Query         gi|254781215|ref|YP_003065628.1| putative phage terminase, large subunit [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 511
No_of_seqs    218 out of 401
Neff          7.5 
Searched_HMMs 39220
Date          Mon May 30 07:09:39 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254781215.hhm -d /home/congqian_1/database/cdd/Cdd.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 pfam03237 Terminase_6 Terminas 100.0   5E-36 1.3E-40  245.8  31.1  356   82-477     2-378 (380)
  2 pfam03354 Terminase_1 Phage Te 100.0 1.7E-24 4.5E-29  173.0  30.8  394   53-477     1-466 (473)
  3 pfam04466 Terminase_3 Phage te 100.0 4.1E-24   1E-28  170.7  29.4  363   81-476     6-385 (387)
  4 COG4626 Phage terminase-like p  99.8 1.2E-15 3.1E-20  117.3  33.8  392   52-477    63-525 (546)
  5 COG5323 Uncharacterized conser  99.7 4.2E-15 1.1E-19  113.8  14.4  343   80-477    39-395 (410)
  6 COG4373 Mu-like prophage FluMu  99.6 5.7E-12 1.4E-16   94.1  23.4  364   79-477    31-473 (509)
  7 pfam05876 Terminase_GpA Phage   99.4   7E-09 1.8E-13   74.6  27.9  394   53-478    19-541 (552)
  8 COG1783 XtmB Phage terminase l  99.2 1.5E-08 3.7E-13   72.6  21.5  342   81-470    28-390 (414)
  9 TIGR01547 phage_term_2 phage t  98.9 5.7E-07 1.5E-11   62.6  17.8  246   81-337     5-301 (462)
 10 COG1061 SSL2 DNA or RNA helica  98.6 5.8E-06 1.5E-10   56.2  14.2  159   50-242    36-196 (442)
 11 smart00487 DEXDc DEAD-like hel  98.5 1.3E-06 3.4E-11   60.2  10.2  167   47-234     5-174 (201)
 12 PRK10875 recD exonuclease V su  98.5 7.9E-06   2E-10   55.4  12.9  157   52-242   149-313 (607)
 13 COG1444 Predicted P-loop ATPas  98.4 3.3E-05 8.3E-10   51.5  14.8  305   55-397   216-591 (758)
 14 pfam04851 ResIII Type III rest  98.4 4.5E-06 1.1E-10   56.9   9.6   99   51-232     4-103 (103)
 15 PRK13766 Hef nuclease; Provisi  98.3 2.3E-05 5.7E-10   52.5  11.9  169   40-233     5-175 (764)
 16 TIGR01448 recD_rel helicase, R  98.3 7.7E-06   2E-10   55.4   9.3  136   52-241   352-507 (769)
 17 KOG2036 consensus               98.1 6.1E-05 1.6E-09   49.8  11.1  144   55-213   258-402 (1011)
 18 PRK00254 ski2-like helicase; P  98.1 0.00018 4.7E-09   46.8  13.2  144   51-229    24-177 (717)
 19 PRK02362 ski2-like helicase; P  98.1 0.00018 4.5E-09   46.8  13.0  152   51-235    24-185 (736)
 20 PRK10536 hypothetical protein;  98.1 0.00047 1.2E-08   44.1  15.2  191   39-273    51-261 (262)
 21 TIGR01447 recD exodeoxyribonuc  98.1 3.8E-05 9.7E-10   51.1   9.5  154   52-230   229-393 (753)
 22 COG1111 MPH1 ERCC4-like helica  98.1 9.3E-05 2.4E-09   48.6  10.7  170   47-242    12-184 (542)
 23 PRK01172 ski2-like helicase; P  98.0 0.00023 5.8E-09   46.2  12.1  156   51-237    23-185 (674)
 24 KOG0354 consensus               98.0 8.3E-05 2.1E-09   48.9   9.4  163   45-234    57-225 (746)
 25 pfam02562 PhoH PhoH-like prote  98.0 0.00042 1.1E-08   44.5  13.0   54   53-118     7-60  (205)
 26 pfam00270 DEAD DEAD/DEAH box h  98.0 0.00015 3.9E-09   47.2  10.4   68   53-133     2-70  (167)
 27 smart00489 DEXDc3 DEAD-like he  97.8  0.0002 5.1E-09   46.5   9.1   81   32-132     1-85  (289)
 28 smart00488 DEXDc2 DEAD-like he  97.8  0.0002 5.1E-09   46.5   9.1   81   32-132     1-85  (289)
 29 KOG0390 consensus               97.6  0.0016   4E-08   40.8  11.4  164   52-234   240-418 (776)
 30 TIGR01054 rgy reverse gyrase;   97.6  0.0015 3.7E-08   41.1  10.4  145   23-200    68-218 (1843)
 31 PRK10590 ATP-dependent RNA hel  97.5   0.002   5E-08   40.2  10.5   75   46-133    19-100 (457)
 32 PRK11192 ATP-dependent RNA hel  97.5  0.0032 8.2E-08   38.9  11.5   74   47-133    22-100 (417)
 33 cd00046 DEXDc DEAD-like helica  97.5 0.00075 1.9E-08   42.9   8.3   52   80-132     3-54  (144)
 34 COG1204 Superfamily II helicas  97.5  0.0063 1.6E-07   37.1  13.0  139   79-238    49-197 (766)
 35 COG1110 Reverse gyrase [DNA re  97.5  0.0023 5.8E-08   39.8  10.5  151   15-200    61-212 (1187)
 36 cd00268 DEADc DEAD-box helicas  97.4  0.0024 6.1E-08   39.7  10.1   72   47-131    18-92  (203)
 37 PTZ00110 helicase; Provisional  97.4  0.0052 1.3E-07   37.6  11.3   79   44-135   198-282 (602)
 38 PRK11634 ATP-dependent RNA hel  97.3  0.0038 9.7E-08   38.4  10.1   75   46-133    24-99  (629)
 39 COG1203 CRISPR-associated heli  97.3  0.0093 2.4E-07   36.0  11.8  170   49-230   194-380 (733)
 40 PRK06305 DNA polymerase III su  97.3  0.0094 2.4E-07   36.0  11.9  151   55-243    22-174 (462)
 41 PRK11776 ATP-dependent RNA hel  97.3  0.0036 9.1E-08   38.6   9.7   77   46-135    22-99  (459)
 42 PRK11448 hsdR type I restricti  97.3   0.014 3.5E-07   34.9  13.4   66   50-122   416-484 (1126)
 43 PRK05563 DNA polymerase III su  97.3  0.0092 2.4E-07   36.0  11.6  156   45-242    15-171 (541)
 44 PRK04537 ATP-dependent RNA hel  97.3   0.011 2.8E-07   35.6  11.8   82   40-134    21-110 (574)
 45 pfam00176 SNF2_N SNF2 family N  97.2  0.0079   2E-07   36.4  10.7  162   54-240     1-168 (295)
 46 PRK08769 DNA polymerase III su  97.2   0.013 3.4E-07   35.0  11.8  153   53-238     7-161 (319)
 47 COG4096 HsdR Type I site-speci  97.2  0.0066 1.7E-07   36.9  10.0   73   44-123   159-231 (875)
 48 pfam07652 Flavi_DEAD Flaviviru  97.2  0.0067 1.7E-07   36.9   9.9  133   85-240    10-144 (146)
 49 COG1205 Distinct helicase fami  97.1  0.0093 2.4E-07   36.0  10.4  165   51-239    71-250 (851)
 50 COG4581 Superfamily II RNA hel  97.1   0.021 5.3E-07   33.8  11.9  155   47-242   117-281 (1041)
 51 COG0513 SrmB Superfamily II DN  97.1   0.012 3.2E-07   35.2  10.6  162   46-229    47-213 (513)
 52 PRK04837 ATP-dependent RNA hel  97.1  0.0069 1.8E-07   36.8   9.1   74   46-132    27-108 (423)
 53 PRK09401 reverse gyrase; Revie  97.1   0.011 2.7E-07   35.6  10.0   93   13-134    52-147 (1176)
 54 PRK07994 DNA polymerase III su  97.1    0.01 2.6E-07   35.7   9.9  149   55-241    21-170 (643)
 55 PRK06871 DNA polymerase III su  96.9   0.031   8E-07   32.7  11.6  153   54-242     5-158 (324)
 56 PRK06645 DNA polymerase III su  96.9    0.03 7.5E-07   32.8  11.2  149   55-241    26-179 (507)
 57 PRK00440 rfc replication facto  96.9   0.025 6.5E-07   33.2  10.8  125   44-229    14-139 (318)
 58 PRK01297 ATP-dependent RNA hel  96.9   0.032 8.1E-07   32.6  12.2   76   44-132   100-183 (472)
 59 PRK05896 DNA polymerase III su  96.9   0.034 8.7E-07   32.4  12.0  155   45-241    15-170 (613)
 60 PRK04914 ATP-dependent helicas  96.9   0.035 8.9E-07   32.4  13.7  173   43-239   140-325 (955)
 61 PRK06647 DNA polymerase III su  96.8   0.037 9.3E-07   32.2  12.0  149   55-242    21-171 (560)
 62 PRK06674 DNA polymerase III su  96.8   0.039 9.9E-07   32.1  11.9  150   55-242    21-171 (563)
 63 PRK12323 DNA polymerase III su  96.8    0.04   1E-06   32.0  11.1  152   55-239    21-173 (721)
 64 pfam05127 DUF699 Putative ATPa  96.8    0.04   1E-06   32.0  13.5   92   98-211     4-95  (160)
 65 PRK12402 replication factor C   96.7   0.038 9.8E-07   32.1  10.8  165   37-238     4-173 (337)
 66 PRK13767 ATP-dependent helicas  96.7   0.033 8.5E-07   32.5  10.4   63   48-123    30-100 (878)
 67 PRK07133 DNA polymerase III su  96.7   0.042 1.1E-06   31.8  11.4  139   55-238    23-166 (718)
 68 PRK08451 DNA polymerase III su  96.7   0.044 1.1E-06   31.7  12.0  149   55-241    19-168 (523)
 69 PRK07764 DNA polymerase III su  96.7  0.0089 2.3E-07   36.1   7.1  152   55-243    20-173 (775)
 70 PRK08691 DNA polymerase III su  96.6    0.05 1.3E-06   31.4  11.5  149   55-241    21-170 (704)
 71 PRK05707 DNA polymerase III su  96.6   0.053 1.4E-06   31.2  10.8  152   79-272    24-176 (328)
 72 COG1199 DinG Rad3-related DNA   96.6   0.023   6E-07   33.5   8.8   65   51-124    16-80  (654)
 73 PRK08058 DNA polymerase III su  96.6   0.055 1.4E-06   31.1  11.9  154   55-276    11-184 (329)
 74 KOG0391 consensus               96.5   0.022 5.7E-07   33.6   8.2  160   51-241   616-784 (1958)
 75 PRK07270 DNA polymerase III su  96.5   0.062 1.6E-06   30.8  11.9  151   55-243    20-171 (557)
 76 PRK06872 DNA polymerase III su  96.5   0.063 1.6E-06   30.8  10.5  149   55-241    21-170 (696)
 77 PRK07003 DNA polymerase III su  96.4   0.071 1.8E-06   30.4  11.7  146   55-238    21-167 (816)
 78 pfam05970 DUF889 PIF1 helicase  96.4   0.014 3.6E-07   34.9   6.5   97   85-216     2-99  (418)
 79 PRK13826 Dtr system oriT relax  96.4   0.051 1.3E-06   31.3   9.3  132   53-241   384-521 (1102)
 80 TIGR02397 dnaX_nterm DNA polym  96.3    0.02   5E-07   33.9   7.1  200   45-308    13-224 (363)
 81 PRK13889 conjugal transfer rel  96.3   0.048 1.2E-06   31.5   8.9  132   54-242   350-487 (992)
 82 PRK05564 DNA polymerase III su  96.3   0.081 2.1E-06   30.1  10.4  151   55-272     9-163 (313)
 83 PRK11747 dinG ATP-dependent DN  96.2   0.085 2.2E-06   29.9  10.6   68   44-118    20-87  (697)
 84 PRK07471 DNA polymerase III su  96.2   0.086 2.2E-06   29.9  11.3  166   55-242    22-191 (363)
 85 COG1875 NYN ribonuclease and A  96.1  0.0074 1.9E-07   36.6   3.9   43   80-122   248-291 (436)
 86 PRK05703 flhF flagellar biosyn  96.1     0.1 2.6E-06   29.4  11.3   38   80-117   213-251 (412)
 87 KOG0952 consensus               96.1     0.1 2.6E-06   29.5   9.6  123   80-213   129-260 (1230)
 88 PRK08074 bifunctional ATP-depe  96.0    0.11 2.7E-06   29.3  10.0   76   45-130   254-329 (932)
 89 PRK08853 DNA polymerase III su  96.0    0.11 2.9E-06   29.2  11.0  149   55-241    21-170 (717)
 90 PRK09112 DNA polymerase III su  96.0    0.12 2.9E-06   29.1  11.1  163   55-243    28-194 (352)
 91 TIGR02621 cas3_GSU0051 CRISPR-  95.8   0.015 3.9E-07   34.6   4.5   84   44-139    10-105 (975)
 92 PRK07993 DNA polymerase III su  95.8    0.13 3.4E-06   28.7  10.3  153   54-241     6-159 (334)
 93 TIGR03499 FlhF flagellar biosy  95.7   0.056 1.4E-06   31.1   7.2   45  353-399   208-259 (282)
 94 COG1484 DnaC DNA replication p  95.7    0.15 3.8E-06   28.4   9.7   74   35-115    69-142 (254)
 95 TIGR00345 arsA arsenite-activa  95.7   0.018 4.7E-07   34.1   4.5   41   87-130     7-51  (330)
 96 PRK09111 DNA polymerase III su  95.7    0.15 3.9E-06   28.3  11.7  152   55-242    28-183 (600)
 97 PRK11057 ATP-dependent DNA hel  95.3    0.11 2.9E-06   29.1   7.4   60   47-123    22-81  (607)
 98 COG5525 Bacteriophage tail ass  95.2   0.049 1.2E-06   31.4   5.4  172   33-233    32-209 (611)
 99 COG3972 Superfamily I DNA and   95.2   0.052 1.3E-06   31.3   5.6  119   85-217   184-321 (660)
100 PRK08699 DNA polymerase III su  95.1    0.23 5.9E-06   27.2  13.8  183   54-279     5-190 (325)
101 KOG0338 consensus               95.1    0.18 4.5E-06   27.9   7.9  154   44-218   197-359 (691)
102 TIGR02782 TrbB_P P-type conjug  95.0    0.08   2E-06   30.1   6.0  100  329-440   170-279 (315)
103 KOG1015 consensus               94.8   0.081 2.1E-06   30.0   5.5  172   54-241   672-870 (1567)
104 TIGR03015 pepcterm_ATPase puta  94.8    0.28 7.3E-06   26.6  10.4  146   43-231    16-166 (269)
105 TIGR02768 TraA_Ti Ti-type conj  94.8   0.088 2.2E-06   29.8   5.7  119   52-230   416-538 (888)
106 KOG0330 consensus               94.6    0.11 2.9E-06   29.1   6.0  217   47-296    80-306 (476)
107 PRK06090 DNA polymerase III su  94.4    0.35 8.8E-06   26.1  15.2  177   54-279     7-185 (319)
108 PRK07940 DNA polymerase III su  94.4    0.35 8.9E-06   26.0  11.9  178   55-277    10-196 (395)
109 PRK06995 flhF flagellar biosyn  94.3    0.36 9.2E-06   26.0  10.4   40   79-118   178-218 (404)
110 COG1201 Lhr Lhr-like helicases  94.3    0.37 9.3E-06   25.9  11.1  129   48-204    20-162 (814)
111 PRK08770 DNA polymerase III su  94.1    0.41   1E-05   25.6  11.3  149   55-241    21-170 (663)
112 PRK13833 conjugal transfer pro  94.0    0.15 3.9E-06   28.3   5.6   32  359-391   206-237 (323)
113 TIGR03158 cas3_cyano CRISPR-as  94.0    0.43 1.1E-05   25.5  12.3   65   55-135     2-66  (357)
114 KOG1805 consensus               94.0    0.11 2.8E-06   29.2   4.7   42   81-124   689-730 (1100)
115 COG2607 Predicted ATPase (AAA+  93.9    0.45 1.1E-05   25.4  13.4   90   33-133    36-135 (287)
116 PRK12377 putative replication   93.9    0.45 1.1E-05   25.4  12.5   59   46-113    74-135 (248)
117 PRK11889 flhF flagellar biosyn  93.8    0.43 1.1E-05   25.5   7.6   28  375-402   388-415 (436)
118 TIGR03117 cas_csf4 CRISPR-asso  93.8    0.46 1.2E-05   25.3   9.1   44   81-124    20-63  (636)
119 pfam02456 Adeno_IVa2 Adenoviru  93.7    0.12 3.2E-06   28.9   4.6   59   79-140    89-147 (370)
120 PRK08181 transposase; Validate  93.6    0.49 1.3E-05   25.1   7.7  105   79-243   108-219 (269)
121 PRK13709 conjugal transfer nic  93.5    0.52 1.3E-05   25.0   8.5  159   10-228   938-1098(1756)
122 PRK10917 ATP-dependent DNA hel  93.5    0.53 1.3E-05   24.9   9.1   75   53-136   260-334 (677)
123 KOG0949 consensus               93.4    0.17 4.4E-06   28.0   4.9   69   48-130   510-578 (1330)
124 KOG2170 consensus               93.4    0.54 1.4E-05   24.9  11.3  123   55-232    91-226 (344)
125 PRK07246 bifunctional ATP-depe  93.3    0.56 1.4E-05   24.8  10.4   78   44-133   240-317 (820)
126 PRK05648 DNA polymerase III su  93.2    0.58 1.5E-05   24.7  11.2  149   55-241    21-170 (705)
127 KOG0389 consensus               93.2    0.34 8.6E-06   26.2   6.1  143   82-234   423-566 (941)
128 PRK06964 DNA polymerase III su  93.1    0.59 1.5E-05   24.6  10.2  192   54-277     5-207 (342)
129 PRK12724 flagellar biosynthesi  93.1     0.6 1.5E-05   24.6  11.9   28  463-490   370-397 (432)
130 PRK07132 DNA polymerase III su  93.1    0.61 1.5E-05   24.5  10.8  130   56-240     4-142 (303)
131 PRK12723 flagellar biosynthesi  93.0    0.61 1.6E-05   24.5  11.0   73  365-443   310-386 (388)
132 PRK07399 DNA polymerase III su  92.8    0.62 1.6E-05   24.5   7.1   75  189-276   123-197 (314)
133 KOG0388 consensus               92.8    0.44 1.1E-05   25.4   6.3  163   53-235   570-738 (1185)
134 KOG0342 consensus               92.7    0.56 1.4E-05   24.8   6.6  149   79-237   121-279 (543)
135 TIGR03029 EpsG chain length de  92.6    0.64 1.6E-05   24.4   6.8   81   33-118    56-143 (274)
136 TIGR02525 plasmid_TraJ plasmid  92.5    0.16   4E-06   28.3   3.6   32   82-113   154-185 (374)
137 PRK13894 conjugal transfer ATP  92.5    0.35 8.8E-06   26.1   5.3   33  358-391   210-242 (320)
138 TIGR00635 ruvB Holliday juncti  92.3    0.56 1.4E-05   24.8   6.2  104   44-218     2-108 (305)
139 KOG0331 consensus               92.2    0.78   2E-05   23.9   8.4  153   44-218   107-267 (519)
140 pfam00580 UvrD-helicase UvrD/R  92.2     0.3 7.6E-06   26.5   4.8   50   79-133    15-66  (494)
141 COG0470 HolB ATPase involved i  92.2    0.78   2E-05   23.8  11.4  108   80-235    27-154 (325)
142 PRK06731 flhF flagellar biosyn  92.0    0.83 2.1E-05   23.7   8.8   86   21-119    28-116 (270)
143 COG2812 DnaX DNA polymerase II  91.9    0.84 2.1E-05   23.6   8.2  149   55-241    21-170 (515)
144 PRK12727 flagellar biosynthesi  91.8    0.87 2.2E-05   23.5  11.9   48  352-399   361-413 (557)
145 KOG0339 consensus               91.7     0.9 2.3E-05   23.5   8.2  136   85-233   268-413 (731)
146 KOG0328 consensus               91.7    0.41   1E-05   25.6   5.0   64   48-123    47-111 (400)
147 TIGR01969 minD_arch cell divis  91.6    0.17 4.3E-06   28.0   3.0  188   79-282     2-204 (258)
148 cd03115 SRP The signal recogni  91.5    0.78   2E-05   23.8   6.3   38   80-118     3-40  (173)
149 COG1200 RecG RecG-like helicas  91.3    0.99 2.5E-05   23.2   9.2   75   52-135   264-338 (677)
150 pfam00448 SRP54 SRP54-type pro  91.1    0.43 1.1E-05   25.5   4.6   39   80-119     4-42  (196)
151 cd01128 rho_factor Transcripti  91.0    0.58 1.5E-05   24.6   5.2   36   79-114    18-53  (249)
152 KOG0335 consensus               90.8    0.53 1.3E-05   24.9   4.8   80   44-136    90-180 (482)
153 pfam05496 RuvB_N Holliday junc  90.6     1.1 2.9E-05   22.8   9.8  106   42-218    20-128 (234)
154 PRK06526 transposase; Provisio  90.6     1.1 2.9E-05   22.8   7.0   33   79-113   100-132 (254)
155 pfam05894 Podovirus_Gp16 Podov  90.3     1.2 3.1E-05   22.6  10.5  144   82-245    22-175 (333)
156 PRK13342 recombination factor   90.3     1.2 3.1E-05   22.6  11.5  120   80-269    40-159 (417)
157 smart00382 AAA ATPases associa  90.1     1.3 3.2E-05   22.5   7.0   39   79-119     4-42  (148)
158 KOG4284 consensus               90.1    0.43 1.1E-05   25.5   3.9  177   50-258    47-234 (980)
159 PRK05917 DNA polymerase III su  90.1     1.3 3.2E-05   22.5  13.2  165   52-271     4-169 (290)
160 PRK09105 putative aminotransfe  90.0     1.2 3.1E-05   22.6   6.1   59   50-121    78-136 (374)
161 pfam05673 DUF815 Protein of un  89.9     1.3 3.3E-05   22.4  12.5   91   34-135     4-105 (248)
162 PRK00411 cdc6 cell division co  89.8     1.3 3.4E-05   22.4  11.4  166   20-234    12-186 (394)
163 COG1702 PhoH Phosphate starvat  89.8    0.39 9.9E-06   25.8   3.5   51   53-115   131-181 (348)
164 COG1149 MinD superfamily P-loo  89.8    0.29 7.5E-06   26.5   2.8   27   77-103     1-28  (284)
165 cd02036 MinD Bacterial cell di  89.7    0.64 1.6E-05   24.4   4.5   32   80-113     2-34  (179)
166 TIGR00348 hsdR type I site-spe  89.7     1.4 3.5E-05   22.3  11.4  196   24-230   270-497 (813)
167 PRK11670 putative ATPase; Prov  89.6     0.7 1.8E-05   24.2   4.6   33   79-113   109-142 (369)
168 KOG0989 consensus               89.5     1.4 3.6E-05   22.3   8.5   58  186-243   124-182 (346)
169 PRK06696 uridine kinase; Valid  89.4    0.84 2.1E-05   23.7   4.9   54   55-113     7-60  (227)
170 PRK10919 ATP-dependent DNA hel  89.3    0.62 1.6E-05   24.5   4.2   43   80-122    18-62  (672)
171 COG1783 XtmB Phage terminase l  89.1    0.15 3.8E-06   28.4   0.9  198  190-390    53-271 (414)
172 PRK06835 DNA replication prote  89.1     1.5 3.8E-05   22.1   7.6   96   13-116   120-221 (330)
173 KOG0385 consensus               89.0     1.5 3.9E-05   22.0   8.8  165   36-234   159-331 (971)
174 PRK09183 transposase/IS protei  89.0     1.5 3.9E-05   22.0   7.3   33   79-113   103-135 (258)
175 PRK09694 hypothetical protein;  88.8     1.6   4E-05   21.9   9.6   57   79-136   305-361 (878)
176 PRK07952 DNA replication prote  88.6     1.6 4.2E-05   21.8  12.8   67   45-116    68-134 (242)
177 PRK12726 flagellar biosynthesi  88.5     1.6 4.2E-05   21.8   6.3  103  333-444   200-312 (407)
178 PRK02731 histidinol-phosphate   88.3     1.7 4.3E-05   21.7   6.9   60   49-121    63-122 (367)
179 KOG0334 consensus               88.2     1.7 4.4E-05   21.7   6.0  135   48-204   385-528 (997)
180 PRK07276 DNA polymerase III su  88.1     1.7 4.4E-05   21.7  12.0  184   53-291     5-190 (290)
181 PRK13341 recombination factor   87.9     1.8 4.6E-05   21.6   8.3   22   79-100    54-75  (726)
182 pfam00931 NB-ARC NB-ARC domain  87.6     1.9 4.8E-05   21.5  10.3  115   76-227    18-134 (285)
183 cd01983 Fer4_NifH The Fer4_Nif  87.6     1.3 3.2E-05   22.5   4.9   33   80-114     2-34  (99)
184 TIGR02868 CydC ABC transporter  87.5    0.57 1.5E-05   24.7   3.0   64   69-137   379-442 (566)
185 cd03110 Fer4_NifH_child This p  87.3     0.5 1.3E-05   25.1   2.7   21   79-99      1-22  (179)
186 PHA00149 DNA encapsidation pro  87.3       2   5E-05   21.3  10.5  187   82-291    22-226 (331)
187 TIGR03305 alt_F1F0_F1_bet alte  87.2     1.9 4.7E-05   21.5   5.5   37   77-113   138-174 (449)
188 PRK03321 putative aminotransfe  87.2     1.8 4.6E-05   21.6   5.5   59   49-120    53-111 (352)
189 cd02038 FleN-like FleN is a me  87.2     1.2 3.2E-05   22.6   4.6   82   80-236     2-84  (139)
190 KOG1803 consensus               87.0     1.3 3.3E-05   22.5   4.6   44   80-125   204-247 (649)
191 KOG3022 consensus               86.9     1.2   3E-05   22.7   4.4   34   78-113    48-82  (300)
192 PRK00149 dnaA chromosomal repl  86.8     1.5 3.9E-05   22.0   4.9   29   89-117    17-45  (447)
193 PRK08939 primosomal protein Dn  86.7     2.1 5.4E-05   21.1   8.3   60   55-117   137-196 (306)
194 KOG1123 consensus               86.6       1 2.5E-05   23.2   3.9  149   43-214   295-445 (776)
195 TIGR03346 chaperone_ClpB ATP-d  86.5     2.1 5.5E-05   21.1  11.2   53   43-105   170-222 (852)
196 COG0003 ArsA Predicted ATPase   86.5     1.1 2.7E-05   23.0   3.9  133   79-239     3-144 (322)
197 pfam09848 DUF2075 Uncharacteri  86.4     2.2 5.5E-05   21.0   7.8   38   80-117     4-42  (348)
198 cd02035 ArsA ArsA ATPase funct  86.3    0.99 2.5E-05   23.2   3.7   27   85-113     7-33  (217)
199 pfam02374 ArsA_ATPase Anion-tr  86.3     1.7 4.2E-05   21.8   4.9   31   82-114     6-36  (304)
200 cd01130 VirB11-like_ATPase Typ  86.2     2.2 5.5E-05   21.1   5.4   49   54-116    13-61  (186)
201 PRK11034 clpA ATP-dependent Cl  86.2     2.2 5.7E-05   21.0   8.9   52   43-104   183-234 (758)
202 cd02025 PanK Pantothenate kina  86.1     1.4 3.7E-05   22.2   4.5   34   80-113     2-35  (220)
203 PRK10037 cell division protein  85.8     1.8 4.6E-05   21.5   4.8   39   77-117     1-40  (250)
204 PRK08233 hypothetical protein;  85.7     1.2 3.1E-05   22.7   3.9   31   79-113     5-35  (182)
205 CHL00175 minD septum-site dete  85.7     1.5 3.9E-05   22.0   4.4   33   79-113    15-48  (279)
206 KOG0340 consensus               85.7     2.4   6E-05   20.8   8.0   92   31-136     9-102 (442)
207 cd00550 ArsA_ATPase Oxyanion-t  85.5     1.2 3.1E-05   22.6   3.9   29   84-114     7-35  (254)
208 COG4962 CpaF Flp pilus assembl  85.5     1.8 4.7E-05   21.5   4.8   56  333-391   211-270 (355)
209 PRK10818 cell division inhibit  85.3     1.7 4.2E-05   21.8   4.5   33   79-113     4-37  (270)
210 COG1647 Esterase/lipase [Gener  85.0     2.5 6.5E-05   20.6   6.4   94   31-137    43-139 (243)
211 pfam00308 Bac_DnaA Bacterial d  85.0     2.1 5.5E-05   21.1   4.9   35   80-114    37-71  (219)
212 PRK07309 aromatic amino acid a  85.0     2.6 6.5E-05   20.6  10.2   25   97-121   105-129 (390)
213 PRK11054 helD DNA helicase IV;  84.7     2.6 6.7E-05   20.5   6.0   78   52-134   175-263 (684)
214 TIGR01074 rep ATP-dependent DN  84.6     2.2 5.6E-05   21.0   4.8   63   55-136     8-72  (677)
215 TIGR01425 SRP54_euk signal rec  84.6     2.7 6.8E-05   20.5   5.8   48   84-135   128-175 (453)
216 PRK10689 transcription-repair   84.6     2.7 6.8E-05   20.5   9.1   55   55-117   605-659 (1148)
217 TIGR02545 ATP_syn_fliI flagell  84.4    0.97 2.5E-05   23.3   3.0   36  354-389   282-330 (439)
218 PRK07324 transaminase; Validat  84.3     2.7 6.9E-05   20.4   6.9   57   56-124    65-121 (373)
219 pfam03205 MobB Molybdopterin g  84.2     2.3   6E-05   20.8   4.8   33   79-113     2-34  (122)
220 PTZ00301 uridine kinase; Provi  84.0     2.3 5.8E-05   20.9   4.7   26   79-104     5-30  (210)
221 cd02034 CooC The accessory pro  84.0     2.4 6.1E-05   20.8   4.8   36   79-116     1-36  (116)
222 CHL00081 chlI Mg-protoporyphyr  83.7     2.9 7.4E-05   20.3   8.0   39   55-99     17-55  (347)
223 cd02037 MRP-like MRP (Multiple  83.6     2.3 5.9E-05   20.9   4.6   32   80-113     2-34  (169)
224 COG0593 DnaA ATPase involved i  83.5     2.9 7.5E-05   20.2   6.7   35   80-114   116-150 (408)
225 PRK05688 fliI flagellum-specif  83.4     1.7 4.3E-05   21.7   3.8   34   77-115   168-201 (451)
226 cd02042 ParA ParA and ParB of   83.3     1.8 4.5E-05   21.6   3.9   28   85-114     8-35  (104)
227 KOG1002 consensus               83.3     1.3 3.3E-05   22.4   3.2  164   52-239   186-364 (791)
228 pfam06564 YhjQ YhjQ protein. T  83.2     2.8 7.1E-05   20.4   4.9   36   77-114     1-37  (244)
229 PRK08149 ATP synthase SpaL; Va  83.2     1.6 4.1E-05   21.9   3.7   36   77-117   150-185 (427)
230 cd01135 V_A-ATPase_B V/A-type   83.2     1.9 4.8E-05   21.5   4.0   41   77-117    69-110 (276)
231 pfam03308 ArgK ArgK protein. T  83.0     3.1 7.9E-05   20.1   6.6   55   54-118    14-70  (267)
232 KOG0350 consensus               82.8     3.1   8E-05   20.0   6.9   78   52-133   161-240 (620)
233 COG2256 MGS1 ATPase related to  82.7     3.2 8.1E-05   20.0   8.6  120   82-270    53-172 (436)
234 TIGR01420 pilT_fam twitching m  82.4     1.1 2.9E-05   22.8   2.6   21   80-100   130-150 (350)
235 COG0514 RecQ Superfamily II DN  82.3     3.3 8.4E-05   19.9   5.8   58   45-122    15-72  (590)
236 PRK08636 aspartate aminotransf  82.3     3.3 8.4E-05   19.9   9.8   18  101-118   113-130 (403)
237 PRK03566 consensus              81.9     3.4 8.6E-05   19.8   7.8   59   50-121    64-122 (365)
238 TIGR03018 pepcterm_TyrKin exop  81.9     3.4 8.7E-05   19.8   7.3   68   49-117     5-76  (207)
239 TIGR01968 minD_bact septum sit  81.6       2 5.1E-05   21.3   3.6   32   80-113     4-36  (272)
240 PRK08118 topology modulation p  81.4     1.4 3.7E-05   22.2   2.8   27   77-103     1-27  (167)
241 PRK13909 putative recombinatio  81.1     3.6 9.2E-05   19.7   5.5   46  194-239   328-379 (911)
242 TIGR00959 ffh signal recogniti  81.0     1.8 4.7E-05   21.5   3.3   93   22-121    44-152 (439)
243 PRK05166 histidinol-phosphate   81.0     3.6 9.3E-05   19.6   6.5   60   49-121    69-128 (374)
244 PRK08972 fliI flagellum-specif  80.7     2.3 5.9E-05   20.9   3.7   33   78-115   161-193 (440)
245 cd01134 V_A-ATPase_A V/A-type   80.7     2.5 6.5E-05   20.6   3.9   22   79-100   159-180 (369)
246 cd01133 F1-ATPase_beta F1 ATP   80.6     3.2 8.1E-05   20.0   4.4   35   78-112    70-104 (274)
247 KOG1802 consensus               80.5     1.9 4.9E-05   21.4   3.2   40   80-120   428-467 (935)
248 COG1703 ArgK Putative periplas  80.4     3.8 9.7E-05   19.5   5.6   53   55-117    37-91  (323)
249 cd02028 UMPK_like Uridine mono  80.4     3.4 8.7E-05   19.8   4.5   34   80-113     2-35  (179)
250 PRK11174 cysteine/glutathione   80.2     3.9 9.9E-05   19.5   9.8   51  336-389   373-423 (588)
251 COG0610 Type I site-specific r  80.1     3.9   1E-04   19.4  17.7  199   12-232   213-415 (962)
252 PRK07721 fliI flagellum-specif  80.0     2.4 6.2E-05   20.8   3.6   23   78-100   157-179 (435)
253 KOG0387 consensus               79.9       4  0.0001   19.4  10.1  170   52-241   207-387 (923)
254 KOG0332 consensus               79.9       2 5.1E-05   21.3   3.2   68   47-124   109-177 (477)
255 TIGR01082 murC UDP-N-acetylmur  79.8       4  0.0001   19.4   5.5   36   79-116   110-145 (491)
256 TIGR00631 uvrb excinuclease AB  79.7       4  0.0001   19.4   7.8  116   55-220    14-132 (667)
257 COG1157 FliI Flagellar biosynt  79.7     2.5 6.3E-05   20.7   3.6   33   78-115   164-196 (441)
258 pfam01695 IstB IstB-like ATP b  79.6     4.1  0.0001   19.3   6.3   66   32-115    18-84  (178)
259 PRK07683 aminotransferase A; V  79.4     4.1  0.0001   19.3   5.5   22   99-120   105-126 (387)
260 pfam05729 NACHT NACHT domain.   79.4     2.4 6.1E-05   20.8   3.5   25   79-103     2-26  (165)
261 PRK04195 replication factor C   79.4     4.1  0.0001   19.3  11.3   56   37-100     3-63  (403)
262 PRK07196 fliI flagellum-specif  79.4     2.8 7.3E-05   20.3   3.8   34   77-115   155-188 (434)
263 TIGR00678 holB DNA polymerase   79.3     4.1 0.00011   19.3   9.3  159   79-276    16-195 (216)
264 PRK04841 transcriptional regul  79.3     4.1 0.00011   19.3  10.7  117   79-228    34-159 (903)
265 PRK12597 F0F1 ATP synthase sub  79.2     3.2 8.2E-05   20.0   4.0   36   77-112   141-176 (459)
266 TIGR01978 sufC FeS assembly AT  79.2     1.5 3.7E-05   22.2   2.3   20   80-99     29-48  (248)
267 PRK13235 nifH nitrogenase redu  79.0     4.2 0.00011   19.2   4.8   35   77-113     1-35  (274)
268 PRK07960 fliI flagellum-specif  79.0     2.9 7.5E-05   20.2   3.8   33   79-116   177-209 (455)
269 COG0455 flhG Antiactivator of   78.9     4.2 0.00011   19.2   4.8   35   78-113     3-38  (262)
270 KOG0951 consensus               78.9     4.3 0.00011   19.2   5.8   76   55-134   306-390 (1674)
271 smart00732 YqgFc Likely ribonu  78.7     4.3 0.00011   19.2   6.6   56  317-375     1-58  (99)
272 PRK11773 uvrD DNA-dependent he  78.7       1 2.5E-05   23.2   1.3   41   80-120    25-67  (722)
273 KOG0346 consensus               78.6     4.3 0.00011   19.1   6.5   56   80-136    59-121 (569)
274 TIGR03498 FliI_clade3 flagella  78.5     3.1 7.8E-05   20.1   3.8   34   77-115   140-173 (418)
275 TIGR03496 FliI_clade1 flagella  78.4     2.8 7.2E-05   20.3   3.6   33   78-115   138-170 (411)
276 KOG0384 consensus               78.0     4.5 0.00012   19.0   9.7  159   51-234   371-539 (1373)
277 KOG1133 consensus               77.9     4.6 0.00012   19.0   5.4   46   50-104    15-62  (821)
278 PRK12414 putative aminotransfe  77.6     4.7 0.00012   19.0   5.5   20  100-119   107-126 (384)
279 PRK13230 nitrogenase reductase  77.4     4.7 0.00012   18.9   5.0   35   77-113     1-35  (292)
280 TIGR01587 cas3_core CRISPR-ass  77.4     4.7 0.00012   18.9   4.8   50   80-130     2-54  (424)
281 PRK07590 L,L-diaminopimelate a  77.1     4.8 0.00012   18.9   7.1   57   55-119    78-134 (409)
282 PRK03158 histidinol-phosphate   77.1     4.8 0.00012   18.9   7.3   59   50-121    61-119 (359)
283 TIGR00643 recG ATP-dependent D  77.0     4.8 0.00012   18.9   8.2  157   54-230   311-472 (721)
284 CHL00060 atpB ATP synthase CF1  77.0     4.8 0.00012   18.9   6.1   37   77-113   155-191 (480)
285 pfam07570 consensus             76.9     2.3   6E-05   20.8   2.8   26   81-106    16-41  (45)
286 PRK06793 fliI flagellum-specif  76.9     3.4 8.7E-05   19.8   3.6   33   78-113   157-189 (432)
287 PRK06002 fliI flagellum-specif  76.9       4  0.0001   19.4   4.0   23   78-100   166-188 (450)
288 cd02040 NifH NifH gene encodes  76.9     4.9 0.00012   18.8   5.0   35   77-113     1-35  (270)
289 COG3640 CooC CO dehydrogenase   76.7     4.9 0.00013   18.8   4.9  116  280-400    99-219 (255)
290 pfam07728 AAA_5 AAA domain (dy  76.7     4.9 0.00013   18.8   7.4   25  194-218    69-93  (139)
291 PHA02518 ParA-like protein; Pr  76.7     3.4 8.8E-05   19.8   3.6   28   85-114     9-36  (211)
292 TIGR01081 mpl UDP-N-acetylmura  76.6       3 7.8E-05   20.1   3.3   53   43-113    84-136 (459)
293 PRK07594 type III secretion sy  76.5     3.1 7.9E-05   20.1   3.3   23   78-100   156-178 (433)
294 PRK13634 cbiO cobalt transport  76.4    0.36 9.2E-06   26.0  -1.5   37   54-98      5-41  (276)
295 PRK07667 uridine kinase; Provi  76.3     2.3   6E-05   20.8   2.7   24   78-101    15-38  (190)
296 PRK08472 fliI flagellum-specif  75.7       3 7.7E-05   20.1   3.1   23   78-100   159-181 (435)
297 KOG0327 consensus               75.6     2.2 5.7E-05   21.0   2.4   66   47-124    45-111 (397)
298 PRK08533 flagellar accessory p  75.6     5.3 0.00013   18.6   6.9   47   73-119    20-66  (230)
299 PRK08927 fliI flagellum-specif  75.3       4  0.0001   19.4   3.6   36   78-118   159-194 (441)
300 COG1074 RecB ATP-dependent exo  75.2     5.4 0.00014   18.6   5.7   57  182-239   370-427 (1139)
301 PRK08116 hypothetical protein;  75.1     5.4 0.00014   18.5   5.7   53   55-113    90-142 (262)
302 PRK06067 flagellar accessory p  75.1     5.4 0.00014   18.5   6.5   48   73-120    28-75  (241)
303 PRK09270 frcK putative fructos  74.9     5.5 0.00014   18.5   6.8   35   78-112    35-69  (230)
304 PRK06217 hypothetical protein;  74.9     2.9 7.4E-05   20.3   2.8   28   77-104     1-28  (185)
305 PRK05480 uridine kinase; Provi  74.9     2.7 6.9E-05   20.4   2.7   24   78-101     7-30  (209)
306 PRK07777 aminotransferase; Val  74.8     5.5 0.00014   18.5   4.4   27  209-238   150-176 (386)
307 PRK06820 type III secretion sy  74.7     2.7 6.9E-05   20.4   2.6   23   78-100   164-186 (445)
308 TIGR03371 cellulose_yhjQ cellu  74.3     5.7 0.00014   18.4   4.5   36   77-114     1-37  (246)
309 PRK08912 hypothetical protein;  74.3     5.7 0.00015   18.4   5.1   23   98-120   102-124 (387)
310 PRK13705 plasmid-partitioning   74.2     5.7 0.00015   18.4   6.2   33   80-114   109-142 (388)
311 PRK13231 nitrogenase reductase  74.2     5.7 0.00015   18.4   4.4   41   77-120     2-44  (264)
312 KOG1411 consensus               74.0     3.3 8.4E-05   19.9   2.9   26  445-472   394-419 (427)
313 KOG2749 consensus               74.0     5.8 0.00015   18.4   4.6   30   75-104   101-130 (415)
314 PRK04196 V-type ATP synthase s  73.9     5.1 0.00013   18.7   3.9   32   78-109   144-175 (460)
315 PRK09280 F0F1 ATP synthase sub  73.9     5.8 0.00015   18.4   6.8   38   76-113   144-181 (466)
316 COG2842 Uncharacterized ATPase  73.9     5.8 0.00015   18.4   7.4  109   78-231    95-203 (297)
317 PRK06348 aspartate aminotransf  73.9     5.8 0.00015   18.3   6.6   60   56-122    69-128 (383)
318 cd02024 NRK1 Nicotinamide ribo  73.8     2.9 7.4E-05   20.2   2.6   21   80-100     2-22  (187)
319 PHA02519 plasmid partition pro  73.7     5.9 0.00015   18.3   6.2   65   54-120    82-148 (387)
320 KOG0257 consensus               73.7     5.9 0.00015   18.3   8.4   26  210-238   164-189 (420)
321 cd04169 RF3 RF3 subfamily.  Pe  73.7     4.5 0.00011   19.1   3.5   27   78-104     3-29  (267)
322 cd02023 UMPK Uridine monophosp  73.7       3 7.6E-05   20.2   2.6   22   80-101     2-23  (198)
323 cd01120 RecA-like_NTPases RecA  73.7     5.9 0.00015   18.3   5.6   36   80-117     2-37  (165)
324 PRK04870 histidinol-phosphate   73.6     5.9 0.00015   18.3  10.0   60   50-121    60-119 (356)
325 COG0572 Udk Uridine kinase [Nu  73.6       3 7.6E-05   20.2   2.6   24   77-100     8-31  (218)
326 pfam00485 PRK Phosphoribulokin  73.5     2.9 7.4E-05   20.2   2.6   22   80-101     2-23  (196)
327 PRK13851 type IV secretion sys  73.2     4.9 0.00012   18.8   3.6   95  334-440   201-303 (343)
328 TIGR00955 3a01204 Pigment prec  72.9     1.8 4.7E-05   21.5   1.4  155   55-243    44-245 (671)
329 pfam01935 DUF87 Domain of unkn  72.8     6.2 0.00016   18.2   4.6   38   79-117    25-62  (218)
330 pfam00437 GSPII_E Type II/IV s  72.7     6.2 0.00016   18.2   6.0   28  361-389   202-229 (283)
331 TIGR01194 cyc_pep_trnsptr cycl  72.7     3.1   8E-05   20.1   2.6   49  338-390   367-417 (555)
332 PRK07261 topology modulation p  72.5     3.5   9E-05   19.7   2.8   26   78-103     1-26  (171)
333 PRK09099 type III secretion sy  72.4     4.5 0.00011   19.1   3.3   23   78-100   164-186 (441)
334 PRK05957 aspartate aminotransf  72.4     6.3 0.00016   18.1   4.8   59   56-120    68-126 (389)
335 PRK10636 putative ABC transpor  72.3     2.9 7.4E-05   20.2   2.3   41  186-228   162-203 (638)
336 PRK13869 plasmid-partitioning   72.1     4.7 0.00012   18.9   3.4   32   81-114   125-157 (405)
337 PRK11147 ABC transporter ATPas  72.1     3.2 8.1E-05   20.0   2.5   43  184-228   167-210 (632)
338 PRK13900 type IV secretion sys  72.0     5.8 0.00015   18.4   3.8   35  356-391   223-257 (332)
339 PRK13232 nifH nitrogenase redu  72.0     6.5 0.00016   18.1   4.8   35   77-113     1-35  (273)
340 PRK11664 ATP-dependent RNA hel  71.8     6.5 0.00017   18.0   6.6   56   58-123     9-64  (812)
341 TIGR01281 DPOR_bchL light-inde  71.7       4  0.0001   19.4   2.9   22  345-366   144-165 (275)
342 TIGR03453 partition_RepA plasm  71.7     4.8 0.00012   18.9   3.3   33   80-114   107-140 (387)
343 TIGR02788 VirB11 P-type DNA tr  71.6     4.9 0.00013   18.8   3.4   21   80-100   161-181 (328)
344 KOG0347 consensus               71.4     3.3 8.4E-05   19.9   2.4  151   45-215   198-365 (731)
345 TIGR00150 TIGR00150 conserved   71.3     4.4 0.00011   19.1   3.1   35   81-120    32-66  (147)
346 pfam00142 Fer4_NifH 4Fe-4S iro  71.0     6.8 0.00017   17.9   4.8   33   79-113     2-34  (269)
347 cd01136 ATPase_flagellum-secre  71.0     4.6 0.00012   19.0   3.1   34   77-115    69-102 (326)
348 TIGR03497 FliI_clade2 flagella  71.0     4.7 0.00012   18.9   3.1   23   78-100   138-160 (413)
349 PRK09082 putative aminotransfe  70.9     6.8 0.00017   17.9   9.7   60   56-121    70-129 (386)
350 TIGR02546 III_secr_ATP type II  70.7     3.5 8.9E-05   19.8   2.4   31   79-114   155-185 (430)
351 PRK06315 type III secretion sy  70.6     3.5   9E-05   19.7   2.5   25   77-101   164-188 (442)
352 TIGR01166 cbiO cobalt ABC tran  70.6     3.9  0.0001   19.4   2.7   26   73-98     14-39  (190)
353 PRK01688 histidinol-phosphate   70.6     6.9 0.00018   17.9   8.5   59   49-120    53-112 (355)
354 cd00984 DnaB_C DnaB helicase C  70.4       7 0.00018   17.9   4.8   35   80-115    16-50  (242)
355 KOG0062 consensus               70.4     5.1 0.00013   18.7   3.2  143   68-221    97-247 (582)
356 cd00009 AAA The AAA+ (ATPases   70.0     7.1 0.00018   17.8  10.4   34   78-113    20-53  (151)
357 PRK09435 arginine/ornithine tr  70.0     7.1 0.00018   17.8   6.4   56   53-118    33-90  (325)
358 PRK13407 bchI magnesium chelat  69.7     7.2 0.00018   17.8   4.6   50  180-232   120-182 (334)
359 pfam01637 Arch_ATPase Archaeal  69.6     7.3 0.00019   17.7  13.7   35   80-116    23-57  (223)
360 PRK07337 aminotransferase; Val  69.3     7.4 0.00019   17.7   5.0   25   96-120   103-127 (388)
361 KOG4181 consensus               69.2     4.8 0.00012   18.9   2.9   13  412-424   361-373 (491)
362 PRK08069 consensus              69.1     7.5 0.00019   17.7   5.1   59   56-121    70-128 (390)
363 pfam09140 MipZ ATPase MipZ. Mi  69.0       7 0.00018   17.8   3.7   32   86-119    10-41  (261)
364 KOG2825 consensus               68.8     3.5   9E-05   19.7   2.1   38   79-116    20-58  (323)
365 PRK04863 mukB cell division pr  68.6     4.2 0.00011   19.2   2.5   34   79-115    29-62  (1486)
366 TIGR00958 3a01208 antigen pept  68.4     3.7 9.5E-05   19.6   2.2   22   80-101   562-583 (770)
367 KOG0920 consensus               68.2     7.8  0.0002   17.6  12.3  158   54-242   177-339 (924)
368 pfam08419 consensus             67.9     7.9  0.0002   17.5   3.9   39   52-99     57-97  (116)
369 COG0488 Uup ATPase components   67.9       5 0.00013   18.8   2.7   26   76-101    28-53  (530)
370 cd01863 Rab18 Rab18 subfamily.  67.9       5 0.00013   18.8   2.7   21   78-98      1-21  (161)
371 PRK11819 putative ABC transpor  67.6     4.8 0.00012   18.9   2.6   37  190-228   180-217 (556)
372 PRK00081 coaE dephospho-CoA ki  67.6     5.1 0.00013   18.7   2.8   31   77-113     2-32  (199)
373 pfam01656 CbiA CobQ/CobB/MinD/  67.5       8  0.0002   17.5   4.1   32   80-113     1-33  (212)
374 PRK05922 type III secretion sy  67.4     7.8  0.0002   17.5   3.7   35   77-116   157-191 (434)
375 TIGR00604 rad3 DNA repair heli  67.3     3.7 9.3E-05   19.6   2.0   72   53-133    18-126 (813)
376 TIGR00580 mfd transcription-re  67.3     8.1 0.00021   17.5   6.3   75   55-137   513-590 (997)
377 PRK06107 aspartate aminotransf  67.3     8.1 0.00021   17.4   5.6   59   56-122    73-132 (402)
378 PRK04192 V-type ATP synthase s  67.2     6.8 0.00017   17.9   3.3   32   79-115   229-260 (585)
379 pfam04310 MukB MukB N-terminal  67.1     5.1 0.00013   18.7   2.6   36   79-117    29-64  (227)
380 PRK05298 excinuclease ABC subu  67.1     8.2 0.00021   17.4   7.6   64   55-131    18-81  (657)
381 cd01886 EF-G Elongation factor  66.8     6.5 0.00016   18.1   3.1  108   80-212     2-113 (270)
382 COG4240 Predicted kinase [Gene  66.5     8.4 0.00021   17.4   4.8   45   56-105    34-78  (300)
383 cd04116 Rab9 Rab9 subfamily.    66.0     6.7 0.00017   17.9   3.1   24   75-98      3-26  (170)
384 PRK06375 consensus              66.0     8.6 0.00022   17.3   5.7   58   56-122    69-127 (381)
385 TIGR00603 rad25 DNA repair hel  65.8     6.3 0.00016   18.2   2.9  147   43-213   262-412 (756)
386 cd01124 KaiC KaiC is a circadi  65.6     8.7 0.00022   17.2   6.2   39   80-120     2-42  (187)
387 cd03289 ABCC_CFTR2 The CFTR su  65.3     6.2 0.00016   18.2   2.8   34   77-113    30-63  (275)
388 PRK13764 ATPase; Provisional    64.7     9.1 0.00023   17.1   4.4   14  463-476   581-594 (605)
389 PRK07367 consensus              64.7     9.1 0.00023   17.1   8.7   58   55-120    67-125 (385)
390 PRK03317 histidinol-phosphate   64.6     9.1 0.00023   17.1   9.5   64   50-121    62-126 (369)
391 PRK13540 cytochrome c biogenes  64.5     6.1 0.00016   18.2   2.7   26   75-100    25-50  (200)
392 KOG0345 consensus               64.4     9.2 0.00023   17.1   8.3   45   79-123    45-95  (567)
393 PRK11331 5-methylcytosine-spec  64.4     9.2 0.00023   17.1   4.2   17  256-272   200-216 (459)
394 cd01869 Rab1_Ypt1 Rab1/Ypt1 su  64.3     7.1 0.00018   17.8   3.0   22   77-98      2-23  (166)
395 PRK06358 threonine-phosphate d  64.1     9.3 0.00024   17.1   6.2   57   50-121    51-107 (354)
396 KOG0781 consensus               64.1     9.3 0.00024   17.1  10.7  158  316-492   377-571 (587)
397 PRK09751 putative ATP-dependen  64.0     9.4 0.00024   17.1   8.0   42   82-123     1-53  (1490)
398 cd03247 ABCC_cytochrome_bd The  63.8     6.3 0.00016   18.1   2.6   36   77-114    28-63  (178)
399 pfam00071 Ras Ras family. Incl  63.6     6.3 0.00016   18.1   2.6   20   79-98      1-20  (162)
400 cd03369 ABCC_NFT1 Domain 2 of   63.5     7.2 0.00018   17.8   2.8   25   76-100    33-57  (207)
401 cd01868 Rab11_like Rab11-like.  63.3     7.7  0.0002   17.6   3.0   22   77-98      3-24  (165)
402 COG0563 Adk Adenylate kinase a  63.3     8.6 0.00022   17.3   3.2   28   79-106     2-29  (178)
403 PRK06936 type III secretion sy  63.0     5.7 0.00015   18.4   2.3   23   78-100   163-185 (439)
404 PRK03262 consensus              63.0     9.8 0.00025   16.9   8.6   60   49-121    53-113 (355)
405 PRK00950 histidinol-phosphate   62.8     9.8 0.00025   16.9   7.7   59   50-120    67-125 (369)
406 PRK13640 cbiO cobalt transport  62.7     6.5 0.00017   18.0   2.5   23   77-99     34-56  (283)
407 PRK13886 conjugal transfer pro  62.7     9.3 0.00024   17.1   3.3   34   85-118    11-44  (241)
408 TIGR00750 lao LAO/AO transport  62.5      10 0.00025   16.9   5.7   34  354-387   122-155 (333)
409 PRK06425 histidinol-phosphate   62.4      10 0.00025   16.9   6.8   58   49-121    36-93  (332)
410 cd04114 Rab30 Rab30 subfamily.  62.4     9.7 0.00025   17.0   3.4   25   74-98      4-28  (169)
411 PRK13543 cytochrome c biogenes  62.3     7.6 0.00019   17.6   2.8   21   78-98     38-58  (214)
412 COG3911 Predicted ATPase [Gene  62.3     8.9 0.00023   17.2   3.2   27   78-104    10-36  (183)
413 cd01892 Miro2 Miro2 subfamily.  62.2     8.7 0.00022   17.2   3.1   23   76-98      3-25  (169)
414 TIGR01313 therm_gnt_kin carboh  62.2     6.3 0.00016   18.1   2.4   47   85-137     6-52  (175)
415 cd03291 ABCC_CFTR1 The CFTR su  62.2     7.2 0.00018   17.8   2.7   23   77-99     63-85  (282)
416 cd01865 Rab3 Rab3 subfamily.    62.1       8  0.0002   17.5   2.9   22   77-98      1-22  (165)
417 PRK03333 coaE dephospho-CoA ki  62.0     7.1 0.00018   17.8   2.6   24   77-100     1-24  (394)
418 COG0210 UvrD Superfamily I DNA  62.0      10 0.00026   16.8   5.6   53   79-136    17-71  (655)
419 cd03277 ABC_SMC5_euk Eukaryoti  62.0     6.6 0.00017   18.0   2.4   21   81-101    27-47  (213)
420 cd03278 ABC_SMC_barmotin Barmo  61.8     8.8 0.00022   17.2   3.1   25   73-98     19-43  (197)
421 PRK13409 putative ATPase RIL;   61.7     7.5 0.00019   17.7   2.7   54   45-98     66-120 (590)
422 cd03249 ABC_MTABC3_MDL1_MDL2 M  61.7     7.6 0.00019   17.6   2.7   26   75-100    27-52  (238)
423 smart00175 RAB Rab subfamily o  61.6     7.7  0.0002   17.6   2.7   21   78-98      1-21  (164)
424 cd04168 TetM_like Tet(M)-like   61.5      10 0.00026   16.8   4.9  109   80-213     2-114 (237)
425 cd04107 Rab32_Rab38 Rab38/Rab3  61.4       8  0.0002   17.5   2.8   21   78-98      1-21  (201)
426 TIGR03539 DapC_actino succinyl  61.4      10 0.00027   16.8   5.6   59   55-120    58-118 (357)
427 cd02032 Bchl_like This family   61.4      10 0.00027   16.8   4.8   34   79-114     2-35  (267)
428 pfam01580 FtsK_SpoIIIE FtsK/Sp  61.3      10 0.00027   16.7   4.6   39   79-117    40-80  (202)
429 PRK13538 cytochrome c biogenes  61.3     7.5 0.00019   17.6   2.6   21   78-98     28-48  (204)
430 pfam07724 AAA_2 AAA domain (Cd  61.3      10 0.00027   16.7   7.5   27  189-216    74-100 (168)
431 cd03246 ABCC_Protease_Secretio  61.3     7.2 0.00018   17.8   2.5   27   75-101    26-52  (173)
432 cd02019 NK Nucleoside/nucleoti  61.1       7 0.00018   17.8   2.5   22   80-101     2-23  (69)
433 cd03223 ABCD_peroxisomal_ALDP   61.1     6.9 0.00018   17.9   2.4   30  193-222   111-141 (166)
434 PRK13849 putative crown gall t  61.0      11 0.00027   16.7   3.7   36   80-117     4-40  (231)
435 cd04127 Rab27A Rab27a subfamil  61.0     8.9 0.00023   17.2   3.0   23   76-98      3-25  (180)
436 PRK09302 circadian clock prote  60.9      11 0.00027   16.7   6.4   49   73-121    20-69  (501)
437 PRK13873 conjugal transfer ATP  60.9      11 0.00027   16.7   4.6   41  354-397   455-496 (815)
438 cd04110 Rab35 Rab35 subfamily.  60.9      10 0.00026   16.9   3.2   24   75-98      4-27  (199)
439 PRK06851 hypothetical protein;  60.8      11 0.00027   16.7   4.5   48   79-126    33-80  (368)
440 PRK07568 aspartate aminotransf  60.7      11 0.00027   16.7   8.9   59   55-121    68-126 (396)
441 PRK04220 2-phosphoglycerate ki  60.6     9.7 0.00025   17.0   3.1   26   76-101    91-116 (306)
442 COG4555 NatA ABC-type Na+ tran  60.6      11 0.00027   16.7   3.9   22   79-100    30-51  (245)
443 TIGR01526 nadR_NMN_Atrans nico  60.4     8.7 0.00022   17.3   2.8   24  279-302   206-229 (346)
444 cd03248 ABCC_TAP TAP, the Tran  60.3       8  0.0002   17.5   2.6   24   78-101    41-64  (226)
445 PRK13233 nifH nitrogenase redu  60.2      11 0.00028   16.6   4.8   40   78-118     3-44  (275)
446 cd00154 Rab Rab family.  Rab G  60.2     8.6 0.00022   17.3   2.8   22   78-99      1-22  (159)
447 cd04119 RJL RJL (RabJ-Like) su  60.1     8.4 0.00021   17.4   2.7   21   78-98      1-21  (168)
448 COG1855 ATPase (PilT family) [  60.0      10 0.00027   16.7   3.2   17  461-477   578-594 (604)
449 COG1239 ChlI Mg-chelatase subu  60.0      11 0.00028   16.6   6.7   38  194-231   147-197 (423)
450 cd04103 Centaurin_gamma Centau  59.6       9 0.00023   17.2   2.8   22   78-99      1-22  (158)
451 cd03228 ABCC_MRP_Like The MRP   59.4     8.7 0.00022   17.3   2.7   37   75-113    26-62  (171)
452 COG1428 Deoxynucleoside kinase  59.3      11 0.00029   16.5   5.3   50   78-132     5-54  (216)
453 cd01131 PilT Pilus retraction   59.3      11 0.00029   16.5   3.8   34   80-114     4-37  (198)
454 PRK08727 hypothetical protein;  59.2      11 0.00029   16.5   4.5   32   80-113    44-75  (233)
455 TIGR02773 addB_Gpos ATP-depend  59.1      11 0.00029   16.5   3.5  157   86-296    10-187 (1192)
456 TIGR02746 TraC-F-type type-IV   59.1      11 0.00029   16.5   4.5   40   79-120   491-532 (900)
457 cd03225 ABC_cobalt_CbiO_domain  59.0     8.8 0.00022   17.2   2.7   20   79-98     29-48  (211)
458 CHL00181 cbbX CbbX; Provisiona  59.0      11 0.00029   16.5  10.7   72  192-269   124-204 (287)
459 KOG2355 consensus               58.9     7.9  0.0002   17.5   2.4   27   72-98     35-61  (291)
460 PRK13632 cbiO cobalt transport  58.9       8  0.0002   17.5   2.4   22   77-98     36-57  (273)
461 TIGR02640 gas_vesic_GvpN gas v  58.8     8.2 0.00021   17.4   2.5  186   76-294    20-222 (265)
462 PRK13539 cytochrome c biogenes  58.8     8.8 0.00022   17.2   2.6   21   78-98     29-49  (206)
463 PRK07543 consensus              58.8      12 0.00029   16.5   9.1   58   55-120    70-128 (400)
464 cd03236 ABC_RNaseL_inhibitor_d  58.7     8.6 0.00022   17.3   2.5   20   79-98     28-47  (255)
465 cd04125 RabA_like RabA-like su  58.6     9.4 0.00024   17.0   2.8   22   78-99      1-22  (188)
466 cd03290 ABCC_SUR1_N The SUR do  58.6     9.1 0.00023   17.1   2.7   23   76-98     26-48  (218)
467 cd01867 Rab8_Rab10_Rab13_like   58.6      10 0.00026   16.8   3.0   22   77-98      3-24  (167)
468 PRK13648 cbiO cobalt transport  58.5       9 0.00023   17.2   2.6   24   76-99     34-57  (269)
469 cd03240 ABC_Rad50 The catalyti  58.5     9.1 0.00023   17.1   2.7   20   79-98     24-43  (204)
470 cd03222 ABC_RNaseL_inhibitor T  58.5     9.1 0.00023   17.1   2.7   21   78-98     26-46  (177)
471 PRK10751 molybdopterin-guanine  58.5      12  0.0003   16.4   4.4   33   80-114     5-37  (170)
472 PRK10247 putative ABC transpor  58.3     9.2 0.00024   17.1   2.7   23   77-99     33-55  (225)
473 TIGR01026 fliI_yscN ATPase Fli  58.3       6 0.00015   18.3   1.7   60   50-114   144-206 (455)
474 PRK13650 cbiO cobalt transport  58.3     8.7 0.00022   17.2   2.5   22   78-99     31-52  (276)
475 KOG0343 consensus               58.2      12  0.0003   16.4   6.3  280   12-323    53-391 (758)
476 cd01861 Rab6 Rab6 subfamily.    58.2     9.5 0.00024   17.0   2.7   20   79-98      2-21  (161)
477 COG1373 Predicted ATPase (AAA+  58.1      12  0.0003   16.4   9.7   37  193-231    96-132 (398)
478 PRK10876 recB exonuclease V su  57.9      12  0.0003   16.4   6.0   52  186-239   373-424 (1181)
479 cd00157 Rho Rho (Ras homology)  57.9     9.8 0.00025   16.9   2.8   21   78-98      1-21  (171)
480 cd04138 H_N_K_Ras_like H-Ras/N  57.7      11 0.00028   16.6   2.9   22   78-99      2-23  (162)
481 COG3421 Uncharacterized protei  57.7      12 0.00031   16.4   3.9   32   85-117     5-36  (812)
482 TIGR02173 cyt_kin_arch cytidyl  57.6     8.8 0.00023   17.2   2.5   36   79-120     2-37  (173)
483 cd00876 Ras Ras family.  The R  57.6     9.3 0.00024   17.1   2.6   21   79-99      1-21  (160)
484 cd03250 ABCC_MRP_domain1 Domai  57.6     9.1 0.00023   17.1   2.5   25   75-99     29-53  (204)
485 pfam03029 ATP_bind_1 Conserved  57.5      12 0.00031   16.3   3.7   32   82-113     1-32  (234)
486 pfam07015 VirC1 VirC1 protein.  57.4      12 0.00031   16.3   3.9   47   80-129     4-51  (231)
487 pfam06733 DEAD_2 DEAD_2. This   57.3     3.9   1E-04   19.4   0.6   24  193-216   141-164 (168)
488 PRK10867 signal recognition pa  57.2      12 0.00031   16.3  15.9   96   20-120    43-143 (453)
489 cd01864 Rab19 Rab19 subfamily.  57.2      11 0.00029   16.5   3.0   22   77-98      3-24  (165)
490 cd04136 Rap_like Rap-like subf  57.1      11 0.00028   16.6   2.9   21   78-98      2-22  (163)
491 KOG0057 consensus               57.0      11 0.00028   16.7   2.8   68  319-389   352-425 (591)
492 cd04123 Rab21 Rab21 subfamily.  57.0      11 0.00027   16.7   2.8   22   78-99      1-22  (162)
493 cd03237 ABC_RNaseL_inhibitor_d  56.9       9 0.00023   17.2   2.4   20   79-98     27-46  (246)
494 cd02026 PRK Phosphoribulokinas  56.8      10 0.00026   16.9   2.6   32   80-113     2-33  (273)
495 PRK10575 iron-hydroxamate tran  56.8     9.5 0.00024   17.0   2.5   22   77-98     37-58  (265)
496 KOG0348 consensus               56.8      12 0.00032   16.3   8.0  136   48-204   157-300 (708)
497 KOG0979 consensus               56.8     8.2 0.00021   17.4   2.2   18   82-99     47-64  (1072)
498 cd03226 ABC_cobalt_CbiO_domain  56.8      10 0.00026   16.9   2.6   22   78-99     27-48  (205)
499 PRK04328 hypothetical protein;  56.7      13 0.00032   16.3   6.9   51   74-124    21-71  (250)
500 PRK00080 ruvB Holliday junctio  56.7      13 0.00032   16.2   9.8  107   42-217    21-128 (328)

No 1  
>pfam03237 Terminase_6 Terminase-like family. This family represents a group of terminase proteins.
Probab=100.00  E-value=5e-36  Score=245.82  Aligned_cols=356  Identities=18%  Similarity=0.113  Sum_probs=255.3

Q ss_pred             EECCCCCCHHHHHHHHHHHHHHHCCCCEEEEEECCHHHHHHHHHHHHHHHHHHCHHCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             50257659789999999999980899669998085899999999999999985500013444322222233344432111
Q gi|254781215|r   82 ISAGRGIGKTTLNAWLVLWLMSTRPGISVICLANSETQLKTTLWAEVSKWLSLLPNKHWFEMQSLSLHPAPWYSDVLHCS  161 (511)
Q Consensus        82 V~sgrG~GKS~l~a~l~lw~l~~~p~~kv~vtApt~~Q~~~ilw~Ei~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  161 (511)
                      +..|||.|||++++..++++++.+|+.+++++++|+.|++.++|+.+..+.......   ........         .+ 
T Consensus         2 ~~ggr~~GKT~~~~~~~~~~a~~~~~~~~~i~~~t~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~---------~i-   68 (380)
T pfam03237         2 ILGSRQSGKTFAFAREALRHALGNGPKNQIILSASKAQARLEFKKGIIEIAGDLLEI---TFEEKNGN---------PI-   68 (380)
T ss_pred             CCCCCCCCHHHHHHHHHHHHHHHCCCCCEEEEECCHHHHHHHHHHHHHHHHHHHCCC---CEEECCCC---------EE-
T ss_conf             426452528399999999999858997289997999999999999999966886387---16727887---------39-


Q ss_pred             CCCCCCEEEEEECCCCCCCCCHHHHCCCCCCEEEEECCHHCCCHHH-HHHH-HHHHCCCCCCEEEEEECCCCCCCCHHHH
Q ss_conf             2357861698530357556100212026761499971110299788-9888-8885079981389982389987655676
Q gi|254781215|r  162 LGIDSKHYSTMCRTYSEERPDTFVGHHNTYGMAIINDEASGTPDVI-NLGI-LGFLTERNANRFWIMTSNPRRLSGKFYE  239 (511)
Q Consensus       162 ~~~~~~~~~~~~~~~s~~~~ea~~G~h~~~~~lvI~DEAsgI~d~i-~e~i-~~~Lt~~g~~~~~i~~~nP~~~~g~fy~  239 (511)
                       ...++..+...   +.+++.+.++++|....++++||++.+++.. +..+ .+.++....+  .+.++||.+...+||+
T Consensus        69 -~~~nGs~i~~~---~~~~~~~~~~~rG~~~~~i~~DE~a~~~~~~~~~~~~~~~~~~~~~~--~~~~stp~~~~~~~~~  142 (380)
T pfam03237        69 -ILPNGAKLYFL---GLESETTAQGYRGASIAGIYFDEATWLPKFQESELVRRLRATKGKWR--KTFFSTPPSPGHWVYD  142 (380)
T ss_pred             -EECCCCEEEEE---ECCCCCCHHHCCCCCCCEEEEEEHHHCCCHHHHHHHHHHHCCCCCCC--EEEEECCCCCCCCHHH
T ss_conf             -91599889996---25776643103485455499830453662789999864410479975--7999889899851989


Q ss_pred             HHHCCC-------CCCEEEEECCCCCCCCCHHHHHHHHHHCCCCHHHHHHHHCCCCCCCCCCEEECHHHHHHHHHCCCCC
Q ss_conf             530352-------4741798404336778977899999751898013544431756666787375599998864076531
Q gi|254781215|r  240 IFNKPL-------DDWKRFQIDTRTVEGIDPSFHEGIIARYGLDSDVTRVEVCGQFPQQDIDSFIPLNIIEEALNREPCP  312 (511)
Q Consensus       240 ~~~~~~-------~~w~~~~i~~~~~p~~~~~~ie~~~~~~geds~~~r~evlgeFp~~~~~~~i~~~~ie~a~~r~~~~  312 (511)
                      .+....       ..|..++++..++|..++++++++++.|++  ..|+++++|+|.. +++++++..+++.+......+
T Consensus       143 ~~~~~~~~~~~~~~~~~~~~~t~~d~~~~~~~~~e~l~~~~~~--~~~~qe~~g~f~~-~~g~if~~~~~~~~~~~~~~~  219 (380)
T pfam03237       143 FWTGWLDDKGKRTFIPADVEVTIEDARALGPEYKEELRALYSD--EEFARLLMGEWVD-TSGSIFKRFELERCDVDEERP  219 (380)
T ss_pred             HHHHHCCCCCCCCEEEEEEECCHHHHCCCCHHHHHHHHHHCCH--HHHHHHHCCCEEC-CCCCEECHHHHHHCCCCCCCC
T ss_conf             9855401677752022067456687132688999999876899--9999985886665-788571478885464675568


Q ss_pred             CCCCEEEEEEECCCC-CCCCEEEEEE---CCC--EEEEEEECCCCCHHHHHHHHHHHHHHCCCCEEEEEECCCCHHHHHH
Q ss_conf             899708999623334-7841799982---275--5899873277898899999999998618882998006876368898
Q gi|254781215|r  313 DPYAPLIMGCDIAEE-GGDNTVVVLR---RGP--VIEHLFDWSKTDLRTTNNKISGLVEKYRPDAIIIDANNTGARTCDY  386 (511)
Q Consensus       313 ~~~~~~viGvDVAr~-G~D~svi~~r---~G~--~v~~~~~~~~~d~~~~a~~i~~~~~~~~~~~i~iD~~GvG~gV~d~  386 (511)
                      .....+++|+|+|.+ ++|.+++++.   .+.  .+......++.++.+++..+.++..+|++..+++|.+|.|.++.+.
T Consensus       220 p~~~~~~~g~D~~~~~~~D~t~~~v~~~~~~~~~~~~~~~~~~~~~~~~~a~~i~~~~~~~~~~~i~id~~~~G~~~~~~  299 (380)
T pfam03237       220 PEHREVIGGVDPAASRGGDYAALVVIAEVDGDKFYVLAREHERGLSPAEQAAIIKKLAERYNVIYIYIDDTGGGESVAQL  299 (380)
T ss_pred             CCCCEEEEEECCCCCCCCCCEEEEEEEECCCCEEEEEEEEEECCCCHHHHHHHHHHHHHHCCCEEEEEECCCCCCHHHHH
T ss_conf             88855999986788888996699999965798599999998368899999999999986438759998378643079999


Q ss_pred             HHHCCCE-EEEECCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCC--CCH---HHHHHHHHCCCEEEECCCCEEEEEECHH
Q ss_conf             9864982-798427777664025522799999999999970899--981---8999998579679987998499984125
Q gi|254781215|r  387 LEMLGYH-VYRVLGQKRAVDLEFCRNRRTELHVKMADWLEFASL--INH---SGLIQNLKSLKSFIVPNTGELAIESKRV  460 (511)
Q Consensus       387 L~~~g~~-v~~v~~~~~~~~~~~y~N~rae~~~~~re~l~~g~l--~~d---~~l~~el~~~~~~~~~~~gki~ie~Kkk  460 (511)
                      |++.+.. .++++.+.+         -|....-.++..++.|++  +.+   ..+++||.... +  +.++      .++
T Consensus       300 l~~~~~~~~~~~~~a~~---------~k~~~~~~v~~l~e~g~v~i~~~~~~~~~i~el~~~~-~--~~~~------~~~  361 (380)
T pfam03237       300 LRRELPGAAFTVRPAPK---------GKNARVLKVSDLIESGRLKVPRGAWCPASFEELEAYH-T--DGGN------ERS  361 (380)
T ss_pred             HHHHCCCCCCCEEECCC---------HHHHHHHHHHHHHHCCCEEEECCCCHHHHHHHHHHHH-H--CCCC------CCC
T ss_conf             99866446711058875---------1999999999999889899947862699999997503-0--3899------899


Q ss_pred             HCCCCCCHHHHHHHHHC
Q ss_conf             48999898999999975
Q gi|254781215|r  461 KGAKSTDYSDGLMYTFA  477 (511)
Q Consensus       461 rg~~SPD~ADAl~l~fa  477 (511)
                      ....|+|.+||+.++..
T Consensus       362 ~~~~hdd~~DAl~yAi~  378 (380)
T pfam03237       362 DVDGHDDAADALRYALN  378 (380)
T ss_pred             CCCCCCHHHHHHHHHHH
T ss_conf             99999889999999986


No 2  
>pfam03354 Terminase_1 Phage Terminase. The majority of the members of this family are bacteriophage proteins, several of which are thought to be terminase large subunit proteins. There are also a number of bacterial proteins of unknown function.
Probab=99.96  E-value=1.7e-24  Score=173.01  Aligned_cols=394  Identities=16%  Similarity=0.116  Sum_probs=240.4

Q ss_pred             HHHHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHH--CCCCEEEEEECCHHHHHHHHHHHHHH
Q ss_conf             8999999999998740565554210124650257659789999999999980--89966999808589999999999999
Q gi|254781215|r   53 SWQLEFMEVVDAHCLNSVNNPNPEVFKGAISAGRGIGKTTLNAWLVLWLMST--RPGISVICLANSETQLKTTLWAEVSK  130 (511)
Q Consensus        53 ~WQ~e~l~~i~~~~~~~~~~~~~~~~r~aV~sgrG~GKS~l~a~l~lw~l~~--~p~~kv~vtApt~~Q~~~ilw~Ei~k  130 (511)
                      +||+.++.+|..+..+.   ..+.++++.+.-|||+|||+++|+++|+.+++  .++..++++|+|.+|++ ++|.++++
T Consensus         1 PwQ~f~i~~ifGw~~~~---g~Rrfr~~~i~v~RkNGKS~l~a~i~ly~~~~~ge~~~ei~~~A~~~~QA~-~~f~~~~~   76 (473)
T pfam03354         1 PWQKFILGLMFGWRKGC---GVRRFREAYVSVGRKNGKSYLMAIRVLYELLLGGKSNQEILVAATTFKQAE-KLFKYVKN   76 (473)
T ss_pred             CCHHHHHHHEEEEEECC---CCEEEEEEEEEEECCCCHHHHHHHHHHHHHHHCCCCCCEEEEEECCHHHHH-HHHHHHHH
T ss_conf             94615625144189289---988999999998268602699999999999709983874999979899999-99999999


Q ss_pred             HHHHCHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCCCCCCCHHHHCCCCCCEEEEECCHHCCC-HHHHH
Q ss_conf             99855000134443222222333444321112357861698530357556100212026761499971110299-78898
Q gi|254781215|r  131 WLSLLPNKHWFEMQSLSLHPAPWYSDVLHCSLGIDSKHYSTMCRTYSEERPDTFVGHHNTYGMAIINDEASGTP-DVINL  209 (511)
Q Consensus       131 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~ea~~G~h~~~~~lvI~DEAsgI~-d~i~e  209 (511)
                      +++.+|........      ..+......+.+...+.  ++...++   ++.+.+|.+   ..++|+||.+..+ ..+++
T Consensus        77 mi~~~p~l~~~~~~------~~~~~~~~~i~~~~t~s--~~~~ls~---~~~~~dG~~---~~~~i~DE~h~~~~~~~~~  142 (473)
T pfam03354        77 QVKLSPFLSIANEN------KLLKSQKDGIEMKINNN--VFKALSN---NGDQYDGGN---PSLAIFDEMHEFKDRELVS  142 (473)
T ss_pred             HHHCCHHHHHHHHC------CCCCCCCEEEEECCCCC--EEEEEEC---CCCCCCCCC---CCEEEEEECCCCCCHHHHH
T ss_conf             99739877755301------10131001589807896--8999857---898766998---7289987223048827899


Q ss_pred             HHHHHHCCCCCCEEEEEECCCCCCCCHHHHHHHC------C---CCCCEEEEE----C-----------CCCCCCC----
Q ss_conf             8888850799813899823899876556765303------5---247417984----0-----------4336778----
Q gi|254781215|r  210 GILGFLTERNANRFWIMTSNPRRLSGKFYEIFNK------P---LDDWKRFQI----D-----------TRTVEGI----  261 (511)
Q Consensus       210 ~i~~~Lt~~g~~~~~i~~~nP~~~~g~fy~~~~~------~---~~~w~~~~i----~-----------~~~~p~~----  261 (511)
                      +++..+........++.+....+..+.+++.+..      .   .++-..+-+    +           ...||.+    
T Consensus       143 ~l~sg~~~r~~~l~~~ITTag~~~~~~~~~~~~~~~~vl~g~~~~~d~~~f~~i~~~d~~dd~~D~~~W~kANP~lg~~~  222 (473)
T pfam03354       143 TIVTGMRKQDNPQTIQITTAGPNRGGPYDEEREYIKRILEGDVERDDDSYFGLIYELDNDDEVKDPAKWIKANPLLGSSL  222 (473)
T ss_pred             HHHHHHHCCCCCEEEEECCCCCCCCCHHHHHHHHHHHHHCCCCCCCCCCEEEEEEECCCCCCCCCHHHHHHHCCCCCCCC
T ss_conf             99876316888719997677889887189999999999708777678766999971698877689899998596767887


Q ss_pred             CHHHHHH-HHHHC--CCCHHHHHHHHCCCCCCCCCCEEECHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCCCEEEEE--
Q ss_conf             9778999-99751--898013544431756666787375599998864076531899708999623334784179998--
Q gi|254781215|r  262 DPSFHEG-IIARY--GLDSDVTRVEVCGQFPQQDIDSFIPLNIIEEALNREPCPDPYAPLIMGCDIAEEGGDNTVVVL--  336 (511)
Q Consensus       262 ~~~~ie~-~~~~~--geds~~~r~evlgeFp~~~~~~~i~~~~ie~a~~r~~~~~~~~~~viGvDVAr~G~D~svi~~--  336 (511)
                      +.+.+.+ ..+..  +...+.|++..++.|..++++.+++.+.+++|... ...-.+.++++|+|.|..+|-.++..+  
T Consensus       223 ~~~~l~~~~~~a~~~p~~~~~f~~k~lN~w~~~~~~~wl~~~~w~~~~~~-~~~~~g~~~~~G~DlS~~~Dlta~~~~~~  301 (473)
T pfam03354       223 TRDNLLKGLIDAIGSPLKMNKFLTKNFNLWMGQDTDSWLTLQDWEQAVFP-PFDINGRRVYIGVDLSMKGDVTALVFVYP  301 (473)
T ss_pred             CHHHHHHHHHHHHHCHHHHHHHHHHHCCCEECCCCCCCCCHHHHHHCCCC-HHHHCCCEEEEEEEECCCCCCCEEEEEEE
T ss_conf             99999999999864937689999972386344544657899999747898-57847996999984035776413799999


Q ss_pred             ECCCE-------------------------------EEEEEECCCCCHHHHHHHHHHHHHHC--CCCEEEEEECCCCHHH
Q ss_conf             22755-------------------------------89987327789889999999999861--8882998006876368
Q gi|254781215|r  337 RRGPV-------------------------------IEHLFDWSKTDLRTTNNKISGLVEKY--RPDAIIIDANNTGART  383 (511)
Q Consensus       337 r~G~~-------------------------------v~~~~~~~~~d~~~~a~~i~~~~~~~--~~~~i~iD~~GvG~gV  383 (511)
                      ..|..                               +..+..-.-.|...+...|.+++.+|  +...|.+|.-+. ...
T Consensus       302 ~~~~~~~~~~~~ip~~~~~~~~~~~~~y~~w~~~G~~l~~~~g~~iD~~~v~~~i~~~~~~~~~~v~~i~yD~~~a-~~~  380 (473)
T pfam03354       302 LDGKFYLHAHSFIPESQAEQIKQDGINYREFIDRGECLTLHDGGMIDPNQIIPWILDFITKTGLDVQAIGYDPWQA-KYF  380 (473)
T ss_pred             ECCEEEEEEEEECCHHHHHHHHCCCCCHHHHHHHCCEEEECCCCEECHHHHHHHHHHHHHHCCCCEEEEEECHHHH-HHH
T ss_conf             7899999998656862766654015568999970987994489832699999999999996299725998466789-999


Q ss_pred             HHHHHHCCC--EEEEECCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCH-HHHHHHHHCCCEEEECCCCEEEEEECHH
Q ss_conf             898986498--2798427777664025522799999999999970899981-8999998579679987998499984125
Q gi|254781215|r  384 CDYLEMLGY--HVYRVLGQKRAVDLEFCRNRRTELHVKMADWLEFASLINH-SGLIQNLKSLKSFIVPNTGELAIESKRV  460 (511)
Q Consensus       384 ~d~L~~~g~--~v~~v~~~~~~~~~~~y~N~rae~~~~~re~l~~g~l~~d-~~l~~el~~~~~~~~~~~gki~ie~Kkk  460 (511)
                      ++.|.+.|.  +++.+.-+.....         ..--.+.+.+.+|++..+ +.++.--.+.=..+.+.+|-+++..  +
T Consensus       381 ~~~le~~g~~~~~v~~~Q~~~~ls---------~~~k~le~~~~~g~i~h~~npvl~w~~~Na~~~~d~~gni~~~K--~  449 (473)
T pfam03354       381 IDRLESTFLDWPLVEIRQGFFSLS---------NPIKELQELVAENKLTHDGNPVMAWALNNAVIKIDAIGNIKINK--K  449 (473)
T ss_pred             HHHHHHCCCCCCEEEECCCCCCCC---------HHHHHHHHHHHCCCEEECCCHHHHHHHCCEEEEECCCCCEEEEC--C
T ss_conf             999996189986698468763007---------79999999997799899968999999709899986999988702--5


Q ss_pred             HCCCCCCHHHHHHHHHC
Q ss_conf             48999898999999975
Q gi|254781215|r  461 KGAKSTDYSDGLMYTFA  477 (511)
Q Consensus       461 rg~~SPD~ADAl~l~fa  477 (511)
                      +--+-=|-++|++||+.
T Consensus       450 ~s~~KID~~~A~v~A~~  466 (473)
T pfam03354       450 KSTDKIDPAVALIMAMG  466 (473)
T ss_pred             CCCCCCCHHHHHHHHHH
T ss_conf             77899489999999999


No 3  
>pfam04466 Terminase_3 Phage terminase large subunit. Initiation of packaging of double-stranded viral DNA involves the specific interaction of the prohead with viral DNA in a process mediated by a phage-encoded terminase protein. The terminase enzymes are usually hetero-oligomers composed of a small and a large subunit. This region is found on the large subunit and possess an endonuclease and ATPase activity that require Mg2+ and a neutral or slightly basic reaction. This region is also found in bacterial sequences.
Probab=99.95  E-value=4.1e-24  Score=170.68  Aligned_cols=363  Identities=16%  Similarity=0.129  Sum_probs=229.4

Q ss_pred             EEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEEECCHHHHHHHHHHHHHHHHHHCHHCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             65025765978999999999998089966999808589999999999999998550001344432222223334443211
Q gi|254781215|r   81 AISAGRGIGKTTLNAWLVLWLMSTRPGISVICLANSETQLKTTLWAEVSKWLSLLPNKHWFEMQSLSLHPAPWYSDVLHC  160 (511)
Q Consensus        81 aV~sgrG~GKS~l~a~l~lw~l~~~p~~kv~vtApt~~Q~~~ilw~Ei~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  160 (511)
                      .+.+|||.|||..+|..++-.++.+| .+++|+.++..++++.+|+++++.+..+.....+..+...+....        
T Consensus         6 v~~GGrgsgKS~~~a~~~i~~~~~~~-~~~l~~r~~~~slr~sv~~~~~~~i~~~~~~~~~~~~~s~~~i~~--------   76 (387)
T pfam04466         6 VAKGGRGSGKSYHIALKLVLKLLMHP-RTNLVIREVKNTIEDSVFTQLQEALSMLGLDHEFKISKSPIEITV--------   76 (387)
T ss_pred             EEEECCCCHHHHHHHHHHHHHHHHCC-CEEEEEECCHHHHHHHHHHHHHHHHHHCCCCCEEEECCCCEEEEE--------
T ss_conf             99908886799999999999998789-869999755688999999999999997699734897376148998--------


Q ss_pred             CCCCCCCEEEEEECCCCCCCCCHHHHCCCCCCEEEEECCHHCCCHHHHHHHHHHHCCCCCCEEEEEECCCCCCCCHHHHH
Q ss_conf             12357861698530357556100212026761499971110299788988888850799813899823899876556765
Q gi|254781215|r  161 SLGIDSKHYSTMCRTYSEERPDTFVGHHNTYGMAIINDEASGTPDVINLGILGFLTERNANRFWIMTSNPRRLSGKFYEI  240 (511)
Q Consensus       161 ~~~~~~~~~~~~~~~~s~~~~ea~~G~h~~~~~lvI~DEAsgI~d~i~e~i~~~Lt~~g~~~~~i~~~nP~~~~g~fy~~  240 (511)
                        . .+++.+...   +.++|+++.|+.+  ..++++|||+.++.+.|+.+.++|...+....++++.||.....++|+.
T Consensus        77 --~-~~gs~i~f~---G~d~~~~iks~~~--i~~~~~eEa~~~~~~~~~~l~~~~r~~~~~~~i~~~~NP~~~~~w~~~~  148 (387)
T pfam04466        77 --K-INGSKFLFY---GMDDPAKIKSIKD--VSDAWIEEAAEFKTEDFDQLIPTIRRPKPGSEIFMSFNPVNKLNWTYKR  148 (387)
T ss_pred             --C-CCCCEEEEE---ECCCHHHHHCCCC--CEEEEEECHHHCCHHHHHHHHHHHCCCCCCEEEEEECCCCCCCCHHHHH
T ss_conf             --7-899699998---5789688416366--1499994124479989999998853178871999982899987748899


Q ss_pred             HHCC-----CCCCEEEEECCCCCCCCCHHHHHHHHHHCCCCHHHHHHHHCCCCCCCCCCEEECHHHHHHHHHCCCCCCCC
Q ss_conf             3035-----24741798404336778977899999751898013544431756666787375599998864076531899
Q gi|254781215|r  241 FNKP-----LDDWKRFQIDTRTVEGIDPSFHEGIIARYGLDSDVTRVEVCGQFPQQDIDSFIPLNIIEEALNREPCPDPY  315 (511)
Q Consensus       241 ~~~~-----~~~w~~~~i~~~~~p~~~~~~ie~~~~~~geds~~~r~evlgeFp~~~~~~~i~~~~ie~a~~r~~~~~~~  315 (511)
                      |-+.     .+++..++..+.|||++++++++++.+.+..|+..|++.++|+|...+..+|-..+..  ...........
T Consensus       149 ~~~~~~~~~~~~~~~~~~ty~DNp~L~~~~i~~~e~~k~~dp~~y~~~~lGe~~~~~g~V~~~~~~~--~~~~~~~~~~~  226 (387)
T pfam04466       149 FFKNDKSELDDDTYIHHSTYRDNPFLPEVDIREIEELKRRNPDYYRIEYLGEFGGLGTLVLPNFEIK--PLWVEAAEDAH  226 (387)
T ss_pred             HHCCCCCCCCCCEEEEEEEECCCCCCCHHHHHHHHHHHHCCHHHHHHHHCCCEEECCCEEEECCEEE--ECCCCCHHHHH
T ss_conf             7417754677885999999616998999999999998703999989977571563487797354455--52326402200


Q ss_pred             CEEEEEEECCCCCCCCEEEEE----ECCCEEEEEEECCCCCHHHHHHHHHHHHHHC--CCCEEEEEECCCCHHHHHHHHH
Q ss_conf             708999623334784179998----2275589987327789889999999999861--8882998006876368898986
Q gi|254781215|r  316 APLIMGCDIAEEGGDNTVVVL----RRGPVIEHLFDWSKTDLRTTNNKISGLVEKY--RPDAIIIDANNTGARTCDYLEM  389 (511)
Q Consensus       316 ~~~viGvDVAr~G~D~svi~~----r~G~~v~~~~~~~~~d~~~~a~~i~~~~~~~--~~~~i~iD~~GvG~gV~d~L~~  389 (511)
                      ..+.+|+|.+- ..|.++++.    ..+..+...+++.+.....+...+.+.....  ....|..|  ..-.-.+..++.
T Consensus       227 ~~~~~G~D~G~-~~dpta~v~~~~~~~~~~lyi~~e~y~~~~~~~~~~~~~~~~~~~~~~~~i~~d--sa~p~~i~~~~~  303 (387)
T pfam04466       227 IKLGFKRDFGF-DESATASVRGALDVKKKVIYLYDEYYDPANQAIDDRTAEVLRDKNYTKEAIKAD--SAEAKSIAALKS  303 (387)
T ss_pred             CCCCCCEECCC-CCCCCEEEEEEEECCCCEEEEEEEEECCCCCCCCHHHHHHHHHCCCCCCEEECC--CCCCCHHHHHHH
T ss_conf             03342135464-378877999999779989999999984678766089999988637666502236--768525679987


Q ss_pred             CC-CEEEEECCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCC-----CCHHHHHHHHHCCCEEEECCCCEEEEEECHHHCC
Q ss_conf             49-82798427777664025522799999999999970899-----9818999998579679987998499984125489
Q gi|254781215|r  390 LG-YHVYRVLGQKRAVDLEFCRNRRTELHVKMADWLEFASL-----INHSGLIQNLKSLKSFIVPNTGELAIESKRVKGA  463 (511)
Q Consensus       390 ~g-~~v~~v~~~~~~~~~~~y~N~rae~~~~~re~l~~g~l-----~~d~~l~~el~~~~~~~~~~~gki~ie~Kkkrg~  463 (511)
                      .+ +.+.+..-+..+.      ....+.--.++..+..+++     +....+++||..-. |+.++.|+..  ++  -.-
T Consensus       304 ~~~~~~~~~~k~~~sv------~~gi~~l~~~~~i~~~~~~~~~~~~~C~~~i~E~~~Y~-w~~d~~g~~~--~~--p~d  372 (387)
T pfam04466       304 PGIFKIVGAKKGPGSV------LQKTRFLDTFRAVLIGEYLDPDDIPRCENTIEELNKYQ-YKKDKNGALI--PD--EMK  372 (387)
T ss_pred             HCCHHHHCCCCCCCCH------HHHHHHHHHHHHHHHCCCCEECCCCCCHHHHHHHHCCE-ECCCCCCCCC--CC--CCC
T ss_conf             1543441230489727------88888999999996057620026878989999997781-3668999988--88--889


Q ss_pred             CCCCHHHHHHHHH
Q ss_conf             9989899999997
Q gi|254781215|r  464 KSTDYSDGLMYTF  476 (511)
Q Consensus       464 ~SPD~ADAl~l~f  476 (511)
                      .-+...||+-++.
T Consensus       373 ~~dH~~DAlRYav  385 (387)
T pfam04466       373 KDPHTIDAIRYAV  385 (387)
T ss_pred             CCCCHHHHHHHHH
T ss_conf             9872577677602


No 4  
>COG4626 Phage terminase-like protein, large subunit [General function prediction only]
Probab=99.83  E-value=1.2e-15  Score=117.27  Aligned_cols=392  Identities=14%  Similarity=0.061  Sum_probs=236.1

Q ss_pred             HHHHHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHH--CCCCEEEEEECCHHHHHHHHHHHHH
Q ss_conf             58999999999998740565554210124650257659789999999999980--8996699980858999999999999
Q gi|254781215|r   52 RSWQLEFMEVVDAHCLNSVNNPNPEVFKGAISAGRGIGKTTLNAWLVLWLMST--RPGISVICLANSETQLKTTLWAEVS  129 (511)
Q Consensus        52 ~~WQ~e~l~~i~~~~~~~~~~~~~~~~r~aV~sgrG~GKS~l~a~l~lw~l~~--~p~~kv~vtApt~~Q~~~ilw~Ei~  129 (511)
                      .+||+.++-+|.....++.+.-  .+--..+.-||+.|||+++|.+.++.++.  +-+..+.+.||+..|+. .+|.+++
T Consensus        63 ~PwQkFiia~l~G~~~k~T~~r--rf~e~fI~v~RkngKt~l~A~i~~~~~l~~~~~~~~~~i~A~s~~qa~-~~F~~ar  139 (546)
T COG4626          63 EPWQKFIVAALFGFYDKQTGIR--RFKEAFIFIPRKNGKSTLAAGIMMTALLLNWRSGAGIYILAPSVEQAA-NSFNPAR  139 (546)
T ss_pred             CCHHHHHHHHHHHEEECCCCEE--EEEEEEEEEECCCCHHHHHHHHHHHHHHHHHCCCCEEEEEECCHHHHH-HHHHHHH
T ss_conf             5189999998760350578706--888999997457855789999999998765304760899834289998-8768999


Q ss_pred             HHHHHCHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCCCCCCCHHHHCCCCCCEEEEECCHHCCCH--HH
Q ss_conf             9998550001344432222223334443211123578616985303575561002120267614999711102997--88
Q gi|254781215|r  130 KWLSLLPNKHWFEMQSLSLHPAPWYSDVLHCSLGIDSKHYSTMCRTYSEERPDTFVGHHNTYGMAIINDEASGTPD--VI  207 (511)
Q Consensus       130 k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~ea~~G~h~~~~~lvI~DEAsgI~d--~i  207 (511)
                      -++...+..        .... .+...+..+.+......  +.+.   +.++...+|.|.   .++|+||-+-..+  +.
T Consensus       140 ~mv~~~~~l--------~~~~-~~~~~s~~i~~~~~~s~--ik~~---aa~~~~~Dg~~~---~~~I~DEih~f~~~~~~  202 (546)
T COG4626         140 DMVKRDDDL--------RDLC-NVQTHSRTITHRKTDST--IKAV---AADPNTVDGLNS---VGAIIDELHLFGKQEDM  202 (546)
T ss_pred             HHHHHCCCH--------HHHC-CCCCCEEEEEECCCCEE--EEEH---HCCCCCCCCCCC---CEEEEEHHHHHCCHHHH
T ss_conf             998737213--------3320-65454048986155111--3301---048875567876---54887637541678999


Q ss_pred             HHHHHHHHCCC-CCCEEEEEECCCCCCCCHHHHHHHCCC---C----CCEEEEEC---------------CCCCCCCC--
Q ss_conf             98888885079-981389982389987655676530352---4----74179840---------------43367789--
Q gi|254781215|r  208 NLGILGFLTER-NANRFWIMTSNPRRLSGKFYEIFNKPL---D----DWKRFQID---------------TRTVEGID--  262 (511)
Q Consensus       208 ~e~i~~~Lt~~-g~~~~~i~~~nP~~~~g~fy~~~~~~~---~----~w~~~~i~---------------~~~~p~~~--  262 (511)
                      +.++.+.|-.. +...+-+.| -+....|+|++..+...   +    +-..+.+-               .-.||++.  
T Consensus       203 ~~~~~~g~~ar~~~l~~~ITT-~g~~~~g~~~q~~~y~k~vl~g~~~d~~~f~~i~e~Dd~~e~~dpe~w~kaNPnlg~s  281 (546)
T COG4626         203 YSEAKGGLGARPEGLVVYITT-SGDPPAGVFKQKLQYAKDVLDGKIKDPHFFPVIYELDEEGEHDDPENWAKANPNLGVS  281 (546)
T ss_pred             HHHHHHHHCCCCCCEEEEEEC-CCCCCCCHHHHHHHHHHHHHCCCCCCCCEEEEEEECCCCCCCCCHHHHHHCCCCCCCE
T ss_conf             999974201576763999966-8988741899999999998669878821079999768820003867774308876514


Q ss_pred             --HHHHHH-HHHHC--CCCHHHHHHHHCCCCCCCCCCEEECHHHHHHHHHC--CCCCCCCCEEEEEEECCCCCCCCEE-E
Q ss_conf             --778999-99751--89801354443175666678737559999886407--6531899708999623334784179-9
Q gi|254781215|r  263 --PSFHEG-IIARY--GLDSDVTRVEVCGQFPQQDIDSFIPLNIIEEALNR--EPCPDPYAPLIMGCDIAEEGGDNTV-V  334 (511)
Q Consensus       263 --~~~ie~-~~~~~--geds~~~r~evlgeFp~~~~~~~i~~~~ie~a~~r--~~~~~~~~~~viGvDVAr~G~D~sv-i  334 (511)
                        .+++.. +++..  +.....|..+-++.|... .+.+++.+.++++..+  +.....+..|++|+|.|...|..++ +
T Consensus       282 v~~~~l~s~~~ka~~~~q~~~dF~tK~lNi~~~~-~~~~~~~~~w~~~~~~~lde~~~~gq~c~~G~Dls~~~D~ts~al  360 (546)
T COG4626         282 VDEAFLYSEYRKARNAPQEARDFMTKHLNIWIGA-SDAWFGADFWEQQGRTVLDEILLRGQVCYGGIDLSGLDDLTSMAL  360 (546)
T ss_pred             EEHHHHHHHHHHHHCCCHHCHHHHHCCCCEEECH-HHCCCCHHHHHHHCCCCCCHHHHCCCEEEEEECCCCCCCCCCEEE
T ss_conf             2077777699987318111227775123315100-102468689997314456535514866899733234555541068


Q ss_pred             EEEC--CCEE-EEEEE-------------------C-----------CCCCHHHHHHHHHHHHHHCCCCEEEEEECCCCH
Q ss_conf             9822--7558-99873-------------------2-----------778988999999999986188829980068763
Q gi|254781215|r  335 VLRR--GPVI-EHLFD-------------------W-----------SKTDLRTTNNKISGLVEKYRPDAIIIDANNTGA  381 (511)
Q Consensus       335 ~~r~--G~~v-~~~~~-------------------~-----------~~~d~~~~a~~i~~~~~~~~~~~i~iD~~GvG~  381 (511)
                      .-|+  +..+ ..-+.                   |           ...|+.++.+.+.+..+.+....|.+|.-|. .
T Consensus       361 ~f~~~~~~~~i~~~h~wv~~~~~~~~k~~~~~~~ew~k~G~lTit~~~~id~~~I~ew~~~~~~~~~i~~v~~D~~g~-~  439 (546)
T COG4626         361 VGRYRETDEWIGWGHAWVHRAAVKRRKSEAPRLQEWVKAGDLTITRRDLIDYAEIVEWFMEIREKFLIKLVGFDPSGA-G  439 (546)
T ss_pred             EEECCCCCEEEEECCCCCHHHHCCCHHHCCHHHHHHHHCCCEEEECCCCCCHHHHHHHHHHHHHHCCCCEEEECCCCH-H
T ss_conf             875378762788424551243113201024668999975927973787313899999999998737851885564432-8


Q ss_pred             HHHHHHHHCCCEEEEECCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCC-CHHHHHHHHHCCCEEEECCCCEEEEEECHH
Q ss_conf             6889898649827984277776640255227999999999999708999-818999998579679987998499984125
Q gi|254781215|r  382 RTCDYLEMLGYHVYRVLGQKRAVDLEFCRNRRTELHVKMADWLEFASLI-NHSGLIQNLKSLKSFIVPNTGELAIESKRV  460 (511)
Q Consensus       382 gV~d~L~~~g~~v~~v~~~~~~~~~~~y~N~rae~~~~~re~l~~g~l~-~d~~l~~el~~~~~~~~~~~gki~ie~Kkk  460 (511)
                      .+.++|.+.|+++.++.-+=.        ++ .+.--.+-..+.+|.+. .|+.+..--+..-....+.++-++.  ||+
T Consensus       440 ~~~~~l~~~g~~lv~i~Q~~~--------~l-~~~~k~~e~~~~~g~i~~~dnp~m~wcv~Nv~~~~~~n~~~~~--kk~  508 (546)
T COG4626         440 EFRDALAEAGIKVVGIPQGFK--------KL-SGAIKTIERKLAEGVLVHGDNPLMEWCVGNVVVEEKGNAIIIT--KKV  508 (546)
T ss_pred             HHHHHHHHCCCCEEECCCHHH--------HH-CCHHHHHHHHHHCCCEEECCCHHHHHHHCCEEEEECCCCCCCC--CCC
T ss_conf             899999847995434450055--------54-7426789999866958978970787753107999628864010--024


Q ss_pred             HCCCCCCHHHHHHHHHC
Q ss_conf             48999898999999975
Q gi|254781215|r  461 KGAKSTDYSDGLMYTFA  477 (511)
Q Consensus       461 rg~~SPD~ADAl~l~fa  477 (511)
                      .+-+-=|.+||+.+|+.
T Consensus       509 ~~~~KID~~~A~v~A~~  525 (546)
T COG4626         509 SGNGKIDPFMALVNAVS  525 (546)
T ss_pred             CCCCCCCHHHHHHHHHH
T ss_conf             77677479999999999


No 5  
>COG5323 Uncharacterized conserved protein [Function unknown]
Probab=99.67  E-value=4.2e-15  Score=113.84  Aligned_cols=343  Identities=17%  Similarity=0.201  Sum_probs=231.7

Q ss_pred             EEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEEECCHHHHHHHHHHHHHHHHHHCH-HCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             465025765978999999999998089966999808589999999999999998550-0013444322222233344432
Q gi|254781215|r   80 GAISAGRGIGKTTLNAWLVLWLMSTRPGISVICLANSETQLKTTLWAEVSKWLSLLP-NKHWFEMQSLSLHPAPWYSDVL  158 (511)
Q Consensus        80 ~aV~sgrG~GKS~l~a~l~lw~l~~~p~~kv~vtApt~~Q~~~ilw~Ei~k~~~~~~-~~~~~~~~~~~~~~~~~~~~~~  158 (511)
                      -.+-.|||.|||...|-.+.|.++-.|  .+..+++|...+++++-.-......... .++-++..-+   ...|.+   
T Consensus        39 WL~~GGRGsGKTrAGAeWv~~~Algkp--SiALvgeTl~DaREVMidGpSGi~~~~~~~RPr~EaSRR---RL~WpN---  110 (410)
T COG5323          39 WLMLGGRGSGKTRAGAEWVTWNALGKP--SIALVGETLHDAREVMIDGPSGIMYHAGASRPRLEASRR---RLDWPN---  110 (410)
T ss_pred             EEEECCCCCCCCCCCCEEEEEHHCCCC--CHHHHHCCCCCHHHHHHCCCHHHHHHHHCCCCHHHHHHH---HHCCCC---
T ss_conf             667636567765555300221102684--065540100114676314827888763014721454556---303688---


Q ss_pred             CCCCCCCCCEEEEEECCCCCCCCCHHHHCCCCCCEEEEECCHHCCC--HHHHHHHHHHHC-CCCCCEEEEEECCCCCCCC
Q ss_conf             1112357861698530357556100212026761499971110299--788988888850-7998138998238998765
Q gi|254781215|r  159 HCSLGIDSKHYSTMCRTYSEERPDTFVGHHNTYGMAIINDEASGTP--DVINLGILGFLT-ERNANRFWIMTSNPRRLSG  235 (511)
Q Consensus       159 ~~~~~~~~~~~~~~~~~~s~~~~ea~~G~h~~~~~lvI~DEAsgI~--d~i~e~i~~~Lt-~~g~~~~~i~~~nP~~~~g  235 (511)
                                 -+.+..+|.+.|+|++|-.   ..+.+.||....+  .+.|.-++=-|. +.+++  .+.+.+|.-.. 
T Consensus       111 -----------GAvA~~FSsEDPeSLRGPQ---Fh~AW~DEl~kWk~PqETw~MLqFGLRLGe~PR--qvVTTTPrp~p-  173 (410)
T COG5323         111 -----------GAVAYAFSSEDPDSLRGPQ---FHLAWTDELLKWKEPQETWAMLQFGLRLGEDPR--QVVTTTPRPIP-  173 (410)
T ss_pred             -----------CCEEEEECCCCHHHCCCCC---CCHHHHHHHHCCCCHHHHHHHHHHHHHHCCCCH--HHEECCCCCCH-
T ss_conf             -----------5014430358803204852---006777887447984889999987665167840--10205998627-


Q ss_pred             HHHHHHHCCCCCCEEEEECCCCCCCCCHHHHHHHHHHCCCCHHHHHHHHCCCCCCCCCCEEECHHHHHHHHHCCCCCCCC
Q ss_conf             56765303524741798404336778977899999751898013544431756666787375599998864076531899
Q gi|254781215|r  236 KFYEIFNKPLDDWKRFQIDTRTVEGIDPSFHEGIIARYGLDSDVTRVEVCGQFPQQDIDSFIPLNIIEEALNREPCPDPY  315 (511)
Q Consensus       236 ~fy~~~~~~~~~w~~~~i~~~~~p~~~~~~ie~~~~~~geds~~~r~evlgeFp~~~~~~~i~~~~ie~a~~r~~~~~~~  315 (511)
                       ....-.....--.++.-.+....+..+.|+..+.+.|| ....-|||..|+..+. +..+...+.++.|++..  +.+-
T Consensus       174 -lLKaLl~dptv~~trm~Ta~NAgNLapgFl~t~a~rYg-GTRLgrQEldGelvee-~GaLw~r~dle~c~ea~--p~pL  248 (410)
T COG5323         174 -LLKALLADPTVALTRMGTAANAGNLAPGFLRTLASRYG-GTRLGRQELDGELVEE-DGALWRREDLERCREAR--PAPL  248 (410)
T ss_pred             -HHHHHHCCCCHHHHHCCCCCCCCCCCHHHHHHHHHHHC-CCCHHHHHCCCEEECC-CCCCCCHHHHHHHHHCC--CCCC
T ss_conf             -89988428612545054322445657799999999845-4411355528778636-77300287899998618--9870


Q ss_pred             CEEEEEEEC-CCCCCCCEEEEE---ECCC-EEEEEEECCCCCHHHHHHHHHHHHHHCCCCEEEEEECCCCHHHHHHHHHC
Q ss_conf             708999623-334784179998---2275-58998732778988999999999986188829980068763688989864
Q gi|254781215|r  316 APLIMGCDI-AEEGGDNTVVVL---RRGP-VIEHLFDWSKTDLRTTNNKISGLVEKYRPDAIIIDANNTGARTCDYLEML  390 (511)
Q Consensus       316 ~~~viGvDV-Ar~G~D~svi~~---r~G~-~v~~~~~~~~~d~~~~a~~i~~~~~~~~~~~i~iD~~GvG~gV~d~L~~~  390 (511)
                      ..+++.||+ |..|.|+|-|.+   +.|. .|+.-++..+......+.+....+..+..++++.+.+--|.-|...|.+.
T Consensus       249 ~RiVVAVDPPA~~g~~sCGIVVaG~~~gr~~VLADes~~g~~PagWArravAa~r~heADa~VAEvNQGGeMVravLa~~  328 (410)
T COG5323         249 DRIVVAVDPPATAGGDSCGIVVAGRRDGRAFVLADESARGLSPAGWARRAVAAARAHEADALVAEVNQGGEMVRAVLAQA  328 (410)
T ss_pred             CEEEEEECCCCCCCCCCEEEEEEEEECCCEEEEECCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHC
T ss_conf             23799726987677875116998850581699612302478821268999999875113478887713417999999604


Q ss_pred             CC--EEEEECCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCH---HHHHHHHHCCCEEEECCCCEEEEEECHHHCCCC
Q ss_conf             98--2798427777664025522799999999999970899981---899999857967998799849998412548999
Q gi|254781215|r  391 GY--HVYRVLGQKRAVDLEFCRNRRTELHVKMADWLEFASLINH---SGLIQNLKSLKSFIVPNTGELAIESKRVKGAKS  465 (511)
Q Consensus       391 g~--~v~~v~~~~~~~~~~~y~N~rae~~~~~re~l~~g~l~~d---~~l~~el~~~~~~~~~~~gki~ie~Kkkrg~~S  465 (511)
                      ..  ++.-+..+-.     +  -.|||-...+   -++|++...   ..|-.|++.     +.+.|          .-.|
T Consensus       329 Dp~~pv~lvRASrG-----K--~~RAEPVAAL---YEQGRVrH~GrF~aLEdem~d-----fgp~g----------LssS  383 (410)
T COG5323         329 DPPCPVKLVRASRG-----K--RARAEPVAAL---YEQGRVRHCGRFVALEDEMMD-----FGPGG----------LSSS  383 (410)
T ss_pred             CCCCCEEEEECCCC-----C--HHCCCHHHHH---HHCCCEEECCCCHHHHHHHHH-----HCCCC----------CCCC
T ss_conf             99986276661456-----3--1013616998---855630004651667898860-----08885----------5678


Q ss_pred             CCHHHHHHHHHC
Q ss_conf             898999999975
Q gi|254781215|r  466 TDYSDGLMYTFA  477 (511)
Q Consensus       466 PD~ADAl~l~fa  477 (511)
                      ||+.|||+.+..
T Consensus       384 PDRlDALVWAv~  395 (410)
T COG5323         384 PDRLDALVWAVS  395 (410)
T ss_pred             CHHHHHHHHHHH
T ss_conf             037788999999


No 6  
>COG4373 Mu-like prophage FluMu protein gp28 [General function prediction only]
Probab=99.58  E-value=5.7e-12  Score=94.11  Aligned_cols=364  Identities=18%  Similarity=0.191  Sum_probs=212.1

Q ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHH---CCCCEEEEEECCHHHHHHHHHHHHHHHHHHCHHCCCCCCCCCCCCCCCC--
Q ss_conf             24650257659789999999999980---8996699980858999999999999999855000134443222222333--
Q gi|254781215|r   79 KGAISAGRGIGKTTLNAWLVLWLMST---RPGISVICLANSETQLKTTLWAEVSKWLSLLPNKHWFEMQSLSLHPAPW--  153 (511)
Q Consensus        79 r~aV~sgrG~GKS~l~a~l~lw~l~~---~p~~kv~vtApt~~Q~~~ilw~Ei~k~~~~~~~~~~~~~~~~~~~~~~~--  153 (511)
                      ++|-. +|.+|-|...|.--+--+..   +-|..|++.......+++-+ .....|.+..-      ..++-++..-+  
T Consensus        31 kIAEK-SRRtGlTwaeA~~dV~~Aak~k~eGG~dVfy~gs~~emArEyI-~acamwar~fN------~~A~d~~E~~f~d  102 (509)
T COG4373          31 KIAEK-SRRTGLTWAEAYEDVRDAAKPKREGGMDVFYSGSDLEMAREYI-RACAMWARIFN------VVATDLGEVVFED  102 (509)
T ss_pred             EHHHH-CCCCCCCHHHHHHHHHHHHCCCCCCCCEEEEECCCHHHHHHHH-HHHHHHHHHHH------HHHHHHHHHHHCC
T ss_conf             15353-0102642888777898752112258852588447489999999-99999999998------8877777876447


Q ss_pred             --CCCCCCCCCCCCCCEEEEEECCCCCCCCCHHHHCCCCCCEEEEECCHHCCC--HHHHHHHHHHHCCCCCCEEEEEECC
Q ss_conf             --444321112357861698530357556100212026761499971110299--7889888888507998138998238
Q gi|254781215|r  154 --YSDVLHCSLGIDSKHYSTMCRTYSEERPDTFVGHHNTYGMAIINDEASGTP--DVINLGILGFLTERNANRFWIMTSN  229 (511)
Q Consensus       154 --~~~~~~~~~~~~~~~~~~~~~~~s~~~~ea~~G~h~~~~~lvI~DEAsgI~--d~i~e~i~~~Lt~~g~~~~~i~~~n  229 (511)
                        ++.+...-+.+.++ ..+.+. +  .||.+++|..+.    |++|||++-.  +++|.++.+ +|-=|.++.++  |+
T Consensus       103 ~dk~~Iltyvi~FasG-fkI~AL-S--SnPknlRg~qG~----VviDEaAFHE~ldEllkAA~a-ltmWGa~vRvi--St  171 (509)
T COG4373         103 SDKSAILTYVIAFASG-FKITAL-S--SNPKNLRGKQGK----VVIDEAAFHEDLDELLKAAAA-LTMWGAPVRVI--ST  171 (509)
T ss_pred             CCHHHHHHHHEEECCC-CEEEEC-C--CCCCCCCCCCCC----EEEEHHHHHHHHHHHHHHHHH-HHHCCCCEEEE--EC
T ss_conf             8756556730320477-467660-4--797455467884----886236656539999998778-76517724899--62


Q ss_pred             CCCCCCHHHHHHH---CCCCCCEEEEECCCC--------------CCCCCHHHHHHHH----HHCCCCHHHHHHHHCCCC
Q ss_conf             9987655676530---352474179840433--------------6778977899999----751898013544431756
Q gi|254781215|r  230 PRRLSGKFYEIFN---KPLDDWKRFQIDTRT--------------VEGIDPSFHEGII----ARYGLDSDVTRVEVCGQF  288 (511)
Q Consensus       230 P~~~~g~fy~~~~---~~~~~w~~~~i~~~~--------------~p~~~~~~ie~~~----~~~geds~~~r~evlgeF  288 (511)
                      .++....|++.-.   ..+++|..+.+.-.|              -|..+++-..+|+    +.-|.+ .-+..||.|. 
T Consensus       172 HNGvDnlFnQ~iQear~grk~ysvH~iTldDAiadGLy~RIc~v~~~~w~pE~Ea~w~a~l~~~a~t~-eda~eEy~C~-  249 (509)
T COG4373         172 HNGVDNLFNQMIQEARQGRKKYSVHSITLDDAIADGLYERICNVDRPAWAPEVEAKWLAELRAIAGTD-EDAQEEYMCN-  249 (509)
T ss_pred             CCCHHHHHHHHHHHHHCCCCCCEEEEEEHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHCCCC-HHHHHHHCCC-
T ss_conf             68701789999999870255531788865777777899999826774567567889999888656981-4457762877-


Q ss_pred             CCCCCCEEECHHHHHHHHHCCCC------------------------------------CCCCCEEEEEEECCCCCCCCE
Q ss_conf             66678737559999886407653------------------------------------189970899962333478417
Q gi|254781215|r  289 PQQDIDSFIPLNIIEEALNREPC------------------------------------PDPYAPLIMGCDIAEEGGDNT  332 (511)
Q Consensus       289 p~~~~~~~i~~~~ie~a~~r~~~------------------------------------~~~~~~~viGvDVAr~G~D~s  332 (511)
                      |..+....||..+||.|+-+++.                                    ..|++....|||.||.+ |-|
T Consensus       250 Pk~s~gAYIphalie~a~~~~vp~l~fe~~~~f~~~~~~~r~~~~~~~cl~~l~P~Lqalnp~~r~~fGvDfaR~~-DLs  328 (509)
T COG4373         250 PKDSTGAYIPHALIEAAVAAEVPDLIFELGSEFHDIPAWLRESEVLTWCLPDLRPALQALNPGGRLYFGVDFARKR-DLS  328 (509)
T ss_pred             CCCCCCCCCCHHHHHHHHHCCCCCEEEECCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCEEECCCCCCCC-CCE
T ss_conf             5667766466789998875479851797574554235664245666653443568987329997165212202256-734


Q ss_pred             EEEEEC--CC----EEEEEEECCCCCHHHHHHHHHHHHHHCCCCE--EEEEECCCCHHHHHHH-HHCCCE-EEEECCCCC
Q ss_conf             999822--75----5899873277898899999999998618882--9980068763688989-864982-798427777
Q gi|254781215|r  333 VVVLRR--GP----VIEHLFDWSKTDLRTTNNKISGLVEKYRPDA--IIIDANNTGARTCDYL-EMLGYH-VYRVLGQKR  402 (511)
Q Consensus       333 vi~~r~--G~----~v~~~~~~~~~d~~~~a~~i~~~~~~~~~~~--i~iD~~GvG~gV~d~L-~~~g~~-v~~v~~~~~  402 (511)
                      |+.+..  |.    -+..++ .....+.+. ..|.-.....-|..  -..|++|.|+-..+.. ...|.. |..|.++++
T Consensus       329 v~~v~e~~~dta~r~v~~le-i~n~pY~qq-~qvmm~ll~~lP~l~gAafDaTGnGgyLAEaAl~~fGs~~v~~V~lneK  406 (509)
T COG4373         329 VLWVWEKVGDTAWRAVVELE-IVNFPYQQQ-EQVMMWLLHLLPMLTGAAFDATGNGGYLAEAALEDFGSEKVTKVTLNEK  406 (509)
T ss_pred             EEEEEEECCCHHHHHEEEEE-EECCCHHHH-HHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHCCCCEEEEEECHH
T ss_conf             99987445523522245898-624864678-9999999986366631223265760476789998627102256762788


Q ss_pred             CCCHHHHHHHHHHHHHHHHHHHHHCC--CCCHHHHHHHHHCCCEEEECCCCEEEEEEC-HHHCCCCCCHHHHHHHHHC
Q ss_conf             66402552279999999999997089--998189999985796799879984999841-2548999898999999975
Q gi|254781215|r  403 AVDLEFCRNRRTELHVKMADWLEFAS--LINHSGLIQNLKSLKSFIVPNTGELAIESK-RVKGAKSTDYSDGLMYTFA  477 (511)
Q Consensus       403 ~~~~~~y~N~rae~~~~~re~l~~g~--l~~d~~l~~el~~~~~~~~~~~gki~ie~K-kkrg~~SPD~ADAl~l~fa  477 (511)
                      =         .-+..-+++-.++++.  +|.++.++.++-.++.  ++...+|-.-.| .+.+-+|.|+|.|+||+--
T Consensus       407 w---------y~ewmpk~Ka~~Ed~~i~~p~~~~v~~D~~hi~v--~ng~P~idk~r~kd~~a~rHgD~avA~cma~R  473 (509)
T COG4373         407 W---------YKEWMPKFKAALEDSSIRLPGTAVVRADFKHIRV--TNGSPSIDKLRKKDRDADRHGDRAVAACMARR  473 (509)
T ss_pred             H---------HHHHHHHHHHHHCCCCEECCCCEEEECCCCCEEE--ECCCCCCCCCCCCCCCCCCCCHHHHHHHHHHH
T ss_conf             8---------8766377786513462334785035101252588--53787644011245444332178999998633


No 7  
>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=99.41  E-value=7e-09  Score=74.61  Aligned_cols=394  Identities=13%  Similarity=0.080  Sum_probs=202.2

Q ss_pred             HHHHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEEECCHHHHHHHHHHHHHHHH
Q ss_conf             89999999999987405655542101246502576597899999999999808996699980858999999999999999
Q gi|254781215|r   53 SWQLEFMEVVDAHCLNSVNNPNPEVFKGAISAGRGIGKTTLNAWLVLWLMSTRPGISVICLANSETQLKTTLWAEVSKWL  132 (511)
Q Consensus        53 ~WQ~e~l~~i~~~~~~~~~~~~~~~~r~aV~sgrG~GKS~l~a~l~lw~l~~~p~~kv~vtApt~~Q~~~ilw~Ei~k~~  132 (511)
                      +||+|+|..+.+          +.+.+|.+..+-|+|||.++-..+-|.+...| +.++++-||...+++..=..|..++
T Consensus        19 Py~~eimd~l~~----------~~v~~V~~~k~aQ~GkT~~~~n~igy~i~~~P-~p~l~v~Pt~~~a~~~s~~rl~Pmi   87 (552)
T pfam05876        19 PYLREIMDALSP----------PSVERVVFMKSAQVGKTELLLNWIGYFIDHDP-APMLVVQPTDDDAKRFSKDRLDPMI   87 (552)
T ss_pred             CHHHHHHHHCCC----------CCCEEEEEEECCCCCHHHHHHHHHHHHHHHCC-CCEEEEECCHHHHHHHHHHHHHHHH
T ss_conf             076999985488----------78449999957870388999999988663089-8879994189999999999899998


Q ss_pred             HHCHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCCCCCCCHHHHCCCCCCEEEEECCHHCCCHHH-----
Q ss_conf             855000134443222222333444321112357861698530357556100212026761499971110299788-----
Q gi|254781215|r  133 SLLPNKHWFEMQSLSLHPAPWYSDVLHCSLGIDSKHYSTMCRTYSEERPDTFVGHHNTYGMAIINDEASGTPDVI-----  207 (511)
Q Consensus       133 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~ea~~G~h~~~~~lvI~DEAsgI~d~i-----  207 (511)
                      +.+|.-........   ..  ..+.......+.++.....    .+.+|.+++.   ...=.+++||....|..+     
T Consensus        88 ~~sP~L~~~~~~~~---~r--~~~nt~~~K~f~gg~l~~~----ga~S~~~L~s---~~~r~l~~DEvD~~~~~~~~eGd  155 (552)
T pfam05876        88 RASPALRERLAPAR---SR--DSDNTLLSKRFPGGSLLLI----GANSPANLRS---RPVRYVILDEVDAYPEDVDGEGD  155 (552)
T ss_pred             HCCHHHHHHHCCCC---CC--CCCCCEEEEEECCCEEEEE----ECCCCHHHHC---CCCCEEEECCHHHCCCCCCCCCC
T ss_conf             61989997507555---65--6677412476078379995----5799614304---86355885134436545677879


Q ss_pred             -HHHHHHHHCCCCCCEEEEEECCCCCCC-CHHHHHHHCC-----------------------------------------
Q ss_conf             -988888850799813899823899876-5567653035-----------------------------------------
Q gi|254781215|r  208 -NLGILGFLTERNANRFWIMTSNPRRLS-GKFYEIFNKP-----------------------------------------  244 (511)
Q Consensus       208 -~e~i~~~Lt~~g~~~~~i~~~nP~~~~-g~fy~~~~~~-----------------------------------------  244 (511)
                       .+-++.=.++.....+.+..|+|+... +.....|...                                         
T Consensus       156 P~~La~~R~~tf~~~~K~~~~STPt~~g~s~I~~~~~~sdqr~~~vpCPhCg~~q~l~~~~l~w~~~~~p~~a~y~C~~C  235 (552)
T pfam05876       156 PISLAEKRTETFGSRRKILAGSTPTIKGTSRIEALYEESDQRRYYVPCPHCGEEQELRWERLKWDKGEAPETARYVCPHC  235 (552)
T ss_pred             HHHHHHHHHHHHCCCCEEEEECCCCCCCCCHHHHHHHCCCEEEEEEECCCCCCCCCCCCCCEEECCCCCCCCEEEECCCC
T ss_conf             89999999875302857999838999996689999866873899868989998655500546647999855349989889


Q ss_pred             -------------------------CCCCEEEEECCCCCCCCCHHHH-HHHHHH--CCCCH--HHHHHHHCCCCCCCCCC
Q ss_conf             -------------------------2474179840433677897789-999975--18980--13544431756666787
Q gi|254781215|r  245 -------------------------LDDWKRFQIDTRTVEGIDPSFH-EGIIAR--YGLDS--DVTRVEVCGQFPQQDID  294 (511)
Q Consensus       245 -------------------------~~~w~~~~i~~~~~p~~~~~~i-e~~~~~--~geds--~~~r~evlgeFp~~~~~  294 (511)
                                               ..+...|+++..-+|..+-..| +++.+.  .|.+.  -.|-.-+||+--+...+
T Consensus       236 g~~i~e~~k~~m~~~G~W~~~~~~~~~~~~gfhl~~lySp~~sw~~ia~~~l~A~~~gd~~~lk~f~Nt~Lge~w~~~~~  315 (552)
T pfam05876       236 GCVIEEHHKRAMLRAGRWIATAPIRRPRHAGFHLNALYSPFRSWGELAAEFLKAERKGDPEKLKTFVNTDLGEPWEEKGE  315 (552)
T ss_pred             CCCCCHHHHHHHHHCCEEEECCCCCCCCCEEEEECHHHCCCCCHHHHHHHHHHHHHCCCHHHHHHEEECCCCCEECCCCC
T ss_conf             88889999998876899980588889981179963574552589999999998776199888635474024424213466


Q ss_pred             EEECHHHHHHHHHCC-CCCCCCCE--EEEEEECCCCCCCCEE---EEEECCC--EEEEEEECCC-CCHHHHHHHHHHHHH
Q ss_conf             375599998864076-53189970--8999623334784179---9982275--5899873277-898899999999998
Q gi|254781215|r  295 SFIPLNIIEEALNRE-PCPDPYAP--LIMGCDIAEEGGDNTV---VVLRRGP--VIEHLFDWSK-TDLRTTNNKISGLVE  365 (511)
Q Consensus       295 ~~i~~~~ie~a~~r~-~~~~~~~~--~viGvDVAr~G~D~sv---i~~r~G~--~v~~~~~~~~-~d~~~~a~~i~~~~~  365 (511)
                      .. ..+.+.+..+.. ...-|.+.  +.+||||-.   |.-.   +.-..|.  +++......| .+..++=..+.++..
T Consensus       316 ~~-~~~~L~~rre~y~~~~vP~g~~~LtagvDvQ~---drle~~v~gwG~~~esW~id~~~i~Gdp~~~~~w~~L~~~l~  391 (552)
T pfam05876       316 AP-DWEELAARAEDYPRGTVPAGVLVLTAGVDVQG---DRLEVEVVGWGRGGESWLIDRGVIWGDPADEETWAALDELLN  391 (552)
T ss_pred             CC-CHHHHHHHHHHCCCCCCCCCEEEEEEEEEECC---CEEEEEEEEECCCCCEEEEEEEEECCCCCCHHHHHHHHHHHH
T ss_conf             78-98999998764466678987069999986149---989999999879985599988886189887789999999972


Q ss_pred             -H--------CCCCEEEEEEC-CCCHHHHHHHHHCC-CEEEEECCCCCCCCH--------HH-------------H----
Q ss_conf             -6--------18882998006-87636889898649-827984277776640--------25-------------5----
Q gi|254781215|r  366 -K--------YRPDAIIIDAN-NTGARTCDYLEMLG-YHVYRVLGQKRAVDL--------EF-------------C----  409 (511)
Q Consensus       366 -~--------~~~~~i~iD~~-GvG~gV~d~L~~~g-~~v~~v~~~~~~~~~--------~~-------------y----  409 (511)
                       .        +.+..++||+. +.-.-|++.++... ..|+++.+.+....+        ..             |    
T Consensus       392 ~~~~~~~G~~~~i~~~~IDsGg~~T~~VY~f~r~~~~~rv~aiKG~~~~~~p~i~~~~~~~~~~~gk~~~~gv~l~~vgt  471 (552)
T pfam05876       392 RTWPHADGGEMRIDAVAIDSGGGVTDEVYAFCRKRRRRRVIAIKGASGYGAPLIGRPSPKDVTKKGKKLRGGVRLWLVGT  471 (552)
T ss_pred             CCCCCCCCCEEEEEEEEEECCCCCHHHHHHHHHHCCCCEEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECC
T ss_conf             74177899883114999989999579999999866886089974688778887567851233666751048835999785


Q ss_pred             HHHHHHHHHHHHHHHHH--CC--CCC--HHHHHHHHHCCCEEEECCCCEEEEEECHHHCCCCCCHHHHHHHHHCC
Q ss_conf             22799999999999970--89--998--18999998579679987998499984125489998989999999759
Q gi|254781215|r  410 RNRRTELHVKMADWLEF--AS--LIN--HSGLIQNLKSLKSFIVPNTGELAIESKRVKGAKSTDYSDGLMYTFAE  478 (511)
Q Consensus       410 ~N~rae~~~~~re~l~~--g~--l~~--d~~l~~el~~~~~~~~~~~gki~ie~Kkkrg~~SPD~ADAl~l~fa~  478 (511)
                      -..|..++..|+-- +.  |.  +|.  +++-.+||++ +.. . ..|+...+=+|++ ++-=-..|..++++|.
T Consensus       472 ~~~K~~l~~rL~~~-~~~~G~~hfp~~~~~~yf~QLtA-E~~-~-~kG~~~~~W~k~~-~~rNE~LDc~vya~Aa  541 (552)
T pfam05876       472 DTAKDRIYARLRRE-EPGPGYIHFPDDLPDEYFEQLTA-EER-V-SKGRPRREWVKPR-GRRNEALDCRVYALAA  541 (552)
T ss_pred             HHHHHHHHHHHCCC-CCCCCEEECCCCCCHHHHHHHHE-EEE-E-CCCCEEEEEECCC-CCCCHHHHHHHHHHHH
T ss_conf             79999999874689-99997598789999999976434-788-5-1797637995389-9987899999999999


No 8  
>COG1783 XtmB Phage terminase large subunit [General function prediction only]
Probab=99.24  E-value=1.5e-08  Score=72.58  Aligned_cols=342  Identities=17%  Similarity=0.154  Sum_probs=199.5

Q ss_pred             EEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEEECCHHHHHHHHHHHHHHHHHHCHHCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             65025765978999999999998089966999808589999999999999998550001344432222223334443211
Q gi|254781215|r   81 AISAGRGIGKTTLNAWLVLWLMSTRPGISVICLANSETQLKTTLWAEVSKWLSLLPNKHWFEMQSLSLHPAPWYSDVLHC  160 (511)
Q Consensus        81 aV~sgrG~GKS~l~a~l~lw~l~~~p~~kv~vtApt~~Q~~~ilw~Ei~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  160 (511)
                      -+.+|||++||...|--++--++-.|++.++|+.--....++.+|.++...++.+-..+.+......+.         .+
T Consensus        28 i~~G~rGS~KSy~~alk~i~kl~~~~~~d~lvIR~v~nt~k~St~~~~~e~l~e~gv~~~f~~~~s~pe---------~i   98 (414)
T COG1783          28 IAKGGRGSSKSYATALKNIEKLLSEPGIDVLVIREVENTHKQSTYALFKEALSELGVTKFFKISKSSPE---------II   98 (414)
T ss_pred             EEECCCCCCHHHHHHHHHHHHHHCCCCCCEEEEEEECCCCCHHHHHHHHHHHHHHCCCCEEEEECCCHH---------HE
T ss_conf             998267775008889999999970778757999972354412089999999998384011577417866---------60


Q ss_pred             CCCCCCCEEEEEECCCCCCCCCHHHHCCCCCCEEEEECCHHCCC-HHHHHHHHHH-HCCCCCCEEEEEECCCCCCCCHHH
Q ss_conf             12357861698530357556100212026761499971110299-7889888888-507998138998238998765567
Q gi|254781215|r  161 SLGIDSKHYSTMCRTYSEERPDTFVGHHNTYGMAIINDEASGTP-DVINLGILGF-LTERNANRFWIMTSNPRRLSGKFY  238 (511)
Q Consensus       161 ~~~~~~~~~~~~~~~~s~~~~ea~~G~h~~~~~lvI~DEAsgI~-d~i~e~i~~~-Lt~~g~~~~~i~~~nP~~~~g~fy  238 (511)
                      ....+.+..|.     .-+.|+-+...+......+++.||+.++ +...|.+..+ ......+  .++.+||...+-+.|
T Consensus        99 ~~~~G~ri~F~-----G~ddp~klKSi~~~~~s~~WfEE~~e~s~e~~~e~l~~l~~~~~~~~--~~~~snpv~~~pw~~  171 (414)
T COG1783          99 LKDTGQRIIFK-----GLDDPAKLKSIAVNWISDLWFEEASEFSYEDDIELLVELRRRELKGH--IILSSNPVSFNPWTY  171 (414)
T ss_pred             ECCCCCEEEEE-----CCCCHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCC--CEEECCCCCCCCCCH
T ss_conf             21258678994-----58987885230100433555787763303456888777641223777--246326434588538


Q ss_pred             HHH----HC--CCCCCEEEEECCCCCCCCCHHHHHHHHHHCCCCHHHHHHHHCCCCCCCCCCEE-----ECHHHHHHHHH
Q ss_conf             653----03--52474179840433677897789999975189801354443175666678737-----55999988640
Q gi|254781215|r  239 EIF----NK--PLDDWKRFQIDTRTVEGIDPSFHEGIIARYGLDSDVTRVEVCGQFPQQDIDSF-----IPLNIIEEALN  307 (511)
Q Consensus       239 ~~~----~~--~~~~w~~~~i~~~~~p~~~~~~ie~~~~~~geds~~~r~evlgeFp~~~~~~~-----i~~~~ie~a~~  307 (511)
                      .-|    ..  .+.+...++-..+++++++...+.++.+.+--|.+.+|+-+.|+|--.+-++|     +|.+++..|++
T Consensus       172 ~~w~~~~~Dek~~~dt~~hhtT~~dn~fL~~~~v~~~ed~k~~d~d~yri~~~gev~v~~~~v~~~~e~~~~d~v~~~i~  251 (414)
T COG1783         172 KHWLEFAVDEKKKADTYIHHTTYRDNLFLGFDDVDELEDLKKNDPDLYRIVRDGEVGVKNGDVFDQFEVKPFDAVKFAID  251 (414)
T ss_pred             HHHHHHHHCCCCCCCEEEEEEECCCCCCCCHHHHHHHHHHHHCCCCCCEEEEEEEEEECCCEECCHHHCCCHHHHHHHHH
T ss_conf             88888874435578668886201356667778999998764128541238997789860752546321577288776677


Q ss_pred             CCCCCCCCCEEEEEEECCCCCCCCEEEEE--ECCCE--EEEEEECCCCCHHHHHHHHHHHHHHCCCC--EEEEEECCCCH
Q ss_conf             76531899708999623334784179998--22755--89987327789889999999999861888--29980068763
Q gi|254781215|r  308 REPCPDPYAPLIMGCDIAEEGGDNTVVVL--RRGPV--IEHLFDWSKTDLRTTNNKISGLVEKYRPD--AIIIDANNTGA  381 (511)
Q Consensus       308 r~~~~~~~~~~viGvDVAr~G~D~svi~~--r~G~~--v~~~~~~~~~d~~~~a~~i~~~~~~~~~~--~i~iD~~GvG~  381 (511)
                      +-..+.      .|+|.+-.-.-..++++  ..|..  ....+......   +-+...+...+++..  .+..|+---  
T Consensus       252 ~i~~~s------~gm~~Gf~~~~n~l~~~~v~~~~k~l~~~~ey~~~~~---~~d~~~~~i~e~n~~k~~~~~dsAe~--  320 (414)
T COG1783         252 NISRPS------TGMDFGFTAKFNRLLKLAVDPGKKYLYIYVEYYANKM---LDDKKTKDISEFNKTKSVIALDSAEP--  320 (414)
T ss_pred             HHCCCC------CCCEEEEEECCCEEEEEEEECCCCEEEEEEECHHHHH---HHHHHHHHHHHHHHCCEEEEECCCCH--
T ss_conf             615565------5402425740757788887046540479861122443---43567899987541122797046347--


Q ss_pred             HHHHHHHHCCCEEEE-ECCCCCCCCHHHHHHHHHHHHHHHHHHHH-HCCCCCHHHHHHHHHCCCEEEECCCCEEEEEECH
Q ss_conf             688989864982798-42777766402552279999999999997-0899981899999857967998799849998412
Q gi|254781215|r  382 RTCDYLEMLGYHVYR-VLGQKRAVDLEFCRNRRTELHVKMADWLE-FASLINHSGLIQNLKSLKSFIVPNTGELAIESKR  459 (511)
Q Consensus       382 gV~d~L~~~g~~v~~-v~~~~~~~~~~~y~N~rae~~~~~re~l~-~g~l~~d~~l~~el~~~~~~~~~~~gki~ie~Kk  459 (511)
                      +.....++.|+.... ..+-++          +.|-.-.+ +.++ .--.|..+..+.++.... |.-+         |+
T Consensus       321 kli~yfk~~G~~~v~a~k~~~s----------~lq~~k~l-~~fk~i~~~p~~en~I~e~~~~~-y~~D---------k~  379 (414)
T COG1783         321 KLIQYFKDVGVGMVYAKKFKGS----------RLQKIKKL-KRFKAIYSSPRCENTINEFNHLE-YKKD---------KK  379 (414)
T ss_pred             HHHHHHHHCCCCCCCCCCCCCC----------HHHHHHHH-HHHCCEEECCCCCCHHHHHEEEE-EEEC---------CC
T ss_conf             7889998628651135567630----------77878988-85125780687652111110113-3201---------22


Q ss_pred             HHCCCCCCHHH
Q ss_conf             54899989899
Q gi|254781215|r  460 VKGAKSTDYSD  470 (511)
Q Consensus       460 krg~~SPD~AD  470 (511)
                      .+++.||...|
T Consensus       380 ~~~i~~p~~id  390 (414)
T COG1783         380 GNGIDSPFTID  390 (414)
T ss_pred             CCCCCCCCCCC
T ss_conf             56889853367


No 9  
>TIGR01547 phage_term_2 phage terminase, large subunit, PBSX family; InterPro: IPR006437   This group of sequences represent a highly divergent family of the large subunit of phage terminase. All members are encoded by phage genomes or within prophage regions of bacterial genomes. This is a distinct family from the phage terminase family represented by IPR005021 from INTERPRO.; GO: 0006323 DNA packaging.
Probab=98.91  E-value=5.7e-07  Score=62.55  Aligned_cols=246  Identities=16%  Similarity=0.157  Sum_probs=165.1

Q ss_pred             EEECCCCCCHHHHHHHHHHHHHHHC-----CCCEEEEEECCHHHHHHHHHHHHHHHHHHCHHC-CCCCCCCCCCCCCCCC
Q ss_conf             6502576597899999999999808-----996699980858999999999999999855000-1344432222223334
Q gi|254781215|r   81 AISAGRGIGKTTLNAWLVLWLMSTR-----PGISVICLANSETQLKTTLWAEVSKWLSLLPNK-HWFEMQSLSLHPAPWY  154 (511)
Q Consensus        81 aV~sgrG~GKS~l~a~l~lw~l~~~-----p~~kv~vtApt~~Q~~~ilw~Ei~k~~~~~~~~-~~~~~~~~~~~~~~~~  154 (511)
                      ...+|++.|||...+-.++-.++..     ++..+++...+....++.++..+...+...-.. ..+.......      
T Consensus         5 ~~~G~~~sgk~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~g~~~~~~~~~~~~~------   78 (462)
T TIGR01547         5 IAKGGRGSGKTFAIALKLVLKLLANKDLYGKPRNILAARKVQNSIRDSVFKDIEDLLSDLGLNLYEFKKSKSPM------   78 (462)
T ss_pred             EECCCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCEEEEEEHHHHHHHHHHHHHHHHHHHCCCHHHHHHHCCCCC------
T ss_conf             63266653157899999999998764531488406887402335665668889999987064022132036662------


Q ss_pred             CCCCCCCCCCCC-CEEEEEECCCCCCCCCHHHHCCCCC--------CEEEEECCHHCCCHHHHHHHHHHHCCCCCC-EEE
Q ss_conf             443211123578-6169853035755610021202676--------149997111029978898888885079981-389
Q gi|254781215|r  155 SDVLHCSLGIDS-KHYSTMCRTYSEERPDTFVGHHNTY--------GMAIINDEASGTPDVINLGILGFLTERNAN-RFW  224 (511)
Q Consensus       155 ~~~~~~~~~~~~-~~~~~~~~~~s~~~~ea~~G~h~~~--------~~lvI~DEAsgI~d~i~e~i~~~Lt~~g~~-~~~  224 (511)
                          .+.+...+ +..+.. .....+++..+.++-+.+        ....+++||+.++...+..+.++++.++.. ..+
T Consensus        79 ----~~~~~~~~~~~~~~f-~G~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ee~~~~~~~~~~~~~~~~r~~~~~~~~~  153 (462)
T TIGR01547        79 ----EIKILNTGGGAYFIF-KGLNSDKPEKLKSGAGLGFTLWEVGLLADLWFEEASELTKEDIKELIPRLREPGGKNKFI  153 (462)
T ss_pred             ----EEEECCCCCCEEEEE-ECCCCCCHHHHHHCCCCCEEEEHHHHHHHHHHHHHHHCCHHHHHHHHHHHCCCCCCEEEE
T ss_conf             ----577615788617996-065756246643104664100014455656555444301446888887640577750699


Q ss_pred             EEECCCCCCCCHHHHHHHCC--CC--CCE---------------EEEECCCCCCCCC----HHHHHHHHHHCCCCHHHHH
Q ss_conf             98238998765567653035--24--741---------------7984043367789----7789999975189801354
Q gi|254781215|r  225 IMTSNPRRLSGKFYEIFNKP--LD--DWK---------------RFQIDTRTVEGID----PSFHEGIIARYGLDSDVTR  281 (511)
Q Consensus       225 i~~~nP~~~~g~fy~~~~~~--~~--~w~---------------~~~i~~~~~p~~~----~~~ie~~~~~~geds~~~r  281 (511)
                      ++-+||.+...+++..|...  .+  .-.               .++....++|+.+    ..+++++...+..+...++
T Consensus       154 ~~~~nP~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~dn~~~~~~~~~~~~~~~~~~~~~~~~~~~  233 (462)
T TIGR01547       154 IFSSNPESPLHWVYKDFIENLGEDEFRICDKPPYEYGVVDKKLYILHSTYRDNPFLSGGDVEEYIQELEKLKDRDPALYR  233 (462)
T ss_pred             EEEECCCCCCCHHHHHHHHCCCCCCHHHHCCCCHHHHHEEECEEEEEEECCCCCCCCCHHHHHHHHHHHHHHCCCHHHHH
T ss_conf             98408898553056665430477601221011013220000002567420346567611589999999986315613433


Q ss_pred             HHHCCCCCCCCCCEEECHHHHH------HHHHC---CCCCCCCCEE--EEEEECCCC-CCCCEEEEEE
Q ss_conf             4431756666787375599998------86407---6531899708--999623334-7841799982
Q gi|254781215|r  282 VEVCGQFPQQDIDSFIPLNIIE------EALNR---EPCPDPYAPL--IMGCDIAEE-GGDNTVVVLR  337 (511)
Q Consensus       282 ~evlgeFp~~~~~~~i~~~~ie------~a~~r---~~~~~~~~~~--viGvDVAr~-G~D~svi~~r  337 (511)
                      ..++|+|...++-+.+...+..      ...+.   .....+..+.  +.|+|.+.. +...++++..
T Consensus       234 ~~~~G~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~  301 (462)
T TIGR01547       234 RILLGEWVSAADVWSLGLPVLTSEGILFKKLDVKAAYIKELPNDPSDFVGGIDAGGVDGNSPSAYVLL  301 (462)
T ss_pred             HHHHCCCCHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCHHEEEECCCCCCCCCCEEEEEE
T ss_conf             44423510122332204444344411121110022123431232100013201476666530367887


No 10 
>COG1061 SSL2 DNA or RNA helicases of superfamily II [Transcription / DNA replication, recombination, and repair]
Probab=98.56  E-value=5.8e-06  Score=56.21  Aligned_cols=159  Identities=23%  Similarity=0.237  Sum_probs=93.6

Q ss_pred             CCHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEEECCHHHHHHHHHHH-H
Q ss_conf             845899999999999874056555421012465025765978999999999998089966999808589999999999-9
Q gi|254781215|r   50 APRSWQLEFMEVVDAHCLNSVNNPNPEVFKGAISAGRGIGKTTLNAWLVLWLMSTRPGISVICLANSETQLKTTLWAE-V  128 (511)
Q Consensus        50 ~P~~WQ~e~l~~i~~~~~~~~~~~~~~~~r~aV~sgrG~GKS~l~a~l~lw~l~~~p~~kv~vtApt~~Q~~~ilw~E-i  128 (511)
                      -||++|.+++.++-.++.. .       .+..|...-|.|||.+++.++-..     ..++++.+|+..-+.+  |.+ +
T Consensus        36 ~lr~yQ~~al~a~~~~~~~-~-------~~gvivlpTGaGKT~va~~~~~~~-----~~~~Lvlv~~~~L~~Q--w~~~~  100 (442)
T COG1061          36 ELRPYQEEALDALVKNRRT-E-------RRGVIVLPTGAGKTVVAAEAIAEL-----KRSTLVLVPTKELLDQ--WAEAL  100 (442)
T ss_pred             CCHHHHHHHHHHHHHHCCC-C-------CCEEEEECCCCCHHHHHHHHHHHH-----CCCEEEEECCHHHHHH--HHHHH
T ss_conf             8859999999999962225-7-------867999679998899999999982-----6988999782999999--99999


Q ss_pred             HHHHHHCHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCCCCCCCHHHHCCCCCCEEEEECCHHCCCHHHH
Q ss_conf             99998550001344432222223334443211123578616985303575561002120267614999711102997889
Q gi|254781215|r  129 SKWLSLLPNKHWFEMQSLSLHPAPWYSDVLHCSLGIDSKHYSTMCRTYSEERPDTFVGHHNTYGMAIINDEASGTPDVIN  208 (511)
Q Consensus       129 ~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~ea~~G~h~~~~~lvI~DEAsgI~d~i~  208 (511)
                      .+.....        .....+      ......... ....+++..+.....  .+.-+...+..|+|+||++.++...+
T Consensus       101 ~~~~~~~--------~~~g~~------~~~~~~~~~-~~i~vat~qtl~~~~--~l~~~~~~~~~liI~DE~Hh~~a~~~  163 (442)
T COG1061         101 KKFLLLN--------DEIGIY------GGGEKELEP-AKVTVATVQTLARRQ--LLDEFLGNEFGLIIFDEVHHLPAPSY  163 (442)
T ss_pred             HHHCCCC--------CCCCEE------CCCCCCCCC-CCEEEEEEHHHHHHH--HHHHHCCCCCCEEEEECCCCCCCHHH
T ss_conf             9734886--------766033------687233577-748999838976415--55540356667599975245784779


Q ss_pred             HHHHHHHCCCCCCEEEEEECCCCCCC-CHHHHHHH
Q ss_conf             88888850799813899823899876-55676530
Q gi|254781215|r  209 LGILGFLTERNANRFWIMTSNPRRLS-GKFYEIFN  242 (511)
Q Consensus       209 e~i~~~Lt~~g~~~~~i~~~nP~~~~-g~fy~~~~  242 (511)
                      ..+...++..-.  .+=++.+|-+.. +...+.+.
T Consensus       164 ~~~~~~~~~~~~--~LGLTATp~R~D~~~~~~l~~  196 (442)
T COG1061         164 RRILELLSAAYP--RLGLTATPEREDGGRIGDLFD  196 (442)
T ss_pred             HHHHHHHHCCCE--EEEEECCCCCCCCCCHHHHHH
T ss_conf             999997510310--467714872448775248774


No 11 
>smart00487 DEXDc DEAD-like helicases superfamily.
Probab=98.53  E-value=1.3e-06  Score=60.20  Aligned_cols=167  Identities=17%  Similarity=0.043  Sum_probs=89.8

Q ss_pred             CCCCCHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEEECCHHHHHHHHHH
Q ss_conf             55784589999999999987405655542101246502576597899999999999808996699980858999999999
Q gi|254781215|r   47 GFSAPRSWQLEFMEVVDAHCLNSVNNPNPEVFKGAISAGRGIGKTTLNAWLVLWLMSTRPGISVICLANSETQLKTTLWA  126 (511)
Q Consensus        47 ~~~~P~~WQ~e~l~~i~~~~~~~~~~~~~~~~r~aV~sgrG~GKS~l~a~l~lw~l~~~p~~kv~vtApt~~Q~~~ilw~  126 (511)
                      .+..|+++|.+++..+....           ..+.|.+.-|.|||..+..+++..+......++++++|+...+.+. ..
T Consensus         5 ~~~~~~~~Q~~~~~~~~~~~-----------~~~~i~~~tGsGKT~~~~~~~~~~~~~~~~~~~li~~P~~~l~~q~-~~   72 (201)
T smart00487        5 GFEPLRPYQKEAIEALLSGL-----------RDVILAAPTGSGKTLAALLPALEALKRGKGKRVLVLVPTRELAEQW-AE   72 (201)
T ss_pred             CCCCCCHHHHHHHHHHHCCC-----------CCEEEECCCCCCHHHHHHHHHHHHHHCCCCCEEEEEECCHHHHHHH-HH
T ss_conf             79999988999999998389-----------9889989999609999999999986338997599990859999999-98


Q ss_pred             HHHHHHHHCHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCC-CEEEEEECCCCCCCCCHHHHCCCCCCEEEEECCHHCCCH
Q ss_conf             9999998550001344432222223334443211123578-616985303575561002120267614999711102997
Q gi|254781215|r  127 EVSKWLSLLPNKHWFEMQSLSLHPAPWYSDVLHCSLGIDS-KHYSTMCRTYSEERPDTFVGHHNTYGMAIINDEASGTPD  205 (511)
Q Consensus       127 Ei~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~s~~~~ea~~G~h~~~~~lvI~DEAsgI~d  205 (511)
                      ++.++.................       ........... ...+++...... ...... .-.....++|+|||+.+.+
T Consensus        73 ~~~~~~~~~~~~~~~~~~~~~~-------~~~~~~~~~~~~~i~i~t~~~l~~-~~~~~~-~~~~~~~~vIiDE~H~~~~  143 (201)
T smart00487       73 ELKKLGPSLGLKVVGLYGGDSK-------REQLRKLESGKTDILVTTPGRLLD-LLENDL-LELSNVDLVILDEAHRLLD  143 (201)
T ss_pred             HHHHCCCCCEEEEEEEECCCCH-------HHHHHHHHCCCCCEEEECHHHHHH-HHHHCC-CCCCCCEEEEEECHHHHHC
T ss_conf             8601021020445565247737-------999999975999899955899999-997275-4525431999989677512


Q ss_pred             -HHHHHHHHHHCCC-CCCEEEEEECCCCCCC
Q ss_conf             -8898888885079-9813899823899876
Q gi|254781215|r  206 -VINLGILGFLTER-NANRFWIMTSNPRRLS  234 (511)
Q Consensus       206 -~i~e~i~~~Lt~~-g~~~~~i~~~nP~~~~  234 (511)
                       .....+...+... ....+++++++|.+..
T Consensus       144 ~~~~~~~~~~~~~~~~~~~~i~lSAT~~~~~  174 (201)
T smart00487      144 GGFGDQLEKLLKLLPKNVQLLLLSATPPEEI  174 (201)
T ss_pred             CCCHHHHHHHHHHCCCCCCEEEECCCCCHHH
T ss_conf             5709999999996799997899924898689


No 12 
>PRK10875 recD exonuclease V subunit alpha; Provisional
Probab=98.47  E-value=7.9e-06  Score=55.36  Aligned_cols=157  Identities=21%  Similarity=0.151  Sum_probs=82.5

Q ss_pred             HHHHHHHHHHHHHHHHCCCCCCCCCCEEEEE-ECCCCCCHHHHHHHHHHHHHHH--CCCCEEEEEECCHHHHHHHHHHHH
Q ss_conf             5899999999999874056555421012465-0257659789999999999980--899669998085899999999999
Q gi|254781215|r   52 RSWQLEFMEVVDAHCLNSVNNPNPEVFKGAI-SAGRGIGKTTLNAWLVLWLMST--RPGISVICLANSETQLKTTLWAEV  128 (511)
Q Consensus        52 ~~WQ~e~l~~i~~~~~~~~~~~~~~~~r~aV-~sgrG~GKS~l~a~l~lw~l~~--~p~~kv~vtApt~~Q~~~ilw~Ei  128 (511)
                      -+||+.+...-..             .+++| +.|=|+|||+.++.++.-.+..  .++.+|..+|||-+-+.... .-|
T Consensus       149 ~dwQk~A~a~Al~-------------~~~~vIsGGPGTGKTttV~~lLa~l~~~~~~~~l~I~LaAPTGKAAaRL~-Esi  214 (607)
T PRK10875        149 VNWQKVAAAVALT-------------RRISVISGGPGTGKTTTVAKLLAALIQLADGERCRIRLAAPTGKAAARLT-ESL  214 (607)
T ss_pred             CCHHHHHHHHHHH-------------CCEEEEECCCCCCHHHHHHHHHHHHHHHCCCCCCEEEEECCHHHHHHHHH-HHH
T ss_conf             5189999999875-------------57789967999877889999999999964589970899882289999999-999


Q ss_pred             HHHHHHCHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCCCCCCCHHHHCCCCCCEEEEECCHHCCCHHHH
Q ss_conf             99998550001344432222223334443211123578616985303575561002120267614999711102997889
Q gi|254781215|r  129 SKWLSLLPNKHWFEMQSLSLHPAPWYSDVLHCSLGIDSKHYSTMCRTYSEERPDTFVGHHNTYGMAIINDEASGTPDVIN  208 (511)
Q Consensus       129 ~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~ea~~G~h~~~~~lvI~DEAsgI~d~i~  208 (511)
                      .+....++..+..      ....+......+--+....++-   .....++||        -...++|+||||.|+-.++
T Consensus       215 ~~~~~~l~~~~~~------~~~~p~~a~TiHRLLg~~p~~~---~f~~~~~nP--------L~~DvlIVDEASMVDl~Lm  277 (607)
T PRK10875        215 GKALRQLPLTDEQ------KKRIPEDASTLHRLLGAQPGSQ---RLRYHAGNP--------LHLDVLVVDEASMIDLPMM  277 (607)
T ss_pred             HHHHHHCCCCHHH------HHCCCCCCEEHHHHCCCCCCCC---CCCCCCCCC--------CCCCEEEEECCHHHHHHHH
T ss_conf             8787534766566------6337655665897529678987---656577999--------9889899907336659999


Q ss_pred             HHHHHHHCCCCCCEEEEEECCC-----CCCCCHHHHHHH
Q ss_conf             8888885079981389982389-----987655676530
Q gi|254781215|r  209 LGILGFLTERNANRFWIMTSNP-----RRLSGKFYEIFN  242 (511)
Q Consensus       209 e~i~~~Lt~~g~~~~~i~~~nP-----~~~~g~fy~~~~  242 (511)
                      ..+..++.. +++  +|..|-+     -+....|.|.+.
T Consensus       278 ~~LL~Alp~-~aR--LILvGD~dQLpSVgaGaVL~DL~~  313 (607)
T PRK10875        278 SRLIDALPD-HAR--VIFLGDRDQLASVEAGAVLGDICA  313 (607)
T ss_pred             HHHHHHCCC-CCE--EEEECCHHHCCCCCCCCCHHHHHH
T ss_conf             999982899-988--999656232478888821799998


No 13 
>COG1444 Predicted P-loop ATPase fused to an acetyltransferase [General function prediction only]
Probab=98.41  E-value=3.3e-05  Score=51.48  Aligned_cols=305  Identities=16%  Similarity=0.081  Sum_probs=137.2

Q ss_pred             HHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHHCC-CCEEEEEECCHHHHHHHHHHHHHHHHH
Q ss_conf             9999999999874056555421012465025765978999999999998089-966999808589999999999999998
Q gi|254781215|r   55 QLEFMEVVDAHCLNSVNNPNPEVFKGAISAGRGIGKTTLNAWLVLWLMSTRP-GISVICLANSETQLKTTLWAEVSKWLS  133 (511)
Q Consensus        55 Q~e~l~~i~~~~~~~~~~~~~~~~r~aV~sgrG~GKS~l~a~l~lw~l~~~p-~~kv~vtApt~~Q~~~ilw~Ei~k~~~  133 (511)
                      |.+++..+..-...+..       -+.+.+.||=|||+++...+ ..+...- ..+|+||||+..-++ ++|.-+.+-++
T Consensus       216 Q~~~l~~~~~l~~~~~~-------~~vlTAdRGRGKSA~lGi~~-~~~~~~~~~~~iiVTAP~~~nv~-~Lf~fa~~~l~  286 (758)
T COG1444         216 QAEALEILERLLDAPKR-------ALVLTADRGRGKSAALGIAL-AAAARLAGSVRIIVTAPTPANVQ-TLFEFAGKGLE  286 (758)
T ss_pred             HHHHHHHHHHHHCCCCC-------EEEEECCCCCCHHHHHHHHH-HHHHHHCCCCEEEEECCCHHHHH-HHHHHHHHHHH
T ss_conf             89999999999708983-------59998677874768874999-99997337720899679778899-99999987699


Q ss_pred             HCHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCCCCCCCHHHHCCCCCCEEEEECCHHCCCHHHHHHHHH
Q ss_conf             55000134443222222333444321112357861698530357556100212026761499971110299788988888
Q gi|254781215|r  134 LLPNKHWFEMQSLSLHPAPWYSDVLHCSLGIDSKHYSTMCRTYSEERPDTFVGHHNTYGMAIINDEASGTPDVINLGILG  213 (511)
Q Consensus       134 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~ea~~G~h~~~~~lvI~DEAsgI~d~i~e~i~~  213 (511)
                      .+=.+.....+            ......... ..++..    ...+|+..+  ..  .-++|+||||+||=.+...+..
T Consensus       287 ~lg~~~~v~~~------------~~g~~~~~~-~~~~~i----~y~~P~~a~--~~--~DllvVDEAAaIplplL~~l~~  345 (758)
T COG1444         287 FLGYKRKVAPD------------ALGEIREVS-GDGFRI----EYVPPDDAQ--EE--ADLLVVDEAAAIPLPLLHKLLR  345 (758)
T ss_pred             HHCCCCCCCCC------------CCCCEEEEC-CCCEEE----EEECCHHHC--CC--CCEEEEEHHHCCCHHHHHHHHH
T ss_conf             82774555634------------424400004-774257----751750012--56--8889981031288699999986


Q ss_pred             HHCCCCCCEEEEEECCCCCCCCH-HHHHHHCC-C-C-CCEEEEECCCCCCCC-CHHHHHHHHHHC----CCC----HHHH
Q ss_conf             85079981389982389987655-67653035-2-4-741798404336778-977899999751----898----0135
Q gi|254781215|r  214 FLTERNANRFWIMTSNPRRLSGK-FYEIFNKP-L-D-DWKRFQIDTRTVEGI-DPSFHEGIIARY----GLD----SDVT  280 (511)
Q Consensus       214 ~Lt~~g~~~~~i~~~nP~~~~g~-fy~~~~~~-~-~-~w~~~~i~~~~~p~~-~~~~ie~~~~~~----ged----s~~~  280 (511)
                      .    -.+..+..|-+..--+|+ |--.|.+. + . +...+++.-.++=.. ..+=||+|.-+-    .|+    ..-.
T Consensus       346 ~----~~rv~~sTTIhGYEGtGRgF~lkf~~~l~~~~~~~~~~~~l~ePIRya~gDPiE~wl~d~LLLdAEp~~~~~~~~  421 (758)
T COG1444         346 R----FPRVLFSTTIHGYEGTGRGFSLKFLARLRKQRDTTLHELELEEPIRYAPGDPIEKWLYDALLLDAEPAELEPEDL  421 (758)
T ss_pred             H----CCCEEEEEEECCCCCCCHHHHHHHHHHHCCCCCCEEEEEECCCCCCCCCCCCHHHHHHHHHCCCCCCCCCCCCCC
T ss_conf             4----481699974024466771799999998431565327998546873168999679999886611787666775434


Q ss_pred             HHHHCCCCCCCCCCEEECHHHHH-------HHHHCCC-----------------CCCCCCEEEEEEECCCCCCC--CEE-
Q ss_conf             44431756666787375599998-------8640765-----------------31899708999623334784--179-
Q gi|254781215|r  281 RVEVCGQFPQQDIDSFIPLNIIE-------EALNREP-----------------CPDPYAPLIMGCDIAEEGGD--NTV-  333 (511)
Q Consensus       281 r~evlgeFp~~~~~~~i~~~~ie-------~a~~r~~-----------------~~~~~~~~viGvDVAr~G~D--~sv-  333 (511)
                      +-...-.++++.+ .+...+...       .|..|..                 ...+..-++..+.||+.|..  .++ 
T Consensus       422 ~~~~~~~~~~~~~-~~~~ee~Lr~~~gllV~AHYRnsP~DL~~L~DaP~h~~~al~~~~~~~va~~qva~EG~l~~~~i~  500 (758)
T COG1444         422 RGSLEILEVDQRD-LLFDEELLRQVYGLLVSAHYRNSPNDLRRLLDAPHHHIFALRAPEGKPVAVWQVAEEGGLSDELID  500 (758)
T ss_pred             CCCEEEEECCHHH-HHHCHHHHHHHHHHHHHHHCCCCHHHHHHHHCCCCCEEEEEECCCCCEEEEEEEECCCCCCHHHHH
T ss_conf             5660255236676-642989999998777533345887789987218877168887599956899986003787288999


Q ss_pred             -------------------------EEEECCCEEEEEEECCCCCHHHHHHH-HHHHHHHCCCCEEEEEECCCCHHHHHHH
Q ss_conf             -------------------------99822755899873277898899999-9999986188829980068763688989
Q gi|254781215|r  334 -------------------------VVLRRGPVIEHLFDWSKTDLRTTNNK-ISGLVEKYRPDAIIIDANNTGARTCDYL  387 (511)
Q Consensus       334 -------------------------i~~r~G~~v~~~~~~~~~d~~~~a~~-i~~~~~~~~~~~i~iD~~GvG~gV~d~L  387 (511)
                                               ++.-.|.++..|.+.+..--+-+..+ +..++++.+   =.+|-.|+|-|+...|
T Consensus       501 ~~~~g~r~~GnlIP~~l~~~~~~~~fa~l~G~RIvRIAvhPe~q~~GiGsrlL~~l~~~a~---~~~DwlgvsFG~t~~L  577 (758)
T COG1444         501 IWLGGRRPRGNLIPDLLAKHHRDPEFAKLVGWRIVRIAVHPELQRMGIGSRLLALLIEEAR---KGLDWLGVSFGYTEEL  577 (758)
T ss_pred             HHHCCCCCCCCCCHHHHHHHHCCHHHHHHCCEEEEEEEECHHHHHCCHHHHHHHHHHHHHH---CCCCEEEECCCCCHHH
T ss_conf             9956878887626799998603423310001268888708878635888999999999984---5898897456788899


Q ss_pred             HH----CCCEEEEE
Q ss_conf             86----49827984
Q gi|254781215|r  388 EM----LGYHVYRV  397 (511)
Q Consensus       388 ~~----~g~~v~~v  397 (511)
                      -.    -|+..+.+
T Consensus       578 ~rFW~rnGF~pVhl  591 (758)
T COG1444         578 LRFWLRNGFVPVHL  591 (758)
T ss_pred             HHHHHHCCEEEEEE
T ss_conf             99999759079873


No 14 
>pfam04851 ResIII Type III restriction enzyme, res subunit.
Probab=98.37  E-value=4.5e-06  Score=56.90  Aligned_cols=99  Identities=26%  Similarity=0.329  Sum_probs=69.3

Q ss_pred             CHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEEECCHHHHHHHHHHHHHH
Q ss_conf             45899999999999874056555421012465025765978999999999998089966999808589999999999999
Q gi|254781215|r   51 PRSWQLEFMEVVDAHCLNSVNNPNPEVFKGAISAGRGIGKTTLNAWLVLWLMSTRPGISVICLANSETQLKTTLWAEVSK  130 (511)
Q Consensus        51 P~~WQ~e~l~~i~~~~~~~~~~~~~~~~r~aV~sgrG~GKS~l~a~l~lw~l~~~p~~kv~vtApt~~Q~~~ilw~Ei~k  130 (511)
                      .|+||.|+++++..+.            +.-|.++-|+|||.+++.++-++.  .++.++++.+|+..-+...       
T Consensus         4 LR~yQ~~a~~~~~~~~------------~~~i~~pTGsGKT~~~~~~i~~~~--~~~~~~lvlvp~~~L~~Q~-------   62 (103)
T pfam04851         4 LRPYQIEAIRNLLEKK------------RGLIVMATGSGKTLTAAKLIARLL--KGKKKVLFLVPRKDLLEQA-------   62 (103)
T ss_pred             CCHHHHHHHHHHHHCC------------CEEEEECCCCCHHHHHHHHHHHHH--HCCCCEEEEECCHHHHHHH-------
T ss_conf             7299999999999639------------869995899987999999999998--4699299990829999999-------


Q ss_pred             HHHHCHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCCCCCCCHHHHCCCCCCEEEEECCHHCCCH-HHHH
Q ss_conf             998550001344432222223334443211123578616985303575561002120267614999711102997-8898
Q gi|254781215|r  131 WLSLLPNKHWFEMQSLSLHPAPWYSDVLHCSLGIDSKHYSTMCRTYSEERPDTFVGHHNTYGMAIINDEASGTPD-VINL  209 (511)
Q Consensus       131 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~ea~~G~h~~~~~lvI~DEAsgI~d-~i~e  209 (511)
                       .+.                                                          .++|+|||+-.+. ..|.
T Consensus        63 -~~~----------------------------------------------------------~lii~DE~H~~~a~~~~~   83 (103)
T pfam04851        63 -LEE----------------------------------------------------------FVIIIDEAHHSSAKTKYR   83 (103)
T ss_pred             -HHH----------------------------------------------------------HHHHHHHHHHCCCHHHHH
T ss_conf             -996----------------------------------------------------------564601635235378999


Q ss_pred             HHHHHHCCCCCCEEEEEECCCCC
Q ss_conf             88888507998138998238998
Q gi|254781215|r  210 GILGFLTERNANRFWIMTSNPRR  232 (511)
Q Consensus       210 ~i~~~Lt~~g~~~~~i~~~nP~~  232 (511)
                      .+...+   .+..++=++.+|.+
T Consensus        84 ~l~~~~---~~~~~lGlTATP~R  103 (103)
T pfam04851        84 KILEYF---KPAFLLGLTATPER  103 (103)
T ss_pred             HHHHHC---CCCEEEEEEECCCC
T ss_conf             999957---72608998008889


No 15 
>PRK13766 Hef nuclease; Provisional
Probab=98.30  E-value=2.3e-05  Score=52.48  Aligned_cols=169  Identities=12%  Similarity=0.060  Sum_probs=81.9

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEEECCHHH
Q ss_conf             57775655578458999999999998740565554210124650257659789999999999980899669998085899
Q gi|254781215|r   40 EKGTPLEGFSAPRSWQLEFMEVVDAHCLNSVNNPNPEVFKGAISAGRGIGKTTLNAWLVLWLMSTRPGISVICLANSETQ  119 (511)
Q Consensus        40 ~~~~~~~~~~~P~~WQ~e~l~~i~~~~~~~~~~~~~~~~r~aV~sgrG~GKS~l~a~l~lw~l~~~p~~kv~vtApt~~Q  119 (511)
                      +|+---+...-||+||.|++..--.   .|          +.|..+.|.|||.+++.++..++- .+++|++..|||..-
T Consensus         5 ~h~~~~p~~ie~R~YQ~el~~~Al~---~N----------tiVvLPTG~GKT~IA~lvi~~~l~-~~~gKilFLaPT~pL   70 (764)
T PRK13766          5 SHPLIKPNTIEARLYQQLLAAKALK---GN----------TLVVLPTGLGKTAIALLVIAERLQ-KYGGKVLILAPTKPL   70 (764)
T ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHH---CC----------EEEEECCCCCHHHHHHHHHHHHHH-HCCCEEEEECCCHHH
T ss_conf             6776586877653879999999985---89----------899959986689999999999997-489889998588889


Q ss_pred             HHHHHHHHHHHHHHHCHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCCCCCCCHHHHCCCCCCEEEEECC
Q ss_conf             99999999999998550001344432222223334443211123578616985303575561002120267614999711
Q gi|254781215|r  120 LKTTLWAEVSKWLSLLPNKHWFEMQSLSLHPAPWYSDVLHCSLGIDSKHYSTMCRTYSEERPDTFVGHHNTYGMAIINDE  199 (511)
Q Consensus       120 ~~~ilw~Ei~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~ea~~G~h~~~~~lvI~DE  199 (511)
                      +.+-. ..+.+.+. .|.. ......+...+.      .+..+-......+++++..-..--.+  -+.-....|+|+||
T Consensus        71 V~Qq~-~~~~~~l~-i~~~-~i~~ltG~~~~~------~r~~~w~~~~Viv~TPQvl~ndL~~g--~i~l~dv~lLVfDE  139 (764)
T PRK13766         71 VEQHA-EFFRKFLN-IDPE-KIVVLTGEISPE------KRAALWEKAKVIVATPQVIENDLLAG--RISLEDVSLLIFDE  139 (764)
T ss_pred             HHHHH-HHHHHHCC-CCCC-EEEEEECCCCHH------HHHHHHCCCCEEEECCHHHHHHHHHC--CCCHHHCCEEEEEC
T ss_conf             99999-99999709-9955-289998887827------68998607999999908999999829--86788822899974


Q ss_pred             HHCC-CHHHH-HHHHHHHCCCCCCEEEEEECCCCCC
Q ss_conf             1029-97889-8888885079981389982389987
Q gi|254781215|r  200 ASGT-PDVIN-LGILGFLTERNANRFWIMTSNPRRL  233 (511)
Q Consensus       200 AsgI-~d~i~-e~i~~~Lt~~g~~~~~i~~~nP~~~  233 (511)
                      |+-- -+.-+ .++.-.+.......++-++.+|...
T Consensus       140 aHha~Gnh~Y~~I~~~y~~~~~~PrILGLTASPGs~  175 (764)
T PRK13766        140 AHRAVGNYAYVFIAERYHEDAKNPLVLGLTASPGSD  175 (764)
T ss_pred             CCCCCCCCCHHHHHHHHHHCCCCCEEEEECCCCCCC
T ss_conf             666667762899999998537785588503688764


No 16 
>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=98.29  E-value=7.7e-06  Score=55.42  Aligned_cols=136  Identities=18%  Similarity=0.174  Sum_probs=86.5

Q ss_pred             HHHHHHHHHHHHHHHHCCCCCCCCCCEEEEEEC-CCCCCHHHHHHHHHHHHHHHC-----------CCCEEEEEECCHHH
Q ss_conf             589999999999987405655542101246502-576597899999999999808-----------99669998085899
Q gi|254781215|r   52 RSWQLEFMEVVDAHCLNSVNNPNPEVFKGAISA-GRGIGKTTLNAWLVLWLMSTR-----------PGISVICLANSETQ  119 (511)
Q Consensus        52 ~~WQ~e~l~~i~~~~~~~~~~~~~~~~r~aV~s-grG~GKS~l~a~l~lw~l~~~-----------p~~kv~vtApt~~Q  119 (511)
                      ..=|+++|..+..+             ||.|-+ |=|+||||++-.++--+....           .+-.|+.+|||-+-
T Consensus       352 ~~~Qk~AL~~~~~~-------------Kv~iLTGGPGTGKtT~t~~i~~~~~~~~gl~l~~~~~vndd~~v~LaAPTGrA  418 (769)
T TIGR01448       352 SEEQKEALKTAIQD-------------KVVILTGGPGTGKTTITKAIIELYEELKGLDLDKDDYVNDDLPVVLAAPTGRA  418 (769)
T ss_pred             HHHHHHHHHHHHCC-------------CEEEEECCCCCCHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCEEEEECCCHHH
T ss_conf             68899999998609-------------48998577888616899999999987168775531245677648873774378


Q ss_pred             HHHHHHHHHHHHHHHCHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCCCCCCCHHHH-CCCC--CCEEEE
Q ss_conf             9999999999999855000134443222222333444321112357861698530357556100212-0267--614999
Q gi|254781215|r  120 LKTTLWAEVSKWLSLLPNKHWFEMQSLSLHPAPWYSDVLHCSLGIDSKHYSTMCRTYSEERPDTFVG-HHNT--YGMAII  196 (511)
Q Consensus       120 ~~~ilw~Ei~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~ea~~G-~h~~--~~~lvI  196 (511)
                      +|..  .|+.-....=+.+           +.+|..+                         +.-.+ .|.+  ...|+|
T Consensus       419 AkRl--~E~TG~~a~TIHR-----------LlG~~~~-------------------------~~~~~k~~~~~~~~DL~I  460 (769)
T TIGR01448       419 AKRL--AEVTGLEALTIHR-----------LLGYGSD-------------------------TKSENKNLEDPIDADLLI  460 (769)
T ss_pred             HHHC--CCCCCCHHHHHHH-----------HHCCCCC-------------------------CCCCCHHHCCCCCCCEEE
T ss_conf             8851--1002621234778-----------6368988-------------------------873211011347877699


Q ss_pred             ECCHHCCCHHHHHHHHHHHCCCCCCEEEEEECC-----CCCCCCHHHHHH
Q ss_conf             711102997889888888507998138998238-----998765567653
Q gi|254781215|r  197 NDEASGTPDVINLGILGFLTERNANRFWIMTSN-----PRRLSGKFYEIF  241 (511)
Q Consensus       197 ~DEAsgI~d~i~e~i~~~Lt~~g~~~~~i~~~n-----P~~~~g~fy~~~  241 (511)
                      +||.|.|++-.+..+..++.+ +++  +|..|=     |-...-.|-|+-
T Consensus       461 vDE~SM~Dt~L~~~lL~a~P~-~a~--lllVGD~DQLPSV~pG~VL~DLi  507 (769)
T TIGR01448       461 VDESSMVDTWLASSLLAAVPD-HAR--LLLVGDADQLPSVGPGQVLKDLI  507 (769)
T ss_pred             EECCCHHHHHHHHHHHHHCCC-CCE--EEEECCCCCCCCCCCCHHHHHHH
T ss_conf             814621889999999861797-777--98883768889886440899998


No 17 
>KOG2036 consensus
Probab=98.13  E-value=6.1e-05  Score=49.76  Aligned_cols=144  Identities=15%  Similarity=0.093  Sum_probs=77.9

Q ss_pred             HHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEEECCHHHHHHHHHHHHHHHHHH
Q ss_conf             99999999998740565554210124650257659789999999999980899669998085899999999999999985
Q gi|254781215|r   55 QLEFMEVVDAHCLNSVNNPNPEVFKGAISAGRGIGKTTLNAWLVLWLMSTRPGISVICLANSETQLKTTLWAEVSKWLSL  134 (511)
Q Consensus        55 Q~e~l~~i~~~~~~~~~~~~~~~~r~aV~sgrG~GKS~l~a~l~lw~l~~~p~~kv~vtApt~~Q~~~ilw~Ei~k~~~~  134 (511)
                      |..++-..-+.+....-+     .-+|..+|||-|||+... +.+..+..+-.++|+||+|+-..+++ +|.-+-|=...
T Consensus       258 Qakav~~f~dai~eK~lr-----~~vsLtA~RGRGKSAALG-lsiA~AVa~GysnIyvtSPspeNlkT-lFeFv~kGfDa  330 (1011)
T KOG2036         258 QAKAVLTFFDAIVEKTLR-----STVSLTASRGRGKSAALG-LSIAGAVAFGYSNIYVTSPSPENLKT-LFEFVFKGFDA  330 (1011)
T ss_pred             HHHHHHHHHHHHHHHHHC-----CEEEEEECCCCCCHHHHH-HHHHHHHHCCCCEEEECCCCHHHHHH-HHHHHHCCHHH
T ss_conf             899999999999875405-----627898547787005564-78999986375037874898388899-99999803123


Q ss_pred             CHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCCCCCCCHHHHCCCCCCEEEEECCHHCCCHH-HHHHHHH
Q ss_conf             500013444322222233344432111235786169853035755610021202676149997111029978-8988888
Q gi|254781215|r  135 LPNKHWFEMQSLSLHPAPWYSDVLHCSLGIDSKHYSTMCRTYSEERPDTFVGHHNTYGMAIINDEASGTPDV-INLGILG  213 (511)
Q Consensus       135 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~ea~~G~h~~~~~lvI~DEAsgI~d~-i~e~i~~  213 (511)
                      +--+.......-.-.-..|..-..++.+....+      +|...-+|.--+-+ +. .-|+|+|||+.||=. +..-+.|
T Consensus       331 L~Yqeh~Dy~iI~s~np~fkkaivRInifr~hr------QtIQYi~P~D~~kl-~q-~eLlVIDEAAAIPLplvk~LigP  402 (1011)
T KOG2036         331 LEYQEHVDYDIIQSTNPDFKKAIVRINIFREHR------QTIQYISPHDHQKL-GQ-AELLVIDEAAAIPLPLVKKLIGP  402 (1011)
T ss_pred             HCCHHHCCHHHHHHCCHHHHHHEEEEEEECCCC------CEEEEECCCHHHHC-CC-CCEEEECHHHCCCHHHHHHHHCC
T ss_conf             131443251146542823140279998742640------13675563005440-67-74898600202777899985165


No 18 
>PRK00254 ski2-like helicase; Provisional
Probab=98.11  E-value=0.00018  Score=46.75  Aligned_cols=144  Identities=15%  Similarity=0.081  Sum_probs=78.7

Q ss_pred             CHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEEECCHHHHHHHHHHHHHH
Q ss_conf             45899999999999874056555421012465025765978999999999998089966999808589999999999999
Q gi|254781215|r   51 PRSWQLEFMEVVDAHCLNSVNNPNPEVFKGAISAGRGIGKTTLNAWLVLWLMSTRPGISVICLANSETQLKTTLWAEVSK  130 (511)
Q Consensus        51 P~~WQ~e~l~~i~~~~~~~~~~~~~~~~r~aV~sgrG~GKS~l~a~l~lw~l~~~p~~kv~vtApt~~Q~~~ilw~Ei~k  130 (511)
                      -.+||.|+|..   ...++.        -+-|+++.|.|||.++-.+++-.++. .+.++++++|...=+.+.. .++++
T Consensus        24 l~p~Q~e~l~~---g~~~g~--------NllvsaPT~sGKTlvAElail~~~l~-~~~k~iyi~P~kALa~EK~-~~f~~   90 (717)
T PRK00254         24 LYPPQAEALTS---GVLEGK--------NLLIAIPTASGKTLIAEIAMVNKLLR-EGGKAVYLVPLKALAEEKF-REFKD   90 (717)
T ss_pred             CCHHHHHHHHH---HHCCCC--------CEEEECCCCCCHHHHHHHHHHHHHHH-CCCEEEEECCHHHHHHHHH-HHHHH
T ss_conf             68999999874---233698--------18998998874899999999999985-2992999926799999999-99987


Q ss_pred             HHHHCHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCCCCCCCHHHHCCC------CCCEEEEECCHHCCC
Q ss_conf             99855000134443222222333444321112357861698530357556100212026------761499971110299
Q gi|254781215|r  131 WLSLLPNKHWFEMQSLSLHPAPWYSDVLHCSLGIDSKHYSTMCRTYSEERPDTFVGHHN------TYGMAIINDEASGTP  204 (511)
Q Consensus       131 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~ea~~G~h~------~~~~lvI~DEAsgI~  204 (511)
                      +-...     ..+.   ...-.+  +.....+  .... .+++      .+|.++.+-.      ...-++|+||.+-|.
T Consensus        91 ~~~~g-----~~V~---~~tGd~--~~~~~~l--~~~d-IiV~------T~Ek~dsl~r~~~~~l~~i~lvViDEiH~ig  151 (717)
T PRK00254         91 WEVLG-----LRVA---MATGDY--DSKDEWL--GKYD-IIIA------TAEKFDSLLRHGSSWIKDVKLLVADEIHLIG  151 (717)
T ss_pred             HHHCC-----CEEE---EEECCC--CCCCCCC--CCCC-EEEE------CHHHHHHHHHCCHHHHHCCCEEEEECEEECC
T ss_conf             77449-----8898---974898--8870104--6899-9998------8899999997162565326989997607888


Q ss_pred             H----HHHHHHHHHHCCCCCCEEEEEECC
Q ss_conf             7----889888888507998138998238
Q gi|254781215|r  205 D----VINLGILGFLTERNANRFWIMTSN  229 (511)
Q Consensus       205 d----~i~e~i~~~Lt~~g~~~~~i~~~n  229 (511)
                      |    .+||.+-.-|.. ..+  +++.|-
T Consensus       152 D~~RG~~lE~~l~~l~~-~~q--iIgLSA  177 (717)
T PRK00254        152 SRDRGATLEFILTHMLG-RAQ--IIGLSA  177 (717)
T ss_pred             CCCCHHHHHHHHHHHHC-CCE--EEEEEE
T ss_conf             98740999999995100-366--999963


No 19 
>PRK02362 ski2-like helicase; Provisional
Probab=98.10  E-value=0.00018  Score=46.82  Aligned_cols=152  Identities=14%  Similarity=0.018  Sum_probs=81.2

Q ss_pred             CHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEEECCHHHHHHHHHHHHHH
Q ss_conf             45899999999999874056555421012465025765978999999999998089966999808589999999999999
Q gi|254781215|r   51 PRSWQLEFMEVVDAHCLNSVNNPNPEVFKGAISAGRGIGKTTLNAWLVLWLMSTRPGISVICLANSETQLKTTLWAEVSK  130 (511)
Q Consensus        51 P~~WQ~e~l~~i~~~~~~~~~~~~~~~~r~aV~sgrG~GKS~l~a~l~lw~l~~~p~~kv~vtApt~~Q~~~ilw~Ei~k  130 (511)
                      -.+||.|++..   ...++.        -+-|+++.|.|||.++-..++-.+.  .+.|+++++|...=+.+++ .+.++
T Consensus        24 Lyp~Q~eal~~---gl~~g~--------NlvvsaPTgsGKTlvAElail~~l~--~g~k~vYi~P~kALa~EK~-~~~~~   89 (736)
T PRK02362         24 LYPPQAEAVEA---GLLEGK--------NLLAAIPTASGKTLLAELAMLKAIA--EGGKALYIVPLRALASEKF-EEFSE   89 (736)
T ss_pred             CCHHHHHHHHH---HHCCCC--------CEEEECCCCCCHHHHHHHHHHHHHH--HCCEEEEECCHHHHHHHHH-HHHHH
T ss_conf             78999999986---435698--------1899799998589999999999998--3997999858799999999-99998


Q ss_pred             HHHHCHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCCCCCCCHHHHCC------CCCCEEEEECCHHCCC
Q ss_conf             9985500013444322222233344432111235786169853035755610021202------6761499971110299
Q gi|254781215|r  131 WLSLLPNKHWFEMQSLSLHPAPWYSDVLHCSLGIDSKHYSTMCRTYSEERPDTFVGHH------NTYGMAIINDEASGTP  204 (511)
Q Consensus       131 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~ea~~G~h------~~~~~lvI~DEAsgI~  204 (511)
                      +...     ...+.   +..-.+......  +  .... .+++      +||-+..+-      -...-++|+||.+-|.
T Consensus        90 ~~~~-----gi~V~---~~tGd~~~~~~~--l--~~~d-IiV~------T~EK~dsl~r~~~~~l~~v~lVViDEiHli~  150 (736)
T PRK02362         90 FSEL-----GLRVG---ISTGDYDRRDEY--L--GRND-IIVA------TSEKTDSLLRNGAPWIDDISCVVADEVHLID  150 (736)
T ss_pred             HHCC-----CCEEE---EEECCCCCCHHH--C--CCCC-EEEE------CHHHHHHHHHCCCHHHHCCCEEEEECCEEEC
T ss_conf             7457-----99899---980898878314--3--6899-9999------9799999984481676508989981767866


Q ss_pred             H----HHHHHHHHHHCCCCCCEEEEEECCCCCCCC
Q ss_conf             7----889888888507998138998238998765
Q gi|254781215|r  205 D----VINLGILGFLTERNANRFWIMTSNPRRLSG  235 (511)
Q Consensus       205 d----~i~e~i~~~Lt~~g~~~~~i~~~nP~~~~g  235 (511)
                      |    .+||.+...|.-.+....+++.|..-.+..
T Consensus       151 d~~RG~~lE~~lskl~~~~~~iqiIgLSATl~N~~  185 (736)
T PRK02362        151 SPNRGPTLEVTLAKLRRLNPDMQVIALSATIGNAD  185 (736)
T ss_pred             CCCCHHHHHHHHHHHHHCCCCCEEEEEECCCCCHH
T ss_conf             88724999999999973387743898624558999


No 20 
>PRK10536 hypothetical protein; Provisional
Probab=98.10  E-value=0.00047  Score=44.14  Aligned_cols=191  Identities=13%  Similarity=0.088  Sum_probs=98.7

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEEECCHH
Q ss_conf             55777565557845899999999999874056555421012465025765978999999999998089966999808589
Q gi|254781215|r   39 GEKGTPLEGFSAPRSWQLEFMEVVDAHCLNSVNNPNPEVFKGAISAGRGIGKTTLNAWLVLWLMSTRPGISVICLANSET  118 (511)
Q Consensus        39 ~~~~~~~~~~~~P~~WQ~e~l~~i~~~~~~~~~~~~~~~~r~aV~sgrG~GKS~l~a~l~lw~l~~~p~~kv~vtApt~~  118 (511)
                      +..+.|+...+.   =|++.+++|.++.            =+-+...-|+|||++++..++-.+....-.++++|-|.-.
T Consensus        51 ~~~~~pi~pkt~---~Q~~yi~~i~~~~------------ivf~~GpAGTGKT~lA~a~Al~~l~~~~~~kIIltRP~V~  115 (262)
T PRK10536         51 SRDTSPILARNE---AQLHYLKAIESKQ------------LIFATGEAGCGKTWISAAKAAEALIHKDVDRIIVTRPVLQ  115 (262)
T ss_pred             CCCCCCCCCCCH---HHHHHHHHHHHCC------------EEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCCC
T ss_conf             788998678986---4999999986198------------3999899987589999999999998588868999667875


Q ss_pred             H----------HHHHHHHHHHHHHHHCHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCCCCCCC-HHHHC
Q ss_conf             9----------999999999999985500013444322222233344432111235786169853035755610-02120
Q gi|254781215|r  119 Q----------LKTTLWAEVSKWLSLLPNKHWFEMQSLSLHPAPWYSDVLHCSLGIDSKHYSTMCRTYSEERPD-TFVGH  187 (511)
Q Consensus       119 Q----------~~~ilw~Ei~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~e-a~~G~  187 (511)
                      -          +.+.+.+.+.-.+..+......      -.....        +....+..-+.        |- -++| 
T Consensus       116 ~ge~lGfLPGdl~EK~~Pyl~Pi~D~L~~~lg~------~~~~~~--------~~~e~G~Iei~--------PlafmRG-  172 (262)
T PRK10536        116 ADEDLGFLPGDIAEKFAPYFRPVYDVLVRRLGA------SFMQYC--------LRPEIGKVEIA--------PFAYMRG-  172 (262)
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHCH------HHHHHH--------HHHHCCCEEEE--------EHHHHCC-
T ss_conf             676667698987998878887899999999685------999999--------87305948998--------7587447-


Q ss_pred             CCCCCEEEEECCHHCCCHHHHHHHHHHHCCCCCCEEEEEECCCCC-------CCCHHHHHHHCCC--CCCEEEEECCCCC
Q ss_conf             267614999711102997889888888507998138998238998-------7655676530352--4741798404336
Q gi|254781215|r  188 HNTYGMAIINDEASGTPDVINLGILGFLTERNANRFWIMTSNPRR-------LSGKFYEIFNKPL--DDWKRFQIDTRTV  258 (511)
Q Consensus       188 h~~~~~lvI~DEAsgI~d~i~e~i~~~Lt~~g~~~~~i~~~nP~~-------~~g~fy~~~~~~~--~~w~~~~i~~~~~  258 (511)
                      +.....++|+|||......-.   .-.||--|...+++.+|.+.-       .+| +.+...+..  +.-..+.++..  
T Consensus       173 rTf~na~IIvDEaQN~T~~qm---k~iLTRiG~~SKiVi~GD~~Q~Dl~~~~~SG-L~~~~~~l~~~~~i~~i~F~~~--  246 (262)
T PRK10536        173 RTFENAVVILDEAQNVTAAQM---KMFLTRLGENVTVIVNGDITQCDLPRGVKSG-LSDALERFEEDEMVGIVRFGKE--  246 (262)
T ss_pred             CCCCCEEEEEEHHHCCCHHHH---HHHHHHCCCCCEEEEECCCCCCCCCCCCCCC-HHHHHHHHCCCCCEEEEECCCC--
T ss_conf             751442899841212899999---8898542599689996882022699999873-9999999569996589983644--


Q ss_pred             CCCCHHHHHHHHHHC
Q ss_conf             778977899999751
Q gi|254781215|r  259 EGIDPSFHEGIIARY  273 (511)
Q Consensus       259 p~~~~~~ie~~~~~~  273 (511)
                      -.+-...+.++...|
T Consensus       247 DIVRs~lVk~Il~aY  261 (262)
T PRK10536        247 DCVRSALCQRTLHAY  261 (262)
T ss_pred             CCCCCHHHHHHHHHC
T ss_conf             401678999999962


No 21 
>TIGR01447 recD exodeoxyribonuclease V, alpha subunit; InterPro: IPR006344   This family describes the exodeoxyribonuclease V alpha subunit, RecD. RecD is part of a RecBCD complex. C-terminal part of the protein matches a domain found in viral RNA helicase, superfamily 1, IPR000606 from INTERPRO. ; GO: 0008854 exodeoxyribonuclease V activity, 0009338 exodeoxyribonuclease V complex.
Probab=98.10  E-value=3.8e-05  Score=51.05  Aligned_cols=154  Identities=17%  Similarity=0.144  Sum_probs=82.4

Q ss_pred             HHHHHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHHCCC-----CEEEEEECCHHHHHHHHHH
Q ss_conf             58999999999998740565554210124650257659789999999999980899-----6699980858999999999
Q gi|254781215|r   52 RSWQLEFMEVVDAHCLNSVNNPNPEVFKGAISAGRGIGKTTLNAWLVLWLMSTRPG-----ISVICLANSETQLKTTLWA  126 (511)
Q Consensus        52 ~~WQ~e~l~~i~~~~~~~~~~~~~~~~r~aV~sgrG~GKS~l~a~l~lw~l~~~p~-----~kv~vtApt~~Q~~~ilw~  126 (511)
                      .+||+=++.-+-..++            +-|..|=|+|||++++-+++-....-+.     .+|.++|||-.-+-.. =.
T Consensus       229 ~D~Q~~a~~~aL~~~f------------~li~GGPGTGKTTTv~~LL~al~~~~~~~G~~~~~I~l~APTGKAa~RL-~e  295 (753)
T TIGR01447       229 TDWQKVAVALALKSNF------------SLITGGPGTGKTTTVARLLLALIKQSPKQGKPRLRIALAAPTGKAAARL-AE  295 (753)
T ss_pred             HHHHHHHHHHHHHCCE------------EEEECCCCCCHHHHHHHHHHHHHHHHHHCCCCCEEEEEECCCHHHHHHH-HH
T ss_conf             3799999999860876------------8998798897789999999999998986499740478866844799999-99


Q ss_pred             HHHHHHHHCHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCCCCCCCHHHHCCCCCCEEEEECCHHCCCHH
Q ss_conf             99999985500013444322222233344432111235786169853035755610021202676149997111029978
Q gi|254781215|r  127 EVSKWLSLLPNKHWFEMQSLSLHPAPWYSDVLHCSLGIDSKHYSTMCRTYSEERPDTFVGHHNTYGMAIINDEASGTPDV  206 (511)
Q Consensus       127 Ei~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~ea~~G~h~~~~~lvI~DEAsgI~d~  206 (511)
                      -|.+....+..... -..+..+...+-...    .+..--+..++....++.+. ++     .-+...+|+||||.|+=.
T Consensus       296 sl~~~~~~L~~~~~-aid~~~~~~~~~~~~----TiHrLLG~~~I~~~~fr~h~-~N-----~L~~DVLvvDEaSMVdl~  364 (753)
T TIGR01447       296 SLRKAVKKLAAENM-AIDEDLIAALPSEAT----TIHRLLGIKPIDTKRFRHHE-RN-----PLPLDVLVVDEASMVDLP  364 (753)
T ss_pred             HHHHHHHHHHHHCC-CCCHHHHCCCCHHHH----HHHHHHCCCCCCCCCCCCCC-CC-----CCCCCEEEECCCHHCCHH
T ss_conf             99988632234236-658798548720456----88886166147876776777-78-----898552787060022679


Q ss_pred             HHHHHHHHHCCCCCC------EEEEEECCC
Q ss_conf             898888885079981------389982389
Q gi|254781215|r  207 INLGILGFLTERNAN------RFWIMTSNP  230 (511)
Q Consensus       207 i~e~i~~~Lt~~g~~------~~~i~~~nP  230 (511)
                      .+.-+-.++.. +++      ..+|++|=+
T Consensus       365 lm~kL~~A~~~-~~k~~KLy~~~LIllGD~  393 (753)
T TIGR01447       365 LMAKLLKALPP-NTKDKKLYADRLILLGDK  393 (753)
T ss_pred             HHHHHHHHCCC-CCCCCCHHHCCCCEECCC
T ss_conf             99999972263-001320101020012267


No 22 
>COG1111 MPH1 ERCC4-like helicases [DNA replication, recombination, and repair]
Probab=98.05  E-value=9.3e-05  Score=48.59  Aligned_cols=170  Identities=16%  Similarity=0.129  Sum_probs=92.0

Q ss_pred             CCCCCHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEEECCHHHHHHHHHH
Q ss_conf             55784589999999999987405655542101246502576597899999999999808996699980858999999999
Q gi|254781215|r   47 GFSAPRSWQLEFMEVVDAHCLNSVNNPNPEVFKGAISAGRGIGKTTLNAWLVLWLMSTRPGISVICLANSETQLKTTLWA  126 (511)
Q Consensus        47 ~~~~P~~WQ~e~l~~i~~~~~~~~~~~~~~~~r~aV~sgrG~GKS~l~a~l~lw~l~~~p~~kv~vtApt~~Q~~~ilw~  126 (511)
                      ....||.||..+....-.+             .+.|+-+.|.|||+++++.+..++--+++ +++..|||..-+-.-. .
T Consensus        12 ~~ie~R~YQ~~i~a~al~~-------------NtLvvlPTGLGKT~IA~~V~~~~l~~~~~-kvlfLAPTKPLV~Qh~-~   76 (542)
T COG1111          12 NTIEPRLYQLNIAAKALFK-------------NTLVVLPTGLGKTFIAAMVIANRLRWFGG-KVLFLAPTKPLVLQHA-E   76 (542)
T ss_pred             CCCCHHHHHHHHHHHHHHC-------------CEEEEECCCCCHHHHHHHHHHHHHHHCCC-EEEEECCCCHHHHHHH-H
T ss_conf             5325889999999998644-------------83899528750799999999999874588-4899658951799999-9


Q ss_pred             HHHHHHHHCHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCCCCCCCHHHHCCC-CCCEEEEECCHHC-CC
Q ss_conf             999999855000134443222222333444321112357861698530357556100212026-7614999711102-99
Q gi|254781215|r  127 EVSKWLSLLPNKHWFEMQSLSLHPAPWYSDVLHCSLGIDSKHYSTMCRTYSEERPDTFVGHHN-TYGMAIINDEASG-TP  204 (511)
Q Consensus       127 Ei~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~ea~~G~h~-~~~~lvI~DEAsg-I~  204 (511)
                      -+.+.....+.  ......+.+.+..      +...-......+++.++-..   +=..|.-. +..+|+|+|||+- +-
T Consensus        77 ~~~~v~~ip~~--~i~~ltGev~p~~------R~~~w~~~kVfvaTPQvveN---Dl~~Grid~~dv~~lifDEAHRAvG  145 (542)
T COG1111          77 FCRKVTGIPED--EIAALTGEVRPEE------REELWAKKKVFVATPQVVEN---DLKAGRIDLDDVSLLIFDEAHRAVG  145 (542)
T ss_pred             HHHHHHCCCHH--HEEEECCCCCHHH------HHHHHHHCCEEEECCHHHHH---HHHCCCCCHHHCEEEEECHHHHCCC
T ss_conf             99998589843--3231117778688------99987517789956387776---8761766767805898623554137


Q ss_pred             HHHH-HHHHHHHCCCCCCEEEEEECCCCCCCCHHHHHHH
Q ss_conf             7889-8888885079981389982389987655676530
Q gi|254781215|r  205 DVIN-LGILGFLTERNANRFWIMTSNPRRLSGKFYEIFN  242 (511)
Q Consensus       205 d~i~-e~i~~~Lt~~g~~~~~i~~~nP~~~~g~fy~~~~  242 (511)
                      +-.| .++.--+...-+..++-++.+|-.....+-+.+.
T Consensus       146 nyAYv~Va~~y~~~~k~~~ilgLTASPGs~~ekI~eV~~  184 (542)
T COG1111         146 NYAYVFVAKEYLRSAKNPLILGLTASPGSDLEKIQEVVE  184 (542)
T ss_pred             CCHHHHHHHHHHHHCCCCEEEEEECCCCCCHHHHHHHHH
T ss_conf             606999999999825684379872389998799999998


No 23 
>PRK01172 ski2-like helicase; Provisional
Probab=98.01  E-value=0.00023  Score=46.16  Aligned_cols=156  Identities=13%  Similarity=0.053  Sum_probs=81.2

Q ss_pred             CHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEEECCHHHHHHHHHHHHHH
Q ss_conf             45899999999999874056555421012465025765978999999999998089966999808589999999999999
Q gi|254781215|r   51 PRSWQLEFMEVVDAHCLNSVNNPNPEVFKGAISAGRGIGKTTLNAWLVLWLMSTRPGISVICLANSETQLKTTLWAEVSK  130 (511)
Q Consensus        51 P~~WQ~e~l~~i~~~~~~~~~~~~~~~~r~aV~sgrG~GKS~l~a~l~lw~l~~~p~~kv~vtApt~~Q~~~ilw~Ei~k  130 (511)
                      +.+||+|.+..+.+    ++        -+-|+++.|.|||.++-.+++-.+.  .+.|+++++|...=+.++ +.++.+
T Consensus        23 l~p~Q~ea~~~~~~----gk--------NllvsaPTgsGKTlvAe~ai~~~l~--~~~k~iyi~P~kAL~~EK-~~~~~~   87 (674)
T PRK01172         23 LYDHQRMAIEQLRK----GE--------NVIVSVPTAAGKTLIAYSAIYETFL--AGLKSIYIVPLRSLAMEK-YEELSR   87 (674)
T ss_pred             CCHHHHHHHHHHHC----CC--------CEEEECCCCCCHHHHHHHHHHHHHH--HCCCEEEECCHHHHHHHH-HHHHHH
T ss_conf             89899999999977----99--------5999789998699999999999998--589799987789999999-999998


Q ss_pred             HHHHCHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCCCCCCCHHHHCC---CCCCEEEEECCHHCCCH--
Q ss_conf             9985500013444322222233344432111235786169853035755610021202---67614999711102997--
Q gi|254781215|r  131 WLSLLPNKHWFEMQSLSLHPAPWYSDVLHCSLGIDSKHYSTMCRTYSEERPDTFVGHH---NTYGMAIINDEASGTPD--  205 (511)
Q Consensus       131 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~ea~~G~h---~~~~~lvI~DEAsgI~d--  205 (511)
                      ...     ..+.+.   ...-.+....   .........+++     .+...++-...   -....++|+||.+.|.|  
T Consensus        88 ~~~-----~g~~v~---~~tGd~~~~~---~~~~~~~I~V~T-----~Ek~~sl~~~~~~~l~~v~~vViDEiH~i~d~~  151 (674)
T PRK01172         88 LRS-----LGMRVK---ISIGDYDDPP---DFIKRYDVVILT-----SEKADSLIHHDPYIINDVGLIVADEIHIIGDED  151 (674)
T ss_pred             HHC-----CCCEEE---EEECCCCCCC---CCCCCCCEEEEC-----HHHHHHHHHCCCHHHCCCCEEEEECCEECCCCC
T ss_conf             873-----798277---8853888980---102558999987-----899999986495022136989982652506877


Q ss_pred             --HHHHHHHHHHCCCCCCEEEEEECCCCCCCCHH
Q ss_conf             --88988888850799813899823899876556
Q gi|254781215|r  206 --VINLGILGFLTERNANRFWIMTSNPRRLSGKF  237 (511)
Q Consensus       206 --~i~e~i~~~Lt~~g~~~~~i~~~nP~~~~g~f  237 (511)
                        .+||.+-..+.--+....++..|-.-.+...+
T Consensus       152 RG~~lE~~l~kl~~l~~~~qiIgLSATi~N~~~l  185 (674)
T PRK01172        152 RGPTLETVLSSARYVNPDARILALSATVSNANEL  185 (674)
T ss_pred             CHHHHHHHHHHHHHCCCCEEEEEECCCCCCHHHH
T ss_conf             2499999999998538660799715786899999


No 24 
>KOG0354 consensus
Probab=97.98  E-value=8.3e-05  Score=48.90  Aligned_cols=163  Identities=16%  Similarity=0.091  Sum_probs=88.9

Q ss_pred             CCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEEECCHHHHHHHH
Q ss_conf             65557845899999999999874056555421012465025765978999999999998089966999808589999999
Q gi|254781215|r   45 LEGFSAPRSWQLEFMEVVDAHCLNSVNNPNPEVFKGAISAGRGIGKTTLNAWLVLWLMSTRPGISVICLANSETQLKTTL  124 (511)
Q Consensus        45 ~~~~~~P~~WQ~e~l~~i~~~~~~~~~~~~~~~~r~aV~sgrG~GKS~l~a~l~lw~l~~~p~~kv~vtApt~~Q~~~il  124 (511)
                      .+....+|.||.|+.+-=   +.+          -+.|+.+.|.|||.++|..++-++-.+|.+||++.|||.-=+..-.
T Consensus        57 ~p~~~~lR~YQ~eivq~A---Lgk----------Ntii~lPTG~GKTfIAa~Vm~nh~rw~p~~KiVF~aP~~pLv~QQ~  123 (746)
T KOG0354          57 YPTNLELRNYQEELVQPA---LGK----------NTIIALPTGSGKTFIAAVIMKNHFEWRPKGKVVFLAPTRPLVNQQI  123 (746)
T ss_pred             CCCCCCCCHHHHHHHHHH---HCC----------CEEEEEECCCCCCCHHHHHHHHHHHCCCCCEEEEEECCCHHHHHHH
T ss_conf             467665607899986786---268----------7699953599861047999999972377643899607711788889


Q ss_pred             HHHHHHHHHHCHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCCCCCCCHHHHCCCC--CCEEEEECCHHC
Q ss_conf             999999998550001344432222223334443211123578616985303575561002120267--614999711102
Q gi|254781215|r  125 WAEVSKWLSLLPNKHWFEMQSLSLHPAPWYSDVLHCSLGIDSKHYSTMCRTYSEERPDTFVGHHNT--YGMAIINDEASG  202 (511)
Q Consensus       125 w~Ei~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~ea~~G~h~~--~~~lvI~DEAsg  202 (511)
                       +........        .+.+.. +.+-.....+..+-......|.++..-...-   -.|.+..  ...|+|+|||+-
T Consensus       124 -a~~~~~~~~--------~~~T~~-l~~~~~~~~r~~i~~s~~vff~TpQil~ndL---~~~~~~~ls~fs~iv~DE~Hr  190 (746)
T KOG0354         124 -ACFSIYLIP--------YSVTGQ-LGDTVPRSNRGEIVASKRVFFRTPQILENDL---KSGLHDELSDFSLIVFDECHR  190 (746)
T ss_pred             -HHHHHCCCC--------CCCEEE-CCCCCCCCCHHHHHCCCCEEEECHHHHHHHC---CCCCCCCCCEEEEEEECCCCC
T ss_conf             -887620676--------010455-0575688762453102635896727634332---543345455179999722244


Q ss_pred             CC-HHHHH-HHHHHHC--CCCCCEEEEEECCCCCCC
Q ss_conf             99-78898-8888850--799813899823899876
Q gi|254781215|r  203 TP-DVINL-GILGFLT--ERNANRFWIMTSNPRRLS  234 (511)
Q Consensus       203 I~-d~i~e-~i~~~Lt--~~g~~~~~i~~~nP~~~~  234 (511)
                      -. +..|. ++.-.|.  -.++++ +-.+.+|-+..
T Consensus       191 a~kn~~Y~~Vmr~~l~~k~~~~qI-LgLTASpG~~~  225 (746)
T KOG0354         191 TSKNHPYNNIMREYLDLKNQGNQI-LGLTASPGSKL  225 (746)
T ss_pred             CCCCCCHHHHHHHHHHHHHCCCCE-EEEECCCCCCH
T ss_conf             555661799999999865146617-99855888458


No 25 
>pfam02562 PhoH PhoH-like protein. PhoH is a cytoplasmic protein and predicted ATPase that is induced by phosphate starvation.
Probab=97.98  E-value=0.00042  Score=44.45  Aligned_cols=54  Identities=15%  Similarity=-0.007  Sum_probs=44.7

Q ss_pred             HHHHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEEECCHH
Q ss_conf             899999999999874056555421012465025765978999999999998089966999808589
Q gi|254781215|r   53 SWQLEFMEVVDAHCLNSVNNPNPEVFKGAISAGRGIGKTTLNAWLVLWLMSTRPGISVICLANSET  118 (511)
Q Consensus        53 ~WQ~e~l~~i~~~~~~~~~~~~~~~~r~aV~sgrG~GKS~l~a~l~lw~l~~~p~~kv~vtApt~~  118 (511)
                      .-|+.++.++.++.            =+.+.+.-|+|||.++...++..+......+++++-|+-.
T Consensus         7 ~~Q~~~~~~l~~~~------------iv~~~GpAGtGKT~la~~~al~~l~~~~~~kiii~Rp~v~   60 (205)
T pfam02562         7 LGQKRYVEAIRKND------------IVFGIGPAGTGKTYLAVAAAVDALKDGKVKRIILTRPAVE   60 (205)
T ss_pred             HHHHHHHHHHHCCC------------EEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEEECCCC
T ss_conf             88999999971798------------0799899986099999999999997189437999757712


No 26 
>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=97.95  E-value=0.00015  Score=47.21  Aligned_cols=68  Identities=19%  Similarity=0.145  Sum_probs=48.4

Q ss_pred             HHHHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHHC-CCCEEEEEECCHHHHHHHHHHHHHHH
Q ss_conf             89999999999987405655542101246502576597899999999999808-99669998085899999999999999
Q gi|254781215|r   53 SWQLEFMEVVDAHCLNSVNNPNPEVFKGAISAGRGIGKTTLNAWLVLWLMSTR-PGISVICLANSETQLKTTLWAEVSKW  131 (511)
Q Consensus        53 ~WQ~e~l~~i~~~~~~~~~~~~~~~~r~aV~sgrG~GKS~l~a~l~lw~l~~~-p~~kv~vtApt~~Q~~~ilw~Ei~k~  131 (511)
                      +-|++++..+..    +.        .+-|.++.|.|||..+...++-.+..+ .+.++++++||..-+.+. ...+.+.
T Consensus         2 ~~Q~~~i~~~~~----g~--------~~iv~~pTGsGKT~~~~~~~l~~~~~~~~~~~~v~l~Pt~aL~~q~-~~~~~~~   68 (167)
T pfam00270         2 PIQAEAIPAILE----GK--------DVLVQAPTGSGKTLAFLLPALQALLKNPDGPQALVLAPTRELAEQI-YEELKKL   68 (167)
T ss_pred             HHHHHHHHHHHC----CC--------CEEEECCCCCCHHHHHHHHHHHHHHHCCCCCEEEEECCHHHHHHHH-HHHHHHH
T ss_conf             459999999976----99--------7899889997589999999999987477898799990608888899-9886432


Q ss_pred             HH
Q ss_conf             98
Q gi|254781215|r  132 LS  133 (511)
Q Consensus       132 ~~  133 (511)
                      ..
T Consensus        69 ~~   70 (167)
T pfam00270        69 GK   70 (167)
T ss_pred             HH
T ss_conf             10


No 27 
>smart00489 DEXDc3 DEAD-like helicases superfamily.
Probab=97.82  E-value=0.0002  Score=46.52  Aligned_cols=81  Identities=28%  Similarity=0.465  Sum_probs=56.9

Q ss_pred             HHHHCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCCCHHH-HHHHHHHHHHHH---CCC
Q ss_conf             7764214557775655578458999999999998740565554210124650257659789-999999999980---899
Q gi|254781215|r   32 VLHFFPWGEKGTPLEGFSAPRSWQLEFMEVVDAHCLNSVNNPNPEVFKGAISAGRGIGKTT-LNAWLVLWLMST---RPG  107 (511)
Q Consensus        32 ~~~~~~w~~~~~~~~~~~~P~~WQ~e~l~~i~~~~~~~~~~~~~~~~r~aV~sgrG~GKS~-l~a~l~lw~l~~---~p~  107 (511)
                      ++|+||..           |++.|.++++.|...+.++.        -+.+-|+.|+|||. +.+..+-|....   ...
T Consensus         1 ~~~~FPy~-----------py~~Q~e~m~~v~~~l~~~~--------~~llEaPTGtGKTlalL~~al~~~~~~~~~~~~   61 (289)
T smart00489        1 LLFYFPYE-----------PYPIQYEFMEELKRVLDRGK--------IGILESPTGTGKTLSLLCLTLTWLRSFPERIQK   61 (289)
T ss_pred             CEECCCCC-----------CCHHHHHHHHHHHHHHHCCC--------EEEEECCCCHHHHHHHHHHHHHHHHHCHHCCCC
T ss_conf             93278999-----------99899999999999997499--------799989996518999999999999967010245


Q ss_pred             CEEEEEECCHHHHHHHHHHHHHHHH
Q ss_conf             6699980858999999999999999
Q gi|254781215|r  108 ISVICLANSETQLKTTLWAEVSKWL  132 (511)
Q Consensus       108 ~kv~vtApt~~Q~~~ilw~Ei~k~~  132 (511)
                      .++++...|..|.... ..|+++..
T Consensus        62 ~ki~~~t~t~~~~~~~-~~elr~~~   85 (289)
T smart00489       62 IKLIYLSRTVSEIEKR-LEELRKLM   85 (289)
T ss_pred             CEEEEEECCHHHHHHH-HHHHHHHC
T ss_conf             6168761537889999-99998632


No 28 
>smart00488 DEXDc2 DEAD-like helicases superfamily.
Probab=97.82  E-value=0.0002  Score=46.52  Aligned_cols=81  Identities=28%  Similarity=0.465  Sum_probs=56.9

Q ss_pred             HHHHCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCCCHHH-HHHHHHHHHHHH---CCC
Q ss_conf             7764214557775655578458999999999998740565554210124650257659789-999999999980---899
Q gi|254781215|r   32 VLHFFPWGEKGTPLEGFSAPRSWQLEFMEVVDAHCLNSVNNPNPEVFKGAISAGRGIGKTT-LNAWLVLWLMST---RPG  107 (511)
Q Consensus        32 ~~~~~~w~~~~~~~~~~~~P~~WQ~e~l~~i~~~~~~~~~~~~~~~~r~aV~sgrG~GKS~-l~a~l~lw~l~~---~p~  107 (511)
                      ++|+||..           |++.|.++++.|...+.++.        -+.+-|+.|+|||. +.+..+-|....   ...
T Consensus         1 ~~~~FPy~-----------py~~Q~e~m~~v~~~l~~~~--------~~llEaPTGtGKTlalL~~al~~~~~~~~~~~~   61 (289)
T smart00488        1 LLFYFPYE-----------PYPIQYEFMEELKRVLDRGK--------IGILESPTGTGKTLSLLCLTLTWLRSFPERIQK   61 (289)
T ss_pred             CEECCCCC-----------CCHHHHHHHHHHHHHHHCCC--------EEEEECCCCHHHHHHHHHHHHHHHHHCHHCCCC
T ss_conf             93278999-----------99899999999999997499--------799989996518999999999999967010245


Q ss_pred             CEEEEEECCHHHHHHHHHHHHHHHH
Q ss_conf             6699980858999999999999999
Q gi|254781215|r  108 ISVICLANSETQLKTTLWAEVSKWL  132 (511)
Q Consensus       108 ~kv~vtApt~~Q~~~ilw~Ei~k~~  132 (511)
                      .++++...|..|.... ..|+++..
T Consensus        62 ~ki~~~t~t~~~~~~~-~~elr~~~   85 (289)
T smart00488       62 IKLIYLSRTVSEIEKR-LEELRKLM   85 (289)
T ss_pred             CEEEEEECCHHHHHHH-HHHHHHHC
T ss_conf             6168761537889999-99998632


No 29 
>KOG0390 consensus
Probab=97.64  E-value=0.0016  Score=40.84  Aligned_cols=164  Identities=19%  Similarity=0.121  Sum_probs=92.6

Q ss_pred             HHHHHHHHHHHHHHHHCCCCCCCC-CCEEEEEECCCCCCHHHHHHHHHHHHHHHCCC-----CEEEEEECCHHHHHHHHH
Q ss_conf             589999999999987405655542-10124650257659789999999999980899-----669998085899999999
Q gi|254781215|r   52 RSWQLEFMEVVDAHCLNSVNNPNP-EVFKGAISAGRGIGKTTLNAWLVLWLMSTRPG-----ISVICLANSETQLKTTLW  125 (511)
Q Consensus        52 ~~WQ~e~l~~i~~~~~~~~~~~~~-~~~r~aV~sgrG~GKS~l~a~l~lw~l~~~p~-----~kv~vtApt~~Q~~~ilw  125 (511)
                      ++=|+|.++-+++..--   .-.| ..--+.++=.=|.|||.+...++.-++-.+|+     ++.+|+||+.--   -.|
T Consensus       240 rPHQ~EG~~FL~knl~g---~~~~~~~~GCImAd~~GlGKTlq~IsflwtlLrq~P~~~~~~~k~lVV~P~sLv---~nW  313 (776)
T KOG0390         240 RPHQREGFEFLYKNLAG---LIRPKNSGGCIMADEPGLGKTLQCISFIWTLLRQFPQAKPLINKPLVVAPSSLV---NNW  313 (776)
T ss_pred             CCHHHHHHHHHHHHHHC---CCCCCCCCCEEEECCCCCCHHHHHHHHHHHHHHHCCCCCCCCCCCEEECCHHHH---HHH
T ss_conf             81578778997864113---111588875472078876407888999999998686755444660798458888---789


Q ss_pred             -HHHHHHHHH-CHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCCCCCCCH----HHHCCCCCCEEEEECC
Q ss_conf             -999999985-5000134443222222333444321112357861698530357556100----2120267614999711
Q gi|254781215|r  126 -AEVSKWLSL-LPNKHWFEMQSLSLHPAPWYSDVLHCSLGIDSKHYSTMCRTYSEERPDT----FVGHHNTYGMAIINDE  199 (511)
Q Consensus       126 -~Ei~k~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~ea----~~G~h~~~~~lvI~DE  199 (511)
                       .|..||... .+.-.-+.......    |........+  ........   ....+-|.    .+-+......|+|+||
T Consensus       314 kkEF~KWl~~~~i~~l~~~~~~~~~----w~~~~sil~~--~~~~~~~~---vli~sye~~~~~~~~il~~~~glLVcDE  384 (776)
T KOG0390         314 KKEFGKWLGNHRINPLDFYSTKKSS----WIKLKSILFL--GYKQFTTP---VLIISYETASDYCRKILLIRPGLLVCDE  384 (776)
T ss_pred             HHHHHHHCCCCCCCEEEEECCCCHH----HHHHHHHHHH--HHHHEEEE---EEECCHHHHHHHHHHHHCCCCCEEEECC
T ss_conf             9999874253555404542345256----6666789886--22112578---7863699999999998547898699779


Q ss_pred             HHCCCH---HHHHHHHHHHCCCCCCEEEEEECCCCCCC
Q ss_conf             102997---88988888850799813899823899876
Q gi|254781215|r  200 ASGTPD---VINLGILGFLTERNANRFWIMTSNPRRLS  234 (511)
Q Consensus       200 AsgI~d---~i~e~i~~~Lt~~g~~~~~i~~~nP~~~~  234 (511)
                      ++-..+   .+|.++..    -..+.+.+.+|+|.-+.
T Consensus       385 GHrlkN~~s~~~kaL~~----l~t~rRVLLSGTp~QNd  418 (776)
T KOG0390         385 GHRLKNSDSLTLKALSS----LKTPRRVLLTGTPIQND  418 (776)
T ss_pred             CCCCCCHHHHHHHHHHH----CCCCCEEEEECCCCCCC
T ss_conf             88856224589999974----68773699607753346


No 30 
>TIGR01054 rgy reverse gyrase; InterPro: IPR005736   DNA topoisomerases regulate the number of topological links between two DNA strands (i.e. change the number of superhelical turns) by catalysing transient single- or double-strand breaks, crossing the strands through one another, then resealing the breaks. These enzymes have several functions: to remove DNA supercoils during transcription and DNA replication; for strand breakage during recombination; for chromosome condensation; and to disentangle intertwined DNA during mitosis , . DNA topoisomerases are divided into two classes: type I enzymes (5.99.1.2 from EC; topoisomerases I, III and V) break single-strand DNA, and type II enzymes (5.99.1.3 from EC; topoisomerases II, IV and VI) break double-strand DNA .   Type I topoisomerases are ATP-independent enzymes (except for reverse gyrase), and can be subdivided according to their structure and reaction mechanisms: type IA (bacterial and archaeal topoisomerase I, topoisomerase III and reverse gyrase) and type IB (eukaryotic topoisomerase I and topoisomerase V). These enzymes are primarily responsible for relaxing positively and/or negatively supercoiled DNA, except for reverse gyrase, which can introduce positive supercoils into DNA.    Reverse gyrase is a type IA topoisomerase that is unique among these enzymes in its requirement for ATP. Reverse gyrase is a hyperthermophile-specific enzyme that acts as a renaturase by positively supercoiling DNA, and by annealing complementary single-strand circles . Hyperthermophilic organisms must protect themselves against heat-induced degradation, and reverse gyrase acts to reduce the rate of double-strand DNA breakage, a function that does not require ATP hydrolysis and which is independent of its positive supercoiling abilities. Reverse gyrase achieves this by recognising nicked DNA and recruiting a protein coat to the site of damage .   More information about this protein can be found at Protein of the Month: DNA Topoisomerase .; GO: 0003677 DNA binding, 0003916 DNA topoisomerase activity, 0006265 DNA topological change, 0006268 DNA unwinding during replication, 0005694 chromosome.
Probab=97.57  E-value=0.0015  Score=41.08  Aligned_cols=145  Identities=19%  Similarity=0.190  Sum_probs=84.7

Q ss_pred             HHHHHHHHHH---HHHCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCCCHHHHHHHHHH
Q ss_conf             6665288667---7642145577756555784589999999999987405655542101246502576597899999999
Q gi|254781215|r   23 EIKLSFSNFV---LHFFPWGEKGTPLEGFSAPRSWQLEFMEVVDAHCLNSVNNPNPEVFKGAISAGRGIGKTTLNAWLVL   99 (511)
Q Consensus        23 ~~~~~~~~~~---~~~~~w~~~~~~~~~~~~P~~WQ~e~l~~i~~~~~~~~~~~~~~~~r~aV~sgrG~GKS~l~a~l~l   99 (511)
                      ....+|.+|.   .++-||+.          =+.|-+.+++.            .    =.|+.++.|+|||++...+.+
T Consensus        68 ~~~k~f~~FF~~~~G~~pws~----------Qk~WAKRv~~~------------~----SFai~APTGVGKttFG~~msl  121 (1843)
T TIGR01054        68 EELKEFEEFFKKAVGSEPWSI----------QKSWAKRVLKG------------D----SFAIVAPTGVGKTTFGLVMSL  121 (1843)
T ss_pred             HHHHHHHHHHHHHHCCCCHHH----------HHHHHHHHHCC------------C----CEEEECCCCCCHHHHHHHHHH
T ss_conf             999999999999718884356----------79999996417------------9----648980588767799999999


Q ss_pred             HHHHHCCCCEEEEEECCHHHHHHHHHHHHHHHHHHCHHCCCCCCC--CCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCC
Q ss_conf             999808996699980858999999999999999855000134443--222222333444321112357861698530357
Q gi|254781215|r  100 WLMSTRPGISVICLANSETQLKTTLWAEVSKWLSLLPNKHWFEMQ--SLSLHPAPWYSDVLHCSLGIDSKHYSTMCRTYS  177 (511)
Q Consensus       100 w~l~~~p~~kv~vtApt~~Q~~~ilw~Ei~k~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s  177 (511)
                      +.+.. .+.+++++=||.-=++++- .-|..+..    +......  ....++.--......+.=.+.++.|-+ -.|++
T Consensus       122 flA~k-KGkR~y~ilPT~lLv~Qv~-~kl~~~~~----k~g~~~~~l~~~yhS~L~~~~kke~~Eri~~GDfdi-litT~  194 (1843)
T TIGR01054       122 FLAKK-KGKRSYIILPTTLLVKQVA-EKLSSLAE----KEGVGIVRLLGAYHSKLSTKEKKEVKERIENGDFDI-LITTS  194 (1843)
T ss_pred             HHHHH-CCCEEEEEECHHHHHHHHH-HHHHHHCC----CCCCCCEEEEEEEECCCCHHHHHHHHHHHHCCCEEE-EHHHH
T ss_conf             98654-2987899947078899999-99875200----257500002221011265456788999873189178-61224


Q ss_pred             CCCCCHHHHCC-CCCCEEEEECCH
Q ss_conf             55610021202-676149997111
Q gi|254781215|r  178 EERPDTFVGHH-NTYGMAIINDEA  200 (511)
Q Consensus       178 ~~~~ea~~G~h-~~~~~lvI~DEA  200 (511)
                      ..-.-++.-++ +.+..|+++|=-
T Consensus       195 ~FL~K~~~~L~~~y~F~liFVDDV  218 (1843)
T TIGR01054       195 MFLSKNFDKLKNQYKFDLIFVDDV  218 (1843)
T ss_pred             HHHHHHHHHCCCCCEEEEEEEECH
T ss_conf             688876651789851448997153


No 31 
>PRK10590 ATP-dependent RNA helicase RhlE; Provisional
Probab=97.52  E-value=0.002  Score=40.23  Aligned_cols=75  Identities=20%  Similarity=0.197  Sum_probs=54.5

Q ss_pred             CCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHHCC-------CCEEEEEECCHH
Q ss_conf             5557845899999999999874056555421012465025765978999999999998089-------966999808589
Q gi|254781215|r   46 EGFSAPRSWQLEFMEVVDAHCLNSVNNPNPEVFKGAISAGRGIGKTTLNAWLVLWLMSTRP-------GISVICLANSET  118 (511)
Q Consensus        46 ~~~~~P~~WQ~e~l~~i~~~~~~~~~~~~~~~~r~aV~sgrG~GKS~l~a~l~lw~l~~~p-------~~kv~vtApt~~  118 (511)
                      .+|+-|-+-|++.+-.+-..      +      -+.+.|..|+|||.....=+|-.+....       +.+++|.+||..
T Consensus        19 ~G~~~PTpIQ~~aIP~iL~G------r------Dvl~~A~TGSGKTlAflLPil~~l~~~~~~~~~~~~~~aLIL~PTRE   86 (457)
T PRK10590         19 QGYREPTPIQQQAIPAVLEG------R------DLMASAQTGTGKTAGFTLPLLQHLITRQPHAKGRRPVRALILTPTRE   86 (457)
T ss_pred             CCCCCCCHHHHHHHHHHHCC------C------CEEEECCCCHHHHHHHHHHHHHHHHHCCCCCCCCCCCEEEEECCHHH
T ss_conf             79999999999999999779------9------88998898118999999999999863676544568824999768799


Q ss_pred             HHHHHHHHHHHHHHH
Q ss_conf             999999999999998
Q gi|254781215|r  119 QLKTTLWAEVSKWLS  133 (511)
Q Consensus       119 Q~~~ilw~Ei~k~~~  133 (511)
                      -+..| ..++..+..
T Consensus        87 LA~Qi-~~~~~~l~~  100 (457)
T PRK10590         87 LAAQI-GENVRDYSK  100 (457)
T ss_pred             HHHHH-HHHHHHHCC
T ss_conf             99999-999997425


No 32 
>PRK11192 ATP-dependent RNA helicase SrmB; Provisional
Probab=97.52  E-value=0.0032  Score=38.91  Aligned_cols=74  Identities=16%  Similarity=0.109  Sum_probs=53.6

Q ss_pred             CCCCCHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHH----CC-CCEEEEEECCHHHHH
Q ss_conf             5578458999999999998740565554210124650257659789999999999980----89-966999808589999
Q gi|254781215|r   47 GFSAPRSWQLEFMEVVDAHCLNSVNNPNPEVFKGAISAGRGIGKTTLNAWLVLWLMST----RP-GISVICLANSETQLK  121 (511)
Q Consensus        47 ~~~~P~~WQ~e~l~~i~~~~~~~~~~~~~~~~r~aV~sgrG~GKS~l~a~l~lw~l~~----~p-~~kv~vtApt~~Q~~  121 (511)
                      +|+-|-+-|++++-.+-+.      +      -+.+.|..|+|||.....=++-.++.    .+ ..+++|.+||..=+.
T Consensus        22 g~~~pT~IQ~~aIp~il~g------~------dvl~~A~TGSGKTlaylLPil~~l~~~~~~~~~~~~~LIl~PTrELa~   89 (417)
T PRK11192         22 GYTRPTAIQAEAIPPALDG------R------DVLGSAPTGTGKTAAFLLPALQHLLDFPRRKSGPPRILILTPTRELAM   89 (417)
T ss_pred             CCCCCCHHHHHHHHHHHCC------C------CEEEECCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEEEECHHHHHH
T ss_conf             9999999999999999779------9------889989998679999999999998752103689964999947199999


Q ss_pred             HHHHHHHHHHHH
Q ss_conf             999999999998
Q gi|254781215|r  122 TTLWAEVSKWLS  133 (511)
Q Consensus       122 ~ilw~Ei~k~~~  133 (511)
                      .+ ..++.+...
T Consensus        90 Qi-~~~~~~l~~  100 (417)
T PRK11192         90 QV-ADQARELAK  100 (417)
T ss_pred             HH-HHHHHHHHC
T ss_conf             99-999998640


No 33 
>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=97.52  E-value=0.00075  Score=42.88  Aligned_cols=52  Identities=21%  Similarity=0.219  Sum_probs=40.1

Q ss_pred             EEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEEECCHHHHHHHHHHHHHHHH
Q ss_conf             46502576597899999999999808996699980858999999999999999
Q gi|254781215|r   80 GAISAGRGIGKTTLNAWLVLWLMSTRPGISVICLANSETQLKTTLWAEVSKWL  132 (511)
Q Consensus        80 ~aV~sgrG~GKS~l~a~l~lw~l~~~p~~kv~vtApt~~Q~~~ilw~Ei~k~~  132 (511)
                      +.|.+.-|.|||..+...++-.+....+.++++++||..-+.++ ..++.+..
T Consensus         3 ~lv~~ptGsGKT~~~~~~~~~~~~~~~~~~~lil~Pt~~L~~q~-~~~~~~~~   54 (144)
T cd00046           3 VLLAAPTGSGKTLAALLPILELLDSLKGGQVLVLAPTRELANQV-AERLKELF   54 (144)
T ss_pred             EEEECCCCCHHHHHHHHHHHHHHHHCCCCEEEEECCHHHHHHHH-HHHHHHHC
T ss_conf             99988997179999999999999756897699974679999999-99999974


No 34 
>COG1204 Superfamily II helicase [General function prediction only]
Probab=97.51  E-value=0.0063  Score=37.05  Aligned_cols=139  Identities=15%  Similarity=0.051  Sum_probs=76.0

Q ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEEECCHHHHHHHHHHHHHHHHHHCHHCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             24650257659789999999999980899669998085899999999999999985500013444322222233344432
Q gi|254781215|r   79 KGAISAGRGIGKTTLNAWLVLWLMSTRPGISVICLANSETQLKTTLWAEVSKWLSLLPNKHWFEMQSLSLHPAPWYSDVL  158 (511)
Q Consensus        79 r~aV~sgrG~GKS~l~a~l~lw~l~~~p~~kv~vtApt~~Q~~~ilw~Ei~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~  158 (511)
                      .+-|+++.|.|||.++-..++=.+.-+ +.++++++|+..=+.++. .+.++|-..-+ +       -.+.    ..+..
T Consensus        49 N~li~aPTgsGKTlIA~lai~~~l~~~-~~k~vYivPlkALa~Ek~-~~~~~~~~~Gi-r-------V~~~----TgD~~  114 (766)
T COG1204          49 NVLISAPTGSGKTLIALLAILSTLLEG-GGKVVYIVPLKALAEEKY-EEFSRLEELGI-R-------VGIS----TGDYD  114 (766)
T ss_pred             CEEEECCCCCCHHHHHHHHHHHHHHHC-CCCEEEEECHHHHHHHHH-HHHHHHHHCCC-E-------EEEE----CCCCC
T ss_conf             679976788866999999999999855-983899907599999999-98666886597-7-------9996----48865


Q ss_pred             CCCCCCCCCEEEEEECCCCCCCCCHHHH-CCCC-----CCEEEEECCHHCCCHH----HHHHHHHHHCCCCCCEEEEEEC
Q ss_conf             1112357861698530357556100212-0267-----6149997111029978----8988888850799813899823
Q gi|254781215|r  159 HCSLGIDSKHYSTMCRTYSEERPDTFVG-HHNT-----YGMAIINDEASGTPDV----INLGILGFLTERNANRFWIMTS  228 (511)
Q Consensus       159 ~~~~~~~~~~~~~~~~~~s~~~~ea~~G-~h~~-----~~~lvI~DEAsgI~d~----i~e~i~~~Lt~~g~~~~~i~~~  228 (511)
                      ...-........+.       .||.++- .|..     ..-++|+||.+-+.|.    +.|++-.-+...+....++..|
T Consensus       115 ~~~~~l~~~~ViVt-------T~EK~Dsl~R~~~~~~~~V~lvViDEiH~l~d~~RG~~lE~iv~r~~~~~~~~rivgLS  187 (766)
T COG1204         115 LDDERLARYDVIVT-------TPEKLDSLTRKRPSWIEEVDLVVIDEIHLLGDRTRGPVLESIVARMRRLNELIRIVGLS  187 (766)
T ss_pred             CCHHHHCCCCEEEE-------CHHHHHHHHHCCCCHHHCCCEEEEEEEEECCCCCCCCEEHHHHHHHHHHCCCEEEEEEE
T ss_conf             55334145887997-------46786676506753334016899942101487565864022798888527551798873


Q ss_pred             CCCCCCCHHH
Q ss_conf             8998765567
Q gi|254781215|r  229 NPRRLSGKFY  238 (511)
Q Consensus       229 nP~~~~g~fy  238 (511)
                      -.-.+.+.+.
T Consensus       188 ATlpN~~evA  197 (766)
T COG1204         188 ATLPNAEEVA  197 (766)
T ss_pred             EECCCHHHHH
T ss_conf             1168889999


No 35 
>COG1110 Reverse gyrase [DNA replication, recombination, and repair]
Probab=97.49  E-value=0.0023  Score=39.82  Aligned_cols=151  Identities=20%  Similarity=0.217  Sum_probs=83.5

Q ss_pred             HHHHHHCHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCCCHHHHH
Q ss_conf             99987070666528866776421455777565557845899999999999874056555421012465025765978999
Q gi|254781215|r   15 LFDLMWSDEIKLSFSNFVLHFFPWGEKGTPLEGFSAPRSWQLEFMEVVDAHCLNSVNNPNPEVFKGAISAGRGIGKTTLN   94 (511)
Q Consensus        15 ~~~~~~~~~~~~~~~~~~~~~~~w~~~~~~~~~~~~P~~WQ~e~l~~i~~~~~~~~~~~~~~~~r~aV~sgrG~GKS~l~   94 (511)
                      +-+-.|+-+...+|..-..++-||+.          -+.|-+.+++.                .-.|+.++.|+|||++.
T Consensus        61 ~~~~~~e~e~~~~fF~k~~G~~~ws~----------QR~WakR~~rg----------------~SFaiiAPTGvGKTTfg  114 (1187)
T COG1110          61 FRRYLWEYEEFEEFFKKATGFRPWSA----------QRVWAKRLVRG----------------KSFAIIAPTGVGKTTFG  114 (1187)
T ss_pred             HHHHHHHHHHHHHHHHHHHCCCCHHH----------HHHHHHHHHCC----------------CCEEEECCCCCCHHHHH
T ss_conf             99999999999999998638986078----------89999998737----------------84489827887654799


Q ss_pred             HHHHHHHHHHCCCCEEEEEECCHHHHHHHHHHHHHHHHHHCHHCCCCCCCCCCCCCCCCCCCC-CCCCCCCCCCEEEEEE
Q ss_conf             999999998089966999808589999999999999998550001344432222223334443-2111235786169853
Q gi|254781215|r   95 AWLVLWLMSTRPGISVICLANSETQLKTTLWAEVSKWLSLLPNKHWFEMQSLSLHPAPWYSDV-LHCSLGIDSKHYSTMC  173 (511)
Q Consensus        95 a~l~lw~l~~~p~~kv~vtApt~~Q~~~ilw~Ei~k~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~  173 (511)
                      +.+.+|++..  +.+++++-||..-++++. ..|.++.+..-     .......|-....... ....-.+.++. |..-
T Consensus       115 ~~~sl~~a~k--gkr~yii~PT~~Lv~Q~~-~kl~~~~e~~~-----~~~~~~~yh~~l~~~ekee~le~i~~gd-fdIl  185 (1187)
T COG1110         115 LLMSLYLAKK--GKRVYIIVPTTTLVRQVY-ERLKKFAEDAG-----SLDVLVVYHSALPTKEKEEALERIESGD-FDIL  185 (1187)
T ss_pred             HHHHHHHHHC--CCEEEEEECCHHHHHHHH-HHHHHHHHHCC-----CCCEEEEECCCCCHHHHHHHHHHHHCCC-CCEE
T ss_conf             9999998755--874999966789999999-99999886537-----8524665312366577999999986599-6399


Q ss_pred             CCCCCCCCCHHHHCCCCCCEEEEECCH
Q ss_conf             035755610021202676149997111
Q gi|254781215|r  174 RTYSEERPDTFVGHHNTYGMAIINDEA  200 (511)
Q Consensus       174 ~~~s~~~~ea~~G~h~~~~~lvI~DEA  200 (511)
                      .+++..-..++.-++.-+..++++|-.
T Consensus       186 itTs~FL~k~~e~L~~~kFdfifVDDV  212 (1187)
T COG1110         186 ITTSQFLSKRFEELSKLKFDFIFVDDV  212 (1187)
T ss_pred             EEEHHHHHHHHHHHCCCCCCEEEECCH
T ss_conf             974787886699840457778998047


No 36 
>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=97.44  E-value=0.0024  Score=39.69  Aligned_cols=72  Identities=19%  Similarity=0.122  Sum_probs=52.0

Q ss_pred             CCCCCHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHHC---CCCEEEEEECCHHHHHHH
Q ss_conf             55784589999999999987405655542101246502576597899999999999808---996699980858999999
Q gi|254781215|r   47 GFSAPRSWQLEFMEVVDAHCLNSVNNPNPEVFKGAISAGRGIGKTTLNAWLVLWLMSTR---PGISVICLANSETQLKTT  123 (511)
Q Consensus        47 ~~~~P~~WQ~e~l~~i~~~~~~~~~~~~~~~~r~aV~sgrG~GKS~l~a~l~lw~l~~~---p~~kv~vtApt~~Q~~~i  123 (511)
                      +|..|-+-|++.+-.+-.    +.        -+.+.|..|+|||.....-++-.+...   .+.++++.+||..-+..+
T Consensus        18 g~~~pt~IQ~~~ip~il~----g~--------dvi~~a~TGSGKTlay~lpil~~l~~~~~~~~~~alil~PTrELa~Qi   85 (203)
T cd00268          18 GFEKPTPIQARAIPPLLS----GR--------DVIGQAQTGSGKTAAFLIPILEKLDPSPKKDGPQALILAPTRELALQI   85 (203)
T ss_pred             CCCCCCHHHHHHHHHHHC----CC--------CEEEECCCCCCCHHHHHHHHHHHHHCCCCCCCCEEEEEECCHHHHHHH
T ss_conf             999999999999999977----99--------889975799722288886999998616676896699996879999999


Q ss_pred             HHHHHHHH
Q ss_conf             99999999
Q gi|254781215|r  124 LWAEVSKW  131 (511)
Q Consensus       124 lw~Ei~k~  131 (511)
                       ..++.+.
T Consensus        86 -~~~~~~l   92 (203)
T cd00268          86 -AEVARKL   92 (203)
T ss_pred             -HHHHHHH
T ss_conf             -9999985


No 37 
>PTZ00110 helicase; Provisional
Probab=97.39  E-value=0.0052  Score=37.60  Aligned_cols=79  Identities=18%  Similarity=0.162  Sum_probs=57.1

Q ss_pred             CCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHHCC------CCEEEEEECCH
Q ss_conf             565557845899999999999874056555421012465025765978999999999998089------96699980858
Q gi|254781215|r   44 PLEGFSAPRSWQLEFMEVVDAHCLNSVNNPNPEVFKGAISAGRGIGKTTLNAWLVLWLMSTRP------GISVICLANSE  117 (511)
Q Consensus        44 ~~~~~~~P~~WQ~e~l~~i~~~~~~~~~~~~~~~~r~aV~sgrG~GKS~l~a~l~lw~l~~~p------~~kv~vtApt~  117 (511)
                      .-.+|+.|-+-|++.+=.+-.      ++      -+...|-.|+|||.....=++-++...|      +..++|.|||.
T Consensus       198 ~~~GF~~PTPIQ~qaIPiaLs------Gr------DvIgiAqTGSGKTLAFlLP~l~hi~~q~~~~~~~gP~aLILaPTR  265 (602)
T PTZ00110        198 EAAGFTEPTPIQVQGWPIALS------GR------DMIGIAETGSGKTLAFLLPAIVHINAQPLLRPGDGPIVLVLAPTR  265 (602)
T ss_pred             HHCCCCCCCHHHHHHHHHHHC------CC------CEEEECCCCCHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEECCHH
T ss_conf             976999999899999879856------98------679987897889999999999998516343678997699973839


Q ss_pred             HHHHHHHHHHHHHHHHHC
Q ss_conf             999999999999999855
Q gi|254781215|r  118 TQLKTTLWAEVSKWLSLL  135 (511)
Q Consensus       118 ~Q~~~ilw~Ei~k~~~~~  135 (511)
                      .=+..| ..|+.++....
T Consensus       266 ELA~QI-~~e~~~~~~~~  282 (602)
T PTZ00110        266 ELAEQI-REQALQFGRSS  282 (602)
T ss_pred             HHHHHH-HHHHHHHHCCC
T ss_conf             999999-99999971547


No 38 
>PRK11634 ATP-dependent RNA helicase DeaD; Provisional
Probab=97.34  E-value=0.0038  Score=38.43  Aligned_cols=75  Identities=16%  Similarity=0.143  Sum_probs=54.4

Q ss_pred             CCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHHC-CCCEEEEEECCHHHHHHHH
Q ss_conf             555784589999999999987405655542101246502576597899999999999808-9966999808589999999
Q gi|254781215|r   46 EGFSAPRSWQLEFMEVVDAHCLNSVNNPNPEVFKGAISAGRGIGKTTLNAWLVLWLMSTR-PGISVICLANSETQLKTTL  124 (511)
Q Consensus        46 ~~~~~P~~WQ~e~l~~i~~~~~~~~~~~~~~~~r~aV~sgrG~GKS~l~a~l~lw~l~~~-p~~kv~vtApt~~Q~~~il  124 (511)
                      -+|..|-+-|++.+-.+-..      +      -+.+.|-.|+|||.....-+|-.+... ...+++|.+||..-+..| 
T Consensus        24 ~Gf~~PTpIQ~~aIP~iL~G------k------Dvi~~AqTGSGKTlAFlLPiL~~l~~~~~~pqaLIL~PTRELA~QV-   90 (629)
T PRK11634         24 LGYEKPSPIQAECIPHLLNG------R------DVLGMAQTGSGKTAAFSLPLLHNLDPELKAPQILVLAPTRELAVQV-   90 (629)
T ss_pred             CCCCCCCHHHHHHHHHHHCC------C------CEEEECCCCCHHHHHHHHHHHHHHHHCCCCCCEEEECCCHHHHHHH-
T ss_conf             79999999999999999679------9------8899788847899999999999866236898689978998999999-


Q ss_pred             HHHHHHHHH
Q ss_conf             999999998
Q gi|254781215|r  125 WAEVSKWLS  133 (511)
Q Consensus       125 w~Ei~k~~~  133 (511)
                      ..++..+..
T Consensus        91 ~~~~~~l~~   99 (629)
T PRK11634         91 AEAMTDFSK   99 (629)
T ss_pred             HHHHHHHHH
T ss_conf             999999972


No 39 
>COG1203 CRISPR-associated helicase Cas3 [Defense mechanisms]
Probab=97.31  E-value=0.0093  Score=35.99  Aligned_cols=170  Identities=16%  Similarity=0.075  Sum_probs=87.2

Q ss_pred             CCCHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHHC--CCCEEEEEECCHHHHHHHHHH
Q ss_conf             784589999999999987405655542101246502576597899999999999808--996699980858999999999
Q gi|254781215|r   49 SAPRSWQLEFMEVVDAHCLNSVNNPNPEVFKGAISAGRGIGKTTLNAWLVLWLMSTR--PGISVICLANSETQLKTTLWA  126 (511)
Q Consensus        49 ~~P~~WQ~e~l~~i~~~~~~~~~~~~~~~~r~aV~sgrG~GKS~l~a~l~lw~l~~~--p~~kv~vtApt~~Q~~~ilw~  126 (511)
                      ..+.+||.++++.+-.....+.        -+-..++.|.|||.+++.+++..+.-.  -.++++.+-|+..-+. .+..
T Consensus       194 ~~~~~~~~~~~~~~~~~~~~~~--------~~vl~aPTG~GKT~asl~~a~~~~~~~~~~~~r~i~vlP~~t~ie-~~~~  264 (733)
T COG1203         194 HEGYELQEKALELILRLEKRSL--------LVVLEAPTGYGKTEASLILALALLDEKIKLKSRVIYVLPFRTIIE-DMYR  264 (733)
T ss_pred             CCHHHHHHHHHHHHHHCCCCCC--------EEEEEECCCCCHHHHHHHHHHHHHHCCCCCCCEEEEECCHHHHHH-HHHH
T ss_conf             5113556799999873225575--------189991688871999999999975311354562899655899999-9999


Q ss_pred             HHHHHHHHCHHCCCCCCCCCCCCCCCCCCCC----CCCCCCCCCCEEEEEECCCCCCCCC--HHHHCCC-----CCCEEE
Q ss_conf             9999998550001344432222223334443----2111235786169853035755610--0212026-----761499
Q gi|254781215|r  127 EVSKWLSLLPNKHWFEMQSLSLHPAPWYSDV----LHCSLGIDSKHYSTMCRTYSEERPD--TFVGHHN-----TYGMAI  195 (511)
Q Consensus       127 Ei~k~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~~~~~~~~~~~~~s~~~~e--a~~G~h~-----~~~~lv  195 (511)
                      .++.+....-.....  ..............    ............+....+.......  +..+++.     -...++
T Consensus       265 r~~~~~~~~~~~~~~--~h~~~~~~~~~~~~~~~~~~~~~~ds~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~S~v  342 (733)
T COG1203         265 RAKEIFGLFSVIGKS--LHSSSKEPLLLEPDQDILLTLTTNDSYKKLLLALIVVTPIQILIFSVKGFKFEFLALLLTSLV  342 (733)
T ss_pred             HHHHHHCCCCCCCCC--CCCCCHHHHHHCCCCCCCEEEEECCCCCCCCCCCEEECHHHHHHHHHCCCCCHHHHHHHHCCE
T ss_conf             998751235543310--013102556517010022588812422362045222069998557404667257788764677


Q ss_pred             EECCHHCCCHH-HHHHHHHH---HCCCCCCEEEEEECCC
Q ss_conf             97111029978-89888888---5079981389982389
Q gi|254781215|r  196 INDEASGTPDV-INLGILGF---LTERNANRFWIMTSNP  230 (511)
Q Consensus       196 I~DEAsgI~d~-i~e~i~~~---Lt~~g~~~~~i~~~nP  230 (511)
                      |+||++.+++. .+.++..+   +...|.+. ++++.|.
T Consensus       343 IlDE~h~~~~~~~~~~l~~~i~~l~~~g~~i-ll~SATl  380 (733)
T COG1203         343 ILDEVHLYADETMLAALLALLEALAEAGVPV-LLMSATL  380 (733)
T ss_pred             EEECHHHCCCCCHHHHHHHHHHHHHHCCCCE-EEEECCC
T ss_conf             8742754165430899999999999689978-9992789


No 40 
>PRK06305 DNA polymerase III subunits gamma and tau; Validated
Probab=97.31  E-value=0.0094  Score=35.96  Aligned_cols=151  Identities=19%  Similarity=0.136  Sum_probs=78.7

Q ss_pred             HHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEE-EEEECCHHHHHHHHHHHHHHHHH
Q ss_conf             99999999998740565554210124650257659789999999999980899669-99808589999999999999998
Q gi|254781215|r   55 QLEFMEVVDAHCLNSVNNPNPEVFKGAISAGRGIGKTTLNAWLVLWLMSTRPGISV-ICLANSETQLKTTLWAEVSKWLS  133 (511)
Q Consensus        55 Q~e~l~~i~~~~~~~~~~~~~~~~r~aV~sgrG~GKS~l~a~l~lw~l~~~p~~kv-~vtApt~~Q~~~ilw~Ei~k~~~  133 (511)
                      |..+.+.+.....++..-|     -.--.+.||+|||+++-.++-...|.++.... .|..-  ..-     .+|    .
T Consensus        22 Q~~vv~~L~nai~~~ri~H-----AyLF~GprGtGKTT~ArilAkaLnC~~~~~~~~pCg~C--~~C-----~~I----~   85 (462)
T PRK06305         22 QDAVVTVLKNALRFNRAAH-----AYLFSGIRGTGKTTLARIFAKALNCQNPTEDQEPCNQC--AIC-----KEI----S   85 (462)
T ss_pred             CHHHHHHHHHHHHCCCCCC-----EEEEECCCCCCHHHHHHHHHHHHCCCCCCCCCCCCCCC--HHH-----HHH----H
T ss_conf             0999999999998499762-----34303899859999999999996799998888988766--888-----998----6


Q ss_pred             HCHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCCCCCCCHHHHCCCCCCEEEEECCHHCCCHHHHHHHHH
Q ss_conf             55000134443222222333444321112357861698530357556100212026761499971110299788988888
Q gi|254781215|r  134 LLPNKHWFEMQSLSLHPAPWYSDVLHCSLGIDSKHYSTMCRTYSEERPDTFVGHHNTYGMAIINDEASGTPDVINLGILG  213 (511)
Q Consensus       134 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~ea~~G~h~~~~~lvI~DEAsgI~d~i~e~i~~  213 (511)
                      .....+.++.++.                 ...  .....|...  .--++....+.+- .+|+||+..+....|+++.-
T Consensus        86 ~g~~~DViEiDaA-----------------s~~--gVddIRel~--e~v~~~P~~~~yK-VyIIDEvhmLs~~AfNALLK  143 (462)
T PRK06305         86 SGTSLDVIEIDGA-----------------SHR--GIEDIRQIN--ETVLFTPSKSQYK-IYIIDEVHMLTKEAFNSLLK  143 (462)
T ss_pred             CCCCCCEEEECCC-----------------CCC--CHHHHHHHH--HHHCCCCCCCCEE-EEEEECHHHCCHHHHHHHHH
T ss_conf             3899986864355-----------------344--668999999--7710088677505-99981521179999999999


Q ss_pred             HHCCCCCCE-EEEEECCCCCCCCHHHHHHHC
Q ss_conf             850799813-899823899876556765303
Q gi|254781215|r  214 FLTERNANR-FWIMTSNPRRLSGKFYEIFNK  243 (511)
Q Consensus       214 ~Lt~~g~~~-~~i~~~nP~~~~g~fy~~~~~  243 (511)
                      +|-++-... +++++..|.+......-.|.+
T Consensus       144 tLEEPP~~v~FILaTTe~~KIp~TIlSRCQr  174 (462)
T PRK06305        144 TLEEPPQHVKFFLATTEIHKIPGTILSRCQK  174 (462)
T ss_pred             HHHCCCCCEEEEEEECCHHHCCHHHHHHHHE
T ss_conf             8618987749999818814285478765402


No 41 
>PRK11776 ATP-dependent RNA helicase DbpA; Provisional
Probab=97.31  E-value=0.0036  Score=38.60  Aligned_cols=77  Identities=16%  Similarity=0.148  Sum_probs=56.0

Q ss_pred             CCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHH-CCCCEEEEEECCHHHHHHHH
Q ss_conf             55578458999999999998740565554210124650257659789999999999980-89966999808589999999
Q gi|254781215|r   46 EGFSAPRSWQLEFMEVVDAHCLNSVNNPNPEVFKGAISAGRGIGKTTLNAWLVLWLMST-RPGISVICLANSETQLKTTL  124 (511)
Q Consensus        46 ~~~~~P~~WQ~e~l~~i~~~~~~~~~~~~~~~~r~aV~sgrG~GKS~l~a~l~lw~l~~-~p~~kv~vtApt~~Q~~~il  124 (511)
                      -+|..|-+-|++.+-.+-+..            -+.+.|..|+|||.....-++-.+.. ....+++|.+||..=+..+ 
T Consensus        22 ~G~~~pTpIQ~~aIP~il~G~------------Dvi~~A~TGSGKTlAfllPil~~l~~~~~~~qaLIL~PTRELa~QV-   88 (459)
T PRK11776         22 LGYTEMTPIQAQSLPAILAGK------------DVIAQAKTGSGKTAAFGLGLLQKLDVKRFRVQALVLCPTRELADQV-   88 (459)
T ss_pred             CCCCCCCHHHHHHHHHHHCCC------------CEEEECCCCCHHHHHHHHHHHHHCCCCCCCCCEEEEECHHHHHHHH-
T ss_conf             799999989999999997799------------8899889985899999999998411367898599996759999999-


Q ss_pred             HHHHHHHHHHC
Q ss_conf             99999999855
Q gi|254781215|r  125 WAEVSKWLSLL  135 (511)
Q Consensus       125 w~Ei~k~~~~~  135 (511)
                      ..+++++.+..
T Consensus        89 ~~~~~~l~~~~   99 (459)
T PRK11776         89 AKEIRRLARFI   99 (459)
T ss_pred             HHHHHHHHHHC
T ss_conf             99999998505


No 42 
>PRK11448 hsdR type I restriction enzyme EcoKI subunit R; Provisional
Probab=97.29  E-value=0.014  Score=34.94  Aligned_cols=66  Identities=18%  Similarity=0.200  Sum_probs=48.8

Q ss_pred             CCHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEEECCH---HHHHH
Q ss_conf             84589999999999987405655542101246502576597899999999999808996699980858---99999
Q gi|254781215|r   50 APRSWQLEFMEVVDAHCLNSVNNPNPEVFKGAISAGRGIGKTTLNAWLVLWLMSTRPGISVICLANSE---TQLKT  122 (511)
Q Consensus        50 ~P~~WQ~e~l~~i~~~~~~~~~~~~~~~~r~aV~sgrG~GKS~l~a~l~lw~l~~~p~~kv~vtApt~---~Q~~~  122 (511)
                      +-|.+|.++++++.+...++.       +|..+.=..|+|||..+..++--++-+.--.+|+..|-..   .|+.+
T Consensus       416 ~lR~YQ~~AI~~v~~a~~~~~-------rraLl~MATGTGKTrtaial~~rLlk~~~~kRILFLvDR~~L~~QA~~  484 (1126)
T PRK11448        416 GLRYYQEDAIQAVEKALANGQ-------REILLAMATGTGKTRTAIALMYRLLKAKRFKRILFLVDRRALGEQALD  484 (1126)
T ss_pred             CCCHHHHHHHHHHHHHHHCCC-------CCEEEEECCCCCHHHHHHHHHHHHHHCCCCCEEEEECCHHHHHHHHHH
T ss_conf             786889999999999998098-------546887248885898999999999965876725798565899999999


No 43 
>PRK05563 DNA polymerase III subunits gamma and tau; Validated
Probab=97.28  E-value=0.0092  Score=36.01  Aligned_cols=156  Identities=16%  Similarity=0.128  Sum_probs=79.2

Q ss_pred             CCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEEECCHHHHHHHH
Q ss_conf             65557845899999999999874056555421012465025765978999999999998089966999808589999999
Q gi|254781215|r   45 LEGFSAPRSWQLEFMEVVDAHCLNSVNNPNPEVFKGAISAGRGIGKTTLNAWLVLWLMSTRPGISVICLANSETQLKTTL  124 (511)
Q Consensus        45 ~~~~~~P~~WQ~e~l~~i~~~~~~~~~~~~~~~~r~aV~sgrG~GKS~l~a~l~lw~l~~~p~~kv~vtApt~~Q~~~il  124 (511)
                      .....|    |..+.+.+.....+++.-|     -.--.+.||+|||+++-.++-..-|.++..--.|-.  -.    .+
T Consensus        15 f~dvvg----Q~~v~~~L~n~i~~~~i~h-----ayLf~GprG~GKTs~Ari~akalnc~~~~~~~pC~~--C~----~C   79 (541)
T PRK05563         15 FEDVVG----QEHITTTLKNQIINNRIAH-----AYLFCGTRGTGKTSTAKIFAKAVNCLNPQDGEPCNE--CE----IC   79 (541)
T ss_pred             HHHHCC----CHHHHHHHHHHHHCCCCCE-----EEEEECCCCCCHHHHHHHHHHHHCCCCCCCCCCCCC--CH----HH
T ss_conf             766248----4999999999998499320-----453038799589999999999957999888985751--48----89


Q ss_pred             HHHHHHHHHHCHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCCCCCCCHHHHCCCCCCEEEEECCHHCCC
Q ss_conf             99999999855000134443222222333444321112357861698530357556100212026761499971110299
Q gi|254781215|r  125 WAEVSKWLSLLPNKHWFEMQSLSLHPAPWYSDVLHCSLGIDSKHYSTMCRTYSEERPDTFVGHHNTYGMAIINDEASGTP  204 (511)
Q Consensus       125 w~Ei~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~ea~~G~h~~~~~lvI~DEAsgI~  204 (511)
                       .+|    .....-+.++..+.                 .+.+  ....|..+..  -.+.-..+.+ -.+|+||++.+.
T Consensus        80 -~~i----~~g~~~Dv~Eidaa-----------------s~~g--vd~iR~~~~~--~~~~p~~~~~-Kv~IiDEvhmls  132 (541)
T PRK05563         80 -KKI----NEGLLMDVIEIDAA-----------------SNNG--VDDIREIIEN--VKYPPQEGKY-KVYIMDEVHMLS  132 (541)
T ss_pred             -HHH----HCCCCCCEEEECCC-----------------CCCC--HHHHHHHHHH--CEECCCCCCE-EEEEEECCCCCC
T ss_conf             -998----56898873662444-----------------4478--8999999976--1048767870-599997723389


Q ss_pred             HHHHHHHHHHHCCCCCC-EEEEEECCCCCCCCHHHHHHH
Q ss_conf             78898888885079981-389982389987655676530
Q gi|254781215|r  205 DVINLGILGFLTERNAN-RFWIMTSNPRRLSGKFYEIFN  242 (511)
Q Consensus       205 d~i~e~i~~~Lt~~g~~-~~~i~~~nP~~~~g~fy~~~~  242 (511)
                      ...|.++.-+|-.+-.. .+++++..|.+..-...-.|.
T Consensus       133 ~~a~nallKtlEePp~~~~Filatte~~ki~~tI~SRcq  171 (541)
T PRK05563        133 QGAVNAFLKTLEEPPSNVIFILATTDPQKLPITILSRCQ  171 (541)
T ss_pred             HHHHHHHHHHHHCCCCCCEEEEECCCCCCCCHHHHHHEE
T ss_conf             999999999985487775699976984427455674213


No 44 
>PRK04537 ATP-dependent RNA helicase RhlB; Provisional
Probab=97.27  E-value=0.011  Score=35.57  Aligned_cols=82  Identities=21%  Similarity=0.116  Sum_probs=58.5

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHHCC--------CCEEE
Q ss_conf             5777565557845899999999999874056555421012465025765978999999999998089--------96699
Q gi|254781215|r   40 EKGTPLEGFSAPRSWQLEFMEVVDAHCLNSVNNPNPEVFKGAISAGRGIGKTTLNAWLVLWLMSTRP--------GISVI  111 (511)
Q Consensus        40 ~~~~~~~~~~~P~~WQ~e~l~~i~~~~~~~~~~~~~~~~r~aV~sgrG~GKS~l~a~l~lw~l~~~p--------~~kv~  111 (511)
                      .++-.-.+|+.|-+-|++.+-.+-+.      +      -+.+.|-.|+|||.....-++-.++..+        +.+++
T Consensus        21 l~aL~~~Gf~~PTpIQ~~aIP~iL~G------k------Dvi~~A~TGSGKTLAYlLPiL~~Ll~~~~l~~~~~~~p~aL   88 (574)
T PRK04537         21 VAGLESAGFTRCTPIQALTLPVALPG------G------DVAGQAQTGTGKTLAFLVAVMNRLLSRPALADRKPEDPRAL   88 (574)
T ss_pred             HHHHHHCCCCCCCHHHHHHHHHHHCC------C------CEEEECCCCCHHHHHHHHHHHHHHHHCCCCCCCCCCCCEEE
T ss_conf             99999779998999999999999579------9------88998489888999999999999983744345778996199


Q ss_pred             EEECCHHHHHHHHHHHHHHHHHH
Q ss_conf             98085899999999999999985
Q gi|254781215|r  112 CLANSETQLKTTLWAEVSKWLSL  134 (511)
Q Consensus       112 vtApt~~Q~~~ilw~Ei~k~~~~  134 (511)
                      |.+||..-+..| +.++.++...
T Consensus        89 ILvPTRELA~QI-~~~~~~l~~~  110 (574)
T PRK04537         89 ILAPTRELAIQI-HKDAVKFGAD  110 (574)
T ss_pred             EECCCHHHHHHH-HHHHHHHHCC
T ss_conf             977989999999-9999998645


No 45 
>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=97.22  E-value=0.0079  Score=36.43  Aligned_cols=162  Identities=19%  Similarity=0.196  Sum_probs=75.8

Q ss_pred             HHHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHHCCC-CEEEEEECCHHHHHHHHHHHHHHHH
Q ss_conf             999999999998740565554210124650257659789999999999980899-6699980858999999999999999
Q gi|254781215|r   54 WQLEFMEVVDAHCLNSVNNPNPEVFKGAISAGRGIGKTTLNAWLVLWLMSTRPG-ISVICLANSETQLKTTLWAEVSKWL  132 (511)
Q Consensus        54 WQ~e~l~~i~~~~~~~~~~~~~~~~r~aV~sgrG~GKS~l~a~l~lw~l~~~p~-~kv~vtApt~~Q~~~ilw~Ei~k~~  132 (511)
                      +|++-++=+......+.+        ...+=-=|.|||.-+-.++.......+. ..++|++|+.--..-  -.|+.+|.
T Consensus         1 yQ~~gv~wl~~~~~~~~g--------giLaDeMGLGKTiq~ia~l~~~~~~~~~~~~~LIV~P~sl~~~W--~~Ei~~~~   70 (295)
T pfam00176         1 YQLEGVNWLISLYNNGLG--------GILADEMGLGKTLQTISLLAYLKELKPLAGPHLVVCPLSTLDNW--LNEFEKWA   70 (295)
T ss_pred             CHHHHHHHHHHHHHCCCC--------EEEECCCCCCHHHHHHHHHHHHHHHCCCCCCEEEEECHHHHHHH--HHHHHHHC
T ss_conf             978899999998727999--------89722787579999999999999838899988999757888767--88999867


Q ss_pred             HHCHHCCCCCCC-CCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCCCCCCCHHHHCCCCCCEEEEECCHHCCCHH---HH
Q ss_conf             855000134443-22222233344432111235786169853035755610021202676149997111029978---89
Q gi|254781215|r  133 SLLPNKHWFEMQ-SLSLHPAPWYSDVLHCSLGIDSKHYSTMCRTYSEERPDTFVGHHNTYGMAIINDEASGTPDV---IN  208 (511)
Q Consensus       133 ~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~ea~~G~h~~~~~lvI~DEAsgI~d~---i~  208 (511)
                      ............ .+......+        .........++....-....+.   ++.-.-..+|+|||+.|.+.   .+
T Consensus        71 ~~~~~~~~~~~~~~r~~~~~~~--------~~~~~~~ivitsY~~~~~~~~~---l~~~~w~~vI~DEaH~iKN~~s~~~  139 (295)
T pfam00176        71 PDLNIVVYYGDGDSRSELLRNV--------LRTGKFDVLITSYEYIRRDKDE---LHKANWRYVILDEGHRIKNAKSKLS  139 (295)
T ss_pred             CCCCEEEEEECHHHHHHHHHHH--------HHCCCCCEEEECHHHHHHHHHH---HHCCCCCEEEEECCCCCCCHHHHHH
T ss_conf             9970799984707689998867--------7416885999309999975999---8408765899876201258788999


Q ss_pred             HHHHHHHCCCCCCEEEEEECCCCCCC-CHHHHH
Q ss_conf             88888850799813899823899876-556765
Q gi|254781215|r  209 LGILGFLTERNANRFWIMTSNPRRLS-GKFYEI  240 (511)
Q Consensus       209 e~i~~~Lt~~g~~~~~i~~~nP~~~~-g~fy~~  240 (511)
                      .++. .|   .++.+|+.+|+|-.+. ..+|-.
T Consensus       140 ~a~~-~l---~~~~r~~LTGTPiqN~l~el~~l  168 (295)
T pfam00176       140 LALK-SL---KTNNRLLLTGTPIQNNLAELWSL  168 (295)
T ss_pred             HHHH-HC---CCCCEEEEECCCCCCCHHHHHHH
T ss_conf             9999-52---35818998687455888999999


No 46 
>PRK08769 DNA polymerase III subunit delta'; Validated
Probab=97.22  E-value=0.013  Score=34.99  Aligned_cols=153  Identities=17%  Similarity=0.186  Sum_probs=77.8

Q ss_pred             HHHHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEEECCHHHHHHHHHHHHHHHH
Q ss_conf             89999999999987405655542101246502576597899999999999808996699980858999999999999999
Q gi|254781215|r   53 SWQLEFMEVVDAHCLNSVNNPNPEVFKGAISAGRGIGKTTLNAWLVLWLMSTRPGISVICLANSETQLKTTLWAEVSKWL  132 (511)
Q Consensus        53 ~WQ~e~l~~i~~~~~~~~~~~~~~~~r~aV~sgrG~GKS~l~a~l~lw~l~~~p~~kv~vtApt~~Q~~~ilw~Ei~k~~  132 (511)
                      +||.+..+.+.....+++.-|     ..-+....|+||+.++-.++-+.++..+++..-+   .-.           +++
T Consensus         7 PWq~~~~~~L~~~i~~~rl~H-----A~Lf~Gp~G~GK~~~A~~~A~~llc~~~~~~~~~---~~~-----------~~i   67 (319)
T PRK08769          7 PWQQRAFDQTVAALDAGRLGH-----GLLICGPEGLGKRAVALALAEHVLASGPDPALAQ---RTR-----------QLI   67 (319)
T ss_pred             CCCHHHHHHHHHHHHCCCCCC-----EEEEECCCCCCHHHHHHHHHHHHHCCCCCCCCCC---HHH-----------HHH
T ss_conf             776899999999997699420-----6875899987899999999999837997976543---388-----------999


Q ss_pred             HHCHHCCCCCCCCCCCCCCCCCC-CCCCCCCCCCCCEEEEEECCCCCCCCCHHHHCCCCCCEEEEECCHHCCCHHHHHHH
Q ss_conf             85500013444322222233344-43211123578616985303575561002120267614999711102997889888
Q gi|254781215|r  133 SLLPNKHWFEMQSLSLHPAPWYS-DVLHCSLGIDSKHYSTMCRTYSEERPDTFVGHHNTYGMAIINDEASGTPDVINLGI  211 (511)
Q Consensus       133 ~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~s~~~~ea~~G~h~~~~~lvI~DEAsgI~d~i~e~i  211 (511)
                      ... ..+.+....    ..+... +..+..+.++      ..|....  --+.....+.+. .+|+|+|..+....++++
T Consensus        68 ~~g-~HPD~~~i~----~~~~~~~~k~k~~I~Id------qiR~l~~--~~~~~p~~g~~K-V~IId~Ad~mn~~AaNal  133 (319)
T PRK08769         68 AAG-THPDLQLVS----FIPNRTGDKLRTEIVIE------QVREISQ--KLALTPQYGIAQ-VVIVDPADAINRSACNAL  133 (319)
T ss_pred             HCC-CCCCEEEEE----CCCCCCCCCCCCCCCHH------HHHHHHH--HHHHCCCCCCCE-EEEECCHHHCCHHHHHHH
T ss_conf             668-998968775----34444543112348699------9999999--961372027956-999806675289999999


Q ss_pred             HHHHCCCCCCEEEEEE-CCCCCCCCHHH
Q ss_conf             8885079981389982-38998765567
Q gi|254781215|r  212 LGFLTERNANRFWIMT-SNPRRLSGKFY  238 (511)
Q Consensus       212 ~~~Lt~~g~~~~~i~~-~nP~~~~g~fy  238 (511)
                      .-+|-++.....++.+ .+|.+..-...
T Consensus       134 LK~LEEPp~~~~~iL~~~~~~~ll~TI~  161 (319)
T PRK08769        134 LKTLEEPSPGRYLWLISAQPARLPATIR  161 (319)
T ss_pred             HHHHCCCCCCEEEEEEECCHHHCCHHHH
T ss_conf             9982279988489998699365824776


No 47 
>COG4096 HsdR Type I site-specific restriction-modification system, R (restriction) subunit and related helicases [Defense mechanisms]
Probab=97.19  E-value=0.0066  Score=36.95  Aligned_cols=73  Identities=18%  Similarity=0.211  Sum_probs=53.8

Q ss_pred             CCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEEECCHHHHHHH
Q ss_conf             56555784589999999999987405655542101246502576597899999999999808996699980858999999
Q gi|254781215|r   44 PLEGFSAPRSWQLEFMEVVDAHCLNSVNNPNPEVFKGAISAGRGIGKTTLNAWLVLWLMSTRPGISVICLANSETQLKTT  123 (511)
Q Consensus        44 ~~~~~~~P~~WQ~e~l~~i~~~~~~~~~~~~~~~~r~aV~sgrG~GKS~l~a~l~lw~l~~~p~~kv~vtApt~~Q~~~i  123 (511)
                      +--.-.+||.+|..+.+.+.++..++..       |+.++=..|+|||..+-.++--.+-+.--.+|+..|-.-.++...
T Consensus       159 ~~~s~i~~RyyQ~~AI~rv~Eaf~~g~~-------raLlvMATGTGKTrTAiaii~rL~r~~~~KRVLFLaDR~~Lv~QA  231 (875)
T COG4096         159 DIDSAIGPRYYQIIAIRRVIEAFSKGQN-------RALLVMATGTGKTRTAIAIIDRLIKSGWVKRVLFLADRNALVDQA  231 (875)
T ss_pred             CCCCCCCCHHHHHHHHHHHHHHHHCCCC-------EEEEEEECCCCCCEEHHHHHHHHHHCCHHHEEEEEECHHHHHHHH
T ss_conf             6322336227889999999999866874-------489997058885231999999999614143056761267899999


No 48 
>pfam07652 Flavi_DEAD Flavivirus DEAD domain.
Probab=97.17  E-value=0.0067  Score=36.90  Aligned_cols=133  Identities=20%  Similarity=0.062  Sum_probs=74.2

Q ss_pred             CCCCCHHHHHHHHHHHHHHHCCCCEEEEEECCHHHHHHHHHHHHHHHHHHCHHCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             57659789999999999980899669998085899999999999999985500013444322222233344432111235
Q gi|254781215|r   85 GRGIGKTTLNAWLVLWLMSTRPGISVICLANSETQLKTTLWAEVSKWLSLLPNKHWFEMQSLSLHPAPWYSDVLHCSLGI  164 (511)
Q Consensus        85 grG~GKS~l~a~l~lw~l~~~p~~kv~vtApt~~Q~~~ilw~Ei~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  164 (511)
                      --|.|||.-.---++--++- ..-+++|.|||.--     -+|+...++..+.+-........                 
T Consensus        10 HPGaGKTr~vLP~~v~~~i~-~~lRtlVLaPTRVV-----~~Em~eAL~g~~vr~~t~a~~~~-----------------   66 (146)
T pfam07652        10 HPGAGKTRKVLPELVRECID-RRLRTLVLAPTRVV-----LAEMEEALRGLPIRYHTPAVSSE-----------------   66 (146)
T ss_pred             CCCCCCCCHHHHHHHHHHHH-CCCEEEEECCHHHH-----HHHHHHHHCCCCCEEECHHHHCC-----------------
T ss_conf             89999702248999999997-28618997727999-----99999997589946752343136-----------------


Q ss_pred             CCCEEEEEECCCCCCCCCHHHHCCCCCCEEEEECCHHCCCHHHH--HHHHHHHCCCCCCEEEEEECCCCCCCCHHHHH
Q ss_conf             78616985303575561002120267614999711102997889--88888850799813899823899876556765
Q gi|254781215|r  165 DSKHYSTMCRTYSEERPDTFVGHHNTYGMAIINDEASGTPDVIN--LGILGFLTERNANRFWIMTSNPRRLSGKFYEI  240 (511)
Q Consensus       165 ~~~~~~~~~~~~s~~~~ea~~G~h~~~~~lvI~DEAsgI~d~i~--e~i~~~Lt~~g~~~~~i~~~nP~~~~g~fy~~  240 (511)
                      ..+.+.+..-......---+.+.+..+..++|+|||++.+..-.  ......+...|.-..++++.+|-+.++.|-++
T Consensus        67 ~~~~~ivdvmCHAT~t~r~l~~~~~~ny~viIMDE~H~~DP~SIAarG~~~~~~~~g~~a~i~mTATPPG~~~~fp~S  144 (146)
T pfam07652        67 HTGREIVDVMCHATFTQRLLSPVRVPNYEVIIMDEAHFTDPASIAARGYISTLVELGEAAAIFMTATPPGTSDPFPES  144 (146)
T ss_pred             CCCCCEEEEECHHHHHHHHHCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCEEEEEEECCCCCCCCCCCCC
T ss_conf             688841889715988889736888564479998512238989999889999885438657999956899989989888


No 49 
>COG1205 Distinct helicase family with a unique C-terminal domain including a metal-binding cysteine cluster [General function prediction only]
Probab=97.14  E-value=0.0093  Score=36.00  Aligned_cols=165  Identities=16%  Similarity=0.111  Sum_probs=93.4

Q ss_pred             CHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEEECCHHHHHHHHHHHHHH
Q ss_conf             45899999999999874056555421012465025765978999999999998089966999808589999999999999
Q gi|254781215|r   51 PRSWQLEFMEVVDAHCLNSVNNPNPEVFKGAISAGRGIGKTTLNAWLVLWLMSTRPGISVICLANSETQLKTTLWAEVSK  130 (511)
Q Consensus        51 P~~WQ~e~l~~i~~~~~~~~~~~~~~~~r~aV~sgrG~GKS~l~a~l~lw~l~~~p~~kv~vtApt~~Q~~~ilw~Ei~k  130 (511)
                      +..-|.++++.+...      +      -|-|.+|.|+|||...-.-+++.++..+.++.++.=||..=+.|-. ..+.+
T Consensus        71 lY~HQ~~A~~~~~~G------~------~vvVtTgTgSGKTe~FllPIld~~l~~~~a~AL~lYPtnALa~DQ~-~rl~~  137 (851)
T COG1205          71 LYSHQVDALRLIREG------R------NVVVTTGTGSGKTESFLLPILDHLLRDPSARALLLYPTNALANDQA-ERLRE  137 (851)
T ss_pred             CCHHHHHHHHHHHCC------C------CEEEECCCCCCHHHHHHHHHHHHHHCCCCCEEEEEECHHHHHHHHH-HHHHH
T ss_conf             007799999999779------9------8899789988545898999999983086650899804377676699-99999


Q ss_pred             HHHHCHHCCCCCCCCCCCCCCCCCCCC--CCC-CCCCCCCEEEEEECC-----CCCCCCCHHHHCCCCCCEEEEECCHHC
Q ss_conf             998550001344432222223334443--211-123578616985303-----575561002120267614999711102
Q gi|254781215|r  131 WLSLLPNKHWFEMQSLSLHPAPWYSDV--LHC-SLGIDSKHYSTMCRT-----YSEERPDTFVGHHNTYGMAIINDEASG  202 (511)
Q Consensus       131 ~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~-~~~~~~~~~~~~~~~-----~s~~~~ea~~G~h~~~~~lvI~DEAsg  202 (511)
                      +....+.+-.+         ..|..+.  .+. .+...+.++..+-..     .-...+...-.+.  +.-++|+||++.
T Consensus       138 ~~~~~~~~v~~---------~~y~Gdt~~~~r~~~~~~pp~IllTNpdMLh~~llr~~~~~~~~~~--~Lk~lVvDElHt  206 (851)
T COG1205         138 LISDLPGKVTF---------GRYTGDTPPEERRAIIRNPPDILLTNPDMLHYLLLRNHDAWLWLLR--NLKYLVVDELHT  206 (851)
T ss_pred             HHHHCCCCEEE---------EEECCCCCHHHHHHHHHCCCCEEEECHHHHHHHHHCCCCCHHHHHH--CCCEEEEECCEE
T ss_conf             99847875135---------4434889678889987389978983889998986368822788873--275899844412


Q ss_pred             CCH----HHHHHH---HHHHCCCCCCEEEEEECCCCCCCCHHHH
Q ss_conf             997----889888---8885079981389982389987655676
Q gi|254781215|r  203 TPD----VINLGI---LGFLTERNANRFWIMTSNPRRLSGKFYE  239 (511)
Q Consensus       203 I~d----~i~e~i---~~~Lt~~g~~~~~i~~~nP~~~~g~fy~  239 (511)
                      -.-    .+.-++   .-.+.-.|+...++++|-.-.+.+.|-.
T Consensus       207 YrGv~GS~vA~llRRL~~~~~~~~~~~q~i~~SAT~~np~e~~~  250 (851)
T COG1205         207 YRGVQGSEVALLLRRLLRRLRRYGSPLQIICTSATLANPGEFAE  250 (851)
T ss_pred             CCCCHHHHHHHHHHHHHHHHHCCCCCCEEEEEECCCCCHHHHHH
T ss_conf             15603788999999999997245899628998312468288999


No 50 
>COG4581 Superfamily II RNA helicase [DNA replication, recombination, and repair]
Probab=97.11  E-value=0.021  Score=33.78  Aligned_cols=155  Identities=15%  Similarity=0.113  Sum_probs=85.1

Q ss_pred             CCCCCHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEEECCHHHHHHHHHH
Q ss_conf             55784589999999999987405655542101246502576597899999999999808996699980858999999999
Q gi|254781215|r   47 GFSAPRSWQLEFMEVVDAHCLNSVNNPNPEVFKGAISAGRGIGKTTLNAWLVLWLMSTRPGISVICLANSETQLKTTLWA  126 (511)
Q Consensus        47 ~~~~P~~WQ~e~l~~i~~~~~~~~~~~~~~~~r~aV~sgrG~GKS~l~a~l~lw~l~~~p~~kv~vtApt~~Q~~~ilw~  126 (511)
                      +|+ ||+||++.+..|...            -.|-|.+..|.|||.+ |-+++..++. .+.++++|+|...-.-.+ +.
T Consensus       117 ~F~-LD~fQ~~a~~~Ler~------------esVlV~ApTssGKTvV-aeyAi~~al~-~~qrviYTsPIKALsNQK-yr  180 (1041)
T COG4581         117 PFE-LDPFQQEAIAILERG------------ESVLVCAPTSSGKTVV-AEYAIALALR-DGQRVIYTSPIKALSNQK-YR  180 (1041)
T ss_pred             CCC-CCHHHHHHHHHHHCC------------CCEEEECCCCCCCCHH-HHHHHHHHHH-CCCCEEECCCHHHHHHHH-HH
T ss_conf             989-678999999998479------------9579973378985559-9999999987-189448616306642067-99


Q ss_pred             HHHHHHHHCHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCC------CCCCCCHHHHCCCCCCEEEEECCH
Q ss_conf             99999985500013444322222233344432111235786169853035------755610021202676149997111
Q gi|254781215|r  127 EVSKWLSLLPNKHWFEMQSLSLHPAPWYSDVLHCSLGIDSKHYSTMCRTY------SEERPDTFVGHHNTYGMAIINDEA  200 (511)
Q Consensus       127 Ei~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~------s~~~~ea~~G~h~~~~~lvI~DEA  200 (511)
                      ++..-....         ++.+.+...-.     .+..+.   -+..-|+      -..+.++.+.     .-.||+||-
T Consensus       181 dl~~~fgdv---------~~~vGL~TGDv-----~IN~~A---~clvMTTEILRnMlyrg~~~~~~-----i~~ViFDEv  238 (1041)
T COG4581         181 DLLAKFGDV---------ADMVGLMTGDV-----SINPDA---PCLVMTTEILRNMLYRGSESLRD-----IEWVVFDEV  238 (1041)
T ss_pred             HHHHHHHHH---------HHHCCCEECCE-----EECCCC---CEEEEEHHHHHHHHCCCCCCCCC-----CCEEEEEEE
T ss_conf             999986005---------65404010543-----427999---66886099999986258610135-----306888766


Q ss_pred             HCCCH----HHHHHHHHHHCCCCCCEEEEEECCCCCCCCHHHHHHH
Q ss_conf             02997----8898888885079981389982389987655676530
Q gi|254781215|r  201 SGTPD----VINLGILGFLTERNANRFWIMTSNPRRLSGKFYEIFN  242 (511)
Q Consensus       201 sgI~d----~i~e~i~~~Lt~~g~~~~~i~~~nP~~~~g~fy~~~~  242 (511)
                      +.|.|    .+||-+.-.+-. +-+  +++.|-...++..|-+...
T Consensus       239 Hyi~D~eRG~VWEE~Ii~lP~-~v~--~v~LSATv~N~~EF~~Wi~  281 (1041)
T COG4581         239 HYIGDRERGVVWEEVIILLPD-HVR--FVFLSATVPNAEEFAEWIQ  281 (1041)
T ss_pred             EECCCCCCCHHHHHHHHHCCC-CCC--EEEEECCCCCHHHHHHHHH
T ss_conf             650463221257899986677-776--8999678898799999997


No 51 
>COG0513 SrmB Superfamily II DNA and RNA helicases [DNA replication, recombination, and repair / Transcription / Translation, ribosomal structure and biogenesis]
Probab=97.09  E-value=0.012  Score=35.20  Aligned_cols=162  Identities=16%  Similarity=-0.037  Sum_probs=86.5

Q ss_pred             CCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHHH--HCCCCE-EEEEECCHHHHHH
Q ss_conf             5557845899999999999874056555421012465025765978999999999998--089966-9998085899999
Q gi|254781215|r   46 EGFSAPRSWQLEFMEVVDAHCLNSVNNPNPEVFKGAISAGRGIGKTTLNAWLVLWLMS--TRPGIS-VICLANSETQLKT  122 (511)
Q Consensus        46 ~~~~~P~~WQ~e~l~~i~~~~~~~~~~~~~~~~r~aV~sgrG~GKS~l~a~l~lw~l~--~~p~~k-v~vtApt~~Q~~~  122 (511)
                      .+|..|.+-|...+-.+-..            .-+.+.|-.|+|||.....=++-.+.  ...... ++|.+||..=+..
T Consensus        47 ~gf~~pt~IQ~~~iP~~l~g------------~Dvi~~A~TGsGKT~Af~lP~l~~i~~~~~~~~~~aLil~PTRELA~Q  114 (513)
T COG0513          47 LGFEEPTPIQLAAIPLILAG------------RDVLGQAQTGTGKTAAFLLPLLQKILKSVERKYVSALILAPTRELAVQ  114 (513)
T ss_pred             CCCCCCCHHHHHHCHHHHCC------------CCEEEECCCCCHHHHHHHHHHHHHHHHCCCCCCCCEEEECCCHHHHHH
T ss_conf             59899898999658776369------------997998689871789999999999740045577756997799999999


Q ss_pred             HHHHHHHHHHHHCH-HCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCCCCCCCHHHHCCCCCCEEEEECCHH
Q ss_conf             99999999998550-00134443222222333444321112357861698530357556100212026761499971110
Q gi|254781215|r  123 TLWAEVSKWLSLLP-NKHWFEMQSLSLHPAPWYSDVLHCSLGIDSKHYSTMCRTYSEERPDTFVGHHNTYGMAIINDEAS  201 (511)
Q Consensus       123 ilw~Ei~k~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~ea~~G~h~~~~~lvI~DEAs  201 (511)
                      | ..++.++....+ .+      ...++- +-........++..  --+.++.+-+.-.--....++..+.-.+|+|||.
T Consensus       115 i-~~~~~~~~~~~~~~~------~~~i~G-G~~~~~q~~~l~~g--~~ivVaTPGRllD~i~~~~l~l~~v~~lVlDEAD  184 (513)
T COG0513         115 I-AEELRKLGKNLGGLR------VAVVYG-GVSIRKQIEALKRG--VDIVVATPGRLLDLIKRGKLDLSGVETLVLDEAD  184 (513)
T ss_pred             H-HHHHHHHHHHCCCCE------EEEEEC-CCCHHHHHHHHHCC--CCEEEECCCHHHHHHHCCCCCCCCEEEEEECCHH
T ss_conf             9-999999986245842------999989-98989999987249--9899979608999986488554650189967617


Q ss_pred             CCCH-HHHHHHHHHHCCCCCCEEEEEECC
Q ss_conf             2997-889888888507998138998238
Q gi|254781215|r  202 GTPD-VINLGILGFLTERNANRFWIMTSN  229 (511)
Q Consensus       202 gI~d-~i~e~i~~~Lt~~g~~~~~i~~~n  229 (511)
                      -+=| .+.+.++..+..-......++||-
T Consensus       185 rmld~gf~~~i~~I~~~~p~~~qtllfSA  213 (513)
T COG0513         185 RMLDMGFIDDIEKILKALPPDRQTLLFSA  213 (513)
T ss_pred             HHCCCCCHHHHHHHHHHCCCCCEEEEEEE
T ss_conf             66388768999999973897748999982


No 52 
>PRK04837 ATP-dependent RNA helicase RhlB; Provisional
Probab=97.06  E-value=0.0069  Score=36.80  Aligned_cols=74  Identities=18%  Similarity=0.079  Sum_probs=52.6

Q ss_pred             CCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHHCC--------CCEEEEEECCH
Q ss_conf             5557845899999999999874056555421012465025765978999999999998089--------96699980858
Q gi|254781215|r   46 EGFSAPRSWQLEFMEVVDAHCLNSVNNPNPEVFKGAISAGRGIGKTTLNAWLVLWLMSTRP--------GISVICLANSE  117 (511)
Q Consensus        46 ~~~~~P~~WQ~e~l~~i~~~~~~~~~~~~~~~~r~aV~sgrG~GKS~l~a~l~lw~l~~~p--------~~kv~vtApt~  117 (511)
                      .+|..|-+-|+..+-.+-...            -+.+.|..|+|||.....-++-.++..+        ..+++|.+||.
T Consensus        27 ~g~~~pTpIQ~~aIP~il~G~------------Dvi~~A~TGSGKTlAfllPil~~ll~~~~~~~~~~~~p~aLIL~PTR   94 (423)
T PRK04837         27 KGFEYCTPIQALALPLTLAGR------------DVAGQAQTGTGKTMAFLTATFHHLLSHPAPEGRKVNQPRALIMAPTR   94 (423)
T ss_pred             CCCCCCCHHHHHHHHHHHCCC------------CEEEECCCCCHHHHHHHHHHHHHHHHCCCCCCCCCCCCEEEEEECCH
T ss_conf             799999999999999996799------------88998999874999999999999983745334556786189993889


Q ss_pred             HHHHHHHHHHHHHHH
Q ss_conf             999999999999999
Q gi|254781215|r  118 TQLKTTLWAEVSKWL  132 (511)
Q Consensus       118 ~Q~~~ilw~Ei~k~~  132 (511)
                      .=+..|. .++..+.
T Consensus        95 ELa~Qi~-~~~~~l~  108 (423)
T PRK04837         95 ELAVQIH-ADAEPLA  108 (423)
T ss_pred             HHHHHHH-HHHHHHH
T ss_conf             9999999-9999974


No 53 
>PRK09401 reverse gyrase; Reviewed
Probab=97.06  E-value=0.011  Score=35.60  Aligned_cols=93  Identities=22%  Similarity=0.307  Sum_probs=62.4

Q ss_pred             HHHHHHHHCHHHHHHHHHHH---HHHCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCCC
Q ss_conf             88999870706665288667---764214557775655578458999999999998740565554210124650257659
Q gi|254781215|r   13 QKLFDLMWSDEIKLSFSNFV---LHFFPWGEKGTPLEGFSAPRSWQLEFMEVVDAHCLNSVNNPNPEVFKGAISAGRGIG   89 (511)
Q Consensus        13 ~~~~~~~~~~~~~~~~~~~~---~~~~~w~~~~~~~~~~~~P~~WQ~e~l~~i~~~~~~~~~~~~~~~~r~aV~sgrG~G   89 (511)
                      ++|...+-......+|.+|-   ..+-||+.          -+.|-+.+|+.                .-.|+.|+.|+|
T Consensus        52 ~~~~~~~~~~~~~~~f~~fF~~~~G~~~w~~----------Qr~WakR~~~g----------------~SFaiiAPTG~G  105 (1176)
T PRK09401         52 KEYEELYSLEEEYKEFEEFFKKKVGSEPWSL----------QRTWAKRLLLG----------------ESFAIIAPTGVG  105 (1176)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHCCCCCHH----------HHHHHHHHHCC----------------CCEEEECCCCCC
T ss_conf             6799999999999999999999868998488----------99999998668----------------974898889988


Q ss_pred             HHHHHHHHHHHHHHHCCCCEEEEEECCHHHHHHHHHHHHHHHHHH
Q ss_conf             789999999999980899669998085899999999999999985
Q gi|254781215|r   90 KTTLNAWLVLWLMSTRPGISVICLANSETQLKTTLWAEVSKWLSL  134 (511)
Q Consensus        90 KS~l~a~l~lw~l~~~p~~kv~vtApt~~Q~~~ilw~Ei~k~~~~  134 (511)
                      ||++...+.+|++.  .+.+++++-||..-++++. .-+..+.+.
T Consensus       106 KTtfgl~~sly~a~--kgkks~~i~PT~~Lv~Q~~-~kl~~~~~~  147 (1176)
T PRK09401        106 KTTFGLVMALYLAK--KGKKSYIIFPTRLLVEQVV-EKLRKLAEK  147 (1176)
T ss_pred             HHHHHHHHHHHHHH--CCCEEEEEECCHHHHHHHH-HHHHHHHHH
T ss_conf             88999999999986--5983999968889999999-999999997


No 54 
>PRK07994 DNA polymerase III subunits gamma and tau; Validated
Probab=97.05  E-value=0.01  Score=35.70  Aligned_cols=149  Identities=15%  Similarity=0.125  Sum_probs=79.0

Q ss_pred             HHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEEECCHHHHHHHHHHHHHHHHHH
Q ss_conf             99999999998740565554210124650257659789999999999980899669998085899999999999999985
Q gi|254781215|r   55 QLEFMEVVDAHCLNSVNNPNPEVFKGAISAGRGIGKTTLNAWLVLWLMSTRPGISVICLANSETQLKTTLWAEVSKWLSL  134 (511)
Q Consensus        55 Q~e~l~~i~~~~~~~~~~~~~~~~r~aV~sgrG~GKS~l~a~l~lw~l~~~p~~kv~vtApt~~Q~~~ilw~Ei~k~~~~  134 (511)
                      |..+++.+...+..++. |.    -..-...||+|||+++-.++-+.-|.....-..|.-  -..-     .+|.    .
T Consensus        21 Q~~v~~~l~na~~~~r~-~h----aylf~G~rG~GKtt~ari~ak~lnc~~~~~~~pcg~--c~~c-----~~i~----~   84 (643)
T PRK07994         21 QEHVLTALANGLSLGRI-HH----AYLFSGTRGVGKTSIARLLAKGLNCETGITATPCGV--CDNC-----REIE----Q   84 (643)
T ss_pred             CHHHHHHHHHHHHHCCC-CC----EEEEECCCCCCHHHHHHHHHHHHCCCCCCCCCCCCC--CHHH-----HHHH----C
T ss_conf             79999999999982986-63----487458998888899999999967999999997876--7768-----9886----5


Q ss_pred             CHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCCCCCCCHHHHCCCCCCEEEEECCHHCCCHHHHHHHHHH
Q ss_conf             50001344432222223334443211123578616985303575561002120267614999711102997889888888
Q gi|254781215|r  135 LPNKHWFEMQSLSLHPAPWYSDVLHCSLGIDSKHYSTMCRTYSEERPDTFVGHHNTYGMAIINDEASGTPDVINLGILGF  214 (511)
Q Consensus       135 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~ea~~G~h~~~~~lvI~DEAsgI~d~i~e~i~~~  214 (511)
                                       +...|...++.....+  ....|... ++ -.+.-.++.+ -.+|+||.+.+....|+++.-+
T Consensus        85 -----------------g~~~d~~eidaas~~~--vd~~rel~-~~-~~y~p~~~r~-kvyiidEvhmls~~afnalLKt  142 (643)
T PRK07994         85 -----------------GRFVDLIEIDAASRTK--VEDTRDLL-DN-VQYAPARGRF-KVYLIDEVHMLSRHSFNALLKT  142 (643)
T ss_pred             -----------------CCCCCEEEEECCCCCC--HHHHHHHH-HH-CCCCCCCCCE-EEEEEECHHHCCHHHHHHHHHH
T ss_conf             -----------------8988758863677788--89999999-84-4668877853-6999722101589999999986


Q ss_pred             HCCCCCCEE-EEEECCCCCCCCHHHHHH
Q ss_conf             507998138-998238998765567653
Q gi|254781215|r  215 LTERNANRF-WIMTSNPRRLSGKFYEIF  241 (511)
Q Consensus       215 Lt~~g~~~~-~i~~~nP~~~~g~fy~~~  241 (511)
                      |-++-...+ ++++..|.+..-...-.|
T Consensus       143 lEePp~hv~filaTT~~~k~p~TilSRC  170 (643)
T PRK07994        143 LEEPPAHVKFLLATTDPQKLPVTILSRC  170 (643)
T ss_pred             HCCCCHHCEEEEECCCHHHCCHHHHHHH
T ss_conf             2378610089986077454847899777


No 55 
>PRK06871 DNA polymerase III subunit delta'; Validated
Probab=96.91  E-value=0.031  Score=32.65  Aligned_cols=153  Identities=18%  Similarity=0.202  Sum_probs=83.5

Q ss_pred             HHHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEEECCHHHHHHHHHHHHHHHHH
Q ss_conf             99999999999874056555421012465025765978999999999998089966999808589999999999999998
Q gi|254781215|r   54 WQLEFMEVVDAHCLNSVNNPNPEVFKGAISAGRGIGKTTLNAWLVLWLMSTRPGISVICLANSETQLKTTLWAEVSKWLS  133 (511)
Q Consensus        54 WQ~e~l~~i~~~~~~~~~~~~~~~~r~aV~sgrG~GKS~l~a~l~lw~l~~~p~~kv~vtApt~~Q~~~ilw~Ei~k~~~  133 (511)
                      ||....+.+......++.-|     ..-+.+.+|+||+.++-.++-|.+|..|+....|..-..=++.         ...
T Consensus         5 Wl~~~~~~l~~~~~~~r~~H-----A~L~~G~~G~Gk~~la~~~a~~llC~~~~~~~~Cg~C~sC~l~---------~~g   70 (324)
T PRK06871          5 WLQPIYQQITQTFLQGRGHH-----ALLFKADSGLGTEQLIRALAQWLMCQAPGDEQPCGQCHSCHLF---------QAG   70 (324)
T ss_pred             CCHHHHHHHHHHHHCCCCCE-----EEEEECCCCCCHHHHHHHHHHHHHCCCCCCCCCCCCCHHHHHH---------HCC
T ss_conf             65799999999998699543-----7876899997899999999999828999999988889899999---------738


Q ss_pred             HCHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCCCCCCCHHHHCCCCCCEEEEECCHHCCCHHHHHHHHH
Q ss_conf             55000134443222222333444321112357861698530357556100212026761499971110299788988888
Q gi|254781215|r  134 LLPNKHWFEMQSLSLHPAPWYSDVLHCSLGIDSKHYSTMCRTYSEERPDTFVGHHNTYGMAIINDEASGTPDVINLGILG  213 (511)
Q Consensus       134 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~ea~~G~h~~~~~lvI~DEAsgI~d~i~e~i~~  213 (511)
                      .-|..+.+.....    +...++..               |....  --+..+..+.+. .+|+|+|..+.....+++.-
T Consensus        71 ~HPD~~~i~~~~~----k~I~vd~I---------------R~l~~--~~~~~~~~g~~K-V~iI~~ae~m~~~AaNALLK  128 (324)
T PRK06871         71 NHPDFHILEPIDG----KDIGVDQV---------------REINE--KVSQFAQQGGNK-VVYIQGAERLTEAAANALLK  128 (324)
T ss_pred             CCCCEEEEECCCC----CCCCHHHH---------------HHHHH--HHHHCCCCCCCE-EEEECCHHHHHHHHHHHHHH
T ss_conf             9998799846788----87889999---------------99999--986462205966-99975888857999999999


Q ss_pred             HHCCCCCCEE-EEEECCCCCCCCHHHHHHH
Q ss_conf             8507998138-9982389987655676530
Q gi|254781215|r  214 FLTERNANRF-WIMTSNPRRLSGKFYEIFN  242 (511)
Q Consensus       214 ~Lt~~g~~~~-~i~~~nP~~~~g~fy~~~~  242 (511)
                      +|-++..... ++.+.+|.+.--..+-++.
T Consensus       129 tLEEPp~~~~fiL~t~~~~~ll~TI~SRCq  158 (324)
T PRK06871        129 TLEEPRPNTYFLLQADLSASLLATIYSRCQ  158 (324)
T ss_pred             HHCCCCCCEEEEEEECCCCCCCCHHHHCCC
T ss_conf             833898783899987870103240862661


No 56 
>PRK06645 DNA polymerase III subunits gamma and tau; Validated
Probab=96.90  E-value=0.03  Score=32.82  Aligned_cols=149  Identities=15%  Similarity=0.092  Sum_probs=72.0

Q ss_pred             HHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEE----EEEECCHHHHHHHHHHHHHH
Q ss_conf             99999999998740565554210124650257659789999999999980899669----99808589999999999999
Q gi|254781215|r   55 QLEFMEVVDAHCLNSVNNPNPEVFKGAISAGRGIGKTTLNAWLVLWLMSTRPGISV----ICLANSETQLKTTLWAEVSK  130 (511)
Q Consensus        55 Q~e~l~~i~~~~~~~~~~~~~~~~r~aV~sgrG~GKS~l~a~l~lw~l~~~p~~kv----~vtApt~~Q~~~ilw~Ei~k  130 (511)
                      |..+.+.+......++--|     -.--.+.||+|||+++-.++--.-|..+...-    .|.  .-..-+.+       
T Consensus        26 Q~~~~~~l~n~i~~~~~~~-----aylf~G~rG~GKTt~Ari~ak~lnc~~~~~~~~~~~~c~--~c~~c~~i-------   91 (507)
T PRK06645         26 QEVLVKVLSYTILNDRLAG-----GYLLTGIRGVGKTTSARIIAKAVNCSALITENTTIKTCE--KCTNCISF-------   91 (507)
T ss_pred             CHHHHHHHHHHHHCCCCCC-----EEEEECCCCCCHHHHHHHHHHHHCCCCCCCCCCCCCCCC--CCHHHHHH-------
T ss_conf             3999999999997399663-----477458799788999999999967999888899888888--87678998-------


Q ss_pred             HHHHCHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCCCCCCCHHHHCCCCCCEEEEECCHHCCCHHHHHH
Q ss_conf             99855000134443222222333444321112357861698530357556100212026761499971110299788988
Q gi|254781215|r  131 WLSLLPNKHWFEMQSLSLHPAPWYSDVLHCSLGIDSKHYSTMCRTYSEERPDTFVGHHNTYGMAIINDEASGTPDVINLG  210 (511)
Q Consensus       131 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~ea~~G~h~~~~~lvI~DEAsgI~d~i~e~  210 (511)
                        .                 .++..+...++-....+  ....|.....  ..+.-..+.+ =.+|+||++.++...|.+
T Consensus        92 --~-----------------~~~~~dv~EiDaas~~g--v~~ir~l~~~--~~~~p~~~~~-kv~iidE~hmls~~a~na  147 (507)
T PRK06645         92 --N-----------------NHNHPDIIEIDAASKTS--VDDIRRIIES--AEYKPLQGKH-KIFIIDEVHMLSKGAFNA  147 (507)
T ss_pred             --H-----------------CCCCCCEEEEECCCCCC--HHHHHHHHHH--CCCCCCCCCE-EEEEECCHHHCCHHHHHH
T ss_conf             --6-----------------58999859963788888--8999999863--5517876743-589952142248999999


Q ss_pred             HHHHHCCCCCCEEEE-EECCCCCCCCHHHHHH
Q ss_conf             888850799813899-8238998765567653
Q gi|254781215|r  211 ILGFLTERNANRFWI-MTSNPRRLSGKFYEIF  241 (511)
Q Consensus       211 i~~~Lt~~g~~~~~i-~~~nP~~~~g~fy~~~  241 (511)
                      +.-+|-.+-...+++ ++..|.+..-..--.|
T Consensus       148 llktlEepp~~~~Fi~atte~~kip~ti~src  179 (507)
T PRK06645        148 LLKTLEEPPPHIIFIFATTEVQKIPATIISRC  179 (507)
T ss_pred             HHHHHHCCCCCEEEEEECCCHHHCCHHHHHHC
T ss_conf             99974278644389997485364837888543


No 57 
>PRK00440 rfc replication factor C small subunit; Reviewed
Probab=96.90  E-value=0.025  Score=33.24  Aligned_cols=125  Identities=18%  Similarity=0.157  Sum_probs=66.0

Q ss_pred             CCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEE-EEECCHHHHHH
Q ss_conf             56555784589999999999987405655542101246502576597899999999999808996699-98085899999
Q gi|254781215|r   44 PLEGFSAPRSWQLEFMEVVDAHCLNSVNNPNPEVFKGAISAGRGIGKTTLNAWLVLWLMSTRPGISVI-CLANSETQLKT  122 (511)
Q Consensus        44 ~~~~~~~P~~WQ~e~l~~i~~~~~~~~~~~~~~~~r~aV~sgrG~GKS~l~a~l~lw~l~~~p~~kv~-vtApt~~Q~~~  122 (511)
                      .+..+.|    |.++...+.....++.   .|.   .-..++.|+|||+++-.++--...-.....++ +-|...+-. +
T Consensus        14 ~l~di~g----~~~~~~~L~~~i~~~~---~ph---lLf~GppG~GKTt~a~~la~~l~~~~~~~~~lelnasd~r~i-d   82 (318)
T PRK00440         14 SLDEVVG----QEEIVERLKSFVKEKN---MPH---LLFAGPPGTGKTTAALALARELYGEYWRENFLELNASDERGI-D   82 (318)
T ss_pred             CHHHHCC----CHHHHHHHHHHHHCCC---CCE---EEEECCCCCCHHHHHHHHHHHHCCCCCCCCEEEECCCCCCCH-H
T ss_conf             8999419----6999999999998799---866---988895998899999999999769864347689516456671-7


Q ss_pred             HHHHHHHHHHHHCHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCCCCCCCHHHHCCCCCCEEEEECCHHC
Q ss_conf             99999999998550001344432222223334443211123578616985303575561002120267614999711102
Q gi|254781215|r  123 TLWAEVSKWLSLLPNKHWFEMQSLSLHPAPWYSDVLHCSLGIDSKHYSTMCRTYSEERPDTFVGHHNTYGMAIINDEASG  202 (511)
Q Consensus       123 ilw~Ei~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~ea~~G~h~~~~~lvI~DEAsg  202 (511)
                      ++=..++...+..                                             +  + + .+. .-++|+|||.+
T Consensus        83 ~vr~~i~~~~~~~---------------------------------------------~--~-~-~~~-~kiiiiDE~d~  112 (318)
T PRK00440         83 VIRNKIKEFARTA---------------------------------------------P--V-G-GAP-FKIIFLDEADN  112 (318)
T ss_pred             HHHHHHHHHHHHC---------------------------------------------C--C-C-CCC-EEEEEEECCCC
T ss_conf             8999999999726---------------------------------------------7--7-8-997-38999868553


Q ss_pred             CCHHHHHHHHHHHCCCCCCEEEEEECC
Q ss_conf             997889888888507998138998238
Q gi|254781215|r  203 TPDVINLGILGFLTERNANRFWIMTSN  229 (511)
Q Consensus       203 I~d~i~e~i~~~Lt~~g~~~~~i~~~n  229 (511)
                      +......++..+|-.......++.+.|
T Consensus       113 l~~~aq~aL~~~mE~~~~~~~fil~~n  139 (318)
T PRK00440        113 LTSDAQQALRRTMEMYSQTTRFILSCN  139 (318)
T ss_pred             CCHHHHHHHHHHHHCCCCCCEEEEECC
T ss_conf             225567888764310566625886348


No 58 
>PRK01297 ATP-dependent RNA helicase RhlB; Provisional
Probab=96.90  E-value=0.032  Score=32.62  Aligned_cols=76  Identities=14%  Similarity=0.078  Sum_probs=55.0

Q ss_pred             CCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHHCC--------CCEEEEEEC
Q ss_conf             565557845899999999999874056555421012465025765978999999999998089--------966999808
Q gi|254781215|r   44 PLEGFSAPRSWQLEFMEVVDAHCLNSVNNPNPEVFKGAISAGRGIGKTTLNAWLVLWLMSTRP--------GISVICLAN  115 (511)
Q Consensus        44 ~~~~~~~P~~WQ~e~l~~i~~~~~~~~~~~~~~~~r~aV~sgrG~GKS~l~a~l~lw~l~~~p--------~~kv~vtAp  115 (511)
                      .--+|..|-+-|++.+-.+-.    +.        -+.+.|..|+|||.....-++-.++..+        ..+++|.+|
T Consensus       100 ~~~Gf~~PTpIQ~~aIP~iL~----Gk--------Dvi~~A~TGSGKTlAyLLPil~~ll~~~~~~~~~~~~p~aLIL~P  167 (472)
T PRK01297        100 HDLGFPYCTPIQAQVLGYTLA----GH--------DAIGRAQTGTGKTAAFLISIINQLLQTPPPKERYMGEPRALIIAP  167 (472)
T ss_pred             HHCCCCCCCHHHHHHHHHHHC----CC--------CEEEECCCCCHHHHHHHHHHHHHHHHCCCCHHCCCCCCEEEEECC
T ss_conf             977999999999999999976----99--------889989998679999999999999717751011368952999879


Q ss_pred             CHHHHHHHHHHHHHHHH
Q ss_conf             58999999999999999
Q gi|254781215|r  116 SETQLKTTLWAEVSKWL  132 (511)
Q Consensus       116 t~~Q~~~ilw~Ei~k~~  132 (511)
                      |..=+.+|. .++....
T Consensus       168 TRELa~QI~-~~~~~L~  183 (472)
T PRK01297        168 TRELVVQIA-KDAAALT  183 (472)
T ss_pred             CHHHHHHHH-HHHHHHH
T ss_conf             999999999-9999974


No 59 
>PRK05896 DNA polymerase III subunits gamma and tau; Validated
Probab=96.86  E-value=0.034  Score=32.42  Aligned_cols=155  Identities=17%  Similarity=0.126  Sum_probs=78.8

Q ss_pred             CCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEEECCHHHHHHHH
Q ss_conf             65557845899999999999874056555421012465025765978999999999998089966999808589999999
Q gi|254781215|r   45 LEGFSAPRSWQLEFMEVVDAHCLNSVNNPNPEVFKGAISAGRGIGKTTLNAWLVLWLMSTRPGISVICLANSETQLKTTL  124 (511)
Q Consensus        45 ~~~~~~P~~WQ~e~l~~i~~~~~~~~~~~~~~~~r~aV~sgrG~GKS~l~a~l~lw~l~~~p~~kv~vtApt~~Q~~~il  124 (511)
                      .....|    |..+.+.+.....+++.-|     -..-.++||+|||++|-.++-...|..+...-.|.....  .+.  
T Consensus        15 F~eIIG----Qe~iv~~L~nAI~~~RiaH-----AYLFsGPrGvGKTTlArifAkaLnC~~~~~~dpCg~C~s--C~~--   81 (613)
T PRK05896         15 FKQIIG----QELIKKILVNAILNNKLTH-----AYIFSGPRGIGKTSIAKIFAKAINCLNPKDGDCCNSCSV--CES--   81 (613)
T ss_pred             HHHHCC----CHHHHHHHHHHHHCCCCCC-----EEEEECCCCCCHHHHHHHHHHHHCCCCCCCCCCCCCCHH--HHH--
T ss_conf             655238----2999999999998499762-----277558998488999999999966999999998888878--999--


Q ss_pred             HHHHHHHHHHCHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCCCCCCCHHHHCCCCCCEEEEECCHHCCC
Q ss_conf             99999999855000134443222222333444321112357861698530357556100212026761499971110299
Q gi|254781215|r  125 WAEVSKWLSLLPNKHWFEMQSLSLHPAPWYSDVLHCSLGIDSKHYSTMCRTYSEERPDTFVGHHNTYGMAIINDEASGTP  204 (511)
Q Consensus       125 w~Ei~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~ea~~G~h~~~~~lvI~DEAsgI~  204 (511)
                             +......+..+..+.                   ........|....  --++.-..+.+. .+|+|||..+.
T Consensus        82 -------I~~g~h~DviEIdaa-------------------sn~gIDeIReLie--~~~~~P~~gkyK-V~IIDEah~Ln  132 (613)
T PRK05896         82 -------INTNQSVDIVELDAA-------------------SNNGVDEIRNIID--NINYLPTTFKYK-VYIIDEAHMLS  132 (613)
T ss_pred             -------HHCCCCCCEEEEECC-------------------CCCCHHHHHHHHH--HHCCCCCCCCCE-EEEECCHHHCC
T ss_conf             -------856999986884065-------------------5578899999999--708587579945-99981622179


Q ss_pred             HHHHHHHHHHHCCCCCC-EEEEEECCCCCCCCHHHHHH
Q ss_conf             78898888885079981-38998238998765567653
Q gi|254781215|r  205 DVINLGILGFLTERNAN-RFWIMTSNPRRLSGKFYEIF  241 (511)
Q Consensus       205 d~i~e~i~~~Lt~~g~~-~~~i~~~nP~~~~g~fy~~~  241 (511)
                      ...|.++.-+|-.+-.. .+++++..|.+..-.-.-+|
T Consensus       133 ~~AaNALLKtLEEPP~~viFIL~Ttep~KLLpTIlSRC  170 (613)
T PRK05896        133 TSAWNALLKTLEEPPKHVVFIFATTEFQKIPLTIISRC  170 (613)
T ss_pred             HHHHHHHHHHCCCCCCCCEEEEEECCHHHCCHHHHHCC
T ss_conf             99999999853489878379998288154937664035


No 60 
>PRK04914 ATP-dependent helicase HepA; Validated
Probab=96.85  E-value=0.035  Score=32.38  Aligned_cols=173  Identities=16%  Similarity=0.177  Sum_probs=85.8

Q ss_pred             CCCCCCCCCH----HHHHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEEECCHH
Q ss_conf             7565557845----899999999999874056555421012465025765978999999999998089966999808589
Q gi|254781215|r   43 TPLEGFSAPR----SWQLEFMEVVDAHCLNSVNNPNPEVFKGAISAGRGIGKTTLNAWLVLWLMSTRPGISVICLANSET  118 (511)
Q Consensus        43 ~~~~~~~~P~----~WQ~e~l~~i~~~~~~~~~~~~~~~~r~aV~sgrG~GKS~l~a~l~lw~l~~~p~~kv~vtApt~~  118 (511)
                      .++-++.|||    +=|-.+.+++...       +   ..|+-++=-=|.|||--+..++-..+....-.+|+|++|..=
T Consensus       140 ~~~~gl~g~r~~l~pHQ~~ia~~v~~r-------~---~PRvLLADEVGLGKTIEAGLIl~ell~rgra~RvLIvvP~~L  209 (955)
T PRK04914        140 SPLRGLRGARAGLIPHQLYIAHEVGRR-------H---APRVLLADEVGLGKTIEAGLIIHQQLLTGRAERVLIIVPETL  209 (955)
T ss_pred             CCCCCCCCCCCCCCCHHHHHHHHHHHC-------C---CCCEEEECCCCCCHHHHHHHHHHHHHHCCCCCEEEEECCHHH
T ss_conf             951132233246563799999999714-------5---884897058888689999999999997487777999927799


Q ss_pred             HHHHHHH-HHHHHHHHHCHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCCCCCCCHHHHCCCCCCEEEEE
Q ss_conf             9999999-999999985500013444322222233344432111235786169853035755610021202676149997
Q gi|254781215|r  119 QLKTTLW-AEVSKWLSLLPNKHWFEMQSLSLHPAPWYSDVLHCSLGIDSKHYSTMCRTYSEERPDTFVGHHNTYGMAIIN  197 (511)
Q Consensus       119 Q~~~ilw-~Ei~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~ea~~G~h~~~~~lvI~  197 (511)
                      +-.   | .|+..-...     .|..-...... ....+..   .-.......+...-+-..++....-+....-.|+|+
T Consensus       210 ~~Q---W~~EL~~KF~L-----~f~i~D~~r~~-~~~~~~~---NpF~~~~~vI~Sld~l~~~~~~~e~l~~a~WDLVIV  277 (955)
T PRK04914        210 QHQ---WLVEMLRRFNL-----RFSLFDEERCA-EAQADAD---NPFETEQLVICSLDFLRKNKKRLEQALDAEWDLLVV  277 (955)
T ss_pred             HHH---HHHHHHHHCCC-----CCEEECCHHHH-HHHCCCC---CCCCCCCEEEEEHHHHCCCHHHHHHHHCCCCCEEEE
T ss_conf             899---99999998399-----80995518888-7533579---975458979987899603967899873389888997


Q ss_pred             CCHHCCC------HHHHHHHHHHHCCCCCCEEEEEECCCCC--CCCHHHH
Q ss_conf             1110299------7889888888507998138998238998--7655676
Q gi|254781215|r  198 DEASGTP------DVINLGILGFLTERNANRFWIMTSNPRR--LSGKFYE  239 (511)
Q Consensus       198 DEAsgI~------d~i~e~i~~~Lt~~g~~~~~i~~~nP~~--~~g~fy~  239 (511)
                      |||+.+.      ..-+..++. |+. ..+..++.+.||..  ..+.|..
T Consensus       278 DEAHhL~~~~~~~s~~y~lve~-La~-~~~~lLLLTATP~QlG~e~~Fa~  325 (955)
T PRK04914        278 DEAHHLVWSEEAPSREYQVVEQ-LAE-VIPGVLLLTATPEQLGQESHFAR  325 (955)
T ss_pred             HHHHHHCCCCCCCCHHHHHHHH-HHH-HCCCEEEEECCCCCCCCHHHHHH
T ss_conf             1344530588788879999999-985-15976998479988986668988


No 61 
>PRK06647 DNA polymerase III subunits gamma and tau; Validated
Probab=96.82  E-value=0.037  Score=32.24  Aligned_cols=149  Identities=15%  Similarity=0.055  Sum_probs=76.0

Q ss_pred             HHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEEE-CCHHHHHHHHHHHHHHHHH
Q ss_conf             999999999987405655542101246502576597899999999999808996699980-8589999999999999998
Q gi|254781215|r   55 QLEFMEVVDAHCLNSVNNPNPEVFKGAISAGRGIGKTTLNAWLVLWLMSTRPGISVICLA-NSETQLKTTLWAEVSKWLS  133 (511)
Q Consensus        55 Q~e~l~~i~~~~~~~~~~~~~~~~r~aV~sgrG~GKS~l~a~l~lw~l~~~p~~kv~vtA-pt~~Q~~~ilw~Ei~k~~~  133 (511)
                      |..+.+.+.....+++.-|     -.--...||+|||+++-.++-...|..++.--.|.- ++-.+        +    .
T Consensus        21 Qe~vv~~L~nai~~~rl~H-----AyLFsGprG~GKTt~ArilAk~LnC~~~~~~~PCg~C~sC~~--------i----~   83 (560)
T PRK06647         21 QDFVVETLKHSIEKNKIAN-----AYIFSGPRGVGKTSSARAFARCLNCVNGPTIMPCGECFSCKS--------I----D   83 (560)
T ss_pred             CHHHHHHHHHHHHCCCCCC-----EEEEECCCCCCHHHHHHHHHHHHCCCCCCCCCCCCCCHHHHH--------H----H
T ss_conf             4999999999997499774-----366328998789999999999965999999888878878888--------7----4


Q ss_pred             HCHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCCCCCCCHHHHCCCCCCEEEEECCHHCCCHHHHHHHHH
Q ss_conf             55000134443222222333444321112357861698530357556100212026761499971110299788988888
Q gi|254781215|r  134 LLPNKHWFEMQSLSLHPAPWYSDVLHCSLGIDSKHYSTMCRTYSEERPDTFVGHHNTYGMAIINDEASGTPDVINLGILG  213 (511)
Q Consensus       134 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~ea~~G~h~~~~~lvI~DEAsgI~d~i~e~i~~  213 (511)
                      .....+.++..+.                 .  .......|...  .--++....+.+. .+|+|||..+....|+++.-
T Consensus        84 ~g~~~DviEidaa-----------------s--n~~VddIR~l~--e~v~~~P~~~~yK-V~IIDEahmLt~~A~NALLK  141 (560)
T PRK06647         84 NDSSLDVIEIDGA-----------------S--NTSVQDVRQIK--EEIMFPPASSRYR-VYIIDEVHMLSNSAFNALLK  141 (560)
T ss_pred             CCCCCCEEEECCC-----------------C--CCCHHHHHHHH--HHHCCCCCCCCEE-EEEECCHHHCCHHHHHHHHH
T ss_conf             5999875764364-----------------5--48889999999--9863287668706-99964656559999999999


Q ss_pred             HHCCCCCCEE-EEEECCCCCCCCHHHHHHH
Q ss_conf             8507998138-9982389987655676530
Q gi|254781215|r  214 FLTERNANRF-WIMTSNPRRLSGKFYEIFN  242 (511)
Q Consensus       214 ~Lt~~g~~~~-~i~~~nP~~~~g~fy~~~~  242 (511)
                      +|-.+-.... ++++..|.+......-+|.
T Consensus       142 tLEEPP~~~~FILaTte~~KI~~TI~SRCQ  171 (560)
T PRK06647        142 TIEEPPPYIVFIFATTEVHKLPATIKSRCQ  171 (560)
T ss_pred             HHHCCCCCEEEEEECCCHHHCHHHHHHHHE
T ss_conf             863488755999977994768489996510


No 62 
>PRK06674 DNA polymerase III subunits gamma and tau; Validated
Probab=96.79  E-value=0.039  Score=32.07  Aligned_cols=150  Identities=14%  Similarity=0.110  Sum_probs=76.3

Q ss_pred             HHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEEECCHHHHHHHHHHHHHHHHHH
Q ss_conf             99999999998740565554210124650257659789999999999980899669998085899999999999999985
Q gi|254781215|r   55 QLEFMEVVDAHCLNSVNNPNPEVFKGAISAGRGIGKTTLNAWLVLWLMSTRPGISVICLANSETQLKTTLWAEVSKWLSL  134 (511)
Q Consensus        55 Q~e~l~~i~~~~~~~~~~~~~~~~r~aV~sgrG~GKS~l~a~l~lw~l~~~p~~kv~vtApt~~Q~~~ilw~Ei~k~~~~  134 (511)
                      |..+.+.+.....+++.-|     -.--.+.||+|||+++-.++-...|.+++..-.|--  -.    .    ... +..
T Consensus        21 Q~~v~~~L~nai~~~ri~H-----AyLF~GprGtGKts~Ari~AkaLnC~~~~~~~pC~~--C~----~----C~~-i~~   84 (563)
T PRK06674         21 QEHVTKTLQNALLQEKVSH-----AYLFSGPRGTGKTSIAKVFAKAVNCEHAPVAEPCNE--CP----S----CLG-ITN   84 (563)
T ss_pred             HHHHHHHHHHHHHCCCCCC-----EEEEECCCCCCHHHHHHHHHHHHCCCCCCCCCCCCC--CH----H----HHH-HHC
T ss_conf             0999999999998499650-----343128998689999999999857999999887766--87----8----999-855


Q ss_pred             CHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCCCCCCCHHHHCCCCCCEEEEECCHHCCCHHHHHHHHHH
Q ss_conf             50001344432222223334443211123578616985303575561002120267614999711102997889888888
Q gi|254781215|r  135 LPNKHWFEMQSLSLHPAPWYSDVLHCSLGIDSKHYSTMCRTYSEERPDTFVGHHNTYGMAIINDEASGTPDVINLGILGF  214 (511)
Q Consensus       135 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~ea~~G~h~~~~~lvI~DEAsgI~d~i~e~i~~~  214 (511)
                      ....+.++..+                 ...++  ....+..+.  --++.-..+.+ =.+|+||+..+....|+++.-+
T Consensus        85 g~~~DviEiDa-----------------asn~g--Vd~IR~i~~--~v~~~P~~~~y-KV~IIDeah~Lt~~A~NALLKt  142 (563)
T PRK06674         85 GSISDVLEIDA-----------------ASNNG--VDEIRDIRD--KVKFAPSAVEY-KVYIIDEVHMLSIGAFNALLKT  142 (563)
T ss_pred             CCCCCEEEECC-----------------CCCCC--HHHHHHHHH--HHCCCCCCCCE-EEEEEECHHHCCHHHHHHHHHH
T ss_conf             89987798525-----------------55578--799999999--82648867873-7999854563799999999998


Q ss_pred             HCCCCCCEE-EEEECCCCCCCCHHHHHHH
Q ss_conf             507998138-9982389987655676530
Q gi|254781215|r  215 LTERNANRF-WIMTSNPRRLSGKFYEIFN  242 (511)
Q Consensus       215 Lt~~g~~~~-~i~~~nP~~~~g~fy~~~~  242 (511)
                      |-.+-...+ ++++.+|.+..-...-.|.
T Consensus       143 LEEPP~~viFILaTtep~ki~~TI~SRCQ  171 (563)
T PRK06674        143 LEEPPGHVIFILATTEPHKIPPTIISRCQ  171 (563)
T ss_pred             HHCCCCCEEEEEECCCHHHCCHHHHHHHE
T ss_conf             63887564999965994758478873310


No 63 
>PRK12323 DNA polymerase III subunits gamma and tau; Provisional
Probab=96.77  E-value=0.04  Score=31.97  Aligned_cols=152  Identities=15%  Similarity=0.125  Sum_probs=79.0

Q ss_pred             HHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEEECCHHHHHHHHHHHHHHHHHH
Q ss_conf             99999999998740565554210124650257659789999999999980899669998085899999999999999985
Q gi|254781215|r   55 QLEFMEVVDAHCLNSVNNPNPEVFKGAISAGRGIGKTTLNAWLVLWLMSTRPGISVICLANSETQLKTTLWAEVSKWLSL  134 (511)
Q Consensus        55 Q~e~l~~i~~~~~~~~~~~~~~~~r~aV~sgrG~GKS~l~a~l~lw~l~~~p~~kv~vtApt~~Q~~~ilw~Ei~k~~~~  134 (511)
                      |.-+++.+...+..++.-|     -..-..-||+|||+++-.++--.-|..++...-+|+.--.+-. .+ .+|    ..
T Consensus        21 Q~~v~~~l~na~~~~r~~h-----aylf~G~rGvGKTt~ari~Ak~lnc~~~~~~~g~~~~pcg~C~-~C-~~i----~~   89 (721)
T PRK12323         21 QEHVVRALTHALEQQRLHH-----AYLFTGTRGVGKTTLSRILAKSLNCTGPDGEGGITAQPCGQCR-AC-TEI----DA   89 (721)
T ss_pred             CHHHHHHHHHHHHCCCCCC-----EEEEECCCCCCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCH-HH-HHH----HC
T ss_conf             5999999999997199754-----4750279988898999999999768998667898788787765-46-877----56


Q ss_pred             CHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCCCCCCCHHHHCCCCCCEEEEECCHHCCCHHHHHHHHHH
Q ss_conf             50001344432222223334443211123578616985303575561002120267614999711102997889888888
Q gi|254781215|r  135 LPNKHWFEMQSLSLHPAPWYSDVLHCSLGIDSKHYSTMCRTYSEERPDTFVGHHNTYGMAIINDEASGTPDVINLGILGF  214 (511)
Q Consensus       135 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~ea~~G~h~~~~~lvI~DEAsgI~d~i~e~i~~~  214 (511)
                                       +...|...++-....+  ....|.... | -.+.-..+.+ -.+|+||.+.+....|+++.-|
T Consensus        90 -----------------g~~~d~~EiDaas~~~--v~~~r~l~~-~-~~y~P~~~~~-KvyiiDevhmls~~afnalLKt  147 (721)
T PRK12323         90 -----------------GRFVDYIEMDAASNRG--VDEMAQLLD-Q-AVYAPTAGRF-KVYMIDEVHMLTNHAFNAMLKT  147 (721)
T ss_pred             -----------------CCCCCEEEEECCCCCC--HHHHHHHHH-H-CCCCCCCCCE-EEEEEECCCCCCHHHHHHHHHH
T ss_conf             -----------------8987647743676788--899999998-5-4558876644-6999854000589999999984


Q ss_pred             HCCCCCCEE-EEEECCCCCCCCHHHH
Q ss_conf             507998138-9982389987655676
Q gi|254781215|r  215 LTERNANRF-WIMTSNPRRLSGKFYE  239 (511)
Q Consensus       215 Lt~~g~~~~-~i~~~nP~~~~g~fy~  239 (511)
                      |-.+=...+ ++++..|.+..-..--
T Consensus       148 lEePP~hv~FilaTT~~~Kip~TilS  173 (721)
T PRK12323        148 LEEPPPHVKFILATTDPQKIPVTVLS  173 (721)
T ss_pred             HCCCCCCEEEEEECCCHHHCCHHHHH
T ss_conf             01797553899943863448588987


No 64 
>pfam05127 DUF699 Putative ATPase (DUF699). This putative domain is about 350 amino acid residues long and appears to have a P-loop motif, suggesting this is an ATPase. This domain is often associated with pfam00583. This domain is found in isolation in the uncharacterized protein HI1254 from Haemophilus influenzae.
Probab=96.77  E-value=0.04  Score=31.97  Aligned_cols=92  Identities=17%  Similarity=0.107  Sum_probs=48.9

Q ss_pred             HHHHHHHCCCCEEEEEECCHHHHHHHHHHHHHHHHHHCHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCC
Q ss_conf             99999808996699980858999999999999999855000134443222222333444321112357861698530357
Q gi|254781215|r   98 VLWLMSTRPGISVICLANSETQLKTTLWAEVSKWLSLLPNKHWFEMQSLSLHPAPWYSDVLHCSLGIDSKHYSTMCRTYS  177 (511)
Q Consensus        98 ~lw~l~~~p~~kv~vtApt~~Q~~~ilw~Ei~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s  177 (511)
                      ++-.++..-.++|+||||+...+. .+|.-+.+-++.+....        .     ..+.....+.......       .
T Consensus         4 a~a~li~~~~~~I~VTAP~~~nv~-~lf~~~~~~L~~lg~~~--------~-----~~~~~~~~~~~~~~~i-------~   62 (160)
T pfam05127         4 AAAALIAQGYSRILVTAPSPANVQ-TLFEFAIKGLDALGYKP--------K-----KREGIIASLRGNGQRI-------R   62 (160)
T ss_pred             HHHHHHHCCCCEEEEECCCHHHHH-HHHHHHHHHHHHCCCCC--------C-----CCCCCEEEEECCCEEE-------E
T ss_conf             999999859973999799989999-99999999998638643--------4-----5655047875287689-------9


Q ss_pred             CCCCCHHHHCCCCCCEEEEECCHHCCCHHHHHHH
Q ss_conf             5561002120267614999711102997889888
Q gi|254781215|r  178 EERPDTFVGHHNTYGMAIINDEASGTPDVINLGI  211 (511)
Q Consensus       178 ~~~~ea~~G~h~~~~~lvI~DEAsgI~d~i~e~i  211 (511)
                      -..|+.+--.. ....++|+||||.||-.+...+
T Consensus        63 f~~Pd~l~~~~-~~~DllvVDEAAaIP~p~L~~l   95 (160)
T pfam05127        63 FIAPDELLKLP-PQADLLVVDEAAAIPLPLLKQL   95 (160)
T ss_pred             EECCHHHHHCC-CCCCEEEEEHHHCCCHHHHHHH
T ss_conf             96808986167-8776899732421888999999


No 65 
>PRK12402 replication factor C small subunit 2; Reviewed
Probab=96.75  E-value=0.038  Score=32.11  Aligned_cols=165  Identities=16%  Similarity=0.078  Sum_probs=75.2

Q ss_pred             CCCCCCC--CCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEEE
Q ss_conf             1455777--56555784589999999999987405655542101246502576597899999999999808996699980
Q gi|254781215|r   37 PWGEKGT--PLEGFSAPRSWQLEFMEVVDAHCLNSVNNPNPEVFKGAISAGRGIGKTTLNAWLVLWLMSTRPGISVICLA  114 (511)
Q Consensus        37 ~w~~~~~--~~~~~~~P~~WQ~e~l~~i~~~~~~~~~~~~~~~~r~aV~sgrG~GKS~l~a~l~lw~l~~~p~~kv~vtA  114 (511)
                      +|-+|-.  .+..+.|    |.++.+.+.....++.   .|.   +-..++.|+|||+++-.++-....-..+..+...-
T Consensus         4 lWveKYRP~~~~dvvG----q~~i~~~L~~~~~~~~---~ph---lLf~GPpG~GKTt~A~~lA~~l~~~~~~~~~~~~n   73 (337)
T PRK12402          4 LWTEKYRPSLFEDILG----QESVVDHLSALAASGN---LPH---LVVYGPSGSGKTAAVRALARELYGDPWENNFTYFN   73 (337)
T ss_pred             CCCCCCCCCCHHHHCC----CHHHHHHHHHHHHCCC---CCE---EEEECCCCCCHHHHHHHHHHHHCCCCCCCCCCEEC
T ss_conf             5321418897998039----7999999999997799---876---98889298489999999999967997567833311


Q ss_pred             CCH--HHHHHHHHHHHHHHHHHCHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCCCCCCCHHHHCCCCCC
Q ss_conf             858--999999999999999855000134443222222333444321112357861698530357556100212026761
Q gi|254781215|r  115 NSE--TQLKTTLWAEVSKWLSLLPNKHWFEMQSLSLHPAPWYSDVLHCSLGIDSKHYSTMCRTYSEERPDTFVGHHNTYG  192 (511)
Q Consensus       115 pt~--~Q~~~ilw~Ei~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~ea~~G~h~~~~  192 (511)
                      .+.  .+-+.    .+..   .....+        .....-...          .......+..-. .-.+..-..+.+ 
T Consensus        74 asd~~~~~~~----~i~~---~~~~~~--------~~~~~~~~~----------~~~~d~i~~ii~-~~a~~~p~~~~~-  126 (337)
T PRK12402         74 VSDFFDQGKK----YLVE---DPRFAH--------FYDDPKRKY----------KSVIDNFKHILK-EYASMRPLSADY-  126 (337)
T ss_pred             CCCCCCCCCC----EEEC---CCCHHH--------HHCCHHHCC----------CCHHHHHHHHHH-HHHCCCCCCCCE-
T ss_conf             6531135640----0101---664234--------420153327----------737899999999-986148877880-


Q ss_pred             EEEEECCHHCCCHHHHHHHHHHHCCCCCCEE-EEEECCCCCCCCHHH
Q ss_conf             4999711102997889888888507998138-998238998765567
Q gi|254781215|r  193 MAIINDEASGTPDVINLGILGFLTERNANRF-WIMTSNPRRLSGKFY  238 (511)
Q Consensus       193 ~lvI~DEAsgI~d~i~e~i~~~Lt~~g~~~~-~i~~~nP~~~~g~fy  238 (511)
                      -++|+|||..+......++..+|-....... ++++.+|.+..-...
T Consensus       127 KiiIlDEad~lt~~Aq~aLlk~lEe~~~~~~fIl~t~~~~~ii~tI~  173 (337)
T PRK12402        127 KLILFDNAEALREDAQQALRRIMERYSETCRFIFSTTQPSKLIPPIR  173 (337)
T ss_pred             EEEEEECCCCCCHHHHHHHHHHHHCCCCCEEEEEECCCCCCCCHHHH
T ss_conf             49997071317999999999887408876699872386444752477


No 66 
>PRK13767 ATP-dependent helicase; Provisional
Probab=96.74  E-value=0.033  Score=32.49  Aligned_cols=63  Identities=19%  Similarity=0.125  Sum_probs=44.3

Q ss_pred             CCCCHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCCCHHHHHHHHH-HHHHHH-------CCCCEEEEEECCHHH
Q ss_conf             578458999999999998740565554210124650257659789999999-999980-------899669998085899
Q gi|254781215|r   48 FSAPRSWQLEFMEVVDAHCLNSVNNPNPEVFKGAISAGRGIGKTTLNAWLV-LWLMST-------RPGISVICLANSETQ  119 (511)
Q Consensus        48 ~~~P~~WQ~e~l~~i~~~~~~~~~~~~~~~~r~aV~sgrG~GKS~l~a~l~-lw~l~~-------~p~~kv~vtApt~~Q  119 (511)
                      |..|.+-|+++...|.+..            -+-|.++.|.||| +++++- +--+..       .++..++++.|...=
T Consensus        30 ~~~p~~~Q~~a~~~i~~G~------------~~Li~ApTGsGKT-lAaflp~l~~l~~~~~~~~~~~~~~~LyIsPLkAL   96 (878)
T PRK13767         30 FGTFTPPQRYAIPLIHEGK------------NVLISSPTGSGKT-LAAFLGIIDELFRLAEEGELEDSVYCIYVSPLRAL   96 (878)
T ss_pred             CCCCCHHHHHHHHHHHCCC------------CEEEECCCCCHHH-HHHHHHHHHHHHHHCCCCCCCCCEEEEEECCHHHH
T ss_conf             7999989999999996799------------8899899981399-99999999999850003677887289996847988


Q ss_pred             HHHH
Q ss_conf             9999
Q gi|254781215|r  120 LKTT  123 (511)
Q Consensus       120 ~~~i  123 (511)
                      ++|+
T Consensus        97 ~~D~  100 (878)
T PRK13767         97 NNDI  100 (878)
T ss_pred             HHHH
T ss_conf             9999


No 67 
>PRK07133 DNA polymerase III subunits gamma and tau; Validated
Probab=96.74  E-value=0.042  Score=31.84  Aligned_cols=139  Identities=16%  Similarity=0.116  Sum_probs=74.9

Q ss_pred             HHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHHCCCC----EEEEEECCHHHHHHHHHHHHHH
Q ss_conf             999999999987405655542101246502576597899999999999808996----6999808589999999999999
Q gi|254781215|r   55 QLEFMEVVDAHCLNSVNNPNPEVFKGAISAGRGIGKTTLNAWLVLWLMSTRPGI----SVICLANSETQLKTTLWAEVSK  130 (511)
Q Consensus        55 Q~e~l~~i~~~~~~~~~~~~~~~~r~aV~sgrG~GKS~l~a~l~lw~l~~~p~~----kv~vtApt~~Q~~~ilw~Ei~k  130 (511)
                      |..+.+.+.....+++.-|     ...-.+.||+|||+++-.++-...|.++..    ...|.+..              
T Consensus        23 Qe~Vv~tL~nAI~~gRIaH-----AYLF~GPRGvGKTT~ARIfAKaLNC~~~~d~~~pC~~C~~~~--------------   83 (718)
T PRK07133         23 QDHIIETLKNIIKSGKISH-----AYLFSGPHGTGKTSVAKIFANALNCSHKTDLIEPCQNCIENF--------------   83 (718)
T ss_pred             CHHHHHHHHHHHHCCCCCC-----EEEEECCCCCCHHHHHHHHHHHHCCCCCCCCCCCCCCHHHCC--------------
T ss_conf             5999999999997499750-----586238998688999999999967999999999770214304--------------


Q ss_pred             HHHHCHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCCCCCCCHHHHCCCCCCEEEEECCHHCCCHHHHHH
Q ss_conf             99855000134443222222333444321112357861698530357556100212026761499971110299788988
Q gi|254781215|r  131 WLSLLPNKHWFEMQSLSLHPAPWYSDVLHCSLGIDSKHYSTMCRTYSEERPDTFVGHHNTYGMAIINDEASGTPDVINLG  210 (511)
Q Consensus       131 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~ea~~G~h~~~~~lvI~DEAsgI~d~i~e~  210 (511)
                        ...                   .+...++.....+  ....|....  .-++....+.+- .+|+||++.+....|.+
T Consensus        84 --~~s-------------------~DViEIDAASn~g--VDdIReLie--~v~y~P~~gkYK-VyIIDEvHMLS~~AfNA  137 (718)
T PRK07133         84 --NNN-------------------LDIIEMDAASNNG--VDEIRELRE--NVKNLPQISKYK-IYIIDEVHMLSKSAFNA  137 (718)
T ss_pred             --CCC-------------------CCEEEECCCCCCC--HHHHHHHHH--HHCCCCCCCCEE-EEEEECCCCCCHHHHHH
T ss_conf             --789-------------------8737754556688--899999999--825588778724-99996620079999999


Q ss_pred             HHHHHCCCCCC-EEEEEECCCCCCCCHHH
Q ss_conf             88885079981-38998238998765567
Q gi|254781215|r  211 ILGFLTERNAN-RFWIMTSNPRRLSGKFY  238 (511)
Q Consensus       211 i~~~Lt~~g~~-~~~i~~~nP~~~~g~fy  238 (511)
                      +.-+|-.+-.. .+++++..|....-..-
T Consensus       138 LLKtLEEPP~hvvFILaTTep~KIP~TIl  166 (718)
T PRK07133        138 LLKTLEEPPKHVIFILATTDVQKIPLTIL  166 (718)
T ss_pred             HHHHHCCCCCCCEEEEEECCHHHCCHHHH
T ss_conf             99850279878279997088254848774


No 68 
>PRK08451 DNA polymerase III subunits gamma and tau; Validated
Probab=96.72  E-value=0.044  Score=31.74  Aligned_cols=149  Identities=18%  Similarity=0.088  Sum_probs=76.8

Q ss_pred             HHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEEECCHHHHHHHHHHHHHHHHHH
Q ss_conf             99999999998740565554210124650257659789999999999980899669998085899999999999999985
Q gi|254781215|r   55 QLEFMEVVDAHCLNSVNNPNPEVFKGAISAGRGIGKTTLNAWLVLWLMSTRPGISVICLANSETQLKTTLWAEVSKWLSL  134 (511)
Q Consensus        55 Q~e~l~~i~~~~~~~~~~~~~~~~r~aV~sgrG~GKS~l~a~l~lw~l~~~p~~kv~vtApt~~Q~~~ilw~Ei~k~~~~  134 (511)
                      |..+.+.+.....+++.-|     -..-.+.||+|||+++-.++-+..|..++..-.|--  -..-+        . +..
T Consensus        19 Qe~iv~~L~nAi~~~Rl~H-----AYLFsGPrGvGKTt~ArifAkaLnC~~~~~~~PCg~--C~sC~--------~-i~~   82 (523)
T PRK08451         19 QESVSKTLSLALDNNRLAH-----AYLFSGLRGSGKTSSARIFSRALVCEQGPSSTPCGT--CAQCQ--------A-ALE   82 (523)
T ss_pred             CHHHHHHHHHHHHCCCCCC-----EEEEECCCCCCHHHHHHHHHHHHCCCCCCCCCCCCC--CHHHH--------H-HHC
T ss_conf             4999999999998599671-----587578998688999999999975999999898887--88899--------9-864


Q ss_pred             CHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCCCCCCCHHHHCCCCCCEEEEECCHHCCCHHHHHHHHHH
Q ss_conf             50001344432222223334443211123578616985303575561002120267614999711102997889888888
Q gi|254781215|r  135 LPNKHWFEMQSLSLHPAPWYSDVLHCSLGIDSKHYSTMCRTYSEERPDTFVGHHNTYGMAIINDEASGTPDVINLGILGF  214 (511)
Q Consensus       135 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~ea~~G~h~~~~~lvI~DEAsgI~d~i~e~i~~~  214 (511)
                      ....+..+..+..-                   ......|....  .-++....+.+. .+|+|||..+....|+++.-+
T Consensus        83 g~hpDViEiDaasn-------------------~gID~IReLie--~~~~~P~~gryK-V~IIDEah~Lt~~A~NALLKT  140 (523)
T PRK08451         83 GRHIDIIEMDAASN-------------------RGIDDIRNLIE--QTKYKPSMARFK-IFIIDEVHMLTKEAFNALLKT  140 (523)
T ss_pred             CCCCCEEEECCCCC-------------------CCHHHHHHHHH--HHCCCCCCCCEE-EEEEECCCCCCHHHHHHHHHH
T ss_conf             89998551055333-------------------68999999999--723588679727-999826030489999999997


Q ss_pred             HCCCCCC-EEEEEECCCCCCCCHHHHHH
Q ss_conf             5079981-38998238998765567653
Q gi|254781215|r  215 LTERNAN-RFWIMTSNPRRLSGKFYEIF  241 (511)
Q Consensus       215 Lt~~g~~-~~~i~~~nP~~~~g~fy~~~  241 (511)
                      |-.+-.. .+++++..|.+..-...-++
T Consensus       141 LEEPP~~vvFILaTTep~KLp~TIlSRC  168 (523)
T PRK08451        141 LEEPPSYVKFILATTDPLKLPATILSRT  168 (523)
T ss_pred             CCCCCCCCEEEEECCCHHHCHHHHHHHH
T ss_conf             0389878379997599476848887420


No 69 
>PRK07764 DNA polymerase III subunits gamma and tau; Validated
Probab=96.68  E-value=0.0089  Score=36.11  Aligned_cols=152  Identities=18%  Similarity=0.117  Sum_probs=78.2

Q ss_pred             HHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEEECCHHHHHHHHHHHHHHHHHH
Q ss_conf             99999999998740565554210124650257659789999999999980899669998085899999999999999985
Q gi|254781215|r   55 QLEFMEVVDAHCLNSVNNPNPEVFKGAISAGRGIGKTTLNAWLVLWLMSTRPGISVICLANSETQLKTTLWAEVSKWLSL  134 (511)
Q Consensus        55 Q~e~l~~i~~~~~~~~~~~~~~~~r~aV~sgrG~GKS~l~a~l~lw~l~~~p~~kv~vtApt~~Q~~~ilw~Ei~k~~~~  134 (511)
                      |..+.+.+...+.+++.-|     -..-...||+|||+++-+++-...|......--|..  -.        ........
T Consensus        20 Qe~v~~~L~~Ai~~gri~H-----AYLFsGprG~GKTt~ARilAkaLNC~~~~~~~PCg~--C~--------sC~~i~~g   84 (775)
T PRK07764         20 QEHVTEPLSTALDSGRINH-----AYLFSGPRGCGKTSSARILARSLNCAQGPTSTPCGV--CD--------SCVALAPG   84 (775)
T ss_pred             CHHHHHHHHHHHHCCCCCC-----EEEEECCCCCCHHHHHHHHHHHHCCCCCCCCCCCCC--CH--------HHHHHHCC
T ss_conf             5999999999998199763-----376237888788899999999966899999898888--76--------37888638


Q ss_pred             C-HHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCCCCCCCHHHHCCCCCCEEEEECCHHCCCHHHHHHHHH
Q ss_conf             5-000134443222222333444321112357861698530357556100212026761499971110299788988888
Q gi|254781215|r  135 L-PNKHWFEMQSLSLHPAPWYSDVLHCSLGIDSKHYSTMCRTYSEERPDTFVGHHNTYGMAIINDEASGTPDVINLGILG  213 (511)
Q Consensus       135 ~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~ea~~G~h~~~~~lvI~DEAsgI~d~i~e~i~~  213 (511)
                      . ...+.++..+                 ..+++  ....|..++  --.+.=..+.+. .+|+||++.+....|+++.-
T Consensus        85 ~~~~~DviEiDA-----------------AS~~g--VddiReL~e--~~~y~P~~~ryK-VyIIDEaHmls~~afNALLK  142 (775)
T PRK07764         85 GPGSLDVVEIDA-----------------ASHGG--VDDARELRE--RAFFAPAQSRYR-IFIIDEAHMVTTAGFNALLK  142 (775)
T ss_pred             CCCCCCEEEECC-----------------CCCCC--HHHHHHHHH--HCCCCCCCCCEE-EEEEECHHHHCHHHHHHHHH
T ss_conf             988886687315-----------------65568--899999998--547687678635-99985354407999999988


Q ss_pred             HHCCCCCCE-EEEEECCCCCCCCHHHHHHHC
Q ss_conf             850799813-899823899876556765303
Q gi|254781215|r  214 FLTERNANR-FWIMTSNPRRLSGKFYEIFNK  243 (511)
Q Consensus       214 ~Lt~~g~~~-~~i~~~nP~~~~g~fy~~~~~  243 (511)
                      +|-+.-... +++++..|.+.-....-.|++
T Consensus       143 tLEEPP~hvvFIlaTTep~kip~TI~SRcq~  173 (775)
T PRK07764        143 IVEEPPEHLIFIFATTEPEKVIGTIRSRTHH  173 (775)
T ss_pred             HHCCCCCCEEEEEECCCHHHCCHHHHHHCCC
T ss_conf             6227864627999548735471677641023


No 70 
>PRK08691 DNA polymerase III subunits gamma and tau; Validated
Probab=96.63  E-value=0.05  Score=31.36  Aligned_cols=149  Identities=17%  Similarity=0.183  Sum_probs=75.9

Q ss_pred             HHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEEECCHHHHHHHHHHHHHHHHHH
Q ss_conf             99999999998740565554210124650257659789999999999980899669998085899999999999999985
Q gi|254781215|r   55 QLEFMEVVDAHCLNSVNNPNPEVFKGAISAGRGIGKTTLNAWLVLWLMSTRPGISVICLANSETQLKTTLWAEVSKWLSL  134 (511)
Q Consensus        55 Q~e~l~~i~~~~~~~~~~~~~~~~r~aV~sgrG~GKS~l~a~l~lw~l~~~p~~kv~vtApt~~Q~~~ilw~Ei~k~~~~  134 (511)
                      |.-+++.+...+.+++. |+.    ..-...||+|||+++-.++...-|..+..--.|..=  ..-     .+|    ..
T Consensus        21 Q~~v~~~L~nal~~~rl-~ha----ylf~G~rGvGKTt~Ari~Ak~lNC~~~~~~~pCg~C--~~C-----~~i----~~   84 (704)
T PRK08691         21 QEHVVKALQNALDEGRL-HHA----YLLTGTRGVGKTTIARILAKSLNCENAQHGEPCGVC--QSC-----TQI----DA   84 (704)
T ss_pred             CHHHHHHHHHHHHHCCC-CCE----EEEECCCCCCHHHHHHHHHHHHCCCCCCCCCCCCCC--HHH-----HHH----HC
T ss_conf             69999999999981997-523----750278987888999999999679999999978777--767-----878----55


Q ss_pred             CHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCCCCCCCHHHHCCCCCCEEEEECCHHCCCHHHHHHHHHH
Q ss_conf             50001344432222223334443211123578616985303575561002120267614999711102997889888888
Q gi|254781215|r  135 LPNKHWFEMQSLSLHPAPWYSDVLHCSLGIDSKHYSTMCRTYSEERPDTFVGHHNTYGMAIINDEASGTPDVINLGILGF  214 (511)
Q Consensus       135 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~ea~~G~h~~~~~lvI~DEAsgI~d~i~e~i~~~  214 (511)
                                       +...|...++-....+  ....|.... + -.+.-..+.+. .+|+||++.+....|+++.-+
T Consensus        85 -----------------g~~~D~~EiDaAs~~~--vdd~R~l~~-~-~~y~P~~~~yK-VyiiDEvhmLs~~afNAlLKt  142 (704)
T PRK08691         85 -----------------GRYVDLLEIDAASNTG--IDNIREVLE-N-AQYAPTAGKYK-VYIIDEVHMLSKSAFNAMLKT  142 (704)
T ss_pred             -----------------CCCCCEEEEECCCCCC--HHHHHHHHH-H-CCCCCCCCCEE-EEEEECHHHCCHHHHHHHHHH
T ss_conf             -----------------8998747742454458--899999998-5-34688678535-999831544389999999986


Q ss_pred             HCCCCCC-EEEEEECCCCCCCCHHHHHH
Q ss_conf             5079981-38998238998765567653
Q gi|254781215|r  215 LTERNAN-RFWIMTSNPRRLSGKFYEIF  241 (511)
Q Consensus       215 Lt~~g~~-~~~i~~~nP~~~~g~fy~~~  241 (511)
                      |-++=.. .+++++..|.+..-..--.|
T Consensus       143 LEEPP~~v~FilaTTdp~Klp~TIlSRC  170 (704)
T PRK08691        143 LEEPPEHVKFILATTDPHKVPVTVLSRC  170 (704)
T ss_pred             HCCCCCCEEEEEECCCHHHCCHHHHHHH
T ss_conf             1479756089985488464758999888


No 71 
>PRK05707 DNA polymerase III subunit delta'; Validated
Probab=96.60  E-value=0.053  Score=31.22  Aligned_cols=152  Identities=15%  Similarity=0.128  Sum_probs=72.1

Q ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEEECCHHHHHHHHHHHHHHHHHHCHHCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             24650257659789999999999980899669998085899999999999999985500013444322222233344432
Q gi|254781215|r   79 KGAISAGRGIGKTTLNAWLVLWLMSTRPGISVICLANSETQLKTTLWAEVSKWLSLLPNKHWFEMQSLSLHPAPWYSDVL  158 (511)
Q Consensus        79 r~aV~sgrG~GKS~l~a~l~lw~l~~~p~~kv~vtApt~~Q~~~ilw~Ei~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~  158 (511)
                      -.-..+..|+||+.++-.++-+.+|.+|...-.|..-..=+.  +       ....-|..++..-...   .....++..
T Consensus        24 A~Lf~G~~G~GK~~lA~~~A~~LlC~~~~~~~~Cg~C~sC~~--~-------~~~~HPD~~~i~pe~~---~~~I~IdqI   91 (328)
T PRK05707         24 AYLLHGPAGIGKRALAERLAAFLLCEAPQGGGACGSCKGCQL--L-------AAGSHPDNFVLEPEEA---DKPIKVDQV   91 (328)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHCCCCCCCCCCCCCHHHHH--H-------HCCCCCCEEEEECCCC---CCCCCHHHH
T ss_conf             464479998679999999999984899999899988889999--8-------7589998799842666---776979999


Q ss_pred             CCCCCCCCCEEEEEECCCCCCCCCHHHHCCCCCCEEEEECCHHCCCHHHHHHHHHHHCCCCCCEEEE-EECCCCCCCCHH
Q ss_conf             1112357861698530357556100212026761499971110299788988888850799813899-823899876556
Q gi|254781215|r  159 HCSLGIDSKHYSTMCRTYSEERPDTFVGHHNTYGMAIINDEASGTPDVINLGILGFLTERNANRFWI-MTSNPRRLSGKF  237 (511)
Q Consensus       159 ~~~~~~~~~~~~~~~~~~s~~~~ea~~G~h~~~~~lvI~DEAsgI~d~i~e~i~~~Lt~~g~~~~~i-~~~nP~~~~g~f  237 (511)
                                     |...  .--+.....+.+. .+|+|+|..+.....+++.-+|-++.....++ .+.+|.+.--..
T Consensus        92 ---------------R~l~--~~~~~~~~~g~~K-V~iI~~Ae~m~~~AaNALLKtLEEPp~~t~fiL~t~~~~~lLpTI  153 (328)
T PRK05707         92 ---------------RELV--SFVVQTAQLGGRK-VVLIEPAEAMNRNAANALLKSLEEPSGQTVLLLISHQPSRLLPTI  153 (328)
T ss_pred             ---------------HHHH--HHHHHCCCCCCCE-EEEEEHHHHHCHHHHHHHHHHHHCCCCCEEEEEEECCHHHCHHHH
T ss_conf             ---------------9999--9983176678957-999502877389999999998507898759998609934482588


Q ss_pred             HHHHHCCCCCCEEEEECCCCCCCCCHHHHHHHHHH
Q ss_conf             76530352474179840433677897789999975
Q gi|254781215|r  238 YEIFNKPLDDWKRFQIDTRTVEGIDPSFHEGIIAR  272 (511)
Q Consensus       238 y~~~~~~~~~w~~~~i~~~~~p~~~~~~ie~~~~~  272 (511)
                      .-++..       +.+     +..+.+.+.+|..+
T Consensus       154 ~SRCq~-------~~~-----~~p~~e~~~~~L~~  176 (328)
T PRK05707        154 KSRCQQ-------LAC-----PLPSNEPSLQWLQQ  176 (328)
T ss_pred             HHCCEE-------EEC-----CCCCHHHHHHHHHH
T ss_conf             741413-------348-----99899999999997


No 72 
>COG1199 DinG Rad3-related DNA helicases [Transcription / DNA replication, recombination, and repair]
Probab=96.59  E-value=0.023  Score=33.46  Aligned_cols=65  Identities=25%  Similarity=0.148  Sum_probs=49.7

Q ss_pred             CHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEEECCHHHHHHHH
Q ss_conf             45899999999999874056555421012465025765978999999999998089966999808589999999
Q gi|254781215|r   51 PRSWQLEFMEVVDAHCLNSVNNPNPEVFKGAISAGRGIGKTTLNAWLVLWLMSTRPGISVICLANSETQLKTTL  124 (511)
Q Consensus        51 P~~WQ~e~l~~i~~~~~~~~~~~~~~~~r~aV~sgrG~GKS~l~a~l~lw~l~~~p~~kv~vtApt~~Q~~~il  124 (511)
                      ||+.|++++..|+.-..++.        .+.+-+|-|+|||...-..++-+..... .++++..+|..+...++
T Consensus        16 ~r~~Q~~~~~~v~~a~~~~~--------~~~iEapTGtGKTl~yL~~al~~~~~~~-~~viist~t~~lq~q~~   80 (654)
T COG1199          16 PRPEQREMAEAVAEALKGGE--------GLLIEAPTGTGKTLAYLLPALAYAREEG-KKVIISTRTKALQEQLL   80 (654)
T ss_pred             CCHHHHHHHHHHHHHHHCCC--------EEEEECCCCCCHHHHHHHHHHHHHHHCC-CEEEEECCCHHHHHHHH
T ss_conf             89899999999999981687--------1899889985175999999998677529-75999899576888987


No 73 
>PRK08058 DNA polymerase III subunit delta'; Validated
Probab=96.57  E-value=0.055  Score=31.10  Aligned_cols=154  Identities=14%  Similarity=0.152  Sum_probs=83.2

Q ss_pred             HHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHHCCC-------------------CEEEEEEC
Q ss_conf             99999999998740565554210124650257659789999999999980899-------------------66999808
Q gi|254781215|r   55 QLEFMEVVDAHCLNSVNNPNPEVFKGAISAGRGIGKTTLNAWLVLWLMSTRPG-------------------ISVICLAN  115 (511)
Q Consensus        55 Q~e~l~~i~~~~~~~~~~~~~~~~r~aV~sgrG~GKS~l~a~l~lw~l~~~p~-------------------~kv~vtAp  115 (511)
                      |..+.+.+..-..+|..-|     -.-..+..|+||+.++-.++-+.+|..+.                   .-+.++.|
T Consensus        11 Q~~i~~~L~~~i~~~rl~H-----A~Lf~Gp~G~GK~~~A~~~A~~LlC~~~~~~~~Cg~C~~C~~~~~~~HPD~~~i~p   85 (329)
T PRK08058         11 QPIVVKMLQNSIAKNRLAH-----AYLFEGAKGTGKKATALWLAKSLFCLERNGVEPCGTCTNCKRIESGNHPDVHLVAP   85 (329)
T ss_pred             HHHHHHHHHHHHHCCCCCC-----EEEEECCCCCCHHHHHHHHHHHHCCCCCCCCCCCCCCHHHHHHHCCCCCCEEEECC
T ss_conf             8999999999998599661-----56557899988999999999997399999999887888999987699997677456


Q ss_pred             CHHHHHHHHHHHHHHHHHHCHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCCCCCCCHHHHCCCCCCEEE
Q ss_conf             58999999999999999855000134443222222333444321112357861698530357556100212026761499
Q gi|254781215|r  116 SETQLKTTLWAEVSKWLSLLPNKHWFEMQSLSLHPAPWYSDVLHCSLGIDSKHYSTMCRTYSEERPDTFVGHHNTYGMAI  195 (511)
Q Consensus       116 t~~Q~~~ilw~Ei~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~ea~~G~h~~~~~lv  195 (511)
                      ...+.+   -.+|+...+..                                               +.....+.+. .+
T Consensus        86 ~~~~i~---idqiR~L~~~~-----------------------------------------------~~~p~~g~~K-V~  114 (329)
T PRK08058         86 DGQSIK---KDQIRYLKEEF-----------------------------------------------SKSGVESNKK-VY  114 (329)
T ss_pred             CCCCCC---HHHHHHHHHHH-----------------------------------------------CCCCCCCCCE-EE
T ss_conf             614077---99999999996-----------------------------------------------4387578867-99


Q ss_pred             EECCHHCCCHHHHHHHHHHHCCCCCCEEEE-EECCCCCCCCHHHHHHHCCCCCCEEEEECCCCCCCCCHHHHHHHHHHCC
Q ss_conf             971110299788988888850799813899-8238998765567653035247417984043367789778999997518
Q gi|254781215|r  196 INDEASGTPDVINLGILGFLTERNANRFWI-MTSNPRRLSGKFYEIFNKPLDDWKRFQIDTRTVEGIDPSFHEGIIARYG  274 (511)
Q Consensus       196 I~DEAsgI~d~i~e~i~~~Lt~~g~~~~~i-~~~nP~~~~g~fy~~~~~~~~~w~~~~i~~~~~p~~~~~~ie~~~~~~g  274 (511)
                      |+|||..+.....+++.-+|-.+.+..+++ .+.+|.+.--...-++       ..+.+     +.++.+.+.++..+-|
T Consensus       115 II~~Ae~m~~~AaNALLKtLEEPp~~t~fIL~t~~~~~lLpTI~SRC-------q~i~f-----~~~~~~~i~~~L~~~~  182 (329)
T PRK08058        115 IIEHADKMTASAANSLLKFLEEPSGDTTAILLTENKHQILPTILSRC-------QVVEF-----RPLPPESLIQRLQEEG  182 (329)
T ss_pred             EEECHHHHCHHHHHHHHHHHHCCCCCCEEEEEECCHHHHHHHHHHCC-------EEEEC-----CCCCHHHHHHHHHHCC
T ss_conf             97347762999999999986468978679987299666436886314-------25658-----8999999999999879


Q ss_pred             CC
Q ss_conf             98
Q gi|254781215|r  275 LD  276 (511)
Q Consensus       275 ed  276 (511)
                      .+
T Consensus       183 i~  184 (329)
T PRK08058        183 IS  184 (329)
T ss_pred             CC
T ss_conf             99


No 74 
>KOG0391 consensus
Probab=96.50  E-value=0.022  Score=33.58  Aligned_cols=160  Identities=18%  Similarity=0.243  Sum_probs=90.0

Q ss_pred             CHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHHCCC-CEEEEEECCHHHHHHHHHH-HH
Q ss_conf             458999999999998740565554210124650257659789999999999980899-6699980858999999999-99
Q gi|254781215|r   51 PRSWQLEFMEVVDAHCLNSVNNPNPEVFKGAISAGRGIGKTTLNAWLVLWLMSTRPG-ISVICLANSETQLKTTLWA-EV  128 (511)
Q Consensus        51 P~~WQ~e~l~~i~~~~~~~~~~~~~~~~r~aV~sgrG~GKS~l~a~l~lw~l~~~p~-~kv~vtApt~~Q~~~ilw~-Ei  128 (511)
                      -|+||.-=|.=++.-..+|.+.        ..+---|.|||.-...++.+.+|-.-+ +--+++-||.--+.   |. |+
T Consensus       616 LReYQkiGLdWLatLYeknlNG--------ILADEmGLGKTIQtISllAhLACeegnWGPHLIVVpTsviLn---WEMEl  684 (1958)
T KOG0391         616 LREYQKIGLDWLATLYEKNLNG--------ILADEMGLGKTIQTISLLAHLACEEGNWGPHLIVVPTSVILN---WEMEL  684 (1958)
T ss_pred             HHHHHHHHHHHHHHHHHHCCCC--------EEHHHHCCCCHHHHHHHHHHHHHCCCCCCCCEEEEECHHHHH---HHHHH
T ss_conf             8888875179999998733443--------222331465145799999998750457787369851322113---36788


Q ss_pred             HHHHHHCHHCC-CCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCCCCCCCHHHHCCC---CCCEEEEECCHHCCC
Q ss_conf             99998550001-34443222222333444321112357861698530357556100212026---761499971110299
Q gi|254781215|r  129 SKWLSLLPNKH-WFEMQSLSLHPAPWYSDVLHCSLGIDSKHYSTMCRTYSEERPDTFVGHHN---TYGMAIINDEASGTP  204 (511)
Q Consensus       129 ~k~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~ea~~G~h~---~~~~lvI~DEAsgI~  204 (511)
                      ++|.-.++.-- +.....++....+|.           .-..|-++.|+-.-   -++++|+   ..--.+|+|||..|.
T Consensus       685 KRwcPglKILTYyGs~kErkeKRqgW~-----------kPnaFHVCItSYkl---v~qd~~AFkrkrWqyLvLDEaqnIK  750 (1958)
T KOG0391         685 KRWCPGLKILTYYGSHKERKEKRQGWA-----------KPNAFHVCITSYKL---VFQDLTAFKRKRWQYLVLDEAQNIK  750 (1958)
T ss_pred             HHHCCCCEEEEECCCHHHHHHHHHCCC-----------CCCEEEEEEHHHHH---HHHHHHHHHHHCCCEEEHHHHHHHC
T ss_conf             652775357652177888888751446-----------88804886310688---8737788876411223214555423


Q ss_pred             H---HHHHHHHHHHCCCCCCEEEEEECCCCCCCCHHHHHH
Q ss_conf             7---889888888507998138998238998765567653
Q gi|254781215|r  205 D---VINLGILGFLTERNANRFWIMTSNPRRLSGKFYEIF  241 (511)
Q Consensus       205 d---~i~e~i~~~Lt~~g~~~~~i~~~nP~~~~g~fy~~~  241 (511)
                      +   .-|+++...    +++..++.+|+|--++  |-+.|
T Consensus       751 nfksqrWQAllnf----nsqrRLLLtgTPLqNs--lmELW  784 (1958)
T KOG0391         751 NFKSQRWQALLNF----NSQRRLLLTGTPLQNS--LMELW  784 (1958)
T ss_pred             CHHHHHHHHHHCC----CHHHEEEECCCCHHHH--HHHHH
T ss_conf             0067889998530----0120022118720467--99999


No 75 
>PRK07270 DNA polymerase III subunits gamma and tau; Validated
Probab=96.49  E-value=0.062  Score=30.80  Aligned_cols=151  Identities=15%  Similarity=0.095  Sum_probs=76.9

Q ss_pred             HHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEEECCHHHHHHHHHHHHHHHHHH
Q ss_conf             99999999998740565554210124650257659789999999999980899669998085899999999999999985
Q gi|254781215|r   55 QLEFMEVVDAHCLNSVNNPNPEVFKGAISAGRGIGKTTLNAWLVLWLMSTRPGISVICLANSETQLKTTLWAEVSKWLSL  134 (511)
Q Consensus        55 Q~e~l~~i~~~~~~~~~~~~~~~~r~aV~sgrG~GKS~l~a~l~lw~l~~~p~~kv~vtApt~~Q~~~ilw~Ei~k~~~~  134 (511)
                      |..+.+.+.....+++.-|     -..-.+.+|+|||+++-.++-...|.++...-.|..  -..-+.+.        + 
T Consensus        20 Qe~i~~~L~nal~~~ri~H-----AyLF~GP~GtGKts~ArifAkaLnC~~~~~~~pC~~--C~~C~~i~--------~-   83 (557)
T PRK07270         20 QEVVATTLKQAVESGKISH-----AYLFSGPRGTGKTSAAKIFAKAMNCPNQVDGEPCNN--CDICRDIT--------N-   83 (557)
T ss_pred             HHHHHHHHHHHHHCCCCCE-----EEEEECCCCCCHHHHHHHHHHHHCCCCCCCCCCCCC--CHHHHHHH--------C-
T ss_conf             1999999999998599540-----442108998689999999999957999899998887--77999987--------5-


Q ss_pred             CHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCCCCCCCHHHHCCCCCCEEEEECCHHCCCHHHHHHHHHH
Q ss_conf             50001344432222223334443211123578616985303575561002120267614999711102997889888888
Q gi|254781215|r  135 LPNKHWFEMQSLSLHPAPWYSDVLHCSLGIDSKHYSTMCRTYSEERPDTFVGHHNTYGMAIINDEASGTPDVINLGILGF  214 (511)
Q Consensus       135 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~ea~~G~h~~~~~lvI~DEAsgI~d~i~e~i~~~  214 (511)
                      ....+.++..+..-                 .+  ....|..+.  --++....+.+ -.+|+||+..+....++++.-+
T Consensus        84 g~~~DviEidaas~-----------------~g--Vd~IRei~~--~~~~~P~~~~y-KV~IIDEah~Ls~~A~NALLKt  141 (557)
T PRK07270         84 GSLEDVIEIDAASN-----------------NG--VDEIRDIRD--KSTYAPSRATY-KVYIIDEVHMLSTGAFNALLKT  141 (557)
T ss_pred             CCCCCEEEECCCCC-----------------CC--HHHHHHHHH--HHCCCCCCCCE-EEEEECCHHHCCHHHHHHHHHH
T ss_conf             89997487347776-----------------78--899999999--84238777883-8999714453499999989998


Q ss_pred             HCCCCCCE-EEEEECCCCCCCCHHHHHHHC
Q ss_conf             50799813-899823899876556765303
Q gi|254781215|r  215 LTERNANR-FWIMTSNPRRLSGKFYEIFNK  243 (511)
Q Consensus       215 Lt~~g~~~-~~i~~~nP~~~~g~fy~~~~~  243 (511)
                      |-.+-... +++++..|....-...-.|.+
T Consensus       142 LEEPP~~~vFIL~Ttep~kIl~TI~SRCQr  171 (557)
T PRK07270        142 LEEPTENVVFILATTELHKIPATILSRVQR  171 (557)
T ss_pred             HHCCCCCEEEEEEECCHHHCCHHHHHHHHH
T ss_conf             528998769999849947592888743000


No 76 
>PRK06872 DNA polymerase III subunits gamma and tau; Provisional
Probab=96.48  E-value=0.063  Score=30.76  Aligned_cols=149  Identities=14%  Similarity=0.125  Sum_probs=78.0

Q ss_pred             HHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEEECCHHHHHHHHHHHHHHHHHH
Q ss_conf             99999999998740565554210124650257659789999999999980899669998085899999999999999985
Q gi|254781215|r   55 QLEFMEVVDAHCLNSVNNPNPEVFKGAISAGRGIGKTTLNAWLVLWLMSTRPGISVICLANSETQLKTTLWAEVSKWLSL  134 (511)
Q Consensus        55 Q~e~l~~i~~~~~~~~~~~~~~~~r~aV~sgrG~GKS~l~a~l~lw~l~~~p~~kv~vtApt~~Q~~~ilw~Ei~k~~~~  134 (511)
                      |.-+++.+...+.+++.-|     -..-..-||+|||+++-.++--.-|......-.|.-  -..-     .+|.     
T Consensus        21 q~~v~~~l~~a~~~~r~~h-----aylf~g~rg~gktt~ari~ak~lnc~~~~~~~pcg~--c~~c-----~~i~-----   83 (696)
T PRK06872         21 QEHILTALSNGLKENRLHH-----AYLFSGTRGVGKTSIARLFAKGLNCVHGVTATPCGE--CENC-----KAIE-----   83 (696)
T ss_pred             CHHHHHHHHHHHHCCCCCC-----EEEEECCCCCCHHHHHHHHHHHHCCCCCCCCCCCCC--CHHH-----HHHH-----
T ss_conf             5999999999997198630-----475117898888899999999867899999997888--6225-----7674-----


Q ss_pred             CHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCCCCCCCHHHHCCCCCCEEEEECCHHCCCHHHHHHHHHH
Q ss_conf             50001344432222223334443211123578616985303575561002120267614999711102997889888888
Q gi|254781215|r  135 LPNKHWFEMQSLSLHPAPWYSDVLHCSLGIDSKHYSTMCRTYSEERPDTFVGHHNTYGMAIINDEASGTPDVINLGILGF  214 (511)
Q Consensus       135 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~ea~~G~h~~~~~lvI~DEAsgI~d~i~e~i~~~  214 (511)
                                      .+...|...++-....+  ....|..- +| -.+.-.++.+. .+|+||.+.++...|+++.-|
T Consensus        84 ----------------~g~~~d~~eidaas~~~--v~~~r~l~-~~-~~~~p~~~~~k-vy~idevhmls~~~fnallkt  142 (696)
T PRK06872         84 ----------------EGNFIDLIEIDAASRTK--VEDTRELL-DN-VQYKPVVGRFK-VYLIDEVHMLSRHSFNALLKT  142 (696)
T ss_pred             ----------------CCCCCCEEEEECCCCCC--HHHHHHHH-HH-CCCCCCCCCEE-EEEEEHHHHCCHHHHHHHHHH
T ss_conf             ----------------47877546750565578--89999999-84-54577677547-999700544389999999875


Q ss_pred             HCCCCCCE-EEEEECCCCCCCCHHHHHH
Q ss_conf             50799813-8998238998765567653
Q gi|254781215|r  215 LTERNANR-FWIMTSNPRRLSGKFYEIF  241 (511)
Q Consensus       215 Lt~~g~~~-~~i~~~nP~~~~g~fy~~~  241 (511)
                      |-.+=... +++++..|.+..-...-.|
T Consensus       143 leepp~~v~f~latt~~~k~p~tilsrc  170 (696)
T PRK06872        143 LEEPPEYVKFLLATTDPQKLPITILSRC  170 (696)
T ss_pred             HCCCCCCEEEEEECCCHHHCCHHHHHHH
T ss_conf             0279754489984386322748898766


No 77 
>PRK07003 DNA polymerase III subunits gamma and tau; Validated
Probab=96.39  E-value=0.071  Score=30.43  Aligned_cols=146  Identities=15%  Similarity=0.127  Sum_probs=71.0

Q ss_pred             HHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEEECCHHHHHHHHHHHHHHHHHH
Q ss_conf             99999999998740565554210124650257659789999999999980899669998085899999999999999985
Q gi|254781215|r   55 QLEFMEVVDAHCLNSVNNPNPEVFKGAISAGRGIGKTTLNAWLVLWLMSTRPGISVICLANSETQLKTTLWAEVSKWLSL  134 (511)
Q Consensus        55 Q~e~l~~i~~~~~~~~~~~~~~~~r~aV~sgrG~GKS~l~a~l~lw~l~~~p~~kv~vtApt~~Q~~~ilw~Ei~k~~~~  134 (511)
                      |.-+++.+..-+..++. |..    ..-...||+|||+++-.++--.-|-.....--|.  +-..-     .+|.    .
T Consensus        21 Q~~v~~~l~nal~~~rl-~ha----ylf~G~rGvGKTt~aRi~Ak~lnC~~~~~~~pcg--~C~~C-----~~i~----~   84 (816)
T PRK07003         21 QEHVVRALTHALDGGRL-HHA----YLFTGTRGVGKTTLSRIFAKALNCETGVTSQPCG--VCRAC-----REID----E   84 (816)
T ss_pred             CHHHHHHHHHHHHCCCC-CCE----EEEECCCCCCHHHHHHHHHHHHCCCCCCCCCCCC--CCHHH-----HHHH----C
T ss_conf             49999999999970986-314----7511789888889999999986789999989787--75557-----8775----5


Q ss_pred             CHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCCCCCCCHHHHCCCCCCEEEEECCHHCCCHHHHHHHHHH
Q ss_conf             50001344432222223334443211123578616985303575561002120267614999711102997889888888
Q gi|254781215|r  135 LPNKHWFEMQSLSLHPAPWYSDVLHCSLGIDSKHYSTMCRTYSEERPDTFVGHHNTYGMAIINDEASGTPDVINLGILGF  214 (511)
Q Consensus       135 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~ea~~G~h~~~~~lvI~DEAsgI~d~i~e~i~~~  214 (511)
                                       +...|...++-....+  ....|.... + -.+.-..+.+ -.+|+||.+.+....|+++.-+
T Consensus        85 -----------------g~~~d~iEiDaAS~~~--vd~~r~l~~-~-~~y~p~~~r~-KvyiiDEvHmls~~afnalLKt  142 (816)
T PRK07003         85 -----------------GRFVDYVEMDAASNRG--VDEMAALLE-R-AVYAPVDARF-KVYMIDEVHMLTNHAFNAMLKT  142 (816)
T ss_pred             -----------------CCCCCEEEEECCCCCC--HHHHHHHHH-H-CCCCCCCCCE-EEEEEECHHHCCHHHHHHHHHH
T ss_conf             -----------------8877547863554357--689999998-6-2247866744-7999841543399999999984


Q ss_pred             HCCCCCCEEE-EEECCCCCCCCHHH
Q ss_conf             5079981389-98238998765567
Q gi|254781215|r  215 LTERNANRFW-IMTSNPRRLSGKFY  238 (511)
Q Consensus       215 Lt~~g~~~~~-i~~~nP~~~~g~fy  238 (511)
                      |-..=...++ +++.-|.+..-..-
T Consensus       143 lEepP~hv~FilaTTd~~k~p~til  167 (816)
T PRK07003        143 LEEPPPHVKFILATTDPQKIPVTVL  167 (816)
T ss_pred             HCCCCCCEEEEEECCCHHHCCHHHH
T ss_conf             0379866489995588011528898


No 78 
>pfam05970 DUF889 PIF1 helicase. The PIF1 helicase inhibits telomerase activity and is cell cycle regulated.
Probab=96.37  E-value=0.014  Score=34.86  Aligned_cols=97  Identities=23%  Similarity=0.087  Sum_probs=52.0

Q ss_pred             CCCCCHHHHHHHHHHHHHHHCCCCEEEEEECCHHHHHHH-HHHHHHHHHHHCHHCCCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             576597899999999999808996699980858999999-9999999998550001344432222223334443211123
Q gi|254781215|r   85 GRGIGKTTLNAWLVLWLMSTRPGISVICLANSETQLKTT-LWAEVSKWLSLLPNKHWFEMQSLSLHPAPWYSDVLHCSLG  163 (511)
Q Consensus        85 grG~GKS~l~a~l~lw~l~~~p~~kv~vtApt~~Q~~~i-lw~Ei~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  163 (511)
                      +=|+|||++.-.++-++-  ..+..+++||||---|.+| -=.-|..+         +..        +  .+       
T Consensus         2 ~AGTGKS~ll~~i~~~l~--~~~~~v~vtA~TGiAA~~i~gG~TiHs~---------~gi--------~--~~-------   53 (418)
T pfam05970         2 YGGTGKTFLWNALSARIR--SRGKIVLNVASSGIAALLLPGGRTAHSR---------FGI--------P--LD-------   53 (418)
T ss_pred             CCCCCHHHHHHHHHHHHH--HCCCEEEEECCHHHHHHCCCCCEEHHHC---------CCC--------C--CC-------
T ss_conf             798879999999999997--6898899989689998516998739852---------698--------9--88-------


Q ss_pred             CCCCEEEEEECCCCCCCCCHHHHCCCCCCEEEEECCHHCCCHHHHHHHHHHHC
Q ss_conf             57861698530357556100212026761499971110299788988888850
Q gi|254781215|r  164 IDSKHYSTMCRTYSEERPDTFVGHHNTYGMAIINDEASGTPDVINLGILGFLT  216 (511)
Q Consensus       164 ~~~~~~~~~~~~~s~~~~ea~~G~h~~~~~lvI~DEAsgI~d~i~e~i~~~Lt  216 (511)
                      ..... .....  +  +.....-++.  ..++|+||.|.|+..+++.+.-.|.
T Consensus        54 ~~~~~-~~~~~--~--~~~~~~~~~~--~~vLIIDEiSMv~~~lfd~id~~lr   99 (418)
T pfam05970        54 IDEDS-TCKIK--R--GSKLAELLKK--ASLIIWDEAPMTHRHCFEALDRTLR   99 (418)
T ss_pred             CCCCC-CEEEC--C--CHHHHHHHHH--CCEEEEECCCCCCHHHHHHHHHHHH
T ss_conf             77420-11213--3--7788998740--8799985411357899999999999


No 79 
>PRK13826 Dtr system oriT relaxase; Provisional
Probab=96.36  E-value=0.051  Score=31.32  Aligned_cols=132  Identities=18%  Similarity=0.082  Sum_probs=69.1

Q ss_pred             HHHHHHHHHHHHHHHCCCCCCCCCCEEEEEE-CCCCCCHHHHHHHHHHHHHHHCCCCEEEEEECCHHHHHHHHHHHHHHH
Q ss_conf             8999999999998740565554210124650-257659789999999999980899669998085899999999999999
Q gi|254781215|r   53 SWQLEFMEVVDAHCLNSVNNPNPEVFKGAIS-AGRGIGKTTLNAWLVLWLMSTRPGISVICLANSETQLKTTLWAEVSKW  131 (511)
Q Consensus        53 ~WQ~e~l~~i~~~~~~~~~~~~~~~~r~aV~-sgrG~GKS~l~a~l~lw~l~~~p~~kv~vtApt~~Q~~~ilw~Ei~k~  131 (511)
                      +=|+++++.|...            .++++. .-=|+|||++++..-..|-.  -|.+|+=.|++-..+... -.+    
T Consensus       384 ~EQ~~Av~hiT~~------------~~Ia~VvG~AGaGKStmL~aAReawEa--~GyrV~GaALsGkAAegL-e~~----  444 (1102)
T PRK13826        384 DEQKTAIEHVAGA------------ERIAAVIGRAGAGKTTMMKAAREAWEA--AGYRVVGGALAGKAAEGL-EKE----  444 (1102)
T ss_pred             HHHHHHHHHHCCC------------CCEEEEEECCCCCHHHHHHHHHHHHHH--CCCEEEEECCCHHHHHHH-HHC----
T ss_conf             9999999985378------------866899842888788999999999997--797798015007899977-534----


Q ss_pred             HHHCHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCCCCCCCHHHHCCCCCCEEEEECCHHCCCHHHHHHH
Q ss_conf             98550001344432222223334443211123578616985303575561002120267614999711102997889888
Q gi|254781215|r  132 LSLLPNKHWFEMQSLSLHPAPWYSDVLHCSLGIDSKHYSTMCRTYSEERPDTFVGHHNTYGMAIINDEASGTPDVINLGI  211 (511)
Q Consensus       132 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~ea~~G~h~~~~~lvI~DEAsgI~d~i~e~i  211 (511)
                             -.........+...|..+                          . .-+. . ..++|+|||+.|...-+.-+
T Consensus       445 -------sGI~SrTlAs~e~~w~~g--------------------------r-~~L~-~-~dVlVIDEAGMVgsrqmarv  488 (1102)
T PRK13826        445 -------AGIASRTLSSWELRWNQG--------------------------R-DQLD-N-KTVFVLDEAGMVSSRQMALF  488 (1102)
T ss_pred             -------CCCCCHHHHHHHHHHCCC--------------------------C-CCCC-C-CCEEEEECCCCCCHHHHHHH
T ss_conf             -------695303389999874358--------------------------6-5567-8-73899845556557999999


Q ss_pred             HHHHCCCCCCEEEEEECC-----CCCCCCHHHHHH
Q ss_conf             888507998138998238-----998765567653
Q gi|254781215|r  212 LGFLTERNANRFWIMTSN-----PRRLSGKFYEIF  241 (511)
Q Consensus       212 ~~~Lt~~g~~~~~i~~~n-----P~~~~g~fy~~~  241 (511)
                      .......|++.  ++.|-     |-.-.+.|....
T Consensus       489 l~~ae~aGAKv--VLVGD~~QLQpIeAGaaFrai~  521 (1102)
T PRK13826        489 VEAVTRAGAKL--VLVGDPEQLQPIEAGAAFRAIA  521 (1102)
T ss_pred             HHHHHHCCCEE--EEECCHHHHCCCCCCHHHHHHH
T ss_conf             99999759989--9968878827610468899999


No 80 
>TIGR02397 dnaX_nterm DNA polymerase III, subunits gamma and tau; InterPro: IPR012763    This entry represents the well-conserved first N-terminal domain of DnaX, approx. 365 aa. The full-length product of the dnaX gene in Escherichia coli encodes the DNA polymerase III tau subunit. A translational frameshift leads to early termination and a truncated protein subunit gamma, about 1/3 shorter than tau and present in roughly equal amounts. This frameshift mechanism is not necessarily universal for species with DNA polymerase III but appears conserved in the extreme thermophile Thermus thermophilis.; GO: 0003887 DNA-directed DNA polymerase activity, 0005524 ATP binding, 0006260 DNA replication, 0009360 DNA polymerase III complex.
Probab=96.33  E-value=0.02  Score=33.92  Aligned_cols=200  Identities=15%  Similarity=0.149  Sum_probs=100.8

Q ss_pred             CCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHHCCC------CEEEEEECCHH
Q ss_conf             655578458999999999998740565554210124650257659789999999999980899------66999808589
Q gi|254781215|r   45 LEGFSAPRSWQLEFMEVVDAHCLNSVNNPNPEVFKGAISAGRGIGKTTLNAWLVLWLMSTRPG------ISVICLANSET  118 (511)
Q Consensus        45 ~~~~~~P~~WQ~e~l~~i~~~~~~~~~~~~~~~~r~aV~sgrG~GKS~l~a~l~lw~l~~~p~------~kv~vtApt~~  118 (511)
                      -....|    |.-+.+.+-..+.+++--|     -.-=++.||+|||++|=.++--.=|. +.      ..-.|.+=+..
T Consensus        13 F~d~~G----Q~~iv~tL~NAi~~~ri~H-----AYLF~GpRGtGKTS~ARIfAKaLNC~-~~~~~PCn~C~~C~~i~~g   82 (363)
T TIGR02397        13 FEDVIG----QEHIVKTLKNAIKNGRIAH-----AYLFSGPRGTGKTSIARIFAKALNCQ-GPDGEPCNECESCKEINSG   82 (363)
T ss_pred             CCCCCC----CHHHHHHHHHHHHHCCCCC-----EEEECCCCCCCHHHHHHHHHHHHCCC-CCCCCCCCCCCHHHHHHCC
T ss_conf             110235----1799999999997189662-----34502859976355899999986588-7877877775022776528


Q ss_pred             HHHHHHHHHHHHHHHHCHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCCCCCCCHHHHCCCCCCEEEEEC
Q ss_conf             99999999999999855000134443222222333444321112357861698530357556100212026761499971
Q gi|254781215|r  119 QLKTTLWAEVSKWLSLLPNKHWFEMQSLSLHPAPWYSDVLHCSLGIDSKHYSTMCRTYSEERPDTFVGHHNTYGMAIIND  198 (511)
Q Consensus       119 Q~~~ilw~Ei~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~ea~~G~h~~~~~lvI~D  198 (511)
                      +.-||+                                  +++...+++  ....|.-.+  --.+.=..+.|-+ +|+|
T Consensus        83 ~~~Dvi----------------------------------EiDAASN~g--VD~IR~l~e--~v~y~P~~~kYKv-YIID  123 (363)
T TIGR02397        83 SSLDVI----------------------------------EIDAASNNG--VDDIRELRE--NVKYAPSKGKYKV-YIID  123 (363)
T ss_pred             CCCCEE----------------------------------EECCCCCCC--HHHHHHHHH--HHCCCCCCCCCCE-EEEE
T ss_conf             986668----------------------------------864865687--889999987--3036875544335-8873


Q ss_pred             CHHCCCHHHHHHHHHHHCCCCCC-EEEEEECCCCCCCCHHHHHHHCCCCCCEEEEECCCCCCCCCHHHHH----HHHHHC
Q ss_conf             11029978898888885079981-3899823899876556765303524741798404336778977899----999751
Q gi|254781215|r  199 EASGTPDVINLGILGFLTERNAN-RFWIMTSNPRRLSGKFYEIFNKPLDDWKRFQIDTRTVEGIDPSFHE----GIIARY  273 (511)
Q Consensus       199 EAsgI~d~i~e~i~~~Lt~~g~~-~~~i~~~nP~~~~g~fy~~~~~~~~~w~~~~i~~~~~p~~~~~~ie----~~~~~~  273 (511)
                      |++..+...|+|+.-||=++=.. .++++|+.|.+-...---+|.+         +   +=..++.+.|-    .+..+-
T Consensus       124 EVHMLS~~AFNALLKTLEEPP~hV~FIlATTE~~KiP~TIlSRCQr---------F---~Fk~i~~~~i~~~L~~I~~~E  191 (363)
T TIGR02397       124 EVHMLSKSAFNALLKTLEEPPEHVVFILATTEPHKIPATILSRCQR---------F---DFKRIPLEDIVERLKKILDKE  191 (363)
T ss_pred             CCCCCCHHHHHHHHHHHCCCCCCEEEEEECCCHHHCCCCCEEECEE---------E---CCCCCCHHHHHHHHHHHHHHH
T ss_conf             2302865689998765227987628887348711205540210003---------1---267899899999999999870


Q ss_pred             CCCHHHHHHHHCCCCCCCCCCEEEC-HHHHHHHHHC
Q ss_conf             8980135444317566667873755-9999886407
Q gi|254781215|r  274 GLDSDVTRVEVCGQFPQQDIDSFIP-LNIIEEALNR  308 (511)
Q Consensus       274 geds~~~r~evlgeFp~~~~~~~i~-~~~ie~a~~r  308 (511)
                      +-+   +-.+-|-.=...+++++.. ..+.|.++.-
T Consensus       192 ~I~---~e~~AL~~IA~~a~GS~RDAlsllDQ~~~~  224 (363)
T TIGR02397       192 GIK---IEDEALELIARAADGSMRDALSLLDQAISF  224 (363)
T ss_pred             CCC---CCHHHHHHHHHHCCCCCCHHHHHHHHHHHH
T ss_conf             883---177899999996289610688999999982


No 81 
>PRK13889 conjugal transfer relaxase TraA; Provisional
Probab=96.30  E-value=0.048  Score=31.51  Aligned_cols=132  Identities=14%  Similarity=0.045  Sum_probs=69.6

Q ss_pred             HHHHHHHHHHHHHHCCCCCCCCCCEEEEEECC-CCCCHHHHHHHHHHHHHHHCCCCEEEEEECCHHHHHHHHHHHHHHHH
Q ss_conf             99999999999874056555421012465025-76597899999999999808996699980858999999999999999
Q gi|254781215|r   54 WQLEFMEVVDAHCLNSVNNPNPEVFKGAISAG-RGIGKTTLNAWLVLWLMSTRPGISVICLANSETQLKTTLWAEVSKWL  132 (511)
Q Consensus        54 WQ~e~l~~i~~~~~~~~~~~~~~~~r~aV~sg-rG~GKS~l~a~l~lw~l~~~p~~kv~vtApt~~Q~~~ilw~Ei~k~~  132 (511)
                      =|+++++.|..            -.+++|.-| =|+|||+++...-.-|-.  -|.+|+=.|++-.-++.. -.+     
T Consensus       350 EQ~~A~~hiT~------------~~~iavVvG~AGtGKStmL~aAReawEa--~GyrV~GaALsGkAAegL-e~~-----  409 (992)
T PRK13889        350 EQADALAHVTD------------GRDLGVVVGYAGTGKSAMLGVAREAWEA--AGYEVRGAALSGIAAENL-EGG-----  409 (992)
T ss_pred             HHHHHHHHHCC------------CCCEEEEEECCCCCHHHHHHHHHHHHHH--CCCEEEEECCCHHHHHHH-HHC-----
T ss_conf             99999998647------------8975899833888788999999999997--798898115006899976-534-----


Q ss_pred             HHCHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCCCCCCCHHHHCCCCCCEEEEECCHHCCCHHHHHHHH
Q ss_conf             85500013444322222233344432111235786169853035755610021202676149997111029978898888
Q gi|254781215|r  133 SLLPNKHWFEMQSLSLHPAPWYSDVLHCSLGIDSKHYSTMCRTYSEERPDTFVGHHNTYGMAIINDEASGTPDVINLGIL  212 (511)
Q Consensus       133 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~ea~~G~h~~~~~lvI~DEAsgI~d~i~e~i~  212 (511)
                            .........-+...|..                           ....+.+.  ..+|+|||+.|...-+.-+.
T Consensus       410 ------sGI~SrTlAs~e~~w~~---------------------------g~~~L~~~--dVlVVDEAGMVgSRqMarll  454 (992)
T PRK13889        410 ------SGIASRTIASLEHGWGQ---------------------------GRDLLTAR--DVLVIDEAGMVGTRQLERVL  454 (992)
T ss_pred             ------CCCCCHHHHHHHHHHHC---------------------------CCCCCCCC--CEEEEECCCCCCHHHHHHHH
T ss_conf             ------79431679999998746---------------------------73347898--58999676557749999999


Q ss_pred             HHHCCCCCCEEEEEECC-----CCCCCCHHHHHHH
Q ss_conf             88507998138998238-----9987655676530
Q gi|254781215|r  213 GFLTERNANRFWIMTSN-----PRRLSGKFYEIFN  242 (511)
Q Consensus       213 ~~Lt~~g~~~~~i~~~n-----P~~~~g~fy~~~~  242 (511)
                      ..-...|++.  +..|-     |-.-.+.|.....
T Consensus       455 ~~Ae~AGAKV--VLVGD~~QLq~IeAGaaFral~e  487 (992)
T PRK13889        455 SHAADAGAKV--VLVGDPQQLQAIEAGAAFRSIHE  487 (992)
T ss_pred             HHHHHCCCEE--EEECCHHHCCCCCCCHHHHHHHH
T ss_conf             9999849989--99488777188646889999998


No 82 
>PRK05564 DNA polymerase III subunit delta'; Validated
Probab=96.28  E-value=0.081  Score=30.05  Aligned_cols=151  Identities=11%  Similarity=0.104  Sum_probs=83.4

Q ss_pred             HHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHHCCC---CEEEEEECCHHHHHHHHHHHHHHH
Q ss_conf             99999999998740565554210124650257659789999999999980899---669998085899999999999999
Q gi|254781215|r   55 QLEFMEVVDAHCLNSVNNPNPEVFKGAISAGRGIGKTTLNAWLVLWLMSTRPG---ISVICLANSETQLKTTLWAEVSKW  131 (511)
Q Consensus        55 Q~e~l~~i~~~~~~~~~~~~~~~~r~aV~sgrG~GKS~l~a~l~lw~l~~~p~---~kv~vtApt~~Q~~~ilw~Ei~k~  131 (511)
                      |.++.+.+.....++..-|     -.--.+.+|+||+.++-.++-+.++...+   .-++...|...+.  |--.+|+..
T Consensus         9 q~~i~~~L~~~i~~~rl~H-----AyLF~Gp~G~GK~~~A~~~A~~ll~~~~~~~~~D~~~~~~~~~~~--I~vd~IR~l   81 (313)
T PRK05564          9 HENIKNRIDNSIIKGKFSH-----ASLIVGEDGIGKSILAKEIANKILGKSEQREYVDIIEYKPINKKS--IGVDDIRNI   81 (313)
T ss_pred             HHHHHHHHHHHHHCCCCCC-----EEEEECCCCCCHHHHHHHHHHHHHCCCCCCCCCCEEEEECCCCCC--CCHHHHHHH
T ss_conf             2999999999998799875-----043279998509999999999982899778898658863322569--998999999


Q ss_pred             HHHCHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCCCCCCCHHHHCCCCCCEEEEECCHHCCCHHHHHHH
Q ss_conf             98550001344432222223334443211123578616985303575561002120267614999711102997889888
Q gi|254781215|r  132 LSLLPNKHWFEMQSLSLHPAPWYSDVLHCSLGIDSKHYSTMCRTYSEERPDTFVGHHNTYGMAIINDEASGTPDVINLGI  211 (511)
Q Consensus       132 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~ea~~G~h~~~~~lvI~DEAsgI~d~i~e~i  211 (511)
                      .+.+                                               ++....+.+. .+|+|||..+.....+++
T Consensus        82 ~~~~-----------------------------------------------~~~p~~g~~K-V~II~~ae~m~~~AaNAL  113 (313)
T PRK05564         82 IEEV-----------------------------------------------NKKPYEGDKK-VIIIYKSEKMTEQAQNAF  113 (313)
T ss_pred             HHHH-----------------------------------------------HHCCCCCCCE-EEEECCHHHHCHHHHHHH
T ss_conf             9998-----------------------------------------------4086258956-999807777589999998


Q ss_pred             HHHHCCCCCCEEEE-EECCCCCCCCHHHHHHHCCCCCCEEEEECCCCCCCCCHHHHHHHHHH
Q ss_conf             88850799813899-82389987655676530352474179840433677897789999975
Q gi|254781215|r  212 LGFLTERNANRFWI-MTSNPRRLSGKFYEIFNKPLDDWKRFQIDTRTVEGIDPSFHEGIIAR  272 (511)
Q Consensus       212 ~~~Lt~~g~~~~~i-~~~nP~~~~g~fy~~~~~~~~~w~~~~i~~~~~p~~~~~~ie~~~~~  272 (511)
                      .-+|-.+-...+++ .+.+|.+.--...-+|..       ++     -+.++.+.+.++..+
T Consensus       114 LKtLEEPP~~t~fIL~t~~~~~lLpTI~SRCQ~-------~~-----f~~l~~~~i~~~L~~  163 (313)
T PRK05564        114 LKTIEEPPKGVFIILLCENLEQILDTIKSRCQI-------YK-----LNRLSKEDIEKFISY  163 (313)
T ss_pred             HHCCCCCCCCEEEEEEECCHHHCCCHHHCCCEE-------EE-----CCCCCHHHHHHHHHH
T ss_conf             455036899858998649835475778706535-------66-----899899999999998


No 83 
>PRK11747 dinG ATP-dependent DNA helicase DinG; Provisional
Probab=96.24  E-value=0.085  Score=29.92  Aligned_cols=68  Identities=19%  Similarity=0.221  Sum_probs=43.5

Q ss_pred             CCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEEECCHH
Q ss_conf             565557845899999999999874056555421012465025765978999999999998089966999808589
Q gi|254781215|r   44 PLEGFSAPRSWQLEFMEVVDAHCLNSVNNPNPEVFKGAISAGRGIGKTTLNAWLVLWLMSTRPGISVICLANSET  118 (511)
Q Consensus        44 ~~~~~~~P~~WQ~e~l~~i~~~~~~~~~~~~~~~~r~aV~sgrG~GKS~l~a~l~lw~l~~~p~~kv~vtApt~~  118 (511)
                      .+++|. ||+=|.+...+|+....+....+     .+.|-||.|+|||..--.-++.++..+ +.+|+|.-+|..
T Consensus        20 ~~~gfe-~R~~Q~~Ma~~V~~al~~~~~~~-----~l~iEAgTGtGKTlaYL~Pai~~a~~~-~~~vvIST~T~~   87 (697)
T PRK11747         20 QLPGFI-PRAGQRQMIAEVAKTLAGEYGRH-----ILVIEAGTGVGKSLAYLLAGIPIARAE-KKKLVISTATVA   87 (697)
T ss_pred             HCCCCC-CCHHHHHHHHHHHHHHHCCCCCC-----EEEEECCCCCHHHHHHHHHHHHHHHHC-CCCEEEECCCHH
T ss_conf             688997-18789999999999961666786-----699989997208999999999999982-997999889889


No 84 
>PRK07471 DNA polymerase III subunit delta'; Validated
Probab=96.24  E-value=0.086  Score=29.89  Aligned_cols=166  Identities=13%  Similarity=0.116  Sum_probs=77.5

Q ss_pred             HHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEEECCHH-HHH--HHHHHHHHHH
Q ss_conf             9999999999874056555421012465025765978999999999998089966999808589-999--9999999999
Q gi|254781215|r   55 QLEFMEVVDAHCLNSVNNPNPEVFKGAISAGRGIGKTTLNAWLVLWLMSTRPGISVICLANSET-QLK--TTLWAEVSKW  131 (511)
Q Consensus        55 Q~e~l~~i~~~~~~~~~~~~~~~~r~aV~sgrG~GKS~l~a~l~lw~l~~~p~~kv~vtApt~~-Q~~--~ilw~Ei~k~  131 (511)
                      |.++.+.+.....++..-|     -.-....+|+||++++=.++-+.+++.+.....+..+... .+.  .-.+..+   
T Consensus        22 qe~~~~~L~~a~~~grl~H-----A~Lf~Gp~GiGK~tlA~~~A~~ll~~~~~~~~~~~~~~~~l~~~~~~p~~r~i---   93 (363)
T PRK07471         22 HAAAEAALLDAYRSGRLHH-----AWLIGGPQGIGKATLAYRMARFLLATPPPGGDAVFPPPASLAVDPDHPVARRI---   93 (363)
T ss_pred             HHHHHHHHHHHHHCCCCCC-----EEEEECCCCCCHHHHHHHHHHHHHCCCCCCCCCCCCCHHHHCCCCCCCHHHHH---
T ss_conf             1999999999998599764-----58767999818899999999998579997777767870531258777289999---


Q ss_pred             HHHCHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCCCCCCCHHHHCCCCCCEEEEECCHHCCCHHHHHHH
Q ss_conf             98550001344432222223334443211123578616985303575561002120267614999711102997889888
Q gi|254781215|r  132 LSLLPNKHWFEMQSLSLHPAPWYSDVLHCSLGIDSKHYSTMCRTYSEERPDTFVGHHNTYGMAIINDEASGTPDVINLGI  211 (511)
Q Consensus       132 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~ea~~G~h~~~~~lvI~DEAsgI~d~i~e~i  211 (511)
                       ......+.+.+      ...+..........+.-.......+.      -++....+.+. .+|+|||..+....++++
T Consensus        94 -~~~~hpdl~~i------~r~~d~k~~~~~~~I~Vd~iR~l~~~------~~~~p~~g~~k-V~IId~ad~mn~~aaNAL  159 (363)
T PRK07471         94 -AAGAHGGLLTL------ERSWNEKGKRLRTVITVDEVRETIGF------FGLTAAEGGWR-VVIVDTADEMNANAANAL  159 (363)
T ss_pred             -HCCCCCCEEEE------ECCCCCCCCCCCCCCCHHHHHHHHHH------HCCCCCCCCCE-EEEEECHHHHCHHHHHHH
T ss_conf             -52699984667------62001133321244539999999999------72485248966-999868787388999999


Q ss_pred             HHHHCCCCCCEEEEEE-CCCCCCCCHHHHHHH
Q ss_conf             8885079981389982-389987655676530
Q gi|254781215|r  212 LGFLTERNANRFWIMT-SNPRRLSGKFYEIFN  242 (511)
Q Consensus       212 ~~~Lt~~g~~~~~i~~-~nP~~~~g~fy~~~~  242 (511)
                      .-+|-.+-.+..++.+ .+|.+.--...-.|.
T Consensus       160 LK~LEEPP~~t~fiLit~~~~~llpTI~SRCq  191 (363)
T PRK07471        160 LKVLEEPPARSLLLLVSHAPARLLPTIRSRCR  191 (363)
T ss_pred             HHHHCCCCCCEEEEEEECCHHHCHHHHHHHCC
T ss_conf             99721589883899863997777799997352


No 85 
>COG1875 NYN ribonuclease and ATPase of PhoH family domains [General    function prediction only]
Probab=96.10  E-value=0.0074  Score=36.62  Aligned_cols=43  Identities=19%  Similarity=0.047  Sum_probs=19.4

Q ss_pred             EEEECCCCCCHHHHHHHHHHHHHHHCC-CCEEEEEECCHHHHHH
Q ss_conf             465025765978999999999998089-9669998085899999
Q gi|254781215|r   80 GAISAGRGIGKTTLNAWLVLWLMSTRP-GISVICLANSETQLKT  122 (511)
Q Consensus        80 ~aV~sgrG~GKS~l~a~l~lw~l~~~p-~~kv~vtApt~~Q~~~  122 (511)
                      |+...--|+|||.|+-...+.-.+-+. ..|++||.|+..--++
T Consensus       248 V~L~G~AGtGKTlLALaAgleqv~e~~~y~KiiVtRp~vpvG~d  291 (436)
T COG1875         248 VSLGGKAGTGKTLLALAAGLEQVLERKRYRKIIVTRPTVPVGED  291 (436)
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHHHHHHHCEEEEECCCCCCCCC
T ss_conf             88633577667699999899999877543027883377677531


No 86 
>PRK05703 flhF flagellar biosynthesis regulator FlhF; Validated
Probab=96.09  E-value=0.1  Score=29.43  Aligned_cols=38  Identities=21%  Similarity=0.108  Sum_probs=17.4

Q ss_pred             EEEECCCCCCHHHHHHHHHHHHHHHCCC-CEEEEEECCH
Q ss_conf             4650257659789999999999980899-6699980858
Q gi|254781215|r   80 GAISAGRGIGKTTLNAWLVLWLMSTRPG-ISVICLANSE  117 (511)
Q Consensus        80 ~aV~sgrG~GKS~l~a~l~lw~l~~~p~-~kv~vtApt~  117 (511)
                      ++...+-|+|||+.+|=|+..+.+.+.. ...++|+-||
T Consensus       213 valVGPTGVGKTTTiAKLAA~~~l~~~~~kV~lIT~Dty  251 (412)
T PRK05703        213 VALVGPTGVGKTTTLAKLAARYALEEGKDKVALITLDTY  251 (412)
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEEEECCC
T ss_conf             999888887567699999999999729981799983767


No 87 
>KOG0952 consensus
Probab=96.05  E-value=0.1  Score=29.46  Aligned_cols=123  Identities=15%  Similarity=0.134  Sum_probs=65.1

Q ss_pred             EEEECCCCCCHHHHHHHHHHHHHHH--------CCCCEEEEEECCHHHHHHHHHHHHHHHHHHCHHCCCCCCCCCCCCCC
Q ss_conf             4650257659789999999999980--------89966999808589999999999999998550001344432222223
Q gi|254781215|r   80 GAISAGRGIGKTTLNAWLVLWLMST--------RPGISVICLANSETQLKTTLWAEVSKWLSLLPNKHWFEMQSLSLHPA  151 (511)
Q Consensus        80 ~aV~sgrG~GKS~l~a~l~lw~l~~--------~p~~kv~vtApt~~Q~~~ilw~Ei~k~~~~~~~~~~~~~~~~~~~~~  151 (511)
                      ..|.|+.|.|||-++---+|-.+-.        ..+-||+++||+..-+-++    +.+|-+++... ...+.....=..
T Consensus       129 MLIcAPTGsGKT~la~L~ILr~ik~~~~~~~i~k~~fKiVYIaPmKALa~Em----~~~~~kkl~~~-gi~v~ELTGD~q  203 (1230)
T KOG0952         129 MLICAPTGSGKTVLAELCILRTIKEHEEQGDIAKDDFKIVYIAPMKALAAEM----VDKFSKKLAPL-GISVRELTGDTQ  203 (1230)
T ss_pred             EEEECCCCCCCHHHHHHHHHHHHHHHCCCCCCCCCCCEEEEEECHHHHHHHH----HHHHHHHCCCC-CCEEEEECCCCH
T ss_conf             7997778997167899999999985014554346871399992568899999----99986642424-625888417545


Q ss_pred             CCCCCCCCCC-CCCCCCEEEEEECCCCCCCCCHHHHCCCCCCEEEEECCHHCCCHHHHHHHHH
Q ss_conf             3344432111-2357861698530357556100212026761499971110299788988888
Q gi|254781215|r  152 PWYSDVLHCS-LGIDSKHYSTMCRTYSEERPDTFVGHHNTYGMAIINDEASGTPDVINLGILG  213 (511)
Q Consensus       152 ~~~~~~~~~~-~~~~~~~~~~~~~~~s~~~~ea~~G~h~~~~~lvI~DEAsgI~d~i~e~i~~  213 (511)
                      -...+..... +-..++-|=...|.+..+  .++.+   . .-|+|+||-+-+.|+--.++|.
T Consensus       204 l~~tei~~tqiiVTTPEKwDvvTRk~~~d--~~l~~---~-V~LviIDEVHlLhd~RGpvlEt  260 (1230)
T KOG0952         204 LTKTEIADTQIIVTTPEKWDVVTRKSVGD--SALFS---L-VRLVIIDEVHLLHDDRGPVLET  260 (1230)
T ss_pred             HHHHHHHHCCEEEECCCCEEEEEEEECCC--HHHHH---H-EEEEEEEEEHHHCCCCCCHHHH
T ss_conf             66778774377970634000466541262--65555---4-2048853001215766406999


No 88 
>PRK08074 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
Probab=96.04  E-value=0.11  Score=29.30  Aligned_cols=76  Identities=22%  Similarity=0.239  Sum_probs=48.8

Q ss_pred             CCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEEECCHHHHHHHH
Q ss_conf             65557845899999999999874056555421012465025765978999999999998089966999808589999999
Q gi|254781215|r   45 LEGFSAPRSWQLEFMEVVDAHCLNSVNNPNPEVFKGAISAGRGIGKTTLNAWLVLWLMSTRPGISVICLANSETQLKTTL  124 (511)
Q Consensus        45 ~~~~~~P~~WQ~e~l~~i~~~~~~~~~~~~~~~~r~aV~sgrG~GKS~l~a~l~lw~l~~~p~~kv~vtApt~~Q~~~il  124 (511)
                      +++|. +|+=|+++..+|++...++.        ..-|-||.|+|||..--.-++.++..+ +.+|+|..+|...-..++
T Consensus       254 ~~~ye-~R~~Q~~ma~~V~~al~~~~--------~l~iEApTGtGKTlaYLlPai~~A~~~-~~~vvIST~T~~LQ~QL~  323 (932)
T PRK08074        254 MPGYE-KREGQQEMMKEVYTALRDSR--------HALIEAGTGTGKTLAYLLPAAYFAKKK-EEPVIISTYTVQLQQQLL  323 (932)
T ss_pred             CCCCC-CCHHHHHHHHHHHHHHHCCC--------CEEEECCCCCCCHHHHHHHHHHHHHHC-CCCEEEEECCHHHHHHHH
T ss_conf             77887-58789999999999985388--------479986888871368799999999975-990999916288999999


Q ss_pred             HHHHHH
Q ss_conf             999999
Q gi|254781215|r  125 WAEVSK  130 (511)
Q Consensus       125 w~Ei~k  130 (511)
                      -.+|..
T Consensus       324 ~kdlp~  329 (932)
T PRK08074        324 EKDIPL  329 (932)
T ss_pred             HHHHHH
T ss_conf             868999


No 89 
>PRK08853 DNA polymerase III subunits gamma and tau; Validated
Probab=96.00  E-value=0.11  Score=29.16  Aligned_cols=149  Identities=17%  Similarity=0.165  Sum_probs=74.5

Q ss_pred             HHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEEECCHHHHHHHHHHHHHHHHHH
Q ss_conf             99999999998740565554210124650257659789999999999980899669998085899999999999999985
Q gi|254781215|r   55 QLEFMEVVDAHCLNSVNNPNPEVFKGAISAGRGIGKTTLNAWLVLWLMSTRPGISVICLANSETQLKTTLWAEVSKWLSL  134 (511)
Q Consensus        55 Q~e~l~~i~~~~~~~~~~~~~~~~r~aV~sgrG~GKS~l~a~l~lw~l~~~p~~kv~vtApt~~Q~~~ilw~Ei~k~~~~  134 (511)
                      |.-+++.+...+..++.-|     -..-...||+|||+++-.++--.=|..+...-.|.-=  .    .+ .+|.    .
T Consensus        21 Q~~v~~~L~nal~~~rl~h-----aylf~G~rGvGKTt~ARi~Ak~lNC~~~~~~~pcg~C--~----~C-~~i~----~   84 (717)
T PRK08853         21 QSHVLTALENALAHNRLHH-----AYLFSGTRGVGKTTIGRLFAKGLNCETGITSTPCGQC--A----TC-KEID----E   84 (717)
T ss_pred             CHHHHHHHHHHHHCCCCCC-----EEEEECCCCCCHHHHHHHHHHHHCCCCCCCCCCCCCC--C----CH-HHHH----C
T ss_conf             5999999999997099740-----5761088988898999999998678999999978887--0----26-7674----4


Q ss_pred             CHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCCCCCCCHHHHCCCCCCEEEEECCHHCCCHHHHHHHHHH
Q ss_conf             50001344432222223334443211123578616985303575561002120267614999711102997889888888
Q gi|254781215|r  135 LPNKHWFEMQSLSLHPAPWYSDVLHCSLGIDSKHYSTMCRTYSEERPDTFVGHHNTYGMAIINDEASGTPDVINLGILGF  214 (511)
Q Consensus       135 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~ea~~G~h~~~~~lvI~DEAsgI~d~i~e~i~~~  214 (511)
                                       +...+...++-....+  ....|... ++ -.+.-.++.+. .+|+||.+.+....|+++..+
T Consensus        85 -----------------g~~~d~~EiDaAs~~~--vdd~rel~-~~-~~y~p~~~~yK-vyiiDEvHmls~~afnAlLKt  142 (717)
T PRK08853         85 -----------------GRFVDLLEIDAASRTK--VEDTRELL-DN-VQYKPARGRFK-VYLIDEVHMLSRHSFNALLKT  142 (717)
T ss_pred             -----------------CCCCCEEEECCCCCCC--HHHHHHHH-HH-CCCCCCCCCEE-EEEEECHHHCCHHHHHHHHHH
T ss_conf             -----------------7877524540565678--89999999-85-55488778547-999830544389999999876


Q ss_pred             HCCCCCCE-EEEEECCCCCCCCHHHHHH
Q ss_conf             50799813-8998238998765567653
Q gi|254781215|r  215 LTERNANR-FWIMTSNPRRLSGKFYEIF  241 (511)
Q Consensus       215 Lt~~g~~~-~~i~~~nP~~~~g~fy~~~  241 (511)
                      |-.+=... +++++..|.+..-...-.|
T Consensus       143 lEEPP~hv~FilaTT~~~kip~TilSRc  170 (717)
T PRK08853        143 LEEPPEYVKFLLATTDPQKLPVTILSRC  170 (717)
T ss_pred             HCCCCCCEEEEEECCCHHHCCHHHHHHH
T ss_conf             0378756489984387343738898765


No 90 
>PRK09112 DNA polymerase III subunit delta'; Validated
Probab=95.97  E-value=0.12  Score=29.09  Aligned_cols=163  Identities=15%  Similarity=0.173  Sum_probs=75.1

Q ss_pred             HHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHHCCCC-EE--EEEECCHHHHHHHHHHHHHHH
Q ss_conf             999999999987405655542101246502576597899999999999808996-69--998085899999999999999
Q gi|254781215|r   55 QLEFMEVVDAHCLNSVNNPNPEVFKGAISAGRGIGKTTLNAWLVLWLMSTRPGI-SV--ICLANSETQLKTTLWAEVSKW  131 (511)
Q Consensus        55 Q~e~l~~i~~~~~~~~~~~~~~~~r~aV~sgrG~GKS~l~a~l~lw~l~~~p~~-kv--~vtApt~~Q~~~ilw~Ei~k~  131 (511)
                      |.++.+.+..-...++.-|     ..-....+|+||++++=.++-+.++ .++. ..  -+..|...   ...+..+.  
T Consensus        28 q~~~~~~L~~a~~~gRl~H-----A~Lf~GP~GiGKaTlA~~~A~~Ll~-~~~~~~~~~~~~~pd~~---~~~~r~i~--   96 (352)
T PRK09112         28 HEEARAFLAQAYREGRLHH-----ALLFEGPEGIGKATLAFHLANHILS-HPDPNEAPETLADPDPA---SPLWRQIA--   96 (352)
T ss_pred             HHHHHHHHHHHHHCCCCCC-----EEEEECCCCCCHHHHHHHHHHHHHC-CCCCCCCCCCCCCCCCC---CHHHHHHH--
T ss_conf             6999999999998499652-----4653589980899999999999866-99866686556788878---77899997--


Q ss_pred             HHHCHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCCCCCCCHHHHCCCCCCEEEEECCHHCCCHHHHHHH
Q ss_conf             98550001344432222223334443211123578616985303575561002120267614999711102997889888
Q gi|254781215|r  132 LSLLPNKHWFEMQSLSLHPAPWYSDVLHCSLGIDSKHYSTMCRTYSEERPDTFVGHHNTYGMAIINDEASGTPDVINLGI  211 (511)
Q Consensus       132 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~ea~~G~h~~~~~lvI~DEAsgI~d~i~e~i  211 (511)
                       . ....+.+... .     .+..........+.-..........      +.....+.+. .+|+|||..+....++++
T Consensus        97 -~-g~hpdl~~i~-r-----~~d~k~~~~~~~I~vd~iR~l~~~~------~~~~~~~~~k-v~Iid~ad~m~~~aaNAL  161 (352)
T PRK09112         97 -Q-GAHPNLLHLT-R-----PFDEKTGKFKTAITVDEIRRVTHFL------SQTSGDGNWR-IVIIDPADDMNRNAANAI  161 (352)
T ss_pred             -C-CCCCCEEEEE-C-----CCCHHHHHHHCCCCHHHHHHHHHHH------CCCCCCCCEE-EEEECCHHHHHHHHHHHH
T ss_conf             -4-8999956553-4-----3220214543357779999999984------5488668806-999818787469999999


Q ss_pred             HHHHCCCCCCEEEEEE-CCCCCCCCHHHHHHHC
Q ss_conf             8885079981389982-3899876556765303
Q gi|254781215|r  212 LGFLTERNANRFWIMT-SNPRRLSGKFYEIFNK  243 (511)
Q Consensus       212 ~~~Lt~~g~~~~~i~~-~nP~~~~g~fy~~~~~  243 (511)
                      .-+|-.+-.+..++.+ .+|.+..-...-.|.+
T Consensus       162 LK~LEEPp~~~~fiLit~~~~~ll~TI~SRCq~  194 (352)
T PRK09112        162 LKTLEEPPARALFILISHSSGRLLPTIRSRCQP  194 (352)
T ss_pred             HHHHHCCCCCEEEEEEECCHHHCHHHHHHHCCC
T ss_conf             998534898748998869977776899974332


No 91 
>TIGR02621 cas3_GSU0051 CRISPR-associated helicase Cas3, Anaes-subtype; InterPro: IPR013444    This entry represents a CRISPR-associated putative DEAH-box helicase, or Cas3, subtype found in Actinomyces naeslundii MG1, Geobacter sulfurreducens PCA, Gemmata obscuriglobus UQM 2246, and Desulfotalea psychrophila. The proteins include both DEAH and HD motifs..
Probab=95.83  E-value=0.015  Score=34.64  Aligned_cols=84  Identities=25%  Similarity=0.303  Sum_probs=49.6

Q ss_pred             CCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCCCHH-HHHHHHHHHHHHHC-----------CCCEEE
Q ss_conf             565557845899999999999874056555421012465025765978-99999999999808-----------996699
Q gi|254781215|r   44 PLEGFSAPRSWQLEFMEVVDAHCLNSVNNPNPEVFKGAISAGRGIGKT-TLNAWLVLWLMSTR-----------PGISVI  111 (511)
Q Consensus        44 ~~~~~~~P~~WQ~e~l~~i~~~~~~~~~~~~~~~~r~aV~sgrG~GKS-~l~a~l~lw~l~~~-----------p~~kv~  111 (511)
                      .+.+..||++||.++..-+.+.       ..|.    +++-+.|.||| .+++..++....-.           -+.+-+
T Consensus        10 ~~~G~~GPfpwQ~~L~~r~~~G-------~~P~----~~s~PTg~GKTlavi~~WlyAl~~~a~~~Grrr~~~~vP~RL~   78 (975)
T TIGR02621        10 ELTGYSGPFPWQLRLAERFVAG-------EPPE----SCSVPTGLGKTLAVIAVWLYALAIDAEQVGRRRRRRKVPRRLV   78 (975)
T ss_pred             HHCCCCCCCHHHHHHHHHHHCC-------CCCC----CCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCCEEECCCEEE
T ss_conf             7358988865899999998548-------9887----6678753236899999999998740003673242133683137


Q ss_pred             EEECCHHHHHHHHHHHHHHHHHHCHHCC
Q ss_conf             9808589999999999999998550001
Q gi|254781215|r  112 CLANSETQLKTTLWAEVSKWLSLLPNKH  139 (511)
Q Consensus       112 vtApt~~Q~~~ilw~Ei~k~~~~~~~~~  139 (511)
                      ++-+ .+.+=|-.+.+..|+.+.++..+
T Consensus        79 yvVd-RR~vVD~~te~a~~i~~aL~~~p  105 (975)
T TIGR02621        79 YVVD-RRTVVDQSTEEAEKIREALGEAP  105 (975)
T ss_pred             EEEE-CCEEECCHHHHHHHHHHHCCCCC
T ss_conf             8871-42453432789999998546888


No 92 
>PRK07993 DNA polymerase III subunit delta'; Validated
Probab=95.82  E-value=0.13  Score=28.68  Aligned_cols=153  Identities=16%  Similarity=0.110  Sum_probs=77.8

Q ss_pred             HHHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEEECCHHHHHHHHHHHHHHHHH
Q ss_conf             99999999999874056555421012465025765978999999999998089966999808589999999999999998
Q gi|254781215|r   54 WQLEFMEVVDAHCLNSVNNPNPEVFKGAISAGRGIGKTTLNAWLVLWLMSTRPGISVICLANSETQLKTTLWAEVSKWLS  133 (511)
Q Consensus        54 WQ~e~l~~i~~~~~~~~~~~~~~~~r~aV~sgrG~GKS~l~a~l~lw~l~~~p~~kv~vtApt~~Q~~~ilw~Ei~k~~~  133 (511)
                      ||...-+.+.....++..-|     -.-+.+..|+||+.++-.++-+.+|..|...-.|..-..=++  +       ...
T Consensus         6 Wl~~~~~~l~~~~~~~rl~H-----A~L~~G~~G~Gk~~la~~~a~~llC~~~~~~~~Cg~C~~C~l--~-------~~~   71 (334)
T PRK07993          6 WLRPDYEKLVGSYQAGRGHH-----ALLIQALPGMGDDALIYALSRYLLCQQPQGHKSCGHCRGCQL--M-------QAG   71 (334)
T ss_pred             CCHHHHHHHHHHHHCCCCCE-----EEEEECCCCCCHHHHHHHHHHHHCCCCCCCCCCCCCCHHHHH--H-------HCC
T ss_conf             87899999999998598104-----675479999889999999999981899999999999978999--8-------668


Q ss_pred             HCHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCCCCCCCHHHHCCCCCCEEEEECCHHCCCHHHHHHHHH
Q ss_conf             55000134443222222333444321112357861698530357556100212026761499971110299788988888
Q gi|254781215|r  134 LLPNKHWFEMQSLSLHPAPWYSDVLHCSLGIDSKHYSTMCRTYSEERPDTFVGHHNTYGMAIINDEASGTPDVINLGILG  213 (511)
Q Consensus       134 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~ea~~G~h~~~~~lvI~DEAsgI~d~i~e~i~~  213 (511)
                      .-|.-++..-...   .....++..               |....  --+.....+.+. .+|+|+|..+....-+++.-
T Consensus        72 ~HPD~~~i~pe~~---~~~I~IdqI---------------R~l~~--~~~~~~~~g~~k-V~iI~~Ae~mn~~AaNaLLK  130 (334)
T PRK07993         72 THPDYYTLTPEKG---KSSLGVDAV---------------REVTE--KLYEHARLGGAK-VVWLPDAALLTDAAANALLK  130 (334)
T ss_pred             CCCCEEEECCCCC---CCCCCHHHH---------------HHHHH--HHHHCCCCCCCE-EEEECCHHHHCHHHHHHHHH
T ss_conf             9998477534223---455999999---------------99999--984366569947-99976677759999999998


Q ss_pred             HHCCCCCCEEEEEE-CCCCCCCCHHHHHH
Q ss_conf             85079981389982-38998765567653
Q gi|254781215|r  214 FLTERNANRFWIMT-SNPRRLSGKFYEIF  241 (511)
Q Consensus       214 ~Lt~~g~~~~~i~~-~nP~~~~g~fy~~~  241 (511)
                      +|-++.....++.. .+|.+.--..+-.+
T Consensus       131 tLEEPp~~t~~iL~t~~~~~lLpTI~SRC  159 (334)
T PRK07993        131 TLEEPPEKTWFFLACREPARLLATLRSRC  159 (334)
T ss_pred             HHCCCCCCEEEEEECCCHHHCCCHHHHHC
T ss_conf             61279988499986698565723887523


No 93 
>TIGR03499 FlhF flagellar biosynthetic protein FlhF.
Probab=95.74  E-value=0.056  Score=31.06  Aligned_cols=45  Identities=16%  Similarity=0.076  Sum_probs=22.7

Q ss_pred             HHHHHHHHHHHHHHCCCC---EEEEEECCCCHHHHHHHHHC----CCEEEEECC
Q ss_conf             889999999999861888---29980068763688989864----982798427
Q gi|254781215|r  353 LRTTNNKISGLVEKYRPD---AIIIDANNTGARTCDYLEML----GYHVYRVLG  399 (511)
Q Consensus       353 ~~~~a~~i~~~~~~~~~~---~i~iD~~GvG~gV~d~L~~~----g~~v~~v~~  399 (511)
                      |+.+|.....+..+++..   -|-+|..=+  |-+++|+.+    |.++.-+..
T Consensus       208 TTTiAKLAa~~~l~~~~~~V~lIT~DtyRi--gA~eQLk~ya~il~vp~~vv~~  259 (282)
T TIGR03499       208 TTTLAKLAARFVLEHGKKKVALITTDTYRI--GAVEQLKTYAKILGVPVKVARD  259 (282)
T ss_pred             HHHHHHHHHHHHHHCCCCCEEEEEECCCCH--HHHHHHHHHHHHHCCEEEEECC
T ss_conf             889999999999973899679998077767--8999999999995974899399


No 94 
>COG1484 DnaC DNA replication protein [DNA replication, recombination, and repair]
Probab=95.70  E-value=0.15  Score=28.40  Aligned_cols=74  Identities=16%  Similarity=-0.022  Sum_probs=49.8

Q ss_pred             HCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEEE
Q ss_conf             42145577756555784589999999999987405655542101246502576597899999999999808996699980
Q gi|254781215|r   35 FFPWGEKGTPLEGFSAPRSWQLEFMEVVDAHCLNSVNNPNPEVFKGAISAGRGIGKTTLNAWLVLWLMSTRPGISVICLA  114 (511)
Q Consensus        35 ~~~w~~~~~~~~~~~~P~~WQ~e~l~~i~~~~~~~~~~~~~~~~r~aV~sgrG~GKS~l~a~l~lw~l~~~p~~kv~vtA  114 (511)
                      .+|.. +.-....|..+..=++..|..+.....+-.     ..--+....+-|+|||+|++.+..-.+ ...-+..+++.
T Consensus        69 ~~p~~-k~~~~~d~~~~~~~~~~~l~~~~~~~~~~~-----~~~nl~l~G~~G~GKthLa~Ai~~~l~-~~g~sv~f~~~  141 (254)
T COG1484          69 SFPAK-KTFEEFDFEFQPGIDKKALEDLASLVEFFE-----RGENLVLLGPPGVGKTHLAIAIGNELL-KAGISVLFITA  141 (254)
T ss_pred             CCCCC-CCCCCCCCCCCCHHHHHHHHHHHHHHHHHC-----CCCCEEEECCCCCCHHHHHHHHHHHHH-HCCCEEEEEEH
T ss_conf             68755-785430235885566999999999998732-----588289989999879999999999999-83984999885


Q ss_pred             C
Q ss_conf             8
Q gi|254781215|r  115 N  115 (511)
Q Consensus       115 p  115 (511)
                      |
T Consensus       142 ~  142 (254)
T COG1484         142 P  142 (254)
T ss_pred             H
T ss_conf             9


No 95 
>TIGR00345 arsA arsenite-activated ATPase (arsA); InterPro: IPR003348   This ATPase is involved in the removal of arsenate, antimonite, and arsenate from the cell.    In Escherichia coli an anion-translocating ATPase has been identified as the product of the arsenical resistance operon of resistance plasmid R773. This ATP-driven oxyanion pump catalyses extrusion of the oxyanions arsenite, antimonite and arsenate. Maintenance of a low intracellular concentration of oxyanion produces resistance to the toxic agents. The pump is composed of two polypeptides, the products of the arsA and arsB genes. This two-subunit enzyme produces resistance to arsenite and antimonite. A third gene, arsC, expands the substrate specificity to allow for arsenate pumping and resistance .   The ArsA and ArsB proteins form a membrane-bound pump that functions as an oxyanion-translocating ATPase. The ArsC protein is an arsenate reductase that reduces arsenate to arsenite, which is subsequently pumped out of the cell .; GO: 0005524 ATP binding, 0006820 anion transport, 0016020 membrane.
Probab=95.68  E-value=0.018  Score=34.14  Aligned_cols=41  Identities=32%  Similarity=0.494  Sum_probs=33.5

Q ss_pred             CCCHHHHHHHHHHHHHHHCCCCEEEEE----ECCHHHHHHHHHHHHHH
Q ss_conf             659789999999999980899669998----08589999999999999
Q gi|254781215|r   87 GIGKTTLNAWLVLWLMSTRPGISVICL----ANSETQLKTTLWAEVSK  130 (511)
Q Consensus        87 G~GKS~l~a~l~lw~l~~~p~~kv~vt----Apt~~Q~~~ilw~Ei~k  130 (511)
                      |||||+++|..++|.+.-.||.|++++    |.+.+|+.+   .|+..
T Consensus         7 GVGKTt~SaAtA~~lAe~qPGkkvLl~STDPAHsL~D~F~---~e~G~   51 (330)
T TIGR00345         7 GVGKTTISAATAIRLAEQQPGKKVLLVSTDPAHSLSDVFE---QELGH   51 (330)
T ss_pred             CCHHHHHHHHHHHHHHHHCCCCEEEEEEECCCHHHHHHHH---HHHCC
T ss_conf             8238889999999998518997799984086002788611---32177


No 96 
>PRK09111 DNA polymerase III subunits gamma and tau; Validated
Probab=95.67  E-value=0.15  Score=28.31  Aligned_cols=152  Identities=16%  Similarity=0.066  Sum_probs=73.6

Q ss_pred             HHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCE-EEEEEC--CHHHHHHHHHHHHHHH
Q ss_conf             9999999999874056555421012465025765978999999999998089966-999808--5899999999999999
Q gi|254781215|r   55 QLEFMEVVDAHCLNSVNNPNPEVFKGAISAGRGIGKTTLNAWLVLWLMSTRPGIS-VICLAN--SETQLKTTLWAEVSKW  131 (511)
Q Consensus        55 Q~e~l~~i~~~~~~~~~~~~~~~~r~aV~sgrG~GKS~l~a~l~lw~l~~~p~~k-v~vtAp--t~~Q~~~ilw~Ei~k~  131 (511)
                      |.-+.+.+......+..-|     ..--...||+|||+++-.++--.=|..|+.. ....-|  .-..-+.|        
T Consensus        28 q~~~~~~l~~~~~~~~~~~-----a~l~~g~rg~gktt~ari~a~~lnc~~~~~~~~~~~~~c~~c~~c~~i--------   94 (600)
T PRK09111         28 QEAMVRTLRNAFETGRIAQ-----AFMLTGVRGVGKTTTARILARALNYKGPDGVGGPTIDPCGVGEHCQAI--------   94 (600)
T ss_pred             CHHHHHHHHHHHHCCCCCC-----EEEEECCCCCCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCHHHHHH--------
T ss_conf             5999999999997298420-----476457898789999999999966988766689988989988658988--------


Q ss_pred             HHHCHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCCCCCCCHHHHCCCCCCEEEEECCHHCCCHHHHHHH
Q ss_conf             98550001344432222223334443211123578616985303575561002120267614999711102997889888
Q gi|254781215|r  132 LSLLPNKHWFEMQSLSLHPAPWYSDVLHCSLGIDSKHYSTMCRTYSEERPDTFVGHHNTYGMAIINDEASGTPDVINLGI  211 (511)
Q Consensus       132 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~ea~~G~h~~~~~lvI~DEAsgI~d~i~e~i  211 (511)
                       ..                 +...+...++.....+  ....|....  --.+.-..+.+ -.+|+||.+.+....|+++
T Consensus        95 -~~-----------------~~~~d~~e~daas~~~--v~~~r~~~~--~~~~~p~~~~~-kv~iidevhmls~~afnal  151 (600)
T PRK09111         95 -ME-----------------GRHVDVIEMDAASHTG--VDDIREIIE--SVRYRPVSARY-KVYIIDEVHMLSTAAFNAL  151 (600)
T ss_pred             -HC-----------------CCCCCEEEEECCCCCC--HHHHHHHHH--HHCCCCCCCCE-EEEEEECCCCCCHHHHHHH
T ss_conf             -66-----------------8998758851554578--889999998--60538877754-6999600110579999999


Q ss_pred             HHHHCCCCCCEEEE-EECCCCCCCCHHHHHHH
Q ss_conf             88850799813899-82389987655676530
Q gi|254781215|r  212 LGFLTERNANRFWI-MTSNPRRLSGKFYEIFN  242 (511)
Q Consensus       212 ~~~Lt~~g~~~~~i-~~~nP~~~~g~fy~~~~  242 (511)
                      .-||-.+=...+++ ++..|.+..-..--.|.
T Consensus       152 lktleepp~~~~fi~att~~~k~p~ti~src~  183 (600)
T PRK09111        152 LKTLEEPPPHVKFIFATTEIRKVPVTVLSRCQ  183 (600)
T ss_pred             HHHHHCCCCCEEEEEECCCHHHCCHHHHHHHH
T ss_conf             98762598654999962853437589985441


No 97 
>PRK11057 ATP-dependent DNA helicase RecQ; Provisional
Probab=95.26  E-value=0.11  Score=29.10  Aligned_cols=60  Identities=17%  Similarity=0.091  Sum_probs=42.3

Q ss_pred             CCCCCHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEEECCHHHHHHH
Q ss_conf             55784589999999999987405655542101246502576597899999999999808996699980858999999
Q gi|254781215|r   47 GFSAPRSWQLEFMEVVDAHCLNSVNNPNPEVFKGAISAGRGIGKTTLNAWLVLWLMSTRPGISVICLANSETQLKTT  123 (511)
Q Consensus        47 ~~~~P~~WQ~e~l~~i~~~~~~~~~~~~~~~~r~aV~sgrG~GKS~l~a~l~lw~l~~~p~~kv~vtApt~~Q~~~i  123 (511)
                      +++.=|+-|+|++.++-...            .+-|..+.|.|||.+--.=++.     .+..++|+.|...-.+|-
T Consensus        22 G~~~Fr~~Q~e~i~~~l~g~------------D~l~~mpTG~GKSlcyQlPal~-----~~g~tiVisPLisLm~DQ   81 (607)
T PRK11057         22 GYQQFRPGQEEIIDTVLSGR------------DCLVVMPTGGGKSLCYQIPALV-----LDGLTLVVSPLISLMKDQ   81 (607)
T ss_pred             CCCCCCHHHHHHHHHHHCCC------------CEEEECCCCCHHHHHHHHHHHH-----CCCCEEEECCHHHHHHHH
T ss_conf             98434576999999998699------------8899878995597999999987-----799889986879999999


No 98 
>COG5525 Bacteriophage tail assembly protein [General function prediction only]
Probab=95.25  E-value=0.049  Score=31.45  Aligned_cols=172  Identities=10%  Similarity=0.041  Sum_probs=92.7

Q ss_pred             HHHCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEE
Q ss_conf             76421455777565557845899999999999874056555421012465025765978999999999998089966999
Q gi|254781215|r   33 LHFFPWGEKGTPLEGFSAPRSWQLEFMEVVDAHCLNSVNNPNPEVFKGAISAGRGIGKTTLNAWLVLWLMSTRPGISVIC  112 (511)
Q Consensus        33 ~~~~~w~~~~~~~~~~~~P~~WQ~e~l~~i~~~~~~~~~~~~~~~~r~aV~sgrG~GKS~l~a~l~lw~l~~~p~~kv~v  112 (511)
                      .|..|=+...++.+=-+.|  .|.+++..+          ..+...+|.+..+-++|||.+....+.|++.+ .+...++
T Consensus        32 ~y~~~~~sa~~~g~W~t~p--~~~~~~n~~----------~~~~~~~V~f~k~ArvG~T~m~~gw~~Y~I~~-~p~~mlv   98 (611)
T COG5525          32 NYMLPKESAYEEGRWETLP--FQIAIMNAM----------GSDEIRAVNFVKSARVGKTKMLLGWIGYFIEH-KPRNMLV   98 (611)
T ss_pred             HCCCCCCCCCCCCCCCCCH--HHHHHHHCC----------CCCCCEEEEEEECCCCCCEEEECCEEEEEEEE-CCCCCEE
T ss_conf             3024765578877776726--899987536----------98641689997402036224542258999986-5765233


Q ss_pred             EECCHHHHHHHHHHHHHHHHHHCHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCCCCCCCHHHHCCCCCC
Q ss_conf             80858999999999999999855000134443222222333444321112357861698530357556100212026761
Q gi|254781215|r  113 LANSETQLKTTLWAEVSKWLSLLPNKHWFEMQSLSLHPAPWYSDVLHCSLGIDSKHYSTMCRTYSEERPDTFVGHHNTYG  192 (511)
Q Consensus       113 tApt~~Q~~~ilw~Ei~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~ea~~G~h~~~~  192 (511)
                      +.||..-+++-+=..+...++.+|.-.        ..+.+...+-+...-.+..+.+++.+-.       |.-..++...
T Consensus        99 ~qpt~~~a~~~~k~k~~pti~~~p~l~--------~~ls~~~~dNn~~~K~f~~G~~l~~g~~-------s~~~~r~~s~  163 (611)
T COG5525          99 VQPTDEKAREHSKTKVEPTIRDVPSLV--------SLLSPSRNDNNLTDKRFPGGVFLMIGWK-------SAKNYRSISV  163 (611)
T ss_pred             ECCCHHHHHHHHHHHCCCCHHCCHHHH--------HHCCCCCCCCCEECCCCCCCEEEEECCC-------CCCCCCCCCH
T ss_conf             336555779988875075020063378--------6527656787311023347727972565-------4565667644


Q ss_pred             EEEEECCHHCCCHHHH------HHHHHHHCCCCCCEEEEEECCCCCC
Q ss_conf             4999711102997889------8888885079981389982389987
Q gi|254781215|r  193 MAIINDEASGTPDVIN------LGILGFLTERNANRFWIMTSNPRRL  233 (511)
Q Consensus       193 ~lvI~DEAsgI~d~i~------e~i~~~Lt~~g~~~~~i~~~nP~~~  233 (511)
                      -.+++||-+.+|+.+-      ..+..=+++ ....+.+.-|+|+-.
T Consensus       164 ~~v~lde~d~fpedv~~EGs~~sl~~kR~~t-~~~~~~l~~stP~i~  209 (611)
T COG5525         164 DVVVLDELDRFPEDVEGEGSATSLASKRITT-MSWGKSLVESTPTIP  209 (611)
T ss_pred             HHHHHHHHHCCCHHHCCCCCHHHHHHHHHCC-CCCCCEEEECCCCCC
T ss_conf             5656667743651222688876778876024-556622441378788


No 99 
>COG3972 Superfamily I DNA and RNA helicases [General function prediction only]
Probab=95.24  E-value=0.052  Score=31.25  Aligned_cols=119  Identities=18%  Similarity=0.079  Sum_probs=65.1

Q ss_pred             CCCCCHHHHHHHHHHHHHHHCCCCEEEEEECCH---HHHHHHHHHHHHH--------HHHHCHHCCCCCCCCCCCCCCCC
Q ss_conf             576597899999999999808996699980858---9999999999999--------99855000134443222222333
Q gi|254781215|r   85 GRGIGKTTLNAWLVLWLMSTRPGISVICLANSE---TQLKTTLWAEVSK--------WLSLLPNKHWFEMQSLSLHPAPW  153 (511)
Q Consensus        85 grG~GKS~l~a~l~lw~l~~~p~~kv~vtApt~---~Q~~~ilw~Ei~k--------~~~~~~~~~~~~~~~~~~~~~~~  153 (511)
                      =-|.|||.+.|.-+...-.++|++++++|--|.   +|.|+. .++.-.        |-..+....|...+.-..+...-
T Consensus       184 LAGSGKT~~La~Kaa~lh~knPd~~I~~Tfftk~L~s~~r~l-v~~F~f~~~e~~pdW~~~l~~h~wgG~t~~g~y~~~~  262 (660)
T COG3972         184 LAGSGKTELLAHKAAELHSKNPDSRIAFTFFTKILASTMRTL-VPEFFFMRVEKQPDWGTKLFCHNWGGLTKEGFYGMYR  262 (660)
T ss_pred             CCCCCCHHHHHHHHHHHHCCCCCCEEEEEEEHHHHHHHHHHH-HHHHHHHHHHCCCCCCCEEEEECCCCCCCCCCHHHHH
T ss_conf             247873029887778974479986389986667888999999-9999998862488724268884357878886038899


Q ss_pred             CCCCCCCCCCCCCCEEEEEECCCCCCC-------CCHHHHCCC-CCCEEEEECCHHCCCHHHHHHHHHHHCC
Q ss_conf             444321112357861698530357556-------100212026-7614999711102997889888888507
Q gi|254781215|r  154 YSDVLHCSLGIDSKHYSTMCRTYSEER-------PDTFVGHHN-TYGMAIINDEASGTPDVINLGILGFLTE  217 (511)
Q Consensus       154 ~~~~~~~~~~~~~~~~~~~~~~~s~~~-------~ea~~G~h~-~~~~lvI~DEAsgI~d~i~e~i~~~Lt~  217 (511)
                      ..-.      .       -.++++..+       .|.++...+ +....+.+||+...|+.+++...-..++
T Consensus       263 ~~~~------~-------~~~~fsg~g~~F~~aC~eli~~~~~~~~yD~ilIDE~QDFP~~F~~Lcf~~tkd  321 (660)
T COG3972         263 YICH------Y-------YEIPFSGFGNGFDAACKELIADINNKKAYDYILIDESQDFPQSFIDLCFMVTKD  321 (660)
T ss_pred             HHHC------C-------CCCCCCCCCCCHHHHHHHHHHHHHCCCCCCEEEECCCCCCCHHHHHHHHHHHCC
T ss_conf             9842------6-------654547877406799999998642564231799424554778999999998247


No 100
>PRK08699 DNA polymerase III subunit delta'; Validated
Probab=95.13  E-value=0.23  Score=27.19  Aligned_cols=183  Identities=13%  Similarity=0.098  Sum_probs=86.5

Q ss_pred             HHHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHHCCCC-EEEEEEC-CHHHHHHHHHHHHHHH
Q ss_conf             9999999999987405655542101246502576597899999999999808996-6999808-5899999999999999
Q gi|254781215|r   54 WQLEFMEVVDAHCLNSVNNPNPEVFKGAISAGRGIGKTTLNAWLVLWLMSTRPGI-SVICLAN-SETQLKTTLWAEVSKW  131 (511)
Q Consensus        54 WQ~e~l~~i~~~~~~~~~~~~~~~~r~aV~sgrG~GKS~l~a~l~lw~l~~~p~~-kv~vtAp-t~~Q~~~ilw~Ei~k~  131 (511)
                      ||.+.-+.+.....+     .|+  -.-..+..|+||+.++-.++-+.+|..|.. ...|..= +-++..          
T Consensus         5 W~~~~w~~l~~~~~r-----l~H--A~L~~Gp~G~Gk~~~A~~~A~~llC~~~~~~~~~Cg~C~sC~~~~----------   67 (325)
T PRK08699          5 WHQEQWRQIAEHWER-----RPN--AWLFVGKKGTGKTAFARFAAKALLCETPAPGCKPCGECMSCHLFG----------   67 (325)
T ss_pred             CCHHHHHHHHHHCCC-----CCE--EEEEECCCCCCHHHHHHHHHHHHHCCCCCCCCCCCCCCHHHHHHH----------
T ss_conf             457999999983445-----011--797579999789999999999982899988899898888899986----------


Q ss_pred             HHHCHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCCCCCCCHHHHCCCCCCEEEEECCHHCCCHHHHHHH
Q ss_conf             98550001344432222223334443211123578616985303575561002120267614999711102997889888
Q gi|254781215|r  132 LSLLPNKHWFEMQSLSLHPAPWYSDVLHCSLGIDSKHYSTMCRTYSEERPDTFVGHHNTYGMAIINDEASGTPDVINLGI  211 (511)
Q Consensus       132 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~ea~~G~h~~~~~lvI~DEAsgI~d~i~e~i  211 (511)
                      ...-|.-.......... ..+..    ...++++      ..|....  --+.....+.+. .+|+|+|..+.....+++
T Consensus        68 ~g~HPD~~~i~p~~~~~-~~g~~----~~~I~id------qiR~l~~--~~~~~~~~~~~k-V~ii~~ae~mn~~aaNaL  133 (325)
T PRK08699         68 QGSHPDFYEITPLADEP-ENGRK----LLQIKID------AVREIID--NVYLTSVRGGLR-VILIHPAESMNVQAANSL  133 (325)
T ss_pred             CCCCCCEEEEECCCCCC-CCCCC----CCCCCHH------HHHHHHH--HHCCCCCCCCCE-EEEECCHHHHCHHHHHHH
T ss_conf             59999968851344530-01665----5667699------9999999--971086568946-999857777589999999


Q ss_pred             HHHHCCCCCCE-EEEEECCCCCCCCHHHHHHHCCCCCCEEEEECCCCCCCCCHHHHHHHHHHCCCCHHH
Q ss_conf             88850799813-899823899876556765303524741798404336778977899999751898013
Q gi|254781215|r  212 LGFLTERNANR-FWIMTSNPRRLSGKFYEIFNKPLDDWKRFQIDTRTVEGIDPSFHEGIIARYGLDSDV  279 (511)
Q Consensus       212 ~~~Lt~~g~~~-~~i~~~nP~~~~g~fy~~~~~~~~~w~~~~i~~~~~p~~~~~~ie~~~~~~geds~~  279 (511)
                      .-+|-++.... +++.+.+|.+.--...-.+..            ..-+..+++.+..|..+.|...+.
T Consensus       134 LK~LEEPp~~~~fiL~t~~~~~llpTI~SRc~~------------~~~~~p~~~~~~~~L~~~gv~~~~  190 (325)
T PRK08699        134 LKVLEEPPPQVVFLLVSHAADKVLPTIKSRCRK------------MVLPAPSHEEALAYLRERGVAEPE  190 (325)
T ss_pred             HHHHCCCCCCEEEEEEECCHHHCCCHHHHCCCC------------CCCCCCCHHHHHHHHHHCCCCCHH
T ss_conf             998417888848999879846462339864542------------108995999999999974897678


No 101
>KOG0338 consensus
Probab=95.10  E-value=0.18  Score=27.94  Aligned_cols=154  Identities=16%  Similarity=0.071  Sum_probs=82.3

Q ss_pred             CCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHHCCC----CEEEEEECCHHH
Q ss_conf             5655578458999999999998740565554210124650257659789999999999980899----669998085899
Q gi|254781215|r   44 PLEGFSAPRSWQLEFMEVVDAHCLNSVNNPNPEVFKGAISAGRGIGKTTLNAWLVLWLMSTRPG----ISVICLANSETQ  119 (511)
Q Consensus        44 ~~~~~~~P~~WQ~e~l~~i~~~~~~~~~~~~~~~~r~aV~sgrG~GKS~l~a~l~lw~l~~~p~----~kv~vtApt~~Q  119 (511)
                      .--+|..|-+-|...+--   .+   .++|      +--.+..|+|||+..+.=+|-.|+.+|-    .+|+|.-||..-
T Consensus       197 ~~lGy~~PTpIQ~a~IPv---al---lgkD------Ica~A~TGsGKTAAF~lPiLERLlYrPk~~~~TRVLVL~PTREL  264 (691)
T KOG0338         197 STLGYKKPTPIQVATIPV---AL---LGKD------ICACAATGSGKTAAFALPILERLLYRPKKVAATRVLVLVPTREL  264 (691)
T ss_pred             HHCCCCCCCCHHHHCCCH---HH---HCCH------HHHEECCCCCCHHHHHHHHHHHHHCCCCCCCCEEEEEEECCHHH
T ss_conf             743878887403310127---75---2222------56401146871145678899998527356761269998350899


Q ss_pred             HHHHHHHHHHHHHHHCHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCCCCCCCHHHHCCCCCCEEEEECC
Q ss_conf             99999999999998550001344432222223334443211123578616985303575561002120267614999711
Q gi|254781215|r  120 LKTTLWAEVSKWLSLLPNKHWFEMQSLSLHPAPWYSDVLHCSLGIDSKHYSTMCRTYSEERPDTFVGHHNTYGMAIINDE  199 (511)
Q Consensus       120 ~~~ilw~Ei~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~ea~~G~h~~~~~lvI~DE  199 (511)
                      +-.+ +.-.++..+..-..       .-+-.-++-...+...+...+...+++.-..-.| --+..+|+-++.-.+|+||
T Consensus       265 aiQv-~sV~~qlaqFt~I~-------~~L~vGGL~lk~QE~~LRs~PDIVIATPGRlIDH-lrNs~sf~ldsiEVLvlDE  335 (691)
T KOG0338         265 AIQV-HSVTKQLAQFTDIT-------VGLAVGGLDLKAQEAVLRSRPDIVIATPGRLIDH-LRNSPSFNLDSIEVLVLDE  335 (691)
T ss_pred             HHHH-HHHHHHHHHHCCCE-------EEEEECCCCHHHHHHHHHHCCCEEEECCHHHHHH-HCCCCCCCCCCEEEEEECH
T ss_conf             9999-99999987660402-------4445247457889999830898799465058887-5158876534325777333


Q ss_pred             HHCC-----CHHHHHHHHHHHCCC
Q ss_conf             1029-----978898888885079
Q gi|254781215|r  200 ASGT-----PDVINLGILGFLTER  218 (511)
Q Consensus       200 AsgI-----~d~i~e~i~~~Lt~~  218 (511)
                      |.-+     .+.+-+.+..+-..+
T Consensus       336 ADRMLeegFademnEii~lcpk~R  359 (691)
T KOG0338         336 ADRMLEEGFADEMNEIIRLCPKNR  359 (691)
T ss_pred             HHHHHHHHHHHHHHHHHHHCCCCC
T ss_conf             888999999999999998551023


No 102
>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=95.05  E-value=0.08  Score=30.11  Aligned_cols=100  Identities=16%  Similarity=0.227  Sum_probs=44.5

Q ss_pred             CCCEEEEEECCC---EEEEEEECCCCCHH-HHHHHHHHHHHHCCCCEEEEEECCCCHHHHHHHHHCC--CE--EEEECCC
Q ss_conf             841799982275---58998732778988-9999999999861888299800687636889898649--82--7984277
Q gi|254781215|r  329 GDNTVVVLRRGP---VIEHLFDWSKTDLR-TTNNKISGLVEKYRPDAIIIDANNTGARTCDYLEMLG--YH--VYRVLGQ  400 (511)
Q Consensus       329 ~D~svi~~r~G~---~v~~~~~~~~~d~~-~~a~~i~~~~~~~~~~~i~iD~~GvG~gV~d~L~~~g--~~--v~~v~~~  400 (511)
                      +|+.||......   ...-...++..|+. -....+....-+||||+|.|=.. =|.--.|-|+-||  .+  +.-++.+
T Consensus       170 ~dR~vIiEDT~ElQC~A~N~V~lrT~d~~Gi~M~~LLk~TLRlRPDRI~VGEV-Rg~eAL~LLKAWNTGHPGGi~TiHAn  248 (315)
T TIGR02782       170 DDRVVIIEDTAELQCAAENLVALRTSDDVGISMTRLLKATLRLRPDRIIVGEV-RGGEALDLLKAWNTGHPGGIATIHAN  248 (315)
T ss_pred             CCEEEEEECCHHHHHCCCCEEEEECCCCCCCCHHHHHHHHHCCCCCCEEEEEE-CCHHHHHHHHHHCCCCCCCCEEECCC
T ss_conf             96189985471320137870687448986614788888750058873356301-43899999864058995302033148


Q ss_pred             CCCCCHHHHHHHHHHHHHHHHHHHHHCCCCC--HHHHHHHHH
Q ss_conf             7766402552279999999999997089998--189999985
Q gi|254781215|r  401 KRAVDLEFCRNRRTELHVKMADWLEFASLIN--HSGLIQNLK  440 (511)
Q Consensus       401 ~~~~~~~~y~N~rae~~~~~re~l~~g~l~~--d~~l~~el~  440 (511)
                      .+          ++ .=-.+-..+.+-...+  .+.|+.|-.
T Consensus       249 ~a----------~~-aL~RLeQLi~E~s~~~kP~~~lI~eav  279 (315)
T TIGR02782       249 NA----------KA-ALRRLEQLIAEVSVSPKPMQELIAEAV  279 (315)
T ss_pred             CH----------HH-HHHHHHHHHHHHCCCCCCHHHHHHHHH
T ss_conf             86----------68-999999999853589972057787541


No 103
>KOG1015 consensus
Probab=94.79  E-value=0.081  Score=30.04  Aligned_cols=172  Identities=15%  Similarity=0.121  Sum_probs=89.0

Q ss_pred             HHHHHHHHHHHHHHCCCCC-CCCCCEEEEEECCCCCCHHHHHHHHH-HHHHHHCCCCE-EEEEECCHHHHHHHHHHHHHH
Q ss_conf             9999999999987405655-54210124650257659789999999-99998089966-999808589999999999999
Q gi|254781215|r   54 WQLEFMEVVDAHCLNSVNN-PNPEVFKGAISAGRGIGKTTLNAWLV-LWLMSTRPGIS-VICLANSETQLKTTLWAEVSK  130 (511)
Q Consensus        54 WQ~e~l~~i~~~~~~~~~~-~~~~~~r~aV~sgrG~GKS~l~a~l~-lw~l~~~p~~k-v~vtApt~~Q~~~ilw~Ei~k  130 (511)
                      -|..=++.+.+.+.....+ --.....+..+-+-|.|||.-+-.++ .-.++...+.+ ++|+.|. ..+-+ -+.|.-+
T Consensus       672 HQv~GvqFMwd~~~eSlkr~~~~~GsGcILAHcMGLGKTlQVvtflhTvL~c~klg~ktaLvV~Pl-Nt~~N-W~~EFek  749 (1567)
T KOG1015         672 HQVDGVQFMWDCCCESLKRTKKSPGSGCILAHCMGLGKTLQVVTFLHTVLLCDKLGFKTALVVCPL-NTALN-WMNEFEK  749 (1567)
T ss_pred             CCCCCHHHHHHHHHHHHHHHCCCCCCCHHHHHHHCCCCEEHHHHHHHHHHHHHCCCCCEEEEECCH-HHHHH-HHHHHHH
T ss_conf             201302589999999988612799863177875045640014678889987420478568997235-99889-9999998


Q ss_pred             HHHHCHHCCCCCCCCCCCC---------CCCCCCCCCCCCCCCCCCEEEEEECC-----CCCCCC-------CHHHHCCC
Q ss_conf             9985500013444322222---------23334443211123578616985303-----575561-------00212026
Q gi|254781215|r  131 WLSLLPNKHWFEMQSLSLH---------PAPWYSDVLHCSLGIDSKHYSTMCRT-----YSEERP-------DTFVGHHN  189 (511)
Q Consensus       131 ~~~~~~~~~~~~~~~~~~~---------~~~~~~~~~~~~~~~~~~~~~~~~~~-----~s~~~~-------ea~~G~h~  189 (511)
                      |.......+-+.+....-+         +..|..+.          ..++.+..     +...++       .-...+-.
T Consensus       750 Wm~~~e~~~~leV~eL~~vkr~e~R~~~L~~W~~~g----------gVmIiGYdmyRnLa~gr~vk~rk~ke~f~k~lvd  819 (1567)
T KOG1015         750 WMEGLEDDEKLEVSELATVKRPEERSYMLQRWQEDG----------GVMIIGYDMYRNLAQGRNVKSRKLKEIFNKALVD  819 (1567)
T ss_pred             HCCCCCCCCCCEEEHHHHCCCHHHHHHHHHHHHHCC----------CEEEEEHHHHHHHHCCCCHHHHHHHHHHHHHCCC
T ss_conf             612422246621202120267488999999997529----------7799736888877514560356799999986057


Q ss_pred             CCCEEEEECCHHCCCHHHH---HHHHHHHCCCCCCEEEEEECCCCCCCCHHHHHH
Q ss_conf             7614999711102997889---888888507998138998238998765567653
Q gi|254781215|r  190 TYGMAIINDEASGTPDVIN---LGILGFLTERNANRFWIMTSNPRRLSGKFYEIF  241 (511)
Q Consensus       190 ~~~~lvI~DEAsgI~d~i~---e~i~~~Lt~~g~~~~~i~~~nP~~~~g~fy~~~  241 (511)
                      ++..+||+|||+-+.++--   .++....+    +..++.+|+|--++-.-|-|.
T Consensus       820 pGPD~vVCDE~HiLKNeksa~Skam~~irt----kRRI~LTGTPLQNNLmEY~CM  870 (1567)
T KOG1015         820 PGPDFVVCDEGHILKNEKSAVSKAMNSIRT----KRRIILTGTPLQNNLMEYHCM  870 (1567)
T ss_pred             CCCCEEEECCHHHHCCCHHHHHHHHHHHHH----HEEEEEECCCHHHHHHHHHHH
T ss_conf             899768724212213524789999998776----404775267113324888788


No 104
>TIGR03015 pepcterm_ATPase putative secretion ATPase, PEP-CTERM locus subfamily. Members of this protein are marked as probable ATPases by the nucleotide binding P-loop motif GXXGXGKTT, a motif DEAQ similar to the DEAD/H box of helicases, and extensive homology to ATPases of MSHA-type pilus systems and to GspA proteins associated with type II protein secretion systems.
Probab=94.79  E-value=0.28  Score=26.61  Aligned_cols=146  Identities=18%  Similarity=0.117  Sum_probs=73.8

Q ss_pred             CCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEEECCHHHHHH
Q ss_conf             75655578458999999999998740565554210124650257659789999999999980899669998085899999
Q gi|254781215|r   43 TPLEGFSAPRSWQLEFMEVVDAHCLNSVNNPNPEVFKGAISAGRGIGKTTLNAWLVLWLMSTRPGISVICLANSETQLKT  122 (511)
Q Consensus        43 ~~~~~~~~P~~WQ~e~l~~i~~~~~~~~~~~~~~~~r~aV~sgrG~GKS~l~a~l~lw~l~~~p~~kv~vtApt~~Q~~~  122 (511)
                      +|-+.|-.|-+-.+++|..+.-......+       =+.|...=|+|||++.-.++--.  -.....++...++.-...+
T Consensus        16 ~pd~~~~y~s~~h~~al~~L~~~l~~~~g-------~~lltGe~GtGKTtllr~l~~~l--~~~~~~~~~i~~~~l~~~~   86 (269)
T TIGR03015        16 LPDPDFFYPSKGHKRAMAYLEYGLSQREG-------FILITGEVGAGKTTLIRNLLKRL--DQERVVAAKLVNTRVDAED   86 (269)
T ss_pred             CCCHHHCCCCHHHHHHHHHHHHHHHCCCC-------EEEEECCCCCCHHHHHHHHHHHC--CCCCEEEEEECCCCCCHHH
T ss_conf             99845414786699999999999964896-------59997299898899999999845--9345489997699999999


Q ss_pred             HHHHHHHHHHHHCHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCCCCCCCHHH--HCCCCCCEEEEECCH
Q ss_conf             999999999985500013444322222233344432111235786169853035755610021--202676149997111
Q gi|254781215|r  123 TLWAEVSKWLSLLPNKHWFEMQSLSLHPAPWYSDVLHCSLGIDSKHYSTMCRTYSEERPDTFV--GHHNTYGMAIINDEA  200 (511)
Q Consensus       123 ilw~Ei~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~ea~~--G~h~~~~~lvI~DEA  200 (511)
                      .+ ..|..-+..-+..    .......                        +..    .+-+.  ...+. ..++|+|||
T Consensus        87 ll-~~i~~~lg~~~~~----~~~~~~~------------------------~~l----~~~L~~~~~~g~-~~vliIDEA  132 (269)
T TIGR03015        87 LL-RMVAADFGLETEG----RDKAALL------------------------REL----EDFLIEQFAAGK-RALLVVDEA  132 (269)
T ss_pred             HH-HHHHHHCCCCCCC----CCHHHHH------------------------HHH----HHHHHHHHHCCC-CEEEEEECH
T ss_conf             99-9999985989889----8999999------------------------999----999999996699-469997242


Q ss_pred             HCCCHHHHHHHHHHH---CCCCCCEEEEEECCCC
Q ss_conf             029978898888885---0799813899823899
Q gi|254781215|r  201 SGTPDVINLGILGFL---TERNANRFWIMTSNPR  231 (511)
Q Consensus       201 sgI~d~i~e~i~~~L---t~~g~~~~~i~~~nP~  231 (511)
                      ..+++++.+.+.-.+   ++..+-..++.+|.|.
T Consensus       133 q~L~~~~Le~Lr~L~n~e~~~~~ll~iiL~Gqpe  166 (269)
T TIGR03015       133 QNLTPELLEELRMLSNFQTDNAKLLQIFLVGQPE  166 (269)
T ss_pred             HHCCHHHHHHHHHHHCCCCCCCCCEEEEEECCHH
T ss_conf             2199999999999970135888704899957867


No 105
>TIGR02768 TraA_Ti Ti-type conjugative transfer relaxase TraA; InterPro: IPR014136   This entry represents the Ti-type conjugative transfer relaxase TraA. TraA contains domains distinctive of a single strand exonuclease (N-terminus, MobA/MobL, IPR005053 from INTERPRO) as well as a helicase domain (central region, homologous to the corresponding region of the F-type relaxase TraI, IPR014129 from INTERPRO). This protein likely fills the same role as TraI(F), nicking (at the oriT site) and unwinding the coiled plasmid prior to conjugative transfer ..
Probab=94.78  E-value=0.088  Score=29.84  Aligned_cols=119  Identities=20%  Similarity=0.103  Sum_probs=64.1

Q ss_pred             HHHHHHHHHHHHHHHHCCCCCCCCCCEEEEEECCC-CCCHHHHHHHHHHHHHHHCCCCEEEEEECCHHHHHHHHHHHHHH
Q ss_conf             58999999999998740565554210124650257-65978999999999998089966999808589999999999999
Q gi|254781215|r   52 RSWQLEFMEVVDAHCLNSVNNPNPEVFKGAISAGR-GIGKTTLNAWLVLWLMSTRPGISVICLANSETQLKTTLWAEVSK  130 (511)
Q Consensus        52 ~~WQ~e~l~~i~~~~~~~~~~~~~~~~r~aV~sgr-G~GKS~l~a~l~lw~l~~~p~~kv~vtApt~~Q~~~ilw~Ei~k  130 (511)
                      .+=|.++++.|..-            .++||.-|+ |+|||+++..+=..|-.-  |-+|+=.| -..-+=+.|      
T Consensus       416 s~EQ~~Av~hvt~s------------~~iavVvG~AGtGKSt~L~aAR~AWe~~--Gy~V~GAA-LsGKAAegL------  474 (888)
T TIGR02768       416 SEEQKEAVRHVTGS------------GDIAVVVGRAGTGKSTMLKAAREAWEAA--GYRVIGAA-LSGKAAEGL------  474 (888)
T ss_pred             HHHHHHHHHHHCCC------------CCEEEEECCCCCCHHHHHHHHHHHHHHC--CCEEEEHH-HHHHHHHHH------
T ss_conf             58999998753289------------9648997489987667899999999873--97787154-555898873------


Q ss_pred             HHHHCHHCCCCCCCCCCC--CCCCCCCCCCCCCCCCCCCEEEEEECCCCCCCCCHHHHCCCCCCEEEEECCHHCCCHHHH
Q ss_conf             998550001344432222--223334443211123578616985303575561002120267614999711102997889
Q gi|254781215|r  131 WLSLLPNKHWFEMQSLSL--HPAPWYSDVLHCSLGIDSKHYSTMCRTYSEERPDTFVGHHNTYGMAIINDEASGTPDVIN  208 (511)
Q Consensus       131 ~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~ea~~G~h~~~~~lvI~DEAsgI~d~i~  208 (511)
                        +..     -....+.+  +..-|..                           ..+-++..+  ++|+|||..|...=+
T Consensus       475 --e~~-----sGI~SRTLASle~aW~~---------------------------G~d~L~~~d--vLviDEAGMV~S~Qm  518 (888)
T TIGR02768       475 --EAE-----SGIESRTLASLEYAWAN---------------------------GRDLLEDKD--VLVIDEAGMVGSRQM  518 (888)
T ss_pred             --HCC-----CCCCHHHHHHHHHHHHC---------------------------CCCCCCCCC--EEEEECCCCHHHHHH
T ss_conf             --002-----68750478879999873---------------------------875224776--689851544146778


Q ss_pred             -HHHHHHHCCCCCCEEEEEECCC
Q ss_conf             -8888885079981389982389
Q gi|254781215|r  209 -LGILGFLTERNANRFWIMTSNP  230 (511)
Q Consensus       209 -e~i~~~Lt~~g~~~~~i~~~nP  230 (511)
                       -++.-+- ..|+++  ++.|=|
T Consensus       519 ~r~l~~A~-~AGaKv--VLvGD~  538 (888)
T TIGR02768       519 ARVLKEAE-EAGAKV--VLVGDP  538 (888)
T ss_pred             HHHHHHHH-HCCCCE--EEECCH
T ss_conf             89999998-727605--984885


No 106
>KOG0330 consensus
Probab=94.64  E-value=0.11  Score=29.13  Aligned_cols=217  Identities=17%  Similarity=0.082  Sum_probs=104.8

Q ss_pred             CCCCCHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHHCC-CCEEEEEECCHHHHHHHHH
Q ss_conf             557845899999999999874056555421012465025765978999999999998089-9669998085899999999
Q gi|254781215|r   47 GFSAPRSWQLEFMEVVDAHCLNSVNNPNPEVFKGAISAGRGIGKTTLNAWLVLWLMSTRP-GISVICLANSETQLKTTLW  125 (511)
Q Consensus        47 ~~~~P~~WQ~e~l~~i~~~~~~~~~~~~~~~~r~aV~sgrG~GKS~l~a~l~lw~l~~~p-~~kv~vtApt~~Q~~~ilw  125 (511)
                      +++.|-+-|++.+-..-.      +      .-|...+-.|+|||...+.=++-.++-.| ...++|.+||..-+..|  
T Consensus        80 ~~~~PT~IQ~~aiP~~L~------g------~dvIglAeTGSGKT~afaLPIl~~LL~~p~~~~~lVLtPtRELA~QI--  145 (476)
T KOG0330          80 GWKKPTKIQSEAIPVALG------G------RDVIGLAETGSGKTGAFALPILQRLLQEPKLFFALVLTPTRELAQQI--  145 (476)
T ss_pred             CCCCCCHHHHHHCCHHHC------C------CCEEEEECCCCCCHHHHHHHHHHHHHCCCCCCEEEEECCCHHHHHHH--
T ss_conf             767874444520655437------9------85799943588840231799999997198774489964828999999--


Q ss_pred             HHHHHHHHHCHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCC-CCCCCHHHHCCCCCCEEEEECCHHCCC
Q ss_conf             9999999855000134443222222333444321112357861698530357-556100212026761499971110299
Q gi|254781215|r  126 AEVSKWLSLLPNKHWFEMQSLSLHPAPWYSDVLHCSLGIDSKHYSTMCRTYS-EERPDTFVGHHNTYGMAIINDEASGTP  204 (511)
Q Consensus       126 ~Ei~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s-~~~~ea~~G~h~~~~~lvI~DEAsgI~  204 (511)
                      +|....+...+.-.   +....    + -.+.....+....+-.+.++.+=+ .+.-++-.|++-+..-.+|+|||.-+=
T Consensus       146 ~e~fe~Lg~~iglr---~~~lv----G-G~~m~~q~~~L~kkPhilVaTPGrL~dhl~~Tkgf~le~lk~LVlDEADrlL  217 (476)
T KOG0330         146 AEQFEALGSGIGLR---VAVLV----G-GMDMMLQANQLSKKPHILVATPGRLWDHLENTKGFSLEQLKFLVLDEADRLL  217 (476)
T ss_pred             HHHHHHHCCCCCEE---EEEEE----C-CCHHHHHHHHHHCCCCEEEECCHHHHHHHHHCCCCCHHHHHHHHHCHHHHHH
T ss_conf             99998753566727---99986----5-8329999887624898798370789999874368408875787633177662


Q ss_pred             HHHH-HHHHHHHCCCCCCEEEEEECCC-CCCCCHHHHHHHCCCCCCEEEEEC--CCCCCCCCHHHHHHHHHHC----CCC
Q ss_conf             7889-8888885079981389982389-987655676530352474179840--4336778977899999751----898
Q gi|254781215|r  205 DVIN-LGILGFLTERNANRFWIMTSNP-RRLSGKFYEIFNKPLDDWKRFQID--TRTVEGIDPSFHEGIIARY----GLD  276 (511)
Q Consensus       205 d~i~-e~i~~~Lt~~g~~~~~i~~~nP-~~~~g~fy~~~~~~~~~w~~~~i~--~~~~p~~~~~~ie~~~~~~----ged  276 (511)
                      |.-| +.+.-.|.---.....+.||-. +...   ......--+.-....++  +..        ++..++.|    +.+
T Consensus       218 d~dF~~~ld~ILk~ip~erqt~LfsATMt~kv---~kL~rasl~~p~~v~~s~ky~t--------v~~lkQ~ylfv~~k~  286 (476)
T KOG0330         218 DMDFEEELDYILKVIPRERQTFLFSATMTKKV---RKLQRASLDNPVKVAVSSKYQT--------VDHLKQTYLFVPGKD  286 (476)
T ss_pred             HHHHHHHHHHHHHHCCCCCEEEEEEEECCHHH---HHHHHHCCCCCEEEECCCHHCC--------HHHHHHHEEECCCCC
T ss_conf             11568999999874674414899986444136---7787641589717860430111--------677664557632666


Q ss_pred             HHHHHHHHCCCCCCCCCCEE
Q ss_conf             01354443175666678737
Q gi|254781215|r  277 SDVTRVEVCGQFPQQDIDSF  296 (511)
Q Consensus       277 s~~~r~evlgeFp~~~~~~~  296 (511)
                      -+.|-+..+.++...+--+|
T Consensus       287 K~~yLV~ll~e~~g~s~iVF  306 (476)
T KOG0330         287 KDTYLVYLLNELAGNSVIVF  306 (476)
T ss_pred             CCHHHHHHHHHHCCCCEEEE
T ss_conf             65238998876359847999


No 107
>PRK06090 DNA polymerase III subunit delta'; Validated
Probab=94.44  E-value=0.35  Score=26.09  Aligned_cols=177  Identities=12%  Similarity=0.114  Sum_probs=90.6

Q ss_pred             HHHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEEECCHHHHHHHHHHHHHHHHH
Q ss_conf             99999999999874056555421012465025765978999999999998089966999808589999999999999998
Q gi|254781215|r   54 WQLEFMEVVDAHCLNSVNNPNPEVFKGAISAGRGIGKTTLNAWLVLWLMSTRPGISVICLANSETQLKTTLWAEVSKWLS  133 (511)
Q Consensus        54 WQ~e~l~~i~~~~~~~~~~~~~~~~r~aV~sgrG~GKS~l~a~l~lw~l~~~p~~kv~vtApt~~Q~~~ilw~Ei~k~~~  133 (511)
                      |+.+..+.+.....+++.-|     ..-+.+..|+||+.++-.++-|.+|..+... .|..-..=++.         ...
T Consensus         7 Wl~~~~~~l~~~~~~~rl~H-----A~L~~g~~G~Gk~~la~~la~~LlC~~~~~~-~Cg~C~sC~l~---------~~g   71 (319)
T PRK06090          7 WLVPVWQNWKSGLDAERIPG-----ALLLQSDEGLGVESLVELFSHALLCQNYQSE-ACGFCHSCELM---------KSG   71 (319)
T ss_pred             CCHHHHHHHHHHHHCCCCCC-----EEEEECCCCCCHHHHHHHHHHHHHCCCCCCC-CCCCCHHHHHH---------HCC
T ss_conf             83799999999998699630-----6766799985799999999999808999999-88778779998---------758


Q ss_pred             HCHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCCCC-CCCHHHHCCCCCCEEEEECCHHCCCHHHHHHHH
Q ss_conf             5500013444322222233344432111235786169853035755-610021202676149997111029978898888
Q gi|254781215|r  134 LLPNKHWFEMQSLSLHPAPWYSDVLHCSLGIDSKHYSTMCRTYSEE-RPDTFVGHHNTYGMAIINDEASGTPDVINLGIL  212 (511)
Q Consensus       134 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~-~~ea~~G~h~~~~~lvI~DEAsgI~d~i~e~i~  212 (511)
                      .-|..+.+.....   .+...++..               |..... ...+.+   +.+. .+|+|+|..+.....+++.
T Consensus        72 ~HPD~~~i~pe~~---~k~I~vd~I---------------R~l~~~~~~~~~~---g~~K-V~iI~~ae~m~~~AaNALL  129 (319)
T PRK06090         72 NHPDLHVIKPEKE---GKSITVEQI---------------RQCNRLAQESSQL---GGYR-LFVIEPADAMNESASNALL  129 (319)
T ss_pred             CCCCCEEEECCCC---CCCCCHHHH---------------HHHHHHHHHCCCC---CCCE-EEEECCHHHCCHHHHHHHH
T ss_conf             9998236612335---676879999---------------9999997545210---6936-9998144434999999999


Q ss_pred             HHHCCCCCCEEEEEE-CCCCCCCCHHHHHHHCCCCCCEEEEECCCCCCCCCHHHHHHHHHHCCCCHHH
Q ss_conf             885079981389982-3899876556765303524741798404336778977899999751898013
Q gi|254781215|r  213 GFLTERNANRFWIMT-SNPRRLSGKFYEIFNKPLDDWKRFQIDTRTVEGIDPSFHEGIIARYGLDSDV  279 (511)
Q Consensus       213 ~~Lt~~g~~~~~i~~-~nP~~~~g~fy~~~~~~~~~w~~~~i~~~~~p~~~~~~ie~~~~~~geds~~  279 (511)
                      -+|-++.....++.. .+|.+.--..+-++.+            ..-+..+.+.+.+|.++-|...+.
T Consensus       130 KtLEEPp~~t~fiL~t~~~~~ll~TI~SRCq~------------~~l~~p~~~~~~~WL~~q~~~~~~  185 (319)
T PRK06090        130 KTLEEPAPNCLFLLVTHNQKRLLPTIVSRCQQ------------WVVTPPSTDQAMQWLKGQGISVPA  185 (319)
T ss_pred             HHHCCCCCCEEEEEEECCHHHCCCCHHHCCCC------------CCCCCCCHHHHHHHHHHHCCCCHH
T ss_conf             98428998838998768512086418761445------------028995999999999884875579


No 108
>PRK07940 DNA polymerase III subunit delta'; Validated
Probab=94.41  E-value=0.35  Score=26.05  Aligned_cols=178  Identities=13%  Similarity=0.169  Sum_probs=84.4

Q ss_pred             HHHHHHHHHHHHHCCCCC-------CCCCCEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEEECCHHHHHHHHHHH
Q ss_conf             999999999987405655-------5421012465025765978999999999998089966999808589999999999
Q gi|254781215|r   55 QLEFMEVVDAHCLNSVNN-------PNPEVFKGAISAGRGIGKTTLNAWLVLWLMSTRPGISVICLANSETQLKTTLWAE  127 (511)
Q Consensus        55 Q~e~l~~i~~~~~~~~~~-------~~~~~~r~aV~sgrG~GKS~l~a~l~lw~l~~~p~~kv~vtApt~~Q~~~ilw~E  127 (511)
                      |..+.+.+..-...+...       .....--.-....+|+||++++-.++--.+|.+|+.. -|.-  -..-+.+    
T Consensus        10 Qe~v~~~L~~A~~~~R~~~~~~~~~~~~~~HAyLF~Gp~G~Gk~~~A~~~A~~l~C~~~~~~-~cg~--C~~C~~i----   82 (395)
T PRK07940         10 QDAVVAELRAAARAARADSAHSAAAGSGMTHAWLFTGPPGSGRSNAARAFAAALQCTDPGVP-GCGE--CRACRTV----   82 (395)
T ss_pred             CHHHHHHHHHHHHHCCCCCCCCCCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHCCCCCCCC-CCCC--CHHHHHH----
T ss_conf             29999999999983634344333346876603763689987889999999999669999999-9987--8789998----


Q ss_pred             HHHHHHHCHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCCCCCCCHHHHCCCCCCEEEEECCHHCCCHHH
Q ss_conf             99999855000134443222222333444321112357861698530357556100212026761499971110299788
Q gi|254781215|r  128 VSKWLSLLPNKHWFEMQSLSLHPAPWYSDVLHCSLGIDSKHYSTMCRTYSEERPDTFVGHHNTYGMAIINDEASGTPDVI  207 (511)
Q Consensus       128 i~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~ea~~G~h~~~~~lvI~DEAsgI~d~i  207 (511)
                         .....|.-+...       +.+       ..++.+      ..|...  ..-++....+.+. .+|+|||..+....
T Consensus        83 ---~~g~hpDv~~i~-------p~~-------~~i~id------~iR~l~--~~~~~~p~~~~~k-v~ii~~a~~m~~~a  136 (395)
T PRK07940         83 ---LAGTHPDVRVVV-------PEG-------LSIGVD------EVREIV--QIAARRPTTGRWR-IVVIEDADRLTERA  136 (395)
T ss_pred             ---HCCCCCCEEEEE-------CCC-------CCCCHH------HHHHHH--HHHHHCCCCCCCE-EEEEECHHHHCHHH
T ss_conf             ---768998718982-------687-------768899------999999--9985273037955-99980778748999


Q ss_pred             HHHHHHHHCCCCCCEEEEE-ECCCCCCCCHHHHHHHCCCCCCEEEEECCCCCCCCCHHHHHHHH-HHCCCCH
Q ss_conf             9888888507998138998-23899876556765303524741798404336778977899999-7518980
Q gi|254781215|r  208 NLGILGFLTERNANRFWIM-TSNPRRLSGKFYEIFNKPLDDWKRFQIDTRTVEGIDPSFHEGII-ARYGLDS  277 (511)
Q Consensus       208 ~e~i~~~Lt~~g~~~~~i~-~~nP~~~~g~fy~~~~~~~~~w~~~~i~~~~~p~~~~~~ie~~~-~~~geds  277 (511)
                      .+++.-+|-.+-....++. +.+|...--...-.+..         +.   -+.++.+.|.++. ++.|.+.
T Consensus       137 ~NalLKtLEEPp~~~~fiL~t~~~~~llpTI~SRcq~---------~~---f~~~~~~~i~~~L~~~~gi~~  196 (395)
T PRK07940        137 ANALLKAVEEPPPRTVWLLCAPSVEDVLPTIRSRCRH---------VA---LRTPSVEAVADVLVRRDGVDP  196 (395)
T ss_pred             HHHHHHHHCCCCCCEEEEEEECCHHHHHHHHHHHHEE---------CC---CCCCCHHHHHHHHHHCCCCCH
T ss_conf             9999985217888869998739978744688744000---------23---799999999999987019998


No 109
>PRK06995 flhF flagellar biosynthesis regulator FlhF; Validated
Probab=94.35  E-value=0.36  Score=25.97  Aligned_cols=40  Identities=23%  Similarity=0.159  Sum_probs=33.0

Q ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHHC-CCCEEEEEECCHH
Q ss_conf             246502576597899999999999808-9966999808589
Q gi|254781215|r   79 KGAISAGRGIGKTTLNAWLVLWLMSTR-PGISVICLANSET  118 (511)
Q Consensus        79 r~aV~sgrG~GKS~l~a~l~lw~l~~~-p~~kv~vtApt~~  118 (511)
                      -++...+.|+|||+.+|=|+.-+.+.+ .....++|+-||+
T Consensus       178 V~alVGPTGVGKTTTiAKLAAr~~l~~g~~kVaLIT~DTYR  218 (404)
T PRK06995        178 VFALVGPTGVGKTTTTAKLAARCVMRHGASKVALLTTDSYR  218 (404)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHHHCCCCEEEEECCCCC
T ss_conf             58986688876375899999999998389837999768754


No 110
>COG1201 Lhr Lhr-like helicases [General function prediction only]
Probab=94.32  E-value=0.37  Score=25.93  Aligned_cols=129  Identities=16%  Similarity=0.038  Sum_probs=74.8

Q ss_pred             CCCCHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHHCC------CCEEEEEECCHHHHH
Q ss_conf             57845899999999999874056555421012465025765978999999999998089------966999808589999
Q gi|254781215|r   48 FSAPRSWQLEFMEVVDAHCLNSVNNPNPEVFKGAISAGRGIGKTTLNAWLVLWLMSTRP------GISVICLANSETQLK  121 (511)
Q Consensus        48 ~~~P~~WQ~e~l~~i~~~~~~~~~~~~~~~~r~aV~sgrG~GKS~l~a~l~lw~l~~~p------~~kv~vtApt~~Q~~  121 (511)
                      |.-|.+=|++++..|.+..            -+-|.|+.|.|||..+=.-++--++-..      +..++++.|-..-.+
T Consensus        20 ~~~~t~~Q~~a~~~i~~G~------------nvLiiAPTGsGKTeAAfLpil~~l~~~~~~~~~~~i~~lYIsPLkALn~   87 (814)
T COG1201          20 FTSLTPPQRYAIPEIHSGE------------NVLIIAPTGSGKTEAAFLPVINELLSLGKGKLEDGIYALYISPLKALNN   87 (814)
T ss_pred             CCCCCHHHHHHHHHHHCCC------------CEEEECCCCCCHHHHHHHHHHHHHHHCCCCCCCCCEEEEEECCHHHHHH
T ss_conf             0899878999999985898------------4699868999737999999999998606888888569999570788878


Q ss_pred             HHHHHHHHHHHHHCHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCCCCCCCHHHHCCC--------CCCE
Q ss_conf             99999999999855000134443222222333444321112357861698530357556100212026--------7614
Q gi|254781215|r  122 TTLWAEVSKWLSLLPNKHWFEMQSLSLHPAPWYSDVLHCSLGIDSKHYSTMCRTYSEERPDTFVGHHN--------TYGM  193 (511)
Q Consensus       122 ~ilw~Ei~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~ea~~G~h~--------~~~~  193 (511)
                      |+. .-|..|.+..=    +..    -.-.+....+.+......+-+..++       .||+++-+-.        .+.-
T Consensus        88 Di~-~rL~~~~~~~G----~~v----~vRhGDT~~~er~r~~~~PPdILiT-------TPEsL~lll~~~~~r~~l~~vr  151 (814)
T COG1201          88 DIR-RRLEEPLRELG----IEV----AVRHGDTPQSEKQKMLKNPPHILIT-------TPESLAILLNSPKFRELLRDVR  151 (814)
T ss_pred             HHH-HHHHHHHHHCC----CCC----CEECCCCCHHHHHHCCCCCCCEEEE-------CHHHHHHHHCCHHHHHHHCCCC
T ss_conf             999-99999999759----844----4422878867763046999968995-------8348999836888999860780


Q ss_pred             EEEECCHHCCC
Q ss_conf             99971110299
Q gi|254781215|r  194 AIINDEASGTP  204 (511)
Q Consensus       194 lvI~DEAsgI~  204 (511)
                      .+|+||.+.+-
T Consensus       152 ~VIVDEiHel~  162 (814)
T COG1201         152 YVIVDEIHALA  162 (814)
T ss_pred             EEEEEHHHHHH
T ss_conf             99951254543


No 111
>PRK08770 DNA polymerase III subunits gamma and tau; Validated
Probab=94.08  E-value=0.41  Score=25.63  Aligned_cols=149  Identities=15%  Similarity=0.160  Sum_probs=76.7

Q ss_pred             HHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEEECCHHHHHHHHHHHHHHHHHH
Q ss_conf             99999999998740565554210124650257659789999999999980899669998085899999999999999985
Q gi|254781215|r   55 QLEFMEVVDAHCLNSVNNPNPEVFKGAISAGRGIGKTTLNAWLVLWLMSTRPGISVICLANSETQLKTTLWAEVSKWLSL  134 (511)
Q Consensus        55 Q~e~l~~i~~~~~~~~~~~~~~~~r~aV~sgrG~GKS~l~a~l~lw~l~~~p~~kv~vtApt~~Q~~~ilw~Ei~k~~~~  134 (511)
                      |.-+++.+...+..++. |..    ..-..-||+|||+++-.++--.-|.....-..|.-  -..-     .+|.    .
T Consensus        21 q~~~~~~l~~~~~~~~~-~~a----~lf~g~rg~gkt~~ar~~a~~lnc~~~~~~~pc~~--c~~c-----~~i~----~   84 (663)
T PRK08770         21 QEHVVRALSNALDSGRV-HHA----FLFTGTRGVGKTTIARIFAKSLNCETGTSADPCGQ--CPAC-----LDID----A   84 (663)
T ss_pred             CHHHHHHHHHHHHCCCC-CEE----EEEECCCCCCHHHHHHHHHHHHCCCCCCCCCCCCC--CHHH-----HHHH----C
T ss_conf             59999999999970997-404----76227998888899999999867899999997877--8778-----9885----4


Q ss_pred             CHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCCCCCCCHHHHCCCCCCEEEEECCHHCCCHHHHHHHHHH
Q ss_conf             50001344432222223334443211123578616985303575561002120267614999711102997889888888
Q gi|254781215|r  135 LPNKHWFEMQSLSLHPAPWYSDVLHCSLGIDSKHYSTMCRTYSEERPDTFVGHHNTYGMAIINDEASGTPDVINLGILGF  214 (511)
Q Consensus       135 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~ea~~G~h~~~~~lvI~DEAsgI~d~i~e~i~~~  214 (511)
                                       +...|...++.....+  ....|..- +| -.+.-.++.+ -.+|+||.+.+....|+++.-|
T Consensus        85 -----------------~~~~d~~e~daas~~~--v~~~r~~~-~~-~~~~p~~~~~-kvy~idevhmls~~~fna~lkt  142 (663)
T PRK08770         85 -----------------GRYIDLLEIDAASNTG--VDDVREVI-EN-AQYMPSRGKF-KVYLIDEVHMLSKAAFNALLKT  142 (663)
T ss_pred             -----------------CCCCCEEEEECCCCCC--HHHHHHHH-HH-CCCCCCCCCE-EEEEEECHHHCCHHHHHHHHHH
T ss_conf             -----------------8988658864676588--89999999-84-4358877743-6999700433289999999874


Q ss_pred             HCCCCCCE-EEEEECCCCCCCCHHHHHH
Q ss_conf             50799813-8998238998765567653
Q gi|254781215|r  215 LTERNANR-FWIMTSNPRRLSGKFYEIF  241 (511)
Q Consensus       215 Lt~~g~~~-~~i~~~nP~~~~g~fy~~~  241 (511)
                      |-.+-... +++++..|.+..-...-.|
T Consensus       143 leepp~~v~f~~att~~~k~p~t~~src  170 (663)
T PRK08770        143 LEEPPEHVKFLLATTDPQKLPVTVLSRC  170 (663)
T ss_pred             HCCCCCCEEEEEECCCHHHCCHHHHHHH
T ss_conf             0278644289985487333748999888


No 112
>PRK13833 conjugal transfer protein TrbB; Provisional
Probab=94.05  E-value=0.15  Score=28.33  Aligned_cols=32  Identities=19%  Similarity=0.313  Sum_probs=20.1

Q ss_pred             HHHHHHHHCCCCEEEEEECCCCHHHHHHHHHCC
Q ss_conf             999999861888299800687636889898649
Q gi|254781215|r  359 KISGLVEKYRPDAIIIDANNTGARTCDYLEMLG  391 (511)
Q Consensus       359 ~i~~~~~~~~~~~i~iD~~GvG~gV~d~L~~~g  391 (511)
                      .+...+-+.+|+.|++-..= |.-..+.|+.++
T Consensus       206 ~Ll~~aLRmrPDRIivGEvR-G~EA~~~L~A~n  237 (323)
T PRK13833        206 RLLKSTMRLRPDRIIVGEVR-DGAALTLLKAWN  237 (323)
T ss_pred             HHHHHHHCCCCCEEEEECCC-CHHHHHHHHHHH
T ss_conf             99999744699758883006-599999999982


No 113
>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=93.99  E-value=0.43  Score=25.51  Aligned_cols=65  Identities=15%  Similarity=0.137  Sum_probs=43.0

Q ss_pred             HHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEEECCHHHHHHHHHHHHHHHHHH
Q ss_conf             99999999998740565554210124650257659789999999999980899669998085899999999999999985
Q gi|254781215|r   55 QLEFMEVVDAHCLNSVNNPNPEVFKGAISAGRGIGKTTLNAWLVLWLMSTRPGISVICLANSETQLKTTLWAEVSKWLSL  134 (511)
Q Consensus        55 Q~e~l~~i~~~~~~~~~~~~~~~~r~aV~sgrG~GKS~l~a~l~lw~l~~~p~~kv~vtApt~~Q~~~ilw~Ei~k~~~~  134 (511)
                      |.|.++++.+-.     .+     =+-+.|+.|.|||..+-.-++     ..+.+++++.||..=+.|+ +..+.++.+.
T Consensus         2 q~~~~~~~~~~~-----~~-----~ivitAPTgsGKT~Aa~lp~l-----~~~~~~lyi~P~kAL~~Dq-~~~l~~~~~~   65 (357)
T TIGR03158         2 QVATFEALQSKD-----AD-----IIFNTAPTGAGKTLAWLTPLL-----HGENDTIALYPTNALIEDQ-TEAIKEFVDV   65 (357)
T ss_pred             HHHHHHHHHCCC-----CC-----EEEEECCCCCCHHHHHHHHHH-----HCCCCEEEECCHHHHHHHH-HHHHHHHHHH
T ss_conf             689999997689-----98-----699989998569999999997-----3898799977789999999-9999999987


Q ss_pred             C
Q ss_conf             5
Q gi|254781215|r  135 L  135 (511)
Q Consensus       135 ~  135 (511)
                      .
T Consensus        66 ~   66 (357)
T TIGR03158        66 F   66 (357)
T ss_pred             H
T ss_conf             4


No 114
>KOG1805 consensus
Probab=93.98  E-value=0.11  Score=29.22  Aligned_cols=42  Identities=26%  Similarity=0.316  Sum_probs=35.8

Q ss_pred             EEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEEECCHHHHHHHH
Q ss_conf             65025765978999999999998089966999808589999999
Q gi|254781215|r   81 AISAGRGIGKTTLNAWLVLWLMSTRPGISVICLANSETQLKTTL  124 (511)
Q Consensus        81 aV~sgrG~GKS~l~a~l~lw~l~~~p~~kv~vtApt~~Q~~~il  124 (511)
                      -|..=-|+|||++++.++--.+.+  +.+|+.|+=|-.-+-+|+
T Consensus       689 LI~GMPGTGKTTtI~~LIkiL~~~--gkkVLLtsyThsAVDNIL  730 (1100)
T KOG1805         689 LILGMPGTGKTTTISLLIKILVAL--GKKVLLTSYTHSAVDNIL  730 (1100)
T ss_pred             EEECCCCCCCHHHHHHHHHHHHHC--CCEEEEEEHHHHHHHHHH
T ss_conf             032699898122599999999973--881899850567889999


No 115
>COG2607 Predicted ATPase (AAA+ superfamily) [General function prediction only]
Probab=93.87  E-value=0.45  Score=25.37  Aligned_cols=90  Identities=19%  Similarity=0.183  Sum_probs=58.6

Q ss_pred             HHHCCCCCCCCCCCCCCCCH----------HHHHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHH
Q ss_conf             76421455777565557845----------89999999999987405655542101246502576597899999999999
Q gi|254781215|r   33 LHFFPWGEKGTPLEGFSAPR----------SWQLEFMEVVDAHCLNSVNNPNPEVFKGAISAGRGIGKTTLNAWLVLWLM  102 (511)
Q Consensus        33 ~~~~~w~~~~~~~~~~~~P~----------~WQ~e~l~~i~~~~~~~~~~~~~~~~r~aV~sgrG~GKS~l~a~l~lw~l  102 (511)
                      .++|-|..+.+.|++..-|+          +=|+++|-.-.....++.    |+ --|-.-..||+|||.++..++.-+.
T Consensus        36 a~~f~~~~~~~~L~pv~~~~~i~L~~l~Gvd~qk~~L~~NT~~F~~G~----pA-NnVLLwGaRGtGKSSLVKA~~~e~~  110 (287)
T COG2607          36 ALAFRWRPAIGYLEPVPDPDPIDLADLVGVDRQKEALVRNTEQFAEGL----PA-NNVLLWGARGTGKSSLVKALLNEYA  110 (287)
T ss_pred             HHHHHCCCCCCCCCCCCCCCCCCHHHHHCCHHHHHHHHHHHHHHHCCC----CC-CCEEEECCCCCCHHHHHHHHHHHHH
T ss_conf             557731335686668898997678987273189999999899997288----65-2367763777774799999999987


Q ss_pred             HHCCCCEEEEEECCHHHHHHHHHHHHHHHHH
Q ss_conf             8089966999808589999999999999998
Q gi|254781215|r  103 STRPGISVICLANSETQLKTTLWAEVSKWLS  133 (511)
Q Consensus       103 ~~~p~~kv~vtApt~~Q~~~ilw~Ei~k~~~  133 (511)
                      -..+  +  .+--+.+++.+  .+-|-..++
T Consensus       111 ~~gl--r--LVEV~k~dl~~--Lp~l~~~Lr  135 (287)
T COG2607         111 DEGL--R--LVEVDKEDLAT--LPDLVELLR  135 (287)
T ss_pred             HCCC--E--EEEECHHHHHH--HHHHHHHHH
T ss_conf             4177--0--79976888865--799999996


No 116
>PRK12377 putative replication protein; Provisional
Probab=93.86  E-value=0.45  Score=25.37  Aligned_cols=59  Identities=20%  Similarity=0.218  Sum_probs=36.7

Q ss_pred             CCCCCCHHHHHHHH---HHHHHHHHCCCCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEE
Q ss_conf             55578458999999---999998740565554210124650257659789999999999980899669998
Q gi|254781215|r   46 EGFSAPRSWQLEFM---EVVDAHCLNSVNNPNPEVFKGAISAGRGIGKTTLNAWLVLWLMSTRPGISVICL  113 (511)
Q Consensus        46 ~~~~~P~~WQ~e~l---~~i~~~~~~~~~~~~~~~~r~aV~sgrG~GKS~l~a~l~lw~l~~~p~~kv~vt  113 (511)
                      ++|.--.+=|+++|   ++++++...+.       .-+-...+-|+|||+|++.+..-.+--  +.+|.++
T Consensus        74 ~ny~~~~~~~~~a~~~a~~~~~~F~~~~-------~NlIf~G~pGtGKTHLA~AIg~~a~~~--G~sVlF~  135 (248)
T PRK12377         74 ANYQVQNDGQRYALSQAKSIADELMTGC-------TNFVFSGKPGTGKNHLAAAIGNRLLAK--GRSVIVV  135 (248)
T ss_pred             CCCCCCCHHHHHHHHHHHHHHHHHHCCC-------CEEEEECCCCCCHHHHHHHHHHHHHHC--CCEEEEE
T ss_conf             4564578789999999999999873188-------608998999987889999999999987--9969998


No 117
>PRK11889 flhF flagellar biosynthesis regulator FlhF; Provisional
Probab=93.85  E-value=0.43  Score=25.50  Aligned_cols=28  Identities=4%  Similarity=-0.005  Sum_probs=10.8

Q ss_pred             EECCCCHHHHHHHHHCCCEEEEECCCCC
Q ss_conf             0068763688989864982798427777
Q gi|254781215|r  375 DANNTGARTCDYLEMLGYHVYRVLGQKR  402 (511)
Q Consensus       375 D~~GvG~gV~d~L~~~g~~v~~v~~~~~  402 (511)
                      |.+...+.++..+.+.+.|+.-+-.|..
T Consensus       388 DET~SlG~ILNv~~~s~LPIsYvTdGQ~  415 (436)
T PRK11889        388 DETASSGELLKIPAVSSAPIVLMTDGQD  415 (436)
T ss_pred             CCCCCCHHHHHHHHHHCCCEEEECCCCC
T ss_conf             2568703788899883998799789985


No 118
>TIGR03117 cas_csf4 CRISPR-associated DEAD/DEAH-box helicase Csf4. Members of this family show up near CRISPR repeats in Acidithiobacillus ferrooxidans ATCC 23270, Azoarcus sp. EbN1, and Rhodoferax ferrireducens DSM 15236. In the latter two species, the CRISPR/cas locus is found on a plasmid. This family is one of several characteristic of a type of CRISPR-associated (cas) gene cluster we designate Aferr after A. ferrooxidans, where it is both chromosomal and the only type of cas gene cluster found. The gene is designated csf4 (CRISPR/cas Subtype as in A. ferrooxidans protein 1), as it lies farthest (fourth closest) from the repeats in the A. ferrooxidans genome.
Probab=93.79  E-value=0.46  Score=25.29  Aligned_cols=44  Identities=18%  Similarity=0.249  Sum_probs=33.0

Q ss_pred             EEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEEECCHHHHHHHH
Q ss_conf             65025765978999999999998089966999808589999999
Q gi|254781215|r   81 AISAGRGIGKTTLNAWLVLWLMSTRPGISVICLANSETQLKTTL  124 (511)
Q Consensus        81 aV~sgrG~GKS~l~a~l~lw~l~~~p~~kv~vtApt~~Q~~~il  124 (511)
                      -|-+|.|+|||..==.-+++++.-+++.+|+|.-+|..--..++
T Consensus        20 lVEAGTGTGKSLAYLvPAl~~a~~~~g~rVVISTaT~aLQeQL~   63 (636)
T TIGR03117        20 MLEASTGVGKTLAMIMAALTMLKERPDQKIAIAVPTLALMGQLW   63 (636)
T ss_pred             EEECCCCCCHHHHHHHHHHHHHHHCCCCCEEEECCCHHHHHHHH
T ss_conf             99899971088999999999998579998899798799999997


No 119
>pfam02456 Adeno_IVa2 Adenovirus IVa2 protein. IVa2 protein can interact with the adenoviral packaging signal and that this interaction involves DNA sequences that have previously been demonstrated to be required for packaging. During the course of lytic infection, the adenovirus major late promoter (MLP) is induced to high levels after replication of viral DNA has started. IVa2 is a transcriptional activator of the major late promoter.
Probab=93.70  E-value=0.12  Score=28.88  Aligned_cols=59  Identities=17%  Similarity=0.196  Sum_probs=46.4

Q ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEEECCHHHHHHHHHHHHHHHHHHCHHCCC
Q ss_conf             24650257659789999999999980899669998085899999999999999985500013
Q gi|254781215|r   79 KGAISAGRGIGKTTLNAWLVLWLMSTRPGISVICLANSETQLKTTLWAEVSKWLSLLPNKHW  140 (511)
Q Consensus        79 r~aV~sgrG~GKS~l~a~l~lw~l~~~p~~kv~vtApt~~Q~~~ilw~Ei~k~~~~~~~~~~  140 (511)
                      =..|-+..|.|||.+.-.++--.++.-++-.|+.++|+.+.+-   -.|+.-|-..+-.-++
T Consensus        89 I~vVYGPTG~GKSQLlRNlis~~lI~P~PETVfFItPq~~mIp---p~E~~aWe~Ql~EGNY  147 (370)
T pfam02456        89 IGVVYGPTGCGKSQLLRNLLSCQLIQPIPETVFFITPQKDMIP---PQEQTAWELQLCEGNY  147 (370)
T ss_pred             EEEEECCCCCCHHHHHHHHHHCCCCCCCCCEEEEECCCCCCCC---HHHHHHHHHHHHHCCC
T ss_conf             9999889987789999998734667799972899767778679---8999999999873577


No 120
>PRK08181 transposase; Validated
Probab=93.62  E-value=0.49  Score=25.10  Aligned_cols=105  Identities=20%  Similarity=0.157  Sum_probs=57.1

Q ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEE-ECCHHHHHHHHHHHHHHHHHHCHHCCCCCCCCCCCCCCCCCCCC
Q ss_conf             24650257659789999999999980899669998-08589999999999999998550001344432222223334443
Q gi|254781215|r   79 KGAISAGRGIGKTTLNAWLVLWLMSTRPGISVICL-ANSETQLKTTLWAEVSKWLSLLPNKHWFEMQSLSLHPAPWYSDV  157 (511)
Q Consensus        79 r~aV~sgrG~GKS~l~a~l~lw~l~~~p~~kv~vt-Apt~~Q~~~ilw~Ei~k~~~~~~~~~~~~~~~~~~~~~~~~~~~  157 (511)
                      -+.+.++-|+|||+++..+..-.+-  -|-+|..+ ++.       +..++........                     
T Consensus       108 Nvil~Gp~GtGKThLA~Alg~~A~~--~G~~V~f~~~~~-------L~~~L~~a~~~~~---------------------  157 (269)
T PRK08181        108 NLLLFGPPGGGKSHLAAAIGLALIE--NGWRVLFTRTTD-------LVQKLQVARRELQ---------------------  157 (269)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHH--CCCEEEEEEHHH-------HHHHHHHHHHCCC---------------------
T ss_conf             0899899998788999999999998--799399978999-------9999999775583---------------------


Q ss_pred             CCCCCCCCCCEEEEEECCCCCCCCCHHHHCCCCCCEEEEECCHHCCC------HHHHHHHHHHHCCCCCCEEEEEECCCC
Q ss_conf             21112357861698530357556100212026761499971110299------788988888850799813899823899
Q gi|254781215|r  158 LHCSLGIDSKHYSTMCRTYSEERPDTFVGHHNTYGMAIINDEASGTP------DVINLGILGFLTERNANRFWIMTSNPR  231 (511)
Q Consensus       158 ~~~~~~~~~~~~~~~~~~~s~~~~ea~~G~h~~~~~lvI~DEAsgI~------d~i~e~i~~~Lt~~g~~~~~i~~~nP~  231 (511)
                                            -...+.-+- . ..|+|+||...+|      +..|+++..-. +.+  . .+.+||  
T Consensus       158 ----------------------~~~~~~~l~-~-~dLLIiDe~G~~~~~~~~~~~lf~lI~~Ry-e~~--S-~IITSn--  207 (269)
T PRK08181        158 ----------------------LESAIAKLD-K-FDLLILDDLAYVTKDQAETSVLFELISARY-ERR--S-ILITAN--  207 (269)
T ss_pred             ----------------------HHHHHHHHH-C-CCEEEEHHCCCCCCCHHHHHHHHHHHHHHH-CCC--C-EEEECC--
T ss_conf             ----------------------999999974-4-460122010566799899999999999985-788--8-899889--


Q ss_pred             CCCCHHHHHHHC
Q ss_conf             876556765303
Q gi|254781215|r  232 RLSGKFYEIFNK  243 (511)
Q Consensus       232 ~~~g~fy~~~~~  243 (511)
                      ...+.+++.|..
T Consensus       208 ~~~~~W~~~f~D  219 (269)
T PRK08181        208 QPFGEWNRVFPD  219 (269)
T ss_pred             CCHHHHHHHCCC
T ss_conf             997788775386


No 121
>PRK13709 conjugal transfer nickase/helicase TraI; Provisional
Probab=93.50  E-value=0.52  Score=24.97  Aligned_cols=159  Identities=14%  Similarity=0.080  Sum_probs=79.9

Q ss_pred             HHHHHHHHHHHCHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCCC
Q ss_conf             67888999870706665288667764214557775655578458999999999998740565554210124650257659
Q gi|254781215|r   10 ETEQKLFDLMWSDEIKLSFSNFVLHFFPWGEKGTPLEGFSAPRSWQLEFMEVVDAHCLNSVNNPNPEVFKGAISAGRGIG   89 (511)
Q Consensus        10 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~w~~~~~~~~~~~~P~~WQ~e~l~~i~~~~~~~~~~~~~~~~r~aV~sgrG~G   89 (511)
                      ++|+.+...+-...-.-.|+.-.       ....-|++.+   +=|++..+-|.+..      |+    =++|..==|+|
T Consensus       938 etEK~IL~~i~~GK~tv~PL~~~-------v~~s~l~~LT---~GQK~At~LIltT~------DR----FvaIQGyAGVG  997 (1756)
T PRK13709        938 EAEKSILRHILEGKEAVTPLMER-------VPGELMEKLT---SGQRAATRMILETS------DR----FTVVQGYAGVG  997 (1756)
T ss_pred             HHHHHHHHHHHCCCCCCCCCHHH-------CCHHHHCCCC---HHHHHHHHHHHCCC------CC----EEEEEECCCCC
T ss_conf             99999999997476656860232-------7556663578---57787775632478------72----59987035566


Q ss_pred             HHHHHHHHH-HHHHHH-CCCCEEEEEECCHHHHHHHHHHHHHHHHHHCHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             789999999-999980-899669998085899999999999999985500013444322222233344432111235786
Q gi|254781215|r   90 KTTLNAWLV-LWLMST-RPGISVICLANSETQLKTTLWAEVSKWLSLLPNKHWFEMQSLSLHPAPWYSDVLHCSLGIDSK  167 (511)
Q Consensus        90 KS~l~a~l~-lw~l~~-~p~~kv~vtApt~~Q~~~ilw~Ei~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  167 (511)
                      ||+.+...+ +-.++- ....+|+=.|||-+.++     |++.   .     ..+...+.-++    ++...        
T Consensus       998 KTTql~avi~ai~tl~~~~rpqViGLAPTH~AV~-----EL~~---~-----GV~AQTlaSfL----~d~~~-------- 1052 (1756)
T PRK13709        998 KTTQFRAVMSAVNMLPESERPRVVGLGPTHRAVG-----EMRS---A-----GVDAQTLASFL----HDTQL-------- 1052 (1756)
T ss_pred             HHHHHHHHHHHHHHCCCCCCCCEEEECCHHHHHH-----HHHH---C-----CCCHHHHHHHH----HHHHH--------
T ss_conf             6778999999997255135872675675178999-----9996---4-----96078999998----62023--------


Q ss_pred             EEEEEECCCCCCCCCHHHHCCCCCCEEEEECCHHCCCHHHHHHHHHHHCCCCCCEEEEEEC
Q ss_conf             1698530357556100212026761499971110299788988888850799813899823
Q gi|254781215|r  168 HYSTMCRTYSEERPDTFVGHHNTYGMAIINDEASGTPDVINLGILGFLTERNANRFWIMTS  228 (511)
Q Consensus       168 ~~~~~~~~~s~~~~ea~~G~h~~~~~lvI~DEAsgI~d~i~e~i~~~Lt~~g~~~~~i~~~  228 (511)
                            ...+   .+..+  +  .+.|+++||+|.|.+.=+..+.......|++.  ++.|
T Consensus      1053 ------~~~~---ge~~d--y--~nTLFllDESSMVgN~dma~~~~lV~asggRA--V~~G 1098 (1756)
T PRK13709       1053 ------QQRS---GETPD--F--SNTLFLLDESSMVGNTDMARAYALIAAGGGRA--VASG 1098 (1756)
T ss_pred             ------HHHC---CCCCC--C--CCEEEEEEHHHCCCHHHHHHHHHHHHHCCCCE--EEEC
T ss_conf             ------4414---89876--5--54289983043147088999999997059837--9727


No 122
>PRK10917 ATP-dependent DNA helicase RecG; Provisional
Probab=93.46  E-value=0.53  Score=24.93  Aligned_cols=75  Identities=20%  Similarity=0.249  Sum_probs=55.0

Q ss_pred             HHHHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEEECCHHHHHHHHHHHHHHHH
Q ss_conf             89999999999987405655542101246502576597899999999999808996699980858999999999999999
Q gi|254781215|r   53 SWQLEFMEVVDAHCLNSVNNPNPEVFKGAISAGRGIGKTTLNAWLVLWLMSTRPGISVICLANSETQLKTTLWAEVSKWL  132 (511)
Q Consensus        53 ~WQ~e~l~~i~~~~~~~~~~~~~~~~r~aV~sgrG~GKS~l~a~l~lw~l~~~p~~kv~vtApt~~Q~~~ilw~Ei~k~~  132 (511)
                      .=|+.++.+|......+..     |.| -+..-=|+|||.++...++-.+.  -+.++++.|||+==++. -+..+++++
T Consensus       260 ~~Q~~~~~ei~~dl~~~~~-----m~r-llqGDVGsGKT~va~~a~~~~~~--~g~q~a~maPTeiLa~Q-h~~~~~~~~  330 (677)
T PRK10917        260 GAQKRVVAEILADLASPKP-----MNR-LLQGDVGSGKTVVAALAALAAIE--AGYQAALMAPTEILAEQ-HYRNLKKWL  330 (677)
T ss_pred             HHHHHHHHHHHHHHCCCCC-----CHH-HHCCCCCCCHHHHHHHHHHHHHH--HCCEEEEECCCHHHHHH-HHHHHHHHH
T ss_conf             8899999999987659954-----277-73287678889999999999998--19948998767999999-999999877


Q ss_pred             HHCH
Q ss_conf             8550
Q gi|254781215|r  133 SLLP  136 (511)
Q Consensus       133 ~~~~  136 (511)
                      ....
T Consensus       331 ~~~~  334 (677)
T PRK10917        331 EPLG  334 (677)
T ss_pred             HHCC
T ss_conf             6349


No 123
>KOG0949 consensus
Probab=93.40  E-value=0.17  Score=27.97  Aligned_cols=69  Identities=25%  Similarity=0.363  Sum_probs=44.0

Q ss_pred             CCCCHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEEECCHHHHHHHHHHH
Q ss_conf             57845899999999999874056555421012465025765978999999999998089966999808589999999999
Q gi|254781215|r   48 FSAPRSWQLEFMEVVDAHCLNSVNNPNPEVFKGAISAGRGIGKTTLNAWLVLWLMSTRPGISVICLANSETQLKTTLWAE  127 (511)
Q Consensus        48 ~~~P~~WQ~e~l~~i~~~~~~~~~~~~~~~~r~aV~sgrG~GKS~l~a~l~lw~l~~~p~~kv~vtApt~~Q~~~ilw~E  127 (511)
                      |. |+.||++.|..+.-..            ..-|.+++-.|||++.=-.+=-.+-......|+.+|||..-+-.+ =++
T Consensus       510 F~-Pd~WQ~elLDsvDr~e------------SavIVAPTSaGKTfisfY~iEKVLResD~~VVIyvaPtKaLVnQv-sa~  575 (1330)
T KOG0949         510 FC-PDEWQRELLDSVDRNE------------SAVIVAPTSAGKTFISFYAIEKVLRESDSDVVIYVAPTKALVNQV-SAN  575 (1330)
T ss_pred             CC-CCHHHHHHHHHHHCCC------------CEEEEEECCCCCEECCHHHHHHHHHHCCCCEEEEECCHHHHHHHH-HHH
T ss_conf             69-8388887766550566------------259982046786100589999998542798799966458776666-677


Q ss_pred             HHH
Q ss_conf             999
Q gi|254781215|r  128 VSK  130 (511)
Q Consensus       128 i~k  130 (511)
                      +..
T Consensus       576 Vya  578 (1330)
T KOG0949         576 VYA  578 (1330)
T ss_pred             HHH
T ss_conf             887


No 124
>KOG2170 consensus
Probab=93.39  E-value=0.54  Score=24.86  Aligned_cols=123  Identities=15%  Similarity=0.093  Sum_probs=69.2

Q ss_pred             HHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHHCCCC---EEEEE---ECCHHHHHHHHHHHH
Q ss_conf             999999999987405655542101246502576597899999999999808996---69998---085899999999999
Q gi|254781215|r   55 QLEFMEVVDAHCLNSVNNPNPEVFKGAISAGRGIGKTTLNAWLVLWLMSTRPGI---SVICL---ANSETQLKTTLWAEV  128 (511)
Q Consensus        55 Q~e~l~~i~~~~~~~~~~~~~~~~r~aV~sgrG~GKS~l~a~l~lw~l~~~p~~---kv~vt---Apt~~Q~~~ilw~Ei  128 (511)
                      +.-++++|..|+.+.+. ..|  +-.|--.+-|+||++++..++--.-.---.+   .-++.   =|..+-+.+ .=.|+
T Consensus        91 ~~~Vv~alk~~~~n~~p-~KP--LvLSfHG~tGTGKN~Va~iiA~n~~~~Gl~S~~V~~fvat~hFP~~~~ie~-Yk~eL  166 (344)
T KOG2170          91 KQLVVNALKSHWANPNP-RKP--LVLSFHGWTGTGKNYVAEIIAENLYRGGLRSPFVHHFVATLHFPHASKIED-YKEEL  166 (344)
T ss_pred             HHHHHHHHHHHHCCCCC-CCC--EEEEECCCCCCCHHHHHHHHHHHHHHCCCCCHHHHHHHHHCCCCCHHHHHH-HHHHH
T ss_conf             99999999998628999-987--589830899875648999999998751125626887655415997678999-99999


Q ss_pred             HHHHHHCHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCCCCCCCHHHHCCCCCCEEEEECCHHCCCHHHH
Q ss_conf             99998550001344432222223334443211123578616985303575561002120267614999711102997889
Q gi|254781215|r  129 SKWLSLLPNKHWFEMQSLSLHPAPWYSDVLHCSLGIDSKHYSTMCRTYSEERPDTFVGHHNTYGMAIINDEASGTPDVIN  208 (511)
Q Consensus       129 ~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~ea~~G~h~~~~~lvI~DEAsgI~d~i~  208 (511)
                      +.|++.                                                +.+  .+. ..++|+||+..+|..+.
T Consensus       167 ~~~v~~------------------------------------------------~v~--~C~-rslFIFDE~DKmp~gLl  195 (344)
T KOG2170         167 KNRVRG------------------------------------------------TVQ--ACQ-RSLFIFDEVDKLPPGLL  195 (344)
T ss_pred             HHHHHH------------------------------------------------HHH--HCC-CCEEEECHHHHCCHHHH
T ss_conf             999999------------------------------------------------998--557-75487310543587699


Q ss_pred             HHHHHHHC-------CCCCCEEEEEECCCCC
Q ss_conf             88888850-------7998138998238998
Q gi|254781215|r  209 LGILGFLT-------ERNANRFWIMTSNPRR  232 (511)
Q Consensus       209 e~i~~~Lt-------~~g~~~~~i~~~nP~~  232 (511)
                      +++.|.|-       ..-.+.+.|..||--+
T Consensus       196 d~lkpfLdyyp~v~gv~frkaIFIfLSN~gg  226 (344)
T KOG2170         196 DVLKPFLDYYPQVSGVDFRKAIFIFLSNAGG  226 (344)
T ss_pred             HHHHHHHCCCCCCCCCCCCCEEEEEECCCCC
T ss_conf             9876663046321355455148999717861


No 125
>PRK07246 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
Probab=93.28  E-value=0.56  Score=24.76  Aligned_cols=78  Identities=24%  Similarity=0.238  Sum_probs=46.8

Q ss_pred             CCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEEECCHHHHHHH
Q ss_conf             56555784589999999999987405655542101246502576597899999999999808996699980858999999
Q gi|254781215|r   44 PLEGFSAPRSWQLEFMEVVDAHCLNSVNNPNPEVFKGAISAGRGIGKTTLNAWLVLWLMSTRPGISVICLANSETQLKTT  123 (511)
Q Consensus        44 ~~~~~~~P~~WQ~e~l~~i~~~~~~~~~~~~~~~~r~aV~sgrG~GKS~l~a~l~lw~l~~~p~~kv~vtApt~~Q~~~i  123 (511)
                      .+.+|. +|+=|.+..+.|++...++.        ...|-||.|+|||..--.-++  +. ....+|+|.-+|..--..+
T Consensus       240 ~~~g~E-~R~~Q~~Ma~~V~~al~~~~--------~l~IEAgTGtGKTlaYLlPai--a~-~~~~~vVIST~T~~LQeQL  307 (820)
T PRK07246        240 ALLGLE-ERPKQEQFAQLVDEDYHDGV--------ASFIEAQTGIGKTYGYLLPLL--AQ-SDQNQIIVSVPTKLLQDQI  307 (820)
T ss_pred             CCCCCC-CCHHHHHHHHHHHHHHCCCC--------CEEEECCCCCCHHHHHHHHHH--HH-CCCCEEEEEECCHHHHHHH
T ss_conf             567986-18899999999999980588--------389988999647999999999--84-3798399990869999999


Q ss_pred             HHHHHHHHHH
Q ss_conf             9999999998
Q gi|254781215|r  124 LWAEVSKWLS  133 (511)
Q Consensus       124 lw~Ei~k~~~  133 (511)
                      +.+++-...+
T Consensus       308 ~~kDlp~L~~  317 (820)
T PRK07246        308 MAGEVKAIQE  317 (820)
T ss_pred             HHHHHHHHHH
T ss_conf             9978999999


No 126
>PRK05648 DNA polymerase III subunits gamma and tau; Reviewed
Probab=93.20  E-value=0.58  Score=24.67  Aligned_cols=149  Identities=17%  Similarity=0.174  Sum_probs=76.0

Q ss_pred             HHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEEECCHHHHHHHHHHHHHHHHHH
Q ss_conf             99999999998740565554210124650257659789999999999980899669998085899999999999999985
Q gi|254781215|r   55 QLEFMEVVDAHCLNSVNNPNPEVFKGAISAGRGIGKTTLNAWLVLWLMSTRPGISVICLANSETQLKTTLWAEVSKWLSL  134 (511)
Q Consensus        55 Q~e~l~~i~~~~~~~~~~~~~~~~r~aV~sgrG~GKS~l~a~l~lw~l~~~p~~kv~vtApt~~Q~~~ilw~Ei~k~~~~  134 (511)
                      |.-+++.+...+..++.-| .    ..-..-||+|||+++-.++--.-|.......-|.-  -..-     .+|.     
T Consensus        21 q~~~~~~l~~~~~~~~~~~-a----~l~~g~rg~gkt~~ar~~ak~lnc~~~~~~~pc~~--c~~c-----~~i~-----   83 (705)
T PRK05648         21 QTHVLKALINALDNQRLHH-A----YLFTGTRGVGKTTIARIIAKCLNCETGVSSTPCGE--CSVC-----REID-----   83 (705)
T ss_pred             HHHHHHHHHHHHHCCCCCC-E----EEEECCCCCCHHHHHHHHHHHHCCCCCCCCCCCCC--CHHH-----HHHH-----
T ss_conf             1999999999997098630-4----65007898889899999999867789998897877--6004-----6662-----


Q ss_pred             CHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCCCCCCCHHHHCCCCCCEEEEECCHHCCCHHHHHHHHHH
Q ss_conf             50001344432222223334443211123578616985303575561002120267614999711102997889888888
Q gi|254781215|r  135 LPNKHWFEMQSLSLHPAPWYSDVLHCSLGIDSKHYSTMCRTYSEERPDTFVGHHNTYGMAIINDEASGTPDVINLGILGF  214 (511)
Q Consensus       135 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~ea~~G~h~~~~~lvI~DEAsgI~d~i~e~i~~~  214 (511)
                                      .+...|...++.....+  ....|... +| -.+.-.++.+. .+|+||.+.+....|+++.-|
T Consensus        84 ----------------~~~~~d~~e~d~as~~~--v~~~r~~~-~~-~~~~p~~~~~k-v~~idevhmls~~~fnallkt  142 (705)
T PRK05648         84 ----------------EGRFVDLIEVDAASRTK--VEDTRELL-DN-VQYAPTRGRYK-VYLIDEVHMLSSHSFNALLKT  142 (705)
T ss_pred             ----------------CCCCCCEEEECCCCCCC--HHHHHHHH-HH-CCCCCCCCCEE-EEEEEHHHHCCHHHHHHHHHH
T ss_conf             ----------------48977634451554478--89999999-85-55177677457-999842654179999999874


Q ss_pred             HCCCCCCE-EEEEECCCCCCCCHHHHHH
Q ss_conf             50799813-8998238998765567653
Q gi|254781215|r  215 LTERNANR-FWIMTSNPRRLSGKFYEIF  241 (511)
Q Consensus       215 Lt~~g~~~-~~i~~~nP~~~~g~fy~~~  241 (511)
                      |-.+-... +++++..|.+..-...-.|
T Consensus       143 leepp~~v~f~~att~~~k~p~t~~src  170 (705)
T PRK05648        143 LEEPPPHVKFLLATTDPQKLPVTILSRC  170 (705)
T ss_pred             CCCCCCCEEEEEECCCHHHCCHHHHHHH
T ss_conf             0479754599984287353758999766


No 127
>KOG0389 consensus
Probab=93.18  E-value=0.34  Score=26.17  Aligned_cols=143  Identities=17%  Similarity=0.097  Sum_probs=70.6

Q ss_pred             EECCCCCCHHHHHHHHHHHHHHHCCCCEEEEEECCHHHHHHHHHHHHHHHHHHCHHCCCCCCCCCCCCCCCC-CCCCCCC
Q ss_conf             502576597899999999999808996699980858999999999999999855000134443222222333-4443211
Q gi|254781215|r   82 ISAGRGIGKTTLNAWLVLWLMSTRPGISVICLANSETQLKTTLWAEVSKWLSLLPNKHWFEMQSLSLHPAPW-YSDVLHC  160 (511)
Q Consensus        82 V~sgrG~GKS~l~a~l~lw~l~~~p~~kv~vtApt~~Q~~~ilw~Ei~k~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~  160 (511)
                      .+--=|.|||-=+-..+.+..-..-++--+|+.|+.. +.+= -+|+.||.-.+..-.+..-..-+..+... ..+.   
T Consensus       423 LADEMGLGKTiQvIaFlayLkq~g~~gpHLVVvPsST-leNW-lrEf~kwCPsl~Ve~YyGSq~ER~~lR~~i~~~~---  497 (941)
T KOG0389         423 LADEMGLGKTIQVIAFLAYLKQIGNPGPHLVVVPSST-LENW-LREFAKWCPSLKVEPYYGSQDERRELRERIKKNK---  497 (941)
T ss_pred             EHHHCCCCCHHHHHHHHHHHHHCCCCCCCEEEECCHH-HHHH-HHHHHHHCCCEEEEECCCCHHHHHHHHHHHHCCC---
T ss_conf             3222057633489999999997299998379920316-8889-9999975975287741576899999999986168---


Q ss_pred             CCCCCCCEEEEEECCCCCCCCCHHHHCCCCCCEEEEECCHHCCCHHHHHHHHHHHCCCCCCEEEEEECCCCCCC
Q ss_conf             12357861698530357556100212026761499971110299788988888850799813899823899876
Q gi|254781215|r  161 SLGIDSKHYSTMCRTYSEERPDTFVGHHNTYGMAIINDEASGTPDVINLGILGFLTERNANRFWIMTSNPRRLS  234 (511)
Q Consensus       161 ~~~~~~~~~~~~~~~~s~~~~ea~~G~h~~~~~lvI~DEAsgI~d~i~e~i~~~Lt~~g~~~~~i~~~nP~~~~  234 (511)
                         .+-.....+-..+. .+.+----++......+|+||++.+.+..-+--...|+-. +.-+++.+|+|--+.
T Consensus       498 ---~~ydVllTTY~la~-~~kdDRsflk~~~~n~viyDEgHmLKN~~SeRy~~LM~I~-An~RlLLTGTPLQNN  566 (941)
T KOG0389         498 ---DDYDVLLTTYNLAA-SSKDDRSFLKNQKFNYVIYDEGHMLKNRTSERYKHLMSIN-ANFRLLLTGTPLQNN  566 (941)
T ss_pred             ---CCCCEEEEEEECCC-CCHHHHHHHHHCCCCEEEECCHHHHHCCCHHHHHHHCCCC-CCCEEEEECCCCCCC
T ss_conf             ---88528998721103-8867789998666667996132654213349888750646-553588518742012


No 128
>PRK06964 DNA polymerase III subunit delta'; Validated
Probab=93.14  E-value=0.59  Score=24.61  Aligned_cols=192  Identities=15%  Similarity=0.112  Sum_probs=86.4

Q ss_pred             HHHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEE-EEEEC-CHHHHHHHHHHHHHHH
Q ss_conf             999999999998740565554210124650257659789999999999980899669-99808-5899999999999999
Q gi|254781215|r   54 WQLEFMEVVDAHCLNSVNNPNPEVFKGAISAGRGIGKTTLNAWLVLWLMSTRPGISV-ICLAN-SETQLKTTLWAEVSKW  131 (511)
Q Consensus        54 WQ~e~l~~i~~~~~~~~~~~~~~~~r~aV~sgrG~GKS~l~a~l~lw~l~~~p~~kv-~vtAp-t~~Q~~~ilw~Ei~k~  131 (511)
                      ||.+..+.+...  .+   .+|+  ........|+||..++-.++-+.+|..|.... .|..- +-.....         
T Consensus         5 W~~~~w~~l~~~--~~---rl~H--A~Lf~Gp~G~Gk~~lA~~~A~~llC~~~~~~~~~Cg~C~sC~~~~~---------   68 (342)
T PRK06964          5 WQTDDWNRLQAL--RA---RWPH--ALLLHGQAGIGKLAFAQHLAQGLLCETPQPNGEPCGTCAACTWFAQ---------   68 (342)
T ss_pred             CCHHHHHHHHHC--CC---CHHE--EEEEECCCCCCHHHHHHHHHHHHHCCCCCCCCCCCCCCHHHHHHHC---------
T ss_conf             556999999980--68---7130--5765799986799999999999838999988897867777888862---------


Q ss_pred             HHHCHHCCCCCCCCCCCCCCCCCCCCCCCCC-----CCC--CC-EEEEEECCCCCCCCCHHHHCCCCCCEEEEECCHHCC
Q ss_conf             9855000134443222222333444321112-----357--86-169853035755610021202676149997111029
Q gi|254781215|r  132 LSLLPNKHWFEMQSLSLHPAPWYSDVLHCSL-----GID--SK-HYSTMCRTYSEERPDTFVGHHNTYGMAIINDEASGT  203 (511)
Q Consensus       132 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-----~~~--~~-~~~~~~~~~s~~~~ea~~G~h~~~~~lvI~DEAsgI  203 (511)
                       ..-|.-++..-............+......     +..  .. ......|...  .--++....+.+. .+|+|.|..+
T Consensus        69 -~~HPD~~~i~Pe~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~I~idqiR~l~--~~l~~~~~~g~~k-VviI~~Ae~m  144 (342)
T PRK06964         69 -GNHPDYRIVRPEALAAEAPGAADDAKAADADEGGKKTRAPSKEIKIEQVRALL--DFCGVGSHRGGAR-VVVLYPAEAL  144 (342)
T ss_pred             -CCCCCEEEECCCHHCCCCCCCCCHHHHHHHHHHCCCCCCCCCCCCHHHHHHHH--HHHHHCCCCCCCE-EEEECCHHHH
T ss_conf             -79997455340021022333210010111222101235655645499999999--9970075458844-9998277873


Q ss_pred             CHHHHHHHHHHHCCCCCCEEEEE-ECCCCCCCCHHHHHHHCCCCCCEEEEECCCCCCCCCHHHHHHHHHHCCCCH
Q ss_conf             97889888888507998138998-238998765567653035247417984043367789778999997518980
Q gi|254781215|r  204 PDVINLGILGFLTERNANRFWIM-TSNPRRLSGKFYEIFNKPLDDWKRFQIDTRTVEGIDPSFHEGIIARYGLDS  277 (511)
Q Consensus       204 ~d~i~e~i~~~Lt~~g~~~~~i~-~~nP~~~~g~fy~~~~~~~~~w~~~~i~~~~~p~~~~~~ie~~~~~~geds  277 (511)
                      ....-+++.-+|-.+.....++. +.+|.+.--...-.+..         +.   -+..+.+.+..|.+..|.+.
T Consensus       145 n~~aaNalLK~LEEPp~~~~~iL~~~~~~~llpTI~SRcq~---------~~---~~~~~~~~~~~~L~~~~v~~  207 (342)
T PRK06964        145 NVAAANALLKTLEEPPPGVVFLLVSARIDRLLPTILSRCRQ---------WP---MTVPAPEAAAAWLAAQGVAD  207 (342)
T ss_pred             CHHHHHHHHHHHCCCCCCEEEEEEECCHHHCCHHHHHCCEE---------EC---CCCCCHHHHHHHHHHCCCCC
T ss_conf             89999999997237987848999869925483688767643---------02---89959999999998739863


No 129
>PRK12724 flagellar biosynthesis regulator FlhF; Provisional
Probab=93.08  E-value=0.6  Score=24.56  Aligned_cols=28  Identities=7%  Similarity=-0.070  Sum_probs=12.6

Q ss_pred             CCCCCHHHHHHHHHCCCCCCCCCCCCCC
Q ss_conf             9998989999999759865000255765
Q gi|254781215|r  463 AKSTDYSDGLMYTFAENPPRSDMDFGRC  490 (511)
Q Consensus       463 ~~SPD~ADAl~l~fa~~~~~~~~~~g~~  490 (511)
                      --+.-++-.|-+......|-+-.+.||+
T Consensus       370 DET~s~G~ilni~~~~~~PisYiT~GQ~  397 (432)
T PRK12724        370 DEADFLGSFLELADTYSKSFTYLSVGQE  397 (432)
T ss_pred             CCCCCCCHHHHHHHHHCCCEEEEECCCC
T ss_conf             2779866999999998898699808997


No 130
>PRK07132 DNA polymerase III subunit delta'; Validated
Probab=93.05  E-value=0.61  Score=24.54  Aligned_cols=130  Identities=9%  Similarity=-0.010  Sum_probs=69.5

Q ss_pred             HHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEEEC--------CHHHHHHHHHHH
Q ss_conf             999999999874056555421012465025765978999999999998089966999808--------589999999999
Q gi|254781215|r   56 LEFMEVVDAHCLNSVNNPNPEVFKGAISAGRGIGKTTLNAWLVLWLMSTRPGISVICLAN--------SETQLKTTLWAE  127 (511)
Q Consensus        56 ~e~l~~i~~~~~~~~~~~~~~~~r~aV~sgrG~GKS~l~a~l~lw~l~~~p~~kv~vtAp--------t~~Q~~~ilw~E  127 (511)
                      ..+.+.+.....+++.-|     -.-..+.+|+||++++..++-...++..+....+..|        ....++.   .+
T Consensus         4 e~iv~~L~nai~~~klsH-----AYLF~G~~G~Gk~~~a~~~a~~l~~~~~~~~~~~~~~~~~~~id~~~~~i~~---~~   75 (303)
T PRK07132          4 NNIIKSLDNLAKQNKISH-----SFLLKSNYNNDLDESILYFLNKFNNLQSLNLNLEELPYNIFLFDIFDEDLSK---EE   75 (303)
T ss_pred             HHHHHHHHHHHHCCCCCE-----EEEEECCCCCCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCEEECCCCCCHHH---HH
T ss_conf             389999999998499761-----6886789986799999999999729987888754565323041332220016---88


Q ss_pred             HHHHHHHCHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCCCCCCCHHHHCCCCCCEEEEECCHHCCCHHH
Q ss_conf             99999855000134443222222333444321112357861698530357556100212026761499971110299788
Q gi|254781215|r  128 VSKWLSLLPNKHWFEMQSLSLHPAPWYSDVLHCSLGIDSKHYSTMCRTYSEERPDTFVGHHNTYGMAIINDEASGTPDVI  207 (511)
Q Consensus       128 i~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~ea~~G~h~~~~~lvI~DEAsgI~d~i  207 (511)
                      +...++.                                         .+...++  +   +.+ =.+|+|||..+....
T Consensus        76 i~~~i~~-----------------------------------------~~~~~~~--~---~~~-Kv~IIdea~~lt~~A  108 (303)
T PRK07132         76 FLSAIEK-----------------------------------------FSFSSFV--S---NQK-KILIIKNIEKTSNSS  108 (303)
T ss_pred             HHHHHHH-----------------------------------------HHHCCCC--C---CCE-EEEEEECHHHCCHHH
T ss_conf             9999999-----------------------------------------9736655--6---870-699981655339999


Q ss_pred             HHHHHHHHCCCCCCEE-EEEECCCCCCCCHHHHH
Q ss_conf             9888888507998138-99823899876556765
Q gi|254781215|r  208 NLGILGFLTERNANRF-WIMTSNPRRLSGKFYEI  240 (511)
Q Consensus       208 ~e~i~~~Lt~~g~~~~-~i~~~nP~~~~g~fy~~  240 (511)
                      +.++.-+|-.+..... ++++.+|.+..-...-+
T Consensus       109 ~NaLLKtLEEPp~~~~fil~t~~~~~il~TI~SR  142 (303)
T PRK07132        109 LNALLKTIEEPSKNTYFLLTTKNINKVIPTIVSR  142 (303)
T ss_pred             HHHHHHHCCCCCCCEEEEEEECCHHHCCHHHHHC
T ss_conf             9999987038986848999728824383778636


No 131
>PRK12723 flagellar biosynthesis regulator FlhF; Provisional
Probab=93.03  E-value=0.61  Score=24.52  Aligned_cols=73  Identities=11%  Similarity=0.143  Sum_probs=43.3

Q ss_pred             HHCCCCEEE---EEECCCCHHHHHHHHHCCCEEEEECCCCCCC-CHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHH
Q ss_conf             861888299---8006876368898986498279842777766-402552279999999999997089998189999985
Q gi|254781215|r  365 EKYRPDAII---IDANNTGARTCDYLEMLGYHVYRVLGQKRAV-DLEFCRNRRTELHVKMADWLEFASLINHSGLIQNLK  440 (511)
Q Consensus       365 ~~~~~~~i~---iD~~GvG~gV~d~L~~~g~~v~~v~~~~~~~-~~~~y~N~rae~~~~~re~l~~g~l~~d~~l~~el~  440 (511)
                      ...+...++   +|.+.-+++++..+.+.+.++.-+-.|..-+ |-+.+ |..     .+...|-..++-+|.+.+.+|.
T Consensus       310 ~~~~~~~~I~TKlDEt~~~G~~l~~~~~~~~Pi~yit~GQ~VPdDie~a-~p~-----~~~~~ilG~~~~~~~~~~~~~~  383 (388)
T PRK12723        310 SPFSYKTVIFTKLDETTCVGNLISLIHEMRKEVSYVTDGQIVPHNISIA-EPL-----TFIKKINGYRISDDAEFIRKLK  383 (388)
T ss_pred             CCCCCCEEEEEECCCCCCCCHHHHHHHHHCCCEEEEECCCCCCCCCCCC-CHH-----HHHHHHHCCCCCCHHHHHHHHH
T ss_conf             2799984999832278986699999999888869993899683020338-999-----9999984871454699999985


Q ss_pred             CCC
Q ss_conf             796
Q gi|254781215|r  441 SLK  443 (511)
Q Consensus       441 ~~~  443 (511)
                      +-.
T Consensus       384 ~~~  386 (388)
T PRK12723        384 SKS  386 (388)
T ss_pred             HCC
T ss_conf             045


No 132
>PRK07399 DNA polymerase III subunit delta'; Validated
Probab=92.83  E-value=0.62  Score=24.47  Aligned_cols=75  Identities=13%  Similarity=0.177  Sum_probs=50.4

Q ss_pred             CCCCEEEEECCHHCCCHHHHHHHHHHHCCCCCCEEEEEECCCCCCCCHHHHHHHCCCCCCEEEEECCCCCCCCCHHHHHH
Q ss_conf             67614999711102997889888888507998138998238998765567653035247417984043367789778999
Q gi|254781215|r  189 NTYGMAIINDEASGTPDVINLGILGFLTERNANRFWIMTSNPRRLSGKFYEIFNKPLDDWKRFQIDTRTVEGIDPSFHEG  268 (511)
Q Consensus       189 ~~~~~lvI~DEAsgI~d~i~e~i~~~Lt~~g~~~~~i~~~nP~~~~g~fy~~~~~~~~~w~~~~i~~~~~p~~~~~~ie~  268 (511)
                      +.+ -.+|+|+|..+.....+++.-+|-.++...+++.+.+|.+.--...-+|..         +..   ..++.+.+.+
T Consensus       123 ~~~-kVvII~~ae~m~~~AaNaLLKtLEEP~~~~fILit~~~~~lLpTI~SRCQ~---------i~F---~~l~~~~i~~  189 (314)
T PRK07399        123 APR-KVVVIEDAETMNEAAANALLKTLEEPGNGTLILIAPSPESLLPTIVSRCQI---------IPF---YRLSDEQLEQ  189 (314)
T ss_pred             CCC-EEEEECCHHHCCHHHHHHHHHHHCCCCCCEEEEEECCHHHCCHHHHCCCEE---------EEC---CCCCHHHHHH
T ss_conf             884-799988978719999999998614787856999979936491466418756---------338---9989999999


Q ss_pred             HHHHCCCC
Q ss_conf             99751898
Q gi|254781215|r  269 IIARYGLD  276 (511)
Q Consensus       269 ~~~~~ged  276 (511)
                      ...+.+..
T Consensus       190 ~L~~~~~~  197 (314)
T PRK07399        190 VLKRLGDN  197 (314)
T ss_pred             HHHHCCCC
T ss_conf             99971664


No 133
>KOG0388 consensus
Probab=92.79  E-value=0.44  Score=25.40  Aligned_cols=163  Identities=17%  Similarity=0.186  Sum_probs=76.1

Q ss_pred             HHHHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHHCC-CCEEEEEECCHHHHHHHHH-HHHHH
Q ss_conf             899999999999874056555421012465025765978999999999998089-9669998085899999999-99999
Q gi|254781215|r   53 SWQLEFMEVVDAHCLNSVNNPNPEVFKGAISAGRGIGKTTLNAWLVLWLMSTRP-GISVICLANSETQLKTTLW-AEVSK  130 (511)
Q Consensus        53 ~WQ~e~l~~i~~~~~~~~~~~~~~~~r~aV~sgrG~GKS~l~a~l~lw~l~~~p-~~kv~vtApt~~Q~~~ilw-~Ei~k  130 (511)
                      ++|-+=|.=++.-...+..        -..+---|.|||.-+..++.+.+-++. .+-.+|+||... +.+  | .||.+
T Consensus       570 EYQlkGLnWLvnlYdqGiN--------GILADeMGLGKTVQsisvlAhLaE~~nIwGPFLVVtpaSt-L~N--WaqEisr  638 (1185)
T KOG0388         570 EYQLKGLNWLVNLYDQGIN--------GILADEMGLGKTVQSISVLAHLAETHNIWGPFLVVTPAST-LHN--WAQEISR  638 (1185)
T ss_pred             HHHHCCHHHHHHHHHCCCC--------CEEHHHHCCCHHHHHHHHHHHHHHHCCCCCCEEEEEHHHH-HHH--HHHHHHH
T ss_conf             8765007899999870344--------1213330453268899999999874458876389602787-767--9999998


Q ss_pred             HHHHCHHC-CCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCCCCCCCHHHHCCCCCCEEEEECCHHCCCH---H
Q ss_conf             99855000-1344432222223334443211123578616985303575561002120267614999711102997---8
Q gi|254781215|r  131 WLSLLPNK-HWFEMQSLSLHPAPWYSDVLHCSLGIDSKHYSTMCRTYSEERPDTFVGHHNTYGMAIINDEASGTPD---V  206 (511)
Q Consensus       131 ~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~ea~~G~h~~~~~lvI~DEAsgI~d---~  206 (511)
                      .+-..... .|.....+.+..+-|.-.-.  .....+-+..++....-.-...-|+-..=++   .|+|||..|..   .
T Consensus       639 FlP~~k~lpywGs~~eRkiLrKfw~rKnm--Y~rna~fhVviTSYQlvVtDeky~qkvKWQY---MILDEAQAIKSSsS~  713 (1185)
T KOG0388         639 FLPSFKVLPYWGSPSERKILRKFWNRKNM--YRRNAPFHVVITSYQLVVTDEKYLQKVKWQY---MILDEAQAIKSSSSS  713 (1185)
T ss_pred             HCCCCEEECCCCCHHHHHHHHHHCCHHHH--HCCCCCCEEEEEEEEEEECHHHHHHHHHHHH---EEHHHHHHHHHHHHH
T ss_conf             58654243476880266899974044444--3047995289975311111599998633452---005578776432256


Q ss_pred             HHHHHHHHHCCCCCCEEEEEECCCCCCCC
Q ss_conf             89888888507998138998238998765
Q gi|254781215|r  207 INLGILGFLTERNANRFWIMTSNPRRLSG  235 (511)
Q Consensus       207 i~e~i~~~Lt~~g~~~~~i~~~nP~~~~g  235 (511)
                      -|..+..    -..+..++.+|+|--++-
T Consensus       714 RWKtLLs----F~cRNRLLLTGTPIQNsM  738 (1185)
T KOG0388         714 RWKTLLS----FKCRNRLLLTGTPIQNSM  738 (1185)
T ss_pred             HHHHHHH----HHCCCEEEECCCCCCHHH
T ss_conf             7887740----210340453188530179


No 134
>KOG0342 consensus
Probab=92.67  E-value=0.56  Score=24.77  Aligned_cols=149  Identities=13%  Similarity=0.107  Sum_probs=73.4

Q ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHH-----CCCCEEEEEECCHHHHHHHHHHHHHHHHHHCHHCCCCCCCCCCCCCCCC
Q ss_conf             24650257659789999999999980-----8996699980858999999999999999855000134443222222333
Q gi|254781215|r   79 KGAISAGRGIGKTTLNAWLVLWLMST-----RPGISVICLANSETQLKTTLWAEVSKWLSLLPNKHWFEMQSLSLHPAPW  153 (511)
Q Consensus        79 r~aV~sgrG~GKS~l~a~l~lw~l~~-----~p~~kv~vtApt~~Q~~~ilw~Ei~k~~~~~~~~~~~~~~~~~~~~~~~  153 (511)
                      .+.+++=.|+|||...-.-++-++..     +++..+++++||..-+..+ ++|.++.+...+..-.    ...+.-..+
T Consensus       121 Dvl~~AKTGtGKTlAFLiPaie~l~k~~~~~r~~~~vlIi~PTRELA~Q~-~~eak~Ll~~h~~~~v----~~viGG~~~  195 (543)
T KOG0342         121 DVLAAAKTGTGKTLAFLLPAIELLRKLKFKPRNGTGVLIICPTRELAMQI-FAEAKELLKYHESITV----GIVIGGNNF  195 (543)
T ss_pred             CCEEEECCCCCCEEEEHHHHHHHHHHCCCCCCCCEEEEEECCCHHHHHHH-HHHHHHHHHHCCCCCE----EEEECCCCC
T ss_conf             31245126887410104689999985365777871489965628999989-9999999972767734----787677410


Q ss_pred             CCCCCCCCCCCCCCEEEEEECCCCC-CCCCHHHHCCCCCCEEEEECCHHCCCHHHH----HHHHHHHCCCCCCEEEEEEC
Q ss_conf             4443211123578616985303575-561002120267614999711102997889----88888850799813899823
Q gi|254781215|r  154 YSDVLHCSLGIDSKHYSTMCRTYSE-ERPDTFVGHHNTYGMAIINDEASGTPDVIN----LGILGFLTERNANRFWIMTS  228 (511)
Q Consensus       154 ~~~~~~~~~~~~~~~~~~~~~~~s~-~~~ea~~G~h~~~~~lvI~DEAsgI~d~i~----e~i~~~Lt~~g~~~~~i~~~  228 (511)
                      ..++++.  .....  ..++.+=+. +.-++-.|+-..+.-++|+|||.-+-|.-|    +-|...+. ...+..+++-+
T Consensus       196 ~~e~~kl--~k~~n--iliATPGRLlDHlqNt~~f~~r~~k~lvlDEADrlLd~GF~~di~~Ii~~lp-k~rqt~LFSAT  270 (543)
T KOG0342         196 SVEADKL--VKGCN--ILIATPGRLLDHLQNTSGFLFRNLKCLVLDEADRLLDIGFEEDVEQIIKILP-KQRQTLLFSAT  270 (543)
T ss_pred             HHHHHHH--HCCCC--EEEECCCHHHHHHHCCCCCHHHCCCEEEEECCHHHHHCCCHHHHHHHHHHCC-CCCCEEEEECC
T ss_conf             5899975--15552--7886784177676557841221220357502035665251888999987523-55304676478


Q ss_pred             CCCCCCCHH
Q ss_conf             899876556
Q gi|254781215|r  229 NPRRLSGKF  237 (511)
Q Consensus       229 nP~~~~g~f  237 (511)
                      .|......+
T Consensus       271 ~~~kV~~l~  279 (543)
T KOG0342         271 QPSKVKDLA  279 (543)
T ss_pred             CCHHHHHHH
T ss_conf             968899999


No 135
>TIGR03029 EpsG chain length determinant protein tyrosine kinase EpsG. The proteins in this family are homologs of the EpsG protein found in Methylobacillus strain 12S and are generally found in operons with other Eps homologs. The protein is believed to function as the protein tyrosine kinase component of the chain length regulator (along with the transmembrane component EpsF).
Probab=92.55  E-value=0.64  Score=24.42  Aligned_cols=81  Identities=15%  Similarity=0.107  Sum_probs=50.8

Q ss_pred             HHHCCCCCCC---C--CCCCCCCCHHHHHHHHHHHHHHHHCC-CCCCCCCCEEEEEEC-CCCCCHHHHHHHHHHHHHHHC
Q ss_conf             7642145577---7--56555784589999999999987405-655542101246502-576597899999999999808
Q gi|254781215|r   33 LHFFPWGEKG---T--PLEGFSAPRSWQLEFMEVVDAHCLNS-VNNPNPEVFKGAISA-GRGIGKTTLNAWLVLWLMSTR  105 (511)
Q Consensus        33 ~~~~~w~~~~---~--~~~~~~~P~~WQ~e~l~~i~~~~~~~-~~~~~~~~~r~aV~s-grG~GKS~l~a~l~lw~l~~~  105 (511)
                      -|-||.-..+   -  +|--..-|..=|.|.||++.....-. .+.+ +  .-++|.| ..|-|||++++.+++-++.  
T Consensus        56 q~~~py~~~~~~~~~~~l~aa~~P~s~~~Ea~R~lRs~l~~~~~~~~-~--~~LaItS~~pGEGKS~vAaNLA~~~Aq--  130 (274)
T TIGR03029        56 QFEYPYLPPNDGSFSPDLIAAYQPFSPQVEALRALRSQLMLRWFSEG-R--KALAVVSAKSGEGCSYIAANLAIVFSQ--  130 (274)
T ss_pred             HCCCCCCCCCCCCCCHHHHHHHCCCCHHHHHHHHHHHHHHHHHCCCC-C--CEEEEECCCCCCCHHHHHHHHHHHHHH--
T ss_conf             62898778455788989987738998899999999999999845788-8--389996899999899999999999996--


Q ss_pred             CCCEEEEEECCHH
Q ss_conf             9966999808589
Q gi|254781215|r  106 PGISVICLANSET  118 (511)
Q Consensus       106 p~~kv~vtApt~~  118 (511)
                      -|.|++++=...+
T Consensus       131 ~G~RvLLVDaDLR  143 (274)
T TIGR03029       131 LGEKTLLIDANLR  143 (274)
T ss_pred             CCCEEEEEECCCC
T ss_conf             7991999958888


No 136
>TIGR02525 plasmid_TraJ plasmid transfer ATPase TraJ; InterPro: IPR013364    Proteins in this entry are predicted ATPases associated with plasmid transfer loci in bacteria. This family is most similar to the DotB ATPase (IPR013363 from INTERPRO) of a type-IV secretion-like system of the obligate intracellular pathogens Legionella pneumophila and Coxiella burnetii..
Probab=92.51  E-value=0.16  Score=28.26  Aligned_cols=32  Identities=28%  Similarity=0.384  Sum_probs=20.8

Q ss_pred             EECCCCCCHHHHHHHHHHHHHHHCCCCEEEEE
Q ss_conf             50257659789999999999980899669998
Q gi|254781215|r   82 ISAGRGIGKTTLNAWLVLWLMSTRPGISVICL  113 (511)
Q Consensus        82 V~sgrG~GKS~l~a~l~lw~l~~~p~~kv~vt  113 (511)
                      |-.-.|+||||++|.+=-+.+-|+|+-||+..
T Consensus       154 iCG~TGSGKSTl~AaiY~~~l~t~pdRKivT~  185 (374)
T TIGR02525       154 ICGETGSGKSTLAAAIYRHCLETYPDRKIVTY  185 (374)
T ss_pred             ECCCCCCCHHHHHHHHHHHHCCCCCCCEEEEE
T ss_conf             21778972899999999985074889707986


No 137
>PRK13894 conjugal transfer ATPase TrbB; Provisional
Probab=92.45  E-value=0.35  Score=26.08  Aligned_cols=33  Identities=21%  Similarity=0.352  Sum_probs=22.3

Q ss_pred             HHHHHHHHHCCCCEEEEEECCCCHHHHHHHHHCC
Q ss_conf             9999999861888299800687636889898649
Q gi|254781215|r  358 NKISGLVEKYRPDAIIIDANNTGARTCDYLEMLG  391 (511)
Q Consensus       358 ~~i~~~~~~~~~~~i~iD~~GvG~gV~d~L~~~g  391 (511)
                      ..+...+-+.+|+.|++-..= |.-+.+.|+.++
T Consensus       210 ~~Ll~~aLR~rPDRIivGEvR-g~Ea~~~l~A~n  242 (320)
T PRK13894        210 TALLKTTLRMRPDRILVGEVR-GPEALDLLMAWN  242 (320)
T ss_pred             HHHHHHHHCCCCCEEEECCCC-CHHHHHHHHHHH
T ss_conf             999999736799858766547-489999999996


No 138
>TIGR00635 ruvB Holliday junction DNA helicase RuvB; InterPro: IPR004605 All proteins in this family for which functions are known are 5'-3' DNA helicases that, as part of a complex with RuvA homologs serve as a 5'-3' Holliday junction helicase. RuvA specifically binds Holliday junctions as a sandwich of two tetramers and maintains the configuration of the junction. It forms a complex with two hexameric rings of RuvB, the subunit that contains helicase activity. The complex drives ATP-dependent branch migration of the Holliday junction recombination intermediate. The endonuclease RuvC resolves junctions.; GO: 0003677 DNA binding, 0005524 ATP binding, 0009378 Holliday junction helicase activity, 0006281 DNA repair, 0006310 DNA recombination.
Probab=92.26  E-value=0.56  Score=24.76  Aligned_cols=104  Identities=15%  Similarity=0.063  Sum_probs=70.7

Q ss_pred             CCCCCCCCHHHHHHHHHHHHHHHHCCCCC--CCCCCEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEE-ECCHHHH
Q ss_conf             56555784589999999999987405655--54210124650257659789999999999980899669998-0858999
Q gi|254781215|r   44 PLEGFSAPRSWQLEFMEVVDAHCLNSVNN--PNPEVFKGAISAGRGIGKTTLNAWLVLWLMSTRPGISVICL-ANSETQL  120 (511)
Q Consensus        44 ~~~~~~~P~~WQ~e~l~~i~~~~~~~~~~--~~~~~~r~aV~sgrG~GKS~l~a~l~lw~l~~~p~~kv~vt-Apt~~Q~  120 (511)
                      .|+.|.|    |.++=+++.-.++.-+.|  .+-   -+-...+=|.|||+|+..++.-     =+.++-+| +|-..-.
T Consensus         2 ~L~eFiG----Q~~vk~~L~l~I~AAk~R~e~LD---H~LL~GPPGLGKTTLA~IiA~E-----mg~~l~iTsGP~L~kP   69 (305)
T TIGR00635         2 LLAEFIG----QEKVKEQLQLFIEAAKMRQEALD---HLLLYGPPGLGKTTLAHIIANE-----MGVNLKITSGPALEKP   69 (305)
T ss_pred             CCHHCCC----CHHHHHHHHHHHHHHHHCCCCCC---CEEEECCCCCCHHHHHHHHHHH-----HCCCCEEEECCCCCCH
T ss_conf             8011058----28899999999999982489734---1663175687467899999998-----3893267406755475


Q ss_pred             HHHHHHHHHHHHHHCHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCCCCCCCHHHHCCCCCCEEEEECCH
Q ss_conf             99999999999985500013444322222233344432111235786169853035755610021202676149997111
Q gi|254781215|r  121 KTTLWAEVSKWLSLLPNKHWFEMQSLSLHPAPWYSDVLHCSLGIDSKHYSTMCRTYSEERPDTFVGHHNTYGMAIINDEA  200 (511)
Q Consensus       121 ~~ilw~Ei~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~ea~~G~h~~~~~lvI~DEA  200 (511)
                      +|.. +-|                                                        .++. ++-+|+| ||-
T Consensus        70 gDla-aiL--------------------------------------------------------t~L~-~gDVLFI-DEI   90 (305)
T TIGR00635        70 GDLA-AIL--------------------------------------------------------TNLE-EGDVLFI-DEI   90 (305)
T ss_pred             HHHH-HHH--------------------------------------------------------HHCC-CCCEEEC-CHH
T ss_conf             7899-999--------------------------------------------------------7056-8963101-256


Q ss_pred             HCCCHHHHHHHHHHHCCC
Q ss_conf             029978898888885079
Q gi|254781215|r  201 SGTPDVINLGILGFLTER  218 (511)
Q Consensus       201 sgI~d~i~e~i~~~Lt~~  218 (511)
                      +=+...+-|.+.|+|-|-
T Consensus        91 HRL~p~~EE~LYpAMEDF  108 (305)
T TIGR00635        91 HRLSPAIEELLYPAMEDF  108 (305)
T ss_pred             HHCCHHHHHHCCCCCCCE
T ss_conf             504833453105300121


No 139
>KOG0331 consensus
Probab=92.25  E-value=0.78  Score=23.87  Aligned_cols=153  Identities=16%  Similarity=0.010  Sum_probs=78.7

Q ss_pred             CCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHH------CC-CCEEEEEECC
Q ss_conf             5655578458999999999998740565554210124650257659789999999999980------89-9669998085
Q gi|254781215|r   44 PLEGFSAPRSWQLEFMEVVDAHCLNSVNNPNPEVFKGAISAGRGIGKTTLNAWLVLWLMST------RP-GISVICLANS  116 (511)
Q Consensus        44 ~~~~~~~P~~WQ~e~l~~i~~~~~~~~~~~~~~~~r~aV~sgrG~GKS~l~a~l~lw~l~~------~p-~~kv~vtApt  116 (511)
                      ...+|..|-+-|+...--+-+      ++      -+-..|..|+|||.....=++-++..      ++ +..++|.|||
T Consensus       107 k~~g~~~PtpIQaq~wp~~l~------Gr------D~v~iA~TGSGKTLay~lP~i~~l~~~~~~~~~~~~P~vLVL~PT  174 (519)
T KOG0331         107 KEQGFEKPTPIQAQGWPIALS------GR------DLVGIARTGSGKTLAYLLPAIVHLNNEQGKLSRGDGPIVLVLAPT  174 (519)
T ss_pred             HHCCCCCCCHHHHCCCCEECC------CC------CEEEEECCCCCCHHHHHHHHHHHHHHCCCCCCCCCCCEEEEECCC
T ss_conf             853999885344144651126------88------657782357862055555799998700444347999869997685


Q ss_pred             HHHHHHHHHHHHHHHHHHCHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCCCCCCCHHHHCCCCCCEEEE
Q ss_conf             89999999999999998550001344432222223334443211123578616985303575561002120267614999
Q gi|254781215|r  117 ETQLKTTLWAEVSKWLSLLPNKHWFEMQSLSLHPAPWYSDVLHCSLGIDSKHYSTMCRTYSEERPDTFVGHHNTYGMAII  196 (511)
Q Consensus       117 ~~Q~~~ilw~Ei~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~ea~~G~h~~~~~lvI  196 (511)
                      ..-+..|- .+..+....+..+.  .|.-+     +.....+...++.+.....++.--.........-.++  ....+|
T Consensus       175 RELA~QV~-~~~~~~~~~~~~~~--~cvyG-----G~~~~~Q~~~l~~gvdiviaTPGRl~d~le~g~~~l~--~v~ylV  244 (519)
T KOG0331         175 RELAVQVQ-AEAREFGKSLRLRS--TCVYG-----GAPKGPQLRDLERGVDVVIATPGRLIDLLEEGSLNLS--RVTYLV  244 (519)
T ss_pred             HHHHHHHH-HHHHHHCCCCCCCE--EEEEC-----CCCCCHHHHHHHCCCCEEEECCHHHHHHHHCCCCCCC--CEEEEE
T ss_conf             99999999-99999707777407--99868-----9886378898755981898077178999974885645--303999


Q ss_pred             ECCHHCCCHHHH-HHHHHHHCCC
Q ss_conf             711102997889-8888885079
Q gi|254781215|r  197 NDEASGTPDVIN-LGILGFLTER  218 (511)
Q Consensus       197 ~DEAsgI~d~i~-e~i~~~Lt~~  218 (511)
                      +|||.-+-|.=| +-++-.+..-
T Consensus       245 LDEADrMldmGFe~qI~~Il~~i  267 (519)
T KOG0331         245 LDEADRMLDMGFEPQIRKILSQI  267 (519)
T ss_pred             ECCHHHHHCCCCHHHHHHHHHHC
T ss_conf             63477663135379999998755


No 140
>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=92.23  E-value=0.3  Score=26.48  Aligned_cols=50  Identities=16%  Similarity=0.218  Sum_probs=38.1

Q ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHH--CCCCEEEEEECCHHHHHHHHHHHHHHHHH
Q ss_conf             24650257659789999999999980--89966999808589999999999999998
Q gi|254781215|r   79 KGAISAGRGIGKTTLNAWLVLWLMST--RPGISVICLANSETQLKTTLWAEVSKWLS  133 (511)
Q Consensus        79 r~aV~sgrG~GKS~l~a~l~lw~l~~--~p~~kv~vtApt~~Q~~~ilw~Ei~k~~~  133 (511)
                      -+.|.+|=|+|||+.....+++.+..  -++.+++++.=|..-+.     |++..+.
T Consensus        15 ~llV~AgAGSGKT~~L~~Ri~~li~~~~~~p~~IL~lTFT~kAA~-----Em~~Ri~   66 (494)
T pfam00580        15 PLLVLAGAGTGKTRVLTERIAYLILEGGIDPEEILAVTFTNKAAR-----EMKERIL   66 (494)
T ss_pred             CEEEEEECCHHHHHHHHHHHHHHHHHCCCCHHHEEEEECHHHHHH-----HHHHHHH
T ss_conf             979997187068999999999999818999747876702899999-----9999999


No 141
>COG0470 HolB ATPase involved in DNA replication [DNA replication, recombination, and repair]
Probab=92.22  E-value=0.78  Score=23.85  Aligned_cols=108  Identities=22%  Similarity=0.223  Sum_probs=64.5

Q ss_pred             EEEECCCCCCHHHHHHHHHHHHHHHCCCC-------------------EEEEEECCHHHHHHHHHHHHHHHHHHCHHCCC
Q ss_conf             46502576597899999999999808996-------------------69998085899999999999999985500013
Q gi|254781215|r   80 GAISAGRGIGKTTLNAWLVLWLMSTRPGI-------------------SVICLANSETQLKTTLWAEVSKWLSLLPNKHW  140 (511)
Q Consensus        80 ~aV~sgrG~GKS~l~a~l~lw~l~~~p~~-------------------kv~vtApt~~Q~~~ilw~Ei~k~~~~~~~~~~  140 (511)
                      +......|+|||+++-.++-+..+..+..                   .++...|+...-.++.-..++...+...    
T Consensus        27 lL~~Gp~G~Gktt~a~~lA~~l~~~~~~~~~~~~~~~~~~~~~~~~~~d~lel~~s~~~~~~i~~~~vr~~~~~~~----  102 (325)
T COG0470          27 LLFYGPPGVGKTTAALALAKELLCENPTGLLPCGHCRSCKLIPAGNHPDFLELNPSDLRKIDIIVEQVRELAEFLS----  102 (325)
T ss_pred             EEEECCCCCCHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHCCCCCCCEEEECCCCCCCCCCHHHHHHHHHHHCC----
T ss_conf             0037999997899999999996586643345520022444320256886599773213333006999999998604----


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCCCCCCCHHHHCCCCCCEEEEECCHHCCCHHHHHHHHHHHCCCCC
Q ss_conf             44432222223334443211123578616985303575561002120267614999711102997889888888507998
Q gi|254781215|r  141 FEMQSLSLHPAPWYSDVLHCSLGIDSKHYSTMCRTYSEERPDTFVGHHNTYGMAIINDEASGTPDVINLGILGFLTERNA  220 (511)
Q Consensus       141 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~ea~~G~h~~~~~lvI~DEAsgI~d~i~e~i~~~Lt~~g~  220 (511)
                                                                 ..+..+.. -++|+|||..+....-.++..++-.+..
T Consensus       103 -------------------------------------------~~~~~~~~-kviiidead~mt~~A~nallk~lEep~~  138 (325)
T COG0470         103 -------------------------------------------ESPLEGGY-KVVIIDEADKLTEDAANALLKTLEEPPK  138 (325)
T ss_pred             -------------------------------------------CCCCCCCC-EEEEEECCCCCCHHHHHHHHHHCCCCCC
T ss_conf             -------------------------------------------46566772-6999732032698888767543324888


Q ss_pred             CEEEEEECC-CCCCCC
Q ss_conf             138998238-998765
Q gi|254781215|r  221 NRFWIMTSN-PRRLSG  235 (511)
Q Consensus       221 ~~~~i~~~n-P~~~~g  235 (511)
                      ...++.++| |.+.-.
T Consensus       139 ~~~~il~~n~~~~il~  154 (325)
T COG0470         139 NTRFILITNDPSKILP  154 (325)
T ss_pred             CEEEEEEECCHHHCHH
T ss_conf             7169997498555647


No 142
>PRK06731 flhF flagellar biosynthesis regulator FlhF; Validated
Probab=92.02  E-value=0.83  Score=23.70  Aligned_cols=86  Identities=15%  Similarity=0.086  Sum_probs=51.4

Q ss_pred             CHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCC---CCCCEEEEEECCCCCCHHHHHHHH
Q ss_conf             70666528866776421455777565557845899999999999874056555---421012465025765978999999
Q gi|254781215|r   21 SDEIKLSFSNFVLHFFPWGEKGTPLEGFSAPRSWQLEFMEVVDAHCLNSVNNP---NPEVFKGAISAGRGIGKTTLNAWL   97 (511)
Q Consensus        21 ~~~~~~~~~~~~~~~~~w~~~~~~~~~~~~P~~WQ~e~l~~i~~~~~~~~~~~---~~~~~r~aV~sgrG~GKS~l~a~l   97 (511)
                      +.++.++|...++--+            .+...++.++++.+.+...+..+..   .....-+......|+|||+.+|=+
T Consensus        28 ~~~vv~~~~~~ik~k~------------~~~~~~~~~vi~~l~~~l~~~~~~~~~~~~~~~vI~lvG~~G~GKTTT~AKL   95 (270)
T PRK06731         28 EQYFIHAYAEKLKVKF------------ENATMITEEVIEYILEDMSSHFNTENVFEKEVQTIALIGPTGVGKTTTLAKM   95 (270)
T ss_pred             CHHHHHHHHHHHHHHH------------CCCCCHHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCCCHHHHHHHH
T ss_conf             8899999999999885------------0455329999999999998750766546799818999888989889999999


Q ss_pred             HHHHHHHCCCCEEEEEECCHHH
Q ss_conf             9999980899669998085899
Q gi|254781215|r   98 VLWLMSTRPGISVICLANSETQ  119 (511)
Q Consensus        98 ~lw~l~~~p~~kv~vtApt~~Q  119 (511)
                      +.|+. .+.....++++-|++-
T Consensus        96 A~~~~-~~~~kV~lia~DtyR~  116 (270)
T PRK06731         96 AWQFH-GKKKTVGFITTDHSRI  116 (270)
T ss_pred             HHHHH-HCCCEEEEEEECCCCH
T ss_conf             99998-6799089998388888


No 143
>COG2812 DnaX DNA polymerase III, gamma/tau subunits [DNA replication, recombination, and repair]
Probab=91.95  E-value=0.84  Score=23.65  Aligned_cols=149  Identities=18%  Similarity=0.156  Sum_probs=75.3

Q ss_pred             HHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEEECCHHHHHHHHHHHHHHHHHH
Q ss_conf             99999999998740565554210124650257659789999999999980899669998085899999999999999985
Q gi|254781215|r   55 QLEFMEVVDAHCLNSVNNPNPEVFKGAISAGRGIGKTTLNAWLVLWLMSTRPGISVICLANSETQLKTTLWAEVSKWLSL  134 (511)
Q Consensus        55 Q~e~l~~i~~~~~~~~~~~~~~~~r~aV~sgrG~GKS~l~a~l~lw~l~~~p~~kv~vtApt~~Q~~~ilw~Ei~k~~~~  134 (511)
                      |.-+.+.+..-+.+++--|     ...-+..||+|||+++-.++--.-|.+...--.|.-=  ..-+.|..+        
T Consensus        21 Qe~v~~~L~nal~~~ri~h-----AYlfsG~RGvGKTt~Ari~AkalNC~~~~~~ePC~~C--~~Ck~I~~g--------   85 (515)
T COG2812          21 QEHVVKTLSNALENGRIAH-----AYLFSGPRGVGKTTIARILAKALNCENGPTAEPCGKC--ISCKEINEG--------   85 (515)
T ss_pred             CHHHHHHHHHHHHHCCCHH-----HHHHCCCCCCCCHHHHHHHHHHHCCCCCCCCCCCHHH--HHHHHHHCC--------
T ss_conf             4899999999998084233-----3651377776710499999999568898777722531--666865148--------


Q ss_pred             CHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCCCCCCCHHHHCCCCCCEEEEECCHHCCCHHHHHHHHHH
Q ss_conf             50001344432222223334443211123578616985303575561002120267614999711102997889888888
Q gi|254781215|r  135 LPNKHWFEMQSLSLHPAPWYSDVLHCSLGIDSKHYSTMCRTYSEERPDTFVGHHNTYGMAIINDEASGTPDVINLGILGF  214 (511)
Q Consensus       135 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~ea~~G~h~~~~~lvI~DEAsgI~d~i~e~i~~~  214 (511)
                                        ...|...++-..+.+  ....|....+  -.+.-..+.+- .+|+||++.+....|+++.-+
T Consensus        86 ------------------~~~DviEiDaASn~g--VddiR~i~e~--v~y~P~~~ryK-VyiIDEvHMLS~~afNALLKT  142 (515)
T COG2812          86 ------------------SLIDVIEIDAASNTG--VDDIREIIEK--VNYAPSEGRYK-VYIIDEVHMLSKQAFNALLKT  142 (515)
T ss_pred             ------------------CCCCCHHHHHHHCCC--HHHHHHHHHH--HCCCCCCCCCE-EEEEECHHHHHHHHHHHHHCC
T ss_conf             ------------------864101136444548--6799999987--24688666641-899831876437888887511


Q ss_pred             HCCCCCC-EEEEEECCCCCCCCHHHHHH
Q ss_conf             5079981-38998238998765567653
Q gi|254781215|r  215 LTERNAN-RFWIMTSNPRRLSGKFYEIF  241 (511)
Q Consensus       215 Lt~~g~~-~~~i~~~nP~~~~g~fy~~~  241 (511)
                      |-.+=.. .+++++..|.+.....--.+
T Consensus       143 LEEPP~hV~FIlATTe~~Kip~TIlSRc  170 (515)
T COG2812         143 LEEPPSHVKFILATTEPQKIPNTILSRC  170 (515)
T ss_pred             CCCCCCCEEEEEECCCCCCCCHHHHHCC
T ss_conf             1368667489985388676840455212


No 144
>PRK12727 flagellar biosynthesis regulator FlhF; Provisional
Probab=91.81  E-value=0.87  Score=23.55  Aligned_cols=48  Identities=10%  Similarity=0.115  Sum_probs=27.0

Q ss_pred             CHHHHHHHHHHHHHHCCCCEEE-EEECCCCHHHHHHHHHC----CCEEEEECC
Q ss_conf             9889999999999861888299-80068763688989864----982798427
Q gi|254781215|r  352 DLRTTNNKISGLVEKYRPDAII-IDANNTGARTCDYLEML----GYHVYRVLG  399 (511)
Q Consensus       352 d~~~~a~~i~~~~~~~~~~~i~-iD~~GvG~gV~d~L~~~----g~~v~~v~~  399 (511)
                      .|+.+++....+..+|+...|. |-.+.+=.|-+++|+-+    |++|.-+..
T Consensus       361 KTTT~aKlAa~~~~~~g~~~valit~DtyRiga~eQL~~y~~ilgvpv~~~~~  413 (557)
T PRK12727        361 KTTTIAKLAQRFAAQHAPRDVALVTTDTQRVGGREQLHSYGRQLGIAVHEADS  413 (557)
T ss_pred             CHHHHHHHHHHHHHHCCCCEEEEEECCCCCHHHHHHHHHHHHHHCCEEEEECC
T ss_conf             31179999999999739981899972664087999999999983975798289


No 145
>KOG0339 consensus
Probab=91.69  E-value=0.9  Score=23.47  Aligned_cols=136  Identities=14%  Similarity=0.084  Sum_probs=69.3

Q ss_pred             CCCCCHHHHHHHHHHHHHHHCC------CCEEEEEECCHHHHHHHHHHHHHHHHHHCHHCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             5765978999999999998089------9669998085899999999999999985500013444322222233344432
Q gi|254781215|r   85 GRGIGKTTLNAWLVLWLMSTRP------GISVICLANSETQLKTTLWAEVSKWLSLLPNKHWFEMQSLSLHPAPWYSDVL  158 (511)
Q Consensus        85 grG~GKS~l~a~l~lw~l~~~p------~~kv~vtApt~~Q~~~ilw~Ei~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~  158 (511)
                      -.|.|||...+|-.+-++.-.|      +.-.++++||..-+..| |.|.++.-... +.+-..+-   .....|+   +
T Consensus       268 ktgSgktaAfi~pm~~himdq~eL~~g~gPi~vilvPTrela~Qi-~~eaKkf~K~y-gl~~v~~y---gGgsk~e---Q  339 (731)
T KOG0339         268 KTGSGKTAAFIWPMIVHIMDQPELKPGEGPIGVILVPTRELASQI-FSEAKKFGKAY-GLRVVAVY---GGGSKWE---Q  339 (731)
T ss_pred             ECCCCCHHHHHHHHHHHHCCHHHHCCCCCCEEEEEECCHHHHHHH-HHHHHHHHHHC-CCEEEEEE---CCCCHHH---H
T ss_conf             115750567777777774140520689997699980638999999-99999863112-64278863---6874888---7


Q ss_pred             CCCCCCCCCEEEEEECCCCCCCCCHHHHCCCCCCEEEEECCHHCCCHHHHH----HHHHHHCCCCCCEEEEEECCCCCC
Q ss_conf             111235786169853035755610021202676149997111029978898----888885079981389982389987
Q gi|254781215|r  159 HCSLGIDSKHYSTMCRTYSEERPDTFVGHHNTYGMAIINDEASGTPDVINL----GILGFLTERNANRFWIMTSNPRRL  233 (511)
Q Consensus       159 ~~~~~~~~~~~~~~~~~~s~~~~ea~~G~h~~~~~lvI~DEAsgI~d~i~e----~i~~~Lt~~g~~~~~i~~~nP~~~  233 (511)
                      ...++-..+  ++++.+-+.-.---+.|..-.+..++|+|||.-+-+-=|+    .|...++   +...+|+|++....
T Consensus       340 ~k~Lk~g~E--ivVaTPgRlid~VkmKatn~~rvS~LV~DEadrmfdmGfe~qVrSI~~hir---pdrQtllFsaTf~~  413 (731)
T KOG0339         340 SKELKEGAE--IVVATPGRLIDMVKMKATNLSRVSYLVLDEADRMFDMGFEPQVRSIKQHIR---PDRQTLLFSATFKK  413 (731)
T ss_pred             HHHHHCCCE--EEEECHHHHHHHHHHHCCCCEEEEEEEEECHHHHHCCCCHHHHHHHHHHCC---CCCEEEEEECCCHH
T ss_conf             776502772--899662888999886033310035788711111312654798999986448---86427986031068


No 146
>KOG0328 consensus
Probab=91.69  E-value=0.41  Score=25.64  Aligned_cols=64  Identities=17%  Similarity=0.111  Sum_probs=46.2

Q ss_pred             CCCCHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHHCC-CCEEEEEECCHHHHHHH
Q ss_conf             57845899999999999874056555421012465025765978999999999998089-96699980858999999
Q gi|254781215|r   48 FSAPRSWQLEFMEVVDAHCLNSVNNPNPEVFKGAISAGRGIGKTTLNAWLVLWLMSTRP-GISVICLANSETQLKTT  123 (511)
Q Consensus        48 ~~~P~~WQ~e~l~~i~~~~~~~~~~~~~~~~r~aV~sgrG~GKS~l~a~l~lw~l~~~p-~~kv~vtApt~~Q~~~i  123 (511)
                      |..|-.-|..++-.|-..            +.|.+.|--|+|||...+.-++=-+-+.. ...+++.+||..-+-.+
T Consensus        47 fekPS~IQqrAi~~IlkG------------rdViaQaqSGTGKTa~~si~vlq~~d~~~r~tQ~lilsPTRELa~Qi  111 (400)
T KOG0328          47 FEKPSAIQQRAIPQILKG------------RDVIAQAQSGTGKTATFSISVLQSLDISVRETQALILSPTRELAVQI  111 (400)
T ss_pred             CCCCHHHHHHHHHHHHCC------------CCEEEEECCCCCCEEEEEEEEEEECCCCCCEEEEEEECCHHHHHHHH
T ss_conf             578167776102456336------------61478704788844789866314034342003578954708999999


No 147
>TIGR01969 minD_arch cell division ATPase MinD; InterPro: IPR010224   Proper placement of the bacterial cell division site requires the site-specific inactivation of other potential division sites. In Escherichia coli, selection of the correct mid-cell site is mediated by the MinC, MinD and MinE proteins. Several members of this family are found in archaeal genomes but their function is uncharacterised. More distantly related proteins include flagellar biosynthesis proteins and ParA chromosome partitioning proteins.    This entry represents the archaeal MinD family. The exact roles of the various archaeal MinD homologs are unknown. .
Probab=91.64  E-value=0.17  Score=28.05  Aligned_cols=188  Identities=16%  Similarity=0.118  Sum_probs=93.9

Q ss_pred             EEEEECCC-CCCHHHHHHHHHHHHHHHCCCCEEEEEECCHHHHHHHHHHHHHHHHHH---CHHCCCCCCCCCCCCCCCCC
Q ss_conf             24650257-659789999999999980899669998085899999999999999985---50001344432222223334
Q gi|254781215|r   79 KGAISAGR-GIGKTTLNAWLVLWLMSTRPGISVICLANSETQLKTTLWAEVSKWLSL---LPNKHWFEMQSLSLHPAPWY  154 (511)
Q Consensus        79 r~aV~sgr-G~GKS~l~a~l~lw~l~~~p~~kv~vtApt~~Q~~~ilw~Ei~k~~~~---~~~~~~~~~~~~~~~~~~~~  154 (511)
                      -++|+||. |+||||.+|.|..-.+-+  |.+|++.=.-...|      =|.-.+.+   .+.-|.--.-+-.+.-.-|.
T Consensus         2 ~I~iASGKGGtGKTT~tANLgVALA~~--Gk~V~~~DADI~MA------NL~LiLgmE~~~VTLhDVLAGeA~i~DAIY~   73 (258)
T TIGR01969         2 IITIASGKGGTGKTTITANLGVALAKL--GKKVLVLDADITMA------NLELILGMEDKPVTLHDVLAGEADIKDAIYE   73 (258)
T ss_pred             EEEEEECCCCCCHHHEEEHHHHHHHHC--CCEEEEEECCHHHH------HHHHHHCCCCCCCCCCCCCCCCCCHHHHCCC
T ss_conf             889997788986140000077889860--97689994676677------6898844688896752213445610011002


Q ss_pred             CCCCCCCCCCCCCEEEEEECCCCCCCCCHHHHCCCCCCEEEEECCHHCCCHHHHHHHHHHHCCCCCCEEEEEECCCCCCC
Q ss_conf             44321112357861698530357556100212026761499971110299788988888850799813899823899876
Q gi|254781215|r  155 SDVLHCSLGIDSKHYSTMCRTYSEERPDTFVGHHNTYGMAIINDEASGTPDVINLGILGFLTERNANRFWIMTSNPRRLS  234 (511)
Q Consensus       155 ~~~~~~~~~~~~~~~~~~~~~~s~~~~ea~~G~h~~~~~lvI~DEAsgI~d~i~e~i~~~Lt~~g~~~~~i~~~nP~~~~  234 (511)
                      .....+..-..+-+|--.-+.--..-+|-+.-+|.+. .++++|-=+|+.-+...++..     +.+.  |.--||==.+
T Consensus        74 gp~GnV~V~PagvSLEg~rKA~~~~L~dV~~~i~~~~-D~lLIDAPAGL~~~a~~Al~~-----a~el--LLVvNPEi~S  145 (258)
T TIGR01969        74 GPEGNVKVIPAGVSLEGLRKADPDKLEDVLKEIIDDT-DFLLIDAPAGLERDAVTALAA-----ADEL--LLVVNPEISS  145 (258)
T ss_pred             CCCCCEEEECCCCCHHHCCCCCHHHHHHHHHHHHCCC-CEEEEECCCCCCHHHHHHHHH-----CCCC--EEEECCCHHH
T ss_conf             8898447850612210001268333289999872043-778874789833789999986-----1866--4866765446


Q ss_pred             --CHHHH--HHHCCCCCCEEEEEC--CCCCCCCCHHHHHHHHHH-----CCCCHHHHHH
Q ss_conf             --55676--530352474179840--433677897789999975-----1898013544
Q gi|254781215|r  235 --GKFYE--IFNKPLDDWKRFQID--TRTVEGIDPSFHEGIIAR-----YGLDSDVTRV  282 (511)
Q Consensus       235 --g~fy~--~~~~~~~~w~~~~i~--~~~~p~~~~~~ie~~~~~-----~geds~~~r~  282 (511)
                        +...-  .-.+..-.=.-.-++  +++....+++.||.+.+-     -+||+.+=|.
T Consensus       146 ItDaLK~k~va~~lGt~ilG~vlNRv~~~~tel~~~eiE~iLevPVl~~vPEDP~VR~A  204 (258)
T TIGR01969       146 ITDALKVKIVAEKLGTAILGVVLNRVTRDKTELGREEIEAILEVPVLGVVPEDPEVRRA  204 (258)
T ss_pred             HHHHHHHHHHHHHCCCCEEEEEEEECCCCCCCCCHHHHHHHHCCCEEEEECCCHHHHHH
T ss_conf             77788999998760883246899602366663788899988479738985698434456


No 148
>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=91.54  E-value=0.78  Score=23.84  Aligned_cols=38  Identities=26%  Similarity=0.299  Sum_probs=28.5

Q ss_pred             EEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEEECCHH
Q ss_conf             465025765978999999999998089966999808589
Q gi|254781215|r   80 GAISAGRGIGKTTLNAWLVLWLMSTRPGISVICLANSET  118 (511)
Q Consensus        80 ~aV~sgrG~GKS~l~a~l~lw~l~~~p~~kv~vtApt~~  118 (511)
                      ++.....|+|||+.+|=++.++. .+...-.++++-|++
T Consensus         3 i~lvGptGvGKTTTiaKLA~~~~-~~~~kV~lit~Dt~R   40 (173)
T cd03115           3 ILLVGLQGVGKTTTAAKLALYLK-KKGKKVLLVAADTYR   40 (173)
T ss_pred             EEEECCCCCCHHHHHHHHHHHHH-HCCCEEEEEECCCCC
T ss_conf             99989999988999999999999-769928999748875


No 149
>COG1200 RecG RecG-like helicase [DNA replication, recombination, and repair / Transcription]
Probab=91.28  E-value=0.99  Score=23.20  Aligned_cols=75  Identities=20%  Similarity=0.280  Sum_probs=53.8

Q ss_pred             HHHHHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEEECCHHHHHHHHHHHHHHH
Q ss_conf             58999999999998740565554210124650257659789999999999980899669998085899999999999999
Q gi|254781215|r   52 RSWQLEFMEVVDAHCLNSVNNPNPEVFKGAISAGRGIGKTTLNAWLVLWLMSTRPGISVICLANSETQLKTTLWAEVSKW  131 (511)
Q Consensus        52 ~~WQ~e~l~~i~~~~~~~~~~~~~~~~r~aV~sgrG~GKS~l~a~l~lw~l~~~p~~kv~vtApt~~Q~~~ilw~Ei~k~  131 (511)
                      -.-|+.++++|........     .|.| -+..-=|+|||-+++..++-...  -|.++..-|||+==|+. -+..+.+|
T Consensus       264 T~aQ~~vi~EI~~Dl~~~~-----~M~R-LlQGDVGSGKTvVA~laml~ai~--~G~Q~ALMAPTEILA~Q-H~~~~~~~  334 (677)
T COG1200         264 TNAQKRVIKEILADLASPV-----PMNR-LLQGDVGSGKTVVALLAMLAAIE--AGYQAALMAPTEILAEQ-HYESLRKW  334 (677)
T ss_pred             CHHHHHHHHHHHHHHCCCH-----HHHH-HHCCCCCCCHHHHHHHHHHHHHH--CCCEEEEECCHHHHHHH-HHHHHHHH
T ss_conf             7899999999986644866-----6678-75267677789999999999987--28816886637999999-99999987


Q ss_pred             HHHC
Q ss_conf             9855
Q gi|254781215|r  132 LSLL  135 (511)
Q Consensus       132 ~~~~  135 (511)
                      +...
T Consensus       335 l~~~  338 (677)
T COG1200         335 LEPL  338 (677)
T ss_pred             HHHC
T ss_conf             6651


No 150
>pfam00448 SRP54 SRP54-type protein, GTPase domain. This family includes relatives of the G-domain of the SRP54 family of proteins.
Probab=91.06  E-value=0.43  Score=25.46  Aligned_cols=39  Identities=23%  Similarity=0.162  Sum_probs=30.1

Q ss_pred             EEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEEECCHHH
Q ss_conf             4650257659789999999999980899669998085899
Q gi|254781215|r   80 GAISAGRGIGKTTLNAWLVLWLMSTRPGISVICLANSETQ  119 (511)
Q Consensus        80 ~aV~sgrG~GKS~l~a~l~lw~l~~~p~~kv~vtApt~~Q  119 (511)
                      +++....|+|||+.+|=++.|+.. +...-.++++-|++-
T Consensus         4 i~lvGptGvGKTTTiaKLAa~~~~-~~~~V~lit~Dt~R~   42 (196)
T pfam00448         4 ILLVGLQGSGKTTTIAKLAAYLKK-QGKKVLLVAADTFRA   42 (196)
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHH-CCCEEEEEECCCCCH
T ss_conf             999899999889999999999997-799289997587768


No 151
>cd01128 rho_factor Transcription termination factor rho is a bacterial ATP-dependent RNA/DNA helicase. It is a homohexamer. Each monomer consists of an N-terminal domain of the OB fold, which is responsible for binding to cysteine rich nucleotides. This alignment is of the C-terminal ATP binding domain.
Probab=91.02  E-value=0.58  Score=24.65  Aligned_cols=36  Identities=31%  Similarity=0.350  Sum_probs=27.6

Q ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEEE
Q ss_conf             246502576597899999999999808996699980
Q gi|254781215|r   79 KGAISAGRGIGKTTLNAWLVLWLMSTRPGISVICLA  114 (511)
Q Consensus        79 r~aV~sgrG~GKS~l~a~l~lw~l~~~p~~kv~vtA  114 (511)
                      |..+-+|.|+|||++...++.-....+++..+++..
T Consensus        18 R~gI~g~~gvGKT~Ll~~i~~~~~~~~~~~~~v~~l   53 (249)
T cd01128          18 RGLIVAPPKAGKTTLLQSIANAITKNHPEVYLIVLL   53 (249)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHHCCCEEEEEEE
T ss_conf             778878999889999999999999858984999999


No 152
>KOG0335 consensus
Probab=90.77  E-value=0.53  Score=24.93  Aligned_cols=80  Identities=18%  Similarity=0.196  Sum_probs=50.5

Q ss_pred             CCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHHC-C----------CCEEEE
Q ss_conf             56555784589999999999987405655542101246502576597899999999999808-9----------966999
Q gi|254781215|r   44 PLEGFSAPRSWQLEFMEVVDAHCLNSVNNPNPEVFKGAISAGRGIGKTTLNAWLVLWLMSTR-P----------GISVIC  112 (511)
Q Consensus        44 ~~~~~~~P~~WQ~e~l~~i~~~~~~~~~~~~~~~~r~aV~sgrG~GKS~l~a~l~lw~l~~~-p----------~~kv~v  112 (511)
                      ...+++.|-+.|+-.+..|.+.            +-+.+.+-.|+|||...-.=++=++.-. +          +..+++
T Consensus        90 ~~~~~~~ptpvQk~sip~i~~G------------rdlmacAqTGsGKT~aFLiPii~~~~~~~~~~~~~~~~~~~P~~lI  157 (482)
T KOG0335          90 KRSGYTKPTPVQKYSIPIISGG------------RDLMACAQTGSGKTAAFLIPIISYLLDEGPEDRGESGGGVYPRALI  157 (482)
T ss_pred             CCCCCCCCCCCEECCCCEEECC------------CCEEEECCCCCCCHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCEEE
T ss_conf             3356668986156042244258------------8427882578851378888899999864865666567788972599


Q ss_pred             EECCHHHHHHHHHHHHHHHHHHCH
Q ss_conf             808589999999999999998550
Q gi|254781215|r  113 LANSETQLKTTLWAEVSKWLSLLP  136 (511)
Q Consensus       113 tApt~~Q~~~ilw~Ei~k~~~~~~  136 (511)
                      .|||..-+- -+|.|..|..-.+-
T Consensus       158 lapTReL~~-Qi~nea~k~~~~s~  180 (482)
T KOG0335         158 LAPTRELVD-QIYNEARKFSYLSG  180 (482)
T ss_pred             EECCHHHHH-HHHHHHHHHCCCCC
T ss_conf             817378766-78888876402212


No 153
>pfam05496 RuvB_N Holliday junction DNA helicase ruvB N-terminus. The RuvB protein makes up part of the RuvABC revolvasome which catalyses the resolution of Holliday junctions that arise during genetic recombination and DNA repair. Branch migration is catalysed by the RuvB protein that is targeted to the Holliday junction by the structure specific RuvA protein. This family contains the N-terminal region of the protein.
Probab=90.62  E-value=1.1  Score=22.82  Aligned_cols=106  Identities=12%  Similarity=0.081  Sum_probs=59.7

Q ss_pred             CCCCCCCCCCHHHHHHHHHHHHHHHHCCC--CCCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEEE-CCHH
Q ss_conf             77565557845899999999999874056--55542101246502576597899999999999808996699980-8589
Q gi|254781215|r   42 GTPLEGFSAPRSWQLEFMEVVDAHCLNSV--NNPNPEVFKGAISAGRGIGKTTLNAWLVLWLMSTRPGISVICLA-NSET  118 (511)
Q Consensus        42 ~~~~~~~~~P~~WQ~e~l~~i~~~~~~~~--~~~~~~~~r~aV~sgrG~GKS~l~a~l~lw~l~~~p~~kv~vtA-pt~~  118 (511)
                      +..++.|-|    |..++..+.--+....  ...++.   +-.-.+.|+|||+++-.++--.     +++..++. |..+
T Consensus        20 P~~l~e~vG----Qehl~~~l~~~i~a~~~~~~~l~h---~lf~GPPG~GKTTlAriiAk~~-----~~~~~~~s~~~i~   87 (234)
T pfam05496        20 PRRLDEYIG----QEKVKENLKIFIEAAKKRGEALDH---VLLYGPPGLGKTTLANIIANEM-----GVNIRITSGPALE   87 (234)
T ss_pred             CCCHHHCCC----HHHHHHHHHHHHHHHHHCCCCCCE---EEEECCCCCCHHHHHHHHHHHH-----CCCEEEECCHHHH
T ss_conf             897666069----499999999999988742777662---7887899998889999999840-----8753761426664


Q ss_pred             HHHHHHHHHHHHHHHHCHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCCCCCCCHHHHCCCCCCEEEEEC
Q ss_conf             99999999999999855000134443222222333444321112357861698530357556100212026761499971
Q gi|254781215|r  119 QLKTTLWAEVSKWLSLLPNKHWFEMQSLSLHPAPWYSDVLHCSLGIDSKHYSTMCRTYSEERPDTFVGHHNTYGMAIIND  198 (511)
Q Consensus       119 Q~~~ilw~Ei~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~ea~~G~h~~~~~lvI~D  198 (511)
                      .++++     ...+.                                                    +.. .+ .++++|
T Consensus        88 ~~~di-----~~~l~----------------------------------------------------~~~-~~-~ILFID  108 (234)
T pfam05496        88 KPGDL-----AAILT----------------------------------------------------NLE-PG-DVLFID  108 (234)
T ss_pred             HHHHH-----HHHHH----------------------------------------------------HCC-CC-CEEEEE
T ss_conf             38999-----99998----------------------------------------------------458-99-889996


Q ss_pred             CHHCCCHHHHHHHHHHHCCC
Q ss_conf             11029978898888885079
Q gi|254781215|r  199 EASGTPDVINLGILGFLTER  218 (511)
Q Consensus       199 EAsgI~d~i~e~i~~~Lt~~  218 (511)
                      |.+-+.....+++.|.|-++
T Consensus       109 EIHr~nK~qqd~Llp~vE~g  128 (234)
T pfam05496       109 EIHRLNRAVEEILYPAMEDF  128 (234)
T ss_pred             CHHHCCHHHHHHCCCCCCCC
T ss_conf             65435876887445533461


No 154
>PRK06526 transposase; Provisional
Probab=90.62  E-value=1.1  Score=22.82  Aligned_cols=33  Identities=24%  Similarity=0.205  Sum_probs=24.6

Q ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEE
Q ss_conf             24650257659789999999999980899669998
Q gi|254781215|r   79 KGAISAGRGIGKTTLNAWLVLWLMSTRPGISVICL  113 (511)
Q Consensus        79 r~aV~sgrG~GKS~l~a~l~lw~l~~~p~~kv~vt  113 (511)
                      -+.+.++-|+|||++++.+..-.+-  -|-+|.++
T Consensus       100 Nvil~G~~GtGKThLA~Alg~~A~~--~G~~v~f~  132 (254)
T PRK06526        100 NVVFLGPPGTGKTHLAIGLGIRACQ--AGHRVLFA  132 (254)
T ss_pred             CEEEECCCCCCHHHHHHHHHHHHHH--CCCCEEEE
T ss_conf             7899899998689999999999998--69967998


No 155
>pfam05894 Podovirus_Gp16 Podovirus DNA encapsidation protein (Gp16). This family consists of several DNA encapsidation protein (Gp16) sequences from the phi-29-like viruses. Gene product 16 catalyses the in vivo and in vitro genome-encapsidation reaction.
Probab=90.28  E-value=1.2  Score=22.63  Aligned_cols=144  Identities=18%  Similarity=0.146  Sum_probs=72.0

Q ss_pred             EECCCCCCHHHHHHHHHHHHHHHCCCCEEEEEECCHHHHHHHHHHHHHHHHHHCHHCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             50257659789999999999980899669998085899999999999999985500013444322222233344432111
Q gi|254781215|r   82 ISAGRGIGKTTLNAWLVLWLMSTRPGISVICLANSETQLKTTLWAEVSKWLSLLPNKHWFEMQSLSLHPAPWYSDVLHCS  161 (511)
Q Consensus        82 V~sgrG~GKS~l~a~l~lw~l~~~p~~kv~vtApt~~Q~~~ilw~Ei~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  161 (511)
                      |-.|||+|||..+...++=-++. .|-+.+...-...        ||++.-..     +|.-.+...--.++.+++.++.
T Consensus        22 vIG~RGiGKTya~k~~~ikd~i~-kGeqFiYLRr~k~--------El~k~~n~-----~F~di~~~fpn~ef~Vkgnki~   87 (333)
T pfam05894        22 VIGARGIGKTYALKERVIKDFIK-KGEQFIYLRRYKT--------ELKKLANE-----FFNDVAHEFPNNEFYVKGNKFY   87 (333)
T ss_pred             EEECCCCCHHHHHHHHHHHHHHH-CCCEEEEEEECCH--------HHHHHHHH-----HHHHHHHHCCCCEEEEECCEEE
T ss_conf             98246554024677888999986-2967999991206--------88877777-----5551665378980799754899


Q ss_pred             CCCCCCEEEEEECCCCCCCCCHHHHCCCCCCEEEEECCH-------HCCCHHH---HHHHHHHHCCCCCCEEEEEECCCC
Q ss_conf             235786169853035755610021202676149997111-------0299788---988888850799813899823899
Q gi|254781215|r  162 LGIDSKHYSTMCRTYSEERPDTFVGHHNTYGMAIINDEA-------SGTPDVI---NLGILGFLTERNANRFWIMTSNPR  231 (511)
Q Consensus       162 ~~~~~~~~~~~~~~~s~~~~ea~~G~h~~~~~lvI~DEA-------sgI~d~i---~e~i~~~Lt~~g~~~~~i~~~nP~  231 (511)
                      +...---|++.-++|.     +..+.-=+...-+++||.       .-+|+++   ...+......+ ....+++.||--
T Consensus        88 ~~~k~igy~i~LS~~q-----~lKS~~Yp~V~~I~fDEfi~ek~~~~Y~pNev~~llnl~~tV~R~R-e~vr~~~lsNAv  161 (333)
T pfam05894        88 IKGELIGYAIPLSNWQ-----ALKSLAYPNVSTIFFDEFVREKDYGSYDPNEVRNFLNLMDTVFRAR-ERVRCICLSNAV  161 (333)
T ss_pred             ECCEEEEEEEEHHHHH-----HHHCCCCCCEEEEEEEEEEEECCCCCCCCHHHHHHHHHHHHHHHHC-CCEEEEEECCHH
T ss_conf             8782899998632455-----6313479855899835112445445789438999999999987503-773899964704


Q ss_pred             CCCCHHHHHHHCCC
Q ss_conf             87655676530352
Q gi|254781215|r  232 RLSGKFYEIFNKPL  245 (511)
Q Consensus       232 ~~~g~fy~~~~~~~  245 (511)
                      ....+.+..++-..
T Consensus       162 ~i~NPYF~~f~~~p  175 (333)
T pfam05894       162 SIVNPYFLLFHIEP  175 (333)
T ss_pred             HCCCHHHEEEECCC
T ss_conf             20472551551136


No 156
>PRK13342 recombination factor protein RarA; Reviewed
Probab=90.27  E-value=1.2  Score=22.63  Aligned_cols=120  Identities=12%  Similarity=0.078  Sum_probs=65.4

Q ss_pred             EEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEEECCHHHHHHHHHHHHHHHHHHCHHCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             46502576597899999999999808996699980858999999999999999855000134443222222333444321
Q gi|254781215|r   80 GAISAGRGIGKTTLNAWLVLWLMSTRPGISVICLANSETQLKTTLWAEVSKWLSLLPNKHWFEMQSLSLHPAPWYSDVLH  159 (511)
Q Consensus        80 ~aV~sgrG~GKS~l~a~l~lw~l~~~p~~kv~vtApt~~Q~~~ilw~Ei~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  159 (511)
                      +..-.+.|+|||+++-.++--.     +...+-...+..-+     ++|++.+......                     
T Consensus        40 ~Il~GPPG~GKTTlA~iiA~~~-----~~~f~~lnA~~~gv-----~dir~ii~~a~~~---------------------   88 (417)
T PRK13342         40 MILWGPPGTGKTTLARIIAGAT-----DAEFEALSAVTSGV-----KDLREVIEEAKQS---------------------   88 (417)
T ss_pred             EEEECCCCCCHHHHHHHHHHHH-----CCCEEEEECCCCCH-----HHHHHHHHHHHHH---------------------
T ss_conf             9988969998999999999986-----89889961410388-----9999999998863---------------------


Q ss_pred             CCCCCCCCEEEEEECCCCCCCCCHHHHCCCCCCEEEEECCHHCCCHHHHHHHHHHHCCCCCCEEEEEECCCCCCCCHHHH
Q ss_conf             11235786169853035755610021202676149997111029978898888885079981389982389987655676
Q gi|254781215|r  160 CSLGIDSKHYSTMCRTYSEERPDTFVGHHNTYGMAIINDEASGTPDVINLGILGFLTERNANRFWIMTSNPRRLSGKFYE  239 (511)
Q Consensus       160 ~~~~~~~~~~~~~~~~~s~~~~ea~~G~h~~~~~lvI~DEAsgI~d~i~e~i~~~Lt~~g~~~~~i~~~nP~~~~g~fy~  239 (511)
                                              .   ++.. .++++||.+-....--+++.+.+-. | .+  +.+|..|.+  +++.
T Consensus        89 ------------------------~---~~~~-tilfiDEIHRfnK~QQD~LLp~vE~-g-~i--iLIgATTEN--P~f~  134 (417)
T PRK13342         89 ------------------------R---LGRR-TILFIDEIHRFNKAQQDALLPHVED-G-TI--TLIGATTEN--PSFE  134 (417)
T ss_pred             ------------------------H---CCCC-EEEEEECHHHCCHHHHHHHHHHHHC-C-CE--EEEEECCCC--CHHH
T ss_conf             ------------------------1---4896-5999978200588999999875112-6-56--999741579--2253


Q ss_pred             HHHCCCCCCEEEEECCCCCCCCCHHHHHHH
Q ss_conf             530352474179840433677897789999
Q gi|254781215|r  240 IFNKPLDDWKRFQIDTRTVEGIDPSFHEGI  269 (511)
Q Consensus       240 ~~~~~~~~w~~~~i~~~~~p~~~~~~ie~~  269 (511)
                      ......++-..+.+.     .++++.+.++
T Consensus       135 in~aLlSRc~vf~l~-----~L~~~di~~i  159 (417)
T PRK13342        135 VNPALLSRAQVFELK-----PLSEEDLEQL  159 (417)
T ss_pred             CCHHHHHHHHHEECC-----CCCHHHHHHH
T ss_conf             489898565700205-----8999999999


No 157
>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=90.10  E-value=1.3  Score=22.54  Aligned_cols=39  Identities=28%  Similarity=0.145  Sum_probs=25.9

Q ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEEECCHHH
Q ss_conf             24650257659789999999999980899669998085899
Q gi|254781215|r   79 KGAISAGRGIGKTTLNAWLVLWLMSTRPGISVICLANSETQ  119 (511)
Q Consensus        79 r~aV~sgrG~GKS~l~a~l~lw~l~~~p~~kv~vtApt~~Q  119 (511)
                      .+.+.++-|+|||+++..++.-.....  ..++.++.....
T Consensus         4 ~ill~G~~GsGKTtl~~~la~~~~~~~--~~v~~~~~~~~~   42 (148)
T smart00382        4 VILIVGPPGSGKTTLARALARELGPPG--GGVIYIDGEDIL   42 (148)
T ss_pred             EEEEECCCCHHHHHHHHHHHHHHCCCC--CCEEEEEHHHHH
T ss_conf             899999997029999999998726689--968998759989


No 158
>KOG4284 consensus
Probab=90.06  E-value=0.43  Score=25.47  Aligned_cols=177  Identities=16%  Similarity=0.091  Sum_probs=82.1

Q ss_pred             CCHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHHCC-CCEEEEEECCHH---HHHHHHH
Q ss_conf             845899999999999874056555421012465025765978999999999998089-966999808589---9999999
Q gi|254781215|r   50 APRSWQLEFMEVVDAHCLNSVNNPNPEVFKGAISAGRGIGKTTLNAWLVLWLMSTRP-GISVICLANSET---QLKTTLW  125 (511)
Q Consensus        50 ~P~~WQ~e~l~~i~~~~~~~~~~~~~~~~r~aV~sgrG~GKS~l~a~l~lw~l~~~p-~~kv~vtApt~~---Q~~~ilw  125 (511)
                      .|-+-|+.++-.+...            ....|.|--|+|||.+.+.+++--+..+- ....++++||..   |+++.++
T Consensus        47 ~ptkiQaaAIP~~~~k------------mDliVQaKSGTGKTlVfsv~av~sl~~~~~~~q~~Iv~PTREiaVQI~~tv~  114 (980)
T KOG4284          47 LPTKIQAAAIPAIFSK------------MDLIVQAKSGTGKTLVFSVLAVESLDSRSSHIQKVIVTPTREIAVQIKETVR  114 (980)
T ss_pred             CCCCHHHHHHHHHHCC------------CCEEEEECCCCCCEEEEEEEEEHHCCCCCCCCEEEEEECCHHHHHHHHHHHH
T ss_conf             7870134321144315------------5358981378885589985430222756676206997143566457999999


Q ss_pred             HHHHHHHHHCHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCCCCCCCHHHHCCCCCCEEEEECCHHCCCH
Q ss_conf             99999998550001344432222223334443211123578616985303575561002120267614999711102997
Q gi|254781215|r  126 AEVSKWLSLLPNKHWFEMQSLSLHPAPWYSDVLHCSLGIDSKHYSTMCRTYSEERPDTFVGHHNTYGMAIINDEASGTPD  205 (511)
Q Consensus       126 ~Ei~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~ea~~G~h~~~~~lvI~DEAsgI~d  205 (511)
                      . |      +|-...+.|.   .+.-+-.+..+...+   +..-+++|.+-+-..---+..+.--+.-|+|+|||..+=+
T Consensus       115 ~-v------~~sf~g~~cs---vfIGGT~~~~d~~rl---k~~rIvIGtPGRi~qL~el~~~n~s~vrlfVLDEADkL~~  181 (980)
T KOG4284         115 K-V------APSFTGARCS---VFIGGTAHKLDLIRL---KQTRIVIGTPGRIAQLVELGAMNMSHVRLFVLDEADKLMD  181 (980)
T ss_pred             H-H------CCCCCCCCEE---EEECCCHHHHHHHHH---HHCEEEECCCHHHHHHHHHCCCCCCCEEEEEECCHHHHHC
T ss_conf             8-6------5244576058---996685435556665---4023784383588999870677711026888431776632


Q ss_pred             -HHH-H---HHHHHHCCCCCCEEEEEECC--CCCCCCHHHHHHHCCCCCCEEEEECCCCC
Q ss_conf             -889-8---88888507998138998238--99876556765303524741798404336
Q gi|254781215|r  206 -VIN-L---GILGFLTERNANRFWIMTSN--PRRLSGKFYEIFNKPLDDWKRFQIDTRTV  258 (511)
Q Consensus       206 -~i~-e---~i~~~Lt~~g~~~~~i~~~n--P~~~~g~fy~~~~~~~~~w~~~~i~~~~~  258 (511)
                       ..| +   .|..+|-  ..+ .++++|-  |.+..    +.-.+.-.+-...+++..++
T Consensus       182 t~sfq~~In~ii~slP--~~r-Qv~a~SATYp~nLd----n~Lsk~mrdp~lVr~n~~d~  234 (980)
T KOG4284         182 TESFQDDINIIINSLP--QIR-QVAAFSATYPRNLD----NLLSKFMRDPALVRFNADDV  234 (980)
T ss_pred             HHHHHHHHHHHHHHCC--HHH-EEEEEECCCCHHHH----HHHHHHHCCCCEEECCCCCC
T ss_conf             0247888999997450--000-25677335735689----99998704622243266774


No 159
>PRK05917 DNA polymerase III subunit delta'; Validated
Probab=90.06  E-value=1.3  Score=22.52  Aligned_cols=165  Identities=13%  Similarity=0.070  Sum_probs=81.6

Q ss_pred             HHHHHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEEECCHHHHHHHHHHHHHHH
Q ss_conf             58999999999998740565554210124650257659789999999999980899669998085899999999999999
Q gi|254781215|r   52 RSWQLEFMEVVDAHCLNSVNNPNPEVFKGAISAGRGIGKTTLNAWLVLWLMSTRPGISVICLANSETQLKTTLWAEVSKW  131 (511)
Q Consensus        52 ~~WQ~e~l~~i~~~~~~~~~~~~~~~~r~aV~sgrG~GKS~l~a~l~lw~l~~~p~~kv~vtApt~~Q~~~ilw~Ei~k~  131 (511)
                      +.||. ++++|...+    .-|     .....+..|+||+.++-.++-..++...+.       ...+..          
T Consensus         4 ~~We~-L~~~i~~~R----l~H-----AyLf~Gp~G~GK~~~A~~~A~~LLc~~~p~-------~~~~i~----------   56 (290)
T PRK05917          4 AAWEA-LLQRVRDQK----VPS-----AILLHGQDLSNLSQYAYELASLILLESSPE-------AQYKIS----------   56 (290)
T ss_pred             HHHHH-HHHHHHCCC----CCE-----EEEEECCCCCCHHHHHHHHHHHHHCCCCCC-------HHHHHH----------
T ss_conf             49999-999998399----660-----687689998659999999999985789961-------688987----------


Q ss_pred             HHHCHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCCCCCCCHHHHCCCCCCEEEEECCHHCCCHHHHHHH
Q ss_conf             98550001344432222223334443211123578616985303575561002120267614999711102997889888
Q gi|254781215|r  132 LSLLPNKHWFEMQSLSLHPAPWYSDVLHCSLGIDSKHYSTMCRTYSEERPDTFVGHHNTYGMAIINDEASGTPDVINLGI  211 (511)
Q Consensus       132 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~ea~~G~h~~~~~lvI~DEAsgI~d~i~e~i  211 (511)
                      ...-|..+++.       +.+ ......++          ..+...  .--++....+.+. .+|+|||..+.....+++
T Consensus        57 ~~~HPD~~~i~-------pe~-k~~~~~Id----------~iR~l~--~~i~~~p~~g~~K-V~IId~Ad~Mn~~AaNAL  115 (290)
T PRK05917         57 QKIHPDIHEFF-------PEG-KGRLHSIE----------TPRAIK--KQIWIHPYEANYK-IYIIHEADRMTLDAISAF  115 (290)
T ss_pred             HCCCCCEEEEC-------CCC-CCCCCCHH----------HHHHHH--HHHCCCCCCCCCE-EEEECCHHHHCHHHHHHH
T ss_conf             46899859961-------577-78878678----------999999--9964186468826-999756776389999999


Q ss_pred             HHHHCCCCCCEEEEEE-CCCCCCCCHHHHHHHCCCCCCEEEEECCCCCCCCCHHHHHHHHH
Q ss_conf             8885079981389982-38998765567653035247417984043367789778999997
Q gi|254781215|r  212 LGFLTERNANRFWIMT-SNPRRLSGKFYEIFNKPLDDWKRFQIDTRTVEGIDPSFHEGIIA  271 (511)
Q Consensus       212 ~~~Lt~~g~~~~~i~~-~nP~~~~g~fy~~~~~~~~~w~~~~i~~~~~p~~~~~~ie~~~~  271 (511)
                      .-+|-++.....++.+ .+|.+.--...-       +=-.++++-.+-..++++.++.+.+
T Consensus       116 LKtLEEPP~~tvfILit~~~~~lLpTI~S-------RCQ~I~i~~~e~~~i~~e~~~~l~~  169 (290)
T PRK05917        116 LKVLEDPPKHSVIILTSAKPQRLPPTIRS-------RSLSIHIPGEEKTLPSKEDIAYLIR  169 (290)
T ss_pred             HHHHCCCCCCEEEEEEECCHHHCCHHHHH-------CCCEEECCCCCCCCCCHHHHHHHHH
T ss_conf             99734798785999986992548237763-------3511677762013478899999999


No 160
>PRK09105 putative aminotransferase; Provisional
Probab=89.96  E-value=1.2  Score=22.61  Aligned_cols=59  Identities=15%  Similarity=-0.018  Sum_probs=39.7

Q ss_pred             CCHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEEECCHHHHH
Q ss_conf             845899999999999874056555421012465025765978999999999998089966999808589999
Q gi|254781215|r   50 APRSWQLEFMEVVDAHCLNSVNNPNPEVFKGAISAGRGIGKTTLNAWLVLWLMSTRPGISVICLANSETQLK  121 (511)
Q Consensus        50 ~P~~WQ~e~l~~i~~~~~~~~~~~~~~~~r~aV~sgrG~GKS~l~a~l~lw~l~~~p~~kv~vtApt~~Q~~  121 (511)
                      +|+..+.++-..|+++..=.  .+     .  |.-  |+|=+.+...++..  ++.|+..+++..||+..-.
T Consensus        78 YPd~~~~~Lr~~lA~~~gv~--~~-----~--I~~--gnGSdE~i~~l~~a--f~~~g~~vv~~~Ptf~~Y~  136 (374)
T PRK09105         78 YLFEMQDELRTLFAAQLGLP--VD-----H--LHA--YAGSSEPLNYAVLA--FTSPEAGLVTADPTYEAGW  136 (374)
T ss_pred             CCCCCHHHHHHHHHHHHCCC--HH-----H--EEE--ECCHHHHHHHHHHH--HHCCCCEEEECCCCHHHHH
T ss_conf             98986899999999997859--02-----4--999--36999999999999--8079986895888779999


No 161
>pfam05673 DUF815 Protein of unknown function (DUF815). This family consists of several bacterial proteins of unknown function.
Probab=89.91  E-value=1.3  Score=22.45  Aligned_cols=91  Identities=20%  Similarity=0.240  Sum_probs=51.4

Q ss_pred             HHCCCCCC-CCCCCCCCCCH----------HHHHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHH
Q ss_conf             64214557-77565557845----------89999999999987405655542101246502576597899999999999
Q gi|254781215|r   34 HFFPWGEK-GTPLEGFSAPR----------SWQLEFMEVVDAHCLNSVNNPNPEVFKGAISAGRGIGKTTLNAWLVLWLM  102 (511)
Q Consensus        34 ~~~~w~~~-~~~~~~~~~P~----------~WQ~e~l~~i~~~~~~~~~~~~~~~~r~aV~sgrG~GKS~l~a~l~lw~l  102 (511)
                      .+|-|... .+.|+...-|+          +=|++.|..-..+..++..-.     -+-.-..||+|||.++-.++.-+.
T Consensus         4 ~AfrW~~~~~g~L~~i~~~d~v~l~~L~Gie~Qk~~l~~NT~~F~~G~pAn-----nvLLwG~RGtGKSSlVKall~~~~   78 (248)
T pfam05673         4 PAFRWRRGESGALEPVPHPDPVDLDDLVGIDRQKEALLRNTEQFLAGLPAN-----NVLLWGARGTGKSSLVKALLNEYA   78 (248)
T ss_pred             CEEEEECCCCCCEEEECCCCCCCHHHHCCHHHHHHHHHHHHHHHHCCCCCC-----CEEEECCCCCCHHHHHHHHHHHHH
T ss_conf             426875389888775178898998893493999999999999998089861-----367676898988899999999863


Q ss_pred             HHCCCCEEEEEECCHHHHHHHHHHHHHHHHHHC
Q ss_conf             808996699980858999999999999999855
Q gi|254781215|r  103 STRPGISVICLANSETQLKTTLWAEVSKWLSLL  135 (511)
Q Consensus       103 ~~~p~~kv~vtApt~~Q~~~ilw~Ei~k~~~~~  135 (511)
                      -  .+-+++=+  ...++.++  +.|-..++..
T Consensus        79 ~--~gLrlIEv--~k~~L~~L--p~i~~~l~~~  105 (248)
T pfam05673        79 D--QGLRLIEV--DKDDLGDL--PDIVDLLRGR  105 (248)
T ss_pred             H--CCCEEEEE--CHHHHCCH--HHHHHHHHCC
T ss_conf             1--49569998--78887219--9999999649


No 162
>PRK00411 cdc6 cell division control protein 6; Reviewed
Probab=89.85  E-value=1.3  Score=22.41  Aligned_cols=166  Identities=14%  Similarity=0.076  Sum_probs=76.5

Q ss_pred             HCHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCCCHHHHHHHHHH
Q ss_conf             07066652886677642145577756555784589999999999987405655542101246502576597899999999
Q gi|254781215|r   20 WSDEIKLSFSNFVLHFFPWGEKGTPLEGFSAPRSWQLEFMEVVDAHCLNSVNNPNPEVFKGAISAGRGIGKTTLNAWLVL   99 (511)
Q Consensus        20 ~~~~~~~~~~~~~~~~~~w~~~~~~~~~~~~P~~WQ~e~l~~i~~~~~~~~~~~~~~~~r~aV~sgrG~GKS~l~a~l~l   99 (511)
                      |++.+..|+--|-.-+-|     ..|++    |+=|.+.|...-....++   ..|  ..+.|...-|+|||+.+-.++-
T Consensus        12 ~~~~if~~~~~L~~~yvP-----~~l~~----Re~Ei~~l~~~l~~~l~g---~~~--~n~~I~G~pGTGKT~~vk~v~~   77 (394)
T PRK00411         12 WDETIFKNEEVLEPDYVP-----ENLPH----REEQIEELAFALRPALRG---SRP--SNVLILGPPGTGKTTTVKKVFE   77 (394)
T ss_pred             CCCCEECCHHHCCCCCCC-----CCCCC----HHHHHHHHHHHHHHHHCC---CCC--CCEEEECCCCCCHHHHHHHHHH
T ss_conf             788615676337998889-----98988----599999999999999759---999--8479988999989999999999


Q ss_pred             HHHHHCCCCEEEEE----ECCHHHHHHHHHHHHHHHHHHCHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECC
Q ss_conf             99980899669998----08589999999999999998550001344432222223334443211123578616985303
Q gi|254781215|r  100 WLMSTRPGISVICL----ANSETQLKTTLWAEVSKWLSLLPNKHWFEMQSLSLHPAPWYSDVLHCSLGIDSKHYSTMCRT  175 (511)
Q Consensus       100 w~l~~~p~~kv~vt----Apt~~Q~~~ilw~Ei~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  175 (511)
                      ..--.-++..++.+    .+|..|+-..++.++..  ...|.+             ++...           ..+.  +.
T Consensus        78 ~l~~~~~~~~~vyINc~~~~t~~~i~~~i~~~L~~--~~~p~~-------------G~s~~-----------~~~~--~l  129 (394)
T PRK00411         78 ELEEAALKVVYVYINCQIDRTRYAILSEIARSLFG--HPPPSS-------------GLSFD-----------ELFD--KI  129 (394)
T ss_pred             HHHHHCCCCEEEEEECCCCCCHHHHHHHHHHHHCC--CCCCCC-------------CCCHH-----------HHHH--HH
T ss_conf             99974689659999696689899999999999569--989877-------------87899-----------9999--99


Q ss_pred             CCCCCCCHHHHCCCCCCEEEEECCHHCCC-----HHHHHHHHHHHCCCCCCEEEEEECCCCCCC
Q ss_conf             57556100212026761499971110299-----788988888850799813899823899876
Q gi|254781215|r  176 YSEERPDTFVGHHNTYGMAIINDEASGTP-----DVINLGILGFLTERNANRFWIMTSNPRRLS  234 (511)
Q Consensus       176 ~s~~~~ea~~G~h~~~~~lvI~DEAsgI~-----d~i~e~i~~~Lt~~g~~~~~i~~~nP~~~~  234 (511)
                           -+.+.. .+. .+++|+||...+-     +.+|...+--=.-.+++..+++++|-....
T Consensus       130 -----~~~l~~-~~~-~~ivvLDEiD~L~~~~~~~vLY~L~r~~~~~~~~~~~vI~IsN~~~~~  186 (394)
T PRK00411        130 -----AEYLDE-RDR-VLIVALDDINYLVEKEGNDVLYSLLRAHEEYPGARIGVIGISSDLTFL  186 (394)
T ss_pred             -----HHHHHC-CCC-EEEEEEECCCCCCCCCCCHHHHHHHHCCCCCCCCCEEEEEEECCCCHH
T ss_conf             -----998616-697-589999655402036650899999854022688738999997687177


No 163
>COG1702 PhoH Phosphate starvation-inducible protein PhoH, predicted ATPase [Signal transduction mechanisms]
Probab=89.81  E-value=0.39  Score=25.77  Aligned_cols=51  Identities=20%  Similarity=0.115  Sum_probs=29.8

Q ss_pred             HHHHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEEEC
Q ss_conf             899999999999874056555421012465025765978999999999998089966999808
Q gi|254781215|r   53 SWQLEFMEVVDAHCLNSVNNPNPEVFKGAISAGRGIGKTTLNAWLVLWLMSTRPGISVICLAN  115 (511)
Q Consensus        53 ~WQ~e~l~~i~~~~~~~~~~~~~~~~r~aV~sgrG~GKS~l~a~l~lw~l~~~p~~kv~vtAp  115 (511)
                      +=|+.-+++|.+|.-           +..+- .=|+|||+|+...+.-.+-..-=.+++.|-|
T Consensus       131 ~~Q~~y~eai~~~di-----------~fGiG-pAGTGKTyLava~av~al~~~~v~rIiLtRP  181 (348)
T COG1702         131 PGQNMYPEAIEEHDI-----------VFGIG-PAGTGKTYLAVAKAVDALGAGQVRRIILTRP  181 (348)
T ss_pred             HHHHHHHHHHHHCCE-----------EEEEC-CCCCCCCHHHHHHHHHHHHCCCHHEEECCCC
T ss_conf             458788999874273-----------66415-6456971112776652654064120100683


No 164
>COG1149 MinD superfamily P-loop ATPase containing an inserted ferredoxin domain [Energy production and conversion]
Probab=89.81  E-value=0.29  Score=26.53  Aligned_cols=27  Identities=37%  Similarity=0.565  Sum_probs=21.8

Q ss_pred             CEEEEEECCC-CCCHHHHHHHHHHHHHH
Q ss_conf             0124650257-65978999999999998
Q gi|254781215|r   77 VFKGAISAGR-GIGKTTLNAWLVLWLMS  103 (511)
Q Consensus        77 ~~r~aV~sgr-G~GKS~l~a~l~lw~l~  103 (511)
                      |.++||.||. |+|||++++.++..+.-
T Consensus         1 mm~vAV~sGKGGtGKTTva~~la~~l~~   28 (284)
T COG1149           1 MMQVAVASGKGGTGKTTVAANLAVLLGD   28 (284)
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHHHHCC
T ss_conf             9279996368877702289999998366


No 165
>cd02036 MinD Bacterial cell division requires the formation of a septum at mid-cell. The site is determined by the min operon products MinC, MinD and MinE. MinC is a nonspecific inhibitor of the septum protein FtsZ. MinE is the supressor of MinC. MinD plays a pivotal role, selecting the mid-cell over other sites through the activation and regulation of MinC and MinE. MinD is a membrane-associated ATPase, related to nitrogenase iron protein. More distantly related proteins include flagellar biosynthesis proteins and ParA chromosome partitioning proteins. MinD is a monomer.
Probab=89.70  E-value=0.64  Score=24.38  Aligned_cols=32  Identities=34%  Similarity=0.469  Sum_probs=25.8

Q ss_pred             EEEECCC-CCCHHHHHHHHHHHHHHHCCCCEEEEE
Q ss_conf             4650257-659789999999999980899669998
Q gi|254781215|r   80 GAISAGR-GIGKTTLNAWLVLWLMSTRPGISVICL  113 (511)
Q Consensus        80 ~aV~sgr-G~GKS~l~a~l~lw~l~~~p~~kv~vt  113 (511)
                      ++|.||+ |+|||++++.++..++..  +.+|+++
T Consensus         2 Iav~s~KGGVGKTT~a~NLA~aLa~~--g~~vllv   34 (179)
T cd02036           2 IVVTSGKGGVGKTTTTANLGTALAQL--GYKVVLI   34 (179)
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHHHC--CCCEEEE
T ss_conf             89973999870999999999999977--9918999


No 166
>TIGR00348 hsdR type I site-specific deoxyribonuclease, HsdR family; InterPro: IPR004473   There are four classes of restriction endonucleases: types I, II,III and IV. All types of enzymes recognise specific short DNA sequences and carry out the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. They differ in their recognition sequence, subunit composition, cleavage position, and cofactor requirements , , as summarised below:    Type I enzymes (3.1.21.3 from EC) cleave at sites remote from recognition site; require both ATP and S-adenosyl-L-methionine to function; multifunctional protein with both restriction and methylase (2.1.1.72 from EC) activities. Type II enzymes (3.1.21.4 from EC) cleave within or at short specific distances from recognition site; most require magnesium; single function (restriction) enzymes independent of methylase. Type III enzymes (3.1.21.5 from EC) cleave at sites a short distance from recognition site; require ATP (but doesn't hydrolyse it); S-adenosyl-L-methionine stimulates reaction but is not required; exists as part of a complex with a modification methylase methylase (2.1.1.72 from EC). Type IV enzymes target methylated DNA.    Type I restriction endonucleases are components of prokaryotic DNA restriction-modification mechanisms that protects the organism against invading foreign DNA. Type I enzymes have three different subunits subunits - M (modification), S (specificity) and R (restriction) - that form multifunctional enzymes with restriction (3.1.21.3 from EC), methylase (2.1.1.72 from EC) and ATPase activities , . The S subunit is required for both restriction and modification and is responsible for recognition of the DNA sequence specific for the system. The M subunit is necessary for modification, and the R subunit is required for restriction. These enzymes use S-Adenosyl-L-methionine (AdoMet) as the methyl group donor in the methylation reaction, and have a requirement for ATP. They recognize asymmetric DNA sequences split into two domains of specific sequence, one 3-4 bp long and another 4-5 bp long, separated by a nonspecific spacer 6-8 bp in length. Cleavage occurs a considerable distance from the recognition sites, rarely less than 400 bp away and up to 7000 bp away. Adenosyl residues are methylated, one on each strand of the recognition sequence. These enzymes are widespread in eubacteria and archaea. In enteric bacteria they have been subdivide into four families: types IA, IB, IC and ID.   This entry represents the R subunit (HsdR) of type I restriction endonucleases such as EcoRI (3.1.21.3 from EC), which recognises the DNA sequence 5'-GAATTC; the R protein (HsdR) is required for both nuclease and ATPase activity , , , .; GO: 0003677 DNA binding, 0005524 ATP binding, 0009035 Type I site-specific deoxyribonuclease activity, 0009307 DNA restriction-modification system.
Probab=89.67  E-value=1.4  Score=22.33  Aligned_cols=196  Identities=17%  Similarity=0.151  Sum_probs=106.3

Q ss_pred             HHHHHHHHHHHHCCCCCCCC-CCCCCCCCHHHHHHHHHHHHHHHHCC-CCCCCCCCEEEEEECCCCCCHHHHHHHHHHHH
Q ss_conf             66528866776421455777-56555784589999999999987405-65554210124650257659789999999999
Q gi|254781215|r   24 IKLSFSNFVLHFFPWGEKGT-PLEGFSAPRSWQLEFMEVVDAHCLNS-VNNPNPEVFKGAISAGRGIGKTTLNAWLVLWL  101 (511)
Q Consensus        24 ~~~~~~~~~~~~~~w~~~~~-~~~~~~~P~~WQ~e~l~~i~~~~~~~-~~~~~~~~~r~aV~sgrG~GKS~l~a~l~lw~  101 (511)
                      -+.++|+|-.+|.....+.. ..--...|+-=|..++..+.+-.... ...+..  .+=.|==-.|+|||-.+=+++.|.
T Consensus       270 kkE~lLd~i~~f~~f~~~~~~g~~~k~~~~y~qy~av~ki~~~~~~~~~~k~~~--n~G~iWHtQGSGKtlTm~f~A~k~  347 (813)
T TIGR00348       270 KKERLLDFIRNFIIFDKEESVGLVTKVIARYMQYRAVKKIVESILRKEKGKDKR--NKGLIWHTQGSGKTLTMLFLARKL  347 (813)
T ss_pred             CCHHHHHHHCCEEEEECCCCCCHHHCCCHHHHHHHHHHHHHHHHHHHHCCCCCC--CCCEEEEEECCCHHHHHHHHHHHH
T ss_conf             703687633121366145110011010038899999999999998531378863--674489850763788999999999


Q ss_pred             H--HHCCCCEEEEEECCHHHHHHHHHHHHHHHH---HHCHHCCCCCCCCCCCCCCCCCCCCC---CCCCCCCCCEEEEEE
Q ss_conf             9--808996699980858999999999999999---85500013444322222233344432---111235786169853
Q gi|254781215|r  102 M--STRPGISVICLANSETQLKTTLWAEVSKWL---SLLPNKHWFEMQSLSLHPAPWYSDVL---HCSLGIDSKHYSTMC  173 (511)
Q Consensus       102 l--~~~p~~kv~vtApt~~Q~~~ilw~Ei~k~~---~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~  173 (511)
                      .  ---..++|+++- -..-|-.-+..++...-   ..++.+    .+.... +.....+..   ..-.....+..+.+.
T Consensus       348 ~~~~~~~~p~v~fvv-DR~eLd~Ql~~~~~~~~~~~~~~~~~----~eS~~~-Lk~~L~~~~~sennPn~~k~g~~~t~I  421 (813)
T TIGR00348       348 RKQKELKNPKVFFVV-DRRELDEQLYKEFSSLKDLIKDCAER----IESIAE-LKELLEKNDESENNPNISKRGIIITTI  421 (813)
T ss_pred             HHHHHHCCCEEEEEE-ECHHHHHHHHHHHHHHHHHCHHHHHC----CCCHHH-HHHHHHHCCCCCCCCCCCCCCEEEEEE
T ss_conf             874652698499997-27277889999998764201010420----678889-999875177645675535676799960


Q ss_pred             CCCCC----CCCCHHHHCC-----CCCCEEEEECCHHCCC-HH------------HHHHHHHHHCCCCCCEEEEEECCC
Q ss_conf             03575----5610021202-----6761499971110299-78------------898888885079981389982389
Q gi|254781215|r  174 RTYSE----ERPDTFVGHH-----NTYGMAIINDEASGTP-DV------------INLGILGFLTERNANRFWIMTSNP  230 (511)
Q Consensus       174 ~~~s~----~~~ea~~G~h-----~~~~~lvI~DEAsgI~-d~------------i~e~i~~~Lt~~g~~~~~i~~~nP  230 (511)
                      +.+..    ...+....++     -...+++|+|||+=.- -.            .-..+..+|-  ++ ..+-.||||
T Consensus       422 qKF~~~~~~k~~e~~~~~~~~i~~~r~~vv~i~DEaHRsqyG~tqklhnGkfqtGla~~~~~~lk--nA-~f~gFTGTP  497 (813)
T TIGR00348       422 QKFDDELLDKLKEEEEKFPESIIIDRKEVVVIIDEAHRSQYGKTQKLHNGKFQTGLAKALKKALK--NA-SFFGFTGTP  497 (813)
T ss_pred             ECCCHHHHHHHHHHHHCCCCEEEEEECCEEEEEECCCCCCCCCCCCCCCCHHHHHHHHHHHHHCH--HH-HHHCCCCCC
T ss_conf             01040344536888743873689871608999706755535341100044135899999987431--12-010122477


No 167
>PRK11670 putative ATPase; Provisional
Probab=89.60  E-value=0.7  Score=24.15  Aligned_cols=33  Identities=36%  Similarity=0.456  Sum_probs=24.3

Q ss_pred             EEEEECCC-CCCHHHHHHHHHHHHHHHCCCCEEEEE
Q ss_conf             24650257-659789999999999980899669998
Q gi|254781215|r   79 KGAISAGR-GIGKTTLNAWLVLWLMSTRPGISVICL  113 (511)
Q Consensus        79 r~aV~sgr-G~GKS~l~a~l~lw~l~~~p~~kv~vt  113 (511)
                      -++|+||. |+|||++++.|++-++-  .|.+|.+.
T Consensus       109 vIAVaSGKGGVGKSTvavNLA~ALA~--~G~kVgll  142 (369)
T PRK11670        109 IIAVSSGKGGVGKSSTAVNLALALAA--EGAKVGIL  142 (369)
T ss_pred             EEEEEECCCCCCHHHHHHHHHHHHHH--CCCCEEEE
T ss_conf             99998589988899999999999996--69937898


No 168
>KOG0989 consensus
Probab=89.54  E-value=1.4  Score=22.27  Aligned_cols=58  Identities=16%  Similarity=0.118  Sum_probs=36.6

Q ss_pred             HCCCCCCEEEEECCHHCCCHHHHHHHHHHHCCCCCC-EEEEEECCCCCCCCHHHHHHHC
Q ss_conf             202676149997111029978898888885079981-3899823899876556765303
Q gi|254781215|r  186 GHHNTYGMAIINDEASGTPDVINLGILGFLTERNAN-RFWIMTSNPRRLSGKFYEIFNK  243 (511)
Q Consensus       186 G~h~~~~~lvI~DEAsgI~d~i~e~i~~~Lt~~g~~-~~~i~~~nP~~~~g~fy~~~~~  243 (511)
                      |.-+...-.+|+|||..+..+.|.++.-+|-..-.. .+++.+.-+.+...+.--.+.+
T Consensus       124 ~~~~~~fKiiIlDEcdsmtsdaq~aLrr~mE~~s~~trFiLIcnylsrii~pi~SRC~K  182 (346)
T KOG0989         124 GYPCPPFKIIILDECDSMTSDAQAALRRTMEDFSRTTRFILICNYLSRIIRPLVSRCQK  182 (346)
T ss_pred             CCCCCCCEEEEEECHHHHHHHHHHHHHHHHHCCCCCEEEEEECCCHHHCCHHHHHHHHH
T ss_conf             78898632899741645309999999999862546659999738856477287746777


No 169
>PRK06696 uridine kinase; Validated
Probab=89.43  E-value=0.84  Score=23.65  Aligned_cols=54  Identities=22%  Similarity=0.166  Sum_probs=37.7

Q ss_pred             HHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEE
Q ss_conf             99999999998740565554210124650257659789999999999980899669998
Q gi|254781215|r   55 QLEFMEVVDAHCLNSVNNPNPEVFKGAISAGRGIGKTTLNAWLVLWLMSTRPGISVICL  113 (511)
Q Consensus        55 Q~e~l~~i~~~~~~~~~~~~~~~~r~aV~sgrG~GKS~l~a~l~lw~l~~~p~~kv~vt  113 (511)
                      -.+++.+|++++..-... +  .++|+|..+=|.|||+++..++--.-.  .+..|+++
T Consensus         7 r~~~~~~~~~~i~~~~p~-r--pl~VgIdG~~gSGKTTlA~~La~~L~~--~G~~V~~v   60 (227)
T PRK06696          7 RKQVVKEIANHILTLNLT-R--PLRVAIDGITASGKTTFANELAEEIKK--RGRPVIRA   60 (227)
T ss_pred             HHHHHHHHHHHHHHCCCC-C--CEEEEEECCCCCCHHHHHHHHHHHHHH--CCCCEEEE
T ss_conf             878999999999835999-8--689997789987879999999999974--69948997


No 170
>PRK10919 ATP-dependent DNA helicase Rep; Provisional
Probab=89.25  E-value=0.62  Score=24.47  Aligned_cols=43  Identities=16%  Similarity=0.196  Sum_probs=34.3

Q ss_pred             EEEECCCCCCHHHHHHHHHHHHHHH--CCCCEEEEEECCHHHHHH
Q ss_conf             4650257659789999999999980--899669998085899999
Q gi|254781215|r   80 GAISAGRGIGKTTLNAWLVLWLMST--RPGISVICLANSETQLKT  122 (511)
Q Consensus        80 ~aV~sgrG~GKS~l~a~l~lw~l~~--~p~~kv~vtApt~~Q~~~  122 (511)
                      +.|.||=|+|||.....-+.|.+..  -++.+|+++.=|..-+.+
T Consensus        18 ~lVlAGaGSGKT~tLt~Ria~Li~~~~v~P~~ILalTFT~kAA~E   62 (672)
T PRK10919         18 CLVLAGAGSGKTRVITNKIAHLIRGCGYQARHIAAVTFTNKAARE   62 (672)
T ss_pred             EEEEECCCHHHHHHHHHHHHHHHHCCCCCCCCEEEECCHHHHHHH
T ss_conf             899973855879999999999986689893338544217999999


No 171
>COG1783 XtmB Phage terminase large subunit [General function prediction only]
Probab=89.14  E-value=0.15  Score=28.39  Aligned_cols=198  Identities=14%  Similarity=-0.013  Sum_probs=113.1

Q ss_pred             CCCEEEEECCHHCCC-HHHHHHHHHHHCCCCCC-EEEEEECCCCCCCCHHHHH--HHCCCCCCEEEEECCCCCCCCCHHH
Q ss_conf             761499971110299-78898888885079981-3899823899876556765--3035247417984043367789778
Q gi|254781215|r  190 TYGMAIINDEASGTP-DVINLGILGFLTERNAN-RFWIMTSNPRRLSGKFYEI--FNKPLDDWKRFQIDTRTVEGIDPSF  265 (511)
Q Consensus       190 ~~~~lvI~DEAsgI~-d~i~e~i~~~Lt~~g~~-~~~i~~~nP~~~~g~fy~~--~~~~~~~w~~~~i~~~~~p~~~~~~  265 (511)
                      +...++++-|-+... +.+|.-+..+++..|.. .+.+..++|....-.++..  |.-..   ....+-|..+|.++.-|
T Consensus        53 ~~~d~lvIR~v~nt~k~St~~~~~e~l~e~gv~~~f~~~~s~pe~i~~~~G~ri~F~G~d---dp~klKSi~~~~~s~~W  129 (414)
T COG1783          53 PGIDVLVIREVENTHKQSTYALFKEALSELGVTKFFKISKSSPEIILKDTGQRIIFKGLD---DPAKLKSIAVNWISDLW  129 (414)
T ss_pred             CCCCEEEEEEECCCCCHHHHHHHHHHHHHHCCCCEEEEECCCHHHEECCCCCEEEEECCC---CHHHHHHHHCCHHHHHH
T ss_conf             787579999723544120899999999983840115774178666021258678994589---87885230100433555


Q ss_pred             HHHHHHHCCCC-----HHHHHHHHCCCCCCCCCCEEECH----HHHHHHHHCC----CCCC---CCCEEEEEEECCCCCC
Q ss_conf             99999751898-----01354443175666678737559----9998864076----5318---9970899962333478
Q gi|254781215|r  266 HEGIIARYGLD-----SDVTRVEVCGQFPQQDIDSFIPL----NIIEEALNRE----PCPD---PYAPLIMGCDIAEEGG  329 (511)
Q Consensus       266 ie~~~~~~ged-----s~~~r~evlgeFp~~~~~~~i~~----~~ie~a~~r~----~~~~---~~~~~viGvDVAr~G~  329 (511)
                      +|+..+--+++     -+.++.+..|+-..++.-+-+..    .|++-+.+..    ..+.   ......++-|.++.+.
T Consensus       130 fEE~~e~s~e~~~e~l~~l~~~~~~~~~~~~snpv~~~pw~~~~w~~~~~Dek~~~dt~~hhtT~~dn~fL~~~~v~~~e  209 (414)
T COG1783         130 FEEASEFSYEDDIELLVELRRRELKGHIILSSNPVSFNPWTYKHWLEFAVDEKKKADTYIHHTTYRDNLFLGFDDVDELE  209 (414)
T ss_pred             HHHHHHHHHHHHHHHHHHHHCCCCCCCCEEECCCCCCCCCCHHHHHHHHHCCCCCCCEEEEEEECCCCCCCCHHHHHHHH
T ss_conf             78776330345688877764122377724632643458853888888874435578668886201356667778999998


Q ss_pred             CCEEEEEECCCEEEEEEEC-CCCCHHHHHHHHHHHHHHCCCCEEEEEECCCCHHHHHHHHHC
Q ss_conf             4179998227558998732-778988999999999986188829980068763688989864
Q gi|254781215|r  330 DNTVVVLRRGPVIEHLFDW-SKTDLRTTNNKISGLVEKYRPDAIIIDANNTGARTCDYLEML  390 (511)
Q Consensus       330 D~svi~~r~G~~v~~~~~~-~~~d~~~~a~~i~~~~~~~~~~~i~iD~~GvG~gV~d~L~~~  390 (511)
                      |..-...+.+..+...+.+ .+.+..+....+..-.-+..++.|.-+.+|++.|+......+
T Consensus       210 d~k~~d~d~yri~~~gev~v~~~~v~~~~e~~~~d~v~~~i~~i~~~s~gm~~Gf~~~~n~l  271 (414)
T COG1783         210 DLKKNDPDLYRIVRDGEVGVKNGDVFDQFEVKPFDAVKFAIDNISRPSTGMDFGFTAKFNRL  271 (414)
T ss_pred             HHHHCCCCCCEEEEEEEEEECCCEECCHHHCCCHHHHHHHHHHHCCCCCCCEEEEEECCCEE
T ss_conf             76412854123899778986075254632157728877667761556554024257407577


No 172
>PRK06835 DNA replication protein DnaC; Validated
Probab=89.11  E-value=1.5  Score=22.07  Aligned_cols=96  Identities=22%  Similarity=0.235  Sum_probs=56.9

Q ss_pred             HHHHHHHHCH------HHHHHHHHHHHHHCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEEECCC
Q ss_conf             8899987070------6665288667764214557775655578458999999999998740565554210124650257
Q gi|254781215|r   13 QKLFDLMWSD------EIKLSFSNFVLHFFPWGEKGTPLEGFSAPRSWQLEFMEVVDAHCLNSVNNPNPEVFKGAISAGR   86 (511)
Q Consensus        13 ~~~~~~~~~~------~~~~~~~~~~~~~~~w~~~~~~~~~~~~P~~WQ~e~l~~i~~~~~~~~~~~~~~~~r~aV~sgr   86 (511)
                      |.+.+.+...      --..+|-+|-+-.|+  .+..+-.+ ..|++-...++........+=. ...   --+-..++-
T Consensus       120 q~~i~~~y~qSnl~~~l~~enF~~F~~~~ys--~~~~~~~~-~sprenm~~i~~~~~~fi~~F~-~~~---~nLlf~G~~  192 (330)
T PRK06835        120 QKLINLYYKQSNLKDILKENNFSNFNLNYYS--DEKDGDEP-ISPRENMENILEKCLNFIKNFD-KNN---ENLLFYGNT  192 (330)
T ss_pred             HHHHHHHHHHCCCCCHHHHCCCCCCCHHHCC--CCCCCCCC-CCHHHHHHHHHHHHHHHHHHCC-CCC---CCEEEECCC
T ss_conf             9999999973163002566143117886539--98788889-8989999999999999987247-888---866988999


Q ss_pred             CCCHHHHHHHHHHHHHHHCCCCEEEEEECC
Q ss_conf             659789999999999980899669998085
Q gi|254781215|r   87 GIGKTTLNAWLVLWLMSTRPGISVICLANS  116 (511)
Q Consensus        87 G~GKS~l~a~l~lw~l~~~p~~kv~vtApt  116 (511)
                      |+|||+|+..++.-.+-.. .+.+++||+.
T Consensus       193 G~GKTfLa~~IA~ell~~g-~sViy~ta~~  221 (330)
T PRK06835        193 GTGKTFLSNCIAKELLDRG-KTVIYRTSDE  221 (330)
T ss_pred             CCCHHHHHHHHHHHHHHCC-CEEEEEEHHH
T ss_conf             9988999999999999879-9499962999


No 173
>KOG0385 consensus
Probab=88.99  E-value=1.5  Score=22.01  Aligned_cols=165  Identities=18%  Similarity=0.186  Sum_probs=84.7

Q ss_pred             CCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHH-CCCCEEEEEE
Q ss_conf             214557775655578458999999999998740565554210124650257659789999999999980-8996699980
Q gi|254781215|r   36 FPWGEKGTPLEGFSAPRSWQLEFMEVVDAHCLNSVNNPNPEVFKGAISAGRGIGKTTLNAWLVLWLMST-RPGISVICLA  114 (511)
Q Consensus        36 ~~w~~~~~~~~~~~~P~~WQ~e~l~~i~~~~~~~~~~~~~~~~r~aV~sgrG~GKS~l~a~l~lw~l~~-~p~~kv~vtA  114 (511)
                      .||+.+++.|      +++|.+=|.=+.--..|+.+        ...+---|.|||--+..++.+..-. .-++--+|++
T Consensus       159 sP~~v~~g~l------r~YQveGlnWLi~l~engin--------gILaDEMGLGKTlQtIs~l~yl~~~~~~~GPfLVi~  224 (971)
T KOG0385         159 SPSYVKGGEL------RDYQLEGLNWLISLYENGIN--------GILADEMGLGKTLQTISLLGYLKGRKGIPGPFLVIA  224 (971)
T ss_pred             CCHHHCCCCC------CHHHHCCHHHHHHHHHCCCC--------CEEEHHCCCCHHHHHHHHHHHHHHHCCCCCCEEEEE
T ss_conf             8322147855------43320337999999865766--------584231045338999999999998517999849981


Q ss_pred             CCHHHHHHHHHHHHHHHHHHCHHCCCC-CCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCCCC---CCCHHHHCCCC
Q ss_conf             858999999999999999855000134-44322222233344432111235786169853035755---61002120267
Q gi|254781215|r  115 NSETQLKTTLWAEVSKWLSLLPNKHWF-EMQSLSLHPAPWYSDVLHCSLGIDSKHYSTMCRTYSEE---RPDTFVGHHNT  190 (511)
Q Consensus       115 pt~~Q~~~ilw~Ei~k~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~---~~ea~~G~h~~  190 (511)
                      |...--  --..|+++|.-.++..-+. ....+.-....         +.. .+ -|.+..|+-+-   .-..+.-+  .
T Consensus       225 P~StL~--NW~~Ef~rf~P~l~~~~~~Gdk~eR~~~~r~---------~~~-~~-~fdV~iTsYEi~i~dk~~lk~~--~  289 (971)
T KOG0385         225 PKSTLD--NWMNEFKRFTPSLNVVVYHGDKEERAALRRD---------IML-PG-RFDVCITSYEIAIKDKSFLKKF--N  289 (971)
T ss_pred             EHHHHH--HHHHHHHHHCCCCCEEEEECCHHHHHHHHHH---------HHC-CC-CCCEEEEHHHHHHHHHHHHHCC--C
T ss_conf             276678--9999999768986349884799999999998---------531-57-8766864078898668898619--9


Q ss_pred             CCEEEEECCHHCCCHH---HHHHHHHHHCCCCCCEEEEEECCCCCCC
Q ss_conf             6149997111029978---8988888850799813899823899876
Q gi|254781215|r  191 YGMAIINDEASGTPDV---INLGILGFLTERNANRFWIMTSNPRRLS  234 (511)
Q Consensus       191 ~~~lvI~DEAsgI~d~---i~e~i~~~Lt~~g~~~~~i~~~nP~~~~  234 (511)
                      . -.+|+|||+-|.+.   ....++-.    .....++.+|+|--++
T Consensus       290 W-~ylvIDEaHRiKN~~s~L~~~lr~f----~~~nrLLlTGTPLQNN  331 (971)
T KOG0385         290 W-RYLVIDEAHRIKNEKSKLSKILREF----KTDNRLLLTGTPLQNN  331 (971)
T ss_pred             C-EEEEECHHHHHCCHHHHHHHHHHHH----CCCCEEEEECCCCCCC
T ss_conf             3-4999523654146244899999985----6655267527854364


No 174
>PRK09183 transposase/IS protein; Provisional
Probab=88.95  E-value=1.5  Score=22.00  Aligned_cols=33  Identities=30%  Similarity=0.286  Sum_probs=24.8

Q ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEE
Q ss_conf             24650257659789999999999980899669998
Q gi|254781215|r   79 KGAISAGRGIGKTTLNAWLVLWLMSTRPGISVICL  113 (511)
Q Consensus        79 r~aV~sgrG~GKS~l~a~l~lw~l~~~p~~kv~vt  113 (511)
                      -+...++-|+|||++++.+..-.+  +-|-+|.++
T Consensus       103 Nvil~G~~GtGKThLA~Alg~~A~--~~G~~v~f~  135 (258)
T PRK09183        103 NIVLLGPSGVGKTHLAIALGYEAV--RAGIKVRFT  135 (258)
T ss_pred             CEEEECCCCCCHHHHHHHHHHHHH--HCCCEEEEE
T ss_conf             679989999868999999999999--879939997


No 175
>PRK09694 hypothetical protein; Provisional
Probab=88.83  E-value=1.6  Score=21.95  Aligned_cols=57  Identities=21%  Similarity=0.124  Sum_probs=41.2

Q ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEEECCHHHHHHHHHHHHHHHHHHCH
Q ss_conf             2465025765978999999999998089966999808589999999999999998550
Q gi|254781215|r   79 KGAISAGRGIGKTTLNAWLVLWLMSTRPGISVICLANSETQLKTTLWAEVSKWLSLLP  136 (511)
Q Consensus        79 r~aV~sgrG~GKS~l~a~l~lw~l~~~p~~kv~vtApt~~Q~~~ilw~Ei~k~~~~~~  136 (511)
                      =+.|-+.-|.|||..+=.++.-.+...-...+++.-||...+ |-||..+.++++++-
T Consensus       305 L~IiEAptG~GKTEAAL~~A~~L~~~~~~~Gl~faLPT~ATa-NaMf~Rv~~~~~~~~  361 (878)
T PRK09694        305 LTVIEAPTGSGKTETALAYAWKLIDQQLADSVIFALPTQATA-NAMLSRMEAAASKLF  361 (878)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHHCCCCCEEEECCHHHHH-HHHHHHHHHHHHHHC
T ss_conf             799975899975899999999999734898369977479889-999999999999736


No 176
>PRK07952 DNA replication protein DnaC; Validated
Probab=88.56  E-value=1.6  Score=21.84  Aligned_cols=67  Identities=18%  Similarity=0.112  Sum_probs=37.0

Q ss_pred             CCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEEECC
Q ss_conf             655578458999999999998740565554210124650257659789999999999980899669998085
Q gi|254781215|r   45 LEGFSAPRSWQLEFMEVVDAHCLNSVNNPNPEVFKGAISAGRGIGKTTLNAWLVLWLMSTRPGISVICLANS  116 (511)
Q Consensus        45 ~~~~~~P~~WQ~e~l~~i~~~~~~~~~~~~~~~~r~aV~sgrG~GKS~l~a~l~lw~l~~~p~~kv~vtApt  116 (511)
                      .++|.-+.+=|+.+|..--....+-..  .  +--..-..+-|+|||+|++.++...+. +-.+.+++|++.
T Consensus        68 Feny~~~~~~q~~al~~a~~y~enf~~--~--~~gLlF~G~~GTGKThLA~aIan~Li~-~G~sVlf~t~~d  134 (242)
T PRK07952         68 FENYRVECEGQMNALSKARQYVEEFDG--N--IASFIFSGKPGTGKNHLAAAICNELLL-RGKSVLIITVAD  134 (242)
T ss_pred             EECEECCCHHHHHHHHHHHHHHHHHCC--C--CCEEEEECCCCCCHHHHHHHHHHHHHH-CCCEEEEEEHHH
T ss_conf             212015877789999999999986543--8--871799789999789999999999998-799499977999


No 177
>PRK12726 flagellar biosynthesis regulator FlhF; Provisional
Probab=88.51  E-value=1.6  Score=21.81  Aligned_cols=103  Identities=8%  Similarity=-0.019  Sum_probs=50.3

Q ss_pred             EEEEECCCEEEEEEECCCCCHHHHHHHHHHHHHHCCCCEEEEEECCCCHHHHHHHHHC----CCEEEEECCCCCCCCHHH
Q ss_conf             9998227558998732778988999999999986188829980068763688989864----982798427777664025
Q gi|254781215|r  333 VVVLRRGPVIEHLFDWSKTDLRTTNNKISGLVEKYRPDAIIIDANNTGARTCDYLEML----GYHVYRVLGQKRAVDLEF  408 (511)
Q Consensus       333 vi~~r~G~~v~~~~~~~~~d~~~~a~~i~~~~~~~~~~~i~iD~~GvG~gV~d~L~~~----g~~v~~v~~~~~~~~~~~  408 (511)
                      .+.+-+|. |.-+.=-+|..-+.++.+++..+.+.+..-.++-++-.=.|-+++|+.+    |.+++.   +.   ++.-
T Consensus       200 ~~~l~~g~-VIaLVGvnGvGKTTTiAKLA~~l~~~gkkV~LVAaDTFRaAAiEQLk~~g~rlgVpV~~---~~---dpa~  272 (407)
T PRK12726        200 SFDLSNHR-IISLIGQTGVGKTTTLVKLGWQLLKQNRTVGFITTDTFRSGAVEQFQGYADKLDVELIV---AT---SPAE  272 (407)
T ss_pred             EEEECCCC-EEEEECCCCCCHHHHHHHHHHHHHHCCCCEEEEECCCCCHHHHHHHHHHHHHHCCEEEE---EC---CHHH
T ss_conf             02303690-89998999897899999999999977991799970667788999999999997964998---18---8899


Q ss_pred             HHHHHHHHHHHHHHHH------HHCCCCCHHHHHHHHHCCCE
Q ss_conf             5227999999999999------70899981899999857967
Q gi|254781215|r  409 CRNRRTELHVKMADWL------EFASLINHSGLIQNLKSLKS  444 (511)
Q Consensus       409 y~N~rae~~~~~re~l------~~g~l~~d~~l~~el~~~~~  444 (511)
                      -.  .+-.+..-+..+      -.||+..+..++.||..+..
T Consensus       273 l~--~av~~~a~~~~~DvVIIDTAGRl~~d~~Lm~EL~ki~~  312 (407)
T PRK12726        273 LE--EAVQYMTYVNCVDHILIDTVGRNYLAEESVSEISAYTD  312 (407)
T ss_pred             HH--HHHHHHHHCCCCCEEEEECCCCCCCCHHHHHHHHHHHH
T ss_conf             99--99999986289998999699988134999999999873


No 178
>PRK02731 histidinol-phosphate aminotransferase; Validated
Probab=88.29  E-value=1.7  Score=21.72  Aligned_cols=60  Identities=20%  Similarity=0.196  Sum_probs=38.0

Q ss_pred             CCCHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEEECCHHHHH
Q ss_conf             7845899999999999874056555421012465025765978999999999998089966999808589999
Q gi|254781215|r   49 SAPRSWQLEFMEVVDAHCLNSVNNPNPEVFKGAISAGRGIGKTTLNAWLVLWLMSTRPGISVICLANSETQLK  121 (511)
Q Consensus        49 ~~P~~WQ~e~l~~i~~~~~~~~~~~~~~~~r~aV~sgrG~GKS~l~a~l~lw~l~~~p~~kv~vtApt~~Q~~  121 (511)
                      .+|+.-..++-++|+++.-  .  + +.  .|.|  |.  |=+.+.  .++..+++.|+.+|++..||+..-.
T Consensus        63 ~YPd~~~~~Lr~aiA~~~~--v--~-~~--~Ilv--~n--Gs~e~i--~l~~~a~~~pgd~Vl~~~P~f~~Y~  122 (367)
T PRK02731         63 RYPDGSGFELKAALAEKFG--V--D-PE--QIIL--GN--GSDEIL--ELLARAYLGPGDEVIYSEHAFAVYP  122 (367)
T ss_pred             CCCCCCHHHHHHHHHHHHC--C--C-HH--HEEE--CC--CHHHHH--HHHHHHHHCCCCEEEECCCCHHHHH
T ss_conf             5959878999999999978--5--8-11--1998--57--899999--9999998479986444798626899


No 179
>KOG0334 consensus
Probab=88.24  E-value=1.7  Score=21.70  Aligned_cols=135  Identities=16%  Similarity=0.053  Sum_probs=70.6

Q ss_pred             CCCCHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHHH-HCC-----CCEEEEEECCHHHHH
Q ss_conf             57845899999999999874056555421012465025765978999999999998-089-----966999808589999
Q gi|254781215|r   48 FSAPRSWQLEFMEVVDAHCLNSVNNPNPEVFKGAISAGRGIGKTTLNAWLVLWLMS-TRP-----GISVICLANSETQLK  121 (511)
Q Consensus        48 ~~~P~~WQ~e~l~~i~~~~~~~~~~~~~~~~r~aV~sgrG~GKS~l~a~l~lw~l~-~~p-----~~kv~vtApt~~Q~~  121 (511)
                      |..|++-|++++=+|-..            +-|...|=-|.|||...--.++=+.. .+|     +.-.++.|||..+++
T Consensus       385 y~k~~~IQ~qAiP~ImsG------------rdvIgvakTgSGKT~af~LPmirhi~dQr~~~~gdGPi~li~aPtrela~  452 (997)
T KOG0334         385 YEKPTPIQAQAIPAIMSG------------RDVIGVAKTGSGKTLAFLLPMIRHIKDQRPLEEGDGPIALILAPTRELAM  452 (997)
T ss_pred             CCCCCCHHHHHCCHHCCC------------CCEEEEECCCCCCCHHHHHHHHHHHCCCCCHHCCCCCEEEEECCCHHHHH
T ss_conf             899875566430122257------------74587732688620344211555420479711078864799737778999


Q ss_pred             HHHHHHHHHHHHHCHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCC---CCCCCHHHHCCCCCCEEEEEC
Q ss_conf             99999999999855000134443222222333444321112357861698530357---556100212026761499971
Q gi|254781215|r  122 TTLWAEVSKWLSLLPNKHWFEMQSLSLHPAPWYSDVLHCSLGIDSKHYSTMCRTYS---EERPDTFVGHHNTYGMAIIND  198 (511)
Q Consensus       122 ~ilw~Ei~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s---~~~~ea~~G~h~~~~~lvI~D  198 (511)
                      .| ..++++....+-  ..+.|..+...     .......++.+.+..+++.-..-   ..|...+--+|  ....+++|
T Consensus       453 QI-~r~~~kf~k~l~--ir~v~vygg~~-----~~~qiaelkRg~eIvV~tpGRmiD~l~~n~grvtnlr--R~t~lv~d  522 (997)
T KOG0334         453 QI-HREVRKFLKLLG--IRVVCVYGGSG-----ISQQIAELKRGAEIVVCTPGRMIDILCANSGRVTNLR--RVTYLVLD  522 (997)
T ss_pred             HH-HHHHHHHHHHCC--CEEEEECCCCC-----HHHHHHHHHCCCCEEEECCCHHHHHHHHCCCCCCCCC--CCCEEEEC
T ss_conf             99-999999877417--62798427851-----8878999867896599645032336661577623310--11035541


Q ss_pred             CHHCCC
Q ss_conf             110299
Q gi|254781215|r  199 EASGTP  204 (511)
Q Consensus       199 EAsgI~  204 (511)
                      ||--.-
T Consensus       523 eaDrmf  528 (997)
T KOG0334         523 EADRMF  528 (997)
T ss_pred             HHHHHH
T ss_conf             123544


No 180
>PRK07276 DNA polymerase III subunit delta'; Validated
Probab=88.11  E-value=1.7  Score=21.65  Aligned_cols=184  Identities=11%  Similarity=0.126  Sum_probs=95.4

Q ss_pred             HHHHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEEEC-CHHHHHHHHHHHHHHH
Q ss_conf             899999999999874056555421012465025765978999999999998089966999808-5899999999999999
Q gi|254781215|r   53 SWQLEFMEVVDAHCLNSVNNPNPEVFKGAISAGRGIGKTTLNAWLVLWLMSTRPGISVICLAN-SETQLKTTLWAEVSKW  131 (511)
Q Consensus        53 ~WQ~e~l~~i~~~~~~~~~~~~~~~~r~aV~sgrG~GKS~l~a~l~lw~l~~~p~~kv~vtAp-t~~Q~~~ilw~Ei~k~  131 (511)
                      +.|-++++....-..+++.-| .     ..=+| |+||..++-+++-+.+|..+.....|.-- +-+++.          
T Consensus         5 ~~Qp~i~~~l~~~i~~~rl~H-A-----yLf~G-~~Gk~~~A~~~A~~l~C~~~~~~~pCg~C~~C~~i~----------   67 (290)
T PRK07276          5 QKQPKLFQRFQTILEQDRLNH-A-----YLFSG-DFASFEMALFLAQSLFCEQKEDVLPCGHCRSCRLIE----------   67 (290)
T ss_pred             HHHHHHHHHHHHHHHCCCCCE-E-----EECCC-CCCHHHHHHHHHHHHHCCCCCCCCCCCCCHHHHHHH----------
T ss_conf             878999999999998499650-5-----42169-868799999999998189999989898899999987----------


Q ss_pred             HHHCHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCCCCCCCHHHHCCCCCCEEEEECCHHCCCHHHHHHH
Q ss_conf             98550001344432222223334443211123578616985303575561002120267614999711102997889888
Q gi|254781215|r  132 LSLLPNKHWFEMQSLSLHPAPWYSDVLHCSLGIDSKHYSTMCRTYSEERPDTFVGHHNTYGMAIINDEASGTPDVINLGI  211 (511)
Q Consensus       132 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~ea~~G~h~~~~~lvI~DEAsgI~d~i~e~i  211 (511)
                      ....|....       +.+.+..       ++.  +    ..|...  +.-+..++.+.+. .+|+|+|..+.....+++
T Consensus        68 ~~~hpDv~~-------i~~~~~~-------I~v--d----~IR~l~--~~~~~~~~~g~~K-V~II~~Ad~mt~~AaNaL  124 (290)
T PRK07276         68 QGDFSDVTV-------IEPQGQV-------IKT--D----TIRELT--ANFSQSGYEGKRQ-VFIIKDADKMHVNAANSL  124 (290)
T ss_pred             CCCCCCCEE-------ECCCCCC-------CCH--H----HHHHHH--HHHHHCCCCCCEE-EEEECCHHHCCHHHHHHH
T ss_conf             699987137-------7167775-------768--8----999999--9984456137827-999776565299999999


Q ss_pred             HHHHCCCCCCEE-EEEECCCCCCCCHHHHHHHCCCCCCEEEEECCCCCCCCCHHHHHHHHHHCCCCHHHHHHHHCCCCCC
Q ss_conf             888507998138-9982389987655676530352474179840433677897789999975189801354443175666
Q gi|254781215|r  212 LGFLTERNANRF-WIMTSNPRRLSGKFYEIFNKPLDDWKRFQIDTRTVEGIDPSFHEGIIARYGLDSDVTRVEVCGQFPQ  290 (511)
Q Consensus       212 ~~~Lt~~g~~~~-~i~~~nP~~~~g~fy~~~~~~~~~w~~~~i~~~~~p~~~~~~ie~~~~~~geds~~~r~evlgeFp~  290 (511)
                      .-+|-++..... ++.+.||.+.--...       ++--.+++     |. +++.+.+..++.|...  +..++++.|..
T Consensus       125 LK~LEEPp~~t~~iLlt~~~~~lLpTI~-------SRCQ~i~f-----p~-~~~~l~~~l~~~gi~~--~~a~~la~~~~  189 (290)
T PRK07276        125 LKVIEEPQSEIYIFLLTNDENKVLPTIK-------SRTQIFHF-----PK-NEAYLYQLLEEKGLLK--TQAKLLAKLAQ  189 (290)
T ss_pred             HHHHCCCCCCCEEEEEECCHHHCCHHHH-------HCCCCCCC-----CC-CHHHHHHHHHHCCCCH--HHHHHHHHHHC
T ss_conf             9970389888379988799254937887-------36601028-----99-6799999999869986--79999999965


Q ss_pred             C
Q ss_conf             6
Q gi|254781215|r  291 Q  291 (511)
Q Consensus       291 ~  291 (511)
                      +
T Consensus       190 ~  190 (290)
T PRK07276        190 S  190 (290)
T ss_pred             C
T ss_conf             9


No 181
>PRK13341 recombination factor protein RarA/unknown domain fusion protein; Reviewed
Probab=87.89  E-value=1.8  Score=21.57  Aligned_cols=22  Identities=27%  Similarity=0.285  Sum_probs=16.3

Q ss_pred             EEEEECCCCCCHHHHHHHHHHH
Q ss_conf             2465025765978999999999
Q gi|254781215|r   79 KGAISAGRGIGKTTLNAWLVLW  100 (511)
Q Consensus        79 r~aV~sgrG~GKS~l~a~l~lw  100 (511)
                      -+..=.+=|+|||+++-.++--
T Consensus        54 S~Il~GPPGtGKTTLA~iIA~~   75 (726)
T PRK13341         54 SLILYGPPGVGKTTLARIIANH   75 (726)
T ss_pred             EEEEECCCCCCHHHHHHHHHHH
T ss_conf             2788897999999999999887


No 182
>pfam00931 NB-ARC NB-ARC domain.
Probab=87.58  E-value=1.9  Score=21.45  Aligned_cols=115  Identities=13%  Similarity=-0.020  Sum_probs=58.8

Q ss_pred             CCEEEEEECCCCCCHHHHHHHHHHHHHH-HCCCCEEEEEECCHHHHHHHHHHHHHHHHHHCHHCCCCCCCCCCCCCCCCC
Q ss_conf             1012465025765978999999999998-089966999808589999999999999998550001344432222223334
Q gi|254781215|r   76 EVFKGAISAGRGIGKTTLNAWLVLWLMS-TRPGISVICLANSETQLKTTLWAEVSKWLSLLPNKHWFEMQSLSLHPAPWY  154 (511)
Q Consensus        76 ~~~r~aV~sgrG~GKS~l~a~l~lw~l~-~~p~~kv~vtApt~~Q~~~ilw~Ei~k~~~~~~~~~~~~~~~~~~~~~~~~  154 (511)
                      .+.-++|..--|+|||+|+..+....-+ .+.+.++.|+..-....++++ ..|.+.+...   .      .     ...
T Consensus        18 ~~~vI~I~G~gGiGKTtLA~~v~~~~~i~~~F~~~~wv~vs~~~~~~~i~-~~i~~~l~~~---~------~-----~~~   82 (285)
T pfam00931        18 NLGVVGIVGMGGVGKTTLAKQIYNDDSVGGHFDSVAWVVVSKTYTEFRLQ-KDILQELGLD---D------S-----DWV   82 (285)
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHCCHHHHHCCCEEEEEEECCCCCHHHHH-HHHHHHHCCC---C------C-----CCC
T ss_conf             95399988999563999999997165565059838999979766689999-9999985666---5------4-----555


Q ss_pred             CCCCCCCCCCCCCEEEEEECCCCCCCCCHH-HHCCCCCCEEEEECCHHCCCHHHHHHHHHHHCCCCCCEEEEEE
Q ss_conf             443211123578616985303575561002-1202676149997111029978898888885079981389982
Q gi|254781215|r  155 SDVLHCSLGIDSKHYSTMCRTYSEERPDTF-VGHHNTYGMAIINDEASGTPDVINLGILGFLTERNANRFWIMT  227 (511)
Q Consensus       155 ~~~~~~~~~~~~~~~~~~~~~~s~~~~ea~-~G~h~~~~~lvI~DEAsgI~d~i~e~i~~~Lt~~g~~~~~i~~  227 (511)
                      .         .+.          .+....+ ..+++. ..|+|+|-..  ....|+.+...+...++..+++.|
T Consensus        83 ~---------~~~----------~~l~~~l~~~L~~k-r~LiVLDDVw--~~~~~~~l~~~~~~~~~gSrIIvT  134 (285)
T pfam00931        83 E---------KNE----------SELAVKIKEALLRK-RFLLVLDDVW--EKNDWDKIGVPFPDGENGSRVIVT  134 (285)
T ss_pred             C---------CCH----------HHHHHHHHHHHCCC-CEEEEECCCC--CHHHHHHHHCCCCCCCCCCEEEEE
T ss_conf             5---------789----------99999999997279-6699963888--789999973457578998279985


No 183
>cd01983 Fer4_NifH The Fer4_NifH superfamily contains a variety of proteins which share a common ATP-binding domain. Functionally, proteins in this superfamily use the energy from hydrolysis of NTP to transfer electron or ion.
Probab=87.57  E-value=1.3  Score=22.51  Aligned_cols=33  Identities=33%  Similarity=0.394  Sum_probs=26.5

Q ss_pred             EEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEEE
Q ss_conf             46502576597899999999999808996699980
Q gi|254781215|r   80 GAISAGRGIGKTTLNAWLVLWLMSTRPGISVICLA  114 (511)
Q Consensus        80 ~aV~sgrG~GKS~l~a~l~lw~l~~~p~~kv~vtA  114 (511)
                      +++.+-.|+|||++++.++.++.-  .+.++++.-
T Consensus         2 i~~~~~kGvGKTT~a~~La~~la~--~g~~Vl~vD   34 (99)
T cd01983           2 IVVTGKGGVGKTTLAANLAAALAK--RGKRVLLID   34 (99)
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHH--CCCEEEEEC
T ss_conf             898589977689999999999998--899699986


No 184
>TIGR02868 CydC ABC transporter, CydDC cysteine exporter (CydDC-E) family, permease/ATP-binding protein CydC; InterPro: IPR014223   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 entry represents CydC, a member of a heterodimeric ATP-binding cassette-type transporter (ABC transporter). It is involved in the export of glutathione from the cytoplasm to the periplasm and is required for the assembly of both cytochrome c and cytochrome bd , , .; GO: 0042626 ATPase activity coupled to transmembrane movement of substances, 0006810 transport, 0016021 integral to membrane.
Probab=87.47  E-value=0.57  Score=24.71  Aligned_cols=64  Identities=25%  Similarity=0.124  Sum_probs=36.5

Q ss_pred             CCCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEEECCHHHHHHHHHHHHHHHHHHCHH
Q ss_conf             565554210124650257659789999999999980899669998085899999999999999985500
Q gi|254781215|r   69 SVNNPNPEVFKGAISAGRGIGKTTLNAWLVLWLMSTRPGISVICLANSETQLKTTLWAEVSKWLSLLPN  137 (511)
Q Consensus        69 ~~~~~~~~~~r~aV~sgrG~GKS~l~a~l~lw~l~~~p~~kv~vtApt~~Q~~~ilw~Ei~k~~~~~~~  137 (511)
                      +...+.+...|++|...=|+|||||.+.+.=.  +--...++.+.--.-.++..   .|+++.+..++.
T Consensus       379 ~V~L~l~~G~r~Ai~G~SG~GKsTLL~~L~G~--l~P~~G~vtl~G~~~~~~~~---~evrr~v~~~aQ  442 (566)
T TIGR02868       379 GVSLDLPPGERVAILGPSGSGKSTLLATLAGL--LDPLQGEVTLDGVPVSSLSE---DEVRRRVSVFAQ  442 (566)
T ss_pred             CCCCCCCCCCCEEEECCCCCCHHHHHHHHHHH--CCCCCCCEEECCCCHHHCCC---CHHEHHEEECCC
T ss_conf             78641138860898668876578999999840--28999917877732432573---110000031278


No 185
>cd03110 Fer4_NifH_child This protein family's function is unkown. It contains nucleotide binding site. It uses NTP as energy source to transfer electron or ion.
Probab=87.28  E-value=0.5  Score=25.06  Aligned_cols=21  Identities=43%  Similarity=0.570  Sum_probs=17.5

Q ss_pred             EEEEECCC-CCCHHHHHHHHHH
Q ss_conf             24650257-6597899999999
Q gi|254781215|r   79 KGAISAGR-GIGKTTLNAWLVL   99 (511)
Q Consensus        79 r~aV~sgr-G~GKS~l~a~l~l   99 (511)
                      |++|.||. |+|||++++.++.
T Consensus         1 kIaV~SgKGGVGKTT~a~nLA~   22 (179)
T cd03110           1 QIAVISGKGGTGKTTVTAALAA   22 (179)
T ss_pred             CEEEEECCCCCHHHHHHHHHHH
T ss_conf             9899958998609999999999


No 186
>PHA00149 DNA encapsidation protein
Probab=87.26  E-value=2  Score=21.34  Aligned_cols=187  Identities=18%  Similarity=0.157  Sum_probs=89.2

Q ss_pred             EECCCCCCHHHHHHHHHHHHHHHCCCCEEEEEECCHHHH--HHHHHHHHHHHHHHCHHCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             502576597899999999999808996699980858999--999999999999855000134443222222333444321
Q gi|254781215|r   82 ISAGRGIGKTTLNAWLVLWLMSTRPGISVICLANSETQL--KTTLWAEVSKWLSLLPNKHWFEMQSLSLHPAPWYSDVLH  159 (511)
Q Consensus        82 V~sgrG~GKS~l~a~l~lw~l~~~p~~kv~vtApt~~Q~--~~ilw~Ei~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  159 (511)
                      |-.|||+|||..+.-.++=-++. .|-+.+...-....+  ++..|+++   ..+-|+ +            ++.+....
T Consensus        22 viG~RgiGKTya~k~~~~k~~i~-kgeqfiyLRr~k~El~~k~~Ff~d~---~~~~~~-~------------ef~Vk~~k   84 (331)
T PHA00149         22 VIGARGIGKTYALKKYLIKRFIK-KGEQFIYLRRYKSELKKKSKFFADI---AQEFPN-T------------EFEVKGRK   84 (331)
T ss_pred             EEECCCCCHHHHHHHHHHHHHHH-CCCEEEEEEECCHHHHHHHHHHHHH---HHHCCC-C------------CEEEEEEE
T ss_conf             98246544035777889999986-2967999993243452021056789---975789-7------------45997008


Q ss_pred             CCCCCCCCEEEEEECCCCCCCCCHHHHCCCCCCEEEEECCH-------HCCCHH---HHHHHHHHHCCCCCCEEEEEECC
Q ss_conf             11235786169853035755610021202676149997111-------029978---89888888507998138998238
Q gi|254781215|r  160 CSLGIDSKHYSTMCRTYSEERPDTFVGHHNTYGMAIINDEA-------SGTPDV---INLGILGFLTERNANRFWIMTSN  229 (511)
Q Consensus       160 ~~~~~~~~~~~~~~~~~s~~~~ea~~G~h~~~~~lvI~DEA-------sgI~d~---i~e~i~~~Lt~~g~~~~~i~~~n  229 (511)
                      +.+...---|++.-+     +.+++.+.-=+...-+++||.       .-+|++   ....+......+ ..+++++.||
T Consensus        85 i~~~~k~igy~i~lS-----~~q~~Ks~~Yp~V~~I~fDEfi~~k~n~~Ylpne~~allnli~tV~R~R-e~i~~~~lsN  158 (331)
T PHA00149         85 IYIKGKLIGYAIPLS-----TWQALKSSAYPNVSTIFFDEFIREKDNKRYLPNEVDALLNLIDTVFRAR-ERVRCICLSN  158 (331)
T ss_pred             EEECCEEEEEEEEHH-----HHHHHCCCCCCCEEEEEEEHHHHHCCCCCCCCCHHHHHHHHHHHHHHHH-CCEEEEEECC
T ss_conf             998680799997044-----6776325689955899712233305433568850899999999987753-5759999758


Q ss_pred             CCCCCCHHHHHHHCCCCCCEEEEECC-CCCCCCCHHHH--HHHHHHCCC---CHHHHHHHHCCCCCCC
Q ss_conf             99876556765303524741798404-33677897789--999975189---8013544431756666
Q gi|254781215|r  230 PRRLSGKFYEIFNKPLDDWKRFQIDT-RTVEGIDPSFH--EGIIARYGL---DSDVTRVEVCGQFPQQ  291 (511)
Q Consensus       230 P~~~~g~fy~~~~~~~~~w~~~~i~~-~~~p~~~~~~i--e~~~~~~ge---ds~~~r~evlgeFp~~  291 (511)
                      -.....+++.-++-..+.=..++... .-..+++.+..  |..+..+|.   .+..+..-...+|...
T Consensus       159 a~~~~NPyF~yf~~~p~~nk~f~~~~~~li~f~~~~~f~~e~~~t~Fgkli~g~ay~e~sldN~F~~n  226 (331)
T PHA00149        159 AVSIVNPYFLYFGLYPDINKRFNVYDEILIEFPNSEDFQSERRKTRFGKLISGTAYYEMSLDNKFSSN  226 (331)
T ss_pred             CCCCCCCHHHEEEEECCCCCEEEECCEEEEEECCHHHHHHHHHHCCHHHCCCCCHHHHHHCCCHHHHC
T ss_conf             54303604423421058994466346189994685886677653103320363125553114221202


No 187
>TIGR03305 alt_F1F0_F1_bet alternate F1F0 ATPase, F1 subunit beta. A small number of taxonomically diverse prokaryotic species have what appears to be a second ATP synthase, in addition to the normal F1F0 ATPase in bacteria and A1A0 ATPase in archaea. These enzymes use ion gradients to synthesize ATP, and in principle may run in either direction. This model represents the F1 beta subunit of this apparent second ATP synthase.
Probab=87.20  E-value=1.9  Score=21.48  Aligned_cols=37  Identities=27%  Similarity=0.453  Sum_probs=28.2

Q ss_pred             CEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEE
Q ss_conf             0124650257659789999999999980899669998
Q gi|254781215|r   77 VFKGAISAGRGIGKTTLNAWLVLWLMSTRPGISVICL  113 (511)
Q Consensus        77 ~~r~aV~sgrG~GKS~l~a~l~lw~l~~~p~~kv~vt  113 (511)
                      .-|+.+-+|+|+|||.++..++.-....+.+..|++.
T Consensus       138 Gqr~gIfggaGvGKT~Ll~e~i~n~~~~~~~v~V~~~  174 (449)
T TIGR03305       138 GGKAGLFGGAGVGKTVLLTEMIHNMVGQHQGVSIFCG  174 (449)
T ss_pred             CCEEEEECCCCCCCCCHHHHHHHHHHHHCCCEEEEEE
T ss_conf             7565665279998410189999865641488689999


No 188
>PRK03321 putative aminotransferase; Provisional
Probab=87.20  E-value=1.8  Score=21.56  Aligned_cols=59  Identities=22%  Similarity=0.251  Sum_probs=36.8

Q ss_pred             CCCHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEEECCHHHH
Q ss_conf             784589999999999987405655542101246502576597899999999999808996699980858999
Q gi|254781215|r   49 SAPRSWQLEFMEVVDAHCLNSVNNPNPEVFKGAISAGRGIGKTTLNAWLVLWLMSTRPGISVICLANSETQL  120 (511)
Q Consensus        49 ~~P~~WQ~e~l~~i~~~~~~~~~~~~~~~~r~aV~sgrG~GKS~l~a~l~lw~l~~~p~~kv~vtApt~~Q~  120 (511)
                      .+|+.-..++-++|+++.-    .+ +.  .  |..|.  |=+.+...+  -.+++.|+.+|++..||+..-
T Consensus        53 ~YPd~~~~~Lr~aiA~~~~----v~-~~--~--I~v~n--Gs~e~i~~~--~~~~~~~gd~Vl~p~P~f~~Y  111 (352)
T PRK03321         53 RYPDNGAVELRAALAEHLG----VA-PE--H--VAVGC--GSVALCQQL--VQATAGPGDEVVFAWRSFEAY  111 (352)
T ss_pred             CCCCCCHHHHHHHHHHHHC----CC-HH--H--EEECC--CHHHHHHHH--HHHHHCCCCEEEECCCCHHHH
T ss_conf             7989986999999999878----78-58--7--99874--699999999--999817979899888853268


No 189
>cd02038 FleN-like FleN is a member of the Fer4_NifH superfamily. It shares the common function as an ATPase, with the ATP-binding domain at the N-terminus. In Pseudomonas aeruginosa, FleN gene is involved in regulating the number of flagella and chemotactic motility by influencing FleQ activity.
Probab=87.19  E-value=1.2  Score=22.58  Aligned_cols=82  Identities=26%  Similarity=0.313  Sum_probs=51.4

Q ss_pred             EEEECCC-CCCHHHHHHHHHHHHHHHCCCCEEEEEECCHHHHHHHHHHHHHHHHHHCHHCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             4650257-659789999999999980899669998085899999999999999985500013444322222233344432
Q gi|254781215|r   80 GAISAGR-GIGKTTLNAWLVLWLMSTRPGISVICLANSETQLKTTLWAEVSKWLSLLPNKHWFEMQSLSLHPAPWYSDVL  158 (511)
Q Consensus        80 ~aV~sgr-G~GKS~l~a~l~lw~l~~~p~~kv~vtApt~~Q~~~ilw~Ei~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~  158 (511)
                      ++|.||. |+|||++++.++.-+.-  .+.+|++.=.-.                               .         
T Consensus         2 i~v~sgKgGvGkt~~~~nLa~~la~--~G~~vll~D~D~-------------------------------g---------   39 (139)
T cd02038           2 IAVTSGKGGVGKTNISANLALALAK--LGKRVLLLDADL-------------------------------G---------   39 (139)
T ss_pred             EEEECCCCCCCHHHHHHHHHHHHHH--CCCCEEEEECCC-------------------------------C---------
T ss_conf             8996499998399999999999997--899699998989-------------------------------9---------


Q ss_pred             CCCCCCCCCEEEEEECCCCCCCCCHHHHCCCCCCEEEEECCHHCCCHHHHHHHHHHHCCCCCCEEEEEECCCCCCCCH
Q ss_conf             111235786169853035755610021202676149997111029978898888885079981389982389987655
Q gi|254781215|r  159 HCSLGIDSKHYSTMCRTYSEERPDTFVGHHNTYGMAIINDEASGTPDVINLGILGFLTERNANRFWIMTSNPRRLSGK  236 (511)
Q Consensus       159 ~~~~~~~~~~~~~~~~~~s~~~~ea~~G~h~~~~~lvI~DEAsgI~d~i~e~i~~~Lt~~g~~~~~i~~~nP~~~~g~  236 (511)
                                               ++.+|-   ..+|+|=++|+.+.+...+.    .. .+..++.++.|+...+.
T Consensus        40 -------------------------~an~~~---D~viiD~~aG~~~~~~~~~~----~a-d~~lvV~tpeptSi~DA   84 (139)
T cd02038          40 -------------------------LANLDY---DYIIIDTGAGISDNVLDFFL----AA-DEVIVVTTPEPTSITDA   84 (139)
T ss_pred             -------------------------CCCCCC---CEEEEECCCCCCHHHHHHHH----HC-CCEEEEECCCHHHHHHH
T ss_conf             -------------------------965799---99999489998778999999----58-95799958970679999


No 190
>KOG1803 consensus
Probab=87.02  E-value=1.3  Score=22.47  Aligned_cols=44  Identities=20%  Similarity=0.142  Sum_probs=37.0

Q ss_pred             EEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEEECCHHHHHHHHH
Q ss_conf             4650257659789999999999980899669998085899999999
Q gi|254781215|r   80 GAISAGRGIGKTTLNAWLVLWLMSTRPGISVICLANSETQLKTTLW  125 (511)
Q Consensus        80 ~aV~sgrG~GKS~l~a~l~lw~l~~~p~~kv~vtApt~~Q~~~ilw  125 (511)
                      .-+-.+-|+|||+...-++.-.+.-  +.+|+|+|||---+.+|+-
T Consensus       204 ~~I~GPPGTGKT~TlvEiI~qlvk~--~k~VLVcaPSn~AVdNive  247 (649)
T KOG1803         204 LIIHGPPGTGKTRTLVEIISQLVKQ--KKRVLVCAPSNVAVDNIVE  247 (649)
T ss_pred             EEEECCCCCCCEEEHHHHHHHHHHC--CCEEEEECCCHHHHHHHHH
T ss_conf             5755799888404399999999972--8859997673678999998


No 191
>KOG3022 consensus
Probab=86.87  E-value=1.2  Score=22.72  Aligned_cols=34  Identities=35%  Similarity=0.406  Sum_probs=27.3

Q ss_pred             EEEEEECCC-CCCHHHHHHHHHHHHHHHCCCCEEEEE
Q ss_conf             124650257-659789999999999980899669998
Q gi|254781215|r   78 FKGAISAGR-GIGKTTLNAWLVLWLMSTRPGISVICL  113 (511)
Q Consensus        78 ~r~aV~sgr-G~GKS~l~a~l~lw~l~~~p~~kv~vt  113 (511)
                      .+++|.||. |+|||++++.+++-.+.  ++.++.+.
T Consensus        48 ~iI~VlSGKGGVGKSTvt~nla~~La~--~g~~vglL   82 (300)
T KOG3022          48 HIILVLSGKGGVGKSTVTVNLALALAS--EGKKVGLL   82 (300)
T ss_pred             EEEEEEECCCCCCHHHHHHHHHHHHHC--CCCCEEEE
T ss_conf             589998678877616899999999861--79717997


No 192
>PRK00149 dnaA chromosomal replication initiation protein; Reviewed
Probab=86.82  E-value=1.5  Score=22.02  Aligned_cols=29  Identities=7%  Similarity=0.215  Sum_probs=14.3

Q ss_pred             CHHHHHHHHHHHHHHHCCCCEEEEEECCH
Q ss_conf             97899999999999808996699980858
Q gi|254781215|r   89 GKTTLNAWLVLWLMSTRPGISVICLANSE  117 (511)
Q Consensus        89 GKS~l~a~l~lw~l~~~p~~kv~vtApt~  117 (511)
                      |....-.|+.---+....+..+++.+|+.
T Consensus        17 ~~~~f~~Wf~pl~~~~~~~~~l~l~vPn~   45 (447)
T PRK00149         17 SEPEYETWIKPLKLEKSSDDTLVLSAPNR   45 (447)
T ss_pred             CHHHHHHHHHHCEEEEEECCEEEEEECCH
T ss_conf             99999999865967686699999997975


No 193
>PRK08939 primosomal protein DnaI; Reviewed
Probab=86.66  E-value=2.1  Score=21.13  Aligned_cols=60  Identities=18%  Similarity=0.029  Sum_probs=40.4

Q ss_pred             HHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEEECCH
Q ss_conf             999999999987405655542101246502576597899999999999808996699980858
Q gi|254781215|r   55 QLEFMEVVDAHCLNSVNNPNPEVFKGAISAGRGIGKTTLNAWLVLWLMSTRPGISVICLANSE  117 (511)
Q Consensus        55 Q~e~l~~i~~~~~~~~~~~~~~~~r~aV~sgrG~GKS~l~a~l~lw~l~~~p~~kv~vtApt~  117 (511)
                      -.+++.++.+.+..-.  ..+....+.+-++-|+|||++++.++.-.+- .--+.+++..|+.
T Consensus       137 R~~a~~~a~~F~~~y~--~~~~~kGlyl~G~~G~GKTyL~~aian~La~-~g~~v~~v~~p~~  196 (306)
T PRK08939        137 RLDALMAALDFLEAYK--PGEKVKGLYLYGDFGVGKTYLLAAIANELAK-KGVSSTLVHFPEF  196 (306)
T ss_pred             HHHHHHHHHHHHHHHC--CCCCCCEEEEECCCCCCHHHHHHHHHHHHHH-CCCEEEEEEHHHH
T ss_conf             9999999999999737--6988877889899999899999999999998-6992999875999


No 194
>KOG1123 consensus
Probab=86.64  E-value=1  Score=23.18  Aligned_cols=149  Identities=17%  Similarity=0.089  Sum_probs=71.5

Q ss_pred             CCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEEECCHHHHHH
Q ss_conf             75655578458999999999998740565554210124650257659789999999999980899669998085899999
Q gi|254781215|r   43 TPLEGFSAPRSWQLEFMEVVDAHCLNSVNNPNPEVFKGAISAGRGIGKTTLNAWLVLWLMSTRPGISVICLANSETQLKT  122 (511)
Q Consensus        43 ~~~~~~~~P~~WQ~e~l~~i~~~~~~~~~~~~~~~~r~aV~sgrG~GKS~l~a~l~lw~l~~~p~~kv~vtApt~~Q~~~  122 (511)
                      -.|..-.-+|++|.+-|+-+..+-+...        .+ +.-+-|.|||-+.--     +.|.-..+++|.+++.-.+..
T Consensus       295 idLKPst~iRpYQEksL~KMFGNgRARS--------Gi-IVLPCGAGKtLVGvT-----Aa~tikK~clvLcts~VSVeQ  360 (776)
T KOG1123         295 IDLKPSTQIRPYQEKSLSKMFGNGRARS--------GI-IVLPCGAGKTLVGVT-----AACTIKKSCLVLCTSAVSVEQ  360 (776)
T ss_pred             CCCCCCCCCCCHHHHHHHHHHCCCCCCC--------CE-EEEECCCCCCEEEEE-----EEEEECCCEEEEECCCCCHHH
T ss_conf             6768545557537878999737885447--------61-898569987425455-----554551427999557566999


Q ss_pred             HHHHHHHHHHHHCHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECC--CCCCCCCHHHHCCCCCCEEEEECCH
Q ss_conf             99999999998550001344432222223334443211123578616985303--5755610021202676149997111
Q gi|254781215|r  123 TLWAEVSKWLSLLPNKHWFEMQSLSLHPAPWYSDVLHCSLGIDSKHYSTMCRT--YSEERPDTFVGHHNTYGMAIINDEA  200 (511)
Q Consensus       123 ilw~Ei~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~s~~~~ea~~G~h~~~~~lvI~DEA  200 (511)
                        |+.-.+++........  +..++-....+..++..+ +    .++-..+.+  -|-+....+.-+++..--|+++||-
T Consensus       361 --WkqQfk~wsti~d~~i--~rFTsd~Ke~~~~~~gvv-v----sTYsMva~t~kRS~eaek~m~~l~~~EWGllllDEV  431 (776)
T KOG1123         361 --WKQQFKQWSTIQDDQI--CRFTSDAKERFPSGAGVV-V----TTYSMVAYTGKRSHEAEKIMDFLRGREWGLLLLDEV  431 (776)
T ss_pred             --HHHHHHHHHCCCCCCE--EEEECCCCCCCCCCCCEE-E----EEEEHHHHCCCCCHHHHHHHHHHHCCEEEEEEEEHH
T ss_conf             --9999874501685545--772024454578988579-9----873131105664277999999984371016884211


Q ss_pred             HCCCHHHHHHHHHH
Q ss_conf             02997889888888
Q gi|254781215|r  201 SGTPDVINLGILGF  214 (511)
Q Consensus       201 sgI~d~i~e~i~~~  214 (511)
                      +-||..+|.-+...
T Consensus       432 HvvPA~MFRRVlsi  445 (776)
T KOG1123         432 HVVPAKMFRRVLSI  445 (776)
T ss_pred             CCCHHHHHHHHHHH
T ss_conf             11269999999999


No 195
>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=86.53  E-value=2.1  Score=21.09  Aligned_cols=53  Identities=19%  Similarity=0.266  Sum_probs=31.2

Q ss_pred             CCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHHC
Q ss_conf             756555784589999999999987405655542101246502576597899999999999808
Q gi|254781215|r   43 TPLEGFSAPRSWQLEFMEVVDAHCLNSVNNPNPEVFKGAISAGRGIGKTTLNAWLVLWLMSTR  105 (511)
Q Consensus        43 ~~~~~~~~P~~WQ~e~l~~i~~~~~~~~~~~~~~~~r~aV~sgrG~GKS~l~a~l~lw~l~~~  105 (511)
                      +.+..+.|=   ..|+-+-|.--+++.++++       -...--|+|||+++-.|+.--+.-.
T Consensus       170 gklDpviGR---d~Ei~r~i~IL~Rr~KNNp-------iLVGepGVGKTAIvEGLA~rI~~g~  222 (852)
T TIGR03346       170 GKLDPVIGR---DEEIRRTIQVLSRRTKNNP-------VLIGEPGVGKTAIVEGLAQRIVNGD  222 (852)
T ss_pred             CCCCCCCCC---HHHHHHHHHHHHHHCCCCC-------CEECCCCCCHHHHHHHHHHHHHCCC
T ss_conf             899977383---6999999999987324897-------2127999879999999999986699


No 196
>COG0003 ArsA Predicted ATPase involved in chromosome partitioning [Cell division and chromosome partitioning]
Probab=86.45  E-value=1.1  Score=23.03  Aligned_cols=133  Identities=17%  Similarity=0.132  Sum_probs=59.1

Q ss_pred             EEEEECC-CCCCHHHHHHHHHHHHHHHCCCCEEEE-E--ECCHHHHHHHHHHHHHHHHHHCHHCCCCCCCCCCCCCCCCC
Q ss_conf             2465025-765978999999999998089966999-8--08589999999999999998550001344432222223334
Q gi|254781215|r   79 KGAISAG-RGIGKTTLNAWLVLWLMSTRPGISVIC-L--ANSETQLKTTLWAEVSKWLSLLPNKHWFEMQSLSLHPAPWY  154 (511)
Q Consensus        79 r~aV~sg-rG~GKS~l~a~l~lw~l~~~p~~kv~v-t--Apt~~Q~~~ilw~Ei~k~~~~~~~~~~~~~~~~~~~~~~~~  154 (511)
                      |+..-+| =|+|||+++|.+++|.+.-... ..++ |  |.+..++.+.   |+..-.++...           .+....
T Consensus         3 riv~f~GKGGVGKTT~aaA~A~~lA~~g~k-vLlvStDPAhsL~d~f~~---elg~~~~~I~~-----------nL~a~e   67 (322)
T COG0003           3 RIVFFTGKGGVGKTTIAAATAVKLAESGKK-VLLVSTDPAHSLGDVFDL---ELGHDPRKVGP-----------NLDALE   67 (322)
T ss_pred             EEEEEECCCCCCHHHHHHHHHHHHHHCCCC-EEEEEECCCCCHHHHHCC---CCCCCHHHCCC-----------CCCEEE
T ss_conf             799993688545899999999999975990-799984898744765423---04785112588-----------875466


Q ss_pred             CCCCCCCCCCCCCEEEEEECCCCCCCCCHHHHCCC-CCCEEEEECCHHCCC--HH--HHHHHHHHHCCCCCCEEEEEECC
Q ss_conf             44321112357861698530357556100212026-761499971110299--78--89888888507998138998238
Q gi|254781215|r  155 SDVLHCSLGIDSKHYSTMCRTYSEERPDTFVGHHN-TYGMAIINDEASGTP--DV--INLGILGFLTERNANRFWIMTSN  229 (511)
Q Consensus       155 ~~~~~~~~~~~~~~~~~~~~~~s~~~~ea~~G~h~-~~~~lvI~DEAsgI~--d~--i~e~i~~~Lt~~g~~~~~i~~~n  229 (511)
                      .++....    .+.|-..        -+.+.+.-. ....-...||+...|  ++  .+..+...+.+.. --.++.=+.
T Consensus        68 iD~~~~l----~ey~~~v--------~~~~~~~~~~~~l~~~~~~e~~~~PGidE~~~l~~i~e~~~~~~-yD~IV~Dta  134 (322)
T COG0003          68 LDPEKAL----EEYWDEV--------KDYLARLLRTRGLGGIYADELATLPGIDEALALLKILEYYVSGE-YDVIVVDTA  134 (322)
T ss_pred             ECHHHHH----HHHHHHH--------HHHHHHHCCCCCCCHHHHHHHHHCCCHHHHHHHHHHHHHHHCCC-CCEEEECCC
T ss_conf             0689999----9999999--------99997412655421257889860988899999999999875268-988998489


Q ss_pred             CCCCCCHHHH
Q ss_conf             9987655676
Q gi|254781215|r  230 PRRLSGKFYE  239 (511)
Q Consensus       230 P~~~~g~fy~  239 (511)
                      ||+.+-+|-.
T Consensus       135 PTG~TLRlL~  144 (322)
T COG0003         135 PTGHTLRLLS  144 (322)
T ss_pred             CHHHHHHHHC
T ss_conf             7087888741


No 197
>pfam09848 DUF2075 Uncharacterized conserved protein (DUF2075). This domain, found in various prokaryotic proteins (including putative ATP/GTP binding proteins), has no known function.
Probab=86.41  E-value=2.2  Score=21.05  Aligned_cols=38  Identities=26%  Similarity=0.278  Sum_probs=24.2

Q ss_pred             EEEECCCCCCHHHHHHHHHHHHHHHCCC-CEEEEEECCH
Q ss_conf             4650257659789999999999980899-6699980858
Q gi|254781215|r   80 GAISAGRGIGKTTLNAWLVLWLMSTRPG-ISVICLANSE  117 (511)
Q Consensus        80 ~aV~sgrG~GKS~l~a~l~lw~l~~~p~-~kv~vtApt~  117 (511)
                      +-|..|=|+|||.++.-++.-......+ ..++++-|..
T Consensus         4 ~~V~G~pGtGKTvv~l~l~~~l~~~~~~~~~~~l~~N~~   42 (348)
T pfam09848         4 FLVTGGPGTGKTVVALNLFAELSDSDLGRTAVFLSGNHP   42 (348)
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHHCCCCCCEEEEECCHH
T ss_conf             999777993899999999999864402682089957866


No 198
>cd02035 ArsA ArsA ATPase functionas as an efflux pump located on the inner membrane of the cell. This ATP-driven oxyanion pump catalyzes the extrusion of arsenite, antimonite and arsenate. Maintenance of a low intracellular concentration of oxyanion produces resistance to the toxic agents. The pump is composed of two subunits, the catalytic ArsA subunit and the membrane subunit ArsB, which are encoded by arsA and arsB genes respectively. Arsenic efflux in bacteria is catalyzed by either ArsB alone or by ArsAB complex. The ATP-coupled pump, however, is more efficient. ArsA is composed of two homologous halves, A1 and A2, connected by a short linker sequence.
Probab=86.33  E-value=0.99  Score=23.20  Aligned_cols=27  Identities=33%  Similarity=0.460  Sum_probs=22.3

Q ss_pred             CCCCCHHHHHHHHHHHHHHHCCCCEEEEE
Q ss_conf             57659789999999999980899669998
Q gi|254781215|r   85 GRGIGKTTLNAWLVLWLMSTRPGISVICL  113 (511)
Q Consensus        85 grG~GKS~l~a~l~lw~l~~~p~~kv~vt  113 (511)
                      ==|+|||++++.+++..+-.  |.|++++
T Consensus         7 KGGVGKTTvAaalA~~lA~~--G~rvLlv   33 (217)
T cd02035           7 KGGVGKTTIAAATAVRLAEE--GKKVLLV   33 (217)
T ss_pred             CCCCCHHHHHHHHHHHHHHC--CCEEEEE
T ss_conf             99661999999999999968--9949999


No 199
>pfam02374 ArsA_ATPase Anion-transporting ATPase. This Pfam family represents a conserved domain, which is sometimes repeated, in an anion-transporting ATPase. The ATPase is involved in the removal of arsenate, antimonite, and arsenate from the cell.
Probab=86.32  E-value=1.7  Score=21.79  Aligned_cols=31  Identities=26%  Similarity=0.407  Sum_probs=24.2

Q ss_pred             EECCCCCCHHHHHHHHHHHHHHHCCCCEEEEEE
Q ss_conf             502576597899999999999808996699980
Q gi|254781215|r   82 ISAGRGIGKTTLNAWLVLWLMSTRPGISVICLA  114 (511)
Q Consensus        82 V~sgrG~GKS~l~a~l~lw~l~~~p~~kv~vtA  114 (511)
                      +..-=|+|||+++|.++++.+-  .+.+++++.
T Consensus         6 ~~GKGGVGKTT~AaA~A~~~A~--~G~rvLlvS   36 (304)
T pfam02374         6 FGGKGGVGKTTVSCATAVRLSE--QGKKVLLVS   36 (304)
T ss_pred             EECCCCCCHHHHHHHHHHHHHH--CCCEEEEEE
T ss_conf             9579857489999999999995--899299994


No 200
>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=86.16  E-value=2.2  Score=21.07  Aligned_cols=49  Identities=27%  Similarity=0.350  Sum_probs=34.7

Q ss_pred             HHHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEEECC
Q ss_conf             999999999998740565554210124650257659789999999999980899669998085
Q gi|254781215|r   54 WQLEFMEVVDAHCLNSVNNPNPEVFKGAISAGRGIGKTTLNAWLVLWLMSTRPGISVICLANS  116 (511)
Q Consensus        54 WQ~e~l~~i~~~~~~~~~~~~~~~~r~aV~sgrG~GKS~l~a~l~lw~l~~~p~~kv~vtApt  116 (511)
                      =|+++|........           -+.|+.+.|.|||+++..++-+.   .+..+++++-.+
T Consensus        13 ~~~~~L~~~v~~~~-----------nIlIsG~tGSGKTTll~al~~~i---~~~~rivtiEd~   61 (186)
T cd01130          13 LQAAYLWLAVEARK-----------NILISGGTGSGKTTLLNALLAFI---PPDERIITIEDT   61 (186)
T ss_pred             HHHHHHHHHHHCCC-----------CEEEECCCCCCHHHHHHHHHHHC---CCCCCEEEECCC
T ss_conf             99999999998599-----------89998999998999999999613---345645984153


No 201
>PRK11034 clpA ATP-dependent Clp protease ATP-binding subunit; Provisional
Probab=86.15  E-value=2.2  Score=20.96  Aligned_cols=52  Identities=19%  Similarity=0.362  Sum_probs=29.0

Q ss_pred             CCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHH
Q ss_conf             75655578458999999999998740565554210124650257659789999999999980
Q gi|254781215|r   43 TPLEGFSAPRSWQLEFMEVVDAHCLNSVNNPNPEVFKGAISAGRGIGKTTLNAWLVLWLMST  104 (511)
Q Consensus        43 ~~~~~~~~P~~WQ~e~l~~i~~~~~~~~~~~~~~~~r~aV~sgrG~GKS~l~a~l~lw~l~~  104 (511)
                      +.+..+.|=   ..|+-+-|.--+++.++++       -...--|+|||+++-.|+.--+.-
T Consensus       183 gklDPviGR---~~Ei~r~i~iL~Rr~KNNp-------iLvGepGVGKTAIvEGLA~rI~~g  234 (758)
T PRK11034        183 GGIDPLIGR---EKELERAIQVLCRRRKNNP-------LLVGESGVGKTAIAEGLAWRIVQG  234 (758)
T ss_pred             CCCCCCCCC---HHHHHHHHHHHHHHCCCCC-------EEECCCCCCHHHHHHHHHHHHHCC
T ss_conf             899987384---8999999999976325896-------021699986999999999999738


No 202
>cd02025 PanK Pantothenate kinase (PanK) catalyzes the phosphorylation of pantothenic acid to form 4'-phosphopantothenic, which is the first of five steps in coenzyme A (CoA) biosynthetic pathway. The reaction carried out by this enzyme is a key regulatory point in CoA biosynthesis.
Probab=86.10  E-value=1.4  Score=22.17  Aligned_cols=34  Identities=21%  Similarity=0.095  Sum_probs=21.7

Q ss_pred             EEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEE
Q ss_conf             4650257659789999999999980899669998
Q gi|254781215|r   80 GAISAGRGIGKTTLNAWLVLWLMSTRPGISVICL  113 (511)
Q Consensus        80 ~aV~sgrG~GKS~l~a~l~lw~l~~~p~~kv~vt  113 (511)
                      ++|++|-|+|||+++..+.--.....++.+|.++
T Consensus         2 IGIaG~sgSGKST~a~~l~~~l~~~~~~~~v~ii   35 (220)
T cd02025           2 IGIAGSVAVGKSTTARVLQALLSRWPDHPNVELI   35 (220)
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHHCCCCCCEEEE
T ss_conf             8978899877999999999986002699948999


No 203
>PRK10037 cell division protein; Provisional
Probab=85.75  E-value=1.8  Score=21.54  Aligned_cols=39  Identities=23%  Similarity=0.280  Sum_probs=27.0

Q ss_pred             CEEEEEECCC-CCCHHHHHHHHHHHHHHHCCCCEEEEEECCH
Q ss_conf             0124650257-6597899999999999808996699980858
Q gi|254781215|r   77 VFKGAISAGR-GIGKTTLNAWLVLWLMSTRPGISVICLANSE  117 (511)
Q Consensus        77 ~~r~aV~sgr-G~GKS~l~a~l~lw~l~~~p~~kv~vtApt~  117 (511)
                      |..++|.|.| |+|||+++|.|+.-..  +-+.+|+++=-.-
T Consensus         1 M~iial~s~kGGVGkTTltAnLA~aL~--~~g~~VlaID~dp   40 (250)
T PRK10037          1 MAILGLQGVRGGVGTTSITAALAWSLQ--MLGENVLVIDACP   40 (250)
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHHHHH--HCCCCEEEEECCH
T ss_conf             937999607888768999999999999--7799189995782


No 204
>PRK08233 hypothetical protein; Provisional
Probab=85.71  E-value=1.2  Score=22.66  Aligned_cols=31  Identities=29%  Similarity=0.182  Sum_probs=23.4

Q ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEE
Q ss_conf             24650257659789999999999980899669998
Q gi|254781215|r   79 KGAISAGRGIGKTTLNAWLVLWLMSTRPGISVICL  113 (511)
Q Consensus        79 r~aV~sgrG~GKS~l~a~l~lw~l~~~p~~kv~vt  113 (511)
                      =++|++|.|.|||+++..++--    .|++.++..
T Consensus         5 IIgIaGgSgSGKTtla~~l~~~----l~~~~~~~~   35 (182)
T PRK08233          5 IITIAAVSGGGKTTLTERLTHK----LKNSKALYF   35 (182)
T ss_pred             EEEEECCCCCCHHHHHHHHHHH----CCCCEEEEE
T ss_conf             9999688867899999999997----467758996


No 205
>CHL00175 minD septum-site determining protein; Validated
Probab=85.68  E-value=1.5  Score=22.01  Aligned_cols=33  Identities=33%  Similarity=0.418  Sum_probs=26.2

Q ss_pred             EEEEECCC-CCCHHHHHHHHHHHHHHHCCCCEEEEE
Q ss_conf             24650257-659789999999999980899669998
Q gi|254781215|r   79 KGAISAGR-GIGKTTLNAWLVLWLMSTRPGISVICL  113 (511)
Q Consensus        79 r~aV~sgr-G~GKS~l~a~l~lw~l~~~p~~kv~vt  113 (511)
                      =++|.||. |+|||++++.++.-.+.  -+.+|+++
T Consensus        15 iIaV~s~KGGVGKTT~a~NLa~aLA~--~G~kVlli   48 (279)
T CHL00175         15 IIVITSGKGGVGKTTTTANLGMSIAR--LGYRVALI   48 (279)
T ss_pred             EEEEECCCCCCCHHHHHHHHHHHHHH--CCCCEEEE
T ss_conf             99997489984489999999999997--89988999


No 206
>KOG0340 consensus
Probab=85.67  E-value=2.4  Score=20.81  Aligned_cols=92  Identities=23%  Similarity=0.144  Sum_probs=62.0

Q ss_pred             HH-HHHCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHHCCCC-
Q ss_conf             67-7642145577756555784589999999999987405655542101246502576597899999999999808996-
Q gi|254781215|r   31 FV-LHFFPWGEKGTPLEGFSAPRSWQLEFMEVVDAHCLNSVNNPNPEVFKGAISAGRGIGKTTLNAWLVLWLMSTRPGI-  108 (511)
Q Consensus        31 ~~-~~~~~w~~~~~~~~~~~~P~~WQ~e~l~~i~~~~~~~~~~~~~~~~r~aV~sgrG~GKS~l~a~l~lw~l~~~p~~-  108 (511)
                      |. |+..||-.+.-.--+.++|-+-|.-.+-.|-+.+            .+.=.+-.|+|||+..|.=++--+.-.|.+ 
T Consensus         9 F~~LGl~~Wlve~l~~l~i~~pTpiQ~~cIpkILeGr------------dcig~AkTGsGKT~AFaLPil~rLsedP~gi   76 (442)
T KOG0340           9 FSILGLSPWLVEQLKALGIKKPTPIQQACIPKILEGR------------DCIGCAKTGSGKTAAFALPILNRLSEDPYGI   76 (442)
T ss_pred             HHHCCCCHHHHHHHHHHCCCCCCCHHHHHHHHHHCCC------------CCCCCCCCCCCCCHHHHHHHHHHHCCCCCCC
T ss_conf             4440763899999998358899826765248785466------------3103134688741122278777613388760


Q ss_pred             EEEEEECCHHHHHHHHHHHHHHHHHHCH
Q ss_conf             6999808589999999999999998550
Q gi|254781215|r  109 SVICLANSETQLKTTLWAEVSKWLSLLP  136 (511)
Q Consensus       109 kv~vtApt~~Q~~~ilw~Ei~k~~~~~~  136 (511)
                      -.++..||..-+..|  +|-...+..+.
T Consensus        77 FalvlTPTrELA~Qi--aEQF~alGk~l  102 (442)
T KOG0340          77 FALVLTPTRELALQI--AEQFIALGKLL  102 (442)
T ss_pred             EEEEECCHHHHHHHH--HHHHHHHCCCC
T ss_conf             699954528888888--89999845645


No 207
>cd00550 ArsA_ATPase Oxyanion-translocating ATPase (ArsA).  This ATPase is involved in transport of arsenite, antimonite or other oxyanions across biological membranes in all three kingdoms of life.  ArsA contains a highly conserved AAA motif present in the AAA+ ATPase superfamily associated with a variety of cellular activities.   To form a functional ATP-driven pump, ArsA interacts with the permease ArsB, which is a channel-forming integral membrane protein. One of the most interesting features of ArsA is the allosteric activation by its transport substrates.  A divalent cation, typically Mg2+, is required for its enzymatic activity.
Probab=85.48  E-value=1.2  Score=22.63  Aligned_cols=29  Identities=31%  Similarity=0.462  Sum_probs=23.0

Q ss_pred             CCCCCCHHHHHHHHHHHHHHHCCCCEEEEEE
Q ss_conf             2576597899999999999808996699980
Q gi|254781215|r   84 AGRGIGKTTLNAWLVLWLMSTRPGISVICLA  114 (511)
Q Consensus        84 sgrG~GKS~l~a~l~lw~l~~~p~~kv~vtA  114 (511)
                      .==|+|||+++|.+++..+..  |.||+++.
T Consensus         7 GKGGVGKTT~AaalA~~lA~~--G~kVLlvs   35 (254)
T cd00550           7 GKGGVGKTTISAATAVRLAEQ--GKKVLLVS   35 (254)
T ss_pred             CCCCCCHHHHHHHHHHHHHHC--CCEEEEEE
T ss_conf             898554899999999999968--99499995


No 208
>COG4962 CpaF Flp pilus assembly protein, ATPase CpaF [Intracellular trafficking and secretion]
Probab=85.47  E-value=1.8  Score=21.51  Aligned_cols=56  Identities=21%  Similarity=0.322  Sum_probs=29.5

Q ss_pred             EEEEECCCEEEEEEECCCC----CHHHHHHHHHHHHHHCCCCEEEEEECCCCHHHHHHHHHCC
Q ss_conf             9998227558998732778----9889999999999861888299800687636889898649
Q gi|254781215|r  333 VVVLRRGPVIEHLFDWSKT----DLRTTNNKISGLVEKYRPDAIIIDANNTGARTCDYLEMLG  391 (511)
Q Consensus       333 vi~~r~G~~v~~~~~~~~~----d~~~~a~~i~~~~~~~~~~~i~iD~~GvG~gV~d~L~~~g  391 (511)
                      .+...+ .++..+++.+..    .-..+.+.+++ +-+.+|+.|+|-. --|.-+.|.|+.+|
T Consensus       211 ELql~~-ph~vrL~TR~~n~Eg~gevtm~dLvkn-~LRmRPDRIiVGE-VRG~Ea~dLL~Amn  270 (355)
T COG4962         211 ELQLAH-PHVVRLETRPPNVEGTGEVTMRDLVKN-ALRMRPDRIIVGE-VRGVEALDLLQAMN  270 (355)
T ss_pred             HHCCCC-CCEEEEEECCCCCCCCCEEEHHHHHHH-HHHCCCCCEEEEE-ECCCCHHHHHHHHC
T ss_conf             644699-855788634887777655889999998-7532865368888-60705999998752


No 209
>PRK10818 cell division inhibitor MinD; Provisional
Probab=85.30  E-value=1.7  Score=21.80  Aligned_cols=33  Identities=27%  Similarity=0.421  Sum_probs=26.7

Q ss_pred             EEEEECCC-CCCHHHHHHHHHHHHHHHCCCCEEEEE
Q ss_conf             24650257-659789999999999980899669998
Q gi|254781215|r   79 KGAISAGR-GIGKTTLNAWLVLWLMSTRPGISVICL  113 (511)
Q Consensus        79 r~aV~sgr-G~GKS~l~a~l~lw~l~~~p~~kv~vt  113 (511)
                      =++|.||. |+|||+++..++..++.  -+.+|+++
T Consensus         4 vIaV~s~KGGVGKTT~avNLA~aLA~--~G~kVlli   37 (270)
T PRK10818          4 IIVVTSGKGGVGKTTSSAAIATGLAQ--KGKKTVVI   37 (270)
T ss_pred             EEEEECCCCCCCHHHHHHHHHHHHHH--CCCCEEEE
T ss_conf             99997899984189999999999997--79968999


No 210
>COG1647 Esterase/lipase [General function prediction only]
Probab=85.03  E-value=2.5  Score=20.62  Aligned_cols=94  Identities=13%  Similarity=0.155  Sum_probs=56.8

Q ss_pred             HHHHHCCCCCCCCCCCCC--CCCHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHHCCCC
Q ss_conf             677642145577756555--784589999999999987405655542101246502576597899999999999808996
Q gi|254781215|r   31 FVLHFFPWGEKGTPLEGF--SAPRSWQLEFMEVVDAHCLNSVNNPNPEVFKGAISAGRGIGKTTLNAWLVLWLMSTRPGI  108 (511)
Q Consensus        31 ~~~~~~~w~~~~~~~~~~--~~P~~WQ~e~l~~i~~~~~~~~~~~~~~~~r~aV~sgrG~GKS~l~a~l~lw~l~~~p~~  108 (511)
                      |--++=-.--||++.+.|  ++|++|=++++..+..-...+-.       .++|..      =.+...+++|.+..+|..
T Consensus        43 yTv~aP~ypGHG~~~e~fl~t~~~DW~~~v~d~Y~~L~~~gy~-------eI~v~G------lSmGGv~alkla~~~p~K  109 (243)
T COG1647          43 YTVYAPRYPGHGTLPEDFLKTTPRDWWEDVEDGYRDLKEAGYD-------EIAVVG------LSMGGVFALKLAYHYPPK  109 (243)
T ss_pred             CEEECCCCCCCCCCHHHHHCCCHHHHHHHHHHHHHHHHHCCCC-------EEEEEE------ECCHHHHHHHHHHHCCCC
T ss_conf             5574688899999989985079999999999999999875798-------589985------120369999998537955


Q ss_pred             EEE-EEECCHHHHHHHHHHHHHHHHHHCHH
Q ss_conf             699-98085899999999999999985500
Q gi|254781215|r  109 SVI-CLANSETQLKTTLWAEVSKWLSLLPN  137 (511)
Q Consensus       109 kv~-vtApt~~Q~~~ilw~Ei~k~~~~~~~  137 (511)
                      +++ ++||+..--..++-.-+.++.++.+.
T Consensus       110 ~iv~m~a~~~~k~~~~iie~~l~y~~~~kk  139 (243)
T COG1647         110 KIVPMCAPVNVKSWRIIIEGLLEYFRNAKK  139 (243)
T ss_pred             CEEEECCCCCCCCCHHHHHHHHHHHHHHHH
T ss_conf             236404776655410345789999998565


No 211
>pfam00308 Bac_DnaA Bacterial dnaA protein.
Probab=85.01  E-value=2.1  Score=21.08  Aligned_cols=35  Identities=29%  Similarity=0.373  Sum_probs=29.6

Q ss_pred             EEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEEE
Q ss_conf             46502576597899999999999808996699980
Q gi|254781215|r   80 GAISAGRGIGKTTLNAWLVLWLMSTRPGISVICLA  114 (511)
Q Consensus        80 ~aV~sgrG~GKS~l~a~l~lw~l~~~p~~kv~vtA  114 (511)
                      +.+-+..|+|||+|...++.-..-..++.++++..
T Consensus        37 l~i~G~~G~GKTHLLqA~~~~~~~~~~~~~v~yl~   71 (219)
T pfam00308        37 LFIYGGVGLGKTHLLHAIGNYALRNFPNLRVVYLT   71 (219)
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEEE
T ss_conf             69988999988899999999999849998288843


No 212
>PRK07309 aromatic amino acid aminotransferase; Validated
Probab=84.96  E-value=2.6  Score=20.61  Aligned_cols=25  Identities=16%  Similarity=0.050  Sum_probs=14.7

Q ss_pred             HHHHHHHHCCCCEEEEEECCHHHHH
Q ss_conf             9999998089966999808589999
Q gi|254781215|r   97 LVLWLMSTRPGISVICLANSETQLK  121 (511)
Q Consensus        97 l~lw~l~~~p~~kv~vtApt~~Q~~  121 (511)
                      .++-.+++.||-.|++..|++....
T Consensus       105 ~~~~~~l~~pGD~Vli~~P~Y~~~~  129 (390)
T PRK07309        105 SASLTAILEPGDKVLLPAPAYPGYE  129 (390)
T ss_pred             HHHHHHHCCCCCEEEECCCCCHHHH
T ss_conf             9999996699898998378744199


No 213
>PRK11054 helD DNA helicase IV; Provisional
Probab=84.70  E-value=2.6  Score=20.53  Aligned_cols=78  Identities=18%  Similarity=0.227  Sum_probs=51.9

Q ss_pred             HHHHHHHHHHHHHHHHCCCCCCCCCC---------EEEEEECCCCCCHHHHHHHHHHHHHHHC--CCCEEEEEECCHHHH
Q ss_conf             58999999999998740565554210---------1246502576597899999999999808--996699980858999
Q gi|254781215|r   52 RSWQLEFMEVVDAHCLNSVNNPNPEV---------FKGAISAGRGIGKTTLNAWLVLWLMSTR--PGISVICLANSETQL  120 (511)
Q Consensus        52 ~~WQ~e~l~~i~~~~~~~~~~~~~~~---------~r~aV~sgrG~GKS~l~a~l~lw~l~~~--p~~kv~vtApt~~Q~  120 (511)
                      ..|....|....+...+....++..-         -.+-|.||=|+|||..+..-+.|.+-..  ++.+|++.+=|..-+
T Consensus       175 ~~~~~~~l~~~~~fF~~~es~PLn~~Qr~Avi~~ed~~LVLAGAGSGKT~vLt~RiayLI~~g~~~P~~ILaLTFT~kAA  254 (684)
T PRK11054        175 QAWTEAMLEEWADFFSQVESSPLNPSQARAVVNGEDSLLVLAGAGSGKTSVLVARAGWLLARGQAQPEQILLLAFGRKAA  254 (684)
T ss_pred             HHHHHHHHHHHHHHHHHHCCCCCCHHHHHHEEECCCCEEEEECCCCCCHHHHHHHHHHHHHCCCCCHHHEEEEECCHHHH
T ss_conf             99999999999999887417999989995727479964898338997077999999999975999866778686349999


Q ss_pred             HHHHHHHHHHHHHH
Q ss_conf             99999999999985
Q gi|254781215|r  121 KTTLWAEVSKWLSL  134 (511)
Q Consensus       121 ~~ilw~Ei~k~~~~  134 (511)
                      .     |++..++.
T Consensus       255 ~-----EMreRl~~  263 (684)
T PRK11054        255 E-----EMDERIRE  263 (684)
T ss_pred             H-----HHHHHHHH
T ss_conf             9-----99999997


No 214
>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=84.63  E-value=2.2  Score=21.04  Aligned_cols=63  Identities=21%  Similarity=0.262  Sum_probs=42.3

Q ss_pred             HHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHHH--HCCCCEEEEEECCHHHHHHHHHHHHHHHH
Q ss_conf             9999999999874056555421012465025765978999999999998--08996699980858999999999999999
Q gi|254781215|r   55 QLEFMEVVDAHCLNSVNNPNPEVFKGAISAGRGIGKTTLNAWLVLWLMS--TRPGISVICLANSETQLKTTLWAEVSKWL  132 (511)
Q Consensus        55 Q~e~l~~i~~~~~~~~~~~~~~~~r~aV~sgrG~GKS~l~a~l~lw~l~--~~p~~kv~vtApt~~Q~~~ilw~Ei~k~~  132 (511)
                      |.++...+..          |    +-|.||=|+|||.++..-|.+.+.  ++++..|+.+.=|=.-|+     |++..+
T Consensus         8 Q~~AV~Y~~G----------P----lLVLAGAGSGKT~VI~~KIayLi~~cgY~a~~IaAvTFTNKAA~-----EMkERV   68 (677)
T TIGR01074         8 QQEAVEYVGG----------P----LLVLAGAGSGKTRVITNKIAYLIQNCGYKAKNIAAVTFTNKAAR-----EMKERV   68 (677)
T ss_pred             HHHHHHHHCC----------C----CEEECCCCCCCCHHHHHHHHHHHHHCCCCCCCEEEEECCHHHHH-----HHHHHH
T ss_conf             7999986158----------7----14651777786357888999987515878761689735237779-----999999


Q ss_pred             HHCH
Q ss_conf             8550
Q gi|254781215|r  133 SLLP  136 (511)
Q Consensus       133 ~~~~  136 (511)
                      ....
T Consensus        69 A~~L   72 (677)
T TIGR01074        69 AKTL   72 (677)
T ss_pred             HHHC
T ss_conf             8522


No 215
>TIGR01425 SRP54_euk signal recognition particle protein SRP54; InterPro: IPR006325    The signal recognition particle (SRP) is a multimeric protein, which along with its conjugate receptor (SR), is involved in targeting secretory proteins to the rough endoplasmic reticulum (RER) membrane in eukaryotes, or to the plasma membrane in prokaryotes , . SRP recognises the signal sequence of the nascent polypeptide on the ribosome, retards its elongation, and docks the SRP-ribosome-polypeptide complex to the RER membrane via the SR receptor. SRP consists of six polypeptides (SRP9, SRP14, SRP19, SRP54, SRP68 and SRP72) and a single 300 nucleotide 7S RNA molecule. The RNA component catalyses the interaction of SRP with its SR receptor . In higher eukaryotes, the SRP complex consists of the Alu domain and the S domain linked by the SRP RNA. The Alu domain consists of a heterodimer of SRP9 and SRP14 bound to the 5' and 3' terminal sequences of SRP RNA. This domain is necessary for retarding the elongation of the nascent polypeptide chain, which gives SRP time to dock the ribosome-polypeptide complex to the RER membrane.    This entry represents the 54 kDa SRP54 component, a GTP-binding protein that interacts with the signal sequence when it emerges from the ribosome. SRP54 of the signal recognition particle has a three-domain structure: an N-terminal helical bundle domain, a GTPase domain, and the M-domain that binds the 7s RNA and also binds the signal sequence. The extreme C-terminal region is glycine-rich and lower in complexity and poorly conserved between species.; GO: 0005525 GTP binding, 0008312 7S RNA binding, 0006614 SRP-dependent cotranslational protein targeting to membrane, 0048500 signal recognition particle.
Probab=84.60  E-value=2.7  Score=20.50  Aligned_cols=48  Identities=15%  Similarity=0.091  Sum_probs=28.6

Q ss_pred             CCCCCCHHHHHHHHHHHHHHHCCCCEEEEEECCHHHHHHHHHHHHHHHHHHC
Q ss_conf             2576597899999999999808996699980858999999999999999855
Q gi|254781215|r   84 AGRGIGKTTLNAWLVLWLMSTRPGISVICLANSETQLKTTLWAEVSKWLSLL  135 (511)
Q Consensus        84 sgrG~GKS~l~a~l~lw~l~~~p~~kv~vtApt~~Q~~~ilw~Ei~k~~~~~  135 (511)
                      .=.|.||||.++=|++||=-- -..-.+|+|-|.+-   .-|-.|+.-..++
T Consensus       128 GLQGaGKTTtctKLA~YYk~r-GfK~~lvCADTFRA---GAFdQLkqNA~kA  175 (453)
T TIGR01425       128 GLQGAGKTTTCTKLAYYYKRR-GFKPALVCADTFRA---GAFDQLKQNATKA  175 (453)
T ss_pred             ECCCCCHHHHHHHHHHHHHCC-CCCEEEECCCCCCC---CHHHHHHHHHHHC
T ss_conf             214887156687877776326-64325651775423---2489998747644


No 216
>PRK10689 transcription-repair coupling factor; Provisional
Probab=84.56  E-value=2.7  Score=20.49  Aligned_cols=55  Identities=15%  Similarity=0.177  Sum_probs=27.8

Q ss_pred             HHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEEECCH
Q ss_conf             999999999987405655542101246502576597899999999999808996699980858
Q gi|254781215|r   55 QLEFMEVVDAHCLNSVNNPNPEVFKGAISAGRGIGKTTLNAWLVLWLMSTRPGISVICLANSE  117 (511)
Q Consensus        55 Q~e~l~~i~~~~~~~~~~~~~~~~r~aV~sgrG~GKS~l~a~l~lw~l~~~p~~kv~vtApt~  117 (511)
                      |..++.+|-........+|     | -|-.==|+|||.++-..+.-.+  ..+..|++.+||-
T Consensus       605 Ql~AI~eV~~DMes~~PMD-----R-LiCGDVGfGKTEVA~RAAFkav--~~gkQVavlvPTT  659 (1148)
T PRK10689        605 QAQAINAVLSDMCQPLAMD-----R-LVCGDVGFGKTEVAMRAAFLAV--ENHKQVAVLVPTT  659 (1148)
T ss_pred             HHHHHHHHHHHHHCCCCCC-----E-EEECCCCCCHHHHHHHHHHHHH--HCCCEEEEEECCC
T ss_conf             9999999987763886774-----1-5676888877999999999999--6398089983662


No 217
>TIGR02545 ATP_syn_fliI flagellar protein export ATPase FliI; InterPro: IPR013379    FliI proteins are involved in bacterial flagellum systems, acting to drive protein export for flagellar biosynthesis. The most closely related proteins are the YscN proteins of bacterial type III secretion systems.; GO: 0016887 ATPase activity, 0001539 ciliary or flagellar motility, 0009296 flagellum biogenesis, 0009288 flagellin-based flagellum.
Probab=84.42  E-value=0.97  Score=23.26  Aligned_cols=36  Identities=8%  Similarity=0.243  Sum_probs=19.1

Q ss_pred             HHHHHHHHHHHHHCC---CC----------EEEEEECCCCHHHHHHHHH
Q ss_conf             899999999998618---88----------2998006876368898986
Q gi|254781215|r  354 RTTNNKISGLVEKYR---PD----------AIIIDANNTGARTCDYLEM  389 (511)
Q Consensus       354 ~~~a~~i~~~~~~~~---~~----------~i~iD~~GvG~gV~d~L~~  389 (511)
                      +-+-..+.++.++=.   ..          .|+||++-.-.+|.|..|.
T Consensus       282 PSVF~~Lp~L~ERaG~~p~~~~~GsITa~yTVLVeGDD~~ePiAD~~Rg  330 (439)
T TIGR02545       282 PSVFSELPRLLERAGIVPGAKGGGSITAFYTVLVEGDDMNEPIADAVRG  330 (439)
T ss_pred             CHHHHHHHHHHHHHCCCCCCCCCCEEEEEEEEEEECCCCCCHHHHHHHH
T ss_conf             0489999999987086469888730568999987368998737877500


No 218
>PRK07324 transaminase; Validated
Probab=84.34  E-value=2.7  Score=20.43  Aligned_cols=57  Identities=25%  Similarity=0.230  Sum_probs=36.1

Q ss_pred             HHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEEECCHHHHHHHH
Q ss_conf             999999999874056555421012465025765978999999999998089966999808589999999
Q gi|254781215|r   56 LEFMEVVDAHCLNSVNNPNPEVFKGAISAGRGIGKTTLNAWLVLWLMSTRPGISVICLANSETQLKTTL  124 (511)
Q Consensus        56 ~e~l~~i~~~~~~~~~~~~~~~~r~aV~sgrG~GKS~l~a~l~lw~l~~~p~~kv~vtApt~~Q~~~il  124 (511)
                      -++-++|+....+. .   |.  .|.|.+|      ...|..++-.+++.||-.|+|..|++.++..+.
T Consensus        65 ~~LR~~Ia~~y~~v-~---~d--~IlvT~G------a~~Al~l~~~~l~~pGD~Viv~~P~Y~~~~~~~  121 (373)
T PRK07324         65 PEFKEAVASLYQNV-K---PD--NILQTNG------ATGANHLVLYALIEPGDHVISVYPTYQQLYDIP  121 (373)
T ss_pred             HHHHHHHHHHHCCC-C---HH--HEEECCC------HHHHHHHHHHHHCCCCCEEEECCCCCHHHHHHH
T ss_conf             99999999986699-8---67--8898687------899999999997599998998899857799999


No 219
>pfam03205 MobB Molybdopterin guanine dinucleotide synthesis protein B. This protein contains a P-loop.
Probab=84.15  E-value=2.3  Score=20.84  Aligned_cols=33  Identities=27%  Similarity=0.269  Sum_probs=26.0

Q ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEE
Q ss_conf             24650257659789999999999980899669998
Q gi|254781215|r   79 KGAISAGRGIGKTTLNAWLVLWLMSTRPGISVICL  113 (511)
Q Consensus        79 r~aV~sgrG~GKS~l~a~l~lw~l~~~p~~kv~vt  113 (511)
                      ++.|....++|||+++..|+.+..-.  +.++++.
T Consensus         2 ~v~i~G~~~sGKttl~~~L~~~~~~~--g~~~~~~   34 (122)
T pfam03205         2 IVLVVGPKDSGKTTLIRKLLNYLKRR--GYRVAVV   34 (122)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHC--CCCEEEE
T ss_conf             79999489998999999999999987--9944899


No 220
>PTZ00301 uridine kinase; Provisional
Probab=84.03  E-value=2.3  Score=20.90  Aligned_cols=26  Identities=35%  Similarity=0.382  Sum_probs=19.9

Q ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHH
Q ss_conf             24650257659789999999999980
Q gi|254781215|r   79 KGAISAGRGIGKTTLNAWLVLWLMST  104 (511)
Q Consensus        79 r~aV~sgrG~GKS~l~a~l~lw~l~~  104 (511)
                      =++|++|-|.|||+++..++--+...
T Consensus         5 iIgIaGgSgSGKTT~a~~i~~~l~~~   30 (210)
T PTZ00301          5 VIGISGASGSGKSSLSTNIVSELMAH   30 (210)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHH
T ss_conf             99996887678999999999998761


No 221
>cd02034 CooC The accessory protein CooC, which contains a nucleotide-binding domain (P-loop) near the N-terminus, participates in the maturation of the nickel center of carbon monoxide dehydrogenase (CODH). CODH from Rhodospirillum rubrum catalyzes the reversible oxidation of CO to CO2. CODH contains a nickel-iron-sulfur cluster (C-center) and an iron-sulfur cluster (B-center). CO oxidation occurs at the C-center. Three accessory proteins encoded by cooCTJ genes are involved in nickel incorporation into a nickel site. CooC functions as a nickel insertase that mobilizes nickel to apoCODH using energy released from ATP hydrolysis. CooC is a homodimer and has NTPase activities. Mutation at the P-loop abolishs its function.
Probab=84.00  E-value=2.4  Score=20.77  Aligned_cols=36  Identities=36%  Similarity=0.534  Sum_probs=27.3

Q ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEEECC
Q ss_conf             24650257659789999999999980899669998085
Q gi|254781215|r   79 KGAISAGRGIGKTTLNAWLVLWLMSTRPGISVICLANS  116 (511)
Q Consensus        79 r~aV~sgrG~GKS~l~a~l~lw~l~~~p~~kv~vtApt  116 (511)
                      |++|+.==|+|||++++.++.+++-.  +.+++++-..
T Consensus         1 kia~~GKGGvGKtt~~~~la~~l~~~--g~~vl~iD~D   36 (116)
T cd02034           1 KIAITGKGGVGKTTIAALLARYLAEK--GKPVLAIDAD   36 (116)
T ss_pred             CEEEECCCCCCHHHHHHHHHHHHHHC--CCEEEEEECC
T ss_conf             97898899774999999999999978--9969999898


No 222
>CHL00081 chlI Mg-protoporyphyrin IX chelatase
Probab=83.67  E-value=2.9  Score=20.25  Aligned_cols=39  Identities=26%  Similarity=0.157  Sum_probs=28.6

Q ss_pred             HHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCCCHHHHHHHHHH
Q ss_conf             999999999987405655542101246502576597899999999
Q gi|254781215|r   55 QLEFMEVVDAHCLNSVNNPNPEVFKGAISAGRGIGKTTLNAWLVL   99 (511)
Q Consensus        55 Q~e~l~~i~~~~~~~~~~~~~~~~r~aV~sgrG~GKS~l~a~l~l   99 (511)
                      |.++-.++--...++.      +--|.|...+|+|||+++=.++-
T Consensus        17 Qe~~k~aLll~av~p~------iGgVLi~G~~GtgKStlvRala~   55 (347)
T CHL00081         17 QEEMKLALLLNVIDPK------IGGVMIMGDRGTGKSTTIRALVD   55 (347)
T ss_pred             HHHHHHHHHHHHCCCC------CCEEEEECCCCCCHHHHHHHHHH
T ss_conf             4999999999825788------78699878998749999999998


No 223
>cd02037 MRP-like MRP (Multiple Resistance and pH adaptation) is a homologue of the Fer4_NifH superfamily. Like the other members of the superfamily, MRP contains a ATP-binding domain at the N-termini. It is found in bacteria as a membrane-spanning protein and functions as a Na+/H+ antiporter.
Probab=83.57  E-value=2.3  Score=20.89  Aligned_cols=32  Identities=38%  Similarity=0.475  Sum_probs=24.2

Q ss_pred             EEEECCC-CCCHHHHHHHHHHHHHHHCCCCEEEEE
Q ss_conf             4650257-659789999999999980899669998
Q gi|254781215|r   80 GAISAGR-GIGKTTLNAWLVLWLMSTRPGISVICL  113 (511)
Q Consensus        80 ~aV~sgr-G~GKS~l~a~l~lw~l~~~p~~kv~vt  113 (511)
                      ++|.||. |+|||++++.+++.+...  +.+|.+.
T Consensus         2 i~v~s~kggvgkst~~~~la~~l~~~--g~~v~~~   34 (169)
T cd02037           2 IAVMSGKGGVGKSTVAVNLALALAKL--GYKVGLL   34 (169)
T ss_pred             EEEECCCCCCCHHHHHHHHHHHHHHC--CCCEEEE
T ss_conf             89974999881999999999999987--9978999


No 224
>COG0593 DnaA ATPase involved in DNA replication initiation [DNA replication, recombination, and repair]
Probab=83.53  E-value=2.9  Score=20.22  Aligned_cols=35  Identities=29%  Similarity=0.298  Sum_probs=27.6

Q ss_pred             EEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEEE
Q ss_conf             46502576597899999999999808996699980
Q gi|254781215|r   80 GAISAGRGIGKTTLNAWLVLWLMSTRPGISVICLA  114 (511)
Q Consensus        80 ~aV~sgrG~GKS~l~a~l~lw~l~~~p~~kv~vtA  114 (511)
                      +-+-+|-|.|||+|+-.+....+...|+.++++..
T Consensus       116 lfi~G~~GlGKTHLl~Aign~~~~~~~~a~v~y~~  150 (408)
T COG0593         116 LFIYGGVGLGKTHLLQAIGNEALANGPNARVVYLT  150 (408)
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEECC
T ss_conf             79987999978999999999998629986488504


No 225
>PRK05688 fliI flagellum-specific ATP synthase; Validated
Probab=83.35  E-value=1.7  Score=21.72  Aligned_cols=34  Identities=21%  Similarity=0.323  Sum_probs=23.9

Q ss_pred             CEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEEEC
Q ss_conf             012465025765978999999999998089966999808
Q gi|254781215|r   77 VFKGAISAGRGIGKTTLNAWLVLWLMSTRPGISVICLAN  115 (511)
Q Consensus        77 ~~r~aV~sgrG~GKS~l~a~l~lw~l~~~p~~kv~vtAp  115 (511)
                      .-|+.+-+|.|+|||++.++++.+     -.+.++|.+-
T Consensus       168 GQR~gIfggsGvGKS~Ll~~i~r~-----~~adv~Vi~l  201 (451)
T PRK05688        168 GQRLGLFAGTGVGKSVLLGMMTRF-----TEADIIVVGL  201 (451)
T ss_pred             CCEEEECCCCCCCHHHHHHHHHHH-----HCCCEEEEEE
T ss_conf             756421048898689999999885-----2798699996


No 226
>cd02042 ParA ParA and ParB of Caulobacter crescentus belong to a conserved family of bacterial proteins implicated in chromosome segregation. ParB binds to DNA sequences adjacent to the origin of replication and localizes to opposite cell poles shortly following the initiation of DNA replication. ParB regulates the ParA ATPase activity by promoting nucleotide exchange in a fashion reminiscent of the exchange factors of eukaryotic G proteins. ADP-bound ParA binds single-stranded DNA, whereas the ATP-bound form dissociates ParB from its DNA binding sites. Increasing the fraction of ParA-ADP in the cell inhibits cell division, suggesting that this simple nucleotide switch may regulate cytokinesis. ParA shares sequence similarity to a conserved and widespread family of ATPases which includes the repA protein of the repABC operon in R. etli Sym plasmid. This operon is involved in the plasmid replication and partition.
Probab=83.30  E-value=1.8  Score=21.61  Aligned_cols=28  Identities=32%  Similarity=0.362  Sum_probs=22.9

Q ss_pred             CCCCCHHHHHHHHHHHHHHHCCCCEEEEEE
Q ss_conf             576597899999999999808996699980
Q gi|254781215|r   85 GRGIGKTTLNAWLVLWLMSTRPGISVICLA  114 (511)
Q Consensus        85 grG~GKS~l~a~l~lw~l~~~p~~kv~vtA  114 (511)
                      ==|+|||+++..++.+++.  .+.+|+++=
T Consensus         8 KGGvGKtt~~~~la~~~a~--~g~~vl~iD   35 (104)
T cd02042           8 KGGVGKTTTAVNLAAALAR--RGKRVLLID   35 (104)
T ss_pred             CCCCCHHHHHHHHHHHHHH--CCCEEEEEE
T ss_conf             9987689999999999997--799299997


No 227
>KOG1002 consensus
Probab=83.26  E-value=1.3  Score=22.43  Aligned_cols=164  Identities=19%  Similarity=0.177  Sum_probs=73.1

Q ss_pred             HHHHHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEEECCHHHHHHHHHH-HHHH
Q ss_conf             589999999999987405655542101246502576597899999999999808996699980858999999999-9999
Q gi|254781215|r   52 RSWQLEFMEVVDAHCLNSVNNPNPEVFKGAISAGRGIGKTTLNAWLVLWLMSTRPGISVICLANSETQLKTTLWA-EVSK  130 (511)
Q Consensus        52 ~~WQ~e~l~~i~~~~~~~~~~~~~~~~r~aV~sgrG~GKS~l~a~l~lw~l~~~p~~kv~vtApt~~Q~~~ilw~-Ei~k  130 (511)
                      -++|+|.|.=.--...       ..+..-..+---|-|||--+..|++--   -..+..+|.||+-.-..   |. ||.+
T Consensus       186 L~fQkE~l~Wl~~QE~-------Ss~~GGiLADEMGMGKTIQtIaLllae---~~ra~tLVvaP~VAlmQ---W~nEI~~  252 (791)
T KOG1002         186 LPFQKEGLAWLTSQEE-------SSVAGGILADEMGMGKTIQTIALLLAE---VDRAPTLVVAPTVALMQ---WKNEIER  252 (791)
T ss_pred             HHHHHHHHHHHHHHHH-------HHHCCCEEHHHHCCCHHHHHHHHHHHC---CCCCCEEEECCHHHHHH---HHHHHHH
T ss_conf             1446777888877355-------431243112431464179999999862---35687069754899999---9999987


Q ss_pred             HHHHCHHCCCCCCCCCCCCCCCCC-CCCCCCCCCCCC---CEEEEEECCCCCCC---------CCHHHHCCCCCCEEEEE
Q ss_conf             998550001344432222223334-443211123578---61698530357556---------10021202676149997
Q gi|254781215|r  131 WLSLLPNKHWFEMQSLSLHPAPWY-SDVLHCSLGIDS---KHYSTMCRTYSEER---------PDTFVGHHNTYGMAIIN  197 (511)
Q Consensus       131 ~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~---~~~~~~~~~~s~~~---------~ea~~G~h~~~~~lvI~  197 (511)
                      .-..+          +..+..... -+...-++-.+.   .++-..-..++.++         -.-..-+|+-...-+|+
T Consensus       253 ~T~gs----------lkv~~YhG~~R~~nikel~~YDvVLTty~vvEs~yRk~~~GfrrKngv~ke~SlLHsi~~~RiIl  322 (791)
T KOG1002         253 HTSGS----------LKVYIYHGAKRDKNIKELMNYDVVLTTYAVVESVYRKQDYGFRRKNGVDKEKSLLHSIKFYRIIL  322 (791)
T ss_pred             HCCCC----------EEEEEEECCCCCCCHHHHHCCCEEEEECHHHHHHHHHCCCCCCCCCCCCCCCCHHHHCEEEEEEH
T ss_conf             62576----------47999726423577888606767997018788898740234211377424532333101023522


Q ss_pred             CCHHCCCHHHHHHHHHHHCCCCCCEEEEEECCCC-CCCCHHHH
Q ss_conf             1110299788988888850799813899823899-87655676
Q gi|254781215|r  198 DEASGTPDVINLGILGFLTERNANRFWIMTSNPR-RLSGKFYE  239 (511)
Q Consensus       198 DEAsgI~d~i~e~i~~~Lt~~g~~~~~i~~~nP~-~~~g~fy~  239 (511)
                      |||++|.+.--..++....-..+.. |..-|+|- +.-|..|-
T Consensus       323 DEAH~IK~R~snTArAV~~L~tt~r-w~LSGTPLQNrigElyS  364 (791)
T KOG1002         323 DEAHNIKDRQSNTARAVFALETTYR-WCLSGTPLQNRIGELYS  364 (791)
T ss_pred             HHHCCCCCCCCCHHHHHHHHHHHHH-HHCCCCCCHHHHHHHHH
T ss_conf             1202531013327888876676653-22058830112789999


No 228
>pfam06564 YhjQ YhjQ protein. This family consists of several bacterial YhjQ proteins. The function of this family is unknown. However, the family does contain a P-loop sequence motif suggesting a nucleotide binding function.
Probab=83.22  E-value=2.8  Score=20.38  Aligned_cols=36  Identities=33%  Similarity=0.350  Sum_probs=26.9

Q ss_pred             CEEEEEECCC-CCCHHHHHHHHHHHHHHHCCCCEEEEEE
Q ss_conf             0124650257-6597899999999999808996699980
Q gi|254781215|r   77 VFKGAISAGR-GIGKTTLNAWLVLWLMSTRPGISVICLA  114 (511)
Q Consensus        77 ~~r~aV~sgr-G~GKS~l~a~l~lw~l~~~p~~kv~vtA  114 (511)
                      |..++|.|+. |+|||++++.|+.-..  ..|.+|+++=
T Consensus         1 MkiIai~s~KGGVGKTT~t~nLa~aLa--~~G~rVLlID   37 (244)
T pfam06564         1 MAVLALQGVRGGVGTTSLTAALGWALQ--QLGESVLVID   37 (244)
T ss_pred             CEEEEEECCCCCCCHHHHHHHHHHHHH--HCCCCEEEEE
T ss_conf             929999669998619999999999999--7799589996


No 229
>PRK08149 ATP synthase SpaL; Validated
Probab=83.19  E-value=1.6  Score=21.88  Aligned_cols=36  Identities=25%  Similarity=0.183  Sum_probs=26.4

Q ss_pred             CEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEEECCH
Q ss_conf             01246502576597899999999999808996699980858
Q gi|254781215|r   77 VFKGAISAGRGIGKTTLNAWLVLWLMSTRPGISVICLANSE  117 (511)
Q Consensus        77 ~~r~aV~sgrG~GKS~l~a~l~lw~l~~~p~~kv~vtApt~  117 (511)
                      .-|+.+-+|.|+|||+|++.++.+     -++.|+|.|---
T Consensus       150 GQR~gIf~gsGvGKs~Ll~~i~~~-----~~adv~Via~IG  185 (427)
T PRK08149        150 GQRMGIFASAGCGKTMLMNMLIEH-----TEADVFVIGLIG  185 (427)
T ss_pred             CCEEECCCCCCCCHHHHHHHHHHH-----CCCCEEEEEEEC
T ss_conf             754000278998677999988863-----589989999702


No 230
>cd01135 V_A-ATPase_B V/A-type ATP synthase (non-catalytic) subunit B. These ATPases couple ATP hydrolysis to the build up of a H+ gradient, but V-type ATPases do not catalyze the reverse reaction. The Vacuolar (V-type) ATPase is found in the membranes of vacuoles, the golgi apparatus and in other coated vesicles in eukaryotes. Archaea have a protein which is similar in sequence to V-ATPases, but functions like an F-ATPase (called A-ATPase).  A similar protein is also found in a few bacteria. This subfamily consists of the non-catalytic beta subunit.
Probab=83.18  E-value=1.9  Score=21.46  Aligned_cols=41  Identities=17%  Similarity=0.031  Sum_probs=28.4

Q ss_pred             CEEEEEECCCCCCHHHHHHHHHHHHHHHCCC-CEEEEEECCH
Q ss_conf             0124650257659789999999999980899-6699980858
Q gi|254781215|r   77 VFKGAISAGRGIGKTTLNAWLVLWLMSTRPG-ISVICLANSE  117 (511)
Q Consensus        77 ~~r~aV~sgrG~GKS~l~a~l~lw~l~~~p~-~kv~vtApt~  117 (511)
                      .-|+.+-+|.|+|||++++.++.-..+...+ +-+.|.+.--
T Consensus        69 GQR~gIfgg~GvGKs~L~~~i~~~~~~~~~~~~~v~V~~~IG  110 (276)
T cd01135          69 GQKIPIFSGSGLPHNELAAQIARQAGVVGEEENFAVVFAAMG  110 (276)
T ss_pred             CCEEEECCCCCCCHHHHHHHHHHHHHHCCCCCCCEEEEEECC
T ss_conf             766332057886367899999998775136887359996155


No 231
>pfam03308 ArgK ArgK protein. The ArgK protein acts as an ATPase enzyme and as a kinase, and phosphorylates periplasmic binding proteins involved in the LAO (lysine, arginine, ornithine)/AO transport systems.
Probab=82.95  E-value=3.1  Score=20.08  Aligned_cols=55  Identities=25%  Similarity=0.165  Sum_probs=41.2

Q ss_pred             HHHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEEE--CCHH
Q ss_conf             9999999999987405655542101246502576597899999999999808996699980--8589
Q gi|254781215|r   54 WQLEFMEVVDAHCLNSVNNPNPEVFKGAISAGRGIGKTTLNAWLVLWLMSTRPGISVICLA--NSET  118 (511)
Q Consensus        54 WQ~e~l~~i~~~~~~~~~~~~~~~~r~aV~sgrG~GKS~l~a~l~lw~l~~~p~~kv~vtA--pt~~  118 (511)
                      .-+++|+.+..+.-        ...++.|...-|+|||++...++..+.-  .+.+|.|.|  ||..
T Consensus        14 ~~~~ll~~~~~~~g--------~a~~iGiTG~PGaGKStli~~l~~~~~~--~g~~vaVlAvDPSS~   70 (267)
T pfam03308        14 EARELLRRLMPLTG--------RAHRVGITGVPGAGKSTLIEALGMELRR--RGHRVAVLAVDPSSP   70 (267)
T ss_pred             HHHHHHHHHHHHCC--------CCEEEEEECCCCCCHHHHHHHHHHHHHH--CCCEEEEEEECCCCC
T ss_conf             79999999874359--------9559987689988799999999999996--898689999789998


No 232
>KOG0350 consensus
Probab=82.80  E-value=3.1  Score=20.04  Aligned_cols=78  Identities=14%  Similarity=0.139  Sum_probs=50.4

Q ss_pred             HHHHHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHHCC--CCEEEEEECCHHHHHHHHHHHHH
Q ss_conf             5899999999999874056555421012465025765978999999999998089--96699980858999999999999
Q gi|254781215|r   52 RSWQLEFMEVVDAHCLNSVNNPNPEVFKGAISAGRGIGKTTLNAWLVLWLMSTRP--GISVICLANSETQLKTTLWAEVS  129 (511)
Q Consensus        52 ~~WQ~e~l~~i~~~~~~~~~~~~~~~~r~aV~sgrG~GKS~l~a~l~lw~l~~~p--~~kv~vtApt~~Q~~~ilw~Ei~  129 (511)
                      ++-|..+|-.+-........   ...+-+.|.|..|.|||-.-+.=|+-.+.-||  --+.+|+-||..-+-.+ ..++.
T Consensus       161 FPVQ~aVlp~ll~~~~~p~~---~r~rDIcV~ApTGSGKTLaY~iPIVQ~L~~R~v~~LRavVivPtr~L~~QV-~~~f~  236 (620)
T KOG0350         161 FPVQYAVLPSLLEEIRSPPP---SRPRDICVNAPTGSGKTLAYVIPIVQLLSSRPVKRLRAVVIVPTRELALQV-YDTFK  236 (620)
T ss_pred             CCHHHHHHHHHHHHHCCCCC---CCCCCEEEECCCCCCCEEEEHHHHHHHHCCCCCCCEEEEEEEEHHHHHHHH-HHHHH
T ss_conf             50588888899986147999---887754775578988456651378999703873405799995479999999-99999


Q ss_pred             HHHH
Q ss_conf             9998
Q gi|254781215|r  130 KWLS  133 (511)
Q Consensus       130 k~~~  133 (511)
                      +|..
T Consensus       237 ~~~~  240 (620)
T KOG0350         237 RLNS  240 (620)
T ss_pred             HHCC
T ss_conf             8566


No 233
>COG2256 MGS1 ATPase related to the helicase subunit of the Holliday junction resolvase [DNA replication, recombination, and repair]
Probab=82.69  E-value=3.2  Score=20.01  Aligned_cols=120  Identities=13%  Similarity=0.098  Sum_probs=68.2

Q ss_pred             EECCCCCCHHHHHHHHHHHHHHHCCCCEEEEEECCHHHHHHHHHHHHHHHHHHCHHCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             50257659789999999999980899669998085899999999999999985500013444322222233344432111
Q gi|254781215|r   82 ISAGRGIGKTTLNAWLVLWLMSTRPGISVICLANSETQLKTTLWAEVSKWLSLLPNKHWFEMQSLSLHPAPWYSDVLHCS  161 (511)
Q Consensus        82 V~sgrG~GKS~l~a~l~lw~l~~~p~~kv~vtApt~~Q~~~ilw~Ei~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  161 (511)
                      .=.+-|+|||+++..++-.     -+..+.-+.++..-++     +|++.++.+..                        
T Consensus        53 l~GPPG~GKTTlA~liA~~-----~~~~f~~~sAv~~gvk-----dlr~i~e~a~~------------------------   98 (436)
T COG2256          53 LWGPPGTGKTTLARLIAGT-----TNAAFEALSAVTSGVK-----DLREIIEEARK------------------------   98 (436)
T ss_pred             EECCCCCCHHHHHHHHHHH-----HCCCEEEECCCCCCHH-----HHHHHHHHHHH------------------------
T ss_conf             7789998888999999876-----1776699515234679-----99999999999------------------------


Q ss_pred             CCCCCCEEEEEECCCCCCCCCHHHHCCCCCCEEEEECCHHCCCHHHHHHHHHHHCCCCCCEEEEEECCCCCCCCHHHHHH
Q ss_conf             23578616985303575561002120267614999711102997889888888507998138998238998765567653
Q gi|254781215|r  162 LGIDSKHYSTMCRTYSEERPDTFVGHHNTYGMAIINDEASGTPDVINLGILGFLTERNANRFWIMTSNPRRLSGKFYEIF  241 (511)
Q Consensus       162 ~~~~~~~~~~~~~~~s~~~~ea~~G~h~~~~~lvI~DEAsgI~d~i~e~i~~~Lt~~g~~~~~i~~~nP~~~~g~fy~~~  241 (511)
                                            ..+ ++.. +++++||-+-....--+++.|.+-.  ..+  +.+|..|-+  ++|+..
T Consensus        99 ----------------------~~~-~gr~-tiLflDEIHRfnK~QQD~lLp~vE~--G~i--ilIGATTEN--PsF~ln  148 (436)
T COG2256          99 ----------------------NRL-LGRR-TILFLDEIHRFNKAQQDALLPHVEN--GTI--ILIGATTEN--PSFELN  148 (436)
T ss_pred             ----------------------HHH-CCCC-EEEEEEHHHHCCHHHHHHHHHHHCC--CEE--EEEECCCCC--CCEEEC
T ss_conf             ----------------------872-5883-4998722533374456551033248--868--999626789--871403


Q ss_pred             HCCCCCCEEEEECCCCCCCCCHHHHHHHH
Q ss_conf             03524741798404336778977899999
Q gi|254781215|r  242 NKPLDDWKRFQIDTRTVEGIDPSFHEGII  270 (511)
Q Consensus       242 ~~~~~~w~~~~i~~~~~p~~~~~~ie~~~  270 (511)
                      +...++-..+.+-..     +.+.|++..
T Consensus       149 ~ALlSR~~vf~lk~L-----~~~di~~~l  172 (436)
T COG2256         149 PALLSRARVFELKPL-----SSEDIKKLL  172 (436)
T ss_pred             HHHHHHHHEEEEECC-----CHHHHHHHH
T ss_conf             888611041565169-----989999999


No 234
>TIGR01420 pilT_fam twitching motility protein; InterPro: IPR006321   These represent the PilT subfamily of proteins related to GspE, a protein involved in type II secretion (also called the General Secretion Pathway). PilT is an apparent cytosolic ATPase associated with type IV pilus systems. It is not required for pilin biogenesis, but is required for twitching motility and social gliding behaviors, shown in some species, powered by pilus retraction . Members of this family may be found in some species that do not have type IV pili but have related structures for DNA uptake and natural transformation. ; GO: 0005524 ATP binding, 0006810 transport.
Probab=82.36  E-value=1.1  Score=22.85  Aligned_cols=21  Identities=24%  Similarity=0.271  Sum_probs=15.2

Q ss_pred             EEEECCCCCCHHHHHHHHHHH
Q ss_conf             465025765978999999999
Q gi|254781215|r   80 GAISAGRGIGKTTLNAWLVLW  100 (511)
Q Consensus        80 ~aV~sgrG~GKS~l~a~l~lw  100 (511)
                      |-|..+-|+|||+..|.++=|
T Consensus       130 iLVTGPTGSGKSTTlAsmIDy  150 (350)
T TIGR01420       130 ILVTGPTGSGKSTTLASMIDY  150 (350)
T ss_pred             EEEECCCCCCHHHHHHHHHHH
T ss_conf             898768898678999999978


No 235
>COG0514 RecQ Superfamily II DNA helicase [DNA replication, recombination, and repair]
Probab=82.30  E-value=3.3  Score=19.92  Aligned_cols=58  Identities=16%  Similarity=0.118  Sum_probs=39.1

Q ss_pred             CCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEEECCHHHHHH
Q ss_conf             655578458999999999998740565554210124650257659789999999999980899669998085899999
Q gi|254781215|r   45 LEGFSAPRSWQLEFMEVVDAHCLNSVNNPNPEVFKGAISAGRGIGKTTLNAWLVLWLMSTRPGISVICLANSETQLKT  122 (511)
Q Consensus        45 ~~~~~~P~~WQ~e~l~~i~~~~~~~~~~~~~~~~r~aV~sgrG~GKS~l~a~l~lw~l~~~p~~kv~vtApt~~Q~~~  122 (511)
                      .+.|-++   |.|++..+.+..            .+.|.=..|.|||.+.-.-++-.     +.-++|+.|-..=.+|
T Consensus        15 y~~FR~g---Q~evI~~~l~g~------------d~lvvmPTGgGKSlCyQiPAll~-----~G~TLVVSPLiSLM~D   72 (590)
T COG0514          15 YASFRPG---QQEIIDALLSGK------------DTLVVMPTGGGKSLCYQIPALLL-----EGLTLVVSPLISLMKD   72 (590)
T ss_pred             CCCCCCC---HHHHHHHHHCCC------------CEEEECCCCCCCCHHHHHHHHHC-----CCCEEEECCHHHHHHH
T ss_conf             1303888---899999996588------------67998538987106743678865-----9978997856888999


No 236
>PRK08636 aspartate aminotransferase; Provisional
Probab=82.30  E-value=3.3  Score=19.92  Aligned_cols=18  Identities=22%  Similarity=0.135  Sum_probs=10.7

Q ss_pred             HHHHCCCCEEEEEECCHH
Q ss_conf             998089966999808589
Q gi|254781215|r  101 LMSTRPGISVICLANSET  118 (511)
Q Consensus       101 ~l~~~p~~kv~vtApt~~  118 (511)
                      .+++.||-.|++..|++.
T Consensus       113 ~al~~pGD~Vli~~P~Y~  130 (403)
T PRK08636        113 QAITNPGDVAIVPDPAYP  130 (403)
T ss_pred             HHHCCCCCEEEECCCCCC
T ss_conf             997799998997788870


No 237
>PRK03566 consensus
Probab=81.95  E-value=3.4  Score=19.84  Aligned_cols=59  Identities=20%  Similarity=0.188  Sum_probs=37.2

Q ss_pred             CCHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEEECCHHHHH
Q ss_conf             845899999999999874056555421012465025765978999999999998089966999808589999
Q gi|254781215|r   50 APRSWQLEFMEVVDAHCLNSVNNPNPEVFKGAISAGRGIGKTTLNAWLVLWLMSTRPGISVICLANSETQLK  121 (511)
Q Consensus        50 ~P~~WQ~e~l~~i~~~~~~~~~~~~~~~~r~aV~sgrG~GKS~l~a~l~lw~l~~~p~~kv~vtApt~~Q~~  121 (511)
                      +|+.-+.++-+.|+++..    .+ +.  .|.|    |+|=+.+.  .++..+++.|+..|++..||+..-.
T Consensus        64 YPd~~~~~Lr~aiA~~~g----v~-~~--~I~v----~~Gs~e~i--~l~~~a~~~pGd~Vl~~~P~y~~Y~  122 (365)
T PRK03566         64 YPDGNGFELKAALAEKLG----VP-PE--QITL----GNGSNDLL--ELLARAFLGPGDEIIYSQYAFAVYP  122 (365)
T ss_pred             CCCCCHHHHHHHHHHHHC----CC-HH--HEEE----CCCHHHHH--HHHHHHHCCCCCEEEECCCCHHHHH
T ss_conf             959668999999999978----48-66--7998----77899999--9999985589987676688668999


No 238
>TIGR03018 pepcterm_TyrKin exopolysaccharide/PEPCTERM locus tyrosine autokinase. Members of this protein family are related to a known protein-tyrosine autokinase and to numerous homologs from exopolysaccharide biosynthesis region proteins, many of which are designated as chain length determinants. Most members of this family contain a short region, immediately C-terminal to the region modeled here, with an abundance of Tyr residues. These C-terminal tyrosine residues are likely to be autophosphorylation sites. Some members of this family are fusion proteins.
Probab=81.86  E-value=3.4  Score=19.82  Aligned_cols=68  Identities=19%  Similarity=0.136  Sum_probs=43.3

Q ss_pred             CCCHHHHHHHHHHHHHHHHCCCCCCCC--CCEEEEEEC-CCCCCHHHHHHHHHHHHHHHCCCCEEEEE-ECCH
Q ss_conf             784589999999999987405655542--101246502-57659789999999999980899669998-0858
Q gi|254781215|r   49 SAPRSWQLEFMEVVDAHCLNSVNNPNP--EVFKGAISA-GRGIGKTTLNAWLVLWLMSTRPGISVICL-ANSE  117 (511)
Q Consensus        49 ~~P~~WQ~e~l~~i~~~~~~~~~~~~~--~~~r~aV~s-grG~GKS~l~a~l~lw~l~~~p~~kv~vt-Apt~  117 (511)
                      .-|+.=+.|.+|.+..+.........+  ...-+.|.| ..|-|||++++.++.-++.. .+.+|+++ |...
T Consensus         5 ~~P~s~~aEa~R~lRt~l~~~~~~~~~~~~~kvi~VTS~~pgeGKTtva~nLA~~lA~~-~~~~VLLVDaDlr   76 (207)
T TIGR03018         5 NSPRSRIAEEFRKIKRPLLANAFSANRKKNNNLIMVTSSLPGEGKSFTAINLAISLAQE-YDKTVLLIDADLR   76 (207)
T ss_pred             CCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCEEEEEECCCCCCCHHHHHHHHHHHHHHH-CCCEEEEEECCCC
T ss_conf             89999899999999998766410103467880999978999998899999999999972-4985999953578


No 239
>TIGR01968 minD_bact septum site-determining protein MinD; InterPro: IPR010223   This entry describes the bacterial and chloroplast form of MinD, a multifunctional cell division protein that guides correct placement of the septum. In Escherichia coli, the cell division site is determined by the cooperative activity of min operon products MinC, MinD, and MinE . MinD is a membrane-associated ATPase and is a septum site-determining factor through the activation and regulation of MinC and MinE. MinD is also known to undergo a rapid pole-to-pole oscillation movement in vivo as observed by fluorescent microscopy. In plants, chloroplast division requires the dimerisation of stromal MinD . The homologous archaeal MinD proteins, with many archaeal genomes having two or more forms, are described by a separate model.; GO: 0016887 ATPase activity, 0000918 selection of site for barrier septum formation.
Probab=81.61  E-value=2  Score=21.29  Aligned_cols=32  Identities=38%  Similarity=0.459  Sum_probs=25.4

Q ss_pred             EEEECCC-CCCHHHHHHHHHHHHHHHCCCCEEEEE
Q ss_conf             4650257-659789999999999980899669998
Q gi|254781215|r   80 GAISAGR-GIGKTTLNAWLVLWLMSTRPGISVICL  113 (511)
Q Consensus        80 ~aV~sgr-G~GKS~l~a~l~lw~l~~~p~~kv~vt  113 (511)
                      +-|.||. |+||||.+|.|-.-.+..  |.||+++
T Consensus         4 iViTSGKGGVGKTTtTANlG~aLA~l--G~kVvli   36 (272)
T TIGR01968         4 IVITSGKGGVGKTTTTANLGTALARL--GKKVVLI   36 (272)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHC--CCEEEEE
T ss_conf             99981788977358989999999961--9828999


No 240
>PRK08118 topology modulation protein; Reviewed
Probab=81.38  E-value=1.4  Score=22.19  Aligned_cols=27  Identities=30%  Similarity=0.132  Sum_probs=22.7

Q ss_pred             CEEEEEECCCCCCHHHHHHHHHHHHHH
Q ss_conf             012465025765978999999999998
Q gi|254781215|r   77 VFKGAISAGRGIGKTTLNAWLVLWLMS  103 (511)
Q Consensus        77 ~~r~aV~sgrG~GKS~l~a~l~lw~l~  103 (511)
                      |.|+.|-.+-|.|||+++..|.--.-+
T Consensus         1 M~rI~IiG~~GsGKSTlAr~L~~~~~i   27 (167)
T PRK08118          1 MKKIILIGSGGSGKSTLARQLGEKLNI   27 (167)
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHHHCC
T ss_conf             967999889998799999999998896


No 241
>PRK13909 putative recombination protein RecB; Provisional
Probab=81.10  E-value=3.6  Score=19.65  Aligned_cols=46  Identities=17%  Similarity=0.188  Sum_probs=28.7

Q ss_pred             EEEECCHHCCCHHHHHHHHHHH----CCCC--CCEEEEEECCCCCCCCHHHH
Q ss_conf             9997111029978898888885----0799--81389982389987655676
Q gi|254781215|r  194 AIINDEASGTPDVINLGILGFL----TERN--ANRFWIMTSNPRRLSGKFYE  239 (511)
Q Consensus       194 lvI~DEAsgI~d~i~e~i~~~L----t~~g--~~~~~i~~~nP~~~~g~fy~  239 (511)
                      .+.+||....+..=|+.+.+.+    ++.+  ...-+++.|=|.-.-+.|+.
T Consensus       328 ~ilVDEFQDTn~~Q~~il~~L~~~~~~g~~~~~~~~lf~VGD~KQSIY~FRg  379 (911)
T PRK13909        328 HILIDEFQDTSLLQYKILLPLIDEIKSGEGQSKNRSFFYVGDVKQSIYRFRG  379 (911)
T ss_pred             EEEEEHHCCCCHHHHHHHHHHHHHHHCCCCCCCCCCEEEECCCCCCHHHCCC
T ss_conf             8996400248999999999999876235556788727997377311022078


No 242
>TIGR00959 ffh signal recognition particle protein; InterPro: IPR004780    The signal recognition particle (SRP) is a multimeric protein, which along with its conjugate receptor (SR), is involved in targeting secretory proteins to the rough endoplasmic reticulum (RER) membrane in eukaryotes, or to the plasma membrane in prokaryotes , . SRP recognises the signal sequence of the nascent polypeptide on the ribosome, retards its elongation, and docks the SRP-ribosome-polypeptide complex to the RER membrane via the SR receptor. SRP consists of six polypeptides (SRP9, SRP14, SRP19, SRP54, SRP68 and SRP72) and a single 300 nucleotide 7S RNA molecule. The RNA component catalyses the interaction of SRP with its SR receptor . In higher eukaryotes, the SRP complex consists of the Alu domain and the S domain linked by the SRP RNA. The Alu domain consists of a heterodimer of SRP9 and SRP14 bound to the 5' and 3' terminal sequences of SRP RNA. This domain is necessary for retarding the elongation of the nascent polypeptide chain, which gives SRP time to dock the ribosome-polypeptide complex to the RER membrane.    This entry represents various SRP subunits.; GO: 0008312 7S RNA binding, 0006614 SRP-dependent cotranslational protein targeting to membrane, 0048500 signal recognition particle.
Probab=81.03  E-value=1.8  Score=21.52  Aligned_cols=93  Identities=23%  Similarity=0.252  Sum_probs=54.9

Q ss_pred             HHHHHHHHHHHHHHCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCC---CCC-------CEEEEEECCCCCCHH
Q ss_conf             0666528866776421455777565557845899999999999874056555---421-------012465025765978
Q gi|254781215|r   22 DEIKLSFSNFVLHFFPWGEKGTPLEGFSAPRSWQLEFMEVVDAHCLNSVNNP---NPE-------VFKGAISAGRGIGKT   91 (511)
Q Consensus        22 ~~~~~~~~~~~~~~~~w~~~~~~~~~~~~P~~WQ~e~l~~i~~~~~~~~~~~---~~~-------~~r~aV~sgrG~GKS   91 (511)
                      -+|..+|++-|+-=    .-|..+..-..|   +..+++-|.|.+-+--+.+   ...       ..-+--+.=.|.|||
T Consensus        44 l~VvK~Fi~~V~ek----A~G~eV~~~~~P---~Qq~iKIV~eEL~~~LG~~~~E~~~L~~~~~~P~vilmvGLQGsGKT  116 (439)
T TIGR00959        44 LQVVKDFIKKVKEK----ALGQEVLKSLSP---GQQFIKIVHEELVAILGGKGRESAELKLAEKRPTVILMVGLQGSGKT  116 (439)
T ss_pred             HHHHHHHHHHHHHH----HHHHHHHCCCCC---CHHEEHHHHHHHHHHCCCCCCCCCCCCCCCCCCEEEEEECCCCCCHH
T ss_conf             68999999988887----522544126780---20120224689998516667325675556786838997313788578


Q ss_pred             HHHHHHHHHHHHHCCCCEEEEEECCH------HHHH
Q ss_conf             99999999999808996699980858------9999
Q gi|254781215|r   92 TLNAWLVLWLMSTRPGISVICLANSE------TQLK  121 (511)
Q Consensus        92 ~l~a~l~lw~l~~~p~~kv~vtApt~------~Q~~  121 (511)
                      |.++=|+.|.+.-..+.+++.+|--.      +||+
T Consensus       117 Tt~gKLA~~ll~kk~~~kvLLva~D~yRPAA~~QL~  152 (439)
T TIGR00959       117 TTAGKLALYLLKKKEGKKVLLVACDLYRPAAIEQLK  152 (439)
T ss_pred             HHHHHHHHHHHHHHCCCCEEEEEHHCCCHHHHHHHH
T ss_conf             899999999999863897034032103478999999


No 243
>PRK05166 histidinol-phosphate aminotransferase; Provisional
Probab=81.00  E-value=3.6  Score=19.63  Aligned_cols=60  Identities=22%  Similarity=0.145  Sum_probs=37.6

Q ss_pred             CCCHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEEECCHHHHH
Q ss_conf             7845899999999999874056555421012465025765978999999999998089966999808589999
Q gi|254781215|r   49 SAPRSWQLEFMEVVDAHCLNSVNNPNPEVFKGAISAGRGIGKTTLNAWLVLWLMSTRPGISVICLANSETQLK  121 (511)
Q Consensus        49 ~~P~~WQ~e~l~~i~~~~~~~~~~~~~~~~r~aV~sgrG~GKS~l~a~l~lw~l~~~p~~kv~vtApt~~Q~~  121 (511)
                      .+|+.-..++-++|+++.-    .+..   .|.|    |+|=+.+...+  -.+++.|+-+|++..||+..-.
T Consensus        69 rYPd~~~~~Lr~aiA~~~g----v~~~---~I~v----~nGs~e~i~~~--~~a~~~pGd~Vl~~~Ptf~~Y~  128 (374)
T PRK05166         69 LYPDPQGRALRAEIAASFG----VPTD---QIIL----GNGSEDLIAVI--CRAVLRPGDRVVTLYPSFPLHE  128 (374)
T ss_pred             CCCCCCHHHHHHHHHHHHC----CCHH---HEEE----CCCHHHHHHHH--HHHHHCCCCEEEECCCCHHHHH
T ss_conf             6979878999999999968----3830---1998----56899999999--9999739998987788777899


No 244
>PRK08972 fliI flagellum-specific ATP synthase; Validated
Probab=80.66  E-value=2.3  Score=20.87  Aligned_cols=33  Identities=24%  Similarity=0.298  Sum_probs=22.8

Q ss_pred             EEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEEEC
Q ss_conf             12465025765978999999999998089966999808
Q gi|254781215|r   78 FKGAISAGRGIGKTTLNAWLVLWLMSTRPGISVICLAN  115 (511)
Q Consensus        78 ~r~aV~sgrG~GKS~l~a~l~lw~l~~~p~~kv~vtAp  115 (511)
                      =|+.+-+|.|+|||.+..+++-+     ..+.++|++-
T Consensus       161 QRigIf~gsGvGKS~Ll~~i~r~-----~~advvVi~l  193 (440)
T PRK08972        161 QRMGLFAGSGVGKSVLLGMMTRG-----TTADVIVVGL  193 (440)
T ss_pred             CEEEECCCCCCCHHHHHHHHHHC-----CCCCEEEEEE
T ss_conf             46663157897589999888751-----4787899986


No 245
>cd01134 V_A-ATPase_A V/A-type ATP synthase catalytic subunit A. These ATPases couple ATP hydrolysis to the build up of a H+ gradient, but V-type ATPases do not catalyze the reverse reaction.  The Vacuolar (V-type) ATPase is found in the membranes of vacuoles, the golgi apparatus and in other coated vesicles in eukaryotes. Archaea have a protein which is similar in sequence to V-ATPases, but functions like an F-ATPase (called A-ATPase).  A similar protein is also found in a few bacteria.
Probab=80.66  E-value=2.5  Score=20.62  Aligned_cols=22  Identities=32%  Similarity=0.394  Sum_probs=10.4

Q ss_pred             EEEEECCCCCCHHHHHHHHHHH
Q ss_conf             2465025765978999999999
Q gi|254781215|r   79 KGAISAGRGIGKTTLNAWLVLW  100 (511)
Q Consensus        79 r~aV~sgrG~GKS~l~a~l~lw  100 (511)
                      |+.+-+++|+|||.+...++-|
T Consensus       159 r~~I~g~~g~GKT~l~~~i~k~  180 (369)
T cd01134         159 TAAIPGPFGCGKTVIQQSLSKY  180 (369)
T ss_pred             EEEEECCCCCCHHHHHHHHHHC
T ss_conf             4677668776899999999853


No 246
>cd01133 F1-ATPase_beta F1 ATP synthase beta subunit, nucleotide-binding domain. The F-ATPase is found in bacterial plasma membranes, mitochondrial inner membranes and in chloroplast thylakoid membranes. It has also been found in the archaea Methanosarcina barkeri. It uses a proton gradient to drive ATP synthesis and hydrolyzes ATP to build the proton gradient. The extrinisic membrane domain, F1,  is composed of alpha, beta, gamma, delta and epsilon subunits with a stoichiometry of 3:3:1:1:1. The beta subunit of ATP synthase is catalytic.
Probab=80.64  E-value=3.2  Score=20.00  Aligned_cols=35  Identities=31%  Similarity=0.325  Sum_probs=24.8

Q ss_pred             EEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEE
Q ss_conf             12465025765978999999999998089966999
Q gi|254781215|r   78 FKGAISAGRGIGKTTLNAWLVLWLMSTRPGISVIC  112 (511)
Q Consensus        78 ~r~aV~sgrG~GKS~l~a~l~lw~l~~~p~~kv~v  112 (511)
                      =|..+-++.|+|||.++..++.-....+.+..|++
T Consensus        70 QR~~I~~~~g~GKt~ll~~ii~~~~~~~~~v~V~~  104 (274)
T cd01133          70 GKIGLFGGAGVGKTVLIMELINNIAKAHGGYSVFA  104 (274)
T ss_pred             CEEEEECCCCCCCCHHHHHHHHHHHHCCCCEEEEE
T ss_conf             57787579999823689999999985089879999


No 247
>KOG1802 consensus
Probab=80.48  E-value=1.9  Score=21.39  Aligned_cols=40  Identities=23%  Similarity=0.321  Sum_probs=31.7

Q ss_pred             EEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEEECCHHHH
Q ss_conf             46502576597899999999999808996699980858999
Q gi|254781215|r   80 GAISAGRGIGKTTLNAWLVLWLMSTRPGISVICLANSETQL  120 (511)
Q Consensus        80 ~aV~sgrG~GKS~l~a~l~lw~l~~~p~~kv~vtApt~~Q~  120 (511)
                      ..+..+-|+|||...| .|++++..+....|+|+||+---+
T Consensus       428 sLIQGPPGTGKTvtsa-~IVyhl~~~~~~~VLvcApSNiAV  467 (935)
T KOG1802         428 SLIQGPPGTGKTVTSA-TIVYHLARQHAGPVLVCAPSNIAV  467 (935)
T ss_pred             EEEECCCCCCCEEHHH-HHHHHHHHHCCCCEEEECCCCHHH
T ss_conf             1554699988331168-999999985289569981650028


No 248
>COG1703 ArgK Putative periplasmic protein kinase ArgK and related GTPases of G3E family [Amino acid transport and metabolism]
Probab=80.43  E-value=3.8  Score=19.51  Aligned_cols=53  Identities=26%  Similarity=0.177  Sum_probs=39.2

Q ss_pred             HHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEEE--CCH
Q ss_conf             999999999987405655542101246502576597899999999999808996699980--858
Q gi|254781215|r   55 QLEFMEVVDAHCLNSVNNPNPEVFKGAISAGRGIGKTTLNAWLVLWLMSTRPGISVICLA--NSE  117 (511)
Q Consensus        55 Q~e~l~~i~~~~~~~~~~~~~~~~r~aV~sgrG~GKS~l~a~l~lw~l~~~p~~kv~vtA--pt~  117 (511)
                      -.++|..++-+.-        ...++-+..--|+|||++...|+.-+  ++.+-+|.|.|  ||.
T Consensus        37 a~~ll~~l~p~tG--------~a~viGITG~PGaGKSTli~~L~~~l--~~~G~rVaVlAVDPSS   91 (323)
T COG1703          37 ARELLRALYPRTG--------NAHVIGITGVPGAGKSTLIEALGREL--RERGHRVAVLAVDPSS   91 (323)
T ss_pred             HHHHHHHHHHCCC--------CCCEEEECCCCCCCHHHHHHHHHHHH--HHCCCEEEEEEECCCC
T ss_conf             9999999731179--------98378731799886688999999999--9779678999988999


No 249
>cd02028 UMPK_like Uridine monophosphate kinase_like (UMPK_like) is a family of proteins highly similar to the uridine monophosphate kinase (UMPK, EC 2.7.1.48), also known as uridine kinase or uridine-cytidine kinase (UCK).
Probab=80.37  E-value=3.4  Score=19.82  Aligned_cols=34  Identities=35%  Similarity=0.280  Sum_probs=23.2

Q ss_pred             EEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEE
Q ss_conf             4650257659789999999999980899669998
Q gi|254781215|r   80 GAISAGRGIGKTTLNAWLVLWLMSTRPGISVICL  113 (511)
Q Consensus        80 ~aV~sgrG~GKS~l~a~l~lw~l~~~p~~kv~vt  113 (511)
                      ++|+.|-|.|||+++..+.--.-.....+.++..
T Consensus         2 IgIaG~SgSGKTT~a~~L~~~l~~~~~~~~vis~   35 (179)
T cd02028           2 VGIAGPSGSGKTTFAKKLSNQLRVNGIGPVVISL   35 (179)
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHHCCCCEEEEEC
T ss_conf             8998989778999999999998464885399954


No 250
>PRK11174 cysteine/glutathione ABC transporter membrane/ATP-binding component; Reviewed
Probab=80.22  E-value=3.9  Score=19.47  Aligned_cols=51  Identities=14%  Similarity=0.153  Sum_probs=23.9

Q ss_pred             EECCCEEEEEEECCCCCHHHHHHHHHHHHHHCCCCEEEEEECCCCHHHHHHHHH
Q ss_conf             822755899873277898899999999998618882998006876368898986
Q gi|254781215|r  336 LRRGPVIEHLFDWSKTDLRTTNNKISGLVEKYRPDAIIIDANNTGARTCDYLEM  389 (511)
Q Consensus       336 ~r~G~~v~~~~~~~~~d~~~~a~~i~~~~~~~~~~~i~iD~~GvG~gV~d~L~~  389 (511)
                      +..|.++-.+ =-.|..-.+++..+..++ .+. ..|.+|+.-+-.=-.+.||+
T Consensus       373 i~~Ge~vaIV-G~SGsGKSTl~~LL~g~~-p~~-G~I~i~g~di~~i~~~~lr~  423 (588)
T PRK11174        373 LPAGQRVALV-GPSGAGKTSLLNALLGFL-PYQ-GSLKINGIELRELDPESWRK  423 (588)
T ss_pred             ECCCCEEEEE-CCCCCCHHHHHHHHHHHC-CCC-CEEEECCEECCCCCHHHHHH
T ss_conf             7499789998-999864999999998728-988-38999998603089999996


No 251
>COG0610 Type I site-specific restriction-modification system, R (restriction) subunit and related helicases [Defense mechanisms]
Probab=80.11  E-value=3.9  Score=19.44  Aligned_cols=199  Identities=17%  Similarity=0.103  Sum_probs=94.8

Q ss_pred             HHHHHHHHHCHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCCCHH
Q ss_conf             88899987070666528866776421455777565557845899999999999874056555421012465025765978
Q gi|254781215|r   12 EQKLFDLMWSDEIKLSFSNFVLHFFPWGEKGTPLEGFSAPRSWQLEFMEVVDAHCLNSVNNPNPEVFKGAISAGRGIGKT   91 (511)
Q Consensus        12 ~~~~~~~~~~~~~~~~~~~~~~~~~~w~~~~~~~~~~~~P~~WQ~e~l~~i~~~~~~~~~~~~~~~~r~aV~sgrG~GKS   91 (511)
                      .+.|...++..+.   .++++.++..-......+--...++-=|..+++....-..+....  ....+-.|=--.|+|||
T Consensus       213 ~~~~~~~~l~~~~---lld~i~~f~vf~k~~~~~~~K~~~~~~q~~a~~~~i~~~~~~~~~--~~~~~G~IWHtqGSGKT  287 (962)
T COG0610         213 LEDLIKGFLAPER---LLDIIRNFIVFDKSDDGLVKKKYQRYAQYRAVQKAIKRILKASNP--GDGKGGYIWHTQGSGKT  287 (962)
T ss_pred             HHHHHHHHHCHHH---HHHHHHHEEEEEECCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCC--CCCCCEEEEECCCCCHH
T ss_conf             9999999859899---999987438996037775211127889999999999999971267--87772389840698378


Q ss_pred             HHHHHHHHHHHHHCCCCEEEEEECCHHHHHHHHHHHHHHHHHHCHHCCCCCCCCCCCCCCCCCCCCCCCCCC-CCCCEEE
Q ss_conf             999999999998089966999808589999999999999998550001344432222223334443211123-5786169
Q gi|254781215|r   92 TLNAWLVLWLMSTRPGISVICLANSETQLKTTLWAEVSKWLSLLPNKHWFEMQSLSLHPAPWYSDVLHCSLG-IDSKHYS  170 (511)
Q Consensus        92 ~l~a~l~lw~l~~~p~~kv~vtApt~~Q~~~ilw~Ei~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~  170 (511)
                      ..+.+++-+.+-.-...+|+++- -..-|-+-+..+....-..+...+  ....+.....         .++ ...+..+
T Consensus       288 ltm~~~A~~l~~~~~~~~v~fvv-DR~dLd~Q~~~~f~~~~~~~~~~~--~~~s~~~Lk~---------~l~~~~~~ii~  355 (962)
T COG0610         288 LTMFKLARLLLELPKNPKVLFVV-DRKDLDDQTSDEFQSFGKVAFNDP--KAESTSELKE---------LLEDGKGKIIV  355 (962)
T ss_pred             HHHHHHHHHHHHCCCCCEEEEEE-CHHHHHHHHHHHHHHHHHHHHCCC--CCCCHHHHHH---------HHHCCCCCEEE
T ss_conf             99999999998365999699996-728899999999999887632044--4457999999---------98658984899


Q ss_pred             EEECCCCCCCCCH-HHHCCCCCCEEEEECCHHCCCH-HHHHHHHHHHCCCCCCEEEEE-ECCCCC
Q ss_conf             8530357556100-2120267614999711102997-889888888507998138998-238998
Q gi|254781215|r  171 TMCRTYSEERPDT-FVGHHNTYGMAIINDEASGTPD-VINLGILGFLTERNANRFWIM-TSNPRR  232 (511)
Q Consensus       171 ~~~~~~s~~~~ea-~~G~h~~~~~lvI~DEAsgI~d-~i~e~i~~~Lt~~g~~~~~i~-~~nP~~  232 (511)
                      .+.+.++....+. ....-.. ...+|+|||+=.-. ..-..+.-++..    ..++. +|+|.-
T Consensus       356 TTIQKf~~~~~~~~~~~~~~~-~ivvI~DEaHRSQ~G~~~~~~~~~~~~----a~~~gFTGTPi~  415 (962)
T COG0610         356 TTIQKFNKAVKEDELELLKRK-NVVVIIDEAHRSQYGELAKLLKKALKK----AIFIGFTGTPIF  415 (962)
T ss_pred             EEECCCCHHHHCCCCCCCCCC-CEEEEEECCCCCCCHHHHHHHHHHHCC----CEEEEEECCCCC
T ss_conf             971026433333320004787-679998640103560789999987036----708975178564


No 252
>PRK07721 fliI flagellum-specific ATP synthase; Validated
Probab=80.05  E-value=2.4  Score=20.76  Aligned_cols=23  Identities=35%  Similarity=0.437  Sum_probs=20.5

Q ss_pred             EEEEEECCCCCCHHHHHHHHHHH
Q ss_conf             12465025765978999999999
Q gi|254781215|r   78 FKGAISAGRGIGKTTLNAWLVLW  100 (511)
Q Consensus        78 ~r~aV~sgrG~GKS~l~a~l~lw  100 (511)
                      -|+.+-+|.|+|||+|++.++-+
T Consensus       157 QRigIf~gsGvGKs~Ll~~iar~  179 (435)
T PRK07721        157 QRVGIFAGSGVGKSTLMGMIARQ  179 (435)
T ss_pred             CEEEECCCCCCCHHHHHHHHHHH
T ss_conf             54100268998789999999887


No 253
>KOG0387 consensus
Probab=79.93  E-value=4  Score=19.41  Aligned_cols=170  Identities=16%  Similarity=0.130  Sum_probs=73.7

Q ss_pred             HHHHHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCCCHHHH-HHHHHH-HHH-HHCCCCEEEEEECCHHHHHHHHHHHH
Q ss_conf             589999999999987405655542101246502576597899-999999-999-80899669998085899999999999
Q gi|254781215|r   52 RSWQLEFMEVVDAHCLNSVNNPNPEVFKGAISAGRGIGKTTL-NAWLVL-WLM-STRPGISVICLANSETQLKTTLWAEV  128 (511)
Q Consensus        52 ~~WQ~e~l~~i~~~~~~~~~~~~~~~~r~aV~sgrG~GKS~l-~a~l~l-w~l-~~~p~~kv~vtApt~~Q~~~ilw~Ei  128 (511)
                      .++|++-++=+.+-...+.+.        .+.--=|.|||.= ++.|+- .+- .+.-++-|+|-|.-..|=.    .|.
T Consensus       207 f~yQreGV~WL~~L~~q~~GG--------ILgDeMGLGKTIQiisFLaaL~~S~k~~~paLIVCP~Tii~qW~----~E~  274 (923)
T KOG0387         207 FPYQREGVQWLWELYCQRAGG--------ILGDEMGLGKTIQIISFLAALHHSGKLTKPALIVCPATIIHQWM----KEF  274 (923)
T ss_pred             HHHHHHHHHHHHHHHHCCCCC--------EECCCCCCCCCHHHHHHHHHHHHCCCCCCCEEEECCHHHHHHHH----HHH
T ss_conf             488898899999997325787--------62012357640158999998750243258659982488999999----999


Q ss_pred             HHHHHHCHHCCCCCCCCCCCCCC---CCCCCCCCCCCCCCCC-EEEEEECCCCCCCCCHHHHCCCCCCEEEEECCHHCCC
Q ss_conf             99998550001344432222223---3344432111235786-1698530357556100212026761499971110299
Q gi|254781215|r  129 SKWLSLLPNKHWFEMQSLSLHPA---PWYSDVLHCSLGIDSK-HYSTMCRTYSEERPDTFVGHHNTYGMAIINDEASGTP  204 (511)
Q Consensus       129 ~k~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~-~~~~~~~~~s~~~~ea~~G~h~~~~~lvI~DEAsgI~  204 (511)
                      ..|+-......+.....+.-+..   -..-+..........+ ....+.-.++...+ -+-|.-  . -.+|+||++-|.
T Consensus       275 ~~w~p~~rv~ilh~t~s~~r~~~~~~~~~~~~~L~r~~~~~~~ilitty~~~r~~~d-~l~~~~--W-~y~ILDEGH~Ir  350 (923)
T KOG0387         275 QTWWPPFRVFILHGTGSGARYDASHSSHKKDKLLIRKVATDGGILITTYDGFRIQGD-DLLGIL--W-DYVILDEGHRIR  350 (923)
T ss_pred             HHHCCCEEEEEEECCCCCCCCCCCHHHHHHHHHHEEEECCCCCEEEEEHHHHCCCCC-CCCCCC--C-CEEEECCCCCCC
T ss_conf             874765379997147765444431013443122203530468479974224200475-234650--3-479823765046


Q ss_pred             HH---HHHHHHHHHCCCCCCEEEEEECCCCCCC-CHHHHHH
Q ss_conf             78---8988888850799813899823899876-5567653
Q gi|254781215|r  205 DV---INLGILGFLTERNANRFWIMTSNPRRLS-GKFYEIF  241 (511)
Q Consensus       205 d~---i~e~i~~~Lt~~g~~~~~i~~~nP~~~~-g~fy~~~  241 (511)
                      ++   +..+..-..|   .. .+++.|+|.-+. ..++..|
T Consensus       351 Npns~islackki~T---~~-RiILSGTPiQNnL~ELwsLf  387 (923)
T KOG0387         351 NPNSKISLACKKIRT---VH-RIILSGTPIQNNLTELWSLF  387 (923)
T ss_pred             CCCCHHHHHHHHCCC---CC-EEEEECCCCCCHHHHHHHHH
T ss_conf             985089999986156---66-48861862101089998776


No 254
>KOG0332 consensus
Probab=79.91  E-value=2  Score=21.26  Aligned_cols=68  Identities=21%  Similarity=0.117  Sum_probs=41.1

Q ss_pred             CCCCCHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHH-CCCCEEEEEECCHHHHHHHH
Q ss_conf             5578458999999999998740565554210124650257659789999999999980-89966999808589999999
Q gi|254781215|r   47 GFSAPRSWQLEFMEVVDAHCLNSVNNPNPEVFKGAISAGRGIGKTTLNAWLVLWLMST-RPGISVICLANSETQLKTTL  124 (511)
Q Consensus        47 ~~~~P~~WQ~e~l~~i~~~~~~~~~~~~~~~~r~aV~sgrG~GKS~l~a~l~lw~l~~-~p~~kv~vtApt~~Q~~~il  124 (511)
                      .|.-|-+-|...|--+-.+--          .-..-.|--|+|||+...--+|-..-. -.-...+|.|||+.-++.++
T Consensus       109 ~F~kPskIQe~aLPlll~~Pp----------~nlIaQsqsGtGKTaaFvL~MLsRvd~~~~~PQ~iCLaPtrELA~Q~~  177 (477)
T KOG0332         109 KFQKPSKIQETALPLLLAEPP----------QNLIAQSQSGTGKTAAFVLTMLSRVDPDVVVPQCICLAPTRELAPQTG  177 (477)
T ss_pred             CCCCCCHHHHHHCCHHHCCCC----------HHHHHHHCCCCCHHHHHHHHHHHHCCCCCCCCCCEEECCHHHHHHHHH
T ss_conf             268832577752125305982----------656655017886058999999873483335877405476177799898


No 255
>TIGR01082 murC UDP-N-acetylmuramate--alanine ligase; InterPro: IPR005758   The bacterial cell wall provides strength and rigidity to counteract internal osmotic pressure, and protection against the environment. The peptidoglycan layer gives the cell wall its strength, and helps maintain the overall shape of the cell. The basic peptidoglycan structure of both Gram-positive and Gram-negative bacteria is comprised of a sheet of glycan chains connected by short cross-linking polypeptides. Biosynthesis of peptidoglycan is a multi-step (11-12 steps) process comprising three main stages:    (1) formation of UDP-N-acetylmuramic acid (UDPMurNAc) from N-acetylglucosamine (GlcNAc). (2) addition of a short polypeptide chain to the UDPMurNAc. (3) addition of a second GlcNAc to the disaccharide-pentapeptide building block and transport of this unit through the cytoplasmic membrane and incorporation into the growing peptidoglycan layer.    Stage two involves four key Mur ligase enzymes: MurC (6.3.2.8 from EC) , MurD (6.3.2.9 from EC) , MurE (6.3.2.13 from EC)  and MurF (6.3.2.10 from EC) . These four Mur ligases are responsible for the successive additions of L-alanine, D-glutamate, meso-diaminopimelate or L-lysine, and D-alanyl-D-alanine to UDP-N-acetylmuramic acid. All four Mur ligases are topologically similar to one another, even though they display low sequence identity. They are each composed of three domains: an N-terminal Rossmann-fold domain responsible for binding the UDPMurNAc substrate; a central domain (similar to ATP-binding domains of several ATPases and GTPases); and a C-terminal domain (similar to dihydrofolate reductase fold) that appears to be associated with binding the incoming amino acid. The conserved sequence motifs found in the four Mur enzymes also map to other members of the Mur ligase family, including folylpolyglutamate synthetase, cyanophycin synthetase and the capB enzyme from Bacillales .    This entry represents UDP-N-acetylmuramate-alanine ligase (MurC). MurC is an essential, cytoplasmic peptidoglycan biosynthetic enzyme, catalyzes the ATP-dependent ligation of L-alanine (Ala) and UDP-N-acetylmuramic acid (UNAM) to form UDP-N-acetylmuramyl-L-alanine (UNAM-Ala). The enzyme is a nonribosomal peptide ligase which utilises ATP to form an amide bond between L-alanine and UNAM.1 Mechanistic studies on the Escherichia coli MurC enzyme using oxygen isotope analyses demonstrated that the enzyme-catalyzed reaction proceeds through an acyl phosphate UNAM intermediate prior to L-alanine addition.; GO: 0005524 ATP binding, 0008763 UDP-N-acetylmuramate-L-alanine ligase activity, 0008360 regulation of cell shape, 0009252 peptidoglycan biosynthetic process, 0009273 peptidoglycan-based cell wall biogenesis, 0051301 cell division, 0005737 cytoplasm.
Probab=79.77  E-value=4  Score=19.38  Aligned_cols=36  Identities=25%  Similarity=0.215  Sum_probs=31.8

Q ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEEECC
Q ss_conf             24650257659789999999999980899669998085
Q gi|254781215|r   79 KGAISAGRGIGKTTLNAWLVLWLMSTRPGISVICLANS  116 (511)
Q Consensus        79 r~aV~sgrG~GKS~l~a~l~lw~l~~~p~~kv~vtApt  116 (511)
                      -++|+..|  |||+.+|+++.-+--+..++.+++....
T Consensus       110 ~iaVaGtH--GKTTTTamia~~~~~aGLdPt~~~GG~~  145 (491)
T TIGR01082       110 SIAVAGTH--GKTTTTAMIAVILKEAGLDPTVIVGGEV  145 (491)
T ss_pred             EEEEECCC--CCHHHHHHHHHHHHHCCCCCCEEECCCC
T ss_conf             07998368--7256899999999844999768986643


No 256
>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=79.69  E-value=4  Score=19.36  Aligned_cols=116  Identities=19%  Similarity=0.210  Sum_probs=70.3

Q ss_pred             HHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEEECCHHHHHHHHHHHHHHHHHH
Q ss_conf             99999999998740565554210124650257659789999999999980899669998085899999999999999985
Q gi|254781215|r   55 QLEFMEVVDAHCLNSVNNPNPEVFKGAISAGRGIGKTTLNAWLVLWLMSTRPGISVICLANSETQLKTTLWAEVSKWLSL  134 (511)
Q Consensus        55 Q~e~l~~i~~~~~~~~~~~~~~~~r~aV~sgrG~GKS~l~a~l~lw~l~~~p~~kv~vtApt~~Q~~~ilw~Ei~k~~~~  134 (511)
                      |=++.+.+.+.+.+|. ++      ....+-.|+|||+.+|++|-=     -+.=++|.|+...=|- -|.+|++...  
T Consensus        14 QP~AI~~L~~~l~~G~-~~------QtLLGvTGsGKTFT~AnVIa~-----~~rPTLV~aHNKTLAA-QLY~EfKefF--   78 (667)
T TIGR00631        14 QPKAIAKLVEGLEAGE-KE------QTLLGVTGSGKTFTMANVIAQ-----VQRPTLVLAHNKTLAA-QLYNEFKEFF--   78 (667)
T ss_pred             HHHHHHHHHHHHHCCC-CC------EEEEEEECCCHHHHHHHHHHH-----HCCCEEEECCCHHHHH-HHHHHHHHHC--
T ss_conf             1899999999985688-71------478532148627889899998-----4798499857776799-9999998638--


Q ss_pred             CHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCCCCCCCHHHHCCCCCCEEEEECCHHCCCHHHHH---HH
Q ss_conf             500013444322222233344432111235786169853035755610021202676149997111029978898---88
Q gi|254781215|r  135 LPNKHWFEMQSLSLHPAPWYSDVLHCSLGIDSKHYSTMCRTYSEERPDTFVGHHNTYGMAIINDEASGTPDVINL---GI  211 (511)
Q Consensus       135 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~ea~~G~h~~~~~lvI~DEAsgI~d~i~e---~i  211 (511)
                       |+      +                     +-++|+.-  +--.+|||.=-    ...++| +=-|.|.|+|=.   ++
T Consensus        79 -Pe------N---------------------AVEYFvSY--YDYYQPEAYvP----~~DtyI-EKdaSINdeIerlR~SA  123 (667)
T TIGR00631        79 -PE------N---------------------AVEYFVSY--YDYYQPEAYVP----SKDTYI-EKDASINDEIERLRLSA  123 (667)
T ss_pred             -CC------C---------------------CEEEEEEC--CCCCCCCCCCC----CCCCEE-ECCCCHHHHHHHHHHHH
T ss_conf             -67------7---------------------24525520--32378732147----988413-04553004676778898


Q ss_pred             HHHHCCCCC
Q ss_conf             888507998
Q gi|254781215|r  212 LGFLTERNA  220 (511)
Q Consensus       212 ~~~Lt~~g~  220 (511)
                      .-+|.++.+
T Consensus       124 T~SLl~RrD  132 (667)
T TIGR00631       124 TKSLLERRD  132 (667)
T ss_pred             HHHHCCCCC
T ss_conf             886423787


No 257
>COG1157 FliI Flagellar biosynthesis/type III secretory pathway ATPase [Cell motility and secretion / Intracellular trafficking and secretion]
Probab=79.69  E-value=2.5  Score=20.71  Aligned_cols=33  Identities=30%  Similarity=0.295  Sum_probs=24.3

Q ss_pred             EEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEEEC
Q ss_conf             12465025765978999999999998089966999808
Q gi|254781215|r   78 FKGAISAGRGIGKTTLNAWLVLWLMSTRPGISVICLAN  115 (511)
Q Consensus        78 ~r~aV~sgrG~GKS~l~a~l~lw~l~~~p~~kv~vtAp  115 (511)
                      -|+-+=||-|+|||+|.++++-.     ..+-++|+|=
T Consensus       164 QRiGIFAgsGVGKStLLgMiar~-----t~aDv~ViaL  196 (441)
T COG1157         164 QRIGIFAGSGVGKSTLLGMIARN-----TEADVNVIAL  196 (441)
T ss_pred             CEEEEEECCCCCHHHHHHHHHCC-----CCCCEEEEEE
T ss_conf             46788716998689999999624-----6698799997


No 258
>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=79.58  E-value=4.1  Score=19.34  Aligned_cols=66  Identities=18%  Similarity=0.080  Sum_probs=36.8

Q ss_pred             HHHHCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEE
Q ss_conf             77642145577756555784589999999999987405655542101246502576597899999999999808996699
Q gi|254781215|r   32 VLHFFPWGEKGTPLEGFSAPRSWQLEFMEVVDAHCLNSVNNPNPEVFKGAISAGRGIGKTTLNAWLVLWLMSTRPGISVI  111 (511)
Q Consensus        32 ~~~~~~w~~~~~~~~~~~~P~~WQ~e~l~~i~~~~~~~~~~~~~~~~r~aV~sgrG~GKS~l~a~l~lw~l~~~p~~kv~  111 (511)
                      .+-.|+|....       +.+++|..-|.. .++..++        .-+....+-|+|||++++.++.-.+  +-+.+|.
T Consensus        18 tle~~d~~~~~-------~~~~~~i~~L~~-~~~i~~~--------~Nlll~G~~GtGKThLA~Ai~~~~~--~~g~~v~   79 (178)
T pfam01695        18 TLEDFDFRAAR-------GLDRRLIAELAG-LDWIEQA--------ENLLLLGPPGVGKTHLACALGHQAC--RAGYSVL   79 (178)
T ss_pred             CHHHCCCCCCC-------CCCHHHHHHHHC-CCCHHCC--------CCEEEECCCCCCHHHHHHHHHHHHH--HCCCEEE
T ss_conf             86336887899-------989999998855-9742158--------7689989999878999999999999--8698599


Q ss_pred             E-EEC
Q ss_conf             9-808
Q gi|254781215|r  112 C-LAN  115 (511)
Q Consensus       112 v-tAp  115 (511)
                      . +++
T Consensus        80 f~~~~   84 (178)
T pfam01695        80 FTRTP   84 (178)
T ss_pred             EEECH
T ss_conf             99616


No 259
>PRK07683 aminotransferase A; Validated
Probab=79.43  E-value=4.1  Score=19.31  Aligned_cols=22  Identities=23%  Similarity=0.160  Sum_probs=12.3

Q ss_pred             HHHHHHCCCCEEEEEECCHHHH
Q ss_conf             9999808996699980858999
Q gi|254781215|r   99 LWLMSTRPGISVICLANSETQL  120 (511)
Q Consensus        99 lw~l~~~p~~kv~vtApt~~Q~  120 (511)
                      +-.+++.||-.|++..|++...
T Consensus       105 ~~~~~~~pGD~Vlv~~P~Y~~~  126 (387)
T PRK07683        105 AFRTILEPGTEVILPAPIYPGY  126 (387)
T ss_pred             HHHHHCCCCCEEEECCCCCCCH
T ss_conf             9999769999899837876656


No 260
>pfam05729 NACHT NACHT domain. This NTPase domain is found in apoptosis proteins as well as those involved in MHC transcription activation. This family is closely related to pfam00931.
Probab=79.42  E-value=2.4  Score=20.78  Aligned_cols=25  Identities=32%  Similarity=0.284  Sum_probs=21.3

Q ss_pred             EEEEECCCCCCHHHHHHHHHHHHHH
Q ss_conf             2465025765978999999999998
Q gi|254781215|r   79 KGAISAGRGIGKTTLNAWLVLWLMS  103 (511)
Q Consensus        79 r~aV~sgrG~GKS~l~a~l~lw~l~  103 (511)
                      +|.|...-|+|||+++..+++-|+.
T Consensus         2 ~i~i~G~aG~GKTtll~kl~~~wa~   26 (165)
T pfam05729         2 TVILQGEAGSGKTTLLQKLALLWAQ   26 (165)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHC
T ss_conf             8999827989899999999999986


No 261
>PRK04195 replication factor C large subunit; Provisional
Probab=79.41  E-value=4.1  Score=19.30  Aligned_cols=56  Identities=21%  Similarity=0.180  Sum_probs=30.9

Q ss_pred             CCCCCCCC--CCCCCCCHHHHHHHHHHHHHHHH---CCCCCCCCCCEEEEEECCCCCCHHHHHHHHHHH
Q ss_conf             14557775--65557845899999999999874---056555421012465025765978999999999
Q gi|254781215|r   37 PWGEKGTP--LEGFSAPRSWQLEFMEVVDAHCL---NSVNNPNPEVFKGAISAGRGIGKTTLNAWLVLW  100 (511)
Q Consensus        37 ~w~~~~~~--~~~~~~P~~WQ~e~l~~i~~~~~---~~~~~~~~~~~r~aV~sgrG~GKS~l~a~l~lw  100 (511)
                      ||-+|-.|  +....|    |.++.+.+..+..   ++...+    .-+-..++.|+|||+++-.++--
T Consensus         3 ~WveKYRPk~~~divg----~~~~v~~l~~Wl~~w~~g~~~~----k~lLL~GPpGvGKTT~a~~lAk~   63 (403)
T PRK04195          3 PWVEKYRPKSLSDVVG----NEKAKKQLREWIESWLKGKPPK----KALLLYGPPGVGKTSLAHALAND   63 (403)
T ss_pred             CCCCCCCCCCHHHHHC----CHHHHHHHHHHHHHHHCCCCCC----CEEEEECCCCCCHHHHHHHHHHH
T ss_conf             8640218998999858----8999999999999987399657----46998893998799999999998


No 262
>PRK07196 fliI flagellum-specific ATP synthase; Validated
Probab=79.38  E-value=2.8  Score=20.31  Aligned_cols=34  Identities=21%  Similarity=0.345  Sum_probs=24.7

Q ss_pred             CEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEEEC
Q ss_conf             012465025765978999999999998089966999808
Q gi|254781215|r   77 VFKGAISAGRGIGKTTLNAWLVLWLMSTRPGISVICLAN  115 (511)
Q Consensus        77 ~~r~aV~sgrG~GKS~l~a~l~lw~l~~~p~~kv~vtAp  115 (511)
                      .-|+.+-+|.|+|||++++.++..     ..+.++|.+-
T Consensus       155 GQRigIfggsGvGKs~Ll~~I~r~-----~~advvVi~l  188 (434)
T PRK07196        155 GQRVGLMAGSGVGKSVLLGMITRY-----TQADVVVVGL  188 (434)
T ss_pred             CCEEEECCCCCCCHHHHHHHHHHH-----HCCCEEEEEE
T ss_conf             524210147899789999999897-----3799899974


No 263
>TIGR00678 holB DNA polymerase III, delta' subunit; InterPro: IPR004622   DNA-directed DNA polymerase (2.7.7.7 from EC) catalyzes DNA-template-directed extension of the 3'-end of an RNA strand by one nucleotide at a time. DNA polymerase III is a complex, multi-chain enzyme responsible for most of the replicative synthesis in bacteria. The enzyme also has 3' to 5' exonuclease activity. It has a core composed of alpha, epsilon and theta chains, that associate with a tau subunit which allows the core dimerisation to form the PolIII' complex. PolIII' associates with the gamma complex (gamma, delta, delta', psi and chi chains) and with the beta chain. This domain is the N-terminal half of the delta' subunit of DNA polymerase III. Delta' is homologous to the gamma and tau subunits, which form an outgroup for phylogenetic comparison. The gamma/tau branch of the tree is much more tightly conserved than the delta' branch, and some members of that branch score more highly against this model than some proteins classified as delta'. The noise cut-off is set to detect weakly scoring delta' subunits rather than to exclude gamma/tau subunits.; GO: 0003887 DNA-directed DNA polymerase activity, 0008408 3'-5' exonuclease activity, 0006260 DNA replication.
Probab=79.31  E-value=4.1  Score=19.28  Aligned_cols=159  Identities=16%  Similarity=0.155  Sum_probs=82.7

Q ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEEECCHHHHHHHHHHHHHHHHHHCHHCCCCCCCCCC-----------
Q ss_conf             246502576597899999999999808996699980858999999999999999855000134443222-----------
Q gi|254781215|r   79 KGAISAGRGIGKTTLNAWLVLWLMSTRPGISVICLANSETQLKTTLWAEVSKWLSLLPNKHWFEMQSLS-----------  147 (511)
Q Consensus        79 r~aV~sgrG~GKS~l~a~l~lw~l~~~p~~kv~vtApt~~Q~~~ilw~Ei~k~~~~~~~~~~~~~~~~~-----------  147 (511)
                      -.-..+..|+||..++-+++-|.+|..+.....|-.-..=+.-.         ..+-|.-+++.-....           
T Consensus        16 A~LF~G~~G~Gk~~~A~~~A~~l~C~~~~~~~~Cg~C~~C~~~~---------~G~HPD~~~~~P~~~~~~~~~de~~~~   86 (216)
T TIGR00678        16 AYLFTGPEGVGKELLALALAKALLCEPRGGGEPCGECHSCRLIE---------AGNHPDLHRLEPEGQSKSLTADEAAEG   86 (216)
T ss_pred             CEEEECCCCCCHHHHHHHHHHHHCCCCCCCCCCCCCCHHHHHHH---------HCCCCCEEEEEEECCCCCCCHHHHHHH
T ss_conf             12544488874899999999998077857788888588899987---------079982378742347777776458976


Q ss_pred             -------CCCCCCCCCCCCCCCCCCCCEEEEEECCCCCCCCCHHHHCCCCCCEEEEECCHHCCCHHHHHHHHHHHCCCCC
Q ss_conf             -------2223334443211123578616985303575561002120267614999711102997889888888507998
Q gi|254781215|r  148 -------LHPAPWYSDVLHCSLGIDSKHYSTMCRTYSEERPDTFVGHHNTYGMAIINDEASGTPDVINLGILGFLTERNA  220 (511)
Q Consensus       148 -------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~ea~~G~h~~~~~lvI~DEAsgI~d~i~e~i~~~Lt~~g~  220 (511)
                             ..+....++..+           ...      ..=+..+..+.+. .||++.|..+.+..-+++.-+|=.+..
T Consensus        87 ~~g~a~~~~~~~Ik~dq~R-----------~l~------~~~~~~~~~~~~r-VviI~~Ae~mn~~AANALLKtLEEPp~  148 (216)
T TIGR00678        87 EEGSAKRRALPQIKVDQVR-----------ELV------EFLSLTPQESGRR-VVIIEDAERMNEAAANALLKTLEEPPP  148 (216)
T ss_pred             HCCCCCCCCCCCCCHHHHH-----------HHH------HHHHHCCCCCCCE-EEEECCHHHCCHHHHHHHHHHEECCCC
T ss_conf             2564211367878727899-----------999------9986064214751-799767323258989865101012798


Q ss_pred             CEEEEEE-CCC--CCCCCHHHHHHHCCCCCCEEEEECCCCCCCCCHHHHHHHHHHCCCC
Q ss_conf             1389982-389--9876556765303524741798404336778977899999751898
Q gi|254781215|r  221 NRFWIMT-SNP--RRLSGKFYEIFNKPLDDWKRFQIDTRTVEGIDPSFHEGIIARYGLD  276 (511)
Q Consensus       221 ~~~~i~~-~nP--~~~~g~fy~~~~~~~~~w~~~~i~~~~~p~~~~~~ie~~~~~~ged  276 (511)
                      +..+|++ .+|  .+.--+..-++..       +     .-+-.+.+.+.+|...-|..
T Consensus       149 ~t~fiL~~~~~DP~~lLpTI~SRCq~-------~-----~f~~l~~~~~~~~L~~~g~~  195 (216)
T TIGR00678       149 NTLFILITHSPDPERLLPTIRSRCQV-------L-----PFPPLSEEALLQWLIEQGIS  195 (216)
T ss_pred             CEEEEEECCCCCHHHHCCCCCCCEEE-------E-----EECCCCHHHHHHHHHHCCCC
T ss_conf             70798850888843322111032015-------8-----62599889999999970878


No 264
>PRK04841 transcriptional regulator MalT; Provisional
Probab=79.29  E-value=4.1  Score=19.28  Aligned_cols=117  Identities=16%  Similarity=0.113  Sum_probs=58.5

Q ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEEECCHHHHHHHHHHHHHHHHHHCHHCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             24650257659789999999999980899669998085899999999999999985500013444322222233344432
Q gi|254781215|r   79 KGAISAGRGIGKTTLNAWLVLWLMSTRPGISVICLANSETQLKTTLWAEVSKWLSLLPNKHWFEMQSLSLHPAPWYSDVL  158 (511)
Q Consensus        79 r~aV~sgrG~GKS~l~a~l~lw~l~~~p~~kv~vtApt~~Q~~~ilw~Ei~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~  158 (511)
                      =+-|.++-|.|||++++.   | +- .......++....+.--...|..+...++.......  ........        
T Consensus        34 l~lv~APaG~GKTtl~a~---w-~~-~~~~~~Wlsld~~d~~~~~f~~~l~~al~~~~~~~~--~~~~~~~~--------   98 (903)
T PRK04841         34 LVLVRSPAGYGKTTLASQ---W-AA-GKNNVGWYSLDESDNQPERFASYLIAALQQATNGHC--SKSEALAE--------   98 (903)
T ss_pred             EEEEECCCCCCHHHHHHH---H-HH-CCCCEEEEECCCCCCCHHHHHHHHHHHHHHHCCCCC--CHHHHCCC--------
T ss_conf             799977999889999999---9-83-499859985885448999999999999998565433--11231135--------


Q ss_pred             CCCCCCCCCEEEEEECCCCCCCCC--------HHHHCCCCCCEEEEECCHHCCCH-HHHHHHHHHHCCCCCCEEEEEEC
Q ss_conf             111235786169853035755610--------02120267614999711102997-88988888850799813899823
Q gi|254781215|r  159 HCSLGIDSKHYSTMCRTYSEERPD--------TFVGHHNTYGMAIINDEASGTPD-VINLGILGFLTERNANRFWIMTS  228 (511)
Q Consensus       159 ~~~~~~~~~~~~~~~~~~s~~~~e--------a~~G~h~~~~~lvI~DEAsgI~d-~i~e~i~~~Lt~~g~~~~~i~~~  228 (511)
                                      .....+.+        .+....  ..+.+|+|....|.+ .+.+.+.-.+........++..|
T Consensus        99 ----------------~~~~~~~~~~~~~l~~~l~~~~--~~~~lvlDD~h~i~~~~~~~~l~~Ll~~~p~~l~lvl~s  159 (903)
T PRK04841         99 ----------------KRQYASLTSLFAQLFIELSDWH--QPLYLVLDDYHLITNPEIHEAMRFFLRHQPENLTLVVLS  159 (903)
T ss_pred             ----------------CCCCCCHHHHHHHHHHHHHCCC--CCEEEEEECCCCCCCHHHHHHHHHHHHHCCCCEEEEEEE
T ss_conf             ----------------5665549999999999975589--986999868364888689999999998389883899876


No 265
>PRK12597 F0F1 ATP synthase subunit beta; Provisional
Probab=79.23  E-value=3.2  Score=19.99  Aligned_cols=36  Identities=31%  Similarity=0.358  Sum_probs=25.7

Q ss_pred             CEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEE
Q ss_conf             012465025765978999999999998089966999
Q gi|254781215|r   77 VFKGAISAGRGIGKTTLNAWLVLWLMSTRPGISVIC  112 (511)
Q Consensus        77 ~~r~aV~sgrG~GKS~l~a~l~lw~l~~~p~~kv~v  112 (511)
                      .-|+.+-+|.|+|||.++..++.-....+.+..|++
T Consensus       141 GqrigIfggaGvGKTvL~~~ii~n~~~~~~~v~V~~  176 (459)
T PRK12597        141 GGKTGLFGGAGVGKTVLMMELIFNISKRHQGSSVFA  176 (459)
T ss_pred             CCEEEEECCCCCCCCHHHHHHHHHHHHHCCCCEEEE
T ss_conf             877774368999821578999998775517836888


No 266
>TIGR01978 sufC FeS assembly ATPase SufC; InterPro: IPR010230   Iron-sulphur (FeS) clusters are important cofactors for numerous proteins involved in electron transfer, in redox and non-redox catalysis, in gene regulation, and as sensors of oxygen and iron. These functions depend on the various FeS cluster prosthetic groups, the most common being [2Fe-2S] and [4Fe-4S] . FeS cluster assembly is a complex process involving the mobilisation of Fe and S atoms from storage sources, their assembly into [Fe-S] form, their transport to specific cellular locations, and their transfer to recipient apoproteins. So far, three FeS assembly machineries have been identified, which are capable of synthesising all types of [Fe-S] clusters: ISC (iron-sulphur cluster), SUF (sulphur assimilation), and NIF (nitrogen fixation) systems.   The ISC system is conserved in eubacteria and eukaryotes (mitochondria), and has broad specificity, targeting general FeS proteins , . It is encoded by the isc operon (iscRSUA-hscBA-fdx-iscX). IscS is a cysteine desulphurase, which obtains S from cysteine (converting it to alanine) and serves as a S donor for FeS cluster assembly. IscU and IscA act as scaffolds to accept S and Fe atoms, assembling clusters and transfering them to recipient apoproteins. HscA is a molecular chaperone and HscB is a co-chaperone. Fdx is a [2Fe-2S]-type ferredoxin. IscR is a transcription factor that regulates expression of the isc operon. IscX (also known as YfhJ) appears to interact with IscS and may function as an Fe donor during cluster assembly .   The SUF system is an alternative pathway to the ISC system that operates under iron starvation and oxidative stress. It is found in eubacteria, archaea and eukaryotes (plastids). The SUF system is encoded by the suf operon (sufABCDSE), and the six encoded proteins are arranged into two complexes (SufSE and SufBCD) and one protein (SufA). SufS is a pyridoxal-phosphate (PLP) protein displaying cysteine desulphurase activity. SufE acts as a scaffold protein that accepts S from SufS and donates it to SufA . SufC is an ATPase with an unorthodox ATP-binding cassette (ABC)-like component. No specific functions have been assigned to SufB and SufD. SufA is homologous to IscA , acting as a scaffold protein in which Fe and S atoms are assembled into [FeS] cluster forms, which can then easily be transferred to apoproteins targets.   In the NIF system, NifS and NifU are required for the formation of metalloclusters of nitrogenase in Azotobacter vinelandii, and other organisms, as well as in the maturation of other FeS proteins. Nitrogenase catalyses the fixation of nitrogen. It contains a complex cluster, the FeMo cofactor, which contains molybdenum, Fe and S. NifS is a cysteine desulphurase. NifU binds one Fe atom at its N-terminal, assembling an FeS cluster that is transferred to nitrogenase apoproteins . Nif proteins involved in the formation of FeS clusters can also be found in organisms that do not fix nitrogen .   This entry represents SufC, which acts as an ATPase in the SUF system. SufC belongs to the ATP-binding cassette transporter family (IPR003439 from INTERPRO) but is no longer thought to be part of a transporter. The complex is reported as cytosolic or associated with the membrane.; GO: 0005524 ATP binding, 0006810 transport.
Probab=79.20  E-value=1.5  Score=22.16  Aligned_cols=20  Identities=35%  Similarity=0.350  Sum_probs=17.3

Q ss_pred             EEEECCCCCCHHHHHHHHHH
Q ss_conf             46502576597899999999
Q gi|254781215|r   80 GAISAGRGIGKTTLNAWLVL   99 (511)
Q Consensus        80 ~aV~sgrG~GKS~l~a~l~l   99 (511)
                      +||=.+.|.|||||+..++=
T Consensus        29 HAiMGPNGsGKSTL~~~iaG   48 (248)
T TIGR01978        29 HAIMGPNGSGKSTLSKTIAG   48 (248)
T ss_pred             EEEECCCCCCHHHHHHHHHC
T ss_conf             99868899847888777617


No 267
>PRK13235 nifH nitrogenase reductase; Reviewed
Probab=79.00  E-value=4.2  Score=19.22  Aligned_cols=35  Identities=34%  Similarity=0.317  Sum_probs=29.0

Q ss_pred             CEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEE
Q ss_conf             0124650257659789999999999980899669998
Q gi|254781215|r   77 VFKGAISAGRGIGKTTLNAWLVLWLMSTRPGISVICL  113 (511)
Q Consensus        77 ~~r~aV~sgrG~GKS~l~a~l~lw~l~~~p~~kv~vt  113 (511)
                      |+++||=.==|+|||+.++.+....+-.  +.||+++
T Consensus         1 m~~iaiyGKGGVGKSTtt~NLaAALA~~--GkkVl~I   35 (274)
T PRK13235          1 MRKVAIYGKGGIGKSTTTQNTVAGLAEM--GKKVMVV   35 (274)
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHHHHHC--CCEEEEE
T ss_conf             9679997998554767899999999978--9979998


No 268
>PRK07960 fliI flagellum-specific ATP synthase; Validated
Probab=78.95  E-value=2.9  Score=20.21  Aligned_cols=33  Identities=24%  Similarity=0.390  Sum_probs=22.1

Q ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEEECC
Q ss_conf             24650257659789999999999980899669998085
Q gi|254781215|r   79 KGAISAGRGIGKTTLNAWLVLWLMSTRPGISVICLANS  116 (511)
Q Consensus        79 r~aV~sgrG~GKS~l~a~l~lw~l~~~p~~kv~vtApt  116 (511)
                      |+.+-+|.|+|||+++++++-.     ..+.++|++--
T Consensus       177 RigIfagsGvGKs~Ll~~iar~-----~~adv~Vi~lI  209 (455)
T PRK07960        177 RMGLFAGSGVGKSVLLGMMARY-----TRADVIVVGLI  209 (455)
T ss_pred             EEECCCCCCCCHHHHHHHHHHH-----HCCCEEEEEEE
T ss_conf             7632489988499999999886-----08985899720


No 269
>COG0455 flhG Antiactivator of flagellar biosynthesis FleN, an ATPase [Cell motility]
Probab=78.95  E-value=4.2  Score=19.21  Aligned_cols=35  Identities=34%  Similarity=0.392  Sum_probs=24.7

Q ss_pred             EEEEEECCC-CCCHHHHHHHHHHHHHHHCCCCEEEEE
Q ss_conf             124650257-659789999999999980899669998
Q gi|254781215|r   78 FKGAISAGR-GIGKTTLNAWLVLWLMSTRPGISVICL  113 (511)
Q Consensus        78 ~r~aV~sgr-G~GKS~l~a~l~lw~l~~~p~~kv~vt  113 (511)
                      ..++|.||+ |+|||++++.+....+-.. +.+|++.
T Consensus         3 ~~Iav~SgKGGvGKTtitanlga~~~~~~-~k~V~~i   38 (262)
T COG0455           3 KVIAVVSGKGGVGKTTITANLGAALAALG-GKVVLLI   38 (262)
T ss_pred             EEEEEEECCCCCCHHHHHHHHHHHHHHHC-CCEEEEE
T ss_conf             89999845887568989986999999648-9769999


No 270
>KOG0951 consensus
Probab=78.87  E-value=4.3  Score=19.20  Aligned_cols=76  Identities=13%  Similarity=0.213  Sum_probs=45.3

Q ss_pred             HHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHHC---------CCCEEEEEECCHHHHHHHHH
Q ss_conf             999999999987405655542101246502576597899999999999808---------99669998085899999999
Q gi|254781215|r   55 QLEFMEVVDAHCLNSVNNPNPEVFKGAISAGRGIGKTTLNAWLVLWLMSTR---------PGISVICLANSETQLKTTLW  125 (511)
Q Consensus        55 Q~e~l~~i~~~~~~~~~~~~~~~~r~aV~sgrG~GKS~l~a~l~lw~l~~~---------p~~kv~vtApt~~Q~~~ilw  125 (511)
                      |.+-|..|+-+.+.-..+-..   -+-+-++.|.|||-.+-.-+|--+--+         .+.+++++||...-+.+++ 
T Consensus       306 g~~sLNrIQS~V~daAl~~~E---nmLlCAPTGaGKTNVAvLtiLqel~~h~r~dgs~nl~~fKIVYIAPmKaLVqE~V-  381 (1674)
T KOG0951         306 GKQSLNRIQSKVYDAALRGDE---NMLLCAPTGAGKTNVAVLTILQELGNHLREDGSVNLAPFKIVYIAPMKALVQEMV-  381 (1674)
T ss_pred             CCHHHHHHHHHHHHHHHCCCC---CEEEECCCCCCCHHHHHHHHHHHHHCCCCCCCCEECCCCEEEEEEEHHHHHHHHH-
T ss_conf             404566788777788755767---3787426788823799999999985354544541025613799842899999999-


Q ss_pred             HHHHHHHHH
Q ss_conf             999999985
Q gi|254781215|r  126 AEVSKWLSL  134 (511)
Q Consensus       126 ~Ei~k~~~~  134 (511)
                      +.+.+++..
T Consensus       382 gsfSkRla~  390 (1674)
T KOG0951         382 GSFSKRLAP  390 (1674)
T ss_pred             HHHHHHCCC
T ss_conf             888864235


No 271
>smart00732 YqgFc Likely ribonuclease with RNase H fold. YqgF proteins are likely to function as an alternative to RuvC in most bacteria, and could be the principal holliday junction resolvases in low-GC Gram-positive bacteria. In Spt6p orthologues, the catalytic residues are substituted indicating that they lack enzymatic functions.
Probab=78.69  E-value=4.3  Score=19.17  Aligned_cols=56  Identities=23%  Similarity=0.403  Sum_probs=42.3

Q ss_pred             EEEEEEECCCCCCCCEEEEEEC--CCEEEEEEECCCCCHHHHHHHHHHHHHHCCCCEEEEE
Q ss_conf             0899962333478417999822--7558998732778988999999999986188829980
Q gi|254781215|r  317 PLIMGCDIAEEGGDNTVVVLRR--GPVIEHLFDWSKTDLRTTNNKISGLVEKYRPDAIIID  375 (511)
Q Consensus       317 ~~viGvDVAr~G~D~svi~~r~--G~~v~~~~~~~~~d~~~~a~~i~~~~~~~~~~~i~iD  375 (511)
                      +.++|+|++   ...+-+++-+  |..+..+..+...+.......+.+++.+++++.|+|-
T Consensus         1 krvLgiD~G---~kriG~Ai~D~~~~~a~pl~~i~~~~~~~~~~~l~~~i~~~~~~~iviG   58 (99)
T smart00732        1 KRVLGLDPG---RKGIGVAVVDETGKLADPLEVIPRTNKEADAARLKKLIKKYQPDLIVIG   58 (99)
T ss_pred             CCEEEEEEC---CCCEEEEEEECCCCEECCCEEEECCCCHHHHHHHHHHHHHHCCCEEEEC
T ss_conf             979999217---8969999998999732131899859826999999999998499889974


No 272
>PRK11773 uvrD DNA-dependent helicase II; Provisional
Probab=78.66  E-value=1  Score=23.19  Aligned_cols=41  Identities=24%  Similarity=0.396  Sum_probs=31.0

Q ss_pred             EEEECCCCCCHHHHHHHHHHHHHHH--CCCCEEEEEECCHHHH
Q ss_conf             4650257659789999999999980--8996699980858999
Q gi|254781215|r   80 GAISAGRGIGKTTLNAWLVLWLMST--RPGISVICLANSETQL  120 (511)
Q Consensus        80 ~aV~sgrG~GKS~l~a~l~lw~l~~--~p~~kv~vtApt~~Q~  120 (511)
                      +.|.||=|+|||.....-+.|.+..  -++.+|+++.=|..-+
T Consensus        25 ~lV~AGaGSGKT~vL~~Ria~Li~~~gv~p~~ILalTFTnkAA   67 (722)
T PRK11773         25 MLVLAGAGSGKTRVLVHRIAWLMQVENASPYSILAVTFTNKAA   67 (722)
T ss_pred             EEEEECCCCHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHH
T ss_conf             7999738715999999999999982999878828984589999


No 273
>KOG0346 consensus
Probab=78.61  E-value=4.3  Score=19.15  Aligned_cols=56  Identities=18%  Similarity=0.184  Sum_probs=38.9

Q ss_pred             EEEECCCCCCHHHHHHHHHHHHHHHC-------CCCEEEEEECCHHHHHHHHHHHHHHHHHHCH
Q ss_conf             46502576597899999999999808-------9966999808589999999999999998550
Q gi|254781215|r   80 GAISAGRGIGKTTLNAWLVLWLMSTR-------PGISVICLANSETQLKTTLWAEVSKWLSLLP  136 (511)
Q Consensus        80 ~aV~sgrG~GKS~l~a~l~lw~l~~~-------p~~kv~vtApt~~Q~~~ilw~Ei~k~~~~~~  136 (511)
                      +-.++-.|.|||..-..=++--++..       -+...++.+||..-++.+ ..++.+....|.
T Consensus        59 vvarArTGSGKT~AYliPllqkll~~k~t~~~e~~~sa~iLvPTkEL~qQv-y~viekL~~~c~  121 (569)
T KOG0346          59 VVARARTGSGKTAAYLIPLLQKLLAEKKTNDGEQGPSAVILVPTKELAQQV-YKVIEKLVEYCS  121 (569)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHHHHCCCCCCCCEEEEEECHHHHHHHH-HHHHHHHHHHHH
T ss_conf             146522688713788999999999764036432463069992509999999-999999999878


No 274
>TIGR03498 FliI_clade3 flagellar protein export ATPase FliI. Members of this protein family are the FliI protein of bacterial flagellum systems. This protein acts to drive protein export for flagellar biosynthesis. The most closely related family is the YscN family of bacterial type III secretion systems. This model represents one (of three) segment of the FliI family tree. These have been modeled separately in order to exclude the type III secretion ATPases more effectively.
Probab=78.48  E-value=3.1  Score=20.10  Aligned_cols=34  Identities=32%  Similarity=0.339  Sum_probs=24.3

Q ss_pred             CEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEEEC
Q ss_conf             012465025765978999999999998089966999808
Q gi|254781215|r   77 VFKGAISAGRGIGKTTLNAWLVLWLMSTRPGISVICLAN  115 (511)
Q Consensus        77 ~~r~aV~sgrG~GKS~l~a~l~lw~l~~~p~~kv~vtAp  115 (511)
                      .-|+.+-+|.|+|||++++.++.+     -.+.++|.|-
T Consensus       140 GQRigIfgg~GvGKt~Ll~~i~~~-----~~adv~V~al  173 (418)
T TIGR03498       140 GQRLGIFAGSGVGKSTLLSMLARN-----TDADVVVIAL  173 (418)
T ss_pred             CCEEECCCCCCCCHHHHHHHHHHH-----CCCCEEEEEE
T ss_conf             766411378999888999999875-----0798689988


No 275
>TIGR03496 FliI_clade1 flagellar protein export ATPase FliI. Members of this protein family are the FliI protein of bacterial flagellum systems. This protein acts to drive protein export for flagellar biosynthesis. The most closely related family is the YscN family of bacterial type III secretion systems. This model represents one (of three) segment of the FliI family tree. These have been modeled separately in order to exclude the type III secretion ATPases more effectively.
Probab=78.44  E-value=2.8  Score=20.32  Aligned_cols=33  Identities=24%  Similarity=0.377  Sum_probs=24.3

Q ss_pred             EEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEEEC
Q ss_conf             12465025765978999999999998089966999808
Q gi|254781215|r   78 FKGAISAGRGIGKTTLNAWLVLWLMSTRPGISVICLAN  115 (511)
Q Consensus        78 ~r~aV~sgrG~GKS~l~a~l~lw~l~~~p~~kv~vtAp  115 (511)
                      =|+.+-+|.|+|||++++.++.+     -.+.++|+|-
T Consensus       138 QR~gIf~g~GvGKs~Ll~~ia~~-----~~adv~Vial  170 (411)
T TIGR03496       138 QRIGIFAGSGVGKSVLLGMMARY-----TEADVVVVGL  170 (411)
T ss_pred             CEEEECCCCCCCHHHHHHHHHHC-----CCCCEEEEEC
T ss_conf             63132279998677999999753-----4898899953


No 276
>KOG0384 consensus
Probab=77.97  E-value=4.5  Score=19.03  Aligned_cols=159  Identities=17%  Similarity=0.151  Sum_probs=82.0

Q ss_pred             CHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHHC-CCCEEEEEECCHHHHHHHHH-HHH
Q ss_conf             4589999999999987405655542101246502576597899999999999808-99669998085899999999-999
Q gi|254781215|r   51 PRSWQLEFMEVVDAHCLNSVNNPNPEVFKGAISAGRGIGKTTLNAWLVLWLMSTR-PGISVICLANSETQLKTTLW-AEV  128 (511)
Q Consensus        51 P~~WQ~e~l~~i~~~~~~~~~~~~~~~~r~aV~sgrG~GKS~l~a~l~lw~l~~~-p~~kv~vtApt~~Q~~~ilw-~Ei  128 (511)
                      -|++|-+=|.=++-.+.++..        +..+--=|.|||-=.-.++-|....+ -.+=.+|++|-..-.-   | .|.
T Consensus       371 LRDYQLeGlNWLl~~W~k~~n--------~ILADEMGLGKTvQtI~FLs~l~~~~~~~GPfLvVvPLSTi~~---W~ref  439 (1373)
T KOG0384         371 LRDYQLEGLNWLLYSWYKRNN--------CILADEMGLGKTVQTITFLSYLFHSLQIHGPFLVVVPLSTITA---WEREF  439 (1373)
T ss_pred             HHHHHHCCHHHHHHHHHCCCC--------EEEECCCCCCCHHHHHHHHHHHHHHCCCCCCEEEEEECCCCHH---HHHHH
T ss_conf             446563132899998864686--------4754002577401345999999984544788699986400078---99999


Q ss_pred             HHHHHHCHHCCCCCCCCCC-CCCCCCCCCCCCCCCCCCCCEEEEEECCCCCC----CCCHHHHCCCCCCEEEEECCHHCC
Q ss_conf             9999855000134443222-22233344432111235786169853035755----610021202676149997111029
Q gi|254781215|r  129 SKWLSLLPNKHWFEMQSLS-LHPAPWYSDVLHCSLGIDSKHYSTMCRTYSEE----RPDTFVGHHNTYGMAIINDEASGT  203 (511)
Q Consensus       129 ~k~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~----~~ea~~G~h~~~~~lvI~DEAsgI  203 (511)
                      ..|..+-..........+. +....|......      ...-|-.-.| +.+    .-+-+..+|   -..+++|||+-+
T Consensus       440 ~~WtdmN~ivY~G~~~SR~~I~qYE~~~~~~~------~~~KFn~LlT-TyE~vLkDk~~L~~i~---W~~~~vDEAHRL  509 (1373)
T KOG0384         440 ETWTDMNVIVYHGNLESRQLIRQYEFYHSSNT------KKLKFNALLT-TYEIVLKDKAELSKIP---WRYLLVDEAHRL  509 (1373)
T ss_pred             HHHHHCCEEEEECCHHHHHHHHHHHEEECCCC------CEEEEEEEEH-HHHHHHCCHHHHCCCC---EEEEEECHHHHH
T ss_conf             98751465888266567899987650454777------5178876400-1898972688864575---278974166550


Q ss_pred             CH---HHHHHHHHHHCCCCCCEEEEEECCCCCCC
Q ss_conf             97---88988888850799813899823899876
Q gi|254781215|r  204 PD---VINLGILGFLTERNANRFWIMTSNPRRLS  234 (511)
Q Consensus       204 ~d---~i~e~i~~~Lt~~g~~~~~i~~~nP~~~~  234 (511)
                      .+   ..++++..+-    ...+++.+|+|--++
T Consensus       510 KN~~s~Ly~~L~~f~----~~hrlLiTGTPLQNs  539 (1373)
T KOG0384         510 KNDESKLYESLNQFK----MNHRLLITGTPLQNS  539 (1373)
T ss_pred             CCCHHHHHHHHHHHH----HCCEEEEECCCCCCC
T ss_conf             650448999999864----307577547854031


No 277
>KOG1133 consensus
Probab=77.87  E-value=4.6  Score=19.01  Aligned_cols=46  Identities=20%  Similarity=0.211  Sum_probs=34.9

Q ss_pred             CCHHHHHHHHHHHHHHHHCCCCCCCCCCEEEE-EECCCCCCHHH-HHHHHHHHHHHH
Q ss_conf             84589999999999987405655542101246-50257659789-999999999980
Q gi|254781215|r   50 APRSWQLEFMEVVDAHCLNSVNNPNPEVFKGA-ISAGRGIGKTT-LNAWLVLWLMST  104 (511)
Q Consensus        50 ~P~~WQ~e~l~~i~~~~~~~~~~~~~~~~r~a-V~sgrG~GKS~-l~a~l~lw~l~~  104 (511)
                      -|-+-|.+++++++--+..++         ++ --|+.|+|||- +++..+-|.-..
T Consensus        15 ~PYdIQ~~lM~elyrvLe~Gk---------IgIfESPTGTGKSLSLiCaaltWL~~~   62 (821)
T KOG1133          15 TPYDIQEDLMRELYRVLEEGK---------IGIFESPTGTGKSLSLICAALTWLRDF   62 (821)
T ss_pred             CCHHHHHHHHHHHHHHHHCCC---------EEEEECCCCCCCHHHHHHHHHHHHHHH
T ss_conf             823699999999999985376---------246757998881178999898998876


No 278
>PRK12414 putative aminotransferase; Provisional
Probab=77.57  E-value=4.7  Score=18.96  Aligned_cols=20  Identities=25%  Similarity=0.185  Sum_probs=10.9

Q ss_pred             HHHHHCCCCEEEEEECCHHH
Q ss_conf             99980899669998085899
Q gi|254781215|r  100 WLMSTRPGISVICLANSETQ  119 (511)
Q Consensus       100 w~l~~~p~~kv~vtApt~~Q  119 (511)
                      -.++++||-.|++..|++..
T Consensus       107 ~~al~~pGD~Vlv~~P~y~~  126 (384)
T PRK12414        107 ISALVHPGDEVIYFEPSFDS  126 (384)
T ss_pred             HHHHCCCCCEEEEECCCCHH
T ss_conf             99967999989990897065


No 279
>PRK13230 nitrogenase reductase-like protein; Reviewed
Probab=77.40  E-value=4.7  Score=18.93  Aligned_cols=35  Identities=31%  Similarity=0.290  Sum_probs=29.5

Q ss_pred             CEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEE
Q ss_conf             0124650257659789999999999980899669998
Q gi|254781215|r   77 VFKGAISAGRGIGKTTLNAWLVLWLMSTRPGISVICL  113 (511)
Q Consensus        77 ~~r~aV~sgrG~GKS~l~a~l~lw~l~~~p~~kv~vt  113 (511)
                      |+++||-.==|+|||+.+..|+.-.+..  +.||+++
T Consensus         1 m~~ia~yGKGGVGKTTTavNLAaALA~~--GkkVLlI   35 (292)
T PRK13230          1 MKQIAFYGKGGIGKSTTVCNLAAALSKS--GKKVIVV   35 (292)
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHHHHHC--CCEEEEE
T ss_conf             9679991799857898999999999987--9959997


No 280
>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=77.38  E-value=4.7  Score=18.93  Aligned_cols=50  Identities=20%  Similarity=0.237  Sum_probs=38.2

Q ss_pred             EEEECCCCCCHHHHHHHHHHH---HHHHCCCCEEEEEECCHHHHHHHHHHHHHH
Q ss_conf             465025765978999999999---998089966999808589999999999999
Q gi|254781215|r   80 GAISAGRGIGKTTLNAWLVLW---LMSTRPGISVICLANSETQLKTTLWAEVSK  130 (511)
Q Consensus        80 ~aV~sgrG~GKS~l~a~l~lw---~l~~~p~~kv~vtApt~~Q~~~ilw~Ei~k  130 (511)
                      +-|.|+-|-|||+++..++..   ..-..--.|++.+-|+...+-++ -..++.
T Consensus         2 ~v~~APTG~GKTe~aL~~A~~sah~~k~~~~~~~I~alP~r~~~na~-~~r~~~   54 (424)
T TIGR01587         2 LVIEAPTGYGKTEAALLWALKSAHLIKKQKADKVIFALPTRVTINAM-YRRLKE   54 (424)
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHHHHHHHHHCCEEEECCHHHHHHHH-HHHHHH
T ss_conf             68861789987899999998636664224440101220268889999-999998


No 281
>PRK07590 L,L-diaminopimelate aminotransferase; Validated
Probab=77.07  E-value=4.8  Score=18.87  Aligned_cols=57  Identities=11%  Similarity=-0.073  Sum_probs=34.2

Q ss_pred             HHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEEECCHHH
Q ss_conf             99999999998740565554210124650257659789999999999980899669998085899
Q gi|254781215|r   55 QLEFMEVVDAHCLNSVNNPNPEVFKGAISAGRGIGKTTLNAWLVLWLMSTRPGISVICLANSETQ  119 (511)
Q Consensus        55 Q~e~l~~i~~~~~~~~~~~~~~~~r~aV~sgrG~GKS~l~a~l~lw~l~~~p~~kv~vtApt~~Q  119 (511)
                      --++-++|+++..+..+.+... -.|.|.+|   +|..+.+.    ..++.||-.|++..|.+..
T Consensus        78 ~~eLReAIa~~~~~~~g~~~~~-~~I~vt~G---a~~~l~~i----~~ll~pGDeViip~P~Yp~  134 (409)
T PRK07590         78 YDFLREKIAENDYQARGCDIDA-EEIFVSDG---AKCDTGNI----LDIFGPDNTIAVTDPVYPV  134 (409)
T ss_pred             CHHHHHHHHHHHHHHHCCCCCH-HHEEECCC---HHHHHHHH----HHHHCCCCEEEECCCCCCC
T ss_conf             4999999999999984899876-88687486---79999999----9983999989966887744


No 282
>PRK03158 histidinol-phosphate aminotransferase; Provisional
Probab=77.05  E-value=4.8  Score=18.87  Aligned_cols=59  Identities=15%  Similarity=0.175  Sum_probs=38.8

Q ss_pred             CCHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEEECCHHHHH
Q ss_conf             845899999999999874056555421012465025765978999999999998089966999808589999
Q gi|254781215|r   50 APRSWQLEFMEVVDAHCLNSVNNPNPEVFKGAISAGRGIGKTTLNAWLVLWLMSTRPGISVICLANSETQLK  121 (511)
Q Consensus        50 ~P~~WQ~e~l~~i~~~~~~~~~~~~~~~~r~aV~sgrG~GKS~l~a~l~lw~l~~~p~~kv~vtApt~~Q~~  121 (511)
                      +|+..+.++-+.|+++..    .+ +.  .+.|    |+|=+.+..  ++..+++.|+.+|++..||+..-.
T Consensus        61 YPd~~~~~Lr~~iA~~~g----v~-~~--~I~v----~nGs~e~i~--~~~~~~~~~g~~vvi~~P~f~~Y~  119 (359)
T PRK03158         61 YPDGYAFELRTKVAKHLG----VK-EE--QLIF----GNGSDEVIQ--IISRALLHEGTNTVMANPTFSQYR  119 (359)
T ss_pred             CCCCCHHHHHHHHHHHHC----CC-HH--HEEE----CCCHHHHHH--HHHHHHHCCCCEEECCCCEEEHHH
T ss_conf             969888999999999868----48-67--7998----478899999--999998079981113798205559


No 283
>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=76.97  E-value=4.8  Score=18.86  Aligned_cols=157  Identities=17%  Similarity=0.133  Sum_probs=79.8

Q ss_pred             HHHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEEECCHHHHHHHHHHHHHHHHH
Q ss_conf             99999999999874056555421012465025765978999999999998089966999808589999999999999998
Q gi|254781215|r   54 WQLEFMEVVDAHCLNSVNNPNPEVFKGAISAGRGIGKTTLNAWLVLWLMSTRPGISVICLANSETQLKTTLWAEVSKWLS  133 (511)
Q Consensus        54 WQ~e~l~~i~~~~~~~~~~~~~~~~r~aV~sgrG~GKS~l~a~l~lw~l~~~p~~kv~vtApt~~Q~~~ilw~Ei~k~~~  133 (511)
                      =|...+.+|-.-.....     .|-| -|..==|+|||-++...++-.+.  -|-++..-|||+==|+. -...+.+|+.
T Consensus       311 aQ~r~v~EI~~DL~~~~-----pMnR-LlQGDVGSGKT~VA~la~l~~i~--~GYQ~ALMAPTEiLA~Q-Hy~~~~~~l~  381 (721)
T TIGR00643       311 AQKRVVKEILQDLKSDV-----PMNR-LLQGDVGSGKTLVAALAMLAAIE--SGYQVALMAPTEILAEQ-HYDSLRNLLA  381 (721)
T ss_pred             HHHHHHHHHHHHHCCCC-----CCCC-CCCCCCCCHHHHHHHHHHHHHHH--CCCEEEEECCHHHHHHH-HHHHHHHHHC
T ss_conf             78999999998614787-----5322-21101066389999999999984--69809991776899999-9999999623


Q ss_pred             HCHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCCCCCCCHHHHCCCCCCEEEEECCHH--CCCH--HHHH
Q ss_conf             55000134443222222333444321112357861698530357556100212026761499971110--2997--8898
Q gi|254781215|r  134 LLPNKHWFEMQSLSLHPAPWYSDVLHCSLGIDSKHYSTMCRTYSEERPDTFVGHHNTYGMAIINDEAS--GTPD--VINL  209 (511)
Q Consensus       134 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~ea~~G~h~~~~~lvI~DEAs--gI~d--~i~e  209 (511)
                      ..-    +.+.......+.-......-.+..+.-. +++| |..- =.|..+ +|  .+-|||+||=+  ||..  ...+
T Consensus       382 p~~----~~vaLLTGs~k~~~r~~~~e~i~~G~~~-~~vG-THAL-iqe~ve-f~--~L~lVIiDEQHRFGV~QR~~L~~  451 (721)
T TIGR00643       382 PLG----IEVALLTGSLKGKQRKELLETIASGEIH-LVVG-THAL-IQEKVE-FK--RLGLVIIDEQHRFGVEQRKKLRE  451 (721)
T ss_pred             CCC----CEEEEEECCCCHHHHHHHHHHHHCCCCE-EEEH-HHHH-HHHHHH-HH--CCCEEEEECCCCCHHHHHHHHHH
T ss_conf             548----5788861566787899999998639520-5733-1355-452144-31--47748993233560789999998


Q ss_pred             HHH-HHHCCCCCCEEEEEECCC
Q ss_conf             888-885079981389982389
Q gi|254781215|r  210 GIL-GFLTERNANRFWIMTSNP  230 (511)
Q Consensus       210 ~i~-~~Lt~~g~~~~~i~~~nP  230 (511)
                      =.. +.+-+-.+. .++|+.||
T Consensus       452 KG~~~~~~G~~PH-~L~MtATP  472 (721)
T TIGR00643       452 KGQEGSMIGFAPH-VLVMTATP  472 (721)
T ss_pred             HHHCCCCCCCCCC-EEEEECCC
T ss_conf             6220688677777-64663788


No 284
>CHL00060 atpB ATP synthase CF1 beta subunit
Probab=76.97  E-value=4.8  Score=18.85  Aligned_cols=37  Identities=30%  Similarity=0.250  Sum_probs=25.1

Q ss_pred             CEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEE
Q ss_conf             0124650257659789999999999980899669998
Q gi|254781215|r   77 VFKGAISAGRGIGKTTLNAWLVLWLMSTRPGISVICL  113 (511)
Q Consensus        77 ~~r~aV~sgrG~GKS~l~a~l~lw~l~~~p~~kv~vt  113 (511)
                      .-|+.+-+|.|+|||.++..++.=..-.+-+..|++.
T Consensus       155 GQRigIfggaGvGKTvLl~eli~niak~~~~v~V~a~  191 (480)
T CHL00060        155 GGKIGLFGGAGVGKTVLIMELINNIAKAHGGVSVFGG  191 (480)
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHHHHCCCCCEEEEEE
T ss_conf             6688765689988789999999612003798899999


No 285
>pfam07570 consensus
Probab=76.94  E-value=2.3  Score=20.84  Aligned_cols=26  Identities=27%  Similarity=0.477  Sum_probs=22.5

Q ss_pred             EEECCCCCCHHHHHHHHHHHHHHHCC
Q ss_conf             65025765978999999999998089
Q gi|254781215|r   81 AISAGRGIGKTTLNAWLVLWLMSTRP  106 (511)
Q Consensus        81 aV~sgrG~GKS~l~a~l~lw~l~~~p  106 (511)
                      -+..|||.+||..+|..++..++..|
T Consensus        16 v~kGgrgS~KS~~~a~~~i~~~~kyp   41 (45)
T pfam07570        16 VAKGGRGSGKSSVIALKIILKLLKYP   41 (45)
T ss_pred             EEECCCCCCCHHHHHHHHHHHHHHCC
T ss_conf             75457676602789999999998342


No 286
>PRK06793 fliI flagellum-specific ATP synthase; Validated
Probab=76.93  E-value=3.4  Score=19.83  Aligned_cols=33  Identities=39%  Similarity=0.467  Sum_probs=23.9

Q ss_pred             EEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEE
Q ss_conf             124650257659789999999999980899669998
Q gi|254781215|r   78 FKGAISAGRGIGKTTLNAWLVLWLMSTRPGISVICL  113 (511)
Q Consensus        78 ~r~aV~sgrG~GKS~l~a~l~lw~l~~~p~~kv~vt  113 (511)
                      =|+.+-+|.|+|||+++++++...   .-+..|++.
T Consensus       157 QR~gIfg~sGvGKstLl~~i~~~~---~adv~Vi~l  189 (432)
T PRK06793        157 QKIGIFAGSGVGKSTLLGMIAKNA---KADINVISL  189 (432)
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHC---CCCCEEEEE
T ss_conf             266663268987899999998724---578657999


No 287
>PRK06002 fliI flagellum-specific ATP synthase; Validated
Probab=76.92  E-value=4  Score=19.40  Aligned_cols=23  Identities=43%  Similarity=0.440  Sum_probs=18.2

Q ss_pred             EEEEEECCCCCCHHHHHHHHHHH
Q ss_conf             12465025765978999999999
Q gi|254781215|r   78 FKGAISAGRGIGKTTLNAWLVLW  100 (511)
Q Consensus        78 ~r~aV~sgrG~GKS~l~a~l~lw  100 (511)
                      =|+.+-+|+|+|||++.++++-.
T Consensus       166 QR~gIfgg~GvGKTtLl~~i~~~  188 (450)
T PRK06002        166 QRIGIFAGSGVGKSTLLAMLARA  188 (450)
T ss_pred             CEEEECCCCCCCHHHHHHHHHHH
T ss_conf             77774268999875999999862


No 288
>cd02040 NifH NifH gene encodes component II (iron protein) of nitrogenase. Nitrogenase is responsible for the biological nitrogen fixation, i.e. reduction of molecular nitrogen to ammonia. NifH consists of two oxygen-sensitive metallosulfur proteins: the mollybdenum-iron (alternatively, vanadium-iron or iron-iron) protein (commonly referred to as component 1), and the iron protein (commonly referred to as component 2). The iron protein is a homodimer, with an Fe4S4 cluster bound between the subunits and two ATP-binding domains. It supplies energy by ATP hydrolysis, and transfers electrons from reduced ferredoxin or flavodoxin to component 1 for the reduction of molecular nitrogen to ammonia.
Probab=76.92  E-value=4.9  Score=18.85  Aligned_cols=35  Identities=31%  Similarity=0.274  Sum_probs=28.2

Q ss_pred             CEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEE
Q ss_conf             0124650257659789999999999980899669998
Q gi|254781215|r   77 VFKGAISAGRGIGKTTLNAWLVLWLMSTRPGISVICL  113 (511)
Q Consensus        77 ~~r~aV~sgrG~GKS~l~a~l~lw~l~~~p~~kv~vt  113 (511)
                      |+.+||..==|+|||+.+..|+.-++.  -+.||+++
T Consensus         1 ~r~Iai~GKGGVGKTTtavNLA~aLa~--~GkkVlli   35 (270)
T cd02040           1 MRQIAIYGKGGIGKSTTTQNLSAALAE--MGKKVMIV   35 (270)
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHHHHH--CCCEEEEE
T ss_conf             958999799857789999999999998--79949998


No 289
>COG3640 CooC CO dehydrogenase maturation factor [Cell division and chromosome partitioning]
Probab=76.73  E-value=4.9  Score=18.81  Aligned_cols=116  Identities=18%  Similarity=0.172  Sum_probs=55.9

Q ss_pred             HHHHHCCCCCCCCCCEEECHHHHHHHHHCCCCCCCCCEEEEEEECC--CCCCCCEEEEEECCCEEEEEEECCCCCHHHHH
Q ss_conf             5444317566667873755999988640765318997089996233--34784179998227558998732778988999
Q gi|254781215|r  280 TRVEVCGQFPQQDIDSFIPLNIIEEALNREPCPDPYAPLIMGCDIA--EEGGDNTVVVLRRGPVIEHLFDWSKTDLRTTN  357 (511)
Q Consensus       280 ~r~evlgeFp~~~~~~~i~~~~ie~a~~r~~~~~~~~~~viGvDVA--r~G~D~svi~~r~G~~v~~~~~~~~~d~~~~a  357 (511)
                      ++.-+.|.--+.++.-+=|...+-.++-++.....+.-+++-..-+  .+|+-     .-+|.....+..-+......++
T Consensus        99 ~~LLvmGkie~~GeGC~Cp~~allR~~l~~l~~~~~e~VivDtEAGiEHfgRg-----~~~~vD~vivVvDpS~~sl~ta  173 (255)
T COG3640          99 IDLLVMGKIEEGGEGCACPMNALLRRLLRHLILNRYEVVIVDTEAGIEHFGRG-----TIEGVDLVIVVVDPSYKSLRTA  173 (255)
T ss_pred             CCEEEECCCCCCCCCCCCHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHCCC-----CCCCCCEEEEEECCCHHHHHHH
T ss_conf             00799525567997431627899999999975166748999633456665656-----3257877999957877888889


Q ss_pred             HHHHHHHHHCCCCEEEEEECCCCH---HHHHHHHHCCCEEEEECCC
Q ss_conf             999999986188829980068763---6889898649827984277
Q gi|254781215|r  358 NKISGLVEKYRPDAIIIDANNTGA---RTCDYLEMLGYHVYRVLGQ  400 (511)
Q Consensus       358 ~~i~~~~~~~~~~~i~iD~~GvG~---gV~d~L~~~g~~v~~v~~~  400 (511)
                      .+|.++.++-....|++=.+=+..   .....+.+.|..+.++--.
T Consensus       174 eri~~L~~elg~k~i~~V~NKv~e~e~~~~~~~~~~~~~vlg~iP~  219 (255)
T COG3640         174 ERIKELAEELGIKRIFVVLNKVDEEEELLRELAEELGLEVLGVIPY  219 (255)
T ss_pred             HHHHHHHHHHCCCEEEEEEEECCCHHHHHHHHHHCCCCEEEEECCC
T ss_conf             9999999871875499999503411577776532279748997169


No 290
>pfam07728 AAA_5 AAA domain (dynein-related subfamily). This Pfam entry includes some of the AAA proteins not detected by the pfam00004 model.
Probab=76.71  E-value=4.9  Score=18.81  Aligned_cols=25  Identities=24%  Similarity=0.282  Sum_probs=20.3

Q ss_pred             EEEECCHHCCCHHHHHHHHHHHCCC
Q ss_conf             9997111029978898888885079
Q gi|254781215|r  194 AIINDEASGTPDVINLGILGFLTER  218 (511)
Q Consensus       194 lvI~DEAsgI~d~i~e~i~~~Lt~~  218 (511)
                      .+++||..-.+..+..++...|-++
T Consensus        69 vl~lDEin~a~~~v~~~L~~~le~~   93 (139)
T pfam07728        69 IAVLDEINRANPDVLNSLLSLLDER   93 (139)
T ss_pred             EEEECCHHHCCHHHHHHHHHHHCCC
T ss_conf             8996343448999999999997489


No 291
>PHA02518 ParA-like protein; Provisional
Probab=76.69  E-value=3.4  Score=19.79  Aligned_cols=28  Identities=36%  Similarity=0.560  Sum_probs=21.8

Q ss_pred             CCCCCHHHHHHHHHHHHHHHCCCCEEEEEE
Q ss_conf             576597899999999999808996699980
Q gi|254781215|r   85 GRGIGKTTLNAWLVLWLMSTRPGISVICLA  114 (511)
Q Consensus        85 grG~GKS~l~a~l~lw~l~~~p~~kv~vtA  114 (511)
                      ==|+|||+++..++.++..  .+.+|+++=
T Consensus         9 KGGvGKTT~a~nLA~~la~--~G~~VlliD   36 (211)
T PHA02518          9 KGGAGKTTVATNLASWLHA--DGHKVLLVD   36 (211)
T ss_pred             CCCCHHHHHHHHHHHHHHH--CCCCEEEEE
T ss_conf             9997499999999999997--899489997


No 292
>TIGR01081 mpl UDP-N-acetylmuramate:L-alanyl-gamma-D-glutamyl-meso-diaminopimelate ligase; InterPro: IPR005757    The tripeptide L-ananyl-gamma-D-glutamyl-meso-diaminopimelic acid is efficiently re-cycled during the formation of bacterial cell wall murein. UDP-N-acetylmuramate:L-alanyl-gamma-D-glutamyl-meso-diaminopimelate ligase is an essential enzyme in this process which links the tripeptide to UDP-N-acetylmuramate.; GO: 0016874 ligase activity, 0007047 cell wall organization and biogenesis.
Probab=76.58  E-value=3  Score=20.12  Aligned_cols=53  Identities=23%  Similarity=0.323  Sum_probs=31.1

Q ss_pred             CCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEE
Q ss_conf             75655578458999999999998740565554210124650257659789999999999980899669998
Q gi|254781215|r   43 TPLEGFSAPRSWQLEFMEVVDAHCLNSVNNPNPEVFKGAISAGRGIGKTTLNAWLVLWLMSTRPGISVICL  113 (511)
Q Consensus        43 ~~~~~~~~P~~WQ~e~l~~i~~~~~~~~~~~~~~~~r~aV~sgrG~GKS~l~a~l~lw~l~~~p~~kv~vt  113 (511)
                      ..|++.+|| .|=.+.|-  .+++            =++|+.-|  |||+.+++++ |-|-..-..-.+++
T Consensus        84 ~nl~Y~SGP-QWL~d~~L--~drW------------VlaV~GTH--GKTTT~~M~~-WvLE~~G~~pGFli  136 (459)
T TIGR01081        84 KNLPYTSGP-QWLHDFVL--RDRW------------VLAVAGTH--GKTTTASMLA-WVLEQCGLKPGFLI  136 (459)
T ss_pred             CCCCCCCCC-CHHHHHHH--HCCE------------EEEEECCC--CCHHHHHHHH-HHHHHCCCCCCCEE
T ss_conf             689502175-10563342--1342------------78950788--6046889999-99986379887267


No 293
>PRK07594 type III secretion system ATPase; Validated
Probab=76.49  E-value=3.1  Score=20.08  Aligned_cols=23  Identities=35%  Similarity=0.328  Sum_probs=19.0

Q ss_pred             EEEEEECCCCCCHHHHHHHHHHH
Q ss_conf             12465025765978999999999
Q gi|254781215|r   78 FKGAISAGRGIGKTTLNAWLVLW  100 (511)
Q Consensus        78 ~r~aV~sgrG~GKS~l~a~l~lw  100 (511)
                      -|+.+-+|.|+|||+++++++..
T Consensus       156 QR~gIfgg~GvGKTtLl~~i~~~  178 (433)
T PRK07594        156 QRVGIFSAPGVGKSTLLAMLCNA  178 (433)
T ss_pred             CEEEECCCCCCCHHHHHHHHHHC
T ss_conf             87420478999855899999842


No 294
>PRK13634 cbiO cobalt transporter ATP-binding subunit; Provisional
Probab=76.44  E-value=0.36  Score=25.97  Aligned_cols=37  Identities=24%  Similarity=0.160  Sum_probs=25.7

Q ss_pred             HHHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCCCHHHHHHHHH
Q ss_conf             999999999998740565554210124650257659789999999
Q gi|254781215|r   54 WQLEFMEVVDAHCLNSVNNPNPEVFKGAISAGRGIGKTTLNAWLV   98 (511)
Q Consensus        54 WQ~e~l~~i~~~~~~~~~~~~~~~~r~aV~sgrG~GKS~l~a~l~   98 (511)
                      +++++|+.|--....+        -.+++....|.|||+++..+.
T Consensus         5 ~e~~AL~~Vsl~i~~G--------e~vaiiG~sGsGKSTLl~~l~   41 (276)
T PRK13634          5 FERRALYDVNVSIPSG--------SYVAIIGHTGSGKSTLLQHLN   41 (276)
T ss_pred             CCCEEEECCEEEECCC--------CEEEEECCCCCHHHHHHHHHH
T ss_conf             9766651447799899--------899999999969999999997


No 295
>PRK07667 uridine kinase; Provisional
Probab=76.30  E-value=2.3  Score=20.85  Aligned_cols=24  Identities=33%  Similarity=0.151  Sum_probs=20.7

Q ss_pred             EEEEEECCCCCCHHHHHHHHHHHH
Q ss_conf             124650257659789999999999
Q gi|254781215|r   78 FKGAISAGRGIGKTTLNAWLVLWL  101 (511)
Q Consensus        78 ~r~aV~sgrG~GKS~l~a~l~lw~  101 (511)
                      +-|+|+.|-|.|||+++.-++--+
T Consensus        15 ~iIgIaG~sgSGKTTla~~L~~~l   38 (190)
T PRK07667         15 FILGIDGLSRSGKTTFVANLKENM   38 (190)
T ss_pred             EEEEEECCCCCCHHHHHHHHHHHH
T ss_conf             999977989788999999999998


No 296
>PRK08472 fliI flagellum-specific ATP synthase; Validated
Probab=75.72  E-value=3  Score=20.14  Aligned_cols=23  Identities=43%  Similarity=0.459  Sum_probs=19.2

Q ss_pred             EEEEEECCCCCCHHHHHHHHHHH
Q ss_conf             12465025765978999999999
Q gi|254781215|r   78 FKGAISAGRGIGKTTLNAWLVLW  100 (511)
Q Consensus        78 ~r~aV~sgrG~GKS~l~a~l~lw  100 (511)
                      =|+.+-+|.|+|||++++.++.+
T Consensus       159 QR~gIf~g~GvGKt~Ll~~i~~~  181 (435)
T PRK08472        159 QKLGIFAGSGVGKSTLMGMIVKG  181 (435)
T ss_pred             CEEECCCCCCCCCCHHHHHHHHH
T ss_conf             66512358999833578888776


No 297
>KOG0327 consensus
Probab=75.61  E-value=2.2  Score=20.96  Aligned_cols=66  Identities=18%  Similarity=0.128  Sum_probs=42.1

Q ss_pred             CCCCCHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHH-CCCCEEEEEECCHHHHHHHH
Q ss_conf             5578458999999999998740565554210124650257659789999999999980-89966999808589999999
Q gi|254781215|r   47 GFSAPRSWQLEFMEVVDAHCLNSVNNPNPEVFKGAISAGRGIGKTTLNAWLVLWLMST-RPGISVICLANSETQLKTTL  124 (511)
Q Consensus        47 ~~~~P~~WQ~e~l~~i~~~~~~~~~~~~~~~~r~aV~sgrG~GKS~l~a~l~lw~l~~-~p~~kv~vtApt~~Q~~~il  124 (511)
                      +|.-|-.-|..++.-+-..            .-+.+.+--|+|||...+..++-.+.+ ..-+.+++.|||...++.+.
T Consensus        45 GFekPSaIQqrAI~p~i~G------------~dv~~qaqsgTgKt~af~i~ilq~iD~~~ke~qalilaPtreLa~q~~  111 (397)
T KOG0327          45 GFEKPSAIQQRAILPCIKG------------HDVIAQAQSGTGKTAAFLISILQQIDMSVKETQALILAPTRELAQQIQ  111 (397)
T ss_pred             CCCCCHHHHHCCCCCCCCC------------CCEEEEEECCCCCHHHHHHHHHHHCCCCHHHHHHHHHCCHHHHHHHHH
T ss_conf             3688227776343553468------------744676302544114667888751374167777988613278889899


No 298
>PRK08533 flagellar accessory protein FlaH; Reviewed
Probab=75.56  E-value=5.3  Score=18.62  Aligned_cols=47  Identities=17%  Similarity=0.100  Sum_probs=29.3

Q ss_pred             CCCCCEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEEECCHHH
Q ss_conf             54210124650257659789999999999980899669998085899
Q gi|254781215|r   73 PNPEVFKGAISAGRGIGKTTLNAWLVLWLMSTRPGISVICLANSETQ  119 (511)
Q Consensus        73 ~~~~~~r~aV~sgrG~GKS~l~a~l~lw~l~~~p~~kv~vtApt~~Q  119 (511)
                      ..|...-+.|..+.|+|||.++..++.-++.....+-.+.|-.|.++
T Consensus        20 Gip~gs~~li~G~~GtGKsi~~~~~~~~~l~~g~~~~yis~e~t~~~   66 (230)
T PRK08533         20 GIPFGSIILIEGDESTGKSILSQRLAYGFLQNGYSVSYVSSQLTTTE   66 (230)
T ss_pred             CCCCCCEEEEECCCCCCHHHHHHHHHHHHHHCCCEEEEEEECCCHHH
T ss_conf             98898489998689987899999999999878986999994389999


No 299
>PRK08927 fliI flagellum-specific ATP synthase; Validated
Probab=75.28  E-value=4  Score=19.36  Aligned_cols=36  Identities=25%  Similarity=0.240  Sum_probs=25.4

Q ss_pred             EEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEEECCHH
Q ss_conf             12465025765978999999999998089966999808589
Q gi|254781215|r   78 FKGAISAGRGIGKTTLNAWLVLWLMSTRPGISVICLANSET  118 (511)
Q Consensus        78 ~r~aV~sgrG~GKS~l~a~l~lw~l~~~p~~kv~vtApt~~  118 (511)
                      -|+.+-+|.|+|||+++++++-.     -.+.+.|.|---.
T Consensus       159 QRigIfagsGvGKs~Ll~~i~r~-----~~adv~VialIGe  194 (441)
T PRK08927        159 QRLGIFAGSGVGKSVLLSMLARN-----TDADVSVIGLIGE  194 (441)
T ss_pred             CEEEECCCCCCCHHHHHHHHHHH-----CCCCCEEEEECCC
T ss_conf             46663168999878999999864-----1677378752265


No 300
>COG1074 RecB ATP-dependent exoDNAse (exonuclease V) beta subunit (contains helicase and exonuclease domains) [DNA replication, recombination, and repair]
Probab=75.25  E-value=5.4  Score=18.57  Aligned_cols=57  Identities=18%  Similarity=0.154  Sum_probs=37.8

Q ss_pred             CHHHHCCCCCCEEEEECCHHCCCHHHHHHHHHHHCCCCC-CEEEEEECCCCCCCCHHHH
Q ss_conf             002120267614999711102997889888888507998-1389982389987655676
Q gi|254781215|r  182 DTFVGHHNTYGMAIINDEASGTPDVINLGILGFLTERNA-NRFWIMTSNPRRLSGKFYE  239 (511)
Q Consensus       182 ea~~G~h~~~~~lvI~DEAsgI~d~i~e~i~~~Lt~~g~-~~~~i~~~nP~~~~g~fy~  239 (511)
                      .-..-++... -.+.+||+..-+..=|.+++...++... ..-+++.|-|.-.-+.|+.
T Consensus       370 ~l~~~lr~~~-~~iLIDEfQDT~~~Q~~Il~~l~~~~~~~~~~lF~VGD~KQSIY~FRg  427 (1139)
T COG1074         370 ELAESLREQY-PHILIDEFQDTDPQQWRILSRLFAGFKAGNRTLFLVGDPKQSIYRFRG  427 (1139)
T ss_pred             HHHHHHHHCC-CEEEEECCCCCCHHHHHHHHHHHHCCCCCCCCEEEECCCHHHHHHHCC
T ss_conf             9999998479-858874034599889999999972566778507997473476553137


No 301
>PRK08116 hypothetical protein; Validated
Probab=75.12  E-value=5.4  Score=18.55  Aligned_cols=53  Identities=17%  Similarity=0.129  Sum_probs=30.5

Q ss_pred             HHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEE
Q ss_conf             99999999998740565554210124650257659789999999999980899669998
Q gi|254781215|r   55 QLEFMEVVDAHCLNSVNNPNPEVFKGAISAGRGIGKTTLNAWLVLWLMSTRPGISVICL  113 (511)
Q Consensus        55 Q~e~l~~i~~~~~~~~~~~~~~~~r~aV~sgrG~GKS~l~a~l~lw~l~~~p~~kv~vt  113 (511)
                      ..++.+..+.+.......    ..-+....+-|+|||+|++.++...+- + +..|+++
T Consensus        90 a~~~a~~Y~~~f~~~~~~----~~GLll~G~~GtGKThLa~aIa~~l~~-~-g~~V~~~  142 (262)
T PRK08116         90 AYKVAVKYVKKFEEMKKE----SVGLLLWGSPGNGKTYLAAAIANELIE-K-GVPVVFV  142 (262)
T ss_pred             HHHHHHHHHHHHHHHCCC----CCEEEEECCCCCCHHHHHHHHHHHHHH-C-CCEEEEE
T ss_conf             999999999989873646----861899898999899999999999998-7-9939998


No 302
>PRK06067 flagellar accessory protein FlaH; Validated
Probab=75.08  E-value=5.4  Score=18.54  Aligned_cols=48  Identities=17%  Similarity=0.034  Sum_probs=30.3

Q ss_pred             CCCCCEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEEECCHHHH
Q ss_conf             542101246502576597899999999999808996699980858999
Q gi|254781215|r   73 PNPEVFKGAISAGRGIGKTTLNAWLVLWLMSTRPGISVICLANSETQL  120 (511)
Q Consensus        73 ~~~~~~r~aV~sgrG~GKS~l~a~l~lw~l~~~p~~kv~vtApt~~Q~  120 (511)
                      -.|...-+.|..+.|+|||.++.-++.-.+.....+-.+.+-.+..|.
T Consensus        28 G~p~g~~~li~G~~G~GKt~~~~~f~~~~~~~g~~~~~~~~ee~~~~~   75 (241)
T PRK06067         28 GIPFGSLILIEGENDTGKSVLSQQFVWGALNQGKRGLAITTENTSKSY   75 (241)
T ss_pred             CCCCCEEEEEECCCCCCHHHHHHHHHHHHHHCCCEEEEEEECCCHHHH
T ss_conf             977990899980799887999999999998679829999942899999


No 303
>PRK09270 frcK putative fructose transport system kinase; Reviewed
Probab=74.90  E-value=5.5  Score=18.51  Aligned_cols=35  Identities=29%  Similarity=0.237  Sum_probs=25.1

Q ss_pred             EEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEE
Q ss_conf             12465025765978999999999998089966999
Q gi|254781215|r   78 FKGAISAGRGIGKTTLNAWLVLWLMSTRPGISVIC  112 (511)
Q Consensus        78 ~r~aV~sgrG~GKS~l~a~l~lw~l~~~p~~kv~v  112 (511)
                      +-++|+.+-|+|||+++..++--.--..+...+++
T Consensus        35 ~lIgIaG~pGSGKSTlA~~l~~~L~~~~~~~~~~~   69 (230)
T PRK09270         35 TVVGIAGPPGAGKSTLAETLWEALSQQGPELPAIQ   69 (230)
T ss_pred             EEEEEECCCCCCHHHHHHHHHHHHHHCCCCCCEEE
T ss_conf             89999899988999999999999862379985799


No 304
>PRK06217 hypothetical protein; Validated
Probab=74.88  E-value=2.9  Score=20.27  Aligned_cols=28  Identities=32%  Similarity=0.279  Sum_probs=22.6

Q ss_pred             CEEEEEECCCCCCHHHHHHHHHHHHHHH
Q ss_conf             0124650257659789999999999980
Q gi|254781215|r   77 VFKGAISAGRGIGKTTLNAWLVLWLMST  104 (511)
Q Consensus        77 ~~r~aV~sgrG~GKS~l~a~l~lw~l~~  104 (511)
                      |.|+.|-..-|.|||+++..+.--.-+.
T Consensus         1 m~rI~i~G~sGsGkSTla~~La~~l~~~   28 (185)
T PRK06217          1 MMRIHITGASGSGTTTLGAALAEALDLP   28 (185)
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHHHCCC
T ss_conf             9679997899887899999999975989


No 305
>PRK05480 uridine kinase; Provisional
Probab=74.87  E-value=2.7  Score=20.45  Aligned_cols=24  Identities=33%  Similarity=0.338  Sum_probs=19.6

Q ss_pred             EEEEEECCCCCCHHHHHHHHHHHH
Q ss_conf             124650257659789999999999
Q gi|254781215|r   78 FKGAISAGRGIGKTTLNAWLVLWL  101 (511)
Q Consensus        78 ~r~aV~sgrG~GKS~l~a~l~lw~  101 (511)
                      +=++|++|-|.|||+++..+.--+
T Consensus         7 ~iIgIaG~SgSGKTT~a~~L~~~l   30 (209)
T PRK05480          7 IIIGIAGGSGSGKTTVASTIYEEL   30 (209)
T ss_pred             EEEEEECCCCCCHHHHHHHHHHHC
T ss_conf             899998999778999999999980


No 306
>PRK07777 aminotransferase; Validated
Probab=74.79  E-value=5.5  Score=18.49  Aligned_cols=27  Identities=11%  Similarity=0.175  Sum_probs=13.5

Q ss_pred             HHHHHHHCCCCCCEEEEEECCCCCCCCHHH
Q ss_conf             888888507998138998238998765567
Q gi|254781215|r  209 LGILGFLTERNANRFWIMTSNPRRLSGKFY  238 (511)
Q Consensus       209 e~i~~~Lt~~g~~~~~i~~~nP~~~~g~fy  238 (511)
                      +.++..++.   +.+.+.+.||+|++|..+
T Consensus       150 ~~l~~~~~~---~tk~iil~~P~NPTG~v~  176 (386)
T PRK07777        150 DALRAAVTP---RTRALIVNSPHNPTGTVL  176 (386)
T ss_pred             HHHHHHCCC---CCEEEEECCCCCCCCCCC
T ss_conf             999974687---776999799969888488


No 307
>PRK06820 type III secretion system ATPase; Validated
Probab=74.70  E-value=2.7  Score=20.44  Aligned_cols=23  Identities=35%  Similarity=0.318  Sum_probs=18.9

Q ss_pred             EEEEEECCCCCCHHHHHHHHHHH
Q ss_conf             12465025765978999999999
Q gi|254781215|r   78 FKGAISAGRGIGKTTLNAWLVLW  100 (511)
Q Consensus        78 ~r~aV~sgrG~GKS~l~a~l~lw  100 (511)
                      -|+.+-+|.|+|||++++.++.+
T Consensus       164 QR~gIfgg~GvGKT~Ll~~i~~~  186 (445)
T PRK06820        164 QRIGIFAAAGVGKSTLLSMLCAD  186 (445)
T ss_pred             CCCEEECCCCCCCCHHHHHHHHH
T ss_conf             74211068999812234456530


No 308
>TIGR03371 cellulose_yhjQ cellulose synthase operon protein YhjQ. Members of this family are the YhjQ protein, found immediately upsteam of bacterial cellulose synthase (bcs) genes in a broad range of bacteria, including both copies of the bcs locus in Klebsiella pneumoniae. In several species it is seen clearly as part of the bcs operon. It is identified as a probable component of the bacterial cellulose metabolic process not only by gene location, but also by partial phylogenetic profiling, or Haft-Selengut algorithm (PMID:16930487), based on a bacterial cellulose biosynthesis genome property profile. Cellulose plays an important role in biofilm formation and structural integrity in some bacteria. Mutants in yhjQ in Escherichia coli, show altered morphology an growth, but the function of YhjQ has not yet been determined.
Probab=74.32  E-value=5.7  Score=18.42  Aligned_cols=36  Identities=33%  Similarity=0.312  Sum_probs=26.2

Q ss_pred             CEEEEEECCC-CCCHHHHHHHHHHHHHHHCCCCEEEEEE
Q ss_conf             0124650257-6597899999999999808996699980
Q gi|254781215|r   77 VFKGAISAGR-GIGKTTLNAWLVLWLMSTRPGISVICLA  114 (511)
Q Consensus        77 ~~r~aV~sgr-G~GKS~l~a~l~lw~l~~~p~~kv~vtA  114 (511)
                      |..++|.++. |+|||+++..++.-++  ..+.+|+++=
T Consensus         1 MkiIav~n~KGGVGKTT~avNLA~~La--~~G~rVLlID   37 (246)
T TIGR03371         1 MKVIAIVGIKGGVGRTTLTAALASALK--LLGEPVLAID   37 (246)
T ss_pred             CEEEEEECCCCCCCHHHHHHHHHHHHH--HCCCCEEEEE
T ss_conf             939999759998549999999999999--6899789997


No 309
>PRK08912 hypothetical protein; Provisional
Probab=74.27  E-value=5.7  Score=18.41  Aligned_cols=23  Identities=17%  Similarity=0.172  Sum_probs=12.3

Q ss_pred             HHHHHHHCCCCEEEEEECCHHHH
Q ss_conf             99999808996699980858999
Q gi|254781215|r   98 VLWLMSTRPGISVICLANSETQL  120 (511)
Q Consensus        98 ~lw~l~~~p~~kv~vtApt~~Q~  120 (511)
                      ++-.+++.||-.|++..|++..-
T Consensus       102 ~~~~al~~pGD~Vlv~~P~y~~y  124 (387)
T PRK08912        102 AALLALVEPGDEVVLFQPLYDSY  124 (387)
T ss_pred             HHHHHHCCCCCEEEEECCCCHHH
T ss_conf             99999669989899948808117


No 310
>PRK13705 plasmid-partitioning protein SopA; Provisional
Probab=74.23  E-value=5.7  Score=18.41  Aligned_cols=33  Identities=24%  Similarity=0.295  Sum_probs=23.8

Q ss_pred             EEEEC-CCCCCHHHHHHHHHHHHHHHCCCCEEEEEE
Q ss_conf             46502-576597899999999999808996699980
Q gi|254781215|r   80 GAISA-GRGIGKTTLNAWLVLWLMSTRPGISVICLA  114 (511)
Q Consensus        80 ~aV~s-grG~GKS~l~a~l~lw~l~~~p~~kv~vtA  114 (511)
                      +||+- ==|+|||+.+..++-+.+.  .|-||+++=
T Consensus       109 IAVaNqKGGvGKTTTavnLA~~LAl--~G~RVLlID  142 (388)
T PRK13705        109 IGVAAHKGGVYKTSVSVHLAQDLAL--KGLRVLLVE  142 (388)
T ss_pred             EEEECCCCCCCHHHHHHHHHHHHHH--CCCEEEEEE
T ss_conf             9995278885599999999999997--799089995


No 311
>PRK13231 nitrogenase reductase-like protein; Reviewed
Probab=74.22  E-value=5.7  Score=18.40  Aligned_cols=41  Identities=24%  Similarity=0.172  Sum_probs=28.7

Q ss_pred             CEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEEE--CCHHHH
Q ss_conf             01246502576597899999999999808996699980--858999
Q gi|254781215|r   77 VFKGAISAGRGIGKTTLNAWLVLWLMSTRPGISVICLA--NSETQL  120 (511)
Q Consensus        77 ~~r~aV~sgrG~GKS~l~a~l~lw~l~~~p~~kv~vtA--pt~~Q~  120 (511)
                      |+++||-.==|+|||+.++.+...++.   +.||+++-  |..+-.
T Consensus         2 m~~iAiyGKGGIGKSTt~~NlaaalA~---g~rVl~igcDpk~dst   44 (264)
T PRK13231          2 LKKIAIYGKGGIGKSTTVSNMAAAYSS---DNSTLVIGCDPKADTT   44 (264)
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHHHHC---CCCEEEECCCCCCCHH
T ss_conf             428999789854788899999999987---9977998568885024


No 312
>KOG1411 consensus
Probab=74.01  E-value=3.3  Score=19.90  Aligned_cols=26  Identities=8%  Similarity=0.290  Sum_probs=14.6

Q ss_pred             EEECCCCEEEEEECHHHCCCCCCHHHHH
Q ss_conf             9987998499984125489998989999
Q gi|254781215|r  445 FIVPNTGELAIESKRVKGAKSTDYSDGL  472 (511)
Q Consensus       445 ~~~~~~gki~ie~Kkkrg~~SPD~ADAl  472 (511)
                      ...+++|||-+-..  ....-|=+|||+
T Consensus       394 iYmT~dGRiS~aG~--ss~nV~yLa~ai  419 (427)
T KOG1411         394 IYLTKDGRISMAGL--SSSNVPYLADAI  419 (427)
T ss_pred             EEECCCCEEEECCC--CCCCCCCCCHHH
T ss_conf             66525863762345--656775411106


No 313
>KOG2749 consensus
Probab=73.96  E-value=5.8  Score=18.36  Aligned_cols=30  Identities=17%  Similarity=0.161  Sum_probs=26.2

Q ss_pred             CCCEEEEEECCCCCCHHHHHHHHHHHHHHH
Q ss_conf             210124650257659789999999999980
Q gi|254781215|r   75 PEVFKGAISAGRGIGKTTLNAWLVLWLMST  104 (511)
Q Consensus        75 ~~~~r~aV~sgrG~GKS~l~a~l~lw~l~~  104 (511)
                      ....|+-|..+..+|||++.-.|+.|.+-.
T Consensus       101 ~~GPrv~vVGp~d~GKsTl~r~L~nyavk~  130 (415)
T KOG2749         101 SYGPRVMVVGPTDVGKSTLCRILLNYAVKQ  130 (415)
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHHHHHHHC
T ss_conf             259779998987656678999999999871


No 314
>PRK04196 V-type ATP synthase subunit B; Provisional
Probab=73.95  E-value=5.1  Score=18.74  Aligned_cols=32  Identities=19%  Similarity=0.070  Sum_probs=25.0

Q ss_pred             EEEEEECCCCCCHHHHHHHHHHHHHHHCCCCE
Q ss_conf             12465025765978999999999998089966
Q gi|254781215|r   78 FKGAISAGRGIGKTTLNAWLVLWLMSTRPGIS  109 (511)
Q Consensus        78 ~r~aV~sgrG~GKS~l~a~l~lw~l~~~p~~k  109 (511)
                      =|+.+-+|.|+|||.+++.++....+...+..
T Consensus       144 Qr~~If~gsGvgks~l~~~i~~qa~~~~~~~~  175 (460)
T PRK04196        144 QKLPIFSGSGLPHNELAAQIARQAKVLGSEEK  175 (460)
T ss_pred             CEEEEECCCCCCCCHHHHHHHHHHHHCCCCCC
T ss_conf             57655338998811699999998775057888


No 315
>PRK09280 F0F1 ATP synthase subunit beta; Validated
Probab=73.88  E-value=5.8  Score=18.35  Aligned_cols=38  Identities=29%  Similarity=0.237  Sum_probs=27.1

Q ss_pred             CCEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEE
Q ss_conf             10124650257659789999999999980899669998
Q gi|254781215|r   76 EVFKGAISAGRGIGKTTLNAWLVLWLMSTRPGISVICL  113 (511)
Q Consensus        76 ~~~r~aV~sgrG~GKS~l~a~l~lw~l~~~p~~kv~vt  113 (511)
                      ..-|+.+-+|.|+|||.++..++.-.+..+.+..|++.
T Consensus       144 kGqrigIfggaGvGKTvLl~eli~n~a~~~~~v~V~a~  181 (466)
T PRK09280        144 KGGKIGLFGGAGVGKTVLIMELINNIAKEHGGYSVFAG  181 (466)
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEE
T ss_conf             77479855799998008999999999986599099997


No 316
>COG2842 Uncharacterized ATPase, putative transposase [General function prediction only]
Probab=73.88  E-value=5.8  Score=18.35  Aligned_cols=109  Identities=14%  Similarity=0.040  Sum_probs=60.6

Q ss_pred             EEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEEECCHHHHHHHHHHHHHHHHHHCHHCCCCCCCCCCCCCCCCCCCC
Q ss_conf             12465025765978999999999998089966999808589999999999999998550001344432222223334443
Q gi|254781215|r   78 FKGAISAGRGIGKTTLNAWLVLWLMSTRPGISVICLANSETQLKTTLWAEVSKWLSLLPNKHWFEMQSLSLHPAPWYSDV  157 (511)
Q Consensus        78 ~r~aV~sgrG~GKS~l~a~l~lw~l~~~p~~kv~vtApt~~Q~~~ilw~Ei~k~~~~~~~~~~~~~~~~~~~~~~~~~~~  157 (511)
                      +-+.|.+.+|.|||..+-.++    -.+ +...++.++....+...+--++...         +..+...+..       
T Consensus        95 ~l~~vyg~~g~gKt~a~~~y~----~s~-p~~~l~~~~p~~~a~~~i~~i~~~~---------~~~~~~~~~d-------  153 (297)
T COG2842          95 SLVVVYGYAGLGKTQAAKNYA----PSN-PNALLIEADPSYTALVLILIICAAA---------FGATDGTIND-------  153 (297)
T ss_pred             CEEEEECCCCCHHHHHHHHHC----CCC-CCCEEECCCHHHHHHHHHHHHHHHH---------HCCCCHHHHH-------
T ss_conf             547886332200689998653----358-6413615881367889999999987---------4014216888-------


Q ss_pred             CCCCCCCCCCEEEEEECCCCCCCCCHHHHCCCCCCEEEEECCHHCCCHHHHHHHHHHHCCCCCCEEEEEECCCC
Q ss_conf             21112357861698530357556100212026761499971110299788988888850799813899823899
Q gi|254781215|r  158 LHCSLGIDSKHYSTMCRTYSEERPDTFVGHHNTYGMAIINDEASGTPDVINLGILGFLTERNANRFWIMTSNPR  231 (511)
Q Consensus       158 ~~~~~~~~~~~~~~~~~~~s~~~~ea~~G~h~~~~~lvI~DEAsgI~d~i~e~i~~~Lt~~g~~~~~i~~~nP~  231 (511)
                                      .+.+  .....    .++.-++++|||-..|-..++.++-..+..|-.  ++..|+|.
T Consensus       154 ----------------~~~~--~~~~l----~~~~~~iivDEA~~L~~~ale~lr~i~d~~Gi~--~vLvG~pr  203 (297)
T COG2842         154 ----------------LTER--LMIRL----RDTVRLIIVDEADRLPYRALEELRRIHDKTGIG--VVLVGMPR  203 (297)
T ss_pred             ----------------HHHH--HHHHH----CCCCCEEEEEHHHCCCHHHHHHHHHHHHHHCCE--EEEECCHH
T ss_conf             ----------------8999--99997----157652665032125868999999988750815--99836768


No 317
>PRK06348 aspartate aminotransferase; Provisional
Probab=73.85  E-value=5.8  Score=18.35  Aligned_cols=60  Identities=18%  Similarity=0.047  Sum_probs=34.8

Q ss_pred             HHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEEECCHHHHHH
Q ss_conf             9999999998740565554210124650257659789999999999980899669998085899999
Q gi|254781215|r   56 LEFMEVVDAHCLNSVNNPNPEVFKGAISAGRGIGKTTLNAWLVLWLMSTRPGISVICLANSETQLKT  122 (511)
Q Consensus        56 ~e~l~~i~~~~~~~~~~~~~~~~r~aV~sgrG~GKS~l~a~l~lw~l~~~p~~kv~vtApt~~Q~~~  122 (511)
                      .++.++|+++..+.-+.+... -.+.+..|      ...+..++-.+++.||-.|++..|++.....
T Consensus        69 ~~lR~aia~~~~~~~g~~~~~-~~I~it~G------~~~al~~~~~~l~~pGD~Vlv~~P~Y~~y~~  128 (383)
T PRK06348         69 KELIEEIINYYKKDYNLSFKE-NEIMAVVG------ACHGMYLALQSILDPGDEVIIHEPYFTPYKD  128 (383)
T ss_pred             HHHHHHHHHHHHHHHCCCCCH-HHEEEECC------HHHHHHHHHHHHCCCCCEEEEECCCCCHHHH
T ss_conf             999999999999987899976-74999489------8999999999965999989980698602699


No 318
>cd02024 NRK1 Nicotinamide riboside kinase (NRK) is an enzyme involved in the metabolism of nicotinamide adenine dinucleotide (NAD+). This enzyme catalyzes the phosphorylation of nicotinamide riboside (NR) to form nicotinamide mononucleotide (NMN). It defines the NR salvage pathway of NAD+ biosynthesis in addition to the pathways through nicotinic acid mononucleotide (NaMN). This enzyme can also phosphorylate the anticancer drug tiazofurin, which is an analog of nicotinamide riboside.
Probab=73.82  E-value=2.9  Score=20.24  Aligned_cols=21  Identities=38%  Similarity=0.238  Sum_probs=18.0

Q ss_pred             EEEECCCCCCHHHHHHHHHHH
Q ss_conf             465025765978999999999
Q gi|254781215|r   80 GAISAGRGIGKTTLNAWLVLW  100 (511)
Q Consensus        80 ~aV~sgrG~GKS~l~a~l~lw  100 (511)
                      ++|+.|-+.|||+++..+.--
T Consensus         2 IgIaG~S~SGKTTla~~L~~~   22 (187)
T cd02024           2 VGISGVTNSGKTTLAKLLQRI   22 (187)
T ss_pred             EEEECCCCCCHHHHHHHHHHH
T ss_conf             899688887599999999998


No 319
>PHA02519 plasmid partition protein SopA; Reviewed
Probab=73.74  E-value=5.9  Score=18.33  Aligned_cols=65  Identities=18%  Similarity=0.281  Sum_probs=38.9

Q ss_pred             HHHHHHHHHHHHHHCCCCCCC-CCCEEEEEEC-CCCCCHHHHHHHHHHHHHHHCCCCEEEEEECCHHHH
Q ss_conf             999999999998740565554-2101246502-576597899999999999808996699980858999
Q gi|254781215|r   54 WQLEFMEVVDAHCLNSVNNPN-PEVFKGAISA-GRGIGKTTLNAWLVLWLMSTRPGISVICLANSETQL  120 (511)
Q Consensus        54 WQ~e~l~~i~~~~~~~~~~~~-~~~~r~aV~s-grG~GKS~l~a~l~lw~l~~~p~~kv~vtApt~~Q~  120 (511)
                      |-.+-+.++..+......+.- .....+||.. ==|+|||+.+..++-+.++.  |-+|+++=-.-.|+
T Consensus        82 ytl~~i~~lR~~l~~~~~rp~~~~~~VIAVaN~KGGVGKTTTavnLA~~LAl~--G~RVL~ID~lDPQa  148 (387)
T PHA02519         82 YTIDQISHMRDHFGNPNQRPDDKNPVVLAVMSHKGGVYKTSSAVHTAQWLALQ--GHRVLLIEGNDPQG  148 (387)
T ss_pred             CCHHHHHHHHHHHCCCCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHC--CCCEEEEECCCCCC
T ss_conf             57999999999864566798988752899861688776999999999999976--99689995988520


No 320
>KOG0257 consensus
Probab=73.71  E-value=5.9  Score=18.33  Aligned_cols=26  Identities=23%  Similarity=0.387  Sum_probs=14.9

Q ss_pred             HHHHHHCCCCCCEEEEEECCCCCCCCHHH
Q ss_conf             88888507998138998238998765567
Q gi|254781215|r  210 GILGFLTERNANRFWIMTSNPRRLSGKFY  238 (511)
Q Consensus       210 ~i~~~Lt~~g~~~~~i~~~nP~~~~g~fy  238 (511)
                      -++.++|..   .++|.+-||+|++|..+
T Consensus       164 ~le~~~t~k---Tk~Ii~ntPhNPtGkvf  189 (420)
T KOG0257         164 ELESKITEK---TKAIILNTPHNPTGKVF  189 (420)
T ss_pred             HHHHHCCCC---CCEEEEECCCCCCCCCC
T ss_conf             998643677---64799948999867305


No 321
>cd04169 RF3 RF3 subfamily.  Peptide chain release factor 3 (RF3) is a protein involved in the termination step of translation in bacteria.  Termination occurs when class I release factors (RF1 or RF2) recognize the stop codon at the A-site of the ribosome and activate the release of the nascent polypeptide.  The class II release factor RF3 then initiates the release of the class I RF from the ribosome.  RF3 binds to the RF/ribosome complex in the inactive (GDP-bound) state.  GDP/GTP exchange occurs, followed by the release of the class I RF.  Subsequent hydrolysis of GTP to GDP triggers the release of RF3 from the ribosome.  RF3 also enhances the efficiency of class I RFs at less preferred stop codons and at stop codons in weak contexts.
Probab=73.71  E-value=4.5  Score=19.09  Aligned_cols=27  Identities=33%  Similarity=0.202  Sum_probs=20.4

Q ss_pred             EEEEEECCCCCCHHHHHHHHHHHHHHH
Q ss_conf             124650257659789999999999980
Q gi|254781215|r   78 FKGAISAGRGIGKTTLNAWLVLWLMST  104 (511)
Q Consensus        78 ~r~aV~sgrG~GKS~l~a~l~lw~l~~  104 (511)
                      +-+++.+-.|.|||+|+-.++.--=.+
T Consensus         3 Rniai~gH~gaGKTtL~EalL~~~G~i   29 (267)
T cd04169           3 RTFAIISHPDAGKTTLTEKLLLFGGAI   29 (267)
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHCCCC
T ss_conf             179998479999899999999866863


No 322
>cd02023 UMPK Uridine monophosphate kinase (UMPK, EC 2.7.1.48), also known as uridine kinase or uridine-cytidine kinase (UCK), catalyzes the reversible phosphoryl transfer from ATP to uridine or cytidine to yield UMP or CMP. In the primidine nucleotide-salvage pathway, this enzyme combined with nucleoside diphosphate kinases further phosphorylates UMP and CMP to form UTP and CTP. This kinase also catalyzes the phosphorylation of several cytotoxic ribonucleoside analogs such as 5-flurrouridine and cyclopentenyl-cytidine.
Probab=73.71  E-value=3  Score=20.20  Aligned_cols=22  Identities=36%  Similarity=0.444  Sum_probs=18.0

Q ss_pred             EEEECCCCCCHHHHHHHHHHHH
Q ss_conf             4650257659789999999999
Q gi|254781215|r   80 GAISAGRGIGKTTLNAWLVLWL  101 (511)
Q Consensus        80 ~aV~sgrG~GKS~l~a~l~lw~  101 (511)
                      ++|+++-|.|||+++..|.--+
T Consensus         2 IgI~G~sgsGKTT~a~~L~~~l   23 (198)
T cd02023           2 IGIAGGSGSGKTTVAEEIIEQL   23 (198)
T ss_pred             EEEECCCCCCHHHHHHHHHHHH
T ss_conf             8988999885999999999980


No 323
>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=73.67  E-value=5.9  Score=18.32  Aligned_cols=36  Identities=31%  Similarity=0.288  Sum_probs=26.9

Q ss_pred             EEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEEECCH
Q ss_conf             46502576597899999999999808996699980858
Q gi|254781215|r   80 GAISAGRGIGKTTLNAWLVLWLMSTRPGISVICLANSE  117 (511)
Q Consensus        80 ~aV~sgrG~GKS~l~a~l~lw~l~~~p~~kv~vtApt~  117 (511)
                      +.|.++.|+|||+++..++.....  ++.++++.+--.
T Consensus         2 ~li~g~~g~GKttl~~~~~~~~~~--~~~~~~~~~~ee   37 (165)
T cd01120           2 ILVFGPTGSGKTTLALQLALNIAT--KGGKVVYVDIEE   37 (165)
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHH--CCCEEEEEECCC
T ss_conf             899989999899999999999876--399799998666


No 324
>PRK04870 histidinol-phosphate aminotransferase; Provisional
Probab=73.62  E-value=5.9  Score=18.31  Aligned_cols=60  Identities=15%  Similarity=0.150  Sum_probs=38.8

Q ss_pred             CCHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEEECCHHHHH
Q ss_conf             845899999999999874056555421012465025765978999999999998089966999808589999
Q gi|254781215|r   50 APRSWQLEFMEVVDAHCLNSVNNPNPEVFKGAISAGRGIGKTTLNAWLVLWLMSTRPGISVICLANSETQLK  121 (511)
Q Consensus        50 ~P~~WQ~e~l~~i~~~~~~~~~~~~~~~~r~aV~sgrG~GKS~l~a~l~lw~l~~~p~~kv~vtApt~~Q~~  121 (511)
                      +|+.-..++-+.|+++.--.      .-..  |..  |+|=+.+...++..  ++.|+.++++..||+..-.
T Consensus        60 YPd~~~~~Lr~~lA~~~gv~------~~~~--Ii~--GnGSdElI~~i~~~--~~~pgd~vl~~~Ptf~~Y~  119 (356)
T PRK04870         60 YPDPRAAALKAALRAAMGVP------AGAD--VLL--GNGSDELIQLIALA--CAKPGAKVLAPVPGFVMYR  119 (356)
T ss_pred             CCCCCHHHHHHHHHHHHCCC------CCCE--EEE--CCCHHHHHHHHHHH--HHCCCCEEEECCCCHHHHH
T ss_conf             98998999999999986879------8776--998--16799999999999--8189898997677766899


No 325
>COG0572 Udk Uridine kinase [Nucleotide transport and metabolism]
Probab=73.60  E-value=3  Score=20.18  Aligned_cols=24  Identities=38%  Similarity=0.338  Sum_probs=19.1

Q ss_pred             CEEEEEECCCCCCHHHHHHHHHHH
Q ss_conf             012465025765978999999999
Q gi|254781215|r   77 VFKGAISAGRGIGKTTLNAWLVLW  100 (511)
Q Consensus        77 ~~r~aV~sgrG~GKS~l~a~l~lw  100 (511)
                      .+=++|+.|.|+|||+++..+.--
T Consensus         8 ~iiIgIaG~SgSGKTTv~~~l~~~   31 (218)
T COG0572           8 VIIIGIAGGSGSGKTTVAKELSEQ   31 (218)
T ss_pred             EEEEEEECCCCCCHHHHHHHHHHH
T ss_conf             699998679877889999999998


No 326
>pfam00485 PRK Phosphoribulokinase / Uridine kinase family. In Arabidopsis the region carries two binding domains, a phosphoribosylpyrophosphate-binding domain and, at the very C-terminus, a uracil-binding domain.
Probab=73.52  E-value=2.9  Score=20.24  Aligned_cols=22  Identities=27%  Similarity=0.341  Sum_probs=18.6

Q ss_pred             EEEECCCCCCHHHHHHHHHHHH
Q ss_conf             4650257659789999999999
Q gi|254781215|r   80 GAISAGRGIGKTTLNAWLVLWL  101 (511)
Q Consensus        80 ~aV~sgrG~GKS~l~a~l~lw~  101 (511)
                      ++|+.|-|.|||+++..+.--+
T Consensus         2 IgIaG~SgSGKTT~a~~L~~~l   23 (196)
T pfam00485         2 IGVAGSSGAGKTTVARTFVSIF   23 (196)
T ss_pred             EEEECCCCCCHHHHHHHHHHHH
T ss_conf             8998998571999999999996


No 327
>PRK13851 type IV secretion system protein VirB11; Provisional
Probab=73.22  E-value=4.9  Score=18.85  Aligned_cols=95  Identities=16%  Similarity=0.225  Sum_probs=49.3

Q ss_pred             EEEECCCEEEEEEECCCCCH-HHHHHHHHHHHHHCCCCEEEEEECCCCHHHHHHHHHCC--CE--EEEECCCCCCCCHHH
Q ss_conf             99822755899873277898-89999999999861888299800687636889898649--82--798427777664025
Q gi|254781215|r  334 VVLRRGPVIEHLFDWSKTDL-RTTNNKISGLVEKYRPDAIIIDANNTGARTCDYLEMLG--YH--VYRVLGQKRAVDLEF  408 (511)
Q Consensus       334 i~~r~G~~v~~~~~~~~~d~-~~~a~~i~~~~~~~~~~~i~iD~~GvG~gV~d~L~~~g--~~--v~~v~~~~~~~~~~~  408 (511)
                      +.+.+-++|..+..-.+... ...+..+...+-+.+|+.|++-.. =|+-..|.|+.++  .+  +.-++.         
T Consensus       201 L~l~~~n~V~l~~~~~~~g~~~vt~~~Ll~~aLRmrPDRIivGEv-RG~EA~d~L~A~nTGH~GsitTiHA---------  270 (343)
T PRK13851        201 LVIPHENHVRLLYSKNGAGLGAVTAEHLLQASLRMRPDRILLGEM-RDDAAWAYLSEVVSGHPGSISTIHG---------  270 (343)
T ss_pred             CCCCCCCEEEEEECCCCCCCCCCCHHHHHHHHHCCCCCEEEEEEE-CCHHHHHHHHHHHCCCCCCCEEECC---------
T ss_conf             258999968999658988858397999999986079982899852-6699999999984699983033567---------


Q ss_pred             HHHHHHHHHHHHHHHHHH---CCCCCHHHHHHHHH
Q ss_conf             522799999999999970---89998189999985
Q gi|254781215|r  409 CRNRRTELHVKMADWLEF---ASLINHSGLIQNLK  440 (511)
Q Consensus       409 y~N~rae~~~~~re~l~~---g~l~~d~~l~~el~  440 (511)
                        |--.+.+-++...+..   |.-.+.+.+...+.
T Consensus       271 --nSa~~a~~RL~~l~~~s~~g~~l~~~~i~~~i~  303 (343)
T PRK13851        271 --ANPVQGFKKLFSLVKSSPQGASLEDRTLIDMLA  303 (343)
T ss_pred             --CCHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHH
T ss_conf             --999999999999987352479999999999999


No 328
>TIGR00955 3a01204 Pigment precourser permease; InterPro: IPR005284   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 different parts of a membrane-spanning permease system necessary for the transport of pigment precursor into pigment cells responsible for eye color. White protein dimerises with brown protein for the transport of guanine and with scarlet protein for the transport of tryptophan.; GO: 0006810 transport.
Probab=72.89  E-value=1.8  Score=21.50  Aligned_cols=155  Identities=17%  Similarity=0.141  Sum_probs=79.9

Q ss_pred             HHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHH--CCCCEEEEE---ECCHHHHHHHHHHHH-
Q ss_conf             99999999998740565554210124650257659789999999999980--899669998---085899999999999-
Q gi|254781215|r   55 QLEFMEVVDAHCLNSVNNPNPEVFKGAISAGRGIGKTTLNAWLVLWLMST--RPGISVICL---ANSETQLKTTLWAEV-  128 (511)
Q Consensus        55 Q~e~l~~i~~~~~~~~~~~~~~~~r~aV~sgrG~GKS~l~a~l~lw~l~~--~p~~kv~vt---Apt~~Q~~~ilw~Ei-  128 (511)
                      ++.+|+.|-.+.+.+.        =+||-.+=|.|||||+..|+-.-.-=  .-+. ++..   .-..+|.+.+. +.+ 
T Consensus        44 ~K~lL~~vSG~a~~Ge--------LlA~mGsSGAGKTTLmn~La~R~~~g~~~~g~-~v~lNG~~~~~~~~~~~s-aYvq  113 (671)
T TIGR00955        44 RKHLLKNVSGVAKPGE--------LLAIMGSSGAGKTTLMNALAFRSPKGLKVSGS-VVLLNGRPIDAKEMRAIS-AYVQ  113 (671)
T ss_pred             CHHHHHCCCEEECCCE--------EEEEECCCCCCHHHHHHHHHCCCCCCCEECCC-EEEECCEECCHHHHHHHH-CHHE
T ss_conf             2011103520210670--------68984787662689999985337478614683-678758375868998540-1220


Q ss_pred             -------------------------------------HHHHHHCHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEE
Q ss_conf             -------------------------------------9999855000134443222222333444321112357861698
Q gi|254781215|r  129 -------------------------------------SKWLSLLPNKHWFEMQSLSLHPAPWYSDVLHCSLGIDSKHYST  171 (511)
Q Consensus       129 -------------------------------------~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  171 (511)
                                                           ...++.+   ....|-.|.+...+..               -.
T Consensus       114 Q~Dlf~~~LTv~E~L~f~A~lRm~~~~~~~~~k~~rV~~vl~~l---~L~~ca~T~IG~pg~~---------------KG  175 (671)
T TIGR00955       114 QDDLFIPTLTVREHLMFQAHLRMKRRVTKKHEKRERVDEVLQAL---GLRKCADTRIGIPGRV---------------KG  175 (671)
T ss_pred             EHHHCCCCCCHHEEEEEEEEEECCCCCCHHHHHHHHHHHHHHHH---CCHHHHCCCCCCCCCE---------------EE
T ss_conf             11004885103000010122334766760579999999999860---4211211343799964---------------55


Q ss_pred             EECCCCCCCCCHHHHCCCCCCEEEEECCH-HCCCHHH-HHHHH--HHHCCCCCCEEEEEECCCCCCCCHHHHHHHC
Q ss_conf             53035755610021202676149997111-0299788-98888--8850799813899823899876556765303
Q gi|254781215|r  172 MCRTYSEERPDTFVGHHNTYGMAIINDEA-SGTPDVI-NLGIL--GFLTERNANRFWIMTSNPRRLSGKFYEIFNK  243 (511)
Q Consensus       172 ~~~~~s~~~~ea~~G~h~~~~~lvI~DEA-sgI~d~i-~e~i~--~~Lt~~g~~~~~i~~~nP~~~~g~fy~~~~~  243 (511)
                      ..-+-+..-+=|..-++.+.  ++++||= ||.|.-. ..|++  --|+..|.- +++.+=.|.   +..|+.|++
T Consensus       176 lSGGErKRLafA~E~ltdP~--~LFcDEPTSGLDSfmA~~Vv~~L~~LA~~G~t-iI~tIHQPS---s~lF~lFd~  245 (671)
T TIGR00955       176 LSGGERKRLAFASELLTDPI--ILFCDEPTSGLDSFMAYSVVQVLKGLAQKGKT-IICTIHQPS---SELFELFDK  245 (671)
T ss_pred             ECCCHHHHHHHHHHHHHCCC--EEEECCCCCHHHHHHHHHHHHHHHHHHCCCCE-EEEEEECCC---HHHHHHHCC
T ss_conf             20113678998878871894--26503889534599999999999998508979-999830561---889851171


No 329
>pfam01935 DUF87 Domain of unknown function DUF87. The function of this prokaryotic domain is unknown. It contains several conserved aspartates and histidines that could be metal ligands.
Probab=72.83  E-value=6.2  Score=18.19  Aligned_cols=38  Identities=24%  Similarity=0.238  Sum_probs=28.7

Q ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEEECCH
Q ss_conf             246502576597899999999999808996699980858
Q gi|254781215|r   79 KGAISAGRGIGKTTLNAWLVLWLMSTRPGISVICLANSE  117 (511)
Q Consensus        79 r~aV~sgrG~GKS~l~a~l~lw~l~~~p~~kv~vtApt~  117 (511)
                      .++|-+..|.|||.+++.++-= ++-.++..+++.=|.-
T Consensus        25 H~aIlg~TGsGKS~tv~vLl~~-l~~~~~~~vlVfDpHg   62 (218)
T pfam01935        25 HFAILGSTGSGKSNTVAVLLEE-LLEKKGATVLIFDPHG   62 (218)
T ss_pred             HEEEECCCCCCHHHHHHHHHHH-HHHCCCCCEEEECCCC
T ss_conf             1478726999769999999999-9854799789982886


No 330
>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=72.75  E-value=6.2  Score=18.18  Aligned_cols=28  Identities=25%  Similarity=0.350  Sum_probs=14.5

Q ss_pred             HHHHHHCCCCEEEEEECCCCHHHHHHHHH
Q ss_conf             99998618882998006876368898986
Q gi|254781215|r  361 SGLVEKYRPDAIIIDANNTGARTCDYLEM  389 (511)
Q Consensus       361 ~~~~~~~~~~~i~iD~~GvG~gV~d~L~~  389 (511)
                      ...+-+.+|+.|+|...- |....+.++.
T Consensus       202 l~~~LR~~PD~IivGEiR-~~Ea~~~l~a  229 (283)
T pfam00437       202 LRAALRQRPDRIMVGEIR-DGETADILRA  229 (283)
T ss_pred             HHHHHCCCCCEEEECCCC-CHHHHHHHHH
T ss_conf             999638899989757869-9899999999


No 331
>TIGR01194 cyc_pep_trnsptr cyclic peptide transporter; InterPro: IPR005898   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).     Bacteria have elaborate pathways for the production of toxins and secondary metabolites. Many such compounds, including syringomycin and pyoverdine are synthesized on non-ribosomal templates consisting of a multienzyme complex. On several occasions the proteins of the complex and transporter protein are present on the same operon. Often times these compounds cross the biological membrane by specific transporters. This model describes a family of cyclic peptide transporters in bacteria. Syringomycin is an amphipathic, cyclic lipodepsipeptide when inserted into host causes formation of channels, permeable to a variety of cations. On the other hand, pyoverdine is a cyclic octa-peptidyl dihydroxyquinoline, which is efficient in sequestering iron for uptake.; GO: 0005524 ATP binding, 0015197 peptide transporter activity, 0015833 peptide transport, 0016021 integral to membrane.
Probab=72.70  E-value=3.1  Score=20.06  Aligned_cols=49  Identities=16%  Similarity=0.234  Sum_probs=22.8

Q ss_pred             CCCEEEEEEECCCCCHHHHHHHHHHHHHHCCCC--EEEEEECCCCHHHHHHHHHC
Q ss_conf             275589987327789889999999999861888--29980068763688989864
Q gi|254781215|r  338 RGPVIEHLFDWSKTDLRTTNNKISGLVEKYRPD--AIIIDANNTGARTCDYLEML  390 (511)
Q Consensus       338 ~G~~v~~~~~~~~~d~~~~a~~i~~~~~~~~~~--~i~iD~~GvG~gV~d~L~~~  390 (511)
                      +|.-|. +.=-||..-.+.++.   ++--|+|+  .+..|+.-|-+..-|.-|++
T Consensus       367 ~G~~Vy-IVG~NGCGK~TL~K~---l~GLY~PQ~G~~LL~G~~V~~~~R~DYR~L  417 (555)
T TIGR01194       367 SGDLVY-IVGENGCGKSTLIKL---LLGLYIPQEGELLLDGEAVSDDSRDDYRDL  417 (555)
T ss_pred             CCCEEE-EECCCCCCHHHHHHH---HHHCCCCCCCCEEECCCCCCCCCCHHHHHH
T ss_conf             352899-964889738999999---972587876754435754563320238999


No 332
>PRK07261 topology modulation protein; Provisional
Probab=72.55  E-value=3.5  Score=19.73  Aligned_cols=26  Identities=35%  Similarity=0.293  Sum_probs=20.9

Q ss_pred             EEEEEECCCCCCHHHHHHHHHHHHHH
Q ss_conf             12465025765978999999999998
Q gi|254781215|r   78 FKGAISAGRGIGKTTLNAWLVLWLMS  103 (511)
Q Consensus        78 ~r~aV~sgrG~GKS~l~a~l~lw~l~  103 (511)
                      .|+.|-.+=|.|||+++..|.--.-+
T Consensus         1 MrI~IiG~sGsGKSTlAr~L~~~~~i   26 (171)
T PRK07261          1 MKIAIIGYSGSGKSTLARFLGQHYNC   26 (171)
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHHCC
T ss_conf             98999889998689999999998797


No 333
>PRK09099 type III secretion system ATPase; Provisional
Probab=72.40  E-value=4.5  Score=19.06  Aligned_cols=23  Identities=30%  Similarity=0.280  Sum_probs=19.6

Q ss_pred             EEEEEECCCCCCHHHHHHHHHHH
Q ss_conf             12465025765978999999999
Q gi|254781215|r   78 FKGAISAGRGIGKTTLNAWLVLW  100 (511)
Q Consensus        78 ~r~aV~sgrG~GKS~l~a~l~lw  100 (511)
                      -|+.+-+|.|+|||++.+.++-+
T Consensus       164 QR~gIf~gsGvGKstLl~~iar~  186 (441)
T PRK09099        164 QRMGIFAPAGVGKSTLMGMFARG  186 (441)
T ss_pred             CEEEEECCCCCCHHHHHHHHHHH
T ss_conf             63300158988789999989875


No 334
>PRK05957 aspartate aminotransferase; Provisional
Probab=72.35  E-value=6.3  Score=18.12  Aligned_cols=59  Identities=15%  Similarity=0.084  Sum_probs=27.1

Q ss_pred             HHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEEECCHHHH
Q ss_conf             99999999987405655542101246502576597899999999999808996699980858999
Q gi|254781215|r   56 LEFMEVVDAHCLNSVNNPNPEVFKGAISAGRGIGKTTLNAWLVLWLMSTRPGISVICLANSETQL  120 (511)
Q Consensus        56 ~e~l~~i~~~~~~~~~~~~~~~~r~aV~sgrG~GKS~l~a~l~lw~l~~~p~~kv~vtApt~~Q~  120 (511)
                      .++-++|+++..+..+.+...--.+.|.+|    -+.  +..++-.+++.||-.|++..|++...
T Consensus        68 ~~LR~aia~~~~~~~g~~~~~~~~I~vt~G----a~~--al~~~~~al~~pGD~Vlv~~P~Y~~~  126 (389)
T PRK05957         68 PPLLEAITQKLQADNGIEINNENAIVVTAG----SNM--AFMNAILAITDPGDEIILNTPYYFNH  126 (389)
T ss_pred             HHHHHHHHHHHHHHHCCCCCCCCEEEECCC----HHH--HHHHHHHHHCCCCCEEEECCCCCCCH
T ss_conf             999999999999996899898988998878----899--99999999759999899778877668


No 335
>PRK10636 putative ABC transporter ATP-binding protein; Provisional
Probab=72.28  E-value=2.9  Score=20.24  Aligned_cols=41  Identities=12%  Similarity=-0.015  Sum_probs=24.4

Q ss_pred             HCCCCCCEEEEECCH-HCCCHHHHHHHHHHHCCCCCCEEEEEEC
Q ss_conf             202676149997111-0299788988888850799813899823
Q gi|254781215|r  186 GHHNTYGMAIINDEA-SGTPDVINLGILGFLTERNANRFWIMTS  228 (511)
Q Consensus       186 G~h~~~~~lvI~DEA-sgI~d~i~e~i~~~Lt~~g~~~~~i~~~  228 (511)
                      ..-....-++++||- ..++-..-..++..|...+...  ++++
T Consensus       162 ~aL~~~PdlLLLDEPTnhLD~~~i~~L~~~L~~~~gtv--ilVS  203 (638)
T PRK10636        162 QALICRSDLLLLDEPTNHLDLDAVIWLEKWLKSYQGTL--ILIS  203 (638)
T ss_pred             HHHCCCCCEEEECCCCCCCCHHHHHHHHHHHHHCCCEE--EEEE
T ss_conf             98558999899708888899899999999999769819--9996


No 336
>PRK13869 plasmid-partitioning protein RepA; Provisional
Probab=72.09  E-value=4.7  Score=18.91  Aligned_cols=32  Identities=34%  Similarity=0.489  Sum_probs=24.2

Q ss_pred             EEEC-CCCCCHHHHHHHHHHHHHHHCCCCEEEEEE
Q ss_conf             6502-576597899999999999808996699980
Q gi|254781215|r   81 AISA-GRGIGKTTLNAWLVLWLMSTRPGISVICLA  114 (511)
Q Consensus        81 aV~s-grG~GKS~l~a~l~lw~l~~~p~~kv~vtA  114 (511)
                      +|.- ==|+|||+.+..++-+++.  .|.+|+++=
T Consensus       125 aVaN~KGGVGKTTtav~LA~~LA~--~G~RVLlID  157 (405)
T PRK13869        125 AVTNFKGGSGKTTTSAHLAQYLAL--QGYRVLAVD  157 (405)
T ss_pred             EEECCCCCCHHHHHHHHHHHHHHH--CCCCEEEEE
T ss_conf             997888776599999999999997--799889996


No 337
>PRK11147 ABC transporter ATPase component; Reviewed
Probab=72.08  E-value=3.2  Score=20.02  Aligned_cols=43  Identities=16%  Similarity=0.048  Sum_probs=27.1

Q ss_pred             HHHCCCCCCEEEEECCH-HCCCHHHHHHHHHHHCCCCCCEEEEEEC
Q ss_conf             21202676149997111-0299788988888850799813899823
Q gi|254781215|r  184 FVGHHNTYGMAIINDEA-SGTPDVINLGILGFLTERNANRFWIMTS  228 (511)
Q Consensus       184 ~~G~h~~~~~lvI~DEA-sgI~d~i~e~i~~~Lt~~g~~~~~i~~~  228 (511)
                      ++..-....-++|+||- ++++-..-+.++..|...+...  +.++
T Consensus       167 LA~aL~~~PdlLlLDEPTn~LD~~~~~~L~~~L~~~~gtv--liIS  210 (632)
T PRK11147        167 LARALVSNPDVLLLDEPTNHLDIETIEWLEGFLKTFQGSI--IFIS  210 (632)
T ss_pred             HHHHHCCCCCEEEEECCCCCCCHHHHHHHHHHHHHCCCEE--EEEE
T ss_conf             9998568999999848876589999999999999759849--9997


No 338
>PRK13900 type IV secretion system ATPase VirB11; Provisional
Probab=71.98  E-value=5.8  Score=18.36  Aligned_cols=35  Identities=26%  Similarity=0.474  Sum_probs=24.4

Q ss_pred             HHHHHHHHHHHCCCCEEEEEECCCCHHHHHHHHHCC
Q ss_conf             999999999861888299800687636889898649
Q gi|254781215|r  356 TNNKISGLVEKYRPDAIIIDANNTGARTCDYLEMLG  391 (511)
Q Consensus       356 ~a~~i~~~~~~~~~~~i~iD~~GvG~gV~d~L~~~g  391 (511)
                      ....+...+-+.+|+.|++-..- |.-..+.|+.++
T Consensus       223 t~~~Ll~~aLR~rPDRIivGEvR-G~EA~~~l~A~n  257 (332)
T PRK13900        223 TTQDLIEACLRLRPDRIIVGELR-GAEAFSFLRAIN  257 (332)
T ss_pred             CHHHHHHHHHCCCCCEEEECCCC-HHHHHHHHHHHH
T ss_conf             69999999756899758445557-199999999997


No 339
>PRK13232 nifH nitrogenase reductase; Reviewed
Probab=71.96  E-value=6.5  Score=18.07  Aligned_cols=35  Identities=29%  Similarity=0.296  Sum_probs=28.9

Q ss_pred             CEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEE
Q ss_conf             0124650257659789999999999980899669998
Q gi|254781215|r   77 VFKGAISAGRGIGKTTLNAWLVLWLMSTRPGISVICL  113 (511)
Q Consensus        77 ~~r~aV~sgrG~GKS~l~a~l~lw~l~~~p~~kv~vt  113 (511)
                      |.++||-.==|+|||+.++.++.-.+..  +.||+++
T Consensus         1 ~~~iaiyGKGGVGKSTTt~NLaAALA~~--GkkVL~I   35 (273)
T PRK13232          1 MRQIAIYGKGGIGKSTTTQNLTAALSTM--GNKILLV   35 (273)
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHHHHHC--CCEEEEE
T ss_conf             9579997998665887899999999977--9969998


No 340
>PRK11664 ATP-dependent RNA helicase HrpB; Provisional
Probab=71.77  E-value=6.5  Score=18.04  Aligned_cols=56  Identities=14%  Similarity=0.077  Sum_probs=37.1

Q ss_pred             HHHHHHHHHHCCCCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEEECCHHHHHHH
Q ss_conf             999999987405655542101246502576597899999999999808996699980858999999
Q gi|254781215|r   58 FMEVVDAHCLNSVNNPNPEVFKGAISAGRGIGKTTLNAWLVLWLMSTRPGISVICLANSETQLKTT  123 (511)
Q Consensus        58 ~l~~i~~~~~~~~~~~~~~~~r~aV~sgrG~GKS~l~a~l~lw~l~~~p~~kv~vtApt~~Q~~~i  123 (511)
                      ++.+|.+...++.        .+-|.+.-|+|||+.+--.++-....  .++|+||-|-.--++.+
T Consensus         9 ~~~~i~~~l~~~~--------~~vl~a~tGsGKtTqvP~~ll~~~~~--~g~I~~~qPRR~AA~s~   64 (812)
T PRK11664          9 VLPELLTALKTAP--------QVLLKAPTGAGKSTWLPLQLLQQGGI--NGKIIMLEPRRLAARNV   64 (812)
T ss_pred             HHHHHHHHHHHCC--------EEEEEECCCCCHHHHHHHHHHHCCCC--CCCEEEECCHHHHHHHH
T ss_conf             9999999999799--------79999089999899999999964688--99389938839999999


No 341
>TIGR01281 DPOR_bchL light-independent protochlorophyllide reductase, iron-sulfur ATP-binding protein; InterPro: IPR005971    Synonym: dark protochlorophyllide reductase    Protochlorophyllide reductase catalyzes the reductive formation of chlorophyllide from protochlorophyllide during biosynthesis of chlorophylls and bacteriochlorophylls. The light-independent (dark) form of protochlorophyllide reductase plays a key role in the ability of gymnosperms, algae, and photosynthetic bacteria to form chlorophyll in the dark. Genetic and sequence analyses have indicated that dark protochlorophyllide reductase consists of three protein subunits that exhibit significant sequence similarity to the three subunits of nitrogenase, which catalyzes the reductive formation of ammonia from dinitrogen. Dark protochlorophyllide reductase activity was shown to be dependent on the presence of all three subunits, ATP, and the reductant dithionite.    The BchL peptide (ChlL in chloroplast and cyanobacteria) is an ATP-binding iron-sulphur protein of the dark form protochlorophyllide reductase, an enzyme similar to nitrogenase . ; GO: 0005524 ATP binding, 0016730 oxidoreductase activity acting on iron-sulfur proteins as donors, 0015995 chlorophyll biosynthetic process, 0019685 photosynthesis dark reaction.
Probab=71.71  E-value=4  Score=19.40  Aligned_cols=22  Identities=18%  Similarity=0.191  Sum_probs=13.0

Q ss_pred             EEECCCCCHHHHHHHHHHHHHH
Q ss_conf             8732778988999999999986
Q gi|254781215|r  345 LFDWSKTDLRTTNNKISGLVEK  366 (511)
Q Consensus       345 ~~~~~~~d~~~~a~~i~~~~~~  366 (511)
                      +.+-|..|..-.|+||..-..+
T Consensus       144 vva~NDFDalFAANRia~av~~  165 (275)
T TIGR01281       144 VVAANDFDALFAANRIAAAVRE  165 (275)
T ss_pred             EEECCCCHHHHHHHHHHHHHHH
T ss_conf             6610772178999999999999


No 342
>TIGR03453 partition_RepA plasmid partitioning protein RepA. Members of this family are the RepA (or ParA) protein involved in replicon partitioning. All known examples occur in bacterial species with two or more replicons, on a plasmid or the smaller chromosome. Note that an apparent exception may be seen as a pseudomolecule from assembly of an incompletely sequenced genome. Members of this family belong to a larger family that also includes the enzyme cobyrinic acid a,c-diamide synthase, but assignment of that name to members of this family would be in error.
Probab=71.67  E-value=4.8  Score=18.88  Aligned_cols=33  Identities=33%  Similarity=0.432  Sum_probs=24.5

Q ss_pred             EEEEC-CCCCCHHHHHHHHHHHHHHHCCCCEEEEEE
Q ss_conf             46502-576597899999999999808996699980
Q gi|254781215|r   80 GAISA-GRGIGKTTLNAWLVLWLMSTRPGISVICLA  114 (511)
Q Consensus        80 ~aV~s-grG~GKS~l~a~l~lw~l~~~p~~kv~vtA  114 (511)
                      ++|.. ==|+|||+.+..++-+.+.  .|.+|+++=
T Consensus       107 Iav~N~KGGVGKTTtav~LA~~LA~--~G~RVLvID  140 (387)
T TIGR03453       107 IAVTNFKGGSGKTTTSAHLAQYLAL--RGYRVLAID  140 (387)
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHHH--CCCCEEEEE
T ss_conf             9997888765699999999999997--799889995


No 343
>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=71.64  E-value=4.9  Score=18.81  Aligned_cols=21  Identities=48%  Similarity=0.373  Sum_probs=14.7

Q ss_pred             EEEECCCCCCHHHHHHHHHHH
Q ss_conf             465025765978999999999
Q gi|254781215|r   80 GAISAGRGIGKTTLNAWLVLW  100 (511)
Q Consensus        80 ~aV~sgrG~GKS~l~a~l~lw  100 (511)
                      +-|+.|-|+||||+.-.++-.
T Consensus       161 Iii~GGTgSGKTTf~kal~~~  181 (328)
T TIGR02788       161 IIISGGTGSGKTTFLKALVKE  181 (328)
T ss_pred             EEEEECCCCHHHHHHHHHHHC
T ss_conf             999906897189999999732


No 344
>KOG0347 consensus
Probab=71.38  E-value=3.3  Score=19.91  Aligned_cols=151  Identities=13%  Similarity=-0.004  Sum_probs=67.8

Q ss_pred             CCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHH---------H-----HCCCCEE
Q ss_conf             6555784589999999999987405655542101246502576597899999999999---------8-----0899669
Q gi|254781215|r   45 LEGFSAPRSWQLEFMEVVDAHCLNSVNNPNPEVFKGAISAGRGIGKTTLNAWLVLWLM---------S-----TRPGISV  110 (511)
Q Consensus        45 ~~~~~~P~~WQ~e~l~~i~~~~~~~~~~~~~~~~r~aV~sgrG~GKS~l~a~l~lw~l---------~-----~~p~~kv  110 (511)
                      -.+|+-|-+-|.-.|-+.--..           .-+.=++-.|.|||-..++=++--+         +     .++-.-.
T Consensus       198 ~~gFs~Pt~IQsl~lp~ai~gk-----------~DIlGaAeTGSGKTLAFGIPiv~~l~~~s~~s~e~~~~~~k~~k~~~  266 (731)
T KOG0347         198 NLGFSRPTEIQSLVLPAAIRGK-----------VDILGAAETGSGKTLAFGIPIVERLLESSDDSQELSNTSAKYVKPIA  266 (731)
T ss_pred             HCCCCCCCCCHHHCCCHHHCCC-----------HHCCCCCCCCCCCEEEECCHHHHHHHHCCCHHHHHHHHHHCCCCCEE
T ss_conf             6478998610441166765463-----------00003334688742441232545433036537654467760576403


Q ss_pred             EEEECCHHHHHHHHHHHHHHHHHHCHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEE-EECCCCCCCCCHH-HHCC
Q ss_conf             9980858999999999999999855000134443222222333444321112357861698-5303575561002-1202
Q gi|254781215|r  111 ICLANSETQLKTTLWAEVSKWLSLLPNKHWFEMQSLSLHPAPWYSDVLHCSLGIDSKHYST-MCRTYSEERPDTF-VGHH  188 (511)
Q Consensus       111 ~vtApt~~Q~~~ilw~Ei~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~s~~~~ea~-~G~h  188 (511)
                      +|.+||..-+-.|. ..+....+.    ..........   +.....+..-+.-.+....+ .||.|..-+..+. -|--
T Consensus       267 LV~tPTRELa~QV~-~Hl~ai~~~----t~i~v~si~G---GLavqKQqRlL~~~p~IVVATPGRlweli~e~n~~l~~~  338 (731)
T KOG0347         267 LVVTPTRELAHQVK-QHLKAIAEK----TQIRVASITG---GLAVQKQQRLLNQRPDIVVATPGRLWELIEEDNTHLGNF  338 (731)
T ss_pred             EEECCHHHHHHHHH-HHHHHHCCC----CCEEEEEEEC---HHHHHHHHHHHHCCCCEEEECCHHHHHHHHHHHHHHHHH
T ss_conf             89637099999999-999986134----6727887523---057999999985299879936628999997510666423


Q ss_pred             CCCCEEEEECCHHCC-CHHHHHHHHHHH
Q ss_conf             676149997111029-978898888885
Q gi|254781215|r  189 NTYGMAIINDEASGT-PDVINLGILGFL  215 (511)
Q Consensus       189 ~~~~~lvI~DEAsgI-~d~i~e~i~~~L  215 (511)
                       ...-++|+|||.-+ .+..|+-++..|
T Consensus       339 -k~vkcLVlDEaDRmvekghF~Els~lL  365 (731)
T KOG0347         339 -KKVKCLVLDEADRMVEKGHFEELSKLL  365 (731)
T ss_pred             -HHCEEEEECCHHHHHHHCCHHHHHHHH
T ss_conf             -324078873477775511099999999


No 345
>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=71.30  E-value=4.4  Score=19.10  Aligned_cols=35  Identities=29%  Similarity=0.204  Sum_probs=27.4

Q ss_pred             EEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEEECCHHHH
Q ss_conf             6502576597899999999999808996699980858999
Q gi|254781215|r   81 AISAGRGIGKTTLNAWLVLWLMSTRPGISVICLANSETQL  120 (511)
Q Consensus        81 aV~sgrG~GKS~l~a~l~lw~l~~~p~~kv~vtApt~~Q~  120 (511)
                      ....==|.|||++.-.++.-     -|-...+++||+.=+
T Consensus        32 ~L~GDlGaGKTtl~~G~~~~-----LG~~~~~~SPTftlv   66 (147)
T TIGR00150        32 LLKGDLGAGKTTLVKGLLQG-----LGITGNVTSPTFTLV   66 (147)
T ss_pred             EEECCCCCCHHHHHHHHHHH-----CCCEEEEECCCCCEE
T ss_conf             97323466658999999983-----792268857932101


No 346
>pfam00142 Fer4_NifH 4Fe-4S iron sulfur cluster binding proteins, NifH/frxC family.
Probab=71.05  E-value=6.8  Score=17.94  Aligned_cols=33  Identities=33%  Similarity=0.277  Sum_probs=26.2

Q ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEE
Q ss_conf             24650257659789999999999980899669998
Q gi|254781215|r   79 KGAISAGRGIGKTTLNAWLVLWLMSTRPGISVICL  113 (511)
Q Consensus        79 r~aV~sgrG~GKS~l~a~l~lw~l~~~p~~kv~vt  113 (511)
                      .+||+.==|+|||+.++.|+.-++-  -+.||.++
T Consensus         2 ~iai~GKGGVGKTTtsvNLA~aLA~--~GkrVlli   34 (269)
T pfam00142         2 KIAIYGKGGIGKSTTSQNTSAALAE--MGKKVLIV   34 (269)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHH--CCCEEEEE
T ss_conf             5899899976889999999999998--79909998


No 347
>cd01136 ATPase_flagellum-secretory_path_III Flagellum-specific ATPase/type III secretory pathway virulence-related protein. This group of ATPases are responsible for the export of flagellum and virulence-related proteins. The bacterial flagellar motor is similar to the F0F1-ATPase, in that they both are proton driven rotary molecular devices. However, the main function of the bacterial flagellar motor is to rotate the flagellar filament for cell motility. Intracellular pathogens such as Salmonella and Chlamydia also have proteins which are similar to the flagellar-specific ATPase, but function in the secretion of virulence-related proteins via the type III secretory pathway.
Probab=70.98  E-value=4.6  Score=18.97  Aligned_cols=34  Identities=29%  Similarity=0.248  Sum_probs=23.5

Q ss_pred             CEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEEEC
Q ss_conf             012465025765978999999999998089966999808
Q gi|254781215|r   77 VFKGAISAGRGIGKTTLNAWLVLWLMSTRPGISVICLAN  115 (511)
Q Consensus        77 ~~r~aV~sgrG~GKS~l~a~l~lw~l~~~p~~kv~vtAp  115 (511)
                      .-|+.+-+|.|+|||++++.++..     ..+.++|.+-
T Consensus        69 GQR~~Ifg~~g~GKt~Ll~~i~~~-----~~~~v~V~~~  102 (326)
T cd01136          69 GQRLGIFAGSGVGKSTLLGMIARG-----TTADVNVIAL  102 (326)
T ss_pred             CCEEEEECCCCCCCCHHHHHHHHC-----CCCCEEEEEE
T ss_conf             987874369999846678768641-----4677599996


No 348
>TIGR03497 FliI_clade2 flagellar protein export ATPase FliI. Members of this protein family are the FliI protein of bacterial flagellum systems. This protein acts to drive protein export for flagellar biosynthesis. The most closely related family is the YscN family of bacterial type III secretion systems. This model represents one (of three) segment of the FliI family tree. These have been modeled separately in order to exclude the type III secretion ATPases more effectively.
Probab=70.98  E-value=4.7  Score=18.94  Aligned_cols=23  Identities=35%  Similarity=0.413  Sum_probs=20.0

Q ss_pred             EEEEEECCCCCCHHHHHHHHHHH
Q ss_conf             12465025765978999999999
Q gi|254781215|r   78 FKGAISAGRGIGKTTLNAWLVLW  100 (511)
Q Consensus        78 ~r~aV~sgrG~GKS~l~a~l~lw  100 (511)
                      =|+.+-+|.|+|||.+++.++..
T Consensus       138 QRigIfag~GvGKt~Ll~~ia~~  160 (413)
T TIGR03497       138 QRVGIFAGSGVGKSTLLGMIARN  160 (413)
T ss_pred             CEEEECCCCCCCHHHHHHHHHHH
T ss_conf             54421058998776999999987


No 349
>PRK09082 putative aminotransferase; Validated
Probab=70.85  E-value=6.8  Score=17.91  Aligned_cols=60  Identities=18%  Similarity=0.165  Sum_probs=26.5

Q ss_pred             HHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEEECCHHHHH
Q ss_conf             999999999874056555421012465025765978999999999998089966999808589999
Q gi|254781215|r   56 LEFMEVVDAHCLNSVNNPNPEVFKGAISAGRGIGKTTLNAWLVLWLMSTRPGISVICLANSETQLK  121 (511)
Q Consensus        56 ~e~l~~i~~~~~~~~~~~~~~~~r~aV~sgrG~GKS~l~a~l~lw~l~~~p~~kv~vtApt~~Q~~  121 (511)
                      .++-++|+++..+..+.....-..|.|.+|=   +   .|..++-.+++.||-.|++..|++....
T Consensus        70 ~~LReaiA~~~~~~~g~~~~p~~eI~vT~Ga---~---~al~~~~~al~~pGD~Vlv~~P~Y~~y~  129 (386)
T PRK09082         70 AALREAIADKTARLYGRRYDADSEITVTAGA---T---EALFAAILALVRPGDEVIVFDPSYDSYA  129 (386)
T ss_pred             HHHHHHHHHHHHHHHCCCCCCCCCEEECCCH---H---HHHHHHHHHHCCCCCEEEEECCCCHHHH
T ss_conf             9999999999999968998988838987788---9---9999999997599998999268628799


No 350
>TIGR02546 III_secr_ATP type III secretion apparatus H+-transporting two-sector ATPase; InterPro: IPR013380    Proteins in this entry are found in a variety of bacteria, and are predicted to be ATPases involved in type III secretion systems. One example is YscN (P40290 from SWISSPROT) from Yersinia enterocolitica, which is thought to energise the YOP (Yersinia outer protein) secretion system .; GO: 0046961 hydrogen ion transporting ATPase activity rotational mechanism, 0030254 protein secretion by the type III secretion system.
Probab=70.71  E-value=3.5  Score=19.76  Aligned_cols=31  Identities=32%  Similarity=0.412  Sum_probs=14.9

Q ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEEE
Q ss_conf             246502576597899999999999808996699980
Q gi|254781215|r   79 KGAISAGRGIGKTTLNAWLVLWLMSTRPGISVICLA  114 (511)
Q Consensus        79 r~aV~sgrG~GKS~l~a~l~lw~l~~~p~~kv~vtA  114 (511)
                      |+-|=|+=|+|||+|+++++-     ...+-|.|+|
T Consensus       155 RiGIFA~aG~GKSTLL~~i~~-----g~~ADv~V~A  185 (430)
T TIGR02546       155 RIGIFAGAGVGKSTLLGMIAR-----GASADVNVIA  185 (430)
T ss_pred             EEEEEECCCCCHHHHHHHHHC-----CCCCCEEEEE
T ss_conf             057870888616689999861-----8988789986


No 351
>PRK06315 type III secretion system ATPase; Provisional
Probab=70.64  E-value=3.5  Score=19.71  Aligned_cols=25  Identities=28%  Similarity=0.286  Sum_probs=20.7

Q ss_pred             CEEEEEECCCCCCHHHHHHHHHHHH
Q ss_conf             0124650257659789999999999
Q gi|254781215|r   77 VFKGAISAGRGIGKTTLNAWLVLWL  101 (511)
Q Consensus        77 ~~r~aV~sgrG~GKS~l~a~l~lw~  101 (511)
                      .-|+.+-+|.|+|||+++.+++...
T Consensus       164 GQR~gIfagsGvGKs~Ll~~i~~~~  188 (442)
T PRK06315        164 GQRIGIFAGAGVGKSSLLGMIARNA  188 (442)
T ss_pred             CCEEECCCCCCCCHHHHHHHHHHHH
T ss_conf             7776403899998889999999744


No 352
>TIGR01166 cbiO cobalt ABC transporter, ATP-binding protein; InterPro: IPR005876   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 entry represents the ATP binding subunit of the multisubunit cobalt transporter in bacteria and its equivalents in archaea. This superfamily includes two groups, one which catalyses the uptake of small molecules, including ions from the external milieu and the other group which is engaged in the efflux of small molecular weight compounds and ions from within the cell. Energy derived from the hydrolysis of ATP drives both the process of uptake and efflux.; GO: 0006824 cobalt ion transport, 0009276 1-2nm peptidoglycan-based cell wall.
Probab=70.60  E-value=3.9  Score=19.42  Aligned_cols=26  Identities=27%  Similarity=0.124  Sum_probs=19.8

Q ss_pred             CCCCCEEEEEECCCCCCHHHHHHHHH
Q ss_conf             54210124650257659789999999
Q gi|254781215|r   73 PNPEVFKGAISAGRGIGKTTLNAWLV   98 (511)
Q Consensus        73 ~~~~~~r~aV~sgrG~GKS~l~a~l~   98 (511)
                      +-+....++.-...|.|||||...+.
T Consensus        14 ~~~~G~~~aLlG~NGaGKsTLl~~Ln   39 (190)
T TIGR01166        14 AVERGEVLALLGANGAGKSTLLLHLN   39 (190)
T ss_pred             EECCCCEEEEECCCCCCHHHHHHHHC
T ss_conf             22057168987289985789988743


No 353
>PRK01688 histidinol-phosphate aminotransferase; Provisional
Probab=70.59  E-value=6.9  Score=17.88  Aligned_cols=59  Identities=14%  Similarity=0.055  Sum_probs=39.4

Q ss_pred             CCCHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHHCCCC-EEEEEECCHHHH
Q ss_conf             784589999999999987405655542101246502576597899999999999808996-699980858999
Q gi|254781215|r   49 SAPRSWQLEFMEVVDAHCLNSVNNPNPEVFKGAISAGRGIGKTTLNAWLVLWLMSTRPGI-SVICLANSETQL  120 (511)
Q Consensus        49 ~~P~~WQ~e~l~~i~~~~~~~~~~~~~~~~r~aV~sgrG~GKS~l~a~l~lw~l~~~p~~-kv~vtApt~~Q~  120 (511)
                      .+||..+.++.++++++..-    + +.  .+  ..  |+|=+.+...++..  ++.|+. .|+++.||+..-
T Consensus        53 rYPD~~~~~Lr~alA~~~gv----~-~e--~I--~v--GnGSdElI~~l~ra--f~~pg~d~vl~~~PtF~~Y  112 (355)
T PRK01688         53 RYPECQPKAVIENYAQYAGV----K-PE--QV--LV--SRGADEGIELLIRA--FCEPGKDAILYCPPTYGMY  112 (355)
T ss_pred             CCCCCCHHHHHHHHHHHHCC----C-HH--HE--EE--ECCHHHHHHHHHHH--HHCCCCCEEEECCCCHHHH
T ss_conf             49799889999999998685----8-77--89--98--16899999999999--8558997499778876899


No 354
>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=70.43  E-value=7  Score=17.86  Aligned_cols=35  Identities=20%  Similarity=0.211  Sum_probs=26.6

Q ss_pred             EEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEEEC
Q ss_conf             465025765978999999999998089966999808
Q gi|254781215|r   80 GAISAGRGIGKTTLNAWLVLWLMSTRPGISVICLAN  115 (511)
Q Consensus        80 ~aV~sgrG~GKS~l~a~l~lw~l~~~p~~kv~vtAp  115 (511)
                      +.|.++-|+|||+++..+++..+.. .+.+|++.+.
T Consensus        16 ~vi~a~~g~GKS~~~~~la~~~a~~-~g~~V~~~Sl   50 (242)
T cd00984          16 IIIAARPSMGKTAFALNIAENIAKK-QGKPVLFFSL   50 (242)
T ss_pred             EEEEECCCCCHHHHHHHHHHHHHHH-CCCCEEEEEC
T ss_conf             9999689999999999999999997-7995999933


No 355
>KOG0062 consensus
Probab=70.40  E-value=5.1  Score=18.71  Aligned_cols=143  Identities=13%  Similarity=-0.021  Sum_probs=67.0

Q ss_pred             CCCCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHHCCCC---EEEEEECCHHHHHHHHHHHHHHHHHHCH---HC-CC
Q ss_conf             05655542101246502576597899999999999808996---6999808589999999999999998550---00-13
Q gi|254781215|r   68 NSVNNPNPEVFKGAISAGRGIGKTTLNAWLVLWLMSTRPGI---SVICLANSETQLKTTLWAEVSKWLSLLP---NK-HW  140 (511)
Q Consensus        68 ~~~~~~~~~~~r~aV~sgrG~GKS~l~a~l~lw~l~~~p~~---kv~vtApt~~Q~~~ilw~Ei~k~~~~~~---~~-~~  140 (511)
                      ++....+...+|.-+..-.|+|||+|.-+++--.+.-.|-.   +...|....+-+..=+|.+  ..+..-+   .+ ..
T Consensus        97 ~~a~L~L~~GrRYGLvGrNG~GKsTLLRaia~~~v~~f~veqE~~g~~t~~~~~~l~~D~~~~--dfl~~e~~l~~~~~l  174 (582)
T KOG0062          97 NKANLTLSRGRRYGLVGRNGIGKSTLLRAIANGQVSGFHVEQEVRGDDTEALQSVLESDTERL--DFLAEEKELLAGLTL  174 (582)
T ss_pred             CCCCEEEECCCCCCEECCCCCCHHHHHHHHHHCCCCCCCCHHHEECCCHHHHHHHHHCCHHHH--HHHHHHHHHHCCCHH
T ss_conf             478555631524321478987589999999845867367612110241587754321237899--998730565300209


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCCCCCCCHHHHCCCCCCEEEEECCHHCCCHHH-HHHHHHHHCCCC
Q ss_conf             4443222222333444321112357861698530357556100212026761499971110299788-988888850799
Q gi|254781215|r  141 FEMQSLSLHPAPWYSDVLHCSLGIDSKHYSTMCRTYSEERPDTFVGHHNTYGMAIINDEASGTPDVI-NLGILGFLTERN  219 (511)
Q Consensus       141 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~ea~~G~h~~~~~lvI~DEAsgI~d~i-~e~i~~~Lt~~g  219 (511)
                      .+.........+|-.+...--.+...+.|.+....++        ++-.+ ..|+.+||-...=|.. -..++.-|.+-.
T Consensus       175 ~ei~~~~L~glGFt~emq~~pt~slSGGWrMrlaLAR--------Alf~~-pDlLLLDEPTNhLDv~av~WLe~yL~t~~  245 (582)
T KOG0062         175 EEIYDKILAGLGFTPEMQLQPTKSLSGGWRMRLALAR--------ALFAK-PDLLLLDEPTNHLDVVAVAWLENYLQTWK  245 (582)
T ss_pred             HHHHHHHHHHCCCCHHHHHCCCCCCCCCHHHHHHHHH--------HHHCC-CCEEEECCCCCCCHHHHHHHHHHHHHHCC
T ss_conf             9999999874799989983650135850426899999--------87249-99886548753101678999999996388


Q ss_pred             CC
Q ss_conf             81
Q gi|254781215|r  220 AN  221 (511)
Q Consensus       220 ~~  221 (511)
                      ..
T Consensus       246 ~T  247 (582)
T KOG0062         246 IT  247 (582)
T ss_pred             CE
T ss_conf             62


No 356
>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=70.05  E-value=7.1  Score=17.80  Aligned_cols=34  Identities=32%  Similarity=0.366  Sum_probs=22.2

Q ss_pred             EEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEE
Q ss_conf             124650257659789999999999980899669998
Q gi|254781215|r   78 FKGAISAGRGIGKTTLNAWLVLWLMSTRPGISVICL  113 (511)
Q Consensus        78 ~r~aV~sgrG~GKS~l~a~l~lw~l~~~p~~kv~vt  113 (511)
                      .-+.+...-|+|||+++..++--..  +.+..++.+
T Consensus        20 ~~ill~GppGtGKT~la~~ia~~~~--~~~~~~~~~   53 (151)
T cd00009          20 KNLLLYGPPGTGKTTLARAIANELF--RPGAPFLYL   53 (151)
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHHC--CCCCCEEEE
T ss_conf             8089989999886599999999712--137982785


No 357
>PRK09435 arginine/ornithine transport system ATPase; Provisional
Probab=70.00  E-value=7.1  Score=17.80  Aligned_cols=56  Identities=27%  Similarity=0.348  Sum_probs=39.6

Q ss_pred             HHHHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEEE--CCHH
Q ss_conf             89999999999987405655542101246502576597899999999999808996699980--8589
Q gi|254781215|r   53 SWQLEFMEVVDAHCLNSVNNPNPEVFKGAISAGRGIGKTTLNAWLVLWLMSTRPGISVICLA--NSET  118 (511)
Q Consensus        53 ~WQ~e~l~~i~~~~~~~~~~~~~~~~r~aV~sgrG~GKS~l~a~l~lw~l~~~p~~kv~vtA--pt~~  118 (511)
                      ..-.++|+.++.|.-        ...++.|...-|+|||++...++..+.-  .+.+|.|.|  ||..
T Consensus        33 ~~~~~ll~~l~~~~g--------~a~~iGiTG~pG~GKStli~~l~~~~~~--~g~~v~vlavDPsS~   90 (325)
T PRK09435         33 ALAQELLDALLPHTG--------NALRIGITGVPGVGKSTFIEALGMHLIE--QGHKVAVLAVDPSST   90 (325)
T ss_pred             HHHHHHHHHHHHCCC--------CCEEEEEECCCCCCHHHHHHHHHHHHHH--CCCEEEEEEECCCCC
T ss_conf             999999998630179--------8259974279998688999999999996--798589999789999


No 358
>PRK13407 bchI magnesium chelatase subunit I; Provisional
Probab=69.70  E-value=7.2  Score=17.76  Aligned_cols=50  Identities=20%  Similarity=0.215  Sum_probs=32.5

Q ss_pred             CCCHHHHCCCCCCEEEEECCHHCCCHHHHHHHHHHHCCCC-------------CCEEEEEECCCCC
Q ss_conf             6100212026761499971110299788988888850799-------------8138998238998
Q gi|254781215|r  180 RPDTFVGHHNTYGMAIINDEASGTPDVINLGILGFLTERN-------------ANRFWIMTSNPRR  232 (511)
Q Consensus       180 ~~ea~~G~h~~~~~lvI~DEAsgI~d~i~e~i~~~Lt~~g-------------~~~~~i~~~nP~~  232 (511)
                      .|.-++-.|+  .+ +.+||.-=.++.+-+++.-.+.++-             ++-.++++.||.-
T Consensus       120 ~PGlLa~Ah~--GV-LylDEinll~~~vld~Ll~~~e~G~~~IeReg~s~~~ParF~LVatmNPeE  182 (334)
T PRK13407        120 EPGLLARANR--GY-LYIDEVNLLEDHIVDLLLDVAQSGENVVEREGLSIRHPARFVLVGSGNPEE  182 (334)
T ss_pred             CCCHHHHCCC--CE-EEEECHHHCCHHHHHHHHHHHHCCCEEEEECCEEEECCCCCEEEEEECCCC
T ss_conf             8605434028--86-787205333388999999887169579997763460366265898208887


No 359
>pfam01637 Arch_ATPase Archaeal ATPase. This family contain a conserved P-loop motif that is involved in binding ATP. This family is almost exclusively found in archaebacteria and particularly in Methanococcus jannaschii that encodes sixteen members of this family.
Probab=69.58  E-value=7.3  Score=17.74  Aligned_cols=35  Identities=26%  Similarity=0.147  Sum_probs=21.1

Q ss_pred             EEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEEECC
Q ss_conf             4650257659789999999999980899669998085
Q gi|254781215|r   80 GAISAGRGIGKTTLNAWLVLWLMSTRPGISVICLANS  116 (511)
Q Consensus        80 ~aV~sgrG~GKS~l~a~l~lw~l~~~p~~kv~vtApt  116 (511)
                      +.|-+.|++|||+|+-..+--.  -.++..++.....
T Consensus        23 ivi~G~RR~GKTsLi~~~~~~~--~~~~~~~i~~~~~   57 (223)
T pfam01637        23 IVVYGPRRCGKTALLREFLEEL--RELGYRVIYYDPL   57 (223)
T ss_pred             EEEECCCCCCHHHHHHHHHHHC--CCCCCEEEEEECH
T ss_conf             9998688787999999999863--3468528999514


No 360
>PRK07337 aminotransferase; Validated
Probab=69.28  E-value=7.4  Score=17.70  Aligned_cols=25  Identities=20%  Similarity=0.037  Sum_probs=15.4

Q ss_pred             HHHHHHHHHCCCCEEEEEECCHHHH
Q ss_conf             9999999808996699980858999
Q gi|254781215|r   96 WLVLWLMSTRPGISVICLANSETQL  120 (511)
Q Consensus        96 ~l~lw~l~~~p~~kv~vtApt~~Q~  120 (511)
                      ..++..+++.||-.|++..|++...
T Consensus       103 l~~~~~~l~~pGD~Vlv~~P~Yp~~  127 (388)
T PRK07337        103 LLLACLALVERGDEVLMPDPSYPCN  127 (388)
T ss_pred             HHHHHHHHCCCCCEEEECCCCCHHH
T ss_conf             9999999669999899858873659


No 361
>KOG4181 consensus
Probab=69.19  E-value=4.8  Score=18.90  Aligned_cols=13  Identities=31%  Similarity=0.363  Sum_probs=5.5

Q ss_pred             HHHHHHHHHHHHH
Q ss_conf             7999999999999
Q gi|254781215|r  412 RRTELHVKMADWL  424 (511)
Q Consensus       412 ~rae~~~~~re~l  424 (511)
                      +|-+|-.++..|+
T Consensus       361 ~rerl~~~~~~l~  373 (491)
T KOG4181         361 QRERLDKKLAYLY  373 (491)
T ss_pred             HHHHHHHHHHHHH
T ss_conf             8988888998885


No 362
>PRK08069 consensus
Probab=69.07  E-value=7.5  Score=17.67  Aligned_cols=59  Identities=10%  Similarity=-0.008  Sum_probs=28.9

Q ss_pred             HHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEEECCHHHHH
Q ss_conf             999999999874056555421012465025765978999999999998089966999808589999
Q gi|254781215|r   56 LEFMEVVDAHCLNSVNNPNPEVFKGAISAGRGIGKTTLNAWLVLWLMSTRPGISVICLANSETQLK  121 (511)
Q Consensus        56 ~e~l~~i~~~~~~~~~~~~~~~~r~aV~sgrG~GKS~l~a~l~lw~l~~~p~~kv~vtApt~~Q~~  121 (511)
                      .++.++|+++..+..+.+... -.|.|.+|    =  ..+..++-.+++.||-.|++..|++....
T Consensus        70 ~~lreaia~~~~~~~g~~~~p-~~V~it~G----~--~~al~~~~~~l~~pGD~Vlv~~P~Y~~y~  128 (390)
T PRK08069         70 QALKQEIVKKFKRDQGLAYDP-SEIIVCTG----A--KHALYTLFQVLLDEGDEVIIPTPYWVSYP  128 (390)
T ss_pred             HHHHHHHHHHHHHHHCCCCCH-HEEEECCC----H--HHHHHHHHHHHCCCCCEEEECCCCCCCHH
T ss_conf             999999999999986899881-11898788----8--99999999972799898998068664279


No 363
>pfam09140 MipZ ATPase MipZ. MipZ is an ATPase that forms a complex with the chromosome partitioning protein ParB near the chromosomal origin of replication. It is responsible for the temporal and spatial regulation of FtsZ ring formation.
Probab=68.96  E-value=7  Score=17.84  Aligned_cols=32  Identities=25%  Similarity=0.277  Sum_probs=23.8

Q ss_pred             CCCCHHHHHHHHHHHHHHHCCCCEEEEEECCHHH
Q ss_conf             7659789999999999980899669998085899
Q gi|254781215|r   86 RGIGKTTLNAWLVLWLMSTRPGISVICLANSETQ  119 (511)
Q Consensus        86 rG~GKS~l~a~l~lw~l~~~p~~kv~vtApt~~Q  119 (511)
                      =|+|||+++..++..++..  +.+|.++=-.-+|
T Consensus        10 GGvGKTTtavnLA~aLA~~--G~rVllIDlDpqq   41 (261)
T pfam09140        10 GGSGKSTTAVHVAVALLYL--GARVATIDLDLRQ   41 (261)
T ss_pred             CCCCHHHHHHHHHHHHHHC--CCCEEEEECCCCC
T ss_conf             9872999999999999988--9978999799999


No 364
>KOG2825 consensus
Probab=68.82  E-value=3.5  Score=19.73  Aligned_cols=38  Identities=29%  Similarity=0.384  Sum_probs=29.6

Q ss_pred             EEEEECC-CCCCHHHHHHHHHHHHHHHCCCCEEEEEECC
Q ss_conf             2465025-7659789999999999980899669998085
Q gi|254781215|r   79 KGAISAG-RGIGKTTLNAWLVLWLMSTRPGISVICLANS  116 (511)
Q Consensus        79 r~aV~sg-rG~GKS~l~a~l~lw~l~~~p~~kv~vtApt  116 (511)
                      |-.-..| -|+|||++++.+++-+...++..-++.|-|.
T Consensus        20 KwifVGGKGGVGKTTcs~sLAvqla~~r~~vLiISTDPA   58 (323)
T KOG2825          20 KWIFVGGKGGVGKTTCSCSLAVQLAKVRESVLIISTDPA   58 (323)
T ss_pred             EEEEECCCCCCCCCCHHHHHHHHHHCCCCCEEEEECCCC
T ss_conf             699976767767653126899998616886478616853


No 365
>PRK04863 mukB cell division protein MukB; Provisional
Probab=68.64  E-value=4.2  Score=19.22  Aligned_cols=34  Identities=32%  Similarity=0.516  Sum_probs=20.5

Q ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEEEC
Q ss_conf             2465025765978999999999998089966999808
Q gi|254781215|r   79 KGAISAGRGIGKTTLNAWLVLWLMSTRPGISVICLAN  115 (511)
Q Consensus        79 r~aV~sgrG~GKS~l~a~l~lw~l~~~p~~kv~vtAp  115 (511)
                      -++.+.|.|.|||++++.++.-.+   |+-+-+-.-|
T Consensus        29 VttLsGgNGAGKSTtMaAf~taLI---PD~tlLhfrn   62 (1486)
T PRK04863         29 VTTLSGGNGAGKSTTMAAFVTALI---PDLTLLHFRN   62 (1486)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHC---CCCCEEECCC
T ss_conf             033005888657989999999967---6430231146


No 366
>TIGR00958 3a01208 antigen peptide transporter 2; InterPro: IPR005293   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).     Proteins of this family are involved in the transport of antigens from the cytoplasm to a membrane-bound compartment for association with MHC class I molecules.; GO: 0005215 transporter activity, 0006810 transport.
Probab=68.41  E-value=3.7  Score=19.56  Aligned_cols=22  Identities=32%  Similarity=0.308  Sum_probs=9.6

Q ss_pred             EEEECCCCCCHHHHHHHHHHHH
Q ss_conf             4650257659789999999999
Q gi|254781215|r   80 GAISAGRGIGKTTLNAWLVLWL  101 (511)
Q Consensus        80 ~aV~sgrG~GKS~l~a~l~lw~  101 (511)
                      ||...+.|.|||+++|.|-.+|
T Consensus       562 vALVGPsGsGKStvaaLL~n~Y  583 (770)
T TIGR00958       562 VALVGPSGSGKSTVAALLQNLY  583 (770)
T ss_pred             EEEECCCCCCHHHHHHHHHHCC
T ss_conf             9986589983999999998557


No 367
>KOG0920 consensus
Probab=68.16  E-value=7.8  Score=17.56  Aligned_cols=158  Identities=14%  Similarity=0.046  Sum_probs=79.5

Q ss_pred             HHHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHH-CCCCEEEEEECCHHHHHHHHHHHHHHHH
Q ss_conf             999999999998740565554210124650257659789999999999980-8996699980858999999999999999
Q gi|254781215|r   54 WQLEFMEVVDAHCLNSVNNPNPEVFKGAISAGRGIGKTTLNAWLVLWLMST-RPGISVICLANSETQLKTTLWAEVSKWL  132 (511)
Q Consensus        54 WQ~e~l~~i~~~~~~~~~~~~~~~~r~aV~sgrG~GKS~l~a~l~lw~l~~-~p~~kv~vtApt~~Q~~~ilw~Ei~k~~  132 (511)
                      -++++|..|..|.            =+.|++..|+|||+-+=-++|-.+.. .+.++|+||-|-.--|-.+  +|-...-
T Consensus       177 ~r~~Il~~i~~~q------------VvvIsGeTGcGKtTQvpQfiLd~~~~~~~~~~IicTQPRRIsAIsv--AeRVa~E  242 (924)
T KOG0920         177 MRDTILDAIEENQ------------VVVISGETGCGKTTQVPQFILDEAIESGAACNIICTQPRRISAISV--AERVAKE  242 (924)
T ss_pred             HHHHHHHHHHHCC------------EEEEECCCCCCCHHHHHHHHHHHHHHCCCCCEEEECCCCHHHHHHH--HHHHHHH
T ss_conf             8999999997496------------6999578898712246699999998628997388667751778999--9999887


Q ss_pred             HHCHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEE-CCCCCCCCCHHHHCCCCCCEEEEECCHHC--CCHHH-H
Q ss_conf             85500013444322222233344432111235786169853-03575561002120267614999711102--99788-9
Q gi|254781215|r  133 SLLPNKHWFEMQSLSLHPAPWYSDVLHCSLGIDSKHYSTMC-RTYSEERPDTFVGHHNTYGMAIINDEASG--TPDVI-N  208 (511)
Q Consensus       133 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~s~~~~ea~~G~h~~~~~lvI~DEAsg--I~d~i-~  208 (511)
                      +....          ...-+|.......... ...-.|++. ...+.-..   .... .+...+|+||.+-  ++.++ .
T Consensus       243 R~~~~----------g~~VGYqvrl~~~~s~-~t~L~fcTtGvLLr~L~~---~~~l-~~~thiivDEVHER~i~~DflL  307 (924)
T KOG0920         243 RGESL----------GEEVGYQVRLESKRSR-ETRLLFCTTGVLLRRLQS---DPTL-SGVTHIIVDEVHERSINTDFLL  307 (924)
T ss_pred             HCCCC----------CCEEEEEEEEECCCCC-CEEEEEECHHHHHHHHCC---CCCC-CCCCEEEEEEEEECCCCCCCHH
T ss_conf             54666----------8713689862013677-516898406899987546---8621-4586654422797167752179


Q ss_pred             HHHHHHHCCCCCCEEEEEECCCCCCCCHHHHHHH
Q ss_conf             8888885079981389982389987655676530
Q gi|254781215|r  209 LGILGFLTERNANRFWIMTSNPRRLSGKFYEIFN  242 (511)
Q Consensus       209 e~i~~~Lt~~g~~~~~i~~~nP~~~~g~fy~~~~  242 (511)
                      .++...|.. ++..+.+.+|-.-+ .-.|.+-|.
T Consensus       308 i~lk~lL~~-~p~LkvILMSAT~d-ae~fs~YF~  339 (924)
T KOG0920         308 ILLKDLLPR-NPDLKVILMSATLD-AELFSDYFG  339 (924)
T ss_pred             HHHHHHHHH-CCCCEEEEEEEECC-HHHHHHHHC
T ss_conf             999988622-88856998621126-288898718


No 368
>pfam08419 consensus
Probab=67.94  E-value=7.9  Score=17.53  Aligned_cols=39  Identities=26%  Similarity=0.327  Sum_probs=25.1

Q ss_pred             HHHHHHHHHHHHHHHHCCCCCCCCCCEEEE-EECCCCC-CHHHHHHHHHH
Q ss_conf             589999999999987405655542101246-5025765-97899999999
Q gi|254781215|r   52 RSWQLEFMEVVDAHCLNSVNNPNPEVFKGA-ISAGRGI-GKTTLNAWLVL   99 (511)
Q Consensus        52 ~~WQ~e~l~~i~~~~~~~~~~~~~~~~r~a-V~sgrG~-GKS~l~a~l~l   99 (511)
                      ++||.+++..+...-     .+    +.+. |=+..|. |||+++--|.+
T Consensus        57 k~WQ~~l~~~l~~~P-----dd----RtI~Wvygp~GgeGKStfak~L~~   97 (116)
T pfam08419        57 RPWQDEVESLLEEEP-----DD----RTIIWVYGPNGGEGKSTFAKHLGL   97 (116)
T ss_pred             CHHHHHHHHHHHCCC-----CC----CEEEEEECCCCCCCHHHHHHHHHH
T ss_conf             169999999983699-----87----469999858998664288886420


No 369
>COG0488 Uup ATPase components of ABC transporters with duplicated ATPase domains [General function prediction only]
Probab=67.91  E-value=5  Score=18.79  Aligned_cols=26  Identities=27%  Similarity=0.136  Sum_probs=20.8

Q ss_pred             CCEEEEEECCCCCCHHHHHHHHHHHH
Q ss_conf             10124650257659789999999999
Q gi|254781215|r   76 EVFKGAISAGRGIGKTTLNAWLVLWL  101 (511)
Q Consensus        76 ~~~r~aV~sgrG~GKS~l~a~l~lw~  101 (511)
                      ..-|+.+..-.|.|||++...++=-.
T Consensus        28 ~G~riGLvG~NGaGKSTLLkilaG~~   53 (530)
T COG0488          28 PGERIGLVGRNGAGKSTLLKILAGEL   53 (530)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHCCC
T ss_conf             99889998999898899999982997


No 370
>cd01863 Rab18 Rab18 subfamily.  Mammalian Rab18 is implicated in endocytic transport and is expressed most highly in polarized epithelial cells. However, trypanosomal Rab, TbRAB18, is upregulated in the BSF (Blood Stream Form) stage and localized predominantly to elements of the Golgi complex.  In human and mouse cells, Rab18 has been identified in lipid droplets, organelles that store neutral lipids. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state.  Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of mos
Probab=67.90  E-value=5  Score=18.77  Aligned_cols=21  Identities=24%  Similarity=0.376  Sum_probs=18.1

Q ss_pred             EEEEEECCCCCCHHHHHHHHH
Q ss_conf             124650257659789999999
Q gi|254781215|r   78 FKGAISAGRGIGKTTLNAWLV   98 (511)
Q Consensus        78 ~r~aV~sgrG~GKS~l~a~l~   98 (511)
                      +|+.|....|+|||.++..++
T Consensus         1 ~KivvvG~~~vGKTsli~r~~   21 (161)
T cd01863           1 LKILLIGDSGVGKSSLLLRFT   21 (161)
T ss_pred             CEEEEECCCCCCHHHHHHHHH
T ss_conf             989999979957999999996


No 371
>PRK11819 putative ABC transporter ATP-binding protein; Reviewed
Probab=67.64  E-value=4.8  Score=18.90  Aligned_cols=37  Identities=11%  Similarity=0.038  Sum_probs=23.6

Q ss_pred             CCCEEEEECCH-HCCCHHHHHHHHHHHCCCCCCEEEEEEC
Q ss_conf             76149997111-0299788988888850799813899823
Q gi|254781215|r  190 TYGMAIINDEA-SGTPDVINLGILGFLTERNANRFWIMTS  228 (511)
Q Consensus       190 ~~~~lvI~DEA-sgI~d~i~e~i~~~Lt~~g~~~~~i~~~  228 (511)
                      ...-++|+||- +.++...-+.++..|.......  +.++
T Consensus       180 ~~PdlLlLDEPTn~LD~~~i~~L~~~L~~~~gtv--ivVS  217 (556)
T PRK11819        180 SKPDMLLLDEPTNHLDAESVAWLEQFLHDYPGTV--VAVT  217 (556)
T ss_pred             CCCCEEEECCCCCCCCHHHHHHHHHHHHHCCCCE--EEEE
T ss_conf             6999899848877789778999999976337877--9999


No 372
>PRK00081 coaE dephospho-CoA kinase; Reviewed
Probab=67.63  E-value=5.1  Score=18.69  Aligned_cols=31  Identities=26%  Similarity=0.373  Sum_probs=24.3

Q ss_pred             CEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEE
Q ss_conf             0124650257659789999999999980899669998
Q gi|254781215|r   77 VFKGAISAGRGIGKTTLNAWLVLWLMSTRPGISVICL  113 (511)
Q Consensus        77 ~~r~aV~sgrG~GKS~l~a~l~lw~l~~~p~~kv~vt  113 (511)
                      |..++|..|=|+|||+++..+--      .|..++..
T Consensus         2 m~~IgiTG~igsGKStv~~~l~~------~G~~vida   32 (199)
T PRK00081          2 MLIIGLTGGIGSGKSTVANIFAE------LGVPVIDA   32 (199)
T ss_pred             CEEEEEECCCCCCHHHHHHHHHH------CCCCEEEH
T ss_conf             78999578887779999999998------89939963


No 373
>pfam01656 CbiA CobQ/CobB/MinD/ParA nucleotide binding domain. This family consists of various cobyrinic acid a,c-diamide synthases. These include CbiA and CbiP from S.typhimurium, and CobQ from R. capsulatus. These amidases catalyse amidations to various side chains of hydrogenobyrinic acid or cobyrinic acid a,c-diamide in the biosynthesis of cobalamin (vitamin B12) from uroporphyrinogen III. Vitamin B12 is an important cofactor and an essential nutrient for many plants and animals and is primarily produced by bacteria. The family also contains dethiobiotin synthetases as well as the plasmid partitioning proteins of the MinD/ParA family.
Probab=67.50  E-value=8  Score=17.47  Aligned_cols=32  Identities=41%  Similarity=0.443  Sum_probs=24.0

Q ss_pred             EEEECC-CCCCHHHHHHHHHHHHHHHCCCCEEEEE
Q ss_conf             465025-7659789999999999980899669998
Q gi|254781215|r   80 GAISAG-RGIGKTTLNAWLVLWLMSTRPGISVICL  113 (511)
Q Consensus        80 ~aV~sg-rG~GKS~l~a~l~lw~l~~~p~~kv~vt  113 (511)
                      ++|.|+ =|+|||++++.++..++.  .+.+|+++
T Consensus         1 Iav~s~KGGVGKTT~a~nLA~~la~--~G~rVlli   33 (212)
T pfam01656         1 IAIAGTKGGVGKTTLAANLARALAK--RGYRVLLI   33 (212)
T ss_pred             CEEECCCCCHHHHHHHHHHHHHHHH--CCCCEEEE
T ss_conf             9897689980699999999999997--89978998


No 374
>PRK05922 type III secretion system ATPase; Validated
Probab=67.39  E-value=7.8  Score=17.53  Aligned_cols=35  Identities=14%  Similarity=0.052  Sum_probs=24.4

Q ss_pred             CEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEEECC
Q ss_conf             0124650257659789999999999980899669998085
Q gi|254781215|r   77 VFKGAISAGRGIGKTTLNAWLVLWLMSTRPGISVICLANS  116 (511)
Q Consensus        77 ~~r~aV~sgrG~GKS~l~a~l~lw~l~~~p~~kv~vtApt  116 (511)
                      .-|+.+-+|.|+|||++++.++..     -...+.|+|.-
T Consensus       157 GQR~gIf~g~GvGKt~Ll~~ia~~-----~~~~v~V~alI  191 (434)
T PRK05922        157 GQRIGVFSEPGSGKSSLLSTIAKG-----SKSTINVIALI  191 (434)
T ss_pred             CCEEEECCCCCCCHHHHHHHHHHC-----CCCCEEEEEEE
T ss_conf             767773079999789999867653-----67875999845


No 375
>TIGR00604 rad3 DNA repair helicase (rad3); InterPro: IPR013020   All proteins in this family for which functions are known are DNA-DNA helicases that function in the initiation of transcription and nucleotide excision repair as part of the TFIIH complex. .
Probab=67.34  E-value=3.7  Score=19.62  Aligned_cols=72  Identities=21%  Similarity=0.270  Sum_probs=45.8

Q ss_pred             HHHHHHHHHHHHHHHCCCCCCCCCCEEEEE-----ECCCCCCHHH------------------HHHH--HHHHHHHHCC-
Q ss_conf             899999999999874056555421012465-----0257659789------------------9999--9999998089-
Q gi|254781215|r   53 SWQLEFMEVVDAHCLNSVNNPNPEVFKGAI-----SAGRGIGKTT------------------LNAW--LVLWLMSTRP-  106 (511)
Q Consensus        53 ~WQ~e~l~~i~~~~~~~~~~~~~~~~r~aV-----~sgrG~GKS~------------------l~a~--l~lw~l~~~p-  106 (511)
                      +=|++.+.++-.-+.+..        ..++     -..-|+|||.                  .+|-  .++-+..-.| 
T Consensus        18 p~q~~~~~~~~~~Ld~~~--------~~~~~~E~dE~PsgtgKt~~GGrisdkdy~~~~~~S~~~SlL~~~~~~~~~~P~   89 (813)
T TIGR00604        18 PEQRSYMRDLKRSLDRGD--------EAILSAEYDEMPSGTGKTIKGGRISDKDYKLDELYSSKVSLLSLILAYQQEKPL   89 (813)
T ss_pred             HHHHHHHHHHHHHHHCCC--------CCCCCCCCCCCCCCCCCEECCCCCCCHHHHHCCCCCHHHHHHHHCCCHHHHCCC
T ss_conf             455444577788771476--------524663556563888740006500201221102440344455423627883889


Q ss_pred             -----------CCEEEEEECCHHHHHHHHHHHHHHHHH
Q ss_conf             -----------966999808589999999999999998
Q gi|254781215|r  107 -----------GISVICLANSETQLKTTLWAEVSKWLS  133 (511)
Q Consensus       107 -----------~~kv~vtApt~~Q~~~ilw~Ei~k~~~  133 (511)
                                 ..|+++++=|..|+... -.|++|...
T Consensus        90 nGdrfdvtnq~~~Ki~Y~SRT~sq~~~~-~~el~kl~~  126 (813)
T TIGR00604        90 NGDRFDVTNQEVLKIIYASRTHSQLEQA-VEELRKLMS  126 (813)
T ss_pred             CCCCEECCCCCCCCEEEECCCCHHHHHH-HHHHHHHHH
T ss_conf             8860000367542227723686278899-999985221


No 376
>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=67.34  E-value=8.1  Score=17.45  Aligned_cols=75  Identities=15%  Similarity=0.160  Sum_probs=53.0

Q ss_pred             HHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHHCCC---CEEEEEECCHHHHHHHHHHHHHHH
Q ss_conf             99999999998740565554210124650257659789999999999980899---669998085899999999999999
Q gi|254781215|r   55 QLEFMEVVDAHCLNSVNNPNPEVFKGAISAGRGIGKTTLNAWLVLWLMSTRPG---ISVICLANSETQLKTTLWAEVSKW  131 (511)
Q Consensus        55 Q~e~l~~i~~~~~~~~~~~~~~~~r~aV~sgrG~GKS~l~a~l~lw~l~~~p~---~kv~vtApt~~Q~~~ilw~Ei~k~  131 (511)
                      |.++..+|..-..+...+|     | -|-.==|.|||.++-..+.- +.+.-+   ..|+|..||-==+.. =|.-+++.
T Consensus       513 Q~~AI~eik~Dm~~~~~MD-----R-L~CGDVGfGKTEVAmRAaFk-Av~~gneylKQVavLVPTT~LA~Q-Hf~tf~~R  584 (997)
T TIGR00580       513 QLKAIEEIKADMESPRPMD-----R-LVCGDVGFGKTEVAMRAAFK-AVLDGNEYLKQVAVLVPTTILAQQ-HFETFKER  584 (997)
T ss_pred             HHHHHHHHHHHHCCCCCCC-----E-EEECCCCCCHHHHHHHHHHH-HHCCCCCEECEEEEECCHHHHHHH-HHHHHHHH
T ss_conf             9999999999740689873-----4-65245488536888878887-633878220116896270442777-88999997


Q ss_pred             HHHCHH
Q ss_conf             985500
Q gi|254781215|r  132 LSLLPN  137 (511)
Q Consensus       132 ~~~~~~  137 (511)
                      ....|.
T Consensus       585 F~~fPv  590 (997)
T TIGR00580       585 FANFPV  590 (997)
T ss_pred             HCCCCE
T ss_conf             378981


No 377
>PRK06107 aspartate aminotransferase; Provisional
Probab=67.31  E-value=8.1  Score=17.45  Aligned_cols=59  Identities=12%  Similarity=0.037  Sum_probs=35.1

Q ss_pred             HHHHHHHHHHHHCCCCCC-CCCCEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEEECCHHHHHH
Q ss_conf             999999999874056555-4210124650257659789999999999980899669998085899999
Q gi|254781215|r   56 LEFMEVVDAHCLNSVNNP-NPEVFKGAISAGRGIGKTTLNAWLVLWLMSTRPGISVICLANSETQLKT  122 (511)
Q Consensus        56 ~e~l~~i~~~~~~~~~~~-~~~~~r~aV~sgrG~GKS~l~a~l~lw~l~~~p~~kv~vtApt~~Q~~~  122 (511)
                      .++.++|+++..+..+.+ .|.  .+.|..|    -+.  +..++-.+++.||-.|++..|++..-..
T Consensus        73 ~eLReAia~~~~~~~g~~v~p~--~I~vt~G----~~~--al~~~~~al~~pGD~Vlv~~P~Y~~y~~  132 (402)
T PRK06107         73 PALRKAIIAKMERRNGLHYADN--EICVGGG----AKQ--AIFLALMATLEEGDEVIIPAPYWVSYPD  132 (402)
T ss_pred             HHHHHHHHHHHHHHHCCCCCCC--EEEECCC----HHH--HHHHHHHHHCCCCCEEEEECCCCCCHHH
T ss_conf             9999999999999868999820--4998688----899--9999999957999989981686653799


No 378
>PRK04192 V-type ATP synthase subunit A; Provisional
Probab=67.18  E-value=6.8  Score=17.94  Aligned_cols=32  Identities=25%  Similarity=0.382  Sum_probs=21.7

Q ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEEEC
Q ss_conf             2465025765978999999999998089966999808
Q gi|254781215|r   79 KGAISAGRGIGKTTLNAWLVLWLMSTRPGISVICLAN  115 (511)
Q Consensus        79 r~aV~sgrG~GKS~l~a~l~lw~l~~~p~~kv~vtAp  115 (511)
                      +.++.+|.|+|||.+...++-|-     ++.++|.+.
T Consensus       229 t~~IpGgfG~GKTvl~~~lak~s-----~aDivVyvg  260 (585)
T PRK04192        229 TAAIPGPFGSGKTVTQHQLAKWA-----DADIVIYVG  260 (585)
T ss_pred             EEECCCCCCCCHHHHHHHHHHCC-----CCCEEEEEE
T ss_conf             23212666666466799997426-----899899997


No 379
>pfam04310 MukB MukB N-terminal. This family represents the N-terminal region of MukB, one of a group of bacterial proteins essential for the movement of nucleoids from mid-cell towards the cell quarters (i.e. chromosome partitioning). The structure of the N-terminal domain consists of an antiparallel six-stranded beta sheet surrounded by one helix on one side and by five helices on the other side. It contains an exposed Walker A loop in an unexpected helix-loop-helix motif (in other proteins, Walker A motifs generally adopt a P loop conformation as part of a strand-loop-helix motif embedded in a conserved topology of alternating helices and (parallel) beta strands).
Probab=67.09  E-value=5.1  Score=18.74  Aligned_cols=36  Identities=31%  Similarity=0.505  Sum_probs=24.6

Q ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEEECCH
Q ss_conf             246502576597899999999999808996699980858
Q gi|254781215|r   79 KGAISAGRGIGKTTLNAWLVLWLMSTRPGISVICLANSE  117 (511)
Q Consensus        79 r~aV~sgrG~GKS~l~a~l~lw~l~~~p~~kv~vtApt~  117 (511)
                      -++.+.|.|.|||++++.++.-.+   |+-+-+-.-||-
T Consensus        29 vttLsG~NGAGKsT~m~Af~talI---PDl~~l~frntt   64 (227)
T pfam04310        29 VTTLSGGNGAGKSTTMAAFITALI---PDLSLLHFRNTT   64 (227)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHC---CCCEEEEECCCC
T ss_conf             688644787654879999999866---664388621556


No 380
>PRK05298 excinuclease ABC subunit B; Provisional
Probab=67.05  E-value=8.2  Score=17.42  Aligned_cols=64  Identities=17%  Similarity=0.151  Sum_probs=45.9

Q ss_pred             HHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEEECCHHHHHHHHHHHHHHH
Q ss_conf             99999999998740565554210124650257659789999999999980899669998085899999999999999
Q gi|254781215|r   55 QLEFMEVVDAHCLNSVNNPNPEVFKGAISAGRGIGKTTLNAWLVLWLMSTRPGISVICLANSETQLKTTLWAEVSKW  131 (511)
Q Consensus        55 Q~e~l~~i~~~~~~~~~~~~~~~~r~aV~sgrG~GKS~l~a~l~lw~l~~~p~~kv~vtApt~~Q~~~ilw~Ei~k~  131 (511)
                      |-+++..+.+...++. +++      ....-.|+|||+.+|.++--     -..-++|.|+...-|- -|+.|++..
T Consensus        18 QP~AI~~L~~gi~~g~-~~Q------~LlGvTGSGKTfTmAnvI~~-----~~rPtLVlahNKTLAA-QLy~Efk~f   81 (657)
T PRK05298         18 QPQAIAELVEGIESGE-KHQ------TLLGVTGSGKTFTMANVIAR-----VQRPTLVLAHNKTLAA-QLYGEFKEF   81 (657)
T ss_pred             CHHHHHHHHHHHHCCC-CEE------EEECCCCCCHHHHHHHHHHH-----HCCCEEEECCCHHHHH-HHHHHHHHH
T ss_conf             7999999998997499-636------99703678566899999998-----6897599766588999-999999976


No 381
>cd01886 EF-G Elongation factor G (EF-G) subfamily.  Translocation is mediated by EF-G (also called translocase).  The structure of EF-G closely resembles that of the complex between EF-Tu and tRNA.  This is an example of molecular mimicry; a protein domain evolved so that it mimics the shape of a tRNA molecule.  EF-G in the GTP form binds to the ribosome, primarily through the interaction of its EF-Tu-like domain with the 50S subunit.  The binding of EF-G to the ribosome in this manner stimulates the GTPase activity of EF-G. On GTP hydrolysis, EF-G undergoes a conformational change that forces its arm deeper into the A site on the 30S subunit.  To accommodate this domain, the peptidyl-tRNA in the A site moves to the P site, carrying the mRNA and the deacylated tRNA with it.  The ribosome may be prepared for these rearrangements by the initial binding of EF-G as well.  The dissociation of EF-G leaves the ribosome ready to accept the next aminoacyl-tRNA into the A site.  This group conta
Probab=66.76  E-value=6.5  Score=18.06  Aligned_cols=108  Identities=11%  Similarity=-0.027  Sum_probs=48.2

Q ss_pred             EEEECCCCCCHHHHHHHHHHHHH-HHCCCCEEEEEECCHHHHHHHHHHHHHHHHHHCHHCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             46502576597899999999999-80899669998085899999999999999985500013444322222233344432
Q gi|254781215|r   80 GAISAGRGIGKTTLNAWLVLWLM-STRPGISVICLANSETQLKTTLWAEVSKWLSLLPNKHWFEMQSLSLHPAPWYSDVL  158 (511)
Q Consensus        80 ~aV~sgrG~GKS~l~a~l~lw~l-~~~p~~kv~vtApt~~Q~~~ilw~Ei~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~  158 (511)
                      +++.+-.|.|||+|+-.++.--= +.+.+ +|-=- +|   +.+-.=-|+++-+........+.|....+          
T Consensus         2 iai~gH~gaGKTtL~EalL~~ag~i~r~G-~v~~g-~t---v~D~~~eE~~R~isi~~~~~~~~w~~~~i----------   66 (270)
T cd01886           2 IGIIAHIDAGKTTTTERILYYTGRIHKIG-EVHGG-GA---TMDFMEQERERGITIQSAATTCFWKDHRI----------   66 (270)
T ss_pred             EEEEECCCCCHHHHHHHHHHHCCCCCCCC-EECCC-CC---CCCCCHHHHHCCCEEECCEEEEEECCEEE----------
T ss_conf             89996899998899999998668735581-55389-75---56684889876870733668999899899----------


Q ss_pred             CCCCCCCCCEEEEEECCCCCCCCCHHHHCCCCCCEEEEECCHHCCC---HHHHHHHH
Q ss_conf             1112357861698530357556100212026761499971110299---78898888
Q gi|254781215|r  159 HCSLGIDSKHYSTMCRTYSEERPDTFVGHHNTYGMAIINDEASGTP---DVINLGIL  212 (511)
Q Consensus       159 ~~~~~~~~~~~~~~~~~~s~~~~ea~~G~h~~~~~lvI~DEAsgI~---d~i~e~i~  212 (511)
                                -+.....+..-..|...+++.--..++|+|-++||.   ..+|+.++
T Consensus        67 ----------nliDTPG~~DF~~e~~~aL~~~D~AviVv~a~~GVe~~T~~~w~~~~  113 (270)
T cd01886          67 ----------NIIDTPGHVDFTIEVERSLRVLDGAVAVFDAVAGVEPQTETVWRQAD  113 (270)
T ss_pred             ----------EEEECCCCHHHHHHHHHHHHHHCEEEEEEECCCCHHHHHHHHHHHHH
T ss_conf             ----------99869696788999999987755599998467644263699998899


No 382
>COG4240 Predicted kinase [General function prediction only]
Probab=66.53  E-value=8.4  Score=17.35  Aligned_cols=45  Identities=27%  Similarity=0.340  Sum_probs=27.4

Q ss_pred             HHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHHC
Q ss_conf             99999999987405655542101246502576597899999999999808
Q gi|254781215|r   56 LEFMEVVDAHCLNSVNNPNPEVFKGAISAGRGIGKTTLNAWLVLWLMSTR  105 (511)
Q Consensus        56 ~e~l~~i~~~~~~~~~~~~~~~~r~aV~sgrG~GKS~l~a~l~lw~l~~~  105 (511)
                      .+++.-|+...+..   ..|.  =+-|+.+.|+|||++++.+..-.+-..
T Consensus        34 Lpll~Kiap~~qe~---grPl--i~gisGpQGSGKStls~~i~~~L~~kg   78 (300)
T COG4240          34 LPLLAKIAPWAQER---GRPL--IVGISGPQGSGKSTLSALIVRLLAAKG   78 (300)
T ss_pred             HHHHHHHHHHHHHC---CCCE--EEEEECCCCCCHHHHHHHHHHHHHHHC
T ss_conf             78898644544212---7963--998526888765359999999999736


No 383
>cd04116 Rab9 Rab9 subfamily.  Rab9 is found in late endosomes, together with mannose 6-phosphate receptors (MPRs) and the tail-interacting protein of 47 kD (TIP47).  Rab9 is a key mediator of vesicular transport from late endosomes to the trans-Golgi network (TGN) by redirecting the MPRs.  Rab9 has been identified as a key component for the replication of several viruses, including HIV1, Ebola, Marburg, and measles, making it a potential target for inhibiting a variety of viruses.  GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state.  Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization.  Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CX
Probab=66.03  E-value=6.7  Score=17.95  Aligned_cols=24  Identities=25%  Similarity=0.412  Sum_probs=20.5

Q ss_pred             CCCEEEEEECCCCCCHHHHHHHHH
Q ss_conf             210124650257659789999999
Q gi|254781215|r   75 PEVFKGAISAGRGIGKTTLNAWLV   98 (511)
Q Consensus        75 ~~~~r~aV~sgrG~GKS~l~a~l~   98 (511)
                      ..++|+.+....|+|||.++..++
T Consensus         3 ~~~~KivvlGd~~VGKTsli~r~~   26 (170)
T cd04116           3 SSLLKVILLGDGGVGKSSLMNRYV   26 (170)
T ss_pred             CEEEEEEEECCCCCCHHHHHHHHH
T ss_conf             608999999999978999999997


No 384
>PRK06375 consensus
Probab=66.02  E-value=8.6  Score=17.29  Aligned_cols=58  Identities=12%  Similarity=0.031  Sum_probs=30.4

Q ss_pred             HHHHHHHHHHHHCCCCC-CCCCCEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEEECCHHHHHH
Q ss_conf             99999999987405655-54210124650257659789999999999980899669998085899999
Q gi|254781215|r   56 LEFMEVVDAHCLNSVNN-PNPEVFKGAISAGRGIGKTTLNAWLVLWLMSTRPGISVICLANSETQLKT  122 (511)
Q Consensus        56 ~e~l~~i~~~~~~~~~~-~~~~~~r~aV~sgrG~GKS~l~a~l~lw~l~~~p~~kv~vtApt~~Q~~~  122 (511)
                      .++-++|+++..+..+. -.|.  .+.| +|   |+.   +..++-.+++.||-+|++..|++.....
T Consensus        69 ~~lR~aia~~~~~~~g~~~~~~--~i~v-t~---~~~---~l~~~~~~l~~pGD~Vii~~P~Y~~y~~  127 (381)
T PRK06375         69 PELREKIALKLKSRNNIDAVAK--NVLV-TP---TKF---GINLAMMVILNPGDEVLIPSPYYVSYPD  127 (381)
T ss_pred             HHHHHHHHHHHHHHCCCCCCCC--EEEE-EC---HHH---HHHHHHHHHCCCCCEEEECCCCCHHHHH
T ss_conf             9999999999998559999957--6998-54---899---9999999866999989981888761999


No 385
>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=65.75  E-value=6.3  Score=18.15  Aligned_cols=147  Identities=16%  Similarity=0.131  Sum_probs=75.8

Q ss_pred             CCCCCCCCCHHHHHHHHH-HHHHHHHCCCCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEEECCHHHHH
Q ss_conf             756555784589999999-9999874056555421012465025765978999999999998089966999808589999
Q gi|254781215|r   43 TPLEGFSAPRSWQLEFME-VVDAHCLNSVNNPNPEVFKGAISAGRGIGKTTLNAWLVLWLMSTRPGISVICLANSETQLK  121 (511)
Q Consensus        43 ~~~~~~~~P~~WQ~e~l~-~i~~~~~~~~~~~~~~~~r~aV~sgrG~GKS~l~a~l~lw~l~~~p~~kv~vtApt~~Q~~  121 (511)
                      =.|.+-+-+|+||.+=|+ -|..+=+...        -| |.=+=|.|||-..--    .+ |+--.+++|.+++.--+.
T Consensus       262 IDLKP~t~~RPYQEKSLrsKMFGNGRARS--------Gi-IVLPCGAGKsLVGvT----AA-CTvkKs~lVLctS~VSV~  327 (756)
T TIGR00603       262 IDLKPTTVLRPYQEKSLRSKMFGNGRARS--------GI-IVLPCGAGKSLVGVT----AA-CTVKKSVLVLCTSAVSVE  327 (756)
T ss_pred             CCCCCCCCCCCCHHHHCCCCCCCCCCCCC--------CC-EECCCCCCCCHHHHH----HH-EEEEEEEEEEECCCHHHH
T ss_conf             45587778897511104445667861105--------51-776778883112254----42-023100789726710088


Q ss_pred             HHHHHHHHHHHHHCHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCCCCCCC---HHHHCCCCCCEEEEEC
Q ss_conf             9999999999985500013444322222233344432111235786169853035755610---0212026761499971
Q gi|254781215|r  122 TTLWAEVSKWLSLLPNKHWFEMQSLSLHPAPWYSDVLHCSLGIDSKHYSTMCRTYSEERPD---TFVGHHNTYGMAIIND  198 (511)
Q Consensus       122 ~ilw~Ei~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~e---a~~G~h~~~~~lvI~D  198 (511)
                      .  |+.=.|++........-.-|...+-.  +...   ..+..  .++-+.+.|.. .+.|   -+.=+++..=-|+|+|
T Consensus       328 Q--W~~QFk~WSti~d~~IcrFTSD~Ke~--~~~~---~gv~v--sTYsMva~t~k-RS~es~k~m~~l~~rEWGl~~LD  397 (756)
T TIGR00603       328 Q--WKQQFKLWSTIDDSQICRFTSDAKEK--FHGE---AGVVV--STYSMVAHTGK-RSYESEKVMEWLTNREWGLILLD  397 (756)
T ss_pred             H--HHHHHHHCCCCCCCCCCCCCCCCCCC--CCCC---CCEEE--ECCCCCCCCCC-CHHHHHHHHHHHHCCCCEEEEEC
T ss_conf             9--99887522688735511025213576--2665---33588--73300024754-31889999999706873179861


Q ss_pred             CHHCCCHHHHHHHHH
Q ss_conf             110299788988888
Q gi|254781215|r  199 EASGTPDVINLGILG  213 (511)
Q Consensus       199 EAsgI~d~i~e~i~~  213 (511)
                      |-+-||-.+|--+..
T Consensus       398 EVHvvPA~mFRrVlt  412 (756)
T TIGR00603       398 EVHVVPAAMFRRVLT  412 (756)
T ss_pred             CCCCCCCCCCCCHHH
T ss_conf             101035001660101


No 386
>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=65.61  E-value=8.7  Score=17.24  Aligned_cols=39  Identities=26%  Similarity=0.351  Sum_probs=26.8

Q ss_pred             EEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEEE--CCHHHH
Q ss_conf             46502576597899999999999808996699980--858999
Q gi|254781215|r   80 GAISAGRGIGKTTLNAWLVLWLMSTRPGISVICLA--NSETQL  120 (511)
Q Consensus        80 ~aV~sgrG~GKS~l~a~l~lw~l~~~p~~kv~vtA--pt~~Q~  120 (511)
                      +-|..+-|+|||.++..++.-.+.-  +-+++++.  -+..|+
T Consensus         2 tLi~G~pGsGKT~~a~qfl~~~a~~--ge~~lyis~eE~~~~l   42 (187)
T cd01124           2 TLLSGGPGTGKTTFALQFLYAGLAR--GEPGLYVTLEESPEEL   42 (187)
T ss_pred             EEEEECCCCCHHHHHHHHHHHHHHC--CCCEEEEEECCCHHHH
T ss_conf             1587689999999999999999876--9978999950799999


No 387
>cd03289 ABCC_CFTR2 The CFTR subfamily domain 2.  The cystic fibrosis transmembrane regulator (CFTR), the product of the gene mutated in patients with cystic fibrosis, has adapted the ABC transporter structural motif to form a tightly regulated anion channel at the apical surface of many epithelia.  Use of the term assembly of a functional ion channel implies the coming together of subunits or at least smaller not-yet functional components of the active whole.  In fact, on the basis of current knowledge only the CFTR polypeptide itself is required to form an ATP- and protein kinase A-dependent low-conductance chloride channel of the type present in the apical membrane of many epithelial cells.  CFTR displays the typical organization (IM-ABC)2 and carries a characteristic hydrophilic R-domain that separates IM1-ABC1 from IM2-ABC2.
Probab=65.26  E-value=6.2  Score=18.18  Aligned_cols=34  Identities=15%  Similarity=0.054  Sum_probs=24.0

Q ss_pred             CEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEE
Q ss_conf             0124650257659789999999999980899669998
Q gi|254781215|r   77 VFKGAISAGRGIGKTTLNAWLVLWLMSTRPGISVICL  113 (511)
Q Consensus        77 ~~r~aV~sgrG~GKS~l~a~l~lw~l~~~p~~kv~vt  113 (511)
                      .-+++|...-|.|||+++..++-  ++. +...|.+-
T Consensus        30 Ge~vaIvG~sGsGKSTLl~lL~g--l~~-~~G~I~id   63 (275)
T cd03289          30 GQRVGLLGRTGSGKSTLLSAFLR--LLN-TEGDIQID   63 (275)
T ss_pred             CCEEEEECCCCCCHHHHHHHHHH--HCC-CCCEEEEC
T ss_conf             99999999999979999999960--357-89539999


No 388
>PRK13764 ATPase; Provisional
Probab=64.68  E-value=9.1  Score=17.13  Aligned_cols=14  Identities=29%  Similarity=0.463  Sum_probs=5.6

Q ss_pred             CCCCCHHHHHHHHH
Q ss_conf             99989899999997
Q gi|254781215|r  463 AKSTDYSDGLMYTF  476 (511)
Q Consensus       463 ~~SPD~ADAl~l~f  476 (511)
                      -++-+.|+.++-+.
T Consensus       581 ~k~S~i~~~l~~a~  594 (605)
T PRK13764        581 AKNSDIAKELLRAI  594 (605)
T ss_pred             CCCCHHHHHHHHHH
T ss_conf             57986899999998


No 389
>PRK07367 consensus
Probab=64.66  E-value=9.1  Score=17.13  Aligned_cols=58  Identities=16%  Similarity=0.098  Sum_probs=29.5

Q ss_pred             HHHHHHHHHHHHHCCCCCC-CCCCEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEEECCHHHH
Q ss_conf             9999999999874056555-42101246502576597899999999999808996699980858999
Q gi|254781215|r   55 QLEFMEVVDAHCLNSVNNP-NPEVFKGAISAGRGIGKTTLNAWLVLWLMSTRPGISVICLANSETQL  120 (511)
Q Consensus        55 Q~e~l~~i~~~~~~~~~~~-~~~~~r~aV~sgrG~GKS~l~a~l~lw~l~~~p~~kv~vtApt~~Q~  120 (511)
                      -.++.++|+++..+..+.+ .|.  .+.|..|    =+  .+..++..+++.||-+|++..|++..-
T Consensus        67 ~~~lR~aia~~~~~~~g~~~~~d--~I~it~G----~~--~al~~~~~~l~~pGD~Vlv~~P~y~~y  125 (385)
T PRK07367         67 EPALREAIAHKLRRENGLDYQAE--NILVTNG----GK--QSLYNLMMALIDPGDEVIIPAPYWLSY  125 (385)
T ss_pred             CHHHHHHHHHHHHHHHCCCCCHH--EEEECCC----HH--HHHHHHHHHHCCCCCEEEECCCCCCCC
T ss_conf             89999999999999858999850--4999089----89--999999999748999899906987771


No 390
>PRK03317 histidinol-phosphate aminotransferase; Provisional
Probab=64.56  E-value=9.1  Score=17.11  Aligned_cols=64  Identities=14%  Similarity=0.038  Sum_probs=36.9

Q ss_pred             CCHHHHHHHHHHHHHHHHCCCCC-CCCCCEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEEECCHHHHH
Q ss_conf             84589999999999987405655-5421012465025765978999999999998089966999808589999
Q gi|254781215|r   50 APRSWQLEFMEVVDAHCLNSVNN-PNPEVFKGAISAGRGIGKTTLNAWLVLWLMSTRPGISVICLANSETQLK  121 (511)
Q Consensus        50 ~P~~WQ~e~l~~i~~~~~~~~~~-~~~~~~r~aV~sgrG~GKS~l~a~l~lw~l~~~p~~kv~vtApt~~Q~~  121 (511)
                      +|+.-..++-+.|++++....+- -.+.  .  |.  =|+|=+.+...+  ..+++.|+.++++..||+..-.
T Consensus        62 YPd~~~~~Lr~alA~~l~~~~~~gv~~e--~--Ii--~gnGSdE~i~~i--~~af~~pGd~vl~~~Ptf~~Y~  126 (369)
T PRK03317         62 YPDRDAVALRTDLAAYLTAQTGVGLGVE--N--VW--AANGSNEILQQL--LQAFGGPGRSALGFVPSYSMHP  126 (369)
T ss_pred             CCCCCHHHHHHHHHHHHHHCCCCCCCHH--H--EE--ECCCHHHHHHHH--HHHHCCCCCEEEECCCCHHHHH
T ss_conf             8997489999999987503026797877--8--78--826899999999--9998289998997478602799


No 391
>PRK13540 cytochrome c biogenesis protein CcmA; Provisional
Probab=64.48  E-value=6.1  Score=18.22  Aligned_cols=26  Identities=27%  Similarity=0.184  Sum_probs=19.6

Q ss_pred             CCCEEEEEECCCCCCHHHHHHHHHHH
Q ss_conf             21012465025765978999999999
Q gi|254781215|r   75 PEVFKGAISAGRGIGKTTLNAWLVLW  100 (511)
Q Consensus        75 ~~~~r~aV~sgrG~GKS~l~a~l~lw  100 (511)
                      +..--+++....|.|||+++-.++=-
T Consensus        25 ~~G~i~~l~G~NGaGKSTLlkli~Gl   50 (200)
T PRK13540         25 PAGGLLHLKGSNGAGKTTLLKLIAGL   50 (200)
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHHCC
T ss_conf             79979999889998799999999778


No 392
>KOG0345 consensus
Probab=64.43  E-value=9.2  Score=17.10  Aligned_cols=45  Identities=16%  Similarity=0.142  Sum_probs=30.2

Q ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHH----CCCC--EEEEEECCHHHHHHH
Q ss_conf             24650257659789999999999980----8996--699980858999999
Q gi|254781215|r   79 KGAISAGRGIGKTTLNAWLVLWLMST----RPGI--SVICLANSETQLKTT  123 (511)
Q Consensus        79 r~aV~sgrG~GKS~l~a~l~lw~l~~----~p~~--kv~vtApt~~Q~~~i  123 (511)
                      -|.|-|..|+|||...-.=++--+.-    .|+.  -.++++||..-+..|
T Consensus        45 DVvveavTGSGKTlAFllP~le~i~rr~~~~~~~~vgalIIsPTRELa~QI   95 (567)
T KOG0345          45 DVVVEAVTGSGKTLAFLLPMLEIIYRREAKTPPGQVGALIISPTRELARQI   95 (567)
T ss_pred             CEEEECCCCCCCCHHHHHHHHHHHHHHCCCCCCCCEEEEEECCCHHHHHHH
T ss_conf             568985678871066899999999861157896512479965719999999


No 393
>PRK11331 5-methylcytosine-specific restriction enzyme subunit McrB; Provisional
Probab=64.40  E-value=9.2  Score=17.10  Aligned_cols=17  Identities=18%  Similarity=0.272  Sum_probs=9.4

Q ss_pred             CCCCCCCHHHHHHHHHH
Q ss_conf             33677897789999975
Q gi|254781215|r  256 RTVEGIDPSFHEGIIAR  272 (511)
Q Consensus       256 ~~~p~~~~~~ie~~~~~  272 (511)
                      .=.|++-+.++.++.+.
T Consensus       200 ~G~pGtGKT~lAk~lA~  216 (459)
T PRK11331        200 QGPPGVGKTFVARRLAY  216 (459)
T ss_pred             ECCCCCCHHHHHHHHHH
T ss_conf             58999887899999999


No 394
>cd01869 Rab1_Ypt1 Rab1/Ypt1 subfamily.  Rab1 is found in every eukaryote and is a key regulatory component for the transport of vesicles from the ER to the Golgi apparatus. Studies on mutations of Ypt1, the yeast homolog of Rab1, showed that this protein is necessary for the budding of vesicles of the ER as well as for their transport to, and fusion with, the Golgi apparatus. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state.  Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization.  Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins.  Due to t
Probab=64.30  E-value=7.1  Score=17.80  Aligned_cols=22  Identities=27%  Similarity=0.434  Sum_probs=19.0

Q ss_pred             CEEEEEECCCCCCHHHHHHHHH
Q ss_conf             0124650257659789999999
Q gi|254781215|r   77 VFKGAISAGRGIGKTTLNAWLV   98 (511)
Q Consensus        77 ~~r~aV~sgrG~GKS~l~a~l~   98 (511)
                      ++|+.+....|+|||.++-.++
T Consensus         2 ~~Kiv~vGd~~vGKTsli~r~~   23 (166)
T cd01869           2 LFKLLLIGDSGVGKSCLLLRFA   23 (166)
T ss_pred             EEEEEEECCCCCCHHHHHHHHH
T ss_conf             6999999999978999999994


No 395
>PRK06358 threonine-phosphate decarboxylase; Provisional
Probab=64.13  E-value=9.3  Score=17.06  Aligned_cols=57  Identities=16%  Similarity=0.047  Sum_probs=33.0

Q ss_pred             CCHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEEECCHHHHH
Q ss_conf             845899999999999874056555421012465025765978999999999998089966999808589999
Q gi|254781215|r   50 APRSWQLEFMEVVDAHCLNSVNNPNPEVFKGAISAGRGIGKTTLNAWLVLWLMSTRPGISVICLANSETQLK  121 (511)
Q Consensus        50 ~P~~WQ~e~l~~i~~~~~~~~~~~~~~~~r~aV~sgrG~GKS~l~a~l~lw~l~~~p~~kv~vtApt~~Q~~  121 (511)
                      +|+.-..++-++|+++.-    .+..   .  |..  |.|=+.+...++..    ..+.++++.+||+..-.
T Consensus        51 YPd~~~~~Lr~aiA~~~g----v~~~---~--I~~--gnGs~e~i~~~~~~----~~~~~v~i~~Ptf~~Y~  107 (354)
T PRK06358         51 YPDIDYLELRKRIASFEQ----LDLE---N--VIL--GNGAAEVIFNIVRV----LKPKKVLILAPTFSEYE  107 (354)
T ss_pred             CCCCCHHHHHHHHHHHHC----CCHH---H--EEE--CCCHHHHHHHHHHH----CCCCEEEEECCCHHHHH
T ss_conf             899977999999999878----3879---9--998--68789999999986----18996999798879999


No 396
>KOG0781 consensus
Probab=64.08  E-value=9.3  Score=17.06  Aligned_cols=158  Identities=11%  Similarity=0.135  Sum_probs=68.1

Q ss_pred             CEEE-EEEECCCCCCCCE--EEEEE--C-CCEEEE--EEECCCCCHHHHHHHHHHHHHHCCCCEEEEEECCCCHHH----
Q ss_conf             7089-9962333478417--99982--2-755899--873277898899999999998618882998006876368----
Q gi|254781215|r  316 APLI-MGCDIAEEGGDNT--VVVLR--R-GPVIEH--LFDWSKTDLRTTNNKISGLVEKYRPDAIIIDANNTGART----  383 (511)
Q Consensus       316 ~~~v-iGvDVAr~G~D~s--vi~~r--~-G~~v~~--~~~~~~~d~~~~a~~i~~~~~~~~~~~i~iD~~GvG~gV----  383 (511)
                      .||+ .-|.|-.-|.-.+  =|+.|  + +.+|..  .++|+..-..++.-.+..+.. ..+..|-+=.-|.|..+    
T Consensus       377 rPYvi~fvGVNGVGKSTNLAKIayWLlqNkfrVlIAACDTFRsGAvEQLrtHv~rl~~-l~~~~v~lfekGYgkd~a~va  455 (587)
T KOG0781         377 RPYVISFVGVNGVGKSTNLAKIAYWLLQNKFRVLIAACDTFRSGAVEQLRTHVERLSA-LHGTMVELFEKGYGKDAAGVA  455 (587)
T ss_pred             CCEEEEEEEECCCCCCCHHHHHHHHHHHCCCEEEEEECCCHHHHHHHHHHHHHHHHHH-HCCCHHHHHHHHCCCCHHHHH
T ss_conf             9759999821476651329999999985783699986243124478999999999987-455204888610477828999


Q ss_pred             ---HHHHHHCCCEEEEECCCCCCCCHHHHHHHHHHHHHHHHHHHHHCC----------CCCHH---HHH---HHHHCC--
Q ss_conf             ---898986498279842777766402552279999999999997089----------99818---999---998579--
Q gi|254781215|r  384 ---CDYLEMLGYHVYRVLGQKRAVDLEFCRNRRTELHVKMADWLEFAS----------LINHS---GLI---QNLKSL--  442 (511)
Q Consensus       384 ---~d~L~~~g~~v~~v~~~~~~~~~~~y~N~rae~~~~~re~l~~g~----------l~~d~---~l~---~el~~~--  442 (511)
                         +...+..|+.|+-+--+++-.+.+.       +.-.+...+....          |-..|   ++.   +.|.-.  
T Consensus       456 k~AI~~a~~~gfDvvLiDTAGRmhn~~~-------LM~~L~kl~~~n~pD~i~~VgEALVG~dsvdq~~~Fn~al~d~~~  528 (587)
T KOG0781         456 KEAIQEARNQGFDVVLIDTAGRMHNNAP-------LMTSLAKLIKVNKPDLILFVGEALVGNDSVDQLKKFNRALADHST  528 (587)
T ss_pred             HHHHHHHHHCCCCEEEEECCCCCCCCHH-------HHHHHHHHHHCCCCCEEEEEHHHHHCCHHHHHHHHHHHHHHCCCC
T ss_conf             9999999866987899835443347806-------789999997447986599850555275589999999998744897


Q ss_pred             CEEEECCCCEEEEEEC----HHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCC
Q ss_conf             6799879984999841----2548999898999999975986500025576540
Q gi|254781215|r  443 KSFIVPNTGELAIESK----RVKGAKSTDYSDGLMYTFAENPPRSDMDFGRCPS  492 (511)
Q Consensus       443 ~~~~~~~~gki~ie~K----kkrg~~SPD~ADAl~l~fa~~~~~~~~~~g~~~s  492 (511)
                      |+ .++  | | |-+|    -.+      ..-|+.|.|+.-.|--=...||+-+
T Consensus       529 ~r-~iD--g-i-lltK~DTvdd~------vG~~v~Mvy~t~~PIlFvG~GQtys  571 (587)
T KOG0781         529 PR-LID--G-I-LLTKFDTVDDK------VGAAVSMVYITGKPILFVGVGQTYS  571 (587)
T ss_pred             CC-CCC--E-E-EEEECCHHHHH------HHHHHHHHEECCCCEEEEECCCCCH
T ss_conf             44-234--3-7-88712506568------8878764200389769984586610


No 397
>PRK09751 putative ATP-dependent helicase Lhr; Provisional
Probab=64.00  E-value=9.4  Score=17.05  Aligned_cols=42  Identities=14%  Similarity=0.073  Sum_probs=25.9

Q ss_pred             EECCCCCCHHHHHHHHHHHHHHHC-----------CCCEEEEEECCHHHHHHH
Q ss_conf             502576597899999999999808-----------996699980858999999
Q gi|254781215|r   82 ISAGRGIGKTTLNAWLVLWLMSTR-----------PGISVICLANSETQLKTT  123 (511)
Q Consensus        82 V~sgrG~GKS~l~a~l~lw~l~~~-----------p~~kv~vtApt~~Q~~~i  123 (511)
                      |.++.|+|||..+=.-+|-.+...           .+.+|+++.|...=+.|+
T Consensus         1 VvAPTGSGKTLAAFL~aLd~L~~~~~~~~~~~~~~~~~~VLYISPLKALa~Dv   53 (1490)
T PRK09751          1 VIAPTGSGKTLAAFLYALDRLFREGGEDTREAHKRKTSRILYISPIKALGTDV   53 (1490)
T ss_pred             CCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCCCCCEEEEEECCHHHHHHHH
T ss_conf             95988743989999999999996145555556788973899959278889999


No 398
>cd03247 ABCC_cytochrome_bd The CYD subfamily implicated in cytochrome bd biogenesis.  The CydC and CydD proteins are important for the formation of cytochrome bd terminal oxidase of E. coli and it has been proposed that they were necessary for biosynthesis of the cytochrome bd quinol oxidase and for periplasmic c-type cytochromes.  CydCD were proposed to determine a heterooligomeric complex important for heme export into the periplasm or to be involved in the maintenance of the proper redox state of the periplasmic space.  In Bacillus subtilius, the absence of CydCD does not affect the presence of halo-cytochrome c in the membrane and this observation suggests that CydCD proteins are not involved in the export of heme in this organism.
Probab=63.85  E-value=6.3  Score=18.13  Aligned_cols=36  Identities=22%  Similarity=-0.033  Sum_probs=24.5

Q ss_pred             CEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEEE
Q ss_conf             01246502576597899999999999808996699980
Q gi|254781215|r   77 VFKGAISAGRGIGKTTLNAWLVLWLMSTRPGISVICLA  114 (511)
Q Consensus        77 ~~r~aV~sgrG~GKS~l~a~l~lw~l~~~p~~kv~vtA  114 (511)
                      .-++++...-|.|||+++..++=-  +.....++.+--
T Consensus        28 Ge~~aivG~sGsGKSTLl~~l~G~--~~p~~G~i~i~g   63 (178)
T cd03247          28 GEKIALLGRSGSGKSTLLQLLTGD--LKPQQGEITLDG   63 (178)
T ss_pred             CCEEEEECCCCCHHHHHHHHHHHC--CCCCCCEEEECC
T ss_conf             999999999987599999999861--766788699999


No 399
>pfam00071 Ras Ras family. Includes sub-families Ras, Rab, Rac, Ral, Ran, Rap Ypt1 and more. Shares P-loop motif with GTP_EFTU, arf and myosin_head. See pfam00009 pfam00025, pfam00063. As regards Rab GTPases, these are important regulators of vesicle formation, motility and fusion. They share a fold in common with all Ras GTPases: this is a six-stranded beta-sheet surrounded by five alpha-helices.
Probab=63.59  E-value=6.3  Score=18.13  Aligned_cols=20  Identities=25%  Similarity=0.391  Sum_probs=17.6

Q ss_pred             EEEEECCCCCCHHHHHHHHH
Q ss_conf             24650257659789999999
Q gi|254781215|r   79 KGAISAGRGIGKTTLNAWLV   98 (511)
Q Consensus        79 r~aV~sgrG~GKS~l~a~l~   98 (511)
                      |++|....|+|||+++..++
T Consensus         1 Ki~vvG~~~vGKTsli~r~~   20 (162)
T pfam00071         1 KLVLVGDGGVGKSSLLIRFT   20 (162)
T ss_pred             CEEEECCCCCCHHHHHHHHH
T ss_conf             98999979977999999996


No 400
>cd03369 ABCC_NFT1 Domain 2 of NFT1 (New full-length MRP-type transporter 1).  NFT1 belongs to the MRP (mulrtidrug resisitance-associated protein) family of ABC transporters.  Some of the MRP members have five additional transmembrane segments in their N-terminas, but the function of these additional membrane-spanning domains is not clear.  The MRP was found in the multidrug-resisting lung cancer cell in which p-glycoprotein was not overexpressed.  MRP exports glutathione by drug stimulation, as well as, certain substrates in conjugated forms with anions such as glutathione, glucuronate, and sulfate.
Probab=63.46  E-value=7.2  Score=17.78  Aligned_cols=25  Identities=32%  Similarity=0.213  Sum_probs=20.4

Q ss_pred             CCEEEEEECCCCCCHHHHHHHHHHH
Q ss_conf             1012465025765978999999999
Q gi|254781215|r   76 EVFKGAISAGRGIGKTTLNAWLVLW  100 (511)
Q Consensus        76 ~~~r~aV~sgrG~GKS~l~a~l~lw  100 (511)
                      ..-++++...-|.|||+++..++=.
T Consensus        33 ~Ge~v~ivG~sGsGKSTLl~ll~g~   57 (207)
T cd03369          33 AGEKIGIVGRTGAGKSTLILALFRF   57 (207)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHHH
T ss_conf             9999999999998799999999987


No 401
>cd01868 Rab11_like Rab11-like.  Rab11a, Rab11b, and Rab25 are closely related, evolutionary conserved Rab proteins that are differentially expressed. Rab11a is ubiquitously synthesized, Rab11b is enriched in brain and heart and Rab25 is only found in epithelia. Rab11/25 proteins seem to regulate recycling pathways from endosomes to the plasma membrane and to the trans-Golgi network. Furthermore, Rab11a is thought to function in the histamine-induced fusion of tubulovesicles containing H+, K+ ATPase with the plasma membrane in gastric parietal cells and in insulin-stimulated insertion of GLUT4 in the plasma membrane of cardiomyocytes. Overexpression of Rab25 has recently been observed in ovarian cancer and breast cancer, and has been correlated with worsened outcomes in both diseases. In addition, Rab25 overexpression has also been observed in prostate cancer, transitional cell carcinoma of the bladder, and invasive breast tumor cells. GTPase activating proteins (GAPs) interact with GTP
Probab=63.31  E-value=7.7  Score=17.58  Aligned_cols=22  Identities=27%  Similarity=0.501  Sum_probs=18.9

Q ss_pred             CEEEEEECCCCCCHHHHHHHHH
Q ss_conf             0124650257659789999999
Q gi|254781215|r   77 VFKGAISAGRGIGKTTLNAWLV   98 (511)
Q Consensus        77 ~~r~aV~sgrG~GKS~l~a~l~   98 (511)
                      .+|+.+....|+|||.+...++
T Consensus         3 ~~Kiv~iGd~~VGKTsli~r~~   24 (165)
T cd01868           3 LFKIVLIGDSGVGKSNLLSRFT   24 (165)
T ss_pred             EEEEEEECCCCCCHHHHHHHHH
T ss_conf             5899999999978999999997


No 402
>COG0563 Adk Adenylate kinase and related kinases [Nucleotide transport and metabolism]
Probab=63.27  E-value=8.6  Score=17.29  Aligned_cols=28  Identities=29%  Similarity=0.140  Sum_probs=22.0

Q ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHHCC
Q ss_conf             2465025765978999999999998089
Q gi|254781215|r   79 KGAISAGRGIGKTTLNAWLVLWLMSTRP  106 (511)
Q Consensus        79 r~aV~sgrG~GKS~l~a~l~lw~l~~~p  106 (511)
                      |+.|-.+=|.|||+++.-++-.+=++|-
T Consensus         2 riiilG~pGaGK~T~A~~La~~~~i~hl   29 (178)
T COG0563           2 RILILGPPGAGKSTLAKKLAKKLGLPHL   29 (178)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHCCCCEE
T ss_conf             7999899999889999999997699785


No 403
>PRK06936 type III secretion system ATPase; Provisional
Probab=63.01  E-value=5.7  Score=18.39  Aligned_cols=23  Identities=39%  Similarity=0.265  Sum_probs=19.5

Q ss_pred             EEEEEECCCCCCHHHHHHHHHHH
Q ss_conf             12465025765978999999999
Q gi|254781215|r   78 FKGAISAGRGIGKTTLNAWLVLW  100 (511)
Q Consensus        78 ~r~aV~sgrG~GKS~l~a~l~lw  100 (511)
                      -|+.+-+|.|+|||++.+.++..
T Consensus       163 QR~gIfagsGvGKs~Ll~~i~r~  185 (439)
T PRK06936        163 QRMGIFAAAGGGKSTLLASLIRS  185 (439)
T ss_pred             CEEECCCCCCCCHHHHHHHHHHH
T ss_conf             70102369999889999999764


No 404
>PRK03262 consensus
Probab=62.95  E-value=9.8  Score=16.93  Aligned_cols=60  Identities=13%  Similarity=0.088  Sum_probs=39.1

Q ss_pred             CCCHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHHCCCC-EEEEEECCHHHHH
Q ss_conf             784589999999999987405655542101246502576597899999999999808996-6999808589999
Q gi|254781215|r   49 SAPRSWQLEFMEVVDAHCLNSVNNPNPEVFKGAISAGRGIGKTTLNAWLVLWLMSTRPGI-SVICLANSETQLK  121 (511)
Q Consensus        49 ~~P~~WQ~e~l~~i~~~~~~~~~~~~~~~~r~aV~sgrG~GKS~l~a~l~lw~l~~~p~~-kv~vtApt~~Q~~  121 (511)
                      .+||....++-.+|+++.-    .+ +.  .  |..  |+|=+.+...++..  ++.|+. .|+++.||+..-.
T Consensus        53 rYPD~~~~~Lr~aiA~~~g----v~-~~--~--I~v--GnGSdE~I~~i~~~--f~~pg~d~vl~~~PtF~~Y~  113 (355)
T PRK03262         53 RYPECQPKAVIENYAQYAG----VK-PE--Q--VLV--SRGADEGIELLIRA--FCEPGKDAILYCPPTYGMYA  113 (355)
T ss_pred             CCCCCCHHHHHHHHHHHHC----CC-HH--H--EEE--ECCHHHHHHHHHHH--HHCCCCCEEEECCCCHHHHH
T ss_conf             3989988999999999868----58-55--7--999--37899999999999--86389977997788859999


No 405
>PRK00950 histidinol-phosphate aminotransferase; Validated
Probab=62.81  E-value=9.8  Score=16.91  Aligned_cols=59  Identities=19%  Similarity=0.093  Sum_probs=37.7

Q ss_pred             CCHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEEECCHHHH
Q ss_conf             84589999999999987405655542101246502576597899999999999808996699980858999
Q gi|254781215|r   50 APRSWQLEFMEVVDAHCLNSVNNPNPEVFKGAISAGRGIGKTTLNAWLVLWLMSTRPGISVICLANSETQL  120 (511)
Q Consensus        50 ~P~~WQ~e~l~~i~~~~~~~~~~~~~~~~r~aV~sgrG~GKS~l~a~l~lw~l~~~p~~kv~vtApt~~Q~  120 (511)
                      +|+.-..++-++|+++.-    .+..   .+.| +  |+|-+.+...++.  +++.||.+|++..||+..-
T Consensus        67 YPd~~~~~Lr~aiA~~~g----v~~e---~ii~-~--gnGs~e~i~~l~~--~~~~~Gd~vl~~~P~y~~Y  125 (369)
T PRK00950         67 YPEPDAPELREAISKYTG----VPVE---NIIV-G--GDGADEIIDVLMR--ILIDEGDEVIIPIPTFTYY  125 (369)
T ss_pred             CCCCCHHHHHHHHHHHHC----CCCC---CEEE-E--CCCHHHHHHHHHH--HHHCCCCEEEECCCCCHHH
T ss_conf             999888999999999868----1975---8799-7--5649999999999--9957999999898873036


No 406
>PRK13640 cbiO cobalt transporter ATP-binding subunit; Provisional
Probab=62.72  E-value=6.5  Score=18.05  Aligned_cols=23  Identities=22%  Similarity=0.140  Sum_probs=18.8

Q ss_pred             CEEEEEECCCCCCHHHHHHHHHH
Q ss_conf             01246502576597899999999
Q gi|254781215|r   77 VFKGAISAGRGIGKTTLNAWLVL   99 (511)
Q Consensus        77 ~~r~aV~sgrG~GKS~l~a~l~l   99 (511)
                      .-.+++....|.|||+++..+.=
T Consensus        34 Ge~vaiiG~nGsGKSTL~~~l~G   56 (283)
T PRK13640         34 GSWTALIGHNGSGKSTISKLING   56 (283)
T ss_pred             CCEEEEECCCCCHHHHHHHHHHC
T ss_conf             99999999999879999999964


No 407
>PRK13886 conjugal transfer protein TraL; Provisional
Probab=62.69  E-value=9.3  Score=17.08  Aligned_cols=34  Identities=15%  Similarity=0.145  Sum_probs=24.5

Q ss_pred             CCCCCHHHHHHHHHHHHHHHCCCCEEEEEECCHH
Q ss_conf             5765978999999999998089966999808589
Q gi|254781215|r   85 GRGIGKTTLNAWLVLWLMSTRPGISVICLANSET  118 (511)
Q Consensus        85 grG~GKS~l~a~l~lw~l~~~p~~kv~vtApt~~  118 (511)
                      ==|+|||.+++.++=|++....+..++=|=|+-.
T Consensus        11 KGGVGKS~va~~LaQY~~~~~~~~~~iDTDpvN~   44 (241)
T PRK13886         11 KGGVGKSMIAATIAQYKAGKGQKPLCIDTDPVNA   44 (241)
T ss_pred             CCCCHHHHHHHHHHHHHHHCCCCCCEEECCCCCC
T ss_conf             8863099999999999983599985560899970


No 408
>TIGR00750 lao LAO/AO transport system ATPase; InterPro: IPR005129   Bacterial periplasmic transport systems require the function of a specific substrate-binding protein, located in the periplasm, and several cytoplasmic membrane transport components. In Escherichia coli K-12, the arginine-ornithine transport system requires an arginine-ornithine-binding protein and the lysine-arginine-ornithine (LAO) transport system includes a LAO-binding protein. Both periplasmic proteins can be phosphorylated by a single kinase, ArgK  resulting in reduced levels of transport activity of the periplasmic transport systems that include each of the binding proteins. The ArgK protein acts as an ATPase enzyme and as a kinase..
Probab=62.52  E-value=10  Score=16.88  Aligned_cols=34  Identities=15%  Similarity=0.336  Sum_probs=16.9

Q ss_pred             HHHHHHHHHHHHHCCCCEEEEEECCCCHHHHHHH
Q ss_conf             8999999999986188829980068763688989
Q gi|254781215|r  354 RTTNNKISGLVEKYRPDAIIIDANNTGARTCDYL  387 (511)
Q Consensus       354 ~~~a~~i~~~~~~~~~~~i~iD~~GvG~gV~d~L  387 (511)
                      ..-+..+..+++-+..|-|+|++.|||-.=+|..
T Consensus       122 s~at~~~~~lldA~G~DVI~vETVGVGQSEVdi~  155 (333)
T TIGR00750       122 SKATRELVKLLDAAGYDVILVETVGVGQSEVDII  155 (333)
T ss_pred             HHHHHHHHHHHHHCCCCEEEEEEECCCHHHHHHH
T ss_conf             7999999999986389879998415752487887


No 409
>PRK06425 histidinol-phosphate aminotransferase; Validated
Probab=62.42  E-value=10  Score=16.87  Aligned_cols=58  Identities=14%  Similarity=0.028  Sum_probs=34.4

Q ss_pred             CCCHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEEECCHHHHH
Q ss_conf             7845899999999999874056555421012465025765978999999999998089966999808589999
Q gi|254781215|r   49 SAPRSWQLEFMEVVDAHCLNSVNNPNPEVFKGAISAGRGIGKTTLNAWLVLWLMSTRPGISVICLANSETQLK  121 (511)
Q Consensus        49 ~~P~~WQ~e~l~~i~~~~~~~~~~~~~~~~r~aV~sgrG~GKS~l~a~l~lw~l~~~p~~kv~vtApt~~Q~~  121 (511)
                      -+|+.=..++-+.|+++..-.     +  -+|  .-  |.|=+.+...++.   ...+ .++++..||+.+=.
T Consensus        36 rYPd~~~~~Lr~~iA~~~~v~-----~--~~I--~v--gnGs~ElI~~l~~---~~~~-~~~~i~~PtF~~Y~   93 (332)
T PRK06425         36 IYPEISYTDIEDQIKIYTQGL-----K--IKV--LI--GPGLTHFIYRLLS---YINV-GNIIIVEPNFNEYK   93 (332)
T ss_pred             HCCCCCHHHHHHHHHHHHCCC-----H--HHE--EE--CCCHHHHHHHHHH---HHCC-CCEEEECCCHHHHH
T ss_conf             294998699999999886968-----6--739--98--2209999999999---8689-99899688889999


No 410
>cd04114 Rab30 Rab30 subfamily.  Rab30 appears to be associated with the Golgi stack. It is expressed in a wide variety of tissue types and in humans maps to chromosome 11.  GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state.  Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization.  Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins.  Due to the presence of truncated sequences in this CD, the lipid modification site is not available for annotation.
Probab=62.41  E-value=9.7  Score=16.96  Aligned_cols=25  Identities=28%  Similarity=0.348  Sum_probs=20.5

Q ss_pred             CCCCEEEEEECCCCCCHHHHHHHHH
Q ss_conf             4210124650257659789999999
Q gi|254781215|r   74 NPEVFKGAISAGRGIGKTTLNAWLV   98 (511)
Q Consensus        74 ~~~~~r~aV~sgrG~GKS~l~a~l~   98 (511)
                      .-..+|+.+....|+|||.++..++
T Consensus         4 ~d~~~KivllGd~~VGKTsli~r~~   28 (169)
T cd04114           4 YDFLFKIVLIGNAGVGKTCLVRRFT   28 (169)
T ss_pred             CCEEEEEEEECCCCCCHHHHHHHHH
T ss_conf             7779899999989979999999998


No 411
>PRK13543 cytochrome c biogenesis protein CcmA; Provisional
Probab=62.34  E-value=7.6  Score=17.62  Aligned_cols=21  Identities=33%  Similarity=0.268  Sum_probs=17.8

Q ss_pred             EEEEEECCCCCCHHHHHHHHH
Q ss_conf             124650257659789999999
Q gi|254781215|r   78 FKGAISAGRGIGKTTLNAWLV   98 (511)
Q Consensus        78 ~r~aV~sgrG~GKS~l~a~l~   98 (511)
                      -.+++....|.|||++.-.++
T Consensus        38 e~~~l~GpNGaGKTTLlr~l~   58 (214)
T PRK13543         38 EALLVQGDNGAGKTTLLRVLA   58 (214)
T ss_pred             CEEEEECCCCCCHHHHHHHHH
T ss_conf             899999999987999999997


No 412
>COG3911 Predicted ATPase [General function prediction only]
Probab=62.28  E-value=8.9  Score=17.19  Aligned_cols=27  Identities=37%  Similarity=0.290  Sum_probs=20.7

Q ss_pred             EEEEEECCCCCCHHHHHHHHHHHHHHH
Q ss_conf             124650257659789999999999980
Q gi|254781215|r   78 FKGAISAGRGIGKTTLNAWLVLWLMST  104 (511)
Q Consensus        78 ~r~aV~sgrG~GKS~l~a~l~lw~l~~  104 (511)
                      .++.++.|-|.|||+|.+.|.--...|
T Consensus        10 ~~fIltGgpGaGKTtLL~aLa~~Gfat   36 (183)
T COG3911          10 KRFILTGGPGAGKTTLLAALARAGFAT   36 (183)
T ss_pred             EEEEEECCCCCCHHHHHHHHHHCCCEE
T ss_conf             389983799976899999999758635


No 413
>cd01892 Miro2 Miro2 subfamily.  Miro (mitochondrial Rho) proteins have tandem GTP-binding domains separated by a linker region containing putative calcium-binding EF hand motifs.  Genes encoding Miro-like proteins were found in several eukaryotic organisms.  This CD represents the putative GTPase domain in the C terminus of Miro proteins.  These atypical Rho GTPases have roles in mitochondrial homeostasis and apoptosis.  Most Rho proteins contain a lipid modification site at the C-terminus; however, Miro is one of few Rho subfamilies that lack this feature.
Probab=62.23  E-value=8.7  Score=17.24  Aligned_cols=23  Identities=26%  Similarity=0.391  Sum_probs=19.6

Q ss_pred             CCEEEEEECCCCCCHHHHHHHHH
Q ss_conf             10124650257659789999999
Q gi|254781215|r   76 EVFKGAISAGRGIGKTTLNAWLV   98 (511)
Q Consensus        76 ~~~r~aV~sgrG~GKS~l~a~l~   98 (511)
                      .++++-|....|+|||.|+-.++
T Consensus         3 ~vfk~~VlG~~~VGKTsLi~rf~   25 (169)
T cd01892           3 NVFLCFVLGAKGSGKSALLRAFL   25 (169)
T ss_pred             EEEEEEEECCCCCCHHHHHHHHH
T ss_conf             08999999999988999999996


No 414
>TIGR01313 therm_gnt_kin carbohydrate kinase, thermoresistant glucokinase family; InterPro: IPR006001    This family of proteins includes thermoresistant and thermosensitve isozymes of gluconate kinase (gluconokinase) in E. coli and other related proteins; members of this family are often named by similarity to the thermostable isozyme. These proteins show homology to shikimate kinases and adenylate kinases but not to gluconate kinases from the FGGY family of carbohydrate kinases (IPR000577 from INTERPRO).; GO: 0016301 kinase activity, 0005975 carbohydrate metabolic process.
Probab=62.20  E-value=6.3  Score=18.13  Aligned_cols=47  Identities=21%  Similarity=0.153  Sum_probs=28.0

Q ss_pred             CCCCCHHHHHHHHHHHHHHHCCCCEEEEEECCHHHHHHHHHHHHHHHHHHCHH
Q ss_conf             57659789999999999980899669998085899999999999999985500
Q gi|254781215|r   85 GRGIGKTTLNAWLVLWLMSTRPGISVICLANSETQLKTTLWAEVSKWLSLLPN  137 (511)
Q Consensus        85 grG~GKS~l~a~l~lw~l~~~p~~kv~vtApt~~Q~~~ilw~Ei~k~~~~~~~  137 (511)
                      -=|+|||++++.++--+-..+|+++.+=. =..+-.+     =|.||-+.-|.
T Consensus         6 vaG~GKs~~a~~l~~~lg~iyPd~~yieG-DdLHP~~-----Ni~KMs~GiPL   52 (175)
T TIGR01313         6 VAGSGKSTIASALAHRLGDIYPDAKYIEG-DDLHPAA-----NIEKMSRGIPL   52 (175)
T ss_pred             CCCCCHHHHHHHHHHHHHHHCCCCCCCCC-CCCCCHH-----HHHHHCCCCCC
T ss_conf             27862889999999985431578875688-6667877-----79873178888


No 415
>cd03291 ABCC_CFTR1 The CFTR subfamily domain 1.  The cystic fibrosis transmembrane regulator (CFTR), the product of the gene mutated in patients with cystic fibrosis, has adapted the ABC transporter structural motif to form a tightly regulated anion channel at the apical surface of many epithelia.  Use of the term assembly of a functional ion channel implies the coming together of subunits, or at least smaller not-yet functional components of the active whole.  In fact, on the basis of current knowledge only the CFTR polypeptide itself is required to form an ATP- and protein kinase A-dependent low-conductance chloride channel of the type present in the apical membrane of many epithelial cells.  CFTR displays the typical organization (IM-ABC)2 and carries a characteristic hydrophilic R-domain that separates IM1-ABC1 from IM2-ABC2.
Probab=62.19  E-value=7.2  Score=17.77  Aligned_cols=23  Identities=30%  Similarity=0.205  Sum_probs=19.2

Q ss_pred             CEEEEEECCCCCCHHHHHHHHHH
Q ss_conf             01246502576597899999999
Q gi|254781215|r   77 VFKGAISAGRGIGKTTLNAWLVL   99 (511)
Q Consensus        77 ~~r~aV~sgrG~GKS~l~a~l~l   99 (511)
                      .-++++...-|.|||+++..++=
T Consensus        63 Ge~vaIVG~sGSGKSTLl~lL~g   85 (282)
T cd03291          63 GEMLAITGSTGSGKTSLLMLILG   85 (282)
T ss_pred             CCEEEEECCCCCHHHHHHHHHHC
T ss_conf             99999999999819999999957


No 416
>cd01865 Rab3 Rab3 subfamily.  The Rab3 subfamily contains Rab3A, Rab3B, Rab3C, and Rab3D.  All four isoforms were found in mouse brain and endocrine tissues, with varying levels of expression.  Rab3A, Rab3B, and Rab3C localized to synaptic and secretory vesicles; Rab3D was expressed at high levels only in adipose tissue, exocrine glands, and the endocrine pituitary, where it is localized to cytoplasmic secretory granules.  Rab3 appears to control Ca2+-regulated exocytosis. The appropriate GDP/GTP exchange cycle of Rab3A is required for Ca2+-regulated exocytosis to occur, and interaction of the GTP-bound form of Rab3A with effector molecule(s) is widely believed to be essential for this process. Functionally, most studies point toward a role for Rab3 in the secretion of hormones and neurotransmitters. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promot
Probab=62.08  E-value=8  Score=17.49  Aligned_cols=22  Identities=27%  Similarity=0.329  Sum_probs=18.1

Q ss_pred             CEEEEEECCCCCCHHHHHHHHH
Q ss_conf             0124650257659789999999
Q gi|254781215|r   77 VFKGAISAGRGIGKTTLNAWLV   98 (511)
Q Consensus        77 ~~r~aV~sgrG~GKS~l~a~l~   98 (511)
                      ++|+.+....|+|||.++..++
T Consensus         1 ~~KivllGd~~VGKTsli~r~~   22 (165)
T cd01865           1 MFKLLIIGNSSVGKTSFLFRYA   22 (165)
T ss_pred             CEEEEEECCCCCCHHHHHHHHH
T ss_conf             9899999999968899999992


No 417
>PRK03333 coaE dephospho-CoA kinase/unknown domain fusion protein; Provisional
Probab=62.01  E-value=7.1  Score=17.82  Aligned_cols=24  Identities=29%  Similarity=0.477  Sum_probs=20.5

Q ss_pred             CEEEEEECCCCCCHHHHHHHHHHH
Q ss_conf             012465025765978999999999
Q gi|254781215|r   77 VFKGAISAGRGIGKTTLNAWLVLW  100 (511)
Q Consensus        77 ~~r~aV~sgrG~GKS~l~a~l~lw  100 (511)
                      |+++.+..|=|+|||+++..+.-.
T Consensus         1 M~~IGLTGGIgsGKStv~~~l~~~   24 (394)
T PRK03333          1 MLRIGLTGGIGAGKSTVSATLAQL   24 (394)
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHC
T ss_conf             949983067555799999999987


No 418
>COG0210 UvrD Superfamily I DNA and RNA helicases [DNA replication, recombination, and repair]
Probab=61.96  E-value=10  Score=16.82  Aligned_cols=53  Identities=19%  Similarity=0.221  Sum_probs=37.5

Q ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHHC--CCCEEEEEECCHHHHHHHHHHHHHHHHHHCH
Q ss_conf             246502576597899999999999808--9966999808589999999999999998550
Q gi|254781215|r   79 KGAISAGRGIGKTTLNAWLVLWLMSTR--PGISVICLANSETQLKTTLWAEVSKWLSLLP  136 (511)
Q Consensus        79 r~aV~sgrG~GKS~l~a~l~lw~l~~~--p~~kv~vtApt~~Q~~~ilw~Ei~k~~~~~~  136 (511)
                      .+-|.+|.|+|||.....-+.|.+...  .+.+|+++.=|-.-++     |++..+..+.
T Consensus        17 p~lV~AGaGsGKT~vlt~Ria~li~~~~v~p~~Il~vTFTnkAA~-----em~~Rl~~~~   71 (655)
T COG0210          17 PLLVLAGAGSGKTRVLTERIAYLIAAGGVDPEQILAITFTNKAAA-----EMRERLLKLL   71 (655)
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHHHCCCCCHHHEEEEEEEHHHHH-----HHHHHHHHHH
T ss_conf             869995799861899999999998738957577177896769999-----9999999873


No 419
>cd03277 ABC_SMC5_euk Eukaryotic SMC5 proteins; SMC proteins are large (approximately 110 to 170 kDa), and each is arranged into five recognizable domains.  Amino-acid sequence homology of SMC proteins between species is largely confined to the amino- and carboxy-terminal globular domains. The amino-terminal domain contains a 'Walker A' nucleotide-binding domain (GxxGxGKS/T, in the single-letter amino-acid code), which by mutational studies has been shown to be essential in several proteins.  The carboxy-terminal domain contains a sequence (the DA-box) that resembles a 'Walker B' motif, and a motif with homology to the signature sequence of the ATP-binding cassette (ABC) family of ATPases.  The sequence homology within the carboxy-terminal domain is relatively high within the SMC1-SMC4 group, whereas SMC5 and SMC6 show some divergence in both of these sequences.  In eukaryotic cells, the proteins are found as heterodimers of SMC1 paired with SMC3, SMC2 with SMC4, and SMC5 with SMC6 (for
Probab=61.95  E-value=6.6  Score=18.01  Aligned_cols=21  Identities=29%  Similarity=0.360  Sum_probs=17.5

Q ss_pred             EEECCCCCCHHHHHHHHHHHH
Q ss_conf             650257659789999999999
Q gi|254781215|r   81 AISAGRGIGKTTLNAWLVLWL  101 (511)
Q Consensus        81 aV~sgrG~GKS~l~a~l~lw~  101 (511)
                      -|....|+|||++++++++-.
T Consensus        27 ~IiGpNGSGKSsIv~AI~lgL   47 (213)
T cd03277          27 MIIGPNGSGKSSIVCAICLGL   47 (213)
T ss_pred             EEECCCCCCHHHHHHHHHHHH
T ss_conf             998899887899999999881


No 420
>cd03278 ABC_SMC_barmotin Barmotin is a tight junction-associated protein expressed in rat epithelial cells which is thought to have an important regulatory role in tight junction barrier function.  Barmotin belongs to the SMC protein family.  SMC proteins are large (approximately 110 to 170 kDa), and each is arranged into five recognizable domains.  Amino-acid sequence homology of SMC proteins between species is largely confined to the amino- and carboxy-terminal globular domains. The amino-terminal domain contains a 'Walker A' nucleotide-binding domain (GxxGxGKS/T, in the single-letter amino-acid code), which by mutational studies has been shown to be essential in several proteins.  The carboxy-terminal domain contains a sequence (the DA-box) that resembles a 'Walker B' motif, and a motif with homology to the signature sequence of the ATP-binding cassette (ABC) family of ATPases.  The sequence homology within the carboxy-terminal domain is relatively high within the SMC1-SMC4 group, w
Probab=61.81  E-value=8.8  Score=17.22  Aligned_cols=25  Identities=28%  Similarity=0.311  Sum_probs=19.0

Q ss_pred             CCCCCEEEEEECCCCCCHHHHHHHHH
Q ss_conf             54210124650257659789999999
Q gi|254781215|r   73 PNPEVFKGAISAGRGIGKTTLNAWLV   98 (511)
Q Consensus        73 ~~~~~~r~aV~sgrG~GKS~l~a~l~   98 (511)
                      .-|.. -+++....|+|||++.-.++
T Consensus        19 ~ip~G-itaIvGpsGsGKSTLl~~i~   43 (197)
T cd03278          19 PFPPG-LTAIVGPNGSGKSNIIDAIR   43 (197)
T ss_pred             ECCCC-EEEEECCCCCCHHHHHHHHH
T ss_conf             73898-28999999998899999999


No 421
>PRK13409 putative ATPase RIL; Provisional
Probab=61.74  E-value=7.5  Score=17.67  Aligned_cols=54  Identities=19%  Similarity=0.185  Sum_probs=28.8

Q ss_pred             CCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCC-CEEEEEECCCCCCHHHHHHHHH
Q ss_conf             65557845899999999999874056555421-0124650257659789999999
Q gi|254781215|r   45 LEGFSAPRSWQLEFMEVVDAHCLNSVNNPNPE-VFKGAISAGRGIGKTTLNAWLV   98 (511)
Q Consensus        45 ~~~~~~P~~WQ~e~l~~i~~~~~~~~~~~~~~-~~r~aV~sgrG~GKS~l~a~l~   98 (511)
                      ......|.+--.+....+..+-++--+.+.|. .-++.+....|.|||+++.+|.
T Consensus        66 i~iinlp~~l~~~~~h~yg~n~f~l~~lp~p~~G~v~GLiG~NGaGKST~lkILs  120 (590)
T PRK13409         66 ISIVNLPEELEEDCVHRYGPNGFKLYGLPIPKEGKVTGILGPNGIGKSTAVKILS  120 (590)
T ss_pred             EEEECCHHHHCCCCEEECCCCCEEEECCCCCCCCCEEEEECCCCCCHHHHHHHHH
T ss_conf             5761483675777605416774356078989998789988999998999999995


No 422
>cd03249 ABC_MTABC3_MDL1_MDL2 MTABC3 (also known as ABCB6) is a mitochondrial ATP-binding cassette protein involved in iron homeostasis and one of four ABC transporters expressed in the mitochondrial inner membrane, the other three being MDL1(ABC7), MDL2, and ATM1.  In fact, the yeast MDL1 (multidrug resistance-like protein 1) and MDL2 (multidrug resistance-like protein 2) transporters are also included in this CD.  MDL1 is an ATP-dependent permease that acts as a high-copy suppressor of ATM1 and is thought to have a role in resistance to oxidative stress. Interestingly, subfamily B is more closely related to the carboxyl-terminal component of subfamily C than the two halves of ABCC molecules are with one another.
Probab=61.73  E-value=7.6  Score=17.61  Aligned_cols=26  Identities=27%  Similarity=0.322  Sum_probs=20.3

Q ss_pred             CCCEEEEEECCCCCCHHHHHHHHHHH
Q ss_conf             21012465025765978999999999
Q gi|254781215|r   75 PEVFKGAISAGRGIGKTTLNAWLVLW  100 (511)
Q Consensus        75 ~~~~r~aV~sgrG~GKS~l~a~l~lw  100 (511)
                      +..-+++|...-|.|||+++..++-.
T Consensus        27 ~~G~~iaIvG~sGsGKSTLl~ll~gl   52 (238)
T cd03249          27 PPGKTVALVGSSGCGKSTVVSLLERF   52 (238)
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHHHC
T ss_conf             69999999999999899999998238


No 423
>smart00175 RAB Rab subfamily of small GTPases. Rab GTPases are implicated in vesicle trafficking.
Probab=61.62  E-value=7.7  Score=17.59  Aligned_cols=21  Identities=29%  Similarity=0.498  Sum_probs=18.2

Q ss_pred             EEEEEECCCCCCHHHHHHHHH
Q ss_conf             124650257659789999999
Q gi|254781215|r   78 FKGAISAGRGIGKTTLNAWLV   98 (511)
Q Consensus        78 ~r~aV~sgrG~GKS~l~a~l~   98 (511)
                      +|+.|....|+|||.++..++
T Consensus         1 ~Ki~vvG~~~vGKTsli~r~~   21 (164)
T smart00175        1 FKIILIGDSGVGKSSLLSRFT   21 (164)
T ss_pred             CEEEEECCCCCCHHHHHHHHH
T ss_conf             989999989977999999994


No 424
>cd04168 TetM_like Tet(M)-like subfamily.  Tet(M), Tet(O), Tet(W), and OtrA are tetracycline resistance genes found in Gram-positive and Gram-negative bacteria.  Tetracyclines inhibit protein synthesis by preventing aminoacyl-tRNA from binding to the ribosomal acceptor site.  This subfamily contains tetracycline resistance proteins that function through ribosomal protection and are typically found on mobile genetic elements, such as transposons or plasmids, and are often conjugative.  Ribosomal protection proteins are homologous to the elongation factors EF-Tu and EF-G.  EF-G and Tet(M) compete for binding on the ribosomes.  Tet(M) has a higher affinity than EF-G, suggesting these two proteins may have overlapping binding sites and that Tet(M) must be released before EF-G can bind.  Tet(M) and Tet(O) have been shown to have ribosome-dependent GTPase activity.  These proteins are part of the GTP translation factor family, which includes EF-G, EF-Tu, EF2, LepA, and SelB.
Probab=61.50  E-value=10  Score=16.77  Aligned_cols=109  Identities=15%  Similarity=0.053  Sum_probs=50.6

Q ss_pred             EEEECCCCCCHHHHHHHHHHH-HHHHCCCCEEEEEECCHHHHHHHHHHHHHHHHHHCHHCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             465025765978999999999-9980899669998085899999999999999985500013444322222233344432
Q gi|254781215|r   80 GAISAGRGIGKTTLNAWLVLW-LMSTRPGISVICLANSETQLKTTLWAEVSKWLSLLPNKHWFEMQSLSLHPAPWYSDVL  158 (511)
Q Consensus        80 ~aV~sgrG~GKS~l~a~l~lw-~l~~~p~~kv~vtApt~~Q~~~ilw~Ei~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~  158 (511)
                      +++.+-.|.|||+|+-.++.- ..+.+.+. |-- -+|.   .+-.=.|..+-+....          ......|..  .
T Consensus         2 iai~gH~~~GKTtL~e~lL~~~g~i~r~G~-v~~-g~t~---~D~~~eE~~r~isi~~----------~~~~~~~~~--~   64 (237)
T cd04168           2 IGILAHVDAGKTTLTESLLYTSGAIRKLGS-VDK-GTTR---TDTMELERQRGITIFS----------AVASFQWED--T   64 (237)
T ss_pred             EEEECCCCCCHHHHHHHHHHHCCHHHHCCC-EEC-CCCC---CCCHHHHHHHCCEEEE----------EEEEEEECC--E
T ss_conf             899938998999999999996571222663-306-8303---7854998984870310----------589999899--8


Q ss_pred             CCCCCCCCCEEEEEECCCCCCCCCHHHHCCCCCCEEEEECCHHCCC---HHHHHHHHH
Q ss_conf             1112357861698530357556100212026761499971110299---788988888
Q gi|254781215|r  159 HCSLGIDSKHYSTMCRTYSEERPDTFVGHHNTYGMAIINDEASGTP---DVINLGILG  213 (511)
Q Consensus       159 ~~~~~~~~~~~~~~~~~~s~~~~ea~~G~h~~~~~lvI~DEAsgI~---d~i~e~i~~  213 (511)
                              ..-++.......-..+...+++.-...++|+|-.+|+.   ..+|+.++-
T Consensus        65 --------~~n~iDtPG~~dF~~e~~~al~~~D~av~Vv~a~~Gv~~~t~~~~~~~~~  114 (237)
T cd04168          65 --------KVNLIDTPGHMDFIAEVERSLSVLDGAILVISAVEGVQAQTRILWRLLRK  114 (237)
T ss_pred             --------EEEEEECCCCHHHHHHHHHHHHHCCCEEEEEECCCCCCCCHHHHHHHHHH
T ss_conf             --------79998898846566689889763481699996588822344999999998


No 425
>cd04107 Rab32_Rab38 Rab38/Rab32 subfamily.  Rab32 and Rab38 are members of the Rab family of small GTPases.  Human Rab32 was first identified in platelets but it is expressed in a variety of cell types, where it functions as an A-kinase anchoring protein (AKAP). Rab38 has been shown to be melanocyte-specific.  GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state.  Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization.  Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins.
Probab=61.42  E-value=8  Score=17.47  Aligned_cols=21  Identities=29%  Similarity=0.403  Sum_probs=18.1

Q ss_pred             EEEEEECCCCCCHHHHHHHHH
Q ss_conf             124650257659789999999
Q gi|254781215|r   78 FKGAISAGRGIGKTTLNAWLV   98 (511)
Q Consensus        78 ~r~aV~sgrG~GKS~l~a~l~   98 (511)
                      +|+.+....|+|||.++-.++
T Consensus         1 fKvvllGd~gVGKTsLi~rf~   21 (201)
T cd04107           1 LKVLVIGDLGVGKTSIIKRYV   21 (201)
T ss_pred             CEEEEECCCCCCHHHHHHHHH
T ss_conf             979999999978999999998


No 426
>TIGR03539 DapC_actino succinyldiaminopimelate transaminase. This family of actinobacterial succinyldiaminopimelate transaminase enzymes (DapC) are members of the pfam00155 superfamily. Many of these genes appear adjacent to other genes encoding enzymes of the lysine biosynthesis via diaminopimelate pathway (GenProp0125).
Probab=61.42  E-value=10  Score=16.76  Aligned_cols=59  Identities=20%  Similarity=0.190  Sum_probs=32.0

Q ss_pred             HHHHHHHHHHHHHCCCCC--CCCCCEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEEECCHHHH
Q ss_conf             999999999987405655--542101246502576597899999999999808996699980858999
Q gi|254781215|r   55 QLEFMEVVDAHCLNSVNN--PNPEVFKGAISAGRGIGKTTLNAWLVLWLMSTRPGISVICLANSETQL  120 (511)
Q Consensus        55 Q~e~l~~i~~~~~~~~~~--~~~~~~r~aV~sgrG~GKS~l~a~l~lw~l~~~p~~kv~vtApt~~Q~  120 (511)
                      -.++-++|+++..+..+.  ..+.  .|.|.+    |=+...+.+ ...+.+.||-.|++..|++..-
T Consensus        58 ~~eLReaia~~~~~~~g~~~~~~~--~I~vt~----G~~~al~~l-~~~l~~~pGD~Vli~~P~y~~y  118 (357)
T TIGR03539        58 TPELREAIVDWLERRRGVPGLDPT--AVLPVI----GTKELVAWL-PTLLGLGPGDTVVIPELAYPTY  118 (357)
T ss_pred             CHHHHHHHHHHHHHHCCCCCCCCC--EEEECC----CHHHHHHHH-HHHHHCCCCCEEEECCCCCCCH
T ss_conf             799999999999997199979957--599868----879999999-9997079999899788877008


No 427
>cd02032 Bchl_like This family of proteins contains bchL and chlL. Protochlorophyllide reductase catalyzes the reductive formation of chlorophyllide from protochlorophyllide during biosynthesis of chlorophylls and bacteriochlorophylls. Three genes, bchL, bchN and bchB, are involved in light-independent protochlorophyllide reduction in bacteriochlorophyll biosynthesis. In cyanobacteria, algae, and gymnosperms, three similar genes, chlL, chlN and chlB are involved in protochlorophyllide reduction during chlorophylls biosynthesis. BchL/chlL, bchN/chlN and bchB/chlB exhibit significant sequence similarity to the nifH, nifD and nifK subunits of nitrogenase, respectively. Nitrogenase catalyzes the reductive formation of ammonia from dinitrogen.
Probab=61.41  E-value=10  Score=16.76  Aligned_cols=34  Identities=29%  Similarity=0.323  Sum_probs=28.0

Q ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEEE
Q ss_conf             246502576597899999999999808996699980
Q gi|254781215|r   79 KGAISAGRGIGKTTLNAWLVLWLMSTRPGISVICLA  114 (511)
Q Consensus        79 r~aV~sgrG~GKS~l~a~l~lw~l~~~p~~kv~vtA  114 (511)
                      ++||-.==|+|||+.+|.+...++.  -+.||+.+-
T Consensus         2 kiaiyGKGGIGKSTttaNl~aaLA~--~G~kVl~Ig   35 (267)
T cd02032           2 VLAVYGKGGIGKSTTSSNLSVALAK--RGKKVLQIG   35 (267)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHH--CCCEEEEEC
T ss_conf             7999779965787789999999998--799599977


No 428
>pfam01580 FtsK_SpoIIIE FtsK/SpoIIIE family. FtsK has extensive sequence similarity to wide variety of proteins from prokaryotes and plasmids, termed the FtsK/SpoIIIE family. This domain contains a putative ATP binding P-loop motif.  It is found in the FtsK cell division protein from E. coli and the stage III sporulation protein E SpoIIIE which has roles in regulation of prespore specific gene expression in B. subtilis. A mutation in FtsK causes a temperature sensitive block in cell division and it is involved in peptidoglycan synthesis or modification. The SpoIIIE protein is implicated in intercellular chromosomal DNA transfer.
Probab=61.32  E-value=10  Score=16.75  Aligned_cols=39  Identities=21%  Similarity=0.254  Sum_probs=30.1

Q ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHHCCC--CEEEEEECCH
Q ss_conf             24650257659789999999999980899--6699980858
Q gi|254781215|r   79 KGAISAGRGIGKTTLNAWLVLWLMSTRPG--ISVICLANSE  117 (511)
Q Consensus        79 r~aV~sgrG~GKS~l~a~l~lw~l~~~p~--~kv~vtApt~  117 (511)
                      -+.|...-|.|||.+.-.+++..+.++.+  .+++++=++.
T Consensus        40 H~Lv~G~tGsGKS~~l~~li~sl~~~~~p~~v~l~liD~K~   80 (202)
T pfam01580        40 HLLIAGATGSGKSTFLNTLILSLAARHSPEEVRLYLIDPKG   80 (202)
T ss_pred             CEEEECCCCCCCCHHHHHHHHHHHHHCCCCEEEEEEECCCC
T ss_conf             68996589998009999999999873796206999974896


No 429
>PRK13538 cytochrome c biogenesis protein CcmA; Provisional
Probab=61.29  E-value=7.5  Score=17.65  Aligned_cols=21  Identities=33%  Similarity=0.259  Sum_probs=17.8

Q ss_pred             EEEEEECCCCCCHHHHHHHHH
Q ss_conf             124650257659789999999
Q gi|254781215|r   78 FKGAISAGRGIGKTTLNAWLV   98 (511)
Q Consensus        78 ~r~aV~sgrG~GKS~l~a~l~   98 (511)
                      -.+++....|.|||++.-.++
T Consensus        28 e~~~l~G~NGaGKSTLl~~l~   48 (204)
T PRK13538         28 ELVQIEGPNGAGKTSLLRILA   48 (204)
T ss_pred             CEEEEECCCCCCHHHHHHHHH
T ss_conf             899999999985999999997


No 430
>pfam07724 AAA_2 AAA domain (Cdc48 subfamily). This Pfam entry includes some of the AAA proteins not detected by the pfam00004 model.
Probab=61.27  E-value=10  Score=16.74  Aligned_cols=27  Identities=19%  Similarity=0.289  Sum_probs=20.2

Q ss_pred             CCCCEEEEECCHHCCCHHHHHHHHHHHC
Q ss_conf             6761499971110299788988888850
Q gi|254781215|r  189 NTYGMAIINDEASGTPDVINLGILGFLT  216 (511)
Q Consensus       189 ~~~~~lvI~DEAsgI~d~i~e~i~~~Lt  216 (511)
                      ..+ ..+++||....+..+|..+...|-
T Consensus        74 ~p~-~VillDEIeKa~~~V~~~LL~ild  100 (168)
T pfam07724        74 KPY-SIVLIDEIEKAHPGVQNDLLQILE  100 (168)
T ss_pred             CCC-CEEEEHHHHHHCHHHHHHHHHHCC
T ss_conf             898-489865776658999999998705


No 431
>cd03246 ABCC_Protease_Secretion This family represents the ABC component of the protease secretion system PrtD, a 60-kDa integral membrane protein sharing 37% identity with HlyB, the ABC component of the alpha-hemolysin secretion pathway, in the C-terminal domain.  They export degradative enzymes by using a type I protein secretion system and  lack an N-terminal signal peptide, but contain a C-terminal secretion signal.  The Type I secretion apparatus is made up of three components, an ABC transporter, a membrane fusion protein (MFP), and an outer membrane protein (OMP).  For the HlyA transporter complex, HlyB (ABC transporter) and HlyD (MFP) reside in the inner membrane of E. coli.  The OMP component is TolC, which is thought to interact with the MFP to form a continuous channel across the periplasm from the cytoplasm to the exterior.  HlyB belongs to the family of ABC transporters, which are ubiquitous, ATP-dependent transmembrane pumps or channels.  The spectrum of transport substra
Probab=61.26  E-value=7.2  Score=17.76  Aligned_cols=27  Identities=30%  Similarity=0.191  Sum_probs=21.3

Q ss_pred             CCCEEEEEECCCCCCHHHHHHHHHHHH
Q ss_conf             210124650257659789999999999
Q gi|254781215|r   75 PEVFKGAISAGRGIGKTTLNAWLVLWL  101 (511)
Q Consensus        75 ~~~~r~aV~sgrG~GKS~l~a~l~lw~  101 (511)
                      +..-.++|...-|.|||+++..++=.+
T Consensus        26 ~~G~~vaIvG~sGsGKSTLl~ll~gl~   52 (173)
T cd03246          26 EPGESLAIIGPSGSGKSTLARLILGLL   52 (173)
T ss_pred             CCCCEEEEECCCCCHHHHHHHHHHCCC
T ss_conf             599999999999980999999996666


No 432
>cd02019 NK Nucleoside/nucleotide kinase (NK) is a protein superfamily consisting of multiple families of enzymes that share structural similarity and are functionally related to the catalysis of the reversible phosphate group transfer from nucleoside triphosphates to nucleosides/nucleotides, nucleoside monophosphates, or sugars. Members of this family play a wide variety of essential roles in nucleotide metabolism, the biosynthesis of coenzymes and aromatic compounds, as well as the metabolism of sugar and sulfate.
Probab=61.11  E-value=7  Score=17.85  Aligned_cols=22  Identities=41%  Similarity=0.442  Sum_probs=19.1

Q ss_pred             EEEECCCCCCHHHHHHHHHHHH
Q ss_conf             4650257659789999999999
Q gi|254781215|r   80 GAISAGRGIGKTTLNAWLVLWL  101 (511)
Q Consensus        80 ~aV~sgrG~GKS~l~a~l~lw~  101 (511)
                      +++..+.|+|||+++..+.--+
T Consensus         2 I~I~G~~gsGKsT~a~~l~~~l   23 (69)
T cd02019           2 IAITGGSGSGKSTVAKKLAEQL   23 (69)
T ss_pred             EEEECCCCCCHHHHHHHHHHHH
T ss_conf             7883688887258999999995


No 433
>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=61.08  E-value=6.9  Score=17.89  Aligned_cols=30  Identities=20%  Similarity=0.125  Sum_probs=20.9

Q ss_pred             EEEEECCH-HCCCHHHHHHHHHHHCCCCCCE
Q ss_conf             49997111-0299788988888850799813
Q gi|254781215|r  193 MAIINDEA-SGTPDVINLGILGFLTERNANR  222 (511)
Q Consensus       193 ~lvI~DEA-sgI~d~i~e~i~~~Lt~~g~~~  222 (511)
                      -++|+||+ ++++...-..+...|...+...
T Consensus       111 ~iliLDEpTs~LD~~~~~~l~~~l~~~~~Tv  141 (166)
T cd03223         111 KFVFLDEATSALDEESEDRLYQLLKELGITV  141 (166)
T ss_pred             CEEEECCCCCCCCHHHHHHHHHHHHHCCCEE
T ss_conf             9999758533289999999999999779989


No 434
>PRK13849 putative crown gall tumor protein VirC1; Provisional
Probab=61.02  E-value=11  Score=16.71  Aligned_cols=36  Identities=31%  Similarity=0.217  Sum_probs=24.7

Q ss_pred             EEEEC-CCCCCHHHHHHHHHHHHHHHCCCCEEEEEECCH
Q ss_conf             46502-576597899999999999808996699980858
Q gi|254781215|r   80 GAISA-GRGIGKTTLNAWLVLWLMSTRPGISVICLANSE  117 (511)
Q Consensus        80 ~aV~s-grG~GKS~l~a~l~lw~l~~~p~~kv~vtApt~  117 (511)
                      +++.+ ==|+|||+++..++.++..  .|.+|.++=..-
T Consensus         4 i~~~~~KGG~GKtT~a~~la~~~~~--~g~~v~~iD~Dp   40 (231)
T PRK13849          4 LTFCSFKGGAGKTTALMGLCAALAS--DGKRVALFEADE   40 (231)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHH--CCCEEEEEECCC
T ss_conf             9996189987699999999999997--899599996899


No 435
>cd04127 Rab27A Rab27a subfamily.  The Rab27a subfamily consists of Rab27a and its highly homologous isoform, Rab27b.  Unlike most Rab proteins whose functions remain poorly defined, Rab27a has many known functions.  Rab27a has multiple effector proteins, and depending on which effector it binds, Rab27a has different functions as well as tissue distribution and/or cellular localization. Putative functions have been assigned to Rab27a when associated with the effector proteins Slp1, Slp2, Slp3, Slp4, Slp5, DmSlp, rabphilin, Dm/Ce-rabphilin, Slac2-a, Slac2-b, Slac2-c, Noc2, JFC1, and Munc13-4. Rab27a has been associated with several human diseases, including hemophagocytic syndrome (Griscelli syndrome or GS), Hermansky-Pudlak syndrome, and choroidermia. In the case of GS, a rare, autosomal recessive disease, a Rab27a mutation is directly responsible for the disorder.  When Rab27a is localized to the secretory granules of pancreatic beta cells, it is believed to mediate glucose-stimulated 
Probab=60.96  E-value=8.9  Score=17.19  Aligned_cols=23  Identities=22%  Similarity=0.176  Sum_probs=19.4

Q ss_pred             CCEEEEEECCCCCCHHHHHHHHH
Q ss_conf             10124650257659789999999
Q gi|254781215|r   76 EVFKGAISAGRGIGKTTLNAWLV   98 (511)
Q Consensus        76 ~~~r~aV~sgrG~GKS~l~a~l~   98 (511)
                      ..+|+.|....|+|||.++..++
T Consensus         3 ~~~KivvvGd~~VGKTsli~r~~   25 (180)
T cd04127           3 YLIKFLALGDSGVGKTSFLYQYT   25 (180)
T ss_pred             EEEEEEEECCCCCCHHHHHHHHH
T ss_conf             78899999999988899999996


No 436
>PRK09302 circadian clock protein KaiC; Reviewed
Probab=60.89  E-value=11  Score=16.70  Aligned_cols=49  Identities=14%  Similarity=0.083  Sum_probs=32.4

Q ss_pred             CCCCCEEEEEECCCCCCHHHHHHHHHHHHHHH-CCCCEEEEEECCHHHHH
Q ss_conf             54210124650257659789999999999980-89966999808589999
Q gi|254781215|r   73 PNPEVFKGAISAGRGIGKTTLNAWLVLWLMST-RPGISVICLANSETQLK  121 (511)
Q Consensus        73 ~~~~~~r~aV~sgrG~GKS~l~a~l~lw~l~~-~p~~kv~vtApt~~Q~~  121 (511)
                      -.|..+-+.|..+-|+|||+++.-.+.-.+-. ...+-.+...-+..++.
T Consensus        20 Glp~g~~~LV~G~pGsGKTtla~QfL~~Ga~~~GE~~lyitl~E~~~~l~   69 (501)
T PRK09302         20 GLPKGRPTLVSGTAGTGKTLFALQFLHNGIKSFGEPGVFVTFEESPEDII   69 (501)
T ss_pred             CCCCCCEEEEEECCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCCHHHHH
T ss_conf             98899779998389999999999999999885599789998579999999


No 437
>PRK13873 conjugal transfer ATPase TrbE; Provisional
Probab=60.88  E-value=11  Score=16.70  Aligned_cols=41  Identities=10%  Similarity=0.079  Sum_probs=21.9

Q ss_pred             HHHHHHHHHHHHHCCCCEEE-EEECCCCHHHHHHHHHCCCEEEEE
Q ss_conf             89999999999861888299-800687636889898649827984
Q gi|254781215|r  354 RTTNNKISGLVEKYRPDAII-IDANNTGARTCDYLEMLGYHVYRV  397 (511)
Q Consensus       354 ~~~a~~i~~~~~~~~~~~i~-iD~~GvG~gV~d~L~~~g~~v~~v  397 (511)
                      ..+...+.....+|.+..|+ .|- |-|.-+.  .+..|-....+
T Consensus       455 Tvll~~l~~q~~ry~~~~vf~FDk-d~s~~i~--~~a~GG~y~~l  496 (815)
T PRK13873        455 SVLLALMALQFRRYPGSQVFAFDF-GGSIRAA--ALAMGGDWHDL  496 (815)
T ss_pred             HHHHHHHHHHHHHCCCCCEEEEEC-CCCHHHH--HHHHCCEEEEC
T ss_conf             999999999986448984899978-9878999--99829987603


No 438
>cd04110 Rab35 Rab35 subfamily.  Rab35 is one of several Rab proteins to be found to participate in the regulation of osteoclast cells in rats. In addition, Rab35 has been identified as a protein that interacts with nucleophosmin-anaplastic lymphoma kinase (NPM-ALK) in human cells.  Overexpression of NPM-ALK is a key oncogenic event in some anaplastic large-cell lymphomas; since Rab35 interacts with N|PM-ALK, it may provide a target for cancer treatments. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state.  Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization.  Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is 
Probab=60.88  E-value=10  Score=16.86  Aligned_cols=24  Identities=29%  Similarity=0.439  Sum_probs=20.2

Q ss_pred             CCCEEEEEECCCCCCHHHHHHHHH
Q ss_conf             210124650257659789999999
Q gi|254781215|r   75 PEVFKGAISAGRGIGKTTLNAWLV   98 (511)
Q Consensus        75 ~~~~r~aV~sgrG~GKS~l~a~l~   98 (511)
                      ..++|+.+....|+|||.++-.++
T Consensus         4 d~~~KIvlvGd~~VGKTSli~r~~   27 (199)
T cd04110           4 DHLFKLLIIGDSGVGKSSLLLRFA   27 (199)
T ss_pred             CEEEEEEEECCCCCCHHHHHHHHH
T ss_conf             757799999979988899999995


No 439
>PRK06851 hypothetical protein; Provisional
Probab=60.75  E-value=11  Score=16.68  Aligned_cols=48  Identities=15%  Similarity=0.168  Sum_probs=36.2

Q ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEEECCHHHHHHHHHH
Q ss_conf             246502576597899999999999808996699980858999999999
Q gi|254781215|r   79 KGAISAGRGIGKTTLNAWLVLWLMSTRPGISVICLANSETQLKTTLWA  126 (511)
Q Consensus        79 r~aV~sgrG~GKS~l~a~l~lw~l~~~p~~kv~vtApt~~Q~~~ilw~  126 (511)
                      -..+.+|-|+|||+++.-+.-.+.-...+...+.++.--+.+--|+.+
T Consensus        33 i~ilKGGpGtGKStlmK~ig~~~~~~GydVE~~hcssD~~SlDGvvip   80 (368)
T PRK06851         33 IFILKGGPGTGKSTLMKKIGEEFLEKGYDVEFLHCSSDNDSLDGVIIP   80 (368)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCCEEEEC
T ss_conf             999968999778999999999999689837999758998864359975


No 440
>PRK07568 aspartate aminotransferase; Provisional
Probab=60.69  E-value=11  Score=16.68  Aligned_cols=59  Identities=14%  Similarity=0.056  Sum_probs=30.1

Q ss_pred             HHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEEECCHHHHH
Q ss_conf             9999999999874056555421012465025765978999999999998089966999808589999
Q gi|254781215|r   55 QLEFMEVVDAHCLNSVNNPNPEVFKGAISAGRGIGKTTLNAWLVLWLMSTRPGISVICLANSETQLK  121 (511)
Q Consensus        55 Q~e~l~~i~~~~~~~~~~~~~~~~r~aV~sgrG~GKS~l~a~l~lw~l~~~p~~kv~vtApt~~Q~~  121 (511)
                      -.++-++|+++..+-...-.|  -.+.|.+|   ++   .+..++..+++.|+-.|++..|++....
T Consensus        68 ~~~LReaia~~~~~~g~~~~~--d~I~iT~G---a~---~al~~~~~~l~~pGD~Vlv~~P~y~~y~  126 (396)
T PRK07568         68 IDSLREAFSKYYKRFNIDFDK--DEIIVTNG---GS---EAILFALMAICDPGDEIIVPEPFYANYN  126 (396)
T ss_pred             CHHHHHHHHHHHHHHCCCCCH--HEEEECCC---HH---HHHHHHHHHHCCCCCEEEEECCCCCCHH
T ss_conf             199999999999986889882--22898578---06---9999999972799898999389753259


No 441
>PRK04220 2-phosphoglycerate kinase; Provisional
Probab=60.65  E-value=9.7  Score=16.97  Aligned_cols=26  Identities=27%  Similarity=0.270  Sum_probs=20.5

Q ss_pred             CCEEEEEECCCCCCHHHHHHHHHHHH
Q ss_conf             10124650257659789999999999
Q gi|254781215|r   76 EVFKGAISAGRGIGKTTLNAWLVLWL  101 (511)
Q Consensus        76 ~~~r~aV~sgrG~GKS~l~a~l~lw~  101 (511)
                      ...=+.+.+.-|+|||++++-|+--.
T Consensus        91 ~pliILigGtsGvGKSTlA~~LA~rL  116 (306)
T PRK04220         91 EPIIILIGGASGVGTSTIAFELASRL  116 (306)
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHHHH
T ss_conf             98799985899887899999999970


No 442
>COG4555 NatA ABC-type Na+ transport system, ATPase component [Energy production and conversion / Inorganic ion transport and metabolism]
Probab=60.59  E-value=11  Score=16.67  Aligned_cols=22  Identities=27%  Similarity=0.288  Sum_probs=17.6

Q ss_pred             EEEEECCCCCCHHHHHHHHHHH
Q ss_conf             2465025765978999999999
Q gi|254781215|r   79 KGAISAGRGIGKTTLNAWLVLW  100 (511)
Q Consensus        79 r~aV~sgrG~GKS~l~a~l~lw  100 (511)
                      =+.+-...|.|||++.-+++-.
T Consensus        30 i~GlLG~NGAGKTT~LRmiatl   51 (245)
T COG4555          30 ITGLLGENGAGKTTLLRMIATL   51 (245)
T ss_pred             EEEEECCCCCCCHHHHHHHHHH
T ss_conf             9998768988712379999983


No 443
>TIGR01526 nadR_NMN_Atrans nicotinamide-nucleotide adenylyltransferase; InterPro: IPR006417   The NadR protein of Escherichia coli and closely related bacteria is both enzyme and regulatory protein. The first 60 or so amino acids, N-terminal region is a DNA-binding helix-turn-helix domain (IPR001387 from INTERPRO) responsible for repressing the nadAB genes of NAD de novo biosynthesis. The NadR homologs in Mycobacterium tuberculosis, Haemophilus influenzae, and others appear to lack the repressor domain. NadR has recently been shown to act as an enzyme of the salvage pathway of NAD biosynthesis, nicotinamide-nucleotide adenylyltransferase; members of this family are presumed to share this activity. E. coli NadR has also been found to regulate the import of its substrate, nicotinamide ribonucleotide, but it is not known if the other members of this family share that activity.  ; GO: 0003677 DNA binding, 0030528 transcription regulator activity, 0006810 transport, 0019363 pyridine nucleotide biosynthetic process, 0045449 regulation of transcription.
Probab=60.36  E-value=8.7  Score=17.25  Aligned_cols=24  Identities=8%  Similarity=-0.241  Sum_probs=9.4

Q ss_pred             HHHHHHCCCCCCCCCCEEECHHHH
Q ss_conf             354443175666678737559999
Q gi|254781215|r  279 VTRVEVCGQFPQQDIDSFIPLNII  302 (511)
Q Consensus       279 ~~r~evlgeFp~~~~~~~i~~~~i  302 (511)
                      .|..+|.-.+.-.++..++..++-
T Consensus       206 Eyar~y~e~~~ggDe~~L~~~dY~  229 (346)
T TIGR01526       206 EYAREYVEAKLGGDEIALQYSDYA  229 (346)
T ss_pred             HHHHHHHHHHCCCCHHHHHCCCHH
T ss_conf             565566665168721454203437


No 444
>cd03248 ABCC_TAP TAP, the Transporter Associated with Antigen Processing; TAP is essential for peptide delivery from the cytosol into the lumen of the endoplasmic reticulum (ER), where these peptides are loaded on major histocompatibility complex (MHC) I molecules.  Loaded MHC I leave the ER and display their antigenic cargo on the cell surface to cytotoxic T cells.  Subsequently, virus-infected or malignantly transformed cells can be eliminated.  TAP belongs to the large family of ATP-binding cassette (ABC) transporters, which translocate a vast variety of solutes across membranes.
Probab=60.26  E-value=8  Score=17.47  Aligned_cols=24  Identities=29%  Similarity=0.263  Sum_probs=20.0

Q ss_pred             EEEEEECCCCCCHHHHHHHHHHHH
Q ss_conf             124650257659789999999999
Q gi|254781215|r   78 FKGAISAGRGIGKTTLNAWLVLWL  101 (511)
Q Consensus        78 ~r~aV~sgrG~GKS~l~a~l~lw~  101 (511)
                      -+++|...-|.|||+++..++-.+
T Consensus        41 e~vaIvG~sGsGKSTL~~ll~gl~   64 (226)
T cd03248          41 EVTALVGPSGSGKSTVVALLENFY   64 (226)
T ss_pred             CEEEEECCCCCHHHHHHHHHHCCC
T ss_conf             999999999984999999996454


No 445
>PRK13233 nifH nitrogenase reductase; Reviewed
Probab=60.22  E-value=11  Score=16.63  Aligned_cols=40  Identities=23%  Similarity=0.079  Sum_probs=30.2

Q ss_pred             EEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEE--ECCHH
Q ss_conf             124650257659789999999999980899669998--08589
Q gi|254781215|r   78 FKGAISAGRGIGKTTLNAWLVLWLMSTRPGISVICL--ANSET  118 (511)
Q Consensus        78 ~r~aV~sgrG~GKS~l~a~l~lw~l~~~p~~kv~vt--Apt~~  118 (511)
                      +++||-.==|+|||+.++.++..++-. .+.||+++  =|..+
T Consensus         3 ~~iaiyGKGGIGKSTTt~NLaaALA~l-~GkrVl~IgcDPk~d   44 (275)
T PRK13233          3 RKIAIYGKGGIGKSTTTQNTAAAMAHF-HDKKVFIHGCDPKAD   44 (275)
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHHHHH-CCCEEEEECCCCCCC
T ss_conf             389998998544654599999999964-798899979788761


No 446
>cd00154 Rab Rab family.  Rab GTPases form the largest family within the Ras superfamily.  There are at least 60 Rab genes in the human genome, and a number of Rab GTPases are conserved from yeast to humans. Rab GTPases are small, monomeric proteins that function as molecular switches to regulate vesicle trafficking pathways.  The different Rab GTPases are localized to the cytosolic face of specific intracellular membranes, where they regulate distinct steps in membrane traffic pathways. In the GTP-bound form, Rab GTPases recruit specific sets of effector proteins onto membranes. Through their effectors, Rab GTPases regulate vesicle formation, actin- and tubulin-dependent vesicle movement, and membrane fusion.  GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state.  Rabs are further regulated by guanine nucleotide di
Probab=60.18  E-value=8.6  Score=17.29  Aligned_cols=22  Identities=36%  Similarity=0.460  Sum_probs=18.7

Q ss_pred             EEEEEECCCCCCHHHHHHHHHH
Q ss_conf             1246502576597899999999
Q gi|254781215|r   78 FKGAISAGRGIGKTTLNAWLVL   99 (511)
Q Consensus        78 ~r~aV~sgrG~GKS~l~a~l~l   99 (511)
                      +|+.|....|+|||.++..++-
T Consensus         1 ~Ki~vvG~~~vGKTsli~~~~~   22 (159)
T cd00154           1 FKIVLIGDSGVGKTSLLLRFVD   22 (159)
T ss_pred             CEEEEECCCCCCHHHHHHHHHH
T ss_conf             9899999699689999999970


No 447
>cd04119 RJL RJL (RabJ-Like) subfamily.  RJLs are found in many protists and as chimeras with C-terminal DNAJ domains in deuterostome metazoa. They are not found in plants, fungi, and protostome metazoa, suggesting a horizontal gene transfer between protists and deuterostome metazoa.  RJLs lack any known membrane targeting signal and contain a degenerate phosphate/magnesium-binding 3 (PM3) motif, suggesting an impaired ability to hydrolyze GTP.  GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state.  Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization.
Probab=60.15  E-value=8.4  Score=17.35  Aligned_cols=21  Identities=19%  Similarity=0.257  Sum_probs=18.1

Q ss_pred             EEEEEECCCCCCHHHHHHHHH
Q ss_conf             124650257659789999999
Q gi|254781215|r   78 FKGAISAGRGIGKTTLNAWLV   98 (511)
Q Consensus        78 ~r~aV~sgrG~GKS~l~a~l~   98 (511)
                      .|+.|....|+|||.|+..++
T Consensus         1 lKivvvG~~~vGKTSLi~r~~   21 (168)
T cd04119           1 IKVISMGNSGVGKSCIIKRYC   21 (168)
T ss_pred             CEEEEECCCCCCHHHHHHHHH
T ss_conf             989999959956899999996


No 448
>COG1855 ATPase (PilT family) [General function prediction only]
Probab=59.96  E-value=10  Score=16.74  Aligned_cols=17  Identities=12%  Similarity=0.089  Sum_probs=8.8

Q ss_pred             HCCCCCCHHHHHHHHHC
Q ss_conf             48999898999999975
Q gi|254781215|r  461 KGAKSTDYSDGLMYTFA  477 (511)
Q Consensus       461 rg~~SPD~ADAl~l~fa  477 (511)
                      |.-++-+.+.+++.+..
T Consensus       578 ri~~~~~~g~~i~~ai~  594 (604)
T COG1855         578 KIRKDSEVGKEIEEAID  594 (604)
T ss_pred             EEECCCHHHHHHHHHHH
T ss_conf             98518768999999986


No 449
>COG1239 ChlI Mg-chelatase subunit ChlI [Coenzyme metabolism]
Probab=59.95  E-value=11  Score=16.60  Aligned_cols=38  Identities=29%  Similarity=0.254  Sum_probs=27.9

Q ss_pred             EEEECCHHCCCHHHHHHHHHHHCCC-C------------CCEEEEEECCCC
Q ss_conf             9997111029978898888885079-9------------813899823899
Q gi|254781215|r  194 AIINDEASGTPDVINLGILGFLTER-N------------ANRFWIMTSNPR  231 (511)
Q Consensus       194 lvI~DEAsgI~d~i~e~i~~~Lt~~-g------------~~~~~i~~~nP~  231 (511)
                      .+.+||---++|.+-+++.-.+..+ |            .+..++.+.||-
T Consensus       147 IlYvDEvnlL~d~lvd~LLd~aaeG~n~vereGisi~hpa~fvligTmNPE  197 (423)
T COG1239         147 ILYVDEVNLLDDHLVDALLDVAAEGVNDVEREGISIRHPARFLLIGTMNPE  197 (423)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHCCCEEEECCEEECCCCCEEEEEECCCC
T ss_conf             798723343518999999999971774033575031367617999644854


No 450
>cd04103 Centaurin_gamma Centaurin gamma.  The centaurins (alpha, beta, gamma, and delta) are large, multi-domain proteins that all contain an ArfGAP domain and ankyrin repeats, and in some cases, numerous additional domains.  Centaurin gamma contains an additional GTPase domain near its N-terminus.  The specific function of this GTPase domain has not been well characterized, but centaurin gamma 2 (CENTG2) may play a role in the development of autism.  Centaurin gamma 1 is also called PIKE (phosphatidyl inositol (PI) 3-kinase enhancer) and centaurin gamma 2 is also known as AGAP (ArfGAP protein with a GTPase-like domain, ankyrin repeats and a Pleckstrin homology domain) or GGAP.  Three isoforms of PIKE have been identified. PIKE-S (short) and PIKE-L (long) are brain-specific isoforms, with PIKE-S restricted to the nucleus and PIKE-L found in multiple cellular compartments.  A third isoform, PIKE-A was identified in human glioblastoma brain cancers and has been found in various tissues. 
Probab=59.60  E-value=9  Score=17.15  Aligned_cols=22  Identities=23%  Similarity=0.184  Sum_probs=18.4

Q ss_pred             EEEEEECCCCCCHHHHHHHHHH
Q ss_conf             1246502576597899999999
Q gi|254781215|r   78 FKGAISAGRGIGKTTLNAWLVL   99 (511)
Q Consensus        78 ~r~aV~sgrG~GKS~l~a~l~l   99 (511)
                      +|+.|....|+|||.++-.++.
T Consensus         1 ~KivllGd~~VGKTsl~~Rf~~   22 (158)
T cd04103           1 LKLGIVGNLQSGKSALVHRYLT   22 (158)
T ss_pred             CEEEEECCCCCCHHHHHHHHHH
T ss_conf             9999999699879999999980


No 451
>cd03228 ABCC_MRP_Like The MRP (Mutidrug Resistance Protein)-like transporters are involved in drug, peptide, and lipid export.  They belong to the subfamily C of the ATP-binding cassette (ABC) superfamily of transport proteins.  The ABCC subfamily contains transporters with a diverse functional spectrum that includes ion transport, cell surface receptor, and toxin secretion activities.  The MRP-like family, simlar to all ABC proteins, have a common four-domain core structure constituted by two membrane-spanning domains, each composed of six transmembrane (TM) helices, and two nucleotide-binding domains (NBD).  ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.
Probab=59.35  E-value=8.7  Score=17.27  Aligned_cols=37  Identities=24%  Similarity=0.135  Sum_probs=24.2

Q ss_pred             CCCEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEE
Q ss_conf             210124650257659789999999999980899669998
Q gi|254781215|r   75 PEVFKGAISAGRGIGKTTLNAWLVLWLMSTRPGISVICL  113 (511)
Q Consensus        75 ~~~~r~aV~sgrG~GKS~l~a~l~lw~l~~~p~~kv~vt  113 (511)
                      +..-++++...-|.|||+++..++=  +..-...+|.+-
T Consensus        26 ~~Ge~i~ivG~sGsGKSTLl~ll~g--l~~p~~G~I~i~   62 (171)
T cd03228          26 KPGEKVAIVGPSGSGKSTLLKLLLR--LYDPTSGEILID   62 (171)
T ss_pred             CCCCEEEEECCCCCHHHHHHHHHHC--CCCCCCCEEEEC
T ss_conf             5998999999999839999999976--775897489999


No 452
>COG1428 Deoxynucleoside kinases [Nucleotide transport and metabolism]
Probab=59.34  E-value=11  Score=16.53  Aligned_cols=50  Identities=18%  Similarity=0.215  Sum_probs=39.4

Q ss_pred             EEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEEECCHHHHHHHHHHHHHHHH
Q ss_conf             1246502576597899999999999808996699980858999999999999999
Q gi|254781215|r   78 FKGAISAGRGIGKTTLNAWLVLWLMSTRPGISVICLANSETQLKTTLWAEVSKWL  132 (511)
Q Consensus        78 ~r~aV~sgrG~GKS~l~a~l~lw~l~~~p~~kv~vtApt~~Q~~~ilw~Ei~k~~  132 (511)
                      ..++|.+-=|+|||+|+..|+--     -++++++=.....+.-+.......+|.
T Consensus         5 ~~IvI~G~IG~GKSTLa~~La~~-----l~~~~~~E~vednp~L~~FY~d~~~ya   54 (216)
T COG1428           5 MVIVIEGMIGAGKSTLAQALAEH-----LGFKVFYELVEDNPFLDLFYEDPERYA   54 (216)
T ss_pred             CEEEEECCCCCCHHHHHHHHHHH-----HCCCEEEECCCCCHHHHHHHHHHHHHH
T ss_conf             08998446446878999999988-----388502222467847999987699741


No 453
>cd01131 PilT Pilus retraction ATPase PilT. PilT is a nucleotide binding protein responsible for the retraction of type IV pili, likely by pili disassembly. This retraction provides the force required for travel of bacteria in low water environments by a mechanism known as twitching motility.
Probab=59.30  E-value=11  Score=16.53  Aligned_cols=34  Identities=15%  Similarity=0.227  Sum_probs=23.7

Q ss_pred             EEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEEE
Q ss_conf             46502576597899999999999808996699980
Q gi|254781215|r   80 GAISAGRGIGKTTLNAWLVLWLMSTRPGISVICLA  114 (511)
Q Consensus        80 ~aV~sgrG~GKS~l~a~l~lw~l~~~p~~kv~vtA  114 (511)
                      +-|..+-|.|||++++.++-+.. .+.+.+++.+-
T Consensus         4 iLitG~TGSGKTTtl~all~~i~-~~~~~~IiTiE   37 (198)
T cd01131           4 VLVTGPTGSGKSTTLAAMIDYIN-KNKTHHILTIE   37 (198)
T ss_pred             EEEECCCCCCHHHHHHHHHHHHC-CCCCCEEEEEC
T ss_conf             99989999979999999998536-37883699964


No 454
>PRK08727 hypothetical protein; Validated
Probab=59.24  E-value=11  Score=16.52  Aligned_cols=32  Identities=31%  Similarity=0.198  Sum_probs=21.5

Q ss_pred             EEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEE
Q ss_conf             4650257659789999999999980899669998
Q gi|254781215|r   80 GAISAGRGIGKTTLNAWLVLWLMSTRPGISVICL  113 (511)
Q Consensus        80 ~aV~sgrG~GKS~l~a~l~lw~l~~~p~~kv~vt  113 (511)
                      +.+-++.|+|||+|+..++......  +.++.+.
T Consensus        44 lyl~G~~GsGKTHLl~a~~~~~~~~--~~~~~yl   75 (233)
T PRK08727         44 LYLSGPAGTGKTHLALSLCAAAEQA--GRSSAYL   75 (233)
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHHC--CCCEEEE
T ss_conf             9998999998899999999999827--9972884


No 455
>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=59.15  E-value=11  Score=16.51  Aligned_cols=157  Identities=13%  Similarity=0.150  Sum_probs=83.1

Q ss_pred             CCCCHHHHHHHHHHHHHHHCC-CCEEEEEECCHHHHHHHHHHHHHHHHHHCHHCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             765978999999999998089-9669998085899999999999999985500013444322222233344432111235
Q gi|254781215|r   86 RGIGKTTLNAWLVLWLMSTRP-GISVICLANSETQLKTTLWAEVSKWLSLLPNKHWFEMQSLSLHPAPWYSDVLHCSLGI  164 (511)
Q Consensus        86 rG~GKS~l~a~l~lw~l~~~p-~~kv~vtApt~~Q~~~ilw~Ei~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  164 (511)
                      =|+|||+++---|---+-..| |..++..+|++-     +|..=...++..-                            
T Consensus        10 aGtGKs~~~i~~Ik~ki~~~p~g~~iillVPdQ~-----TFq~E~~l~~~~e----------------------------   56 (1192)
T TIGR02773        10 AGTGKSTFIIDEIKQKIKENPLGKPIILLVPDQM-----TFQMEKALLNDIE----------------------------   56 (1192)
T ss_pred             CCCCHHHHHHHHHHHHHHCCCCCCCEEEECCCCC-----HHHHHHHHHCCCC----------------------------
T ss_conf             6875457888999999710789895378768852-----4899999816777----------------------------


Q ss_pred             CCCEEEEEECCCCCCCCCHHHHCCCCCCEEEEECCHHCCCHHHHH-HH-----HHHHCCCCCCEEEEEECCCCCCCCHHH
Q ss_conf             786169853035755610021202676149997111029978898-88-----888507998138998238998765567
Q gi|254781215|r  165 DSKHYSTMCRTYSEERPDTFVGHHNTYGMAIINDEASGTPDVINL-GI-----LGFLTERNANRFWIMTSNPRRLSGKFY  238 (511)
Q Consensus       165 ~~~~~~~~~~~~s~~~~ea~~G~h~~~~~lvI~DEAsgI~d~i~e-~i-----~~~Lt~~g~~~~~i~~~nP~~~~g~fy  238 (511)
                      .++...+...        ||.-  =.+.   |+-|..|....+.. +.     .-.+-+...  .|=++.+=.+..|+.-
T Consensus        57 ~~g~lraqvl--------SF~R--LA~r---VlqE~GG~tr~~l~~~G~~M~i~K~~ee~k~--~lkvy~~A~~~~GF~~  121 (1192)
T TIGR02773        57 LNGSLRAQVL--------SFSR--LAWR---VLQETGGLTRQFLTQAGIEMLIRKVIEEHKD--ELKVYQKASRKKGFLA  121 (1192)
T ss_pred             CCCCCCCEEE--------EHHH--HHHH---HHHHCCCCHHHHHHHHHHHHHHHHHHHHHCC--HHHHHHHHHCCCCHHH
T ss_conf             6874441132--------0447--6556---8763376026779887589999999986011--1247888623253489


Q ss_pred             HHHHCCCCCCEEEEEC--------------CCCCCCCCHHHHHHHHHHCCCCHHHHHHHHCCCCCCCCCCEE
Q ss_conf             6530352474179840--------------433677897789999975189801354443175666678737
Q gi|254781215|r  239 EIFNKPLDDWKRFQID--------------TRTVEGIDPSFHEGIIARYGLDSDVTRVEVCGQFPQQDIDSF  296 (511)
Q Consensus       239 ~~~~~~~~~w~~~~i~--------------~~~~p~~~~~~ie~~~~~~geds~~~r~evlgeFp~~~~~~~  296 (511)
                      ..-..-. ..+.+.++              .+-+|.+-..-++++.--|.    .|--...+.|.++.| .+
T Consensus       122 ~l~~~it-EfKry~v~pe~L~~~~~~~~~~~~~~~~~l~~KL~Dl~~iY~----~fe~~L~~~y~~~ED-~L  187 (1192)
T TIGR02773       122 KLSEMIT-EFKRYEVTPEDLRKAAEELEDSERRSERVLKEKLEDLSLIYQ----EFEERLADEYIDSED-QL  187 (1192)
T ss_pred             HHHHHHH-HHHHHCCCHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHH----HHHHHHCCCCCCCHH-HH
T ss_conf             9999988-762206898899999861013202441667766899999999----999987077577334-48


No 456
>TIGR02746 TraC-F-type type-IV secretion system protein TraC; InterPro: IPR014117   The proteins in this entry are found in the F, P and I-like type IV secretion systems. Gene symbols include TraC (F-type), TrbE/VirB4 (P-type) and TraU (I-type). The proteins contain the Walker A and B motifs and so are putative nucleotide triphosphatases..
Probab=59.09  E-value=11  Score=16.50  Aligned_cols=40  Identities=28%  Similarity=0.351  Sum_probs=23.8

Q ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEE--ECCHHHH
Q ss_conf             24650257659789999999999980899669998--0858999
Q gi|254781215|r   79 KGAISAGRGIGKTTLNAWLVLWLMSTRPGISVICL--ANSETQL  120 (511)
Q Consensus        79 r~aV~sgrG~GKS~l~a~l~lw~l~~~p~~kv~vt--Apt~~Q~  120 (511)
                      -++|.++=|.|||.++-.++.=.+.  -|++|.|+  --++.-|
T Consensus       491 N~~~~g~sG~GKSf~~Q~~~~~~L~--~G~kv~viDvG~Sy~KL  532 (900)
T TIGR02746       491 NIAVVGGSGAGKSFFMQELIVSVLS--RGGKVWVIDVGRSYKKL  532 (900)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHH--CCCEEEEEEECCCHHHH
T ss_conf             4899728898716879899999851--79848999607884888


No 457
>cd03225 ABC_cobalt_CbiO_domain1 Domain I of the ABC component of a cobalt transport family found in bacteria, archaea, and eukaryota.  The transition metal cobalt is an essential component of many enzymes and must be transported into cells in appropriate amounts when needed.  This ABC transport system of the CbiMNQO family is involved in cobalt transport in association with the cobalamin (vitamin B12) biosynthetic pathways.  Most of cobalt (Cbi) transport systems possess a separate CbiN component, the cobalt-binding periplasmic protein, and they are encoded by the conserved gene cluster cbiMNQO.  Both the CbiM and CbiQ proteins are integral cytoplasmic membrane proteins, and the CbiO protein has the linker peptide and the Walker A and B motifs commonly found in the ATPase components of the ABC-type transport systems.
Probab=59.04  E-value=8.8  Score=17.23  Aligned_cols=20  Identities=35%  Similarity=0.243  Sum_probs=17.8

Q ss_pred             EEEEECCCCCCHHHHHHHHH
Q ss_conf             24650257659789999999
Q gi|254781215|r   79 KGAISAGRGIGKTTLNAWLV   98 (511)
Q Consensus        79 r~aV~sgrG~GKS~l~a~l~   98 (511)
                      -+++....|.|||+++..++
T Consensus        29 i~~iiG~nGaGKSTLlk~i~   48 (211)
T cd03225          29 FVLIVGPNGSGKSTLLRLLN   48 (211)
T ss_pred             EEEEECCCCCCHHHHHHHHH
T ss_conf             99998899998999999996


No 458
>CHL00181 cbbX CbbX; Provisional
Probab=58.98  E-value=11  Score=16.49  Aligned_cols=72  Identities=19%  Similarity=0.125  Sum_probs=39.8

Q ss_pred             CEEEEECCHHCCC---------HHHHHHHHHHHCCCCCCEEEEEECCCCCCCCHHHHHHHCCCCCCEEEEECCCCCCCCC
Q ss_conf             1499971110299---------7889888888507998138998238998765567653035247417984043367789
Q gi|254781215|r  192 GMAIINDEASGTP---------DVINLGILGFLTERNANRFWIMTSNPRRLSGKFYEIFNKPLDDWKRFQIDTRTVEGID  262 (511)
Q Consensus       192 ~~lvI~DEAsgI~---------d~i~e~i~~~Lt~~g~~~~~i~~~nP~~~~g~fy~~~~~~~~~w~~~~i~~~~~p~~~  262 (511)
                      .+|+| |||..+.         .++.+.+...|.+...+.++|..|=|... ..|.....-.++++...    ..=|..+
T Consensus       124 GVLfI-DEAY~L~~~~~~~dfg~eaidtLl~~me~~~~~lvvI~AGY~~eM-~~fl~~NpGL~sRf~~~----i~F~dYt  197 (287)
T CHL00181        124 GVLFI-DEAYYLYKPDNERDYGAEAIEILLQVMENQRDDLVVIFAGYKDRM-DKFYESNPGLSSRVANH----VDFPDYT  197 (287)
T ss_pred             CEEEE-ECHHHHCCCCCCCCCHHHHHHHHHHHHHHCCCCEEEEEECCHHHH-HHHHHHCCCHHHHCCCE----EECCCCC
T ss_conf             87998-244653578899983799999999998707998899984678999-99998590478768872----3779859


Q ss_pred             HHHHHHH
Q ss_conf             7789999
Q gi|254781215|r  263 PSFHEGI  269 (511)
Q Consensus       263 ~~~ie~~  269 (511)
                      ++.+-++
T Consensus       198 ~~EL~~I  204 (287)
T CHL00181        198 PEELLQI  204 (287)
T ss_pred             HHHHHHH
T ss_conf             9999999


No 459
>KOG2355 consensus
Probab=58.92  E-value=7.9  Score=17.51  Aligned_cols=27  Identities=30%  Similarity=0.246  Sum_probs=17.0

Q ss_pred             CCCCCCEEEEEECCCCCCHHHHHHHHH
Q ss_conf             554210124650257659789999999
Q gi|254781215|r   72 NPNPEVFKGAISAGRGIGKTTLNAWLV   98 (511)
Q Consensus        72 ~~~~~~~r~aV~sgrG~GKS~l~a~l~   98 (511)
                      .++|...|+.+....|.|||++...+.
T Consensus        35 ldlp~gsRcLlVGaNGaGKtTlLKiLs   61 (291)
T KOG2355          35 LDLPAGSRCLLVGANGAGKTTLLKILS   61 (291)
T ss_pred             ECCCCCCEEEEEECCCCCHHHHHHHHC
T ss_conf             026889647998058875454698865


No 460
>PRK13632 cbiO cobalt transporter ATP-binding subunit; Provisional
Probab=58.91  E-value=8  Score=17.50  Aligned_cols=22  Identities=32%  Similarity=0.232  Sum_probs=18.2

Q ss_pred             CEEEEEECCCCCCHHHHHHHHH
Q ss_conf             0124650257659789999999
Q gi|254781215|r   77 VFKGAISAGRGIGKTTLNAWLV   98 (511)
Q Consensus        77 ~~r~aV~sgrG~GKS~l~a~l~   98 (511)
                      .-.+++....|+|||+++..+.
T Consensus        36 Ge~vaivG~nGsGKSTLlk~l~   57 (273)
T PRK13632         36 GEYVAILGHNGSGKSTISKILT   57 (273)
T ss_pred             CCEEEEECCCCCHHHHHHHHHH
T ss_conf             9899999999986999999997


No 461
>TIGR02640 gas_vesic_GvpN gas vesicle protein GvpN; InterPro: IPR013462    The GvpN protein is associated with the production of gas vesicles produced in some prokaryotes to give cells buoyancy , . It belongs to a larger family of ATPases .; GO: 0000166 nucleotide binding, 0005524 ATP binding, 0031412 gas vesicle organization and biogenesis, 0031411 gas vesicle.
Probab=58.85  E-value=8.2  Score=17.42  Aligned_cols=186  Identities=17%  Similarity=0.109  Sum_probs=97.1

Q ss_pred             CCEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEEECCHHHHHHHHHHHHHHHHHHCHHCCCCCCCCCCCCCCCCCC
Q ss_conf             10124650257659789999999999980899669998085899999999999999985500013444322222233344
Q gi|254781215|r   76 EVFKGAISAGRGIGKTTLNAWLVLWLMSTRPGISVICLANSETQLKTTLWAEVSKWLSLLPNKHWFEMQSLSLHPAPWYS  155 (511)
Q Consensus        76 ~~~r~aV~sgrG~GKS~l~a~l~lw~l~~~p~~kv~vtApt~~Q~~~ilw~Ei~k~~~~~~~~~~~~~~~~~~~~~~~~~  155 (511)
                      ..+=|+...+-|+|||+||-.++--    +.-+-+++.-+.+=.-+|.+ ++-....++             ...-.|.+
T Consensus        20 ~G~PvHl~GPaG~GKT~LA~hvA~~----r~RPV~l~~Gd~eL~~~DLv-G~~~g~~~~-------------kv~Dqfih   81 (265)
T TIGR02640        20 SGYPVHLRGPAGTGKTTLAMHVARK----RDRPVVLINGDAELTTSDLV-GSYAGYTRK-------------KVVDQFIH   81 (265)
T ss_pred             CCCCEEEECCCCCCHHHHHHHHHHH----CCCCEEEEECCCCCCCCCCC-CCCCCCEEE-------------EEEECCEE
T ss_conf             7886674478885568999999973----68968998658232654423-154675222-------------23201211


Q ss_pred             CCCCCCCCCCCCEEEEEECCCCCCCCCHHHHCCCCCCEEEEECCHHCCCHHHHHHHH-----HHHCCCC-----------
Q ss_conf             432111235786169853035755610021202676149997111029978898888-----8850799-----------
Q gi|254781215|r  156 DVLHCSLGIDSKHYSTMCRTYSEERPDTFVGHHNTYGMAIINDEASGTPDVINLGIL-----GFLTERN-----------  219 (511)
Q Consensus       156 ~~~~~~~~~~~~~~~~~~~~~s~~~~ea~~G~h~~~~~lvI~DEAsgI~d~i~e~i~-----~~Lt~~g-----------  219 (511)
                      .-.+.+ ..-...|... +..     .|   .+ ++.+ +|-||.+=..++.-+++.     +.|.=++           
T Consensus        82 nV~K~~-d~~~~~W~D~-rLt-----~A---v~-eG~T-LVYdEF~RskP~~nNVLLSvlEE~vL~LPg~~~~~~Yv~Vh  149 (265)
T TIGR02640        82 NVVKLE-DIVRQNWVDN-RLT-----LA---VR-EGFT-LVYDEFTRSKPETNNVLLSVLEEGVLELPGKRGESRYVDVH  149 (265)
T ss_pred             EEECCC-CCCCCCCCCC-HHH-----HH---HH-CCCE-EEECCCCCCCCHHHHHHHHHHHHHHHCCCCCCCCCCCEEEC
T ss_conf             134251-2200266783-578-----99---75-6972-76647578862045656755552321588878778722578


Q ss_pred             CCEEEEEECCCCCCCCHHHHHHHCCCCCCEEEEECCCCCCCCCHHHHHHHHHHCCCCHHHHHHHHCCCCC-CCCCC
Q ss_conf             8138998238998765567653035247417984043367789778999997518980135444317566-66787
Q gi|254781215|r  220 ANRFWIMTSNPRRLSGKFYEIFNKPLDDWKRFQIDTRTVEGIDPSFHEGIIARYGLDSDVTRVEVCGQFP-QQDID  294 (511)
Q Consensus       220 ~~~~~i~~~nP~~~~g~fy~~~~~~~~~w~~~~i~~~~~p~~~~~~ie~~~~~~geds~~~r~evlgeFp-~~~~~  294 (511)
                      +.=..|.||||.-..|. |+.+-..-++=.++.+++.|  ......|-..+-...+.+...-+++.-+|= .+++.
T Consensus       150 P~FR~IfTSNp~EYAGV-h~~QDALlDRL~ti~~D~~D--~~~e~ai~~~~t~~~~~~a~~IV~lv~~~R~a~g~e  222 (265)
T TIGR02640       150 PEFRVIFTSNPVEYAGV-HETQDALLDRLVTISMDYPD--EDTETAILRAKTDVAEESAATIVRLVRELRLASGDE  222 (265)
T ss_pred             CCCCEEECCCCCCCCCC-CCHHHHHHHHHCCCCCCCCC--HHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHCCCC
T ss_conf             87024631487010576-77166776644004578544--478999999860612467899999999984212553


No 462
>PRK13539 cytochrome c biogenesis protein CcmA; Provisional
Probab=58.82  E-value=8.8  Score=17.22  Aligned_cols=21  Identities=33%  Similarity=0.292  Sum_probs=17.4

Q ss_pred             EEEEEECCCCCCHHHHHHHHH
Q ss_conf             124650257659789999999
Q gi|254781215|r   78 FKGAISAGRGIGKTTLNAWLV   98 (511)
Q Consensus        78 ~r~aV~sgrG~GKS~l~a~l~   98 (511)
                      --+++....|.|||++...++
T Consensus        29 ei~~l~G~NGaGKTTLlk~i~   49 (206)
T PRK13539         29 EALVLTGPNGSGKTTLLRLLA   49 (206)
T ss_pred             CEEEEECCCCCCHHHHHHHHH
T ss_conf             499998999998999999995


No 463
>PRK07543 consensus
Probab=58.80  E-value=12  Score=16.47  Aligned_cols=58  Identities=22%  Similarity=0.224  Sum_probs=32.9

Q ss_pred             HHHHHHHHHHHHHCCCCCC-CCCCEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEEECCHHHH
Q ss_conf             9999999999874056555-42101246502576597899999999999808996699980858999
Q gi|254781215|r   55 QLEFMEVVDAHCLNSVNNP-NPEVFKGAISAGRGIGKTTLNAWLVLWLMSTRPGISVICLANSETQL  120 (511)
Q Consensus        55 Q~e~l~~i~~~~~~~~~~~-~~~~~r~aV~sgrG~GKS~l~a~l~lw~l~~~p~~kv~vtApt~~Q~  120 (511)
                      -.++-++|+++..+..+.+ .|.  .|.|.+|   ++..+   ..+-.+++.||-+|++..|++..-
T Consensus        70 ~~eLR~aia~~~~~~~g~~~~pd--~V~vt~G---~~~al---~~~~~al~~pGD~Vlv~~P~Y~~y  128 (400)
T PRK07543         70 IPELKQAICAKFKRENGLDYKPE--QVIVGTG---GKQIL---YNALMATLNPGDEVIIPAPYWVSY  128 (400)
T ss_pred             HHHHHHHHHHHHHHHHCCCCCCC--EEEEECC---CHHHH---HHHHHHHCCCCCEEEEECCCCCCC
T ss_conf             09999999999999848998804--2899278---26999---999998579999899827866553


No 464
>cd03236 ABC_RNaseL_inhibitor_domain1 The ATPase domain 1 of RNase L inhibitor.  The ABC ATPase, RNase L inhibitor (RLI), is a key enzyme in ribosomal biogenesis, formation of translation preinitiation complexes, and assembly of HIV capsids.  RLI s are not transport proteins and thus cluster with a group of soluble proteins that lack the transmembrane components commonly found in other members of the family.  Structurally, RLIs have an N-terminal Fe-S domain and two nucleotide binding domains which are arranged to form two composite active sites in their interface cleft.  RLI is one of the most conserved enzymes between archaea and eukaryotes with a sequence identity more than 48%.  The high degree of evolutionary conservation suggests that RLI performs a central role in archaeal and eukaryotic physiology.
Probab=58.66  E-value=8.6  Score=17.30  Aligned_cols=20  Identities=30%  Similarity=0.293  Sum_probs=17.2

Q ss_pred             EEEEECCCCCCHHHHHHHHH
Q ss_conf             24650257659789999999
Q gi|254781215|r   79 KGAISAGRGIGKTTLNAWLV   98 (511)
Q Consensus        79 r~aV~sgrG~GKS~l~a~l~   98 (511)
                      -+++....|.|||+++..++
T Consensus        28 i~gLiGpNGaGKSTLlk~i~   47 (255)
T cd03236          28 VLGLVGPNGIGKSTALKILA   47 (255)
T ss_pred             EEEEECCCCCCHHHHHHHHH
T ss_conf             99998999970999999996


No 465
>cd04125 RabA_like RabA-like subfamily.  RabA was first identified in D. discoideum, where its expression levels were compared to other Rabs in growing and developing cells.  The RabA mRNA levels were below the level of detection by Northern blot analysis, suggesting a very low level of expression.  The function of RabA remains unknown.  GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state.  Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization.  Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins.
Probab=58.64  E-value=9.4  Score=17.04  Aligned_cols=22  Identities=32%  Similarity=0.436  Sum_probs=18.2

Q ss_pred             EEEEEECCCCCCHHHHHHHHHH
Q ss_conf             1246502576597899999999
Q gi|254781215|r   78 FKGAISAGRGIGKTTLNAWLVL   99 (511)
Q Consensus        78 ~r~aV~sgrG~GKS~l~a~l~l   99 (511)
                      +|+.|....|+|||.++..++-
T Consensus         1 ~KivvvGd~~VGKTsli~r~~~   22 (188)
T cd04125           1 FKVVIIGDYGVGKSSLLKRFTE   22 (188)
T ss_pred             CEEEEECCCCCCHHHHHHHHHH
T ss_conf             9799999999789999999951


No 466
>cd03290 ABCC_SUR1_N The SUR domain 1.  The sulfonylurea receptor SUR is an ATP transporter of the ABCC/MRP family with tandem ATPase binding domains.  Unlike other ABC proteins, it has no intrinsic transport function, neither active nor passive, but associates with the potassium channel proteins Kir6.1 or Kir6.2 to form the ATP-sensitive potassium (K(ATP)) channel.  Within the channel complex, SUR serves as a regulatory subunit that fine-tunes the gating of Kir6.x in response to alterations in cellular metabolism.  It constitutes a major pharmaceutical target as it binds numerous drugs, K(ATP) channel openers and blockers, capable of up- or down-regulating channel activity.
Probab=58.63  E-value=9.1  Score=17.12  Aligned_cols=23  Identities=22%  Similarity=0.143  Sum_probs=18.2

Q ss_pred             CCEEEEEECCCCCCHHHHHHHHH
Q ss_conf             10124650257659789999999
Q gi|254781215|r   76 EVFKGAISAGRGIGKTTLNAWLV   98 (511)
Q Consensus        76 ~~~r~aV~sgrG~GKS~l~a~l~   98 (511)
                      ..-.++|...-|+|||++...++
T Consensus        26 ~Ge~~~IvG~sGsGKSTLl~~l~   48 (218)
T cd03290          26 TGQLTMIVGQVGCGKSSLLLAIL   48 (218)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHH
T ss_conf             99999999999980999999985


No 467
>cd01867 Rab8_Rab10_Rab13_like Rab8/Sec4/Ypt2.  Rab8/Sec4/Ypt2 are known or suspected to be involved in post-Golgi transport to the plasma membrane. It is likely that these Rabs have functions that are specific to the mammalian lineage and have no orthologs in plants. Rab8 modulates polarized membrane transport through reorganization of actin and microtubules, induces the formation of new surface extensions, and has an important role in directed membrane transport to cell surfaces. The Ypt2 gene of the fission yeast Schizosaccharomyces pombe encodes a member of the Ypt/Rab family of small GTP-binding proteins, related in sequence to Sec4p of Saccharomyces cerevisiae but closer to mammalian Rab8.  GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state.  Rabs are further regulated by guanine nucleotide dissociation inhi
Probab=58.57  E-value=10  Score=16.77  Aligned_cols=22  Identities=27%  Similarity=0.418  Sum_probs=19.1

Q ss_pred             CEEEEEECCCCCCHHHHHHHHH
Q ss_conf             0124650257659789999999
Q gi|254781215|r   77 VFKGAISAGRGIGKTTLNAWLV   98 (511)
Q Consensus        77 ~~r~aV~sgrG~GKS~l~a~l~   98 (511)
                      ++|+.+...-|+|||.++..++
T Consensus         3 ~~KivlvGd~~vGKTsli~r~~   24 (167)
T cd01867           3 LFKLLLIGDSGVGKSCLLLRFS   24 (167)
T ss_pred             EEEEEEECCCCCCHHHHHHHHH
T ss_conf             8999999999978899999996


No 468
>PRK13648 cbiO cobalt transporter ATP-binding subunit; Provisional
Probab=58.53  E-value=9  Score=17.15  Aligned_cols=24  Identities=21%  Similarity=0.220  Sum_probs=19.5

Q ss_pred             CCEEEEEECCCCCCHHHHHHHHHH
Q ss_conf             101246502576597899999999
Q gi|254781215|r   76 EVFKGAISAGRGIGKTTLNAWLVL   99 (511)
Q Consensus        76 ~~~r~aV~sgrG~GKS~l~a~l~l   99 (511)
                      ..-.+++-...|+|||+++..++=
T Consensus        34 ~Ge~vaiiG~sGsGKSTLl~ll~G   57 (269)
T PRK13648         34 KGQWTSIVGHNGSGKSTIAKLMIG   57 (269)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHC
T ss_conf             998999999999979999999964


No 469
>cd03240 ABC_Rad50 The catalytic domains of Rad50 are similar to the ATP-binding cassette of ABC transporters, but are not associated with membrane-spanning domains.  The conserved ATP-binding motifs common to Rad50 and the ABC transporter family include the Walker A and Walker B motifs, the Q loop, a histidine residue in the switch region, a D-loop, and a conserved LSGG sequence.  This conserved sequence, LSGG, is the most specific and characteristic motif of this family and is thus known as the ABC signature sequence.
Probab=58.51  E-value=9.1  Score=17.14  Aligned_cols=20  Identities=35%  Similarity=0.297  Sum_probs=16.3

Q ss_pred             EEEEECCCCCCHHHHHHHHH
Q ss_conf             24650257659789999999
Q gi|254781215|r   79 KGAISAGRGIGKTTLNAWLV   98 (511)
Q Consensus        79 r~aV~sgrG~GKS~l~a~l~   98 (511)
                      -+++....|.|||++...+.
T Consensus        24 itaivG~NGaGKSTLl~~i~   43 (204)
T cd03240          24 LTLIVGQNGAGKTTIIEALK   43 (204)
T ss_pred             EEEEECCCCCCHHHHHHHHH
T ss_conf             89999899999999999986


No 470
>cd03222 ABC_RNaseL_inhibitor The ABC ATPase RNase L inhibitor (RLI) is a key enzyme in ribosomal biogenesis, formation of translation preinitiation complexes, and assembly of HIV capsids.  RLI's are not transport proteins, and thus cluster with a group of soluble proteins that lack the transmembrane components commonly found in other members of the family.  Structurally, RLI's have an N-terminal Fe-S domain and two nucleotide-binding domains, which are arranged to form two composite active sites in their interface cleft.  RLI is one of the most conserved enzymes between archaea and eukaryotes with a sequence identity more than 48%.  The high degree of evolutionary conservation suggests that RLI performs a central role in archaeal and eukaryotic physiology.
Probab=58.50  E-value=9.1  Score=17.13  Aligned_cols=21  Identities=33%  Similarity=0.191  Sum_probs=18.0

Q ss_pred             EEEEEECCCCCCHHHHHHHHH
Q ss_conf             124650257659789999999
Q gi|254781215|r   78 FKGAISAGRGIGKTTLNAWLV   98 (511)
Q Consensus        78 ~r~aV~sgrG~GKS~l~a~l~   98 (511)
                      -.+++....|.|||++...++
T Consensus        26 Eiv~ilGpNGaGKSTllk~i~   46 (177)
T cd03222          26 EVIGIVGPNGTGKTTAVKILA   46 (177)
T ss_pred             CEEEEECCCCCCHHHHHHHHH
T ss_conf             899998999999999999996


No 471
>PRK10751 molybdopterin-guanine dinucleotide biosynthesis protein B; Provisional
Probab=58.47  E-value=12  Score=16.44  Aligned_cols=33  Identities=39%  Similarity=0.291  Sum_probs=26.2

Q ss_pred             EEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEEE
Q ss_conf             46502576597899999999999808996699980
Q gi|254781215|r   80 GAISAGRGIGKTTLNAWLVLWLMSTRPGISVICLA  114 (511)
Q Consensus        80 ~aV~sgrG~GKS~l~a~l~lw~l~~~p~~kv~vtA  114 (511)
                      ++|.+-.|+|||+|+.-++-++.-  .|-+|.++=
T Consensus         5 i~ivG~s~SGKTTLi~kli~~l~~--~G~rV~~IK   37 (170)
T PRK10751          5 LAIAAWSGTGKTTLLKKLIPALCA--RGIRPGLIK   37 (170)
T ss_pred             EEEEECCCCCHHHHHHHHHHHHHH--CCCEEEEEE
T ss_conf             999946999999999999999998--798499994


No 472
>PRK10247 putative ABC transporter ATP-binding protein YbbL; Provisional
Probab=58.33  E-value=9.2  Score=17.09  Aligned_cols=23  Identities=26%  Similarity=0.137  Sum_probs=18.7

Q ss_pred             CEEEEEECCCCCCHHHHHHHHHH
Q ss_conf             01246502576597899999999
Q gi|254781215|r   77 VFKGAISAGRGIGKTTLNAWLVL   99 (511)
Q Consensus        77 ~~r~aV~sgrG~GKS~l~a~l~l   99 (511)
                      .-.+++....|.|||+++..++=
T Consensus        33 Ge~~~i~G~sGsGKSTLlk~i~g   55 (225)
T PRK10247         33 GEFKLITGPSGCGKSTLLKIVAS   55 (225)
T ss_pred             CCEEEEECCCCCCHHHHHHHHHC
T ss_conf             96999999999999999999964


No 473
>TIGR01026 fliI_yscN ATPase FliI/YscN family; InterPro: IPR005714    Proteins in this entry show extensive homology to the ATP synthase F1 beta subunit, and are involved in type III protein secretion. They fall into the two separate functional groups outlined below.   The first group, exemplified by the Salmonella typhimurium FliI protein (P26465 from SWISSPROT), is needed for flagellar assembly. Most structural components of the bacterial flagellum are translocated through the central channel of the growing flagellar structure by the type III flagellar protein-export apparatus in an ATPase-driven manner, to be assembled at the growing end. FliI is the ATPase that couples ATP hydrolysis to the translocation reaction , .   The second group couples ATP hydrolysis to protein translocation in non-flagellar type III secretion systems. Often these systems are involved in virulence and pathogenicity. YscN (P40290 from SWISSPROT) from pathogenic Yersinia species, for example, energises the injection of antihost factors directly into eukaryotic cells, thus overcoming host defences .; GO: 0016887 ATPase activity, 0009058 biosynthetic process, 0015031 protein transport, 0005737 cytoplasm.
Probab=58.30  E-value=6  Score=18.26  Aligned_cols=60  Identities=20%  Similarity=0.171  Sum_probs=32.6

Q ss_pred             CCHHHHHHHHHHHHHHHHCCCCCCCC--CCEEEEEECCCCCCHHHHHHHHHH-HHHHHCCCCEEEEEE
Q ss_conf             84589999999999987405655542--101246502576597899999999-999808996699980
Q gi|254781215|r   50 APRSWQLEFMEVVDAHCLNSVNNPNP--EVFKGAISAGRGIGKTTLNAWLVL-WLMSTRPGISVICLA  114 (511)
Q Consensus        50 ~P~~WQ~e~l~~i~~~~~~~~~~~~~--~~~r~aV~sgrG~GKS~l~a~l~l-w~l~~~p~~kv~vtA  114 (511)
                      .|.+=+|..++++-.-=.+.-+-=++  -.=|+-+=||=|+|||+|+.|++- .     ..+-|.|+|
T Consensus       144 ~~nPl~R~~i~~~~~tGVR~iD~LLTvGkGQR~GIFAGSGVGKStLlGMIARn~-----~~ADv~ViA  206 (455)
T TIGR01026       144 PINPLKREPIREILSTGVRSIDGLLTVGKGQRIGIFAGSGVGKSTLLGMIARNN-----TEADVNVIA  206 (455)
T ss_pred             CCCCCCCCCCHHHEECCCEEECCCCCCCCCCCEEEEECCCCCHHHHHHHHHHCC-----CCCCEEEEE
T ss_conf             988667630002100364531010355566501355037600344566763006-----789827998


No 474
>PRK13650 cbiO cobalt transporter ATP-binding subunit; Provisional
Probab=58.29  E-value=8.7  Score=17.25  Aligned_cols=22  Identities=23%  Similarity=0.006  Sum_probs=17.9

Q ss_pred             EEEEEECCCCCCHHHHHHHHHH
Q ss_conf             1246502576597899999999
Q gi|254781215|r   78 FKGAISAGRGIGKTTLNAWLVL   99 (511)
Q Consensus        78 ~r~aV~sgrG~GKS~l~a~l~l   99 (511)
                      -.+++....|.|||+++..++=
T Consensus        31 E~vaivG~nGsGKSTL~~~l~G   52 (276)
T PRK13650         31 EWLSIIGHNGSGKSTTVRLIDG   52 (276)
T ss_pred             CEEEEECCCCCHHHHHHHHHHC
T ss_conf             8999999999879999999973


No 475
>KOG0343 consensus
Probab=58.24  E-value=12  Score=16.41  Aligned_cols=280  Identities=14%  Similarity=0.076  Sum_probs=127.1

Q ss_pred             HHHHHHHHHCHHHHHHHHHHHHHHCCCCC-CCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCCCH
Q ss_conf             88899987070666528866776421455-77756555784589999999999987405655542101246502576597
Q gi|254781215|r   12 EQKLFDLMWSDEIKLSFSNFVLHFFPWGE-KGTPLEGFSAPRSWQLEFMEVVDAHCLNSVNNPNPEVFKGAISAGRGIGK   90 (511)
Q Consensus        12 ~~~~~~~~~~~~~~~~~~~~~~~~~~w~~-~~~~~~~~~~P~~WQ~e~l~~i~~~~~~~~~~~~~~~~r~aV~sgrG~GK   90 (511)
                      -++|+..|-.-. ...|..|.-+-..|-. +|-.-..|..|-+-|++.+-    +-..+        .-|.=+|-.|+||
T Consensus        53 i~~l~~ky~ei~-~~~~~kF~dlpls~~t~kgLke~~fv~~teiQ~~~Ip----~aL~G--------~DvlGAAkTGSGK  119 (758)
T KOG0343          53 IEELKQKYAEID-STTIKKFADLPLSQKTLKGLKEAKFVKMTEIQRDTIP----MALQG--------HDVLGAAKTGSGK  119 (758)
T ss_pred             HHHHHHHHHHHH-HHHHHHHHHCCCCHHHHHHHHHCCCCCHHHHHHHHCC----HHCCC--------CCCCCCCCCCCCC
T ss_conf             999999999864-3425568748876678876765487569999876414----22057--------5000102358884


Q ss_pred             HHHHHHHHHHHHHH-----CCCCEEEEEECCHHHHHHHHHHHHHHHHHHCHHCCCCCCCCCCCCCCCCCCCCCC--CCCC
Q ss_conf             89999999999980-----8996699980858999999999999999855000134443222222333444321--1123
Q gi|254781215|r   91 TTLNAWLVLWLMST-----RPGISVICLANSETQLKTTLWAEVSKWLSLLPNKHWFEMQSLSLHPAPWYSDVLH--CSLG  163 (511)
Q Consensus        91 S~l~a~l~lw~l~~-----~p~~kv~vtApt~~Q~~~ilw~Ei~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~  163 (511)
                      |-..-+-+|-.+.-     ..|--++++.||..-+-.+ |.-|.+.-..    |.|.+        +...+...  ....
T Consensus       120 TLAFlvPvlE~L~r~kWs~~DGlGalIISPTRELA~Qt-FevL~kvgk~----h~fSa--------GLiiGG~~~k~E~e  186 (758)
T KOG0343         120 TLAFLVPVLEALYRLKWSPTDGLGALIISPTRELALQT-FEVLNKVGKH----HDFSA--------GLIIGGKDVKFELE  186 (758)
T ss_pred             EEEEHHHHHHHHHHCCCCCCCCCEEEEECCHHHHHHHH-HHHHHHHHHC----CCCCC--------CEEECCCHHHHHHH
T ss_conf             46543999999997177887883269956529999999-9999987520----56431--------13665712688997


Q ss_pred             CCCCEEEEEECCCCCC-CCCHHHHCCCCCCEEEEECCHHCCCHH-HHHHHHHHHCCCCC-CEEEEEECCCCCCCCHHHHH
Q ss_conf             5786169853035755-610021202676149997111029978-89888888507998-13899823899876556765
Q gi|254781215|r  164 IDSKHYSTMCRTYSEE-RPDTFVGHHNTYGMAIINDEASGTPDV-INLGILGFLTERNA-NRFWIMTSNPRRLSGKFYEI  240 (511)
Q Consensus       164 ~~~~~~~~~~~~~s~~-~~ea~~G~h~~~~~lvI~DEAsgI~d~-i~e~i~~~Lt~~g~-~~~~i~~~nP~~~~g~fy~~  240 (511)
                      .-+..-+.++.+-+.- .-+-.-+++..+.-++|+|||.-+=|- +-..+.+.++.--. +--++.-.++++..-.....
T Consensus       187 Ri~~mNILVCTPGRLLQHmde~~~f~t~~lQmLvLDEADR~LDMGFk~tL~~Ii~~lP~~RQTLLFSATqt~svkdLaRL  266 (758)
T KOG0343         187 RISQMNILVCTPGRLLQHMDENPNFSTSNLQMLVLDEADRMLDMGFKKTLNAIIENLPKKRQTLLFSATQTKSVKDLARL  266 (758)
T ss_pred             HHHCCCEEEECHHHHHHHHHHCCCCCCCCCEEEEECCHHHHHHHHHHHHHHHHHHHCCHHHEEEEEECCCCHHHHHHHHH
T ss_conf             66257769966178998754167878776047873208889877678889999873772330466632551139999975


Q ss_pred             HHCCCCCCEEEEECC-CCCCC-----------CC-----------------------HH---HHHHHH----------HH
Q ss_conf             303524741798404-33677-----------89-----------------------77---899999----------75
Q gi|254781215|r  241 FNKPLDDWKRFQIDT-RTVEG-----------ID-----------------------PS---FHEGII----------AR  272 (511)
Q Consensus       241 ~~~~~~~w~~~~i~~-~~~p~-----------~~-----------------------~~---~ie~~~----------~~  272 (511)
                      .. ..+.+...+... ...|-           .+                       ..   ++-+.-          .-
T Consensus       267 sL-~dP~~vsvhe~a~~atP~~L~Q~y~~v~l~~Ki~~L~sFI~shlk~K~iVF~SscKqvkf~~e~F~rlrpg~~l~~L  345 (758)
T KOG0343         267 SL-KDPVYVSVHENAVAATPSNLQQSYVIVPLEDKIDMLWSFIKSHLKKKSIVFLSSCKQVKFLYEAFCRLRPGIPLLAL  345 (758)
T ss_pred             HC-CCCCEEEEECCCCCCCHHHHHHEEEEEEHHHHHHHHHHHHHHCCCCCEEEEEEHHHHHHHHHHHHHHCCCCCCEEEE
T ss_conf             34-79857997235333683645332799760147899999998452543699986006899999999850899832542


Q ss_pred             CCCCHHHHHHHHCCCCCCCCCCEEECHHHHHHHHHCCCCCCCCCEEEEEEE
Q ss_conf             189801354443175666678737559999886407653189970899962
Q gi|254781215|r  273 YGLDSDVTRVEVCGQFPQQDIDSFIPLNIIEEALNREPCPDPYAPLIMGCD  323 (511)
Q Consensus       273 ~geds~~~r~evlgeFp~~~~~~~i~~~~ie~a~~r~~~~~~~~~~viGvD  323 (511)
                      +|.-+-.-|.++..+|.+....++|..+..-...+.     |.-.+|+-+|
T Consensus       346 ~G~~~Q~~R~ev~~~F~~~~~~vLF~TDv~aRGLDF-----paVdwViQ~D  391 (758)
T KOG0343         346 HGTMSQKKRIEVYKKFVRKRAVVLFCTDVAARGLDF-----PAVDWVIQVD  391 (758)
T ss_pred             CCCHHHHHHHHHHHHHHHHCCEEEEEEHHHHCCCCC-----CCCCEEEEEC
T ss_conf             163137788999999987555589860255436898-----6433699806


No 476
>cd01861 Rab6 Rab6 subfamily.  Rab6 is involved in microtubule-dependent transport pathways through the Golgi and from endosomes to the Golgi. Rab6A of mammals is implicated in retrograde transport through the Golgi stack, and is also required for a slow, COPI-independent, retrograde transport pathway from the Golgi to the endoplasmic reticulum (ER). This pathway may allow Golgi residents to be recycled through the ER for scrutiny by ER quality-control systems. Yeast Ypt6p, the homolog of the mammalian Rab6 GTPase, is not essential for cell viability. Ypt6p acts in endosome-to-Golgi, in intra-Golgi retrograde transport, and possibly also in Golgi-to-ER trafficking.  GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state.  Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate
Probab=58.22  E-value=9.5  Score=17.00  Aligned_cols=20  Identities=20%  Similarity=0.332  Sum_probs=17.5

Q ss_pred             EEEEECCCCCCHHHHHHHHH
Q ss_conf             24650257659789999999
Q gi|254781215|r   79 KGAISAGRGIGKTTLNAWLV   98 (511)
Q Consensus        79 r~aV~sgrG~GKS~l~a~l~   98 (511)
                      |+.|....|+|||+|+..++
T Consensus         2 Ki~vvG~~~vGKTsli~r~~   21 (161)
T cd01861           2 KLVFLGDQSVGKTSIITRFM   21 (161)
T ss_pred             EEEEECCCCCCHHHHHHHHH
T ss_conf             79999979978999999993


No 477
>COG1373 Predicted ATPase (AAA+ superfamily) [General function prediction only]
Probab=58.11  E-value=12  Score=16.40  Aligned_cols=37  Identities=27%  Similarity=0.271  Sum_probs=23.3

Q ss_pred             EEEEECCHHCCCHHHHHHHHHHHCCCCCCEEEEEECCCC
Q ss_conf             499971110299788988888850799813899823899
Q gi|254781215|r  193 MAIINDEASGTPDVINLGILGFLTERNANRFWIMTSNPR  231 (511)
Q Consensus       193 ~lvI~DEAsgI~d~i~e~i~~~Lt~~g~~~~~i~~~nP~  231 (511)
                      ..+++||.+.+++  |+-.-..+-+.+....++..||..
T Consensus        96 ~yifLDEIq~v~~--W~~~lk~l~d~~~~~v~itgsss~  132 (398)
T COG1373          96 SYIFLDEIQNVPD--WERALKYLYDRGNLDVLITGSSSS  132 (398)
T ss_pred             CEEEEEEECCCHH--HHHHHHHHHCCCCCEEEEECCCHH
T ss_conf             4599983337610--899999997567750999837167


No 478
>PRK10876 recB exonuclease V subunit beta; Provisional
Probab=57.93  E-value=12  Score=16.38  Aligned_cols=52  Identities=10%  Similarity=0.065  Sum_probs=34.5

Q ss_pred             HCCCCCCEEEEECCHHCCCHHHHHHHHHHHCCCCCCEEEEEECCCCCCCCHHHH
Q ss_conf             202676149997111029978898888885079981389982389987655676
Q gi|254781215|r  186 GHHNTYGMAIINDEASGTPDVINLGILGFLTERNANRFWIMTSNPRRLSGKFYE  239 (511)
Q Consensus       186 G~h~~~~~lvI~DEAsgI~d~i~e~i~~~Lt~~g~~~~~i~~~nP~~~~g~fy~  239 (511)
                      -++..+. .+.+||....+..=|+.+........ ..-+++.|-|.-.-+.|+.
T Consensus       373 ~l~~ry~-~iLIDEFQDTd~~Q~~I~~~l~~~~~-~~~LfmVGDpKQSIY~FRg  424 (1181)
T PRK10876        373 AIRTRFP-VAMIDEFQDTDPQQYRIFRRIWGHQP-ETALLLIGDPKQAIYAFRG  424 (1181)
T ss_pred             HHHHHCC-EEEEHHHCCCCHHHHHHHHHHHCCCC-CCCEEEEECCHHHHHHCCC
T ss_conf             9985185-64402320488999999999964799-8816998264366552256


No 479
>cd00157 Rho Rho (Ras homology) family.  Members of the Rho family include RhoA, Cdc42, Rac, Rnd, Wrch1, RhoBTB, and Rop.  There are 22 human Rho family members identified currently.  These proteins are all involved in the reorganization of the actin cytoskeleton in response to external stimuli.  They also have roles in cell transformation by Ras in cytokinesis, in focal adhesion formation and in the stimulation of stress-activated kinase.  These various functions are controlled through distinct effector proteins and mediated through a GTP-binding/GTPase cycle involving three classes of regulating proteins: GAPs (GTPase-activating proteins), GEFs (guanine nucleotide exchange factors), and GDIs (guanine nucleotide dissociation inhibitors).  Most Rho proteins contain a lipid modification site at the C-terminus, with a typical sequence motif CaaX, where a = an aliphatic amino acid and X = any amino acid.  Lipid binding is essential for membrane attachment, a key feature of most Rho protein
Probab=57.88  E-value=9.8  Score=16.91  Aligned_cols=21  Identities=24%  Similarity=0.221  Sum_probs=17.8

Q ss_pred             EEEEEECCCCCCHHHHHHHHH
Q ss_conf             124650257659789999999
Q gi|254781215|r   78 FKGAISAGRGIGKTTLNAWLV   98 (511)
Q Consensus        78 ~r~aV~sgrG~GKS~l~a~l~   98 (511)
                      +|+.+....|+|||.++..++
T Consensus         1 iKi~llGd~~VGKTsli~r~~   21 (171)
T cd00157           1 IKIVVVGDGAVGKTCLLISYT   21 (171)
T ss_pred             CEEEEECCCCCCHHHHHHHHH
T ss_conf             989999999966999999996


No 480
>cd04138 H_N_K_Ras_like H-Ras/N-Ras/K-Ras subfamily.  H-Ras, N-Ras, and K-Ras4A/4B are the prototypical members of the Ras family.  These isoforms generate distinct signal outputs despite interacting with a common set of activators and effectors, and are strongly associated with oncogenic progression in tumor initiation.  Mutated versions of Ras that are insensitive to GAP stimulation (and are therefore constitutively active) are found in a significant fraction of human cancers.  Many Ras guanine nucleotide exchange factors (GEFs) have been identified.  They are sequestered in the cytosol until activation by growth factors triggers recruitment to the plasma membrane or Golgi, where the GEF colocalizes with Ras.  Active (GTP-bound) Ras interacts with several effector proteins that stimulate a variety of diverse cytoplasmic signaling activities.  Some are known to positively mediate the oncogenic properties of Ras, including Raf, phosphatidylinositol 3-kinase (PI3K), RalGEFs, and Tiam1.  
Probab=57.69  E-value=11  Score=16.65  Aligned_cols=22  Identities=27%  Similarity=0.519  Sum_probs=18.7

Q ss_pred             EEEEEECCCCCCHHHHHHHHHH
Q ss_conf             1246502576597899999999
Q gi|254781215|r   78 FKGAISAGRGIGKTTLNAWLVL   99 (511)
Q Consensus        78 ~r~aV~sgrG~GKS~l~a~l~l   99 (511)
                      +|+.+....|+|||.++..++-
T Consensus         2 ~KvvlvGd~~VGKTsli~r~~~   23 (162)
T cd04138           2 YKLVVVGAGGVGKSALTIQLIQ   23 (162)
T ss_pred             EEEEEECCCCCCHHHHHHHHHH
T ss_conf             3999989999889999999983


No 481
>COG3421 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=57.69  E-value=12  Score=16.36  Aligned_cols=32  Identities=25%  Similarity=0.231  Sum_probs=21.3

Q ss_pred             CCCCCHHHHHHHHHHHHHHHCCCCEEEEEECCH
Q ss_conf             576597899999999999808996699980858
Q gi|254781215|r   85 GRGIGKTTLNAWLVLWLMSTRPGISVICLANSE  117 (511)
Q Consensus        85 grG~GKS~l~a~l~lw~l~~~p~~kv~vtApt~  117 (511)
                      ..|.|||.++|.|||....... -+.+..-|..
T Consensus         5 atgsgkt~~ma~lil~~y~kgy-r~flffvnq~   36 (812)
T COG3421           5 ATGSGKTLVMAGLILECYKKGY-RNFLFFVNQA   36 (812)
T ss_pred             CCCCCHHHHHHHHHHHHHHHCH-HHEEEEECCH
T ss_conf             3588700599999999997340-4189985211


No 482
>TIGR02173 cyt_kin_arch cytidylate kinase, putative; InterPro: IPR011892    Proteins in this family are believed to be cytidylate kinase. Members of this family are found in the archaea and in spirochaetes, and differ considerably from the common bacterial form of cytidylate kinase described by IPR003136 from INTERPRO.; GO: 0004127 cytidylate kinase activity, 0005524 ATP binding, 0006139 nucleobase nucleoside nucleotide and nucleic acid metabolic process.
Probab=57.63  E-value=8.8  Score=17.21  Aligned_cols=36  Identities=31%  Similarity=0.182  Sum_probs=25.3

Q ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEEECCHHHH
Q ss_conf             246502576597899999999999808996699980858999
Q gi|254781215|r   79 KGAISAGRGIGKTTLNAWLVLWLMSTRPGISVICLANSETQL  120 (511)
Q Consensus        79 r~aV~sgrG~GKS~l~a~l~lw~l~~~p~~kv~vtApt~~Q~  120 (511)
                      -+.|+..=|+|||++|..++--+-+      =.+.|...+|+
T Consensus         2 ~I~ISGpPGSGktTvA~~lA~~Lsl------~~iSaG~iRel   37 (173)
T TIGR02173         2 IITISGPPGSGKTTVAKILAEKLSL------KLISAGDIREL   37 (173)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHCCC------CEECCCHHHHH
T ss_conf             7887358968647899999986398------31202007889


No 483
>cd00876 Ras Ras family.  The Ras family of the Ras superfamily includes classical N-Ras, H-Ras, and K-Ras, as well as R-Ras, Rap, Ral, Rheb, Rhes, ARHI, RERG, Rin/Rit, RSR1, RRP22, Ras2, Ras-dva, and RGK proteins.  Ras proteins regulate cell growth, proliferation and differentiation.  Ras is activated by guanine nucleotide exchange factors (GEFs) that release GDP and allow GTP binding.  Many RasGEFs have been identified.  These are sequestered in the cytosol until activation by growth factors triggers recruitment to the plasma membrane or Golgi, where the GEF colocalizes with Ras.  Active GTP-bound Ras interacts with several effector proteins: among the best characterized are the Raf kinases, phosphatidylinositol 3-kinase (PI3K), RalGEFs and NORE/MST1.  Most Ras proteins contain a lipid modification site at the C-terminus, with a typical sequence motif CaaX, where a = an aliphatic amino acid and X = any amino acid.  Lipid binding is essential for membrane attachment, a key feature of m
Probab=57.60  E-value=9.3  Score=17.08  Aligned_cols=21  Identities=24%  Similarity=0.409  Sum_probs=17.3

Q ss_pred             EEEEECCCCCCHHHHHHHHHH
Q ss_conf             246502576597899999999
Q gi|254781215|r   79 KGAISAGRGIGKTTLNAWLVL   99 (511)
Q Consensus        79 r~aV~sgrG~GKS~l~a~l~l   99 (511)
                      |+.|....|+|||.++..++-
T Consensus         1 Ki~ivG~~~vGKTsli~r~~~   21 (160)
T cd00876           1 KVVVLGAGGVGKSAITIQFVK   21 (160)
T ss_pred             CEEEECCCCCCHHHHHHHHHH
T ss_conf             999999699679999999961


No 484
>cd03250 ABCC_MRP_domain1 Domain 1 of the ABC subfamily C.  This family is also known as MRP (mulrtidrug resisitance-associated protein).  Some of the MRP members have five additional transmembrane segments in their N-terminas, but the function of these additional membrane-spanning domains is not clear.  The MRP was found in the multidrug-resisting lung cancer cell in which p-glycoprotein was not overexpressed. MRP exports glutathione by drug stimulation, as well as, certain substrates in conjugated forms with anions, such as glutathione, glucuronate, and sulfate.
Probab=57.57  E-value=9.1  Score=17.14  Aligned_cols=25  Identities=32%  Similarity=0.215  Sum_probs=19.8

Q ss_pred             CCCEEEEEECCCCCCHHHHHHHHHH
Q ss_conf             2101246502576597899999999
Q gi|254781215|r   75 PEVFKGAISAGRGIGKTTLNAWLVL   99 (511)
Q Consensus        75 ~~~~r~aV~sgrG~GKS~l~a~l~l   99 (511)
                      +..-.+++...-|.|||+++..++=
T Consensus        29 ~~Ge~~~IvG~sGsGKSTLl~~i~G   53 (204)
T cd03250          29 PKGELVAIVGPVGSGKSSLLSALLG   53 (204)
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHCC
T ss_conf             6998999999999858999999818


No 485
>pfam03029 ATP_bind_1 Conserved hypothetical ATP binding protein. Members of this family are found in a range of archaea and eukaryotes and have hypothesized ATP binding activity.
Probab=57.49  E-value=12  Score=16.33  Aligned_cols=32  Identities=31%  Similarity=0.324  Sum_probs=22.9

Q ss_pred             EECCCCCCHHHHHHHHHHHHHHHCCCCEEEEE
Q ss_conf             50257659789999999999980899669998
Q gi|254781215|r   82 ISAGRGIGKTTLNAWLVLWLMSTRPGISVICL  113 (511)
Q Consensus        82 V~sgrG~GKS~l~a~l~lw~l~~~p~~kv~vt  113 (511)
                      |..+-|+|||++.+.+.-|.-.......++=.
T Consensus         1 ViGpaGSGKTT~~~~l~~~l~~~~r~~~vvNL   32 (234)
T pfam03029         1 VVGGAGSGKTTFVGALSEILPLRGRSVYVVNL   32 (234)
T ss_pred             CCCCCCCCHHHHHHHHHHHHHHCCCCEEEEEC
T ss_conf             98989898899999999999977997599978


No 486
>pfam07015 VirC1 VirC1 protein. This family consists of several bacterial VirC1 proteins. In Agrobacterium tumefaciens, a cis-active 24-base-pair sequence adjacent to the right border of the T-DNA, called overdrive, stimulates tumour formation by increasing the level of T-DNA processing. It is thought that the virC operon which enhances T-DNA processing probably does so because the VirC1 protein interacts with overdrive. It has now been shown that the virC1 gene product binds to overdrive but not to the right border of T-DNA.
Probab=57.44  E-value=12  Score=16.33  Aligned_cols=47  Identities=30%  Similarity=0.277  Sum_probs=28.7

Q ss_pred             EEEEC-CCCCCHHHHHHHHHHHHHHHCCCCEEEEEECCHHHHHHHHHHHHH
Q ss_conf             46502-576597899999999999808996699980858999999999999
Q gi|254781215|r   80 GAISA-GRGIGKTTLNAWLVLWLMSTRPGISVICLANSETQLKTTLWAEVS  129 (511)
Q Consensus        80 ~aV~s-grG~GKS~l~a~l~lw~l~~~p~~kv~vtApt~~Q~~~ilw~Ei~  129 (511)
                      +++.+ ==|+|||+++..++..+..  .|.+|.++=..-+| .-.-|.+..
T Consensus         4 i~~~~~KGG~GKtT~a~~la~~~~~--~g~~V~liD~Dpq~-s~~~W~~~a   51 (231)
T pfam07015         4 ITFCSFKGGAGKTTALMGLCSALAS--DGKRVALFEADENR-PLTKWRENA   51 (231)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHH--CCCEEEEEECCCCC-CHHHHHHHH
T ss_conf             9996179986599999999999996--89959999689986-889999987


No 487
>pfam06733 DEAD_2 DEAD_2. This represents a conserved region within a number of RAD3-like DNA-binding helicases that are seemingly ubiquitous - members include proteins of eukaryotic, bacterial and archaeal origin. RAD3 is involved in nucleotide excision repair, and forms part of the transcription factor TFIIH in yeast.
Probab=57.33  E-value=3.9  Score=19.44  Aligned_cols=24  Identities=25%  Similarity=0.141  Sum_probs=16.7

Q ss_pred             EEEEECCHHCCCHHHHHHHHHHHC
Q ss_conf             499971110299788988888850
Q gi|254781215|r  193 MAIINDEASGTPDVINLGILGFLT  216 (511)
Q Consensus       193 ~lvI~DEAsgI~d~i~e~i~~~Lt  216 (511)
                      .++|+|||+.|++..-++..-.+|
T Consensus       141 ~IvI~DEAHNl~~~~~~~~S~~ls  164 (168)
T pfam06733       141 SIVIFDEAHNIEDVCISSLSFEIS  164 (168)
T ss_pred             EEEEEECCCCHHHHHHHHCCCEEC
T ss_conf             499998813759999996187615


No 488
>PRK10867 signal recognition particle protein; Provisional
Probab=57.24  E-value=12  Score=16.31  Aligned_cols=96  Identities=16%  Similarity=0.006  Sum_probs=53.0

Q ss_pred             HCHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCC----CEEEEEECCCCCCHHHHHH
Q ss_conf             070666528866776421455777565557845899999999999874056555421----0124650257659789999
Q gi|254781215|r   20 WSDEIKLSFSNFVLHFFPWGEKGTPLEGFSAPRSWQLEFMEVVDAHCLNSVNNPNPE----VFKGAISAGRGIGKTTLNA   95 (511)
Q Consensus        20 ~~~~~~~~~~~~~~~~~~w~~~~~~~~~~~~P~~WQ~e~l~~i~~~~~~~~~~~~~~----~~r~aV~sgrG~GKS~l~a   95 (511)
                      .+-++..+|.+-++--. -   +........|++.=.+++++--.............    ..-+-+..=.|+|||+.+|
T Consensus        43 V~~~vvk~~i~~vke~~-~---g~~v~~~l~p~q~i~kiv~~eL~~lLg~~~~~l~~~~~~p~VIm~vGLqGsGKTTT~a  118 (453)
T PRK10867         43 VALPVVREFINRVKEKA-V---GHEVNKSLTPGQEFVKIVRNELVAAMGEENQTLNLAAQPPAVVLMAGLQGAGKTTSVG  118 (453)
T ss_pred             CCHHHHHHHHHHHHHHH-C---CCCCCCCCCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCEEEEEECCCCCCHHHHHH
T ss_conf             88799999999999996-3---3513578988999999999999998588876663378999699997468885185899


Q ss_pred             HHHHHHHHHCCCCEEE-EEECCHHHH
Q ss_conf             9999999808996699-980858999
Q gi|254781215|r   96 WLVLWLMSTRPGISVI-CLANSETQL  120 (511)
Q Consensus        96 ~l~lw~l~~~p~~kv~-vtApt~~Q~  120 (511)
                      =|+.|+--- -+.+|+ |.|-|++-+
T Consensus       119 KLA~~lk~k-~~k~vllvaaDt~Rpa  143 (453)
T PRK10867        119 KLGKFLREK-HKKKVLVVSADVYRPA  143 (453)
T ss_pred             HHHHHHHHC-CCCEEEEECCCCCHHH
T ss_conf             999999973-8983798558877058


No 489
>cd01864 Rab19 Rab19 subfamily.  Rab19 proteins are associated with Golgi stacks. Similarity analysis indicated that Rab41 is closely related to Rab19. However, the function of these Rabs is not yet chracterized. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state.  Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins.  Due to the presence of truncated sequences in this CD, the lipid modification site is not available for annotation.
Probab=57.23  E-value=11  Score=16.54  Aligned_cols=22  Identities=23%  Similarity=0.327  Sum_probs=19.1

Q ss_pred             CEEEEEECCCCCCHHHHHHHHH
Q ss_conf             0124650257659789999999
Q gi|254781215|r   77 VFKGAISAGRGIGKTTLNAWLV   98 (511)
Q Consensus        77 ~~r~aV~sgrG~GKS~l~a~l~   98 (511)
                      .+|+.+....|+|||.++..++
T Consensus         3 ~~Kiv~lGd~~vGKTsli~r~~   24 (165)
T cd01864           3 LFKIILIGDSNVGKTCVVQRFK   24 (165)
T ss_pred             EEEEEEECCCCCCHHHHHHHHH
T ss_conf             8999999999958999999996


No 490
>cd04136 Rap_like Rap-like subfamily.  The Rap subfamily consists of the Rap1, Rap2, and RSR1.  Rap subfamily proteins perform different cellular functions, depending on the isoform and its subcellular localization. For example, in rat salivary gland, neutrophils, and platelets, Rap1 localizes to secretory granules and is believed to regulate exocytosis or the formation of secretory granules.  Rap1 has also been shown to localize in the Golgi of rat fibroblasts, zymogen granules, plasma membrane, and microsomal membrane of the pancreatic acini, as well as in the endocytic compartment of skeletal muscle cells and fibroblasts.   Rap1 localizes in the nucleus of human oropharyngeal squamous cell carcinomas (SCCs) and cell lines.  Rap1 plays a role in phagocytosis by controlling the binding of adhesion receptors (typically integrins) to their ligands.  In yeast, Rap1 has been implicated in multiple functions, including activation and silencing of transcription and maintenance of telomeres. 
Probab=57.07  E-value=11  Score=16.58  Aligned_cols=21  Identities=29%  Similarity=0.555  Sum_probs=18.1

Q ss_pred             EEEEEECCCCCCHHHHHHHHH
Q ss_conf             124650257659789999999
Q gi|254781215|r   78 FKGAISAGRGIGKTTLNAWLV   98 (511)
Q Consensus        78 ~r~aV~sgrG~GKS~l~a~l~   98 (511)
                      +|+.+....|+|||.++..++
T Consensus         2 fKivllGd~~VGKTsli~r~~   22 (163)
T cd04136           2 YKVVVLGSGGVGKSALTVQFV   22 (163)
T ss_pred             EEEEEECCCCCCHHHHHHHHH
T ss_conf             199998999988999999997


No 491
>KOG0057 consensus
Probab=57.04  E-value=11  Score=16.65  Aligned_cols=68  Identities=16%  Similarity=0.222  Sum_probs=38.2

Q ss_pred             EEEEECC-CCCCCCEE-----EEEECCCEEEEEEECCCCCHHHHHHHHHHHHHHCCCCEEEEEECCCCHHHHHHHHH
Q ss_conf             9996233-34784179-----99822755899873277898899999999998618882998006876368898986
Q gi|254781215|r  319 IMGCDIA-EEGGDNTV-----VVLRRGPVIEHLFDWSKTDLRTTNNKISGLVEKYRPDAIIIDANNTGARTCDYLEM  389 (511)
Q Consensus       319 viGvDVA-r~G~D~sv-----i~~r~G~~v~~~~~~~~~d~~~~a~~i~~~~~~~~~~~i~iD~~GvG~gV~d~L~~  389 (511)
                      +.-.||. .+|+..-+     +-+..|.+|-.+ --+|..-..+...+-.+.+ |. ..|.||+.-+-.--.+.||+
T Consensus       352 I~F~dV~f~y~~k~~iL~gvsf~I~kGekVaIv-G~nGsGKSTilr~LlrF~d-~s-G~I~IdG~dik~~~~~SlR~  425 (591)
T KOG0057         352 IEFDDVHFSYGPKRKVLKGVSFTIPKGEKVAIV-GSNGSGKSTILRLLLRFFD-YS-GSILIDGQDIKEVSLESLRQ  425 (591)
T ss_pred             EEEEEEEEEECCCCCEECCEEEEECCCCEEEEE-CCCCCCHHHHHHHHHHHHC-CC-CCEEECCEEHHHHCHHHHHH
T ss_conf             799865787479774003605886489789897-8999878899999999744-68-85999873376507577652


No 492
>cd04123 Rab21 Rab21 subfamily.  The localization and function of Rab21 are not clearly defined, with conflicting data reported.  Rab21 has been reported to localize in the ER in human intestinal epithelial cells, with partial colocalization with alpha-glucosidase, a late endosomal/lysosomal marker.  More recently, Rab21 was shown to colocalize with and affect the morphology of early endosomes. In Dictyostelium, GTP-bound Rab21, together with two novel LIM domain proteins, LimF and ChLim, has been shown to regulate phagocytosis. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state.  Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization.  Most Rab GTPases contain a lipid modification site
Probab=56.96  E-value=11  Score=16.71  Aligned_cols=22  Identities=32%  Similarity=0.333  Sum_probs=18.4

Q ss_pred             EEEEEECCCCCCHHHHHHHHHH
Q ss_conf             1246502576597899999999
Q gi|254781215|r   78 FKGAISAGRGIGKTTLNAWLVL   99 (511)
Q Consensus        78 ~r~aV~sgrG~GKS~l~a~l~l   99 (511)
                      +|+.|....|+|||+++..++-
T Consensus         1 ~Ki~vvG~~~vGKTsli~r~~~   22 (162)
T cd04123           1 FKVVLLGEGRVGKTSLVLRYVE   22 (162)
T ss_pred             CEEEEECCCCCCHHHHHHHHHH
T ss_conf             9899999999679999999983


No 493
>cd03237 ABC_RNaseL_inhibitor_domain2 The ATPase domain 2 of RNase L inhibitor.  The ABC ATPase, RNase L inhibitor (RLI), is a key enzyme in ribosomal biogenesis, formation of translation preinitiation complexes, and assembly of HIV capsids.  RLI's are not transport proteins and thus cluster with a group of soluble proteins that lack the transmembrane components commonly found in other members of the family.  Structurally, RLI's have an N-terminal Fe-S domain and two nucleotide-binding domains which are arranged to form two composite active sites in their interface cleft.  RLI is one of the most conserved enzymes between archaea and eukaryotes with a sequence identity of more than 48%.  The high degree of evolutionary conservation suggests that RLI performs a central role in archaeal and eukaryotic physiology.
Probab=56.90  E-value=9  Score=17.17  Aligned_cols=20  Identities=40%  Similarity=0.380  Sum_probs=17.1

Q ss_pred             EEEEECCCCCCHHHHHHHHH
Q ss_conf             24650257659789999999
Q gi|254781215|r   79 KGAISAGRGIGKTTLNAWLV   98 (511)
Q Consensus        79 r~aV~sgrG~GKS~l~a~l~   98 (511)
                      .+++....|.|||++.-.++
T Consensus        27 iv~liGpNGaGKSTLlk~l~   46 (246)
T cd03237          27 VIGILGPNGIGKTTFIKMLA   46 (246)
T ss_pred             EEEEECCCCCHHHHHHHHHH
T ss_conf             99999799976999999997


No 494
>cd02026 PRK Phosphoribulokinase (PRK) is an enzyme involved in the Benson-Calvin cycle in chloroplasts or photosynthetic prokaryotes. This enzyme catalyzes the phosphorylation of D-ribulose 5-phosphate to form D-ribulose 1, 5-biphosphate, using ATP and NADPH produced by the primary reactions of photosynthesis.
Probab=56.82  E-value=10  Score=16.87  Aligned_cols=32  Identities=28%  Similarity=0.428  Sum_probs=21.8

Q ss_pred             EEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEE
Q ss_conf             4650257659789999999999980899669998
Q gi|254781215|r   80 GAISAGRGIGKTTLNAWLVLWLMSTRPGISVICL  113 (511)
Q Consensus        80 ~aV~sgrG~GKS~l~a~l~lw~l~~~p~~kv~vt  113 (511)
                      ++|++|-|.|||+++-.+.--+  -.....+++.
T Consensus         2 IgVaG~SGSGKTTv~~~i~~if--g~~~v~vI~~   33 (273)
T cd02026           2 IGVAGDSGCGKSTFLRRLTSLF--GSDLVTVICL   33 (273)
T ss_pred             EEEECCCCCCHHHHHHHHHHHH--CCCCEEEEEC
T ss_conf             8997888786999999999985--8487699965


No 495
>PRK10575 iron-hydroxamate transporter ATP-binding subunit; Provisional
Probab=56.81  E-value=9.5  Score=17.01  Aligned_cols=22  Identities=27%  Similarity=0.160  Sum_probs=17.9

Q ss_pred             CEEEEEECCCCCCHHHHHHHHH
Q ss_conf             0124650257659789999999
Q gi|254781215|r   77 VFKGAISAGRGIGKTTLNAWLV   98 (511)
Q Consensus        77 ~~r~aV~sgrG~GKS~l~a~l~   98 (511)
                      .--+++....|.|||+++..+.
T Consensus        37 Ge~~~liG~NGaGKSTLl~~l~   58 (265)
T PRK10575         37 GKVTGLIGHNGSGKSTLLKMLG   58 (265)
T ss_pred             CCEEEEECCCCCHHHHHHHHHH
T ss_conf             9899999999980999999995


No 496
>KOG0348 consensus
Probab=56.77  E-value=12  Score=16.26  Aligned_cols=136  Identities=15%  Similarity=0.067  Sum_probs=73.5

Q ss_pred             CCCCHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHHCC-------CCEEEEEECCHHHH
Q ss_conf             57845899999999999874056555421012465025765978999999999998089-------96699980858999
Q gi|254781215|r   48 FSAPRSWQLEFMEVVDAHCLNSVNNPNPEVFKGAISAGRGIGKTTLNAWLVLWLMSTRP-------GISVICLANSETQL  120 (511)
Q Consensus        48 ~~~P~~WQ~e~l~~i~~~~~~~~~~~~~~~~r~aV~sgrG~GKS~l~a~l~lw~l~~~p-------~~kv~vtApt~~Q~  120 (511)
                      +..|-.-|++.+-.|-.      ++      .+-|.|-.|.|||-.-..=++-.+...+       |.-.+|++||..-+
T Consensus       157 i~~pTsVQkq~IP~lL~------gr------D~lV~aQTGSGKTLAYllPiVq~Lq~m~~ki~Rs~G~~ALVivPTREL~  224 (708)
T KOG0348         157 ISAPTSVQKQAIPVLLE------GR------DALVRAQTGSGKTLAYLLPIVQSLQAMEPKIQRSDGPYALVIVPTRELA  224 (708)
T ss_pred             CCCCCHHHHCCHHHHHC------CC------CEEEECCCCCCCCHHHHHHHHHHHHHCCCCCCCCCCCEEEEEECHHHHH
T ss_conf             57640676502035525------86------3478857788621799999999997268655556883489980419999


Q ss_pred             HHHHHHHHHHHHHHCHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCCC-CCCCHHHHCCCCCCEEEEECC
Q ss_conf             9999999999998550001344432222223334443211123578616985303575-561002120267614999711
Q gi|254781215|r  121 KTTLWAEVSKWLSLLPNKHWFEMQSLSLHPAPWYSDVLHCSLGIDSKHYSTMCRTYSE-ERPDTFVGHHNTYGMAIINDE  199 (511)
Q Consensus       121 ~~ilw~Ei~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~-~~~ea~~G~h~~~~~lvI~DE  199 (511)
                      ..+ +.-+.|.+..   .+|..--.   .+-+=...+++..+  ..+.-+.++.+-+. +.-.+-..+|-...-.+|+||
T Consensus       225 ~Q~-y~~~qKLl~~---~hWIVPg~---lmGGEkkKSEKARL--RKGiNILIgTPGRLvDHLknT~~i~~s~LRwlVlDE  295 (708)
T KOG0348         225 LQI-YETVQKLLKP---FHWIVPGV---LMGGEKKKSEKARL--RKGINILIGTPGRLVDHLKNTKSIKFSRLRWLVLDE  295 (708)
T ss_pred             HHH-HHHHHHHHCC---CEEEEECE---EECCCCCCCHHHHH--HCCCEEEECCCHHHHHHHHCCCHHEEEEEEEEEECC
T ss_conf             999-9999987257---43773021---22363310178887--548548975842788987430022100356898534


Q ss_pred             HHCCC
Q ss_conf             10299
Q gi|254781215|r  200 ASGTP  204 (511)
Q Consensus       200 AsgI~  204 (511)
                      |.-+=
T Consensus       296 aDrll  300 (708)
T KOG0348         296 ADRLL  300 (708)
T ss_pred             HHHHH
T ss_conf             36787


No 497
>KOG0979 consensus
Probab=56.75  E-value=8.2  Score=17.43  Aligned_cols=18  Identities=28%  Similarity=0.433  Sum_probs=7.8

Q ss_pred             EECCCCCCHHHHHHHHHH
Q ss_conf             502576597899999999
Q gi|254781215|r   82 ISAGRGIGKTTLNAWLVL   99 (511)
Q Consensus        82 V~sgrG~GKS~l~a~l~l   99 (511)
                      |.++.|+|||+++++++|
T Consensus        47 IiGpNGSGKSSiVcAIcL   64 (1072)
T KOG0979          47 IIGPNGSGKSSIVCAICL   64 (1072)
T ss_pred             EECCCCCCCHHHHHHHHH
T ss_conf             877898970488999999


No 498
>cd03226 ABC_cobalt_CbiO_domain2 Domain II of the ABC component of a cobalt transport family found in bacteria, archaea, and eukaryota.  The transition metal cobalt is an essential component of many enzymes and must be transported into cells in appropriate amounts when needed.  The CbiMNQO family ABC transport system is involved in cobalt transport in association with the cobalamin (vitamin B12) biosynthetic pathways.  Most cobalt (Cbi) transport systems possess a separate CbiN component, the cobalt-binding periplasmic protein, and they are encoded by the conserved gene cluster cbiMNQO.  Both the CbiM and CbiQ proteins are integral cytoplasmic membrane proteins, and the CbiO protein has the linker peptide and the Walker A and B motifs commonly found in the ATPase components of the ABC-type transport systems.
Probab=56.75  E-value=10  Score=16.87  Aligned_cols=22  Identities=36%  Similarity=0.270  Sum_probs=18.1

Q ss_pred             EEEEEECCCCCCHHHHHHHHHH
Q ss_conf             1246502576597899999999
Q gi|254781215|r   78 FKGAISAGRGIGKTTLNAWLVL   99 (511)
Q Consensus        78 ~r~aV~sgrG~GKS~l~a~l~l   99 (511)
                      --+++....|.|||+++-.++=
T Consensus        27 ei~~iiG~nGaGKSTLl~~i~G   48 (205)
T cd03226          27 EIIALTGKNGAGKTTLAKILAG   48 (205)
T ss_pred             CEEEEECCCCCCHHHHHHHHHC
T ss_conf             8999988999989999999956


No 499
>PRK04328 hypothetical protein; Provisional
Probab=56.73  E-value=13  Score=16.26  Aligned_cols=51  Identities=18%  Similarity=0.199  Sum_probs=0.0

Q ss_pred             CCCCEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEEECCHHHHHHHH
Q ss_conf             421012465025765978999999999998089966999808589999999
Q gi|254781215|r   74 NPEVFKGAISAGRGIGKTTLNAWLVLWLMSTRPGISVICLANSETQLKTTL  124 (511)
Q Consensus        74 ~~~~~r~aV~sgrG~GKS~l~a~l~lw~l~~~p~~kv~vtApt~~Q~~~il  124 (511)
                      .|...-+.|+.+-|+|||.++.-.+.-.+.....+-.+.+--+..|+..-+
T Consensus        21 lp~gs~~Lv~G~pGtGKT~la~qFl~~g~~~GE~~lyis~eE~~~~l~~~~   71 (250)
T PRK04328         21 IPERNVVLLSGGPGTGKSIFSQQFLWNGLQMGEPGIYVALEEHPVQVRRNM   71 (250)
T ss_pred             CCCCEEEEEEECCCCCHHHHHHHHHHHHHHCCCCEEEEEEECCHHHHHHHH
T ss_conf             879969999828999989999999999987699779999727999999999


No 500
>PRK00080 ruvB Holliday junction DNA helicase RuvB; Reviewed
Probab=56.68  E-value=13  Score=16.25  Aligned_cols=107  Identities=15%  Similarity=0.147  Sum_probs=0.0

Q ss_pred             CCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEE-ECCHHHH
Q ss_conf             775655578458999999999998740565554210124650257659789999999999980899669998-0858999
Q gi|254781215|r   42 GTPLEGFSAPRSWQLEFMEVVDAHCLNSVNNPNPEVFKGAISAGRGIGKTTLNAWLVLWLMSTRPGISVICL-ANSETQL  120 (511)
Q Consensus        42 ~~~~~~~~~P~~WQ~e~l~~i~~~~~~~~~~~~~~~~r~aV~sgrG~GKS~l~a~l~lw~l~~~p~~kv~vt-Apt~~Q~  120 (511)
                      +..+..|.|-++--..+--.|.....++...|     -+-...+-|.|||+++..++.-     -++++-+| +|.....
T Consensus        21 P~~l~efiGQ~~i~~~L~v~i~Aak~r~e~ld-----H~Ll~GPPGlGKTTLA~iiA~E-----~~~~~~~tsGP~lek~   90 (328)
T PRK00080         21 PKSLDEFIGQEKVKENLKIFIEAAKKRGEALD-----HVLLYGPPGLGKTTLANIIANE-----MGVNIRITSGPALEKA   90 (328)
T ss_pred             CCCHHHCCCHHHHHHHHHHHHHHHHHCCCCCC-----CEEEECCCCCCHHHHHHHHHHH-----HCCCCEECCCCCCCCH
T ss_conf             88576635959999999999999996499988-----0576588998899999999998-----6888156245001674


Q ss_pred             HHHHHHHHHHHHHHCHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCCCCCCCHHHHCCCCCCEEEEECCH
Q ss_conf             99999999999985500013444322222233344432111235786169853035755610021202676149997111
Q gi|254781215|r  121 KTTLWAEVSKWLSLLPNKHWFEMQSLSLHPAPWYSDVLHCSLGIDSKHYSTMCRTYSEERPDTFVGHHNTYGMAIINDEA  200 (511)
Q Consensus       121 ~~ilw~Ei~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~ea~~G~h~~~~~lvI~DEA  200 (511)
                           +-+...+.++                                                      .....+++||.
T Consensus        91 -----~DL~~iLt~l------------------------------------------------------~~~dvLFIDEI  111 (328)
T PRK00080         91 -----GDLAALLTNL------------------------------------------------------EEGDVLFIDEI  111 (328)
T ss_pred             -----HHHHHHHHHC------------------------------------------------------CCCCEEEEHHH
T ss_conf             -----7899999608------------------------------------------------------87876765065


Q ss_pred             HCCCHHHHHHHHHHHCC
Q ss_conf             02997889888888507
Q gi|254781215|r  201 SGTPDVINLGILGFLTE  217 (511)
Q Consensus       201 sgI~d~i~e~i~~~Lt~  217 (511)
                      +-++..+-|.+.++|-+
T Consensus       112 HRl~~~vEE~LY~AMED  128 (328)
T PRK00080        112 HRLSPVVEEILYPAMED  128 (328)
T ss_pred             HHCCHHHHHHHHHHHHH
T ss_conf             32488899885798775


Done!