCCCCCCCEEEEEEECC
T ss_conf             987559-818980771789999748856453039996347-7663--135379999998---755897522788865464


Q ss_pred             HHHHHHHHHHHHHHHCCCC--CCCCC-CC-C---CCEECCCCCCCCCCCCCCCHHHHHHHHHHH-CCCCEEEEEECCCCE
Q ss_conf             2467753212344412432--23676-54-3---321102222332224547989999998862-265517997422200
Q gi|254780619|r  362 IESRVNGISRRYHSVHLST--RYRNS-AL-P---HLQVIDMRGQTIAQGKSLSPEMIDGIRHTL-ARNEQTLLFLNRRGY  433 (731)
Q Consensus       362 les~~~~~~g~~~~~~l~~--R~~~~-~~-P---~i~ivDm~~~~~~~~~~lS~~l~~~i~~~l-~~g~qvll~lnRrGy  433 (731)
                      -+....+..  |  +..+.  +..+. .+ +   -.++++.-.+..     .-..|.+.+++.. ..+.+||||.+.+= 
T Consensus       283 ~~v~~lA~~--f--l~~~~~i~ig~~~~~~a~~~i~qive~~~~~~-----K~~~l~~lL~~~~~~~~~KvIIFc~tkr-  352 (519)
T KOG0331         283 KEVRQLAED--F--LNNPIQINVGNKKELKANHNIRQIVEVCDETA-----KLRKLGKLLEDISSDSEGKVIIFCETKR-  352 (519)
T ss_pred             HHHHHHHHH--H--HCCCEEEEECCHHHHHHHCCHHHHHHHCCHHH-----HHHHHHHHHHHHHCCCCCCEEEEECCHH-
T ss_conf             889999999--8--45964899612145544333146511268788-----9887999999973568986899964336-


Q ss_pred             EHHCCCCCCCCCCCCCCCCCEEEEECCCCCCEECHHHCCCCCCCCCCCCCCCCEECCCCCCHHHHHHHHHHCCCCCHHHH
Q ss_conf             00002356543431014652012113578320000210244655566678741100135428998888520485200010
Q gi|254780619|r  434 APLTLCQVCGNRLKCLHCSCWLVEHRSKKKLYCHQCGHSAIYSQSCVVCGSSGKMIACGFGIERIAEEVCEYFPLARISI  513 (731)
Q Consensus       434 a~~~~C~~Cg~~~~C~~C~~~l~~h~~~~~l~Ch~Cg~~~~~~~~Cp~Cg~~~~l~~~G~Gte~~~e~l~~~fp~~~v~~  513 (731)
                                                                                  ..++++..+++.  +.+..-
T Consensus       353 ------------------------------------------------------------~~~~l~~~l~~~--~~~a~~  370 (519)
T KOG0331         353 ------------------------------------------------------------TCDELARNLRRK--GWPAVA  370 (519)
T ss_pred             ------------------------------------------------------------HHHHHHHHHHHC--CCCEEE
T ss_conf             ------------------------------------------------------------499999887751--766155


Q ss_pred             CCCCCCCCHHHHHHHHHHHCCCCCCEEEEEHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCC
Q ss_conf             23211358678999998621257657987044302311345201233000344310245578999998754311025667
Q gi|254780619|r  514 LSSDLEGGGGRLQLQLSAIAKGEIDIIIGTQLVAKGHNFPRMSLVGVVDGDLGLTNADLRSSERTFQLLSQVTGRAGRFG  593 (731)
Q Consensus       514 ~d~d~~~~~~~~~~~~~~~~~~~~~ilvgTq~i~kg~~fp~v~lv~il~aD~~l~~pd~ra~E~~~qll~qv~gRagr~~  593 (731)
                      +..|.+  ....+..|+.|.+|+..|||+|.+.|.|+|+|+|.+|+-.|  .=.+.-||          +.=.||.||+.
T Consensus       371 iHGd~s--Q~eR~~~L~~FreG~~~vLVATdVAaRGLDi~dV~lVInyd--fP~~vEdY----------VHRiGRTGRa~  436 (519)
T KOG0331         371 IHGDKS--QSERDWVLKGFREGKSPVLVATDVAARGLDVPDVDLVINYD--FPNNVEDY----------VHRIGRTGRAG  436 (519)
T ss_pred             ECCCCC--HHHHHHHHHHCCCCCCCEEEECCCCCCCCCCCCCCEEEECC--CCCCHHHH----------HHHCCCCCCCC
T ss_conf             006664--88999999750268854698815312568876664799678--99998998----------86537654578


Q ss_pred             CCCEEEE
Q ss_conf             8868999
Q gi|254780619|r  594 LKSLGLI  600 (731)
Q Consensus       594 ~~g~v~i  600 (731)
                      +.|..+.
T Consensus       437 ~~G~A~t  443 (519)
T KOG0331         437 KKGTAIT  443 (519)
T ss_pred             CCCEEEE
T ss_conf             8824899


No 38 
>COG1201 Lhr Lhr-like helicases [General function prediction only]
Probab=99.45  E-value=8e-11  Score=101.87  Aligned_cols=303  Identities=21%  Similarity=0.240  Sum_probs=188.6

Q ss_pred             CCCCHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHHHHH-HHHHHC-------CCCEEEEECCCHHHHHHHHHHH-
Q ss_conf             6688378999999987520489619984475315799999999-998514-------6847997152100134455543-
Q gi|254780619|r  197 PILDKNQQDVVEQVVPLCTKGFAVSLISGVTGSGKTEVYLEIV-AAVLHL-------GKQVLILLPEISLTSAILERFQ-  267 (731)
Q Consensus       197 ~~Lt~eQ~~a~~~i~~~~~~~f~~~LL~GvTGSGKTEVYl~li-~~~L~~-------GkqvLiLvPEI~Lt~Q~~~rl~-  267 (731)
                      ..+|+-|..|+..|...     ...|+--=|||||||-.+-.+ ...++.       |=.||+.-|=-+|...+..|+. 
T Consensus        21 ~~~t~~Q~~a~~~i~~G-----~nvLiiAPTGsGKTeAAfLpil~~l~~~~~~~~~~~i~~lYIsPLkALn~Di~~rL~~   95 (814)
T COG1201          21 TSLTPPQRYAIPEIHSG-----ENVLIIAPTGSGKTEAAFLPVINELLSLGKGKLEDGIYALYISPLKALNNDIRRRLEE   95 (814)
T ss_pred             CCCCHHHHHHHHHHHCC-----CCEEEECCCCCCHHHHHHHHHHHHHHHCCCCCCCCCEEEEEECCHHHHHHHHHHHHHH
T ss_conf             89987899999998589-----8469986899973799999999999860688888856999957078887899999999


Q ss_pred             --CCCCCEEEEEECCCCCHHHHHHHHHHHCCCCEEEEECCHHH---HHH------HCCCEEEEEEECCCCCCHHCCCCCC
Q ss_conf             --03897689962355723566789999719973999400121---100------1000136774055321000024432
Q gi|254780619|r  268 --KRFGVKPAEWHSSLSTSMREKIWRQVARGAISVIVGVRSAL---FLP------FKKLGLIVIDEEHDISYKQEEGILY  336 (731)
Q Consensus       268 --~rF~~~v~v~HS~ls~~eR~~~w~~i~~G~~~IVIGtRSAi---f~P------~~nLglIIvDEEHd~sykq~~~pry  336 (731)
                        +++|..|.+.|+..++++|..    ....-++|+|-|.-.+   +.+      |.|+.-+||||=|+-.    ++=|=
T Consensus        96 ~~~~~G~~v~vRhGDT~~~er~r----~~~~PPdILiTTPEsL~lll~~~~~r~~l~~vr~VIVDEiHel~----~sKRG  167 (814)
T COG1201          96 PLRELGIEVAVRHGDTPQSEKQK----MLKNPPHILITTPESLAILLNSPKFRELLRDVRYVIVDEIHALA----ESKRG  167 (814)
T ss_pred             HHHHCCCCCCEECCCCCHHHHHH----CCCCCCCEEEECHHHHHHHHCCHHHHHHHCCCCEEEEEHHHHHH----CCCCC
T ss_conf             99975984444228788677630----46999968995834899983688899986078099951254543----45653


Q ss_pred             CHHHHHHHHHHHCC--CCEECCCCCCCH-H--HHHHHHHH-HHHHHCCCCCCCCCCCCCCEECCCCCCCCCCCCCCCHHH
Q ss_conf             24899999751103--210000245432-4--67753212-344412432236765433211022223322245479899
Q gi|254780619|r  337 NARDMSIVRGKIES--FPVVLVSATPSI-E--SRVNGISR-RYHSVHLSTRYRNSALPHLQVIDMRGQTIAQGKSLSPEM  410 (731)
Q Consensus       337 ~aRdvA~~Ra~~~~--~~lilgSATPSl-e--s~~~~~~g-~~~~~~l~~R~~~~~~P~i~ivDm~~~~~~~~~~lS~~l  410 (731)
                      +---+++.|.+..-  ..-|=-|||=+- +  .-+.+..+ ....+.    ....+.+++.++.........+ .....+
T Consensus       168 ~~Lsl~LeRL~~l~~~~qRIGLSATV~~~~~varfL~g~~~~~~Iv~----~~~~k~~~i~v~~p~~~~~~~~-~~~~~~  242 (814)
T COG1201         168 VQLALSLERLRELAGDFQRIGLSATVGPPEEVAKFLVGFGDPCEIVD----VSAAKKLEIKVISPVEDLIYDE-ELWAAL  242 (814)
T ss_pred             HHHHHHHHHHHHHCCCCEEEEEHHCCCCHHHHHHHHCCCCCCEEEEE----CCCCCCCEEEEEECCCCCCCCC-CHHHHH
T ss_conf             13433299998517553797540215888999998547898429997----4567753179980477500026-246789


Q ss_pred             HHHHHHHHCCCCEEEEEECCCCEEHHCCCCCCCCCCCCCCCCCEEEEECCCCCCEECHHHCCCCCCCCCCCCCCCCEECC
Q ss_conf             99998862265517997422200000023565434310146520121135783200002102446555666787411001
Q gi|254780619|r  411 IDGIRHTLARNEQTLLFLNRRGYAPLTLCQVCGNRLKCLHCSCWLVEHRSKKKLYCHQCGHSAIYSQSCVVCGSSGKMIA  490 (731)
Q Consensus       411 ~~~i~~~l~~g~qvll~lnRrGya~~~~C~~Cg~~~~C~~C~~~l~~h~~~~~l~Ch~Cg~~~~~~~~Cp~Cg~~~~l~~  490 (731)
                      ++.|.+.+++...+|+|.|.|.-|                                                        
T Consensus       243 ~~~i~~~v~~~~ttLIF~NTR~~a--------------------------------------------------------  266 (814)
T COG1201         243 YERIAELVKKHRTTLIFTNTRSGA--------------------------------------------------------  266 (814)
T ss_pred             HHHHHHHHHHCCCEEEEEECHHHH--------------------------------------------------------
T ss_conf             999999996168589997272789--------------------------------------------------------


Q ss_pred             CCCCHHHHHHHHHHCCCCCHHHHCCCCCCCCHHHHHHHHHHHCCCCCCEEEEEHHHCCCCCCCCCCHHHHHHHHHHHHHH
Q ss_conf             35428998888520485200010232113586789999986212576579870443023113452012330003443102
Q gi|254780619|r  491 CGFGIERIAEEVCEYFPLARISILSSDLEGGGGRLQLQLSAIAKGEIDIIIGTQLVAKGHNFPRMSLVGVVDGDLGLTNA  570 (731)
Q Consensus       491 ~G~Gte~~~e~l~~~fp~~~v~~~d~d~~~~~~~~~~~~~~~~~~~~~ilvgTq~i~kg~~fp~v~lv~il~aD~~l~~p  570 (731)
                           |++...|++.++ .+| ....-+. ++......-++|.+|+.+.+|.|.-+..|.|.-+|.||+-+++=      
T Consensus       267 -----E~l~~~L~~~~~-~~i-~~HHgSl-Sre~R~~vE~~lk~G~lravV~TSSLELGIDiG~vdlVIq~~SP------  332 (814)
T COG1201         267 -----ERLAFRLKKLGP-DII-EVHHGSL-SRELRLEVEERLKEGELKAVVATSSLELGIDIGDIDLVIQLGSP------  332 (814)
T ss_pred             -----HHHHHHHHHHCC-CCE-EEECCCC-CHHHHHHHHHHHHCCCCEEEEECCCHHHCCCCCCCEEEEEECCC------
T ss_conf             -----999999987268-755-6531666-57789999999866886299980642205024774299981793------


Q ss_pred             HHHHHHHHHHHHHHHHHCCCCCC
Q ss_conf             45578999998754311025667
Q gi|254780619|r  571 DLRSSERTFQLLSQVTGRAGRFG  593 (731)
Q Consensus       571 d~ra~E~~~qll~qv~gRagr~~  593 (731)
                            +-..-+.|=.||||..-
T Consensus       333 ------~sV~r~lQRiGRsgHr~  349 (814)
T COG1201         333 ------KSVNRFLQRIGRAGHRL  349 (814)
T ss_pred             ------HHHHHHHHHCCCCCCCC
T ss_conf             ------88888868503146656


No 39 
>COG0514 RecQ Superfamily II DNA helicase [DNA replication, recombination, and repair]
Probab=99.44  E-value=1.4e-10  Score=99.91  Aligned_cols=316  Identities=23%  Similarity=0.309  Sum_probs=198.7

Q ss_pred             CCHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHCCCCCEEEEEE
Q ss_conf             88378999999987520489619984475315799999999998514684799715210013445554303897689962
Q gi|254780619|r  199 LDKNQQDVVEQVVPLCTKGFAVSLISGVTGSGKTEVYLEIVAAVLHLGKQVLILLPEISLTSAILERFQKRFGVKPAEWH  278 (731)
Q Consensus       199 Lt~eQ~~a~~~i~~~~~~~f~~~LL~GvTGSGKTEVYl~li~~~L~~GkqvLiLvPEI~Lt~Q~~~rl~~rF~~~v~v~H  278 (731)
                      .-+.|+.+++.+....+   ...++  =||+||.-.|.  |-..+..| =+||+-|=|+|-..-++.++.. |..++-+|
T Consensus        18 FR~gQ~evI~~~l~g~d---~lvvm--PTGgGKSlCyQ--iPAll~~G-~TLVVSPLiSLM~DQV~~l~~~-Gi~A~~ln   88 (590)
T COG0514          18 FRPGQQEIIDALLSGKD---TLVVM--PTGGGKSLCYQ--IPALLLEG-LTLVVSPLISLMKDQVDQLEAA-GIRAAYLN   88 (590)
T ss_pred             CCCCHHHHHHHHHCCCC---EEEEC--CCCCCCCHHHH--HHHHHCCC-CEEEECCHHHHHHHHHHHHHHC-CCEEEHHH
T ss_conf             38888999999965886---79985--38987106743--67886599-7899785688899999999975-96520442


Q ss_pred             CCCCCHHHHHHHHHHHCCCCEEEEEC----CHHHHHH---HCCCEEEEEEECCCCCCHHCC-CCCCCHHHHHHHHHHHCC
Q ss_conf             35572356678999971997399940----0121100---100013677405532100002-443224899999751103
Q gi|254780619|r  279 SSLSTSMREKIWRQVARGAISVIVGV----RSALFLP---FKKLGLIVIDEEHDISYKQEE-GILYNARDMSIVRGKIES  350 (731)
Q Consensus       279 S~ls~~eR~~~w~~i~~G~~~IVIGt----RSAif~P---~~nLglIIvDEEHd~sykq~~-~pry~aRdvA~~Ra~~~~  350 (731)
                      |.++..||..+|..+.+|+.+++-=+    .+.-|..   --.+++++|||-|=-|  |.- .+|=+-|.+..+++.+-+
T Consensus        89 S~l~~~e~~~v~~~l~~g~~klLyisPErl~~~~f~~~L~~~~i~l~vIDEAHCiS--qWGhdFRP~Y~~lg~l~~~~~~  166 (590)
T COG0514          89 STLSREERQQVLNQLKSGQLKLLYISPERLMSPRFLELLKRLPISLVAIDEAHCIS--QWGHDFRPDYRRLGRLRAGLPN  166 (590)
T ss_pred             CCCCHHHHHHHHHHHHCCCEEEEEECCHHHCCHHHHHHHHHCCCCEEEECHHHHHH--HCCCCCCHHHHHHHHHHHHCCC
T ss_conf             43678779999999864964599988136317689999970887569962177776--4177437768999999851799


Q ss_pred             CCEECCCCCCCHHHHHHHHHHHHHHHCCCC---CCCCCCCCCCEECCCCCCCCCCCCCCCHHHHHHHHHHHCCCCEEEEE
Q ss_conf             210000245432467753212344412432---23676543321102222332224547989999998862265517997
Q gi|254780619|r  351 FPVVLVSATPSIESRVNGISRRYHSVHLST---RYRNSALPHLQVIDMRGQTIAQGKSLSPEMIDGIRHTLARNEQTLLF  427 (731)
Q Consensus       351 ~~lilgSATPSles~~~~~~g~~~~~~l~~---R~~~~~~P~i~ivDm~~~~~~~~~~lS~~l~~~i~~~l~~g~qvll~  427 (731)
                      +|++--+||-...+-.-+..    .+.+..   ...+...|++..                ....    ..+--.|..++
T Consensus       167 ~p~~AlTATA~~~v~~DI~~----~L~l~~~~~~~~sfdRpNi~~----------------~v~~----~~~~~~q~~fi  222 (590)
T COG0514         167 PPVLALTATATPRVRDDIRE----QLGLQDANIFRGSFDRPNLAL----------------KVVE----KGEPSDQLAFL  222 (590)
T ss_pred             CCEEEEECCCCHHHHHHHHH----HHCCCCCCEEEECCCCCHHHH----------------HHHH----CCCHHHHHHHH
T ss_conf             97799737898678999999----846788664871589852345----------------5642----56478889998


Q ss_pred             E---CCCCEEHHCCCCCCCCCCCCCCCCCEEEEECCCCCCEECHHHCCCCCCCCCCCCCCCCEECCCCCCHHHHHHHHHH
Q ss_conf             4---2220000002356543431014652012113578320000210244655566678741100135428998888520
Q gi|254780619|r  428 L---NRRGYAPLTLCQVCGNRLKCLHCSCWLVEHRSKKKLYCHQCGHSAIYSQSCVVCGSSGKMIACGFGIERIAEEVCE  504 (731)
Q Consensus       428 l---nRrGya~~~~C~~Cg~~~~C~~C~~~l~~h~~~~~l~Ch~Cg~~~~~~~~Cp~Cg~~~~l~~~G~Gte~~~e~l~~  504 (731)
                      .   ++.+=+..++                                           |.|.       .+.|.+.+.|..
T Consensus       223 ~~~~~~~~~~GIIY-------------------------------------------c~sR-------k~~E~ia~~L~~  252 (590)
T COG0514         223 ATVLPQLSKSGIIY-------------------------------------------CLTR-------KKVEELAEWLRK  252 (590)
T ss_pred             HHHCCCCCCCEEEE-------------------------------------------EEEH-------HHHHHHHHHHHH
T ss_conf             74132468972899-------------------------------------------9337-------759999999997


Q ss_pred             CCCCCHHHHCCCCCCCCHHHHHHHHHHHCCCCCCEEEEEHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             48520001023211358678999998621257657987044302311345201233000344310245578999998754
Q gi|254780619|r  505 YFPLARISILSSDLEGGGGRLQLQLSAIAKGEIDIIIGTQLVAKGHNFPRMSLVGVVDGDLGLTNADLRSSERTFQLLSQ  584 (731)
Q Consensus       505 ~fp~~~v~~~d~d~~~~~~~~~~~~~~~~~~~~~ilvgTq~i~kg~~fp~v~lv~il~aD~~l~~pd~ra~E~~~qll~q  584 (731)
                      .  +.++.....+.  .+...+..-+.|..++..|+|.|-.-.=|.|-|||..|+=.|.=        ++-|-    ++|
T Consensus       253 ~--g~~a~~YHaGl--~~~eR~~~q~~f~~~~~~iiVAT~AFGMGIdKpdVRfViH~~lP--------~s~Es----YyQ  316 (590)
T COG0514         253 N--GISAGAYHAGL--SNEERERVQQAFLNDEIKVMVATNAFGMGIDKPDVRFVIHYDLP--------GSIES----YYQ  316 (590)
T ss_pred             C--CCCEEEECCCC--CHHHHHHHHHHHHCCCCCEEEEECCCCCCCCCCCCEEEEEECCC--------CCHHH----HHH
T ss_conf             7--97257751898--89999999999716998689996462477678884079980699--------89899----999


Q ss_pred             HHHCCCCCCCCCEEEEEECCCCC-HHHHHHHHC
Q ss_conf             31102566788689999329864-888999958
Q gi|254780619|r  585 VTGRAGRFGLKSLGLIQAYQPTH-PVMQALVSG  616 (731)
Q Consensus       585 v~gRagr~~~~g~v~iQt~~p~~-~~~~~~~~~  616 (731)
                      =+|||||...+.+.++ -|.|+. ...++....
T Consensus       317 E~GRAGRDG~~a~ail-l~~~~D~~~~~~~i~~  348 (590)
T COG0514         317 ETGRAGRDGLPAEAIL-LYSPEDIRWQRYLIEQ  348 (590)
T ss_pred             HHHHCCCCCCCCEEEE-EECCCCHHHHHHHHHH
T ss_conf             9713567877021788-6063007999999985


No 40 
>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=99.43  E-value=2.1e-12  Score=113.92  Aligned_cols=132  Identities=32%  Similarity=0.460  Sum_probs=100.8

Q ss_pred             EEEEECCCCHHHHHHHHHHHHHHHH--CCCCEEEEECCCHHHHHHHHHHHCCCC--CEEEEEECCCCCHHHHHHHHHHHC
Q ss_conf             1998447531579999999999851--468479971521001344555430389--768996235572356678999971
Q gi|254780619|r  220 VSLISGVTGSGKTEVYLEIVAAVLH--LGKQVLILLPEISLTSAILERFQKRFG--VKPAEWHSSLSTSMREKIWRQVAR  295 (731)
Q Consensus       220 ~~LL~GvTGSGKTEVYl~li~~~L~--~GkqvLiLvPEI~Lt~Q~~~rl~~rF~--~~v~v~HS~ls~~eR~~~w~~i~~  295 (731)
                      ..++.+-||||||..|+-.+.+.+.  .++++|+++|...|+.|+.++|+..++  ..+...+++.+..++.    ....
T Consensus         2 ~~lv~~ptGsGKT~~~~~~~~~~~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~   77 (144)
T cd00046           2 DVLLAAPTGSGKTLAALLPILELLDSLKGGQVLVLAPTRELANQVAERLKELFGEGIKVGYLIGGTSIKQQE----KLLS   77 (144)
T ss_pred             CEEEECCCCCHHHHHHHHHHHHHHHHCCCCEEEEECCHHHHHHHHHHHHHHHCCCCCEEEEEECCCCHHHHH----HHHC
T ss_conf             999988997179999999999999756897699974679999999999999748871799996136367789----8745


Q ss_pred             CCCEEEEECCHHHH-------HHHCCCEEEEEEECCCCCCHHCCCCCCCHHHHHHHHHHHCCCCEECCCCCC
Q ss_conf             99739994001211-------001000136774055321000024432248999997511032100002454
Q gi|254780619|r  296 GAISVIVGVRSALF-------LPFKKLGLIVIDEEHDISYKQEEGILYNARDMSIVRGKIESFPVVLVSATP  360 (731)
Q Consensus       296 G~~~IVIGtRSAif-------~P~~nLglIIvDEEHd~sykq~~~pry~aRdvA~~Ra~~~~~~lilgSATP  360 (731)
                      +...|+|+|...+.       ..+.++++||+||-|.-..     ..|-..-..+.+....++++++-||||
T Consensus        78 ~~~~ilv~T~~~l~~~~~~~~~~~~~~~~vViDEaH~~~~-----~~~~~~~~~~~~~~~~~~~~l~lSATp  144 (144)
T cd00046          78 GKTDIVVGTPGRLLDELERLKLSLKKLDLLILDEAHRLLN-----QGFGLLGLKILLKLPKDRQVLLLSATP  144 (144)
T ss_pred             CCCCEEECCHHHHHHHHHCCCCCCCCCCEEEEECHHHHHC-----CCCHHHHHHHHHHCCCCCCEEEECCCC
T ss_conf             8984998288999999973876555100999988887643-----796999999999679999489982899


No 41 
>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=99.43  E-value=2.4e-11  Score=105.84  Aligned_cols=153  Identities=19%  Similarity=0.231  Sum_probs=92.2

Q ss_pred             HHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHCC---C--CCEEEEE
Q ss_conf             8999999987520489619984475315799999999998514684799715210013445554303---8--9768996
Q gi|254780619|r  203 QQDVVEQVVPLCTKGFAVSLISGVTGSGKTEVYLEIVAAVLHLGKQVLILLPEISLTSAILERFQKR---F--GVKPAEW  277 (731)
Q Consensus       203 Q~~a~~~i~~~~~~~f~~~LL~GvTGSGKTEVYl~li~~~L~~GkqvLiLvPEI~Lt~Q~~~rl~~r---F--~~~v~v~  277 (731)
                      |.++++.+....   -...++.-=|||||||-|+--   +|.++..+|++.|-.+|+.+..+++++.   |  +.++.++
T Consensus         2 q~~~~~~~~~~~---~~~ivitAPTgsGKT~Aa~lp---~l~~~~~~lyi~P~kAL~~Dq~~~l~~~~~~~~~~~~~~~~   75 (357)
T TIGR03158         2 QVATFEALQSKD---ADIIFNTAPTGAGKTLAWLTP---LLHGENDTIALYPTNALIEDQTEAIKEFVDVFKPERDVNLL   75 (357)
T ss_pred             HHHHHHHHHCCC---CCEEEEECCCCCCHHHHHHHH---HHHCCCCEEEECCHHHHHHHHHHHHHHHHHHHCCCCCCCEE
T ss_conf             689999997689---986999899985699999999---97389879997778999999999999999874423464402


Q ss_pred             E--CCC-----------CC---HHH-HHHH-HHHHCCCCEEEEECCHHHHH---------------HHCCCEEEEEEECC
Q ss_conf             2--355-----------72---356-6789-99971997399940012110---------------01000136774055
Q gi|254780619|r  278 H--SSL-----------ST---SMR-EKIW-RQVARGAISVIVGVRSALFL---------------PFKKLGLIVIDEEH  324 (731)
Q Consensus       278 H--S~l-----------s~---~eR-~~~w-~~i~~G~~~IVIGtRSAif~---------------P~~nLglIIvDEEH  324 (731)
                      |  +..           ..   ++. +... ..+....+.|++.|--.+..               =+.++..|||||=|
T Consensus        76 ~~~~~~~~~~~~~~~d~~~~~~g~~~~~~~r~~~~~~~p~ILlTtPd~l~~~l~~~~~~~~~~~~~~~~~l~~VViDEiH  155 (357)
T TIGR03158        76 HVSKATLKDIKEYANDKVGSSKGEKLYNLLRNPIGTSTPIILLTNPDIFVYLTRFAYIDRGDIAAGFYTKFSTVIFDEFH  155 (357)
T ss_pred             ECCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCCEEEEECHHHHHHHHHHHCCCCCHHHHHHHHCCCEEEEEEEH
T ss_conf             11464323344465555343445410256654302589909992889999997620136510399998516747756200


Q ss_pred             CCCCHHCCC--CCCCHHHHHHHHHHHCCCCEECCCCCCCHH
Q ss_conf             321000024--432248999997511032100002454324
Q gi|254780619|r  325 DISYKQEEG--ILYNARDMSIVRGKIESFPVVLVSATPSIE  363 (731)
Q Consensus       325 d~sykq~~~--pry~aRdvA~~Ra~~~~~~lilgSATPSle  363 (731)
                        +|-....  .-+..+..-..+....+.++++.||||...
T Consensus       156 --~y~~~~~~~~~~~l~~~~~~~~~~~~~~~i~lSAT~~~~  194 (357)
T TIGR03158       156 --LYDAKQLVGMLFLLAYMQLIRFFECRRKFVFLSATPDPA  194 (357)
T ss_pred             --CCCCCCHHHHHHHHHHHHHHHHCCCCCEEEEECCCCCHH
T ss_conf             --006762089999999999986336898089982799803


No 42 
>KOG0354 consensus
Probab=99.41  E-value=2.3e-10  Score=98.40  Aligned_cols=380  Identities=18%  Similarity=0.144  Sum_probs=188.3

Q ss_pred             CCCCCCCHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHHHHHHHHHHC--CCCEEEEECCCHHHHHHHHHHHCCC-
Q ss_conf             4666688378999999987520489619984475315799999999998514--6847997152100134455543038-
Q gi|254780619|r  194 FSLPILDKNQQDVVEQVVPLCTKGFAVSLISGVTGSGKTEVYLEIVAAVLHL--GKQVLILLPEISLTSAILERFQKRF-  270 (731)
Q Consensus       194 ~~~~~Lt~eQ~~a~~~i~~~~~~~f~~~LL~GvTGSGKTEVYl~li~~~L~~--GkqvLiLvPEI~Lt~Q~~~rl~~rF-  270 (731)
                      ...-.|-+.|..+++...      |...|+.-=||||||.|..-.|.+.+..  ..-|++|+|.+-|..|..++|..++ 
T Consensus        58 p~~~~lR~YQ~eivq~AL------gkNtii~lPTG~GKTfIAa~Vm~nh~rw~p~~KiVF~aP~~pLv~QQ~a~~~~~~~  131 (746)
T KOG0354          58 PTNLELRNYQEELVQPAL------GKNTIIALPTGSGKTFIAAVIMKNHFEWRPKGKVVFLAPTRPLVNQQIACFSIYLI  131 (746)
T ss_pred             CCCCCCCHHHHHHHHHHH------CCCEEEEEECCCCCCCHHHHHHHHHHHCCCCCEEEEEECCCHHHHHHHHHHHHCCC
T ss_conf             676656078999867862------68769995359986104799999997237764389960771178888988762067


Q ss_pred             CCEEEEEECC-CCCHHHHHHHHHHHCCCCEEEEECC--------HHHHHHHCCCEEEEEEECCCCCCHHCCCCCCCHHHH
Q ss_conf             9768996235-5723566789999719973999400--------121100100013677405532100002443224899
Q gi|254780619|r  271 GVKPAEWHSS-LSTSMREKIWRQVARGAISVIVGVR--------SALFLPFKKLGLIVIDEEHDISYKQEEGILYNARDM  341 (731)
Q Consensus       271 ~~~v~v~HS~-ls~~eR~~~w~~i~~G~~~IVIGtR--------SAif~P~~nLglIIvDEEHd~sykq~~~pry~aRdv  341 (731)
                      +-.+-..+++ .+.+.|-+.|.     ..+|++-|-        ++.--++.+..+||+||-|..+   -+.| |+---=
T Consensus       132 ~~~~T~~l~~~~~~~~r~~i~~-----s~~vff~TpQil~ndL~~~~~~~ls~fs~iv~DE~Hra~---kn~~-Y~~Vmr  202 (746)
T KOG0354         132 PYSVTGQLGDTVPRSNRGEIVA-----SKRVFFRTPQILENDLKSGLHDELSDFSLIVFDECHRTS---KNHP-YNNIMR  202 (746)
T ss_pred             CCCCEEECCCCCCCCCHHHHHC-----CCCEEEECHHHHHHHCCCCCCCCCCEEEEEEECCCCCCC---CCCC-HHHHHH
T ss_conf             6010455057568876245310-----263589672763433254334545517999972224455---5661-799999


Q ss_pred             HHHHHHHCCCCEECCCCCCCHHHHHHHHHHHHHHH-CCCCCCCCC---CCC-----CCEECCCCCCCCCCCCCCCHHHHH
Q ss_conf             99975110321000024543246775321234441-243223676---543-----321102222332224547989999
Q gi|254780619|r  342 SIVRGKIESFPVVLVSATPSIESRVNGISRRYHSV-HLSTRYRNS---ALP-----HLQVIDMRGQTIAQGKSLSPEMID  412 (731)
Q Consensus       342 A~~Ra~~~~~~lilgSATPSles~~~~~~g~~~~~-~l~~R~~~~---~~P-----~i~ivDm~~~~~~~~~~lS~~l~~  412 (731)
                      .++.-+.++..++=-||||. .....+++--+.|. .|.-|-...   ...     ....+|+..+...    +++.+..
T Consensus       203 ~~l~~k~~~~qILgLTASpG-~~~~~v~~~I~~L~asldvr~~ssi~~~y~~lr~~~~i~v~~~~~~~~----~~~~f~~  277 (746)
T KOG0354         203 EYLDLKNQGNQILGLTASPG-SKLEQVQNVIDNLCASLDVRTESSIKSNYEELREHVQIPVDLSLCERD----IEDPFGM  277 (746)
T ss_pred             HHHHHHHCCCCEEEEECCCC-CCHHHHHHHHHHHHEECCCCHHHHHHHHHHHHHCCCCCCCCHHHHHHH----HHHHHHH
T ss_conf             99986514661799855888-458999999985203325550445654189872467524758876411----3436999


Q ss_pred             HHHHHHCC--CCEEEEEECCCC--EEHHCC--C--CCCCCCCCCCCC--CCEEEEECCCCCCEECHHH----CCCCCCCC
Q ss_conf             99886226--551799742220--000002--3--565434310146--5201211357832000021----02446555
Q gi|254780619|r  413 GIRHTLAR--NEQTLLFLNRRG--YAPLTL--C--QVCGNRLKCLHC--SCWLVEHRSKKKLYCHQCG----HSAIYSQS  478 (731)
Q Consensus       413 ~i~~~l~~--g~qvll~lnRrG--ya~~~~--C--~~Cg~~~~C~~C--~~~l~~h~~~~~l~Ch~Cg----~~~~~~~~  478 (731)
                      .|+.-+..  ++. |.-++.++  |.-.++  =  ..=++...=++|  ...+.+| ....|.||.=-    +... -+.
T Consensus       278 ~i~p~l~~l~~~~-l~~~~~~~~~~~~~~~~~~~~~~~~~~~~q~~~f~~~~~~~~-~~~ll~~~gir~~~~l~~~-~~f  354 (746)
T KOG0354         278 IIEPLLQQLQEEG-LIEISDKSTSYEQWVVQAEKAAAPNGPENQRNCFYALHLRKY-NLALLISDGIRFVDALDYL-EDF  354 (746)
T ss_pred             HHHHHHHHHHHCC-CCCCCCCCCCCCCHHHHHHHHHCCCCCCCCHHHHHHHHHHHH-HHHHHHHCCHHHHHHHHHH-HHH
T ss_conf             9999999998638-541024333444404330022236887432036789999987-8888763234037777655-543


Q ss_pred             CCCCCCCC----------------------EECC---CC-CCHHHHHHHHHHCC---CCCHHHHCCC-------------
Q ss_conf             66678741----------------------1001---35-42899888852048---5200010232-------------
Q gi|254780619|r  479 CVVCGSSG----------------------KMIA---CG-FGIERIAEEVCEYF---PLARISILSS-------------  516 (731)
Q Consensus       479 Cp~Cg~~~----------------------~l~~---~G-~Gte~~~e~l~~~f---p~~~v~~~d~-------------  516 (731)
                      =++|+...                      .+..   +| .=.|++.+.|...|   |+.+++.+-.             
T Consensus       355 ~~e~~~~k~~~~~~e~~~~~~~~~~m~~~~~l~~~~~~~npkle~l~~~l~e~f~~~~dsR~IIFve~R~sa~~l~~~l~  434 (746)
T KOG0354         355 YEEVALKKYLKLELEARLIRNFTENMNELEHLSLDPPKENPKLEKLVEILVEQFEQNPDSRTIIFVETRESALALKKWLL  434 (746)
T ss_pred             CCCCCHHHHHHHHHCCHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHCCCCCCEEEEEEHHHHHHHHHHHHH
T ss_conf             00000467889874221067788988764432027876684699999999998605988507999732889999999997


Q ss_pred             ----C----------------CCCCHHHHHHHHHHHCCCCCCEEEEEHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf             ----1----------------13586789999986212576579870443023113452012330003443102455789
Q gi|254780619|r  517 ----D----------------LEGGGGRLQLQLSAIAKGEIDIIIGTQLVAKGHNFPRMSLVGVVDGDLGLTNADLRSSE  576 (731)
Q Consensus       517 ----d----------------~~~~~~~~~~~~~~~~~~~~~ilvgTq~i~kg~~fp~v~lv~il~aD~~l~~pd~ra~E  576 (731)
                          +                +--+...-...+.+|.+|+.+|||+|.+..-|+|.+.++||+--|+         -++|
T Consensus       435 ~~~~~~ir~~~fiGq~~s~~~~gmtqk~Q~evl~~Fr~G~~NvLVATSV~EEGLDI~ec~lVIcYd~---------~snp  505 (746)
T KOG0354         435 QLHELGIKAEIFIGQGKSTQSTGMTQKEQKEVLDKFRDGEINVLVATSVAEEGLDIGECNLVICYDY---------SSNP  505 (746)
T ss_pred             HHHHCCCCCCEEEECCCCCCCCCCCHHHHHHHHHHHHCCCCCEEEEECCHHCCCCCCCCCEEEEECC---------CCCH
T ss_conf             5401354402156035445444457899999999985798027998101004677421128999657---------7668


Q ss_pred             HHHHHHHHHHHCCCCCCCCCEEEEEECCCCCHHH
Q ss_conf             9999875431102566788689999329864888
Q gi|254780619|r  577 RTFQLLSQVTGRAGRFGLKSLGLIQAYQPTHPVM  610 (731)
Q Consensus       577 ~~~qll~qv~gRagr~~~~g~v~iQt~~p~~~~~  610 (731)
                      -   -+.|-.|| ||.+ .|++++-|..-++..+
T Consensus       506 I---rmIQrrGR-gRa~-ns~~vll~t~~~~~~~  534 (746)
T KOG0354         506 I---RMVQRRGR-GRAR-NSKCVLLTTGSEVIEF  534 (746)
T ss_pred             H---HHHHHHCC-CCCC-CCEEEEEECCHHHHHH
T ss_conf             8---99998631-0101-8769999725168899


No 43 
>KOG0330 consensus
Probab=99.37  E-value=5.7e-11  Score=102.97  Aligned_cols=349  Identities=19%  Similarity=0.223  Sum_probs=188.9

Q ss_pred             HCCCHHHHHHHHHCCHHHHHHHHHCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHHHHH
Q ss_conf             09998999752455722344554102356654344666688378999999987520489619984475315799999999
Q gi|254780619|r  160 SQVSSHVIDGLKAQGVIKQIFEVISPVVDSPNLYFSLPILDKNQQDVVEQVVPLCTKGFAVSLISGVTGSGKTEVYLEIV  239 (731)
Q Consensus       160 ~~~s~~~i~~L~~kglI~~~~~~~~~~~~~~~~~~~~~~Lt~eQ~~a~~~i~~~~~~~f~~~LL~GvTGSGKTEVYl~li  239 (731)
                      .++....++++...||-                     ..|+=|++++-...   ..+  -.+--.-||||||--|+-=|
T Consensus        66 Lgv~~~L~~ac~~l~~~---------------------~PT~IQ~~aiP~~L---~g~--dvIglAeTGSGKT~afaLPI  119 (476)
T KOG0330          66 LGVHPELLEACQELGWK---------------------KPTKIQSEAIPVAL---GGR--DVIGLAETGSGKTGAFALPI  119 (476)
T ss_pred             CCCCHHHHHHHHHHCCC---------------------CCCHHHHHHCCHHH---CCC--CEEEEECCCCCCHHHHHHHH
T ss_conf             37689999999984767---------------------87444452065543---798--57999435888402317999


Q ss_pred             HHHHHCCC---CEEEEECCCHHHHHHHHHHHCC---CCCEEEEEECCCCCHHHHHHHHHHHCCCCEEEEECCHHHHHH--
Q ss_conf             99851468---4799715210013445554303---897689962355723566789999719973999400121100--
Q gi|254780619|r  240 AAVLHLGK---QVLILLPEISLTSAILERFQKR---FGVKPAEWHSSLSTSMREKIWRQVARGAISVIVGVRSALFLP--  311 (731)
Q Consensus       240 ~~~L~~Gk---qvLiLvPEI~Lt~Q~~~rl~~r---F~~~v~v~HS~ls~~eR~~~w~~i~~G~~~IVIGtRSAif~P--  311 (731)
                      -+.|-+..   -+|||+|.=-|+.|+.+-|...   .|.+++++-+++.-..-    .....-++.|+|+|-.+++=-  
T Consensus       120 l~~LL~~p~~~~~lVLtPtRELA~QI~e~fe~Lg~~iglr~~~lvGG~~m~~q----~~~L~kkPhilVaTPGrL~dhl~  195 (476)
T KOG0330         120 LQRLLQEPKLFFALVLTPTRELAQQIAEQFEALGSGIGLRVAVLVGGMDMMLQ----ANQLSKKPHILVATPGRLWDHLE  195 (476)
T ss_pred             HHHHHCCCCCCEEEEECCCHHHHHHHHHHHHHHCCCCCEEEEEEECCCHHHHH----HHHHHCCCCEEEECCHHHHHHHH
T ss_conf             99997198774489964828999999999987535667279998658329999----88762489879837078999987


Q ss_pred             ------HCCCEEEEEEECCCCCCHHCCCCCCCHHHHHHHHHHHCCCCEECCCCCCCHHHHHHHHHHHHHHHCCCCCCCCC
Q ss_conf             ------10001367740553210000244322489999975110321000024543246775321234441243223676
Q gi|254780619|r  312 ------FKKLGLIVIDEEHDISYKQEEGILYNARDMSIVRGKIESFPVVLVSATPSIESRVNGISRRYHSVHLSTRYRNS  385 (731)
Q Consensus       312 ------~~nLglIIvDEEHd~sykq~~~pry~aRdvA~~Ra~~~~~~lilgSATPSles~~~~~~g~~~~~~l~~R~~~~  385 (731)
                            ++.|.-.|+||. |--.-++-.+-   -|- +++---.+...+|-|||-+-+.      ++.....+.+-..-+
T Consensus       196 ~Tkgf~le~lk~LVlDEA-DrlLd~dF~~~---ld~-ILk~ip~erqt~LfsATMt~kv------~kL~rasl~~p~~v~  264 (476)
T KOG0330         196 NTKGFSLEQLKFLVLDEA-DRLLDMDFEEE---LDY-ILKVIPRERQTFLFSATMTKKV------RKLQRASLDNPVKVA  264 (476)
T ss_pred             HCCCCCHHHHHHHHHCHH-HHHHHHHHHHH---HHH-HHHHCCCCCEEEEEEEECCHHH------HHHHHHCCCCCEEEE
T ss_conf             436840887578763317-76621156899---999-9874674414899986444136------778764158971786


Q ss_pred             CCCCCEECCCCCCCCCCCCCCCHHHHHHHHHHHCCCCEEEEEECCCCEEHHCCCCCCCCCCCCCCCCCEEEEECCCCCCE
Q ss_conf             54332110222233222454798999999886226551799742220000002356543431014652012113578320
Q gi|254780619|r  386 ALPHLQVIDMRGQTIAQGKSLSPEMIDGIRHTLARNEQTLLFLNRRGYAPLTLCQVCGNRLKCLHCSCWLVEHRSKKKLY  465 (731)
Q Consensus       386 ~~P~i~ivDm~~~~~~~~~~lS~~l~~~i~~~l~~g~qvll~lnRrGya~~~~C~~Cg~~~~C~~C~~~l~~h~~~~~l~  465 (731)
                      .--..+.||                      +|   .|..+|++-+--                  +..|+|--+     
T Consensus       265 ~s~ky~tv~----------------------~l---kQ~ylfv~~k~K------------------~~yLV~ll~-----  296 (476)
T KOG0330         265 VSSKYQTVD----------------------HL---KQTYLFVPGKDK------------------DTYLVYLLN-----  296 (476)
T ss_pred             CCCHHCCHH----------------------HH---HHHEEECCCCCC------------------CHHHHHHHH-----
T ss_conf             043011167----------------------76---645576326666------------------523899887-----


Q ss_pred             ECHHHCCCCCCCCCCCCCCCCEECCCCCCHHHHHHHHHHCCCCCHHHHCCCCCCCCHHHHHHHHHHHCCCCCCEEEEEHH
Q ss_conf             00021024465556667874110013542899888852048520001023211358678999998621257657987044
Q gi|254780619|r  466 CHQCGHSAIYSQSCVVCGSSGKMIACGFGIERIAEEVCEYFPLARISILSSDLEGGGGRLQLQLSAIAKGEIDIIIGTQL  545 (731)
Q Consensus       466 Ch~Cg~~~~~~~~Cp~Cg~~~~l~~~G~Gte~~~e~l~~~fp~~~v~~~d~d~~~~~~~~~~~~~~~~~~~~~ilvgTq~  545 (731)
                       |.-|  ..+--.|..|..          |+++.-.|..+  +..-+.+..|...  ......++.|.++.-+|||.|-.
T Consensus       297 -e~~g--~s~iVF~~t~~t----------t~~la~~L~~l--g~~a~~LhGqmsq--~~Rlg~l~~Fk~~~r~iLv~TDV  359 (476)
T KOG0330         297 -ELAG--NSVIVFCNTCNT----------TRFLALLLRNL--GFQAIPLHGQMSQ--SKRLGALNKFKAGARSILVCTDV  359 (476)
T ss_pred             -HHCC--CCEEEEEECCCH----------HHHHHHHHHHC--CCCEECCCCHHHH--HHHHHHHHHHHCCCCCEEEECCH
T ss_conf             -6359--847999834640----------89999999862--7643205660357--78877899875147767986130


Q ss_pred             HCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEECCCCCHHHHHHHHCCHHHHHHHH
Q ss_conf             30231134520123300034431024557899999875431102566788689999329864888999958979999999
Q gi|254780619|r  546 VAKGHNFPRMSLVGVVDGDLGLTNADLRSSERTFQLLSQVTGRAGRFGLKSLGLIQAYQPTHPVMQALVSGDADSFYESE  625 (731)
Q Consensus       546 i~kg~~fp~v~lv~il~aD~~l~~pd~ra~E~~~qll~qv~gRagr~~~~g~v~iQt~~p~~~~~~~~~~~d~~~f~~~e  625 (731)
                      -+.|+|.|.|.+|  +|-|.-.++-||          .-=.||.||....|++|--       +-|    +|.+.|-+-|
T Consensus       360 aSRGLDip~Vd~V--VNyDiP~~skDY----------IHRvGRtaRaGrsG~~Itl-------Vtq----yDve~~qrIE  416 (476)
T KOG0330         360 ASRGLDIPHVDVV--VNYDIPTHSKDY----------IHRVGRTARAGRSGKAITL-------VTQ----YDVELVQRIE  416 (476)
T ss_pred             HCCCCCCCCCEEE--EECCCCCCHHHH----------HHHCCCCCCCCCCCCEEEE-------EEH----HHHHHHHHHH
T ss_conf             1046898771079--953789837888----------8870430016777514898-------744----5569999999


Q ss_pred             HHHHHHCCCCCC
Q ss_conf             999998188880
Q gi|254780619|r  626 IRARESVNLPPF  637 (731)
Q Consensus       626 l~~R~~~~~PPf  637 (731)
                      ...|+.+-.||-
T Consensus       417 ~~~gkkl~~~~~  428 (476)
T KOG0330         417 HALGKKLPEYKV  428 (476)
T ss_pred             HHHHCCCCCCCC
T ss_conf             998547875676


No 44 
>COG1202 Superfamily II helicase, archaea-specific [General function prediction only]
Probab=99.35  E-value=2.2e-11  Score=106.12  Aligned_cols=294  Identities=23%  Similarity=0.274  Sum_probs=162.9

Q ss_pred             EEECCCCHHHHHHH-HHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHCCC---CCEEEE--EECCCCCHHHHHHHHHH-H
Q ss_conf             98447531579999-99999985146847997152100134455543038---976899--62355723566789999-7
Q gi|254780619|r  222 LISGVTGSGKTEVY-LEIVAAVLHLGKQVLILLPEISLTSAILERFQKRF---GVKPAE--WHSSLSTSMREKIWRQV-A  294 (731)
Q Consensus       222 LL~GvTGSGKTEVY-l~li~~~L~~GkqvLiLvPEI~Lt~Q~~~rl~~rF---~~~v~v--~HS~ls~~eR~~~w~~i-~  294 (731)
                      |.-.-|+||||.|- |--+..++..|+--|+|||=++|+.|-+..|+.|.   |..+++  =-|.+...++-   ... -
T Consensus       236 lVVSaTasGKTLIgElAGi~~~l~~g~KmlfLvPLVALANQKy~dF~~rYs~LglkvairVG~srIk~~~~p---v~~~t  312 (830)
T COG1202         236 LVVSATASGKTLIGELAGIPRLLSGGKKMLFLVPLVALANQKYEDFKERYSKLGLKVAIRVGMSRIKTREEP---VVVDT  312 (830)
T ss_pred             EEEECCCCCCCHHHHHHCCHHHHHCCCEEEEEEHHHHHHCCHHHHHHHHHHCCCCEEEEEECHHHHCCCCCC---CCCCC
T ss_conf             999405777514777637387883787289973168763111899999865016627888423452246775---35689


Q ss_pred             CCCCEEEEECCHHHH------HHHCCCEEEEEEECCCCCCHH-CCCCCCCHHHHHHHHHHHCCCCEECCCCCCC-HHHHH
Q ss_conf             199739994001211------001000136774055321000-0244322489999975110321000024543-24677
Q gi|254780619|r  295 RGAISVIVGVRSALF------LPFKKLGLIVIDEEHDISYKQ-EEGILYNARDMSIVRGKIESFPVVLVSATPS-IESRV  366 (731)
Q Consensus       295 ~G~~~IVIGtRSAif------~P~~nLglIIvDEEHd~sykq-~~~pry~aRdvA~~Ra~~~~~~lilgSATPS-les~~  366 (731)
                      .-.++|||||.-++=      --+.|.|.+||||=|-  ..- +.+||.+.- ++.+|--..++.+|.-|||-- .+-+.
T Consensus       313 ~~dADIIVGTYEGiD~lLRtg~~lgdiGtVVIDEiHt--L~deERG~RLdGL-I~RLr~l~~~AQ~i~LSATVgNp~elA  389 (830)
T COG1202         313 SPDADIIVGTYEGIDYLLRTGKDLGDIGTVVIDEIHT--LEDEERGPRLDGL-IGRLRYLFPGAQFIYLSATVGNPEELA  389 (830)
T ss_pred             CCCCCEEEEECHHHHHHHHCCCCCCCCCEEEEEEEEE--CCCHHCCCCHHHH-HHHHHHHCCCCEEEEEEEECCCHHHHH
T ss_conf             9877679861110789987078555443599650120--4401016323528-999998677774999874338869999


Q ss_pred             HHHHHHHHHHCCCCCCCCCCCC-CCEECCCCCCCCCCCCCCCHHHHHHHHHHHCCC--CEEEEEECCCCEEHHCCCCCCC
Q ss_conf             5321234441243223676543-321102222332224547989999998862265--5179974222000000235654
Q gi|254780619|r  367 NGISRRYHSVHLSTRYRNSALP-HLQVIDMRGQTIAQGKSLSPEMIDGIRHTLARN--EQTLLFLNRRGYAPLTLCQVCG  443 (731)
Q Consensus       367 ~~~~g~~~~~~l~~R~~~~~~P-~i~ivDm~~~~~~~~~~lS~~l~~~i~~~l~~g--~qvll~lnRrGya~~~~C~~Cg  443 (731)
                      ...  ..+++.-.+|    +-| .-++|=-+.+..+.+ .++.-...+-...-.+|  .|.|+|.|-|        ++|.
T Consensus       390 ~~l--~a~lV~y~~R----PVplErHlvf~~~e~eK~~-ii~~L~k~E~~~~sskg~rGQtIVFT~SR--------rr~h  454 (830)
T COG1202         390 KKL--GAKLVLYDER----PVPLERHLVFARNESEKWD-IIARLVKREFSTESSKGYRGQTIVFTYSR--------RRCH  454 (830)
T ss_pred             HHH--CCEEEEECCC----CCCHHHEEEEECCCHHHHH-HHHHHHHHHHHHHHCCCCCCCEEEEECCH--------HHHH
T ss_conf             883--8725865588----7873670664048167778-99999999975441137677369994216--------6699


Q ss_pred             CCCCCCCCCCEEEEECCCCCCEECHHHCCCCCCCCCCCCCCCCEECCCCCCHHHHHHHHHHCCCCCHHHHCCCCCCCCHH
Q ss_conf             34310146520121135783200002102446555666787411001354289988885204852000102321135867
Q gi|254780619|r  444 NRLKCLHCSCWLVEHRSKKKLYCHQCGHSAIYSQSCVVCGSSGKMIACGFGIERIAEEVCEYFPLARISILSSDLEGGGG  523 (731)
Q Consensus       444 ~~~~C~~C~~~l~~h~~~~~l~Ch~Cg~~~~~~~~Cp~Cg~~~~l~~~G~Gte~~~e~l~~~fp~~~v~~~d~d~~~~~~  523 (731)
                      ..+      ..|+-   .        |..               -.++-.|....+                        
T Consensus       455 ~lA------~~L~~---k--------G~~---------------a~pYHaGL~y~e------------------------  478 (830)
T COG1202         455 ELA------DALTG---K--------GLK---------------AAPYHAGLPYKE------------------------  478 (830)
T ss_pred             HHH------HHHHC---C--------CCC---------------CCCCCCCCCHHH------------------------
T ss_conf             999------88610---7--------866---------------654437986788------------------------


Q ss_pred             HHHHHHHHHCCCCCCEEEEEHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCC--CCCEEEEE
Q ss_conf             8999998621257657987044302311345201233000344310245578999998754311025667--88689999
Q gi|254780619|r  524 RLQLQLSAIAKGEIDIIIGTQLVAKGHNFPRMSLVGVVDGDLGLTNADLRSSERTFQLLSQVTGRAGRFG--LKSLGLIQ  601 (731)
Q Consensus       524 ~~~~~~~~~~~~~~~ilvgTq~i~kg~~fp~v~lv~il~aD~~l~~pd~ra~E~~~qll~qv~gRagr~~--~~g~v~iQ  601 (731)
                       ...+-..|.+++.+.+|.|-.++-|.|||.-. |+.   +++.-.-|+=+.    |-..|..|||||-.  ..|+|++-
T Consensus       479 -Rk~vE~~F~~q~l~~VVTTAAL~AGVDFPASQ-VIF---EsLaMG~~WLs~----~EF~QM~GRAGRp~yHdrGkVyll  549 (830)
T COG1202         479 -RKSVERAFAAQELAAVVTTAALAAGVDFPASQ-VIF---ESLAMGIEWLSV----REFQQMLGRAGRPDYHDRGKVYLL  549 (830)
T ss_pred             -HHHHHHHHHCCCCCEEEEHHHHHCCCCCCHHH-HHH---HHHHCCCCCCCH----HHHHHHHCCCCCCCCCCCCEEEEE
T ss_conf             -88899997608755576424564478875189-999---998710432789----999998504699872337339999


No 45 
>KOG0345 consensus
Probab=99.34  E-value=2.6e-10  Score=97.90  Aligned_cols=301  Identities=17%  Similarity=0.179  Sum_probs=159.8

Q ss_pred             CCCHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHHHHHHHHH-H-----CCC--CEEEEECCCHHHHHHHHHH---
Q ss_conf             6883789999999875204896199844753157999999999985-1-----468--4799715210013445554---
Q gi|254780619|r  198 ILDKNQQDVVEQVVPLCTKGFAVSLISGVTGSGKTEVYLEIVAAVL-H-----LGK--QVLILLPEISLTSAILERF---  266 (731)
Q Consensus       198 ~Lt~eQ~~a~~~i~~~~~~~f~~~LL~GvTGSGKTEVYl~li~~~L-~-----~Gk--qvLiLvPEI~Lt~Q~~~rl---  266 (731)
                      ..|+-|..++-.+...     .-...+.+||||||.-|+-=+-+.+ .     .+.  .+||+.|.=-|+.|+..-.   
T Consensus        28 ~mTpVQa~tIPlll~~-----KDVvveavTGSGKTlAFllP~le~i~rr~~~~~~~~vgalIIsPTRELa~QI~~V~~~F  102 (567)
T KOG0345          28 KMTPVQAATIPLLLKN-----KDVVVEAVTGSGKTLAFLLPMLEIIYRREAKTPPGQVGALIISPTRELARQIREVAQPF  102 (567)
T ss_pred             CCCHHHHHHHHHHHCC-----CCEEEECCCCCCCCHHHHHHHHHHHHHHCCCCCCCCEEEEEECCCHHHHHHHHHHHHHH
T ss_conf             3687787466788527-----85689856788710668999999998611578965124799657199999999999999


Q ss_pred             HCC-CCCEEEEEECCCCCHHHHHHHHHHHCCCCEEEEECCH---------HHHHHHCCCEEEEEEECCCCCCHHCCCCCC
Q ss_conf             303-8976899623557235667899997199739994001---------211001000136774055321000024432
Q gi|254780619|r  267 QKR-FGVKPAEWHSSLSTSMREKIWRQVARGAISVIVGVRS---------ALFLPFKKLGLIVIDEEHDISYKQEEGILY  336 (731)
Q Consensus       267 ~~r-F~~~v~v~HS~ls~~eR~~~w~~i~~G~~~IVIGtRS---------Aif~P~~nLglIIvDEEHd~sykq~~~pry  336 (731)
                      -.. ++.+...|-++.+-.+-+   ...+...+.|+|||..         +.++-|++|.+.|+||.. --  -+.++-=
T Consensus       103 ~~~l~~l~~~l~vGG~~v~~Di---~~fkee~~nIlVgTPGRL~di~~~~~~~l~~rsLe~LVLDEAD-rL--ldmgFe~  176 (567)
T KOG0345         103 LEHLPNLNCELLVGGRSVEEDI---KTFKEEGPNILVGTPGRLLDILQREAEKLSFRSLEILVLDEAD-RL--LDMGFEA  176 (567)
T ss_pred             HHHCCCCCEEEEECCCCHHHHH---HHHHHHCCCEEEECCHHHHHHHHCHHHCCCCCCCCEEEECCHH-HH--HCCCHHH
T ss_conf             9850365459997686477799---9999709958994762499998453000361331157751467-67--4432799


Q ss_pred             CHHHHHHHHHHHCCCCEECCCCCC--CHHHHHHHHHHHHHHHCCCCCCCCCCCCCCEECCCCCCCCCCCCCCCHHHHHHH
Q ss_conf             248999997511032100002454--324677532123444124322367654332110222233222454798999999
Q gi|254780619|r  337 NARDMSIVRGKIESFPVVLVSATP--SIESRVNGISRRYHSVHLSTRYRNSALPHLQVIDMRGQTIAQGKSLSPEMIDGI  414 (731)
Q Consensus       337 ~aRdvA~~Ra~~~~~~lilgSATP--Sles~~~~~~g~~~~~~l~~R~~~~~~P~i~ivDm~~~~~~~~~~lS~~l~~~i  414 (731)
                      +...+.-..-++-..-+.  |||-  .++.+..  .|    +        +.                            
T Consensus       177 ~~n~ILs~LPKQRRTGLF--SATq~~~v~dL~r--aG----L--------RN----------------------------  212 (567)
T KOG0345         177 SVNTILSFLPKQRRTGLF--SATQTQEVEDLAR--AG----L--------RN----------------------------  212 (567)
T ss_pred             HHHHHHHHCCCCCCCCCC--EEHHHHHHHHHHH--HH----C--------CC----------------------------
T ss_conf             999999866210002443--0021466889998--53----5--------68----------------------------


Q ss_pred             HHHHCCCCEEEEEECCCCE--EH------HCCCCCCCCCCCCCCCCCEEEEECCCCCCEECHHHCCC-CCCCCCCCCCCC
Q ss_conf             8862265517997422200--00------00235654343101465201211357832000021024-465556667874
Q gi|254780619|r  415 RHTLARNEQTLLFLNRRGY--AP------LTLCQVCGNRLKCLHCSCWLVEHRSKKKLYCHQCGHSA-IYSQSCVVCGSS  485 (731)
Q Consensus       415 ~~~l~~g~qvll~lnRrGy--a~------~~~C~~Cg~~~~C~~C~~~l~~h~~~~~l~Ch~Cg~~~-~~~~~Cp~Cg~~  485 (731)
                              +|-+-++-++-  +|      ++.|.--....                .|.--.|+++. ..--.-|.|.+.
T Consensus       213 --------pv~V~V~~k~~~~tPS~L~~~Y~v~~a~eK~~----------------~lv~~L~~~~~kK~iVFF~TCasV  268 (567)
T KOG0345         213 --------PVRVSVKEKSKSATPSSLALEYLVCEADEKLS----------------QLVHLLNNNKDKKCIVFFPTCASV  268 (567)
T ss_pred             --------CEEEEECCCCCCCCCHHHHHEEEEECHHHHHH----------------HHHHHHHCCCCCCEEEEECCCCHH
T ss_conf             --------63654123445558423111256757788899----------------999999624546279993475409


Q ss_pred             CEECCCCCCHHHHHHHHHHCCCCCHHHHCCCCCCCCHHHHHHHHHHHCCCCCCEEEEEHHHCCCCCCCCCCHHHHHHHHH
Q ss_conf             11001354289988885204852000102321135867899999862125765798704430231134520123300034
Q gi|254780619|r  486 GKMIACGFGIERIAEEVCEYFPLARISILSSDLEGGGGRLQLQLSAIAKGEIDIIIGTQLVAKGHNFPRMSLVGVVDGDL  565 (731)
Q Consensus       486 ~~l~~~G~Gte~~~e~l~~~fp~~~v~~~d~d~~~~~~~~~~~~~~~~~~~~~ilvgTq~i~kg~~fp~v~lv~il~aD~  565 (731)
                      .   ++|.       .+..+.+...+.-+.... +. ....+.+++|.+..-.+|..|-..|.|+|+|+|.+|+=.|.-.
T Consensus       269 e---Yf~~-------~~~~~l~~~~i~~iHGK~-~q-~~R~k~~~~F~~~~~~vl~~TDVaARGlDip~iD~VvQ~DpP~  336 (567)
T KOG0345         269 E---YFGK-------LFSRLLKKREIFSIHGKM-SQ-KARAKVLEAFRKLSNGVLFCTDVAARGLDIPGIDLVVQFDPPK  336 (567)
T ss_pred             H---HHHH-------HHHHHHCCCCEEEECCHH-CC-HHHHHHHHHHHHCCCCEEEEEHHHHCCCCCCCCEEEEECCCCC
T ss_conf             9---9998-------888760787479862201-23-4688999998715686188604555368988970799707999


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCEEEEE
Q ss_conf             431024557899999875431102566788689999
Q gi|254780619|r  566 GLTNADLRSSERTFQLLSQVTGRAGRFGLKSLGLIQ  601 (731)
Q Consensus       566 ~l~~pd~ra~E~~~qll~qv~gRagr~~~~g~v~iQ  601 (731)
                      -            ....+-=+||+||..+.|+.|+-
T Consensus       337 ~------------~~~FvHR~GRTaR~gr~G~Aivf  360 (567)
T KOG0345         337 D------------PSSFVHRCGRTARAGREGNAIVF  360 (567)
T ss_pred             C------------HHHHHHHCCHHHHCCCCCCEEEE
T ss_conf             8------------14777741214435676634899


No 46 
>KOG0344 consensus
Probab=99.31  E-value=3.9e-10  Score=96.63  Aligned_cols=303  Identities=19%  Similarity=0.267  Sum_probs=164.7

Q ss_pred             CEEEEECCCCHHHHHHHHHHHHHHH--------HCCCCEEEEECCCHHHHHHHHHHHCCC-----CCEEEEEECCCCCHH
Q ss_conf             6199844753157999999999985--------146847997152100134455543038-----976899623557235
Q gi|254780619|r  219 AVSLISGVTGSGKTEVYLEIVAAVL--------HLGKQVLILLPEISLTSAILERFQKRF-----GVKPAEWHSSLSTSM  285 (731)
Q Consensus       219 ~~~LL~GvTGSGKTEVYl~li~~~L--------~~GkqvLiLvPEI~Lt~Q~~~rl~~rF-----~~~v~v~HS~ls~~e  285 (731)
                      ...|-.+.||||||--|.-=+-.-|        ..|-+++|+.|.-.|..|++..+.++-     +..++..+-...+++
T Consensus       174 r~~lAcapTGsgKtlaf~~Pil~~L~~~~~~~~~~gl~a~Il~ptreLa~Qi~re~~k~~~~~~t~~~a~~~~~~~~~~q  253 (593)
T KOG0344         174 RDVLACAPTGSGKTLAFNLPILQHLKDLSQEKHKVGLRALILSPTRELAAQIYREMRKYSIDEGTSLRAAQFSKPAYPSQ  253 (593)
T ss_pred             CCEEEECCCCCCCHHHHHHHHHHHHHHHHCCCCCCCEEEEEECCHHHHHHHHHHHHHHCCCCCCCCHHHHHCCCCCCHHH
T ss_conf             30588635788620565569999998752035765427888444499999999999855777787534551666653110


Q ss_pred             HHHHHHHHHCCCCEEEEECCHHHH----H-----HHCCCEEEEEEECCCCCCHHCCCCCC-CHHHHHHHHHHHCCCCEEC
Q ss_conf             667899997199739994001211----0-----01000136774055321000024432-2489999975110321000
Q gi|254780619|r  286 REKIWRQVARGAISVIVGVRSALF----L-----PFKKLGLIVIDEEHDISYKQEEGILY-NARDMSIVRGKIESFPVVL  355 (731)
Q Consensus       286 R~~~w~~i~~G~~~IVIGtRSAif----~-----P~~nLglIIvDEEHd~sykq~~~pry-~aRdvA~~Ra~~~~~~lil  355 (731)
                      +.......   ..+|.|+|..-+-    .     -+.+.--.|+| |.|--+.. +..+= +|+=+...  .-.++.+=|
T Consensus       254 k~a~~~~~---k~dili~TP~ri~~~~~~~~~~idl~~V~~lV~d-EaD~lfe~-~~f~~Qla~I~sac--~s~~i~~a~  326 (593)
T KOG0344         254 KPAFLSDE---KYDILISTPMRIVGLLGLGKLNIDLSKVEWLVVD-EADLLFEP-EFFVEQLADIYSAC--QSPDIRVAL  326 (593)
T ss_pred             CCCHHHHH---HHHHHHCCHHHHHHHHCCCCCCCHHHEEEEEEEC-HHHHHHCH-HHHHHHHHHHHHHH--CCCCHHHHH
T ss_conf             33246777---8878861879999985589753201203567664-68765081-56999999999985--285222566


Q ss_pred             CCCCCCHHHHHHHHHHHHHHHCCCCCCCCCCCCCCEECCCCCCCCCCCCCCCHHHHHHHHHHHCCC--CEEEEEECCCCE
Q ss_conf             024543246775321234441243223676543321102222332224547989999998862265--517997422200
Q gi|254780619|r  356 VSATPSIESRVNGISRRYHSVHLSTRYRNSALPHLQVIDMRGQTIAQGKSLSPEMIDGIRHTLARN--EQTLLFLNRRGY  433 (731)
Q Consensus       356 gSATPSles~~~~~~g~~~~~~l~~R~~~~~~P~i~ivDm~~~~~~~~~~lS~~l~~~i~~~l~~g--~qvll~lnRrGy  433 (731)
                      =|||-+.+.=-+++.-+-.++.+   .-+..--....||  ++..-.|.  -..-+-++++-+..|  -++|||+-    
T Consensus       327 FSat~~~~VEE~~~~i~~~~~~v---ivg~~~sa~~~V~--QelvF~gs--e~~K~lA~rq~v~~g~~PP~lIfVQ----  395 (593)
T KOG0344         327 FSATISVYVEEWAELIKSDLKRV---IVGLRNSANETVD--QELVFCGS--EKGKLLALRQLVASGFKPPVLIFVQ----  395 (593)
T ss_pred             HHCCCCHHHHHHHHHHHCCCEEE---EEECCHHHHHHHH--HHHEEEEC--CHHHHHHHHHHHHCCCCCCEEEEEE----
T ss_conf             32146077999999865053368---9842525765545--55121104--3457788999986158997489885----


Q ss_pred             EHHCCCCCCCCCCCCCCCCCEEEEECCCCCCEECHHHCCCCCCCCCCCCCCCCEECCCCCCHHHHHHHHHHCCCCCHHHH
Q ss_conf             00002356543431014652012113578320000210244655566678741100135428998888520485200010
Q gi|254780619|r  434 APLTLCQVCGNRLKCLHCSCWLVEHRSKKKLYCHQCGHSAIYSQSCVVCGSSGKMIACGFGIERIAEEVCEYFPLARISI  513 (731)
Q Consensus       434 a~~~~C~~Cg~~~~C~~C~~~l~~h~~~~~l~Ch~Cg~~~~~~~~Cp~Cg~~~~l~~~G~Gte~~~e~l~~~fp~~~v~~  513 (731)
                                                                              ..--| ..+.++|. .|++.+|..
T Consensus       396 --------------------------------------------------------s~eRa-k~L~~~L~-~~~~i~v~v  417 (593)
T KOG0344         396 --------------------------------------------------------SKERA-KQLFEELE-IYDNINVDV  417 (593)
T ss_pred             --------------------------------------------------------CHHHH-HHHHHHHH-HCCCCCEEE
T ss_conf             --------------------------------------------------------38889-99999864-235766346


Q ss_pred             CCCCCCCCHHHHHHHHHHHCCCCCCEEEEEHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCC
Q ss_conf             23211358678999998621257657987044302311345201233000344310245578999998754311025667
Q gi|254780619|r  514 LSSDLEGGGGRLQLQLSAIAKGEIDIIIGTQLVAKGHNFPRMSLVGVVDGDLGLTNADLRSSERTFQLLSQVTGRAGRFG  593 (731)
Q Consensus       514 ~d~d~~~~~~~~~~~~~~~~~~~~~ilvgTq~i~kg~~fp~v~lv~il~aD~~l~~pd~ra~E~~~qll~qv~gRagr~~  593 (731)
                      +.++.  .....++.++.|+.|++.+||.|-+++.|.||-+|++|+.-|.      |.+     ..+.+.++ ||+||+.
T Consensus       418 Ih~e~--~~~qrde~~~~FR~g~IwvLicTdll~RGiDf~gvn~VInyD~------p~s-----~~syihrI-GRtgRag  483 (593)
T KOG0344         418 IHGER--SQKQRDETMERFRIGKIWVLICTDLLARGIDFKGVNLVINYDF------PQS-----DLSYIHRI-GRTGRAG  483 (593)
T ss_pred             EECCC--CHHHHHHHHHHHHCCCEEEEEEHHHHHCCCCCCCCCEEEECCC------CCH-----HHHHHHHH-HCCCCCC
T ss_conf             76366--6667789999985067068885046654556457636895378------722-----47888873-0257889


Q ss_pred             CCCEEEEEECCCC--CHHHHHH
Q ss_conf             8868999932986--4888999
Q gi|254780619|r  594 LKSLGLIQAYQPT--HPVMQAL  613 (731)
Q Consensus       594 ~~g~v~iQt~~p~--~~~~~~~  613 (731)
                      +.|+.+  |+.+|  -+.++.+
T Consensus       484 ~~g~Ai--tfytd~d~~~ir~i  503 (593)
T KOG0344         484 RSGKAI--TFYTDQDMPRIRSI  503 (593)
T ss_pred             CCCCEE--EEECCCCCHHHHHH
T ss_conf             886169--98632553455568


No 47 
>PRK09401 reverse gyrase; Reviewed
Probab=99.26  E-value=3.2e-09  Score=89.67  Aligned_cols=269  Identities=20%  Similarity=0.288  Sum_probs=155.2

Q ss_pred             CCCHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHCC---C--CC
Q ss_conf             688378999999987520489619984475315799999999998514684799715210013445554303---8--97
Q gi|254780619|r  198 ILDKNQQDVVEQVVPLCTKGFAVSLISGVTGSGKTEVYLEIVAAVLHLGKQVLILLPEISLTSAILERFQKR---F--GV  272 (731)
Q Consensus       198 ~Lt~eQ~~a~~~i~~~~~~~f~~~LL~GvTGSGKTEVYl~li~~~L~~GkqvLiLvPEI~Lt~Q~~~rl~~r---F--~~  272 (731)
                      .+..-|......+..  .   ..|-|=.=||.|||-.=+-+..-.-.+|+-+++++|.-.|..|.++|++..   +  +.
T Consensus        78 ~~w~~Qr~WakR~~~--g---~SFaiiAPTG~GKTtfgl~~sly~a~kgkks~~i~PT~~Lv~Q~~~kl~~~~~~~~~~~  152 (1176)
T PRK09401         78 EPWSLQRTWAKRLLL--G---ESFAIIAPTGVGKTTFGLVMALYLAKKGKKSYIIFPTRLLVEQVVEKLRKLAEKVGVKV  152 (1176)
T ss_pred             CCCHHHHHHHHHHHC--C---CCEEEECCCCCCHHHHHHHHHHHHHHCCCEEEEEECCHHHHHHHHHHHHHHHHHHCCCC
T ss_conf             984889999999866--8---97489888998888999999999986598399996888999999999999999709984


Q ss_pred             EEEEEECCCCCHHHHHHHHHHHCCCCEEEEECCHHHHH-------HHCCCEEEEEEECCCCCCHHCCCC-------CC--
Q ss_conf             68996235572356678999971997399940012110-------010001367740553210000244-------32--
Q gi|254780619|r  273 KPAEWHSSLSTSMREKIWRQVARGAISVIVGVRSALFL-------PFKKLGLIVIDEEHDISYKQEEGI-------LY--  336 (731)
Q Consensus       273 ~v~v~HS~ls~~eR~~~w~~i~~G~~~IVIGtRSAif~-------P~~nLglIIvDEEHd~sykq~~~p-------ry--  336 (731)
                      ++..|||+|+.++|.+...++.+|+-+|.|.|-  .|+       |=.+.++|.||+- |+-.|...+.       -|  
T Consensus       153 ~~~~y~~~~~~~~kee~~~~~~~gdfdIlitT~--~fl~kn~~~l~~~~f~fifvDDV-Ds~LKssKnid~~l~llGf~~  229 (1176)
T PRK09401        153 RLLYYHSSLKKKEKEEFLERLEEGDFDILVTTS--QFLSKNFDELPKDRFDFVFVDDV-DAVLKSSKNIDKLLKLLGFSE  229 (1176)
T ss_pred             EEEEEECCCCHHHHHHHHHHHHCCCCCEEEEEH--HHHHHHHHHCCCCCCCEEEEECH-HHHHHHHHHHHHHHHHCCCCH
T ss_conf             089985677666789999886559986899856--76765487603568888999341-877752340999999839999


Q ss_pred             CHHHHHHH------------------------HHHHCCCCEECCCCCCCHHHHHHHHHHHHHHHCCCCCCCCCCCCCCEE
Q ss_conf             24899999------------------------751103210000245432467753212344412432236765433211
Q gi|254780619|r  337 NARDMSIV------------------------RGKIESFPVVLVSATPSIESRVNGISRRYHSVHLSTRYRNSALPHLQV  392 (731)
Q Consensus       337 ~aRdvA~~------------------------Ra~~~~~~lilgSATPSles~~~~~~g~~~~~~l~~R~~~~~~P~i~i  392 (731)
                      ..-+-|+.                        ..+.....+|.+|||-...+..--.-.  .++-.  .++....---.|
T Consensus       230 e~i~~a~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~livsSAT~~prg~r~~lfr--eLlgF--evg~~~~~lRni  305 (1176)
T PRK09401        230 EDIEKAMELIKLKRKTEELKEEIEELEEKIREIRKKKKGVLVVSSATGRPRGIRIKLFR--ELLGF--EVGRPRFYLRNI  305 (1176)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCEEEEEECCCCCCCCCHHHHHH--HHHCC--CCCCCCCCEEEE
T ss_conf             99999999999752343444567788999998743687499997577788885389999--98298--678864230212


Q ss_pred             CCCCCCCCCCCCCCCHHHHHHHHHHHCCCCEEEEEECCCCEEHHCCCCCCCCCCCCCCCCCEEEEECCCCCCEECHHHCC
Q ss_conf             02222332224547989999998862265517997422200000023565434310146520121135783200002102
Q gi|254780619|r  393 IDMRGQTIAQGKSLSPEMIDGIRHTLARNEQTLLFLNRRGYAPLTLCQVCGNRLKCLHCSCWLVEHRSKKKLYCHQCGHS  472 (731)
Q Consensus       393 vDm~~~~~~~~~~lS~~l~~~i~~~l~~g~qvll~lnRrGya~~~~C~~Cg~~~~C~~C~~~l~~h~~~~~l~Ch~Cg~~  472 (731)
                      +|+..+...    +-+.+.+.+ +.|-.|  -|+|++                                           
T Consensus       306 ~D~y~~~~~----~~~~~~e~v-~~lG~G--gLifv~-------------------------------------------  335 (1176)
T PRK09401        306 VDVYIEPED----LVEKLVELV-KRLGDG--GLVFVP-------------------------------------------  335 (1176)
T ss_pred             EEEECCCCC----HHHHHHHHH-HHHCCC--EEEEEE-------------------------------------------
T ss_conf             577605766----889999999-984895--499976-------------------------------------------


Q ss_pred             CCCCCCCCCCCCCCEECCCCCCH---HHHHHHHHHCCCCCHHHHCCCCCCCCHHHHHHHHHHHCCCCCCEEEEEH----H
Q ss_conf             44655566678741100135428---9988885204852000102321135867899999862125765798704----4
Q gi|254780619|r  473 AIYSQSCVVCGSSGKMIACGFGI---ERIAEEVCEYFPLARISILSSDLEGGGGRLQLQLSAIAKGEIDIIIGTQ----L  545 (731)
Q Consensus       473 ~~~~~~Cp~Cg~~~~l~~~G~Gt---e~~~e~l~~~fp~~~v~~~d~d~~~~~~~~~~~~~~~~~~~~~ilvgTq----~  545 (731)
                                        ...|.   +++.+.|...  +.++....+   .+    .+.+++|++|++|+|||..    .
T Consensus       336 ------------------~~~g~e~~~~~~~~l~~~--g~~a~~~~~---~~----~~~le~f~~Ge~dvLvG~asyyg~  388 (1176)
T PRK09401        336 ------------------TDYGKEYAEELKEYLESH--GIKAEAYSG---RK----KEFLEKFEEGEIDVLIGVASYYGV  388 (1176)
T ss_pred             ------------------CCCCHHHHHHHHHHHHHC--CCEEEEEEC---CC----HHHHHHHHCCCCCEEEEECCCCCC
T ss_conf             ------------------765889999999999976--966999605---88----668889757886489997012452


Q ss_pred             HCCCCCCCCC
Q ss_conf             3023113452
Q gi|254780619|r  546 VAKGHNFPRM  555 (731)
Q Consensus       546 i~kg~~fp~v  555 (731)
                      ++.|+|.|.+
T Consensus       389 lvRGiDlP~~  398 (1176)
T PRK09401        389 LVRGIDLPER  398 (1176)
T ss_pred             CCCCCCCCCE
T ss_conf             1015776411


No 48 
>PRK09694 hypothetical protein; Provisional
Probab=99.26  E-value=2.1e-09  Score=91.00  Aligned_cols=312  Identities=20%  Similarity=0.192  Sum_probs=164.5

Q ss_pred             CCCHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHHHHHHHHHHCC--CCEEEEECCCHHHHHHHHHHHC----CCC
Q ss_conf             6883789999999875204896199844753157999999999985146--8479971521001344555430----389
Q gi|254780619|r  198 ILDKNQQDVVEQVVPLCTKGFAVSLISGVTGSGKTEVYLEIVAAVLHLG--KQVLILLPEISLTSAILERFQK----RFG  271 (731)
Q Consensus       198 ~Lt~eQ~~a~~~i~~~~~~~f~~~LL~GvTGSGKTEVYl~li~~~L~~G--kqvLiLvPEI~Lt~Q~~~rl~~----rF~  271 (731)
                      .-++-|+.+ +++    ..+...+.|.-.|||||||-.|-++....++|  ..+.+.+|.-+-+.+|++|+.+    .|+
T Consensus       288 ~PrplQ~~~-~~l----~~~PgL~IiEAptG~GKTEAAL~~A~~L~~~~~~~Gl~faLPT~ATaNaMf~Rv~~~~~~~~~  362 (878)
T PRK09694        288 QPRQLQTLV-DAL----PLAPGLTVIEAPTGSGKTETALAYAWKLIDQQLADSVIFALPTQATANAMLSRMEAAASKLFP  362 (878)
T ss_pred             CCCHHHHHH-HHC----CCCCCEEEEECCCCCCHHHHHHHHHHHHHHHCCCCCEEEECCHHHHHHHHHHHHHHHHHHHCC
T ss_conf             996799999-845----679987999758999758999999999997348983699774798899999999999997368


Q ss_pred             C-EEEEEECCC--CCH------------------HHHHHHHH--HHCC-CCEEEEECCH-HHH--HHHC-----CC----
Q ss_conf             7-689962355--723------------------56678999--9719-9739994001-211--0010-----00----
Q gi|254780619|r  272 V-KPAEWHSSL--STS------------------MREKIWRQ--VARG-AISVIVGVRS-ALF--LPFK-----KL----  315 (731)
Q Consensus       272 ~-~v~v~HS~l--s~~------------------eR~~~w~~--i~~G-~~~IVIGtRS-Aif--~P~~-----nL----  315 (731)
                      + .+.+.||.-  +..                  .....|..  -+++ -+.+.|||=- +++  +|++     -+    
T Consensus       363 ~~~v~LaHg~a~l~~~~~~l~~~~~~~~~~~~~~~~~~~W~~~~~Kr~LLap~~VGTiDQaLla~L~~kH~~LR~~gLa~  442 (878)
T PRK09694        363 SPNLILAHGNSRFNHLFQSIKSRAITEQGQEEAWVQCCQWLSQSNKRVFLGQIGVCTIDQVLISVLPVKHRFIRGLGIGR  442 (878)
T ss_pred             CCCEEEECCHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHCCCHHHHHCCCCEECCHHHHHHHHHCCCHHHHHHHHHCC
T ss_conf             99769744736550566651013676544543015777664111022313771546799999987461489999998628


Q ss_pred             EEEEEEECCCCC-CHHCCCCCCCHHHHHHHHHHHCCCCEECCCCCCCHH---HHHHHHHHHHHHHCCCCCCCCCCCCCCE
Q ss_conf             136774055321-000024432248999997511032100002454324---6775321234441243223676543321
Q gi|254780619|r  316 GLIVIDEEHDIS-YKQEEGILYNARDMSIVRGKIESFPVVLVSATPSIE---SRVNGISRRYHSVHLSTRYRNSALPHLQ  391 (731)
Q Consensus       316 glIIvDEEHd~s-ykq~~~pry~aRdvA~~Ra~~~~~~lilgSATPSle---s~~~~~~g~~~~~~l~~R~~~~~~P~i~  391 (731)
                      +.+||||=|-.. |-+    .|= ..+..+.+ ..++++||-|||-.-.   .+..+-.+.-.-.     .....-|-+.
T Consensus       443 kvvIiDEVHAYD~Ym~----~lL-~~lL~wl~-~~g~~viLLSATLP~~~R~~L~~ay~~~~~~~-----~~~~~YP~it  511 (878)
T PRK09694        443 SVLIVDEVHAYDAYMN----GLL-EAVLKAQA-QVGGSVILLSATLPMTQKQKLLDTYGLHTDPV-----ENNSAYPLIN  511 (878)
T ss_pred             CEEEEECCCCCCHHHH----HHH-HHHHHHHH-HCCCCEEEEECCCCHHHHHHHHHHHCCCCCCC-----CCCCCCCEEE
T ss_conf             7489725333458899----999-99999999-83998899927898999999999755688766-----6677886136


Q ss_pred             ECCC-------------------CCCCCCCCCCC-CHHHHHHHHHHHCCCCEEEEEECCCCEEHHCCCCCCCCCCCCCCC
Q ss_conf             1022-------------------22332224547-989999998862265517997422200000023565434310146
Q gi|254780619|r  392 VIDM-------------------RGQTIAQGKSL-SPEMIDGIRHTLARNEQTLLFLNRRGYAPLTLCQVCGNRLKCLHC  451 (731)
Q Consensus       392 ivDm-------------------~~~~~~~~~~l-S~~l~~~i~~~l~~g~qvll~lnRrGya~~~~C~~Cg~~~~C~~C  451 (731)
                      .++.                   .-+....+... ...+++.+.+.++.|..|+++.|.=.-|--++..    ...+...
T Consensus       512 ~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~l~~~~~~G~~v~vI~NTV~rAq~~y~~----L~~~~~~  587 (878)
T PRK09694        512 WRGVNGAQRFDLLAHQLPPRFSIQPEPICLADMLPDLTMLERMIAAANAGAQVCVICNLVDDAQVCYQR----LKELNNT  587 (878)
T ss_pred             ECCCCCCCCCCCCCCCCCCCCEEEEEEEECCCCCCCHHHHHHHHHHHHCCCEEEEEECCHHHHHHHHHH----HHHHCCC
T ss_conf             315566675344655567772378887631444764899999999997899599993889999999999----9985289


Q ss_pred             CCEE-EEECCCCCCEECHHHCCCCCCCCCCCCCCCCEECCCCCCHHHHHHHHHHCCCCCHHHHCCCCCCCCHHHHHHHHH
Q ss_conf             5201-211357832000021024465556667874110013542899888852048520001023211358678999998
Q gi|254780619|r  452 SCWL-VEHRSKKKLYCHQCGHSAIYSQSCVVCGSSGKMIACGFGIERIAEEVCEYFPLARISILSSDLEGGGGRLQLQLS  530 (731)
Q Consensus       452 ~~~l-~~h~~~~~l~Ch~Cg~~~~~~~~Cp~Cg~~~~l~~~G~Gte~~~e~l~~~fp~~~v~~~d~d~~~~~~~~~~~~~  530 (731)
                      +..+ -+|                         |.  |...  -=+++|+++-+.|-.        +..           
T Consensus       588 ~~~v~L~H-------------------------sR--F~~~--DR~~~E~~vl~~~Gk--------~~~-----------  619 (878)
T PRK09694        588 QVDIDLFH-------------------------AR--FTFN--DRREKENRVISNFGK--------NGK-----------  619 (878)
T ss_pred             CCCEEEEE-------------------------CC--CCHH--HHHHHHHHHHHHHCC--------CCC-----------
T ss_conf             98779986-------------------------88--8776--699999999998688--------988-----------


Q ss_pred             HHCCCCCCEEEEEHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCC
Q ss_conf             62125765798704430231134520123300034431024557899999875431102566788
Q gi|254780619|r  531 AIAKGEIDIIIGTQLVAKGHNFPRMSLVGVVDGDLGLTNADLRSSERTFQLLSQVTGRAGRFGLK  595 (731)
Q Consensus       531 ~~~~~~~~ilvgTq~i~kg~~fp~v~lv~il~aD~~l~~pd~ra~E~~~qll~qv~gRagr~~~~  595 (731)
                         .....||||||.|...+|         +|+|.+.  .|.--    .-+|.|=+||--|+.+.
T Consensus       620 ---r~~g~IlVaTQVvEQSLD---------iDfD~li--TDLAP----iDlLlQR~GRLhRH~R~  666 (878)
T PRK09694        620 ---RNVGRILVATQVVEQSLD---------LDFDWLI--TQHCP----ADLLFQRMGRLHRHHRK  666 (878)
T ss_pred             ---CCCCEEEEECCEEEEEEC---------CCCCHHH--CCCCC----HHHHHHHHHHHHCCCCC
T ss_conf             ---999869997733324303---------3533011--04686----99999874232058998


No 49 
>KOG0333 consensus
Probab=99.25  E-value=5.3e-09  Score=87.95  Aligned_cols=315  Identities=23%  Similarity=0.336  Sum_probs=165.1

Q ss_pred             EEEEECCCCHHHHHHHH-HHH---------H--HHHHCCCCEEEEECCCHHHHHHHH---HHHCCCCCEEEEEECCCCCH
Q ss_conf             19984475315799999-999---------9--985146847997152100134455---54303897689962355723
Q gi|254780619|r  220 VSLISGVTGSGKTEVYL-EIV---------A--AVLHLGKQVLILLPEISLTSAILE---RFQKRFGVKPAEWHSSLSTS  284 (731)
Q Consensus       220 ~~LL~GvTGSGKTEVYl-~li---------~--~~L~~GkqvLiLvPEI~Lt~Q~~~---rl~~rF~~~v~v~HS~ls~~  284 (731)
                      -.+.---||||||--++ .+.         .  .-...|.-+++|.|.=-|++|+..   .|-..+|.++...-++++--
T Consensus       284 D~igvaETgsGktaaf~ipLl~~IsslP~~~~~en~~~gpyaiilaptReLaqqIeeEt~kf~~~lg~r~vsvigg~s~E  363 (673)
T KOG0333         284 DPIGVAETGSGKTAAFLIPLLIWISSLPPMARLENNIEGPYAIILAPTRELAQQIEEETNKFGKPLGIRTVSVIGGLSFE  363 (673)
T ss_pred             CEEEEEECCCCCCCCCHHHHHHHHHCCCCCCHHHHCCCCCEEEEECHHHHHHHHHHHHHHHHCCCCCCEEEEEECCCCHH
T ss_conf             72368731677532000158899870898414442346860012033799999999999875030143289985463366


Q ss_pred             HHHHHHHHHHCCCCEEEEECCHHHHHHH-------CCCEEEEEEE---CCCCCCHHC-----C-CCCCCHH-------HH
Q ss_conf             5667899997199739994001211001-------0001367740---553210000-----2-4432248-------99
Q gi|254780619|r  285 MREKIWRQVARGAISVIVGVRSALFLPF-------KKLGLIVIDE---EHDISYKQE-----E-GILYNAR-------DM  341 (731)
Q Consensus       285 eR~~~w~~i~~G~~~IVIGtRSAif~P~-------~nLglIIvDE---EHd~sykq~-----~-~pry~aR-------dv  341 (731)
                      |.   =.++..| +.|||||..-+..-+       ....-+|.||   +-|..|-.+     + -|--|+.       +.
T Consensus       364 Eq---~fqls~g-ceiviatPgrLid~Lenr~lvl~qctyvvldeadrmiDmgfE~dv~~iL~~mPssn~k~~tde~~~~  439 (673)
T KOG0333         364 EQ---GFQLSMG-CEIVIATPGRLIDSLENRYLVLNQCTYVVLDEADRMIDMGFEPDVQKILEQMPSSNAKPDTDEKEGE  439 (673)
T ss_pred             HH---HHHHHCC-CEEEECCCHHHHHHHHHHHHHHCCCCEEECCCHHHHHCCCCCHHHHHHHHHCCCCCCCCCCCCHHHH
T ss_conf             53---0246415-4144247407888777788875058467624066654246667788899838763458886310218


Q ss_pred             HHHHHHHC-----CCCEECCCCC--CCHHHHHHHHHHHHHHHCCCCCCCCCCCCCC-EECCCCCCCCCCCCCCCHHHHHH
Q ss_conf             99975110-----3210000245--4324677532123444124322367654332-11022223322245479899999
Q gi|254780619|r  342 SIVRGKIE-----SFPVVLVSAT--PSIESRVNGISRRYHSVHLSTRYRNSALPHL-QVIDMRGQTIAQGKSLSPEMIDG  413 (731)
Q Consensus       342 A~~Ra~~~-----~~~lilgSAT--PSles~~~~~~g~~~~~~l~~R~~~~~~P~i-~ivDm~~~~~~~~~~lS~~l~~~  413 (731)
                      -.+|+.+.     ...+.| |||  |.+|-+..---.+--.++.  -..+.+.|.+ +.|-|-.+        ++. ..+
T Consensus       440 ~~~~~~~~~~k~yrqT~mf-tatm~p~verlar~ylr~pv~vti--g~~gk~~~rveQ~v~m~~e--------d~k-~kk  507 (673)
T KOG0333         440 ERVRKNFSSSKKYRQTVMF-TATMPPAVERLARSYLRRPVVVTI--GSAGKPTPRVEQKVEMVSE--------DEK-RKK  507 (673)
T ss_pred             HHHHHHCCCCCCEEEEEEE-ECCCCHHHHHHHHHHHHCCEEEEE--CCCCCCCCCHHEEEEEECC--------HHH-HHH
T ss_conf             8887510312102578998-447876799999998527769995--4678986021117888155--------688-999


Q ss_pred             HHHHHCCC--CEEEEEECCCCEEHHCCCCCCCCCCCCCCCCCEEEEECCCCCCEECHHHCCCCCCCCCCCCCCCCEECCC
Q ss_conf             98862265--5179974222000000235654343101465201211357832000021024465556667874110013
Q gi|254780619|r  414 IRHTLARN--EQTLLFLNRRGYAPLTLCQVCGNRLKCLHCSCWLVEHRSKKKLYCHQCGHSAIYSQSCVVCGSSGKMIAC  491 (731)
Q Consensus       414 i~~~l~~g--~qvll~lnRrGya~~~~C~~Cg~~~~C~~C~~~l~~h~~~~~l~Ch~Cg~~~~~~~~Cp~Cg~~~~l~~~  491 (731)
                      +.+.|+++  .++++|+|.+--        |.++++                                            
T Consensus       508 L~eil~~~~~ppiIIFvN~kk~--------~d~lAk--------------------------------------------  535 (673)
T KOG0333         508 LIEILESNFDPPIIIFVNTKKG--------ADALAK--------------------------------------------  535 (673)
T ss_pred             HHHHHHHCCCCCEEEEEECHHH--------HHHHHH--------------------------------------------
T ss_conf             9999984799987999831324--------899999--------------------------------------------


Q ss_pred             CCCHHHHHHHHHHCCCCCHHHHCCCCCCCCHHHHHHHHHHHCCCCCCEEEEEHHHCCCCCCCCCCHHHHHHHHHHHHHHH
Q ss_conf             54289988885204852000102321135867899999862125765798704430231134520123300034431024
Q gi|254780619|r  492 GFGIERIAEEVCEYFPLARISILSSDLEGGGGRLQLQLSAIAKGEIDIIIGTQLVAKGHNFPRMSLVGVVDGDLGLTNAD  571 (731)
Q Consensus       492 G~Gte~~~e~l~~~fp~~~v~~~d~d~~~~~~~~~~~~~~~~~~~~~ilvgTq~i~kg~~fp~v~lv~il~aD~~l~~pd  571 (731)
                               -|.++  +.++.++..  -++....+..|..|..+..||||+|-..+.|.|.|||.+|  +|.|..-+.-|
T Consensus       536 ---------~LeK~--g~~~~tlHg--~k~qeQRe~aL~~fr~~t~dIlVaTDvAgRGIDIpnVSlV--inydmaksieD  600 (673)
T KOG0333         536 ---------ILEKA--GYKVTTLHG--GKSQEQRENALADFREGTGDILVATDVAGRGIDIPNVSLV--INYDMAKSIED  600 (673)
T ss_pred             ---------HHHHC--CCEEEEEEC--CCCHHHHHHHHHHHHHCCCCEEEEECCCCCCCCCCCCCEE--EECCHHHHHHH
T ss_conf             ---------98644--324799617--8527789999999871578779983221257777761214--62205565899


Q ss_pred             HHHHHHHHHHHHHHHHCCCCCCCCCEEEEEECCCCC-HHHHHHHHCCHHHHHHHHHHHHHHCCCCCC
Q ss_conf             557899999875431102566788689999329864-888999958979999999999998188880
Q gi|254780619|r  572 LRSSERTFQLLSQVTGRAGRFGLKSLGLIQAYQPTH-PVMQALVSGDADSFYESEIRARESVNLPPF  637 (731)
Q Consensus       572 ~ra~E~~~qll~qv~gRagr~~~~g~v~iQt~~p~~-~~~~~~~~~d~~~f~~~el~~R~~~~~PPf  637 (731)
                      |          +-=.||.||+.+.|.++- -+.|++ .++-.|         .+.|.+--..+-||-
T Consensus       601 Y----------tHRIGRTgRAGk~GtaiS-flt~~dt~v~ydL---------kq~l~es~~s~~P~E  647 (673)
T KOG0333         601 Y----------THRIGRTGRAGKSGTAIS-FLTPADTAVFYDL---------KQALRESVKSHCPPE  647 (673)
T ss_pred             H----------HHHHCCCCCCCCCCEEEE-EECCCHHHHHHHH---------HHHHHHHHHCCCCHH
T ss_conf             9----------887423444666753689-8640111778999---------999998642269822


No 50 
>KOG0348 consensus
Probab=99.22  E-value=1.6e-09  Score=92.00  Aligned_cols=347  Identities=19%  Similarity=0.261  Sum_probs=180.1

Q ss_pred             CCCHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHHHHHHHHHH---------CCCCEEEEECCCHHHHHHHHHHHC
Q ss_conf             68837899999998752048961998447531579999999999851---------468479971521001344555430
Q gi|254780619|r  198 ILDKNQQDVVEQVVPLCTKGFAVSLISGVTGSGKTEVYLEIVAAVLH---------LGKQVLILLPEISLTSAILERFQK  268 (731)
Q Consensus       198 ~Lt~eQ~~a~~~i~~~~~~~f~~~LL~GvTGSGKTEVYl~li~~~L~---------~GkqvLiLvPEI~Lt~Q~~~rl~~  268 (731)
                      .+|.-|++++-.+...     .-.|++.-||||||.-|+--+-+.|+         .|-=+||+||.--|+.|+++-.++
T Consensus       159 ~pTsVQkq~IP~lL~g-----rD~lV~aQTGSGKTLAYllPiVq~Lq~m~~ki~Rs~G~~ALVivPTREL~~Q~y~~~qK  233 (708)
T KOG0348         159 APTSVQKQAIPVLLEG-----RDALVRAQTGSGKTLAYLLPIVQSLQAMEPKIQRSDGPYALVIVPTRELALQIYETVQK  233 (708)
T ss_pred             CCCHHHHCCHHHHHCC-----CCEEEECCCCCCCCHHHHHHHHHHHHHCCCCCCCCCCCEEEEEECHHHHHHHHHHHHHH
T ss_conf             6406765020355258-----63478857788621799999999997268655556883489980419999999999998


Q ss_pred             CCCCEEEEEECCC-CCHHHHHHHHHHHCCCCEEEEECCHHHH--------HHHCCCEEEEEEECC---CCCCHHCCCCCC
Q ss_conf             3897689962355-7235667899997199739994001211--------001000136774055---321000024432
Q gi|254780619|r  269 RFGVKPAEWHSSL-STSMREKIWRQVARGAISVIVGVRSALF--------LPFKKLGLIVIDEEH---DISYKQEEGILY  336 (731)
Q Consensus       269 rF~~~v~v~HS~l-s~~eR~~~w~~i~~G~~~IVIGtRSAif--------~P~~nLglIIvDEEH---d~sykq~~~pry  336 (731)
                      -...--.+.-..+ +...|...-.+++.| +.|+|||..-+.        .-+.+|..+|.||-.   |-.|-       
T Consensus       234 Ll~~~hWIVPg~lmGGEkkKSEKARLRKG-iNILIgTPGRLvDHLknT~~i~~s~LRwlVlDEaDrlleLGfe-------  305 (708)
T KOG0348         234 LLKPFHWIVPGVLMGGEKKKSEKARLRKG-INILIGTPGRLVDHLKNTKSIKFSRLRWLVLDEADRLLELGFE-------  305 (708)
T ss_pred             HHCCCEEEEECEEECCCCCCCHHHHHHCC-CEEEECCCHHHHHHHHCCCHHEEEEEEEEEECCHHHHHHCCCH-------
T ss_conf             72574377302122363310178887548-5489758427889874300221003568985343678762430-------


Q ss_pred             CHHHHHHHHHHH--------CC--CC----EECCCCCCCHH--HHHHHHHHHHHHHCCCCCCCCCCCCCCEECCCCCCCC
Q ss_conf             248999997511--------03--21----00002454324--6775321234441243223676543321102222332
Q gi|254780619|r  337 NARDMSIVRGKI--------ES--FP----VVLVSATPSIE--SRVNGISRRYHSVHLSTRYRNSALPHLQVIDMRGQTI  400 (731)
Q Consensus       337 ~aRdvA~~Ra~~--------~~--~~----lilgSATPSle--s~~~~~~g~~~~~~l~~R~~~~~~P~i~ivDm~~~~~  400 (731)
                        +|+....-..        +.  +|    -+|.|||-.--  -+....-..+.++.|.+-. ....|+.+-+++-....
T Consensus       306 --kdit~Il~~v~~~~~~e~~~~~lp~q~q~mLlSATLtd~V~rLa~~sLkDpv~I~ld~s~-~~~~p~~~a~~ev~~~~  382 (708)
T KOG0348         306 --KDITQILKAVHSIQNAECKDPKLPHQLQNMLLSATLTDGVNRLADLSLKDPVYISLDKSH-SQLNPKDKAVQEVDDGP  382 (708)
T ss_pred             --HHHHHHHHHHHHCCCHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCEEEECCCHH-HHCCCCHHHHHHCCCCC
T ss_conf             --039999998750020010255663787767666556777888763315685564043012-20386314566337753


Q ss_pred             CCC----CCCCHHHH----------------HHHHHHHC--CCCEEEEEECCCCEEHHCCCCCCCCCCCCCCCCCEEEEE
Q ss_conf             224----54798999----------------99988622--655179974222000000235654343101465201211
Q gi|254780619|r  401 AQG----KSLSPEMI----------------DGIRHTLA--RNEQTLLFLNRRGYAPLTLCQVCGNRLKCLHCSCWLVEH  458 (731)
Q Consensus       401 ~~~----~~lS~~l~----------------~~i~~~l~--~g~qvll~lnRrGya~~~~C~~Cg~~~~C~~C~~~l~~h  458 (731)
                      .++    ..+++.|+                ..+.+..+  ....+++|+         +            |.-..-||
T Consensus       383 ~~~~l~~~~iPeqL~qry~vVPpKLRLV~Laa~L~~~~k~~~~qk~iVF~---------S------------~~d~VeFH  441 (708)
T KOG0348         383 AGDKLDSFAIPEQLLQRYTVVPPKLRLVALAALLLNKVKFEEKQKMIVFF---------S------------CSDSVEFH  441 (708)
T ss_pred             CCCCCCCCCCCHHHHHCEEECCCCHHHHHHHHHHHHHHHHHHHCEEEEEE---------E------------CHHHHHHH
T ss_conf             45632012386876500685287410899999999986544423069999---------6------------32578999


Q ss_pred             CCCCCCEECHHHCCCCCCCCCCCCCCCCEECCCCCCHHHHHHHHHHCCCCCHHHHCCCCCCCCHHHHHHHHHHHCCCCCC
Q ss_conf             35783200002102446555666787411001354289988885204852000102321135867899999862125765
Q gi|254780619|r  459 RSKKKLYCHQCGHSAIYSQSCVVCGSSGKMIACGFGIERIAEEVCEYFPLARISILSSDLEGGGGRLQLQLSAIAKGEID  538 (731)
Q Consensus       459 ~~~~~l~Ch~Cg~~~~~~~~Cp~Cg~~~~l~~~G~Gte~~~e~l~~~fp~~~v~~~d~d~~~~~~~~~~~~~~~~~~~~~  538 (731)
                      -  ..+.|..-       ..  .-|+....-.-|         +..+|-+.++.|+.....  .......++.|+..+-.
T Consensus       442 y--~lf~~~l~-------~~--~e~~s~~~~s~g---------~~~l~~~~k~~rLHGsm~--QeeRts~f~~Fs~~~~~  499 (708)
T KOG0348         442 Y--SLFSEALL-------SH--LEGSSGAPDSEG---------LPPLFMDLKFYRLHGSME--QEERTSVFQEFSHSRRA  499 (708)
T ss_pred             H--HHHHHHHH-------CC--CCCCCCCCCCCC---------CHHHHHCCEEEEECCCHH--HHHHHHHHHHHCCCCCE
T ss_conf             9--99986540-------23--236667866679---------810331463788427434--88999998753035442


Q ss_pred             EEEEEHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEECCC-CCHHHHHHHHC
Q ss_conf             7987044302311345201233000344310245578999998754311025667886899993298-64888999958
Q gi|254780619|r  539 IIIGTQLVAKGHNFPRMSLVGVVDGDLGLTNADLRSSERTFQLLSQVTGRAGRFGLKSLGLIQAYQP-THPVMQALVSG  616 (731)
Q Consensus       539 ilvgTq~i~kg~~fp~v~lv~il~aD~~l~~pd~ra~E~~~qll~qv~gRagr~~~~g~v~iQt~~p-~~~~~~~~~~~  616 (731)
                      ||..|-..|.|+|+|+|++|+=.|+-       |-..|-    +. -.||..|....|+.++= ..| +...+.++..+
T Consensus       500 VLLcTDVAaRGLDlP~V~~vVQYd~P-------~s~ady----lH-RvGRTARaG~kG~alLf-L~P~Eaey~~~l~~~  565 (708)
T KOG0348         500 VLLCTDVAARGLDLPHVGLVVQYDPP-------FSTADY----LH-RVGRTARAGEKGEALLF-LLPSEAEYVNYLKKH  565 (708)
T ss_pred             EEEEHHHHHCCCCCCCCCEEEEECCC-------CCHHHH----HH-HHHHHHHCCCCCCEEEE-ECCCHHHHHHHHHHH
T ss_conf             78850345426888776769982799-------988999----99-84045434677715788-665179999988750


No 51 
>KOG0951 consensus
Probab=99.19  E-value=1.1e-09  Score=93.32  Aligned_cols=352  Identities=21%  Similarity=0.241  Sum_probs=189.3

Q ss_pred             CCCHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHHHHHHHHHHCCCC-----------EEEEECCCHHHHHHHHHH
Q ss_conf             688378999999987520489619984475315799999999998514684-----------799715210013445554
Q gi|254780619|r  198 ILDKNQQDVVEQVVPLCTKGFAVSLISGVTGSGKTEVYLEIVAAVLHLGKQ-----------VLILLPEISLTSAILERF  266 (731)
Q Consensus       198 ~Lt~eQ~~a~~~i~~~~~~~f~~~LL~GvTGSGKTEVYl~li~~~L~~Gkq-----------vLiLvPEI~Lt~Q~~~rl  266 (731)
                      .||..|..+.+.....    -...||-|=||+|||-|.+.-|-+.++.+.-           +-+.+|--+|...++..|
T Consensus       309 sLNrIQS~V~daAl~~----~EnmLlCAPTGaGKTNVAvLtiLqel~~h~r~dgs~nl~~fKIVYIAPmKaLVqE~Vgsf  384 (1674)
T KOG0951         309 SLNRIQSKVYDAALRG----DENMLLCAPTGAGKTNVAVLTILQELGNHLREDGSVNLAPFKIVYIAPMKALVQEMVGSF  384 (1674)
T ss_pred             HHHHHHHHHHHHHHCC----CCCEEEECCCCCCCHHHHHHHHHHHHHCCCCCCCCEECCCCEEEEEEEHHHHHHHHHHHH
T ss_conf             5667887777887557----673787426788823799999999985354544541025613799842899999999888


Q ss_pred             HCCC---CCEEEEEECCCCCHHHHHHHHHHHCCCCEEEEEC--------CHHH-HHHHCCCEEEEEEECCCCCCHHCCCC
Q ss_conf             3038---9768996235572356678999971997399940--------0121-10010001367740553210000244
Q gi|254780619|r  267 QKRF---GVKPAEWHSSLSTSMREKIWRQVARGAISVIVGV--------RSAL-FLPFKKLGLIVIDEEHDISYKQEEGI  334 (731)
Q Consensus       267 ~~rF---~~~v~v~HS~ls~~eR~~~w~~i~~G~~~IVIGt--------RSAi-f~P~~nLglIIvDEEHd~sykq~~~p  334 (731)
                      ++|+   |..|+.+.+..+-+...     +  -+..|++||        |-+= -+=.+-..|.||||=|=.  .-+.||
T Consensus       385 SkRla~~GItV~ElTgD~~l~~~q-----i--eeTQVIVtTPEKwDiITRk~gdraY~qlvRLlIIDEIHLL--hDdRGp  455 (1674)
T KOG0951         385 SKRLAPLGITVLELTGDSQLGKEQ-----I--EETQVIVTTPEKWDIITRKSGDRAYEQLVRLLIIDEIHLL--HDDRGP  455 (1674)
T ss_pred             HHHCCCCCCEEEEECCCCCCHHHH-----H--HCCEEEEECCCHHHHHHCCCCCHHHHHHHHHHHHHHHHHC--CCCCCH
T ss_conf             864235671798732654100443-----2--1220287064222211104674238888888765444321--556640


Q ss_pred             CC---CHHHHHHHHHHHCCCCEECCCCC-CCH---HHHHHHHHHHHHHHCCCCCCCCCCCCCCEECCCCCC-CCCCCCCC
Q ss_conf             32---24899999751103210000245-432---467753212344412432236765433211022223-32224547
Q gi|254780619|r  335 LY---NARDMSIVRGKIESFPVVLVSAT-PSI---ESRVNGISRRYHSVHLSTRYRNSALPHLQVIDMRGQ-TIAQGKSL  406 (731)
Q Consensus       335 ry---~aRdvA~~Ra~~~~~~lilgSAT-PSl---es~~~~~~g~~~~~~l~~R~~~~~~P~i~ivDm~~~-~~~~~~~l  406 (731)
                      --   -||-.-..-...+++.++=-||| |--   +++-.+....  +.....-++..++ .-++|..+.. +...-..+
T Consensus       456 VLESIVaRt~r~ses~~e~~RlVGLSATLPNy~DV~~Fl~v~~~g--lf~fd~syRpvPL-~qq~Igitek~~~~~~qam  532 (1674)
T KOG0951         456 VLESIVARTFRRSESTEEGSRLVGLSATLPNYEDVASFLRVDPEG--LFYFDSSYRPVPL-KQQYIGITEKKPLKRFQAM  532 (1674)
T ss_pred             HHHHHHHHHHHHHHHCCCCCEEEEECCCCCCHHHHHHHHCCCCCC--CCCCCCCCCCCCC-CCEEECCCCCCCHHHHHHH
T ss_conf             788999999998651245743641015578616557775558532--4135755576776-4147633037806777777


Q ss_pred             CHHHHHHHHHHHCCCCEEEEEECCCCEEHHCCCCCCCCCCCC--CCCCCEEEEE---CCC----CCCEECHHHCCCCCCC
Q ss_conf             989999998862265517997422200000023565434310--1465201211---357----8320000210244655
Q gi|254780619|r  407 SPEMIDGIRHTLARNEQTLLFLNRRGYAPLTLCQVCGNRLKC--LHCSCWLVEH---RSK----KKLYCHQCGHSAIYSQ  477 (731)
Q Consensus       407 S~~l~~~i~~~l~~g~qvll~lnRrGya~~~~C~~Cg~~~~C--~~C~~~l~~h---~~~----~~l~Ch~Cg~~~~~~~  477 (731)
                      -+...+++-++..+ .|||+|+.-|--..        .+++-  ..|---=|.|   ++.    ..|+|+--.  .    
T Consensus       533 Ne~~yeKVme~agk-~qVLVFVHsRKET~--------ktA~aIRd~~le~dtls~fmre~s~s~eilrtea~~--~----  597 (1674)
T KOG0951         533 NEACYEKVLEHAGK-NQVLVFVHSRKETA--------KTARAIRDKALEEDTLSRFMREDSASREILRTEAGQ--A----  597 (1674)
T ss_pred             HHHHHHHHHHHCCC-CCEEEEEEECHHHH--------HHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHC--C----
T ss_conf             89999999973787-85899998335788--------999999998864537999876344114565544420--1----


Q ss_pred             CCCCCCCCCEECCCCCCHHHHHHHHHHCCCCCHHHHCCCCCCCCHHHHHHHHHHHCCCCCCEEEEEHHHCCCCCCCCCCH
Q ss_conf             56667874110013542899888852048520001023211358678999998621257657987044302311345201
Q gi|254780619|r  478 SCVVCGSSGKMIACGFGIERIAEEVCEYFPLARISILSSDLEGGGGRLQLQLSAIAKGEIDIIIGTQLVAKGHNFPRMSL  557 (731)
Q Consensus       478 ~Cp~Cg~~~~l~~~G~Gte~~~e~l~~~fp~~~v~~~d~d~~~~~~~~~~~~~~~~~~~~~ilvgTq~i~kg~~fp~v~l  557 (731)
                      .-|+-   ..|.+.|+|+.           +|..-|-|++.      -|   +-|++|+++++|.|--+|-|.+.|.=| 
T Consensus       598 kn~dL---kdLLpygfaIH-----------hAGl~R~dR~~------~E---dLf~~g~iqvlvstatlawgvnlpaht-  653 (1674)
T KOG0951         598 KNPDL---KDLLPYGFAIH-----------HAGLNRKDREL------VE---DLFADGHIQVLVSTATLAWGVNLPAHT-  653 (1674)
T ss_pred             CCHHH---HHHHHCCCEEE-----------CCCCCCCHHHH------HH---HHHHCCCEEEEEEEHHHHHHCCCCCCE-
T ss_conf             58307---87731351331-----------16778623778------99---987448626887502456424777626-


Q ss_pred             HHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHCCCCCC--CCCEEEEEECCCC
Q ss_conf             233000344310245-578999998754311025667--8868999932986
Q gi|254780619|r  558 VGVVDGDLGLTNADL-RSSERTFQLLSQVTGRAGRFG--LKSLGLIQAYQPT  606 (731)
Q Consensus       558 v~il~aD~~l~~pd~-ra~E~~~qll~qv~gRagr~~--~~g~v~iQt~~p~  606 (731)
                      |+|=.  ...+.|+= |=.|..-+=.+|-.|||||-.  ..|+.+|-|...+
T Consensus       654 Viikg--tqvy~pekg~w~elsp~dv~qmlgragrp~~D~~gegiiit~~se  703 (1674)
T KOG0951         654 VIIKG--TQVYDPEKGRWTELSPLDVMQMLGRAGRPQYDTCGEGIIITDHSE  703 (1674)
T ss_pred             EEECC--CCCCCCCCCCCCCCCHHHHHHHHHHCCCCCCCCCCCEEECCCCHH
T ss_conf             89607--621583457666278799999975448976476786455047067


No 52 
>COG1110 Reverse gyrase [DNA replication, recombination, and repair]
Probab=99.17  E-value=4.9e-09  Score=88.22  Aligned_cols=118  Identities=27%  Similarity=0.407  Sum_probs=86.6

Q ss_pred             CCHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHCCC---C-CEE
Q ss_conf             883789999999875204896199844753157999999999985146847997152100134455543038---9-768
Q gi|254780619|r  199 LDKNQQDVVEQVVPLCTKGFAVSLISGVTGSGKTEVYLEIVAAVLHLGKQVLILLPEISLTSAILERFQKRF---G-VKP  274 (731)
Q Consensus       199 Lt~eQ~~a~~~i~~~~~~~f~~~LL~GvTGSGKTEVYl~li~~~L~~GkqvLiLvPEI~Lt~Q~~~rl~~rF---~-~~v  274 (731)
                      +-..|......+..  .+   .|-+-.=||.|||-.=+-+..-.-.+|+.+++++|.-.|..|..+|+++.-   + -++
T Consensus        83 ~ws~QR~WakR~~r--g~---SFaiiAPTGvGKTTfg~~~sl~~a~kgkr~yii~PT~~Lv~Q~~~kl~~~~e~~~~~~~  157 (1187)
T COG1110          83 PWSAQRVWAKRLVR--GK---SFAIIAPTGVGKTTFGLLMSLYLAKKGKRVYIIVPTTTLVRQVYERLKKFAEDAGSLDV  157 (1187)
T ss_pred             CHHHHHHHHHHHHC--CC---CEEEECCCCCCHHHHHHHHHHHHHHCCCEEEEEECCHHHHHHHHHHHHHHHHHCCCCCE
T ss_conf             60788999999873--78---44898278876547999999998755874999966789999999999998865378524


Q ss_pred             -EEEECCCCCHHHHHHHHHHHCCCCEEEEECCHHHHHH--H-----CCCEEEEEEEC
Q ss_conf             -9962355723566789999719973999400121100--1-----00013677405
Q gi|254780619|r  275 -AEWHSSLSTSMREKIWRQVARGAISVIVGVRSALFLP--F-----KKLGLIVIDEE  323 (731)
Q Consensus       275 -~v~HS~ls~~eR~~~w~~i~~G~~~IVIGtRSAif~P--~-----~nLglIIvDEE  323 (731)
                       .+|||.|+.++|.+...++.+|..+|+|.|-  .|++  |     .+..+|.||+-
T Consensus       158 ~~~yh~~l~~~ekee~le~i~~gdfdIlitTs--~FL~k~~e~L~~~kFdfifVDDV  212 (1187)
T COG1110         158 LVVYHSALPTKEKEEALERIESGDFDILITTS--QFLSKRFEELSKLKFDFIFVDDV  212 (1187)
T ss_pred             EEEECCCCCHHHHHHHHHHHHCCCCCEEEEEH--HHHHHHHHHHCCCCCCEEEECCH
T ss_conf             66531236657799999998659963999747--87886699840457778998047


No 53 
>PRK09751 putative ATP-dependent helicase Lhr; Provisional
Probab=99.16  E-value=4.4e-09  Score=88.59  Aligned_cols=312  Identities=20%  Similarity=0.223  Sum_probs=152.3

Q ss_pred             CCHHHHHHHHHHHHHHH-H------------CCCCEEEEECCCHHHHHHHHHHHC----------C-----CCCEEEEEE
Q ss_conf             53157999999999985-1------------468479971521001344555430----------3-----897689962
Q gi|254780619|r  227 TGSGKTEVYLEIVAAVL-H------------LGKQVLILLPEISLTSAILERFQK----------R-----FGVKPAEWH  278 (731)
Q Consensus       227 TGSGKTEVYl~li~~~L-~------------~GkqvLiLvPEI~Lt~Q~~~rl~~----------r-----F~~~v~v~H  278 (731)
                      ||||||+-++-.+-.-| .            .|-+||++-|--+|...+.++++.          +     .+..|.+.|
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             CCCCCHHHHHHHHHHHCCCCEEEEECCHHHHHH--------HCCCEEEEEEECCCCCCHHCCCCCCCHHHHHHHH--HHH
Q ss_conf             355723566789999719973999400121100--------1000136774055321000024432248999997--511
Q gi|254780619|r  279 SSLSTSMREKIWRQVARGAISVIVGVRSALFLP--------FKKLGLIVIDEEHDISYKQEEGILYNARDMSIVR--GKI  348 (731)
Q Consensus       279 S~ls~~eR~~~w~~i~~G~~~IVIGtRSAif~P--------~~nLglIIvDEEHd~sykq~~~pry~aRdvA~~R--a~~  348 (731)
                      +..+.+||..    ....-++|+|-|-=.+|+-        |.++..|||||=|.-.    .+-|=.--.+++.|  +-.
T Consensus        85 GDT~~~eR~r----~~r~PPdILITTPESL~LlLtsk~r~~L~~v~~VIVDEiHala----gsKRGahLaLsLeRL~~l~  156 (1490)
T PRK09751         85 GDTPAQERSK----LTRNPPDILITTPESLYLMLTSRARETLRGVETVIIDEVHAVA----GSKRGAHLALSLERLDALL  156 (1490)
T ss_pred             CCCCHHHHHH----HHHCCCCEEEECHHHHHHHHHHHHHHHHCCCCEEEECCCHHHH----CCCCHHHHHHHHHHHHHHC
T ss_conf             9999999999----8508998398488999998735699997799899962864420----5883999999999999865


Q ss_pred             -CCCCEECCCCCC-CHHHHHHHHHHHHHHHCCCCCCCCCCCCCCEEC----CCCCCCCCC---------C--CCCCHHHH
Q ss_conf             -032100002454-324677532123444124322367654332110----222233222---------4--54798999
Q gi|254780619|r  349 -ESFPVVLVSATP-SIESRVNGISRRYHSVHLSTRYRNSALPHLQVI----DMRGQTIAQ---------G--KSLSPEMI  411 (731)
Q Consensus       349 -~~~~lilgSATP-Sles~~~~~~g~~~~~~l~~R~~~~~~P~i~iv----Dm~~~~~~~---------~--~~lS~~l~  411 (731)
                       ..+.-|--|||= .+|.......|. .-....+ ....+..+++++    ||..-....         +  ..+-+.+.
T Consensus       157 ~~~~qRIGLSATv~p~e~vA~fLgg~-rpv~IV~-~~~~k~~~l~v~vPv~d~~~~~~~~~~~g~~~~~~~~~siw~~v~  234 (1490)
T PRK09751        157 HTSAQRIGLSATVRSASDVAAFLGGD-RPVTVVN-PPAMRHPQIRIVVPVANMDDVSSVASGTGEDSHAGREGSIWPYIE  234 (1490)
T ss_pred             CCCCCEEEEECCCCCHHHHHHHHCCC-CCEEEEC-CCCCCCCEEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHH
T ss_conf             89996899977668999999873799-9837868-888887527997046653333323567763223555453167889


Q ss_pred             HHHHHHHCCCCEEEEEECCCCEEHHCCCCCCCCCCCCCCCCCEEEEECCCCCCEECHHHCCCCCCCCCCCCCCCCEECCC
Q ss_conf             99988622655179974222000000235654343101465201211357832000021024465556667874110013
Q gi|254780619|r  412 DGIRHTLARNEQTLLFLNRRGYAPLTLCQVCGNRLKCLHCSCWLVEHRSKKKLYCHQCGHSAIYSQSCVVCGSSGKMIAC  491 (731)
Q Consensus       412 ~~i~~~l~~g~qvll~lnRrGya~~~~C~~Cg~~~~C~~C~~~l~~h~~~~~l~Ch~Cg~~~~~~~~Cp~Cg~~~~l~~~  491 (731)
                      ..|-+.+.+++.+|+|.|.|+-+-.+ |..=....              ..++     +...+.+  -+.  .. .-...
T Consensus       235 ~~i~~~i~~hrsTLVF~NTR~~AErl-~~~L~el~--------------~erl-----~~~~~~~--~~~--~~-~~~~~  289 (1490)
T PRK09751        235 TGILDEVLRHRSTIVFTNSRGLAEKL-TARLNELY--------------AARL-----QRSPSIA--VDA--AH-FESTS  289 (1490)
T ss_pred             HHHHHHHHHCCCEEEEECCHHHHHHH-HHHHHHHH--------------HHHH-----CCCCCCC--CCC--CC-CCCCC
T ss_conf             99999997268769997887999999-99999999--------------9873-----2464322--110--00-01112


Q ss_pred             CCCHHHHHHHHHHCCCCCHHHHCCCCCCCCHHHHHHHHHHHCCCCCCEEEEEHHHCCCCCCCCCCHHHHHHHHHHHHHHH
Q ss_conf             54289988885204852000102321135867899999862125765798704430231134520123300034431024
Q gi|254780619|r  492 GFGIERIAEEVCEYFPLARISILSSDLEGGGGRLQLQLSAIAKGEIDIIIGTQLVAKGHNFPRMSLVGVVDGDLGLTNAD  571 (731)
Q Consensus       492 G~Gte~~~e~l~~~fp~~~v~~~d~d~~~~~~~~~~~~~~~~~~~~~ilvgTq~i~kg~~fp~v~lv~il~aD~~l~~pd  571 (731)
                      |.++.++..     . +.-+.+...-+.+ |.....+=+.+++|+...+|.|.-+.=|.|+-.|.+|+-+.+=       
T Consensus       290 ~~~~~~~~g-----~-~~~ia~aHHGSlS-ke~R~~vE~~LK~G~LraVVaTSSLELGIDiG~VDlVVQvgsP-------  355 (1490)
T PRK09751        290 GATSNRVQS-----S-DVFIARSHHGSVS-KEQRAITEQALKSGELRCVVATSSLELGIDMGAVDLVIQVATP-------  355 (1490)
T ss_pred             CCCCCCCCC-----C-CCCCCCCCCCCCC-HHHHHHHHHHHHCCCCCEEEECCCHHHCCCCCCCCEEEEECCC-------
T ss_conf             222112356-----6-5433445557689-9999999999867997789977805407764465579980696-------


Q ss_pred             HHHHHHHHHHHHHHHHCCCCC
Q ss_conf             557899999875431102566
Q gi|254780619|r  572 LRSSERTFQLLSQVTGRAGRF  592 (731)
Q Consensus       572 ~ra~E~~~qll~qv~gRagr~  592 (731)
                           +...-+.|=+||||-.
T Consensus       356 -----~sVAs~lQRvGRAGH~  371 (1490)
T PRK09751        356 -----LSVASGLQRIGRAGHQ  371 (1490)
T ss_pred             -----HHHHHHHHHHCCCCCC
T ss_conf             -----6788999971012578


No 54 
>PRK11448 hsdR type I restriction enzyme EcoKI subunit R; Provisional
Probab=99.14  E-value=1.1e-09  Score=93.17  Aligned_cols=170  Identities=21%  Similarity=0.228  Sum_probs=113.6

Q ss_pred             CCCCHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHHHHHHHHHHCC--CCEEEEECCCHHHHHHHHHHHCCCCCEE
Q ss_conf             66883789999999875204896199844753157999999999985146--8479971521001344555430389768
Q gi|254780619|r  197 PILDKNQQDVVEQVVPLCTKGFAVSLISGVTGSGKTEVYLEIVAAVLHLG--KQVLILLPEISLTSAILERFQKRFGVKP  274 (731)
Q Consensus       197 ~~Lt~eQ~~a~~~i~~~~~~~f~~~LL~GvTGSGKTEVYl~li~~~L~~G--kqvLiLvPEI~Lt~Q~~~rl~~rF~~~v  274 (731)
                      ..|-.-|..|+..+.....++..-.||.=-||+|||.+.+.++...++.|  +-||+||=-.+|..|..+.|+..-... 
T Consensus       415 i~lR~YQ~~AI~~v~~a~~~~~rraLl~MATGTGKTrtaial~~rLlk~~~~kRILFLvDR~~L~~QA~~~F~~~~~~~-  493 (1126)
T PRK11448        415 LGLRYYQEDAIQAVEKALANGQREILLAMATGTGKTRTAIALMYRLLKAKRFKRILFLVDRRALGEQALDAFKDTKIEG-  493 (1126)
T ss_pred             CCCCHHHHHHHHHHHHHHHCCCCCEEEEECCCCCHHHHHHHHHHHHHHCCCCCEEEEECCHHHHHHHHHHHHHHCCCCC-
T ss_conf             7786889999999999998098546887248885898999999999965876725798565899999999875434545-


Q ss_pred             EEEECCCCCHHHHHHH---HHHHCCCCEEEEECCHHHH-----------HHHCCCEEEEEEECCCCCCHHCCCCC---CC
Q ss_conf             9962355723566789---9997199739994001211-----------00100013677405532100002443---22
Q gi|254780619|r  275 AEWHSSLSTSMREKIW---RQVARGAISVIVGVRSALF-----------LPFKKLGLIVIDEEHDISYKQEEGIL---YN  337 (731)
Q Consensus       275 ~v~HS~ls~~eR~~~w---~~i~~G~~~IVIGtRSAif-----------~P~~nLglIIvDEEHd~sykq~~~pr---y~  337 (731)
                           ..+-.+-|.+-   .....++.+|+|.|--++.           .|.-.-.||||||-|-+ |--+..+.   ..
T Consensus       494 -----~~~~~~~~~v~~l~~~~~~~~~rv~isT~q~m~~~i~~~~~~~~~~~~~FDlIIiDEaHRg-y~ld~em~e~e~~  567 (1126)
T PRK11448        494 -----NQTFASIYDIKGLTDKFPEDETKVHVATVQSMVKRILQSDDSEPPPVGQYDCIVVDEAHRG-YTLDKEMTEGELQ  567 (1126)
T ss_pred             -----CCCCCHHHHHHHCCCCCCCCCCEEEEECHHHHHHHHHCCCCCCCCCCCCCCEEEEECCCCC-CCCCCCCCCCHHC
T ss_conf             -----6664002200102567878777199973078998752357677999985137989778788-7433231100010


Q ss_pred             HHH----HHHHHH--HHCCCCEECCCCCCCHHHHHHHHHHHH
Q ss_conf             489----999975--110321000024543246775321234
Q gi|254780619|r  338 ARD----MSIVRG--KIESFPVVLVSATPSIESRVNGISRRY  373 (731)
Q Consensus       338 aRd----vA~~Ra--~~~~~~lilgSATPSles~~~~~~g~~  373 (731)
                      .||    +..+|+  .+.++.+|=-+|||...||-....-.|
T Consensus       568 ~rd~~s~~skyr~IldYFDA~~iGLTATP~~~T~~~Fg~P~~  609 (1126)
T PRK11448        568 FRDQLDYVSKYRRVLDYFDAVKIGLTATPALHTTEIFGEPVY  609 (1126)
T ss_pred             CCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHCCCCE
T ss_conf             232024777899998762155404767999555677099730


No 55 
>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=99.12  E-value=4e-09  Score=88.89  Aligned_cols=174  Identities=24%  Similarity=0.257  Sum_probs=117.3

Q ss_pred             HCCCHHHHHHHHHCCHHHHHHHHHCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHHHHH
Q ss_conf             09998999752455722344554102356654344666688378999999987520489619984475315799999999
Q gi|254780619|r  160 SQVSSHVIDGLKAQGVIKQIFEVISPVVDSPNLYFSLPILDKNQQDVVEQVVPLCTKGFAVSLISGVTGSGKTEVYLEIV  239 (731)
Q Consensus       160 ~~~s~~~i~~L~~kglI~~~~~~~~~~~~~~~~~~~~~~Lt~eQ~~a~~~i~~~~~~~f~~~LL~GvTGSGKTEVYl~li  239 (731)
                      .+.+...+++|.+.|+-                     .+|+=|+.++-.+...     .-.++..-||||||..|+=-+
T Consensus         4 l~L~~~ll~~l~~~g~~---------------------~pt~IQ~~~ip~il~g-----~dvi~~a~TGSGKTlay~lpi   57 (203)
T cd00268           4 LGLSPELLRGIYALGFE---------------------KPTPIQARAIPPLLSG-----RDVIGQAQTGSGKTAAFLIPI   57 (203)
T ss_pred             CCCCHHHHHHHHHCCCC---------------------CCCHHHHHHHHHHHCC-----CCEEEECCCCCCCHHHHHHHH
T ss_conf             96599999999987999---------------------9999999999999779-----988997579972228888699


Q ss_pred             HHHH-----HCCCCEEEEECCCHHHHHHHHHHHCC---CCCEEEEEECCCCCHHHHHHHHHHHCCCCEEEEECCHHHH--
Q ss_conf             9985-----14684799715210013445554303---8976899623557235667899997199739994001211--
Q gi|254780619|r  240 AAVL-----HLGKQVLILLPEISLTSAILERFQKR---FGVKPAEWHSSLSTSMREKIWRQVARGAISVIVGVRSALF--  309 (731)
Q Consensus       240 ~~~L-----~~GkqvLiLvPEI~Lt~Q~~~rl~~r---F~~~v~v~HS~ls~~eR~~~w~~i~~G~~~IVIGtRSAif--  309 (731)
                      -+.+     ..+-|+|||+|.-.|+.|+.+.|...   .+.++..++++.+-.+..   ..+.. .++|+|||-.-++  
T Consensus        58 l~~l~~~~~~~~~~alil~PTrELa~Qi~~~~~~l~~~~~i~~~~~~gg~~~~~~~---~~l~~-~~~IlI~TPgrl~~~  133 (203)
T cd00268          58 LEKLDPSPKKDGPQALILAPTRELALQIAEVARKLGKHTNLKVVVIYGGTSIDKQI---RKLKR-GPHIVVATPGRLLDL  133 (203)
T ss_pred             HHHHHCCCCCCCCEEEEEECCHHHHHHHHHHHHHHCCCCCEEEEEEECCCCHHHHH---HHHHC-CCEEEEECCHHHHHH
T ss_conf             99986166768966999968799999999999985057983899983898879999---99853-875999681899999


Q ss_pred             -----HHHCCCEEEEEEECCCCCCHHCCCCCCCHHHHHHHHHHHCCCCEECCCCCCCHHHHHHH
Q ss_conf             -----00100013677405532100002443224899999751103210000245432467753
Q gi|254780619|r  310 -----LPFKKLGLIVIDEEHDISYKQEEGILYNARDMSIVRGKIESFPVVLVSATPSIESRVNG  368 (731)
Q Consensus       310 -----~P~~nLglIIvDEEHd~sykq~~~pry~aRdvA~~Ra~~~~~~lilgSATPSles~~~~  368 (731)
                           ..+.++..+|+||-+.- +  +.+..=+...+  ++.--.+...+|-|||=+-+....+
T Consensus       134 l~~~~~~l~~l~~lVlDEAD~l-l--~~gf~~~i~~I--~~~l~~~~Q~~lfSAT~~~~v~~l~  192 (203)
T cd00268         134 LERGKLDLSKVKYLVLDEADRM-L--DMGFEDQIREI--LKLLPKDRQTLLFSATMPKEVRDLA  192 (203)
T ss_pred             HHCCCCCCCCCCEEEEECHHHH-H--HCCCHHHHHHH--HHHCCCCCEEEEEEECCCHHHHHHH
T ss_conf             9848865132248999858888-7--47769999999--9858967779999804998899999


No 56 
>KOG0342 consensus
Probab=99.12  E-value=5.8e-09  Score=87.64  Aligned_cols=326  Identities=17%  Similarity=0.148  Sum_probs=170.3

Q ss_pred             CCCHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHHH-HHHHHHH------CCCCEEEEECCCHHHHHHHHHHHCCC
Q ss_conf             6883789999999875204896199844753157999999-9999851------46847997152100134455543038
Q gi|254780619|r  198 ILDKNQQDVVEQVVPLCTKGFAVSLISGVTGSGKTEVYLE-IVAAVLH------LGKQVLILLPEISLTSAILERFQKRF  270 (731)
Q Consensus       198 ~Lt~eQ~~a~~~i~~~~~~~f~~~LL~GvTGSGKTEVYl~-li~~~L~------~GkqvLiLvPEI~Lt~Q~~~rl~~rF  270 (731)
                      .+|.-|+..+..+....     -.|-..-||||||--+|- +++..++      .|-.|+|+.|.=-|+-|+.+-.+.-.
T Consensus       104 ~MT~VQ~~ti~pll~gk-----Dvl~~AKTGtGKTlAFLiPaie~l~k~~~~~r~~~~vlIi~PTRELA~Q~~~eak~Ll  178 (543)
T KOG0342         104 TMTPVQQKTIPPLLEGK-----DVLAAAKTGTGKTLAFLLPAIELLRKLKFKPRNGTGVLIICPTRELAMQIFAEAKELL  178 (543)
T ss_pred             CCHHHHHHHCCCCCCCC-----CCEEEECCCCCCEEEEHHHHHHHHHHCCCCCCCCEEEEEECCCHHHHHHHHHHHHHHH
T ss_conf             00288874267667984-----3124512688741010468999998536577787148996562899998999999999


Q ss_pred             CCEEEEEE-CCCCCHHHHHHHHHHHCCCCEEEEECCHHHHH--------HHCCCEEEEEEECCCCCCHHCCCCCCCHHHH
Q ss_conf             97689962-35572356678999971997399940012110--------0100013677405532100002443224899
Q gi|254780619|r  271 GVKPAEWH-SSLSTSMREKIWRQVARGAISVIVGVRSALFL--------PFKKLGLIVIDEEHDISYKQEEGILYNARDM  341 (731)
Q Consensus       271 ~~~v~v~H-S~ls~~eR~~~w~~i~~G~~~IVIGtRSAif~--------P~~nLglIIvDEEHd~sykq~~~pry~aRdv  341 (731)
                      ...-..+- .-++...|...-.++.. .+.|+|.|..-+.-        -++|+...|+||.---   .+.+++=+...+
T Consensus       179 ~~h~~~~v~~viGG~~~~~e~~kl~k-~~niliATPGRLlDHlqNt~~f~~r~~k~lvlDEADrl---Ld~GF~~di~~I  254 (543)
T KOG0342         179 KYHESITVGIVIGGNNFSVEADKLVK-GCNILIATPGRLLDHLQNTSGFLFRNLKCLVLDEADRL---LDIGFEEDVEQI  254 (543)
T ss_pred             HHCCCCCEEEEECCCCCHHHHHHHHC-CCCEEEECCCHHHHHHHCCCCCHHHCCCEEEEECCHHH---HHCCCHHHHHHH
T ss_conf             72767734787677410589997515-55278867841776765578412212203575020356---652518889999


Q ss_pred             HHHHHHHCCCCEECCCCCCCHHHHHHHHHHHHHHHCCCCCCCCCCCCCCEECCCCCCCCCCCCCCCHHHHHHHHHHHCCC
Q ss_conf             99975110321000024543246775321234441243223676543321102222332224547989999998862265
Q gi|254780619|r  342 SIVRGKIESFPVVLVSATPSIESRVNGISRRYHSVHLSTRYRNSALPHLQVIDMRGQTIAQGKSLSPEMIDGIRHTLARN  421 (731)
Q Consensus       342 A~~Ra~~~~~~lilgSATPSles~~~~~~g~~~~~~l~~R~~~~~~P~i~ivDm~~~~~~~~~~lS~~l~~~i~~~l~~g  421 (731)
                      --..-  .+..-.|=|||-+-+.--.+      .+.|..+     .--|.++|-+..                 .+-++.
T Consensus       255 i~~lp--k~rqt~LFSAT~~~kV~~l~------~~~L~~d-----~~~v~~~d~~~~-----------------~The~l  304 (543)
T KOG0342         255 IKILP--KQRQTLLFSATQPSKVKDLA------RGALKRD-----PVFVNVDDGGER-----------------ETHERL  304 (543)
T ss_pred             HHHCC--CCCCEEEEECCCCHHHHHHH------HHHHCCC-----CEEEECCCCCCC-----------------CHHHCC
T ss_conf             87523--55304676478968899999------8763377-----468624789973-----------------023246


Q ss_pred             CEEEEEECCCCEEHHCCCCCCCCCCCCCCCCCEEEEE-CCCCCCEECHHHCCCCCCCCCCCCCCCCEECCCCCCHHHHHH
Q ss_conf             5179974222000000235654343101465201211-357832000021024465556667874110013542899888
Q gi|254780619|r  422 EQTLLFLNRRGYAPLTLCQVCGNRLKCLHCSCWLVEH-RSKKKLYCHQCGHSAIYSQSCVVCGSSGKMIACGFGIERIAE  500 (731)
Q Consensus       422 ~qvll~lnRrGya~~~~C~~Cg~~~~C~~C~~~l~~h-~~~~~l~Ch~Cg~~~~~~~~Cp~Cg~~~~l~~~G~Gte~~~e  500 (731)
                      +|-           +++|..=.+        ..+.|+ .+.+.     -.  +.+--.||.|.+.. +         ..+
T Consensus       305 ~Qg-----------yvv~~~~~~--------f~ll~~~LKk~~-----~~--~KiiVF~sT~~~vk-~---------~~~  348 (543)
T KOG0342         305 EQG-----------YVVAPSDSR--------FSLLYTFLKKNI-----KR--YKIIVFFSTCMSVK-F---------HAE  348 (543)
T ss_pred             CCE-----------EEECCCCCH--------HHHHHHHHHHHC-----CC--CEEEEEECHHHHHH-H---------HHH
T ss_conf             640-----------796265411--------799999999734-----77--24999933026799-9---------999


Q ss_pred             HHHHCCCCCHHHHCCCCCCCCHHHHHHHHHHHCCCCCCEEEEEHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             85204852000102321135867899999862125765798704430231134520123300034431024557899999
Q gi|254780619|r  501 EVCEYFPLARISILSSDLEGGGGRLQLQLSAIAKGEIDIIIGTQLVAKGHNFPRMSLVGVVDGDLGLTNADLRSSERTFQ  580 (731)
Q Consensus       501 ~l~~~fp~~~v~~~d~d~~~~~~~~~~~~~~~~~~~~~ilvgTq~i~kg~~fp~v~lv~il~aD~~l~~pd~ra~E~~~q  580 (731)
                      .|+  .-+.+|..+.+-.+..  .......+|.+-+..|||.|-..|.|+|||+|++|+=+|.      ||=+.     |
T Consensus       349 lL~--~~dlpv~eiHgk~~Q~--kRT~~~~~F~kaesgIL~cTDVaARGlD~P~V~~VvQ~~~------P~d~~-----~  413 (543)
T KOG0342         349 LLN--YIDLPVLEIHGKQKQN--KRTSTFFEFCKAESGILVCTDVAARGLDIPDVDWVVQYDP------PSDPE-----Q  413 (543)
T ss_pred             HHH--HCCCCHHHHHCCCCCC--CCCHHHHHHHHCCCCEEEECCHHHCCCCCCCCEEEEEECC------CCCHH-----H
T ss_conf             985--0687532442578532--2023899886106643996032213688888407998589------99989-----9


Q ss_pred             HHHHHHHCCCCCCCCCEEEEEECCCCCHHHHHHH
Q ss_conf             8754311025667886899993298648889999
Q gi|254780619|r  581 LLSQVTGRAGRFGLKSLGLIQAYQPTHPVMQALV  614 (731)
Q Consensus       581 ll~qv~gRagr~~~~g~v~iQt~~p~~~~~~~~~  614 (731)
                      .++ =.||.||..+.|+.++--.--+-+.++++.
T Consensus       414 YIH-RvGRTaR~gk~G~alL~l~p~El~Flr~LK  446 (543)
T KOG0342         414 YIH-RVGRTAREGKEGKALLLLAPWELGFLRYLK  446 (543)
T ss_pred             HHH-HHCCCCCCCCCCEEEEEECHHHHHHHHHHH
T ss_conf             898-732122368986389996766778999986


No 57 
>KOG0335 consensus
Probab=99.01  E-value=1.1e-07  Score=77.85  Aligned_cols=326  Identities=19%  Similarity=0.171  Sum_probs=167.2

Q ss_pred             CCCHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHHH-HHHHHHHC------------CCCEEEEECCCHHHHHHHH
Q ss_conf             6883789999999875204896199844753157999999-99998514------------6847997152100134455
Q gi|254780619|r  198 ILDKNQQDVVEQVVPLCTKGFAVSLISGVTGSGKTEVYLE-IVAAVLHL------------GKQVLILLPEISLTSAILE  264 (731)
Q Consensus       198 ~Lt~eQ~~a~~~i~~~~~~~f~~~LL~GvTGSGKTEVYl~-li~~~L~~------------GkqvLiLvPEI~Lt~Q~~~  264 (731)
                      ..|+-|+.++..|...     .-.+-.+=||||||--||- ++...+..            +-++|||+|.=.|.-|++.
T Consensus        96 ~ptpvQk~sip~i~~G-----rdlmacAqTGsGKT~aFLiPii~~~~~~~~~~~~~~~~~~~P~~lIlapTReL~~Qi~n  170 (482)
T KOG0335          96 KPTPVQKYSIPIISGG-----RDLMACAQTGSGKTAAFLIPIISYLLDEGPEDRGESGGGVYPRALILAPTRELVDQIYN  170 (482)
T ss_pred             CCCCCEECCCCEEECC-----CCEEEECCCCCCCHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCEEEEECCHHHHHHHHH
T ss_conf             8986156042244258-----84278825788513788888999998648656665677889725998173787667888


Q ss_pred             HHHCCC---CCEEEEEECCCCCHHHHHHHHHHHCCCCEEEEECCHHHH-------HHHCCCEEEEEEECCCCCCHHC-CC
Q ss_conf             543038---976899623557235667899997199739994001211-------0010001367740553210000-24
Q gi|254780619|r  265 RFQKRF---GVKPAEWHSSLSTSMREKIWRQVARGAISVIVGVRSALF-------LPFKKLGLIVIDEEHDISYKQE-EG  333 (731)
Q Consensus       265 rl~~rF---~~~v~v~HS~ls~~eR~~~w~~i~~G~~~IVIGtRSAif-------~P~~nLglIIvDEEHd~sykq~-~~  333 (731)
                      +-++.-   +.++.++-.+  ...+ .+...+.+ ..+|+++|---+-       .-+.+++.+|+||-- -  --+ .+
T Consensus       171 ea~k~~~~s~~~~~~~ygg--~~~~-~q~~~~~~-gcdIlvaTpGrL~d~~e~g~i~l~~~k~~vLDEAD-r--MlD~mg  243 (482)
T KOG0335         171 EARKFSYLSGMKSVVVYGG--TDLG-AQLRFIKR-GCDILVATPGRLKDLIERGKISLDNCKFLVLDEAD-R--MLDEMG  243 (482)
T ss_pred             HHHHHCCCCCCEEEEEECC--CCHH-HHHHHHCC-CCCEEEECCCHHHHHHHCCEEEHHHCCEEEECCHH-H--HHHHCC
T ss_conf             8876402212203300578--4454-42233325-75578855750564554151126238589952367-7--666326


Q ss_pred             CCCCHHHHHHHHHH---HCCCCEECCCCCCCHHHHHHHHHHHHHHHCCCCCCCCCCCCCCEECCCCCCCCCCCCCCCHHH
Q ss_conf             43224899999751---103210000245432467753212344412432236765433211022223322245479899
Q gi|254780619|r  334 ILYNARDMSIVRGK---IESFPVVLVSATPSIESRVNGISRRYHSVHLSTRYRNSALPHLQVIDMRGQTIAQGKSLSPEM  410 (731)
Q Consensus       334 pry~aRdvA~~Ra~---~~~~~lilgSATPSles~~~~~~g~~~~~~l~~R~~~~~~P~i~ivDm~~~~~~~~~~lS~~l  410 (731)
                      +-=+.|.+-..-.+   ...-++.| |||=+-+.-..                                           
T Consensus       244 F~p~Ir~Iv~~~~~~~~~~~qt~mF-SAtfp~~iq~l-------------------------------------------  279 (482)
T KOG0335         244 FEPQIRKIVEQLGMPPKNNRQTLLF-SATFPKEIQRL-------------------------------------------  279 (482)
T ss_pred             CCHHHHHHHCCCCCCCCCCEEEEEE-ECCCCHHHHHH-------------------------------------------
T ss_conf             6620799962558887466137887-35577566644-------------------------------------------


Q ss_pred             HHHHHHHHCCCCEEEEEECCCCEEHHCCCCCCCCCCCCCCCCCEEEEECCCCCCEECHHHCCCCCCCCCCCCC-----CC
Q ss_conf             9999886226551799742220000002356543431014652012113578320000210244655566678-----74
Q gi|254780619|r  411 IDGIRHTLARNEQTLLFLNRRGYAPLTLCQVCGNRLKCLHCSCWLVEHRSKKKLYCHQCGHSAIYSQSCVVCG-----SS  485 (731)
Q Consensus       411 ~~~i~~~l~~g~qvll~lnRrGya~~~~C~~Cg~~~~C~~C~~~l~~h~~~~~l~Ch~Cg~~~~~~~~Cp~Cg-----~~  485 (731)
                         +...+..+ .+++-+-|-|-++       ..+.+|    +..+.   +...+|+.=.-- ....-||.=+     ..
T Consensus       280 ---~~~fl~~~-yi~laV~rvg~~~-------~ni~q~----i~~V~---~~~kr~~Lldll-~~~~~~~~~~~~~~e~t  340 (482)
T KOG0335         280 ---AADFLKDN-YIFLAVGRVGSTS-------ENITQK----ILFVN---EMEKRSKLLDLL-NKDDGPPSDGEPKWEKT  340 (482)
T ss_pred             ---HHHHHHHC-CEEEEEEEECCCC-------CCCEEE----EEEEC---CHHHHHHHHHHH-HCCCCCCCCCCCCCCEE
T ss_conf             ---78876415-1388875304666-------563467----66421---113578999886-13467866577643138


Q ss_pred             CEECCCCCCHHHHHHHHHHCCCCCHHHHCCCCCCCCHHHHHHHHHHHCCCCCCEEEEEHHHCCCCCCCCCCHHHHHHHHH
Q ss_conf             11001354289988885204852000102321135867899999862125765798704430231134520123300034
Q gi|254780619|r  486 GKMIACGFGIERIAEEVCEYFPLARISILSSDLEGGGGRLQLQLSAIAKGEIDIIIGTQLVAKGHNFPRMSLVGVVDGDL  565 (731)
Q Consensus       486 ~~l~~~G~Gte~~~e~l~~~fp~~~v~~~d~d~~~~~~~~~~~~~~~~~~~~~ilvgTq~i~kg~~fp~v~lv~il~aD~  565 (731)
                      .-|...--+.-.++..|...+-.  ..-+..|  .+....+..++.|+.|...+||.|-+.|.|+|+|+|+-|+..|.=.
T Consensus       341 lvFvEt~~~~d~l~~~l~~~~~~--~~sIhg~--~tq~er~~al~~Fr~g~~pvlVaT~VaaRGlDi~~V~hVInyDmP~  416 (482)
T KOG0335         341 LVFVETKRGADELAAFLSSNGYP--AKSIHGD--RTQIEREQALNDFRNGKAPVLVATNVAARGLDIPNVKHVINYDMPA  416 (482)
T ss_pred             EEEEECCHHHHHHHHHHHCCCCC--CEEECCH--HHHHHHHHHHHHHHCCCCCEEEEEHHHHCCCCCCCCCEEEEEECCC
T ss_conf             99961300326999998617987--4560332--5563799998776469866798703665478876874358863675


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEECCCCCHHHHHHH
Q ss_conf             4310245578999998754311025667886899993298648889999
Q gi|254780619|r  566 GLTNADLRSSERTFQLLSQVTGRAGRFGLKSLGLIQAYQPTHPVMQALV  614 (731)
Q Consensus       566 ~l~~pd~ra~E~~~qll~qv~gRagr~~~~g~v~iQt~~p~~~~~~~~~  614 (731)
                      .  +.||          .-=.||.||.+..|++.--...++..+.+.|.
T Consensus       417 d--~d~Y----------vHRIGRTGR~Gn~G~atsf~n~~~~~i~~~L~  453 (482)
T KOG0335         417 D--IDDY----------VHRIGRTGRVGNGGRATSFFNEKNQNIAKALV  453 (482)
T ss_pred             C--HHHH----------HHHCCCCCCCCCCCEEEEEECCCCCHHHHHHH
T ss_conf             2--4667----------77415435577773268876474300689999


No 58 
>pfam04851 ResIII Type III restriction enzyme, res subunit.
Probab=99.00  E-value=1.6e-09  Score=91.93  Aligned_cols=64  Identities=33%  Similarity=0.412  Sum_probs=56.9

Q ss_pred             CCCHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHH
Q ss_conf             688378999999987520489619984475315799999999998514684799715210013445554
Q gi|254780619|r  198 ILDKNQQDVVEQVVPLCTKGFAVSLISGVTGSGKTEVYLEIVAAVLHLGKQVLILLPEISLTSAILERF  266 (731)
Q Consensus       198 ~Lt~eQ~~a~~~i~~~~~~~f~~~LL~GvTGSGKTEVYl~li~~~L~~GkqvLiLvPEI~Lt~Q~~~rl  266 (731)
                      .|.+.|+++++.+...     ...++..-||||||.+.+.+++...+.++.+||+||...|..|+.++|
T Consensus         3 ~LR~yQ~~a~~~~~~~-----~~~~i~~pTGsGKT~~~~~~i~~~~~~~~~~lvlvp~~~L~~Q~~~~~   66 (103)
T pfam04851         3 ELRPYQIEAIRNLLEK-----KRGLIVMATGSGKTLTAAKLIARLLKGKKKVLFLVPRKDLLEQALEEF   66 (103)
T ss_pred             CCCHHHHHHHHHHHHC-----CCEEEEECCCCCHHHHHHHHHHHHHHCCCCEEEEECCHHHHHHHHHHH
T ss_conf             8729999999999963-----986999589998799999999999846992999908299999999965


No 59 
>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=99.00  E-value=4.1e-08  Score=81.13  Aligned_cols=328  Identities=22%  Similarity=0.238  Sum_probs=180.4

Q ss_pred             EEEECCCCHHHHHHHHHHHHH---HHHCCC--CEEEEECCCHHHHHHHHHHHC----CCCC--EEEEEEC------CCC-
Q ss_conf             998447531579999999999---851468--479971521001344555430----3897--6899623------557-
Q gi|254780619|r  221 SLISGVTGSGKTEVYLEIVAA---VLHLGK--QVLILLPEISLTSAILERFQK----RFGV--KPAEWHS------SLS-  282 (731)
Q Consensus       221 ~LL~GvTGSGKTEVYl~li~~---~L~~Gk--qvLiLvPEI~Lt~Q~~~rl~~----rF~~--~v~v~HS------~ls-  282 (731)
                      .+|.-=||+||||..|-.+.+   .++++.  .+++.+|-=+.+-.|..|+++    -||+  .+...||      ..+ 
T Consensus         2 ~v~~APTG~GKTe~aL~~A~~sah~~k~~~~~~~I~alP~r~~~na~~~r~~~sash~Fg~P~~~~~~~ssrfnh~~~~i   81 (424)
T TIGR01587         2 LVIEAPTGYGKTEAALLWALKSAHLIKKQKADKVIFALPTRVTINAMYRRLKESASHLFGSPELVLLLHSSRFNHLASSI   81 (424)
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHHHHHHHHHCCEEEECCHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHHH
T ss_conf             68861789987899999998636664224440101220268889999999998677541785432334552267899999


Q ss_pred             ------CHHHHHHHHHH----HCCCCEEEE----------------ECCHHHH----HHHCCC--EEEEEEECCCCCCHH
Q ss_conf             ------23566789999----719973999----------------4001211----001000--136774055321000
Q gi|254780619|r  283 ------TSMREKIWRQV----ARGAISVIV----------------GVRSALF----LPFKKL--GLIVIDEEHDISYKQ  330 (731)
Q Consensus       283 ------~~eR~~~w~~i----~~G~~~IVI----------------GtRSAif----~P~~nL--glIIvDEEHd~sykq  330 (731)
                            ...--..|..+    ..+..++..                ++-|+-|    .-..++  .+||+||=|  .|  
T Consensus        82 k~~~~~~~~d~~~~~~~~~~~~~~~~~~~~~pi~~~T~d~~~~~~~~~ssGs~~~~~~~~~~~~~S~~i~DE~h--~y--  157 (424)
T TIGR01587        82 KLRKIKEKGDSEELEKLVKLYIHSNKKLFLKPITVCTIDQVLKSVFGESSGSFGHYEITLASIANSLIIFDEVH--AY--  157 (424)
T ss_pred             HHHHHHCCCCHHHHHHHHHHHCCCCHHEEECCCCCCCHHHHHEEEECCCCCCCHHHHHHHHHHHHHHHHHHHHH--HH--
T ss_conf             98776304782799999985224212101317885341220000005534452056888877776765625367--77--


Q ss_pred             CCCCCCCHHHHHHHHHH-HCCCCEECCCCCCCHHHHHHHHHHHHHHHCCCCCCCCCCCCCCE------ECCC--------
Q ss_conf             02443224899999751-10321000024543246775321234441243223676543321------1022--------
Q gi|254780619|r  331 EEGILYNARDMSIVRGK-IESFPVVLVSATPSIESRVNGISRRYHSVHLSTRYRNSALPHLQ------VIDM--------  395 (731)
Q Consensus       331 ~~~pry~aRdvA~~Ra~-~~~~~lilgSATPSles~~~~~~g~~~~~~l~~R~~~~~~P~i~------ivDm--------  395 (731)
                      ++.+.=+.--+|+.+.+ .-+.|++|-|||=+.+ +..-....+....+...-....+-.++      -.|+        
T Consensus       158 ~~~~~~~~~l~~L~~~~~~~~~~~~lMsATlP~~-~~~~l~~~~~~~~~~~~~~~~~~~~~~GvnGaqrfdllahPe~~~  236 (424)
T TIGR01587       158 EEYTLALTILAALEVLKIDNDVKILLMSATLPRE-LKKFLKEYLEKIEYVEENELLDLKEVEGVNGAQRFDLLAHPEFKE  236 (424)
T ss_pred             HHHHHHHHHHHHHHHHHHHCCCCEEEEECCCCHH-HHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCHHHHHHHCCCHHHH
T ss_conf             6425555699999999987389889984056757-899999873104763333557866435464202333321720210


Q ss_pred             -CCCCC-----CCCCCCCHHHHHHH-HHHHCCCCEEEEEECCCCEEHHCCCCCCCCCCCCCCCCCEEEEECCCCCCEECH
Q ss_conf             -22332-----22454798999999-886226551799742220000002356543431014652012113578320000
Q gi|254780619|r  396 -RGQTI-----AQGKSLSPEMIDGI-RHTLARNEQTLLFLNRRGYAPLTLCQVCGNRLKCLHCSCWLVEHRSKKKLYCHQ  468 (731)
Q Consensus       396 -~~~~~-----~~~~~lS~~l~~~i-~~~l~~g~qvll~lnRrGya~~~~C~~Cg~~~~C~~C~~~l~~h~~~~~l~Ch~  468 (731)
                       |.+..     ..........++.| -+.+.++.+++|++|.=+-|-.                                
T Consensus       237 ~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ii~NtV~~A~~--------------------------------  284 (424)
T TIGR01587       237 KRFENHRISLIEKDKVGEISSLERLLLEELKKGGKVLIIVNTVDRAQE--------------------------------  284 (424)
T ss_pred             HHHHCCCCCHHHHHCCCCHHHHHHHHHHHCCCCCCEEEEEECHHHHHH--------------------------------
T ss_conf             022157642134320331346666778741577866999854389999--------------------------------


Q ss_pred             HHCCCCCCCCCCCCCCCCEECCCCCCHHHHHHHHHHCCCCCH-HHHCCC-----CCCCCHHHHHHHHHHHCC-----CCC
Q ss_conf             210244655566678741100135428998888520485200-010232-----113586789999986212-----576
Q gi|254780619|r  469 CGHSAIYSQSCVVCGSSGKMIACGFGIERIAEEVCEYFPLAR-ISILSS-----DLEGGGGRLQLQLSAIAK-----GEI  537 (731)
Q Consensus       469 Cg~~~~~~~~Cp~Cg~~~~l~~~G~Gte~~~e~l~~~fp~~~-v~~~d~-----d~~~~~~~~~~~~~~~~~-----~~~  537 (731)
                                                   ++..+++.-|... |.-+.+     |. ..|++-...+..|.+     ++.
T Consensus       285 -----------------------------~Y~~~kE~~p~~~~~~L~HsRF~~~DR-~~KEde~~~l~e~~~S~~~~~~~  334 (424)
T TIGR01587       285 -----------------------------FYQKLKEKAPELEEVILLHSRFTEKDR-AKKEDEAELLKELKKSAWKDNEK  334 (424)
T ss_pred             -----------------------------HHHHHHHCCCCCCCEEEEECCCCHHHH-HHHHHHHHHHHHHHCCCCCCCCC
T ss_conf             -----------------------------999985126520021244044770036-67767999999851013544577


Q ss_pred             CEEEEEHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCC-C-----EEEEEECCCCCHHHH
Q ss_conf             5798704430231134520123300034431024557899999875431102566788-6-----899993298648889
Q gi|254780619|r  538 DIIIGTQLVAKGHNFPRMSLVGVVDGDLGLTNADLRSSERTFQLLSQVTGRAGRFGLK-S-----LGLIQAYQPTHPVMQ  611 (731)
Q Consensus       538 ~ilvgTq~i~kg~~fp~v~lv~il~aD~~l~~pd~ra~E~~~qll~qv~gRagr~~~~-g-----~v~iQt~~p~~~~~~  611 (731)
                      -|+|+||+|.-|+|         +|+|.+..  |.-    ....|.|=.||.-|.+++ |     +|+|-|-.+++.-..
T Consensus       335 ~v~V~TQv~E~SlD---------~s~D~~iT--e~a----P~d~LiQR~GR~~R~~~~~~d~~~~~~y~~~~~~~~~e~a  399 (424)
T TIGR01587       335 FVIVATQVIEVSLD---------ISVDVMIT--ELA----PIDSLIQRLGRLNRYGRKIGDIENREVYILTILLEDKELA  399 (424)
T ss_pred             EEEEEEEEEEEEEE---------CCCCHHHH--HCC----CHHHHHHHHHHHCCCCCCCCCCCCCCEEEEEECCCCCCCC
T ss_conf             06998787888642---------04441343--115----0123355421110113565788987203785257888756


Q ss_pred             HHHHCCHHHHHHHHHHHHHH
Q ss_conf             99958979999999999998
Q gi|254780619|r  612 ALVSGDADSFYESEIRARES  631 (731)
Q Consensus       612 ~~~~~d~~~f~~~el~~R~~  631 (731)
                       -...|--.+|..++-+|-.
T Consensus       400 -ry~~~~~~~~~~~~~~~T~  418 (424)
T TIGR01587       400 -RYKDDRHLVYPYELVERTI  418 (424)
T ss_pred             -CCCCCCCCCCCHHHHHHHH
T ss_conf             -4224564116567789899


No 60 
>COG4096 HsdR Type I site-specific restriction-modification system, R (restriction) subunit and related helicases [Defense mechanisms]
Probab=98.98  E-value=1.3e-08  Score=84.90  Aligned_cols=323  Identities=19%  Similarity=0.195  Sum_probs=178.9

Q ss_pred             CCCCCHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHHHHHHHHHHCC--CCEEEEECCCHHHHHHHHHHHCCCCCE
Q ss_conf             666883789999999875204896199844753157999999999985146--847997152100134455543038976
Q gi|254780619|r  196 LPILDKNQQDVVEQVVPLCTKGFAVSLISGVTGSGKTEVYLEIVAAVLHLG--KQVLILLPEISLTSAILERFQKRFGVK  273 (731)
Q Consensus       196 ~~~Lt~eQ~~a~~~i~~~~~~~f~~~LL~GvTGSGKTEVYl~li~~~L~~G--kqvLiLvPEI~Lt~Q~~~rl~~rF~~~  273 (731)
                      ...+-.-|+.|+..+.....++-.-.||-=-||+|||-..+.+|...++.|  |.||+|+=--+|..|.+.-|...+++.
T Consensus       163 ~i~~RyyQ~~AI~rv~Eaf~~g~~raLlvMATGTGKTrTAiaii~rL~r~~~~KRVLFLaDR~~Lv~QA~~af~~~~P~~  242 (875)
T COG4096         163 AIGPRYYQIIAIRRVIEAFSKGQNRALLVMATGTGKTRTAIAIIDRLIKSGWVKRVLFLADRNALVDQAYGAFEDFLPFG  242 (875)
T ss_pred             CCCCHHHHHHHHHHHHHHHHCCCCEEEEEEECCCCCCEEHHHHHHHHHHCCHHHEEEEEECHHHHHHHHHHHHHHHCCCC
T ss_conf             33622788999999999986687448999705888523199999999961414305676126789999999999639886


Q ss_pred             --EEEEECCCCCHHHHHHHHHHHCCCCEEEEECCHHHH----------HHHCC--CEEEEEEECCCCCCHHCCCC--CCC
Q ss_conf             --899623557235667899997199739994001211----------00100--01367740553210000244--322
Q gi|254780619|r  274 --PAEWHSSLSTSMREKIWRQVARGAISVIVGVRSALF----------LPFKK--LGLIVIDEEHDISYKQEEGI--LYN  337 (731)
Q Consensus       274 --v~v~HS~ls~~eR~~~w~~i~~G~~~IVIGtRSAif----------~P~~n--LglIIvDEEHd~sykq~~~p--ry~  337 (731)
                        .-.......            .+...|.++|--++.          -||.-  ..||||||-|-++|+..++.  +|+
T Consensus       243 ~~~n~i~~~~~------------~~s~~i~lsTyqt~~~~~~~~~~~~~~f~~g~FDlIvIDEaHRgi~~~~~~I~dYFd  310 (875)
T COG4096         243 TKMNKIEDKKG------------DTSSEIYLSTYQTMTGRIEQKEDEYRRFGPGFFDLIVIDEAHRGIYSEWSSILDYFD  310 (875)
T ss_pred             CCEEEECCCCC------------CCCEEEEEEEHHHHHHHHHCCCCCCCCCCCCCEEEEEECHHHHHHHHHHHHHHHHHH
T ss_conf             40123201467------------863058876037787564065456556788831289960666667876678988999


Q ss_pred             HHHHHHHHHHHCCCCEECCCCCCCH----HHHHHHHHHHHH-HHCCCCCCCCCCC--CCCEECCCCCCCCCCCCC---CC
Q ss_conf             4899999751103210000245432----467753212344-4124322367654--332110222233222454---79
Q gi|254780619|r  338 ARDMSIVRGKIESFPVVLVSATPSI----ESRVNGISRRYH-SVHLSTRYRNSAL--PHLQVIDMRGQTIAQGKS---LS  407 (731)
Q Consensus       338 aRdvA~~Ra~~~~~~lilgSATPSl----es~~~~~~g~~~-~~~l~~R~~~~~~--P~i~ivDm~~~~~~~~~~---lS  407 (731)
                      |.-            ++| +|||--    .||--. +|.-. .+.+.+-+...-+  +++.-|+.+.  ...|..   +|
T Consensus       311 A~~------------~gL-TATP~~~~d~~T~~~F-~g~Pt~~YsleeAV~DG~Lvpy~vi~i~~~~--~~~G~~~~~~s  374 (875)
T COG4096         311 AAT------------QGL-TATPKETIDRSTYGFF-NGEPTYAYSLEEAVEDGFLVPYKVIRIDTDF--DLDGWKPDAGS  374 (875)
T ss_pred             HHH------------HHH-CCCCCCCCCCCCCCCC-CCCCCEEECHHHHHHCCCCCCCCCEEEEEEC--CCCCCCCCCCC
T ss_conf             988------------761-2576211132310133-7970224128888521545788633766431--56674767552


Q ss_pred             HHHHHHHHHHHCCCCEEEEEECCCCEEHHCCCCCCCCCCCCCCCCCEEEEECCCCCCE----ECHHHCC--CC-CCCCCC
Q ss_conf             8999999886226551799742220000002356543431014652012113578320----0002102--44-655566
Q gi|254780619|r  408 PEMIDGIRHTLARNEQTLLFLNRRGYAPLTLCQVCGNRLKCLHCSCWLVEHRSKKKLY----CHQCGHS--AI-YSQSCV  480 (731)
Q Consensus       408 ~~l~~~i~~~l~~g~qvll~lnRrGya~~~~C~~Cg~~~~C~~C~~~l~~h~~~~~l~----Ch~Cg~~--~~-~~~~Cp  480 (731)
                      + -.+...+.+...++.   -+++-+...+.|..                   .+..+    -+||-..  -. ++.+--
T Consensus       375 e-rek~~g~~i~~dd~~---~~~~d~dr~~v~~~-------------------~~~~V~r~~~e~l~~~~~g~~~~KTIv  431 (875)
T COG4096         375 E-REKLQGEAIDEDDQN---FEARDFDRTLVIPF-------------------RTETVARELTEYLKRGATGDEIGKTIV  431 (875)
T ss_pred             H-HHHHHCCCCCCCCCC---CCCCCCCHHEECCC-------------------HHHHHHHHHHHHHCCCCCCCCCCCEEE
T ss_conf             3-233313436865446---33355320000312-------------------478999999998425668886684589


Q ss_pred             CCCCCCEECCCCCCHHHHHHHHHHCCCCCH---HHHCCCCCCCCHHHHHHHHHHHCC--CCCCEEEEEHHHCCCCCCCCC
Q ss_conf             678741100135428998888520485200---010232113586789999986212--576579870443023113452
Q gi|254780619|r  481 VCGSSGKMIACGFGIERIAEEVCEYFPLAR---ISILSSDLEGGGGRLQLQLSAIAK--GEIDIIIGTQLVAKGHNFPRM  555 (731)
Q Consensus       481 ~Cg~~~~l~~~G~Gte~~~e~l~~~fp~~~---v~~~d~d~~~~~~~~~~~~~~~~~--~~~~ilvgTq~i~kg~~fp~v  555 (731)
                      -|.+.       .-.|++.+.+.+.||+.+   +..+..|....+.    .+..|..  .-|.|.|.--|+.-|.|.|.|
T Consensus       432 Fa~n~-------dHAe~i~~~~~~~ype~~~~~a~~IT~d~~~~q~----~Id~f~~ke~~P~IaitvdlL~TGiDvpev  500 (875)
T COG4096         432 FAKNH-------DHAERIREALVNEYPEYNGRYAMKITGDAEQAQA----LIDNFIDKEKYPRIAITVDLLTTGVDVPEV  500 (875)
T ss_pred             EEECC-------HHHHHHHHHHHHHCCCCCCCEEEEEECCCHHHHH----HHHHHHHCCCCCCEEEEHHHHHCCCCCHHE
T ss_conf             96270-------7899999999874801067459998444065689----999887437898358761245427876220


Q ss_pred             CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCC
Q ss_conf             0123300034431024557899999875431102566
Q gi|254780619|r  556 SLVGVVDGDLGLTNADLRSSERTFQLLSQVTGRAGRF  592 (731)
Q Consensus       556 ~lv~il~aD~~l~~pd~ra~E~~~qll~qv~gRagr~  592 (731)
                      -+++.        .-+-||--++.    |..||.-|-
T Consensus       501 ~nlVF--------~r~V~SktkF~----QMvGRGTRl  525 (875)
T COG4096         501 VNLVF--------DRKVRSKTKFK----QMVGRGTRL  525 (875)
T ss_pred             EEEEE--------HHHHHHHHHHH----HHHCCCCCC
T ss_conf             45643--------14446689999----986676543


No 61 
>PRK11664 ATP-dependent RNA helicase HrpB; Provisional
Probab=98.96  E-value=1.1e-07  Score=77.97  Aligned_cols=70  Identities=19%  Similarity=0.263  Sum_probs=52.1

Q ss_pred             HHHHHHHHHC-CCCEEEEECCCHHHHHHHHHHHCCCCC--EEEEEECCCCCHHHHHHHHHHHCCCCEEEEECC
Q ss_conf             9999998514-684799715210013445554303897--689962355723566789999719973999400
Q gi|254780619|r  236 LEIVAAVLHL-GKQVLILLPEISLTSAILERFQKRFGV--KPAEWHSSLSTSMREKIWRQVARGAISVIVGVR  305 (731)
Q Consensus       236 l~li~~~L~~-GkqvLiLvPEI~Lt~Q~~~rl~~rF~~--~v~v~HS~ls~~eR~~~w~~i~~G~~~IVIGtR  305 (731)
                      ..++...+.. .+.+|+-+|-+.-..++.++++++++.  .+..+||.|+.++...++.....|.-+||+.|-
T Consensus       201 ~~~i~~~~~~~~G~iLvFLPG~~EI~~~~~~L~~~~~~~~~i~pL~g~l~~~~Q~~~~~~~~~g~rKvIlaTn  273 (812)
T PRK11664        201 AVATAELLRQESGSLLLFLPGVGEIQRVQEQLASRVGSDVLLCPLYGALSLAEQQKAILPAPAGMRKVVLATN  273 (812)
T ss_pred             HHHHHHHHHCCCCCEEEECCCHHHHHHHHHHHHHHCCCCEEEEECCCCCCHHHHHHHHCCCCCCCEEEEEECC
T ss_conf             9999999735899889976998999999999863355780899644789988987760679999537999502


No 62 
>KOG0346 consensus
Probab=98.93  E-value=8.9e-09  Score=86.24  Aligned_cols=385  Identities=21%  Similarity=0.248  Sum_probs=182.8

Q ss_pred             HHHCCCHHHHHHHHHCCHHHHHHHHHCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHHH
Q ss_conf             77099989997524557223445541023566543446666883789999999875204896199844753157999999
Q gi|254780619|r  158 RASQVSSHVIDGLKAQGVIKQIFEVISPVVDSPNLYFSLPILDKNQQDVVEQVVPLCTKGFAVSLISGVTGSGKTEVYLE  237 (731)
Q Consensus       158 ~~~~~s~~~i~~L~~kglI~~~~~~~~~~~~~~~~~~~~~~Lt~eQ~~a~~~i~~~~~~~f~~~LL~GvTGSGKTEVYl~  237 (731)
                      ...+..+..++++.+.||-+.                     |--|+.|+--+   .+.+  -.+-..-||||||--|+-
T Consensus        22 e~~gLD~RllkAi~~lG~ekp---------------------TlIQs~aIpla---LEgK--DvvarArTGSGKT~AYli   75 (569)
T KOG0346          22 EEFGLDSRLLKAITKLGWEKP---------------------TLIQSSAIPLA---LEGK--DVVARARTGSGKTAAYLI   75 (569)
T ss_pred             HHHCCCHHHHHHHHHHCCCCC---------------------CHHHHCCCCHH---HCCC--CEEEEECCCCCCHHHHHH
T ss_conf             871888899999997176776---------------------23443221243---2486--314652268871378899


Q ss_pred             -HHHHHHH--------CCCCEEEEECCCHHHHHHHHHHHCC---CC--CEEEEEECCCCCHHHHHHHHHHHCCCCEEEEE
Q ss_conf             -9999851--------4684799715210013445554303---89--76899623557235667899997199739994
Q gi|254780619|r  238 -IVAAVLH--------LGKQVLILLPEISLTSAILERFQKR---FG--VKPAEWHSSLSTSMREKIWRQVARGAISVIVG  303 (731)
Q Consensus       238 -li~~~L~--------~GkqvLiLvPEI~Lt~Q~~~rl~~r---F~--~~v~v~HS~ls~~eR~~~w~~i~~G~~~IVIG  303 (731)
                       +++..|+        +|-+++||||.--|+.|.+..+.+-   .+  .+++-+.|.++++.-. +   +..+.++||||
T Consensus        76 Pllqkll~~k~t~~~e~~~sa~iLvPTkEL~qQvy~viekL~~~c~k~lr~~nl~s~~sdsv~~-~---~L~d~pdIvV~  151 (569)
T KOG0346          76 PLLQKLLAEKKTNDGEQGPSAVILVPTKELAQQVYKVIEKLVEYCSKDLRAINLASSMSDSVNS-V---ALMDLPDIVVA  151 (569)
T ss_pred             HHHHHHHHHHHCCCCCCCCEEEEEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHH-H---HHCCCCCEEEE
T ss_conf             9999999764036432463069992509999999999999999878765554210331167778-8---87059975871


Q ss_pred             CCHHHH--------HHHCCCEEEEEEECCCC--CCHHCCCCCCCHHHHHHHHHHH-CCCCEECCCCCCCHHHHHH---HH
Q ss_conf             001211--------00100013677405532--1000024432248999997511-0321000024543246775---32
Q gi|254780619|r  304 VRSALF--------LPFKKLGLIVIDEEHDI--SYKQEEGILYNARDMSIVRGKI-ESFPVVLVSATPSIESRVN---GI  369 (731)
Q Consensus       304 tRSAif--------~P~~nLglIIvDEEHd~--sykq~~~pry~aRdvA~~Ra~~-~~~~lilgSATPSles~~~---~~  369 (731)
                      |.+-+.        .+...|...||||- |-  ||      -|. -|+--.+..+ -.+..+|.|||-|-..-..   +.
T Consensus       152 TP~~ll~~~~~~~~~~~~~l~~LVvDEA-DLllsf------GYe-edlk~l~~~LPr~~Q~~LmSATl~dDv~~LKkL~l  223 (569)
T KOG0346         152 TPAKLLRHLAAGVLEYLDSLSFLVVDEA-DLLLSF------GYE-EDLKKLRSHLPRIYQCFLMSATLSDDVQALKKLFL  223 (569)
T ss_pred             CHHHHHHHHHHCCCHHHHHEEEEEECHH-HHHHHC------CCH-HHHHHHHHHCCCHHHHEEEHHHHHHHHHHHHHHHC
T ss_conf             7188999986063021201025785035-666423------608-88999987488256502003135567999999751


Q ss_pred             HHHHHHHCCCCC--CCCCCCCCCEECCCCCCCCCCCCCCCHHHHHHHHHHHCCCCEEEEEECC--CCEEHHCCCCCCCCC
Q ss_conf             123444124322--3676543321102222332224547989999998862265517997422--200000023565434
Q gi|254780619|r  370 SRRYHSVHLSTR--YRNSALPHLQVIDMRGQTIAQGKSLSPEMIDGIRHTLARNEQTLLFLNR--RGYAPLTLCQVCGNR  445 (731)
Q Consensus       370 ~g~~~~~~l~~R--~~~~~~P~i~ivDm~~~~~~~~~~lS~~l~~~i~~~l~~g~qvll~lnR--rGya~~~~C~~Cg~~  445 (731)
                      .+-. .++|++-  .+...+-+..+.   -+  +...+  --+...++-.|-+| ..|||+|.  |||-=-+.-..-|-.
T Consensus       224 ~nPv-iLkl~e~el~~~dqL~Qy~v~---cs--e~DKf--lllyallKL~LI~g-KsliFVNtIdr~YrLkLfLeqFGik  294 (569)
T KOG0346         224 HNPV-ILKLTEGELPNPDQLTQYQVK---CS--EEDKF--LLLYALLKLRLIRG-KSLIFVNTIDRCYRLKLFLEQFGIK  294 (569)
T ss_pred             CCCE-EEEECCCCCCCCCCCEEEEEE---EC--CCHHH--HHHHHHHHHHHHCC-CEEEEEECHHHHHHHHHHHHHHCCH
T ss_conf             6976-898326668984522589997---03--53068--89999999988627-5499985002468899999980737


Q ss_pred             CCCCCCCCEEEEECCCCCCEECHHHCCCCCCCCCCCCCCCCEECCCC--CCHHHHHHHHHHCCCCCHHHHCCCCCCCCHH
Q ss_conf             31014652012113578320000210244655566678741100135--4289988885204852000102321135867
Q gi|254780619|r  446 LKCLHCSCWLVEHRSKKKLYCHQCGHSAIYSQSCVVCGSSGKMIACG--FGIERIAEEVCEYFPLARISILSSDLEGGGG  523 (731)
Q Consensus       446 ~~C~~C~~~l~~h~~~~~l~Ch~Cg~~~~~~~~Cp~Cg~~~~l~~~G--~Gte~~~e~l~~~fp~~~v~~~d~d~~~~~~  523 (731)
                      ..--  ++-|     .-.-+||.-.   ++..     |..+.++...  .-+++++|+.+.-=    -..-+.+..+++.
T Consensus       295 sciL--NseL-----P~NSR~Hii~---QFNk-----G~YdivIAtD~s~~~~~~eee~kgk~----~e~~~kndkkskk  355 (569)
T KOG0346         295 SCIL--NSEL-----PANSRCHIIE---QFNK-----GLYDIVIATDDSADGDKLEEEVKGKS----DEKNPKNDKKSKK  355 (569)
T ss_pred             HHHH--CCCC-----CCCCHHHHHH---HHHC-----CCEEEEEECCCCCCHHHHHCCCCCCC----CCCCCCCCCCCCC
T ss_conf             6652--5646-----6432122898---8607-----61159997067641355521112544----4568877421244


Q ss_pred             HHHHHHHHHCCCCCCEEEEEHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEC
Q ss_conf             89999986212576579870443023113452012330003443102455789999987543110256678868999932
Q gi|254780619|r  524 RLQLQLSAIAKGEIDIIIGTQLVAKGHNFPRMSLVGVVDGDLGLTNADLRSSERTFQLLSQVTGRAGRFGLKSLGLIQAY  603 (731)
Q Consensus       524 ~~~~~~~~~~~~~~~ilvgTq~i~kg~~fp~v~lv~il~aD~~l~~pd~ra~E~~~qll~qv~gRagr~~~~g~v~iQt~  603 (731)
                      +.        +.|.       =++.|.||.+|..|.  |.|.--         .+-+ +.--+||.+|+.++|.++-- -
T Consensus       356 K~--------D~E~-------GVsRGIDF~~V~~Vl--NFD~P~---------t~~s-YIHRvGRTaRg~n~GtalSf-v  407 (569)
T KOG0346         356 KL--------DKES-------GVSRGIDFHHVSNVL--NFDFPE---------TVTS-YIHRVGRTARGNNKGTALSF-V  407 (569)
T ss_pred             CC--------CCHH-------CHHCCCCCHHEEEEE--ECCCCC---------CHHH-HHHHCCCCCCCCCCCCEEEE-E
T ss_conf             45--------7011-------212165401211456--137898---------5478-88861222347898725999-6


Q ss_pred             CCCCHHHHHHHHCCHHHHHHHHHHHHHHCCCCCCHHE
Q ss_conf             9864888999958979999999999998188880118
Q gi|254780619|r  604 QPTHPVMQALVSGDADSFYESEIRARESVNLPPFGRL  640 (731)
Q Consensus       604 ~p~~~~~~~~~~~d~~~f~~~el~~R~~~~~PPf~~~  640 (731)
                      .|....    ...+-+.+...|-..+..--+-||...
T Consensus       408 ~P~e~~----g~~~le~~~~d~~~~~~~qilqPY~f~  440 (569)
T KOG0346         408 SPKEEF----GKESLESILKDENRQEGRQILQPYQFR  440 (569)
T ss_pred             CCHHHH----HHHHHHHHHHHHHHHCCCCCCCCCCCH
T ss_conf             646776----066799997437764274204665100


No 63 
>KOG0338 consensus
Probab=98.92  E-value=1.4e-07  Score=76.98  Aligned_cols=290  Identities=21%  Similarity=0.285  Sum_probs=142.9

Q ss_pred             CCCCHHHHHHHHH-HHHHHHHCCC-----CEEEEECCCHHHHHHHHHHH---CCCCCEEEEEECCCCCHHHHHHHHHHHC
Q ss_conf             4753157999999-9999851468-----47997152100134455543---0389768996235572356678999971
Q gi|254780619|r  225 GVTGSGKTEVYLE-IVAAVLHLGK-----QVLILLPEISLTSAILERFQ---KRFGVKPAEWHSSLSTSMREKIWRQVAR  295 (731)
Q Consensus       225 GvTGSGKTEVYl~-li~~~L~~Gk-----qvLiLvPEI~Lt~Q~~~rl~---~rF~~~v~v~HS~ls~~eR~~~w~~i~~  295 (731)
                      .+||||||--|+- .++..|-+-+     .||||||.--|+.|....++   +...-.+.+--++|+-++-    ..+..
T Consensus       225 A~TGsGKTAAF~lPiLERLlYrPk~~~~TRVLVL~PTRELaiQv~sV~~qlaqFt~I~~~L~vGGL~lk~Q----E~~LR  300 (691)
T KOG0338         225 AATGSGKTAAFALPILERLLYRPKKVAATRVLVLVPTRELAIQVHSVTKQLAQFTDITVGLAVGGLDLKAQ----EAVLR  300 (691)
T ss_pred             ECCCCCCHHHHHHHHHHHHHCCCCCCCCEEEEEEECCHHHHHHHHHHHHHHHHHCCCEEEEEECCCCHHHH----HHHHH
T ss_conf             11468711456788999985273567612699983508999999999999876604024445247457889----99983


Q ss_pred             CCCEEEEECCHHHH--------HHHCCCEEEEEEECCCCCCHHCCCCCCCHHHHHHHHHHHCCCCEECCCCCCCHHHHHH
Q ss_conf             99739994001211--------0010001367740553210000244322489999975110321000024543246775
Q gi|254780619|r  296 GAISVIVGVRSALF--------LPFKKLGLIVIDEEHDISYKQEEGILYNARDMSIVRGKIESFPVVLVSATPSIESRVN  367 (731)
Q Consensus       296 G~~~IVIGtRSAif--------~P~~nLglIIvDEEHd~sykq~~~pry~aRdvA~~Ra~~~~~~lilgSATPSles~~~  367 (731)
                      ..++|||.|..-+.        .-+.|+...|+||-. --  -++++.=.--+  ++|.--.+-.-.|=|||.+-|.--+
T Consensus       301 s~PDIVIATPGRlIDHlrNs~sf~ldsiEVLvlDEAD-RM--LeegFademnE--ii~lcpk~RQTmLFSATMteeVkdL  375 (691)
T KOG0338         301 SRPDIVIATPGRLIDHLRNSPSFNLDSIEVLVLDEAD-RM--LEEGFADEMNE--IIRLCPKNRQTMLFSATMTEEVKDL  375 (691)
T ss_pred             HCCCEEEECCHHHHHHHCCCCCCCCCCEEEEEECHHH-HH--HHHHHHHHHHH--HHHHCCCCCCCEEEHHHHHHHHHHH
T ss_conf             0898799465058887515887653432577733388-89--99999999999--9985510230012112257889999


Q ss_pred             HHHHHHHHHCCCCCCCCCCCCCCEECCC--------CCCCCC--CCC-CCCHH-HHHHHHHHHCCCCEEEEEECCCCEEH
Q ss_conf             3212344412432236765433211022--------223322--245-47989-99999886226551799742220000
Q gi|254780619|r  368 GISRRYHSVHLSTRYRNSALPHLQVIDM--------RGQTIA--QGK-SLSPE-MIDGIRHTLARNEQTLLFLNRRGYAP  435 (731)
Q Consensus       368 ~~~g~~~~~~l~~R~~~~~~P~i~ivDm--------~~~~~~--~~~-~lS~~-l~~~i~~~l~~g~qvll~lnRrGya~  435 (731)
                      +      .+.|.+       |---.||-        ++|...  .++ ..-+. +...+..+..+  .+++|+-++-.  
T Consensus       376 ~------slSL~k-------Pvrifvd~~~~~a~~LtQEFiRIR~~re~dRea~l~~l~~rtf~~--~~ivFv~tKk~--  438 (691)
T KOG0338         376 A------SLSLNK-------PVRIFVDPNKDTAPKLTQEFIRIRPKREGDREAMLASLITRTFQD--RTIVFVRTKKQ--  438 (691)
T ss_pred             H------HHHCCC-------CEEEEECCCCCCCHHHHHHHHEECCCCCCCCHHHHHHHHHHHCCC--CEEEEEEHHHH--
T ss_conf             9------755179-------858985786544404447781005564444178999999876043--36999720877--


Q ss_pred             HCCCCCCCCCCCCCCCCCEEEEECCCCCCEECHHHCCCCCCCCCCCCCCCCEECCCC-CCHHHHHHHHHHCCCCCHHHHC
Q ss_conf             002356543431014652012113578320000210244655566678741100135-4289988885204852000102
Q gi|254780619|r  436 LTLCQVCGNRLKCLHCSCWLVEHRSKKKLYCHQCGHSAIYSQSCVVCGSSGKMIACG-FGIERIAEEVCEYFPLARISIL  514 (731)
Q Consensus       436 ~~~C~~Cg~~~~C~~C~~~l~~h~~~~~l~Ch~Cg~~~~~~~~Cp~Cg~~~~l~~~G-~Gte~~~e~l~~~fp~~~v~~~  514 (731)
                                                                    |+ ..+ +-+| .|.  -.-||+..+..      
T Consensus       439 ----------------------------------------------AH-Rl~-IllGLlgl--~agElHGsLtQ------  462 (691)
T KOG0338         439 ----------------------------------------------AH-RLR-ILLGLLGL--KAGELHGSLTQ------  462 (691)
T ss_pred             ----------------------------------------------HH-HHH-HHHHHHHC--HHHHHCCCCCH------
T ss_conf             ----------------------------------------------88-999-99987301--06655054108------


Q ss_pred             CCCCCCCHHHHHHHHHHHCCCCCCEEEEEHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCC
Q ss_conf             32113586789999986212576579870443023113452012330003443102455789999987543110256678
Q gi|254780619|r  515 SSDLEGGGGRLQLQLSAIAKGEIDIIIGTQLVAKGHNFPRMSLVGVVDGDLGLTNADLRSSERTFQLLSQVTGRAGRFGL  594 (731)
Q Consensus       515 d~d~~~~~~~~~~~~~~~~~~~~~ilvgTq~i~kg~~fp~v~lv~il~aD~~l~~pd~ra~E~~~qll~qv~gRagr~~~  594 (731)
                              ...-..+++|.++++|+||.|-..+.|+|+++|..|+-.++      |  ++.|   +.++.| ||..|+.+
T Consensus       463 --------~QRlesL~kFk~~eidvLiaTDvAsRGLDI~gV~tVINy~m------P--~t~e---~Y~HRV-GRTARAGR  522 (691)
T KOG0338         463 --------EQRLESLEKFKKEEIDVLIATDVASRGLDIEGVQTVINYAM------P--KTIE---HYLHRV-GRTARAGR  522 (691)
T ss_pred             --------HHHHHHHHHHHHCCCCEEEEECHHHCCCCCCCEEEEEECCC------C--HHHH---HHHHHH-HHHHHCCC
T ss_conf             --------88999999877456877987204444677655168884267------5--2689---999874-00332456


Q ss_pred             CCEEEEEECCCCCHHHHHHHHC
Q ss_conf             8689999329864888999958
Q gi|254780619|r  595 KSLGLIQAYQPTHPVMQALVSG  616 (731)
Q Consensus       595 ~g~v~iQt~~p~~~~~~~~~~~  616 (731)
                      .|+-+----.-|-.+++.+.+.
T Consensus       523 aGrsVtlvgE~dRkllK~iik~  544 (691)
T KOG0338         523 AGRSVTLVGESDRKLLKEIIKS  544 (691)
T ss_pred             CCCEEEEECCCCHHHHHHHHHH
T ss_conf             7643787445408899999851


No 64 
>KOG0343 consensus
Probab=98.89  E-value=1.7e-07  Score=76.34  Aligned_cols=313  Identities=21%  Similarity=0.288  Sum_probs=165.3

Q ss_pred             HCCCHHHHHHHHHCCHHHHHHHHHCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHHHHH
Q ss_conf             09998999752455722344554102356654344666688378999999987520489619984475315799999999
Q gi|254780619|r  160 SQVSSHVIDGLKAQGVIKQIFEVISPVVDSPNLYFSLPILDKNQQDVVEQVVPLCTKGFAVSLISGVTGSGKTEVYLEIV  239 (731)
Q Consensus       160 ~~~s~~~i~~L~~kglI~~~~~~~~~~~~~~~~~~~~~~Lt~eQ~~a~~~i~~~~~~~f~~~LL~GvTGSGKTEVYl~li  239 (731)
                      +.+|....+.|.+.+++.                     +|+-|+..+--.    -++ .-.|=-.-||||||.-++--+
T Consensus        74 lpls~~t~kgLke~~fv~---------------------~teiQ~~~Ip~a----L~G-~DvlGAAkTGSGKTLAFlvPv  127 (758)
T KOG0343          74 LPLSQKTLKGLKEAKFVK---------------------MTEIQRDTIPMA----LQG-HDVLGAAKTGSGKTLAFLVPV  127 (758)
T ss_pred             CCCCHHHHHHHHHCCCCC---------------------HHHHHHHHCCHH----CCC-CCCCCCCCCCCCCEEEEHHHH
T ss_conf             887667887676548756---------------------999987641422----057-500010235888446543999


Q ss_pred             HHHHH-------CCCCEEEEECCCHHHHHHHHHHHCC---CCCEEEEEECCCCCHHHHHHHHHHHCCCCEEEEECCHHHH
Q ss_conf             99851-------4684799715210013445554303---8976899623557235667899997199739994001211
Q gi|254780619|r  240 AAVLH-------LGKQVLILLPEISLTSAILERFQKR---FGVKPAEWHSSLSTSMREKIWRQVARGAISVIVGVRSALF  309 (731)
Q Consensus       240 ~~~L~-------~GkqvLiLvPEI~Lt~Q~~~rl~~r---F~~~v~v~HS~ls~~eR~~~w~~i~~G~~~IVIGtRSAif  309 (731)
                      -+.|-       -|-.|||.-|.--|+.|++.-+...   -+....+.-++   ++  -.+.+-+-.+..|+|+|..-++
T Consensus       128 lE~L~r~kWs~~DGlGalIISPTRELA~QtFevL~kvgk~h~fSaGLiiGG---~~--~k~E~eRi~~mNILVCTPGRLL  202 (758)
T KOG0343         128 LEALYRLKWSPTDGLGALIISPTRELALQTFEVLNKVGKHHDFSAGLIIGG---KD--VKFELERISQMNILVCTPGRLL  202 (758)
T ss_pred             HHHHHHCCCCCCCCCEEEEECCHHHHHHHHHHHHHHHHHCCCCCCCEEECC---CH--HHHHHHHHHCCCEEEECHHHHH
T ss_conf             999997177887883269956529999999999998752056431136657---12--6889976625776996617899


Q ss_pred             --------HHHCCCEEEEEEECC---CCCCHHCCCCCCCHHHHHHHHHHHCCCC----EECCCCCCCHHH--HHHHHHHH
Q ss_conf             --------001000136774055---3210000244322489999975110321----000024543246--77532123
Q gi|254780619|r  310 --------LPFKKLGLIVIDEEH---DISYKQEEGILYNARDMSIVRGKIESFP----VVLVSATPSIES--RVNGISRR  372 (731)
Q Consensus       310 --------~P~~nLglIIvDEEH---d~sykq~~~pry~aRdvA~~Ra~~~~~~----lilgSATPSles--~~~~~~g~  372 (731)
                              .--.||.+.|.||..   |..||-.-            -+-.++.|    .+|=|||++-.+  +.+.--..
T Consensus       203 QHmde~~~f~t~~lQmLvLDEADR~LDMGFk~tL------------~~Ii~~lP~~RQTLLFSATqt~svkdLaRLsL~d  270 (758)
T KOG0343         203 QHMDENPNFSTSNLQMLVLDEADRMLDMGFKKTL------------NAIIENLPKKRQTLLFSATQTKSVKDLARLSLKD  270 (758)
T ss_pred             HHHHHCCCCCCCCCEEEEECCHHHHHHHHHHHHH------------HHHHHHCCHHHEEEEEECCCCHHHHHHHHHHCCC
T ss_conf             8754167878776047873208889877678889------------9998737723304666325511399999753479


Q ss_pred             HHHHCCCCCCCCCCCC----CCEECCCCCCCCCCCCCCCHHHHHHHHHHHCCCCEEEEEECCCCEEHHCCCCCCCCCCCC
Q ss_conf             4441243223676543----321102222332224547989999998862265517997422200000023565434310
Q gi|254780619|r  373 YHSVHLSTRYRNSALP----HLQVIDMRGQTIAQGKSLSPEMIDGIRHTLARNEQTLLFLNRRGYAPLTLCQVCGNRLKC  448 (731)
Q Consensus       373 ~~~~~l~~R~~~~~~P----~i~ivDm~~~~~~~~~~lS~~l~~~i~~~l~~g~qvll~lnRrGya~~~~C~~Cg~~~~C  448 (731)
                      +.++...+.... ..|    +..++ |.-+     . --..|..-|+.+++.+  .|+|+.                   
T Consensus       271 P~~vsvhe~a~~-atP~~L~Q~y~~-v~l~-----~-Ki~~L~sFI~shlk~K--~iVF~S-------------------  321 (758)
T KOG0343         271 PVYVSVHENAVA-ATPSNLQQSYVI-VPLE-----D-KIDMLWSFIKSHLKKK--SIVFLS-------------------  321 (758)
T ss_pred             CCEEEEECCCCC-CCHHHHHHEEEE-EEHH-----H-HHHHHHHHHHHCCCCC--EEEEEE-------------------
T ss_conf             857997235333-683645332799-7601-----4-7899999998452543--699986-------------------


Q ss_pred             CCCCCEEEEECCCCCCEECHHHCCCCCCCCCCCCCCCCEECCCCCCHHHHHHHHHHCCCCCHHHHCCCCCCCCHHHHHHH
Q ss_conf             14652012113578320000210244655566678741100135428998888520485200010232113586789999
Q gi|254780619|r  449 LHCSCWLVEHRSKKKLYCHQCGHSAIYSQSCVVCGSSGKMIACGFGIERIAEEVCEYFPLARISILSSDLEGGGGRLQLQ  528 (731)
Q Consensus       449 ~~C~~~l~~h~~~~~l~Ch~Cg~~~~~~~~Cp~Cg~~~~l~~~G~Gte~~~e~l~~~fp~~~v~~~d~d~~~~~~~~~~~  528 (731)
                                                      .|..          ..-+.|...++=|+.++.-+..-.  +....-..
T Consensus       322 --------------------------------scKq----------vkf~~e~F~rlrpg~~l~~L~G~~--~Q~~R~ev  357 (758)
T KOG0343         322 --------------------------------SCKQ----------VKFLYEAFCRLRPGIPLLALHGTM--SQKKRIEV  357 (758)
T ss_pred             --------------------------------HHHH----------HHHHHHHHHHCCCCCCEEEECCCH--HHHHHHHH
T ss_conf             --------------------------------0068----------999999998508998325421631--37788999


Q ss_pred             HHHHCCCCCCEEEEEHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCEEEE
Q ss_conf             986212576579870443023113452012330003443102455789999987543110256678868999
Q gi|254780619|r  529 LSAIAKGEIDIIIGTQLVAKGHNFPRMSLVGVVDGDLGLTNADLRSSERTFQLLSQVTGRAGRFGLKSLGLI  600 (731)
Q Consensus       529 ~~~~~~~~~~ilvgTq~i~kg~~fp~v~lv~il~aD~~l~~pd~ra~E~~~qll~qv~gRagr~~~~g~v~i  600 (731)
                      +.+|......||..|-+.|.|+|||.|+-|+=+|.           .|..-+.++ -+||+.|....|+-++
T Consensus       358 ~~~F~~~~~~vLF~TDv~aRGLDFpaVdwViQ~DC-----------Pedv~tYIH-RvGRtAR~~~~G~sll  417 (758)
T KOG0343         358 YKKFVRKRAVVLFCTDVAARGLDFPAVDWVIQVDC-----------PEDVDTYIH-RVGRTARYKERGESLL  417 (758)
T ss_pred             HHHHHHHCCEEEEEEHHHHCCCCCCCCCEEEEECC-----------CHHHHHHHH-HHHHHHCCCCCCCEEE
T ss_conf             99998755558986025543689864336998068-----------205889998-7212211367785689


No 65 
>KOG0351 consensus
Probab=98.84  E-value=3.6e-07  Score=73.94  Aligned_cols=322  Identities=20%  Similarity=0.268  Sum_probs=177.0

Q ss_pred             CCHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHCCCCCEEEEEE
Q ss_conf             88378999999987520489619984475315799999999998514684799715210013445554303897689962
Q gi|254780619|r  199 LDKNQQDVVEQVVPLCTKGFAVSLISGVTGSGKTEVYLEIVAAVLHLGKQVLILLPEISLTSAILERFQKRFGVKPAEWH  278 (731)
Q Consensus       199 Lt~eQ~~a~~~i~~~~~~~f~~~LL~GvTGSGKTEVYl~li~~~L~~GkqvLiLvPEI~Lt~Q~~~rl~~rF~~~v~v~H  278 (731)
                      .-+.|.+|+..+..    +-.+ ++-=.||+||-.-|   ---++-.++-.+|.-|=|+|-...+.-| ...+.....+|
T Consensus       265 FR~~Q~eaI~~~l~----Gkd~-fvlmpTG~GKSLCY---QlPA~l~~gitvVISPL~SLm~DQv~~L-~~~~I~a~~L~  335 (941)
T KOG0351         265 FRPNQLEAINATLS----GKDC-FVLMPTGGGKSLCY---QLPALLLGGVTVVISPLISLMQDQVTHL-SKKGIPACFLS  335 (941)
T ss_pred             CCHHHHHHHHHHHC----CCCE-EEEEECCCCEEEEE---ECCCCCCCCCEEEECCHHHHHHHHHHHH-HHCCCCEEECC
T ss_conf             88439999999974----8846-99953488625676---6661013893699633899999999743-21485413235


Q ss_pred             CCCCCHHHHHHHHHHHCC--CCEEEEECC-----HHHH----HHHCC---CEEEEEEECCCCCCHHCCCCCCCHHHHHHH
Q ss_conf             355723566789999719--973999400-----1211----00100---013677405532100002443224899999
Q gi|254780619|r  279 SSLSTSMREKIWRQVARG--AISVIVGVR-----SALF----LPFKK---LGLIVIDEEHDISYKQEEGILYNARDMSIV  344 (731)
Q Consensus       279 S~ls~~eR~~~w~~i~~G--~~~IVIGtR-----SAif----~P~~n---LglIIvDEEHd~sykq~~~pry~aRdvA~~  344 (731)
                      |.++..+|..+|..+++|  ..+|+-=|-     |.-+    .-+..   +.++||||-|.-|=.-. -+|=+-+.+..+
T Consensus       336 s~q~~~~~~~i~q~l~~~~~~ikilYvtPE~v~~~~~l~~~~~~L~~~~~lal~vIDEAHCVSqWgH-dFRp~Yk~l~~l  414 (941)
T KOG0351         336 SIQTAAERLAILQKLANGNPIIKILYVTPEKVVASEGLLESLADLYARGLLALFVIDEAHCVSQWGH-DFRPSYKRLGLL  414 (941)
T ss_pred             CCCCHHHHHHHHHHHHCCCCEEEEEEECHHHHHCCCCHHHHHHHCCCCCEEEEEEECHHHHHHHHCC-CCCHHHHHHHHH
T ss_conf             6566888999999985788767899967788633321566787506787048887227887664223-334778999999


Q ss_pred             HHHHCCCCEECCCCCCCHHHHHHHHHHHHHHHCCCCC--CC-CCCCCCCEECCCCCCCCCCCCCCCHHHHHHHHHHHCCC
Q ss_conf             7511032100002454324677532123444124322--36-76543321102222332224547989999998862265
Q gi|254780619|r  345 RGKIESFPVVLVSATPSIESRVNGISRRYHSVHLSTR--YR-NSALPHLQVIDMRGQTIAQGKSLSPEMIDGIRHTLARN  421 (731)
Q Consensus       345 Ra~~~~~~lilgSATPSles~~~~~~g~~~~~~l~~R--~~-~~~~P~i~ivDm~~~~~~~~~~lS~~l~~~i~~~l~~g  421 (731)
                      |-+..++|++=-+||-+..+    .......|.|.+-  +. ....|+... ..+.+   .+.--.......++... .+
T Consensus       415 ~~~~~~vP~iALTATAT~~v----~~DIi~~L~l~~~~~~~~sfnR~NL~y-eV~~k---~~~~~~~~~~~~~~~~~-~~  485 (941)
T KOG0351         415 RIRFPGVPFIALTATATERV----REDVIRSLGLRNPELFKSSFNRPNLKY-EVSPK---TDKDALLDILEESKLRH-PD  485 (941)
T ss_pred             HHHCCCCCEEEEEHHCCHHH----HHHHHHHHCCCCCCEECCCCCCCCCEE-EEEEC---CCCCCHHHHHHHHHHCC-CC
T ss_conf             85278997687530020889----999999827888632225679988559-99856---67531688988765128-99


Q ss_pred             CEEEEEECCCCEEHHCCCCCCCCCCCCCCCCCEEEEECCCCCCEECHHHCCCCCCCCCCCCCCCCEECCCCCCHHHHHHH
Q ss_conf             51799742220000002356543431014652012113578320000210244655566678741100135428998888
Q gi|254780619|r  422 EQTLLFLNRRGYAPLTLCQVCGNRLKCLHCSCWLVEHRSKKKLYCHQCGHSAIYSQSCVVCGSSGKMIACGFGIERIAEE  501 (731)
Q Consensus       422 ~qvll~lnRrGya~~~~C~~Cg~~~~C~~C~~~l~~h~~~~~l~Ch~Cg~~~~~~~~Cp~Cg~~~~l~~~G~Gte~~~e~  501 (731)
                                 -+..++|.   ..                                  .+             +|++...
T Consensus       486 -----------~s~IIYC~---sr----------------------------------~~-------------ce~vs~~  504 (941)
T KOG0351         486 -----------QSGIIYCL---SR----------------------------------KE-------------CEQVSAV  504 (941)
T ss_pred             -----------CCEEEEEC---CC----------------------------------CH-------------HHHHHHH
T ss_conf             -----------98379968---82----------------------------------31-------------9999999


Q ss_pred             HHHCCCCCHHHHCCCCCCCCHHHHHHHHHHHCCCCCCEEEEEHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             52048520001023211358678999998621257657987044302311345201233000344310245578999998
Q gi|254780619|r  502 VCEYFPLARISILSSDLEGGGGRLQLQLSAIAKGEIDIIIGTQLVAKGHNFPRMSLVGVVDGDLGLTNADLRSSERTFQL  581 (731)
Q Consensus       502 l~~~fp~~~v~~~d~d~~~~~~~~~~~~~~~~~~~~~ilvgTq~i~kg~~fp~v~lv~il~aD~~l~~pd~ra~E~~~ql  581 (731)
                      |.+.--.+--  ...-  -.++..+.+-.+|..++..|+|+|=+-.-|.|+|+|.+|.=..      .|      +.|-.
T Consensus       505 L~~~~~~a~~--YHAG--l~~~~R~~Vq~~w~~~~~~VivATVAFGMGIdK~DVR~ViH~~------lP------ks~E~  568 (941)
T KOG0351         505 LRSLGKSAAF--YHAG--LPPKERETVQKAWMSDKIRVIVATVAFGMGIDKPDVRFVIHYS------LP------KSFEG  568 (941)
T ss_pred             HHHHCHHHHH--HHCC--CCHHHHHHHHHHHHCCCCEEEEEEEECCCCCCCCCEEEEEECC------CC------HHHHH
T ss_conf             9873520575--5267--8878889999998568870899985224787778635999777------86------14788


Q ss_pred             HHHHHHCCCCCCCCCEE-EEEECCCCCHHHHHHHHCC
Q ss_conf             75431102566788689-9993298648889999589
Q gi|254780619|r  582 LSQVTGRAGRFGLKSLG-LIQAYQPTHPVMQALVSGD  617 (731)
Q Consensus       582 l~qv~gRagr~~~~g~v-~iQt~~p~~~~~~~~~~~d  617 (731)
                      .+|-+|||||-..+..- +.-++. |..-++.++..+
T Consensus       569 YYQE~GRAGRDG~~s~C~l~y~~~-D~~~l~~ll~s~  604 (941)
T KOG0351         569 YYQEAGRAGRDGLPSSCVLLYGYA-DISELRRLLTSG  604 (941)
T ss_pred             HHHHCCCCCCCCCCCEEEEECCHH-HHHHHHHHHHCC
T ss_conf             887403367678800267742613-789999998726


No 66 
>COG4581 Superfamily II RNA helicase [DNA replication, recombination, and repair]
Probab=98.82  E-value=1.3e-07  Score=77.36  Aligned_cols=143  Identities=24%  Similarity=0.285  Sum_probs=105.3

Q ss_pred             CCCCCHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHCCCCCE--
Q ss_conf             666883789999999875204896199844753157999999999985146847997152100134455543038976--
Q gi|254780619|r  196 LPILDKNQQDVVEQVVPLCTKGFAVSLISGVTGSGKTEVYLEIVAAVLHLGKQVLILLPEISLTSAILERFQKRFGVK--  273 (731)
Q Consensus       196 ~~~Lt~eQ~~a~~~i~~~~~~~f~~~LL~GvTGSGKTEVYl~li~~~L~~GkqvLiLvPEI~Lt~Q~~~rl~~rF~~~--  273 (731)
                      +..|.+-|+.++..+....     ..+.--=||||||-|--=+|+.++..|..|++.-|=-+|..|.+.+|..+||+-  
T Consensus       117 ~F~LD~fQ~~a~~~Ler~e-----sVlV~ApTssGKTvVaeyAi~~al~~~qrviYTsPIKALsNQKyrdl~~~fgdv~~  191 (1041)
T COG4581         117 PFELDPFQQEAIAILERGE-----SVLVCAPTSSGKTVVAEYAIALALRDGQRVIYTSPIKALSNQKYRDLLAKFGDVAD  191 (1041)
T ss_pred             CCCCCHHHHHHHHHHHCCC-----CEEEECCCCCCCCHHHHHHHHHHHHCCCCEEECCCHHHHHHHHHHHHHHHHHHHHH
T ss_conf             9896789999999984799-----57997337898555999999999871894486163066420679999998600565


Q ss_pred             -EEEEECCCCCHHHHHHHHHHHCCCCEEEEEC----CHHHHHH---HCCCEEEEEEECCCCCCHHC--CCCCCCHHHHHH
Q ss_conf             -8996235572356678999971997399940----0121100---10001367740553210000--244322489999
Q gi|254780619|r  274 -PAEWHSSLSTSMREKIWRQVARGAISVIVGV----RSALFLP---FKKLGLIVIDEEHDISYKQE--EGILYNARDMSI  343 (731)
Q Consensus       274 -v~v~HS~ls~~eR~~~w~~i~~G~~~IVIGt----RSAif~P---~~nLglIIvDEEHd~sykq~--~~pry~aRdvA~  343 (731)
                       +.++.+..+           .++.+.++|=|    ||=++.+   +.++.-||.||-|   |-.|  +++-|   +..+
T Consensus       192 ~vGL~TGDv~-----------IN~~A~clvMTTEILRnMlyrg~~~~~~i~~ViFDEvH---yi~D~eRG~VW---EE~I  254 (1041)
T COG4581         192 MVGLMTGDVS-----------INPDAPCLVMTTEILRNMLYRGSESLRDIEWVVFDEVH---YIGDRERGVVW---EEVI  254 (1041)
T ss_pred             HCCCEECCEE-----------ECCCCCEEEEEHHHHHHHHCCCCCCCCCCCEEEEEEEE---ECCCCCCCHHH---HHHH
T ss_conf             4040105434-----------27999668860999999862586101353068887666---50463221257---8999


Q ss_pred             HHHHHCCCCEECCCCCCC
Q ss_conf             975110321000024543
Q gi|254780619|r  344 VRGKIESFPVVLVSATPS  361 (731)
Q Consensus       344 ~Ra~~~~~~lilgSATPS  361 (731)
                      ...- .++++|+-|||=+
T Consensus       255 i~lP-~~v~~v~LSATv~  271 (1041)
T COG4581         255 ILLP-DHVRFVFLSATVP  271 (1041)
T ss_pred             HHCC-CCCCEEEEECCCC
T ss_conf             8667-7776899967889


No 67 
>KOG0350 consensus
Probab=98.75  E-value=1.8e-06  Score=68.57  Aligned_cols=331  Identities=19%  Similarity=0.215  Sum_probs=161.9

Q ss_pred             CCHHHHHHHHHHHHHHCC--CC--CEEEEECCCCHHHHHHHHHHHHHHHHCC----CCEEEEECCCHHHHHHHHHHHCCC
Q ss_conf             883789999999875204--89--6199844753157999999999985146----847997152100134455543038
Q gi|254780619|r  199 LDKNQQDVVEQVVPLCTK--GF--AVSLISGVTGSGKTEVYLEIVAAVLHLG----KQVLILLPEISLTSAILERFQKRF  270 (731)
Q Consensus       199 Lt~eQ~~a~~~i~~~~~~--~f--~~~LL~GvTGSGKTEVYl~li~~~L~~G----kqvLiLvPEI~Lt~Q~~~rl~~rF  270 (731)
                      +-+-|..++..+......  .|  .-...-.-||||||.-|.-=|-++|.+-    -+++|+||.--|+-|.++.|...-
T Consensus       160 ~FPVQ~aVlp~ll~~~~~p~~~r~rDIcV~ApTGSGKTLaY~iPIVQ~L~~R~v~~LRavVivPtr~L~~QV~~~f~~~~  239 (620)
T KOG0350         160 LFPVQYAVLPSLLEEIRSPPPSRPRDICVNAPTGSGKTLAYVIPIVQLLSSRPVKRLRAVVIVPTRELALQVYDTFKRLN  239 (620)
T ss_pred             CCCHHHHHHHHHHHHHCCCCCCCCCCEEEECCCCCCCEEEEHHHHHHHHCCCCCCCEEEEEEEEHHHHHHHHHHHHHHHC
T ss_conf             45058888889998614799988775477557898845665137899970387340579999547999999999999856


Q ss_pred             ---CCEEEEEECCCCCHHHHHHHHHHHCCCC----EEEEECCHHHH--------HHHCCCEEEEEEECC---CCCCHHCC
Q ss_conf             ---9768996235572356678999971997----39994001211--------001000136774055---32100002
Q gi|254780619|r  271 ---GVKPAEWHSSLSTSMREKIWRQVARGAI----SVIVGVRSALF--------LPFKKLGLIVIDEEH---DISYKQEE  332 (731)
Q Consensus       271 ---~~~v~v~HS~ls~~eR~~~w~~i~~G~~----~IVIGtRSAif--------~P~~nLglIIvDEEH---d~sykq~~  332 (731)
                         |-.|..|. +.+.=+ -++ .++.+-.+    +|+|.|..-+.        .-+++|...||||-.   |.||..+ 
T Consensus       240 ~~tgL~V~~~s-gq~sl~-~E~-~qL~~~~~~~~~DIlVaTPGRLVDHl~~~k~f~Lk~LrfLVIDEADRll~qsfQ~W-  315 (620)
T KOG0350         240 SGTGLAVCSLS-GQNSLE-DEA-RQLASDPPECRIDILVATPGRLVDHLNNTKSFDLKHLRFLVIDEADRLLDQSFQEW-  315 (620)
T ss_pred             CCCCEEEEECC-CCCCHH-HHH-HHHHCCCCCCCCCEEECCCHHHHHHCCCCCCCCHHHCEEEEECHHHHHHHHHHHHH-
T ss_conf             68865988601-454057-899-99725997654366973726888860489875644535777525778999999988-


Q ss_pred             CCCCCHHHHHHHHHHHCCC-----CEECC--CCCCCHHHHHHHHHHHHHHHCCCCCCCCCCCCCCEECCCCCCCCCCCCC
Q ss_conf             4432248999997511032-----10000--2454324677532123444124322367654332110222233222454
Q gi|254780619|r  333 GILYNARDMSIVRGKIESF-----PVVLV--SATPSIESRVNGISRRYHSVHLSTRYRNSALPHLQVIDMRGQTIAQGKS  405 (731)
Q Consensus       333 ~pry~aRdvA~~Ra~~~~~-----~lilg--SATPSles~~~~~~g~~~~~~l~~R~~~~~~P~i~ivDm~~~~~~~~~~  405 (731)
                        .++    .....+-..+     .++=+  +++|+.  +-..+++.+.+          ..|...++-        ..-
T Consensus       316 --l~~----v~~~~~~~k~~~~~~nii~~~~~~~pt~--~~e~~t~~~~~----------~~~l~kL~~--------sat  369 (620)
T KOG0350         316 --LDT----VMSLCKTMKRVACLDNIIRQRQAPQPTV--LSELLTKLGKL----------YPPLWKLVF--------SAT  369 (620)
T ss_pred             --HHH----HHHHHCCCHHHCCHHHHHHHCCCCCCHH--HHHHHHHCCCC----------CCHHHHHHC--------CHH
T ss_conf             --999----9998377401047154441014677400--58777412776----------752676530--------133


Q ss_pred             CCHHHHHHHHHHHCCCCEEEEE-ECCC-C-EE--HHCCCCCCCCCCCCCCCCCEE-EEEC----CCCCCEECHHHCCCCC
Q ss_conf             7989999998862265517997-4222-0-00--000235654343101465201-2113----5783200002102446
Q gi|254780619|r  406 LSPEMIDGIRHTLARNEQTLLF-LNRR-G-YA--PLTLCQVCGNRLKCLHCSCWL-VEHR----SKKKLYCHQCGHSAIY  475 (731)
Q Consensus       406 lS~~l~~~i~~~l~~g~qvll~-lnRr-G-ya--~~~~C~~Cg~~~~C~~C~~~l-~~h~----~~~~l~Ch~Cg~~~~~  475 (731)
                      ||...-+..  .|.-+.+-++. .+.- | |+  +.+.|..|-.-.+    --|+ .||.    +-+++.|--       
T Consensus       370 LsqdP~Kl~--~l~l~~Prl~~v~~~~~~ryslp~~l~~~~vv~~~~----~kpl~~~~lI~~~k~~r~lcf~-------  436 (620)
T KOG0350         370 LSQDPSKLK--DLTLHIPRLFHVSKPLIGRYSLPSSLSHRLVVTEPK----FKPLAVYALITSNKLNRTLCFV-------  436 (620)
T ss_pred             HHCCHHHHH--HHHCCCCCEEEEECCCCEEEECCHHHHHCEEECCCC----CCHHHHHHHHHHHHCCEEEEEE-------
T ss_conf             304968876--533279835886225432661575542133420235----5437699999774010489995-------


Q ss_pred             CCCCCCCCCCCEECCCCCCHHHHHHHHHHCCC--CCHHHHCCCCCCCCHHHHHHHHHHHCCCCCCEEEEEHHHCCCCCCC
Q ss_conf             55566678741100135428998888520485--2000102321135867899999862125765798704430231134
Q gi|254780619|r  476 SQSCVVCGSSGKMIACGFGIERIAEEVCEYFP--LARISILSSDLEGGGGRLQLQLSAIAKGEIDIIIGTQLVAKGHNFP  553 (731)
Q Consensus       476 ~~~Cp~Cg~~~~l~~~G~Gte~~~e~l~~~fp--~~~v~~~d~d~~~~~~~~~~~~~~~~~~~~~ilvgTq~i~kg~~fp  553 (731)
                             .|.       --+-|+...|+-.|-  +.++.-+.+.  -++....+++.+|+.|++.+||.+-++|.|.|.-
T Consensus       437 -------~S~-------~sa~Rl~~~L~v~~~~~~~~~s~~t~~--l~~k~r~k~l~~f~~g~i~vLIcSD~laRGiDv~  500 (620)
T KOG0350         437 -------NSV-------SSANRLAHVLKVEFCSDNFKVSEFTGQ--LNGKRRYKMLEKFAKGDINVLICSDALARGIDVN  500 (620)
T ss_pred             -------CCH-------HHHHHHHHHHHHHHCCCCCHHHHHHHH--HHHHHHHHHHHHHHCCCCEEEEEHHHHHCCCCCC
T ss_conf             -------246-------889999999999862644025565234--4388999999987538952998523655477602


Q ss_pred             CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCEEEE
Q ss_conf             52012330003443102455789999987543110256678868999
Q gi|254780619|r  554 RMSLVGVVDGDLGLTNADLRSSERTFQLLSQVTGRAGRFGLKSLGLI  600 (731)
Q Consensus       554 ~v~lv~il~aD~~l~~pd~ra~E~~~qll~qv~gRagr~~~~g~v~i  600 (731)
                      +|+-|+--|.  -++          -+.++-=+||.+|+...|.++-
T Consensus       501 ~v~~VINYd~--P~~----------~ktyVHR~GRTARAgq~G~a~t  535 (620)
T KOG0350         501 DVDNVINYDP--PAS----------DKTYVHRAGRTARAGQDGYAIT  535 (620)
T ss_pred             CCCEEEECCC--CCH----------HHHHHHHHCCCCCCCCCCEEEE
T ss_conf             4604763589--812----------6578776022100567744789


No 68 
>KOG0334 consensus
Probab=98.73  E-value=3.5e-06  Score=66.35  Aligned_cols=287  Identities=21%  Similarity=0.274  Sum_probs=156.0

Q ss_pred             CHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHH-HHHHHHHHH-------CCCCEEEEECCCHHHHHHHHH---HHC
Q ss_conf             837899999998752048961998447531579999-999999851-------468479971521001344555---430
Q gi|254780619|r  200 DKNQQDVVEQVVPLCTKGFAVSLISGVTGSGKTEVY-LEIVAAVLH-------LGKQVLILLPEISLTSAILER---FQK  268 (731)
Q Consensus       200 t~eQ~~a~~~i~~~~~~~f~~~LL~GvTGSGKTEVY-l~li~~~L~-------~GkqvLiLvPEI~Lt~Q~~~r---l~~  268 (731)
                      ++=|.+|+=.|..    + ...+=++-||||||--| |-++.+...       .|--+|||.|.=.|..|+.+-   |..
T Consensus       389 ~~IQ~qAiP~Ims----G-rdvIgvakTgSGKT~af~LPmirhi~dQr~~~~gdGPi~li~aPtrela~QI~r~~~kf~k  463 (997)
T KOG0334         389 TPIQAQAIPAIMS----G-RDVIGVAKTGSGKTLAFLLPMIRHIKDQRPLEEGDGPIALILAPTRELAMQIHREVRKFLK  463 (997)
T ss_pred             CCHHHHHCCHHCC----C-CCEEEEECCCCCCCHHHHHHHHHHHCCCCCHHCCCCCEEEEECCCHHHHHHHHHHHHHHHH
T ss_conf             7556643012225----7-7458773268862034421155542047971107886479973777899999999999877


Q ss_pred             CCCCEEE-EEECCCCCHHHHHHHHHHHCCCCEEEEECCHHHHH-------HHCCCE---EEEEEECCCCCCHHCCC--CC
Q ss_conf             3897689-96235572356678999971997399940012110-------010001---36774055321000024--43
Q gi|254780619|r  269 RFGVKPA-EWHSSLSTSMREKIWRQVARGAISVIVGVRSALFL-------PFKKLG---LIVIDEEHDISYKQEEG--IL  335 (731)
Q Consensus       269 rF~~~v~-v~HS~ls~~eR~~~w~~i~~G~~~IVIGtRSAif~-------P~~nLg---lIIvDEEHd~sykq~~~--pr  335 (731)
                      -.+-.++ +|    +...+.+.-..+++| +.|||+|-+-..-       ++.||.   -++.||- |--|  +.+  |-
T Consensus       464 ~l~ir~v~vy----gg~~~~~qiaelkRg-~eIvV~tpGRmiD~l~~n~grvtnlrR~t~lv~dea-Drmf--dmgfePq  535 (997)
T KOG0334         464 LLGIRVVCVY----GGSGISQQIAELKRG-AEIVVCTPGRMIDILCANSGRVTNLRRVTYLVLDEA-DRMF--DMGFEPQ  535 (997)
T ss_pred             HCCCEEEEEC----CCCCHHHHHHHHHCC-CCEEEECCCHHHHHHHHCCCCCCCCCCCCEEEECHH-HHHH--HCCCCCC
T ss_conf             4176279842----785188789998678-965996450323366615776233101103554112-3544--0045754


Q ss_pred             CCHHHHHHHHHHHCCCCEECCCCCC--CHHHHHHHHHHHHHHHCCCCCCCCCCCCCCEECCCCC------------CCCC
Q ss_conf             2248999997511032100002454--3246775321234441243223676543321102222------------3322
Q gi|254780619|r  336 YNARDMSIVRGKIESFPVVLVSATP--SIESRVNGISRRYHSVHLSTRYRNSALPHLQVIDMRG------------QTIA  401 (731)
Q Consensus       336 y~aRdvA~~Ra~~~~~~lilgSATP--Sles~~~~~~g~~~~~~l~~R~~~~~~P~i~ivDm~~------------~~~~  401 (731)
                       +.| + +... ...-..+|-|||=  ++|++.+-      .++         +|---+|+.+.            ... 
T Consensus       536 -~~~-I-i~nl-rpdrQtvlfSatfpr~m~~la~~------vl~---------~Pveiiv~~~svV~k~V~q~v~V~~~-  595 (997)
T KOG0334         536 -ITR-I-LQNL-RPDRQTVLFSATFPRSMEALARK------VLK---------KPVEIIVGGRSVVCKEVTQVVRVCAI-  595 (997)
T ss_pred             -CEE-H-HHHC-CHHHHHHHHHHHHHHHHHHHHHH------HHC---------CCEEEEECCCEEEECCEEEEEEEECC-
T ss_conf             -040-9-7646-60354345662206999999988------615---------88089974630574240489998148-


Q ss_pred             CCCCCCHHHHHHHHHHHCCCCEEEEEECCCCEEHHCCCCCCCCCCCCCCCCCEEEEECCCCCCEECHHHCCCCCCCCCCC
Q ss_conf             24547989999998862265517997422200000023565434310146520121135783200002102446555666
Q gi|254780619|r  402 QGKSLSPEMIDGIRHTLARNEQTLLFLNRRGYAPLTLCQVCGNRLKCLHCSCWLVEHRSKKKLYCHQCGHSAIYSQSCVV  481 (731)
Q Consensus       402 ~~~~lS~~l~~~i~~~l~~g~qvll~lnRrGya~~~~C~~Cg~~~~C~~C~~~l~~h~~~~~l~Ch~Cg~~~~~~~~Cp~  481 (731)
                      .+..| ..|++.|.+.-+++ .+++|           |.+|+...-|+   -.|.                 ..+..|-.
T Consensus       596 e~eKf-~kL~eLl~e~~e~~-~tiiF-----------v~~qe~~d~l~---~~L~-----------------~ag~~~~s  642 (997)
T KOG0334         596 ENEKF-LKLLELLGERYEDG-KTIIF-----------VDKQEKADALL---RDLQ-----------------KAGYNCDS  642 (997)
T ss_pred             CHHHH-HHHHHHHHHHHHCC-CEEEE-----------ECCCHHHHHHH---HHHH-----------------HCCCCHHH
T ss_conf             36779-99999999886248-87999-----------84714788999---9998-----------------56860543


Q ss_pred             CCCCCEECCCCCCHHHHHHHHHHCCCCCHHHHCCCCCCCCHHHHHHHHHHHCCCCCCEEEEEHHHCCCCCCCCCCHHHHH
Q ss_conf             78741100135428998888520485200010232113586789999986212576579870443023113452012330
Q gi|254780619|r  482 CGSSGKMIACGFGIERIAEEVCEYFPLARISILSSDLEGGGGRLQLQLSAIAKGEIDIIIGTQLVAKGHNFPRMSLVGVV  561 (731)
Q Consensus       482 Cg~~~~l~~~G~Gte~~~e~l~~~fp~~~v~~~d~d~~~~~~~~~~~~~~~~~~~~~ilvgTq~i~kg~~fp~v~lv~il  561 (731)
                                          |+.--|              ....+..+++|.++...+||.|-.+|.|+|+.++-||+.-
T Consensus       643 --------------------lHGgv~--------------q~dR~sti~dfK~~~~~LLvaTsvvarGLdv~~l~Lvvny  688 (997)
T KOG0334         643 --------------------LHGGVD--------------QHDRSSTIEDFKNGVVNLLVATSVVARGLDVKELILVVNY  688 (997)
T ss_pred             --------------------HCCCCC--------------HHHHHHHHHHHHCCCCEEEEEHHHHHCCCCCCCEEEEEEC
T ss_conf             --------------------057875--------------6778858999745674289851454267666540589973


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCEE
Q ss_conf             0034431024557899999875431102566788689
Q gi|254780619|r  562 DGDLGLTNADLRSSERTFQLLSQVTGRAGRFGLKSLG  598 (731)
Q Consensus       562 ~aD~~l~~pd~ra~E~~~qll~qv~gRagr~~~~g~v  598 (731)
                      |  .-=+.+|          +.--.||+||..+.|..
T Consensus       689 d--~pnh~ed----------yvhR~gRTgragrkg~A  713 (997)
T KOG0334         689 D--FPNHYED----------YVHRVGRTGRAGRKGAA  713 (997)
T ss_pred             C--CCHHHHH----------HHHHHCCCCCCCCCCEE
T ss_conf             6--6312799----------99985135667776337


No 69 
>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=98.73  E-value=2.8e-06  Score=67.16  Aligned_cols=336  Identities=19%  Similarity=0.292  Sum_probs=204.1

Q ss_pred             CCHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHCCCCCEEEEEE
Q ss_conf             88378999999987520489619984475315799999999998514684799715210013445554303897689962
Q gi|254780619|r  199 LDKNQQDVVEQVVPLCTKGFAVSLISGVTGSGKTEVYLEIVAAVLHLGKQVLILLPEISLTSAILERFQKRFGVKPAEWH  278 (731)
Q Consensus       199 Lt~eQ~~a~~~i~~~~~~~f~~~LL~GvTGSGKTEVYl~li~~~L~~GkqvLiLvPEI~Lt~Q~~~rl~~rF~~~v~v~H  278 (731)
                      --+.|+.+++.+....+   ...++-  ||-||--=| ++  -+|=.+.=.+|.-|=|||=.--++.|+.- |..-+.+.
T Consensus        14 FR~gQe~II~~vL~g~~---~l~vmP--TGGGKSlCY-Q~--PALll~Glt~VISPLIsLMkDQVd~L~~~-Gv~Aa~lN   84 (607)
T TIGR01389        14 FRGGQEEIIEHVLDGRD---VLVVMP--TGGGKSLCY-QV--PALLLKGLTVVISPLISLMKDQVDQLRAA-GVAAAYLN   84 (607)
T ss_pred             CCCHHHHHHHHHHCCCC---EEEECC--CCCCHHHHH-HH--HHHHHCCCEEEECCHHHHHHHHHHHHHHC-CCEEEEEC
T ss_conf             77315899999847798---589738--998512777-21--78872898799842363147799999860-70145203


Q ss_pred             CCCCCHHHHHHHHHHHCCCCEEE-EEC-C--HHHHH---HHCCCEEEEEEECCCCCCHHCCC-CCCCHHHHHHHHHHHCC
Q ss_conf             35572356678999971997399-940-0--12110---01000136774055321000024-43224899999751103
Q gi|254780619|r  279 SSLSTSMREKIWRQVARGAISVI-VGV-R--SALFL---PFKKLGLIVIDEEHDISYKQEEG-ILYNARDMSIVRGKIES  350 (731)
Q Consensus       279 S~ls~~eR~~~w~~i~~G~~~IV-IGt-R--SAif~---P~~nLglIIvDEEHd~sykq~~~-pry~aRdvA~~Ra~~~~  350 (731)
                      |.+|..|..++|.++.+|+.++. |.. |  +.-|+   -=.++.|+=|||-|=-|  |+-. +|=.=+.++.+.-..-+
T Consensus        85 St~s~~E~~~i~~~~~~G~~~LLYvAPERL~~~~Fl~~L~~~~i~L~AvDEAHCvS--QWGHDFRPeY~~L~~l~~~fp~  162 (607)
T TIGR01389        85 STLSAKEQQEIEKALVNGELKLLYVAPERLEQDYFLNMLKRLTIALLAVDEAHCVS--QWGHDFRPEYRRLGELAERFPQ  162 (607)
T ss_pred             CCCCHHHHHHHHHHHHCCCEEEEEECCHHHHHHHHHHHHHCCCCEEEEEECCCCCC--CCCCCCCHHHHHHHHHHHHCCC
T ss_conf             77888899999999841981577516713211899988731993089983250216--6888875658999999986789


Q ss_pred             CCEECC-CCCCCHHHHHHHHHHHHHHHCCCCC---CCCCCCCCCEECCCCCCCCCCCCCCCHHHHHHHHHHHCCCCEEEE
Q ss_conf             210000-2454324677532123444124322---367654332110222233222454798999999886226551799
Q gi|254780619|r  351 FPVVLV-SATPSIESRVNGISRRYHSVHLSTR---YRNSALPHLQVIDMRGQTIAQGKSLSPEMIDGIRHTLARNEQTLL  426 (731)
Q Consensus       351 ~~lilg-SATPSles~~~~~~g~~~~~~l~~R---~~~~~~P~i~ivDm~~~~~~~~~~lS~~l~~~i~~~l~~g~qvll  426 (731)
                      .|++++ +||=..++-.-+.    +.|+|..-   +.+...|++..-=+++..      -...+++-|+           
T Consensus       163 ~P~~iALTATAd~~t~~DI~----~~L~L~~~~~f~~SFdRpNl~~~v~~k~n------~~~~l~~yl~-----------  221 (607)
T TIGR01389       163 VPTRIALTATADAETRQDIV----ELLRLKDANEFISSFDRPNLRFSVVKKNN------KKKFLLEYLK-----------  221 (607)
T ss_pred             CCEEEEEECCCCHHHHHHHH----HHCCCCCCCCCCCCCCCHHHHHHHHHHCC------CCHHHHHHHH-----------
T ss_conf             86699872489987899999----97088986541256775114334312037------8136899975-----------


Q ss_pred             EECCCCEEHHCCCCCCCCCCCCCCCCCEEEEECCCCCCEECHHHCCCCCCCCCCCCCCCCEECCCCCCHHHHHHHHHHCC
Q ss_conf             74222000000235654343101465201211357832000021024465556667874110013542899888852048
Q gi|254780619|r  427 FLNRRGYAPLTLCQVCGNRLKCLHCSCWLVEHRSKKKLYCHQCGHSAIYSQSCVVCGSSGKMIACGFGIERIAEEVCEYF  506 (731)
Q Consensus       427 ~lnRrGya~~~~C~~Cg~~~~C~~C~~~l~~h~~~~~l~Ch~Cg~~~~~~~~Cp~Cg~~~~l~~~G~Gte~~~e~l~~~f  506 (731)
                       .+|-|-|..++|                                           .|.       -+||++++.|... 
T Consensus       222 -~~~~G~SGIIYa-------------------------------------------~sR-------~~VE~~~~~L~s~-  249 (607)
T TIGR01389       222 -KHREGQSGIIYA-------------------------------------------SSR-------KKVEELAERLESQ-  249 (607)
T ss_pred             -CCCCCCCEEEEC-------------------------------------------CCH-------HHHHHHHHHHHHC-
T ss_conf             -079995347876-------------------------------------------770-------4589999999747-


Q ss_pred             CCCHHHHCCCCCCCCHHHHHHHHHHHCCCCCCEEEEEHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             52000102321135867899999862125765798704430231134520123300034431024557899999875431
Q gi|254780619|r  507 PLARISILSSDLEGGGGRLQLQLSAIAKGEIDIIIGTQLVAKGHNFPRMSLVGVVDGDLGLTNADLRSSERTFQLLSQVT  586 (731)
Q Consensus       507 p~~~v~~~d~d~~~~~~~~~~~~~~~~~~~~~ilvgTq~i~kg~~fp~v~lv~il~aD~~l~~pd~ra~E~~~qll~qv~  586 (731)
                       +++.+....--  ...-.++..++|-..+..|+|+|=.=-=|.|=|||-.|+=.|.      |  ++-|..    +|=+
T Consensus       250 -G~~A~~YHAGL--~~~~R~e~Q~~Fl~d~~~vmVAT~AFGMGIdKpnVRFViH~d~------P--~~~EsY----YQE~  314 (607)
T TIGR01389       250 -GISALAYHAGL--SNKVRAENQEDFLYDDVKVMVATNAFGMGIDKPNVRFVIHADM------P--KNIESY----YQEA  314 (607)
T ss_pred             -CCCEEECCCCC--CHHHHHHHHHHHHHHCCEEEEEEECCCCCCCCCCCCEEEEECC------C--CCHHHH----HCCC
T ss_conf             -96204036798--7768999975444625548888712358747876548886368------7--421113----1035


Q ss_pred             HCCCCCCCCCEEEEEECCCC-CHHHHHHHHCCHHHHHHHHHHHHHHCCC
Q ss_conf             10256678868999932986-4888999958979999999999998188
Q gi|254780619|r  587 GRAGRFGLKSLGLIQAYQPT-HPVMQALVSGDADSFYESEIRARESVNL  634 (731)
Q Consensus       587 gRagr~~~~g~v~iQt~~p~-~~~~~~~~~~d~~~f~~~el~~R~~~~~  634 (731)
                      |||||-..|.+.++- |.+. =.+.+..++..--.+-.+..+.+|.-.+
T Consensus       315 GRAGRDGlpae~~ll-y~~~D~~l~~~~I~~s~~~~~~K~~e~~KL~~m  362 (607)
T TIGR01389       315 GRAGRDGLPAEAILL-YSLADIALLKRFIEQSEADEDRKQIEREKLDAM  362 (607)
T ss_pred             CCCCCCCCHHHHHHH-CCHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHH
T ss_conf             546887526778672-477789999999741588488999999999999


No 70 
>KOG0339 consensus
Probab=98.73  E-value=3.2e-06  Score=66.73  Aligned_cols=289  Identities=21%  Similarity=0.272  Sum_probs=166.1

Q ss_pred             CCCHHHHHHHHHHH-HHH-----HH--CCCCEEEEECCCHHHHHHHH---HHHCCCCCEEEEEECCCCCHHHHHHHHHHH
Q ss_conf             75315799999999-998-----51--46847997152100134455---543038976899623557235667899997
Q gi|254780619|r  226 VTGSGKTEVYLEIV-AAV-----LH--LGKQVLILLPEISLTSAILE---RFQKRFGVKPAEWHSSLSTSMREKIWRQVA  294 (731)
Q Consensus       226 vTGSGKTEVYl~li-~~~-----L~--~GkqvLiLvPEI~Lt~Q~~~---rl~~rF~~~v~v~HS~ls~~eR~~~w~~i~  294 (731)
                      -||||||--|+.-+ -++     |+  .|-=.+||||.-.|+.|+..   +|.+..|-+++-.|.+.|.-   ++...++
T Consensus       268 ktgSgktaAfi~pm~~himdq~eL~~g~gPi~vilvPTrela~Qi~~eaKkf~K~ygl~~v~~ygGgsk~---eQ~k~Lk  344 (731)
T KOG0339         268 KTGSGKTAAFIWPMIVHIMDQPELKPGEGPIGVILVPTRELASQIFSEAKKFGKAYGLRVVAVYGGGSKW---EQSKELK  344 (731)
T ss_pred             ECCCCCHHHHHHHHHHHHCCHHHHCCCCCCEEEEEECCHHHHHHHHHHHHHHHHHCCCEEEEEECCCCHH---HHHHHHH
T ss_conf             1157505677777777741405206899976999806389999999999986311264278863687488---8777650


Q ss_pred             CCCCEEEEECCHHHH-------HHHCCCEEEEEEECCCCCCHHCCCCCCCHHHHHHHHHHHCCCCEECCCCCCCHHHHHH
Q ss_conf             199739994001211-------0010001367740553210000244322489999975110321000024543246775
Q gi|254780619|r  295 RGAISVIVGVRSALF-------LPFKKLGLIVIDEEHDISYKQEEGILYNARDMSIVRGKIESFPVVLVSATPSIESRVN  367 (731)
Q Consensus       295 ~G~~~IVIGtRSAif-------~P~~nLglIIvDEEHd~sykq~~~pry~aRdvA~~Ra~~~~~~lilgSATPSles~~~  367 (731)
                       -.+-|||.|.--+.       +-+.+..+.|+||- |.-|  +.+.-+.+|.+.-.-.-  +-..+|=|||=+-..-.+
T Consensus       345 -~g~EivVaTPgRlid~VkmKatn~~rvS~LV~DEa-drmf--dmGfe~qVrSI~~hirp--drQtllFsaTf~~kIe~l  418 (731)
T KOG0339         345 -EGAEIVVATPGRLIDMVKMKATNLSRVSYLVLDEA-DRMF--DMGFEPQVRSIKQHIRP--DRQTLLFSATFKKKIEKL  418 (731)
T ss_pred             -CCCEEEEECHHHHHHHHHHHCCCCEEEEEEEEECH-HHHH--CCCCHHHHHHHHHHCCC--CCEEEEEECCCHHHHHHH
T ss_conf             -27728996628889998860333100357887111-1131--26547989999864488--642798603106889999


Q ss_pred             HHHHHHHHHCCCCCCCCCCCCCCEECCCCCCCCCCCCCCCHHHHHHHHHHHCCCCEEEEEECCCCEEHHCCCCCCCCCCC
Q ss_conf             32123444124322367654332110222233222454798999999886226551799742220000002356543431
Q gi|254780619|r  368 GISRRYHSVHLSTRYRNSALPHLQVIDMRGQTIAQGKSLSPEMIDGIRHTLARNEQTLLFLNRRGYAPLTLCQVCGNRLK  447 (731)
Q Consensus       368 ~~~g~~~~~~l~~R~~~~~~P~i~ivDm~~~~~~~~~~lS~~l~~~i~~~l~~g~qvll~lnRrGya~~~~C~~Cg~~~~  447 (731)
                      +..           +..-   .|++|-  .+-...|.-        |       .|+                    +..
T Consensus       419 ard-----------~L~d---pVrvVq--g~vgean~d--------I-------TQ~--------------------V~V  447 (731)
T KOG0339         419 ARD-----------ILSD---PVRVVQ--GEVGEANED--------I-------TQT--------------------VSV  447 (731)
T ss_pred             HHH-----------HHCC---CEEEEE--EEHHCCCCC--------H-------HHE--------------------EEE
T ss_conf             999-----------7359---726787--401025665--------2-------424--------------------652


Q ss_pred             CCCCCCEEEEECCCCCCEECHHHCCCCCCCCCCCCCCCCEECCCCCCHHHHHHHHHHCCCCCHHHHCCCCCCCCHHHHHH
Q ss_conf             01465201211357832000021024465556667874110013542899888852048520001023211358678999
Q gi|254780619|r  448 CLHCSCWLVEHRSKKKLYCHQCGHSAIYSQSCVVCGSSGKMIACGFGIERIAEEVCEYFPLARISILSSDLEGGGGRLQL  527 (731)
Q Consensus       448 C~~C~~~l~~h~~~~~l~Ch~Cg~~~~~~~~Cp~Cg~~~~l~~~G~Gte~~~e~l~~~fp~~~v~~~d~d~~~~~~~~~~  527 (731)
                      ||+=.      ++-+.|.||.-++...        |+...|...-.-.|.|+..|+-  -+..|.-+..|.-.  ....+
T Consensus       448 ~~s~~------~Kl~wl~~~L~~f~S~--------gkvlifVTKk~~~e~i~a~Lkl--k~~~v~llhgdkdq--a~rn~  509 (731)
T KOG0339         448 CPSEE------KKLNWLLRHLVEFSSE--------GKVLIFVTKKADAEEIAANLKL--KGFNVSLLHGDKDQ--AERNE  509 (731)
T ss_pred             CCCCH------HHHHHHHHHHHHHCCC--------CCEEEEEECCCCHHHHHHHHCC--CCCEEEEECCCHHH--HHHHH
T ss_conf             36817------8889999975501367--------8479999422789999987320--56325652274566--77777


Q ss_pred             HHHHHCCCCCCEEEEEHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEECCCC
Q ss_conf             9986212576579870443023113452012330003443102455789999987543110256678868999932986
Q gi|254780619|r  528 QLSAIAKGEIDIIIGTQLVAKGHNFPRMSLVGVVDGDLGLTNADLRSSERTFQLLSQVTGRAGRFGLKSLGLIQAYQPT  606 (731)
Q Consensus       528 ~~~~~~~~~~~ilvgTq~i~kg~~fp~v~lv~il~aD~~l~~pd~ra~E~~~qll~qv~gRagr~~~~g~v~iQt~~p~  606 (731)
                      .+.+|..+...|||.|-.-+.|+|.|.+..|+..|  .      +|.-|    ..+|-.||.||+...|-.+  |+-.+
T Consensus       510 ~ls~fKkk~~~VlvatDvaargldI~~ikTVvnyD--~------ardId----ththrigrtgRag~kGvay--TlvTe  574 (731)
T KOG0339         510 VLSKFKKKRKPVLVATDVAARGLDIPSIKTVVNYD--F------ARDID----THTHRIGRTGRAGEKGVAY--TLVTE  574 (731)
T ss_pred             HHHHHHHCCCCEEEEEEHHHCCCCCCCCCEEECCC--C------CCHHH----HHHHHHHHCCCCCCCCEEE--EEECH
T ss_conf             99987624775488840765178752201023432--2------21067----7887751023355565136--87335


No 71 
>KOG4284 consensus
Probab=98.72  E-value=5e-08  Score=80.48  Aligned_cols=312  Identities=19%  Similarity=0.269  Sum_probs=155.6

Q ss_pred             CHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHHHHHHHHHHC---CCCEEEEECCCHHHHHHHHHHH---CCC-CC
Q ss_conf             8378999999987520489619984475315799999999998514---6847997152100134455543---038-97
Q gi|254780619|r  200 DKNQQDVVEQVVPLCTKGFAVSLISGVTGSGKTEVYLEIVAAVLHL---GKQVLILLPEISLTSAILERFQ---KRF-GV  272 (731)
Q Consensus       200 t~eQ~~a~~~i~~~~~~~f~~~LL~GvTGSGKTEVYl~li~~~L~~---GkqvLiLvPEI~Lt~Q~~~rl~---~rF-~~  272 (731)
                      |+-|..|+-.+...+     -.+++.-.|.|||.||--++-+.|..   .-|.+|++|.--++-|+-..|.   ..| |.
T Consensus        49 tkiQaaAIP~~~~km-----DliVQaKSGTGKTlVfsv~av~sl~~~~~~~q~~Iv~PTREiaVQI~~tv~~v~~sf~g~  123 (980)
T KOG4284          49 TKIQAAAIPAIFSKM-----DLIVQAKSGTGKTLVFSVLAVESLDSRSSHIQKVIVTPTREIAVQIKETVRKVAPSFTGA  123 (980)
T ss_pred             CCHHHHHHHHHHCCC-----CEEEEECCCCCCEEEEEEEEEHHCCCCCCCCEEEEEECCHHHHHHHHHHHHHHCCCCCCC
T ss_conf             701343211443155-----358981378885589985430222756676206997143566457999999865244576


Q ss_pred             EEEEEECCCCCHHHHHHHHHHHCCCCEEEEECCHHHH-------HHHCCCEEEEEEECCCCCCHHCCCCCCCHHHHHHHH
Q ss_conf             6899623557235667899997199739994001211-------001000136774055321000024432248999997
Q gi|254780619|r  273 KPAEWHSSLSTSMREKIWRQVARGAISVIVGVRSALF-------LPFKKLGLIVIDEEHDISYKQEEGILYNARDMSIVR  345 (731)
Q Consensus       273 ~v~v~HS~ls~~eR~~~w~~i~~G~~~IVIGtRSAif-------~P~~nLglIIvDEEHd~sykq~~~pry~aRdvA~~R  345 (731)
                      +..++-++..-+.     -+++-.+.+|||||..-+.       +-+..+.|.|.||. |--| +.+.++ |  |+-+..
T Consensus       124 ~csvfIGGT~~~~-----d~~rlk~~rIvIGtPGRi~qL~el~~~n~s~vrlfVLDEA-DkL~-~t~sfq-~--~In~ii  193 (980)
T KOG4284         124 RCSVFIGGTAHKL-----DLIRLKQTRIVIGTPGRIAQLVELGAMNMSHVRLFVLDEA-DKLM-DTESFQ-D--DINIII  193 (980)
T ss_pred             CEEEEECCCHHHH-----HHHHHHHCEEEECCCHHHHHHHHHCCCCCCCEEEEEECCH-HHHH-CHHHHH-H--HHHHHH
T ss_conf             0589966854355-----5666540237843835889998706777110268884317-7663-202478-8--899999


Q ss_pred             HHHCCC-CEECCCCCCCHHHHHHHHHHHH---HHHCCCCCCCCCCCCCCEECCCCCCCCCCC-CCCCHHHHHHHHHHHCC
Q ss_conf             511032-1000024543246775321234---441243223676543321102222332224-54798999999886226
Q gi|254780619|r  346 GKIESF-PVVLVSATPSIESRVNGISRRY---HSVHLSTRYRNSALPHLQVIDMRGQTIAQG-KSLSPEMIDGIRHTLAR  420 (731)
Q Consensus       346 a~~~~~-~lilgSATPSles~~~~~~g~~---~~~~l~~R~~~~~~P~i~ivDm~~~~~~~~-~~lS~~l~~~i~~~l~~  420 (731)
                      ..+-.+ .++-.|||=- +-+-+.....+   .++++..+       .+.++-+++--...+ ...|-+-++..-+.|  
T Consensus       194 ~slP~~rQv~a~SATYp-~nLdn~Lsk~mrdp~lVr~n~~-------d~~L~GikQyv~~~~s~nnsveemrlklq~L--  263 (980)
T KOG4284         194 NSLPQIRQVAAFSATYP-RNLDNLLSKFMRDPALVRFNAD-------DVQLFGIKQYVVAKCSPNNSVEEMRLKLQKL--  263 (980)
T ss_pred             HHCCHHHEEEEEECCCC-HHHHHHHHHHHCCCCEEECCCC-------CCEEECHHHEEEECCCCCCHHHHHHHHHHHH--
T ss_conf             74500002567733573-5689999987046222432667-------7425301020352268863589999999999--


Q ss_pred             CCEEEEEECCCCEEHHCCCCCCCCCCCCCCCCCEEEEECCCCCCEECHHHCCCCCCCCCCCCCCCCEECCCCCCHHHHHH
Q ss_conf             55179974222000000235654343101465201211357832000021024465556667874110013542899888
Q gi|254780619|r  421 NEQTLLFLNRRGYAPLTLCQVCGNRLKCLHCSCWLVEHRSKKKLYCHQCGHSAIYSQSCVVCGSSGKMIACGFGIERIAE  500 (731)
Q Consensus       421 g~qvll~lnRrGya~~~~C~~Cg~~~~C~~C~~~l~~h~~~~~l~Ch~Cg~~~~~~~~Cp~Cg~~~~l~~~G~Gte~~~e  500 (731)
                       .+++   |+--|-..++  -|....+|.+-...    .+..-+-||.-              |.. +.           
T Consensus       264 -~~vf---~~ipy~QAlV--F~~~~sra~~~a~~----L~ssG~d~~~I--------------Sga-M~-----------  307 (980)
T KOG4284         264 -THVF---KSIPYVQALV--FCDQISRAEPIATH----LKSSGLDVTFI--------------SGA-MS-----------  307 (980)
T ss_pred             -HHHH---HHCCHHHHHH--HHHHHHHHHHHHHH----HHCCCCCEEEE--------------CCC-CC-----------
T ss_conf             -9998---6072677776--54134210478877----51169871774--------------141-12-----------


Q ss_pred             HHHHCCCCCHHHHCCCCCCCCHHHHHHHHHHHCCCCCCEEEEEHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             85204852000102321135867899999862125765798704430231134520123300034431024557899999
Q gi|254780619|r  501 EVCEYFPLARISILSSDLEGGGGRLQLQLSAIAKGEIDIIIGTQLVAKGHNFPRMSLVGVVDGDLGLTNADLRSSERTFQ  580 (731)
Q Consensus       501 ~l~~~fp~~~v~~~d~d~~~~~~~~~~~~~~~~~~~~~ilvgTq~i~kg~~fp~v~lv~il~aD~~l~~pd~ra~E~~~q  580 (731)
                                          - +.....++..+.-...|||.|-+.|.|.|-|+|+||+-+|+-         +.|.|| 
T Consensus       308 --------------------Q-~~Rl~a~~~lr~f~~rILVsTDLtaRGIDa~~vNLVVNiD~p---------~d~eTY-  356 (980)
T KOG4284         308 --------------------Q-KDRLLAVDQLRAFRVRILVSTDLTARGIDADNVNLVVNIDAP---------ADEETY-  356 (980)
T ss_pred             --------------------H-HHHHHHHHHHHHCEEEEEEECCHHHCCCCCCCCCEEEECCCC---------CCHHHH-
T ss_conf             --------------------3-578899987420168999852312226786555369835877---------306789-


Q ss_pred             HHHHHHHCCCCCCCCCEEEEEECCCCC
Q ss_conf             875431102566788689999329864
Q gi|254780619|r  581 LLSQVTGRAGRFGLKSLGLIQAYQPTH  607 (731)
Q Consensus       581 ll~qv~gRagr~~~~g~v~iQt~~p~~  607 (731)
                        +--.|||||+...|-.+  |+.-+-
T Consensus       357 --~HRIGRAgRFG~~G~aV--T~~~~~  379 (980)
T KOG4284         357 --FHRIGRAGRFGAHGAAV--TLLEDE  379 (980)
T ss_pred             --HHHHHHCCCCCCCCEEE--EEECCC
T ss_conf             --98840000145565068--886060


No 72 
>KOG0328 consensus
Probab=98.71  E-value=1.2e-08  Score=85.35  Aligned_cols=323  Identities=22%  Similarity=0.347  Sum_probs=176.8

Q ss_pred             CHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHHHHHHHHHH---CCCCEEEEECCCHHHHHHHHHHH---CCCCCE
Q ss_conf             837899999998752048961998447531579999999999851---46847997152100134455543---038976
Q gi|254780619|r  200 DKNQQDVVEQVVPLCTKGFAVSLISGVTGSGKTEVYLEIVAAVLH---LGKQVLILLPEISLTSAILERFQ---KRFGVK  273 (731)
Q Consensus       200 t~eQ~~a~~~i~~~~~~~f~~~LL~GvTGSGKTEVYl~li~~~L~---~GkqvLiLvPEI~Lt~Q~~~rl~---~rF~~~  273 (731)
                      +.-|+.|+-.|.+..     -..-+.-.|.|||--|---+-+.+.   +.-|||+|-|.--|+.|+.+-..   ...+.+
T Consensus        51 S~IQqrAi~~IlkGr-----dViaQaqSGTGKTa~~si~vlq~~d~~~r~tQ~lilsPTRELa~Qi~~vi~alg~~mnvq  125 (400)
T KOG0328          51 SAIQQRAIPQILKGR-----DVIAQAQSGTGKTATFSISVLQSLDISVRETQALILSPTRELAVQIQKVILALGDYMNVQ  125 (400)
T ss_pred             HHHHHHHHHHHHCCC-----CEEEEECCCCCCEEEEEEEEEEECCCCCCEEEEEEECCHHHHHHHHHHHHHHHCCCCCCE
T ss_conf             677761024563366-----147870478884478986631403434200357895470899999999999832423644


Q ss_pred             EEEEECCCCCHHHHHHHHHHHCCCCEEEEECCHHHH-------HHHCCCEEEEEEECCCC---CCHHCCCCCCCHHHHHH
Q ss_conf             899623557235667899997199739994001211-------00100013677405532---10000244322489999
Q gi|254780619|r  274 PAEWHSSLSTSMREKIWRQVARGAISVIVGVRSALF-------LPFKKLGLIVIDEEHDI---SYKQEEGILYNARDMSI  343 (731)
Q Consensus       274 v~v~HS~ls~~eR~~~w~~i~~G~~~IVIGtRSAif-------~P~~nLglIIvDEEHd~---sykq~~~pry~aRdvA~  343 (731)
                      .-.--++-+-++   ...+.-.| ..+|.||..-+|       +-.++..++|.||..+-   .||+|-   |   |  +
T Consensus       126 ~hacigg~n~ge---dikkld~G-~hvVsGtPGrv~dmikr~~L~tr~vkmlVLDEaDemL~kgfk~Qi---y---d--i  193 (400)
T KOG0328         126 CHACIGGKNLGE---DIKKLDYG-QHVVSGTPGRVLDMIKRRSLRTRAVKMLVLDEADEMLNKGFKEQI---Y---D--I  193 (400)
T ss_pred             EEEEECCCCCCH---HHHHHCCC-CEEEECCCCHHHHHHHHCCCCCCCEEEEEECCHHHHHHHHHHHHH---H---H--H
T ss_conf             898735775103---45653256-147507981599999862310114268985458999875677889---9---9--9


Q ss_pred             HHHHHCCCCEECCCCCCCHHHHHHHHHHHHHHHCCCCCCCCCCCCCCEECCCCCCCCCCCCCCCHHHHHHHHHHHCCCCE
Q ss_conf             97511032100002454324677532123444124322367654332110222233222454798999999886226551
Q gi|254780619|r  344 VRGKIESFPVVLVSATPSIESRVNGISRRYHSVHLSTRYRNSALPHLQVIDMRGQTIAQGKSLSPEMIDGIRHTLARNEQ  423 (731)
Q Consensus       344 ~Ra~~~~~~lilgSATPSles~~~~~~g~~~~~~l~~R~~~~~~P~i~ivDm~~~~~~~~~~lS~~l~~~i~~~l~~g~q  423 (731)
                      +|.--.++.++|.|||-+-|.+           ++++.+-+.   .|++.--|.+.       +   ++.|+       |
T Consensus       194 yr~lp~~~Qvv~~SATlp~eil-----------emt~kfmtd---pvrilvkrdel-------t---lEgIK-------q  242 (400)
T KOG0328         194 YRYLPPGAQVVLVSATLPHEIL-----------EMTEKFMTD---PVRILVKRDEL-------T---LEGIK-------Q  242 (400)
T ss_pred             HHHCCCCCEEEEEECCCCHHHH-----------HHHHHHCCC---CEEEEEECCCC-------C---HHHHH-------H
T ss_conf             9847998669999645869999-----------999874488---52688705777-------6---66655-------5


Q ss_pred             EEEEECCCCEEHHCCCCCCCCCCCCCCCCCEEEEECCCCCCEECHHHCCCCCCCCCCCCCCCCEECCCCCCHHHHHHHHH
Q ss_conf             79974222000000235654343101465201211357832000021024465556667874110013542899888852
Q gi|254780619|r  424 TLLFLNRRGYAPLTLCQVCGNRLKCLHCSCWLVEHRSKKKLYCHQCGHSAIYSQSCVVCGSSGKMIACGFGIERIAEEVC  503 (731)
Q Consensus       424 vll~lnRrGya~~~~C~~Cg~~~~C~~C~~~l~~h~~~~~l~Ch~Cg~~~~~~~~Cp~Cg~~~~l~~~G~Gte~~~e~l~  503 (731)
                      -++-+.+-           .|...- -||.+=++.                +...---|...   ..+..=+||..+.. 
T Consensus       243 f~v~ve~E-----------ewKfdt-LcdLYd~Lt----------------ItQavIFcnTk---~kVdwLtekm~~~n-  290 (400)
T KOG0328         243 FFVAVEKE-----------EWKFDT-LCDLYDTLT----------------ITQAVIFCNTK---RKVDWLTEKMREAN-  290 (400)
T ss_pred             HEEEECHH-----------HHHHHH-HHHHHHHHE----------------HHEEEEEECCC---CHHHHHHHHHHHHC-
T ss_conf             42441322-----------553768-988864306----------------11479996264---04368899988617-


Q ss_pred             HCCCCCHHHHCCCCCCCCHHHHHHHHHHHCCCCCCEEEEEHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             04852000102321135867899999862125765798704430231134520123300034431024557899999875
Q gi|254780619|r  504 EYFPLARISILSSDLEGGGGRLQLQLSAIAKGEIDIIIGTQLVAKGHNFPRMSLVGVVDGDLGLTNADLRSSERTFQLLS  583 (731)
Q Consensus       504 ~~fp~~~v~~~d~d~~~~~~~~~~~~~~~~~~~~~ilvgTq~i~kg~~fp~v~lv~il~aD~~l~~pd~ra~E~~~qll~  583 (731)
                           ..|.-|..|...  +..+++.++|++|+..+||.|-.-|.|.|.|.|+||+--|      .|.+|      +++.
T Consensus       291 -----ftVssmHGDm~q--kERd~im~dFRsg~SrvLitTDVwaRGiDv~qVslviNYD------LP~nr------e~YI  351 (400)
T KOG0328         291 -----FTVSSMHGDMEQ--KERDKIMNDFRSGKSRVLITTDVWARGIDVQQVSLVINYD------LPNNR------ELYI  351 (400)
T ss_pred             -----CEEEECCCCCCH--HHHHHHHHHHHCCCCEEEEEECHHHCCCCCCEEEEEEECC------CCCCH------HHHH
T ss_conf             -----336630577645--6799999876547834999710444258750057899437------88548------7876


Q ss_pred             HHHHCCCCCCCCCEEEEEECCCCCHHHHHHHHCCHHHHHHHHH
Q ss_conf             4311025667886899993298648889999589799999999
Q gi|254780619|r  584 QVTGRAGRFGLKSLGLIQAYQPTHPVMQALVSGDADSFYESEI  626 (731)
Q Consensus       584 qv~gRagr~~~~g~v~iQt~~p~~~~~~~~~~~d~~~f~~~el  626 (731)
                      --.||+||+.++|-++=  +.. +.-++.+  .|.+.||...+
T Consensus       352 HRIGRSGRFGRkGvain--FVk-~~d~~~l--rdieq~yst~i  389 (400)
T KOG0328         352 HRIGRSGRFGRKGVAIN--FVK-SDDLRIL--RDIEQYYSTQI  389 (400)
T ss_pred             HHHCCCCCCCCCCEEEE--EEC-HHHHHHH--HHHHHHHHHHC
T ss_conf             65013565677606998--751-7889999--99999976411


No 73 
>KOG0327 consensus
Probab=98.67  E-value=5.8e-07  Score=72.37  Aligned_cols=324  Identities=21%  Similarity=0.311  Sum_probs=171.1

Q ss_pred             CHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHHHHHHHHHH---CCCCEEEEECCCHHHHHHHHHHHCCCCCEEEE
Q ss_conf             837899999998752048961998447531579999999999851---46847997152100134455543038976899
Q gi|254780619|r  200 DKNQQDVVEQVVPLCTKGFAVSLISGVTGSGKTEVYLEIVAAVLH---LGKQVLILLPEISLTSAILERFQKRFGVKPAE  276 (731)
Q Consensus       200 t~eQ~~a~~~i~~~~~~~f~~~LL~GvTGSGKTEVYl~li~~~L~---~GkqvLiLvPEI~Lt~Q~~~rl~~rF~~~v~v  276 (731)
                      +.=||.|+--+.+    + .-...+--+|+|||-.|+-.+.+-+.   .-.|||+|+|.-.|+.|..+.+..-+.. .-+
T Consensus        50 SaIQqrAI~p~i~----G-~dv~~qaqsgTgKt~af~i~ilq~iD~~~ke~qalilaPtreLa~q~~~v~~~lg~~-~~~  123 (397)
T KOG0327          50 SAIQQRAILPCIK----G-HDVIAQAQSGTGKTAAFLISILQQIDMSVKETQALILAPTRELAQQIQKVVRALGDH-MDV  123 (397)
T ss_pred             HHHHHCCCCCCCC----C-CCEEEEEECCCCCHHHHHHHHHHHCCCCHHHHHHHHHCCHHHHHHHHHHHHHHHHCC-CCE
T ss_conf             2777634355346----8-744676302544114667888751374167777988613278889899998864112-461


Q ss_pred             EECCCCCHH-HHHHHHHHHCCCCEEEEECCHHHH-------HHHCCCEEEEEEECCCCCCHHCCCCCCCHHH--HHHHHH
Q ss_conf             623557235-667899997199739994001211-------0010001367740553210000244322489--999975
Q gi|254780619|r  277 WHSSLSTSM-REKIWRQVARGAISVIVGVRSALF-------LPFKKLGLIVIDEEHDISYKQEEGILYNARD--MSIVRG  346 (731)
Q Consensus       277 ~HS~ls~~e-R~~~w~~i~~G~~~IVIGtRSAif-------~P~~nLglIIvDEEHd~sykq~~~pry~aRd--vA~~Ra  346 (731)
                      .-+.+...- +...=.+++.-.+-||+||.--+|       +...+..+.++||. |..      .-.+.+|  -++++.
T Consensus       124 ~v~~~igg~~~~~~~~~i~~~~~hivvGTpgrV~dml~~~~l~~~~iKmfvlDEa-DEm------Ls~gfkdqI~~if~~  196 (397)
T KOG0327         124 SVHACIGGTNVRREDQALLKDKPHIVVGTPGRVFDMLNRGSLSTDGIKMFVLDEA-DEM------LSRGFKDQIYDIFQE  196 (397)
T ss_pred             EEEEECCCCCCHHHHHHHHCCCCEEECCCCHHHHHHHCCCCCCCCCEEEEEECCH-HHH------HCCCHHHHHHHHHHH
T ss_conf             4665317641003455552047635437850577764136456665467752436-766------305648999999987


Q ss_pred             HHCCCCEECCCCCCCHHHHHHHHHHHHHHHCCCCCCCCCCCCCCEECCCCCCCCCCCCCCCHHHHHHHHHHHCCCCEEEE
Q ss_conf             11032100002454324677532123444124322367654332110222233222454798999999886226551799
Q gi|254780619|r  347 KIESFPVVLVSATPSIESRVNGISRRYHSVHLSTRYRNSALPHLQVIDMRGQTIAQGKSLSPEMIDGIRHTLARNEQTLL  426 (731)
Q Consensus       347 ~~~~~~lilgSATPSles~~~~~~g~~~~~~l~~R~~~~~~P~i~ivDm~~~~~~~~~~lS~~l~~~i~~~l~~g~qvll  426 (731)
                      --.+..++|-|||--.+..+.++.           +..    ....|..+++..      .   ++.|+       |.  
T Consensus       197 lp~~vQv~l~SAT~p~~vl~vt~~-----------f~~----~pv~i~vkk~~l------t---l~gik-------q~--  243 (397)
T KOG0327         197 LPSDVQVVLLSATMPSDVLEVTKK-----------FMR----EPVRILVKKDEL------T---LEGIK-------QF--  243 (397)
T ss_pred             CCCCHHHEEECCCCCHHHHHHHHH-----------HCC----CCEEEEECCHHH------H---HHHEE-------EE--
T ss_conf             594322010013685889999887-----------404----756899520020------1---22200-------22--


Q ss_pred             EECCCCEEHHCCCCCCCCCCCCCCCCCEEEEECCCCCCEECHHHCCCCCCCCCCCCCCCCEECCCCCCHHHHHHHHHHCC
Q ss_conf             74222000000235654343101465201211357832000021024465556667874110013542899888852048
Q gi|254780619|r  427 FLNRRGYAPLTLCQVCGNRLKCLHCSCWLVEHRSKKKLYCHQCGHSAIYSQSCVVCGSSGKMIACGFGIERIAEEVCEYF  506 (731)
Q Consensus       427 ~lnRrGya~~~~C~~Cg~~~~C~~C~~~l~~h~~~~~l~Ch~Cg~~~~~~~~Cp~Cg~~~~l~~~G~Gte~~~e~l~~~f  506 (731)
                      ++|-.-=+          ...| -|+             ||.     .....---|.+.       -+...+.+.| ..+
T Consensus       244 ~i~v~k~~----------k~~~-l~d-------------l~~-----~~~q~~if~nt~-------r~v~~l~~~L-~~~  286 (397)
T KOG0327         244 YINVEKEE----------KLDT-LCD-------------LYR-----RVTQAVIFCNTR-------RKVDNLTDKL-RAH  286 (397)
T ss_pred             EEECCCCC----------CCCH-HHH-------------HHH-----HHHCCEEEECCH-------HHHHHHHHHH-HHC
T ss_conf             20105431----------1227-999-------------998-----643105785104-------5677789998-627


Q ss_pred             CCCHHHHCCCCCCCCHHHHHHHHHHHCCCCCCEEEEEHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             52000102321135867899999862125765798704430231134520123300034431024557899999875431
Q gi|254780619|r  507 PLARISILSSDLEGGGGRLQLQLSAIAKGEIDIIIGTQLVAKGHNFPRMSLVGVVDGDLGLTNADLRSSERTFQLLSQVT  586 (731)
Q Consensus       507 p~~~v~~~d~d~~~~~~~~~~~~~~~~~~~~~ilvgTq~i~kg~~fp~v~lv~il~aD~~l~~pd~ra~E~~~qll~qv~  586 (731)
                      + ..+.-+..|+..  ...+.++.+|..|+..+||-|-..|.|+|+.++.+|+..|+-           .|. +-+.-=+
T Consensus       287 ~-~~~s~i~~d~~q--~~R~~~~~~f~~g~srvlIttdl~argidv~~~slvinydlP-----------~r~-~~yihR~  351 (397)
T KOG0327         287 G-FTVSAIHGDMEQ--NERDTLMREFRSGSSRVLITTDLLARGIDVQQVSLVVNYDLP-----------ARK-ENYIHRI  351 (397)
T ss_pred             C-CEEEEEECCCCH--HHHHHHHHHHHCCCCEEEEECCCCCCCCCHHHCCEEEEECCC-----------CCH-HHHHHHC
T ss_conf             7-337876346430--034689998645872377412212465411101225650165-----------206-6666525


Q ss_pred             HCCCCCCCCCEEEEEECCCCCHHHHHHHHCCHHHHHHHHH
Q ss_conf             1025667886899993298648889999589799999999
Q gi|254780619|r  587 GRAGRFGLKSLGLIQAYQPTHPVMQALVSGDADSFYESEI  626 (731)
Q Consensus       587 gRagr~~~~g~v~iQt~~p~~~~~~~~~~~d~~~f~~~el  626 (731)
                      ||+||..++|.++=  +..+|.+ +.+  .|.+.||..-+
T Consensus       352 gr~gr~grkg~~in--~v~~~d~-~~l--k~ie~~y~~~i  386 (397)
T KOG0327         352 GRAGRFGRKGVAIN--FVTEEDV-RDL--KDIEKFYNTPI  386 (397)
T ss_pred             CCCCCCCCCCEEEE--EEHHHHH-HHH--HHHHHHCCCCC
T ss_conf             54565677713555--2017568-888--73898638720


No 74 
>KOG0336 consensus
Probab=98.66  E-value=1.5e-05  Score=61.52  Aligned_cols=283  Identities=20%  Similarity=0.291  Sum_probs=147.9

Q ss_pred             EEEEECC-------CCHHHHHHHHHH-HHHHH--------HCCCCEEEEECCCHHHHHHHHHHHCC-C-CC-EEEEEECC
Q ss_conf             1998447-------531579999999-99985--------14684799715210013445554303-8-97-68996235
Q gi|254780619|r  220 VSLISGV-------TGSGKTEVYLEI-VAAVL--------HLGKQVLILLPEISLTSAILERFQKR-F-GV-KPAEWHSS  280 (731)
Q Consensus       220 ~~LL~Gv-------TGSGKTEVYl~l-i~~~L--------~~GkqvLiLvPEI~Lt~Q~~~rl~~r-F-~~-~v~v~HS~  280 (731)
                      +.||+|.       ||+|||.-||.- +-+.+        ..|-.+|+|.|.=-|+.|+....+.+ + |- .+.+|   
T Consensus       252 PI~LQG~DliGVAQTgtgKtL~~L~pg~ihi~aqp~~~~qr~~p~~lvl~ptreLalqie~e~~kysyng~ksvc~y---  328 (629)
T KOG0336         252 PILLQGIDLIGVAQTGTGKTLAFLLPGFIHIDAQPKRREQRNGPGVLVLTPTRELALQIEGEVKKYSYNGLKSVCVY---  328 (629)
T ss_pred             CEEECCCCEEEEEECCCCCCHHHHCCCEEEEECCCHHHHCCCCCCEEEEECCHHHHHHHHHHHHHHHHCCCCEEEEE---
T ss_conf             20113764477874489847787505401451461112036898549983338889988767767643584328875---


Q ss_pred             CCCHHHHHHHHHHHCCCCEEEEECCHHH---H-HHHCCC---EEEEEEECCCCCCHHCCCCCCCHHHHHHHHHHHCCCCE
Q ss_conf             5723566789999719973999400121---1-001000---13677405532100002443224899999751103210
Q gi|254780619|r  281 LSTSMREKIWRQVARGAISVIVGVRSAL---F-LPFKKL---GLIVIDEEHDISYKQEEGILYNARDMSIVRGKIESFPV  353 (731)
Q Consensus       281 ls~~eR~~~w~~i~~G~~~IVIGtRSAi---f-~P~~nL---glIIvDEEHd~sykq~~~pry~aRdvA~~Ra~~~~~~l  353 (731)
                       +.+.|-++-..++.| ..|+|.|.-.+   | .-+-||   ..+|+||.. --  -++++--..|.+.+-  -.-+-..
T Consensus       329 -gggnR~eqie~lkrg-veiiiatPgrlndL~~~n~i~l~siTYlVlDEAD-rM--LDMgFEpqIrkilld--iRPDRqt  401 (629)
T KOG0336         329 -GGGNRNEQIEDLKRG-VEIIIATPGRLNDLQMDNVINLASITYLVLDEAD-RM--LDMGFEPQIRKILLD--IRPDRQT  401 (629)
T ss_pred             -CCCCCHHHHHHHHCC-CEEEEECCCHHHHHHHCCEEEEEEEEEEEECCHH-HH--HCCCCCHHHHHHHHH--CCCCCEE
T ss_conf             -487854689987457-4177607851765553172001125889861266-66--445662888988652--2776225


Q ss_pred             ECCCCCCCHHHHHHHHHHHHHHHCCCCCCCCCCCC------CCEECCCCCCCCCCCCCCCHHHHHHHHHHHCCCCEEEEE
Q ss_conf             00024543246775321234441243223676543------321102222332224547989999998862265517997
Q gi|254780619|r  354 VLVSATPSIESRVNGISRRYHSVHLSTRYRNSALP------HLQVIDMRGQTIAQGKSLSPEMIDGIRHTLARNEQTLLF  427 (731)
Q Consensus       354 ilgSATPSles~~~~~~g~~~~~~l~~R~~~~~~P------~i~ivDm~~~~~~~~~~lS~~l~~~i~~~l~~g~qvll~  427 (731)
                      +|.|||=.--.-.++++  |..--+.--.+.-.+.      +.-+|  ..+...    +  .+.+..-++......|++|
T Consensus       402 vmTSATWP~~VrrLa~s--Y~Kep~~v~vGsLdL~a~~sVkQ~i~v--~~d~~k----~--~~~~~f~~~ms~ndKvIiF  471 (629)
T KOG0336         402 VMTSATWPEGVRRLAQS--YLKEPMIVYVGSLDLVAVKSVKQNIIV--TTDSEK----L--EIVQFFVANMSSNDKVIIF  471 (629)
T ss_pred             EEECCCCCHHHHHHHHH--HHHCCEEEEECCCCEEEEEEEEEEEEE--CCCHHH----H--HHHHHHHHHCCCCCEEEEE
T ss_conf             53105586689999998--640854999614343554101025884--361899----9--9999999855888618999


Q ss_pred             ECCCCEEHHCCCCCCCCCCCCCCCCCEEEEECCCCCCEECHHHCCCCCCCCCCCCCCCCEECCCCCCHHHHHHHHHHCCC
Q ss_conf             42220000002356543431014652012113578320000210244655566678741100135428998888520485
Q gi|254780619|r  428 LNRRGYAPLTLCQVCGNRLKCLHCSCWLVEHRSKKKLYCHQCGHSAIYSQSCVVCGSSGKMIACGFGIERIAEEVCEYFP  507 (731)
Q Consensus       428 lnRrGya~~~~C~~Cg~~~~C~~C~~~l~~h~~~~~l~Ch~Cg~~~~~~~~Cp~Cg~~~~l~~~G~Gte~~~e~l~~~fp  507 (731)
                      +-|+--|-.++-                           .                    |...|+-+|    -|+.   
T Consensus       472 v~~K~~AD~LSS---------------------------d--------------------~~l~gi~~q----~lHG---  497 (629)
T KOG0336         472 VSRKVMADHLSS---------------------------D--------------------FCLKGISSQ----SLHG---  497 (629)
T ss_pred             EECHHHHHHCCC---------------------------H--------------------HHHCCCCHH----HCCC---
T ss_conf             831032210231---------------------------0--------------------211461011----0258---


Q ss_pred             CCHHHHCCCCCCCCHHHHHHHHHHHCCCCCCEEEEEHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             20001023211358678999998621257657987044302311345201233000344310245578999998754311
Q gi|254780619|r  508 LARISILSSDLEGGGGRLQLQLSAIAKGEIDIIIGTQLVAKGHNFPRMSLVGVVDGDLGLTNADLRSSERTFQLLSQVTG  587 (731)
Q Consensus       508 ~~~v~~~d~d~~~~~~~~~~~~~~~~~~~~~ilvgTq~i~kg~~fp~v~lv~il~aD~~l~~pd~ra~E~~~qll~qv~g  587 (731)
                             +    +...+.|..+++|..|+..|||.|-+.+.|+|.|++|-|  +|-|.-.+.-.|          +--.|
T Consensus       498 -------~----r~Q~DrE~al~~~ksG~vrILvaTDlaSRGlDv~DiTHV--~NyDFP~nIeeY----------VHRvG  554 (629)
T KOG0336         498 -------N----REQSDREMALEDFKSGEVRILVATDLASRGLDVPDITHV--YNYDFPRNIEEY----------VHRVG  554 (629)
T ss_pred             -------C----HHHHHHHHHHHHHHCCCEEEEEEECHHHCCCCCHHCCEE--ECCCCCCCHHHH----------HHHHC
T ss_conf             -------7----224359999976415816999972234337882002035--405787559999----------98712


Q ss_pred             CCCCCCCCCEEE
Q ss_conf             025667886899
Q gi|254780619|r  588 RAGRFGLKSLGL  599 (731)
Q Consensus       588 Ragr~~~~g~v~  599 (731)
                      |.||+.+.|+-+
T Consensus       555 rtGRaGr~G~si  566 (629)
T KOG0336         555 RTGRAGRTGTSI  566 (629)
T ss_pred             CCCCCCCCCCEE
T ss_conf             356577776327


No 75 
>KOG0347 consensus
Probab=98.63  E-value=1.2e-06  Score=70.02  Aligned_cols=348  Identities=16%  Similarity=0.226  Sum_probs=175.0

Q ss_pred             HCCCHHHHHHHHHCCHHHHHHHHHCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHH-HHH
Q ss_conf             0999899975245572234455410235665434466668837899999998752048961998447531579999-999
Q gi|254780619|r  160 SQVSSHVIDGLKAQGVIKQIFEVISPVVDSPNLYFSLPILDKNQQDVVEQVVPLCTKGFAVSLISGVTGSGKTEVY-LEI  238 (731)
Q Consensus       160 ~~~s~~~i~~L~~kglI~~~~~~~~~~~~~~~~~~~~~~Lt~eQ~~a~~~i~~~~~~~f~~~LL~GvTGSGKTEVY-l~l  238 (731)
                      +.++..++.+|-..|+.+.                     |+=|..++-.+.   ..++ -.|=-..||||||.-| +-+
T Consensus       186 l~lp~~iL~aL~~~gFs~P---------------------t~IQsl~lp~ai---~gk~-DIlGaAeTGSGKTLAFGIPi  240 (731)
T KOG0347         186 LFLPMEILRALSNLGFSRP---------------------TEIQSLVLPAAI---RGKV-DILGAAETGSGKTLAFGIPI  240 (731)
T ss_pred             CCCCHHHHHHHHHCCCCCC---------------------CCCHHHCCCHHH---CCCH-HCCCCCCCCCCCEEEECCHH
T ss_conf             8989999999986478998---------------------610441166765---4630-00033346887424412325


Q ss_pred             HH-------------HHHHCCCC--EEEEECCCHHHHHHHHHHH---CCCCCEEEEEECCCCCHHHHHHHHHHHCCCCEE
Q ss_conf             99-------------98514684--7997152100134455543---038976899623557235667899997199739
Q gi|254780619|r  239 VA-------------AVLHLGKQ--VLILLPEISLTSAILERFQ---KRFGVKPAEWHSSLSTSMREKIWRQVARGAISV  300 (731)
Q Consensus       239 i~-------------~~L~~Gkq--vLiLvPEI~Lt~Q~~~rl~---~rF~~~v~v~HS~ls~~eR~~~w~~i~~G~~~I  300 (731)
                      ++             .+=+++.|  +||+.|.--|+-|...-|.   ..-+-.++.+.++|+-..-    .++.+-.+.|
T Consensus       241 v~~l~~~s~~s~e~~~~~~k~~k~~~LV~tPTRELa~QV~~Hl~ai~~~t~i~v~si~GGLavqKQ----qRlL~~~p~I  316 (731)
T KOG0347         241 VERLLESSDDSQELSNTSAKYVKPIALVVTPTRELAHQVKQHLKAIAEKTQIRVASITGGLAVQKQ----QRLLNQRPDI  316 (731)
T ss_pred             HHHHHHCCCHHHHHHHHHHCCCCCEEEEECCHHHHHHHHHHHHHHHCCCCCEEEEEEECHHHHHHH----HHHHHCCCCE
T ss_conf             454330365376544677605764038963709999999999998613467278875230579999----9998529987


Q ss_pred             EEECCHHHH----------HHHCCCEEEEEEECCCCCCHHCCCCCC-CHHHHHHHH---H-HHCCCCEECCCCCCCHHHH
Q ss_conf             994001211----------001000136774055321000024432-248999997---5-1103210000245432467
Q gi|254780619|r  301 IVGVRSALF----------LPFKKLGLIVIDEEHDISYKQEEGILY-NARDMSIVR---G-KIESFPVVLVSATPSIESR  365 (731)
Q Consensus       301 VIGtRSAif----------~P~~nLglIIvDEEHd~sykq~~~pry-~aRdvA~~R---a-~~~~~~lilgSATPSles~  365 (731)
                      ||.|..-+|          .-|+++.-.|+||-.-.  -| ++ .| --+.+.-+.   . +.+.-.+|| |||-++-..
T Consensus       317 VVATPGRlweli~e~n~~l~~~k~vkcLVlDEaDRm--ve-kg-hF~Els~lL~~L~e~~~~~qrQTlVF-SATlt~~~~  391 (731)
T KOG0347         317 VVATPGRLWELIEEDNTHLGNFKKVKCLVLDEADRM--VE-KG-HFEELSKLLKHLNEEQKNRQRQTLVF-SATLTLVLQ  391 (731)
T ss_pred             EEECCHHHHHHHHHHHHHHHHHHHCEEEEECCHHHH--HH-HC-CHHHHHHHHHHHHHHHCCCCCCEEEE-EEEEEHHHC
T ss_conf             993662899999751066642332407887347777--55-11-09999999998603110510125899-877633321


Q ss_pred             HHHHHHHHHHHCCCCCCCCCCCCCCEECCCCCCCCCCCCCCCHHHHHHHHHHHCCCCEEEEEECCC-CEEHHCCCCCCCC
Q ss_conf             753212344412432236765433211022223322245479899999988622655179974222-0000002356543
Q gi|254780619|r  366 VNGISRRYHSVHLSTRYRNSALPHLQVIDMRGQTIAQGKSLSPEMIDGIRHTLARNEQTLLFLNRR-GYAPLTLCQVCGN  444 (731)
Q Consensus       366 ~~~~~g~~~~~~l~~R~~~~~~P~i~ivDm~~~~~~~~~~lS~~l~~~i~~~l~~g~qvll~lnRr-Gya~~~~C~~Cg~  444 (731)
                      ......        .+..+.            + .    .....+...|++.=-+|.+.+|=+||- +-|..+.    ..
T Consensus       392 ~~~~~~--------~k~~~k------------~-~----~~~~kiq~Lmk~ig~~~kpkiiD~t~q~~ta~~l~----Es  442 (731)
T KOG0347         392 QPLSSS--------RKKKDK------------E-D----ELNAKIQHLMKKIGFRGKPKIIDLTPQSATASTLT----ES  442 (731)
T ss_pred             CHHHHH--------HHCCCH------------H-H----HHHHHHHHHHHHHCCCCCCEEEECCCCHHHHHHHH----HH
T ss_conf             705776--------542211------------4-5----56679999999847568982676682044788888----77


Q ss_pred             CCCCC--CCCCEEEEECCCCCCEECHHHCCCCCCCCCCCCCCCCEECCCCCCHHHHHHHHHHCCCCCHHHHCCCCCCCCH
Q ss_conf             43101--4652012113578320000210244655566678741100135428998888520485200010232113586
Q gi|254780619|r  445 RLKCL--HCSCWLVEHRSKKKLYCHQCGHSAIYSQSCVVCGSSGKMIACGFGIERIAEEVCEYFPLARISILSSDLEGGG  522 (731)
Q Consensus       445 ~~~C~--~C~~~l~~h~~~~~l~Ch~Cg~~~~~~~~Cp~Cg~~~~l~~~G~Gte~~~e~l~~~fp~~~v~~~d~d~~~~~  522 (731)
                      .+.||  +=|.+|.|.      .-.|=|.+.-      -|+|-+       -+-|+.-.|+.+  +++-+-+.+..+ -|
T Consensus       443 ~I~C~~~eKD~ylyYf------l~ryPGrTlV------F~NsId-------~vKRLt~~L~~L--~i~p~~LHA~M~-QK  500 (731)
T KOG0347         443 LIECPPLEKDLYLYYF------LTRYPGRTLV------FCNSID-------CVKRLTVLLNNL--DIPPLPLHASMI-QK  500 (731)
T ss_pred             HHCCCCCCCCEEEEEE------EEECCCCEEE------EECHHH-------HHHHHHHHHHHC--CCCCCHHHHHHH-HH
T ss_conf             6358854454068998------8636983599------841188-------999999997416--999710257788-99


Q ss_pred             HHHHHHHHHHCCCCCCEEEEEHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEE
Q ss_conf             78999998621257657987044302311345201233000344310245578999998754311025667886899993
Q gi|254780619|r  523 GRLQLQLSAIAKGEIDIIIGTQLVAKGHNFPRMSLVGVVDGDLGLTNADLRSSERTFQLLSQVTGRAGRFGLKSLGLIQA  602 (731)
Q Consensus       523 ~~~~~~~~~~~~~~~~ilvgTq~i~kg~~fp~v~lv~il~aD~~l~~pd~ra~E~~~qll~qv~gRagr~~~~g~v~iQt  602 (731)
                      .. -+-|+.|.+....+||+|-..|.|+|+|+|+-|+-...      |      |+.-.++--+||..|+...|--++- 
T Consensus       501 qR-LknLEkF~~~~~~VLiaTDVAARGLDIp~V~HVIHYqV------P------rtseiYVHRSGRTARA~~~Gvsvml-  566 (731)
T KOG0347         501 QR-LKNLEKFKQSPSGVLIATDVAARGLDIPGVQHVIHYQV------P------RTSEIYVHRSGRTARANSEGVSVML-  566 (731)
T ss_pred             HH-HHHHHHHHCCCCEEEEEEHHHHCCCCCCCCCEEEEEEC------C------CCCCEEEECCCCCCCCCCCCEEEEE-
T ss_conf             99-87699874488817996234442588878636789606------8------7532467626653225678837998-


Q ss_pred             CCCC
Q ss_conf             2986
Q gi|254780619|r  603 YQPT  606 (731)
Q Consensus       603 ~~p~  606 (731)
                      -.|.
T Consensus       567 ~~P~  570 (731)
T KOG0347         567 CGPQ  570 (731)
T ss_pred             ECHH
T ss_conf             6817


No 76 
>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=98.60  E-value=1.9e-07  Score=76.08  Aligned_cols=116  Identities=23%  Similarity=0.377  Sum_probs=83.9

Q ss_pred             HHHHHHHHHHHCCCCEEEEEECCCCEEHHCCCCCCCCCCCCCCCCCEEEEECCCCCCEECHHHCCCCCCCCCCCCCCCCE
Q ss_conf             89999998862265517997422200000023565434310146520121135783200002102446555666787411
Q gi|254780619|r  408 PEMIDGIRHTLARNEQTLLFLNRRGYAPLTLCQVCGNRLKCLHCSCWLVEHRSKKKLYCHQCGHSAIYSQSCVVCGSSGK  487 (731)
Q Consensus       408 ~~l~~~i~~~l~~g~qvll~lnRrGya~~~~C~~Cg~~~~C~~C~~~l~~h~~~~~l~Ch~Cg~~~~~~~~Cp~Cg~~~~  487 (731)
                      +.+.+.|++.+++|+++|+|.|.+..+                                                     
T Consensus        15 ~~l~~~i~~~~~~~~kviIF~~~~~~~-----------------------------------------------------   41 (131)
T cd00079          15 EALLELLKEHLKKGGKVLIFCPSKKML-----------------------------------------------------   41 (131)
T ss_pred             HHHHHHHHHHHHCCCEEEEEECCHHHH-----------------------------------------------------
T ss_conf             999999999997899099997889999-----------------------------------------------------


Q ss_pred             ECCCCCCHHHHHHHHHHCCCCCHHHHCCCCCCCCHHHHHHHHHHHCCCCCCEEEEEHHHCCCCCCCCCCHHHHHHHHHHH
Q ss_conf             00135428998888520485200010232113586789999986212576579870443023113452012330003443
Q gi|254780619|r  488 MIACGFGIERIAEEVCEYFPLARISILSSDLEGGGGRLQLQLSAIAKGEIDIIIGTQLVAKGHNFPRMSLVGVVDGDLGL  567 (731)
Q Consensus       488 l~~~G~Gte~~~e~l~~~fp~~~v~~~d~d~~~~~~~~~~~~~~~~~~~~~ilvgTq~i~kg~~fp~v~lv~il~aD~~l  567 (731)
                              +.+++.|++  ++.++..++++..  ....+.+++.|.+++.+|||+|.+++-|+|+|.++.|++.|..   
T Consensus        42 --------~~l~~~L~~--~~~~~~~~~~~~~--~~~R~~~~~~F~~~~~~ilv~t~~~~~Gldl~~~~~vI~~~~~---  106 (131)
T cd00079          42 --------DELAELLRK--PGIKVAALHGDGS--QEEREEVLKDFREGEIVVLVATDVIARGIDLPNVSVVINYDLP---  106 (131)
T ss_pred             --------HHHHHHHHH--CCCCEEEEECCCC--HHHHHHHHHHHHHHCEEEEEEEECCEECCCCCCCCEEEEECCC---
T ss_conf             --------999999955--8998999989999--9999999999775401048875112003661028799997899---


Q ss_pred             HHHHHHHHHHHHHHHHHHHHCCCCCCCCCEEEE
Q ss_conf             102455789999987543110256678868999
Q gi|254780619|r  568 TNADLRSSERTFQLLSQVTGRAGRFGLKSLGLI  600 (731)
Q Consensus       568 ~~pd~ra~E~~~qll~qv~gRagr~~~~g~v~i  600 (731)
                          +     ....+.|..||+||...+|.+++
T Consensus       107 ----~-----s~~~~~Q~~GR~~R~gq~~~~~~  130 (131)
T cd00079         107 ----W-----SPSSYLQRIGRAGRAGQKGTAIL  130 (131)
T ss_pred             ----C-----CHHHHHHHHHCCCCCCCCEEEEE
T ss_conf             ----6-----98999989721670899637997


No 77 
>KOG0352 consensus
Probab=98.56  E-value=4.8e-06  Score=65.32  Aligned_cols=333  Identities=20%  Similarity=0.243  Sum_probs=185.0

Q ss_pred             CCHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHCCCCCEEEEEE
Q ss_conf             88378999999987520489619984475315799999999998514684799715210013445554303897689962
Q gi|254780619|r  199 LDKNQQDVVEQVVPLCTKGFAVSLISGVTGSGKTEVYLEIVAAVLHLGKQVLILLPEISLTSAILERFQKRFGVKPAEWH  278 (731)
Q Consensus       199 Lt~eQ~~a~~~i~~~~~~~f~~~LL~GvTGSGKTEVYl~li~~~L~~GkqvLiLvPEI~Lt~Q~~~rl~~rF~~~v~v~H  278 (731)
                      -++-|..|+.-+.+...    -....=-||+||..-|- + -..+..| =.+|.-|-|+|...-++-+.. +...+..++
T Consensus        21 Ks~LQE~A~~c~VK~k~----DVyVsMPTGaGKSLCyQ-L-PaL~~~g-ITIV~SPLiALIkDQiDHL~~-LKVp~~SLN   92 (641)
T KOG0352          21 KSRLQEQAINCIVKRKC----DVYVSMPTGAGKSLCYQ-L-PALVHGG-ITIVISPLIALIKDQIDHLKR-LKVPCESLN   92 (641)
T ss_pred             CCHHHHHHHHHHHHCCC----CEEEECCCCCCHHHHHH-C-HHHHHCC-EEEEECHHHHHHHHHHHHHHH-HCCCHHHHH
T ss_conf             37578998999883467----37996468876014542-6-5877288-189930789999999877874-056166640


Q ss_pred             CCCCCHHHHHHHHHHHCCCCEE---EEEC---CHHHHHHH-------CCCEEEEEEECCCCCCH-HCCCCCCCHHHHHHH
Q ss_conf             3557235667899997199739---9940---01211001-------00013677405532100-002443224899999
Q gi|254780619|r  279 SSLSTSMREKIWRQVARGAISV---IVGV---RSALFLPF-------KKLGLIVIDEEHDISYK-QEEGILYNARDMSIV  344 (731)
Q Consensus       279 S~ls~~eR~~~w~~i~~G~~~I---VIGt---RSAif~P~-------~nLglIIvDEEHd~syk-q~~~pry~aRdvA~~  344 (731)
                      |+||..||-++...+..-++.+   .|..   -+.-|-|+       .-|..++|||.|=-|-. .+-.|  +--.+.-+
T Consensus        93 SKlSt~ER~ri~~DL~~ekp~~K~LYITPE~AAt~~FQ~lLn~L~~r~~L~Y~vVDEAHCVSQWGHDFRP--DYL~LG~L  170 (641)
T KOG0352          93 SKLSTVERSRIMGDLAKEKPTIKMLYITPEGAATDGFQKLLNGLANRDVLRYIVVDEAHCVSQWGHDFRP--DYLTLGSL  170 (641)
T ss_pred             CHHHHHHHHHHHHHHHHCCCCEEEEEECHHHHHHHHHHHHHHHHHHHCEEEEEEECHHHHHHHHCCCCCC--CHHHHHHH
T ss_conf             1210788999988887437751489976315556668999998874140224773346667762666682--04446667


Q ss_pred             HHHHCCCCEECCCCCCCHHHHHHHHHHHHHHHCCCCCCCCCCCCCCEE---CC--CCCCCCCCCCCCCHHH---HHHHHH
Q ss_conf             751103210000245432467753212344412432236765433211---02--2223322245479899---999988
Q gi|254780619|r  345 RGKIESFPVVLVSATPSIESRVNGISRRYHSVHLSTRYRNSALPHLQV---ID--MRGQTIAQGKSLSPEM---IDGIRH  416 (731)
Q Consensus       345 Ra~~~~~~lilgSATPSles~~~~~~g~~~~~~l~~R~~~~~~P~i~i---vD--m~~~~~~~~~~lS~~l---~~~i~~  416 (731)
                      |+++.++|.+--+||-+.+.    +...|.-++|.+-......|.++-   -|  |+       ..|++.+   -+--+.
T Consensus       171 RS~~~~vpwvALTATA~~~V----qEDi~~qL~L~~PVAiFkTP~FR~NLFYD~~~K-------~~I~D~~~~LaDF~~~  239 (641)
T KOG0352         171 RSVCPGVPWVALTATANAKV----QEDIAFQLKLRNPVAIFKTPTFRDNLFYDNHMK-------SFITDCLTVLADFSSS  239 (641)
T ss_pred             HHHCCCCCEEEEECCCCHHH----HHHHHHHHHCCCCHHHHCCCCHHHHHHHHHHHH-------HHHCCHHHHHHHHHHH
T ss_conf             74469996698543467767----799999976058544405741454445788888-------7641377789999998


Q ss_pred             HHCCCCEEEEEECCCCEEHHCCCCCCCCCCCCCCCCCEEEEECCCCCCEECHHHCCCCCCCCCCCCCCCCEECCCCCCHH
Q ss_conf             62265517997422200000023565434310146520121135783200002102446555666787411001354289
Q gi|254780619|r  417 TLARNEQTLLFLNRRGYAPLTLCQVCGNRLKCLHCSCWLVEHRSKKKLYCHQCGHSAIYSQSCVVCGSSGKMIACGFGIE  496 (731)
Q Consensus       417 ~l~~g~qvll~lnRrGya~~~~C~~Cg~~~~C~~C~~~l~~h~~~~~l~Ch~Cg~~~~~~~~Cp~Cg~~~~l~~~G~Gte  496 (731)
                      +|-+  +--..-|.+|+..               |++  +           ||-.+    +.|-.-.  -.+.-.|.|.-
T Consensus       240 ~LG~--~~~~~~~~K~~~G---------------CGI--V-----------YCRTR----~~cEq~A--I~l~~~Gi~A~  283 (641)
T KOG0352         240 NLGK--HEKASQNKKTFTG---------------CGI--V-----------YCRTR----NECEQVA--IMLEIAGIPAM  283 (641)
T ss_pred             HCCC--CHHHHCCCCCCCC---------------CEE--E-----------EECCH----HHHHHHH--HHHHHCCCCHH
T ss_conf             6289--0444117877777---------------327--9-----------96028----8999898--87532476267


Q ss_pred             HHHHHHHHCCCCCHHHHCCCCCCCCHHHHHHHHHHHCCCCCCEEEEEHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf             98888520485200010232113586789999986212576579870443023113452012330003443102455789
Q gi|254780619|r  497 RIAEEVCEYFPLARISILSSDLEGGGGRLQLQLSAIAKGEIDIIIGTQLVAKGHNFPRMSLVGVVDGDLGLTNADLRSSE  576 (731)
Q Consensus       497 ~~~e~l~~~fp~~~v~~~d~d~~~~~~~~~~~~~~~~~~~~~ilvgTq~i~kg~~fp~v~lv~il~aD~~l~~pd~ra~E  576 (731)
                      ---.-|+                  ++.....-++..+++.-|+++|---.-|.|=|+|..|+--|.-            
T Consensus       284 AYHAGLK------------------~~ERTeVQe~WM~~~~PvI~AT~SFGMGVDKp~VRFViHW~~~------------  333 (641)
T KOG0352         284 AYHAGLK------------------KKERTEVQEKWMNNEIPVIAATVSFGMGVDKPDVRFVIHWSPS------------  333 (641)
T ss_pred             HHHHHCC------------------CCHHHHHHHHHHCCCCCEEEEEECCCCCCCCCCEEEEEECCHH------------
T ss_conf             7650014------------------1126889999862788779996024446687761599951705------------


Q ss_pred             HHHHHHHHHHHCCCCCCCCCEEEE-EECCCCCHHHHHHHHCCHH
Q ss_conf             999987543110256678868999-9329864888999958979
Q gi|254780619|r  577 RTFQLLSQVTGRAGRFGLKSLGLI-QAYQPTHPVMQALVSGDAD  619 (731)
Q Consensus       577 ~~~qll~qv~gRagr~~~~g~v~i-Qt~~p~~~~~~~~~~~d~~  619 (731)
                      +...-+.|-+|||||..+++-.=+ -+++ |-..+..|+.++-.
T Consensus       334 qn~AgYYQESGRAGRDGk~SyCRLYYsR~-D~~~i~FLi~~e~a  376 (641)
T KOG0352         334 QNLAGYYQESGRAGRDGKRSYCRLYYSRQ-DKNALNFLVSGELA  376 (641)
T ss_pred             HHHHHHHHHCCCCCCCCCCCCEEEEECCC-CHHHHHHHHHHHHH
T ss_conf             65789988615356677725201333214-05777799776789


No 78 
>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=98.49  E-value=7.7e-07  Score=71.41  Aligned_cols=114  Identities=26%  Similarity=0.451  Sum_probs=83.7

Q ss_pred             HHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHHHHHHHHHHC--CCCEEEEECCCHHHHHHHHHHHCCC---C--CE
Q ss_conf             378999999987520489619984475315799999999998514--6847997152100134455543038---9--76
Q gi|254780619|r  201 KNQQDVVEQVVPLCTKGFAVSLISGVTGSGKTEVYLEIVAAVLHL--GKQVLILLPEISLTSAILERFQKRF---G--VK  273 (731)
Q Consensus       201 ~eQ~~a~~~i~~~~~~~f~~~LL~GvTGSGKTEVYl~li~~~L~~--GkqvLiLvPEI~Lt~Q~~~rl~~rF---~--~~  273 (731)
                      .-|+.....+..  .+.|   =+=-=||=|||=.= -+|+..|+.  |+.|++++|+--|+.|..+++++.-   |  ..
T Consensus        87 s~Qk~WAKRv~~--~~SF---ai~APTGVGKttFG-~~mslflA~kKGkR~y~ilPT~lLv~Qv~~kl~~~~~k~g~~~~  160 (1843)
T TIGR01054        87 SIQKSWAKRVLK--GDSF---AIVAPTGVGKTTFG-LVMSLFLAKKKGKRSYIILPTTLLVKQVAEKLSSLAEKEGVGIV  160 (1843)
T ss_pred             HHHHHHHHHHHC--CCCE---EEECCCCCCHHHHH-HHHHHHHHHHCCCEEEEEECHHHHHHHHHHHHHHHCCCCCCCCE
T ss_conf             567999999641--7964---89805887677999-99999986542987899947078899999998752002575000


Q ss_pred             --EEEEECCCCCHHHHHHHHHHHCCCCEEEEECCHHHHH-------H-HCCCEEEEEEE
Q ss_conf             --8996235572356678999971997399940012110-------0-10001367740
Q gi|254780619|r  274 --PAEWHSSLSTSMREKIWRQVARGAISVIVGVRSALFL-------P-FKKLGLIVIDE  322 (731)
Q Consensus       274 --v~v~HS~ls~~eR~~~w~~i~~G~~~IVIGtRSAif~-------P-~~nLglIIvDE  322 (731)
                        +..|||.|+.++|.+.-.++.+|..+|+|+|  +.|+       + =.+-.+|+||+
T Consensus       161 ~l~~~yhS~L~~~~kke~~Eri~~GDfdilitT--~~FL~K~~~~L~~~y~F~liFVDD  217 (1843)
T TIGR01054       161 RLLGAYHSKLSTKEKKEVKERIENGDFDILITT--SMFLSKNFDKLKNQYKFDLIFVDD  217 (1843)
T ss_pred             EEEEEEECCCCHHHHHHHHHHHHCCCEEEEHHH--HHHHHHHHHHCCCCCEEEEEEEEC
T ss_conf             022210112654567889998731891786122--468887665178985144899715


No 79 
>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=98.40  E-value=0.00037  Score=50.86  Aligned_cols=344  Identities=21%  Similarity=0.251  Sum_probs=207.0

Q ss_pred             CCHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHCCCCCEEEEEE
Q ss_conf             88378999999987520489619984475315799999999998514684799715210013445554303897689962
Q gi|254780619|r  199 LDKNQQDVVEQVVPLCTKGFAVSLISGVTGSGKTEVYLEIVAAVLHLGKQVLILLPEISLTSAILERFQKRFGVKPAEWH  278 (731)
Q Consensus       199 Lt~eQ~~a~~~i~~~~~~~f~~~LL~GvTGSGKTEVYl~li~~~L~~GkqvLiLvPEI~Lt~Q~~~rl~~rF~~~v~v~H  278 (731)
                      --+.|.++++........    .|+==-||-||-.=| ++-  ++-.++=.||.-|=|+|-..-+..|+. +|..-..|.
T Consensus        12 Frp~Q~e~I~~~L~g~RD----~~vvMpTG~GKSLCY-Q~P--a~~~~G~t~VIsPLiSLm~DQV~~L~~-~~i~A~~L~   83 (497)
T TIGR00614        12 FRPVQLEVINAVLEGRRD----CLVVMPTGGGKSLCY-QLP--ALYSDGLTLVISPLISLMEDQVLQLKA-SGIPATFLN   83 (497)
T ss_pred             CCHHHHHHHHHHHCCCCC----EEEEECCCCCHHHHH-HHH--HHHCCCCEEEECCHHHHHHHHHHHHHH-CCCCEECCC
T ss_conf             551489999987548975----699815898603676-405--675089649973636568999999874-486301044


Q ss_pred             CCCCCHHHHHHHHHH--HCCCCEEEEEC-----CH-HHHHHH------CCCEEEEEEECCCCCCHHCCC-CCCCHHHHHH
Q ss_conf             355723566789999--71997399940-----01-211001------000136774055321000024-4322489999
Q gi|254780619|r  279 SSLSTSMREKIWRQV--ARGAISVIVGV-----RS-ALFLPF------KKLGLIVIDEEHDISYKQEEG-ILYNARDMSI  343 (731)
Q Consensus       279 S~ls~~eR~~~w~~i--~~G~~~IVIGt-----RS-Aif~P~------~nLglIIvDEEHd~sykq~~~-pry~aRdvA~  343 (731)
                      |..|..+..++...+  ++|+.+++==|     .+ .+|--+      .++.+|.|||-|=-|  |+-. +|=+-+.+..
T Consensus        84 s~~s~~~~~~v~~~~~~k~g~~kllYvtPE~~~~~~~ll~~Le~~Y~~~~~~~iAvDEAHCiS--qWGHDFR~~Y~~LG~  161 (497)
T TIGR00614        84 SSQSKEQQKEVLTDLSKKDGKLKLLYVTPEKISKSKSLLQTLEKLYERKGITLIAVDEAHCIS--QWGHDFRPDYKALGS  161 (497)
T ss_pred             CCCCHHHHHHHHHHHHHHCCCEEEEEECHHHHHCCHHHHHHHHHHHHHCCCEEEEEECEEEEC--CCCCCCCHHHHHHHH
T ss_conf             325778999999998730797589971634653464789999998864496699983215435--888874079999657


Q ss_pred             HHHHHCCCCEECCCCCCCHHHHHHHHHHHHHHHCCCC---CCCCCCCCCCEECCCCCCCCCCCCCCCHHHHHHHH-HHHC
Q ss_conf             9751103210000245432467753212344412432---23676543321102222332224547989999998-8622
Q gi|254780619|r  344 VRGKIESFPVVLVSATPSIESRVNGISRRYHSVHLST---RYRNSALPHLQVIDMRGQTIAQGKSLSPEMIDGIR-HTLA  419 (731)
Q Consensus       344 ~Ra~~~~~~lilgSATPSles~~~~~~g~~~~~~l~~---R~~~~~~P~i~ivDm~~~~~~~~~~lS~~l~~~i~-~~l~  419 (731)
                      +|.+.=++|++=-|||-+-.+..-+    .+.|.|.+   -......|+++.-=+++....  ..+...|.+-|. +.=.
T Consensus       162 Lk~~fP~vP~~ALTATA~~~~~~Di----~~~L~l~~p~~~~~SFdRPNl~y~v~~K~~n~--~~~~~dl~~f~~~~~~s  235 (497)
T TIGR00614       162 LKQKFPNVPIMALTATASPSVREDI----LRILNLKNPQVFITSFDRPNLYYEVRRKTSNT--KKILEDLLRFIVKKASS  235 (497)
T ss_pred             HHHHCCCCCEEEEECCCCHHHHHHH----HHHHCCCCCCEEEECCCCCCCEEEEECCCCCH--HHHHHHHHHHHHHHCCC
T ss_conf             8885488743643405786789999----98722136624640466876303400578970--25899999998752035


Q ss_pred             CCCEEEEEECCCCEEHHCCCCCCCCCCCCCCCCCEEEEECCCCCCEECHHHCCCCCCCCCCCCCCCCEECCCCCCHHHHH
Q ss_conf             65517997422200000023565434310146520121135783200002102446555666787411001354289988
Q gi|254780619|r  420 RNEQTLLFLNRRGYAPLTLCQVCGNRLKCLHCSCWLVEHRSKKKLYCHQCGHSAIYSQSCVVCGSSGKMIACGFGIERIA  499 (731)
Q Consensus       420 ~g~qvll~lnRrGya~~~~C~~Cg~~~~C~~C~~~l~~h~~~~~l~Ch~Cg~~~~~~~~Cp~Cg~~~~l~~~G~Gte~~~  499 (731)
                      .+++       +|-++.++|                                           -|..       -+|++.
T Consensus       236 ~~~~-------~G~sGIIYC-------------------------------------------~SR~-------~~e~~a  258 (497)
T TIGR00614       236 AWEF-------KGKSGIIYC-------------------------------------------PSRK-------KSEQVA  258 (497)
T ss_pred             CCCC-------CCCCEEEEC-------------------------------------------CCCH-------HHHHHH
T ss_conf             6524-------588302752-------------------------------------------8723-------489999


Q ss_pred             HHHHHCCCCCHHHHCCCCCCCCHHHHHHHHHHHC-CCCCCEEEEEHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             8852048520001023211358678999998621-257657987044302311345201233000344310245578999
Q gi|254780619|r  500 EEVCEYFPLARISILSSDLEGGGGRLQLQLSAIA-KGEIDIIIGTQLVAKGHNFPRMSLVGVVDGDLGLTNADLRSSERT  578 (731)
Q Consensus       500 e~l~~~fp~~~v~~~d~d~~~~~~~~~~~~~~~~-~~~~~ilvgTq~i~kg~~fp~v~lv~il~aD~~l~~pd~ra~E~~  578 (731)
                      ++|++.==.+.-.----.    ....+.+=.+|. ..++.|+|+|=.=.=|.|=|+|..|+=-++=        |+-|-.
T Consensus       259 ~~L~~~G~~a~aYHAGl~----~~~R~~V~~~f~nrD~~QvVvATvAFGMGInKpdvRfViH~~~P--------k~~EsY  326 (497)
T TIGR00614       259 AELQKLGIAAGAYHAGLE----ISARKEVQHKFQNRDEIQVVVATVAFGMGINKPDVRFVIHYSLP--------KSMESY  326 (497)
T ss_pred             HHHHHCCCEEEHHHCCCC----HHHHHHHHHHHHCCCCCEEEEEEEECCCCCCCCCCCEEEEECCC--------CCCCCC
T ss_conf             999755861002402688----64778999987503885799987212688876353678850788--------562110


Q ss_pred             HHHHHHHHHCCCCCCCCCEEEEEECCC-CCHHHHHHHHCCHHH-HHHHHHHHHHHC
Q ss_conf             998754311025667886899993298-648889999589799-999999999981
Q gi|254780619|r  579 FQLLSQVTGRAGRFGLKSLGLIQAYQP-THPVMQALVSGDADS-FYESEIRARESV  632 (731)
Q Consensus       579 ~qll~qv~gRagr~~~~g~v~iQt~~p-~~~~~~~~~~~d~~~-f~~~el~~R~~~  632 (731)
                          .|=+|||||-+-+...++- |.| |-..++.++.-..++ +...+.-+++.+
T Consensus       327 ----YQE~GRAGRDgl~s~c~lf-y~~aD~~~~~~~l~e~~~~~~ht~~~~~~~~~  377 (497)
T TIGR00614       327 ----YQESGRAGRDGLPSECVLF-YAPADIARLRRLLVEEPDGKYHTQRTYKLKLL  377 (497)
T ss_pred             ----CCCCCCCCCCCCCCCEEEE-ECHHHHHHHHHHHEECCCCCHHHHHHHHHHHH
T ss_conf             ----1355556789732010233-04356999988740045775157899999999


No 80 
>KOG0947 consensus
Probab=98.38  E-value=5.8e-06  Score=64.72  Aligned_cols=138  Identities=21%  Similarity=0.334  Sum_probs=95.6

Q ss_pred             CCCHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHCCCCCEEEEE
Q ss_conf             68837899999998752048961998447531579999999999851468479971521001344555430389768996
Q gi|254780619|r  198 ILDKNQQDVVEQVVPLCTKGFAVSLISGVTGSGKTEVYLEIVAAVLHLGKQVLILLPEISLTSAILERFQKRFGVKPAEW  277 (731)
Q Consensus       198 ~Lt~eQ~~a~~~i~~~~~~~f~~~LL~GvTGSGKTEVYl~li~~~L~~GkqvLiLvPEI~Lt~Q~~~rl~~rF~~~v~v~  277 (731)
                      .+..-|+.|+....    .+- ....-.-|.||||-|.=-+|+-+-+.+..+++--|=-+|..|-++.|++.||+.- ++
T Consensus       297 elD~FQk~Ai~~le----rg~-SVFVAAHTSAGKTvVAEYAialaq~h~TR~iYTSPIKALSNQKfRDFk~tF~Dvg-Ll  370 (1248)
T KOG0947         297 ELDTFQKEAIYHLE----RGD-SVFVAAHTSAGKTVVAEYAIALAQKHMTRTIYTSPIKALSNQKFRDFKETFGDVG-LL  370 (1248)
T ss_pred             CCCHHHHHHHHHHH----CCC-EEEEEECCCCCCCHHHHHHHHHHHHHCCCEEECCHHHHHCCCHHHHHHHHCCCCC-EE
T ss_conf             76678999999997----278-1799713778843699999999886355157526346540015788877426665-45


Q ss_pred             ECCCCCHHHHHHHHHHHCCCCEEEEEC----CHHHHH---HHCCCEEEEEEECCCCCCHHCC--CCCCCHHHHHHHHHHH
Q ss_conf             235572356678999971997399940----012110---0100013677405532100002--4432248999997511
Q gi|254780619|r  278 HSSLSTSMREKIWRQVARGAISVIVGV----RSALFL---PFKKLGLIVIDEEHDISYKQEE--GILYNARDMSIVRGKI  348 (731)
Q Consensus       278 HS~ls~~eR~~~w~~i~~G~~~IVIGt----RSAif~---P~~nLglIIvDEEHd~sykq~~--~pry~aRdvA~~Ra~~  348 (731)
                      ++...           .+-++.++|=|    ||-++-   =..|+..||.||-|   |-.+.  +.-|-  +|-+|.-+ 
T Consensus       371 TGDvq-----------inPeAsCLIMTTEILRsMLYrgadliRDvE~VIFDEVH---YiND~eRGvVWE--EViIMlP~-  433 (1248)
T KOG0947         371 TGDVQ-----------INPEASCLIMTTEILRSMLYRGADLIRDVEFVIFDEVH---YINDVERGVVWE--EVIIMLPR-  433 (1248)
T ss_pred             ECCEE-----------ECCCCCEEEEHHHHHHHHHHCCCCHHHCCCEEEEEEEE---ECCCCCCCCCCE--EEEEECCC-
T ss_conf             14433-----------27775467656999999875155432113369874035---414413562210--12253255-


Q ss_pred             CCCCEECCCCC
Q ss_conf             03210000245
Q gi|254780619|r  349 ESFPVVLVSAT  359 (731)
Q Consensus       349 ~~~~lilgSAT  359 (731)
                       .+.+||-|||
T Consensus       434 -HV~~IlLSAT  443 (1248)
T KOG0947         434 -HVNFILLSAT  443 (1248)
T ss_pred             -CCEEEEEECC
T ss_conf             -4159998465


No 81 
>KOG0332 consensus
Probab=98.35  E-value=4.7e-06  Score=65.42  Aligned_cols=285  Identities=21%  Similarity=0.276  Sum_probs=151.2

Q ss_pred             ECCCCHHHHHHHHHHHHHHHHC---CCCEEEEECCCHHHHHHHHHHHCC--CC-CEE-EEEECC-CCCHHHHHHHHHHHC
Q ss_conf             4475315799999999998514---684799715210013445554303--89-768-996235-572356678999971
Q gi|254780619|r  224 SGVTGSGKTEVYLEIVAAVLHL---GKQVLILLPEISLTSAILERFQKR--FG-VKP-AEWHSS-LSTSMREKIWRQVAR  295 (731)
Q Consensus       224 ~GvTGSGKTEVYl~li~~~L~~---GkqvLiLvPEI~Lt~Q~~~rl~~r--F~-~~v-~v~HS~-ls~~eR~~~w~~i~~  295 (731)
                      +.-.|+|||--+.-.+-.-+..   --|++-|.|+--|++|+..-|.+-  |- ... +.|-.+ ...+...        
T Consensus       135 QsqsGtGKTaaFvL~MLsRvd~~~~~PQ~iCLaPtrELA~Q~~eVv~eMGKf~~ita~yair~sk~~rG~~l--------  206 (477)
T KOG0332         135 QSQSGTGKTAAFVLTMLSRVDPDVVVPQCICLAPTRELAPQTGEVVEEMGKFTELTASYAIRGSKAKRGNKL--------  206 (477)
T ss_pred             HHCCCCCHHHHHHHHHHHHCCCCCCCCCCEEECCHHHHHHHHHHHHHHHCCCEEEEEEEEECCCCCCCCCCC--------
T ss_conf             501788605899999987348333587740547617779989899998467011468998537644467733--------


Q ss_pred             CCCEEEEECCHHHH--------HHHCCCEEEEEEECCCCCCHHCCCCCCCHHHHHHHHHHHCCCCEECCCCCCCHHHHHH
Q ss_conf             99739994001211--------0010001367740553210000244322489999975110321000024543246775
Q gi|254780619|r  296 GAISVIVGVRSALF--------LPFKKLGLIVIDEEHDISYKQEEGILYNARDMSIVRGKIESFPVVLVSATPSIESRVN  367 (731)
Q Consensus       296 G~~~IVIGtRSAif--------~P~~nLglIIvDEEHd~sykq~~~pry~aRdvA~~Ra~~~~~~lilgSATPSles~~~  367 (731)
                       ...|||||-.-+.        .-+..+...+.||- |.+--++ +..=++  +-++|.--.++.++|=|||=.=..+.-
T Consensus       207 -~eqIviGTPGtv~Dl~~klk~id~~kikvfVlDEA-D~Mi~tq-G~~D~S--~rI~~~lP~~~QllLFSATf~e~V~~F  281 (477)
T KOG0332         207 -TEQIVIGTPGTVLDLMLKLKCIDLEKIKVFVLDEA-DVMIDTQ-GFQDQS--IRIMRSLPRNQQLLLFSATFVEKVAAF  281 (477)
T ss_pred             -HHHEEECCCCCHHHHHHHHHHHCHHHCEEEEECCH-HHHHHCC-CCCCCC--HHHHHHCCCCCEEEEEECHHHHHHHHH
T ss_conf             -22213179942899999987427666438885322-5554313-665543--104431687623776401037799999


Q ss_pred             HHHHHHHHHCCCCCCCCCCCCCCEECCCCCCCCCCCCCCCHHHHHHHHHHHCCCCEEEEEECCCCEEHHCCCCC--CCCC
Q ss_conf             32123444124322367654332110222233222454798999999886226551799742220000002356--5434
Q gi|254780619|r  368 GISRRYHSVHLSTRYRNSALPHLQVIDMRGQTIAQGKSLSPEMIDGIRHTLARNEQTLLFLNRRGYAPLTLCQV--CGNR  445 (731)
Q Consensus       368 ~~~g~~~~~~l~~R~~~~~~P~i~ivDm~~~~~~~~~~lS~~l~~~i~~~l~~g~qvll~lnRrGya~~~~C~~--Cg~~  445 (731)
                      +      ..-         .|+-..+-++.+...         +..|+       |-           ++.|..  -.+.
T Consensus       282 a------~ki---------vpn~n~i~Lk~eel~---------L~~Ik-------Ql-----------yv~C~~~~~K~~  319 (477)
T KOG0332         282 A------LKI---------VPNANVIILKREELA---------LDNIK-------QL-----------YVLCACRDDKYQ  319 (477)
T ss_pred             H------HHH---------CCCCCEEEEEHHHCC---------CCCHH-------HH-----------EEECCCHHHHHH
T ss_conf             9------985---------489840365634306---------42134-------31-----------366555166799


Q ss_pred             CCCCCCCCEEEEECCCCCCEECHHHCCCCCCCCCCCCCCCCEECCCCCCHHHHHHHHHHCCCCCHHHHCCCCCCCCHHHH
Q ss_conf             31014652012113578320000210244655566678741100135428998888520485200010232113586789
Q gi|254780619|r  446 LKCLHCSCWLVEHRSKKKLYCHQCGHSAIYSQSCVVCGSSGKMIACGFGIERIAEEVCEYFPLARISILSSDLEGGGGRL  525 (731)
Q Consensus       446 ~~C~~C~~~l~~h~~~~~l~Ch~Cg~~~~~~~~Cp~Cg~~~~l~~~G~Gte~~~e~l~~~fp~~~v~~~d~d~~~~~~~~  525 (731)
                      +.|. -=+.+|.                         |+..-|-....-.+++.+++...  +..|..+..|.+.  ...
T Consensus       320 ~l~~-lyg~~ti-------------------------gqsiIFc~tk~ta~~l~~~m~~~--Gh~V~~l~G~l~~--~~R  369 (477)
T KOG0332         320 ALVN-LYGLLTI-------------------------GQSIIFCHTKATAMWLYEEMRAE--GHQVSLLHGDLTV--EQR  369 (477)
T ss_pred             HHHH-HHHHHHH-------------------------HHEEEEEEEHHHHHHHHHHHHHC--CCEEEEEECCCHH--HHH
T ss_conf             9999-8701111-------------------------00589996202699999999843--7536785065306--788


Q ss_pred             HHHHHHHCCCCCCEEEEEHHHCCCCCCCCCCHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHCCCCCCCCCEEEE
Q ss_conf             99998621257657987044302311345201233000344-3102455789999987543110256678868999
Q gi|254780619|r  526 QLQLSAIAKGEIDIIIGTQLVAKGHNFPRMSLVGVVDGDLG-LTNADLRSSERTFQLLSQVTGRAGRFGLKSLGLI  600 (731)
Q Consensus       526 ~~~~~~~~~~~~~ilvgTq~i~kg~~fp~v~lv~il~aD~~-l~~pd~ra~E~~~qll~qv~gRagr~~~~g~v~i  600 (731)
                      ..++..|+.|+..+||.|-.+|.|.|.+.|++|+-.|.-.- -..||+-.       +.--.||+||+.+.|-++=
T Consensus       370 ~~ii~~Fr~g~~kVLitTnV~ARGiDv~qVs~VvNydlP~~~~~~pD~et-------YlHRiGRtGRFGkkG~a~n  438 (477)
T KOG0332         370 AAIIDRFREGKEKVLITTNVCARGIDVAQVSVVVNYDLPVKYTGEPDYET-------YLHRIGRTGRFGKKGLAIN  438 (477)
T ss_pred             HHHHHHHHCCCCEEEEEECHHHCCCCCCEEEEEEECCCCCCCCCCCCHHH-------HHHHHCCCCCCCCCCEEEE
T ss_conf             99999986576069987011123565313799994477645578987788-------9887023465665524898


No 82 
>PRK04914 ATP-dependent helicase HepA; Validated
Probab=98.31  E-value=2e-05  Score=60.54  Aligned_cols=156  Identities=22%  Similarity=0.240  Sum_probs=96.1

Q ss_pred             CCCHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHHHHHHHHHHCC--CCEEEEECCCHHHHHHHHHHHCCCCCEEE
Q ss_conf             6883789999999875204896199844753157999999999985146--84799715210013445554303897689
Q gi|254780619|r  198 ILDKNQQDVVEQVVPLCTKGFAVSLISGVTGSGKTEVYLEIVAAVLHLG--KQVLILLPEISLTSAILERFQKRFGVKPA  275 (731)
Q Consensus       198 ~Lt~eQ~~a~~~i~~~~~~~f~~~LL~GvTGSGKTEVYl~li~~~L~~G--kqvLiLvPEI~Lt~Q~~~rl~~rF~~~v~  275 (731)
                      .|-+.|-.+..++.....-   =+||=-..|=|||--.--++.+.+..|  +.+||+||+ +|..||...+..+|+-...
T Consensus       151 ~l~pHQ~~ia~~v~~r~~P---RvLLADEVGLGKTIEAGLIl~ell~rgra~RvLIvvP~-~L~~QW~~EL~~KF~L~f~  226 (955)
T PRK04914        151 GLIPHQLYIAHEVGRRHAP---RVLLADEVGLGKTIEAGLIIHQQLLTGRAERVLIIVPE-TLQHQWLVEMLRRFNLRFS  226 (955)
T ss_pred             CCCCHHHHHHHHHHHCCCC---CEEEECCCCCCHHHHHHHHHHHHHHCCCCCEEEEECCH-HHHHHHHHHHHHHCCCCCE
T ss_conf             6563799999999714588---48970588886899999999999974877779999277-9989999999998399809


Q ss_pred             EEECCCCCHHHHHHHHHH-HC--CCCEEEEECCH--------HHHHHHCCCEEEEEEECCCCCCHHCC-CCCCCHHHHHH
Q ss_conf             962355723566789999-71--99739994001--------21100100013677405532100002-44322489999
Q gi|254780619|r  276 EWHSSLSTSMREKIWRQV-AR--GAISVIVGVRS--------ALFLPFKKLGLIVIDEEHDISYKQEE-GILYNARDMSI  343 (731)
Q Consensus       276 v~HS~ls~~eR~~~w~~i-~~--G~~~IVIGtRS--------Aif~P~~nLglIIvDEEHd~sykq~~-~pry~aRdvA~  343 (731)
                      ++.+     +|...-..- .+  ....+||..-.        .-++.-.+-.|+||||-|.-.+..+. +..|..   ..
T Consensus       227 i~D~-----~r~~~~~~~~~NpF~~~~~vI~Sld~l~~~~~~~e~l~~a~WDLVIVDEAHhL~~~~~~~s~~y~l---ve  298 (955)
T PRK04914        227 LFDE-----ERCAEAQADADNPFETEQLVICSLDFLRKNKKRLEQALDAEWDLLVVDEAHHLVWSEEAPSREYQV---VE  298 (955)
T ss_pred             EECC-----HHHHHHHCCCCCCCCCCCEEEEEHHHHCCCHHHHHHHHCCCCCEEEEHHHHHHCCCCCCCCHHHHH---HH
T ss_conf             9551-----888875335799754589799878996039678998733898889971344530588788879999---99


Q ss_pred             HHHHHCCCCEECCCCCC---CHHHHH
Q ss_conf             97511032100002454---324677
Q gi|254780619|r  344 VRGKIESFPVVLVSATP---SIESRV  366 (731)
Q Consensus       344 ~Ra~~~~~~lilgSATP---Sles~~  366 (731)
                      ..|.... .++|-||||   ..++++
T Consensus       299 ~La~~~~-~lLLLTATP~QlG~e~~F  323 (955)
T PRK04914        299 QLAEVIP-GVLLLTATPEQLGQESHF  323 (955)
T ss_pred             HHHHHCC-CEEEEECCCCCCCCHHHH
T ss_conf             9985159-769984799889866689


No 83 
>KOG0326 consensus
Probab=98.29  E-value=8.2e-06  Score=63.53  Aligned_cols=279  Identities=22%  Similarity=0.325  Sum_probs=143.6

Q ss_pred             CCCHHHHHHHHHHHHHHHHC---CCCEEEEEC--CCHH-HHHHHHHHHCCCCCEEEEEECCCCCHHHHHHHHHHHCCCCE
Q ss_conf             75315799999999998514---684799715--2100-13445554303897689962355723566789999719973
Q gi|254780619|r  226 VTGSGKTEVYLEIVAAVLHL---GKQVLILLP--EISL-TSAILERFQKRFGVKPAEWHSSLSTSMREKIWRQVARGAIS  299 (731)
Q Consensus       226 vTGSGKTEVYl~li~~~L~~---GkqvLiLvP--EI~L-t~Q~~~rl~~rF~~~v~v~HS~ls~~eR~~~w~~i~~G~~~  299 (731)
                      -.|.|||--|.--+-+-+..   .=|+++|||  |.+| |.|...++.+..+..+.+-.++.+-.+-   -.++ ++...
T Consensus       130 KNGTGKT~a~~IP~Lekid~~~~~IQ~~ilVPtrelALQtSqvc~~lskh~~i~vmvttGGT~lrDD---I~Rl-~~~VH  205 (459)
T KOG0326         130 KNGTGKTAAYCIPVLEKIDPKKNVIQAIILVPTRELALQTSQVCKELSKHLGIKVMVTTGGTSLRDD---IMRL-NQTVH  205 (459)
T ss_pred             CCCCCCCCCEECHHHHHCCCCCCCEEEEEEEECCHHHHHHHHHHHHHHCCCCEEEEEECCCCCCCCC---EEEE-CCCEE
T ss_conf             1898873304412566528221004479996163266788799999860468499994388654432---0561-58269


Q ss_pred             EEEECCHHHH-------HHHCCCEEEEEEECCCCCCHHCCCCCCCHHHHHHHHHHHCCCCEECCCCCCCHHHHHHHHHHH
Q ss_conf             9994001211-------001000136774055321000024432248999997511032100002454324677532123
Q gi|254780619|r  300 VIVGVRSALF-------LPFKKLGLIVIDEEHDISYKQEEGILYNARDMSIVRGKIESFPVVLVSATPSIESRVNGISRR  372 (731)
Q Consensus       300 IVIGtRSAif-------~P~~nLglIIvDEEHd~sykq~~~pry~aRdvA~~Ra~~~~~~lilgSATPSles~~~~~~g~  372 (731)
                      ++|||..-++       +-+.+-.++|+||. |--.-++-+|-  .-++..+.-+  .-.++|=|||=.+-.     .+-
T Consensus       206 ~~vgTPGRIlDL~~KgVa~ls~c~~lV~DEA-DKlLs~~F~~~--~e~li~~lP~--~rQillySATFP~tV-----k~F  275 (459)
T KOG0326         206 LVVGTPGRILDLAKKGVADLSDCVILVMDEA-DKLLSVDFQPI--VEKLISFLPK--ERQILLYSATFPLTV-----KGF  275 (459)
T ss_pred             EEECCCHHHHHHHHCCCCCCHHCEEEEECHH-HHHHCHHHHHH--HHHHHHHCCC--CCEEEEEECCCCHHH-----HHH
T ss_conf             9972871788888626522001147874105-54414145678--9999875785--420467631364058-----889


Q ss_pred             HHHHCCCCCCCCCCCCCCEECCCCCCCCCCCCCCCHHHHHHHHHHHCCC-CEEEEEECCCCEEHHCCCCCCCCCCCCCCC
Q ss_conf             4441243223676543321102222332224547989999998862265-517997422200000023565434310146
Q gi|254780619|r  373 YHSVHLSTRYRNSALPHLQVIDMRGQTIAQGKSLSPEMIDGIRHTLARN-EQTLLFLNRRGYAPLTLCQVCGNRLKCLHC  451 (731)
Q Consensus       373 ~~~~~l~~R~~~~~~P~i~ivDm~~~~~~~~~~lS~~l~~~i~~~l~~g-~qvll~lnRrGya~~~~C~~Cg~~~~C~~C  451 (731)
                      + --.|.+-         ..|++-+|...                  +| .|-        |                  
T Consensus       276 m-~~~l~kP---------y~INLM~eLtl------------------~GvtQy--------Y------------------  301 (459)
T KOG0326         276 M-DRHLKKP---------YEINLMEELTL------------------KGVTQY--------Y------------------  301 (459)
T ss_pred             H-HHHCCCC---------CEEEHHHHHHH------------------CCHHHH--------E------------------
T ss_conf             9-9860586---------02204656320------------------352321--------0------------------


Q ss_pred             CCEEEEECCCCCCEECHHHCCC-CCCCCCCCCCCCCEECCCCCCHHHHHHH---HH--HCCCCCHHHHCCCCCCCCHHHH
Q ss_conf             5201211357832000021024-4655566678741100135428998888---52--0485200010232113586789
Q gi|254780619|r  452 SCWLVEHRSKKKLYCHQCGHSA-IYSQSCVVCGSSGKMIACGFGIERIAEE---VC--EYFPLARISILSSDLEGGGGRL  525 (731)
Q Consensus       452 ~~~l~~h~~~~~l~Ch~Cg~~~-~~~~~Cp~Cg~~~~l~~~G~Gte~~~e~---l~--~~fp~~~v~~~d~d~~~~~~~~  525 (731)
                          +|-++..++.|-.--+.. .+...---|.|..+       .|-++.-   |+  -.|-.++..         ....
T Consensus       302 ----afV~e~qKvhCLntLfskLqINQsIIFCNS~~r-------VELLAkKITelGyscyyiHakM~---------Q~hR  361 (459)
T KOG0326         302 ----AFVEERQKVHCLNTLFSKLQINQSIIFCNSTNR-------VELLAKKITELGYSCYYIHAKMA---------QEHR  361 (459)
T ss_pred             ----EEECHHHHHHHHHHHHHHHCCCCEEEEECCCHH-------HHHHHHHHHHCCCHHHHHHHHHH---------HHHH
T ss_conf             ----110235555649989887500445999636317-------67989888861643667788887---------7654


Q ss_pred             HHHHHHHCCCCCCEEEEEHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCEEEE-EECC
Q ss_conf             999986212576579870443023113452012330003443102455789999987543110256678868999-9329
Q gi|254780619|r  526 QLQLSAIAKGEIDIIIGTQLVAKGHNFPRMSLVGVVDGDLGLTNADLRSSERTFQLLSQVTGRAGRFGLKSLGLI-QAYQ  604 (731)
Q Consensus       526 ~~~~~~~~~~~~~ilvgTq~i~kg~~fp~v~lv~il~aD~~l~~pd~ra~E~~~qll~qv~gRagr~~~~g~v~i-Qt~~  604 (731)
                      ...+.+|++|....||.|-++..|.|.++|+.|  +|.|.-      +.+|..    .--.||+||+...|..|= -||.
T Consensus       362 NrVFHdFr~G~crnLVctDL~TRGIDiqavNvV--INFDfp------k~aEtY----LHRIGRsGRFGhlGlAInLitye  429 (459)
T KOG0326         362 NRVFHDFRNGKCRNLVCTDLFTRGIDIQAVNVV--INFDFP------KNAETY----LHRIGRSGRFGHLGLAINLITYE  429 (459)
T ss_pred             HHHHHHHHCCCCCEEEEHHHHHCCCCCCEEEEE--EECCCC------CCHHHH----HHHCCCCCCCCCCCEEEEEEEHH
T ss_conf             245565432532012420233046554102599--963788------777899----98716776578762479987503


No 84 
>COG4889 Predicted helicase [General function prediction only]
Probab=98.26  E-value=0.0002  Score=52.99  Aligned_cols=369  Identities=17%  Similarity=0.151  Sum_probs=188.7

Q ss_pred             CCCCCHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHCCC--CCE
Q ss_conf             666883789999999875204896199844753157999999999985146847997152100134455543038--976
Q gi|254780619|r  196 LPILDKNQQDVVEQVVPLCTKGFAVSLISGVTGSGKTEVYLEIVAAVLHLGKQVLILLPEISLTSAILERFQKRF--GVK  273 (731)
Q Consensus       196 ~~~Lt~eQ~~a~~~i~~~~~~~f~~~LL~GvTGSGKTEVYl~li~~~L~~GkqvLiLvPEI~Lt~Q~~~rl~~rF--~~~  273 (731)
                      ++.+.+.||.|++........+-+--|+- -.|.|||=--|++++..-+  .-+|+|||-|+|..|+.+.....-  ..+
T Consensus       159 ~kk~R~hQq~Aid~a~~~F~~n~RGkLIM-AcGTGKTfTsLkisEala~--~~iL~LvPSIsLLsQTlrew~~~~~l~~~  235 (1518)
T COG4889         159 PKKPRPHQQTAIDAAKEGFSDNDRGKLIM-ACGTGKTFTSLKISEALAA--ARILFLVPSISLLSQTLREWTAQKELDFR  235 (1518)
T ss_pred             CCCCCHHHHHHHHHHHHHCCCCCCCCEEE-ECCCCCCCHHHHHHHHHHH--HHEEEECCHHHHHHHHHHHHHHCCCCCCE
T ss_conf             78998367899999986255166775898-3378862137889999864--02365435189999999988534665512


Q ss_pred             EEEEECC----------------CCC----HHHHHHHHHHHC-CCCEEEEECCHHHH-------HHHCCCEEEEEEECCC
Q ss_conf             8996235----------------572----356678999971-99739994001211-------0010001367740553
Q gi|254780619|r  274 PAEWHSS----------------LST----SMREKIWRQVAR-GAISVIVGVRSALF-------LPFKKLGLIVIDEEHD  325 (731)
Q Consensus       274 v~v~HS~----------------ls~----~eR~~~w~~i~~-G~~~IVIGtRSAif-------~P~~nLglIIvDEEHd  325 (731)
                      .....|.                +..    ..-...|...+. ..--||-.|.-++-       +-+....|||+||.|-
T Consensus       236 a~aVcSD~kvsrs~eDik~sdl~~p~sT~~~~il~~~~~~~k~~~~~vvFsTYQSl~~i~eAQe~G~~~fDliicDEAHR  315 (1518)
T COG4889         236 ASAVCSDDKVSRSAEDIKASDLPIPVSTDLEDILSEMEHRQKANGLTVVFSTYQSLPRIKEAQEAGLDEFDLIICDEAHR  315 (1518)
T ss_pred             EEEEECCCCCCCCCCCCCHHCCCCCCCCCHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHHHCCCCCCCEEEECCHHC
T ss_conf             57886365234441232120478887574999999998753337838999702114878999974999753797440001


Q ss_pred             CC---CHHCCCC---CCCHHHHHHHHHHHCCCCEECCCCCCCHHHHHHHHHHHHHHHCCCCCCCCCCCCCCEECCCCCCC
Q ss_conf             21---0000244---32248999997511032100002454324677532123444124322367654332110222233
Q gi|254780619|r  326 IS---YKQEEGI---LYNARDMSIVRGKIESFPVVLVSATPSIESRVNGISRRYHSVHLSTRYRNSALPHLQVIDMRGQT  399 (731)
Q Consensus       326 ~s---ykq~~~p---ry~aRdvA~~Ra~~~~~~lilgSATPSles~~~~~~g~~~~~~l~~R~~~~~~P~i~ivDm~~~~  399 (731)
                      ..   |-.++.-   |.|.-.-      .-.+.=++.+|||-+=+  -..++         ++   .-....+.-|-.+.
T Consensus       316 TtGa~~a~dd~saFt~vHs~~n------iKa~kRlYmTATPkiy~--eS~K~---------kA---kd~s~~l~SMDDe~  375 (1518)
T COG4889         316 TTGATLAGDDKSAFTRVHSDQN------IKAAKRLYMTATPKIYS--ESSKA---------KA---KDHSAELSSMDDEL  375 (1518)
T ss_pred             CCCCEECCCCCCCCEEECCCCC------HHHHHHHHCCCCCHHHC--HHHHH---------HH---HHCCCEEECCCHHH
T ss_conf             4462322577201045337641------58887666006860212--25453---------03---21143011255265


Q ss_pred             CCCCCCCCHHHHHHHHHHHCCCCEEEEEECCCCE-EHHCCCCCCCCCCCCCCCCCEEEEECCCCCCEECH----------
Q ss_conf             2224547989999998862265517997422200-00002356543431014652012113578320000----------
Q gi|254780619|r  400 IAQGKSLSPEMIDGIRHTLARNEQTLLFLNRRGY-APLTLCQVCGNRLKCLHCSCWLVEHRSKKKLYCHQ----------  468 (731)
Q Consensus       400 ~~~~~~lS~~l~~~i~~~l~~g~qvll~lnRrGy-a~~~~C~~Cg~~~~C~~C~~~l~~h~~~~~l~Ch~----------  468 (731)
                      .-+..+.--.--+++...|-..-.|+++.-+++- ++.+.|.--|--       ..|....-....-||.          
T Consensus       376 ~fGeef~rl~FgeAv~rdlLTDYKVmvlaVd~~~i~~~~~~~~~~~~-------~~L~~dd~~kIvG~wnGlakr~g~~n  448 (1518)
T COG4889         376 TFGEEFHRLGFGEAVERDLLTDYKVMVLAVDKEVIAGVLQSVLSGPS-------KGLALDDVSKIVGCWNGLAKRNGEDN  448 (1518)
T ss_pred             HHCHHHHCCCHHHHHHHHHHCCCEEEEEEECHHHHHHHHHHHCCCCC-------CCCCHHHHHHHHHHHHHHHHHCCCCC
T ss_conf             54546621226778764010052589998317665245656306864-------34243445677777665665325536


Q ss_pred             --HHCCC---CCCC---CCCCCCCCCEECC-CCCCHHHHHHHHHHCCCCCHHHHCCCCCCCCHH---HHHHHHHHHCCCC
Q ss_conf             --21024---4655---5666787411001-354289988885204852000102321135867---8999998621257
Q gi|254780619|r  469 --CGHSA---IYSQ---SCVVCGSSGKMIA-CGFGIERIAEEVCEYFPLARISILSSDLEGGGG---RLQLQLSAIAKGE  536 (731)
Q Consensus       469 --Cg~~~---~~~~---~Cp~Cg~~~~l~~-~G~Gte~~~e~l~~~fp~~~v~~~d~d~~~~~~---~~~~~~~~~~~~~  536 (731)
                        -|..+   +.-+   .|..-..+..+.. +-.=.|---+||++-|++..+..-..|-+-+..   ++......|...+
T Consensus       449 ~~~~~~~d~ap~~RAIaF~k~I~tSK~i~~sFe~Vve~Y~~Elk~d~~nL~iSi~HvDGtmNal~R~~l~~l~~~~~~ne  528 (1518)
T COG4889         449 DLKNIKADTAPMQRAIAFAKDIKTSKQIAESFETVVEAYDEELKKDFKNLKISIDHVDGTMNALERLDLLELKNTFEPNE  528 (1518)
T ss_pred             CCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEEEEECCCCCCHHHHHHHHHHCCCCCCCCH
T ss_conf             54367677507889999987667788788888999999999997326683688751467300888877886158899421


Q ss_pred             CCEEEEEHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCC---CCEEEEEECCCC
Q ss_conf             6579870443023113452012330003443102455789999987543110256678---868999932986
Q gi|254780619|r  537 IDIIIGTQLVAKGHNFPRMSLVGVVDGDLGLTNADLRSSERTFQLLSQVTGRAGRFGL---KSLGLIQAYQPT  606 (731)
Q Consensus       537 ~~ilvgTq~i~kg~~fp~v~lv~il~aD~~l~~pd~ra~E~~~qll~qv~gRagr~~~---~g~v~iQt~~p~  606 (731)
                      ..||---.-++.|.|.|.+..|+.+|.-..+            -=++|..||+-|..+   -|-+|+--.-|+
T Consensus       529 ckIlSNaRcLSEGVDVPaLDsViFf~pr~sm------------VDIVQaVGRVMRKa~gK~yGYIILPIalpe  589 (1518)
T COG4889         529 CKILSNARCLSEGVDVPALDSVIFFDPRSSM------------VDIVQAVGRVMRKAKGKKYGYIILPIALPE  589 (1518)
T ss_pred             HEEECCCHHHHCCCCCCCCCEEEEECCCHHH------------HHHHHHHHHHHHHCCCCCCCEEEEEECCCC
T ss_conf             0110133154237885341237986685128------------899999999987276876656998731587


No 85 
>PRK12904 preprotein translocase subunit SecA; Reviewed
Probab=98.17  E-value=0.00066  Score=48.95  Aligned_cols=77  Identities=19%  Similarity=0.176  Sum_probs=59.5

Q ss_pred             CCCHHHHHHHHHHHHHHHHCCCCEEEEECCCHHHH---HHHHHHHCCCCCEEEEEECCCCCHHHHHHHHHHHCCCCEEEE
Q ss_conf             75315799999999998514684799715210013---445554303897689962355723566789999719973999
Q gi|254780619|r  226 VTGSGKTEVYLEIVAAVLHLGKQVLILLPEISLTS---AILERFQKRFGVKPAEWHSSLSTSMREKIWRQVARGAISVIV  302 (731)
Q Consensus       226 vTGSGKTEVYl~li~~~L~~GkqvLiLvPEI~Lt~---Q~~~rl~~rF~~~v~v~HS~ls~~eR~~~w~~i~~G~~~IVI  302 (731)
                      -||-|||.+..-.+--.--.|+.|-|+-..=-|+.   ++...+...+|-.|.+..+++++.+|...|.      ++|+-
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             ECCHHH
Q ss_conf             400121
Q gi|254780619|r  303 GVRSAL  308 (731)
Q Consensus       303 GtRSAi  308 (731)
                      ||-+.+
T Consensus       176 ~tn~e~  181 (833)
T PRK12904        176 GTNNEF  181 (833)
T ss_pred             ECCCCC
T ss_conf             125432


No 86 
>KOG0340 consensus
Probab=98.17  E-value=0.00024  Score=52.31  Aligned_cols=117  Identities=22%  Similarity=0.232  Sum_probs=71.1

Q ss_pred             CCCHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHHHHHHHHHHC---CCCEEEEECCCHHHHHHHHHHHC---CCC
Q ss_conf             688378999999987520489619984475315799999999998514---68479971521001344555430---389
Q gi|254780619|r  198 ILDKNQQDVVEQVVPLCTKGFAVSLISGVTGSGKTEVYLEIVAAVLHL---GKQVLILLPEISLTSAILERFQK---RFG  271 (731)
Q Consensus       198 ~Lt~eQ~~a~~~i~~~~~~~f~~~LL~GvTGSGKTEVYl~li~~~L~~---GkqvLiLvPEI~Lt~Q~~~rl~~---rF~  271 (731)
                      .-|+-|+..+-.|....+     .+=-.-||||||--+.-=|-+-|+.   |-=+|||-|.--|+-|+.+.|..   -.+
T Consensus        29 ~pTpiQ~~cIpkILeGrd-----cig~AkTGsGKT~AFaLPil~rLsedP~giFalvlTPTrELA~QiaEQF~alGk~l~  103 (442)
T KOG0340          29 KPTPIQQACIPKILEGRD-----CIGCAKTGSGKTAAFALPILNRLSEDPYGIFALVLTPTRELALQIAEQFIALGKLLN  103 (442)
T ss_pred             CCCCHHHHHHHHHHCCCC-----CCCCCCCCCCCCHHHHHHHHHHHCCCCCCCEEEEECCHHHHHHHHHHHHHHHCCCCC
T ss_conf             998267652487854663-----103134688741122278777613388760699954528888888899998456456


Q ss_pred             CEEEEEECCCCCHHHHHHHHHHHCCCCEEEEECC--HHHH---------HHHCCCEEEEEEEC
Q ss_conf             7689962355723566789999719973999400--1211---------00100013677405
Q gi|254780619|r  272 VKPAEWHSSLSTSMREKIWRQVARGAISVIVGVR--SALF---------LPFKKLGLIVIDEE  323 (731)
Q Consensus       272 ~~v~v~HS~ls~~eR~~~w~~i~~G~~~IVIGtR--SAif---------~P~~nLglIIvDEE  323 (731)
                      .++.+.-++++--    .-......++.+||.|-  -|-.         .-|.++...++||.
T Consensus       104 lK~~vivGG~d~i----~qa~~L~~rPHvVvatPGRlad~l~sn~~~~~~~~~rlkflVlDEA  162 (442)
T KOG0340         104 LKVSVIVGGTDMI----MQAAILSDRPHVVVATPGRLADHLSSNLGVCSWIFQRLKFLVLDEA  162 (442)
T ss_pred             CEEEEEECCHHHH----HHHHHCCCCCCEEECCCCCCCCCCCCCCCCCHHHHHCEEEEEECCH
T ss_conf             3279997568876----4544426698757517633354112687655255530046774130


No 87 
>COG1643 HrpA HrpA-like helicases [DNA replication, recombination, and repair]
Probab=98.17  E-value=5.2e-05  Score=57.40  Aligned_cols=59  Identities=17%  Similarity=0.319  Sum_probs=32.2

Q ss_pred             CCEEEEECCCHHHHHHHHHHHC-CCC--CEEEEEECCCCCHHHHHHHHHHHCCCCEEEEECC
Q ss_conf             8479971521001344555430-389--7689962355723566789999719973999400
Q gi|254780619|r  247 KQVLILLPEISLTSAILERFQK-RFG--VKPAEWHSSLSTSMREKIWRQVARGAISVIVGVR  305 (731)
Q Consensus       247 kqvLiLvPEI~Lt~Q~~~rl~~-rF~--~~v~v~HS~ls~~eR~~~w~~i~~G~~~IVIGtR  305 (731)
                      +++|+.+|=.....++.+.+++ .++  ..|.-+||.|+..|-..+|.-.-.|.=+||+.|.
T Consensus       260 GdILvFLpG~~EI~~~~~~L~~~~l~~~~~i~PLy~~L~~~eQ~rvF~p~~~~~RKVVlATN  321 (845)
T COG1643         260 GSILVFLPGQREIERTAEWLEKAELGDDLEILPLYGALSAEEQVRVFEPAPGGKRKVVLATN  321 (845)
T ss_pred             CCEEEECCCHHHHHHHHHHHHHCCCCCCCEEEECCCCCCHHHHHHHCCCCCCCCCEEEEECC
T ss_conf             98899778689999999999732447883894040359989998662878888604999751


No 88 
>smart00490 HELICc helicase superfamily c-terminal domain.
Probab=98.17  E-value=1.3e-06  Score=69.69  Aligned_cols=81  Identities=26%  Similarity=0.354  Sum_probs=65.8

Q ss_pred             HHHHHHHHHCCCCCHHHHCCCCCCCCHHHHHHHHHHHCCCCCCEEEEEHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHH
Q ss_conf             99888852048520001023211358678999998621257657987044302311345201233000344310245578
Q gi|254780619|r  496 ERIAEEVCEYFPLARISILSSDLEGGGGRLQLQLSAIAKGEIDIIIGTQLVAKGHNFPRMSLVGVVDGDLGLTNADLRSS  575 (731)
Q Consensus       496 e~~~e~l~~~fp~~~v~~~d~d~~~~~~~~~~~~~~~~~~~~~ilvgTq~i~kg~~fp~v~lv~il~aD~~l~~pd~ra~  575 (731)
                      |.+.+.|++.  +.++..+++++.  +...+++++.|.+++.+|||+|++++.|.|+|+++.|++.+..           
T Consensus         1 ~~l~~~l~~~--g~~~~~i~g~~~--~~~R~~~~~~f~~~~~~ilv~t~~~~~Gidl~~~~~vI~~~~~-----------   65 (82)
T smart00490        1 EELAELLKEL--GIKVARLHGGLS--QEEREEILEKFNNGKIKVLVATDVAERGLDLPGVDLVIIYDLP-----------   65 (82)
T ss_pred             CHHHHHHHHC--CCCEEEEECCCC--HHHHHHHHHHHHCCCCEEEEEEEEEEEECCCCCCCEEEEECCC-----------
T ss_conf             9789999888--991999989699--9999999999987997199995024211489889999997899-----------


Q ss_pred             HHHHHHHHHHHHCCCCC
Q ss_conf             99999875431102566
Q gi|254780619|r  576 ERTFQLLSQVTGRAGRF  592 (731)
Q Consensus       576 E~~~qll~qv~gRagr~  592 (731)
                       ...+.+.|..||+||.
T Consensus        66 -~~~~~~~Q~~GR~~R~   81 (82)
T smart00490       66 -WSPASYIQRIGRAGRA   81 (82)
T ss_pred             -CCHHHHHHHHCCCCCC
T ss_conf             -6989999997258789


No 89 
>pfam07652 Flavi_DEAD Flavivirus DEAD domain.
Probab=98.10  E-value=2.1e-05  Score=60.50  Aligned_cols=123  Identities=23%  Similarity=0.319  Sum_probs=82.3

Q ss_pred             EEEECCCCHHHH-HHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHCCCCCEEEEEECCCCCHHHHHHHHHHHCCCCE
Q ss_conf             998447531579-9999999998514684799715210013445554303897689962355723566789999719973
Q gi|254780619|r  221 SLISGVTGSGKT-EVYLEIVAAVLHLGKQVLILLPEISLTSAILERFQKRFGVKPAEWHSSLSTSMREKIWRQVARGAIS  299 (731)
Q Consensus       221 ~LL~GvTGSGKT-EVYl~li~~~L~~GkqvLiLvPEI~Lt~Q~~~rl~~rF~~~v~v~HS~ls~~eR~~~w~~i~~G~~~  299 (731)
                      ..|+=-.||||| .|--+++.++++++.++|||.|.=.-...+.+-++.    ..+-+|+..-.+++        .|..-
T Consensus         5 t~ld~HPGaGKTr~vLP~~v~~~i~~~lRtlVLaPTRVV~~Em~eAL~g----~~vr~~t~a~~~~~--------~~~~i   72 (146)
T pfam07652         5 TVLDLHPGAGKTRKVLPELVRECIDRRLRTLVLAPTRVVLAEMEEALRG----LPIRYHTPAVSSEH--------TGREI   72 (146)
T ss_pred             EEEECCCCCCCCCHHHHHHHHHHHHCCCEEEEECCHHHHHHHHHHHHCC----CCCEEECHHHHCCC--------CCCCE
T ss_conf             7985389999702248999999997286189977279999999999758----99467523431366--------88841


Q ss_pred             EEEECCHHHH-------HHHCCCEEEEEEECCCCCCHHCCCCCCCHHHHHHHHHHHCCCCEECCCCCCC
Q ss_conf             9994001211-------0010001367740553210000244322489999975110321000024543
Q gi|254780619|r  300 VIVGVRSALF-------LPFKKLGLIVIDEEHDISYKQEEGILYNARDMSIVRGKIESFPVVLVSATPS  361 (731)
Q Consensus       300 IVIGtRSAif-------~P~~nLglIIvDEEHd~sykq~~~pry~aRdvA~~Ra~~~~~~lilgSATPS  361 (731)
                      |-+-.+ |-|       .+..|-.+||+||-|=.     +.----+|-....+++...+.+|+.||||.
T Consensus        73 vdvmCH-AT~t~r~l~~~~~~ny~viIMDE~H~~-----DP~SIAarG~~~~~~~~g~~a~i~mTATPP  135 (146)
T pfam07652        73 VDVMCH-ATFTQRLLSPVRVPNYEVIIMDEAHFT-----DPASIAARGYISTLVELGEAAAIFMTATPP  135 (146)
T ss_pred             EEEECH-HHHHHHHHCCCCCCCEEEEEEECCCCC-----CHHHHHHHHHHHHHHHCCCEEEEEEECCCC
T ss_conf             889715-988889736888564479998512238-----989999889999885438657999956899


No 90 
>KOG0337 consensus
Probab=98.09  E-value=9.3e-05  Score=55.49  Aligned_cols=244  Identities=19%  Similarity=0.200  Sum_probs=120.4

Q ss_pred             CCCCHHHHHHHHHHHHHHHHCC----CCEEEEECCCHHHHHHHHHHHCC--C-CCEEE-EEECCCCCHHHHHHHHHHHCC
Q ss_conf             4753157999999999985146----84799715210013445554303--8-97689-962355723566789999719
Q gi|254780619|r  225 GVTGSGKTEVYLEIVAAVLHLG----KQVLILLPEISLTSAILERFQKR--F-GVKPA-EWHSSLSTSMREKIWRQVARG  296 (731)
Q Consensus       225 GvTGSGKTEVYl~li~~~L~~G----kqvLiLvPEI~Lt~Q~~~rl~~r--F-~~~v~-v~HS~ls~~eR~~~w~~i~~G  296 (731)
                      +-||||||--|+--+.+.|+..    -.+|++.|.=-|+.|+.+-+++.  | +-+.+ ++| +-+   .-+.|..+ ++
T Consensus        65 artgsgktaaf~ipm~e~Lk~~s~~g~RalilsptreLa~qtlkvvkdlgrgt~lr~s~~~g-gD~---~eeqf~~l-~~  139 (529)
T KOG0337          65 ARTGSGKTAAFLIPMIEKLKSHSQTGLRALILSPTRELALQTLKVVKDLGRGTKLRQSLLVG-GDS---IEEQFILL-NE  139 (529)
T ss_pred             EECCCCCHHHHHHHHHHHHHHCCCCCCCEEECCCCHHHHHHHHHHHHHHCCCCCHHHHHHCC-CCH---HHHHHHHH-CC
T ss_conf             52278610467889999986136446202432670889999999999851542112101126-324---88999984-15


Q ss_pred             CCEEEEECCH-----HHH--HHHCCCEEEEEEECCCCCCHHCCCCCCCHHHHHHHHHHH-CCCCEECCCCC-CCH-HHHH
Q ss_conf             9739994001-----211--001000136774055321000024432248999997511-03210000245-432-4677
Q gi|254780619|r  297 AISVIVGVRS-----ALF--LPFKKLGLIVIDEEHDISYKQEEGILYNARDMSIVRGKI-ESFPVVLVSAT-PSI-ESRV  366 (731)
Q Consensus       297 ~~~IVIGtRS-----Aif--~P~~nLglIIvDEEHd~sykq~~~pry~aRdvA~~Ra~~-~~~~lilgSAT-PSl-es~~  366 (731)
                      .++|||.|-.     ++=  +-+.....+|.||- |.-|+.-=.++.|     -..++. ++..-+|-||| |+. -.+.
T Consensus       140 npDii~ATpgr~~h~~vem~l~l~sveyVVfdEa-drlfemgfqeql~-----e~l~rl~~~~QTllfSatlp~~lv~fa  213 (529)
T KOG0337         140 NPDIIIATPGRLLHLGVEMTLTLSSVEYVVFDEA-DRLFEMGFQEQLH-----EILSRLPESRQTLLFSATLPRDLVDFA  213 (529)
T ss_pred             CCCEEEECCCEEEEEEHHEECCCCCEEEEEEHHH-HHHHHHHHHHHHH-----HHHHHCCCCCEEEEEECCCCHHHHHHH
T ss_conf             9987982485134200210012132256641013-4787653689999-----998757776307998523764467788


Q ss_pred             HHHHHHHHHHCCCCCCCCCCCC-CCEECCCCC----------CCCCCCCCCCHHHHHHHHHHHCCCCEEEEEECCCCEEH
Q ss_conf             5321234441243223676543-321102222----------33222454798999999886226551799742220000
Q gi|254780619|r  367 NGISRRYHSVHLSTRYRNSALP-HLQVIDMRG----------QTIAQGKSLSPEMIDGIRHTLARNEQTLLFLNRRGYAP  435 (731)
Q Consensus       367 ~~~~g~~~~~~l~~R~~~~~~P-~i~ivDm~~----------~~~~~~~~lS~~l~~~i~~~l~~g~qvll~lnRrGya~  435 (731)
                        +.|             ...| .|+ +|...          ....... --..|+....+... .+|.++|..+++.+-
T Consensus       214 --kaG-------------l~~p~lVR-ldvetkise~lk~~f~~~~~a~-K~aaLl~il~~~~~-~~~t~vf~~tk~hve  275 (529)
T KOG0337         214 --KAG-------------LVPPVLVR-LDVETKISELLKVRFFRVRKAE-KEAALLSILGGRIK-DKQTIVFVATKHHVE  275 (529)
T ss_pred             --HCC-------------CCCCCEEE-EEHHHHCCHHHHHHEEEECCHH-HHHHHHHHHHCCCC-CCCEEEEECCCCHHH
T ss_conf             --706-------------88871687-4014210545451422306178-89999999851256-665069831530478


Q ss_pred             HCCCCCCCCCCCCCCCCCEEEEECCCCCCEECHHHCCCCCCCCCCCCCCCCEECCCCCCHHHHHHHHHHCCCCCHHHHCC
Q ss_conf             00235654343101465201211357832000021024465556667874110013542899888852048520001023
Q gi|254780619|r  436 LTLCQVCGNRLKCLHCSCWLVEHRSKKKLYCHQCGHSAIYSQSCVVCGSSGKMIACGFGIERIAEEVCEYFPLARISILS  515 (731)
Q Consensus       436 ~~~C~~Cg~~~~C~~C~~~l~~h~~~~~l~Ch~Cg~~~~~~~~Cp~Cg~~~~l~~~G~Gte~~~e~l~~~fp~~~v~~~d  515 (731)
                      ++.-                         .-+-||+      -|..|+|..                             
T Consensus       276 ~~~~-------------------------ll~~~g~------~~s~iyssl-----------------------------  295 (529)
T KOG0337         276 YVRG-------------------------LLRDFGG------EGSDIYSSL-----------------------------  295 (529)
T ss_pred             HHHH-------------------------HHHHCCC------CCCCCCCCC-----------------------------
T ss_conf             9887-------------------------8986398------744111445-----------------------------


Q ss_pred             CCCCCCHHHHHHHHHHHCCCCCCEEEEEHHHCCCCCCCCCCHHHHHH
Q ss_conf             21135867899999862125765798704430231134520123300
Q gi|254780619|r  516 SDLEGGGGRLQLQLSAIAKGEIDIIIGTQLVAKGHNFPRMSLVGVVD  562 (731)
Q Consensus       516 ~d~~~~~~~~~~~~~~~~~~~~~ilvgTq~i~kg~~fp~v~lv~il~  562 (731)
                       |...+    ..-+.+|..++..|+|-|..-|.|.|.|...-|+-+|
T Consensus       296 -D~~aR----k~~~~~F~~~k~~~lvvTdvaaRG~diplldnvinyd  337 (529)
T KOG0337         296 -DQEAR----KINGRDFRGRKTSILVVTDVAARGLDIPLLDNVINYD  337 (529)
T ss_pred             -CHHHH----HHCCCCCCCCCCCEEEEEHHHHCCCCCCCCCCCCCCC
T ss_conf             -86766----5042034677552599842333358876544656456


No 91 
>PRK11131 ATP-dependent RNA helicase HrpA; Provisional
Probab=97.99  E-value=0.00086  Score=48.08  Aligned_cols=147  Identities=22%  Similarity=0.293  Sum_probs=83.2

Q ss_pred             CCCHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHHHHHHHHHH--CCCCEEEEECC------CHHHHHHHHHHHCC
Q ss_conf             68837899999998752048961998447531579999999999851--46847997152------10013445554303
Q gi|254780619|r  198 ILDKNQQDVVEQVVPLCTKGFAVSLISGVTGSGKTEVYLEIVAAVLH--LGKQVLILLPE------ISLTSAILERFQKR  269 (731)
Q Consensus       198 ~Lt~eQ~~a~~~i~~~~~~~f~~~LL~GvTGSGKTEVYl~li~~~L~--~GkqvLiLvPE------I~Lt~Q~~~rl~~r  269 (731)
                      +.+.....+++.|..     .++..+-|.||||||-   ++-+-+++  .|....|.+-.      |+++..........
T Consensus        74 Pi~~~r~~i~~~i~~-----nqVvii~GeTGsGKTT---QiPq~~le~g~g~~~~I~~TQPRRiAA~svA~RVA~E~~~~  145 (1295)
T PRK11131         74 PVSQKKQDILEAIRD-----HQVVIVAGETGSGKTT---QLPKICLELGRGIKGLIGHTQPRRLAARTVANRIAEELETE  145 (1295)
T ss_pred             CCHHHHHHHHHHHHH-----CCEEEEECCCCCCHHH---HHHHHHHHCCCCCCCEEEECCCHHHHHHHHHHHHHHHHCCC
T ss_conf             961899999999997-----9969997689998788---99999996279999989977965999999999999981999


Q ss_pred             CCCEEEE---EECCCCCHHHHHHHHHHHCCCCEEEEECCHHHH-----HH-HCCCEEEEEEECCCCCCHHCCCCCCCHHH
Q ss_conf             8976899---623557235667899997199739994001211-----00-10001367740553210000244322489
Q gi|254780619|r  270 FGVKPAE---WHSSLSTSMREKIWRQVARGAISVIVGVRSALF-----LP-FKKLGLIVIDEEHDISYKQEEGILYNARD  340 (731)
Q Consensus       270 F~~~v~v---~HS~ls~~eR~~~w~~i~~G~~~IVIGtRSAif-----~P-~~nLglIIvDEEHd~sykq~~~pry~aRd  340 (731)
                      .|..|.-   +.+..|             .+..|..=|-.-++     -| +.+-+.|||||-|+=|-.-|=-.-| .++
T Consensus       146 lG~~VGY~VRf~~~~s-------------~~t~i~~~TdGiLL~e~~~d~~L~~y~~iIiDEaHERsl~~D~LLg~-Lk~  211 (1295)
T PRK11131        146 LGGCVGYKVRFNDQVS-------------DNTMVKLMTDGILLAEIQQDRLLMQYDTIIIDEAHERSLNIDFILGY-LKE  211 (1295)
T ss_pred             CCCEEEEEECCCCCCC-------------CCCEEEEECCHHHHHHHHHCCCCCCCCEEEEECCCCCCCHHHHHHHH-HHH
T ss_conf             8998888945698879-------------99779997656999986209987887779986855688019999999-999


Q ss_pred             HHHHHHHHCCCCEECCCCCCCHHHHHHHH
Q ss_conf             99997511032100002454324677532
Q gi|254780619|r  341 MSIVRGKIESFPVVLVSATPSIESRVNGI  369 (731)
Q Consensus       341 vA~~Ra~~~~~~lilgSATPSles~~~~~  369 (731)
                      +..   +.-+..||+.|||.-.|.+.+.-
T Consensus       212 ll~---~R~dLKvIimSATid~e~fs~yF  237 (1295)
T PRK11131        212 LLP---RRPDLKVIITSATIDPERFSRHF  237 (1295)
T ss_pred             HHH---HCCCCEEEEECCCCCHHHHHHHC
T ss_conf             983---39998899955868979999657


No 92 
>PRK12906 secA preprotein translocase subunit SecA; Reviewed
Probab=97.94  E-value=0.00036  Score=50.98  Aligned_cols=92  Identities=20%  Similarity=0.219  Sum_probs=67.6

Q ss_pred             CCCHHHHHHHHHHHHHHHHCCCCEEEEECCCHHHH---HHHHHHHCCCCCEEEEEECCCCCHHHHHHHHHHHCCCCEEEE
Q ss_conf             75315799999999998514684799715210013---445554303897689962355723566789999719973999
Q gi|254780619|r  226 VTGSGKTEVYLEIVAAVLHLGKQVLILLPEISLTS---AILERFQKRFGVKPAEWHSSLSTSMREKIWRQVARGAISVIV  302 (731)
Q Consensus       226 vTGSGKTEVYl~li~~~L~~GkqvLiLvPEI~Lt~---Q~~~rl~~rF~~~v~v~HS~ls~~eR~~~w~~i~~G~~~IVI  302 (731)
                      -||-|||.|..-.+--.--.|+.|-|+-..=-|+.   ++...+...+|-.|.+..+.+++.+|...|.      ++|+=
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             ECCHHH-H-------------HHHCCCEEEEEEEC
Q ss_conf             400121-1-------------00100013677405
Q gi|254780619|r  303 GVRSAL-F-------------LPFKKLGLIVIDEE  323 (731)
Q Consensus       303 GtRSAi-f-------------~P~~nLglIIvDEE  323 (731)
                      ||-+-+ |             .=...+...||||-
T Consensus       175 ~Tn~e~gFDYLRDnm~~~~~~~vqr~~~~aIvDEv  209 (823)
T PRK12906        175 STNSELGFDYLRDNMVVYKEQMVQRPLNYAIVDEV  209 (823)
T ss_pred             ECCCCEECCCCCCCCCCCHHHHCCCCCCEEEEECH
T ss_conf             25655021113544126888834788855898541


No 93 
>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=97.90  E-value=7.4e-06  Score=63.87  Aligned_cols=72  Identities=22%  Similarity=0.315  Sum_probs=57.7

Q ss_pred             CCCHHHHCCCCCCCCHHHHHHHHHHHCCCCCCEEEEEHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             52000102321135867899999862125765798704430231134520123300034431024557899999875431
Q gi|254780619|r  507 PLARISILSSDLEGGGGRLQLQLSAIAKGEIDIIIGTQLVAKGHNFPRMSLVGVVDGDLGLTNADLRSSERTFQLLSQVT  586 (731)
Q Consensus       507 p~~~v~~~d~d~~~~~~~~~~~~~~~~~~~~~ilvgTq~i~kg~~fp~v~lv~il~aD~~l~~pd~ra~E~~~qll~qv~  586 (731)
                      ++.++..+++++  .....+.++++|.+++.+|||+|++++.|+|+|+++.|++.|..            .....+.|..
T Consensus         6 ~g~~~~~i~g~~--~~~~R~~~~~~f~~~~~~ilv~t~~~~~Gid~~~~~~vi~~~~~------------~s~~~~~Q~~   71 (78)
T pfam00271         6 PGIKVARLHGGL--SQEEREEILEDFRNGKSKVLVATDVAGRGIDLPDVNVVINYDLP------------WNPASYIQRI   71 (78)
T ss_pred             CCCCEEEEECCC--CHHHHHHHHHHHHCCCCEEEEEECCCCCCCCCCCCCEEEEECCC------------CCHHHHHHHH
T ss_conf             898599986979--99999999999987997399992565256778789999997899------------6989999997


Q ss_pred             HCCCCC
Q ss_conf             102566
Q gi|254780619|r  587 GRAGRF  592 (731)
Q Consensus       587 gRagr~  592 (731)
                      ||+||.
T Consensus        72 GR~~R~   77 (78)
T pfam00271        72 GRAGRA   77 (78)
T ss_pred             CCCCCC
T ss_conf             268779


No 94 
>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=97.86  E-value=0.00022  Score=52.58  Aligned_cols=159  Identities=16%  Similarity=0.243  Sum_probs=93.7

Q ss_pred             CCCHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHHHHHHHHHHCC-CCEEEEECCCHHHHHH-HHHHHCCCCCEEE
Q ss_conf             6883789999999875204896199844753157999999999985146-8479971521001344-5554303897689
Q gi|254780619|r  198 ILDKNQQDVVEQVVPLCTKGFAVSLISGVTGSGKTEVYLEIVAAVLHLG-KQVLILLPEISLTSAI-LERFQKRFGVKPA  275 (731)
Q Consensus       198 ~Lt~eQ~~a~~~i~~~~~~~f~~~LL~GvTGSGKTEVYl~li~~~L~~G-kqvLiLvPEI~Lt~Q~-~~rl~~rF~~~v~  275 (731)
                      ..++-|..+.+.+...   ......+-+=+-+||||+-+.++...+.+. ..+|++.|...++... ..||..-|.+..+
T Consensus        16 ~~~Py~~eimd~l~~~---~v~~V~~~k~aQ~GkT~~~~n~igy~i~~~P~p~l~v~Pt~~~a~~~s~~rl~Pmi~~sP~   92 (552)
T pfam05876        16 DRTPYLREIMDALSPP---SVERVVFMKSAQVGKTELLLNWIGYFIDHDPAPMLVVQPTDDDAKRFSKDRLDPMIRASPA   92 (552)
T ss_pred             CCCCHHHHHHHHCCCC---CCEEEEEEECCCCCHHHHHHHHHHHHHHHCCCCEEEEECCHHHHHHHHHHHHHHHHHCCHH
T ss_conf             8880769999854887---8449999957870388999999988663089887999418999999999989999861989


Q ss_pred             EEECCCCCH---HH-HHHHHHHHCCCCEEEEECCHHHHHHHCCCEEEEEEECCCCCCHHCCCCCCCHHHHHHHHHHHC-C
Q ss_conf             962355723---56-678999971997399940012110010001367740553210000244322489999975110-3
Q gi|254780619|r  276 EWHSSLSTS---MR-EKIWRQVARGAISVIVGVRSALFLPFKKLGLIVIDEEHDISYKQEEGILYNARDMSIVRGKIE-S  350 (731)
Q Consensus       276 v~HS~ls~~---eR-~~~w~~i~~G~~~IVIGtRSAif~P~~nLglIIvDEEHd~sykq~~~pry~aRdvA~~Ra~~~-~  350 (731)
                       +...+++.   +. -....+--.|-.-.++|+-|+-=+--.....+++||- | .|-.+-+--=+..++|..|..-. .
T Consensus        93 -L~~~~~~~~~r~~~nt~~~K~f~gg~l~~~ga~S~~~L~s~~~r~l~~DEv-D-~~~~~~~~eGdP~~La~~R~~tf~~  169 (552)
T pfam05876        93 -LRERLAPARSRDSDNTLLSKRFPGGSLLLIGANSPANLRSRPVRYVILDEV-D-AYPEDVDGEGDPISLAEKRTETFGS  169 (552)
T ss_pred             -HHHHHCCCCCCCCCCCEEEEEECCCEEEEEECCCCHHHHCCCCCEEEECCH-H-HCCCCCCCCCCHHHHHHHHHHHHCC
T ss_conf             -997507555656677412476078379995579961430486355885134-4-3654567787989999999875302


Q ss_pred             CCEECCCCCCCH
Q ss_conf             210000245432
Q gi|254780619|r  351 FPVVLVSATPSI  362 (731)
Q Consensus       351 ~~lilgSATPSl  362 (731)
                      -.-++...||.+
T Consensus       170 ~~K~~~~STPt~  181 (552)
T pfam05876       170 RRKILAGSTPTI  181 (552)
T ss_pred             CCEEEEECCCCC
T ss_conf             857999838999


No 95 
>KOG0920 consensus
Probab=97.84  E-value=0.00036  Score=50.99  Aligned_cols=330  Identities=19%  Similarity=0.178  Sum_probs=154.4

Q ss_pred             CHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHHH-HHHHHHHCCCCEEEEE--CCCHHHHHHHHHHHCC----CCC
Q ss_conf             83789999999875204896199844753157999999-9999851468479971--5210013445554303----897
Q gi|254780619|r  200 DKNQQDVVEQVVPLCTKGFAVSLISGVTGSGKTEVYLE-IVAAVLHLGKQVLILL--PEISLTSAILERFQKR----FGV  272 (731)
Q Consensus       200 t~eQ~~a~~~i~~~~~~~f~~~LL~GvTGSGKTEVYl~-li~~~L~~GkqvLiLv--PEI~Lt~Q~~~rl~~r----F~~  272 (731)
                      .+.+..+++.|..     .++.++-|.||+|||-=--+ +.+..+..|.-+=|++  |-.--+.-+.+|....    .|.
T Consensus       175 ~~~r~~Il~~i~~-----~qVvvIsGeTGcGKtTQvpQfiLd~~~~~~~~~~IicTQPRRIsAIsvAeRVa~ER~~~~g~  249 (924)
T KOG0920         175 YKMRDTILDAIEE-----NQVVVISGETGCGKTTQVPQFILDEAIESGAACNIICTQPRRISAISVAERVAKERGESLGE  249 (924)
T ss_pred             HHHHHHHHHHHHH-----CCEEEEECCCCCCCHHHHHHHHHHHHHHCCCCCEEEECCCCHHHHHHHHHHHHHHHCCCCCC
T ss_conf             7789999999974-----96699957889871224669999999862899738866775177899999998875466687


Q ss_pred             EEEEEECCCCCHHHHHHHHHHHCCCCEEEEECCHHHHH------H-HCCCEEEEEEECCCCCCHHCCCCCCCHHHHHHHH
Q ss_conf             68996235572356678999971997399940012110------0-1000136774055321000024432248999997
Q gi|254780619|r  273 KPAEWHSSLSTSMREKIWRQVARGAISVIVGVRSALFL------P-FKKLGLIVIDEEHDISYKQEEGILYNARDMSIVR  345 (731)
Q Consensus       273 ~v~v~HS~ls~~eR~~~w~~i~~G~~~IVIGtRSAif~------P-~~nLglIIvDEEHd~sykq~~~pry~aRdvA~~R  345 (731)
                      .| -|+=+          +.-+.+.-..+...-.++++      | +.+.+-|||||=|+=+-- .+..-+..+++...|
T Consensus       250 ~V-GYqvr----------l~~~~s~~t~L~fcTtGvLLr~L~~~~~l~~~thiivDEVHER~i~-~DflLi~lk~lL~~~  317 (924)
T KOG0920         250 EV-GYQVR----------LESKRSRETRLLFCTTGVLLRRLQSDPTLSGVTHIIVDEVHERSIN-TDFLLILLKDLLPRN  317 (924)
T ss_pred             EE-EEEEE----------EECCCCCCEEEEEECHHHHHHHHCCCCCCCCCCEEEEEEEEECCCC-CCCHHHHHHHHHHHC
T ss_conf             13-68986----------2013677516898406899987546862145866544227971677-521799999886228


Q ss_pred             HHHCCCCEECCCCCCCHHHHHHHHHHHHHHHCCCCCCCCCCCCCCEECCCCCCCCCCCCCCCHHHHHHHHHHHCCCCEEE
Q ss_conf             51103210000245432467753212344412432236765433211022223322245479899999988622655179
Q gi|254780619|r  346 GKIESFPVVLVSATPSIESRVNGISRRYHSVHLSTRYRNSALPHLQVIDMRGQTIAQGKSLSPEMIDGIRHTLARNEQTL  425 (731)
Q Consensus       346 a~~~~~~lilgSATPSles~~~~~~g~~~~~~l~~R~~~~~~P~i~ivDm~~~~~~~~~~lS~~l~~~i~~~l~~g~qvl  425 (731)
                         -+-.+||.|||--.|.+...-.| ...+    ++.+++.|...             .+-+..+..+....+...+- 
T Consensus       318 ---p~LkvILMSAT~dae~fs~YF~~-~pvi----~i~grtfpV~~-------------~fLEDil~~~~~~~~~~~~~-  375 (924)
T KOG0920         318 ---PDLKVILMSATLDAELFSDYFGG-CPVI----TIPGRTFPVKE-------------YFLEDILSKTGYVSEDDSAR-  375 (924)
T ss_pred             ---CCCEEEEEEEECCHHHHHHHHCC-CCEE----EECCCCCCHHH-------------HHHHHHHHHHCCCCCCCCCC-
T ss_conf             ---88569986211262888987189-9358----64687864588-------------78999998751444455655-


Q ss_pred             EEECCCCEEHHCCCCCCCCCCCCCCCCCEEEEECCC----CCCEECHHHCCCCCCCCCCCCCCCCEECCCCCCHHHHHHH
Q ss_conf             974222000000235654343101465201211357----8320000210244655566678741100135428998888
Q gi|254780619|r  426 LFLNRRGYAPLTLCQVCGNRLKCLHCSCWLVEHRSK----KKLYCHQCGHSAIYSQSCVVCGSSGKMIACGFGIERIAEE  501 (731)
Q Consensus       426 l~lnRrGya~~~~C~~Cg~~~~C~~C~~~l~~h~~~----~~l~Ch~Cg~~~~~~~~Cp~Cg~~~~l~~~G~Gte~~~e~  501 (731)
                       ....+|         +...+.     ..+....-+    ..|.||.|..          +.... +--+=+|.+.|..-
T Consensus       376 -~~~~~~---------~~~~~~-----~~~~~~~id~~Li~~li~~I~~~----------~~~Ga-ILVFLPG~~eI~~~  429 (924)
T KOG0920         376 -SGPERS---------QLRLAR-----LKLWEPEIDYDLIEDLIEYIDER----------EFEGA-ILVFLPGWEEILQL  429 (924)
T ss_pred             -CCCCCC---------CCCCCC-----CHHCCCCCCHHHHHHHHHHCCCC----------CCCCE-EEEECCCHHHHHHH
T ss_conf             -555667---------443222-----00115421477999998740557----------88742-89974888999999


Q ss_pred             HHHC-----CCC-CH--HHHCCCCCCCCHHHHHHHHHHHCCCCCCEEEEEHHHCCCCCCCCCCHHHHHHH--------HH
Q ss_conf             5204-----852-00--01023211358678999998621257657987044302311345201233000--------34
Q gi|254780619|r  502 VCEY-----FPL-AR--ISILSSDLEGGGGRLQLQLSAIAKGEIDIIIGTQLVAKGHNFPRMSLVGVVDG--------DL  565 (731)
Q Consensus       502 l~~~-----fp~-~~--v~~~d~d~~~~~~~~~~~~~~~~~~~~~ilvgTq~i~kg~~fp~v~lv~il~a--------D~  565 (731)
                      ..++     |-+ .+  |..+.+-.  .....+.++.....|.-.|++.|-+..-....|+|.-  |+|.        |.
T Consensus       430 ~~~L~~~~~f~~~~~~~ilplHs~~--~~~eQ~~VF~~pp~g~RKIIlaTNIAETSITIdDVvy--VIDsG~~Ke~~yD~  505 (924)
T KOG0920         430 KELLEVNLPFADSLKFAILPLHSSI--PSEEQQAVFKRPPKGTRKIILATNIAETSITIDDVVY--VIDSGLVKEKSYDP  505 (924)
T ss_pred             HHHHHHCCCCCCCCCEEEEECCCCC--CHHHHHHHCCCCCCCCCHHHHHHHHHHHCCCCCCEEE--EEECCEEEEEEECC
T ss_conf             9975415665666625887051008--8688998617899995123222013753452367479--98647154444056


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCEEE
Q ss_conf             4310245578999998754311025667886899
Q gi|254780619|r  566 GLTNADLRSSERTFQLLSQVTGRAGRFGLKSLGL  599 (731)
Q Consensus       566 ~l~~pd~ra~E~~~qll~qv~gRagr~~~~g~v~  599 (731)
                      ..+..-+...=-....-.|-+|||||-. +|.++
T Consensus       506 ~~~~s~l~~~wvSkAna~QR~GRAGRv~-~G~cy  538 (924)
T KOG0920         506 ERKVSCLLLSWVSKANAKQRRGRAGRVR-PGICY  538 (924)
T ss_pred             CCCCCCCEEEECCCCCHHHHCCCCCCCC-CCEEE
T ss_conf             6785400024201003677545555645-76268


No 96 
>PRK10917 ATP-dependent DNA helicase RecG; Provisional
Probab=97.80  E-value=0.00036  Score=50.98  Aligned_cols=85  Identities=16%  Similarity=0.294  Sum_probs=41.6

Q ss_pred             HHHHHHHHCCCCEEEEECCCH--------HHHHHHHHHHCCCCC-EEEEEECCCCCHHHHHHHHHHHCCCCEEEEECCHH
Q ss_conf             999998514684799715210--------013445554303897-68996235572356678999971997399940012
Q gi|254780619|r  237 EIVAAVLHLGKQVLILLPEIS--------LTSAILERFQKRFGV-KPAEWHSSLSTSMREKIWRQVARGAISVIVGVRSA  307 (731)
Q Consensus       237 ~li~~~L~~GkqvLiLvPEI~--------Lt~Q~~~rl~~rF~~-~v~v~HS~ls~~eR~~~w~~i~~G~~~IVIGtRSA  307 (731)
                      +.+++.+++|+||-++.|=|.        -..++++++++.|++ +|+++|++|++.|+-++..+-++|+.+|.|.|---
T Consensus       458 ~~i~~~~~~g~q~y~v~p~ieese~~~~~~~~~~~~~l~~~~~~~~v~~~hG~m~~~ek~~~m~~F~~g~~~iLvsTtvi  537 (677)
T PRK10917        458 ERIREEIAKGRQAYVVCPLIEESEKLDLQSAEETYEELQKALPELRVGLLHGRMKPAEKDAVMAAFKAGEIDILVATTVI  537 (677)
T ss_pred             HHHHHHHHCCCEEEEEECCCCCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCCCHHHHHHHHHHHHCCCCCEEEECCEE
T ss_conf             99999997599289994131123320177799999999844899759983078987899999999983999999989897


Q ss_pred             -HHHHHCCCEEEEEE
Q ss_conf             -11001000136774
Q gi|254780619|r  308 -LFLPFKKLGLIVID  321 (731)
Q Consensus       308 -if~P~~nLglIIvD  321 (731)
                       +=.-++|-..+||.
T Consensus       538 EvGvdvpna~~mvi~  552 (677)
T PRK10917        538 EVGVDVPNATVMVIE  552 (677)
T ss_pred             ECCCCCCCCCEEEEE
T ss_conf             558678888589997


No 97 
>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=97.70  E-value=0.00028  Score=51.80  Aligned_cols=87  Identities=18%  Similarity=0.404  Sum_probs=53.3

Q ss_pred             HHHHHHHHHHHHHCCCCEEEEEC---CCHHHH------HHHHHHHCCC-CC-EEEEEECCCCCHHHHHHHHHHHCCCCEE
Q ss_conf             99999999998514684799715---210013------4455543038-97-6899623557235667899997199739
Q gi|254780619|r  232 TEVYLEIVAAVLHLGKQVLILLP---EISLTS------AILERFQKRF-GV-KPAEWHSSLSTSMREKIWRQVARGAISV  300 (731)
Q Consensus       232 TEVYl~li~~~L~~GkqvLiLvP---EI~Lt~------Q~~~rl~~rF-~~-~v~v~HS~ls~~eR~~~w~~i~~G~~~I  300 (731)
                      ++.-++.+++-+++|+||-|..|   |...+|      .+..++++.| +. +|+++||+|++.||-++...=++|+.+|
T Consensus       514 ~~~v~~~~~~E~~~GrQaYvv~PlI~ESE~lp~lk~A~~~~~~l~~~f~~~~~v~LlHGrm~~~eK~~vm~~F~~~~~~I  593 (721)
T TIGR00643       514 IDIVYEFIEEEIAKGRQAYVVYPLIEESEKLPDLKAAEALYERLKKAFLPKYNVGLLHGRMKSDEKEAVMEEFREGEVDI  593 (721)
T ss_pred             HHHHHHHHHHHHHCCCCEEEEECCCCCCCCCCHHHHHHHHHHHHHHHHCCCCEEEEECCCCCHHHHHHHHHHHHHCCCEE
T ss_conf             68999999999832890899964403200471689999999998886122100113306898478999999852158369


Q ss_pred             EEECCHHHH---HHHCCCEEEEE
Q ss_conf             994001211---00100013677
Q gi|254780619|r  301 IVGVRSALF---LPFKKLGLIVI  320 (731)
Q Consensus       301 VIGtRSAif---~P~~nLglIIv  320 (731)
                      .|.|-  |-   .-++|..++||
T Consensus       594 LVsTT--VIEVGVDVPnAtvMVI  614 (721)
T TIGR00643       594 LVSTT--VIEVGVDVPNATVMVI  614 (721)
T ss_pred             EEEEE--EEEEEEECCCCCEEEE
T ss_conf             99976--8999861797727888


No 98 
>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=97.59  E-value=0.0056  Score=41.88  Aligned_cols=119  Identities=20%  Similarity=0.283  Sum_probs=76.8

Q ss_pred             HHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHHHHHHHHHHCC---CCEEEEECCCHHHHHHHHHHHCCCCC-EEEEEE
Q ss_conf             89999999875204896199844753157999999999985146---84799715210013445554303897-689962
Q gi|254780619|r  203 QQDVVEQVVPLCTKGFAVSLISGVTGSGKTEVYLEIVAAVLHLG---KQVLILLPEISLTSAILERFQKRFGV-KPAEWH  278 (731)
Q Consensus       203 Q~~a~~~i~~~~~~~f~~~LL~GvTGSGKTEVYl~li~~~L~~G---kqvLiLvPEI~Lt~Q~~~rl~~rF~~-~v~v~H  278 (731)
                      |...+.-......++. --+|-=..|-|||---+-++......+   +-+||++|. +|..|+...++..++. .+.++|
T Consensus         2 Q~~gv~wl~~~~~~~~-ggiLaDeMGLGKTiq~ia~l~~~~~~~~~~~~~LIV~P~-sl~~~W~~Ei~~~~~~~~~~~~~   79 (295)
T pfam00176         2 QLEGVNWLISLYNNGL-GGILADEMGLGKTLQTISLLAYLKELKPLAGPHLVVCPL-STLDNWLNEFEKWAPDLNIVVYY   79 (295)
T ss_pred             HHHHHHHHHHHHHCCC-CEEEECCCCCCHHHHHHHHHHHHHHHCCCCCCEEEEECH-HHHHHHHHHHHHHCCCCCEEEEE
T ss_conf             7889999999872799-989722787579999999999999838899988999757-88876788999867997079998


Q ss_pred             CCCCCHHHHHHHHH-HHCCCCEEEEECCHHHH---HHHCC--CEEEEEEECCC
Q ss_conf             35572356678999-97199739994001211---00100--01367740553
Q gi|254780619|r  279 SSLSTSMREKIWRQ-VARGAISVIVGVRSALF---LPFKK--LGLIVIDEEHD  325 (731)
Q Consensus       279 S~ls~~eR~~~w~~-i~~G~~~IVIGtRSAif---~P~~n--LglIIvDEEHd  325 (731)
                      ..-  +.|...+.. ...+..+|||-|...+-   .++.+  -..||+||.|-
T Consensus        80 ~~~--~~r~~~~~~~~~~~~~~ivitsY~~~~~~~~~l~~~~w~~vI~DEaH~  130 (295)
T pfam00176        80 GDG--DSRSELLRNVLRTGKFDVLITSYEYIRRDKDELHKANWRYVILDEGHR  130 (295)
T ss_pred             ECH--HHHHHHHHHHHHCCCCCEEEECHHHHHHHHHHHHCCCCCEEEEECCCC
T ss_conf             470--768999886774168859993099999759998408765899876201


No 99 
>COG1200 RecG RecG-like helicase [DNA replication, recombination, and repair / Transcription]
Probab=97.58  E-value=0.00067  Score=48.91  Aligned_cols=92  Identities=17%  Similarity=0.326  Sum_probs=56.6

Q ss_pred             HHHHHHHHHHHHHHHHCCCCEEEEECCCH--------HHHHHHHHHHCCCCC-EEEEEECCCCCHHHHHHHHHHHCCCCE
Q ss_conf             15799999999998514684799715210--------013445554303897-689962355723566789999719973
Q gi|254780619|r  229 SGKTEVYLEIVAAVLHLGKQVLILLPEIS--------LTSAILERFQKRFGV-KPAEWHSSLSTSMREKIWRQVARGAIS  299 (731)
Q Consensus       229 SGKTEVYl~li~~~L~~GkqvLiLvPEI~--------Lt~Q~~~rl~~rF~~-~v~v~HS~ls~~eR~~~w~~i~~G~~~  299 (731)
                      ..+.+|| +.|.+.+.+|+||-+..|=|.        .+..+.+.++..|+. +|.++|++|++.||-.+..+-++|+.+
T Consensus       457 ~~~~~v~-e~i~~ei~~GrQaY~VcPLIeeSE~l~l~~a~~~~~~L~~~~~~~~vgL~HGrm~~~eKd~vM~~Fk~~e~~  535 (677)
T COG1200         457 ERRPEVY-ERIREEIAKGRQAYVVCPLIEESEKLELQAAEELYEELKSFLPELKVGLVHGRMKPAEKDAVMEAFKEGEID  535 (677)
T ss_pred             CCHHHHH-HHHHHHHHCCCEEEEEECCCCCCCCCHHHHHHHHHHHHHHHCCCCEEEEEECCCCHHHHHHHHHHHHCCCCC
T ss_conf             4479999-999999974997999952535433113654999999999870546367775689867799999999808876


Q ss_pred             EEEECCHH-HHHHHCCCEEEEEE
Q ss_conf             99940012-11001000136774
Q gi|254780619|r  300 VIVGVRSA-LFLPFKKLGLIVID  321 (731)
Q Consensus       300 IVIGtRSA-if~P~~nLglIIvD  321 (731)
                      |.|.|--- |=.-++|..++||.
T Consensus       536 ILVaTTVIEVGVdVPnATvMVIe  558 (677)
T COG1200         536 ILVATTVIEVGVDVPNATVMVIE  558 (677)
T ss_pred             EEEEEEEEEECCCCCCCEEEEEE
T ss_conf             89981389952357887079996


No 100
>PRK11747 dinG ATP-dependent DNA helicase DinG; Provisional
Probab=97.41  E-value=0.0058  Score=41.75  Aligned_cols=65  Identities=20%  Similarity=0.288  Sum_probs=41.3

Q ss_pred             CHHHHHHHHHHHHHHC--CCCCEEEEECCCCHHHHHHHHH-HHHHHHHCCCCEEEEECCCHHHHHHHH
Q ss_conf             8378999999987520--4896199844753157999999-999985146847997152100134455
Q gi|254780619|r  200 DKNQQDVVEQVVPLCT--KGFAVSLISGVTGSGKTEVYLE-IVAAVLHLGKQVLILLPEISLTSAILE  264 (731)
Q Consensus       200 t~eQ~~a~~~i~~~~~--~~f~~~LL~GvTGSGKTEVYl~-li~~~L~~GkqvLiLvPEI~Lt~Q~~~  264 (731)
                      -++|.+-...|.....  .+-...+++--||.|||-=||= ++..+...|+.|+|-.+.|+|-.|++.
T Consensus        27 R~~Q~~Ma~~V~~al~~~~~~~~l~iEAgTGtGKTlaYL~Pai~~a~~~~~~vvIST~T~~LQeQL~~   94 (697)
T PRK11747         27 RAGQRQMIAEVAKTLAGEYGRHILVIEAGTGVGKSLAYLLAGIPIARAEKKKLVISTATVALQEQLVH   94 (697)
T ss_pred             CHHHHHHHHHHHHHHHCCCCCCEEEEECCCCCHHHHHHHHHHHHHHHHCCCCEEEECCCHHHHHHHHH
T ss_conf             87899999999999616667866999899972089999999999999829979998898899999987


No 101
>PRK08074 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
Probab=97.41  E-value=0.0048  Score=42.38  Aligned_cols=127  Identities=26%  Similarity=0.362  Sum_probs=84.4

Q ss_pred             CCHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHHH-HHHHHHHCCCCEEEEECCCHHHHHHHHH----HHCCCC--
Q ss_conf             883789999999875204896199844753157999999-9999851468479971521001344555----430389--
Q gi|254780619|r  199 LDKNQQDVVEQVVPLCTKGFAVSLISGVTGSGKTEVYLE-IVAAVLHLGKQVLILLPEISLTSAILER----FQKRFG--  271 (731)
Q Consensus       199 Lt~eQ~~a~~~i~~~~~~~f~~~LL~GvTGSGKTEVYl~-li~~~L~~GkqvLiLvPEI~Lt~Q~~~r----l~~rF~--  271 (731)
                      --+.|......+......+ ...++..-||.|||-=||- ++..+.+.|+.|+|-.+.+.|-.|++.+    +++.++  
T Consensus       259 ~R~~Q~~ma~~V~~al~~~-~~l~iEApTGtGKTlaYLlPai~~A~~~~~~vvIST~T~~LQ~QL~~kdlp~L~~~l~~~  337 (932)
T PRK08074        259 KREGQQEMMKEVYTALRDS-RHALIEAGTGTGKTLAYLLPAAYFAKKKEEPVIISTYTVQLQQQLLEKDIPLLQKIFPFP  337 (932)
T ss_pred             CCHHHHHHHHHHHHHHHCC-CCEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEECCHHHHHHHHHHHHHHHHHHHCCC
T ss_conf             5878999999999998538-847998688887136879999999997599099991628899999986899999971998


Q ss_pred             CEEEEEECCC-------------------------------------------C-CHHHHHHHHHHH-------------
Q ss_conf             7689962355-------------------------------------------7-235667899997-------------
Q gi|254780619|r  272 VKPAEWHSSL-------------------------------------------S-TSMREKIWRQVA-------------  294 (731)
Q Consensus       272 ~~v~v~HS~l-------------------------------------------s-~~eR~~~w~~i~-------------  294 (731)
                      .+.+++-++-                                           + +......|.++.             
T Consensus       338 ~~~~llKGr~nYlCl~k~~~~l~~~~~~~~~~~~~~~il~Wl~~T~tGD~del~~~~~~~~~w~~i~~~~~~~~~~~c~~  417 (932)
T PRK08074        338 VKAALLKGRSHYLCLRKFEQALQEEDDNYDVALTKAQLLVWLTETETGDLDELNLPSGGKLLWNRIASDGHSPGGKQSPW  417 (932)
T ss_pred             CCEEEEECCHHCCCHHHHHHHHCCCCCCHHHHHHHHHHHHHHHCCCCCCHHHCCCCCCHHHHHHHHCCCCCCCCCCCCCC
T ss_conf             60899966141277688999853545415578889999998726888688763699634889988455753202355887


Q ss_pred             ------------CCCCEEEEECCHHHHHHHC-------CCEEEEEEECCCC
Q ss_conf             ------------1997399940012110010-------0013677405532
Q gi|254780619|r  295 ------------RGAISVIVGVRSALFLPFK-------KLGLIVIDEEHDI  326 (731)
Q Consensus       295 ------------~G~~~IVIGtRSAif~P~~-------nLglIIvDEEHd~  326 (731)
                                  .-.++|||..++=+|.++.       .-..+||||-|.-
T Consensus       418 ~~~Cf~~~ar~~a~~AdvvI~NHalL~~d~~~~~~ilp~~~~lViDEAH~L  468 (932)
T PRK08074        418 FSRCFYQRAKNKAKFADIVITNHALLLTDFTSEEPLLPSYEHIIIDEAHHF  468 (932)
T ss_pred             CCCCHHHHHHHHHHHCCEEEECHHHHHHHHHCCCCCCCCCCEEEEECHHHH
T ss_conf             577989999997642999998889985656414776887676997313231


No 102
>pfam09848 DUF2075 Uncharacterized conserved protein (DUF2075). This domain, found in various prokaryotic proteins (including putative ATP/GTP binding proteins), has no known function.
Probab=97.36  E-value=0.0012  Score=47.01  Aligned_cols=83  Identities=25%  Similarity=0.388  Sum_probs=52.8

Q ss_pred             CEEEEECCCCHHHHHHHHHHHHHHH--HCCCCEEEEECCCHHHHHHHHHHHCCCCCEEEEEECCCCCHHHHHHHHHHHCC
Q ss_conf             6199844753157999999999985--14684799715210013445554303897689962355723566789999719
Q gi|254780619|r  219 AVSLISGVTGSGKTEVYLEIVAAVL--HLGKQVLILLPEISLTSAILERFQKRFGVKPAEWHSSLSTSMREKIWRQVARG  296 (731)
Q Consensus       219 ~~~LL~GvTGSGKTEVYl~li~~~L--~~GkqvLiLvPEI~Lt~Q~~~rl~~rF~~~v~v~HS~ls~~eR~~~w~~i~~G  296 (731)
                      +++++.|+.|+|||-|-+.++....  ..+..+.+|.+.=.|..-+...+....+...                      
T Consensus         2 ~v~~V~G~pGtGKTvv~l~l~~~l~~~~~~~~~~~l~~N~~~~~~l~~~l~~~~~~~~----------------------   59 (348)
T pfam09848         2 AVFLVTGGPGTGKTVVALNLFAELSDSDLGRTAVFLSGNHPLVLVLYEALAGDLKVRK----------------------   59 (348)
T ss_pred             EEEEEECCCCCCHHHHHHHHHHHHHHCCCCCCEEEEECCHHHHHHHHHHHHHHCCHHH----------------------
T ss_conf             7999977799389999999999986440268208995786699999999860412001----------------------


Q ss_pred             CCEEEEECCHHHH-----HHHCCCEEEEEEECCCC
Q ss_conf             9739994001211-----00100013677405532
Q gi|254780619|r  297 AISVIVGVRSALF-----LPFKKLGLIVIDEEHDI  326 (731)
Q Consensus       297 ~~~IVIGtRSAif-----~P~~nLglIIvDEEHd~  326 (731)
                       ...+.+.  .-|     .+.+...++||||-|-.
T Consensus        60 -~~~~~~~--~~fi~~~~~~~~~~dvvivDEAhRl   91 (348)
T pfam09848        60 -KKLFRKP--TSFINNLHKAPPHEDVVIVDEAHRL   91 (348)
T ss_pred             -CCCCCCC--HHHHCCCCCCCCCCCEEEEEHHHHH
T ss_conf             -0200072--5231652357986778998317866


No 103
>PRK07952 DNA replication protein DnaC; Validated
Probab=97.36  E-value=0.0016  Score=45.95  Aligned_cols=93  Identities=25%  Similarity=0.353  Sum_probs=67.6

Q ss_pred             CCCHHHHHHHHHHH---HHHCCCCCEEEEECCCCHHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHCCCCCEE
Q ss_conf             68837899999998---752048961998447531579999999999851468479971521001344555430389768
Q gi|254780619|r  198 ILDKNQQDVVEQVV---PLCTKGFAVSLISGVTGSGKTEVYLEIVAAVLHLGKQVLILLPEISLTSAILERFQKRFGVKP  274 (731)
Q Consensus       198 ~Lt~eQ~~a~~~i~---~~~~~~f~~~LL~GvTGSGKTEVYl~li~~~L~~GkqvLiLvPEI~Lt~Q~~~rl~~rF~~~v  274 (731)
                      .-++.|+.|++...   .....++...|++|-.|.|||-..--++.+.+.+|++|++..     ++.++.++++-|++. 
T Consensus        73 ~~~~~q~~al~~a~~y~enf~~~~~gLlF~G~~GTGKThLA~aIan~Li~~G~sVlf~t-----~~dLl~~lr~t~~~~-  146 (242)
T PRK07952         73 VECEGQMNALSKARQYVEEFDGNIASFIFSGKPGTGKNHLAAAICNELLLRGKSVLIIT-----VADIMSAMKDTFRNS-  146 (242)
T ss_pred             CCCHHHHHHHHHHHHHHHHHCCCCCEEEEECCCCCCHHHHHHHHHHHHHHCCCEEEEEE-----HHHHHHHHHHHHHCC-
T ss_conf             58777899999999999865438871799789999789999999999998799499977-----999999999998068-


Q ss_pred             EEEECCCCCHHHHHHHHHHHCCCCEEEEECCHHHHHHHCCCEEEEEEEC
Q ss_conf             9962355723566789999719973999400121100100013677405
Q gi|254780619|r  275 AEWHSSLSTSMREKIWRQVARGAISVIVGVRSALFLPFKKLGLIVIDEE  323 (731)
Q Consensus       275 ~v~HS~ls~~eR~~~w~~i~~G~~~IVIGtRSAif~P~~nLglIIvDEE  323 (731)
                           +.+..                      -++..+.+..|+|+||=
T Consensus       147 -----~~~e~----------------------~~l~~l~~~dLLIiDdl  168 (242)
T PRK07952        147 -----ETSEE----------------------QLLNDLSNVDLLVIDEI  168 (242)
T ss_pred             -----CCCHH----------------------HHHHHHHCCCEEEEECC
T ss_conf             -----75699----------------------99998631898987301


No 104
>KOG0950 consensus
Probab=97.32  E-value=0.0033  Score=43.67  Aligned_cols=136  Identities=25%  Similarity=0.338  Sum_probs=76.1

Q ss_pred             EEEEC-CCCHHHHHHHHH-HHHHHHHCCCCEEEEECCCHHHHHHHHH---HHCCCCCEEEEEECCCCCHHHHHHHHHHHC
Q ss_conf             99844-753157999999-9999851468479971521001344555---430389768996235572356678999971
Q gi|254780619|r  221 SLISG-VTGSGKTEVYLE-IVAAVLHLGKQVLILLPEISLTSAILER---FQKRFGVKPAEWHSSLSTSMREKIWRQVAR  295 (731)
Q Consensus       221 ~LL~G-vTGSGKTEVYl~-li~~~L~~GkqvLiLvPEI~Lt~Q~~~r---l~~rF~~~v~v~HS~ls~~eR~~~w~~i~~  295 (731)
                      .|++| =|+-|||.|.== +.+.+|-..|-|++.+|=++-...-..-   |..-+|..|-.|-++.++..|.+       
T Consensus       242 nliys~Pts~gktlvaeilml~~~l~~rr~~llilp~vsiv~Ek~~~l~~~~~~~G~~ve~y~g~~~p~~~~k-------  314 (1008)
T KOG0950         242 NLIYSLPTSAGKTLVAEILMLREVLCRRRNVLLILPYVSIVQEKISALSPFSIDLGFPVEEYAGRFPPEKRRK-------  314 (1008)
T ss_pred             CEEEECCCCCCHHHHHHHHHHHHHHHHHHCEEEECCEEEHHHHHHHHHHHHCCCCCCCCHHHCCCCCCCCCCC-------
T ss_conf             5588578764067999999999998874211674242102587776400220335886221126689988644-------


Q ss_pred             CCCEEEEEC--CHHHH-------HHHCCCEEEEEEECCCCCCHHCCCCCCCHHH-HHH--HHHHHCCCCEECCCCC-C--
Q ss_conf             997399940--01211-------0010001367740553210000244322489-999--9751103210000245-4--
Q gi|254780619|r  296 GAISVIVGV--RSALF-------LPFKKLGLIVIDEEHDISYKQEEGILYNARD-MSI--VRGKIESFPVVLVSAT-P--  360 (731)
Q Consensus       296 G~~~IVIGt--RSAif-------~P~~nLglIIvDEEHd~sykq~~~pry~aRd-vA~--~Ra~~~~~~lilgSAT-P--  360 (731)
                       ...+-|-|  ++...       --..-+|+|+|||-|=-.   +.+--|+--. ++.  +-+......+|=.||| |  
T Consensus       315 -~~sv~i~tiEkanslin~lie~g~~~~~g~vvVdElhmi~---d~~rg~~lE~~l~k~~y~~~~~~~~iIGMSATi~N~  390 (1008)
T KOG0950         315 -RESVAIATIEKANSLINSLIEQGRLDFLGMVVVDELHMIG---DKGRGAILELLLAKILYENLETSVQIIGMSATIPNN  390 (1008)
T ss_pred             -CEEEEEEEHHHHHHHHHHHHHCCCCCCCCCEEEEEEEEEE---CCCCCHHHHHHHHHHHHHCCCCCEEEEEEECCCCCH
T ss_conf             -1045542037667688888761783304728975224640---356355899999999996325634676552414774


Q ss_pred             -CHHHHHH
Q ss_conf             -3246775
Q gi|254780619|r  361 -SIESRVN  367 (731)
Q Consensus       361 -Sles~~~  367 (731)
                       -+++|.+
T Consensus       391 ~lL~~~L~  398 (1008)
T KOG0950         391 SLLQDWLD  398 (1008)
T ss_pred             HHHHHHHH
T ss_conf             88998864


No 105
>KOG1805 consensus
Probab=97.27  E-value=0.004  Score=42.99  Aligned_cols=122  Identities=21%  Similarity=0.288  Sum_probs=76.3

Q ss_pred             CCCCCCHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHCCCCCEE
Q ss_conf             66668837899999998752048961998447531579999999999851468479971521001344555430389768
Q gi|254780619|r  195 SLPILDKNQQDVVEQVVPLCTKGFAVSLISGVTGSGKTEVYLEIVAAVLHLGKQVLILLPEISLTSAILERFQKRFGVKP  274 (731)
Q Consensus       195 ~~~~Lt~eQ~~a~~~i~~~~~~~f~~~LL~GvTGSGKTEVYl~li~~~L~~GkqvLiLvPEI~Lt~Q~~~rl~~rF~~~v  274 (731)
                      ....||++|++|+..+...  ..|  .|+.|-.|+|||-.--.+|+-.+..|+.||+-.=.-+-..-+.-+++   +..+
T Consensus       666 ~~~~LN~dQr~A~~k~L~a--edy--~LI~GMPGTGKTTtI~~LIkiL~~~gkkVLLtsyThsAVDNILiKL~---~~~i  738 (1100)
T KOG1805         666 ILLRLNNDQRQALLKALAA--EDY--ALILGMPGTGKTTTISLLIKILVALGKKVLLTSYTHSAVDNILIKLK---GFGI  738 (1100)
T ss_pred             HHHHCCHHHHHHHHHHHHC--CCH--HEEECCCCCCCHHHHHHHHHHHHHCCCEEEEEEHHHHHHHHHHHHHH---CCCC
T ss_conf             8753188999999998730--332--20326998981225999999999738818998505678899999875---0671


Q ss_pred             EEE--ECCC-----------CC--HHH-HHHHHHHHCCCCEEEEECCHHHHHHH---CCCEEEEEEECC
Q ss_conf             996--2355-----------72--356-67899997199739994001211001---000136774055
Q gi|254780619|r  275 AEW--HSSL-----------ST--SMR-EKIWRQVARGAISVIVGVRSALFLPF---KKLGLIVIDEEH  324 (731)
Q Consensus       275 ~v~--HS~l-----------s~--~eR-~~~w~~i~~G~~~IVIGtRSAif~P~---~nLglIIvDEEH  324 (731)
                      +++  -|.-           +.  +++ +... +-.-+.+.||.+|=-++--|+   +....+||||..
T Consensus       739 ~~lRLG~~~kih~~v~e~~~~~~~s~ks~~~l-~~~~~~~~IVa~TClgi~~plf~~R~FD~cIiDEAS  806 (1100)
T KOG1805         739 YILRLGSEEKIHPDVEEFTLTNETSEKSYADL-KKFLDQTSIVACTCLGINHPLFVNRQFDYCIIDEAS  806 (1100)
T ss_pred             CEEECCCCCCCCHHHHHHHCCCCCCHHHHHHH-HHHHCCCCEEEEECCCCCCHHHHCCCCCEEEECCCC
T ss_conf             10344872224468998712344545339999-997289767999715788655521426789986511


No 106
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=97.17  E-value=0.0085  Score=40.50  Aligned_cols=26  Identities=31%  Similarity=0.500  Sum_probs=15.9

Q ss_pred             CHHHHHHHHHHCCCCCH-HHHCCCCCCCC
Q ss_conf             28998888520485200-01023211358
Q gi|254780619|r  494 GIERIAEEVCEYFPLAR-ISILSSDLEGG  521 (731)
Q Consensus       494 Gte~~~e~l~~~fp~~~-v~~~d~d~~~~  521 (731)
                      |||-+..-  -.||++. |..+|.|+.-.
T Consensus       540 GTQmiaKG--~~fp~vtLVgvl~aD~~L~  566 (730)
T COG1198         540 GTQMIAKG--HDFPNVTLVGVLDADTGLG  566 (730)
T ss_pred             CCHHHHCC--CCCCCCEEEEEEECHHHHC
T ss_conf             41666427--8866631899996314315


No 107
>PRK10689 transcription-repair coupling factor; Provisional
Probab=97.17  E-value=0.0043  Score=42.73  Aligned_cols=75  Identities=23%  Similarity=0.314  Sum_probs=50.6

Q ss_pred             ECCCCCCHHHHHHHHHHCCCCCH--HHHCCCCCCCCHHHHHHHHHHHCCCCCCEEEEE-HHHCCCCCCCCCCHHHHHHHH
Q ss_conf             00135428998888520485200--010232113586789999986212576579870-443023113452012330003
Q gi|254780619|r  488 MIACGFGIERIAEEVCEYFPLAR--ISILSSDLEGGGGRLQLQLSAIAKGEIDIIIGT-QLVAKGHNFPRMSLVGVVDGD  564 (731)
Q Consensus       488 l~~~G~Gte~~~e~l~~~fp~~~--v~~~d~d~~~~~~~~~~~~~~~~~~~~~ilvgT-q~i~kg~~fp~v~lv~il~aD  564 (731)
                      +.+--.=.++=.+-.++-|.+.+  |..+++=  .++....++++.+.+|++||+||| .++.|...|.|++|++| |-.
T Consensus       655 lvPTTiLA~QH~~tF~~Rf~~~pv~i~~LsRf--~s~ke~~~i~~~l~~G~idIvIGTH~ll~~dv~f~~LGLlIi-DEE  731 (1148)
T PRK10689        655 LVPTTLLAQQHYDNFRDRFANWPVRIEMLSRF--RSAKEQTQILAEAAEGKIDILIGTHKLLQSDVKWKDLGLLIV-DEE  731 (1148)
T ss_pred             EECCCCCHHHHHHHHHHHHHCCCCEEEEECCC--CCHHHHHHHHHHHHCCCCCEEEHHHHHHCCCCCCCCCCEEEE-CCC
T ss_conf             83662237999999998764157337750388--889999999999866998776204888669865466643786-010


Q ss_pred             H
Q ss_conf             4
Q gi|254780619|r  565 L  565 (731)
Q Consensus       565 ~  565 (731)
                      +
T Consensus       732 q  732 (1148)
T PRK10689        732 H  732 (1148)
T ss_pred             H
T ss_conf             2


No 108
>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=97.16  E-value=0.0099  Score=39.99  Aligned_cols=92  Identities=25%  Similarity=0.383  Sum_probs=72.5

Q ss_pred             CHHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHCCCCCEEEEEECCCCCHHHHHHHHHHHCCCCEEEEECCHH
Q ss_conf             31579999999999851468479971521001344555430389768996235572356678999971997399940012
Q gi|254780619|r  228 GSGKTEVYLEIVAAVLHLGKQVLILLPEISLTSAILERFQKRFGVKPAEWHSSLSTSMREKIWRQVARGAISVIVGVRSA  307 (731)
Q Consensus       228 GSGKTEVYl~li~~~L~~GkqvLiLvPEI~Lt~Q~~~rl~~rF~~~v~v~HS~ls~~eR~~~w~~i~~G~~~IVIGtRSA  307 (731)
                      -|.|-+.-++.+.+.+..|.++||.++.+..+..+...|++ .+..+..+|++++..+|..+-.+.++|+..|++.|-.+
T Consensus        10 ~~~K~~~l~~~i~~~~~~~~kviIF~~~~~~~~~l~~~L~~-~~~~~~~~~~~~~~~~R~~~~~~F~~~~~~ilv~t~~~   88 (131)
T cd00079          10 EDEKLEALLELLKEHLKKGGKVLIFCPSKKMLDELAELLRK-PGIKVAALHGDGSQEEREEVLKDFREGEIVVLVATDVI   88 (131)
T ss_pred             CHHHHHHHHHHHHHHHHCCCEEEEEECCHHHHHHHHHHHHH-CCCCEEEEECCCCHHHHHHHHHHHHHHCEEEEEEEECC
T ss_conf             66999999999999997899099997889999999999955-89989999899999999999999775401048875112


Q ss_pred             HH-HHHCCCEEEEE
Q ss_conf             11-00100013677
Q gi|254780619|r  308 LF-LPFKKLGLIVI  320 (731)
Q Consensus       308 if-~P~~nLglIIv  320 (731)
                      -- +-+++...+|+
T Consensus        89 ~~Gldl~~~~~vI~  102 (131)
T cd00079          89 ARGIDLPNVSVVIN  102 (131)
T ss_pred             EECCCCCCCCEEEE
T ss_conf             00366102879999


No 109
>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=97.15  E-value=0.0014  Score=46.55  Aligned_cols=113  Identities=28%  Similarity=0.442  Sum_probs=63.6

Q ss_pred             CEEEEECCCCHHHHHHHHH-HHHHHHHCCCCEEEEECCCHHHHHHHHHHHCCCCCEEEEEECCCCCHHHHHHHHHHHCCC
Q ss_conf             6199844753157999999-999985146847997152100134455543038976899623557235667899997199
Q gi|254780619|r  219 AVSLISGVTGSGKTEVYLE-IVAAVLHLGKQVLILLPEISLTSAILERFQKRFGVKPAEWHSSLSTSMREKIWRQVARGA  297 (731)
Q Consensus       219 ~~~LL~GvTGSGKTEVYl~-li~~~L~~GkqvLiLvPEI~Lt~Q~~~rl~~rF~~~v~v~HS~ls~~eR~~~w~~i~~G~  297 (731)
                      +.+|+.|+.|||||--.+. .+..++++||.|..=+|++.     .+.+.+.++...-.   ....-+-...|..     
T Consensus         1 MI~litG~pGsGKS~~aV~~~i~~al~~GR~V~tNI~gL~-----~~~~~~~~~~~~~~---~~~~~~~~~~w~~-----   67 (183)
T pfam05707         1 MIYLITGKPGSGKTLEAVSYHILPALKKGRKVITNIDGLN-----LERFPKVFGEDVRE---RLEDIGYMDPWRT-----   67 (183)
T ss_pred             CEEEEECCCCCCCCHHHHHHHHHHHHHCCCEEEECCCCCC-----CHHCCCCCCCCCCC---CCCCCCCCHHHCC-----
T ss_conf             9799935999962299999999999878998998786535-----22101223444543---2000012223314-----


Q ss_pred             CEEEEECCHHHHHHHCCCEEEEEEECCCCCCHHCCC--C-CCCHHHHHHHHHHHCCCCEECCCCCCC
Q ss_conf             739994001211001000136774055321000024--4-322489999975110321000024543
Q gi|254780619|r  298 ISVIVGVRSALFLPFKKLGLIVIDEEHDISYKQEEG--I-LYNARDMSIVRGKIESFPVVLVSATPS  361 (731)
Q Consensus       298 ~~IVIGtRSAif~P~~nLglIIvDEEHd~sykq~~~--p-ry~aRdvA~~Ra~~~~~~lilgSATPS  361 (731)
                                    .++=+||||||-|.- |-...+  + .=+..  ++......|..++|.+-.|+
T Consensus        68 --------------~p~g~liViDE~~~~-~~~r~~~~~~~~~i~--~l~~HRH~G~DiiliTQ~~~  117 (183)
T pfam05707        68 --------------YPKGALLVIDEAQTW-FPSRRGGDKVPPVLD--AFSTHRHLGWDIILITQNPS  117 (183)
T ss_pred             --------------CCCCCEEEEECCHHH-CCCCCCCCCCCHHHH--HHHHCCCCCCEEEEEECCHH
T ss_conf             --------------999879999897655-488777888838999--99980778820899918979


No 110
>KOG0341 consensus
Probab=97.06  E-value=0.0014  Score=46.52  Aligned_cols=96  Identities=22%  Similarity=0.350  Sum_probs=59.1

Q ss_pred             HHHHHHHHHHCCCCCCEEEEEHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCEE--EE
Q ss_conf             7899999862125765798704430231134520123300034431024557899999875431102566788689--99
Q gi|254780619|r  523 GRLQLQLSAIAKGEIDIIIGTQLVAKGHNFPRMSLVGVVDGDLGLTNADLRSSERTFQLLSQVTGRAGRFGLKSLG--LI  600 (731)
Q Consensus       523 ~~~~~~~~~~~~~~~~ilvgTq~i~kg~~fp~v~lv~il~aD~~l~~pd~ra~E~~~qll~qv~gRagr~~~~g~v--~i  600 (731)
                      ......++.|+.|+.|+||+|-..+||+|||++.-|+-.|.      |     |..-. ++--.||.||..+.|-.  +|
T Consensus       458 edR~~ai~afr~gkKDVLVATDVASKGLDFp~iqHVINyDM------P-----~eIEN-YVHRIGRTGRsg~~GiATTfI  525 (610)
T KOG0341         458 EDRHYAIEAFRAGKKDVLVATDVASKGLDFPDIQHVINYDM------P-----EEIEN-YVHRIGRTGRSGKTGIATTFI  525 (610)
T ss_pred             HHHHHHHHHHHCCCCCEEEEECCHHCCCCCCCCHHHCCCCC------H-----HHHHH-HHHHHCCCCCCCCCCEEEEEE
T ss_conf             67888999986578745887310003689745044404788------0-----88999-999712467788864022211


Q ss_pred             EECCCCCHHHHHHHHCCHHHHHHHHHHHHHHCCCCCCHHEE
Q ss_conf             93298648889999589799999999999981888801189
Q gi|254780619|r  601 QAYQPTHPVMQALVSGDADSFYESEIRARESVNLPPFGRLA  641 (731)
Q Consensus       601 Qt~~p~~~~~~~~~~~d~~~f~~~el~~R~~~~~PPf~~~~  641 (731)
                      --.+ +..++-.         .++.|.+-++- .|||-...
T Consensus       526 NK~~-~esvLlD---------LK~LL~EakQ~-vP~~L~~L  555 (610)
T KOG0341         526 NKNQ-EESVLLD---------LKHLLQEAKQE-VPPVLAEL  555 (610)
T ss_pred             CCCC-HHHHHHH---------HHHHHHHHHCC-CCHHHHHH
T ss_conf             4563-1888987---------99999986510-88799974


No 111
>PRK05582 DNA topoisomerase I; Validated
Probab=97.00  E-value=0.001  Score=47.59  Aligned_cols=40  Identities=33%  Similarity=0.625  Sum_probs=22.3

Q ss_pred             CCCCCCCEEEEECCC--C-CCEEC---HHHCC---CCCCCCCCCCCCCC
Q ss_conf             101465201211357--8-32000---02102---44655566678741
Q gi|254780619|r  447 KCLHCSCWLVEHRSK--K-KLYCH---QCGHS---AIYSQSCVVCGSSG  486 (731)
Q Consensus       447 ~C~~C~~~l~~h~~~--~-~l~Ch---~Cg~~---~~~~~~Cp~Cg~~~  486 (731)
                      .||.|++.|+..++.  + .+-|.   -|.|.   .+....||.||+..
T Consensus       622 ~CP~C~~~l~~r~~k~gk~F~gCs~yp~C~~~~~~~p~~~~Cp~Cg~~~  670 (692)
T PRK05582        622 KCPECGGKIVKRKSKKGKKFYGCSNYPKCNFISNYEPSNEKCPECGSYM  670 (692)
T ss_pred             CCCCCCCEEEEEECCCCCEEEECCCCCCCCCCCCCCCCCCCCCCCCCHH
T ss_conf             7999997747885489998997489999997738899999699998157


No 112
>PHA00350 putative assembly protein
Probab=96.95  E-value=0.0033  Score=43.66  Aligned_cols=125  Identities=26%  Similarity=0.287  Sum_probs=71.4

Q ss_pred             CEEEEECCCCHHHHH--HHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHCCCCC---E---EEEEECCCCCHHHHHHH
Q ss_conf             619984475315799--999999998514684799715210013445554303897---6---89962355723566789
Q gi|254780619|r  219 AVSLISGVTGSGKTE--VYLEIVAAVLHLGKQVLILLPEISLTSAILERFQKRFGV---K---PAEWHSSLSTSMREKIW  290 (731)
Q Consensus       219 ~~~LL~GvTGSGKTE--VYl~li~~~L~~GkqvLiLvPEI~Lt~Q~~~rl~~rF~~---~---v~v~HS~ls~~eR~~~w  290 (731)
                      +.++++|..|||||=  |+++ |-.+|++||-|+==+|.  |.   .+.+.++|++   .   +-+-+....+-+.+..|
T Consensus         2 ~I~~~~G~pGSyKS~~av~~~-ilPALk~GR~ViTNi~g--l~---le~i~k~~~~~p~~~~liri~~~~~~~~~~~~~~   75 (402)
T PHA00350          2 MIYAIVGRPGSYKSYEAVVYH-IIPALKDGRKVITNIPG--LN---LDVFEKVFGEFPDTAELIRIVDRNLEDFESMNRP   75 (402)
T ss_pred             CEEEEECCCCCCCCEEEEHHH-HHHHHHCCCEEEECCCC--CC---HHHHHHHCCCCCCCHHEEEEECCCCCCHHHHHCC
T ss_conf             179982599997660110867-68898569989977899--88---8999987178836032278743786422222020


Q ss_pred             HHHHCCCCEEEEECCHHHHHHHCCCE-EEEEEECCCCC-----CHHCCC---------C----CCCHHHHHHHHHHHCCC
Q ss_conf             99971997399940012110010001-36774055321-----000024---------4----32248999997511032
Q gi|254780619|r  291 RQVARGAISVIVGVRSALFLPFKKLG-LIVIDEEHDIS-----YKQEEG---------I----LYNARDMSIVRGKIESF  351 (731)
Q Consensus       291 ~~i~~G~~~IVIGtRSAif~P~~nLg-lIIvDEEHd~s-----ykq~~~---------p----ry~aRdvA~~Ra~~~~~  351 (731)
                      ..                +.|   .| ||||||-|+.-     +|..+.         |    +=..-.-+.+|.+..|.
T Consensus        76 f~----------------W~p---~galiviDE~q~~~~~~~~~~~~~~~~~p~~~~~~~~~~~p~~~~~~~~~HRh~~w  136 (402)
T PHA00350         76 FS----------------WRP---RGALYVIDEAQMIFPKRLGFKMANIFKRPFTDFEPHLPEGPENFLEAFMRHRHYNW  136 (402)
T ss_pred             CC----------------CCC---CCCEEEEECHHHHCCCCCCCCHHHHHCCCCCCCCCCCCCCCHHHHHHHHHHCCCCC
T ss_conf             12----------------367---77789996313324654330023321266642000267884569999997321586


Q ss_pred             CEECCCCCCCHHHHHHHHH
Q ss_conf             1000024543246775321
Q gi|254780619|r  352 PVVLVSATPSIESRVNGIS  370 (731)
Q Consensus       352 ~lilgSATPSles~~~~~~  370 (731)
                      .++|.  ||+..-.+....
T Consensus       137 DI~L~--Tp~~~~i~~~ir  153 (402)
T PHA00350        137 DIILL--TPNIRKIHSDIR  153 (402)
T ss_pred             CEEEE--CCCHHHHHHHHH
T ss_conf             67996--788789859999


No 113
>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=96.92  E-value=0.0097  Score=40.05  Aligned_cols=50  Identities=28%  Similarity=0.367  Sum_probs=39.7

Q ss_pred             CEEEEECCCCHHHHHHHHHHHHHH-HHCCCCEEEEECCCHHHHHHHHHHHCC
Q ss_conf             619984475315799999999998-514684799715210013445554303
Q gi|254780619|r  219 AVSLISGVTGSGKTEVYLEIVAAV-LHLGKQVLILLPEISLTSAILERFQKR  269 (731)
Q Consensus       219 ~~~LL~GvTGSGKTEVYl~li~~~-L~~GkqvLiLvPEI~Lt~Q~~~rl~~r  269 (731)
                      ..+++-|-||+|||-+-++++.++ +++|+.|+++-.|-+ ..++..|+-..
T Consensus        20 ~l~vi~g~pg~GKS~~~~~~a~~~a~~~g~~Vl~~slEm~-~~~~~~R~~a~   70 (186)
T pfam03796        20 DLIIIAARPSMGKTAFALNIARNAALKQDKPVLFFSLEMS-AEQLAERLLSS   70 (186)
T ss_pred             CEEEEEECCCCCHHHHHHHHHHHHHHHCCCCEEEECCCCC-HHHHHHHHHHH
T ss_conf             1799996799987999999999999970996687547552-99999999998


No 114
>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=96.92  E-value=0.0081  Score=40.65  Aligned_cols=128  Identities=18%  Similarity=0.156  Sum_probs=85.9

Q ss_pred             EEECCCCHHHHHHHHHHHHHHHHCCCCEEEEECCCHHHH---HHHHHHHCCCCCEEEEEECCCCCHHHHHHHHHHHCCCC
Q ss_conf             984475315799999999998514684799715210013---44555430389768996235572356678999971997
Q gi|254780619|r  222 LISGVTGSGKTEVYLEIVAAVLHLGKQVLILLPEISLTS---AILERFQKRFGVKPAEWHSSLSTSMREKIWRQVARGAI  298 (731)
Q Consensus       222 LL~GvTGSGKTEVYl~li~~~L~~GkqvLiLvPEI~Lt~---Q~~~rl~~rF~~~v~v~HS~ls~~eR~~~w~~i~~G~~  298 (731)
                      +.+=-||-|||.+..-.+.-.--.|+.|-|+-..=-|+.   ++...+.+.||-.|.+..+++++.+|...|.      .
T Consensus        94 IaEM~TGEGKTL~atl~a~l~AL~Gk~VhvvTvNdYLA~RDae~m~~vy~~LGLsvg~i~~~~~~~err~aY~------~  167 (381)
T pfam07517        94 IAEMKTGEGKTLTATLPAYLNALSGKGVHVVTVNDYLAKRDAEWMGPLYEFLGLSVGVITSDMSPEERREAYN------C  167 (381)
T ss_pred             EEEEECCCCCHHHHHHHHHHHHCCCCCCEEEECCHHHHHHHHHHHHHHHHHHCCEEEECCCCCCHHHHHHHHH------C
T ss_conf             2588769981199999999997379974899758888688999979999984860542278898488898751------6


Q ss_pred             EEEEECCHHH-H-------------HHHCCCEEEEEEECCCCCCHHCCCCCCCHHHHHHHHHHHCCCCEECCCCCCCHHH
Q ss_conf             3999400121-1-------------0010001367740553210000244322489999975110321000024543246
Q gi|254780619|r  299 SVIVGVRSAL-F-------------LPFKKLGLIVIDEEHDISYKQEEGILYNARDMSIVRGKIESFPVVLVSATPSIES  364 (731)
Q Consensus       299 ~IVIGtRSAi-f-------------~P~~nLglIIvDEEHd~sykq~~~pry~aRdvA~~Ra~~~~~~lilgSATPSles  364 (731)
                      +|+=||-|-+ |             .-.+.+...||||- |+=.              +   -....|+|+++.+|-...
T Consensus       168 DItYgTn~e~gFDYLRDnm~~~~~~~vqR~~~~aIVDEv-DSiL--------------I---DEArtPLIISg~~~~~~~  229 (381)
T pfam07517       168 DITYGTNSELGFDYLRDNMALSKEDKVQRGLNFAIVDEV-DSIL--------------I---DEARTPLIISGPVEDESE  229 (381)
T ss_pred             CCEECCHHHHHHHHHHHHHHCCHHHHCCCCCCEEEEECC-CHHE--------------E---ECCCCCCEECCCCCCCCH
T ss_conf             605503223214453234415825434577776999745-1121--------------2---046786354078876305


Q ss_pred             HHHHHHHHH
Q ss_conf             775321234
Q gi|254780619|r  365 RVNGISRRY  373 (731)
Q Consensus       365 ~~~~~~g~~  373 (731)
                      .|.......
T Consensus       230 ~y~~~~~~~  238 (381)
T pfam07517       230 LYLIADALV  238 (381)
T ss_pred             HHHHHHHHH
T ss_conf             899999999


No 115
>PRK05580 primosome assembly protein PriA; Validated
Probab=96.91  E-value=0.028  Score=36.54  Aligned_cols=25  Identities=16%  Similarity=0.434  Sum_probs=16.9

Q ss_pred             CCCEEEEE-CCCCHHHHHHHHHHHHH
Q ss_conf             89619984-47531579999999999
Q gi|254780619|r  217 GFAVSLIS-GVTGSGKTEVYLEIVAA  241 (731)
Q Consensus       217 ~f~~~LL~-GvTGSGKTEVYl~li~~  241 (731)
                      +..+.++| +.|.+-|.++|+++...
T Consensus       239 g~~v~v~HS~ls~~eR~~~w~~i~~G  264 (699)
T PRK05580        239 GARVAVLHSGLSDGERYRAWLAALRG  264 (699)
T ss_pred             CCCEEEECCCCCHHHHHHHHHHHHCC
T ss_conf             99579964889857999999999769


No 116
>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=96.83  E-value=0.021  Score=37.43  Aligned_cols=138  Identities=16%  Similarity=0.112  Sum_probs=77.7

Q ss_pred             CEEEEECCCCHHHHHHHHHHHHHHHH-CCCCEEEEECCCHHHHHHHHHHHCCC-CCEEE-EEECCCCCHHHHHHHHHHHC
Q ss_conf             61998447531579999999999851-46847997152100134455543038-97689-96235572356678999971
Q gi|254780619|r  219 AVSLISGVTGSGKTEVYLEIVAAVLH-LGKQVLILLPEISLTSAILERFQKRF-GVKPA-EWHSSLSTSMREKIWRQVAR  295 (731)
Q Consensus       219 ~~~LL~GvTGSGKTEVYl~li~~~L~-~GkqvLiLvPEI~Lt~Q~~~rl~~rF-~~~v~-v~HS~ls~~eR~~~w~~i~~  295 (731)
                      ...++-|.||+|||.+-++++..... .|..|++.-.|-.- .|+..|+-... +.... .........++++.|..-..
T Consensus        31 eL~viaarpg~GKT~f~~~~a~~~~~~~g~~vl~~SlEm~~-~~~~~Rlls~~~g~~~~~~~~~~~~~~e~~~~~~~~~~  109 (271)
T cd01122          31 ELIILTAGTGVGKTTFLREYALDLITQHGVRVGTISLEEPV-VRTARRLLGQYAGKRLHLPDTVFIYTLEEFDAAFDEFE  109 (271)
T ss_pred             CEEEEEECCCCCHHHHHHHHHHHHHHHCCCEEEEEECCCCH-HHHHHHHHHHHHCCCHHHCCCCCCCHHHHHHHHHHHHC
T ss_conf             08999968998699999999999999769908999704999-99999999998299711034467780999999999970


Q ss_pred             CCCEEEE----EC------CHHH--HHHHCCCEEEEEEECCCCCC-HHCCCCCCCH-----HHHHHHHHHHCCCCEECCC
Q ss_conf             9973999----40------0121--10010001367740553210-0002443224-----8999997511032100002
Q gi|254780619|r  296 GAISVIV----GV------RSAL--FLPFKKLGLIVIDEEHDISY-KQEEGILYNA-----RDMSIVRGKIESFPVVLVS  357 (731)
Q Consensus       296 G~~~IVI----Gt------RSAi--f~P~~nLglIIvDEEHd~sy-kq~~~pry~a-----RdvA~~Ra~~~~~~lilgS  357 (731)
                      +...+.|    |.      ++.+  +.--.++++||||-=+--.- .+...-++.+     |.+ ...|+.++|++++.|
T Consensus       110 ~~~~l~i~d~~~~~~~~~i~~~ir~~~~~~~~~~vvIDylqll~~~~~~~~d~~~~i~~i~~~L-k~lAke~~v~Vi~ls  188 (271)
T cd01122         110 GTGRLFMYDSFGEYSMDSVLEKVRYMAVSHGIQHIIIDNLSIMVSDERASGDERKALDEIMTKL-RGFATEHGIHITLVS  188 (271)
T ss_pred             CCCCEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEEHHHHCCCCCCCCCCHHHHHHHHHHHH-HHHHHHHCCCEEEEE
T ss_conf             7998088789999889999999999998289988998317850367867731899999999999-999999799779995


Q ss_pred             C
Q ss_conf             4
Q gi|254780619|r  358 A  358 (731)
Q Consensus       358 A  358 (731)
                      .
T Consensus       189 Q  189 (271)
T cd01122         189 H  189 (271)
T ss_pred             C
T ss_conf             2


No 117
>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=96.83  E-value=0.026  Score=36.76  Aligned_cols=37  Identities=30%  Similarity=0.355  Sum_probs=25.7

Q ss_pred             CCCEEEEECCCCHHHHHHHHHHHHHHHHCCCCEEEEE
Q ss_conf             8961998447531579999999999851468479971
Q gi|254780619|r  217 GFAVSLISGVTGSGKTEVYLEIVAAVLHLGKQVLILL  253 (731)
Q Consensus       217 ~f~~~LL~GvTGSGKTEVYl~li~~~L~~GkqvLiLv  253 (731)
                      +..+..|+|-+|||||-.---+..++.+.|++++++-
T Consensus        37 ~~~~l~i~G~~GsGKTHLl~a~~~~~~~~~~~~~yl~   73 (226)
T TIGR03420        37 GDRFLYLWGESGSGKSHLLQAACAAAEERGKSAIYLP   73 (226)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHHHHHCCCCCEEEEC
T ss_conf             8886999899999889999999999862699579952


No 118
>PRK12377 putative replication protein; Provisional
Probab=96.73  E-value=0.027  Score=36.64  Aligned_cols=95  Identities=20%  Similarity=0.360  Sum_probs=66.1

Q ss_pred             CCCCCCHHHHHHHHHHH---HHHCCCCCEEEEECCCCHHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHCCCC
Q ss_conf             66668837899999998---752048961998447531579999999999851468479971521001344555430389
Q gi|254780619|r  195 SLPILDKNQQDVVEQVV---PLCTKGFAVSLISGVTGSGKTEVYLEIVAAVLHLGKQVLILLPEISLTSAILERFQKRFG  271 (731)
Q Consensus       195 ~~~~Lt~eQ~~a~~~i~---~~~~~~f~~~LL~GvTGSGKTEVYl~li~~~L~~GkqvLiLvPEI~Lt~Q~~~rl~~rF~  271 (731)
                      +...-++.|+.|+.+..   .....++...++.|-+|.|||-...-+..+++.+|++|++.-     ++.++.+++..+.
T Consensus        75 ny~~~~~~~~~a~~~a~~~~~~F~~~~~NlIf~G~pGtGKTHLA~AIg~~a~~~G~sVlF~t-----~~dLv~~L~~a~~  149 (248)
T PRK12377         75 NYQVQNDGQRYALSQAKSIADELMTGCTNFVFSGKPGTGKNHLAAAIGNRLLAKGRSVIVVT-----VPDVMSRLHESYD  149 (248)
T ss_pred             CCCCCCHHHHHHHHHHHHHHHHHHCCCCEEEEECCCCCCHHHHHHHHHHHHHHCCCEEEEEE-----HHHHHHHHHHHHH
T ss_conf             56457878999999999999987318860899899998788999999999998799699988-----9999999999998


Q ss_pred             CEEEEEECCCCCHHHHHHHHHHHCCCCEEEEECCHHHHHHHCCCEEEEEEEC
Q ss_conf             7689962355723566789999719973999400121100100013677405
Q gi|254780619|r  272 VKPAEWHSSLSTSMREKIWRQVARGAISVIVGVRSALFLPFKKLGLIVIDEE  323 (731)
Q Consensus       272 ~~v~v~HS~ls~~eR~~~w~~i~~G~~~IVIGtRSAif~P~~nLglIIvDEE  323 (731)
                      +                       |+      +...++-.+.+..|+|+||=
T Consensus       150 ~-----------------------g~------~~~k~l~~l~~~dLLIIDEl  172 (248)
T PRK12377        150 N-----------------------GQ------SGEKFLQELCKVDLLVLDEI  172 (248)
T ss_pred             C-----------------------CC------CHHHHHHHHHCCCEEEEHHC
T ss_conf             4-----------------------85------09999999733898986000


No 119
>pfam02562 PhoH PhoH-like protein. PhoH is a cytoplasmic protein and predicted ATPase that is induced by phosphate starvation.
Probab=96.72  E-value=0.0071  Score=41.10  Aligned_cols=168  Identities=15%  Similarity=0.163  Sum_probs=84.9

Q ss_pred             CCCCHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHHHHHHHHHHCCC--CEEEEECCCHHHHHHHHHHHCCCCCEE
Q ss_conf             668837899999998752048961998447531579999999999851468--479971521001344555430389768
Q gi|254780619|r  197 PILDKNQQDVVEQVVPLCTKGFAVSLISGVTGSGKTEVYLEIVAAVLHLGK--QVLILLPEISLTSAILERFQKRFGVKP  274 (731)
Q Consensus       197 ~~Lt~eQ~~a~~~i~~~~~~~f~~~LL~GvTGSGKTEVYl~li~~~L~~Gk--qvLiLvPEI~Lt~Q~~~rl~~rF~~~v  274 (731)
                      .+.|.+|+.+++.+..   .  ....+.|-+|||||-+.+.++.+.+..|+  .+++.=|-+..            |..+
T Consensus         3 ~P~~~~Q~~~~~~l~~---~--~iv~~~GpAGtGKT~la~~~al~~l~~~~~~kiii~Rp~v~~------------g~~i   65 (205)
T pfam02562         3 KPKTLGQKRYVEAIRK---N--DIVFGIGPAGTGKTYLAVAAAVDALKDGKVKRIILTRPAVEA------------GEKL   65 (205)
T ss_pred             CCCCHHHHHHHHHHHC---C--CEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEEECCCCC------------CCCC
T ss_conf             7898889999999717---9--807998999860999999999999971894379997577125------------7754


Q ss_pred             EEEECCCCCHHHHHHHHHHHCCCCEEEEECCH---------HHHHHHC-------CCEEEEEEECCCCCCHHCCCCCCCH
Q ss_conf             99623557235667899997199739994001---------2110010-------0013677405532100002443224
Q gi|254780619|r  275 AEWHSSLSTSMREKIWRQVARGAISVIVGVRS---------ALFLPFK-------KLGLIVIDEEHDISYKQEEGILYNA  338 (731)
Q Consensus       275 ~v~HS~ls~~eR~~~w~~i~~G~~~IVIGtRS---------Aif~P~~-------nLglIIvDEEHd~sykq~~~pry~a  338 (731)
                      ..+-+  +..|+.+-|..-......-++|...         =-|.|+.       +=..|||||-++.+.        |.
T Consensus        66 GfLPG--~~~eK~~p~~~p~~d~l~~~~~~~~~~~l~~~~~Ie~~pl~~iRGrTf~n~~iIvDEaQN~t~--------~~  135 (205)
T pfam02562        66 GFLPG--DLEEKVDPYLRPLYDALYDMLGAEKVEKLIERGVIEIAPLAYMRGRTLNDAFIILDEAQNTTP--------EQ  135 (205)
T ss_pred             CCCCC--CHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHCCCEEECCHHHHCCCCCCCCEEEEECHHCCCH--------HH
T ss_conf             55889--789999999999999999872899999999759756614676554762568899972213999--------99


Q ss_pred             HHHHHHHHHHCCCCEECCCCCCCHHHHH-HHHHHHHHHHCCCCCCCCCCCCCCEECCCCCC
Q ss_conf             8999997511032100002454324677-53212344412432236765433211022223
Q gi|254780619|r  339 RDMSIVRGKIESFPVVLVSATPSIESRV-NGISRRYHSVHLSTRYRNSALPHLQVIDMRGQ  398 (731)
Q Consensus       339 RdvA~~Ra~~~~~~lilgSATPSles~~-~~~~g~~~~~~l~~R~~~~~~P~i~ivDm~~~  398 (731)
                      -...+-|.- +|+.+|+..-+ +--... ...+|   +..+.++..+  .+.+.++++..+
T Consensus       136 lk~ilTRiG-~~SK~vi~GD~-~Q~D~~~~~~nG---l~~~~~~l~~--~~~~~~i~f~~~  189 (205)
T pfam02562       136 MKMFLTRIG-FNSKMVVTGDI-TQIDLPKGQKSG---LADALEILKG--VEGIGFIEFTLK  189 (205)
T ss_pred             HHHHHHHCC-CCCEEEEECCH-HHCCCCCCCCCC---HHHHHHHHCC--CCCEEEEEECCC
T ss_conf             999984217-99689994786-651789999872---9999999669--998599993586


No 120
>TIGR00373 TIGR00373 conserved hypothetical protein TIGR00373; InterPro: IPR005241    This family of proteins is, so far, restricted to archaeal genomes. The family appears to be distantly related to the N-terminal region of the eukaryotic transcription initiation factor IIE alpha chain. .
Probab=96.72  E-value=0.0019  Score=45.44  Aligned_cols=64  Identities=20%  Similarity=0.348  Sum_probs=46.2

Q ss_pred             HHHHHHHHHHHCCCCEEEEEECCCCEEHHCCCCCCCCCCCCCCCCCEEEEECCCCCCEECHHHCCCCCCCCCCCCCCCCE
Q ss_conf             89999998862265517997422200000023565434310146520121135783200002102446555666787411
Q gi|254780619|r  408 PEMIDGIRHTLARNEQTLLFLNRRGYAPLTLCQVCGNRLKCLHCSCWLVEHRSKKKLYCHQCGHSAIYSQSCVVCGSSGK  487 (731)
Q Consensus       408 ~~l~~~i~~~l~~g~qvll~lnRrGya~~~~C~~Cg~~~~C~~C~~~l~~h~~~~~l~Ch~Cg~~~~~~~~Cp~Cg~~~~  487 (731)
                      +.+++.+++.|+.-+..+.|+                   ||||.+..||..            ......+||.||+.  
T Consensus        93 ~e~~kkLreklEfE~nn~ff~-------------------CpN~~vrftf~e------------Ame~nFtCP~CG~~--  139 (168)
T TIGR00373        93 EELVKKLREKLEFEKNNMFFV-------------------CPNMNVRFTFDE------------AMELNFTCPECGAM--  139 (168)
T ss_pred             HHHHHHHHHHHHHHCCCEEEE-------------------ECCCEEEEEHHH------------HHCCCCCCCCCCCH--
T ss_conf             999999998742310772587-------------------138405740422------------31167988331323--


Q ss_pred             ECCCC--CCHHHHHHHHHH
Q ss_conf             00135--428998888520
Q gi|254780619|r  488 MIACG--FGIERIAEEVCE  504 (731)
Q Consensus       488 l~~~G--~Gte~~~e~l~~  504 (731)
                      |..+-  -=++.|+|+++.
T Consensus       140 l~~~DnSe~I~~ieee~~~  158 (168)
T TIGR00373       140 LDYLDNSELIKEIEEEVKL  158 (168)
T ss_pred             HHHHHHHHHHHHHHHHHHH
T ss_conf             2241027899999999988


No 121
>PRK08620 DNA topoisomerase III; Provisional
Probab=96.69  E-value=0.0012  Score=46.97  Aligned_cols=51  Identities=29%  Similarity=0.616  Sum_probs=35.7

Q ss_pred             CCCCCCCCCCEEEEE--CCCCCCEECH--HHCCCCCC----CCCCCCCCCCEECCCCCC
Q ss_conf             343101465201211--3578320000--21024465----556667874110013542
Q gi|254780619|r  444 NRLKCLHCSCWLVEH--RSKKKLYCHQ--CGHSAIYS----QSCVVCGSSGKMIACGFG  494 (731)
Q Consensus       444 ~~~~C~~C~~~l~~h--~~~~~l~Ch~--Cg~~~~~~----~~Cp~Cg~~~~l~~~G~G  494 (731)
                      .-..||.|+.+|..-  +.+..|.|.-  |+|+.++.    .+||.||....++.-|.|
T Consensus       608 t~~~Cp~Cg~~m~~~~gr~Gkf~~C~~peC~~~k~~~~~~~~~Cp~C~~~~~~~~~~~g  666 (726)
T PRK08620        608 TGTKCPDCGKFMLEVKGKNGKMLVCQDRECGHRKNVSRKTNARCPNCKKKLELRGEGEG  666 (726)
T ss_pred             CCCCCCCCCCCCEEEECCCCCEEECCCCCCCCCCCCHHHCCCCCCCCCCEEEEEECCCC
T ss_conf             89856426832116858987557468998999777102128949999985689856778


No 122
>PRK08620 DNA topoisomerase III; Provisional
Probab=96.63  E-value=0.0014  Score=46.47  Aligned_cols=53  Identities=28%  Similarity=0.595  Sum_probs=38.4

Q ss_pred             CCEEEEEECCCCEEHHCCCCC--CCCC--------CCCCCCCCEEEEECC--CCCCEECHHHCCCCCC
Q ss_conf             551799742220000002356--5434--------310146520121135--7832000021024465
Q gi|254780619|r  421 NEQTLLFLNRRGYAPLTLCQV--CGNR--------LKCLHCSCWLVEHRS--KKKLYCHQCGHSAIYS  476 (731)
Q Consensus       421 g~qvll~lnRrGya~~~~C~~--Cg~~--------~~C~~C~~~l~~h~~--~~~l~Ch~Cg~~~~~~  476 (731)
                      |...+...-|.|  .++.|.+  |++.        ++||+|+..|+.+++  +..+.|. |||.+...
T Consensus       616 g~~m~~~~gr~G--kf~~C~~peC~~~k~~~~~~~~~Cp~C~~~~~~~~~~~g~~~~c~-~~~~e~~~  680 (726)
T PRK08620        616 GKFMLEVKGKNG--KMLVCQDRECGHRKNVSRKTNARCPNCKKKLELRGEGEGQIFVCV-CGHREKLS  680 (726)
T ss_pred             CCCCEEEECCCC--CEEECCCCCCCCCCCCHHHCCCCCCCCCCEEEEEECCCCCEEEEC-CCCHHHHH
T ss_conf             832116858987--557468998999777102128949999985689856778789973-89887888


No 123
>PRK05636 replicative DNA helicase; Provisional
Probab=96.62  E-value=0.077  Score=33.16  Aligned_cols=131  Identities=20%  Similarity=0.292  Sum_probs=77.0

Q ss_pred             EEEEECCCCHHHHHHHHHHHHHH-HHCCCCEEEEECCCHHHHHHHHHHHCCC-CCEE-EEEECCCCCHHHHHHHHHHH-C
Q ss_conf             19984475315799999999998-5146847997152100134455543038-9768-99623557235667899997-1
Q gi|254780619|r  220 VSLISGVTGSGKTEVYLEIVAAV-LHLGKQVLILLPEISLTSAILERFQKRF-GVKP-AEWHSSLSTSMREKIWRQVA-R  295 (731)
Q Consensus       220 ~~LL~GvTGSGKTEVYl~li~~~-L~~GkqvLiLvPEI~Lt~Q~~~rl~~rF-~~~v-~v~HS~ls~~eR~~~w~~i~-~  295 (731)
                      ...|=|-+|.|||-..+.++..+ +.+|+.|++.-.|-+ ..|+..|+-... +... -+.+..+++.+-......+. -
T Consensus       269 LiIiAARPsmGKTalAlnia~n~A~~~g~~v~~fSLEMs-~~ql~~Rlla~~s~V~~~~ir~g~l~~~~~~~l~~a~~~l  347 (507)
T PRK05636        269 MIIVAARPGVGKSTIALDFMRSASIKNNKASVIFSLEMS-KSEIVMRLLSAEAEVRLADMRGGKMDEDAWEKLVQRLGKI  347 (507)
T ss_pred             EEEEEECCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCC-HHHHHHHHHHHHCCCCHHHHHCCCCCHHHHHHHHHHHHHH
T ss_conf             799973787866899999999999876993799715699-8999999999847988788855887889999999999998


Q ss_pred             CCCEEEEECCHHH-----------HHHHCCCEEEEEEECCCCCCHHCCCC--CCCHHH--HH------HHHHHHCCCCEE
Q ss_conf             9973999400121-----------10010001367740553210000244--322489--99------997511032100
Q gi|254780619|r  296 GAISVIVGVRSAL-----------FLPFKKLGLIVIDEEHDISYKQEEGI--LYNARD--MS------IVRGKIESFPVV  354 (731)
Q Consensus       296 G~~~IVIGtRSAi-----------f~P~~nLglIIvDEEHd~sykq~~~p--ry~aRd--vA------~~Ra~~~~~~li  354 (731)
                      .+..|.|=-.+.+           ...-.+|++||||      |=|-..+  +...|.  |+      ...|+..+||||
T Consensus       348 ~~~pl~IdD~~~lti~~Ira~aRrlk~~~~l~livVD------YLQLm~~~~~~~~R~~ev~~ISr~LK~lAkel~vpVi  421 (507)
T PRK05636        348 AQAPIFIDDSANLTMMEIRSKARRLKQKHDLKMIVVD------YLQLMSSGKRVESRQQEVSEFSRQLKLLAKELDVPLI  421 (507)
T ss_pred             HHCCEEEECCCCCCHHHHHHHHHHHHHHCCCCEEEEE------HHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCEE
T ss_conf             6198899849997699999999999861799989984------5884568888766899999999999999999799889


Q ss_pred             CCC
Q ss_conf             002
Q gi|254780619|r  355 LVS  357 (731)
Q Consensus       355 lgS  357 (731)
                      +.|
T Consensus       422 ~Ls  424 (507)
T PRK05636        422 AIS  424 (507)
T ss_pred             EEC
T ss_conf             971


No 124
>COG1197 Mfd Transcription-repair coupling factor (superfamily II helicase) [DNA replication, recombination, and repair / Transcription]
Probab=96.61  E-value=0.018  Score=38.08  Aligned_cols=165  Identities=19%  Similarity=0.270  Sum_probs=91.1

Q ss_pred             ECCCCCCHHHHHHHHHHCCCCCHHH--HCCCCCCCCHHHHHHHHHHHCCCCCCEEEEE-HHHCCCCCCCCCCHHHHHHHH
Q ss_conf             0013542899888852048520001--0232113586789999986212576579870-443023113452012330003
Q gi|254780619|r  488 MIACGFGIERIAEEVCEYFPLARIS--ILSSDLEGGGGRLQLQLSAIAKGEIDIIIGT-QLVAKGHNFPRMSLVGVVDGD  564 (731)
Q Consensus       488 l~~~G~Gte~~~e~l~~~fp~~~v~--~~d~d~~~~~~~~~~~~~~~~~~~~~ilvgT-q~i~kg~~fp~v~lv~il~aD  564 (731)
                      +.+--.=.|+=.+-+++-|-+.+|-  .+|+=  ++++....+++.+.+|++||+||| .++.|+..|.|++|++| |-.
T Consensus       649 LVPTTlLA~QHy~tFkeRF~~fPV~I~~LSRF--~s~kE~~~il~~la~G~vDIvIGTHrLL~kdv~FkdLGLlII-DEE  725 (1139)
T COG1197         649 LVPTTLLAQQHYETFKERFAGFPVRIEVLSRF--RSAKEQKEILKGLAEGKVDIVIGTHRLLSKDVKFKDLGLLII-DEE  725 (1139)
T ss_pred             ECCCHHHHHHHHHHHHHHHCCCCEEEEEECCC--CCHHHHHHHHHHHHCCCCCEEEECHHHHCCCCEEECCCEEEE-ECH
T ss_conf             92607868998999998733898258886055--788999999999856984589963176478967704764897-443


Q ss_pred             HHHHHHHHHHHH--------------------HHHHH-HHHHHHCCCCC-CCCCEEEEEECCCCC--HHHHHH-----HH
Q ss_conf             443102455789--------------------99998-75431102566-788689999329864--888999-----95
Q gi|254780619|r  565 LGLTNADLRSSE--------------------RTFQL-LSQVTGRAGRF-GLKSLGLIQAYQPTH--PVMQAL-----VS  615 (731)
Q Consensus       565 ~~l~~pd~ra~E--------------------~~~ql-l~qv~gRagr~-~~~g~v~iQt~~p~~--~~~~~~-----~~  615 (731)
                      +-+..   +--|                    ||.+| |..+...+==. ...+|.=||||--++  .+++.+     .+
T Consensus       726 qRFGV---k~KEkLK~Lr~~VDvLTLSATPIPRTL~Msm~GiRdlSvI~TPP~~R~pV~T~V~~~d~~~ireAI~REl~R  802 (1139)
T COG1197         726 QRFGV---KHKEKLKELRANVDVLTLSATPIPRTLNMSLSGIRDLSVIATPPEDRLPVKTFVSEYDDLLIREAILRELLR  802 (1139)
T ss_pred             HHCCC---CHHHHHHHHHCCCCEEEEECCCCCCHHHHHHHCCHHHHHCCCCCCCCCCEEEEEECCCHHHHHHHHHHHHHC
T ss_conf             53271---178999877505728974178875447777744303311147998772128887158828999999998715


Q ss_pred             CC--------HHHHHHHHHHHHHHCCCCCCHHEEEEEEECCCHHHHHHHHHHHHH
Q ss_conf             89--------799999999999981888801189998845998999999999998
Q gi|254780619|r  616 GD--------ADSFYESEIRARESVNLPPFGRLAAVIISGTKYQEVENYAYNLKE  662 (731)
Q Consensus       616 ~d--------~~~f~~~el~~R~~~~~PPf~~~~~i~~~~~~~~~~~~~~~~~~~  662 (731)
                      +.        -+...+..   .+.-.+=|-.|++ +.-....+.+.++....+.+
T Consensus       803 gGQvfYv~NrV~~Ie~~~---~~L~~LVPEarI~-vaHGQM~e~eLE~vM~~F~~  853 (1139)
T COG1197         803 GGQVFYVHNRVESIEKKA---ERLRELVPEARIA-VAHGQMRERELEEVMLDFYN  853 (1139)
T ss_pred             CCEEEEEECCCCCHHHHH---HHHHHHCCCEEEE-EEECCCCHHHHHHHHHHHHC
T ss_conf             987999943331299999---9999859846888-85258888999999999972


No 125
>KOG1803 consensus
Probab=96.59  E-value=0.0054  Score=41.99  Aligned_cols=67  Identities=27%  Similarity=0.490  Sum_probs=51.6

Q ss_pred             CCCCCHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHHHHHHHHHHCCCCEEEEECC-CHHHHHHHHHHH
Q ss_conf             666883789999999875204896199844753157999999999985146847997152-100134455543
Q gi|254780619|r  196 LPILDKNQQDVVEQVVPLCTKGFAVSLISGVTGSGKTEVYLEIVAAVLHLGKQVLILLPE-ISLTSAILERFQ  267 (731)
Q Consensus       196 ~~~Lt~eQ~~a~~~i~~~~~~~f~~~LL~GvTGSGKTEVYl~li~~~L~~GkqvLiLvPE-I~Lt~Q~~~rl~  267 (731)
                      .+.|+..|+.|+....   ..+ .+..+||=.|.|||-.-.++|.+.+++|++||++.|. +++ .-+.+|+.
T Consensus       183 ~~~ln~SQk~Av~~~~---~~k-~l~~I~GPPGTGKT~TlvEiI~qlvk~~k~VLVcaPSn~AV-dNiverl~  250 (649)
T KOG1803         183 NKNLNSSQKAAVSFAI---NNK-DLLIIHGPPGTGKTRTLVEIISQLVKQKKRVLVCAPSNVAV-DNIVERLT  250 (649)
T ss_pred             CCCCCHHHHHHHHHHH---CCC-CCEEEECCCCCCCEEEHHHHHHHHHHCCCEEEEECCCHHHH-HHHHHHHC
T ss_conf             7432377999999973---568-83575579988840439999999997288599976736789-99998750


No 126
>KOG0948 consensus
Probab=96.58  E-value=0.03  Score=36.34  Aligned_cols=369  Identities=17%  Similarity=0.193  Sum_probs=184.3

Q ss_pred             CCCCHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHCCCCCEEEE
Q ss_conf             66883789999999875204896199844753157999999999985146847997152100134455543038976899
Q gi|254780619|r  197 PILDKNQQDVVEQVVPLCTKGFAVSLISGVTGSGKTEVYLEIVAAVLHLGKQVLILLPEISLTSAILERFQKRFGVKPAE  276 (731)
Q Consensus       197 ~~Lt~eQ~~a~~~i~~~~~~~f~~~LL~GvTGSGKTEVYl~li~~~L~~GkqvLiLvPEI~Lt~Q~~~rl~~rF~~~v~v  276 (731)
                      ..|.+-|..++.-|..     -...|...-|.+|||-|.==+|+.+|.....|++--|=-+|..|-++.|.+-|++- .+
T Consensus       128 F~LDpFQ~~aI~Cidr-----~eSVLVSAHTSAGKTVVAeYAIA~sLr~kQRVIYTSPIKALSNQKYREl~~EF~DV-GL  201 (1041)
T KOG0948         128 FTLDPFQSTAIKCIDR-----GESVLVSAHTSAGKTVVAEYAIAMSLREKQRVIYTSPIKALSNQKYRELLEEFKDV-GL  201 (1041)
T ss_pred             CCCCCHHHHHHHHHCC-----CCEEEEEEECCCCCCHHHHHHHHHHHHHCCEEEEECHHHHHCCHHHHHHHHHHCCC-CE
T ss_conf             4348067654531127-----96389984057885237999999998764858960731554115489999884636-52


Q ss_pred             EECCCCCHHHHHHHHHHHCCCCEEEEEC---CHHHHH---HHCCCEEEEEEECCCCCCHHC---------------CCCC
Q ss_conf             6235572356678999971997399940---012110---010001367740553210000---------------2443
Q gi|254780619|r  277 WHSSLSTSMREKIWRQVARGAISVIVGV---RSALFL---PFKKLGLIVIDEEHDISYKQE---------------EGIL  335 (731)
Q Consensus       277 ~HS~ls~~eR~~~w~~i~~G~~~IVIGt---RSAif~---P~~nLglIIvDEEHd~sykq~---------------~~pr  335 (731)
                      +++..|=.          -....+|..|   ||-++-   =++..+.||.||=|   |--|               +..|
T Consensus       202 MTGDVTIn----------P~ASCLVMTTEILRsMLYRGSEvmrEVaWVIFDEIH---YMRDkERGVVWEETIIllP~~vr  268 (1041)
T KOG0948         202 MTGDVTIN----------PDASCLVMTTEILRSMLYRGSEVMREVAWVIFDEIH---YMRDKERGVVWEETIILLPDNVR  268 (1041)
T ss_pred             EECCEEEC----------CCCCEEEEHHHHHHHHHHCCCHHHHEEEEEEEEEEH---HCCCCCCCEEEEEEEEECCCCCE
T ss_conf             30544668----------987545337999999874331675523148862001---00134456023566785366603


Q ss_pred             C--------CHHHHHHHHHHHCCCC--EECCCCCCCHHHHH--HH-HHHHHHHHCCCCCCCCCC-------CCCCEECC-
Q ss_conf             2--------2489999975110321--00002454324677--53-212344412432236765-------43321102-
Q gi|254780619|r  336 Y--------NARDMSIVRGKIESFP--VVLVSATPSIESRV--NG-ISRRYHSVHLSTRYRNSA-------LPHLQVID-  394 (731)
Q Consensus       336 y--------~aRdvA~~Ra~~~~~~--lilgSATPSles~~--~~-~~g~~~~~~l~~R~~~~~-------~P~i~ivD-  394 (731)
                      |        |||+.|-+-+++|.-|  +|+.---|..=..|  -+ ..|-|..+.-+..++...       +++-.--| 
T Consensus       269 ~VFLSATiPNA~qFAeWI~~ihkQPcHVVYTdyRPTPLQHyifP~ggdGlylvVDek~~FrednF~~am~~l~~~~~~~~  348 (1041)
T KOG0948         269 FVFLSATIPNARQFAEWICHIHKQPCHVVYTDYRPTPLQHYIFPAGGDGLYLVVDEKGKFREDNFQKAMSVLRKAGESDG  348 (1041)
T ss_pred             EEEEECCCCCHHHHHHHHHHHHCCCCEEEEECCCCCCCEEEEECCCCCEEEEEEECCCCCCHHHHHHHHHHHHCCCCCCC
T ss_conf             89995658777999999999755874289505878864144530799806999705664226779999997632577864


Q ss_pred             --CCCCC-CCCC----CCCCHHHHHHHHHHHC-CCCEEEEEECCCCEEHHCCCCCCCCCCCCCCCCCEEEEECCC-CCCE
Q ss_conf             --22233-2224----5479899999988622-655179974222000000235654343101465201211357-8320
Q gi|254780619|r  395 --MRGQT-IAQG----KSLSPEMIDGIRHTLA-RNEQTLLFLNRRGYAPLTLCQVCGNRLKCLHCSCWLVEHRSK-KKLY  465 (731)
Q Consensus       395 --m~~~~-~~~~----~~lS~~l~~~i~~~l~-~g~qvll~lnRrGya~~~~C~~Cg~~~~C~~C~~~l~~h~~~-~~l~  465 (731)
                        .-... .+++    ..-.+.+.+.++-.+. +..+|++|-        ++=++|..-+.--   ..|-+.... +.+ 
T Consensus       349 ~~~~~~k~~kG~~~~~~~~~s~i~kiVkmi~~~~~~PVIvFS--------FSkkeCE~~Alqm---~kldfN~deEk~~-  416 (1041)
T KOG0948         349 KKKANKKGRKGGTGGKGPGDSDIYKIVKMIMERNYLPVIVFS--------FSKKECEAYALQM---SKLDFNTDEEKEL-  416 (1041)
T ss_pred             CCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHCCCCEEEEE--------ECHHHHHHHHHHH---CCCCCCCHHHHHH-
T ss_conf             445554456577678898743199999999962689669998--------1476799999765---1576788568889-


Q ss_pred             ECHHHCCCCCCCCCCCCCCCCEECCCCCCHHHHHHHHHHCCCCCHHHHCCCCCC-CCHHHHHHHHHHHCCCCCCEEEEEH
Q ss_conf             000210244655566678741100135428998888520485200010232113-5867899999862125765798704
Q gi|254780619|r  466 CHQCGHSAIYSQSCVVCGSSGKMIACGFGIERIAEEVCEYFPLARISILSSDLE-GGGGRLQLQLSAIAKGEIDIIIGTQ  544 (731)
Q Consensus       466 Ch~Cg~~~~~~~~Cp~Cg~~~~l~~~G~Gte~~~e~l~~~fp~~~v~~~d~d~~-~~~~~~~~~~~~~~~~~~~ilvgTq  544 (731)
                            ...+.+.--.|=|..     .-+.-+|+.-|--+-.++.|..  |--. --|.-.|.   -|..|=..+|-+|.
T Consensus       417 ------V~~iF~nAi~~Lsee-----Dr~LPqie~iLPLL~RGIGIHH--sGLLPIlKE~IEI---LFqEGLvKvLFATE  480 (1041)
T KOG0948         417 ------VETIFNNAIDQLSEE-----DRELPQIENILPLLRRGIGIHH--SGLLPILKEVIEI---LFQEGLVKVLFATE  480 (1041)
T ss_pred             ------HHHHHHHHHHHCCHH-----HCCCHHHHHHHHHHHHCCCCCC--CCCHHHHHHHHHH---HHHCCHHHHHHHHH
T ss_conf             ------999999999854853-----3155178888999873554344--5504789999999---98502798877541


Q ss_pred             HHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCC--CCEEEEEECCCC-CHHHHHHHHC
Q ss_conf             43023113452012330003443102455789999987543110256678--868999932986-4888999958
Q gi|254780619|r  545 LVAKGHNFPRMSLVGVVDGDLGLTNADLRSSERTFQLLSQVTGRAGRFGL--KSLGLIQAYQPT-HPVMQALVSG  616 (731)
Q Consensus       545 ~i~kg~~fp~v~lv~il~aD~~l~~pd~ra~E~~~qll~qv~gRagr~~~--~g~v~iQt~~p~-~~~~~~~~~~  616 (731)
                      --+=|++.|.=| |+..++- -+...+||=-  .---+.|.+|||||...  .|-||+--..+- -.+.+.+.++
T Consensus       481 TFsiGLNMPAkT-VvFT~~r-KfDG~~fRwi--ssGEYIQMSGRAGRRG~DdrGivIlmiDekm~~~~ak~m~kG  551 (1041)
T KOG0948         481 TFSIGLNMPAKT-VVFTAVR-KFDGKKFRWI--SSGEYIQMSGRAGRRGIDDRGIVILMIDEKMEPQVAKDMLKG  551 (1041)
T ss_pred             HHHHCCCCCCEE-EEEEECC-CCCCCCEEEE--CCCCEEEECCCCCCCCCCCCCEEEEEECCCCCHHHHHHHHCC
T ss_conf             231005886405-8874011-1478640453--366357741534556778775299995676797899998638


No 127
>PRK05642 DNA replication initiation factor; Validated
Probab=96.56  E-value=0.034  Score=35.88  Aligned_cols=48  Identities=17%  Similarity=0.219  Sum_probs=27.8

Q ss_pred             HHHHHHHHHHHC-CCCCEEEEECCCCHHHHHHHHHHH-HHHHHCCCCEEEE
Q ss_conf             999999987520-489619984475315799999999-9985146847997
Q gi|254780619|r  204 QDVVEQVVPLCT-KGFAVSLISGVTGSGKTEVYLEIV-AAVLHLGKQVLIL  252 (731)
Q Consensus       204 ~~a~~~i~~~~~-~~f~~~LL~GvTGSGKTEVYl~li-~~~L~~GkqvLiL  252 (731)
                      -.++..+..... ....+..|||-+|||||-. ++++ .++-+.|+.++++
T Consensus        30 ~~~~~~l~~~~~~~~~~~l~i~G~~G~GKTHL-L~A~~~~~~~~~~~~~yl   79 (234)
T PRK05642         30 LGYVERLCEADAGWTESLIYLWGKDGVGRSHL-LQAACLRFEQRGEPAVYL   79 (234)
T ss_pred             HHHHHHHHHCCCCCCCCEEEEECCCCCCHHHH-HHHHHHHHHHCCCCEEEE
T ss_conf             99999987606787788389988999988999-999999998079967997


No 128
>TIGR01074 rep ATP-dependent DNA helicase Rep; InterPro: IPR005752    RepA hexameric DNA helicase contain ATP-binding domains similar to those seen in monomeric helicases but which are arranged in a ring. There is compelling evidence to suggest that a single ssDNA molecule passes through the centre of the hexameric ring. Activity of the enzyme is based upon two separate but coupled activities, ssDNA translocation and duplex destabilisation, and is driven by energy derived from the continuous ATP-binding and hydrolysis events that take place in the active-site cleft. The resulting conformational changes that accompany these events underpin the coupling process and allow the helicase to translocate along the DNA, destabilizing the duplex and separating the two strands in an active process  ; GO: 0004003 ATP-dependent DNA helicase activity, 0006268 DNA unwinding during replication, 0005737 cytoplasm.
Probab=96.53  E-value=0.0041  Score=42.90  Aligned_cols=117  Identities=23%  Similarity=0.323  Sum_probs=76.2

Q ss_pred             CCCHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHHHHHHHHHHC-CCCEEEEECCCHHHHHHHHHHHCCCCCEEEE
Q ss_conf             688378999999987520489619984475315799999999998514-6847997152100134455543038976899
Q gi|254780619|r  198 ILDKNQQDVVEQVVPLCTKGFAVSLISGVTGSGKTEVYLEIVAAVLHL-GKQVLILLPEISLTSAILERFQKRFGVKPAE  276 (731)
Q Consensus       198 ~Lt~eQ~~a~~~i~~~~~~~f~~~LL~GvTGSGKTEVYl~li~~~L~~-GkqvLiLvPEI~Lt~Q~~~rl~~rF~~~v~v  276 (731)
                      .||+.|+.|+.-+..       |.|+=---|||||.|=.+=|+..+.+ |.++                     ..-+||
T Consensus         3 ~LNp~Q~~AV~Y~~G-------PlLVLAGAGSGKT~VI~~KIayLi~~cgY~a---------------------~~IaAv   54 (677)
T TIGR01074         3 KLNPQQQEAVEYVGG-------PLLVLAGAGSGKTRVITNKIAYLIQNCGYKA---------------------KNIAAV   54 (677)
T ss_pred             CCCHHHHHHHHHHCC-------CCEEECCCCCCCCHHHHHHHHHHHHHCCCCC---------------------CCEEEE
T ss_conf             887437999986158-------7146517777863578889999875158787---------------------616897


Q ss_pred             EECCCCCHHH-HHHHHHHHCCCCE-EEEECCHHHHHHHCCCEEEEEEECCCC-CCHHCCCCCCCHHHHHHHHHHHCC
Q ss_conf             6235572356-6789999719973-999400121100100013677405532-100002443224899999751103
Q gi|254780619|r  277 WHSSLSTSMR-EKIWRQVARGAIS-VIVGVRSALFLPFKKLGLIVIDEEHDI-SYKQEEGILYNARDMSIVRGKIES  350 (731)
Q Consensus       277 ~HS~ls~~eR-~~~w~~i~~G~~~-IVIGtRSAif~P~~nLglIIvDEEHd~-sykq~~~pry~aRdvA~~Ra~~~~  350 (731)
                      ---.=++.|- -++=..+..++++ ++|-|       |.+|||=|+=+||+. .||.--+. |+..|-..+...+..
T Consensus        55 TFTNKAA~EMkERVA~~L~~~~~~GL~isT-------FH~LGL~Ii~~E~~~lG~K~nFSl-FD~~D~~all~eL~~  123 (677)
T TIGR01074        55 TFTNKAAREMKERVAKTLGKGQAKGLTIST-------FHTLGLKIIRREHNALGLKSNFSL-FDETDQLALLKELLE  123 (677)
T ss_pred             ECCHHHHHHHHHHHHHHCCCCCCCCCEEEC-------CHHHHHHHHHHHHHHCCCCCCCCC-CCHHHHHHHHHHHHH
T ss_conf             352377799999998522654558544752-------057338999999986488999642-067889999998752


No 129
>COG0610 Type I site-specific restriction-modification system, R (restriction) subunit and related helicases [Defense mechanisms]
Probab=96.51  E-value=0.09  Score=32.65  Aligned_cols=331  Identities=17%  Similarity=0.195  Sum_probs=148.6

Q ss_pred             CEEEEECCCCHHHHHHHHHHHHHHHHC--CCCEEEEECCCHHHHHHHHHHHCCCCCEEEEEECCCCCHHHHHHHHHH-HC
Q ss_conf             619984475315799999999998514--684799715210013445554303897689962355723566789999-71
Q gi|254780619|r  219 AVSLISGVTGSGKTEVYLEIVAAVLHL--GKQVLILLPEISLTSAILERFQKRFGVKPAEWHSSLSTSMREKIWRQV-AR  295 (731)
Q Consensus       219 ~~~LL~GvTGSGKTEVYl~li~~~L~~--GkqvLiLvPEI~Lt~Q~~~rl~~rF~~~v~v~HS~ls~~eR~~~w~~i-~~  295 (731)
                      ...++|=.||||||--=+.++...++.  .-.|+++|=-..|-.|+.+-|++.-....- -+    .++-.+...+. ..
T Consensus       274 ~~G~IWHtqGSGKTltm~~~A~~l~~~~~~~~v~fvvDR~dLd~Q~~~~f~~~~~~~~~-~~----~~~s~~~Lk~~l~~  348 (962)
T COG0610         274 KGGYIWHTQGSGKTLTMFKLARLLLELPKNPKVLFVVDRKDLDDQTSDEFQSFGKVAFN-DP----KAESTSELKELLED  348 (962)
T ss_pred             CCEEEEECCCCCHHHHHHHHHHHHHHCCCCCEEEEEECHHHHHHHHHHHHHHHHHHHHC-CC----CCCCHHHHHHHHHC
T ss_conf             72389840698378999999999983659996999967288999999999998876320-44----44579999999865


Q ss_pred             CCCEEEEEC----CHHHH----HHHCCCEE-EEEEECCCCCCHHCCCCCCCHHHHHHHHHHHCCCCEECCCCCCCHHHHH
Q ss_conf             997399940----01211----00100013-6774055321000024432248999997511032100002454324677
Q gi|254780619|r  296 GAISVIVGV----RSALF----LPFKKLGL-IVIDEEHDISYKQEEGILYNARDMSIVRGKIESFPVVLVSATPSIESRV  366 (731)
Q Consensus       296 G~~~IVIGt----RSAif----~P~~nLgl-IIvDEEHd~sykq~~~pry~aRdvA~~Ra~~~~~~lilgSATPSles~~  366 (731)
                      +...|||-|    ..++.    ....+... +|+||-|-+-|    | .    .-+.++....++..+==+-||-.+.-.
T Consensus       349 ~~~~ii~TTIQKf~~~~~~~~~~~~~~~~ivvI~DEaHRSQ~----G-~----~~~~~~~~~~~a~~~gFTGTPi~~~d~  419 (962)
T COG0610         349 GKGKIIVTTIQKFNKAVKEDELELLKRKNVVVIIDEAHRSQY----G-E----LAKLLKKALKKAIFIGFTGTPIFKEDK  419 (962)
T ss_pred             CCCCEEEEEECCCCHHHHCCCCCCCCCCCEEEEEECCCCCCC----H-H----HHHHHHHHHCCCEEEEEECCCCCCCCC
T ss_conf             898489997102643333332000478767999864010356----0-7----899999870367089751785640224


Q ss_pred             HH---HHHHHH-HHCCCCCCC-CCCCCCC----EECCCCCCCCCCCCCCCHHH--------HHHHHHHHCCCCEEEEEEC
Q ss_conf             53---212344-412432236-7654332----11022223322245479899--------9999886226551799742
Q gi|254780619|r  367 NG---ISRRYH-SVHLSTRYR-NSALPHL----QVIDMRGQTIAQGKSLSPEM--------IDGIRHTLARNEQTLLFLN  429 (731)
Q Consensus       367 ~~---~~g~~~-~~~l~~R~~-~~~~P~i----~ivDm~~~~~~~~~~lS~~l--------~~~i~~~l~~g~qvll~ln  429 (731)
                      .+   .-|.|- -...+.-+. ++.+|-.    .-+++..+.......+.+..        ...+++...+. ..+...+
T Consensus       420 ~tt~~~fg~ylh~Y~i~~aI~Dg~vl~i~y~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~~~-~~~~~~~  498 (962)
T COG0610         420 DTTKDVFGDYLHTYTITDAIRDGAVLPVYYENRVELELIEESIKEEAEELDERIEEITEDILEKIKKKTKNL-EFLAMLA  498 (962)
T ss_pred             CCHHHHHCCEEEEEECCHHHCCCCEEEEEECCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHCH
T ss_conf             203555174479986522323576332584031234532001245666669998422799999999987555-6875144


Q ss_pred             CCCEEHHC-CCCCCCCCCCCCCCCCEEEEECCCCCCEECHHHCCCCCCCCCCCCCCCCEECCCCCCHHHHHHHHHHCCCC
Q ss_conf             22000000-23565434310146520121135783200002102446555666787411001354289988885204852
Q gi|254780619|r  430 RRGYAPLT-LCQVCGNRLKCLHCSCWLVEHRSKKKLYCHQCGHSAIYSQSCVVCGSSGKMIACGFGIERIAEEVCEYFPL  508 (731)
Q Consensus       430 RrGya~~~-~C~~Cg~~~~C~~C~~~l~~h~~~~~l~Ch~Cg~~~~~~~~Cp~Cg~~~~l~~~G~Gte~~~e~l~~~fp~  508 (731)
                      .|+.--+. +-..+-... =..=-+.+++ .+.. .   -|......-..++.|++. .... + -++.........++.
T Consensus       499 ~r~~~~a~~~~~~f~~~~-~~~~kam~V~-~sr~-~---~~~~~~~~~~~~~~~~~~-~~~~-~-~i~~~~~~~~~~~~~  569 (962)
T COG0610         499 VRLIRAAKDIYDHFKKEE-VFDLKAMVVA-SSRK-V---AVELYEAEIAARLDWHSK-ESLE-G-AIKDYNTEFETDFDK  569 (962)
T ss_pred             HHHHHHHHHHHHHHHHHC-CCCCEEEEEE-ECHH-H---HHHHHHHHHHHHHHHHHH-HHHH-H-HHHHHHHHCCCCCHH
T ss_conf             889999999999998611-5583599998-4168-7---877678887751556665-3005-2-899986132232023


Q ss_pred             CHHHHCCCCCCCCHHHHHHHHHH--HCCCCCCEEEEEHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             00010232113586789999986--2125765798704430231134520123300034431024557899999875431
Q gi|254780619|r  509 ARISILSSDLEGGGGRLQLQLSA--IAKGEIDIIIGTQLVAKGHNFPRMSLVGVVDGDLGLTNADLRSSERTFQLLSQVT  586 (731)
Q Consensus       509 ~~v~~~d~d~~~~~~~~~~~~~~--~~~~~~~ilvgTq~i~kg~~fp~v~lv~il~aD~~l~~pd~ra~E~~~qll~qv~  586 (731)
                      ..-      ....+...+.....  .....++|||=+-|..-|+|-|.+..   +..|.-|..          ..|+|+.
T Consensus       570 ~~~------~~~~~~~~~~~~~r~~~~~d~~kllIV~dMlLTGFDaP~L~T---mYvDK~Lk~----------H~L~QAi  630 (962)
T COG0610         570 KQS------HAKLKDEKKDLIKRFKLKDDPLDLLIVVDMLLTGFDAPCLNT---LYVDKPLKY----------HNLIQAI  630 (962)
T ss_pred             HHH------HHHHHHHHHHHHHHHCCCCCCCCEEEEECCCCCCCCCCCCCE---EEECCCCCC----------CHHHHHH
T ss_conf             445------577777765332321275778768999776204677542012---674455443----------3189999


Q ss_pred             HCCCCC
Q ss_conf             102566
Q gi|254780619|r  587 GRAGRF  592 (731)
Q Consensus       587 gRagr~  592 (731)
                      -|+-|-
T Consensus       631 sRtNR~  636 (962)
T COG0610         631 SRTNRV  636 (962)
T ss_pred             HHHCCC
T ss_conf             886458


No 130
>PRK08938 DNA topoisomerase I; Validated
Probab=96.48  E-value=0.0044  Score=42.66  Aligned_cols=60  Identities=27%  Similarity=0.606  Sum_probs=33.2

Q ss_pred             EEEECCCCEEHHCCCC---CCCCC--------CCCCCCC-CEEEEECCCC---CCEEC---HHHCC---CCCCCCCCCCC
Q ss_conf             9974222000000235---65434--------3101465-2012113578---32000---02102---44655566678
Q gi|254780619|r  425 LLFLNRRGYAPLTLCQ---VCGNR--------LKCLHCS-CWLVEHRSKK---KLYCH---QCGHS---AIYSQSCVVCG  483 (731)
Q Consensus       425 ll~lnRrGya~~~~C~---~Cg~~--------~~C~~C~-~~l~~h~~~~---~l~Ch---~Cg~~---~~~~~~Cp~Cg  483 (731)
                      ++-..|.|  .|+.|.   +|.++        ..||.|+ +.+...++.+   .+-|.   -|.|.   .+....||.||
T Consensus       588 ~~k~gr~G--~F~~Cs~yP~Ck~t~~~~~~~~~~CP~C~~g~l~~r~sk~g~~f~gCs~yp~C~~~~~~~p~~~~Cp~Cg  665 (692)
T PRK08938        588 VIKMGRYG--KFYACSNFPDCRNTKAIVKEIGVTCPKCHKGQVIERKSKKNRIFYGCDRYPECDFVSWDKPIGRDCPKCG  665 (692)
T ss_pred             EEEECCCC--CEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCEEEECCCCCCCCEECCCCCCCCCCCCCC
T ss_conf             68815788--4334789988888677665568829599997457551478987774898998983167887488499999


Q ss_pred             CCC
Q ss_conf             741
Q gi|254780619|r  484 SSG  486 (731)
Q Consensus       484 ~~~  486 (731)
                      +..
T Consensus       666 ~~~  668 (692)
T PRK08938        666 HYL  668 (692)
T ss_pred             CCC
T ss_conf             604


No 131
>PRK10590 ATP-dependent RNA helicase RhlE; Provisional
Probab=96.48  E-value=0.094  Score=32.51  Aligned_cols=123  Identities=21%  Similarity=0.226  Sum_probs=81.5

Q ss_pred             EECCCCHHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHCCCCCEEEEEECCCCCHHHHHHHHHHHCCCCEEEE
Q ss_conf             84475315799999999998514684799715210013445554303897689962355723566789999719973999
Q gi|254780619|r  223 ISGVTGSGKTEVYLEIVAAVLHLGKQVLILLPEISLTSAILERFQKRFGVKPAEWHSSLSTSMREKIWRQVARGAISVIV  302 (731)
Q Consensus       223 L~GvTGSGKTEVYl~li~~~L~~GkqvLiLvPEI~Lt~Q~~~rl~~rF~~~v~v~HS~ls~~eR~~~w~~i~~G~~~IVI  302 (731)
                      ++=+...-|.++..+++..  ...+++||-+....-+..+...|.+ .|..++.+|++++..+|..+...-++|+..|+|
T Consensus       224 ~~~v~~~~k~~~L~~ll~~--~~~~~~iIF~~tk~~a~~l~~~L~~-~g~~~~~lHg~~sq~~R~~~l~~F~~g~~~vLV  300 (457)
T PRK10590        224 VHFVDKKRKRELLSQMIGK--GNWQQVLVFTRTKHGANHLAEQLNK-DGIRSAAIHGNKSQGARTRALADFKSGDIRVLV  300 (457)
T ss_pred             EEEECHHHHHHHHHHHHHH--CCCCCEEEEECHHHHHHHHHHHHHH-CCCCCEEEECCCCHHHHHHHHHHHHCCCCCEEE
T ss_conf             9995667899999999861--5866335884119999999999855-699823232478999999999999869982999


Q ss_pred             ECCHHH-HHHHCCCEEEEE-EECCC-CCCHHCCCCCCCHHHHHHHHHHHCCCCEECC
Q ss_conf             400121-100100013677-40553-2100002443224899999751103210000
Q gi|254780619|r  303 GVRSAL-FLPFKKLGLIVI-DEEHD-ISYKQEEGILYNARDMSIVRGKIESFPVVLV  356 (731)
Q Consensus       303 GtRSAi-f~P~~nLglIIv-DEEHd-~sykq~~~pry~aRdvA~~Ra~~~~~~lilg  356 (731)
                      .|=-|. =+.++++.+||- |=-.+ .+|-.--     .|   -=||-..|..+.|.
T Consensus       301 aTDvaaRGiDi~~V~~VInyD~P~~~e~YvHRi-----GR---TGRaG~~G~ait~v  349 (457)
T PRK10590        301 ATDIAARGLDIEELPHVVNYELPNVPEDYVHRI-----GR---TGRAAATGEALSLV  349 (457)
T ss_pred             ECCCCCCCCCCCCCCEEEEECCCCCHHHEECCC-----CC---CCCCCCCEEEEEEE
T ss_conf             577011556635688799938999744500226-----70---60589953699986


No 132
>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=96.45  E-value=0.0047  Score=42.43  Aligned_cols=67  Identities=25%  Similarity=0.320  Sum_probs=50.5

Q ss_pred             CCHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHHHHHHHHHHC-C---CCEEEEECCCHHHHHHHHHHHCCCCC
Q ss_conf             88378999999987520489619984475315799999999998514-6---84799715210013445554303897
Q gi|254780619|r  199 LDKNQQDVVEQVVPLCTKGFAVSLISGVTGSGKTEVYLEIVAAVLHL-G---KQVLILLPEISLTSAILERFQKRFGV  272 (731)
Q Consensus       199 Lt~eQ~~a~~~i~~~~~~~f~~~LL~GvTGSGKTEVYl~li~~~L~~-G---kqvLiLvPEI~Lt~Q~~~rl~~rF~~  272 (731)
                      ||++|+.|+...       -.+.|+-+.-|||||.+-.+-+...+.. |   .++|++.-.=.-+..|-.|+.+.++.
T Consensus         1 Ln~~Q~~av~~~-------~~~llV~AgAGSGKT~~L~~Ri~~li~~~~~~p~~IL~lTFT~kAA~Em~~Ri~~~l~~   71 (494)
T pfam00580         1 LNPEQRKAVTHL-------GGPLLVLAGAGTGKTRVLTERIAYLILEGGIDPEEILAVTFTNKAAREMKERILKLLGK   71 (494)
T ss_pred             CCHHHHHHHCCC-------CCCEEEEEECCHHHHHHHHHHHHHHHHHCCCCHHHEEEEECHHHHHHHHHHHHHHHCCC
T ss_conf             998899998099-------99979997187068999999999999818999747876702899999999999987383


No 133
>COG1201 Lhr Lhr-like helicases [General function prediction only]
Probab=96.44  E-value=0.018  Score=38.03  Aligned_cols=71  Identities=21%  Similarity=0.213  Sum_probs=65.7

Q ss_pred             HHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHCCCCCEEEEEECCCCCHHHHHHHHHHHCCCCEEEEECCH
Q ss_conf             99999985146847997152100134455543038976899623557235667899997199739994001
Q gi|254780619|r  236 LEIVAAVLHLGKQVLILLPEISLTSAILERFQKRFGVKPAEWHSSLSTSMREKIWRQVARGAISVIVGVRS  306 (731)
Q Consensus       236 l~li~~~L~~GkqvLiLvPEI~Lt~Q~~~rl~~rF~~~v~v~HS~ls~~eR~~~w~~i~~G~~~IVIGtRS  306 (731)
                      +..+.+.+++.+++||-+.....|.-+..+++..++..+.+-||++|..+|.++=.+.++|+.+.||-|-|
T Consensus       243 ~~~i~~~v~~~~ttLIF~NTR~~aE~l~~~L~~~~~~~i~~HHgSlSre~R~~vE~~lk~G~lravV~TSS  313 (814)
T COG1201         243 YERIAELVKKHRTTLIFTNTRSGAERLAFRLKKLGPDIIEVHHGSLSRELRLEVEERLKEGELKAVVATSS  313 (814)
T ss_pred             HHHHHHHHHHCCCEEEEEECHHHHHHHHHHHHHHCCCCEEEECCCCCHHHHHHHHHHHHCCCCEEEEECCC
T ss_conf             99999999616858999727278999999998726875565316665778999999986688629998064


No 134
>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=96.42  E-value=0.038  Score=35.55  Aligned_cols=45  Identities=31%  Similarity=0.443  Sum_probs=36.5

Q ss_pred             EEEECCCCHHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHH
Q ss_conf             9984475315799999999998514684799715210013445554
Q gi|254780619|r  221 SLISGVTGSGKTEVYLEIVAAVLHLGKQVLILLPEISLTSAILERF  266 (731)
Q Consensus       221 ~LL~GvTGSGKTEVYl~li~~~L~~GkqvLiLvPEI~Lt~Q~~~rl  266 (731)
                      .|+.|.+|+|||-.-++++.++..+|..|++..-|... .|...|+
T Consensus         2 ~li~g~~g~GKttl~~~~~~~~~~~~~~~~~~~~ee~~-~q~~~~~   46 (165)
T cd01120           2 ILVFGPTGSGKTTLALQLALNIATKGGKVVYVDIEEEI-EELTERL   46 (165)
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHHCCCEEEEEECCCCH-HHHHHHH
T ss_conf             89998999989999999999987639979999866644-8999999


No 135
>PRK08413 consensus
Probab=96.41  E-value=0.0043  Score=42.73  Aligned_cols=49  Identities=22%  Similarity=0.396  Sum_probs=28.3

Q ss_pred             CCCCCCCCEEEEECC--CCCCEEC---HHHCCCCCC--------CCCCCCCCCCEECCCCCC
Q ss_conf             310146520121135--7832000---021024465--------556667874110013542
Q gi|254780619|r  446 LKCLHCSCWLVEHRS--KKKLYCH---QCGHSAIYS--------QSCVVCGSSGKMIACGFG  494 (731)
Q Consensus       446 ~~C~~C~~~l~~h~~--~~~l~Ch---~Cg~~~~~~--------~~Cp~Cg~~~~l~~~G~G  494 (731)
                      ..||.|+..|...+.  +..+.|.   -|.++.+++        ..||.||+.+.++....|
T Consensus       570 ~~Cp~Cg~~l~~~~~r~G~F~~Cs~yP~Ck~t~~~~~~~~~~~~~~c~~cg~~m~~k~gr~g  631 (733)
T PRK08413        570 ESCPKCGGELVKRKGRYGEFIACSNFPKCKYSKNTESENKEASEEVCEKCGGPMVQKFGRNG  631 (733)
T ss_pred             CCCCCCCCCCEEECCCCCEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHEEECCCC
T ss_conf             98743585411331677406842899875554567665432345668767841321205787


No 136
>PRK07219 DNA topoisomerase I; Validated
Probab=96.39  E-value=0.0031  Score=43.84  Aligned_cols=39  Identities=28%  Similarity=0.539  Sum_probs=17.8

Q ss_pred             CCCCCCCEEEEECCC--C-CCEEC---HHHCCCCCC---------CCCCCCCCC
Q ss_conf             101465201211357--8-32000---021024465---------556667874
Q gi|254780619|r  447 KCLHCSCWLVEHRSK--K-KLYCH---QCGHSAIYS---------QSCVVCGSS  485 (731)
Q Consensus       447 ~C~~C~~~l~~h~~~--~-~l~Ch---~Cg~~~~~~---------~~Cp~Cg~~  485 (731)
                      .||.|++.|+..++.  . .+-|.   -|.++.+.|         ..||.||+.
T Consensus       672 ~CP~cgg~lv~r~sk~gk~F~gCs~yP~C~~t~~lp~~~~~~~~~e~Cp~Cg~~  725 (769)
T PRK07219        672 ECPADGGRLVLRQSRYGKRFLGCSNYPKCTVTYPLPQKGIIKKTGEKCPYCGAP  725 (769)
T ss_pred             CCCCCCCEEEEECCCCCCEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCE
T ss_conf             288999779986378998565179999997525075447645058847778983


No 137
>PRK08082 consensus
Probab=96.39  E-value=0.1  Score=32.16  Aligned_cols=132  Identities=17%  Similarity=0.214  Sum_probs=79.7

Q ss_pred             CEEEEECCCCHHHHHHHHHHHHH-HHHCCCCEEEEECCCHHHHHHHHHHHCCC-CCEE-EEEECCCCCHHHHHHHHHHH-
Q ss_conf             61998447531579999999999-85146847997152100134455543038-9768-99623557235667899997-
Q gi|254780619|r  219 AVSLISGVTGSGKTEVYLEIVAA-VLHLGKQVLILLPEISLTSAILERFQKRF-GVKP-AEWHSSLSTSMREKIWRQVA-  294 (731)
Q Consensus       219 ~~~LL~GvTGSGKTEVYl~li~~-~L~~GkqvLiLvPEI~Lt~Q~~~rl~~rF-~~~v-~v~HS~ls~~eR~~~w~~i~-  294 (731)
                      ..++|=|-+|.|||-..+.++.. ++.+|+.|++.--|-+ ..|+..|+-... +... .+-++.+++.+....-..+. 
T Consensus       204 ~LiviaaRPsmGKTa~alnia~~~a~~~~~~V~~fSlEM~-~~~l~~R~la~~s~i~~~~i~~g~l~~~e~~~i~~a~~~  282 (453)
T PRK08082        204 DLIIVAARPSVGKTAFALNIAQNVATKTDENVAIFSLEMG-ADQLVMRMLCAEGNIDAQRLRTGSLTSDDWGKLTMAMGS  282 (453)
T ss_pred             CEEEEEECCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCC-HHHHHHHHHHCCCCCCHHHHHCCCCCHHHHHHHHHHHHH
T ss_conf             5799986788757899999999999855994899731389-899999999715588866775189999999999999998


Q ss_pred             CCCCEEEEECCHHH-----------HHHHCCCEEEEEEECCCCCCHHCCC-------CCCC-----HHHHHHHHHHHCCC
Q ss_conf             19973999400121-----------1001000136774055321000024-------4322-----48999997511032
Q gi|254780619|r  295 RGAISVIVGVRSAL-----------FLPFKKLGLIVIDEEHDISYKQEEG-------ILYN-----ARDMSIVRGKIESF  351 (731)
Q Consensus       295 ~G~~~IVIGtRSAi-----------f~P~~nLglIIvDEEHd~sykq~~~-------pry~-----aRdvA~~Ra~~~~~  351 (731)
                      -.+..+.|--.+++           +..-.++++||||      |=|--.       .|+.     .|.+ ...|+..++
T Consensus       283 l~~~~l~idd~~~~~i~~i~~~~r~~~~~~~~~livID------YlqLi~~~~~~~~~r~~ev~~isr~L-K~lAkel~i  355 (453)
T PRK08082        283 LSNAGIYIDDTPGIRVNEIRAKCRRLKQEQGLGMILID------YLQLIQGSGRSGENRQQEVSEISRTL-KALARELEV  355 (453)
T ss_pred             HCCCCEEEECCCCCCHHHHHHHHHHHHHHCCCCEEEEE------CHHHCCCCCCCCCCHHHHHHHHHHHH-HHHHHHHCC
T ss_conf             50697389789999899999999999986699889995------07733778988878999999999999-999999699


Q ss_pred             CEECCCC
Q ss_conf             1000024
Q gi|254780619|r  352 PVVLVSA  358 (731)
Q Consensus       352 ~lilgSA  358 (731)
                      |||+.|-
T Consensus       356 pvi~lsQ  362 (453)
T PRK08082        356 PVIALSQ  362 (453)
T ss_pred             CEEEECC
T ss_conf             7999644


No 138
>CHL00122 secA preprotein translocase subunit SecA; Validated
Probab=96.38  E-value=0.1  Score=32.24  Aligned_cols=92  Identities=22%  Similarity=0.222  Sum_probs=66.2

Q ss_pred             CCCHHHHHHHHHHHHHHHHCCCCEEEEECCCHHHH---HHHHHHHCCCCCEEEEEECCCCCHHHHHHHHHHHCCCCEEEE
Q ss_conf             75315799999999998514684799715210013---445554303897689962355723566789999719973999
Q gi|254780619|r  226 VTGSGKTEVYLEIVAAVLHLGKQVLILLPEISLTS---AILERFQKRFGVKPAEWHSSLSTSMREKIWRQVARGAISVIV  302 (731)
Q Consensus       226 vTGSGKTEVYl~li~~~L~~GkqvLiLvPEI~Lt~---Q~~~rl~~rF~~~v~v~HS~ls~~eR~~~w~~i~~G~~~IVI  302 (731)
                      -||-|||.+..-.+--.--.|+.|-|+-..=-|+.   ++...+...+|-.|.+..+++++.+|...|.      ++|+=
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             ECCHHH-H-------------HHHCCCEEEEEEEC
Q ss_conf             400121-1-------------00100013677405
Q gi|254780619|r  303 GVRSAL-F-------------LPFKKLGLIVIDEE  323 (731)
Q Consensus       303 GtRSAi-f-------------~P~~nLglIIvDEE  323 (731)
                      ||-+.+ |             .=...+...||||-
T Consensus       171 ~Tn~e~gFDyLRDnm~~~~~~~vqr~~~~aIvDEv  205 (891)
T CHL00122        171 VTNSELGFDYLRDNMALSLSEVVQRPFNYCIIDEV  205 (891)
T ss_pred             ECCCCEECCCCCCCCCCCHHHHHCCCCCEEEEECH
T ss_conf             78876222566633236878840889973788640


No 139
>PRK10919 ATP-dependent DNA helicase Rep; Provisional
Probab=96.30  E-value=0.0072  Score=41.05  Aligned_cols=25  Identities=28%  Similarity=0.509  Sum_probs=19.5

Q ss_pred             CEEEEEHHHCCCCCCCCCCHHHHHH
Q ss_conf             5798704430231134520123300
Q gi|254780619|r  538 DIIIGTQLVAKGHNFPRMSLVGVVD  562 (731)
Q Consensus       538 ~ilvgTq~i~kg~~fp~v~lv~il~  562 (731)
                      .|-+-|===|||+.||.|=++|+-+
T Consensus       551 ~V~LmTiH~SKGLEf~~Vfl~gl~e  575 (672)
T PRK10919        551 QVQLMTLHASKGLEFPYVYMVGMEE  575 (672)
T ss_pred             EEEEEEHHHHHCCCCCEEEEECCCC
T ss_conf             0899648862310368799967838


No 140
>PRK11634 ATP-dependent RNA helicase DeaD; Provisional
Probab=96.29  E-value=0.12  Score=31.75  Aligned_cols=125  Identities=20%  Similarity=0.287  Sum_probs=84.3

Q ss_pred             ECCCCHHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHCCCCCEEEEEECCCCCHHHHHHHHHHHCCCCEEEEE
Q ss_conf             44753157999999999985146847997152100134455543038976899623557235667899997199739994
Q gi|254780619|r  224 SGVTGSGKTEVYLEIVAAVLHLGKQVLILLPEISLTSAILERFQKRFGVKPAEWHSSLSTSMREKIWRQVARGAISVIVG  303 (731)
Q Consensus       224 ~GvTGSGKTEVYl~li~~~L~~GkqvLiLvPEI~Lt~Q~~~rl~~rF~~~v~v~HS~ls~~eR~~~w~~i~~G~~~IVIG  303 (731)
                      +-|.+.-|.+..++++..  ....++||-+....-+..+...|.. .|..++.+|+.|+..+|..+..+.++|+.+|+|.
T Consensus       225 ~~v~~~~K~~aL~~~L~~--~~~~~~IIF~~Tk~~~~~l~~~L~~-~g~~~~~LHgdm~q~~R~~~l~~Fr~g~~~ILVa  301 (629)
T PRK11634        225 WTVWGMRKNEALVRFLEA--EDFDAAIIFVRTKNATLEVAEALER-NGYNSAALNGDMNQALREQTLERLKDGRLDILIA  301 (629)
T ss_pred             EEECCHHHHHHHHHHHHH--CCCCEEEEEEECHHHHHHHHHHHHH-CCCCEEEEECCCCHHHHHHHHHHHHCCCCCEEEE
T ss_conf             996524579999999861--5888489998227889999999997-6996576568999999999999997599988987


Q ss_pred             CCHHH-HHHHCCCEEEEE-EECCC-CCCHHCCCCCCCHHHHHHHHHHHCCCCEECCCCCCC
Q ss_conf             00121-100100013677-40553-210000244322489999975110321000024543
Q gi|254780619|r  304 VRSAL-FLPFKKLGLIVI-DEEHD-ISYKQEEGILYNARDMSIVRGKIESFPVVLVSATPS  361 (731)
Q Consensus       304 tRSAi-f~P~~nLglIIv-DEEHd-~sykq~~~pry~aRdvA~~Ra~~~~~~lilgSATPS  361 (731)
                      |=-|. =+-++++.+||- |=-.| .+|-.--+     |   -=||-..|..+.|.  ||.
T Consensus       302 TDvaARGLDi~~V~~VINyDlP~d~e~YVHRiG-----R---TGRaGr~G~Aitfv--~~~  352 (629)
T PRK11634        302 TDVAARGLDVERISLVVNYDIPMDSESYVHRIG-----R---TGRAGRAGRALLFV--ENR  352 (629)
T ss_pred             CCCCCCCCCCCCCCEEEEECCCCCHHHCCCCCC-----C---CCCCCCCEEEEEEE--CHH
T ss_conf             862105577256888999689897434010258-----3---31689964699988--889


No 141
>PRK11192 ATP-dependent RNA helicase SrmB; Provisional
Probab=96.25  E-value=0.049  Score=34.66  Aligned_cols=119  Identities=13%  Similarity=0.208  Sum_probs=77.7

Q ss_pred             CHHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHCCCCCEEEEEECCCCCHHHHHHHHHHHCCCCEEEEECCHH
Q ss_conf             31579999999999851468479971521001344555430389768996235572356678999971997399940012
Q gi|254780619|r  228 GSGKTEVYLEIVAAVLHLGKQVLILLPEISLTSAILERFQKRFGVKPAEWHSSLSTSMREKIWRQVARGAISVIVGVRSA  307 (731)
Q Consensus       228 GSGKTEVYl~li~~~L~~GkqvLiLvPEI~Lt~Q~~~rl~~rF~~~v~v~HS~ls~~eR~~~w~~i~~G~~~IVIGtRSA  307 (731)
                      -..|.+.-.+++..  ....++||-+....-+..+...|.+. |..++.+|++++..+|.++..+-++|+.+|+|.|--|
T Consensus       231 ~~~k~~~L~~ll~~--~~~~k~iIF~~t~~~~~~l~~~L~~~-g~~~~~lhg~l~q~~R~~~l~~F~~g~~~vLVaTDva  307 (417)
T PRK11192        231 LEHKTALLCHLLKQ--EEVTRSIVFVRTRERVHELAGWLRKA-GINCCYLEGEMVQKKRNEAIKRLTDGRVNVLVATDVA  307 (417)
T ss_pred             HHHHHHHHHHHHHC--CCCCCCEEEECCHHHHHHHHHHHHCC-CCCEEEECCCCCHHHHHHHHHHHHCCCCCEEEECCHH
T ss_conf             89999999999853--47665215311246676898865314-8835754001799999999999976999899981243


Q ss_pred             H-HHHHCCCEEEEE-EECCC-CCCHHCCCCCCCHHHHHHHHHHHCCCCEECCC
Q ss_conf             1-100100013677-40553-21000024432248999997511032100002
Q gi|254780619|r  308 L-FLPFKKLGLIVI-DEEHD-ISYKQEEGILYNARDMSIVRGKIESFPVVLVS  357 (731)
Q Consensus       308 i-f~P~~nLglIIv-DEEHd-~sykq~~~pry~aRdvA~~Ra~~~~~~lilgS  357 (731)
                      . =+.++++..||- |=-.+ .+|-+.-|     |   .=|+-..|..+-|.+
T Consensus       308 aRGiDi~~V~~VInyd~P~~~~~YvHRiG-----R---TGR~G~~G~ait~v~  352 (417)
T PRK11192        308 ARGIDIDDISHVINFDMPRSADTYLHRIG-----R---TGRAGKKGTAISLVE  352 (417)
T ss_pred             HCCCCCCCCCEEEEECCCCCHHHHHHHCC-----H---HHCCCCCEEEEEEEC
T ss_conf             46777046988999799998889233067-----7---234899548999874


No 142
>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=96.24  E-value=0.014  Score=38.83  Aligned_cols=118  Identities=24%  Similarity=0.299  Sum_probs=70.7

Q ss_pred             EEEEECCCCHHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHCCCCC----------EEEEEE-CCCCCHHHHH
Q ss_conf             19984475315799999999998514684799715210013445554303897----------689962-3557235667
Q gi|254780619|r  220 VSLISGVTGSGKTEVYLEIVAAVLHLGKQVLILLPEISLTSAILERFQKRFGV----------KPAEWH-SSLSTSMREK  288 (731)
Q Consensus       220 ~~LL~GvTGSGKTEVYl~li~~~L~~GkqvLiLvPEI~Lt~Q~~~rl~~rF~~----------~v~v~H-S~ls~~eR~~  288 (731)
                      ..=+||-.|||||-|-|.++-.+..+|+.|++.=-|=+|.+   +||++-+++          ++.|+. +.+.+.++  
T Consensus        14 iTQiYGp~G~GKTn~c~~~a~~a~~~Gk~v~YiDTEGGLS~---ER~~q~~~~~~~D~e~~~~~~iv~~~~~f~eQ~~--   88 (223)
T TIGR02237        14 ITQIYGPPGSGKTNICLILAVNAARQGKKVVYIDTEGGLSP---ERFKQIAEDRALDPERVLSNVIVFEVFDFDEQEV--   88 (223)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHCCCCEEEEECCCCCHH---HHHHHHHHCCCCCHHHHHCCEEEECCCCHHHHHH--
T ss_conf             88987589986789999999999861895899962898328---9999986305889888841535523535678999--


Q ss_pred             HHHHHHCCCCEEEEECCHHHHHHH--CCCEEEEEE--------ECCCCCCHHCCCCCCCHHH--HHHHHHHHCCCCEEC
Q ss_conf             899997199739994001211001--000136774--------0553210000244322489--999975110321000
Q gi|254780619|r  289 IWRQVARGAISVIVGVRSALFLPF--KKLGLIVID--------EEHDISYKQEEGILYNARD--MSIVRGKIESFPVVL  355 (731)
Q Consensus       289 ~w~~i~~G~~~IVIGtRSAif~P~--~nLglIIvD--------EEHd~sykq~~~pry~aRd--vA~~Ra~~~~~~lil  355 (731)
                         .|.          +.+-|+--  ...+|||||        |+.|++-|+.+--+==++.  +....|+..++++|.
T Consensus        89 ---ai~----------~~~~~~~~~G~~~~LvVvDs~t~~YRle~~~d~nk~~~~~~~l~~Ql~~Ll~lArk~~~AVvi  154 (223)
T TIGR02237        89 ---AIQ----------KTSKLIDRDGDKADLVVVDSFTALYRLERSDDRNKQISLNRELARQLTLLLSLARKKDLAVVI  154 (223)
T ss_pred             ---HHH----------HHHHHHHCCCCEEEEEEEECCHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCEEE
T ss_conf             ---999----------999998606883314888153345420257860256799999999999999998764997899


No 143
>PRK12326 preprotein translocase subunit SecA; Reviewed
Probab=96.23  E-value=0.025  Score=36.95  Aligned_cols=92  Identities=20%  Similarity=0.207  Sum_probs=66.7

Q ss_pred             CCCHHHHHHHHHHHHHHHHCCCCEEEEECCCHHHH---HHHHHHHCCCCCEEEEEECCCCCHHHHHHHHHHHCCCCEEEE
Q ss_conf             75315799999999998514684799715210013---445554303897689962355723566789999719973999
Q gi|254780619|r  226 VTGSGKTEVYLEIVAAVLHLGKQVLILLPEISLTS---AILERFQKRFGVKPAEWHSSLSTSMREKIWRQVARGAISVIV  302 (731)
Q Consensus       226 vTGSGKTEVYl~li~~~L~~GkqvLiLvPEI~Lt~---Q~~~rl~~rF~~~v~v~HS~ls~~eR~~~w~~i~~G~~~IVI  302 (731)
                      -||-|||.+..-.+--.--.|+.|-|+-..=-|+.   ++...+...||-.|++..+++++.+|...|.      ++|+-
T Consensus       110 ~TGEGKTL~atlpaylnAL~GkgVHvVTvNDYLA~RDaewm~piy~fLGLtvg~i~~~~~~~err~aY~------~DItY  183 (775)
T PRK12326        110 ATGEGKTLAGAIAAAGYALGGRRVHVITVNDYLARRDAEWMGPLLEAFGLTVGWITEESTAEERRAAYA------CDVTY  183 (775)
T ss_pred             ECCCCHHHHHHHHHHHHHHCCCCCEEEECCHHHHHHHHHHHHHHHHHHCCEECCCCCCCCHHHHHHHCC------CCCCC
T ss_conf             068858999999999996369980898225687887699999999982977653789999799998446------87731


Q ss_pred             ECCHHH-H-------------HHHCCCEEEEEEEC
Q ss_conf             400121-1-------------00100013677405
Q gi|254780619|r  303 GVRSAL-F-------------LPFKKLGLIVIDEE  323 (731)
Q Consensus       303 GtRSAi-f-------------~P~~nLglIIvDEE  323 (731)
                      ||-+.+ |             .=.+.+...||||-
T Consensus       184 ~Tn~E~GFDYLRDnm~~~~~~~vqr~~~faIVDEv  218 (775)
T PRK12326        184 ASVNEIGFDVLRDQLVTDVADLVSPNPDVAIIDEA  218 (775)
T ss_pred             CCCCCCCCCCCHHHHCCCHHHHCCCCCCEEEEECC
T ss_conf             15555324455132126988843677875998642


No 144
>PRK05298 excinuclease ABC subunit B; Provisional
Probab=96.23  E-value=0.059  Score=34.05  Aligned_cols=277  Identities=19%  Similarity=0.160  Sum_probs=128.9

Q ss_pred             ECCCCHHHHHHHHHHHHHHHH--------CCCCEEEEECCCHHHHHHHHHHHCCCCCEEEEE--ECCCCCHHHHHHHHHH
Q ss_conf             447531579999999999851--------468479971521001344555430389768996--2355723566789999
Q gi|254780619|r  224 SGVTGSGKTEVYLEIVAAVLH--------LGKQVLILLPEISLTSAILERFQKRFGVKPAEW--HSSLSTSMREKIWRQV  293 (731)
Q Consensus       224 ~GvTGSGKTEVYl~li~~~L~--------~GkqvLiLvPEI~Lt~Q~~~rl~~rF~~~v~v~--HS~ls~~eR~~~w~~i  293 (731)
                      |=||...+.+..+..|++-|+        +||=          .  =..|+++|-...+-.+  -+-++.-|   +|.+-
T Consensus       249 hyVt~~e~l~~Ai~~I~~EL~eRl~~f~~~gKl----------l--EAqRL~qRT~yDlEMl~E~GyCsGIE---NYSRh  313 (657)
T PRK05298        249 HYVTPRERLERAIESIKEELEERLKELEKEGKL----------L--EAQRLEQRTRYDLEMLRELGYCSGIE---NYSRH  313 (657)
T ss_pred             CCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCH----------H--HHHHHHHHHHHHHHHHHHCCCCCCHH---HHHHH
T ss_conf             768997999999999999999999999976777----------9--88899999887999999828775601---21565


Q ss_pred             HCCCCEEEEECCH-HHHHHHCCCEEEEEEECCCCCCHHCCCCCC---CHHHHHHH-H-----HHH------------CCC
Q ss_conf             7199739994001-211001000136774055321000024432---24899999-7-----511------------032
Q gi|254780619|r  294 ARGAISVIVGVRS-ALFLPFKKLGLIVIDEEHDISYKQEEGILY---NARDMSIV-R-----GKI------------ESF  351 (731)
Q Consensus       294 ~~G~~~IVIGtRS-Aif~P~~nLglIIvDEEHd~sykq~~~pry---~aRdvA~~-R-----a~~------------~~~  351 (731)
                      .+|+.   -|.|- .+|==|++--|+||||.|=. --|-.+. |   .+|--.+. -     +.+            .--
T Consensus       314 l~gR~---pGe~P~tLlDYfp~DfLl~iDESHvt-vPQi~gM-y~GDrsRK~~LVe~GFRLPSAlDNRPL~feEFe~~~~  388 (657)
T PRK05298        314 LSGRA---PGEPPPTLLDYFPDDFLLFIDESHVT-VPQIGGM-YNGDRSRKETLVEYGFRLPSALDNRPLKFEEFEAKVP  388 (657)
T ss_pred             CCCCC---CCCCCCHHHHHCCCCEEEEECCCCCC-CHHHHHH-HCCCHHHHHHHHHHCCCCCCCCCCCCCCHHHHHHHCC
T ss_conf             06999---88789448875775659998321124-0878878-6231577888987057787233489978899997448


Q ss_pred             CEECCCCCCCHHHHHHHHHHHHHHHCCCCCCCCCCCCCCEECCCCCCCCCCCCCCCHHHHHHHHHHHCCCCEEEEEECCC
Q ss_conf             10000245432467753212344412432236765433211022223322245479899999988622655179974222
Q gi|254780619|r  352 PVVLVSATPSIESRVNGISRRYHSVHLSTRYRNSALPHLQVIDMRGQTIAQGKSLSPEMIDGIRHTLARNEQTLLFLNRR  431 (731)
Q Consensus       352 ~lilgSATPSles~~~~~~g~~~~~~l~~R~~~~~~P~i~ivDm~~~~~~~~~~lS~~l~~~i~~~l~~g~qvll~lnRr  431 (731)
                      .+|+.||||.-  |-.-.+|.  .++.--|+.|--=|.|+|-     + ..|.  =+.|+.+|+++.++|+.||+..=.+
T Consensus       389 q~iyVSATPg~--yEl~~s~~--vvEQiIRPTGLlDP~ievr-----p-~~~Q--iddl~~ei~~~~~~~er~LvttlTk  456 (657)
T PRK05298        389 QTIYVSATPGD--YELEKSGQ--VVEQIIRPTGLLDPEIEVR-----P-TKGQ--VDDLLSEIRKRVAKGERVLVTTLTK  456 (657)
T ss_pred             CEEEEECCCCH--HHHHHCCC--EEEEEECCCCCCCCCEEEE-----C-CCCC--HHHHHHHHHHHHHCCCEEEEEECHH
T ss_conf             77999569858--98873667--3457777887879845996-----4-8787--9999999999963697699995459


Q ss_pred             CEEHHCCCCCCCCCCCCCCCCCEEEEECCCCCCEECHHHCCCCCCCC-----CCCCCCCCEECCCCCCHHHHHHHHHHCC
Q ss_conf             00000023565434310146520121135783200002102446555-----6667874110013542899888852048
Q gi|254780619|r  432 GYAPLTLCQVCGNRLKCLHCSCWLVEHRSKKKLYCHQCGHSAIYSQS-----CVVCGSSGKMIACGFGIERIAEEVCEYF  506 (731)
Q Consensus       432 Gya~~~~C~~Cg~~~~C~~C~~~l~~h~~~~~l~Ch~Cg~~~~~~~~-----Cp~Cg~~~~l~~~G~Gte~~~e~l~~~f  506 (731)
                      --|--                  ||-+-.....+|+|--.......+     --.-|..+-+    .|+--+-|-|  -.
T Consensus       457 kmaEd------------------Lt~yl~~~~ik~~YlHs~i~t~eR~eIl~~LR~G~~DVl----VGINLLREGL--Dl  512 (657)
T PRK05298        457 RMAED------------------LTDYLKELGIKVRYLHSDIDTLERVEIIRDLRLGEFDVL----VGINLLREGL--DI  512 (657)
T ss_pred             HHHHH------------------HHHHHHHCCCEEEEEECCCCHHHHHHHHHHHHCCCCCEE----EEECHHHCCC--CC
T ss_conf             89999------------------999999679807996266618899999999858887589----7500220457--87


Q ss_pred             CCCH-HHHCCCCCCCCHHHHHHHHHHHCCCCCCEEEEEHHHCCCCCCCCCCHHHHHHHHHHHHHHHH
Q ss_conf             5200-01023211358678999998621257657987044302311345201233000344310245
Q gi|254780619|r  507 PLAR-ISILSSDLEGGGGRLQLQLSAIAKGEIDIIIGTQLVAKGHNFPRMSLVGVVDGDLGLTNADL  572 (731)
Q Consensus       507 p~~~-v~~~d~d~~~~~~~~~~~~~~~~~~~~~ilvgTq~i~kg~~fp~v~lv~il~aD~~l~~pd~  572 (731)
                      |++. |..+|.|..+--.+...++              |+|.  ---.|++=-+|+.||..-.+-.-
T Consensus       513 PEVSLVaILDADKeGFLRs~~SLi--------------QtiG--RAARN~~G~vIlYAD~iT~SM~~  563 (657)
T PRK05298        513 PEVSLVAILDADKEGFLRSERSLI--------------QTIG--RAARNVNGKVILYADKITDSMQK  563 (657)
T ss_pred             CCEEEEEEEECCCCCCCCCCCHHH--------------HHHH--HHHHCCCCEEEEEECCCCHHHHH
T ss_conf             613579887068522103520599--------------9987--88625797499981545099999


No 145
>PRK12903 secA preprotein translocase subunit SecA; Reviewed
Probab=96.19  E-value=0.052  Score=34.47  Aligned_cols=92  Identities=21%  Similarity=0.252  Sum_probs=66.1

Q ss_pred             CCCHHHHHHHHHHHHHHHHCCCCEEEEECCCHHHH---HHHHHHHCCCCCEEEEEECCCCCHHHHHHHHHHHCCCCEEEE
Q ss_conf             75315799999999998514684799715210013---445554303897689962355723566789999719973999
Q gi|254780619|r  226 VTGSGKTEVYLEIVAAVLHLGKQVLILLPEISLTS---AILERFQKRFGVKPAEWHSSLSTSMREKIWRQVARGAISVIV  302 (731)
Q Consensus       226 vTGSGKTEVYl~li~~~L~~GkqvLiLvPEI~Lt~---Q~~~rl~~rF~~~v~v~HS~ls~~eR~~~w~~i~~G~~~IVI  302 (731)
                      -||-|||.+..-.+--.--.|+.|-|+-..=-|+.   ++...+...+|-.|.+..+++++.+|...|.      ++|+-
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             ECCHHH-H-------------HHHCCCEEEEEEEC
Q ss_conf             400121-1-------------00100013677405
Q gi|254780619|r  303 GVRSAL-F-------------LPFKKLGLIVIDEE  323 (731)
Q Consensus       303 GtRSAi-f-------------~P~~nLglIIvDEE  323 (731)
                      ||-+.+ |             .-...+...||||-
T Consensus       173 ~tn~e~gFDyLrDnm~~~~~~~vqr~~~~aIvDEv  207 (885)
T PRK12903        173 STHSELGFDYLRDNMVSSYEEKVQRGLNFCLIDEV  207 (885)
T ss_pred             ECCCCEEECCCCCCCCCCHHHHCCCCCCEEEEECC
T ss_conf             77865030114001135837725889980366541


No 146
>PRK13767 ATP-dependent helicase; Provisional
Probab=96.16  E-value=0.023  Score=37.25  Aligned_cols=84  Identities=23%  Similarity=0.358  Sum_probs=65.6

Q ss_pred             HHHHHHHHCCCCEEEEECCCHHHHHHHHHHHCCCC-----CEEEEEECCCCCHHHHHHHHHHHCCCCEEEEECCHHHH-H
Q ss_conf             99999851468479971521001344555430389-----76899623557235667899997199739994001211-0
Q gi|254780619|r  237 EIVAAVLHLGKQVLILLPEISLTSAILERFQKRFG-----VKPAEWHSSLSTSMREKIWRQVARGAISVIVGVRSALF-L  310 (731)
Q Consensus       237 ~li~~~L~~GkqvLiLvPEI~Lt~Q~~~rl~~rF~-----~~v~v~HS~ls~~eR~~~w~~i~~G~~~IVIGtRSAif-~  310 (731)
                      +.+.+.++.++++||-+=.=+.+..+..+++++++     ..|+++|++++..+|.++=.+.++|+.+.||-|-|-=+ .
T Consensus       275 ~~l~~~i~~~~~tLvF~NtR~~aE~~~~~L~~~~~~~~~~~~i~~HHgSls~e~R~~vE~~lk~G~l~~vV~TsSLELGI  354 (878)
T PRK13767        275 ETLDELIQEHRTTLIFTNTRSGAERVVYKLRKRYPEEYDEDNIGAHHSSLSREVRLEVEEKLKRGELKVVVSSTSLELGI  354 (878)
T ss_pred             HHHHHHHHHCCCEEEEECCHHHHHHHHHHHHHHHHHCCCCCCEEEECCCCCHHHHHHHHHHHHCCCCCEEEEECHHHCCC
T ss_conf             99999998389779991558999999999998534306754322201778999999999998579986899827365077


Q ss_pred             HHCCCEEEEE
Q ss_conf             0100013677
Q gi|254780619|r  311 PFKKLGLIVI  320 (731)
Q Consensus       311 P~~nLglIIv  320 (731)
                      .+-++.+||-
T Consensus       355 DiG~Vd~Viq  364 (878)
T PRK13767        355 DIGYIDLVVL  364 (878)
T ss_pred             CCCCCCEEEE
T ss_conf             7775258997


No 147
>COG4098 comFA Superfamily II DNA/RNA helicase required for DNA uptake (late competence protein) [DNA replication, recombination, and repair]
Probab=96.14  E-value=0.047  Score=34.79  Aligned_cols=85  Identities=21%  Similarity=0.394  Sum_probs=66.7

Q ss_pred             HHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHCCCCC-EEEEEECCCCCHHHHHHHHHHHCCCCEEEEECCHHHH---HH
Q ss_conf             9999998514684799715210013445554303897-6899623557235667899997199739994001211---00
Q gi|254780619|r  236 LEIVAAVLHLGKQVLILLPEISLTSAILERFQKRFGV-KPAEWHSSLSTSMREKIWRQVARGAISVIVGVRSALF---LP  311 (731)
Q Consensus       236 l~li~~~L~~GkqvLiLvPEI~Lt~Q~~~rl~~rF~~-~v~v~HS~ls~~eR~~~w~~i~~G~~~IVIGtRSAif---~P  311 (731)
                      .+.+++....|+-+|+-+|||.-..|..+-|+..|+. .++..||.  +..|.+.-...++|+.+|+|.|-  ++   .-
T Consensus       295 ~~~lekq~~~~~P~liF~p~I~~~eq~a~~lk~~~~~~~i~~Vhs~--d~~R~EkV~~fR~G~~~lLiTTT--ILERGVT  370 (441)
T COG4098         295 KRWLEKQRKTGRPVLIFFPEIETMEQVAAALKKKLPKETIASVHSE--DQHRKEKVEAFRDGKITLLITTT--ILERGVT  370 (441)
T ss_pred             HHHHHHHHHCCCCEEEEECCHHHHHHHHHHHHHHCCCCCEEEEECC--CCCHHHHHHHHHCCCEEEEEEEE--HHHCCCC
T ss_conf             9999998743882899925058899999999861886421565336--70178999998758638999844--0332664


Q ss_pred             HCCCEEEEEEECC
Q ss_conf             1000136774055
Q gi|254780619|r  312 FKKLGLIVIDEEH  324 (731)
Q Consensus       312 ~~nLglIIvDEEH  324 (731)
                      |+|+...|++-||
T Consensus       371 fp~vdV~Vlgaeh  383 (441)
T COG4098         371 FPNVDVFVLGAEH  383 (441)
T ss_pred             CCCCEEEEECCCC
T ss_conf             3562399954776


No 148
>PRK13104 secA preprotein translocase subunit SecA; Reviewed
Probab=96.06  E-value=0.097  Score=32.41  Aligned_cols=92  Identities=18%  Similarity=0.237  Sum_probs=66.2

Q ss_pred             CCCHHHHHHHHHHHHHHHHCCCCEEEEECCCHHHH---HHHHHHHCCCCCEEEEEECCCCCHHHHHHHHHHHCCCCEEEE
Q ss_conf             75315799999999998514684799715210013---445554303897689962355723566789999719973999
Q gi|254780619|r  226 VTGSGKTEVYLEIVAAVLHLGKQVLILLPEISLTS---AILERFQKRFGVKPAEWHSSLSTSMREKIWRQVARGAISVIV  302 (731)
Q Consensus       226 vTGSGKTEVYl~li~~~L~~GkqvLiLvPEI~Lt~---Q~~~rl~~rF~~~v~v~HS~ls~~eR~~~w~~i~~G~~~IVI  302 (731)
                      -||-|||.|..-.+--.--.|+.|-|+-..=-|+.   ++...+...+|-.|.+..+++++.+|...|.      ++|+-
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             ECCHHH-H-------------HHHCCCEEEEEEEC
Q ss_conf             400121-1-------------00100013677405
Q gi|254780619|r  303 GVRSAL-F-------------LPFKKLGLIVIDEE  323 (731)
Q Consensus       303 GtRSAi-f-------------~P~~nLglIIvDEE  323 (731)
                      ||-+-+ |             .-...+...||||-
T Consensus       177 ~Tn~e~gFDyLrDnm~~~~~~~vqr~~~~aivDEv  211 (896)
T PRK13104        177 GTNNEYGFDYLRDNMAFSLTDKVQRELNFAIVDEV  211 (896)
T ss_pred             ECCCCCCCCCCCCCHHCCHHHHCCCCCCEEEEECH
T ss_conf             67865415235721113847625667764787422


No 149
>PRK07263 consensus
Probab=96.06  E-value=0.15  Score=30.93  Aligned_cols=132  Identities=21%  Similarity=0.240  Sum_probs=79.2

Q ss_pred             CEEEEECCCCHHHHHHHHHHHHHH-HHCCCCEEEEECCCHHHHHHHHHHHCCC-CCEE-EEEECCCCCHHHHHHHHHHH-
Q ss_conf             619984475315799999999998-5146847997152100134455543038-9768-99623557235667899997-
Q gi|254780619|r  219 AVSLISGVTGSGKTEVYLEIVAAV-LHLGKQVLILLPEISLTSAILERFQKRF-GVKP-AEWHSSLSTSMREKIWRQVA-  294 (731)
Q Consensus       219 ~~~LL~GvTGSGKTEVYl~li~~~-L~~GkqvLiLvPEI~Lt~Q~~~rl~~rF-~~~v-~v~HS~ls~~eR~~~w~~i~-  294 (731)
                      ....|=|-+|.|||-..++++..+ +.+|+.|++.--|-+ ..|+..|+-..- +... .+..+.+++.+.......+. 
T Consensus       204 dLiviaaRPsmGKTa~alnia~~iA~~~~~~V~~fSlEMs-~~ql~~R~la~~~~i~~~~i~~g~l~~~e~~~~~~a~~~  282 (453)
T PRK07263        204 QLIILAARPAVGKTAFVLNIAQNVGTKQKKTVAIFSLEMG-AESLVDRMLAAEGMVDSHSLRTGQLTDQDWNNVTIAQGA  282 (453)
T ss_pred             CEEEEEECCCCCHHHHHHHHHHHHHHHCCCEEEEEECCCC-HHHHHHHHHHHHCCCCHHCCCCCCCCHHHHHHHHHHHHH
T ss_conf             6899972788847899999999999855982899924699-899999999986173310331365247999999999987


Q ss_pred             CCCCEEEEECCHHH---------H--HH-H-CCCEEEEEEECCCCCCHHCC-CCCCCHHH--H------HHHHHHHCCCC
Q ss_conf             19973999400121---------1--00-1-00013677405532100002-44322489--9------99975110321
Q gi|254780619|r  295 RGAISVIVGVRSAL---------F--LP-F-KKLGLIVIDEEHDISYKQEE-GILYNARD--M------SIVRGKIESFP  352 (731)
Q Consensus       295 ~G~~~IVIGtRSAi---------f--~P-~-~nLglIIvDEEHd~sykq~~-~pry~aRd--v------A~~Ra~~~~~~  352 (731)
                      -.+..+.|-..+.+         =  .. . .+|++||||      |=|-. +++-.-|.  +      ....|+..++|
T Consensus       283 l~~~~l~idd~~~~~i~~i~~~~r~~~~~~~~~l~livID------YlqLi~~~~~~~r~~ev~~isr~lK~lAkel~ip  356 (453)
T PRK07263        283 LAEAPIYIDDTPGIKITEIRARSRKLSQEVDGGLGLIVID------YLQLITGTKPENRQQEVSDISRQLKILAKELKVP  356 (453)
T ss_pred             HCCCCEEEECCCCCCHHHHHHHHHHHHHHHCCCCCEEEEE------HHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHCCC
T ss_conf             4068589978999998999999999998605898689973------6764468885359999999999999999987997


Q ss_pred             EECCC
Q ss_conf             00002
Q gi|254780619|r  353 VVLVS  357 (731)
Q Consensus       353 lilgS  357 (731)
                      ||+.|
T Consensus       357 vi~ls  361 (453)
T PRK07263        357 VIALS  361 (453)
T ss_pred             EEEEC
T ss_conf             99974


No 150
>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=96.02  E-value=0.057  Score=34.15  Aligned_cols=134  Identities=20%  Similarity=0.181  Sum_probs=75.7

Q ss_pred             CCCCCHHHHHHHHHHHHHHCC-C--CCEEEEECCCCHHHHHHHHHHHHHHHHC--CCCEE-EEEC----CCHH-HHHHHH
Q ss_conf             666883789999999875204-8--9619984475315799999999998514--68479-9715----2100-134455
Q gi|254780619|r  196 LPILDKNQQDVVEQVVPLCTK-G--FAVSLISGVTGSGKTEVYLEIVAAVLHL--GKQVL-ILLP----EISL-TSAILE  264 (731)
Q Consensus       196 ~~~Lt~eQ~~a~~~i~~~~~~-~--f~~~LL~GvTGSGKTEVYl~li~~~L~~--GkqvL-iLvP----EI~L-t~Q~~~  264 (731)
                      ...--++|-..+.......-. |  +...+|||-||+|||-|--.++++.=..  ++.+- |-+=    ++.- -.|++.
T Consensus        18 ~i~hRdeqI~~l~~~L~~~l~PG~~P~Ni~iYGkTGtGKT~vt~~v~~~l~~~~~~~d~~D~~~~~~NC~~~~T~y~~~~   97 (383)
T TIGR02928        18 RIVHRDEQIEELAKALRPILRPGSRPSNIFIYGKTGTGKTAVTKYVMKELEEAAEDRDVRDVSTVYINCQILDTSYQVLV   97 (383)
T ss_pred             CCCCCHHHHHHHHHHHHHHHCCCCCCCCEEEECCCCCCHHHHHHHHHHHHHHHHHCCCCCCEEEEEECCCCCCCHHHHHH
T ss_conf             46686789999999988750674898725887888987889999999999998622699715899977854684699999


Q ss_pred             HHHCCC---CCEEEEEECCCCCHHHHHHHHHHHC-CCCEEEEECCHHHHHHHCCCEEE-EEEECCCCCC-HHCCCCCCCH
Q ss_conf             543038---9768996235572356678999971-99739994001211001000136-7740553210-0002443224
Q gi|254780619|r  265 RFQKRF---GVKPAEWHSSLSTSMREKIWRQVAR-GAISVIVGVRSALFLPFKKLGLI-VIDEEHDISY-KQEEGILYNA  338 (731)
Q Consensus       265 rl~~rF---~~~v~v~HS~ls~~eR~~~w~~i~~-G~~~IVIGtRSAif~P~~nLglI-IvDEEHd~sy-kq~~~pry~a  338 (731)
                      ++-+.|   +...-+=+.|+|.++-|+......+ ..                +-.+| |.||= |.=. +..+.|-|.-
T Consensus        98 ~L~~~ln~~~~~~~vP~tG~s~~~~~~~l~~~l~~~~----------------~~~~~ivLDEi-D~Lv~~~~d~PAyS~  160 (383)
T TIGR02928        98 ELANQLNRRGSGEEVPTTGLSTSEVFRELYKELNRER----------------GDSLIIVLDEI-DKLVRKDDDDPAYSK  160 (383)
T ss_pred             HHHHHHCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHC----------------CCEEEEEECCC-CHHHCCCCCCHHHHH
T ss_conf             9999851577888898877878999999999983201----------------88799986231-022158888807878


Q ss_pred             HHHHHHHH
Q ss_conf             89999975
Q gi|254780619|r  339 RDMSIVRG  346 (731)
Q Consensus       339 RdvA~~Ra  346 (731)
                      -=..+-||
T Consensus       161 ~LY~L~Ra  168 (383)
T TIGR02928       161 LLYQLSRA  168 (383)
T ss_pred             HHHHHHHH
T ss_conf             85343310


No 151
>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=96.02  E-value=0.083  Score=32.92  Aligned_cols=75  Identities=19%  Similarity=0.251  Sum_probs=48.4

Q ss_pred             CCCHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHHHHHHHHHHCCCCEEEEECCCHHHH-HHHHHHHCCCCCE
Q ss_conf             688378999999987520489619984475315799999999998514684799715210013-4455543038976
Q gi|254780619|r  198 ILDKNQQDVVEQVVPLCTKGFAVSLISGVTGSGKTEVYLEIVAAVLHLGKQVLILLPEISLTS-AILERFQKRFGVK  273 (731)
Q Consensus       198 ~Lt~eQ~~a~~~i~~~~~~~f~~~LL~GvTGSGKTEVYl~li~~~L~~GkqvLiLvPEI~Lt~-Q~~~rl~~rF~~~  273 (731)
                      ..++..+.++..+......+-...+|-|..|||||-+.-.++ +.+.......++++.-.+++ .+...+...||..
T Consensus        23 y~s~~h~~al~~L~~~l~~~~g~~lltGe~GtGKTtllr~l~-~~l~~~~~~~~~i~~~~l~~~~ll~~i~~~lg~~   98 (269)
T TIGR03015        23 YPSKGHKRAMAYLEYGLSQREGFILITGEVGAGKTTLIRNLL-KRLDQERVVAAKLVNTRVDAEDLLRMVAADFGLE   98 (269)
T ss_pred             CCCHHHHHHHHHHHHHHHCCCCEEEEECCCCCCHHHHHHHHH-HHCCCCCEEEEEECCCCCCHHHHHHHHHHHCCCC
T ss_conf             478669999999999996489659997299898899999999-8459345489997699999999999999985989


No 152
>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=96.01  E-value=0.11  Score=31.98  Aligned_cols=136  Identities=24%  Similarity=0.295  Sum_probs=70.8

Q ss_pred             CEEEEECCCCHHHHHHHHHHHHHH-HHCCCCEEEEECCCHHHHHHHHHHHCCC-CCEEEEEECC-CCCHHHHHHHHHHH-
Q ss_conf             619984475315799999999998-5146847997152100134455543038-9768996235-57235667899997-
Q gi|254780619|r  219 AVSLISGVTGSGKTEVYLEIVAAV-LHLGKQVLILLPEISLTSAILERFQKRF-GVKPAEWHSS-LSTSMREKIWRQVA-  294 (731)
Q Consensus       219 ~~~LL~GvTGSGKTEVYl~li~~~-L~~GkqvLiLvPEI~Lt~Q~~~rl~~rF-~~~v~v~HS~-ls~~eR~~~w~~i~-  294 (731)
                      ..+++-|-||.|||...++++.+. ..+|..|++.-.|-+ ..++..|+-... +....-+.++ +++.+. ..+.+.. 
T Consensus        14 ~L~vi~a~~g~GKS~~~~~la~~~a~~~g~~V~~~SlEm~-~~~~~~R~~s~~~~i~~~~i~~~~~~~~~~-~~~~~~~~   91 (242)
T cd00984          14 DLIIIAARPSMGKTAFALNIAENIAKKQGKPVLFFSLEMS-KEQLLQRLLASESGISLSKLRTGSLSDEDW-ERLAEAIG   91 (242)
T ss_pred             CEEEEEECCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCC-HHHHHHHHHHHHHCCCHHHHHCCCCCHHHH-HHHHHHHH
T ss_conf             1899996899999999999999999977995999933353-889999999998297745530265227999-99999999


Q ss_pred             -CCCCEEEE-ECCH----HH------HHHHCCCEEEEEEECC--CCCCHHCCCCCCC-----HHHHHHHHHHHCCCCEEC
Q ss_conf             -19973999-4001----21------1001000136774055--3210000244322-----489999975110321000
Q gi|254780619|r  295 -RGAISVIV-GVRS----AL------FLPFKKLGLIVIDEEH--DISYKQEEGILYN-----ARDMSIVRGKIESFPVVL  355 (731)
Q Consensus       295 -~G~~~IVI-GtRS----Ai------f~P~~nLglIIvDEEH--d~sykq~~~pry~-----aRdvA~~Ra~~~~~~lil  355 (731)
                       -.+..+.| .+.+    .+      +.--.++.+||||-=+  .++-  ...-+|.     +|++ ...|+..++|+|+
T Consensus        92 ~~~~~~l~i~d~~~~t~~~i~~~ir~~~~~~~~~~vvvDylql~~~~~--~~~~~~~~i~~i~~~L-k~lA~e~~v~Vi~  168 (242)
T cd00984          92 ELKELPIYIDDSSSLTVSDIRSRARRLKKEHGLGLIVIDYLQLMSGSK--KKGNRQQEVAEISRSL-KLLAKELNVPVIA  168 (242)
T ss_pred             HHCCCCEEEECCCCCCHHHHHHHHHHHHHHCCCCEEEEEHHHHCCCCC--CCCCHHHHHHHHHHHH-HHHHHHHCCEEEE
T ss_conf             861698899669999999999999999883699899982698546777--6657999999999999-9999997993999


Q ss_pred             CCCC
Q ss_conf             0245
Q gi|254780619|r  356 VSAT  359 (731)
Q Consensus       356 gSAT  359 (731)
                      .|..
T Consensus       169 ~sQl  172 (242)
T cd00984         169 LSQL  172 (242)
T ss_pred             EECC
T ss_conf             8467


No 153
>PRK00349 uvrA excinuclease ABC subunit A; Reviewed
Probab=95.99  E-value=0.028  Score=36.50  Aligned_cols=67  Identities=21%  Similarity=0.274  Sum_probs=35.3

Q ss_pred             HHHHHHHHHHCCCCEEEEEECCCCEEHHCCCCCCCCCCCCCCCCCEEEEECCCCCCEECHHHCCCCCCCCCCCCCCCCEE
Q ss_conf             99999988622655179974222000000235654343101465201211357832000021024465556667874110
Q gi|254780619|r  409 EMIDGIRHTLARNEQTLLFLNRRGYAPLTLCQVCGNRLKCLHCSCWLVEHRSKKKLYCHQCGHSAIYSQSCVVCGSSGKM  488 (731)
Q Consensus       409 ~l~~~i~~~l~~g~qvll~lnRrGya~~~~C~~Cg~~~~C~~C~~~l~~h~~~~~l~Ch~Cg~~~~~~~~Cp~Cg~~~~l  488 (731)
                      .+++.||+-.++-.++    -.|||.+...--+- .-.+||.|.+.=+..-+-+        |-......||.|++. ++
T Consensus       707 g~~d~IR~lFA~~~~a----k~rg~~~~~FSfN~-~gGrC~~C~G~G~~~~~m~--------Fl~d~~~~C~~C~G~-R~  772 (944)
T PRK00349        707 GVFDPIRELFAGTPEA----KARGYKPGRFSFNV-KGGRCEACQGDGVIKIEMH--------FLPDVYVPCDVCKGK-RY  772 (944)
T ss_pred             CCHHHHHHHHHCCHHH----HHHCCCCCCCCCCC-CCCCCCCCCCCCCEEEEHH--------CCCCCEEECCCCCCC-CC
T ss_conf             4579999998419487----97099976067799-8964887654472898410--------289853479998984-56


Q ss_pred             C
Q ss_conf             0
Q gi|254780619|r  489 I  489 (731)
Q Consensus       489 ~  489 (731)
                      .
T Consensus       773 ~  773 (944)
T PRK00349        773 N  773 (944)
T ss_pred             C
T ss_conf             9


No 154
>PRK01297 ATP-dependent RNA helicase RhlB; Provisional
Probab=95.99  E-value=0.088  Score=32.74  Aligned_cols=23  Identities=13%  Similarity=0.186  Sum_probs=15.0

Q ss_pred             HHHHHHHHHHHHHCCCCEEEEECC
Q ss_conf             999999999985146847997152
Q gi|254780619|r  232 TEVYLEIVAAVLHLGKQVLILLPE  255 (731)
Q Consensus       232 TEVYl~li~~~L~~GkqvLiLvPE  255 (731)
                      |+|=-++|-.+| +|+.+++..|.
T Consensus       108 TpIQ~~aIP~iL-~GkDvi~~A~T  130 (472)
T PRK01297        108 TPIQAQVLGYTL-AGHDAIGRAQT  130 (472)
T ss_pred             CHHHHHHHHHHH-CCCCEEEECCC
T ss_conf             999999999997-69988998999


No 155
>PRK09137 DNA topoisomerase I; Validated
Probab=95.96  E-value=0.015  Score=38.69  Aligned_cols=29  Identities=21%  Similarity=0.433  Sum_probs=11.7

Q ss_pred             CCCCCCCEEEEE--CCCCCCEE---CHHHCCCCC
Q ss_conf             101465201211--35783200---002102446
Q gi|254780619|r  447 KCLHCSCWLVEH--RSKKKLYC---HQCGHSAIY  475 (731)
Q Consensus       447 ~C~~C~~~l~~h--~~~~~l~C---h~Cg~~~~~  475 (731)
                      .||.|+.+|..-  +.+..+-|   .-|.++.++
T Consensus       591 ~Cp~Cg~~l~~r~g~~G~F~~Cs~yP~Ck~t~~~  624 (761)
T PRK09137        591 KCPECGKPLSIKLGKRGRFIACTGYPECKYTRNL  624 (761)
T ss_pred             CCCCCCCEEEEEECCCCCEEECCCCCCCCCCCCC
T ss_conf             7888998238995587765766798766675767


No 156
>KOG0353 consensus
Probab=95.96  E-value=0.17  Score=30.61  Aligned_cols=298  Identities=21%  Similarity=0.263  Sum_probs=153.4

Q ss_pred             CEEEEECCCCHHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHCCCCCEEEEEECCCCCHHHHHHHHHHH--CC
Q ss_conf             6199844753157999999999985146847997152100134455543038976899623557235667899997--19
Q gi|254780619|r  219 AVSLISGVTGSGKTEVYLEIVAAVLHLGKQVLILLPEISLTSAILERFQKRFGVKPAEWHSSLSTSMREKIWRQVA--RG  296 (731)
Q Consensus       219 ~~~LL~GvTGSGKTEVYl~li~~~L~~GkqvLiLvPEI~Lt~Q~~~rl~~rF~~~v~v~HS~ls~~eR~~~w~~i~--~G  296 (731)
                      .++|+- -||-||..-|--   -+|-.+.=+|+..|-|+|...-+-.+++ +|.....++..-|..+-.++-..+.  +.
T Consensus       111 d~~lil-~tgggkslcyql---pal~adg~alvi~plislmedqil~lkq-lgi~as~lnansske~~k~v~~~i~nkds  185 (695)
T KOG0353         111 DAFLIL-PTGGGKSLCYQL---PALCADGFALVICPLISLMEDQILQLKQ-LGIDASMLNANSSKEEAKRVEAAITNKDS  185 (695)
T ss_pred             CEEEEE-ECCCCCCHHHHH---HHHHCCCCEEEECHHHHHHHHHHHHHHH-HCCCHHHCCCCCCHHHHHHHHHHHCCCCC
T ss_conf             469998-379961245223---5876287457610268888999999998-08644430575548889899998707776


Q ss_pred             CCEEEEEC-----CHHHHH-------HHCCCEEEEEEECCCCC-CHHCCCCCCCHHHHHHHHHHHCCCCEECCCCCCCHH
Q ss_conf             97399940-----012110-------01000136774055321-000024432248999997511032100002454324
Q gi|254780619|r  297 AISVIVGV-----RSALFL-------PFKKLGLIVIDEEHDIS-YKQEEGILYNARDMSIVRGKIESFPVVLVSATPSIE  363 (731)
Q Consensus       297 ~~~IVIGt-----RSAif~-------P~~nLglIIvDEEHd~s-ykq~~~pry~aRdvA~~Ra~~~~~~lilgSATPSle  363 (731)
                      +-+++--|     .|-.|+       ....+.+|-|||-|--| |-.+-.|-|.+-.+  +.-+.-|+|++=-+||-.-.
T Consensus       186 e~kliyvtpekiaksk~~mnkleka~~~~~~~~iaidevhccsqwghdfr~dy~~l~i--lkrqf~~~~iigltatatn~  263 (695)
T KOG0353         186 EFKLIYVTPEKIAKSKKFMNKLEKALEAGFFKLIAIDEVHCCSQWGHDFRPDYKALGI--LKRQFKGAPIIGLTATATNH  263 (695)
T ss_pred             EEEEEEECHHHHHHHHHHHHHHHHHHHCCEEEEEEECCEEEHHHHCCCCCCCHHHHHH--HHHHCCCCCEEEEEHHHHCC
T ss_conf             1589996489987779999999987642604898531023265437665741688889--99757999656323110000


Q ss_pred             HHHHHHHHHHHHHC--CCCCCCCCCCCCCEECCCCCCCCCCCCCCCHHHHHHHHHHHCCCCEEEEEECCCCEEHHCCCC-
Q ss_conf             67753212344412--432236765433211022223322245479899999988622655179974222000000235-
Q gi|254780619|r  364 SRVNGISRRYHSVH--LSTRYRNSALPHLQVIDMRGQTIAQGKSLSPEMIDGIRHTLARNEQTLLFLNRRGYAPLTLCQ-  440 (731)
Q Consensus       364 s~~~~~~g~~~~~~--l~~R~~~~~~P~i~ivDm~~~~~~~~~~lS~~l~~~i~~~l~~g~qvll~lnRrGya~~~~C~-  440 (731)
                      .+-.++.  +--++  ++=|+ +...|+..- ..++.+  ++   .+..++.|-+.++..        =.|-+..++|- 
T Consensus       264 vl~d~k~--il~ie~~~tf~a-~fnr~nl~y-ev~qkp--~n---~dd~~edi~k~i~~~--------f~gqsgiiyc~s  326 (695)
T KOG0353         264 VLDDAKD--ILCIEAAFTFRA-GFNRPNLKY-EVRQKP--GN---EDDCIEDIAKLIKGD--------FAGQSGIIYCFS  326 (695)
T ss_pred             HHHHHHH--HHHHHHHHEEEC-CCCCCCCEE-EEEECC--CC---HHHHHHHHHHHHCCC--------CCCCCCEEEEEC
T ss_conf             3567888--774786511202-368887326-745189--97---577899999985444--------378765699953


Q ss_pred             --CCCCCCCCCCCCCEEEEECCCCCCEECHHHCCCCCCCCCCCCCCCCEECCCCCCHHHHHHHHHHCCCCCHHHHCCCCC
Q ss_conf             --654343101465201211357832000021024465556667874110013542899888852048520001023211
Q gi|254780619|r  441 --VCGNRLKCLHCSCWLVEHRSKKKLYCHQCGHSAIYSQSCVVCGSSGKMIACGFGIERIAEEVCEYFPLARISILSSDL  518 (731)
Q Consensus       441 --~Cg~~~~C~~C~~~l~~h~~~~~l~Ch~Cg~~~~~~~~Cp~Cg~~~~l~~~G~Gte~~~e~l~~~fp~~~v~~~d~d~  518 (731)
                        +|..+++      .|.-|   +.-.-||-.                                 .+-|.      |   
T Consensus       327 q~d~ekva~------alkn~---gi~a~~yha---------------------------------~lep~------d---  355 (695)
T KOG0353         327 QKDCEKVAK------ALKNH---GIHAGAYHA---------------------------------NLEPE------D---  355 (695)
T ss_pred             CCCHHHHHH------HHHHC---CCCCCCCCC---------------------------------CCCCC------C---
T ss_conf             465899999------99855---835221405---------------------------------56853------4---


Q ss_pred             CCCHHHHHHHHHHHCCCCCCEEEEEHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHH--------HHH-------
Q ss_conf             35867899999862125765798704430231134520123300034431024557899999--------875-------
Q gi|254780619|r  519 EGGGGRLQLQLSAIAKGEIDIIIGTQLVAKGHNFPRMSLVGVVDGDLGLTNADLRSSERTFQ--------LLS-------  583 (731)
Q Consensus       519 ~~~~~~~~~~~~~~~~~~~~ilvgTq~i~kg~~fp~v~lv~il~aD~~l~~pd~ra~E~~~q--------ll~-------  583 (731)
                        +.+.|+.    ...|++.++|+|-...-|.|-|+|..|+--..-        .+-|..||        +-.       
T Consensus       356 --ks~~hq~----w~a~eiqvivatvafgmgidkpdvrfvihhsl~--------ksienyyqasarillrmtkqknksdt  421 (695)
T KOG0353         356 --KSGAHQG----WIAGEIQVIVATVAFGMGIDKPDVRFVIHHSLP--------KSIENYYQASARILLRMTKQKNKSDT  421 (695)
T ss_pred             --CCCCCCC----CCCCCEEEEEEEEEECCCCCCCCEEEEEECCCC--------HHHHHHHHHHHHHHHHHHHHCCCCCC
T ss_conf             --4540003----304606899998640256788871699953661--------66899998878999987652255567


Q ss_pred             ------------------------HHHHCCCCCCCCCEEEEEECCC
Q ss_conf             ------------------------4311025667886899993298
Q gi|254780619|r  584 ------------------------QVTGRAGRFGLKSLGLIQAYQP  605 (731)
Q Consensus       584 ------------------------qv~gRagr~~~~g~v~iQt~~p  605 (731)
                                              .-+|||||.+-+...|+--...
T Consensus       422 ggstqinilevctnfkiffavfsekesgragrd~~~a~cilyy~~~  467 (695)
T KOG0353         422 GGSTQINILEVCTNFKIFFAVFSEKESGRAGRDDMKADCILYYGFA  467 (695)
T ss_pred             CCCCEEEHHHHHCCCEEEEEEECCHHCCCCCCCCCCCCEEEEECHH
T ss_conf             8753000433401310122220311025556688866479984247


No 157
>COG3973 Superfamily I DNA and RNA helicases [General function prediction only]
Probab=95.95  E-value=0.016  Score=38.34  Aligned_cols=53  Identities=32%  Similarity=0.482  Sum_probs=39.8

Q ss_pred             CCCHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHHHHHHHHHH------CCCCEEEEECCC
Q ss_conf             68837899999998752048961998447531579999999999851------468479971521
Q gi|254780619|r  198 ILDKNQQDVVEQVVPLCTKGFAVSLISGVTGSGKTEVYLEIVAAVLH------LGKQVLILLPEI  256 (731)
Q Consensus       198 ~Lt~eQ~~a~~~i~~~~~~~f~~~LL~GvTGSGKTEVYl~li~~~L~------~GkqvLiLvPEI  256 (731)
                      ++.+||.+++-.      .+-.+...+|..|||||-|.||-++-.|-      ++++|||+.|.-
T Consensus       212 TIQkEQneIIR~------ek~~ilVVQGaAGSGKTtiALHRvAyLlY~~R~~l~~k~vlvl~PN~  270 (747)
T COG3973         212 TIQKEQNEIIRF------EKNKILVVQGAAGSGKTTIALHRVAYLLYGYRGPLQAKPVLVLGPNR  270 (747)
T ss_pred             HHHHHHHHHHHC------CCCCEEEEECCCCCCCHHHHHHHHHHHHHCCCCCCCCCCEEEECCCH
T ss_conf             861767778755------57874899558888713588999999985356624668659982838


No 158
>KOG0953 consensus
Probab=95.95  E-value=0.018  Score=38.04  Aligned_cols=103  Identities=20%  Similarity=0.342  Sum_probs=61.2

Q ss_pred             HHCC--CCCCEEEEEHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHCCCCCCCC-CEEEEEECCC-
Q ss_conf             6212--576579870443023113452012330003443102455789-9999875431102566788-6899993298-
Q gi|254780619|r  531 AIAK--GEIDIIIGTQLVAKGHNFPRMSLVGVVDGDLGLTNADLRSSE-RTFQLLSQVTGRAGRFGLK-SLGLIQAYQP-  605 (731)
Q Consensus       531 ~~~~--~~~~ilvgTq~i~kg~~fp~v~lv~il~aD~~l~~pd~ra~E-~~~qll~qv~gRagr~~~~-g~v~iQt~~p-  605 (731)
                      .|.+  ++.||||+|-.|.-|++. ++.-|+.-+    |.-++=|..| -+....-|.||||||+..+ ..-++-|.+. 
T Consensus       402 ~FNd~~~e~dvlVAsDAIGMGLNL-~IrRiiF~s----l~Kysg~e~~~it~sqikQIAGRAGRf~s~~~~G~vTtl~~e  476 (700)
T KOG0953         402 LFNDPSNECDVLVASDAIGMGLNL-NIRRIIFYS----LIKYSGRETEDITVSQIKQIAGRAGRFGSKYPQGEVTTLHSE  476 (700)
T ss_pred             HHCCCCCCCCEEEEECCCCCCCCC-CEEEEEEEE----CCCCCCCCCEECCHHHHHHHHHCCCCCCCCCCCCEEEEEEHH
T ss_conf             737988762568862321455444-311798750----356776621025689999885101544567767457774186


Q ss_pred             CCHHHHHHHHCCHHH------HHHHHHHHHHHCCCCCCH
Q ss_conf             648889999589799------999999999981888801
Q gi|254780619|r  606 THPVMQALVSGDADS------FYESEIRARESVNLPPFG  638 (731)
Q Consensus       606 ~~~~~~~~~~~d~~~------f~~~el~~R~~~~~PPf~  638 (731)
                      |-..++.+.+.-.+-      |...|.-++=...+|+-+
T Consensus       477 DL~~L~~~l~~p~epi~~agl~pt~eqie~fa~~~Pd~t  515 (700)
T KOG0953         477 DLKLLKRILKRPVEPIKNAGLWPTDEQIELFAYHLPDAT  515 (700)
T ss_pred             HHHHHHHHHHCCCHHHHHCCCCCCHHHHHHHHHHCCCCC
T ss_conf             699999998479567776357863999999998689824


No 159
>PRK08903 hypothetical protein; Validated
Probab=95.92  E-value=0.17  Score=30.52  Aligned_cols=36  Identities=31%  Similarity=0.390  Sum_probs=26.0

Q ss_pred             CEEEEECCCCHHHHHHHHHHHHHHHHCCCCEEEEEC
Q ss_conf             619984475315799999999998514684799715
Q gi|254780619|r  219 AVSLISGVTGSGKTEVYLEIVAAVLHLGKQVLILLP  254 (731)
Q Consensus       219 ~~~LL~GvTGSGKTEVYl~li~~~L~~GkqvLiLvP  254 (731)
                      ....|||-+|||||-.---+..++.+.|+.+.++-.
T Consensus        43 ~~l~i~G~~G~GKTHLl~a~~~~~~~~~~~~~yl~~   78 (227)
T PRK08903         43 RFFYLWGEAGSGRSHLLQALVAAASEGGKNARYLDP   78 (227)
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHHHHCCCCEEEECC
T ss_conf             669998999998889999999999806997499651


No 160
>PRK11776 ATP-dependent RNA helicase DbpA; Provisional
Probab=95.90  E-value=0.098  Score=32.36  Aligned_cols=126  Identities=15%  Similarity=0.184  Sum_probs=86.7

Q ss_pred             EECCCCHHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHCCCCCEEEEEECCCCCHHHHHHHHHHHCCCCEEEE
Q ss_conf             84475315799999999998514684799715210013445554303897689962355723566789999719973999
Q gi|254780619|r  223 ISGVTGSGKTEVYLEIVAAVLHLGKQVLILLPEISLTSAILERFQKRFGVKPAEWHSSLSTSMREKIWRQVARGAISVIV  302 (731)
Q Consensus       223 L~GvTGSGKTEVYl~li~~~L~~GkqvLiLvPEI~Lt~Q~~~rl~~rF~~~v~v~HS~ls~~eR~~~w~~i~~G~~~IVI  302 (731)
                      .+-+....|.+.-.+++..  ....++||-+....-+..+...|++ .|..+..+|++|+..+|..+..+-++|+.+|+|
T Consensus       221 ~~~v~~~~K~~~L~~ll~~--~~~~~~IIFcntk~~v~~l~~~L~~-~g~~~~~lHg~m~q~~R~~~l~~F~~g~~~iLV  297 (459)
T PRK11776        221 FYEVDPDERLPALQRLLLH--YRPESCVVFCNTKKECQEVADALNA-QGFSALALHGDLEQRDRDQVLVRFANRSCSVLV  297 (459)
T ss_pred             EEEECHHHHHHHHHHHHHH--CCCCCEEEEECCHHHHHHHHHHHHH-CCCCEEEEECCCCHHHHHHHHHHHHCCCCCEEE
T ss_conf             9997718789999999973--6876603761748999999999986-799689987999999999999999779997998


Q ss_pred             ECCHHHH-HHHCCCEEEEE-EECCCC-CCHHCCCCCCCHHHHHHHHHHHCCCCEECCCCCCC
Q ss_conf             4001211-00100013677-405532-10000244322489999975110321000024543
Q gi|254780619|r  303 GVRSALF-LPFKKLGLIVI-DEEHDI-SYKQEEGILYNARDMSIVRGKIESFPVVLVSATPS  361 (731)
Q Consensus       303 GtRSAif-~P~~nLglIIv-DEEHd~-sykq~~~pry~aRdvA~~Ra~~~~~~lilgSATPS  361 (731)
                      .|=-|.= +.++++..||- |=-.|. +|-+-     -.|   -=||-..|..+.|.  ||.
T Consensus       298 aTDvaaRGIDi~~V~~VInyDlP~~~e~YvHR-----iGR---TGRaG~~G~ait~v--t~~  349 (459)
T PRK11776        298 ATDVAARGLDIKSLEAVINYELARDPEVHVHR-----IGR---TGRAGSKGLALSLV--APE  349 (459)
T ss_pred             EHHHHHCCCCCCCCCEEEEECCCCCHHHHHHC-----CCH---HHCCCCCEEEEEEE--CHH
T ss_conf             81043476771359889997898974552020-----525---13789965799998--689


No 161
>KOG0926 consensus
Probab=95.87  E-value=0.051  Score=34.55  Aligned_cols=204  Identities=25%  Similarity=0.312  Sum_probs=94.4

Q ss_pred             CCCCCHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHHHHHHHHHHCCCCEE-EEECC-CHHHH-------HHHHHH
Q ss_conf             6668837899999998752048961998447531579999999999851468479-97152-10013-------445554
Q gi|254780619|r  196 LPILDKNQQDVVEQVVPLCTKGFAVSLISGVTGSGKTEVYLEIVAAVLHLGKQVL-ILLPE-ISLTS-------AILERF  266 (731)
Q Consensus       196 ~~~Lt~eQ~~a~~~i~~~~~~~f~~~LL~GvTGSGKTEVYl~li~~~L~~GkqvL-iLvPE-I~Lt~-------Q~~~rl  266 (731)
                      +|.+-.| +.+.+.|...     .+..+.|-||||||-=   +=.=..++|...= .--|+ |+.|.       .|.+|.
T Consensus       255 LPI~aeE-q~IMEaIn~n-----~vvIIcGeTGsGKTTQ---vPQFLYEAGf~s~~~~~~gmIGITqPRRVAaiamAkRV  325 (1172)
T KOG0926         255 LPIVAEE-QRIMEAINEN-----PVVIICGETGSGKTTQ---VPQFLYEAGFASEQSSSPGMIGITQPRRVAAIAMAKRV  325 (1172)
T ss_pred             CCHHHHH-HHHHHHHHCC-----CEEEEECCCCCCCCCC---CHHHHHHCCCCCCCCCCCCEEEECCCHHHHHHHHHHHH
T ss_conf             7636789-9999986228-----7499954888886443---41899871347766799870540572278999999999


Q ss_pred             HCCCCCEEEEEECCCCCHHHHHHHHHHHCCCCEEEEECCHHHHH------HHCCCEEEEEEECCCCCCHHCCCCCCCHHH
Q ss_conf             30389768996235572356678999971997399940012110------010001367740553210000244322489
Q gi|254780619|r  267 QKRFGVKPAEWHSSLSTSMREKIWRQVARGAISVIVGVRSALFL------PFKKLGLIVIDEEHDISYKQEEGILYNARD  340 (731)
Q Consensus       267 ~~rF~~~v~v~HS~ls~~eR~~~w~~i~~G~~~IVIGtRSAif~------P~~nLglIIvDEEHd~sykq~~~pry~aRd  340 (731)
                      ..-+|.    +-|..|=.-||+   .-......|--=|-.-++-      =+..-..||+||.|+-|-..|--.---.| 
T Consensus       326 a~EL~~----~~~eVsYqIRfd---~ti~e~T~IkFMTDGVLLrEi~~DflL~kYSvIIlDEAHERSvnTDILiGmLSR-  397 (1172)
T KOG0926         326 AFELGV----LGSEVSYQIRFD---GTIGEDTSIKFMTDGVLLREIENDFLLTKYSVIILDEAHERSVNTDILIGMLSR-  397 (1172)
T ss_pred             HHHHCC----CCCCEEEEEEEC---CCCCCCCEEEEECCHHHHHHHHHHHHHHHCEEEEECHHHHCCCHHHHHHHHHHH-
T ss_conf             998525----764114899853---656887404774023889998876755420157851254303127899999988-


Q ss_pred             HHHHHHHHCC-------CCEECCCCCCCHHHHHHHHHHHHHHHCCCCCCCCCCCCCCEECCCCCCCCCC--CCC-CCHHH
Q ss_conf             9999751103-------2100002454324677532123444124322367654332110222233222--454-79899
Q gi|254780619|r  341 MSIVRGKIES-------FPVVLVSATPSIESRVNGISRRYHSVHLSTRYRNSALPHLQVIDMRGQTIAQ--GKS-LSPEM  410 (731)
Q Consensus       341 vA~~Ra~~~~-------~~lilgSATPSles~~~~~~g~~~~~~l~~R~~~~~~P~i~ivDm~~~~~~~--~~~-lS~~l  410 (731)
                      +.-+|++++.       -.||+.|||-.++.+.-           .+|-.....| +--||.|+-+..-  +.. -.+.+
T Consensus       398 iV~LR~k~~ke~~~~kpLKLIIMSATLRVsDFte-----------nk~LFpi~pP-likVdARQfPVsIHF~krT~~DYi  465 (1172)
T KOG0926         398 IVPLRQKYYKEQCQIKPLKLIIMSATLRVSDFTE-----------NKRLFPIPPP-LIKVDARQFPVSIHFNKRTPDDYI  465 (1172)
T ss_pred             HHHHHHHHHHHHCCCCCEEEEEEEEEEEECCCCC-----------CCEECCCCCC-EEEEECCCCCEEEEECCCCCCHHH
T ss_conf             7788899766413567616999741477110246-----------7542478996-055304528568873267984178


Q ss_pred             HHH------HHHHHCCCCEEEEEEC
Q ss_conf             999------9886226551799742
Q gi|254780619|r  411 IDG------IRHTLARNEQTLLFLN  429 (731)
Q Consensus       411 ~~~------i~~~l~~g~qvll~ln  429 (731)
                      -++      |.+.|-.| -.|+|+-
T Consensus       466 ~eAfrKtc~IH~kLP~G-~ILVFvT  489 (1172)
T KOG0926         466 AEAFRKTCKIHKKLPPG-GILVFVT  489 (1172)
T ss_pred             HHHHHHHHHHHHCCCCC-CEEEEEE
T ss_conf             99999999886108998-2799980


No 162
>PRK13107 preprotein translocase subunit SecA; Reviewed
Probab=95.81  E-value=0.17  Score=30.61  Aligned_cols=92  Identities=20%  Similarity=0.186  Sum_probs=65.6

Q ss_pred             CCCHHHHHHHHHHHHHHHHCCCCEEEEECCCHHHH---HHHHHHHCCCCCEEEEEECCCCCHHHHHHHHHHHCCCCEEEE
Q ss_conf             75315799999999998514684799715210013---445554303897689962355723566789999719973999
Q gi|254780619|r  226 VTGSGKTEVYLEIVAAVLHLGKQVLILLPEISLTS---AILERFQKRFGVKPAEWHSSLSTSMREKIWRQVARGAISVIV  302 (731)
Q Consensus       226 vTGSGKTEVYl~li~~~L~~GkqvLiLvPEI~Lt~---Q~~~rl~~rF~~~v~v~HS~ls~~eR~~~w~~i~~G~~~IVI  302 (731)
                      -||-|||.|..-.+--.--.|+.|-|+-..=-|+.   ++...+..++|-.|.+..+++++.+|...|.      .+|+-
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             ECCHHH-H---------HH----HCCCEEEEEEEC
Q ss_conf             400121-1---------00----100013677405
Q gi|254780619|r  303 GVRSAL-F---------LP----FKKLGLIVIDEE  323 (731)
Q Consensus       303 GtRSAi-f---------~P----~~nLglIIvDEE  323 (731)
                      ||-+-+ |         .+    ...+-..||||-
T Consensus       177 ~Tn~e~gFDYLRDnm~~~~~~~vqr~~~~aivDEv  211 (908)
T PRK13107        177 GTNNEFGFDYLRDNMAFSPQERVQRPLHYALIDEV  211 (908)
T ss_pred             ECCCCCCCCCCCCCCCCCHHHHCCCCCCEEEEECH
T ss_conf             35764234235743015758753567764887422


No 163
>PRK04537 ATP-dependent RNA helicase RhlB; Provisional
Probab=95.77  E-value=0.1  Score=32.20  Aligned_cols=121  Identities=13%  Similarity=0.246  Sum_probs=82.1

Q ss_pred             CCCHHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHCCCCCEEEEEECCCCCHHHHHHHHHHHCCCCEEEEECC
Q ss_conf             75315799999999998514684799715210013445554303897689962355723566789999719973999400
Q gi|254780619|r  226 VTGSGKTEVYLEIVAAVLHLGKQVLILLPEISLTSAILERFQKRFGVKPAEWHSSLSTSMREKIWRQVARGAISVIVGVR  305 (731)
Q Consensus       226 vTGSGKTEVYl~li~~~L~~GkqvLiLvPEI~Lt~Q~~~rl~~rF~~~v~v~HS~ls~~eR~~~w~~i~~G~~~IVIGtR  305 (731)
                      +...-|.+..+.++..  ..+.++||-+.....+..+...|+. .+..+..+|++++..+|..+..+-++|+..|+|.|=
T Consensus       239 ~~~~~K~~~L~~LL~~--~~~~k~IIF~nT~~~ve~l~~~L~~-~g~~v~~LHG~lsQ~eR~~~L~~Fk~G~~~VLVaTD  315 (574)
T PRK04537        239 PSDEEKQTLLLGLLSR--SEGARTMVFVNTKAFVERVARTLER-HGYRVGVLSGDVPQKKRESLLNRFQKGQLEILVATD  315 (574)
T ss_pred             CCHHHHHHHHHHHHHH--CCCCCCEEECCHHHHHHHHHHHHHH-CCCCEEEEECCCCHHHHHHHHHHHHCCCCCEEEECC
T ss_conf             7778999999999972--6776511533418999999999997-799689970999999999999999769997997735


Q ss_pred             HHHH-HHHCCCEEEEE-EECCC-CCCHHCCCCCCCHHHHHHHHHHHCCCCEECCC
Q ss_conf             1211-00100013677-40553-21000024432248999997511032100002
Q gi|254780619|r  306 SALF-LPFKKLGLIVI-DEEHD-ISYKQEEGILYNARDMSIVRGKIESFPVVLVS  357 (731)
Q Consensus       306 SAif-~P~~nLglIIv-DEEHd-~sykq~~~pry~aRdvA~~Ra~~~~~~lilgS  357 (731)
                      -|.= +-++++.+||- |=-+| .+|-+-     -.|   .=|+-..|..+-|.|
T Consensus       316 VAARGIDIp~V~~VINYDlP~~~e~YVHR-----IGR---TGRaGr~G~AITfv~  362 (574)
T PRK04537        316 VAARGLHIDGVKYVYNYDLPFDAEDYVHR-----IGR---TARLGEEGDAISFAC  362 (574)
T ss_pred             CCCCCCCCCCCCEEEEECCCCCHHHHHCC-----CCH---HHCCCCCEEEEEEEC
T ss_conf             00233571469979995796982141124-----535---037899335999877


No 164
>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=95.75  E-value=0.063  Score=33.84  Aligned_cols=46  Identities=28%  Similarity=0.278  Sum_probs=35.4

Q ss_pred             CEEEEECCCCHHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHH
Q ss_conf             6199844753157999999999985146847997152100134455
Q gi|254780619|r  219 AVSLISGVTGSGKTEVYLEIVAAVLHLGKQVLILLPEISLTSAILE  264 (731)
Q Consensus       219 ~~~LL~GvTGSGKTEVYl~li~~~L~~GkqvLiLvPEI~Lt~Q~~~  264 (731)
                      ...+|.|-+|||||.+-..++......+..++.+.++.........
T Consensus         3 ~~ill~G~~GsGKTtl~~~la~~~~~~~~~v~~~~~~~~~~~~~~~   48 (148)
T smart00382        3 EVILIVGPPGSGKTTLARALARELGPPGGGVIYIDGEDILEEVLDQ   48 (148)
T ss_pred             CEEEEECCCCHHHHHHHHHHHHHHCCCCCCEEEEEHHHHHHHHHHH
T ss_conf             7899999997029999999998726689968998759989888987


No 165
>PRK08116 hypothetical protein; Validated
Probab=95.75  E-value=0.094  Score=32.52  Aligned_cols=109  Identities=21%  Similarity=0.432  Sum_probs=62.8

Q ss_pred             CEEEEECCCCHHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHCCCCCEEEEEECCCCCHHHHHHHHHHHCCCC
Q ss_conf             61998447531579999999999851468479971521001344555430389768996235572356678999971997
Q gi|254780619|r  219 AVSLISGVTGSGKTEVYLEIVAAVLHLGKQVLILLPEISLTSAILERFQKRFGVKPAEWHSSLSTSMREKIWRQVARGAI  298 (731)
Q Consensus       219 ~~~LL~GvTGSGKTEVYl~li~~~L~~GkqvLiLvPEI~Lt~Q~~~rl~~rF~~~v~v~HS~ls~~eR~~~w~~i~~G~~  298 (731)
                      ...||+|-+|+|||-+..-++...+++|.+|++.-     .+.++.++++-|+..     +..+                
T Consensus       109 ~GLll~G~~GtGKThLa~aIa~~l~~~g~~V~~~~-----~~~ll~~lk~~~~~~-----~~~~----------------  162 (262)
T PRK08116        109 VGLLLWGSPGNGKTYLAAAIANELIEKGVPVVFVN-----VPELLNRIKSTYNSE-----GKED----------------  162 (262)
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHHHHCCCEEEEEE-----HHHHHHHHHHHHHCC-----CCHH----------------
T ss_conf             61899898999899999999999998799399988-----999999999998635-----6101----------------


Q ss_pred             EEEEECCHHHHHHHCCCEEEEEEEC---CCCCCHHCCCCCCCHHHHHHHHHHH-CCCCEECCCCCCCHHHHHH
Q ss_conf             3999400121100100013677405---5321000024432248999997511-0321000024543246775
Q gi|254780619|r  299 SVIVGVRSALFLPFKKLGLIVIDEE---HDISYKQEEGILYNARDMSIVRGKI-ESFPVVLVSATPSIESRVN  367 (731)
Q Consensus       299 ~IVIGtRSAif~P~~nLglIIvDEE---Hd~sykq~~~pry~aRdvA~~Ra~~-~~~~lilgSATPSles~~~  367 (731)
                            ...++-.+.+..|.|+|+=   ..+.|-.+.  -|+     +.-.++ .+-|.|+.|=- +++.+..
T Consensus       163 ------~~e~l~~l~~~dLLIiDDlG~e~~t~w~~e~--lf~-----IIn~Ry~~~kptIiTTNl-~~~eL~~  221 (262)
T PRK08116        163 ------ENEIIRALDNADLLILDDLGAEKDTEWVREK--LYN-----IIDSRYRKGLPTIFTTNL-SLEELKN  221 (262)
T ss_pred             ------HHHHHHHHHCCCEEEEEHHCCCCCCHHHHHH--HHH-----HHHHHHHCCCCEEEECCC-CHHHHHH
T ss_conf             ------9999998612998998322145698789999--999-----999999769998998799-9999999


No 166
>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=95.74  E-value=0.013  Score=38.98  Aligned_cols=126  Identities=16%  Similarity=0.228  Sum_probs=69.6

Q ss_pred             CEEEEECCCCHHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHCCCCCEE-EEEECCCCCHHHHHHHHHHHCCC
Q ss_conf             61998447531579999999999851468479971521001344555430389768-99623557235667899997199
Q gi|254780619|r  219 AVSLISGVTGSGKTEVYLEIVAAVLHLGKQVLILLPEISLTSAILERFQKRFGVKP-AEWHSSLSTSMREKIWRQVARGA  297 (731)
Q Consensus       219 ~~~LL~GvTGSGKTEVYl~li~~~L~~GkqvLiLvPEI~Lt~Q~~~rl~~rF~~~v-~v~HS~ls~~eR~~~w~~i~~G~  297 (731)
                      +-.|+||.||||||+.=.++++.+=++|--|+|.==+=.       -...+|.... .+|+.==+-..-++.|..+.+- 
T Consensus       209 Qh~L~~GTtG~GKs~~lr~LL~~iR~rGd~AIiYDkgC~-------f~~~fyd~~~DviLNP~D~RCA~Wd~W~Ec~~~-  280 (613)
T TIGR02759       209 QHILIHGTTGSGKSVALRKLLRWIRQRGDRAIIYDKGCT-------FVSRFYDPSQDVILNPLDERCANWDVWRECKDK-  280 (613)
T ss_pred             CCEEEECCCCCHHHHHHHHHHHHHHHCCCEEEEEECCCC-------CCCCCCCCCCCEEECCCCCCCCCCCCCCCCCCC-
T ss_conf             252664541743899999999999863985899825742-------021326888874606744355548835035889-


Q ss_pred             CEEEEECCHHHHHHHCCCEEEEEEECCCCCCHHCCCCCC--CHHH----HHHH-HHHHCCCC------EECCCCCCCHHH
Q ss_conf             739994001211001000136774055321000024432--2489----9999-75110321------000024543246
Q gi|254780619|r  298 ISVIVGVRSALFLPFKKLGLIVIDEEHDISYKQEEGILY--NARD----MSIV-RGKIESFP------VVLVSATPSIES  364 (731)
Q Consensus       298 ~~IVIGtRSAif~P~~nLglIIvDEEHd~sykq~~~pry--~aRd----vA~~-Ra~~~~~~------lilgSATPSles  364 (731)
                      ++  -++=+..|.|..      +|+--        -|.|  .||-    +|.. |-...+|.      ++|   |-++|.
T Consensus       281 ~d--Fen~A~~LIPm~------~~~sm--------DPFW~~SARtiF~S~A~~m~~d~~rcs~~~Ll~~lL---t~~Le~  341 (613)
T TIGR02759       281 TD--FENMAEALIPMH------GDGSM--------DPFWVDSARTIFTSTAYKMRNDPKRCSTSKLLDLLL---TSELEE  341 (613)
T ss_pred             CC--HHHHHHHHCCCC------CCCCC--------CCHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHC---CHHHHH
T ss_conf             88--789999838898------88887--------712243236789999999730256788899998750---402678


Q ss_pred             HHHHHHH
Q ss_conf             7753212
Q gi|254780619|r  365 RVNGISR  371 (731)
Q Consensus       365 ~~~~~~g  371 (731)
                      +.+..+|
T Consensus       342 L~~~L~g  348 (613)
T TIGR02759       342 LRDYLKG  348 (613)
T ss_pred             HHHHHCC
T ss_conf             8876347


No 167
>PRK06835 DNA replication protein DnaC; Validated
Probab=95.71  E-value=0.049  Score=34.64  Aligned_cols=60  Identities=25%  Similarity=0.353  Sum_probs=43.0

Q ss_pred             HHHHHHHHH---HHCCCCCEEEEECCCCHHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHC
Q ss_conf             999999987---52048961998447531579999999999851468479971521001344555430
Q gi|254780619|r  204 QDVVEQVVP---LCTKGFAVSLISGVTGSGKTEVYLEIVAAVLHLGKQVLILLPEISLTSAILERFQK  268 (731)
Q Consensus       204 ~~a~~~i~~---~~~~~f~~~LL~GvTGSGKTEVYl~li~~~L~~GkqvLiLvPEI~Lt~Q~~~rl~~  268 (731)
                      +.+++....   ...+.+...|++|-||.|||-...-++.+.+.+|.+|+++-     ++++++.+++
T Consensus       166 ~~i~~~~~~fi~~F~~~~~nLlf~G~~G~GKTfLa~~IA~ell~~g~sViy~t-----a~~L~~~l~~  228 (330)
T PRK06835        166 ENILEKCLNFIKNFDKNNENLLFYGNTGTGKTFLSNCIAKELLDRGKTVIYRT-----SDELIENLRE  228 (330)
T ss_pred             HHHHHHHHHHHHHCCCCCCCEEEECCCCCCHHHHHHHHHHHHHHCCCEEEEEE-----HHHHHHHHHH
T ss_conf             99999999998724788886698899999889999999999998799499962-----9999999999


No 168
>KOG0329 consensus
Probab=95.69  E-value=0.014  Score=38.75  Aligned_cols=135  Identities=27%  Similarity=0.340  Sum_probs=87.8

Q ss_pred             EEEECCCCHHHHHHHHHHHHHHHHC-CCC--EEEEECCCHHHHHH---HHHHHCCCC-CEEEEEECCCCCHHHHHHHHHH
Q ss_conf             9984475315799999999998514-684--79971521001344---555430389-7689962355723566789999
Q gi|254780619|r  221 SLISGVTGSGKTEVYLEIVAAVLHL-GKQ--VLILLPEISLTSAI---LERFQKRFG-VKPAEWHSSLSTSMREKIWRQV  293 (731)
Q Consensus       221 ~LL~GvTGSGKTEVYl~li~~~L~~-Gkq--vLiLvPEI~Lt~Q~---~~rl~~rF~-~~v~v~HS~ls~~eR~~~w~~i  293 (731)
                      .|-+.-.|-|||-|+.-+.-+.++- ..|  ||++.-.--|+-|+   +.||.++.+ .+++++.++++-++-.+.... 
T Consensus        82 vlcqaksgmgktavfvl~tlqqiepv~g~vsvlvmchtrelafqi~~ey~rfskymP~vkvaVFfGG~~Ikkdee~lk~-  160 (387)
T KOG0329          82 VLCQAKSGMGKTAVFVLATLQQIEPVDGQVSVLVMCHTRELAFQISKEYERFSKYMPSVKVSVFFGGLFIKKDEELLKN-  160 (387)
T ss_pred             HHEECCCCCCCEEEEEHHHHHHCCCCCCEEEEEEEECCHHHHHHHHHHHHHHHHHCCCCEEEEEECCEECCCCHHHHHC-
T ss_conf             2010025788436552223552378898079999962189999988999999754888458999755310346998827-


Q ss_pred             HCCCCEEEEECCHHHHHH-------HCCCEEEEEEECCCCCCHHCCCCCCCHHHHH-HHHHHHCCCCEECCCCCCCHHH
Q ss_conf             719973999400121100-------1000136774055321000024432248999-9975110321000024543246
Q gi|254780619|r  294 ARGAISVIVGVRSALFLP-------FKKLGLIVIDEEHDISYKQEEGILYNARDMS-IVRGKIESFPVVLVSATPSIES  364 (731)
Q Consensus       294 ~~G~~~IVIGtRSAif~P-------~~nLglIIvDEEHd~sykq~~~pry~aRdvA-~~Ra~~~~~~lilgSATPSles  364 (731)
                         -+.|||||..-+.+-       ++|..-.|+||- |--..|-+ .|   ||+- +.|+.-+.-.+.+.|||-|-|.
T Consensus       161 ---~PhivVgTPGrilALvr~k~l~lk~vkhFvlDEc-dkmle~lD-Mr---RDvQEifr~tp~~KQvmmfsatlskei  231 (387)
T KOG0329         161 ---CPHIVVGTPGRILALVRNRSLNLKNVKHFVLDEC-DKMLEQLD-MR---RDVQEIFRMTPHEKQVMMFSATLSKEI  231 (387)
T ss_pred             ---CCEEEECCCHHHHHHHHHCCCCHHHCCEEEHHHH-HHHHHHHH-HH---HHHHHHHHCCCCCCEEEEEEEECCHHH
T ss_conf             ---9908976828899998724575320321123337-78999878-88---879998632865320345420131566


No 169
>COG1203 CRISPR-associated helicase Cas3 [Defense mechanisms]
Probab=95.64  E-value=0.067  Score=33.61  Aligned_cols=24  Identities=4%  Similarity=0.076  Sum_probs=9.4

Q ss_pred             HHHHHHHHHHCCCCC-CEEEEEHHH
Q ss_conf             789999986212576-579870443
Q gi|254780619|r  523 GRLQLQLSAIAKGEI-DIIIGTQLV  546 (731)
Q Consensus       523 ~~~~~~~~~~~~~~~-~ilvgTq~i  546 (731)
                      ....+++..+..... -.|+-+++.
T Consensus       451 ~~Aie~Y~~Lk~~~~~v~LlHSRf~  475 (733)
T COG1203         451 DRAIELYEKLKEKGPKVLLLHSRFT  475 (733)
T ss_pred             HHHHHHHHHHHCCCCCEEEEECCCC
T ss_conf             9999999998555895799886355


No 170
>KOG0951 consensus
Probab=95.64  E-value=0.22  Score=29.70  Aligned_cols=195  Identities=22%  Similarity=0.284  Sum_probs=108.4

Q ss_pred             EEEECCCCHHHHHHHHHHHHHHHHCCCCEEEEEC--CCH--HHHHHHHHHHCCCCCEEEEEECCCCCHHHHHHHHHHHCC
Q ss_conf             9984475315799999999998514684799715--210--013445554303897689962355723566789999719
Q gi|254780619|r  221 SLISGVTGSGKTEVYLEIVAAVLHLGKQVLILLP--EIS--LTSAILERFQKRFGVKPAEWHSSLSTSMREKIWRQVARG  296 (731)
Q Consensus       221 ~LL~GvTGSGKTEVYl~li~~~L~~GkqvLiLvP--EI~--Lt~Q~~~rl~~rF~~~v~v~HS~ls~~eR~~~w~~i~~G  296 (731)
                      .++---+|||||-+.--++..--..| .+....|  ||+  ....+.++|..-.|-.+..+.+.-|-.-+.     +.  
T Consensus      1162 v~vga~~gsgkt~~ae~a~l~~~~~~-~~vyi~p~~~i~~~~~~~w~~~f~~~~G~~~~~l~ge~s~dlkl-----~~-- 1233 (1674)
T KOG0951        1162 VLVGAPNGSGKTACAELALLRPDTIG-RAVYIAPLEEIADEQYRDWEKKFSKLLGLRIVKLTGETSLDLKL-----LQ-- 1233 (1674)
T ss_pred             EEEECCCCCCHHHHHHHHHCCCCCCE-EEEEECCHHHHHHHHHHHHHHHHCCCCCCEEEECCCCCCCCHHH-----HH--
T ss_conf             89945788734488999862886632-79984366899999999998753104580688517865525677-----64--


Q ss_pred             CCEEEEECCHH--HHHHHCCCEEEEEEECCCCCCHHCCCCCC----CHHHHHHHHHHHCCCCEECCCCCCCHHHHHHHHH
Q ss_conf             97399940012--11001000136774055321000024432----2489999975110321000024543246775321
Q gi|254780619|r  297 AISVIVGVRSA--LFLPFKKLGLIVIDEEHDISYKQEEGILY----NARDMSIVRGKIESFPVVLVSATPSIESRVNGIS  370 (731)
Q Consensus       297 ~~~IVIGtRSA--if~P~~nLglIIvDEEHd~sykq~~~pry----~aRdvA~~Ra~~~~~~lilgSATPSles~~~~~~  370 (731)
                      ...|+|.|...  +.--.+++.+-|+||-|--+  -..++-|    ..|-+|...-+  ++.++--|     .++.|+..
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 1304 (1674)
T KOG0951        1234 KGQVIISTPEQWDLLQSIQQVDLFIVDELHLIG--GVYGAVYEVICSMRYIASQLEK--KIRVVALS-----SSLANARD 1304 (1674)
T ss_pred             HCCEEEECHHHHHHHHHHHHCCEEEEEHHHHHC--CCCCCEEEEEEEHHHHHHHHHH--HEEEEEEE-----HHHCCCHH
T ss_conf             245588663577777554321168610234414--6577348987447999999986--50588732-----22304122


Q ss_pred             HHHHHHCCCCCCCC-----CCCC---CCEECCCCCCCCCCCCCCCHHHHHHHHHHHCCCCEEEEEECCCCEEHH
Q ss_conf             23444124322367-----6543---321102222332224547989999998862265517997422200000
Q gi|254780619|r  371 RRYHSVHLSTRYRN-----SALP---HLQVIDMRGQTIAQGKSLSPEMIDGIRHTLARNEQTLLFLNRRGYAPL  436 (731)
Q Consensus       371 g~~~~~~l~~R~~~-----~~~P---~i~ivDm~~~~~~~~~~lS~~l~~~i~~~l~~g~qvll~lnRrGya~~  436 (731)
                      +-+   .-+.+..+     ++-|   +|+.+|.... ............++|.+....+++.++|++.|-.+-.
T Consensus      1305 ~ig---~s~~~v~Nf~p~~R~~Pl~i~i~~~~~~~~-~s~~~am~~~~~~ai~~~a~~~k~~~vf~p~rk~~~~ 1374 (1674)
T KOG0951        1305 LIG---ASSSGVFNFSPSVRPVPLEIHIQSVDISHF-ESRMLAMTKPTYTAIVRHAGNRKPAIVFLPTRKHARL 1374 (1674)
T ss_pred             HCC---CCCCCEEECCCCCCCCCEEEEEEEECCCHH-HHHHHHHHHHHHHHHHHHHCCCCCEEEEECCCHHHHH
T ss_conf             205---354553605866688760688887324015-7888774312799999985489972798034014322


No 171
>PRK13103 secA preprotein translocase subunit SecA; Reviewed
Probab=95.60  E-value=0.13  Score=31.41  Aligned_cols=92  Identities=22%  Similarity=0.196  Sum_probs=65.7

Q ss_pred             CCCHHHHHHHHHHHHHHHHCCCCEEEEECCCHHHH---HHHHHHHCCCCCEEEEEECCCCCHHHHHHHHHHHCCCCEEEE
Q ss_conf             75315799999999998514684799715210013---445554303897689962355723566789999719973999
Q gi|254780619|r  226 VTGSGKTEVYLEIVAAVLHLGKQVLILLPEISLTS---AILERFQKRFGVKPAEWHSSLSTSMREKIWRQVARGAISVIV  302 (731)
Q Consensus       226 vTGSGKTEVYl~li~~~L~~GkqvLiLvPEI~Lt~---Q~~~rl~~rF~~~v~v~HS~ls~~eR~~~w~~i~~G~~~IVI  302 (731)
                      -||-|||.|..-.+--.--.|+.|-|+-..=-|+.   ++...+...+|-.|.+..+.+++.+|...|      .++|+-
T Consensus       103 ~TGEGKTL~atlp~ylnal~g~gvhvvTvNdYLA~RDae~m~~~y~~lGltvg~i~~~~~~~~r~~aY------~~DitY  176 (913)
T PRK13103        103 RTGEGKTLVGTLAVYLNALSGKGVHVVTVNDYLARRDANWMRPLYEFLGLSVGIVTPFQPPEEKRAAY------AADITY  176 (913)
T ss_pred             CCCCCHHHHHHHHHHHHHHCCCCEEEECCCHHHHHHHHHHHHHHHHHHCCEEEECCCCCCHHHHHHHC------CCCCEE
T ss_conf             17885599999999998755997099726536558669999999998197685518999979999746------688644


Q ss_pred             ECCHHH-H-------------HHHCCCEEEEEEEC
Q ss_conf             400121-1-------------00100013677405
Q gi|254780619|r  303 GVRSAL-F-------------LPFKKLGLIVIDEE  323 (731)
Q Consensus       303 GtRSAi-f-------------~P~~nLglIIvDEE  323 (731)
                      ||-+-+ |             .--..+...||||-
T Consensus       177 ~tn~e~gFDyLRDnm~~~~~~~vqr~~~~aivDEv  211 (913)
T PRK13103        177 GTNNEFGFDYLRDNMAFSLDDKFQRELNFAVIDEV  211 (913)
T ss_pred             ECCCCCCCCCCCCCHHCCHHHHCCCCCCEEEEECH
T ss_conf             35764335345733104878843667764787423


No 172
>smart00489 DEXDc3 DEAD-like helicases superfamily.
Probab=95.58  E-value=0.13  Score=31.44  Aligned_cols=45  Identities=22%  Similarity=0.320  Sum_probs=35.1

Q ss_pred             CHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHHHHHHHHHHC
Q ss_conf             8378999999987520489619984475315799999999998514
Q gi|254780619|r  200 DKNQQDVVEQVVPLCTKGFAVSLISGVTGSGKTEVYLEIVAAVLHL  245 (731)
Q Consensus       200 t~eQ~~a~~~i~~~~~~~f~~~LL~GvTGSGKTEVYl~li~~~L~~  245 (731)
                      -+.|....+.+......+ ...|++.=||+|||--||-.+-..+..
T Consensus        10 y~~Q~e~m~~v~~~l~~~-~~~llEaPTGtGKTlalL~~al~~~~~   54 (289)
T smart00489       10 YPIQYEFMEELKRVLDRG-KIGILESPTGTGKTLSLLCLTLTWLRS   54 (289)
T ss_pred             CHHHHHHHHHHHHHHHCC-CEEEEECCCCHHHHHHHHHHHHHHHHH
T ss_conf             989999999999999749-979998999651899999999999996


No 173
>smart00488 DEXDc2 DEAD-like helicases superfamily.
Probab=95.58  E-value=0.13  Score=31.44  Aligned_cols=45  Identities=22%  Similarity=0.320  Sum_probs=35.1

Q ss_pred             CHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHHHHHHHHHHC
Q ss_conf             8378999999987520489619984475315799999999998514
Q gi|254780619|r  200 DKNQQDVVEQVVPLCTKGFAVSLISGVTGSGKTEVYLEIVAAVLHL  245 (731)
Q Consensus       200 t~eQ~~a~~~i~~~~~~~f~~~LL~GvTGSGKTEVYl~li~~~L~~  245 (731)
                      -+.|....+.+......+ ...|++.=||+|||--||-.+-..+..
T Consensus        10 y~~Q~e~m~~v~~~l~~~-~~~llEaPTGtGKTlalL~~al~~~~~   54 (289)
T smart00488       10 YPIQYEFMEELKRVLDRG-KIGILESPTGTGKTLSLLCLTLTWLRS   54 (289)
T ss_pred             CHHHHHHHHHHHHHHHCC-CEEEEECCCCHHHHHHHHHHHHHHHHH
T ss_conf             989999999999999749-979998999651899999999999996


No 174
>PRK06904 replicative DNA helicase; Validated
Probab=95.56  E-value=0.23  Score=29.52  Aligned_cols=132  Identities=19%  Similarity=0.232  Sum_probs=77.6

Q ss_pred             CEEEEECCCCHHHHHHHHHHHHHH-HHCCCCEEEEECCCHHHHHHHHHHHCCC-CCEEE-EEECC-CCCHH--HHHHHHH
Q ss_conf             619984475315799999999998-5146847997152100134455543038-97689-96235-57235--6678999
Q gi|254780619|r  219 AVSLISGVTGSGKTEVYLEIVAAV-LHLGKQVLILLPEISLTSAILERFQKRF-GVKPA-EWHSS-LSTSM--REKIWRQ  292 (731)
Q Consensus       219 ~~~LL~GvTGSGKTEVYl~li~~~-L~~GkqvLiLvPEI~Lt~Q~~~rl~~rF-~~~v~-v~HS~-ls~~e--R~~~w~~  292 (731)
                      ..++|=|-+|.|||-..+.++..+ +..|+.|++.--|-+ ..|+..|+-... +...- +..+. +++.+  +...+..
T Consensus       222 ~LiViAaRPsmGKTa~alnia~n~A~~~~~~V~~fSLEM~-~~~l~~R~ls~~s~v~~~~i~~g~~l~~~e~~~~~~~~~  300 (472)
T PRK06904        222 DLIIVAARPSMGKTTFAMNLCENAAMASEKPVLVFSLEMP-AEQIMMRMLASLSRVDQTKIRTGQNLDQQDWAKISSTVG  300 (472)
T ss_pred             CEEEEEECCCCCHHHHHHHHHHHHHHHCCCCEEEECCCCC-HHHHHHHHHHHHCCCCHHHHHCCCCCHHHHHHHHHHHHH
T ss_conf             5799973798756899999999999955995799778799-999999999986499988864688560999999999999


Q ss_pred             HHCCCCEEEEECCHHH------------HHHHCCCEEEEEEECCCCCCHHCC-CCCC-CHHH--HH------HHHHHHCC
Q ss_conf             9719973999400121------------100100013677405532100002-4432-2489--99------99751103
Q gi|254780619|r  293 VARGAISVIVGVRSAL------------FLPFKKLGLIVIDEEHDISYKQEE-GILY-NARD--MS------IVRGKIES  350 (731)
Q Consensus       293 i~~G~~~IVIGtRSAi------------f~P~~nLglIIvDEEHd~sykq~~-~pry-~aRd--vA------~~Ra~~~~  350 (731)
                      ..+..+.+.|=..+.+            .-.-.++++||||      |=|-. .+.+ .-|.  ++      ...|+..+
T Consensus       301 ~l~~~~~l~idd~~~~t~~~i~~~~r~~~~~~~~l~~vvID------YLqL~~~~~~~~~r~~ei~~isr~LK~lAkel~  374 (472)
T PRK06904        301 MFKQKPNLYIDDSSGLTPTELRSRARRVYRENGGLSLIMVD------YLQLMRAPGFEDNRTLEIAEISRSLKALAKELK  374 (472)
T ss_pred             HHHCCCCEEEECCCCCCHHHHHHHHHHHHHHCCCCCEEEEE------HHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHC
T ss_conf             98468981684699999999999999999873899789963------886604888777788999999999999999979


Q ss_pred             CCEECCC
Q ss_conf             2100002
Q gi|254780619|r  351 FPVVLVS  357 (731)
Q Consensus       351 ~~lilgS  357 (731)
                      +|||+.|
T Consensus       375 ipvi~Ls  381 (472)
T PRK06904        375 VPVVALS  381 (472)
T ss_pred             CCEEEEC
T ss_conf             9889973


No 175
>PRK08084 DNA replication initiation factor; Provisional
Probab=95.56  E-value=0.21  Score=29.77  Aligned_cols=37  Identities=19%  Similarity=0.261  Sum_probs=26.3

Q ss_pred             CCCCEEEEECCCCHHHHHHHHHHH-HHHHHCCCCEEEEE
Q ss_conf             489619984475315799999999-99851468479971
Q gi|254780619|r  216 KGFAVSLISGVTGSGKTEVYLEIV-AAVLHLGKQVLILL  253 (731)
Q Consensus       216 ~~f~~~LL~GvTGSGKTEVYl~li-~~~L~~GkqvLiLv  253 (731)
                      .+.....|||-+|||||-. ++++ .++.++|+++.++-
T Consensus        43 ~~~~~l~l~G~~G~GKTHL-LqA~~~~~~~~~~~~~yl~   80 (235)
T PRK08084         43 EHSGYIYLWGREGAGRSHL-LHAACAELSQRGDAVGYVP   80 (235)
T ss_pred             CCCCEEEEECCCCCCHHHH-HHHHHHHHHCCCCCEEEEE
T ss_conf             8987699989999888999-9999999970798579987


No 176
>PRK11057 ATP-dependent DNA helicase RecQ; Provisional
Probab=95.54  E-value=0.041  Score=35.30  Aligned_cols=86  Identities=23%  Similarity=0.374  Sum_probs=69.1

Q ss_pred             CCCCEEEEECCCHHHHHHHHHHHCCCCCEEEEEECCCCCHHHHHHHHHHHCCCCEEEEECCHHHH---HHHCCCEEEEEE
Q ss_conf             46847997152100134455543038976899623557235667899997199739994001211---001000136774
Q gi|254780619|r  245 LGKQVLILLPEISLTSAILERFQKRFGVKPAEWHSSLSTSMREKIWRQVARGAISVIVGVRSALF---LPFKKLGLIVID  321 (731)
Q Consensus       245 ~GkqvLiLvPEI~Lt~Q~~~rl~~rF~~~v~v~HS~ls~~eR~~~w~~i~~G~~~IVIGtRSAif---~P~~nLglIIvD  321 (731)
                      .|.+.||.++...-+.++..+|+.. |..+..||++|++.+|..+-..-.+|+.+|||.|-  +|   .--+|...||=-
T Consensus       235 ~~~sgIIYc~trk~~e~la~~L~~~-G~~~~~YHagl~~~~R~~~q~~f~~~~~~vivAT~--AFGMGIdk~dVR~ViH~  311 (607)
T PRK11057        235 RGKSGIIYCNSRAKVEDTAARLQSR-GISAAAYHAGLDNDVRADVQEAFQRDDLQIVVATV--AFGMGINKPNVRFVVHF  311 (607)
T ss_pred             CCCCEEEEECCHHHHHHHHHHHHHC-CCCEEECCCCCCHHHHHHHHHHHHCCCCCEEEEEH--HHHCCCCCCCCCEEEEC
T ss_conf             8997799969289999999999857-97545305899978999999987568875899750--11057677776679977


Q ss_pred             E--CCCCCCHHCCC
Q ss_conf             0--55321000024
Q gi|254780619|r  322 E--EHDISYKQEEG  333 (731)
Q Consensus       322 E--EHd~sykq~~~  333 (731)
                      .  ..=++|.|+-|
T Consensus       312 ~~P~s~e~yyQE~G  325 (607)
T PRK11057        312 DIPRNIESYYQETG  325 (607)
T ss_pred             CCCCCHHHHHHHHH
T ss_conf             89999999999886


No 177
>KOG0987 consensus
Probab=95.54  E-value=0.029  Score=36.43  Aligned_cols=77  Identities=26%  Similarity=0.278  Sum_probs=54.3

Q ss_pred             CCCCCHHHHHHHHHHHHHHCC-CCCEEEEECCCCHHHHHHHHHHHHHHHHCCCCEEEEECC-CHHHHHHHHH-HHCCCCC
Q ss_conf             666883789999999875204-896199844753157999999999985146847997152-1001344555-4303897
Q gi|254780619|r  196 LPILDKNQQDVVEQVVPLCTK-GFAVSLISGVTGSGKTEVYLEIVAAVLHLGKQVLILLPE-ISLTSAILER-FQKRFGV  272 (731)
Q Consensus       196 ~~~Lt~eQ~~a~~~i~~~~~~-~f~~~LL~GvTGSGKTEVYl~li~~~L~~GkqvLiLvPE-I~Lt~Q~~~r-l~~rF~~  272 (731)
                      ...||.+|+.+++.+.....+ .-..+. +|--|.|||=+|-.+++..-+.|++++...+- |+..+-.-.| ...+||.
T Consensus       115 ~~~l~~eqk~v~d~~~~~v~~~~g~~ff-~g~~gtgKt~l~~t~~~~~~~~g~~~~~v~~s~ia~~~l~gg~T~~s~fgi  193 (540)
T KOG0987         115 PKKLTPEQKRVYDAILEAVENNLGGVFF-YGFGGTGKTYLLKTLIAALRSRGKIVLNVASSGIAALLLEGGRTAHSRFGI  193 (540)
T ss_pred             HHHCCHHHHHHHHHHHHHHHCCCCCEEE-CCCCCCCCEEEHHHHHHHHHHCCCCEEEEEECCHHHHHCCCCCCCCHHHCC
T ss_conf             6655987763799999998547876534-367886540237889999974587146653301244315688530043166


Q ss_pred             E
Q ss_conf             6
Q gi|254780619|r  273 K  273 (731)
Q Consensus       273 ~  273 (731)
                      .
T Consensus       194 ~  194 (540)
T KOG0987         194 P  194 (540)
T ss_pred             C
T ss_conf             5


No 178
>PRK09361 radB DNA repair and recombination protein RadB; Provisional
Probab=95.52  E-value=0.12  Score=31.76  Aligned_cols=37  Identities=30%  Similarity=0.540  Sum_probs=34.4

Q ss_pred             CEEEEECCCCHHHHHHHHHHHHHHHHCCCCEEEEECC
Q ss_conf             6199844753157999999999985146847997152
Q gi|254780619|r  219 AVSLISGVTGSGKTEVYLEIVAAVLHLGKQVLILLPE  255 (731)
Q Consensus       219 ~~~LL~GvTGSGKTEVYl~li~~~L~~GkqvLiLvPE  255 (731)
                      +..++.|..|||||-+-++++.++..+|..|+++-=|
T Consensus        24 ~itei~G~pG~GKTtl~lq~a~~~~~~g~~vlYidtE   60 (224)
T PRK09361         24 TITQIYGPPGSGKTNICIQLAVEAARQGKKVIYIDTE   60 (224)
T ss_pred             EEEEEECCCCCCHHHHHHHHHHHHHHCCCCEEEECCC
T ss_conf             7999989999859999999999999749909996787


No 179
>pfam00308 Bac_DnaA Bacterial dnaA protein.
Probab=95.49  E-value=0.078  Score=33.14  Aligned_cols=167  Identities=17%  Similarity=0.215  Sum_probs=73.8

Q ss_pred             HHHHHHHHCCCCCEEEEECCCCHHHHHHHHHHHHHHH-HC--CCCEEEEECCCHHHHHHHHHHHCCCCCEEEEEECCCCC
Q ss_conf             9999875204896199844753157999999999985-14--68479971521001344555430389768996235572
Q gi|254780619|r  207 VEQVVPLCTKGFAVSLISGVTGSGKTEVYLEIVAAVL-HL--GKQVLILLPEISLTSAILERFQKRFGVKPAEWHSSLST  283 (731)
Q Consensus       207 ~~~i~~~~~~~f~~~LL~GvTGSGKTEVYl~li~~~L-~~--GkqvLiLvPEI~Lt~Q~~~rl~~rF~~~v~v~HS~ls~  283 (731)
                      .+.+.......+.+.+|||-+|||||-. ++++.... ++  +..|.++-.|-                           
T Consensus        23 ~~~i~~~~~~~~npl~i~G~~G~GKTHL-LqA~~~~~~~~~~~~~v~yl~~~~---------------------------   74 (219)
T pfam00308        23 ALAVAEAPGKAYNPLFIYGGVGLGKTHL-LHAIGNYALRNFPNLRVVYLTSEE---------------------------   74 (219)
T ss_pred             HHHHHHCCCCCCCCEEEECCCCCCHHHH-HHHHHHHHHHHCCCCEEEEEEHHH---------------------------
T ss_conf             9999967587678269988999988899-999999999849998288843999---------------------------


Q ss_pred             HHHHHHHHHH-HCCCCEEEEECCHHHHHHHCCCEEEEEEECCCCCCHH-CCCCCCCHHHHHHHHHHHCCCCEECCCCCCC
Q ss_conf             3566789999-7199739994001211001000136774055321000-0244322489999975110321000024543
Q gi|254780619|r  284 SMREKIWRQV-ARGAISVIVGVRSALFLPFKKLGLIVIDEEHDISYKQ-EEGILYNARDMSIVRGKIESFPVVLVSATPS  361 (731)
Q Consensus       284 ~eR~~~w~~i-~~G~~~IVIGtRSAif~P~~nLglIIvDEEHd~sykq-~~~pry~aRdvA~~Ra~~~~~~lilgSATPS  361 (731)
                        -...+..+ .++.       -.+...-+.++.+++||+=|--+=++ .+.--||.-+    +....+.+++++|..|.
T Consensus        75 --~~~~~~~~l~~~~-------~~~f~~~l~~~d~l~iDDi~~l~~~~~~ee~lf~l~N----~~~~~~~~lllts~~~p  141 (219)
T pfam00308        75 --FLNDFVDALRDNK-------IEAFKKSYRNVDLLLIDDIQFLAGKEKTQEEFFHTFN----ALHENNKQIVLTSDRPP  141 (219)
T ss_pred             --HHHHHHHHHHCCC-------HHHHHHHHHHCCHHHHCCHHHHCCCHHHHHHHHHHHH----HHHHCCCEEEEECCCCC
T ss_conf             --9998899998188-------8899999763233652236765686478999999999----99972986999779981


Q ss_pred             HHHHHHHHHHHHHHHCCCCCCCCCCCCCCEECC-------CCCCCCCCCCCCCHHHHHHHHHHHCCC
Q ss_conf             246775321234441243223676543321102-------222332224547989999998862265
Q gi|254780619|r  362 IESRVNGISRRYHSVHLSTRYRNSALPHLQVID-------MRGQTIAQGKSLSPEMIDGIRHTLARN  421 (731)
Q Consensus       362 les~~~~~~g~~~~~~l~~R~~~~~~P~i~ivD-------m~~~~~~~~~~lS~~l~~~i~~~l~~g  421 (731)
                      -+.-       ..+-.|..|......-.+...|       +++.....|-.+++...+-|-+++.+.
T Consensus       142 ~~l~-------~~~~dL~SRL~~g~~~~i~~pdd~~~~~iL~~~a~~r~l~l~~~v~~yl~~r~~R~  201 (219)
T pfam00308       142 KELE-------GFEDRLRSRFEWGLIIAIEPPDLETRLAILRKKAEEENINIPNEVLNFIAQRITDN  201 (219)
T ss_pred             CCCC-------CCCHHHHHHHHCCEEEECCCCCHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHCCCC
T ss_conf             0024-------53277999986875661169999999999999999849999999999999842798


No 180
>COG0468 RecA RecA/RadA recombinase [DNA replication, recombination, and repair]
Probab=95.49  E-value=0.1  Score=32.22  Aligned_cols=88  Identities=22%  Similarity=0.226  Sum_probs=57.9

Q ss_pred             CEEEEECCCCHHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHCCCCCEEEEEECCCCCHHHHHHHHHHHCCCC
Q ss_conf             61998447531579999999999851468479971521001344555430389768996235572356678999971997
Q gi|254780619|r  219 AVSLISGVTGSGKTEVYLEIVAAVLHLGKQVLILLPEISLTSAILERFQKRFGVKPAEWHSSLSTSMREKIWRQVARGAI  298 (731)
Q Consensus       219 ~~~LL~GvTGSGKTEVYl~li~~~L~~GkqvLiLvPEI~Lt~Q~~~rl~~rF~~~v~v~HS~ls~~eR~~~w~~i~~G~~  298 (731)
                      ...=++|--|||||-+.++++..+...|..|++.=-|=+|-|+-...+...+-+++.+..-.-...+..-+=..+..+. 
T Consensus        61 ~ItEiyG~~gsGKT~lal~~~~~aq~~g~~a~fIDtE~~l~p~r~~~l~~~~~d~l~v~~~~~~e~q~~i~~~~~~~~~-  139 (279)
T COG0468          61 RITEIYGPESSGKTTLALQLVANAQKPGGKAAFIDTEHALDPERAKQLGVDLLDNLLVSQPDTGEQQLEIAEKLARSGA-  139 (279)
T ss_pred             EEEEEECCCCCCHHHHHHHHHHHHHCCCCEEEEEECCCCCCHHHHHHHHHHHHCCEEEECCCCHHHHHHHHHHHHHHCC-
T ss_conf             5899846887654668999988865379808999589998999999988754215368668977999999999987546-


Q ss_pred             EEEEECCHHHHHHHCCCEEEEEE
Q ss_conf             39994001211001000136774
Q gi|254780619|r  299 SVIVGVRSALFLPFKKLGLIVID  321 (731)
Q Consensus       299 ~IVIGtRSAif~P~~nLglIIvD  321 (731)
                            +        +.+|||||
T Consensus       140 ------~--------~i~LvVVD  148 (279)
T COG0468         140 ------E--------KIDLLVVD  148 (279)
T ss_pred             ------C--------CCCEEEEE
T ss_conf             ------8--------87889982


No 181
>cd01123 Rad51_DMC1_radA Rad51_DMC1_radA,B. This group of recombinases includes the eukaryotic proteins RAD51, RAD55/57 and the meiosis-specific protein DMC1, and the archaeal proteins radA and radB. They are closely related to the bacterial RecA group. Rad51 proteins catalyze a similiar recombination reaction as RecA, using ATP-dependent DNA binding activity and a DNA-dependent ATPase. However, this reaction is less efficient and requires accessory proteins such as RAD55/57 .
Probab=95.48  E-value=0.19  Score=30.25  Aligned_cols=43  Identities=23%  Similarity=0.315  Sum_probs=32.8

Q ss_pred             CEEEEECCCCHHHHHHHHHHHHHHHH------CCCCEEEEECCCHHHHH
Q ss_conf             61998447531579999999999851------46847997152100134
Q gi|254780619|r  219 AVSLISGVTGSGKTEVYLEIVAAVLH------LGKQVLILLPEISLTSA  261 (731)
Q Consensus       219 ~~~LL~GvTGSGKTEVYl~li~~~L~------~GkqvLiLvPEI~Lt~Q  261 (731)
                      +...|+|..|||||.+-|+++..+..      .|..|+++-=|=++.++
T Consensus        20 ~itEi~G~~GsGKTql~lqla~~~~~~~~~~g~~~~vvyIdtE~~f~~~   68 (235)
T cd01123          20 SITEIFGEFGSGKTQLCHQLAVTVQLPIELGGLEGKAVYIDTEGTFRPE   68 (235)
T ss_pred             EEEEEECCCCCCHHHHHHHHHHHHHHHHHHCCCCCEEEEEECCCCCCHH
T ss_conf             7999999999849999999999984247536789629999536775889


No 182
>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=95.48  E-value=0.15  Score=31.04  Aligned_cols=48  Identities=25%  Similarity=0.335  Sum_probs=36.9

Q ss_pred             CEEEEECCCCHHHHHHHHHHHHHHHHCC------CCEEEEECCCHHHHHHHHHH
Q ss_conf             6199844753157999999999985146------84799715210013445554
Q gi|254780619|r  219 AVSLISGVTGSGKTEVYLEIVAAVLHLG------KQVLILLPEISLTSAILERF  266 (731)
Q Consensus       219 ~~~LL~GvTGSGKTEVYl~li~~~L~~G------kqvLiLvPEI~Lt~Q~~~rl  266 (731)
                      +...++|..|||||.+-++++..+...|      +.|+++-=|=+..++.+..+
T Consensus        20 ~ItEi~G~~gsGKT~l~lqla~~~q~~~~~~~~~g~vvyIDtE~~f~~~rl~~i   73 (226)
T cd01393          20 RITEIFGEFGSGKTQLCLQLAVEAQLPGELGGLEGKVVYIDTEGAFRPERLVQL   73 (226)
T ss_pred             EEEEEECCCCCCHHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCCCHHHHHHH
T ss_conf             399999999998999999999998542211699961999955775319999999


No 183
>PRK11054 helD DNA helicase IV; Provisional
Probab=95.47  E-value=0.048  Score=34.77  Aligned_cols=77  Identities=26%  Similarity=0.318  Sum_probs=54.9

Q ss_pred             CCCCCHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHHHHHHHHHHCCC----CEEEEECCCHHHHHHHHHHHCCCC
Q ss_conf             6668837899999998752048961998447531579999999999851468----479971521001344555430389
Q gi|254780619|r  196 LPILDKNQQDVVEQVVPLCTKGFAVSLISGVTGSGKTEVYLEIVAAVLHLGK----QVLILLPEISLTSAILERFQKRFG  271 (731)
Q Consensus       196 ~~~Lt~eQ~~a~~~i~~~~~~~f~~~LL~GvTGSGKTEVYl~li~~~L~~Gk----qvLiLvPEI~Lt~Q~~~rl~~rF~  271 (731)
                      ..+||++|..|+-.-       -...|+=.--|||||.|-..-|+..++.|.    ++|.|.=.-.=+..|-+|+++++|
T Consensus       194 s~PLn~~Qr~Avi~~-------ed~~LVLAGAGSGKT~vLt~RiayLI~~g~~~P~~ILaLTFT~kAA~EMreRl~~~lg  266 (684)
T PRK11054        194 SSPLNPSQARAVVNG-------EDSLLVLAGAGSGKTSVLVARAGWLLARGQAQPEQILLLAFGRKAAEEMDERIRERLG  266 (684)
T ss_pred             CCCCCHHHHHHEEEC-------CCCEEEEECCCCCCHHHHHHHHHHHHHCCCCCHHHEEEEECCHHHHHHHHHHHHHHCC
T ss_conf             799998999572747-------9964898338997077999999999975999866778686349999999999997549


Q ss_pred             C---EEEEEEC
Q ss_conf             7---6899623
Q gi|254780619|r  272 V---KPAEWHS  279 (731)
Q Consensus       272 ~---~v~v~HS  279 (731)
                      .   .+.-+||
T Consensus       267 ~~~v~~~TFHS  277 (684)
T PRK11054        267 TEDITARTFHA  277 (684)
T ss_pred             CCCEEEEEHHH
T ss_conf             99837865999


No 184
>COG1199 DinG Rad3-related DNA helicases [Transcription / DNA replication, recombination, and repair]
Probab=95.47  E-value=0.11  Score=32.10  Aligned_cols=77  Identities=23%  Similarity=0.176  Sum_probs=46.9

Q ss_pred             HHHHHHHCCCCC-CEEEEEHHHCCCCCCCCCCHHHHHHHHHHHHHHH---H----HHHH-------------HHHHHHHH
Q ss_conf             999986212576-5798704430231134520123300034431024---5----5789-------------99998754
Q gi|254780619|r  526 QLQLSAIAKGEI-DIIIGTQLVAKGHNFPRMSLVGVVDGDLGLTNAD---L----RSSE-------------RTFQLLSQ  584 (731)
Q Consensus       526 ~~~~~~~~~~~~-~ilvgTq~i~kg~~fp~v~lv~il~aD~~l~~pd---~----ra~E-------------~~~qll~q  584 (731)
                      +.+++.|..... .++|||.-.+-|.|||+=.+.+|+-+-.-+-.||   .    +..+             .+..-+.|
T Consensus       517 ~~~l~~f~~~~~~~~lv~~gsf~EGVD~~g~~l~~vvI~~lPfp~p~dp~~~~r~~~~~~~g~~~f~~~~l~~A~~~l~Q  596 (654)
T COG1199         517 EELLEKFKASGEGLILVGGGSFWEGVDFPGDALRLVVIVGLPFPNPDDPLLKARLEFLKRLGGDPFEEFYLPPAVIKLRQ  596 (654)
T ss_pred             HHHHHHHHHCCCCEEEEEECCEECCEECCCCCEEEEEEEECCCCCCCCHHHHHHHHHHHHHCCCCCCEEEHHHHHHHHHH
T ss_conf             99999997147864999723310315168876579999826899899899999999998726997103458999999998


Q ss_pred             HHHCCCCCCCC-CEEEEEE
Q ss_conf             31102566788-6899993
Q gi|254780619|r  585 VTGRAGRFGLK-SLGLIQA  602 (731)
Q Consensus       585 v~gRagr~~~~-g~v~iQt  602 (731)
                      ..||+=|+... |-|+|.-
T Consensus       597 avGRlIR~~~D~G~ivllD  615 (654)
T COG1199         597 AVGRLIRSEDDRGVIVLLD  615 (654)
T ss_pred             HHCCCCCCCCCCEEEEEEC
T ss_conf             7430104788716999971


No 185
>PRK00149 dnaA chromosomal replication initiation protein; Reviewed
Probab=95.46  E-value=0.028  Score=36.52  Aligned_cols=116  Identities=17%  Similarity=0.268  Sum_probs=62.8

Q ss_pred             HHHHHHHHHHCCCCCEEEEECCCCHHHHHHHHHHHHHHHH-C--CCCEEEEECCCHHHHHHHHHHHCCCCCEEEEEECCC
Q ss_conf             9999998752048961998447531579999999999851-4--684799715210013445554303897689962355
Q gi|254780619|r  205 DVVEQVVPLCTKGFAVSLISGVTGSGKTEVYLEIVAAVLH-L--GKQVLILLPEISLTSAILERFQKRFGVKPAEWHSSL  281 (731)
Q Consensus       205 ~a~~~i~~~~~~~f~~~LL~GvTGSGKTEVYl~li~~~L~-~--GkqvLiLvPEI~Lt~Q~~~rl~~rF~~~v~v~HS~l  281 (731)
                      .|...+.......|.|.+|||-+|.|||-. |++|...+. +  ++.|+++-.|= .+.+++.-+               
T Consensus       132 aAA~~Va~~pg~~yNPLfIyG~~GlGKTHL-l~AIgn~~~~~~p~~~v~Y~tae~-F~~~~v~al---------------  194 (447)
T PRK00149        132 AAALAVAENPGKAYNPLFIYGGVGLGKTHL-LHAIGNYILEKNPNAKVVYVSSEK-FTNDFVKAL---------------  194 (447)
T ss_pred             HHHHHHHHCCCCCCCCEEEECCCCCCHHHH-HHHHHHHHHHHCCCCEEEEEEHHH-HHHHHHHHH---------------
T ss_conf             999999837676778558977998878899-999999999858997289954999-999999998---------------


Q ss_pred             CCHHHHHHHHHHHCCCCEEEEECCHHHH-HHHCCCEEEEEEECCCCCCHHCC-CCCCCHHHHHHHHHHHCCCCEECCCCC
Q ss_conf             7235667899997199739994001211-00100013677405532100002-443224899999751103210000245
Q gi|254780619|r  282 STSMREKIWRQVARGAISVIVGVRSALF-LPFKKLGLIVIDEEHDISYKQEE-GILYNARDMSIVRGKIESFPVVLVSAT  359 (731)
Q Consensus       282 s~~eR~~~w~~i~~G~~~IVIGtRSAif-~P~~nLglIIvDEEHd~sykq~~-~pry~aRdvA~~Ra~~~~~~lilgSAT  359 (731)
                                  +++.        ..-| --+.+..+.+||+=|.-+-|+.. .--||.-+-.    ...|-.+|+.|.-
T Consensus       195 ------------~~~~--------~~~Fr~~yr~~DvLliDDiqfl~gk~~tqeeff~~fn~l----~~~~kqiv~tsd~  250 (447)
T PRK00149        195 ------------RNNA--------MEEFKEKYRSVDVLLIDDIQFLAGKEKTQEEFFHTFNAL----HENNKQIVITSDR  250 (447)
T ss_pred             ------------HCCC--------HHHHHHHHHCCCEEEECHHHHHHCCHHHHHHHHHHHHHH----HHCCCEEEEECCC
T ss_conf             ------------5186--------999999997288543214888605577999999999999----9849968995788


Q ss_pred             CC
Q ss_conf             43
Q gi|254780619|r  360 PS  361 (731)
Q Consensus       360 PS  361 (731)
                      |.
T Consensus       251 ~P  252 (447)
T PRK00149        251 PP  252 (447)
T ss_pred             CH
T ss_conf             96


No 186
>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=95.41  E-value=0.1  Score=32.18  Aligned_cols=158  Identities=21%  Similarity=0.255  Sum_probs=84.0

Q ss_pred             HHHHHHHCCCCCHH--HHCCCCCCCCHHHHHHHHHHHCCCCCCEEEEEH-HHCCCCCCCCCCHHHHHHHHHHHHHHH---
Q ss_conf             88885204852000--102321135867899999862125765798704-430231134520123300034431024---
Q gi|254780619|r  498 IAEEVCEYFPLARI--SILSSDLEGGGGRLQLQLSAIAKGEIDIIIGTQ-LVAKGHNFPRMSLVGVVDGDLGLTNAD---  571 (731)
Q Consensus       498 ~~e~l~~~fp~~~v--~~~d~d~~~~~~~~~~~~~~~~~~~~~ilvgTq-~i~kg~~fp~v~lv~il~aD~~l~~pd---  571 (731)
                      =.+-+++-|-+.||  ..+|+=.  +.....+++.++.+|++||||||+ ++.|...|-|++|++| |=.+=+..-+   
T Consensus       577 Hf~tf~~RF~~fPv~I~~LSRF~--~~~E~~~iL~~la~G~iDI~IGTH~lL~k~v~FKdLGLlIi-DEEQRFGV~~KE~  653 (997)
T TIGR00580       577 HFETFKERFANFPVTIELLSRFR--SAKEKKEILKELASGKIDILIGTHKLLQKDVKFKDLGLLII-DEEQRFGVKQKEK  653 (997)
T ss_pred             HHHHHHHHHCCCCEEEEECCCCC--CCHHHHHHHHHHHCCCEEEEECCHHHHCCCEEEECCCCEEE-ECCCCCCCCHHHH
T ss_conf             88999997378981687527756--73789999999755942266301041278546863864698-3143488311555


Q ss_pred             ---HHHH-----------HHHHHH-HHHHHHCCCCCCC-CCEEEEEECCCCC--HHHHHHHH-------------CCHHH
Q ss_conf             ---5578-----------999998-7543110256678-8689999329864--88899995-------------89799
Q gi|254780619|r  572 ---LRSS-----------ERTFQL-LSQVTGRAGRFGL-KSLGLIQAYQPTH--PVMQALVS-------------GDADS  620 (731)
Q Consensus       572 ---~ra~-----------E~~~ql-l~qv~gRagr~~~-~g~v~iQt~~p~~--~~~~~~~~-------------~d~~~  620 (731)
                         .|++           =||.+| |.++-+.+==.-. .+|.=|+||--++  .+++.++.             ++-+.
T Consensus       654 lK~~~~~VDvLtlsATPIPRTL~MSl~g~RdlS~I~TPP~~R~pv~T~v~~~~~~~~~~AI~rEL~RgGQvFyv~Nrie~  733 (997)
T TIGR00580       654 LKELKTSVDVLTLSATPIPRTLHMSLSGIRDLSIIATPPEDRLPVRTFVMEYDDELVREAIRRELLRGGQVFYVHNRIES  733 (997)
T ss_pred             HCCCCCCCCEEEEECCCCHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCHHHHHHHHHHHHCCCCEEEEEECCCCC
T ss_conf             30015676567633789605589998755332210578887742488774278689999999753139818998088135


Q ss_pred             HHHHHHHHHHHCCCCCCHHEEEEEEECCCHHHHHHHHHHHHH
Q ss_conf             999999999981888801189998845998999999999998
Q gi|254780619|r  621 FYESEIRARESVNLPPFGRLAAVIISGTKYQEVENYAYNLKE  662 (731)
Q Consensus       621 f~~~el~~R~~~~~PPf~~~~~i~~~~~~~~~~~~~~~~~~~  662 (731)
                      ..+-+-..|   .+=|--|++... .-..+++.++...++.+
T Consensus       734 i~~~~~~l~---~LVP~arIaiaH-GqM~e~eLE~~m~~F~~  771 (997)
T TIGR00580       734 IEKLKTQLR---ELVPEARIAIAH-GQMTENELEEVMLEFYK  771 (997)
T ss_pred             HHHHHHHHH---HCCCCEEEEEEE-CCCCHHHHHHHHHHHHC
T ss_conf             789999998---508432678883-35684568999998626


No 187
>PRK08006 replicative DNA helicase; Provisional
Probab=95.39  E-value=0.26  Score=29.10  Aligned_cols=133  Identities=21%  Similarity=0.228  Sum_probs=80.0

Q ss_pred             CEEEEECCCCHHHHHHHHHHHHH-HHHCCCCEEEEECCCHHHHHHHHHHHCCC-CCEE-EEEECCCCCHHHHHHHH--HH
Q ss_conf             61998447531579999999999-85146847997152100134455543038-9768-99623557235667899--99
Q gi|254780619|r  219 AVSLISGVTGSGKTEVYLEIVAA-VLHLGKQVLILLPEISLTSAILERFQKRF-GVKP-AEWHSSLSTSMREKIWR--QV  293 (731)
Q Consensus       219 ~~~LL~GvTGSGKTEVYl~li~~-~L~~GkqvLiLvPEI~Lt~Q~~~rl~~rF-~~~v-~v~HS~ls~~eR~~~w~--~i  293 (731)
                      ..+.|=|-+|.|||-..+.++.. ++.+|+.|++.-.|-+ ..|+..|+-... +... -+..+.+++.+....-.  ..
T Consensus       225 ~LiviaaRPsmGKTalalnia~~~a~~~~~~V~~fSlEMs-~~ql~~Rlla~~s~v~~~~i~~g~l~~~e~~~l~~~~~~  303 (471)
T PRK08006        225 DLIIVAARPSMGKTTFAMNLCENAAMLQDKPVLIFSLEMP-GEQIMMRMLASLSRVDQTRIRTGQLDDEDWARISGTMGI  303 (471)
T ss_pred             CEEEEEECCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCC-HHHHHHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHHHHH
T ss_conf             3899994699876999999999999866995799816799-999999999974477755453688799999999999999


Q ss_pred             HCCCCEEEEECCHHHH------------HHHCCCEEEEEEECCCCCCHHCCC-CCC-CHH--HHH------HHHHHHCCC
Q ss_conf             7199739994001211------------001000136774055321000024-432-248--999------997511032
Q gi|254780619|r  294 ARGAISVIVGVRSALF------------LPFKKLGLIVIDEEHDISYKQEEG-ILY-NAR--DMS------IVRGKIESF  351 (731)
Q Consensus       294 ~~G~~~IVIGtRSAif------------~P~~nLglIIvDEEHd~sykq~~~-pry-~aR--dvA------~~Ra~~~~~  351 (731)
                      ......+.|=..+.+=            -....+++||||      |=|-.. +.. +-|  +++      ...|+..+|
T Consensus       304 ~~~~~~l~idd~~~~t~~~i~a~~r~~~~~~~gl~lvvID------YLqL~~~~~~~~~r~~ei~~isr~lK~lAkel~i  377 (471)
T PRK08006        304 LLEKRNMYIDDSSGLTPTEVRSRARRIFREHGGLSLIMID------YLQLMRVPSLSDNRTLEIAEISRSLKALAKELQV  377 (471)
T ss_pred             HHHCCCEEEECCCCCCHHHHHHHHHHHHHHCCCCCEEEEE------HHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHCC
T ss_conf             9751885773689998999999999999864898689963------8866167874410668999999999999999699


Q ss_pred             CEECCCC
Q ss_conf             1000024
Q gi|254780619|r  352 PVVLVSA  358 (731)
Q Consensus       352 ~lilgSA  358 (731)
                      |||+.|-
T Consensus       378 pVi~LsQ  384 (471)
T PRK08006        378 PVVALSQ  384 (471)
T ss_pred             CEEEECC
T ss_conf             6899701


No 188
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=95.37  E-value=0.0074  Score=40.95  Aligned_cols=40  Identities=25%  Similarity=0.699  Sum_probs=31.2

Q ss_pred             HCCCCCCCCCC---------CCCCCCCEEEEECCCCCCEECHHHCCCCCCCCCCCCC
Q ss_conf             00235654343---------1014652012113578320000210244655566678
Q gi|254780619|r  436 LTLCQVCGNRL---------KCLHCSCWLVEHRSKKKLYCHQCGHSAIYSQSCVVCG  483 (731)
Q Consensus       436 ~~~C~~Cg~~~---------~C~~C~~~l~~h~~~~~l~Ch~Cg~~~~~~~~Cp~Cg  483 (731)
                      .-.|.+||+.+         .||+|+--+.+       +|+.|- +...+.+||+||
T Consensus         9 ~~~CtSCg~~i~p~e~~v~F~CPnCGe~~I~-------Rc~~CR-k~g~~Y~Cp~CG   57 (61)
T COG2888           9 PPVCTSCGREIAPGETAVKFPCPNCGEVEIY-------RCAKCR-KLGNPYRCPKCG   57 (61)
T ss_pred             CCEECCCCCEECCCCCEEEEECCCCCCEEEE-------HHHHHH-HCCCCEECCCCC
T ss_conf             8521237877046875008648999824241-------056687-749944788767


No 189
>COG0593 DnaA ATPase involved in DNA replication initiation [DNA replication, recombination, and repair]
Probab=95.31  E-value=0.22  Score=29.67  Aligned_cols=39  Identities=26%  Similarity=0.327  Sum_probs=25.6

Q ss_pred             HHHHHCCCCCEEEEECCCCHHHHHHHHHHHH-HHHHCCCCE
Q ss_conf             9875204896199844753157999999999-985146847
Q gi|254780619|r  210 VVPLCTKGFAVSLISGVTGSGKTEVYLEIVA-AVLHLGKQV  249 (731)
Q Consensus       210 i~~~~~~~f~~~LL~GvTGSGKTEVYl~li~-~~L~~Gkqv  249 (731)
                      +.......+.+.+|||-+|+|||-. ++++. .+++.+..+
T Consensus       105 va~~~g~~~nplfi~G~~GlGKTHL-l~Aign~~~~~~~~a  144 (408)
T COG0593         105 VAENPGGAYNPLFIYGGVGLGKTHL-LQAIGNEALANGPNA  144 (408)
T ss_pred             HHHCCCCCCCCEEEECCCCCCHHHH-HHHHHHHHHHHCCCC
T ss_conf             8756688689579987999978999-999999998629986


No 190
>PRK04837 ATP-dependent RNA helicase RhlB; Provisional
Probab=95.29  E-value=0.17  Score=30.53  Aligned_cols=119  Identities=14%  Similarity=0.189  Sum_probs=73.8

Q ss_pred             CHHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHCCCCCEEEEEECCCCCHHHHHHHHHHHCCCCEEEEECCHH
Q ss_conf             31579999999999851468479971521001344555430389768996235572356678999971997399940012
Q gi|254780619|r  228 GSGKTEVYLEIVAAVLHLGKQVLILLPEISLTSAILERFQKRFGVKPAEWHSSLSTSMREKIWRQVARGAISVIVGVRSA  307 (731)
Q Consensus       228 GSGKTEVYl~li~~~L~~GkqvLiLvPEI~Lt~Q~~~rl~~rF~~~v~v~HS~ls~~eR~~~w~~i~~G~~~IVIGtRSA  307 (731)
                      ..-|....+.++++.  ...+++|-+....-+..+...|. ..|..++.+||.++..+|..+..+-++|+..|+|.|=-|
T Consensus       240 ~~~K~~~L~~ll~~~--~~~k~iIF~nt~~~~~~l~~~L~-~~g~~~~~lhg~~~q~~R~~~l~~F~~g~~~vLVaTDva  316 (423)
T PRK04837        240 NEEKMRLLQTLIEEE--WPDRAIIFANTKHRCEEIWGHLA-ADGHRVGLLTGDVPQKKRLRILEQFTRGDLDILVATDVA  316 (423)
T ss_pred             HHHHHHHHHHHHHHH--CCCCEEEECCHHHHHHHHHHHHH-HCCCCEEEECCCCCHHHHHHHHHHHHCCCCCEEEEHHHH
T ss_conf             277999999999840--88746886162888999999997-659817872254579999999999976999899870043


Q ss_pred             HH-HHHCCCEEEEE-EECCC-CCCHHCCCCCCCHHHHHHHHHHHCCCCEECCC
Q ss_conf             11-00100013677-40553-21000024432248999997511032100002
Q gi|254780619|r  308 LF-LPFKKLGLIVI-DEEHD-ISYKQEEGILYNARDMSIVRGKIESFPVVLVS  357 (731)
Q Consensus       308 if-~P~~nLglIIv-DEEHd-~sykq~~~pry~aRdvA~~Ra~~~~~~lilgS  357 (731)
                      .= +-++++..||- |=-.| .+|-.-     -.|   -=||-..|..+-|.+
T Consensus       317 aRGLDi~~V~~VInyD~P~~~~~YiHR-----iGR---TgRaG~~G~aitf~~  361 (423)
T PRK04837        317 ARGLHIPDVTHVFNYDLPDDCEDYVHR-----IGR---TGRAGASGHSISFAC  361 (423)
T ss_pred             HCCCCCCCCCEEEEECCCCCHHHEECC-----CCH---HHCCCCCEEEEEEEC
T ss_conf             277772679889996998974551004-----654---127899468999873


No 191
>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=95.23  E-value=0.058  Score=34.13  Aligned_cols=130  Identities=21%  Similarity=0.307  Sum_probs=81.2

Q ss_pred             CCCCHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHHHHHHHHHHCC-------------CCEEEEECCCHHHHHHH
Q ss_conf             66883789999999875204896199844753157999999999985146-------------84799715210013445
Q gi|254780619|r  197 PILDKNQQDVVEQVVPLCTKGFAVSLISGVTGSGKTEVYLEIVAAVLHLG-------------KQVLILLPEISLTSAIL  263 (731)
Q Consensus       197 ~~Lt~eQ~~a~~~i~~~~~~~f~~~LL~GvTGSGKTEVYl~li~~~L~~G-------------kqvLiLvPEI~Lt~Q~~  263 (731)
                      ..|..+|++|+..+...     .+++|-|-.|.|||=|-=-.++-+-+-+             ..|++-+|    |-.-.
T Consensus       349 ~~l~~~Qk~AL~~~~~~-----Kv~iLTGGPGTGKtT~t~~i~~~~~~~~gl~l~~~~~vndd~~v~LaAP----TGrAA  419 (769)
T TIGR01448       349 LKLSEEQKEALKTAIQD-----KVVILTGGPGTGKTTITKAIIELYEELKGLDLDKDDYVNDDLPVVLAAP----TGRAA  419 (769)
T ss_pred             CCHHHHHHHHHHHHHCC-----CEEEEECCCCCCHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCEEEEECC----CHHHH
T ss_conf             77068899999998609-----4899857788861689999999998716877553124567764887377----43788


Q ss_pred             HHHHCCCCCEEEEEECCCCCHHHHHHHHHHHCCCCEEEEECCHHHHHHHCCCEEEEEEECCCCCCHHCCCCCCCHHHHHH
Q ss_conf             55430389768996235572356678999971997399940012110010001367740553210000244322489999
Q gi|254780619|r  264 ERFQKRFGVKPAEWHSSLSTSMREKIWRQVARGAISVIVGVRSALFLPFKKLGLIVIDEEHDISYKQEEGILYNARDMSI  343 (731)
Q Consensus       264 ~rl~~rF~~~v~v~HS~ls~~eR~~~w~~i~~G~~~IVIGtRSAif~P~~nLglIIvDEEHd~sykq~~~pry~aRdvA~  343 (731)
                      +|+.+.-|..-.-.|+-|.-...-....+...              =| -|-.||||||-.             =-|-++
T Consensus       420 kRl~E~TG~~a~TIHRLlG~~~~~~~~~k~~~--------------~~-~~~DL~IvDE~S-------------M~Dt~L  471 (769)
T TIGR01448       420 KRLAEVTGLEALTIHRLLGYGSDTKSENKNLE--------------DP-IDADLLIVDESS-------------MVDTWL  471 (769)
T ss_pred             HHCCCCCCCHHHHHHHHHCCCCCCCCCCHHHC--------------CC-CCCCEEEEECCC-------------HHHHHH
T ss_conf             85110026212347786368988873211011--------------34-787769981462-------------188999


Q ss_pred             HHHHH----CCCCEECCCCC---CCHH
Q ss_conf             97511----03210000245---4324
Q gi|254780619|r  344 VRGKI----ESFPVVLVSAT---PSIE  363 (731)
Q Consensus       344 ~Ra~~----~~~~lilgSAT---PSle  363 (731)
                      +..-+    .+|.|+|..-+   ||+.
T Consensus       472 ~~~lL~a~P~~a~lllVGD~DQLPSV~  498 (769)
T TIGR01448       472 ASSLLAAVPDHARLLLVGDADQLPSVG  498 (769)
T ss_pred             HHHHHHHCCCCCEEEEECCCCCCCCCC
T ss_conf             999986179777798883768889886


No 192
>pfam04216 FdhE Protein involved in formate dehydrogenase formation. The function of these proteins is unknown. They may possibly be involved in the formation of formate dehydrogenase.
Probab=95.21  E-value=0.0098  Score=40.01  Aligned_cols=45  Identities=22%  Similarity=0.421  Sum_probs=29.8

Q ss_pred             CCCCCCCCEEE---EEC----CCCCCEECHHHCCCCCCC-CCCCCCCCCEECC
Q ss_conf             31014652012---113----578320000210244655-5666787411001
Q gi|254780619|r  446 LKCLHCSCWLV---EHR----SKKKLYCHQCGHSAIYSQ-SCVVCGSSGKMIA  490 (731)
Q Consensus       446 ~~C~~C~~~l~---~h~----~~~~l~Ch~Cg~~~~~~~-~Cp~Cg~~~~l~~  490 (731)
                      -.||.|+++=+   .+.    ..+.|.|..|+++..+.+ .||.||++..+..
T Consensus       167 ~~CPvCGs~P~~s~~~~~~~~G~Ryl~Cs~C~teW~~~R~~C~~Cg~~~~~~~  219 (283)
T pfam04216       167 GLCPVCGSAPVASVIRGGGAQGLRYLHCSLCETEWHFVRVKCTNCGSTKGLAY  219 (283)
T ss_pred             CCCCCCCCCCHHHEEECCCCCCCEEEECCCCCCCCCCCCCCCCCCCCCCCCCE
T ss_conf             96999998100011313787883688658887832422654799999996430


No 193
>PRK09137 DNA topoisomerase I; Validated
Probab=95.20  E-value=0.03  Score=36.30  Aligned_cols=64  Identities=23%  Similarity=0.503  Sum_probs=38.9

Q ss_pred             EEEEEECCCCEEHHCCC---CCCCCC------------------CCCCCCCCEEEEEC--CCCCCEE---CHHHCCCCCC
Q ss_conf             17997422200000023---565434------------------31014652012113--5783200---0021024465
Q gi|254780619|r  423 QTLLFLNRRGYAPLTLC---QVCGNR------------------LKCLHCSCWLVEHR--SKKKLYC---HQCGHSAIYS  476 (731)
Q Consensus       423 qvll~lnRrGya~~~~C---~~Cg~~------------------~~C~~C~~~l~~h~--~~~~l~C---h~Cg~~~~~~  476 (731)
                      +.++-..|+|.  |+.|   .+|.++                  ..||.|+.+|+.-+  .+..+.|   ..|.+..++.
T Consensus       598 ~l~~r~g~~G~--F~~Cs~yP~Ck~t~~~~~~~~~~~~~~~~~~~~Cp~Cg~~mv~k~gr~G~f~~Cs~yP~Ck~~~~~~  675 (761)
T PRK09137        598 PLSIKLGKRGR--FIACTGYPECKYTRNLDEDEEEAAEEEVVEGRKCPKCGSPLHIKQGRYGKFIGCSNYPECKHMEPLE  675 (761)
T ss_pred             EEEEEECCCCC--EEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCEEECCCCCCCCCCCCCC
T ss_conf             23899558776--5766798766675767765555556665578869889971278614676345337998766777666


Q ss_pred             ------CCCCCCCCCCEEC
Q ss_conf             ------5566678741100
Q gi|254780619|r  477 ------QSCVVCGSSGKMI  489 (731)
Q Consensus       477 ------~~Cp~Cg~~~~l~  489 (731)
                            -.||.||+. .+.
T Consensus       676 k~~~~~~~CP~C~~g-~~~  693 (761)
T PRK09137        676 KPKDTGVTCPKCKKG-ELV  693 (761)
T ss_pred             CCCCCCCCCCCCCCC-CEE
T ss_conf             766677619899998-777


No 194
>COG0210 UvrD Superfamily I DNA and RNA helicases [DNA replication, recombination, and repair]
Probab=95.18  E-value=0.068  Score=33.57  Aligned_cols=26  Identities=38%  Similarity=0.581  Sum_probs=18.1

Q ss_pred             CEEEEEHHHCCCCCCCCCCHHHHHHH
Q ss_conf             57987044302311345201233000
Q gi|254780619|r  538 DIIIGTQLVAKGHNFPRMSLVGVVDG  563 (731)
Q Consensus       538 ~ilvgTq~i~kg~~fp~v~lv~il~a  563 (731)
                      .|-+-|==-+||+.||.|-++|+-+.
T Consensus       554 ~V~lmT~H~aKGlEf~~Vfl~g~~eg  579 (655)
T COG0210         554 QVNLMTIHAAKGLEFPYVFLVGLEEG  579 (655)
T ss_pred             CEEEEEHHHHCCCCCCEEEEECCCCC
T ss_conf             46997201313776875678555368


No 195
>PRK04023 DNA polymerase II large subunit; Validated
Probab=95.12  E-value=0.022  Score=37.36  Aligned_cols=61  Identities=20%  Similarity=0.526  Sum_probs=40.2

Q ss_pred             HHHHHHCCCCEEEEEECCCCEEHHCCCCCCCCC---CCCCCCCCEEEEECCCCCCEECHHHCCCCCCCCCCCCCCC
Q ss_conf             998862265517997422200000023565434---3101465201211357832000021024465556667874
Q gi|254780619|r  413 GIRHTLARNEQTLLFLNRRGYAPLTLCQVCGNR---LKCLHCSCWLVEHRSKKKLYCHQCGHSAIYSQSCVVCGSS  485 (731)
Q Consensus       413 ~i~~~l~~g~qvll~lnRrGya~~~~C~~Cg~~---~~C~~C~~~l~~h~~~~~l~Ch~Cg~~~~~~~~Cp~Cg~~  485 (731)
                      .|.++.++++.+-+-+      +.-.|.+||..   .+|++|+..     ......|..||.... ...|+.|+..
T Consensus       616 ~I~~Aa~~~g~i~vev------g~R~Cp~Cg~eT~~~~C~~CG~~-----T~~~~~c~~C~~~~~-~~~c~~c~~~  679 (1128)
T PRK04023        616 SINKAAEKGGTIEVEV------GNRKCPSCGKETFYRRCPFCGTH-----TEPVYRCPRCGIEVD-EEVCPKCGRE  679 (1128)
T ss_pred             HHHHHHHCCCCEEEEE------EEEECCCCCCCCCCCCCCCCCCC-----CCCCCCCCCCCCCCC-CCCCCCCCCC
T ss_conf             3999983369369998------20288999983575578777996-----654324776666556-6535445776


No 196
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=95.12  E-value=0.0087  Score=40.39  Aligned_cols=33  Identities=24%  Similarity=0.474  Sum_probs=26.4

Q ss_pred             CCCCEECHHHCCCCCCC-CCCCCCCCCEECCCCC
Q ss_conf             78320000210244655-5666787411001354
Q gi|254780619|r  461 KKKLYCHQCGHSAIYSQ-SCVVCGSSGKMIACGF  493 (731)
Q Consensus       461 ~~~l~Ch~Cg~~~~~~~-~Cp~Cg~~~~l~~~G~  493 (731)
                      .+.|.|..|+.+..+.+ +|+.||++..+.+.++
T Consensus       210 ~RyL~CslC~teW~~~R~~C~~C~~~~~l~y~~~  243 (307)
T PRK03564        210 LRYLHCNLCESEWHVVRVKCSNCEQSGKLHYWSL  243 (307)
T ss_pred             EEEEECCCCCCCCCCCCCCCCCCCCCCCEEEEEE
T ss_conf             0688648777740213534688889888203666


No 197
>COG0556 UvrB Helicase subunit of the DNA excision repair complex [DNA replication, recombination, and repair]
Probab=95.10  E-value=0.21  Score=29.89  Aligned_cols=118  Identities=22%  Similarity=0.349  Sum_probs=87.0

Q ss_pred             CCHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHHHHHHHHHHC-CCCEEEEECCCHHHHHHHHHHHCCCCCEEEEE
Q ss_conf             88378999999987520489619984475315799999999998514-68479971521001344555430389768996
Q gi|254780619|r  199 LDKNQQDVVEQVVPLCTKGFAVSLISGVTGSGKTEVYLEIVAAVLHL-GKQVLILLPEISLTSAILERFQKRFGVKPAEW  277 (731)
Q Consensus       199 Lt~eQ~~a~~~i~~~~~~~f~~~LL~GvTGSGKTEVYl~li~~~L~~-GkqvLiLvPEI~Lt~Q~~~rl~~rF~~~v~v~  277 (731)
                      -+.+|-.|++++.....++-.--.|-||||||||=-    |+.++++ ++-.|||.|.--|+.|++..|++.|+++-+.|
T Consensus        13 PaGDQP~AI~~Lv~gi~~g~~~QtLLGvTGSGKTfT----~AnVI~~~~rPtLV~AhNKTLAaQLy~Efk~fFP~NaVEY   88 (663)
T COG0556          13 PAGDQPEAIAELVEGIENGLKHQTLLGVTGSGKTFT----MANVIAKVQRPTLVLAHNKTLAAQLYSEFKEFFPENAVEY   88 (663)
T ss_pred             CCCCCHHHHHHHHHHHHCCCEEEEEEEECCCCCHHH----HHHHHHHHCCCEEEEECCHHHHHHHHHHHHHHCCCCCEEE
T ss_conf             999867999999988863860258862036883107----9999998689719982555479999999997686764588


Q ss_pred             E-CC----------------------CC---CHHHHHHHHHHHCCCCEEEEECCHHHH---HHHCCCEEEEE
Q ss_conf             2-35----------------------57---235667899997199739994001211---00100013677
Q gi|254780619|r  278 H-SS----------------------LS---TSMREKIWRQVARGAISVIVGVRSALF---LPFKKLGLIVI  320 (731)
Q Consensus       278 H-S~----------------------ls---~~eR~~~w~~i~~G~~~IVIGtRSAif---~P~~nLglIIv  320 (731)
                      - |.                      .+   +.-|...-.++..-+--|||++-|+++   .|-.-+.+.+.
T Consensus        89 FVSYYDYYQPEAYvp~tDtyIEKdasiNdeId~mR~SAt~sLleR~DVIVVaSVScIYGlG~P~~y~~~~~~  160 (663)
T COG0556          89 FVSYYDYYQPEAYVPSTDTYIEKDASINDEIDRLRHSATRSLLERRDVIVVASVSCIYGLGSPEEYLKMMLS  160 (663)
T ss_pred             EEEECCCCCCCCCCCCCCCEEECCCCHHHHHHHHHHHHHHHHHCCCCEEEEEEEEEECCCCCHHHHHHHEEE
T ss_conf             864001468513457777357536506789999999988877504786999987651048986998753799


No 198
>COG1110 Reverse gyrase [DNA replication, recombination, and repair]
Probab=95.10  E-value=0.023  Score=37.19  Aligned_cols=55  Identities=25%  Similarity=0.477  Sum_probs=39.8

Q ss_pred             HCCCCEEEEECC---CHHHHHHHHHHHCCCCCEEEEEECCCCCHHHHHHHHHHHCCCCEEEEEC
Q ss_conf             146847997152---1001344555430389768996235572356678999971997399940
Q gi|254780619|r  244 HLGKQVLILLPE---ISLTSAILERFQKRFGVKPAEWHSSLSTSMREKIWRQVARGAISVIVGV  304 (731)
Q Consensus       244 ~~GkqvLiLvPE---I~Lt~Q~~~rl~~rF~~~v~v~HS~ls~~eR~~~w~~i~~G~~~IVIGt  304 (731)
                      .-|...||.||-   ...+..+.+++++ .|.++..+||+     +...+..-..|++++.||.
T Consensus       333 ~lG~GgLIfV~~d~G~e~aeel~e~Lr~-~Gi~a~~~~a~-----~~~~le~F~~GeidvLVGv  390 (1187)
T COG1110         333 KLGDGGLIFVPIDYGREKAEELAEYLRS-HGINAELIHAE-----KEEALEDFEEGEVDVLVGV  390 (1187)
T ss_pred             HHCCCEEEEEECHHHHHHHHHHHHHHHH-CCCEEEEEECC-----CHHHHHHHCCCCEEEEEEE
T ss_conf             8489749999717738999999999986-69607986232-----0224566506760179985


No 199
>PRK10416 cell division protein FtsY; Provisional
Probab=95.10  E-value=0.29  Score=28.77  Aligned_cols=39  Identities=28%  Similarity=0.352  Sum_probs=32.5

Q ss_pred             CCCEEEEECCCCHHHHHHHHHHHHHHHHCCCCEEEEECC
Q ss_conf             896199844753157999999999985146847997152
Q gi|254780619|r  217 GFAVSLISGVTGSGKTEVYLEIVAAVLHLGKQVLILLPE  255 (731)
Q Consensus       217 ~f~~~LL~GvTGSGKTEVYl~li~~~L~~GkqvLiLvPE  255 (731)
                      +..+.|+-||.|||||----.++...-++|+.|++-.=.
T Consensus       294 ~P~VIl~vGvNG~GKTTTigKLA~~~~~~gkkVllaA~D  332 (499)
T PRK10416        294 TPFVILMVGVNGVGKTTTIGKLARQFEQQGKSVMLAAGD  332 (499)
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHHHHHHCCCCEEEEEEC
T ss_conf             987999974787878989999999999779953788406


No 200
>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=95.05  E-value=0.12  Score=31.68  Aligned_cols=265  Identities=18%  Similarity=0.196  Sum_probs=143.8

Q ss_pred             CCCHHHHHHHHHHHHHHHHCCCCEEEEECCCHHHH---HHHHHHHCCCCCEEEEEECCCCCHHHHHHHHHHHCCCCEEEE
Q ss_conf             75315799999999998514684799715210013---445554303897689962355723566789999719973999
Q gi|254780619|r  226 VTGSGKTEVYLEIVAAVLHLGKQVLILLPEISLTS---AILERFQKRFGVKPAEWHSSLSTSMREKIWRQVARGAISVIV  302 (731)
Q Consensus       226 vTGSGKTEVYl~li~~~L~~GkqvLiLvPEI~Lt~---Q~~~rl~~rF~~~v~v~HS~ls~~eR~~~w~~i~~G~~~IVI  302 (731)
                      =||-|||.|..-.+---==.||+|-|.-=-==|+.   .+..++-.++|-.|.+.-|+|++.+|..+|.      ++|+=
T Consensus        81 kTGEGKTL~AtLpaYLNAL~GkGVHvVTVNdYLA~RD~e~m~~v~~FLGL~VGl~~~~m~~~eRr~aY~------cDITY  154 (904)
T TIGR00963        81 KTGEGKTLVATLPAYLNALTGKGVHVVTVNDYLARRDAEWMGQVYRFLGLSVGLILSSMSPEERREAYA------CDITY  154 (904)
T ss_pred             CCCCCHHHHHHHHHHHHHHCCCCCEEEEECCHHHHHHHHHHHHHHHHCCCEEEEECCCCCHHHHHHHHC------CCEEE
T ss_conf             148862899999999876517962799635044488899878999684936888617998589999854------98165


Q ss_pred             EC----------------------CHHHHHHHCCCEEEEEEE-----------C-CCCCCH-----------HCCCCCCC
Q ss_conf             40----------------------012110010001367740-----------5-532100-----------00244322
Q gi|254780619|r  303 GV----------------------RSALFLPFKKLGLIVIDE-----------E-HDISYK-----------QEEGILYN  337 (731)
Q Consensus       303 Gt----------------------RSAif~P~~nLglIIvDE-----------E-Hd~syk-----------q~~~pry~  337 (731)
                      ||                      |.=-||=+.-..-|.|||           | +-.-|.           -+..|  -
T Consensus       155 ~TNnELGFDYLRDNM~~~~ee~vqR~f~FAIIDEVDSILIDEARTPLIISGpae~~~~~Y~ev~~~~~~l~e~~~~p--~  232 (904)
T TIGR00963       155 GTNNELGFDYLRDNMALSKEEKVQRPFNFAIIDEVDSILIDEARTPLIISGPAEKSTEKYLEVNKLVDPLKETDKLP--Q  232 (904)
T ss_pred             ECCCCCCHHHHHHHHHCCHHHHHCCCCCCEEEEEECCEEECCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHCCCCCC--C
T ss_conf             32654202466676411501210167222688642446423336865235766786301001787886641665575--0


Q ss_pred             HHHHHHHHH-H-HCCCC-------EE-------C-CCCCCCHH-------HHHHHHHH-HHHHHC----------CCCCC
Q ss_conf             489999975-1-10321-------00-------0-02454324-------67753212-344412----------43223
Q gi|254780619|r  338 ARDMSIVRG-K-IESFP-------VV-------L-VSATPSIE-------SRVNGISR-RYHSVH----------LSTRY  382 (731)
Q Consensus       338 aRdvA~~Ra-~-~~~~~-------li-------l-gSATPSle-------s~~~~~~g-~~~~~~----------l~~R~  382 (731)
                      |-++|-... . -.+-.       |.       . +=-.=.++       ++|...+. +.+++.          -..-|
T Consensus       233 a~~~~~~l~e~W~~dY~vDeK~r~v~Lte~G~~~WaE~~L~~~g~~~~~~nLyd~~n~~~~hyi~nALkA~~lf~kDvdY  312 (904)
T TIGR00963       233 ANEVAKALKEKWDVDYEVDEKNRNVLLTEKGMKKWAEDLLGVDGIIKGAVNLYDLENSPLIHYILNALKAKELFEKDVDY  312 (904)
T ss_pred             HHHHHHHHHHHCCCCCEEECCCCEEEECCCCHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCE
T ss_conf             44568998631167703510417465140117899987532432144301301245334588899999999987439835


Q ss_pred             CCCCCCCCEECCC-CCCCCCCCCCCCHHHHHHHHHHHCCCCEEEEEECCCCEEHHCCCCCCCCCCCCCCCCCEEEEECCC
Q ss_conf             6765433211022-223322245479899999988622655179974222000000235654343101465201211357
Q gi|254780619|r  383 RNSALPHLQVIDM-RGQTIAQGKSLSPEMIDGIRHTLARNEQTLLFLNRRGYAPLTLCQVCGNRLKCLHCSCWLVEHRSK  461 (731)
Q Consensus       383 ~~~~~P~i~ivDm-~~~~~~~~~~lS~~l~~~i~~~l~~g~qvll~lnRrGya~~~~C~~Cg~~~~C~~C~~~l~~h~~~  461 (731)
                      -- .=-+|.|||= +.+.+ .|+..|+-|++||    +++|.|=|--=-.=.|+                   -||   .
T Consensus       313 IV-~dgeV~IVDEFTGRim-~GRR~SdGLHQAi----EAKE~V~I~~En~T~At-------------------ITy---Q  364 (904)
T TIGR00963       313 IV-RDGEVVIVDEFTGRIM-EGRRWSDGLHQAI----EAKEGVEIQNENQTLAT-------------------ITY---Q  364 (904)
T ss_pred             EE-ECCEEEEEEEECCCCC-CCCCCCCHHHHHH----HHHCCCEEECCCCEEEE-------------------HHH---H
T ss_conf             88-8887899873058338-8961242257999----97468601035522440-------------------445---7


Q ss_pred             CCCEECHHHCCCCCCCCCCCCCCCCEECCCCCCHHHHHH-HHHHCC-------CC-CHHHHCCC-CC--CCCHHHHHHH-
Q ss_conf             832000021024465556667874110013542899888-852048-------52-00010232-11--3586789999-
Q gi|254780619|r  462 KKLYCHQCGHSAIYSQSCVVCGSSGKMIACGFGIERIAE-EVCEYF-------PL-ARISILSS-DL--EGGGGRLQLQ-  528 (731)
Q Consensus       462 ~~l~Ch~Cg~~~~~~~~Cp~Cg~~~~l~~~G~Gte~~~e-~l~~~f-------p~-~~v~~~d~-d~--~~~~~~~~~~-  528 (731)
                      |.            ..-=      .+|... +||-++|+ |+.+.+       |. -++.|-|. |.  .+-..++.-+ 
T Consensus       365 Nf------------FrlY------~KLsGM-TGTA~TE~~EF~~IYnL~Vv~vPTNrp~~R~D~~DlvY~te~~Kw~Av~  425 (904)
T TIGR00963       365 NF------------FRLY------EKLSGM-TGTAKTEEEEFEKIYNLEVVVVPTNRPVIRKDLPDLVYKTEEEKWKAVV  425 (904)
T ss_pred             HH------------HHHH------HHHCCC-CCCHHHHHHHHHCCCCCEEEECCCCCCCCCCCCCCCEECCHHHHHHHHH
T ss_conf             67------------6542------654468-7756899998404577513551667723446777734647688999999


Q ss_pred             ---HHHHCCCCCCEEEEEHHH
Q ss_conf             ---986212576579870443
Q gi|254780619|r  529 ---LSAIAKGEIDIIIGTQLV  546 (731)
Q Consensus       529 ---~~~~~~~~~~ilvgTq~i  546 (731)
                         .+.-..|+| |||||.-|
T Consensus       426 ~e~~~~h~~GqP-vLvGT~sv  445 (904)
T TIGR00963       426 DEIKEIHAKGQP-VLVGTTSV  445 (904)
T ss_pred             HHHHHHHHCCCC-EEEEECCH
T ss_conf             999998746898-77752217


No 201
>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=95.03  E-value=0.063  Score=33.85  Aligned_cols=146  Identities=21%  Similarity=0.332  Sum_probs=104.4

Q ss_pred             CCHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHHHHHHHHHHC-CCCEEEEECCCHHHHHHHHHHHCCCCCEEEEE
Q ss_conf             88378999999987520489619984475315799999999998514-68479971521001344555430389768996
Q gi|254780619|r  199 LDKNQQDVVEQVVPLCTKGFAVSLISGVTGSGKTEVYLEIVAAVLHL-GKQVLILLPEISLTSAILERFQKRFGVKPAEW  277 (731)
Q Consensus       199 Lt~eQ~~a~~~i~~~~~~~f~~~LL~GvTGSGKTEVYl~li~~~L~~-GkqvLiLvPEI~Lt~Q~~~rl~~rF~~~v~v~  277 (731)
                      -+.+|=+|+.++......|-.---|=||||||||    --|++++++ ||=+|||+|.--|+.|++.-|++.|++|-++|
T Consensus        10 P~GDQP~AI~~L~~~l~~G~~~QtLLGvTGsGKT----FT~AnVIa~~~rPTLV~aHNKTLAAQLY~EfKefFPeNAVEY   85 (667)
T TIGR00631        10 PAGDQPKAIAKLVEGLEAGEKEQTLLGVTGSGKT----FTMANVIAQVQRPTLVLAHNKTLAAQLYNEFKEFFPENAVEY   85 (667)
T ss_pred             CCCCHHHHHHHHHHHHHCCCCCEEEEEEECCCHH----HHHHHHHHHHCCCEEEECCCHHHHHHHHHHHHHHCCCCCEEE
T ss_conf             6788189999999998568871478532148627----889899998479849985777679999999986386772452


Q ss_pred             E-----------------------CCCC---CHHHHHHHHHHHCCCCEEEEECCHHHH---HHHCCCEEEEE-EECCCCC
Q ss_conf             2-----------------------3557---235667899997199739994001211---00100013677-4055321
Q gi|254780619|r  278 H-----------------------SSLS---TSMREKIWRQVARGAISVIVGVRSALF---LPFKKLGLIVI-DEEHDIS  327 (731)
Q Consensus       278 H-----------------------S~ls---~~eR~~~w~~i~~G~~~IVIGtRSAif---~P~~nLglIIv-DEEHd~s  327 (731)
                      -                       |..+   +.-|..+-.++..=+--|||+|=|+++   .|=.-+.+.+. ....+-+
T Consensus        86 FvSYYDYYQPEAYvP~~DtyIEKdaSINdeIerlR~SAT~SLl~RrDVIVVASVScIYGLG~P~~Y~~~~~~l~vG~~~~  165 (667)
T TIGR00631        86 FVSYYDYYQPEAYVPSKDTYIEKDASINDEIERLRLSATKSLLERRDVIVVASVSCIYGLGSPEEYLKMVLHLEVGKEID  165 (667)
T ss_pred             EEECCCCCCCCCCCCCCCCEEECCCCHHHHHHHHHHHHHHHHCCCCCEEEEEEEEEECCCCCCHHHHCCEEEEEECCCCC
T ss_conf             55203237873214798841304553004676778898886423787899987552068888255642278654078558


Q ss_pred             CHHC----CCCCCCHHHHHHHHHHH
Q ss_conf             0000----24432248999997511
Q gi|254780619|r  328 YKQE----EGILYNARDMSIVRGKI  348 (731)
Q Consensus       328 ykq~----~~pry~aRdvA~~Ra~~  348 (731)
                      .++-    =..-|..=|+.+.|++.
T Consensus       166 ~~~ll~~LV~lqY~RNd~~f~RG~F  190 (667)
T TIGR00631       166 RRELLRRLVELQYERNDVDFQRGTF  190 (667)
T ss_pred             HHHHHHHHHHHCEEECCEECCCCCE
T ss_conf             8999988634030571234057712


No 202
>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=95.02  E-value=0.078  Score=33.12  Aligned_cols=69  Identities=19%  Similarity=0.282  Sum_probs=44.5

Q ss_pred             EEEEECCCCHHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHCCCCCEEEEEECCCCCHHHHHHHHHHH
Q ss_conf             199844753157999999999985146847997152100134455543038976899623557235667899997
Q gi|254780619|r  220 VSLISGVTGSGKTEVYLEIVAAVLHLGKQVLILLPEISLTSAILERFQKRFGVKPAEWHSSLSTSMREKIWRQVA  294 (731)
Q Consensus       220 ~~LL~GvTGSGKTEVYl~li~~~L~~GkqvLiLvPEI~Lt~Q~~~rl~~rF~~~v~v~HS~ls~~eR~~~w~~i~  294 (731)
                      -.|+.|-||||||-++.+++.+++.+|..++|.=|.=.    +.++|...=++  ++++---..+..++-|..+.
T Consensus        44 H~lv~G~tGsGKT~~i~~li~~~~~rg~~~II~DpkGe----~~~~fy~~~~d--~ilnP~d~rs~~wnp~~ei~  112 (410)
T cd01127          44 HTMIIGTTGTGKTTQIRELLASIRARGDRAIIYDPNGG----FVSKFYRPATD--IILNPFDARCAGWSLFNEIR  112 (410)
T ss_pred             CEEEECCCCCCHHHHHHHHHHHHHHCCCEEEEEECCCH----HHHHHHCCCCC--EEECCCCCCCCCCCHHHHHC
T ss_conf             47998899998899999999999986990999958854----99997544776--68676643577777578846


No 203
>COG3587 Restriction endonuclease [Defense mechanisms]
Probab=94.99  E-value=0.15  Score=30.93  Aligned_cols=31  Identities=32%  Similarity=0.589  Sum_probs=17.1

Q ss_pred             CCCHHHHHHHHHHHHHHHHC-CC-CEEEEECCC
Q ss_conf             75315799999999998514-68-479971521
Q gi|254780619|r  226 VTGSGKTEVYLEIVAAVLHL-GK-QVLILLPEI  256 (731)
Q Consensus       226 vTGSGKTEVYl~li~~~L~~-Gk-qvLiLvPEI  256 (731)
                      .||.|||=+|++.|-+.=++ |- --+|+||.+
T Consensus        82 ETGTGKTy~YlrtmfeLhk~YG~~KFIivVPs~  114 (985)
T COG3587          82 ETGTGKTYTYLRTMFELHKKYGLFKFIIVVPSL  114 (985)
T ss_pred             ECCCCCEEEHHHHHHHHHHHHCCEEEEEEECCH
T ss_conf             327884331799999999974845599993538


No 204
>PRK10536 hypothetical protein; Provisional
Probab=94.98  E-value=0.12  Score=31.77  Aligned_cols=54  Identities=17%  Similarity=0.250  Sum_probs=40.2

Q ss_pred             CCCCCHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHHHHHHHHHHCCC--CEEEEEC
Q ss_conf             6668837899999998752048961998447531579999999999851468--4799715
Q gi|254780619|r  196 LPILDKNQQDVVEQVVPLCTKGFAVSLISGVTGSGKTEVYLEIVAAVLHLGK--QVLILLP  254 (731)
Q Consensus       196 ~~~Lt~eQ~~a~~~i~~~~~~~f~~~LL~GvTGSGKTEVYl~li~~~L~~Gk--qvLiLvP  254 (731)
                      ..+-|.+|+..++.|...     ......|-.|+|||-+.+-++.+.|..++  ..++.=|
T Consensus        57 i~pkt~~Q~~yi~~i~~~-----~ivf~~GpAGTGKT~lA~a~Al~~l~~~~~~kIIltRP  112 (262)
T PRK10536         57 ILARNEAQLHYLKAIESK-----QLIFATGEAGCGKTWISAAKAAEALIHKDVDRIIVTRP  112 (262)
T ss_pred             CCCCCHHHHHHHHHHHHC-----CEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECC
T ss_conf             678986499999998619-----83999899987589999999999998588868999667


No 205
>PRK08760 replicative DNA helicase; Provisional
Probab=94.96  E-value=0.34  Score=28.20  Aligned_cols=131  Identities=20%  Similarity=0.214  Sum_probs=79.5

Q ss_pred             CEEEEECCCCHHHHHHHHHHHHHH-HHCCCCEEEEECCCHHHHHHHHHHHCCC-CCEE-EEEECCCCCHHHHHHHHHHHC
Q ss_conf             619984475315799999999998-5146847997152100134455543038-9768-996235572356678999971
Q gi|254780619|r  219 AVSLISGVTGSGKTEVYLEIVAAV-LHLGKQVLILLPEISLTSAILERFQKRF-GVKP-AEWHSSLSTSMREKIWRQVAR  295 (731)
Q Consensus       219 ~~~LL~GvTGSGKTEVYl~li~~~-L~~GkqvLiLvPEI~Lt~Q~~~rl~~rF-~~~v-~v~HS~ls~~eR~~~w~~i~~  295 (731)
                      ..+.|=|-+|.|||-..+.++..+ ++.|+.|++.--|-+ ..|+..|+-... +... -+....+++.+.......+..
T Consensus       230 ~LiViaaRPsmGKTalalnia~~~A~~~~~~V~~fSLEMs-~~ql~~Rlls~~s~v~~~~i~~g~l~~~e~~~~~~a~~~  308 (476)
T PRK08760        230 DLIILAARPAMGKTTFALNIAEYAAIKSKKGVAVFSMEMS-ASQLAMRLISSNGRINAQRLRTGALEDEDWARVTGAIKM  308 (476)
T ss_pred             CEEEEEECCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCC-HHHHHHHHHHHHCCCCHHHHHCCCCCHHHHHHHHHHHHH
T ss_conf             7799987788747899999999999837997899703699-999999999983389767776489999999999999999


Q ss_pred             -CCCEEEEECCHHH-----------HHHHCCCEEEEEEECCCCCCHHCCC------CCC-----CHHHHHHHHHHHCCCC
Q ss_conf             -9973999400121-----------1001000136774055321000024------432-----2489999975110321
Q gi|254780619|r  296 -GAISVIVGVRSAL-----------FLPFKKLGLIVIDEEHDISYKQEEG------ILY-----NARDMSIVRGKIESFP  352 (731)
Q Consensus       296 -G~~~IVIGtRSAi-----------f~P~~nLglIIvDEEHd~sykq~~~------pry-----~aRdvA~~Ra~~~~~~  352 (731)
                       .+..+.|--.+++           +..-.++++||||      |=|-..      .|+     =+|.+ ...|+..+||
T Consensus       309 l~~~~l~idD~~~~t~~~ir~~~R~~k~~~~l~lvvID------YLqL~~~~~~~~~r~~~v~~isr~l-K~lAkel~vp  381 (476)
T PRK08760        309 LKETKIFIDDTPGVSPEVLRSKCRRLKREHDLGLIVID------YLQLMSVPGNSENRATEISEISRSL-KGLAKELNVP  381 (476)
T ss_pred             HHHCCCEEECCCCCCHHHHHHHHHHHHHHCCCCEEEEE------HHHHCCCCCCCCCHHHHHHHHHHHH-HHHHHHHCCC
T ss_conf             86088168579999999999999999872799879997------0764158888744889999999999-9999997997


Q ss_pred             EECCC
Q ss_conf             00002
Q gi|254780619|r  353 VVLVS  357 (731)
Q Consensus       353 lilgS  357 (731)
                      ||+.|
T Consensus       382 Vi~Ls  386 (476)
T PRK08760        382 VIALS  386 (476)
T ss_pred             EEEEC
T ss_conf             89963


No 206
>PRK06526 transposase; Provisional
Probab=94.94  E-value=0.092  Score=32.59  Aligned_cols=130  Identities=17%  Similarity=0.251  Sum_probs=73.6

Q ss_pred             CCCCHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHCCCCCEEEE
Q ss_conf             66883789999999875204896199844753157999999999985146847997152100134455543038976899
Q gi|254780619|r  197 PILDKNQQDVVEQVVPLCTKGFAVSLISGVTGSGKTEVYLEIVAAVLHLGKQVLILLPEISLTSAILERFQKRFGVKPAE  276 (731)
Q Consensus       197 ~~Lt~eQ~~a~~~i~~~~~~~f~~~LL~GvTGSGKTEVYl~li~~~L~~GkqvLiLvPEI~Lt~Q~~~rl~~rF~~~v~v  276 (731)
                      +.++..|-.-+...  .+-......++.|-||.|||-+..-+..++..+|..|++.-     +++++.+|..-       
T Consensus        79 ~~l~~~~i~~La~~--~fi~~~~Nvil~G~~GtGKThLA~Alg~~A~~~G~~v~f~~-----~~~L~~~L~~a-------  144 (254)
T PRK06526         79 RSLKRDTIAHLGTL--DFVTGKENVVFLGPPGTGKTHLAIGLGIRACQAGHRVLFAT-----AAQWVARLAAA-------  144 (254)
T ss_pred             CCCCHHHHHHHHCC--CHHHCCCCEEEECCCCCCHHHHHHHHHHHHHHCCCCEEEEE-----HHHHHHHHHHH-------
T ss_conf             89899999998637--17765887899899998689999999999998699679987-----79999999998-------


Q ss_pred             EECCCCCHHHHHHHHHHHCCCCEEEEECCHHHHHHHCCCEEEEEEECCCCCCHHCCCCCCCHHHH-HHHHHHHCCCCEEC
Q ss_conf             62355723566789999719973999400121100100013677405532100002443224899-99975110321000
Q gi|254780619|r  277 WHSSLSTSMREKIWRQVARGAISVIVGVRSALFLPFKKLGLIVIDEEHDISYKQEEGILYNARDM-SIVRGKIESFPVVL  355 (731)
Q Consensus       277 ~HS~ls~~eR~~~w~~i~~G~~~IVIGtRSAif~P~~nLglIIvDEEHd~sykq~~~pry~aRdv-A~~Ra~~~~~~lil  355 (731)
                                       ..      -|+-...+.-+....|+|+||=   .|..-+.  -.+.++ -++=..++..++|+
T Consensus       145 -----------------~~------~g~~~~~~~~l~~~dLLIiDe~---g~~~~~~--~~a~~lf~li~~Rye~~S~Ii  196 (254)
T PRK06526        145 -----------------HH------AGRLQDELVKLGRIPLLIVDEV---GYIPFEA--EAANLFFQLVSSRYERASLIV  196 (254)
T ss_pred             -----------------HH------CCCHHHHHHHHHCCCEEEEECC---CCCCCCH--HHHHHHHHHHHHHHCCCCEEE
T ss_conf             -----------------85------5809999998513687765021---3644788--999999999999974588676


Q ss_pred             CCCCCCHHHHHHHH
Q ss_conf             02454324677532
Q gi|254780619|r  356 VSATPSIESRVNGI  369 (731)
Q Consensus       356 gSATPSles~~~~~  369 (731)
                      .|--| ++.|+.+.
T Consensus       197 TSn~~-~~~W~~~f  209 (254)
T PRK06526        197 TSNKP-FGRWGEVF  209 (254)
T ss_pred             ECCCC-HHHHHHHC
T ss_conf             65898-66888864


No 207
>PRK08506 replicative DNA helicase; Provisional
Probab=94.90  E-value=0.36  Score=28.07  Aligned_cols=132  Identities=20%  Similarity=0.248  Sum_probs=79.9

Q ss_pred             CEEEEECCCCHHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHCCCC-CEEE-EEECCCCCHHHHHHHHHH-HC
Q ss_conf             61998447531579999999999851468479971521001344555430389-7689-962355723566789999-71
Q gi|254780619|r  219 AVSLISGVTGSGKTEVYLEIVAAVLHLGKQVLILLPEISLTSAILERFQKRFG-VKPA-EWHSSLSTSMREKIWRQV-AR  295 (731)
Q Consensus       219 ~~~LL~GvTGSGKTEVYl~li~~~L~~GkqvLiLvPEI~Lt~Q~~~rl~~rF~-~~v~-v~HS~ls~~eR~~~w~~i-~~  295 (731)
                      ....|=|-+|-|||-..+.++..++.+|+.|++.--|-+ ..|+..|+-...+ ...- +-...+++.+....-..+ .-
T Consensus       194 dLiIIAARPsmGKTAfAlniA~~~a~~~~~V~~FSLEMs-~~ql~~Rlls~~s~V~~~~lr~g~l~~~e~~~~~~a~~~l  272 (473)
T PRK08506        194 DLIIIAARPSMGKTTLVLNMVLKALNQGKGVAFFSLEMP-AEQLMLRMLSAKTSIPLQNLRTGDLDDDEWENLSDACDEL  272 (473)
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHHHHCCCCEEEEECCCC-HHHHHHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHHHHHH
T ss_conf             279995079986789999999999965996589822479-9999999999728878310006899999999999999998


Q ss_pred             CCCEEEEECCHHH---------H-H--HHCCCEEEEEEECCCCCCHHCCCC--CCCHHH--HH------HHHHHHCCCCE
Q ss_conf             9973999400121---------1-0--010001367740553210000244--322489--99------99751103210
Q gi|254780619|r  296 GAISVIVGVRSAL---------F-L--PFKKLGLIVIDEEHDISYKQEEGI--LYNARD--MS------IVRGKIESFPV  353 (731)
Q Consensus       296 G~~~IVIGtRSAi---------f-~--P~~nLglIIvDEEHd~sykq~~~p--ry~aRd--vA------~~Ra~~~~~~l  353 (731)
                      .+..+.|=-.+.+         = +  -..+|++||||      |=|-..+  +..-|.  |+      ...|+..++||
T Consensus       273 ~~~~l~IdD~~~lti~~Ira~~Rr~k~~~~~l~livID------YLQLm~~~~~~~~R~~ev~~ISr~LK~lAkEl~vPV  346 (473)
T PRK08506        273 SQKKLFVYDSGYVNIHQVRAQLRKLKSQHPEIGLAVID------YLQLMSGSKNFKDRHLQISEISRGLKLLARELDIPI  346 (473)
T ss_pred             HCCCEEEECCCCCCHHHHHHHHHHHHHHCCCCCEEEEE------HHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCE
T ss_conf             65988998899999999999999999976998789963------675546888753088999999999999999969979


Q ss_pred             ECCC
Q ss_conf             0002
Q gi|254780619|r  354 VLVS  357 (731)
Q Consensus       354 ilgS  357 (731)
                      |+-|
T Consensus       347 iaLS  350 (473)
T PRK08506        347 IALS  350 (473)
T ss_pred             EEEC
T ss_conf             9970


No 208
>KOG0922 consensus
Probab=94.89  E-value=0.23  Score=29.56  Aligned_cols=136  Identities=21%  Similarity=0.297  Sum_probs=70.0

Q ss_pred             CCEEEEECCCCHHHHHHHHH-HHHHHHHCCCCEEEEECC----CHHHHHHHHHHHCCCCCEEEEEECCCCCHHHHHHHHH
Q ss_conf             96199844753157999999-999985146847997152----1001344555430389768996235572356678999
Q gi|254780619|r  218 FAVSLISGVTGSGKTEVYLE-IVAAVLHLGKQVLILLPE----ISLTSAILERFQKRFGVKPAEWHSSLSTSMREKIWRQ  292 (731)
Q Consensus       218 f~~~LL~GvTGSGKTEVYl~-li~~~L~~GkqvLiLvPE----I~Lt~Q~~~rl~~rF~~~v~v~HS~ls~~eR~~~w~~  292 (731)
                      .++..+-|.||||||-=-=+ +.+.-+.+.+.+-+-=|-    ++|+...........|..|. |+      -|+   ..
T Consensus        66 nqvlIviGeTGsGKSTQipQyL~eaG~~~~g~I~~TQPRRVAavslA~RVAeE~~~~lG~~VG-Y~------IRF---ed  135 (674)
T KOG0922          66 NQVLIVIGETGSGKSTQIPQYLAEAGFASSGKIACTQPRRVAAVSLAKRVAEEMGCQLGEEVG-YT------IRF---ED  135 (674)
T ss_pred             CCEEEEECCCCCCCCCCHHHHHHHCCCCCCCCEEEECCCHHHHHHHHHHHHHHHCCCCCCEEE-EE------EEE---CC
T ss_conf             877999848989853327699986265668827750671677888999999985897676222-69------984---56


Q ss_pred             HHCCCCEEEEEC-----CHHHHHH-HCCCEEEEEEECCCCCCHHCCCCCCCHHHHHHHHH---HHCCCCEECCCCCCCHH
Q ss_conf             971997399940-----0121100-10001367740553210000244322489999975---11032100002454324
Q gi|254780619|r  293 VARGAISVIVGV-----RSALFLP-FKKLGLIVIDEEHDISYKQEEGILYNARDMSIVRG---KIESFPVVLVSATPSIE  363 (731)
Q Consensus       293 i~~G~~~IVIGt-----RSAif~P-~~nLglIIvDEEHd~sykq~~~pry~aRdvA~~Ra---~~~~~~lilgSATPSle  363 (731)
                      ..+++.+|..=|     |-++.=| +..-..||+||-|+-|-.-|-       =+++++.   +.-.-.||+.|||--.+
T Consensus       136 ~ts~~TrikymTDG~LLRE~l~Dp~LskYsvIIlDEAHERsl~TDi-------LlGlLKki~~~R~~LklIimSATlda~  208 (674)
T KOG0922         136 STSKDTRIKYMTDGMLLREILKDPLLSKYSVIILDEAHERSLHTDI-------LLGLLKKILKKRPDLKLIIMSATLDAE  208 (674)
T ss_pred             CCCCCEEEEEECCHHHHHHHHCCCCCCCCCEEEEECHHHHHHHHHH-------HHHHHHHHHHCCCCCEEEEEEEEECHH
T ss_conf             6787336999613599998850876454448998322310157889-------999999987327783699992352489


Q ss_pred             HHHHHHH
Q ss_conf             6775321
Q gi|254780619|r  364 SRVNGIS  370 (731)
Q Consensus       364 s~~~~~~  370 (731)
                      -+...-+
T Consensus       209 kfS~yF~  215 (674)
T KOG0922         209 KFSEYFN  215 (674)
T ss_pred             HHHHHHC
T ss_conf             9999864


No 209
>PRK08181 transposase; Validated
Probab=94.86  E-value=0.25  Score=29.29  Aligned_cols=132  Identities=17%  Similarity=0.247  Sum_probs=74.4

Q ss_pred             CCCCHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHCCCCCEEEE
Q ss_conf             66883789999999875204896199844753157999999999985146847997152100134455543038976899
Q gi|254780619|r  197 PILDKNQQDVVEQVVPLCTKGFAVSLISGVTGSGKTEVYLEIVAAVLHLGKQVLILLPEISLTSAILERFQKRFGVKPAE  276 (731)
Q Consensus       197 ~~Lt~eQ~~a~~~i~~~~~~~f~~~LL~GvTGSGKTEVYl~li~~~L~~GkqvLiLvPEI~Lt~Q~~~rl~~rF~~~v~v  276 (731)
                      +.++..|-..+.... .+-......+|.|-||.|||-+..-+..+++.+|..|++.-     ++.++..|..        
T Consensus        86 p~i~~~~i~~L~~~~-~fi~~~~Nvil~Gp~GtGKThLA~Alg~~A~~~G~~V~f~~-----~~~L~~~L~~--------  151 (269)
T PRK08181         86 PMISKAQVMALAAGD-SWLAKGANLLLFGPPGGGKSHLAAAIGLALIENGWRVLFTR-----TTDLVQKLQV--------  151 (269)
T ss_pred             CCCCHHHHHHHHCCC-HHHHCCCEEEEECCCCCCHHHHHHHHHHHHHHCCCEEEEEE-----HHHHHHHHHH--------
T ss_conf             998999999996567-58864870899899998788999999999998799399978-----9999999999--------


Q ss_pred             EECCCCCHHHHHHHHHHHCCCCEEEEECCHHHHHHHCCCEEEEEEECCCCCCHHCCCCCCCHHHHHH-HHHHHCCCCEEC
Q ss_conf             6235572356678999971997399940012110010001367740553210000244322489999-975110321000
Q gi|254780619|r  277 WHSSLSTSMREKIWRQVARGAISVIVGVRSALFLPFKKLGLIVIDEEHDISYKQEEGILYNARDMSI-VRGKIESFPVVL  355 (731)
Q Consensus       277 ~HS~ls~~eR~~~w~~i~~G~~~IVIGtRSAif~P~~nLglIIvDEEHd~sykq~~~pry~aRdvA~-~Ra~~~~~~lil  355 (731)
                                      +..      =|+-...+.-+.+..|+|+||   -.|..-+.  -.+.++-- +=..++..++|+
T Consensus       152 ----------------a~~------~~~~~~~~~~l~~~dLLIiDe---~G~~~~~~--~~~~~lf~lI~~Rye~~S~II  204 (269)
T PRK08181        152 ----------------ARR------ELQLESAIAKLDKFDLLILDD---LAYVTKDQ--AETSVLFELISARYERRSILI  204 (269)
T ss_pred             ----------------HHH------CCCHHHHHHHHHCCCEEEEHH---CCCCCCCH--HHHHHHHHHHHHHHCCCCEEE
T ss_conf             ----------------775------583999999974446012201---05667998--999999999999857888899


Q ss_pred             CCCCCCHHHHHHHHH
Q ss_conf             024543246775321
Q gi|254780619|r  356 VSATPSIESRVNGIS  370 (731)
Q Consensus       356 gSATPSles~~~~~~  370 (731)
                      .|--| ++.|+.+-.
T Consensus       205 TSn~~-~~~W~~~f~  218 (269)
T PRK08181        205 TANQP-FGEWNRVFP  218 (269)
T ss_pred             ECCCC-HHHHHHHCC
T ss_conf             88999-778877538


No 210
>KOG0952 consensus
Probab=94.84  E-value=0.068  Score=33.60  Aligned_cols=73  Identities=22%  Similarity=0.292  Sum_probs=53.5

Q ss_pred             HHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHH----------------------CCCCCEEEEEECCCCCHHHHHH
Q ss_conf             999999999985146847997152100134455543----------------------0389768996235572356678
Q gi|254780619|r  232 TEVYLEIVAAVLHLGKQVLILLPEISLTSAILERFQ----------------------KRFGVKPAEWHSSLSTSMREKI  289 (731)
Q Consensus       232 TEVYl~li~~~L~~GkqvLiLvPEI~Lt~Q~~~rl~----------------------~rF~~~v~v~HS~ls~~eR~~~  289 (731)
                      -|+|...+.+.++.|.||++-|+-=+-|..+.+.|.                      +-|..-+++-|.++.-++|.-+
T Consensus       335 d~~~~~kv~e~~~~g~qVlvFvhsR~~Ti~tA~~l~~~a~~~g~~~~f~~~~~~k~l~elf~~g~~iHhAGm~r~DR~l~  414 (1230)
T KOG0952         335 DEVCYDKVVEFLQEGHQVLVFVHSRNETIRTAKKLRERAETNGEKDLFLPSPRNKQLKELFQQGMGIHHAGMLRSDRQLV  414 (1230)
T ss_pred             HHHHHHHHHHHHHCCCEEEEEEECCHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCHHHHHHH
T ss_conf             77899999999974985999996574899999999999886286565678836678999987401020256431468999


Q ss_pred             HHHHHCCCCEEEEEC
Q ss_conf             999971997399940
Q gi|254780619|r  290 WRQVARGAISVIVGV  304 (731)
Q Consensus       290 w~~i~~G~~~IVIGt  304 (731)
                      =.--+.|..+|..-|
T Consensus       415 E~~F~~G~i~vL~cT  429 (1230)
T KOG0952         415 EKEFKEGHIKVLCCT  429 (1230)
T ss_pred             HHHHHCCCCEEEEEC
T ss_conf             999855982289961


No 211
>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=94.83  E-value=0.24  Score=29.39  Aligned_cols=38  Identities=26%  Similarity=0.407  Sum_probs=34.3

Q ss_pred             CEEEEECCCCHHHHHHHHHHHHHHHHCCCCEEEEECCC
Q ss_conf             61998447531579999999999851468479971521
Q gi|254780619|r  219 AVSLISGVTGSGKTEVYLEIVAAVLHLGKQVLILLPEI  256 (731)
Q Consensus       219 ~~~LL~GvTGSGKTEVYl~li~~~L~~GkqvLiLvPEI  256 (731)
                      +..+|.|..|+|||-+-++++.++.++|..|++.-=|=
T Consensus        20 ~it~i~G~pG~GKStl~lq~a~~~~~~g~~v~YidtE~   57 (218)
T cd01394          20 TVTQVYGPPGTGKTNIAIQLAVETAGQGKKVAYIDTEG   57 (218)
T ss_pred             EEEEEECCCCCCHHHHHHHHHHHHHHCCCEEEEEECCC
T ss_conf             79999899998499999999999863698699996655


No 212
>PRK08074 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
Probab=94.79  E-value=0.1  Score=32.17  Aligned_cols=33  Identities=18%  Similarity=0.240  Sum_probs=19.0

Q ss_pred             HHHHHHHHCCCCCCEEEEEHHHCCCCCCCCCCH
Q ss_conf             999998621257657987044302311345201
Q gi|254780619|r  525 LQLQLSAIAKGEIDIIIGTQLVAKGHNFPRMSL  557 (731)
Q Consensus       525 ~~~~~~~~~~~~~~ilvgTq~i~kg~~fp~v~l  557 (731)
                      .+++++.|..++..||+||..-.-|.|||+-.|
T Consensus       797 r~~ll~~F~~~~~svLlGt~SFwEGVDlpGd~L  829 (932)
T PRK08074        797 RARLMKKFQQFDKAILLGTSSFWEGIDIPGDEL  829 (932)
T ss_pred             HHHHHHHHHHCCCEEEEECCCCCCCCCCCCCCE
T ss_conf             999999998479849996566435622799886


No 213
>PRK08727 hypothetical protein; Validated
Probab=94.79  E-value=0.38  Score=27.87  Aligned_cols=36  Identities=31%  Similarity=0.400  Sum_probs=27.7

Q ss_pred             CCCEEEEECCCCHHHHHHHHHHHHHHHHCCCCEEEE
Q ss_conf             896199844753157999999999985146847997
Q gi|254780619|r  217 GFAVSLISGVTGSGKTEVYLEIVAAVLHLGKQVLIL  252 (731)
Q Consensus       217 ~f~~~LL~GvTGSGKTEVYl~li~~~L~~GkqvLiL  252 (731)
                      ......|||-+|||||-.-.-+...+-..|+.+.++
T Consensus        40 ~~~~lyl~G~~GsGKTHLl~a~~~~~~~~~~~~~yl   75 (233)
T PRK08727         40 SSDWLYLSGPAGTGKTHLALSLCAAAEQAGRSSAYL   75 (233)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHHHHHHCCCCEEEE
T ss_conf             889899989999988999999999998279972884


No 214
>PRK09694 hypothetical protein; Provisional
Probab=94.78  E-value=0.2  Score=30.06  Aligned_cols=39  Identities=8%  Similarity=0.105  Sum_probs=21.1

Q ss_pred             CCEECCCCCCCCCCCCCCCHHHHHHHHHHHCCCCEEEEEECC
Q ss_conf             321102222332224547989999998862265517997422
Q gi|254780619|r  389 HLQVIDMRGQTIAQGKSLSPEMIDGIRHTLARNEQTLLFLNR  430 (731)
Q Consensus       389 ~i~ivDm~~~~~~~~~~lS~~l~~~i~~~l~~g~qvll~lnR  430 (731)
                      ++-|||   |-.......+..|...++-.-.-|.+|+|+...
T Consensus       443 kvvIiD---EVHAYD~Ym~~lL~~lL~wl~~~g~~viLLSAT  481 (878)
T PRK09694        443 SVLIVD---EVHAYDAYMNGLLEAVLKAQAQVGGSVILLSAT  481 (878)
T ss_pred             CEEEEE---CCCCCCHHHHHHHHHHHHHHHHCCCCEEEEECC
T ss_conf             748972---533345889999999999999839988999278


No 215
>KOG0344 consensus
Probab=94.77  E-value=0.036  Score=35.73  Aligned_cols=83  Identities=20%  Similarity=0.278  Sum_probs=58.1

Q ss_pred             EECCCCHHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHCCCCCEEE-EEECCCCCHHHHHHHHH-HHCCCCEE
Q ss_conf             84475315799999999998514684799715210013445554303897689-96235572356678999-97199739
Q gi|254780619|r  223 ISGVTGSGKTEVYLEIVAAVLHLGKQVLILLPEISLTSAILERFQKRFGVKPA-EWHSSLSTSMREKIWRQ-VARGAISV  300 (731)
Q Consensus       223 L~GvTGSGKTEVYl~li~~~L~~GkqvLiLvPEI~Lt~Q~~~rl~~rF~~~v~-v~HS~ls~~eR~~~w~~-i~~G~~~I  300 (731)
                      |-|+-|-|||++-+..++..+-- .+.+++-| +.+..|+..-++..+.-.+- -+-| -+-+..-+.|.. ++.+-..|
T Consensus       273 i~~~~~~~~~~idl~~V~~lV~d-EaD~lfe~-~~f~~Qla~I~sac~s~~i~~a~FS-at~~~~VEE~~~~i~~~~~~v  349 (593)
T KOG0344         273 IVGLLGLGKLNIDLSKVEWLVVD-EADLLFEP-EFFVEQLADIYSACQSPDIRVALFS-ATISVYVEEWAELIKSDLKRV  349 (593)
T ss_pred             HHHHHCCCCCCCHHHEEEEEEEC-HHHHHHCH-HHHHHHHHHHHHHHCCCCHHHHHHH-CCCCHHHHHHHHHHHCCCEEE
T ss_conf             99985589753201203567664-68765081-5699999999998528522256632-146077999999865053368


Q ss_pred             EEECCHHH
Q ss_conf             99400121
Q gi|254780619|r  301 IVGVRSAL  308 (731)
Q Consensus       301 VIGtRSAi  308 (731)
                      +||+|++.
T Consensus       350 ivg~~~sa  357 (593)
T KOG0344         350 IVGLRNSA  357 (593)
T ss_pred             EEECCHHH
T ss_conf             98425257


No 216
>PRK06319 DNA topoisomerase I/SWI domain fusion protein; Validated
Probab=94.77  E-value=0.045  Score=34.95  Aligned_cols=10  Identities=20%  Similarity=0.281  Sum_probs=4.9

Q ss_pred             CCCCHHHHHHHH
Q ss_conf             454324677532
Q gi|254780619|r  358 ATPSIESRVNGI  369 (731)
Q Consensus       358 ATPSles~~~~~  369 (731)
                      -|||  ||..+.
T Consensus       494 GRPS--TyA~II  503 (864)
T PRK06319        494 GRPS--TYATIM  503 (864)
T ss_pred             CCCH--HHHHHH
T ss_conf             9501--069999


No 217
>KOG0924 consensus
Probab=94.74  E-value=0.39  Score=27.79  Aligned_cols=134  Identities=22%  Similarity=0.276  Sum_probs=65.8

Q ss_pred             CCEEEEECCCCHHHHHHHHHHHHHHHHCCC--CEEE--EECC----CHHHHHHHHHHHCCCCCEEEEEECCCCCHHHHHH
Q ss_conf             961998447531579999999999851468--4799--7152----1001344555430389768996235572356678
Q gi|254780619|r  218 FAVSLISGVTGSGKTEVYLEIVAAVLHLGK--QVLI--LLPE----ISLTSAILERFQKRFGVKPAEWHSSLSTSMREKI  289 (731)
Q Consensus       218 f~~~LL~GvTGSGKTEVYl~li~~~L~~Gk--qvLi--LvPE----I~Lt~Q~~~rl~~rF~~~v~v~HS~ls~~eR~~~  289 (731)
                      .++.++-|.||||||   -++..-.++.|.  .-+|  --|-    |+++......+.-.+|+.|.-       +-|+  
T Consensus       371 n~vvvivgETGSGKT---TQl~QyL~edGY~~~GmIGcTQPRRvAAiSVAkrVa~EM~~~lG~~VGY-------sIRF--  438 (1042)
T KOG0924         371 NQVVVIVGETGSGKT---TQLAQYLYEDGYADNGMIGCTQPRRVAAISVAKRVAEEMGVTLGDTVGY-------SIRF--  438 (1042)
T ss_pred             CCEEEEEECCCCCCH---HHHHHHHHHCCCCCCCEEEECCCHHHHHHHHHHHHHHHHCCCCCCCCCE-------EEEE--
T ss_conf             857999935889850---1667999862245587154357227899999999999858764531124-------8885--


Q ss_pred             HHHHHCCCCEEEEECCHHHHH-------HHCCCEEEEEEECCCCCCHHCCCCCCCHHHHHHHHHHHCCCCEECCCCCCCH
Q ss_conf             999971997399940012110-------0100013677405532100002443224899999751103210000245432
Q gi|254780619|r  290 WRQVARGAISVIVGVRSALFL-------PFKKLGLIVIDEEHDISYKQEEGILYNARDMSIVRGKIESFPVVLVSATPSI  362 (731)
Q Consensus       290 w~~i~~G~~~IVIGtRSAif~-------P~~nLglIIvDEEHd~sykq~~~pry~aRdvA~~Ra~~~~~~lilgSATPSl  362 (731)
                       ..+......|=-=|- ++++       -+..-..||+||.|+-|..-+--.- -.+++   .|...+..+|..|||--.
T Consensus       439 -EdvT~~~T~IkymTD-GiLLrEsL~d~~L~kYSviImDEAHERslNtDilfG-llk~~---larRrdlKliVtSATm~a  512 (1042)
T KOG0924         439 -EDVTSEDTKIKYMTD-GILLRESLKDRDLDKYSVIIMDEAHERSLNTDILFG-LLKKV---LARRRDLKLIVTSATMDA  512 (1042)
T ss_pred             -EECCCCCEEEEEECC-CHHHHHHHHHHHHHHEEEEEECHHHHCCCCHHHHHH-HHHHH---HHHHCCCEEEEEECCCCH
T ss_conf             -204787605787423-057797763300444017885114330300589999-99999---874226359976220248


Q ss_pred             HHHHHHH
Q ss_conf             4677532
Q gi|254780619|r  363 ESRVNGI  369 (731)
Q Consensus       363 es~~~~~  369 (731)
                      +-+.+.-
T Consensus       513 ~kf~nfF  519 (1042)
T KOG0924         513 QKFSNFF  519 (1042)
T ss_pred             HHHHHHH
T ss_conf             9998872


No 218
>PRK11788 hypothetical protein; Provisional
Probab=94.61  E-value=0.011  Score=39.53  Aligned_cols=32  Identities=22%  Similarity=0.505  Sum_probs=22.3

Q ss_pred             CCCCCEECHHHCCC-CCCCCCCCCCCCCEECCC
Q ss_conf             57832000021024-465556667874110013
Q gi|254780619|r  460 SKKKLYCHQCGHSA-IYSQSCVVCGSSGKMIAC  491 (731)
Q Consensus       460 ~~~~l~Ch~Cg~~~-~~~~~Cp~Cg~~~~l~~~  491 (731)
                      .....+|++|||+. .+.|.||.|++=..++|.
T Consensus       351 ~~~~Y~C~~CGF~~~~~~WqCPsC~~W~Si~P~  383 (389)
T PRK11788        351 RKPRYRCRNCGFTARTLYWHCPSCKAWETIKPI  383 (389)
T ss_pred             CCCCEECCCCCCCCCCEEEECCCCCCCCCCCCC
T ss_conf             799976999999888314579099986784898


No 219
>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=94.61  E-value=0.42  Score=27.57  Aligned_cols=131  Identities=24%  Similarity=0.291  Sum_probs=71.5

Q ss_pred             CEEEEECCCCHHHHHHHHHHHHH-HHHCCCCEEEEECCCHHHHHHHHHHHCCC-CCEEEEE-ECCCCCHHHHHHHHHHH-
Q ss_conf             61998447531579999999999-85146847997152100134455543038-9768996-23557235667899997-
Q gi|254780619|r  219 AVSLISGVTGSGKTEVYLEIVAA-VLHLGKQVLILLPEISLTSAILERFQKRF-GVKPAEW-HSSLSTSMREKIWRQVA-  294 (731)
Q Consensus       219 ~~~LL~GvTGSGKTEVYl~li~~-~L~~GkqvLiLvPEI~Lt~Q~~~rl~~rF-~~~v~v~-HS~ls~~eR~~~w~~i~-  294 (731)
                      ....|=|-+|.|||-..++++.. ++.+|+.|++.--|-+ ..|+..|+-... +....-+ .+.+++.+....-..+. 
T Consensus       195 ~LiIiaARPsmGKTafalnia~n~A~~~g~~Vl~fSLEMs-~eql~~R~la~~s~i~~~~i~~g~l~~~~~~~~~~a~~~  273 (421)
T TIGR03600       195 DLIVIGARPSMGKTTLALNIAENVALREGKPVLFFSLEMS-AEQLGERLLASKSGINTGNIRTGRFNDSDFNRLLNAVDR  273 (421)
T ss_pred             CEEEEEEECCCCHHHHHHHHHHHHHHHCCCEEEEEECCCC-HHHHHHHHHHHHCCCCHHHHHCCCCCHHHHHHHHHHHHH
T ss_conf             6899985467874599999999999866983899925799-999999999985489776665289998999999999998


Q ss_pred             CCCCEEEEECCHHH-----------H-HHHCCCEEEEEEECCCCCCHHCCCC-----CCC-----HHHHHHHHHHHCCCC
Q ss_conf             19973999400121-----------1-0010001367740553210000244-----322-----489999975110321
Q gi|254780619|r  295 RGAISVIVGVRSAL-----------F-LPFKKLGLIVIDEEHDISYKQEEGI-----LYN-----ARDMSIVRGKIESFP  352 (731)
Q Consensus       295 ~G~~~IVIGtRSAi-----------f-~P~~nLglIIvDEEHd~sykq~~~p-----ry~-----aRdvA~~Ra~~~~~~  352 (731)
                      -.+..+.|=-.+.+           + .-...+++||||      |=|--.+     |+.     +|.+ ...|+..++|
T Consensus       274 l~~~~l~i~d~~~~ti~~ir~~~r~~~~~~~~l~livID------YLqLi~~~~~~~r~~ei~~Isr~L-K~lAkel~ip  346 (421)
T TIGR03600       274 LSEKDLYIDDTGGLTVAQIRSIARRIKRKKGGLDLIVVD------YIQLMAPTRGRDRNEELGGISRGL-KALAKELDVP  346 (421)
T ss_pred             HHCCCEEEECCCCCCHHHHHHHHHHHHHHCCCCCEEEEC------HHHHCCCCCCCCHHHHHHHHHHHH-HHHHHHHCCC
T ss_conf             616878996699887678999999999862898699975------786537888888899999999999-9999997997


Q ss_pred             EECCC
Q ss_conf             00002
Q gi|254780619|r  353 VVLVS  357 (731)
Q Consensus       353 lilgS  357 (731)
                      ||+.|
T Consensus       347 Vi~ls  351 (421)
T TIGR03600       347 VVLLA  351 (421)
T ss_pred             EEEEC
T ss_conf             89970


No 220
>COG1435 Tdk Thymidine kinase [Nucleotide transport and metabolism]
Probab=94.60  E-value=0.3  Score=28.61  Aligned_cols=105  Identities=25%  Similarity=0.336  Sum_probs=65.0

Q ss_pred             EEEEECCCCHHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHCCCCCEEEEEECCCCCHHHHHHHHHHHCCCCE
Q ss_conf             19984475315799999999998514684799715210013445554303897689962355723566789999719973
Q gi|254780619|r  220 VSLISGVTGSGKTEVYLEIVAAVLHLGKQVLILLPEISLTSAILERFQKRFGVKPAEWHSSLSTSMREKIWRQVARGAIS  299 (731)
Q Consensus       220 ~~LL~GvTGSGKTEVYl~li~~~L~~GkqvLiLvPEI~Lt~Q~~~rl~~rF~~~v~v~HS~ls~~eR~~~w~~i~~G~~~  299 (731)
                      ..++.|--+|||||--|+.+...-.+|+-|++.-|+|.          .||+.....=|.+++..              .
T Consensus         6 l~~i~gpM~SGKT~eLl~r~~~~~~~g~~v~vfkp~iD----------~R~~~~~V~Sr~G~~~~--------------A   61 (201)
T COG1435           6 LEFIYGPMFSGKTEELLRRARRYKEAGMKVLVFKPAID----------TRYGVGKVSSRIGLSSE--------------A   61 (201)
T ss_pred             EEEEECCCCCCCHHHHHHHHHHHHHCCCEEEEEECCCC----------CCCCCCEEEECCCCCCC--------------C
T ss_conf             99997157686359999999999975980899852533----------53564336531587665--------------3


Q ss_pred             EEEECCHHHHHHHCC------CEEEEEEECCCCCCHHCCCCCCCHHHHHHHHHHHCCCCEECC
Q ss_conf             999400121100100------013677405532100002443224899999751103210000
Q gi|254780619|r  300 VIVGVRSALFLPFKK------LGLIVIDEEHDISYKQEEGILYNARDMSIVRGKIESFPVVLV  356 (731)
Q Consensus       300 IVIGtRSAif~P~~n------LglIIvDEEHd~sykq~~~pry~aRdvA~~Ra~~~~~~lilg  356 (731)
                      ++|-.-..+|.-+..      .+.|.|||-+   |-.+     +--++.-..|..+|+||+..
T Consensus        62 ~~i~~~~~i~~~i~~~~~~~~~~~v~IDEaQ---F~~~-----~~v~~l~~lad~lgi~Vi~~  116 (201)
T COG1435          62 VVIPSDTDIFDEIAALHEKPPVDCVLIDEAQ---FFDE-----ELVYVLNELADRLGIPVICY  116 (201)
T ss_pred             EECCCHHHHHHHHHHCCCCCCCCEEEEEHHH---HCCH-----HHHHHHHHHHHHCCCEEEEE
T ss_conf             5638757899999851347875789996167---1897-----89999999986149889995


No 221
>KOG1002 consensus
Probab=94.58  E-value=0.38  Score=27.91  Aligned_cols=120  Identities=18%  Similarity=0.268  Sum_probs=73.2

Q ss_pred             CCCHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHHHHHHHHHHC--CCCEEEEECCCHHHHHHHHHHHCCC-C-CE
Q ss_conf             688378999999987520489619984475315799999999998514--6847997152100134455543038-9-76
Q gi|254780619|r  198 ILDKNQQDVVEQVVPLCTKGFAVSLISGVTGSGKTEVYLEIVAAVLHL--GKQVLILLPEISLTSAILERFQKRF-G-VK  273 (731)
Q Consensus       198 ~Lt~eQ~~a~~~i~~~~~~~f~~~LL~GvTGSGKTEVYl~li~~~L~~--GkqvLiLvPEI~Lt~Q~~~rl~~rF-~-~~  273 (731)
                      +|-+-|+..+.=......+.+.--.|--.-|-|||   ++.|+-+|+.  +.+.||++|-++|. |+.......- | -.
T Consensus       184 ~LL~fQkE~l~Wl~~QE~Ss~~GGiLADEMGMGKT---IQtIaLllae~~ra~tLVvaP~VAlm-QW~nEI~~~T~gslk  259 (791)
T KOG1002         184 PLLPFQKEGLAWLTSQEESSVAGGILADEMGMGKT---IQTIALLLAEVDRAPTLVVAPTVALM-QWKNEIERHTSGSLK  259 (791)
T ss_pred             CCHHHHHHHHHHHHHHHHHHHCCCEEHHHHCCCHH---HHHHHHHHHCCCCCCEEEECCHHHHH-HHHHHHHHHCCCCEE
T ss_conf             13144677788887735543124311243146417---99999998623568706975489999-999999876257647


Q ss_pred             EEEEECCCCCHHHHHHHHHHHCCCCEEEEECCHHHH--------------------HHHCCCE--EEEEEECCCCC
Q ss_conf             899623557235667899997199739994001211--------------------0010001--36774055321
Q gi|254780619|r  274 PAEWHSSLSTSMREKIWRQVARGAISVIVGVRSALF--------------------LPFKKLG--LIVIDEEHDIS  327 (731)
Q Consensus       274 v~v~HS~ls~~eR~~~w~~i~~G~~~IVIGtRSAif--------------------~P~~nLg--lIIvDEEHd~s  327 (731)
                      +++||+.--++    +-....  ..++|+.|.+.+=                    .++.+..  -||+||.|+--
T Consensus       260 v~~YhG~~R~~----nikel~--~YDvVLTty~vvEs~yRk~~~GfrrKngv~ke~SlLHsi~~~RiIlDEAH~IK  329 (791)
T KOG1002         260 VYIYHGAKRDK----NIKELM--NYDVVLTTYAVVESVYRKQDYGFRRKNGVDKEKSLLHSIKFYRIILDEAHNIK  329 (791)
T ss_pred             EEEEECCCCCC----CHHHHH--CCCEEEEECHHHHHHHHHCCCCCCCCCCCCCCCCHHHHCEEEEEEHHHHCCCC
T ss_conf             99972642357----788860--67679970187888987402342113774245323331010235221202531


No 222
>PRK09200 preprotein translocase subunit SecA; Reviewed
Probab=94.57  E-value=0.42  Score=27.51  Aligned_cols=92  Identities=21%  Similarity=0.212  Sum_probs=62.9

Q ss_pred             CCCHHHHHHHHHHHHHHHHCCCCEEEEECCCHHHH---HHHHHHHCCCCCEEEEEECCC-----CCHHHHHHHHHHHCCC
Q ss_conf             75315799999999998514684799715210013---445554303897689962355-----7235667899997199
Q gi|254780619|r  226 VTGSGKTEVYLEIVAAVLHLGKQVLILLPEISLTS---AILERFQKRFGVKPAEWHSSL-----STSMREKIWRQVARGA  297 (731)
Q Consensus       226 vTGSGKTEVYl~li~~~L~~GkqvLiLvPEI~Lt~---Q~~~rl~~rF~~~v~v~HS~l-----s~~eR~~~w~~i~~G~  297 (731)
                      -||-|||.+..-.+--.--.|+.|-|+-..=-|+.   ++...+...+|-.|.+.-|++     ++.+|...|.      
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             CEEEEECCHHHHH--------------HHCCCEEEEEEEC
Q ss_conf             7399940012110--------------0100013677405
Q gi|254780619|r  298 ISVIVGVRSALFL--------------PFKKLGLIVIDEE  323 (731)
Q Consensus       298 ~~IVIGtRSAif~--------------P~~nLglIIvDEE  323 (731)
                      ++|+=||-|.+=.              =...+...||||-
T Consensus       173 ~di~Y~tn~e~gfDyLrDn~~~~~~~~v~r~~~~aivDEv  212 (799)
T PRK09200        173 ADIIYTTNSELGFDYLRDNLADSKEDKVLRPLNYAIIDEV  212 (799)
T ss_pred             CCCEECCCCCCHHHHHCCCCCCCHHHCCCCCCCEEEEECH
T ss_conf             7722235654003453012015676525778966898532


No 223
>KOG0736 consensus
Probab=94.57  E-value=0.28  Score=28.90  Aligned_cols=109  Identities=28%  Similarity=0.399  Sum_probs=53.1

Q ss_pred             CCEEEEECCCCHHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHCCCCCEEEEEECCCCCHHHHHHHHHHHCCC
Q ss_conf             96199844753157999999999985146847997152100134455543038976899623557235667899997199
Q gi|254780619|r  218 FAVSLISGVTGSGKTEVYLEIVAAVLHLGKQVLILLPEISLTSAILERFQKRFGVKPAEWHSSLSTSMREKIWRQVARGA  297 (731)
Q Consensus       218 f~~~LL~GvTGSGKTEVYl~li~~~L~~GkqvLiLvPEI~Lt~Q~~~rl~~rF~~~v~v~HS~ls~~eR~~~w~~i~~G~  297 (731)
                      +..+||||.+|||||-+- ++++.-+  |..+ +=++=-.|+.                =.++.+.......|.+++.-+
T Consensus       431 ~~~vLLhG~~g~GK~t~V-~~vas~l--g~h~-~evdc~el~~----------------~s~~~~etkl~~~f~~a~~~~  490 (953)
T KOG0736         431 NPSVLLHGPPGSGKTTVV-RAVASEL--GLHL-LEVDCYELVA----------------ESASHTETKLQAIFSRARRCS  490 (953)
T ss_pred             CEEEEEECCCCCCHHHHH-HHHHHHH--CCCE-EECCHHHHHH----------------CCCCHHHHHHHHHHHHHHHCC
T ss_conf             537998679998757999-9999983--8725-7013898864----------------363313789999999875268


Q ss_pred             CEEEEECCHHHHHHHCCCEEEEEEECCCCCCHHCCCCCCCHHHHHHHHHHHC-------CCCEECCCCCCCHHHH
Q ss_conf             7399940012110010001367740553210000244322489999975110-------3210000245432467
Q gi|254780619|r  298 ISVIVGVRSALFLPFKKLGLIVIDEEHDISYKQEEGILYNARDMSIVRGKIE-------SFPVVLVSATPSIESR  365 (731)
Q Consensus       298 ~~IVIGtRSAif~P~~nLglIIvDEEHd~sykq~~~pry~aRdvA~~Ra~~~-------~~~lilgSATPSles~  365 (731)
                      +.|+.         +.|+..+-+|.+.-          -++|-...+|-..+       ..++++..+|-|.|..
T Consensus       491 pavif---------l~~~dvl~id~dgg----------ed~rl~~~i~~~ls~e~~~~~~~~~ivv~t~~s~~~l  546 (953)
T KOG0736         491 PAVLF---------LRNLDVLGIDQDGG----------EDARLLKVIRHLLSNEDFKFSCPPVIVVATTSSIEDL  546 (953)
T ss_pred             CEEEE---------EECCCEEEECCCCC----------HHHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCCCC
T ss_conf             62898---------72242455337774----------4277999999997202356779965999962530239


No 224
>PRK08413 consensus
Probab=94.56  E-value=0.046  Score=34.86  Aligned_cols=27  Identities=22%  Similarity=0.525  Sum_probs=15.5

Q ss_pred             EEHHCCCC---CCCCCC------------CCCCCCCEEEEEC
Q ss_conf             00000235---654343------------1014652012113
Q gi|254780619|r  433 YAPLTLCQ---VCGNRL------------KCLHCSCWLVEHR  459 (731)
Q Consensus       433 ya~~~~C~---~Cg~~~------------~C~~C~~~l~~h~  459 (731)
                      |-.|+.|.   +|.++.            .||.|+.+|..+.
T Consensus       586 ~G~F~~Cs~yP~Ck~t~~~~~~~~~~~~~~c~~cg~~m~~k~  627 (733)
T PRK08413        586 YGEFIACSNFPKCKYSKNTESENKEASEEVCEKCGGPMVQKF  627 (733)
T ss_pred             CCEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHEEE
T ss_conf             740684289987555456766543234566876784132120


No 225
>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=94.54  E-value=0.26  Score=29.11  Aligned_cols=79  Identities=27%  Similarity=0.302  Sum_probs=55.2

Q ss_pred             CEEEEECCCCHHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHCCCCCEE-EEEECCCCCHH-HHHHHHHH-HC
Q ss_conf             61998447531579999999999851468479971521001344555430389768-99623557235-66789999-71
Q gi|254780619|r  219 AVSLISGVTGSGKTEVYLEIVAAVLHLGKQVLILLPEISLTSAILERFQKRFGVKP-AEWHSSLSTSM-REKIWRQV-AR  295 (731)
Q Consensus       219 ~~~LL~GvTGSGKTEVYl~li~~~L~~GkqvLiLvPEI~Lt~Q~~~rl~~rF~~~v-~v~HS~ls~~e-R~~~w~~i-~~  295 (731)
                      +..-++|-.+||||-+.+++++++-+.|..|+++=-|-++.|.+.+.+    |.++ -+++++-...| -.++...+ ++
T Consensus        56 Rivei~G~essGKTtlal~~ia~aQk~gg~~~~iDaE~a~d~~~a~~l----GVD~~~l~~~qp~~~Eq~l~i~~~li~s  131 (325)
T cd00983          56 RIIEIYGPESSGKTTLALHAIAEAQKLGGTVAFIDAEHALDPVYAKKL----GVDLDNLLISQPDTGEQALEIADSLVRS  131 (325)
T ss_pred             EEEEEECCCCCCHHHHHHHHHHHHHHCCCEEEEEEHHHCCCHHHHHHC----CCCHHHEEEECCCHHHHHHHHHHHHHCC
T ss_conf             089998898777999999999998735983999962542598999980----9984675896663899999999997515


Q ss_pred             CCCEEE
Q ss_conf             997399
Q gi|254780619|r  296 GAISVI  301 (731)
Q Consensus       296 G~~~IV  301 (731)
                      |..++|
T Consensus       132 ~~~dli  137 (325)
T cd00983         132 GAVDLI  137 (325)
T ss_pred             CCCCEE
T ss_conf             887679


No 226
>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=94.52  E-value=0.12  Score=31.66  Aligned_cols=48  Identities=23%  Similarity=0.308  Sum_probs=38.1

Q ss_pred             CCCCEEEEECCCCHHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHC
Q ss_conf             48961998447531579999999999851468479971521001344555430
Q gi|254780619|r  216 KGFAVSLISGVTGSGKTEVYLEIVAAVLHLGKQVLILLPEISLTSAILERFQK  268 (731)
Q Consensus       216 ~~f~~~LL~GvTGSGKTEVYl~li~~~L~~GkqvLiLvPEI~Lt~Q~~~rl~~  268 (731)
                      ......+|.|-||.|||-+..-+..+++++|.+|++.-     ++.++++++.
T Consensus        45 ~~~~Nlll~G~~GtGKThLA~Ai~~~~~~~g~~v~f~~-----~~~L~~~l~~   92 (178)
T pfam01695        45 EQAENLLLLGPPGVGKTHLACALGHQACRAGYSVLFTR-----TPDLVEQLKR   92 (178)
T ss_pred             HCCCCEEEECCCCCCHHHHHHHHHHHHHHCCCEEEEEE-----CHHHHHHHHH
T ss_conf             15876899899998789999999999998698599996-----1679999998


No 227
>PRK05595 replicative DNA helicase; Provisional
Probab=94.49  E-value=0.44  Score=27.38  Aligned_cols=130  Identities=22%  Similarity=0.228  Sum_probs=75.5

Q ss_pred             CEEEEECCCCHHHHHHHHHHHHH-HHHCCCCEEEEECCCHHHHHHHHHHHCCC-CCEEEE-EECCCCCHHHHHHHHHHH-
Q ss_conf             61998447531579999999999-85146847997152100134455543038-976899-623557235667899997-
Q gi|254780619|r  219 AVSLISGVTGSGKTEVYLEIVAA-VLHLGKQVLILLPEISLTSAILERFQKRF-GVKPAE-WHSSLSTSMREKIWRQVA-  294 (731)
Q Consensus       219 ~~~LL~GvTGSGKTEVYl~li~~-~L~~GkqvLiLvPEI~Lt~Q~~~rl~~rF-~~~v~v-~HS~ls~~eR~~~w~~i~-  294 (731)
                      ...+|=|-+|.|||-..++++.. ++.+|+.|++.--|-+ ..|+..|+-... +....- -.+.+++.+-.. +..+. 
T Consensus       202 dLiiiaaRP~mGKTa~alnia~~~a~~~g~~V~~fSlEMs-~~ql~~R~ls~~s~i~~~~i~~g~l~~~~~~~-~~~a~~  279 (444)
T PRK05595        202 DMILIAARPSMGKTTFALNIAEYAALREGKSVVIFSLEMS-KEQLAYKLLCSEANVDMLRLRTGNLEDKDWEN-IARASG  279 (444)
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHHHHHCCCCEEEEECCCC-HHHHHHHHHHHHCCCCCCCCCCCCCCHHHHHH-HHHHHH
T ss_conf             7799985798980799999999999866993799958899-99999999996469884423268979999999-999999


Q ss_pred             -CCCCEEEEECCHHH-----------HHHHCCCEEEEEEECCCCCCHHCCC------CCCCH-----HHHHHHHHHHCCC
Q ss_conf             -19973999400121-----------1001000136774055321000024------43224-----8999997511032
Q gi|254780619|r  295 -RGAISVIVGVRSAL-----------FLPFKKLGLIVIDEEHDISYKQEEG------ILYNA-----RDMSIVRGKIESF  351 (731)
Q Consensus       295 -~G~~~IVIGtRSAi-----------f~P~~nLglIIvDEEHd~sykq~~~------pry~a-----RdvA~~Ra~~~~~  351 (731)
                       -.+..+.|=-.+.+           +..-.++++||||      |=|-..      .|+..     |.+ ...|+..++
T Consensus       280 ~l~~~~l~i~d~~~~ti~~i~~~~r~~~~~~~~~liiiD------YlqLi~~~~~~~~r~~ev~~isr~L-K~lAkel~i  352 (444)
T PRK05595        280 PLAAAKIYIDDTAGVSVMEMRSKCRRLKIEHGIDLILID------YLQLMSGGKSSESRQQEVSEISRSI-KALAKEMEC  352 (444)
T ss_pred             HHHCCCCCCCCCCCCCHHHHHHHHHHHHHHCCCCEEEEE------HHHHCCCCCCCCCHHHHHHHHHHHH-HHHHHHHCC
T ss_conf             985489705489996489999999999987399989982------3763578988888999999999999-999999699


Q ss_pred             CEECCC
Q ss_conf             100002
Q gi|254780619|r  352 PVVLVS  357 (731)
Q Consensus       352 ~lilgS  357 (731)
                      |||+.|
T Consensus       353 pvi~ls  358 (444)
T PRK05595        353 PVIALS  358 (444)
T ss_pred             CEEEEC
T ss_conf             799970


No 228
>PRK11773 uvrD DNA-dependent helicase II; Provisional
Probab=94.49  E-value=0.021  Score=37.42  Aligned_cols=33  Identities=33%  Similarity=0.394  Sum_probs=23.0

Q ss_pred             CEEEEEHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf             5798704430231134520123300034431024557
Q gi|254780619|r  538 DIIIGTQLVAKGHNFPRMSLVGVVDGDLGLTNADLRS  574 (731)
Q Consensus       538 ~ilvgTq~i~kg~~fp~v~lv~il~aD~~l~~pd~ra  574 (731)
                      .|-+-|===|||+.||.|=++|+-+.    ..|..|+
T Consensus       553 ~V~LmTiH~AKGLEFp~Vfl~gl~eg----~fP~~~s  585 (722)
T PRK11773        553 AVQLMTLHSAKGLEFPLVFLVGMEEG----LFPSQMS  585 (722)
T ss_pred             EEEEEEEECCCCCCCCEEEEECCCCC----CCCCCCC
T ss_conf             28999612026866776898066179----8886334


No 229
>PRK09354 recA recombinase A; Provisional
Probab=94.47  E-value=0.35  Score=28.16  Aligned_cols=90  Identities=24%  Similarity=0.259  Sum_probs=61.5

Q ss_pred             CEEEEECCCCHHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHCCCCCEEE-EEECCCCCH-HHHHHHHHH-HC
Q ss_conf             619984475315799999999998514684799715210013445554303897689-962355723-566789999-71
Q gi|254780619|r  219 AVSLISGVTGSGKTEVYLEIVAAVLHLGKQVLILLPEISLTSAILERFQKRFGVKPA-EWHSSLSTS-MREKIWRQV-AR  295 (731)
Q Consensus       219 ~~~LL~GvTGSGKTEVYl~li~~~L~~GkqvLiLvPEI~Lt~Q~~~rl~~rF~~~v~-v~HS~ls~~-eR~~~w~~i-~~  295 (731)
                      +..-++|-.+||||-+.+++++++-+.|+.|+++=-|-++.|+..+.+    |.++- ++.|+-... +-+++...+ ++
T Consensus        61 RivEi~G~esSGKTtlal~~iaeaQk~Gg~~a~iDaE~ald~~~a~~l----GVd~d~llv~qpd~~Eqal~i~e~Lvrs  136 (350)
T PRK09354         61 RIVEIYGPESSGKTTLALHAIAEAQKAGGTAAFIDAEHALDPVYAKKL----GVDIDNLLVSQPDTGEQALEIADALVRS  136 (350)
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHHHHCCCCEEEEEECCCCCHHHHHHC----CCCHHHEEEECCCHHHHHHHHHHHHHHC
T ss_conf             089998898777999999999999975994799960002798899984----9771571785686799999999999854


Q ss_pred             CCCEEEEECCHHHHHHH
Q ss_conf             99739994001211001
Q gi|254780619|r  296 GAISVIVGVRSALFLPF  312 (731)
Q Consensus       296 G~~~IVIGtRSAif~P~  312 (731)
                      |..++||=---|.+.|-
T Consensus       137 g~vd~IVvDSVaAL~pk  153 (350)
T PRK09354        137 GAVDLIVVDSVAALVPK  153 (350)
T ss_pred             CCCCEEEEECCCCCCCH
T ss_conf             88418998253345768


No 230
>PRK01172 ski2-like helicase; Provisional
Probab=94.43  E-value=0.23  Score=29.49  Aligned_cols=84  Identities=21%  Similarity=0.238  Sum_probs=57.9

Q ss_pred             HHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHH------------------------CCCCCEEEEEECCCCCHHHHHHH
Q ss_conf             999999985146847997152100134455543------------------------03897689962355723566789
Q gi|254780619|r  235 YLEIVAAVLHLGKQVLILLPEISLTSAILERFQ------------------------KRFGVKPAEWHSSLSTSMREKIW  290 (731)
Q Consensus       235 Yl~li~~~L~~GkqvLiLvPEI~Lt~Q~~~rl~------------------------~rF~~~v~v~HS~ls~~eR~~~w  290 (731)
                      +..++.+++..|.||||-+|.=.-+.++...+.                        +....-|+..|++|++.+|.-+=
T Consensus       225 ~~~l~~~~~~~~~~~LVF~~sR~~~e~~A~~l~~~~~~~~~~~~~~~~~~~~~~~L~~~l~~GVafHHaGL~~~eR~lVE  304 (674)
T PRK01172        225 INSLIKETVNDGGQVLVFVSSRKNAEDYAEMLIQHFPEFNDFKVSSENNNVYDDSLNEMLPHGVAFHHAGLSNEQRRFIE  304 (674)
T ss_pred             HHHHHHHHHHCCCCEEEEEECHHHHHHHHHHHHHHHHHCCCHHCCHHHHHCCCHHHHHHHHCCEEEECCCCCHHHHHHHH
T ss_conf             99999999966994799950758899999999985321010010315431120999999962828306899989999999


Q ss_pred             HHHHCCCCEEEEECCH---HHHHHHCCCEEEEEE
Q ss_conf             9997199739994001---211001000136774
Q gi|254780619|r  291 RQVARGAISVIVGVRS---ALFLPFKKLGLIVID  321 (731)
Q Consensus       291 ~~i~~G~~~IVIGtRS---Aif~P~~nLglIIvD  321 (731)
                      ..-++|..+|++.|-.   +|=+|.   ..+||.
T Consensus       305 ~~f~~g~i~vl~aT~TLAaGVNlPA---r~VIi~  335 (674)
T PRK01172        305 EMFRNRYIKVIVATPTLAAGVNLPA---RLVIVR  335 (674)
T ss_pred             HHHHCCCCEEEEECCHHHHHCCCCE---EEEEEE
T ss_conf             9998699649971446765447860---599993


No 231
>pfam05621 TniB Bacterial TniB protein. This family consists of several bacterial TniB NTP-binding proteins. TniB is a probable ATP-binding protein which is involved in Tn5053 mercury resistance transposition.
Probab=94.41  E-value=0.46  Score=27.25  Aligned_cols=68  Identities=22%  Similarity=0.252  Sum_probs=40.7

Q ss_pred             CCCEEEEEEECCC---CCCHHCCCCCCCHHHHHHHHHHHCCCCEECCCCCCCHHHHHHHHHHHHHHHCCCCCCCCCCCCC
Q ss_conf             0001367740553---2100002443224899999751103210000245432467753212344412432236765433
Q gi|254780619|r  313 KKLGLIVIDEEHD---ISYKQEEGILYNARDMSIVRGKIESFPVVLVSATPSIESRVNGISRRYHSVHLSTRYRNSALPH  389 (731)
Q Consensus       313 ~nLglIIvDEEHd---~sykq~~~pry~aRdvA~~Ra~~~~~~lilgSATPSles~~~~~~g~~~~~~l~~R~~~~~~P~  389 (731)
                      -+..++||||=|.   .|+.++..    .-++..+.+...++|+|+.. |+.  . +++.+..   -+|.+|+....+|.
T Consensus       144 ~~vrmLIIDEiHnlL~Gs~~~qr~----~ln~LK~L~Nel~IpiV~vG-t~e--A-~~ai~tD---~QlasRF~~~~Lp~  212 (302)
T pfam05621       144 VGVRMLVIDELHNVLAGNSVNRRE----FLNLLRFLGNELRIPLVGVG-TRD--A-YLAIRSD---DQLENRFEPMLLPP  212 (302)
T ss_pred             CCCCEEEEECHHHHCCCCHHHHHH----HHHHHHHHHHCCCCCEEEEC-CHH--H-HHHHHCC---HHHHHHCCCCCCCC
T ss_conf             498789985436560486889999----99999998636587869953-199--9-9997068---88885058611688


Q ss_pred             CE
Q ss_conf             21
Q gi|254780619|r  390 LQ  391 (731)
Q Consensus       390 i~  391 (731)
                      =+
T Consensus       213 W~  214 (302)
T pfam05621       213 WE  214 (302)
T ss_pred             CC
T ss_conf             88


No 232
>PRK08694 consensus
Probab=94.38  E-value=0.46  Score=27.20  Aligned_cols=131  Identities=24%  Similarity=0.310  Sum_probs=76.3

Q ss_pred             CEEEEECCCCHHHHHHHHHHHHHHHHCCC-CEEEEECCCHHHHHHHHHHHCCCC-CEEE-EEECCCCCHHHHHHHHHHH-
Q ss_conf             61998447531579999999999851468-479971521001344555430389-7689-9623557235667899997-
Q gi|254780619|r  219 AVSLISGVTGSGKTEVYLEIVAAVLHLGK-QVLILLPEISLTSAILERFQKRFG-VKPA-EWHSSLSTSMREKIWRQVA-  294 (731)
Q Consensus       219 ~~~LL~GvTGSGKTEVYl~li~~~L~~Gk-qvLiLvPEI~Lt~Q~~~rl~~rF~-~~v~-v~HS~ls~~eR~~~w~~i~-  294 (731)
                      ..++|=|-+|.|||-..+.++..+..+|+ .|++.--|-+ ..|+..|+-...+ .... +-.+.+++.+.......+. 
T Consensus       219 ~LiVIaaRPsmGKTalalnia~~~a~~~~~~V~~fSLEMs-~~~l~~Rlla~~s~v~~~~i~~g~l~~~e~~~~~~a~~~  297 (468)
T PRK08694        219 DLIIVAGRPSMGKTAFSINIAEHVAVEGKLPVAVFSMEMG-GAQLVMRMLGSVGRLDQSVLKTGRLEDEHWGRLNEAVVK  297 (468)
T ss_pred             CEEEEEECCCCCHHHHHHHHHHHHHHHCCCCEEEECCCCC-HHHHHHHHHHHHCCCCHHHCCCCCCCHHHHHHHHHHHHH
T ss_conf             4799961786537899999999999847984799778899-999999999972598632110489999999999999999


Q ss_pred             CCCCEEEEECCHHHH-----HH-------H-CCCEEEEEEECCCCCCHHCCC------CCCC-----HHHHHHHHHHHCC
Q ss_conf             199739994001211-----00-------1-000136774055321000024------4322-----4899999751103
Q gi|254780619|r  295 RGAISVIVGVRSALF-----LP-------F-KKLGLIVIDEEHDISYKQEEG------ILYN-----ARDMSIVRGKIES  350 (731)
Q Consensus       295 ~G~~~IVIGtRSAif-----~P-------~-~nLglIIvDEEHd~sykq~~~------pry~-----aRdvA~~Ra~~~~  350 (731)
                      -.+..+.|--.+.+=     +-       . ..+++||||      |=|-..      .|+.     .|.+ ...|+..+
T Consensus       298 l~~~pl~idd~~~~t~~~i~a~~r~~~~~~~~kl~~vvID------YLqLi~~~~~~~~r~~~i~~isr~L-K~lAkel~  370 (468)
T PRK08694        298 LSDAPVYIDETPGLTALELRARARRLARQFNNKLGLIVID------YLQLMAGSGRSDNRASELGEISRSL-KALAKELQ  370 (468)
T ss_pred             HHCCCEEEECCCCCCHHHHHHHHHHHHHHHCCCCCEEEEE------HHHHCCCCCCCCCHHHHHHHHHHHH-HHHHHHHC
T ss_conf             8629968976999988799999999999838987389973------6754168887655999999999999-99999979


Q ss_pred             CCEECCC
Q ss_conf             2100002
Q gi|254780619|r  351 FPVVLVS  357 (731)
Q Consensus       351 ~~lilgS  357 (731)
                      ||||+.|
T Consensus       371 ipvi~Ls  377 (468)
T PRK08694        371 VPIIALS  377 (468)
T ss_pred             CCEEEEC
T ss_conf             9899963


No 233
>PRK05582 DNA topoisomerase I; Validated
Probab=94.31  E-value=0.037  Score=35.58  Aligned_cols=41  Identities=24%  Similarity=0.477  Sum_probs=28.7

Q ss_pred             CCCCCCCCEEEEECC--CCCCEECH---HHCCCCCC-----------CCCCCCCCCC
Q ss_conf             310146520121135--78320000---21024465-----------5566678741
Q gi|254780619|r  446 LKCLHCSCWLVEHRS--KKKLYCHQ---CGHSAIYS-----------QSCVVCGSSG  486 (731)
Q Consensus       446 ~~C~~C~~~l~~h~~--~~~l~Ch~---Cg~~~~~~-----------~~Cp~Cg~~~  486 (731)
                      ..||.|+.+|+..+.  +..+.|..   |.++.++.           ..||.||+..
T Consensus       574 ~~Cp~Cg~~l~~r~~~~G~F~~Cs~yP~Ck~t~~~~~~~~~~~~~~~~~CP~C~~~l  630 (692)
T PRK05582        574 RKCPKCGRELVIKHGRYGEFIACSNYPKCKYTKPIEEEEKLASEELDVKCPECGGKI  630 (692)
T ss_pred             CCCCCCCCCCEEEECCCCCEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEE
T ss_conf             877567982026726889626578998788977687644444453699799999774


No 234
>KOG4439 consensus
Probab=94.30  E-value=0.1  Score=32.16  Aligned_cols=122  Identities=17%  Similarity=0.246  Sum_probs=78.6

Q ss_pred             CCCHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHHHHHHHHH-----HC--CCC---EEEEECCCHHHHHHHHHHH
Q ss_conf             6883789999999875204896199844753157999999999985-----14--684---7997152100134455543
Q gi|254780619|r  198 ILDKNQQDVVEQVVPLCTKGFAVSLISGVTGSGKTEVYLEIVAAVL-----HL--GKQ---VLILLPEISLTSAILERFQ  267 (731)
Q Consensus       198 ~Lt~eQ~~a~~~i~~~~~~~f~~~LL~GvTGSGKTEVYl~li~~~L-----~~--Gkq---vLiLvPEI~Lt~Q~~~rl~  267 (731)
                      .|-+.|+.++.=..-...+..+--.|-..-|=|||..-+.+|.+.=     ..  |-+   .||.+|. +|..|+...+.
T Consensus       325 ~LmpHQkaal~Wl~wRE~q~~~GGILaddmGLGKTlsmislil~qK~~~~~~~~~~~~a~~TLII~Pa-Sli~qW~~Ev~  403 (901)
T KOG4439         325 ELMPHQKAALRWLLWRESQPPSGGILADDMGLGKTLSMISLILHQKAARKAREKKGESASKTLIICPA-SLIHQWEAEVA  403 (901)
T ss_pred             ECCHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHCCCCCCCCCEEEECCH-HHHHHHHHHHH
T ss_conf             44514665414310013479998650213345530679999998899987541445655772886739-99998899999


Q ss_pred             CCCCC---EEEEEECCCCCHHHHHHHHHHHCCCCEEEEECCHHHH-------------HHHCCCE--EEEEEECCC
Q ss_conf             03897---6899623557235667899997199739994001211-------------0010001--367740553
Q gi|254780619|r  268 KRFGV---KPAEWHSSLSTSMREKIWRQVARGAISVIVGVRSALF-------------LPFKKLG--LIVIDEEHD  325 (731)
Q Consensus       268 ~rF~~---~v~v~HS~ls~~eR~~~w~~i~~G~~~IVIGtRSAif-------------~P~~nLg--lIIvDEEHd  325 (731)
                      .|...   .|++||+.-.    .++=.+... ..+|||.|.+-+-             .|+.+..  -||.||.|.
T Consensus       404 ~rl~~n~LsV~~~HG~n~----r~i~~~~L~-~YDvViTTY~lva~~~~~e~~~~~~~spL~~I~W~RVILDEAH~  474 (901)
T KOG4439         404 RRLEQNALSVYLYHGPNK----REISAKELR-KYDVVITTYNLVANKPDDELEEGKNSSPLARIAWSRVILDEAHN  474 (901)
T ss_pred             HHHHHCCEEEEEECCCCC----CCCCHHHHH-HCCEEEEEEECCCCCCCHHHHCCCCCCHHHHHHHHHHHHHHHHH
T ss_conf             998635007998617861----547888873-25669985211015773033315674277775677753424554


No 235
>PRK06921 hypothetical protein; Provisional
Probab=94.24  E-value=0.2  Score=29.96  Aligned_cols=49  Identities=18%  Similarity=0.183  Sum_probs=34.2

Q ss_pred             CCCCEEEEECCCCHHHHHHHHHHHHHHHHC-CCCEEEEECCCHHHHHHHHHHHCC
Q ss_conf             489619984475315799999999998514-684799715210013445554303
Q gi|254780619|r  216 KGFAVSLISGVTGSGKTEVYLEIVAAVLHL-GKQVLILLPEISLTSAILERFQKR  269 (731)
Q Consensus       216 ~~f~~~LL~GvTGSGKTEVYl~li~~~L~~-GkqvLiLvPEI~Lt~Q~~~rl~~r  269 (731)
                      ..+...++.|-+|+|||-.-.-++.+.+.+ |.+||++.     .++++..+++-
T Consensus       114 ~~~~~l~f~G~~G~GKThLa~aIa~~Ll~~~~~~Vly~~-----~~~~~~~lk~~  163 (265)
T PRK06921        114 CRKNSIALLGQPGSGKTHLLTAAANELMRKKGVPVLYFP-----FVEGFGDLKDD  163 (265)
T ss_pred             CCCCCEEEECCCCCCHHHHHHHHHHHHHHHCCCEEEEEE-----HHHHHHHHHHH
T ss_conf             776627997289898899999999999996297199988-----79999999988


No 236
>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=94.23  E-value=0.11  Score=31.98  Aligned_cols=38  Identities=37%  Similarity=0.512  Sum_probs=28.0

Q ss_pred             CCCCCCCCHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHH
Q ss_conf             446666883789999999875204896199844753157999
Q gi|254780619|r  193 YFSLPILDKNQQDVVEQVVPLCTKGFAVSLISGVTGSGKTEV  234 (731)
Q Consensus       193 ~~~~~~Lt~eQ~~a~~~i~~~~~~~f~~~LL~GvTGSGKTEV  234 (731)
                      |.....+|..|..++.+.....    +..|+-|-||||||=.
T Consensus       118 YV~~gimtaaQ~d~l~~Av~ar----~NIlv~GGTGSGKTTL  155 (315)
T TIGR02782       118 YVEAGIMTAAQRDVLREAVAAR----KNILVVGGTGSGKTTL  155 (315)
T ss_pred             HHHHCCCCHHHHHHHHHHHHHC----CCEEEECCCCCCHHHH
T ss_conf             7640445578999999999712----9889981458857999


No 237
>COG0513 SrmB Superfamily II DNA and RNA helicases [DNA replication, recombination, and repair / Transcription / Translation, ribosomal structure and biogenesis]
Probab=94.23  E-value=0.41  Score=27.60  Aligned_cols=117  Identities=21%  Similarity=0.328  Sum_probs=75.6

Q ss_pred             HHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHCCCCCEEEEEECCCCCHHHHHHHHHHHCCCCEEEEECCHHH-
Q ss_conf             5799999999998514684799715210013445554303897689962355723566789999719973999400121-
Q gi|254780619|r  230 GKTEVYLEIVAAVLHLGKQVLILLPEISLTSAILERFQKRFGVKPAEWHSSLSTSMREKIWRQVARGAISVIVGVRSAL-  308 (731)
Q Consensus       230 GKTEVYl~li~~~L~~GkqvLiLvPEI~Lt~Q~~~rl~~rF~~~v~v~HS~ls~~eR~~~w~~i~~G~~~IVIGtRSAi-  308 (731)
                      .|.+.-.+++...  ...++||-+.....+..+...+..+ |..++.+|++++..+|.++...-++|+.+|.|.|=-|. 
T Consensus       259 ~k~~~L~~ll~~~--~~~~~IVF~~tk~~~~~l~~~l~~~-g~~~~~lhG~l~q~~R~~~l~~F~~g~~~iLVaTDvaaR  335 (513)
T COG0513         259 EKLELLLKLLKDE--DEGRVIVFVRTKRLVEELAESLRKR-GFKVAALHGDLPQEERDRALEKFKDGELRVLVATDVAAR  335 (513)
T ss_pred             HHHHHHHHHHHCC--CCCEEEEEECCHHHHHHHHHHHHHC-CCEEEEEECCCCHHHHHHHHHHHHCCCCCEEEEECHHHC
T ss_conf             7999999998278--8883999957677699999999978-965999738899889999999997599898998065446


Q ss_pred             HHHHCCCEEEEE-EECCC-CCCHHCCCCCCCHHHHHH-HHHHHCCCCEECCCC
Q ss_conf             100100013677-40553-210000244322489999-975110321000024
Q gi|254780619|r  309 FLPFKKLGLIVI-DEEHD-ISYKQEEGILYNARDMSI-VRGKIESFPVVLVSA  358 (731)
Q Consensus       309 f~P~~nLglIIv-DEEHd-~sykq~~~pry~aRdvA~-~Ra~~~~~~lilgSA  358 (731)
                      =+.++++..||= |=..| .+|-       | | +-. =||-..|..+.|.+.
T Consensus       336 GiDi~~v~~VinyD~p~~~e~yv-------H-R-iGRTgRaG~~G~ai~fv~~  379 (513)
T COG0513         336 GLDIPDVSHVINYDLPLDPEDYV-------H-R-IGRTGRAGRKGVAISFVTE  379 (513)
T ss_pred             CCCCCCCCEEEECCCCCCCCCCC-------C-C-CCCCCCCCCCCEEEEEECC
T ss_conf             89966674799787999804131-------7-3-4534348998727998556


No 238
>PRK08840 replicative DNA helicase; Provisional
Probab=94.19  E-value=0.51  Score=26.92  Aligned_cols=132  Identities=19%  Similarity=0.236  Sum_probs=78.6

Q ss_pred             CEEEEECCCCHHHHHHHHHHHHHH-HHCCCCEEEEECCCHHHHHHHHHHHCCC-CCEE-EEEECCCCCHHHHHHHHHH--
Q ss_conf             619984475315799999999998-5146847997152100134455543038-9768-9962355723566789999--
Q gi|254780619|r  219 AVSLISGVTGSGKTEVYLEIVAAV-LHLGKQVLILLPEISLTSAILERFQKRF-GVKP-AEWHSSLSTSMREKIWRQV--  293 (731)
Q Consensus       219 ~~~LL~GvTGSGKTEVYl~li~~~-L~~GkqvLiLvPEI~Lt~Q~~~rl~~rF-~~~v-~v~HS~ls~~eR~~~w~~i--  293 (731)
                      ..++|=|-+|.|||-..++++.++ +++|+.|++.--|-+ ..|+..|+-... +... -+-.+.+++.+....-..+  
T Consensus       218 ~LiviaaRPsmGKTalalnia~n~a~~~~~~v~~fSlEMs-~~ql~~Rlls~~s~i~~~~ir~g~l~~~e~~~i~~a~~~  296 (464)
T PRK08840        218 DLIIVAARPSMGKTTFAMNLCENAAMDQDKPVLIFSLEMP-AEQLMMRMLASLSRVDQTKIRTGQLDDEDWARISSTMGI  296 (464)
T ss_pred             CEEEEEECCCCCHHHHHHHHHHHHHHHCCCCEEEECCCCC-HHHHHHHHHHHHCCCCCCHHHCCCCCHHHHHHHHHHHHH
T ss_conf             6799983798736899999999999965996799767799-899999999985389820111488899999999999999


Q ss_pred             HCCCCEEEEECCHHH-----------HHHHC-CCEEEEEEECCCCCCHHCC-CCCC-CHH--HHH------HHHHHHCCC
Q ss_conf             719973999400121-----------10010-0013677405532100002-4432-248--999------997511032
Q gi|254780619|r  294 ARGAISVIVGVRSAL-----------FLPFK-KLGLIVIDEEHDISYKQEE-GILY-NAR--DMS------IVRGKIESF  351 (731)
Q Consensus       294 ~~G~~~IVIGtRSAi-----------f~P~~-nLglIIvDEEHd~sykq~~-~pry-~aR--dvA------~~Ra~~~~~  351 (731)
                      ......+.|=-.+.+           +..-. .|++||||      |=|-. .+.. +-|  +++      ...|+..++
T Consensus       297 ~~~~~~l~idd~~~~t~~~i~a~~r~~~~~~~~l~lvvID------YLqL~~~~~~~~~r~~~i~~isr~lK~lAkel~v  370 (464)
T PRK08840        297 LMEKKNMYIDDSSGLTPTEVRSRARRVAREHGGLSMIMVD------YLQLMRVPALQDNRTLEIAEISRSLKALAKELNV  370 (464)
T ss_pred             HHHCCCEEEECCCCCCHHHHHHHHHHHHHHCCCCCEEEEE------HHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHCC
T ss_conf             9847995885699875799999999999864898789961------8866067886403678999999999999999699


Q ss_pred             CEECCC
Q ss_conf             100002
Q gi|254780619|r  352 PVVLVS  357 (731)
Q Consensus       352 ~lilgS  357 (731)
                      |||+.|
T Consensus       371 pVv~ls  376 (464)
T PRK08840        371 PVVALS  376 (464)
T ss_pred             CEEEEC
T ss_conf             899963


No 239
>PTZ00110 helicase; Provisional
Probab=94.18  E-value=0.51  Score=26.91  Aligned_cols=35  Identities=26%  Similarity=0.469  Sum_probs=16.2

Q ss_pred             EECCCCCCCCCCCCCCCHHHHHHHHHHHCCCCEEEEEE
Q ss_conf             11022223322245479899999988622655179974
Q gi|254780619|r  391 QVIDMRGQTIAQGKSLSPEMIDGIRHTLARNEQTLLFL  428 (731)
Q Consensus       391 ~ivDm~~~~~~~~~~lS~~l~~~i~~~l~~g~qvll~l  428 (731)
                      -|+|=-++...-|  +-+. ++.|-+.+....|+++|-
T Consensus       333 LVLDEADRMLDmG--Fe~q-I~~Il~~i~pdRQTlLFS  367 (602)
T PTZ00110        333 LVLDEADRMLDMG--FEPQ-IRKIVSQIRPDRQTLMWS  367 (602)
T ss_pred             EEEECHHHHHCCC--CHHH-HHHHHHHCCCCCEEEEEE
T ss_conf             9987577663546--2999-999998589787799995


No 240
>PRK09165 replicative DNA helicase; Provisional
Probab=94.18  E-value=0.51  Score=26.91  Aligned_cols=132  Identities=21%  Similarity=0.211  Sum_probs=76.9

Q ss_pred             CEEEEECCCCHHHHHHHHHHHHHHH---------------HCCCCEEEEECCCHHHHHHHHHHHCCC-CCEEE-EEECCC
Q ss_conf             6199844753157999999999985---------------146847997152100134455543038-97689-962355
Q gi|254780619|r  219 AVSLISGVTGSGKTEVYLEIVAAVL---------------HLGKQVLILLPEISLTSAILERFQKRF-GVKPA-EWHSSL  281 (731)
Q Consensus       219 ~~~LL~GvTGSGKTEVYl~li~~~L---------------~~GkqvLiLvPEI~Lt~Q~~~rl~~rF-~~~v~-v~HS~l  281 (731)
                      ....|=|-+|.|||-..+.++..+-               .+|+.|++.--|-+ ..|+..|+-..- +.... +..+.+
T Consensus       206 dLiIIAARPsmGKTafaLniA~n~A~~~~~~~~~~~~~~~~~g~~V~~FSLEMs-~~ql~~Rlls~~s~V~~~~ir~g~l  284 (484)
T PRK09165        206 DLIILAGRPSMGKTALATNIAFNAAKAYLREAQPDGSKKAVNGGVVGFFSLEMS-AEQLATRILSEQSEISSSKIRRGKI  284 (484)
T ss_pred             CEEEEEECCCCCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCEEEEEECCCC-HHHHHHHHHHHHHCCCHHHHHCCCC
T ss_conf             379996079997789999999999987410222233211368984899947799-9999999999972686135544899


Q ss_pred             CCHHHHHHHHHHH-CCCCEEEEECCHHH-----------HHHHCCCEEEEEEECCCCCCHHCCCC--C--CCHH--HHH-
Q ss_conf             7235667899997-19973999400121-----------10010001367740553210000244--3--2248--999-
Q gi|254780619|r  282 STSMREKIWRQVA-RGAISVIVGVRSAL-----------FLPFKKLGLIVIDEEHDISYKQEEGI--L--YNAR--DMS-  342 (731)
Q Consensus       282 s~~eR~~~w~~i~-~G~~~IVIGtRSAi-----------f~P~~nLglIIvDEEHd~sykq~~~p--r--y~aR--dvA-  342 (731)
                      ++.+.......+. -.+..+.|--.+.+           +..-.++++||||      |=|-..+  +  ..-|  +|+ 
T Consensus       285 ~~~e~~~i~~a~~~l~~~~l~IdD~~~~ti~~Ira~~Rr~k~~~gl~livID------YLqLi~~~~~~~~~~R~~ev~~  358 (484)
T PRK09165        285 SEEDFEKLVDASQELQKLPLYIDDTPALSISALRARARRLKRQHGLDLLVID------YLQLIRGSSKRSQDNRVQEISE  358 (484)
T ss_pred             CHHHHHHHHHHHHHHHCCCEEEECCCCCCHHHHHHHHHHHHHHHCCCEEEEE------CHHHCCCCCCCCCHHHHHHHHH
T ss_conf             9999999999999997198489779998799999999999986099889995------1763578888861219999999


Q ss_pred             -----HHHHHHCCCCEECCC
Q ss_conf             -----997511032100002
Q gi|254780619|r  343 -----IVRGKIESFPVVLVS  357 (731)
Q Consensus       343 -----~~Ra~~~~~~lilgS  357 (731)
                           ...|+..+||||+-|
T Consensus       359 Isr~LK~lAkel~ipVi~Ls  378 (484)
T PRK09165        359 ITQGLKALAKELNIPVIALS  378 (484)
T ss_pred             HHHHHHHHHHHHCCCEEEEC
T ss_conf             99999999999699699974


No 241
>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=94.16  E-value=0.22  Score=29.76  Aligned_cols=116  Identities=19%  Similarity=0.117  Sum_probs=64.1

Q ss_pred             CHHHHHHHHHHCCCCCHHHHCCCCCCCCHHHHHHHHHHHCCCCCCEEEEEHHHCCCCCCC--------C--CCHHHHHHH
Q ss_conf             289988885204852000102321135867899999862125765798704430231134--------5--201233000
Q gi|254780619|r  494 GIERIAEEVCEYFPLARISILSSDLEGGGGRLQLQLSAIAKGEIDIIIGTQLVAKGHNFP--------R--MSLVGVVDG  563 (731)
Q Consensus       494 Gte~~~e~l~~~fp~~~v~~~d~d~~~~~~~~~~~~~~~~~~~~~ilvgTq~i~kg~~fp--------~--v~lv~il~a  563 (731)
                      ..+++.|.|...++. +++.--.|. ......+++++.|.+++..||.||.-.--|.|+|        +  +++|+|.-.
T Consensus       482 ~~~~~ae~l~~~l~~-~~l~Qge~~-~~~~l~~~~~~~f~~~~~svLfGT~SfWEGVDvpG~~~~~~~Gd~Ls~VII~rL  559 (636)
T TIGR03117       482 HISAIGQLVELGIPA-EIVIQSEKN-RLASAEQQFLALYANGIQPVLIAAGGAWTGIDLTHKPVSPDKDNLLTDLIITCA  559 (636)
T ss_pred             HHHHHHHHHHHCCCC-CEEEECCCC-CHHHHHHHHHHHHHCCCCCEEEECCCCCCCCCCCCCCCCCCCCCCCEEEEEECC
T ss_conf             999999999722788-658745764-035689999998727899689867764066257886667887774206657569


Q ss_pred             HHHHHHHHH-----HHH----------HHHHHHHHHHHHCCCCCC---CCCEEEEEECCCCCHHHHHH
Q ss_conf             344310245-----578----------999998754311025667---88689999329864888999
Q gi|254780619|r  564 DLGLTNADL-----RSS----------ERTFQLLSQVTGRAGRFG---LKSLGLIQAYQPTHPVMQAL  613 (731)
Q Consensus       564 D~~l~~pd~-----ra~----------E~~~qll~qv~gRagr~~---~~g~v~iQt~~p~~~~~~~~  613 (731)
                      -..  .||=     |+.          -.+.=.|.|-+||-=|..   ..|.|.|--....+|.+..+
T Consensus       560 PF~--~p~~p~~~~r~~~~~g~~~~~vp~A~i~lkQG~GRLIRs~d~~D~G~vaiLD~RI~~~~~~~~  625 (636)
T TIGR03117       560 PFG--LNRSLSMLKRIRKTSVRPWEIINESLMMLRQGLGRLVRHPDMPQNRRIHMLDGRIHWPYMESW  625 (636)
T ss_pred             CCC--CCCCHHHHHHHHHCCCCHHHHHHHHHHHHHHHCCCEECCCCCCCCEEEEEECCCCCHHHHHHH
T ss_conf             989--998789999997149987777999999997745730314778896589996475532443146


No 242
>COG1484 DnaC DNA replication protein [DNA replication, recombination, and repair]
Probab=94.15  E-value=0.26  Score=29.09  Aligned_cols=88  Identities=23%  Similarity=0.379  Sum_probs=57.9

Q ss_pred             CCHHHHHHHHHHHH---HHCCCCCEEEEECCCCHHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHCCCCCEEE
Q ss_conf             88378999999987---520489619984475315799999999998514684799715210013445554303897689
Q gi|254780619|r  199 LDKNQQDVVEQVVP---LCTKGFAVSLISGVTGSGKTEVYLEIVAAVLHLGKQVLILLPEISLTSAILERFQKRFGVKPA  275 (731)
Q Consensus       199 Lt~eQ~~a~~~i~~---~~~~~f~~~LL~GvTGSGKTEVYl~li~~~L~~GkqvLiLvPEI~Lt~Q~~~rl~~rF~~~v~  275 (731)
                      .+..++.++..+..   ... .....+|+|-+|.|||-+..-+..++++.|.+|++.-     ++.++.+++.-|++   
T Consensus        84 ~~~~~~~~l~~~~~~~~~~~-~~~nl~l~G~~G~GKthLa~Ai~~~l~~~g~sv~f~~-----~~el~~~Lk~~~~~---  154 (254)
T COG1484          84 QPGIDKKALEDLASLVEFFE-RGENLVLLGPPGVGKTHLAIAIGNELLKAGISVLFIT-----APDLLSKLKAAFDE---  154 (254)
T ss_pred             CCHHHHHHHHHHHHHHHHHC-CCCCEEEECCCCCCHHHHHHHHHHHHHHCCCEEEEEE-----HHHHHHHHHHHHHC---
T ss_conf             85566999999999998732-5882899899998799999999999998398499988-----59999999998745---


Q ss_pred             EEECCCCCHHHHHHHHHHHCCCCEEEEECCHHHHHH-HCCCEEEEEEE
Q ss_conf             962355723566789999719973999400121100-10001367740
Q gi|254780619|r  276 EWHSSLSTSMREKIWRQVARGAISVIVGVRSALFLP-FKKLGLIVIDE  322 (731)
Q Consensus       276 v~HS~ls~~eR~~~w~~i~~G~~~IVIGtRSAif~P-~~nLglIIvDE  322 (731)
                                                 |+.-.-+.- +.+..+.|+||
T Consensus       155 ---------------------------~~~~~~l~~~l~~~dlLIiDD  175 (254)
T COG1484         155 ---------------------------GRLEEKLLRELKKVDLLIIDD  175 (254)
T ss_pred             ---------------------------CCHHHHHHHHHHHCCEEEEEC
T ss_conf             ---------------------------526899998875289899823


No 243
>PRK12726 flagellar biosynthesis regulator FlhF; Provisional
Probab=94.11  E-value=0.48  Score=27.10  Aligned_cols=37  Identities=22%  Similarity=0.325  Sum_probs=31.9

Q ss_pred             CEEEEECCCCHHHHHHHHHHHHHHHHCCCCEEEEECC
Q ss_conf             6199844753157999999999985146847997152
Q gi|254780619|r  219 AVSLISGVTGSGKTEVYLEIVAAVLHLGKQVLILLPE  255 (731)
Q Consensus       219 ~~~LL~GvTGSGKTEVYl~li~~~L~~GkqvLiLvPE  255 (731)
                      .+.+|=|+||||||=---.++.....+|++|++..=.
T Consensus       207 ~VIaLVGvnGvGKTTTiAKLA~~l~~~gkkV~LVAaD  243 (407)
T PRK12726        207 RIISLIGQTGVGKTTTLVKLGWQLLKQNRTVGFITTD  243 (407)
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHHHHCCCCEEEEECC
T ss_conf             0899989998978999999999999779917999706


No 244
>COG0552 FtsY Signal recognition particle GTPase [Intracellular trafficking and secretion]
Probab=94.09  E-value=0.52  Score=26.86  Aligned_cols=39  Identities=33%  Similarity=0.386  Sum_probs=33.4

Q ss_pred             CCCCEEEEECCCCHHHHHHHHHHHHHHHHCCCCEEEEEC
Q ss_conf             489619984475315799999999998514684799715
Q gi|254780619|r  216 KGFAVSLISGVTGSGKTEVYLEIVAAVLHLGKQVLILLP  254 (731)
Q Consensus       216 ~~f~~~LL~GvTGSGKTEVYl~li~~~L~~GkqvLiLvP  254 (731)
                      ++..++|+-||.|+|||----.++....++|+.|++-.=
T Consensus       137 ~~p~Vil~vGVNG~GKTTTIaKLA~~l~~~g~~VllaA~  175 (340)
T COG0552         137 KKPFVILFVGVNGVGKTTTIAKLAKYLKQQGKSVLLAAG  175 (340)
T ss_pred             CCCEEEEEEECCCCCHHHHHHHHHHHHHHCCCEEEEEEC
T ss_conf             986799999348886371799999999978986999823


No 245
>PRK12422 chromosomal replication initiation protein; Provisional
Probab=94.09  E-value=0.21  Score=29.77  Aligned_cols=105  Identities=19%  Similarity=0.308  Sum_probs=59.6

Q ss_pred             CCCEEEEECCCCHHHHHHHHHHHHHHHHC-CCCEEEEECCCHHHHHHHHHHHCCCCCEEEEEECCCCCHHHHHHHHHHHC
Q ss_conf             89619984475315799999999998514-68479971521001344555430389768996235572356678999971
Q gi|254780619|r  217 GFAVSLISGVTGSGKTEVYLEIVAAVLHL-GKQVLILLPEISLTSAILERFQKRFGVKPAEWHSSLSTSMREKIWRQVAR  295 (731)
Q Consensus       217 ~f~~~LL~GvTGSGKTEVYl~li~~~L~~-GkqvLiLvPEI~Lt~Q~~~rl~~rF~~~v~v~HS~ls~~eR~~~w~~i~~  295 (731)
                      .|.|..|||-+|.|||-. |++|...+.. ++.|+++-.|- .+.+++.-                           +++
T Consensus       140 ~yNPLfIyG~~GlGKTHL-L~AIgn~i~~~~~kV~Yvtae~-F~~~~v~a---------------------------i~~  190 (455)
T PRK12422        140 PFNPIYLFGPEGSGKTHL-MQAAVSALRESGGKILYVSSEL-FTEHLVSA---------------------------IRS  190 (455)
T ss_pred             CCCCEEEECCCCCCHHHH-HHHHHHHHHCCCCEEEEECHHH-HHHHHHHH---------------------------HHC
T ss_conf             678758878999978999-9999998537998699974999-99999999---------------------------975


Q ss_pred             CCCEEEEECCHHHH-HHHCCCEEEEEEECCCCCCHHC-CCCCCCHHHHHHHHHHHCCCCEECCCCCCCH
Q ss_conf             99739994001211-0010001367740553210000-2443224899999751103210000245432
Q gi|254780619|r  296 GAISVIVGVRSALF-LPFKKLGLIVIDEEHDISYKQE-EGILYNARDMSIVRGKIESFPVVLVSATPSI  362 (731)
Q Consensus       296 G~~~IVIGtRSAif-~P~~nLglIIvDEEHd~sykq~-~~pry~aRdvA~~Ra~~~~~~lilgSATPSl  362 (731)
                      |+.        .-| --+.+..+.+||+=|--+-|.. +.--||.-+-..    ..|-.+|+.|..|.-
T Consensus       191 ~~~--------~~Fr~~yr~~DvLLIDDIQfl~gK~~tqeEff~tfN~L~----~~~KQIVitsDr~P~  247 (455)
T PRK12422        191 GEM--------QRFRSFYRNVDALFIEDIEVFSGKGATQEEFFHTFNSLH----TEGKLIVISSSYAPG  247 (455)
T ss_pred             CCH--------HHHHHHHHCCCEEEEEHHHHHHCCHHHHHHHHHHHHHHH----HCCCEEEEECCCCHH
T ss_conf             889--------999999963887763147887284889999999999999----859969996898957


No 246
>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=94.07  E-value=0.53  Score=26.78  Aligned_cols=290  Identities=21%  Similarity=0.333  Sum_probs=162.0

Q ss_pred             EEEEECCCCHHHH-HHHHHHHHHHHHCCCCEEEEECC-C---HHHHHHHHHHHCCCCCEEEE---EECCCCCHHHHHHHH
Q ss_conf             1998447531579-99999999985146847997152-1---00134455543038976899---623557235667899
Q gi|254780619|r  220 VSLISGVTGSGKT-EVYLEIVAAVLHLGKQVLILLPE-I---SLTSAILERFQKRFGVKPAE---WHSSLSTSMREKIWR  291 (731)
Q Consensus       220 ~~LL~GvTGSGKT-EVYl~li~~~L~~GkqvLiLvPE-I---~Lt~Q~~~rl~~rF~~~v~v---~HS~ls~~eR~~~w~  291 (731)
                      -.+|.-=||-||| -|=|.+..+-+..|+..|+|=|= +   +-+.-|...+.+.-|+.|..   .-|+.|+..|.++  
T Consensus        19 ~vvL~APpGAGKsT~~PLaLL~~pW~~~~kIimLEPRRlAAR~~A~rlA~~LgE~VG~tVGyRvR~enkVs~~TRlEv--   96 (858)
T TIGR01970        19 QVVLEAPPGAGKSTAVPLALLDAPWLIGGKIIMLEPRRLAARSAAQRLASQLGEEVGDTVGYRVRLENKVSARTRLEV--   96 (858)
T ss_pred             CEEEECCCCCCHHHHHHHHHHHHHHHCCCEEEEECCHHHHHHHHHHHHHHHHCCCCCCCCCEEEECCCCCCCCCCEEE--
T ss_conf             506416722471105889976626434880787474478999999999997088988620405771132587754578--


Q ss_pred             HHHCCCCEEEEECCHHHHHH-HCCCEEEEEEECCCCCCHHCCCCCCCHHHHHHHHHHHCC--CCEECCCCCCCHHHHHHH
Q ss_conf             99719973999400121100-100013677405532100002443224899999751103--210000245432467753
Q gi|254780619|r  292 QVARGAISVIVGVRSALFLP-FKKLGLIVIDEEHDISYKQEEGILYNARDMSIVRGKIES--FPVVLVSATPSIESRVNG  368 (731)
Q Consensus       292 ~i~~G~~~IVIGtRSAif~P-~~nLglIIvDEEHd~sykq~~~pry~aRdvA~~Ra~~~~--~~lilgSATPSles~~~~  368 (731)
                       +..|     |=||.=-==| +...|+||.||-||=|-.-|=+.=+ |+||  .-.=.++  -+|+..|||=+=+-+.+-
T Consensus        97 -VTEG-----iLTRMlQ~DP~L~GVg~liFDEFHERsL~aDLaLAL-aLdV--Qs~LRdDPPLkil~MSATLdg~rLs~L  167 (858)
T TIGR01970        97 -VTEG-----ILTRMLQDDPELEGVGLLIFDEFHERSLDADLALAL-ALDV--QSALRDDPPLKILIMSATLDGERLSSL  167 (858)
T ss_pred             -EECC-----HHHHHCCCCCCCCCCCEEEECHHHHHHHHHHHHHHH-HHHH--HHHHCCCCCCEEHHCCCCCHHHHHHHH
T ss_conf             -7232-----687740168884535232311022434678899999-8853--343106864000000026327999974


Q ss_pred             HHHHHHHHCCCCCCCCCCCCCCEECCCCCCC-CCCCCCCCHHHHHHHHHHHCCC-CE----EEEEECCCCEEHHCCCCCC
Q ss_conf             2123444124322367654332110222233-2224547989999998862265-51----7997422200000023565
Q gi|254780619|r  369 ISRRYHSVHLSTRYRNSALPHLQVIDMRGQT-IAQGKSLSPEMIDGIRHTLARN-EQ----TLLFLNRRGYAPLTLCQVC  442 (731)
Q Consensus       369 ~~g~~~~~~l~~R~~~~~~P~i~ivDm~~~~-~~~~~~lS~~l~~~i~~~l~~g-~q----vll~lnRrGya~~~~C~~C  442 (731)
                      ... --+++-    .|+..|    ||.+-.. ...+..|-+.+..++.+.|+.. .-    +|+|||=.|=         
T Consensus       168 L~~-Ap~v~S----~GR~fP----Ve~rY~~P~~~~e~l~~~~~r~v~~~La~~~GSGPqd~LvFLPG~aE---------  229 (858)
T TIGR01970       168 LPD-APVVES----EGRSFP----VEIRYLPPLREDERLEDRVSRAVEHALAEESGSGPQDVLVFLPGQAE---------  229 (858)
T ss_pred             CCC-CCEEEE----CCCCCC----EECCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCCCCCHHEECCCHHH---------
T ss_conf             330-264200----787876----11022767875553347899999999961678863301001687778---------


Q ss_pred             CCCCCCCCCCCEEEEECCCCCCEECHHHCCCCCCCCCCCCCCCCEECCCCCCHHHHHHHHHHCC---CCCHHHHCCCCCC
Q ss_conf             4343101465201211357832000021024465556667874110013542899888852048---5200010232113
Q gi|254780619|r  443 GNRLKCLHCSCWLVEHRSKKKLYCHQCGHSAIYSQSCVVCGSSGKMIACGFGIERIAEEVCEYF---PLARISILSSDLE  519 (731)
Q Consensus       443 g~~~~C~~C~~~l~~h~~~~~l~Ch~Cg~~~~~~~~Cp~Cg~~~~l~~~G~Gte~~~e~l~~~f---p~~~v~~~d~d~~  519 (731)
                                                                          +.|+++.|.+.+   |++.|.=+-..- 
T Consensus       230 ----------------------------------------------------I~Rv~~~L~e~L~~rs~v~lcPLYG~L-  256 (858)
T TIGR01970       230 ----------------------------------------------------IRRVQEQLAERLDARSEVLLCPLYGEL-  256 (858)
T ss_pred             ----------------------------------------------------HHHHHHHHHHHHCCCCCCHHCCCCCCC-
T ss_conf             ----------------------------------------------------999999999975178710005767888-


Q ss_pred             CCHHHHHHHHHHHCCCCCCEEEEEHHHCCCCCCCCCCHHHHHHHHHHHH-HHHHH--HH------HHHHH-HHHHHHHCC
Q ss_conf             5867899999862125765798704430231134520123300034431-02455--78------99999-875431102
Q gi|254780619|r  520 GGGGRLQLQLSAIAKGEIDIIIGTQLVAKGHNFPRMSLVGVVDGDLGLT-NADLR--SS------ERTFQ-LLSQVTGRA  589 (731)
Q Consensus       520 ~~~~~~~~~~~~~~~~~~~ilvgTq~i~kg~~fp~v~lv~il~aD~~l~-~pd~r--a~------E~~~q-ll~qv~gRa  589 (731)
                       ..+.-++.+..-.+|-=.|+..|-+-.-.+.+++|.+|    .|+++. .|.|.  +.      .|..| --+|=||||
T Consensus       257 -~~~aQ~~AI~P~a~GrRKVVLATNiAEtSLTIeGvRvV----iDsGl~R~arFDP~sG~TRL~~~RisqASA~QRAGRA  331 (858)
T TIGR01970       257 -ELAAQDRAIKPAAAGRRKVVLATNIAETSLTIEGVRVV----IDSGLARVARFDPKSGITRLETQRISQASATQRAGRA  331 (858)
T ss_pred             -CHHHHHHHCCCCCCCCCEEEEEHHHHHHHEEECCEEEE----EECCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCC
T ss_conf             -97899987087746673434200012221001763588----7156556763478887402445788973376512633


Q ss_pred             CCCCCCCE
Q ss_conf             56678868
Q gi|254780619|r  590 GRFGLKSL  597 (731)
Q Consensus       590 gr~~~~g~  597 (731)
                      ||-. +|-
T Consensus       332 GRle-pGv  338 (858)
T TIGR01970       332 GRLE-PGV  338 (858)
T ss_pred             CCCC-CCH
T ss_conf             2211-141


No 247
>PRK05748 replicative DNA helicase; Provisional
Probab=94.05  E-value=0.54  Score=26.73  Aligned_cols=130  Identities=22%  Similarity=0.247  Sum_probs=76.4

Q ss_pred             CEEEEECCCCHHHHHHHHHHHHHH-HHCCCCEEEEECCCHHHHHHHHHHHCCCC-CEEE-EEECCCCCHHHHHHHH--HH
Q ss_conf             619984475315799999999998-51468479971521001344555430389-7689-9623557235667899--99
Q gi|254780619|r  219 AVSLISGVTGSGKTEVYLEIVAAV-LHLGKQVLILLPEISLTSAILERFQKRFG-VKPA-EWHSSLSTSMREKIWR--QV  293 (731)
Q Consensus       219 ~~~LL~GvTGSGKTEVYl~li~~~-L~~GkqvLiLvPEI~Lt~Q~~~rl~~rF~-~~v~-v~HS~ls~~eR~~~w~--~i  293 (731)
                      ...+|=|-+|.|||-..+.++..+ +++|+.|++.--|-+ ..|+..|+-...+ .... +-.+.+++.+....-.  ..
T Consensus       204 ~LiviaaRP~mGKTa~alnia~~~a~~~~~~v~~fSlEM~-~~~l~~R~la~~s~v~~~~i~~g~l~~~~~~~~~~a~~~  282 (448)
T PRK05748        204 DLIIVAARPSVGKTAFALNIAQNVATKTDKNVAIFSLEMG-AESLVMRMLCAEGRIDQQKLRTGQLTDEDWPKLTIAVGS  282 (448)
T ss_pred             CEEEEEECCCCCHHHHHHHHHHHHHHHCCCEEEEEECCCC-HHHHHHHHHHHHHCCCHHHHHCCCCCHHHHHHHHHHHHH
T ss_conf             3799984799876899999999999856980899817788-889999999997467777776289999999999999999


Q ss_pred             HCCCCEEEEECCHHH-----------HHH-HCCCEEEEEEECCCCCCHHCCC-C------CCC-----HHHHHHHHHHHC
Q ss_conf             719973999400121-----------100-1000136774055321000024-4------322-----489999975110
Q gi|254780619|r  294 ARGAISVIVGVRSAL-----------FLP-FKKLGLIVIDEEHDISYKQEEG-I------LYN-----ARDMSIVRGKIE  349 (731)
Q Consensus       294 ~~G~~~IVIGtRSAi-----------f~P-~~nLglIIvDEEHd~sykq~~~-p------ry~-----aRdvA~~Ra~~~  349 (731)
                      .. +..+.|-..+.+           +.. ..++++||||      |=|--. |      |+.     .|.+ ...|+..
T Consensus       283 l~-~~~l~i~d~~~~ti~~i~~~~r~~~~~~~~~~~vviD------Ylqli~~~~~~~~~r~~ev~~isr~l-K~lAkel  354 (448)
T PRK05748        283 LS-DAPIYIDDTPGIKVTEIRARCRRLAQEHGGLGLIVID------YLQLIQGSGRSGENRQQEVSEISRSL-KALAKEL  354 (448)
T ss_pred             HH-CCCEEEECCCCCCHHHHHHHHHHHHHHCCCCCEEEEE------HHHHCCCCCCCCCCHHHHHHHHHHHH-HHHHHHH
T ss_conf             86-5983785589886899999999999975998899971------68644777877643999999999999-9999996


Q ss_pred             CCCEECCC
Q ss_conf             32100002
Q gi|254780619|r  350 SFPVVLVS  357 (731)
Q Consensus       350 ~~~lilgS  357 (731)
                      ++|||+.|
T Consensus       355 ~ipvi~ls  362 (448)
T PRK05748        355 KVPVIALS  362 (448)
T ss_pred             CCCEEEEC
T ss_conf             99889970


No 248
>CHL00174 accD acetyl-CoA carboxylase beta subunit; Reviewed
Probab=94.04  E-value=0.024  Score=37.10  Aligned_cols=121  Identities=17%  Similarity=0.142  Sum_probs=54.0

Q ss_pred             CCCCCCCCEEEEECC--CCCCEECHHHCCCCCCCCCCCCCCCCEECC-CCCCHHHHHHHHHHCCCCCHHHHCCCCCCCCH
Q ss_conf             310146520121135--783200002102446555666787411001-35428998888520485200010232113586
Q gi|254780619|r  446 LKCLHCSCWLVEHRS--KKKLYCHQCGHSAIYSQSCVVCGSSGKMIA-CGFGIERIAEEVCEYFPLARISILSSDLEGGG  522 (731)
Q Consensus       446 ~~C~~C~~~l~~h~~--~~~l~Ch~Cg~~~~~~~~Cp~Cg~~~~l~~-~G~Gte~~~e~l~~~fp~~~v~~~d~d~~~~~  522 (731)
                      .+||+|+..+ |++.  +|..+|..|||..+++.+       .++.. +..|+   .+|+.........+-+-.|+.+-+
T Consensus        49 ~KCp~C~~~i-y~kdLe~Nl~VCp~C~~H~ri~a~-------eRi~~L~D~gs---feEi~~~l~~~DPL~F~~D~K~Y~  117 (305)
T CHL00174         49 VQCENCYGLN-YKKFLKSKMNICEQCGYHLKMSSS-------DRIELLIDPGT---WNPMDEDMVSLDPIEFHSEEEPYK  117 (305)
T ss_pred             CCCCCCCCHH-HHHHHHHHCCCCCCCCCCCCCCHH-------HHHHHHCCCCC---CEECCCCCCCCCCCCCCCCCCCHH
T ss_conf             5498766224-599999839899299799733999-------99999827996---168678878888444755543378


Q ss_pred             HHHHHHHHHHCCCCCCEEEEEHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             7899999862125765798704430231134520123300034431024557899999875
Q gi|254780619|r  523 GRLQLQLSAIAKGEIDIIIGTQLVAKGHNFPRMSLVGVVDGDLGLTNADLRSSERTFQLLS  583 (731)
Q Consensus       523 ~~~~~~~~~~~~~~~~ilvgTq~i~kg~~fp~v~lv~il~aD~~l~~pd~ra~E~~~qll~  583 (731)
                      .+++..-++-... -.+++|+--| .|++    ..+++.|...+-.+-.--..|+.....-
T Consensus       118 dRL~~arkkTg~~-dAvv~g~G~I-~g~~----vvv~vmDF~FmGGSMGsvvGEki~ra~e  172 (305)
T CHL00174        118 DRIDSYQKKTGLT-DAVQTGIGQL-NGIP----VALGVMDFQFMGGSMGSVVGEKITRLIE  172 (305)
T ss_pred             HHHHHHHHHHCCC-EEEEEEEEEE-CCEE----EEEEEEECCCCCCCCHHHHHHHHHHHHH
T ss_conf             9999999971998-0799999999-9977----9999972401156520788999999999


No 249
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=93.96  E-value=0.041  Score=35.29  Aligned_cols=35  Identities=23%  Similarity=0.486  Sum_probs=21.5

Q ss_pred             CCEEEEECCCCCCEECHHHCCCCCC------------------------CCCCCCCCCC
Q ss_conf             5201211357832000021024465------------------------5566678741
Q gi|254780619|r  452 SCWLVEHRSKKKLYCHQCGHSAIYS------------------------QSCVVCGSSG  486 (731)
Q Consensus       452 ~~~l~~h~~~~~l~Ch~Cg~~~~~~------------------------~~Cp~Cg~~~  486 (731)
                      +..|....-.-..+|+.||+.+.+.                        ..||.|||..
T Consensus        59 gA~L~Ie~vp~~~~C~~Cg~ef~~~~~~~~~~~~~~~~~h~~pe~~~~~~~CP~Cgs~~  117 (135)
T PRK03824         59 GAEIIFEEEEAVLKCRNCGYEWSLKEVKDKLDEEIREAIHFIPEVVHAFLKCPKCGSRD  117 (135)
T ss_pred             CCEEEEEECCCEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
T ss_conf             98999996175689233898724443332100000111123421235566290998988


No 250
>PRK06893 DNA replication initiation factor; Validated
Probab=93.96  E-value=0.36  Score=28.05  Aligned_cols=33  Identities=18%  Similarity=0.215  Sum_probs=24.7

Q ss_pred             EEEEECCCCHHHHHHHHHHHHHHHHCCCCEEEE
Q ss_conf             199844753157999999999985146847997
Q gi|254780619|r  220 VSLISGVTGSGKTEVYLEIVAAVLHLGKQVLIL  252 (731)
Q Consensus       220 ~~LL~GvTGSGKTEVYl~li~~~L~~GkqvLiL  252 (731)
                      ...|||.+|||||-.---+..++..+++.++++
T Consensus        41 ~l~i~G~~gsGKTHLLqa~~~~~~~~~~~~~yi   73 (229)
T PRK06893         41 FFYIWGGKSSGKSHLLKAVSNHYLLNQRTAIYI   73 (229)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHHCCCEEEE
T ss_conf             799989999988999999999999718985999


No 251
>PRK06319 DNA topoisomerase I/SWI domain fusion protein; Validated
Probab=93.90  E-value=0.042  Score=35.22  Aligned_cols=10  Identities=20%  Similarity=0.405  Sum_probs=4.8

Q ss_pred             CCCCCCEEEE
Q ss_conf             0146520121
Q gi|254780619|r  448 CLHCSCWLVE  457 (731)
Q Consensus       448 C~~C~~~l~~  457 (731)
                      ||.|+.+|++
T Consensus       648 Cp~Cg~~mv~  657 (864)
T PRK06319        648 CPLCGGEMKV  657 (864)
T ss_pred             CCCCCCCCEE
T ss_conf             7678970113


No 252
>PRK12902 secA preprotein translocase subunit SecA; Reviewed
Probab=93.90  E-value=0.25  Score=29.21  Aligned_cols=92  Identities=23%  Similarity=0.200  Sum_probs=66.1

Q ss_pred             CCCHHHHHHHHHHHHHHHHCCCCEEEEECCCHHHH---HHHHHHHCCCCCEEEEEECCCCCHHHHHHHHHHHCCCCEEEE
Q ss_conf             75315799999999998514684799715210013---445554303897689962355723566789999719973999
Q gi|254780619|r  226 VTGSGKTEVYLEIVAAVLHLGKQVLILLPEISLTS---AILERFQKRFGVKPAEWHSSLSTSMREKIWRQVARGAISVIV  302 (731)
Q Consensus       226 vTGSGKTEVYl~li~~~L~~GkqvLiLvPEI~Lt~---Q~~~rl~~rF~~~v~v~HS~ls~~eR~~~w~~i~~G~~~IVI  302 (731)
                      -||-|||.|..-.+--.--.|+.|-|+-..=-|+.   .+...+...+|-.|.+..+++++.+|...|      .++|+=
T Consensus       106 ~TGEGKTL~atlp~ylnAL~GkgvHvvTvNdYLA~RDae~m~~vy~fLGltvg~i~~~~~~~er~~aY------~~DItY  179 (946)
T PRK12902        106 KTGEGKTLVATLPSYLNALTGKGVHVVTVNDYLARRDAEWMGQVHRFLGLSVGLIQQDMSPEERKKNY------ACDITY  179 (946)
T ss_pred             CCCCCHHHHHHHHHHHHHHCCCCEEEECCCHHHHHHHHHHHHHHHHHHCCEEEEECCCCCHHHHHHHH------CCCCEE
T ss_conf             17884799999999998655997099726526568679999999998197783548998989999985------898279


Q ss_pred             ECCHHHH--------------HHHCCCEEEEEEEC
Q ss_conf             4001211--------------00100013677405
Q gi|254780619|r  303 GVRSALF--------------LPFKKLGLIVIDEE  323 (731)
Q Consensus       303 GtRSAif--------------~P~~nLglIIvDEE  323 (731)
                      ||-|-+=              .-...+...||||-
T Consensus       180 ~Tn~E~gFDYLRDnm~~~~~~~vqr~~~~aIvDEv  214 (946)
T PRK12902        180 ATNSELGFDYLRDNMATDISEVVQRPFNYCVIDEV  214 (946)
T ss_pred             ECCCCCCCCCCCCCCCCCHHHHHCCCCCEEEEECH
T ss_conf             78887577235304478868843879965898542


No 253
>COG3857 AddB ATP-dependent nuclease, subunit B [DNA replication, recombination, and repair]
Probab=93.86  E-value=0.13  Score=31.48  Aligned_cols=67  Identities=15%  Similarity=0.058  Sum_probs=29.6

Q ss_pred             HHHHHHHHHHHHHHHHH-----------HHHHH--HHHCCCCCC---CCCEEEEEECCCCCHHHHHHHHCCHHHHHHHHH
Q ss_conf             03443102455789999-----------98754--311025667---886899993298648889999589799999999
Q gi|254780619|r  563 GDLGLTNADLRSSERTF-----------QLLSQ--VTGRAGRFG---LKSLGLIQAYQPTHPVMQALVSGDADSFYESEI  626 (731)
Q Consensus       563 aD~~l~~pd~ra~E~~~-----------qll~q--v~gRagr~~---~~g~v~iQt~~p~~~~~~~~~~~d~~~f~~~el  626 (731)
                      .|..+..-||.++-+.|           ||++=  ++++.+-..   ..|-.+++-.+   |.++.-...+-+...+.-.
T Consensus       912 ~~~~l~IvDYKSsa~~f~l~~vYyGL~lQlmTYLdai~q~~~~~~~~p~GalYfhm~e---P~i~~~~~~~l~~i~~el~  988 (1108)
T COG3857         912 KDGYLGIVDYKSSAHQFDLTDVYYGLSLQLMTYLDAIKQNAPEDDVKPGGALYFHMHE---PEIKLNSDLGLDKIEQELK  988 (1108)
T ss_pred             CCCCEEEEEECCCCCCCCHHHHCCCHHHHHHHHHHHHHHHHHHHCCCCCCEEEEEECC---HHHHHCCCCCHHHHHHHHH
T ss_conf             5881588872365211452432144128799999999874043115644147888438---5653023444688999998


Q ss_pred             HHHHHC
Q ss_conf             999981
Q gi|254780619|r  627 RARESV  632 (731)
Q Consensus       627 ~~R~~~  632 (731)
                      +.++.-
T Consensus       989 Ks~k~k  994 (1108)
T COG3857         989 KSMKYK  994 (1108)
T ss_pred             HHHHHH
T ss_conf             756530


No 254
>KOG0390 consensus
Probab=93.80  E-value=0.59  Score=26.40  Aligned_cols=128  Identities=20%  Similarity=0.209  Sum_probs=81.5

Q ss_pred             CCCHHHHHHHHHHHHHHCC-----CCCEEEEECCCCHHHHHHHHHHHHHHHHCCCC-------EEEEECCCHHHHHHHHH
Q ss_conf             6883789999999875204-----89619984475315799999999998514684-------79971521001344555
Q gi|254780619|r  198 ILDKNQQDVVEQVVPLCTK-----GFAVSLISGVTGSGKTEVYLEIVAAVLHLGKQ-------VLILLPEISLTSAILER  265 (731)
Q Consensus       198 ~Lt~eQ~~a~~~i~~~~~~-----~f~~~LL~GvTGSGKTEVYl~li~~~L~~Gkq-------vLiLvPEI~Lt~Q~~~r  265 (731)
                      .|-+.|+..+..+......     +..-..+--.-|+|||.--+-++-..|+++-|       .||++|- +|..-+.+-
T Consensus       238 ~LrPHQ~EG~~FL~knl~g~~~~~~~~GCImAd~~GlGKTlq~IsflwtlLrq~P~~~~~~~k~lVV~P~-sLv~nWkkE  316 (776)
T KOG0390         238 ILRPHQREGFEFLYKNLAGLIRPKNSGGCIMADEPGLGKTLQCISFIWTLLRQFPQAKPLINKPLVVAPS-SLVNNWKKE  316 (776)
T ss_pred             HCCCHHHHHHHHHHHHHHCCCCCCCCCCEEEECCCCCCHHHHHHHHHHHHHHHCCCCCCCCCCCEEECCH-HHHHHHHHH
T ss_conf             1281578778997864113111588875472078876407888999999998686755444660798458-888789999


Q ss_pred             HHCCCCC-EEEEEECCCCCHH---HHHHHHHHH---CCCCEEEEECCHH----HHHHHCCCEEEEEEECCCC
Q ss_conf             4303897-6899623557235---667899997---1997399940012----1100100013677405532
Q gi|254780619|r  266 FQKRFGV-KPAEWHSSLSTSM---REKIWRQVA---RGAISVIVGVRSA----LFLPFKKLGLIVIDEEHDI  326 (731)
Q Consensus       266 l~~rF~~-~v~v~HS~ls~~e---R~~~w~~i~---~G~~~IVIGtRSA----if~P~~nLglIIvDEEHd~  326 (731)
                      |.+-.+. ++-.+-=....++   ....|..+.   -..+-.+++.=.+    --.=...+||.|.||-|+.
T Consensus       317 F~KWl~~~~i~~l~~~~~~~~~w~~~~sil~~~~~~~~~~vli~sye~~~~~~~~il~~~~glLVcDEGHrl  388 (776)
T KOG0390         317 FGKWLGNHRINPLDFYSTKKSSWIKLKSILFLGYKQFTTPVLIISYETASDYCRKILLIRPGLLVCDEGHRL  388 (776)
T ss_pred             HHHHCCCCCCCEEEEECCCCHHHHHHHHHHHHHHHHEEEEEEECCHHHHHHHHHHHHCCCCCEEEECCCCCC
T ss_conf             987425355540454234525666667898862211257878636999999999985478986997798885


No 255
>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=93.73  E-value=0.59  Score=26.40  Aligned_cols=70  Identities=23%  Similarity=0.206  Sum_probs=51.7

Q ss_pred             CEEEEECCCCHHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHCCCCCEEE-EEECCCCC-HHHHHHHHH
Q ss_conf             619984475315799999999998514684799715210013445554303897689-96235572-356678999
Q gi|254780619|r  219 AVSLISGVTGSGKTEVYLEIVAAVLHLGKQVLILLPEISLTSAILERFQKRFGVKPA-EWHSSLST-SMREKIWRQ  292 (731)
Q Consensus       219 ~~~LL~GvTGSGKTEVYl~li~~~L~~GkqvLiLvPEI~Lt~Q~~~rl~~rF~~~v~-v~HS~ls~-~eR~~~w~~  292 (731)
                      +...++|-.+||||-+.+++++++-++|..|+++=-|-++++++.+.+    |.++- ++.+.-.. .+-.++...
T Consensus        53 Ri~ei~G~essGKTtlal~~ia~aQk~gg~~~~iD~E~a~d~~~a~~l----GVD~~~l~~~qpd~~Eqal~i~~~  124 (322)
T pfam00154        53 RIIEIYGPESSGKTTLALHAIAEAQKAGGTAAFIDAEHALDPVYAKKL----GVDIDNLLVSQPDTGEQALEIADM  124 (322)
T ss_pred             EEEEEECCCCCCHHHHHHHHHHHHHHCCCEEEEEEHHHHCCHHHHHHC----CCCHHHEEEECCCHHHHHHHHHHH
T ss_conf             089998898777899999999999734993899853660598899980----988025389778839999999999


No 256
>PRK07219 DNA topoisomerase I; Validated
Probab=93.73  E-value=0.09  Score=32.67  Aligned_cols=18  Identities=17%  Similarity=0.339  Sum_probs=9.4

Q ss_pred             HCCCH----HHHHHHHHCCHHH
Q ss_conf             09998----9997524557223
Q gi|254780619|r  160 SQVSS----HVIDGLKAQGVIK  177 (731)
Q Consensus       160 ~~~s~----~~i~~L~~kglI~  177 (731)
                      .++|.    .+.+.|-.+|+|.
T Consensus       290 lg~s~~kTm~iAQ~LYe~GlIT  311 (769)
T PRK07219        290 IGIMPTKAMSIAEKLYMRGLIS  311 (769)
T ss_pred             CCCCHHHHHHHHHHHHHCCCCC
T ss_conf             1899999999999886489544


No 257
>PRK12898 secA preprotein translocase subunit SecA; Reviewed
Probab=93.72  E-value=0.3  Score=28.64  Aligned_cols=78  Identities=17%  Similarity=0.123  Sum_probs=59.5

Q ss_pred             CCCCHHHHHHHHHHHHHHHHCCCCEEEEECCCHHHH---HHHHHHHCCCCCEEEEEECCCCCHHHHHHHHHHHCCCCEEE
Q ss_conf             475315799999999998514684799715210013---44555430389768996235572356678999971997399
Q gi|254780619|r  225 GVTGSGKTEVYLEIVAAVLHLGKQVLILLPEISLTS---AILERFQKRFGVKPAEWHSSLSTSMREKIWRQVARGAISVI  301 (731)
Q Consensus       225 GvTGSGKTEVYl~li~~~L~~GkqvLiLvPEI~Lt~---Q~~~rl~~rF~~~v~v~HS~ls~~eR~~~w~~i~~G~~~IV  301 (731)
                      =-||-|||.+..-.+--.--.|+.|-|.-..=-|+.   ++...+...+|-.|.+..+++++.+|...|.      ++|+
T Consensus       138 M~TGEGKTL~atlpaylnAL~G~gVHvvTvNDYLA~RDae~mg~iy~fLGLsvg~i~~~~~~~eRr~aY~------~DIt  211 (673)
T PRK12898        138 MQTGEGKTLTATLPAGTAALAGRPVHVITVNDYLAERDAEQMRPLYEALGVTVGCVIEDQDPEERRAAYG------ADVT  211 (673)
T ss_pred             EECCCCHHHHHHHHHHHHHHCCCCEEEEECCHHHHHHHHHHHHHHHHHHCCEEEEECCCCCHHHHHHHHC------CCCE
T ss_conf             5078858999999999997369970898045577787699999999982977845179999799999726------9957


Q ss_pred             EECCHHH
Q ss_conf             9400121
Q gi|254780619|r  302 VGVRSAL  308 (731)
Q Consensus       302 IGtRSAi  308 (731)
                      =||-+.+
T Consensus       212 YgTn~E~  218 (673)
T PRK12898        212 YCTNKEL  218 (673)
T ss_pred             EECCHHH
T ss_conf             9565233


No 258
>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=93.69  E-value=0.12  Score=31.62  Aligned_cols=36  Identities=33%  Similarity=0.528  Sum_probs=32.2

Q ss_pred             EEEEECCCCHHHHHHHHHHHHHHHHCCCCEEEEECC
Q ss_conf             199844753157999999999985146847997152
Q gi|254780619|r  220 VSLISGVTGSGKTEVYLEIVAAVLHLGKQVLILLPE  255 (731)
Q Consensus       220 ~~LL~GvTGSGKTEVYl~li~~~L~~GkqvLiLvPE  255 (731)
                      -.|+-|-||||||..+..++..++..|.+++|.=|-
T Consensus        17 H~lviG~tGsGKT~~i~~~i~~~~~~~~s~iv~DpK   52 (386)
T pfam10412        17 HILIVGTTGTGKTQALRELLDQIRARGDRAIIYDPT   52 (386)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHCCCCEEEEECC
T ss_conf             589988999988879999999999779919999587


No 259
>TIGR00064 ftsY signal recognition particle-docking protein FtsY; InterPro: IPR004390   ABC transporters belong to the ATP-Binding Cassette (ABC) superfamily, which uses the hydrolysis of ATP to energize diverse biological systems. ABC transporters are minimally constituted of two conserved regions: a highly conserved ATP binding cassette (ABC) and a less conserved transmembrane domain (TMD). These regions can be found on the same protein or on two different ones. Most ABC transporters function as a dimer and therefore are constituted of four domains, two ABC modules and two TMDs.   ABC transporters are involved in the export or import of a wide variety of substrates ranging from small ions to macromolecules. The major function of ABC import systems is to provide essential nutrients to bacteria. They are found only in prokaryotes and their four constitutive domains are usually encoded by independent polypeptides (two ABC proteins and two TMD proteins). Prokaryotic importers require additional extracytoplasmic binding proteins (one or more per systems) for function. In contrast, export systems are involved in the extrusion of noxious substances, the export of extracellular toxins and the targeting of membrane components. They are found in all living organisms and in general the TMD is fused to the ABC module in a variety of combinations. Some eukaryotic exporters encode the four domains on the same polypeptide chain .    The ABC module (approximately two hundred amino acid residues) is known to bind and hydrolyze ATP, thereby coupling transport to ATP hydrolysis in a large number of biological processes. The cassette is duplicated in several subfamilies. Its primary sequence is highly conserved, displaying a typical phosphate-binding loop: Walker A, and a magnesium binding site: Walker B. Besides these two regions, three other conserved motifs are present in the ABC cassette: the switch region which contains a histidine loop, postulated to polarize the attaching water molecule for hydrolysis, the signature conserved motif (LSGGQ) specific to the ABC transporter, and the Q-motif (between Walker A and the signature), which interacts with the gamma phosphate through a water bond. The Walker A, Walker B, Q-loop and switch region form the nucleotide binding site , , .   The 3D structure of a monomeric ABC module adopts a stubby L-shape with two distinct arms. ArmI (mainly beta-strand) contains Walker A and Walker B. The important residues for ATP hydrolysis and/or binding are located in the P-loop. The ATP-binding pocket is located at the extremity of armI. The perpendicular armII contains mostly the alpha helical subdomain with the signature motif. It only seems to be required for structural integrity of the ABC module. ArmII is in direct contact with the TMD. The hinge between armI and armII contains both the histidine loop and the Q-loop, making contact with the gamma phosphate of the ATP molecule. ATP hydrolysis leads to a conformational change that could facilitate ADP release. In the dimer the two ABC cassettes contact each other through hydrophobic interactions at the antiparallel beta-sheet of armI by a two-fold axis , , , , , .   Proteins known to belong to this family are classified in several functional subfamilies depending on the substrate used (for further information see http://www.tcdb.org/tcdb/index.php?tc=3.A.1).  This family includes the cell division ABC transporter and the periplasmic substrate-binding protein FtsY. There is a weak division between FtsY and SRP54; both are GTPases. In Escherichia coli, ftsY is an essential gene located in an operon with cell division genes ftsE and ftsX, but its apparent function is as the signal recognition particle docking protein.; GO: 0005525 GTP binding.
Probab=93.68  E-value=0.59  Score=26.43  Aligned_cols=40  Identities=33%  Similarity=0.391  Sum_probs=34.0

Q ss_pred             HCCCCCEEEEECCCCHHHHHHHHHHHHHHHHCCCCEEEEE
Q ss_conf             2048961998447531579999999999851468479971
Q gi|254780619|r  214 CTKGFAVSLISGVTGSGKTEVYLEIVAAVLHLGKQVLILL  253 (731)
Q Consensus       214 ~~~~f~~~LL~GvTGSGKTEVYl~li~~~L~~GkqvLiLv  253 (731)
                      ..++..++|+-||.|+|||===-.++....++|++|++=+
T Consensus        78 ~~~kp~Vil~VGVNG~GKTTTIaKLA~~l~~~Gk~V~laA  117 (284)
T TIGR00064        78 EEKKPNVILFVGVNGVGKTTTIAKLANKLKKQGKSVLLAA  117 (284)
T ss_pred             CCCCCEEEEEEEEECCCHHHHHHHHHHHHHHCCCEEEEEC
T ss_conf             4789779999844088601028899999987499089982


No 260
>PRK00411 cdc6 cell division control protein 6; Reviewed
Probab=93.66  E-value=0.62  Score=26.22  Aligned_cols=44  Identities=20%  Similarity=0.248  Sum_probs=27.1

Q ss_pred             CCHHHHHHHHH-HHHHHC-CCCCEEEEECCCCHHHHHHHHHHHHHH
Q ss_conf             88378999999-987520-489619984475315799999999998
Q gi|254780619|r  199 LDKNQQDVVEQ-VVPLCT-KGFAVSLISGVTGSGKTEVYLEIVAAV  242 (731)
Q Consensus       199 Lt~eQ~~a~~~-i~~~~~-~~f~~~LL~GvTGSGKTEVYl~li~~~  242 (731)
                      --++|...+.. +..... ......+++|.||+|||-+--..+++.
T Consensus        34 ~Re~Ei~~l~~~l~~~l~g~~~~n~~I~G~pGTGKT~~vk~v~~~l   79 (394)
T PRK00411         34 HREEQIEELAFALRPALRGSRPSNVLILGPPGTGKTTTVKKVFEEL   79 (394)
T ss_pred             CHHHHHHHHHHHHHHHHCCCCCCCEEEECCCCCCHHHHHHHHHHHH
T ss_conf             8599999999999999759999847998899998999999999999


No 261
>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=93.63  E-value=0.13  Score=31.38  Aligned_cols=42  Identities=38%  Similarity=0.618  Sum_probs=25.4

Q ss_pred             HHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHHHHHHHHHHCCCCEE
Q ss_conf             99999998752048961998447531579999999999851468479
Q gi|254780619|r  204 QDVVEQVVPLCTKGFAVSLISGVTGSGKTEVYLEIVAAVLHLGKQVL  250 (731)
Q Consensus       204 ~~a~~~i~~~~~~~f~~~LL~GvTGSGKTEVYl~li~~~L~~GkqvL  250 (731)
                      +.+++.+... ...+...+|.|-||||||++--.+    =.+|.|||
T Consensus       114 ~~v~~~l~~~-~~~~~~~vl~G~TG~GKT~iL~~L----~~~G~qvi  155 (311)
T TIGR03167       114 RFVIDQLEEL-PQPFPLIVLGGMTGSGKTELLHAL----ANAGAQVL  155 (311)
T ss_pred             HHHHHHHHHC-CCCCCEEEEECCCCCCHHHHHHHH----HHCCCCCC
T ss_conf             9999999714-546876998788887789999999----97699742


No 262
>PRK07220 DNA topoisomerase I; Validated
Probab=93.55  E-value=0.056  Score=34.22  Aligned_cols=41  Identities=29%  Similarity=0.477  Sum_probs=32.1

Q ss_pred             CCCCCCCCCEEEEECCC---CCCEEC---HHHCCCCCCC---------CCCCCCCC
Q ss_conf             43101465201211357---832000---0210244655---------56667874
Q gi|254780619|r  445 RLKCLHCSCWLVEHRSK---KKLYCH---QCGHSAIYSQ---------SCVVCGSS  485 (731)
Q Consensus       445 ~~~C~~C~~~l~~h~~~---~~l~Ch---~Cg~~~~~~~---------~Cp~Cg~~  485 (731)
                      ...||.|+..|.+.+..   ..+-|.   -|.++.++|.         .||.||-+
T Consensus       589 ~~~CP~Cg~~l~~r~~k~g~~FigCs~YP~C~~t~pLp~~g~~~~~~~~C~~~~~~  644 (740)
T PRK07220        589 IGKCSLCGSELMVRRSKRGSRFIGCSGYPNCTFSLPLPKSGQIIVTDKVCEAHGLH  644 (740)
T ss_pred             CCCCCCCCCCCEEEECCCCCEEEECCCCCCCCCCEECCCCCCEEECCCCCCCCCCE
T ss_conf             89788899600477458799788589899999852269998463478868779983


No 263
>PRK02362 ski2-like helicase; Provisional
Probab=93.55  E-value=0.4  Score=27.72  Aligned_cols=84  Identities=25%  Similarity=0.283  Sum_probs=55.8

Q ss_pred             HHHHHHHHHHCCCCEEEEECCCHHHHHHHH-----------------------H------------HHCCCCCEEEEEEC
Q ss_conf             999999985146847997152100134455-----------------------5------------43038976899623
Q gi|254780619|r  235 YLEIVAAVLHLGKQVLILLPEISLTSAILE-----------------------R------------FQKRFGVKPAEWHS  279 (731)
Q Consensus       235 Yl~li~~~L~~GkqvLiLvPEI~Lt~Q~~~-----------------------r------------l~~rF~~~v~v~HS  279 (731)
                      .+.++.+++.+|+|+||-+|.=.-+..+..                       +            +.+....-|+..|+
T Consensus       232 ~~~l~~~~~~~~~~~LVF~~SR~~~e~~A~~la~~~~~~~~~~~~~~l~~~~~~i~~~~~~~~~~~L~~~l~~GVafHHA  311 (736)
T PRK02362        232 DLNLVLDTLDEGGQCLVFVSSRRNAEAFAKRAASALKKALSAEEREALAGIAEEIREVSETDTSKVLADCVRSGAAFHHA  311 (736)
T ss_pred             HHHHHHHHHHCCCCEEEEEECHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHCCEEEECC
T ss_conf             89999999973990699982499999999999875242157566889999999997344420359999999609485159


Q ss_pred             CCCCHHHHHHHHHHHCCCCEEEEECCHH---HHHHHCCCEEEEEE
Q ss_conf             5572356678999971997399940012---11001000136774
Q gi|254780619|r  280 SLSTSMREKIWRQVARGAISVIVGVRSA---LFLPFKKLGLIVID  321 (731)
Q Consensus       280 ~ls~~eR~~~w~~i~~G~~~IVIGtRSA---if~P~~nLglIIvD  321 (731)
                      +|++.+|.-+=..-++|..+|++.|-.=   |=+|.   ..+||.
T Consensus       312 GL~~~~R~lVE~~Fr~g~Ikvl~aTsTLA~GVNLPA---r~VIi~  353 (736)
T PRK02362        312 GLSREHRELVEEGFRDGLIKVISSTPTLAAGLNLPA---RRVIIR  353 (736)
T ss_pred             CCCHHHHHHHHHHHHCCCCCEEEECCHHHCCCCCCE---EEEEEE
T ss_conf             999899999999998799838972516650557852---699980


No 264
>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=93.55  E-value=0.2  Score=30.00  Aligned_cols=49  Identities=27%  Similarity=0.290  Sum_probs=36.2

Q ss_pred             CCEEEEECCCCHHHHHHHHHHHHH-HHHCCCCEEEEECCCHHHHHHHHHHH
Q ss_conf             961998447531579999999999-85146847997152100134455543
Q gi|254780619|r  218 FAVSLISGVTGSGKTEVYLEIVAA-VLHLGKQVLILLPEISLTSAILERFQ  267 (731)
Q Consensus       218 f~~~LL~GvTGSGKTEVYl~li~~-~L~~GkqvLiLvPEI~Lt~Q~~~rl~  267 (731)
                      -++.|+.|.+|||||-.-++.+.+ ++++|..|+++--|-. ..++.++++
T Consensus        19 gs~~LI~G~pGsGKT~la~qfl~~ga~~~ge~~lYis~ee~-~~~l~~~~~   68 (231)
T pfam06745        19 GRVVLITGGPGTGKTIFGLQFLYNGALEYGEPGVYVTLEEP-PEDLRENAK   68 (231)
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEEECCC-HHHHHHHHH
T ss_conf             96999985897259999999999999865896899981379-999999999


No 265
>COG0514 RecQ Superfamily II DNA helicase [DNA replication, recombination, and repair]
Probab=93.51  E-value=0.47  Score=27.15  Aligned_cols=73  Identities=21%  Similarity=0.355  Sum_probs=56.5

Q ss_pred             CCCCEEEEECCCHHHHHHHHHHHCCCCCEEEEEECCCCCHHHHHHHHHHHCCCCEEEEECCHHHHHHH--CCCEEEE
Q ss_conf             46847997152100134455543038976899623557235667899997199739994001211001--0001367
Q gi|254780619|r  245 LGKQVLILLPEISLTSAILERFQKRFGVKPAEWHSSLSTSMREKIWRQVARGAISVIVGVRSALFLPF--KKLGLIV  319 (731)
Q Consensus       245 ~GkqvLiLvPEI~Lt~Q~~~rl~~rF~~~v~v~HS~ls~~eR~~~w~~i~~G~~~IVIGtRSAif~P~--~nLglII  319 (731)
                      .++..+|-+..-.-+.++.+++.+. |.+++.||++|++.+|..+-.+-.+++.+|+|.|- |.=+=+  +|+..+|
T Consensus       229 ~~~~GIIYc~sRk~~E~ia~~L~~~-g~~a~~YHaGl~~~eR~~~q~~f~~~~~~iiVAT~-AFGMGIdKpdVRfVi  303 (590)
T COG0514         229 LSKSGIIYCLTRKKVEELAEWLRKN-GISAGAYHAGLSNEERERVQQAFLNDEIKVMVATN-AFGMGIDKPDVRFVI  303 (590)
T ss_pred             CCCCEEEEEEEHHHHHHHHHHHHHC-CCCEEEECCCCCHHHHHHHHHHHHCCCCCEEEEEC-CCCCCCCCCCCEEEE
T ss_conf             6897289993377599999999977-97257751898899999999997169986899964-624776788840799


No 266
>PRK06321 replicative DNA helicase; Provisional
Probab=93.50  E-value=0.66  Score=26.04  Aligned_cols=132  Identities=17%  Similarity=0.183  Sum_probs=78.0

Q ss_pred             CEEEEECCCCHHHHHHHHHHHHHHH-HCCCCEEEEECCCHHHHHHHHHHHCCC-CCEEE-EEECCCCCHHHHHHHHHHHC
Q ss_conf             6199844753157999999999985-146847997152100134455543038-97689-96235572356678999971
Q gi|254780619|r  219 AVSLISGVTGSGKTEVYLEIVAAVL-HLGKQVLILLPEISLTSAILERFQKRF-GVKPA-EWHSSLSTSMREKIWRQVAR  295 (731)
Q Consensus       219 ~~~LL~GvTGSGKTEVYl~li~~~L-~~GkqvLiLvPEI~Lt~Q~~~rl~~rF-~~~v~-v~HS~ls~~eR~~~w~~i~~  295 (731)
                      ..++|=|-+|.|||-..++++.++. +.++.|++.--|-+ ..|+..|+-... +.... +-.+.+++.+.......+..
T Consensus       227 dliviaaRPsmGKTalalnia~~~a~~~~~~v~~fSLEMs-~~ql~~R~ls~~s~i~~~~i~~g~l~~~e~~~~~~a~~~  305 (472)
T PRK06321        227 NLMILAARPAMGKTALALNIAENFCFQNRLPVGIFSLEMT-VDQLIHRIICSRSEVESKKISVGDLSGRDFQRIVSVVNE  305 (472)
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEECCCCC-HHHHHHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHHHHH
T ss_conf             5799853899977999999999999856994699757799-999999998740376755210479999999999999999


Q ss_pred             -CCCEEEEECCHHH-----------HHHHCCCEEEEEEECCCCCCHHCCCC----CC-CHHH--HH------HHHHHHCC
Q ss_conf             -9973999400121-----------10010001367740553210000244----32-2489--99------99751103
Q gi|254780619|r  296 -GAISVIVGVRSAL-----------FLPFKKLGLIVIDEEHDISYKQEEGI----LY-NARD--MS------IVRGKIES  350 (731)
Q Consensus       296 -G~~~IVIGtRSAi-----------f~P~~nLglIIvDEEHd~sykq~~~p----ry-~aRd--vA------~~Ra~~~~  350 (731)
                       .+..+.|--.+++           +-.-.++++||||      |=|-..+    +. ..|.  ++      ...|+..+
T Consensus       306 l~~~~l~idd~~~~ti~~i~~~~r~~k~~~~l~~vvID------YlqL~~~~~~~~~~~~r~~~i~~isr~lK~lAkel~  379 (472)
T PRK06321        306 MQEHTLLIDDQPGLKITDLRARARRMKESYDIQFLIID------YLQLLSGSGTLRNSESRQTEISEISRMLKNLARELN  379 (472)
T ss_pred             HHHCCEEEECCCCCCHHHHHHHHHHHHHHCCCCEEEEE------EHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHC
T ss_conf             85487578679999899999999999873899879997------277416777777788899999999999999999979


Q ss_pred             CCEECCC
Q ss_conf             2100002
Q gi|254780619|r  351 FPVVLVS  357 (731)
Q Consensus       351 ~~lilgS  357 (731)
                      +|||+.|
T Consensus       380 vpvi~Ls  386 (472)
T PRK06321        380 IPILCLS  386 (472)
T ss_pred             CCEEEEC
T ss_conf             9799972


No 267
>COG3357 Predicted transcriptional regulator containing an HTH domain fused to a Zn-ribbon [Transcription]
Probab=93.47  E-value=0.076  Score=33.22  Aligned_cols=50  Identities=22%  Similarity=0.397  Sum_probs=33.4

Q ss_pred             HHHHHHHHCCCCEEEEEECCCCEEHHCCCCCCCCCCCCCCCCCEEEEECCCCCCEECHHHCCCCCCCCCCCCCCCCEECC
Q ss_conf             99998862265517997422200000023565434310146520121135783200002102446555666787411001
Q gi|254780619|r  411 IDGIRHTLARNEQTLLFLNRRGYAPLTLCQVCGNRLKCLHCSCWLVEHRSKKKLYCHQCGHSAIYSQSCVVCGSSGKMIA  490 (731)
Q Consensus       411 ~~~i~~~l~~g~qvll~lnRrGya~~~~C~~Cg~~~~C~~C~~~l~~h~~~~~l~Ch~Cg~~~~~~~~Cp~Cg~~~~l~~  490 (731)
                      ++-|.+.|.+....|++.+       ..|++||+...-.                      ....|.+||.|.|. ++..
T Consensus        40 L~hiak~lkr~g~~Llv~P-------a~CkkCGfef~~~----------------------~ik~pSRCP~CKSE-~Ie~   89 (97)
T COG3357          40 LEHIAKSLKRKGKRLLVRP-------ARCKKCGFEFRDD----------------------KIKKPSRCPKCKSE-WIEE   89 (97)
T ss_pred             HHHHHHHHHHCCCEEEECC-------HHHCCCCCCCCCC----------------------CCCCCCCCCCCHHH-CCCC
T ss_conf             9999999974786688547-------3222268623655----------------------46786669853143-0458


No 268
>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=93.46  E-value=0.39  Score=27.80  Aligned_cols=126  Identities=24%  Similarity=0.407  Sum_probs=77.8

Q ss_pred             CCCCCCCCCCCCCCCCHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHH
Q ss_conf             23566543446666883789999999875204896199844753157999999999985146847997152100134455
Q gi|254780619|r  185 PVVDSPNLYFSLPILDKNQQDVVEQVVPLCTKGFAVSLISGVTGSGKTEVYLEIVAAVLHLGKQVLILLPEISLTSAILE  264 (731)
Q Consensus       185 ~~~~~~~~~~~~~~Lt~eQ~~a~~~i~~~~~~~f~~~LL~GvTGSGKTEVYl~li~~~L~~GkqvLiLvPEI~Lt~Q~~~  264 (731)
                      ...+.|+.......-+.+-+++++++..-..+         -+||++.           ..|.+-+|..|-=.-+.|+..
T Consensus       200 ~SFdRPNl~y~v~~K~~n~~~~~~dl~~f~~~---------~~~s~~~-----------~~G~sGIIYC~SR~~~e~~a~  259 (497)
T TIGR00614       200 TSFDRPNLYYEVRRKTSNTKKILEDLLRFIVK---------KASSAWE-----------FKGKSGIIYCPSRKKSEQVAA  259 (497)
T ss_pred             ECCCCCCCEEEEECCCCCHHHHHHHHHHHHHH---------HCCCCCC-----------CCCCCEEEECCCCHHHHHHHH
T ss_conf             04668763034005789702589999999875---------2035652-----------458830275287234899999


Q ss_pred             HHHCCCCCEEEEEECCCCCHHHHHHHHHHH-CCCCEEEEECCHHHH-HHH--CCCEEEEE-EECC-CCCCHHCCC
Q ss_conf             543038976899623557235667899997-199739994001211-001--00013677-4055-321000024
Q gi|254780619|r  265 RFQKRFGVKPAEWHSSLSTSMREKIWRQVA-RGAISVIVGVRSALF-LPF--KKLGLIVI-DEEH-DISYKQEEG  333 (731)
Q Consensus       265 rl~~rF~~~v~v~HS~ls~~eR~~~w~~i~-~G~~~IVIGtRSAif-~P~--~nLglIIv-DEEH-d~sykq~~~  333 (731)
                      .|++. |-.-+-||.+|+.++|.++-.+=. ..+..|||.|=  +| +=.  +|..-||= |=-- =+||.||.|
T Consensus       260 ~L~~~-G~~a~aYHAGl~~~~R~~V~~~f~nrD~~QvVvATv--AFGMGInKpdvRfViH~~~Pk~~EsYYQE~G  331 (497)
T TIGR00614       260 ELQKL-GIAAGAYHAGLEISARKEVQHKFQNRDEIQVVVATV--AFGMGINKPDVRFVIHYSLPKSMESYYQESG  331 (497)
T ss_pred             HHHHC-CCEEEHHHCCCCHHHHHHHHHHHHCCCCCEEEEEEE--ECCCCCCCCCCCEEEEECCCCCCCCCCCCCC
T ss_conf             99755-861002402688647789999875038857999872--1268887635367885078856211013555


No 269
>PRK13700 conjugal transfer protein TraD; Provisional
Probab=93.39  E-value=0.14  Score=31.24  Aligned_cols=37  Identities=24%  Similarity=0.307  Sum_probs=33.6

Q ss_pred             CEEEEECCCCHHHHHHHHHHHHHHHHCCCCEEEEECC
Q ss_conf             6199844753157999999999985146847997152
Q gi|254780619|r  219 AVSLISGVTGSGKTEVYLEIVAAVLHLGKQVLILLPE  255 (731)
Q Consensus       219 ~~~LL~GvTGSGKTEVYl~li~~~L~~GkqvLiLvPE  255 (731)
                      +-+|++|.||||||.+-.+++.++-++|.-|+|.=|.
T Consensus       186 qH~li~GTtGtGKS~~ir~LL~qIR~RGdrAIIyD~~  222 (732)
T PRK13700        186 QNFCLHGTVGAGKSEVIRRLANYARQRGDMVVIYDRS  222 (732)
T ss_pred             HEEEEECCCCCCHHHHHHHHHHHHHHCCCCEEEECCC
T ss_conf             1267746888889999999999999729958999399


No 270
>PRK12900 secA preprotein translocase subunit SecA; Reviewed
Probab=93.38  E-value=0.32  Score=28.49  Aligned_cols=92  Identities=17%  Similarity=0.199  Sum_probs=65.6

Q ss_pred             CCCHHHHHHHHHHHHHHHHCCCCEEEEECCCHHHH---HHHHHHHCCCCCEEEEEECCCCCHHHHHHHHHHHCCCCEEEE
Q ss_conf             75315799999999998514684799715210013---445554303897689962355723566789999719973999
Q gi|254780619|r  226 VTGSGKTEVYLEIVAAVLHLGKQVLILLPEISLTS---AILERFQKRFGVKPAEWHSSLSTSMREKIWRQVARGAISVIV  302 (731)
Q Consensus       226 vTGSGKTEVYl~li~~~L~~GkqvLiLvPEI~Lt~---Q~~~rl~~rF~~~v~v~HS~ls~~eR~~~w~~i~~G~~~IVI  302 (731)
                      -||-|||.|..-.+--.--.|+.|-|+-..=-|+.   .+...+...+|-.|.+..+++++.+|...|.      ++|+=
T Consensus       115 ~TGEGKTLvatlp~ylnaL~GkgvHvvTvNdYLA~RDae~m~~vy~fLGlsvg~i~~~~~~~err~aY~------~DItY  188 (983)
T PRK12900        115 ATGEGKTLVSTLPTFLNALTGRGVHVVTVNDYLAQRDKEWMNPVFEFHGLSVGVILNSMRPEERREQYL------CDITY  188 (983)
T ss_pred             CCCCCHHHHHHHHHHHHHHCCCCCEEECCCHHHHHHHHHHHHHHHHHHCCEEEEECCCCCHHHHHHHHC------CCCEE
T ss_conf             178858999999999986369982898145676786799999999984977703089999899999875------99578


Q ss_pred             ECCHHH-H-------------HHHCCCEEEEEEEC
Q ss_conf             400121-1-------------00100013677405
Q gi|254780619|r  303 GVRSAL-F-------------LPFKKLGLIVIDEE  323 (731)
Q Consensus       303 GtRSAi-f-------------~P~~nLglIIvDEE  323 (731)
                      ||-+-+ |             .-...+-..||||-
T Consensus       189 gTn~E~gFDYLRDnm~~~~~~~vqr~~~~aIVDEv  223 (983)
T PRK12900        189 GTNNEFGFDYLRDNMAGSPEEMVQRDFYFAIVDEV  223 (983)
T ss_pred             ECCCCCCCCCCHHCCCCCHHHHCCCCCCEEEEECH
T ss_conf             78985424021004477868842788855898441


No 271
>PRK08939 primosomal protein DnaI; Reviewed
Probab=93.37  E-value=0.46  Score=27.27  Aligned_cols=50  Identities=14%  Similarity=0.167  Sum_probs=35.5

Q ss_pred             CEEEEECCCCHHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHCCCCCE
Q ss_conf             6199844753157999999999985146847997152100134455543038976
Q gi|254780619|r  219 AVSLISGVTGSGKTEVYLEIVAAVLHLGKQVLILLPEISLTSAILERFQKRFGVK  273 (731)
Q Consensus       219 ~~~LL~GvTGSGKTEVYl~li~~~L~~GkqvLiLvPEI~Lt~Q~~~rl~~rF~~~  273 (731)
                      .-.+|+|..|.|||-+.--++.+..++|..|+++.     .|.++..+++.|++.
T Consensus       158 kGlyl~G~~G~GKTyL~~aian~La~~g~~v~~v~-----~p~~~~~lK~s~~d~  207 (306)
T PRK08939        158 KGLYLYGDFGVGKTYLLAAIANELAKKGVSSTLVH-----FPEFIRELKNAISDG  207 (306)
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHHHHCCCEEEEEE-----HHHHHHHHHHHHCCC
T ss_conf             77889899999899999999999998699299987-----599999999986489


No 272
>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=93.33  E-value=0.7  Score=25.85  Aligned_cols=36  Identities=31%  Similarity=0.483  Sum_probs=30.4

Q ss_pred             CEEEEECCCCHHHHHHHHHHHHHHHHCCCCEEEEEC
Q ss_conf             619984475315799999999998514684799715
Q gi|254780619|r  219 AVSLISGVTGSGKTEVYLEIVAAVLHLGKQVLILLP  254 (731)
Q Consensus       219 ~~~LL~GvTGSGKTEVYl~li~~~L~~GkqvLiLvP  254 (731)
                      ++.+|-|.||+|||---.+++.....+|+.|.+.-=
T Consensus         1 ~Vi~lvGptGvGKTTTiaKLA~~~~~~~~kV~lit~   36 (173)
T cd03115           1 TVILLVGLQGVGKTTTAAKLALYLKKKGKKVLLVAA   36 (173)
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHHHHCCCEEEEEEC
T ss_conf             999998999998899999999999976992899974


No 273
>PRK12899 secA preprotein translocase subunit SecA; Reviewed
Probab=93.28  E-value=0.37  Score=28.00  Aligned_cols=76  Identities=21%  Similarity=0.214  Sum_probs=57.5

Q ss_pred             CCCHHHHHHHHHHHHHHHHCCCCEEEEECCCHHHH---HHHHHHHCCCCCEEEEEECCCCCHHHHHHHHHHHCCCCEEEE
Q ss_conf             75315799999999998514684799715210013---445554303897689962355723566789999719973999
Q gi|254780619|r  226 VTGSGKTEVYLEIVAAVLHLGKQVLILLPEISLTS---AILERFQKRFGVKPAEWHSSLSTSMREKIWRQVARGAISVIV  302 (731)
Q Consensus       226 vTGSGKTEVYl~li~~~L~~GkqvLiLvPEI~Lt~---Q~~~rl~~rF~~~v~v~HS~ls~~eR~~~w~~i~~G~~~IVI  302 (731)
                      -||-|||.|..-.+--.--.|+.|-|+-..=-|+.   .+...+...+|-.|.+..+++++.+|...|.      ++|+=
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             ECCHH
Q ss_conf             40012
Q gi|254780619|r  303 GVRSA  307 (731)
Q Consensus       303 GtRSA  307 (731)
                      ||-+-
T Consensus       189 gTn~E  193 (969)
T PRK12899        189 GTASE  193 (969)
T ss_pred             ECCCC
T ss_conf             78866


No 274
>KOG0340 consensus
Probab=93.27  E-value=0.53  Score=26.75  Aligned_cols=74  Identities=26%  Similarity=0.422  Sum_probs=46.8

Q ss_pred             HHHHHHCCCCCCEEEEEHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCEEE-EEECCC
Q ss_conf             9998621257657987044302311345201233000344310245578999998754311025667886899-993298
Q gi|254780619|r  527 LQLSAIAKGEIDIIIGTQLVAKGHNFPRMSLVGVVDGDLGLTNADLRSSERTFQLLSQVTGRAGRFGLKSLGL-IQAYQP  605 (731)
Q Consensus       527 ~~~~~~~~~~~~ilvgTq~i~kg~~fp~v~lv~il~aD~~l~~pd~ra~E~~~qll~qv~gRagr~~~~g~v~-iQt~~p  605 (731)
                      ..+..|+++.+.|||+|-..+.|+|.|.|.||+--|.-.   -|      +.|  ++ -.||..|+.+.|..| |-| .-
T Consensus       295 ~aLsrFrs~~~~iliaTDVAsRGLDIP~V~LVvN~diPr---~P------~~y--iH-RvGRtARAGR~G~aiSivt-~r  361 (442)
T KOG0340         295 AALSRFRSNAARILIATDVASRGLDIPTVELVVNHDIPR---DP------KDY--IH-RVGRTARAGRKGMAISIVT-QR  361 (442)
T ss_pred             HHHHHHHHCCCCEEEEECHHHCCCCCCCEEEEEECCCCC---CH------HHH--HH-HHCCHHCCCCCCCEEEEEC-HH
T ss_conf             899877626740899731343278988446787068899---87------888--87-6030120567764289862-42


Q ss_pred             CCHHHHHH
Q ss_conf             64888999
Q gi|254780619|r  606 THPVMQAL  613 (731)
Q Consensus       606 ~~~~~~~~  613 (731)
                      |-.+++++
T Consensus       362 Dv~l~~ai  369 (442)
T KOG0340         362 DVELLQAI  369 (442)
T ss_pred             HHHHHHHH
T ss_conf             27999999


No 275
>PRK08938 DNA topoisomerase I; Validated
Probab=93.26  E-value=0.087  Score=32.76  Aligned_cols=45  Identities=20%  Similarity=0.439  Sum_probs=30.6

Q ss_pred             CCCCCCCCEEEEEC--CCCCCEECH---HHCCCCCC----CCCCCCCCCCEECCC
Q ss_conf             31014652012113--578320000---21024465----556667874110013
Q gi|254780619|r  446 LKCLHCSCWLVEHR--SKKKLYCHQ---CGHSAIYS----QSCVVCGSSGKMIAC  491 (731)
Q Consensus       446 ~~C~~C~~~l~~h~--~~~~l~Ch~---Cg~~~~~~----~~Cp~Cg~~~~l~~~  491 (731)
                      ..||.|+.+|+.-.  .+..+-|.-   |.++.+++    ..||.||.. .+..+
T Consensus       578 ~~Cp~Cg~~l~~k~gr~G~F~~Cs~yP~Ck~t~~~~~~~~~~CP~C~~g-~l~~r  631 (692)
T PRK08938        578 FDCEVCGSPMVIKMGRYGKFYACSNFPDCRNTKAIVKEIGVTCPKCHKG-QVIER  631 (692)
T ss_pred             CCCCCCCCCCEEEECCCCCEEECCCCCCCCCCCCCCCCCCCCCCCCCCC-CEEEE
T ss_conf             9886788600688157884334789988888677665568829599997-45755


No 276
>PRK05973 replicative DNA helicase; Provisional
Probab=93.25  E-value=0.3  Score=28.64  Aligned_cols=113  Identities=19%  Similarity=0.212  Sum_probs=67.2

Q ss_pred             CEEEEECCCCHHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHCC------CCCEEEEE-ECCCCCHHHHHHHH
Q ss_conf             619984475315799999999998514684799715210013445554303------89768996-23557235667899
Q gi|254780619|r  219 AVSLISGVTGSGKTEVYLEIVAAVLHLGKQVLILLPEISLTSAILERFQKR------FGVKPAEW-HSSLSTSMREKIWR  291 (731)
Q Consensus       219 ~~~LL~GvTGSGKTEVYl~li~~~L~~GkqvLiLvPEI~Lt~Q~~~rl~~r------F~~~v~v~-HS~ls~~eR~~~w~  291 (731)
                      ...+|=|-.|=|||-.-|+++.++.++|+.|+|--=|-. ..|+..|+..-      ++....+- ...++..+-   -.
T Consensus        65 DLIIlAARPsMGKTafaLnla~~A~k~g~~v~fFSLEM~-~~ql~~RL~~~~~~~~~~~~~~~iD~sd~i~~~~i---~r  140 (237)
T PRK05973         65 DLVLLGARPGQGKTLLGLELAVEAMKSGRTGVFFTLEYT-EKDVLDRLRALGVDRAQFADLFEFDTSDAICADYI---IA  140 (237)
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHHHHHCCCEEEEEECCC-HHHHHHHHHHCCCCHHHCCCCCEECCCHHHHHHHH---HH
T ss_conf             779994289887899999999999995996699961599-99999999972778334067510038303339999---99


Q ss_pred             HHHCCCCEEEEECCHHHHHHHCCCEEEEEEECCCCCCHHCCC-----CCC--CHHHHHHHHHHHCCCCEECCCC
Q ss_conf             997199739994001211001000136774055321000024-----432--2489999975110321000024
Q gi|254780619|r  292 QVARGAISVIVGVRSALFLPFKKLGLIVIDEEHDISYKQEEG-----ILY--NARDMSIVRGKIESFPVVLVSA  358 (731)
Q Consensus       292 ~i~~G~~~IVIGtRSAif~P~~nLglIIvDEEHd~sykq~~~-----pry--~aRdvA~~Ra~~~~~~lilgSA  358 (731)
                                      -...-.+.+|||||      |=|-..     +--  -.|.+ ...|+..++|+|+-|-
T Consensus       141 ----------------rl~~~~~~~LIVID------YLQLM~~~r~~~eiseisRsL-K~lAkEl~vPVvaLSQ  191 (237)
T PRK05973        141 ----------------RLASAPRGTLVVID------YLQLLDQRREKPDLSVQVRAL-KSFARKRGVILVFISQ  191 (237)
T ss_pred             ----------------HHHHCCCCCEEEEE------CHHHHCCCCCCCCHHHHHHHH-HHHHHHHCCCEEEEEC
T ss_conf             ----------------98527899689997------677526677886689999999-9999986993999400


No 277
>PRK08769 DNA polymerase III subunit delta'; Validated
Probab=93.25  E-value=0.2  Score=30.04  Aligned_cols=49  Identities=33%  Similarity=0.337  Sum_probs=39.2

Q ss_pred             CCCHHHHHHHHHHHHHHCCC--CCEEEEECCCCHHHHHHHHHHHHHHHHCC
Q ss_conf             68837899999998752048--96199844753157999999999985146
Q gi|254780619|r  198 ILDKNQQDVVEQVVPLCTKG--FAVSLISGVTGSGKTEVYLEIVAAVLHLG  246 (731)
Q Consensus       198 ~Lt~eQ~~a~~~i~~~~~~~--f~~~LL~GvTGSGKTEVYl~li~~~L~~G  246 (731)
                      ..+++|+.+++.+.....++  .-.+|++|-.|+||+.....+++..+..+
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 278
>cd01126 TraG_VirD4 The TraG/TraD/VirD4 family are bacterial conjugation proteins involved in type IV secretion. These proteins aid the transfer of DNA from the plasmid into the host bacterial chromosome. They contain an ATP binding domain. VirD4 is involved in DNA transfer to plant cells and is required for virulence.
Probab=93.23  E-value=0.33  Score=28.35  Aligned_cols=55  Identities=20%  Similarity=0.267  Sum_probs=39.8

Q ss_pred             EEEECCCCHHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHCCCCCEEEEEE
Q ss_conf             9984475315799999999998514684799715210013445554303897689962
Q gi|254780619|r  221 SLISGVTGSGKTEVYLEIVAAVLHLGKQVLILLPEISLTSAILERFQKRFGVKPAEWH  278 (731)
Q Consensus       221 ~LL~GvTGSGKTEVYl~li~~~L~~GkqvLiLvPEI~Lt~Q~~~rl~~rF~~~v~v~H  278 (731)
                      .|+-|-||||||.-|  ++-..++.+.+++|.=|-=-+. ....++++.+|.+|.++.
T Consensus         2 ~lvig~tGsGKt~~~--vip~ll~~~~s~vv~D~Kgel~-~~t~~~~~~~G~~v~v~n   56 (384)
T cd01126           2 VLVFAPTRSGKGVGF--VIPNLLTWPGSVVVLDPKGENF-ELTSEHRRALGRKVFVFD   56 (384)
T ss_pred             EEEECCCCCCHHHHH--HHHHHHHCCCCEEEEECCHHHH-HHHHHHHHHCCCEEEEEE
T ss_conf             799889999731899--9999981899889994878999-999999998799689981


No 279
>TIGR02788 VirB11 P-type DNA transfer ATPase VirB11; InterPro: IPR014155   This entry contains VirB11, a protein that is found in the vir locus of Agrobacterium Ti plasmids where it is involved in the type IV secretion system for DNA transfer . VirB11 is believed to be an ATPase  and is a homologue of the P-like conjugation system TrbB protein and the Flp pilus system protein TadA ..
Probab=93.20  E-value=0.12  Score=31.75  Aligned_cols=51  Identities=12%  Similarity=0.148  Sum_probs=33.4

Q ss_pred             HCCCCC---C-CHHHHHHHHHHHHHC--CCCHHH----HHHHHCCCCCCCCCCCCCHHCCC
Q ss_conf             406689---9-989999999998530--887889----99985753223333200000133
Q gi|254780619|r   78 VFDCPP---L-SRQMCEFVKWVADYT--FSPMGL----VARMVVSALSETEKMEEKIQFTG  128 (731)
Q Consensus        78 VlD~~~---L-~~~ll~L~~wiA~yY--~~plG~----vLk~aLP~~~k~~~~~~~~~~~~  128 (731)
                      -+|.|.   | .+.+..|+.-+|++.  .=.+.+    +|.+.||.+.+..-.-......+
T Consensus        31 ~~d~P~rkaLT~~~l~~La~~~A~~~nt~q~is~y~~P~LSa~LP~G~RvQ~V~PPAc~~~   91 (328)
T TIGR02788        31 RFDVPERKALTFSHLRRLARAVASFSNTKQSISEYENPILSATLPGGERVQIVIPPACEND   91 (328)
T ss_pred             EEECCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCCCCEEEEECCCCCEEEEEECCCCCCC
T ss_conf             8726752244189999999998876537862010228637888699947999806875898


No 280
>PRK07246 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
Probab=93.18  E-value=0.52  Score=26.81  Aligned_cols=65  Identities=25%  Similarity=0.269  Sum_probs=48.8

Q ss_pred             CCHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHH
Q ss_conf             8837899999998752048961998447531579999999999851468479971521001344555
Q gi|254780619|r  199 LDKNQQDVVEQVVPLCTKGFAVSLISGVTGSGKTEVYLEIVAAVLHLGKQVLILLPEISLTSAILER  265 (731)
Q Consensus       199 Lt~eQ~~a~~~i~~~~~~~f~~~LL~GvTGSGKTEVYl~li~~~L~~GkqvLiLvPEI~Lt~Q~~~r  265 (731)
                      .-++|..-...+......+ ...++.--||.|||--||--+- +...++.|+|-...+.|-.|++.+
T Consensus       246 ~R~~Q~~Ma~~V~~al~~~-~~l~IEAgTGtGKTlaYLlPai-a~~~~~~vVIST~T~~LQeQL~~k  310 (820)
T PRK07246        246 ERPKQEQFAQLVDEDYHDG-VASFIEAQTGIGKTYGYLLPLL-AQSDQNQIIVSVPTKLLQDQIMAG  310 (820)
T ss_pred             CCHHHHHHHHHHHHHHCCC-CCEEEECCCCCCHHHHHHHHHH-HHCCCCEEEEEECCHHHHHHHHHH
T ss_conf             1889999999999998058-8389988999647999999999-843798399990869999999997


No 281
>TIGR00515 accD acetyl-CoA carboxylase, carboxyl transferase, beta subunit; InterPro: IPR000438 Fatty acid synthesis involves a set of reactions, commencing with carboxylation of acetyl-CoA to malonyl-CoA. This is an irreversible reaction, catalysed by the acetyl-CoA carboxylase complex (6.4.1.2 from EC); a heterohexamer of biotin carboxyl carrier protein, biotin carboxylase and two non-identical carboxyl transferase subunits (alpha and beta) in a 2:2 association . The reaction involves two steps:   Biotin carrier protein + ATP + HCO_3^- = Carboxybiotin carrier protein + ADP + P_i  Carboxybiotin carrier protein + Acetyl-CoA = Malonyl-CoA + Biotin carrier protein   In the first step, biotin carboxylase catalyses the carboxylation of the carrier protein to form an intermediate. Next, the transcarboxylase complex transfers the carboxyl group from the intermediate to acetyl-CoA forming malonyl-CoA.; GO: 0003989 acetyl-CoA carboxylase activity, 0006633 fatty acid biosynthetic process, 0009317 acetyl-CoA carboxylase complex.
Probab=93.18  E-value=0.11  Score=32.07  Aligned_cols=96  Identities=23%  Similarity=0.302  Sum_probs=42.8

Q ss_pred             CCCCCCCCCCCEEEEECC--CCCCEECHHHCCCCCCCCCCCCCCCCEECCCCCCHHHHH--------HHHHHCCCCCHHH
Q ss_conf             434310146520121135--783200002102446555666787411001354289988--------8852048520001
Q gi|254780619|r  443 GNRLKCLHCSCWLVEHRS--KKKLYCHQCGHSAIYSQSCVVCGSSGKMIACGFGIERIA--------EEVCEYFPLARIS  512 (731)
Q Consensus       443 g~~~~C~~C~~~l~~h~~--~~~l~Ch~Cg~~~~~~~~Cp~Cg~~~~l~~~G~Gte~~~--------e~l~~~fp~~~v~  512 (731)
                      |.-.+||.|.. +.||++  .|.-+|-.|||..++             ..    -|||+        +|+.+.+--..++
T Consensus        31 g~wtKCp~C~~-~~Y~keL~~n~~VC~~C~hH~R~-------------~A----~eRi~~L~D~~S~~E~~~~L~P~D~L   92 (292)
T TIGR00515        31 GVWTKCPKCGQ-LLYTKELQRNLSVCLKCDHHFRM-------------DA----RERIESLLDEGSFEEFNEHLRPKDPL   92 (292)
T ss_pred             CCEECCCHHHH-HHHHHHHHCCCEECCCCCCCCCC-------------CH----HHHHHHHCCCHHHHHHHCCCCCCCCC
T ss_conf             73001442434-43466530355574237987746-------------87----99998741500237773147878876


Q ss_pred             HCCCCCCCCHHHHHHHHHHHCCCCCCEEEEEHHHCCCCCCCCCCHHHHHHH
Q ss_conf             023211358678999998621257657987044302311345201233000
Q gi|254780619|r  513 ILSSDLEGGGGRLQLQLSAIAKGEIDIIIGTQLVAKGHNFPRMSLVGVVDG  563 (731)
Q Consensus       513 ~~d~d~~~~~~~~~~~~~~~~~~~~~ilvgTq~i~kg~~fp~v~lv~il~a  563 (731)
                      .+ .|..+-|.++++.-++-.. +-.++.|+--|.   ..|-+  |+|.|.
T Consensus        93 ~F-~D~k~Ykdri~~~~k~T~~-~dAv~tg~G~l~---~~P~~--~av~dF  136 (292)
T TIGR00515        93 KF-KDKKSYKDRIKKAQKETGL-KDAVVTGKGTLY---GMPIV--VAVMDF  136 (292)
T ss_pred             CC-CCCHHHHHHHHHHHHHCCC-CCCEEEEEEEEC---CCCEE--EEEECC
T ss_conf             78-9856689999998741288-651686003754---84279--997514


No 282
>PRK04023 DNA polymerase II large subunit; Validated
Probab=93.14  E-value=0.044  Score=35.04  Aligned_cols=35  Identities=26%  Similarity=0.451  Sum_probs=23.5

Q ss_pred             CCCCCCCCCEEEEECCCCCCEECHHHCCCCCCCCCCCCCCC
Q ss_conf             43101465201211357832000021024465556667874
Q gi|254780619|r  445 RLKCLHCSCWLVEHRSKKKLYCHQCGHSAIYSQSCVVCGSS  485 (731)
Q Consensus       445 ~~~C~~C~~~l~~h~~~~~l~Ch~Cg~~~~~~~~Cp~Cg~~  485 (731)
                      .-+||.|+..      .-..+|+.||........||.||..
T Consensus       633 ~R~Cp~Cg~e------T~~~~C~~CG~~T~~~~~c~~C~~~  667 (1128)
T PRK04023        633 NRKCPSCGKE------TFYRRCPFCGTHTEPVYRCPRCGIE  667 (1128)
T ss_pred             EEECCCCCCC------CCCCCCCCCCCCCCCCCCCCCCCCC
T ss_conf             0288999983------5755787779966543247766665


No 283
>PRK04328 hypothetical protein; Provisional
Probab=93.14  E-value=0.16  Score=30.71  Aligned_cols=38  Identities=26%  Similarity=0.336  Sum_probs=33.8

Q ss_pred             CCEEEEECCCCHHHHHHHHHHHHHHHHCCCCEEEEECC
Q ss_conf             96199844753157999999999985146847997152
Q gi|254780619|r  218 FAVSLISGVTGSGKTEVYLEIVAAVLHLGKQVLILLPE  255 (731)
Q Consensus       218 f~~~LL~GvTGSGKTEVYl~li~~~L~~GkqvLiLvPE  255 (731)
                      .++.|+.|.+|||||-.-++.+.+.+++|..+|++.=|
T Consensus        24 gs~~Lv~G~pGtGKT~la~qFl~~g~~~GE~~lyis~e   61 (250)
T PRK04328         24 RNVVLLSGGPGTGKSIFSQQFLWNGLQMGEPGIYVALE   61 (250)
T ss_pred             CEEEEEEECCCCCHHHHHHHHHHHHHHCCCCEEEEEEE
T ss_conf             96999982899998999999999998769977999972


No 284
>PRK13342 recombination factor protein RarA; Reviewed
Probab=93.05  E-value=0.66  Score=26.02  Aligned_cols=73  Identities=16%  Similarity=0.225  Sum_probs=36.3

Q ss_pred             CHHHHHHHHHHCCCCCHHHHCCCCCCCCHHHHHHHHHHHCCCCCC--EEEEEHHHCCCCCCCCC--CHHHHHHHHHHHHH
Q ss_conf             289988885204852000102321135867899999862125765--79870443023113452--01233000344310
Q gi|254780619|r  494 GIERIAEEVCEYFPLARISILSSDLEGGGGRLQLQLSAIAKGEID--IIIGTQLVAKGHNFPRM--SLVGVVDGDLGLTN  569 (731)
Q Consensus       494 Gte~~~e~l~~~fp~~~v~~~d~d~~~~~~~~~~~~~~~~~~~~~--ilvgTq~i~kg~~fp~v--~lv~il~aD~~l~~  569 (731)
                      ..+.+++.+++     +..+.|.+-...-.-.--+.+.++...+|  +-=-..||.-|-|..-+  .|+++-.-|.+|.-
T Consensus       213 ~~~~~~~~~~~-----~~~~yDk~gd~HYd~iSAf~KSiRGSDpdAAlyyLarml~~GEDp~~IaRRLii~AsEDIGlAd  287 (417)
T PRK13342        213 TLELLEEALQR-----RAARYDKDGDEHYDLISALHKSIRGSDPDAALYYLARMLEAGEDPLFIARRLVIIASEDIGLAD  287 (417)
T ss_pred             CHHHHHHHHHH-----CCCCCCCCCCHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHCCCC
T ss_conf             89999999844-----1035777863478999999998516995489999999997599979999999998854403678


Q ss_pred             HH
Q ss_conf             24
Q gi|254780619|r  570 AD  571 (731)
Q Consensus       570 pd  571 (731)
                      |.
T Consensus       288 P~  289 (417)
T PRK13342        288 PN  289 (417)
T ss_pred             HH
T ss_conf             78


No 285
>PRK06696 uridine kinase; Validated
Probab=92.95  E-value=0.36  Score=28.03  Aligned_cols=32  Identities=31%  Similarity=0.438  Sum_probs=25.5

Q ss_pred             EEEECCCCHHHHHHHHHHHHHHHHCCCCEEEE
Q ss_conf             99844753157999999999985146847997
Q gi|254780619|r  221 SLISGVTGSGKTEVYLEIVAAVLHLGKQVLIL  252 (731)
Q Consensus       221 ~LL~GvTGSGKTEVYl~li~~~L~~GkqvLiL  252 (731)
                      .-+.|.+|||||-+.=++++..=++|.+|+++
T Consensus        29 VgIdG~~gSGKTTlA~~La~~L~~~G~~V~~v   60 (227)
T PRK06696         29 VAIDGITASGKTTFANELAEEIKKRGRPVIRA   60 (227)
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHHCCCCEEEE
T ss_conf             99778998787999999999997469948997


No 286
>PRK05654 acetyl-CoA carboxylase subunit beta; Validated
Probab=92.95  E-value=0.13  Score=31.41  Aligned_cols=112  Identities=17%  Similarity=0.202  Sum_probs=49.9

Q ss_pred             CCCCCCCCEEEEECC--CCCCEECHHHCCCCCCCCCCCCCCCCEECCCCCCHHHHHHHHHH-CC-------CCCHHHHCC
Q ss_conf             310146520121135--78320000210244655566678741100135428998888520-48-------520001023
Q gi|254780619|r  446 LKCLHCSCWLVEHRS--KKKLYCHQCGHSAIYSQSCVVCGSSGKMIACGFGIERIAEEVCE-YF-------PLARISILS  515 (731)
Q Consensus       446 ~~C~~C~~~l~~h~~--~~~l~Ch~Cg~~~~~~~~Cp~Cg~~~~l~~~G~Gte~~~e~l~~-~f-------p~~~v~~~d  515 (731)
                      .+||+|+.. .|++.  .|..             .||+||.+..+.+.    ||++-.+-. .|       +....+-+.
T Consensus        31 ~kCp~C~~~-i~~~dL~~n~~-------------VCp~C~~H~ri~a~----~Ri~~l~D~gsfee~~~~~~~~DpL~F~   92 (288)
T PRK05654         31 TKCPSCGQV-LYRKELEANLN-------------VCPKCGHHMRISAR----ERLDLLLDEGSFVELDAELEPKDPLKFR   92 (288)
T ss_pred             CCCCCCCHH-HHHHHHHHHCC-------------CCCCCCCCCCCCHH----HHHHHHCCCCCEEECCCCCCCCCCCCCC
T ss_conf             228776503-50999998387-------------89299798631999----9999970799778847887889985888


Q ss_pred             CCCCCCHHHHHHHHHHHCCCCCCEEEEEHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             2113586789999986212576579870443023113452012330003443102455789999987
Q gi|254780619|r  516 SDLEGGGGRLQLQLSAIAKGEIDIIIGTQLVAKGHNFPRMSLVGVVDGDLGLTNADLRSSERTFQLL  582 (731)
Q Consensus       516 ~d~~~~~~~~~~~~~~~~~~~~~ilvgTq~i~kg~~fp~v~lv~il~aD~~l~~pd~ra~E~~~qll  582 (731)
                       |+.+-+.+++..-++-.. +-.+++|+-.| .|.+    ..+++.|...+-.+-.--..|+.....
T Consensus        93 -d~k~Y~drl~~a~kkTg~-~dav~~g~G~I-~g~~----v~~~~~df~F~GGSmG~~~GEki~~a~  152 (288)
T PRK05654         93 -DSKKYKDRLKAAQKKTGL-KDAVVTGKGTI-EGMP----VVLAVMDFSFMGGSMGSVVGEKIVRAV  152 (288)
T ss_pred             -CCCHHHHHHHHHHHHCCC-CCEEEEEEEEE-CCEE----EEEEEECHHHHCCCCCHHHHHHHHHHH
T ss_conf             -853178999999987097-50799989999-9999----999995214542664578999999999


No 287
>COG0846 SIR2 NAD-dependent protein deacetylases, SIR2 family [Transcription]
Probab=92.93  E-value=0.15  Score=30.86  Aligned_cols=47  Identities=26%  Similarity=0.399  Sum_probs=25.8

Q ss_pred             CCCCCCCCCCCEECCCCCCHHHHHHHHHHCCCCCHHHHCCCCCCCCHHHHHHHHHHHCCCCCCEEEEEH
Q ss_conf             555666787411001354289988885204852000102321135867899999862125765798704
Q gi|254780619|r  476 SQSCVVCGSSGKMIACGFGIERIAEEVCEYFPLARISILSSDLEGGGGRLQLQLSAIAKGEIDIIIGTQ  544 (731)
Q Consensus       476 ~~~Cp~Cg~~~~l~~~G~Gte~~~e~l~~~fp~~~v~~~d~d~~~~~~~~~~~~~~~~~~~~~ilvgTq  544 (731)
                      +..||.||+. .+++.   +    -..++..|.              ..++..++.....+.-|+|||.
T Consensus       146 ~p~C~~Cg~~-~lrP~---V----V~fGE~lp~--------------~~~~~~~~~~~~~d~liviGTS  192 (250)
T COG0846         146 IPRCPKCGGP-VLRPD---V----VWFGEPLPA--------------SFLDEALEALKEADLLIVIGTS  192 (250)
T ss_pred             CCCCCCCCCC-CCCCC---E----EEECCCCCH--------------HHHHHHHHHHCCCCEEEEECCC
T ss_conf             9868767996-24688---7----880798988--------------9999999984469999997864


No 288
>COG1379 PHP family phosphoesterase with a Zn ribbon [General function prediction only]
Probab=92.86  E-value=0.5  Score=26.97  Aligned_cols=61  Identities=16%  Similarity=0.273  Sum_probs=32.1

Q ss_pred             CEEEEECCCHHHHHHHHHHHCCCCCEEE--EEECCCCCHHHHHHHHHHHCCCCEEEEECCHHHHHHHCC
Q ss_conf             4799715210013445554303897689--962355723566789999719973999400121100100
Q gi|254780619|r  248 QVLILLPEISLTSAILERFQKRFGVKPA--EWHSSLSTSMREKIWRQVARGAISVIVGVRSALFLPFKK  314 (731)
Q Consensus       248 qvLiLvPEI~Lt~Q~~~rl~~rF~~~v~--v~HS~ls~~eR~~~w~~i~~G~~~IVIGtRSAif~P~~n  314 (731)
                      .+|+++|.++-..++..++.++-.+-..  --|=.++..+-    ..+.+ +....+|.- -+|.|+..
T Consensus        84 HhLlilPSl~~~~El~~~l~~~skni~~~grprv~~tg~el----~e~v~-dlggL~gPa-HaFtPwts  146 (403)
T COG1379          84 HHLLILPSLSAAEELSEWLSKYSKNIETEGRPRVYLTGAEL----AEIVK-DLGGLIGPA-HAFTPWTS  146 (403)
T ss_pred             EEEEECCCHHHHHHHHHHHHHHHCCCCCCCCCEEECCHHHH----HHHHH-HCCCCEECC-CCCCCCHH
T ss_conf             69997185889999999998741476435885552368999----99998-726604032-21686177


No 289
>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=92.82  E-value=0.17  Score=30.55  Aligned_cols=47  Identities=32%  Similarity=0.396  Sum_probs=37.0

Q ss_pred             EEEEECCCCHHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHH
Q ss_conf             199844753157999999999985146847997152100134455543
Q gi|254780619|r  220 VSLISGVTGSGKTEVYLEIVAAVLHLGKQVLILLPEISLTSAILERFQ  267 (731)
Q Consensus       220 ~~LL~GvTGSGKTEVYl~li~~~L~~GkqvLiLvPEI~Lt~Q~~~rl~  267 (731)
                      +.|+.|.+|||||-.-++.+.+.+++|..||++-=|-. ..++.++++
T Consensus         1 stLi~G~pGsGKT~~a~qfl~~~a~~ge~~lyis~eE~-~~~l~~~~~   47 (187)
T cd01124           1 STLLSGGPGTGKTTFALQFLYAGLARGEPGLYVTLEES-PEELIENAE   47 (187)
T ss_pred             CEEEEECCCCCHHHHHHHHHHHHHHCCCCEEEEEECCC-HHHHHHHHH
T ss_conf             91587689999999999999999876997899995079-999999999


No 290
>PRK00481 NAD-dependent deacetylase; Provisional
Probab=92.81  E-value=0.12  Score=31.61  Aligned_cols=48  Identities=25%  Similarity=0.425  Sum_probs=23.6

Q ss_pred             CCCCCCCCCCCEECCCCCCHHHHHHHHHHCCCCCHHHHCCCCCCCCHHHHHHHHHHHCCCCCCEEEEEHHH
Q ss_conf             55566678741100135428998888520485200010232113586789999986212576579870443
Q gi|254780619|r  476 SQSCVVCGSSGKMIACGFGIERIAEEVCEYFPLARISILSSDLEGGGGRLQLQLSAIAKGEIDIIIGTQLV  546 (731)
Q Consensus       476 ~~~Cp~Cg~~~~l~~~G~Gte~~~e~l~~~fp~~~v~~~d~d~~~~~~~~~~~~~~~~~~~~~ilvgTq~i  546 (731)
                      ...||.||+.  +++--.       ..++..|..              .+++..+...+-+.-|+|||.+.
T Consensus       142 ~p~C~~Cgg~--lrP~VV-------~FGE~lp~~--------------~~~~a~~~~~~aDlllvvGTSl~  189 (239)
T PRK00481        142 PPRCPKCGGI--LRPDVV-------LFGEMLPEE--------------AIDRAYEALEEADLFIVIGTSLV  189 (239)
T ss_pred             CCCCCCCCCE--ECCCEE-------ECCCCCCHH--------------HHHHHHHHHHCCCEEEEECCCCE
T ss_conf             9988567997--464221-------367789867--------------99999999972998999678855


No 291
>TIGR03676 aRF1/eRF1 peptide chain release factor 1, archaeal and eukaryotic forms. Directs the termination of nascent peptide synthesis (translation) in response to the termination codons UAA, UAG and UGA. This model identifies both archaeal (aRF1) and eukaryotic (eRF1) of the protein. Also known as translation termination factor 1.
Probab=92.80  E-value=0.41  Score=27.64  Aligned_cols=91  Identities=24%  Similarity=0.308  Sum_probs=45.8

Q ss_pred             HHHHHHHHCCCC--EEEEEECCCCEEHHCCCCCCCCCCCCCCCCCEEEEECCCCCCEECHHHCCCCCCCCCCCCCCCCEE
Q ss_conf             999988622655--179974222000000235654343101465201211357832000021024465556667874110
Q gi|254780619|r  411 IDGIRHTLARNE--QTLLFLNRRGYAPLTLCQVCGNRLKCLHCSCWLVEHRSKKKLYCHQCGHSAIYSQSCVVCGSSGKM  488 (731)
Q Consensus       411 ~~~i~~~l~~g~--qvll~lnRrGya~~~~C~~Cg~~~~C~~C~~~l~~h~~~~~l~Ch~Cg~~~~~~~~Cp~Cg~~~~l  488 (731)
                      .+.++++|+.|-  ..|+.=|=+..         ++..+|++|+.-...+...+         .......||.||+...+
T Consensus       293 ~~ev~kALemGAVetLLIsE~L~~~---------R~~~kc~~c~~e~~~~~~~~---------~~~~~~~c~~cg~~~e~  354 (403)
T TIGR03676       293 EEEVRKALEMGAVDTLLISEDLRKI---------RVTFKCPNCGYEEEKTVKPE---------EGDKSEACPKCGSELEI  354 (403)
T ss_pred             HHHHHHHHHCCCCCEEEEECCCCCE---------EEEEECCCCCCEEEEECCCC---------CCCCCCCCCCCCCCEEE
T ss_conf             9999999862973169873256622---------79997688882588731544---------34456688556872046


Q ss_pred             CCCCCCHHHHHHHHHHCCCCCHHHHCCCCCCCC
Q ss_conf             013542899888852048520001023211358
Q gi|254780619|r  489 IACGFGIERIAEEVCEYFPLARISILSSDLEGG  521 (731)
Q Consensus       489 ~~~G~Gte~~~e~l~~~fp~~~v~~~d~d~~~~  521 (731)
                      ...-.=+|++.+.-++ | +++|..++.|+..+
T Consensus       355 ~e~~dliE~L~e~ak~-~-Ga~ve~IS~~seEG  385 (403)
T TIGR03676       355 VEEEDIIEELSELAEE-S-GAKVEIISTDTEEG  385 (403)
T ss_pred             EECCCHHHHHHHHHHH-C-CCEEEEEECCCCCH
T ss_conf             4136189999999997-3-98899990898107


No 292
>cd03223 ABCD_peroxisomal_ALDP Peroxisomal ATP-binding cassette transporter (Pat) is involved in the import of very long-chain fatty acids (VLCFA) into the peroxisome.  The peroxisomal membrane forms a permeability barrier for a wide variety of metabolites required for and formed during fatty acid beta-oxidation.  To communicate with the cytoplasm and mitochondria, peroxisomes need dedicated proteins to transport such hydrophilic molecules across their membranes.  X-linked adrenoleukodystrophy (X-ALD) is caused by mutations in the ALD gene, which encodes ALDP (adrenoleukodystrophy protein ), a peroxisomal integral membrane protein that is a member of the ATP-binding cassette (ABC) transporter protein family.  The disease is characterized by a striking and unpredictable variation in phenotypic expression.  Phenotypes include the rapidly progressive childhood cerebral form (CCALD), the milder adult form, adrenomyeloneuropathy (AMN), and variants without neurologic involvement (i.e. asympt
Probab=92.80  E-value=0.22  Score=29.69  Aligned_cols=119  Identities=18%  Similarity=0.265  Sum_probs=58.9

Q ss_pred             CEEEEECCCCHHHHHHHHHHHHHHHHCCCCEEEEEC---CCHHHHHHHHHHHCCCCCEE-EEEECCCCCHHHHHHHHHHH
Q ss_conf             619984475315799999999998514684799715---21001344555430389768-99623557235667899997
Q gi|254780619|r  219 AVSLISGVTGSGKTEVYLEIVAAVLHLGKQVLILLP---EISLTSAILERFQKRFGVKP-AEWHSSLSTSMREKIWRQVA  294 (731)
Q Consensus       219 ~~~LL~GvTGSGKTEVYl~li~~~L~~GkqvLiLvP---EI~Lt~Q~~~rl~~rF~~~v-~v~HS~ls~~eR~~~w~~i~  294 (731)
                      ....|-|-+|||||-. ++++...+.-...-+. .|   .|+..||----+...+.+++ +.|...||.+||.++-..  
T Consensus        28 e~v~i~G~sGsGKSTL-l~~l~Gl~~~~~G~i~-~~~~~~i~~v~Q~~~l~~~tl~e~l~~p~~~~LSGGqkQRvalA--  103 (166)
T cd03223          28 DRLLITGPSGTGKSSL-FRALAGLWPWGSGRIG-MPEGEDLLFLPQRPYLPLGTLREQLIYPWDDVLSGGEQQRLAFA--  103 (166)
T ss_pred             CEEEEECCCCCCHHHH-HHHHCCCCCCCCCEEE-ECCCCCEEEECCCCCCCCCCHHHHHHCCCCCCCCHHHHHHHHHH--
T ss_conf             9999995899988999-9998698769986799-76998799985646658875999963615467899999999999--


Q ss_pred             CCCCEEEEECCHHHHHHHCCCEEEEEEECCCCCCHHCCCCCCCHHHHHHHHHHHCCCCEECCCCCCCH
Q ss_conf             19973999400121100100013677405532100002443224899999751103210000245432
Q gi|254780619|r  295 RGAISVIVGVRSALFLPFKKLGLIVIDEEHDISYKQEEGILYNARDMSIVRGKIESFPVVLVSATPSI  362 (731)
Q Consensus       295 ~G~~~IVIGtRSAif~P~~nLglIIvDEEHd~sykq~~~pry~aRdvA~~Ra~~~~~~lilgSATPSl  362 (731)
                                | |+   +.+..++|.||-- ++-   | + -..+.+.-.. +..+..+|+.|.-+++
T Consensus       104 ----------R-al---~~~p~iliLDEpT-s~L---D-~-~~~~~l~~~l-~~~~~Tvi~VtH~~~~  150 (166)
T cd03223         104 ----------R-LL---LHKPKFVFLDEAT-SAL---D-E-ESEDRLYQLL-KELGITVISVGHRPSL  150 (166)
T ss_pred             ----------H-HH---HCCCCEEEECCCC-CCC---C-H-HHHHHHHHHH-HHCCCEEEEEECCHHH
T ss_conf             ----------9-99---6499999975853-328---9-9-9999999999-9779989999434699


No 293
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=92.76  E-value=0.11  Score=31.98  Aligned_cols=42  Identities=19%  Similarity=0.256  Sum_probs=23.7

Q ss_pred             CCCCCCCEEEEECCCCCCEECHHHCCCCCCCCCCCCCCCCEECCCCCCHHHHHHHHHH
Q ss_conf             1014652012113578320000210244655566678741100135428998888520
Q gi|254780619|r  447 KCLHCSCWLVEHRSKKKLYCHQCGHSAIYSQSCVVCGSSGKMIACGFGIERIAEEVCE  504 (731)
Q Consensus       447 ~C~~C~~~l~~h~~~~~l~Ch~Cg~~~~~~~~Cp~Cg~~~~l~~~G~Gte~~~e~l~~  504 (731)
                      .||+|+..++|..            ......+||.||+.  |..+  -.+++.+.|++
T Consensus       119 ~C~~c~~R~tFee------------Ame~~F~CP~CG~~--Le~~--DN~~~i~~Lk~  160 (178)
T PRK06266        119 VCPNGHPKFTFDE------------AMEYGFRCPQCGEM--LEEY--DNSKDIEELKE  160 (178)
T ss_pred             ECCCCCCCCCHHH------------HHHCCCCCCCCCCC--CEEC--CCHHHHHHHHH
T ss_conf             8899983005999------------98839969999886--6322--37999999999


No 294
>PRK10246 exonuclease subunit SbcC; Provisional
Probab=92.73  E-value=0.11  Score=31.88  Aligned_cols=34  Identities=21%  Similarity=0.167  Sum_probs=14.7

Q ss_pred             CCCCCCHHHHHHHHHHHHHCCCCHHHHHHHH-CCC
Q ss_conf             6689998999999999853088788999985-753
Q gi|254780619|r   80 DCPPLSRQMCEFVKWVADYTFSPMGLVARMV-VSA  113 (731)
Q Consensus        80 D~~~L~~~ll~L~~wiA~yY~~plG~vLk~a-LP~  113 (731)
                      |..++....-+-...|.+--.-+..+..+.+ ||.
T Consensus       121 dg~~~~~k~~~v~~~I~~llGLd~~qF~q~v~LpQ  155 (1047)
T PRK10246        121 DGKILADKVKDKLELTATLTGLDYGRFTRSMLLSQ  155 (1047)
T ss_pred             CCCCCCCCHHHHHHHHHHHHCCCHHHHHHHHEECC
T ss_conf             98850563788999999997999999114306751


No 295
>smart00490 HELICc helicase superfamily c-terminal domain.
Probab=92.72  E-value=0.35  Score=28.18  Aligned_cols=58  Identities=31%  Similarity=0.428  Sum_probs=45.0

Q ss_pred             HHHHHCCCCCEEEEEECCCCCHHHHHHHHHHHCCCCEEEEECCHHHH-HHHCCCEEEEEE
Q ss_conf             55543038976899623557235667899997199739994001211-001000136774
Q gi|254780619|r  263 LERFQKRFGVKPAEWHSSLSTSMREKIWRQVARGAISVIVGVRSALF-LPFKKLGLIVID  321 (731)
Q Consensus       263 ~~rl~~rF~~~v~v~HS~ls~~eR~~~w~~i~~G~~~IVIGtRSAif-~P~~nLglIIvD  321 (731)
                      .+.|++. |..++.+||+++..+|.++..+-.+|+.+|+|+|..+-- .-+++...||+-
T Consensus         4 ~~~l~~~-g~~~~~i~g~~~~~~R~~~~~~f~~~~~~ilv~t~~~~~Gidl~~~~~vI~~   62 (82)
T smart00490        4 AELLKEL-GIKVARLHGGLSQEEREEILEKFNNGKIKVLVATDVAERGLDLPGVDLVIIY   62 (82)
T ss_pred             HHHHHHC-CCCEEEEECCCCHHHHHHHHHHHHCCCCEEEEEEEEEEEECCCCCCCEEEEE
T ss_conf             9999888-9919999896999999999999987997199995024211489889999997


No 296
>COG1618 Predicted nucleotide kinase [Nucleotide transport and metabolism]
Probab=92.67  E-value=0.13  Score=31.52  Aligned_cols=38  Identities=32%  Similarity=0.489  Sum_probs=30.8

Q ss_pred             EEEEECCCCHHHHHHHHHHHHHHHHCCCCEE-EEECCCH
Q ss_conf             1998447531579999999999851468479-9715210
Q gi|254780619|r  220 VSLISGVTGSGKTEVYLEIVAAVLHLGKQVL-ILLPEIS  257 (731)
Q Consensus       220 ~~LL~GvTGSGKTEVYl~li~~~L~~GkqvL-iLvPEI~  257 (731)
                      -..+-|-.|||||.+-+.+++..-+.|..|- ++.|||-
T Consensus         7 ki~ITG~PGvGKtTl~~ki~e~L~~~g~kvgGf~t~EVR   45 (179)
T COG1618           7 KIFITGRPGVGKTTLVLKIAEKLREKGYKVGGFITPEVR   45 (179)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHCCCEEEEEEEEEEE
T ss_conf             999867998458999999999998559665139831142


No 297
>PRK09401 reverse gyrase; Reviewed
Probab=92.64  E-value=0.23  Score=29.47  Aligned_cols=51  Identities=27%  Similarity=0.448  Sum_probs=35.3

Q ss_pred             CCEECHHHCCCCC-CCCCCCCCCCCEECCCCCCHHHHHHHHHHCCCCCHHHHCCCCC
Q ss_conf             3200002102446-5556667874110013542899888852048520001023211
Q gi|254780619|r  463 KLYCHQCGHSAIY-SQSCVVCGSSGKMIACGFGIERIAEEVCEYFPLARISILSSDL  518 (731)
Q Consensus       463 ~l~Ch~Cg~~~~~-~~~Cp~Cg~~~~l~~~G~Gte~~~e~l~~~fp~~~v~~~d~d~  518 (731)
                      .=+|.-||++..- ...||.|||.. +.    +.+++.+.|+++=-++.-+.+-+|-
T Consensus       677 IkrC~~cg~qft~~~~~cP~Cgs~~-i~----dk~~vv~aLR~lA~EvDeVyIATDP  728 (1176)
T PRK09401        677 IKRCRDCGHQFTDESDRCPRCGSTN-ID----DKEEIIEALRELALEVDEVLIATDP  728 (1176)
T ss_pred             HHHHHHCCCCCCCCCCCCCCCCCCC-CC----CHHHHHHHHHHHHHHCCEEEECCCC
T ss_conf             7677535860124666688778887-56----6899999999998755989987899


No 298
>PRK11664 ATP-dependent RNA helicase HrpB; Provisional
Probab=92.64  E-value=0.42  Score=27.50  Aligned_cols=300  Identities=18%  Similarity=0.267  Sum_probs=146.5

Q ss_pred             HHHHHHHHCCCCCEEEEECCCCHHHHH-HHHHHHHHHHHCCCCEEEEECC----CHHHHHHHHHHHCCCCCEEEEEECCC
Q ss_conf             999987520489619984475315799-9999999985146847997152----10013445554303897689962355
Q gi|254780619|r  207 VEQVVPLCTKGFAVSLISGVTGSGKTE-VYLEIVAAVLHLGKQVLILLPE----ISLTSAILERFQKRFGVKPAEWHSSL  281 (731)
Q Consensus       207 ~~~i~~~~~~~f~~~LL~GvTGSGKTE-VYl~li~~~L~~GkqvLiLvPE----I~Lt~Q~~~rl~~rF~~~v~v~HS~l  281 (731)
                      .++|.....+ ..+.+|.|-||||||- |=+.+.++....| .++++=|-    ++++..+..-+....|..|. |.=  
T Consensus        10 ~~~i~~~l~~-~~~~vl~a~tGsGKtTqvP~~ll~~~~~~g-~I~~~qPRR~AA~s~A~RvA~e~~e~~G~~VG-Y~v--   84 (812)
T PRK11664         10 LPELLTALKT-APQVLLKAPTGAGKSTWLPLQLLQQGGING-KIIMLEPRRLAARNVAQRLAEQLGEKPGETVG-YRM--   84 (812)
T ss_pred             HHHHHHHHHH-CCEEEEEECCCCCHHHHHHHHHHHCCCCCC-CEEEECCHHHHHHHHHHHHHHHHCCCCCCEEE-EEE--
T ss_conf             9999999997-997999908999989999999996468899-38993883999999999999972999998675-782--


Q ss_pred             CCHHHHHHHHHHHCCCCEEEEECCHHHHH------H-HCCCEEEEEEECCCCCCHHCCCCCCCHHHHHHHHHHHCCCCEE
Q ss_conf             72356678999971997399940012110------0-1000136774055321000024432248999997511032100
Q gi|254780619|r  282 STSMREKIWRQVARGAISVIVGVRSALFL------P-FKKLGLIVIDEEHDISYKQEEGILYNARDMSIVRGKIESFPVV  354 (731)
Q Consensus       282 s~~eR~~~w~~i~~G~~~IVIGtRSAif~------P-~~nLglIIvDEEHd~sykq~~~pry~aRdvA~~Ra~~~~~~li  354 (731)
                          |.+.   -.+.+.+|.+=|- ++|+      | +.+.+.||+||-|+=|-..|-..- =.+++  .++...+..||
T Consensus        85 ----R~e~---~~s~~Tri~~~T~-GiLlr~l~~dp~L~~~~~vI~DE~HER~l~~Dl~l~-l~~~~--~~~~r~dLklv  153 (812)
T PRK11664         85 ----RAES---KVGPNTRLEVVTE-GILTRMIQRDPELSGVGLVILDEFHERSLQADLALA-LLLDV--QQGLRDDLKLL  153 (812)
T ss_pred             ----CCCC---CCCCCCEEEEECH-HHHHHHHHHCCCCCCCCEEEEECCCCCCHHHHHHHH-HHHHH--HHHHCCCCEEE
T ss_conf             ----5677---8899857999755-899999724977677888999575468751899999-99999--98618982899


Q ss_pred             CCCCCCCHHHHHHHHHHHHHHHCCCCCCCCCCCCCCEECCCCCCCCCCCCCCCHHHHHHHHHHHCCC-CEEEEEECCCCE
Q ss_conf             0024543246775321234441243223676543321102222332224547989999998862265-517997422200
Q gi|254780619|r  355 LVSATPSIESRVNGISRRYHSVHLSTRYRNSALPHLQVIDMRGQTIAQGKSLSPEMIDGIRHTLARN-EQTLLFLNRRGY  433 (731)
Q Consensus       355 lgSATPSles~~~~~~g~~~~~~l~~R~~~~~~P~i~ivDm~~~~~~~~~~lS~~l~~~i~~~l~~g-~qvll~lnRrGy  433 (731)
                      +.|||.-.+.+.....+ ...++-    .+...| |+   .+-.+......+.....+.++..++.. .-+|+|++--+-
T Consensus       154 vMSATld~~~~~~~~~~-~~~i~~----~gr~fp-V~---~~y~~~~~~~~~~~~~~~~i~~~~~~~~G~iLvFLPG~~E  224 (812)
T PRK11664        154 IMSATLDNDRLQQLLPD-APYIES----EGRSFP-VE---RRYQPLPAHQRFDEAVAVATAELLRQESGSLLLFLPGVGE  224 (812)
T ss_pred             EECCCCCHHHHHHHCCC-CCEEEE----CCCCCC-EE---EEECCCCCCCHHHHHHHHHHHHHHHCCCCCEEEECCCHHH
T ss_conf             98478884889975899-988987----874331-15---7854688520699999999999973589988997699899


Q ss_pred             EHHCCCCCCCCCCCCCCCCCEEEEECCCCCCEECHHHCCCCCCCCCCCCCCCCEECCCCCCHHHHHHHHHHCCC-CCHHH
Q ss_conf             00002356543431014652012113578320000210244655566678741100135428998888520485-20001
Q gi|254780619|r  434 APLTLCQVCGNRLKCLHCSCWLVEHRSKKKLYCHQCGHSAIYSQSCVVCGSSGKMIACGFGIERIAEEVCEYFP-LARIS  512 (731)
Q Consensus       434 a~~~~C~~Cg~~~~C~~C~~~l~~h~~~~~l~Ch~Cg~~~~~~~~Cp~Cg~~~~l~~~G~Gte~~~e~l~~~fp-~~~v~  512 (731)
                      .                                                             +++.+.|...++ +..|.
T Consensus       225 I-------------------------------------------------------------~~~~~~L~~~~~~~~~i~  243 (812)
T PRK11664        225 I-------------------------------------------------------------QRVQEQLASRVGSDVLLC  243 (812)
T ss_pred             H-------------------------------------------------------------HHHHHHHHHHCCCCEEEE
T ss_conf             9-------------------------------------------------------------999999863355780899


Q ss_pred             HCCCCCCCCHHHHHHHHHHHCCCCCCEEEEEHHHCCCCCCCCCCHHHHHHHHHHHH-HHHHHHHHHHH---------HHH
Q ss_conf             02321135867899999862125765798704430231134520123300034431-02455789999---------987
Q gi|254780619|r  513 ILSSDLEGGGGRLQLQLSAIAKGEIDIIIGTQLVAKGHNFPRMSLVGVVDGDLGLT-NADLRSSERTF---------QLL  582 (731)
Q Consensus       513 ~~d~d~~~~~~~~~~~~~~~~~~~~~ilvgTq~i~kg~~fp~v~lv~il~aD~~l~-~pd~ra~E~~~---------qll  582 (731)
                      -+.++.  .....+..+..-..|.-.|++.|-+-.-.+..|+|..|+    |+++. .+.|...-..-         .--
T Consensus       244 pL~g~l--~~~~Q~~~~~~~~~g~rKvIlaTnIAEtSlTI~gV~~VI----DsG~~r~~~~d~~~g~~~L~~~~iSkasa  317 (812)
T PRK11664        244 PLYGAL--SLAEQQKAILPAPAGMRKVVLATNIAETSLTIEGIRLVV----DSGLERVARFDPKTGLTRLETQRISQASM  317 (812)
T ss_pred             ECCCCC--CHHHHHHHHCCCCCCCEEEEEECCCHHCEEEECCEEEEE----ECHHHHHHEECCCCCCCEEEEEECCHHHH
T ss_conf             644789--988987760679999537999502000202017814897----40223443234357975676770454435


Q ss_pred             HHHHHCCCCCCCCCEEE
Q ss_conf             54311025667886899
Q gi|254780619|r  583 SQVTGRAGRFGLKSLGL  599 (731)
Q Consensus       583 ~qv~gRagr~~~~g~v~  599 (731)
                      .|=+|||||- .+|.++
T Consensus       318 ~QRaGRAGR~-~pG~cy  333 (812)
T PRK11664        318 TQRAGRAGRL-EPGICL  333 (812)
T ss_pred             HCCCCCCCCC-CCCEEE
T ss_conf             3136767888-997078


No 299
>TIGR02487 NrdD anaerobic ribonucleoside-triphosphate reductase; InterPro: IPR012833    This entry is found in the oxygen-sensitive (anaerobic, class III) ribonucleotide reductase. The mechanism of the enzyme involves a glycine-centred radical , a C-terminal zinc binding site , and a set of conserved active site cysteines and asparagines . This enzyme requires an activating component, NrdG, a radical-SAM domain containing enzyme (IPR012837 from INTERPRO). Together the two form an alpha-2/beta-2 heterodimer.; GO: 0008998 ribonucleoside-triphosphate reductase activity, 0016491 oxidoreductase activity.
Probab=92.61  E-value=0.047  Score=34.79  Aligned_cols=39  Identities=26%  Similarity=0.394  Sum_probs=24.4

Q ss_pred             CCEECHHH-CCCCCC-----CCCCCCCCCCEECCCCCCHHHHHHHHH
Q ss_conf             32000021-024465-----556667874110013542899888852
Q gi|254780619|r  463 KLYCHQCG-HSAIYS-----QSCVVCGSSGKMIACGFGIERIAEEVC  503 (731)
Q Consensus       463 ~l~Ch~Cg-~~~~~~-----~~Cp~Cg~~~~l~~~G~Gte~~~e~l~  503 (731)
                      .=.|+-|| |.....     ..||.|||++. ... -.+.||--+|.
T Consensus       590 ~~~C~~Cg~y~~~~~~t~~g~~CP~CGs~D~-~~~-~~~sRitGYL~  634 (655)
T TIGR02487       590 VDVCEDCGEYTGEGLNTEKGDKCPKCGSHDE-TDI-EVISRITGYLR  634 (655)
T ss_pred             CCEECCCCCCHHCCCCCCCCCCCCCCCCCCH-HHE-EEEEEEEEECC
T ss_conf             7652576532000000115566889887622-110-13000355226


No 300
>PRK04195 replication factor C large subunit; Provisional
Probab=92.56  E-value=0.88  Score=25.08  Aligned_cols=17  Identities=35%  Similarity=0.493  Sum_probs=14.6

Q ss_pred             CEEEEECCCCHHHHHHH
Q ss_conf             61998447531579999
Q gi|254780619|r  219 AVSLISGVTGSGKTEVY  235 (731)
Q Consensus       219 ~~~LL~GvTGSGKTEVY  235 (731)
                      .+.||+|-.|.|||=..
T Consensus        41 k~lLL~GPpGvGKTT~a   57 (403)
T PRK04195         41 KALLLYGPPGVGKTSLA   57 (403)
T ss_pred             CEEEEECCCCCCHHHHH
T ss_conf             46998893998799999


No 301
>PRK11823 DNA repair protein RadA; Provisional
Probab=92.54  E-value=0.057  Score=34.15  Aligned_cols=156  Identities=27%  Similarity=0.374  Sum_probs=87.4

Q ss_pred             CEEEEECCCCHHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHCCCC---CEEEEEECCCCCHHHHHHHHHHHC
Q ss_conf             61998447531579999999999851468479971521001344555430389---768996235572356678999971
Q gi|254780619|r  219 AVSLISGVTGSGKTEVYLEIVAAVLHLGKQVLILLPEISLTSAILERFQKRFG---VKPAEWHSSLSTSMREKIWRQVAR  295 (731)
Q Consensus       219 ~~~LL~GvTGSGKTEVYl~li~~~L~~GkqvLiLvPEI~Lt~Q~~~rl~~rF~---~~v~v~HS~ls~~eR~~~w~~i~~  295 (731)
                      ++.||-|..|-||.-.-|+++.. +++|+.||+.-=|-+. .|+-.|.. |++   +++.++.    +..--.+...+..
T Consensus        91 S~iLlgGePGIGKSTLlLQ~a~~-la~~~~vLYvSGEES~-~Qik~RA~-RLg~~~~~l~l~~----et~l~~Il~~i~~  163 (454)
T PRK11823         91 SVVLIGGDPGIGKSTLLLQVAAA-LAAGGKVLYVSGEESL-QQIKLRAE-RLGLPSDNLYLLA----ETNLEDILATIEE  163 (454)
T ss_pred             EEEEECCCCCCCHHHHHHHHHHH-HHCCCCEEEECCCHHH-HHHHHHHH-HHCCCCCCCEEEE----CCCHHHHHHHHHH
T ss_conf             48995079988899999999999-8559957998150157-89999999-7588888737885----3689999999986


Q ss_pred             CCCEEEEECCHHHHHHHCCCEEEEEEECCCCCCHH--CCCCC--CCHHHHHHH---HHHHCCCCEECCCC--------CC
Q ss_conf             99739994001211001000136774055321000--02443--224899999---75110321000024--------54
Q gi|254780619|r  296 GAISVIVGVRSALFLPFKKLGLIVIDEEHDISYKQ--EEGIL--YNARDMSIV---RGKIESFPVVLVSA--------TP  360 (731)
Q Consensus       296 G~~~IVIGtRSAif~P~~nLglIIvDEEHd~sykq--~~~pr--y~aRdvA~~---Ra~~~~~~lilgSA--------TP  360 (731)
                                       .++.++|||-=+-- |-.  +..|-  -..|++|..   .|+..+++++|...        =|
T Consensus       164 -----------------~~P~~lIIDSIQT~-~~~~~~s~pGsvsQVre~a~~L~~~AK~~~i~~~lVGHVTKdG~iAGP  225 (454)
T PRK11823        164 -----------------EKPDLVVIDSIQTM-YSPELESAPGSVSQVRECAAELTRLAKQSGIAVFLVGHVTKEGAIAGP  225 (454)
T ss_pred             -----------------HCCCEEEEECHHEE-EECCCCCCCCCHHHHHHHHHHHHHHHHHCCCCEEEEEEECCCCCCCCC
T ss_conf             -----------------09988999431115-415667789978999999999999997449828999977267764661


Q ss_pred             -CHHHHHHH-------HHHHHHHHC-CCCCCCCCCCCCCEECCCCCCCCC
Q ss_conf             -32467753-------212344412-432236765433211022223322
Q gi|254780619|r  361 -SIESRVNG-------ISRRYHSVH-LSTRYRNSALPHLQVIDMRGQTIA  401 (731)
Q Consensus       361 -Sles~~~~-------~~g~~~~~~-l~~R~~~~~~P~i~ivDm~~~~~~  401 (731)
                       .||.+.-+       ....|+.++ .++||+...  ++-+..|+.+-+.
T Consensus       226 kvLEHmVDtVl~fEGd~~~~~RiLR~~KNRFG~t~--EiGvFeM~~~GL~  273 (454)
T PRK11823        226 RVLEHMVDTVLYFEGDRHSRFRILRAVKNRFGATN--EIGVFEMTEKGLR  273 (454)
T ss_pred             HHHHHHHCEEEEECCCCCCCCEEEEEECCCCCCCC--EEEEEEECCCCCE
T ss_conf             45222010468751576655024563124677666--0589986168845


No 302
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=92.53  E-value=0.086  Score=32.81  Aligned_cols=35  Identities=26%  Similarity=0.396  Sum_probs=23.0

Q ss_pred             CCEEEEECCCCCCEECHHHCCCCCC----CCCCCCCCCC
Q ss_conf             5201211357832000021024465----5566678741
Q gi|254780619|r  452 SCWLVEHRSKKKLYCHQCGHSAIYS----QSCVVCGSSG  486 (731)
Q Consensus       452 ~~~l~~h~~~~~l~Ch~Cg~~~~~~----~~Cp~Cg~~~  486 (731)
                      +.-|....-.-..+|..||+.....    ..||.|||..
T Consensus        60 ~A~L~Ie~~p~~~~C~~Cg~~f~~~~~~~~~CP~Cgs~~   98 (117)
T PRK00564         60 DAILDIVDEKVELECKDCSHVFKPNALDYGVCEKCHSKN   98 (117)
T ss_pred             CCEEEEEEECCEEECCCCCCEEECCCCCCCCCCCCCCCC
T ss_conf             979999973878991008998822774068590988999


No 303
>KOG0949 consensus
Probab=92.52  E-value=0.12  Score=31.62  Aligned_cols=142  Identities=24%  Similarity=0.387  Sum_probs=86.3

Q ss_pred             CHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHHHHHHHHHHC--CCCEEEEECCCHHHHHHHHHHHCCCCCE----
Q ss_conf             8378999999987520489619984475315799999999998514--6847997152100134455543038976----
Q gi|254780619|r  200 DKNQQDVVEQVVPLCTKGFAVSLISGVTGSGKTEVYLEIVAAVLHL--GKQVLILLPEISLTSAILERFQKRFGVK----  273 (731)
Q Consensus       200 t~eQ~~a~~~i~~~~~~~f~~~LL~GvTGSGKTEVYl~li~~~L~~--GkqvLiLvPEI~Lt~Q~~~rl~~rF~~~----  273 (731)
                      +.+|..-.+.....     ...+|---|.||||=+=.-+|+++|..  .+=|+..+|+-+|..|.......||...    
T Consensus       513 d~WQ~elLDsvDr~-----eSavIVAPTSaGKTfisfY~iEKVLResD~~VVIyvaPtKaLVnQvsa~VyaRF~~~t~~r  587 (1330)
T KOG0949         513 DEWQRELLDSVDRN-----ESAVIVAPTSAGKTFISFYAIEKVLRESDSDVVIYVAPTKALVNQVSANVYARFDTKTFLR  587 (1330)
T ss_pred             CHHHHHHHHHHHCC-----CCEEEEEECCCCCEECCHHHHHHHHHHCCCCEEEEECCHHHHHHHHHHHHHHHHCCCCCCC
T ss_conf             38888776655056-----6259982046786100589999998542798799966458776666677887633676563


Q ss_pred             EEEEECCCCCHHHHHHHHHHHCCCCEEEEEC----CHHHHHH------HCCCEEEEEEECCCCCCHHCCCCCCCHHHHHH
Q ss_conf             8996235572356678999971997399940----0121100------10001367740553210000244322489999
Q gi|254780619|r  274 PAEWHSSLSTSMREKIWRQVARGAISVIVGV----RSALFLP------FKKLGLIVIDEEHDISYKQEEGILYNARDMSI  343 (731)
Q Consensus       274 v~v~HS~ls~~eR~~~w~~i~~G~~~IVIGt----RSAif~P------~~nLglIIvDEEHd~sykq~~~pry~aRdvA~  343 (731)
                      ...+-+.++.--+...|.      ..|.|..    -|-+..|      .+...-||.||-|-.. ..+++-   .++-.+
T Consensus       588 g~sl~g~ltqEYsinp~n------CQVLITvPecleslLlspp~~q~~cerIRyiIfDEVH~iG-~~ed~l---~~Eqll  657 (1330)
T KOG0949         588 GVSLLGDLTQEYSINPWN------CQVLITVPECLESLLLSPPHHQKFCERIRYIIFDEVHLIG-NEEDGL---LWEQLL  657 (1330)
T ss_pred             CHHHHHHHHHHHCCCCHH------CEEEEECHHHHHHHHCCCHHHHHHHHCCEEEEECHHHHCC-CCCCCH---HHHHHH
T ss_conf             134676666773578411------3599974678998863856653022400589711233246-524341---899877


Q ss_pred             HHHHHCCCCEECCCCC
Q ss_conf             9751103210000245
Q gi|254780619|r  344 VRGKIESFPVVLVSAT  359 (731)
Q Consensus       344 ~Ra~~~~~~lilgSAT  359 (731)
                         -+-.||.+--|||
T Consensus       658 ---~li~CP~L~LSAT  670 (1330)
T KOG0949         658 ---LLIPCPFLVLSAT  670 (1330)
T ss_pred             ---HHCCCCEEEEECC
T ss_conf             ---7457870687413


No 304
>TIGR00416 sms DNA repair protein RadA; InterPro: IPR004504   RadA/Sms is a highly conserved eubacterial protein that shares sequence similarity with both RecA strand transferase and lon protease. The RadA/Sms family are probable ATP-dependent proteases involved in both DNA repair and degradation of proteins, peptides, glycopeptides. They are classified in as non-peptidase homologues and unassigned peptidases in MEROPS peptidase family S16 (lon protease family, clan SJ).   RadA/Sms is involved in recombination and recombinational repair, most likely involving the stabilisation or processing of branched DNA molecules or blocked replication forks because of its genetic redundancy with RecG and RuvABC .; GO: 0003684 damaged DNA binding, 0005524 ATP binding, 0006281 DNA repair.
Probab=92.50  E-value=0.048  Score=34.74  Aligned_cols=171  Identities=19%  Similarity=0.286  Sum_probs=94.4

Q ss_pred             CEEEEECCCCHHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHCCCCCEEEEEECCCCCHHHHHHHHHH-HCCC
Q ss_conf             619984475315799999999998514684799715210013445554303897689962355723566789999-7199
Q gi|254780619|r  219 AVSLISGVTGSGKTEVYLEIVAAVLHLGKQVLILLPEISLTSAILERFQKRFGVKPAEWHSSLSTSMREKIWRQV-ARGA  297 (731)
Q Consensus       219 ~~~LL~GvTGSGKTEVYl~li~~~L~~GkqvLiLvPEI~Lt~Q~~~rl~~rF~~~v~v~HS~ls~~eR~~~w~~i-~~G~  297 (731)
                      +..|+=|..|=||-=.-|+.+.+.-++-..+|+.-=|-++ .|+.-| ..|+|..     .=.++++-.+-...+ ..|+
T Consensus       104 sliLiGG~PG~GKSTLLLqV~~~LA~~~~~~LYVsGEES~-~Q~klR-A~RLGit-----~~~~~sqaqdGinnlahdG~  176 (481)
T TIGR00416       104 SLILIGGDPGIGKSTLLLQVACQLAKNSMKVLYVSGEESL-QQIKLR-ATRLGIT-----DLVEPSQAQDGINNLAHDGN  176 (481)
T ss_pred             CEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEEECCHH-HHHHHH-HHHCCCC-----CCCCHHHHHHHHHHHHCCCC
T ss_conf             1698468899635678999999984048816899723016-778888-7545532-----47870234432454302675


Q ss_pred             CEEEEECCHH-HH--HHHCCCEEEEEEECCCCCCHHC--CCCC--CCHHHHHHHH---HHHCCCCEECCCC--------C
Q ss_conf             7399940012-11--0010001367740553210000--2443--2248999997---5110321000024--------5
Q gi|254780619|r  298 ISVIVGVRSA-LF--LPFKKLGLIVIDEEHDISYKQE--EGIL--YNARDMSIVR---GKIESFPVVLVSA--------T  359 (731)
Q Consensus       298 ~~IVIGtRSA-if--~P~~nLglIIvDEEHd~sykq~--~~pr--y~aRdvA~~R---a~~~~~~lilgSA--------T  359 (731)
                      -.+.==|--- +.  +---|+.++|||==+ .=|-.+  .+|-  =.+|+++-+.   ||..++++++..+        =
T Consensus       177 L~~L~Et~~e~I~~~~e~~~P~~~ViDSIQ-~ly~~di~SaPGSVsQVRE~t~~Lmr~AKt~~iaifiVGHVTKeGsiAG  255 (481)
T TIGR00416       177 LYVLSETNLEQICAEIEELNPQVVVIDSIQ-TLYLPDISSAPGSVSQVRECTAELMRLAKTRGIAIFIVGHVTKEGSIAG  255 (481)
T ss_pred             CCCCCCCCHHHHHHHHHHHCCCEEEEECCC-CCCCHHHCCCCCCHHHHHHHHHHHHHHHHHCCCCEEEEEEECCCCCCCC
T ss_conf             321575798999999985299489991421-0000000258884238889999998765216865799700435675434


Q ss_pred             CCH-HH-----HHHH-H-HHHHHHHC-CCCCCCCCCCCCCEECCCCCCC
Q ss_conf             432-46-----7753-2-12344412-4322367654332110222233
Q gi|254780619|r  360 PSI-ES-----RVNG-I-SRRYHSVH-LSTRYRNSALPHLQVIDMRGQT  399 (731)
Q Consensus       360 PSl-es-----~~~~-~-~g~~~~~~-l~~R~~~~~~P~i~ivDm~~~~  399 (731)
                      |-+ |.     +|.- . ...|+.|+ .++||+...  ++-|..|+++-
T Consensus       256 PkvLEH~vD~vLyfeGd~~~~~R~LRS~KNRFGat~--E~G~FeM~e~G  302 (481)
T TIGR00416       256 PKVLEHMVDTVLYFEGDRDSRFRILRSVKNRFGATN--EIGIFEMTEQG  302 (481)
T ss_pred             CHHHHHHHHHHEECCCCCCCCCCHHHCCCCCCCCCC--CCCCCCCCHHH
T ss_conf             046663433110115887534440100015678734--21010000233


No 305
>COG3972 Superfamily I DNA and RNA helicases [General function prediction only]
Probab=92.45  E-value=0.17  Score=30.52  Aligned_cols=121  Identities=20%  Similarity=0.205  Sum_probs=67.3

Q ss_pred             CCEEEEECCCCHHHHHHHHHHHHHHHHCC--CCEEEEECCCHHHHHHHHHHHCCC-------C--CEEEEEE--CCCCCH
Q ss_conf             96199844753157999999999985146--847997152100134455543038-------9--7689962--355723
Q gi|254780619|r  218 FAVSLISGVTGSGKTEVYLEIVAAVLHLG--KQVLILLPEISLTSAILERFQKRF-------G--VKPAEWH--SSLSTS  284 (731)
Q Consensus       218 f~~~LL~GvTGSGKTEVYl~li~~~L~~G--kqvLiLvPEI~Lt~Q~~~rl~~rF-------~--~~v~v~H--S~ls~~  284 (731)
                      |.+-.+.|-.||||||+-++-+++.-..+  -+.++-+=.-.|..|+-.+..+.|       +  .+..+.|  .+++..
T Consensus       176 ~G~qrIrGLAGSGKT~~La~Kaa~lh~knPd~~I~~Tfftk~L~s~~r~lv~~F~f~~~e~~pdW~~~l~~h~wgG~t~~  255 (660)
T COG3972         176 FGKQRIRGLAGSGKTELLAHKAAELHSKNPDSRIAFTFFTKILASTMRTLVPEFFFMRVEKQPDWGTKLFCHNWGGLTKE  255 (660)
T ss_pred             CCHHHHHCCCCCCCHHHHHHHHHHHHCCCCCCEEEEEEEHHHHHHHHHHHHHHHHHHHHHCCCCCCCEEEEECCCCCCCC
T ss_conf             73465200247873029887778974479986389986667888999999999999886248872426888435787888


Q ss_pred             HHHHHHHHHHCCCCEEEEECCHHHH--------HHHCC---CEEEEEEECCCCCCHHCCCCCCCHHHHHHHHHH
Q ss_conf             5667899997199739994001211--------00100---013677405532100002443224899999751
Q gi|254780619|r  285 MREKIWRQVARGAISVIVGVRSALF--------LPFKK---LGLIVIDEEHDISYKQEEGILYNARDMSIVRGK  347 (731)
Q Consensus       285 eR~~~w~~i~~G~~~IVIGtRSAif--------~P~~n---LglIIvDEEHd~sykq~~~pry~aRdvA~~Ra~  347 (731)
                      --|.-+..+. +...+--|.+..-|        .-.+|   +..|.|||-+|-       |- .--|+..+.++
T Consensus       256 g~y~~~~~~~-~~~~~~fsg~g~~F~~aC~eli~~~~~~~~yD~ilIDE~QDF-------P~-~F~~Lcf~~tk  320 (660)
T COG3972         256 GFYGMYRYIC-HYYEIPFSGFGNGFDAACKELIADINNKKAYDYILIDESQDF-------PQ-SFIDLCFMVTK  320 (660)
T ss_pred             CCHHHHHHHH-CCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCCEEEECCCCCC-------CH-HHHHHHHHHHC
T ss_conf             6038899984-266545478774067999999986425642317994245547-------78-99999999824


No 306
>PRK07111 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=92.44  E-value=0.053  Score=34.42  Aligned_cols=28  Identities=18%  Similarity=0.300  Sum_probs=14.9

Q ss_pred             HHHHHHCCCCEEEEEEC--------CCCEEHHCCCC
Q ss_conf             99886226551799742--------22000000235
Q gi|254780619|r  413 GIRHTLARNEQTLLFLN--------RRGYAPLTLCQ  440 (731)
Q Consensus       413 ~i~~~l~~g~qvll~ln--------RrGya~~~~C~  440 (731)
                      +++-+-+++-+-+++++        ..|+.+...|.
T Consensus       353 a~~~taK~~~P~f~~~d~~~~~~~~~~~~~~~~~~~  388 (703)
T PRK07111        353 ACRVAAKRLFPNFMFLDAPFNKEYYDKGRPETEVAT  388 (703)
T ss_pred             HHHHHHHHCCCCEEECCCCCCHHHCCCCCCCCCCCC
T ss_conf             999988756886780576411330356778877777


No 307
>KOG0949 consensus
Probab=92.36  E-value=0.36  Score=28.07  Aligned_cols=69  Identities=23%  Similarity=0.310  Sum_probs=46.6

Q ss_pred             HHCCCCCCEEEEEHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCC--CCCEEEEEECCCCCH
Q ss_conf             621257657987044302311345201233000344310245578999998754311025667--886899993298648
Q gi|254780619|r  531 AIAKGEIDIIIGTQLVAKGHNFPRMSLVGVVDGDLGLTNADLRSSERTFQLLSQVTGRAGRFG--LKSLGLIQAYQPTHP  608 (731)
Q Consensus       531 ~~~~~~~~ilvgTq~i~kg~~fp~v~lv~il~aD~~l~~pd~ra~E~~~qll~qv~gRagr~~--~~g~v~iQt~~p~~~  608 (731)
                      -|+.|...+|++|.-++=|.+.|.=|.|--.  |++-.-|         -...|.||||||..  .-|.|+.-. -|-|.
T Consensus       983 LFR~g~L~VlfaT~TLsLGiNMPCrTVvF~g--DsLQL~p---------lny~QmaGRAGRRGFD~lGnV~Fmg-iP~~k 1050 (1330)
T KOG0949         983 LFRQGHLQVLFATETLSLGINMPCRTVVFAG--DSLQLDP---------LNYKQMAGRAGRRGFDTLGNVVFMG-IPRQK 1050 (1330)
T ss_pred             HHHCCCEEEEEEEEEHHCCCCCCCEEEEEEC--CCCCCCC---------HHHHHHHCCCCCCCCCCCCCEEEEE-CCHHH
T ss_conf             8644856899982110112688741689703--5221371---------4577662403344555556558872-75999


Q ss_pred             HHH
Q ss_conf             889
Q gi|254780619|r  609 VMQ  611 (731)
Q Consensus       609 ~~~  611 (731)
                      +-+
T Consensus      1051 v~r 1053 (1330)
T KOG0949        1051 VQR 1053 (1330)
T ss_pred             HHH
T ss_conf             999


No 308
>PRK08270 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=92.30  E-value=0.062  Score=33.87  Aligned_cols=78  Identities=21%  Similarity=0.262  Sum_probs=42.6

Q ss_pred             EEECC-CCHHHH--------HHHHHHHHHHHH------CCCCEEEEECCCHHHHHHHHHHHCCCCCEEEEEECCCCCHHH
Q ss_conf             98447-531579--------999999999851------468479971521001344555430389768996235572356
Q gi|254780619|r  222 LISGV-TGSGKT--------EVYLEIVAAVLH------LGKQVLILLPEISLTSAILERFQKRFGVKPAEWHSSLSTSMR  286 (731)
Q Consensus       222 LL~Gv-TGSGKT--------EVYl~li~~~L~------~GkqvLiLvPEI~Lt~Q~~~rl~~rF~~~v~v~HS~ls~~eR  286 (731)
                      |.+|- +|.|+.        .+++..|.+.+.      .|.|++-.+ ...|+|              ++...+|+..|-
T Consensus       180 l~~Gf~~~~g~i~s~ppk~~~tA~~~~~~~i~~~q~~~~Ggqa~~~f-D~~LAP--------------yv~~d~l~~~ei  244 (681)
T PRK08270        180 LLEGFNGVPGKVESKPPKHFRSALGQIVNFLGTLQNEWAGAQAFSSF-DTYLAP--------------FVRKDNLSYAEV  244 (681)
T ss_pred             HHHCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHCCEEHHHH-HHHHCC--------------HHHHCCCCHHHH
T ss_conf             98274888886501898679999999999999986554314138768-887200--------------462146989999


Q ss_pred             HHHHHHHHCCCCEEEEECCHHHHHHHCCCEE
Q ss_conf             6789999719973999400121100100013
Q gi|254780619|r  287 EKIWRQVARGAISVIVGVRSALFLPFKKLGL  317 (731)
Q Consensus       287 ~~~w~~i~~G~~~IVIGtRSAif~P~~nLgl  317 (731)
                      ++.++...-+ ..  .=+|+.-=+||.++++
T Consensus       245 kqa~Q~fvy~-lN--t~sr~ggQtPFt~i~~  272 (681)
T PRK08270        245 KQALQEFVFN-LN--VPSRWGFQTPFTNLTF  272 (681)
T ss_pred             HHHHHHHHHH-HC--CCCCCCCCCCCEEEEE
T ss_conf             9999999998-54--6566789788157783


No 309
>TIGR02642 phage_xxxx uncharacterized phage protein; InterPro: IPR013464    This uncharacterised protein is found in prophage regions of Shewanella oneidensis MR-1, Vibrio vulnificus (strain YJ016), Yersinia pseudotuberculosis IP 32953, and Aeromonas hydrophila ATCC7966. It appears to have regions of sequence similarity to the phage lambda antitermination protein Q..
Probab=92.30  E-value=0.07  Score=33.48  Aligned_cols=65  Identities=22%  Similarity=0.491  Sum_probs=38.4

Q ss_pred             HHHHHHHHCCCCEEEEEECCCCEEHHCCCCCCCCCCCCCCCCC-EEEEECCCCCCEECHHHCCCCCCCCCCCCCCCCEEC
Q ss_conf             9999886226551799742220000002356543431014652-012113578320000210244655566678741100
Q gi|254780619|r  411 IDGIRHTLARNEQTLLFLNRRGYAPLTLCQVCGNRLKCLHCSC-WLVEHRSKKKLYCHQCGHSAIYSQSCVVCGSSGKMI  489 (731)
Q Consensus       411 ~~~i~~~l~~g~qvll~lnRrGya~~~~C~~Cg~~~~C~~C~~-~l~~h~~~~~l~Ch~Cg~~~~~~~~Cp~Cg~~~~l~  489 (731)
                      +++.+..++.-+.+|     |-||..    .-+..-+||+|-+ .+++|               +-|..|++|++++++.
T Consensus       157 I~~~~~~I~TE~~~L-----rd~a~~----~a~~~~~CP~C~Gtg~~~~---------------~~P~~C~~C~G~G~~~  212 (270)
T TIGR02642       157 IKALKAKIDTERRAL-----RDYAVA----KAAESRKCPRCRGTGLRLR---------------RQPEECDKCAGTGRLL  212 (270)
T ss_pred             HHHHHHHHHHHHHHH-----HHHHHH----HHHHCCCCCCCCCCCCCCC---------------CCCCCCCCCCCCCCCC
T ss_conf             999987767778889-----999999----8741488798656678889---------------7788777778643303


Q ss_pred             CCCCCHHHHHHHHHHCC
Q ss_conf             13542899888852048
Q gi|254780619|r  490 ACGFGIERIAEEVCEYF  506 (731)
Q Consensus       490 ~~G~Gte~~~e~l~~~f  506 (731)
                      +       .+|.+.+-|
T Consensus       213 ~-------~~e~l~ks~  222 (270)
T TIGR02642       213 P-------TVEDLSKSF  222 (270)
T ss_pred             C-------CHHHHHHHH
T ss_conf             0-------089999988


No 310
>COG3267 ExeA Type II secretory pathway, component ExeA (predicted ATPase) [Intracellular trafficking and secretion]
Probab=92.28  E-value=0.71  Score=25.80  Aligned_cols=113  Identities=19%  Similarity=0.237  Sum_probs=60.5

Q ss_pred             CCHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHCCCCCEEEEEE
Q ss_conf             88378999999987520489619984475315799999999998514684799715210013445554303897689962
Q gi|254780619|r  199 LDKNQQDVVEQVVPLCTKGFAVSLISGVTGSGKTEVYLEIVAAVLHLGKQVLILLPEISLTSAILERFQKRFGVKPAEWH  278 (731)
Q Consensus       199 Lt~eQ~~a~~~i~~~~~~~f~~~LL~GvTGSGKTEVYl~li~~~L~~GkqvLiLvPEI~Lt~Q~~~rl~~rF~~~v~v~H  278 (731)
                      ...+-+.++..+......+-....+-|..|||||-+- +++.+.+..++-+.+.+|--.++                   
T Consensus        32 ~~a~h~e~l~~l~~~i~d~qg~~~vtGevGsGKTv~~-Ral~~s~~~d~~~~v~i~~~~~s-------------------   91 (269)
T COG3267          32 WAADHNEALLMLHAAIADGQGILAVTGEVGSGKTVLR-RALLASLNEDQVAVVVIDKPTLS-------------------   91 (269)
T ss_pred             HHHHHHHHHHHHHHHHHCCCCEEEEEECCCCCHHHHH-HHHHHHCCCCCEEEEEECCCCHH-------------------
T ss_conf             3200159999977777517855999744777636999-99998557885179983576301-------------------


Q ss_pred             CCCCCHHHHHHHHHHHCCCCEEEEEC------C--HHHHHHHCCCEEEEEEECCCCCCHHCCCCC
Q ss_conf             35572356678999971997399940------0--121100100013677405532100002443
Q gi|254780619|r  279 SSLSTSMREKIWRQVARGAISVIVGV------R--SALFLPFKKLGLIVIDEEHDISYKQEEGIL  335 (731)
Q Consensus       279 S~ls~~eR~~~w~~i~~G~~~IVIGt------R--SAif~P~~nLglIIvDEEHd~sykq~~~pr  335 (731)
                          ...-.+.|..-..+.++.-+-+      |  -|++.--++.-..+|||-||.++-+.++-|
T Consensus        92 ----~~~~~~ai~~~l~~~p~~~~~~~~e~~~~~L~al~~~g~r~v~l~vdEah~L~~~~le~Lr  152 (269)
T COG3267          92 ----DATLLEAIVADLESQPKVNVNAVLEQIDRELAALVKKGKRPVVLMVDEAHDLNDSALEALR  152 (269)
T ss_pred             ----HHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHCCCCEEEEEHHHHHHCHHHHHHHH
T ss_conf             ----7889999999840583200688999999999999981788737850167661754899999


No 311
>PRK06450 threonine synthase; Validated
Probab=92.25  E-value=0.087  Score=32.76  Aligned_cols=35  Identities=20%  Similarity=0.173  Sum_probs=15.0

Q ss_pred             HHHHCCCCEEEEECCCHHHHHHHHHHHCCCCCEEEEE
Q ss_conf             9851468479971521001344555430389768996
Q gi|254780619|r  241 AVLHLGKQVLILLPEISLTSAILERFQKRFGVKPAEW  277 (731)
Q Consensus       241 ~~L~~GkqvLiLvPEI~Lt~Q~~~rl~~rF~~~v~v~  277 (731)
                      .+-..|-.+.|.+|+  -+|+--...-..+|.+|...
T Consensus       113 yaa~~Gi~~~I~vP~--~~~~~K~~~~~~yGA~vv~v  147 (336)
T PRK06450        113 YGAAAGIKVKIFVPE--TASGGKLKQIEAYGAEVIKV  147 (336)
T ss_pred             HHHHCCCCEEEECCC--CCCHHHHHHHHHCCCEEEEE
T ss_conf             999849968998268--89999999999769999997


No 312
>PRK04296 thymidine kinase; Provisional
Probab=92.21  E-value=0.83  Score=25.29  Aligned_cols=105  Identities=22%  Similarity=0.312  Sum_probs=61.2

Q ss_pred             EEEEECCCCHHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHCCCCCEEEEEECCCCCHHHHHHHHHHHCCCCE
Q ss_conf             19984475315799999999998514684799715210013445554303897689962355723566789999719973
Q gi|254780619|r  220 VSLISGVTGSGKTEVYLEIVAAVLHLGKQVLILLPEISLTSAILERFQKRFGVKPAEWHSSLSTSMREKIWRQVARGAIS  299 (731)
Q Consensus       220 ~~LL~GvTGSGKTEVYl~li~~~L~~GkqvLiLvPEI~Lt~Q~~~rl~~rF~~~v~v~HS~ls~~eR~~~w~~i~~G~~~  299 (731)
                      ..++.|--.||||.--++.+...-..|+.+++.-|++.          .|++..-.+-|++++-              ..
T Consensus         4 L~~i~GpMfSGKTteLi~~~~~~~~~gkkvl~~kp~~D----------~Ry~~~~I~Sh~g~~~--------------~~   59 (197)
T PRK04296          4 LYFIYGAMNSGKSTELLQRAYNYEERGMKVLVFTPAID----------DRYGEGKVVSRIGLSR--------------EA   59 (197)
T ss_pred             EEEEECCCCCHHHHHHHHHHHHHHHCCCEEEEEEECCC----------CCCCCCCEECCCCCEE--------------EE
T ss_conf             99999342788899999999999987995999985344----------6577785786789834--------------68


Q ss_pred             EEEECCHHHH------HHHCCCEEEEEEECCCCCCHHCCCCCCCHHHHHHHHHHHCCCCEECC
Q ss_conf             9994001211------00100013677405532100002443224899999751103210000
Q gi|254780619|r  300 VIVGVRSALF------LPFKKLGLIVIDEEHDISYKQEEGILYNARDMSIVRGKIESFPVVLV  356 (731)
Q Consensus       300 IVIGtRSAif------~P~~nLglIIvDEEHd~sykq~~~pry~aRdvA~~Ra~~~~~~lilg  356 (731)
                      +.+..---+|      .-..+...|.|||-|  .|. +    -+..+++... ...|..|+..
T Consensus        60 ~~v~~~~~i~~~~~~~~~~~~~dvI~IDEaQ--Ff~-~----~~i~~~~~~~-~~~~~~Viv~  114 (197)
T PRK04296         60 ILISSDTDIFELIEEEHEGGKIDCVLIDEAQ--FLD-K----EQVVQLAEVV-DDLGIPVICY  114 (197)
T ss_pred             EEECCHHHHHHHHHHHHCCCCCCEEEECCHH--CCC-H----HHHHHHHHHH-HHCCCEEEEE
T ss_conf             9948789999999876304785689972021--279-8----9999999999-8318589997


No 313
>KOG1123 consensus
Probab=92.15  E-value=0.51  Score=26.86  Aligned_cols=113  Identities=19%  Similarity=0.256  Sum_probs=72.4

Q ss_pred             CCCHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHCCC---CCEE
Q ss_conf             6883789999999875204896199844753157999999999985146847997152100134455543038---9768
Q gi|254780619|r  198 ILDKNQQDVVEQVVPLCTKGFAVSLISGVTGSGKTEVYLEIVAAVLHLGKQVLILLPEISLTSAILERFQKRF---GVKP  274 (731)
Q Consensus       198 ~Lt~eQ~~a~~~i~~~~~~~f~~~LL~GvTGSGKTEVYl~li~~~L~~GkqvLiLvPEI~Lt~Q~~~rl~~rF---~~~v  274 (731)
                      .+.+-|..-+...-......-...+|  --|+|||.|=+-++.   .-.|+||+|.---.-..|+-..|+.--   ++.+
T Consensus       302 ~iRpYQEksL~KMFGNgRARSGiIVL--PCGAGKtLVGvTAa~---tikK~clvLcts~VSVeQWkqQfk~wsti~d~~i  376 (776)
T KOG1123         302 QIRPYQEKSLSKMFGNGRARSGIIVL--PCGAGKTLVGVTAAC---TIKKSCLVLCTSAVSVEQWKQQFKQWSTIQDDQI  376 (776)
T ss_pred             CCCCHHHHHHHHHHCCCCCCCCEEEE--ECCCCCCEEEEEEEE---EECCCEEEEECCCCCHHHHHHHHHHHHCCCCCCE
T ss_conf             55753787899973788544761898--569987425455554---5514279995575669999999874501685545


Q ss_pred             EEEECCCCCHHHHHHHHHHHCCCCEEEEECCHHH---------------HHHHCCCEEEEEEECC
Q ss_conf             9962355723566789999719973999400121---------------1001000136774055
Q gi|254780619|r  275 AEWHSSLSTSMREKIWRQVARGAISVIVGVRSAL---------------FLPFKKLGLIVIDEEH  324 (731)
Q Consensus       275 ~v~HS~ls~~eR~~~w~~i~~G~~~IVIGtRSAi---------------f~P~~nLglIIvDEEH  324 (731)
                      +.+.|.-.+.-         .+.+.|||.|.|-+               |+-=..-|+++.||-|
T Consensus       377 ~rFTsd~Ke~~---------~~~~gvvvsTYsMva~t~kRS~eaek~m~~l~~~EWGllllDEVH  432 (776)
T KOG1123         377 CRFTSDAKERF---------PSGAGVVVTTYSMVAYTGKRSHEAEKIMDFLRGREWGLLLLDEVH  432 (776)
T ss_pred             EEEECCCCCCC---------CCCCCEEEEEEEHHHHCCCCCHHHHHHHHHHHCCEEEEEEEEHHC
T ss_conf             77202445457---------898857998731311056642779999999843710168842111


No 314
>PRK05823 consensus
Probab=92.14  E-value=0.093  Score=32.53  Aligned_cols=39  Identities=26%  Similarity=0.597  Sum_probs=19.9

Q ss_pred             CCCCCCCEEEEECC--C--CCCEEC---HHHCCCCC-----------CCCCCCCCCC
Q ss_conf             10146520121135--7--832000---02102446-----------5556667874
Q gi|254780619|r  447 KCLHCSCWLVEHRS--K--KKLYCH---QCGHSAIY-----------SQSCVVCGSS  485 (731)
Q Consensus       447 ~C~~C~~~l~~h~~--~--~~l~Ch---~Cg~~~~~-----------~~~Cp~Cg~~  485 (731)
                      .||.|+.+|..-+.  +  ..+-|.   -|.+....           ...||.||+.
T Consensus       603 ~CP~Cg~~l~~r~~~~g~~~F~~Cs~yp~Ck~~~~~~~~~~~~~~~~~~~CP~Cg~~  659 (691)
T PRK05823        603 DCPKCASDLLYRRTRRGNEKFVGCSNFPKCKFTEFSEQKPLEKPEELEELCPECNSK  659 (691)
T ss_pred             CCCCCCCCCEEEECCCCCCEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCH
T ss_conf             898889820367426888604557999988787777877666633258859999824


No 315
>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=92.10  E-value=0.05  Score=34.63  Aligned_cols=29  Identities=28%  Similarity=0.308  Sum_probs=15.3

Q ss_pred             CEEEEECCC-----CHHHHHHHHHHHHHHHHCCCCEE
Q ss_conf             619984475-----31579999999999851468479
Q gi|254780619|r  219 AVSLISGVT-----GSGKTEVYLEIVAAVLHLGKQVL  250 (731)
Q Consensus       219 ~~~LL~GvT-----GSGKTEVYl~li~~~L~~GkqvL  250 (731)
                      .++|+-++.     +||.|   =++.+-.|-+|-|++
T Consensus       560 ~~ylvvpD~~tYiQASGRT---SRl~aGGlTkGlS~V  593 (1843)
T TIGR01054       560 KLYLVVPDVKTYIQASGRT---SRLYAGGLTKGLSVV  593 (1843)
T ss_pred             EEEEEECCCCCCCCCCCHH---HHHHHHHHHHCCEEE
T ss_conf             2599966877442467415---665542323053489


No 316
>PRK06067 flagellar accessory protein FlaH; Validated
Probab=92.10  E-value=0.37  Score=27.96  Aligned_cols=49  Identities=24%  Similarity=0.358  Sum_probs=38.4

Q ss_pred             CCEEEEECCCCHHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHH
Q ss_conf             96199844753157999999999985146847997152100134455543
Q gi|254780619|r  218 FAVSLISGVTGSGKTEVYLEIVAAVLHLGKQVLILLPEISLTSAILERFQ  267 (731)
Q Consensus       218 f~~~LL~GvTGSGKTEVYl~li~~~L~~GkqvLiLvPEI~Lt~Q~~~rl~  267 (731)
                      .+..|+.|-+|+|||-+-++.+...+++|..++++.=|-. +.+++++.+
T Consensus        32 g~~~li~G~~G~GKt~~~~~f~~~~~~~g~~~~~~~~ee~-~~~~~~~~~   80 (241)
T PRK06067         32 GSLILIEGENDTGKSVLSQQFVWGALNQGKRGLAITTENT-SKSYLKQME   80 (241)
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHHHHHCCCEEEEEEECCC-HHHHHHHHH
T ss_conf             9089998079988799999999999867982999994289-999999999


No 317
>PRK13826 Dtr system oriT relaxase; Provisional
Probab=92.06  E-value=1  Score=24.64  Aligned_cols=103  Identities=19%  Similarity=0.252  Sum_probs=64.7

Q ss_pred             CCCCHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHHHHHHHHHHC-CCCEEEEECC----------CHHHHHHHHH
Q ss_conf             6688378999999987520489619984475315799999999998514-6847997152----------1001344555
Q gi|254780619|r  197 PILDKNQQDVVEQVVPLCTKGFAVSLISGVTGSGKTEVYLEIVAAVLHL-GKQVLILLPE----------ISLTSAILER  265 (731)
Q Consensus       197 ~~Lt~eQ~~a~~~i~~~~~~~f~~~LL~GvTGSGKTEVYl~li~~~L~~-GkqvLiLvPE----------I~Lt~Q~~~r  265 (731)
                      ..|++||..|+..|...    -...++.|.-|.|||-+ |.++.++++. |..|+=+.|-          -+...+++.-
T Consensus       380 ~~Ls~EQ~~Av~hiT~~----~~Ia~VvG~AGaGKStm-L~aAReawEa~GyrV~GaALsGkAAegLe~~sGI~SrTlAs  454 (1102)
T PRK13826        380 ARLSDEQKTAIEHVAGA----ERIAAVIGRAGAGKTTM-MKAAREAWEAAGYRVVGGALAGKAAEGLEKEAGIASRTLSS  454 (1102)
T ss_pred             CCCCHHHHHHHHHHCCC----CCEEEEEECCCCCHHHH-HHHHHHHHHHCCCEEEEECCCHHHHHHHHHCCCCCCHHHHH
T ss_conf             13899999999985378----86689984288878899-99999999977977980150078999775346953033899


Q ss_pred             HH-----CC--CC-CEEE-EEECCCCCHHHHHHHHHHH--CCCCEEEEEC
Q ss_conf             43-----03--89-7689-9623557235667899997--1997399940
Q gi|254780619|r  266 FQ-----KR--FG-VKPA-EWHSSLSTSMREKIWRQVA--RGAISVIVGV  304 (731)
Q Consensus       266 l~-----~r--F~-~~v~-v~HS~ls~~eR~~~w~~i~--~G~~~IVIGt  304 (731)
                      +.     .+  ++ ..|. +=-.+|-.+.-+.-..+..  .|.--|.||-
T Consensus       455 ~e~~w~~gr~~L~~~dVlVIDEAGMVgsrqmarvl~~ae~aGAKvVLVGD  504 (1102)
T PRK13826        455 WELRWNQGRDQLDNKTVFVLDEAGMVSSRQMALFVEAVTRAGAKLVLVGD  504 (1102)
T ss_pred             HHHHHCCCCCCCCCCCEEEEECCCCCCHHHHHHHHHHHHHCCCEEEEECC
T ss_conf             99874358655678738998455565579999999999975998999688


No 318
>COG0068 HypF Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]
Probab=92.05  E-value=0.11  Score=32.08  Aligned_cols=90  Identities=18%  Similarity=0.108  Sum_probs=39.7

Q ss_pred             HHHHHHCCCC---CEEEEEECCCCCHHHHHHH----HH-HHCCCCEEEEECCHHHHHHH----CCCEEE-EEEECCCCCC
Q ss_conf             4555430389---7689962355723566789----99-97199739994001211001----000136-7740553210
Q gi|254780619|r  262 ILERFQKRFG---VKPAEWHSSLSTSMREKIW----RQ-VARGAISVIVGVRSALFLPF----KKLGLI-VIDEEHDISY  328 (731)
Q Consensus       262 ~~~rl~~rF~---~~v~v~HS~ls~~eR~~~w----~~-i~~G~~~IVIGtRSAif~P~----~nLglI-IvDEEHd~sy  328 (731)
                      .+.+++.|.+   ...|++--.+...+.+-.-    .. +.+-...||+=-++-.|...    ++|.-| ||-       
T Consensus       232 aV~~LR~rk~Rp~KPFAvM~kdl~~i~~~a~~~~~E~~lL~S~~rPIVll~Kk~~~~~~~~iAP~l~~iGVML-------  304 (750)
T COG0068         232 AVAKLRKRKNRPLKPFAVMAKDLETIEEFAEVNDEEEELLTSPSRPIVLLKKKKVFLLESNIAPGLHTIGVML-------  304 (750)
T ss_pred             HHHHHHHHCCCCCCCCEEEECCHHHHHHHHCCCHHHHHHHCCCCCCEEEECCCCCCCCCCCCCCCCCCCCEEE-------
T ss_conf             9999998518988883465064887877624567889874586676798636666664122589998752662-------


Q ss_pred             HHCCCCCCCHHHHHHHHHHHCCCCEECCCCCCCHHHH
Q ss_conf             0002443224899999751103210000245432467
Q gi|254780619|r  329 KQEEGILYNARDMSIVRGKIESFPVVLVSATPSIESR  365 (731)
Q Consensus       329 kq~~~pry~aRdvA~~Ra~~~~~~lilgSATPSles~  365 (731)
                           | |.--.-. +.-...+.++|+.||-.|-|.+
T Consensus       305 -----P-YtpLhhL-Ll~~~~~~~~VmTSaNl~g~Pm  334 (750)
T COG0068         305 -----P-YTPLHHL-LLQESLDIPYVMTSANLPGEPM  334 (750)
T ss_pred             -----C-CCCHHHH-HHHHCCCCEEEEECCCCCCCCC
T ss_conf             -----2-7816665-4331368329980588889985


No 319
>KOG1802 consensus
Probab=91.94  E-value=0.45  Score=27.32  Aligned_cols=69  Identities=30%  Similarity=0.454  Sum_probs=49.9

Q ss_pred             CCCCCCCCHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHHHHHHHHHHC-CCCEEEEEC-CCHHHHHHHHHHH
Q ss_conf             44666688378999999987520489619984475315799999999998514-684799715-2100134455543
Q gi|254780619|r  193 YFSLPILDKNQQDVVEQVVPLCTKGFAVSLISGVTGSGKTEVYLEIVAAVLHL-GKQVLILLP-EISLTSAILERFQ  267 (731)
Q Consensus       193 ~~~~~~Lt~eQ~~a~~~i~~~~~~~f~~~LL~GvTGSGKTEVYl~li~~~L~~-GkqvLiLvP-EI~Lt~Q~~~rl~  267 (731)
                      .+..|.||..|..|+......     ...||+|=.|.|||-+-..++-+...+ +..||+.+| .|+ ..|+.+.+.
T Consensus       405 ~~~lpkLN~SQ~~AV~~VL~r-----plsLIQGPPGTGKTvtsa~IVyhl~~~~~~~VLvcApSNiA-VDqLaeKIh  475 (935)
T KOG1802         405 VPNLPKLNASQSNAVKHVLQR-----PLSLIQGPPGTGKTVTSATIVYHLARQHAGPVLVCAPSNIA-VDQLAEKIH  475 (935)
T ss_pred             CCCCHHHCHHHHHHHHHHHCC-----CCEEEECCCCCCCEEHHHHHHHHHHHHCCCCEEEECCCCHH-HHHHHHHHH
T ss_conf             789612246789999999759-----85155469998833116899999998528956998165002-899999998


No 320
>cd01130 VirB11-like_ATPase Type IV secretory pathway component VirB11, and related ATPases. The homohexamer, VirB11 is one of eleven Vir proteins, which are required for T-pilus biogenesis and virulence in the transfer of T-DNA from the Ti (tumor-inducing) plasmid of bacterial to plant cells. The pilus is a fibrous cell surface organelle, which mediates adhesion between bacteria during conjugative transfer or between bacteria and host eukaryotic cells during infection. VirB11- related ATPases include the archaeal flagella biosynthesis protein and the pilus assembly proteins CpaF/TadA and TrbB.  This alignment contains the C-terminal domain, which is the ATPase.
Probab=91.94  E-value=0.51  Score=26.86  Aligned_cols=49  Identities=27%  Similarity=0.267  Sum_probs=32.3

Q ss_pred             CCCHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHHHHHHHHHHCCCCEEE
Q ss_conf             688378999999987520489619984475315799999999998514684799
Q gi|254780619|r  198 ILDKNQQDVVEQVVPLCTKGFAVSLISGVTGSGKTEVYLEIVAAVLHLGKQVLI  251 (731)
Q Consensus       198 ~Lt~eQ~~a~~~i~~~~~~~f~~~LL~GvTGSGKTEVYl~li~~~L~~GkqvLi  251 (731)
                      .++++|...+......    -...|+-|-||||||..- .++...+.....++.
T Consensus         9 ~~~~~~~~~L~~~v~~----~~nIlIsG~tGSGKTTll-~al~~~i~~~~rivt   57 (186)
T cd01130           9 TFSPLQAAYLWLAVEA----RKNILISGGTGSGKTTLL-NALLAFIPPDERIIT   57 (186)
T ss_pred             CCCHHHHHHHHHHHHC----CCCEEEECCCCCCHHHHH-HHHHHHCCCCCCEEE
T ss_conf             9999999999999985----998999899999899999-999961334564598


No 321
>PRK06731 flhF flagellar biosynthesis regulator FlhF; Validated
Probab=91.83  E-value=1.1  Score=24.46  Aligned_cols=37  Identities=22%  Similarity=0.184  Sum_probs=29.0

Q ss_pred             CCEEEEECCCCHHHHHHHHHHHHHHHHCCCCEEEEEC
Q ss_conf             9619984475315799999999998514684799715
Q gi|254780619|r  218 FAVSLISGVTGSGKTEVYLEIVAAVLHLGKQVLILLP  254 (731)
Q Consensus       218 f~~~LL~GvTGSGKTEVYl~li~~~L~~GkqvLiLvP  254 (731)
                      ..+.++-|.||||||=--..++.....+|+.|++..=
T Consensus        75 ~~vI~lvG~~G~GKTTT~AKLA~~~~~~~~kV~lia~  111 (270)
T PRK06731         75 VQTIALIGPTGVGKTTTLAKMAWQFHGKKKTVGFITT  111 (270)
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHHHHHCCCEEEEEEE
T ss_conf             8189998889898899999999999867990899983


No 322
>PRK13889 conjugal transfer relaxase TraA; Provisional
Probab=91.82  E-value=1.1  Score=24.46  Aligned_cols=103  Identities=17%  Similarity=0.195  Sum_probs=65.1

Q ss_pred             CCCCHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHHHHHHHHHH-CCCCEEEEECC----------CHHHHHHHHH
Q ss_conf             668837899999998752048961998447531579999999999851-46847997152----------1001344555
Q gi|254780619|r  197 PILDKNQQDVVEQVVPLCTKGFAVSLISGVTGSGKTEVYLEIVAAVLH-LGKQVLILLPE----------ISLTSAILER  265 (731)
Q Consensus       197 ~~Lt~eQ~~a~~~i~~~~~~~f~~~LL~GvTGSGKTEVYl~li~~~L~-~GkqvLiLvPE----------I~Lt~Q~~~r  265 (731)
                      ..|++||..|+..|...    -...++-|--|.|||=+ |.++.++++ +|..|+=+.|-          -+...+++..
T Consensus       345 ~~Ls~EQ~~A~~hiT~~----~~iavVvG~AGtGKStm-L~aAReawEa~GyrV~GaALsGkAAegLe~~sGI~SrTlAs  419 (992)
T PRK13889        345 LVLSGEQADALAHVTDG----RDLGVVVGYAGTGKSAM-LGVAREAWEAAGYEVRGAALSGIAAENLEGGSGIASRTIAS  419 (992)
T ss_pred             CCCCHHHHHHHHHHCCC----CCEEEEEECCCCCHHHH-HHHHHHHHHHCCCEEEEECCCHHHHHHHHHCCCCCCHHHHH
T ss_conf             88799999999986478----97589983388878899-99999999977988981150068999765347943167999


Q ss_pred             HHCCC-------C-CEEE-EEECCCCCHHHHHHHHHHH--CCCCEEEEEC
Q ss_conf             43038-------9-7689-9623557235667899997--1997399940
Q gi|254780619|r  266 FQKRF-------G-VKPA-EWHSSLSTSMREKIWRQVA--RGAISVIVGV  304 (731)
Q Consensus       266 l~~rF-------~-~~v~-v~HS~ls~~eR~~~w~~i~--~G~~~IVIGt  304 (731)
                      +.-..       + ..|. |=-.+|-.+.-+....++.  .|.--|.||-
T Consensus       420 ~e~~w~~g~~~L~~~dVlVVDEAGMVgSRqMarll~~Ae~AGAKVVLVGD  469 (992)
T PRK13889        420 LEHGWGQGRDLLTARDVLVIDEAGMVGTRQLERVLSHAADAGAKVVLVGD  469 (992)
T ss_pred             HHHHHHCCCCCCCCCCEEEEECCCCCCHHHHHHHHHHHHHCCCEEEEECC
T ss_conf             99987467334789858999676557749999999999984998999488


No 323
>pfam08423 Rad51 Rad51. Rad51 is a DNA repair and recombination protein and is a homologue of the bacterial ATPase RecA protein.
Probab=91.80  E-value=0.78  Score=25.48  Aligned_cols=53  Identities=17%  Similarity=0.255  Sum_probs=36.7

Q ss_pred             CEEEEECCCCHHHHHHHHHHHHHHH---H---CCCCEEEEECCCHHHHHHHHHHHCCCC
Q ss_conf             6199844753157999999999985---1---468479971521001344555430389
Q gi|254780619|r  219 AVSLISGVTGSGKTEVYLEIVAAVL---H---LGKQVLILLPEISLTSAILERFQKRFG  271 (731)
Q Consensus       219 ~~~LL~GvTGSGKTEVYl~li~~~L---~---~GkqvLiLvPEI~Lt~Q~~~rl~~rF~  271 (731)
                      ...=++|.-|||||-+-++++-.+-   +   .+..|+++=-|=++.|.-+..+.++|+
T Consensus        44 ~ITEi~G~~gsGKTQlc~qlav~~qlp~~~gg~~g~vvyIDTEg~f~~eRl~qia~~~~  102 (261)
T pfam08423        44 SITEVFGEFRTGKTQLCHTLCVTCQLPLEMGGGEGKALYIDTEGTFRPERIVAIAERFG  102 (261)
T ss_pred             EEEEEECCCCCCHHHHHHHHHHHHHCHHHHCCCCCEEEEEECCCCCCHHHHHHHHHHHC
T ss_conf             29999899888789999999999407096569997289993688869899999999829


No 324
>KOG0925 consensus
Probab=91.79  E-value=0.36  Score=28.07  Aligned_cols=34  Identities=21%  Similarity=0.200  Sum_probs=16.4

Q ss_pred             CHHHHHHHHHHCCCCCHHHHCCCCCCCCHHHHHHHHHHHCCCC
Q ss_conf             2899888852048520001023211358678999998621257
Q gi|254780619|r  494 GIERIAEEVCEYFPLARISILSSDLEGGGGRLQLQLSAIAKGE  536 (731)
Q Consensus       494 Gte~~~e~l~~~fp~~~v~~~d~d~~~~~~~~~~~~~~~~~~~  536 (731)
                      +.++.+.+.++.|-.     .|.|.    -.+-+++..|.+++
T Consensus       505 ~a~kaAdeak~~f~H-----~dGDH----lTLlnVYhAfkq~~  538 (699)
T KOG0925         505 SASKAADEAKETFAH-----IDGDH----LTLLNVYHAFKQNN  538 (699)
T ss_pred             HHHHHHHHHHHHHCC-----CCCCH----HHHHHHHHHHHHCC
T ss_conf             688889999887458-----88635----78999999998359


No 325
>PRK11784 tRNA 2-selenouridine synthase; Provisional
Probab=91.77  E-value=0.17  Score=30.46  Aligned_cols=28  Identities=39%  Similarity=0.660  Sum_probs=19.1

Q ss_pred             CEEEEECCCCHHHHHHHHHHHHHHHHCCCCEE
Q ss_conf             61998447531579999999999851468479
Q gi|254780619|r  219 AVSLISGVTGSGKTEVYLEIVAAVLHLGKQVL  250 (731)
Q Consensus       219 ~~~LL~GvTGSGKTEVYl~li~~~L~~GkqvL  250 (731)
                      ...+|.|-||||||++--.    .=..|.|||
T Consensus       138 ~~~vl~G~TG~GKT~lL~~----L~~~G~~vi  165 (333)
T PRK11784        138 PLVVLGGMTGSGKTRLLQA----LANAGAQVL  165 (333)
T ss_pred             CCEEEECCCCCCHHHHHHH----HHHCCCCEE
T ss_conf             8599867888778999999----997599743


No 326
>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=91.71  E-value=0.19  Score=30.15  Aligned_cols=141  Identities=23%  Similarity=0.331  Sum_probs=70.1

Q ss_pred             CCCHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHHHHHHHHHHCCCCEEEEECCCHHHH-------HHHHHH----
Q ss_conf             688378999999987520489619984475315799999999998514684799715210013-------445554----
Q gi|254780619|r  198 ILDKNQQDVVEQVVPLCTKGFAVSLISGVTGSGKTEVYLEIVAAVLHLGKQVLILLPEISLTS-------AILERF----  266 (731)
Q Consensus       198 ~Lt~eQ~~a~~~i~~~~~~~f~~~LL~GvTGSGKTEVYl~li~~~L~~GkqvLiLvPEI~Lt~-------Q~~~rl----  266 (731)
                      +-+.-.+.+.+.|..     .++..|=|.||||||   -++=+=||+-|+.+==|   ||-|+       -...|+    
T Consensus        69 PvS~kRedI~~AI~~-----nQVviiAGETGSGKT---TQLPKICLELGrG~~Gl---IGHTQPRRlAAR~VA~R~AeEL  137 (1320)
T TIGR01967        69 PVSAKREDIAKAIAE-----NQVVIIAGETGSGKT---TQLPKICLELGRGSRGL---IGHTQPRRLAARSVAERVAEEL  137 (1320)
T ss_pred             CHHHHHHHHHHHHHH-----CCEEEEECCCCCCCC---CCCHHHHHHHCCCCCCC---CCCCCHHHHHHHHHHHHHHHHH
T ss_conf             711118999999984-----898999724487620---23216777542787654---1247146889999999999983


Q ss_pred             HCCCCCEEE--E-EECCCCCHHHHHHHHHHHCCCCEEEEECCHHHHHH------HCCCEEEEEEECCCCCCHHCCCCCCC
Q ss_conf             303897689--9-62355723566789999719973999400121100------10001367740553210000244322
Q gi|254780619|r  267 QKRFGVKPA--E-WHSSLSTSMREKIWRQVARGAISVIVGVRSALFLP------FKKLGLIVIDEEHDISYKQEEGILYN  337 (731)
Q Consensus       267 ~~rF~~~v~--v-~HS~ls~~eR~~~w~~i~~G~~~IVIGtRSAif~P------~~nLglIIvDEEHd~sykq~~~pry~  337 (731)
                      ..-+|..|.  | +|-.+++.    +..+++         |=.=++|-      +..=..|||||-|+=|..=|==.-| 
T Consensus       138 gtplGe~VGYkVRF~D~v~~~----t~VKLm---------TDGiLLAE~Q~DRfL~~YDTIIIDEAHERSLNIDFLLGY-  203 (1320)
T TIGR01967       138 GTPLGELVGYKVRFEDQVSSN----TLVKLM---------TDGILLAETQQDRFLERYDTIIIDEAHERSLNIDFLLGY-  203 (1320)
T ss_pred             CCCCCCCCCCEEEECCCCCCC----CEEEEH---------HHHHHHHHHHHHHHHHHCCCEEECCHHHHHHHHHHHHHH-
T ss_conf             889886132036631426885----436303---------223589985200222106733651123112338899988-


Q ss_pred             HHHHHHHHHHHCCCCEECCCCCCCHHHHH
Q ss_conf             48999997511032100002454324677
Q gi|254780619|r  338 ARDMSIVRGKIESFPVVLVSATPSIESRV  366 (731)
Q Consensus       338 aRdvA~~Ra~~~~~~lilgSATPSles~~  366 (731)
                      -+.+.   -+.=+-+||-.|||=-+|=+.
T Consensus       204 LK~lL---~rRPDLKiIITSATID~ERFs  229 (1320)
T TIGR01967       204 LKQLL---PRRPDLKIIITSATIDPERFS  229 (1320)
T ss_pred             HHHHC---CCCCCCCEEEECCCCCHHHHH
T ss_conf             87632---668865257400235744687


No 327
>TIGR00143 hypF [NiFe] hydrogenase maturation protein HypF; InterPro: IPR004421   The large subunit of [NiFe]-hydrogenase, as well as other nickel metalloenzymes, is synthesized as a precursor devoid of the metalloenzyme active site. This precursor then undergoes a complex post-translational maturation process that requires a number of accessory proteins , , . Members of the HypF family are accessory proteins involved in hydrogenase maturation. They contain the following domains: acylphosphatase, zinc fingers (2 repeats), a YrdC-like domain, and a C-terminal domain with a putative O-carbamoyltransferase motif.   The presence of CO and CN- ligands of the active site iron atoms is essential for [NiFe]-hydrogenase enzyme activity . Both ligands have been suggested to originate from carbamoylphosphate , which is required for maturation of [NiFe]-hydrogenases . Escherichia coli HypF interacts with carbamoylphosphate as a substrate and releases inorganic phosphate . In addition, HypF also cleaves ATP into AMP and pyrophosphate in the presence of carbamoylphosphate. This, and the fact that HypF catalyzes a carbamoylphosphate-dependent pyrophosphate ATP exchange reaction, suggest that the protein catalyzes the activation of carbamoylphosphate .   The mechanism of action of HypF, as well as of its individual domains, is not yet clear. Mutations in any of the three major signature motifs, the acylphosphatase, the zinc fingers, and the O-carbamoyltransferase motif, can block carbamoylphosphate phosphatase activity. This indicates an integrated cooperativity between these domains in the cleavage reaction .   The N-terminal acylphosphatase (ACP) domain is thought to support the conversion of carbamoylphosphate into CO and CN- , . Biochemical results demonstrating its ACP activity are not available , . ACPs are small enzymes that specifically catalyze the hydrolysis of carboxylphosphate bonds in acylphosphates, including carbamoylphosphate . Zinc fingers have been implicated in bivalent cation binding or as part of a chaperone domain interacting with the large subunit precursor, but experimental studies on such a function are lacking thus far. The YrdC-like domain is present in protein families with regulatory functions (IPR012200 from INTERPRO, IPR010923 from INTERPRO) and has been implicated in RNA binding . It is not clear what function it may have in members of the HypF family. A C-terminal domain is distantly related to peptidase M22, but contains a conserved O-carbamoyltransferase motif required for the carbamoylphosphate phosphatase activity . The function of this domain is not clear.   Nomenclature note: the following names are used as synonyms of HypF: HupY in Azotobacter chroococcum, HupN in Rhizobium leguminosarum, HydA in Escherichia coli. In other organisms, these names are used to designate various "hydrogenase cluster" proteins unrelated to the members of this family. ; GO: 0030528 transcription regulator activity.
Probab=91.68  E-value=0.096  Score=32.46  Aligned_cols=86  Identities=17%  Similarity=0.240  Sum_probs=52.0

Q ss_pred             HHHHHHHHCCCC--C-EEEEEECCCCCHHHHHHH-----HHHHCCCCEEEEECCHHHH-HHH----CCCEEE-EEEECCC
Q ss_conf             344555430389--7-689962355723566789-----9997199739994001211-001----000136-7740553
Q gi|254780619|r  260 SAILERFQKRFG--V-KPAEWHSSLSTSMREKIW-----RQVARGAISVIVGVRSALF-LPF----KKLGLI-VIDEEHD  325 (731)
Q Consensus       260 ~Q~~~rl~~rF~--~-~v~v~HS~ls~~eR~~~w-----~~i~~G~~~IVIGtRSAif-~P~----~nLglI-IvDEEHd  325 (731)
                      -+.+.||+.+.+  . ..|++-..++..+++-..     ..+.+-...|||=-.|-.+ .++    +||.-| ||     
T Consensus       231 ~~~V~~LR~~k~RP~kPfAvM~~~l~~~~~~A~~~~~E~~~L~S~aaPIVl~~Kk~dy~~~~~~iAp~l~~iGVM-----  305 (799)
T TIGR00143       231 DEVVERLRLRKNRPAKPFAVMSPDLESIEEHAELNNLEKELLLSPAAPIVLLRKKKDYIKLFENIAPNLDTIGVM-----  305 (799)
T ss_pred             HHHHHHHHHHCCCCCCCCEECCCCCCCHHHHHCCCHHHHHHHCCCCCCEEEEECCCCCCCCCCCCCCCCCCEEEE-----
T ss_conf             489999986457889751441530200155505586899851166477677615757443560116796932586-----


Q ss_pred             CCCHHCCCCCCCHHHHHHHHHHHCCCCEECCCCC
Q ss_conf             2100002443224899999751103210000245
Q gi|254780619|r  326 ISYKQEEGILYNARDMSIVRGKIESFPVVLVSAT  359 (731)
Q Consensus       326 ~sykq~~~pry~aRdvA~~Ra~~~~~~lilgSAT  359 (731)
                              ..|.--.-.+++ ....+|+|+.||=
T Consensus       306 --------LPYtPLHhLLL~-~~~~~p~VmTSaN  330 (799)
T TIGR00143       306 --------LPYTPLHHLLLQ-ELLAKPLVMTSAN  330 (799)
T ss_pred             --------CCCCHHHHHHHH-HHCCCCEEEECCC
T ss_conf             --------488645789867-6227771660267


No 328
>PRK05541 adenylylsulfate kinase; Provisional
Probab=91.67  E-value=1.1  Score=24.34  Aligned_cols=62  Identities=24%  Similarity=0.250  Sum_probs=44.7

Q ss_pred             CCEEEEECCCCHHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHCCCCCEEEEEECCCCCHHHHHHHHHHH
Q ss_conf             96199844753157999999999985146847997152100134455543038976899623557235667899997
Q gi|254780619|r  218 FAVSLISGVTGSGKTEVYLEIVAAVLHLGKQVLILLPEISLTSAILERFQKRFGVKPAEWHSSLSTSMREKIWRQVA  294 (731)
Q Consensus       218 f~~~LL~GvTGSGKTEVYl~li~~~L~~GkqvLiLvPEI~Lt~Q~~~rl~~rF~~~v~v~HS~ls~~eR~~~w~~i~  294 (731)
                      ..+.-+-|-.|||||-+.-.+-...-++|..+.+|=-         +.+++.|+.      .+-|..+|.++..++.
T Consensus         7 g~viW~TGLsGSGKTTiA~~l~~~L~~~g~~~~~LDG---------D~lR~~~~~------~gfs~~~R~~n~~r~~   68 (176)
T PRK05541          7 GYVIWITGLAGSGKTTIAKALYERLKLKYSNVIYLDG---------DELREIFGH------SGYDKESRIEMALKRA   68 (176)
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHHHHHCCCCEEEECC---------HHHHHHHCC------CCCCHHHHHHHHHHHH
T ss_conf             6799978999998999999999999975997799886---------899987365------8989999999999999


No 329
>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=91.65  E-value=1.1  Score=24.33  Aligned_cols=33  Identities=24%  Similarity=0.291  Sum_probs=21.9

Q ss_pred             CCCCEEEEECCCCHHHHHHHHHHHHHHHHCCCC
Q ss_conf             489619984475315799999999998514684
Q gi|254780619|r  216 KGFAVSLISGVTGSGKTEVYLEIVAAVLHLGKQ  248 (731)
Q Consensus       216 ~~f~~~LL~GvTGSGKTEVYl~li~~~L~~Gkq  248 (731)
                      ......||+|-+|+|||-+.-.++...-..+..
T Consensus        17 ~~~~~ill~GppGtGKT~la~~ia~~~~~~~~~   49 (151)
T cd00009          17 PPPKNLLLYGPPGTGKTTLARAIANELFRPGAP   49 (151)
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHHHHHCCCCCC
T ss_conf             799808998999988659999999971213798


No 330
>pfam07191 DUF1407 Protein of unknown function (DUF1407). This family consists of several short, hypothetical bacterial proteins of around 70 residues in length. Members of this family have 8 highly conserved cysteine residues, which form two zinc ribbon domains.
Probab=91.65  E-value=0.081  Score=33.00  Aligned_cols=38  Identities=24%  Similarity=0.407  Sum_probs=32.9

Q ss_pred             CCCCCCCCEEEEECCCCCCEECHHHCCCCCCCCCCCCCCC
Q ss_conf             3101465201211357832000021024465556667874
Q gi|254780619|r  446 LKCLHCSCWLVEHRSKKKLYCHQCGHSAIYSQSCVVCGSS  485 (731)
Q Consensus       446 ~~C~~C~~~l~~h~~~~~l~Ch~Cg~~~~~~~~Cp~Cg~~  485 (731)
                      ..||.|...|..  .++...|..|+.....-..||+|+..
T Consensus         2 ~~CP~C~~~l~~--~~~~~~C~~C~~~~~~~a~CP~C~~~   39 (70)
T pfam07191         2 LICPQCQQELEW--KGGHYHCDQCQKDFKKQALCPDCHQE   39 (70)
T ss_pred             CCCCCCCCCCEE--CCCCEECHHHCCEEEEEEECCCCCCH
T ss_conf             728889995243--39977970330101478989762437


No 331
>PRK06620 hypothetical protein; Validated
Probab=91.62  E-value=1.1  Score=24.43  Aligned_cols=36  Identities=19%  Similarity=0.172  Sum_probs=21.6

Q ss_pred             CCHHHHHHHHHHHHHHCC----C-CCEEEEECCCCHHHHHH
Q ss_conf             883789999999875204----8-96199844753157999
Q gi|254780619|r  199 LDKNQQDVVEQVVPLCTK----G-FAVSLISGVTGSGKTEV  234 (731)
Q Consensus       199 Lt~eQ~~a~~~i~~~~~~----~-f~~~LL~GvTGSGKTEV  234 (731)
                      -++..+.|++.+......    . ....+|+|-.|||||-.
T Consensus        20 vs~~N~~A~~~i~~wp~~~~~~~~~~~l~I~Gp~gSGKTHL   60 (214)
T PRK06620         20 VSSSNDQAYNIIKNWQCMFGVNPYKFTLLIKGPSSSGKTYL   60 (214)
T ss_pred             ECCCHHHHHHHHHHCHHCCCCCCCCCEEEEECCCCCCHHHH
T ss_conf             76869999999983630256686555599987999988999


No 332
>COG1675 TFA1 Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=91.58  E-value=0.15  Score=30.97  Aligned_cols=46  Identities=20%  Similarity=0.310  Sum_probs=27.0

Q ss_pred             CCCCCCCEEEEECCCCCCEECHHHCCCCCCCCCCCCCCCCEECCCCCCHHHHHHHHHH
Q ss_conf             1014652012113578320000210244655566678741100135428998888520
Q gi|254780619|r  447 KCLHCSCWLVEHRSKKKLYCHQCGHSAIYSQSCVVCGSSGKMIACGFGIERIAEEVCE  504 (731)
Q Consensus       447 ~C~~C~~~l~~h~~~~~l~Ch~Cg~~~~~~~~Cp~Cg~~~~l~~~G~Gte~~~e~l~~  504 (731)
                      .||+|.+++++..            ....-..||.||+.....--+...+.+++++.+
T Consensus       115 ~C~~~~~r~sfde------------A~~~~F~Cp~Cg~~L~~~d~s~~i~~l~~~i~~  160 (176)
T COG1675         115 VCPNCHVKYSFDE------------AMELGFTCPKCGEDLEEYDSSEEIEELESELDE  160 (176)
T ss_pred             ECCCCCCCCCHHH------------HHHHCCCCCCCCCHHHHCCCHHHHHHHHHHHHH
T ss_conf             6778877314999------------998379888777424440462789999999999


No 333
>PRK08665 ribonucleotide-diphosphate reductase subunit alpha; Validated
Probab=91.57  E-value=0.096  Score=32.43  Aligned_cols=24  Identities=21%  Similarity=0.163  Sum_probs=8.9

Q ss_pred             CCCCEEEEECCHHHHHHHCCCEEE
Q ss_conf             199739994001211001000136
Q gi|254780619|r  295 RGAISVIVGVRSALFLPFKKLGLI  318 (731)
Q Consensus       295 ~G~~~IVIGtRSAif~P~~nLglI  318 (731)
                      +|++-|+-=.+-=-.-|.+++|-|
T Consensus       242 tgePgi~F~D~iN~~n~~~~~g~I  265 (733)
T PRK08665        242 NGEPGIVFLDRINRDNPTPHVGEI  265 (733)
T ss_pred             HCCCEEEECCHHHHCCCCCCCCEE
T ss_conf             589632011447646998777834


No 334
>COG0777 AccD Acetyl-CoA carboxylase beta subunit [Lipid metabolism]
Probab=91.55  E-value=0.4  Score=27.70  Aligned_cols=119  Identities=19%  Similarity=0.279  Sum_probs=54.1

Q ss_pred             CCCCCCCCCCCEEEEECCCCCCEECHHHCCCCCCCCCCCCCCCCEECCCCCCHHHHHHHHHH-CC--------CCCHHHH
Q ss_conf             43431014652012113578320000210244655566678741100135428998888520-48--------5200010
Q gi|254780619|r  443 GNRLKCLHCSCWLVEHRSKKKLYCHQCGHSAIYSQSCVVCGSSGKMIACGFGIERIAEEVCE-YF--------PLARISI  513 (731)
Q Consensus       443 g~~~~C~~C~~~l~~h~~~~~l~Ch~Cg~~~~~~~~Cp~Cg~~~~l~~~G~Gte~~~e~l~~-~f--------p~~~v~~  513 (731)
                      |.-.+||.|..- .|+++-           ...-+.||.|+.+.++..    .||++..+-. -|        |.-+.-.
T Consensus        26 ~lw~KCp~c~~~-~y~~eL-----------~~n~~vcp~c~~h~ri~A----~~Ri~~llD~gsf~el~~~l~~~dPL~F   89 (294)
T COG0777          26 GLWTKCPSCGEM-LYRKEL-----------ESNLKVCPKCGHHMRISA----RERLEALLDEGSFEELDSPLEPKDPLKF   89 (294)
T ss_pred             CCEEECCCCCCE-EEHHHH-----------HHHHHCCCCCCCCCCCCH----HHHHHHHHCCCCCEECCCCCCCCCCCCC
T ss_conf             835477875535-468878-----------733232655676465699----9999986289851011568776886558


Q ss_pred             CCCCCCCCHHHHHHHHHHHCCCC-CCEEEEEHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             23211358678999998621257-65798704430231134520123300034431024557899999875431
Q gi|254780619|r  514 LSSDLEGGGGRLQLQLSAIAKGE-IDIIIGTQLVAKGHNFPRMSLVGVVDGDLGLTNADLRSSERTFQLLSQVT  586 (731)
Q Consensus       514 ~d~d~~~~~~~~~~~~~~~~~~~-~~ilvgTq~i~kg~~fp~v~lv~il~aD~~l~~pd~ra~E~~~qll~qv~  586 (731)
                        .|+.+-+..++..-.+  .|. -.|++|+-.| +|+  |-  .+++.|...+-.+-.--+.||..+.+-+..
T Consensus        90 --~d~k~Y~~rL~~a~~~--tg~~davvtg~g~i-~G~--pv--v~av~df~FmgGSmGsVvGeki~ra~E~A~  154 (294)
T COG0777          90 --PDSKKYKDRLEAARKK--TGLDDAVVTGEGTI-NGL--PV--VLAVMDFAFMGGSMGSVVGEKITRAIERAI  154 (294)
T ss_pred             --CCCHHHHHHHHHHHHH--CCCCCCEEEEEEEE-CCE--EE--EEEEEECCCCCCCCHHHHHHHHHHHHHHHH
T ss_conf             --7521257999998751--19985159875478-886--78--999974244245505899999999999999


No 335
>pfam10083 DUF2321 Uncharacterized protein conserved in bacteria (DUF2321). Members of this family of hypothetical bacterial proteins have no known function.
Probab=91.51  E-value=0.054  Score=34.33  Aligned_cols=48  Identities=23%  Similarity=0.400  Sum_probs=31.2

Q ss_pred             HCCCCCCCCC--CCCCCCCCEEEEECCCCCCEECHHHCCCCCCCCCCCCCCC
Q ss_conf             0023565434--3101465201211357832000021024465556667874
Q gi|254780619|r  436 LTLCQVCGNR--LKCLHCSCWLVEHRSKKKLYCHQCGHSAIYSQSCVVCGSS  485 (731)
Q Consensus       436 ~~~C~~Cg~~--~~C~~C~~~l~~h~~~~~l~Ch~Cg~~~~~~~~Cp~Cg~~  485 (731)
                      .-+|.+||..  ..||+|+.+..-+-.- .-++-. |.....|.-|-+||+.
T Consensus        28 ~~fC~kCG~~TI~~Cp~C~t~IrG~y~v-~GV~~l-g~~y~~PsyC~nCG~p   77 (158)
T pfam10083        28 ENFCSKCGAATITSCPHCSTPIRGFYYV-DGVLGL-GSDYDAPSYCHNCGKP   77 (158)
T ss_pred             HHHHHHHHHHHHHHCCCCCCCCCCCCCC-CCEEEC-CCCCCCCHHHHHCCCC
T ss_conf             9999876689997586899986775026-873644-8889995468747998


No 336
>PRK08533 flagellar accessory protein FlaH; Reviewed
Probab=91.42  E-value=1.2  Score=24.16  Aligned_cols=38  Identities=21%  Similarity=0.324  Sum_probs=35.4

Q ss_pred             CEEEEECCCCHHHHHHHHHHHHHHHHCCCCEEEEECCC
Q ss_conf             61998447531579999999999851468479971521
Q gi|254780619|r  219 AVSLISGVTGSGKTEVYLEIVAAVLHLGKQVLILLPEI  256 (731)
Q Consensus       219 ~~~LL~GvTGSGKTEVYl~li~~~L~~GkqvLiLvPEI  256 (731)
                      +..|+.|..|+|||-.-.+.+...+++|..|+++--|-
T Consensus        25 s~~li~G~~GtGKsi~~~~~~~~~l~~g~~~~yis~e~   62 (230)
T PRK08533         25 SIILIEGDESTGKSILSQRLAYGFLQNGYSVSYVSSQL   62 (230)
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHHHHCCCEEEEEEECC
T ss_conf             48999868998789999999999987898699999438


No 337
>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=91.41  E-value=0.21  Score=29.88  Aligned_cols=197  Identities=21%  Similarity=0.298  Sum_probs=94.8

Q ss_pred             CHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHH-HHHHHHHHHHHCCCCEEEEECCCH-HHHHHHHHHHCCCCCEEEEE
Q ss_conf             8378999999987520489619984475315799-999999998514684799715210-01344555430389768996
Q gi|254780619|r  200 DKNQQDVVEQVVPLCTKGFAVSLISGVTGSGKTE-VYLEIVAAVLHLGKQVLILLPEIS-LTSAILERFQKRFGVKPAEW  277 (731)
Q Consensus       200 t~eQ~~a~~~i~~~~~~~f~~~LL~GvTGSGKTE-VYl~li~~~L~~GkqvLiLvPEI~-Lt~Q~~~rl~~rF~~~v~v~  277 (731)
                      +++|++-|-+.   ..+++.+.|.-|=||||||- .|-     +|     -++=-||+. .|           -+++++.
T Consensus       311 eP~Qk~~fL~A---i~kPqGMvLVTGPTGSGKTVSLYT-----aL-----niLN~~~~NIST-----------AEDPVEI  366 (577)
T TIGR02538       311 EPDQKALFLEA---IHKPQGMVLVTGPTGSGKTVSLYT-----AL-----NILNTEEVNIST-----------AEDPVEI  366 (577)
T ss_pred             CHHHHHHHHHH---HHCCCCCEEEECCCCCCHHHHHHH-----HH-----CCCCCCCCCCCC-----------CCCCEEE
T ss_conf             88899999999---707997288626659841687876-----31-----125776745011-----------4477246


Q ss_pred             E-CCC-----CCHHHHHHHHHHHCCCCEEEEECCHHHHHHHCCCEEEEEEECCCCCCHHCCCCC-CCHHHHHHHHHHHCC
Q ss_conf             2-355-----723566789999719973999400121100100013677405532100002443-224899999751103
Q gi|254780619|r  278 H-SSL-----STSMREKIWRQVARGAISVIVGVRSALFLPFKKLGLIVIDEEHDISYKQEEGIL-YNARDMSIVRGKIES  350 (731)
Q Consensus       278 H-S~l-----s~~eR~~~w~~i~~G~~~IVIGtRSAif~P~~nLglIIvDEEHd~sykq~~~pr-y~aRdvA~~Ra~~~~  350 (731)
                      . -|.     +++. =-+|..+++            .|+ -+|+..|.|=|           -| .-+=|+|++=|+  -
T Consensus       367 NLpGINQVnvNpK~-GLTFAaALr------------SFL-RQDPDIIMVGE-----------IRDLETAEIAiKAAq--T  419 (577)
T TIGR02538       367 NLPGINQVNVNPKI-GLTFAAALR------------SFL-RQDPDIIMVGE-----------IRDLETAEIAIKAAQ--T  419 (577)
T ss_pred             EECCCCEECCCCCC-CCCHHHHHH------------HHC-CCCCCEEEEEC-----------CCCHHHHHHHHHHHC--C
T ss_conf             40771512046678-878799998------------640-68998898706-----------664215899999840--4


Q ss_pred             CCEECCCCCCCHHHHHHHHHHHHHHHCCCCCCCCCCCCCCEECCCCCCCCCCCCCCCHHHHHHHHHHHCCCCEEEEEECC
Q ss_conf             21000024543246775321234441243223676543321102222332224547989999998862265517997422
Q gi|254780619|r  351 FPVVLVSATPSIESRVNGISRRYHSVHLSTRYRNSALPHLQVIDMRGQTIAQGKSLSPEMIDGIRHTLARNEQTLLFLNR  430 (731)
Q Consensus       351 ~~lilgSATPSles~~~~~~g~~~~~~l~~R~~~~~~P~i~ivDm~~~~~~~~~~lS~~l~~~i~~~l~~g~qvll~lnR  430 (731)
                      .-+||                    -+|..  +.|+--=.++++|--.+    ..|.+.+-=-|-|+|++.         
T Consensus       420 GHLVl--------------------STLHT--NdAp~Tl~RL~NMGiap----FNIASSV~LI~AQRLARR---------  464 (577)
T TIGR02538       420 GHLVL--------------------STLHT--NDAPETLARLVNMGIAP----FNIASSVNLIMAQRLARR---------  464 (577)
T ss_pred             CCCEE--------------------CCCCC--CCHHHHHHHHHHCCCHH----HHHHHHHHHHHHHHHHHH---------
T ss_conf             87210--------------------10001--68589999997538413----799999999999975524---------


Q ss_pred             CCEEHHCCCCCCCCC-CCCCCCCC-EEEEECCCCCCEECHHHCCCCCCCCCCCCCCCCEECCCCCCH
Q ss_conf             200000023565434-31014652-012113578320000210244655566678741100135428
Q gi|254780619|r  431 RGYAPLTLCQVCGNR-LKCLHCSC-WLVEHRSKKKLYCHQCGHSAIYSQSCVVCGSSGKMIACGFGI  495 (731)
Q Consensus       431 rGya~~~~C~~Cg~~-~~C~~C~~-~l~~h~~~~~l~Ch~Cg~~~~~~~~Cp~Cg~~~~l~~~G~Gt  495 (731)
                             .|.+|..+ ..-|.=.. .|=||..  -|-=  -|++.=-|.=|-+|-+++ ++.+ .|+
T Consensus       465 -------LCs~CK~~~~~~p~~~Ll~lGF~~e--dL~~--Pg~~ly~pvGC~~C~~~G-YKGR-vGi  518 (577)
T TIGR02538       465 -------LCSHCKAPVEEVPEEALLELGFTEE--DLAD--PGLKLYGPVGCEECSNTG-YKGR-VGI  518 (577)
T ss_pred             -------CCCCCCCCCCCCCHHHHHHCCCCHH--HHCC--CCCEECCCCCCCCCCCCC-CEEE-EEE
T ss_conf             -------0313687766468599985688868--9269--993861762610037987-2010-213


No 338
>PRK07004 replicative DNA helicase; Provisional
Probab=91.41  E-value=1.2  Score=24.15  Aligned_cols=131  Identities=21%  Similarity=0.261  Sum_probs=76.1

Q ss_pred             CEEEEECCCCHHHHHHHHHHHHHH-HHCCCCEEEEECCCHHHHHHHHHHHCCCC-CEE-EEEECCCCCHHHHHHHHHHH-
Q ss_conf             619984475315799999999998-51468479971521001344555430389-768-99623557235667899997-
Q gi|254780619|r  219 AVSLISGVTGSGKTEVYLEIVAAV-LHLGKQVLILLPEISLTSAILERFQKRFG-VKP-AEWHSSLSTSMREKIWRQVA-  294 (731)
Q Consensus       219 ~~~LL~GvTGSGKTEVYl~li~~~-L~~GkqvLiLvPEI~Lt~Q~~~rl~~rF~-~~v-~v~HS~ls~~eR~~~w~~i~-  294 (731)
                      ....|=|-+|.|||-..+.++..+ +++|+.|++.--|-+ ..|+..|+-...+ ... .+..+.+++.+....-..+. 
T Consensus       214 dLiIIAARPsmGKTafAlniA~n~A~~~g~~V~~FSLEMs-~eql~~Rlls~~s~I~~~~ir~g~l~~~e~~~i~~a~~~  292 (460)
T PRK07004        214 ELIIVAGRPSMGKTAFSMNIGEYVAVEYGLPVAVFSMEMP-GTQLAMRMLGSVGRLDQHRMRTGRLTDEDWPKLTHAVQK  292 (460)
T ss_pred             CEEEEEECCCCCHHHHHHHHHHHHHHHCCCCEEEECCCCC-HHHHHHHHHHHCCCCCCCHHHCCCCCHHHHHHHHHHHHH
T ss_conf             5799973687642699999999998725886699847799-999999999860698821100788999999999999999


Q ss_pred             CCCCEEEEECCHH---------H--HHHH-CCCEEEEEEECCCCCCHHCCC------CCC-----CHHHHHHHHHHHCCC
Q ss_conf             1997399940012---------1--1001-000136774055321000024------432-----248999997511032
Q gi|254780619|r  295 RGAISVIVGVRSA---------L--FLPF-KKLGLIVIDEEHDISYKQEEG------ILY-----NARDMSIVRGKIESF  351 (731)
Q Consensus       295 ~G~~~IVIGtRSA---------i--f~P~-~nLglIIvDEEHd~sykq~~~------pry-----~aRdvA~~Ra~~~~~  351 (731)
                      -.+..+.|=..+.         +  +..- .++++||||      |=|--.      .|.     =.|.+ ...|+..++
T Consensus       293 l~~~~l~IdD~~~lt~~~ira~~Rr~~~~~g~l~lvviD------Ylqli~~~~~~~~r~~ei~~isr~l-K~lAkel~i  365 (460)
T PRK07004        293 MSEAQLFIDETGGLNPMELRSRARRLARQCGKLGLIIID------YLQLMSGSSQGENRATEISEISRSL-KSLAKELDV  365 (460)
T ss_pred             HHCCCEEEECCCCCHHHHHHHHHHHHHHHCCCCCEEEEE------HHHHCCCCCCCCCHHHHHHHHHHHH-HHHHHHHCC
T ss_conf             855974896898730789999999999743588899850------7754478888888999999999999-999999699


Q ss_pred             CEECCC
Q ss_conf             100002
Q gi|254780619|r  352 PVVLVS  357 (731)
Q Consensus       352 ~lilgS  357 (731)
                      |||+.|
T Consensus       366 pvi~ls  371 (460)
T PRK07004        366 PVIALS  371 (460)
T ss_pred             CEEEEC
T ss_conf             789970


No 339
>PRK00254 ski2-like helicase; Provisional
Probab=91.38  E-value=0.83  Score=25.27  Aligned_cols=83  Identities=20%  Similarity=0.240  Sum_probs=55.1

Q ss_pred             HHHHHHHHHCCCCEEEEECCCHHHHH----HHHHH----------------------------HCCCCCEEEEEECCCCC
Q ss_conf             99999985146847997152100134----45554----------------------------30389768996235572
Q gi|254780619|r  236 LEIVAAVLHLGKQVLILLPEISLTSA----ILERF----------------------------QKRFGVKPAEWHSSLST  283 (731)
Q Consensus       236 l~li~~~L~~GkqvLiLvPEI~Lt~Q----~~~rl----------------------------~~rF~~~v~v~HS~ls~  283 (731)
                      .+++.+++..|+|+||-+|.=.-+.+    +..++                            .+-+..-|+..|++|++
T Consensus       227 ~~l~~~~~~~~~~~LVF~~tR~~~e~~A~~la~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~L~~~l~~GVafHHAGL~~  306 (717)
T PRK00254        227 EELVYDAVKRGKGALIFVNMRRKAEKTALELAKKIKNLLTKPELRELKELADSLEENPTNEKLAKALRGGVAFHHAGLGR  306 (717)
T ss_pred             HHHHHHHHHCCCCCEEEEECHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHCCCCHHHHHHHHHCHHHHCCCCCH
T ss_conf             89999999749981899955799999999999988763076889999999999873765189999997083121589998


Q ss_pred             HHHHHHHHHHHCCCCEEEEECCHH---HHHHHCCCEEEEEE
Q ss_conf             356678999971997399940012---11001000136774
Q gi|254780619|r  284 SMREKIWRQVARGAISVIVGVRSA---LFLPFKKLGLIVID  321 (731)
Q Consensus       284 ~eR~~~w~~i~~G~~~IVIGtRSA---if~P~~nLglIIvD  321 (731)
                      .+|.-+=..-++|..+|++-|-.=   |=+|..   .+||.
T Consensus       307 ~~R~lVE~~Fr~g~Ikvl~aTsTLA~GVNLPAr---~VIi~  344 (717)
T PRK00254        307 DERVLVEDNFRKGLIKVVVATPTLSAGINTPAF---RVIIR  344 (717)
T ss_pred             HHHHHHHHHHHCCCCEEEEECCHHHCCCCCCCE---EEEEE
T ss_conf             899999999987995899816446504577605---99992


No 340
>PRK06260 threonine synthase; Validated
Probab=91.38  E-value=0.097  Score=32.40  Aligned_cols=12  Identities=33%  Similarity=0.670  Sum_probs=5.5

Q ss_pred             HCCCCEEEEECC
Q ss_conf             146847997152
Q gi|254780619|r  244 HLGKQVLILLPE  255 (731)
Q Consensus       244 ~~GkqvLiLvPE  255 (731)
                      ..|-.+.|.+|+
T Consensus       139 ~~Gl~~~I~vP~  150 (400)
T PRK06260        139 RAGLKCYVLLPA  150 (400)
T ss_pred             HCCCCEEEEEEC
T ss_conf             839977999858


No 341
>TIGR00354 polC DNA polymerase II, large subunit DP2; InterPro: IPR004475 This family represents the large subunit, DP2, of a two subunit novel archaebacterial replicative DNA polymerase first characterised for Pyrococcus furiosus. The structure of DP2 appears to be organised as a ~950 residue component separated from a ~300 residue component by a ~150 residue intein. The other subunit, DP1, has sequence similarity to the eukaryotic DNA polymerase delta small subunit.; GO: 0003677 DNA binding, 0003887 DNA-directed DNA polymerase activity, 0006260 DNA replication, 0006308 DNA catabolic process.
Probab=91.36  E-value=0.082  Score=32.97  Aligned_cols=49  Identities=12%  Similarity=0.014  Sum_probs=24.3

Q ss_pred             CCCEEEEEEEEEC--CCCCCCCCHHCCCHHHHCCCCC---CCHHHHHHH-HHHHH
Q ss_conf             9968999999824--8876788011141888406689---998999999-99985
Q gi|254780619|r   49 RSRTVLGIVWYNS--EEKYKIDSLKLRPIEYVFDCPP---LSRQMCEFV-KWVAD   97 (731)
Q Consensus        49 g~r~~~GiVv~~~--~~~~~~~~~kLK~I~~VlD~~~---L~~~ll~L~-~wiA~   97 (731)
                      .+|-+.-||-++-  .-++....|+|+.=-.--..-.   +.|.++.|+ +|||=
T Consensus       315 ~~Ky~sdiiaGRPVlahPS~kGgFRLRYGRaRNtGfAt~GvhPAtMyLldeF~AV  369 (1173)
T TIGR00354       315 DDKYVSDIIAGRPVLAHPSKKGGFRLRYGRARNTGFATVGVHPATMYLLDEFLAV  369 (1173)
T ss_pred             CCCEEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCHHCCCCHHHHHHHHHHHHH
T ss_conf             7745432205875111577667611234433221201037765789988756530


No 342
>PRK09087 hypothetical protein; Validated
Probab=91.35  E-value=1.2  Score=24.11  Aligned_cols=34  Identities=26%  Similarity=0.306  Sum_probs=22.3

Q ss_pred             HHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHH
Q ss_conf             3789999999875204896199844753157999
Q gi|254780619|r  201 KNQQDVVEQVVPLCTKGFAVSLISGVTGSGKTEV  234 (731)
Q Consensus       201 ~eQ~~a~~~i~~~~~~~f~~~LL~GvTGSGKTEV  234 (731)
                      +..+.|++-+............|+|-.|||||-.
T Consensus        27 ~~N~~a~~~l~~~~~w~~~~~~L~Gp~gsGKTHL   60 (226)
T PRK09087         27 ESNRAAVSLVDRWPNWPSPVVVLAGPVGSGKTHL   60 (226)
T ss_pred             CCHHHHHHHHHHCCCCCCCEEEEECCCCCCHHHH
T ss_conf             7699999999847267777589989999988699


No 343
>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=91.23  E-value=0.52  Score=26.83  Aligned_cols=53  Identities=25%  Similarity=0.340  Sum_probs=42.1

Q ss_pred             CCCCEEEEEECCCCCHHHHHHHHHHHCCCCEEEEECCHHHH-HHHCCCEEEEEE
Q ss_conf             38976899623557235667899997199739994001211-001000136774
Q gi|254780619|r  269 RFGVKPAEWHSSLSTSMREKIWRQVARGAISVIVGVRSALF-LPFKKLGLIVID  321 (731)
Q Consensus       269 rF~~~v~v~HS~ls~~eR~~~w~~i~~G~~~IVIGtRSAif-~P~~nLglIIvD  321 (731)
                      ..|..++.+||+++..+|.++....++|+.+|+|+|...-- +-+++...||.-
T Consensus         5 ~~g~~~~~i~g~~~~~~R~~~~~~f~~~~~~ilv~t~~~~~Gid~~~~~~vi~~   58 (78)
T pfam00271         5 KPGIKVARLHGGLSQEEREEILEDFRNGKSKVLVATDVAGRGIDLPDVNVVINY   58 (78)
T ss_pred             HCCCCEEEEECCCCHHHHHHHHHHHHCCCCEEEEEECCCCCCCCCCCCCEEEEE
T ss_conf             689859998697999999999999987997399992565256778789999997


No 344
>pfam09332 Mcm10 Mcm10 replication factor. Mcm10 is a eukaryotic DNA replication factor that regulates the stability and chromatin association of DNA polymerase alpha.
Probab=91.20  E-value=0.11  Score=31.97  Aligned_cols=57  Identities=21%  Similarity=0.372  Sum_probs=41.4

Q ss_pred             HHCCCCCCCCCCC-----CCCCCCEEEEECCCC-CCEECHHHCCC----CCC-CCCCCCCCCCEECCCC
Q ss_conf             0002356543431-----014652012113578-32000021024----465-5566678741100135
Q gi|254780619|r  435 PLTLCQVCGNRLK-----CLHCSCWLVEHRSKK-KLYCHQCGHSA----IYS-QSCVVCGSSGKMIACG  492 (731)
Q Consensus       435 ~~~~C~~Cg~~~~-----C~~C~~~l~~h~~~~-~l~Ch~Cg~~~----~~~-~~Cp~Cg~~~~l~~~G  492 (731)
                      .++.|..|.|+..     |..=.-+|.+|.... .+.|.-||.+.    .+| ..|.+||+.. +...|
T Consensus       253 k~V~C~~CkYt~f~~se~Ck~e~H~l~~~da~KRFFkC~dC~~Rtisl~r~P~~~C~~Cg~~k-weR~~  320 (346)
T pfam09332       253 KAVTCKQCKYTAFKAADRCVEENHDLHWHDAVKRFFKCPDCGNRTISLDRLPKKHCKNCGLFK-WERDA  320 (346)
T ss_pred             EEEEECCCCCEEECHHHHHHHCCCCEEEEECEEEEEECCCCCCCEEEEECCCCCCCCCCCCCC-EEEHH
T ss_conf             589823566613262677886089517860333224568878744562107622232367751-10011


No 345
>PRK09001 DNA topoisomerase I; Validated
Probab=91.19  E-value=0.14  Score=31.29  Aligned_cols=12  Identities=25%  Similarity=0.296  Sum_probs=6.1

Q ss_pred             HHHHHHHHCCHH
Q ss_conf             999752455722
Q gi|254780619|r  165 HVIDGLKAQGVI  176 (731)
Q Consensus       165 ~~i~~L~~kglI  176 (731)
                      .+.+.|-..|+|
T Consensus       311 ~iAQ~LYE~GlI  322 (869)
T PRK09001        311 MMAQRLYEAGYI  322 (869)
T ss_pred             HHHHHHHHCCEE
T ss_conf             999999847756


No 346
>PRK09183 transposase/IS protein; Provisional
Probab=91.18  E-value=0.54  Score=26.71  Aligned_cols=130  Identities=15%  Similarity=0.172  Sum_probs=70.5

Q ss_pred             CCCCHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHCCCCCEEEE
Q ss_conf             66883789999999875204896199844753157999999999985146847997152100134455543038976899
Q gi|254780619|r  197 PILDKNQQDVVEQVVPLCTKGFAVSLISGVTGSGKTEVYLEIVAAVLHLGKQVLILLPEISLTSAILERFQKRFGVKPAE  276 (731)
Q Consensus       197 ~~Lt~eQ~~a~~~i~~~~~~~f~~~LL~GvTGSGKTEVYl~li~~~L~~GkqvLiLvPEI~Lt~Q~~~rl~~rF~~~v~v  276 (731)
                      +.++..|-.-+...  .+-......+|.|-||.|||-+..-+..++..+|..|++.-     ++.++.++.....+    
T Consensus        82 ~~l~~~~i~~La~~--~fi~~~~Nvil~G~~GtGKThLA~Alg~~A~~~G~~v~f~~-----~~~L~~~L~~a~~~----  150 (258)
T PRK09183         82 TGAPQKQLQSLRSL--SFIERNENIVLLGPSGVGKTHLAIALGYEAVRAGIKVRFTT-----AADLLLQLSTAQRQ----  150 (258)
T ss_pred             CCCCHHHHHHHHCC--CHHHCCCCEEEECCCCCCHHHHHHHHHHHHHHCCCEEEEEE-----HHHHHHHHHHHHHC----
T ss_conf             86238999988258--16655886799899998689999999999998799399978-----99999999999876----


Q ss_pred             EECCCCCHHHHHHHHHHHCCCCEEEEECCHHHHH-HHCCCEEEEEEECCCCCCHHCCCCCCCHHHHH-HHHHHHCCCCEE
Q ss_conf             6235572356678999971997399940012110-01000136774055321000024432248999-997511032100
Q gi|254780619|r  277 WHSSLSTSMREKIWRQVARGAISVIVGVRSALFL-PFKKLGLIVIDEEHDISYKQEEGILYNARDMS-IVRGKIESFPVV  354 (731)
Q Consensus       277 ~HS~ls~~eR~~~w~~i~~G~~~IVIGtRSAif~-P~~nLglIIvDEEHd~sykq~~~pry~aRdvA-~~Ra~~~~~~li  354 (731)
                                 ..+.               ..+. -+....|+|+||   -.|..-+.  ..+.++- ++=..++..++|
T Consensus       151 -----------~~~~---------------~~l~r~l~~~dLLIiDd---lG~~~~~~--~~~~~lfeli~~Rye~~S~I  199 (258)
T PRK09183        151 -----------GRYK---------------TTLQRGVMAPRLLIIDE---IGYLPFSQ--EEANLFFQVIAKRYEKGAMI  199 (258)
T ss_pred             -----------CCHH---------------HHHHHHHCCCCEEEEHH---HHCCCCCH--HHHHHHHHHHHHHHCCCCEE
T ss_conf             -----------8599---------------99998743465144313---31546888--89999999999985767789


Q ss_pred             CCCCCCCHHHHHHHH
Q ss_conf             002454324677532
Q gi|254780619|r  355 LVSATPSIESRVNGI  369 (731)
Q Consensus       355 lgSATPSles~~~~~  369 (731)
                      +.|--| ++.|+.+-
T Consensus       200 iTSn~~-~~~W~~~f  213 (258)
T PRK09183        200 LTSNLP-FGQWDQTF  213 (258)
T ss_pred             EECCCC-HHHHHHHC
T ss_conf             988999-78985651


No 347
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=91.17  E-value=0.1  Score=32.21  Aligned_cols=40  Identities=28%  Similarity=0.684  Sum_probs=25.2

Q ss_pred             HHHHHHHHHHHCCCCEEEEEECCCCEEHHCCCCCCCCCCCCCCCCCEEEEECCCCCCEECHHHCCCCCCCCCCCCCCC
Q ss_conf             899999988622655179974222000000235654343101465201211357832000021024465556667874
Q gi|254780619|r  408 PEMIDGIRHTLARNEQTLLFLNRRGYAPLTLCQVCGNRLKCLHCSCWLVEHRSKKKLYCHQCGHSAIYSQSCVVCGSS  485 (731)
Q Consensus       408 ~~l~~~i~~~l~~g~qvll~lnRrGya~~~~C~~Cg~~~~C~~C~~~l~~h~~~~~l~Ch~Cg~~~~~~~~Cp~Cg~~  485 (731)
                      ..++....+.+.+|+             +.+|.-||++..                         -..|.+||.||.+
T Consensus       119 ~~~~~~~Le~~~~~~-------------~~vC~vCGy~~~-------------------------ge~P~~CPiCga~  158 (166)
T COG1592         119 AEMFRGLLERLEEGK-------------VWVCPVCGYTHE-------------------------GEAPEVCPICGAP  158 (166)
T ss_pred             HHHHHHHHHHHHCCC-------------EEECCCCCCCCC-------------------------CCCCCCCCCCCCH
T ss_conf             999999998660387-------------787687888126-------------------------8998769999981


No 348
>pfam01155 HypA Hydrogenase expression/synthesis hypA family. Four conserved cysteines lie either side of the least conserved region.
Probab=91.13  E-value=0.17  Score=30.57  Aligned_cols=55  Identities=22%  Similarity=0.288  Sum_probs=35.0

Q ss_pred             CCHHHHHHHHHHHCCCCEEEEEECCCCEEHHCCCCCCCCCCCCCCCCCEEEEECCCCCCEECHHHCCCCC---CCCCCCC
Q ss_conf             7989999998862265517997422200000023565434310146520121135783200002102446---5556667
Q gi|254780619|r  406 LSPEMIDGIRHTLARNEQTLLFLNRRGYAPLTLCQVCGNRLKCLHCSCWLVEHRSKKKLYCHQCGHSAIY---SQSCVVC  482 (731)
Q Consensus       406 lS~~l~~~i~~~l~~g~qvll~lnRrGya~~~~C~~Cg~~~~C~~C~~~l~~h~~~~~l~Ch~Cg~~~~~---~~~Cp~C  482 (731)
                      +.+..++..-+.+.+|-  +                      |  =+.-|....-.-..+|+.||+....   ...||.|
T Consensus        38 V~pe~L~f~f~~~~~~T--~----------------------~--e~A~L~ie~vp~~~~C~~Cg~~~~~~~~~~~CP~C   91 (112)
T pfam01155        38 VEPEALRFAFEVAAEGT--L----------------------A--EGAELEIEEVPGVARCRDCGQEFELEERFFRCPKC   91 (112)
T ss_pred             CCHHHHHHHHHHHHCCC--C----------------------C--CCCEEEEEECCCEEECCCCCCEECCCCCCCCCCCC
T ss_conf             28999999999984588--7----------------------6--89899999518748998999714257776799089


Q ss_pred             CCCC
Q ss_conf             8741
Q gi|254780619|r  483 GSSG  486 (731)
Q Consensus       483 g~~~  486 (731)
                      ||..
T Consensus        92 gs~~   95 (112)
T pfam01155        92 GSLD   95 (112)
T ss_pred             CCCC
T ss_conf             7998


No 349
>KOG0387 consensus
Probab=91.07  E-value=1.3  Score=23.91  Aligned_cols=364  Identities=15%  Similarity=0.158  Sum_probs=168.0

Q ss_pred             CCCHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHH---HHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHCCCC-CE
Q ss_conf             688378999999987520489619984475315799---99999999851468479971521001344555430389-76
Q gi|254780619|r  198 ILDKNQQDVVEQVVPLCTKGFAVSLISGVTGSGKTE---VYLEIVAAVLHLGKQVLILLPEISLTSAILERFQKRFG-VK  273 (731)
Q Consensus       198 ~Lt~eQ~~a~~~i~~~~~~~f~~~LL~GvTGSGKTE---VYl~li~~~L~~GkqvLiLvPEI~Lt~Q~~~rl~~rF~-~~  273 (731)
                      .|-+-|+.-++=......++.. -.|--.-|=|||-   ++|.++.+.=.--+-|||+.|- .+.+|+.+.|+.-++ .+
T Consensus       205 ~Lf~yQreGV~WL~~L~~q~~G-GILgDeMGLGKTIQiisFLaaL~~S~k~~~paLIVCP~-Tii~qW~~E~~~w~p~~r  282 (923)
T KOG0387         205 KLFPYQREGVQWLWELYCQRAG-GILGDEMGLGKTIQIISFLAALHHSGKLTKPALIVCPA-TIIHQWMKEFQTWWPPFR  282 (923)
T ss_pred             HHHHHHHHHHHHHHHHHHCCCC-CEECCCCCCCCCHHHHHHHHHHHHCCCCCCCEEEECCH-HHHHHHHHHHHHHCCCEE
T ss_conf             8648889889999999732578-76201235764015899999875024325865998248-899999999987476537


Q ss_pred             EEEEECCCCCHH-----HHHHHHH----HHCCCCEEEEECCHHHHHH---HCC--CEEEEEEECCCCCCHHCCCCCCCHH
Q ss_conf             899623557235-----6678999----9719973999400121100---100--0136774055321000024432248
Q gi|254780619|r  274 PAEWHSSLSTSM-----REKIWRQ----VARGAISVIVGVRSALFLP---FKK--LGLIVIDEEHDISYKQEEGILYNAR  339 (731)
Q Consensus       274 v~v~HS~ls~~e-----R~~~w~~----i~~G~~~IVIGtRSAif~P---~~n--LglIIvDEEHd~sykq~~~pry~aR  339 (731)
                      |.+||+.-+.+.     -..-|-.    ...-...|.|-|.+..-+-   +.+  -+.+|.||-|--     ..|. ..+
T Consensus       283 v~ilh~t~s~~r~~~~~~~~~~~~~L~r~~~~~~~ilitty~~~r~~~d~l~~~~W~y~ILDEGH~I-----rNpn-s~i  356 (923)
T KOG0387         283 VFILHGTGSGARYDASHSSHKKDKLLIRKVATDGGILITTYDGFRIQGDDLLGILWDYVILDEGHRI-----RNPN-SKI  356 (923)
T ss_pred             EEEEECCCCCCCCCCCHHHHHHHHHHEEEECCCCCEEEEEHHHHCCCCCCCCCCCCCEEEECCCCCC-----CCCC-CHH
T ss_conf             9997147765444431013443122203530468479974224200475234650347982376504-----6985-089


Q ss_pred             HHHHHHHHHCCCCEECCCCCCCH----HHHHHH---HHHH----------HHHHCCCCCCCCCCCCCCEE--CCCCCCCC
Q ss_conf             99999751103210000245432----467753---2123----------44412432236765433211--02222332
Q gi|254780619|r  340 DMSIVRGKIESFPVVLVSATPSI----ESRVNG---ISRR----------YHSVHLSTRYRNSALPHLQV--IDMRGQTI  400 (731)
Q Consensus       340 dvA~~Ra~~~~~~lilgSATPSl----es~~~~---~~g~----------~~~~~l~~R~~~~~~P~i~i--vDm~~~~~  400 (731)
                      .+|..-.+- .-.+|| |-||--    |.|...   --|+          |.+.  .++-..+.-+.+++  -+  +...
T Consensus       357 slackki~T-~~RiIL-SGTPiQNnL~ELwsLfDFv~PG~Lgt~~~F~~~f~~p--I~~GgyaNAs~~qv~~ay--kca~  430 (923)
T KOG0387         357 SLACKKIRT-VHRIIL-SGTPIQNNLTELWSLFDFVFPGKLGTLPVFQQNFEHP--INRGGYANASPRQVQTAY--KCAV  430 (923)
T ss_pred             HHHHHHCCC-CCEEEE-ECCCCCCHHHHHHHHHHHCCCCCCCCHHHHHHHHHHH--EECCCCCCCCHHHHHHHH--HHHH
T ss_conf             999986156-664886-1862101089998776640677445517787630111--003565789879999999--9999


Q ss_pred             CCCCCCCHHHHHHHHHHHC------CCCEEEEE----ECCCCE-----EHHCCCC-------CCCCCCCCCCCCCEEEEE
Q ss_conf             2245479899999988622------65517997----422200-----0000235-------654343101465201211
Q gi|254780619|r  401 AQGKSLSPEMIDGIRHTLA------RNEQTLLF----LNRRGY-----APLTLCQ-------VCGNRLKCLHCSCWLVEH  458 (731)
Q Consensus       401 ~~~~~lS~~l~~~i~~~l~------~g~qvll~----lnRrGy-----a~~~~C~-------~Cg~~~~C~~C~~~l~~h  458 (731)
                      .-...|++.++..++.-..      +.++|++-    .-|+=|     ++-+.|-       -||-...=.-|+-|.-+.
T Consensus       431 ~Lr~lI~PylLRR~K~dv~~~~Lp~K~E~VlfC~LT~~QR~~Y~~fl~s~~v~~i~ng~~~~l~Gi~iLrkICnHPdll~  510 (923)
T KOG0387         431 ALRDLISPYLLRRMKSDVKGLKLPKKEEIVLFCRLTKLQRRLYQRFLNSSEVNKILNGKRNCLSGIDILRKICNHPDLLD  510 (923)
T ss_pred             HHHHHHHHHHHHHHHHHHHHCCCCCCCCEEEEEECCHHHHHHHHHHHHHHHHHHHHCCCCCCEECHHHHHHHCCCCCCCC
T ss_conf             99987679999999988644217886525899856699999999986059899997498441215188886458941026


Q ss_pred             CCC--------CCCEECHHHCCCCCCCC---CCCCCCCCEECCCCCCHHHHHHHHHHC---CCCCHHHHCCCCCCCCHHH
Q ss_conf             357--------83200002102446555---666787411001354289988885204---8520001023211358678
Q gi|254780619|r  459 RSK--------KKLYCHQCGHSAIYSQS---CVVCGSSGKMIACGFGIERIAEEVCEY---FPLARISILSSDLEGGGGR  524 (731)
Q Consensus       459 ~~~--------~~l~Ch~Cg~~~~~~~~---Cp~Cg~~~~l~~~G~Gte~~~e~l~~~---fp~~~v~~~d~d~~~~~~~  524 (731)
                      +..        -..---.||........   --.=|.. .+. + .-+.+.-+.|...   -+++.-+|||.-|..  ..
T Consensus       511 ~~~~~~~~~~D~~g~~k~sGKm~vl~~ll~~W~kqg~r-vll-F-sqs~~mLdilE~fL~~~~~ysylRmDGtT~~--~~  585 (923)
T KOG0387         511 RRDEDEKQGPDYEGDPKRSGKMKVLAKLLKDWKKQGDR-VLL-F-SQSRQMLDILESFLRRAKGYSYLRMDGTTPA--AL  585 (923)
T ss_pred             CCCCCCCCCCCCCCCHHHCCHHHHHHHHHHHHHHCCCE-EEE-E-HHHHHHHHHHHHHHHHCCCCEEEEECCCCCC--CH
T ss_conf             76421235887678956521699999999998617977-998-4-1377999999999873478538971588862--01


Q ss_pred             HHHHHHHHCCCC-CCE-EEEEHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             999998621257-657-987044302311345201233000344310245578999998
Q gi|254780619|r  525 LQLQLSAIAKGE-IDI-IIGTQLVAKGHNFPRMSLVGVVDGDLGLTNADLRSSERTFQL  581 (731)
Q Consensus       525 ~~~~~~~~~~~~-~~i-lvgTq~i~kg~~fp~v~lv~il~aD~~l~~pd~ra~E~~~ql  581 (731)
                      ...++++|.+++ +.| |+.|+.=.=|++.-..+=|+|.|.|- =-+.|--|.||+|.+
T Consensus       586 R~~lVd~Fne~~s~~VFLLTTrvGGLGlNLTgAnRVIIfDPdW-NPStD~QAreRawRi  643 (923)
T KOG0387         586 RQKLVDRFNEDESIFVFLLTTRVGGLGLNLTGANRVIIFDPDW-NPSTDNQARERAWRI  643 (923)
T ss_pred             HHHHHHHHCCCCCEEEEEEEECCCCCCCCCCCCCEEEEECCCC-CCCCCHHHHHHHHHH
T ss_conf             0578986367874579999730355411245675589979999-976425788888863


No 350
>pfam02146 SIR2 Sir2 family. This region is characteristic of Silent information regulator 2 (Sir2) proteins, or sirtuins. These are protein deacetylases that depend on nicotine adenine dinucleotide (NAD). They are found in many subcellular locations, including the nucleus, cytoplasm and mitochondria. Eukaryotic forms play in important role in the regulation of transcriptional repression. Moreover, they are involved in microtubule organisation and DNA damage repair processes.
Probab=90.98  E-value=0.34  Score=28.21  Aligned_cols=18  Identities=28%  Similarity=0.564  Sum_probs=10.9

Q ss_pred             HHHHHCCCCCCEEEEEHH
Q ss_conf             998621257657987044
Q gi|254780619|r  528 QLSAIAKGEIDIIIGTQL  545 (731)
Q Consensus       528 ~~~~~~~~~~~ilvgTq~  545 (731)
                      ..+.+.+-+.-|+|||.+
T Consensus       156 a~~~~~~aDl~lviGTSl  173 (177)
T pfam02146       156 AYEDVEEADLLIVIGTSL  173 (177)
T ss_pred             HHHHHHCCCEEEEECCCC
T ss_conf             999996399999968681


No 351
>PRK08579 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=90.97  E-value=0.095  Score=32.48  Aligned_cols=37  Identities=11%  Similarity=0.161  Sum_probs=20.9

Q ss_pred             CCCCCHHHHHHHHHHHCCCCEEEEECCHHHHHHHCCCEEE
Q ss_conf             3557235667899997199739994001211001000136
Q gi|254780619|r  279 SSLSTSMREKIWRQVARGAISVIVGVRSALFLPFKKLGLI  318 (731)
Q Consensus       279 S~ls~~eR~~~w~~i~~G~~~IVIGtRSAif~P~~nLglI  318 (731)
                      ++|+..|-.+.++...-   .+-+=+|+.-=+||.|+.+-
T Consensus       144 d~l~~~evkq~~Q~fvy---nlN~~sr~g~QtPFtni~~~  180 (623)
T PRK08579        144 DGLDYRKIKQNIQRLVY---NLNYPSRVGMQTPFTNFTVT  180 (623)
T ss_pred             CCCCHHHHHHHHHHHHH---HCCCCCCCCCCCCCEEEEEC
T ss_conf             34789999999999887---60464667887871578965


No 352
>COG4260 Membrane protease subunit, stomatin/prohibitin family [Amino acid    transport and metabolism]
Probab=90.96  E-value=0.089  Score=32.69  Aligned_cols=38  Identities=32%  Similarity=0.678  Sum_probs=28.7

Q ss_pred             CEEHHCCCCCCCCCCCCCCCCCEEEEECCCCCCEECHHHCCCC----CCCCCCCCCCC
Q ss_conf             0000002356543431014652012113578320000210244----65556667874
Q gi|254780619|r  432 GYAPLTLCQVCGNRLKCLHCSCWLVEHRSKKKLYCHQCGHSAI----YSQSCVVCGSS  485 (731)
Q Consensus       432 Gya~~~~C~~Cg~~~~C~~C~~~l~~h~~~~~l~Ch~Cg~~~~----~~~~Cp~Cg~~  485 (731)
                      +=+..-.|.+|+..--|++|+                ||.+..    .+..||+||..
T Consensus       302 ~pa~t~~~~r~~k~nfc~ncG----------------~~~t~~~~ng~a~fcp~cgq~  343 (345)
T COG4260         302 APAATWPCARCAKLNFCLNCG----------------CGTTADFDNGKAKFCPECGQG  343 (345)
T ss_pred             CCCCCCCCHHCCCCCCCCCCC----------------CCCCCCCCCCHHHHCHHHCCC
T ss_conf             875568510005655033468----------------654468764300207654577


No 353
>TIGR01384 TFS_arch transcription factor S; InterPro: IPR006288   DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme . The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length . The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel.   RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise:  RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors.  RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs.  Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kD, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits.   These sequences are the archaeal DNA-directed RNA polymerase, subunit M (also known as transcription factor S), a protein related in size and sequence to certain eukaryotic RNA polymerase small subunits, and in sequence and function to the much larger eukaryotic transcription factor IIS (TFIIS). Although originally suggested to be a subunit of the archaeal RNA polymerase, it elutes separately from active polymerase in gel filtration experiments and acts, like TFIIs, as an induction factor for RNA cleavage by RNA polymerase . ; GO: 0003677 DNA binding, 0003700 transcription factor activity, 0003899 DNA-directed RNA polymerase activity, 0006350 transcription.
Probab=90.96  E-value=0.085  Score=32.83  Aligned_cols=30  Identities=23%  Similarity=0.664  Sum_probs=26.0

Q ss_pred             CCCCCCEEEEECCCC--CCEECHHHCCCCCCC
Q ss_conf             014652012113578--320000210244655
Q gi|254780619|r  448 CLHCSCWLVEHRSKK--KLYCHQCGHSAIYSQ  477 (731)
Q Consensus       448 C~~C~~~l~~h~~~~--~l~Ch~Cg~~~~~~~  477 (731)
                      ||.|+.-|+=.|+++  .++|..|||+.++..
T Consensus         3 CPKCgs~M~P~K~~Gkn~~~C~~CGYE~~~T~   34 (111)
T TIGR01384         3 CPKCGSLMVPDKKNGKNKYKCRKCGYEKEITK   34 (111)
T ss_pred             CCCCCCCCCCCCCCCCCEEECCCCCCCCCCCC
T ss_conf             78669715854306950116288887330466


No 354
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=90.95  E-value=0.091  Score=32.62  Aligned_cols=27  Identities=30%  Similarity=0.704  Sum_probs=21.9

Q ss_pred             CCCCCCCCEEEEECCCCCCEECHHHCCCC
Q ss_conf             31014652012113578320000210244
Q gi|254780619|r  446 LKCLHCSCWLVEHRSKKKLYCHQCGHSAI  474 (731)
Q Consensus       446 ~~C~~C~~~l~~h~~~~~l~Ch~Cg~~~~  474 (731)
                      ++|.+|..+|.+  ..+.|.|..||+++.
T Consensus       150 A~CsrC~~~L~~--~~~~l~Cp~Cg~tEk  176 (188)
T COG1096         150 ARCSRCRAPLVK--KGNMLKCPNCGNTEK  176 (188)
T ss_pred             EECCCCCCCEEE--CCCEEECCCCCCEEE
T ss_conf             983677762088--475998887798776


No 355
>COG0529 CysC Adenylylsulfate kinase and related kinases [Inorganic ion transport and metabolism]
Probab=90.91  E-value=0.9  Score=25.00  Aligned_cols=140  Identities=23%  Similarity=0.233  Sum_probs=80.4

Q ss_pred             CCCCCEEEEECCCCHHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHCCCCCEE-EEEEC--CCCCHHHHHHHH
Q ss_conf             048961998447531579999999999851468479971521001344555430389768-99623--557235667899
Q gi|254780619|r  215 TKGFAVSLISGVTGSGKTEVYLEIVAAVLHLGKQVLILLPEISLTSAILERFQKRFGVKP-AEWHS--SLSTSMREKIWR  291 (731)
Q Consensus       215 ~~~f~~~LL~GvTGSGKTEVYl~li~~~L~~GkqvLiLvPEI~Lt~Q~~~rl~~rF~~~v-~v~HS--~ls~~eR~~~w~  291 (731)
                      .++..+.-+-|-.|||||-+.-.+-++..++|+++-+|=                 |+++ --+.+  +.|..+|.+++.
T Consensus        20 ~~~~~viW~TGLSGsGKSTiA~ale~~L~~~G~~~y~LD-----------------GDnvR~gL~~dLgFs~edR~eniR   82 (197)
T COG0529          20 GQKGAVIWFTGLSGSGKSTIANALEEKLFAKGYHVYLLD-----------------GDNVRHGLNRDLGFSREDRIENIR   82 (197)
T ss_pred             CCCCEEEEEECCCCCCHHHHHHHHHHHHHHCCCEEEEEC-----------------CHHHHHCCCCCCCCCHHHHHHHHH
T ss_conf             799859996468888787999999999997597589855-----------------746765005788978678999999


Q ss_pred             HHHCCCCEEEEECCHHHHHHHCCCEEEEEEECCCCCCHHCCCCCCCHHHHHHHHHHHCCCCEECCCCCCCHH--------
Q ss_conf             997199739994001211001000136774055321000024432248999997511032100002454324--------
Q gi|254780619|r  292 QVARGAISVIVGVRSALFLPFKKLGLIVIDEEHDISYKQEEGILYNARDMSIVRGKIESFPVVLVSATPSIE--------  363 (731)
Q Consensus       292 ~i~~G~~~IVIGtRSAif~P~~nLglIIvDEEHd~sykq~~~pry~aRdvA~~Ra~~~~~~lilgSATPSle--------  363 (731)
                      ++..=          |=  -|.+-|+|++-     |+   =+|.=..|+.|..+-.....-=|+.- ||--+        
T Consensus        83 Rvaev----------Ak--ll~daG~iviv-----a~---ISP~r~~R~~aR~~~~~~~FiEVyV~-~pl~vce~RDpKG  141 (197)
T COG0529          83 RVAEV----------AK--LLADAGLIVIV-----AF---ISPYREDRQMARELLGEGEFIEVYVD-TPLEVCERRDPKG  141 (197)
T ss_pred             HHHHH----------HH--HHHHCCEEEEE-----EE---ECCCHHHHHHHHHHHCCCCEEEEEEC-CCHHHHHHCCCHH
T ss_conf             99999----------99--99878908999-----75---17309999999997276862899957-9899998618257


Q ss_pred             HHHHHHHHHHHHHC-CCCCCCCCCCCCCEE
Q ss_conf             67753212344412-432236765433211
Q gi|254780619|r  364 SRVNGISRRYHSVH-LSTRYRNSALPHLQV  392 (731)
Q Consensus       364 s~~~~~~g~~~~~~-l~~R~~~~~~P~i~i  392 (731)
                      .|..|.+|.+..++ ...-|....-|.+.+
T Consensus       142 LYkKAr~GeI~~fTGid~pYE~P~~Pel~l  171 (197)
T COG0529         142 LYKKARAGEIKNFTGIDSPYEAPENPELHL  171 (197)
T ss_pred             HHHHHHCCCCCCCCCCCCCCCCCCCCEEEE
T ss_conf             899997598778757788888999982675


No 356
>COG1439 Predicted nucleic acid-binding protein, consists of a PIN domain and a Zn-ribbon module [General function prediction only]
Probab=90.84  E-value=0.12  Score=31.66  Aligned_cols=74  Identities=27%  Similarity=0.352  Sum_probs=39.3

Q ss_pred             CCCHHHHHHHHHHHCCCCE--EEEEECCCCEEHHCCCCCCCCCCCCCCCCC-EEEEEC-----CCCCCEECHHHCCCCCC
Q ss_conf             4798999999886226551--799742220000002356543431014652-012113-----57832000021024465
Q gi|254780619|r  405 SLSPEMIDGIRHTLARNEQ--TLLFLNRRGYAPLTLCQVCGNRLKCLHCSC-WLVEHR-----SKKKLYCHQCGHSAIYS  476 (731)
Q Consensus       405 ~lS~~l~~~i~~~l~~g~q--vll~lnRrGya~~~~C~~Cg~~~~C~~C~~-~l~~h~-----~~~~l~Ch~Cg~~~~~~  476 (731)
                      +||++=++.+.-+++-+++  |.++..  -|+=       ..++.=-.=.. +..++.     ..-.++||-|+..++.|
T Consensus        82 ~LS~tDi~VlalAlel~~~~~v~l~Td--Dysv-------QNVa~~Lgi~~~~~~~~~~I~~v~~w~~rC~GC~~~f~~~  152 (177)
T COG1439          82 NLSPTDIEVLALALELGEEVQVALATD--DYSV-------QNVALQLGLNVRSISYKGKIKKVRKWRLRCHGCKRIFPEP  152 (177)
T ss_pred             CCCHHHHHHHHHHHHHCCCCCEEEEEC--CHHH-------HHHHHHHCCEEEEEECCCCCCEEEEEEEEEECCCEECCCC
T ss_conf             157555999998886156546069954--4578-------7899972946774001576114753568984575250898


Q ss_pred             -CCCCCCCCCCE
Q ss_conf             -55666787411
Q gi|254780619|r  477 -QSCVVCGSSGK  487 (731)
Q Consensus       477 -~~Cp~Cg~~~~  487 (731)
                       ..||.|||...
T Consensus       153 ~~~Cp~CG~~~~  164 (177)
T COG1439         153 KDFCPICGSPLK  164 (177)
T ss_pred             CCCCCCCCCCEE
T ss_conf             880778999117


No 357
>PRK09263 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=90.82  E-value=0.098  Score=32.38  Aligned_cols=18  Identities=11%  Similarity=0.270  Sum_probs=9.6

Q ss_pred             HHHHHHHHHHHH------CCCCEE
Q ss_conf             999999999851------468479
Q gi|254780619|r  233 EVYLEIVAAVLH------LGKQVL  250 (731)
Q Consensus       233 EVYl~li~~~L~------~GkqvL  250 (731)
                      ++++..+.+.+.      .|.|++
T Consensus       202 ~tA~~~~~~~l~~~q~~~~Ggqa~  225 (711)
T PRK09263        202 QTATAVTAQIIAQVASSQYGGCTI  225 (711)
T ss_pred             HHHHHHHHHHHHHHHHHHHCCEEH
T ss_conf             999999999999998765357111


No 358
>PRK07667 uridine kinase; Provisional
Probab=90.76  E-value=0.35  Score=28.18  Aligned_cols=33  Identities=24%  Similarity=0.308  Sum_probs=24.9

Q ss_pred             EEEEECCCCHHHHHHHHHHHHHHHHCCCCEEEE
Q ss_conf             199844753157999999999985146847997
Q gi|254780619|r  220 VSLISGVTGSGKTEVYLEIVAAVLHLGKQVLIL  252 (731)
Q Consensus       220 ~~LL~GvTGSGKTEVYl~li~~~L~~GkqvLiL  252 (731)
                      ..=+.|.+|||||-+.-++++..-+.|..++++
T Consensus        16 iIgIaG~sgSGKTTla~~L~~~l~~~~~~v~v~   48 (190)
T PRK07667         16 ILGIDGLSRSGKTTFVANLKENMKQEGIPFHIF   48 (190)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHCCCCEEEE
T ss_conf             999779897889999999999986659837999


No 359
>cd01409 SIRT4 SIRT4: Eukaryotic and prokaryotic group (class2) which includes human sirtuin SIRT4 and several bacterial homologs; and are members of the SIR2 family of proteins, silent information regulator 2 (Sir2) enzymes which catalyze NAD+-dependent protein/histone deacetylation. Sir2 proteins have been shown to regulate gene silencing, DNA repair, metabolic enzymes, and life span.
Probab=90.71  E-value=0.34  Score=28.20  Aligned_cols=17  Identities=29%  Similarity=0.575  Sum_probs=11.9

Q ss_pred             CCEEHHCCCCCCCCCCC
Q ss_conf             20000002356543431
Q gi|254780619|r  431 RGYAPLTLCQVCGNRLK  447 (731)
Q Consensus       431 rGya~~~~C~~Cg~~~~  447 (731)
                      .|-...+.|..|++..-
T Consensus       113 HGsl~~~~C~~C~~~~~  129 (260)
T cd01409         113 HGSLHRVVCLSCGFRTP  129 (260)
T ss_pred             ECCCCEEEECCCCCCCC
T ss_conf             42548558189989576


No 360
>cd03214 ABC_Iron-Siderophores_B12_Hemin ABC transporters, involved in the uptake of siderophores, heme, and vitamin B12, are widely conserved in bacteria and archaea.  Only very few species lack representatives of the siderophore family transporters.  The E. coli BtuCD protein is an ABC transporter mediating vitamin B12 uptake.  The two ATP-binding cassettes (BtuD) are in close contact with each other, as are the two membrane-spanning subunits (BtuC); this arrangement is distinct from that observed for the E. coli lipid flippase MsbA.  The BtuC subunits provide 20 transmembrane helices grouped around a translocation pathway that is closed to the cytoplasm by a gate region, whereas the dimer arrangement of the BtuD subunits resembles the ATP-bound form of the Rad50 DNA repair enzyme.  A prominent cytoplasmic loop of BtuC forms the contact region with the ATP-binding cassette and represent a conserved motif among the ABC transporters.
Probab=90.66  E-value=0.98  Score=24.72  Aligned_cols=116  Identities=18%  Similarity=0.215  Sum_probs=59.3

Q ss_pred             CEEEEECCCCHHHHHHHHHHHHHHHHCC-CCEEEE------EC------CCHHHHHHHHHHHC-CC-CCEEEEEECCCCC
Q ss_conf             6199844753157999999999985146-847997------15------21001344555430-38-9768996235572
Q gi|254780619|r  219 AVSLISGVTGSGKTEVYLEIVAAVLHLG-KQVLIL------LP------EISLTSAILERFQK-RF-GVKPAEWHSSLST  283 (731)
Q Consensus       219 ~~~LL~GvTGSGKTEVYl~li~~~L~~G-kqvLiL------vP------EI~Lt~Q~~~rl~~-rF-~~~v~v~HS~ls~  283 (731)
                      ...-|=|-.|||||.. ++++...+... .++.+-      .|      .|+..+|..+++.- .| +..+    ..||.
T Consensus        26 e~~~liG~nGsGKTTL-l~~i~G~~~~~~G~I~~~g~~i~~~~~~~~~~~i~~v~Q~l~~~~l~~~~~~~~----~~LSG  100 (180)
T cd03214          26 EIVGILGPNGAGKSTL-LKTLAGLLKPSSGEILLDGKDLASLSPKELARKIAYVPQALELLGLAHLADRPF----NELSG  100 (180)
T ss_pred             CEEEEECCCCCCHHHH-HHHHHCCCCCCCCEEEECCEECCCCCHHHHHCCCCHHHHHHHHCCCHHHHCCCH----HHCCH
T ss_conf             7999998999889999-999957989987289999999896999999554649999999859977864991----03799


Q ss_pred             HHHHHHHHHHHCCCCEEEEECCHHHHHHHCCCEEEEEEECCCCCCHHCCCCCCCHHHHHHHHHHHCCCCEECCCC
Q ss_conf             356678999971997399940012110010001367740553210000244322489999975110321000024
Q gi|254780619|r  284 SMREKIWRQVARGAISVIVGVRSALFLPFKKLGLIVIDEEHDISYKQEEGILYNARDMSIVRGKIESFPVVLVSA  358 (731)
Q Consensus       284 ~eR~~~w~~i~~G~~~IVIGtRSAif~P~~nLglIIvDEEHd~sykq~~~pry~aRdvA~~Ra~~~~~~lilgSA  358 (731)
                      +||.++-...                +=+.|+.++|.||--..   -|-.-+....++-....+.++..+++.|.
T Consensus       101 GqkQrv~iA~----------------aL~~~P~ililDEPts~---LD~~~~~~i~~~i~~l~~~~~~tii~itH  156 (180)
T cd03214         101 GERQRVLLAR----------------ALAQEPPILLLDEPTSH---LDIAHQIELLELLRRLARERGKTVVMVLH  156 (180)
T ss_pred             HHHHHHHHHH----------------HHHHCCCEEEECCCCCC---CCHHHHHHHHHHHHHHHHHCCCEEEEEEC
T ss_conf             9999999999----------------99868964788587544---79999999999999999846989999907


No 361
>PRK13894 conjugal transfer ATPase TrbB; Provisional
Probab=90.51  E-value=1.4  Score=23.55  Aligned_cols=41  Identities=29%  Similarity=0.403  Sum_probs=26.0

Q ss_pred             CCCHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHHHHHHHH
Q ss_conf             688378999999987520489619984475315799999999998
Q gi|254780619|r  198 ILDKNQQDVVEQVVPLCTKGFAVSLISGVTGSGKTEVYLEIVAAV  242 (731)
Q Consensus       198 ~Lt~eQ~~a~~~i~~~~~~~f~~~LL~GvTGSGKTEVYl~li~~~  242 (731)
                      .++.+|...+......    ....|+-|-||||||..---++...
T Consensus       133 ~~~~~~a~~L~~~V~~----r~nilI~G~TgsGKTTll~all~~i  173 (320)
T PRK13894        133 IMTAEQREAIIAAVRA----HRNILVIGGTGSGKTTLVNAIINEM  173 (320)
T ss_pred             CCCHHHHHHHHHHHHC----CCCEEEECCCCCCHHHHHHHHHHHH
T ss_conf             9999999999999972----8758998588865689999998632


No 362
>PRK11827 hypothetical protein; Provisional
Probab=90.50  E-value=0.12  Score=31.60  Aligned_cols=34  Identities=18%  Similarity=0.281  Sum_probs=29.5

Q ss_pred             CCCCCCCCCCEEEEECCCCCCEECHHHCCCCCCC
Q ss_conf             3431014652012113578320000210244655
Q gi|254780619|r  444 NRLKCLHCSCWLVEHRSKKKLYCHQCGHSAIYSQ  477 (731)
Q Consensus       444 ~~~~C~~C~~~l~~h~~~~~l~Ch~Cg~~~~~~~  477 (731)
                      .+..||.|.++|.|++..+.|.|..|+-.+++-+
T Consensus         7 ~ILvCP~ckg~L~yd~~~~ELic~~~~LAyPIrd   40 (60)
T PRK11827          7 EIIACPVCNGKLWYNQEKQELICKLDNLAFPLRD   40 (60)
T ss_pred             HEEECCCCCCCCEECCCCCEEEECCCCEECCCCC
T ss_conf             2255778899033987689886066474265538


No 363
>TIGR00376 TIGR00376 DNA helicase, putative; InterPro: IPR004483 Eukaryotic members of this family have been characterised as binding certain single-stranded G-rich DNA sequences (GGGGT and GGGCT). A number of related proteins are characterised as helicases.; GO: 0003677 DNA binding, 0005524 ATP binding.
Probab=90.45  E-value=1.2  Score=24.12  Aligned_cols=73  Identities=26%  Similarity=0.423  Sum_probs=57.9

Q ss_pred             CCCCHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHHHHHHHHHHCCC--CEEEEECCCHHHHHHHHHHHCCCCCE
Q ss_conf             668837899999998752048961998447531579999999999851468--47997152100134455543038976
Q gi|254780619|r  197 PILDKNQQDVVEQVVPLCTKGFAVSLISGVTGSGKTEVYLEIVAAVLHLGK--QVLILLPEISLTSAILERFQKRFGVK  273 (731)
Q Consensus       197 ~~Lt~eQ~~a~~~i~~~~~~~f~~~LL~GvTGSGKTEVYl~li~~~L~~Gk--qvLiLvPEI~Lt~Q~~~rl~~rF~~~  273 (731)
                      +.++..|+.++.......    ..+++||-.|.|||....+++.+.+..|.  .+++..|.-.-...++.++...++..
T Consensus       201 ~~l~~~~~~~~~~~~~~~----~~~~~~gp~g~g~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~d~~~~~~~~~~p~~  275 (709)
T TIGR00376       201 PNLNESQKEAVGFALSSK----DLFLIHGPPGTGKTRTLVELIRQLVKRGPEERVLVTAPSNIAVDNLLERLAPLYPDL  275 (709)
T ss_pred             CCCCHHHHHHHHHHHCCC----CEEEEECCCCCCCHHHHHHHHHHHHHCCCCCCEEEECCCCHHHHHHHHHHHHHCCCC
T ss_conf             232234677765431234----416872677776215689999999852853306762353103778888876414541


No 364
>COG4306 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=90.44  E-value=0.095  Score=32.47  Aligned_cols=45  Identities=27%  Similarity=0.425  Sum_probs=29.1

Q ss_pred             CCCCCCC--CCCCCCCCCEEE--EECCCCCCEECHHHCCCCCCCCCCCCCCCC
Q ss_conf             2356543--431014652012--113578320000210244655566678741
Q gi|254780619|r  438 LCQVCGN--RLKCLHCSCWLV--EHRSKKKLYCHQCGHSAIYSQSCVVCGSSG  486 (731)
Q Consensus       438 ~C~~Cg~--~~~C~~C~~~l~--~h~~~~~l~Ch~Cg~~~~~~~~Cp~Cg~~~  486 (731)
                      .|..||.  +..||.|+.+..  ||-+ +.|   --|..+.+|..|-+||+..
T Consensus        30 fcskcgeati~qcp~csasirgd~~ve-gvl---glg~dye~psfchncgs~f   78 (160)
T COG4306          30 FCSKCGEATITQCPICSASIRGDYYVE-GVL---GLGGDYEPPSFCHNCGSRF   78 (160)
T ss_pred             HHHHHCHHHHHCCCCCCCCCCCCCEEE-EEE---CCCCCCCCCCHHHCCCCCC
T ss_conf             986514688853875677545640012-221---1587878940654179988


No 365
>PRK00133 metG methionyl-tRNA synthetase; Reviewed
Probab=90.43  E-value=0.89  Score=25.03  Aligned_cols=14  Identities=29%  Similarity=0.316  Sum_probs=7.5

Q ss_pred             HHHHHHHHHCCHHH
Q ss_conf             89997524557223
Q gi|254780619|r  164 SHVIDGLKAQGVIK  177 (731)
Q Consensus       164 ~~~i~~L~~kglI~  177 (731)
                      ..++..|.++|.|.
T Consensus       104 q~~f~~l~~~G~iy  117 (666)
T PRK00133        104 QEIYLKLKENGYIY  117 (666)
T ss_pred             HHHHHHHHHCCCEE
T ss_conf             99999999789989


No 366
>cd01410 SIRT7 SIRT7: Eukaryotic and prokaryotic group (class4) which includes human sirtuin SIRT6, SIRT7, and several bacterial homologs; and are members of the SIR2 family of proteins, silent information regulator 2 (Sir2) enzymes which catalyze NAD+-dependent protein/histone deacetylation. Sir2 proteins have been shown to regulate gene silencing, DNA repair, metabolic enzymes, and life span.
Probab=90.43  E-value=0.23  Score=29.54  Aligned_cols=47  Identities=23%  Similarity=0.458  Sum_probs=24.3

Q ss_pred             CCCCCCCCCCCCEECCC--CCCHHHHHHHHHHCCCCCHHHHCCCCCCCCHHHHHHHHHHHCCCCCCEEEEEHHH
Q ss_conf             65556667874110013--5428998888520485200010232113586789999986212576579870443
Q gi|254780619|r  475 YSQSCVVCGSSGKMIAC--GFGIERIAEEVCEYFPLARISILSSDLEGGGGRLQLQLSAIAKGEIDIIIGTQLV  546 (731)
Q Consensus       475 ~~~~Cp~Cg~~~~l~~~--G~Gte~~~e~l~~~fp~~~v~~~d~d~~~~~~~~~~~~~~~~~~~~~ilvgTq~i  546 (731)
                      .+..||.||+.  +++-  =+|         +..|.              ..++...+.+.+-+.-|+|||.+.
T Consensus       119 ~~p~C~~Cgg~--lrP~VV~FG---------E~lp~--------------~~~~~a~~~~~~aDlllviGTSl~  167 (206)
T cd01410         119 TGRRCHACGGI--LKDTIVDFG---------ERLPP--------------ENWMGAAAAACRADLFLCLGTSLQ  167 (206)
T ss_pred             CCCCCCCCCCC--CCCCEEECC---------CCCCH--------------HHHHHHHHHHHHCCEEEEECCCCE
T ss_conf             89988233897--046488735---------65998--------------999999999984998999767955


No 367
>PRK12901 secA preprotein translocase subunit SecA; Reviewed
Probab=90.42  E-value=1.2  Score=23.99  Aligned_cols=92  Identities=18%  Similarity=0.163  Sum_probs=62.3

Q ss_pred             CCCHHHHHHHHHHHHHHHHCCCCEEEEECCCHHHH---HHHHHHHCCCCCEEEEEECC-CCCHHHHHHHHHHHCCCCEEE
Q ss_conf             75315799999999998514684799715210013---44555430389768996235-572356678999971997399
Q gi|254780619|r  226 VTGSGKTEVYLEIVAAVLHLGKQVLILLPEISLTS---AILERFQKRFGVKPAEWHSS-LSTSMREKIWRQVARGAISVI  301 (731)
Q Consensus       226 vTGSGKTEVYl~li~~~L~~GkqvLiLvPEI~Lt~---Q~~~rl~~rF~~~v~v~HS~-ls~~eR~~~w~~i~~G~~~IV  301 (731)
                      -||-|||.|..-.+--.--.|+.|-|+-..=-|+.   ++...+...+|-.|.+..+. +++.+|...|.      ++|+
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             EECCHHHHH--------------HHCCCEEEEEEEC
Q ss_conf             940012110--------------0100013677405
Q gi|254780619|r  302 VGVRSALFL--------------PFKKLGLIVIDEE  323 (731)
Q Consensus       302 IGtRSAif~--------------P~~nLglIIvDEE  323 (731)
                      -||-+.+=.              =-..+...||||-
T Consensus       266 YgTn~EfGFDYLRDnm~~~~~~~vqr~~~~aIVDEv  301 (1111)
T PRK12901        266 YGTNNEFGFDYLRDNMAVSPKDLVQRKHNYAIVDEV  301 (1111)
T ss_pred             ECCCCCCCHHHHHHHCCCCHHHHCCCCCCEEEEECH
T ss_conf             415654102435640157878725677765888423


No 368
>PRK03846 adenylylsulfate kinase; Provisional
Probab=90.40  E-value=1.4  Score=23.48  Aligned_cols=67  Identities=22%  Similarity=0.267  Sum_probs=46.4

Q ss_pred             HCCCCCEEEEECCCCHHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHCCCCCEEEEEECCCCCHHHHHHHHHH
Q ss_conf             20489619984475315799999999998514684799715210013445554303897689962355723566789999
Q gi|254780619|r  214 CTKGFAVSLISGVTGSGKTEVYLEIVAAVLHLGKQVLILLPEISLTSAILERFQKRFGVKPAEWHSSLSTSMREKIWRQV  293 (731)
Q Consensus       214 ~~~~f~~~LL~GvTGSGKTEVYl~li~~~L~~GkqvLiLvPEI~Lt~Q~~~rl~~rF~~~v~v~HS~ls~~eR~~~w~~i  293 (731)
                      ..++..+.-|-|-.|||||-+.-.+.+...+.|..+++|=-         +.++..|+...     +-|..+|.++-.++
T Consensus        20 ~~~kg~viWlTGLSGSGKTTlA~~L~~~L~~~~~~~~~LDG---------D~lR~~l~~dl-----gfs~~dR~~n~~r~   85 (198)
T PRK03846         20 HGHKGVVLWFTGLSGSGKSTVAGALEEALHELGVHTYLLDG---------DNVRHGLCSDL-----GFSDADRKENIRRV   85 (198)
T ss_pred             HCCCCEEEEEECCCCCCHHHHHHHHHHHHHHCCCCEEEECH---------HHHHHHHCCCC-----CCCHHHHHHHHHHH
T ss_conf             68998699987999998899999999999975997599777---------99987436678-----98999999999999


Q ss_pred             H
Q ss_conf             7
Q gi|254780619|r  294 A  294 (731)
Q Consensus       294 ~  294 (731)
                      .
T Consensus        86 ~   86 (198)
T PRK03846         86 G   86 (198)
T ss_pred             H
T ss_conf             9


No 369
>KOG0923 consensus
Probab=90.33  E-value=0.44  Score=27.41  Aligned_cols=138  Identities=25%  Similarity=0.347  Sum_probs=67.5

Q ss_pred             CCEEEEECCCCHHHHHHHHH-HHHHHHHC-CCCEEEEECCCHHHHHHHHHHHCCCCCEEEEEECCCCCHHHHHHHHHHHC
Q ss_conf             96199844753157999999-99998514-68479971521001344555430389768996235572356678999971
Q gi|254780619|r  218 FAVSLISGVTGSGKTEVYLE-IVAAVLHL-GKQVLILLPEISLTSAILERFQKRFGVKPAEWHSSLSTSMREKIWRQVAR  295 (731)
Q Consensus       218 f~~~LL~GvTGSGKTEVYl~-li~~~L~~-GkqvLiLvPEI~Lt~Q~~~rl~~rF~~~v~v~HS~ls~~eR~~~w~~i~~  295 (731)
                      .++.++-|.||||||-=-=+ +.+.-+.. |+-+-.--|-=.-+--..+|..+-.|.+..   -..+=+-|++   ...+
T Consensus       280 ~QVLiI~GeTGSGKTTQiPQyL~EaGytk~gk~IgcTQPRRVAAmSVAaRVA~EMgvkLG---~eVGYsIRFE---dcTS  353 (902)
T KOG0923         280 HQVLIIVGETGSGKTTQIPQYLYEAGYTKGGKKIGCTQPRRVAAMSVAARVAEEMGVKLG---HEVGYSIRFE---DCTS  353 (902)
T ss_pred             CCEEEEECCCCCCCCCCCCHHHHHCCCCCCCCEEEECCCCHHHHHHHHHHHHHHHCCCCC---CCCCEEEEEC---CCCC
T ss_conf             708999757889864456289885421358946740685068877799999998574014---3144488850---3567


Q ss_pred             CCCEEEEECCHHH---HHHHCCC---EEEEEEECCCCCCHHCCCCCC-CHHHHHHHHHHHCCCCEECCCCCCCHHHHH
Q ss_conf             9973999400121---1001000---136774055321000024432-248999997511032100002454324677
Q gi|254780619|r  296 GAISVIVGVRSAL---FLPFKKL---GLIVIDEEHDISYKQEEGILY-NARDMSIVRGKIESFPVVLVSATPSIESRV  366 (731)
Q Consensus       296 G~~~IVIGtRSAi---f~P~~nL---glIIvDEEHd~sykq~~~pry-~aRdvA~~Ra~~~~~~lilgSATPSles~~  366 (731)
                      .+..|=.=|-.-+   |+-=++|   ..|||||-|+-...-|  .-| -..|+|.+|   -.-.|++.|||--.|-+.
T Consensus       354 ekTvlKYMTDGmLlREfL~epdLasYSViiiDEAHERTL~TD--ILfgLvKDIar~R---pdLKllIsSAT~DAekFS  426 (902)
T KOG0923         354 EKTVLKYMTDGMLLREFLSEPDLASYSVIIVDEAHERTLHTD--ILFGLVKDIARFR---PDLKLLISSATMDAEKFS  426 (902)
T ss_pred             CCEEEEEECCHHHHHHHHCCCCCCCEEEEEEEHHHHHHHHHH--HHHHHHHHHHHHC---CCCEEEEECCCCCHHHHH
T ss_conf             412243224306799871463422335999602432003456--7999878887508---760477322226789998


No 370
>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=90.32  E-value=1.4  Score=23.44  Aligned_cols=67  Identities=33%  Similarity=0.275  Sum_probs=51.9

Q ss_pred             CHHHHHHHHHHHHHHCCC-CCEEEEECCCCHHHHHHHHHHHHHHHH-CCCCEEEEECCCHHHHHHHHHH
Q ss_conf             837899999998752048-961998447531579999999999851-4684799715210013445554
Q gi|254780619|r  200 DKNQQDVVEQVVPLCTKG-FAVSLISGVTGSGKTEVYLEIVAAVLH-LGKQVLILLPEISLTSAILERF  266 (731)
Q Consensus       200 t~eQ~~a~~~i~~~~~~~-f~~~LL~GvTGSGKTEVYl~li~~~L~-~GkqvLiLvPEI~Lt~Q~~~rl  266 (731)
                      -++|..-.+.+......| -...||.--||+|||-=||=.|...=. .+++|+|=++.|-|=.|++++-
T Consensus       262 R~~Q~~la~~v~~~l~~Gt~~~~lIEA~tG~GKtlgYLLPal~~~~~~~~~vviST~Tk~LQ~QL~E~d  330 (944)
T TIGR01407       262 REEQLKLAELVEDELTHGTEEKSLIEAPTGTGKTLGYLLPALYLAKEEEKPVVISTATKVLQSQLLEKD  330 (944)
T ss_pred             HHHHHHHHHHHHHHHCCCCCHHHHEECCCCCCHHHHHHHHHHHHCCCCCCCEEEEECCHHHHHHHHHHH
T ss_conf             388999999999984157661133023766432589999999731378885699836366565656888


No 371
>PRK09194 prolyl-tRNA synthetase; Provisional
Probab=90.31  E-value=0.42  Score=27.57  Aligned_cols=18  Identities=28%  Similarity=0.479  Sum_probs=9.6

Q ss_pred             ECCCCCCHHHHHHHHHHC
Q ss_conf             001354289988885204
Q gi|254780619|r  488 MIACGFGIERIAEEVCEY  505 (731)
Q Consensus       488 l~~~G~Gte~~~e~l~~~  505 (731)
                      +--+|.|+.|+-.-+-+.
T Consensus       440 MGCYGIGVsRllaAiiEq  457 (570)
T PRK09194        440 MGCYGIGVSRLVAAAIEQ  457 (570)
T ss_pred             EEEEECCHHHHHHHHHHH
T ss_conf             562002467899999998


No 372
>TIGR03346 chaperone_ClpB ATP-dependent chaperone ClpB. Members of this protein family are the bacterial ATP-dependent chaperone ClpB. This protein belongs to the AAA family, ATPases associated with various cellular activities (pfam00004). This molecular chaperone does not act as a protease, but rather serves to disaggregate misfolded and aggregated proteins.
Probab=90.20  E-value=0.74  Score=25.67  Aligned_cols=174  Identities=18%  Similarity=0.193  Sum_probs=89.4

Q ss_pred             CCEECHHHCCCCCCCCCCCCCCCCEECCCCCCHHHHHHHHHH-CCCC-CHHHHCCCCCCCCHHHHHHHHHHHCCCCCCEE
Q ss_conf             320000210244655566678741100135428998888520-4852-00010232113586789999986212576579
Q gi|254780619|r  463 KLYCHQCGHSAIYSQSCVVCGSSGKMIACGFGIERIAEEVCE-YFPL-ARISILSSDLEGGGGRLQLQLSAIAKGEIDII  540 (731)
Q Consensus       463 ~l~Ch~Cg~~~~~~~~Cp~Cg~~~~l~~~G~Gte~~~e~l~~-~fp~-~~v~~~d~d~~~~~~~~~~~~~~~~~~~~~il  540 (731)
                      .+++..-|-.-+   .=|- ||...+-+-|.|-..+...|.+ +|.+ ..++|+|..--..            .+...-|
T Consensus       580 aI~~sraGL~dp---~rP~-GsFlf~GptGvGKTELAKaLAe~Lfg~~~~LIriDMSEy~E------------~hsvsrL  643 (852)
T TIGR03346       580 AIRRSRAGLSDP---NRPI-GSFLFLGPTGVGKTELAKALAEFLFDDEDAMVRIDMSEYME------------KHSVARL  643 (852)
T ss_pred             HHHHHHCCCCCC---CCCC-EEEEEECCCCCCHHHHHHHHHHHHHCCCCCEEEECHHHHCC------------HHHHHHH
T ss_conf             999997188889---9974-58998678877689999999999855852069843044301------------2247785


Q ss_pred             EEEHHHCCCCCCCCC---------CHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHH--HCC----CCC-CCCCEEEEEEC
Q ss_conf             870443023113452---------01233000344310245-57899999875431--102----566-78868999932
Q gi|254780619|r  541 IGTQLVAKGHNFPRM---------SLVGVVDGDLGLTNADL-RSSERTFQLLSQVT--GRA----GRF-GLKSLGLIQAY  603 (731)
Q Consensus       541 vgTq~i~kg~~fp~v---------~lv~il~aD~~l~~pd~-ra~E~~~qll~qv~--gRa----gr~-~~~g~v~iQt~  603 (731)
                      ||+.-=--||+-.+.         --|+++|        .+ .|.-..|.+|.|+.  ||-    ||- +-...+||-|.
T Consensus       644 iGaPPGYVGy~egG~Lte~vr~~PysVvL~D--------EIEKAh~~V~~~lLQilD~G~ltD~~Gr~vdF~NtiiimTS  715 (852)
T TIGR03346       644 IGAPPGYVGYEEGGQLTEAVRRKPYSVVLFD--------EVEKAHPDVFNVLLQVLDDGRLTDGQGRTVDFRNTVIIMTS  715 (852)
T ss_pred             CCCCCCCCCCCCCCEECHHHHHCCCEEEEEC--------CHHHHCHHHHHHHHHHHCCCEEECCCCCEEEEEEEEEEEEC
T ss_conf             5899976776878742398981988799853--------05430768999999882367430799988853556898615


Q ss_pred             CCCCHHHHHHH-HCCHHHHHHHHHHHHHHCCCCCCH-HE-EEEEEECCCHHHHHHHHHHH
Q ss_conf             98648889999-589799999999999981888801-18-99988459989999999999
Q gi|254780619|r  604 QPTHPVMQALV-SGDADSFYESEIRARESVNLPPFG-RL-AAVIISGTKYQEVENYAYNL  660 (731)
Q Consensus       604 ~p~~~~~~~~~-~~d~~~f~~~el~~R~~~~~PPf~-~~-~~i~~~~~~~~~~~~~~~~~  660 (731)
                      |-....+.... ..+++..-+.-.++=+...=|-|- |+ ..|.|..-+.+.+.+++...
T Consensus       716 N~Ga~~i~~~~~~~~~~~~~~~~~~~~~~~F~PEflnRid~ii~F~~L~~~~l~~I~~~~  775 (852)
T TIGR03346       716 NLGSQFIQELAGGDDYEEMREAVMEVLRAHFRPEFLNRIDEIVVFHPLGREQIARIVEIQ  775 (852)
T ss_pred             CCCHHHHHHHCCCCCHHHHHHHHHHHHHHHCCHHHHHHCCEEEEECCCCHHHHHHHHHHH
T ss_conf             406599974114555799999999999965899899637868983789999999999999


No 373
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=90.13  E-value=0.21  Score=29.86  Aligned_cols=35  Identities=17%  Similarity=0.481  Sum_probs=25.1

Q ss_pred             CCEEEEECCCCCCEECHHHCCCCC----CCCCCCCCCCC
Q ss_conf             520121135783200002102446----55566678741
Q gi|254780619|r  452 SCWLVEHRSKKKLYCHQCGHSAIY----SQSCVVCGSSG  486 (731)
Q Consensus       452 ~~~l~~h~~~~~l~Ch~Cg~~~~~----~~~Cp~Cg~~~  486 (731)
                      +.-|..+.-.-..+|+.||.....    ...||.|||..
T Consensus        59 gA~L~Ie~vp~~~~C~~C~~~~~~~~~~~~~CP~Cgs~~   97 (114)
T PRK03681         59 GCKLHLEEQEAECWCETCQQYVTLLTQRVRRCPQCHGDM   97 (114)
T ss_pred             CCEEEEEECCCEEECCCCCCEEEECCCCCCCCCCCCCCC
T ss_conf             979999952858996559985540677677390883997


No 374
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=90.12  E-value=0.13  Score=31.40  Aligned_cols=35  Identities=17%  Similarity=0.379  Sum_probs=21.0

Q ss_pred             CCCCCCCCCCEEEEECCCCCCEECHHHCCCCCCCCC
Q ss_conf             343101465201211357832000021024465556
Q gi|254780619|r  444 NRLKCLHCSCWLVEHRSKKKLYCHQCGHSAIYSQSC  479 (731)
Q Consensus       444 ~~~~C~~C~~~l~~h~~~~~l~Ch~Cg~~~~~~~~C  479 (731)
                      ..++||.|+..|-= +..+-++|..||++.+-...+
T Consensus       349 ~~p~Cp~Cg~~m~S-~G~~g~rC~kCg~~~~~~~~~  383 (421)
T COG1571         349 VNPVCPRCGGRMKS-AGRNGFRCKKCGTRARETLIK  383 (421)
T ss_pred             CCCCCCCCCCCHHH-CCCCCCCCCCCCCCCCCCCCC
T ss_conf             17889766771311-678985266426617755323


No 375
>cd01675 RNR_III Class III ribonucleotide reductase. Ribonucleotide reductase (RNR) catalyzes the reductive synthesis of deoxyribonucleotides from their corresponding ribonucleotides. It provides the precursors necessary for DNA synthesis. RNRs are separated into three classes based on their metallocofactor usage. Class I RNRs, found in eukaryotes, bacteria, and bacteriophage, use a diiron-tyrosyl radical. Class II RNRs, found in bacteria, bacteriophage, algae and archaea, use coenzyme B12 (adenosylcobalamin, AdoCbl). Class III RNRs, found in strict or facultative anaerobic bacteria, bacteriophage, and archaea, use an FeS cluster and S-adenosylmethionine to generate a glycyl radical. Many organisms have more than one class of RNR present in their genomes. All three RNRs have a ten-stranded alpha-beta barrel domain that is structurally similar to the domain of PFL (pyruvate formate lyase). The class III enzyme from phage T4 consists of two subunits, this model covers the larger subunit w
Probab=89.96  E-value=0.13  Score=31.34  Aligned_cols=35  Identities=11%  Similarity=0.051  Sum_probs=16.5

Q ss_pred             CCHHHHHHHHHHHCCCCEEEEECCHHHHHHHCCCEEEE
Q ss_conf             72356678999971997399940012110010001367
Q gi|254780619|r  282 STSMREKIWRQVARGAISVIVGVRSALFLPFKKLGLIV  319 (731)
Q Consensus       282 s~~eR~~~w~~i~~G~~~IVIGtRSAif~P~~nLglII  319 (731)
                      +.++-++.++...-+   +=.=+|+.-=.||.|+.+-.
T Consensus       130 ~~~ei~q~~Q~fvy~---lN~~sr~g~Q~PFtni~~~~  164 (555)
T cd01675         130 TRKEIKQAMQGFIYN---LNTLSRRGGQTPFTNITLGL  164 (555)
T ss_pred             HHHHHHHHHHHEEEE---EECCCCCCCCCCCEEEEECC
T ss_conf             299999998760675---31133356877735899725


No 376
>PRK04011 peptide chain release factor 1; Provisional
Probab=89.94  E-value=1.5  Score=23.22  Aligned_cols=89  Identities=19%  Similarity=0.259  Sum_probs=42.7

Q ss_pred             HHHHHHHHCCCC--EEEEEECCCCEEHHCCCCCCCCCCCCCCCCCEEEEECCCCCCEECHHHCCCCCCCCCCCCCCCCEE
Q ss_conf             999988622655--179974222000000235654343101465201211357832000021024465556667874110
Q gi|254780619|r  411 IDGIRHTLARNE--QTLLFLNRRGYAPLTLCQVCGNRLKCLHCSCWLVEHRSKKKLYCHQCGHSAIYSQSCVVCGSSGKM  488 (731)
Q Consensus       411 ~~~i~~~l~~g~--qvll~lnRrGya~~~~C~~Cg~~~~C~~C~~~l~~h~~~~~l~Ch~Cg~~~~~~~~Cp~Cg~~~~l  488 (731)
                      .+.++++|+.|-  ..|+.=|=+..--.+.|.+|++..         ....+.+.          .....||.||+...+
T Consensus       300 ~~et~~ALe~GAVetLLisE~L~~~R~~~~c~~c~~~~---------~~~~~~~~----------~~~~~cp~cg~~~~~  360 (409)
T PRK04011        300 EEEVRKALEMGAVDTLLISEDLRKVRVTYKCNNCGYEE---------EKTVKEEE----------PKTGTCPKCGSALEI  360 (409)
T ss_pred             HHHHHHHHHCCCCEEEEEECCCCCEEEEEECCCCCCEE---------EEECCCCC----------CCCCCCCCCCCCCEE
T ss_conf             99999998759750899973653016899759987178---------87215332----------234689755751024


Q ss_pred             CCCCCCHHHHHHHHHHCCCCCHHHHCCCCCCC
Q ss_conf             01354289988885204852000102321135
Q gi|254780619|r  489 IACGFGIERIAEEVCEYFPLARISILSSDLEG  520 (731)
Q Consensus       489 ~~~G~Gte~~~e~l~~~fp~~~v~~~d~d~~~  520 (731)
                      ...-.=+|++.+.-++ | +++|..++.|+..
T Consensus       361 ~e~~dliE~L~e~a~~-~-Ga~ve~IS~~seE  390 (409)
T PRK04011        361 EEEEDIVEELSELAEE-S-GTKVEVISTDTEE  390 (409)
T ss_pred             EECCCHHHHHHHHHHH-C-CCEEEEECCCCHH
T ss_conf             3237489999999997-3-9889998599752


No 377
>KOG4150 consensus
Probab=89.86  E-value=0.89  Score=25.05  Aligned_cols=68  Identities=29%  Similarity=0.294  Sum_probs=46.2

Q ss_pred             HHHHHHHCCCCCCEEEEEHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCE-EEEEECC
Q ss_conf             999986212576579870443023113452012330003443102455789999987543110256678868-9999329
Q gi|254780619|r  526 QLQLSAIAKGEIDIIIGTQLVAKGHNFPRMSLVGVVDGDLGLTNADLRSSERTFQLLSQVTGRAGRFGLKSL-GLIQAYQ  604 (731)
Q Consensus       526 ~~~~~~~~~~~~~ilvgTq~i~kg~~fp~v~lv~il~aD~~l~~pd~ra~E~~~qll~qv~gRagr~~~~g~-v~iQt~~  604 (731)
                      .++-.++-.|+..=+|.|-.+.-|.|.      |-|||-..+..|-      ..+-++|-+|||||..++.. |+|....
T Consensus       573 RKIE~~~F~G~L~giIaTNALELGIDI------G~LDAVl~~GFP~------S~aNl~QQ~GRAGRRNk~SLavyva~~~  640 (1034)
T KOG4150         573 RKIESDLFGGKLCGIIATNALELGIDI------GHLDAVLHLGFPG------SIANLWQQAGRAGRRNKPSLAVYVAFLG  640 (1034)
T ss_pred             HHHHHHHHCCEEEEEEECCHHHHCCCC------CCCCEEEECCCCC------HHHHHHHHHHHCCCCCCCCEEEEEEECC
T ss_conf             777888517826899853607444243------5643689826850------6778998721101568984489997427


Q ss_pred             C
Q ss_conf             8
Q gi|254780619|r  605 P  605 (731)
Q Consensus       605 p  605 (731)
                      |
T Consensus       641 P  641 (1034)
T KOG4150         641 P  641 (1034)
T ss_pred             C
T ss_conf             6


No 378
>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=89.78  E-value=1.2  Score=23.95  Aligned_cols=38  Identities=29%  Similarity=0.456  Sum_probs=31.9

Q ss_pred             CCEEEEECCCCHHHHHHHHHHHHHHHHCCCCEEEEECCC
Q ss_conf             961998447531579999999999851468479971521
Q gi|254780619|r  218 FAVSLISGVTGSGKTEVYLEIVAAVLHLGKQVLILLPEI  256 (731)
Q Consensus       218 f~~~LL~GvTGSGKTEVYl~li~~~L~~GkqvLiLvPEI  256 (731)
                      -.-++|+|..|||||-.-.+++.-+..+| -+++-+|+.
T Consensus        23 ~~r~vL~G~~GsGKS~~L~q~v~~A~~~~-wiVl~vP~~   60 (274)
T pfam10236        23 VVRFVLTGERGSGKSVLLAQAMAYALTQG-WVVLHVPEA   60 (274)
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHHHHHCC-EEEEECCCH
T ss_conf             51899889799779999999999998599-899984988


No 379
>COG2835 Uncharacterized conserved protein [Function unknown]
Probab=89.75  E-value=0.18  Score=30.27  Aligned_cols=34  Identities=26%  Similarity=0.447  Sum_probs=29.5

Q ss_pred             CCCCCCCCCCEEEEECCCCCCEECHHHCCCCCCC
Q ss_conf             3431014652012113578320000210244655
Q gi|254780619|r  444 NRLKCLHCSCWLVEHRSKKKLYCHQCGHSAIYSQ  477 (731)
Q Consensus       444 ~~~~C~~C~~~l~~h~~~~~l~Ch~Cg~~~~~~~  477 (731)
                      ++.-||-|.++|.|++.++.|.|+.|+-.+++-+
T Consensus         7 eiLaCP~~kg~L~~~~~~~~L~c~~~~~aYpI~d   40 (60)
T COG2835           7 EILACPVCKGPLVYDEEKQELICPRCKLAYPIRD   40 (60)
T ss_pred             EEEECCCCCCCCEEECCCCEEEECCCCCEEECCC
T ss_conf             1466667589506815689897153481313346


No 380
>PRK05333 NAD-dependent deacetylase; Provisional
Probab=89.75  E-value=0.45  Score=27.31  Aligned_cols=17  Identities=29%  Similarity=0.473  Sum_probs=11.8

Q ss_pred             CCEEHHCCCCCCCCCCC
Q ss_conf             20000002356543431
Q gi|254780619|r  431 RGYAPLTLCQVCGNRLK  447 (731)
Q Consensus       431 rGya~~~~C~~Cg~~~~  447 (731)
                      -|-.....|.+||+...
T Consensus       123 HGsl~~~~C~~C~~~~~  139 (285)
T PRK05333        123 HGRLDGVRCMGCGARHP  139 (285)
T ss_pred             ECCEEEEEECCCCCCCC
T ss_conf             36576589899998365


No 381
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=89.74  E-value=0.25  Score=29.31  Aligned_cols=35  Identities=17%  Similarity=0.414  Sum_probs=22.5

Q ss_pred             CCEEEEECCCCCCEECHHHCCCCCC---CCCCCCCCCC
Q ss_conf             5201211357832000021024465---5566678741
Q gi|254780619|r  452 SCWLVEHRSKKKLYCHQCGHSAIYS---QSCVVCGSSG  486 (731)
Q Consensus       452 ~~~l~~h~~~~~l~Ch~Cg~~~~~~---~~Cp~Cg~~~  486 (731)
                      +.-|..+.-.-..+|..||....+.   ..||.|||..
T Consensus        59 gA~L~I~~~p~~~~C~~C~~~~~~~~~~~~CP~Cgs~~   96 (113)
T PRK12380         59 GCDLHIVYKPAQAWCWDCSQVVEIHQHDAQCPHCHGER   96 (113)
T ss_pred             CCEEEEEECCCEEECCCCCCEEECCCCCCCCCCCCCCC
T ss_conf             98999995485799655999872478888390697996


No 382
>cd01129 PulE-GspE PulE/GspE The type II secretory pathway is the main terminal branch of the general secretory pathway (GSP).  It is responsible for the export the majority of Gram-negative bacterial exoenzymes and toxins. PulE is a cytoplasmic protein of the GSP, which contains an ATP binding site and a tetracysteine motif. This subgroup also includes PillB and HofB.
Probab=89.74  E-value=1.3  Score=23.86  Aligned_cols=51  Identities=22%  Similarity=0.420  Sum_probs=31.3

Q ss_pred             CCHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHHHHHHHHHHCCCCEEEE
Q ss_conf             883789999999875204896199844753157999999999985146847997
Q gi|254780619|r  199 LDKNQQDVVEQVVPLCTKGFAVSLISGVTGSGKTEVYLEIVAAVLHLGKQVLIL  252 (731)
Q Consensus       199 Lt~eQ~~a~~~i~~~~~~~f~~~LL~GvTGSGKTEVYl~li~~~L~~GkqvLiL  252 (731)
                      ++++|...+..+.   .......|+-|-||||||--.-.++.+.-..++.++-+
T Consensus        64 ~~~~~~~~l~~~~---~~~~GlilitGptGSGKtTtl~a~l~~~~~~~~~i~ti  114 (264)
T cd01129          64 LKPENLEIFRKLL---EKPHGIILVTGPTGSGKTTTLYSALSELNTPEKNIITV  114 (264)
T ss_pred             CCHHHHHHHHHHH---HCCCCEEEEECCCCCCHHHHHHHHHHHHCCCCCEEEEE
T ss_conf             9999999999997---08998899978999977999999998643688508998


No 383
>PRK09302 circadian clock protein KaiC; Reviewed
Probab=89.72  E-value=0.7  Score=25.85  Aligned_cols=167  Identities=20%  Similarity=0.174  Sum_probs=78.6

Q ss_pred             CCEEEEECCCCHHHHHHHHHHHHHHHHC-CCCEEEEECCCHHHHHHHHHHHCCCCC---------EEEEEECCCCCHHHH
Q ss_conf             9619984475315799999999998514-684799715210013445554303897---------689962355723566
Q gi|254780619|r  218 FAVSLISGVTGSGKTEVYLEIVAAVLHL-GKQVLILLPEISLTSAILERFQKRFGV---------KPAEWHSSLSTSMRE  287 (731)
Q Consensus       218 f~~~LL~GvTGSGKTEVYl~li~~~L~~-GkqvLiLvPEI~Lt~Q~~~rl~~rF~~---------~v~v~HS~ls~~eR~  287 (731)
                      .+++|+.|..|||||-.-++.+-+-+++ |..+|+..=  +-++.-+.+.-+.||.         .+.+.|-....++..
T Consensus        24 g~~~LV~G~pGsGKTtla~QfL~~Ga~~~GE~~lyitl--~E~~~~l~~~~~~~g~~~~~~~~~~~l~i~d~~~~~~~~~  101 (501)
T PRK09302         24 GRPTLVSGTAGTGKTLFALQFLHNGIKSFGEPGVFVTF--EESPEDIIRNVASFGWDLQKLIDEGKLFILDASPDPSEQE  101 (501)
T ss_pred             CCEEEEEECCCCCHHHHHHHHHHHHHHHCCCCEEEEEC--CCCHHHHHHHHHHCCCCHHHHHHCCCEEEEECCCCCCCCC
T ss_conf             97799983899999999999999998855997899985--7999999999998499868973268389996156743111


Q ss_pred             HHHHHHHCCCCEEEEECCHHHHH------HHCCCEEEEEEECCC--CCCHHCCCCCCCHHHHHHHHHHHCCCCEECCCCC
Q ss_conf             78999971997399940012110------010001367740553--2100002443224899999751103210000245
Q gi|254780619|r  288 KIWRQVARGAISVIVGVRSALFL------PFKKLGLIVIDEEHD--ISYKQEEGILYNARDMSIVRGKIESFPVVLVSAT  359 (731)
Q Consensus       288 ~~w~~i~~G~~~IVIGtRSAif~------P~~nLglIIvDEEHd--~sykq~~~pry~aRdvA~~Ra~~~~~~lilgSAT  359 (731)
                      .      .|+.++     ++++.      --.+...||||==-.  ..+......|....++..+.+ ..+|.+++.|..
T Consensus       102 ~------~~~~dL-----~~l~~~I~~~v~~~~~~RvViDSlt~l~~~~~~~~~~R~~l~~L~~~l~-~~g~T~llt~E~  169 (501)
T PRK09302        102 E------AGEYDL-----SALIERIEYAIRKIKAKRVVIDSIEALFQQYDNPAVVRRELFRLFAWLK-QKGVTAVMTGER  169 (501)
T ss_pred             C------CCCCCH-----HHHHHHHHHHHHHHCCCEEEECCHHHHHHHCCCHHHHHHHHHHHHHHHH-HCCCEEEEEECC
T ss_conf             3------344768-----9999999999997199999999978998763587899999999999998-779779998756


Q ss_pred             CC---------HHHHHHHHHHHHHHHCCCCCCC-CCCCCCCEECCCCCCCCCCC
Q ss_conf             43---------2467753212344412432236-76543321102222332224
Q gi|254780619|r  360 PS---------IESRVNGISRRYHSVHLSTRYR-NSALPHLQVIDMRGQTIAQG  403 (731)
Q Consensus       360 PS---------les~~~~~~g~~~~~~l~~R~~-~~~~P~i~ivDm~~~~~~~~  403 (731)
                      +.         +|.|  +-.|..   .|..+.. +...=.++|+-||......|
T Consensus       170 ~~~~~~~~~~g~Ee~--vaDGVI---~L~~~~~~~~~~R~L~V~KmRGs~~~~g  218 (501)
T PRK09302        170 GDEYGPIARYGVEEF--VSDCVV---ILRNVLEGEKRTRTLEILKYRGTTHGKG  218 (501)
T ss_pred             CCCCCCCCCCCHHHH--HCCEEE---EEEEECCCCCCEEEEEEEECCCCCCCCC
T ss_conf             666787543452442--013078---8765414885258999998358866687


No 384
>TIGR02773 addB_Gpos ATP-dependent nuclease subunit B; InterPro: IPR014140   DNA repair is accomplished by several different systems in prokaryotes. Recombinational repair of double-stranded DNA breaks involves the RecBCD pathway in some lineages, and AddAB (also called RexAB) in others. AddA is conserved between the firmicutes and the alphaproteobacteria, while its partner protein (RexB) is not. This entry describes the ATP-dependent nuclease subunit B (AddB/RexB) protein as found Bacillus subtilis and related species. Although the RexB protein of Streptococcus and Lactococcus is considered to be orthologous and functionally equivalent, merely named differently, all members of this protein family have a P-loop nucleotide binding motif GxxGxGK[ST] at the N-terminus, unlike RexB proteins, and a CxxCxxxxxC motif at the C-terminus, both of which may be relevant to function..
Probab=89.62  E-value=0.6  Score=26.38  Aligned_cols=146  Identities=14%  Similarity=0.137  Sum_probs=70.7

Q ss_pred             HHHHHHHHHHHHHHH--HH-----------HHHHHHH------HHHCC---CCCCCCCEEEEEECCCCCHHHHHHHH---
Q ss_conf             000344310245578--99-----------9998754------31102---56678868999932986488899995---
Q gi|254780619|r  561 VDGDLGLTNADLRSS--ER-----------TFQLLSQ------VTGRA---GRFGLKSLGLIQAYQPTHPVMQALVS---  615 (731)
Q Consensus       561 l~aD~~l~~pd~ra~--E~-----------~~qll~q------v~gRa---gr~~~~g~v~iQt~~p~~~~~~~~~~---  615 (731)
                      .+-.+.|.+=||.|+  -+           ..|||+=      =|-+-   |..-.||=|+-  |+-++|.+++=..   
T Consensus       967 ~e~~~ylRIIDYKSsnPsk~LDL~~VYYGl~LQmLtYLD~~l~~s~~~~~lg~~a~PaGvLY--Fhihdp~~~a~~~Gel 1044 (1192)
T TIGR02773       967 KEDETYLRIIDYKSSNPSKKLDLTEVYYGLALQMLTYLDIVLTNSEKWLKLGNQAKPAGVLY--FHIHDPIVSAKKDGEL 1044 (1192)
T ss_pred             CCCCEEEEEEEECCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCEEEE--EEECCCEEEECCCCCC
T ss_conf             58981488887037888735435776668999999999999985899997106547760455--6643723300788765


Q ss_pred             ----CCHHHHHHHHHHHHHHCCCCCCHHEEEEEEECCCHHHHHHHHHHHHHHCCCCCCCEEECCCCCHHHHHCCEEEE-E
Q ss_conf             ----89799999999999981888801189998845998999999999998573438849981767526885882379-9
Q gi|254780619|r  616 ----GDADSFYESEIRARESVNLPPFGRLAAVIISGTKYQEVENYAYNLKEHAPRSSDIVVFGPAESPLFMVRGRYRF-R  690 (731)
Q Consensus       616 ----~d~~~f~~~el~~R~~~~~PPf~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~GP~~~~~~k~~~~~r~-~  690 (731)
                          =.-+...+.-+++=|.-|+         ..+.  . +|.+......+... .++  |   +||.+-|-.+-+.. .
T Consensus      1045 eDDaLt~e~i~~E~~K~~Kl~GL---------lL~d--~-~vV~~MD~~LE~G~-~S~--I---vPA~lKKdG~l~~~Gs 1106 (1192)
T TIGR02773      1045 EDDALTEEEIEKELLKEYKLKGL---------LLSD--L-DVVKLMDTTLEEGK-SSN--I---VPASLKKDGSLGSRGS 1106 (1192)
T ss_pred             CCCCCCHHHHHHHHHHHHHHCCC---------CCCC--H-HHHHHHHHHCCCCC-CCC--E---EECCCCCCCCCCCCCC
T ss_conf             30247888999998777643055---------3677--8-99999763035786-334--4---7142145856564642


Q ss_pred             EEEECCCHHHHHHHHHHHHHH-HHHCCCCCEEEEEECCHH
Q ss_conf             999809938999999999986-421037868999706802
Q gi|254780619|r  691 LLIHGKRNSNLQGFFSQMYDN-TIKRSNALRVQFDIDPQN  729 (731)
Q Consensus       691 ~~ik~~~~~~l~~~l~~~~~~-~~~~~~~~~~~iDvDP~~  729 (731)
                      =++--..-..|.+.++....+ ..+.-.|   .|||+|.-
T Consensus      1107 ~~~~~~~Fe~l~khv~~~~~~~g~~i~~G---~v~i~PyK 1143 (1192)
T TIGR02773      1107 KVATEEEFELLRKHVKKKFKEAGENILEG---KVSIEPYK 1143 (1192)
T ss_pred             CCCCHHHHHHHHHHHHHHHHHHHHHHCCC---CEEECCCC
T ss_conf             00367889999999988999998765079---40013565


No 385
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=89.59  E-value=1.4  Score=23.54  Aligned_cols=97  Identities=19%  Similarity=0.175  Sum_probs=56.9

Q ss_pred             CCCHHHHHHHHHHHCCCCCCHHHHHHHHCCCHHHH----HHHHHCCHHHHHHHHHCCCCCCCCC-CCCCCCCCHHHHHHH
Q ss_conf             58688999999988098878788887709998999----7524557223445541023566543-446666883789999
Q gi|254780619|r  133 INTVARLRVLDKIKDGKIWEKRDLIRASQVSSHVI----DGLKAQGVIKQIFEVISPVVDSPNL-YFSLPILDKNQQDVV  207 (731)
Q Consensus       133 ~~~~~~~~~l~~l~~~~~~~~~el~~~~~~s~~~i----~~L~~kglI~~~~~~~~~~~~~~~~-~~~~~~Lt~eQ~~a~  207 (731)
                      .......+++..|.+++..+..++.+..++|.+.+    +.|.+.|+|+...-..+|..-.... ..-...+.......+
T Consensus        11 ~LD~~D~~IL~~Lq~daR~s~~eLA~~vglS~stv~~RikrLe~~GiI~gy~a~id~~~lG~~~~a~v~i~l~~~~~~~~   90 (164)
T PRK11169         11 DLDRIDRNILNELQKDGRISNVELSKRVGLSPTPCLERVRRLERQGFIQGYTALLNPHYLDASLLVFVEITLNRGAPDVF   90 (164)
T ss_pred             CHHHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEEEEEECCCCCCCCEEEEEEEEECCCCHHHH
T ss_conf             55199999999999848999999999989299999999999997898866899976000798749999999658886899


Q ss_pred             HHHHHHHCCCCCEEEEECCCCH
Q ss_conf             9998752048961998447531
Q gi|254780619|r  208 EQVVPLCTKGFAVSLISGVTGS  229 (731)
Q Consensus       208 ~~i~~~~~~~f~~~LL~GvTGS  229 (731)
                      +++......-..+.-.|-+||+
T Consensus        91 ~~~~~~l~~~peV~~~~~vtG~  112 (164)
T PRK11169         91 EQFNAAVQKLEEIQECHLVSGD  112 (164)
T ss_pred             HHHHHHHHCCCCEEEEEEEECC
T ss_conf             9999998429978999983077


No 386
>PRK09001 DNA topoisomerase I; Validated
Probab=89.58  E-value=0.31  Score=28.55  Aligned_cols=12  Identities=33%  Similarity=0.717  Sum_probs=5.1

Q ss_pred             CCCCCCCCEECC
Q ss_conf             666787411001
Q gi|254780619|r  479 CVVCGSSGKMIA  490 (731)
Q Consensus       479 Cp~Cg~~~~l~~  490 (731)
                      |+.||+.+.++.
T Consensus       716 C~kCg~~m~lk~  727 (869)
T PRK09001        716 CDKCGSEMHLKT  727 (869)
T ss_pred             CCCCCCCCEEEC
T ss_conf             655798545503


No 387
>KOG2324 consensus
Probab=89.54  E-value=0.41  Score=27.58  Aligned_cols=158  Identities=17%  Similarity=0.209  Sum_probs=68.3

Q ss_pred             CHHCCCCCC---CHHHHHHHHHHHCCCCEECCCCCCCHHHHHHHHHHHHHHHCCCCCCCCCCCCCCEECCCCCCCCCCCC
Q ss_conf             000024432---24899999751103210000245432467753212344412432236765433211022223322245
Q gi|254780619|r  328 YKQEEGILY---NARDMSIVRGKIESFPVVLVSATPSIESRVNGISRRYHSVHLSTRYRNSALPHLQVIDMRGQTIAQGK  404 (731)
Q Consensus       328 ykq~~~pry---~aRdvA~~Ra~~~~~~lilgSATPSles~~~~~~g~~~~~~l~~R~~~~~~P~i~ivDm~~~~~~~~~  404 (731)
                      |+-+-.||+   -+|+..+.-..-..     .++--+.+||..+..- |..+     +..-.+|-|.+-   ...-.-|.
T Consensus       145 fRDElrpRfGLlRgREFlMKDmYsFd-----~~~etA~qTy~~v~~a-Y~~i-----FkqL~~pfVkv~---AdsG~iGG  210 (457)
T KOG2324         145 FRDELRPRFGLLRGREFLMKDMYSFD-----SDEETAQQTYQLVDQA-YDRI-----FKQLGLPFVKVW---ADSGDIGG  210 (457)
T ss_pred             HHHCCCCCCCCHHHHHHHHHHHHCCC-----CCHHHHHHHHHHHHHH-HHHH-----HHHCCCCEEEEE---ECCCCCCC
T ss_conf             44134754230124788876533025-----8888999999999999-9999-----997399769986---03566476


Q ss_pred             CCCHHHHHHHHHHHCCCCEEEEEECCCCEEHHCCCCCCCCC-----------CCCCCCCC-EEEEECCCCCCEECHHHCC
Q ss_conf             47989999998862265517997422200000023565434-----------31014652-0121135783200002102
Q gi|254780619|r  405 SLSPEMIDGIRHTLARNEQTLLFLNRRGYAPLTLCQVCGNR-----------LKCLHCSC-WLVEHRSKKKLYCHQCGHS  472 (731)
Q Consensus       405 ~lS~~l~~~i~~~l~~g~qvll~lnRrGya~~~~C~~Cg~~-----------~~C~~C~~-~l~~h~~~~~l~Ch~Cg~~  472 (731)
                      .+|.+-.    -.-.-||-+           ...|.+||+.           +.||+|.. +|+--+.-..-.--|-|.+
T Consensus       211 ~vShEfh----l~~~vgED~-----------l~~C~~C~~s~n~e~~~~sk~~~Cp~C~~~~L~~~~~IEVgHtF~LG~k  275 (457)
T KOG2324         211 EVSHEFH----LIHPVGEDT-----------LMSCPSCGYSKNSEDLDLSKIASCPKCNEGRLTKTKSIEVGHTFLLGTK  275 (457)
T ss_pred             EEEEEEE----CCCCCCCCC-----------EEECCCCCCCCCHHHHCCCCCCCCCCCCCCCCCCCCCEEEEEEEEECCC
T ss_conf             1012575----257667500-----------3446767755760121377656687656777511243477778871430


Q ss_pred             CCCCCC---CCCCCCC--CEECCCCCCHHHHHHHHHHCCCCCHHHHC
Q ss_conf             446555---6667874--11001354289988885204852000102
Q gi|254780619|r  473 AIYSQS---CVVCGSS--GKMIACGFGIERIAEEVCEYFPLARISIL  514 (731)
Q Consensus       473 ~~~~~~---Cp~Cg~~--~~l~~~G~Gte~~~e~l~~~fp~~~v~~~  514 (731)
                      +.-|-.   --.||..  ..+--+|.|+.|+-........+.+-+|+
T Consensus       276 YS~~lna~f~~~~gKpe~l~MgCyGIGVtRllaAa~evls~~~~lrw  322 (457)
T KOG2324         276 YSKPLNAKFVNVEGKPEFLHMGCYGIGVTRLLAAAAEVLSDDKGLRW  322 (457)
T ss_pred             CCCCCCCEEEEECCCCCEEEECCEECCHHHHHHHHHHHHCCCCCCCC
T ss_conf             15434765544059840687402000489899999998156554315


No 388
>PRK07418 acetolactate synthase 3 catalytic subunit; Reviewed
Probab=89.54  E-value=0.46  Score=27.20  Aligned_cols=10  Identities=30%  Similarity=0.518  Sum_probs=4.8

Q ss_pred             CCCEEEEECC
Q ss_conf             9973999400
Q gi|254780619|r  296 GAISVIVGVR  305 (731)
Q Consensus       296 G~~~IVIGtR  305 (731)
                      -..-|+||+|
T Consensus       291 aDlvl~vG~r  300 (615)
T PRK07418        291 CDLLIAVGAR  300 (615)
T ss_pred             CCEEEEECCC
T ss_conf             8869996576


No 389
>COG2956 Predicted N-acetylglucosaminyl transferase [Carbohydrate transport and metabolism]
Probab=89.51  E-value=0.15  Score=31.03  Aligned_cols=31  Identities=23%  Similarity=0.540  Sum_probs=19.1

Q ss_pred             CCCCCEECHHHCCC-CCCCCCCCCCCCCEECC
Q ss_conf             57832000021024-46555666787411001
Q gi|254780619|r  460 SKKKLYCHQCGHSA-IYSQSCVVCGSSGKMIA  490 (731)
Q Consensus       460 ~~~~l~Ch~Cg~~~-~~~~~Cp~Cg~~~~l~~  490 (731)
                      .+-..+|+.|||+. .+.|.||+|..=..++|
T Consensus       351 ~~~~YRC~~CGF~a~~l~W~CPsC~~W~TikP  382 (389)
T COG2956         351 RKPRYRCQNCGFTAHTLYWHCPSCRAWETIKP  382 (389)
T ss_pred             HCCCCEECCCCCCHHEEEEECCCCCCCCCCCC
T ss_conf             16772100168631013541887565224177


No 390
>TIGR01073 pcrA ATP-dependent DNA helicase PcrA; InterPro: IPR005751    The DNA helicase PcrA is found mainly in Gram-positive bacteria and belongs to a superfamily of helicases, together with Rep and UvrD helicases from Escherichia coli. The action of the 3'5' bacterial DNA helicase is based upon two separate but coupled activities, ssDNA translocation and duplex destabilisation, and is driven by energy derived from the continuous ATP-binding and hydrolysis events that take place in the active-site cleft. The resulting conformational changes that accompany these events underpin the coupling process and allow the helicase to translocate along the DNA, destabilising the duplex and separating the two strands in an active process .; GO: 0004003 ATP-dependent DNA helicase activity, 0006268 DNA unwinding during replication, 0005737 cytoplasm.
Probab=89.50  E-value=0.31  Score=28.51  Aligned_cols=64  Identities=30%  Similarity=0.329  Sum_probs=39.2

Q ss_pred             CCCHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHHHHHHHHHHCCCCEEEEECCCHH--------HHHHHHHHHCC
Q ss_conf             6883789999999875204896199844753157999999999985146847997152100--------13445554303
Q gi|254780619|r  198 ILDKNQQDVVEQVVPLCTKGFAVSLISGVTGSGKTEVYLEIVAAVLHLGKQVLILLPEISL--------TSAILERFQKR  269 (731)
Q Consensus       198 ~Lt~eQ~~a~~~i~~~~~~~f~~~LL~GvTGSGKTEVYl~li~~~L~~GkqvLiLvPEI~L--------t~Q~~~rl~~r  269 (731)
                      .||++|+.|+..-.       .|.||=---|||||.|--+-|++.+.+..    ..|+=-|        +..|-+|+++-
T Consensus         4 ~LN~~Q~~AV~tt~-------GPLLi~AGAGSGKTRVLThRIA~L~~e~~----v~P~nILAiTFTNKAArEMkERv~~L   72 (811)
T TIGR01073         4 GLNPEQREAVKTTE-------GPLLIMAGAGSGKTRVLTHRIAHLLAEKN----VAPWNILAITFTNKAAREMKERVEKL   72 (811)
T ss_pred             CCCHHHHHHHHHCC-------CCCEEEECCCCCCCHHHHHHHHHHHHHCC----CCCCCEEEEECCHHHHHHHHHHHHHH
T ss_conf             02489999973037-------84101013788731057899999997223----69850465532205316789999998


Q ss_pred             CCC
Q ss_conf             897
Q gi|254780619|r  270 FGV  272 (731)
Q Consensus       270 F~~  272 (731)
                      ||.
T Consensus        73 ~g~   75 (811)
T TIGR01073        73 LGP   75 (811)
T ss_pred             HHH
T ss_conf             524


No 391
>pfam00448 SRP54 SRP54-type protein, GTPase domain. This family includes relatives of the G-domain of the SRP54 family of proteins.
Probab=89.38  E-value=1.7  Score=22.92  Aligned_cols=36  Identities=36%  Similarity=0.556  Sum_probs=29.1

Q ss_pred             CEEEEECCCCHHHHHHHHHHHHHHHHCCCCEEEEEC
Q ss_conf             619984475315799999999998514684799715
Q gi|254780619|r  219 AVSLISGVTGSGKTEVYLEIVAAVLHLGKQVLILLP  254 (731)
Q Consensus       219 ~~~LL~GvTGSGKTEVYl~li~~~L~~GkqvLiLvP  254 (731)
                      .+.++-|.||+|||=--.+++.....+|+.|.+.-=
T Consensus         2 ~vi~lvGptGvGKTTTiaKLAa~~~~~~~~V~lit~   37 (196)
T pfam00448         2 NVILLVGLQGSGKTTTIAKLAAYLKKQGKKVLLVAA   37 (196)
T ss_pred             EEEEEECCCCCCHHHHHHHHHHHHHHCCCEEEEEEC
T ss_conf             699998999998899999999999977992899975


No 392
>PRK10220 hypothetical protein; Provisional
Probab=89.34  E-value=0.19  Score=30.23  Aligned_cols=30  Identities=17%  Similarity=0.387  Sum_probs=22.5

Q ss_pred             CCCCCCCCCCEEEEECCCCCCEECHHHCCCC
Q ss_conf             3431014652012113578320000210244
Q gi|254780619|r  444 NRLKCLHCSCWLVEHRSKKKLYCHQCGHSAI  474 (731)
Q Consensus       444 ~~~~C~~C~~~l~~h~~~~~l~Ch~Cg~~~~  474 (731)
                      ..+.||.|+...||+ ....+.|.-|||+..
T Consensus         2 tlP~CP~C~seytYe-dg~~~vCpeC~hEW~   31 (111)
T PRK10220          2 SLPHCPKCNSEYTYE-DNGMYICPECAHEWN   31 (111)
T ss_pred             CCCCCCCCCCCCEEC-CCCEEECCCCCCCCC
T ss_conf             888699898924382-799789977647479


No 393
>pfam12340 DUF3638 Protein of unknown function (DUF3638). This domain family is found in eukaryotes, and is approximately 230 amino acids in length. There are two conserved sequence motifs: LLE and NMG.
Probab=89.33  E-value=0.62  Score=26.26  Aligned_cols=109  Identities=21%  Similarity=0.296  Sum_probs=67.1

Q ss_pred             CCCHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHHHHHHHHHHCCCCEE-EEECCCHHHHHHHHHHHCCCCC----
Q ss_conf             68837899999998752048961998447531579999999999851468479-9715210013445554303897----
Q gi|254780619|r  198 ILDKNQQDVVEQVVPLCTKGFAVSLISGVTGSGKTEVYLEIVAAVLHLGKQVL-ILLPEISLTSAILERFQKRFGV----  272 (731)
Q Consensus       198 ~Lt~eQ~~a~~~i~~~~~~~f~~~LL~GvTGSGKTEVYl~li~~~L~~GkqvL-iLvPEI~Lt~Q~~~rl~~rF~~----  272 (731)
                      .+-+.|..+........ . .....++=..|.|||-|-+-+....|+.|.+.. +.|| -+|..|+..-++.+||.    
T Consensus        23 liR~~Q~~va~~~i~~~-~-~~n~v~QlnMGeGKTsVI~Pmla~~LAdg~~Lvr~vvp-~~Ll~q~~~~L~~~lggll~r   99 (229)
T pfam12340        23 LIRPVQVDVARAMISPS-S-GSNSVLQLNMGEGKTSVIVPMVAAVLADGSRLVRVIVP-KPLLRQMAQMLQSRLGGLLGR   99 (229)
T ss_pred             EECHHHHHHHHHHHCCC-C-CCCEEEHHHCCCCCCEEEHHHHHHHHCCCCCEEEEECC-HHHHHHHHHHHHHHHHHHCCC
T ss_conf             54289999999985755-7-88722011206996224378899997488845899826-889999999999986421377


Q ss_pred             EEEEEE-CC-C--CCHH--H-HHHHHHHHCCCCEEEEECCHHHHH
Q ss_conf             689962-35-5--7235--6-678999971997399940012110
Q gi|254780619|r  273 KPAEWH-SS-L--STSM--R-EKIWRQVARGAISVIVGVRSALFL  310 (731)
Q Consensus       273 ~v~v~H-S~-l--s~~e--R-~~~w~~i~~G~~~IVIGtRSAif~  310 (731)
                      .|+.+. |+ +  ++++  + ......++. +-.|++.+-..+..
T Consensus       100 ~v~~lPFsR~~~~~~~~~~~~~~~~~~~~~-~~GIll~~PEhilS  143 (229)
T pfam12340       100 EIYHLPFSRRTPTTESEINLYRQLHEECMK-EGGVLLAQPEHILS  143 (229)
T ss_pred             CEEEECCCCCCCCCHHHHHHHHHHHHHHHH-CCCEEEECCHHHHH
T ss_conf             059840347688998999999999999997-29879968078776


No 394
>KOG2041 consensus
Probab=89.26  E-value=0.22  Score=29.69  Aligned_cols=25  Identities=12%  Similarity=0.219  Sum_probs=19.4

Q ss_pred             ECCCCCCHHHHHHHHHHCCCCCHHH
Q ss_conf             0013542899888852048520001
Q gi|254780619|r  488 MIACGFGIERIAEEVCEYFPLARIS  512 (731)
Q Consensus       488 l~~~G~Gte~~~e~l~~~fp~~~v~  512 (731)
                      |.++|.-.|-++..|+.-.|.+-|.
T Consensus       862 f~svGMC~qAV~a~Lr~s~pkaAv~  886 (1189)
T KOG2041         862 FTSVGMCDQAVEAYLRRSLPKAAVH  886 (1189)
T ss_pred             HHHHCHHHHHHHHHHHCCCCHHHHH
T ss_conf             8750408899999986058188999


No 395
>pfam09862 DUF2089 Protein of unknown function(DUF2089). This domain, found in various hypothetical prokaryotic proteins, has no known function.
Probab=89.26  E-value=0.28  Score=28.91  Aligned_cols=58  Identities=24%  Similarity=0.479  Sum_probs=30.4

Q ss_pred             CCCCCCEEEEECCCCCCEECHHHCCCCC-CCCCCCCCCCC--------EECCCCCCHHHHHHHHHHCCCCCH
Q ss_conf             0146520121135783200002102446-55566678741--------100135428998888520485200
Q gi|254780619|r  448 CLHCSCWLVEHRSKKKLYCHQCGHSAIY-SQSCVVCGSSG--------KMIACGFGIERIAEEVCEYFPLAR  510 (731)
Q Consensus       448 C~~C~~~l~~h~~~~~l~Ch~Cg~~~~~-~~~Cp~Cg~~~--------~l~~~G~Gte~~~e~l~~~fp~~~  510 (731)
                      ||.|+..|..    .+|.|..|+....- ...|.-|.=+.        .+...| -...++.+++-.+|.++
T Consensus         1 CPvCg~~l~V----t~L~C~~C~t~ieG~F~l~~f~~L~~E~l~Fi~~fi~~~G-nlke~~~~lgiSYpTvR   67 (113)
T pfam09862         1 CPVCGEELTV----TRLECSKCGTTIEGRFTLCKFCRLTPEQLEFVELFIKCRG-NIKEVEKELGISYPTVR   67 (113)
T ss_pred             CCCCCCCEEE----EEEECCCCCCEEEEEECCCHHHCCCHHHHHHHHHHHHHCC-CHHHHHHHHCCCCHHHH
T ss_conf             9989981389----9988489986797365340652389999999999999168-89999999788818899


No 396
>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=89.26  E-value=1.1  Score=24.41  Aligned_cols=52  Identities=25%  Similarity=0.287  Sum_probs=32.8

Q ss_pred             CCEEEEECCCCHHHHHHHHHHHHHHHHC-CCCEEEEECCCHHHHHHHHHHHCCCCCEEEEEECC
Q ss_conf             9619984475315799999999998514-68479971521001344555430389768996235
Q gi|254780619|r  218 FAVSLISGVTGSGKTEVYLEIVAAVLHL-GKQVLILLPEISLTSAILERFQKRFGVKPAEWHSS  280 (731)
Q Consensus       218 f~~~LL~GvTGSGKTEVYl~li~~~L~~-GkqvLiLvPEI~Lt~Q~~~rl~~rF~~~v~v~HS~  280 (731)
                      -.+.+|.|+-|||||    -+.+..++. |=|.-+--|+=.|       ...+=..+.-+||=.
T Consensus        28 ~~v~~L~GDlGaGKT----tl~~G~~~~LG~~~~~~SPTftl-------v~~Y~~~~~~~YH~D   80 (147)
T TIGR00150        28 GTVVLLKGDLGAGKT----TLVKGLLQGLGITGNVTSPTFTL-------VNEYNEGNLPLYHFD   80 (147)
T ss_pred             CEEEEEECCCCCCHH----HHHHHHHHHCCCEEEEECCCCCE-------EEEEECCCCCEEEEE
T ss_conf             538997323466658----99999998379226885793210-------100113785153333


No 397
>PRK00762 hypA hydrogenase nickel incorporation protein; Provisional
Probab=89.22  E-value=0.3  Score=28.66  Aligned_cols=33  Identities=24%  Similarity=0.588  Sum_probs=17.3

Q ss_pred             CEEEEECCCCCCEECHHHCCCCC----------CCCCCCCCCCC
Q ss_conf             20121135783200002102446----------55566678741
Q gi|254780619|r  453 CWLVEHRSKKKLYCHQCGHSAIY----------SQSCVVCGSSG  486 (731)
Q Consensus       453 ~~l~~h~~~~~l~Ch~Cg~~~~~----------~~~Cp~Cg~~~  486 (731)
                      ..|....-.-..+| .||+....          ...||.|||..
T Consensus        60 A~L~Ie~vp~~~~C-~Cg~~~~~~~~~~~~~~~~~~CP~Cgs~~  102 (124)
T PRK00762         60 ADIIVEMIPPELEC-ECGYKGVVDEDEIDHYAAVMECPVCGNKH  102 (124)
T ss_pred             CEEEEEECCCEEEE-ECCCCCCCCCCCCCCCCCCCCCCCCCCCC
T ss_conf             89999971725996-28995553321000256777191887977


No 398
>TIGR02012 tigrfam_recA protein RecA; InterPro: IPR001553   The recA gene product is a multifunctional enzyme that plays a role in homologous recombination, DNA repair and induction of the SOS response . In homologous recombination, the protein functions as a DNA-dependent ATPase, promoting synapsis, heteroduplex formation and strand exchange between homologous DNAs . RecA also acts as a protease cofactor that promotes autodigestion of the lexA product and phage repressors. The proteolytic inactivation of the lexA repressor by an activated form of recA may cause a derepression of the 20 or so genes involved in the SOS response, which regulates DNA repair, induced mutagenesis, delayed cell division and prophage induction in response to DNA damage .    RecA is a protein of about 350 amino-acid residues. Its sequence is very well conserved , ,  among eubacterial species. It is also found in the chloroplast of plants . RecA-like proteins are found in archaea and diverse eukaryotic organisms, like fission yeast, mouse or human. In the filament visualised by X-ray crystallography, -strand 3, the loop C-terminal to -strand 2, and alpha-helix D of the core domain form one surface that packs against alpha-helix A and -strand 0 (the N-terminal domain) of an adjacent monomer during polymerisation [Lusetti and Cox, Annu. Rev. Biochem. 2002. 71:71-100.]. The core ATP-binding site domain is well conserved, with 14 invariant residues. It contains the nucleotide binding loop between -strand 1 and alpha-helix C. The Escherichia coli sequence GPESSGKT matches the consensus sequence of amino acids (G/A)XXXXGK(T/S) for the Walker A box (also referred to as the P-loop) found in a number of nucleoside triphosphate (NTP)-binding proteins. Another nucleotide binding motif, the Walker B box is found at -strand 4 in the RecA structure. The Walker B box is characterised by four hydrophobic amino acids followed by an acidic residue (usually aspartate). Nucleotide specificity and additional ATP binding interactions are contributed by the amino acid residues at -strand 2 and the loop C-terminal to that strand, all of which are greater than 90
Probab=89.18  E-value=1.7  Score=22.82  Aligned_cols=92  Identities=25%  Similarity=0.272  Sum_probs=66.7

Q ss_pred             CEEEEECCCCHHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHCCCCCEE-EEEECCCCCHH-HHHHHHH-HHC
Q ss_conf             61998447531579999999999851468479971521001344555430389768-99623557235-6678999-971
Q gi|254780619|r  219 AVSLISGVTGSGKTEVYLEIVAAVLHLGKQVLILLPEISLTSAILERFQKRFGVKP-AEWHSSLSTSM-REKIWRQ-VAR  295 (731)
Q Consensus       219 ~~~LL~GvTGSGKTEVYl~li~~~L~~GkqvLiLvPEI~Lt~Q~~~rl~~rF~~~v-~v~HS~ls~~e-R~~~w~~-i~~  295 (731)
                      +..=+||.-.||||-+.+++|+++=+.|..+.+.=-|-+|=|.-...    +|.++ -++-|+=-.+| -.++... +++
T Consensus        56 Ri~EiYGpESsGKTTLal~~iA~~Qk~Gg~~afiDAEHAlD~~YA~~----LGv~~~~L~~sQPd~GE~ALeI~~~L~rS  131 (322)
T TIGR02012        56 RIIEIYGPESSGKTTLALHVIAEAQKAGGVAAFIDAEHALDPVYAKK----LGVDIDNLLVSQPDTGEQALEIAETLVRS  131 (322)
T ss_pred             EEEEEECCCCCCHHHHHHHHHHHHHHCCCEEEEEECHHHCCHHHHHH----HCCCHHHHEEECCCCCHHHHHHHHHHHHC
T ss_conf             07998548988478999999999974398389984513037788998----36452471120888714699999998723


Q ss_pred             CCCEEEEECCHHHHHHHCC
Q ss_conf             9973999400121100100
Q gi|254780619|r  296 GAISVIVGVRSALFLPFKK  314 (731)
Q Consensus       296 G~~~IVIGtRSAif~P~~n  314 (731)
                      |..+|||=---|.+.|-..
T Consensus       132 gAvD~iVvDSVAAL~P~aE  150 (322)
T TIGR02012       132 GAVDIIVVDSVAALVPKAE  150 (322)
T ss_pred             CCCEEEEECCCCCCCCHHH
T ss_conf             7611799734001387123


No 399
>cd01413 SIR2_Af2 SIR2_Af2: Archaeal and prokaryotic group which includes Archaeoglobus fulgidus Sir2-Af2, Sulfolobus solfataricus ssSir2, and several bacterial homologs; and are members of the SIR2 family of proteins, silent information regulator 2 (Sir2) enzymes which catalyze NAD+-dependent protein/histone deacetylation. Sir2 proteins have been shown to regulate gene silencing, DNA repair, metabolic enzymes, and life span. The Sir2 homolog from the archaea Sulfolobus solftaricus deacetylates the non-specific DNA protein Alba to mediate transcription repression.
Probab=89.12  E-value=0.4  Score=27.74  Aligned_cols=74  Identities=24%  Similarity=0.388  Sum_probs=35.1

Q ss_pred             CCEEHHCCCCCCCCCCCCCCCCCEEEEECCCCCCEECHHHCCCCCCCCCCCCCCCCEECCC--CCCHHHHHHHHHHCCCC
Q ss_conf             2000000235654343101465201211357832000021024465556667874110013--54289988885204852
Q gi|254780619|r  431 RGYAPLTLCQVCGNRLKCLHCSCWLVEHRSKKKLYCHQCGHSAIYSQSCVVCGSSGKMIAC--GFGIERIAEEVCEYFPL  508 (731)
Q Consensus       431 rGya~~~~C~~Cg~~~~C~~C~~~l~~h~~~~~l~Ch~Cg~~~~~~~~Cp~Cg~~~~l~~~--G~Gte~~~e~l~~~fp~  508 (731)
                      -|....+.|.+||......   -.. .             .....+..||.||+.  +++-  =+|         +..|.
T Consensus       108 HG~l~~~~C~~C~~~~~~~---~~~-~-------------~~~~~~P~C~~C~g~--lrP~VV~FG---------E~lp~  159 (222)
T cd01413         108 HGTLQTAYCVNCGSKYDLE---EVK-Y-------------AKKHEVPRCPKCGGI--IRPDVVLFG---------EPLPQ  159 (222)
T ss_pred             EEEECEEEECCCCCCCCHH---HHH-H-------------HHHCCCCCCCCCCCC--CCCCEEECC---------CCCCH
T ss_conf             8725757828999837788---987-7-------------752589977455883--367577757---------77987


Q ss_pred             CHHHHCCCCCCCCHHHHHHHHHHHCCCCCCEEEEEHHH
Q ss_conf             00010232113586789999986212576579870443
Q gi|254780619|r  509 ARISILSSDLEGGGGRLQLQLSAIAKGEIDIIIGTQLV  546 (731)
Q Consensus       509 ~~v~~~d~d~~~~~~~~~~~~~~~~~~~~~ilvgTq~i  546 (731)
                      .              .++...+.+.+-+.-|+|||.+.
T Consensus       160 ~--------------~~~~a~~~~~~aDlllvvGTSl~  183 (222)
T cd01413         160 A--------------LLREAIEAAKEADLFIVLGSSLV  183 (222)
T ss_pred             H--------------HHHHHHHHHHCCCEEEEECCCCE
T ss_conf             8--------------99999999973998999787864


No 400
>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=89.07  E-value=0.6  Score=26.37  Aligned_cols=111  Identities=23%  Similarity=0.341  Sum_probs=73.9

Q ss_pred             CCCHHHHHHHHHHHHHHCCC---CCEEEEECCCCHHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHCCC---C
Q ss_conf             68837899999998752048---96199844753157999999999985146847997152100134455543038---9
Q gi|254780619|r  198 ILDKNQQDVVEQVVPLCTKG---FAVSLISGVTGSGKTEVYLEIVAAVLHLGKQVLILLPEISLTSAILERFQKRF---G  271 (731)
Q Consensus       198 ~Lt~eQ~~a~~~i~~~~~~~---f~~~LL~GvTGSGKTEVYl~li~~~L~~GkqvLiLvPEI~Lt~Q~~~rl~~rF---~  271 (731)
                      .+-+-|.+-+.  ++...+|   -.+..|-  -|.|||.|=+-|+..+   -|+||||.---.-..||-..|+.=-   +
T Consensus       269 ~~RPYQEKSLr--sKMFGNGRARSGiIVLP--CGAGKsLVGvTAACTv---kKs~lVLctS~VSV~QW~~QFk~WSti~d  341 (756)
T TIGR00603       269 VLRPYQEKSLR--SKMFGNGRARSGIIVLP--CGAGKSLVGVTAACTV---KKSVLVLCTSAVSVEQWKQQFKLWSTIDD  341 (756)
T ss_pred             CCCCCHHHHCC--CCCCCCCCCCCCCEECC--CCCCCCHHHHHHHEEE---EEEEEEEECCCHHHHHHHHHHHHCCCCCC
T ss_conf             88975111044--45667861105517767--7888311225442023---10078972671008899988752268873


Q ss_pred             CEEEEEECCCCCHHHHHHHHHHHCCCCEEEEECCHHH---------------HHHHCCCEEEEEEECC
Q ss_conf             7689962355723566789999719973999400121---------------1001000136774055
Q gi|254780619|r  272 VKPAEWHSSLSTSMREKIWRQVARGAISVIVGVRSAL---------------FLPFKKLGLIVIDEEH  324 (731)
Q Consensus       272 ~~v~v~HS~ls~~eR~~~w~~i~~G~~~IVIGtRSAi---------------f~P~~nLglIIvDEEH  324 (731)
                      ..|+.++|.-.++  ..       |++.|+|.|.|=|               |+-=+-=||||+||=|
T Consensus       342 ~~IcrFTSD~Ke~--~~-------~~~gv~vsTYsMva~t~kRS~es~k~m~~l~~rEWGl~~LDEVH  400 (756)
T TIGR00603       342 SQICRFTSDAKEK--FH-------GEAGVVVSTYSMVAHTGKRSYESEKVMEWLTNREWGLILLDEVH  400 (756)
T ss_pred             CCCCCCCCCCCCC--CC-------CCCCEEEECCCCCCCCCCCHHHHHHHHHHHHCCCCEEEEECCCC
T ss_conf             5511025213576--26-------65335887330002475431889999999706873179861101


No 401
>PRK06749 replicative DNA helicase; Provisional
Probab=89.04  E-value=1.8  Score=22.75  Aligned_cols=131  Identities=19%  Similarity=0.230  Sum_probs=71.6

Q ss_pred             CEEEEECCCCHHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHCCC-CCEEEEEEC---CCCCHHHHHHHHHHH
Q ss_conf             6199844753157999999999985146847997152100134455543038-976899623---557235667899997
Q gi|254780619|r  219 AVSLISGVTGSGKTEVYLEIVAAVLHLGKQVLILLPEISLTSAILERFQKRF-GVKPAEWHS---SLSTSMREKIWRQVA  294 (731)
Q Consensus       219 ~~~LL~GvTGSGKTEVYl~li~~~L~~GkqvLiLvPEI~Lt~Q~~~rl~~rF-~~~v~v~HS---~ls~~eR~~~w~~i~  294 (731)
                      ....|=|-+|.|||-..++++..+..+|+.|++.--|-+ ..|+..|+-..- +....-+.+   .+++.+-......+.
T Consensus       187 ~LiviaaRPsmGKTa~alnia~~~a~~g~~v~~fSlEMs-~~~l~~R~ls~~s~v~~~~i~~~~~~~~~~~~~~~~~a~~  265 (428)
T PRK06749        187 DFVVLGARPSMGKTAFALNVGLHAAKSGAAVGLFSLEMS-SKQLLKRMASCVGEVSGGRLKNPKHRFAMEDWEKVSKAFA  265 (428)
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHHHHCCCCEEEEECCCC-HHHHHHHHHHHHCCCCHHHHHCCCCCCCHHHHHHHHHHHH
T ss_conf             689996279897689999999999964992799837899-9999999999754998888627767799999999999999


Q ss_pred             -CCCCEEEEECCHHHH-----HHHC--------CCEEEEEEECCCCCCHHCCC--C-----CCC-----HHHHHHHHHHH
Q ss_conf             -199739994001211-----0010--------00136774055321000024--4-----322-----48999997511
Q gi|254780619|r  295 -RGAISVIVGVRSALF-----LPFK--------KLGLIVIDEEHDISYKQEEG--I-----LYN-----ARDMSIVRGKI  348 (731)
Q Consensus       295 -~G~~~IVIGtRSAif-----~P~~--------nLglIIvDEEHd~sykq~~~--p-----ry~-----aRdvA~~Ra~~  348 (731)
                       -.+..+.|=..+.+=     +-..        ++++||||      |=|-..  +     |+.     +|.+ ...|+.
T Consensus       266 ~l~~~~l~i~d~~~~ti~~i~~~~r~~~~~~g~~~~livID------YlqLi~~~~~~~~~r~~ev~~isr~l-K~lAke  338 (428)
T PRK06749        266 EIGELPLEIYDNAGVTVQDIWMQTRKLKRKHGDKKVLIIVD------YLQLITGDPKHKGNRFQEISEISRKL-KLLARE  338 (428)
T ss_pred             HHHCCCEEEECCCCCCHHHHHHHHHHHHHHCCCCCEEEEEE------HHHHCCCCCCCCCCHHHHHHHHHHHH-HHHHHH
T ss_conf             98559659975899767999999999999749987699976------77650578777778999999999999-999999


Q ss_pred             CCCCEECCC
Q ss_conf             032100002
Q gi|254780619|r  349 ESFPVVLVS  357 (731)
Q Consensus       349 ~~~~lilgS  357 (731)
                      .+||+|+.|
T Consensus       339 l~vpvi~ls  347 (428)
T PRK06749        339 LNVCVVALS  347 (428)
T ss_pred             HCCCEEEEC
T ss_conf             699899971


No 402
>cd01675 RNR_III Class III ribonucleotide reductase. Ribonucleotide reductase (RNR) catalyzes the reductive synthesis of deoxyribonucleotides from their corresponding ribonucleotides. It provides the precursors necessary for DNA synthesis. RNRs are separated into three classes based on their metallocofactor usage. Class I RNRs, found in eukaryotes, bacteria, and bacteriophage, use a diiron-tyrosyl radical. Class II RNRs, found in bacteria, bacteriophage, algae and archaea, use coenzyme B12 (adenosylcobalamin, AdoCbl). Class III RNRs, found in strict or facultative anaerobic bacteria, bacteriophage, and archaea, use an FeS cluster and S-adenosylmethionine to generate a glycyl radical. Many organisms have more than one class of RNR present in their genomes. All three RNRs have a ten-stranded alpha-beta barrel domain that is structurally similar to the domain of PFL (pyruvate formate lyase). The class III enzyme from phage T4 consists of two subunits, this model covers the larger subunit w
Probab=89.04  E-value=0.51  Score=26.87  Aligned_cols=25  Identities=16%  Similarity=0.089  Sum_probs=18.3

Q ss_pred             CHHHHHHHHHHHCCCCEECCCCCCCH
Q ss_conf             24899999751103210000245432
Q gi|254780619|r  337 NARDMSIVRGKIESFPVVLVSATPSI  362 (731)
Q Consensus       337 ~aRdvA~~Ra~~~~~~lilgSATPSl  362 (731)
                      |.||.+..-.+..|...-| -|||+=
T Consensus       398 ~m~~~~~~~~~e~g~~~~l-~~TPAE  422 (555)
T cd01675         398 HIRERADEFKEETGLLYSV-EATPAE  422 (555)
T ss_pred             HHHHHHHHHHHHHCCCEEE-EECCCC
T ss_conf             9999999998986993489-976436


No 403
>PRK00889 adenylylsulfate kinase; Provisional
Probab=88.95  E-value=1.8  Score=22.70  Aligned_cols=106  Identities=21%  Similarity=0.275  Sum_probs=60.7

Q ss_pred             CCCCEEEEECCCCHHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHCCCCCEEEEEECCCCCHHHHHHHHHHHC
Q ss_conf             48961998447531579999999999851468479971521001344555430389768996235572356678999971
Q gi|254780619|r  216 KGFAVSLISGVTGSGKTEVYLEIVAAVLHLGKQVLILLPEISLTSAILERFQKRFGVKPAEWHSSLSTSMREKIWRQVAR  295 (731)
Q Consensus       216 ~~f~~~LL~GvTGSGKTEVYl~li~~~L~~GkqvLiLvPEI~Lt~Q~~~rl~~rF~~~v~v~HS~ls~~eR~~~w~~i~~  295 (731)
                      ++| +.-+-|-.|||||-+.-.+.+..-+.|..+.+|=-         +.++.-|....     +.|..+|.++..++..
T Consensus         3 kg~-viWltGlsgSGKTTia~~l~~~L~~~~~~~~~LDG---------D~lR~~l~~~l-----gfs~~dR~~n~~r~~~   67 (175)
T PRK00889          3 RGV-TVWFTGLSGAGKTTISHALAEKLRARGYPVEVLDG---------DIVRTNLSKGL-----GFSKEDRDTNIRRIGF   67 (175)
T ss_pred             CCE-EEEEECCCCCCHHHHHHHHHHHHHHCCCCEEEECC---------HHHHHHHCCCC-----CCCHHHHHHHHHHHHH
T ss_conf             888-99988989999999999999999986996799776---------88887536788-----9898999999999999


Q ss_pred             CCCEEEEECCHHHHHHHCCCEEEEEEECCCCCCHHCCCCCCCHHHHHHHHHHHCCCCEECCCC
Q ss_conf             997399940012110010001367740553210000244322489999975110321000024
Q gi|254780619|r  296 GAISVIVGVRSALFLPFKKLGLIVIDEEHDISYKQEEGILYNARDMSIVRGKIESFPVVLVSA  358 (731)
Q Consensus       296 G~~~IVIGtRSAif~P~~nLglIIvDEEHd~sykq~~~pry~aRdvA~~Ra~~~~~~lilgSA  358 (731)
                      =          |-+  +.+-|.++|--        --+|.-..|+-+..  ...+.--|+..+
T Consensus        68 l----------a~~--l~~~g~~vIvs--------~isp~~~~R~~~r~--~~~~~~EIyv~~  108 (175)
T PRK00889         68 V----------AHL--LTRHGVIVLVS--------AISPYRETREEVRG--TIGNFVEVFVNA  108 (175)
T ss_pred             H----------HHH--HHHCCCEEEEE--------ECCCCHHHHHHHHH--HCCCCEEEEECC
T ss_conf             9----------999--98189868885--------04799999999998--578766998428


No 404
>cd01412 SIRT5_Af1_CobB SIRT5_Af1_CobB: Eukaryotic, archaeal and prokaryotic group (class3) which includes human sirtuin SIRT5, Archaeoglobus fulgidus Sir2-Af1, and E. coli CobB; and are members of the SIR2 family of proteins, silent information regulator 2 (Sir2) enzymes which catalyze NAD+-dependent protein/histone deacetylation. Sir2 proteins have been shown to regulate gene silencing, DNA repair, metabolic enzymes, and life span. CobB is a bacterial sirtuin that deacetylates acetyl-CoA synthetase at an active site lysine to stimulate its enzymatic activity.
Probab=88.86  E-value=0.41  Score=27.63  Aligned_cols=39  Identities=18%  Similarity=0.260  Sum_probs=20.0

Q ss_pred             CCEEHHCCCCCCCCCCCCCCCCCEEEEECCCCCCEECHHHCCCCCCCCCCCCCCCCEECC
Q ss_conf             200000023565434310146520121135783200002102446555666787411001
Q gi|254780619|r  431 RGYAPLTLCQVCGNRLKCLHCSCWLVEHRSKKKLYCHQCGHSAIYSQSCVVCGSSGKMIA  490 (731)
Q Consensus       431 rGya~~~~C~~Cg~~~~C~~C~~~l~~h~~~~~l~Ch~Cg~~~~~~~~Cp~Cg~~~~l~~  490 (731)
                      -|-...+.|.+|++.....           ..       -.... +..||.||+.  +++
T Consensus       104 HG~~~~~~C~~C~~~~~~~-----------~~-------~~~~~-~p~C~~Cgg~--lrP  142 (224)
T cd01412         104 HGSLFRVRCSSCGYVGENN-----------EE-------IPEEE-LPRCPKCGGL--LRP  142 (224)
T ss_pred             ECEECEEEECCCCCCCCCC-----------CC-------CCCCC-CCCCCCCCCE--ECC
T ss_conf             0301669989998988552-----------22-------12367-9977467997--055


No 405
>pfam00437 GSPII_E Type II/IV secretion system protein. This family contains both type II and type IV pathway secretion proteins from bacteria. VirB11 ATPase is a subunit of the Agrobacterium tumefaciens transfer DNA (T-DNA) transfer system, a type IV secretion pathway required for delivery of T-DNA and effector proteins to plant cells during infection.
Probab=88.80  E-value=1.8  Score=22.63  Aligned_cols=49  Identities=24%  Similarity=0.386  Sum_probs=29.0

Q ss_pred             CCHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHHHHHHHHHHC-CCCEEEE
Q ss_conf             88378999999987520489619984475315799999999998514-6847997
Q gi|254780619|r  199 LDKNQQDVVEQVVPLCTKGFAVSLISGVTGSGKTEVYLEIVAAVLHL-GKQVLIL  252 (731)
Q Consensus       199 Lt~eQ~~a~~~i~~~~~~~f~~~LL~GvTGSGKTEVYl~li~~~L~~-GkqvLiL  252 (731)
                      +++++...+.....    .....|+-|-||||||..- .++...+.. ++.++.+
T Consensus       124 ~~~~~~~~L~~~v~----~~~~ilIsG~TGSGKTT~l-~all~~i~~~~~riiti  173 (283)
T pfam00437       124 FDADIAEFLRQAVQ----ARGNILVSGGTGSGKTTLL-YALLNEINTDDERIVTI  173 (283)
T ss_pred             CHHHHHHHHHHHHH----CCCEEEEECCCCCCHHHHH-HHHHHHCCCCCCCEEEE
T ss_conf             85999999999998----1975999889999889999-99998408777627873


No 406
>smart00492 HELICc3 helicase superfamily c-terminal domain.
Probab=88.79  E-value=1.2  Score=24.01  Aligned_cols=79  Identities=23%  Similarity=0.198  Sum_probs=45.3

Q ss_pred             HHHHHHHHHHCC-CCCCEEEEEHHHCCCCCCCCCC--HHHHH---H--HHH-HHH-HHHH-------HHHH-----HHHH
Q ss_conf             789999986212-5765798704430231134520--12330---0--034-431-0245-------5789----