Query         gi|254781187|ref|YP_003065600.1| putative phage terminase, large subunit [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 367
No_of_seqs    184 out of 358
Neff          7.3 
Searched_HMMs 39220
Date          Mon May 30 07:52:43 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254781187.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 2.6E-28 6.6E-33  192.6  19.9  247   82-350     2-261 (380)
  2 pfam04466 Terminase_3 Phage te  99.9 3.3E-25 8.5E-30  173.5  19.2  253   77-350     3-264 (387)
  3 pfam03354 Terminase_1 Phage Te  99.8 3.1E-18 7.9E-23  130.8  18.7  261   53-336     1-298 (473)
  4 COG5323 Uncharacterized conser  99.4 2.3E-13   6E-18  100.9   6.8  238   80-345    39-281 (410)
  5 COG4626 Phage terminase-like p  99.4 3.2E-10 8.1E-15   81.7  19.9  306    1-338     7-364 (546)
  6 COG1783 XtmB Phage terminase l  99.2 6.3E-10 1.6E-14   79.8  14.6  233   79-336    27-273 (414)
  7 TIGR01547 phage_term_2 phage t  99.1   7E-09 1.8E-13   73.4  15.8  248   80-340     4-304 (462)
  8 pfam05876 Terminase_GpA Phage   98.9 4.9E-07 1.2E-11   62.1  16.1  166   52-242    18-192 (552)
  9 COG4373 Mu-like prophage FluMu  98.8 2.5E-07 6.3E-12   64.0  14.2  236   79-336    31-332 (509)
 10 COG1061 SSL2 DNA or RNA helica  98.7   1E-06 2.6E-11   60.1  13.9  162   48-242    34-196 (442)
 11 COG1444 Predicted P-loop ATPas  98.6 3.6E-06 9.1E-11   56.8  14.4  149   54-236   215-364 (758)
 12 smart00487 DEXDc DEAD-like hel  98.6   1E-06 2.6E-11   60.1  10.8  173   46-240     4-180 (201)
 13 PRK10875 recD exonuclease V su  98.5 1.6E-05   4E-10   52.9  14.1  156   52-241   149-312 (607)
 14 PRK13766 Hef nuclease; Provisi  98.4 5.9E-06 1.5E-10   55.5  11.7  159   48-231    13-173 (764)
 15 TIGR01448 recD_rel helicase, R  98.4 4.2E-06 1.1E-10   56.4  10.3  138   52-243   352-509 (769)
 16 pfam04851 ResIII Type III rest  98.3 6.8E-06 1.7E-10   55.1  10.0  100   50-232     3-103 (103)
 17 TIGR01447 recD exodeoxyribonuc  98.2 3.8E-05 9.6E-10   50.5  11.4  156   52-232   229-395 (753)
 18 pfam02562 PhoH PhoH-like prote  98.2 1.4E-05 3.5E-10   53.2   9.0   56   51-118     5-60  (205)
 19 PRK10536 hypothetical protein;  98.2 5.5E-05 1.4E-09   49.6  12.1  184   51-273    60-261 (262)
 20 PRK02362 ski2-like helicase; P  98.2 8.7E-05 2.2E-09   48.3  12.8  158   47-237    20-187 (736)
 21 PRK01172 ski2-like helicase; P  98.2  0.0001 2.6E-09   47.9  13.1  160   50-239    22-187 (674)
 22 COG1111 MPH1 ERCC4-like helica  98.2 5.4E-05 1.4E-09   49.6  11.3  167   48-241    13-183 (542)
 23 PRK00254 ski2-like helicase; P  98.1 0.00022 5.6E-09   45.9  13.2  143   48-223    21-173 (717)
 24 KOG0354 consensus               98.1 8.1E-05 2.1E-09   48.5  10.5  156   50-233    62-224 (746)
 25 smart00488 DEXDc2 DEAD-like he  98.0 4.9E-05 1.3E-09   49.8   9.1   80   33-132     2-85  (289)
 26 smart00489 DEXDc3 DEAD-like he  98.0 4.9E-05 1.3E-09   49.8   9.1   80   33-132     2-85  (289)
 27 pfam00270 DEAD DEAD/DEAH box h  98.0 9.5E-05 2.4E-09   48.1  10.5   69   52-133     1-70  (167)
 28 PRK10590 ATP-dependent RNA hel  98.0 0.00016 4.1E-09   46.7  10.9  138   45-204    18-162 (457)
 29 KOG2036 consensus               97.9 0.00037 9.5E-09   44.5  11.5  145   52-211   255-399 (1011)
 30 PRK11192 ATP-dependent RNA hel  97.9 0.00049 1.2E-08   43.7  11.9   75   46-133    21-100 (417)
 31 PRK04837 ATP-dependent RNA hel  97.9 0.00017 4.4E-09   46.5   9.3   76   45-133    26-109 (423)
 32 PRK11634 ATP-dependent RNA hel  97.8 0.00045 1.2E-08   43.9  10.8   76   45-133    23-99  (629)
 33 cd00268 DEADc DEAD-box helicas  97.8 0.00041   1E-08   44.2   9.9   74   46-132    17-93  (203)
 34 PRK04537 ATP-dependent RNA hel  97.7  0.0008   2E-08   42.4  10.9   79   44-135    25-111 (574)
 35 PTZ00110 helicase; Provisional  97.7 0.00074 1.9E-08   42.6  10.6  159   45-227   199-368 (602)
 36 cd00046 DEXDc DEAD-like helica  97.7 0.00027 6.9E-09   45.3   8.3   53   79-132     2-54  (144)
 37 PRK01297 ATP-dependent RNA hel  97.7 0.00052 1.3E-08   43.6   9.7   77   43-132    99-183 (472)
 38 COG1204 Superfamily II helicas  97.7  0.0023 5.8E-08   39.7  12.7  158   57-239    31-198 (766)
 39 PRK11776 ATP-dependent RNA hel  97.6 0.00097 2.5E-08   41.9  10.4   78   45-135    21-99  (459)
 40 PRK06305 DNA polymerase III su  97.6  0.0029 7.4E-08   39.0  12.2  138   54-229    21-159 (462)
 41 PRK13709 conjugal transfer nic  97.5  0.0016 4.1E-08   40.5  10.4  159   10-229   938-1099(1756)
 42 COG1203 CRISPR-associated heli  97.5  0.0052 1.3E-07   37.5  12.0  171   50-231   195-381 (733)
 43 COG4096 HsdR Type I site-speci  97.4  0.0021 5.4E-08   39.8   9.7   74   44-124   159-232 (875)
 44 COG0513 SrmB Superfamily II DN  97.4  0.0032   8E-08   38.8  10.2  159   46-226    47-212 (513)
 45 PRK09112 DNA polymerase III su  97.3  0.0096 2.5E-07   35.8  11.9  159   45-230    13-180 (352)
 46 PRK04914 ATP-dependent helicas  97.3   0.013 3.4E-07   35.0  13.9  176   40-238   137-324 (955)
 47 PRK05896 DNA polymerase III su  97.3   0.011 2.8E-07   35.4  12.0  138   54-229    20-157 (613)
 48 PRK05563 DNA polymerase III su  97.3  0.0089 2.3E-07   36.0  11.5  136   54-227    20-155 (541)
 49 pfam00176 SNF2_N SNF2 family N  97.3  0.0051 1.3E-07   37.5  10.1  137   81-233    20-160 (295)
 50 PRK08058 DNA polymerase III su  97.3   0.013 3.2E-07   35.1  12.0  123   50-228     6-147 (329)
 51 COG4581 Superfamily II RNA hel  97.3   0.015 3.8E-07   34.7  13.1  159   47-244   116-283 (1041)
 52 PRK06647 DNA polymerase III su  97.3   0.012 3.1E-07   35.2  11.9  137   54-229    20-157 (560)
 53 PRK06674 DNA polymerase III su  97.2   0.013 3.4E-07   34.9  12.0  138   54-229    20-157 (563)
 54 PRK08769 DNA polymerase III su  97.2  0.0062 1.6E-07   37.0  10.0  147   51-229     5-151 (319)
 55 PRK08451 DNA polymerase III su  97.2   0.016 4.2E-07   34.4  12.0  136   55-228    19-154 (523)
 56 COG1484 DnaC DNA replication p  97.2  0.0083 2.1E-07   36.2  10.5   71   35-113    69-139 (254)
 57 PRK11448 hsdR type I restricti  97.2   0.018 4.6E-07   34.1  13.1   72   44-122   410-484 (1126)
 58 PRK08074 bifunctional ATP-depe  97.1  0.0078   2E-07   36.4   9.9   72   50-130   258-332 (932)
 59 TIGR02782 TrbB_P P-type conjug  97.1  0.0018 4.5E-08   40.3   6.6   56   52-118   125-181 (315)
 60 PRK11747 dinG ATP-dependent DN  97.1    0.01 2.6E-07   35.7  10.4   68   50-123    25-92  (697)
 61 PRK07133 DNA polymerase III su  97.1   0.021 5.3E-07   33.8  11.9  129   54-227    22-154 (718)
 62 PRK05707 DNA polymerase III su  97.1   0.012 3.1E-07   35.2  10.6   36  194-229   109-144 (328)
 63 PRK07270 DNA polymerase III su  97.1   0.021 5.4E-07   33.7  12.1  138   54-229    19-156 (557)
 64 KOG0390 consensus               97.1   0.021 5.4E-07   33.7  11.8  173   52-242   240-424 (776)
 65 pfam07652 Flavi_DEAD Flaviviru  97.1   0.008   2E-07   36.3   9.5  131   81-240     6-144 (146)
 66 PRK00440 rfc replication facto  97.1   0.022 5.7E-07   33.5  11.8  119   55-230    21-140 (318)
 67 PRK06871 DNA polymerase III su  97.1    0.02   5E-07   33.9  11.3  140   54-229     5-144 (324)
 68 PRK07994 DNA polymerase III su  97.0   0.012 3.2E-07   35.1  10.2  134   54-225    20-153 (643)
 69 TIGR03015 pepcterm_ATPase puta  97.0   0.021 5.3E-07   33.7  11.3  152   38-231     6-166 (269)
 70 PRK06645 DNA polymerase III su  97.0    0.02 5.1E-07   33.8  11.2  142   54-229    25-166 (507)
 71 PRK07471 DNA polymerase III su  96.9  0.0075 1.9E-07   36.5   8.4  160   47-230     9-178 (363)
 72 pfam05970 DUF889 PIF1 helicase  96.9   0.002 5.2E-08   39.9   5.5   97   85-216     2-99  (418)
 73 PRK13826 Dtr system oriT relax  96.9   0.013 3.3E-07   35.0   9.6  114   81-240   401-520 (1102)
 74 COG1875 NYN ribonuclease and A  96.9  0.0015 3.9E-08   40.7   4.8  156   53-237   231-394 (436)
 75 PRK06090 DNA polymerase III su  96.9    0.03 7.7E-07   32.8  11.5  134   60-229    13-146 (319)
 76 PRK08181 transposase; Validate  96.9   0.024 6.2E-07   33.3  10.5  128   50-244    87-220 (269)
 77 TIGR01054 rgy reverse gyrase;   96.8   0.015 3.8E-07   34.6   9.3  200   80-286   102-375 (1843)
 78 PRK13889 conjugal transfer rel  96.8   0.018 4.6E-07   34.1   9.3  131   53-241   349-486 (992)
 79 pfam05127 DUF699 Putative ATPa  96.7   0.043 1.1E-06   31.8  12.2   85  106-212    12-96  (160)
 80 PRK05564 DNA polymerase III su  96.7   0.036 9.1E-07   32.3  10.5  121   54-229     8-131 (313)
 81 KOG1805 consensus               96.7  0.0085 2.2E-07   36.1   7.0  130   78-230   687-829 (1100)
 82 PRK07246 bifunctional ATP-depe  96.7   0.035 8.8E-07   32.4  10.1   74   50-134   245-318 (820)
 83 COG1205 Distinct helicase fami  96.7    0.02 5.1E-07   33.9   8.8   74   51-137    71-144 (851)
 84 PRK12323 DNA polymerase III su  96.6    0.05 1.3E-06   31.4  11.4  140   54-226    20-159 (721)
 85 PRK12377 putative replication   96.6   0.051 1.3E-06   31.4  13.3   60   45-113    73-135 (248)
 86 COG1199 DinG Rad3-related DNA   96.6   0.023 5.8E-07   33.5   8.9   67   49-124    14-80  (654)
 87 PRK07764 DNA polymerase III su  96.6   0.025 6.3E-07   33.3   9.0  137   55-227    20-156 (775)
 88 PRK08691 DNA polymerase III su  96.6   0.052 1.3E-06   31.3  11.4  134   54-225    20-153 (704)
 89 COG1201 Lhr Lhr-like helicases  96.6   0.023 5.7E-07   33.5   8.6   78   46-136    18-101 (814)
 90 KOG0952 consensus               96.5   0.023   6E-07   33.4   8.5  139   53-213   113-263 (1230)
 91 PRK10917 ATP-dependent DNA hel  96.5   0.061 1.6E-06   30.9  11.8   83   42-137   253-335 (677)
 92 COG1110 Reverse gyrase [DNA re  96.5   0.018 4.7E-07   34.1   7.7  109   79-200    99-212 (1187)
 93 PRK12402 replication factor C   96.5   0.063 1.6E-06   30.8  11.8   35  193-227   127-161 (337)
 94 TIGR02397 dnaX_nterm DNA polym  96.4   0.067 1.7E-06   30.7  11.0  119   54-230    18-154 (363)
 95 KOG0338 consensus               96.3   0.012   3E-07   35.3   6.0  197   44-267   197-404 (691)
 96 PRK08699 DNA polymerase III su  96.3   0.071 1.8E-06   30.5   9.9  127   79-229    23-151 (325)
 97 KOG0335 consensus               96.3   0.038 9.6E-07   32.2   8.4  167   43-233    89-273 (482)
 98 COG3972 Superfamily I DNA and   96.3   0.018 4.7E-07   34.1   6.7  134   82-224   181-327 (660)
 99 PRK07003 DNA polymerase III su  96.3   0.085 2.2E-06   30.0  11.7  135   54-226    20-154 (816)
100 TIGR00345 arsA arsenite-activa  96.2  0.0057 1.4E-07   37.2   3.9   44   87-130     7-51  (330)
101 PRK11057 ATP-dependent DNA hel  96.1   0.021 5.3E-07   33.8   6.4   62   46-124    21-82  (607)
102 PRK05703 flhF flagellar biosyn  96.1   0.054 1.4E-06   31.2   8.4   68   51-118   184-252 (412)
103 PRK13767 ATP-dependent helicas  96.0   0.043 1.1E-06   31.8   7.6   89    7-124     6-101 (878)
104 TIGR03499 FlhF flagellar biosy  96.0   0.037 9.5E-07   32.2   7.1   70   50-119   165-237 (282)
105 TIGR02525 plasmid_TraJ plasmid  96.0  0.0086 2.2E-07   36.1   3.8   35   80-114   152-186 (374)
106 PRK06872 DNA polymerase III su  96.0   0.067 1.7E-06   30.6   8.4  135   54-226    20-154 (696)
107 TIGR03346 chaperone_ClpB ATP-d  96.0    0.12   3E-06   29.2  10.3   48   54-101   569-619 (852)
108 pfam01695 IstB IstB-like ATP b  96.0    0.08   2E-06   30.2   8.7   55   50-115    29-83  (178)
109 KOG0330 consensus               95.9   0.028   7E-07   33.0   6.2  156   47-224    80-240 (476)
110 PRK09183 transposase/IS protei  95.9    0.12   3E-06   29.2   9.4   68   35-114    66-136 (258)
111 PRK06526 transposase; Provisio  95.9    0.13 3.2E-06   29.0   9.3  127   50-244    80-212 (254)
112 PRK08853 DNA polymerase III su  95.8    0.14 3.5E-06   28.8  11.1  134   54-225    20-153 (717)
113 TIGR02621 cas3_GSU0051 CRISPR-  95.8    0.03 7.6E-07   32.8   6.0  158   45-216    11-215 (975)
114 KOG0331 consensus               95.7   0.035 8.8E-07   32.4   6.1  260   45-331   108-407 (519)
115 PRK07952 DNA replication prote  95.7    0.15 3.8E-06   28.5  12.9   65   45-115    68-133 (242)
116 PRK13833 conjugal transfer pro  95.7   0.036 9.2E-07   32.3   6.1   55   52-117   130-184 (323)
117 KOG0949 consensus               95.7   0.057 1.5E-06   31.1   7.1  167   50-242   511-682 (1330)
118 KOG0333 consensus               95.7   0.034 8.6E-07   32.4   5.8  144   38-203   247-408 (673)
119 PRK09111 DNA polymerase III su  95.6    0.16   4E-06   28.3  12.0  139   54-226    27-166 (600)
120 PRK08770 DNA polymerase III su  95.4    0.17 4.3E-06   28.2   8.5  135   54-226    20-154 (663)
121 KOG0391 consensus               95.3    0.11 2.8E-06   29.3   7.5  167   49-242   614-785 (1958)
122 COG1200 RecG RecG-like helicas  95.3     0.2 5.2E-06   27.7   9.5   82   42-136   258-339 (677)
123 PRK05648 DNA polymerase III su  95.3    0.19 4.9E-06   27.8   8.5  135   54-226    20-154 (705)
124 KOG0340 consensus               95.2    0.15 3.8E-06   28.5   7.9  158   37-218    16-184 (442)
125 TIGR03117 cas_csf4 CRISPR-asso  95.2    0.23 5.9E-06   27.3   9.1   45   80-124    19-63  (636)
126 PRK07993 DNA polymerase III su  95.1    0.25 6.3E-06   27.2  10.4  134   61-229    13-146 (334)
127 PRK13894 conjugal transfer ATP  94.9   0.077   2E-06   30.2   5.8   55   53-118   136-190 (320)
128 TIGR02768 TraA_Ti Ti-type conj  94.7    0.28 7.2E-06   26.8   8.2  122   53-231   417-539 (888)
129 KOG0350 consensus               94.7    0.17 4.4E-06   28.1   7.1  149   54-214   163-318 (620)
130 PRK07399 DNA polymerase III su  94.7     0.2 5.2E-06   27.7   7.3   41  189-230   123-163 (314)
131 TIGR00643 recG ATP-dependent D  94.7     0.3 7.5E-06   26.7   8.1   81   42-135   303-383 (721)
132 COG0470 HolB ATPase involved i  94.6    0.32 8.2E-06   26.5  11.8  103   79-229    26-147 (325)
133 PRK13342 recombination factor   94.6    0.32 8.2E-06   26.5  10.2  112   78-254    38-149 (417)
134 CHL00095 clpC Clp protease ATP  94.6    0.33 8.5E-06   26.4   9.0  127   54-222   513-647 (823)
135 KOG2170 consensus               94.5    0.34 8.7E-06   26.3  10.1  126   52-232    88-226 (344)
136 PRK06964 DNA polymerase III su  94.4    0.35   9E-06   26.2  10.4   37  193-229   134-170 (342)
137 KOG0389 consensus               94.4    0.19 4.8E-06   27.9   6.7  144   81-233   422-565 (941)
138 COG4889 Predicted helicase [Ge  94.3    0.37 9.5E-06   26.1   8.9   91   23-127   134-225 (1518)
139 PRK12723 flagellar biosynthesi  94.3    0.33 8.5E-06   26.4   7.7   73   49-121   145-221 (388)
140 PRK07132 DNA polymerase III su  94.3    0.39 9.9E-06   26.0  11.9  119   56-229     4-130 (303)
141 pfam05894 Podovirus_Gp16 Podov  94.2    0.39   1E-05   25.9  13.3  145   78-243    19-173 (333)
142 PRK07276 DNA polymerase III su  94.2    0.41   1E-05   25.8  11.5  136   53-228     5-141 (290)
143 PRK05917 DNA polymerase III su  94.1    0.41   1E-05   25.8  11.2  166   52-271     4-169 (290)
144 KOG0342 consensus               94.1    0.42 1.1E-05   25.7   8.0  168   45-234    99-276 (543)
145 PRK07940 DNA polymerase III su  94.0    0.44 1.1E-05   25.6  11.7  138   55-229    10-158 (395)
146 pfam00580 UvrD-helicase UvrD/R  93.9     0.1 2.6E-06   29.5   4.5   45   79-123    15-61  (494)
147 KOG1015 consensus               93.7    0.21 5.3E-06   27.6   5.8  160   80-242   699-871 (1567)
148 TIGR00631 uvrb excinuclease AB  93.7    0.48 1.2E-05   25.4   7.6  189   55-302    14-215 (667)
149 PRK11034 clpA ATP-dependent Cl  93.7     0.5 1.3E-05   25.3   8.2   47   54-100   462-511 (758)
150 PHA00149 DNA encapsidation pro  93.6    0.51 1.3E-05   25.2  10.5  143   77-243    18-172 (331)
151 PRK12724 flagellar biosynthesi  93.6    0.51 1.3E-05   25.2   7.6   42   79-120   225-266 (432)
152 PRK00411 cdc6 cell division co  93.5    0.53 1.4E-05   25.1  11.6   70   57-128    37-110 (394)
153 COG4962 CpaF Flp pilus assembl  93.4    0.18 4.5E-06   28.1   4.9   51   53-117   160-210 (355)
154 KOG0339 consensus               93.3    0.54 1.4E-05   25.1   7.3  158   48-230   243-410 (731)
155 PRK10416 cell division protein  93.3    0.58 1.5E-05   24.9  10.4  106   74-214   294-402 (499)
156 KOG0334 consensus               93.0    0.45 1.1E-05   25.6   6.6   75   48-135   385-465 (997)
157 pfam02456 Adeno_IVa2 Adenoviru  92.9    0.21 5.3E-06   27.6   4.7   84   52-138    58-145 (370)
158 PRK06731 flhF flagellar biosyn  92.9    0.67 1.7E-05   24.5  13.8   69   50-120    45-117 (270)
159 smart00382 AAA ATPases associa  92.7    0.68 1.7E-05   24.5   7.1   40   79-120     4-43  (148)
160 TIGR03158 cas3_cyano CRISPR-as  92.7     0.7 1.8E-05   24.4   7.8   65   55-135     2-66  (357)
161 TIGR01074 rep ATP-dependent DN  92.7    0.26 6.7E-06   27.0   5.0   89   55-158     8-98  (677)
162 PRK00149 dnaA chromosomal repl  92.7    0.66 1.7E-05   24.5   7.0   56   53-115   128-183 (447)
163 COG0593 DnaA ATPase involved i  92.6    0.63 1.6E-05   24.7   6.9   36   80-115   116-151 (408)
164 COG1702 PhoH Phosphate starvat  92.6    0.17 4.3E-06   28.2   3.9  150   50-232   128-281 (348)
165 PRK10919 ATP-dependent DNA hel  92.6    0.25 6.3E-06   27.2   4.7   45   80-124    18-64  (672)
166 PRK12727 flagellar biosynthesi  92.5    0.74 1.9E-05   24.2  10.1   40   80-119   351-391 (557)
167 TIGR01420 pilT_fam twitching m  92.5    0.18 4.6E-06   28.0   3.9   27   79-105   129-155 (350)
168 TIGR03345 VI_ClpV1 type VI sec  92.4    0.76 1.9E-05   24.2   9.4   48   54-101   570-620 (852)
169 PRK08116 hypothetical protein;  92.3     0.8   2E-05   24.0  12.5   33   80-114   111-143 (262)
170 PRK06835 DNA replication prote  92.3    0.61 1.6E-05   24.7   6.4   82   25-115   138-220 (330)
171 COG2812 DnaX DNA polymerase II  92.2    0.82 2.1E-05   24.0   7.3  134   54-225    20-153 (515)
172 KOG0352 consensus               92.2    0.82 2.1E-05   24.0   7.2  166   53-243    23-223 (641)
173 cd01130 VirB11-like_ATPase Typ  92.1    0.46 1.2E-05   25.5   5.6   51   53-117    12-62  (186)
174 PRK06995 flhF flagellar biosyn  92.1     0.3 7.8E-06   26.6   4.7   41   80-120   179-220 (404)
175 PRK06696 uridine kinase; Valid  92.0    0.74 1.9E-05   24.2   6.6   54   55-113     7-60  (227)
176 cd01128 rho_factor Transcripti  91.9    0.43 1.1E-05   25.7   5.3   35   79-113    18-52  (249)
177 PRK11054 helD DNA helicase IV;  91.6    0.43 1.1E-05   25.7   5.0   46   79-124   211-258 (684)
178 PRK10865 protein disaggregatio  91.5    0.97 2.5E-05   23.5   8.5   48   54-101   572-622 (857)
179 PRK04195 replication factor C   91.1     1.1 2.7E-05   23.3  12.0   22   79-100    42-63  (403)
180 KOG0328 consensus               91.1    0.17 4.2E-06   28.2   2.5  151   47-221    46-202 (400)
181 PRK09270 frcK putative fructos  91.0    0.85 2.2E-05   23.9   6.1   38   76-113    33-70  (230)
182 COG5525 Bacteriophage tail ass  90.9    0.21 5.3E-06   27.6   2.8  152   52-231    49-207 (611)
183 TIGR03305 alt_F1F0_F1_bet alte  90.8    0.78   2E-05   24.1   5.7   51   79-130   140-191 (449)
184 COG5410 Uncharacterized protei  90.8    0.84 2.2E-05   23.9   5.9  187    5-223     3-203 (305)
185 COG0003 ArsA Predicted ATPase   90.5    0.38 9.8E-06   26.0   3.9   47   81-128     6-52  (322)
186 COG0514 RecQ Superfamily II DN  90.5    0.69 1.7E-05   24.4   5.2   61   47-124    14-74  (590)
187 pfam02374 ArsA_ATPase Anion-tr  90.4    0.64 1.6E-05   24.6   5.0   42   81-124     5-47  (304)
188 KOG0947 consensus               90.3     1.3 3.2E-05   22.8   8.1   68   50-132   297-364 (1248)
189 KOG0332 consensus               90.3    0.22 5.7E-06   27.4   2.5   72   43-124   105-177 (477)
190 KOG0781 consensus               90.2     1.3 3.3E-05   22.8   9.5  137   55-230   362-506 (587)
191 pfam03308 ArgK ArgK protein. T  90.2     1.3 3.3E-05   22.8   6.7   54   55-118    15-70  (267)
192 pfam05496 RuvB_N Holliday junc  90.0     1.3 3.4E-05   22.6   9.5   26  193-218   103-128 (234)
193 TIGR01978 sufC FeS assembly AT  89.8    0.25 6.3E-06   27.2   2.5   72  192-272   166-243 (248)
194 pfam00437 GSPII_E Type II/IV s  89.8     1.4 3.5E-05   22.6   6.8   37   79-117   141-177 (283)
195 KOG4284 consensus               89.8    0.68 1.7E-05   24.5   4.7  137   47-208    44-185 (980)
196 PRK11889 flhF flagellar biosyn  89.7     1.4 3.6E-05   22.5  13.0   60   58-120   223-283 (436)
197 pfam00448 SRP54 SRP54-type pro  89.3     1.5 3.8E-05   22.4  12.0   52   80-135     4-55  (196)
198 KOG0991 consensus               89.3     1.1 2.9E-05   23.1   5.5   94   74-216    45-138 (333)
199 PRK08939 primosomal protein Dn  89.2     1.5 3.9E-05   22.3   7.7   70   45-117   127-196 (306)
200 PRK10037 cell division protein  89.2    0.73 1.9E-05   24.3   4.5   43   77-121     1-45  (250)
201 TIGR00580 mfd transcription-re  89.2     1.5 3.9E-05   22.3   7.0   60   51-117   509-571 (997)
202 PRK11773 uvrD DNA-dependent he  89.1    0.34 8.5E-06   26.3   2.7   44   80-123    25-70  (722)
203 KOG0989 consensus               88.8     1.7 4.2E-05   22.1   9.7  172   54-274    40-221 (346)
204 cd02025 PanK Pantothenate kina  88.7     0.9 2.3E-05   23.7   4.7   34   80-113     2-35  (220)
205 COG1703 ArgK Putative periplas  88.6     1.5 3.8E-05   22.4   5.7   75   25-117    13-91  (323)
206 PRK09401 reverse gyrase; Revie  88.6     1.7 4.3E-05   22.0  17.0  110   79-201    95-209 (1176)
207 PRK11664 ATP-dependent RNA hel  88.4     1.7 4.5E-05   21.9  14.7  145   79-243    22-170 (812)
208 TIGR00678 holB DNA polymerase   88.3     1.8 4.5E-05   21.9   7.5  132   79-230    16-158 (216)
209 COG1239 ChlI Mg-chelatase subu  88.3     1.8 4.5E-05   21.9   7.2  161   48-233    19-199 (423)
210 cd02035 ArsA ArsA ATPase funct  88.3    0.67 1.7E-05   24.5   3.8   31   82-114     4-34  (217)
211 PRK13900 type IV secretion sys  88.3     1.5 3.9E-05   22.3   5.6   37   78-117   161-197 (332)
212 cd03115 SRP The signal recogni  88.3     1.1 2.7E-05   23.2   4.8   52   80-135     3-54  (173)
213 pfam01637 Arch_ATPase Archaeal  88.1     1.8 4.6E-05   21.8  10.8   52   57-116     6-57  (223)
214 cd01983 Fer4_NifH The Fer4_Nif  88.1     1.2 3.1E-05   22.9   5.0   33   80-114     2-34  (99)
215 cd02036 MinD Bacterial cell di  88.0     1.1 2.7E-05   23.3   4.7   32   80-113     2-34  (179)
216 TIGR01425 SRP54_euk signal rec  87.9     1.7 4.3E-05   22.0   5.7   94   84-209   128-223 (453)
217 cd00550 ArsA_ATPase Oxyanion-t  87.9    0.74 1.9E-05   24.2   3.8   40   82-123     5-45  (254)
218 PRK13851 type IV secretion sys  87.8     1.2 3.2E-05   22.9   4.9  101   78-220   163-263 (343)
219 KOG0337 consensus               87.8     1.2 3.1E-05   23.0   4.8   74   45-131    38-113 (529)
220 PRK08233 hypothetical protein;  87.7    0.96 2.4E-05   23.6   4.3   32   79-114     5-36  (182)
221 KOG1123 consensus               87.7    0.57 1.5E-05   24.9   3.1  147   41-210   293-441 (776)
222 KOG1002 consensus               87.6     1.9   5E-05   21.7   7.0  216    3-233   119-357 (791)
223 PRK07667 uridine kinase; Provi  87.6    0.63 1.6E-05   24.7   3.3   27   75-101    12-38  (190)
224 TIGR00750 lao LAO/AO transport  87.6       2   5E-05   21.7   5.9   58   50-117    17-78  (333)
225 PTZ00301 uridine kinase; Provi  87.5     1.3 3.4E-05   22.7   4.9   26   79-104     5-30  (210)
226 KOG0923 consensus               87.3       2 5.2E-05   21.6  10.0  160   54-243   269-431 (902)
227 cd02034 CooC The accessory pro  87.1     1.5 3.8E-05   22.4   5.0   37   79-117     1-37  (116)
228 pfam07517 SecA_DEAD SecA DEAD-  87.1     2.1 5.3E-05   21.5   7.9  143   79-242    93-235 (381)
229 COG2842 Uncharacterized ATPase  87.0     2.1 5.4E-05   21.5   6.5  107   80-231    97-203 (297)
230 pfam07570 consensus             86.6    0.79   2E-05   24.1   3.3   28   78-106    14-41  (45)
231 TIGR03029 EpsG chain length de  86.3     2.3 5.9E-05   21.2   7.1   77   37-117    63-142 (274)
232 KOG0347 consensus               86.0    0.64 1.6E-05   24.6   2.6  265   45-336   198-538 (731)
233 COG2607 Predicted ATPase (AAA+  85.7     2.5 6.3E-05   21.0  12.9   92   33-135    36-137 (287)
234 pfam02500 DNA_pack_N Probable   85.6     1.3 3.2E-05   22.8   4.0   51   83-134   186-236 (276)
235 cd02028 UMPK_like Uridine mono  85.4     1.8 4.5E-05   21.9   4.7   38   80-117     2-39  (179)
236 cd01135 V_A-ATPase_B V/A-type   85.2     1.4 3.6E-05   22.5   4.1   44   79-122    71-115 (276)
237 TIGR01969 minD_arch cell divis  84.9    0.95 2.4E-05   23.6   3.1  191   80-285     3-207 (258)
238 PRK06921 hypothetical protein;  84.8     2.7 6.9E-05   20.8   9.0   59   51-114    94-152 (265)
239 pfam03205 MobB Molybdopterin g  84.8     2.3 5.8E-05   21.2   5.0   34   78-113     1-34  (122)
240 pfam10236 DAP3 Mitochondrial r  84.7     2.4 6.2E-05   21.1   5.1   27   77-103    23-49  (274)
241 KOG0348 consensus               84.6     2.8 7.1E-05   20.7   7.7  139   45-204   154-300 (708)
242 TIGR02562 cas3_yersinia CRISPR  84.6     1.3 3.3E-05   22.8   3.6  262   53-326   423-776 (1153)
243 pfam09848 DUF2075 Uncharacteri  84.6     2.8 7.1E-05   20.7   8.0   39   80-118     4-42  (348)
244 CHL00060 atpB ATP synthase CF1  84.6     2.8 7.1E-05   20.7   6.2   50   79-129   157-207 (480)
245 CHL00081 chlI Mg-protoporyphyr  84.5     2.8 7.2E-05   20.7   9.1   52  179-233   130-194 (347)
246 cd01133 F1-ATPase_beta F1 ATP   84.4     2.8 7.2E-05   20.7   5.8   33   79-111    71-103 (274)
247 TIGR00959 ffh signal recogniti  84.2     1.1 2.9E-05   23.1   3.2  112   80-225   105-227 (439)
248 PRK13407 bchI magnesium chelat  84.2     2.9 7.4E-05   20.6   8.1   54  177-233   117-183 (334)
249 KOG3022 consensus               84.2       2 5.2E-05   21.5   4.5   34   78-113    48-82  (300)
250 cd01134 V_A-ATPase_A V/A-type   84.1     2.9 7.5E-05   20.6   5.5   37   79-120   159-195 (369)
251 cd02042 ParA ParA and ParB of   84.0     1.6 4.1E-05   22.2   3.9   28   86-115     9-36  (104)
252 PRK12597 F0F1 ATP synthase sub  83.9       3 7.6E-05   20.5   6.4   44   79-122   143-187 (459)
253 pfam05673 DUF815 Protein of un  83.9       3 7.6E-05   20.5  11.2   52   79-136    55-106 (248)
254 PRK05298 excinuclease ABC subu  83.9       3 7.6E-05   20.5   7.9   68   51-131    14-81  (657)
255 COG3640 CooC CO dehydrogenase   83.8     2.8 7.1E-05   20.7   5.1   34   79-113     2-35  (255)
256 pfam00308 Bac_DnaA Bacterial d  83.7       3 7.7E-05   20.5   7.0   36   80-115    37-72  (219)
257 pfam06564 YhjQ YhjQ protein. T  83.7     2.2 5.7E-05   21.3   4.6   36   77-114     1-37  (244)
258 PRK11670 putative ATPase; Prov  83.6     2.4 6.1E-05   21.1   4.7   34   79-114   109-143 (369)
259 PRK08118 topology modulation p  83.3     1.2   3E-05   23.0   3.0   26   77-102     1-26  (167)
260 PRK11131 ATP-dependent RNA hel  83.3     3.2 8.1E-05   20.4  14.2  161   53-244    77-240 (1295)
261 PRK13341 recombination factor   83.2     3.2 8.1E-05   20.4  10.0   41   78-123    53-93  (726)
262 KOG1803 consensus               82.9     2.6 6.6E-05   20.9   4.6   45   80-126   204-248 (649)
263 PRK04220 2-phosphoglycerate ki  82.9     2.5 6.4E-05   21.0   4.5   89   10-124    42-131 (306)
264 PRK07568 aspartate aminotransf  82.8     3.3 8.4E-05   20.3   7.6   64   51-122    64-127 (396)
265 cd02038 FleN-like FleN is a me  82.8     2.7 6.9E-05   20.8   4.7   33   80-114     2-35  (139)
266 COG1373 Predicted ATPase (AAA+  82.5     3.4 8.7E-05   20.2  10.4   16   79-94     39-54  (398)
267 cd04169 RF3 RF3 subfamily.  Pe  82.4     3.4 8.7E-05   20.2   5.4  140   78-243     3-146 (267)
268 COG1149 MinD superfamily P-loo  82.3     1.3 3.3E-05   22.7   2.9   72  192-275   164-240 (284)
269 TIGR00603 rad25 DNA repair hel  82.3     1.4 3.6E-05   22.5   3.1  148   41-211   260-411 (756)
270 TIGR01587 cas3_core CRISPR-ass  82.3     3.3 8.4E-05   20.3   5.0   50   80-130     2-54  (424)
271 cd01120 RecA-like_NTPases RecA  82.3     3.4 8.8E-05   20.1   6.2   42   80-123     2-45  (165)
272 cd02024 NRK1 Nicotinamide ribo  82.2       2 5.2E-05   21.5   3.9   21   80-100     2-22  (187)
273 cd01869 Rab1_Ypt1 Rab1/Ypt1 su  82.1     1.6 4.1E-05   22.2   3.3   23   76-98      1-23  (166)
274 cd03110 Fer4_NifH_child This p  82.0     1.3 3.3E-05   22.8   2.8   36  190-232    91-126 (179)
275 TIGR02788 VirB11 P-type DNA tr  81.9     1.3 3.2E-05   22.8   2.7   94   78-191   159-270 (328)
276 KOG0345 consensus               81.9     3.6 9.1E-05   20.0   8.6  122   79-208    45-174 (567)
277 KOG2228 consensus               81.8     3.6 9.2E-05   20.0   7.9   81   43-134    24-105 (408)
278 PRK09280 F0F1 ATP synthase sub  81.5     3.7 9.4E-05   20.0   6.8   34   79-112   147-180 (466)
279 COG1643 HrpA HrpA-like helicas  81.5     3.7 9.4E-05   20.0  13.1  161   53-244    53-217 (845)
280 cd01886 EF-G Elongation factor  81.4    0.78   2E-05   24.1   1.5  133   79-242     1-138 (270)
281 pfam01935 DUF87 Domain of unkn  81.4     3.2 8.2E-05   20.3   4.7   39   79-118    25-63  (218)
282 PRK02731 histidinol-phosphate   81.3     2.5 6.4E-05   21.0   4.1   58   51-121    65-122 (367)
283 TIGR01075 uvrD DNA helicase II  81.2     3.7 9.5E-05   19.9   4.9   55   79-136    19-73  (741)
284 COG0210 UvrD Superfamily I DNA  81.1     3.8 9.7E-05   19.9   6.0   45   79-123    17-63  (655)
285 KOG0742 consensus               80.9     3.9 9.9E-05   19.8  11.5   77   57-135   365-441 (630)
286 PRK06793 fliI flagellum-specif  80.8     3.2 8.2E-05   20.3   4.5   41   79-122   158-199 (432)
287 pfam00931 NB-ARC NB-ARC domain  80.7     3.9  0.0001   19.8  10.7   48   76-123    18-66  (285)
288 TIGR01407 dinG_rel DnaQ family  80.7     3.9  0.0001   19.8   7.4   76   51-133   261-339 (944)
289 COG4240 Predicted kinase [Gene  80.7     3.9  0.0001   19.8   5.1   52   56-114    34-86  (300)
290 cd01868 Rab11_like Rab11-like.  80.4       2 5.1E-05   21.6   3.3   23   76-98      2-24  (165)
291 COG0610 Type I site-specific r  80.3       4  0.0001   19.7  12.4  138   51-203   249-388 (962)
292 CHL00175 minD septum-site dete  80.3     3.5   9E-05   20.1   4.6   36   76-113    11-48  (279)
293 pfam00155 Aminotran_1_2 Aminot  79.8     4.2 0.00011   19.6   6.0   69   49-124    35-104 (351)
294 COG1074 RecB ATP-dependent exo  79.7     4.2 0.00011   19.6   6.4   47  184-231   372-419 (1139)
295 pfam05729 NACHT NACHT domain.   79.6     2.5 6.5E-05   21.0   3.6   27   79-105     2-28  (165)
296 TIGR01968 minD_bact septum sit  79.6     2.6 6.6E-05   20.9   3.7  123   80-214     4-136 (272)
297 PRK06067 flagellar accessory p  79.6     4.3 0.00011   19.6   6.2   40   79-120    34-75  (241)
298 TIGR02545 ATP_syn_fliI flagell  78.9     1.4 3.7E-05   22.5   2.2   46   79-134   160-205 (439)
299 KOG4181 consensus               78.8     2.8 7.2E-05   20.7   3.7   62   55-123   171-232 (491)
300 COG4178 ABC-type uncharacteriz  78.6     4.6 0.00012   19.4   5.9   49  183-231   525-574 (604)
301 PRK05480 uridine kinase; Provi  78.6     2.3 5.9E-05   21.2   3.2   24   78-101     7-30  (209)
302 PRK10818 cell division inhibit  78.6     4.4 0.00011   19.5   4.6   32   80-113     5-37  (270)
303 PRK08149 ATP synthase SpaL; Va  78.4     2.8 7.1E-05   20.7   3.6   38   79-121   152-189 (427)
304 KOG0385 consensus               78.4     4.6 0.00012   19.3   9.5  172   36-241   159-336 (971)
305 TIGR03496 FliI_clade1 flagella  78.2     4.7 0.00012   19.3   5.2   36   79-119   139-174 (411)
306 COG0455 flhG Antiactivator of   78.2     4.7 0.00012   19.3   4.9   35   78-112     3-38  (262)
307 PRK10689 transcription-repair   78.1     4.7 0.00012   19.3   8.0   59   54-120   604-662 (1148)
308 cd01863 Rab18 Rab18 subfamily.  78.0     2.2 5.7E-05   21.3   2.9   21   78-98      1-21  (161)
309 TIGR02868 CydC ABC transporter  78.0     2.5 6.3E-05   21.0   3.1   72   55-141   373-447 (566)
310 PRK08927 fliI flagellum-specif  78.0     3.3 8.4E-05   20.3   3.8   39   79-122   160-198 (441)
311 TIGR02746 TraC-F-type type-IV   77.9     4.8 0.00012   19.3   5.5   47   78-124   490-536 (900)
312 PRK07960 fliI flagellum-specif  77.9     2.7 6.8E-05   20.8   3.3   39   79-122   177-215 (455)
313 PRK13235 nifH nitrogenase redu  77.9     4.8 0.00012   19.3   4.9   43   77-121     1-45  (274)
314 pfam00485 PRK Phosphoribulokin  77.9     2.1 5.3E-05   21.5   2.8   22   80-101     2-23  (196)
315 PRK07721 fliI flagellum-specif  77.9     3.6 9.2E-05   20.0   4.0   38   79-121   158-195 (435)
316 PRK03321 putative aminotransfe  77.9     4.8 0.00012   19.3   5.2   58   51-121    55-112 (352)
317 PRK05688 fliI flagellum-specif  77.9     2.2 5.6E-05   21.3   2.9   46   79-134   170-215 (451)
318 PRK03158 histidinol-phosphate   77.8     2.9 7.3E-05   20.6   3.5   59   51-122    62-120 (359)
319 cd01131 PilT Pilus retraction   77.7     3.8 9.7E-05   19.9   4.1   35   80-115     4-38  (198)
320 PRK09435 arginine/ornithine tr  77.7     4.9 0.00012   19.2   7.1   59   53-121    33-93  (325)
321 PRK07594 type III secretion sy  77.6     3.3 8.5E-05   20.2   3.7   38   79-121   157-194 (433)
322 COG1419 FlhF Flagellar GTP-bin  77.6     4.9 0.00013   19.2   9.3   62   55-118   183-245 (407)
323 cd02023 UMPK Uridine monophosp  77.6     2.2 5.6E-05   21.3   2.8   22   80-101     2-23  (198)
324 COG0556 UvrB Helicase subunit   77.5     4.9 0.00013   19.2   7.0   69   51-132    13-81  (663)
325 pfam03266 DUF265 Protein of un  77.5     4.9 0.00013   19.2   7.1   60  191-255    95-157 (168)
326 PRK12289 ribosome-associated G  77.4     2.5 6.4E-05   21.0   3.1   16   82-97    176-191 (351)
327 cd01864 Rab19 Rab19 subfamily.  77.4     2.8 7.1E-05   20.7   3.3   23   76-98      2-24  (165)
328 PRK12422 chromosomal replicati  77.4       5 0.00013   19.2   6.2   53   57-115   124-177 (455)
329 cd00009 AAA The AAA+ (ATPases   77.4       5 0.00013   19.2  11.8   35   79-115    21-55  (151)
330 cd01892 Miro2 Miro2 subfamily.  77.2     3.1 7.9E-05   20.4   3.5   23   76-98      3-25  (169)
331 PRK10263 DNA translocase FtsK;  77.2     3.4 8.6E-05   20.2   3.7   47   70-116  1003-1051(1355)
332 PRK08972 fliI flagellum-specif  77.1     3.8 9.7E-05   19.9   3.9   38   79-121   162-199 (440)
333 cd01867 Rab8_Rab10_Rab13_like   77.0     2.9 7.5E-05   20.6   3.3   23   76-98      2-24  (167)
334 PRK08533 flagellar accessory p  77.0     5.1 0.00013   19.1   6.4   44   75-120    22-67  (230)
335 cd01865 Rab3 Rab3 subfamily.    77.0     2.6 6.6E-05   20.9   3.1   23   77-99      1-23  (165)
336 pfam02367 UPF0079 Uncharacteri  76.9     4.1 0.00011   19.7   4.1   49   57-118     3-51  (123)
337 PRK06002 fliI flagellum-specif  76.8     2.3 5.9E-05   21.2   2.7   21   79-99    167-187 (450)
338 pfam01580 FtsK_SpoIIIE FtsK/Sp  76.7     5.2 0.00013   19.0   4.6   41   77-117    38-80  (202)
339 PRK00741 prfC peptide chain re  76.7     2.6 6.5E-05   20.9   2.9  137   77-241    10-152 (526)
340 PHA02518 ParA-like protein; Pr  76.6     3.1   8E-05   20.4   3.4   28   85-114     9-36  (211)
341 PRK08472 fliI flagellum-specif  76.6     3.1   8E-05   20.4   3.4   22   79-100   160-181 (435)
342 PRK13909 putative recombinatio  76.6     5.2 0.00013   19.0   6.4   40  191-231   325-371 (911)
343 cd04122 Rab14 Rab14 subfamily.  76.5     2.9 7.5E-05   20.6   3.2   24   76-99      1-24  (166)
344 PRK06217 hypothetical protein;  76.4     2.7 6.8E-05   20.8   3.0   28   77-104     1-28  (185)
345 pfam07726 AAA_3 ATPase family   76.4     5.3 0.00013   19.0   7.5   24  194-217    65-88  (131)
346 COG0552 FtsY Signal recognitio  76.3     5.3 0.00014   19.0   9.7  124   75-234   139-272 (340)
347 TIGR02784 addA_alphas double-s  76.3     2.9 7.4E-05   20.6   3.1   24  192-215   397-420 (1190)
348 KOG0327 consensus               76.2     3.7 9.5E-05   19.9   3.7   67   46-124    44-111 (397)
349 COG0563 Adk Adenylate kinase a  76.2     3.5   9E-05   20.1   3.5   29   79-107     2-30  (178)
350 PRK03566 consensus              76.2     1.5 3.7E-05   22.4   1.6   54   55-121    69-122 (365)
351 PRK13231 nitrogenase reductase  76.0     5.4 0.00014   18.9   4.6   45   77-124     2-48  (264)
352 cd04138 H_N_K_Ras_like H-Ras/N  75.9       3 7.8E-05   20.5   3.2   22   78-99      2-23  (162)
353 cd04110 Rab35 Rab35 subfamily.  75.8     3.2 8.2E-05   20.3   3.3   24   75-98      4-27  (199)
354 PRK06820 type III secretion sy  75.8     4.3 0.00011   19.6   3.9   35   79-118   165-199 (445)
355 PRK07196 fliI flagellum-specif  75.7     5.5 0.00014   18.9   5.8   38   79-121   157-194 (434)
356 TIGR00958 3a01208 antigen pept  75.6     2.5 6.3E-05   21.0   2.6   23   79-101   561-583 (770)
357 CHL00059 atpA ATP synthase CF1  75.6     5.6 0.00014   18.9   4.9   22   79-100   165-186 (501)
358 cd01866 Rab2 Rab2 subfamily.    75.6     3.2 8.2E-05   20.3   3.2   23   76-98      3-25  (168)
359 pfam07728 AAA_5 AAA domain (dy  75.5     5.6 0.00014   18.8   7.7   25  193-217    68-92  (139)
360 PRK07324 transaminase; Validat  75.5     5.6 0.00014   18.8   6.2   60   53-124    62-121 (373)
361 cd04116 Rab9 Rab9 subfamily.    75.4     3.4 8.8E-05   20.2   3.3   23   76-98      4-26  (170)
362 smart00175 RAB Rab subfamily o  75.4     2.9 7.3E-05   20.6   2.9   21   78-98      1-21  (164)
363 PRK06315 type III secretion sy  75.2     2.6 6.5E-05   20.9   2.6   22   79-100   166-187 (442)
364 cd04114 Rab30 Rab30 subfamily.  75.1     4.1  0.0001   19.7   3.7   24   75-98      5-28  (169)
365 PRK11331 5-methylcytosine-spec  75.1     5.7 0.00015   18.8   4.4   40   79-118   196-237 (459)
366 pfam00735 Septin Septin. Membe  74.8     3.3 8.4E-05   20.3   3.1   23   77-99      4-26  (280)
367 cd04136 Rap_like Rap-like subf  74.8     3.3 8.5E-05   20.2   3.1   22   78-99      2-23  (163)
368 KOG0920 consensus               74.8     5.8 0.00015   18.7  14.1  186   53-273   176-365 (924)
369 PRK00081 coaE dephospho-CoA ki  74.6     3.1   8E-05   20.4   3.0   31   77-113     2-32  (199)
370 PRK04863 mukB cell division pr  74.6     4.1  0.0001   19.7   3.5   36   79-117    29-64  (1486)
371 cd04107 Rab32_Rab38 Rab38/Rab3  74.5     3.2 8.2E-05   20.3   3.0   21   78-98      1-21  (201)
372 PRK07261 topology modulation p  74.5     3.3 8.4E-05   20.3   3.0   22   79-100     2-23  (171)
373 PRK13705 plasmid-partitioning   74.4       6 0.00015   18.7   7.5   87   23-114    50-142 (388)
374 TIGR00955 3a01204 Pigment prec  74.4       2   5E-05   21.6   1.9  233   55-305    44-325 (671)
375 KOG1133 consensus               74.3       6 0.00015   18.7   5.5   47   50-104    15-62  (821)
376 PRK09265 aminotransferase AlaT  74.3       6 0.00015   18.7   8.9   61   51-119    70-131 (404)
377 PRK06936 type III secretion sy  74.1     6.1 0.00015   18.6   6.0   36   79-119   164-199 (439)
378 cd04127 Rab27A Rab27a subfamil  74.0     3.9 9.9E-05   19.8   3.3   23   76-98      3-25  (180)
379 TIGR03497 FliI_clade2 flagella  74.0     6.1 0.00016   18.6   5.4   41   79-122   139-180 (413)
380 PRK13768 GTPase; Provisional    73.9     6.2 0.00016   18.6   4.9   36   78-113     3-38  (253)
381 PRK13230 nitrogenase reductase  73.8     6.2 0.00016   18.6   5.0   35   77-113     1-35  (292)
382 COG0572 Udk Uridine kinase [Nu  73.8     3.2 8.1E-05   20.4   2.8   23   77-99      8-30  (218)
383 cd04125 RabA_like RabA-like su  73.8     3.4 8.6E-05   20.2   2.9   22   78-99      1-22  (188)
384 cd04123 Rab21 Rab21 subfamily.  73.6     3.5 8.9E-05   20.1   3.0   22   78-99      1-22  (162)
385 TIGR01166 cbiO cobalt ABC tran  73.4     3.3 8.4E-05   20.2   2.8   43  179-222   133-180 (190)
386 PRK13634 cbiO cobalt transport  73.4    0.53 1.3E-05   25.1  -1.3   37   55-99      6-42  (276)
387 cd02037 MRP-like MRP (Multiple  73.4     6.3 0.00016   18.5   4.5   32   80-113     2-34  (169)
388 COG0396 sufC Cysteine desulfur  73.3     2.9 7.3E-05   20.6   2.5   81  182-272   154-238 (251)
389 smart00173 RAS Ras subfamily o  73.3     3.6 9.2E-05   20.0   3.0   21   78-98      1-21  (164)
390 COG2805 PilT Tfp pilus assembl  73.3     6.4 0.00016   18.5   5.5   34   79-113   127-160 (353)
391 cd04113 Rab4 Rab4 subfamily.    73.3     3.5 8.9E-05   20.1   2.9   21   78-98      1-21  (161)
392 cd04175 Rap1 Rap1 subgroup.  T  73.2     3.8 9.7E-05   19.9   3.1   22   78-99      2-23  (164)
393 cd03277 ABC_SMC5_euk Eukaryoti  73.2       3 7.7E-05   20.5   2.6   21   79-100    26-46  (213)
394 COG3421 Uncharacterized protei  73.1     6.4 0.00016   18.5   5.0   33   85-118     5-37  (812)
395 KOG0344 consensus               72.8     6.5 0.00017   18.4   6.2   74   46-132   154-233 (593)
396 KOG4439 consensus               72.8     6.5 0.00017   18.4   6.8  138   81-235   349-506 (901)
397 PRK04196 V-type ATP synthase s  72.7     5.8 0.00015   18.8   3.9   45   79-123   145-193 (460)
398 pfam04665 Pox_A32 Poxvirus A32  72.7     5.1 0.00013   19.1   3.7   43   78-122    14-56  (241)
399 cd04148 RGK RGK subfamily.  Th  72.6     3.6 9.3E-05   20.0   2.9   21   78-98      1-21  (221)
400 COG2256 MGS1 ATPase related to  72.6     6.6 0.00017   18.4   7.4   40   79-123    50-89  (436)
401 cd01860 Rab5_related Rab5-rela  72.6       4  0.0001   19.7   3.1   22   78-99      2-23  (163)
402 cd00154 Rab Rab family.  Rab G  72.5     3.8 9.7E-05   19.9   3.0   22   78-99      1-22  (159)
403 PRK10751 molybdopterin-guanine  72.4     6.7 0.00017   18.4   4.5   38   79-118     4-41  (170)
404 cd01850 CDC_Septin CDC/Septin.  72.3     4.1  0.0001   19.7   3.1   24   76-99      3-26  (276)
405 KOG0336 consensus               72.3     4.6 0.00012   19.4   3.4  149   80-243   260-421 (629)
406 cd04103 Centaurin_gamma Centau  72.1       4  0.0001   19.8   3.0   22   78-99      1-22  (158)
407 TIGR03498 FliI_clade3 flagella  72.0     3.7 9.3E-05   20.0   2.8   35   79-118   142-176 (418)
408 PRK09099 type III secretion sy  72.0     3.8 9.7E-05   19.9   2.9   23   79-101   165-187 (441)
409 cd01870 RhoA_like RhoA-like su  71.8     4.1  0.0001   19.7   3.0   22   78-99      2-23  (175)
410 cd04177 RSR1 RSR1 subgroup.  R  71.7     4.3 0.00011   19.5   3.1   22   78-99      2-23  (168)
411 TIGR03324 alt_F1F0_F1_al alter  71.7     6.9 0.00018   18.3   4.3   21   79-99    164-184 (497)
412 pfam00071 Ras Ras family. Incl  71.7     3.7 9.4E-05   20.0   2.7   20   79-98      1-20  (162)
413 cd01136 ATPase_flagellum-secre  71.5       5 0.00013   19.1   3.4   36   79-119    71-106 (326)
414 PRK05922 type III secretion sy  71.4     6.2 0.00016   18.6   3.8   35   79-118   159-193 (434)
415 cd04121 Rab40 Rab40 subfamily.  71.4       5 0.00013   19.2   3.3   23   76-98      5-27  (189)
416 cd02040 NifH NifH gene encodes  71.4       7 0.00018   18.2   4.8   35   77-113     1-35  (270)
417 PRK13764 ATPase; Provisional    71.2     7.1 0.00018   18.2   5.0   26   79-104   261-286 (605)
418 COG1197 Mfd Transcription-repa  71.2     7.1 0.00018   18.2   7.1   75   53-136   597-671 (1139)
419 KOG0346 consensus               71.0     7.2 0.00018   18.2   6.6   77   47-136    38-121 (569)
420 COG1157 FliI Flagellar biosynt  70.9     4.1  0.0001   19.7   2.8   47   79-135   165-211 (441)
421 KOG0979 consensus               70.8     3.2 8.2E-05   20.3   2.3   18   82-99     47-64  (1072)
422 cd03116 MobB Molybdenum is an   70.7     7.3 0.00019   18.1   4.8   39   79-119     3-41  (159)
423 COG3973 Superfamily I DNA and   70.5     7.4 0.00019   18.1   5.2   51   79-134   228-282 (747)
424 PRK13721 conjugal transfer ATP  70.5     7.4 0.00019   18.1   5.4   42   78-121   475-518 (864)
425 cd03289 ABCC_CFTR2 The CFTR su  70.5     4.6 0.00012   19.4   3.0   31   79-112    32-62  (275)
426 pfam04310 MukB MukB N-terminal  70.3     4.2 0.00011   19.6   2.8   36   79-117    29-64  (227)
427 TIGR01526 nadR_NMN_Atrans nico  70.2     4.9 0.00012   19.2   3.1   35   65-101   165-199 (346)
428 PRK10636 putative ABC transpor  70.2     3.7 9.5E-05   19.9   2.5   34  189-222   165-199 (638)
429 pfam07015 VirC1 VirC1 protein.  70.2     7.5 0.00019   18.1   6.1  100   80-212     4-104 (231)
430 COG1674 FtsK DNA segregation A  70.1     6.5 0.00017   18.4   3.7   50   67-116   520-571 (858)
431 cd04139 RalA_RalB RalA/RalB su  70.1     4.7 0.00012   19.3   3.0   22   78-99      1-22  (164)
432 cd04145 M_R_Ras_like M-Ras/R-R  70.1     5.1 0.00013   19.1   3.2   22   77-98      2-23  (164)
433 TIGR02546 III_secr_ATP type II  70.0       7 0.00018   18.3   3.8  129   79-243   155-321 (430)
434 PRK13646 cbiO cobalt transport  69.9     1.3 3.2E-05   22.8   0.0   37   54-98     18-54  (286)
435 cd04168 TetM_like Tet(M)-like   69.8     7.6 0.00019   18.0   5.6  135   79-244     1-140 (237)
436 cd04176 Rap2 Rap2 subgroup.  T  69.8     5.1 0.00013   19.1   3.1   22   78-99      2-23  (163)
437 KOG1802 consensus               69.8       5 0.00013   19.1   3.1   37   80-117   428-464 (935)
438 cd00157 Rho Rho (Ras homology)  69.7     4.7 0.00012   19.3   2.9   21   78-98      1-21  (171)
439 TIGR00150 TIGR00150 conserved   69.7     5.2 0.00013   19.1   3.1   38   79-121    29-67  (147)
440 pfam03029 ATP_bind_1 Conserved  69.7     6.8 0.00017   18.3   3.7   35   82-116     1-35  (234)
441 PRK11147 ABC transporter ATPas  69.6     4.2 0.00011   19.6   2.7   42  185-228   168-210 (632)
442 PRK06851 hypothetical protein;  69.4     1.7 4.3E-05   22.1   0.6   51   79-129    33-83  (368)
443 TIGR03371 cellulose_yhjQ cellu  69.2     7.8  0.0002   18.0   4.6   36   77-114     1-37  (246)
444 PRK13695 putative NTPase; Prov  69.2     7.8  0.0002   18.0   6.7  164   77-268     3-169 (174)
445 pfam01656 CbiA CobQ/CobB/MinD/  69.2     7.9  0.0002   17.9   4.1   31   81-113     2-33  (212)
446 cd01124 KaiC KaiC is a circadi  69.1     7.9  0.0002   17.9   6.2   34   80-115     2-35  (187)
447 TIGR02030 BchI-ChlI magnesium   68.9       8  0.0002   17.9   4.5  138   73-218    21-161 (340)
448 cd04170 EF-G_bact Elongation f  68.6     4.7 0.00012   19.3   2.7  134   79-243     1-139 (268)
449 PRK13343 F0F1 ATP synthase sub  68.6     8.1 0.00021   17.9   4.1   21   79-99    164-184 (502)
450 TIGR00064 ftsY signal recognit  68.6     8.1 0.00021   17.9   7.0  130   70-235    77-218 (284)
451 COG5008 PilU Tfp pilus assembl  68.4     7.1 0.00018   18.2   3.6   29   80-108   130-158 (375)
452 cd01122 GP4d_helicase GP4d_hel  68.4     8.2 0.00021   17.8   7.0   44   80-124    33-78  (271)
453 TIGR01281 DPOR_bchL light-inde  68.3     4.6 0.00012   19.4   2.6   42   80-123     3-46  (275)
454 cd04140 ARHI_like ARHI subfami  68.2     5.6 0.00014   18.8   3.1   22   78-99      2-23  (165)
455 cd04141 Rit_Rin_Ric Rit/Rin/Ri  68.2     5.9 0.00015   18.7   3.2   22   78-99      3-24  (172)
456 cd01129 PulE-GspE PulE/GspE Th  68.1     8.3 0.00021   17.8   6.6   54   50-115    63-116 (264)
457 pfam09140 MipZ ATPase MipZ. Mi  68.1     7.2 0.00018   18.2   3.6   30   86-117    10-39  (261)
458 KOG0388 consensus               68.0     8.3 0.00021   17.8   8.0  163   53-234   570-737 (1185)
459 TIGR00486 TIGR00486 conserved   67.9     8.3 0.00021   17.8   4.5   75   45-128   193-278 (325)
460 cd04117 Rab15 Rab15 subfamily.  67.9     5.3 0.00013   19.0   2.9   22   78-99      1-22  (161)
461 PRK03333 coaE dephospho-CoA ki  67.9       5 0.00013   19.1   2.7   23   77-99      1-23  (394)
462 cd03291 ABCC_CFTR1 The CFTR su  67.8     5.4 0.00014   19.0   2.9   33   58-98     52-84  (282)
463 PRK13873 conjugal transfer ATP  67.8     8.4 0.00021   17.8   4.7   33   79-112   443-475 (815)
464 cd04115 Rab33B_Rab33A Rab33B/R  67.6     6.4 0.00016   18.5   3.3   23   77-99      2-24  (170)
465 cd00877 Ran Ran (Ras-related n  67.6     5.7 0.00015   18.8   3.0   21   78-98      1-21  (166)
466 cd04119 RJL RJL (RabJ-Like) su  67.5     5.6 0.00014   18.9   2.9   20   79-98      2-21  (168)
467 cd03247 ABCC_cytochrome_bd The  67.4     5.4 0.00014   18.9   2.8   21   79-99     30-50  (178)
468 cd04111 Rab39 Rab39 subfamily.  67.3     6.6 0.00017   18.4   3.3   24   76-99      1-24  (211)
469 PRK13637 cbiO cobalt transport  67.2     1.1 2.7E-05   23.3  -0.8   37   54-98     18-54  (287)
470 cd03246 ABCC_Protease_Secretio  67.1     5.7 0.00015   18.8   2.9   21   79-99     30-50  (173)
471 KOG1969 consensus               67.1     8.7 0.00022   17.7   9.1  107   51-217   306-413 (877)
472 cd03369 ABCC_NFT1 Domain 2 of   67.0     6.1 0.00016   18.6   3.1   22   79-100    36-57  (207)
473 pfam02689 Herpes_Helicase Heli  67.0     8.7 0.00022   17.7   4.5   37   73-117    57-93  (801)
474 PRK09694 hypothetical protein;  66.8     8.8 0.00022   17.6   8.7   76   47-135   285-360 (878)
475 cd03249 ABC_MTABC3_MDL1_MDL2 M  66.5       6 0.00015   18.7   2.9   21   79-99     31-51  (238)
476 cd04129 Rho2 Rho2 subfamily.    66.3     6.5 0.00017   18.4   3.1   22   78-99      2-23  (187)
477 PRK11819 putative ABC transpor  66.3     5.7 0.00015   18.8   2.8   39  188-228   178-217 (556)
478 cd00984 DnaB_C DnaB helicase C  66.3       9 0.00023   17.6   6.7   35   80-115    16-50  (242)
479 PRK13233 nifH nitrogenase redu  66.2       9 0.00023   17.6   5.0   44   78-122     3-48  (275)
480 PRK13645 cbiO cobalt transport  66.1     1.1 2.7E-05   23.2  -1.0   38   53-98     21-58  (289)
481 PRK13640 cbiO cobalt transport  66.1     5.7 0.00015   18.8   2.8   34   58-99     23-56  (283)
482 cd03114 ArgK-like The function  66.0     9.1 0.00023   17.6   4.7   36   80-117     2-37  (148)
483 COG1341 Predicted GTPase or GT  66.0     9.1 0.00023   17.6   6.0   56   47-104    45-100 (398)
484 cd01862 Rab7 Rab7 subfamily.    66.0     6.3 0.00016   18.5   3.0   21   78-98      1-21  (172)
485 COG1136 SalX ABC-type antimicr  65.9     5.7 0.00015   18.8   2.7   33   79-114    33-65  (226)
486 cd01861 Rab6 Rab6 subfamily.    65.9     6.3 0.00016   18.5   2.9   21   79-99      2-22  (161)
487 cd00615 Orn_deC_like Ornithine  65.9     9.2 0.00023   17.5   6.1   31   94-124    86-116 (294)
488 PRK00080 ruvB Holliday junctio  65.8     9.2 0.00023   17.5   8.1   94   55-217    30-128 (328)
489 cd04112 Rab26 Rab26 subfamily.  65.7     6.5 0.00017   18.5   3.0   21   78-98      1-21  (191)
490 cd00876 Ras Ras family.  The R  65.6     5.9 0.00015   18.7   2.7   21   79-99      1-21  (160)
491 cd03248 ABCC_TAP TAP, the Tran  65.1     6.4 0.00016   18.5   2.9   22   79-100    42-63  (226)
492 PRK07367 consensus              65.0     9.5 0.00024   17.4   7.0   64   51-122    63-127 (385)
493 COG0542 clpA ATP-binding subun  64.9     9.6 0.00024   17.4  11.2  134   54-229   495-642 (786)
494 cd03240 ABC_Rad50 The catalyti  64.8     6.5 0.00016   18.5   2.8   20   79-98     24-43  (204)
495 PTZ00132 GTP-binding nuclear p  64.8     7.5 0.00019   18.1   3.1   56  221-277   110-169 (209)
496 PRK10790 putative multidrug tr  64.8     6.6 0.00017   18.4   2.9   18   80-97    370-387 (593)
497 cd03223 ABCD_peroxisomal_ALDP   64.8     5.9 0.00015   18.7   2.6   37  190-228   108-145 (166)
498 TIGR01082 murC UDP-N-acetylmur  64.4     9.8 0.00025   17.4   5.2   52   55-119    96-148 (491)
499 PRK13886 conjugal transfer pro  64.4     8.5 0.00022   17.7   3.4   30   87-116    13-42  (241)
500 cd01875 RhoG RhoG subfamily.    64.2       8  0.0002   17.9   3.2   21   78-98      4-24  (191)

No 1  
>pfam03237 Terminase_6 Terminase-like family. This family represents a group of terminase proteins.
Probab=99.97  E-value=2.6e-28  Score=192.55  Aligned_cols=247  Identities=16%  Similarity=0.084  Sum_probs=183.6

Q ss_pred             EECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             61488678899999999999970899779997153799999999999999986231211233332100012333221111
Q gi|254781187|r   82 ISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLKNTLWAEVSKWLSMLPHRHWFEMQSLSLHPSGWYAELLEQS  161 (367)
Q Consensus        82 v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~~~lw~ei~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  161 (367)
                      +.+|||+|||++++..++++++.+++.+++++++|..|++.++++.+..++......              .+.......
T Consensus         2 ~~ggr~~GKT~~~~~~~~~~a~~~~~~~~~i~~~t~~~~~~~~~~~~~~~~~~~~~~--------------~~~~~~~~~   67 (380)
T pfam03237         2 ILGSRQSGKTFAFAREALRHALGNGPKNQIILSASKAQARLEFKKGIIEIAGDLLEI--------------TFEEKNGNP   67 (380)
T ss_pred             CCCCCCCCHHHHHHHHHHHHHHHCCCCCEEEEECCHHHHHHHHHHHHHHHHHHHCCC--------------CEEECCCCE
T ss_conf             426452528399999999999858997289997999999999999999966886387--------------167278873


Q ss_pred             CCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCEEEEECCCCCCHHHH-HHH-HHHHHCCCCCEEEEEEECCCCCCCHHHH
Q ss_conf             34577612662101354455652101135862899975455998899-998-9874069882589998078999876887
Q gi|254781187|r  162 MGIDSKHYTITCRTYSEERPDTFVGPHNTHGMAVFNDEASGTPDIIN-KSI-LGFFTELNPNRFWIMTSNTRRLNGWFYD  239 (367)
Q Consensus       162 ~~~~~~~~~~~a~~~~~~~~ea~~g~h~~~~~l~ivDEAsgI~d~i~-e~i-~g~Lt~~~~~~~~i~igNP~r~~g~Fye  239 (367)
                      +...+|+.+....   .+++.+.++++|....++++||++.+++..+ ..+ .+.++....+  .+.++||+.+.++||+
T Consensus        68 i~~~nGs~i~~~~---~~~~~~~~~~rG~~~~~i~~DE~a~~~~~~~~~~~~~~~~~~~~~~--~~~~stp~~~~~~~~~  142 (380)
T pfam03237        68 IILPNGAKLYFLG---LESETTAQGYRGASIAGIYFDEATWLPKFQESELVRRLRATKGKWR--KTFFSTPPSPGHWVYD  142 (380)
T ss_pred             EEECCCCEEEEEE---CCCCCCHHHCCCCCCCEEEEEEHHHCCCHHHHHHHHHHHCCCCCCC--EEEEECCCCCCCCHHH
T ss_conf             9915998899962---5776643103485455499830453662789999864410479975--7999889899851989


Q ss_pred             HHHCCC-------CCEEEEEECCCCCCCCCHHHHHHHHHHCCCCCCEEEEEEEEEECCCCCCEEECHHHHHHHHCCCCCC
Q ss_conf             541122-------3504675233328888988999999621688000268886443277898078299986443157777
Q gi|254781187|r  240 IFNIPL-------EDWKRYQIDTRTVEGIDSGFHEGIISRYGLDSDVARIEILGQFPQQEVNNFIPHNYIEEAMSREAID  312 (367)
Q Consensus       240 ~~~~~~-------~~w~~~~~~~~d~p~~~~~~i~~~~~~~gedS~~~r~ev~G~Fp~~~~d~~ip~~~ie~a~~~~~~~  312 (367)
                      .|....       ..|..++++..++|..++++++++++.|++.  .|+++++|+|. .+++++|+..+++.+......+
T Consensus       143 ~~~~~~~~~~~~~~~~~~~~~t~~d~~~~~~~~~e~l~~~~~~~--~~~qe~~g~f~-~~~g~if~~~~~~~~~~~~~~~  219 (380)
T pfam03237       143 FWTGWLDDKGKRTFIPADVEVTIEDARALGPEYKEELRALYSDE--EFARLLMGEWV-DTSGSIFKRFELERCDVDEERP  219 (380)
T ss_pred             HHHHHCCCCCCCCEEEEEEECCHHHHCCCCHHHHHHHHHHCCHH--HHHHHHCCCEE-CCCCCEECHHHHHHCCCCCCCC
T ss_conf             98554016777520220674566871326889999998768999--99998588666-5788571478885464675568


Q ss_pred             CCCCCEEEEEECCC-CCCCEEEEEEE---CCCEEEEEHHHCH
Q ss_conf             88984899996387-78810899997---0883687042030
Q gi|254781187|r  313 DLYAPLIMGCDIAG-EGGDKTVVVFR---RGNIIEHIFDWSA  350 (367)
Q Consensus       313 ~~~~p~viGvDvAr-~G~D~Tvi~~r---~G~~v~~i~~~~~  350 (367)
                      ....++++|+|+|. .++|+|++++.   .++....+.++..
T Consensus       220 p~~~~~~~g~D~~~~~~~D~t~~~v~~~~~~~~~~~~~~~~~  261 (380)
T pfam03237       220 PEHREVIGGVDPAASRGGDYAALVVIAEVDGDKFYVLAREHE  261 (380)
T ss_pred             CCCCEEEEEECCCCCCCCCCEEEEEEEECCCCEEEEEEEEEE
T ss_conf             888559999867888889966999999657985999999983


No 2  
>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=99.94  E-value=3.3e-25  Score=173.49  Aligned_cols=253  Identities=18%  Similarity=0.153  Sum_probs=185.9

Q ss_pred             EEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             12477614886788999999999999708997799971537999999999999999862312112333321000123332
Q gi|254781187|r   77 IFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLKNTLWAEVSKWLSMLPHRHWFEMQSLSLHPSGWYAE  156 (367)
Q Consensus        77 ~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~~~lw~ei~k~~~~~~~~~~~~~~~~~~~~~~~~~~  156 (367)
                      +|+++. +|||+|||..+|..++-.++.+| .+++|++.+.+++++.+|+++++.++.+...+.+..+...+..      
T Consensus         3 r~~v~~-GGrgsgKS~~~a~~~i~~~~~~~-~~~l~~r~~~~slr~sv~~~~~~~i~~~~~~~~~~~~~s~~~i------   74 (387)
T pfam04466         3 RYKVAK-GGRGSGKSYHIALKLVLKLLMHP-RTNLVIREVKNTIEDSVFTQLQEALSMLGLDHEFKISKSPIEI------   74 (387)
T ss_pred             CEEEEE-ECCCCHHHHHHHHHHHHHHHHCC-CEEEEEECCHHHHHHHHHHHHHHHHHHCCCCCEEEECCCCEEE------
T ss_conf             689999-08886799999999999998789-8699997556889999999999999976997348973761489------


Q ss_pred             CCCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCEEEEECCCCCCHHHHHHHHHHHHCCCCCEEEEEEECCCCCCCH
Q ss_conf             21111345776126621013544556521011358628999754559988999989874069882589998078999876
Q gi|254781187|r  157 LLEQSMGIDSKHYTITCRTYSEERPDTFVGPHNTHGMAVFNDEASGTPDIINKSILGFFTELNPNRFWIMTSNTRRLNGW  236 (367)
Q Consensus       157 ~~~~~~~~~~~~~~~~a~~~~~~~~ea~~g~h~~~~~l~ivDEAsgI~d~i~e~i~g~Lt~~~~~~~~i~igNP~r~~g~  236 (367)
                           ....+|+.+.+. +.  ++|+++.|+.+  ..++++|||+.++...|+.+.++++.......+++..||.....|
T Consensus        75 -----~~~~~gs~i~f~-G~--d~~~~iks~~~--i~~~~~eEa~~~~~~~~~~l~~~~r~~~~~~~i~~~~NP~~~~~w  144 (387)
T pfam04466        75 -----TVKINGSKFLFY-GM--DDPAKIKSIKD--VSDAWIEEAAEFKTEDFDQLIPTIRRPKPGSEIFMSFNPVNKLNW  144 (387)
T ss_pred             -----EECCCCCEEEEE-EC--CCHHHHHCCCC--CEEEEEECHHHCCHHHHHHHHHHHCCCCCCEEEEEECCCCCCCCH
T ss_conf             -----987899699998-57--89688416366--149999412447998999999885317887199998289998774


Q ss_pred             HHHHHHCC-----CCCEEEEEECCCCCCCCCHHHHHHHHHHCCCCCCEEEEEEEEEECCCCCCEEECHHHHHHHHCCCCC
Q ss_conf             88754112-----2350467523332888898899999962168800026888644327789807829998644315777
Q gi|254781187|r  237 FYDIFNIP-----LEDWKRYQIDTRTVEGIDSGFHEGIISRYGLDSDVARIEILGQFPQQEVNNFIPHNYIEEAMSREAI  311 (367)
Q Consensus       237 Fye~~~~~-----~~~w~~~~~~~~d~p~~~~~~i~~~~~~~gedS~~~r~ev~G~Fp~~~~d~~ip~~~ie~a~~~~~~  311 (367)
                      .|+.|-+.     ..++..++....|||++++++++++++.+..++..|++.++|+|.. .++.+|+.-.+ ........
T Consensus       145 ~~~~~~~~~~~~~~~~~~~~~~ty~DNp~L~~~~i~~~e~~k~~dp~~y~~~~lGe~~~-~~g~V~~~~~~-~~~~~~~~  222 (387)
T pfam04466       145 TYKRFFKNDKSELDDDTYIHHSTYRDNPFLPEVDIREIEELKRRNPDYYRIEYLGEFGG-LGTLVLPNFEI-KPLWVEAA  222 (387)
T ss_pred             HHHHHHCCCCCCCCCCEEEEEEEECCCCCCCHHHHHHHHHHHHCCHHHHHHHHCCCEEE-CCCEEEECCEE-EECCCCCH
T ss_conf             88997417754677885999999616998999999999998703999989977571563-48779735445-55232640


Q ss_pred             CCCCCCEEEEEECCCCCCCEEEEEE----ECCCEEEEEHHHCH
Q ss_conf             7889848999963877881089999----70883687042030
Q gi|254781187|r  312 DDLYAPLIMGCDIAGEGGDKTVVVF----RRGNIIEHIFDWSA  350 (367)
Q Consensus       312 ~~~~~p~viGvDvAr~G~D~Tvi~~----r~G~~v~~i~~~~~  350 (367)
                      .+....+.+|+|. |+-.|.|+++.    ..|+.+....++.+
T Consensus       223 ~~~~~~~~~G~D~-G~~~dpta~v~~~~~~~~~~lyi~~e~y~  264 (387)
T pfam04466       223 EDAHIKLGFKRDF-GFDESATASVRGALDVKKKVIYLYDEYYD  264 (387)
T ss_pred             HHHHCCCCCCEEC-CCCCCCCEEEEEEEECCCCEEEEEEEEEC
T ss_conf             2200033421354-64378877999999779989999999984


No 3  
>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=99.82  E-value=3.1e-18  Score=130.78  Aligned_cols=261  Identities=15%  Similarity=0.147  Sum_probs=159.3

Q ss_pred             HHHHHHHHHHHHHHHCCCCCCCCCEEE-EEEECCCCCCHHHHHHHHHHHHHHHC--CCCEEEEECCCHHHHHHHHHHHHH
Q ss_conf             899999998888751245555541124-77614886788999999999999708--997799971537999999999999
Q gi|254781187|r   53 RWQLEFMEAVDVHCHSNVNNSNPTIFK-CAISAGRGIGKTTLNAWMMLWLISTR--PGMSIICIANSETQLKNTLWAEVS  129 (367)
Q Consensus        53 ~wq~~~l~~~~~~~~~~~~~~~~~~~~-~~v~sgrg~GKS~~~a~~~lw~~~~~--~~~~v~~~A~t~~Q~~~~lw~ei~  129 (367)
                      +||.-++..|.-.-..    ...-+|| +.+.-|||.|||.++|+++++.++..  ++..++++|++.+|++ ++|.+++
T Consensus         1 PwQ~f~i~~ifGw~~~----~g~Rrfr~~~i~v~RkNGKS~l~a~i~ly~~~~~ge~~~ei~~~A~~~~QA~-~~f~~~~   75 (473)
T pfam03354         1 PWQKFILGLMFGWRKG----CGVRRFREAYVSVGRKNGKSYLMAIRVLYELLLGGKSNQEILVAATTFKQAE-KLFKYVK   75 (473)
T ss_pred             CCHHHHHHHEEEEEEC----CCCEEEEEEEEEEECCCCHHHHHHHHHHHHHHHCCCCCCEEEEEECCHHHHH-HHHHHHH
T ss_conf             9461562514418928----9988999999998268602699999999999709983874999979899999-9999999


Q ss_pred             HHHHHCCCCCC-CCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCEEEEECCCCCC-HHH
Q ss_conf             99986231211-2333321000123332211113457761266210135445565210113586289997545599-889
Q gi|254781187|r  130 KWLSMLPHRHW-FEMQSLSLHPSGWYAELLEQSMGIDSKHYTITCRTYSEERPDTFVGPHNTHGMAVFNDEASGTP-DII  207 (367)
Q Consensus       130 k~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~ea~~g~h~~~~~l~ivDEAsgI~-d~i  207 (367)
                      ++++..|...- +...       ...  ..+..+........+...++   ++++..|   .+..++|+||..-.+ +.+
T Consensus        76 ~mi~~~p~l~~~~~~~-------~~~--~~~~~i~~~~t~s~~~~ls~---~~~~~dG---~~~~~~i~DE~h~~~~~~~  140 (473)
T pfam03354        76 NQVKLSPFLSIANENK-------LLK--SQKDGIEMKINNNVFKALSN---NGDQYDG---GNPSLAIFDEMHEFKDREL  140 (473)
T ss_pred             HHHHCCHHHHHHHHCC-------CCC--CCCEEEEECCCCCEEEEEEC---CCCCCCC---CCCCEEEEEECCCCCCHHH
T ss_conf             9997398777553011-------013--10015898078968999857---8987669---9872899872230488278


Q ss_pred             HHHHHHHHHCCCCCEEEEEEECC-CCCCCHHHHHHHCCC---------CC--E--EEEEECCC-----------CCCCC-
Q ss_conf             99989874069882589998078-999876887541122---------35--0--46752333-----------28888-
Q gi|254781187|r  208 NKSILGFFTELNPNRFWIMTSNT-RRLNGWFYDIFNIPL---------ED--W--KRYQIDTR-----------TVEGI-  261 (367)
Q Consensus       208 ~e~i~g~Lt~~~~~~~~i~igNP-~r~~g~Fye~~~~~~---------~~--w--~~~~~~~~-----------d~p~~-  261 (367)
                      +++++..+......++ +.|+|. +...+.+++.+...+         ++  .  ..+..+..           -||.+ 
T Consensus       141 ~~~l~sg~~~r~~~l~-~~ITTag~~~~~~~~~~~~~~~~vl~g~~~~~d~~~f~~i~~~d~~dd~~D~~~W~kANP~lg  219 (473)
T pfam03354       141 VSTIVTGMRKQDNPQT-IQITTAGPNRGGPYDEEREYIKRILEGDVERDDDSYFGLIYELDNDDEVKDPAKWIKANPLLG  219 (473)
T ss_pred             HHHHHHHHHCCCCCEE-EEECCCCCCCCCHHHHHHHHHHHHHCCCCCCCCCCEEEEEEECCCCCCCCCHHHHHHHCCCCC
T ss_conf             9999876316888719-997677889887189999999999708777678766999971698877689899998596767


Q ss_pred             ---CHHHHHHHHH-HCCCC--CCEEEEEEEEEECCCCCCEEECHHHHHHHHCCCCCCCCCCCEEEEEECCCCCCCEEEEE
Q ss_conf             ---9889999996-21688--00026888644327789807829998644315777788984899996387788108999
Q gi|254781187|r  262 ---DSGFHEGIIS-RYGLD--SDVARIEILGQFPQQEVNNFIPHNYIEEAMSREAIDDLYAPLIMGCDIAGEGGDKTVVV  335 (367)
Q Consensus       262 ---~~~~i~~~~~-~~ged--S~~~r~ev~G~Fp~~~~d~~ip~~~ie~a~~~~~~~~~~~p~viGvDvAr~G~D~Tvi~  335 (367)
                         +.+.+.+..+ .....  -+.|+...+.++...+++++++.+.+++|.. +...-.+.++++|+|+|.. +|-|+++
T Consensus       220 ~~~~~~~l~~~~~~a~~~p~~~~~f~~k~lN~w~~~~~~~wl~~~~w~~~~~-~~~~~~g~~~~~G~DlS~~-~Dlta~~  297 (473)
T pfam03354       220 SSLTRDNLLKGLIDAIGSPLKMNKFLTKNFNLWMGQDTDSWLTLQDWEQAVF-PPFDINGRRVYIGVDLSMK-GDVTALV  297 (473)
T ss_pred             CCCCHHHHHHHHHHHHHCHHHHHHHHHHHCCCEECCCCCCCCCHHHHHHCCC-CHHHHCCCEEEEEEEECCC-CCCCEEE
T ss_conf             8879999999999986493768999997238634454465789999974789-8578479969999840357-7641379


Q ss_pred             E
Q ss_conf             9
Q gi|254781187|r  336 F  336 (367)
Q Consensus       336 ~  336 (367)
                      +
T Consensus       298 ~  298 (473)
T pfam03354       298 F  298 (473)
T ss_pred             E
T ss_conf             9


No 4  
>COG5323 Uncharacterized conserved protein [Function unknown]
Probab=99.44  E-value=2.3e-13  Score=100.87  Aligned_cols=238  Identities=17%  Similarity=0.187  Sum_probs=170.2

Q ss_pred             EEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             77614886788999999999999708997799971537999999999999999862312112333321000123332211
Q gi|254781187|r   80 CAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLKNTLWAEVSKWLSMLPHRHWFEMQSLSLHPSGWYAELLE  159 (367)
Q Consensus        80 ~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~~~lw~ei~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  159 (367)
                      -.+..|||+|||..-|-++.|.++-.|.  +..+++|.+.+++++..-...+....- .+...+++.            +
T Consensus        39 WL~~GGRGsGKTrAGAeWv~~~AlgkpS--iALvgeTl~DaREVMidGpSGi~~~~~-~~RPr~EaS------------R  103 (410)
T COG5323          39 WLMLGGRGSGKTRAGAEWVTWNALGKPS--IALVGETLHDAREVMIDGPSGIMYHAG-ASRPRLEAS------------R  103 (410)
T ss_pred             EEEECCCCCCCCCCCCEEEEEHHCCCCC--HHHHHCCCCCHHHHHHCCCHHHHHHHH-CCCCHHHHH------------H
T ss_conf             6676365677655553002211026840--655401001146763148278887630-147214545------------5


Q ss_pred             CCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCEEEEECCCCC--CHHHHHHHHHHHHCCCCCEEEEEEECCCCCCCHH
Q ss_conf             11345776126621013544556521011358628999754559--9889999898740698825899980789998768
Q gi|254781187|r  160 QSMGIDSKHYTITCRTYSEERPDTFVGPHNTHGMAVFNDEASGT--PDIINKSILGFFTELNPNRFWIMTSNTRRLNGWF  237 (367)
Q Consensus       160 ~~~~~~~~~~~~~a~~~~~~~~ea~~g~h~~~~~l~ivDEAsgI--~d~i~e~i~g~Lt~~~~~~~~i~igNP~r~~g~F  237 (367)
                      ..+.-++|   +.+..+|.+.|+++.|   ..+++.+.||....  |++.|+.++=.|.-+..+... . .+++++....
T Consensus       104 RRL~WpNG---AvA~~FSsEDPeSLRG---PQFh~AW~DEl~kWk~PqETw~MLqFGLRLGe~PRqv-V-TTTPrp~plL  175 (410)
T COG5323         104 RRLDWPNG---AVAYAFSSEDPDSLRG---PQFHLAWTDELLKWKEPQETWAMLQFGLRLGEDPRQV-V-TTTPRPIPLL  175 (410)
T ss_pred             HHHCCCCC---CEEEEECCCCHHHCCC---CCCCHHHHHHHHCCCCHHHHHHHHHHHHHHCCCCHHH-E-ECCCCCCHHH
T ss_conf             63036885---0144303588032048---5200677788744798488999998766516784010-2-0599862789


Q ss_pred             HHHHHCCCCCEEEEEECCCCCCCCCHHHHHHHHHHCCCCCCEEEEEEEEEECCCCCCEEECHHHHHHHHCCCCCCCCCCC
Q ss_conf             87541122350467523332888898899999962168800026888644327789807829998644315777788984
Q gi|254781187|r  238 YDIFNIPLEDWKRYQIDTRTVEGIDSGFHEGIISRYGLDSDVARIEILGQFPQQEVNNFIPHNYIEEAMSREAIDDLYAP  317 (367)
Q Consensus       238 ye~~~~~~~~w~~~~~~~~d~p~~~~~~i~~~~~~~gedS~~~r~ev~G~Fp~~~~d~~ip~~~ie~a~~~~~~~~~~~p  317 (367)
                      --+..++. --..+.-.+.+..++.+.|++.+.+.||- ...-|||+.|+..+. ++.++..+.++.|++  ..|.|-+.
T Consensus       176 KaLl~dpt-v~~trm~Ta~NAgNLapgFl~t~a~rYgG-TRLgrQEldGelvee-~GaLw~r~dle~c~e--a~p~pL~R  250 (410)
T COG5323         176 KALLADPT-VALTRMGTAANAGNLAPGFLRTLASRYGG-TRLGRQELDGELVEE-DGALWRREDLERCRE--ARPAPLDR  250 (410)
T ss_pred             HHHHCCCC-HHHHHCCCCCCCCCCCHHHHHHHHHHHCC-CCHHHHHCCCEEECC-CCCCCCHHHHHHHHH--CCCCCCCE
T ss_conf             98842861-25450543224456577999999998454-411355528778636-773002878999986--18987023


Q ss_pred             EEEEEECC-CCCCCEEEEEE--ECCCEEEEE
Q ss_conf             89999638-77881089999--708836870
Q gi|254781187|r  318 LIMGCDIA-GEGGDKTVVVF--RRGNIIEHI  345 (367)
Q Consensus       318 ~viGvDvA-r~G~D~Tvi~~--r~G~~v~~i  345 (367)
                      +++.||+- ..|+|++-|.+  +...+.+.+
T Consensus       251 iVVAVDPPA~~g~~sCGIVVaG~~~gr~~VL  281 (410)
T COG5323         251 IVVAVDPPATAGGDSCGIVVAGRRDGRAFVL  281 (410)
T ss_pred             EEEEECCCCCCCCCCEEEEEEEEECCCEEEE
T ss_conf             7997269876778751169988505816996


No 5  
>COG4626 Phage terminase-like protein, large subunit [General function prediction only]
Probab=99.39  E-value=3.2e-10  Score=81.66  Aligned_cols=306  Identities=15%  Similarity=0.116  Sum_probs=171.5

Q ss_pred             CCCCCCCCCCCHHHHHHHHCCCCCC--CCHH--HHHHHHHCCCCC---------CCCCCCCCCCHHHHHHHHHHHHHHHH
Q ss_conf             9755545723378999975232012--5988--885543014668---------88443666842899999998888751
Q gi|254781187|r    1 MPRLISTDQKLEQELHEMLMHAECV--LSFK--NFVMRFFPWGIK---------GKPLEHFSQPHRWQLEFMEAVDVHCH   67 (367)
Q Consensus         1 ~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~--~f~~~~~~w~~~---------~~~~~~~~~p~~wq~~~l~~~~~~~~   67 (367)
                      +++.+.+-+...|.+.-.+  .++.  .++.  .|+..+|.  ++         |.|+    .-.+||.-++-.|.-...
T Consensus         7 ~dg~~~a~~~~k~a~kr~~--~DL~~~~~~e~~~~~i~~~e--~~~~~~~~~~~~~p~----~l~PwQkFiia~l~G~~~   78 (546)
T COG4626           7 IDGWITACKDWKQAAKRHL--SDLPAPIYPEQAERAIAIFE--QLRIVDGPGSPGFPE----SLEPWQKFIVAALFGFYD   78 (546)
T ss_pred             CCCCCCCCHHHHHHHHHHH--HHHHCCCCHHHHHHHHHHHH--HCCCCCCCCCCCCCC----CCCCHHHHHHHHHHHEEE
T ss_conf             4773125788999999777--74104247555236665544--002103677789863----435189999998760350


Q ss_pred             CCCCCCCCCEEEE-EEECCCCCCHHHHHHHHHHHHHHHCC--CCEEEEECCCHHHHHHHHHHHHHHHHHHCCCCCCCCCC
Q ss_conf             2455555411247-76148867889999999999997089--97799971537999999999999999862312112333
Q gi|254781187|r   68 SNVNNSNPTIFKC-AISAGRGIGKTTLNAWMMLWLISTRP--GMSIICIANSETQLKNTLWAEVSKWLSMLPHRHWFEMQ  144 (367)
Q Consensus        68 ~~~~~~~~~~~~~-~v~sgrg~GKS~~~a~~~lw~~~~~~--~~~v~~~A~t~~Q~~~~lw~ei~k~~~~~~~~~~~~~~  144 (367)
                      .+...   -+|+. .|.-+|+-|||+++|.+++..++...  +..+.++||+..|+.+ +|.+++..+...+..      
T Consensus        79 k~T~~---rrf~e~fI~v~RkngKt~l~A~i~~~~~l~~~~~~~~~~i~A~s~~qa~~-~F~~ar~mv~~~~~l------  148 (546)
T COG4626          79 KQTGI---RRFKEAFIFIPRKNGKSTLAAGIMMTALLLNWRSGAGIYILAPSVEQAAN-SFNPARDMVKRDDDL------  148 (546)
T ss_pred             CCCCE---EEEEEEEEEEECCCCHHHHHHHHHHHHHHHHHCCCCEEEEEECCHHHHHH-HHHHHHHHHHHCCCH------
T ss_conf             57870---68889999974578557899999999987653047608998342899988-768999998737213------


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCEEEEECCCCCCH--HHHHHHHHHHHCCCCCE
Q ss_conf             3210001233322111134577612662101354455652101135862899975455998--89999898740698825
Q gi|254781187|r  145 SLSLHPSGWYAELLEQSMGIDSKHYTITCRTYSEERPDTFVGPHNTHGMAVFNDEASGTPD--IINKSILGFFTELNPNR  222 (367)
Q Consensus       145 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~ea~~g~h~~~~~l~ivDEAsgI~d--~i~e~i~g~Lt~~~~~~  222 (367)
                        +....   ....+..+........+-+.++   ++....|.|   ..++|+||-.-..+  +.+.++.+.|-..-+. 
T Consensus       149 --~~~~~---~~~~s~~i~~~~~~s~ik~~aa---~~~~~Dg~~---~~~~I~DEih~f~~~~~~~~~~~~g~~ar~~~-  216 (546)
T COG4626         149 --RDLCN---VQTHSRTITHRKTDSTIKAVAA---DPNTVDGLN---SVGAIIDELHLFGKQEDMYSEAKGGLGARPEG-  216 (546)
T ss_pred             --HHHCC---CCCCEEEEEECCCCEEEEEHHC---CCCCCCCCC---CCEEEEEHHHHHCCHHHHHHHHHHHHCCCCCC-
T ss_conf             --33206---5454048986155111330104---887556787---65488763754167899999997420157676-


Q ss_pred             EEEEEECC-CCCCCHHHHHHHCCC---CC-------EE-EEEECCC-----------CCCCCC----HHHHHH-HHHHCC
Q ss_conf             89998078-999876887541122---35-------04-6752333-----------288889----889999-996216
Q gi|254781187|r  223 FWIMTSNT-RRLNGWFYDIFNIPL---ED-------WK-RYQIDTR-----------TVEGID----SGFHEG-IISRYG  274 (367)
Q Consensus       223 ~~i~igNP-~r~~g~Fye~~~~~~---~~-------w~-~~~~~~~-----------d~p~~~----~~~i~~-~~~~~g  274 (367)
                      +++.|+|- .-..|+|++..+..+   ++       .. ....+..           .||++.    .+++.. .++...
T Consensus       217 l~~~ITT~g~~~~g~~~q~~~y~k~vl~g~~~d~~~f~~i~e~Dd~~e~~dpe~w~kaNPnlg~sv~~~~l~s~~~ka~~  296 (546)
T COG4626         217 LVVYITTSGDPPAGVFKQKLQYAKDVLDGKIKDPHFFPVIYELDEEGEHDDPENWAKANPNLGVSVDEAFLYSEYRKARN  296 (546)
T ss_pred             EEEEEECCCCCCCCHHHHHHHHHHHHHCCCCCCCCEEEEEEECCCCCCCCCHHHHHHCCCCCCCEEEHHHHHHHHHHHHC
T ss_conf             39999668988741899999999998669878821079999768820003867774308876514207777769998731


Q ss_pred             CC--CCEEEEEEEEEECCCCCCEEECHHHHHHHHCC--CCCCCCCCCEEEEEECCCCCCCEEEEEE--EC
Q ss_conf             88--00026888644327789807829998644315--7777889848999963877881089999--70
Q gi|254781187|r  275 LD--SDVARIEILGQFPQQEVNNFIPHNYIEEAMSR--EAIDDLYAPLIMGCDIAGEGGDKTVVVF--RR  338 (367)
Q Consensus       275 ed--S~~~r~ev~G~Fp~~~~d~~ip~~~ie~a~~~--~~~~~~~~p~viGvDvAr~G~D~Tvi~~--r~  338 (367)
                      ..  -..|..+-+..|... .+.+++.+.+++|..+  +.....+..++.|+|.|+. .|-|.+++  |.
T Consensus       297 ~~q~~~dF~tK~lNi~~~~-~~~~~~~~~w~~~~~~~lde~~~~gq~c~~G~Dls~~-~D~ts~al~f~~  364 (546)
T COG4626         297 APQEARDFMTKHLNIWIGA-SDAWFGADFWEQQGRTVLDEILLRGQVCYGGIDLSGL-DDLTSMALVGRY  364 (546)
T ss_pred             CCHHCHHHHHCCCCEEECH-HHCCCCHHHHHHHCCCCCCHHHHCCCEEEEEECCCCC-CCCCCEEEEEEC
T ss_conf             8111227775123315100-1024686899973144565355148668997332345-555410688753


No 6  
>COG1783 XtmB Phage terminase large subunit [General function prediction only]
Probab=99.24  E-value=6.3e-10  Score=79.85  Aligned_cols=233  Identities=18%  Similarity=0.150  Sum_probs=163.6

Q ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             47761488678899999999999970899779997153799999999999999986231211233332100012333221
Q gi|254781187|r   79 KCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLKNTLWAEVSKWLSMLPHRHWFEMQSLSLHPSGWYAELL  158 (367)
Q Consensus        79 ~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~~~lw~ei~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~  158 (367)
                      .+ +.+|||++||..+|--++--++..|+..++|+....+..++.+|.+++-.++.+-..+.|.....           .
T Consensus        27 ~i-~~G~rGS~KSy~~alk~i~kl~~~~~~d~lvIR~v~nt~k~St~~~~~e~l~e~gv~~~f~~~~s-----------~   94 (414)
T COG1783          27 FI-AKGGRGSSKSYATALKNIEKLLSEPGIDVLVIREVENTHKQSTYALFKEALSELGVTKFFKISKS-----------S   94 (414)
T ss_pred             EE-EECCCCCCHHHHHHHHHHHHHHCCCCCCEEEEEEECCCCCHHHHHHHHHHHHHHCCCCEEEEECC-----------C
T ss_conf             99-98267775008889999999970778757999972354412089999999998384011577417-----------8


Q ss_pred             CCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCEEEEECCCCCC-HHHHHHHHHH-HHCCCCCEEEEEEECCCCCCCH
Q ss_conf             1113457761266210135445565210113586289997545599-8899998987-4069882589998078999876
Q gi|254781187|r  159 EQSMGIDSKHYTITCRTYSEERPDTFVGPHNTHGMAVFNDEASGTP-DIINKSILGF-FTELNPNRFWIMTSNTRRLNGW  236 (367)
Q Consensus       159 ~~~~~~~~~~~~~~a~~~~~~~~ea~~g~h~~~~~l~ivDEAsgI~-d~i~e~i~g~-Lt~~~~~~~~i~igNP~r~~g~  236 (367)
                      ...+..++|..+++..   ...|..+.+++......+|+.||+.++ ..-.|.+..+ ......+  +++.+||-.-.+|
T Consensus        95 pe~i~~~~G~ri~F~G---~ddp~klKSi~~~~~s~~WfEE~~e~s~e~~~e~l~~l~~~~~~~~--~~~~snpv~~~pw  169 (414)
T COG1783          95 PEIILKDTGQRIIFKG---LDDPAKLKSIAVNWISDLWFEEASEFSYEDDIELLVELRRRELKGH--IILSSNPVSFNPW  169 (414)
T ss_pred             HHHEECCCCCEEEEEC---CCCHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCC--CEEECCCCCCCCC
T ss_conf             6660212586789945---8987885230100433555787763303456888777641223777--2463264345885


Q ss_pred             HHHHHHC------CCCCEEEEEECCCCCCCCCHHHHHHHHHHCCCCCCEEEEEEEEEECCCCCCEEE------CHHHHHH
Q ss_conf             8875411------223504675233328888988999999621688000268886443277898078------2999864
Q gi|254781187|r  237 FYDIFNI------PLEDWKRYQIDTRTVEGIDSGFHEGIISRYGLDSDVARIEILGQFPQQEVNNFI------PHNYIEE  304 (367)
Q Consensus       237 Fye~~~~------~~~~w~~~~~~~~d~p~~~~~~i~~~~~~~gedS~~~r~ev~G~Fp~~~~d~~i------p~~~ie~  304 (367)
                      -|..|-.      .+.+...++-...|+++++...+++.+....-+.+.||.-+.|+|-- ...-++      |.+++..
T Consensus       170 ~~~~w~~~~~Dek~~~dt~~hhtT~~dn~fL~~~~v~~~ed~k~~d~d~yri~~~gev~v-~~~~v~~~~e~~~~d~v~~  248 (414)
T COG1783         170 TYKHWLEFAVDEKKKADTYIHHTTYRDNLFLGFDDVDELEDLKKNDPDLYRIVRDGEVGV-KNGDVFDQFEVKPFDAVKF  248 (414)
T ss_pred             CHHHHHHHHHCCCCCCCEEEEEEECCCCCCCCHHHHHHHHHHHHCCCCCCEEEEEEEEEE-CCCEECCHHHCCCHHHHHH
T ss_conf             388888887443557866888620135666777899999876412854123899778986-0752546321577288776


Q ss_pred             HHCCCCCCCCCCCEEEEEECCCCCCCEEEEEE
Q ss_conf             43157777889848999963877881089999
Q gi|254781187|r  305 AMSREAIDDLYAPLIMGCDIAGEGGDKTVVVF  336 (367)
Q Consensus       305 a~~~~~~~~~~~p~viGvDvAr~G~D~Tvi~~  336 (367)
                      |.++-..+      ..|+|. |+-.+.++|+.
T Consensus       249 ~i~~i~~~------s~gm~~-Gf~~~~n~l~~  273 (414)
T COG1783         249 AIDNISRP------STGMDF-GFTAKFNRLLK  273 (414)
T ss_pred             HHHHHCCC------CCCCEE-EEEECCCEEEE
T ss_conf             67761556------554024-25740757788


No 7  
>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=99.14  E-value=7e-09  Score=73.43  Aligned_cols=248  Identities=16%  Similarity=0.155  Sum_probs=170.9

Q ss_pred             EEEECCCCCCHHHHHHHHHHHHHHHC-----CCCEEEEECCCHHHHHHHHHHHHHHHHHHCCCC-CCCCCCCCCCCCCCC
Q ss_conf             77614886788999999999999708-----997799971537999999999999999862312-112333321000123
Q gi|254781187|r   80 CAISAGRGIGKTTLNAWMMLWLISTR-----PGMSIICIANSETQLKNTLWAEVSKWLSMLPHR-HWFEMQSLSLHPSGW  153 (367)
Q Consensus        80 ~~v~sgrg~GKS~~~a~~~lw~~~~~-----~~~~v~~~A~t~~Q~~~~lw~ei~k~~~~~~~~-~~~~~~~~~~~~~~~  153 (367)
                      ....+|+++|||+.++..++-.++..     ++..++++..+....++.++..+...+...-.. +.+.......     
T Consensus         4 ~~~~G~~~sgk~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~g~~~~~~~~~~~~~-----   78 (462)
T TIGR01547         4 IIAKGGRGSGKTFAIALKLVLKLLANKDLYGKPRNILAARKVQNSIRDSVFKDIEDLLSDLGLNLYEFKKSKSPM-----   78 (462)
T ss_pred             EEECCCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCEEEEEEHHHHHHHHHHHHHHHHHHHCCCHHHHHHHCCCCC-----
T ss_conf             663266653157899999999998764531488406887402335665668889999987064022132036662-----


Q ss_pred             CCCCCCCCCCCCC---CCEEEEECCCCCCCCCCCCCCCCC--------CCCEEEEECCCCCCHHHHHHHHHHHHCCCCC-
Q ss_conf             3322111134577---612662101354455652101135--------8628999754559988999989874069882-
Q gi|254781187|r  154 YAELLEQSMGIDS---KHYTITCRTYSEERPDTFVGPHNT--------HGMAVFNDEASGTPDIINKSILGFFTELNPN-  221 (367)
Q Consensus       154 ~~~~~~~~~~~~~---~~~~~~a~~~~~~~~ea~~g~h~~--------~~~l~ivDEAsgI~d~i~e~i~g~Lt~~~~~-  221 (367)
                             ..+..+   +..++.. +...+.+..+.+..+.        ....++++||+.++...++.+.++++..+.+ 
T Consensus        79 -------~~~~~~~~~~~~~~f~-G~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ee~~~~~~~~~~~~~~~~r~~~~~~  150 (462)
T TIGR01547        79 -------EIKILNTGGGAYFIFK-GLNSDKPEKLKSGAGLGFTLWEVGLLADLWFEEASELTKEDIKELIPRLREPGGKN  150 (462)
T ss_pred             -------EEEECCCCCCEEEEEE-CCCCCCHHHHHHCCCCCEEEEHHHHHHHHHHHHHHHCCHHHHHHHHHHHCCCCCCE
T ss_conf             -------5776157886179960-65756246643104664100014455656555444301446888887640577750


Q ss_pred             EEEEEEECCCCCCCHHHHHHHCC--C--CCEE---------------EEEECCCCCCCCC----HHHHHHHHHHCCCCCC
Q ss_conf             58999807899987688754112--2--3504---------------6752333288889----8899999962168800
Q gi|254781187|r  222 RFWIMTSNTRRLNGWFYDIFNIP--L--EDWK---------------RYQIDTRTVEGID----SGFHEGIISRYGLDSD  278 (367)
Q Consensus       222 ~~~i~igNP~r~~g~Fye~~~~~--~--~~w~---------------~~~~~~~d~p~~~----~~~i~~~~~~~gedS~  278 (367)
                      ..+++-.||.....++++.|...  .  ....               .++....|+|+++    ..++++....+..+..
T Consensus       151 ~~~~~~~nP~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~dn~~~~~~~~~~~~~~~~~~~~~~~~  230 (462)
T TIGR01547       151 KFIIFSSNPESPLHWVYKDFIENLGEDEFRICDKPPYEYGVVDKKLYILHSTYRDNPFLSGGDVEEYIQELEKLKDRDPA  230 (462)
T ss_pred             EEEEEEECCCCCCCHHHHHHHHCCCCCCHHHHCCCCHHHHHEEECEEEEEEECCCCCCCCCHHHHHHHHHHHHHHCCCHH
T ss_conf             69998408898553056665430477601221011013220000002567420346567611589999999986315613


Q ss_pred             EEEEEEEEEECCCCCCEEECHHHH------HHHHC---CCCCCCCCCCE--EEEEECCCC-CCCEEEEEEECCC
Q ss_conf             026888644327789807829998------64431---57777889848--999963877-8810899997088
Q gi|254781187|r  279 VARIEILGQFPQQEVNNFIPHNYI------EEAMS---REAIDDLYAPL--IMGCDIAGE-GGDKTVVVFRRGN  340 (367)
Q Consensus       279 ~~r~ev~G~Fp~~~~d~~ip~~~i------e~a~~---~~~~~~~~~p~--viGvDvAr~-G~D~Tvi~~r~G~  340 (367)
                      .||..++|+|...++-+.+...+.      ....+   ..+...+..+.  +.|.|.+.. |...++++.....
T Consensus       231 ~~~~~~~G~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~  304 (462)
T TIGR01547       231 LYRRILLGEWVSAADVWSLGLPVLTSEGILFKKLDVKAAYIKELPNDPSDFVGGIDAGGVDGNSPSAYVLLGIE  304 (462)
T ss_pred             HHHHHHHCCCCHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCHHEEEECCCCCCCCCCEEEEEEEEE
T ss_conf             43344423510122332204444344411121110022123431232100013201476666530367887200


No 8  
>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=98.86  E-value=4.9e-07  Score=62.12  Aligned_cols=166  Identities=10%  Similarity=0.053  Sum_probs=102.9

Q ss_pred             HHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHHHHH
Q ss_conf             28999999988887512455555411247761488678899999999999970899779997153799999999999999
Q gi|254781187|r   52 HRWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLKNTLWAEVSKW  131 (367)
Q Consensus        52 ~~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~~~lw~ei~k~  131 (367)
                      .++|.++++.+.+.          .+.+|.+..+-|+|||.+.-.++-|.+...| ..++++-||...+++..=..|...
T Consensus        18 ~Py~~eimd~l~~~----------~v~~V~~~k~aQ~GkT~~~~n~igy~i~~~P-~p~l~v~Pt~~~a~~~s~~rl~Pm   86 (552)
T pfam05876        18 TPYLREIMDALSPP----------SVERVVFMKSAQVGKTELLLNWIGYFIDHDP-APMLVVQPTDDDAKRFSKDRLDPM   86 (552)
T ss_pred             CCHHHHHHHHCCCC----------CCEEEEEEECCCCCHHHHHHHHHHHHHHHCC-CCEEEEECCHHHHHHHHHHHHHHH
T ss_conf             80769999854887----------8449999957870388999999988663089-887999418999999999989999


Q ss_pred             HHHCCCCCC-CCCCCCCCCCCCCCCCCCCCCCC-CCCCCEEEEECCCCCCCCCCCCCCCCCCCCEEEEECCCCCCHH---
Q ss_conf             986231211-23333210001233322111134-5776126621013544556521011358628999754559988---
Q gi|254781187|r  132 LSMLPHRHW-FEMQSLSLHPSGWYAELLEQSMG-IDSKHYTITCRTYSEERPDTFVGPHNTHGMAVFNDEASGTPDI---  206 (367)
Q Consensus       132 ~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~a~~~~~~~~ea~~g~h~~~~~l~ivDEAsgI~d~---  206 (367)
                      ++..|.-.. +...    .   .....+....+ +.+|.....+       +.+..++++...-++++||....+..   
T Consensus        87 i~~sP~L~~~~~~~----~---~r~~~nt~~~K~f~gg~l~~~g-------a~S~~~L~s~~~r~l~~DEvD~~~~~~~~  152 (552)
T pfam05876        87 IRASPALRERLAPA----R---SRDSDNTLLSKRFPGGSLLLIG-------ANSPANLRSRPVRYVILDEVDAYPEDVDG  152 (552)
T ss_pred             HHCCHHHHHHHCCC----C---CCCCCCCEEEEEECCCEEEEEE-------CCCCHHHHCCCCCEEEECCHHHCCCCCCC
T ss_conf             86198999750755----5---6566774124760783799955-------79961430486355885134436545677


Q ss_pred             ---HHHHHHHHHHCCCCCEEEEEEECCCCC-CCHHHHHHH
Q ss_conf             ---999989874069882589998078999-876887541
Q gi|254781187|r  207 ---INKSILGFFTELNPNRFWIMTSNTRRL-NGWFYDIFN  242 (367)
Q Consensus       207 ---i~e~i~g~Lt~~~~~~~~i~igNP~r~-~g~Fye~~~  242 (367)
                         ..+-++.-.++...+.+.+..|+|+.. ++.-...|.
T Consensus       153 eGdP~~La~~R~~tf~~~~K~~~~STPt~~g~s~I~~~~~  192 (552)
T pfam05876       153 EGDPISLAEKRTETFGSRRKILAGSTPTIKGTSRIEALYE  192 (552)
T ss_pred             CCCHHHHHHHHHHHHCCCCEEEEECCCCCCCCCHHHHHHH
T ss_conf             8798999999987530285799983899999668999986


No 9  
>COG4373 Mu-like prophage FluMu protein gp28 [General function prediction only]
Probab=98.84  E-value=2.5e-07  Score=63.96  Aligned_cols=236  Identities=19%  Similarity=0.238  Sum_probs=144.4

Q ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHH---CCCCEEEEECCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             47761488678899999999999970---899779997153799999999999999986231211233332100012333
Q gi|254781187|r   79 KCAISAGRGIGKTTLNAWMMLWLIST---RPGMSIICIANSETQLKNTLWAEVSKWLSMLPHRHWFEMQSLSLHPSGWYA  155 (367)
Q Consensus        79 ~~~v~sgrg~GKS~~~a~~~lw~~~~---~~~~~v~~~A~t~~Q~~~~lw~ei~k~~~~~~~~~~~~~~~~~~~~~~~~~  155 (367)
                      ++|-.| |.+|-|+..|.--+--+..   .-|..|.++......+++-+ .....|.+.+-.      -++.+.......
T Consensus        31 kIAEKS-RRtGlTwaeA~~dV~~Aak~k~eGG~dVfy~gs~~emArEyI-~acamwar~fN~------~A~d~~E~~f~d  102 (509)
T COG4373          31 KIAEKS-RRTGLTWAEAYEDVRDAAKPKREGGMDVFYSGSDLEMAREYI-RACAMWARIFNV------VATDLGEVVFED  102 (509)
T ss_pred             EHHHHC-CCCCCCHHHHHHHHHHHHCCCCCCCCEEEEECCCHHHHHHHH-HHHHHHHHHHHH------HHHHHHHHHHCC
T ss_conf             153530-102642888777898752112258852588447489999999-999999999988------877777876447


Q ss_pred             C---CCCCC-CCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCEEEEECCCCCC--HHHHHHHHHHHHCCCCCEEEEEEEC
Q ss_conf             2---21111-3457761266210135445565210113586289997545599--8899998987406988258999807
Q gi|254781187|r  156 E---LLEQS-MGIDSKHYTITCRTYSEERPDTFVGPHNTHGMAVFNDEASGTP--DIINKSILGFFTELNPNRFWIMTSN  229 (367)
Q Consensus       156 ~---~~~~~-~~~~~~~~~~~a~~~~~~~~ea~~g~h~~~~~l~ivDEAsgI~--d~i~e~i~g~Lt~~~~~~~~i~igN  229 (367)
                      .   ...++ +.+.+|. -+.+   -..||.++.|..|.    +++|||++-.  ++++.++.+ ++-=+.++-  .||+
T Consensus       103 ~dk~~Iltyvi~FasGf-kI~A---LSSnPknlRg~qG~----VviDEaAFHE~ldEllkAA~a-ltmWGa~vR--viSt  171 (509)
T COG4373         103 SDKSAILTYVIAFASGF-KITA---LSSNPKNLRGKQGK----VVIDEAAFHEDLDELLKAAAA-LTMWGAPVR--VIST  171 (509)
T ss_pred             CCHHHHHHHHEEECCCC-EEEE---CCCCCCCCCCCCCC----EEEEHHHHHHHHHHHHHHHHH-HHHCCCCEE--EEEC
T ss_conf             87565567303204774-6766---04797455467884----886236656539999998778-765177248--9962


Q ss_pred             CCCCCCHHHHHHHC---CCCCEEEEEECCCC------------------CCCCCHHHHHHHHHHCCCCCCEEEEEEEEEE
Q ss_conf             89998768875411---22350467523332------------------8888988999999621688000268886443
Q gi|254781187|r  230 TRRLNGWFYDIFNI---PLEDWKRYQIDTRT------------------VEGIDSGFHEGIISRYGLDSDVARIEILGQF  288 (367)
Q Consensus       230 P~r~~g~Fye~~~~---~~~~w~~~~~~~~d------------------~p~~~~~~i~~~~~~~gedS~~~r~ev~G~F  288 (367)
                      -++..+.|+++-..   +++.|.++.+.-.|                  .|..-..|..+..+.-|.+ +-+..|+.|. 
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             CCCCCCEEECHHHHHHHHCCCCCC------------------------------------CCCCCEEEEEECCCCCCCEE
Q ss_conf             277898078299986443157777------------------------------------88984899996387788108
Q gi|254781187|r  289 PQQEVNNFIPHNYIEEAMSREAID------------------------------------DLYAPLIMGCDIAGEGGDKT  332 (367)
Q Consensus       289 p~~~~d~~ip~~~ie~a~~~~~~~------------------------------------~~~~p~viGvDvAr~G~D~T  332 (367)
                      |..+.+++||..+|++++-+++..                                    .|......|||.||. +|-|
T Consensus       250 Pk~s~gAYIphalie~a~~~~vp~l~fe~~~~f~~~~~~~r~~~~~~~cl~~l~P~Lqalnp~~r~~fGvDfaR~-~DLs  328 (509)
T COG4373         250 PKDSTGAYIPHALIEAAVAAEVPDLIFELGSEFHDIPAWLRESEVLTWCLPDLRPALQALNPGGRLYFGVDFARK-RDLS  328 (509)
T ss_pred             CCCCCCCCCCHHHHHHHHHCCCCCEEEECCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCEEECCCCCCC-CCCE
T ss_conf             566776646678999887547985179757455423566424566665344356898732999716521220225-6734


Q ss_pred             EEEE
Q ss_conf             9999
Q gi|254781187|r  333 VVVF  336 (367)
Q Consensus       333 vi~~  336 (367)
                      |+++
T Consensus       329 v~~v  332 (509)
T COG4373         329 VLWV  332 (509)
T ss_pred             EEEE
T ss_conf             9998


No 10 
>COG1061 SSL2 DNA or RNA helicases of superfamily II [Transcription / DNA replication, recombination, and repair]
Probab=98.71  E-value=1e-06  Score=60.14  Aligned_cols=162  Identities=18%  Similarity=0.143  Sum_probs=97.7

Q ss_pred             CCCCHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHH
Q ss_conf             66842899999998888751245555541124776148867889999999999997089977999715379999999999
Q gi|254781187|r   48 FSQPHRWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLKNTLWAE  127 (367)
Q Consensus        48 ~~~p~~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~~~lw~e  127 (367)
                      .-.|+.+|.+.++++-.+... ..       |..|..+-|.|||.+++..+-..-     .++++++|+..-+.+-- ..
T Consensus        34 ~~~lr~yQ~~al~a~~~~~~~-~~-------~gvivlpTGaGKT~va~~~~~~~~-----~~~Lvlv~~~~L~~Qw~-~~   99 (442)
T COG1061          34 EFELRPYQEEALDALVKNRRT-ER-------RGVIVLPTGAGKTVVAAEAIAELK-----RSTLVLVPTKELLDQWA-EA   99 (442)
T ss_pred             CCCCHHHHHHHHHHHHHHCCC-CC-------CEEEEECCCCCHHHHHHHHHHHHC-----CCEEEEECCHHHHHHHH-HH
T ss_conf             788859999999999962225-78-------679996799988999999999826-----98899978299999999-99


Q ss_pred             HHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCEEEEECCCCCCHHH
Q ss_conf             99999862312112333321000123332211113457761266210135445565210113586289997545599889
Q gi|254781187|r  128 VSKWLSMLPHRHWFEMQSLSLHPSGWYAELLEQSMGIDSKHYTITCRTYSEERPDTFVGPHNTHGMAVFNDEASGTPDII  207 (367)
Q Consensus       128 i~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~ea~~g~h~~~~~l~ivDEAsgI~d~i  207 (367)
                      +.+.......          +    ............ ....+++-++.....  .+.-+.+.++.|+|+||+..++...
T Consensus       100 ~~~~~~~~~~----------~----g~~~~~~~~~~~-~~i~vat~qtl~~~~--~l~~~~~~~~~liI~DE~Hh~~a~~  162 (442)
T COG1061         100 LKKFLLLNDE----------I----GIYGGGEKELEP-AKVTVATVQTLARRQ--LLDEFLGNEFGLIIFDEVHHLPAPS  162 (442)
T ss_pred             HHHHCCCCCC----------C----CEECCCCCCCCC-CCEEEEEEHHHHHHH--HHHHHCCCCCCEEEEECCCCCCCHH
T ss_conf             9973488676----------6----033687233577-748999838976415--5554035666759997524578477


Q ss_pred             HHHHHHHHHCCCCCEEEEEEECCCCCC-CHHHHHHH
Q ss_conf             999898740698825899980789998-76887541
Q gi|254781187|r  208 NKSILGFFTELNPNRFWIMTSNTRRLN-GWFYDIFN  242 (367)
Q Consensus       208 ~e~i~g~Lt~~~~~~~~i~igNP~r~~-g~Fye~~~  242 (367)
                      +..+...++....  ..-++.+|.|.. +...+.+.
T Consensus       163 ~~~~~~~~~~~~~--~LGLTATp~R~D~~~~~~l~~  196 (442)
T COG1061         163 YRRILELLSAAYP--RLGLTATPEREDGGRIGDLFD  196 (442)
T ss_pred             HHHHHHHHHCCCE--EEEEECCCCCCCCCCHHHHHH
T ss_conf             9999997510310--467714872448775248774


No 11 
>COG1444 Predicted P-loop ATPase fused to an acetyltransferase [General function prediction only]
Probab=98.62  E-value=3.6e-06  Score=56.83  Aligned_cols=149  Identities=19%  Similarity=0.143  Sum_probs=84.1

Q ss_pred             HHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCC-CCEEEEECCCHHHHHHHHHHHHHHHH
Q ss_conf             99999998888751245555541124776148867889999999999997089-97799971537999999999999999
Q gi|254781187|r   54 WQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRP-GMSIICIANSETQLKNTLWAEVSKWL  132 (367)
Q Consensus        54 wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~-~~~v~~~A~t~~Q~~~~lw~ei~k~~  132 (367)
                      =|.+++..+....+.+..       -++|.|.||=|||++....+ ..+...- ..+|+||||+...+. .++.-+.+-+
T Consensus       215 dQ~~~l~~~~~l~~~~~~-------~~vlTAdRGRGKSA~lGi~~-~~~~~~~~~~~iiVTAP~~~nv~-~Lf~fa~~~l  285 (758)
T COG1444         215 DQAEALEILERLLDAPKR-------ALVLTADRGRGKSAALGIAL-AAAARLAGSVRIIVTAPTPANVQ-TLFEFAGKGL  285 (758)
T ss_pred             HHHHHHHHHHHHHCCCCC-------EEEEECCCCCCHHHHHHHHH-HHHHHHCCCCEEEEECCCHHHHH-HHHHHHHHHH
T ss_conf             189999999999708983-------59998677874768874999-99997337720899679778899-9999998769


Q ss_pred             HHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCEEEEECCCCCCHHHHHHHH
Q ss_conf             86231211233332100012333221111345776126621013544556521011358628999754559988999989
Q gi|254781187|r  133 SMLPHRHWFEMQSLSLHPSGWYAELLEQSMGIDSKHYTITCRTYSEERPDTFVGPHNTHGMAVFNDEASGTPDIINKSIL  212 (367)
Q Consensus       133 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~ea~~g~h~~~~~l~ivDEAsgI~d~i~e~i~  212 (367)
                      +.+-.++....+..-             ++....+..+.    ..=.+|..-+  ..  ..++++||||+||=.+...+.
T Consensus       286 ~~lg~~~~v~~~~~g-------------~~~~~~~~~~~----i~y~~P~~a~--~~--~DllvVDEAAaIplplL~~l~  344 (758)
T COG1444         286 EFLGYKRKVAPDALG-------------EIREVSGDGFR----IEYVPPDDAQ--EE--ADLLVVDEAAAIPLPLLHKLL  344 (758)
T ss_pred             HHHCCCCCCCCCCCC-------------CEEEECCCCEE----EEEECCHHHC--CC--CCEEEEEHHHCCCHHHHHHHH
T ss_conf             982774555634424-------------40000477425----7751750012--56--888998103128869999998


Q ss_pred             HHHHCCCCCEEEEEEECCCCCCCH
Q ss_conf             874069882589998078999876
Q gi|254781187|r  213 GFFTELNPNRFWIMTSNTRRLNGW  236 (367)
Q Consensus       213 g~Lt~~~~~~~~i~igNP~r~~g~  236 (367)
                          ..-.+.++..+.+=..++|.
T Consensus       345 ----~~~~rv~~sTTIhGYEGtGR  364 (758)
T COG1444         345 ----RRFPRVLFSTTIHGYEGTGR  364 (758)
T ss_pred             ----HHCCCEEEEEEECCCCCCCH
T ss_conf             ----64481699974024466771


No 12 
>smart00487 DEXDc DEAD-like helicases superfamily.
Probab=98.58  E-value=1e-06  Score=60.14  Aligned_cols=173  Identities=13%  Similarity=0.023  Sum_probs=92.5

Q ss_pred             CCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHH
Q ss_conf             36668428999999988887512455555411247761488678899999999999970899779997153799999999
Q gi|254781187|r   46 EHFSQPHRWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLKNTLW  125 (367)
Q Consensus        46 ~~~~~p~~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~~~lw  125 (367)
                      ..+..|+++|.++++.+....           ..+.|.++-|+|||..++.+++..+......++++++|+...+.+. .
T Consensus         4 ~~~~~~~~~Q~~~~~~~~~~~-----------~~~~i~~~tGsGKT~~~~~~~~~~~~~~~~~~~li~~P~~~l~~q~-~   71 (201)
T smart00487        4 FGFEPLRPYQKEAIEALLSGL-----------RDVILAAPTGSGKTLAALLPALEALKRGKGKRVLVLVPTRELAEQW-A   71 (201)
T ss_pred             CCCCCCCHHHHHHHHHHHCCC-----------CCEEEECCCCCCHHHHHHHHHHHHHHCCCCCEEEEEECCHHHHHHH-H
T ss_conf             379999988999999998389-----------9889989999609999999999986338997599990859999999-9


Q ss_pred             HHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC-CCEEEEECCCCCCCCCCCCCCCCCCCCEEEEECCCCCC
Q ss_conf             99999998623121123333210001233322111134577-61266210135445565210113586289997545599
Q gi|254781187|r  126 AEVSKWLSMLPHRHWFEMQSLSLHPSGWYAELLEQSMGIDS-KHYTITCRTYSEERPDTFVGPHNTHGMAVFNDEASGTP  204 (367)
Q Consensus       126 ~ei~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~a~~~~~~~~ea~~g~h~~~~~l~ivDEAsgI~  204 (367)
                      .++.++........-........       ........... ...+.+-..... ...... .......++|+|||..+.
T Consensus        72 ~~~~~~~~~~~~~~~~~~~~~~~-------~~~~~~~~~~~~~i~i~t~~~l~~-~~~~~~-~~~~~~~~vIiDE~H~~~  142 (201)
T smart00487       72 EELKKLGPSLGLKVVGLYGGDSK-------REQLRKLESGKTDILVTTPGRLLD-LLENDL-LELSNVDLVILDEAHRLL  142 (201)
T ss_pred             HHHHHCCCCCEEEEEEEECCCCH-------HHHHHHHHCCCCCEEEECHHHHHH-HHHHCC-CCCCCCEEEEEECHHHHH
T ss_conf             88601021020445565247737-------999999975999899955899999-997275-452543199998967751


Q ss_pred             H-HHHHHHHHHHH--CCCCCEEEEEEECCCCCCCHHHHH
Q ss_conf             8-89999898740--698825899980789998768875
Q gi|254781187|r  205 D-IINKSILGFFT--ELNPNRFWIMTSNTRRLNGWFYDI  240 (367)
Q Consensus       205 d-~i~e~i~g~Lt--~~~~~~~~i~igNP~r~~g~Fye~  240 (367)
                      + .....+...+.  ..+.+ ++++.+||+...-.+...
T Consensus       143 ~~~~~~~~~~~~~~~~~~~~-~i~lSAT~~~~~~~~~~~  180 (201)
T smart00487      143 DGGFGDQLEKLLKLLPKNVQ-LLLLSATPPEEIENLLEL  180 (201)
T ss_pred             CCCCHHHHHHHHHHCCCCCC-EEEECCCCCHHHHHHHHH
T ss_conf             25709999999996799997-899924898689999999


No 13 
>PRK10875 recD exonuclease V subunit alpha; Provisional
Probab=98.45  E-value=1.6e-05  Score=52.92  Aligned_cols=156  Identities=20%  Similarity=0.154  Sum_probs=83.7

Q ss_pred             HHHHHHHHHHHHHHHHCCCCCCCCCEEEE-EEECCCCCCHHHHHHHHHHHH--HHHCCCCEEEEECCCHHHHHHHHHHHH
Q ss_conf             28999999988887512455555411247-761488678899999999999--970899779997153799999999999
Q gi|254781187|r   52 HRWQLEFMEAVDVHCHSNVNNSNPTIFKC-AISAGRGIGKTTLNAWMMLWL--ISTRPGMSIICIANSETQLKNTLWAEV  128 (367)
Q Consensus        52 ~~wq~~~l~~~~~~~~~~~~~~~~~~~~~-~v~sgrg~GKS~~~a~~~lw~--~~~~~~~~v~~~A~t~~Q~~~~lw~ei  128 (367)
                      ..||+.+...   -+++          ++ .|.+|=|+|||+.++.++.-+  +...++.+|..+|||.+-+.... .-+
T Consensus       149 ~dwQk~A~a~---Al~~----------~~~vIsGGPGTGKTttV~~lLa~l~~~~~~~~l~I~LaAPTGKAAaRL~-Esi  214 (607)
T PRK10875        149 VNWQKVAAAV---ALTR----------RISVISGGPGTGKTTTVAKLLAALIQLADGERCRIRLAAPTGKAAARLT-ESL  214 (607)
T ss_pred             CCHHHHHHHH---HHHC----------CEEEEECCCCCCHHHHHHHHHHHHHHHCCCCCCEEEEECCHHHHHHHHH-HHH
T ss_conf             5189999999---8755----------7789967999877889999999999964589970899882289999999-999


Q ss_pred             HHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCEEEEECCCCCCHHHH
Q ss_conf             99998623121123333210001233322111134577612662101354455652101135862899975455998899
Q gi|254781187|r  129 SKWLSMLPHRHWFEMQSLSLHPSGWYAELLEQSMGIDSKHYTITCRTYSEERPDTFVGPHNTHGMAVFNDEASGTPDIIN  208 (367)
Q Consensus       129 ~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~ea~~g~h~~~~~l~ivDEAsgI~d~i~  208 (367)
                      .+.+..++.....      ....+....-.-.-++..+++..   .....+||-        ...++||||||.|+-..+
T Consensus       215 ~~~~~~l~~~~~~------~~~~p~~a~TiHRLLg~~p~~~~---f~~~~~nPL--------~~DvlIVDEASMVDl~Lm  277 (607)
T PRK10875        215 GKALRQLPLTDEQ------KKRIPEDASTLHRLLGAQPGSQR---LRYHAGNPL--------HLDVLVVDEASMIDLPMM  277 (607)
T ss_pred             HHHHHHCCCCHHH------HHCCCCCCEEHHHHCCCCCCCCC---CCCCCCCCC--------CCCEEEEECCHHHHHHHH
T ss_conf             8787534766566------63376556658975296789876---565779999--------889899907336659999


Q ss_pred             HHHHHHHHCCCCCEEEEEEECCC-----CCCCHHHHHH
Q ss_conf             99898740698825899980789-----9987688754
Q gi|254781187|r  209 KSILGFFTELNPNRFWIMTSNTR-----RLNGWFYDIF  241 (367)
Q Consensus       209 e~i~g~Lt~~~~~~~~i~igNP~-----r~~g~Fye~~  241 (367)
                      ..+.-++.. +.++  +++|.|.     +.+..|.|+.
T Consensus       278 ~~LL~Alp~-~aRL--ILvGD~dQLpSVgaGaVL~DL~  312 (607)
T PRK10875        278 SRLIDALPD-HARV--IFLGDRDQLASVEAGAVLGDIC  312 (607)
T ss_pred             HHHHHHCCC-CCEE--EEECCHHHCCCCCCCCCHHHHH
T ss_conf             999982899-9889--9965623247888882179999


No 14 
>PRK13766 Hef nuclease; Provisional
Probab=98.44  E-value=5.9e-06  Score=55.47  Aligned_cols=159  Identities=11%  Similarity=0.068  Sum_probs=80.7

Q ss_pred             CCCCHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHH
Q ss_conf             66842899999998888751245555541124776148867889999999999997089977999715379999999999
Q gi|254781187|r   48 FSQPHRWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLKNTLWAE  127 (367)
Q Consensus        48 ~~~p~~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~~~lw~e  127 (367)
                      .-.+|.+|.++++.--.   +          ++.|+.+.|+|||.+++.++..++- .++.|++.+|||-.-+.+-. ..
T Consensus        13 ~ie~R~YQ~el~~~Al~---~----------NtiVvLPTG~GKT~IA~lvi~~~l~-~~~gKilFLaPT~pLV~Qq~-~~   77 (764)
T PRK13766         13 TIEARLYQQLLAAKALK---G----------NTLVVLPTGLGKTAIALLVIAERLQ-KYGGKVLILAPTKPLVEQHA-EF   77 (764)
T ss_pred             CCCCCHHHHHHHHHHHH---C----------CEEEEECCCCCHHHHHHHHHHHHHH-HCCCEEEEECCCHHHHHHHH-HH
T ss_conf             77653879999999985---8----------9899959986689999999999997-48988999858888999999-99


Q ss_pred             HHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCEEEEECCCCC-CHH
Q ss_conf             9999986231211233332100012333221111345776126621013544556521011358628999754559-988
Q gi|254781187|r  128 VSKWLSMLPHRHWFEMQSLSLHPSGWYAELLEQSMGIDSKHYTITCRTYSEERPDTFVGPHNTHGMAVFNDEASGT-PDI  206 (367)
Q Consensus       128 i~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~ea~~g~h~~~~~l~ivDEAsgI-~d~  206 (367)
                      +++.......+-. ..+ +...+      ..+...-......+++.+.....-..+  -+.-..+.|+|+|||... .+.
T Consensus        78 ~~~~l~i~~~~i~-~lt-G~~~~------~~r~~~w~~~~Viv~TPQvl~ndL~~g--~i~l~dv~lLVfDEaHha~Gnh  147 (764)
T PRK13766         78 FRKFLNIDPEKIV-VLT-GEISP------EKRAALWEKAKVIVATPQVIENDLLAG--RISLEDVSLLIFDEAHRAVGNY  147 (764)
T ss_pred             HHHHCCCCCCEEE-EEE-CCCCH------HHHHHHHCCCCEEEECCHHHHHHHHHC--CCCHHHCCEEEEECCCCCCCCC
T ss_conf             9997099955289-998-88782------768998607999999908999999829--8678882289997466666776


Q ss_pred             HH-HHHHHHHHCCCCCEEEEEEECCC
Q ss_conf             99-99898740698825899980789
Q gi|254781187|r  207 IN-KSILGFFTELNPNRFWIMTSNTR  231 (367)
Q Consensus       207 i~-e~i~g~Lt~~~~~~~~i~igNP~  231 (367)
                      .+ .++.-.+.......+.-++.+|.
T Consensus       148 ~Y~~I~~~y~~~~~~PrILGLTASPG  173 (764)
T PRK13766        148 AYVFIAERYHEDAKNPLVLGLTASPG  173 (764)
T ss_pred             CHHHHHHHHHHCCCCCEEEEECCCCC
T ss_conf             28999999985377855885036887


No 15 
>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=98.41  E-value=4.2e-06  Score=56.37  Aligned_cols=138  Identities=17%  Similarity=0.205  Sum_probs=89.9

Q ss_pred             HHHHHHHHHHHHHHHHCCCCCCCCCEEEEE-EECCCCCCHHHHHHHHHHHHHHHC-----------CCCEEEEECCCHHH
Q ss_conf             289999999888875124555554112477-614886788999999999999708-----------99779997153799
Q gi|254781187|r   52 HRWQLEFMEAVDVHCHSNVNNSNPTIFKCA-ISAGRGIGKTTLNAWMMLWLISTR-----------PGMSIICIANSETQ  119 (367)
Q Consensus        52 ~~wq~~~l~~~~~~~~~~~~~~~~~~~~~~-v~sgrg~GKS~~~a~~~lw~~~~~-----------~~~~v~~~A~t~~Q  119 (367)
                      ..=|+++|..+..+             ||. +.+|=|+|||+++-..+-.+....           .+.+|+..|||.+=
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             HHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCCCCCCCCC-CCC--CCCCEEE
Q ss_conf             9999999999999862312112333321000123332211113457761266210135445565210-113--5862899
Q gi|254781187|r  120 LKNTLWAEVSKWLSMLPHRHWFEMQSLSLHPSGWYAELLEQSMGIDSKHYTITCRTYSEERPDTFVG-PHN--THGMAVF  196 (367)
Q Consensus       120 ~~~~lw~ei~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~ea~~g-~h~--~~~~l~i  196 (367)
                      +|..  .|+---...-++++                      ++.+..              +.-.+ .|-  -++.|+|
T Consensus       419 AkRl--~E~TG~~a~TIHRL----------------------lG~~~~--------------~~~~~k~~~~~~~~DL~I  460 (769)
T TIGR01448       419 AKRL--AEVTGLEALTIHRL----------------------LGYGSD--------------TKSENKNLEDPIDADLLI  460 (769)
T ss_pred             HHHC--CCCCCCHHHHHHHH----------------------HCCCCC--------------CCCCCHHHCCCCCCCEEE
T ss_conf             8851--10026212347786----------------------368988--------------873211011347877699


Q ss_pred             EECCCCCCHHHHHHHHHHHHCCCCCEEEEEEEC-----CCCCCCHHHHHHHC
Q ss_conf             975455998899998987406988258999807-----89998768875411
Q gi|254781187|r  197 NDEASGTPDIINKSILGFFTELNPNRFWIMTSN-----TRRLNGWFYDIFNI  243 (367)
Q Consensus       197 vDEAsgI~d~i~e~i~g~Lt~~~~~~~~i~igN-----P~r~~g~Fye~~~~  243 (367)
                      |||.|.|++-.+..+..++.+ +++++  ++|-     |-.++..|-|+-+.
T Consensus       461 vDE~SM~Dt~L~~~lL~a~P~-~a~ll--lVGD~DQLPSV~pG~VL~DLi~s  509 (769)
T TIGR01448       461 VDESSMVDTWLASSLLAAVPD-HARLL--LVGDADQLPSVGPGQVLKDLIQS  509 (769)
T ss_pred             EECCCHHHHHHHHHHHHHCCC-CCEEE--EECCCCCCCCCCCCHHHHHHHHC
T ss_conf             814621889999999861797-77798--88376888988644089999846


No 16 
>pfam04851 ResIII Type III restriction enzyme, res subunit.
Probab=98.34  E-value=6.8e-06  Score=55.12  Aligned_cols=100  Identities=20%  Similarity=0.295  Sum_probs=69.1

Q ss_pred             CCHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHHH
Q ss_conf             84289999999888875124555554112477614886788999999999999708997799971537999999999999
Q gi|254781187|r   50 QPHRWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLKNTLWAEVS  129 (367)
Q Consensus        50 ~p~~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~~~lw~ei~  129 (367)
                      ..|+||.++++++.++-            |..|.++-|+|||.+++.++.++.  .++.++++++|+..-+.+.      
T Consensus         3 ~LR~yQ~~a~~~~~~~~------------~~~i~~pTGsGKT~~~~~~i~~~~--~~~~~~lvlvp~~~L~~Q~------   62 (103)
T pfam04851         3 ELRPYQIEAIRNLLEKK------------RGLIVMATGSGKTLTAAKLIARLL--KGKKKVLFLVPRKDLLEQA------   62 (103)
T ss_pred             CCCHHHHHHHHHHHHCC------------CEEEEECCCCCHHHHHHHHHHHHH--HCCCCEEEEECCHHHHHHH------
T ss_conf             87299999999999639------------869995899987999999999998--4699299990829999999------


Q ss_pred             HHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCEEEEECCCCCCHH-HH
Q ss_conf             99986231211233332100012333221111345776126621013544556521011358628999754559988-99
Q gi|254781187|r  130 KWLSMLPHRHWFEMQSLSLHPSGWYAELLEQSMGIDSKHYTITCRTYSEERPDTFVGPHNTHGMAVFNDEASGTPDI-IN  208 (367)
Q Consensus       130 k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~ea~~g~h~~~~~l~ivDEAsgI~d~-i~  208 (367)
                        .+.                                                          .++|+|||...+.. .|
T Consensus        63 --~~~----------------------------------------------------------~lii~DE~H~~~a~~~~   82 (103)
T pfam04851        63 --LEE----------------------------------------------------------FVIIIDEAHHSSAKTKY   82 (103)
T ss_pred             --HHH----------------------------------------------------------HHHHHHHHHHCCCHHHH
T ss_conf             --996----------------------------------------------------------56460163523537899


Q ss_pred             HHHHHHHHCCCCCEEEEEEECCCC
Q ss_conf             998987406988258999807899
Q gi|254781187|r  209 KSILGFFTELNPNRFWIMTSNTRR  232 (367)
Q Consensus       209 e~i~g~Lt~~~~~~~~i~igNP~r  232 (367)
                      ..+...+.   ....+-++.+|.|
T Consensus        83 ~~l~~~~~---~~~~lGlTATP~R  103 (103)
T pfam04851        83 RKILEYFK---PAFLLGLTATPER  103 (103)
T ss_pred             HHHHHHCC---CCEEEEEEECCCC
T ss_conf             99999577---2608998008889


No 17 
>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=98.21  E-value=3.8e-05  Score=50.55  Aligned_cols=156  Identities=19%  Similarity=0.161  Sum_probs=86.6

Q ss_pred             HHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCC-----CEEEEECCCHHHHHHHHHH
Q ss_conf             28999999988887512455555411247761488678899999999999970899-----7799971537999999999
Q gi|254781187|r   52 HRWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPG-----MSIICIANSETQLKNTLWA  126 (367)
Q Consensus        52 ~~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~-----~~v~~~A~t~~Q~~~~lw~  126 (367)
                      +.||.=++...-.   ++        | ..|.+|=|+|||+.++-+++=....-+.     .+|.++|||++=+. .+-.
T Consensus       229 ~D~Q~~a~~~aL~---~~--------f-~li~GGPGTGKTTTv~~LL~al~~~~~~~G~~~~~I~l~APTGKAa~-RL~e  295 (753)
T TIGR01447       229 TDWQKVAVALALK---SN--------F-SLITGGPGTGKTTTVARLLLALIKQSPKQGKPRLRIALAAPTGKAAA-RLAE  295 (753)
T ss_pred             HHHHHHHHHHHHH---CC--------E-EEEECCCCCCHHHHHHHHHHHHHHHHHHCCCCCEEEEEECCCHHHHH-HHHH
T ss_conf             3799999999860---87--------6-89987988977899999999999989864997404788668447999-9999


Q ss_pred             HHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCEEEEECCCCCCHH
Q ss_conf             99999986231211233332100012333221111345776126621013544556521011358628999754559988
Q gi|254781187|r  127 EVSKWLSMLPHRHWFEMQSLSLHPSGWYAELLEQSMGIDSKHYTITCRTYSEERPDTFVGPHNTHGMAVFNDEASGTPDI  206 (367)
Q Consensus       127 ei~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~ea~~g~h~~~~~l~ivDEAsgI~d~  206 (367)
                      -|.+....+....- .+.  +...........+  +.---|...+....++.+....      -....+||||||.|+=.
T Consensus       296 sl~~~~~~L~~~~~-aid--~~~~~~~~~~~~T--iHrLLG~~~I~~~~fr~h~~N~------L~~DVLvvDEaSMVdl~  364 (753)
T TIGR01447       296 SLRKAVKKLAAENM-AID--EDLIAALPSEATT--IHRLLGIKPIDTKRFRHHERNP------LPLDVLVVDEASMVDLP  364 (753)
T ss_pred             HHHHHHHHHHHHCC-CCC--HHHHCCCCHHHHH--HHHHHCCCCCCCCCCCCCCCCC------CCCCEEEECCCHHCCHH
T ss_conf             99988632234236-658--7985487204568--8886166147876776777788------98552787060022679


Q ss_pred             HHHHHHHHHHCCCCC------EEEEEEECCCC
Q ss_conf             999989874069882------58999807899
Q gi|254781187|r  207 INKSILGFFTELNPN------RFWIMTSNTRR  232 (367)
Q Consensus       207 i~e~i~g~Lt~~~~~------~~~i~igNP~r  232 (367)
                      .+..+.-++.... |      .-+|++|-++-
T Consensus       365 lm~kL~~A~~~~~-k~~KLy~~~LIllGD~nQ  395 (753)
T TIGR01447       365 LMAKLLKALPPNT-KDKKLYADRLILLGDKNQ  395 (753)
T ss_pred             HHHHHHHHCCCCC-CCCCHHHCCCCEECCCCC
T ss_conf             9999997226300-132010102001226788


No 18 
>pfam02562 PhoH PhoH-like protein. PhoH is a cytoplasmic protein and predicted ATPase that is induced by phosphate starvation.
Probab=98.21  E-value=1.4e-05  Score=53.24  Aligned_cols=56  Identities=18%  Similarity=0.025  Sum_probs=46.2

Q ss_pred             CHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHH
Q ss_conf             42899999998888751245555541124776148867889999999999997089977999715379
Q gi|254781187|r   51 PHRWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSET  118 (367)
Q Consensus        51 p~~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~  118 (367)
                      -++-|+.+++.+.++.            -+.+.++-|+|||++++..++..+......+++++.|.-.
T Consensus         5 ~~~~Q~~~~~~l~~~~------------iv~~~GpAGtGKT~la~~~al~~l~~~~~~kiii~Rp~v~   60 (205)
T pfam02562         5 KTLGQKRYVEAIRKND------------IVFGIGPAGTGKTYLAVAAAVDALKDGKVKRIILTRPAVE   60 (205)
T ss_pred             CCHHHHHHHHHHHCCC------------EEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEEECCCC
T ss_conf             9888999999971798------------0799899986099999999999997189437999757712


No 19 
>PRK10536 hypothetical protein; Provisional
Probab=98.20  E-value=5.5e-05  Score=49.56  Aligned_cols=184  Identities=16%  Similarity=0.121  Sum_probs=95.3

Q ss_pred             CHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHH---------
Q ss_conf             42899999998888751245555541124776148867889999999999997089977999715379999---------
Q gi|254781187|r   51 PHRWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLK---------  121 (367)
Q Consensus        51 p~~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~---------  121 (367)
                      -++-|.+.++.|.++.            -+-..++-|+|||++++.+++-.+....-.++++|.|.-.--+         
T Consensus        60 kt~~Q~~yi~~i~~~~------------ivf~~GpAGTGKT~lA~a~Al~~l~~~~~~kIIltRP~V~~ge~lGfLPGdl  127 (262)
T PRK10536         60 RNEAQLHYLKAIESKQ------------LIFATGEAGCGKTWISAAKAAEALIHKDVDRIIVTRPVLQADEDLGFLPGDI  127 (262)
T ss_pred             CCHHHHHHHHHHHHCC------------EEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCCCCCCCCCH
T ss_conf             9864999999986198------------3999899987589999999999998588868999667875676667698987


Q ss_pred             -HHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCEEEEECC
Q ss_conf             -9999999999986231211233332100012333221111345776126621013544556521011358628999754
Q gi|254781187|r  122 -NTLWAEVSKWLSMLPHRHWFEMQSLSLHPSGWYAELLEQSMGIDSKHYTITCRTYSEERPDTFVGPHNTHGMAVFNDEA  200 (367)
Q Consensus       122 -~~lw~ei~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~ea~~g~h~~~~~l~ivDEA  200 (367)
                       +.+.+.+.-.+..+-..           +.   ....+..+....|..-+        .|-++---+..+-.++|+|||
T Consensus       128 ~EK~~Pyl~Pi~D~L~~~-----------lg---~~~~~~~~~~e~G~Iei--------~PlafmRGrTf~na~IIvDEa  185 (262)
T PRK10536        128 AEKFAPYFRPVYDVLVRR-----------LG---ASFMQYCLRPEIGKVEI--------APFAYMRGRTFENAVVILDEA  185 (262)
T ss_pred             HHHHHHHHHHHHHHHHHH-----------HC---HHHHHHHHHHHCCCEEE--------EEHHHHCCCCCCCEEEEEEHH
T ss_conf             998878887899999999-----------68---59999998730594899--------875874477514428998412


Q ss_pred             CCCCHHHHHHHHHHHHCCCCCEEEEEEECCCCC------CCHHHHHHHCCC--CCEEEEEECCCCCCCCCHHHHHHHHHH
Q ss_conf             559988999989874069882589998078999------876887541122--350467523332888898899999962
Q gi|254781187|r  201 SGTPDIINKSILGFFTELNPNRFWIMTSNTRRL------NGWFYDIFNIPL--EDWKRYQIDTRTVEGIDSGFHEGIISR  272 (367)
Q Consensus       201 sgI~d~i~e~i~g~Lt~~~~~~~~i~igNP~r~------~g~Fye~~~~~~--~~w~~~~~~~~d~p~~~~~~i~~~~~~  272 (367)
                      +-....-...+.   |--+....+++.|.+.-.      .+-+.+......  +....+.++..|  .+....+.+....
T Consensus       186 QN~T~~qmk~iL---TRiG~~SKiVi~GD~~Q~Dl~~~~~SGL~~~~~~l~~~~~i~~i~F~~~D--IVRs~lVk~Il~a  260 (262)
T PRK10536        186 QNVTAAQMKMFL---TRLGENVTVIVNGDITQCDLPRGVKSGLSDALERFEEDEMVGIVRFGKED--CVRSALCQRTLHA  260 (262)
T ss_pred             HCCCHHHHHHHH---HHCCCCCEEEEECCCCCCCCCCCCCCCHHHHHHHHCCCCCEEEEECCCCC--CCCCHHHHHHHHH
T ss_conf             128999998898---54259968999688202269999987399999995699965899836444--0167899999996


Q ss_pred             C
Q ss_conf             1
Q gi|254781187|r  273 Y  273 (367)
Q Consensus       273 ~  273 (367)
                      |
T Consensus       261 Y  261 (262)
T PRK10536        261 Y  261 (262)
T ss_pred             C
T ss_conf             2


No 20 
>PRK02362 ski2-like helicase; Provisional
Probab=98.19  E-value=8.7e-05  Score=48.31  Aligned_cols=158  Identities=16%  Similarity=0.032  Sum_probs=83.6

Q ss_pred             CCCCCHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHH
Q ss_conf             66684289999999888875124555554112477614886788999999999999708997799971537999999999
Q gi|254781187|r   47 HFSQPHRWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLKNTLWA  126 (367)
Q Consensus        47 ~~~~p~~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~~~lw~  126 (367)
                      +++.--+||.++++.   .+..+.        ++.|+++.|+|||.++-..++-.+.  .+.|+++++|...=+.+.. .
T Consensus        20 gI~~Lyp~Q~eal~~---gl~~g~--------NlvvsaPTgsGKTlvAElail~~l~--~g~k~vYi~P~kALa~EK~-~   85 (736)
T PRK02362         20 GIEELYPPQAEAVEA---GLLEGK--------NLLAAIPTASGKTLLAELAMLKAIA--EGGKALYIVPLRALASEKF-E   85 (736)
T ss_pred             CCCCCCHHHHHHHHH---HHCCCC--------CEEEECCCCCCHHHHHHHHHHHHHH--HCCEEEEECCHHHHHHHHH-H
T ss_conf             997578999999986---435698--------1899799998589999999999998--3997999858799999999-9


Q ss_pred             HHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCCCCCCCCCCC------CCCCCEEEEECC
Q ss_conf             99999986231211233332100012333221111345776126621013544556521011------358628999754
Q gi|254781187|r  127 EVSKWLSMLPHRHWFEMQSLSLHPSGWYAELLEQSMGIDSKHYTITCRTYSEERPDTFVGPH------NTHGMAVFNDEA  200 (367)
Q Consensus       127 ei~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~ea~~g~h------~~~~~l~ivDEA  200 (367)
                      +++++...-..            ............-...... ++.+.      ||.+..+-      -.+.-++|+||.
T Consensus        86 ~~~~~~~~gi~------------V~~~tGd~~~~~~~l~~~d-IiV~T------~EK~dsl~r~~~~~l~~v~lVViDEi  146 (736)
T PRK02362         86 EFSEFSELGLR------------VGISTGDYDRRDEYLGRND-IIVAT------SEKTDSLLRNGAPWIDDISCVVADEV  146 (736)
T ss_pred             HHHHHHCCCCE------------EEEEECCCCCCHHHCCCCC-EEEEC------HHHHHHHHHCCCHHHHCCCEEEEECC
T ss_conf             99987457998------------9998089887831436899-99999------79999998448167650898998176


Q ss_pred             CCCCH----HHHHHHHHHHHCCCCCEEEEEEECCCCCCCHH
Q ss_conf             55998----89999898740698825899980789998768
Q gi|254781187|r  201 SGTPD----IINKSILGFFTELNPNRFWIMTSNTRRLNGWF  237 (367)
Q Consensus       201 sgI~d----~i~e~i~g~Lt~~~~~~~~i~igNP~r~~g~F  237 (367)
                      ..|.|    .++|++...+..-+...-.+..|.+-.+...+
T Consensus       147 Hli~d~~RG~~lE~~lskl~~~~~~iqiIgLSATl~N~~~l  187 (736)
T PRK02362        147 HLIDSPNRGPTLEVTLAKLRRLNPDMQVIALSATIGNADEL  187 (736)
T ss_pred             EEECCCCCHHHHHHHHHHHHHCCCCCEEEEEECCCCCHHHH
T ss_conf             78668872499999999997338774389862455899999


No 21 
>PRK01172 ski2-like helicase; Provisional
Probab=98.18  E-value=0.0001  Score=47.92  Aligned_cols=160  Identities=12%  Similarity=-0.023  Sum_probs=81.9

Q ss_pred             CCHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHHH
Q ss_conf             84289999999888875124555554112477614886788999999999999708997799971537999999999999
Q gi|254781187|r   50 QPHRWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLKNTLWAEVS  129 (367)
Q Consensus        50 ~p~~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~~~lw~ei~  129 (367)
                      .+.+||++.+..+.++-            ++.|+++.|.|||.++-..++-.+.  .+.|+++++|...=+.+.. .+++
T Consensus        22 ~l~p~Q~ea~~~~~~gk------------NllvsaPTgsGKTlvAe~ai~~~l~--~~~k~iyi~P~kAL~~EK~-~~~~   86 (674)
T PRK01172         22 ELYDHQRMAIEQLRKGE------------NVIVSVPTAAGKTLIAYSAIYETFL--AGLKSIYIVPLRSLAMEKY-EELS   86 (674)
T ss_pred             CCCHHHHHHHHHHHCCC------------CEEEECCCCCCHHHHHHHHHHHHHH--HCCCEEEECCHHHHHHHHH-HHHH
T ss_conf             88989999999997799------------5999789998699999999999998--5897999877899999999-9999


Q ss_pred             HHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCEEEEECCCCCCH----
Q ss_conf             9998623121123333210001233322111134577612662101354455652101135862899975455998----
Q gi|254781187|r  130 KWLSMLPHRHWFEMQSLSLHPSGWYAELLEQSMGIDSKHYTITCRTYSEERPDTFVGPHNTHGMAVFNDEASGTPD----  205 (367)
Q Consensus       130 k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~ea~~g~h~~~~~l~ivDEAsgI~d----  205 (367)
                      ++.... .    .+.       ..........-...... ++.+..-..++--+-+.-.-.+..++|+||...|.|    
T Consensus        87 ~~~~~g-~----~v~-------~~tGd~~~~~~~~~~~~-I~V~T~Ek~~sl~~~~~~~l~~v~~vViDEiH~i~d~~RG  153 (674)
T PRK01172         87 RLRSLG-M----RVK-------ISIGDYDDPPDFIKRYD-VVILTSEKADSLIHHDPYIINDVGLIVADEIHIIGDEDRG  153 (674)
T ss_pred             HHHCCC-C----EEE-------EEECCCCCCCCCCCCCC-EEEECHHHHHHHHHCCCHHHCCCCEEEEECCEECCCCCCH
T ss_conf             887379-8----277-------88538889801025589-9998789999998649502213698998265250687724


Q ss_pred             HHHHHHHHHHH--CCCCCEEEEEEECCCCCCCHHHH
Q ss_conf             89999898740--69882589998078999876887
Q gi|254781187|r  206 IINKSILGFFT--ELNPNRFWIMTSNTRRLNGWFYD  239 (367)
Q Consensus       206 ~i~e~i~g~Lt--~~~~~~~~i~igNP~r~~g~Fye  239 (367)
                      .+||.+...+.  .++.++  +..|-+-.+...+.+
T Consensus       154 ~~lE~~l~kl~~l~~~~qi--IgLSATi~N~~~la~  187 (674)
T PRK01172        154 PTLETVLSSARYVNPDARI--LALSATVSNANELAQ  187 (674)
T ss_pred             HHHHHHHHHHHHCCCCEEE--EEECCCCCCHHHHHH
T ss_conf             9999999999853866079--971578689999998


No 22 
>COG1111 MPH1 ERCC4-like helicases [DNA replication, recombination, and repair]
Probab=98.16  E-value=5.4e-05  Score=49.61  Aligned_cols=167  Identities=13%  Similarity=0.075  Sum_probs=88.6

Q ss_pred             CCCCHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHH
Q ss_conf             66842899999998888751245555541124776148867889999999999997089977999715379999999999
Q gi|254781187|r   48 FSQPHRWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLKNTLWAE  127 (367)
Q Consensus        48 ~~~p~~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~~~lw~e  127 (367)
                      ...||.+|..+....-.   +          ++.|+-+.|.|||+++++.+..++--.++ +++.+|||..-+-+-. .-
T Consensus        13 ~ie~R~YQ~~i~a~al~---~----------NtLvvlPTGLGKT~IA~~V~~~~l~~~~~-kvlfLAPTKPLV~Qh~-~~   77 (542)
T COG1111          13 TIEPRLYQLNIAAKALF---K----------NTLVVLPTGLGKTFIAAMVIANRLRWFGG-KVLFLAPTKPLVLQHA-EF   77 (542)
T ss_pred             CCCHHHHHHHHHHHHHH---C----------CEEEEECCCCCHHHHHHHHHHHHHHHCCC-EEEEECCCCHHHHHHH-HH
T ss_conf             32588999999999864---4----------83899528750799999999999874588-4899658951799999-99


Q ss_pred             HHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC-CEEEEECCCCCCCCCCCCC-CCCCCCCEEEEECCC-CCC
Q ss_conf             9999986231211233332100012333221111345776-1266210135445565210-113586289997545-599
Q gi|254781187|r  128 VSKWLSMLPHRHWFEMQSLSLHPSGWYAELLEQSMGIDSK-HYTITCRTYSEERPDTFVG-PHNTHGMAVFNDEAS-GTP  204 (367)
Q Consensus       128 i~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~a~~~~~~~~ea~~g-~h~~~~~l~ivDEAs-gI~  204 (367)
                      +++.....++. -...+ +.+.+       .+.......+ ..+++-++..  | +=..| +--+...|+|+|||. .+-
T Consensus        78 ~~~v~~ip~~~-i~~lt-Gev~p-------~~R~~~w~~~kVfvaTPQvve--N-Dl~~Grid~~dv~~lifDEAHRAvG  145 (542)
T COG1111          78 CRKVTGIPEDE-IAALT-GEVRP-------EEREELWAKKKVFVATPQVVE--N-DLKAGRIDLDDVSLLIFDEAHRAVG  145 (542)
T ss_pred             HHHHHCCCHHH-EEEEC-CCCCH-------HHHHHHHHHCCEEEECCHHHH--H-HHHCCCCCHHHCEEEEECHHHHCCC
T ss_conf             99985898433-23111-77786-------889998751778995638777--6-8761766767805898623554137


Q ss_pred             HHHH-HHHHHHHHCCCCCEEEEEEECCCCCCCHHHHHH
Q ss_conf             8899-998987406988258999807899987688754
Q gi|254781187|r  205 DIIN-KSILGFFTELNPNRFWIMTSNTRRLNGWFYDIF  241 (367)
Q Consensus       205 d~i~-e~i~g~Lt~~~~~~~~i~igNP~r~~g~Fye~~  241 (367)
                      +..| .++.--+....+..+.-++.+|-......-+..
T Consensus       146 nyAYv~Va~~y~~~~k~~~ilgLTASPGs~~ekI~eV~  183 (542)
T COG1111         146 NYAYVFVAKEYLRSAKNPLILGLTASPGSDLEKIQEVV  183 (542)
T ss_pred             CCHHHHHHHHHHHHCCCCEEEEEECCCCCCHHHHHHHH
T ss_conf             60699999999982568437987238999879999999


No 23 
>PRK00254 ski2-like helicase; Provisional
Probab=98.08  E-value=0.00022  Score=45.87  Aligned_cols=143  Identities=13%  Similarity=0.041  Sum_probs=80.9

Q ss_pred             CCCCHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHH
Q ss_conf             66842899999998888751245555541124776148867889999999999997089977999715379999999999
Q gi|254781187|r   48 FSQPHRWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLKNTLWAE  127 (367)
Q Consensus        48 ~~~p~~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~~~lw~e  127 (367)
                      ++.--+||.++|+.   ++..+.        ++.|+++.|.|||.++-..++-.+.. .+.++++++|...=+.+.. .+
T Consensus        21 I~~l~p~Q~e~l~~---g~~~g~--------NllvsaPT~sGKTlvAElail~~~l~-~~~k~iyi~P~kALa~EK~-~~   87 (717)
T PRK00254         21 IEELYPPQAEALTS---GVLEGK--------NLLIAIPTASGKTLIAEIAMVNKLLR-EGGKAVYLVPLKALAEEKF-RE   87 (717)
T ss_pred             CCCCCHHHHHHHHH---HHCCCC--------CEEEECCCCCCHHHHHHHHHHHHHHH-CCCEEEEECCHHHHHHHHH-HH
T ss_conf             87268999999874---233698--------18998998874899999999999985-2992999926799999999-99


Q ss_pred             HHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCCCCCCCCCCC------CCCCCEEEEECCC
Q ss_conf             9999986231211233332100012333221111345776126621013544556521011------3586289997545
Q gi|254781187|r  128 VSKWLSMLPHRHWFEMQSLSLHPSGWYAELLEQSMGIDSKHYTITCRTYSEERPDTFVGPH------NTHGMAVFNDEAS  201 (367)
Q Consensus       128 i~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~ea~~g~h------~~~~~l~ivDEAs  201 (367)
                      +++|-..-. +           ............-... ..-++.+.      +|.+..+-      -.+.-++|+||+.
T Consensus        88 f~~~~~~g~-~-----------V~~~tGd~~~~~~~l~-~~dIiV~T------~Ek~dsl~r~~~~~l~~i~lvViDEiH  148 (717)
T PRK00254         88 FKDWEVLGL-R-----------VAMATGDYDSKDEWLG-KYDIIIAT------AEKFDSLLRHGSSWIKDVKLLVADEIH  148 (717)
T ss_pred             HHHHHHCCC-E-----------EEEEECCCCCCCCCCC-CCCEEEEC------HHHHHHHHHCCHHHHHCCCEEEEECEE
T ss_conf             987774498-8-----------9897489888701046-89999988------899999997162565326989997607


Q ss_pred             CCCH----HHHHHHHHHHHCCCCCEE
Q ss_conf             5998----899998987406988258
Q gi|254781187|r  202 GTPD----IINKSILGFFTELNPNRF  223 (367)
Q Consensus       202 gI~d----~i~e~i~g~Lt~~~~~~~  223 (367)
                      .|.|    .+||.+..-+.. ..+++
T Consensus       149 ~igD~~RG~~lE~~l~~l~~-~~qiI  173 (717)
T PRK00254        149 LIGSRDRGATLEFILTHMLG-RAQII  173 (717)
T ss_pred             ECCCCCCHHHHHHHHHHHHC-CCEEE
T ss_conf             88898740999999995100-36699


No 24 
>KOG0354 consensus
Probab=98.05  E-value=8.1e-05  Score=48.51  Aligned_cols=156  Identities=14%  Similarity=0.096  Sum_probs=84.9

Q ss_pred             CCHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHHH
Q ss_conf             84289999999888875124555554112477614886788999999999999708997799971537999999999999
Q gi|254781187|r   50 QPHRWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLKNTLWAEVS  129 (367)
Q Consensus        50 ~p~~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~~~lw~ei~  129 (367)
                      .+|.+|.++... |=+            -++.|+++.|.|||+++|..+.-++-.+|..||+.+||+.--+..-. +.++
T Consensus        62 ~lR~YQ~eivq~-ALg------------kNtii~lPTG~GKTfIAa~Vm~nh~rw~p~~KiVF~aP~~pLv~QQ~-a~~~  127 (746)
T KOG0354          62 ELRNYQEELVQP-ALG------------KNTIIALPTGSGKTFIAAVIMKNHFEWRPKGKVVFLAPTRPLVNQQI-ACFS  127 (746)
T ss_pred             CCCHHHHHHHHH-HHC------------CCEEEEEECCCCCCCHHHHHHHHHHHCCCCCEEEEEECCCHHHHHHH-HHHH
T ss_conf             560789998678-626------------87699953599861047999999972377643899607711788889-8876


Q ss_pred             HHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCC---CCCEEEEECCCCC-CH
Q ss_conf             9998623121123333210001233322111134577612662101354455652101135---8628999754559-98
Q gi|254781187|r  130 KWLSMLPHRHWFEMQSLSLHPSGWYAELLEQSMGIDSKHYTITCRTYSEERPDTFVGPHNT---HGMAVFNDEASGT-PD  205 (367)
Q Consensus       130 k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~ea~~g~h~~---~~~l~ivDEAsgI-~d  205 (367)
                      .....    +-....-+..-+.     ....++-......+.+.+.-.    ..++.....   .+.|+|+|||..- .+
T Consensus       128 ~~~~~----~~~T~~l~~~~~~-----~~r~~i~~s~~vff~TpQil~----ndL~~~~~~~ls~fs~iv~DE~Hra~kn  194 (746)
T KOG0354         128 IYLIP----YSVTGQLGDTVPR-----SNRGEIVASKRVFFRTPQILE----NDLKSGLHDELSDFSLIVFDECHRTSKN  194 (746)
T ss_pred             HCCCC----CCCEEECCCCCCC-----CCHHHHHCCCCEEEECHHHHH----HHCCCCCCCCCCEEEEEEECCCCCCCCC
T ss_conf             20676----0104550575688-----762453102635896727634----3325433454551799997222445556


Q ss_pred             HHH-HHHHHHH--HCCCCCEEEEEEECCCCC
Q ss_conf             899-9989874--069882589998078999
Q gi|254781187|r  206 IIN-KSILGFF--TELNPNRFWIMTSNTRRL  233 (367)
Q Consensus       206 ~i~-e~i~g~L--t~~~~~~~~i~igNP~r~  233 (367)
                      ..| .++.--+  ...+.+++ .++.+|-..
T Consensus       195 ~~Y~~Vmr~~l~~k~~~~qIL-gLTASpG~~  224 (746)
T KOG0354         195 HPYNNIMREYLDLKNQGNQIL-GLTASPGSK  224 (746)
T ss_pred             CCHHHHHHHHHHHHHCCCCEE-EEECCCCCC
T ss_conf             617999999998651466179-985588845


No 25 
>smart00488 DEXDc2 DEAD-like helicases superfamily.
Probab=98.03  E-value=4.9e-05  Score=49.84  Aligned_cols=80  Identities=24%  Similarity=0.431  Sum_probs=57.9

Q ss_pred             HHHHCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHH-HHHHHHHHHHHC---CCC
Q ss_conf             5430146688844366684289999999888875124555554112477614886788999-999999999708---997
Q gi|254781187|r   33 MRFFPWGIKGKPLEHFSQPHRWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTL-NAWMMLWLISTR---PGM  108 (367)
Q Consensus        33 ~~~~~w~~~~~~~~~~~~p~~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~-~a~~~lw~~~~~---~~~  108 (367)
                      .|.||.           .|++.|.++++.|.+.++++.        .+.+-||.|+|||.. .+..+-|.....   ...
T Consensus         2 ~~~FPy-----------~py~~Q~e~m~~v~~~l~~~~--------~~llEaPTGtGKTlalL~~al~~~~~~~~~~~~~   62 (289)
T smart00488        2 LFYFPY-----------EPYPIQYEFMEELKRVLDRGK--------IGILESPTGTGKTLSLLCLTLTWLRSFPERIQKI   62 (289)
T ss_pred             EECCCC-----------CCCHHHHHHHHHHHHHHHCCC--------EEEEECCCCHHHHHHHHHHHHHHHHHCHHCCCCC
T ss_conf             327899-----------999899999999999997499--------7999899965189999999999999670102456


Q ss_pred             EEEEECCCHHHHHHHHHHHHHHHH
Q ss_conf             799971537999999999999999
Q gi|254781187|r  109 SIICIANSETQLKNTLWAEVSKWL  132 (367)
Q Consensus       109 ~v~~~A~t~~Q~~~~lw~ei~k~~  132 (367)
                      ++++...|.+|....+ .|+++..
T Consensus        63 ki~~~t~t~~~~~~~~-~elr~~~   85 (289)
T smart00488       63 KLIYLSRTVSEIEKRL-EELRKLM   85 (289)
T ss_pred             EEEEEECCHHHHHHHH-HHHHHHC
T ss_conf             1687615378899999-9998632


No 26 
>smart00489 DEXDc3 DEAD-like helicases superfamily.
Probab=98.03  E-value=4.9e-05  Score=49.84  Aligned_cols=80  Identities=24%  Similarity=0.431  Sum_probs=57.9

Q ss_pred             HHHHCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHH-HHHHHHHHHHHC---CCC
Q ss_conf             5430146688844366684289999999888875124555554112477614886788999-999999999708---997
Q gi|254781187|r   33 MRFFPWGIKGKPLEHFSQPHRWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTL-NAWMMLWLISTR---PGM  108 (367)
Q Consensus        33 ~~~~~w~~~~~~~~~~~~p~~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~-~a~~~lw~~~~~---~~~  108 (367)
                      .|.||.           .|++.|.++++.|.+.++++.        .+.+-||.|+|||.. .+..+-|.....   ...
T Consensus         2 ~~~FPy-----------~py~~Q~e~m~~v~~~l~~~~--------~~llEaPTGtGKTlalL~~al~~~~~~~~~~~~~   62 (289)
T smart00489        2 LFYFPY-----------EPYPIQYEFMEELKRVLDRGK--------IGILESPTGTGKTLSLLCLTLTWLRSFPERIQKI   62 (289)
T ss_pred             EECCCC-----------CCCHHHHHHHHHHHHHHHCCC--------EEEEECCCCHHHHHHHHHHHHHHHHHCHHCCCCC
T ss_conf             327899-----------999899999999999997499--------7999899965189999999999999670102456


Q ss_pred             EEEEECCCHHHHHHHHHHHHHHHH
Q ss_conf             799971537999999999999999
Q gi|254781187|r  109 SIICIANSETQLKNTLWAEVSKWL  132 (367)
Q Consensus       109 ~v~~~A~t~~Q~~~~lw~ei~k~~  132 (367)
                      ++++...|.+|....+ .|+++..
T Consensus        63 ki~~~t~t~~~~~~~~-~elr~~~   85 (289)
T smart00489       63 KLIYLSRTVSEIEKRL-EELRKLM   85 (289)
T ss_pred             EEEEEECCHHHHHHHH-HHHHHHC
T ss_conf             1687615378899999-9998632


No 27 
>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=98.03  E-value=9.5e-05  Score=48.11  Aligned_cols=69  Identities=20%  Similarity=0.149  Sum_probs=48.6

Q ss_pred             HHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCC-CCEEEEECCCHHHHHHHHHHHHHH
Q ss_conf             2899999998888751245555541124776148867889999999999997089-977999715379999999999999
Q gi|254781187|r   52 HRWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRP-GMSIICIANSETQLKNTLWAEVSK  130 (367)
Q Consensus        52 ~~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~-~~~v~~~A~t~~Q~~~~lw~ei~k  130 (367)
                      ++.|.+++..+..+.            .+.|.++.|+|||......++-.+.... +.++++++|+..-+.+.. ..+++
T Consensus         1 ~~~Q~~~i~~~~~g~------------~~iv~~pTGsGKT~~~~~~~l~~~~~~~~~~~~v~l~Pt~aL~~q~~-~~~~~   67 (167)
T pfam00270         1 TPIQAEAIPAILEGK------------DVLVQAPTGSGKTLAFLLPALQALLKNPDGPQALVLAPTRELAEQIY-EELKK   67 (167)
T ss_pred             CHHHHHHHHHHHCCC------------CEEEECCCCCCHHHHHHHHHHHHHHHCCCCCEEEEECCHHHHHHHHH-HHHHH
T ss_conf             945999999997699------------78998899975899999999999874778987999906088888999-88643


Q ss_pred             HHH
Q ss_conf             998
Q gi|254781187|r  131 WLS  133 (367)
Q Consensus       131 ~~~  133 (367)
                      ...
T Consensus        68 ~~~   70 (167)
T pfam00270        68 LGK   70 (167)
T ss_pred             HHH
T ss_conf             210


No 28 
>PRK10590 ATP-dependent RNA helicase RhlE; Provisional
Probab=97.98  E-value=0.00016  Score=46.67  Aligned_cols=138  Identities=16%  Similarity=0.053  Sum_probs=77.8

Q ss_pred             CCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCC-------CCEEEEECCCH
Q ss_conf             43666842899999998888751245555541124776148867889999999999997089-------97799971537
Q gi|254781187|r   45 LEHFSQPHRWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRP-------GMSIICIANSE  117 (367)
Q Consensus        45 ~~~~~~p~~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~-------~~~v~~~A~t~  117 (367)
                      -.+|..|++-|.+.+-.+-+..            -+.+.|..|+|||.....=++-.+....       +.+++|++||.
T Consensus        18 ~~G~~~PTpIQ~~aIP~iL~Gr------------Dvl~~A~TGSGKTlAflLPil~~l~~~~~~~~~~~~~~aLIL~PTR   85 (457)
T PRK10590         18 EQGYREPTPIQQQAIPAVLEGR------------DLMASAQTGTGKTAGFTLPLLQHLITRQPHAKGRRPVRALILTPTR   85 (457)
T ss_pred             HCCCCCCCHHHHHHHHHHHCCC------------CEEEECCCCHHHHHHHHHHHHHHHHHCCCCCCCCCCCEEEEECCHH
T ss_conf             7799999999999999997799------------8899889811899999999999986367654456882499976879


Q ss_pred             HHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCEEEE
Q ss_conf             99999999999999986231211233332100012333221111345776126621013544556521011358628999
Q gi|254781187|r  118 TQLKNTLWAEVSKWLSMLPHRHWFEMQSLSLHPSGWYAELLEQSMGIDSKHYTITCRTYSEERPDTFVGPHNTHGMAVFN  197 (367)
Q Consensus       118 ~Q~~~~lw~ei~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~ea~~g~h~~~~~l~iv  197 (367)
                      .-+.++ ..+++++...+..+.      ..+.   ..............+.-++.+.+-+...-..-..+.-.+.-++|+
T Consensus        86 ELA~Qi-~~~~~~l~~~~~~~~------~~~~---Gg~~~~~q~~~l~~~~dIlVaTPGRLldl~~~~~~~l~~v~~lVl  155 (457)
T PRK10590         86 ELAAQI-GENVRDYSKYLNIRS------LVVF---GGVSINPQMMKLRGGVDVLVATPGRLLDLEHQNAVKLDQVEILVL  155 (457)
T ss_pred             HHHHHH-HHHHHHHCCCCCCEE------EEEE---CCCCHHHHHHHHCCCCCEEEECCHHHHHHHHCCCCCCCCCEEEEE
T ss_conf             999999-999997425589459------9997---997775999986189998998928889888626776575239998


Q ss_pred             ECCCCCC
Q ss_conf             7545599
Q gi|254781187|r  198 DEASGTP  204 (367)
Q Consensus       198 DEAsgI~  204 (367)
                      |||--+=
T Consensus       156 DEAD~mL  162 (457)
T PRK10590        156 DEADRML  162 (457)
T ss_pred             ECCHHHH
T ss_conf             3705651


No 29 
>KOG2036 consensus
Probab=97.90  E-value=0.00037  Score=44.46  Aligned_cols=145  Identities=14%  Similarity=0.054  Sum_probs=77.6

Q ss_pred             HHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHHHHH
Q ss_conf             28999999988887512455555411247761488678899999999999970899779997153799999999999999
Q gi|254781187|r   52 HRWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLKNTLWAEVSKW  131 (367)
Q Consensus        52 ~~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~~~lw~ei~k~  131 (367)
                      +.-|.+++-...+.+.....     ..-+++.||||-|||+.....+. .+..+-...|.+|+|+-..+++. |--+-|=
T Consensus       255 T~dQakav~~f~dai~eK~l-----r~~vsLtA~RGRGKSAALGlsiA-~AVa~GysnIyvtSPspeNlkTl-FeFv~kG  327 (1011)
T KOG2036         255 TLDQAKAVLTFFDAIVEKTL-----RSTVSLTASRGRGKSAALGLSIA-GAVAFGYSNIYVTSPSPENLKTL-FEFVFKG  327 (1011)
T ss_pred             HHHHHHHHHHHHHHHHHHHH-----CCEEEEEECCCCCCHHHHHHHHH-HHHHCCCCEEEECCCCHHHHHHH-HHHHHCC
T ss_conf             17789999999999987540-----56278985477870055647899-99863750378748983888999-9999803


Q ss_pred             HHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCEEEEECCCCCCHHHHHHH
Q ss_conf             98623121123333210001233322111134577612662101354455652101135862899975455998899998
Q gi|254781187|r  132 LSMLPHRHWFEMQSLSLHPSGWYAELLEQSMGIDSKHYTITCRTYSEERPDTFVGPHNTHGMAVFNDEASGTPDIINKSI  211 (367)
Q Consensus       132 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~ea~~g~h~~~~~l~ivDEAsgI~d~i~e~i  211 (367)
                      ...+-.+....++...-....+.....+..+..+-+      ++..--+|..-+-+.  ...|+++|||+.||=.+--.+
T Consensus       328 fDaL~Yqeh~Dy~iI~s~np~fkkaivRInifr~hr------QtIQYi~P~D~~kl~--q~eLlVIDEAAAIPLplvk~L  399 (1011)
T KOG2036         328 FDALEYQEHVDYDIIQSTNPDFKKAIVRINIFREHR------QTIQYISPHDHQKLG--QAELLVIDEAAAIPLPLVKKL  399 (1011)
T ss_pred             HHHHCCHHHCCHHHHHHCCHHHHHHEEEEEEECCCC------CEEEEECCCHHHHCC--CCCEEEECHHHCCCHHHHHHH
T ss_conf             123131443251146542823140279998742640------136755630054406--774898600202777899985


No 30 
>PRK11192 ATP-dependent RNA helicase SrmB; Provisional
Probab=97.89  E-value=0.00049  Score=43.74  Aligned_cols=75  Identities=15%  Similarity=0.079  Sum_probs=53.7

Q ss_pred             CCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHH----CC-CCEEEEECCCHHHH
Q ss_conf             36668428999999988887512455555411247761488678899999999999970----89-97799971537999
Q gi|254781187|r   46 EHFSQPHRWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLIST----RP-GMSIICIANSETQL  120 (367)
Q Consensus        46 ~~~~~p~~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~----~~-~~~v~~~A~t~~Q~  120 (367)
                      .+|..|++-|.+.+-.+-++.            -+.+.|..|+|||.....=++-.+.-    .+ ..++++++||..=+
T Consensus        21 ~g~~~pT~IQ~~aIp~il~g~------------dvl~~A~TGSGKTlaylLPil~~l~~~~~~~~~~~~~LIl~PTrELa   88 (417)
T PRK11192         21 KGYTRPTAIQAEAIPPALDGR------------DVLGSAPTGTGKTAAFLLPALQHLLDFPRRKSGPPRILILTPTRELA   88 (417)
T ss_pred             CCCCCCCHHHHHHHHHHHCCC------------CEEEECCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEEEECHHHHH
T ss_conf             799999999999999997799------------88998999867999999999999875210368996499994719999


Q ss_pred             HHHHHHHHHHHHH
Q ss_conf             9999999999998
Q gi|254781187|r  121 KNTLWAEVSKWLS  133 (367)
Q Consensus       121 ~~~lw~ei~k~~~  133 (367)
                      .++ ..+++++..
T Consensus        89 ~Qi-~~~~~~l~~  100 (417)
T PRK11192         89 MQV-ADQARELAK  100 (417)
T ss_pred             HHH-HHHHHHHHC
T ss_conf             999-999998640


No 31 
>PRK04837 ATP-dependent RNA helicase RhlB; Provisional
Probab=97.86  E-value=0.00017  Score=46.51  Aligned_cols=76  Identities=14%  Similarity=0.031  Sum_probs=54.4

Q ss_pred             CCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCC--------CEEEEECCC
Q ss_conf             436668428999999988887512455555411247761488678899999999999970899--------779997153
Q gi|254781187|r   45 LEHFSQPHRWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPG--------MSIICIANS  116 (367)
Q Consensus        45 ~~~~~~p~~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~--------~~v~~~A~t  116 (367)
                      -.+|..|++-|...+-.+-++.            -+.+.|..|+|||.....-++-.++..+.        .+++|++||
T Consensus        26 ~~g~~~pTpIQ~~aIP~il~G~------------Dvi~~A~TGSGKTlAfllPil~~ll~~~~~~~~~~~~p~aLIL~PT   93 (423)
T PRK04837         26 KKGFEYCTPIQALALPLTLAGR------------DVAGQAQTGTGKTMAFLTATFHHLLSHPAPEGRKVNQPRALIMAPT   93 (423)
T ss_pred             HCCCCCCCHHHHHHHHHHHCCC------------CEEEECCCCCHHHHHHHHHHHHHHHHCCCCCCCCCCCCEEEEEECC
T ss_conf             7799999999999999996799------------8899899987499999999999998374533455678618999388


Q ss_pred             HHHHHHHHHHHHHHHHH
Q ss_conf             79999999999999998
Q gi|254781187|r  117 ETQLKNTLWAEVSKWLS  133 (367)
Q Consensus       117 ~~Q~~~~lw~ei~k~~~  133 (367)
                      ..=+.++ ..+++.+..
T Consensus        94 RELa~Qi-~~~~~~l~~  109 (423)
T PRK04837         94 RELAVQI-HADAEPLAQ  109 (423)
T ss_pred             HHHHHHH-HHHHHHHHC
T ss_conf             9999999-999999743


No 32 
>PRK11634 ATP-dependent RNA helicase DeaD; Provisional
Probab=97.81  E-value=0.00045  Score=43.94  Aligned_cols=76  Identities=14%  Similarity=0.100  Sum_probs=55.5

Q ss_pred             CCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHC-CCCEEEEECCCHHHHHHH
Q ss_conf             4366684289999999888875124555554112477614886788999999999999708-997799971537999999
Q gi|254781187|r   45 LEHFSQPHRWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTR-PGMSIICIANSETQLKNT  123 (367)
Q Consensus        45 ~~~~~~p~~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~-~~~~v~~~A~t~~Q~~~~  123 (367)
                      -.+|..|++-|.+.+-.+-+.    .        -+.+.|-.|+|||...+.-++-.+... ....++|++||..-+.++
T Consensus        23 ~~Gf~~PTpIQ~~aIP~iL~G----k--------Dvi~~AqTGSGKTlAFlLPiL~~l~~~~~~pqaLIL~PTRELA~QV   90 (629)
T PRK11634         23 DLGYEKPSPIQAECIPHLLNG----R--------DVLGMAQTGSGKTAAFSLPLLHNLDPELKAPQILVLAPTRELAVQV   90 (629)
T ss_pred             HCCCCCCCHHHHHHHHHHHCC----C--------CEEEECCCCCHHHHHHHHHHHHHHHHCCCCCCEEEECCCHHHHHHH
T ss_conf             879999999999999999679----9--------8899788847899999999999866236898689978998999999


Q ss_pred             HHHHHHHHHH
Q ss_conf             9999999998
Q gi|254781187|r  124 LWAEVSKWLS  133 (367)
Q Consensus       124 lw~ei~k~~~  133 (367)
                       ..+++++..
T Consensus        91 -~~~~~~l~~   99 (629)
T PRK11634         91 -AEAMTDFSK   99 (629)
T ss_pred             -HHHHHHHHH
T ss_conf             -999999972


No 33 
>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=97.76  E-value=0.00041  Score=44.21  Aligned_cols=74  Identities=18%  Similarity=0.088  Sum_probs=53.7

Q ss_pred             CCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCC---CCEEEEECCCHHHHHH
Q ss_conf             3666842899999998888751245555541124776148867889999999999997089---9779997153799999
Q gi|254781187|r   46 EHFSQPHRWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRP---GMSIICIANSETQLKN  122 (367)
Q Consensus        46 ~~~~~p~~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~---~~~v~~~A~t~~Q~~~  122 (367)
                      .+|..|++-|.+.+..+-++    .        .+.+.|..|+|||.....-++-.+...+   +.++++++||..-+.+
T Consensus        17 ~g~~~pt~IQ~~~ip~il~g----~--------dvi~~a~TGSGKTlay~lpil~~l~~~~~~~~~~alil~PTrELa~Q   84 (203)
T cd00268          17 LGFEKPTPIQARAIPPLLSG----R--------DVIGQAQTGSGKTAAFLIPILEKLDPSPKKDGPQALILAPTRELALQ   84 (203)
T ss_pred             CCCCCCCHHHHHHHHHHHCC----C--------CEEEECCCCCCCHHHHHHHHHHHHHCCCCCCCCEEEEEECCHHHHHH
T ss_conf             79999999999999999779----9--------88997579972228888699999861667689669999687999999


Q ss_pred             HHHHHHHHHH
Q ss_conf             9999999999
Q gi|254781187|r  123 TLWAEVSKWL  132 (367)
Q Consensus       123 ~lw~ei~k~~  132 (367)
                      + ..++++..
T Consensus        85 i-~~~~~~l~   93 (203)
T cd00268          85 I-AEVARKLG   93 (203)
T ss_pred             H-HHHHHHHC
T ss_conf             9-99999850


No 34 
>PRK04537 ATP-dependent RNA helicase RhlB; Provisional
Probab=97.73  E-value=0.0008  Score=42.42  Aligned_cols=79  Identities=16%  Similarity=0.063  Sum_probs=57.9

Q ss_pred             CCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCC--------CCEEEEECC
Q ss_conf             443666842899999998888751245555541124776148867889999999999997089--------977999715
Q gi|254781187|r   44 PLEHFSQPHRWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRP--------GMSIICIAN  115 (367)
Q Consensus        44 ~~~~~~~p~~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~--------~~~v~~~A~  115 (367)
                      .-.+|..|++-|.+.+-.+-+.    .        .+.+.|..|+|||.....-++-.+...+        +.+++|++|
T Consensus        25 ~~~Gf~~PTpIQ~~aIP~iL~G----k--------Dvi~~A~TGSGKTLAYlLPiL~~Ll~~~~l~~~~~~~p~aLILvP   92 (574)
T PRK04537         25 ESAGFTRCTPIQALTLPVALPG----G--------DVAGQAQTGTGKTLAFLVAVMNRLLSRPALADRKPEDPRALILAP   92 (574)
T ss_pred             HHCCCCCCCHHHHHHHHHHHCC----C--------CEEEECCCCCHHHHHHHHHHHHHHHHCCCCCCCCCCCCEEEEECC
T ss_conf             9779998999999999999579----9--------889984898889999999999999837443457789961999779


Q ss_pred             CHHHHHHHHHHHHHHHHHHC
Q ss_conf             37999999999999999862
Q gi|254781187|r  116 SETQLKNTLWAEVSKWLSML  135 (367)
Q Consensus       116 t~~Q~~~~lw~ei~k~~~~~  135 (367)
                      |..-+.++ ..++.++...+
T Consensus        93 TRELA~QI-~~~~~~l~~~~  111 (574)
T PRK04537         93 TRELAIQI-HKDAVKFGADL  111 (574)
T ss_pred             CHHHHHHH-HHHHHHHHCCC
T ss_conf             89999999-99999986458


No 35 
>PTZ00110 helicase; Provisional
Probab=97.72  E-value=0.00074  Score=42.63  Aligned_cols=159  Identities=12%  Similarity=-0.022  Sum_probs=84.1

Q ss_pred             CCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCC------CCEEEEECCCHH
Q ss_conf             43666842899999998888751245555541124776148867889999999999997089------977999715379
Q gi|254781187|r   45 LEHFSQPHRWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRP------GMSIICIANSET  118 (367)
Q Consensus        45 ~~~~~~p~~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~------~~~v~~~A~t~~  118 (367)
                      -.+|+.|++-|.+.+=.+-.   .   +      -+...|-.|+|||.....=++-.+...+      +..++|+|||..
T Consensus       199 ~~GF~~PTPIQ~qaIPiaLs---G---r------DvIgiAqTGSGKTLAFlLP~l~hi~~q~~~~~~~gP~aLILaPTRE  266 (602)
T PTZ00110        199 AAGFTEPTPIQVQGWPIALS---G---R------DMIGIAETGSGKTLAFLLPAIVHINAQPLLRPGDGPIVLVLAPTRE  266 (602)
T ss_pred             HCCCCCCCHHHHHHHHHHHC---C---C------CEEEECCCCCHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEECCHHH
T ss_conf             76999999899999879856---9---8------6799878978899999999999985163436789976999738399


Q ss_pred             HHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCEEEEE
Q ss_conf             99999999999999862312112333321000123332211113457761266210135445565210113586289997
Q gi|254781187|r  119 QLKNTLWAEVSKWLSMLPHRHWFEMQSLSLHPSGWYAELLEQSMGIDSKHYTITCRTYSEERPDTFVGPHNTHGMAVFND  198 (367)
Q Consensus       119 Q~~~~lw~ei~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~ea~~g~h~~~~~l~ivD  198 (367)
                      =+.++ ..++.++......+      ...++   ..............+.-++.|.+-|...--.-..+.-..+.++|+|
T Consensus       267 LA~QI-~~e~~~~~~~~~ir------~~~i~---GG~~~~~Q~~~L~~G~dIvVATPGRLiDlL~~~~~~L~~v~yLVLD  336 (602)
T PTZ00110        267 LAEQI-REQALQFGRSSKLK------NSVAY---GGVPKRFQTYALRRGVEILIACPGRLIDFLESNVTNLRRVTYLVLD  336 (602)
T ss_pred             HHHHH-HHHHHHHHCCCCCE------EEEEE---CCCCHHHHHHHHCCCCCEEEECCHHHHHHHHCCCCCCCCEEEEEEE
T ss_conf             99999-99999971547854------99997---9968799999871699999979238999996499874310289987


Q ss_pred             CCCCCCH-----HHHHHHHHHHHCCCCCEEEEEE
Q ss_conf             5455998-----8999989874069882589998
Q gi|254781187|r  199 EASGTPD-----IINKSILGFFTELNPNRFWIMT  227 (367)
Q Consensus       199 EAsgI~d-----~i~e~i~g~Lt~~~~~~~~i~i  227 (367)
                      ||--.=|     .+-..+ ..+ ..+..++++..
T Consensus       337 EADRMLDmGFe~qI~~Il-~~i-~pdRQTlLFSA  368 (602)
T PTZ00110        337 EADRMLDMGFEPQIRKIV-SQI-RPDRQTLMWSA  368 (602)
T ss_pred             CHHHHHCCCCHHHHHHHH-HHC-CCCCEEEEEEC
T ss_conf             577663546299999999-858-97877999955


No 36 
>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=97.71  E-value=0.00027  Score=45.31  Aligned_cols=53  Identities=17%  Similarity=0.236  Sum_probs=41.5

Q ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHHHHHH
Q ss_conf             477614886788999999999999708997799971537999999999999999
Q gi|254781187|r   79 KCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLKNTLWAEVSKWL  132 (367)
Q Consensus        79 ~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~~~lw~ei~k~~  132 (367)
                      .+.|.++-|+|||..+...++-.+....+.++++++|+..-+.+. ..++.+..
T Consensus         2 ~~lv~~ptGsGKT~~~~~~~~~~~~~~~~~~~lil~Pt~~L~~q~-~~~~~~~~   54 (144)
T cd00046           2 DVLLAAPTGSGKTLAALLPILELLDSLKGGQVLVLAPTRELANQV-AERLKELF   54 (144)
T ss_pred             CEEEECCCCCHHHHHHHHHHHHHHHHCCCCEEEEECCHHHHHHHH-HHHHHHHC
T ss_conf             999988997179999999999999756897699974679999999-99999974


No 37 
>PRK01297 ATP-dependent RNA helicase RhlB; Provisional
Probab=97.70  E-value=0.00052  Score=43.58  Aligned_cols=77  Identities=13%  Similarity=0.013  Sum_probs=56.0

Q ss_pred             CCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCC--------CCEEEEEC
Q ss_conf             8443666842899999998888751245555541124776148867889999999999997089--------97799971
Q gi|254781187|r   43 KPLEHFSQPHRWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRP--------GMSIICIA  114 (367)
Q Consensus        43 ~~~~~~~~p~~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~--------~~~v~~~A  114 (367)
                      +.-.+|..|++-|.+.+-.+-.+    .        -+.+.|..|+|||.....=++-.+...+        ..+++|++
T Consensus        99 L~~~Gf~~PTpIQ~~aIP~iL~G----k--------Dvi~~A~TGSGKTlAyLLPil~~ll~~~~~~~~~~~~p~aLIL~  166 (472)
T PRK01297         99 IHDLGFPYCTPIQAQVLGYTLAG----H--------DAIGRAQTGTGKTAAFLISIINQLLQTPPPKERYMGEPRALIIA  166 (472)
T ss_pred             HHHCCCCCCCHHHHHHHHHHHCC----C--------CEEEECCCCCHHHHHHHHHHHHHHHHCCCCHHCCCCCCEEEEEC
T ss_conf             99779999999999999999769----9--------88998999867999999999999971775101136895299987


Q ss_pred             CCHHHHHHHHHHHHHHHH
Q ss_conf             537999999999999999
Q gi|254781187|r  115 NSETQLKNTLWAEVSKWL  132 (367)
Q Consensus       115 ~t~~Q~~~~lw~ei~k~~  132 (367)
                      ||..=+.++. ..++...
T Consensus       167 PTRELa~QI~-~~~~~L~  183 (472)
T PRK01297        167 PTRELVVQIA-KDAAALT  183 (472)
T ss_pred             CCHHHHHHHH-HHHHHHH
T ss_conf             9999999999-9999974


No 38 
>COG1204 Superfamily II helicase [General function prediction only]
Probab=97.68  E-value=0.0023  Score=39.66  Aligned_cols=158  Identities=16%  Similarity=0.060  Sum_probs=85.3

Q ss_pred             HHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHHHHHHHHCC
Q ss_conf             99998888751245555541124776148867889999999999997089977999715379999999999999998623
Q gi|254781187|r   57 EFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLKNTLWAEVSKWLSMLP  136 (367)
Q Consensus        57 ~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~~~lw~ei~k~~~~~~  136 (367)
                      +++-.++.+...+... .   -++.|+++.|+|||.++-..++=.+.-+ +.++++++|+..=+.++. .++++|-..-+
T Consensus        31 el~~~qq~av~~~~~~-~---~N~li~aPTgsGKTlIA~lai~~~l~~~-~~k~vYivPlkALa~Ek~-~~~~~~~~~Gi  104 (766)
T COG1204          31 ELFNPQQEAVEKGLLS-D---ENVLISAPTGSGKTLIALLAILSTLLEG-GGKVVYIVPLKALAEEKY-EEFSRLEELGI  104 (766)
T ss_pred             HHHHHHHHHHHCCCCC-C---CCEEEECCCCCCHHHHHHHHHHHHHHHC-CCCEEEEECHHHHHHHHH-HHHHHHHHCCC
T ss_conf             7557899874111257-9---8679976788866999999999999855-983899907599999999-98666886597


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCCCCCCCCCCC------CCCCCEEEEECCCCCCHH----
Q ss_conf             1211233332100012333221111345776126621013544556521011------358628999754559988----
Q gi|254781187|r  137 HRHWFEMQSLSLHPSGWYAELLEQSMGIDSKHYTITCRTYSEERPDTFVGPH------NTHGMAVFNDEASGTPDI----  206 (367)
Q Consensus       137 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~ea~~g~h------~~~~~l~ivDEAsgI~d~----  206 (367)
                                  +...........+-...... ++.+      .||.+..+-      .....|+|+||+.-+.|.    
T Consensus       105 ------------rV~~~TgD~~~~~~~l~~~~-ViVt------T~EK~Dsl~R~~~~~~~~V~lvViDEiH~l~d~~RG~  165 (766)
T COG1204         105 ------------RVGISTGDYDLDDERLARYD-VIVT------TPEKLDSLTRKRPSWIEEVDLVVIDEIHLLGDRTRGP  165 (766)
T ss_pred             ------------EEEEECCCCCCCHHHHCCCC-EEEE------CHHHHHHHHHCCCCHHHCCCEEEEEEEEECCCCCCCC
T ss_conf             ------------79996488655533414588-7997------4678667650675333401689994210148756586


Q ss_pred             HHHHHHHHHHCCCCCEEEEEEECCCCCCCHHHH
Q ss_conf             999989874069882589998078999876887
Q gi|254781187|r  207 INKSILGFFTELNPNRFWIMTSNTRRLNGWFYD  239 (367)
Q Consensus       207 i~e~i~g~Lt~~~~~~~~i~igNP~r~~g~Fye  239 (367)
                      +.|++..-+...+...-.+..|-+-.+.+-+.+
T Consensus       166 ~lE~iv~r~~~~~~~~rivgLSATlpN~~evA~  198 (766)
T COG1204         166 VLESIVARMRRLNELIRIVGLSATLPNAEEVAD  198 (766)
T ss_pred             EEHHHHHHHHHHCCCEEEEEEEEECCCHHHHHH
T ss_conf             402279888852755179887311688899999


No 39 
>PRK11776 ATP-dependent RNA helicase DbpA; Provisional
Probab=97.65  E-value=0.00097  Score=41.90  Aligned_cols=78  Identities=12%  Similarity=0.101  Sum_probs=56.7

Q ss_pred             CCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHC-CCCEEEEECCCHHHHHHH
Q ss_conf             4366684289999999888875124555554112477614886788999999999999708-997799971537999999
Q gi|254781187|r   45 LEHFSQPHRWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTR-PGMSIICIANSETQLKNT  123 (367)
Q Consensus        45 ~~~~~~p~~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~-~~~~v~~~A~t~~Q~~~~  123 (367)
                      -.+|..|++-|.+.+-.+-++.            -+.+.|..|+|||.....-++-.+-.. ....+++++||..=+.++
T Consensus        21 ~~G~~~pTpIQ~~aIP~il~G~------------Dvi~~A~TGSGKTlAfllPil~~l~~~~~~~qaLIL~PTRELa~QV   88 (459)
T PRK11776         21 ELGYTEMTPIQAQSLPAILAGK------------DVIAQAKTGSGKTAAFGLGLLQKLDVKRFRVQALVLCPTRELADQV   88 (459)
T ss_pred             HCCCCCCCHHHHHHHHHHHCCC------------CEEEECCCCCHHHHHHHHHHHHHCCCCCCCCCEEEEECHHHHHHHH
T ss_conf             7799999989999999997799------------8899889985899999999998411367898599996759999999


Q ss_pred             HHHHHHHHHHHC
Q ss_conf             999999999862
Q gi|254781187|r  124 LWAEVSKWLSML  135 (367)
Q Consensus       124 lw~ei~k~~~~~  135 (367)
                       ..+++++.+.+
T Consensus        89 -~~~~~~l~~~~   99 (459)
T PRK11776         89 -AKEIRRLARFI   99 (459)
T ss_pred             -HHHHHHHHHHC
T ss_conf             -99999998505


No 40 
>PRK06305 DNA polymerase III subunits gamma and tau; Validated
Probab=97.59  E-value=0.0029  Score=38.98  Aligned_cols=138  Identities=17%  Similarity=0.100  Sum_probs=71.9

Q ss_pred             HHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEE-EEECCCHHHHHHHHHHHHHHHH
Q ss_conf             999999988887512455555411247761488678899999999999970899779-9971537999999999999999
Q gi|254781187|r   54 WQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSI-ICIANSETQLKNTLWAEVSKWL  132 (367)
Q Consensus        54 wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v-~~~A~t~~Q~~~~lw~ei~k~~  132 (367)
                      .|..+.+.+...+..+.. .+.    ..-.+.||+|||+++-.++-...|.++.... -|-.-      .. +.+|..  
T Consensus        21 GQ~~vv~~L~nai~~~ri-~HA----yLF~GprGtGKTT~ArilAkaLnC~~~~~~~~pCg~C------~~-C~~I~~--   86 (462)
T PRK06305         21 GQDAVVTVLKNALRFNRA-AHA----YLFSGIRGTGKTTLARIFAKALNCQNPTEDQEPCNQC------AI-CKEISS--   86 (462)
T ss_pred             CCHHHHHHHHHHHHCCCC-CCE----EEEECCCCCCHHHHHHHHHHHHCCCCCCCCCCCCCCC------HH-HHHHHC--
T ss_conf             909999999999984997-623----4303899859999999999996799998888988766------88-899863--


Q ss_pred             HHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCEEEEECCCCCCHHHHHHHH
Q ss_conf             86231211233332100012333221111345776126621013544556521011358628999754559988999989
Q gi|254781187|r  133 SMLPHRHWFEMQSLSLHPSGWYAELLEQSMGIDSKHYTITCRTYSEERPDTFVGPHNTHGMAVFNDEASGTPDIINKSIL  212 (367)
Q Consensus       133 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~ea~~g~h~~~~~l~ivDEAsgI~d~i~e~i~  212 (367)
                        -.....++..+                 ...+|  .-..+-..+  .-.+....+.+. .+|+||+...+...|.+++
T Consensus        87 --g~~~DViEiDa-----------------As~~g--VddIRel~e--~v~~~P~~~~yK-VyIIDEvhmLs~~AfNALL  142 (462)
T PRK06305         87 --GTSLDVIEIDG-----------------ASHRG--IEDIRQINE--TVLFTPSKSQYK-IYIIDEVHMLTKEAFNSLL  142 (462)
T ss_pred             --CCCCCEEEECC-----------------CCCCC--HHHHHHHHH--HHCCCCCCCCEE-EEEEECHHHCCHHHHHHHH
T ss_conf             --89998686435-----------------53446--689999997--710088677505-9998152117999999999


Q ss_pred             HHHHCCCCCEEEEEEEC
Q ss_conf             87406988258999807
Q gi|254781187|r  213 GFFTELNPNRFWIMTSN  229 (367)
Q Consensus       213 g~Lt~~~~~~~~i~igN  229 (367)
                      .+|-.+-...+.+++.|
T Consensus       143 KtLEEPP~~v~FILaTT  159 (462)
T PRK06305        143 KTLEEPPQHVKFFLATT  159 (462)
T ss_pred             HHHHCCCCCEEEEEEEC
T ss_conf             98618987749999818


No 41 
>PRK13709 conjugal transfer nickase/helicase TraI; Provisional
Probab=97.55  E-value=0.0016  Score=40.53  Aligned_cols=159  Identities=16%  Similarity=0.184  Sum_probs=89.7

Q ss_pred             CCHHHHHHHHCCCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCC
Q ss_conf             33789999752320125988885543014668884436668428999999988887512455555411247761488678
Q gi|254781187|r   10 KLEQELHEMLMHAECVLSFKNFVMRFFPWGIKGKPLEHFSQPHRWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIG   89 (367)
Q Consensus        10 ~~~~~~~~~~~~~~~~~~~~~f~~~~~~w~~~~~~~~~~~~p~~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~G   89 (367)
                      ++|+.+...+-..+--.-|  |+.-+        |-....+-+..|.+..+-|.+.         +.+| ++|.+-=|+|
T Consensus       938 etEK~IL~~i~~GK~tv~P--L~~~v--------~~s~l~~LT~GQK~At~LIltT---------~DRF-vaIQGyAGVG  997 (1756)
T PRK13709        938 EAEKSILRHILEGKEAVTP--LMERV--------PGELMEKLTSGQRAATRMILET---------SDRF-TVVQGYAGVG  997 (1756)
T ss_pred             HHHHHHHHHHHCCCCCCCC--CHHHC--------CHHHHCCCCHHHHHHHHHHHCC---------CCCE-EEEEECCCCC
T ss_conf             9999999999747665686--02327--------5566635785778777563247---------8725-9987035566


Q ss_pred             HHHHHHHHHHHHHHHCCC---CEEEEECCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             899999999999970899---77999715379999999999999998623121123333210001233322111134577
Q gi|254781187|r   90 KTTLNAWMMLWLISTRPG---MSIICIANSETQLKNTLWAEVSKWLSMLPHRHWFEMQSLSLHPSGWYAELLEQSMGIDS  166 (367)
Q Consensus        90 KS~~~a~~~lw~~~~~~~---~~v~~~A~t~~Q~~~~lw~ei~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  166 (367)
                      ||+..-..+- .+-+-|.   .+|+=.|||.+.++++==.-|             ..+.+.-++.             +.
T Consensus       998 KTTql~avi~-ai~tl~~~~rpqViGLAPTH~AV~EL~~~GV-------------~AQTlaSfL~-------------d~ 1050 (1756)
T PRK13709        998 KTTQFRAVMS-AVNMLPESERPRVVGLGPTHRAVGEMRSAGV-------------DAQTLASFLH-------------DT 1050 (1756)
T ss_pred             HHHHHHHHHH-HHHHCCCCCCCCEEEECCHHHHHHHHHHCCC-------------CHHHHHHHHH-------------HH
T ss_conf             6778999999-9972551358726756751789999996496-------------0789999986-------------20


Q ss_pred             CCEEEEECCCCCCCCCCCCCCCCCCCCEEEEECCCCCCHHHHHHHHHHHHCCCCCEEEEEEEC
Q ss_conf             612662101354455652101135862899975455998899998987406988258999807
Q gi|254781187|r  167 KHYTITCRTYSEERPDTFVGPHNTHGMAVFNDEASGTPDIINKSILGFFTELNPNRFWIMTSN  229 (367)
Q Consensus       167 ~~~~~~a~~~~~~~~ea~~g~h~~~~~l~ivDEAsgI~d~i~e~i~g~Lt~~~~~~~~i~igN  229 (367)
                      .     ......+.|+ +      ...|+++||+|.|.+.=+..+...+..+++|.  ++.|-
T Consensus      1051 ~-----~~~~~ge~~d-y------~nTLFllDESSMVgN~dma~~~~lV~asggRA--V~~GD 1099 (1756)
T PRK13709       1051 Q-----LQQRSGETPD-F------SNTLFLLDESSMVGNTDMARAYALIAAGGGRA--VASGD 1099 (1756)
T ss_pred             H-----HHHHCCCCCC-C------CCEEEEEEHHHCCCHHHHHHHHHHHHHCCCCE--EEECC
T ss_conf             2-----3441489876-5------54289983043147088999999997059837--97277


No 42 
>COG1203 CRISPR-associated helicase Cas3 [Defense mechanisms]
Probab=97.46  E-value=0.0052  Score=37.46  Aligned_cols=171  Identities=13%  Similarity=0.049  Sum_probs=87.4

Q ss_pred             CCHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHC--CCCEEEEECCCHHHHHHHHHHH
Q ss_conf             84289999999888875124555554112477614886788999999999999708--9977999715379999999999
Q gi|254781187|r   50 QPHRWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTR--PGMSIICIANSETQLKNTLWAE  127 (367)
Q Consensus        50 ~p~~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~--~~~~v~~~A~t~~Q~~~~lw~e  127 (367)
                      ++.+||.++++.+-....+..        -+.+.++.|.|||.+++.+++..+.-.  -..+++.+-|+..-+. .+...
T Consensus       195 ~~~~~~~~~~~~~~~~~~~~~--------~~vl~aPTG~GKT~asl~~a~~~~~~~~~~~~r~i~vlP~~t~ie-~~~~r  265 (733)
T COG1203         195 EGYELQEKALELILRLEKRSL--------LVVLEAPTGYGKTEASLILALALLDEKIKLKSRVIYVLPFRTIIE-DMYRR  265 (733)
T ss_pred             CHHHHHHHHHHHHHHCCCCCC--------EEEEEECCCCCHHHHHHHHHHHHHHCCCCCCCEEEEECCHHHHHH-HHHHH
T ss_conf             113556799999873225575--------189991688871999999999975311354562899655899999-99999


Q ss_pred             HHHHHHHCCCCCCCCCCCCCCCCCCCCCC--CCCCCCCCCCCCEEE---EECCCCCCCCCCCCCCC-----CCCCCEEEE
Q ss_conf             99999862312112333321000123332--211113457761266---21013544556521011-----358628999
Q gi|254781187|r  128 VSKWLSMLPHRHWFEMQSLSLHPSGWYAE--LLEQSMGIDSKHYTI---TCRTYSEERPDTFVGPH-----NTHGMAVFN  197 (367)
Q Consensus       128 i~k~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~---~a~~~~~~~~ea~~g~h-----~~~~~l~iv  197 (367)
                      ++.+....-....................  ...............   ...+.+-.+ ....+.+     .-...++|+
T Consensus       266 ~~~~~~~~~~~~~~~h~~~~~~~~~~~~~~~~~~~~~~ds~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~l~~S~vIl  344 (733)
T COG1203         266 AKEIFGLFSVIGKSLHSSSKEPLLLEPDQDILLTLTTNDSYKKLLLALIVVTPIQILI-FSVKGFKFEFLALLLTSLVIL  344 (733)
T ss_pred             HHHHHCCCCCCCCCCCCCCHHHHHHCCCCCCCEEEEECCCCCCCCCCCEEECHHHHHH-HHHCCCCCHHHHHHHHCCEEE
T ss_conf             9875123554331001310255651701002258881242236204522206999855-740466725778876467787


Q ss_pred             ECCCCCCHH-HHHHHHHHH---HCCCCCEEEEEEECCC
Q ss_conf             754559988-999989874---0698825899980789
Q gi|254781187|r  198 DEASGTPDI-INKSILGFF---TELNPNRFWIMTSNTR  231 (367)
Q Consensus       198 DEAsgI~d~-i~e~i~g~L---t~~~~~~~~i~igNP~  231 (367)
                      ||+...++. .+.++.+++   ...|.+++ ++..|.|
T Consensus       345 DE~h~~~~~~~~~~l~~~i~~l~~~g~~il-l~SATlP  381 (733)
T COG1203         345 DEVHLYADETMLAALLALLEALAEAGVPVL-LMSATLP  381 (733)
T ss_pred             ECHHHCCCCCHHHHHHHHHHHHHHCCCCEE-EEECCCC
T ss_conf             427541654308999999999996899789-9927899


No 43 
>COG4096 HsdR Type I site-specific restriction-modification system, R (restriction) subunit and related helicases [Defense mechanisms]
Probab=97.43  E-value=0.0021  Score=39.85  Aligned_cols=74  Identities=15%  Similarity=0.167  Sum_probs=55.2

Q ss_pred             CCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHH
Q ss_conf             44366684289999999888875124555554112477614886788999999999999708997799971537999999
Q gi|254781187|r   44 PLEHFSQPHRWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLKNT  123 (367)
Q Consensus        44 ~~~~~~~p~~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~~~  123 (367)
                      +-....+||.+|..+.+.+.++..++..+      -+.|. ..|+|||..+-.++--++-+.--++|+-.|-.-.++.+.
T Consensus       159 ~~~s~i~~RyyQ~~AI~rv~Eaf~~g~~r------aLlvM-ATGTGKTrTAiaii~rL~r~~~~KRVLFLaDR~~Lv~QA  231 (875)
T COG4096         159 DIDSAIGPRYYQIIAIRRVIEAFSKGQNR------ALLVM-ATGTGKTRTAIAIIDRLIKSGWVKRVLFLADRNALVDQA  231 (875)
T ss_pred             CCCCCCCCHHHHHHHHHHHHHHHHCCCCE------EEEEE-ECCCCCCEEHHHHHHHHHHCCHHHEEEEEECHHHHHHHH
T ss_conf             63223362278899999999998668744------89997-058885231999999999614143056761267899999


Q ss_pred             H
Q ss_conf             9
Q gi|254781187|r  124 L  124 (367)
Q Consensus       124 l  124 (367)
                      .
T Consensus       232 ~  232 (875)
T COG4096         232 Y  232 (875)
T ss_pred             H
T ss_conf             9


No 44 
>COG0513 SrmB Superfamily II DNA and RNA helicases [DNA replication, recombination, and repair / Transcription / Translation, ribosomal structure and biogenesis]
Probab=97.39  E-value=0.0032  Score=38.77  Aligned_cols=159  Identities=14%  Similarity=-0.023  Sum_probs=87.3

Q ss_pred             CCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHH--HCCCCE-EEEECCCHHHHHH
Q ss_conf             3666842899999998888751245555541124776148867889999999999997--089977-9997153799999
Q gi|254781187|r   46 EHFSQPHRWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLIS--TRPGMS-IICIANSETQLKN  122 (367)
Q Consensus        46 ~~~~~p~~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~--~~~~~~-v~~~A~t~~Q~~~  122 (367)
                      .+|..|++-|...+-.+-..            .-+.+.|-.|+|||.....=++-.+.  ...... .++++||..=+.+
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             HHHHHHHHHHHHCC-CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCEEEEECCC
Q ss_conf             99999999998623-12112333321000123332211113457761266210135445565210113586289997545
Q gi|254781187|r  123 TLWAEVSKWLSMLP-HRHWFEMQSLSLHPSGWYAELLEQSMGIDSKHYTITCRTYSEERPDTFVGPHNTHGMAVFNDEAS  201 (367)
Q Consensus       123 ~lw~ei~k~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~ea~~g~h~~~~~l~ivDEAs  201 (367)
                      + ..++.++....+ .+      ...+.  .......+. .....+.-++.+.+-+...--....++..+.-.+|+|||.
T Consensus       115 i-~~~~~~~~~~~~~~~------~~~i~--GG~~~~~q~-~~l~~g~~ivVaTPGRllD~i~~~~l~l~~v~~lVlDEAD  184 (513)
T COG0513         115 I-AEELRKLGKNLGGLR------VAVVY--GGVSIRKQI-EALKRGVDIVVATPGRLLDLIKRGKLDLSGVETLVLDEAD  184 (513)
T ss_pred             H-HHHHHHHHHHCCCCE------EEEEE--CCCCHHHHH-HHHHCCCCEEEECCCHHHHHHHCCCCCCCCEEEEEECCHH
T ss_conf             9-999999986245842------99998--998989999-9872499899979608999986488554650189967617


Q ss_pred             CCCH-HHHHHHHHHHH--CCCCCEEEEE
Q ss_conf             5998-89999898740--6988258999
Q gi|254781187|r  202 GTPD-IINKSILGFFT--ELNPNRFWIM  226 (367)
Q Consensus       202 gI~d-~i~e~i~g~Lt--~~~~~~~~i~  226 (367)
                      -+=| .+.+.++..+.  ..+..++++.
T Consensus       185 rmld~gf~~~i~~I~~~~p~~~qtllfS  212 (513)
T COG0513         185 RMLDMGFIDDIEKILKALPPDRQTLLFS  212 (513)
T ss_pred             HHCCCCCHHHHHHHHHHCCCCCEEEEEE
T ss_conf             6638876899999997389774899998


No 45 
>PRK09112 DNA polymerase III subunit delta'; Validated
Probab=97.30  E-value=0.0096  Score=35.79  Aligned_cols=159  Identities=14%  Similarity=0.186  Sum_probs=78.2

Q ss_pred             CCCCCCCHH-----HHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEE--EEECCCH
Q ss_conf             436668428-----999999988887512455555411247761488678899999999999970899779--9971537
Q gi|254781187|r   45 LEHFSQPHR-----WQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSI--ICIANSE  117 (367)
Q Consensus        45 ~~~~~~p~~-----wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v--~~~A~t~  117 (367)
                      +++..+|+.     .|.++.+.+..-.+.+...+     -....+.+|+||++++=.++-+.++...+...  -+..|-.
T Consensus        13 ~~g~p~Pr~~~~liGq~~~~~~L~~a~~~gRl~H-----A~Lf~GP~GiGKaTlA~~~A~~Ll~~~~~~~~~~~~~~pd~   87 (352)
T PRK09112         13 IDGVPSPSENNRLFGHEEARAFLAQAYREGRLHH-----ALLFEGPEGIGKATLAFHLANHILSHPDPNEAPETLADPDP   87 (352)
T ss_pred             CCCCCCCCCHHHHCCHHHHHHHHHHHHHCCCCCC-----EEEEECCCCCCHHHHHHHHHHHHHCCCCCCCCCCCCCCCCC
T ss_conf             8999896446462786999999999998499652-----46535899808999999999998669986668655678887


Q ss_pred             HHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCC--CCCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCEE
Q ss_conf             999999999999999862312112333321000123332--211113457761266210135445565210113586289
Q gi|254781187|r  118 TQLKNTLWAEVSKWLSMLPHRHWFEMQSLSLHPSGWYAE--LLEQSMGIDSKHYTITCRTYSEERPDTFVGPHNTHGMAV  195 (367)
Q Consensus       118 ~Q~~~~lw~ei~k~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~a~~~~~~~~ea~~g~h~~~~~l~  195 (367)
                      +   ...++.+..  ...|+  .+.+.      +++...  ..+..+..+.      .+....  --+.....+.+ -.+
T Consensus        88 ~---~~~~r~i~~--g~hpd--l~~i~------r~~d~k~~~~~~~I~vd~------iR~l~~--~~~~~~~~~~~-kv~  145 (352)
T PRK09112         88 A---SPLWRQIAQ--GAHPN--LLHLT------RPFDEKTGKFKTAITVDE------IRRVTH--FLSQTSGDGNW-RIV  145 (352)
T ss_pred             C---CHHHHHHHC--CCCCC--EEEEE------CCCCHHHHHHHCCCCHHH------HHHHHH--HHCCCCCCCCE-EEE
T ss_conf             8---778999974--89999--56553------432202145433577799------999999--84548866880-699


Q ss_pred             EEECCCCCCHHHHHHHHHHHHCCCCCEEEEEEECC
Q ss_conf             99754559988999989874069882589998078
Q gi|254781187|r  196 FNDEASGTPDIINKSILGFFTELNPNRFWIMTSNT  230 (367)
Q Consensus       196 ivDEAsgI~d~i~e~i~g~Lt~~~~~~~~i~igNP  230 (367)
                      |+|||.......+.++..+|-.+-.+.+.+++++-
T Consensus       146 Iid~ad~m~~~aaNALLK~LEEPp~~~~fiLit~~  180 (352)
T PRK09112        146 IIDPADDMNRNAANAILKTLEEPPARALFILISHS  180 (352)
T ss_pred             EECCHHHHHHHHHHHHHHHHHCCCCCEEEEEEECC
T ss_conf             98187874699999999985348987489988699


No 46 
>PRK04914 ATP-dependent helicase HepA; Validated
Probab=97.30  E-value=0.013  Score=34.97  Aligned_cols=176  Identities=13%  Similarity=0.134  Sum_probs=90.4

Q ss_pred             CCCCCCCCCCCCH----HHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECC
Q ss_conf             6888443666842----899999998888751245555541124776148867889999999999997089977999715
Q gi|254781187|r   40 IKGKPLEHFSQPH----RWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIAN  115 (367)
Q Consensus        40 ~~~~~~~~~~~p~----~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~  115 (367)
                      ....|+.++-||+    +-|.-+.+++...       +.   +|+.++=-=|.|||.-+..++--.+....-.+|+|+.|
T Consensus       137 ~~~~~~~gl~g~r~~l~pHQ~~ia~~v~~r-------~~---PRvLLADEVGLGKTIEAGLIl~ell~rgra~RvLIvvP  206 (955)
T PRK04914        137 QFQSPLRGLRGARAGLIPHQLYIAHEVGRR-------HA---PRVLLADEVGLGKTIEAGLIIHQQLLTGRAERVLIIVP  206 (955)
T ss_pred             HHCCCCCCCCCCCCCCCCHHHHHHHHHHHC-------CC---CCEEEECCCCCCHHHHHHHHHHHHHHCCCCCEEEEECC
T ss_conf             726951132233246563799999999714-------58---84897058888689999999999997487777999927


Q ss_pred             CHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCEE
Q ss_conf             37999999999999999862312112333321000123332211113457761266210135445565210113586289
Q gi|254781187|r  116 SETQLKNTLWAEVSKWLSMLPHRHWFEMQSLSLHPSGWYAELLEQSMGIDSKHYTITCRTYSEERPDTFVGPHNTHGMAV  195 (367)
Q Consensus       116 t~~Q~~~~lw~ei~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~ea~~g~h~~~~~l~  195 (367)
                      ..  +..-.-.|+..-.+..     |..-.............    .-+......+.+.-+-..++....-+......|+
T Consensus       207 ~~--L~~QW~~EL~~KF~L~-----f~i~D~~r~~~~~~~~~----NpF~~~~~vI~Sld~l~~~~~~~e~l~~a~WDLV  275 (955)
T PRK04914        207 ET--LQHQWLVEMLRRFNLR-----FSLFDEERCAEAQADAD----NPFETEQLVICSLDFLRKNKKRLEQALDAEWDLL  275 (955)
T ss_pred             HH--HHHHHHHHHHHHCCCC-----CEEECCHHHHHHHCCCC----CCCCCCCEEEEEHHHHCCCHHHHHHHHCCCCCEE
T ss_conf             79--9899999999983998-----09955188887533579----9754589799878996039678998733898889


Q ss_pred             EEECCCCC------CHHHHHHHHHHHHCCCCCEEEEEEECCCC--CCCHHH
Q ss_conf             99754559------98899998987406988258999807899--987688
Q gi|254781187|r  196 FNDEASGT------PDIINKSILGFFTELNPNRFWIMTSNTRR--LNGWFY  238 (367)
Q Consensus       196 ivDEAsgI------~d~i~e~i~g~Lt~~~~~~~~i~igNP~r--~~g~Fy  238 (367)
                      |||||..+      +..-+..++. |+... +.+.+++.||-.  ..+.|.
T Consensus       276 IVDEAHhL~~~~~~~s~~y~lve~-La~~~-~~lLLLTATP~QlG~e~~Fa  324 (955)
T PRK04914        276 VVDEAHHLVWSEEAPSREYQVVEQ-LAEVI-PGVLLLTATPEQLGQESHFA  324 (955)
T ss_pred             EEHHHHHHCCCCCCCCHHHHHHHH-HHHHC-CCEEEEECCCCCCCCHHHHH
T ss_conf             971344530588788879999999-98515-97699847998898666898


No 47 
>PRK05896 DNA polymerase III subunits gamma and tau; Validated
Probab=97.28  E-value=0.011  Score=35.43  Aligned_cols=138  Identities=14%  Similarity=0.093  Sum_probs=71.2

Q ss_pred             HHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHHHHHHH
Q ss_conf             99999998888751245555541124776148867889999999999997089977999715379999999999999998
Q gi|254781187|r   54 WQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLKNTLWAEVSKWLS  133 (367)
Q Consensus        54 wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~~~lw~ei~k~~~  133 (367)
                      .|..+.+.+..-++++... |.    ....++||+||++++-.++-...|..+...-.|-.-.  ..+     .+..  .
T Consensus        20 GQe~iv~~L~nAI~~~Ria-HA----YLFsGPrGvGKTTlArifAkaLnC~~~~~~dpCg~C~--sC~-----~I~~--g   85 (613)
T PRK05896         20 GQELIKKILVNAILNNKLT-HA----YIFSGPRGIGKTSIAKIFAKAINCLNPKDGDCCNSCS--VCE-----SINT--N   85 (613)
T ss_pred             CCHHHHHHHHHHHHCCCCC-CE----EEEECCCCCCHHHHHHHHHHHHCCCCCCCCCCCCCCH--HHH-----HHHC--C
T ss_conf             8299999999999849976-22----7755899848899999999996699999999888887--899-----9856--9


Q ss_pred             HCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCEEEEECCCCCCHHHHHHHHH
Q ss_conf             62312112333321000123332211113457761266210135445565210113586289997545599889999898
Q gi|254781187|r  134 MLPHRHWFEMQSLSLHPSGWYAELLEQSMGIDSKHYTITCRTYSEERPDTFVGPHNTHGMAVFNDEASGTPDIINKSILG  213 (367)
Q Consensus       134 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~ea~~g~h~~~~~l~ivDEAsgI~d~i~e~i~g  213 (367)
                      ..|.-  .+..                 .....|  .-..+.....  -++....|.+. .+|+|||.......|.+++-
T Consensus        86 ~h~Dv--iEId-----------------aasn~g--IDeIReLie~--~~~~P~~gkyK-V~IIDEah~Ln~~AaNALLK  141 (613)
T PRK05896         86 QSVDI--VELD-----------------AASNNG--VDEIRNIIDN--INYLPTTFKYK-VYIIDEAHMLSTSAWNALLK  141 (613)
T ss_pred             CCCCE--EEEE-----------------CCCCCC--HHHHHHHHHH--HCCCCCCCCCE-EEEECCHHHCCHHHHHHHHH
T ss_conf             99986--8840-----------------655578--8999999997--08587579945-99981622179999999998


Q ss_pred             HHHCCCCCEEEEEEEC
Q ss_conf             7406988258999807
Q gi|254781187|r  214 FFTELNPNRFWIMTSN  229 (367)
Q Consensus       214 ~Lt~~~~~~~~i~igN  229 (367)
                      +|-.+-...+.+++++
T Consensus       142 tLEEPP~~viFIL~Tt  157 (613)
T PRK05896        142 TLEEPPKHVVFIFATT  157 (613)
T ss_pred             HCCCCCCCCEEEEEEC
T ss_conf             5348987837999828


No 48 
>PRK05563 DNA polymerase III subunits gamma and tau; Validated
Probab=97.28  E-value=0.0089  Score=35.99  Aligned_cols=136  Identities=14%  Similarity=0.107  Sum_probs=67.4

Q ss_pred             HHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHHHHHHH
Q ss_conf             99999998888751245555541124776148867889999999999997089977999715379999999999999998
Q gi|254781187|r   54 WQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLKNTLWAEVSKWLS  133 (367)
Q Consensus        54 wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~~~lw~ei~k~~~  133 (367)
                      .|..+.+.+...+..+... |.    ..-++.||+|||+++-+++--.-|.++..---|-     + ...+ .++..   
T Consensus        20 gQ~~v~~~L~n~i~~~~i~-ha----yLf~GprG~GKTs~Ari~akalnc~~~~~~~pC~-----~-C~~C-~~i~~---   84 (541)
T PRK05563         20 GQEHITTTLKNQIINNRIA-HA----YLFCGTRGTGKTSTAKIFAKAVNCLNPQDGEPCN-----E-CEIC-KKINE---   84 (541)
T ss_pred             CCHHHHHHHHHHHHCCCCC-EE----EEEECCCCCCHHHHHHHHHHHHCCCCCCCCCCCC-----C-CHHH-HHHHC---
T ss_conf             8499999999999849932-04----5303879958999999999995799988898575-----1-4889-99856---


Q ss_pred             HCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCEEEEECCCCCCHHHHHHHHH
Q ss_conf             62312112333321000123332211113457761266210135445565210113586289997545599889999898
Q gi|254781187|r  134 MLPHRHWFEMQSLSLHPSGWYAELLEQSMGIDSKHYTITCRTYSEERPDTFVGPHNTHGMAVFNDEASGTPDIINKSILG  213 (367)
Q Consensus       134 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~ea~~g~h~~~~~l~ivDEAsgI~d~i~e~i~g  213 (367)
                          ..              ...+.+  +........-..+-.++..  .+.-..+.+ -.+|+||+...+...|.+++-
T Consensus        85 ----g~--------------~~Dv~E--idaas~~gvd~iR~~~~~~--~~~p~~~~~-Kv~IiDEvhmls~~a~nallK  141 (541)
T PRK05563         85 ----GL--------------LMDVIE--IDAASNNGVDDIREIIENV--KYPPQEGKY-KVYIMDEVHMLSQGAVNAFLK  141 (541)
T ss_pred             ----CC--------------CCCEEE--ECCCCCCCHHHHHHHHHHC--EECCCCCCE-EEEEEECCCCCCHHHHHHHHH
T ss_conf             ----89--------------887366--2444447889999999761--048767870-599997723389999999999


Q ss_pred             HHHCCCCCEEEEEE
Q ss_conf             74069882589998
Q gi|254781187|r  214 FFTELNPNRFWIMT  227 (367)
Q Consensus       214 ~Lt~~~~~~~~i~i  227 (367)
                      +|-.+-.....++.
T Consensus       142 tlEePp~~~~Fila  155 (541)
T PRK05563        142 TLEEPPSNVIFILA  155 (541)
T ss_pred             HHHCCCCCCEEEEE
T ss_conf             98548777569997


No 49 
>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=97.26  E-value=0.0051  Score=37.46  Aligned_cols=137  Identities=16%  Similarity=0.167  Sum_probs=68.3

Q ss_pred             EEECCCCCCHHHHHHHHHHHHHHHCCC-CEEEEECCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             761488678899999999999970899-7799971537999999999999999862312112333321000123332211
Q gi|254781187|r   81 AISAGRGIGKTTLNAWMMLWLISTRPG-MSIICIANSETQLKNTLWAEVSKWLSMLPHRHWFEMQSLSLHPSGWYAELLE  159 (367)
Q Consensus        81 ~v~sgrg~GKS~~~a~~~lw~~~~~~~-~~v~~~A~t~~Q~~~~lw~ei~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  159 (367)
                      ..+=-=|.|||.-+-.++.......+. .+++|++|..  +....-.|+++|...............+.       ....
T Consensus        20 iLaDeMGLGKTiq~ia~l~~~~~~~~~~~~~LIV~P~s--l~~~W~~Ei~~~~~~~~~~~~~~~~~~r~-------~~~~   90 (295)
T pfam00176        20 ILADEMGLGKTLQTISLLAYLKELKPLAGPHLVVCPLS--TLDNWLNEFEKWAPDLNIVVYYGDGDSRS-------ELLR   90 (295)
T ss_pred             EEECCCCCCHHHHHHHHHHHHHHHCCCCCCEEEEECHH--HHHHHHHHHHHHCCCCCEEEEEECHHHHH-------HHHH
T ss_conf             97227875799999999999998388999889997578--88767889998679970799984707689-------9988


Q ss_pred             CCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCEEEEECCCCCCHHH---HHHHHHHHHCCCCCEEEEEEECCCCC
Q ss_conf             113457761266210135445565210113586289997545599889---99989874069882589998078999
Q gi|254781187|r  160 QSMGIDSKHYTITCRTYSEERPDTFVGPHNTHGMAVFNDEASGTPDII---NKSILGFFTELNPNRFWIMTSNTRRL  233 (367)
Q Consensus       160 ~~~~~~~~~~~~~a~~~~~~~~ea~~g~h~~~~~l~ivDEAsgI~d~i---~e~i~g~Lt~~~~~~~~i~igNP~r~  233 (367)
                      .......-...+.....-....   .-++......+|+|||..|.+.-   +.++. .|   ..+..|+++|||-.+
T Consensus        91 ~~~~~~~~~ivitsY~~~~~~~---~~l~~~~w~~vI~DEaH~iKN~~s~~~~a~~-~l---~~~~r~~LTGTPiqN  160 (295)
T pfam00176        91 NVLRTGKFDVLITSYEYIRRDK---DELHKANWRYVILDEGHRIKNAKSKLSLALK-SL---KTNNRLLLTGTPIQN  160 (295)
T ss_pred             HHHHCCCCCEEEECHHHHHHHH---HHHHCCCCCEEEEECCCCCCCHHHHHHHHHH-HC---CCCCEEEEECCCCCC
T ss_conf             6774168859993099999759---9984087658998762012587889999999-52---358189986874558


No 50 
>PRK08058 DNA polymerase III subunit delta'; Validated
Probab=97.25  E-value=0.013  Score=35.06  Aligned_cols=123  Identities=14%  Similarity=0.160  Sum_probs=75.9

Q ss_pred             CCHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCC-------------------EE
Q ss_conf             84289999999888875124555554112477614886788999999999999708997-------------------79
Q gi|254781187|r   50 QPHRWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGM-------------------SI  110 (367)
Q Consensus        50 ~p~~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~-------------------~v  110 (367)
                      ....-|..+.+.+..-+++|... |    .....+.+|+||+.++-.++-+.+|..+..                   .+
T Consensus         6 ~~~~~Q~~i~~~L~~~i~~~rl~-H----A~Lf~Gp~G~GK~~~A~~~A~~LlC~~~~~~~~Cg~C~~C~~~~~~~HPD~   80 (329)
T PRK08058          6 QLTALQPIVVKMLQNSIAKNRLA-H----AYLFEGAKGTGKKATALWLAKSLFCLERNGVEPCGTCTNCKRIESGNHPDV   80 (329)
T ss_pred             HHHHHHHHHHHHHHHHHHCCCCC-C----EEEEECCCCCCHHHHHHHHHHHHCCCCCCCCCCCCCCHHHHHHHCCCCCCE
T ss_conf             88831899999999999859966-1----565578999889999999999973999999998878889999876999976


Q ss_pred             EEECCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCC
Q ss_conf             99715379999999999999998623121123333210001233322111134577612662101354455652101135
Q gi|254781187|r  111 ICIANSETQLKNTLWAEVSKWLSMLPHRHWFEMQSLSLHPSGWYAELLEQSMGIDSKHYTITCRTYSEERPDTFVGPHNT  190 (367)
Q Consensus       111 ~~~A~t~~Q~~~~lw~ei~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~ea~~g~h~~  190 (367)
                      ..+.|...+.+-   ..|+...+.+                                               +.....|.
T Consensus        81 ~~i~p~~~~i~i---dqiR~L~~~~-----------------------------------------------~~~p~~g~  110 (329)
T PRK08058         81 HLVAPDGQSIKK---DQIRYLKEEF-----------------------------------------------SKSGVESN  110 (329)
T ss_pred             EEECCCCCCCCH---HHHHHHHHHH-----------------------------------------------CCCCCCCC
T ss_conf             774566140779---9999999996-----------------------------------------------43875788


Q ss_pred             CCCEEEEECCCCCCHHHHHHHHHHHHCCCCCEEEEEEE
Q ss_conf             86289997545599889999898740698825899980
Q gi|254781187|r  191 HGMAVFNDEASGTPDIINKSILGFFTELNPNRFWIMTS  228 (367)
Q Consensus       191 ~~~l~ivDEAsgI~d~i~e~i~g~Lt~~~~~~~~i~ig  228 (367)
                      +. .+|+|||.........++..+|-.+-..+++++++
T Consensus       111 ~K-V~II~~Ae~m~~~AaNALLKtLEEPp~~t~fIL~t  147 (329)
T PRK08058        111 KK-VYIIEHADKMTASAANSLLKFLEEPSGDTTAILLT  147 (329)
T ss_pred             CE-EEEEECHHHHCHHHHHHHHHHHHCCCCCCEEEEEE
T ss_conf             67-99973477629999999999864689786799872


No 51 
>COG4581 Superfamily II RNA helicase [DNA replication, recombination, and repair]
Probab=97.25  E-value=0.015  Score=34.67  Aligned_cols=159  Identities=13%  Similarity=0.064  Sum_probs=87.1

Q ss_pred             CCCCCHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHH
Q ss_conf             66684289999999888875124555554112477614886788999999999999708997799971537999999999
Q gi|254781187|r   47 HFSQPHRWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLKNTLWA  126 (367)
Q Consensus        47 ~~~~p~~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~~~lw~  126 (367)
                      +.-.+++||.+.+..|....            .|-|+|..|.|||.+ |-+++..++.+ +.++++|+|...-..+. ++
T Consensus       116 ~~F~LD~fQ~~a~~~Ler~e------------sVlV~ApTssGKTvV-aeyAi~~al~~-~qrviYTsPIKALsNQK-yr  180 (1041)
T COG4581         116 YPFELDPFQQEAIAILERGE------------SVLVCAPTSSGKTVV-AEYAIALALRD-GQRVIYTSPIKALSNQK-YR  180 (1041)
T ss_pred             CCCCCCHHHHHHHHHHHCCC------------CEEEECCCCCCCCHH-HHHHHHHHHHC-CCCEEECCCHHHHHHHH-HH
T ss_conf             89896789999999984799------------579973378985559-99999999871-89448616306642067-99


Q ss_pred             HHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECC-----CCCCCCCCCCCCCCCCCCEEEEECCC
Q ss_conf             9999998623121123333210001233322111134577612662101-----35445565210113586289997545
Q gi|254781187|r  127 EVSKWLSMLPHRHWFEMQSLSLHPSGWYAELLEQSMGIDSKHYTITCRT-----YSEERPDTFVGPHNTHGMAVFNDEAS  201 (367)
Q Consensus       127 ei~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~-----~~~~~~ea~~g~h~~~~~l~ivDEAs  201 (367)
                      ++..-.... ...|-..|               .+....+...+..-.|     +--...+..+     ....+|+||..
T Consensus       181 dl~~~fgdv-~~~vGL~T---------------GDv~IN~~A~clvMTTEILRnMlyrg~~~~~-----~i~~ViFDEvH  239 (1041)
T COG4581         181 DLLAKFGDV-ADMVGLMT---------------GDVSINPDAPCLVMTTEILRNMLYRGSESLR-----DIEWVVFDEVH  239 (1041)
T ss_pred             HHHHHHHHH-HHHCCCEE---------------CCEEECCCCCEEEEEHHHHHHHHCCCCCCCC-----CCCEEEEEEEE
T ss_conf             999986005-65404010---------------5434279996688609999998625861013-----53068887666


Q ss_pred             CCCH----HHHHHHHHHHHCCCCCEEEEEEECCCCCCCHHHHHHHCC
Q ss_conf             5998----899998987406988258999807899987688754112
Q gi|254781187|r  202 GTPD----IINKSILGFFTELNPNRFWIMTSNTRRLNGWFYDIFNIP  244 (367)
Q Consensus       202 gI~d----~i~e~i~g~Lt~~~~~~~~i~igNP~r~~g~Fye~~~~~  244 (367)
                      .|.|    .+||-..-.+-.. -+  ++++|-+..+.-.|.+....-
T Consensus       240 yi~D~eRG~VWEE~Ii~lP~~-v~--~v~LSATv~N~~EF~~Wi~~~  283 (1041)
T COG4581         240 YIGDRERGVVWEEVIILLPDH-VR--FVFLSATVPNAEEFAEWIQRV  283 (1041)
T ss_pred             ECCCCCCCHHHHHHHHHCCCC-CC--EEEEECCCCCHHHHHHHHHHC
T ss_conf             504632212578999866777-76--899967889879999999740


No 52 
>PRK06647 DNA polymerase III subunits gamma and tau; Validated
Probab=97.25  E-value=0.012  Score=35.19  Aligned_cols=137  Identities=18%  Similarity=0.112  Sum_probs=71.0

Q ss_pred             HHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEEC-CCHHHHHHHHHHHHHHHH
Q ss_conf             9999999888875124555554112477614886788999999999999708997799971-537999999999999999
Q gi|254781187|r   54 WQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIA-NSETQLKNTLWAEVSKWL  132 (367)
Q Consensus        54 wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A-~t~~Q~~~~lw~ei~k~~  132 (367)
                      .|..+.+.+...++.+... |.    ..-++.||+|||+++-+++-...|..++.---|-. ++-        .++..  
T Consensus        20 GQe~vv~~L~nai~~~rl~-HA----yLFsGprG~GKTt~ArilAk~LnC~~~~~~~PCg~C~sC--------~~i~~--   84 (560)
T PRK06647         20 GQDFVVETLKHSIEKNKIA-NA----YIFSGPRGVGKTSSARAFARCLNCVNGPTIMPCGECFSC--------KSIDN--   84 (560)
T ss_pred             CCHHHHHHHHHHHHCCCCC-CE----EEEECCCCCCHHHHHHHHHHHHCCCCCCCCCCCCCCHHH--------HHHHC--
T ss_conf             9499999999999749977-43----663289987899999999999659999998888788788--------88745--


Q ss_pred             HHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCEEEEECCCCCCHHHHHHHH
Q ss_conf             86231211233332100012333221111345776126621013544556521011358628999754559988999989
Q gi|254781187|r  133 SMLPHRHWFEMQSLSLHPSGWYAELLEQSMGIDSKHYTITCRTYSEERPDTFVGPHNTHGMAVFNDEASGTPDIINKSIL  212 (367)
Q Consensus       133 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~ea~~g~h~~~~~l~ivDEAsgI~d~i~e~i~  212 (367)
                      ...++  .++..+                   .........+-...  .-.+....+.+ -.+|+|||...+...|.+++
T Consensus        85 g~~~D--viEida-------------------asn~~VddIR~l~e--~v~~~P~~~~y-KV~IIDEahmLt~~A~NALL  140 (560)
T PRK06647         85 DSSLD--VIEIDG-------------------ASNTSVQDVRQIKE--EIMFPPASSRY-RVYIIDEVHMLSNSAFNALL  140 (560)
T ss_pred             CCCCC--EEEECC-------------------CCCCCHHHHHHHHH--HHCCCCCCCCE-EEEEECCHHHCCHHHHHHHH
T ss_conf             99987--576436-------------------45488899999999--86328766870-69996465655999999999


Q ss_pred             HHHHCCCCCEEEEEEEC
Q ss_conf             87406988258999807
Q gi|254781187|r  213 GFFTELNPNRFWIMTSN  229 (367)
Q Consensus       213 g~Lt~~~~~~~~i~igN  229 (367)
                      -+|-.+-...+.+++.|
T Consensus       141 KtLEEPP~~~~FILaTt  157 (560)
T PRK06647        141 KTIEEPPPYIVFIFATT  157 (560)
T ss_pred             HHHHCCCCCEEEEEECC
T ss_conf             98634887559999779


No 53 
>PRK06674 DNA polymerase III subunits gamma and tau; Validated
Probab=97.24  E-value=0.013  Score=34.92  Aligned_cols=138  Identities=12%  Similarity=0.086  Sum_probs=71.4

Q ss_pred             HHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHHHHHHH
Q ss_conf             99999998888751245555541124776148867889999999999997089977999715379999999999999998
Q gi|254781187|r   54 WQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLKNTLWAEVSKWLS  133 (367)
Q Consensus        54 wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~~~lw~ei~k~~~  133 (367)
                      .|..+.+.+..-+..+.. .|.    ..-.+.||+|||.++-.++-...|.+++..--|-  .    ...+ ..+..  .
T Consensus        20 GQ~~v~~~L~nai~~~ri-~HA----yLF~GprGtGKts~Ari~AkaLnC~~~~~~~pC~--~----C~~C-~~i~~--g   85 (563)
T PRK06674         20 GQEHVTKTLQNALLQEKV-SHA----YLFSGPRGTGKTSIAKVFAKAVNCEHAPVAEPCN--E----CPSC-LGITN--G   85 (563)
T ss_pred             CHHHHHHHHHHHHHCCCC-CCE----EEEECCCCCCHHHHHHHHHHHHCCCCCCCCCCCC--C----CHHH-HHHHC--C
T ss_conf             809999999999984996-503----4312899868999999999985799999988776--6----8789-99855--8


Q ss_pred             HCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCEEEEECCCCCCHHHHHHHHH
Q ss_conf             62312112333321000123332211113457761266210135445565210113586289997545599889999898
Q gi|254781187|r  134 MLPHRHWFEMQSLSLHPSGWYAELLEQSMGIDSKHYTITCRTYSEERPDTFVGPHNTHGMAVFNDEASGTPDIINKSILG  213 (367)
Q Consensus       134 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~ea~~g~h~~~~~l~ivDEAsgI~d~i~e~i~g  213 (367)
                      ..+.  ..+.                 +....+|  ....+-.+..  -.+....+.+ -.+|+||+...+...|.+++.
T Consensus        86 ~~~D--viEi-----------------Daasn~g--Vd~IR~i~~~--v~~~P~~~~y-KV~IIDeah~Lt~~A~NALLK  141 (563)
T PRK06674         86 SISD--VLEI-----------------DAASNNG--VDEIRDIRDK--VKFAPSAVEY-KVYIIDEVHMLSIGAFNALLK  141 (563)
T ss_pred             CCCC--EEEE-----------------CCCCCCC--HHHHHHHHHH--HCCCCCCCCE-EEEEEECHHHCCHHHHHHHHH
T ss_conf             9987--7985-----------------2555578--7999999998--2648867873-799985456379999999999


Q ss_pred             HHHCCCCCEEEEEEEC
Q ss_conf             7406988258999807
Q gi|254781187|r  214 FFTELNPNRFWIMTSN  229 (367)
Q Consensus       214 ~Lt~~~~~~~~i~igN  229 (367)
                      +|-.+-...+.+++.|
T Consensus       142 tLEEPP~~viFILaTt  157 (563)
T PRK06674        142 TLEEPPGHVIFILATT  157 (563)
T ss_pred             HHHCCCCCEEEEEECC
T ss_conf             8638875649999659


No 54 
>PRK08769 DNA polymerase III subunit delta'; Validated
Probab=97.21  E-value=0.0062  Score=36.97  Aligned_cols=147  Identities=13%  Similarity=0.162  Sum_probs=77.4

Q ss_pred             CHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHHHH
Q ss_conf             42899999998888751245555541124776148867889999999999997089977999715379999999999999
Q gi|254781187|r   51 PHRWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLKNTLWAEVSK  130 (367)
Q Consensus        51 p~~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~~~lw~ei~k  130 (367)
                      -.+||.+..+.+...+++|...+     ...+.+..|+||+.++-.++-+.+|..++....+-.      ...    +. 
T Consensus         5 ~~PWq~~~~~~L~~~i~~~rl~H-----A~Lf~Gp~G~GK~~~A~~~A~~llc~~~~~~~~~~~------~~~----i~-   68 (319)
T PRK08769          5 FSPWQQRAFDQTVAALDAGRLGH-----GLLICGPEGLGKRAVALALAEHVLASGPDPALAQRT------RQL----IA-   68 (319)
T ss_pred             CCCCCHHHHHHHHHHHHCCCCCC-----EEEEECCCCCCHHHHHHHHHHHHHCCCCCCCCCCHH------HHH----HH-
T ss_conf             58776899999999997699420-----687589998789999999999983799797654338------899----96-


Q ss_pred             HHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCEEEEECCCCCCHHHHHH
Q ss_conf             99862312112333321000123332211113457761266210135445565210113586289997545599889999
Q gi|254781187|r  131 WLSMLPHRHWFEMQSLSLHPSGWYAELLEQSMGIDSKHYTITCRTYSEERPDTFVGPHNTHGMAVFNDEASGTPDIINKS  210 (367)
Q Consensus       131 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~ea~~g~h~~~~~l~ivDEAsgI~d~i~e~  210 (367)
                       ....|+-+.....     +... ....+.+++.+.-.-.+..        -+.....|.+ -.+|+|||.........+
T Consensus        69 -~g~HPD~~~i~~~-----~~~~-~~k~k~~I~IdqiR~l~~~--------~~~~p~~g~~-KV~IId~Ad~mn~~AaNa  132 (319)
T PRK08769         69 -AGTHPDLQLVSFI-----PNRT-GDKLRTEIVIEQVREISQK--------LALTPQYGIA-QVVIVDPADAINRSACNA  132 (319)
T ss_pred             -CCCCCCEEEEECC-----CCCC-CCCCCCCCCHHHHHHHHHH--------HHHCCCCCCC-EEEEECCHHHCCHHHHHH
T ss_conf             -6899896877534-----4445-4311234869999999999--------6137202795-699980667528999999


Q ss_pred             HHHHHHCCCCCEEEEEEEC
Q ss_conf             8987406988258999807
Q gi|254781187|r  211 ILGFFTELNPNRFWIMTSN  229 (367)
Q Consensus       211 i~g~Lt~~~~~~~~i~igN  229 (367)
                      +..+|-.+....+++++++
T Consensus       133 lLK~LEEPp~~~~~iL~~~  151 (319)
T PRK08769        133 LLKTLEEPSPGRYLWLISA  151 (319)
T ss_pred             HHHHHCCCCCCEEEEEEEC
T ss_conf             9998227998848999869


No 55 
>PRK08451 DNA polymerase III subunits gamma and tau; Validated
Probab=97.19  E-value=0.016  Score=34.37  Aligned_cols=136  Identities=15%  Similarity=0.082  Sum_probs=69.5

Q ss_pred             HHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHHHHHHHH
Q ss_conf             99999988887512455555411247761488678899999999999970899779997153799999999999999986
Q gi|254781187|r   55 QLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLKNTLWAEVSKWLSM  134 (367)
Q Consensus        55 q~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~~~lw~ei~k~~~~  134 (367)
                      |..+.+.+..-++++... |    -....++||+||++++-.++-...|..++..--|-.  -.    .+ ..+..  ..
T Consensus        19 Qe~iv~~L~nAi~~~Rl~-H----AYLFsGPrGvGKTt~ArifAkaLnC~~~~~~~PCg~--C~----sC-~~i~~--g~   84 (523)
T PRK08451         19 QESVSKTLSLALDNNRLA-H----AYLFSGLRGSGKTSSARIFSRALVCEQGPSSTPCGT--CA----QC-QAALE--GR   84 (523)
T ss_pred             CHHHHHHHHHHHHCCCCC-C----EEEEECCCCCCHHHHHHHHHHHHCCCCCCCCCCCCC--CH----HH-HHHHC--CC
T ss_conf             499999999999859967-1----587578998688999999999975999999898887--88----89-99864--89


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCEEEEECCCCCCHHHHHHHHHH
Q ss_conf             23121123333210001233322111134577612662101354455652101135862899975455998899998987
Q gi|254781187|r  135 LPHRHWFEMQSLSLHPSGWYAELLEQSMGIDSKHYTITCRTYSEERPDTFVGPHNTHGMAVFNDEASGTPDIINKSILGF  214 (367)
Q Consensus       135 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~ea~~g~h~~~~~l~ivDEAsgI~d~i~e~i~g~  214 (367)
                      .|+  ..+..+.                   .....-..+.....  -.+....+.+. .+|+|||.......+.+++-+
T Consensus        85 hpD--ViEiDaa-------------------sn~gID~IReLie~--~~~~P~~gryK-V~IIDEah~Lt~~A~NALLKT  140 (523)
T PRK08451         85 HID--IIEMDAA-------------------SNRGIDDIRNLIEQ--TKYKPSMARFK-IFIIDEVHMLTKEAFNALLKT  140 (523)
T ss_pred             CCC--EEEECCC-------------------CCCCHHHHHHHHHH--HCCCCCCCCEE-EEEEECCCCCCHHHHHHHHHH
T ss_conf             998--5510553-------------------33689999999997--23588679727-999826030489999999997


Q ss_pred             HHCCCCCEEEEEEE
Q ss_conf             40698825899980
Q gi|254781187|r  215 FTELNPNRFWIMTS  228 (367)
Q Consensus       215 Lt~~~~~~~~i~ig  228 (367)
                      |-.+-...+.+++.
T Consensus       141 LEEPP~~vvFILaT  154 (523)
T PRK08451        141 LEEPPSYVKFILAT  154 (523)
T ss_pred             CCCCCCCCEEEEEC
T ss_conf             03898783799975


No 56 
>COG1484 DnaC DNA replication protein [DNA replication, recombination, and repair]
Probab=97.18  E-value=0.0083  Score=36.18  Aligned_cols=71  Identities=20%  Similarity=0.129  Sum_probs=52.8

Q ss_pred             HHCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEE
Q ss_conf             3014668884436668428999999988887512455555411247761488678899999999999970899779997
Q gi|254781187|r   35 FFPWGIKGKPLEHFSQPHRWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICI  113 (367)
Q Consensus        35 ~~~w~~~~~~~~~~~~p~~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~  113 (367)
                      .+|.. +...+..|..+..-+.+++..+....+.-.     ....+.+.++-|+|||++++++..-.+  ..+..|+++
T Consensus        69 ~~p~~-k~~~~~d~~~~~~~~~~~l~~~~~~~~~~~-----~~~nl~l~G~~G~GKthLa~Ai~~~l~--~~g~sv~f~  139 (254)
T COG1484          69 SFPAK-KTFEEFDFEFQPGIDKKALEDLASLVEFFE-----RGENLVLLGPPGVGKTHLAIAIGNELL--KAGISVLFI  139 (254)
T ss_pred             CCCCC-CCCCCCCCCCCCHHHHHHHHHHHHHHHHHC-----CCCCEEEECCCCCCHHHHHHHHHHHHH--HCCCEEEEE
T ss_conf             68755-785430235885566999999999998732-----588289989999879999999999999--839849998


No 57 
>PRK11448 hsdR type I restriction enzyme EcoKI subunit R; Provisional
Probab=97.17  E-value=0.018  Score=34.11  Aligned_cols=72  Identities=17%  Similarity=0.221  Sum_probs=52.4

Q ss_pred             CCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCH---HHH
Q ss_conf             44366684289999999888875124555554112477614886788999999999999708997799971537---999
Q gi|254781187|r   44 PLEHFSQPHRWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSE---TQL  120 (367)
Q Consensus        44 ~~~~~~~p~~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~---~Q~  120 (367)
                      |...-.+-|.+|.++.+++.+.+..+..       |..+.=..|+|||..+..++--++-+.--.+|+..+-..   +|+
T Consensus       410 ~~~~~i~lR~YQ~~AI~~v~~a~~~~~r-------raLl~MATGTGKTrtaial~~rLlk~~~~kRILFLvDR~~L~~QA  482 (1126)
T PRK11448        410 PFDYELGLRYYQEDAIQAVEKALANGQR-------EILLAMATGTGKTRTAIALMYRLLKAKRFKRILFLVDRRALGEQA  482 (1126)
T ss_pred             CCCCCCCCCHHHHHHHHHHHHHHHCCCC-------CEEEEECCCCCHHHHHHHHHHHHHHCCCCCEEEEECCHHHHHHHH
T ss_conf             9877777868899999999999980985-------468872488858989999999999658767257985658999999


Q ss_pred             HH
Q ss_conf             99
Q gi|254781187|r  121 KN  122 (367)
Q Consensus       121 ~~  122 (367)
                      .+
T Consensus       483 ~~  484 (1126)
T PRK11448        483 LD  484 (1126)
T ss_pred             HH
T ss_conf             99


No 58 
>PRK08074 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
Probab=97.14  E-value=0.0078  Score=36.38  Aligned_cols=72  Identities=21%  Similarity=0.190  Sum_probs=49.9

Q ss_pred             CCHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCH---HHHHHHHHH
Q ss_conf             84289999999888875124555554112477614886788999999999999708997799971537---999999999
Q gi|254781187|r   50 QPHRWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSE---TQLKNTLWA  126 (367)
Q Consensus        50 ~p~~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~---~Q~~~~lw~  126 (367)
                      .+|+-|.+|...|++.+..+.        .+.|-||.|+|||..--.-++.++..+ +.+|++..+|.   +|+-..-.+
T Consensus       258 e~R~~Q~~ma~~V~~al~~~~--------~l~iEApTGtGKTlaYLlPai~~A~~~-~~~vvIST~T~~LQ~QL~~kdlp  328 (932)
T PRK08074        258 EKREGQQEMMKEVYTALRDSR--------HALIEAGTGTGKTLAYLLPAAYFAKKK-EEPVIISTYTVQLQQQLLEKDIP  328 (932)
T ss_pred             CCCHHHHHHHHHHHHHHHCCC--------CEEEECCCCCCCHHHHHHHHHHHHHHC-CCCEEEEECCHHHHHHHHHHHHH
T ss_conf             758789999999999985388--------479986888871368799999999975-99099991628899999986899


Q ss_pred             HHHH
Q ss_conf             9999
Q gi|254781187|r  127 EVSK  130 (367)
Q Consensus       127 ei~k  130 (367)
                      .+++
T Consensus       329 ~L~~  332 (932)
T PRK08074        329 LLQK  332 (932)
T ss_pred             HHHH
T ss_conf             9999


No 59 
>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=97.12  E-value=0.0018  Score=40.30  Aligned_cols=56  Identities=18%  Similarity=0.261  Sum_probs=45.8

Q ss_pred             HHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHH-HCCCCEEEEECCCHH
Q ss_conf             2899999998888751245555541124776148867889999999999997-089977999715379
Q gi|254781187|r   52 HRWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLIS-TRPGMSIICIANSET  118 (367)
Q Consensus        52 ~~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~-~~~~~~v~~~A~t~~  118 (367)
                      +.-|.++|.+--. .+          .++.|.+|.|+|||+|+-+++--... +.|+-|++++.-|..
T Consensus       125 taaQ~d~l~~Av~-ar----------~NIlv~GGTGSGKTTLaNAlla~I~~l~~P~dR~vIiEDT~E  181 (315)
T TIGR02782       125 TAAQRDVLREAVA-AR----------KNILVVGGTGSGKTTLANALLAEIAKLNDPDDRVVIIEDTAE  181 (315)
T ss_pred             CHHHHHHHHHHHH-HC----------CCEEEECCCCCCHHHHHHHHHHHHHHCCCCCCEEEEEECCHH
T ss_conf             5789999999997-12----------988998145885799999999988521699961899854713


No 60 
>PRK11747 dinG ATP-dependent DNA helicase DinG; Provisional
Probab=97.12  E-value=0.01  Score=35.69  Aligned_cols=68  Identities=13%  Similarity=0.131  Sum_probs=44.3

Q ss_pred             CCHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHH
Q ss_conf             84289999999888875124555554112477614886788999999999999708997799971537999999
Q gi|254781187|r   50 QPHRWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLKNT  123 (367)
Q Consensus        50 ~p~~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~~~  123 (367)
                      .||+-|.+|..+|++.+......     -.+.|-||.|+|||..--.-++.++.. .+.+|+|..+|..--..+
T Consensus        25 e~R~~Q~~Ma~~V~~al~~~~~~-----~~l~iEAgTGtGKTlaYL~Pai~~a~~-~~~~vvIST~T~~LQeQL   92 (697)
T PRK11747         25 IPRAGQRQMIAEVAKTLAGEYGR-----HILVIEAGTGVGKSLAYLLAGIPIARA-EKKKLVISTATVALQEQL   92 (697)
T ss_pred             CCCHHHHHHHHHHHHHHHCCCCC-----CEEEEECCCCCHHHHHHHHHHHHHHHH-CCCCEEEECCCHHHHHHH
T ss_conf             71878999999999996166678-----669998999720899999999999998-299799988988999999


No 61 
>PRK07133 DNA polymerase III subunits gamma and tau; Validated
Probab=97.11  E-value=0.021  Score=33.77  Aligned_cols=129  Identities=16%  Similarity=0.106  Sum_probs=70.5

Q ss_pred             HHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCC----EEEEECCCHHHHHHHHHHHHH
Q ss_conf             9999999888875124555554112477614886788999999999999708997----799971537999999999999
Q gi|254781187|r   54 WQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGM----SIICIANSETQLKNTLWAEVS  129 (367)
Q Consensus        54 wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~----~v~~~A~t~~Q~~~~lw~ei~  129 (367)
                      .|..+.+.+..-++++... |    ...-+++||+|||+++-.++-...|.++..    ...|.+...            
T Consensus        22 GQe~Vv~tL~nAI~~gRIa-H----AYLF~GPRGvGKTT~ARIfAKaLNC~~~~d~~~pC~~C~~~~~------------   84 (718)
T PRK07133         22 GQDHIIETLKNIIKSGKIS-H----AYLFSGPHGTGKTSVAKIFANALNCSHKTDLIEPCQNCIENFN------------   84 (718)
T ss_pred             CCHHHHHHHHHHHHCCCCC-C----EEEEECCCCCCHHHHHHHHHHHHCCCCCCCCCCCCCCHHHCCC------------
T ss_conf             8599999999999749975-0----5862389986889999999999679999999997702143047------------


Q ss_pred             HHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCEEEEECCCCCCHHHHH
Q ss_conf             99986231211233332100012333221111345776126621013544556521011358628999754559988999
Q gi|254781187|r  130 KWLSMLPHRHWFEMQSLSLHPSGWYAELLEQSMGIDSKHYTITCRTYSEERPDTFVGPHNTHGMAVFNDEASGTPDIINK  209 (367)
Q Consensus       130 k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~ea~~g~h~~~~~l~ivDEAsgI~d~i~e  209 (367)
                              .+               ...  .++........-..+...+.  -.+....|.+. .+|+|||...+...|.
T Consensus        85 --------~s---------------~DV--iEIDAASn~gVDdIReLie~--v~y~P~~gkYK-VyIIDEvHMLS~~AfN  136 (718)
T PRK07133         85 --------NN---------------LDI--IEMDAASNNGVDEIRELREN--VKNLPQISKYK-IYIIDEVHMLSKSAFN  136 (718)
T ss_pred             --------CC---------------CCE--EEECCCCCCCHHHHHHHHHH--HCCCCCCCCEE-EEEEECCCCCCHHHHH
T ss_conf             --------89---------------873--77545566888999999998--25588778724-9999662007999999


Q ss_pred             HHHHHHHCCCCCEEEEEE
Q ss_conf             989874069882589998
Q gi|254781187|r  210 SILGFFTELNPNRFWIMT  227 (367)
Q Consensus       210 ~i~g~Lt~~~~~~~~i~i  227 (367)
                      +++-+|-.+-..++.++.
T Consensus       137 ALLKtLEEPP~hvvFILa  154 (718)
T PRK07133        137 ALLKTLEEPPKHVIFILA  154 (718)
T ss_pred             HHHHHHCCCCCCCEEEEE
T ss_conf             999850279878279997


No 62 
>PRK05707 DNA polymerase III subunit delta'; Validated
Probab=97.10  E-value=0.012  Score=35.20  Aligned_cols=36  Identities=14%  Similarity=0.168  Sum_probs=30.4

Q ss_pred             EEEEECCCCCCHHHHHHHHHHHHCCCCCEEEEEEEC
Q ss_conf             899975455998899998987406988258999807
Q gi|254781187|r  194 AVFNDEASGTPDIINKSILGFFTELNPNRFWIMTSN  229 (367)
Q Consensus       194 l~ivDEAsgI~d~i~e~i~g~Lt~~~~~~~~i~igN  229 (367)
                      .+|+|+|.........++..+|-.+-..++++++++
T Consensus       109 V~iI~~Ae~m~~~AaNALLKtLEEPp~~t~fiL~t~  144 (328)
T PRK05707        109 VVLIEPAEAMNRNAANALLKSLEEPSGQTVLLLISH  144 (328)
T ss_pred             EEEEEHHHHHCHHHHHHHHHHHHCCCCCEEEEEEEC
T ss_conf             999502877389999999998507898759998609


No 63 
>PRK07270 DNA polymerase III subunits gamma and tau; Validated
Probab=97.09  E-value=0.021  Score=33.68  Aligned_cols=138  Identities=14%  Similarity=0.093  Sum_probs=69.5

Q ss_pred             HHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHHHHHHH
Q ss_conf             99999998888751245555541124776148867889999999999997089977999715379999999999999998
Q gi|254781187|r   54 WQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLKNTLWAEVSKWLS  133 (367)
Q Consensus        54 wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~~~lw~ei~k~~~  133 (367)
                      .|..+.+.+..-++++... |.    ..-.++||+|||.++-.++-...|.++...--|-.  -..-+.+.     .  .
T Consensus        19 GQe~i~~~L~nal~~~ri~-HA----yLF~GP~GtGKts~ArifAkaLnC~~~~~~~pC~~--C~~C~~i~-----~--g   84 (557)
T PRK07270         19 GQEVVATTLKQAVESGKIS-HA----YLFSGPRGTGKTSAAKIFAKAMNCPNQVDGEPCNN--CDICRDIT-----N--G   84 (557)
T ss_pred             CHHHHHHHHHHHHHCCCCC-EE----EEEECCCCCCHHHHHHHHHHHHCCCCCCCCCCCCC--CHHHHHHH-----C--C
T ss_conf             8199999999999859954-04----42108998689999999999957999899998887--77999987-----5--8


Q ss_pred             HCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCEEEEECCCCCCHHHHHHHHH
Q ss_conf             62312112333321000123332211113457761266210135445565210113586289997545599889999898
Q gi|254781187|r  134 MLPHRHWFEMQSLSLHPSGWYAELLEQSMGIDSKHYTITCRTYSEERPDTFVGPHNTHGMAVFNDEASGTPDIINKSILG  213 (367)
Q Consensus       134 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~ea~~g~h~~~~~l~ivDEAsgI~d~i~e~i~g  213 (367)
                      ..++  .++..+.                 ...|  .-..+-.+.  --++....+.+ -.+|+|||...+...+.+++-
T Consensus        85 ~~~D--viEidaa-----------------s~~g--Vd~IRei~~--~~~~~P~~~~y-KV~IIDEah~Ls~~A~NALLK  140 (557)
T PRK07270         85 SLED--VIEIDAA-----------------SNNG--VDEIRDIRD--KSTYAPSRATY-KVYIIDEVHMLSTGAFNALLK  140 (557)
T ss_pred             CCCC--EEEECCC-----------------CCCC--HHHHHHHHH--HHCCCCCCCCE-EEEEECCHHHCCHHHHHHHHH
T ss_conf             9997--4873477-----------------7678--899999999--84238777883-899971445349999998999


Q ss_pred             HHHCCCCCEEEEEEEC
Q ss_conf             7406988258999807
Q gi|254781187|r  214 FFTELNPNRFWIMTSN  229 (367)
Q Consensus       214 ~Lt~~~~~~~~i~igN  229 (367)
                      +|-.+-...+.+++.|
T Consensus       141 tLEEPP~~~vFIL~Tt  156 (557)
T PRK07270        141 TLEEPTENVVFILATT  156 (557)
T ss_pred             HHHCCCCCEEEEEEEC
T ss_conf             8528998769999849


No 64 
>KOG0390 consensus
Probab=97.09  E-value=0.021  Score=33.72  Aligned_cols=173  Identities=20%  Similarity=0.119  Sum_probs=94.1

Q ss_pred             HHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCC-----CEEEEECCCHHHHHHHHHH
Q ss_conf             28999999988887512455555411247761488678899999999999970899-----7799971537999999999
Q gi|254781187|r   52 HRWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPG-----MSIICIANSETQLKNTLWA  126 (367)
Q Consensus        52 ~~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~-----~~v~~~A~t~~Q~~~~lw~  126 (367)
                      ++-|.|.++=+.+.+-.......+  .-..++-.=|+|||.++-.++.-++..+|+     .+.+|++|+.  +-...-+
T Consensus       240 rPHQ~EG~~FL~knl~g~~~~~~~--~GCImAd~~GlGKTlq~IsflwtlLrq~P~~~~~~~k~lVV~P~s--Lv~nWkk  315 (776)
T KOG0390         240 RPHQREGFEFLYKNLAGLIRPKNS--GGCIMADEPGLGKTLQCISFIWTLLRQFPQAKPLINKPLVVAPSS--LVNNWKK  315 (776)
T ss_pred             CCHHHHHHHHHHHHHHCCCCCCCC--CCEEEECCCCCCHHHHHHHHHHHHHHHCCCCCCCCCCCEEECCHH--HHHHHHH
T ss_conf             815787789978641131115888--754720788764078889999999986867554446607984588--8878999


Q ss_pred             HHHHHHHH-CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCE---EEEECCCCCCCCCCCCCCCCCCCCEEEEECCCC
Q ss_conf             99999986-23121123333210001233322111134577612---662101354455652101135862899975455
Q gi|254781187|r  127 EVSKWLSM-LPHRHWFEMQSLSLHPSGWYAELLEQSMGIDSKHY---TITCRTYSEERPDTFVGPHNTHGMAVFNDEASG  202 (367)
Q Consensus       127 ei~k~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~a~~~~~~~~ea~~g~h~~~~~l~ivDEAsg  202 (367)
                      |+.||... .++...+.......|++    ..-...+.+..-+.   .+..-+++    ...+-+......++|+||..-
T Consensus       316 EF~KWl~~~~i~~l~~~~~~~~~w~~----~~sil~~~~~~~~~~vli~sye~~~----~~~~~il~~~~glLVcDEGHr  387 (776)
T KOG0390         316 EFGKWLGNHRINPLDFYSTKKSSWIK----LKSILFLGYKQFTTPVLIISYETAS----DYCRKILLIRPGLLVCDEGHR  387 (776)
T ss_pred             HHHHHCCCCCCCEEEEECCCCHHHHH----HHHHHHHHHHHEEEEEEECCHHHHH----HHHHHHHCCCCCEEEECCCCC
T ss_conf             99874253555404542345256666----6789886221125787863699999----999998547898699779888


Q ss_pred             CCH---HHHHHHHHHHHCCCCCEEEEEEECCCCCCCHHHHHHH
Q ss_conf             998---8999989874069882589998078999876887541
Q gi|254781187|r  203 TPD---IINKSILGFFTELNPNRFWIMTSNTRRLNGWFYDIFN  242 (367)
Q Consensus       203 I~d---~i~e~i~g~Lt~~~~~~~~i~igNP~r~~g~Fye~~~  242 (367)
                      -.+   .+|.++-    .-..+.-.++.|||--  |-|-|.|+
T Consensus       388 lkN~~s~~~kaL~----~l~t~rRVLLSGTp~Q--Ndl~EyFn  424 (776)
T KOG0390         388 LKNSDSLTLKALS----SLKTPRRVLLTGTPIQ--NDLKEYFN  424 (776)
T ss_pred             CCCHHHHHHHHHH----HCCCCCEEEEECCCCC--CCHHHHHH
T ss_conf             5622458999997----4687736996077533--46999978


No 65 
>pfam07652 Flavi_DEAD Flavivirus DEAD domain.
Probab=97.07  E-value=0.008  Score=36.29  Aligned_cols=131  Identities=18%  Similarity=0.090  Sum_probs=74.7

Q ss_pred             EEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             76148867889999999999997089977999715379999999999999998623121123333210001233322111
Q gi|254781187|r   81 AISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLKNTLWAEVSKWLSMLPHRHWFEMQSLSLHPSGWYAELLEQ  160 (367)
Q Consensus        81 ~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~~~lw~ei~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  160 (367)
                      .+--.=|.|||.-.---++-. +.....++++.|||.     ++-+|+.+.++..+.+.....-..              
T Consensus         6 ~ld~HPGaGKTr~vLP~~v~~-~i~~~lRtlVLaPTR-----VV~~Em~eAL~g~~vr~~t~a~~~--------------   65 (146)
T pfam07652         6 VLDLHPGAGKTRKVLPELVRE-CIDRRLRTLVLAPTR-----VVLAEMEEALRGLPIRYHTPAVSS--------------   65 (146)
T ss_pred             EEECCCCCCCCCHHHHHHHHH-HHHCCCEEEEECCHH-----HHHHHHHHHHCCCCCEEECHHHHC--------------
T ss_conf             985389999702248999999-997286189977279-----999999999758994675234313--------------


Q ss_pred             CCCCCCCCEEEE-----ECCCCCCCCCCCCCCCCCCCCEEEEECCCCCCHHHHHHHHHHH---HCCCCCEEEEEEECCCC
Q ss_conf             134577612662-----1013544556521011358628999754559988999989874---06988258999807899
Q gi|254781187|r  161 SMGIDSKHYTIT-----CRTYSEERPDTFVGPHNTHGMAVFNDEASGTPDIINKSILGFF---TELNPNRFWIMTSNTRR  232 (367)
Q Consensus       161 ~~~~~~~~~~~~-----a~~~~~~~~ea~~g~h~~~~~l~ivDEAsgI~d~i~e~i~g~L---t~~~~~~~~i~igNP~r  232 (367)
                         ...+...+.     ..+-+.     +.+.+.-+..++|+|||.+.+.....+ .|-+   ...+.-.+.+++.+|++
T Consensus        66 ---~~~~~~ivdvmCHAT~t~r~-----l~~~~~~ny~viIMDE~H~~DP~SIAa-rG~~~~~~~~g~~a~i~mTATPPG  136 (146)
T pfam07652        66 ---EHTGREIVDVMCHATFTQRL-----LSPVRVPNYEVIIMDEAHFTDPASIAA-RGYISTLVELGEAAAIFMTATPPG  136 (146)
T ss_pred             ---CCCCCCEEEEECHHHHHHHH-----HCCCCCCCEEEEEEECCCCCCHHHHHH-HHHHHHHHHCCCEEEEEEECCCCC
T ss_conf             ---66888418897159888897-----368885644799985122389899998-899998854386579999568999


Q ss_pred             CCCHHHHH
Q ss_conf             98768875
Q gi|254781187|r  233 LNGWFYDI  240 (367)
Q Consensus       233 ~~g~Fye~  240 (367)
                      .++.|-++
T Consensus       137 ~~~~fp~S  144 (146)
T pfam07652       137 TSDPFPES  144 (146)
T ss_pred             CCCCCCCC
T ss_conf             89989888


No 66 
>PRK00440 rfc replication factor C small subunit; Reviewed
Probab=97.07  E-value=0.022  Score=33.55  Aligned_cols=119  Identities=16%  Similarity=0.170  Sum_probs=61.6

Q ss_pred             HHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEE-CCCHHHHHHHHHHHHHHHHH
Q ss_conf             99999988887512455555411247761488678899999999999970899779997-15379999999999999998
Q gi|254781187|r   55 QLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICI-ANSETQLKNTLWAEVSKWLS  133 (367)
Q Consensus        55 q~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~-A~t~~Q~~~~lw~ei~k~~~  133 (367)
                      |.++...+...++.+.   .|   .+.+.++.|+|||+++-.++--..+-.....++-. |...+.+. ++-..++...+
T Consensus        21 ~~~~~~~L~~~i~~~~---~p---hlLf~GppG~GKTt~a~~la~~l~~~~~~~~~lelnasd~r~id-~vr~~i~~~~~   93 (318)
T PRK00440         21 QEEIVERLKSFVKEKN---MP---HLLFAGPPGTGKTTAALALARELYGEYWRENFLELNASDERGID-VIRNKIKEFAR   93 (318)
T ss_pred             CHHHHHHHHHHHHCCC---CC---EEEEECCCCCCHHHHHHHHHHHHCCCCCCCCEEEECCCCCCCHH-HHHHHHHHHHH
T ss_conf             6999999999998799---86---69888959988999999999997698643476895164566717-89999999997


Q ss_pred             HCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCEEEEECCCCCCHHHHHHHHH
Q ss_conf             62312112333321000123332211113457761266210135445565210113586289997545599889999898
Q gi|254781187|r  134 MLPHRHWFEMQSLSLHPSGWYAELLEQSMGIDSKHYTITCRTYSEERPDTFVGPHNTHGMAVFNDEASGTPDIINKSILG  213 (367)
Q Consensus       134 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~ea~~g~h~~~~~l~ivDEAsgI~d~i~e~i~g  213 (367)
                      ..+                                               +.   +...-++|+|||.+.......++..
T Consensus        94 ~~~-----------------------------------------------~~---~~~~kiiiiDE~d~l~~~aq~aL~~  123 (318)
T PRK00440         94 TAP-----------------------------------------------VG---GAPFKIIFLDEADNLTSDAQQALRR  123 (318)
T ss_pred             HCC-----------------------------------------------CC---CCCEEEEEEECCCCCCHHHHHHHHH
T ss_conf             267-----------------------------------------------78---9973899986855322556788876


Q ss_pred             HHHCCCCCEEEEEEECC
Q ss_conf             74069882589998078
Q gi|254781187|r  214 FFTELNPNRFWIMTSNT  230 (367)
Q Consensus       214 ~Lt~~~~~~~~i~igNP  230 (367)
                      +|-........+++.|.
T Consensus       124 ~mE~~~~~~~fil~~n~  140 (318)
T PRK00440        124 TMEMYSQTTRFILSCNY  140 (318)
T ss_pred             HHHCCCCCCEEEEECCC
T ss_conf             43105666258863488


No 67 
>PRK06871 DNA polymerase III subunit delta'; Validated
Probab=97.05  E-value=0.02  Score=33.91  Aligned_cols=140  Identities=16%  Similarity=0.288  Sum_probs=72.8

Q ss_pred             HHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHHHHHHH
Q ss_conf             99999998888751245555541124776148867889999999999997089977999715379999999999999998
Q gi|254781187|r   54 WQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLKNTLWAEVSKWLS  133 (367)
Q Consensus        54 wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~~~lw~ei~k~~~  133 (367)
                      ||....+.+....+.+...+     ...+.+.+|+||+.++-.++-|.+|..|+...-|-.-..=++       +.  ..
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-----ALLFKADSGLGTEQLIRALAQWLMCQAPGDEQPCGQCHSCHL-------FQ--AG   70 (324)
T ss_pred             CCHHHHHHHHHHHHCCCCCE-----EEEEECCCCCCHHHHHHHHHHHHHCCCCCCCCCCCCCHHHHH-------HH--CC
T ss_conf             65799999999998699543-----787689999789999999999982899999998888989999-------97--38


Q ss_pred             HCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCEEEEECCCCCCHHHHHHHHH
Q ss_conf             62312112333321000123332211113457761266210135445565210113586289997545599889999898
Q gi|254781187|r  134 MLPHRHWFEMQSLSLHPSGWYAELLEQSMGIDSKHYTITCRTYSEERPDTFVGPHNTHGMAVFNDEASGTPDIINKSILG  213 (367)
Q Consensus       134 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~ea~~g~h~~~~~l~ivDEAsgI~d~i~e~i~g  213 (367)
                      .-|+-++.....             ..+++.+.-.....     .-+-.+.+|   .+ -.+|+|+|.........++..
T Consensus        71 ~HPD~~~i~~~~-------------~k~I~vd~IR~l~~-----~~~~~~~~g---~~-KV~iI~~ae~m~~~AaNALLK  128 (324)
T PRK06871         71 NHPDFHILEPID-------------GKDIGVDQVREINE-----KVSQFAQQG---GN-KVVYIQGAERLTEAAANALLK  128 (324)
T ss_pred             CCCCEEEEECCC-------------CCCCCHHHHHHHHH-----HHHHCCCCC---CC-EEEEECCHHHHHHHHHHHHHH
T ss_conf             999879984678-------------88788999999999-----986462205---96-699975888857999999999


Q ss_pred             HHHCCCCCEEEEEEEC
Q ss_conf             7406988258999807
Q gi|254781187|r  214 FFTELNPNRFWIMTSN  229 (367)
Q Consensus       214 ~Lt~~~~~~~~i~igN  229 (367)
                      +|-.+...++.+++++
T Consensus       129 tLEEPp~~~~fiL~t~  144 (324)
T PRK06871        129 TLEEPRPNTYFLLQAD  144 (324)
T ss_pred             HHCCCCCCEEEEEEEC
T ss_conf             8338987838999878


No 68 
>PRK07994 DNA polymerase III subunits gamma and tau; Validated
Probab=97.04  E-value=0.012  Score=35.11  Aligned_cols=134  Identities=15%  Similarity=0.144  Sum_probs=72.5

Q ss_pred             HHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHHHHHHH
Q ss_conf             99999998888751245555541124776148867889999999999997089977999715379999999999999998
Q gi|254781187|r   54 WQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLKNTLWAEVSKWLS  133 (367)
Q Consensus        54 wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~~~lw~ei~k~~~  133 (367)
                      .|..+++.+...+..+.. ++.    ....+.||+|||+++-.++-.+-|.....-.-|    . + ... ..+|..   
T Consensus        20 GQ~~v~~~l~na~~~~r~-~ha----ylf~G~rG~GKtt~ari~ak~lnc~~~~~~~pc----g-~-c~~-c~~i~~---   84 (643)
T PRK07994         20 GQEHVLTALANGLSLGRI-HHA----YLFSGTRGVGKTSIARLLAKGLNCETGITATPC----G-V-CDN-CREIEQ---   84 (643)
T ss_pred             CCHHHHHHHHHHHHHCCC-CCE----EEEECCCCCCHHHHHHHHHHHHCCCCCCCCCCC----C-C-CHH-HHHHHC---
T ss_conf             879999999999982986-634----874589988888999999999679999999978----7-6-776-898865---


Q ss_pred             HCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCEEEEECCCCCCHHHHHHHHH
Q ss_conf             62312112333321000123332211113457761266210135445565210113586289997545599889999898
Q gi|254781187|r  134 MLPHRHWFEMQSLSLHPSGWYAELLEQSMGIDSKHYTITCRTYSEERPDTFVGPHNTHGMAVFNDEASGTPDIINKSILG  213 (367)
Q Consensus       134 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~ea~~g~h~~~~~l~ivDEAsgI~d~i~e~i~g  213 (367)
                                        ..+....+.+  ...+...-..+-..+  --.+.-.+|.+. .+|+||....+...|.+++.
T Consensus        85 ------------------g~~~d~~eid--aas~~~vd~~rel~~--~~~y~p~~~r~k-vyiidEvhmls~~afnalLK  141 (643)
T PRK07994         85 ------------------GRFVDLIEID--AASRTKVEDTRDLLD--NVQYAPARGRFK-VYLIDEVHMLSRHSFNALLK  141 (643)
T ss_pred             ------------------CCCCCEEEEE--CCCCCCHHHHHHHHH--HCCCCCCCCCEE-EEEEECHHHCCHHHHHHHHH
T ss_conf             ------------------8988758863--677788899999998--446688778536-99972210158999999998


Q ss_pred             HHHCCCCCEEEE
Q ss_conf             740698825899
Q gi|254781187|r  214 FFTELNPNRFWI  225 (367)
Q Consensus       214 ~Lt~~~~~~~~i  225 (367)
                      +|-.+-...+.+
T Consensus       142 tlEePp~hv~fi  153 (643)
T PRK07994        142 TLEEPPAHVKFL  153 (643)
T ss_pred             HHCCCCHHCEEE
T ss_conf             623786100899


No 69 
>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=97.03  E-value=0.021  Score=33.73  Aligned_cols=152  Identities=14%  Similarity=0.142  Sum_probs=72.5

Q ss_pred             CCCCCCCCCCCCCCH-----HHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCC-CCEEE
Q ss_conf             466888443666842-----899999998888751245555541124776148867889999999999997089-97799
Q gi|254781187|r   38 WGIKGKPLEHFSQPH-----RWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRP-GMSII  111 (367)
Q Consensus        38 w~~~~~~~~~~~~p~-----~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~-~~~v~  111 (367)
                      ||-+..|+..-..|+     +-..++|..+.-.++....      + +.|.+.=|+|||++.-.++-..   .+ ...++
T Consensus         6 fgl~~~PF~~~pd~~~~y~s~~h~~al~~L~~~l~~~~g------~-~lltGe~GtGKTtllr~l~~~l---~~~~~~~~   75 (269)
T TIGR03015         6 FGFTTKPFQLLPDPDFFYPSKGHKRAMAYLEYGLSQREG------F-ILITGEVGAGKTTLIRNLLKRL---DQERVVAA   75 (269)
T ss_pred             CCCCCCCCCCCCCHHHCCCCHHHHHHHHHHHHHHHCCCC------E-EEEECCCCCCHHHHHHHHHHHC---CCCCEEEE
T ss_conf             499989999999845414786699999999999964896------5-9997299898899999999845---93454899


Q ss_pred             EECCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCC
Q ss_conf             97153799999999999999986231211233332100012333221111345776126621013544556521011358
Q gi|254781187|r  112 CIANSETQLKNTLWAEVSKWLSMLPHRHWFEMQSLSLHPSGWYAELLEQSMGIDSKHYTITCRTYSEERPDTFVGPHNTH  191 (367)
Q Consensus       112 ~~A~t~~Q~~~~lw~ei~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~ea~~g~h~~~  191 (367)
                      .+.++.-...+.+ ..|..-+..-+...    ......          ..         +....    . +  ....+..
T Consensus        76 ~i~~~~l~~~~ll-~~i~~~lg~~~~~~----~~~~~~----------~~---------l~~~L----~-~--~~~~g~~  124 (269)
T TIGR03015        76 KLVNTRVDAEDLL-RMVAADFGLETEGR----DKAALL----------RE---------LEDFL----I-E--QFAAGKR  124 (269)
T ss_pred             EECCCCCCHHHHH-HHHHHHCCCCCCCC----CHHHHH----------HH---------HHHHH----H-H--HHHCCCC
T ss_conf             9769999999999-99999859898898----999999----------99---------99999----9-9--9966994


Q ss_pred             CCEEEEECCCCCCHHHHHHHHHHH---HCCCCCEEEEEEECCC
Q ss_conf             628999754559988999989874---0698825899980789
Q gi|254781187|r  192 GMAVFNDEASGTPDIINKSILGFF---TELNPNRFWIMTSNTR  231 (367)
Q Consensus       192 ~~l~ivDEAsgI~d~i~e~i~g~L---t~~~~~~~~i~igNP~  231 (367)
                       .++|+|||..+++++.+.+.-.+   ++..+-.-.+++|.|.
T Consensus       125 -~vliIDEAq~L~~~~Le~Lr~L~n~e~~~~~ll~iiL~Gqpe  166 (269)
T TIGR03015       125 -ALLVVDEAQNLTPELLEELRMLSNFQTDNAKLLQIFLVGQPE  166 (269)
T ss_pred             -EEEEEECHHHCCHHHHHHHHHHHCCCCCCCCCEEEEEECCHH
T ss_conf             -699972422199999999999970135888704899957867


No 70 
>PRK06645 DNA polymerase III subunits gamma and tau; Validated
Probab=97.02  E-value=0.02  Score=33.83  Aligned_cols=142  Identities=15%  Similarity=0.096  Sum_probs=68.2

Q ss_pred             HHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHHHHHHH
Q ss_conf             99999998888751245555541124776148867889999999999997089977999715379999999999999998
Q gi|254781187|r   54 WQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLKNTLWAEVSKWLS  133 (367)
Q Consensus        54 wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~~~lw~ei~k~~~  133 (367)
                      .|..+.+.+...+..+... +    ...-.+.||+|||+.+-.++--.-|..+...--...|-..  ...+ ..+..   
T Consensus        25 GQ~~~~~~l~n~i~~~~~~-~----aylf~G~rG~GKTt~Ari~ak~lnc~~~~~~~~~~~~c~~--c~~c-~~i~~---   93 (507)
T PRK06645         25 GQEVLVKVLSYTILNDRLA-G----GYLLTGIRGVGKTTSARIIAKAVNCSALITENTTIKTCEK--CTNC-ISFNN---   93 (507)
T ss_pred             CCHHHHHHHHHHHHCCCCC-C----EEEEECCCCCCHHHHHHHHHHHHCCCCCCCCCCCCCCCCC--CHHH-HHHHC---
T ss_conf             9399999999999739966-3----4774587997889999999999679998888998888888--7678-99865---


Q ss_pred             HCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCEEEEECCCCCCHHHHHHHHH
Q ss_conf             62312112333321000123332211113457761266210135445565210113586289997545599889999898
Q gi|254781187|r  134 MLPHRHWFEMQSLSLHPSGWYAELLEQSMGIDSKHYTITCRTYSEERPDTFVGPHNTHGMAVFNDEASGTPDIINKSILG  213 (367)
Q Consensus       134 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~ea~~g~h~~~~~l~ivDEAsgI~d~i~e~i~g  213 (367)
                                        .....+.+.+  .......-..+...+.  -.+.-..+.+ -.+|+||+...+...|.+++-
T Consensus        94 ------------------~~~~dv~EiD--aas~~gv~~ir~l~~~--~~~~p~~~~~-kv~iidE~hmls~~a~nallk  150 (507)
T PRK06645         94 ------------------HNHPDIIEID--AASKTSVDDIRRIIES--AEYKPLQGKH-KIFIIDEVHMLSKGAFNALLK  150 (507)
T ss_pred             ------------------CCCCCEEEEE--CCCCCCHHHHHHHHHH--CCCCCCCCCE-EEEEECCHHHCCHHHHHHHHH
T ss_conf             ------------------8999859963--7888888999999863--5517876743-589952142248999999999


Q ss_pred             HHHCCCCCEEEEEEEC
Q ss_conf             7406988258999807
Q gi|254781187|r  214 FFTELNPNRFWIMTSN  229 (367)
Q Consensus       214 ~Lt~~~~~~~~i~igN  229 (367)
                      +|-.+-.....++..|
T Consensus       151 tlEepp~~~~Fi~att  166 (507)
T PRK06645        151 TLEEPPPHIIFIFATT  166 (507)
T ss_pred             HHHCCCCCEEEEEECC
T ss_conf             7427864438999748


No 71 
>PRK07471 DNA polymerase III subunit delta'; Validated
Probab=96.95  E-value=0.0075  Score=36.47  Aligned_cols=160  Identities=16%  Similarity=0.169  Sum_probs=79.8

Q ss_pred             CCCCCHH-----HHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHH-HH
Q ss_conf             6668428-----99999998888751245555541124776148867889999999999997089977999715379-99
Q gi|254781187|r   47 HFSQPHR-----WQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSET-QL  120 (367)
Q Consensus        47 ~~~~p~~-----wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~-Q~  120 (367)
                      +..+|+.     .|.++...+..-.+.+...+     -....+.+|+||++++=.++-+.+|+.++....+...... .+
T Consensus         9 ~~p~P~~~~~liGqe~~~~~L~~a~~~grl~H-----A~Lf~Gp~GiGK~tlA~~~A~~ll~~~~~~~~~~~~~~~~l~~   83 (363)
T PRK07471          9 ADPHPRETTALFGHAAAEAALLDAYRSGRLHH-----AWLIGGPQGIGKATLAYRMARFLLATPPPGGDAVFPPPASLAV   83 (363)
T ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCC-----EEEEECCCCCCHHHHHHHHHHHHHCCCCCCCCCCCCCHHHHCC
T ss_conf             99599982731681999999999998599764-----5876799981889999999999857999777776787053125


Q ss_pred             --HHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCC--CCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCEEE
Q ss_conf             --9999999999998623121123333210001233322--111134577612662101354455652101135862899
Q gi|254781187|r  121 --KNTLWAEVSKWLSMLPHRHWFEMQSLSLHPSGWYAEL--LEQSMGIDSKHYTITCRTYSEERPDTFVGPHNTHGMAVF  196 (367)
Q Consensus       121 --~~~lw~ei~k~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~a~~~~~~~~ea~~g~h~~~~~l~i  196 (367)
                        ..-.++.+.    .......+.+.      +.+....  .+..+..+.      .+..  ..--++....|.+. .+|
T Consensus        84 ~~~~p~~r~i~----~~~hpdl~~i~------r~~d~k~~~~~~~I~Vd~------iR~l--~~~~~~~p~~g~~k-V~I  144 (363)
T PRK07471         84 DPDHPVARRIA----AGAHGGLLTLE------RSWNEKGKRLRTVITVDE------VRET--IGFFGLTAAEGGWR-VVI  144 (363)
T ss_pred             CCCCCHHHHHH----CCCCCCEEEEE------CCCCCCCCCCCCCCCHHH------HHHH--HHHHCCCCCCCCCE-EEE
T ss_conf             87772899995----26999846676------200113332124453999------9999--99972485248966-999


Q ss_pred             EECCCCCCHHHHHHHHHHHHCCCCCEEEEEEECC
Q ss_conf             9754559988999989874069882589998078
Q gi|254781187|r  197 NDEASGTPDIINKSILGFFTELNPNRFWIMTSNT  230 (367)
Q Consensus       197 vDEAsgI~d~i~e~i~g~Lt~~~~~~~~i~igNP  230 (367)
                      +|||.......+.+++.+|-.+-.+++++++++-
T Consensus       145 Id~ad~mn~~aaNALLK~LEEPP~~t~fiLit~~  178 (363)
T PRK07471        145 VDTADEMNANAANALLKVLEEPPARSLLLLVSHA  178 (363)
T ss_pred             EECHHHHCHHHHHHHHHHHCCCCCCEEEEEEECC
T ss_conf             8687873889999999972158988389986399


No 72 
>pfam05970 DUF889 PIF1 helicase. The PIF1 helicase inhibits telomerase activity and is cell cycle regulated.
Probab=96.95  E-value=0.002  Score=39.94  Aligned_cols=97  Identities=14%  Similarity=-0.003  Sum_probs=54.0

Q ss_pred             CCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHH-HHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             886788999999999999708997799971537999999-9999999998623121123333210001233322111134
Q gi|254781187|r   85 GRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLKNT-LWAEVSKWLSMLPHRHWFEMQSLSLHPSGWYAELLEQSMG  163 (367)
Q Consensus        85 grg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~~~-lw~ei~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  163 (367)
                      +=|+|||++.-.++-++-  ..+..+++||||.--|..+ --.-+-.|..                    ..      +.
T Consensus         2 ~AGTGKS~ll~~i~~~l~--~~~~~v~vtA~TGiAA~~i~gG~TiHs~~g--------------------i~------~~   53 (418)
T pfam05970         2 YGGTGKTFLWNALSARIR--SRGKIVLNVASSGIAALLLPGGRTAHSRFG--------------------IP------LD   53 (418)
T ss_pred             CCCCCHHHHHHHHHHHHH--HCCCEEEEECCHHHHHHCCCCCEEHHHCCC--------------------CC------CC
T ss_conf             798879999999999997--689889998968999851699873985269--------------------89------88


Q ss_pred             CCCCCEEEEECCCCCCCCCCCCCCCCCCCCEEEEECCCCCCHHHHHHHHHHHH
Q ss_conf             57761266210135445565210113586289997545599889999898740
Q gi|254781187|r  164 IDSKHYTITCRTYSEERPDTFVGPHNTHGMAVFNDEASGTPDIINKSILGFFT  216 (367)
Q Consensus       164 ~~~~~~~~~a~~~~~~~~ea~~g~h~~~~~l~ivDEAsgI~d~i~e~i~g~Lt  216 (367)
                      .......-.  ..   +.....-++  +..++|+||.|.|+...|+.+.-.|.
T Consensus        54 ~~~~~~~~~--~~---~~~~~~~~~--~~~vLIIDEiSMv~~~lfd~id~~lr   99 (418)
T pfam05970        54 IDEDSTCKI--KR---GSKLAELLK--KASLIIWDEAPMTHRHCFEALDRTLR   99 (418)
T ss_pred             CCCCCCEEE--CC---CHHHHHHHH--HCCEEEEECCCCCCHHHHHHHHHHHH
T ss_conf             774201121--33---778899874--08799985411357899999999999


No 73 
>PRK13826 Dtr system oriT relaxase; Provisional
Probab=96.94  E-value=0.013  Score=35.01  Aligned_cols=114  Identities=16%  Similarity=0.123  Sum_probs=64.6

Q ss_pred             EEECCCCCCHHHHHHH-HHHHHHHHCCCCEEEEECCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             7614886788999999-999999708997799971537999999999999999862312112333321000123332211
Q gi|254781187|r   81 AISAGRGIGKTTLNAW-MMLWLISTRPGMSIICIANSETQLKNTLWAEVSKWLSMLPHRHWFEMQSLSLHPSGWYAELLE  159 (367)
Q Consensus        81 ~v~sgrg~GKS~~~a~-~~lw~~~~~~~~~v~~~A~t~~Q~~~~lw~ei~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  159 (367)
                      +|.+-=|.|||++... --.|-.   .|.+|+=.|++...+... =.+- .          ....    .+..|...   
T Consensus       401 ~VvG~AGaGKStmL~aAReawEa---~GyrV~GaALsGkAAegL-e~~s-G----------I~Sr----TlAs~e~~---  458 (1102)
T PRK13826        401 AVIGRAGAGKTTMMKAAREAWEA---AGYRVVGGALAGKAAEGL-EKEA-G----------IASR----TLSSWELR---  458 (1102)
T ss_pred             EEEECCCCCHHHHHHHHHHHHHH---CCCEEEEECCCHHHHHHH-HHCC-C----------CCCH----HHHHHHHH---
T ss_conf             99842888788999999999997---797798015007899977-5346-9----------5303----38999987---


Q ss_pred             CCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCEEEEECCCCCCHHHHHHHHHHHHCCCCCEEEEEEECC-----CCCC
Q ss_conf             11345776126621013544556521011358628999754559988999989874069882589998078-----9998
Q gi|254781187|r  160 QSMGIDSKHYTITCRTYSEERPDTFVGPHNTHGMAVFNDEASGTPDIINKSILGFFTELNPNRFWIMTSNT-----RRLN  234 (367)
Q Consensus       160 ~~~~~~~~~~~~~a~~~~~~~~ea~~g~h~~~~~l~ivDEAsgI~d~i~e~i~g~Lt~~~~~~~~i~igNP-----~r~~  234 (367)
                          ..              + +. .-+  ....++|+|||+.|....+.-+.......|.+++  +.|-|     -..+
T Consensus       459 ----w~--------------~-gr-~~L--~~~dVlVIDEAGMVgsrqmarvl~~ae~aGAKvV--LVGD~~QLQpIeAG  514 (1102)
T PRK13826        459 ----WN--------------Q-GR-DQL--DNKTVFVLDEAGMVSSRQMALFVEAVTRAGAKLV--LVGDPEQLQPIEAG  514 (1102)
T ss_pred             ----HC--------------C-CC-CCC--CCCCEEEEECCCCCCHHHHHHHHHHHHHCCCEEE--EECCHHHHCCCCCC
T ss_conf             ----43--------------5-86-556--7873899845556557999999999997599899--96887882761046


Q ss_pred             CHHHHH
Q ss_conf             768875
Q gi|254781187|r  235 GWFYDI  240 (367)
Q Consensus       235 g~Fye~  240 (367)
                      +.|-.+
T Consensus       515 aaFrai  520 (1102)
T PRK13826        515 AAFRAI  520 (1102)
T ss_pred             HHHHHH
T ss_conf             889999


No 74 
>COG1875 NYN ribonuclease and ATPase of PhoH family domains [General    function prediction only]
Probab=96.94  E-value=0.0015  Score=40.71  Aligned_cols=156  Identities=13%  Similarity=0.042  Sum_probs=82.6

Q ss_pred             HHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCC-CCEEEEECCCHHHHHHHHHHHHHHH
Q ss_conf             899999998888751245555541124776148867889999999999997089-9779997153799999999999999
Q gi|254781187|r   53 RWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRP-GMSIICIANSETQLKNTLWAEVSKW  131 (367)
Q Consensus        53 ~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~-~~~v~~~A~t~~Q~~~~lw~ei~k~  131 (367)
                      ..|+=.|+.+-+          +.+-=|...+--|+|||.++-+..+.-..-+. ..|++++.|+..--+++-|      
T Consensus       231 ~eQ~~ALdlLld----------~dI~lV~L~G~AGtGKTlLALaAgleqv~e~~~y~KiiVtRp~vpvG~dIGf------  294 (436)
T COG1875         231 AEQRVALDLLLD----------DDIDLVSLGGKAGTGKTLLALAAGLEQVLERKRYRKIIVTRPTVPVGEDIGF------  294 (436)
T ss_pred             HHHHHHHHHHCC----------CCCCEEEEECCCCCCHHHHHHHHHHHHHHHHHHHCEEEEECCCCCCCCCCCC------
T ss_conf             888888998638----------7778488633577667699999899999877543027883377677531376------


Q ss_pred             HHHCCCCCCCCCCCCCCCCCCCCCCC----CCCCCCCCCCCEEEEECCC-CCCCCCCCCCCCCCC--CCEEEEECCCCCC
Q ss_conf             98623121123333210001233322----1111345776126621013-544556521011358--6289997545599
Q gi|254781187|r  132 LSMLPHRHWFEMQSLSLHPSGWYAEL----LEQSMGIDSKHYTITCRTY-SEERPDTFVGPHNTH--GMAVFNDEASGTP  204 (367)
Q Consensus       132 ~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~~~~~~~~~a~~~-~~~~~ea~~g~h~~~--~~l~ivDEAsgI~  204 (367)
                         +|       -....+|.||.-..    .........++........ ..-.-+++--+||.+  -.++|+|||+...
T Consensus       295 ---LP-------G~eEeKm~PWmq~i~DnLE~L~~~~~~~~~~l~~~l~~~~iev~alt~IRGRSl~~~FiIIDEaQNLT  364 (436)
T COG1875         295 ---LP-------GTEEEKMGPWMQAIFDNLEVLFSPNEPGDRALEEILSRGRIEVEALTYIRGRSLPDSFIIIDEAQNLT  364 (436)
T ss_pred             ---CC-------CCHHHHCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCEEEEEEEEECCCCCCCCEEEEEHHHCCC
T ss_conf             ---88-------84366506157676667998726665536789988741542566520131665553069971212178


Q ss_pred             HHHHHHHHHHHHCCCCCEEEEEEECCCCCCCHH
Q ss_conf             889999898740698825899980789998768
Q gi|254781187|r  205 DIINKSILGFFTELNPNRFWIMTSNTRRLNGWF  237 (367)
Q Consensus       205 d~i~e~i~g~Lt~~~~~~~~i~igNP~r~~g~F  237 (367)
                      ....-.|.- -.+.+++  .+++|||.-..+++
T Consensus       365 pheikTilt-R~G~GsK--IVl~gd~aQiD~~y  394 (436)
T COG1875         365 PHELKTILT-RAGEGSK--IVLTGDPAQIDTPY  394 (436)
T ss_pred             HHHHHHHHH-HHCCCCE--EEEECCHHHCCCCC
T ss_conf             888899987-6069977--99808988827754


No 75 
>PRK06090 DNA polymerase III subunit delta'; Validated
Probab=96.92  E-value=0.03  Score=32.75  Aligned_cols=134  Identities=10%  Similarity=0.118  Sum_probs=68.7

Q ss_pred             HHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHHHHHHHHCCCCC
Q ss_conf             98888751245555541124776148867889999999999997089977999715379999999999999998623121
Q gi|254781187|r   60 EAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLKNTLWAEVSKWLSMLPHRH  139 (367)
Q Consensus        60 ~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~~~lw~ei~k~~~~~~~~~  139 (367)
                      +.+....+.+... +    .+.+.+.+|+||+.++-.++-|.+|..+... .|-.-..      + ..+.  ...-|+-+
T Consensus        13 ~~l~~~~~~~rl~-H----A~L~~g~~G~Gk~~la~~la~~LlC~~~~~~-~Cg~C~s------C-~l~~--~g~HPD~~   77 (319)
T PRK06090         13 QNWKSGLDAERIP-G----ALLLQSDEGLGVESLVELFSHALLCQNYQSE-ACGFCHS------C-ELMK--SGNHPDLH   77 (319)
T ss_pred             HHHHHHHHCCCCC-C----EEEEECCCCCCHHHHHHHHHHHHHCCCCCCC-CCCCCHH------H-HHHH--CCCCCCCE
T ss_conf             9999999869963-0----6766799985799999999999808999999-8877877------9-9987--58999823


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCEEEEECCCCCCHHHHHHHHHHHHCCC
Q ss_conf             12333321000123332211113457761266210135445565210113586289997545599889999898740698
Q gi|254781187|r  140 WFEMQSLSLHPSGWYAELLEQSMGIDSKHYTITCRTYSEERPDTFVGPHNTHGMAVFNDEASGTPDIINKSILGFFTELN  219 (367)
Q Consensus       140 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~ea~~g~h~~~~~l~ivDEAsgI~d~i~e~i~g~Lt~~~  219 (367)
                      +...+.            ....++.+.-....     +.....+.+|   -+ -.+|+|+|.........++..+|-++.
T Consensus        78 ~i~pe~------------~~k~I~vd~IR~l~-----~~~~~~~~~g---~~-KV~iI~~ae~m~~~AaNALLKtLEEPp  136 (319)
T PRK06090         78 VIKPEK------------EGKSITVEQIRQCN-----RLAQESSQLG---GY-RLFVIEPADAMNESASNALLKTLEEPA  136 (319)
T ss_pred             EEECCC------------CCCCCCHHHHHHHH-----HHHHHCCCCC---CC-EEEEECCHHHCCHHHHHHHHHHHCCCC
T ss_conf             661233------------56768799999999-----9975452106---93-699981444349999999999842899


Q ss_pred             CCEEEEEEEC
Q ss_conf             8258999807
Q gi|254781187|r  220 PNRFWIMTSN  229 (367)
Q Consensus       220 ~~~~~i~igN  229 (367)
                      .+++.+++++
T Consensus       137 ~~t~fiL~t~  146 (319)
T PRK06090        137 PNCLFLLVTH  146 (319)
T ss_pred             CCEEEEEEEC
T ss_conf             8838998768


No 76 
>PRK08181 transposase; Validated
Probab=96.86  E-value=0.024  Score=33.31  Aligned_cols=128  Identities=14%  Similarity=0.107  Sum_probs=68.9

Q ss_pred             CCHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHHH
Q ss_conf             84289999999888875124555554112477614886788999999999999708997799971537999999999999
Q gi|254781187|r   50 QPHRWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLKNTLWAEVS  129 (367)
Q Consensus        50 ~p~~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~~~lw~ei~  129 (367)
                      ++.+-|..-|..--.+++++.        ++.+.++-|+|||+++.++..-  .++.|.+|..+.-..      +..++.
T Consensus        87 ~i~~~~i~~L~~~~~fi~~~~--------Nvil~Gp~GtGKThLA~Alg~~--A~~~G~~V~f~~~~~------L~~~L~  150 (269)
T PRK08181         87 MISKAQVMALAAGDSWLAKGA--------NLLLFGPPGGGKSHLAAAIGLA--LIENGWRVLFTRTTD------LVQKLQ  150 (269)
T ss_pred             CCCHHHHHHHHCCCHHHHCCC--------EEEEECCCCCCHHHHHHHHHHH--HHHCCCEEEEEEHHH------HHHHHH
T ss_conf             989999999965675886487--------0899899998788999999999--998799399978999------999999


Q ss_pred             HHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCEEEEECCCCCC-----
Q ss_conf             999862312112333321000123332211113457761266210135445565210113586289997545599-----
Q gi|254781187|r  130 KWLSMLPHRHWFEMQSLSLHPSGWYAELLEQSMGIDSKHYTITCRTYSEERPDTFVGPHNTHGMAVFNDEASGTP-----  204 (367)
Q Consensus       130 k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~ea~~g~h~~~~~l~ivDEAsgI~-----  204 (367)
                      ......                                ..           ...+.-+  ....|+|+||...+|     
T Consensus       151 ~a~~~~--------------------------------~~-----------~~~~~~l--~~~dLLIiDe~G~~~~~~~~  185 (269)
T PRK08181        151 VARREL--------------------------------QL-----------ESAIAKL--DKFDLLILDDLAYVTKDQAE  185 (269)
T ss_pred             HHHHCC--------------------------------CH-----------HHHHHHH--HCCCEEEEHHCCCCCCCHHH
T ss_conf             977558--------------------------------39-----------9999997--44460122010566799899


Q ss_pred             -HHHHHHHHHHHHCCCCCEEEEEEECCCCCCCHHHHHHHCC
Q ss_conf             -8899998987406988258999807899987688754112
Q gi|254781187|r  205 -DIINKSILGFFTELNPNRFWIMTSNTRRLNGWFYDIFNIP  244 (367)
Q Consensus       205 -d~i~e~i~g~Lt~~~~~~~~i~igNP~r~~g~Fye~~~~~  244 (367)
                       +..|+.+..--   +.+. .+++  .+.+.+..++.|.++
T Consensus       186 ~~~lf~lI~~Ry---e~~S-~IIT--Sn~~~~~W~~~f~D~  220 (269)
T PRK08181        186 TSVLFELISARY---ERRS-ILIT--ANQPFGEWNRVFPDP  220 (269)
T ss_pred             HHHHHHHHHHHH---CCCC-EEEE--CCCCHHHHHHHCCCH
T ss_conf             999999999985---7888-8998--899977887753868


No 77 
>TIGR01054 rgy reverse gyrase; InterPro: IPR005736   DNA topoisomerases regulate the number of topological links between two DNA strands (i.e. change the number of superhelical turns) by catalysing transient single- or double-strand breaks, crossing the strands through one another, then resealing the breaks. These enzymes have several functions: to remove DNA supercoils during transcription and DNA replication; for strand breakage during recombination; for chromosome condensation; and to disentangle intertwined DNA during mitosis , . DNA topoisomerases are divided into two classes: type I enzymes (5.99.1.2 from EC; topoisomerases I, III and V) break single-strand DNA, and type II enzymes (5.99.1.3 from EC; topoisomerases II, IV and VI) break double-strand DNA .   Type I topoisomerases are ATP-independent enzymes (except for reverse gyrase), and can be subdivided according to their structure and reaction mechanisms: type IA (bacterial and archaeal topoisomerase I, topoisomerase III and reverse gyrase) and type IB (eukaryotic topoisomerase I and topoisomerase V). These enzymes are primarily responsible for relaxing positively and/or negatively supercoiled DNA, except for reverse gyrase, which can introduce positive supercoils into DNA.    Reverse gyrase is a type IA topoisomerase that is unique among these enzymes in its requirement for ATP. Reverse gyrase is a hyperthermophile-specific enzyme that acts as a renaturase by positively supercoiling DNA, and by annealing complementary single-strand circles . Hyperthermophilic organisms must protect themselves against heat-induced degradation, and reverse gyrase acts to reduce the rate of double-strand DNA breakage, a function that does not require ATP hydrolysis and which is independent of its positive supercoiling abilities. Reverse gyrase achieves this by recognising nicked DNA and recruiting a protein coat to the site of damage .   More information about this protein can be found at Protein of the Month: DNA Topoisomerase .; GO: 0003677 DNA binding, 0003916 DNA topoisomerase activity, 0006265 DNA topological change, 0006268 DNA unwinding during replication, 0005694 chromosome.
Probab=96.85  E-value=0.015  Score=34.62  Aligned_cols=200  Identities=18%  Similarity=0.101  Sum_probs=104.7

Q ss_pred             EEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHHHHHHHHCCCCCCCCCC--CCCCCCCCCCCCC
Q ss_conf             77614886788999999999999708997799971537999999999999999862312112333--3210001233322
Q gi|254781187|r   80 CAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLKNTLWAEVSKWLSMLPHRHWFEMQ--SLSLHPSGWYAEL  157 (367)
Q Consensus        80 ~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~~~lw~ei~k~~~~~~~~~~~~~~--~~~~~~~~~~~~~  157 (367)
                      -|+.|+.|+|||++...+.+++++- .|.++.++=||..=++++- ..|++...+.-    ....  ....+.+....+.
T Consensus       102 Fai~APTGVGKttFG~~mslflA~k-KGkR~y~ilPT~lLv~Qv~-~kl~~~~~k~g----~~~~~l~~~yhS~L~~~~k  175 (1843)
T TIGR01054       102 FAIVAPTGVGKTTFGLVMSLFLAKK-KGKRSYIILPTTLLVKQVA-EKLSSLAEKEG----VGIVRLLGAYHSKLSTKEK  175 (1843)
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHHH-CCCEEEEEECHHHHHHHHH-HHHHHHCCCCC----CCCEEEEEEEECCCCHHHH
T ss_conf             4898058876779999999998654-2987899947078899999-99875200257----5000022210112654567


Q ss_pred             CCCCCCCCCCCEEEEECCCCCCCCCCCCCCC-CCCCCEEEEECCCCC----------------CH----HHHHHH-----
Q ss_conf             1111345776126621013544556521011-358628999754559----------------98----899998-----
Q gi|254781187|r  158 LEQSMGIDSKHYTITCRTYSEERPDTFVGPH-NTHGMAVFNDEASGT----------------PD----IINKSI-----  211 (367)
Q Consensus       158 ~~~~~~~~~~~~~~~a~~~~~~~~ea~~g~h-~~~~~l~ivDEAsgI----------------~d----~i~e~i-----  211 (367)
                      ...--++.+|.+-+.-.| +..-.=++.-++ +.++.|++||---.+                +.    ..|+.|     
T Consensus       176 ke~~Eri~~GDfdilitT-~~FL~K~~~~L~~~y~F~liFVDDVDa~Lk~skNVD~~L~LlGF~eE~i~~a~~~i~L~~k  254 (1843)
T TIGR01054       176 KEVKERIENGDFDILITT-SMFLSKNFDKLKNQYKFDLIFVDDVDALLKASKNVDKILKLLGFSEELIEKAYELIKLKLK  254 (1843)
T ss_pred             HHHHHHHHCCCEEEEHHH-HHHHHHHHHHCCCCCEEEEEEEECHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
T ss_conf             889998731891786122-4688876651789851448997153676316555667775517889999999999999887


Q ss_pred             ---------------------------------HHHHHCCCCCEEEEEEECCC-CCCCHHHHHHHCCC-------CCE-E
Q ss_conf             ---------------------------------98740698825899980789-99876887541122-------350-4
Q gi|254781187|r  212 ---------------------------------LGFFTELNPNRFWIMTSNTR-RLNGWFYDIFNIPL-------EDW-K  249 (367)
Q Consensus       212 ---------------------------------~g~Lt~~~~~~~~i~igNP~-r~~g~Fye~~~~~~-------~~w-~  249 (367)
                                                       +.......++.-++++|+-| ++-|-=..+|+..-       ... -
T Consensus       255 ~~k~~~~~~~~~~~~R~E~~~~~LE~~~r~~~~~a~~~~krGr~g~LivsSATG~prG~r~~LFR~LL~FevG~~~~~GL  334 (1843)
T TIGR01054       255 ENKLEEDLAREKIVVRLEARKKLLEAKRRLEKLEAEIKKKRGRKGVLIVSSATGKPRGKRVKLFRELLGFEVGKGSDTGL  334 (1843)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEEEEEEECCCCCCCCHHHHHHHHCCCCCCCCCCCCC
T ss_conf             64357788888886467888999999999898776474324886469998514888761336536552710057642233


Q ss_pred             EEEECCCCCCCC-CHHHHHH---HHHHCCCCCCEEEEEEEE
Q ss_conf             675233328888-9889999---996216880002688864
Q gi|254781187|r  250 RYQIDTRTVEGI-DSGFHEG---IISRYGLDSDVARIEILG  286 (367)
Q Consensus       250 ~~~~~~~d~p~~-~~~~i~~---~~~~~gedS~~~r~ev~G  286 (367)
                      .--++..+++.- =.+-+.+   ..+.+|..--+|=.--+|
T Consensus       335 RnvvD~y~~~~d~v~E~~~~sve~v~~LG~GGlVyvs~~yG  375 (1843)
T TIGR01054       335 RNVVDVYEEDEDGVKEKLLESVELVKKLGKGGLVYVSIDYG  375 (1843)
T ss_pred             CCEEEEEECCCCCHHHHHHHHHHHHHHHCCCEEEEEECCCC
T ss_conf             21388511488844688999999999847943999712225


No 78 
>PRK13889 conjugal transfer relaxase TraA; Provisional
Probab=96.78  E-value=0.018  Score=34.14  Aligned_cols=131  Identities=12%  Similarity=0.019  Sum_probs=72.6

Q ss_pred             HHHHHHHHHHHHHHHCCCCCCCCCEEEEE-EECCCCCCHHHHHHH-HHHHHHHHCCCCEEEEECCCHHHHHHHHHHHHHH
Q ss_conf             89999999888875124555554112477-614886788999999-9999997089977999715379999999999999
Q gi|254781187|r   53 RWQLEFMEAVDVHCHSNVNNSNPTIFKCA-ISAGRGIGKTTLNAW-MMLWLISTRPGMSIICIANSETQLKNTLWAEVSK  130 (367)
Q Consensus        53 ~wq~~~l~~~~~~~~~~~~~~~~~~~~~~-v~sgrg~GKS~~~a~-~~lw~~~~~~~~~v~~~A~t~~Q~~~~lw~ei~k  130 (367)
                      .=|++.++.|...          .  +++ |.+-=|.|||++... --.|-   ..|.+|+=.|++..-+...- .+-  
T Consensus       349 ~EQ~~A~~hiT~~----------~--~iavVvG~AGtGKStmL~aAReawE---a~GyrV~GaALsGkAAegLe-~~s--  410 (992)
T PRK13889        349 GEQADALAHVTDG----------R--DLGVVVGYAGTGKSAMLGVAREAWE---AAGYEVRGAALSGIAAENLE-GGS--  410 (992)
T ss_pred             HHHHHHHHHHCCC----------C--CEEEEEECCCCCHHHHHHHHHHHHH---HCCCEEEEECCCHHHHHHHH-HCC--
T ss_conf             9999999986478----------9--7589983388878899999999999---77988981150068999765-347--


Q ss_pred             HHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCEEEEECCCCCCHHHHHH
Q ss_conf             99862312112333321000123332211113457761266210135445565210113586289997545599889999
Q gi|254781187|r  131 WLSMLPHRHWFEMQSLSLHPSGWYAELLEQSMGIDSKHYTITCRTYSEERPDTFVGPHNTHGMAVFNDEASGTPDIINKS  210 (367)
Q Consensus       131 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~ea~~g~h~~~~~l~ivDEAsgI~d~i~e~  210 (367)
                          -+     ...    .+..|...                   +  .  .....+.  ....+|||||+.|+...+.-
T Consensus       411 ----GI-----~Sr----TlAs~e~~-------------------w--~--~g~~~L~--~~dVlVVDEAGMVgSRqMar  452 (992)
T PRK13889        411 ----GI-----ASR----TIASLEHG-------------------W--G--QGRDLLT--ARDVLVIDEAGMVGTRQLER  452 (992)
T ss_pred             ----CC-----CCH----HHHHHHHH-------------------H--H--CCCCCCC--CCCEEEEECCCCCCHHHHHH
T ss_conf             ----94-----316----79999998-------------------7--4--6733478--98589996765577499999


Q ss_pred             HHHHHHCCCCCEEEEEEECC-----CCCCCHHHHHH
Q ss_conf             89874069882589998078-----99987688754
Q gi|254781187|r  211 ILGFFTELNPNRFWIMTSNT-----RRLNGWFYDIF  241 (367)
Q Consensus       211 i~g~Lt~~~~~~~~i~igNP-----~r~~g~Fye~~  241 (367)
                      +.......+.+++  ++|-|     ...++.|-.+.
T Consensus       453 ll~~Ae~AGAKVV--LVGD~~QLq~IeAGaaFral~  486 (992)
T PRK13889        453 VLSHAADAGAKVV--LVGDPQQLQAIEAGAAFRSIH  486 (992)
T ss_pred             HHHHHHHCCCEEE--EECCHHHCCCCCCCHHHHHHH
T ss_conf             9999998499899--948877718864688999999


No 79 
>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=96.73  E-value=0.043  Score=31.82  Aligned_cols=85  Identities=21%  Similarity=0.153  Sum_probs=47.0

Q ss_pred             CCCEEEEECCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCCCCCCCC
Q ss_conf             99779997153799999999999999986231211233332100012333221111345776126621013544556521
Q gi|254781187|r  106 PGMSIICIANSETQLKNTLWAEVSKWLSMLPHRHWFEMQSLSLHPSGWYAELLEQSMGIDSKHYTITCRTYSEERPDTFV  185 (367)
Q Consensus       106 ~~~~v~~~A~t~~Q~~~~lw~ei~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~ea~~  185 (367)
                      -..+|+||||+...+. .+|.-+.+-++.+.....        .     .......+....       +..+-..|+..-
T Consensus        12 ~~~~I~VTAP~~~nv~-~lf~~~~~~L~~lg~~~~--------~-----~~~~~~~~~~~~-------~~i~f~~Pd~l~   70 (160)
T pfam05127        12 GYSRILVTAPSPANVQ-TLFEFAIKGLDALGYKPK--------K-----REGIIASLRGNG-------QRIRFIAPDELL   70 (160)
T ss_pred             CCCEEEEECCCHHHHH-HHHHHHHHHHHHCCCCCC--------C-----CCCCEEEEECCC-------EEEEEECCHHHH
T ss_conf             9973999799989999-999999999986386434--------5-----655047875287-------689996808986


Q ss_pred             CCCCCCCCEEEEECCCCCCHHHHHHHH
Q ss_conf             011358628999754559988999989
Q gi|254781187|r  186 GPHNTHGMAVFNDEASGTPDIINKSIL  212 (367)
Q Consensus       186 g~h~~~~~l~ivDEAsgI~d~i~e~i~  212 (367)
                      ... ....+++|||||.||-.+...+.
T Consensus        71 ~~~-~~~DllvVDEAAaIP~p~L~~ll   96 (160)
T pfam05127        71 KLP-PQADLLVVDEAAAIPLPLLKQLL   96 (160)
T ss_pred             HCC-CCCCEEEEEHHHCCCHHHHHHHH
T ss_conf             167-87768997324218889999998


No 80 
>PRK05564 DNA polymerase III subunit delta'; Validated
Probab=96.73  E-value=0.036  Score=32.32  Aligned_cols=121  Identities=12%  Similarity=0.067  Sum_probs=71.4

Q ss_pred             HHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCC---EEEEECCCHHHHHHHHHHHHHH
Q ss_conf             9999999888875124555554112477614886788999999999999708997---7999715379999999999999
Q gi|254781187|r   54 WQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGM---SIICIANSETQLKNTLWAEVSK  130 (367)
Q Consensus        54 wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~---~v~~~A~t~~Q~~~~lw~ei~k  130 (367)
                      .|.++.+.+...++.+.. .|.    ....+.+|+||+.++-.++-..+|...+.   -++...+...+.  +--..|+.
T Consensus         8 Gq~~i~~~L~~~i~~~rl-~HA----yLF~Gp~G~GK~~~A~~~A~~ll~~~~~~~~~D~~~~~~~~~~~--I~vd~IR~   80 (313)
T PRK05564          8 GHENIKNRIDNSIIKGKF-SHA----SLIVGEDGIGKSILAKEIANKILGKSEQREYVDIIEYKPINKKS--IGVDDIRN   80 (313)
T ss_pred             CHHHHHHHHHHHHHCCCC-CCE----EEEECCCCCCHHHHHHHHHHHHHCCCCCCCCCCEEEEECCCCCC--CCHHHHHH
T ss_conf             829999999999987998-750----43279998509999999999982899778898658863322569--99899999


Q ss_pred             HHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCEEEEECCCCCCHHHHHH
Q ss_conf             99862312112333321000123332211113457761266210135445565210113586289997545599889999
Q gi|254781187|r  131 WLSMLPHRHWFEMQSLSLHPSGWYAELLEQSMGIDSKHYTITCRTYSEERPDTFVGPHNTHGMAVFNDEASGTPDIINKS  210 (367)
Q Consensus       131 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~ea~~g~h~~~~~l~ivDEAsgI~d~i~e~  210 (367)
                      .++.+                                               ++....|.+ -.+|+|||.........+
T Consensus        81 l~~~~-----------------------------------------------~~~p~~g~~-KV~II~~ae~m~~~AaNA  112 (313)
T PRK05564         81 IIEEV-----------------------------------------------NKKPYEGDK-KVIIIYKSEKMTEQAQNA  112 (313)
T ss_pred             HHHHH-----------------------------------------------HHCCCCCCC-EEEEECCHHHHCHHHHHH
T ss_conf             99998-----------------------------------------------408625895-699980777758999999


Q ss_pred             HHHHHHCCCCCEEEEEEEC
Q ss_conf             8987406988258999807
Q gi|254781187|r  211 ILGFFTELNPNRFWIMTSN  229 (367)
Q Consensus       211 i~g~Lt~~~~~~~~i~igN  229 (367)
                      +..+|-.+-..++.+++.+
T Consensus       113 LLKtLEEPP~~t~fIL~t~  131 (313)
T PRK05564        113 FLKTIEEPPKGVFIILLCE  131 (313)
T ss_pred             HHHCCCCCCCCEEEEEEEC
T ss_conf             8455036899858998649


No 81 
>KOG1805 consensus
Probab=96.68  E-value=0.0085  Score=36.12  Aligned_cols=130  Identities=17%  Similarity=0.107  Sum_probs=70.0

Q ss_pred             EEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             24776148867889999999999997089977999715379999999999999998623121123333210001233322
Q gi|254781187|r   78 FKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLKNTLWAEVSKWLSMLPHRHWFEMQSLSLHPSGWYAEL  157 (367)
Q Consensus        78 ~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~~~lw~ei~k~~~~~~~~~~~~~~~~~~~~~~~~~~~  157 (367)
                      |++ |.+=-|+|||++++.++--++.+  +++|+.|+-|..-+.+++-+..+--+..+           ++......++.
T Consensus       687 y~L-I~GMPGTGKTTtI~~LIkiL~~~--gkkVLLtsyThsAVDNILiKL~~~~i~~l-----------RLG~~~kih~~  752 (1100)
T KOG1805         687 YAL-ILGMPGTGKTTTISLLIKILVAL--GKKVLLTSYTHSAVDNILIKLKGFGIYIL-----------RLGSEEKIHPD  752 (1100)
T ss_pred             HHE-EECCCCCCCHHHHHHHHHHHHHC--CCEEEEEEHHHHHHHHHHHHHHCCCCCEE-----------ECCCCCCCCHH
T ss_conf             220-32699898122599999999973--88189985056788999998750671103-----------44872224468


Q ss_pred             CCCCC-------------CCCCCCEEEEECCCCCCCCCCCCCCCCCCCCEEEEECCCCCCHHHHHHHHHHHHCCCCCEEE
Q ss_conf             11113-------------45776126621013544556521011358628999754559988999989874069882589
Q gi|254781187|r  158 LEQSM-------------GIDSKHYTITCRTYSEERPDTFVGPHNTHGMAVFNDEASGTPDIINKSILGFFTELNPNRFW  224 (367)
Q Consensus       158 ~~~~~-------------~~~~~~~~~~a~~~~~~~~ea~~g~h~~~~~l~ivDEAsgI~d~i~e~i~g~Lt~~~~~~~~  224 (367)
                      .+...             +.-.+..-+.|.|.-.-+ +-+-.-  ..+.++|+|||+.|+..+   ..|.|.-.+ +  .
T Consensus       753 v~e~~~~~~~s~ks~~~l~~~~~~~~IVa~TClgi~-~plf~~--R~FD~cIiDEASQI~lP~---~LgPL~~s~-k--F  823 (1100)
T KOG1805         753 VEEFTLTNETSEKSYADLKKFLDQTSIVACTCLGIN-HPLFVN--RQFDYCIIDEASQILLPL---CLGPLSFSN-K--F  823 (1100)
T ss_pred             HHHHHCCCCCCHHHHHHHHHHHCCCCEEEEECCCCC-CHHHHC--CCCCEEEECCCCCCCCCH---HHHHHHHCC-E--E
T ss_conf             998712344545339999997289767999715788-655521--426789986511114342---121021123-5--8


Q ss_pred             EEEECC
Q ss_conf             998078
Q gi|254781187|r  225 IMTSNT  230 (367)
Q Consensus       225 i~igNP  230 (367)
                      ++.|-+
T Consensus       824 VLVGDh  829 (1100)
T KOG1805         824 VLVGDH  829 (1100)
T ss_pred             EEECCC
T ss_conf             996463


No 82 
>PRK07246 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
Probab=96.67  E-value=0.035  Score=32.39  Aligned_cols=74  Identities=23%  Similarity=0.205  Sum_probs=48.0

Q ss_pred             CCHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHHH
Q ss_conf             84289999999888875124555554112477614886788999999999999708997799971537999999999999
Q gi|254781187|r   50 QPHRWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLKNTLWAEVS  129 (367)
Q Consensus        50 ~p~~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~~~lw~ei~  129 (367)
                      .+|+-|.+|.+.|++.+..+.        .+.|-||.|+|||..--.-+   +....+.+|++..+|..--.+.+.+++.
T Consensus       245 E~R~~Q~~Ma~~V~~al~~~~--------~l~IEAgTGtGKTlaYLlPa---ia~~~~~~vVIST~T~~LQeQL~~kDlp  313 (820)
T PRK07246        245 EERPKQEQFAQLVDEDYHDGV--------ASFIEAQTGIGKTYGYLLPL---LAQSDQNQIIVSVPTKLLQDQIMAGEVK  313 (820)
T ss_pred             CCCHHHHHHHHHHHHHHCCCC--------CEEEECCCCCCHHHHHHHHH---HHHCCCCEEEEEECCHHHHHHHHHHHHH
T ss_conf             618899999999999980588--------38998899964799999999---9843798399990869999999997899


Q ss_pred             HHHHH
Q ss_conf             99986
Q gi|254781187|r  130 KWLSM  134 (367)
Q Consensus       130 k~~~~  134 (367)
                      ...+.
T Consensus       314 ~L~~~  318 (820)
T PRK07246        314 AIQEQ  318 (820)
T ss_pred             HHHHH
T ss_conf             99998


No 83 
>COG1205 Distinct helicase family with a unique C-terminal domain including a metal-binding cysteine cluster [General function prediction only]
Probab=96.67  E-value=0.02  Score=33.88  Aligned_cols=74  Identities=15%  Similarity=0.192  Sum_probs=64.6

Q ss_pred             CHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHHHH
Q ss_conf             42899999998888751245555541124776148867889999999999997089977999715379999999999999
Q gi|254781187|r   51 PHRWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLKNTLWAEVSK  130 (367)
Q Consensus        51 p~~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~~~lw~ei~k  130 (367)
                      +-.-|.+.++.+.+..            .+.|.+|.|+|||-..-.-+++.++..+..+.+++-||-.=+.|-. ..+++
T Consensus        71 lY~HQ~~A~~~~~~G~------------~vvVtTgTgSGKTe~FllPIld~~l~~~~a~AL~lYPtnALa~DQ~-~rl~~  137 (851)
T COG1205          71 LYSHQVDALRLIREGR------------NVVVTTGTGSGKTESFLLPILDHLLRDPSARALLLYPTNALANDQA-ERLRE  137 (851)
T ss_pred             CCHHHHHHHHHHHCCC------------CEEEECCCCCCHHHHHHHHHHHHHHCCCCCEEEEEECHHHHHHHHH-HHHHH
T ss_conf             0077999999997799------------8899789988545898999999983086650899804377676699-99999


Q ss_pred             HHHHCCC
Q ss_conf             9986231
Q gi|254781187|r  131 WLSMLPH  137 (367)
Q Consensus       131 ~~~~~~~  137 (367)
                      +.+.++.
T Consensus       138 ~~~~~~~  144 (851)
T COG1205         138 LISDLPG  144 (851)
T ss_pred             HHHHCCC
T ss_conf             9984787


No 84 
>PRK12323 DNA polymerase III subunits gamma and tau; Provisional
Probab=96.64  E-value=0.05  Score=31.41  Aligned_cols=140  Identities=17%  Similarity=0.159  Sum_probs=73.6

Q ss_pred             HHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHHHHHHH
Q ss_conf             99999998888751245555541124776148867889999999999997089977999715379999999999999998
Q gi|254781187|r   54 WQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLKNTLWAEVSKWLS  133 (367)
Q Consensus        54 wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~~~lw~ei~k~~~  133 (367)
                      .|.-+++.+..-+..+... +.    ..-.+.||+|||+++-.++--+-|.+++...-+++.--.+- .. +.+|..   
T Consensus        20 GQ~~v~~~l~na~~~~r~~-ha----ylf~G~rGvGKTt~ari~Ak~lnc~~~~~~~g~~~~pcg~C-~~-C~~i~~---   89 (721)
T PRK12323         20 GQEHVVRALTHALEQQRLH-HA----YLFTGTRGVGKTTLSRILAKSLNCTGPDGEGGITAQPCGQC-RA-CTEIDA---   89 (721)
T ss_pred             CCHHHHHHHHHHHHCCCCC-CE----EEEECCCCCCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCC-HH-HHHHHC---
T ss_conf             8599999999999719975-44----75027998889899999999976899866789878878776-54-687756---


Q ss_pred             HCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCEEEEECCCCCCHHHHHHHHH
Q ss_conf             62312112333321000123332211113457761266210135445565210113586289997545599889999898
Q gi|254781187|r  134 MLPHRHWFEMQSLSLHPSGWYAELLEQSMGIDSKHYTITCRTYSEERPDTFVGPHNTHGMAVFNDEASGTPDIINKSILG  213 (367)
Q Consensus       134 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~ea~~g~h~~~~~l~ivDEAsgI~d~i~e~i~g  213 (367)
                                        ..+..+.  ++....++..-..+-..+..  .+.-..|.+. .+|+||....+...|.+++.
T Consensus        90 ------------------g~~~d~~--EiDaas~~~v~~~r~l~~~~--~y~P~~~~~K-vyiiDevhmls~~afnalLK  146 (721)
T PRK12323         90 ------------------GRFVDYI--EMDAASNRGVDEMAQLLDQA--VYAPTAGRFK-VYMIDEVHMLTNHAFNAMLK  146 (721)
T ss_pred             ------------------CCCCCEE--EEECCCCCCHHHHHHHHHHC--CCCCCCCCEE-EEEEECCCCCCHHHHHHHHH
T ss_conf             ------------------8987647--74367678889999999854--5588766446-99985400058999999998


Q ss_pred             HHHCCCCCEEEEE
Q ss_conf             7406988258999
Q gi|254781187|r  214 FFTELNPNRFWIM  226 (367)
Q Consensus       214 ~Lt~~~~~~~~i~  226 (367)
                      +|-..=...+.++
T Consensus       147 tlEePP~hv~Fil  159 (721)
T PRK12323        147 TLEEPPPHVKFIL  159 (721)
T ss_pred             HHCCCCCCEEEEE
T ss_conf             4017975538999


No 85 
>PRK12377 putative replication protein; Provisional
Probab=96.63  E-value=0.051  Score=31.36  Aligned_cols=60  Identities=18%  Similarity=0.217  Sum_probs=39.2

Q ss_pred             CCCCCCCHHHHHHHHH---HHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEE
Q ss_conf             4366684289999999---88887512455555411247761488678899999999999970899779997
Q gi|254781187|r   45 LEHFSQPHRWQLEFME---AVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICI  113 (367)
Q Consensus        45 ~~~~~~p~~wq~~~l~---~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~  113 (367)
                      ++++.--.+-|++++.   .++++...+       .-.+...++-|+|||++++++..-.+-  .|.+|+.+
T Consensus        73 f~ny~~~~~~~~~a~~~a~~~~~~F~~~-------~~NlIf~G~pGtGKTHLA~AIg~~a~~--~G~sVlF~  135 (248)
T PRK12377         73 FANYQVQNDGQRYALSQAKSIADELMTG-------CTNFVFSGKPGTGKNHLAAAIGNRLLA--KGRSVIVV  135 (248)
T ss_pred             CCCCCCCCHHHHHHHHHHHHHHHHHHCC-------CCEEEEECCCCCCHHHHHHHHHHHHHH--CCCEEEEE
T ss_conf             3456457878999999999999987318-------860899899998788999999999998--79969998


No 86 
>COG1199 DinG Rad3-related DNA helicases [Transcription / DNA replication, recombination, and repair]
Probab=96.62  E-value=0.023  Score=33.51  Aligned_cols=67  Identities=22%  Similarity=0.143  Sum_probs=51.7

Q ss_pred             CCCHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHH
Q ss_conf             6842899999998888751245555541124776148867889999999999997089977999715379999999
Q gi|254781187|r   49 SQPHRWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLKNTL  124 (367)
Q Consensus        49 ~~p~~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~~~l  124 (367)
                      -.||+.|.++...|++-+.++.        .+.|-||-|+|||...-..++-+..... .++++..+|..+....+
T Consensus        14 ~~~r~~Q~~~~~~v~~a~~~~~--------~~~iEapTGtGKTl~yL~~al~~~~~~~-~~viist~t~~lq~q~~   80 (654)
T COG1199          14 FEPRPEQREMAEAVAEALKGGE--------GLLIEAPTGTGKTLAYLLPALAYAREEG-KKVIISTRTKALQEQLL   80 (654)
T ss_pred             CCCCHHHHHHHHHHHHHHHCCC--------EEEEECCCCCCHHHHHHHHHHHHHHHCC-CEEEEECCCHHHHHHHH
T ss_conf             9989899999999999981687--------1899889985175999999998677529-75999899576888987


No 87 
>PRK07764 DNA polymerase III subunits gamma and tau; Validated
Probab=96.62  E-value=0.025  Score=33.31  Aligned_cols=137  Identities=17%  Similarity=0.100  Sum_probs=69.4

Q ss_pred             HHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHHHHHHHH
Q ss_conf             99999988887512455555411247761488678899999999999970899779997153799999999999999986
Q gi|254781187|r   55 QLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLKNTLWAEVSKWLSM  134 (367)
Q Consensus        55 q~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~~~lw~ei~k~~~~  134 (367)
                      |..+.+.+..-++.+.. .|.    ..-++.||+|||+++=+++--+.|.+....--|-.      ...+ ..|..  ..
T Consensus        20 Qe~v~~~L~~Ai~~gri-~HA----YLFsGprG~GKTt~ARilAkaLNC~~~~~~~PCg~------C~sC-~~i~~--g~   85 (775)
T PRK07764         20 QEHVTEPLSTALDSGRI-NHA----YLFSGPRGCGKTSSARILARSLNCAQGPTSTPCGV------CDSC-VALAP--GG   85 (775)
T ss_pred             CHHHHHHHHHHHHCCCC-CCE----EEEECCCCCCHHHHHHHHHHHHCCCCCCCCCCCCC------CHHH-HHHHC--CC
T ss_conf             59999999999981997-633----76237888788899999999966899999898888------7637-88863--89


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCEEEEECCCCCCHHHHHHHHHH
Q ss_conf             23121123333210001233322111134577612662101354455652101135862899975455998899998987
Q gi|254781187|r  135 LPHRHWFEMQSLSLHPSGWYAELLEQSMGIDSKHYTITCRTYSEERPDTFVGPHNTHGMAVFNDEASGTPDIINKSILGF  214 (367)
Q Consensus       135 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~ea~~g~h~~~~~l~ivDEAsgI~d~i~e~i~g~  214 (367)
                      ..+-...++.                   ...+..+...+-.++  --.+.-..+.+. .+|+||+..++...|++++.+
T Consensus        86 ~~~~DviEiD-------------------AAS~~gVddiReL~e--~~~y~P~~~ryK-VyIIDEaHmls~~afNALLKt  143 (775)
T PRK07764         86 PGSLDVVEID-------------------AASHGGVDDARELRE--RAFFAPAQSRYR-IFIIDEAHMVTTAGFNALLKI  143 (775)
T ss_pred             CCCCCEEEEC-------------------CCCCCCHHHHHHHHH--HCCCCCCCCCEE-EEEEECHHHHCHHHHHHHHHH
T ss_conf             8888668731-------------------565568899999998--547687678635-999853544079999999886


Q ss_pred             HHCCCCCEEEEEE
Q ss_conf             4069882589998
Q gi|254781187|r  215 FTELNPNRFWIMT  227 (367)
Q Consensus       215 Lt~~~~~~~~i~i  227 (367)
                      |-..-...++|+.
T Consensus       144 LEEPP~hvvFIla  156 (775)
T PRK07764        144 VEEPPEHLIFIFA  156 (775)
T ss_pred             HCCCCCCEEEEEE
T ss_conf             2278646279995


No 88 
>PRK08691 DNA polymerase III subunits gamma and tau; Validated
Probab=96.61  E-value=0.052  Score=31.30  Aligned_cols=134  Identities=16%  Similarity=0.126  Sum_probs=68.8

Q ss_pred             HHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHHHHHHH
Q ss_conf             99999998888751245555541124776148867889999999999997089977999715379999999999999998
Q gi|254781187|r   54 WQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLKNTLWAEVSKWLS  133 (367)
Q Consensus        54 wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~~~lw~ei~k~~~  133 (367)
                      .|.-+++.+..-+..|.. .+.    ..-.+.||+|||+++-.++.-+-|..+..---|-.      ... +.+|..   
T Consensus        20 GQ~~v~~~L~nal~~~rl-~ha----ylf~G~rGvGKTt~Ari~Ak~lNC~~~~~~~pCg~------C~~-C~~i~~---   84 (704)
T PRK08691         20 GQEHVVKALQNALDEGRL-HHA----YLLTGTRGVGKTTIARILAKSLNCENAQHGEPCGV------CQS-CTQIDA---   84 (704)
T ss_pred             CCHHHHHHHHHHHHHCCC-CCE----EEEECCCCCCHHHHHHHHHHHHCCCCCCCCCCCCC------CHH-HHHHHC---
T ss_conf             869999999999981997-523----75027898788899999999967999999997877------776-787855---


Q ss_pred             HCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCEEEEECCCCCCHHHHHHHHH
Q ss_conf             62312112333321000123332211113457761266210135445565210113586289997545599889999898
Q gi|254781187|r  134 MLPHRHWFEMQSLSLHPSGWYAELLEQSMGIDSKHYTITCRTYSEERPDTFVGPHNTHGMAVFNDEASGTPDIINKSILG  213 (367)
Q Consensus       134 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~ea~~g~h~~~~~l~ivDEAsgI~d~i~e~i~g  213 (367)
                       .                 .+..+...+  ...+...-..+-..+.  -.+.-..|.+. .+|+||+...+...|.+++.
T Consensus        85 -g-----------------~~~D~~EiD--aAs~~~vdd~R~l~~~--~~y~P~~~~yK-VyiiDEvhmLs~~afNAlLK  141 (704)
T PRK08691         85 -G-----------------RYVDLLEID--AASNTGIDNIREVLEN--AQYAPTAGKYK-VYIIDEVHMLSKSAFNAMLK  141 (704)
T ss_pred             -C-----------------CCCCEEEEE--CCCCCCHHHHHHHHHH--CCCCCCCCCEE-EEEEECHHHCCHHHHHHHHH
T ss_conf             -8-----------------998747742--4544588999999985--34688678535-99983154438999999998


Q ss_pred             HHHCCCCCEEEE
Q ss_conf             740698825899
Q gi|254781187|r  214 FFTELNPNRFWI  225 (367)
Q Consensus       214 ~Lt~~~~~~~~i  225 (367)
                      +|-.+=...+.+
T Consensus       142 tLEEPP~~v~Fi  153 (704)
T PRK08691        142 TLEEPPEHVKFI  153 (704)
T ss_pred             HHCCCCCCEEEE
T ss_conf             614797560899


No 89 
>COG1201 Lhr Lhr-like helicases [General function prediction only]
Probab=96.58  E-value=0.023  Score=33.53  Aligned_cols=78  Identities=15%  Similarity=0.071  Sum_probs=60.6

Q ss_pred             CCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCC------CCEEEEECCCHHH
Q ss_conf             3666842899999998888751245555541124776148867889999999999997089------9779997153799
Q gi|254781187|r   46 EHFSQPHRWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRP------GMSIICIANSETQ  119 (367)
Q Consensus        46 ~~~~~p~~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~------~~~v~~~A~t~~Q  119 (367)
                      +.|..|++-|+.++..|.+..            .+.|.|+.|+|||-.+=.-++-.+....      +..+++++|-..-
T Consensus        18 ~~~~~~t~~Q~~a~~~i~~G~------------nvLiiAPTGsGKTeAAfLpil~~l~~~~~~~~~~~i~~lYIsPLkAL   85 (814)
T COG1201          18 RKFTSLTPPQRYAIPEIHSGE------------NVLIIAPTGSGKTEAAFLPVINELLSLGKGKLEDGIYALYISPLKAL   85 (814)
T ss_pred             HHCCCCCHHHHHHHHHHHCCC------------CEEEECCCCCCHHHHHHHHHHHHHHHCCCCCCCCCEEEEEECCHHHH
T ss_conf             850899878999999985898------------46998689997379999999999986068888885699995707888


Q ss_pred             HHHHHHHHHHHHHHHCC
Q ss_conf             99999999999998623
Q gi|254781187|r  120 LKNTLWAEVSKWLSMLP  136 (367)
Q Consensus       120 ~~~~lw~ei~k~~~~~~  136 (367)
                      .+|+. .-+..|.+.+-
T Consensus        86 n~Di~-~rL~~~~~~~G  101 (814)
T COG1201          86 NNDIR-RRLEEPLRELG  101 (814)
T ss_pred             HHHHH-HHHHHHHHHCC
T ss_conf             78999-99999999759


No 90 
>KOG0952 consensus
Probab=96.55  E-value=0.023  Score=33.43  Aligned_cols=139  Identities=19%  Similarity=0.189  Sum_probs=74.6

Q ss_pred             HHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHH--------CCCCEEEEECCCHHHHHHHH
Q ss_conf             8999999988887512455555411247761488678899999999999970--------89977999715379999999
Q gi|254781187|r   53 RWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLIST--------RPGMSIICIANSETQLKNTL  124 (367)
Q Consensus        53 ~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~--------~~~~~v~~~A~t~~Q~~~~l  124 (367)
                      .-|-++....+.-        +.   +..|+|+.|.|||.++-.-+|-.+-.        ..+.||+++||...-+.++ 
T Consensus       113 ~iQS~vFp~aY~S--------ne---NMLIcAPTGsGKT~la~L~ILr~ik~~~~~~~i~k~~fKiVYIaPmKALa~Em-  180 (1230)
T KOG0952         113 RIQSEVFPVAYKS--------NE---NMLICAPTGSGKTVLAELCILRTIKEHEEQGDIAKDDFKIVYIAPMKALAAEM-  180 (1230)
T ss_pred             HHHHHHHHHHHCC--------CC---CEEEECCCCCCCHHHHHHHHHHHHHHHCCCCCCCCCCCEEEEEECHHHHHHHH-
T ss_conf             7787741465147--------88---77997778997167899999999985014554346871399992568899999-


Q ss_pred             HHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCC-CCCCCEEEEECCCCCCCCCCCCCCCCCCCCEEEEECCCCC
Q ss_conf             999999998623121123333210001233322111134-5776126621013544556521011358628999754559
Q gi|254781187|r  125 WAEVSKWLSMLPHRHWFEMQSLSLHPSGWYAELLEQSMG-IDSKHYTITCRTYSEERPDTFVGPHNTHGMAVFNDEASGT  203 (367)
Q Consensus       125 w~ei~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~a~~~~~~~~ea~~g~h~~~~~l~ivDEAsgI  203 (367)
                         +.+|-.++--... .+....--+.....+...+++. ..++.|=+..+-+...  .++.+.    .-|+|+||-.-+
T Consensus       181 ---~~~~~kkl~~~gi-~v~ELTGD~ql~~tei~~tqiiVTTPEKwDvvTRk~~~d--~~l~~~----V~LviIDEVHlL  250 (1230)
T KOG0952         181 ---VDKFSKKLAPLGI-SVRELTGDTQLTKTEIADTQIIVTTPEKWDVVTRKSVGD--SALFSL----VRLVIIDEVHLL  250 (1230)
T ss_pred             ---HHHHHHHCCCCCC-EEEEECCCCHHHHHHHHHCCEEEECCCCEEEEEEEECCC--HHHHHH----EEEEEEEEEHHH
T ss_conf             ---9998664242462-588841754566778774377970634000466541262--655554----204885300121


Q ss_pred             CHH---HHHHHHH
Q ss_conf             988---9999898
Q gi|254781187|r  204 PDI---INKSILG  213 (367)
Q Consensus       204 ~d~---i~e~i~g  213 (367)
                      .|+   +.|+|-.
T Consensus       251 hd~RGpvlEtiVa  263 (1230)
T KOG0952         251 HDDRGPVLETIVA  263 (1230)
T ss_pred             CCCCCCHHHHHHH
T ss_conf             5766406999999


No 91 
>PRK10917 ATP-dependent DNA helicase RecG; Provisional
Probab=96.50  E-value=0.061  Score=30.86  Aligned_cols=83  Identities=19%  Similarity=0.241  Sum_probs=62.7

Q ss_pred             CCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHH
Q ss_conf             88443666842899999998888751245555541124776148867889999999999997089977999715379999
Q gi|254781187|r   42 GKPLEHFSQPHRWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLK  121 (367)
Q Consensus        42 ~~~~~~~~~p~~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~  121 (367)
                      .+|.    .++.-|.+++++|...+..+.     .|.|+ +.+-=|+|||.++...++-  ...-|..++++|||+==++
T Consensus       253 ~LPF----~LT~~Q~~~~~ei~~dl~~~~-----~m~rl-lqGDVGsGKT~va~~a~~~--~~~~g~q~a~maPTeiLa~  320 (677)
T PRK10917        253 SLPF----ELTGAQKRVVAEILADLASPK-----PMNRL-LQGDVGSGKTVVAALAALA--AIEAGYQAALMAPTEILAE  320 (677)
T ss_pred             HCCC----CCCHHHHHHHHHHHHHHCCCC-----CCHHH-HCCCCCCCHHHHHHHHHHH--HHHHCCEEEEECCCHHHHH
T ss_conf             0999----889889999999998765995-----42777-3287678889999999999--9981994899876799999


Q ss_pred             HHHHHHHHHHHHHCCC
Q ss_conf             9999999999986231
Q gi|254781187|r  122 NTLWAEVSKWLSMLPH  137 (367)
Q Consensus       122 ~~lw~ei~k~~~~~~~  137 (367)
                      + -+..+++++..+..
T Consensus       321 Q-h~~~~~~~~~~~~i  335 (677)
T PRK10917        321 Q-HYRNLKKWLEPLGI  335 (677)
T ss_pred             H-HHHHHHHHHHHCCC
T ss_conf             9-99999987763498


No 92 
>COG1110 Reverse gyrase [DNA replication, recombination, and repair]
Probab=96.50  E-value=0.018  Score=34.07  Aligned_cols=109  Identities=22%  Similarity=0.225  Sum_probs=64.1

Q ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             47761488678899999999999970899779997153799999999999999986231211233332100012333221
Q gi|254781187|r   79 KCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLKNTLWAEVSKWLSMLPHRHWFEMQSLSLHPSGWYAELL  158 (367)
Q Consensus        79 ~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~~~lw~ei~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~  158 (367)
                      -.|+.|+.|+|||+..+.+.+|++.-.  .+++++-||..-+++.. ..++++.+..-..        ...+. |+...-
T Consensus        99 SFaiiAPTGvGKTTfg~~~sl~~a~kg--kr~yii~PT~~Lv~Q~~-~kl~~~~e~~~~~--------~~~~~-yh~~l~  166 (1187)
T COG1110          99 SFAIIAPTGVGKTTFGLLMSLYLAKKG--KRVYIIVPTTTLVRQVY-ERLKKFAEDAGSL--------DVLVV-YHSALP  166 (1187)
T ss_pred             CEEEECCCCCCHHHHHHHHHHHHHHCC--CEEEEEECCHHHHHHHH-HHHHHHHHHCCCC--------CEEEE-ECCCCC
T ss_conf             448982788765479999999987558--74999966789999999-9999988653785--------24665-312366


Q ss_pred             -----CCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCEEEEECC
Q ss_conf             -----111345776126621013544556521011358628999754
Q gi|254781187|r  159 -----EQSMGIDSKHYTITCRTYSEERPDTFVGPHNTHGMAVFNDEA  200 (367)
Q Consensus       159 -----~~~~~~~~~~~~~~a~~~~~~~~ea~~g~h~~~~~l~ivDEA  200 (367)
                           ..--.+.+|.+-+ -.+.+..-+-++.-++.-++.|+++|-.
T Consensus       167 ~~ekee~le~i~~gdfdI-litTs~FL~k~~e~L~~~kFdfifVDDV  212 (1187)
T COG1110         167 TKEKEEALERIESGDFDI-LITTSQFLSKRFEELSKLKFDFIFVDDV  212 (1187)
T ss_pred             HHHHHHHHHHHHCCCCCE-EEEEHHHHHHHHHHHCCCCCCEEEECCH
T ss_conf             577999999986599639-9974787886699840457778998047


No 93 
>PRK12402 replication factor C small subunit 2; Reviewed
Probab=96.49  E-value=0.063  Score=30.81  Aligned_cols=35  Identities=9%  Similarity=0.154  Sum_probs=26.5

Q ss_pred             CEEEEECCCCCCHHHHHHHHHHHHCCCCCEEEEEE
Q ss_conf             28999754559988999989874069882589998
Q gi|254781187|r  193 MAVFNDEASGTPDIINKSILGFFTELNPNRFWIMT  227 (367)
Q Consensus       193 ~l~ivDEAsgI~d~i~e~i~g~Lt~~~~~~~~i~i  227 (367)
                      -++|+|||..+......++..+|-........+++
T Consensus       127 KiiIlDEad~lt~~Aq~aLlk~lEe~~~~~~fIl~  161 (337)
T PRK12402        127 KLILFDNAEALREDAQQALRRIMERYSETCRFIFS  161 (337)
T ss_pred             EEEEEECCCCCCHHHHHHHHHHHHCCCCCEEEEEE
T ss_conf             49997071317999999999887408876699872


No 94 
>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=96.44  E-value=0.067  Score=30.65  Aligned_cols=119  Identities=13%  Similarity=0.101  Sum_probs=72.2

Q ss_pred             HHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCC----C--EEEEECCCHHHHHHHH---
Q ss_conf             999999988887512455555411247761488678899999999999970899----7--7999715379999999---
Q gi|254781187|r   54 WQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPG----M--SIICIANSETQLKNTL---  124 (367)
Q Consensus        54 wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~----~--~v~~~A~t~~Q~~~~l---  124 (367)
                      .|.=+.+.+..-+..+.- .|.+    .=++.||+|||+++=.++-=+=|. +.    |  --.|.+-+..+.-|++   
T Consensus        18 GQ~~iv~tL~NAi~~~ri-~HAY----LF~GpRGtGKTS~ARIfAKaLNC~-~~~~~PCn~C~~C~~i~~g~~~DviEiD   91 (363)
T TIGR02397        18 GQEHIVKTLKNAIKNGRI-AHAY----LFSGPRGTGKTSIARIFAKALNCQ-GPDGEPCNECESCKEINSGSSLDVIEID   91 (363)
T ss_pred             CCHHHHHHHHHHHHHCCC-CCEE----EECCCCCCCHHHHHHHHHHHHCCC-CCCCCCCCCCCHHHHHHCCCCCCEEEEC
T ss_conf             517999999999971896-6234----502859976355899999986588-7877877775022776528986668864


Q ss_pred             ------H---HHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCEE
Q ss_conf             ------9---9999999862312112333321000123332211113457761266210135445565210113586289
Q gi|254781187|r  125 ------W---AEVSKWLSMLPHRHWFEMQSLSLHPSGWYAELLEQSMGIDSKHYTITCRTYSEERPDTFVGPHNTHGMAV  195 (367)
Q Consensus       125 ------w---~ei~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~ea~~g~h~~~~~l~  195 (367)
                            -   ++|..-+.                                                  +.-..+.+.+ +
T Consensus        92 AASN~gVD~IR~l~e~v~--------------------------------------------------y~P~~~kYKv-Y  120 (363)
T TIGR02397        92 AASNNGVDDIRELRENVK--------------------------------------------------YAPSKGKYKV-Y  120 (363)
T ss_pred             CCCCCCHHHHHHHHHHHC--------------------------------------------------CCCCCCCCCE-E
T ss_conf             865687889999987303--------------------------------------------------6875544335-8


Q ss_pred             EEECCCCCCHHHHHHHHHHHHCCCCCEEEEEEECC
Q ss_conf             99754559988999989874069882589998078
Q gi|254781187|r  196 FNDEASGTPDIINKSILGFFTELNPNRFWIMTSNT  230 (367)
Q Consensus       196 ivDEAsgI~d~i~e~i~g~Lt~~~~~~~~i~igNP  230 (367)
                      |+||+...+...|.|++-||=.+=...+.+ +-||
T Consensus       121 IIDEVHMLS~~AFNALLKTLEEPP~hV~FI-lATT  154 (363)
T TIGR02397       121 IIDEVHMLSKSAFNALLKTLEEPPEHVVFI-LATT  154 (363)
T ss_pred             EEECCCCCCHHHHHHHHHHHCCCCCCEEEE-EECC
T ss_conf             873230286568999876522798762888-7348


No 95 
>KOG0338 consensus
Probab=96.33  E-value=0.012  Score=35.25  Aligned_cols=197  Identities=14%  Similarity=0.103  Sum_probs=94.6

Q ss_pred             CCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCC----CEEEEECCCHHH
Q ss_conf             4436668428999999988887512455555411247761488678899999999999970899----779997153799
Q gi|254781187|r   44 PLEHFSQPHRWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPG----MSIICIANSETQ  119 (367)
Q Consensus        44 ~~~~~~~p~~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~----~~v~~~A~t~~Q  119 (367)
                      ...+|..|++.|...+-   -.+..   .      -+.-+|..|+|||+..+.=+|-.|+.+|-    .+|+|.-||..-
T Consensus       197 ~~lGy~~PTpIQ~a~IP---vallg---k------DIca~A~TGsGKTAAF~lPiLERLlYrPk~~~~TRVLVL~PTREL  264 (691)
T KOG0338         197 STLGYKKPTPIQVATIP---VALLG---K------DICACAATGSGKTAAFALPILERLLYRPKKVAATRVLVLVPTREL  264 (691)
T ss_pred             HHCCCCCCCCHHHHCCC---HHHHC---C------HHHHEECCCCCCHHHHHHHHHHHHHCCCCCCCCEEEEEEECCHHH
T ss_conf             74387888740331012---77522---2------256401146871145678899998527356761269998350899


Q ss_pred             HHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCEEEEEC
Q ss_conf             99999999999998623121123333210001233322111134577612662101354455652101135862899975
Q gi|254781187|r  120 LKNTLWAEVSKWLSMLPHRHWFEMQSLSLHPSGWYAELLEQSMGIDSKHYTITCRTYSEERPDTFVGPHNTHGMAVFNDE  199 (367)
Q Consensus       120 ~~~~lw~ei~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~ea~~g~h~~~~~l~ivDE  199 (367)
                      +-++ ....++.....-...-+...-+.++..       ...++..+...+++--..-. ---|..+++-++.-.+|+||
T Consensus       265 aiQv-~sV~~qlaqFt~I~~~L~vGGL~lk~Q-------E~~LRs~PDIVIATPGRlID-HlrNs~sf~ldsiEVLvlDE  335 (691)
T KOG0338         265 AIQV-HSVTKQLAQFTDITVGLAVGGLDLKAQ-------EAVLRSRPDIVIATPGRLID-HLRNSPSFNLDSIEVLVLDE  335 (691)
T ss_pred             HHHH-HHHHHHHHHHCCCEEEEEECCCCHHHH-------HHHHHHCCCEEEECCHHHHH-HHCCCCCCCCCCEEEEEECH
T ss_conf             9999-999999876604024445247457889-------99983089879946505888-75158876534325777333


Q ss_pred             CCCCC-----HHHHHHHHHHHHCCCCCEEEEEEECCCCCCCHHHHHHHCCCCC-EEEEEEC-CCCCCCCCHHHHH
Q ss_conf             45599-----8899998987406988258999807899987688754112235-0467523-3328888988999
Q gi|254781187|r  200 ASGTP-----DIINKSILGFFTELNPNRFWIMTSNTRRLNGWFYDIFNIPLED-WKRYQID-TRTVEGIDSGFHE  267 (367)
Q Consensus       200 AsgI~-----d~i~e~i~g~Lt~~~~~~~~i~igNP~r~~g~Fye~~~~~~~~-w~~~~~~-~~d~p~~~~~~i~  267 (367)
                      |.-.=     +.+-|.|.  |+..+...+  +||- | .+.-.-++-.--.+. ...+--+ -...|.+.++|+.
T Consensus       336 ADRMLeegFademnEii~--lcpk~RQTm--LFSA-T-MteeVkdL~slSL~kPvrifvd~~~~~a~~LtQEFiR  404 (691)
T KOG0338         336 ADRMLEEGFADEMNEIIR--LCPKNRQTM--LFSA-T-MTEEVKDLASLSLNKPVRIFVDPNKDTAPKLTQEFIR  404 (691)
T ss_pred             HHHHHHHHHHHHHHHHHH--HCCCCCCCE--EEHH-H-HHHHHHHHHHHHCCCCEEEEECCCCCCCHHHHHHHHE
T ss_conf             888999999999999998--551023001--2112-2-5788999997551798589857865444044477810


No 96 
>PRK08699 DNA polymerase III subunit delta'; Validated
Probab=96.33  E-value=0.071  Score=30.47  Aligned_cols=127  Identities=15%  Similarity=0.135  Sum_probs=61.4

Q ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHHCCCCE-EEEEC-CCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             4776148867889999999999997089977-99971-537999999999999999862312112333321000123332
Q gi|254781187|r   79 KCAISAGRGIGKTTLNAWMMLWLISTRPGMS-IICIA-NSETQLKNTLWAEVSKWLSMLPHRHWFEMQSLSLHPSGWYAE  156 (367)
Q Consensus        79 ~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~-v~~~A-~t~~Q~~~~lw~ei~k~~~~~~~~~~~~~~~~~~~~~~~~~~  156 (367)
                      -....+..|+||..++-.++-+++|..|... .-|-. ++=+....          ..-|+-++.......  ..   ..
T Consensus        23 A~L~~Gp~G~Gk~~~A~~~A~~llC~~~~~~~~~Cg~C~sC~~~~~----------g~HPD~~~i~p~~~~--~~---~g   87 (325)
T PRK08699         23 AWLFVGKKGTGKTAFARFAAKALLCETPAPGCKPCGECMSCHLFGQ----------GSHPDFYEITPLADE--PE---NG   87 (325)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHCCCCCCCCCCCCCCHHHHHHHC----------CCCCCEEEEECCCCC--CC---CC
T ss_conf             7975799997899999999999828999888998988888999865----------999996885134453--00---16


Q ss_pred             CCCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCEEEEECCCCCCHHHHHHHHHHHHCCCCCEEEEEEEC
Q ss_conf             2111134577612662101354455652101135862899975455998899998987406988258999807
Q gi|254781187|r  157 LLEQSMGIDSKHYTITCRTYSEERPDTFVGPHNTHGMAVFNDEASGTPDIINKSILGFFTELNPNRFWIMTSN  229 (367)
Q Consensus       157 ~~~~~~~~~~~~~~~~a~~~~~~~~ea~~g~h~~~~~l~ivDEAsgI~d~i~e~i~g~Lt~~~~~~~~i~igN  229 (367)
                      .....++.+.-      +-....  -+.....|.+ -.+|+|+|.......-.++..+|-.+-..++.+++++
T Consensus        88 ~~~~~I~idqi------R~l~~~--~~~~~~~~~~-kV~ii~~ae~mn~~aaNaLLK~LEEPp~~~~fiL~t~  151 (325)
T PRK08699         88 RKLLQIKIDAV------REIIDN--VYLTSVRGGL-RVILIHPAESMNVQAANSLLKVLEEPPPQVVFLLVSH  151 (325)
T ss_pred             CCCCCCCHHHH------HHHHHH--HCCCCCCCCC-EEEEECCHHHHCHHHHHHHHHHHCCCCCCEEEEEEEC
T ss_conf             65566769999------999999--7108656894-6999857777589999999998417888848999879


No 97 
>KOG0335 consensus
Probab=96.30  E-value=0.038  Score=32.17  Aligned_cols=167  Identities=13%  Similarity=-0.020  Sum_probs=85.4

Q ss_pred             CCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHC-C----------CCEEE
Q ss_conf             844366684289999999888875124555554112477614886788999999999999708-9----------97799
Q gi|254781187|r   43 KPLEHFSQPHRWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTR-P----------GMSII  111 (367)
Q Consensus        43 ~~~~~~~~p~~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~-~----------~~~v~  111 (367)
                      ....++..|++.|.-.+-.|.+.            .-+.++|-.|+|||...-.=++=.+.-. +          ...++
T Consensus        89 ~~~~~~~~ptpvQk~sip~i~~G------------rdlmacAqTGsGKT~aFLiPii~~~~~~~~~~~~~~~~~~~P~~l  156 (482)
T KOG0335          89 IKRSGYTKPTPVQKYSIPIISGG------------RDLMACAQTGSGKTAAFLIPIISYLLDEGPEDRGESGGGVYPRAL  156 (482)
T ss_pred             CCCCCCCCCCCCEECCCCEEECC------------CCEEEECCCCCCCHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCEE
T ss_conf             23356668986156042244258------------842788257885137888889999986486566656778897259


Q ss_pred             EECCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCC
Q ss_conf             97153799999999999999986231211233332100012333221111345776126621013544556521011358
Q gi|254781187|r  112 CIANSETQLKNTLWAEVSKWLSMLPHRHWFEMQSLSLHPSGWYAELLEQSMGIDSKHYTITCRTYSEERPDTFVGPHNTH  191 (367)
Q Consensus       112 ~~A~t~~Q~~~~lw~ei~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~ea~~g~h~~~  191 (367)
                      +.|||..-+. -++.|.+|....+-.+.-.-+.         .............+.-++.+..-+...-..-.-+--.+
T Consensus       157 IlapTReL~~-Qi~nea~k~~~~s~~~~~~~yg---------g~~~~~q~~~~~~gcdIlvaTpGrL~d~~e~g~i~l~~  226 (482)
T KOG0335         157 ILAPTRELVD-QIYNEARKFSYLSGMKSVVVYG---------GTDLGAQLRFIKRGCDILVATPGRLKDLIERGKISLDN  226 (482)
T ss_pred             EEECCHHHHH-HHHHHHHHHCCCCCCEEEEEEC---------CCCHHHHHHHHCCCCCEEEECCCHHHHHHHCCEEEHHH
T ss_conf             9817378766-7888887640221220330057---------84454422333257557885575056455415112623


Q ss_pred             CCEEEEECCC-------CCCHHHHHHHHHHHHCCCCCEEEEEEECCCCC
Q ss_conf             6289997545-------59988999989874069882589998078999
Q gi|254781187|r  192 GMAVFNDEAS-------GTPDIINKSILGFFTELNPNRFWIMTSNTRRL  233 (367)
Q Consensus       192 ~~l~ivDEAs-------gI~d~i~e~i~g~Lt~~~~~~~~i~igNP~r~  233 (367)
                      +-++++|||-       |.|+.=+-+....+...+.+.- ++|+ ++-+
T Consensus       227 ~k~~vLDEADrMlD~mgF~p~Ir~Iv~~~~~~~~~~~qt-~mFS-Atfp  273 (482)
T KOG0335         227 CKFLVLDEADRMLDEMGFEPQIRKIVEQLGMPPKNNRQT-LLFS-ATFP  273 (482)
T ss_pred             CCEEEECCHHHHHHHCCCCHHHHHHHCCCCCCCCCCEEE-EEEE-CCCC
T ss_conf             858995236776663266620799962558887466137-8873-5577


No 98 
>COG3972 Superfamily I DNA and RNA helicases [General function prediction only]
Probab=96.29  E-value=0.018  Score=34.08  Aligned_cols=134  Identities=15%  Similarity=0.120  Sum_probs=66.7

Q ss_pred             EECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCH---HHHHHHHHHHHH-H-------HHHHCCCCCCCCCCCCCCCC
Q ss_conf             614886788999999999999708997799971537---999999999999-9-------99862312112333321000
Q gi|254781187|r   82 ISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSE---TQLKNTLWAEVS-K-------WLSMLPHRHWFEMQSLSLHP  150 (367)
Q Consensus        82 v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~---~Q~~~~lw~ei~-k-------~~~~~~~~~~~~~~~~~~~~  150 (367)
                      |++=-|+|||.+.|..+.....++|+.+|++|--|.   +|.|+.+ ++.- .       |-+++....|...+....+-
T Consensus       181 IrGLAGSGKT~~La~Kaa~lh~knPd~~I~~Tfftk~L~s~~r~lv-~~F~f~~~e~~pdW~~~l~~h~wgG~t~~g~y~  259 (660)
T COG3972         181 IRGLAGSGKTELLAHKAAELHSKNPDSRIAFTFFTKILASTMRTLV-PEFFFMRVEKQPDWGTKLFCHNWGGLTKEGFYG  259 (660)
T ss_pred             HHCCCCCCCHHHHHHHHHHHHCCCCCCEEEEEEEHHHHHHHHHHHH-HHHHHHHHHCCCCCCCEEEEECCCCCCCCCCHH
T ss_conf             2002478730298877789744799863899866678889999999-999998862488724268884357878886038


Q ss_pred             -CCCCCCCCCCCCCCCCCCEEEEECCCCCCCCCCCCCCCC-CCCCEEEEECCCCCCHHHHHHHHHHHHCCCCCEEE
Q ss_conf             -123332211113457761266210135445565210113-58628999754559988999989874069882589
Q gi|254781187|r  151 -SGWYAELLEQSMGIDSKHYTITCRTYSEERPDTFVGPHN-THGMAVFNDEASGTPDIINKSILGFFTELNPNRFW  224 (367)
Q Consensus       151 -~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~ea~~g~h~-~~~~l~ivDEAsgI~d~i~e~i~g~Lt~~~~~~~~  224 (367)
                       ..+...+.+......+       ..++..-.|.++...+ .....+++||++..|+..++-..-..+ .-+++.|
T Consensus       260 ~~~~~~~~~~~~fsg~g-------~~F~~aC~eli~~~~~~~~yD~ilIDE~QDFP~~F~~Lcf~~tk-d~Krlvy  327 (660)
T COG3972         260 MYRYICHYYEIPFSGFG-------NGFDAACKELIADINNKKAYDYILIDESQDFPQSFIDLCFMVTK-DKKRLVY  327 (660)
T ss_pred             HHHHHHCCCCCCCCCCC-------CCHHHHHHHHHHHHHCCCCCCEEEECCCCCCCHHHHHHHHHHHC-CCCEEEE
T ss_conf             89998426654547877-------40679999999864256423179942455477899999999824-7543898


No 99 
>PRK07003 DNA polymerase III subunits gamma and tau; Validated
Probab=96.25  E-value=0.085  Score=29.98  Aligned_cols=135  Identities=17%  Similarity=0.159  Sum_probs=66.3

Q ss_pred             HHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHHHHHHH
Q ss_conf             99999998888751245555541124776148867889999999999997089977999715379999999999999998
Q gi|254781187|r   54 WQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLKNTLWAEVSKWLS  133 (367)
Q Consensus        54 wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~~~lw~ei~k~~~  133 (367)
                      .|.-+++.+..-+..+... +.    ..-.+.||+|||+++-.++--+-|......--|    . + ... +.+|..   
T Consensus        20 GQ~~v~~~l~nal~~~rl~-ha----ylf~G~rGvGKTt~aRi~Ak~lnC~~~~~~~pc----g-~-C~~-C~~i~~---   84 (816)
T PRK07003         20 GQEHVVRALTHALDGGRLH-HA----YLFTGTRGVGKTTLSRIFAKALNCETGVTSQPC----G-V-CRA-CREIDE---   84 (816)
T ss_pred             CCHHHHHHHHHHHHCCCCC-CE----EEEECCCCCCHHHHHHHHHHHHCCCCCCCCCCC----C-C-CHH-HHHHHC---
T ss_conf             8499999999999709863-14----751178988888999999998678999998978----7-7-555-787755---


Q ss_pred             HCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCEEEEECCCCCCHHHHHHHHH
Q ss_conf             62312112333321000123332211113457761266210135445565210113586289997545599889999898
Q gi|254781187|r  134 MLPHRHWFEMQSLSLHPSGWYAELLEQSMGIDSKHYTITCRTYSEERPDTFVGPHNTHGMAVFNDEASGTPDIINKSILG  213 (367)
Q Consensus       134 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~ea~~g~h~~~~~l~ivDEAsgI~d~i~e~i~g  213 (367)
                                        ..+..+.+.+-  ..+...-..+-..+..  .+.-..|.+ -.+|+||....+...|.+++.
T Consensus        85 ------------------g~~~d~iEiDa--AS~~~vd~~r~l~~~~--~y~p~~~r~-KvyiiDEvHmls~~afnalLK  141 (816)
T PRK07003         85 ------------------GRFVDYVEMDA--ASNRGVDEMAALLERA--VYAPVDARF-KVYMIDEVHMLTNHAFNAMLK  141 (816)
T ss_pred             ------------------CCCCCEEEEEC--CCCCCHHHHHHHHHHC--CCCCCCCCE-EEEEEECHHHCCHHHHHHHHH
T ss_conf             ------------------88775478635--5435768999999862--247866744-799984154339999999998


Q ss_pred             HHHCCCCCEEEEE
Q ss_conf             7406988258999
Q gi|254781187|r  214 FFTELNPNRFWIM  226 (367)
Q Consensus       214 ~Lt~~~~~~~~i~  226 (367)
                      +|-..=...+.++
T Consensus       142 tlEepP~hv~Fil  154 (816)
T PRK07003        142 TLEEPPPHVKFIL  154 (816)
T ss_pred             HHCCCCCCEEEEE
T ss_conf             4037986648999


No 100
>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=96.24  E-value=0.0057  Score=37.21  Aligned_cols=44  Identities=25%  Similarity=0.489  Sum_probs=34.8

Q ss_pred             CCCHHHHHHHHHHHHHHHCCCCEEEEECCC-HHHHHHHHHHHHHH
Q ss_conf             678899999999999970899779997153-79999999999999
Q gi|254781187|r   87 GIGKTTLNAWMMLWLISTRPGMSIICIANS-ETQLKNTLWAEVSK  130 (367)
Q Consensus        87 g~GKS~~~a~~~lw~~~~~~~~~v~~~A~t-~~Q~~~~lw~ei~k  130 (367)
                      |||||+++|+.++|++--.||.|+++++.- .+.+.|++=.|+.+
T Consensus         7 GVGKTt~SaAtA~~lAe~qPGkkvLl~STDPAHsL~D~F~~e~G~   51 (330)
T TIGR00345         7 GVGKTTISAATAIRLAEQQPGKKVLLVSTDPAHSLSDVFEQELGH   51 (330)
T ss_pred             CCHHHHHHHHHHHHHHHHCCCCEEEEEEECCCHHHHHHHHHHHCC
T ss_conf             823888999999999851899779998408600278861132177


No 101
>PRK11057 ATP-dependent DNA helicase RecQ; Provisional
Probab=96.13  E-value=0.021  Score=33.75  Aligned_cols=62  Identities=16%  Similarity=0.102  Sum_probs=44.0

Q ss_pred             CCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHH
Q ss_conf             3666842899999998888751245555541124776148867889999999999997089977999715379999999
Q gi|254781187|r   46 EHFSQPHRWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLKNTL  124 (367)
Q Consensus        46 ~~~~~p~~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~~~l  124 (367)
                      .+++..++-|.+++.++-..-            -+.+..+.|.|||.+--.=++-    . +..++|++|..+-++|-+
T Consensus        21 FG~~~Fr~~Q~e~i~~~l~g~------------D~l~~mpTG~GKSlcyQlPal~----~-~g~tiVisPLisLm~DQv   82 (607)
T PRK11057         21 FGYQQFRPGQEEIIDTVLSGR------------DCLVVMPTGGGKSLCYQIPALV----L-DGLTLVVSPLISLMKDQV   82 (607)
T ss_pred             CCCCCCCHHHHHHHHHHHCCC------------CEEEECCCCCHHHHHHHHHHHH----C-CCCEEEECCHHHHHHHHH
T ss_conf             698434576999999998699------------8899878995597999999987----7-998899868799999999


No 102
>PRK05703 flhF flagellar biosynthesis regulator FlhF; Validated
Probab=96.12  E-value=0.054  Score=31.21  Aligned_cols=68  Identities=15%  Similarity=0.027  Sum_probs=43.0

Q ss_pred             CHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCC-CEEEEECCCHH
Q ss_conf             428999999988887512455555411247761488678899999999999970899-77999715379
Q gi|254781187|r   51 PHRWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPG-MSIICIANSET  118 (367)
Q Consensus        51 p~~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~-~~v~~~A~t~~  118 (367)
                      +..-...++..+.+.+.-..........-+++.++-|+|||+.+|=++..+.+.+.. ...++|+.|++
T Consensus       184 ~~~~~~~l~~~L~~~l~~~~~~~~~~~~vvalVGPTGVGKTTTiAKLAA~~~l~~~~~kV~lIT~DtyR  252 (412)
T PRK05703        184 PREAWRYLLELLANMLPTRVEDILEQGGVVALVGPTGVGKTTTLAKLAARYALEEGKDKVALITLDTYR  252 (412)
T ss_pred             HHHHHHHHHHHHHHHCCCCCCCCCCCCCEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEEEECCCC
T ss_conf             799999999999975788876654567369998888875676999999999997299817999837677


No 103
>PRK13767 ATP-dependent helicase; Provisional
Probab=96.03  E-value=0.043  Score=31.82  Aligned_cols=89  Identities=15%  Similarity=0.066  Sum_probs=56.5

Q ss_pred             CCCCCHHHHHHHHCCCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCC
Q ss_conf             57233789999752320125988885543014668884436668428999999988887512455555411247761488
Q gi|254781187|r    7 TDQKLEQELHEMLMHAECVLSFKNFVMRFFPWGIKGKPLEHFSQPHRWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGR   86 (367)
Q Consensus         7 ~~~~~~~~~~~~~~~~~~~~~~~~f~~~~~~w~~~~~~~~~~~~p~~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgr   86 (367)
                      |..+++++.++++       +|.-  .-   |=     -..|..|++.|+++...|.+.-            .+.|.|+.
T Consensus         6 ~~~~~~~~~~~~l-------~p~v--~~---wf-----~~~~~~p~~~Q~~a~~~i~~G~------------~~Li~ApT   56 (878)
T PRK13767          6 TKEYSDEEILSLL-------HPYV--AE---WF-----KRKFGTFTPPQRYAIPLIHEGK------------NVLISSPT   56 (878)
T ss_pred             HCCCCHHHHHHHC-------CHHH--HH---HH-----HHCCCCCCHHHHHHHHHHHCCC------------CEEEECCC
T ss_conf             1026757677627-------9899--99---99-----8537999989999999996799------------88998999


Q ss_pred             CCCHHHHHHHHHHHHHHH-------CCCCEEEEECCCHHHHHHHH
Q ss_conf             678899999999999970-------89977999715379999999
Q gi|254781187|r   87 GIGKTTLNAWMMLWLIST-------RPGMSIICIANSETQLKNTL  124 (367)
Q Consensus        87 g~GKS~~~a~~~lw~~~~-------~~~~~v~~~A~t~~Q~~~~l  124 (367)
                      |+|||..+-.-++-.+..       ..+..+++++|...=++|+.
T Consensus        57 GsGKTlAaflp~l~~l~~~~~~~~~~~~~~~LyIsPLkAL~~D~~  101 (878)
T PRK13767         57 GSGKTLAAFLGIIDELFRLAEEGELEDSVYCIYVSPLRALNNDIH  101 (878)
T ss_pred             CCHHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEECCHHHHHHHHH
T ss_conf             813999999999999985000367788728999684798899999


No 104
>TIGR03499 FlhF flagellar biosynthetic protein FlhF.
Probab=95.99  E-value=0.037  Score=32.18  Aligned_cols=70  Identities=13%  Similarity=0.013  Sum_probs=45.3

Q ss_pred             CCHHHHHHHHHHHHHHHHCCCCCCC--CCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCE-EEEECCCHHH
Q ss_conf             8428999999988887512455555--41124776148867889999999999997089977-9997153799
Q gi|254781187|r   50 QPHRWQLEFMEAVDVHCHSNVNNSN--PTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMS-IICIANSETQ  119 (367)
Q Consensus        50 ~p~~wq~~~l~~~~~~~~~~~~~~~--~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~-v~~~A~t~~Q  119 (367)
                      .++.....+...+++.+........  ....-+++.++.|+|||+.+|-++..+...+...+ .++|.-|++-
T Consensus       165 ~~~~~~~~l~~~L~~~i~~~~~~~~~~~~~~vi~lvGPTGVGKTTTiAKLAa~~~l~~~~~~V~lIT~DtyRi  237 (282)
T TIGR03499       165 DAESAWRWLREALENMLPVKPEEDEILEQGGVIALVGPTGVGKTTTLAKLAARFVLEHGKKKVALITTDTYRI  237 (282)
T ss_pred             CHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCEEEEECCCCCCHHHHHHHHHHHHHHHCCCCCEEEEEECCCCH
T ss_conf             9789999999999964777887655445672799977888757889999999999973899679998077767


No 105
>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=95.98  E-value=0.0086  Score=36.08  Aligned_cols=35  Identities=29%  Similarity=0.335  Sum_probs=32.1

Q ss_pred             EEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEEC
Q ss_conf             77614886788999999999999708997799971
Q gi|254781187|r   80 CAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIA  114 (367)
Q Consensus        80 ~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A  114 (367)
                      -.|++-.|+|||+++|.+=-+.+-|+|+.||+++.
T Consensus       152 GLiCG~TGSGKSTl~AaiY~~~l~t~pdRKivT~E  186 (374)
T TIGR02525       152 GLICGETGSGKSTLAAAIYRHCLETYPDRKIVTYE  186 (374)
T ss_pred             EEECCCCCCCHHHHHHHHHHHHCCCCCCCEEEEEE
T ss_conf             02217789728999999999850748897079865


No 106
>PRK06872 DNA polymerase III subunits gamma and tau; Provisional
Probab=95.98  E-value=0.067  Score=30.62  Aligned_cols=135  Identities=15%  Similarity=0.140  Sum_probs=70.6

Q ss_pred             HHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHHHHHHH
Q ss_conf             99999998888751245555541124776148867889999999999997089977999715379999999999999998
Q gi|254781187|r   54 WQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLKNTLWAEVSKWLS  133 (367)
Q Consensus        54 wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~~~lw~ei~k~~~  133 (367)
                      .|.-+++.+..-+..+... +.    ....+.||+|||+++-.++--+-|......--|-.      ... +.+|..   
T Consensus        20 gq~~v~~~l~~a~~~~r~~-ha----ylf~g~rg~gktt~ari~ak~lnc~~~~~~~pcg~------c~~-c~~i~~---   84 (696)
T PRK06872         20 GQEHILTALSNGLKENRLH-HA----YLFSGTRGVGKTSIARLFAKGLNCVHGVTATPCGE------CEN-CKAIEE---   84 (696)
T ss_pred             CCHHHHHHHHHHHHCCCCC-CE----EEEECCCCCCHHHHHHHHHHHHCCCCCCCCCCCCC------CHH-HHHHHC---
T ss_conf             8599999999999719863-04----75117898888899999999867899999997888------622-576744---


Q ss_pred             HCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCEEEEECCCCCCHHHHHHHHH
Q ss_conf             62312112333321000123332211113457761266210135445565210113586289997545599889999898
Q gi|254781187|r  134 MLPHRHWFEMQSLSLHPSGWYAELLEQSMGIDSKHYTITCRTYSEERPDTFVGPHNTHGMAVFNDEASGTPDIINKSILG  213 (367)
Q Consensus       134 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~ea~~g~h~~~~~l~ivDEAsgI~d~i~e~i~g  213 (367)
                                        ..+..+.+  +....++..-..+-..+.  -.+.-.+|.+. .+|+||....+...|.+++.
T Consensus        85 ------------------g~~~d~~e--idaas~~~v~~~r~l~~~--~~~~p~~~~~k-vy~idevhmls~~~fnallk  141 (696)
T PRK06872         85 ------------------GNFIDLIE--IDAASRTKVEDTRELLDN--VQYKPVVGRFK-VYLIDEVHMLSRHSFNALLK  141 (696)
T ss_pred             ------------------CCCCCEEE--EECCCCCCHHHHHHHHHH--CCCCCCCCCEE-EEEEEHHHHCCHHHHHHHHH
T ss_conf             ------------------78775467--505655788999999984--54577677547-99970054438999999987


Q ss_pred             HHHCCCCCEEEEE
Q ss_conf             7406988258999
Q gi|254781187|r  214 FFTELNPNRFWIM  226 (367)
Q Consensus       214 ~Lt~~~~~~~~i~  226 (367)
                      +|-..=...+.++
T Consensus       142 tleepp~~v~f~l  154 (696)
T PRK06872        142 TLEEPPEYVKFLL  154 (696)
T ss_pred             HHCCCCCCEEEEE
T ss_conf             5027975448998


No 107
>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=95.98  E-value=0.12  Score=29.16  Aligned_cols=48  Identities=29%  Similarity=0.259  Sum_probs=29.1

Q ss_pred             HHHHHHHHHHHHHHCC-CCCCCCC--EEEEEEECCCCCCHHHHHHHHHHHH
Q ss_conf             9999999888875124-5555541--1247761488678899999999999
Q gi|254781187|r   54 WQLEFMEAVDVHCHSN-VNNSNPT--IFKCAISAGRGIGKTTLNAWMMLWL  101 (367)
Q Consensus        54 wq~~~l~~~~~~~~~~-~~~~~~~--~~~~~v~sgrg~GKS~~~a~~~lw~  101 (367)
                      .|.++++.|++.+++. ..-..|.  +--....++-|+|||.++-.++-.+
T Consensus       569 GQd~AI~~I~~aI~~sraGL~dp~rP~GsFlf~GptGvGKTELAKaLAe~L  619 (852)
T TIGR03346       569 GQDEAVEAVSDAIRRSRAGLSDPNRPIGSFLFLGPTGVGKTELAKALAEFL  619 (852)
T ss_pred             CHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCCCHHHHHHHHHHHH
T ss_conf             709999999999999971888899974589986788776899999999998


No 108
>pfam01695 IstB IstB-like ATP binding protein. This protein contains an ATP/GTP binding P-loop motif. It is found associated with IS21 family insertion sequences. The function of this protein is unknown, but it may perform a transposase function.
Probab=95.97  E-value=0.08  Score=30.17  Aligned_cols=55  Identities=16%  Similarity=0.118  Sum_probs=34.9

Q ss_pred             CCHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECC
Q ss_conf             842899999998888751245555541124776148867889999999999997089977999715
Q gi|254781187|r   50 QPHRWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIAN  115 (367)
Q Consensus        50 ~p~~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~  115 (367)
                      +.+++|..-|.. .+.+.++        .++.+.++-|+|||++++++..-. + ..+.+|..+.-
T Consensus        29 ~~~~~~i~~L~~-~~~i~~~--------~Nlll~G~~GtGKThLA~Ai~~~~-~-~~g~~v~f~~~   83 (178)
T pfam01695        29 GLDRRLIAELAG-LDWIEQA--------ENLLLLGPPGVGKTHLACALGHQA-C-RAGYSVLFTRT   83 (178)
T ss_pred             CCCHHHHHHHHC-CCCHHCC--------CCEEEECCCCCCHHHHHHHHHHHH-H-HCCCEEEEEEC
T ss_conf             989999998855-9742158--------768998999987899999999999-9-86985999961


No 109
>KOG0330 consensus
Probab=95.93  E-value=0.028  Score=33.00  Aligned_cols=156  Identities=15%  Similarity=0.056  Sum_probs=83.6

Q ss_pred             CCCCCHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCC-CEEEEECCCHHHHHHHHH
Q ss_conf             6668428999999988887512455555411247761488678899999999999970899-779997153799999999
Q gi|254781187|r   47 HFSQPHRWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPG-MSIICIANSETQLKNTLW  125 (367)
Q Consensus        47 ~~~~p~~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~-~~v~~~A~t~~Q~~~~lw  125 (367)
                      +++.|++-|.+.+-.   -++. .        -+..+|-.|+|||...+.=++-.|+-.|. ..++|.+||..-+.++  
T Consensus        80 ~~~~PT~IQ~~aiP~---~L~g-~--------dvIglAeTGSGKT~afaLPIl~~LL~~p~~~~~lVLtPtRELA~QI--  145 (476)
T KOG0330          80 GWKKPTKIQSEAIPV---ALGG-R--------DVIGLAETGSGKTGAFALPILQRLLQEPKLFFALVLTPTRELAQQI--  145 (476)
T ss_pred             CCCCCCHHHHHHCCH---HHCC-C--------CEEEEECCCCCCHHHHHHHHHHHHHCCCCCCEEEEECCCHHHHHHH--
T ss_conf             767874444520655---4379-8--------5799943588840231799999997198774489964828999999--


Q ss_pred             HHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCC-CCCCCCCCCCCCCCCCEEEEECCCCCC
Q ss_conf             9999999862312112333321000123332211113457761266210135-445565210113586289997545599
Q gi|254781187|r  126 AEVSKWLSMLPHRHWFEMQSLSLHPSGWYAELLEQSMGIDSKHYTITCRTYS-EERPDTFVGPHNTHGMAVFNDEASGTP  204 (367)
Q Consensus       126 ~ei~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~-~~~~ea~~g~h~~~~~l~ivDEAsgI~  204 (367)
                      +|.-..+...+.-   .+.    -.... ......-.-...+..++.|.+-+ -+--++-.|++-+..-++++|||.-+=
T Consensus       146 ~e~fe~Lg~~igl---r~~----~lvGG-~~m~~q~~~L~kkPhilVaTPGrL~dhl~~Tkgf~le~lk~LVlDEADrlL  217 (476)
T KOG0330         146 AEQFEALGSGIGL---RVA----VLVGG-MDMMLQANQLSKKPHILVATPGRLWDHLENTKGFSLEQLKFLVLDEADRLL  217 (476)
T ss_pred             HHHHHHHCCCCCE---EEE----EEECC-CHHHHHHHHHHCCCCEEEECCHHHHHHHHHCCCCCHHHHHHHHHCHHHHHH
T ss_conf             9999875356672---799----98658-329999887624898798370789999874368408875787633177662


Q ss_pred             HHHHH-HHHHHHH--CCCCCEEE
Q ss_conf             88999-9898740--69882589
Q gi|254781187|r  205 DIINK-SILGFFT--ELNPNRFW  224 (367)
Q Consensus       205 d~i~e-~i~g~Lt--~~~~~~~~  224 (367)
                      |.-|+ .+.-.|.  ....+++.
T Consensus       218 d~dF~~~ld~ILk~ip~erqt~L  240 (476)
T KOG0330         218 DMDFEEELDYILKVIPRERQTFL  240 (476)
T ss_pred             HHHHHHHHHHHHHHCCCCCEEEE
T ss_conf             11568999999874674414899


No 110
>PRK09183 transposase/IS protein; Provisional
Probab=95.91  E-value=0.12  Score=29.15  Aligned_cols=68  Identities=21%  Similarity=0.194  Sum_probs=38.6

Q ss_pred             HHCCCCCCCCCCCCC---CCHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEE
Q ss_conf             301466888443666---84289999999888875124555554112477614886788999999999999708997799
Q gi|254781187|r   35 FFPWGIKGKPLEHFS---QPHRWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSII  111 (367)
Q Consensus        35 ~~~w~~~~~~~~~~~---~p~~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~  111 (367)
                      -||+. +..+-..|+   +..+.|..-|.. .++++++        .++.+.++-|+|||++++++..  ..++.|.+|.
T Consensus        66 ~fp~~-ktle~fDf~~~~~l~~~~i~~La~-~~fi~~~--------~Nvil~G~~GtGKThLA~Alg~--~A~~~G~~v~  133 (258)
T PRK09183         66 AFPAV-KTFEEYDFTFATGAPQKQLQSLRS-LSFIERN--------ENIVLLGPSGVGKTHLAIALGY--EAVRAGIKVR  133 (258)
T ss_pred             CCCCC-CCHHHCCCCCCCCCCHHHHHHHHC-CCHHHCC--------CCEEEECCCCCCHHHHHHHHHH--HHHHCCCEEE
T ss_conf             99998-777555654688623899998825-8166558--------8679989999868999999999--9998799399


Q ss_pred             EEC
Q ss_conf             971
Q gi|254781187|r  112 CIA  114 (367)
Q Consensus       112 ~~A  114 (367)
                      .+.
T Consensus       134 f~~  136 (258)
T PRK09183        134 FTT  136 (258)
T ss_pred             EEE
T ss_conf             978


No 111
>PRK06526 transposase; Provisional
Probab=95.86  E-value=0.13  Score=28.96  Aligned_cols=127  Identities=14%  Similarity=0.139  Sum_probs=66.3

Q ss_pred             CCHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHHH
Q ss_conf             84289999999888875124555554112477614886788999999999999708997799971537999999999999
Q gi|254781187|r   50 QPHRWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLKNTLWAEVS  129 (367)
Q Consensus        50 ~p~~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~~~lw~ei~  129 (367)
                      +..+-|.+-|.. .+++.++.        ++.+.++-|+|||++++++..- + |+.|.+|.++.-..      +..++.
T Consensus        80 ~l~~~~i~~La~-~~fi~~~~--------Nvil~G~~GtGKThLA~Alg~~-A-~~~G~~v~f~~~~~------L~~~L~  142 (254)
T PRK06526         80 SLKRDTIAHLGT-LDFVTGKE--------NVVFLGPPGTGKTHLAIGLGIR-A-CQAGHRVLFATAAQ------WVARLA  142 (254)
T ss_pred             CCCHHHHHHHHC-CCHHHCCC--------CEEEECCCCCCHHHHHHHHHHH-H-HHCCCCEEEEEHHH------HHHHHH
T ss_conf             989999999863-71776588--------7899899998689999999999-9-98699679987799------999999


Q ss_pred             HHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCEEEEECCCCCC-----
Q ss_conf             999862312112333321000123332211113457761266210135445565210113586289997545599-----
Q gi|254781187|r  130 KWLSMLPHRHWFEMQSLSLHPSGWYAELLEQSMGIDSKHYTITCRTYSEERPDTFVGPHNTHGMAVFNDEASGTP-----  204 (367)
Q Consensus       130 k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~ea~~g~h~~~~~l~ivDEAsgI~-----  204 (367)
                      .....                                +.           -...+.-+  ....|+|+||....|     
T Consensus       143 ~a~~~--------------------------------g~-----------~~~~~~~l--~~~dLLIiDe~g~~~~~~~~  177 (254)
T PRK06526        143 AAHHA--------------------------------GR-----------LQDELVKL--GRIPLLIVDEVGYIPFEAEA  177 (254)
T ss_pred             HHHHC--------------------------------CC-----------HHHHHHHH--HCCCEEEEECCCCCCCCHHH
T ss_conf             98855--------------------------------80-----------99999985--13687765021364478899


Q ss_pred             -HHHHHHHHHHHHCCCCCEEEEEEECCCCCCCHHHHHHHCC
Q ss_conf             -8899998987406988258999807899987688754112
Q gi|254781187|r  205 -DIINKSILGFFTELNPNRFWIMTSNTRRLNGWFYDIFNIP  244 (367)
Q Consensus       205 -d~i~e~i~g~Lt~~~~~~~~i~igNP~r~~g~Fye~~~~~  244 (367)
                       +..|+++..--   +.+. .++++  +.+....++.|.++
T Consensus       178 a~~lf~li~~Ry---e~~S-~IiTS--n~~~~~W~~~f~D~  212 (254)
T PRK06526        178 ANLFFQLVSSRY---ERAS-LIVTS--NKPFGRWGEVFGDD  212 (254)
T ss_pred             HHHHHHHHHHHH---CCCC-EEEEC--CCCHHHHHHHCCCH
T ss_conf             999999999997---4588-67665--89866888864868


No 112
>PRK08853 DNA polymerase III subunits gamma and tau; Validated
Probab=95.82  E-value=0.14  Score=28.75  Aligned_cols=134  Identities=19%  Similarity=0.159  Sum_probs=67.8

Q ss_pred             HHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHHHHHHH
Q ss_conf             99999998888751245555541124776148867889999999999997089977999715379999999999999998
Q gi|254781187|r   54 WQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLKNTLWAEVSKWLS  133 (367)
Q Consensus        54 wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~~~lw~ei~k~~~  133 (367)
                      .|.-+++.+..-+..+... +.    ..-.+.||+|||+++-.++--+-|......--|.-      ... +.+|..   
T Consensus        20 GQ~~v~~~L~nal~~~rl~-ha----ylf~G~rGvGKTt~ARi~Ak~lNC~~~~~~~pcg~------C~~-C~~i~~---   84 (717)
T PRK08853         20 GQSHVLTALENALAHNRLH-HA----YLFSGTRGVGKTTIGRLFAKGLNCETGITSTPCGQ------CAT-CKEIDE---   84 (717)
T ss_pred             CCHHHHHHHHHHHHCCCCC-CE----EEEECCCCCCHHHHHHHHHHHHCCCCCCCCCCCCC------CCC-HHHHHC---
T ss_conf             8599999999999709974-05----76108898889899999999867899999997888------702-676744---


Q ss_pred             HCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCEEEEECCCCCCHHHHHHHHH
Q ss_conf             62312112333321000123332211113457761266210135445565210113586289997545599889999898
Q gi|254781187|r  134 MLPHRHWFEMQSLSLHPSGWYAELLEQSMGIDSKHYTITCRTYSEERPDTFVGPHNTHGMAVFNDEASGTPDIINKSILG  213 (367)
Q Consensus       134 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~ea~~g~h~~~~~l~ivDEAsgI~d~i~e~i~g  213 (367)
                                        ..+..+.+.+  ...+...-..+-..+ + -.+.-.+|.+. .+|+||....+...|.+++.
T Consensus        85 ------------------g~~~d~~EiD--aAs~~~vdd~rel~~-~-~~y~p~~~~yK-vyiiDEvHmls~~afnAlLK  141 (717)
T PRK08853         85 ------------------GRFVDLLEID--AASRTKVEDTRELLD-N-VQYKPARGRFK-VYLIDEVHMLSRHSFNALLK  141 (717)
T ss_pred             ------------------CCCCCEEEEC--CCCCCCHHHHHHHHH-H-CCCCCCCCCEE-EEEEECHHHCCHHHHHHHHH
T ss_conf             ------------------7877524540--565678899999998-5-55488778547-99983054438999999987


Q ss_pred             HHHCCCCCEEEE
Q ss_conf             740698825899
Q gi|254781187|r  214 FFTELNPNRFWI  225 (367)
Q Consensus       214 ~Lt~~~~~~~~i  225 (367)
                      +|-.+=...+.+
T Consensus       142 tlEEPP~hv~Fi  153 (717)
T PRK08853        142 TLEEPPEYVKFL  153 (717)
T ss_pred             HHCCCCCCEEEE
T ss_conf             603787564899


No 113
>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=95.80  E-value=0.03  Score=32.78  Aligned_cols=158  Identities=17%  Similarity=0.138  Sum_probs=81.3

Q ss_pred             CCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHH-HHHHHHHHHHHHHC-----------CCCEEEE
Q ss_conf             43666842899999998888751245555541124776148867889-99999999999708-----------9977999
Q gi|254781187|r   45 LEHFSQPHRWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKT-TLNAWMMLWLISTR-----------PGMSIIC  112 (367)
Q Consensus        45 ~~~~~~p~~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS-~~~a~~~lw~~~~~-----------~~~~v~~  112 (367)
                      +.+.+||.+||.++.+.+.+.       ..|+    ++.-+.|+||| .+++.+++-...-.           -+.+-++
T Consensus        11 ~~G~~GPfpwQ~~L~~r~~~G-------~~P~----~~s~PTg~GKTlavi~~WlyAl~~~a~~~Grrr~~~~vP~RL~y   79 (975)
T TIGR02621        11 LTGYSGPFPWQLRLAERFVAG-------EPPE----SCSVPTGLGKTLAVIAVWLYALAIDAEQVGRRRRRRKVPRRLVY   79 (975)
T ss_pred             HCCCCCCCHHHHHHHHHHHCC-------CCCC----CCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCCEEECCCEEEE
T ss_conf             358988865899999998548-------9887----66787532368999999999987400036732421336831378


Q ss_pred             ECCCHHHHHHHHHHHHHHHHHHCCCCCCCC------CCCCCC-------------CCCCCCCCCC--CCCCCCCCC-CEE
Q ss_conf             715379999999999999998623121123------333210-------------0012333221--111345776-126
Q gi|254781187|r  113 IANSETQLKNTLWAEVSKWLSMLPHRHWFE------MQSLSL-------------HPSGWYAELL--EQSMGIDSK-HYT  170 (367)
Q Consensus       113 ~A~t~~Q~~~~lw~ei~k~~~~~~~~~~~~------~~~~~~-------------~~~~~~~~~~--~~~~~~~~~-~~~  170 (367)
                      +-+- +.+=|-.+.+..|+.+.|+......      +.....             .++..+....  -++...++. ..+
T Consensus        80 vVdR-R~vVD~~te~a~~i~~aL~~~pe~~Av~~vl~slr~~~~~Pa~a~pl~v~~LRGg~ad~~rDltew~~~P~rPav  158 (975)
T TIGR02621        80 VVDR-RTVVDQSTEEAEKIREALGEAPELPAVRYVLESLRSAFAIPAEAEPLAVSTLRGGFADNDRDLTEWTRDPSRPAV  158 (975)
T ss_pred             EEEC-CEEECCHHHHHHHHHHHCCCCCCHHHHHHHHHHHCCCCCCCCCCCCCEEEECCCCCCCHHHHHHHHHHCCCCCEE
T ss_conf             8714-245343278999999854688877899999997323678776566523311167553022323345317899669


Q ss_pred             EEE-------------CCCCCCCCCCCCCCCCCCCCEEEEECCCCCCHHHHHHHHHHHH
Q ss_conf             621-------------0135445565210113586289997545599889999898740
Q gi|254781187|r  171 ITC-------------RTYSEERPDTFVGPHNTHGMAVFNDEASGTPDIINKSILGFFT  216 (367)
Q Consensus       171 ~~a-------------~~~~~~~~ea~~g~h~~~~~l~ivDEAsgI~d~i~e~i~g~Lt  216 (367)
                      |.+             .+.+-.+.-=-+|+-|.. .|+++||| +++..+-|.+.-..+
T Consensus       159 ivgTvDm~gSRLLFrGYg~spk~rpihAal~G~D-Al~VlDEA-Hl~~~f~e~L~~i~~  215 (975)
T TIGR02621       159 IVGTVDMIGSRLLFRGYGCSPKSRPIHAALLGQD-ALIVLDEA-HLSPAFQETLKQIRS  215 (975)
T ss_pred             EEECCCCHHHHHHHHCCCCCCCCCCHHHHHHHCH-HHHHHHHH-HCCHHHHHHHHHHHH
T ss_conf             9834420234354413456766551122213110-66543343-058789999999851


No 114
>KOG0331 consensus
Probab=95.74  E-value=0.035  Score=32.39  Aligned_cols=260  Identities=11%  Similarity=0.014  Sum_probs=118.9

Q ss_pred             CCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHH------CC-CCEEEEECCCH
Q ss_conf             436668428999999988887512455555411247761488678899999999999970------89-97799971537
Q gi|254781187|r   45 LEHFSQPHRWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLIST------RP-GMSIICIANSE  117 (367)
Q Consensus        45 ~~~~~~p~~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~------~~-~~~v~~~A~t~  117 (367)
                      ..+|..|++-|+...--+-+    +        .-+...|..|+|||.....=++-++..      +. +.+++|.+||.
T Consensus       108 ~~g~~~PtpIQaq~wp~~l~----G--------rD~v~iA~TGSGKTLay~lP~i~~l~~~~~~~~~~~~P~vLVL~PTR  175 (519)
T KOG0331         108 EQGFEKPTPIQAQGWPIALS----G--------RDLVGIARTGSGKTLAYLLPAIVHLNNEQGKLSRGDGPIVLVLAPTR  175 (519)
T ss_pred             HCCCCCCCHHHHCCCCEECC----C--------CCEEEEECCCCCCHHHHHHHHHHHHHHCCCCCCCCCCCEEEEECCCH
T ss_conf             53999885344144651126----8--------86577823578620555557999987004443479998699976859


Q ss_pred             HHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCEEEE
Q ss_conf             99999999999999986231211233332100012333221111345776126621013544556521011358628999
Q gi|254781187|r  118 TQLKNTLWAEVSKWLSMLPHRHWFEMQSLSLHPSGWYAELLEQSMGIDSKHYTITCRTYSEERPDTFVGPHNTHGMAVFN  197 (367)
Q Consensus       118 ~Q~~~~lw~ei~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~ea~~g~h~~~~~l~iv  197 (367)
                      .-+..+ -.+..++...+..+.--.....+..+...         ....|.-.+.+.+-+-..--....+.-..+.++++
T Consensus       176 ELA~QV-~~~~~~~~~~~~~~~~cvyGG~~~~~Q~~---------~l~~gvdiviaTPGRl~d~le~g~~~l~~v~ylVL  245 (519)
T KOG0331         176 ELAVQV-QAEAREFGKSLRLRSTCVYGGAPKGPQLR---------DLERGVDVVIATPGRLIDLLEEGSLNLSRVTYLVL  245 (519)
T ss_pred             HHHHHH-HHHHHHHCCCCCCCEEEEECCCCCCHHHH---------HHHCCCCEEEECCHHHHHHHHCCCCCCCCEEEEEE
T ss_conf             999999-99999970777740799868988637889---------87559818980771789999748856453039996


Q ss_pred             ECCCCCCHHHH-HHHHHHHHC---CCCCEEEEEEECCCCCCCHHHHHHHCCCCCEEEEEECCCC----CCC-------C-
Q ss_conf             75455998899-998987406---9882589998078999876887541122350467523332----888-------8-
Q gi|254781187|r  198 DEASGTPDIIN-KSILGFFTE---LNPNRFWIMTSNTRRLNGWFYDIFNIPLEDWKRYQIDTRT----VEG-------I-  261 (367)
Q Consensus       198 DEAsgI~d~i~-e~i~g~Lt~---~~~~~~~i~igNP~r~~g~Fye~~~~~~~~w~~~~~~~~d----~p~-------~-  261 (367)
                      |||--.-|.=| +.++-.+..   ....++|... +-++..-.+.+.|..   +...+.+-..+    +..       . 
T Consensus       246 DEADrMldmGFe~qI~~Il~~i~~~~rQtlm~sa-Twp~~v~~lA~~fl~---~~~~i~ig~~~~~~a~~~i~qive~~~  321 (519)
T KOG0331         246 DEADRMLDMGFEPQIRKILSQIPRPDRQTLMFSA-TWPKEVRQLAEDFLN---NPIQINVGNKKELKANHNIRQIVEVCD  321 (519)
T ss_pred             CCHHHHHCCCCHHHHHHHHHHCCCCCCCEEEEEE-ECCHHHHHHHHHHHC---CCEEEEECCHHHHHHHCCHHHHHHHCC
T ss_conf             3477663135379999998755897522788865-464889999999845---964899612145544333146511268


Q ss_pred             ---CHHHHHHHHHHCCCCCCEEEEEEEEEECCCCC------------CEEECHHHHHHHHCC--CCCCCCCCCEEEEEEC
Q ss_conf             ---98899999962168800026888644327789------------807829998644315--7777889848999963
Q gi|254781187|r  262 ---DSGFHEGIISRYGLDSDVARIEILGQFPQQEV------------NNFIPHNYIEEAMSR--EAIDDLYAPLIMGCDI  324 (367)
Q Consensus       262 ---~~~~i~~~~~~~gedS~~~r~ev~G~Fp~~~~------------d~~ip~~~ie~a~~~--~~~~~~~~p~viGvDv  324 (367)
                         ...-+.+.++.+.. ...-++.+.|+--+..+            ..-|..+.-+.-.+.  .......-|+.+.=||
T Consensus       322 ~~~K~~~l~~lL~~~~~-~~~~KvIIFc~tkr~~~~l~~~l~~~~~~a~~iHGd~sQ~eR~~~L~~FreG~~~vLVATdV  400 (519)
T KOG0331         322 ETAKLRKLGKLLEDISS-DSEGKVIIFCETKRTCDELARNLRRKGWPAVAIHGDKSQSERDWVLKGFREGKSPVLVATDV  400 (519)
T ss_pred             HHHHHHHHHHHHHHHHC-CCCCCEEEEECCHHHHHHHHHHHHHCCCCEEEECCCCCHHHHHHHHHHCCCCCCCEEEECCC
T ss_conf             78898879999999735-68986899964336499999887751766155006664889999997502688546988153


Q ss_pred             CCCCCCE
Q ss_conf             8778810
Q gi|254781187|r  325 AGEGGDK  331 (367)
Q Consensus       325 Ar~G~D~  331 (367)
                      |..|=|=
T Consensus       401 AaRGLDi  407 (519)
T KOG0331         401 AARGLDV  407 (519)
T ss_pred             CCCCCCC
T ss_conf             1256887


No 115
>PRK07952 DNA replication protein DnaC; Validated
Probab=95.72  E-value=0.15  Score=28.50  Aligned_cols=65  Identities=18%  Similarity=0.187  Sum_probs=39.9

Q ss_pred             CCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEE-ECC
Q ss_conf             43666842899999998888751245555541124776148867889999999999997089977999-715
Q gi|254781187|r   45 LEHFSQPHRWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIIC-IAN  115 (367)
Q Consensus        45 ~~~~~~p~~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~-~A~  115 (367)
                      ++++.-..+-|.++|..--.+.++-    ....--+...++-|+|||+++++++.-.+.  .+..|++ +++
T Consensus        68 Feny~~~~~~q~~al~~a~~y~enf----~~~~~gLlF~G~~GTGKThLA~aIan~Li~--~G~sVlf~t~~  133 (242)
T PRK07952         68 FENYRVECEGQMNALSKARQYVEEF----DGNIASFIFSGKPGTGKNHLAAAICNELLL--RGKSVLIITVA  133 (242)
T ss_pred             EECEECCCHHHHHHHHHHHHHHHHH----CCCCCEEEEECCCCCCHHHHHHHHHHHHHH--CCCEEEEEEHH
T ss_conf             2120158777899999999999865----438871799789999789999999999998--79949997799


No 116
>PRK13833 conjugal transfer protein TrbB; Provisional
Probab=95.71  E-value=0.036  Score=32.29  Aligned_cols=55  Identities=20%  Similarity=0.295  Sum_probs=42.7

Q ss_pred             HHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCH
Q ss_conf             289999999888875124555554112477614886788999999999999708997799971537
Q gi|254781187|r   52 HRWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSE  117 (367)
Q Consensus        52 ~~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~  117 (367)
                      .+.|.++|+..-..           ..++.|++|.|+|||++..+++-......|+.+++++-.+.
T Consensus       130 t~~~~~~L~~aV~~-----------r~nilVsGgTGSGKTTllnaL~~~i~~~~p~eRivtIEDt~  184 (323)
T PRK13833        130 TEAQASTIRSAISS-----------RLNIVISGGTGSGKTTLANAVIAEIVASAPEDRLVILEDTA  184 (323)
T ss_pred             CHHHHHHHHHHHHC-----------CCCEEEECCCCCCHHHHHHHHHHHHCCCCCHHEEEEECCCC
T ss_conf             99999999999981-----------89689991777756899999998640289323399945750


No 117
>KOG0949 consensus
Probab=95.70  E-value=0.057  Score=31.05  Aligned_cols=167  Identities=14%  Similarity=0.113  Sum_probs=78.5

Q ss_pred             CCHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHHH
Q ss_conf             84289999999888875124555554112477614886788999999999999708997799971537999999999999
Q gi|254781187|r   50 QPHRWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLKNTLWAEVS  129 (367)
Q Consensus        50 ~p~~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~~~lw~ei~  129 (367)
                      -|+.||.+.|..+.-.      .      .+.|.|++-.|||++.=-.+=-.+-......|+.+||+..-+..+. +.+.
T Consensus       511 ~Pd~WQ~elLDsvDr~------e------SavIVAPTSaGKTfisfY~iEKVLResD~~VVIyvaPtKaLVnQvs-a~Vy  577 (1330)
T KOG0949         511 CPDEWQRELLDSVDRN------E------SAVIVAPTSAGKTFISFYAIEKVLRESDSDVVIYVAPTKALVNQVS-ANVY  577 (1330)
T ss_pred             CCCHHHHHHHHHHHCC------C------CEEEEEECCCCCEECCHHHHHHHHHHCCCCEEEEECCHHHHHHHHH-HHHH
T ss_conf             9838888776655056------6------2599820467861005899999985427987999664587766666-7788


Q ss_pred             H-HHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCEEEEECCCCC----C
Q ss_conf             9-9986231211233332100012333221111345776126621013544556521011358628999754559----9
Q gi|254781187|r  130 K-WLSMLPHRHWFEMQSLSLHPSGWYAELLEQSMGIDSKHYTITCRTYSEERPDTFVGPHNTHGMAVFNDEASGT----P  204 (367)
Q Consensus       130 k-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~ea~~g~h~~~~~l~ivDEAsgI----~  204 (367)
                      - .-...++...+.+..   ..+.|-......+..+.-.. +....   -.+|-.-+++- +..-.+|+||-.-|    .
T Consensus       578 aRF~~~t~~rg~sl~g~---ltqEYsinp~nCQVLITvPe-clesl---Llspp~~q~~c-erIRyiIfDEVH~iG~~ed  649 (1330)
T KOG0949         578 ARFDTKTFLRGVSLLGD---LTQEYSINPWNCQVLITVPE-CLESL---LLSPPHHQKFC-ERIRYIIFDEVHLIGNEED  649 (1330)
T ss_pred             HHHCCCCCCCCHHHHHH---HHHHHCCCCHHCEEEEECHH-HHHHH---HCCCHHHHHHH-HCCEEEEECHHHHCCCCCC
T ss_conf             76336765631346766---66773578411359997467-89988---63856653022-4005897112332465243


Q ss_pred             HHHHHHHHHHHHCCCCCEEEEEEECCCCCCCHHHHHHH
Q ss_conf             88999989874069882589998078999876887541
Q gi|254781187|r  205 DIINKSILGFFTELNPNRFWIMTSNTRRLNGWFYDIFN  242 (367)
Q Consensus       205 d~i~e~i~g~Lt~~~~~~~~i~igNP~r~~g~Fye~~~  242 (367)
                      ..+||-+.-..+- .--.+-..+|||.    .|+.-.+
T Consensus       650 ~l~~Eqll~li~C-P~L~LSATigN~~----l~qkWln  682 (1330)
T KOG0949         650 GLLWEQLLLLIPC-PFLVLSATIGNPN----LFQKWLN  682 (1330)
T ss_pred             CHHHHHHHHHCCC-CEEEEECCCCCHH----HHHHHHH
T ss_conf             4189987774578-7068741338888----9999999


No 118
>KOG0333 consensus
Probab=95.67  E-value=0.034  Score=32.44  Aligned_cols=144  Identities=19%  Similarity=0.149  Sum_probs=82.1

Q ss_pred             CCCCCCCCC--------CCCCCHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHH-HHHHHHHHHCC--
Q ss_conf             466888443--------6668428999999988887512455555411247761488678899999-99999997089--
Q gi|254781187|r   38 WGIKGKPLE--------HFSQPHRWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNA-WMMLWLISTRP--  106 (367)
Q Consensus        38 w~~~~~~~~--------~~~~p~~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a-~~~lw~~~~~~--  106 (367)
                      |.+.+.|++        ++..|++-|+.+   |.-.+|+..        =+-| +-.|+|||...- -+++|...+-|  
T Consensus       247 wEE~~~P~e~l~~I~~~~y~eptpIqR~a---ipl~lQ~rD--------~igv-aETgsGktaaf~ipLl~~IsslP~~~  314 (673)
T KOG0333         247 WEESGFPLELLSVIKKPGYKEPTPIQRQA---IPLGLQNRD--------PIGV-AETGSGKTAAFLIPLLIWISSLPPMA  314 (673)
T ss_pred             HHHCCCCHHHHHHHHHCCCCCCCHHHHHH---CCCHHCCCC--------EEEE-EECCCCCCCCCHHHHHHHHHCCCCCC
T ss_conf             32238988999999734899984678863---110101477--------2368-73167753200015889987089841


Q ss_pred             -------CCEEEEECCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCC
Q ss_conf             -------9779997153799999999999999986231211233332100012333221111345776126621013544
Q gi|254781187|r  107 -------GMSIICIANSETQLKNTLWAEVSKWLSMLPHRHWFEMQSLSLHPSGWYAELLEQSMGIDSKHYTITCRTYSEE  179 (367)
Q Consensus       107 -------~~~v~~~A~t~~Q~~~~lw~ei~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~  179 (367)
                             |...+++|||..-+ ..+..|..|+...+-++         ..............+....|.-+..|.+.+..
T Consensus       315 ~~en~~~gpyaiilaptReLa-qqIeeEt~kf~~~lg~r---------~vsvigg~s~EEq~fqls~gceiviatPgrLi  384 (673)
T KOG0333         315 RLENNIEGPYAIILAPTRELA-QQIEEETNKFGKPLGIR---------TVSVIGGLSFEEQGFQLSMGCEIVIATPGRLI  384 (673)
T ss_pred             HHHHCCCCCEEEEECHHHHHH-HHHHHHHHHHCCCCCCE---------EEEEECCCCHHHHHHHHHCCCEEEECCCHHHH
T ss_conf             444234686001203379999-99999998750301432---------89985463366530246415414424740788


Q ss_pred             CCCCCCCCCCCCCCEEEEECCCCC
Q ss_conf             556521011358628999754559
Q gi|254781187|r  180 RPDTFVGPHNTHGMAVFNDEASGT  203 (367)
Q Consensus       180 ~~ea~~g~h~~~~~l~ivDEAsgI  203 (367)
                      ..--=.-+-...+..+++|||.-.
T Consensus       385 d~Lenr~lvl~qctyvvldeadrm  408 (673)
T KOG0333         385 DSLENRYLVLNQCTYVVLDEADRM  408 (673)
T ss_pred             HHHHHHHHHHCCCCEEECCCHHHH
T ss_conf             877778887505846762406665


No 119
>PRK09111 DNA polymerase III subunits gamma and tau; Validated
Probab=95.65  E-value=0.16  Score=28.34  Aligned_cols=139  Identities=15%  Similarity=0.094  Sum_probs=69.3

Q ss_pred             HHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCE-EEEECCCHHHHHHHHHHHHHHHH
Q ss_conf             99999998888751245555541124776148867889999999999997089977-99971537999999999999999
Q gi|254781187|r   54 WQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMS-IICIANSETQLKNTLWAEVSKWL  132 (367)
Q Consensus        54 wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~-v~~~A~t~~Q~~~~lw~ei~k~~  132 (367)
                      .|.-+.+.+..-+..|... |.    ....+.||+|||+++-.++--+-|..|+.. .....|-..  ... +.+|..  
T Consensus        27 gq~~~~~~l~~~~~~~~~~-~a----~l~~g~rg~gktt~ari~a~~lnc~~~~~~~~~~~~~c~~--c~~-c~~i~~--   96 (600)
T PRK09111         27 GQEAMVRTLRNAFETGRIA-QA----FMLTGVRGVGKTTTARILARALNYKGPDGVGGPTIDPCGV--GEH-CQAIME--   96 (600)
T ss_pred             CCHHHHHHHHHHHHCCCCC-CE----EEEECCCCCCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCC--CHH-HHHHHC--
T ss_conf             8599999999999729842-04----7645789878999999999996698876668998898998--865-898866--


Q ss_pred             HHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCEEEEECCCCCCHHHHHHHH
Q ss_conf             86231211233332100012333221111345776126621013544556521011358628999754559988999989
Q gi|254781187|r  133 SMLPHRHWFEMQSLSLHPSGWYAELLEQSMGIDSKHYTITCRTYSEERPDTFVGPHNTHGMAVFNDEASGTPDIINKSIL  212 (367)
Q Consensus       133 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~ea~~g~h~~~~~l~ivDEAsgI~d~i~e~i~  212 (367)
                                         ..+..+.  ++....++..-..+-..+..  .+.-..+.+. .+|+||....+...|.+++
T Consensus        97 -------------------~~~~d~~--e~daas~~~v~~~r~~~~~~--~~~p~~~~~k-v~iidevhmls~~afnall  152 (600)
T PRK09111         97 -------------------GRHVDVI--EMDAASHTGVDDIREIIESV--RYRPVSARYK-VYIIDEVHMLSTAAFNALL  152 (600)
T ss_pred             -------------------CCCCCEE--EEECCCCCCHHHHHHHHHHH--CCCCCCCCEE-EEEEECCCCCCHHHHHHHH
T ss_conf             -------------------8998758--85155457888999999860--5388777546-9996001105799999999


Q ss_pred             HHHHCCCCCEEEEE
Q ss_conf             87406988258999
Q gi|254781187|r  213 GFFTELNPNRFWIM  226 (367)
Q Consensus       213 g~Lt~~~~~~~~i~  226 (367)
                      .+|-.+=...+.++
T Consensus       153 ktleepp~~~~fi~  166 (600)
T PRK09111        153 KTLEEPPPHVKFIF  166 (600)
T ss_pred             HHHHCCCCCEEEEE
T ss_conf             87625986549999


No 120
>PRK08770 DNA polymerase III subunits gamma and tau; Validated
Probab=95.37  E-value=0.17  Score=28.19  Aligned_cols=135  Identities=19%  Similarity=0.186  Sum_probs=70.1

Q ss_pred             HHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHHHHHHH
Q ss_conf             99999998888751245555541124776148867889999999999997089977999715379999999999999998
Q gi|254781187|r   54 WQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLKNTLWAEVSKWLS  133 (367)
Q Consensus        54 wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~~~lw~ei~k~~~  133 (367)
                      .|.-+++.+..-+..+... +.    ..-.+-||+|||+++-.++--+-|.. |.+.   .|-. + ... +.+|..   
T Consensus        20 gq~~~~~~l~~~~~~~~~~-~a----~lf~g~rg~gkt~~ar~~a~~lnc~~-~~~~---~pc~-~-c~~-c~~i~~---   84 (663)
T PRK08770         20 GQEHVVRALSNALDSGRVH-HA----FLFTGTRGVGKTTIARIFAKSLNCET-GTSA---DPCG-Q-CPA-CLDIDA---   84 (663)
T ss_pred             CCHHHHHHHHHHHHCCCCC-EE----EEEECCCCCCHHHHHHHHHHHHCCCC-CCCC---CCCC-C-CHH-HHHHHC---
T ss_conf             8599999999999709974-04----76227998888899999999867899-9999---9787-7-877-898854---


Q ss_pred             HCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCEEEEECCCCCCHHHHHHHHH
Q ss_conf             62312112333321000123332211113457761266210135445565210113586289997545599889999898
Q gi|254781187|r  134 MLPHRHWFEMQSLSLHPSGWYAELLEQSMGIDSKHYTITCRTYSEERPDTFVGPHNTHGMAVFNDEASGTPDIINKSILG  213 (367)
Q Consensus       134 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~ea~~g~h~~~~~l~ivDEAsgI~d~i~e~i~g  213 (367)
                                        ..+..+.+.+  ...+...-..+-..+.  -.+.-.+|.+. .+|+||....+...|.+++.
T Consensus        85 ------------------~~~~d~~e~d--aas~~~v~~~r~~~~~--~~~~p~~~~~k-vy~idevhmls~~~fna~lk  141 (663)
T PRK08770         85 ------------------GRYIDLLEID--AASNTGVDDVREVIEN--AQYMPSRGKFK-VYLIDEVHMLSKAAFNALLK  141 (663)
T ss_pred             ------------------CCCCCEEEEE--CCCCCCHHHHHHHHHH--CCCCCCCCCEE-EEEEECHHHCCHHHHHHHHH
T ss_conf             ------------------8988658864--6765888999999984--43588777436-99970043328999999987


Q ss_pred             HHHCCCCCEEEEE
Q ss_conf             7406988258999
Q gi|254781187|r  214 FFTELNPNRFWIM  226 (367)
Q Consensus       214 ~Lt~~~~~~~~i~  226 (367)
                      +|-.+=...+.++
T Consensus       142 tleepp~~v~f~~  154 (663)
T PRK08770        142 TLEEPPEHVKFLL  154 (663)
T ss_pred             HHCCCCCCEEEEE
T ss_conf             4027864428998


No 121
>KOG0391 consensus
Probab=95.34  E-value=0.11  Score=29.32  Aligned_cols=167  Identities=14%  Similarity=0.159  Sum_probs=89.4

Q ss_pred             CCCHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCC-CEEEEECCCHHHHHHHHHHH
Q ss_conf             68428999999988887512455555411247761488678899999999999970899-77999715379999999999
Q gi|254781187|r   49 SQPHRWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPG-MSIICIANSETQLKNTLWAE  127 (367)
Q Consensus        49 ~~p~~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~-~~v~~~A~t~~Q~~~~lw~e  127 (367)
                      ..-|.+|.-=|.=++.--++|.+        -..+---|.|||.-+-.++.+++|..-+ .--+++-||..-+.-  ==|
T Consensus       614 GqLReYQkiGLdWLatLYeknlN--------GILADEmGLGKTIQtISllAhLACeegnWGPHLIVVpTsviLnW--EME  683 (1958)
T KOG0391         614 GQLREYQKIGLDWLATLYEKNLN--------GILADEMGLGKTIQTISLLAHLACEEGNWGPHLIVVPTSVILNW--EME  683 (1958)
T ss_pred             HHHHHHHHHHHHHHHHHHHHCCC--------CEEHHHHCCCCHHHHHHHHHHHHHCCCCCCCCEEEEECHHHHHH--HHH
T ss_conf             77888887517999999873344--------32223314651457999999987504577873698513221133--678


Q ss_pred             HHHHHHHCCC-CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCEEEEECCCCCCH-
Q ss_conf             9999986231-21123333210001233322111134577612662101354455652101135862899975455998-
Q gi|254781187|r  128 VSKWLSMLPH-RHWFEMQSLSLHPSGWYAELLEQSMGIDSKHYTITCRTYSEERPDTFVGPHNTHGMAVFNDEASGTPD-  205 (367)
Q Consensus       128 i~k~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~ea~~g~h~~~~~l~ivDEAsgI~d-  205 (367)
                      +|+|.-.+.. -+.-.....+.+-+.|...           ..|-.+.++=...--....+.....-++|+|||..|.+ 
T Consensus       684 lKRwcPglKILTYyGs~kErkeKRqgW~kP-----------naFHVCItSYklv~qd~~AFkrkrWqyLvLDEaqnIKnf  752 (1958)
T KOG0391         684 LKRWCPGLKILTYYGSHKERKEKRQGWAKP-----------NAFHVCITSYKLVFQDLTAFKRKRWQYLVLDEAQNIKNF  752 (1958)
T ss_pred             HHHHCCCCEEEEECCCHHHHHHHHHCCCCC-----------CEEEEEEHHHHHHHHHHHHHHHHCCCEEEHHHHHHHCCH
T ss_conf             865277535765217788888875144688-----------804886310688873778887641122321455542300


Q ss_pred             --HHHHHHHHHHHCCCCCEEEEEEECCCCCCCHHHHHHH
Q ss_conf             --8999989874069882589998078999876887541
Q gi|254781187|r  206 --IINKSILGFFTELNPNRFWIMTSNTRRLNGWFYDIFN  242 (367)
Q Consensus       206 --~i~e~i~g~Lt~~~~~~~~i~igNP~r~~g~Fye~~~  242 (367)
                        .-|+++...-+.  .+  .+++|+|-.  |-|-++|.
T Consensus       753 ksqrWQAllnfnsq--rR--LLLtgTPLq--NslmELWS  785 (1958)
T KOG0391         753 KSQRWQALLNFNSQ--RR--LLLTGTPLQ--NSLMELWS  785 (1958)
T ss_pred             HHHHHHHHHCCCHH--HE--EEECCCCHH--HHHHHHHH
T ss_conf             67889998530012--00--221187204--67999999


No 122
>COG1200 RecG RecG-like helicase [DNA replication, recombination, and repair / Transcription]
Probab=95.33  E-value=0.2  Score=27.67  Aligned_cols=82  Identities=21%  Similarity=0.277  Sum_probs=61.0

Q ss_pred             CCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHH
Q ss_conf             88443666842899999998888751245555541124776148867889999999999997089977999715379999
Q gi|254781187|r   42 GKPLEHFSQPHRWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLK  121 (367)
Q Consensus        42 ~~~~~~~~~p~~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~  121 (367)
                      .+|+    .++..|..++++|...+.++.     .|-|+ +.+-=|+|||..++..++-. . .-|..+..+|||+==|+
T Consensus       258 ~LPF----~LT~aQ~~vi~EI~~Dl~~~~-----~M~RL-lQGDVGSGKTvVA~laml~a-i-~~G~Q~ALMAPTEILA~  325 (677)
T COG1200         258 ALPF----KLTNAQKRVIKEILADLASPV-----PMNRL-LQGDVGSGKTVVALLAMLAA-I-EAGYQAALMAPTEILAE  325 (677)
T ss_pred             HCCC----CCCHHHHHHHHHHHHHHCCCH-----HHHHH-HCCCCCCCHHHHHHHHHHHH-H-HCCCEEEEECCHHHHHH
T ss_conf             5899----767899999999986644866-----66787-52676777899999999999-8-72881688663799999


Q ss_pred             HHHHHHHHHHHHHCC
Q ss_conf             999999999998623
Q gi|254781187|r  122 NTLWAEVSKWLSMLP  136 (367)
Q Consensus       122 ~~lw~ei~k~~~~~~  136 (367)
                      + -+..+++|+..+-
T Consensus       326 Q-H~~~~~~~l~~~~  339 (677)
T COG1200         326 Q-HYESLRKWLEPLG  339 (677)
T ss_pred             H-HHHHHHHHHHHCC
T ss_conf             9-9999998766519


No 123
>PRK05648 DNA polymerase III subunits gamma and tau; Reviewed
Probab=95.26  E-value=0.19  Score=27.83  Aligned_cols=135  Identities=16%  Similarity=0.205  Sum_probs=69.6

Q ss_pred             HHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHHHHHHH
Q ss_conf             99999998888751245555541124776148867889999999999997089977999715379999999999999998
Q gi|254781187|r   54 WQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLKNTLWAEVSKWLS  133 (367)
Q Consensus        54 wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~~~lw~ei~k~~~  133 (367)
                      .|.-+++.+..-+..+... |.    ..-.+.||+|||+++-.++--+-| ..|...   .|-. + ... +.+|..   
T Consensus        20 gq~~~~~~l~~~~~~~~~~-~a----~l~~g~rg~gkt~~ar~~ak~lnc-~~~~~~---~pc~-~-c~~-c~~i~~---   84 (705)
T PRK05648         20 GQTHVLKALINALDNQRLH-HA----YLFTGTRGVGKTTIARIIAKCLNC-ETGVSS---TPCG-E-CSV-CREIDE---   84 (705)
T ss_pred             CHHHHHHHHHHHHHCCCCC-CE----EEEECCCCCCHHHHHHHHHHHHCC-CCCCCC---CCCC-C-CHH-HHHHHC---
T ss_conf             8199999999999709863-04----650078988898999999998677-899988---9787-7-600-466624---


Q ss_pred             HCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCEEEEECCCCCCHHHHHHHHH
Q ss_conf             62312112333321000123332211113457761266210135445565210113586289997545599889999898
Q gi|254781187|r  134 MLPHRHWFEMQSLSLHPSGWYAELLEQSMGIDSKHYTITCRTYSEERPDTFVGPHNTHGMAVFNDEASGTPDIINKSILG  213 (367)
Q Consensus       134 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~ea~~g~h~~~~~l~ivDEAsgI~d~i~e~i~g  213 (367)
                                        ..+..+.+.+  ...+...-..+-..+.  -.+.-.+|.+. .+|+||....+...|.+++.
T Consensus        85 ------------------~~~~d~~e~d--~as~~~v~~~r~~~~~--~~~~p~~~~~k-v~~idevhmls~~~fnallk  141 (705)
T PRK05648         85 ------------------GRFVDLIEVD--AASRTKVEDTRELLDN--VQYAPTRGRYK-VYLIDEVHMLSSHSFNALLK  141 (705)
T ss_pred             ------------------CCCCCEEEEC--CCCCCCHHHHHHHHHH--CCCCCCCCCEE-EEEEEHHHHCCHHHHHHHHH
T ss_conf             ------------------8977634451--5544788999999985--55177677457-99984265417999999987


Q ss_pred             HHHCCCCCEEEEE
Q ss_conf             7406988258999
Q gi|254781187|r  214 FFTELNPNRFWIM  226 (367)
Q Consensus       214 ~Lt~~~~~~~~i~  226 (367)
                      +|-.+=...+.++
T Consensus       142 tleepp~~v~f~~  154 (705)
T PRK05648        142 TLEEPPPHVKFLL  154 (705)
T ss_pred             HCCCCCCCEEEEE
T ss_conf             4047975459998


No 124
>KOG0340 consensus
Probab=95.24  E-value=0.15  Score=28.50  Aligned_cols=158  Identities=15%  Similarity=0.015  Sum_probs=84.3

Q ss_pred             CCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCE-EEEECC
Q ss_conf             1466888443666842899999998888751245555541124776148867889999999999997089977-999715
Q gi|254781187|r   37 PWGIKGKPLEHFSQPHRWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMS-IICIAN  115 (367)
Q Consensus        37 ~w~~~~~~~~~~~~p~~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~-v~~~A~  115 (367)
                      ||=.+-+--.+..+|++-|....-.|-+..            -+.=+|-.|+|||+..|.-++-.+.-+|... .++..|
T Consensus        16 ~Wlve~l~~l~i~~pTpiQ~~cIpkILeGr------------dcig~AkTGsGKT~AFaLPil~rLsedP~giFalvlTP   83 (442)
T KOG0340          16 PWLVEQLKALGIKKPTPIQQACIPKILEGR------------DCIGCAKTGSGKTAAFALPILNRLSEDPYGIFALVLTP   83 (442)
T ss_pred             HHHHHHHHHHCCCCCCCHHHHHHHHHHCCC------------CCCCCCCCCCCCCHHHHHHHHHHHCCCCCCCEEEEECC
T ss_conf             899999998358899826765248785466------------31031346887411222787776133887606999545


Q ss_pred             CHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCCCC------CCCCCCCC
Q ss_conf             379999999999999998623121123333210001233322111134577612662101354455------65210113
Q gi|254781187|r  116 SETQLKNTLWAEVSKWLSMLPHRHWFEMQSLSLHPSGWYAELLEQSMGIDSKHYTITCRTYSEERP------DTFVGPHN  189 (367)
Q Consensus       116 t~~Q~~~~lw~ei~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~------ea~~g~h~  189 (367)
                      |..-+-.+  +|--..+.++.+..--        .................+...+.+..-+...+      +..-++  
T Consensus        84 TrELA~Qi--aEQF~alGk~l~lK~~--------vivGG~d~i~qa~~L~~rPHvVvatPGRlad~l~sn~~~~~~~~--  151 (442)
T KOG0340          84 TRELALQI--AEQFIALGKLLNLKVS--------VIVGGTDMIMQAAILSDRPHVVVATPGRLADHLSSNLGVCSWIF--  151 (442)
T ss_pred             HHHHHHHH--HHHHHHHCCCCCCEEE--------EEECCHHHHHHHHHCCCCCCEEECCCCCCCCCCCCCCCCCHHHH--
T ss_conf             28888888--8999984564563279--------99756887645444266987575176333541126876552555--


Q ss_pred             CCCCEEEEECCCCCC----HHHHHHHHHHHHCC
Q ss_conf             586289997545599----88999989874069
Q gi|254781187|r  190 THGMAVFNDEASGTP----DIINKSILGFFTEL  218 (367)
Q Consensus       190 ~~~~l~ivDEAsgI~----d~i~e~i~g~Lt~~  218 (367)
                      ...-++++|||.-+=    ++..+.++-.+-..
T Consensus       152 ~rlkflVlDEADrvL~~~f~d~L~~i~e~lP~~  184 (442)
T KOG0340         152 QRLKFLVLDEADRVLAGCFPDILEGIEECLPKP  184 (442)
T ss_pred             HCEEEEEECCHHHHHCCCHHHHHHHHHCCCCCC
T ss_conf             300467741302654156056776665048876


No 125
>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=95.16  E-value=0.23  Score=27.34  Aligned_cols=45  Identities=20%  Similarity=0.248  Sum_probs=35.4

Q ss_pred             EEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHH
Q ss_conf             776148867889999999999997089977999715379999999
Q gi|254781187|r   80 CAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLKNTL  124 (367)
Q Consensus        80 ~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~~~l  124 (367)
                      ..|-||.|+|||..--.-++.++.-+++.+|+|..+|..--.+.+
T Consensus        19 ~lVEAGTGTGKSLAYLvPAl~~a~~~~g~rVVISTaT~aLQeQL~   63 (636)
T TIGR03117        19 GMLEASTGVGKTLAMIMAALTMLKERPDQKIAIAVPTLALMGQLW   63 (636)
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHHHCCCCCEEEECCCHHHHHHHH
T ss_conf             999899971088999999999998579998899798799999997


No 126
>PRK07993 DNA polymerase III subunit delta'; Validated
Probab=95.07  E-value=0.25  Score=27.17  Aligned_cols=134  Identities=13%  Similarity=0.113  Sum_probs=68.9

Q ss_pred             HHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHHHHHHHHCCCCCC
Q ss_conf             88887512455555411247761488678899999999999970899779997153799999999999999986231211
Q gi|254781187|r   61 AVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLKNTLWAEVSKWLSMLPHRHW  140 (367)
Q Consensus        61 ~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~~~lw~ei~k~~~~~~~~~~  140 (367)
                      .+....+.+...+     .+.+.+..|+||+.++-.++-+.+|..|...--|-.-..  -+     .+.  ...-|+-++
T Consensus        13 ~l~~~~~~~rl~H-----A~L~~G~~G~Gk~~la~~~a~~llC~~~~~~~~Cg~C~~--C~-----l~~--~~~HPD~~~   78 (334)
T PRK07993         13 KLVGSYQAGRGHH-----ALLIQALPGMGDDALIYALSRYLLCQQPQGHKSCGHCRG--CQ-----LMQ--AGTHPDYYT   78 (334)
T ss_pred             HHHHHHHCCCCCE-----EEEEECCCCCCHHHHHHHHHHHHCCCCCCCCCCCCCCHH--HH-----HHH--CCCCCCEEE
T ss_conf             9999998598104-----675479999889999999999981899999999999978--99-----986--689998477


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCEEEEECCCCCCHHHHHHHHHHHHCCCC
Q ss_conf             23333210001233322111134577612662101354455652101135862899975455998899998987406988
Q gi|254781187|r  141 FEMQSLSLHPSGWYAELLEQSMGIDSKHYTITCRTYSEERPDTFVGPHNTHGMAVFNDEASGTPDIINKSILGFFTELNP  220 (367)
Q Consensus       141 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~ea~~g~h~~~~~l~ivDEAsgI~d~i~e~i~g~Lt~~~~  220 (367)
                      ...+.            ....++.+.-.-..      .  --+.....|.+. .+|+|+|.......-.++..+|-.+..
T Consensus        79 i~pe~------------~~~~I~IdqIR~l~------~--~~~~~~~~g~~k-V~iI~~Ae~mn~~AaNaLLKtLEEPp~  137 (334)
T PRK07993         79 LTPEK------------GKSSLGVDAVREVT------E--KLYEHARLGGAK-VVWLPDAALLTDAAANALLKTLEEPPE  137 (334)
T ss_pred             ECCCC------------CCCCCCHHHHHHHH------H--HHHHCCCCCCCE-EEEECCHHHHCHHHHHHHHHHHCCCCC
T ss_conf             53422------------34559999999999------9--984366569947-999766777599999999986127998


Q ss_pred             CEEEEEEEC
Q ss_conf             258999807
Q gi|254781187|r  221 NRFWIMTSN  229 (367)
Q Consensus       221 ~~~~i~igN  229 (367)
                      .++.+++++
T Consensus       138 ~t~~iL~t~  146 (334)
T PRK07993        138 KTWFFLACR  146 (334)
T ss_pred             CEEEEEECC
T ss_conf             849998669


No 127
>PRK13894 conjugal transfer ATPase TrbB; Provisional
Probab=94.95  E-value=0.077  Score=30.25  Aligned_cols=55  Identities=22%  Similarity=0.171  Sum_probs=41.0

Q ss_pred             HHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHH
Q ss_conf             899999998888751245555541124776148867889999999999997089977999715379
Q gi|254781187|r   53 RWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSET  118 (367)
Q Consensus        53 ~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~  118 (367)
                      +-|.++|+..-..           ..++.|++|.|+|||++..+++-......|..+++++..+..
T Consensus       136 ~~~a~~L~~~V~~-----------r~nilI~G~TgsGKTTll~all~~i~~~~p~eRivtIED~~E  190 (320)
T PRK13894        136 AEQREAIIAAVRA-----------HRNILVIGGTGSGKTTLVNAIINEMVIQDPTERVFIIEDTGE  190 (320)
T ss_pred             HHHHHHHHHHHHC-----------CCCEEEECCCCCCHHHHHHHHHHHHCCCCCCCCEEEECCHHH
T ss_conf             9999999999972-----------875899858886568999999863202695201775258788


No 128
>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=94.74  E-value=0.28  Score=26.79  Aligned_cols=122  Identities=18%  Similarity=0.019  Sum_probs=67.7

Q ss_pred             HHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCC-CCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHHHHH
Q ss_conf             8999999988887512455555411247761488-678899999999999970899779997153799999999999999
Q gi|254781187|r   53 RWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGR-GIGKTTLNAWMMLWLISTRPGMSIICIANSETQLKNTLWAEVSKW  131 (367)
Q Consensus        53 ~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgr-g~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~~~lw~ei~k~  131 (367)
                      .=|.++++.|...-            ++||.-|+ |.|||++...+=..|-.-.  -+|+=-|=+.+-++ -|-++    
T Consensus       417 ~EQ~~Av~hvt~s~------------~iavVvG~AGtGKSt~L~aAR~AWe~~G--y~V~GAALsGKAAe-gLe~~----  477 (888)
T TIGR02768       417 EEQKEAVRHVTGSG------------DIAVVVGRAGTGKSTMLKAAREAWEAAG--YRVIGAALSGKAAE-GLEAE----  477 (888)
T ss_pred             HHHHHHHHHHCCCC------------CEEEEECCCCCCHHHHHHHHHHHHHHCC--CEEEEHHHHHHHHH-HHHCC----
T ss_conf             89999987532899------------6489974899876678999999998739--77871545558988-73002----


Q ss_pred             HHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCEEEEECCCCCCHHHHHHH
Q ss_conf             98623121123333210001233322111134577612662101354455652101135862899975455998899998
Q gi|254781187|r  132 LSMLPHRHWFEMQSLSLHPSGWYAELLEQSMGIDSKHYTITCRTYSEERPDTFVGPHNTHGMAVFNDEASGTPDIINKSI  211 (367)
Q Consensus       132 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~ea~~g~h~~~~~l~ivDEAsgI~d~i~e~i  211 (367)
                                 +-.....++-|...             +          .....-++..  ..+|+|||..|.-.-+.=+
T Consensus       478 -----------sGI~SRTLASle~a-------------W----------~~G~d~L~~~--dvLviDEAGMV~S~Qm~r~  521 (888)
T TIGR02768       478 -----------SGIESRTLASLEYA-------------W----------ANGRDLLEDK--DVLVIDEAGMVGSRQMARV  521 (888)
T ss_pred             -----------CCCCHHHHHHHHHH-------------H----------HCCCCCCCCC--CEEEEECCCCHHHHHHHHH
T ss_conf             -----------68750478879999-------------8----------7387522477--6689851544146778899


Q ss_pred             HHHHHCCCCCEEEEEEECCC
Q ss_conf             98740698825899980789
Q gi|254781187|r  212 LGFFTELNPNRFWIMTSNTR  231 (367)
Q Consensus       212 ~g~Lt~~~~~~~~i~igNP~  231 (367)
                      ...-...+.|+  +++|-|.
T Consensus       522 l~~A~~AGaKv--VLvGD~~  539 (888)
T TIGR02768       522 LKEAEEAGAKV--VLVGDPE  539 (888)
T ss_pred             HHHHHHCCCCE--EEECCHH
T ss_conf             99998727605--9848857


No 129
>KOG0350 consensus
Probab=94.73  E-value=0.17  Score=28.12  Aligned_cols=149  Identities=15%  Similarity=0.041  Sum_probs=75.2

Q ss_pred             HHHHHHHHHHHHHHCCCCCCCCC-EEEEEEECCCCCCHHHHHHHHHHHHHHHCCC--CEEEEECCCHHHHHHHHHHHHHH
Q ss_conf             99999998888751245555541-1247761488678899999999999970899--77999715379999999999999
Q gi|254781187|r   54 WQLEFMEAVDVHCHSNVNNSNPT-IFKCAISAGRGIGKTTLNAWMMLWLISTRPG--MSIICIANSETQLKNTLWAEVSK  130 (367)
Q Consensus        54 wq~~~l~~~~~~~~~~~~~~~~~-~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~--~~v~~~A~t~~Q~~~~lw~ei~k  130 (367)
                      -|.-+|--+-+.++.    ..|. -.-++|.|+.|+|||-.-+.=|+=.+..+|-  .+++++-||..-+-++ ...+++
T Consensus       163 VQ~aVlp~ll~~~~~----p~~~r~rDIcV~ApTGSGKTLaY~iPIVQ~L~~R~v~~LRavVivPtr~L~~QV-~~~f~~  237 (620)
T KOG0350         163 VQYAVLPSLLEEIRS----PPPSRPRDICVNAPTGSGKTLAYVIPIVQLLSSRPVKRLRAVVIVPTRELALQV-YDTFKR  237 (620)
T ss_pred             HHHHHHHHHHHHHCC----CCCCCCCCEEEECCCCCCCEEEEHHHHHHHHCCCCCCCEEEEEEEEHHHHHHHH-HHHHHH
T ss_conf             588888899986147----999887754775578988456651378999703873405799995479999999-999998


Q ss_pred             HHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC---CEEEEECCCCC-CCCCCCCCCCCCCCCEEEEECCCCCCHH
Q ss_conf             9986231211233332100012333221111345776---12662101354-4556521011358628999754559988
Q gi|254781187|r  131 WLSMLPHRHWFEMQSLSLHPSGWYAELLEQSMGIDSK---HYTITCRTYSE-ERPDTFVGPHNTHGMAVFNDEASGTPDI  206 (367)
Q Consensus       131 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~a~~~~~-~~~ea~~g~h~~~~~l~ivDEAsgI~d~  206 (367)
                      |....-.   .-+...    ...-.+.....+..+..   .-+..+.+.|. .--.+..|+--.+.-++|+|||.-+=+.
T Consensus       238 ~~~~tgL---~V~~~s----gq~sl~~E~~qL~~~~~~~~~DIlVaTPGRLVDHl~~~k~f~Lk~LrfLVIDEADRll~q  310 (620)
T KOG0350         238 LNSGTGL---AVCSLS----GQNSLEDEARQLASDPPECRIDILVATPGRLVDHLNNTKSFDLKHLRFLVIDEADRLLDQ  310 (620)
T ss_pred             HCCCCCE---EEEECC----CCCCHHHHHHHHHCCCCCCCCCEEECCCHHHHHHCCCCCCCCHHHCEEEEECHHHHHHHH
T ss_conf             5668865---988601----454057899997259976543669737268888604898756445357775257789999


Q ss_pred             HHHHHHHH
Q ss_conf             99998987
Q gi|254781187|r  207 INKSILGF  214 (367)
Q Consensus       207 i~e~i~g~  214 (367)
                      .|+-=.++
T Consensus       311 sfQ~Wl~~  318 (620)
T KOG0350         311 SFQEWLDT  318 (620)
T ss_pred             HHHHHHHH
T ss_conf             99988999


No 130
>PRK07399 DNA polymerase III subunit delta'; Validated
Probab=94.69  E-value=0.2  Score=27.69  Aligned_cols=41  Identities=10%  Similarity=0.179  Sum_probs=30.3

Q ss_pred             CCCCCEEEEECCCCCCHHHHHHHHHHHHCCCCCEEEEEEECC
Q ss_conf             358628999754559988999989874069882589998078
Q gi|254781187|r  189 NTHGMAVFNDEASGTPDIINKSILGFFTELNPNRFWIMTSNT  230 (367)
Q Consensus       189 ~~~~~l~ivDEAsgI~d~i~e~i~g~Lt~~~~~~~~i~igNP  230 (367)
                      |.+ -.+|+|+|.........++..+|-.+.+.++.++..+|
T Consensus       123 ~~~-kVvII~~ae~m~~~AaNaLLKtLEEP~~~~fILit~~~  163 (314)
T PRK07399        123 APR-KVVVIEDAETMNEAAANALLKTLEEPGNGTLILIAPSP  163 (314)
T ss_pred             CCC-EEEEECCHHHCCHHHHHHHHHHHCCCCCCEEEEEECCH
T ss_conf             884-79998897871999999999861478785699997993


No 131
>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=94.67  E-value=0.3  Score=26.68  Aligned_cols=81  Identities=22%  Similarity=0.295  Sum_probs=60.9

Q ss_pred             CCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHH
Q ss_conf             88443666842899999998888751245555541124776148867889999999999997089977999715379999
Q gi|254781187|r   42 GKPLEHFSQPHRWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLK  121 (367)
Q Consensus        42 ~~~~~~~~~p~~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~  121 (367)
                      .+|.    .+|.-|...+.+|...+.++.     .|-|+ |.+==|+|||..++..++-.+  .-|-++..+|||+==|+
T Consensus       303 ~LPF----~LT~aQ~r~v~EI~~DL~~~~-----pMnRL-lQGDVGSGKT~VA~la~l~~i--~~GYQ~ALMAPTEiLA~  370 (721)
T TIGR00643       303 SLPF----ELTRAQKRVVKEILQDLKSDV-----PMNRL-LQGDVGSGKTLVAALAMLAAI--ESGYQVALMAPTEILAE  370 (721)
T ss_pred             CCCC----CCCHHHHHHHHHHHHHHCCCC-----CCCCC-CCCCCCCHHHHHHHHHHHHHH--HCCCEEEEECCHHHHHH
T ss_conf             2888----776778999999998614787-----53222-110106638999999999998--46980999177689999


Q ss_pred             HHHHHHHHHHHHHC
Q ss_conf             99999999999862
Q gi|254781187|r  122 NTLWAEVSKWLSML  135 (367)
Q Consensus       122 ~~lw~ei~k~~~~~  135 (367)
                      + -...+.+|+..+
T Consensus       371 Q-Hy~~~~~~l~p~  383 (721)
T TIGR00643       371 Q-HYDSLRNLLAPL  383 (721)
T ss_pred             H-HHHHHHHHHCCC
T ss_conf             9-999999962354


No 132
>COG0470 HolB ATPase involved in DNA replication [DNA replication, recombination, and repair]
Probab=94.63  E-value=0.32  Score=26.47  Aligned_cols=103  Identities=18%  Similarity=0.165  Sum_probs=64.3

Q ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHHCCCC-------------------EEEEECCCHHHHHHHHHHHHHHHHHHCCCCC
Q ss_conf             477614886788999999999999708997-------------------7999715379999999999999998623121
Q gi|254781187|r   79 KCAISAGRGIGKTTLNAWMMLWLISTRPGM-------------------SIICIANSETQLKNTLWAEVSKWLSMLPHRH  139 (367)
Q Consensus        79 ~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~-------------------~v~~~A~t~~Q~~~~lw~ei~k~~~~~~~~~  139 (367)
                      .+.+.+..|+|||+++-+++-++.+..+..                   .++-+.|+.....++.-..+++..+...   
T Consensus        26 alL~~Gp~G~Gktt~a~~lA~~l~~~~~~~~~~~~~~~~~~~~~~~~~~d~lel~~s~~~~~~i~~~~vr~~~~~~~---  102 (325)
T COG0470          26 ALLFYGPPGVGKTTAALALAKELLCENPTGLLPCGHCRSCKLIPAGNHPDFLELNPSDLRKIDIIVEQVRELAEFLS---  102 (325)
T ss_pred             CEEEECCCCCCHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHCCCCCCCEEEECCCCCCCCCCHHHHHHHHHHHCC---
T ss_conf             10037999997899999999996586643345520022444320256886599773213333006999999998604---


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCEEEEECCCCCCHHHHHHHHHHHHCCC
Q ss_conf             12333321000123332211113457761266210135445565210113586289997545599889999898740698
Q gi|254781187|r  140 WFEMQSLSLHPSGWYAELLEQSMGIDSKHYTITCRTYSEERPDTFVGPHNTHGMAVFNDEASGTPDIINKSILGFFTELN  219 (367)
Q Consensus       140 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~ea~~g~h~~~~~l~ivDEAsgI~d~i~e~i~g~Lt~~~  219 (367)
                                                                  ..+..+. .-++|+|||..+....-.+++.++-.+.
T Consensus       103 --------------------------------------------~~~~~~~-~kviiidead~mt~~A~nallk~lEep~  137 (325)
T COG0470         103 --------------------------------------------ESPLEGG-YKVVIIDEADKLTEDAANALLKTLEEPP  137 (325)
T ss_pred             --------------------------------------------CCCCCCC-CEEEEEECCCCCCHHHHHHHHHHCCCCC
T ss_conf             --------------------------------------------4656677-2699973203269888876754332488


Q ss_pred             CCEEEEEEEC
Q ss_conf             8258999807
Q gi|254781187|r  220 PNRFWIMTSN  229 (367)
Q Consensus       220 ~~~~~i~igN  229 (367)
                      .+...+++.|
T Consensus       138 ~~~~~il~~n  147 (325)
T COG0470         138 KNTRFILITN  147 (325)
T ss_pred             CCEEEEEEEC
T ss_conf             8716999749


No 133
>PRK13342 recombination factor protein RarA; Reviewed
Probab=94.62  E-value=0.32  Score=26.46  Aligned_cols=112  Identities=12%  Similarity=0.117  Sum_probs=64.4

Q ss_pred             EEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             24776148867889999999999997089977999715379999999999999998623121123333210001233322
Q gi|254781187|r   78 FKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLKNTLWAEVSKWLSMLPHRHWFEMQSLSLHPSGWYAEL  157 (367)
Q Consensus        78 ~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~~~lw~ei~k~~~~~~~~~~~~~~~~~~~~~~~~~~~  157 (367)
                      +.+..-++.|+|||+++-.++--.     +...+-...+.+.+++     +++.++....                    
T Consensus        38 ~s~Il~GPPG~GKTTlA~iiA~~~-----~~~f~~lnA~~~gv~d-----ir~ii~~a~~--------------------   87 (417)
T PRK13342         38 SSMILWGPPGTGKTTLARIIAGAT-----DAEFEALSAVTSGVKD-----LREVIEEAKQ--------------------   87 (417)
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHH-----CCCEEEEECCCCCHHH-----HHHHHHHHHH--------------------
T ss_conf             759988969998999999999986-----8988996141038899-----9999999886--------------------


Q ss_pred             CCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCEEEEECCCCCCHHHHHHHHHHHHCCCCCEEEEEEECCCCCCCHH
Q ss_conf             11113457761266210135445565210113586289997545599889999898740698825899980789998768
Q gi|254781187|r  158 LEQSMGIDSKHYTITCRTYSEERPDTFVGPHNTHGMAVFNDEASGTPDIINKSILGFFTELNPNRFWIMTSNTRRLNGWF  237 (367)
Q Consensus       158 ~~~~~~~~~~~~~~~a~~~~~~~~ea~~g~h~~~~~l~ivDEAsgI~d~i~e~i~g~Lt~~~~~~~~i~igNP~r~~g~F  237 (367)
                                               ...   +.. .++++||..-..-...+++++.+-.+  .  .++||.+|.  |++
T Consensus        88 -------------------------~~~---~~~-tilfiDEIHRfnK~QQD~LLp~vE~g--~--iiLIgATTE--NP~  132 (417)
T PRK13342         88 -------------------------SRL---GRR-TILFIDEIHRFNKAQQDALLPHVEDG--T--ITLIGATTE--NPS  132 (417)
T ss_pred             -------------------------HHC---CCC-EEEEEECHHHCCHHHHHHHHHHHHCC--C--EEEEEECCC--CCH
T ss_conf             -------------------------314---896-59999782005889999998751126--5--699974157--922


Q ss_pred             HHHHHCCCCCEEEEEEC
Q ss_conf             87541122350467523
Q gi|254781187|r  238 YDIFNIPLEDWKRYQID  254 (367)
Q Consensus       238 ye~~~~~~~~w~~~~~~  254 (367)
                      +..-..-.++-.++.+.
T Consensus       133 f~in~aLlSRc~vf~l~  149 (417)
T PRK13342        133 FEVNPALLSRAQVFELK  149 (417)
T ss_pred             HHCCHHHHHHHHHEECC
T ss_conf             53489898565700205


No 134
>CHL00095 clpC Clp protease ATP binding subunit
Probab=94.56  E-value=0.33  Score=26.37  Aligned_cols=127  Identities=20%  Similarity=0.178  Sum_probs=62.9

Q ss_pred             HHHHHHHHHHHHHHCC-CCCCCCCEE--EEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHHHH
Q ss_conf             9999999888875124-555554112--4776148867889999999999997089977999715379999999999999
Q gi|254781187|r   54 WQLEFMEAVDVHCHSN-VNNSNPTIF--KCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLKNTLWAEVSK  130 (367)
Q Consensus        54 wq~~~l~~~~~~~~~~-~~~~~~~~~--~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~~~lw~ei~k  130 (367)
                      .|.++++.|++.+++. ..-..|..+  -..-+++-|+|||.++-.++-.+.-......-+=++.....      ..+.+
T Consensus       513 GQd~AI~~vs~ai~rsraGl~~~~rPigsFlf~GPTGvGKTElAK~LA~~LFg~e~~liR~DMSEy~E~------hsvsr  586 (823)
T CHL00095        513 GQDEAVVAVSKAIRRARVGLKNPNRPIASFIFCGPTGVGKTELTKALASYFFGSEEAMIRLDMSEYMEK------HTVSK  586 (823)
T ss_pred             CCHHHHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHCCCCCCEEEECCCCCCCC------CCHHH
T ss_conf             769999999999999970899899974689987899887799999999997478202588535101554------20767


Q ss_pred             HHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCEEEEECCCCCCHHHHHH
Q ss_conf             99862312112333321000123332211113457761266210135445565210113586289997545599889999
Q gi|254781187|r  131 WLSMLPHRHWFEMQSLSLHPSGWYAELLEQSMGIDSKHYTITCRTYSEERPDTFVGPHNTHGMAVFNDEASGTPDIINKS  210 (367)
Q Consensus       131 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~ea~~g~h~~~~~l~ivDEAsgI~d~i~e~  210 (367)
                      .+...|                 .      +.+++.|..          -.|+..  +..+ ..+++||-..-.+++|+.
T Consensus       587 LIGaPP-----------------G------YVGy~eGG~----------LTeaVr--r~Py-sVvLfDEIEKAHpdV~ni  630 (823)
T CHL00095        587 LIGSPP-----------------G------YVGYNEGGQ----------LTEAVR--KKPY-TVVLFDEIEKAHPDIFNL  630 (823)
T ss_pred             HCCCCC-----------------C------CCCCCCCCC----------HHHHHH--CCCC-EEEEECHHHHCCHHHHHH
T ss_conf             458998-----------------7------667787882----------019887--1998-699862131138899998


Q ss_pred             HH-----HHHHCCCCCE
Q ss_conf             89-----8740698825
Q gi|254781187|r  211 IL-----GFFTELNPNR  222 (367)
Q Consensus       211 i~-----g~Lt~~~~~~  222 (367)
                      +.     |.||++.++.
T Consensus       631 lLQvlDdG~LtD~~Gr~  647 (823)
T CHL00095        631 LLQILDDGRLTDSKGRT  647 (823)
T ss_pred             HHHHCCCCCCCCCCCCE
T ss_conf             87651688434899998


No 135
>KOG2170 consensus
Probab=94.51  E-value=0.34  Score=26.31  Aligned_cols=126  Identities=13%  Similarity=0.089  Sum_probs=70.8

Q ss_pred             HHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEE--EEE----CCCHHHHHHHHH
Q ss_conf             28999999988887512455555411247761488678899999999999970899779--997----153799999999
Q gi|254781187|r   52 HRWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSI--ICI----ANSETQLKNTLW  125 (367)
Q Consensus        52 ~~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v--~~~----A~t~~Q~~~~lw  125 (367)
                      ..-+.-+++.|-.|..+.. ...|-  -+|.-++-|+||++.+-.++--+..-.-.+..  ..+    =|..+-+. -.-
T Consensus        88 Hla~~~Vv~alk~~~~n~~-p~KPL--vLSfHG~tGTGKN~Va~iiA~n~~~~Gl~S~~V~~fvat~hFP~~~~ie-~Yk  163 (344)
T KOG2170          88 HLAKQLVVNALKSHWANPN-PRKPL--VLSFHGWTGTGKNYVAEIIAENLYRGGLRSPFVHHFVATLHFPHASKIE-DYK  163 (344)
T ss_pred             HHHHHHHHHHHHHHHCCCC-CCCCE--EEEECCCCCCCHHHHHHHHHHHHHHCCCCCHHHHHHHHHCCCCCHHHHH-HHH
T ss_conf             8799999999999862899-99875--8983089987564899999999875112562688765541599767899-999


Q ss_pred             HHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCEEEEECCCCCCH
Q ss_conf             99999998623121123333210001233322111134577612662101354455652101135862899975455998
Q gi|254781187|r  126 AEVSKWLSMLPHRHWFEMQSLSLHPSGWYAELLEQSMGIDSKHYTITCRTYSEERPDTFVGPHNTHGMAVFNDEASGTPD  205 (367)
Q Consensus       126 ~ei~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~ea~~g~h~~~~~l~ivDEAsgI~d  205 (367)
                      .++++|++.                                                +.+   +-...++|+||+...|.
T Consensus       164 ~eL~~~v~~------------------------------------------------~v~---~C~rslFIFDE~DKmp~  192 (344)
T KOG2170         164 EELKNRVRG------------------------------------------------TVQ---ACQRSLFIFDEVDKLPP  192 (344)
T ss_pred             HHHHHHHHH------------------------------------------------HHH---HCCCCEEEECHHHHCCH
T ss_conf             999999999------------------------------------------------998---55775487310543587


Q ss_pred             HHHHHHHHHHH-------CCCCCEEEEEEECCCC
Q ss_conf             89999898740-------6988258999807899
Q gi|254781187|r  206 IINKSILGFFT-------ELNPNRFWIMTSNTRR  232 (367)
Q Consensus       206 ~i~e~i~g~Lt-------~~~~~~~~i~igNP~r  232 (367)
                      ...++|.|.|-       ....+.+.+..||..+
T Consensus       193 gLld~lkpfLdyyp~v~gv~frkaIFIfLSN~gg  226 (344)
T KOG2170         193 GLLDVLKPFLDYYPQVSGVDFRKAIFIFLSNAGG  226 (344)
T ss_pred             HHHHHHHHHHCCCCCCCCCCCCCEEEEEECCCCC
T ss_conf             6999876663046321355455148999717861


No 136
>PRK06964 DNA polymerase III subunit delta'; Validated
Probab=94.44  E-value=0.35  Score=26.21  Aligned_cols=37  Identities=16%  Similarity=0.152  Sum_probs=30.2

Q ss_pred             CEEEEECCCCCCHHHHHHHHHHHHCCCCCEEEEEEEC
Q ss_conf             2899975455998899998987406988258999807
Q gi|254781187|r  193 MAVFNDEASGTPDIINKSILGFFTELNPNRFWIMTSN  229 (367)
Q Consensus       193 ~l~ivDEAsgI~d~i~e~i~g~Lt~~~~~~~~i~igN  229 (367)
                      -.+|+|.|.......-.++..+|-.+...++.+++++
T Consensus       134 kVviI~~Ae~mn~~aaNalLK~LEEPp~~~~~iL~~~  170 (342)
T PRK06964        134 RVVVLYPAEALNVAAANALLKTLEEPPPGVVFLLVSA  170 (342)
T ss_pred             EEEEECCHHHHCHHHHHHHHHHHCCCCCCEEEEEEEC
T ss_conf             4999827787389999999997237987848999869


No 137
>KOG0389 consensus
Probab=94.43  E-value=0.19  Score=27.89  Aligned_cols=144  Identities=14%  Similarity=0.102  Sum_probs=79.0

Q ss_pred             EEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             76148867889999999999997089977999715379999999999999998623121123333210001233322111
Q gi|254781187|r   81 AISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLKNTLWAEVSKWLSMLPHRHWFEMQSLSLHPSGWYAELLEQ  160 (367)
Q Consensus        81 ~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~~~lw~ei~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  160 (367)
                      ..+--=|.|||.=+-++..++.--.-+.--+|+.|+. .+. -+-+|+.||.-.+.......-+..+..++.....   .
T Consensus       422 ILADEMGLGKTiQvIaFlayLkq~g~~gpHLVVvPsS-Tle-NWlrEf~kwCPsl~Ve~YyGSq~ER~~lR~~i~~---~  496 (941)
T KOG0389         422 ILADEMGLGKTIQVIAFLAYLKQIGNPGPHLVVVPSS-TLE-NWLREFAKWCPSLKVEPYYGSQDERRELRERIKK---N  496 (941)
T ss_pred             EEHHHCCCCCHHHHHHHHHHHHHCCCCCCCEEEECCH-HHH-HHHHHHHHHCCCEEEEECCCCHHHHHHHHHHHHC---C
T ss_conf             5322205763348999999999729999837992031-688-8999999759752877415768999999999861---6


Q ss_pred             CCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCEEEEECCCCCCHHHHHHHHHHHHCCCCCEEEEEEECCCCC
Q ss_conf             1345776126621013544556521011358628999754559988999989874069882589998078999
Q gi|254781187|r  161 SMGIDSKHYTITCRTYSEERPDTFVGPHNTHGMAVFNDEASGTPDIINKSILGFFTELNPNRFWIMTSNTRRL  233 (367)
Q Consensus       161 ~~~~~~~~~~~~a~~~~~~~~ea~~g~h~~~~~l~ivDEAsgI~d~i~e~i~g~Lt~~~~~~~~i~igNP~r~  233 (367)
                      ...+   ....+.-..-..+.+.-.-++..++.++|.||+....+..-+-....|+-..+..+ +++|+|--+
T Consensus       497 ~~~y---dVllTTY~la~~~kdDRsflk~~~~n~viyDEgHmLKN~~SeRy~~LM~I~An~Rl-LLTGTPLQN  565 (941)
T KOG0389         497 KDDY---DVLLTTYNLAASSKDDRSFLKNQKFNYVIYDEGHMLKNRTSERYKHLMSINANFRL-LLTGTPLQN  565 (941)
T ss_pred             CCCC---CEEEEEEECCCCCHHHHHHHHHCCCCEEEECCHHHHHCCCHHHHHHHCCCCCCCEE-EEECCCCCC
T ss_conf             8885---28998721103886778999866666799613265421334988875064655358-851874201


No 138
>COG4889 Predicted helicase [General function prediction only]
Probab=94.34  E-value=0.37  Score=26.07  Aligned_cols=91  Identities=23%  Similarity=0.137  Sum_probs=60.1

Q ss_pred             CCCCCHHHHHHHHHC-CCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHH
Q ss_conf             012598888554301-4668884436668428999999988887512455555411247761488678899999999999
Q gi|254781187|r   23 ECVLSFKNFVMRFFP-WGIKGKPLEHFSQPHRWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWL  101 (367)
Q Consensus        23 ~~~~~~~~f~~~~~~-w~~~~~~~~~~~~p~~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~  101 (367)
                      ++..+|...-.+ .| =-+.++||.....||+.|-.+..+.-+|.+.|.      +-++..+  -|+|||+.+--+.--.
T Consensus       134 ei~es~IDW~~f-~p~e~~~nl~l~~~kk~R~hQq~Aid~a~~~F~~n~------RGkLIMA--cGTGKTfTsLkisEal  204 (1518)
T COG4889         134 EIAESPIDWDIF-DPTELQDNLPLKKPKKPRPHQQTAIDAAKEGFSDND------RGKLIMA--CGTGKTFTSLKISEAL  204 (1518)
T ss_pred             HHHCCCCCHHHC-CCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHCCCCC------CCCEEEE--CCCCCCCHHHHHHHHH
T ss_conf             873288775434-953266565647878998367899999986255166------7758983--3788621378899998


Q ss_pred             HHHCCCCEEEEECCCHHHHHHHHHHH
Q ss_conf             97089977999715379999999999
Q gi|254781187|r  102 ISTRPGMSIICIANSETQLKNTLWAE  127 (367)
Q Consensus       102 ~~~~~~~~v~~~A~t~~Q~~~~lw~e  127 (367)
                      +.    .+++..+|+.+-+.+.+ +|
T Consensus       205 a~----~~iL~LvPSIsLLsQTl-re  225 (1518)
T COG4889         205 AA----ARILFLVPSISLLSQTL-RE  225 (1518)
T ss_pred             HH----HHEEEECCHHHHHHHHH-HH
T ss_conf             64----02365435189999999-98


No 139
>PRK12723 flagellar biosynthesis regulator FlhF; Provisional
Probab=94.28  E-value=0.33  Score=26.36  Aligned_cols=73  Identities=10%  Similarity=-0.060  Sum_probs=42.4

Q ss_pred             CCCHHHHHHHHHHHHHHHHCCCCCCCCCEEE-EEEECCCCCCHHHHHHHHHHHHHHHCCCC---EEEEECCCHHHHH
Q ss_conf             6842899999998888751245555541124-77614886788999999999999708997---7999715379999
Q gi|254781187|r   49 SQPHRWQLEFMEAVDVHCHSNVNNSNPTIFK-CAISAGRGIGKTTLNAWMMLWLISTRPGM---SIICIANSETQLK  121 (367)
Q Consensus        49 ~~p~~wq~~~l~~~~~~~~~~~~~~~~~~~~-~~v~sgrg~GKS~~~a~~~lw~~~~~~~~---~v~~~A~t~~Q~~  121 (367)
                      +..++-+..++..+.+.+..........-.| ++..++.|+|||+.+|=++..+.+.....   ..++|+.|++-+.
T Consensus       145 ~~~~~v~~~l~~~i~~~i~~~~~~~~~~k~~vi~lVGPTGvGKTTTiAKLAa~~~l~~~~k~~~V~lit~DtyRigA  221 (388)
T PRK12723        145 DDYDKVRDSVIIYIAKTIKCSGSIIDNLKKRIFILVGPTGVGKTTTIAKLAAIYGINSDDKSLNIKIITIDNYRIGA  221 (388)
T ss_pred             CCHHHHHHHHHHHHHHHHCCCCCCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCCCCEEEEEECCCCHHH
T ss_conf             40879999999999976223666533557628999899887578799999999998626767737999807875889


No 140
>PRK07132 DNA polymerase III subunit delta'; Validated
Probab=94.26  E-value=0.39  Score=25.96  Aligned_cols=119  Identities=10%  Similarity=0.051  Sum_probs=66.3

Q ss_pred             HHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECC--------CHHHHHHHHHHH
Q ss_conf             999998888751245555541124776148867889999999999997089977999715--------379999999999
Q gi|254781187|r   56 LEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIAN--------SETQLKNTLWAE  127 (367)
Q Consensus        56 ~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~--------t~~Q~~~~lw~e  127 (367)
                      +.+.+.+..-++++.. .|.+    ...+.||+||+.++..++-...|+..+....+..+        ....++.   ..
T Consensus         4 e~iv~~L~nai~~~kl-sHAY----LF~G~~G~Gk~~~a~~~a~~l~~~~~~~~~~~~~~~~~~~id~~~~~i~~---~~   75 (303)
T PRK07132          4 NNIIKSLDNLAKQNKI-SHSF----LLKSNYNNDLDESILYFLNKFNNLQSLNLNLEELPYNIFLFDIFDEDLSK---EE   75 (303)
T ss_pred             HHHHHHHHHHHHCCCC-CEEE----EEECCCCCCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCEEECCCCCCHHH---HH
T ss_conf             3899999999984997-6168----86789986799999999999729987888754565323041332220016---88


Q ss_pred             HHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCEEEEECCCCCCHHH
Q ss_conf             99999862312112333321000123332211113457761266210135445565210113586289997545599889
Q gi|254781187|r  128 VSKWLSMLPHRHWFEMQSLSLHPSGWYAELLEQSMGIDSKHYTITCRTYSEERPDTFVGPHNTHGMAVFNDEASGTPDII  207 (367)
Q Consensus       128 i~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~ea~~g~h~~~~~l~ivDEAsgI~d~i  207 (367)
                      +...++.                                         .....++  +   |.+ -.+|+|||.......
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             HHHHHHHHHCCCCCEEEEEEEC
Q ss_conf             9998987406988258999807
Q gi|254781187|r  208 NKSILGFFTELNPNRFWIMTSN  229 (367)
Q Consensus       208 ~e~i~g~Lt~~~~~~~~i~igN  229 (367)
                      +.+++-+|-.+....+.+++.+
T Consensus       109 ~NaLLKtLEEPp~~~~fil~t~  130 (303)
T PRK07132        109 LNALLKTIEEPSKNTYFLLTTK  130 (303)
T ss_pred             HHHHHHHCCCCCCCEEEEEEEC
T ss_conf             9999987038986848999728


No 141
>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=94.21  E-value=0.39  Score=25.91  Aligned_cols=145  Identities=19%  Similarity=0.192  Sum_probs=74.7

Q ss_pred             EEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             24776148867889999999999997089977999715379999999999999998623121123333210001233322
Q gi|254781187|r   78 FKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLKNTLWAEVSKWLSMLPHRHWFEMQSLSLHPSGWYAEL  157 (367)
Q Consensus        78 ~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~~~lw~ei~k~~~~~~~~~~~~~~~~~~~~~~~~~~~  157 (367)
                      .+..| +|||+|||+.+--.++--++.. |.+.+...-...-++..-=.-........|+.. |.            ...
T Consensus        19 lnfvI-G~RGiGKTya~k~~~ikd~i~k-GeqFiYLRr~k~El~k~~n~~F~di~~~fpn~e-f~------------Vkg   83 (333)
T pfam05894        19 LNFVI-GARGIGKTYALKERVIKDFIKK-GEQFIYLRRYKTELKKLANEFFNDVAHEFPNNE-FY------------VKG   83 (333)
T ss_pred             EEEEE-ECCCCCHHHHHHHHHHHHHHHC-CCEEEEEEECCHHHHHHHHHHHHHHHHHCCCCE-EE------------EEC
T ss_conf             79998-2465540246778889999862-967999991206888777775551665378980-79------------975


Q ss_pred             CCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCEEEEECC-------CCCCHHHHH---HHHHHHHCCCCCEEEEEE
Q ss_conf             1111345776126621013544556521011358628999754-------559988999---989874069882589998
Q gi|254781187|r  158 LEQSMGIDSKHYTITCRTYSEERPDTFVGPHNTHGMAVFNDEA-------SGTPDIINK---SILGFFTELNPNRFWIMT  227 (367)
Q Consensus       158 ~~~~~~~~~~~~~~~a~~~~~~~~ea~~g~h~~~~~l~ivDEA-------sgI~d~i~e---~i~g~Lt~~~~~~~~i~i  227 (367)
                      ++..+...--.+++.-.+|     .+..+..=.+..-+++||.       ..+|+++-.   .+.-..+. .....+++.
T Consensus        84 nki~~~~k~igy~i~LS~~-----q~lKS~~Yp~V~~I~fDEfi~ek~~~~Y~pNev~~llnl~~tV~R~-Re~vr~~~l  157 (333)
T pfam05894        84 NKFYIKGELIGYAIPLSNW-----QALKSLAYPNVSTIFFDEFVREKDYGSYDPNEVRNFLNLMDTVFRA-RERVRCICL  157 (333)
T ss_pred             CEEEECCEEEEEEEEHHHH-----HHHHCCCCCCEEEEEEEEEEEECCCCCCCCHHHHHHHHHHHHHHHH-CCCEEEEEE
T ss_conf             4899878289999863245-----5631347985589983511244544578943899999999998750-377389996


Q ss_pred             ECCCCCCCHHHHHHHC
Q ss_conf             0789998768875411
Q gi|254781187|r  228 SNTRRLNGWFYDIFNI  243 (367)
Q Consensus       228 gNP~r~~g~Fye~~~~  243 (367)
                      ||--...|+.+..|+-
T Consensus       158 sNAv~i~NPYF~~f~~  173 (333)
T pfam05894       158 SNAVSIVNPYFLLFHI  173 (333)
T ss_pred             CCHHHCCCHHHEEEEC
T ss_conf             4704204725515511


No 142
>PRK07276 DNA polymerase III subunit delta'; Validated
Probab=94.15  E-value=0.41  Score=25.83  Aligned_cols=136  Identities=11%  Similarity=0.099  Sum_probs=69.7

Q ss_pred             HHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECC-CHHHHHHHHHHHHHHH
Q ss_conf             899999998888751245555541124776148867889999999999997089977999715-3799999999999999
Q gi|254781187|r   53 RWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIAN-SETQLKNTLWAEVSKW  131 (367)
Q Consensus        53 ~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~-t~~Q~~~~lw~ei~k~  131 (367)
                      +.|-++...+..-++++.. .|.+.|     +| |+||..++-+++-+.+|..+....-|-.- .-+++..         
T Consensus         5 ~~Qp~i~~~l~~~i~~~rl-~HAyLf-----~G-~~Gk~~~A~~~A~~l~C~~~~~~~pCg~C~~C~~i~~---------   68 (290)
T PRK07276          5 QKQPKLFQRFQTILEQDRL-NHAYLF-----SG-DFASFEMALFLAQSLFCEQKEDVLPCGHCRSCRLIEQ---------   68 (290)
T ss_pred             HHHHHHHHHHHHHHHCCCC-CEEEEC-----CC-CCCHHHHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHC---------
T ss_conf             8789999999999984996-505421-----69-8687999999999981899999898988999999876---------


Q ss_pred             HHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCEEEEECCCCCCHHHHHHH
Q ss_conf             98623121123333210001233322111134577612662101354455652101135862899975455998899998
Q gi|254781187|r  132 LSMLPHRHWFEMQSLSLHPSGWYAELLEQSMGIDSKHYTITCRTYSEERPDTFVGPHNTHGMAVFNDEASGTPDIINKSI  211 (367)
Q Consensus       132 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~ea~~g~h~~~~~l~ivDEAsgI~d~i~e~i  211 (367)
                       ...|+-+....+.              ..++.+.  ..-...      .-+..+..|.+ -.+|+|+|.........++
T Consensus        69 -~~hpDv~~i~~~~--------------~~I~vd~--IR~l~~------~~~~~~~~g~~-KV~II~~Ad~mt~~AaNaL  124 (290)
T PRK07276         69 -GDFSDVTVIEPQG--------------QVIKTDT--IRELTA------NFSQSGYEGKR-QVFIIKDADKMHVNAANSL  124 (290)
T ss_pred             -CCCCCCEEECCCC--------------CCCCHHH--HHHHHH------HHHHCCCCCCE-EEEEECCHHHCCHHHHHHH
T ss_conf             -9998713771677--------------7576889--999999------98445613782-7999776565299999999


Q ss_pred             HHHHHCCCCCEEEEEEE
Q ss_conf             98740698825899980
Q gi|254781187|r  212 LGFFTELNPNRFWIMTS  228 (367)
Q Consensus       212 ~g~Lt~~~~~~~~i~ig  228 (367)
                      ..+|-.+....+++++.
T Consensus       125 LK~LEEPp~~t~~iLlt  141 (290)
T PRK07276        125 LKVIEEPQSEIYIFLLT  141 (290)
T ss_pred             HHHHCCCCCCCEEEEEE
T ss_conf             99703898883799887


No 143
>PRK05917 DNA polymerase III subunit delta'; Validated
Probab=94.14  E-value=0.41  Score=25.83  Aligned_cols=166  Identities=10%  Similarity=-0.008  Sum_probs=80.8

Q ss_pred             HHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHHHHH
Q ss_conf             28999999988887512455555411247761488678899999999999970899779997153799999999999999
Q gi|254781187|r   52 HRWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLKNTLWAEVSKW  131 (367)
Q Consensus        52 ~~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~~~lw~ei~k~  131 (367)
                      ..||.     +...++++.. .|    .....+..|+||+.++-.++-..+|...+..       ..+        +.. 
T Consensus         4 ~~We~-----L~~~i~~~Rl-~H----AyLf~Gp~G~GK~~~A~~~A~~LLc~~~p~~-------~~~--------i~~-   57 (290)
T PRK05917          4 AAWEA-----LLQRVRDQKV-PS----AILLHGQDLSNLSQYAYELASLILLESSPEA-------QYK--------ISQ-   57 (290)
T ss_pred             HHHHH-----HHHHHHCCCC-CE----EEEEECCCCCCHHHHHHHHHHHHHCCCCCCH-------HHH--------HHH-
T ss_conf             49999-----9999983996-60----6876899986599999999999857899616-------889--------874-


Q ss_pred             HHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCEEEEECCCCCCHHHHHHH
Q ss_conf             98623121123333210001233322111134577612662101354455652101135862899975455998899998
Q gi|254781187|r  132 LSMLPHRHWFEMQSLSLHPSGWYAELLEQSMGIDSKHYTITCRTYSEERPDTFVGPHNTHGMAVFNDEASGTPDIINKSI  211 (367)
Q Consensus       132 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~ea~~g~h~~~~~l~ivDEAsgI~d~i~e~i  211 (367)
                       ..-|+-+++......        ..    .+.+.      .+....  --++....|.+ -.+|+|||.........++
T Consensus        58 -~~HPD~~~i~pe~k~--------~~----~~Id~------iR~l~~--~i~~~p~~g~~-KV~IId~Ad~Mn~~AaNAL  115 (290)
T PRK05917         58 -KIHPDIHEFFPEGKG--------RL----HSIET------PRAIKK--QIWIHPYEANY-KIYIIHEADRMTLDAISAF  115 (290)
T ss_pred             -CCCCCEEEECCCCCC--------CC----CCHHH------HHHHHH--HHCCCCCCCCC-EEEEECCHHHHCHHHHHHH
T ss_conf             -689985996157778--------87----86789------999999--96418646882-6999756776389999999


Q ss_pred             HHHHHCCCCCEEEEEEECCCCCCCHHHHHHHCCCCCEEEEEECCCCCCCCCHHHHHHHHH
Q ss_conf             987406988258999807899987688754112235046752333288889889999996
Q gi|254781187|r  212 LGFFTELNPNRFWIMTSNTRRLNGWFYDIFNIPLEDWKRYQIDTRTVEGIDSGFHEGIIS  271 (367)
Q Consensus       212 ~g~Lt~~~~~~~~i~igNP~r~~g~Fye~~~~~~~~w~~~~~~~~d~p~~~~~~i~~~~~  271 (367)
                      ..+|-.+...++.+++.+-+  .    ..-.-=+.+=..++++-.+-...+++.++.+.+
T Consensus       116 LKtLEEPP~~tvfILit~~~--~----~lLpTI~SRCQ~I~i~~~e~~~i~~e~~~~l~~  169 (290)
T PRK05917        116 LKVLEDPPKHSVIILTSAKP--Q----RLPPTIRSRSLSIHIPGEEKTLPSKEDIAYLIR  169 (290)
T ss_pred             HHHHCCCCCCEEEEEEECCH--H----HCCHHHHHCCCEEECCCCCCCCCCHHHHHHHHH
T ss_conf             99734798785999986992--5----482377633511677762013478899999999


No 144
>KOG0342 consensus
Probab=94.08  E-value=0.42  Score=25.74  Aligned_cols=168  Identities=13%  Similarity=0.061  Sum_probs=85.9

Q ss_pred             CCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHH---H--CCCCEEEEECCCHHH
Q ss_conf             43666842899999998888751245555541124776148867889999999999997---0--899779997153799
Q gi|254781187|r   45 LEHFSQPHRWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLIS---T--RPGMSIICIANSETQ  119 (367)
Q Consensus        45 ~~~~~~p~~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~---~--~~~~~v~~~A~t~~Q  119 (367)
                      -++|..=+.-|.+.+..+-+..            .+.++|-.|+|||...-.-++-++.   +  +++..+++++||..-
T Consensus        99 ~~GF~~MT~VQ~~ti~pll~gk------------Dvl~~AKTGtGKTlAFLiPaie~l~k~~~~~r~~~~vlIi~PTREL  166 (543)
T KOG0342          99 EMGFETMTPVQQKTIPPLLEGK------------DVLAAAKTGTGKTLAFLLPAIELLRKLKFKPRNGTGVLIICPTREL  166 (543)
T ss_pred             HCCCCCCHHHHHHHCCCCCCCC------------CCEEEECCCCCCEEEEHHHHHHHHHHCCCCCCCCEEEEEECCCHHH
T ss_conf             3585300288874267667984------------3124512688741010468999998536577787148996562899


Q ss_pred             HHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCC-CCCCCCCCCCCCCCCEEEEE
Q ss_conf             99999999999998623121123333210001233322111134577612662101354-45565210113586289997
Q gi|254781187|r  120 LKNTLWAEVSKWLSMLPHRHWFEMQSLSLHPSGWYAELLEQSMGIDSKHYTITCRTYSE-ERPDTFVGPHNTHGMAVFND  198 (367)
Q Consensus       120 ~~~~lw~ei~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~-~~~ea~~g~h~~~~~l~ivD  198 (367)
                      +.++ ++|+++.+.-.+. .+..     +-+-+........  +...+.....|.+-+. +--++-.|+-..+.-++|+|
T Consensus       167 A~Q~-~~eak~Ll~~h~~-~~v~-----~viGG~~~~~e~~--kl~k~~niliATPGRLlDHlqNt~~f~~r~~k~lvlD  237 (543)
T KOG0342         167 AMQI-FAEAKELLKYHES-ITVG-----IVIGGNNFSVEAD--KLVKGCNILIATPGRLLDHLQNTSGFLFRNLKCLVLD  237 (543)
T ss_pred             HHHH-HHHHHHHHHHCCC-CCEE-----EEECCCCCHHHHH--HHHCCCCEEEECCCHHHHHHHCCCCCHHHCCCEEEEE
T ss_conf             9989-9999999972767-7347-----8767741058999--7515552788678417767655784122122035750


Q ss_pred             CCCCCCHHHH----HHHHHHHHCCCCCEEEEEEECCCCCC
Q ss_conf             5455998899----99898740698825899980789998
Q gi|254781187|r  199 EASGTPDIIN----KSILGFFTELNPNRFWIMTSNTRRLN  234 (367)
Q Consensus       199 EAsgI~d~i~----e~i~g~Lt~~~~~~~~i~igNP~r~~  234 (367)
                      ||.-+-|.-|    +-|...+.. ..+.+++...-|++-.
T Consensus       238 EADrlLd~GF~~di~~Ii~~lpk-~rqt~LFSAT~~~kV~  276 (543)
T KOG0342         238 EADRLLDIGFEEDVEQIIKILPK-QRQTLLFSATQPSKVK  276 (543)
T ss_pred             CCHHHHHCCCHHHHHHHHHHCCC-CCCEEEEECCCCHHHH
T ss_conf             20356652518889999875235-5304676478968899


No 145
>PRK07940 DNA polymerase III subunit delta'; Validated
Probab=93.98  E-value=0.44  Score=25.63  Aligned_cols=138  Identities=15%  Similarity=0.190  Sum_probs=72.1

Q ss_pred             HHHHHHHHHHHHHCCC-----------CCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHH
Q ss_conf             9999998888751245-----------55554112477614886788999999999999708997799971537999999
Q gi|254781187|r   55 QLEFMEAVDVHCHSNV-----------NNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLKNT  123 (367)
Q Consensus        55 q~~~l~~~~~~~~~~~-----------~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~~~  123 (367)
                      |+.+.+.+..-++.+.           ...|.+    ...+++|+||+.++-+++--++|.+++..- |-  .-.    .
T Consensus        10 Qe~v~~~L~~A~~~~R~~~~~~~~~~~~~~HAy----LF~Gp~G~Gk~~~A~~~A~~l~C~~~~~~~-cg--~C~----~   78 (395)
T PRK07940         10 QDAVVAELRAAARAARADSAHSAAAGSGMTHAW----LFTGPPGSGRSNAARAFAAALQCTDPGVPG-CG--ECR----A   78 (395)
T ss_pred             CHHHHHHHHHHHHHCCCCCCCCCCCCCCCCEEE----EEECCCCCCHHHHHHHHHHHHCCCCCCCCC-CC--CCH----H
T ss_conf             299999999999836343443333468766037----636899878899999999996699999999-98--787----8


Q ss_pred             HHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCEEEEECCCCC
Q ss_conf             99999999986231211233332100012333221111345776126621013544556521011358628999754559
Q gi|254781187|r  124 LWAEVSKWLSMLPHRHWFEMQSLSLHPSGWYAELLEQSMGIDSKHYTITCRTYSEERPDTFVGPHNTHGMAVFNDEASGT  203 (367)
Q Consensus       124 lw~ei~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~ea~~g~h~~~~~l~ivDEAsgI  203 (367)
                      + ..+.  ....|+-++.......              ++.+.      .+-..  ..-++....|.+. .+|+|||...
T Consensus        79 C-~~i~--~g~hpDv~~i~p~~~~--------------i~id~------iR~l~--~~~~~~p~~~~~k-v~ii~~a~~m  132 (395)
T PRK07940         79 C-RTVL--AGTHPDVRVVVPEGLS--------------IGVDE------VREIV--QIAARRPTTGRWR-IVVIEDADRL  132 (395)
T ss_pred             H-HHHH--CCCCCCEEEEECCCCC--------------CCHHH------HHHHH--HHHHHCCCCCCCE-EEEEECHHHH
T ss_conf             9-9987--6899871898268776--------------88999------99999--9985273037955-9998077874


Q ss_pred             CHHHHHHHHHHHHCCCCCEEEEEEEC
Q ss_conf             98899998987406988258999807
Q gi|254781187|r  204 PDIINKSILGFFTELNPNRFWIMTSN  229 (367)
Q Consensus       204 ~d~i~e~i~g~Lt~~~~~~~~i~igN  229 (367)
                      .....+++..+|-.+-...++++..+
T Consensus       133 ~~~a~NalLKtLEEPp~~~~fiL~t~  158 (395)
T PRK07940        133 TERAANALLKAVEEPPPRTVWLLCAP  158 (395)
T ss_pred             CHHHHHHHHHHHCCCCCCEEEEEEEC
T ss_conf             89999999985217888869998739


No 146
>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=93.92  E-value=0.1  Score=29.53  Aligned_cols=45  Identities=20%  Similarity=0.266  Sum_probs=36.3

Q ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHHC--CCCEEEEECCCHHHHHHH
Q ss_conf             477614886788999999999999708--997799971537999999
Q gi|254781187|r   79 KCAISAGRGIGKTTLNAWMMLWLISTR--PGMSIICIANSETQLKNT  123 (367)
Q Consensus        79 ~~~v~sgrg~GKS~~~a~~~lw~~~~~--~~~~v~~~A~t~~Q~~~~  123 (367)
                      .+.|.||=|+|||+....-+++++...  ++.+|+++.-|.+-+.++
T Consensus        15 ~llV~AgAGSGKT~~L~~Ri~~li~~~~~~p~~IL~lTFT~kAA~Em   61 (494)
T pfam00580        15 PLLVLAGAGTGKTRVLTERIAYLILEGGIDPEEILAVTFTNKAAREM   61 (494)
T ss_pred             CEEEEEECCHHHHHHHHHHHHHHHHHCCCCHHHEEEEECHHHHHHHH
T ss_conf             97999718706899999999999981899974787670289999999


No 147
>KOG1015 consensus
Probab=93.73  E-value=0.21  Score=27.61  Aligned_cols=160  Identities=16%  Similarity=0.127  Sum_probs=78.7

Q ss_pred             EEEECCCCCCHHHHHHHHH-HHHHHHCCC-CEEEEECCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCC--------
Q ss_conf             7761488678899999999-999970899-779997153799999999999999986231211233332100--------
Q gi|254781187|r   80 CAISAGRGIGKTTLNAWMM-LWLISTRPG-MSIICIANSETQLKNTLWAEVSKWLSMLPHRHWFEMQSLSLH--------  149 (367)
Q Consensus        80 ~~v~sgrg~GKS~~~a~~~-lw~~~~~~~-~~v~~~A~t~~Q~~~~lw~ei~k~~~~~~~~~~~~~~~~~~~--------  149 (367)
                      ..++-+-|.|||.-+-.++ .-++|..-+ .+++|+.|. +.+- -.+.|+.+|...+.+..-+++..+..+        
T Consensus       699 cILAHcMGLGKTlQVvtflhTvL~c~klg~ktaLvV~Pl-Nt~~-NW~~EFekWm~~~e~~~~leV~eL~~vkr~e~R~~  776 (1567)
T KOG1015         699 CILAHCMGLGKTLQVVTFLHTVLLCDKLGFKTALVVCPL-NTAL-NWMNEFEKWMEGLEDDEKLEVSELATVKRPEERSY  776 (1567)
T ss_pred             HHHHHHHCCCCEEHHHHHHHHHHHHHCCCCCEEEEECCH-HHHH-HHHHHHHHHCCCCCCCCCCEEEHHHHCCCHHHHHH
T ss_conf             177875045640014678889987420478568997235-9988-99999998612422246621202120267488999


Q ss_pred             -CCCCCCCCCCCCCCCCCCCEEEEECCC--CCCCCCCCCCCCCCCCCEEEEECCCCCCHHHHHHHHHHHHCCCCCEEEEE
Q ss_conf             -012333221111345776126621013--54455652101135862899975455998899998987406988258999
Q gi|254781187|r  150 -PSGWYAELLEQSMGIDSKHYTITCRTY--SEERPDTFVGPHNTHGMAVFNDEASGTPDIINKSILGFFTELNPNRFWIM  226 (367)
Q Consensus       150 -~~~~~~~~~~~~~~~~~~~~~~~a~~~--~~~~~ea~~g~h~~~~~l~ivDEAsgI~d~i~e~i~g~Lt~~~~~~~~i~  226 (367)
                       +..|....-..-++++.=...+.++.-  +.....-.+.+-.....+++.|||.-+.++--.+...+..-...+.+ |+
T Consensus       777 ~L~~W~~~ggVmIiGYdmyRnLa~gr~vk~rk~ke~f~k~lvdpGPD~vVCDE~HiLKNeksa~Skam~~irtkRRI-~L  855 (1567)
T KOG1015         777 MLQRWQEDGGVMIIGYDMYRNLAQGRNVKSRKLKEIFNKALVDPGPDFVVCDEGHILKNEKSAVSKAMNSIRTKRRI-IL  855 (1567)
T ss_pred             HHHHHHHCCCEEEEEHHHHHHHHCCCCHHHHHHHHHHHHHCCCCCCCEEEECCHHHHCCCHHHHHHHHHHHHHHEEE-EE
T ss_conf             99999752977997368888775145603567999999860578997687242122135247899999987764047-75


Q ss_pred             EECCCCCCCHHHHHHH
Q ss_conf             8078999876887541
Q gi|254781187|r  227 TSNTRRLNGWFYDIFN  242 (367)
Q Consensus       227 igNP~r~~g~Fye~~~  242 (367)
                      +|+|--+.=.-|-|+-
T Consensus       856 TGTPLQNNLmEY~CMV  871 (1567)
T KOG1015         856 TGTPLQNNLMEYHCMV  871 (1567)
T ss_pred             ECCCHHHHHHHHHHHH
T ss_conf             2671133248887888


No 148
>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=93.72  E-value=0.48  Score=25.38  Aligned_cols=189  Identities=15%  Similarity=0.138  Sum_probs=104.3

Q ss_pred             HHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHHHHHHHH
Q ss_conf             99999988887512455555411247761488678899999999999970899779997153799999999999999986
Q gi|254781187|r   55 QLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLKNTLWAEVSKWLSM  134 (367)
Q Consensus        55 q~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~~~lw~ei~k~~~~  134 (367)
                      |=++.+.+.+.++.|..      +.+ ..+-.|+|||+.+|++|-=     -+.=.+|+|+.. .|.--|..|+|.+   
T Consensus        14 QP~AI~~L~~~l~~G~~------~Qt-LLGvTGsGKTFT~AnVIa~-----~~rPTLV~aHNK-TLAAQLY~EfKef---   77 (667)
T TIGR00631        14 QPKAIAKLVEGLEAGEK------EQT-LLGVTGSGKTFTMANVIAQ-----VQRPTLVLAHNK-TLAAQLYNEFKEF---   77 (667)
T ss_pred             HHHHHHHHHHHHHCCCC------CEE-EEEEECCCHHHHHHHHHHH-----HCCCEEEECCCH-HHHHHHHHHHHHH---
T ss_conf             18999999999856887------147-8532148627889899998-----479849985777-6799999999863---


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCEEEEECCCCCCHHHH---HHH
Q ss_conf             23121123333210001233322111134577612662101354455652101135862899975455998899---998
Q gi|254781187|r  135 LPHRHWFEMQSLSLHPSGWYAELLEQSMGIDSKHYTITCRTYSEERPDTFVGPHNTHGMAVFNDEASGTPDIIN---KSI  211 (367)
Q Consensus       135 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~ea~~g~h~~~~~l~ivDEAsgI~d~i~---e~i  211 (367)
                      .|+.      +     -    +++..+              .+=.+|||+=--.    .+.| +==|.|-|+|-   =.+
T Consensus        78 FPeN------A-----V----EYFvSY--------------YDYYQPEAYvP~~----DtyI-EKdaSINdeIerlR~SA  123 (667)
T TIGR00631        78 FPEN------A-----V----EYFVSY--------------YDYYQPEAYVPSK----DTYI-EKDASINDEIERLRLSA  123 (667)
T ss_pred             CCCC------C-----E----EEEEEC--------------CCCCCCCCCCCCC----CCEE-ECCCCHHHHHHHHHHHH
T ss_conf             8677------2-----4----525520--------------3237873214798----8413-04553004676778898


Q ss_pred             HHHHHCCCCCEEEEEEECCCCCCCHHHHHHHCCCCCEEEEEECCCCCCCCCHHHHHHHHHH---------CCCCCCEEEE
Q ss_conf             9874069882589998078999876887541122350467523332888898899999962---------1688000268
Q gi|254781187|r  212 LGFFTELNPNRFWIMTSNTRRLNGWFYDIFNIPLEDWKRYQIDTRTVEGIDSGFHEGIISR---------YGLDSDVARI  282 (367)
Q Consensus       212 ~g~Lt~~~~~~~~i~igNP~r~~g~Fye~~~~~~~~w~~~~~~~~d~p~~~~~~i~~~~~~---------~gedS~~~r~  282 (367)
                      .-+|.+..--+...++|.=-+.         .....|..+.++-.-...++.+.+.+..-.         +..++..+|=
T Consensus       124 T~SLl~RrDVIVVASVScIYGL---------G~P~~Y~~~~~~l~vG~~~~~~~ll~~LV~lqY~RNd~~f~RG~FRvrG  194 (667)
T TIGR00631       124 TKSLLERRDVIVVASVSCIYGL---------GSPEEYLKMVLHLEVGKEIDRRELLRRLVELQYERNDVDFQRGTFRVRG  194 (667)
T ss_pred             HHHHCCCCCEEEEEEEEEECCC---------CCCHHHHCCEEEEEECCCCCHHHHHHHHHHHCEEECCEECCCCCEEEEE
T ss_conf             8864237878999875520688---------8825564227865407855889999886340305712340577125763


Q ss_pred             EEEEEEC-CCCCCEEECHHHH
Q ss_conf             8864432-7789807829998
Q gi|254781187|r  283 EILGQFP-QQEVNNFIPHNYI  302 (367)
Q Consensus       283 ev~G~Fp-~~~~d~~ip~~~i  302 (367)
                      .|-=.|| ..+++-.+-.++.
T Consensus       195 DVvEIfP~~~~~~~~~RiEfF  215 (667)
T TIGR00631       195 DVVEIFPAAYEDEFAVRIEFF  215 (667)
T ss_pred             EEEEEECCCCCCCCEEEEEEE
T ss_conf             189863477677724899852


No 149
>PRK11034 clpA ATP-dependent Clp protease ATP-binding subunit; Provisional
Probab=93.68  E-value=0.5  Score=25.29  Aligned_cols=47  Identities=15%  Similarity=0.094  Sum_probs=26.4

Q ss_pred             HHHHHHHHHHHHHHCC-CCCCCC--CEEEEEEECCCCCCHHHHHHHHHHH
Q ss_conf             9999999888875124-555554--1124776148867889999999999
Q gi|254781187|r   54 WQLEFMEAVDVHCHSN-VNNSNP--TIFKCAISAGRGIGKTTLNAWMMLW  100 (367)
Q Consensus        54 wq~~~l~~~~~~~~~~-~~~~~~--~~~~~~v~sgrg~GKS~~~a~~~lw  100 (367)
                      .|.+++..+++.+++. ..-..|  .+--..-.++.|+|||.++-.++-.
T Consensus       462 GQ~~Ai~~v~~ai~~~raGL~~~~rPigsFlf~GPTGVGKTElak~LA~~  511 (758)
T PRK11034        462 GQDKAIEALTEAIKMSRAGLGHEHKPVGSFLFAGPTGVGKTEVTVQLSKA  511 (758)
T ss_pred             CCHHHHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCCCHHHHHHHHHHH
T ss_conf             54999999999999986388899997058999789987779999999999


No 150
>PHA00149 DNA encapsidation protein
Probab=93.62  E-value=0.51  Score=25.23  Aligned_cols=143  Identities=20%  Similarity=0.241  Sum_probs=76.1

Q ss_pred             EEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHH--HHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCC
Q ss_conf             1247761488678899999999999970899779997153799999--99999999998623121123333210001233
Q gi|254781187|r   77 IFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLKN--TLWAEVSKWLSMLPHRHWFEMQSLSLHPSGWY  154 (367)
Q Consensus        77 ~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~~--~lw~ei~k~~~~~~~~~~~~~~~~~~~~~~~~  154 (367)
                      +.+..| ++||+|||+.+--.++--++.. |.+.+...-...-++.  ..++.+   ....|+ +-|..           
T Consensus        18 ~l~fvi-G~RgiGKTya~k~~~~k~~i~k-geqfiyLRr~k~El~~k~~Ff~d~---~~~~~~-~ef~V-----------   80 (331)
T PHA00149         18 ILNFVI-GARGIGKTYALKKYLIKRFIKK-GEQFIYLRRYKSELKKKSKFFADI---AQEFPN-TEFEV-----------   80 (331)
T ss_pred             EEEEEE-ECCCCCHHHHHHHHHHHHHHHC-CCEEEEEEECCHHHHHHHHHHHHH---HHHCCC-CCEEE-----------
T ss_conf             469998-2465440357778899999862-967999993243452021056789---975789-74599-----------


Q ss_pred             CCCCCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCEEEEECC-------CCCCHHHH---HHHHHHHHCCCCCEEE
Q ss_conf             3221111345776126621013544556521011358628999754-------55998899---9989874069882589
Q gi|254781187|r  155 AELLEQSMGIDSKHYTITCRTYSEERPDTFVGPHNTHGMAVFNDEA-------SGTPDIIN---KSILGFFTELNPNRFW  224 (367)
Q Consensus       155 ~~~~~~~~~~~~~~~~~~a~~~~~~~~ea~~g~h~~~~~l~ivDEA-------sgI~d~i~---e~i~g~Lt~~~~~~~~  224 (367)
                       ..++..+...--.+.+.-+     +..++.|..=.+..-+++||.       ..+|+++-   ..+.-..+.. ....+
T Consensus        81 -k~~ki~~~~k~igy~i~lS-----~~q~~Ks~~Yp~V~~I~fDEfi~~k~n~~Ylpne~~allnli~tV~R~R-e~i~~  153 (331)
T PHA00149         81 -KGRKIYIKGKLIGYAIPLS-----TWQALKSSAYPNVSTIFFDEFIREKDNKRYLPNEVDALLNLIDTVFRAR-ERVRC  153 (331)
T ss_pred             -EEEEEEECCEEEEEEEEHH-----HHHHHCCCCCCCEEEEEEEHHHHHCCCCCCCCCHHHHHHHHHHHHHHHH-CCEEE
T ss_conf             -7008998680799997044-----6776325689955899712233305433568850899999999987753-57599


Q ss_pred             EEEECCCCCCCHHHHHHHC
Q ss_conf             9980789998768875411
Q gi|254781187|r  225 IMTSNTRRLNGWFYDIFNI  243 (367)
Q Consensus       225 i~igNP~r~~g~Fye~~~~  243 (367)
                      +++||-.-..|+++.-|+-
T Consensus       154 ~~lsNa~~~~NPyF~yf~~  172 (331)
T PHA00149        154 ICLSNAVSIVNPYFLYFGL  172 (331)
T ss_pred             EEECCCCCCCCCHHHEEEE
T ss_conf             9975854303604423421


No 151
>PRK12724 flagellar biosynthesis regulator FlhF; Provisional
Probab=93.59  E-value=0.51  Score=25.22  Aligned_cols=42  Identities=14%  Similarity=-0.036  Sum_probs=34.0

Q ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHH
Q ss_conf             477614886788999999999999708997799971537999
Q gi|254781187|r   79 KCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQL  120 (367)
Q Consensus        79 ~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~  120 (367)
                      -++..++.|+|||+.+|=++.-+.+.+.....++|+.|++=+
T Consensus       225 vi~lVGPTGVGKTTTiAKLAA~~~l~~~kkVaLIT~DTYRIg  266 (432)
T PRK12724        225 VVFFVGPTGSGKTTSIAKLAAKYFLHMGKSVSLYTTDNYRIA  266 (432)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHHCCCEEEEEECCCCCHH
T ss_conf             999989999888999999999999974992799952665377


No 152
>PRK00411 cdc6 cell division control protein 6; Reviewed
Probab=93.51  E-value=0.53  Score=25.11  Aligned_cols=70  Identities=17%  Similarity=0.156  Sum_probs=36.9

Q ss_pred             HHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEE----CCCHHHHHHHHHHHH
Q ss_conf             999988887512455555411247761488678899999999999970899779997----153799999999999
Q gi|254781187|r   57 EFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICI----ANSETQLKNTLWAEV  128 (367)
Q Consensus        57 ~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~----A~t~~Q~~~~lw~ei  128 (367)
                      +-++.|+.+++.-.....|  .++.|.+.-|+|||..+-..+-.+--...+..++.+    .+|..|+-..++..+
T Consensus        37 ~Ei~~l~~~l~~~l~g~~~--~n~~I~G~pGTGKT~~vk~v~~~l~~~~~~~~~vyINc~~~~t~~~i~~~i~~~L  110 (394)
T PRK00411         37 EQIEELAFALRPALRGSRP--SNVLILGPPGTGKTTTVKKVFEELEEAALKVVYVYINCQIDRTRYAILSEIARSL  110 (394)
T ss_pred             HHHHHHHHHHHHHHCCCCC--CCEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEEECCCCCCHHHHHHHHHHHH
T ss_conf             9999999999999759999--8479988999989999999999999746896599996966898999999999995


No 153
>COG4962 CpaF Flp pilus assembly protein, ATPase CpaF [Intracellular trafficking and secretion]
Probab=93.37  E-value=0.18  Score=28.06  Aligned_cols=51  Identities=25%  Similarity=0.274  Sum_probs=38.2

Q ss_pred             HHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCH
Q ss_conf             89999999888875124555554112477614886788999999999999708997799971537
Q gi|254781187|r   53 RWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSE  117 (367)
Q Consensus        53 ~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~  117 (367)
                      .=|.++|+.+...           +.++.|++|.|+|||++..++...   --++.+++|+-.|.
T Consensus       160 ~~~a~~L~~av~~-----------r~NILisGGTGSGKTTlLNal~~~---i~~~eRvItiEDta  210 (355)
T COG4962         160 RRAAKFLRRAVGI-----------RCNILISGGTGSGKTTLLNALSGF---IDSDERVITIEDTA  210 (355)
T ss_pred             HHHHHHHHHHHHH-----------CEEEEEECCCCCCHHHHHHHHHHC---CCCCCEEEEEEEHH
T ss_conf             8999999999862-----------015999678788799999999715---79765089981236


No 154
>KOG0339 consensus
Probab=93.31  E-value=0.54  Score=25.07  Aligned_cols=158  Identities=18%  Similarity=0.133  Sum_probs=82.8

Q ss_pred             CCCCHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCC------CCEEEEECCCHHHHH
Q ss_conf             66842899999998888751245555541124776148867889999999999997089------977999715379999
Q gi|254781187|r   48 FSQPHRWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRP------GMSIICIANSETQLK  121 (367)
Q Consensus        48 ~~~p~~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~------~~~v~~~A~t~~Q~~  121 (367)
                      |..|+.-|+.+|-...         ....+  +-| |-.|+||+...+|-++-++.-.|      +.-.++++||..-+.
T Consensus       243 y~kptpiq~qalptal---------sgrdv--igI-AktgSgktaAfi~pm~~himdq~eL~~g~gPi~vilvPTrela~  310 (731)
T KOG0339         243 YEKPTPIQCQALPTAL---------SGRDV--IGI-AKTGSGKTAAFIWPMIVHIMDQPELKPGEGPIGVILVPTRELAS  310 (731)
T ss_pred             CCCCCCCCCCCCCCCC---------CCCCC--HHE-EECCCCCHHHHHHHHHHHHCCHHHHCCCCCCEEEEEECCHHHHH
T ss_conf             0467752334355224---------66521--111-21157505677777777741405206899976999806389999


Q ss_pred             HHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCEEEEECCC
Q ss_conf             99999999999862312112333321000123332211113457761266210135445565210113586289997545
Q gi|254781187|r  122 NTLWAEVSKWLSMLPHRHWFEMQSLSLHPSGWYAELLEQSMGIDSKHYTITCRTYSEERPDTFVGPHNTHGMAVFNDEAS  201 (367)
Q Consensus       122 ~~lw~ei~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~ea~~g~h~~~~~l~ivDEAs  201 (367)
                      ++ +.|.|++-...-...-..+.-...|         ...-....|.-++.|.+-|.-.--.+.+..-.+..++++|||.
T Consensus       311 Qi-~~eaKkf~K~ygl~~v~~ygGgsk~---------eQ~k~Lk~g~EivVaTPgRlid~VkmKatn~~rvS~LV~DEad  380 (731)
T KOG0339         311 QI-FSEAKKFGKAYGLRVVAVYGGGSKW---------EQSKELKEGAEIVVATPGRLIDMVKMKATNLSRVSYLVLDEAD  380 (731)
T ss_pred             HH-HHHHHHHHHHCCCEEEEEECCCCHH---------HHHHHHHCCCEEEEECHHHHHHHHHHHCCCCEEEEEEEEECHH
T ss_conf             99-9999986311264278863687488---------8777650277289966288899988603331003578871111


Q ss_pred             CCCHHHHH----HHHHHHHCCCCCEEEEEEECC
Q ss_conf             59988999----989874069882589998078
Q gi|254781187|r  202 GTPDIINK----SILGFFTELNPNRFWIMTSNT  230 (367)
Q Consensus       202 gI~d~i~e----~i~g~Lt~~~~~~~~i~igNP  230 (367)
                      -.=+.=|+    .|-..++. +...  ++|+++
T Consensus       381 rmfdmGfe~qVrSI~~hirp-drQt--llFsaT  410 (731)
T KOG0339         381 RMFDMGFEPQVRSIKQHIRP-DRQT--LLFSAT  410 (731)
T ss_pred             HHHCCCCHHHHHHHHHHCCC-CCEE--EEEECC
T ss_conf             13126547989999864488-6427--986031


No 155
>PRK10416 cell division protein FtsY; Provisional
Probab=93.28  E-value=0.58  Score=24.89  Aligned_cols=106  Identities=15%  Similarity=0.165  Sum_probs=56.8

Q ss_pred             CCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEE-CCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCC
Q ss_conf             5411247761488678899999999999970899779997-153799999999999999986231211233332100012
Q gi|254781187|r   74 NPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICI-ANSETQLKNTLWAEVSKWLSMLPHRHWFEMQSLSLHPSG  152 (367)
Q Consensus        74 ~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~-A~t~~Q~~~~lw~ei~k~~~~~~~~~~~~~~~~~~~~~~  152 (367)
                      .|.+  +.+.+=.|+|||+.++=++.|+.-  .+.+|++. +-|++-+-   ...++.|.++.-.               
T Consensus       294 ~P~V--Il~vGvNG~GKTTTigKLA~~~~~--~gkkVllaA~DTfRaAA---ieQL~~w~~r~~v---------------  351 (499)
T PRK10416        294 TPFV--ILMVGVNGVGKTTTIGKLARQFEQ--QGKSVMLAAGDTFRAAA---VEQLQVWGQRNNI---------------  351 (499)
T ss_pred             CCEE--EEEECCCCCCHHHHHHHHHHHHHH--CCCCEEEEEECCCCHHH---HHHHHHHHCCCCC---------------
T ss_conf             9879--999747878789899999999997--79953788406675689---9999998424573---------------


Q ss_pred             CCCCCCCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCEEEEECCCCCC--HHHHHHHHHH
Q ss_conf             3332211113457761266210135445565210113586289997545599--8899998987
Q gi|254781187|r  153 WYAELLEQSMGIDSKHYTITCRTYSEERPDTFVGPHNTHGMAVFNDEASGTP--DIINKSILGF  214 (367)
Q Consensus       153 ~~~~~~~~~~~~~~~~~~~~a~~~~~~~~ea~~g~h~~~~~l~ivDEAsgI~--d~i~e~i~g~  214 (367)
                         .......+.++....          -++++.....+...+|+|-|.-..  ...++-+...
T Consensus       352 ---~vi~~~~g~Dpa~V~----------~dai~~a~~~~~DvviiDTAGRl~~~~~LM~EL~ki  402 (499)
T PRK10416        352 ---PVIAQHTGADSASVI----------FDAIQAAKARNVDVLIADTAGRLQNKSHLMEELKKI  402 (499)
T ss_pred             ---EEEECCCCCCHHHHH----------HHHHHHHHHCCCCEEEEECCCCCCCCHHHHHHHHHH
T ss_conf             ---698368999979999----------999999997299989985776432609999999999


No 156
>KOG0334 consensus
Probab=93.03  E-value=0.45  Score=25.57  Aligned_cols=75  Identities=24%  Similarity=0.252  Sum_probs=47.6

Q ss_pred             CCCCHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHH-HHHCC-----CCEEEEECCCHHHHH
Q ss_conf             668428999999988887512455555411247761488678899999999999-97089-----977999715379999
Q gi|254781187|r   48 FSQPHRWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWL-ISTRP-----GMSIICIANSETQLK  121 (367)
Q Consensus        48 ~~~p~~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~-~~~~~-----~~~v~~~A~t~~Q~~  121 (367)
                      +..|+..|..++-.|-..            .-|...|=-|+|||...-..++=+ ...++     |...+++|||..++.
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             HHHHHHHHHHHHHC
Q ss_conf             99999999999862
Q gi|254781187|r  122 NTLWAEVSKWLSML  135 (367)
Q Consensus       122 ~~lw~ei~k~~~~~  135 (367)
                      ++ .++++++...+
T Consensus       453 QI-~r~~~kf~k~l  465 (997)
T KOG0334         453 QI-HREVRKFLKLL  465 (997)
T ss_pred             HH-HHHHHHHHHHC
T ss_conf             99-99999987741


No 157
>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=92.88  E-value=0.21  Score=27.62  Aligned_cols=84  Identities=11%  Similarity=0.033  Sum_probs=56.0

Q ss_pred             HHHHHHHHHHHHHHHHCCCC----CCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHH
Q ss_conf             28999999988887512455----55541124776148867889999999999997089977999715379999999999
Q gi|254781187|r   52 HRWQLEFMEAVDVHCHSNVN----NSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLKNTLWAE  127 (367)
Q Consensus        52 ~~wq~~~l~~~~~~~~~~~~----~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~~~lw~e  127 (367)
                      ..-..+++..-..+++.+..    ++.-.=+=..|-++.|.|||.+.-.++---++.-++.+|+.++|+...+-   -.|
T Consensus        58 ~~~~~~~~n~~~~~L~~dG~~~SLNy~~qP~I~vVYGPTG~GKSQLlRNlis~~lI~P~PETVfFItPq~~mIp---p~E  134 (370)
T pfam02456        58 MEAVHGQLNEASRYLRPDGELPSLNYGLQPVIGVVYGPTGCGKSQLLRNLLSCQLIQPIPETVFFITPQKDMIP---PQE  134 (370)
T ss_pred             HHHHHHHHHHHHHHHCCCCCCCCCCCCCCCEEEEEECCCCCCHHHHHHHHHHCCCCCCCCCEEEEECCCCCCCC---HHH
T ss_conf             99999999863154066896575546787449999889987789999998734667799972899767778679---899


Q ss_pred             HHHHHHHCCCC
Q ss_conf             99999862312
Q gi|254781187|r  128 VSKWLSMLPHR  138 (367)
Q Consensus       128 i~k~~~~~~~~  138 (367)
                      +.-|-..+-..
T Consensus       135 ~~aWe~Ql~EG  145 (370)
T pfam02456       135 QTAWELQLCEG  145 (370)
T ss_pred             HHHHHHHHHHC
T ss_conf             99999998735


No 158
>PRK06731 flhF flagellar biosynthesis regulator FlhF; Validated
Probab=92.88  E-value=0.67  Score=24.52  Aligned_cols=69  Identities=17%  Similarity=0.117  Sum_probs=41.7

Q ss_pred             CCHHHHHHHHHHHHHHHHCCCCC---CCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEE-EEECCCHHHH
Q ss_conf             84289999999888875124555---55411247761488678899999999999970899779-9971537999
Q gi|254781187|r   50 QPHRWQLEFMEAVDVHCHSNVNN---SNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSI-ICIANSETQL  120 (367)
Q Consensus        50 ~p~~wq~~~l~~~~~~~~~~~~~---~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v-~~~A~t~~Q~  120 (367)
                      +...++.++++.+.+.+......   ......-+.+.+..|+|||+.+|=++.|+. .+ +.++ ++++-|++-+
T Consensus        45 ~~~~~~~~vi~~l~~~l~~~~~~~~~~~~~~~vI~lvG~~G~GKTTT~AKLA~~~~-~~-~~kV~lia~DtyR~a  117 (270)
T PRK06731         45 NATMITEEVIEYILEDMSSHFNTENVFEKEVQTIALIGPTGVGKTTTLAKMAWQFH-GK-KKTVGFITTDHSRIG  117 (270)
T ss_pred             CCCCHHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHH-HC-CCEEEEEEECCCCHH
T ss_conf             45532999999999999875076654679981899988898988999999999998-67-990899983888888


No 159
>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=92.73  E-value=0.68  Score=24.47  Aligned_cols=40  Identities=25%  Similarity=0.137  Sum_probs=26.5

Q ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHH
Q ss_conf             477614886788999999999999708997799971537999
Q gi|254781187|r   79 KCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQL  120 (367)
Q Consensus        79 ~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~  120 (367)
                      .+.+.++-|+|||+++..++.-.....  ..++.++......
T Consensus         4 ~ill~G~~GsGKTtl~~~la~~~~~~~--~~v~~~~~~~~~~   43 (148)
T smart00382        4 VILIVGPPGSGKTTLARALARELGPPG--GGVIYIDGEDILE   43 (148)
T ss_pred             EEEEECCCCHHHHHHHHHHHHHHCCCC--CCEEEEEHHHHHH
T ss_conf             899999997029999999998726689--9689987599898


No 160
>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=92.71  E-value=0.7  Score=24.38  Aligned_cols=65  Identities=15%  Similarity=0.175  Sum_probs=45.0

Q ss_pred             HHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHHHHHHHH
Q ss_conf             99999988887512455555411247761488678899999999999970899779997153799999999999999986
Q gi|254781187|r   55 QLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLKNTLWAEVSKWLSM  134 (367)
Q Consensus        55 q~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~~~lw~ei~k~~~~  134 (367)
                      |.|+++++.+..       .+   =+.+.|+.|+|||..+-.-++     ..+.+++++.|+..-+.|.. ..++++++.
T Consensus         2 q~~~~~~~~~~~-------~~---~ivitAPTgsGKT~Aa~lp~l-----~~~~~~lyi~P~kAL~~Dq~-~~l~~~~~~   65 (357)
T TIGR03158         2 QVATFEALQSKD-------AD---IIFNTAPTGAGKTLAWLTPLL-----HGENDTIALYPTNALIEDQT-EAIKEFVDV   65 (357)
T ss_pred             HHHHHHHHHCCC-------CC---EEEEECCCCCCHHHHHHHHHH-----HCCCCEEEECCHHHHHHHHH-HHHHHHHHH
T ss_conf             689999997689-------98---699989998569999999997-----38987999777899999999-999999987


Q ss_pred             C
Q ss_conf             2
Q gi|254781187|r  135 L  135 (367)
Q Consensus       135 ~  135 (367)
                      +
T Consensus        66 ~   66 (357)
T TIGR03158        66 F   66 (357)
T ss_pred             H
T ss_conf             4


No 161
>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=92.70  E-value=0.26  Score=27.01  Aligned_cols=89  Identities=21%  Similarity=0.120  Sum_probs=63.8

Q ss_pred             HHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHH--HHCCCCEEEEECCCHHHHHHHHHHHHHHHH
Q ss_conf             999999888875124555554112477614886788999999999999--708997799971537999999999999999
Q gi|254781187|r   55 QLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLI--STRPGMSIICIANSETQLKNTLWAEVSKWL  132 (367)
Q Consensus        55 q~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~--~~~~~~~v~~~A~t~~Q~~~~lw~ei~k~~  132 (367)
                      |.++.+.+.=          |    +.|.||=|+|||.++--.|.+++  |+.++.+|+.+.=|=+-|+++= -.|++.+
T Consensus         8 Q~~AV~Y~~G----------P----lLVLAGAGSGKT~VI~~KIayLi~~cgY~a~~IaAvTFTNKAA~EMk-ERVA~~L   72 (677)
T TIGR01074         8 QQEAVEYVGG----------P----LLVLAGAGSGKTRVITNKIAYLIQNCGYKAKNIAAVTFTNKAAREMK-ERVAKTL   72 (677)
T ss_pred             HHHHHHHHCC----------C----CEEECCCCCCCCHHHHHHHHHHHHHCCCCCCCEEEEECCHHHHHHHH-HHHHHHC
T ss_conf             7999986158----------7----14651777786357888999987515878761689735237779999-9998522


Q ss_pred             HHCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             86231211233332100012333221
Q gi|254781187|r  133 SMLPHRHWFEMQSLSLHPSGWYAELL  158 (367)
Q Consensus       133 ~~~~~~~~~~~~~~~~~~~~~~~~~~  158 (367)
                      .+.-.+.+.-+|...+-+.....+.+
T Consensus        73 ~~~~~~GL~isTFH~LGL~Ii~~E~~   98 (677)
T TIGR01074        73 GKGQAKGLTISTFHTLGLKIIRREHN   98 (677)
T ss_pred             CCCCCCCCEEECCHHHHHHHHHHHHH
T ss_conf             65455854475205733899999998


No 162
>PRK00149 dnaA chromosomal replication initiation protein; Reviewed
Probab=92.68  E-value=0.66  Score=24.54  Aligned_cols=56  Identities=23%  Similarity=0.315  Sum_probs=41.9

Q ss_pred             HHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECC
Q ss_conf             899999998888751245555541124776148867889999999999997089977999715
Q gi|254781187|r   53 RWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIAN  115 (367)
Q Consensus        53 ~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~  115 (367)
                      +.=..+.+++++.   +...++|    +-|-++-|+|||+|..++....+-.+|+.+|+++..
T Consensus       128 ~lA~aAA~~Va~~---pg~~yNP----LfIyG~~GlGKTHLl~AIgn~~~~~~p~~~v~Y~ta  183 (447)
T PRK00149        128 RLAHAAALAVAEN---PGKAYNP----LFIYGGVGLGKTHLLHAIGNYILEKNPNAKVVYVSS  183 (447)
T ss_pred             HHHHHHHHHHHHC---CCCCCCC----EEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEEEH
T ss_conf             9999999999837---6767785----589779988788999999999998589972899549


No 163
>COG0593 DnaA ATPase involved in DNA replication initiation [DNA replication, recombination, and repair]
Probab=92.63  E-value=0.63  Score=24.68  Aligned_cols=36  Identities=22%  Similarity=0.307  Sum_probs=32.5

Q ss_pred             EEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECC
Q ss_conf             776148867889999999999997089977999715
Q gi|254781187|r   80 CAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIAN  115 (367)
Q Consensus        80 ~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~  115 (367)
                      +-+.+|-|+|||++..++....+...|..++++...
T Consensus       116 lfi~G~~GlGKTHLl~Aign~~~~~~~~a~v~y~~s  151 (408)
T COG0593         116 LFIYGGVGLGKTHLLQAIGNEALANGPNARVVYLTS  151 (408)
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEECCH
T ss_conf             799879999789999999999986299864885048


No 164
>COG1702 PhoH Phosphate starvation-inducible protein PhoH, predicted ATPase [Signal transduction mechanisms]
Probab=92.60  E-value=0.17  Score=28.17  Aligned_cols=150  Identities=18%  Similarity=0.117  Sum_probs=75.6

Q ss_pred             CCHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHHH
Q ss_conf             84289999999888875124555554112477614886788999999999999708997799971537999999999999
Q gi|254781187|r   50 QPHRWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLKNTLWAEVS  129 (367)
Q Consensus        50 ~p~~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~~~lw~ei~  129 (367)
                      .-+.-|..-+++|.+|.-           +..+ +.=|+|||+++...++-.+-...=.+|+.|.|.- .+-        
T Consensus       128 ~kt~~Q~~y~eai~~~di-----------~fGi-GpAGTGKTyLava~av~al~~~~v~rIiLtRPaV-EAG--------  186 (348)
T COG1702         128 PKTPGQNMYPEAIEEHDI-----------VFGI-GPAGTGKTYLAVAKAVDALGAGQVRRIILTRPAV-EAG--------  186 (348)
T ss_pred             ECCHHHHHHHHHHHHCCE-----------EEEE-CCCCCCCCHHHHHHHHHHHHCCCHHEEECCCCCH-HCC--------
T ss_conf             668458788999874273-----------6641-5645697111277665265406412010068313-036--------


Q ss_pred             HHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC--CCCCEEEEECCCCCCCCCCCCCCCCCC--CCEEEEECCCCCCH
Q ss_conf             99986231211233332100012333221111345--776126621013544556521011358--62899975455998
Q gi|254781187|r  130 KWLSMLPHRHWFEMQSLSLHPSGWYAELLEQSMGI--DSKHYTITCRTYSEERPDTFVGPHNTH--GMAVFNDEASGTPD  205 (367)
Q Consensus       130 k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~a~~~~~~~~ea~~g~h~~~--~~l~ivDEAsgI~d  205 (367)
                         ++    --|..-+.+.+..||.-+........  .........++.-+-.|-++  .+|++  -.++|+|||+--. 
T Consensus       187 ---Ek----lGfLPGdl~eKvdPylRPLyDAl~d~l~~~~~~~~~e~~vIEiAPlAy--MRGRTL~dAfVIlDEaQNtT-  256 (348)
T COG1702         187 ---EK----LGFLPGDLREKVDPYLRPLYDALYDILGAERVEALDERGVIEIAPLAY--MRGRTLNDAFVILDEAQNTT-  256 (348)
T ss_pred             ---CC----CCCCCCCHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHCCEEEECHHH--HHCCCCCCEEEEEECCCCCC-
T ss_conf             ---42----370788234324611041789999986489773055509487602456--53587787289985510050-


Q ss_pred             HHHHHHHHHHHCCCCCEEEEEEECCCC
Q ss_conf             899998987406988258999807899
Q gi|254781187|r  206 IINKSILGFFTELNPNRFWIMTSNTRR  232 (367)
Q Consensus       206 ~i~e~i~g~Lt~~~~~~~~i~igNP~r  232 (367)
                        -+-+.=.||--+..+.|+.+|.++-
T Consensus       257 --~~QmKMfLTRiGf~skmvItGD~tQ  281 (348)
T COG1702         257 --VGQMKMFLTRIGFESKMVITGDITQ  281 (348)
T ss_pred             --HHHHCEEEEEECCCCEEEEECCCCC
T ss_conf             --6451340033137742699757521


No 165
>PRK10919 ATP-dependent DNA helicase Rep; Provisional
Probab=92.59  E-value=0.25  Score=27.17  Aligned_cols=45  Identities=22%  Similarity=0.307  Sum_probs=36.2

Q ss_pred             EEEECCCCCCHHHHHHHHHHHHHHH--CCCCEEEEECCCHHHHHHHH
Q ss_conf             7761488678899999999999970--89977999715379999999
Q gi|254781187|r   80 CAISAGRGIGKTTLNAWMMLWLIST--RPGMSIICIANSETQLKNTL  124 (367)
Q Consensus        80 ~~v~sgrg~GKS~~~a~~~lw~~~~--~~~~~v~~~A~t~~Q~~~~l  124 (367)
                      +.|.||=|+|||.....-+.|++..  -++.+|+++.=|.+-+.++-
T Consensus        18 ~lVlAGaGSGKT~tLt~Ria~Li~~~~v~P~~ILalTFT~kAA~Emk   64 (672)
T PRK10919         18 CLVLAGAGSGKTRVITNKIAHLIRGCGYQARHIAAVTFTNKAAREMK   64 (672)
T ss_pred             EEEEECCCHHHHHHHHHHHHHHHHCCCCCCCCEEEECCHHHHHHHHH
T ss_conf             89997385587999999999998668989333854421799999999


No 166
>PRK12727 flagellar biosynthesis regulator FlhF; Provisional
Probab=92.51  E-value=0.74  Score=24.22  Aligned_cols=40  Identities=18%  Similarity=0.169  Sum_probs=31.8

Q ss_pred             EEEECCCCCCHHHHHHHHHHHHHHHCC-CCEEEEECCCHHH
Q ss_conf             776148867889999999999997089-9779997153799
Q gi|254781187|r   80 CAISAGRGIGKTTLNAWMMLWLISTRP-GMSIICIANSETQ  119 (367)
Q Consensus        80 ~~v~sgrg~GKS~~~a~~~lw~~~~~~-~~~v~~~A~t~~Q  119 (367)
                      ++..++.|+|||+.+|-++.-++..+- .+..++|..|++-
T Consensus       351 ~AlvGpTGvGKTTT~aKlAa~~~~~~g~~~valit~DtyRi  391 (557)
T PRK12727        351 IALVGPTGAGKTTTIAKLAQRFAAQHAPRDVALVTTDTQRV  391 (557)
T ss_pred             EEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEEECCCCCH
T ss_conf             78743777673117999999999973998189997266408


No 167
>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=92.48  E-value=0.18  Score=27.99  Aligned_cols=27  Identities=22%  Similarity=0.279  Sum_probs=19.8

Q ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHHC
Q ss_conf             477614886788999999999999708
Q gi|254781187|r   79 KCAISAGRGIGKTTLNAWMMLWLISTR  105 (367)
Q Consensus        79 ~~~v~sgrg~GKS~~~a~~~lw~~~~~  105 (367)
                      =+.|.++-|+|||+..|.+|=+.=-+.
T Consensus       129 LiLVTGPTGSGKSTTlAsmIDyIN~~~  155 (350)
T TIGR01420       129 LILVTGPTGSGKSTTLASMIDYINKNK  155 (350)
T ss_pred             CEEEECCCCCCHHHHHHHHHHHHHCCC
T ss_conf             389876889867899999997874038


No 168
>TIGR03345 VI_ClpV1 type VI secretion ATPase, ClpV1 family. Members of this protein family are homologs of ClpB, an ATPase associated with chaperone-related functions. These ClpB homologs, designated ClpV1, are a key component of the bacterial pathogenicity-associated type VI secretion system.
Probab=92.43  E-value=0.76  Score=24.16  Aligned_cols=48  Identities=17%  Similarity=0.151  Sum_probs=27.7

Q ss_pred             HHHHHHHHHHHHHHCC---CCCCCCCEEEEEEECCCCCCHHHHHHHHHHHH
Q ss_conf             9999999888875124---55555411247761488678899999999999
Q gi|254781187|r   54 WQLEFMEAVDVHCHSN---VNNSNPTIFKCAISAGRGIGKTTLNAWMMLWL  101 (367)
Q Consensus        54 wq~~~l~~~~~~~~~~---~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~  101 (367)
                      .|.++++.|++.+++.   .....-..--..-.++.|+|||.++-.++-.+
T Consensus       570 GQ~~Av~~v~~ai~~sraGl~d~~rPigsFLFlGPTGVGKTElAK~LA~~L  620 (852)
T TIGR03345       570 GQDHALEAIAERIRTARAGLEDPRKPLGVFLLVGPSGVGKTETALALAELL  620 (852)
T ss_pred             CHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCCCHHHHHHHHHHHH
T ss_conf             849999999999999871799999985689987899877899999999997


No 169
>PRK08116 hypothetical protein; Validated
Probab=92.26  E-value=0.8  Score=24.03  Aligned_cols=33  Identities=27%  Similarity=0.359  Sum_probs=23.7

Q ss_pred             EEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEEC
Q ss_conf             77614886788999999999999708997799971
Q gi|254781187|r   80 CAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIA  114 (367)
Q Consensus        80 ~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A  114 (367)
                      +...++-|+|||+++++++...+ .+ +..|+++.
T Consensus       111 Lll~G~~GtGKThLa~aIa~~l~-~~-g~~V~~~~  143 (262)
T PRK08116        111 LLLWGSPGNGKTYLAAAIANELI-EK-GVPVVFVN  143 (262)
T ss_pred             EEEECCCCCCHHHHHHHHHHHHH-HC-CCEEEEEE
T ss_conf             89989899989999999999999-87-99399988


No 170
>PRK06835 DNA replication protein DnaC; Validated
Probab=92.25  E-value=0.61  Score=24.73  Aligned_cols=82  Identities=16%  Similarity=0.169  Sum_probs=50.1

Q ss_pred             CCCHHHHHHHHHCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHH
Q ss_conf             25988885543014668884436668428999999988887512455555411247761488678899999999999970
Q gi|254781187|r   25 VLSFKNFVMRFFPWGIKGKPLEHFSQPHRWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLIST  104 (367)
Q Consensus        25 ~~~~~~f~~~~~~w~~~~~~~~~~~~p~~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~  104 (367)
                      ..+|.+|=+-.|+- +.+ | .....|++-=.+++...-++.++    +...--.+...++-|+|||+++++++.-.+-.
T Consensus       138 ~enF~~F~~~~ys~-~~~-~-~~~~sprenm~~i~~~~~~fi~~----F~~~~~nLlf~G~~G~GKTfLa~~IA~ell~~  210 (330)
T PRK06835        138 ENNFSNFNLNYYSD-EKD-G-DEPISPRENMENILEKCLNFIKN----FDKNNENLLFYGNTGTGKTFLSNCIAKELLDR  210 (330)
T ss_pred             HCCCCCCCHHHCCC-CCC-C-CCCCCHHHHHHHHHHHHHHHHHH----CCCCCCCEEEECCCCCCHHHHHHHHHHHHHHC
T ss_conf             61431178865399-878-8-88989899999999999999872----47888866988999998899999999999987


Q ss_pred             CCCCEEEE-ECC
Q ss_conf             89977999-715
Q gi|254781187|r  105 RPGMSIIC-IAN  115 (367)
Q Consensus       105 ~~~~~v~~-~A~  115 (367)
                      .  ..|++ +|+
T Consensus       211 g--~sViy~ta~  220 (330)
T PRK06835        211 G--KTVIYRTSD  220 (330)
T ss_pred             C--CEEEEEEHH
T ss_conf             9--949996299


No 171
>COG2812 DnaX DNA polymerase III, gamma/tau subunits [DNA replication, recombination, and repair]
Probab=92.16  E-value=0.82  Score=23.96  Aligned_cols=134  Identities=15%  Similarity=0.104  Sum_probs=65.6

Q ss_pred             HHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHHHHHHH
Q ss_conf             99999998888751245555541124776148867889999999999997089977999715379999999999999998
Q gi|254781187|r   54 WQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLKNTLWAEVSKWLS  133 (367)
Q Consensus        54 wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~~~lw~ei~k~~~  133 (367)
                      .|+-+.+.+..-+..+.. .+.+    .-++.||+|||+++-.++--+-|.+...--.|     .+.. .+ .+|..=  
T Consensus        20 GQe~v~~~L~nal~~~ri-~hAY----lfsG~RGvGKTt~Ari~AkalNC~~~~~~ePC-----~~C~-~C-k~I~~g--   85 (515)
T COG2812          20 GQEHVVKTLSNALENGRI-AHAY----LFSGPRGVGKTTIARILAKALNCENGPTAEPC-----GKCI-SC-KEINEG--   85 (515)
T ss_pred             CCHHHHHHHHHHHHHCCC-HHHH----HHCCCCCCCCHHHHHHHHHHHCCCCCCCCCCC-----HHHH-HH-HHHHCC--
T ss_conf             648999999999980842-3336----51377776710499999999568898777722-----5316-66-865148--


Q ss_pred             HCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCEEEEECCCCCCHHHHHHHHH
Q ss_conf             62312112333321000123332211113457761266210135445565210113586289997545599889999898
Q gi|254781187|r  134 MLPHRHWFEMQSLSLHPSGWYAELLEQSMGIDSKHYTITCRTYSEERPDTFVGPHNTHGMAVFNDEASGTPDIINKSILG  213 (367)
Q Consensus       134 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~ea~~g~h~~~~~l~ivDEAsgI~d~i~e~i~g  213 (367)
                      ..                   ..+  +++........-.-+-..+.  -.+.-..+.+. .+|+||+...+...|.++..
T Consensus        86 ~~-------------------~Dv--iEiDaASn~gVddiR~i~e~--v~y~P~~~ryK-VyiIDEvHMLS~~afNALLK  141 (515)
T COG2812          86 SL-------------------IDV--IEIDAASNTGVDDIREIIEK--VNYAPSEGRYK-VYIIDEVHMLSKQAFNALLK  141 (515)
T ss_pred             CC-------------------CCC--HHHHHHHCCCHHHHHHHHHH--HCCCCCCCCCE-EEEEECHHHHHHHHHHHHHC
T ss_conf             86-------------------410--11364445486799999987--24688666641-89983187643788888751


Q ss_pred             HHHCCCCCEEEE
Q ss_conf             740698825899
Q gi|254781187|r  214 FFTELNPNRFWI  225 (367)
Q Consensus       214 ~Lt~~~~~~~~i  225 (367)
                      +|-.+=...+.+
T Consensus       142 TLEEPP~hV~FI  153 (515)
T COG2812         142 TLEEPPSHVKFI  153 (515)
T ss_pred             CCCCCCCCEEEE
T ss_conf             113686674899


No 172
>KOG0352 consensus
Probab=92.16  E-value=0.82  Score=23.95  Aligned_cols=166  Identities=15%  Similarity=0.114  Sum_probs=75.6

Q ss_pred             HHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHHHHH-
Q ss_conf             8999999988887512455555411247761488678899999999999970899779997153799999999999999-
Q gi|254781187|r   53 RWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLKNTLWAEVSKW-  131 (367)
Q Consensus        53 ~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~~~lw~ei~k~-  131 (367)
                      +-|+.....+...-+           -|-|+-+.|.|||-+.-.-.|    ...+ -.||++|-..-+++.+ ..+.+. 
T Consensus        23 ~LQE~A~~c~VK~k~-----------DVyVsMPTGaGKSLCyQLPaL----~~~g-ITIV~SPLiALIkDQi-DHL~~LK   85 (641)
T KOG0352          23 RLQEQAINCIVKRKC-----------DVYVSMPTGAGKSLCYQLPAL----VHGG-ITIVISPLIALIKDQI-DHLKRLK   85 (641)
T ss_pred             HHHHHHHHHHHHCCC-----------CEEEECCCCCCHHHHHHCHHH----HHCC-EEEEECHHHHHHHHHH-HHHHHHC
T ss_conf             578998999883467-----------379964688760145426587----7288-1899307899999998-7787405


Q ss_pred             --HHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEC-CCCCCCCCCCCCCCCCCCC-EEEEECCCCCCH--
Q ss_conf             --9862312112333321000123332211113457761266210-1354455652101135862-899975455998--
Q gi|254781187|r  132 --LSMLPHRHWFEMQSLSLHPSGWYAELLEQSMGIDSKHYTITCR-TYSEERPDTFVGPHNTHGM-AVFNDEASGTPD--  205 (367)
Q Consensus       132 --~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~-~~~~~~~ea~~g~h~~~~~-l~ivDEAsgI~d--  205 (367)
                        .+. .|......+   +..........+..++    ..+|+-- .++..=-.-++++|..+.+ +++||||.-|++  
T Consensus        86 Vp~~S-LNSKlSt~E---R~ri~~DL~~ekp~~K----~LYITPE~AAt~~FQ~lLn~L~~r~~L~Y~vVDEAHCVSQWG  157 (641)
T KOG0352          86 VPCES-LNSKLSTVE---RSRIMGDLAKEKPTIK----MLYITPEGAATDGFQKLLNGLANRDVLRYIVVDEAHCVSQWG  157 (641)
T ss_pred             CCHHH-HHCHHHHHH---HHHHHHHHHHCCCCEE----EEEECHHHHHHHHHHHHHHHHHHHCEEEEEEECHHHHHHHHC
T ss_conf             61666-401210788---9999888874377514----899763155566689999988741402247733466677626


Q ss_pred             -H--HHHHHHHHHHCCCCCEEEEE-------------------------EECCCCCCCHHHHHHHC
Q ss_conf             -8--99998987406988258999-------------------------80789998768875411
Q gi|254781187|r  206 -I--INKSILGFFTELNPNRFWIM-------------------------TSNTRRLNGWFYDIFNI  243 (367)
Q Consensus       206 -~--i~e~i~g~Lt~~~~~~~~i~-------------------------igNP~r~~g~Fye~~~~  243 (367)
                       +  .-.--+|.|++.-.-..|++                         +.+|.-..|.|||...+
T Consensus       158 HDFRPDYL~LG~LRS~~~~vpwvALTATA~~~VqEDi~~qL~L~~PVAiFkTP~FR~NLFYD~~~K  223 (641)
T KOG0352         158 HDFRPDYLTLGSLRSVCPGVPWVALTATANAKVQEDIAFQLKLRNPVAIFKTPTFRDNLFYDNHMK  223 (641)
T ss_pred             CCCCCCHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHHHHHHCCCCHHHHCCCCHHHHHHHHHHHH
T ss_conf             666820444666774469996698543467767799999976058544405741454445788888


No 173
>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=92.09  E-value=0.46  Score=25.49  Aligned_cols=51  Identities=27%  Similarity=0.330  Sum_probs=36.8

Q ss_pred             HHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCH
Q ss_conf             89999999888875124555554112477614886788999999999999708997799971537
Q gi|254781187|r   53 RWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSE  117 (367)
Q Consensus        53 ~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~  117 (367)
                      +=|.++|+.....-           .++.|+++.|+|||++...++-+.   .+..+++++..+.
T Consensus        12 ~~~~~~L~~~v~~~-----------~nIlIsG~tGSGKTTll~al~~~i---~~~~rivtiEd~~   62 (186)
T cd01130          12 PLQAAYLWLAVEAR-----------KNILISGGTGSGKTTLLNALLAFI---PPDERIITIEDTA   62 (186)
T ss_pred             HHHHHHHHHHHHCC-----------CCEEEECCCCCCHHHHHHHHHHHC---CCCCCEEEECCCH
T ss_conf             99999999999859-----------989998999998999999999613---3456459841535


No 174
>PRK06995 flhF flagellar biosynthesis regulator FlhF; Validated
Probab=92.07  E-value=0.3  Score=26.60  Aligned_cols=41  Identities=20%  Similarity=0.138  Sum_probs=33.3

Q ss_pred             EEEECCCCCCHHHHHHHHHHHHHHHCC-CCEEEEECCCHHHH
Q ss_conf             776148867889999999999997089-97799971537999
Q gi|254781187|r   80 CAISAGRGIGKTTLNAWMMLWLISTRP-GMSIICIANSETQL  120 (367)
Q Consensus        80 ~~v~sgrg~GKS~~~a~~~lw~~~~~~-~~~v~~~A~t~~Q~  120 (367)
                      ++..++.|+|||+.+|=++..+.+.+- ....++|..|++-.
T Consensus       179 ~alVGPTGVGKTTTiAKLAAr~~l~~g~~kVaLIT~DTYRIg  220 (404)
T PRK06995        179 FALVGPTGVGKTTTTAKLAARCVMRHGASKVALLTTDSYRIG  220 (404)
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHHHHCCCCEEEEECCCCCHH
T ss_conf             898668887637589999999999838983799976875478


No 175
>PRK06696 uridine kinase; Validated
Probab=92.01  E-value=0.74  Score=24.24  Aligned_cols=54  Identities=17%  Similarity=0.129  Sum_probs=37.1

Q ss_pred             HHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEE
Q ss_conf             99999988887512455555411247761488678899999999999970899779997
Q gi|254781187|r   55 QLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICI  113 (367)
Q Consensus        55 q~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~  113 (367)
                      ...++.+|++++....-   .-.++|+|.++=|+|||+++..++--+-.  .+..++++
T Consensus         7 r~~~~~~~~~~i~~~~p---~rpl~VgIdG~~gSGKTTlA~~La~~L~~--~G~~V~~v   60 (227)
T PRK06696          7 RKQVVKEIANHILTLNL---TRPLRVAIDGITASGKTTFANELAEEIKK--RGRPVIRA   60 (227)
T ss_pred             HHHHHHHHHHHHHHCCC---CCCEEEEEECCCCCCHHHHHHHHHHHHHH--CCCCEEEE
T ss_conf             87899999999983599---98689997789987879999999999974--69948997


No 176
>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=91.91  E-value=0.43  Score=25.70  Aligned_cols=35  Identities=26%  Similarity=0.263  Sum_probs=26.9

Q ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEE
Q ss_conf             47761488678899999999999970899779997
Q gi|254781187|r   79 KCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICI  113 (367)
Q Consensus        79 ~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~  113 (367)
                      |..|-+|+|+|||++...++.-....+++..+++.
T Consensus        18 R~gI~g~~gvGKT~Ll~~i~~~~~~~~~~~~~v~~   52 (249)
T cd01128          18 RGLIVAPPKAGKTTLLQSIANAITKNHPEVYLIVL   52 (249)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHHCCCEEEEEE
T ss_conf             77887899988999999999999985898499999


No 177
>PRK11054 helD DNA helicase IV; Provisional
Probab=91.59  E-value=0.43  Score=25.67  Aligned_cols=46  Identities=22%  Similarity=0.260  Sum_probs=38.7

Q ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHHC--CCCEEEEECCCHHHHHHHH
Q ss_conf             477614886788999999999999708--9977999715379999999
Q gi|254781187|r   79 KCAISAGRGIGKTTLNAWMMLWLISTR--PGMSIICIANSETQLKNTL  124 (367)
Q Consensus        79 ~~~v~sgrg~GKS~~~a~~~lw~~~~~--~~~~v~~~A~t~~Q~~~~l  124 (367)
                      ++.|.||=|+|||..+..-+.|++...  ++.+|++++=|.+-+.++-
T Consensus       211 ~~LVLAGAGSGKT~vLt~RiayLI~~g~~~P~~ILaLTFT~kAA~EMr  258 (684)
T PRK11054        211 SLLVLAGAGSGKTSVLVARAGWLLARGQAQPEQILLLAFGRKAAEEMD  258 (684)
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHHHCCCCCHHHEEEEECCHHHHHHHH
T ss_conf             648983389970779999999999759998667786863499999999


No 178
>PRK10865 protein disaggregation chaperone; Provisional
Probab=91.53  E-value=0.97  Score=23.53  Aligned_cols=48  Identities=25%  Similarity=0.206  Sum_probs=30.2

Q ss_pred             HHHHHHHHHHHHHHCC-CCCCCCCE--EEEEEECCCCCCHHHHHHHHHHHH
Q ss_conf             9999999888875124-55555411--247761488678899999999999
Q gi|254781187|r   54 WQLEFMEAVDVHCHSN-VNNSNPTI--FKCAISAGRGIGKTTLNAWMMLWL  101 (367)
Q Consensus        54 wq~~~l~~~~~~~~~~-~~~~~~~~--~~~~v~sgrg~GKS~~~a~~~lw~  101 (367)
                      .|.++++.|++.+++. ..-..|..  --....++-|+|||.++-.++-.+
T Consensus       572 GQd~AI~~v~~aI~~sraGL~dp~rPiGsFLFlGPTGVGKTElAK~LA~~L  622 (857)
T PRK10865        572 GQNEAVEAVSNAIRRSRAGLSDPNRPIGSFLFLGPTGVGKTELCKALANFM  622 (857)
T ss_pred             CHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHH
T ss_conf             809999999999999863899999973899986898788899999999998


No 179
>PRK04195 replication factor C large subunit; Provisional
Probab=91.11  E-value=1.1  Score=23.27  Aligned_cols=22  Identities=23%  Similarity=0.191  Sum_probs=17.4

Q ss_pred             EEEEECCCCCCHHHHHHHHHHH
Q ss_conf             4776148867889999999999
Q gi|254781187|r   79 KCAISAGRGIGKTTLNAWMMLW  100 (367)
Q Consensus        79 ~~~v~sgrg~GKS~~~a~~~lw  100 (367)
                      -+.+.++.|+|||+++-+++--
T Consensus        42 ~lLL~GPpGvGKTT~a~~lAk~   63 (403)
T PRK04195         42 ALLLYGPPGVGKTSLAHALAND   63 (403)
T ss_pred             EEEEECCCCCCHHHHHHHHHHH
T ss_conf             6998893998799999999998


No 180
>KOG0328 consensus
Probab=91.11  E-value=0.17  Score=28.21  Aligned_cols=151  Identities=13%  Similarity=-0.006  Sum_probs=74.2

Q ss_pred             CCCCCHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCC-CCEEEEECCCHHHHHHHHH
Q ss_conf             666842899999998888751245555541124776148867889999999999997089-9779997153799999999
Q gi|254781187|r   47 HFSQPHRWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRP-GMSIICIANSETQLKNTLW  125 (367)
Q Consensus        47 ~~~~p~~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~-~~~v~~~A~t~~Q~~~~lw  125 (367)
                      +|..|-.-|..++-.|-.    +        ..|.+.|--|+|||...+.-++=-+-... ...+++.+||..-+..+  
T Consensus        46 GfekPS~IQqrAi~~Ilk----G--------rdViaQaqSGTGKTa~~si~vlq~~d~~~r~tQ~lilsPTRELa~Qi--  111 (400)
T KOG0328          46 GFEKPSAIQQRAIPQILK----G--------RDVIAQAQSGTGKTATFSISVLQSLDISVRETQALILSPTRELAVQI--  111 (400)
T ss_pred             CCCCCHHHHHHHHHHHHC----C--------CCEEEEECCCCCCEEEEEEEEEEECCCCCCEEEEEEECCHHHHHHHH--
T ss_conf             257816777610245633----6--------61478704788844789866314034342003578954708999999--


Q ss_pred             HHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCEEEEECCC----
Q ss_conf             9999999862312112333321000123332211113457761266210135445565210113586289997545----
Q gi|254781187|r  126 AEVSKWLSMLPHRHWFEMQSLSLHPSGWYAELLEQSMGIDSKHYTITCRTYSEERPDTFVGPHNTHGMAVFNDEAS----  201 (367)
Q Consensus       126 ~ei~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~ea~~g~h~~~~~l~ivDEAs----  201 (367)
                      .++-..+...-+-.-+.|..        ....-..--+.+-|...+.+.+-+...--..+.++-...-++++|||.    
T Consensus       112 ~~vi~alg~~mnvq~hacig--------g~n~gedikkld~G~hvVsGtPGrv~dmikr~~L~tr~vkmlVLDEaDemL~  183 (400)
T KOG0328         112 QKVILALGDYMNVQCHACIG--------GKNLGEDIKKLDYGQHVVSGTPGRVLDMIKRRSLRTRAVKMLVLDEADEMLN  183 (400)
T ss_pred             HHHHHHHCCCCCCEEEEEEC--------CCCCCHHHHHHCCCCEEEECCCCHHHHHHHHCCCCCCCEEEEEECCHHHHHH
T ss_conf             99999832423644898735--------7751034565325614750798159999986231011426898545899987


Q ss_pred             -CCCHHHHHHHHHHHHCCCCC
Q ss_conf             -59988999989874069882
Q gi|254781187|r  202 -GTPDIINKSILGFFTELNPN  221 (367)
Q Consensus       202 -gI~d~i~e~i~g~Lt~~~~~  221 (367)
                       |..+.+|++..-  -.++..
T Consensus       184 kgfk~Qiydiyr~--lp~~~Q  202 (400)
T KOG0328         184 KGFKEQIYDIYRY--LPPGAQ  202 (400)
T ss_pred             HHHHHHHHHHHHH--CCCCCE
T ss_conf             5677889999984--799866


No 181
>PRK09270 frcK putative fructose transport system kinase; Reviewed
Probab=91.03  E-value=0.85  Score=23.88  Aligned_cols=38  Identities=24%  Similarity=0.244  Sum_probs=27.2

Q ss_pred             CEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEE
Q ss_conf             11247761488678899999999999970899779997
Q gi|254781187|r   76 TIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICI  113 (367)
Q Consensus        76 ~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~  113 (367)
                      .++-++|+++=|+|||+++..++--+-...+...++++
T Consensus        33 rR~lIgIaG~pGSGKSTlA~~l~~~L~~~~~~~~~~~v   70 (230)
T PRK09270         33 RRTVVGIAGPPGAGKSTLAETLWEALSQQGPELPAIQV   70 (230)
T ss_pred             CEEEEEEECCCCCCHHHHHHHHHHHHHHCCCCCCEEEE
T ss_conf             71899998999889999999999998623799857997


No 182
>COG5525 Bacteriophage tail assembly protein [General function prediction only]
Probab=90.92  E-value=0.21  Score=27.64  Aligned_cols=152  Identities=12%  Similarity=0.080  Sum_probs=83.3

Q ss_pred             HHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHHHHH
Q ss_conf             28999999988887512455555411247761488678899999999999970899779997153799999999999999
Q gi|254781187|r   52 HRWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLKNTLWAEVSKW  131 (367)
Q Consensus        52 ~~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~~~lw~ei~k~  131 (367)
                      .+.|.++...+          ...+..+|.+..+-++|||.+.-..+.+++.+.| ..-+++.||...+++-+-..+..-
T Consensus        49 ~p~~~~~~n~~----------~~~~~~~V~f~k~ArvG~T~m~~gw~~Y~I~~~p-~~mlv~qpt~~~a~~~~k~k~~pt  117 (611)
T COG5525          49 LPFQIAIMNAM----------GSDEIRAVNFVKSARVGKTKMLLGWIGYFIEHKP-RNMLVVQPTDEKAREHSKTKVEPT  117 (611)
T ss_pred             CHHHHHHHHCC----------CCCCCEEEEEEECCCCCCEEEECCEEEEEEEECC-CCCEEECCCHHHHHHHHHHHCCCC
T ss_conf             26899987536----------9864168999740203622454225899998657-652333365557799888750750


Q ss_pred             HHHCCC-CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCEEEEECCCCCCHHHHH-
Q ss_conf             986231-211233332100012333221111345776126621013544556521011358628999754559988999-
Q gi|254781187|r  132 LSMLPH-RHWFEMQSLSLHPSGWYAELLEQSMGIDSKHYTITCRTYSEERPDTFVGPHNTHGMAVFNDEASGTPDIINK-  209 (367)
Q Consensus       132 ~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~ea~~g~h~~~~~l~ivDEAsgI~d~i~e-  209 (367)
                      ++-.|. .+.         +.+.....+...-.+..|..+..+-       .+....++.+..++.+||-+.++.++-. 
T Consensus       118 i~~~p~l~~~---------ls~~~~dNn~~~K~f~~G~~l~~g~-------~s~~~~r~~s~~~v~lde~d~fpedv~~E  181 (611)
T COG5525         118 IRDVPSLVSL---------LSPSRNDNNLTDKRFPGGVFLMIGW-------KSAKNYRSISVDVVVLDELDRFPEDVEGE  181 (611)
T ss_pred             HHCCHHHHHH---------CCCCCCCCCEECCCCCCCEEEEECC-------CCCCCCCCCCHHHHHHHHHHCCCHHHCCC
T ss_conf             2006337865---------2765678731102334772797256-------54565667644565666774365122268


Q ss_pred             -----HHHHHHHCCCCCEEEEEEECCC
Q ss_conf             -----9898740698825899980789
Q gi|254781187|r  210 -----SILGFFTELNPNRFWIMTSNTR  231 (367)
Q Consensus       210 -----~i~g~Lt~~~~~~~~i~igNP~  231 (367)
                           .+..-+++ ....+.+..|+|+
T Consensus       182 Gs~~sl~~kR~~t-~~~~~~l~~stP~  207 (611)
T COG5525         182 GSATSLASKRITT-MSWGKSLVESTPT  207 (611)
T ss_pred             CCHHHHHHHHHCC-CCCCCEEEECCCC
T ss_conf             8876778876024-5566224413787


No 183
>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=90.83  E-value=0.78  Score=24.08  Aligned_cols=51  Identities=29%  Similarity=0.526  Sum_probs=35.4

Q ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEE-ECCCHHHHHHHHHHHHHH
Q ss_conf             4776148867889999999999997089977999-715379999999999999
Q gi|254781187|r   79 KCAISAGRGIGKTTLNAWMMLWLISTRPGMSIIC-IANSETQLKNTLWAEVSK  130 (367)
Q Consensus        79 ~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~-~A~t~~Q~~~~lw~ei~k  130 (367)
                      |+.+-+|+|+|||.++..++.-....+.+..|++ +....+.+.+ ++.++++
T Consensus       140 r~gIfggaGvGKT~Ll~e~i~n~~~~~~~v~V~~~IGER~rE~~e-~~~el~~  191 (449)
T TIGR03305       140 KAGLFGGAGVGKTVLLTEMIHNMVGQHQGVSIFCGIGERCREGEE-LYREMKE  191 (449)
T ss_pred             EEEEECCCCCCCCCHHHHHHHHHHHHCCCEEEEEEEEEEHHHHHH-HHHHHHH
T ss_conf             656652799984101899998656414886899997452167999-9999875


No 184
>COG5410 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=90.83  E-value=0.84  Score=23.89  Aligned_cols=187  Identities=15%  Similarity=0.089  Sum_probs=88.0

Q ss_pred             CCCCCCCHHHHHHHHCCCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEEC
Q ss_conf             54572337899997523201259888855430146688844366684289999999888875124555554112477614
Q gi|254781187|r    5 ISTDQKLEQELHEMLMHAECVLSFKNFVMRFFPWGIKGKPLEHFSQPHRWQLEFMEAVDVHCHSNVNNSNPTIFKCAISA   84 (367)
Q Consensus         5 ~~~~~~~~~~~~~~~~~~~~~~~~~~f~~~~~~w~~~~~~~~~~~~p~~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~s   84 (367)
                      .++|.-+++.|..+|    |.++-+.|.+++|-....+ .- +   | -|-.+++-+.-+|.+.+.      .-++.+--
T Consensus         3 ~~~~~~~~EaL~~~L----~~~~h~f~~r~f~T~~~~~-~Y-~---~-~~H~~iI~~~L~~Vi~G~------~k~~Iin~   66 (305)
T COG5410           3 RSTEQAQEEALIKAL----CEADHLFFTRYFFTQRQQL-RY-R---V-NWHHHVIAGVLDDVIAGR------RKDVIINV   66 (305)
T ss_pred             CCHHHHHHHHHHHHH----HHHHHHHHHHHHHEECCCC-EE-C---C-HHHHHHHHHHHHHHHCCC------CEEEEEEC
T ss_conf             203777799999999----9999988867652116653-00-2---1-155799998888886363------10489966


Q ss_pred             CCCCCHHHHHHH-HHHHHHHHCCCCEEEEECCCHHHHHHHHHHHHHH-HHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             886788999999-9999997089977999715379999999999999-99862312112333321000123332211113
Q gi|254781187|r   85 GRGIGKTTLNAW-MMLWLISTRPGMSIICIANSETQLKNTLWAEVSK-WLSMLPHRHWFEMQSLSLHPSGWYAELLEQSM  162 (367)
Q Consensus        85 grg~GKS~~~a~-~~lw~~~~~~~~~v~~~A~t~~Q~~~~lw~ei~k-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  162 (367)
                      +-+.-||.+++. +-.++|..+|.+++++++.+.  +-.+.+.+-.+ .+++-....+|..+..     +..+....-.+
T Consensus        67 PP~~skS~~Vs~~~PaY~L~~NP~KR~~~~SYSd--~La~~~s~~~r~ii~sd~y~~LFp~~I~-----~~~~~~k~w~i  139 (305)
T COG5410          67 PPGSSKSELVAINVPAYGLALNPYKRFLHISYSD--DLALLNSETAREIVQSDEYRALFPLEIA-----DDAKSKKRWNV  139 (305)
T ss_pred             CCCCCCCEEEEEECCHHEEEECCCCEEEEEEHHH--HHHHHHCHHHHHHHHCCCHHHCCCEEEC-----CCCCCCCCEEE
T ss_conf             9852323478850541125507633189854767--8998834467898722103320763204-----67667632368


Q ss_pred             CCCCCCEEEEECCCCCCCCCCCCCCCCCCCCEEEEECCCC--------CCHHHHHHHHHHH----HCCCCCEE
Q ss_conf             4577612662101354455652101135862899975455--------9988999989874----06988258
Q gi|254781187|r  163 GIDSKHYTITCRTYSEERPDTFVGPHNTHGMAVFNDEASG--------TPDIINKSILGFF----TELNPNRF  223 (367)
Q Consensus       163 ~~~~~~~~~~a~~~~~~~~ea~~g~h~~~~~l~ivDEAsg--------I~d~i~e~i~g~L----t~~~~~~~  223 (367)
                      ..++|..+++..+         .+.-|+...++|+|.--.        |-++++.-.+.++    ..++..++
T Consensus       140 ~~~gGg~yaTs~g---------G~ATG~GaD~LIIDDP~k~e~a~SktIR~K~Yr~~~st~~sr~~~~~s~ii  203 (305)
T COG5410         140 VVDGGGVYATSLG---------GQATGFGADALIIDDPLKVEDAYSKTIRSKAYRKLVSTVKSRKASPDTPII  203 (305)
T ss_pred             EEECCEEEEEECC---------CCCCCCCCCEEEECCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCEE
T ss_conf             9428878887305---------654577874698659988777545689999999999998753038997189


No 185
>COG0003 ArsA Predicted ATPase involved in chromosome partitioning [Cell division and chromosome partitioning]
Probab=90.54  E-value=0.38  Score=25.98  Aligned_cols=47  Identities=19%  Similarity=0.254  Sum_probs=29.2

Q ss_pred             EEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHH
Q ss_conf             761488678899999999999970899779997153799999999999
Q gi|254781187|r   81 AISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLKNTLWAEV  128 (367)
Q Consensus        81 ~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~~~lw~ei  128 (367)
                      .+.+==|+|||+++|+.++|.+.-... ..++.....+.+.+++=-++
T Consensus         6 ~f~GKGGVGKTT~aaA~A~~lA~~g~k-vLlvStDPAhsL~d~f~~el   52 (322)
T COG0003           6 FFTGKGGVGKTTIAAATAVKLAESGKK-VLLVSTDPAHSLGDVFDLEL   52 (322)
T ss_pred             EEECCCCCCHHHHHHHHHHHHHHCCCC-EEEEEECCCCCHHHHHCCCC
T ss_conf             993688545899999999999975990-79998489874476542304


No 186
>COG0514 RecQ Superfamily II DNA helicase [DNA replication, recombination, and repair]
Probab=90.53  E-value=0.69  Score=24.44  Aligned_cols=61  Identities=16%  Similarity=0.151  Sum_probs=40.9

Q ss_pred             CCCCCHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHH
Q ss_conf             666842899999998888751245555541124776148867889999999999997089977999715379999999
Q gi|254781187|r   47 HFSQPHRWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLKNTL  124 (367)
Q Consensus        47 ~~~~p~~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~~~l  124 (367)
                      ++++.|+-|.++++.+.+..            ++.|.=+.|.|||-+.-.-++-.    +| -++|++|-.+=.+|-+
T Consensus        14 Gy~~FR~gQ~evI~~~l~g~------------d~lvvmPTGgGKSlCyQiPAll~----~G-~TLVVSPLiSLM~DQV   74 (590)
T COG0514          14 GYASFRPGQQEIIDALLSGK------------DTLVVMPTGGGKSLCYQIPALLL----EG-LTLVVSPLISLMKDQV   74 (590)
T ss_pred             CCCCCCCCHHHHHHHHHCCC------------CEEEECCCCCCCCHHHHHHHHHC----CC-CEEEECCHHHHHHHHH
T ss_conf             91303888899999996588------------67998538987106743678865----99-7899785688899999


No 187
>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=90.40  E-value=0.64  Score=24.62  Aligned_cols=42  Identities=19%  Similarity=0.389  Sum_probs=26.5

Q ss_pred             EEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEEC-CCHHHHHHHH
Q ss_conf             7614886788999999999999708997799971-5379999999
Q gi|254781187|r   81 AISAGRGIGKTTLNAWMMLWLISTRPGMSIICIA-NSETQLKNTL  124 (367)
Q Consensus        81 ~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A-~t~~Q~~~~l  124 (367)
                      -+.+-=|+|||+++|+++++.+-  .|.|+++++ .-.+.+.+++
T Consensus         5 ~~~GKGGVGKTT~AaA~A~~~A~--~G~rvLlvStDPAhsL~D~~   47 (304)
T pfam02374         5 FFGGKGGVGKTTVSCATAVRLSE--QGKKVLLVSTDPAHSLSDSF   47 (304)
T ss_pred             EEECCCCCCHHHHHHHHHHHHHH--CCCEEEEEECCCCCHHHHHH
T ss_conf             99579857489999999999995--89929999469721488984


No 188
>KOG0947 consensus
Probab=90.34  E-value=1.3  Score=22.84  Aligned_cols=68  Identities=13%  Similarity=0.165  Sum_probs=46.6

Q ss_pred             CCHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHHH
Q ss_conf             84289999999888875124555554112477614886788999999999999708997799971537999999999999
Q gi|254781187|r   50 QPHRWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLKNTLWAEVS  129 (367)
Q Consensus        50 ~p~~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~~~lw~ei~  129 (367)
                      .|+..|+++...+--+.            -|-|+|..-.|||.++- +++ -++.....+.++|+|-. -+.+-=|+..+
T Consensus       297 elD~FQk~Ai~~lerg~------------SVFVAAHTSAGKTvVAE-YAi-alaq~h~TR~iYTSPIK-ALSNQKfRDFk  361 (1248)
T KOG0947         297 ELDTFQKEAIYHLERGD------------SVFVAAHTSAGKTVVAE-YAI-ALAQKHMTRTIYTSPIK-ALSNQKFRDFK  361 (1248)
T ss_pred             CCCHHHHHHHHHHHCCC------------EEEEEECCCCCCCHHHH-HHH-HHHHHHCCCEEECCHHH-HHCCCHHHHHH
T ss_conf             76678999999997278------------17997137788436999-999-99886355157526346-54001578887


Q ss_pred             HHH
Q ss_conf             999
Q gi|254781187|r  130 KWL  132 (367)
Q Consensus       130 k~~  132 (367)
                      .-.
T Consensus       362 ~tF  364 (1248)
T KOG0947         362 ETF  364 (1248)
T ss_pred             HHC
T ss_conf             742


No 189
>KOG0332 consensus
Probab=90.26  E-value=0.22  Score=27.43  Aligned_cols=72  Identities=18%  Similarity=0.122  Sum_probs=44.6

Q ss_pred             CCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHC-CCCEEEEECCCHHHHH
Q ss_conf             844366684289999999888875124555554112477614886788999999999999708-9977999715379999
Q gi|254781187|r   43 KPLEHFSQPHRWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTR-PGMSIICIANSETQLK  121 (367)
Q Consensus        43 ~~~~~~~~p~~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~-~~~~v~~~A~t~~Q~~  121 (367)
                      +-.+.|+-|.+.|+..|--+-.+--         . ++.-.|--|+|||+....-+|-.+--. .-..++|+|||..-++
T Consensus       105 ly~M~F~kPskIQe~aLPlll~~Pp---------~-nlIaQsqsGtGKTaaFvL~MLsRvd~~~~~PQ~iCLaPtrELA~  174 (477)
T KOG0332         105 LYAMKFQKPSKIQETALPLLLAEPP---------Q-NLIAQSQSGTGKTAAFVLTMLSRVDPDVVVPQCICLAPTRELAP  174 (477)
T ss_pred             HHHHCCCCCCHHHHHHCCHHHCCCC---------H-HHHHHHCCCCCHHHHHHHHHHHHCCCCCCCCCCEEECCHHHHHH
T ss_conf             8875268832577752125305982---------6-56655017886058999999873483335877405476177799


Q ss_pred             HHH
Q ss_conf             999
Q gi|254781187|r  122 NTL  124 (367)
Q Consensus       122 ~~l  124 (367)
                      .++
T Consensus       175 Q~~  177 (477)
T KOG0332         175 QTG  177 (477)
T ss_pred             HHH
T ss_conf             898


No 190
>KOG0781 consensus
Probab=90.20  E-value=1.3  Score=22.77  Aligned_cols=137  Identities=15%  Similarity=0.267  Sum_probs=74.9

Q ss_pred             HHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEEC-CCH-----HHHHHHHHHHH
Q ss_conf             999999888875124555554112477614886788999999999999708997799971-537-----99999999999
Q gi|254781187|r   55 QLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIA-NSE-----TQLKNTLWAEV  128 (367)
Q Consensus        55 q~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A-~t~-----~Q~~~~lw~ei  128 (367)
                      -.++||+|..--++.    -|++  ++..+=.|+|||+-.|-++.|++-..  .+|++.| .|.     .|++.-    +
T Consensus       362 sVDlLrdI~~ar~~k----rPYv--i~fvGVNGVGKSTNLAKIayWLlqNk--frVlIAACDTFRsGAvEQLrtH----v  429 (587)
T KOG0781         362 SVDLLRDIMSARRRK----RPYV--ISFVGVNGVGKSTNLAKIAYWLLQNK--FRVLIAACDTFRSGAVEQLRTH----V  429 (587)
T ss_pred             HHHHHHHHHHHHHCC----CCEE--EEEEEECCCCCCCHHHHHHHHHHHCC--CEEEEEECCCHHHHHHHHHHHH----H
T ss_conf             066999999987468----9759--99982147665132999999998578--3699986243124478999999----9


Q ss_pred             HHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCEEEEECCCCCCH--H
Q ss_conf             99998623121123333210001233322111134577612662101354455652101135862899975455998--8
Q gi|254781187|r  129 SKWLSMLPHRHWFEMQSLSLHPSGWYAELLEQSMGIDSKHYTITCRTYSEERPDTFVGPHNTHGMAVFNDEASGTPD--I  206 (367)
Q Consensus       129 ~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~ea~~g~h~~~~~l~ivDEAsgI~d--~  206 (367)
                      ++...+.+       +.-.++.+.|.            ++   .+.-+    -++++-.+..++..+++|-|.-..+  .
T Consensus       430 ~rl~~l~~-------~~v~lfekGYg------------kd---~a~va----k~AI~~a~~~gfDvvLiDTAGRmhn~~~  483 (587)
T KOG0781         430 ERLSALHG-------TMVELFEKGYG------------KD---AAGVA----KEAIQEARNQGFDVVLIDTAGRMHNNAP  483 (587)
T ss_pred             HHHHHHCC-------CHHHHHHHHCC------------CC---HHHHH----HHHHHHHHHCCCCEEEEECCCCCCCCHH
T ss_conf             99987455-------20488861047------------78---28999----9999999866987899835443347806


Q ss_pred             HHHHHHHHHHCCCCCEEEEEEECC
Q ss_conf             999989874069882589998078
Q gi|254781187|r  207 INKSILGFFTELNPNRFWIMTSNT  230 (367)
Q Consensus       207 i~e~i~g~Lt~~~~~~~~i~igNP  230 (367)
                      .+.++.. |...+.+-+.+..|--
T Consensus       484 LM~~L~k-l~~~n~pD~i~~VgEA  506 (587)
T KOG0781         484 LMTSLAK-LIKVNKPDLILFVGEA  506 (587)
T ss_pred             HHHHHHH-HHHCCCCCEEEEEHHH
T ss_conf             7899999-9744798659985055


No 191
>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=90.20  E-value=1.3  Score=22.77  Aligned_cols=54  Identities=19%  Similarity=0.191  Sum_probs=40.2

Q ss_pred             HHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEE--CCCHH
Q ss_conf             99999988887512455555411247761488678899999999999970899779997--15379
Q gi|254781187|r   55 QLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICI--ANSET  118 (367)
Q Consensus        55 q~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~--A~t~~  118 (367)
                      -.++|+.+..+..        ...++-|...-|+|||+++..++..+.-.  +.+|.|+  -|+..
T Consensus        15 ~~~ll~~~~~~~g--------~a~~iGiTG~PGaGKStli~~l~~~~~~~--g~~vaVlAvDPSS~   70 (267)
T pfam03308        15 ARELLRRLMPLTG--------RAHRVGITGVPGAGKSTLIEALGMELRRR--GHRVAVLAVDPSSP   70 (267)
T ss_pred             HHHHHHHHHHHCC--------CCEEEEEECCCCCCHHHHHHHHHHHHHHC--CCEEEEEEECCCCC
T ss_conf             9999999874359--------95599876899887999999999999968--98689999789998


No 192
>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=89.95  E-value=1.3  Score=22.64  Aligned_cols=26  Identities=12%  Similarity=0.189  Sum_probs=21.4

Q ss_pred             CEEEEECCCCCCHHHHHHHHHHHHCC
Q ss_conf             28999754559988999989874069
Q gi|254781187|r  193 MAVFNDEASGTPDIINKSILGFFTEL  218 (367)
Q Consensus       193 ~l~ivDEAsgI~d~i~e~i~g~Lt~~  218 (367)
                      .++++||..-......++++|.+-++
T Consensus       103 ~ILFIDEIHr~nK~qqd~Llp~vE~g  128 (234)
T pfam05496       103 DVLFIDEIHRLNRAVEEILYPAMEDF  128 (234)
T ss_pred             CEEEEECHHHCCHHHHHHCCCCCCCC
T ss_conf             88999665435876887445533461


No 193
>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=89.83  E-value=0.25  Score=27.17  Aligned_cols=72  Identities=19%  Similarity=0.228  Sum_probs=47.0

Q ss_pred             CCEEEEECC-CCCC-HH---HHHHHHHHHHCCC-CCEEEEEEECCCCCCCHHHHHHHCCCCCEEEEEECCCCCCCCCHHH
Q ss_conf             628999754-5599-88---9999898740698-8258999807899987688754112235046752333288889889
Q gi|254781187|r  192 GMAVFNDEA-SGTP-DI---INKSILGFFTELN-PNRFWIMTSNTRRLNGWFYDIFNIPLEDWKRYQIDTRTVEGIDSGF  265 (367)
Q Consensus       192 ~~l~ivDEA-sgI~-d~---i~e~i~g~Lt~~~-~~~~~i~igNP~r~~g~Fye~~~~~~~~w~~~~~~~~d~p~~~~~~  265 (367)
                      +.|+|+||- ||.+ |.   |.+.+. .+++.. .+.++ +++       ++-+++..=+.++..+-++-+-+..=+.+.
T Consensus       166 P~laiLDE~DSGLDiDALk~V~~~in-~lr~~~P~~~~l-iiT-------HY~rlL~~I~PD~VhVl~~GrIV~sGd~~L  236 (248)
T TIGR01978       166 PKLAILDEIDSGLDIDALKIVAEGIN-RLREEHPDRAFL-IIT-------HYQRLLNYIKPDVVHVLVDGRIVKSGDVEL  236 (248)
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHHHH-HHHCCCCCCEEE-EEE-------CHHHHHHHCCCCEEEEEECCEEEEECCHHH
T ss_conf             95798606888763788899999999-873068980089-987-------517884131898899974675876489899


Q ss_pred             HHHHHHH
Q ss_conf             9999962
Q gi|254781187|r  266 HEGIISR  272 (367)
Q Consensus       266 i~~~~~~  272 (367)
                      ..+..++
T Consensus       237 a~~le~~  243 (248)
T TIGR01978       237 AKELEEK  243 (248)
T ss_pred             HHHHHHH
T ss_conf             9999860


No 194
>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=89.79  E-value=1.4  Score=22.56  Aligned_cols=37  Identities=27%  Similarity=0.321  Sum_probs=25.7

Q ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCH
Q ss_conf             477614886788999999999999708997799971537
Q gi|254781187|r   79 KCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSE  117 (367)
Q Consensus        79 ~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~  117 (367)
                      .+.|+++.|+|||++..+++-..  -.++.+++++..+.
T Consensus       141 ~ilIsG~TGSGKTT~l~all~~i--~~~~~riitiED~~  177 (283)
T pfam00437       141 NILVSGGTGSGKTTLLYALLNEI--NTDDERIVTIEDPV  177 (283)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHC--CCCCCCEEEECCCC
T ss_conf             59998899998899999999840--87776278733785


No 195
>KOG4284 consensus
Probab=89.78  E-value=0.68  Score=24.46  Aligned_cols=137  Identities=15%  Similarity=0.094  Sum_probs=69.6

Q ss_pred             CCCCCHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCC-CEEEEECCCHH---HHHH
Q ss_conf             6668428999999988887512455555411247761488678899999999999970899-77999715379---9999
Q gi|254781187|r   47 HFSQPHRWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPG-MSIICIANSET---QLKN  122 (367)
Q Consensus        47 ~~~~p~~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~-~~v~~~A~t~~---Q~~~  122 (367)
                      .|--|++-|..++-.+...+            -+.|.|--|+|||-+.+.+++--+-.+-. ..+++++||..   |+++
T Consensus        44 ~f~~ptkiQaaAIP~~~~km------------DliVQaKSGTGKTlVfsv~av~sl~~~~~~~q~~Iv~PTREiaVQI~~  111 (980)
T KOG4284          44 AFALPTKIQAAAIPAIFSKM------------DLIVQAKSGTGKTLVFSVLAVESLDSRSSHIQKVIVTPTREIAVQIKE  111 (980)
T ss_pred             CCCCCCCHHHHHHHHHHCCC------------CEEEEECCCCCCEEEEEEEEEHHCCCCCCCCEEEEEECCHHHHHHHHH
T ss_conf             34578701343211443155------------358981378885589985430222756676206997143566457999


Q ss_pred             HHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCEEEEECCCC
Q ss_conf             99999999998623121123333210001233322111134577612662101354455652101135862899975455
Q gi|254781187|r  123 TLWAEVSKWLSMLPHRHWFEMQSLSLHPSGWYAELLEQSMGIDSKHYTITCRTYSEERPDTFVGPHNTHGMAVFNDEASG  202 (367)
Q Consensus       123 ~lw~ei~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~ea~~g~h~~~~~l~ivDEAsg  202 (367)
                      .+++.       +|.-..++|.   .+...-.+..+.+.+   +.+.++.+.+-+-..---+..+.--+.-|+|+|||..
T Consensus       112 tv~~v-------~~sf~g~~cs---vfIGGT~~~~d~~rl---k~~rIvIGtPGRi~qL~el~~~n~s~vrlfVLDEADk  178 (980)
T KOG4284         112 TVRKV-------APSFTGARCS---VFIGGTAHKLDLIRL---KQTRIVIGTPGRIAQLVELGAMNMSHVRLFVLDEADK  178 (980)
T ss_pred             HHHHH-------CCCCCCCCEE---EEECCCHHHHHHHHH---HHCEEEECCCHHHHHHHHHCCCCCCCEEEEEECCHHH
T ss_conf             99986-------5244576058---996685435556665---4023784383588999870677711026888431776


Q ss_pred             CCH-HHH
Q ss_conf             998-899
Q gi|254781187|r  203 TPD-IIN  208 (367)
Q Consensus       203 I~d-~i~  208 (367)
                      .=+ ..|
T Consensus       179 L~~t~sf  185 (980)
T KOG4284         179 LMDTESF  185 (980)
T ss_pred             HHCHHHH
T ss_conf             6320247


No 196
>PRK11889 flhF flagellar biosynthesis regulator FlhF; Provisional
Probab=89.67  E-value=1.4  Score=22.51  Aligned_cols=60  Identities=18%  Similarity=0.108  Sum_probs=38.7

Q ss_pred             HHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCC-EEEEECCCHHHH
Q ss_conf             999888875124555554112477614886788999999999999708997-799971537999
Q gi|254781187|r   58 FMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGM-SIICIANSETQL  120 (367)
Q Consensus        58 ~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~-~v~~~A~t~~Q~  120 (367)
                      +|+++.-|... .+.+.-++--+|..++.|+|||+.+|=++..+.  ..+. ..++|..|++-+
T Consensus       223 ~~~~~~~~~~~-~~~~~~~~q~IALVGPTGVGKTTTIAKLAArf~--~~~KkVALITtDTYRIG  283 (436)
T PRK11889        223 ILEDMRSHFNT-ENVFEKEVQTIALIGPTGVGKTTTLAKMAWQFH--GKKKTVGFITTDHSRIG  283 (436)
T ss_pred             HHHHHHHHCCH-HHHHHHHCEEEEEECCCCCCHHHHHHHHHHHHH--CCCCEEEEEECCCCHHH
T ss_conf             99998874031-013364171799989999888999999999986--16980899980663476


No 197
>pfam00448 SRP54 SRP54-type protein, GTPase domain. This family includes relatives of the G-domain of the SRP54 family of proteins.
Probab=89.34  E-value=1.5  Score=22.35  Aligned_cols=52  Identities=17%  Similarity=0.155  Sum_probs=33.9

Q ss_pred             EEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHHHHHHHHC
Q ss_conf             77614886788999999999999708997799971537999999999999999862
Q gi|254781187|r   80 CAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLKNTLWAEVSKWLSML  135 (367)
Q Consensus        80 ~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~~~lw~ei~k~~~~~  135 (367)
                      +++.++.|+|||+.+|-++.|+.. +.....++++.|++-.-   ...++.+.+.+
T Consensus         4 i~lvGptGvGKTTTiaKLAa~~~~-~~~~V~lit~Dt~R~gA---~eQL~~ya~~l   55 (196)
T pfam00448         4 ILLVGLQGSGKTTTIAKLAAYLKK-QGKKVLLVAADTFRAAA---IEQLKQLAERL   55 (196)
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHH-CCCEEEEEECCCCCHHH---HHHHHHHHHHC
T ss_conf             999899999889999999999997-79928999758776889---99999999863


No 198
>KOG0991 consensus
Probab=89.29  E-value=1.1  Score=23.13  Aligned_cols=94  Identities=15%  Similarity=0.115  Sum_probs=52.4

Q ss_pred             CCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCC
Q ss_conf             54112477614886788999999999999708997799971537999999999999999862312112333321000123
Q gi|254781187|r   74 NPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLKNTLWAEVSKWLSMLPHRHWFEMQSLSLHPSGW  153 (367)
Q Consensus        74 ~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~~~lw~ei~k~~~~~~~~~~~~~~~~~~~~~~~  153 (367)
                      ..+|+.+.+++.-|+|||+.+-.++--++-.....-++-.-.+...--+++-..||.+..+-.                 
T Consensus        45 ~gnmP~liisGpPG~GKTTsi~~LAr~LLG~~~ke~vLELNASdeRGIDvVRn~IK~FAQ~kv-----------------  107 (333)
T KOG0991          45 EGNMPNLIISGPPGTGKTTSILCLARELLGDSYKEAVLELNASDERGIDVVRNKIKMFAQKKV-----------------  107 (333)
T ss_pred             CCCCCCEEEECCCCCCHHHHHHHHHHHHHCHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHC-----------------
T ss_conf             289986675279998616489999999838066657632057655460899999999987203-----------------


Q ss_pred             CCCCCCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCEEEEECCCCCCHHHHHHHHHHHH
Q ss_conf             332211113457761266210135445565210113586289997545599889999898740
Q gi|254781187|r  154 YAELLEQSMGIDSKHYTITCRTYSEERPDTFVGPHNTHGMAVFNDEASGTPDIINKSILGFFT  216 (367)
Q Consensus       154 ~~~~~~~~~~~~~~~~~~~a~~~~~~~~ea~~g~h~~~~~l~ivDEAsgI~d~i~e~i~g~Lt  216 (367)
                                                  .-..|   ++ -.+|+|||....+..-.+++-+|-
T Consensus       108 ----------------------------~lp~g---rh-KIiILDEADSMT~gAQQAlRRtME  138 (333)
T KOG0991         108 ----------------------------TLPPG---RH-KIIILDEADSMTAGAQQALRRTME  138 (333)
T ss_pred             ----------------------------CCCCC---CE-EEEEEECCCHHHHHHHHHHHHHHH
T ss_conf             ----------------------------48998---52-489961522020689999999999


No 199
>PRK08939 primosomal protein DnaI; Reviewed
Probab=89.23  E-value=1.5  Score=22.30  Aligned_cols=70  Identities=16%  Similarity=-0.003  Sum_probs=43.5

Q ss_pred             CCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCH
Q ss_conf             4366684289999999888875124555554112477614886788999999999999708997799971537
Q gi|254781187|r   45 LEHFSQPHRWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSE  117 (367)
Q Consensus        45 ~~~~~~p~~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~  117 (367)
                      |..+.--+.-..+++.++.+++..-.  ..+...-+-+.+.-|+|||+++++++--++ ..--..+++..|+.
T Consensus       127 ~~d~~~~d~~R~~a~~~a~~F~~~y~--~~~~~kGlyl~G~~G~GKTyL~~aian~La-~~g~~v~~v~~p~~  196 (306)
T PRK08939        127 LADIDLDDLDRLDALMAALDFLEAYK--PGEKVKGLYLYGDFGVGKTYLLAAIANELA-KKGVSSTLVHFPEF  196 (306)
T ss_pred             HHHCCCCCHHHHHHHHHHHHHHHHHC--CCCCCCEEEEECCCCCCHHHHHHHHHHHHH-HCCCEEEEEEHHHH
T ss_conf             98648897789999999999999737--698887788989999989999999999999-86992999875999


No 200
>PRK10037 cell division protein; Provisional
Probab=89.22  E-value=0.73  Score=24.27  Aligned_cols=43  Identities=19%  Similarity=0.323  Sum_probs=28.7

Q ss_pred             EEEEEEECCC-CCCHHHHHHHHHHHHHHHCCCCEEEEECC-CHHHHH
Q ss_conf             1247761488-67889999999999997089977999715-379999
Q gi|254781187|r   77 IFKCAISAGR-GIGKTTLNAWMMLWLISTRPGMSIICIAN-SETQLK  121 (367)
Q Consensus        77 ~~~~~v~sgr-g~GKS~~~a~~~lw~~~~~~~~~v~~~A~-t~~Q~~  121 (367)
                      |..++|.|.| |+|||+++|.++.  ++..-+.+|+++=- -++.++
T Consensus         1 M~iial~s~kGGVGkTTltAnLA~--aL~~~g~~VlaID~dpqN~Lr   45 (250)
T PRK10037          1 MAILGLQGVRGGVGTTSITAALAW--SLQMLGENVLVIDACPDNLLR   45 (250)
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHH--HHHHCCCCEEEEECCHHHHHH
T ss_conf             937999607888768999999999--999779918999578256678


No 201
>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=89.18  E-value=1.5  Score=22.28  Aligned_cols=60  Identities=13%  Similarity=0.144  Sum_probs=48.0

Q ss_pred             CHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCC---CEEEEECCCH
Q ss_conf             428999999988887512455555411247761488678899999999999970899---7799971537
Q gi|254781187|r   51 PHRWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPG---MSIICIANSE  117 (367)
Q Consensus        51 p~~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~---~~v~~~A~t~  117 (367)
                      +|+=|.++..+|-..+++....|     |+ ||+==|.|||-++...+. .+.+.-.   ..|+++.||-
T Consensus       509 eT~DQ~~AI~eik~Dm~~~~~MD-----RL-~CGDVGfGKTEVAmRAaF-kAv~~gneylKQVavLVPTT  571 (997)
T TIGR00580       509 ETPDQLKAIEEIKADMESPRPMD-----RL-VCGDVGFGKTEVAMRAAF-KAVLDGNEYLKQVAVLVPTT  571 (997)
T ss_pred             CCHHHHHHHHHHHHHHCCCCCCC-----EE-EECCCCCCHHHHHHHHHH-HHHCCCCCEECEEEEECCHH
T ss_conf             97789999999999740689873-----46-524548853688887888-76338782201168962704


No 202
>PRK11773 uvrD DNA-dependent helicase II; Provisional
Probab=89.15  E-value=0.34  Score=26.35  Aligned_cols=44  Identities=23%  Similarity=0.394  Sum_probs=33.7

Q ss_pred             EEEECCCCCCHHHHHHHHHHHHHHH--CCCCEEEEECCCHHHHHHH
Q ss_conf             7761488678899999999999970--8997799971537999999
Q gi|254781187|r   80 CAISAGRGIGKTTLNAWMMLWLIST--RPGMSIICIANSETQLKNT  123 (367)
Q Consensus        80 ~~v~sgrg~GKS~~~a~~~lw~~~~--~~~~~v~~~A~t~~Q~~~~  123 (367)
                      +.|.||=|+|||.....-+.|++..  -++.+|+++.=|.+-+.++
T Consensus        25 ~lV~AGaGSGKT~vL~~Ria~Li~~~gv~p~~ILalTFTnkAA~Em   70 (722)
T PRK11773         25 MLVLAGAGSGKTRVLVHRIAWLMQVENASPYSILAVTFTNKAAAEM   70 (722)
T ss_pred             EEEEECCCCHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHH
T ss_conf             7999738715999999999999982999878828984589999999


No 203
>KOG0989 consensus
Probab=88.76  E-value=1.7  Score=22.10  Aligned_cols=172  Identities=12%  Similarity=0.054  Sum_probs=80.9

Q ss_pred             HHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCC-CCEEEEECCCHHHHHHHHHHHHHHHH
Q ss_conf             99999998888751245555541124776148867889999999999997089-97799971537999999999999999
Q gi|254781187|r   54 WQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRP-GMSIICIANSETQLKNTLWAEVSKWL  132 (367)
Q Consensus        54 wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~-~~~v~~~A~t~~Q~~~~lw~ei~k~~  132 (367)
                      .|..+...+-.-+.+   +.+|.   ..--+++|+|||..+-+++--..+-.. +++++-.-.+...-..+.-..++.+.
T Consensus        40 gQe~vV~~L~~a~~~---~~lp~---~LFyGPpGTGKTStalafar~L~~~~~~~~rvl~lnaSderGisvvr~Kik~fa  113 (346)
T KOG0989          40 GQEHVVQVLKNALLR---RILPH---YLFYGPPGTGKTSTALAFARALNCEQLFPCRVLELNASDERGISVVREKIKNFA  113 (346)
T ss_pred             CHHHHHHHHHHHHHH---CCCCE---EEEECCCCCCHHHHHHHHHHHHCCCCCCCCCHHHHCCCCCCCCCCHHHHHCCHH
T ss_conf             159999999999860---68860---786689998676899999998557423555424313660014310066523799


Q ss_pred             HHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCEEEEECCCCCCHHHHHHHH
Q ss_conf             86231211233332100012333221111345776126621013544556521011358628999754559988999989
Q gi|254781187|r  133 SMLPHRHWFEMQSLSLHPSGWYAELLEQSMGIDSKHYTITCRTYSEERPDTFVGPHNTHGMAVFNDEASGTPDIINKSIL  212 (367)
Q Consensus       133 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~ea~~g~h~~~~~l~ivDEAsgI~d~i~e~i~  212 (367)
                      ...                                         ....  ...+.-..-+-.+|+|||...+.+.|.++.
T Consensus       114 kl~-----------------------------------------~~~~--~~~~~~~~~fKiiIlDEcdsmtsdaq~aLr  150 (346)
T KOG0989         114 KLT-----------------------------------------VLLK--RSDGYPCPPFKIIILDECDSMTSDAQAALR  150 (346)
T ss_pred             HHH-----------------------------------------HCCC--CCCCCCCCCCEEEEEECHHHHHHHHHHHHH
T ss_conf             875-----------------------------------------0255--656788986328997416453099999999


Q ss_pred             HHHHCCCCCEEEEEEECC-CCCCCHHH-H--HHH-CCCCC----EEEEEECCCCCCCCCHHHHHHHHHHCC
Q ss_conf             874069882589998078-99987688-7--541-12235----046752333288889889999996216
Q gi|254781187|r  213 GFFTELNPNRFWIMTSNT-RRLNGWFY-D--IFN-IPLED----WKRYQIDTRTVEGIDSGFHEGIISRYG  274 (367)
Q Consensus       213 g~Lt~~~~~~~~i~igNP-~r~~g~Fy-e--~~~-~~~~~----w~~~~~~~~d~p~~~~~~i~~~~~~~g  274 (367)
                      -+|-.....+-.|++.|- .+--.+.- +  -|+ ++-++    -....+.+.++=-++++-++.+...-+
T Consensus       151 r~mE~~s~~trFiLIcnylsrii~pi~SRC~KfrFk~L~d~~iv~rL~~Ia~~E~v~~d~~al~~I~~~S~  221 (346)
T KOG0989         151 RTMEDFSRTTRFILICNYLSRIIRPLVSRCQKFRFKKLKDEDIVDRLEKIASKEGVDIDDDALKLIAKISD  221 (346)
T ss_pred             HHHHCCCCCEEEEEECCCHHHCCHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHCC
T ss_conf             99862546659999738856477287746777128876447899999999888589978789999999738


No 204
>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=88.72  E-value=0.9  Score=23.72  Aligned_cols=34  Identities=18%  Similarity=0.128  Sum_probs=21.6

Q ss_pred             EEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEE
Q ss_conf             7761488678899999999999970899779997
Q gi|254781187|r   80 CAISAGRGIGKTTLNAWMMLWLISTRPGMSIICI  113 (367)
Q Consensus        80 ~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~  113 (367)
                      +.|++|-|+|||+++..+.--+.....+.+|.++
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 205
>COG1703 ArgK Putative periplasmic protein kinase ArgK and related GTPases of G3E family [Amino acid transport and metabolism]
Probab=88.60  E-value=1.5  Score=22.38  Aligned_cols=75  Identities=19%  Similarity=0.154  Sum_probs=48.8

Q ss_pred             CCCHHHHHHHHHCCCCCCCCCCCCCCCHH--HHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHH
Q ss_conf             25988885543014668884436668428--9999999888875124555554112477614886788999999999999
Q gi|254781187|r   25 VLSFKNFVMRFFPWGIKGKPLEHFSQPHR--WQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLI  102 (367)
Q Consensus        25 ~~~~~~f~~~~~~w~~~~~~~~~~~~p~~--wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~  102 (367)
                      +.|-..-.+.+.        |..-..|+.  --.++|+.++.+.-        ...++-|.+.=|+|||+++-.++.-+ 
T Consensus        13 ~GdrrAlARaIT--------lvEs~~~~h~~~a~~ll~~l~p~tG--------~a~viGITG~PGaGKSTli~~L~~~l-   75 (323)
T COG1703          13 AGDRRALARAIT--------LVESRRPDHRALARELLRALYPRTG--------NAHVIGITGVPGAGKSTLIEALGREL-   75 (323)
T ss_pred             CCCHHHHHHHHH--------HHHCCCCHHHHHHHHHHHHHHHCCC--------CCCEEEECCCCCCCHHHHHHHHHHHH-
T ss_conf             479989999989--------9764795024679999999731179--------98378731799886688999999999-


Q ss_pred             HHCCCCEEEEEC--CCH
Q ss_conf             708997799971--537
Q gi|254781187|r  103 STRPGMSIICIA--NSE  117 (367)
Q Consensus       103 ~~~~~~~v~~~A--~t~  117 (367)
                       .+.+.+|.|+|  |+.
T Consensus        76 -~~~G~rVaVlAVDPSS   91 (323)
T COG1703          76 -RERGHRVAVLAVDPSS   91 (323)
T ss_pred             -HHCCCEEEEEEECCCC
T ss_conf             -9779678999988999


No 206
>PRK09401 reverse gyrase; Reviewed
Probab=88.60  E-value=1.7  Score=22.04  Aligned_cols=110  Identities=21%  Similarity=0.198  Sum_probs=62.7

Q ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCC-
Q ss_conf             4776148867889999999999997089977999715379999999999999998623121123333210001233322-
Q gi|254781187|r   79 KCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLKNTLWAEVSKWLSMLPHRHWFEMQSLSLHPSGWYAEL-  157 (367)
Q Consensus        79 ~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~~~lw~ei~k~~~~~~~~~~~~~~~~~~~~~~~~~~~-  157 (367)
                      ..|+.|+.|+|||++...+.+|++.  .+.|++++-||..-++++. ..+..+.++.-..         +....++... 
T Consensus        95 SFaiiAPTG~GKTtfgl~~sly~a~--kgkks~~i~PT~~Lv~Q~~-~kl~~~~~~~~~~---------~~~~~y~~~~~  162 (1176)
T PRK09401         95 SFAIIAPTGVGKTTFGLVMALYLAK--KGKKSYIIFPTRLLVEQVV-EKLRKLAEKVGVK---------VRLLYYHSSLK  162 (1176)
T ss_pred             CEEEECCCCCCHHHHHHHHHHHHHH--CCCEEEEEECCHHHHHHHH-HHHHHHHHHHCCC---------CEEEEEECCCC
T ss_conf             7489888998888999999999986--5983999968889999999-9999999970998---------40899856776


Q ss_pred             ----CCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCEEEEECCC
Q ss_conf             ----11113457761266210135445565210113586289997545
Q gi|254781187|r  158 ----LEQSMGIDSKHYTITCRTYSEERPDTFVGPHNTHGMAVFNDEAS  201 (367)
Q Consensus       158 ----~~~~~~~~~~~~~~~a~~~~~~~~ea~~g~h~~~~~l~ivDEAs  201 (367)
                          .+..-....|..-+. .+.+..-+-++.-+....+.++.||-.-
T Consensus       163 ~~~kee~~~~~~~gdfdIl-itT~~fl~kn~~~l~~~~f~fifvDDVD  209 (1176)
T PRK09401        163 KKEKEEFLERLEEGDFDIL-VTTSQFLSKNFDELPKDRFDFVFVDDVD  209 (1176)
T ss_pred             HHHHHHHHHHHHCCCCCEE-EEEHHHHHHHHHHCCCCCCCEEEEECHH
T ss_conf             6678999988655998689-9856767654876035688889993418


No 207
>PRK11664 ATP-dependent RNA helicase HrpB; Provisional
Probab=88.38  E-value=1.7  Score=21.95  Aligned_cols=145  Identities=16%  Similarity=0.072  Sum_probs=64.9

Q ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             47761488678899999999999970899779997153799999999999999986231211233332100012333221
Q gi|254781187|r   79 KCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLKNTLWAEVSKWLSMLPHRHWFEMQSLSLHPSGWYAELL  158 (367)
Q Consensus        79 ~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~~~lw~ei~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~  158 (367)
                      .+.|.+.-|+|||+.+--+++-....  ..+|+||-|-.=-++.+ -..++.......            ....++....
T Consensus        22 ~~vl~a~tGsGKtTqvP~~ll~~~~~--~g~I~~~qPRR~AA~s~-A~RvA~e~~e~~------------G~~VGY~vR~   86 (812)
T PRK11664         22 QVLLKAPTGAGKSTWLPLQLLQQGGI--NGKIIMLEPRRLAARNV-AQRLAEQLGEKP------------GETVGYRMRA   86 (812)
T ss_pred             EEEEEECCCCCHHHHHHHHHHHCCCC--CCCEEEECCHHHHHHHH-HHHHHHHHCCCC------------CCEEEEEECC
T ss_conf             79999089999899999999964688--99389938839999999-999999729999------------9867578256


Q ss_pred             CCCCCCCCCCEEEE-ECCCCCCCCCCCCCCCCCCCCEEEEECCC--CCCHHH-HHHHHHHHHCCCCCEEEEEEECCCCCC
Q ss_conf             11134577612662-10135445565210113586289997545--599889-999898740698825899980789998
Q gi|254781187|r  159 EQSMGIDSKHYTIT-CRTYSEERPDTFVGPHNTHGMAVFNDEAS--GTPDII-NKSILGFFTELNPNRFWIMTSNTRRLN  234 (367)
Q Consensus       159 ~~~~~~~~~~~~~~-a~~~~~~~~ea~~g~h~~~~~l~ivDEAs--gI~d~i-~e~i~g~Lt~~~~~~~~i~igNP~r~~  234 (367)
                      .......+...|++ +...+....+  ..+  ..+.++|+||+.  .+.-++ +-.+.-...........++.| -|-..
T Consensus        87 e~~~s~~Tri~~~T~GiLlr~l~~d--p~L--~~~~~vI~DE~HER~l~~Dl~l~l~~~~~~~~r~dLklvvMS-ATld~  161 (812)
T PRK11664         87 ESKVGPNTRLEVVTEGILTRMIQRD--PEL--SGVGLVILDEFHERSLQADLALALLLDVQQGLRDDLKLLIMS-ATLDN  161 (812)
T ss_pred             CCCCCCCCEEEEECHHHHHHHHHHC--CCC--CCCCEEEEECCCCCCHHHHHHHHHHHHHHHHHCCCCEEEEEC-CCCCH
T ss_conf             7788998579997558999997249--776--778889995754687518999999999998618982899984-78884


Q ss_pred             CHHHHHHHC
Q ss_conf             768875411
Q gi|254781187|r  235 GWFYDIFNI  243 (367)
Q Consensus       235 g~Fye~~~~  243 (367)
                      ..|.+.|..
T Consensus       162 ~~~~~~~~~  170 (812)
T PRK11664        162 DRLQQLLPD  170 (812)
T ss_pred             HHHHHHCCC
T ss_conf             889975899


No 208
>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=88.35  E-value=1.8  Score=21.93  Aligned_cols=132  Identities=16%  Similarity=0.160  Sum_probs=70.5

Q ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCC---------
Q ss_conf             47761488678899999999999970899779997153799999999999999986231211233332100---------
Q gi|254781187|r   79 KCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLKNTLWAEVSKWLSMLPHRHWFEMQSLSLH---------  149 (367)
Q Consensus        79 ~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~~~lw~ei~k~~~~~~~~~~~~~~~~~~~---------  149 (367)
                      -....+..|+||..++-+++-|++|..+....-|-.-..-+.-.         ...-|+-+++..+.....         
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             --CCCCCCCCCCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCEEEEECCCCCCHHHHHHHHHHHHCCCCCEEEEEE
Q ss_conf             --012333221111345776126621013544556521011358628999754559988999989874069882589998
Q gi|254781187|r  150 --PSGWYAELLEQSMGIDSKHYTITCRTYSEERPDTFVGPHNTHGMAVFNDEASGTPDIINKSILGFFTELNPNRFWIMT  227 (367)
Q Consensus       150 --~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~ea~~g~h~~~~~l~ivDEAsgI~d~i~e~i~g~Lt~~~~~~~~i~i  227 (367)
                        .. .. ...+..++.+.=-..        ...=+..+..+.+. .+|+|.|.-.....=.+++.+|=.+..+++++++
T Consensus        87 ~~g~-a~-~~~~~~Ik~dq~R~l--------~~~~~~~~~~~~~r-VviI~~Ae~mn~~AANALLKtLEEPp~~t~fiL~  155 (216)
T TIGR00678        87 EEGS-AK-RRALPQIKVDQVREL--------VEFLSLTPQESGRR-VVIIEDAERMNEAAANALLKTLEEPPPNTLFILI  155 (216)
T ss_pred             HCCC-CC-CCCCCCCCHHHHHHH--------HHHHHHCCCCCCCE-EEEECCHHHCCHHHHHHHHHHEECCCCCEEEEEE
T ss_conf             2564-21-136787872789999--------99986064214751-7997673232589898651010127987079885


Q ss_pred             ECC
Q ss_conf             078
Q gi|254781187|r  228 SNT  230 (367)
Q Consensus       228 gNP  230 (367)
                      +.-
T Consensus       156 ~~~  158 (216)
T TIGR00678       156 THS  158 (216)
T ss_pred             CCC
T ss_conf             088


No 209
>COG1239 ChlI Mg-chelatase subunit ChlI [Coenzyme metabolism]
Probab=88.32  E-value=1.8  Score=21.92  Aligned_cols=161  Identities=14%  Similarity=0.068  Sum_probs=73.5

Q ss_pred             CCCCHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEE-----CCCHHHHHH
Q ss_conf             668428999999988887512455555411247761488678899999999999970899779997-----153799999
Q gi|254781187|r   48 FSQPHRWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICI-----ANSETQLKN  122 (367)
Q Consensus        48 ~~~p~~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~-----A~t~~Q~~~  122 (367)
                      ..|-++|-.=++.+          .-.|.+-.+.|++-+|+|||+++=+++-    .-|+..++.-     -|+..-   
T Consensus        19 ivGqd~lk~aL~l~----------av~P~iggvLI~G~kGtaKSt~~Rala~----LLp~~~~V~gc~f~cdP~~P~---   81 (423)
T COG1239          19 IVGQDPLKLALGLN----------AVDPQIGGALIAGEKGTAKSTLARALAD----LLPEIEVVIGCPFNCDPDDPE---   81 (423)
T ss_pred             HCCCHHHHHHHHHH----------HCCCCCCEEEEECCCCCCHHHHHHHHHH----HCCCCCEECCCCCCCCCCCHH---
T ss_conf             43753777887653----------0263104268766887527799999998----679633216887889988705---


Q ss_pred             HHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCC-C-CCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCEEEEECC
Q ss_conf             99999999998623121123333210001233322111-1-345776126621013544556521011358628999754
Q gi|254781187|r  123 TLWAEVSKWLSMLPHRHWFEMQSLSLHPSGWYAELLEQ-S-MGIDSKHYTITCRTYSEERPDTFVGPHNTHGMAVFNDEA  200 (367)
Q Consensus       123 ~lw~ei~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~-~~~~~~~~~~~a~~~~~~~~ea~~g~h~~~~~l~ivDEA  200 (367)
                      .+..+.++-....   .|.....  +++..-..+...+ + +-++-....+....-....|.-+.-.|   .-.++|||-
T Consensus        82 ~~c~~c~~k~~e~---~~~~~~~--r~v~~v~lPl~ateDrvvGslDi~ka~~~g~~af~PGlLa~An---RGIlYvDEv  153 (423)
T COG1239          82 EMCDECRAKGDEL---EWLPREK--RKVPFVALPLGATEDRLVGSLDIEKALEEGPKAFQPGLLARAN---RGILYVDEV  153 (423)
T ss_pred             HHHHHHHHHCCCC---CCCCCCC--EECCEECCCCCCCHHHHCCCCCHHHHHHCCCCCCCCCCHHHCC---CCEEEEECC
T ss_conf             5519998620232---4454221--0031223887630433004567999972683002775110035---887987233


Q ss_pred             CCCCHHHHHHHHHHHHCC-------------CCCEEEEEEECCCCC
Q ss_conf             559988999989874069-------------882589998078999
Q gi|254781187|r  201 SGTPDIINKSILGFFTEL-------------NPNRFWIMTSNTRRL  233 (367)
Q Consensus       201 sgI~d~i~e~i~g~Lt~~-------------~~~~~~i~igNP~r~  233 (367)
                      .-++|.+-+++.-.+..+             -.+.+++.+.||-.+
T Consensus       154 nlL~d~lvd~LLd~aaeG~n~vereGisi~hpa~fvligTmNPEeG  199 (423)
T COG1239         154 NLLDDHLVDALLDVAAEGVNDVEREGISIRHPARFLLIGTMNPEEG  199 (423)
T ss_pred             CCCCHHHHHHHHHHHHHCCCEEEECCEEECCCCCEEEEEECCCCCC
T ss_conf             4351899999999997177403357503136761799964485446


No 210
>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=88.31  E-value=0.67  Score=24.49  Aligned_cols=31  Identities=26%  Similarity=0.461  Sum_probs=23.6

Q ss_pred             EECCCCCCHHHHHHHHHHHHHHHCCCCEEEEEC
Q ss_conf             614886788999999999999708997799971
Q gi|254781187|r   82 ISAGRGIGKTTLNAWMMLWLISTRPGMSIICIA  114 (367)
Q Consensus        82 v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A  114 (367)
                      +.+==|+|||++++.+++.++-.  |.|++++.
T Consensus         4 ~sGKGGVGKTTvAaalA~~lA~~--G~rvLlvs   34 (217)
T cd02035           4 FTGKGGVGKTTIAAATAVRLAEE--GKKVLLVS   34 (217)
T ss_pred             EECCCCCCHHHHHHHHHHHHHHC--CCEEEEEE
T ss_conf             97899661999999999999968--99499995


No 211
>PRK13900 type IV secretion system ATPase VirB11; Provisional
Probab=88.26  E-value=1.5  Score=22.28  Aligned_cols=37  Identities=22%  Similarity=0.206  Sum_probs=27.7

Q ss_pred             EEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCH
Q ss_conf             2477614886788999999999999708997799971537
Q gi|254781187|r   78 FKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSE  117 (367)
Q Consensus        78 ~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~  117 (367)
                      .++.|++|.|+|||++..+++-.   .-++.+++++-.+.
T Consensus       161 ~NilI~G~TgSGKTTll~aL~~~---ip~~eRiitIEDt~  197 (332)
T PRK13900        161 KNIIISGGTSTGKTTFTNAALRE---IPAIERLITVEDAR  197 (332)
T ss_pred             CCEEEECCCCCCHHHHHHHHHHC---CCCCCCEEEECCCH
T ss_conf             71999888898899999999835---89535356631406


No 212
>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=88.26  E-value=1.1  Score=23.24  Aligned_cols=52  Identities=17%  Similarity=0.198  Sum_probs=32.8

Q ss_pred             EEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHHHHHHHHC
Q ss_conf             77614886788999999999999708997799971537999999999999999862
Q gi|254781187|r   80 CAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLKNTLWAEVSKWLSML  135 (367)
Q Consensus        80 ~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~~~lw~ei~k~~~~~  135 (367)
                      +++.+..|+|||+.+|-++.++. .+.....++++.|++-.-   ...++.+.+.+
T Consensus         3 i~lvGptGvGKTTTiaKLA~~~~-~~~~kV~lit~Dt~R~gA---~eQL~~~a~~l   54 (173)
T cd03115           3 ILLVGLQGVGKTTTAAKLALYLK-KKGKKVLLVAADTYRPAA---IEQLRVLGEQV   54 (173)
T ss_pred             EEEECCCCCCHHHHHHHHHHHHH-HCCCEEEEEECCCCCHHH---HHHHHHHHHHC
T ss_conf             99989999988999999999999-769928999748875779---99999999974


No 213
>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=88.12  E-value=1.8  Score=21.85  Aligned_cols=52  Identities=13%  Similarity=0.082  Sum_probs=28.2

Q ss_pred             HHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCC
Q ss_conf             999988887512455555411247761488678899999999999970899779997153
Q gi|254781187|r   57 EFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANS  116 (367)
Q Consensus        57 ~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t  116 (367)
                      +-|+.+.+.++++...      -++|-+.|++|||.++-..+-=  .-.++..++.....
T Consensus         6 ~EL~~L~~~~~~~~~~------~ivi~G~RR~GKTsLi~~~~~~--~~~~~~~~i~~~~~   57 (223)
T pfam01637         6 KELKELEEWAERGTYP------IIVVYGPRRCGKTALLREFLEE--LRELGYRVIYYDPL   57 (223)
T ss_pred             HHHHHHHHHHHCCCCC------EEEEECCCCCCHHHHHHHHHHH--CCCCCCEEEEEECH
T ss_conf             9999999999669971------8999868878799999999986--33468528999514


No 214
>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=88.10  E-value=1.2  Score=22.90  Aligned_cols=33  Identities=30%  Similarity=0.423  Sum_probs=26.4

Q ss_pred             EEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEEC
Q ss_conf             77614886788999999999999708997799971
Q gi|254781187|r   80 CAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIA  114 (367)
Q Consensus        80 ~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A  114 (367)
                      +++.+--|+|||++++.++..+..  .+.+++++-
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 215
>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=88.01  E-value=1.1  Score=23.27  Aligned_cols=32  Identities=31%  Similarity=0.503  Sum_probs=25.0

Q ss_pred             EEEECCC-CCCHHHHHHHHHHHHHHHCCCCEEEEE
Q ss_conf             7761488-678899999999999970899779997
Q gi|254781187|r   80 CAISAGR-GIGKTTLNAWMMLWLISTRPGMSIICI  113 (367)
Q Consensus        80 ~~v~sgr-g~GKS~~~a~~~lw~~~~~~~~~v~~~  113 (367)
                      ++|+||. |+|||++++.++..++..  +.+++++
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 216
>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=87.94  E-value=1.7  Score=22.03  Aligned_cols=94  Identities=11%  Similarity=0.090  Sum_probs=56.3

Q ss_pred             CCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             48867889999999999997089977999715379999999999999998623121123333210001233322111134
Q gi|254781187|r   84 AGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLKNTLWAEVSKWLSMLPHRHWFEMQSLSLHPSGWYAELLEQSMG  163 (367)
Q Consensus        84 sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~~~lw~ei~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  163 (367)
                      +=.|+|||+.+.=|++|+=--. ...++|+|-|.   |-.-|..+++-..+..              -|++..    +.+
T Consensus       128 GLQGaGKTTtctKLA~YYk~rG-fK~~lvCADTF---RAGAFdQLkqNA~kA~--------------iPFYGs----y~E  185 (453)
T TIGR01425       128 GLQGAGKTTTCTKLAYYYKRRG-FKPALVCADTF---RAGAFDQLKQNATKAK--------------IPFYGS----YLE  185 (453)
T ss_pred             ECCCCCHHHHHHHHHHHHHCCC-CCEEEECCCCC---CCCHHHHHHHHHHHCC--------------CCCCCC----CCC
T ss_conf             2148871566878777763266-43256517754---2324899987476448--------------971201----048


Q ss_pred             CCCCCEEEEECCCCCCCCCCCCCCCCCCCCEEEEECCCCC--CHHHHH
Q ss_conf             5776126621013544556521011358628999754559--988999
Q gi|254781187|r  164 IDSKHYTITCRTYSEERPDTFVGPHNTHGMAVFNDEASGT--PDIINK  209 (367)
Q Consensus       164 ~~~~~~~~~a~~~~~~~~ea~~g~h~~~~~l~ivDEAsgI--~d~i~e  209 (367)
                      .|+  ..+.        .|..+-++.|+..++|||-..-=  .+..|+
T Consensus       186 ~DP--VkiA--------~EGv~~Fk~E~~diIivDTSGRHkQe~~LF~  223 (453)
T TIGR01425       186 SDP--VKIA--------SEGVEKFKKEKFDIIIVDTSGRHKQEEELFE  223 (453)
T ss_pred             CCC--EEEE--------CCCHHHHHCCCCCEEEEECCCCCHHHHHHHH
T ss_conf             987--0780--------0201132212784799837987322588889


No 217
>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=87.91  E-value=0.74  Score=24.24  Aligned_cols=40  Identities=23%  Similarity=0.432  Sum_probs=26.6

Q ss_pred             EECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCC-HHHHHHH
Q ss_conf             61488678899999999999970899779997153-7999999
Q gi|254781187|r   82 ISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANS-ETQLKNT  123 (367)
Q Consensus        82 v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t-~~Q~~~~  123 (367)
                      +.+==|+|||+++|.+++..+-.  |.|+++++-. .+.+.++
T Consensus         5 ~~GKGGVGKTT~AaalA~~lA~~--G~kVLlvstDPahsLsd~   45 (254)
T cd00550           5 FGGKGGVGKTTISAATAVRLAEQ--GKKVLLVSTDPAHSLSDS   45 (254)
T ss_pred             EECCCCCCHHHHHHHHHHHHHHC--CCEEEEEECCCCCCHHHH
T ss_conf             96898554899999999999968--994999958986448898


No 218
>PRK13851 type IV secretion system protein VirB11; Provisional
Probab=87.80  E-value=1.2  Score=22.86  Aligned_cols=101  Identities=13%  Similarity=0.084  Sum_probs=54.4

Q ss_pred             EEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             24776148867889999999999997089977999715379999999999999998623121123333210001233322
Q gi|254781187|r   78 FKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLKNTLWAEVSKWLSMLPHRHWFEMQSLSLHPSGWYAEL  157 (367)
Q Consensus        78 ~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~~~lw~ei~k~~~~~~~~~~~~~~~~~~~~~~~~~~~  157 (367)
                      .++.|++|.|+|||++..+++-.   .-++.+++++-.+..-         .     ++..++....    +        
T Consensus       163 ~NIlIsGgTGSGKTTllnALl~~---IP~~eRIvtIEDt~EL---------~-----l~~~n~V~l~----~--------  213 (343)
T PRK13851        163 LTMLLCGPTGSGKTTMSKTLISA---IPPQERLITIEDTLEL---------V-----IPHENHVRLL----Y--------  213 (343)
T ss_pred             CCEEEECCCCCCHHHHHHHHHHC---CCCCCCEEEECCCCCC---------C-----CCCCCEEEEE----E--------
T ss_conf             88999888986199999999962---8965527996115002---------5-----8999968999----6--------


Q ss_pred             CCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCEEEEECCCCCCHHHHHHHHHHHHCCCC
Q ss_conf             111134577612662101354455652101135862899975455998899998987406988
Q gi|254781187|r  158 LEQSMGIDSKHYTITCRTYSEERPDTFVGPHNTHGMAVFNDEASGTPDIINKSILGFFTELNP  220 (367)
Q Consensus       158 ~~~~~~~~~~~~~~~a~~~~~~~~ea~~g~h~~~~~l~ivDEAsgI~d~i~e~i~g~Lt~~~~  220 (367)
                          .+...+..   ..+.......+   +| .+..-+|+-|.-|  ++.|+-+...-|+..+
T Consensus       214 ----~~~~~g~~---~vt~~~Ll~~a---LR-mrPDRIivGEvRG--~EA~d~L~A~nTGH~G  263 (343)
T PRK13851        214 ----SKNGAGLG---AVTAEHLLQAS---LR-MRPDRILLGEMRD--DAAWAYLSEVVSGHPG  263 (343)
T ss_pred             ----CCCCCCCC---CCCHHHHHHHH---HC-CCCCEEEEEEECC--HHHHHHHHHHHCCCCC
T ss_conf             ----58988858---39799999998---60-7998289985266--9999999998469998


No 219
>KOG0337 consensus
Probab=87.77  E-value=1.2  Score=22.95  Aligned_cols=74  Identities=16%  Similarity=0.128  Sum_probs=46.7

Q ss_pred             CCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCC--CCEEEEECCCHHHHHH
Q ss_conf             43666842899999998888751245555541124776148867889999999999997089--9779997153799999
Q gi|254781187|r   45 LEHFSQPHRWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRP--GMSIICIANSETQLKN  122 (367)
Q Consensus        45 ~~~~~~p~~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~--~~~v~~~A~t~~Q~~~  122 (367)
                      -++|..|++-|++-.-.   +++.         .-+.-.|--|+|||...-+=++-.|..+-  +.+.++..||..-+-.
T Consensus        38 kkg~~~ptpiqRKTipl---iLe~---------~dvv~martgsgktaaf~ipm~e~Lk~~s~~g~RalilsptreLa~q  105 (529)
T KOG0337          38 KKGFNTPTPIQRKTIPL---ILEG---------RDVVGMARTGSGKTAAFLIPMIEKLKSHSQTGLRALILSPTRELALQ  105 (529)
T ss_pred             HHHCCCCCCHHCCCCCC---EEEC---------CCCCEEEECCCCCHHHHHHHHHHHHHHCCCCCCCEEECCCCHHHHHH
T ss_conf             86238998411034420---0314---------52100552278610467889999986136446202432670889999


Q ss_pred             HHHHHHHHH
Q ss_conf             999999999
Q gi|254781187|r  123 TLWAEVSKW  131 (367)
Q Consensus       123 ~lw~ei~k~  131 (367)
                      . +.-++..
T Consensus       106 t-lkvvkdl  113 (529)
T KOG0337         106 T-LKVVKDL  113 (529)
T ss_pred             H-HHHHHHH
T ss_conf             9-9999985


No 220
>PRK08233 hypothetical protein; Provisional
Probab=87.74  E-value=0.96  Score=23.55  Aligned_cols=32  Identities=25%  Similarity=0.174  Sum_probs=24.2

Q ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEEC
Q ss_conf             477614886788999999999999708997799971
Q gi|254781187|r   79 KCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIA  114 (367)
Q Consensus        79 ~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A  114 (367)
                      =++|++|.|+|||+++-.++--    .|+..++..-
T Consensus         5 IIgIaGgSgSGKTtla~~l~~~----l~~~~~~~~D   36 (182)
T PRK08233          5 IITIAAVSGGGKTTLTERLTHK----LKNSKALYFD   36 (182)
T ss_pred             EEEEECCCCCCHHHHHHHHHHH----CCCCEEEEEC
T ss_conf             9999688867899999999997----4677589966


No 221
>KOG1123 consensus
Probab=87.70  E-value=0.57  Score=24.93  Aligned_cols=147  Identities=13%  Similarity=0.081  Sum_probs=73.4

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHH
Q ss_conf             88844366684289999999888875124555554112477614886788999999999999708997799971537999
Q gi|254781187|r   41 KGKPLEHFSQPHRWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQL  120 (367)
Q Consensus        41 ~~~~~~~~~~p~~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~  120 (367)
                      ++..|--...+|++|++-|+.+.-.-+-   ++     -+.|. +-|.|||-..-     -++|.-..+++|.+++.-.+
T Consensus       293 l~idLKPst~iRpYQEksL~KMFGNgRA---RS-----GiIVL-PCGAGKtLVGv-----TAa~tikK~clvLcts~VSV  358 (776)
T KOG1123         293 LDIDLKPSTQIRPYQEKSLSKMFGNGRA---RS-----GIIVL-PCGAGKTLVGV-----TAACTIKKSCLVLCTSAVSV  358 (776)
T ss_pred             CCCCCCCCCCCCCHHHHHHHHHHCCCCC---CC-----CEEEE-ECCCCCCEEEE-----EEEEEECCCEEEEECCCCCH
T ss_conf             8867685455575378789997378854---47-----61898-56998742545-----55545514279995575669


Q ss_pred             HHHHHHH-HHHHHHHCCCCCCCCCCCCCCCCCCCCC-CCCCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCEEEEE
Q ss_conf             9999999-9999986231211233332100012333-2211113457761266210135445565210113586289997
Q gi|254781187|r  121 KNTLWAE-VSKWLSMLPHRHWFEMQSLSLHPSGWYA-ELLEQSMGIDSKHYTITCRTYSEERPDTFVGPHNTHGMAVFND  198 (367)
Q Consensus       121 ~~~lw~e-i~k~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~a~~~~~~~~ea~~g~h~~~~~l~ivD  198 (367)
                      .+  |+. .+.|...-+. ..-..+....-..+... ....++      +..+....-+-+......-+++...-|+++|
T Consensus       359 eQ--WkqQfk~wsti~d~-~i~rFTsd~Ke~~~~~~gvvvsTY------sMva~t~kRS~eaek~m~~l~~~EWGllllD  429 (776)
T KOG1123         359 EQ--WKQQFKQWSTIQDD-QICRFTSDAKERFPSGAGVVVTTY------SMVAYTGKRSHEAEKIMDFLRGREWGLLLLD  429 (776)
T ss_pred             HH--HHHHHHHHHCCCCC-CEEEEECCCCCCCCCCCCEEEEEE------EHHHHCCCCCHHHHHHHHHHHCCEEEEEEEE
T ss_conf             99--99998745016855-457720244545789885799873------1311056642779999999843710168842


Q ss_pred             CCCCCCHHHHHH
Q ss_conf             545599889999
Q gi|254781187|r  199 EASGTPDIINKS  210 (367)
Q Consensus       199 EAsgI~d~i~e~  210 (367)
                      |..-||...|--
T Consensus       430 EVHvvPA~MFRR  441 (776)
T KOG1123         430 EVHVVPAKMFRR  441 (776)
T ss_pred             HHCCCHHHHHHH
T ss_conf             111126999999


No 222
>KOG1002 consensus
Probab=87.65  E-value=1.9  Score=21.67  Aligned_cols=216  Identities=13%  Similarity=0.058  Sum_probs=92.7

Q ss_pred             CCCCCCCCCHHHHHHHHCCCCCCCCHHHHHHHHH-------CCCCCC----CCCCCCCCCH-------HHHHHHHHHHHH
Q ss_conf             5554572337899997523201259888855430-------146688----8443666842-------899999998888
Q gi|254781187|r    3 RLISTDQKLEQELHEMLMHAECVLSFKNFVMRFF-------PWGIKG----KPLEHFSQPH-------RWQLEFMEAVDV   64 (367)
Q Consensus         3 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~~~~~-------~w~~~~----~~~~~~~~p~-------~wq~~~l~~~~~   64 (367)
                      |..++--+.-..++...|.++..-.-.|..++.-       -|..++    -..+...+|.       ++|.|.|.=...
T Consensus       119 rrk~~ark~k~~~s~~k~q~k~~p~er~~~rl~eh~pE~~~v~~dlde~~p~i~e~aeqP~dlii~LL~fQkE~l~Wl~~  198 (791)
T KOG1002         119 RRKPTARKKKKKTSTEKKQPKVTPYERNTLRLYEHHPELRNVFTDLDEANPVIAERAEQPDDLIIPLLPFQKEGLAWLTS  198 (791)
T ss_pred             CCCCCHHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHCCCHHHHCCCCCCCCEECCHHHHHHHHHHHHH
T ss_conf             45752355554333554276558410003556541803444453231237401220369601342131446777888877


Q ss_pred             HHHCCCCCCCCCEEEEE-EECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHHHHHHHHCCC--CCCC
Q ss_conf             75124555554112477-61488678899999999999970899779997153799999999999999986231--2112
Q gi|254781187|r   65 HCHSNVNNSNPTIFKCA-ISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLKNTLWAEVSKWLSMLPH--RHWF  141 (367)
Q Consensus        65 ~~~~~~~~~~~~~~~~~-v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~~~lw~ei~k~~~~~~~--~~~~  141 (367)
                      +.+.        .++-- .+---|.|||.-+-.+++-   --.....+|+||+-.-.  ..-.||.+.-+..-.  -+.-
T Consensus       199 QE~S--------s~~GGiLADEMGMGKTIQtIaLlla---e~~ra~tLVvaP~VAlm--QW~nEI~~~T~gslkv~~YhG  265 (791)
T KOG1002         199 QEES--------SVAGGILADEMGMGKTIQTIALLLA---EVDRAPTLVVAPTVALM--QWKNEIERHTSGSLKVYIYHG  265 (791)
T ss_pred             HHHH--------HHCCCEEHHHHCCCHHHHHHHHHHH---CCCCCCEEEECCHHHHH--HHHHHHHHHCCCCEEEEEEEC
T ss_conf             3554--------3124311243146417999999986---23568706975489999--999999876257647999726


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCC--CCCCCCCCCCCCCCEEEEECCCCCCHHHHHHHHHHHHCCC
Q ss_conf             33332100012333221111345776126621013544--5565210113586289997545599889999898740698
Q gi|254781187|r  142 EMQSLSLHPSGWYAELLEQSMGIDSKHYTITCRTYSEE--RPDTFVGPHNTHGMAVFNDEASGTPDIINKSILGFFTELN  219 (367)
Q Consensus       142 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~--~~ea~~g~h~~~~~l~ivDEAsgI~d~i~e~i~g~Lt~~~  219 (367)
                      ......+.....+..+..++....+.. .-.-.+++..  .-....-+|+-.+.-+|+|||.+|.+..-..+.....-..
T Consensus       266 ~~R~~nikel~~YDvVLTty~vvEs~y-Rk~~~GfrrKngv~ke~SlLHsi~~~RiIlDEAH~IK~R~snTArAV~~L~t  344 (791)
T KOG1002         266 AKRDKNIKELMNYDVVLTTYAVVESVY-RKQDYGFRRKNGVDKEKSLLHSIKFYRIILDEAHNIKDRQSNTARAVFALET  344 (791)
T ss_pred             CCCCCCHHHHHCCCEEEEECHHHHHHH-HHCCCCCCCCCCCCCCCCHHHHCEEEEEEHHHHCCCCCCCCCHHHHHHHHHH
T ss_conf             423577888606767997018788898-7402342113774245323331010235221202531013327888876676


Q ss_pred             CCEEEEEEECCCCC
Q ss_conf             82589998078999
Q gi|254781187|r  220 PNRFWIMTSNTRRL  233 (367)
Q Consensus       220 ~~~~~i~igNP~r~  233 (367)
                      ... ||+-|+|-.+
T Consensus       345 t~r-w~LSGTPLQN  357 (791)
T KOG1002         345 TYR-WCLSGTPLQN  357 (791)
T ss_pred             HHH-HHCCCCCCHH
T ss_conf             653-2205883011


No 223
>PRK07667 uridine kinase; Provisional
Probab=87.64  E-value=0.63  Score=24.65  Aligned_cols=27  Identities=26%  Similarity=0.129  Sum_probs=22.7

Q ss_pred             CCEEEEEEECCCCCCHHHHHHHHHHHH
Q ss_conf             411247761488678899999999999
Q gi|254781187|r   75 PTIFKCAISAGRGIGKTTLNAWMMLWL  101 (367)
Q Consensus        75 ~~~~~~~v~sgrg~GKS~~~a~~~lw~  101 (367)
                      .++|-++|++|-|+|||+++.-++--+
T Consensus        12 ~~r~iIgIaG~sgSGKTTla~~L~~~l   38 (190)
T PRK07667         12 ENRFILGIDGLSRSGKTTFVANLKENM   38 (190)
T ss_pred             CCEEEEEEECCCCCCHHHHHHHHHHHH
T ss_conf             986999977989788999999999998


No 224
>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=87.60  E-value=2  Score=21.65  Aligned_cols=58  Identities=24%  Similarity=0.341  Sum_probs=42.2

Q ss_pred             CCH--HHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEEC--CCH
Q ss_conf             842--89999999888875124555554112477614886788999999999999708997799971--537
Q gi|254781187|r   50 QPH--RWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIA--NSE  117 (367)
Q Consensus        50 ~p~--~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A--~t~  117 (367)
                      +|+  .-=.++|+.|...+        .+.-++=|.+-=|+|||++...++-  .+-+.|.+|.|+|  ||.
T Consensus        17 ~p~H~~~a~~ll~~i~p~~--------GnA~~vG~TG~PGaGKSTl~~~l~~--~lrRrG~~VaViAvDP~S   78 (333)
T TIGR00750        17 EPEHRELAKELLERILPKT--------GNAHVVGITGVPGAGKSTLVEKLIM--ELRRRGLKVAVIAVDPSS   78 (333)
T ss_pred             CCHHHHHHHHHHHHHHHHC--------CCCEEEEEECCCCCCHHHHHHHHHH--HHHHCCCEEEEEEECCCC
T ss_conf             9704799999999862432--------7907876646888857779999989--997659768999887975


No 225
>PTZ00301 uridine kinase; Provisional
Probab=87.49  E-value=1.3  Score=22.68  Aligned_cols=26  Identities=27%  Similarity=0.376  Sum_probs=20.0

Q ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHH
Q ss_conf             47761488678899999999999970
Q gi|254781187|r   79 KCAISAGRGIGKTTLNAWMMLWLIST  104 (367)
Q Consensus        79 ~~~v~sgrg~GKS~~~a~~~lw~~~~  104 (367)
                      =+.|++|-|+|||+++..++--+...
T Consensus         5 iIgIaGgSgSGKTT~a~~i~~~l~~~   30 (210)
T PTZ00301          5 VIGISGASGSGKSSLSTNIVSELMAH   30 (210)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHH
T ss_conf             99996887678999999999998761


No 226
>KOG0923 consensus
Probab=87.34  E-value=2  Score=21.56  Aligned_cols=160  Identities=17%  Similarity=0.062  Sum_probs=80.9

Q ss_pred             HHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHHHH-HH
Q ss_conf             99999998888751245555541124776148867889999999999997089977999715379999999999999-99
Q gi|254781187|r   54 WQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLKNTLWAEVSK-WL  132 (367)
Q Consensus        54 wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~~~lw~ei~k-~~  132 (367)
                      +..++|.+|.+|.            -+.|.+-.|+|||+-+--++.---.|.-+.+|.||-|-.--+..+- +.+++ +-
T Consensus       269 ykdell~av~e~Q------------VLiI~GeTGSGKTTQiPQyL~EaGytk~gk~IgcTQPRRVAAmSVA-aRVA~EMg  335 (902)
T KOG0923         269 YKDELLKAVKEHQ------------VLIIVGETGSGKTTQIPQYLYEAGYTKGGKKIGCTQPRRVAAMSVA-ARVAEEMG  335 (902)
T ss_pred             HHHHHHHHHHHCC------------EEEEECCCCCCCCCCCCHHHHHCCCCCCCCEEEECCCCHHHHHHHH-HHHHHHHC
T ss_conf             3999999998670------------8999757889864456289885421358946740685068877799-99999857


Q ss_pred             HHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCEEEEECCCC--CCHHHHHH
Q ss_conf             8623121123333210001233322111134577612662101354455652101135862899975455--99889999
Q gi|254781187|r  133 SMLPHRHWFEMQSLSLHPSGWYAELLEQSMGIDSKHYTITCRTYSEERPDTFVGPHNTHGMAVFNDEASG--TPDIINKS  210 (367)
Q Consensus       133 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~ea~~g~h~~~~~l~ivDEAsg--I~d~i~e~  210 (367)
                      -++-+  ...++.  .+   -.....++-+++     ...+-..++...|-.    -.+...+|+|||.-  ...+|.=.
T Consensus       336 vkLG~--eVGYsI--RF---EdcTSekTvlKY-----MTDGmLlREfL~epd----LasYSViiiDEAHERTL~TDILfg  399 (902)
T KOG0923         336 VKLGH--EVGYSI--RF---EDCTSEKTVLKY-----MTDGMLLREFLSEPD----LASYSVIIVDEAHERTLHTDILFG  399 (902)
T ss_pred             CCCCC--CCCEEE--EE---CCCCCCCEEEEE-----ECCHHHHHHHHCCCC----CCCEEEEEEEHHHHHHHHHHHHHH
T ss_conf             40143--144488--85---035674122432-----243067998714634----223359996024320034567999


Q ss_pred             HHHHHHCCCCCEEEEEEECCCCCCCHHHHHHHC
Q ss_conf             898740698825899980789998768875411
Q gi|254781187|r  211 ILGFFTELNPNRFWIMTSNTRRLNGWFYDIFNI  243 (367)
Q Consensus       211 i~g~Lt~~~~~~~~i~igNP~r~~g~Fye~~~~  243 (367)
                      +..-+......+. +++++-|...--|-..|-.
T Consensus       400 LvKDIar~RpdLK-llIsSAT~DAekFS~fFDd  431 (902)
T KOG0923         400 LVKDIARFRPDLK-LLISSATMDAEKFSAFFDD  431 (902)
T ss_pred             HHHHHHHHCCCCE-EEEECCCCCHHHHHHHCCC
T ss_conf             8788875087604-7732222678999876168


No 227
>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=87.13  E-value=1.5  Score=22.41  Aligned_cols=37  Identities=32%  Similarity=0.541  Sum_probs=28.0

Q ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCH
Q ss_conf             477614886788999999999999708997799971537
Q gi|254781187|r   79 KCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSE  117 (367)
Q Consensus        79 ~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~  117 (367)
                      |++|+.==|+|||++++.++.+++-.  +.+++++-.--
T Consensus         1 kia~~GKGGvGKtt~~~~la~~l~~~--g~~vl~iD~Dp   37 (116)
T cd02034           1 KIAITGKGGVGKTTIAALLARYLAEK--GKPVLAIDADP   37 (116)
T ss_pred             CEEEECCCCCCHHHHHHHHHHHHHHC--CCEEEEEECCC
T ss_conf             97898899774999999999999978--99699998989


No 228
>pfam07517 SecA_DEAD SecA DEAD-like domain. SecA protein binds to the plasma membrane where it interacts with proOmpA to support translocation of proOmpA through the membrane. SecA protein achieves this translocation, in association with SecY protein, in an ATP dependent manner. This domain represents the N-terminal ATP-dependent helicase domain, which is related to the pfam00270.
Probab=87.12  E-value=2.1  Score=21.48  Aligned_cols=143  Identities=11%  Similarity=-0.034  Sum_probs=63.5

Q ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             47761488678899999999999970899779997153799999999999999986231211233332100012333221
Q gi|254781187|r   79 KCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLKNTLWAEVSKWLSMLPHRHWFEMQSLSLHPSGWYAELL  158 (367)
Q Consensus        79 ~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~~~lw~ei~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~  158 (367)
                      ++|=.. .|=|||-.++..+.-.+++..+.- +||.|.+=--|+.  ..+...++.+-...-.-.......   -.....
T Consensus        93 ~IaEM~-TGEGKTL~atl~a~l~AL~Gk~Vh-vvTvNdYLA~RDa--e~m~~vy~~LGLsvg~i~~~~~~~---err~aY  165 (381)
T pfam07517        93 KIAEMK-TGEGKTLTATLPAYLNALSGKGVH-VVTVNDYLAKRDA--EWMGPLYEFLGLSVGVITSDMSPE---ERREAY  165 (381)
T ss_pred             CEEEEE-CCCCCHHHHHHHHHHHHCCCCCCE-EEECCHHHHHHHH--HHHHHHHHHHCCEEEECCCCCCHH---HHHHHH
T ss_conf             725887-699811999999999973799748-9975888868899--997999998486054227889848---889875


Q ss_pred             CCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCEEEEECCCCCCHHHHHHHHHHHHCCCCCEEEEEEECCCCCCCHHH
Q ss_conf             11134577612662101354455652101135862899975455998899998987406988258999807899987688
Q gi|254781187|r  159 EQSMGIDSKHYTITCRTYSEERPDTFVGPHNTHGMAVFNDEASGTPDIINKSILGFFTELNPNRFWIMTSNTRRLNGWFY  238 (367)
Q Consensus       159 ~~~~~~~~~~~~~~a~~~~~~~~ea~~g~h~~~~~l~ivDEAsgI~d~i~e~i~g~Lt~~~~~~~~i~igNP~r~~g~Fy  238 (367)
                      ..++-+...+-+.+-..-. .-..+....-.....++||||+-.|           |-+....-+  ++|.|......+|
T Consensus       166 ~~DItYgTn~e~gFDYLRD-nm~~~~~~~vqR~~~~aIVDEvDSi-----------LIDEArtPL--IISg~~~~~~~~y  231 (381)
T pfam07517       166 NCDITYGTNSELGFDYLRD-NMALSKEDKVQRGLNFAIVDEVDSI-----------LIDEARTPL--IISGPVEDESELY  231 (381)
T ss_pred             HCCCEECCHHHHHHHHHHH-HHHCCHHHHCCCCCCEEEEECCCHH-----------EEECCCCCC--EECCCCCCCCHHH
T ss_conf             1660550322321445323-4415825434577776999745112-----------120467863--5407887630589


Q ss_pred             HHHH
Q ss_conf             7541
Q gi|254781187|r  239 DIFN  242 (367)
Q Consensus       239 e~~~  242 (367)
                      ..+.
T Consensus       232 ~~~~  235 (381)
T pfam07517       232 LIAD  235 (381)
T ss_pred             HHHH
T ss_conf             9999


No 229
>COG2842 Uncharacterized ATPase, putative transposase [General function prediction only]
Probab=87.03  E-value=2.1  Score=21.45  Aligned_cols=107  Identities=10%  Similarity=0.046  Sum_probs=60.6

Q ss_pred             EEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             77614886788999999999999708997799971537999999999999999862312112333321000123332211
Q gi|254781187|r   80 CAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLKNTLWAEVSKWLSMLPHRHWFEMQSLSLHPSGWYAELLE  159 (367)
Q Consensus        80 ~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~~~lw~ei~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  159 (367)
                      ++|-+.+|+||+...-.+    +-.+ +...++.++....+...+-.+.......         +.+.+.          
T Consensus        97 ~~vyg~~g~gKt~a~~~y----~~s~-p~~~l~~~~p~~~a~~~i~~i~~~~~~~---------~~~~~~----------  152 (297)
T COG2842          97 VVVYGYAGLGKTQAAKNY----APSN-PNALLIEADPSYTALVLILIICAAAFGA---------TDGTIN----------  152 (297)
T ss_pred             EEEECCCCCHHHHHHHHH----CCCC-CCCEEECCCHHHHHHHHHHHHHHHHHCC---------CCHHHH----------
T ss_conf             788633220068999865----3358-6413615881367889999999987401---------421688----------


Q ss_pred             CCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCEEEEECCCCCCHHHHHHHHHHHHCCCCCEEEEEEECCC
Q ss_conf             113457761266210135445565210113586289997545599889999898740698825899980789
Q gi|254781187|r  160 QSMGIDSKHYTITCRTYSEERPDTFVGPHNTHGMAVFNDEASGTPDIINKSILGFFTELNPNRFWIMTSNTR  231 (367)
Q Consensus       160 ~~~~~~~~~~~~~a~~~~~~~~ea~~g~h~~~~~l~ivDEAsgI~d~i~e~i~g~Lt~~~~~~~~i~igNP~  231 (367)
                                 .  .+      ++.........-++++|||...+-..++.++-.....+--  ++.+|+|.
T Consensus       153 -----------d--~~------~~~~~~l~~~~~~iivDEA~~L~~~ale~lr~i~d~~Gi~--~vLvG~pr  203 (297)
T COG2842         153 -----------D--LT------ERLMIRLRDTVRLIIVDEADRLPYRALEELRRIHDKTGIG--VVLVGMPR  203 (297)
T ss_pred             -----------H--HH------HHHHHHHCCCCCEEEEEHHHCCCHHHHHHHHHHHHHHCCE--EEEECCHH
T ss_conf             -----------8--89------9999997157652665032125868999999988750815--99836768


No 230
>pfam07570 consensus
Probab=86.57  E-value=0.79  Score=24.06  Aligned_cols=28  Identities=25%  Similarity=0.478  Sum_probs=22.6

Q ss_pred             EEEEEECCCCCCHHHHHHHHHHHHHHHCC
Q ss_conf             24776148867889999999999997089
Q gi|254781187|r   78 FKCAISAGRGIGKTTLNAWMMLWLISTRP  106 (367)
Q Consensus        78 ~~~~v~sgrg~GKS~~~a~~~lw~~~~~~  106 (367)
                      +++ +.+|||++||..+|..++..+.-.|
T Consensus        14 y~v-~kGgrgS~KS~~~a~~~i~~~~kyp   41 (45)
T pfam07570        14 YIV-AKGGRGSGKSSVIALKIILKLLKYP   41 (45)
T ss_pred             EEE-EECCCCCCCHHHHHHHHHHHHHHCC
T ss_conf             077-5457676602789999999998342


No 231
>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=86.33  E-value=2.3  Score=21.22  Aligned_cols=77  Identities=17%  Similarity=0.055  Sum_probs=49.7

Q ss_pred             CCCCCCC--CCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEEC-CCCCCHHHHHHHHHHHHHHHCCCCEEEEE
Q ss_conf             1466888--44366684289999999888875124555554112477614-88678899999999999970899779997
Q gi|254781187|r   37 PWGIKGK--PLEHFSQPHRWQLEFMEAVDVHCHSNVNNSNPTIFKCAISA-GRGIGKTTLNAWMMLWLISTRPGMSIICI  113 (367)
Q Consensus        37 ~w~~~~~--~~~~~~~p~~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~s-grg~GKS~~~a~~~lw~~~~~~~~~v~~~  113 (367)
                      ++|+-+.  +|--.-.|.-=|.|.+|.+...+--.--..  ...-++|.| ..|-|||+++|.+++-++-.  |.|++.+
T Consensus        63 ~~~~~~~~~~l~aa~~P~s~~~Ea~R~lRs~l~~~~~~~--~~~~LaItS~~pGEGKS~vAaNLA~~~Aq~--G~RvLLV  138 (274)
T TIGR03029        63 PPNDGSFSPDLIAAYQPFSPQVEALRALRSQLMLRWFSE--GRKALAVVSAKSGEGCSYIAANLAIVFSQL--GEKTLLI  138 (274)
T ss_pred             CCCCCCCCHHHHHHHCCCCHHHHHHHHHHHHHHHHHCCC--CCCEEEEECCCCCCCHHHHHHHHHHHHHHC--CCEEEEE
T ss_conf             845578898998773899889999999999999984578--883899968999998999999999999967--9919999


Q ss_pred             CCCH
Q ss_conf             1537
Q gi|254781187|r  114 ANSE  117 (367)
Q Consensus       114 A~t~  117 (367)
                      -.-.
T Consensus       139 DaDL  142 (274)
T TIGR03029       139 DANL  142 (274)
T ss_pred             ECCC
T ss_conf             5888


No 232
>KOG0347 consensus
Probab=85.99  E-value=0.64  Score=24.61  Aligned_cols=265  Identities=14%  Similarity=0.100  Sum_probs=118.4

Q ss_pred             CCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHH--------------HHCCCCEE
Q ss_conf             4366684289999999888875124555554112477614886788999999999999--------------70899779
Q gi|254781187|r   45 LEHFSQPHRWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLI--------------STRPGMSI  110 (367)
Q Consensus        45 ~~~~~~p~~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~--------------~~~~~~~v  110 (367)
                      -.+|+.|++.|...|-+.   ++...        -+.=+|-.|+|||-..+.=++-.+              .-++-.-.
T Consensus       198 ~~gFs~Pt~IQsl~lp~a---i~gk~--------DIlGaAeTGSGKTLAFGIPiv~~l~~~s~~s~e~~~~~~k~~k~~~  266 (731)
T KOG0347         198 NLGFSRPTEIQSLVLPAA---IRGKV--------DILGAAETGSGKTLAFGIPIVERLLESSDDSQELSNTSAKYVKPIA  266 (731)
T ss_pred             HCCCCCCCCCHHHCCCHH---HCCCH--------HCCCCCCCCCCCEEEECCHHHHHHHHCCCHHHHHHHHHHCCCCCEE
T ss_conf             647899861044116676---54630--------0003334688742441232545433036537654467760576403


Q ss_pred             EEECCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCC-CCCCCCCCCEEEEE---CCCCCCCCCCCCC
Q ss_conf             9971537999999999999999862312112333321000123332211-11345776126621---0135445565210
Q gi|254781187|r  111 ICIANSETQLKNTLWAEVSKWLSMLPHRHWFEMQSLSLHPSGWYAELLE-QSMGIDSKHYTITC---RTYSEERPDTFVG  186 (367)
Q Consensus       111 ~~~A~t~~Q~~~~lw~ei~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~a---~~~~~~~~ea~~g  186 (367)
                      +|++||..-+-.+. ..++.+.+..    ..  ....+  ..+....-+ +-+...+  -++.|   +.|...+..+.--
T Consensus       267 LV~tPTRELa~QV~-~Hl~ai~~~t----~i--~v~si--~GGLavqKQqRlL~~~p--~IVVATPGRlweli~e~n~~l  335 (731)
T KOG0347         267 LVVTPTRELAHQVK-QHLKAIAEKT----QI--RVASI--TGGLAVQKQQRLLNQRP--DIVVATPGRLWELIEEDNTHL  335 (731)
T ss_pred             EEECCHHHHHHHHH-HHHHHHCCCC----CE--EEEEE--ECHHHHHHHHHHHHCCC--CEEEECCHHHHHHHHHHHHHH
T ss_conf             89637099999999-9999861346----72--78875--23057999999985299--879936628999997510666


Q ss_pred             CCCCCCCEEEEECCCCC-CHHHHHHHHHHH---HC----CCCCEEEEEEECCCCCCCHHHHHHHCCCCC-----E-----
Q ss_conf             11358628999754559-988999989874---06----988258999807899987688754112235-----0-----
Q gi|254781187|r  187 PHNTHGMAVFNDEASGT-PDIINKSILGFF---TE----LNPNRFWIMTSNTRRLNGWFYDIFNIPLED-----W-----  248 (367)
Q Consensus       187 ~h~~~~~l~ivDEAsgI-~d~i~e~i~g~L---t~----~~~~~~~i~igNP~r~~g~Fye~~~~~~~~-----w-----  248 (367)
                      ..-....|+++|||.-. .+..|+-+.-.|   -+    .....+  .+| -|-.-+.+.......++.     .     
T Consensus       336 ~~~k~vkcLVlDEaDRmvekghF~Els~lL~~L~e~~~~~qrQTl--VFS-ATlt~~~~~~~~~~~k~~~k~~~~~~kiq  412 (731)
T KOG0347         336 GNFKKVKCLVLDEADRMVEKGHFEELSKLLKHLNEEQKNRQRQTL--VFS-ATLTLVLQQPLSSSRKKKDKEDELNAKIQ  412 (731)
T ss_pred             HHHHHCEEEEECCHHHHHHHCCHHHHHHHHHHHHHHHCCCCCCEE--EEE-EEEEHHHCCHHHHHHHCCCHHHHHHHHHH
T ss_conf             423324078873477775511099999999986031105101258--998-77633321705776542211455667999


Q ss_pred             ----------EEEEECCCCCCCCCHHHHHHHHHHCCCCCCEEEEEEEEEECCCCCCEEECH--HHHH-------------
Q ss_conf             ----------467523332888898899999962168800026888644327789807829--9986-------------
Q gi|254781187|r  249 ----------KRYQIDTRTVEGIDSGFHEGIISRYGLDSDVARIEILGQFPQQEVNNFIPH--NYIE-------------  303 (367)
Q Consensus       249 ----------~~~~~~~~d~p~~~~~~i~~~~~~~gedS~~~r~ev~G~Fp~~~~d~~ip~--~~ie-------------  303 (367)
                                ...-++..-...+.....+..+..-.-.-+.|-+.++-.||..  +-+|.-  +.+.             
T Consensus       413 ~Lmk~ig~~~kpkiiD~t~q~~ta~~l~Es~I~C~~~eKD~ylyYfl~ryPGr--TlVF~NsId~vKRLt~~L~~L~i~p  490 (731)
T KOG0347         413 HLMKKIGFRGKPKIIDLTPQSATASTLTESLIECPPLEKDLYLYYFLTRYPGR--TLVFCNSIDCVKRLTVLLNNLDIPP  490 (731)
T ss_pred             HHHHHHCCCCCCEEEECCCCHHHHHHHHHHHHCCCCCCCCEEEEEEEEECCCC--EEEEECHHHHHHHHHHHHHHCCCCC
T ss_conf             99998475689826766820447888887763588544540689988636983--5998411889999999974169997


Q ss_pred             ----HHHC-----CCC--CCCCCCCEEEEEECCCCCCC----EEEEEE
Q ss_conf             ----4431-----577--77889848999963877881----089999
Q gi|254781187|r  304 ----EAMS-----REA--IDDLYAPLIMGCDIAGEGGD----KTVVVF  336 (367)
Q Consensus       304 ----~a~~-----~~~--~~~~~~p~viGvDvAr~G~D----~Tvi~~  336 (367)
                          ++|.     .+.  .-.....+.+.-|||-.|=|    ..||+.
T Consensus       491 ~~LHA~M~QKqRLknLEkF~~~~~~VLiaTDVAARGLDIp~V~HVIHY  538 (731)
T KOG0347         491 LPLHASMIQKQRLKNLEKFKQSPSGVLIATDVAARGLDIPGVQHVIHY  538 (731)
T ss_pred             CHHHHHHHHHHHHHHHHHHHCCCCEEEEEEHHHHCCCCCCCCCEEEEE
T ss_conf             102577889999876998744888179962344425888786367896


No 233
>COG2607 Predicted ATPase (AAA+ superfamily) [General function prediction only]
Probab=85.69  E-value=2.5  Score=21.02  Aligned_cols=92  Identities=15%  Similarity=0.139  Sum_probs=53.0

Q ss_pred             HHHHCCCCCCCCCCCCCCCHH----------HHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHH
Q ss_conf             543014668884436668428----------9999999888875124555554112477614886788999999999999
Q gi|254781187|r   33 MRFFPWGIKGKPLEHFSQPHR----------WQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLI  102 (367)
Q Consensus        33 ~~~~~w~~~~~~~~~~~~p~~----------wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~  102 (367)
                      .++|-|+..+.-|.....|..          =|.++|-+=....-.+.-.     -.|..-+.||+|||.++-++..-+.
T Consensus        36 a~~f~~~~~~~~L~pv~~~~~i~L~~l~Gvd~qk~~L~~NT~~F~~G~pA-----NnVLLwGaRGtGKSSLVKA~~~e~~  110 (287)
T COG2607          36 ALAFRWRPAIGYLEPVPDPDPIDLADLVGVDRQKEALVRNTEQFAEGLPA-----NNVLLWGARGTGKSSLVKALLNEYA  110 (287)
T ss_pred             HHHHHCCCCCCCCCCCCCCCCCCHHHHHCCHHHHHHHHHHHHHHHCCCCC-----CCEEEECCCCCCHHHHHHHHHHHHH
T ss_conf             55773133568666889899767898727318999999989999728865-----2367763777774799999999987


Q ss_pred             HHCCCCEEEEECCCHHHHHHHHHHHHHHHHHHC
Q ss_conf             708997799971537999999999999999862
Q gi|254781187|r  103 STRPGMSIICIANSETQLKNTLWAEVSKWLSML  135 (367)
Q Consensus       103 ~~~~~~~v~~~A~t~~Q~~~~lw~ei~k~~~~~  135 (367)
                      ...+  +  .+.-+.+++.+  .+.+-..++..
T Consensus       111 ~~gl--r--LVEV~k~dl~~--Lp~l~~~Lr~~  137 (287)
T COG2607         111 DEGL--R--LVEVDKEDLAT--LPDLVELLRAR  137 (287)
T ss_pred             HCCC--E--EEEECHHHHHH--HHHHHHHHHCC
T ss_conf             4177--0--79976888865--79999999618


No 234
>pfam02500 DNA_pack_N Probable DNA packing protein, N-terminus. This family includes proteins that are probably involved in DNA packing in herpesvirus. This domain is normally found at the N-terminus of the protein.
Probab=85.55  E-value=1.3  Score=22.79  Aligned_cols=51  Identities=22%  Similarity=0.285  Sum_probs=43.1

Q ss_pred             ECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHHHHHHHH
Q ss_conf             1488678899999999999970899779997153799999999999999986
Q gi|254781187|r   83 SAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLKNTLWAEVSKWLSM  134 (367)
Q Consensus        83 ~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~~~lw~ei~k~~~~  134 (367)
                      .-+|.=|||++.-.+|--.|....|.+|-+||. ++-+.+-+|.||..-+++
T Consensus       186 LVPRRHGKTWfvVpiIsllL~s~egI~IGYvAH-qkhvs~~VF~EI~~rl~r  236 (276)
T pfam02500       186 LVPRRHGKTWFVVPIISLLLSSFEGIHIGYVAH-QKHVSEPVFTEIINRLRR  236 (276)
T ss_pred             EEECCCCCEEEHHHHHHHHHHHCCCCEEEEHHH-HHHHHHHHHHHHHHHHHH
T ss_conf             731578973553999999997315855542688-887438999999999998


No 235
>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=85.44  E-value=1.8  Score=21.92  Aligned_cols=38  Identities=24%  Similarity=0.225  Sum_probs=25.8

Q ss_pred             EEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCH
Q ss_conf             77614886788999999999999708997799971537
Q gi|254781187|r   80 CAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSE  117 (367)
Q Consensus        80 ~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~  117 (367)
                      ++|++|-|+|||+++..+.--+-.....+.++.+-.-+
T Consensus         2 IgIaG~SgSGKTT~a~~L~~~l~~~~~~~~vis~D~yy   39 (179)
T cd02028           2 VGIAGPSGSGKTTFAKKLSNQLRVNGIGPVVISLDDYY   39 (179)
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHHCCCCEEEEECCCCC
T ss_conf             89989897789999999999984648853999546664


No 236
>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=85.20  E-value=1.4  Score=22.49  Aligned_cols=44  Identities=16%  Similarity=0.116  Sum_probs=29.2

Q ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHHCC-CCEEEEECCCHHHHHH
Q ss_conf             4776148867889999999999997089-9779997153799999
Q gi|254781187|r   79 KCAISAGRGIGKTTLNAWMMLWLISTRP-GMSIICIANSETQLKN  122 (367)
Q Consensus        79 ~~~v~sgrg~GKS~~~a~~~lw~~~~~~-~~~v~~~A~t~~Q~~~  122 (367)
                      |+.|-+|+|+|||++.+.++.--..... ...+++.+-.....++
T Consensus        71 R~gIfgg~GvGKs~L~~~i~~~~~~~~~~~~~v~V~~~IGer~re  115 (276)
T cd01135          71 KIPIFSGSGLPHNELAAQIARQAGVVGEEENFAVVFAAMGITMED  115 (276)
T ss_pred             EEEECCCCCCCHHHHHHHHHHHHHHCCCCCCCEEEEEECCEEHHH
T ss_conf             633205788636789999999877513688735999615553257


No 237
>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=84.90  E-value=0.95  Score=23.58  Aligned_cols=191  Identities=13%  Similarity=0.060  Sum_probs=94.1

Q ss_pred             EEEECCC-CCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             7761488-678899999999999970899779997153799999999999999986231211233332100012333221
Q gi|254781187|r   80 CAISAGR-GIGKTTLNAWMMLWLISTRPGMSIICIANSETQLKNTLWAEVSKWLSMLPHRHWFEMQSLSLHPSGWYAELL  158 (367)
Q Consensus        80 ~~v~sgr-g~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~~~lw~ei~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~  158 (367)
                      ++|+||- |+||||++|.+.+-+.-+  |.+|+++=.--..+.=.+   |=.+=.+-+.-|-.....-.+..+.|.+...
T Consensus         3 I~iASGKGGtGKTT~tANLgVALA~~--Gk~V~~~DADI~MANL~L---iLgmE~~~VTLhDVLAGeA~i~DAIY~gp~G   77 (258)
T TIGR01969         3 ITIASGKGGTGKTTITANLGVALAKL--GKKVLVLDADITMANLEL---ILGMEDKPVTLHDVLAGEADIKDAIYEGPEG   77 (258)
T ss_pred             EEEEECCCCCCHHHEEEHHHHHHHHC--CCEEEEEECCHHHHHHHH---HHCCCCCCCCCCCCCCCCCCHHHHCCCCCCC
T ss_conf             89997788986140000077889860--976899946766776898---8446888967522134456100110028898


Q ss_pred             CCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCEEEEECCCCCCHHHHHHHHHHHHCCCCCEEEEEEECCCCCCCHHH
Q ss_conf             11134577612662101354455652101135862899975455998899998987406988258999807899987688
Q gi|254781187|r  159 EQSMGIDSKHYTITCRTYSEERPDTFVGPHNTHGMAVFNDEASGTPDIINKSILGFFTELNPNRFWIMTSNTRRLNGWFY  238 (367)
Q Consensus       159 ~~~~~~~~~~~~~~a~~~~~~~~ea~~g~h~~~~~l~ivDEAsgI~d~i~e~i~g~Lt~~~~~~~~i~igNP~r~~g~Fy  238 (367)
                      ..+.--..=++--.-+.--+.-+|-...++.. ..++++|==||+--+...++.    .. .+.+  +.-||-= + ---
T Consensus        78 nV~V~PagvSLEg~rKA~~~~L~dV~~~i~~~-~D~lLIDAPAGL~~~a~~Al~----~a-~elL--LVvNPEi-~-SIt  147 (258)
T TIGR01969        78 NVKVIPAGVSLEGLRKADPDKLEDVLKEIIDD-TDFLLIDAPAGLERDAVTALA----AA-DELL--LVVNPEI-S-SIT  147 (258)
T ss_pred             CEEEECCCCCHHHCCCCCHHHHHHHHHHHHCC-CCEEEEECCCCCCHHHHHHHH----HC-CCCE--EEECCCH-H-HHH
T ss_conf             44785061221000126833328999987204-377887478983378999998----61-8664--8667654-4-677


Q ss_pred             HHHH---CCCC-CE----EEEEECCCCCCCCCHHHHHHHHHH-----CCCCCCEEEEEEE
Q ss_conf             7541---1223-50----467523332888898899999962-----1688000268886
Q gi|254781187|r  239 DIFN---IPLE-DW----KRYQIDTRTVEGIDSGFHEGIISR-----YGLDSDVARIEIL  285 (367)
Q Consensus       239 e~~~---~~~~-~w----~~~~~~~~d~p~~~~~~i~~~~~~-----~gedS~~~r~ev~  285 (367)
                      |...   -+++ +-    -..---.++.-.++++.+|...+-     -.||+.+-|.=..
T Consensus       148 DaLK~k~va~~lGt~ilG~vlNRv~~~~tel~~~eiE~iLevPVl~~vPEDP~VR~AAa~  207 (258)
T TIGR01969       148 DALKVKIVAEKLGTAILGVVLNRVTRDKTELGREEIEAILEVPVLGVVPEDPEVRRAAAF  207 (258)
T ss_pred             HHHHHHHHHHHCCCCEEEEEEEECCCCCCCCCHHHHHHHHCCCEEEEECCCHHHHHHHHC
T ss_conf             788999998760883246899602366663788899988479738985698434456424


No 238
>PRK06921 hypothetical protein; Provisional
Probab=84.84  E-value=2.7  Score=20.78  Aligned_cols=59  Identities=19%  Similarity=0.068  Sum_probs=34.3

Q ss_pred             CHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEEC
Q ss_conf             4289999999888875124555554112477614886788999999999999708997799971
Q gi|254781187|r   51 PHRWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIA  114 (367)
Q Consensus        51 p~~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A  114 (367)
                      +.+.-..+++.+.++.+--..+.+    .+...+.-|+|||+++++++-.++-. .+..|+++.
T Consensus        94 ~k~a~~~a~eY~~~F~~i~~~~~~----~l~f~G~~G~GKThLa~aIa~~Ll~~-~~~~Vly~~  152 (265)
T PRK06921         94 IKDAYECAVEYVKDFEKIQGCRKN----SIALLGQPGSGKTHLLTAAANELMRK-KGVPVLYFP  152 (265)
T ss_pred             HHHHHHHHHHHHHHHHHHHCCCCC----CEEEECCCCCCHHHHHHHHHHHHHHH-CCCEEEEEE
T ss_conf             999999999999977876077766----27997289898899999999999996-297199988


No 239
>pfam03205 MobB Molybdopterin guanine dinucleotide synthesis protein B. This protein contains a P-loop.
Probab=84.77  E-value=2.3  Score=21.23  Aligned_cols=34  Identities=21%  Similarity=0.262  Sum_probs=26.1

Q ss_pred             EEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEE
Q ss_conf             247761488678899999999999970899779997
Q gi|254781187|r   78 FKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICI  113 (367)
Q Consensus        78 ~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~  113 (367)
                      +|+.|.+..++|||+++..++-+.+-.  +.++++.
T Consensus         1 p~v~i~G~~~sGKttl~~~L~~~~~~~--g~~~~~~   34 (122)
T pfam03205         1 PIVLVVGPKDSGKTTLIRKLLNYLKRR--GYRVAVV   34 (122)
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHHHHC--CCCEEEE
T ss_conf             979999489998999999999999987--9944899


No 240
>pfam10236 DAP3 Mitochondrial ribosomal death-associated protein 3. This is a family of conserved proteins which were originally described as death-associated-protein-3 (DAP-3). The proteins carry a P-loop DNA-binding motif, and induce apoptosis. DAP3 has been shown to be a pro-apoptotic factor in the mitochondrial matrix and to be crucial for mitochondrial biogenesis and so has also been designated as MRP-S29 (mitochondrial ribosomal protein subunit 29).
Probab=84.72  E-value=2.4  Score=21.09  Aligned_cols=27  Identities=26%  Similarity=0.498  Sum_probs=22.2

Q ss_pred             EEEEEEECCCCCCHHHHHHHHHHHHHH
Q ss_conf             124776148867889999999999997
Q gi|254781187|r   77 IFKCAISAGRGIGKTTLNAWMMLWLIS  103 (367)
Q Consensus        77 ~~~~~v~sgrg~GKS~~~a~~~lw~~~  103 (367)
                      ..|+.+-+.+|+|||.+.+-++.|-..
T Consensus        23 ~~r~vL~G~~GsGKS~~L~q~v~~A~~   49 (274)
T pfam10236        23 VVRFVLTGERGSGKSVLLAQAMAYALT   49 (274)
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHHHHH
T ss_conf             518998897997799999999999985


No 241
>KOG0348 consensus
Probab=84.61  E-value=2.8  Score=20.72  Aligned_cols=139  Identities=13%  Similarity=0.026  Sum_probs=78.8

Q ss_pred             CCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCC-------CCEEEEECCCH
Q ss_conf             43666842899999998888751245555541124776148867889999999999997089-------97799971537
Q gi|254781187|r   45 LEHFSQPHRWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRP-------GMSIICIANSE  117 (367)
Q Consensus        45 ~~~~~~p~~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~-------~~~v~~~A~t~  117 (367)
                      ...+..|+--|...+-.|-+      ++      -+.|.|-.|+|||-.-+.=++-.+...+       |.-.+|++||.
T Consensus       154 ~m~i~~pTsVQkq~IP~lL~------gr------D~lV~aQTGSGKTLAYllPiVq~Lq~m~~ki~Rs~G~~ALVivPTR  221 (708)
T KOG0348         154 KMKISAPTSVQKQAIPVLLE------GR------DALVRAQTGSGKTLAYLLPIVQSLQAMEPKIQRSDGPYALVIVPTR  221 (708)
T ss_pred             HHCCCCCCHHHHCCHHHHHC------CC------CEEEECCCCCCCCHHHHHHHHHHHHHCCCCCCCCCCCEEEEEECHH
T ss_conf             74557640676502035525------86------3478857788621799999999997268655556883489980419


Q ss_pred             HHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCC-CCCCCCCCCCCCCCCEEE
Q ss_conf             9999999999999998623121123333210001233322111134577612662101354-455652101135862899
Q gi|254781187|r  118 TQLKNTLWAEVSKWLSMLPHRHWFEMQSLSLHPSGWYAELLEQSMGIDSKHYTITCRTYSE-ERPDTFVGPHNTHGMAVF  196 (367)
Q Consensus       118 ~Q~~~~lw~ei~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~-~~~ea~~g~h~~~~~l~i  196 (367)
                      .-+-.+ +.-+.|.+.   ..+|.-.     -.-.+....-+-..+...|..+..+.+-|. +--.+-..+|-...-.+|
T Consensus       222 EL~~Q~-y~~~qKLl~---~~hWIVP-----g~lmGGEkkKSEKARLRKGiNILIgTPGRLvDHLknT~~i~~s~LRwlV  292 (708)
T KOG0348         222 ELALQI-YETVQKLLK---PFHWIVP-----GVLMGGEKKKSEKARLRKGINILIGTPGRLVDHLKNTKSIKFSRLRWLV  292 (708)
T ss_pred             HHHHHH-HHHHHHHHC---CCEEEEE-----CEEECCCCCCCHHHHHHCCCEEEECCCHHHHHHHHCCCHHEEEEEEEEE
T ss_conf             999999-999998725---7437730-----2122363310178887548548975842788987430022100356898


Q ss_pred             EECCCCCC
Q ss_conf             97545599
Q gi|254781187|r  197 NDEASGTP  204 (367)
Q Consensus       197 vDEAsgI~  204 (367)
                      +|||.-|=
T Consensus       293 lDEaDrll  300 (708)
T KOG0348         293 LDEADRLL  300 (708)
T ss_pred             ECCHHHHH
T ss_conf             53436787


No 242
>TIGR02562 cas3_yersinia CRISPR-associated helicase Cas3, Yersinia-type; InterPro: IPR013395    The helicase encoded in many CRISPR-associated (cas) gene clusters is designated Cas3. The Yersinia-type helicase Cas3 proteins differ from the more common Cas3 proteins by being considerably larger, though they still share a number of motifs, and replace Cas3 in some CRISPR/cas loci in a number of Proteobacteria, including Yersinia pestis, Chromobacterium violaceum, Erwinia carotovora subsp. atroseptica SCRI1043, Photorhabdus luminescens subsp. laumondii TTO1, Legionella pneumophila, etc..
Probab=84.60  E-value=1.3  Score=22.78  Aligned_cols=262  Identities=15%  Similarity=0.121  Sum_probs=116.0

Q ss_pred             HHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECC-------CH--------
Q ss_conf             899999998888751245555541124776148867889999999999997089977999715-------37--------
Q gi|254781187|r   53 RWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIAN-------SE--------  117 (367)
Q Consensus        53 ~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~-------t~--------  117 (367)
                      .||-++......-.++- ......++++   ||.|+|||..-|.++--+---.+|+++.+-=+       |+        
T Consensus       423 ~WQ~kA~~~a~~~~~~~-~~~G~f~vN~---AsTGcGKT~aNar~~yaL~~~~~G~R~a~ALgLR~LTLQTG~ALk~~L~  498 (1153)
T TIGR02562       423 RWQNKAFNLAQKLRQKS-EEQGAFGVNM---ASTGCGKTLANARLMYALRDDKQGLRFAIALGLRSLTLQTGSALKKRLN  498 (1153)
T ss_pred             HHHHHHHHHHHHHHHHH-HHCCCEEEEC---CCCCCHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHCC
T ss_conf             67889999999988735-4279469862---6468437999999986177888874001343224678888899997417


Q ss_pred             -----------HHHHHHHHHHHHHHHHHC------CCCCCCCCCC---CCCCCCCCCCCCCCCCCCCCCCC---------
Q ss_conf             -----------999999999999999862------3121123333---21000123332211113457761---------
Q gi|254781187|r  118 -----------TQLKNTLWAEVSKWLSML------PHRHWFEMQS---LSLHPSGWYAELLEQSMGIDSKH---------  168 (367)
Q Consensus       118 -----------~Q~~~~lw~ei~k~~~~~------~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~---------  168 (367)
                                 .++...+|..-+.-++..      +...|+....   ...+..+.........+-.+.+.         
T Consensus       499 L~d~~lAv~iG~~~~~~Lf~~~~ek~e~~~~~gs~s~~~f~~~~~~~~~~~~~~~~~~~~~~~~ls~d~k~~~lL~aP~l  578 (1153)
T TIGR02562       499 LSDDDLAVLIGGTAVKKLFDLSKEKIEQVDEDGSESAEKFLEEGQDCNLVDYDGALDTEELLSRLSKDDKLKKLLAAPVL  578 (1153)
T ss_pred             CCCCCEEEEECCHHHHHHHHHHHHHHHHHCCCCCCCHHHHHCCCCCCCCCCCCCCCCCHHHHHHHCCCHHHHHHHHCCHH
T ss_conf             88576367865288899999877652020035688615550432116863236775414675431025455466525126


Q ss_pred             -EEEEECCCCCCCCCCCCCCCCCCCCE------EEEECCCCCCHHHHHHH-----HHHHHCCCCCEEEEEEECC---CCC
Q ss_conf             -26621013544556521011358628------99975455998899998-----9874069882589998078---999
Q gi|254781187|r  169 -YTITCRTYSEERPDTFVGPHNTHGMA------VFNDEASGTPDIINKSI-----LGFFTELNPNRFWIMTSNT---RRL  233 (367)
Q Consensus       169 -~~~~a~~~~~~~~ea~~g~h~~~~~l------~ivDEAsgI~d~i~e~i-----~g~Lt~~~~~~~~i~igNP---~r~  233 (367)
                       ..+.--.   --.|+.+|-|-=..||      +|+||--+-+.+-.-++     ...|  -|.+.++   |+-   +.-
T Consensus       579 vcTiDhLi---~A~Es~rgG~~i~p~LRllsSDLiLDE~Ddy~~~dLpAl~RLV~lAgL--~GsrVll---SSATL~p~l  650 (1153)
T TIGR02562       579 VCTIDHLI---PATESVRGGHHIAPMLRLLSSDLILDEPDDYEREDLPALLRLVQLAGL--LGSRVLL---SSATLPPAL  650 (1153)
T ss_pred             HHHHHHCC---CCCCCCCCCEEHHHHHHHHHHHHEECCCCCCCHHHHHHHHHHHHHHHH--HCCHHHH---HCCCCCHHH
T ss_conf             65543200---467754456107889987532320048888871234899999999998--4441422---213660889


Q ss_pred             CCHHHHHHHCCC----------CCEEEEEECCCCCCCCC--------------HHHHHHHHHHCCCCCCEEEEEEEE--E
Q ss_conf             876887541122----------35046752333288889--------------889999996216880002688864--4
Q gi|254781187|r  234 NGWFYDIFNIPL----------EDWKRYQIDTRTVEGID--------------SGFHEGIISRYGLDSDVARIEILG--Q  287 (367)
Q Consensus       234 ~g~Fye~~~~~~----------~~w~~~~~~~~d~p~~~--------------~~~i~~~~~~~gedS~~~r~ev~G--~  287 (367)
                      -.-.|+.|..++          +.-..+++.|.|-+.+-              .+|+..+...+...+..-+.+++.  +
T Consensus       651 v~~lF~AY~aGr~~y~~~~G~~~~~~~~cc~w~de~~~~~~~~~q~~~F~~~h~~F~~~r~~~L~~~p~~R~AeLLsLS~  730 (1153)
T TIGR02562       651 VKTLFKAYEAGRKIYQALKGQPKKPLNICCAWVDEPQVVQADCNQKEEFIQRHQDFVRKRAEKLAKKPVRRLAELLSLSS  730 (1153)
T ss_pred             HHHHHHHHHHHHHHHHHHCCCCCCCEEEEEECCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHCCCCCC
T ss_conf             99999999999999997467988860556532464679998642169999998889999999862676223020036888


Q ss_pred             E-CCCCCCEEECH---HHHHHH---HCCCCCCCCCCCEEEEEECCC
Q ss_conf             3-27789807829---998644---315777788984899996387
Q gi|254781187|r  288 F-PQQEVNNFIPH---NYIEEA---MSREAIDDLYAPLIMGCDIAG  326 (367)
Q Consensus       288 F-p~~~~d~~ip~---~~ie~a---~~~~~~~~~~~p~viGvDvAr  326 (367)
                      - |+.++.++++.   .+.+.+   +.-...-+|.....+.|-+=|
T Consensus       731 ~kpr~Gn~s~~~~la~~ll~~~~~LH~~h~~t~p~~~K~vSvGLiR  776 (1153)
T TIGR02562       731 LKPRKGNESVYLALAESLLEGALRLHQLHAQTDPKSEKKVSVGLIR  776 (1153)
T ss_pred             CCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEEEEE
T ss_conf             8865650567999999999999999860266777678778886154


No 243
>pfam09848 DUF2075 Uncharacterized conserved protein (DUF2075). This domain, found in various prokaryotic proteins (including putative ATP/GTP binding proteins), has no known function.
Probab=84.59  E-value=2.8  Score=20.71  Aligned_cols=39  Identities=18%  Similarity=0.325  Sum_probs=24.7

Q ss_pred             EEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHH
Q ss_conf             776148867889999999999997089977999715379
Q gi|254781187|r   80 CAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSET  118 (367)
Q Consensus        80 ~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~  118 (367)
                      +.|.++=|+|||.+..-++.-......+...+.......
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 244
>CHL00060 atpB ATP synthase CF1 beta subunit
Probab=84.58  E-value=2.8  Score=20.71  Aligned_cols=50  Identities=22%  Similarity=0.383  Sum_probs=30.1

Q ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEE-ECCCHHHHHHHHHHHHH
Q ss_conf             4776148867889999999999997089977999-71537999999999999
Q gi|254781187|r   79 KCAISAGRGIGKTTLNAWMMLWLISTRPGMSIIC-IANSETQLKNTLWAEVS  129 (367)
Q Consensus        79 ~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~-~A~t~~Q~~~~lw~ei~  129 (367)
                      |+.+-+|+|+|||+++..++.-..-.+.+..|++ +-...+.+++ ++.|++
T Consensus       157 RigIfggaGvGKTvLl~eli~niak~~~~v~V~a~IGER~RE~~e-~~~e~~  207 (480)
T CHL00060        157 KIGLFGGAGVGKTVLIMELINNIAKAHGGVSVFGGVGERTREGND-LYMEMK  207 (480)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHCCCCCEEEEEEECCCCHHHHH-HHHHHH
T ss_conf             887656899887899999996120037988999996677367999-999998


No 245
>CHL00081 chlI Mg-protoporyphyrin IX chelatase
Probab=84.48  E-value=2.8  Score=20.68  Aligned_cols=52  Identities=13%  Similarity=0.026  Sum_probs=32.8

Q ss_pred             CCCCCCCCCCCCCCCEEEEECCCCCCHHHHHHHHHHHHCCC-------------CCEEEEEEECCCCC
Q ss_conf             45565210113586289997545599889999898740698-------------82589998078999
Q gi|254781187|r  179 ERPDTFVGPHNTHGMAVFNDEASGTPDIINKSILGFFTELN-------------PNRFWIMTSNTRRL  233 (367)
Q Consensus       179 ~~~ea~~g~h~~~~~l~ivDEAsgI~d~i~e~i~g~Lt~~~-------------~~~~~i~igNP~r~  233 (367)
                      ..|.-++..|   .-++++||.--.+|.+-+++.-++..+.             .+.+.+++.||-.+
T Consensus       130 f~pGlLa~A~---rGiLyvDEINll~d~~v~~LLda~a~G~~~VEReG~S~~~Pa~F~liaT~NPeEg  194 (347)
T CHL00081        130 FEPGLLAKAN---RGILYVDEVNLLDDHLVDILLDSAASGWNTVEREGISIRHPARFVLIGSGNPEEG  194 (347)
T ss_pred             CCCCHHHHCC---CCEEEEEHHHHHHHHHHHHHHHHHHCCEEEECCCCEEECCCCCEEEEECCCCCCC
T ss_conf             5653122203---8858861454323799999999985580898046423305750068855786556


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=84.44  E-value=2.8  Score=20.67  Aligned_cols=33  Identities=27%  Similarity=0.409  Sum_probs=24.2

Q ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEE
Q ss_conf             477614886788999999999999708997799
Q gi|254781187|r   79 KCAISAGRGIGKTTLNAWMMLWLISTRPGMSII  111 (367)
Q Consensus        79 ~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~  111 (367)
                      |+.|-+++|+|||++.+.++.-....+.+..|+
T Consensus        71 R~~I~~~~g~GKt~ll~~ii~~~~~~~~~v~V~  103 (274)
T cd01133          71 KIGLFGGAGVGKTVLIMELINNIAKAHGGYSVF  103 (274)
T ss_pred             EEEEECCCCCCCCHHHHHHHHHHHHCCCCEEEE
T ss_conf             778757999982368999999998508987999


No 247
>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=84.20  E-value=1.1  Score=23.10  Aligned_cols=112  Identities=14%  Similarity=0.160  Sum_probs=62.8

Q ss_pred             EEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCH------HHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCC
Q ss_conf             77614886788999999999999708997799971537------999999999999999862312112333321000123
Q gi|254781187|r   80 CAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSE------TQLKNTLWAEVSKWLSMLPHRHWFEMQSLSLHPSGW  153 (367)
Q Consensus        80 ~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~------~Q~~~~lw~ei~k~~~~~~~~~~~~~~~~~~~~~~~  153 (367)
                      +-.++=.|+||||.+|=++.|.+.-..+.+++.+|---      +||+..     .+.+.                 .  
T Consensus       105 ilmvGLQGsGKTTt~gKLA~~ll~kk~~~kvLLva~D~yRPAA~~QL~~L-----g~Q~g-----------------V--  160 (439)
T TIGR00959       105 ILMVGLQGSGKTTTAGKLALYLLKKKEGKKVLLVACDLYRPAAIEQLKVL-----GEQVG-----------------V--  160 (439)
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHHHHCCCCEEEEEHHCCCHHHHHHHHHH-----HHHCC-----------------C--
T ss_conf             99731378857889999999999986389703403210347899999997-----67528-----------------8--


Q ss_pred             CCCCCC-CCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCEEEEECCC--CCCHHHHHHHH--HHHHCCCCCEEEE
Q ss_conf             332211-113457761266210135445565210113586289997545--59988999989--8740698825899
Q gi|254781187|r  154 YAELLE-QSMGIDSKHYTITCRTYSEERPDTFVGPHNTHGMAVFNDEAS--GTPDIINKSIL--GFFTELNPNRFWI  225 (367)
Q Consensus       154 ~~~~~~-~~~~~~~~~~~~~a~~~~~~~~ea~~g~h~~~~~l~ivDEAs--gI~d~i~e~i~--g~Lt~~~~~~~~i  225 (367)
                        +++. ...+.++-+  . .-++    ..+.+-+...++..+|+|-|.  .|++..++=+.  -..+.++ +++.+
T Consensus       161 --pvf~h~~~~~~p~~--P-v~ia----~~Al~~Ak~~~~D~vI~DTAGRL~ID~~LM~EL~~iK~~~nP~-EiLlV  227 (439)
T TIGR00959       161 --PVFAHLGKGQSPDD--P-VEIA----RQALEEAKENGFDVVIVDTAGRLQIDEELMEELAEIKEILNPD-EILLV  227 (439)
T ss_pred             --CCCCCCCCCCCCCC--H-HHHH----HHHHHHHHHCCCCEEEEECCCCHHHHHHHHHHHHHHHHHHCCC-EEEEC
T ss_conf             --71100478889887--7-8999----9999999974897899726751255599999999998886887-05412


No 248
>PRK13407 bchI magnesium chelatase subunit I; Provisional
Probab=84.17  E-value=2.9  Score=20.60  Aligned_cols=54  Identities=13%  Similarity=0.054  Sum_probs=35.4

Q ss_pred             CCCCCCCCCCCCCCCCCEEEEECCCCCCHHHHHHHHHHHHCC-------------CCCEEEEEEECCCCC
Q ss_conf             544556521011358628999754559988999989874069-------------882589998078999
Q gi|254781187|r  177 SEERPDTFVGPHNTHGMAVFNDEASGTPDIINKSILGFFTEL-------------NPNRFWIMTSNTRRL  233 (367)
Q Consensus       177 ~~~~~ea~~g~h~~~~~l~ivDEAsgI~d~i~e~i~g~Lt~~-------------~~~~~~i~igNP~r~  233 (367)
                      +...|.-++-.|+   -.+++||..-.++.+-+++.-.+.++             -.+...+++.||-.+
T Consensus       117 ~~~~PGlLa~Ah~---GVLylDEinll~~~vld~Ll~~~e~G~~~IeReg~s~~~ParF~LVatmNPeEg  183 (334)
T PRK13407        117 KAFEPGLLARANR---GYLYIDEVNLLEDHIVDLLLDVAQSGENVVEREGLSIRHPARFVLVGSGNPEEG  183 (334)
T ss_pred             CCCCCCHHHHCCC---CEEEEECHHHCCHHHHHHHHHHHHCCCEEEEECCEEEECCCCCEEEEEECCCCC
T ss_conf             7788605434028---867872053333889999998871695799977634603662658982088877


No 249
>KOG3022 consensus
Probab=84.16  E-value=2  Score=21.54  Aligned_cols=34  Identities=26%  Similarity=0.411  Sum_probs=26.3

Q ss_pred             EEEEEECCC-CCCHHHHHHHHHHHHHHHCCCCEEEEE
Q ss_conf             247761488-678899999999999970899779997
Q gi|254781187|r   78 FKCAISAGR-GIGKTTLNAWMMLWLISTRPGMSIICI  113 (367)
Q Consensus        78 ~~~~v~sgr-g~GKS~~~a~~~lw~~~~~~~~~v~~~  113 (367)
                      -.++|+||- |+|||+.++.+++-++.  ++.++.+.
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 250
>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=84.08  E-value=2.9  Score=20.58  Aligned_cols=37  Identities=19%  Similarity=0.239  Sum_probs=24.8

Q ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHH
Q ss_conf             477614886788999999999999708997799971537999
Q gi|254781187|r   79 KCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQL  120 (367)
Q Consensus        79 ~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~  120 (367)
                      |..|-+++|+|||.+...++-|     .+..+++.+.-.+..
T Consensus       159 r~~I~g~~g~GKT~l~~~i~k~-----~~~dv~Vyv~iGeRg  195 (369)
T cd01134         159 TAAIPGPFGCGKTVIQQSLSKY-----SNSDIVIYVGCGERG  195 (369)
T ss_pred             EEEEECCCCCCHHHHHHHHHHC-----CCCCEEEEEEEECCH
T ss_conf             4677668776899999999853-----799889999971141


No 251
>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=84.04  E-value=1.6  Score=22.16  Aligned_cols=28  Identities=29%  Similarity=0.334  Sum_probs=22.3

Q ss_pred             CCCCHHHHHHHHHHHHHHHCCCCEEEEECC
Q ss_conf             867889999999999997089977999715
Q gi|254781187|r   86 RGIGKTTLNAWMMLWLISTRPGMSIICIAN  115 (367)
Q Consensus        86 rg~GKS~~~a~~~lw~~~~~~~~~v~~~A~  115 (367)
                      =|+|||+++..++..+..  .+.+++++--
T Consensus         9 GGvGKtt~~~~la~~~a~--~g~~vl~iD~   36 (104)
T cd02042           9 GGVGKTTTAVNLAAALAR--RGKRVLLIDL   36 (104)
T ss_pred             CCCCHHHHHHHHHHHHHH--CCCEEEEEEC
T ss_conf             987689999999999997--7992999977


No 252
>PRK12597 F0F1 ATP synthase subunit beta; Provisional
Probab=83.93  E-value=3  Score=20.54  Aligned_cols=44  Identities=20%  Similarity=0.370  Sum_probs=29.4

Q ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEE-ECCCHHHHHH
Q ss_conf             4776148867889999999999997089977999-7153799999
Q gi|254781187|r   79 KCAISAGRGIGKTTLNAWMMLWLISTRPGMSIIC-IANSETQLKN  122 (367)
Q Consensus        79 ~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~-~A~t~~Q~~~  122 (367)
                      |+.+-+|.|+|||.++..++.-....+.+..|++ +-...+.+++
T Consensus       143 rigIfggaGvGKTvL~~~ii~n~~~~~~~v~V~~~iGER~rEv~e  187 (459)
T PRK12597        143 KTGLFGGAGVGKTVLMMELIFNISKRHQGSSVFAGVGERSREGHE  187 (459)
T ss_pred             EEEEECCCCCCCCHHHHHHHHHHHHHCCCCEEEEEECCCHHHHHH
T ss_conf             777436899982157899999877551783688862454688999


No 253
>pfam05673 DUF815 Protein of unknown function (DUF815). This family consists of several bacterial proteins of unknown function.
Probab=83.89  E-value=3  Score=20.53  Aligned_cols=52  Identities=19%  Similarity=0.326  Sum_probs=32.0

Q ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHHHHHHHHCC
Q ss_conf             4776148867889999999999997089977999715379999999999999998623
Q gi|254781187|r   79 KCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLKNTLWAEVSKWLSMLP  136 (367)
Q Consensus        79 ~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~~~lw~ei~k~~~~~~  136 (367)
                      .+.+-+.||+|||.++-+++.-+.  ..+.++|=+.  .+++.+.  +.|-..++..|
T Consensus        55 nvLLwG~RGtGKSSlVKall~~~~--~~gLrlIEv~--k~~L~~L--p~i~~~l~~~~  106 (248)
T pfam05673        55 NVLLWGARGTGKSSLVKALLNEYA--DQGLRLIEVD--KDDLGDL--PDIVDLLRGRP  106 (248)
T ss_pred             CEEEECCCCCCHHHHHHHHHHHHH--HCCCEEEEEC--HHHHCCH--HHHHHHHHCCC
T ss_conf             367676898988899999999863--1495699987--8887219--99999996499


No 254
>PRK05298 excinuclease ABC subunit B; Provisional
Probab=83.88  E-value=3  Score=20.52  Aligned_cols=68  Identities=18%  Similarity=0.162  Sum_probs=48.2

Q ss_pred             CHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHHHH
Q ss_conf             42899999998888751245555541124776148867889999999999997089977999715379999999999999
Q gi|254781187|r   51 PHRWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLKNTLWAEVSK  130 (367)
Q Consensus        51 p~~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~~~lw~ei~k  130 (367)
                      |.-=|-++...+.+++++|..      +.+ +.+-.|+|||+.+|..+--     -..-.+++|+...-| .-++.|++.
T Consensus        14 P~GDQP~AI~~L~~gi~~g~~------~Q~-LlGvTGSGKTfTmAnvI~~-----~~rPtLVlahNKTLA-AQLy~Efk~   80 (657)
T PRK05298         14 PAGDQPQAIAELVEGIESGEK------HQT-LLGVTGSGKTFTMANVIAR-----VQRPTLVLAHNKTLA-AQLYGEFKE   80 (657)
T ss_pred             CCCCCHHHHHHHHHHHHCCCC------EEE-EECCCCCCHHHHHHHHHHH-----HCCCEEEECCCHHHH-HHHHHHHHH
T ss_conf             999879999999989974996------369-9703678566899999998-----689759976658899-999999997


Q ss_pred             H
Q ss_conf             9
Q gi|254781187|r  131 W  131 (367)
Q Consensus       131 ~  131 (367)
                      +
T Consensus        81 f   81 (657)
T PRK05298         81 F   81 (657)
T ss_pred             H
T ss_conf             6


No 255
>COG3640 CooC CO dehydrogenase maturation factor [Cell division and chromosome partitioning]
Probab=83.84  E-value=2.8  Score=20.70  Aligned_cols=34  Identities=32%  Similarity=0.542  Sum_probs=26.7

Q ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEE
Q ss_conf             47761488678899999999999970899779997
Q gi|254781187|r   79 KCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICI  113 (367)
Q Consensus        79 ~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~  113 (367)
                      ++||++=-|+|||+++|.++.-++..+. .+|+++
T Consensus         2 kIaI~GKGG~GKTtiaalll~~l~~~~~-~~VLvV   35 (255)
T COG3640           2 KIAITGKGGVGKTTIAALLLKRLLSKGG-YNVLVV   35 (255)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHCCC-CEEEEE
T ss_conf             6999659976589999999999986489-549999


No 256
>pfam00308 Bac_DnaA Bacterial dnaA protein.
Probab=83.74  E-value=3  Score=20.49  Aligned_cols=36  Identities=22%  Similarity=0.379  Sum_probs=30.4

Q ss_pred             EEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECC
Q ss_conf             776148867889999999999997089977999715
Q gi|254781187|r   80 CAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIAN  115 (367)
Q Consensus        80 ~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~  115 (367)
                      +-|-+.-|+|||++..+++.-..-..++.+++++..
T Consensus        37 l~i~G~~G~GKTHLLqA~~~~~~~~~~~~~v~yl~~   72 (219)
T pfam00308        37 LFIYGGVGLGKTHLLHAIGNYALRNFPNLRVVYLTS   72 (219)
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEEEH
T ss_conf             699889999888999999999998499982888439


No 257
>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=83.71  E-value=2.2  Score=21.29  Aligned_cols=36  Identities=31%  Similarity=0.396  Sum_probs=26.5

Q ss_pred             EEEEEEECCC-CCCHHHHHHHHHHHHHHHCCCCEEEEEC
Q ss_conf             1247761488-6788999999999999708997799971
Q gi|254781187|r   77 IFKCAISAGR-GIGKTTLNAWMMLWLISTRPGMSIICIA  114 (367)
Q Consensus        77 ~~~~~v~sgr-g~GKS~~~a~~~lw~~~~~~~~~v~~~A  114 (367)
                      |..++|+++. |+|||++++.+..-+  ...|.+|+++=
T Consensus         1 MkiIai~s~KGGVGKTT~t~nLa~aL--a~~G~rVLlID   37 (244)
T pfam06564         1 MAVLALQGVRGGVGTTSLTAALGWAL--QQLGESVLVID   37 (244)
T ss_pred             CEEEEEECCCCCCCHHHHHHHHHHHH--HHCCCCEEEEE
T ss_conf             92999966999861999999999999--97799589996


No 258
>PRK11670 putative ATPase; Provisional
Probab=83.56  E-value=2.4  Score=21.10  Aligned_cols=34  Identities=26%  Similarity=0.438  Sum_probs=26.0

Q ss_pred             EEEEECCC-CCCHHHHHHHHHHHHHHHCCCCEEEEEC
Q ss_conf             47761488-6788999999999999708997799971
Q gi|254781187|r   79 KCAISAGR-GIGKTTLNAWMMLWLISTRPGMSIICIA  114 (367)
Q Consensus        79 ~~~v~sgr-g~GKS~~~a~~~lw~~~~~~~~~v~~~A  114 (367)
                      -++|+||- |+|||+.++.+++-+..  .|.+|.+.=
T Consensus       109 vIAVaSGKGGVGKSTvavNLA~ALA~--~G~kVgllD  143 (369)
T PRK11670        109 IIAVSSGKGGVGKSSTAVNLALALAA--EGAKVGILD  143 (369)
T ss_pred             EEEEEECCCCCCHHHHHHHHHHHHHH--CCCCEEEEE
T ss_conf             99998589988899999999999996--699378982


No 259
>PRK08118 topology modulation protein; Reviewed
Probab=83.31  E-value=1.2  Score=23.00  Aligned_cols=26  Identities=27%  Similarity=0.189  Sum_probs=21.5

Q ss_pred             EEEEEEECCCCCCHHHHHHHHHHHHH
Q ss_conf             12477614886788999999999999
Q gi|254781187|r   77 IFKCAISAGRGIGKTTLNAWMMLWLI  102 (367)
Q Consensus        77 ~~~~~v~sgrg~GKS~~~a~~~lw~~  102 (367)
                      |-|+.|-++-|+|||+++..+.--.-
T Consensus         1 M~rI~IiG~~GsGKSTlAr~L~~~~~   26 (167)
T PRK08118          1 MKKIILIGSGGSGKSTLARQLGEKLN   26 (167)
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHHHC
T ss_conf             96799988999879999999999889


No 260
>PRK11131 ATP-dependent RNA helicase HrpA; Provisional
Probab=83.28  E-value=3.2  Score=20.37  Aligned_cols=161  Identities=15%  Similarity=0.007  Sum_probs=77.4

Q ss_pred             HHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHHHHHH
Q ss_conf             89999999888875124555554112477614886788999999999999708997799971537999999999999999
Q gi|254781187|r   53 RWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLKNTLWAEVSKWL  132 (367)
Q Consensus        53 ~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~~~lw~ei~k~~  132 (367)
                      ....+++..|.+|.            =+.|++-.|+|||+=+-=+++- +.....++|+||-|-.=-+..+ -..+..-.
T Consensus        77 ~~r~~i~~~i~~nq------------Vvii~GeTGsGKTTQiPq~~le-~g~g~~~~I~~TQPRRiAA~sv-A~RVA~E~  142 (1295)
T PRK11131         77 QKKQDILEAIRDHQ------------VVIVAGETGSGKTTQLPKICLE-LGRGIKGLIGHTQPRRLAARTV-ANRIAEEL  142 (1295)
T ss_pred             HHHHHHHHHHHHCC------------EEEEECCCCCCHHHHHHHHHHH-CCCCCCCEEEECCCHHHHHHHH-HHHHHHHH
T ss_conf             89999999999799------------6999768999878899999996-2799999899779659999999-99999981


Q ss_pred             HHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEE-EEECCCCCCCCCCCCCCCCCCCCEEEEECCCC--CCHHHHH
Q ss_conf             86231211233332100012333221111345776126-62101354455652101135862899975455--9988999
Q gi|254781187|r  133 SMLPHRHWFEMQSLSLHPSGWYAELLEQSMGIDSKHYT-ITCRTYSEERPDTFVGPHNTHGMAVFNDEASG--TPDIINK  209 (367)
Q Consensus       133 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~a~~~~~~~~ea~~g~h~~~~~l~ivDEAsg--I~d~i~e  209 (367)
                      ... ...           ..++...+.......+...+ -.+...++-..+  ..+  .....+|+|||.-  +.-++.-
T Consensus       143 ~~~-lG~-----------~VGY~VRf~~~~s~~t~i~~~TdGiLL~e~~~d--~~L--~~y~~iIiDEaHERsl~~D~LL  206 (1295)
T PRK11131        143 ETE-LGG-----------CVGYKVRFNDQVSDNTMVKLMTDGILLAEIQQD--RLL--MQYDTIIIDEAHERSLNIDFIL  206 (1295)
T ss_pred             CCC-CCC-----------EEEEEECCCCCCCCCCEEEEECCHHHHHHHHHC--CCC--CCCCEEEEECCCCCCCHHHHHH
T ss_conf             999-899-----------888894569887999779997656999986209--987--8877799868556880199999


Q ss_pred             HHHHHHHCCCCCEEEEEEECCCCCCCHHHHHHHCC
Q ss_conf             98987406988258999807899987688754112
Q gi|254781187|r  210 SILGFFTELNPNRFWIMTSNTRRLNGWFYDIFNIP  244 (367)
Q Consensus       210 ~i~g~Lt~~~~~~~~i~igNP~r~~g~Fye~~~~~  244 (367)
                      .+.-.+-........+++ +-|-....|-+.|...
T Consensus       207 g~Lk~ll~~R~dLKvIim-SATid~e~fs~yF~~a  240 (1295)
T PRK11131        207 GYLKELLPRRPDLKVIIT-SATIDPERFSRHFNNA  240 (1295)
T ss_pred             HHHHHHHHHCCCCEEEEE-CCCCCHHHHHHHCCCC
T ss_conf             999999833999889995-5868979999657999


No 261
>PRK13341 recombination factor protein RarA/unknown domain fusion protein; Reviewed
Probab=83.23  E-value=3.2  Score=20.36  Aligned_cols=41  Identities=17%  Similarity=0.138  Sum_probs=26.3

Q ss_pred             EEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHH
Q ss_conf             2477614886788999999999999708997799971537999999
Q gi|254781187|r   78 FKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLKNT  123 (367)
Q Consensus        78 ~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~~~  123 (367)
                      ..+..-++=|+|||+++-.++--     -+...+....+...++++
T Consensus        53 ~S~Il~GPPGtGKTTLA~iIA~~-----t~~~F~~lsAv~sgvkdl   93 (726)
T PRK13341         53 GSLILYGPPGVGKTTLARIIANH-----TRAHFSSLNAVLAGVKDL   93 (726)
T ss_pred             CEEEEECCCCCCHHHHHHHHHHH-----HCCCEEEEECCCCCHHHH
T ss_conf             82788897999999999999887-----488679985620377999


No 262
>KOG1803 consensus
Probab=82.91  E-value=2.6  Score=20.90  Aligned_cols=45  Identities=20%  Similarity=0.190  Sum_probs=36.9

Q ss_pred             EEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHH
Q ss_conf             77614886788999999999999708997799971537999999999
Q gi|254781187|r   80 CAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLKNTLWA  126 (367)
Q Consensus        80 ~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~~~lw~  126 (367)
                      ..|.++-|+|||+...-++.=.+.-  +.+|+|+|||--.+.+++=+
T Consensus       204 ~~I~GPPGTGKT~TlvEiI~qlvk~--~k~VLVcaPSn~AVdNiver  248 (649)
T KOG1803         204 LIIHGPPGTGKTRTLVEIISQLVKQ--KKRVLVCAPSNVAVDNIVER  248 (649)
T ss_pred             EEEECCCCCCCEEEHHHHHHHHHHC--CCEEEEECCCHHHHHHHHHH
T ss_conf             5755799888404399999999972--88599976736789999987


No 263
>PRK04220 2-phosphoglycerate kinase; Provisional
Probab=82.86  E-value=2.5  Score=20.98  Aligned_cols=89  Identities=12%  Similarity=0.134  Sum_probs=46.8

Q ss_pred             CCHHHHHHHHCCCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCHHHHH-HHHHHHHHHHHCCCCCCCCCEEEEEEECCCCC
Q ss_conf             33789999752320125988885543014668884436668428999-99998888751245555541124776148867
Q gi|254781187|r   10 KLEQELHEMLMHAECVLSFKNFVMRFFPWGIKGKPLEHFSQPHRWQL-EFMEAVDVHCHSNVNNSNPTIFKCAISAGRGI   88 (367)
Q Consensus        10 ~~~~~~~~~~~~~~~~~~~~~f~~~~~~w~~~~~~~~~~~~p~~wq~-~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~   88 (367)
                      +.|+.|.+.....-.+++....|+..         |....+|..-++ ++.+.+. +      ...|.  =+.|.+.-|+
T Consensus        42 ei~~~L~~~~~~~i~~~el~~~v~~~---------l~~~~~~~~a~rY~~~r~~r-~------~~~pl--iILigGtsGv  103 (306)
T PRK04220         42 EIEEELKKEGITKITKEELRRRVYYK---------LIEKDYEEIAEKYLLWRRIR-K------SKEPI--IILIGGASGV  103 (306)
T ss_pred             HHHHHHHHCCCEEECHHHHHHHHHHH---------HHHHCCHHHHHHHHHHHHHH-C------CCCCE--EEEEECCCCC
T ss_conf             99999986577163599999999999---------99844099999999999985-3------69987--9998589988


Q ss_pred             CHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHH
Q ss_conf             889999999999997089977999715379999999
Q gi|254781187|r   89 GKTTLNAWMMLWLISTRPGMSIICIANSETQLKNTL  124 (367)
Q Consensus        89 GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~~~l  124 (367)
                      |||++++-++--     -+-+.++-.   +.+|.++
T Consensus       104 GKSTlA~~LA~r-----LgI~~visT---D~IREVm  131 (306)
T PRK04220        104 GTSTIAFELASR-----LGIRSVIGT---DSIREVM  131 (306)
T ss_pred             CHHHHHHHHHHH-----HCCCEEECC---HHHHHHH
T ss_conf             789999999997-----098834222---1699999


No 264
>PRK07568 aspartate aminotransferase; Provisional
Probab=82.81  E-value=3.3  Score=20.26  Aligned_cols=64  Identities=14%  Similarity=0.093  Sum_probs=39.7

Q ss_pred             CHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHH
Q ss_conf             428999999988887512455555411247761488678899999999999970899779997153799999
Q gi|254781187|r   51 PHRWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLKN  122 (367)
Q Consensus        51 p~~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~~  122 (367)
                      |...-.++-++|+++.++-.....|+  ++.|.+|   ++   .|..++..++++||-.|++..|++.....
T Consensus        64 ~~~G~~~LReaia~~~~~~g~~~~~d--~I~iT~G---a~---~al~~~~~~l~~pGD~Vlv~~P~y~~y~~  127 (396)
T PRK07568         64 HSAGIDSLREAFSKYYKRFNIDFDKD--EIIVTNG---GS---EAILFALMAICDPGDEIIVPEPFYANYNG  127 (396)
T ss_pred             CCCCCHHHHHHHHHHHHHHCCCCCHH--EEEECCC---HH---HHHHHHHHHHCCCCCEEEEECCCCCCHHH
T ss_conf             98671999999999999868898822--2898578---06---99999999727998989993897532599


No 265
>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=82.77  E-value=2.7  Score=20.80  Aligned_cols=33  Identities=30%  Similarity=0.562  Sum_probs=23.7

Q ss_pred             EEEECC-CCCCHHHHHHHHHHHHHHHCCCCEEEEEC
Q ss_conf             776148-86788999999999999708997799971
Q gi|254781187|r   80 CAISAG-RGIGKTTLNAWMMLWLISTRPGMSIICIA  114 (367)
Q Consensus        80 ~~v~sg-rg~GKS~~~a~~~lw~~~~~~~~~v~~~A  114 (367)
                      ++|+|| -|+|||++++.+..-+.  +.|.+++++=
T Consensus         2 i~v~sgKgGvGkt~~~~nLa~~la--~~G~~vll~D   35 (139)
T cd02038           2 IAVTSGKGGVGKTNISANLALALA--KLGKRVLLLD   35 (139)
T ss_pred             EEEECCCCCCCHHHHHHHHHHHHH--HCCCCEEEEE
T ss_conf             899649999839999999999999--7899699998


No 266
>COG1373 Predicted ATPase (AAA+ superfamily) [General function prediction only]
Probab=82.47  E-value=3.4  Score=20.18  Aligned_cols=16  Identities=44%  Similarity=0.397  Sum_probs=14.5

Q ss_pred             EEEEECCCCCCHHHHH
Q ss_conf             4776148867889999
Q gi|254781187|r   79 KCAISAGRGIGKTTLN   94 (367)
Q Consensus        79 ~~~v~sgrg~GKS~~~   94 (367)
                      -+.|.+.||+|||++.
T Consensus        39 i~~i~GpR~~GKTtll   54 (398)
T COG1373          39 IILILGPRQVGKTTLL   54 (398)
T ss_pred             EEEEECCCCCCHHHHH
T ss_conf             4999888647789999


No 267
>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=82.39  E-value=3.4  Score=20.16  Aligned_cols=140  Identities=14%  Similarity=0.048  Sum_probs=67.7

Q ss_pred             EEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             24776148867889999999999997089977999715379999999999999998623121123333210001233322
Q gi|254781187|r   78 FKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLKNTLWAEVSKWLSMLPHRHWFEMQSLSLHPSGWYAEL  157 (367)
Q Consensus        78 ~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~~~lw~ei~k~~~~~~~~~~~~~~~~~~~~~~~~~~~  157 (367)
                      +++++.+..|.|||+++=+++.---....-.+|--=....+.+.|-.=-|.++-+.....-..+.|..            
T Consensus         3 Rniai~gH~gaGKTtL~EalL~~~G~i~r~G~V~~~~~~g~t~~D~~~eE~~R~iSi~~~~~~~~w~~------------   70 (267)
T cd04169           3 RTFAIISHPDAGKTTLTEKLLLFGGAIREAGAVKARKSRKHATSDWMEIEKQRGISVTSSVMQFEYRD------------   70 (267)
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHCCCCCCCCEEEECCCCCCCCCCCHHHHHHCCCEEECCEEEEEECC------------
T ss_conf             17999847999989999999986686333854630368886046887999865944863637887899------------


Q ss_pred             CCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCEEEEECCCCCCH---HHHHHHHHHHHCCCCCEEEEEEECCC-CC
Q ss_conf             111134577612662101354455652101135862899975455998---89999898740698825899980789-99
Q gi|254781187|r  158 LEQSMGIDSKHYTITCRTYSEERPDTFVGPHNTHGMAVFNDEASGTPD---IINKSILGFFTELNPNRFWIMTSNTR-RL  233 (367)
Q Consensus       158 ~~~~~~~~~~~~~~~a~~~~~~~~ea~~g~h~~~~~l~ivDEAsgI~d---~i~e~i~g~Lt~~~~~~~~i~igNP~-r~  233 (367)
                              .+..++.+-+......|...+++.-...++++|=.+||.-   .+|+.+.    ..+-+.+ + +-|=- +.
T Consensus        71 --------~kinliDTPG~~DF~~e~~~al~v~D~AviVv~a~~GVe~~T~~~w~~a~----~~~iP~i-i-fINKmDr~  136 (267)
T cd04169          71 --------CVINLLDTPGHEDFSEDTYRTLTAVDSAVMVIDAAKGVEPQTRKLFEVCR----LRGIPII-T-FINKLDRE  136 (267)
T ss_pred             --------EEEEEEECCCCHHHHHHHHHHHHHHHCEEEEEECCCCCCHHHHHHHHHHH----HCCCCEE-E-EEECCCCC
T ss_conf             --------89999979697789999999998864547995256665355899999999----7299979-9-98534567


Q ss_pred             CCHHHHHHHC
Q ss_conf             8768875411
Q gi|254781187|r  234 NGWFYDIFNI  243 (367)
Q Consensus       234 ~g~Fye~~~~  243 (367)
                      ..-|.++...
T Consensus       137 ~adf~~~l~~  146 (267)
T cd04169         137 GRDPLELLDE  146 (267)
T ss_pred             CCCHHHHHHH
T ss_conf             8987899999


No 268
>COG1149 MinD superfamily P-loop ATPase containing an inserted ferredoxin domain [Energy production and conversion]
Probab=82.35  E-value=1.3  Score=22.74  Aligned_cols=72  Identities=18%  Similarity=0.077  Sum_probs=38.0

Q ss_pred             CCEEEEECCCCCCHHHHHHHHHHHHCCCCCEEEEEEECCCCCCCHHHHHHHC--CC---CCEEEEEECCCCCCCCCHHHH
Q ss_conf             6289997545599889999898740698825899980789998768875411--22---350467523332888898899
Q gi|254781187|r  192 GMAVFNDEASGTPDIINKSILGFFTELNPNRFWIMTSNTRRLNGWFYDIFNI--PL---EDWKRYQIDTRTVEGIDSGFH  266 (367)
Q Consensus       192 ~~l~ivDEAsgI~d~i~e~i~g~Lt~~~~~~~~i~igNP~r~~g~Fye~~~~--~~---~~w~~~~~~~~d~p~~~~~~i  266 (367)
                      .-++|+|-|+|+.-.+..++.+    .+.   .+++.-|| +.| ++|+-+-  ..   +--..+-++-. ++..+  .+
T Consensus       164 ~~~~IIDsaaG~gCpVi~sl~~----aD~---ai~VTEPT-p~g-lhD~kr~~el~~~f~ip~~iViNr~-~~g~s--~i  231 (284)
T COG1149         164 ADLLIIDSAAGTGCPVIASLKG----ADL---AILVTEPT-PFG-LHDLKRALELVEHFGIPTGIVINRY-NLGDS--EI  231 (284)
T ss_pred             CCEEEEECCCCCCCHHHHHHCC----CCE---EEEEECCC-CCC-HHHHHHHHHHHHHHCCCEEEEEECC-CCCCH--HH
T ss_conf             2125885799789717776416----877---99981688-523-6689999999998399549999667-77720--89


Q ss_pred             HHHHHHCCC
Q ss_conf             999962168
Q gi|254781187|r  267 EGIISRYGL  275 (367)
Q Consensus       267 ~~~~~~~ge  275 (367)
                      ++.-+.+|-
T Consensus       232 e~~~~e~gi  240 (284)
T COG1149         232 EEYCEEEGI  240 (284)
T ss_pred             HHHHHHCCC
T ss_conf             998887399


No 269
>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=82.34  E-value=1.4  Score=22.52  Aligned_cols=148  Identities=11%  Similarity=0.084  Sum_probs=76.1

Q ss_pred             CCCCCCCCCCCHHHHHHHHH-HHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHH
Q ss_conf             88844366684289999999-88887512455555411247761488678899999999999970899779997153799
Q gi|254781187|r   41 KGKPLEHFSQPHRWQLEFME-AVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQ  119 (367)
Q Consensus        41 ~~~~~~~~~~p~~wq~~~l~-~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q  119 (367)
                      ++..|==...+|++|+|=|+ .+.=.=|   =|+     =|.|. +=|.|||-.--     -++|.--++|+|.+++.=.
T Consensus       260 L~IDLKP~t~~RPYQEKSLrsKMFGNGR---ARS-----GiIVL-PCGAGKsLVGv-----TAACTvkKs~lVLctS~VS  325 (756)
T TIGR00603       260 LNIDLKPTTVLRPYQEKSLRSKMFGNGR---ARS-----GIIVL-PCGAGKSLVGV-----TAACTVKKSVLVLCTSAVS  325 (756)
T ss_pred             CCCCCCCCCCCCCCHHHHCCCCCCCCCC---CCC-----CCEEC-CCCCCCCHHHH-----HHHEEEEEEEEEEECCCHH
T ss_conf             6745587778897511104445667861---105-----51776-77888311225-----4420231007897267100


Q ss_pred             HHHHHHHHH-HHHHHHCCCCCCCCCCCCCCCCCCC-CCCCCCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCEEEE
Q ss_conf             999999999-9999862312112333321000123-33221111345776126621013544556521011358628999
Q gi|254781187|r  120 LKNTLWAEV-SKWLSMLPHRHWFEMQSLSLHPSGW-YAELLEQSMGIDSKHYTITCRTYSEERPDTFVGPHNTHGMAVFN  197 (367)
Q Consensus       120 ~~~~lw~ei-~k~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~a~~~~~~~~ea~~g~h~~~~~l~iv  197 (367)
                      +.+  |+.- +.|-+.-+ ..--..|....-.... -....+      +=+..+.+.--|.+..--+.=+++...=|+|+
T Consensus       326 V~Q--W~~QFk~WSti~d-~~IcrFTSD~Ke~~~~~~gv~vs------TYsMva~t~kRS~es~k~m~~l~~rEWGl~~L  396 (756)
T TIGR00603       326 VEQ--WKQQFKLWSTIDD-SQICRFTSDAKEKFHGEAGVVVS------TYSMVAHTGKRSYESEKVMEWLTNREWGLILL  396 (756)
T ss_pred             HHH--HHHHHHHCCCCCC-CCCCCCCCCCCCCCCCCCCEEEE------CCCCCCCCCCCHHHHHHHHHHHHCCCCEEEEE
T ss_conf             889--9988752268873-55110252135762665335887------33000247543188999999970687317986


Q ss_pred             ECCCCCCHHHH-HHH
Q ss_conf             75455998899-998
Q gi|254781187|r  198 DEASGTPDIIN-KSI  211 (367)
Q Consensus       198 DEAsgI~d~i~-e~i  211 (367)
                      ||-.-||...| -|+
T Consensus       397 DEVHvvPA~mFRrVl  411 (756)
T TIGR00603       397 DEVHVVPAAMFRRVL  411 (756)
T ss_pred             CCCCCCCCCCCCCHH
T ss_conf             110103500166010


No 270
>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=82.30  E-value=3.3  Score=20.26  Aligned_cols=50  Identities=20%  Similarity=0.232  Sum_probs=36.3

Q ss_pred             EEEECCCCCCHHHHHHHHHHH---HHHHCCCCEEEEECCCHHHHHHHHHHHHHH
Q ss_conf             776148867889999999999---997089977999715379999999999999
Q gi|254781187|r   80 CAISAGRGIGKTTLNAWMMLW---LISTRPGMSIICIANSETQLKNTLWAEVSK  130 (367)
Q Consensus        80 ~~v~sgrg~GKS~~~a~~~lw---~~~~~~~~~v~~~A~t~~Q~~~~lw~ei~k  130 (367)
                      +.|.|+-|-|||.++..++..   ..-...-.|++.+=|+...+.++. ..++.
T Consensus         2 ~v~~APTG~GKTe~aL~~A~~sah~~k~~~~~~~I~alP~r~~~na~~-~r~~~   54 (424)
T TIGR01587         2 LVIEAPTGYGKTEAALLWALKSAHLIKKQKADKVIFALPTRVTINAMY-RRLKE   54 (424)
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHHHHHHHHHCCEEEECCHHHHHHHHH-HHHHH
T ss_conf             688617899878999999986366642244401012202688899999-99998


No 271
>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=82.30  E-value=3.4  Score=20.14  Aligned_cols=42  Identities=21%  Similarity=0.274  Sum_probs=29.3

Q ss_pred             EEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECC--CHHHHHHH
Q ss_conf             776148867889999999999997089977999715--37999999
Q gi|254781187|r   80 CAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIAN--SETQLKNT  123 (367)
Q Consensus        80 ~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~--t~~Q~~~~  123 (367)
                      +.|.++.|+|||+++..++.....  ++.++++++-  +.+|++..
T Consensus         2 ~li~g~~g~GKttl~~~~~~~~~~--~~~~~~~~~~ee~~~q~~~~   45 (165)
T cd01120           2 ILVFGPTGSGKTTLALQLALNIAT--KGGKVVYVDIEEEIEELTER   45 (165)
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHH--CCCEEEEEECCCCHHHHHHH
T ss_conf             899989999899999999999876--39979999866644899999


No 272
>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=82.16  E-value=2  Score=21.53  Aligned_cols=21  Identities=33%  Similarity=0.279  Sum_probs=17.9

Q ss_pred             EEEECCCCCCHHHHHHHHHHH
Q ss_conf             776148867889999999999
Q gi|254781187|r   80 CAISAGRGIGKTTLNAWMMLW  100 (367)
Q Consensus        80 ~~v~sgrg~GKS~~~a~~~lw  100 (367)
                      ++|++|-|+|||+++..+.--
T Consensus         2 IgIaG~S~SGKTTla~~L~~~   22 (187)
T cd02024           2 VGISGVTNSGKTTLAKLLQRI   22 (187)
T ss_pred             EEEECCCCCCHHHHHHHHHHH
T ss_conf             899688887599999999998


No 273
>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=82.14  E-value=1.6  Score=22.20  Aligned_cols=23  Identities=26%  Similarity=0.427  Sum_probs=20.1

Q ss_pred             CEEEEEEECCCCCCHHHHHHHHH
Q ss_conf             11247761488678899999999
Q gi|254781187|r   76 TIFKCAISAGRGIGKTTLNAWMM   98 (367)
Q Consensus        76 ~~~~~~v~sgrg~GKS~~~a~~~   98 (367)
                      ++||+++.+..|+|||.++-.++
T Consensus         1 y~~Kiv~vGd~~vGKTsli~r~~   23 (166)
T cd01869           1 YLFKLLLIGDSGVGKSCLLLRFA   23 (166)
T ss_pred             CEEEEEEECCCCCCHHHHHHHHH
T ss_conf             96999999999978999999994


No 274
>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=82.00  E-value=1.3  Score=22.79  Aligned_cols=36  Identities=8%  Similarity=0.097  Sum_probs=23.1

Q ss_pred             CCCCEEEEECCCCCCHHHHHHHHHHHHCCCCCEEEEEEECCCC
Q ss_conf             5862899975455998899998987406988258999807899
Q gi|254781187|r  190 THGMAVFNDEASGTPDIINKSILGFFTELNPNRFWIMTSNTRR  232 (367)
Q Consensus       190 ~~~~l~ivDEAsgI~d~i~e~i~g~Lt~~~~~~~~i~igNP~r  232 (367)
                      +.+.++|+|=.+|+.+.+..++.    ..+ ..  +...+|..
T Consensus        91 ~~~D~viiD~Ppg~~~~~~~al~----~ad-~~--iiVttP~~  126 (179)
T cd03110          91 EGAELIIIDGPPGIGCPVIASLT----GAD-AA--LLVTEPTP  126 (179)
T ss_pred             CCCCEEEEECCCCCCHHHHHHHH----CCC-EE--EEECCCCH
T ss_conf             37998998189997578999997----399-49--99819947


No 275
>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=81.87  E-value=1.3  Score=22.80  Aligned_cols=94  Identities=18%  Similarity=0.146  Sum_probs=51.0

Q ss_pred             EEEEEECCCCCCHHHHHHHHHHH---------------HHHHC-CCCEEEEECCC-HHHHHHHHHHHH-HHHHHHCCCCC
Q ss_conf             24776148867889999999999---------------99708-99779997153-799999999999-99998623121
Q gi|254781187|r   78 FKCAISAGRGIGKTTLNAWMMLW---------------LISTR-PGMSIICIANS-ETQLKNTLWAEV-SKWLSMLPHRH  139 (367)
Q Consensus        78 ~~~~v~sgrg~GKS~~~a~~~lw---------------~~~~~-~~~~v~~~A~t-~~Q~~~~lw~ei-~k~~~~~~~~~  139 (367)
                      ..+.|++|-|+|||++.-+++-.               ..+-+ |+..-+.-+-. .+|...+.-+.+ +-.+++-|   
T Consensus       159 knIii~GGTgSGKTTf~kal~~~IP~~ER~iTIED~~E~~~~hhpN~V~L~ysk~v~~g~~~vt~~~Ll~scLRMrP---  235 (328)
T TIGR02788       159 KNIIISGGTGSGKTTFLKALVKEIPKDERLITIEDTRELFLPHHPNKVHLFYSKGVGQGSAKVTPKDLLESCLRMRP---  235 (328)
T ss_pred             CEEEEEECCCCHHHHHHHHHHHCCCCCCCEEEEEEEECCCCCCCCCEEEEEECCCCCCCCCCCCHHHHHHHHHCCCC---
T ss_conf             91999906897189999999732762252788852011478889864565534642344356898999999711774---


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCC
Q ss_conf             1233332100012333221111345776126621013544556521011358
Q gi|254781187|r  140 WFEMQSLSLHPSGWYAELLEQSMGIDSKHYTITCRTYSEERPDTFVGPHNTH  191 (367)
Q Consensus       140 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~ea~~g~h~~~  191 (367)
                            .++.+..         ++.+  ..|.+-+-...+-|.++-.+|+.+
T Consensus       236 ------DRI~LgE---------LRG~--Eaf~F~~~~nsGHpGsiTT~HA~s  270 (328)
T TIGR02788       236 ------DRILLGE---------LRGD--EAFDFIRAVNSGHPGSITTVHAGS  270 (328)
T ss_pred             ------CHHHHHH---------HCCH--HHHHHHHHHCCCCCCCEEEEEECC
T ss_conf             ------0576743---------0332--578888752059886056787189


No 276
>KOG0345 consensus
Probab=81.86  E-value=3.6  Score=20.04  Aligned_cols=122  Identities=15%  Similarity=-0.020  Sum_probs=59.0

Q ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHHC----CCC--EEEEECCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCC
Q ss_conf             477614886788999999999999708----997--79997153799999999999999986231211233332100012
Q gi|254781187|r   79 KCAISAGRGIGKTTLNAWMMLWLISTR----PGM--SIICIANSETQLKNTLWAEVSKWLSMLPHRHWFEMQSLSLHPSG  152 (367)
Q Consensus        79 ~~~v~sgrg~GKS~~~a~~~lw~~~~~----~~~--~v~~~A~t~~Q~~~~lw~ei~k~~~~~~~~~~~~~~~~~~~~~~  152 (367)
                      -|+|-|..|+|||...-.=++-.+.-+    |+.  -.++++||..-+++| ..-+..+++.+++-....+.-       
T Consensus        45 DVvveavTGSGKTlAFllP~le~i~rr~~~~~~~~vgalIIsPTRELa~QI-~~V~~~F~~~l~~l~~~l~vG-------  116 (567)
T KOG0345          45 DVVVEAVTGSGKTLAFLLPMLEIIYRREAKTPPGQVGALIISPTRELARQI-REVAQPFLEHLPNLNCELLVG-------  116 (567)
T ss_pred             CEEEECCCCCCCCHHHHHHHHHHHHHHCCCCCCCCEEEEEECCCHHHHHHH-HHHHHHHHHHCCCCCEEEEEC-------
T ss_conf             568985678871066899999999861157896512479965719999999-999999998503654599976-------


Q ss_pred             CCCCCCCCCCCCCCCCEEEEECCCCCCCCCC--CCCCCCCCCCEEEEECCCCCCHHHH
Q ss_conf             3332211113457761266210135445565--2101135862899975455998899
Q gi|254781187|r  153 WYAELLEQSMGIDSKHYTITCRTYSEERPDT--FVGPHNTHGMAVFNDEASGTPDIIN  208 (367)
Q Consensus       153 ~~~~~~~~~~~~~~~~~~~~a~~~~~~~~ea--~~g~h~~~~~l~ivDEAsgI~d~i~  208 (367)
                      ...........-..+..+..+.+-+...--.  ...+...+..++|+|||.-.=|--|
T Consensus       117 G~~v~~Di~~fkee~~nIlVgTPGRL~di~~~~~~~l~~rsLe~LVLDEADrLldmgF  174 (567)
T KOG0345         117 GRSVEEDIKTFKEEGPNILVGTPGRLLDILQREAEKLSFRSLEILVLDEADRLLDMGF  174 (567)
T ss_pred             CCCHHHHHHHHHHHCCCEEEECCHHHHHHHHCHHHCCCCCCCCEEEECCHHHHHCCCH
T ss_conf             8647779999997099589947624999984530003613311577514676744327


No 277
>KOG2228 consensus
Probab=81.79  E-value=3.6  Score=20.02  Aligned_cols=81  Identities=20%  Similarity=0.187  Sum_probs=44.1

Q ss_pred             CCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEE-CCCHHHHH
Q ss_conf             84436668428999999988887512455555411247761488678899999999999970899779997-15379999
Q gi|254781187|r   43 KPLEHFSQPHRWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICI-ANSETQLK  121 (367)
Q Consensus        43 ~~~~~~~~p~~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~-A~t~~Q~~  121 (367)
                      ++|.+.+.-++=-.++++.-..|-+.         --+++.++||+|||.+.+-.+.-  .-..+.+.+++ =|-.=|..
T Consensus        24 ~~l~g~~~~~~~l~~~lkqt~~~gEs---------nsviiigprgsgkT~li~~~Ls~--~q~~~E~~l~v~Lng~~~~d   92 (408)
T KOG2228          24 INLFGVQDEQKHLSELLKQTILHGES---------NSVIIIGPRGSGKTILIDTRLSD--IQENGENFLLVRLNGELQTD   92 (408)
T ss_pred             CCEEEHHHHHHHHHHHHHHHHHHCCC---------CCEEEECCCCCCCEEEEHHHHHH--HHHCCCEEEEEEECCCCHHH
T ss_conf             65000587899999999999984477---------72699814778816740778766--77517727999878500155


Q ss_pred             HHHHHHHHHHHHH
Q ss_conf             9999999999986
Q gi|254781187|r  122 NTLWAEVSKWLSM  134 (367)
Q Consensus       122 ~~lw~ei~k~~~~  134 (367)
                      .+...+|.+.++.
T Consensus        93 k~al~~I~rql~~  105 (408)
T KOG2228          93 KIALKGITRQLAL  105 (408)
T ss_pred             HHHHHHHHHHHHH
T ss_conf             8999999999999


No 278
>PRK09280 F0F1 ATP synthase subunit beta; Validated
Probab=81.52  E-value=3.7  Score=19.97  Aligned_cols=34  Identities=26%  Similarity=0.395  Sum_probs=26.1

Q ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEE
Q ss_conf             4776148867889999999999997089977999
Q gi|254781187|r   79 KCAISAGRGIGKTTLNAWMMLWLISTRPGMSIIC  112 (367)
Q Consensus        79 ~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~  112 (367)
                      |+.+-+|.|+|||.+...++.-....+.+..|++
T Consensus       147 rigIfggaGvGKTvLl~eli~n~a~~~~~v~V~a  180 (466)
T PRK09280        147 KIGLFGGAGVGKTVLIMELINNIAKEHGGYSVFA  180 (466)
T ss_pred             EEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEE
T ss_conf             7985579999800899999999998659909999


No 279
>COG1643 HrpA HrpA-like helicases [DNA replication, recombination, and repair]
Probab=81.47  E-value=3.7  Score=19.95  Aligned_cols=161  Identities=15%  Similarity=0.043  Sum_probs=77.4

Q ss_pred             HHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHHHHHH
Q ss_conf             89999999888875124555554112477614886788999999999999708997799971537999999999999999
Q gi|254781187|r   53 RWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLKNTLWAEVSKWL  132 (367)
Q Consensus        53 ~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~~~lw~ei~k~~  132 (367)
                      .-..+++..|..|.            .+.|.+.-|+|||+-.--+++-.-. .-+.+|+||-|-.=-++++    .++..
T Consensus        53 ~~~~~i~~ai~~~~------------vvii~getGsGKTTqlP~~lle~g~-~~~g~I~~tQPRRlAArsv----A~RvA  115 (845)
T COG1643          53 AVRDEILKAIEQNQ------------VVIIVGETGSGKTTQLPQFLLEEGL-GIAGKIGCTQPRRLAARSV----AERVA  115 (845)
T ss_pred             HHHHHHHHHHHHCC------------EEEEECCCCCCHHHHHHHHHHHHHC-CCCCEEEECCCHHHHHHHH----HHHHH
T ss_conf             88999999998697------------8998679988758788999996001-6687599658438999999----99999


Q ss_pred             HHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC-EEEEECCCCCCCCCCCCCCCCCCCCEEEEECCCC--CCHHHHH
Q ss_conf             862312112333321000123332211113457761-2662101354455652101135862899975455--9988999
Q gi|254781187|r  133 SMLPHRHWFEMQSLSLHPSGWYAELLEQSMGIDSKH-YTITCRTYSEERPDTFVGPHNTHGMAVFNDEASG--TPDIINK  209 (367)
Q Consensus       133 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~a~~~~~~~~ea~~g~h~~~~~l~ivDEAsg--I~d~i~e  209 (367)
                      +.+-.+.         ...-++...+.......... ..-.+...+.-.-+.    .-....++|+|||.-  +..++--
T Consensus       116 eel~~~~---------G~~VGY~iRfe~~~s~~Trik~mTdGiLlrei~~D~----~Ls~ys~vIiDEaHERSl~tDilL  182 (845)
T COG1643         116 EELGEKL---------GETVGYSIRFESKVSPRTRIKVMTDGILLREIQNDP----LLSGYSVVIIDEAHERSLNTDILL  182 (845)
T ss_pred             HHHCCCC---------CCEEEEEEEEECCCCCCCEEEEECCHHHHHHHHHCC----CCCCCCEEEEECHHHHHHHHHHHH
T ss_conf             9838986---------765437999622678771468951479999984380----204587799701335568889999


Q ss_pred             HHHHH-HHCCCCCEEEEEEECCCCCCCHHHHHHHCC
Q ss_conf             98987-406988258999807899987688754112
Q gi|254781187|r  210 SILGF-FTELNPNRFWIMTSNTRRLNGWFYDIFNIP  244 (367)
Q Consensus       210 ~i~g~-Lt~~~~~~~~i~igNP~r~~g~Fye~~~~~  244 (367)
                      .+..- +........ +++.+-|-+...|...|..+
T Consensus       183 gllk~~~~~rr~DLK-iIimSATld~~rfs~~f~~a  217 (845)
T COG1643         183 GLLKDLLARRRDDLK-LIIMSATLDAERFSAYFGNA  217 (845)
T ss_pred             HHHHHHHHHCCCCCE-EEEEECCCCHHHHHHHCCCC
T ss_conf             999999864688705-99972535889999762899


No 280
>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=81.42  E-value=0.78  Score=24.09  Aligned_cols=133  Identities=13%  Similarity=0.094  Sum_probs=65.2

Q ss_pred             EEEEECCCCCCHHHHHHHHHHHH-HHHCCCCEEEEECCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             47761488678899999999999-97089977999715379999999999999998623121123333210001233322
Q gi|254781187|r   79 KCAISAGRGIGKTTLNAWMMLWL-ISTRPGMSIICIANSETQLKNTLWAEVSKWLSMLPHRHWFEMQSLSLHPSGWYAEL  157 (367)
Q Consensus        79 ~~~v~sgrg~GKS~~~a~~~lw~-~~~~~~~~v~~~A~t~~Q~~~~lw~ei~k~~~~~~~~~~~~~~~~~~~~~~~~~~~  157 (367)
                      +++|.+..|.|||+++-.++.-- +..+.|. |    ...+.+.+-.=-|.++-+.....-..+.|+..           
T Consensus         1 Niai~gH~gaGKTtL~EalL~~ag~i~r~G~-v----~~g~tv~D~~~eE~~R~isi~~~~~~~~w~~~-----------   64 (270)
T cd01886           1 NIGIIAHIDAGKTTTTERILYYTGRIHKIGE-V----HGGGATMDFMEQERERGITIQSAATTCFWKDH-----------   64 (270)
T ss_pred             CEEEEECCCCCHHHHHHHHHHHCCCCCCCCE-E----CCCCCCCCCCHHHHHCCCEEECCEEEEEECCE-----------
T ss_conf             9899968999988999999986687355815-5----38975566848898768707336689998998-----------


Q ss_pred             CCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCEEEEECCCCCC---HHHHHHHHHHHHCCCCCEEEEEEECC-CCC
Q ss_conf             11113457761266210135445565210113586289997545599---88999989874069882589998078-999
Q gi|254781187|r  158 LEQSMGIDSKHYTITCRTYSEERPDTFVGPHNTHGMAVFNDEASGTP---DIINKSILGFFTELNPNRFWIMTSNT-RRL  233 (367)
Q Consensus       158 ~~~~~~~~~~~~~~~a~~~~~~~~ea~~g~h~~~~~l~ivDEAsgI~---d~i~e~i~g~Lt~~~~~~~~i~igNP-~r~  233 (367)
                               +..++.+-+......|...+++.-...++++|=++||.   ..+|+.+.    ..+-+.+  .+-|= .|.
T Consensus        65 ---------~inliDTPG~~DF~~e~~~aL~~~D~AviVv~a~~GVe~~T~~~w~~~~----~~~lP~i--~fINKmDre  129 (270)
T cd01886          65 ---------RINIIDTPGHVDFTIEVERSLRVLDGAVAVFDAVAGVEPQTETVWRQAD----RYNVPRI--AFVNKMDRT  129 (270)
T ss_pred             ---------EEEEEECCCCHHHHHHHHHHHHHHCEEEEEEECCCCHHHHHHHHHHHHH----HCCCCEE--EEEECCCCC
T ss_conf             ---------9999869696788999999987755599998467644263699998899----8499989--999887877


Q ss_pred             CCHHHHHHH
Q ss_conf             876887541
Q gi|254781187|r  234 NGWFYDIFN  242 (367)
Q Consensus       234 ~g~Fye~~~  242 (367)
                      ..-|.+...
T Consensus       130 ~ad~~~~l~  138 (270)
T cd01886         130 GADFFRVVE  138 (270)
T ss_pred             CCCCHHHHH
T ss_conf             887166899


No 281
>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=81.39  E-value=3.2  Score=20.31  Aligned_cols=39  Identities=18%  Similarity=0.269  Sum_probs=29.1

Q ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHH
Q ss_conf             4776148867889999999999997089977999715379
Q gi|254781187|r   79 KCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSET  118 (367)
Q Consensus        79 ~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~  118 (367)
                      .++|.+-.|+|||++++.++- .+.-.++..+++.=|...
T Consensus        25 H~aIlg~TGsGKS~tv~vLl~-~l~~~~~~~vlVfDpHgE   63 (218)
T pfam01935        25 HFAILGSTGSGKSNTVAVLLE-ELLEKKGATVLIFDPHGE   63 (218)
T ss_pred             HEEEECCCCCCHHHHHHHHHH-HHHHCCCCCEEEECCCCC
T ss_conf             147872699976999999999-998547997899828863


No 282
>PRK02731 histidinol-phosphate aminotransferase; Validated
Probab=81.30  E-value=2.5  Score=21.01  Aligned_cols=58  Identities=16%  Similarity=0.182  Sum_probs=34.5

Q ss_pred             CHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHH
Q ss_conf             42899999998888751245555541124776148867889999999999997089977999715379999
Q gi|254781187|r   51 PHRWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLK  121 (367)
Q Consensus        51 p~~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~  121 (367)
                      |+.-..++-++|+++..=+.  +     ++.|  |.|  =+  .+..++..+++.|+.+|++..|++..-.
T Consensus        65 Pd~~~~~Lr~aiA~~~~v~~--~-----~Ilv--~nG--s~--e~i~l~~~a~~~pgd~Vl~~~P~f~~Y~  122 (367)
T PRK02731         65 PDGSGFELKAALAEKFGVDP--E-----QIIL--GNG--SD--EILELLARAYLGPGDEVIYSEHAFAVYP  122 (367)
T ss_pred             CCCCHHHHHHHHHHHHCCCH--H-----HEEE--CCC--HH--HHHHHHHHHHHCCCCEEEECCCCHHHHH
T ss_conf             59878999999999978581--1-----1998--578--99--9999999998479986444798626899


No 283
>TIGR01075 uvrD DNA helicase II; InterPro: IPR005753    The SOS response is required for efficient nucleotide excision repair (NER) of the major ultraviolet light (UV) induced DNA lesions. The expression of three NER genes, uvrA, uvrB, and uvrD, is upregulated as part of the SOS response. UvrD differs from the others in that it is not involved in lesion recognition but rather in promoting the post-incision steps of NER, including turnover of the UvrBC incision complex . The form of the UvrD helicase with optimal helicase activity is oligomeric with at least two sites for binding the DNA substrate, where one site contacts regions of the 3'-ssDNA tail that are distal from the single-stranded/double-stranded DNA junction.; GO: 0004003 ATP-dependent DNA helicase activity, 0006268 DNA unwinding during replication, 0005737 cytoplasm.
Probab=81.20  E-value=3.7  Score=19.93  Aligned_cols=55  Identities=27%  Similarity=0.317  Sum_probs=40.7

Q ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHHHHHHHHCC
Q ss_conf             4776148867889999999999997089977999715379999999999999998623
Q gi|254781187|r   79 KCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLKNTLWAEVSKWLSMLP  136 (367)
Q Consensus        79 ~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~~~lw~ei~k~~~~~~  136 (367)
                      ...|.||=|+|||-+..-=|.|++....=+.-=++|-|..   +.--+|++.-+..+.
T Consensus        19 ~~LvLAGAGSGKTRVL~hRIaWL~~v~~~s~~SiMAVTFT---NKAA~Em~~Ri~~~~   73 (741)
T TIGR01075        19 NLLVLAGAGSGKTRVLTHRIAWLLSVENASPHSIMAVTFT---NKAAAEMRHRIEALL   73 (741)
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHHHCCCCCCCCEEEECHH---HHHHHHHHHHHHHHH
T ss_conf             5548730688850247888998874078998535632003---478999999999986


No 284
>COG0210 UvrD Superfamily I DNA and RNA helicases [DNA replication, recombination, and repair]
Probab=81.12  E-value=3.8  Score=19.88  Aligned_cols=45  Identities=22%  Similarity=0.270  Sum_probs=35.2

Q ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHHC--CCCEEEEECCCHHHHHHH
Q ss_conf             477614886788999999999999708--997799971537999999
Q gi|254781187|r   79 KCAISAGRGIGKTTLNAWMMLWLISTR--PGMSIICIANSETQLKNT  123 (367)
Q Consensus        79 ~~~v~sgrg~GKS~~~a~~~lw~~~~~--~~~~v~~~A~t~~Q~~~~  123 (367)
                      .+.|.||.|+|||.....-+.|++...  .+..|+++.=|-+-++.+
T Consensus        17 p~lV~AGaGsGKT~vlt~Ria~li~~~~v~p~~Il~vTFTnkAA~em   63 (655)
T COG0210          17 PLLVLAGAGSGKTRVLTERIAYLIAAGGVDPEQILAITFTNKAAAEM   63 (655)
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHHHCCCCCHHHEEEEEEEHHHHHHH
T ss_conf             86999579986189999999999873895757717789676999999


No 285
>KOG0742 consensus
Probab=80.88  E-value=3.9  Score=19.83  Aligned_cols=77  Identities=13%  Similarity=0.069  Sum_probs=48.6

Q ss_pred             HHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHHHHHHHHC
Q ss_conf             9999888875124555554112477614886788999999999999708997799971537999999999999999862
Q gi|254781187|r   57 EFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLKNTLWAEVSKWLSML  135 (367)
Q Consensus        57 ~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~~~lw~ei~k~~~~~  135 (367)
                      +-++.|+.-- .|.+.++...+++..-++-|+|||..+--++..--+-+.=.+.-=+||-..|+-+.+ .++-+|..++
T Consensus       365 ~Rie~lA~aT-aNTK~h~apfRNilfyGPPGTGKTm~ArelAr~SGlDYA~mTGGDVAPlG~qaVTki-H~lFDWakkS  441 (630)
T KOG0742         365 KRIEDLAIAT-ANTKKHQAPFRNILFYGPPGTGKTMFARELARHSGLDYAIMTGGDVAPLGAQAVTKI-HKLFDWAKKS  441 (630)
T ss_pred             HHHHHHHHHH-CCCCCCCCHHHHEEEECCCCCCHHHHHHHHHHHCCCCEEHHCCCCCCCCHHHHHHHH-HHHHHHHHHC
T ss_conf             9999998874-043002430440032479998604999999885287410013787555217889999-9987887515


No 286
>PRK06793 fliI flagellum-specific ATP synthase; Validated
Probab=80.78  E-value=3.2  Score=20.33  Aligned_cols=41  Identities=27%  Similarity=0.465  Sum_probs=26.0

Q ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEE-CCCHHHHHH
Q ss_conf             47761488678899999999999970899779997-153799999
Q gi|254781187|r   79 KCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICI-ANSETQLKN  122 (367)
Q Consensus        79 ~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~-A~t~~Q~~~  122 (367)
                      |+.|-+|+|+|||++.++++..-   .-+..|++. ....+-+++
T Consensus       158 R~gIfg~sGvGKstLl~~i~~~~---~adv~Vi~lIGeRgrEv~e  199 (432)
T PRK06793        158 KIGIFAGSGVGKSTLLGMIAKNA---KADINVISLVGERGREVKD  199 (432)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHC---CCCCEEEEEEEEECHHHHH
T ss_conf             66663268987899999998724---5786579998886279999


No 287
>pfam00931 NB-ARC NB-ARC domain.
Probab=80.73  E-value=3.9  Score=19.80  Aligned_cols=48  Identities=15%  Similarity=0.006  Sum_probs=29.9

Q ss_pred             CEEEEEEECCCCCCHHHHHHHHHHHH-HHHCCCCEEEEECCCHHHHHHH
Q ss_conf             11247761488678899999999999-9708997799971537999999
Q gi|254781187|r   76 TIFKCAISAGRGIGKTTLNAWMMLWL-ISTRPGMSIICIANSETQLKNT  123 (367)
Q Consensus        76 ~~~~~~v~sgrg~GKS~~~a~~~lw~-~~~~~~~~v~~~A~t~~Q~~~~  123 (367)
                      ++.-++|.+--|+|||+++..+.-.. .-.+.+.++.++........++
T Consensus        18 ~~~vI~I~G~gGiGKTtLA~~v~~~~~i~~~F~~~~wv~vs~~~~~~~i   66 (285)
T pfam00931        18 NLGVVGIVGMGGVGKTTLAKQIYNDDSVGGHFDSVAWVVVSKTYTEFRL   66 (285)
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHCCHHHHHCCCEEEEEEECCCCCHHHH
T ss_conf             9539998899956399999999716556505983899997976668999


No 288
>TIGR01407 dinG_rel DnaQ family exonuclease/DinG family helicase, putative; InterPro: IPR006310   These are a family of proteins in Gram-positive bacteria. The N-terminal region of about 200 amino acids resembles the epsilon subunit of E. coli DNA polymerase III and the homologous region of the Gram-positive type DNA polymerase III alpha subunit. The epsilon subunit contains an exonuclease domain. The remainder of this protein family resembles a predicted ATP-dependent helicase, the DNA damage-inducible protein DinG of Escherichia coli. .
Probab=80.67  E-value=3.9  Score=19.79  Aligned_cols=76  Identities=21%  Similarity=0.187  Sum_probs=49.8

Q ss_pred             CHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCH---HHHHHHHHHH
Q ss_conf             4289999999888875124555554112477614886788999999999999708997799971537---9999999999
Q gi|254781187|r   51 PHRWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSE---TQLKNTLWAE  127 (367)
Q Consensus        51 p~~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~---~Q~~~~lw~e  127 (367)
                      =|.=|.++...|.+++.+|...      .+-|-||-|+|||..==--++ +....++..|++-.+|.   +|+-+.-.+.
T Consensus       261 ~R~~Q~~la~~v~~~l~~Gt~~------~~lIEA~tG~GKtlgYLLPal-~~~~~~~~~vviST~Tk~LQ~QL~E~d~P~  333 (944)
T TIGR01407       261 YREEQLKLAELVEDELTHGTEE------KSLIEAPTGTGKTLGYLLPAL-YLAKEEEKPVVISTATKVLQSQLLEKDIPL  333 (944)
T ss_pred             HHHHHHHHHHHHHHHHCCCCCH------HHHEECCCCCCHHHHHHHHHH-HHCCCCCCCEEEEECCHHHHHHHHHHHHHH
T ss_conf             1388999999999984157661------133023766432589999999-731378885699836366565656888898


Q ss_pred             HHHHHH
Q ss_conf             999998
Q gi|254781187|r  128 VSKWLS  133 (367)
Q Consensus       128 i~k~~~  133 (367)
                      +++.+.
T Consensus       334 l~~~~~  339 (944)
T TIGR01407       334 LNKILN  339 (944)
T ss_pred             HHHHCC
T ss_conf             886518


No 289
>COG4240 Predicted kinase [General function prediction only]
Probab=80.65  E-value=3.9  Score=19.78  Aligned_cols=52  Identities=21%  Similarity=0.312  Sum_probs=30.8

Q ss_pred             HHHHHHHHHH-HHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEEC
Q ss_conf             9999988887-5124555554112477614886788999999999999708997799971
Q gi|254781187|r   56 LEFMEAVDVH-CHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIA  114 (367)
Q Consensus        56 ~~~l~~~~~~-~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A  114 (367)
                      .+++..|+.. .+++    .|  +=+-|+++.|+|||++++.+...+....- .++...+
T Consensus        34 Lpll~Kiap~~qe~g----rP--li~gisGpQGSGKStls~~i~~~L~~kg~-ert~~lS   86 (300)
T COG4240          34 LPLLAKIAPWAQERG----RP--LIVGISGPQGSGKSTLSALIVRLLAAKGL-ERTATLS   86 (300)
T ss_pred             HHHHHHHHHHHHHCC----CC--EEEEEECCCCCCHHHHHHHHHHHHHHHCC-CCEEEEE
T ss_conf             788986445442127----96--39985268887653599999999997365-3068866


No 290
>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=80.43  E-value=2  Score=21.59  Aligned_cols=23  Identities=26%  Similarity=0.501  Sum_probs=20.0

Q ss_pred             CEEEEEEECCCCCCHHHHHHHHH
Q ss_conf             11247761488678899999999
Q gi|254781187|r   76 TIFKCAISAGRGIGKTTLNAWMM   98 (367)
Q Consensus        76 ~~~~~~v~sgrg~GKS~~~a~~~   98 (367)
                      +.||+.|.+..|+|||.++..++
T Consensus         2 y~~Kiv~iGd~~VGKTsli~r~~   24 (165)
T cd01868           2 YLFKIVLIGDSGVGKSNLLSRFT   24 (165)
T ss_pred             EEEEEEEECCCCCCHHHHHHHHH
T ss_conf             35899999999978999999997


No 291
>COG0610 Type I site-specific restriction-modification system, R (restriction) subunit and related helicases [Defense mechanisms]
Probab=80.34  E-value=4  Score=19.72  Aligned_cols=138  Identities=13%  Similarity=0.060  Sum_probs=68.5

Q ss_pred             CHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHHHH
Q ss_conf             42899999998888751245555541124776148867889999999999997089977999715379999999999999
Q gi|254781187|r   51 PHRWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLKNTLWAEVSK  130 (367)
Q Consensus        51 p~~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~~~lw~ei~k  130 (367)
                      ++.-|..++....+-.......  ...-+-.|=--.|+|||..+.+++-+.+-.-...+|+++-- ..-+.+-+..++++
T Consensus       249 ~~~~q~~a~~~~i~~~~~~~~~--~~~~~G~IWHtqGSGKTltm~~~A~~l~~~~~~~~v~fvvD-R~dLd~Q~~~~f~~  325 (962)
T COG0610         249 QRYAQYRAVQKAIKRILKASNP--GDGKGGYIWHTQGSGKTLTMFKLARLLLELPKNPKVLFVVD-RKDLDDQTSDEFQS  325 (962)
T ss_pred             HHHHHHHHHHHHHHHHHHHCCC--CCCCCEEEEECCCCCHHHHHHHHHHHHHHCCCCCEEEEEEC-HHHHHHHHHHHHHH
T ss_conf             7889999999999999971267--87772389840698378999999999983659996999967-28899999999999


Q ss_pred             HHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC-CCCCEEEEECCCCCCCCCC-CCCCCCCCCCEEEEECCCCC
Q ss_conf             9986231211233332100012333221111345-7761266210135445565-21011358628999754559
Q gi|254781187|r  131 WLSMLPHRHWFEMQSLSLHPSGWYAELLEQSMGI-DSKHYTITCRTYSEERPDT-FVGPHNTHGMAVFNDEASGT  203 (367)
Q Consensus       131 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~a~~~~~~~~ea-~~g~h~~~~~l~ivDEAsgI  203 (367)
                      .-......+  .....         ...+..++. ..+..+.+-+.+.....+. .....+.+ ..+|+|||.--
T Consensus       326 ~~~~~~~~~--~~~s~---------~~Lk~~l~~~~~~ii~TTIQKf~~~~~~~~~~~~~~~~-ivvI~DEaHRS  388 (962)
T COG0610         326 FGKVAFNDP--KAEST---------SELKELLEDGKGKIIVTTIQKFNKAVKEDELELLKRKN-VVVIIDEAHRS  388 (962)
T ss_pred             HHHHHHCCC--CCCCH---------HHHHHHHHCCCCCEEEEEECCCCHHHHCCCCCCCCCCC-EEEEEECCCCC
T ss_conf             887632044--44579---------99999986589848999710264333333200047876-79998640103


No 292
>CHL00175 minD septum-site determining protein; Validated
Probab=80.33  E-value=3.5  Score=20.07  Aligned_cols=36  Identities=31%  Similarity=0.484  Sum_probs=26.2

Q ss_pred             CEEE-EEEECCC-CCCHHHHHHHHHHHHHHHCCCCEEEEE
Q ss_conf             1124-7761488-678899999999999970899779997
Q gi|254781187|r   76 TIFK-CAISAGR-GIGKTTLNAWMMLWLISTRPGMSIICI  113 (367)
Q Consensus        76 ~~~~-~~v~sgr-g~GKS~~~a~~~lw~~~~~~~~~v~~~  113 (367)
                      .|-| ++|++|. |+|||++++.+..-++.  .+.||+++
T Consensus        11 ~m~kiIaV~s~KGGVGKTT~a~NLa~aLA~--~G~kVlli   48 (279)
T CHL00175         11 TMTRIIVITSGKGGVGKTTTTANLGMSIAR--LGYRVALI   48 (279)
T ss_pred             CCCEEEEEECCCCCCCHHHHHHHHHHHHHH--CCCCEEEE
T ss_conf             988699997489984489999999999997--89988999


No 293
>pfam00155 Aminotran_1_2 Aminotransferase class I and II.
Probab=79.83  E-value=4.2  Score=19.62  Aligned_cols=69  Identities=14%  Similarity=0.085  Sum_probs=42.7

Q ss_pred             CCCHHHHHHHHHHHHHHHHCCCCCC-CCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHH
Q ss_conf             6842899999998888751245555-541124776148867889999999999997089977999715379999999
Q gi|254781187|r   49 SQPHRWQLEFMEAVDVHCHSNVNNS-NPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLKNTL  124 (367)
Q Consensus        49 ~~p~~wq~~~l~~~~~~~~~~~~~~-~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~~~l  124 (367)
                      -+|..--.++-++|+++.++..... .|+ -.+.+.+|  .  +  .+..++-.+++.|+-.|++-.|++......+
T Consensus        35 Y~~~~G~~~LR~aia~~~~~~~~~~~~~e-~~I~~t~G--~--~--~~l~~~~~~l~~~gd~Vli~~P~y~~~~~~~  104 (351)
T pfam00155        35 YGPTDGLPELREALAKFLGRSPVLKLDRE-AAVVFGSG--A--G--ANIEALIFLLANPGDAILVPAPTYASYIRIA  104 (351)
T ss_pred             CCCCHHHHHHHHHHHHHHHHHCCCCCCCC-CEEEECCC--H--H--HHHHHHHHHHCCCCCEEEECCCCCHHHHHHH
T ss_conf             79818789999999998601029999947-48998113--9--9--9999999996699499998899868899999


No 294
>COG1074 RecB ATP-dependent exoDNAse (exonuclease V) beta subunit (contains helicase and exonuclease domains) [DNA replication, recombination, and repair]
Probab=79.72  E-value=4.2  Score=19.59  Aligned_cols=47  Identities=13%  Similarity=0.128  Sum_probs=29.9

Q ss_pred             CCCCCCCCCCEEEEECCCCCCHHHHHHHHHHHHCCCC-CEEEEEEECCC
Q ss_conf             2101135862899975455998899998987406988-25899980789
Q gi|254781187|r  184 FVGPHNTHGMAVFNDEASGTPDIINKSILGFFTELNP-NRFWIMTSNTR  231 (367)
Q Consensus       184 ~~g~h~~~~~l~ivDEAsgI~d~i~e~i~g~Lt~~~~-~~~~i~igNP~  231 (367)
                      ...++.. +-.+++||++--+..-|.++....++... ....+++|-|-
T Consensus       372 ~~~lr~~-~~~iLIDEfQDT~~~Q~~Il~~l~~~~~~~~~~lF~VGD~K  419 (1139)
T COG1074         372 AESLREQ-YPHILIDEFQDTDPQQWRILSRLFAGFKAGNRTLFLVGDPK  419 (1139)
T ss_pred             HHHHHHC-CCEEEEECCCCCCHHHHHHHHHHHHCCCCCCCCEEEECCCH
T ss_conf             9999847-98588740345998899999999725667785079974734


No 295
>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=79.62  E-value=2.5  Score=20.96  Aligned_cols=27  Identities=26%  Similarity=0.298  Sum_probs=21.7

Q ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHHC
Q ss_conf             477614886788999999999999708
Q gi|254781187|r   79 KCAISAGRGIGKTTLNAWMMLWLISTR  105 (367)
Q Consensus        79 ~~~v~sgrg~GKS~~~a~~~lw~~~~~  105 (367)
                      ++.|.+.-|+|||+++..+++-|+--.
T Consensus         2 ~i~i~G~aG~GKTtll~kl~~~wa~g~   28 (165)
T pfam05729         2 TVILQGEAGSGKTTLLQKLALLWAQGK   28 (165)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHCCC
T ss_conf             899982798989999999999998698


No 296
>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=79.61  E-value=2.6  Score=20.92  Aligned_cols=123  Identities=19%  Similarity=0.179  Sum_probs=59.2

Q ss_pred             EEEECCC-CCCHHHHHHHHHHHHHHHCCCCEEEEE-CCCH-HHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             7761488-678899999999999970899779997-1537-999999999999999862312112333321000123332
Q gi|254781187|r   80 CAISAGR-GIGKTTLNAWMMLWLISTRPGMSIICI-ANSE-TQLKNTLWAEVSKWLSMLPHRHWFEMQSLSLHPSGWYAE  156 (367)
Q Consensus        80 ~~v~sgr-g~GKS~~~a~~~lw~~~~~~~~~v~~~-A~t~-~Q~~~~lw~ei~k~~~~~~~~~~~~~~~~~~~~~~~~~~  156 (367)
                      +.|.||- |+||||.+|.+-.=++..  |.||+++ +-.. +-| |++-..=.+.+.-+.+----.|+         ...
T Consensus         4 iViTSGKGGVGKTTtTANlG~aLA~l--G~kVvliD~DiGLRNL-D~~lGLEnRivYt~vDVveG~C~---------l~q   71 (272)
T TIGR01968         4 IVITSGKGGVGKTTTTANLGTALARL--GKKVVLIDADIGLRNL-DLLLGLENRIVYTLVDVVEGECR---------LQQ   71 (272)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHC--CCEEEEEECCCCCHHH-HHHHCCCHHHHHHHHHHHCCCCC---------CCC
T ss_conf             99981788977358989999999961--9828999547570345-77742310354535543248421---------100


Q ss_pred             CCCCCCCCCCCCEEEEECCCCCCC--CCCC----CCCCCC-CCCEEEEECCCCCCHHHHHHHHHH
Q ss_conf             211113457761266210135445--5652----101135-862899975455998899998987
Q gi|254781187|r  157 LLEQSMGIDSKHYTITCRTYSEER--PDTF----VGPHNT-HGMAVFNDEASGTPDIINKSILGF  214 (367)
Q Consensus       157 ~~~~~~~~~~~~~~~~a~~~~~~~--~ea~----~g~h~~-~~~l~ivDEAsgI~d~i~e~i~g~  214 (367)
                      +...+-+..+=..-+.+|+.+.+.  +|.+    +.+..+ ++.++|+|==|||..-+-.|+.|+
T Consensus        72 ALikDKr~~NL~LLpAsQ~rdK~~~~~E~~~~lv~~Lk~~~~FDYviIDcPAGIE~GF~nAv~~A  136 (272)
T TIGR01968        72 ALIKDKRLENLYLLPASQTRDKDAVTPEQMKKLVNELKEEEHFDYVIIDCPAGIESGFRNAVAPA  136 (272)
T ss_pred             CCCCCCCCHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHCCCCEEEEEECCCCHHHHHHHHHHHC
T ss_conf             10012675235663653023613469778999999985437930799737877435689987526


No 297
>PRK06067 flagellar accessory protein FlaH; Validated
Probab=79.59  E-value=4.3  Score=19.57  Aligned_cols=40  Identities=18%  Similarity=0.202  Sum_probs=26.8

Q ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEEC--CCHHHH
Q ss_conf             477614886788999999999999708997799971--537999
Q gi|254781187|r   79 KCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIA--NSETQL  120 (367)
Q Consensus        79 ~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A--~t~~Q~  120 (367)
                      -+.|.++.|+|||.++.-++. ..+.+ +.++++++  .+.+|+
T Consensus        34 ~~li~G~~G~GKt~~~~~f~~-~~~~~-g~~~~~~~~ee~~~~~   75 (241)
T PRK06067         34 LILIEGENDTGKSVLSQQFVW-GALNQ-GKRGLAITTENTSKSY   75 (241)
T ss_pred             EEEEECCCCCCHHHHHHHHHH-HHHHC-CCEEEEEEECCCHHHH
T ss_conf             899980799887999999999-99867-9829999942899999


No 298
>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=78.94  E-value=1.4  Score=22.47  Aligned_cols=46  Identities=26%  Similarity=0.348  Sum_probs=30.0

Q ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHHHHHHHH
Q ss_conf             47761488678899999999999970899779997153799999999999999986
Q gi|254781187|r   79 KCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLKNTLWAEVSKWLSM  134 (367)
Q Consensus        79 ~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~~~lw~ei~k~~~~  134 (367)
                      |+-|-||=|+|||+|.++++-+     -..-|+|+|=-..-=     +|++.+++.
T Consensus       160 R~GIFAGSGVGKSTLLGMiAr~-----t~ADV~VIALIGERG-----REV~EFiE~  205 (439)
T TIGR02545       160 RLGIFAGSGVGKSTLLGMIARY-----TEADVNVIALIGERG-----REVKEFIED  205 (439)
T ss_pred             EEEEECCCCHHHHHHHHHHHCC-----CCCCEEEEEEECCCC-----CCCHHHHHH
T ss_conf             0266337744478898887506-----658878998444656-----643135543


No 299
>KOG4181 consensus
Probab=78.82  E-value=2.8  Score=20.66  Aligned_cols=62  Identities=15%  Similarity=0.112  Sum_probs=34.6

Q ss_pred             HHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHH
Q ss_conf             999999888875124555554112477614886788999999999999708997799971537999999
Q gi|254781187|r   55 QLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLKNT  123 (367)
Q Consensus        55 q~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~~~  123 (367)
                      |..+..++.+.+.     +.+++--+.|.+|.|+|||++.+.++.=  ..+.+.+..+-.|...-+++.
T Consensus       171 ~g~~~d~a~~ll~-----~~tdf~VIgvlG~QgsGKStllslLaan--s~~~dyr~yvFRpvS~Ea~E~  232 (491)
T KOG4181         171 NGIFNDNARKLLH-----KTTDFTVIGVLGGQGSGKSTLLSLLAAN--SLDYDYRQYVFRPVSPEADEC  232 (491)
T ss_pred             CCCHHHHHHHHHH-----CCCCEEEEEEECCCCCCHHHHHHHHHCC--CHHHHHHHHHCCCCCHHHHHH
T ss_conf             5512368999961-----4898169974047775488999998426--847766777303578556665


No 300
>COG4178 ABC-type uncharacterized transport system, permease and ATPase components [General function prediction only]
Probab=78.64  E-value=4.6  Score=19.39  Aligned_cols=49  Identities=20%  Similarity=0.164  Sum_probs=22.2

Q ss_pred             CCCCCCCCCCCEEEEECC-CCCCHHHHHHHHHHHHCCCCCEEEEEEECCC
Q ss_conf             521011358628999754-5599889999898740698825899980789
Q gi|254781187|r  183 TFVGPHNTHGMAVFNDEA-SGTPDIINKSILGFFTELNPNRFWIMTSNTR  231 (367)
Q Consensus       183 a~~g~h~~~~~l~ivDEA-sgI~d~i~e~i~g~Lt~~~~~~~~i~igNP~  231 (367)
                      +|+-+--.....+++||| +.++++.-..+.-++.+.=.....+.+|-.+
T Consensus       525 afARilL~kP~~v~LDEATsALDe~~e~~l~q~l~~~lp~~tvISV~Hr~  574 (604)
T COG4178         525 AFARLLLHKPKWVFLDEATSALDEETEDRLYQLLKEELPDATVISVGHRP  574 (604)
T ss_pred             HHHHHHHCCCCEEEEECCHHCCCHHHHHHHHHHHHHHCCCCEEEEECCCH
T ss_conf             99999970999899806011259578999999998548997899955600


No 301
>PRK05480 uridine kinase; Provisional
Probab=78.63  E-value=2.3  Score=21.18  Aligned_cols=24  Identities=33%  Similarity=0.393  Sum_probs=19.7

Q ss_pred             EEEEEECCCCCCHHHHHHHHHHHH
Q ss_conf             247761488678899999999999
Q gi|254781187|r   78 FKCAISAGRGIGKTTLNAWMMLWL  101 (367)
Q Consensus        78 ~~~~v~sgrg~GKS~~~a~~~lw~  101 (367)
                      +-++|++|-|+|||+++..+.--+
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 302
>PRK10818 cell division inhibitor MinD; Provisional
Probab=78.62  E-value=4.4  Score=19.48  Aligned_cols=32  Identities=31%  Similarity=0.492  Sum_probs=25.1

Q ss_pred             EEEECCC-CCCHHHHHHHHHHHHHHHCCCCEEEEE
Q ss_conf             7761488-678899999999999970899779997
Q gi|254781187|r   80 CAISAGR-GIGKTTLNAWMMLWLISTRPGMSIICI  113 (367)
Q Consensus        80 ~~v~sgr-g~GKS~~~a~~~lw~~~~~~~~~v~~~  113 (367)
                      ++|++|. |+|||+++..++.-++.  .+.+++++
T Consensus         5 IaV~s~KGGVGKTT~avNLA~aLA~--~G~kVlli   37 (270)
T PRK10818          5 IVVTSGKGGVGKTTSSAAIATGLAQ--KGKKTVVI   37 (270)
T ss_pred             EEEECCCCCCCHHHHHHHHHHHHHH--CCCCEEEE
T ss_conf             9997899984189999999999997--79968999


No 303
>PRK08149 ATP synthase SpaL; Validated
Probab=78.45  E-value=2.8  Score=20.70  Aligned_cols=38  Identities=21%  Similarity=0.238  Sum_probs=26.7

Q ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHH
Q ss_conf             4776148867889999999999997089977999715379999
Q gi|254781187|r   79 KCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLK  121 (367)
Q Consensus        79 ~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~  121 (367)
                      |+.|-+|.|+|||++.++++-+     -+..++|.|--...-+
T Consensus       152 R~gIf~gsGvGKs~Ll~~i~~~-----~~adv~Via~IGeRgr  189 (427)
T PRK08149        152 RMGIFASAGCGKTMLMNMLIEH-----TEADVFVIGLIGERGR  189 (427)
T ss_pred             EEECCCCCCCCHHHHHHHHHHH-----CCCCEEEEEEECCCHH
T ss_conf             4000278998677999988863-----5899899997023378


No 304
>KOG0385 consensus
Probab=78.42  E-value=4.6  Score=19.35  Aligned_cols=172  Identities=16%  Similarity=0.138  Sum_probs=86.4

Q ss_pred             HCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHH-CCCCEEEEEC
Q ss_conf             014668884436668428999999988887512455555411247761488678899999999999970-8997799971
Q gi|254781187|r   36 FPWGIKGKPLEHFSQPHRWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLIST-RPGMSIICIA  114 (367)
Q Consensus        36 ~~w~~~~~~~~~~~~p~~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~-~~~~~v~~~A  114 (367)
                      -||+.++..      .+.+|.+=|.=+.---+++.+        ...+---|.|||.-+-.++.++... .-+.-.+|++
T Consensus       159 sP~~v~~g~------lr~YQveGlnWLi~l~engin--------gILaDEMGLGKTlQtIs~l~yl~~~~~~~GPfLVi~  224 (971)
T KOG0385         159 SPSYVKGGE------LRDYQLEGLNWLISLYENGIN--------GILADEMGLGKTLQTISLLGYLKGRKGIPGPFLVIA  224 (971)
T ss_pred             CCHHHCCCC------CCHHHHCCHHHHHHHHHCCCC--------CEEEHHCCCCHHHHHHHHHHHHHHHCCCCCCEEEEE
T ss_conf             832214785------543320337999999865766--------584231045338999999999998517999849981


Q ss_pred             CCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCC---CCCCCCCCCCCCC
Q ss_conf             5379999999999999998623121123333210001233322111134577612662101354---4556521011358
Q gi|254781187|r  115 NSETQLKNTLWAEVSKWLSMLPHRHWFEMQSLSLHPSGWYAELLEQSMGIDSKHYTITCRTYSE---ERPDTFVGPHNTH  191 (367)
Q Consensus       115 ~t~~Q~~~~lw~ei~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~---~~~ea~~g~h~~~  191 (367)
                      |.. .+. -...|+++|.-.++.-....-...+..        ...++.. .+ .+....|+=+   .....+.   ..+
T Consensus       225 P~S-tL~-NW~~Ef~rf~P~l~~~~~~Gdk~eR~~--------~~r~~~~-~~-~fdV~iTsYEi~i~dk~~lk---~~~  289 (971)
T KOG0385         225 PKS-TLD-NWMNEFKRFTPSLNVVVYHGDKEERAA--------LRRDIML-PG-RFDVCITSYEIAIKDKSFLK---KFN  289 (971)
T ss_pred             EHH-HHH-HHHHHHHHHCCCCCEEEEECCHHHHHH--------HHHHHHC-CC-CCCEEEEHHHHHHHHHHHHH---CCC
T ss_conf             276-678-999999976898634988479999999--------9998531-57-87668640788986688986---199


Q ss_pred             CCEEEEECCCCCCHHH--HHHHHHHHHCCCCCEEEEEEECCCCCCCHHHHHH
Q ss_conf             6289997545599889--9998987406988258999807899987688754
Q gi|254781187|r  192 GMAVFNDEASGTPDII--NKSILGFFTELNPNRFWIMTSNTRRLNGWFYDIF  241 (367)
Q Consensus       192 ~~l~ivDEAsgI~d~i--~e~i~g~Lt~~~~~~~~i~igNP~r~~g~Fye~~  241 (367)
                      .-++|+|||.-|.+.-  ...+.--+.. .+++  +++|+|--+  -.+++|
T Consensus       290 W~ylvIDEaHRiKN~~s~L~~~lr~f~~-~nrL--LlTGTPLQN--NL~ELW  336 (971)
T KOG0385         290 WRYLVIDEAHRIKNEKSKLSKILREFKT-DNRL--LLTGTPLQN--NLHELW  336 (971)
T ss_pred             CEEEEECHHHHHCCHHHHHHHHHHHHCC-CCEE--EEECCCCCC--CHHHHH
T ss_conf             3499952365414624489999998566-5526--752785436--499999


No 305
>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=78.24  E-value=4.7  Score=19.32  Aligned_cols=36  Identities=22%  Similarity=0.407  Sum_probs=25.3

Q ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHH
Q ss_conf             47761488678899999999999970899779997153799
Q gi|254781187|r   79 KCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQ  119 (367)
Q Consensus        79 ~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q  119 (367)
                      |+.|-+|.|+|||++.++++-+     -+..++|++--...
T Consensus       139 R~gIf~g~GvGKs~Ll~~ia~~-----~~adv~VialIGeR  174 (411)
T TIGR03496       139 RIGIFAGSGVGKSVLLGMMARY-----TEADVVVVGLIGER  174 (411)
T ss_pred             EEEECCCCCCCHHHHHHHHHHC-----CCCCEEEEECCCCC
T ss_conf             3132279998677999999753-----48988999532530


No 306
>COG0455 flhG Antiactivator of flagellar biosynthesis FleN, an ATPase [Cell motility]
Probab=78.17  E-value=4.7  Score=19.30  Aligned_cols=35  Identities=26%  Similarity=0.328  Sum_probs=24.6

Q ss_pred             EEEEEECCC-CCCHHHHHHHHHHHHHHHCCCCEEEE
Q ss_conf             247761488-67889999999999997089977999
Q gi|254781187|r   78 FKCAISAGR-GIGKTTLNAWMMLWLISTRPGMSIIC  112 (367)
Q Consensus        78 ~~~~v~sgr-g~GKS~~~a~~~lw~~~~~~~~~v~~  112 (367)
                      ..++|.||. |+|||+++|.+....+.......+++
T Consensus         3 ~~Iav~SgKGGvGKTtitanlga~~~~~~~k~V~~i   38 (262)
T COG0455           3 KVIAVVSGKGGVGKTTITANLGAALAALGGKVVLLI   38 (262)
T ss_pred             EEEEEEECCCCCCHHHHHHHHHHHHHHHCCCEEEEE
T ss_conf             899998458875689899869999996489769999


No 307
>PRK10689 transcription-repair coupling factor; Provisional
Probab=78.12  E-value=4.7  Score=19.29  Aligned_cols=59  Identities=12%  Similarity=0.131  Sum_probs=37.2

Q ss_pred             HHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHH
Q ss_conf             9999999888875124555554112477614886788999999999999708997799971537999
Q gi|254781187|r   54 WQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQL  120 (367)
Q Consensus        54 wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~  120 (367)
                      =|.++..+|-+..+++.     .|=|+ ||+==|.|||-++...+.  .+...|..|.+.+||.==+
T Consensus       604 DQl~AI~eV~~DMes~~-----PMDRL-iCGDVGfGKTEVA~RAAF--kav~~gkQVavlvPTTiLA  662 (1148)
T PRK10689        604 DQAQAINAVLSDMCQPL-----AMDRL-VCGDVGFGKTEVAMRAAF--LAVENHKQVAVLVPTTLLA  662 (1148)
T ss_pred             HHHHHHHHHHHHHHCCC-----CCCEE-EECCCCCCHHHHHHHHHH--HHHHCCCEEEEEECCCCCH
T ss_conf             89999999987763886-----77415-676888877999999999--9996398089983662237


No 308
>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=77.99  E-value=2.2  Score=21.31  Aligned_cols=21  Identities=24%  Similarity=0.414  Sum_probs=18.5

Q ss_pred             EEEEEECCCCCCHHHHHHHHH
Q ss_conf             247761488678899999999
Q gi|254781187|r   78 FKCAISAGRGIGKTTLNAWMM   98 (367)
Q Consensus        78 ~~~~v~sgrg~GKS~~~a~~~   98 (367)
                      +|++|.+..|+|||.++..++
T Consensus         1 ~KivvvG~~~vGKTsli~r~~   21 (161)
T cd01863           1 LKILLIGDSGVGKSSLLLRFT   21 (161)
T ss_pred             CEEEEECCCCCCHHHHHHHHH
T ss_conf             989999979957999999996


No 309
>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=77.96  E-value=2.5  Score=21.05  Aligned_cols=72  Identities=21%  Similarity=0.200  Sum_probs=41.1

Q ss_pred             HHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCE--EEEECCCHHHHHHHHHHHHHHHH
Q ss_conf             9999998888751245555541124776148867889999999999997089977--99971537999999999999999
Q gi|254781187|r   55 QLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMS--IICIANSETQLKNTLWAEVSKWL  132 (367)
Q Consensus        55 q~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~--v~~~A~t~~Q~~~~lw~ei~k~~  132 (367)
                      |..+|+.|.=++.        .-.|++|.+.=|+|||++.+.+.=    ..|+.+  +.+.--.-.++.   -.|+.+.+
T Consensus       373 ~~~vl~~V~L~l~--------~G~r~Ai~G~SG~GKsTLL~~L~G----~l~P~~G~vtl~G~~~~~~~---~~evrr~v  437 (566)
T TIGR02868       373 PPNVLDGVSLDLP--------PGERVAILGPSGSGKSTLLATLAG----LLDPLQGEVTLDGVPVSSLS---EDEVRRRV  437 (566)
T ss_pred             CHHHHCCCCCCCC--------CCCCEEEECCCCCCHHHHHHHHHH----HCCCCCCCEEECCCCHHHCC---CCHHEHHE
T ss_conf             3465427864113--------886089866887657899999984----02899991787773243257---31100000


Q ss_pred             HHCCC-CCCC
Q ss_conf             86231-2112
Q gi|254781187|r  133 SMLPH-RHWF  141 (367)
Q Consensus       133 ~~~~~-~~~~  141 (367)
                      ..++- -|.|
T Consensus       438 ~~~aQ~aHlF  447 (566)
T TIGR02868       438 SVFAQDAHLF  447 (566)
T ss_pred             EECCCCCCCC
T ss_conf             3127886211


No 310
>PRK08927 fliI flagellum-specific ATP synthase; Validated
Probab=77.96  E-value=3.3  Score=20.26  Aligned_cols=39  Identities=21%  Similarity=0.266  Sum_probs=27.1

Q ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHH
Q ss_conf             47761488678899999999999970899779997153799999
Q gi|254781187|r   79 KCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLKN  122 (367)
Q Consensus        79 ~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~~  122 (367)
                      |+.|-+|.|+|||++.++++-.     -...++|.|--...-++
T Consensus       160 RigIfagsGvGKs~Ll~~i~r~-----~~adv~VialIGeRgrE  198 (441)
T PRK08927        160 RLGIFAGSGVGKSVLLSMLARN-----TDADVSVIGLIGERGRE  198 (441)
T ss_pred             EEEECCCCCCCHHHHHHHHHHH-----CCCCCEEEEECCCCHHH
T ss_conf             6663168999878999999864-----16773787522651899


No 311
>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=77.93  E-value=4.8  Score=19.26  Aligned_cols=47  Identities=21%  Similarity=0.326  Sum_probs=37.1

Q ss_pred             EEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHH
Q ss_conf             24776148867889999999999997089977999715379999999
Q gi|254781187|r   78 FKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLKNTL  124 (367)
Q Consensus        78 ~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~~~l  124 (367)
                      |+++|.++=|.|||+++-.+++=.+...-..-|+=+--++..+...+
T Consensus       490 YN~~~~g~sG~GKSf~~Q~~~~~~L~~G~kv~viDvG~Sy~KLC~~l  536 (900)
T TIGR02746       490 YNIAVVGGSGAGKSFFMQELIVSVLSRGGKVWVIDVGRSYKKLCEML  536 (900)
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHHHHCCCEEEEEEECCCHHHHHHHH
T ss_conf             14899728898716879899999851798489996078848887651


No 312
>PRK07960 fliI flagellum-specific ATP synthase; Validated
Probab=77.92  E-value=2.7  Score=20.82  Aligned_cols=39  Identities=21%  Similarity=0.366  Sum_probs=26.7

Q ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHH
Q ss_conf             47761488678899999999999970899779997153799999
Q gi|254781187|r   79 KCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLKN  122 (367)
Q Consensus        79 ~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~~  122 (367)
                      |+.|-+|.|+|||++.++++-.     ....++|++--...-++
T Consensus       177 RigIfagsGvGKs~Ll~~iar~-----~~adv~Vi~lIGERgrE  215 (455)
T PRK07960        177 RMGLFAGSGVGKSVLLGMMARY-----TRADVIVVGLIGERGRE  215 (455)
T ss_pred             EEECCCCCCCCHHHHHHHHHHH-----HCCCEEEEEEECEEHHH
T ss_conf             7632489988499999999886-----08985899720406289


No 313
>PRK13235 nifH nitrogenase reductase; Reviewed
Probab=77.91  E-value=4.8  Score=19.26  Aligned_cols=43  Identities=23%  Similarity=0.298  Sum_probs=31.8

Q ss_pred             EEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEE--CCCHHHHH
Q ss_conf             1247761488678899999999999970899779997--15379999
Q gi|254781187|r   77 IFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICI--ANSETQLK  121 (367)
Q Consensus        77 ~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~--A~t~~Q~~  121 (367)
                      |.++||-.==|+|||+.++.+...++-.  |.||+++  =|..+..+
T Consensus         1 m~~iaiyGKGGVGKSTtt~NLaAALA~~--GkkVl~IgcDPk~dsT~   45 (274)
T PRK13235          1 MRKVAIYGKGGIGKSTTTQNTVAGLAEM--GKKVMVVGCDPKADSTR   45 (274)
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHHHHHC--CCEEEEECCCCCCCHHH
T ss_conf             9679997998554767899999999978--99799989898453667


No 314
>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=77.90  E-value=2.1  Score=21.49  Aligned_cols=22  Identities=23%  Similarity=0.359  Sum_probs=18.6

Q ss_pred             EEEECCCCCCHHHHHHHHHHHH
Q ss_conf             7761488678899999999999
Q gi|254781187|r   80 CAISAGRGIGKTTLNAWMMLWL  101 (367)
Q Consensus        80 ~~v~sgrg~GKS~~~a~~~lw~  101 (367)
                      +.|++|-|+|||+++..+.--+
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 315
>PRK07721 fliI flagellum-specific ATP synthase; Validated
Probab=77.88  E-value=3.6  Score=20.02  Aligned_cols=38  Identities=26%  Similarity=0.302  Sum_probs=26.2

Q ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHH
Q ss_conf             4776148867889999999999997089977999715379999
Q gi|254781187|r   79 KCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLK  121 (367)
Q Consensus        79 ~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~  121 (367)
                      |+.|-+|.|+|||++.++++-+-     ...++|.+--...-+
T Consensus       158 RigIf~gsGvGKs~Ll~~iar~~-----~adv~V~~liGeR~r  195 (435)
T PRK07721        158 RVGIFAGSGVGKSTLMGMIARQT-----SADLNVIALIGERGR  195 (435)
T ss_pred             EEEECCCCCCCHHHHHHHHHHHH-----CCCEEEEEEECCCHH
T ss_conf             41002689987899999998874-----488258999332028


No 316
>PRK03321 putative aminotransferase; Provisional
Probab=77.87  E-value=4.8  Score=19.25  Aligned_cols=58  Identities=21%  Similarity=0.230  Sum_probs=35.2

Q ss_pred             CHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHH
Q ss_conf             42899999998888751245555541124776148867889999999999997089977999715379999
Q gi|254781187|r   51 PHRWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLK  121 (367)
Q Consensus        51 p~~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~  121 (367)
                      |+....++-++|+++..-...       ++.|  |.|+  +.+  ...+-.+++.|+.+|++..|++..-.
T Consensus        55 Pd~~~~~Lr~aiA~~~~v~~~-------~I~v--~nGs--~e~--i~~~~~~~~~~gd~Vl~p~P~f~~Y~  112 (352)
T PRK03321         55 PDNGAVELRAALAEHLGVAPE-------HVAV--GCGS--VAL--CQQLVQATAGPGDEVVFAWRSFEAYP  112 (352)
T ss_pred             CCCCHHHHHHHHHHHHCCCHH-------HEEE--CCCH--HHH--HHHHHHHHHCCCCEEEECCCCHHHHH
T ss_conf             899869999999998787858-------7998--7469--999--99999998179798998888532689


No 317
>PRK05688 fliI flagellum-specific ATP synthase; Validated
Probab=77.86  E-value=2.2  Score=21.33  Aligned_cols=46  Identities=24%  Similarity=0.380  Sum_probs=28.4

Q ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHHHHHHHH
Q ss_conf             47761488678899999999999970899779997153799999999999999986
Q gi|254781187|r   79 KCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLKNTLWAEVSKWLSM  134 (367)
Q Consensus        79 ~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~~~lw~ei~k~~~~  134 (367)
                      |+.|-+|+|+|||++.++++-+     -...++|++--....     +|++.+++.
T Consensus       170 R~gIfggsGvGKS~Ll~~i~r~-----~~adv~Vi~lIGERg-----rEv~efi~~  215 (451)
T PRK05688        170 RLGLFAGTGVGKSVLLGMMTRF-----TEADIIVVGLIGERG-----REVKEFIEH  215 (451)
T ss_pred             EEEECCCCCCCHHHHHHHHHHH-----HCCCEEEEEEEEEEH-----HHHHHHHHH
T ss_conf             6421048898689999999885-----279869999612775-----999999999


No 318
>PRK03158 histidinol-phosphate aminotransferase; Provisional
Probab=77.85  E-value=2.9  Score=20.62  Aligned_cols=59  Identities=14%  Similarity=0.219  Sum_probs=36.5

Q ss_pred             CHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHH
Q ss_conf             428999999988887512455555411247761488678899999999999970899779997153799999
Q gi|254781187|r   51 PHRWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLKN  122 (367)
Q Consensus        51 p~~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~~  122 (367)
                      |+.-..++-+.|+++..-...       .+.|  |.  |=+-  +..++..+++.|+.+|++.+|++..-..
T Consensus        62 Pd~~~~~Lr~~iA~~~gv~~~-------~I~v--~n--Gs~e--~i~~~~~~~~~~g~~vvi~~P~f~~Y~~  120 (359)
T PRK03158         62 PDGYAFELRTKVAKHLGVKEE-------QLIF--GN--GSDE--VIQIISRALLHEGTNTVMANPTFSQYRH  120 (359)
T ss_pred             CCCCHHHHHHHHHHHHCCCHH-------HEEE--CC--CHHH--HHHHHHHHHHCCCCEEECCCCEEEHHHH
T ss_conf             698889999999998684867-------7998--47--8899--9999999980799811137982055599


No 319
>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=77.74  E-value=3.8  Score=19.87  Aligned_cols=35  Identities=23%  Similarity=0.339  Sum_probs=25.7

Q ss_pred             EEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECC
Q ss_conf             776148867889999999999997089977999715
Q gi|254781187|r   80 CAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIAN  115 (367)
Q Consensus        80 ~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~  115 (367)
                      +.|+++-|+|||+..+.++-+. ..+.+.+++.+..
T Consensus         4 iLitG~TGSGKTTtl~all~~i-~~~~~~~IiTiED   38 (198)
T cd01131           4 VLVTGPTGSGKSTTLAAMIDYI-NKNKTHHILTIED   38 (198)
T ss_pred             EEEECCCCCCHHHHHHHHHHHH-CCCCCCEEEEECC
T ss_conf             9998999997999999999853-6378836999647


No 320
>PRK09435 arginine/ornithine transport system ATPase; Provisional
Probab=77.72  E-value=4.9  Score=19.22  Aligned_cols=59  Identities=22%  Similarity=0.330  Sum_probs=40.4

Q ss_pred             HHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEE--ECCCHHHHH
Q ss_conf             899999998888751245555541124776148867889999999999997089977999--715379999
Q gi|254781187|r   53 RWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIIC--IANSETQLK  121 (367)
Q Consensus        53 ~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~--~A~t~~Q~~  121 (367)
                      ..-.++|+.+..|.        ...+++-|.+.-|+|||+++..++..+...  +.+|.|  +-|+..-..
T Consensus        33 ~~~~~ll~~l~~~~--------g~a~~iGiTG~pG~GKStli~~l~~~~~~~--g~~v~vlavDPsS~~sg   93 (325)
T PRK09435         33 ALAQELLDALLPHT--------GNALRIGITGVPGVGKSTFIEALGMHLIEQ--GHKVAVLAVDPSSTRTG   93 (325)
T ss_pred             HHHHHHHHHHHHCC--------CCCEEEEEECCCCCCHHHHHHHHHHHHHHC--CCEEEEEEECCCCCCCC
T ss_conf             99999999863017--------982599742799986889999999999967--98589999789999888


No 321
>PRK07594 type III secretion system ATPase; Validated
Probab=77.61  E-value=3.3  Score=20.23  Aligned_cols=38  Identities=21%  Similarity=0.258  Sum_probs=25.2

Q ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHH
Q ss_conf             4776148867889999999999997089977999715379999
Q gi|254781187|r   79 KCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLK  121 (367)
Q Consensus        79 ~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~  121 (367)
                      |+.|-+|+|+|||++.++++.     +....+.|.+--...-+
T Consensus       157 R~gIfgg~GvGKTtLl~~i~~-----~~~adv~V~~lIGERgr  194 (433)
T PRK07594        157 RVGIFSAPGVGKSTLLAMLCN-----APDADSNVLVLIGERGR  194 (433)
T ss_pred             EEEECCCCCCCHHHHHHHHHH-----CCCCCCEEEEEECCCHH
T ss_conf             742047899985589999984-----24798159999410048


No 322
>COG1419 FlhF Flagellar GTP-binding protein [Cell motility and secretion]
Probab=77.61  E-value=4.9  Score=19.20  Aligned_cols=62  Identities=16%  Similarity=0.061  Sum_probs=37.4

Q ss_pred             HHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCC-CCEEEEECCCHH
Q ss_conf             9999998888751245555541124776148867889999999999997089-977999715379
Q gi|254781187|r   55 QLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRP-GMSIICIANSET  118 (367)
Q Consensus        55 q~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~-~~~v~~~A~t~~  118 (367)
                      -.+.++.+-.+.-.+....+  -.-++..++.|+|||+..|=++.-+..... ....++|-.|++
T Consensus       183 ~~~~l~~~~~~~~~~~~~~~--~~vi~LVGPTGVGKTTTlAKLAar~~~~~~~~kVaiITtDtYR  245 (407)
T COG1419         183 FSEKLRKLLLSLIENLIVEQ--KRVIALVGPTGVGKTTTLAKLAARYVMLKKKKKVAIITTDTYR  245 (407)
T ss_pred             HHHHHHHHHHHHCCCCCCCC--CCEEEEECCCCCCHHHHHHHHHHHHHHHCCCCCEEEEEECCCH
T ss_conf             79999998876441111246--8579998998875887999999999753257606899714411


No 323
>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=77.60  E-value=2.2  Score=21.32  Aligned_cols=22  Identities=36%  Similarity=0.481  Sum_probs=18.3

Q ss_pred             EEEECCCCCCHHHHHHHHHHHH
Q ss_conf             7761488678899999999999
Q gi|254781187|r   80 CAISAGRGIGKTTLNAWMMLWL  101 (367)
Q Consensus        80 ~~v~sgrg~GKS~~~a~~~lw~  101 (367)
                      ++|+++-|+|||+++..+.--+
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 324
>COG0556 UvrB Helicase subunit of the DNA excision repair complex [DNA replication, recombination, and repair]
Probab=77.55  E-value=4.9  Score=19.19  Aligned_cols=69  Identities=17%  Similarity=0.184  Sum_probs=47.9

Q ss_pred             CHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHHHH
Q ss_conf             42899999998888751245555541124776148867889999999999997089977999715379999999999999
Q gi|254781187|r   51 PHRWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLKNTLWAEVSK  130 (367)
Q Consensus        51 p~~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~~~lw~ei~k  130 (367)
                      |.-=|-++.+.+.+.++++..      +.+ ..+-.|+|||+.+|..+--     -..-.+|+|+...-+ .-++.|+|.
T Consensus        13 PaGDQP~AI~~Lv~gi~~g~~------~Qt-LLGvTGSGKTfT~AnVI~~-----~~rPtLV~AhNKTLA-aQLy~Efk~   79 (663)
T COG0556          13 PAGDQPEAIAELVEGIENGLK------HQT-LLGVTGSGKTFTMANVIAK-----VQRPTLVLAHNKTLA-AQLYSEFKE   79 (663)
T ss_pred             CCCCCHHHHHHHHHHHHCCCE------EEE-EEEECCCCCHHHHHHHHHH-----HCCCEEEEECCHHHH-HHHHHHHHH
T ss_conf             999867999999988863860------258-8620368831079999998-----689719982555479-999999997


Q ss_pred             HH
Q ss_conf             99
Q gi|254781187|r  131 WL  132 (367)
Q Consensus       131 ~~  132 (367)
                      +.
T Consensus        80 fF   81 (663)
T COG0556          80 FF   81 (663)
T ss_pred             HC
T ss_conf             68


No 325
>pfam03266 DUF265 Protein of unknown function, DUF265.
Probab=77.50  E-value=4.9  Score=19.19  Aligned_cols=60  Identities=13%  Similarity=0.120  Sum_probs=35.4

Q ss_pred             CCCEEEEECCCCC---CHHHHHHHHHHHHCCCCCEEEEEEECCCCCCCHHHHHHHCCCCCEEEEEECC
Q ss_conf             8628999754559---9889999898740698825899980789998768875411223504675233
Q gi|254781187|r  191 HGMAVFNDEASGT---PDIINKSILGFFTELNPNRFWIMTSNTRRLNGWFYDIFNIPLEDWKRYQIDT  255 (367)
Q Consensus       191 ~~~l~ivDEAsgI---~d~i~e~i~g~Lt~~~~~~~~i~igNP~r~~g~Fye~~~~~~~~w~~~~~~~  255 (367)
                      +..++++||-...   +..+.++++..|.+ +.+.+  ++- |.+....|-+...+ +.+...+.++.
T Consensus        95 ~~dlivIDEIG~mEl~s~~F~~~v~~~l~~-~~~vl--~ti-~~~~~~~~v~~i~~-~~d~~i~~vt~  157 (168)
T pfam03266        95 EADLIIIDEIGPMELKSPKFREAIEEVLSS-NKPVL--AVV-HRRSDSPLVERIRR-RPDVKIFVVTE  157 (168)
T ss_pred             CCCEEEEECCCHHHHHHHHHHHHHHHHHCC-CCCEE--EEE-EECCCCHHHHHHHC-CCCCEEEEECH
T ss_conf             898999976314533149999999999669-99799--999-72589838999741-79938999786


No 326
>PRK12289 ribosome-associated GTPase; Reviewed
Probab=77.44  E-value=2.5  Score=20.97  Aligned_cols=16  Identities=25%  Similarity=0.574  Sum_probs=8.9

Q ss_pred             EECCCCCCHHHHHHHH
Q ss_conf             6148867889999999
Q gi|254781187|r   82 ISAGRGIGKTTLNAWM   97 (367)
Q Consensus        82 v~sgrg~GKS~~~a~~   97 (367)
                      +++.-|+|||+++-.+
T Consensus       176 ~~G~SGVGKSSLIN~L  191 (351)
T PRK12289        176 VAGPSGVGKSSLINRL  191 (351)
T ss_pred             EECCCCCCHHHHHHHH
T ss_conf             9817988788988763


No 327
>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=77.44  E-value=2.8  Score=20.70  Aligned_cols=23  Identities=22%  Similarity=0.343  Sum_probs=20.3

Q ss_pred             CEEEEEEECCCCCCHHHHHHHHH
Q ss_conf             11247761488678899999999
Q gi|254781187|r   76 TIFKCAISAGRGIGKTTLNAWMM   98 (367)
Q Consensus        76 ~~~~~~v~sgrg~GKS~~~a~~~   98 (367)
                      ++||+.+.+..|+|||.++..++
T Consensus         2 ~~~Kiv~lGd~~vGKTsli~r~~   24 (165)
T cd01864           2 FLFKIILIGDSNVGKTCVVQRFK   24 (165)
T ss_pred             EEEEEEEECCCCCCHHHHHHHHH
T ss_conf             58999999999958999999996


No 328
>PRK12422 chromosomal replication initiation protein; Provisional
Probab=77.42  E-value=5  Score=19.17  Aligned_cols=53  Identities=19%  Similarity=0.188  Sum_probs=35.1

Q ss_pred             HHHHHHHHHHHCC-CCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECC
Q ss_conf             9999888875124-5555541124776148867889999999999997089977999715
Q gi|254781187|r   57 EFMEAVDVHCHSN-VNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIAN  115 (367)
Q Consensus        57 ~~l~~~~~~~~~~-~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~  115 (367)
                      .+..+++.....+ ...++|    +-|-++-|.|||+|.-++....  ..++.+|+++..
T Consensus       124 ~aa~~va~~~~~~~g~~yNP----LfIyG~~GlGKTHLL~AIgn~i--~~~~~kV~Yvta  177 (455)
T PRK12422        124 RILQEFAKVSEQGKGFPFNP----IYLFGPEGSGKTHLMQAAVSAL--RESGGKILYVSS  177 (455)
T ss_pred             HHHHHHHHCCCCCCCCCCCC----EEEECCCCCCHHHHHHHHHHHH--HCCCCEEEEECH
T ss_conf             99999983755358876787----5887899997899999999985--379986999749


No 329
>cd00009 AAA The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC, RecA-like, VirD4-like, PilT-like, and SF1/2 helicases. Members of the AAA+ ATPases function as molecular chaperons, ATPase subunits of proteases, helicases, or nucleic-acid stimulated ATPases. The AAA+ proteins contain several distinct features in addition to the conserved alpha-beta-alpha core domain structure and the Walker A and B motifs of the P-loop NTPases.
Probab=77.36  E-value=5  Score=19.16  Aligned_cols=35  Identities=26%  Similarity=0.358  Sum_probs=23.3

Q ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECC
Q ss_conf             4776148867889999999999997089977999715
Q gi|254781187|r   79 KCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIAN  115 (367)
Q Consensus        79 ~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~  115 (367)
                      .+.+.+.-|+|||+++..++- .+. +.+..++.+..
T Consensus        21 ~ill~GppGtGKT~la~~ia~-~~~-~~~~~~~~~~~   55 (151)
T cd00009          21 NLLLYGPPGTGKTTLARAIAN-ELF-RPGAPFLYLNA   55 (151)
T ss_pred             EEEEECCCCCCHHHHHHHHHH-HHC-CCCCCEEEEEH
T ss_conf             089989999886599999999-712-13798278547


No 330
>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=77.23  E-value=3.1  Score=20.44  Aligned_cols=23  Identities=26%  Similarity=0.585  Sum_probs=20.3

Q ss_pred             CEEEEEEECCCCCCHHHHHHHHH
Q ss_conf             11247761488678899999999
Q gi|254781187|r   76 TIFKCAISAGRGIGKTTLNAWMM   98 (367)
Q Consensus        76 ~~~~~~v~sgrg~GKS~~~a~~~   98 (367)
                      ++|++.|.+-.|+|||.++-.++
T Consensus         3 ~vfk~~VlG~~~VGKTsLi~rf~   25 (169)
T cd01892           3 NVFLCFVLGAKGSGKSALLRAFL   25 (169)
T ss_pred             EEEEEEEECCCCCCHHHHHHHHH
T ss_conf             08999999999988999999996


No 331
>PRK10263 DNA translocase FtsK; Provisional
Probab=77.21  E-value=3.4  Score=20.21  Aligned_cols=47  Identities=17%  Similarity=0.156  Sum_probs=34.4

Q ss_pred             CCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCC--CEEEEECCC
Q ss_conf             55555411247761488678899999999999970899--779997153
Q gi|254781187|r   70 VNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPG--MSIICIANS  116 (367)
Q Consensus        70 ~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~--~~v~~~A~t  116 (367)
                      ...++..|.-+.|++..|+|||.++-.+|+=+|....+  .|.|.+-|+
T Consensus      1003 vv~DLaKMPHLLIAGtTGSGKSV~iNsmI~SlLyk~~PdevrlImIDPK 1051 (1355)
T PRK10263       1003 VVADLAKMPHLLVAGTTGSGKSVGVNAMILSMLYKAQPEDVRFIMIDPK 1051 (1355)
T ss_pred             EEEEHHHCCCEEEECCCCCCCHHHHHHHHHHHHHCCCHHHEEEEEECCC
T ss_conf             7747421971134046788830439999999984388879479986687


No 332
>PRK08972 fliI flagellum-specific ATP synthase; Validated
Probab=77.06  E-value=3.8  Score=19.88  Aligned_cols=38  Identities=21%  Similarity=0.330  Sum_probs=26.6

Q ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHH
Q ss_conf             4776148867889999999999997089977999715379999
Q gi|254781187|r   79 KCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLK  121 (367)
Q Consensus        79 ~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~  121 (367)
                      |+.|-+|.|+|||++.++++-     +....++|++--...-+
T Consensus       162 RigIf~gsGvGKS~Ll~~i~r-----~~~advvVi~lIGERgr  199 (440)
T PRK08972        162 RMGLFAGSGVGKSVLLGMMTR-----GTTADVIVVGLVGERGR  199 (440)
T ss_pred             EEEECCCCCCCHHHHHHHHHH-----CCCCCEEEEEEECEEHH
T ss_conf             666315789758999988875-----14787899986231369


No 333
>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=77.02  E-value=2.9  Score=20.58  Aligned_cols=23  Identities=26%  Similarity=0.417  Sum_probs=20.1

Q ss_pred             CEEEEEEECCCCCCHHHHHHHHH
Q ss_conf             11247761488678899999999
Q gi|254781187|r   76 TIFKCAISAGRGIGKTTLNAWMM   98 (367)
Q Consensus        76 ~~~~~~v~sgrg~GKS~~~a~~~   98 (367)
                      +.+|+.+.+..|+|||.++..++
T Consensus         2 y~~KivlvGd~~vGKTsli~r~~   24 (167)
T cd01867           2 YLFKLLLIGDSGVGKSCLLLRFS   24 (167)
T ss_pred             EEEEEEEECCCCCCHHHHHHHHH
T ss_conf             68999999999978899999996


No 334
>PRK08533 flagellar accessory protein FlaH; Reviewed
Probab=77.02  E-value=5.1  Score=19.10  Aligned_cols=44  Identities=18%  Similarity=0.192  Sum_probs=27.8

Q ss_pred             CCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEE--CCCHHHH
Q ss_conf             411247761488678899999999999970899779997--1537999
Q gi|254781187|r   75 PTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICI--ANSETQL  120 (367)
Q Consensus        75 ~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~--A~t~~Q~  120 (367)
                      |.-.-+.|.+..|+|||.++.-++. ..+. .+.+++++  ..|.++.
T Consensus        22 p~gs~~li~G~~GtGKsi~~~~~~~-~~l~-~g~~~~yis~e~t~~~~   67 (230)
T PRK08533         22 PFGSIILIEGDESTGKSILSQRLAY-GFLQ-NGYSVSYVSSQLTTTEF   67 (230)
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHHH-HHHH-CCCEEEEEEECCCHHHH
T ss_conf             8984899986899878999999999-9987-89869999943899999


No 335
>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=77.00  E-value=2.6  Score=20.89  Aligned_cols=23  Identities=26%  Similarity=0.297  Sum_probs=19.2

Q ss_pred             EEEEEEECCCCCCHHHHHHHHHH
Q ss_conf             12477614886788999999999
Q gi|254781187|r   77 IFKCAISAGRGIGKTTLNAWMML   99 (367)
Q Consensus        77 ~~~~~v~sgrg~GKS~~~a~~~l   99 (367)
                      +||+.+.+..|+|||.++..++-
T Consensus         1 ~~KivllGd~~VGKTsli~r~~~   23 (165)
T cd01865           1 MFKLLIIGNSSVGKTSFLFRYAD   23 (165)
T ss_pred             CEEEEEECCCCCCHHHHHHHHHC
T ss_conf             98999999999688999999924


No 336
>pfam02367 UPF0079 Uncharacterized P-loop hydrolase UPF0079. This uncharacterized family contains a P-loop.
Probab=76.90  E-value=4.1  Score=19.65  Aligned_cols=49  Identities=18%  Similarity=0.105  Sum_probs=34.8

Q ss_pred             HHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHH
Q ss_conf             99998888751245555541124776148867889999999999997089977999715379
Q gi|254781187|r   57 EFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSET  118 (367)
Q Consensus        57 ~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~  118 (367)
                      ++-+.++..++.+.        -+...+.=|+|||+++-.++--+     +...-|++||+.
T Consensus         3 ~lg~~ia~~l~~G~--------vi~L~G~LGaGKTtfvr~i~~~l-----g~~~~V~SPTF~   51 (123)
T pfam02367         3 NLGKRLAQLLKAGD--------VVLLSGDLGAGKTTFVRGLAKGL-----GITGNVTSPTFT   51 (123)
T ss_pred             HHHHHHHHHCCCCC--------EEEEECCCCCCHHHHHHHHHHHC-----CCCCCCCCCCEE
T ss_conf             99999997689997--------99998887788999999999985-----998873799558


No 337
>PRK06002 fliI flagellum-specific ATP synthase; Validated
Probab=76.76  E-value=2.3  Score=21.22  Aligned_cols=21  Identities=43%  Similarity=0.602  Sum_probs=18.0

Q ss_pred             EEEEECCCCCCHHHHHHHHHH
Q ss_conf             477614886788999999999
Q gi|254781187|r   79 KCAISAGRGIGKTTLNAWMML   99 (367)
Q Consensus        79 ~~~v~sgrg~GKS~~~a~~~l   99 (367)
                      |+.|-+|+|+|||++.++++-
T Consensus       167 R~gIfgg~GvGKTtLl~~i~~  187 (450)
T PRK06002        167 RIGIFAGSGVGKSTLLAMLAR  187 (450)
T ss_pred             EEEECCCCCCCHHHHHHHHHH
T ss_conf             777426899987599999986


No 338
>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=76.71  E-value=5.2  Score=19.05  Aligned_cols=41  Identities=20%  Similarity=0.245  Sum_probs=31.6

Q ss_pred             EEEEEEECCCCCCHHHHHHHHHHHHHHHCCC--CEEEEECCCH
Q ss_conf             1247761488678899999999999970899--7799971537
Q gi|254781187|r   77 IFKCAISAGRGIGKTTLNAWMMLWLISTRPG--MSIICIANSE  117 (367)
Q Consensus        77 ~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~--~~v~~~A~t~  117 (367)
                      ...+.|.+.-|+|||.+.-.++..++..+.+  .+++++-++.
T Consensus        38 ~pH~Lv~G~tGsGKS~~l~~li~sl~~~~~p~~v~l~liD~K~   80 (202)
T pfam01580        38 MPHLLIAGATGSGKSTFLNTLILSLAARHSPEEVRLYLIDPKG   80 (202)
T ss_pred             CCCEEEECCCCCCCCHHHHHHHHHHHHHCCCCEEEEEEECCCC
T ss_conf             8868996589998009999999999873796206999974896


No 339
>PRK00741 prfC peptide chain release factor 3; Provisional
Probab=76.68  E-value=2.6  Score=20.94  Aligned_cols=137  Identities=13%  Similarity=0.066  Sum_probs=67.4

Q ss_pred             EEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCC--HHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCC
Q ss_conf             1247761488678899999999999970899779997153--79999999999999998623121123333210001233
Q gi|254781187|r   77 IFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANS--ETQLKNTLWAEVSKWLSMLPHRHWFEMQSLSLHPSGWY  154 (367)
Q Consensus        77 ~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t--~~Q~~~~lw~ei~k~~~~~~~~~~~~~~~~~~~~~~~~  154 (367)
                      +++++|.|.-|.|||+++-.+++.--..+.-.+|  -+.+  .+...|  |-++.+-....+......        ..|.
T Consensus        10 ~RniaIi~H~dAGKTTLtE~lL~~~GaI~~~G~V--~~~~~~~~~~sD--~~~~E~~RgiSI~ssv~~--------~e~~   77 (526)
T PRK00741         10 RRTFAIISHPDAGKTTLTEKLLLFGGAIQEAGTV--KGRKSGRHATSD--WMEMEKQRGISVTSSVMQ--------FPYR   77 (526)
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHHCCCCCCCCEE--ECCCCCCCCCCC--CCHHHHHCCCEEECCEEE--------EEEC
T ss_conf             1779999378989899999999746752448466--314678864678--858899759648615177--------8678


Q ss_pred             CCCCCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCEEEEECCCCCC---HHHHHHHHHHHHCCCCCEEEEEEECCC
Q ss_conf             32211113457761266210135445565210113586289997545599---889999898740698825899980789
Q gi|254781187|r  155 AELLEQSMGIDSKHYTITCRTYSEERPDTFVGPHNTHGMAVFNDEASGTP---DIINKSILGFFTELNPNRFWIMTSNTR  231 (367)
Q Consensus       155 ~~~~~~~~~~~~~~~~~~a~~~~~~~~ea~~g~h~~~~~l~ivDEAsgI~---d~i~e~i~g~Lt~~~~~~~~i~igNP~  231 (367)
                      .  .        ...++..-+......|...+++.-...++++|=++||.   ..+|+++.    ..+-+.+  ++-|=-
T Consensus        78 ~--~--------~iNliDTPGh~DF~~e~~raL~a~D~Av~Vida~~GVe~qTe~~w~~~~----~~~iP~i--~FINKm  141 (526)
T PRK00741         78 D--C--------LINLLDTPGHEDFSEDTYRTLTAVDSALMVIDAAKGVEPQTRKLMEVCR----LRDTPIF--TFINKL  141 (526)
T ss_pred             C--E--------EEEEEECCCCHHHHHHHHHHHHHHCEEEEEEECCCCCCHHHHHHHHHHH----HCCCCEE--EEEECC
T ss_conf             9--8--------9999909894677899999998737599999777552333689999988----6399889--999656


Q ss_pred             C-CCCHHHHHH
Q ss_conf             9-987688754
Q gi|254781187|r  232 R-LNGWFYDIF  241 (367)
Q Consensus       232 r-~~g~Fye~~  241 (367)
                      . ..--|.++.
T Consensus       142 DR~~ad~~~~l  152 (526)
T PRK00741        142 DRDGREPLELL  152 (526)
T ss_pred             CCCCCCHHHHH
T ss_conf             76789878988


No 340
>PHA02518 ParA-like protein; Provisional
Probab=76.63  E-value=3.1  Score=20.40  Aligned_cols=28  Identities=29%  Similarity=0.548  Sum_probs=21.2

Q ss_pred             CCCCCHHHHHHHHHHHHHHHCCCCEEEEEC
Q ss_conf             886788999999999999708997799971
Q gi|254781187|r   85 GRGIGKTTLNAWMMLWLISTRPGMSIICIA  114 (367)
Q Consensus        85 grg~GKS~~~a~~~lw~~~~~~~~~v~~~A  114 (367)
                      ==|+|||+++..++.++..  .+.+|+++=
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 341
>PRK08472 fliI flagellum-specific ATP synthase; Validated
Probab=76.59  E-value=3.1  Score=20.39  Aligned_cols=22  Identities=41%  Similarity=0.531  Sum_probs=19.6

Q ss_pred             EEEEECCCCCCHHHHHHHHHHH
Q ss_conf             4776148867889999999999
Q gi|254781187|r   79 KCAISAGRGIGKTTLNAWMMLW  100 (367)
Q Consensus        79 ~~~v~sgrg~GKS~~~a~~~lw  100 (367)
                      |+.|-+|+|+|||++.+.++.+
T Consensus       160 R~gIf~g~GvGKt~Ll~~i~~~  181 (435)
T PRK08472        160 KLGIFAGSGVGKSTLMGMIVKG  181 (435)
T ss_pred             EEECCCCCCCCCCHHHHHHHHH
T ss_conf             6512358999833578888776


No 342
>PRK13909 putative recombination protein RecB; Provisional
Probab=76.57  E-value=5.2  Score=19.02  Aligned_cols=40  Identities=13%  Similarity=0.146  Sum_probs=26.2

Q ss_pred             CCCEEEEECCCCCCHHHHHHHHHHHH----C---CCCCEEEEEEECCC
Q ss_conf             86289997545599889999898740----6---98825899980789
Q gi|254781187|r  191 HGMAVFNDEASGTPDIINKSILGFFT----E---LNPNRFWIMTSNTR  231 (367)
Q Consensus       191 ~~~l~ivDEAsgI~d~i~e~i~g~Lt----~---~~~~~~~i~igNP~  231 (367)
                      .+-.++|||++-.+..-|+.+.+.+.    +   .+.+. .+++|-|.
T Consensus       325 ~~~~ilVDEFQDTn~~Q~~il~~L~~~~~~g~~~~~~~~-lf~VGD~K  371 (911)
T PRK13909        325 KISHILIDEFQDTSLLQYKILLPLIDEIKSGEGQSKNRS-FFYVGDVK  371 (911)
T ss_pred             CCCEEEEEHHCCCCHHHHHHHHHHHHHHHCCCCCCCCCC-EEEECCCC
T ss_conf             576899640024899999999999987623555678872-79973773


No 343
>cd04122 Rab14 Rab14 subfamily.  Rab14 GTPases are localized to biosynthetic compartments, including the rough ER, the Golgi complex, and the trans-Golgi network, and to endosomal compartments, including early endosomal vacuoles and associated vesicles.  Rab14 is believed to function in both the biosynthetic and recycling pathways between the Golgi and endosomal compartments.  Rab14 has also been identified on GLUT4 vesicles, and has been suggested to help regulate GLUT4 translocation.  In addition, Rab14 is believed to play a role in the regulation of 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 GT
Probab=76.47  E-value=2.9  Score=20.56  Aligned_cols=24  Identities=33%  Similarity=0.394  Sum_probs=20.7

Q ss_pred             CEEEEEEECCCCCCHHHHHHHHHH
Q ss_conf             112477614886788999999999
Q gi|254781187|r   76 TIFKCAISAGRGIGKTTLNAWMML   99 (367)
Q Consensus        76 ~~~~~~v~sgrg~GKS~~~a~~~l   99 (367)
                      +.||+.+.+-.|+|||.++..++-
T Consensus         1 y~~KivlvGd~~VGKTsli~r~~~   24 (166)
T cd04122           1 YIFKYIIIGDMGVGKSCLLHQFTE   24 (166)
T ss_pred             CEEEEEEECCCCCCHHHHHHHHHC
T ss_conf             949999999999579999999912


No 344
>PRK06217 hypothetical protein; Validated
Probab=76.43  E-value=2.7  Score=20.83  Aligned_cols=28  Identities=29%  Similarity=0.297  Sum_probs=21.9

Q ss_pred             EEEEEEECCCCCCHHHHHHHHHHHHHHH
Q ss_conf             1247761488678899999999999970
Q gi|254781187|r   77 IFKCAISAGRGIGKTTLNAWMMLWLIST  104 (367)
Q Consensus        77 ~~~~~v~sgrg~GKS~~~a~~~lw~~~~  104 (367)
                      |.|+.|.+.-|+|||+++..+.--.-+.
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 345
>pfam07726 AAA_3 ATPase family associated with various cellular activities (AAA). This Pfam entry includes some of the AAA proteins not detected by the pfam00004 model.
Probab=76.42  E-value=5.3  Score=19.00  Aligned_cols=24  Identities=21%  Similarity=0.371  Sum_probs=20.1

Q ss_pred             EEEEECCCCCCHHHHHHHHHHHHC
Q ss_conf             899975455998899998987406
Q gi|254781187|r  194 AVFNDEASGTPDIINKSILGFFTE  217 (367)
Q Consensus       194 l~ivDEAsgI~d~i~e~i~g~Lt~  217 (367)
                      ++++||....++.+..++...|.+
T Consensus        65 vl~lDEin~a~~~v~~~Ll~~l~e   88 (131)
T pfam07726        65 VLLADEINRAPPKTQSALLEAMQE   88 (131)
T ss_pred             CEEEEHHHCCCHHHHHHHHHHHHC
T ss_conf             056401203998999999976326


No 346
>COG0552 FtsY Signal recognition particle GTPase [Intracellular trafficking and secretion]
Probab=76.30  E-value=5.3  Score=18.98  Aligned_cols=124  Identities=17%  Similarity=0.150  Sum_probs=65.9

Q ss_pred             CCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEEC-CCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCC
Q ss_conf             4112477614886788999999999999708997799971-537999999999999999862312112333321000123
Q gi|254781187|r   75 PTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIA-NSETQLKNTLWAEVSKWLSMLPHRHWFEMQSLSLHPSGW  153 (367)
Q Consensus        75 ~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A-~t~~Q~~~~lw~ei~k~~~~~~~~~~~~~~~~~~~~~~~  153 (367)
                      |++  +.+.+=.|+|||+.+|=++-|+..  .+.+|++.| -|.+-+-   -..++-|.+++-..               
T Consensus       139 p~V--il~vGVNG~GKTTTIaKLA~~l~~--~g~~VllaA~DTFRAaA---iEQL~~w~er~gv~---------------  196 (340)
T COG0552         139 PFV--ILFVGVNGVGKTTTIAKLAKYLKQ--QGKSVLLAAGDTFRAAA---IEQLEVWGERLGVP---------------  196 (340)
T ss_pred             CEE--EEEEECCCCCHHHHHHHHHHHHHH--CCCEEEEEECCHHHHHH---HHHHHHHHHHHCCE---------------
T ss_conf             679--999934888637179999999997--89869998233478999---99999999995992---------------


Q ss_pred             CCCCCCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCEEEEECCCCCCH--HHHHHH-------HHHHHCCCCCEEE
Q ss_conf             3322111134577612662101354455652101135862899975455998--899998-------9874069882589
Q gi|254781187|r  154 YAELLEQSMGIDSKHYTITCRTYSEERPDTFVGPHNTHGMAVFNDEASGTPD--IINKSI-------LGFFTELNPNRFW  224 (367)
Q Consensus       154 ~~~~~~~~~~~~~~~~~~~a~~~~~~~~ea~~g~h~~~~~l~ivDEAsgI~d--~i~e~i-------~g~Lt~~~~~~~~  224 (367)
                         ..+...+.|+-+..          -++.+...+.+...+++|-|.-..+  ..++-+       .+.+.+.--++++
T Consensus       197 ---vI~~~~G~DpAaVa----------fDAi~~Akar~~DvvliDTAGRLhnk~nLM~EL~KI~rV~~k~~~~ap~e~ll  263 (340)
T COG0552         197 ---VISGKEGADPAAVA----------FDAIQAAKARGIDVVLIDTAGRLHNKKNLMDELKKIVRVIKKDDPDAPHEILL  263 (340)
T ss_pred             ---EECCCCCCCCHHHH----------HHHHHHHHHCCCCEEEEECCCCCCCCHHHHHHHHHHHHHHCCCCCCCCCEEEE
T ss_conf             ---78259999808999----------99999999769999999675544573668999999999846456899842899


Q ss_pred             EEEECCCCCC
Q ss_conf             9980789998
Q gi|254781187|r  225 IMTSNTRRLN  234 (367)
Q Consensus       225 i~igNP~r~~  234 (367)
                      + +-..++..
T Consensus       264 v-lDAttGqn  272 (340)
T COG0552         264 V-LDATTGQN  272 (340)
T ss_pred             E-EECCCCHH
T ss_conf             9-77564756


No 347
>TIGR02784 addA_alphas double-strand break repair helicase AddA; InterPro: IPR014151   AddAB, also called RexAB, substitutes for RecBCD in several bacterial lineages. These DNA recombination proteins act before synapse and are particularly important for DNA repair of double-stranded breaks by homologous recombination. The term AddAB is used broadly, with AddA homologues between the alphaproteobacteria and the Firmicutes, while the partner AddB proteins show no strong homology across the two groups of species..
Probab=76.26  E-value=2.9  Score=20.61  Aligned_cols=24  Identities=21%  Similarity=0.025  Sum_probs=19.7

Q ss_pred             CCEEEEECCCCCCHHHHHHHHHHH
Q ss_conf             628999754559988999989874
Q gi|254781187|r  192 GMAVFNDEASGTPDIINKSILGFF  215 (367)
Q Consensus       192 ~~l~ivDEAsgI~d~i~e~i~g~L  215 (367)
                      +..++||||+--++.-|++|+-.-
T Consensus       397 iDHILvDEAQDTSP~QW~iI~~LA  420 (1190)
T TIGR02784       397 IDHILVDEAQDTSPEQWEIIQALA  420 (1190)
T ss_pred             CCEEEECCHHCCCHHHHHHHHHHH
T ss_conf             043771220048865899999998


No 348
>KOG0327 consensus
Probab=76.19  E-value=3.7  Score=19.93  Aligned_cols=67  Identities=16%  Similarity=0.106  Sum_probs=41.4

Q ss_pred             CCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCC-CEEEEECCCHHHHHHHH
Q ss_conf             36668428999999988887512455555411247761488678899999999999970899-77999715379999999
Q gi|254781187|r   46 EHFSQPHRWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPG-MSIICIANSETQLKNTL  124 (367)
Q Consensus        46 ~~~~~p~~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~-~~v~~~A~t~~Q~~~~l  124 (367)
                      ++|..|.--|-.+   |..-+..      +   .+-+.+--|+||+...+..++-.+.+... +.+++.||+...+..+.
T Consensus        44 ~GFekPSaIQqrA---I~p~i~G------~---dv~~qaqsgTgKt~af~i~ilq~iD~~~ke~qalilaPtreLa~q~~  111 (397)
T KOG0327          44 YGFEKPSAIQQRA---ILPCIKG------H---DVIAQAQSGTGKTAAFLISILQQIDMSVKETQALILAPTRELAQQIQ  111 (397)
T ss_pred             HCCCCCHHHHHCC---CCCCCCC------C---CEEEEEECCCCCHHHHHHHHHHHCCCCHHHHHHHHHCCHHHHHHHHH
T ss_conf             0368822777634---3553468------7---44676302544114667888751374167777988613278889899


No 349
>COG0563 Adk Adenylate kinase and related kinases [Nucleotide transport and metabolism]
Probab=76.16  E-value=3.5  Score=20.07  Aligned_cols=29  Identities=24%  Similarity=0.141  Sum_probs=22.7

Q ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHHCCC
Q ss_conf             47761488678899999999999970899
Q gi|254781187|r   79 KCAISAGRGIGKTTLNAWMMLWLISTRPG  107 (367)
Q Consensus        79 ~~~v~sgrg~GKS~~~a~~~lw~~~~~~~  107 (367)
                      |+.|.++=|+|||+++..++-.+=+.|-+
T Consensus         2 riiilG~pGaGK~T~A~~La~~~~i~hls   30 (178)
T COG0563           2 RILILGPPGAGKSTLAKKLAKKLGLPHLD   30 (178)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHCCCCEEC
T ss_conf             79998999998899999999976997855


No 350
>PRK03566 consensus
Probab=76.16  E-value=1.5  Score=22.43  Aligned_cols=54  Identities=17%  Similarity=0.134  Sum_probs=31.8

Q ss_pred             HHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHH
Q ss_conf             9999998888751245555541124776148867889999999999997089977999715379999
Q gi|254781187|r   55 QLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLK  121 (367)
Q Consensus        55 q~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~  121 (367)
                      ..++-++|+++..-..     +  ++.|  |.  |=+.  +..++..+++.|+.+|++..|++..-.
T Consensus        69 ~~~Lr~aiA~~~gv~~-----~--~I~v--~~--Gs~e--~i~l~~~a~~~pGd~Vl~~~P~y~~Y~  122 (365)
T PRK03566         69 GFELKAALAEKLGVPP-----E--QITL--GN--GSND--LLELLARAFLGPGDEIIYSQYAFAVYP  122 (365)
T ss_pred             HHHHHHHHHHHHCCCH-----H--HEEE--CC--CHHH--HHHHHHHHHCCCCCEEEECCCCHHHHH
T ss_conf             8999999999978486-----6--7998--77--8999--999999985589987676688668999


No 351
>PRK13231 nitrogenase reductase-like protein; Reviewed
Probab=75.97  E-value=5.4  Score=18.93  Aligned_cols=45  Identities=24%  Similarity=0.217  Sum_probs=32.2

Q ss_pred             EEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEE--CCCHHHHHHHH
Q ss_conf             1247761488678899999999999970899779997--15379999999
Q gi|254781187|r   77 IFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICI--ANSETQLKNTL  124 (367)
Q Consensus        77 ~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~--A~t~~Q~~~~l  124 (367)
                      |.++||-.==|+|||+.++.+..-++ .  +.||+.+  -|+.+..+..+
T Consensus         2 m~~iAiyGKGGIGKSTt~~NlaaalA-~--g~rVl~igcDpk~dst~~L~   48 (264)
T PRK13231          2 LKKIAIYGKGGIGKSTTVSNMAAAYS-S--DNSTLVIGCDPKADTTRTLV   48 (264)
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHHHH-C--CCCEEEECCCCCCCHHHHHH
T ss_conf             42899978985478889999999998-7--99779985688850246761


No 352
>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=75.91  E-value=3  Score=20.47  Aligned_cols=22  Identities=23%  Similarity=0.536  Sum_probs=19.4

Q ss_pred             EEEEEECCCCCCHHHHHHHHHH
Q ss_conf             2477614886788999999999
Q gi|254781187|r   78 FKCAISAGRGIGKTTLNAWMML   99 (367)
Q Consensus        78 ~~~~v~sgrg~GKS~~~a~~~l   99 (367)
                      ||+.+.+..|+|||.++..++-
T Consensus         2 ~KvvlvGd~~VGKTsli~r~~~   23 (162)
T cd04138           2 YKLVVVGAGGVGKSALTIQLIQ   23 (162)
T ss_pred             EEEEEECCCCCCHHHHHHHHHH
T ss_conf             3999989999889999999983


No 353
>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=75.84  E-value=3.2  Score=20.32  Aligned_cols=24  Identities=29%  Similarity=0.466  Sum_probs=20.9

Q ss_pred             CCEEEEEEECCCCCCHHHHHHHHH
Q ss_conf             411247761488678899999999
Q gi|254781187|r   75 PTIFKCAISAGRGIGKTTLNAWMM   98 (367)
Q Consensus        75 ~~~~~~~v~sgrg~GKS~~~a~~~   98 (367)
                      ...||+.+.+..|+|||.++-.++
T Consensus         4 d~~~KIvlvGd~~VGKTSli~r~~   27 (199)
T cd04110           4 DHLFKLLIIGDSGVGKSSLLLRFA   27 (199)
T ss_pred             CEEEEEEEECCCCCCHHHHHHHHH
T ss_conf             757799999979988899999995


No 354
>PRK06820 type III secretion system ATPase; Validated
Probab=75.84  E-value=4.3  Score=19.57  Aligned_cols=35  Identities=23%  Similarity=0.302  Sum_probs=24.0

Q ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHH
Q ss_conf             4776148867889999999999997089977999715379
Q gi|254781187|r   79 KCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSET  118 (367)
Q Consensus        79 ~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~  118 (367)
                      |+.|-+|+|+|||++.+.++.+     -...++|.+--..
T Consensus       165 R~gIfgg~GvGKT~Ll~~i~~~-----~~adv~V~~~IGe  199 (445)
T PRK06820        165 RIGIFAAAGVGKSTLLSMLCAD-----SAADVMVLALIGE  199 (445)
T ss_pred             CCEEECCCCCCCCHHHHHHHHH-----CCCCEEEEEEEEE
T ss_conf             4211068999812234456530-----6788799998744


No 355
>PRK07196 fliI flagellum-specific ATP synthase; Validated
Probab=75.65  E-value=5.5  Score=18.87  Aligned_cols=38  Identities=16%  Similarity=0.365  Sum_probs=25.8

Q ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHH
Q ss_conf             4776148867889999999999997089977999715379999
Q gi|254781187|r   79 KCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLK  121 (367)
Q Consensus        79 ~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~  121 (367)
                      |+.|-+|.|+|||++.++++-.     ....++|.+--...-+
T Consensus       157 RigIfggsGvGKs~Ll~~I~r~-----~~advvVi~lIGeRgr  194 (434)
T PRK07196        157 RVGLMAGSGVGKSVLLGMITRY-----TQADVVVVGLIGERGR  194 (434)
T ss_pred             EEEECCCCCCCHHHHHHHHHHH-----HCCCEEEEEECCEEHH
T ss_conf             4210147899789999999897-----3799899974222349


No 356
>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=75.63  E-value=2.5  Score=21.05  Aligned_cols=23  Identities=26%  Similarity=0.307  Sum_probs=19.2

Q ss_pred             EEEEECCCCCCHHHHHHHHHHHH
Q ss_conf             47761488678899999999999
Q gi|254781187|r   79 KCAISAGRGIGKTTLNAWMMLWL  101 (367)
Q Consensus        79 ~~~v~sgrg~GKS~~~a~~~lw~  101 (367)
                      =+|+.++-|.|||+++|.+-..+
T Consensus       561 vvALVGPsGsGKStvaaLL~n~Y  583 (770)
T TIGR00958       561 VVALVGPSGSGKSTVAALLQNLY  583 (770)
T ss_pred             EEEEECCCCCCHHHHHHHHHHCC
T ss_conf             59986589983999999998557


No 357
>CHL00059 atpA ATP synthase CF1 alpha subunit
Probab=75.58  E-value=5.6  Score=18.86  Aligned_cols=22  Identities=27%  Similarity=0.252  Sum_probs=17.9

Q ss_pred             EEEEECCCCCCHHHHHHHHHHH
Q ss_conf             4776148867889999999999
Q gi|254781187|r   79 KCAISAGRGIGKTTLNAWMMLW  100 (367)
Q Consensus        79 ~~~v~sgrg~GKS~~~a~~~lw  100 (367)
                      |..|-++||+|||+++.-.++-
T Consensus       165 R~lI~Gd~gvGKTtl~~d~Iin  186 (501)
T CHL00059        165 RELIIGDRQTGKTAVATDTILN  186 (501)
T ss_pred             EEEEECCCCCCHHHHHHHHHHH
T ss_conf             6677557884477999999985


No 358
>cd01866 Rab2 Rab2 subfamily.  Rab2 is localized on cis-Golgi membranes and interacts with Golgi matrix proteins. Rab2 is also implicated in the maturation of vesicular tubular clusters (VTCs), which are microtubule-associated intermediates in transport between the ER and Golgi apparatus. In plants, Rab2 regulates vesicle trafficking between the ER and the Golgi bodies and is important to pollen tube growth.  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 featur
Probab=75.56  E-value=3.2  Score=20.31  Aligned_cols=23  Identities=30%  Similarity=0.450  Sum_probs=20.3

Q ss_pred             CEEEEEEECCCCCCHHHHHHHHH
Q ss_conf             11247761488678899999999
Q gi|254781187|r   76 TIFKCAISAGRGIGKTTLNAWMM   98 (367)
Q Consensus        76 ~~~~~~v~sgrg~GKS~~~a~~~   98 (367)
                      +.||+.+.+..|+|||.++..++
T Consensus         3 y~~KivlvGd~~VGKTsli~r~~   25 (168)
T cd01866           3 YLFKYIIIGDTGVGKSCLLLQFT   25 (168)
T ss_pred             EEEEEEEECCCCCCHHHHHHHHH
T ss_conf             88899999989978899999991


No 359
>pfam07728 AAA_5 AAA domain (dynein-related subfamily). This Pfam entry includes some of the AAA proteins not detected by the pfam00004 model.
Probab=75.49  E-value=5.6  Score=18.85  Aligned_cols=25  Identities=20%  Similarity=0.201  Sum_probs=20.4

Q ss_pred             CEEEEECCCCCCHHHHHHHHHHHHC
Q ss_conf             2899975455998899998987406
Q gi|254781187|r  193 MAVFNDEASGTPDIINKSILGFFTE  217 (367)
Q Consensus       193 ~l~ivDEAsgI~d~i~e~i~g~Lt~  217 (367)
                      -.+++||....+..+..++...|-+
T Consensus        68 ~vl~lDEin~a~~~v~~~L~~~le~   92 (139)
T pfam07728        68 EIAVLDEINRANPDVLNSLLSLLDE   92 (139)
T ss_pred             CEEEECCHHHCCHHHHHHHHHHHCC
T ss_conf             6899634344899999999999748


No 360
>PRK07324 transaminase; Validated
Probab=75.46  E-value=5.6  Score=18.84  Aligned_cols=60  Identities=23%  Similarity=0.231  Sum_probs=39.0

Q ss_pred             HHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHH
Q ss_conf             899999998888751245555541124776148867889999999999997089977999715379999999
Q gi|254781187|r   53 RWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLKNTL  124 (367)
Q Consensus        53 ~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~~~l  124 (367)
                      +.--++-++|+..-+ +...+     ++.|.+|      ...|..++-.+++.||-.|++..|++.+...+.
T Consensus        62 ~G~~~LR~~Ia~~y~-~v~~d-----~IlvT~G------a~~Al~l~~~~l~~pGD~Viv~~P~Y~~~~~~~  121 (373)
T PRK07324         62 EGSPEFKEAVASLYQ-NVKPD-----NILQTNG------ATGANHLVLYALIEPGDHVISVYPTYQQLYDIP  121 (373)
T ss_pred             CCCHHHHHHHHHHHC-CCCHH-----HEEECCC------HHHHHHHHHHHHCCCCCEEEECCCCCHHHHHHH
T ss_conf             898999999999866-99867-----8898687------899999999997599998998899857799999


No 361
>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=75.44  E-value=3.4  Score=20.15  Aligned_cols=23  Identities=22%  Similarity=0.476  Sum_probs=20.5

Q ss_pred             CEEEEEEECCCCCCHHHHHHHHH
Q ss_conf             11247761488678899999999
Q gi|254781187|r   76 TIFKCAISAGRGIGKTTLNAWMM   98 (367)
Q Consensus        76 ~~~~~~v~sgrg~GKS~~~a~~~   98 (367)
                      .++|+.|.+..|+|||.++..++
T Consensus         4 ~~~KivvlGd~~VGKTsli~r~~   26 (170)
T cd04116           4 SLLKVILLGDGGVGKSSLMNRYV   26 (170)
T ss_pred             EEEEEEEECCCCCCHHHHHHHHH
T ss_conf             08999999999978999999997


No 362
>smart00175 RAB Rab subfamily of small GTPases. Rab GTPases are implicated in vesicle trafficking.
Probab=75.41  E-value=2.9  Score=20.62  Aligned_cols=21  Identities=29%  Similarity=0.536  Sum_probs=18.8

Q ss_pred             EEEEEECCCCCCHHHHHHHHH
Q ss_conf             247761488678899999999
Q gi|254781187|r   78 FKCAISAGRGIGKTTLNAWMM   98 (367)
Q Consensus        78 ~~~~v~sgrg~GKS~~~a~~~   98 (367)
                      ||+.|.+..|+|||.++..++
T Consensus         1 ~Ki~vvG~~~vGKTsli~r~~   21 (164)
T smart00175        1 FKIILIGDSGVGKSSLLSRFT   21 (164)
T ss_pred             CEEEEECCCCCCHHHHHHHHH
T ss_conf             989999989977999999994


No 363
>PRK06315 type III secretion system ATPase; Provisional
Probab=75.17  E-value=2.6  Score=20.93  Aligned_cols=22  Identities=32%  Similarity=0.466  Sum_probs=19.5

Q ss_pred             EEEEECCCCCCHHHHHHHHHHH
Q ss_conf             4776148867889999999999
Q gi|254781187|r   79 KCAISAGRGIGKTTLNAWMMLW  100 (367)
Q Consensus        79 ~~~v~sgrg~GKS~~~a~~~lw  100 (367)
                      |+.|-+|+|+|||++.++++..
T Consensus       166 R~gIfagsGvGKs~Ll~~i~~~  187 (442)
T PRK06315        166 RIGIFAGAGVGKSSLLGMIARN  187 (442)
T ss_pred             EEECCCCCCCCHHHHHHHHHHH
T ss_conf             7640389999888999999974


No 364
>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=75.10  E-value=4.1  Score=19.67  Aligned_cols=24  Identities=29%  Similarity=0.452  Sum_probs=20.6

Q ss_pred             CCEEEEEEECCCCCCHHHHHHHHH
Q ss_conf             411247761488678899999999
Q gi|254781187|r   75 PTIFKCAISAGRGIGKTTLNAWMM   98 (367)
Q Consensus        75 ~~~~~~~v~sgrg~GKS~~~a~~~   98 (367)
                      ...||+.+.+..|+|||.++..++
T Consensus         5 d~~~KivllGd~~VGKTsli~r~~   28 (169)
T cd04114           5 DFLFKIVLIGNAGVGKTCLVRRFT   28 (169)
T ss_pred             CEEEEEEEECCCCCCHHHHHHHHH
T ss_conf             779899999989979999999998


No 365
>PRK11331 5-methylcytosine-specific restriction enzyme subunit McrB; Provisional
Probab=75.09  E-value=5.7  Score=18.79  Aligned_cols=40  Identities=15%  Similarity=0.233  Sum_probs=30.7

Q ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEE--CCCHH
Q ss_conf             47761488678899999999999970899779997--15379
Q gi|254781187|r   79 KCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICI--ANSET  118 (367)
Q Consensus        79 ~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~--A~t~~  118 (367)
                      .+...+.-|+|||+++-+++-+.+....+.++..+  .|+++
T Consensus       196 nvIL~G~pGtGKT~lAk~lA~~l~g~~~~~rv~~Vqfhpsys  237 (459)
T PRK11331        196 NIILQGPPGVGKTFVARRLAYLLTGEKAPQRVNMVQFHQSYS  237 (459)
T ss_pred             CEEEECCCCCCHHHHHHHHHHHHHCCCCCCCEEEEEECCCCC
T ss_conf             279658999887899999999970788778468998358866


No 366
>pfam00735 Septin Septin. Members of this family include CDC3, CDC10, CDC11 and CDC12/Septin. Members of this family bind GTP. As regards the septins, these are polypeptides of 30-65kDa with three characteristic GTPase motifs (G-1, G-3 and G-4) that are similar to those of the Ras family. The G-4 motif is strictly conserved with a unique septin consensus of AKAD. Most septins are thought to have at least one coiled-coil region, which in some cases is necessary for intermolecular interactions that allow septins to polymerize to form rod-shaped complexes. In turn, these are arranged into tandem arrays to form filaments. They are multifunctional proteins, with roles in cytokinesis, sporulation, germ cell development, exocytosis and apoptosis.
Probab=74.82  E-value=3.3  Score=20.26  Aligned_cols=23  Identities=35%  Similarity=0.475  Sum_probs=19.2

Q ss_pred             EEEEEEECCCCCCHHHHHHHHHH
Q ss_conf             12477614886788999999999
Q gi|254781187|r   77 IFKCAISAGRGIGKTTLNAWMML   99 (367)
Q Consensus        77 ~~~~~v~sgrg~GKS~~~a~~~l   99 (367)
                      -|.+-|++.+|+|||+++--+.-
T Consensus         4 ~fnimvvG~sGlGKTTfiNtL~~   26 (280)
T pfam00735         4 DFTLMVVGESGLGKTTLINTLFL   26 (280)
T ss_pred             EEEEEEECCCCCCHHHHHHHHHC
T ss_conf             78999977999978999999857


No 367
>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=74.81  E-value=3.3  Score=20.23  Aligned_cols=22  Identities=23%  Similarity=0.522  Sum_probs=19.2

Q ss_pred             EEEEEECCCCCCHHHHHHHHHH
Q ss_conf             2477614886788999999999
Q gi|254781187|r   78 FKCAISAGRGIGKTTLNAWMML   99 (367)
Q Consensus        78 ~~~~v~sgrg~GKS~~~a~~~l   99 (367)
                      ||+.+.+..|+|||.++..++-
T Consensus         2 fKivllGd~~VGKTsli~r~~~   23 (163)
T cd04136           2 YKVVVLGSGGVGKSALTVQFVQ   23 (163)
T ss_pred             EEEEEECCCCCCHHHHHHHHHH
T ss_conf             1999989999889999999971


No 368
>KOG0920 consensus
Probab=74.80  E-value=5.8  Score=18.74  Aligned_cols=186  Identities=19%  Similarity=0.156  Sum_probs=89.0

Q ss_pred             HHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHH-HHCCCCEEEEECCCHHHHHHHHHHHHHHH
Q ss_conf             89999999888875124555554112477614886788999999999999-70899779997153799999999999999
Q gi|254781187|r   53 RWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLI-STRPGMSIICIANSETQLKNTLWAEVSKW  131 (367)
Q Consensus        53 ~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~-~~~~~~~v~~~A~t~~Q~~~~lw~ei~k~  131 (367)
                      +-++++|..|.++.            -+.|++..|.|||+-+--+++-.. ...+.++|+||-|-.-.|-.+ -..+++-
T Consensus       176 ~~r~~Il~~i~~~q------------VvvIsGeTGcGKtTQvpQfiLd~~~~~~~~~~IicTQPRRIsAIsv-AeRVa~E  242 (924)
T KOG0920         176 KMRDTILDAIEENQ------------VVVISGETGCGKTTQVPQFILDEAIESGAACNIICTQPRRISAISV-AERVAKE  242 (924)
T ss_pred             HHHHHHHHHHHHCC------------EEEEECCCCCCCHHHHHHHHHHHHHHCCCCCEEEECCCCHHHHHHH-HHHHHHH
T ss_conf             78999999997496------------6999578898712246699999998628997388667751778999-9999887


Q ss_pred             HHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC-CEEEEECCCCCCCCCCCCCCCCCCCCEEEEECCC--CCCHHHH
Q ss_conf             986231211233332100012333221111345776-1266210135445565210113586289997545--5998899
Q gi|254781187|r  132 LSMLPHRHWFEMQSLSLHPSGWYAELLEQSMGIDSK-HYTITCRTYSEERPDTFVGPHNTHGMAVFNDEAS--GTPDIIN  208 (367)
Q Consensus       132 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~a~~~~~~~~ea~~g~h~~~~~l~ivDEAs--gI~d~i~  208 (367)
                      ....+.           ....|-.... ........ ....++...+....+  ..  ..+...+|+||..  .+..+..
T Consensus       243 R~~~~g-----------~~VGYqvrl~-~~~s~~t~L~fcTtGvLLr~L~~~--~~--l~~~thiivDEVHER~i~~Dfl  306 (924)
T KOG0920         243 RGESLG-----------EEVGYQVRLE-SKRSRETRLLFCTTGVLLRRLQSD--PT--LSGVTHIIVDEVHERSINTDFL  306 (924)
T ss_pred             HCCCCC-----------CEEEEEEEEE-CCCCCCEEEEEECHHHHHHHHCCC--CC--CCCCCEEEEEEEEECCCCCCCH
T ss_conf             546668-----------7136898620-136775168984068999875468--62--1458665442279716775217


Q ss_pred             HHHHHHHHCCCCCEEEEEEECCCCCCCHHHHHHHCCCCCEEEEEECCCCCCCCCHHHHHHHHHHC
Q ss_conf             99898740698825899980789998768875411223504675233328888988999999621
Q gi|254781187|r  209 KSILGFFTELNPNRFWIMTSNTRRLNGWFYDIFNIPLEDWKRYQIDTRTVEGIDSGFHEGIISRY  273 (367)
Q Consensus       209 e~i~g~Lt~~~~~~~~i~igNP~r~~g~Fye~~~~~~~~w~~~~~~~~d~p~~~~~~i~~~~~~~  273 (367)
                      -.+.--+-..+.....++.| -|-+.-.|-+-|.    .-.+++++.+.-| +..-++++..+..
T Consensus       307 Li~lk~lL~~~p~LkvILMS-AT~dae~fs~YF~----~~pvi~i~grtfp-V~~~fLEDil~~~  365 (924)
T KOG0920         307 LILLKDLLPRNPDLKVILMS-ATLDAELFSDYFG----GCPVITIPGRTFP-VKEYFLEDILSKT  365 (924)
T ss_pred             HHHHHHHHHHCCCCEEEEEE-EECCHHHHHHHHC----CCCEEEECCCCCC-HHHHHHHHHHHHH
T ss_conf             99999886228885699862-1126288898718----9935864687864-5887899999875


No 369
>PRK00081 coaE dephospho-CoA kinase; Reviewed
Probab=74.59  E-value=3.1  Score=20.39  Aligned_cols=31  Identities=23%  Similarity=0.392  Sum_probs=24.0

Q ss_pred             EEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEE
Q ss_conf             1247761488678899999999999970899779997
Q gi|254781187|r   77 IFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICI  113 (367)
Q Consensus        77 ~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~  113 (367)
                      |..+.|.+|-|+|||+++..+--      .|..++..
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 370
>PRK04863 mukB cell division protein MukB; Provisional
Probab=74.59  E-value=4.1  Score=19.70  Aligned_cols=36  Identities=25%  Similarity=0.392  Sum_probs=27.4

Q ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCH
Q ss_conf             477614886788999999999999708997799971537
Q gi|254781187|r   79 KCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSE  117 (367)
Q Consensus        79 ~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~  117 (367)
                      =++.++|.|.|||+++++++.-   .-||.+-+-..||.
T Consensus        29 VttLsGgNGAGKSTtMaAf~ta---LIPD~tlLhfrntt   64 (1486)
T PRK04863         29 VTTLSGGNGAGKSTTMAAFVTA---LIPDLTLLHFRNTT   64 (1486)
T ss_pred             EEEEECCCCCCHHHHHHHHHHH---HCCCCCEEECCCCC
T ss_conf             0330058886579899999999---67643023114666


No 371
>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=74.52  E-value=3.2  Score=20.32  Aligned_cols=21  Identities=24%  Similarity=0.423  Sum_probs=18.7

Q ss_pred             EEEEEECCCCCCHHHHHHHHH
Q ss_conf             247761488678899999999
Q gi|254781187|r   78 FKCAISAGRGIGKTTLNAWMM   98 (367)
Q Consensus        78 ~~~~v~sgrg~GKS~~~a~~~   98 (367)
                      ||+.+.+..|+|||.++-.++
T Consensus         1 fKvvllGd~gVGKTsLi~rf~   21 (201)
T cd04107           1 LKVLVIGDLGVGKTSIIKRYV   21 (201)
T ss_pred             CEEEEECCCCCCHHHHHHHHH
T ss_conf             979999999978999999998


No 372
>PRK07261 topology modulation protein; Provisional
Probab=74.47  E-value=3.3  Score=20.28  Aligned_cols=22  Identities=36%  Similarity=0.383  Sum_probs=19.0

Q ss_pred             EEEEECCCCCCHHHHHHHHHHH
Q ss_conf             4776148867889999999999
Q gi|254781187|r   79 KCAISAGRGIGKTTLNAWMMLW  100 (367)
Q Consensus        79 ~~~v~sgrg~GKS~~~a~~~lw  100 (367)
                      |+.|-++=|+|||+++..+.--
T Consensus         2 rI~IiG~sGsGKSTlAr~L~~~   23 (171)
T PRK07261          2 KIAIIGYSGSGKSTLARFLGQH   23 (171)
T ss_pred             EEEEECCCCCCHHHHHHHHHHH
T ss_conf             8999889998689999999998


No 373
>PRK13705 plasmid-partitioning protein SopA; Provisional
Probab=74.44  E-value=6  Score=18.68  Aligned_cols=87  Identities=10%  Similarity=0.090  Sum_probs=45.6

Q ss_pred             CCCCCHHHHHHHHHCCCCCCCCCCCCCCC---HH-HHHHHHHHHHHHHHCCCCCCCCCEE-EEEEEC-CCCCCHHHHHHH
Q ss_conf             01259888855430146688844366684---28-9999999888875124555554112-477614-886788999999
Q gi|254781187|r   23 ECVLSFKNFVMRFFPWGIKGKPLEHFSQP---HR-WQLEFMEAVDVHCHSNVNNSNPTIF-KCAISA-GRGIGKTTLNAW   96 (367)
Q Consensus        23 ~~~~~~~~f~~~~~~w~~~~~~~~~~~~p---~~-wq~~~l~~~~~~~~~~~~~~~~~~~-~~~v~s-grg~GKS~~~a~   96 (367)
                      .+..+   +++-...-|.+-.|.....|-   |. |-.+-+.++.+.+.....+...+.. -+||+- ==|+|||+.+..
T Consensus        50 gvs~~---~lr~~~~~g~~P~p~~~~~gr~~~R~~Ytl~~i~~lR~~~~~~p~R~~g~~~~VIAVaNqKGGvGKTTTavn  126 (388)
T PRK13705         50 GVSSQ---AIRDAEKAGRLPHPDMEMRGRVEQRVGYTIEQINHMRDVFGTRLRRAEDEFPPVIGVAAHKGGVYKTSVSVH  126 (388)
T ss_pred             CCCHH---HHHHHHHCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHCCCCCCCCCCCCEEEEEECCCCCCCHHHHHHH
T ss_conf             99999---999786468999997687776554551069999999999643889999998728999527888559999999


Q ss_pred             HHHHHHHHCCCCEEEEEC
Q ss_conf             999999708997799971
Q gi|254781187|r   97 MMLWLISTRPGMSIICIA  114 (367)
Q Consensus        97 ~~lw~~~~~~~~~v~~~A  114 (367)
                      ++-.++.  .|.||+++=
T Consensus       127 LA~~LAl--~G~RVLlID  142 (388)
T PRK13705        127 LAQDLAL--KGLRVLLVE  142 (388)
T ss_pred             HHHHHHH--CCCEEEEEE
T ss_conf             9999997--799089995


No 374
>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=74.43  E-value=2  Score=21.65  Aligned_cols=233  Identities=11%  Similarity=0.005  Sum_probs=103.2

Q ss_pred             HHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCC-CE-EEE--ECCCHHHHHHHHHHHHHH
Q ss_conf             99999988887512455555411247761488678899999999999970899-77-999--715379999999999999
Q gi|254781187|r   55 QLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPG-MS-IIC--IANSETQLKNTLWAEVSK  130 (367)
Q Consensus        55 q~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~-~~-v~~--~A~t~~Q~~~~lw~ei~k  130 (367)
                      +..+|..+.=+.+.|.        =+||.++=|.|||+|..+++---.---.. .. |++  ..-..++.+.+. +.+.+
T Consensus        44 ~K~lL~~vSG~a~~Ge--------LlA~mGsSGAGKTTLmn~La~R~~~g~~~~g~~v~lNG~~~~~~~~~~~s-aYvqQ  114 (671)
T TIGR00955        44 RKHLLKNVSGVAKPGE--------LLAIMGSSGAGKTTLMNALAFRSPKGLKVSGSVVLLNGRPIDAKEMRAIS-AYVQQ  114 (671)
T ss_pred             CHHHHHCCCEEECCCE--------EEEEECCCCCCHHHHHHHHHCCCCCCCEECCCEEEECCEECCHHHHHHHH-CHHEE
T ss_conf             2011103520210670--------68984787662689999985337478614683678758375868998540-12201


Q ss_pred             ---HHHHCCCCCCCCCCCCCCCCCCCCCCCCC-----------------CCCCCCCCCEEEEECCCCCCCCCCCCCCCCC
Q ss_conf             ---99862312112333321000123332211-----------------1134577612662101354455652101135
Q gi|254781187|r  131 ---WLSMLPHRHWFEMQSLSLHPSGWYAELLE-----------------QSMGIDSKHYTITCRTYSEERPDTFVGPHNT  190 (367)
Q Consensus       131 ---~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-----------------~~~~~~~~~~~~~a~~~~~~~~ea~~g~h~~  190 (367)
                         .+..+=....+..++.-+-.+-......+                 ....+.+|..-..+-+-++--+=|..-+  .
T Consensus       115 ~Dlf~~~LTv~E~L~f~A~lRm~~~~~~~~~k~~rV~~vl~~l~L~~ca~T~IG~pg~~KGlSGGErKRLafA~E~l--t  192 (671)
T TIGR00955       115 DDLFIPTLTVREHLMFQAHLRMKRRVTKKHEKRERVDEVLQALGLRKCADTRIGIPGRVKGLSGGERKRLAFASELL--T  192 (671)
T ss_pred             HHHCCCCCCHHEEEEEEEEEECCCCCCHHHHHHHHHHHHHHHHCCHHHHCCCCCCCCCEEEECCCHHHHHHHHHHHH--H
T ss_conf             10048851030000101223347667605799999999998604211211343799964552011367899887887--1


Q ss_pred             CCCEEEEEC-CCCCCH----HHHHHHHHHHHCCCCCEEEEEEECCCCCCCHHHHHHHCC----CC-------------CE
Q ss_conf             862899975-455998----899998987406988258999807899987688754112----23-------------50
Q gi|254781187|r  191 HGMAVFNDE-ASGTPD----IINKSILGFFTELNPNRFWIMTSNTRRLNGWFYDIFNIP----LE-------------DW  248 (367)
Q Consensus       191 ~~~l~ivDE-AsgI~d----~i~e~i~g~Lt~~~~~~~~i~igNP~r~~g~Fye~~~~~----~~-------------~w  248 (367)
                      ++.++++|| -||.|-    .+-.++. .|+..|+ ++.+.|=.|.   ...|+.|.+=    .+             .+
T Consensus       193 dP~~LFcDEPTSGLDSfmA~~Vv~~L~-~LA~~G~-tiI~tIHQPS---s~lF~lFd~i~lla~Grvvy~G~p~~a~~FF  267 (671)
T TIGR00955       193 DPIILFCDEPTSGLDSFMAYSVVQVLK-GLAQKGK-TIICTIHQPS---SELFELFDKIILLAEGRVVYLGSPDQAVPFF  267 (671)
T ss_pred             CCCEEEECCCCCHHHHHHHHHHHHHHH-HHHCCCC-EEEEEEECCC---HHHHHHHCCEEEEECCEEEEECCCHHHHHHH
T ss_conf             894265038895345999999999999-9850897-9999830561---8898511716775277279827810368989


Q ss_pred             EEEE--ECCCCCCCCCHHHHHHHHHHCCCCCCE-EEEEEEEEECCCCCCEEECHHHHHHH
Q ss_conf             4675--233328888988999999621688000-26888644327789807829998644
Q gi|254781187|r  249 KRYQ--IDTRTVEGIDSGFHEGIISRYGLDSDV-ARIEILGQFPQQEVNNFIPHNYIEEA  305 (367)
Q Consensus       249 ~~~~--~~~~d~p~~~~~~i~~~~~~~gedS~~-~r~ev~G~Fp~~~~d~~ip~~~ie~a  305 (367)
                      ..+-  ..+..+ +.+.||+.+..+.-..+... -|.+..... +.....-+..+.....
T Consensus       268 ~~~Gpd~~cP~~-yNPADF~~~~la~~p~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~  325 (671)
T TIGR00955       268 SELGPDFPCPEN-YNPADFYLQVLAVIPGSENERSRETIEKIC-DAFAVSDIGRSMLVNT  325 (671)
T ss_pred             HHCCCCCCCCCC-CCCHHHHHHHHHCCCCCCHHHHHHHHHHHH-HHHHCCHHHHHHHHHH
T ss_conf             844888789788-888889999973155520034799999998-7651450246789988


No 375
>KOG1133 consensus
Probab=74.32  E-value=6  Score=18.67  Aligned_cols=47  Identities=17%  Similarity=0.167  Sum_probs=34.5

Q ss_pred             CCHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHH-HHHHHHHHHHH
Q ss_conf             84289999999888875124555554112477614886788999-99999999970
Q gi|254781187|r   50 QPHRWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTL-NAWMMLWLIST  104 (367)
Q Consensus        50 ~p~~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~-~a~~~lw~~~~  104 (367)
                      .|-..|.+++++++-.+..+..        -..-|+.|+|||-. +++.+-|+-..
T Consensus        15 ~PYdIQ~~lM~elyrvLe~GkI--------gIfESPTGTGKSLSLiCaaltWL~~~   62 (821)
T KOG1133          15 TPYDIQEDLMRELYRVLEEGKI--------GIFESPTGTGKSLSLICAALTWLRDF   62 (821)
T ss_pred             CCHHHHHHHHHHHHHHHHCCCE--------EEEECCCCCCCHHHHHHHHHHHHHHH
T ss_conf             8236999999999999853762--------46757998881178999898998876


No 376
>PRK09265 aminotransferase AlaT; Validated
Probab=74.30  E-value=6  Score=18.66  Aligned_cols=61  Identities=10%  Similarity=-0.006  Sum_probs=38.3

Q ss_pred             CHHHHHHHHHHHHHHHHCCCC-CCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHH
Q ss_conf             428999999988887512455-555411247761488678899999999999970899779997153799
Q gi|254781187|r   51 PHRWQLEFMEAVDVHCHSNVN-NSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQ  119 (367)
Q Consensus        51 p~~wq~~~l~~~~~~~~~~~~-~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q  119 (367)
                      |...-.++-++|+++.++... ...|+  ++.|..    |-+.  |...+-.++++||-.|++-+|.+..
T Consensus        70 ~~~G~~eLReaIA~~~~~~~~~~~~p~--~I~vT~----Ga~~--al~~~~~all~pGDeVlvp~P~Yp~  131 (404)
T PRK09265         70 DSKGLFSARKAIMQYYQQKGIPDVDVD--DIYIGN----GVSE--LIVMAMQALLNNGDEVLVPAPDYPL  131 (404)
T ss_pred             CCCCCHHHHHHHHHHHHHHCCCCCCHH--HEEECC----CHHH--HHHHHHHHHCCCCCEEEEECCCCCH
T ss_conf             888889999999999997569998889--978758----8899--9999999964998989994688730


No 377
>PRK06936 type III secretion system ATPase; Provisional
Probab=74.10  E-value=6.1  Score=18.63  Aligned_cols=36  Identities=25%  Similarity=0.228  Sum_probs=24.7

Q ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHH
Q ss_conf             47761488678899999999999970899779997153799
Q gi|254781187|r   79 KCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQ  119 (367)
Q Consensus        79 ~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q  119 (367)
                      |+.|-+|.|+|||++.++++..   +..+  ++|.+--...
T Consensus       164 R~gIfagsGvGKs~Ll~~i~r~---~~ad--v~V~alIGER  199 (439)
T PRK06936        164 RMGIFAAAGGGKSTLLASLIRS---AEVD--VTVLALIGER  199 (439)
T ss_pred             EEECCCCCCCCHHHHHHHHHHH---HCCC--CEEEEEECCC
T ss_conf             0102369999889999999764---3269--5799980730


No 378
>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=74.04  E-value=3.9  Score=19.81  Aligned_cols=23  Identities=22%  Similarity=0.254  Sum_probs=19.9

Q ss_pred             CEEEEEEECCCCCCHHHHHHHHH
Q ss_conf             11247761488678899999999
Q gi|254781187|r   76 TIFKCAISAGRGIGKTTLNAWMM   98 (367)
Q Consensus        76 ~~~~~~v~sgrg~GKS~~~a~~~   98 (367)
                      +.+|+.|.+..|+|||.++..++
T Consensus         3 ~~~KivvvGd~~VGKTsli~r~~   25 (180)
T cd04127           3 YLIKFLALGDSGVGKTSFLYQYT   25 (180)
T ss_pred             EEEEEEEECCCCCCHHHHHHHHH
T ss_conf             78899999999988899999996


No 379
>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=73.99  E-value=6.1  Score=18.62  Aligned_cols=41  Identities=24%  Similarity=0.478  Sum_probs=25.9

Q ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEE-ECCCHHHHHH
Q ss_conf             4776148867889999999999997089977999-7153799999
Q gi|254781187|r   79 KCAISAGRGIGKTTLNAWMMLWLISTRPGMSIIC-IANSETQLKN  122 (367)
Q Consensus        79 ~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~-~A~t~~Q~~~  122 (367)
                      |+.+-+|.|+|||++.++++-+-   ..+..|++ +....+.+++
T Consensus       139 RigIfag~GvGKt~Ll~~ia~~~---~adv~Vi~liGERgrEv~e  180 (413)
T TIGR03497       139 RVGIFAGSGVGKSTLLGMIARNA---KADINVIALIGERGREVRD  180 (413)
T ss_pred             EEEECCCCCCCHHHHHHHHHHHH---CCCCCEEEEEEEECHHHHH
T ss_conf             44210589987769999999874---3785238886332289999


No 380
>PRK13768 GTPase; Provisional
Probab=73.87  E-value=6.2  Score=18.60  Aligned_cols=36  Identities=25%  Similarity=0.340  Sum_probs=27.7

Q ss_pred             EEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEE
Q ss_conf             247761488678899999999999970899779997
Q gi|254781187|r   78 FKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICI  113 (367)
Q Consensus        78 ~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~  113 (367)
                      +-+.|.+.-|+|||+..+.+--|.........++=.
T Consensus         3 ~~~~ViGpaGSGKsT~~~~l~~~l~~~~r~~~vvNL   38 (253)
T PRK13768          3 YIVFFLGTAGSGKTTLVGALSDWLEEQGYDVAIVNL   38 (253)
T ss_pred             EEEEEECCCCCCHHHHHHHHHHHHHHCCCCEEEEEC
T ss_conf             189998999998899999999999976997599978


No 381
>PRK13230 nitrogenase reductase-like protein; Reviewed
Probab=73.84  E-value=6.2  Score=18.59  Aligned_cols=35  Identities=26%  Similarity=0.324  Sum_probs=28.2

Q ss_pred             EEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEE
Q ss_conf             1247761488678899999999999970899779997
Q gi|254781187|r   77 IFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICI  113 (367)
Q Consensus        77 ~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~  113 (367)
                      |.++||-.==|+|||+.+..+..-++..  |.||+++
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 382
>COG0572 Udk Uridine kinase [Nucleotide transport and metabolism]
Probab=73.82  E-value=3.2  Score=20.36  Aligned_cols=23  Identities=30%  Similarity=0.413  Sum_probs=18.9

Q ss_pred             EEEEEEECCCCCCHHHHHHHHHH
Q ss_conf             12477614886788999999999
Q gi|254781187|r   77 IFKCAISAGRGIGKTTLNAWMML   99 (367)
Q Consensus        77 ~~~~~v~sgrg~GKS~~~a~~~l   99 (367)
                      ++=+.|++|.|+|||+++-.+.-
T Consensus         8 ~iiIgIaG~SgSGKTTv~~~l~~   30 (218)
T COG0572           8 VIIIGIAGGSGSGKTTVAKELSE   30 (218)
T ss_pred             EEEEEEECCCCCCHHHHHHHHHH
T ss_conf             69999867987788999999999


No 383
>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=73.77  E-value=3.4  Score=20.19  Aligned_cols=22  Identities=32%  Similarity=0.471  Sum_probs=19.0

Q ss_pred             EEEEEECCCCCCHHHHHHHHHH
Q ss_conf             2477614886788999999999
Q gi|254781187|r   78 FKCAISAGRGIGKTTLNAWMML   99 (367)
Q Consensus        78 ~~~~v~sgrg~GKS~~~a~~~l   99 (367)
                      ||+.|.+..|+|||.++..++-
T Consensus         1 ~KivvvGd~~VGKTsli~r~~~   22 (188)
T cd04125           1 FKVVIIGDYGVGKSSLLKRFTE   22 (188)
T ss_pred             CEEEEECCCCCCHHHHHHHHHH
T ss_conf             9799999999789999999951


No 384
>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=73.56  E-value=3.5  Score=20.10  Aligned_cols=22  Identities=27%  Similarity=0.353  Sum_probs=19.2

Q ss_pred             EEEEEECCCCCCHHHHHHHHHH
Q ss_conf             2477614886788999999999
Q gi|254781187|r   78 FKCAISAGRGIGKTTLNAWMML   99 (367)
Q Consensus        78 ~~~~v~sgrg~GKS~~~a~~~l   99 (367)
                      ||++|.+..|+|||.++..++-
T Consensus         1 ~Ki~vvG~~~vGKTsli~r~~~   22 (162)
T cd04123           1 FKVVLLGEGRVGKTSLVLRYVE   22 (162)
T ss_pred             CEEEEECCCCCCHHHHHHHHHH
T ss_conf             9899999999679999999983


No 385
>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=73.45  E-value=3.3  Score=20.25  Aligned_cols=43  Identities=9%  Similarity=0.071  Sum_probs=27.6

Q ss_pred             CCCCCCCCCCCCCCCEEEEEC-CCCCCHH----HHHHHHHHHHCCCCCE
Q ss_conf             455652101135862899975-4559988----9999898740698825
Q gi|254781187|r  179 ERPDTFVGPHNTHGMAVFNDE-ASGTPDI----INKSILGFFTELNPNR  222 (367)
Q Consensus       179 ~~~ea~~g~h~~~~~l~ivDE-AsgI~d~----i~e~i~g~Lt~~~~~~  222 (367)
                      ...-|++|+=+.+...+|+|| .||++..    +.+.|. -|+..++.+
T Consensus       133 kkRvAIAGAvAM~Pd~l~LDEPTAGLDp~G~~q~~~~l~-~L~~~G~tv  180 (190)
T TIGR01166       133 KKRVAIAGAVAMRPDVLLLDEPTAGLDPAGAEQLLAILR-RLRAEGTTV  180 (190)
T ss_pred             HHHHHHHHHHHHCCCEEEEECCCCCCCHHHHHHHHHHHH-HHHHCCCEE
T ss_conf             357777758861663466427888978747999999988-787239989


No 386
>PRK13634 cbiO cobalt transporter ATP-binding subunit; Provisional
Probab=73.41  E-value=0.53  Score=25.14  Aligned_cols=37  Identities=27%  Similarity=0.198  Sum_probs=25.0

Q ss_pred             HHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHH
Q ss_conf             999999888875124555554112477614886788999999999
Q gi|254781187|r   55 QLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMML   99 (367)
Q Consensus        55 q~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~l   99 (367)
                      +.++|++|.=.++.+.        .++|.+..|+|||++.-.+.-
T Consensus         6 e~~AL~~Vsl~i~~Ge--------~vaiiG~sGsGKSTLl~~l~G   42 (276)
T PRK13634          6 ERRALYDVNVSIPSGS--------YVAIIGHTGSGKSTLLQHLNG   42 (276)
T ss_pred             CCEEEECCEEEECCCC--------EEEEECCCCCHHHHHHHHHHC
T ss_conf             7666514477998998--------999999999699999999974


No 387
>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=73.37  E-value=6.3  Score=18.52  Aligned_cols=32  Identities=28%  Similarity=0.478  Sum_probs=22.7

Q ss_pred             EEEECCC-CCCHHHHHHHHHHHHHHHCCCCEEEEE
Q ss_conf             7761488-678899999999999970899779997
Q gi|254781187|r   80 CAISAGR-GIGKTTLNAWMMLWLISTRPGMSIICI  113 (367)
Q Consensus        80 ~~v~sgr-g~GKS~~~a~~~lw~~~~~~~~~v~~~  113 (367)
                      ++|.||. |+|||++++.+++-+...  +.++.+.
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 388
>COG0396 sufC Cysteine desulfurase activator ATPase [Posttranslational modification, protein turnover, chaperones]
Probab=73.29  E-value=2.9  Score=20.63  Aligned_cols=81  Identities=16%  Similarity=0.059  Sum_probs=40.5

Q ss_pred             CCCCCCCCCCCCEEEEECC-CCCCHHHHH-HHH--HHHHCCCCCEEEEEEECCCCCCCHHHHHHHCCCCCEEEEEECCCC
Q ss_conf             6521011358628999754-559988999-989--874069882589998078999876887541122350467523332
Q gi|254781187|r  182 DTFVGPHNTHGMAVFNDEA-SGTPDIINK-SIL--GFFTELNPNRFWIMTSNTRRLNGWFYDIFNIPLEDWKRYQIDTRT  257 (367)
Q Consensus       182 ea~~g~h~~~~~l~ivDEA-sgI~d~i~e-~i~--g~Lt~~~~~~~~i~igNP~r~~g~Fye~~~~~~~~w~~~~~~~~d  257 (367)
                      |-+|-.- -..-++|+||- ||++=+... +..  ..|.+.+.-.+ + | |      +.-+....-..+...+-.+-+-
T Consensus       154 EilQ~~~-lePkl~ILDE~DSGLDIdalk~V~~~i~~lr~~~~~~l-i-I-T------Hy~rll~~i~pD~vhvl~~GrI  223 (251)
T COG0396         154 EILQLLL-LEPKLAILDEPDSGLDIDALKIVAEGINALREEGRGVL-I-I-T------HYQRLLDYIKPDKVHVLYDGRI  223 (251)
T ss_pred             HHHHHHH-CCCCEEEECCCCCCCCHHHHHHHHHHHHHHHCCCCEEE-E-E-E------CHHHHHHHCCCCEEEEEECCEE
T ss_conf             9999984-59988995588767558999999999999865897299-9-9-5------5799984268887999988889


Q ss_pred             CCCCCHHHHHHHHHH
Q ss_conf             888898899999962
Q gi|254781187|r  258 VEGIDSGFHEGIISR  272 (367)
Q Consensus       258 ~p~~~~~~i~~~~~~  272 (367)
                      +-.-+++..++.+++
T Consensus       224 v~sG~~el~~~le~~  238 (251)
T COG0396         224 VKSGDPELAEELEEK  238 (251)
T ss_pred             EECCCHHHHHHHHHH
T ss_conf             832998999999971


No 389
>smart00173 RAS Ras subfamily of RAS small GTPases. Similar in fold and function to the bacterial EF-Tu GTPase. p21Ras couples receptor Tyr kinases and G protein receptors  to protein kinase cascades
Probab=73.29  E-value=3.6  Score=20.03  Aligned_cols=21  Identities=24%  Similarity=0.534  Sum_probs=18.5

Q ss_pred             EEEEEECCCCCCHHHHHHHHH
Q ss_conf             247761488678899999999
Q gi|254781187|r   78 FKCAISAGRGIGKTTLNAWMM   98 (367)
Q Consensus        78 ~~~~v~sgrg~GKS~~~a~~~   98 (367)
                      ||+.|.+..|+|||.++-.++
T Consensus         1 fKiv~vGd~~vGKTsli~r~~   21 (164)
T smart00173        1 YKLVVLGSGGVGKSALTIQFV   21 (164)
T ss_pred             CEEEEECCCCCCHHHHHHHHH
T ss_conf             989999999978999999997


No 390
>COG2805 PilT Tfp pilus assembly protein, pilus retraction ATPase PilT [Cell motility and secretion / Intracellular trafficking and secretion]
Probab=73.28  E-value=6.4  Score=18.51  Aligned_cols=34  Identities=24%  Similarity=0.300  Sum_probs=22.7

Q ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEE
Q ss_conf             47761488678899999999999970899779997
Q gi|254781187|r   79 KCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICI  113 (367)
Q Consensus        79 ~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~  113 (367)
                      -+.|.++.|+|||+..|.++-+.=-+.+ ..|+.+
T Consensus       127 LILVTGpTGSGKSTTlAamId~iN~~~~-~HIlTI  160 (353)
T COG2805         127 LILVTGPTGSGKSTTLAAMIDYINKHKA-KHILTI  160 (353)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHCCCC-CCEEEE
T ss_conf             6998679999678799999999841477-516872


No 391
>cd04113 Rab4 Rab4 subfamily.  Rab4 has been implicated in numerous functions within the cell.  It helps regulate endocytosis through the sorting, recycling, and degradation of early endosomes. Mammalian Rab4 is involved in the regulation of many surface proteins including G-protein-coupled receptors, transferrin receptor, integrins, and surfactant protein A.  Experimental data implicate Rab4 in regulation of the recycling of internalized receptors back to the plasma membrane.  It is also believed to influence receptor-mediated antigen processing in B-lymphocytes, in calcium-dependent exocytosis in platelets, in alpha-amylase secretion in pancreatic cells, and in insulin-induced translocation of Glut4 from internal vesicles to the cell surface. Rab4 is known to share effector proteins with Rab5 and Rab11.  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 p
Probab=73.25  E-value=3.5  Score=20.10  Aligned_cols=21  Identities=33%  Similarity=0.479  Sum_probs=18.8

Q ss_pred             EEEEEECCCCCCHHHHHHHHH
Q ss_conf             247761488678899999999
Q gi|254781187|r   78 FKCAISAGRGIGKTTLNAWMM   98 (367)
Q Consensus        78 ~~~~v~sgrg~GKS~~~a~~~   98 (367)
                      ||+.+.+..|+|||.++..++
T Consensus         1 ~Kivl~Gd~~vGKTsli~r~~   21 (161)
T cd04113           1 FKFIIIGSSGTGKSCLLHRFV   21 (161)
T ss_pred             CEEEEECCCCCCHHHHHHHHH
T ss_conf             989999949967999999997


No 392
>cd04175 Rap1 Rap1 subgroup.  The Rap1 subgroup is part of the Rap subfamily of the Ras family.  It can be further divided into the Rap1a and Rap1b isoforms.  In humans, Rap1a and Rap1b share 95% sequence homology, but are products of two different genes located on chromosomes 1 and 12, respectively.  Rap1a is sometimes called smg p21 or Krev1 in the older literature.  Rap1 proteins are believed to perform different cellular functions, depending on the isoform, its subcellular localization, and the effector proteins it binds.  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 the microsomal membrane of pancreatic acini, as well as in the endocytic compartment of skeletal muscle cells and fibroblasts.  High expression of Rap1 has been observed in the n
Probab=73.21  E-value=3.8  Score=19.88  Aligned_cols=22  Identities=23%  Similarity=0.499  Sum_probs=19.3

Q ss_pred             EEEEEECCCCCCHHHHHHHHHH
Q ss_conf             2477614886788999999999
Q gi|254781187|r   78 FKCAISAGRGIGKTTLNAWMML   99 (367)
Q Consensus        78 ~~~~v~sgrg~GKS~~~a~~~l   99 (367)
                      ||+.+.+..|+|||.++..++-
T Consensus         2 fKIvllGd~~VGKTsli~r~~~   23 (164)
T cd04175           2 YKLVVLGSGGVGKSALTVQFVQ   23 (164)
T ss_pred             EEEEEECCCCCCHHHHHHHHHH
T ss_conf             2999989999759999999970


No 393
>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=73.16  E-value=3  Score=20.49  Aligned_cols=21  Identities=24%  Similarity=0.287  Sum_probs=17.5

Q ss_pred             EEEEECCCCCCHHHHHHHHHHH
Q ss_conf             4776148867889999999999
Q gi|254781187|r   79 KCAISAGRGIGKTTLNAWMMLW  100 (367)
Q Consensus        79 ~~~v~sgrg~GKS~~~a~~~lw  100 (367)
                      ++ |.+..|+|||++++++++=
T Consensus        26 N~-IiGpNGSGKSsIv~AI~lg   46 (213)
T cd03277          26 NM-IIGPNGSGKSSIVCAICLG   46 (213)
T ss_pred             EE-EECCCCCCHHHHHHHHHHH
T ss_conf             79-9889988789999999988


No 394
>COG3421 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=73.13  E-value=6.4  Score=18.49  Aligned_cols=33  Identities=21%  Similarity=0.203  Sum_probs=20.2

Q ss_pred             CCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHH
Q ss_conf             8867889999999999997089977999715379
Q gi|254781187|r   85 GRGIGKTTLNAWMMLWLISTRPGMSIICIANSET  118 (367)
Q Consensus        85 grg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~  118 (367)
                      ..|+|||.++|.+||...--. ..+.+.--|..+
T Consensus         5 atgsgkt~~ma~lil~~y~kg-yr~flffvnq~n   37 (812)
T COG3421           5 ATGSGKTLVMAGLILECYKKG-YRNFLFFVNQAN   37 (812)
T ss_pred             CCCCCHHHHHHHHHHHHHHHC-HHHEEEEECCHH
T ss_conf             358870059999999999734-041899852116


No 395
>KOG0344 consensus
Probab=72.80  E-value=6.5  Score=18.44  Aligned_cols=74  Identities=18%  Similarity=0.213  Sum_probs=48.5

Q ss_pred             CCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCC------CCEEEEECCCHHH
Q ss_conf             3666842899999998888751245555541124776148867889999999999997089------9779997153799
Q gi|254781187|r   46 EHFSQPHRWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRP------GMSIICIANSETQ  119 (367)
Q Consensus        46 ~~~~~p~~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~------~~~v~~~A~t~~Q  119 (367)
                      -.|++|.+-|+.+   |.-.+++         ..+..++.-|.|||.....=++=.+.-+-      +-+.++++|+..-
T Consensus       154 ~~F~~Pt~iq~~a---ipvfl~~---------r~~lAcapTGsgKtlaf~~Pil~~L~~~~~~~~~~gl~a~Il~ptreL  221 (593)
T KOG0344         154 LGFDEPTPIQKQA---IPVFLEK---------RDVLACAPTGSGKTLAFNLPILQHLKDLSQEKHKVGLRALILSPTREL  221 (593)
T ss_pred             CCCCCCCCCCCHH---HHHHHCC---------CCEEEECCCCCCCHHHHHHHHHHHHHHHHCCCCCCCEEEEEECCHHHH
T ss_conf             7888877310011---5666413---------305886357886205655699999987520357654278884444999


Q ss_pred             HHHHHHHHHHHHH
Q ss_conf             9999999999999
Q gi|254781187|r  120 LKNTLWAEVSKWL  132 (367)
Q Consensus       120 ~~~~lw~ei~k~~  132 (367)
                      +.++ ..|..++-
T Consensus       222 a~Qi-~re~~k~~  233 (593)
T KOG0344         222 AAQI-YREMRKYS  233 (593)
T ss_pred             HHHH-HHHHHHCC
T ss_conf             9999-99998557


No 396
>KOG4439 consensus
Probab=72.76  E-value=6.5  Score=18.43  Aligned_cols=138  Identities=17%  Similarity=0.149  Sum_probs=61.8

Q ss_pred             EEECCCCCCHHHHHHHHHHHHHHHCC-------C-CEEEEECCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCC
Q ss_conf             76148867889999999999997089-------9-779997153799999999999999986231211233332100012
Q gi|254781187|r   81 AISAGRGIGKTTLNAWMMLWLISTRP-------G-MSIICIANSETQLKNTLWAEVSKWLSMLPHRHWFEMQSLSLHPSG  152 (367)
Q Consensus        81 ~v~sgrg~GKS~~~a~~~lw~~~~~~-------~-~~v~~~A~t~~Q~~~~lw~ei~k~~~~~~~~~~~~~~~~~~~~~~  152 (367)
                      .++--+|.|||..+-.+++.--..+.       . .+.++++|.. -+ --.-+|+++-++.....         .++. 
T Consensus       349 ILaddmGLGKTlsmislil~qK~~~~~~~~~~~~a~~TLII~PaS-li-~qW~~Ev~~rl~~n~Ls---------V~~~-  416 (901)
T KOG4439         349 ILADDMGLGKTLSMISLILHQKAARKAREKKGESASKTLIICPAS-LI-HQWEAEVARRLEQNALS---------VYLY-  416 (901)
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHHHHHHCCCCCCCCCEEEECCHH-HH-HHHHHHHHHHHHHCCEE---------EEEE-
T ss_conf             502133455306799999988999875414456557728867399-99-98899999998635007---------9986-


Q ss_pred             CCCCCCCCCCCCCC--C-CEEEEECCCCCCCCCCCCCCCCCC-------CCEEEEECCCCCCHHHHHHHHH--HHHCCCC
Q ss_conf             33322111134577--6-126621013544556521011358-------6289997545599889999898--7406988
Q gi|254781187|r  153 WYAELLEQSMGIDS--K-HYTITCRTYSEERPDTFVGPHNTH-------GMAVFNDEASGTPDIINKSILG--FFTELNP  220 (367)
Q Consensus       153 ~~~~~~~~~~~~~~--~-~~~~~a~~~~~~~~ea~~g~h~~~-------~~l~ivDEAsgI~d~i~e~i~g--~Lt~~~~  220 (367)
                        +.-++.++....  . ...++....-...|.+-.+.++..       ..-+|+|||.-|.+.--.....  .|+... 
T Consensus       417 --HG~n~r~i~~~~L~~YDvViTTY~lva~~~~~e~~~~~~~spL~~I~W~RVILDEAH~IrN~~tq~S~AVC~L~a~~-  493 (901)
T KOG4439         417 --HGPNKREISAKELRKYDVVITTYNLVANKPDDELEEGKNSSPLARIAWSRVILDEAHNIRNSNTQCSKAVCKLSAKS-  493 (901)
T ss_pred             --CCCCCCCCCHHHHHHCCEEEEEEECCCCCCCHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHCC-
T ss_conf             --17861547888873256699852110157730333156742777756777534245541366306788988776204-


Q ss_pred             CEEEEEEECCCCCCC
Q ss_conf             258999807899987
Q gi|254781187|r  221 NRFWIMTSNTRRLNG  235 (367)
Q Consensus       221 ~~~~i~igNP~r~~g  235 (367)
                        -||.+|+|-.+..
T Consensus       494 --RWclTGTPiqNn~  506 (901)
T KOG4439         494 --RWCLTGTPIQNNL  506 (901)
T ss_pred             --EEECCCCCCCCCH
T ss_conf             --1331267544441


No 397
>PRK04196 V-type ATP synthase subunit B; Provisional
Probab=72.72  E-value=5.8  Score=18.76  Aligned_cols=45  Identities=13%  Similarity=0.054  Sum_probs=29.4

Q ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHHCCCCE-EEE---ECCCHHHHHHH
Q ss_conf             4776148867889999999999997089977-999---71537999999
Q gi|254781187|r   79 KCAISAGRGIGKTTLNAWMMLWLISTRPGMS-IIC---IANSETQLKNT  123 (367)
Q Consensus        79 ~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~-v~~---~A~t~~Q~~~~  123 (367)
                      |+.|-+|.|+|||.+++.++........+.. ++|   +....+.+.+.
T Consensus       145 r~~If~gsGvgks~l~~~i~~qa~~~~~~~~~~vV~~~iGeR~~E~~e~  193 (460)
T PRK04196        145 KLPIFSGSGLPHNELAAQIARQAKVLGSEEKFAVVFAAMGITFEEANFF  193 (460)
T ss_pred             EEEEECCCCCCCCHHHHHHHHHHHHCCCCCCCEEEEEECCEECHHHHHH
T ss_conf             7655338998811699999998775057888159997320760689999


No 398
>pfam04665 Pox_A32 Poxvirus A32 protein. The A32 protein is thought to be involved in viral DNA packaging.
Probab=72.68  E-value=5.1  Score=19.10  Aligned_cols=43  Identities=26%  Similarity=0.280  Sum_probs=28.7

Q ss_pred             EEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHH
Q ss_conf             247761488678899999999999970899779997153799999
Q gi|254781187|r   78 FKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLKN  122 (367)
Q Consensus        78 ~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~~  122 (367)
                      ||+|+.+|-|+|||+..--+..-+..-.  .-|....|..+.+.+
T Consensus        14 FrmaivGgSGSGKT~yLlsLf~tlv~ky--khIfLfTpv~N~~Yd   56 (241)
T pfam04665        14 FRMAIVGGSGSGKTTYLLSLLRTLVRKF--KHIFLFTPVYNNAYD   56 (241)
T ss_pred             CEEEEEECCCCCHHHHHHHHHHHHHHHH--EEEEEECCCCCCCCC
T ss_conf             3599981588756699999999997741--589996244673236


No 399
>cd04148 RGK RGK subfamily.  The RGK (Rem, Rem2, Rad, Gem/Kir) subfamily of Ras GTPases are expressed in a tissue-specific manner and are dynamically regulated by transcriptional and posttranscriptional mechanisms in response to environmental cues.   RGK proteins bind to the beta subunit of L-type calcium channels, causing functional down-regulation of these voltage-dependent calcium channels, and either termination of calcium-dependent secretion or modulation of electrical conduction and contractile function.  Inhibition of L-type calcium channels by Rem2 may provide a mechanism for modulating calcium-triggered exocytosis in hormone-secreting cells, and has been proposed to influence the secretion of insulin in pancreatic beta cells.  RGK proteins also interact with and inhibit the Rho/Rho kinase pathway to modulate remodeling of the cytoskeleton.  Two characteristics of RGK proteins cited in the literature are N-terminal and C-terminal extensions beyond the GTPase domain typical of Ra
Probab=72.61  E-value=3.6  Score=19.99  Aligned_cols=21  Identities=19%  Similarity=0.539  Sum_probs=18.8

Q ss_pred             EEEEEECCCCCCHHHHHHHHH
Q ss_conf             247761488678899999999
Q gi|254781187|r   78 FKCAISAGRGIGKTTLNAWMM   98 (367)
Q Consensus        78 ~~~~v~sgrg~GKS~~~a~~~   98 (367)
                      ||+.+.+..|+|||.++..++
T Consensus         1 yKVvllGd~gVGKTSLi~rf~   21 (221)
T cd04148           1 YRVVMLGSPGVGKSSLASQFT   21 (221)
T ss_pred             CEEEEECCCCCHHHHHHHHHH
T ss_conf             979999989970999999998


No 400
>COG2256 MGS1 ATPase related to the helicase subunit of the Holliday junction resolvase [DNA replication, recombination, and repair]
Probab=72.60  E-value=6.6  Score=18.41  Aligned_cols=40  Identities=18%  Similarity=0.182  Sum_probs=27.1

Q ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHH
Q ss_conf             477614886788999999999999708997799971537999999
Q gi|254781187|r   79 KCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLKNT  123 (367)
Q Consensus        79 ~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~~~  123 (367)
                      ....=++=|+|||+++..++--     -+..+.-++.+.+.++++
T Consensus        50 SmIl~GPPG~GKTTlA~liA~~-----~~~~f~~~sAv~~gvkdl   89 (436)
T COG2256          50 SMILWGPPGTGKTTLARLIAGT-----TNAAFEALSAVTSGVKDL   89 (436)
T ss_pred             EEEEECCCCCCHHHHHHHHHHH-----HCCCEEEECCCCCCHHHH
T ss_conf             0577789998888999999876-----177669951523467999


No 401
>cd01860 Rab5_related Rab5-related subfamily.  This subfamily includes Rab5 and Rab22 of mammals, Ypt51/Ypt52/Ypt53 of yeast, and RabF of plants. The members of this subfamily are involved in endocytosis and endocytic-sorting pathways.  In mammals, Rab5 GTPases localize to early endosomes and regulate fusion of clathrin-coated vesicles to early endosomes and fusion between early endosomes. In yeast, Ypt51p family members similarly regulate membrane trafficking through prevacuolar compartments. 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 mo
Probab=72.57  E-value=4  Score=19.75  Aligned_cols=22  Identities=23%  Similarity=0.400  Sum_probs=19.4

Q ss_pred             EEEEEECCCCCCHHHHHHHHHH
Q ss_conf             2477614886788999999999
Q gi|254781187|r   78 FKCAISAGRGIGKTTLNAWMML   99 (367)
Q Consensus        78 ~~~~v~sgrg~GKS~~~a~~~l   99 (367)
                      ||+.|.+..|+|||.++..++-
T Consensus         2 ~KivviGd~~vGKTsli~r~~~   23 (163)
T cd01860           2 FKLVLLGDSSVGKSSLVLRFVK   23 (163)
T ss_pred             EEEEEECCCCCCHHHHHHHHHH
T ss_conf             7999999599689999999943


No 402
>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=72.51  E-value=3.8  Score=19.89  Aligned_cols=22  Identities=32%  Similarity=0.478  Sum_probs=19.0

Q ss_pred             EEEEEECCCCCCHHHHHHHHHH
Q ss_conf             2477614886788999999999
Q gi|254781187|r   78 FKCAISAGRGIGKTTLNAWMML   99 (367)
Q Consensus        78 ~~~~v~sgrg~GKS~~~a~~~l   99 (367)
                      +|+.|.+..|+|||.++..++-
T Consensus         1 ~Ki~vvG~~~vGKTsli~~~~~   22 (159)
T cd00154           1 FKIVLIGDSGVGKTSLLLRFVD   22 (159)
T ss_pred             CEEEEECCCCCCHHHHHHHHHH
T ss_conf             9899999699689999999970


No 403
>PRK10751 molybdopterin-guanine dinucleotide biosynthesis protein B; Provisional
Probab=72.37  E-value=6.7  Score=18.38  Aligned_cols=38  Identities=32%  Similarity=0.248  Sum_probs=29.9

Q ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHH
Q ss_conf             4776148867889999999999997089977999715379
Q gi|254781187|r   79 KCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSET  118 (367)
Q Consensus        79 ~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~  118 (367)
                      =++|.+-.|+|||+++..++-.+  +..|.+|.++-.+..
T Consensus         4 ii~ivG~s~SGKTTLi~kli~~l--~~~G~rV~~IKH~~H   41 (170)
T PRK10751          4 LLAIAAWSGTGKTTLLKKLIPAL--CARGIRPGLIKHTHH   41 (170)
T ss_pred             EEEEEECCCCCHHHHHHHHHHHH--HHCCCEEEEEECCCC
T ss_conf             79999469999999999999999--987984999945777


No 404
>cd01850 CDC_Septin CDC/Septin.  Septins are a conserved family of GTP-binding proteins associated with diverse processes in dividing and non-dividing cells.  They were first discovered in the budding yeast S. cerevisiae as a set of genes (CDC3, CDC10, CDC11 and CDC12) required for normal bud morphology. Septins are also present in metazoan cells, where they are required for cytokinesis in some systems, and implicated in a variety of other processes involving organization of the cell cortex and exocytosis.  In humans, 12 septin genes generate dozens of polypeptides, many of which comprise heterooligomeric complexes. Since septin mutants are commonly defective in cytokinesis and formation of the neck formation of the neck filaments/septin rings, septins have been considered to be the primary constituents of the neck filaments.  Septins belong to the GTPase superfamily for their conserved GTPase motifs and enzymatic activities.
Probab=72.35  E-value=4.1  Score=19.71  Aligned_cols=24  Identities=21%  Similarity=0.328  Sum_probs=20.0

Q ss_pred             CEEEEEEECCCCCCHHHHHHHHHH
Q ss_conf             112477614886788999999999
Q gi|254781187|r   76 TIFKCAISAGRGIGKTTLNAWMML   99 (367)
Q Consensus        76 ~~~~~~v~sgrg~GKS~~~a~~~l   99 (367)
                      .-|.+-|++.+|+|||+++--+..
T Consensus         3 ~~fnimVvG~sGlGKsTfiNtLf~   26 (276)
T cd01850           3 FQFNIMVVGESGLGKSTFINTLFN   26 (276)
T ss_pred             CEEEEEEECCCCCCHHHHHHHHHC
T ss_conf             579999976899988999999747


No 405
>KOG0336 consensus
Probab=72.31  E-value=4.6  Score=19.37  Aligned_cols=149  Identities=16%  Similarity=0.038  Sum_probs=65.2

Q ss_pred             EEEECCCCCCHHHHHHHHHHHH-------HHHCCCCEEEEECCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCC
Q ss_conf             7761488678899999999999-------970899779997153799999999999999986231211233332100012
Q gi|254781187|r   80 CAISAGRGIGKTTLNAWMMLWL-------ISTRPGMSIICIANSETQLKNTLWAEVSKWLSMLPHRHWFEMQSLSLHPSG  152 (367)
Q Consensus        80 ~~v~sgrg~GKS~~~a~~~lw~-------~~~~~~~~v~~~A~t~~Q~~~~lw~ei~k~~~~~~~~~~~~~~~~~~~~~~  152 (367)
                      +...|-.|.||+-..-.-.+-+       .-.+++..+++.+||..-+-. +=.|.++....--       ....++-..
T Consensus       260 liGVAQTgtgKtL~~L~pg~ihi~aqp~~~~qr~~p~~lvl~ptreLalq-ie~e~~kysyng~-------ksvc~yggg  331 (629)
T KOG0336         260 LIGVAQTGTGKTLAFLLPGFIHIDAQPKRREQRNGPGVLVLTPTRELALQ-IEGEVKKYSYNGL-------KSVCVYGGG  331 (629)
T ss_pred             EEEEEECCCCCCHHHHCCCEEEEECCCHHHHCCCCCCEEEEECCHHHHHH-HHHHHHHHHHCCC-------CEEEEECCC
T ss_conf             47787448984778750540145146111203689854998333888998-8767767643584-------328875487


Q ss_pred             CCCCCCCCCCCCCCCCEEEEECCCCCCC--CCCCCCCCCCCCCEEEEECCCCCCHHHHH-HHHHHHHC--CCCCEEEEEE
Q ss_conf             3332211113457761266210135445--56521011358628999754559988999-98987406--9882589998
Q gi|254781187|r  153 WYAELLEQSMGIDSKHYTITCRTYSEER--PDTFVGPHNTHGMAVFNDEASGTPDIINK-SILGFFTE--LNPNRFWIMT  227 (367)
Q Consensus       153 ~~~~~~~~~~~~~~~~~~~~a~~~~~~~--~ea~~g~h~~~~~l~ivDEAsgI~d~i~e-~i~g~Lt~--~~~~~~~i~i  227 (367)
                         ..+...-....|.-.+.+.+-+...  -+++-.+  .+..++++|||...=|.=|| .|...|-+  ++..+.  ++
T Consensus       332 ---nR~eqie~lkrgveiiiatPgrlndL~~~n~i~l--~siTYlVlDEADrMLDMgFEpqIrkilldiRPDRqtv--mT  404 (629)
T KOG0336         332 ---NRNEQIEDLKRGVEIIIATPGRLNDLQMDNVINL--ASITYLVLDEADRMLDMGFEPQIRKILLDIRPDRQTV--MT  404 (629)
T ss_pred             ---CCHHHHHHHHCCCEEEEECCCHHHHHHHCCEEEE--EEEEEEEECCHHHHHCCCCCHHHHHHHHHCCCCCEEE--EE
T ss_conf             ---8546899874574177607851765553172001--1258898612666644566288898865227762255--31


Q ss_pred             EC-CCCCCCHHHHHHHC
Q ss_conf             07-89998768875411
Q gi|254781187|r  228 SN-TRRLNGWFYDIFNI  243 (367)
Q Consensus       228 gN-P~r~~g~Fye~~~~  243 (367)
                      |- -+.+.-...+.|.+
T Consensus       405 SATWP~~VrrLa~sY~K  421 (629)
T KOG0336         405 SATWPEGVRRLAQSYLK  421 (629)
T ss_pred             CCCCCHHHHHHHHHHHH
T ss_conf             05586689999998640


No 406
>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=72.10  E-value=4  Score=19.76  Aligned_cols=22  Identities=23%  Similarity=0.240  Sum_probs=19.2

Q ss_pred             EEEEEECCCCCCHHHHHHHHHH
Q ss_conf             2477614886788999999999
Q gi|254781187|r   78 FKCAISAGRGIGKTTLNAWMML   99 (367)
Q Consensus        78 ~~~~v~sgrg~GKS~~~a~~~l   99 (367)
                      +|++|.+..|+|||.++..++-
T Consensus         1 ~KivllGd~~VGKTsl~~Rf~~   22 (158)
T cd04103           1 LKLGIVGNLQSGKSALVHRYLT   22 (158)
T ss_pred             CEEEEECCCCCCHHHHHHHHHH
T ss_conf             9999999699879999999980


No 407
>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=72.02  E-value=3.7  Score=19.99  Aligned_cols=35  Identities=29%  Similarity=0.385  Sum_probs=24.5

Q ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHH
Q ss_conf             4776148867889999999999997089977999715379
Q gi|254781187|r   79 KCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSET  118 (367)
Q Consensus        79 ~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~  118 (367)
                      |+.+-+|.|+|||++.+.++-+     -+..++|.+--..
T Consensus       142 RigIfgg~GvGKt~Ll~~i~~~-----~~adv~V~aliGe  176 (418)
T TIGR03498       142 RLGIFAGSGVGKSTLLSMLARN-----TDADVVVIALVGE  176 (418)
T ss_pred             EEECCCCCCCCHHHHHHHHHHH-----CCCCEEEEEEEEE
T ss_conf             6411378999888999999875-----0798689988302


No 408
>PRK09099 type III secretion system ATPase; Provisional
Probab=71.96  E-value=3.8  Score=19.87  Aligned_cols=23  Identities=30%  Similarity=0.319  Sum_probs=19.9

Q ss_pred             EEEEECCCCCCHHHHHHHHHHHH
Q ss_conf             47761488678899999999999
Q gi|254781187|r   79 KCAISAGRGIGKTTLNAWMMLWL  101 (367)
Q Consensus        79 ~~~v~sgrg~GKS~~~a~~~lw~  101 (367)
                      |+.|-+|+|+|||++.++++-+.
T Consensus       165 R~gIf~gsGvGKstLl~~iar~~  187 (441)
T PRK09099        165 RMGIFAPAGVGKSTLMGMFARGT  187 (441)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHH
T ss_conf             33001589887899999898751


No 409
>cd01870 RhoA_like RhoA-like subfamily.  The RhoA subfamily consists of RhoA, RhoB, and RhoC.  RhoA promotes the formation of stress fibers and focal adhesions, regulating cell shape, attachment, and motility.  RhoA can bind to multiple effector proteins, thereby triggering different downstream responses.  In many cell types, RhoA mediates local assembly of the contractile ring, which is necessary for cytokinesis.  RhoA is vital for muscle contraction; in vascular smooth muscle cells, RhoA plays a key role in cell contraction, differentiation, migration, and proliferation.  RhoA activities appear to be elaborately regulated in a time- and space-dependent manner to control cytoskeletal changes.  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 proteins.  RhoA and RhoC are observed only in geranyl
Probab=71.79  E-value=4.1  Score=19.69  Aligned_cols=22  Identities=27%  Similarity=0.123  Sum_probs=19.0

Q ss_pred             EEEEEECCCCCCHHHHHHHHHH
Q ss_conf             2477614886788999999999
Q gi|254781187|r   78 FKCAISAGRGIGKTTLNAWMML   99 (367)
Q Consensus        78 ~~~~v~sgrg~GKS~~~a~~~l   99 (367)
                      .|+++.+..|+|||.++..++-
T Consensus         2 ~Ki~liGd~~VGKTsli~r~~~   23 (175)
T cd01870           2 KKLVIVGDGACGKTCLLIVFSK   23 (175)
T ss_pred             CEEEEECCCCCCHHHHHHHHHC
T ss_conf             0999999899669999999970


No 410
>cd04177 RSR1 RSR1 subgroup.  RSR1/Bud1p is a member of the Rap subfamily of the Ras family that is found in fungi.  In budding yeasts, RSR1 is involved in selecting a site for bud growth on the cell cortex, which directs the establishment of cell polarization.  The Rho family GTPase cdc42 and its GEF, cdc24, then establish an axis of polarized growth by organizing the actin cytoskeleton and secretory apparatus at the bud site.  It is believed that cdc42 interacts directly with RSR1 in vivo.  In filamentous fungi, polar growth occurs at the tips of hypha and at novel growth sites along the extending hypha.  In Ashbya gossypii, RSR1 is a key regulator of hyphal growth, localizing at the tip region and regulating in apical polarization of the actin cytoskeleton.  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 featu
Probab=71.74  E-value=4.3  Score=19.55  Aligned_cols=22  Identities=23%  Similarity=0.507  Sum_probs=19.6

Q ss_pred             EEEEEECCCCCCHHHHHHHHHH
Q ss_conf             2477614886788999999999
Q gi|254781187|r   78 FKCAISAGRGIGKTTLNAWMML   99 (367)
Q Consensus        78 ~~~~v~sgrg~GKS~~~a~~~l   99 (367)
                      ||+.+.+..|+|||.++..++-
T Consensus         2 fKivlvGd~~VGKTsli~rf~~   23 (168)
T cd04177           2 YKIVVLGAGGVGKSALTVQFVQ   23 (168)
T ss_pred             EEEEEECCCCCCHHHHHHHHHH
T ss_conf             1999989999779999999961


No 411
>TIGR03324 alt_F1F0_F1_al alternate F1F0 ATPase, F1 subunit alpha. A small number of taxonomically diverse prokaryotic species, including Methanosarcina barkeri, 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 alpha subunit of this apparent second ATP synthase.
Probab=71.70  E-value=6.9  Score=18.28  Aligned_cols=21  Identities=29%  Similarity=0.310  Sum_probs=16.9

Q ss_pred             EEEEECCCCCCHHHHHHHHHH
Q ss_conf             477614886788999999999
Q gi|254781187|r   79 KCAISAGRGIGKTTLNAWMML   99 (367)
Q Consensus        79 ~~~v~sgrg~GKS~~~a~~~l   99 (367)
                      |..|-++||+|||+++...++
T Consensus       164 RelIigdrgtGKTtla~dtIi  184 (497)
T TIGR03324       164 RELILGDRQTGKTAIAIDTIL  184 (497)
T ss_pred             EEEEECCCCCCHHHHHHHHHH
T ss_conf             677645888880088999997


No 412
>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=71.69  E-value=3.7  Score=19.96  Aligned_cols=20  Identities=25%  Similarity=0.423  Sum_probs=17.9

Q ss_pred             EEEEECCCCCCHHHHHHHHH
Q ss_conf             47761488678899999999
Q gi|254781187|r   79 KCAISAGRGIGKTTLNAWMM   98 (367)
Q Consensus        79 ~~~v~sgrg~GKS~~~a~~~   98 (367)
                      |++|.+..|+|||.++..++
T Consensus         1 Ki~vvG~~~vGKTsli~r~~   20 (162)
T pfam00071         1 KLVLVGDGGVGKSSLLIRFT   20 (162)
T ss_pred             CEEEECCCCCCHHHHHHHHH
T ss_conf             98999979977999999996


No 413
>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=71.54  E-value=5  Score=19.14  Aligned_cols=36  Identities=28%  Similarity=0.303  Sum_probs=24.1

Q ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHH
Q ss_conf             47761488678899999999999970899779997153799
Q gi|254781187|r   79 KCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQ  119 (367)
Q Consensus        79 ~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q  119 (367)
                      |+.|-+|+|+|||++.+.++..     ....++|.+--...
T Consensus        71 R~~Ifg~~g~GKt~Ll~~i~~~-----~~~~v~V~~~IGer  106 (326)
T cd01136          71 RLGIFAGSGVGKSTLLGMIARG-----TTADVNVIALIGER  106 (326)
T ss_pred             EEEEECCCCCCCCHHHHHHHHC-----CCCCEEEEEEECCC
T ss_conf             7874369999846678768641-----46775999960533


No 414
>PRK05922 type III secretion system ATPase; Validated
Probab=71.43  E-value=6.2  Score=18.58  Aligned_cols=35  Identities=20%  Similarity=0.145  Sum_probs=24.3

Q ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHH
Q ss_conf             4776148867889999999999997089977999715379
Q gi|254781187|r   79 KCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSET  118 (367)
Q Consensus        79 ~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~  118 (367)
                      |+.+-+|.|+|||++.+.++..     ....+.|++--..
T Consensus       159 R~gIf~g~GvGKt~Ll~~ia~~-----~~~~v~V~alIGe  193 (434)
T PRK05922        159 RIGVFSEPGSGKSSLLSTIAKG-----SKSTINVIALIGE  193 (434)
T ss_pred             EEEECCCCCCCHHHHHHHHHHC-----CCCCEEEEEEEEE
T ss_conf             7773079999789999867653-----6787599984551


No 415
>cd04121 Rab40 Rab40 subfamily.  This subfamily contains Rab40a, Rab40b, and Rab40c, which are all highly homologous.  In rat, Rab40c is localized to the perinuclear recycling compartment (PRC), and is distributed in a tissue-specific manor, with high expression in brain, heart, kidney, and testis, low expression in lung and liver, and no expression in spleen and skeletal muscle.  Rab40c is highly expressed in differentiated oligodendrocytes but minimally expressed in oligodendrocyte progenitors, suggesting a role in the vesicular transport of myelin components.  Unlike most other Ras-superfamily proteins, Rab40c was shown to have a much lower affinity for GTP, and an affinity for GDP that is lower than for 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 d
Probab=71.37  E-value=5  Score=19.17  Aligned_cols=23  Identities=17%  Similarity=0.274  Sum_probs=20.0

Q ss_pred             CEEEEEEECCCCCCHHHHHHHHH
Q ss_conf             11247761488678899999999
Q gi|254781187|r   76 TIFKCAISAGRGIGKTTLNAWMM   98 (367)
Q Consensus        76 ~~~~~~v~sgrg~GKS~~~a~~~   98 (367)
                      +.+|+.|.+..|+|||.++..++
T Consensus         5 y~~KivllGd~~VGKTsl~~r~~   27 (189)
T cd04121           5 YLLKFLLVGDSDVGKGEILASLQ   27 (189)
T ss_pred             EEEEEEEECCCCCCHHHHHHHHH
T ss_conf             89999999989978999999997


No 416
>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=71.37  E-value=7  Score=18.24  Aligned_cols=35  Identities=26%  Similarity=0.315  Sum_probs=27.5

Q ss_pred             EEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEE
Q ss_conf             1247761488678899999999999970899779997
Q gi|254781187|r   77 IFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICI  113 (367)
Q Consensus        77 ~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~  113 (367)
                      |+.+||..==|+|||+.++.++.-++.  -|.||+++
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 417
>PRK13764 ATPase; Provisional
Probab=71.25  E-value=7.1  Score=18.22  Aligned_cols=26  Identities=19%  Similarity=0.275  Sum_probs=22.7

Q ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHH
Q ss_conf             47761488678899999999999970
Q gi|254781187|r   79 KCAISAGRGIGKTTLNAWMMLWLIST  104 (367)
Q Consensus        79 ~~~v~sgrg~GKS~~~a~~~lw~~~~  104 (367)
                      -+.|++.-|.|||+++.+++-++...
T Consensus       261 GilIaG~PGaGKsTfaqalA~~~~~~  286 (605)
T PRK13764        261 GILIAGAPGAGKSTFAQALAEFYADM  286 (605)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHC
T ss_conf             49997799997789999999999847


No 418
>COG1197 Mfd Transcription-repair coupling factor (superfamily II helicase) [DNA replication, recombination, and repair / Transcription]
Probab=71.19  E-value=7.1  Score=18.21  Aligned_cols=75  Identities=16%  Similarity=0.192  Sum_probs=48.2

Q ss_pred             HHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHHHHHH
Q ss_conf             89999999888875124555554112477614886788999999999999708997799971537999999999999999
Q gi|254781187|r   53 RWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLKNTLWAEVSKWL  132 (367)
Q Consensus        53 ~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~~~lw~ei~k~~  132 (367)
                      +=|...+.+|-...+.+.-.     =|+ |++-=|+|||-++...+.  .....|..|.+..||-==+.+= +.-+++-.
T Consensus       597 ~DQl~AI~eVk~DM~~~kpM-----DRL-iCGDVGFGKTEVAmRAAF--kAV~~GKQVAvLVPTTlLA~QH-y~tFkeRF  667 (1139)
T COG1197         597 PDQLKAIEEVKRDMESGKPM-----DRL-ICGDVGFGKTEVAMRAAF--KAVMDGKQVAVLVPTTLLAQQH-YETFKERF  667 (1139)
T ss_pred             HHHHHHHHHHHHHHCCCCCC-----HHE-EECCCCCCHHHHHHHHHH--HHHCCCCEEEEECCCHHHHHHH-HHHHHHHH
T ss_conf             78999999999886069866-----102-565768759999999999--9863797499992607868998-99999873


Q ss_pred             HHCC
Q ss_conf             8623
Q gi|254781187|r  133 SMLP  136 (367)
Q Consensus       133 ~~~~  136 (367)
                      .-.|
T Consensus       668 ~~fP  671 (1139)
T COG1197         668 AGFP  671 (1139)
T ss_pred             CCCC
T ss_conf             3898


No 419
>KOG0346 consensus
Probab=71.00  E-value=7.2  Score=18.19  Aligned_cols=77  Identities=14%  Similarity=0.165  Sum_probs=51.1

Q ss_pred             CCCCCHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCC-------CCEEEEECCCHHH
Q ss_conf             666842899999998888751245555541124776148867889999999999997089-------9779997153799
Q gi|254781187|r   47 HFSQPHRWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRP-------GMSIICIANSETQ  119 (367)
Q Consensus        47 ~~~~p~~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~-------~~~v~~~A~t~~Q  119 (367)
                      +++.|+.-|..++--+   ++. .        .+..+|-.|+|||..-+.=++=.++...       +...++.+||..-
T Consensus        38 G~ekpTlIQs~aIpla---LEg-K--------DvvarArTGSGKT~AYliPllqkll~~k~t~~~e~~~sa~iLvPTkEL  105 (569)
T KOG0346          38 GWEKPTLIQSSAIPLA---LEG-K--------DVVARARTGSGKTAAYLIPLLQKLLAEKKTNDGEQGPSAVILVPTKEL  105 (569)
T ss_pred             CCCCCCHHHHCCCCHH---HCC-C--------CEEEEECCCCCCHHHHHHHHHHHHHHHHHCCCCCCCCEEEEEECHHHH
T ss_conf             7677623443221243---248-6--------314652268871378899999999976403643246306999250999


Q ss_pred             HHHHHHHHHHHHHHHCC
Q ss_conf             99999999999998623
Q gi|254781187|r  120 LKNTLWAEVSKWLSMLP  136 (367)
Q Consensus       120 ~~~~lw~ei~k~~~~~~  136 (367)
                      +.++ ..++.+....++
T Consensus       106 ~qQv-y~viekL~~~c~  121 (569)
T KOG0346         106 AQQV-YKVIEKLVEYCS  121 (569)
T ss_pred             HHHH-HHHHHHHHHHHH
T ss_conf             9999-999999999878


No 420
>COG1157 FliI Flagellar biosynthesis/type III secretory pathway ATPase [Cell motility and secretion / Intracellular trafficking and secretion]
Probab=70.88  E-value=4.1  Score=19.68  Aligned_cols=47  Identities=26%  Similarity=0.298  Sum_probs=31.1

Q ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHHHHHHHHC
Q ss_conf             477614886788999999999999708997799971537999999999999999862
Q gi|254781187|r   79 KCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLKNTLWAEVSKWLSML  135 (367)
Q Consensus        79 ~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~~~lw~ei~k~~~~~  135 (367)
                      |+-|=||-|+|||++.++++-     +....++|+|=-...-     +|++.+++..
T Consensus       165 RiGIFAgsGVGKStLLgMiar-----~t~aDv~ViaLIGERG-----REVrEFIE~~  211 (441)
T COG1157         165 RIGIFAGSGVGKSTLLGMIAR-----NTEADVNVIALIGERG-----REVREFIEKD  211 (441)
T ss_pred             EEEEEECCCCCHHHHHHHHHC-----CCCCCEEEEEEEECCC-----HHHHHHHHHH
T ss_conf             678871699868999999962-----4669879999760664-----0599999986


No 421
>KOG0979 consensus
Probab=70.76  E-value=3.2  Score=20.32  Aligned_cols=18  Identities=28%  Similarity=0.410  Sum_probs=9.7

Q ss_pred             EECCCCCCHHHHHHHHHH
Q ss_conf             614886788999999999
Q gi|254781187|r   82 ISAGRGIGKTTLNAWMML   99 (367)
Q Consensus        82 v~sgrg~GKS~~~a~~~l   99 (367)
                      |.++.|+|||.++++++|
T Consensus        47 IiGpNGSGKSSiVcAIcL   64 (1072)
T KOG0979          47 IIGPNGSGKSSIVCAICL   64 (1072)
T ss_pred             EECCCCCCCHHHHHHHHH
T ss_conf             877898970488999999


No 422
>cd03116 MobB Molybdenum is an essential trace element in the form of molybdenum cofactor (Moco) which is associated with the metabolism of nitrogen, carbon and sulfur by redox active enzymes. In E. coli, the synthesis of Moco involves genes from several loci: moa, mob, mod, moe and mog. The mob locus contains mobA and mobB genes. MobB catalyzes the attachment of the guanine dinucleotide to molybdopterin.
Probab=70.68  E-value=7.3  Score=18.14  Aligned_cols=39  Identities=23%  Similarity=0.278  Sum_probs=30.5

Q ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHH
Q ss_conf             47761488678899999999999970899779997153799
Q gi|254781187|r   79 KCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQ  119 (367)
Q Consensus        79 ~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q  119 (367)
                      =++|.+-.++|||+++..++-.+  +..|.+|.++=...+.
T Consensus         3 ii~ivG~snSGKTTLi~kli~~l--~~~G~~V~~iKH~~H~   41 (159)
T cd03116           3 VIGFVGYSGSGKTTLLEKLIPAL--SARGLRVAVIKHDHHD   41 (159)
T ss_pred             EEEEEECCCCCHHHHHHHHHHHH--HHCCCEEEEEEECCCC
T ss_conf             99999679999999999999999--9779859899734767


No 423
>COG3973 Superfamily I DNA and RNA helicases [General function prediction only]
Probab=70.51  E-value=7.4  Score=18.12  Aligned_cols=51  Identities=18%  Similarity=0.301  Sum_probs=37.8

Q ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHHCCC----CEEEEECCCHHHHHHHHHHHHHHHHHH
Q ss_conf             47761488678899999999999970899----779997153799999999999999986
Q gi|254781187|r   79 KCAISAGRGIGKTTLNAWMMLWLISTRPG----MSIICIANSETQLKNTLWAEVSKWLSM  134 (367)
Q Consensus        79 ~~~v~sgrg~GKS~~~a~~~lw~~~~~~~----~~v~~~A~t~~Q~~~~lw~ei~k~~~~  134 (367)
                      -+.|.++-|+|||+++--=+.|++..+.+    .-|++.+|..     ++-..++..+-.
T Consensus       228 ilVVQGaAGSGKTtiALHRvAyLlY~~R~~l~~k~vlvl~PN~-----vFleYis~VLPe  282 (747)
T COG3973         228 ILVVQGAAGSGKTTIALHRVAYLLYGYRGPLQAKPVLVLGPNR-----VFLEYISRVLPE  282 (747)
T ss_pred             EEEEECCCCCCCHHHHHHHHHHHHHCCCCCCCCCCEEEECCCH-----HHHHHHHHHCHH
T ss_conf             4899558888713588999999985356624668659982838-----999999875544


No 424
>PRK13721 conjugal transfer ATP-binding protein TraC; Provisional
Probab=70.47  E-value=7.4  Score=18.12  Aligned_cols=42  Identities=19%  Similarity=0.277  Sum_probs=30.7

Q ss_pred             EEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEE--CCCHHHHH
Q ss_conf             247761488678899999999999970899779997--15379999
Q gi|254781187|r   78 FKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICI--ANSETQLK  121 (367)
Q Consensus        78 ~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~--A~t~~Q~~  121 (367)
                      |+++|.++-|.|||+++-.++.=++..  |.+|+++  -.++..+.
T Consensus       475 ~N~~I~g~SGsGKSf~~q~l~~~~~~~--G~~V~IID~G~SY~~lc  518 (864)
T PRK13721        475 YNMAVCGTSGAGKTGLIQPLIRSVLDS--GGFAVVFDMGDGYKSLC  518 (864)
T ss_pred             CCEEEECCCCCCHHHHHHHHHHHHHHC--CCEEEEEECCCCHHHHH
T ss_conf             006998289986899999999999857--99799996997899999


No 425
>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=70.46  E-value=4.6  Score=19.36  Aligned_cols=31  Identities=19%  Similarity=0.228  Sum_probs=22.1

Q ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEE
Q ss_conf             4776148867889999999999997089977999
Q gi|254781187|r   79 KCAISAGRGIGKTTLNAWMMLWLISTRPGMSIIC  112 (367)
Q Consensus        79 ~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~  112 (367)
                      +++|.+.-|+|||+++..++-  +.. +...|.+
T Consensus        32 ~vaIvG~sGsGKSTLl~lL~g--l~~-~~G~I~i   62 (275)
T cd03289          32 RVGLLGRTGSGKSTLLSAFLR--LLN-TEGDIQI   62 (275)
T ss_pred             EEEEECCCCCCHHHHHHHHHH--HCC-CCCEEEE
T ss_conf             999999999979999999960--357-8953999


No 426
>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=70.31  E-value=4.2  Score=19.60  Aligned_cols=36  Identities=28%  Similarity=0.407  Sum_probs=27.6

Q ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCH
Q ss_conf             477614886788999999999999708997799971537
Q gi|254781187|r   79 KCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSE  117 (367)
Q Consensus        79 ~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~  117 (367)
                      -++..+|.|.|||++.++++.-   .-|+.+-+-..||.
T Consensus        29 vttLsG~NGAGKsT~m~Af~ta---lIPDl~~l~frntt   64 (227)
T pfam04310        29 VTTLSGGNGAGKSTTMAAFITA---LIPDLSLLHFRNTT   64 (227)
T ss_pred             EEEEECCCCCCHHHHHHHHHHH---HCCCCEEEEECCCC
T ss_conf             6886447876548799999998---66664388621556


No 427
>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=70.24  E-value=4.9  Score=19.22  Aligned_cols=35  Identities=29%  Similarity=0.244  Sum_probs=26.0

Q ss_pred             HHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHH
Q ss_conf             7512455555411247761488678899999999999
Q gi|254781187|r   65 HCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWL  101 (367)
Q Consensus        65 ~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~  101 (367)
                      |+.+-..++  .+.+|||.+|--+|||+|+-.++--+
T Consensus       165 hIpr~~rp~--F~k~V~ilG~eStGKstLv~~lA~~~  199 (346)
T TIGR01526       165 HIPREVRPF--FVKTVAILGGESTGKSTLVNKLAEKL  199 (346)
T ss_pred             HCCCEECCC--EEEEEEEECCCCCCHHHHHHHHHHHH
T ss_conf             147202322--04588885588863689999999984


No 428
>PRK10636 putative ABC transporter ATP-binding protein; Provisional
Probab=70.20  E-value=3.7  Score=19.92  Aligned_cols=34  Identities=6%  Similarity=-0.130  Sum_probs=22.3

Q ss_pred             CCCCCEEEEECC-CCCCHHHHHHHHHHHHCCCCCE
Q ss_conf             358628999754-5599889999898740698825
Q gi|254781187|r  189 NTHGMAVFNDEA-SGTPDIINKSILGFFTELNPNR  222 (367)
Q Consensus       189 ~~~~~l~ivDEA-sgI~d~i~e~i~g~Lt~~~~~~  222 (367)
                      .....++++||- ++.+-.....++..|...+.-+
T Consensus       165 ~~~PdlLLLDEPTnhLD~~~i~~L~~~L~~~~gtv  199 (638)
T PRK10636        165 ICRSDLLLLDEPTNHLDLDAVIWLEKWLKSYQGTL  199 (638)
T ss_pred             CCCCCEEEECCCCCCCCHHHHHHHHHHHHHCCCEE
T ss_conf             58999899708888899899999999999769819


No 429
>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=70.15  E-value=7.5  Score=18.07  Aligned_cols=100  Identities=15%  Similarity=0.112  Sum_probs=49.1

Q ss_pred             EEEEC-CCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             77614-88678899999999999970899779997153799999999999999986231211233332100012333221
Q gi|254781187|r   80 CAISA-GRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLKNTLWAEVSKWLSMLPHRHWFEMQSLSLHPSGWYAELL  158 (367)
Q Consensus        80 ~~v~s-grg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~~~lw~ei~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~  158 (367)
                      +++++ -=|+|||+++..++..+.  ..|.+|.++-.--++ .-.-|.+...-.....                      
T Consensus         4 i~~~~~KGG~GKtT~a~~la~~~~--~~g~~V~liD~Dpq~-s~~~W~~~a~~~~~~~----------------------   58 (231)
T pfam07015         4 ITFCSFKGGAGKTTALMGLCSALA--SDGKRVALFEADENR-PLTKWRENALRKGTWD----------------------   58 (231)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHH--HCCCEEEEEECCCCC-CHHHHHHHHHHCCCCC----------------------
T ss_conf             999617998659999999999999--689959999689986-8899999876468888----------------------


Q ss_pred             CCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCEEEEECCCCCCHHHHHHHH
Q ss_conf             111345776126621013544556521011358628999754559988999989
Q gi|254781187|r  159 EQSMGIDSKHYTITCRTYSEERPDTFVGPHNTHGMAVFNDEASGTPDIINKSIL  212 (367)
Q Consensus       159 ~~~~~~~~~~~~~~a~~~~~~~~ea~~g~h~~~~~l~ivDEAsgI~d~i~e~i~  212 (367)
                             +......... ...-.......+...+.++|+|-+..+++.+-.++.
T Consensus        59 -------~~~~v~~~~~-~~~l~~~~~~~~~~~yD~VIIDtpg~~s~~~~~AI~  104 (231)
T pfam07015        59 -------PACEIFNADE-LPLLEQAYEHAEGSGFDYALADTHGGSSELNNTIIA  104 (231)
T ss_pred             -------CCCCEECCCC-HHHHHHHHHHHHHCCCCEEEECCCCCCCHHHHHHHH
T ss_conf             -------7652220566-015899999886579998998399857589999999


No 430
>COG1674 FtsK DNA segregation ATPase FtsK/SpoIIIE and related proteins [Cell division and chromosome partitioning]
Probab=70.10  E-value=6.5  Score=18.44  Aligned_cols=50  Identities=18%  Similarity=0.113  Sum_probs=35.9

Q ss_pred             HCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCC--EEEEECCC
Q ss_conf             124555554112477614886788999999999999708997--79997153
Q gi|254781187|r   67 HSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGM--SIICIANS  116 (367)
Q Consensus        67 ~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~--~v~~~A~t  116 (367)
                      +....-+...+..+.|++..|+|||+..-.+++=++.++.+.  +.+++-|.
T Consensus       520 ~~~~~~dlak~~hlli~G~tgsGKSv~lnt~i~Sll~~~~P~ev~~~~iD~k  571 (858)
T COG1674         520 QEPIVIDLAKAGHLLIAGATGSGKSVALNTMILSLLYTHSPEEVRFYIIDPK  571 (858)
T ss_pred             CCCEEEECCCCCCEEEECCCCCCHHHHHHHHHHHHHHCCCCHHEEEEEECCC
T ss_conf             8813855356888788248886515589999999875189068499997478


No 431
>cd04139 RalA_RalB RalA/RalB subfamily.  The Ral (Ras-like) subfamily consists of the highly homologous RalA and RalB.  Ral proteins are believed to play a crucial role in tumorigenesis, metastasis, endocytosis, and actin cytoskeleton dynamics.  Despite their high sequence similarity (80% sequence identity), nonoverlapping and opposing functions have been assigned to RalA and RalBs in tumor migration.  In human bladder and prostate cancer cells, RalB promotes migration while RalA inhibits it.  A Ral-specific set of GEFs has been identified that are activated by Ras binding.  This RalGEF activity is enhanced by Ras binding to another of its target proteins, phosphatidylinositol 3-kinase (PI3K).   Ral effectors include RLIP76/RalBP1, a Rac/cdc42 GAP, and the exocyst (Sec6/8) complex, a heterooctomeric protein complex that is involved in tethering vesicles to specific sites on the plasma membrane prior to exocytosis.  In rat kidney cells, RalB is required for functional assembly of the exo
Probab=70.09  E-value=4.7  Score=19.32  Aligned_cols=22  Identities=27%  Similarity=0.572  Sum_probs=19.1

Q ss_pred             EEEEEECCCCCCHHHHHHHHHH
Q ss_conf             2477614886788999999999
Q gi|254781187|r   78 FKCAISAGRGIGKTTLNAWMML   99 (367)
Q Consensus        78 ~~~~v~sgrg~GKS~~~a~~~l   99 (367)
                      ||+.+.+.-|+|||.++..++-
T Consensus         1 fKvvlvGd~~VGKTsli~r~~~   22 (164)
T cd04139           1 YKVIVVGAGGVGKSALTLQFMY   22 (164)
T ss_pred             CEEEEECCCCCCHHHHHHHHHH
T ss_conf             9799999999889999999971


No 432
>cd04145 M_R_Ras_like M-Ras/R-Ras-like subfamily.  This subfamily contains R-Ras2/TC21, M-Ras/R-Ras3, and related members of the Ras family. M-Ras is expressed in lympho-hematopoetic cells.  It interacts with some of the known Ras effectors, but appears to also have its own effectors.  Expression of mutated M-Ras leads to transformation of several types of cell lines, including hematopoietic cells, mammary epithelial cells, and fibroblasts.  Overexpression of M-Ras is observed in carcinomas from breast, uterus, thyroid, stomach, colon, kidney, lung, and rectum.  In addition, expression of a constitutively active M-Ras mutant in murine bone marrow induces a malignant mast cell leukemia that is distinct from the monocytic leukemia induced by H-Ras.  TC21, along with H-Ras, has been shown to regulate the branching morphogenesis of ureteric bud cell branching in mice.  Most Ras proteins contain a lipid modification site at the C-terminus, with a typical sequence motif CaaX, where a = an ali
Probab=70.08  E-value=5.1  Score=19.09  Aligned_cols=22  Identities=27%  Similarity=0.625  Sum_probs=19.0

Q ss_pred             EEEEEEECCCCCCHHHHHHHHH
Q ss_conf             1247761488678899999999
Q gi|254781187|r   77 IFKCAISAGRGIGKTTLNAWMM   98 (367)
Q Consensus        77 ~~~~~v~sgrg~GKS~~~a~~~   98 (367)
                      -||+.|.+.-|+|||.++..++
T Consensus         2 t~Kiv~lGd~~VGKTsli~r~~   23 (164)
T cd04145           2 TYKLVVVGGGGVGKSALTIQFI   23 (164)
T ss_pred             CEEEEEECCCCCCHHHHHHHHH
T ss_conf             3799999999978899999998


No 433
>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=69.95  E-value=7  Score=18.26  Aligned_cols=129  Identities=16%  Similarity=0.164  Sum_probs=67.7

Q ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             47761488678899999999999970899779997153799999999999999986231211233332100012333221
Q gi|254781187|r   79 KCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLKNTLWAEVSKWLSMLPHRHWFEMQSLSLHPSGWYAELL  158 (367)
Q Consensus        79 ~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~~~lw~ei~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~  158 (367)
                      |+=|=|+=|+|||+|.++++     -...+.|+|+|=-..-=     +|++.+++..--.                    
T Consensus       155 RiGIFA~aG~GKSTLL~~i~-----~g~~ADv~V~ALIGERG-----REVREFiE~~lg~--------------------  204 (430)
T TIGR02546       155 RIGIFAGAGVGKSTLLGMIA-----RGASADVNVIALIGERG-----REVREFIEHLLGE--------------------  204 (430)
T ss_pred             EEEEEECCCCCHHHHHHHHH-----CCCCCCEEEEEECCCCC-----HHHHHHHHHCCCH--------------------
T ss_conf             05787088861668999986-----18988789986027876-----0478887520783--------------------


Q ss_pred             CCCCCCCCCCEEEEECCCCCCCCCCCCCCC------------CCCCCEEEEEC--------------------CCCCCHH
Q ss_conf             111345776126621013544556521011------------35862899975--------------------4559988
Q gi|254781187|r  159 EQSMGIDSKHYTITCRTYSEERPDTFVGPH------------NTHGMAVFNDE--------------------ASGTPDI  206 (367)
Q Consensus       159 ~~~~~~~~~~~~~~a~~~~~~~~ea~~g~h------------~~~~~l~ivDE--------------------AsgI~d~  206 (367)
                          + ...-..+.+.|++.-..|..+..+            |.+ +|+++|=                    +.|.|+-
T Consensus       205 ----e-~~~RsVlVvsTSDrss~eR~~AAy~ATaIAEYFRDQGk~-VlLmmDSlTRfARA~REiGLAaGEP~aR~GyPPS  278 (430)
T TIGR02546       205 ----E-GRKRSVLVVSTSDRSSLERLKAAYTATAIAEYFRDQGKR-VLLMMDSLTRFARALREIGLAAGEPPARRGYPPS  278 (430)
T ss_pred             ----H-HCCCEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHCCCE-EEEEEECHHHHHHHHHHHHHHCCCCCCCCCCCCC
T ss_conf             ----0-524248996079866799999987887999999973990-7988402779999987788753784002577873


Q ss_pred             HHHHHHHHH--HCCCCCEEEEEEEC----CCCCCCHHHHHHHC
Q ss_conf             999989874--06988258999807----89998768875411
Q gi|254781187|r  207 INKSILGFF--TELNPNRFWIMTSN----TRRLNGWFYDIFNI  243 (367)
Q Consensus       207 i~e~i~g~L--t~~~~~~~~i~igN----P~r~~g~Fye~~~~  243 (367)
                      +|..+=-.|  ++.+.+..+-++.|    ++..+.++.|--+.
T Consensus       279 VF~~LPRLLERaG~~e~GSITA~YTVLvEgDd~~dP~ADEvRS  321 (430)
T TIGR02546       279 VFSSLPRLLERAGNSEKGSITALYTVLVEGDDMNDPIADEVRS  321 (430)
T ss_pred             HHHHCCHHHCCCCCCCCCCEEEEEEEEECCCCCCCCHHHHHHH
T ss_conf             6650750122786112962534567876277799843665544


No 434
>PRK13646 cbiO cobalt transporter ATP-binding subunit; Provisional
Probab=69.86  E-value=1.3  Score=22.82  Aligned_cols=37  Identities=24%  Similarity=0.270  Sum_probs=25.6

Q ss_pred             HHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHH
Q ss_conf             999999988887512455555411247761488678899999999
Q gi|254781187|r   54 WQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMM   98 (367)
Q Consensus        54 wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~   98 (367)
                      .+.++|++|.=.+.++.        .++|.+..|+|||++.-.+.
T Consensus        18 ~~~~aL~~vsl~I~~Ge--------~~aiiG~nGsGKSTLl~~l~   54 (286)
T PRK13646         18 YQHQAIHDVNTEFEQGK--------YYAIVGQTGSGKSTLIQNIN   54 (286)
T ss_pred             CCCCEEECEEEEECCCC--------EEEEECCCCCHHHHHHHHHH
T ss_conf             70506624177986998--------99999999981999999997


No 435
>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=69.83  E-value=7.6  Score=18.03  Aligned_cols=135  Identities=16%  Similarity=0.124  Sum_probs=67.4

Q ss_pred             EEEEECCCCCCHHHHHHHHHHH-HHHHCCCCEEEEECCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             4776148867889999999999-997089977999715379999999999999998623121123333210001233322
Q gi|254781187|r   79 KCAISAGRGIGKTTLNAWMMLW-LISTRPGMSIICIANSETQLKNTLWAEVSKWLSMLPHRHWFEMQSLSLHPSGWYAEL  157 (367)
Q Consensus        79 ~~~v~sgrg~GKS~~~a~~~lw-~~~~~~~~~v~~~A~t~~Q~~~~lw~ei~k~~~~~~~~~~~~~~~~~~~~~~~~~~~  157 (367)
                      ++++.+..|.|||+++-.++.- ....+.|. |-    ..+...+..=-|.++-+.....-..+.|..            
T Consensus         1 Niai~gH~~~GKTtL~e~lL~~~g~i~r~G~-v~----~g~t~~D~~~eE~~r~isi~~~~~~~~~~~------------   63 (237)
T cd04168           1 NIGILAHVDAGKTTLTESLLYTSGAIRKLGS-VD----KGTTRTDTMELERQRGITIFSAVASFQWED------------   63 (237)
T ss_pred             CEEEECCCCCCHHHHHHHHHHHCCHHHHCCC-EE----CCCCCCCCHHHHHHHCCEEEEEEEEEEECC------------
T ss_conf             9899938998999999999996571222663-30----683037854998984870310589999899------------


Q ss_pred             CCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCEEEEECCCCCCH---HHHHHHHHHHHCCCCCEEEEEEECC-CCC
Q ss_conf             111134577612662101354455652101135862899975455998---8999989874069882589998078-999
Q gi|254781187|r  158 LEQSMGIDSKHYTITCRTYSEERPDTFVGPHNTHGMAVFNDEASGTPD---IINKSILGFFTELNPNRFWIMTSNT-RRL  233 (367)
Q Consensus       158 ~~~~~~~~~~~~~~~a~~~~~~~~ea~~g~h~~~~~l~ivDEAsgI~d---~i~e~i~g~Lt~~~~~~~~i~igNP-~r~  233 (367)
                              ....++.+-+......+...+++.-...++++|=.+||..   .+|..+.    ..+-+.+ +. -|= .|.
T Consensus        64 --------~~~n~iDtPG~~dF~~e~~~al~~~D~av~Vv~a~~Gv~~~t~~~~~~~~----~~~~P~i-if-iNKmDre  129 (237)
T cd04168          64 --------TKVNLIDTPGHMDFIAEVERSLSVLDGAILVISAVEGVQAQTRILWRLLR----KLNIPTI-IF-VNKIDRA  129 (237)
T ss_pred             --------EEEEEEECCCCHHHHHHHHHHHHHCCCEEEEEECCCCCCCCHHHHHHHHH----HCCCCEE-EE-EECCCCC
T ss_conf             --------87999889884656668988976348169999658882234499999999----8599859-98-6244578


Q ss_pred             CCHHHHHHHCC
Q ss_conf             87688754112
Q gi|254781187|r  234 NGWFYDIFNIP  244 (367)
Q Consensus       234 ~g~Fye~~~~~  244 (367)
                      .--|.+....-
T Consensus       130 ~adf~~~l~~i  140 (237)
T cd04168         130 GADLEKVYQEI  140 (237)
T ss_pred             CCCHHHHHHHH
T ss_conf             99999999999


No 436
>cd04176 Rap2 Rap2 subgroup.  The Rap2 subgroup is part of the Rap subfamily of the Ras family.  It consists of Rap2a, Rap2b, and Rap2c.  Both isoform 3 of the human mitogen-activated protein kinase kinase kinase kinase 4 (MAP4K4) and Traf2- and Nck-interacting kinase (TNIK) are putative effectors of Rap2 in mediating the activation of c-Jun N-terminal kinase (JNK) to regulate the actin cytoskeleton.  In human platelets, Rap2 was shown to interact with the cytoskeleton by binding the actin filaments.  In embryonic Xenopus development, Rap2 is necessary for the Wnt/beta-catenin signaling pathway.  The Rap2 interacting protein 9 (RPIP9) is highly expressed in human breast carcinomas and correlates with a poor prognosis, suggesting a role for Rap2 in breast cancer oncogenesis.  Rap2b, but not Rap2a, Rap2c, Rap1a, or Rap1b, is expressed in human red blood cells, where it is believed to be involved in vesiculation.  A number of additional effector proteins for Rap2 have been identified, incl
Probab=69.80  E-value=5.1  Score=19.08  Aligned_cols=22  Identities=23%  Similarity=0.514  Sum_probs=19.2

Q ss_pred             EEEEEECCCCCCHHHHHHHHHH
Q ss_conf             2477614886788999999999
Q gi|254781187|r   78 FKCAISAGRGIGKTTLNAWMML   99 (367)
Q Consensus        78 ~~~~v~sgrg~GKS~~~a~~~l   99 (367)
                      ||+.+.+.-|+|||.++..++-
T Consensus         2 ~KivllGd~~VGKTsli~r~~~   23 (163)
T cd04176           2 YKVVVLGSGGVGKSALTVQFVS   23 (163)
T ss_pred             EEEEEECCCCCCHHHHHHHHHH
T ss_conf             3999989999789999999970


No 437
>KOG1802 consensus
Probab=69.80  E-value=5  Score=19.13  Aligned_cols=37  Identities=22%  Similarity=0.281  Sum_probs=29.6

Q ss_pred             EEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCH
Q ss_conf             77614886788999999999999708997799971537
Q gi|254781187|r   80 CAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSE  117 (367)
Q Consensus        80 ~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~  117 (367)
                      ..|.++-|+|||..+|.++. .+..+....|+|+||+-
T Consensus       428 sLIQGPPGTGKTvtsa~IVy-hl~~~~~~~VLvcApSN  464 (935)
T KOG1802         428 SLIQGPPGTGKTVTSATIVY-HLARQHAGPVLVCAPSN  464 (935)
T ss_pred             EEEECCCCCCCEEHHHHHHH-HHHHHCCCCEEEECCCC
T ss_conf             15546999883311689999-99985289569981650


No 438
>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=69.74  E-value=4.7  Score=19.30  Aligned_cols=21  Identities=24%  Similarity=0.262  Sum_probs=18.3

Q ss_pred             EEEEEECCCCCCHHHHHHHHH
Q ss_conf             247761488678899999999
Q gi|254781187|r   78 FKCAISAGRGIGKTTLNAWMM   98 (367)
Q Consensus        78 ~~~~v~sgrg~GKS~~~a~~~   98 (367)
                      +|+.+.+..|+|||.++..++
T Consensus         1 iKi~llGd~~VGKTsli~r~~   21 (171)
T cd00157           1 IKIVVVGDGAVGKTCLLISYT   21 (171)
T ss_pred             CEEEEECCCCCCHHHHHHHHH
T ss_conf             989999999966999999996


No 439
>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=69.65  E-value=5.2  Score=19.06  Aligned_cols=38  Identities=21%  Similarity=0.214  Sum_probs=28.7

Q ss_pred             EEEE-ECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHH
Q ss_conf             4776-148867889999999999997089977999715379999
Q gi|254781187|r   79 KCAI-SAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLK  121 (367)
Q Consensus        79 ~~~v-~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~  121 (367)
                      .|.+ .+==|.|||+++-+++.     +-|....+++||++=+.
T Consensus        29 ~v~~L~GDlGaGKTtl~~G~~~-----~LG~~~~~~SPTftlv~   67 (147)
T TIGR00150        29 TVVLLKGDLGAGKTTLVKGLLQ-----GLGITGNVTSPTFTLVN   67 (147)
T ss_pred             EEEEEECCCCCCHHHHHHHHHH-----HCCCEEEEECCCCCEEE
T ss_conf             3899732346665899999998-----37922688579321010


No 440
>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=69.65  E-value=6.8  Score=18.33  Aligned_cols=35  Identities=20%  Similarity=0.250  Sum_probs=25.5

Q ss_pred             EECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCC
Q ss_conf             61488678899999999999970899779997153
Q gi|254781187|r   82 ISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANS  116 (367)
Q Consensus        82 v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t  116 (367)
                      |.++-|+|||+..+.+.-|.-..+....++=.=|-
T Consensus         1 ViGpaGSGKTT~~~~l~~~l~~~~r~~~vvNLDPA   35 (234)
T pfam03029         1 VVGGAGSGKTTFVGALSEILPLRGRSVYVVNLDPA   35 (234)
T ss_pred             CCCCCCCCHHHHHHHHHHHHHHCCCCEEEEECCCC
T ss_conf             98989898899999999999977997599978986


No 441
>PRK11147 ABC transporter ATPase component; Reviewed
Probab=69.63  E-value=4.2  Score=19.60  Aligned_cols=42  Identities=14%  Similarity=0.088  Sum_probs=27.4

Q ss_pred             CCCCCCCCCEEEEECC-CCCCHHHHHHHHHHHHCCCCCEEEEEEE
Q ss_conf             1011358628999754-5599889999898740698825899980
Q gi|254781187|r  185 VGPHNTHGMAVFNDEA-SGTPDIINKSILGFFTELNPNRFWIMTS  228 (367)
Q Consensus       185 ~g~h~~~~~l~ivDEA-sgI~d~i~e~i~g~Lt~~~~~~~~i~ig  228 (367)
                      +..-..+..++|+||- ++.+-...+.++..|...+.-+  ++++
T Consensus       168 A~aL~~~PdlLlLDEPTn~LD~~~~~~L~~~L~~~~gtv--liIS  210 (632)
T PRK11147        168 ARALVSNPDVLLLDEPTNHLDIETIEWLEGFLKTFQGSI--IFIS  210 (632)
T ss_pred             HHHHCCCCCEEEEECCCCCCCHHHHHHHHHHHHHCCCEE--EEEE
T ss_conf             998568999999848876589999999999999759849--9997


No 442
>PRK06851 hypothetical protein; Provisional
Probab=69.42  E-value=1.7  Score=22.07  Aligned_cols=51  Identities=16%  Similarity=0.228  Sum_probs=41.1

Q ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHHH
Q ss_conf             477614886788999999999999708997799971537999999999999
Q gi|254781187|r   79 KCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLKNTLWAEVS  129 (367)
Q Consensus        79 ~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~~~lw~ei~  129 (367)
                      -..+.+|-|+|||+++-.+.--++....+...+.++.--+.+.-++.++++
T Consensus        33 i~ilKGGpGtGKStlmK~ig~~~~~~GydVE~~hcssD~~SlDGvvip~lk   83 (368)
T PRK06851         33 IFILKGGPGTGKSTLMKKIGEEFLEKGYDVEFLHCSSDNDSLDGVIIPELK   83 (368)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCCEEEECCCC
T ss_conf             999968999778999999999999689837999758998864359975787


No 443
>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=69.23  E-value=7.8  Score=17.95  Aligned_cols=36  Identities=31%  Similarity=0.341  Sum_probs=25.0

Q ss_pred             EEEEEEECCC-CCCHHHHHHHHHHHHHHHCCCCEEEEEC
Q ss_conf             1247761488-6788999999999999708997799971
Q gi|254781187|r   77 IFKCAISAGR-GIGKTTLNAWMMLWLISTRPGMSIICIA  114 (367)
Q Consensus        77 ~~~~~v~sgr-g~GKS~~~a~~~lw~~~~~~~~~v~~~A  114 (367)
                      |..++|.++. |+|||++++.++.-+.  ..|.+|+++=
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 444
>PRK13695 putative NTPase; Provisional
Probab=69.22  E-value=7.8  Score=17.95  Aligned_cols=164  Identities=11%  Similarity=0.043  Sum_probs=69.5

Q ss_pred             EEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             12477614886788999999999999708997799971537999999999999999862312112333321000123332
Q gi|254781187|r   77 IFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLKNTLWAEVSKWLSMLPHRHWFEMQSLSLHPSGWYAE  156 (367)
Q Consensus        77 ~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~~~lw~ei~k~~~~~~~~~~~~~~~~~~~~~~~~~~  156 (367)
                      ..|+-+.+--|+|||+++.-++--+-.-......++|.+....-+.+-                |.+-...-....+...
T Consensus         3 ~~kI~iTG~PGvGKTTli~Kv~~~L~~~g~~v~GF~T~Evre~G~R~G----------------F~vv~l~~g~~~~lA~   66 (174)
T PRK13695          3 ALRIGITGMPGVGKTTLVLKIAELLAREGYKVGGFITEEVREGGKRIG----------------FKIIDLDTGEEGILAR   66 (174)
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHHHHHCCCEEEEEEEEEEECCCEEEE----------------EEEEECCCCCEEEEEE
T ss_conf             429998789998899999999999863696174699525603882850----------------5999905885687675


Q ss_pred             CCCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCEEEEECCCCC---CHHHHHHHHHHHHCCCCCEEEEEEECCCCC
Q ss_conf             21111345776126621013544556521011358628999754559---988999989874069882589998078999
Q gi|254781187|r  157 LLEQSMGIDSKHYTITCRTYSEERPDTFVGPHNTHGMAVFNDEASGT---PDIINKSILGFFTELNPNRFWIMTSNTRRL  233 (367)
Q Consensus       157 ~~~~~~~~~~~~~~~~a~~~~~~~~ea~~g~h~~~~~l~ivDEAsgI---~d~i~e~i~g~Lt~~~~~~~~i~igNP~r~  233 (367)
                      ... .....-|.+.+....+....-.+++-.. .+..++++||-...   +..+.++++..|.+ +.+.+ ..+  | + 
T Consensus        67 ~~~-~~~~~VgkY~V~~~~~e~~~~~~l~~a~-~~~dlivIDEIG~MEl~s~~F~~~V~~~L~s-~kpvl-~ti--h-~-  138 (174)
T PRK13695         67 VGA-VSRPRVGKYVVNLEDLERIAIPAISRAL-READLIIIDEIGPMELKSKKFVSAVEEVLKS-EKPVI-ATV--H-R-  138 (174)
T ss_pred             CCC-CCCCCCCCEEEEHHHHHHHHHHHHHHCC-CCCCEEEEECCCHHHHHHHHHHHHHHHHHCC-CCCEE-EEE--C-H-
T ss_conf             378-8985545668716897899899998353-5787999963103311049999999999738-99899-997--7-5-


Q ss_pred             CCHHHHHHHCCCCCEEEEEECCCCCCCCCHHHHHH
Q ss_conf             87688754112235046752333288889889999
Q gi|254781187|r  234 NGWFYDIFNIPLEDWKRYQIDTRTVEGIDSGFHEG  268 (367)
Q Consensus       234 ~g~Fye~~~~~~~~w~~~~~~~~d~p~~~~~~i~~  268 (367)
                        .|-+.... ++ -..+.++-.+-..+..+-++.
T Consensus       139 --p~v~~ik~-~~-~~v~~vT~~NRd~l~~~Il~~  169 (174)
T PRK13695        139 --PVVQRIRS-LG-GEVFWLTPENRNILPEEILNR  169 (174)
T ss_pred             --HHHHHHHC-CC-CEEEEECHHHHHHHHHHHHHH
T ss_conf             --88898633-79-899998934677559999999


No 445
>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=69.19  E-value=7.9  Score=17.95  Aligned_cols=31  Identities=39%  Similarity=0.498  Sum_probs=22.7

Q ss_pred             EEEC-CCCCCHHHHHHHHHHHHHHHCCCCEEEEE
Q ss_conf             7614-88678899999999999970899779997
Q gi|254781187|r   81 AISA-GRGIGKTTLNAWMMLWLISTRPGMSIICI  113 (367)
Q Consensus        81 ~v~s-grg~GKS~~~a~~~lw~~~~~~~~~v~~~  113 (367)
                      +|.+ -=|+|||++++.++..+.-  .+.+|+++
T Consensus         2 av~s~KGGVGKTT~a~nLA~~la~--~G~rVlli   33 (212)
T pfam01656         2 AIAGTKGGVGKTTLAANLARALAK--RGYRVLLI   33 (212)
T ss_pred             EEECCCCCHHHHHHHHHHHHHHHH--CCCCEEEE
T ss_conf             897689980699999999999997--89978998


No 446
>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=69.08  E-value=7.9  Score=17.93  Aligned_cols=34  Identities=24%  Similarity=0.305  Sum_probs=25.5

Q ss_pred             EEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECC
Q ss_conf             776148867889999999999997089977999715
Q gi|254781187|r   80 CAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIAN  115 (367)
Q Consensus        80 ~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~  115 (367)
                      +.|.++-|+|||.++.-++.-.+.  .+.++++++-
T Consensus         2 tLi~G~pGsGKT~~a~qfl~~~a~--~ge~~lyis~   35 (187)
T cd01124           2 TLLSGGPGTGKTTFALQFLYAGLA--RGEPGLYVTL   35 (187)
T ss_pred             EEEEECCCCCHHHHHHHHHHHHHH--CCCCEEEEEE
T ss_conf             158768999999999999999987--6997899995


No 447
>TIGR02030 BchI-ChlI magnesium chelatase ATPase subunit I; InterPro: IPR011775    This entry represents one of two ATPase subunits of the trimeric magnesium chelatase responsible for insertion of magnesium ion into protoporphyrin IX. This is an essential step in the biosynthesis of both chlorophyll and bacteriochlorophyll . This subunit is found in green plants, photosynthetic algae, cyanobacteria and other photosynthetic bacteria. It is also found in certain archaea not known to make chlorins.; GO: 0005524 ATP binding, 0016851 magnesium chelatase activity, 0006779 porphyrin biosynthetic process.
Probab=68.85  E-value=8  Score=17.90  Aligned_cols=138  Identities=12%  Similarity=0.036  Sum_probs=68.0

Q ss_pred             CCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCH--HHHHHHHHHHHHHHHHHC-CCCCCCCCCCCCCC
Q ss_conf             554112477614886788999999999999708997799971537--999999999999999862-31211233332100
Q gi|254781187|r   73 SNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSE--TQLKNTLWAEVSKWLSML-PHRHWFEMQSLSLH  149 (367)
Q Consensus        73 ~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~--~Q~~~~lw~ei~k~~~~~-~~~~~~~~~~~~~~  149 (367)
                      -+|..==|-|.+-||+|||+.+=+|+-    .-|.-+++---|.-  -..+..+..|.+-..... ..+... +-..+..
T Consensus        21 idP~IGGVmvmGdRGTgKSTavRALAa----lLP~IkaVagcP~n~~Ps~~~~~c~e~r~~~~~~Gkt~~~~-~i~~pvp   95 (340)
T TIGR02030        21 IDPKIGGVMVMGDRGTGKSTAVRALAA----LLPEIKAVAGCPFNSAPSDREELCEEVRILEDSSGKTKKLA-VIEKPVP   95 (340)
T ss_pred             ECCCCCEEEEECCCCCCHHHHHHHHHH----HCCCEEEECCCCCCCCCCCCCCCCHHHHHHHHCCCCCCCCE-EEECCCC
T ss_conf             068856288867789835689999997----49940786176878888886135767777531268656751-5515765


Q ss_pred             CCCCCCCCCCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCEEEEECCCCCCHHHHHHHHHHHHCC
Q ss_conf             012333221111345776126621013544556521011358628999754559988999989874069
Q gi|254781187|r  150 PSGWYAELLEQSMGIDSKHYTITCRTYSEERPDTFVGPHNTHGMAVFNDEASGTPDIINKSILGFFTEL  218 (367)
Q Consensus       150 ~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~ea~~g~h~~~~~l~ivDEAsgI~d~i~e~i~g~Lt~~  218 (367)
                      +-.......+.-.-+.--.-.+-+++-....|.=++-   .|+=++++||---..|++-++++=.-.++
T Consensus        96 vVDLPLGaTEDRVcGtlDIerALt~GvkAFePGLLAr---ANRG~LYiDEVNLLeDHlVDvLLDvAasG  161 (340)
T TIGR02030        96 VVDLPLGATEDRVCGTLDIERALTEGVKAFEPGLLAR---ANRGYLYIDEVNLLEDHLVDVLLDVAASG  161 (340)
T ss_pred             EEECCCCCCCCCEECHHHHHHHHHCCCCCCCCCCHHH---HCCCCEEEEEEHHHHHHHHHHHHHHCCCC
T ss_conf             3647988621313440247677504721036630466---61784255210001245665665220478


No 448
>cd04170 EF-G_bact 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
Probab=68.63  E-value=4.7  Score=19.33  Aligned_cols=134  Identities=19%  Similarity=0.111  Sum_probs=67.5

Q ss_pred             EEEEECCCCCCHHHHHHHHHHHHH-HHCCCCEEEEECCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             477614886788999999999999-7089977999715379999999999999998623121123333210001233322
Q gi|254781187|r   79 KCAISAGRGIGKTTLNAWMMLWLI-STRPGMSIICIANSETQLKNTLWAEVSKWLSMLPHRHWFEMQSLSLHPSGWYAEL  157 (367)
Q Consensus        79 ~~~v~sgrg~GKS~~~a~~~lw~~-~~~~~~~v~~~A~t~~Q~~~~lw~ei~k~~~~~~~~~~~~~~~~~~~~~~~~~~~  157 (367)
                      ++++.+.-|.|||+++-.++..-- ..+.|. |    ...+.+.|-+=-|.++-+.....-..+.|+.            
T Consensus         1 Ni~iigH~~aGKTtL~E~lL~~~g~i~~~G~-V----~~g~t~~D~~~~E~~RgiSi~s~~~~~~w~~------------   63 (268)
T cd04170           1 NIALVGHSGSGKTTLAEALLYATGAIDRLGS-V----EDGTTVSDYDPEEIKRKMSISTSVAPLEWKG------------   63 (268)
T ss_pred             CEEEEECCCCCHHHHHHHHHHHCCCCCCCCC-C----CCCCCCCCCCHHHHHCCCCEECCEEEEEECC------------
T ss_conf             9899908999989999999996699665765-4----5897357787889867967513557888899------------


Q ss_pred             CCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCEEEEECCCCCCH---HHHHHHHHHHHCCCCCEEEEEEECCC-CC
Q ss_conf             111134577612662101354455652101135862899975455998---89999898740698825899980789-99
Q gi|254781187|r  158 LEQSMGIDSKHYTITCRTYSEERPDTFVGPHNTHGMAVFNDEASGTPD---IINKSILGFFTELNPNRFWIMTSNTR-RL  233 (367)
Q Consensus       158 ~~~~~~~~~~~~~~~a~~~~~~~~ea~~g~h~~~~~l~ivDEAsgI~d---~i~e~i~g~Lt~~~~~~~~i~igNP~-r~  233 (367)
                              ....++..-+......|...+++.-...++++|=.+||..   .+|+.+.    ..+-+.+  ++-|=- |.
T Consensus        64 --------~~inliDTPG~~DF~~e~~~aL~v~D~Av~Vida~~GVe~~T~~~w~~~~----~~~iP~i--~fINKmDr~  129 (268)
T cd04170          64 --------HKINLIDTPGYADFVGETRAALRAADAALVVVSAQSGVEVGTEKLWEFAD----EAGIPRI--IFINKMDRE  129 (268)
T ss_pred             --------EEEEEEECCCCHHHHHHHHHHHCCCCEEEEEECCCCCHHHHHHHHHHHHH----HCCCCEE--EEEECCCCC
T ss_conf             --------79999869897579999999840478399994187547687999999999----8599989--999787878


Q ss_pred             CCHHHHHHHC
Q ss_conf             8768875411
Q gi|254781187|r  234 NGWFYDIFNI  243 (367)
Q Consensus       234 ~g~Fye~~~~  243 (367)
                      .--|.++...
T Consensus       130 ~ad~~~~l~~  139 (268)
T cd04170         130 RADFDKTLAA  139 (268)
T ss_pred             CCCHHHHHHH
T ss_conf             9964779999


No 449
>PRK13343 F0F1 ATP synthase subunit alpha; Provisional
Probab=68.62  E-value=8.1  Score=17.87  Aligned_cols=21  Identities=24%  Similarity=0.294  Sum_probs=17.1

Q ss_pred             EEEEECCCCCCHHHHHHHHHH
Q ss_conf             477614886788999999999
Q gi|254781187|r   79 KCAISAGRGIGKTTLNAWMML   99 (367)
Q Consensus        79 ~~~v~sgrg~GKS~~~a~~~l   99 (367)
                      |+.|-+|+|+|||+++.-.++
T Consensus       164 R~gIfg~~GvGKT~L~~~~I~  184 (502)
T PRK13343        164 RELIIGDRQTGKTAIAIDAII  184 (502)
T ss_pred             EEECCCCCCCCCCHHHHHHHH
T ss_conf             775136788880489999999


No 450
>TIGR00064 ftsY signal recognition particle-docking protein FtsY; InterPro: IPR004390   ABC transporters belong to the ATP-Binding Cassette (ABC) superfamily, which uses the hydrolysis of ATP to energize diverse biological systems. ABC transporters are minimally constituted of two conserved regions: a highly conserved ATP binding cassette (ABC) and a less conserved transmembrane domain (TMD). These regions can be found on the same protein or on two different ones. Most ABC transporters function as a dimer and therefore are constituted of four domains, two ABC modules and two TMDs.   ABC transporters are involved in the export or import of a wide variety of substrates ranging from small ions to macromolecules. The major function of ABC import systems is to provide essential nutrients to bacteria. They are found only in prokaryotes and their four constitutive domains are usually encoded by independent polypeptides (two ABC proteins and two TMD proteins). Prokaryotic importers require additional extracytoplasmic binding proteins (one or more per systems) for function. In contrast, export systems are involved in the extrusion of noxious substances, the export of extracellular toxins and the targeting of membrane components. They are found in all living organisms and in general the TMD is fused to the ABC module in a variety of combinations. Some eukaryotic exporters encode the four domains on the same polypeptide chain .    The ABC module (approximately two hundred amino acid residues) is known to bind and hydrolyze ATP, thereby coupling transport to ATP hydrolysis in a large number of biological processes. The cassette is duplicated in several subfamilies. Its primary sequence is highly conserved, displaying a typical phosphate-binding loop: Walker A, and a magnesium binding site: Walker B. Besides these two regions, three other conserved motifs are present in the ABC cassette: the switch region which contains a histidine loop, postulated to polarize the attaching water molecule for hydrolysis, the signature conserved motif (LSGGQ) specific to the ABC transporter, and the Q-motif (between Walker A and the signature), which interacts with the gamma phosphate through a water bond. The Walker A, Walker B, Q-loop and switch region form the nucleotide binding site , , .   The 3D structure of a monomeric ABC module adopts a stubby L-shape with two distinct arms. ArmI (mainly beta-strand) contains Walker A and Walker B. The important residues for ATP hydrolysis and/or binding are located in the P-loop. The ATP-binding pocket is located at the extremity of armI. The perpendicular armII contains mostly the alpha helical subdomain with the signature motif. It only seems to be required for structural integrity of the ABC module. ArmII is in direct contact with the TMD. The hinge between armI and armII contains both the histidine loop and the Q-loop, making contact with the gamma phosphate of the ATP molecule. ATP hydrolysis leads to a conformational change that could facilitate ADP release. In the dimer the two ABC cassettes contact each other through hydrophobic interactions at the antiparallel beta-sheet of armI by a two-fold axis , , , , , .   Proteins known to belong to this family are classified in several functional subfamilies depending on the substrate used (for further information see http://www.tcdb.org/tcdb/index.php?tc=3.A.1).  This family includes the cell division ABC transporter and the periplasmic substrate-binding protein FtsY. There is a weak division between FtsY and SRP54; both are GTPases. In Escherichia coli, ftsY is an essential gene located in an operon with cell division genes ftsE and ftsX, but its apparent function is as the signal recognition particle docking protein.; GO: 0005525 GTP binding.
Probab=68.61  E-value=8.1  Score=17.87  Aligned_cols=130  Identities=17%  Similarity=0.198  Sum_probs=72.7

Q ss_pred             CCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEE-ECCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCC
Q ss_conf             5555541124776148867889999999999997089977999-715379999999999999998623121123333210
Q gi|254781187|r   70 VNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIIC-IANSETQLKNTLWAEVSKWLSMLPHRHWFEMQSLSL  148 (367)
Q Consensus        70 ~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~-~A~t~~Q~~~~lw~ei~k~~~~~~~~~~~~~~~~~~  148 (367)
                      .....|+++  .+.+=.|+|||+.+|=++-++.--.  .+|++ -+-|.+=+-   -..+..|.+++-.           
T Consensus        77 ~~~~kp~Vi--l~VGVNG~GKTTTIaKLA~~l~~~G--k~V~laAgDTFRAAA---~EQL~~Wa~R~gv-----------  138 (284)
T TIGR00064        77 PEEKKPNVI--LFVGVNGVGKTTTIAKLANKLKKQG--KSVLLAAGDTFRAAA---IEQLEVWAKRLGV-----------  138 (284)
T ss_pred             CCCCCCEEE--EEEEEECCCHHHHHHHHHHHHHHCC--CEEEEECCCHHHHHH---HHHHHHHHHHHCC-----------
T ss_conf             147897799--9984408860102889999998749--908998275247999---9999998988387-----------


Q ss_pred             CCCCCCCCCCCCCCC-CCCCCEEEEECCCCCCCCCCCCCCCCCCCCEEEEECCCCCCH---------HHHHHHHHHHH-C
Q ss_conf             001233322111134-577612662101354455652101135862899975455998---------89999898740-6
Q gi|254781187|r  149 HPSGWYAELLEQSMG-IDSKHYTITCRTYSEERPDTFVGPHNTHGMAVFNDEASGTPD---------IINKSILGFFT-E  217 (367)
Q Consensus       149 ~~~~~~~~~~~~~~~-~~~~~~~~~a~~~~~~~~ea~~g~h~~~~~l~ivDEAsgI~d---------~i~e~i~g~Lt-~  217 (367)
                             ...+...+ .|+-+..-          ++.+...+.+...+++|-|.-...         +|.-++.-... +
T Consensus       139 -------~vi~~~~gn~DPAaV~f----------DAi~~Ak~~niDvvliDTAGRLqnk~NLm~EL~KI~RV~~k~~~~~  201 (284)
T TIGR00064       139 -------DVIKQKEGNADPAAVIF----------DAIQAAKARNIDVVLIDTAGRLQNKVNLMDELKKIKRVIKKVDPVD  201 (284)
T ss_pred             -------EEEECCCCCCCCHHHHH----------HHHHHHHHCCCCEEEEECCCCCCCCHHHHHHHHHHHHHHHHHHCCC
T ss_conf             -------55407889887178999----------9899998749978997347545466203999999999873210257


Q ss_pred             CCCCEEEEEEECCCCCCC
Q ss_conf             988258999807899987
Q gi|254781187|r  218 LNPNRFWIMTSNTRRLNG  235 (367)
Q Consensus       218 ~~~~~~~i~igNP~r~~g  235 (367)
                      .-...+ +.+-..++.++
T Consensus       202 aP~e~l-LVlDAt~Gqna  218 (284)
T TIGR00064       202 APDEVL-LVLDATTGQNA  218 (284)
T ss_pred             CCCEEE-EEEHHHHHHHH
T ss_conf             875575-42202220308


No 451
>COG5008 PilU Tfp pilus assembly protein, ATPase PilU [Cell motility and secretion / Intracellular trafficking and secretion]
Probab=68.39  E-value=7.1  Score=18.20  Aligned_cols=29  Identities=28%  Similarity=0.280  Sum_probs=18.4

Q ss_pred             EEEECCCCCCHHHHHHHHHHHHHHHCCCC
Q ss_conf             77614886788999999999999708997
Q gi|254781187|r   80 CAISAGRGIGKTTLNAWMMLWLISTRPGM  108 (367)
Q Consensus        80 ~~v~sgrg~GKS~~~a~~~lw~~~~~~~~  108 (367)
                      +.|.++.|+|||+..|.++-+.--..++.
T Consensus       130 viiVGaTGSGKSTtmAaMi~yRN~~s~gH  158 (375)
T COG5008         130 VIIVGATGSGKSTTMAAMIGYRNKNSTGH  158 (375)
T ss_pred             EEEECCCCCCCHHHHHHHHCCCCCCCCCC
T ss_conf             99987788884016899860134688773


No 452
>cd01122 GP4d_helicase GP4d_helicase is a homohexameric 5'-3' helicases. Helicases couple NTP hydrolysis to the unwinding of nucleic acid duplexes into their component strands.
Probab=68.37  E-value=8.2  Score=17.84  Aligned_cols=44  Identities=30%  Similarity=0.396  Sum_probs=29.1

Q ss_pred             EEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEEC--CCHHHHHHHH
Q ss_conf             77614886788999999999999708997799971--5379999999
Q gi|254781187|r   80 CAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIA--NSETQLKNTL  124 (367)
Q Consensus        80 ~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A--~t~~Q~~~~l  124 (367)
                      +.|+|.-|+|||+++.-+++..+. ..+.+|++.+  -+..|+...+
T Consensus        33 ~viaarpg~GKT~f~~~~a~~~~~-~~g~~vl~~SlEm~~~~~~~Rl   78 (271)
T cd01122          33 IILTAGTGVGKTTFLREYALDLIT-QHGVRVGTISLEEPVVRTARRL   78 (271)
T ss_pred             EEEEECCCCCHHHHHHHHHHHHHH-HCCCEEEEEECCCCHHHHHHHH
T ss_conf             999968998699999999999999-7699089997049999999999


No 453
>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=68.30  E-value=4.6  Score=19.38  Aligned_cols=42  Identities=19%  Similarity=0.230  Sum_probs=29.7

Q ss_pred             EEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEE--ECCCHHHHHHH
Q ss_conf             776148867889999999999997089977999--71537999999
Q gi|254781187|r   80 CAISAGRGIGKTTLNAWMMLWLISTRPGMSIIC--IANSETQLKNT  123 (367)
Q Consensus        80 ~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~--~A~t~~Q~~~~  123 (367)
                      +||=.==|+|||+.+|.+.+-++  +.|+||+=  +=|+.+...++
T Consensus         3 lAvYGKGGiGKSTTssNLSvA~A--~~GkkVlQIGCDPKhDSTFTL   46 (275)
T TIGR01281         3 LAVYGKGGIGKSTTSSNLSVALA--KKGKKVLQIGCDPKHDSTFTL   46 (275)
T ss_pred             EEEECCCCCCCHHHHHHHHHHHH--HCCCEEEEECCCCCCCCCCCC
T ss_conf             88863888770046789999998--469918985257888877454


No 454
>cd04140 ARHI_like ARHI subfamily.  ARHI (A Ras homolog member I) is a member of the Ras family with several unique structural and functional properties.  ARHI is expressed in normal human ovarian and breast tissue, but its expression is decreased or eliminated in breast and ovarian cancer.  ARHI contains an N-terminal extension of 34 residues (human) that is required to retain its tumor suppressive activity.   Unlike most other Ras family members, ARHI is maintained in the constitutively active (GTP-bound) state in resting cells and has modest GTPase activity.  ARHI inhibits STAT3 (signal transducers and activators of transcription 3), a latent transcription factor whose abnormal activation plays a critical role in oncogenesis.  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 most Ras proteins.  Due to
Probab=68.21  E-value=5.6  Score=18.83  Aligned_cols=22  Identities=18%  Similarity=0.468  Sum_probs=19.5

Q ss_pred             EEEEEECCCCCCHHHHHHHHHH
Q ss_conf             2477614886788999999999
Q gi|254781187|r   78 FKCAISAGRGIGKTTLNAWMML   99 (367)
Q Consensus        78 ~~~~v~sgrg~GKS~~~a~~~l   99 (367)
                      ||+.|.+--|+|||.++..++-
T Consensus         2 ~KivllGd~~VGKTsli~r~~~   23 (165)
T cd04140           2 YRVVVFGAGGVGKSSLVLRFVK   23 (165)
T ss_pred             EEEEEECCCCCCHHHHHHHHHH
T ss_conf             0999989999769999999964


No 455
>cd04141 Rit_Rin_Ric Rit/Rin/Ric subfamily.  Rit (Ras-like protein in all tissues), Rin (Ras-like protein in neurons) and Ric (Ras-related protein which interacts with calmodulin) form a subfamily with several unique structural and functional characteristics.   These proteins all lack a the C-terminal CaaX lipid-binding motif typical of Ras family proteins, and Rin and Ric contain calmodulin-binding domains.  Rin, which is expressed only in neurons, induces neurite outgrowth in rat pheochromocytoma cells through its association with calmodulin and its activation of endogenous Rac/cdc42.  Rit, which is ubiquitously expressed in mammals, inhibits growth-factor withdrawl-mediated apoptosis and induces neurite extension in pheochromocytoma cells.  Rit and Rin are both able to form a ternary complex with PAR6, a cell polarity-regulating protein, and Rac/cdc42.  This ternary complex is proposed to have physiological function in processes such as tumorigenesis.  Activated Ric is likely to sign
Probab=68.20  E-value=5.9  Score=18.73  Aligned_cols=22  Identities=18%  Similarity=0.459  Sum_probs=19.5

Q ss_pred             EEEEEECCCCCCHHHHHHHHHH
Q ss_conf             2477614886788999999999
Q gi|254781187|r   78 FKCAISAGRGIGKTTLNAWMML   99 (367)
Q Consensus        78 ~~~~v~sgrg~GKS~~~a~~~l   99 (367)
                      ||+.|.+..|+|||.++..++-
T Consensus         3 ~Kiv~lGd~~VGKTsli~r~~~   24 (172)
T cd04141           3 YKIVMLGAGGVGKSAVTMQFIS   24 (172)
T ss_pred             EEEEEECCCCCCHHHHHHHHHH
T ss_conf             6999999999779999999970


No 456
>cd01129 PulE-GspE PulE/GspE The type II secretory pathway is the main terminal branch of the general secretory pathway (GSP).  It is responsible for the export the majority of Gram-negative bacterial exoenzymes and toxins. PulE is a cytoplasmic protein of the GSP, which contains an ATP binding site and a tetracysteine motif. This subgroup also includes PillB and HofB.
Probab=68.12  E-value=8.3  Score=17.81  Aligned_cols=54  Identities=20%  Similarity=0.153  Sum_probs=34.8

Q ss_pred             CCHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECC
Q ss_conf             842899999998888751245555541124776148867889999999999997089977999715
Q gi|254781187|r   50 QPHRWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIAN  115 (367)
Q Consensus        50 ~p~~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~  115 (367)
                      |..+-|.+.|+.+....+.          -+.|++.-|+|||+....++-.  +..++.+|+.+..
T Consensus        63 G~~~~~~~~l~~~~~~~~G----------lilitGptGSGKtTtl~a~l~~--~~~~~~~i~tiEd  116 (264)
T cd01129          63 GLKPENLEIFRKLLEKPHG----------IILVTGPTGSGKTTTLYSALSE--LNTPEKNIITVED  116 (264)
T ss_pred             CCCHHHHHHHHHHHHCCCC----------EEEEECCCCCCHHHHHHHHHHH--HCCCCCEEEEEEC
T ss_conf             7999999999999708998----------8999789999779999999986--4368850899867


No 457
>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=68.09  E-value=7.2  Score=18.19  Aligned_cols=30  Identities=23%  Similarity=0.267  Sum_probs=22.3

Q ss_pred             CCCCHHHHHHHHHHHHHHHCCCCEEEEECCCH
Q ss_conf             86788999999999999708997799971537
Q gi|254781187|r   86 RGIGKTTLNAWMMLWLISTRPGMSIICIANSE  117 (367)
Q Consensus        86 rg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~  117 (367)
                      =|+|||+.+..++..++..  |.+|+++=-.-
T Consensus        10 GGvGKTTtavnLA~aLA~~--G~rVllIDlDp   39 (261)
T pfam09140        10 GGSGKSTTAVHVAVALLYL--GARVATIDLDL   39 (261)
T ss_pred             CCCCHHHHHHHHHHHHHHC--CCCEEEEECCC
T ss_conf             9872999999999999988--99789997999


No 458
>KOG0388 consensus
Probab=67.96  E-value=8.3  Score=17.79  Aligned_cols=163  Identities=15%  Similarity=0.144  Sum_probs=78.1

Q ss_pred             HHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCC-CCEEEEECCCHHHHHHHHHHHHHHH
Q ss_conf             899999998888751245555541124776148867889999999999997089-9779997153799999999999999
Q gi|254781187|r   53 RWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRP-GMSIICIANSETQLKNTLWAEVSKW  131 (367)
Q Consensus        53 ~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~-~~~v~~~A~t~~Q~~~~lw~ei~k~  131 (367)
                      ++|.+=|.=++.--..+.+        -..+---|.|||.-+-.++.+++-++. ..-.+|++|. +.+. -.-.||.++
T Consensus       570 EYQlkGLnWLvnlYdqGiN--------GILADeMGLGKTVQsisvlAhLaE~~nIwGPFLVVtpa-StL~-NWaqEisrF  639 (1185)
T KOG0388         570 EYQLKGLNWLVNLYDQGIN--------GILADEMGLGKTVQSISVLAHLAETHNIWGPFLVVTPA-STLH-NWAQEISRF  639 (1185)
T ss_pred             HHHHCCHHHHHHHHHCCCC--------CEEHHHHCCCHHHHHHHHHHHHHHHCCCCCCEEEEEHH-HHHH-HHHHHHHHH
T ss_conf             8765007899999870344--------12133304532688999999998744588763896027-8776-799999985


Q ss_pred             HHHCCC-CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCEEEEECCCCCCH---HH
Q ss_conf             986231-21123333210001233322111134577612662101354455652101135862899975455998---89
Q gi|254781187|r  132 LSMLPH-RHWFEMQSLSLHPSGWYAELLEQSMGIDSKHYTITCRTYSEERPDTFVGPHNTHGMAVFNDEASGTPD---II  207 (367)
Q Consensus       132 ~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~ea~~g~h~~~~~l~ivDEAsgI~d---~i  207 (367)
                      +-.+.. .+|-..+...+--+.|.....  +-+..+-...++.--.-.....=++..   ..-+.|+|||+.|..   .-
T Consensus       640 lP~~k~lpywGs~~eRkiLrKfw~rKnm--Y~rna~fhVviTSYQlvVtDeky~qkv---KWQYMILDEAQAIKSSsS~R  714 (1185)
T KOG0388         640 LPSFKVLPYWGSPSERKILRKFWNRKNM--YRRNAPFHVVITSYQLVVTDEKYLQKV---KWQYMILDEAQAIKSSSSSR  714 (1185)
T ss_pred             CCCCEEECCCCCHHHHHHHHHHCCHHHH--HCCCCCCEEEEEEEEEEECHHHHHHHH---HHHHEEHHHHHHHHHHHHHH
T ss_conf             8654243476880266899974044444--304799528997531111159999863---34520055787764322567


Q ss_pred             HHHHHHHHHCCCCCEEEEEEECCCCCC
Q ss_conf             999898740698825899980789998
Q gi|254781187|r  208 NKSILGFFTELNPNRFWIMTSNTRRLN  234 (367)
Q Consensus       208 ~e~i~g~Lt~~~~~~~~i~igNP~r~~  234 (367)
                      |..+...-+  .+++  +++|+|-.++
T Consensus       715 WKtLLsF~c--RNRL--LLTGTPIQNs  737 (1185)
T KOG0388         715 WKTLLSFKC--RNRL--LLTGTPIQNS  737 (1185)
T ss_pred             HHHHHHHHC--CCEE--EECCCCCCHH
T ss_conf             887740210--3404--5318853017


No 459
>TIGR00486 TIGR00486 conserved hypothetical protein TIGR00486; InterPro: IPR002678   This family contains several NIF3 (NGG1p interacting factor 3) protein homologues. NIF3 interacts with the yeast transcriptional coactivator NGG1p which is part of the ADA complex, the exact function of this interaction is unknown ..
Probab=67.94  E-value=8.3  Score=17.79  Aligned_cols=75  Identities=13%  Similarity=0.186  Sum_probs=49.8

Q ss_pred             CCCCCCCHHHHHHHHHHHHHHHHCC----CCCCC------CCEEEEEEECCCCCC-HHHHHHHHHHHHHHHCCCCEEEEE
Q ss_conf             4366684289999999888875124----55555------411247761488678-899999999999970899779997
Q gi|254781187|r   45 LEHFSQPHRWQLEFMEAVDVHCHSN----VNNSN------PTIFKCAISAGRGIG-KTTLNAWMMLWLISTRPGMSIICI  113 (367)
Q Consensus        45 ~~~~~~p~~wq~~~l~~~~~~~~~~----~~~~~------~~~~~~~v~sgrg~G-KS~~~a~~~lw~~~~~~~~~v~~~  113 (367)
                      +..+..+..- .+++..+...+.++    .....      ..+.||||+||-|.+ ||++...+.       .+.-+.+|
T Consensus       193 ~~~~~~~~~~-~~~~~~~~~~L~v~~~~~~~~~~PsaWnq~~v~kvA~vsG~G~s~ks~~~~a~~-------~gvd~yiT  264 (325)
T TIGR00486       193 VGELKASIES-KEEVLEIKKKLNVKPLLVVKKGEPSAWNQEKVKKVAVVSGSGLSDKSFIMKALR-------EGVDLYIT  264 (325)
T ss_pred             EEEECCCCCH-HHHHHHHHHHCCCCCEEEEECCCCCCCCCCCCCEEEEEECCCCCHHHHHHHHHH-------CCCCEEEC
T ss_conf             6753455105-788888887449971788506887523102166389995578752789999997-------08968971


Q ss_pred             CCCHHHHHHHHHHHH
Q ss_conf             153799999999999
Q gi|254781187|r  114 ANSETQLKNTLWAEV  128 (367)
Q Consensus       114 A~t~~Q~~~~lw~ei  128 (367)
                      -....|.. .+|+|+
T Consensus       265 Gd~~h~~~-~~A~e~  278 (325)
T TIGR00486       265 GDLSHHTA-HLAREL  278 (325)
T ss_pred             CCCHHHHH-HHHHHC
T ss_conf             65406678-876438


No 460
>cd04117 Rab15 Rab15 subfamily.  Rab15 colocalizes with the transferrin receptor in early endosome compartments, but not with late endosomal markers. It codistributes with Rab4 and Rab5 on early/sorting endosomes, and with Rab11 on pericentriolar recycling endosomes. It is believed to function as an inhibitory GTPase that regulates distinct steps in early endocytic 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 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
Probab=67.87  E-value=5.3  Score=19.01  Aligned_cols=22  Identities=27%  Similarity=0.407  Sum_probs=19.0

Q ss_pred             EEEEEECCCCCCHHHHHHHHHH
Q ss_conf             2477614886788999999999
Q gi|254781187|r   78 FKCAISAGRGIGKTTLNAWMML   99 (367)
Q Consensus        78 ~~~~v~sgrg~GKS~~~a~~~l   99 (367)
                      ||+.+.+..|+|||.++..++-
T Consensus         1 ~KIvllGd~~VGKTsli~r~~~   22 (161)
T cd04117           1 FRLLLIGDSGVGKTCLLCRFTD   22 (161)
T ss_pred             CEEEEECCCCCCHHHHHHHHHC
T ss_conf             9899999499858999999942


No 461
>PRK03333 coaE dephospho-CoA kinase/unknown domain fusion protein; Provisional
Probab=67.87  E-value=5  Score=19.15  Aligned_cols=23  Identities=26%  Similarity=0.541  Sum_probs=18.3

Q ss_pred             EEEEEEECCCCCCHHHHHHHHHH
Q ss_conf             12477614886788999999999
Q gi|254781187|r   77 IFKCAISAGRGIGKTTLNAWMML   99 (367)
Q Consensus        77 ~~~~~v~sgrg~GKS~~~a~~~l   99 (367)
                      |+++.+.+|=|+|||+.+.++.-
T Consensus         1 M~~IGLTGGIgsGKStv~~~l~~   23 (394)
T PRK03333          1 MLRIGLTGGIGAGKSTVSATLAQ   23 (394)
T ss_pred             CEEEEEECCCCCCHHHHHHHHHH
T ss_conf             94998306755579999999998


No 462
>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=67.82  E-value=5.4  Score=18.97  Aligned_cols=33  Identities=21%  Similarity=0.391  Sum_probs=24.7

Q ss_pred             HHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHH
Q ss_conf             99988887512455555411247761488678899999999
Q gi|254781187|r   58 FMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMM   98 (367)
Q Consensus        58 ~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~   98 (367)
                      +|+.|.=.+..+.        +++|.+.-|+|||+++..++
T Consensus        52 VLk~Isf~I~~Ge--------~vaIVG~sGSGKSTLl~lL~   84 (282)
T cd03291          52 VLKNINLKIEKGE--------MLAITGSTGSGKTSLLMLIL   84 (282)
T ss_pred             EEECEEEEECCCC--------EEEEECCCCCHHHHHHHHHH
T ss_conf             1416489984999--------99999999981999999995


No 463
>PRK13873 conjugal transfer ATPase TrbE; Provisional
Probab=67.77  E-value=8.4  Score=17.77  Aligned_cols=33  Identities=27%  Similarity=0.413  Sum_probs=19.6

Q ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEE
Q ss_conf             4776148867889999999999997089977999
Q gi|254781187|r   79 KCAISAGRGIGKTTLNAWMMLWLISTRPGMSIIC  112 (367)
Q Consensus        79 ~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~  112 (367)
                      ...|.++-|.|||++.+.++.= ..-+++.+|++
T Consensus       443 HtlI~GpTGsGKTvll~~l~~q-~~ry~~~~vf~  475 (815)
T PRK13873        443 HTLVVGPTGAGKSVLLALMALQ-FRRYPGSQVFA  475 (815)
T ss_pred             CEEEECCCCCCHHHHHHHHHHH-HHHCCCCCEEE
T ss_conf             4389788999899999999999-86448984899


No 464
>cd04115 Rab33B_Rab33A Rab33B/Rab33A subfamily.  Rab33B is ubiquitously expressed in mouse tissues and cells, where it is localized to the medial Golgi cisternae. It colocalizes with alpha-mannose II.  Together with the other cisternal Rabs, Rab6A and Rab6A', it is believed to regulate the Golgi response to stress and is likely a molecular target in stress-activated signaling pathways. Rab33A (previously known as S10) is expressed primarily in the brain and immune system cells.  In humans, it is located on the X chromosome at Xq26 and its expression is down-regulated in tuberculosis patients. Experimental evidence suggests that Rab33A is a novel CD8+ T cell factor that likely plays a role in tuberculosis disease processes.  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 
Probab=67.65  E-value=6.4  Score=18.49  Aligned_cols=23  Identities=30%  Similarity=0.429  Sum_probs=19.2

Q ss_pred             EEEEEEECCCCCCHHHHHHHHHH
Q ss_conf             12477614886788999999999
Q gi|254781187|r   77 IFKCAISAGRGIGKTTLNAWMML   99 (367)
Q Consensus        77 ~~~~~v~sgrg~GKS~~~a~~~l   99 (367)
                      .||+.+.+..|+|||.++-.++-
T Consensus         2 ~~Kiv~lGd~~VGKTsli~r~~~   24 (170)
T cd04115           2 IFKIIVIGDSNVGKTCLTYRFCA   24 (170)
T ss_pred             EEEEEEECCCCCCHHHHHHHHHC
T ss_conf             69999999799779999999953


No 465
>cd00877 Ran Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases. Ran GTPase is involved in diverse biological functions, such as nuclear transport, spindle formation during mitosis, DNA replication, and cell division.  Among the Ras superfamily, Ran is a unique small G protein.  It does not have a lipid modification motif at the C-terminus to bind to the membrane, which is often observed within the Ras superfamily.  Ran may therefore interact with a wide range of proteins in various intracellular locations.  Like other GTPases, Ran exists in GTP- and GDP-bound conformations that interact differently with effectors.  Conversion between these forms and the assembly or disassembly of effector complexes requires the interaction of regulator proteins.  The intrinsic GTPase activity of Ran is very low, but it is greatly stimulated by a GTPase-activating protein (RanGAP1) located in the cytoplasm. By contrast, RCC1, a guanine nucleotide exchange factor that generates RanGTP, is
Probab=67.55  E-value=5.7  Score=18.79  Aligned_cols=21  Identities=33%  Similarity=0.482  Sum_probs=18.1

Q ss_pred             EEEEEECCCCCCHHHHHHHHH
Q ss_conf             247761488678899999999
Q gi|254781187|r   78 FKCAISAGRGIGKTTLNAWMM   98 (367)
Q Consensus        78 ~~~~v~sgrg~GKS~~~a~~~   98 (367)
                      ||+.+.+..|+|||.++-.++
T Consensus         1 ~KivlvGd~~VGKTsli~r~~   21 (166)
T cd00877           1 FKLVLVGDGGTGKTTFVKRHL   21 (166)
T ss_pred             CEEEEECCCCCCHHHHHHHHH
T ss_conf             989999999988899999998


No 466
>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=67.52  E-value=5.6  Score=18.87  Aligned_cols=20  Identities=20%  Similarity=0.290  Sum_probs=17.9

Q ss_pred             EEEEECCCCCCHHHHHHHHH
Q ss_conf             47761488678899999999
Q gi|254781187|r   79 KCAISAGRGIGKTTLNAWMM   98 (367)
Q Consensus        79 ~~~v~sgrg~GKS~~~a~~~   98 (367)
                      |+.|.+..|+|||.++..++
T Consensus         2 KivvvG~~~vGKTSLi~r~~   21 (168)
T cd04119           2 KVISMGNSGVGKSCIIKRYC   21 (168)
T ss_pred             EEEEECCCCCCHHHHHHHHH
T ss_conf             89999959956899999996


No 467
>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=67.41  E-value=5.4  Score=18.94  Aligned_cols=21  Identities=33%  Similarity=0.335  Sum_probs=18.4

Q ss_pred             EEEEECCCCCCHHHHHHHHHH
Q ss_conf             477614886788999999999
Q gi|254781187|r   79 KCAISAGRGIGKTTLNAWMML   99 (367)
Q Consensus        79 ~~~v~sgrg~GKS~~~a~~~l   99 (367)
                      +++|.+.-|+|||++...++=
T Consensus        30 ~~aivG~sGsGKSTLl~~l~G   50 (178)
T cd03247          30 KIALLGRSGSGKSTLLQLLTG   50 (178)
T ss_pred             EEEEECCCCCHHHHHHHHHHH
T ss_conf             999999998759999999986


No 468
>cd04111 Rab39 Rab39 subfamily.  Found in eukaryotes, Rab39 is mainly found in epithelial cell lines, but is distributed widely in various human tissues and cell lines.  It is believed to be a novel Rab protein involved in regulating Golgi-associated vesicular transport during cellular endocytosis. 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=67.32  E-value=6.6  Score=18.39  Aligned_cols=24  Identities=17%  Similarity=0.242  Sum_probs=20.6

Q ss_pred             CEEEEEEECCCCCCHHHHHHHHHH
Q ss_conf             112477614886788999999999
Q gi|254781187|r   76 TIFKCAISAGRGIGKTTLNAWMML   99 (367)
Q Consensus        76 ~~~~~~v~sgrg~GKS~~~a~~~l   99 (367)
                      +.||+.+.+.-|+|||.++..++-
T Consensus         1 y~fKivllGd~~VGKTsL~~rf~~   24 (211)
T cd04111           1 YQFRLIVIGDSTVGKSSLLKRFTE   24 (211)
T ss_pred             CEEEEEEECCCCCCHHHHHHHHHH
T ss_conf             979999999999619999999981


No 469
>PRK13637 cbiO cobalt transporter ATP-binding subunit; Provisional
Probab=67.16  E-value=1.1  Score=23.30  Aligned_cols=37  Identities=19%  Similarity=0.300  Sum_probs=26.0

Q ss_pred             HHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHH
Q ss_conf             999999988887512455555411247761488678899999999
Q gi|254781187|r   54 WQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMM   98 (367)
Q Consensus        54 wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~   98 (367)
                      ++..+|++|.=.++.+.        .+++.+..|+|||++...+.
T Consensus        18 ~~~~aL~~isl~i~~GE--------~v~iiG~nGsGKSTLl~~l~   54 (287)
T PRK13637         18 FEKKALDNVNIEIEDGE--------FVALIGHTGSGKSTLIQHLN   54 (287)
T ss_pred             CCCEEEECEEEEECCCC--------EEEEECCCCCHHHHHHHHHH
T ss_conf             73817532076987998--------99999999939999999997


No 470
>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=67.10  E-value=5.7  Score=18.79  Aligned_cols=21  Identities=33%  Similarity=0.379  Sum_probs=18.6

Q ss_pred             EEEEECCCCCCHHHHHHHHHH
Q ss_conf             477614886788999999999
Q gi|254781187|r   79 KCAISAGRGIGKTTLNAWMML   99 (367)
Q Consensus        79 ~~~v~sgrg~GKS~~~a~~~l   99 (367)
                      .++|.+.-|+|||++...++=
T Consensus        30 ~vaIvG~sGsGKSTLl~ll~g   50 (173)
T cd03246          30 SLAIIGPSGSGKSTLARLILG   50 (173)
T ss_pred             EEEEECCCCCHHHHHHHHHHC
T ss_conf             999999999809999999966


No 471
>KOG1969 consensus
Probab=67.05  E-value=8.7  Score=17.68  Aligned_cols=107  Identities=18%  Similarity=0.226  Sum_probs=59.9

Q ss_pred             CHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEE-CCCHHHHHHHHHHHHH
Q ss_conf             428999999988887512455555411247761488678899999999999970899779997-1537999999999999
Q gi|254781187|r   51 PHRWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICI-ANSETQLKNTLWAEVS  129 (367)
Q Consensus        51 p~~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~-A~t~~Q~~~~lw~ei~  129 (367)
                      +-+|-.|++...-+.++|....      -+..++.-|.|||+++-.++-     +-|-+|+=+ |-.++.+. .    ++
T Consensus       306 ~~~~~ke~~~~~~~~s~RP~kK------ilLL~GppGlGKTTLAHViAk-----qaGYsVvEINASDeRt~~-~----v~  369 (877)
T KOG1969         306 KGPTEKEVLDMELDPSKRPPKK------ILLLCGPPGLGKTTLAHVIAK-----QAGYSVVEINASDERTAP-M----VK  369 (877)
T ss_pred             CCCCHHHHHHCCCCCCCCCCCC------EEEEECCCCCCHHHHHHHHHH-----HCCCEEEEECCCCCCCHH-H----HH
T ss_conf             4664345563246866798400------687536887872479999998-----628548873255543478-8----99


Q ss_pred             HHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCEEEEECCCCCCHHHHH
Q ss_conf             99986231211233332100012333221111345776126621013544556521011358628999754559988999
Q gi|254781187|r  130 KWLSMLPHRHWFEMQSLSLHPSGWYAELLEQSMGIDSKHYTITCRTYSEERPDTFVGPHNTHGMAVFNDEASGTPDIINK  209 (367)
Q Consensus       130 k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~ea~~g~h~~~~~l~ivDEAsgI~d~i~e  209 (367)
                      +-++.+.            .                +               ++.-+. +....|+|+||--|-+....+
T Consensus       370 ~kI~~av------------q----------------~---------------~s~l~a-dsrP~CLViDEIDGa~~~~Vd  405 (877)
T KOG1969         370 EKIENAV------------Q----------------N---------------HSVLDA-DSRPVCLVIDEIDGAPRAAVD  405 (877)
T ss_pred             HHHHHHH------------H----------------H---------------CCCCCC-CCCCCEEEEECCCCCCHHHHH
T ss_conf             9999988------------6----------------4---------------112256-888635998424687289999


Q ss_pred             HHHHHHHC
Q ss_conf             98987406
Q gi|254781187|r  210 SILGFFTE  217 (367)
Q Consensus       210 ~i~g~Lt~  217 (367)
                      +|+..+..
T Consensus       406 vilslv~a  413 (877)
T KOG1969         406 VILSLVKA  413 (877)
T ss_pred             HHHHHHHH
T ss_conf             99999974


No 472
>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=67.02  E-value=6.1  Score=18.61  Aligned_cols=22  Identities=32%  Similarity=0.406  Sum_probs=18.8

Q ss_pred             EEEEECCCCCCHHHHHHHHHHH
Q ss_conf             4776148867889999999999
Q gi|254781187|r   79 KCAISAGRGIGKTTLNAWMMLW  100 (367)
Q Consensus        79 ~~~v~sgrg~GKS~~~a~~~lw  100 (367)
                      +++|.+.-|+|||+++..+.=.
T Consensus        36 ~v~ivG~sGsGKSTLl~ll~g~   57 (207)
T cd03369          36 KIGIVGRTGAGKSTLILALFRF   57 (207)
T ss_pred             EEEEECCCCCCHHHHHHHHHHH
T ss_conf             9999999998799999999987


No 473
>pfam02689 Herpes_Helicase Helicase. This family consists of Helicases from the Herpes viruses. Helicases are responsible for the unwinding of DNA and are essential for replication and completion of the viral life cycle.
Probab=66.96  E-value=8.7  Score=17.67  Aligned_cols=37  Identities=16%  Similarity=0.161  Sum_probs=24.3

Q ss_pred             CCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCH
Q ss_conf             554112477614886788999999999999708997799971537
Q gi|254781187|r   73 SNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSE  117 (367)
Q Consensus        73 ~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~  117 (367)
                      .+|.. -..|.+--|.|||+.+..+.-       ...+++|..|.
T Consensus        57 ~LPFs-~ylITGtAGaGKSTsIq~L~~-------~LdCvITGaT~   93 (801)
T pfam02689        57 ELPFS-AYLITGTAGAGKSTSIQTLNE-------NLDCLITGATR   93 (801)
T ss_pred             CCCCE-EEEEECCCCCCCHHHHHHHHH-------HCCEEEECCHH
T ss_conf             67725-899953788870518999997-------53928956158


No 474
>PRK09694 hypothetical protein; Provisional
Probab=66.77  E-value=8.8  Score=17.65  Aligned_cols=76  Identities=22%  Similarity=0.205  Sum_probs=48.7

Q ss_pred             CCCCCHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHH
Q ss_conf             66684289999999888875124555554112477614886788999999999999708997799971537999999999
Q gi|254781187|r   47 HFSQPHRWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLKNTLWA  126 (367)
Q Consensus        47 ~~~~p~~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~~~lw~  126 (367)
                      ....|++-|..+ .++..         .|-  =+.|-+.-|.|||-.+-+++.-++...-...+++.-||...+. -||.
T Consensus       285 ~~~~PrplQ~~~-~~l~~---------~Pg--L~IiEAptG~GKTEAAL~~A~~L~~~~~~~Gl~faLPT~ATaN-aMf~  351 (878)
T PRK09694        285 NGYQPRQLQTLV-DALPL---------APG--LTVIEAPTGSGKTETALAYAWKLIDQQLADSVIFALPTQATAN-AMLS  351 (878)
T ss_pred             CCCCCCHHHHHH-HHCCC---------CCC--EEEEECCCCCCHHHHHHHHHHHHHHHCCCCCEEEECCHHHHHH-HHHH
T ss_conf             899996799999-84567---------998--7999758999758999999999997348983699774798899-9999


Q ss_pred             HHHHHHHHC
Q ss_conf             999999862
Q gi|254781187|r  127 EVSKWLSML  135 (367)
Q Consensus       127 ei~k~~~~~  135 (367)
                      .+.++++.+
T Consensus       352 Rv~~~~~~~  360 (878)
T PRK09694        352 RMEAAASKL  360 (878)
T ss_pred             HHHHHHHHH
T ss_conf             999999973


No 475
>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=66.54  E-value=6  Score=18.66  Aligned_cols=21  Identities=24%  Similarity=0.365  Sum_probs=18.1

Q ss_pred             EEEEECCCCCCHHHHHHHHHH
Q ss_conf             477614886788999999999
Q gi|254781187|r   79 KCAISAGRGIGKTTLNAWMML   99 (367)
Q Consensus        79 ~~~v~sgrg~GKS~~~a~~~l   99 (367)
                      +++|.+.-|+|||+++..++-
T Consensus        31 ~iaIvG~sGsGKSTLl~ll~g   51 (238)
T cd03249          31 TVALVGSSGCGKSTVVSLLER   51 (238)
T ss_pred             EEEEECCCCCCHHHHHHHHHH
T ss_conf             999999999989999999823


No 476
>cd04129 Rho2 Rho2 subfamily.  Rho2 is a fungal GTPase that plays a role in cell morphogenesis, control of cell wall integrity, control of growth polarity, and maintenance of growth direction.  Rho2 activates the protein kinase C homolog Pck2, and Pck2 controls Mok1, the major (1-3) alpha-D-glucan synthase.  Together with Rho1 (RhoA), Rho2 regulates the construction of the cell wall.  Unlike Rho1, Rho2 is not an essential protein, but its overexpression is lethal.  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 proper intracellular localization via membrane attachment.  As with other Rho family GTPases, the GDP/GTP cycling is regulated by GEFs (guanine nucleotide exchange factors), GAPs (GTPase-activating proteins) and GDIs (guanine nucleotide dissociation inhibitors).
Probab=66.32  E-value=6.5  Score=18.44  Aligned_cols=22  Identities=32%  Similarity=0.288  Sum_probs=19.0

Q ss_pred             EEEEEECCCCCCHHHHHHHHHH
Q ss_conf             2477614886788999999999
Q gi|254781187|r   78 FKCAISAGRGIGKTTLNAWMML   99 (367)
Q Consensus        78 ~~~~v~sgrg~GKS~~~a~~~l   99 (367)
                      .|+.+.+..|+|||.++..++-
T Consensus         2 ~KivllGd~~VGKTsLi~r~~~   23 (187)
T cd04129           2 RKLVIVGDGACGKTSLLSVFTL   23 (187)
T ss_pred             EEEEEECCCCCCHHHHHHHHHH
T ss_conf             1999999899768999999982


No 477
>PRK11819 putative ABC transporter ATP-binding protein; Reviewed
Probab=66.29  E-value=5.7  Score=18.79  Aligned_cols=39  Identities=8%  Similarity=-0.011  Sum_probs=25.3

Q ss_pred             CCCCCCEEEEECC-CCCCHHHHHHHHHHHHCCCCCEEEEEEE
Q ss_conf             1358628999754-5599889999898740698825899980
Q gi|254781187|r  188 HNTHGMAVFNDEA-SGTPDIINKSILGFFTELNPNRFWIMTS  228 (367)
Q Consensus       188 h~~~~~l~ivDEA-sgI~d~i~e~i~g~Lt~~~~~~~~i~ig  228 (367)
                      -.....++|+||- +..+...-+.++..|......+  ++++
T Consensus       178 L~~~PdlLlLDEPTn~LD~~~i~~L~~~L~~~~gtv--ivVS  217 (556)
T PRK11819        178 LLSKPDMLLLDEPTNHLDAESVAWLEQFLHDYPGTV--VAVT  217 (556)
T ss_pred             HHCCCCEEEECCCCCCCCHHHHHHHHHHHHHCCCCE--EEEE
T ss_conf             846999899848877789778999999976337877--9999


No 478
>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=66.28  E-value=9  Score=17.59  Aligned_cols=35  Identities=17%  Similarity=0.251  Sum_probs=26.5

Q ss_pred             EEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECC
Q ss_conf             776148867889999999999997089977999715
Q gi|254781187|r   80 CAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIAN  115 (367)
Q Consensus        80 ~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~  115 (367)
                      +.|+|+-|+|||+++.-+++..+. +.+.+|++.+.
T Consensus        16 ~vi~a~~g~GKS~~~~~la~~~a~-~~g~~V~~~Sl   50 (242)
T cd00984          16 IIIAARPSMGKTAFALNIAENIAK-KQGKPVLFFSL   50 (242)
T ss_pred             EEEEECCCCCHHHHHHHHHHHHHH-HCCCCEEEEEC
T ss_conf             999968999999999999999999-77995999933


No 479
>PRK13233 nifH nitrogenase reductase; Reviewed
Probab=66.23  E-value=9  Score=17.58  Aligned_cols=44  Identities=18%  Similarity=0.086  Sum_probs=32.6

Q ss_pred             EEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEE--CCCHHHHHH
Q ss_conf             247761488678899999999999970899779997--153799999
Q gi|254781187|r   78 FKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICI--ANSETQLKN  122 (367)
Q Consensus        78 ~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~--A~t~~Q~~~  122 (367)
                      .++||-.==|+|||+.++.+...++-. .+.||+++  =|..+..+.
T Consensus         3 ~~iaiyGKGGIGKSTTt~NLaaALA~l-~GkrVl~IgcDPk~dST~~   48 (275)
T PRK13233          3 RKIAIYGKGGIGKSTTTQNTAAAMAHF-HDKKVFIHGCDPKADSTRL   48 (275)
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHHHHH-CCCEEEEECCCCCCCHHHH
T ss_conf             389998998544654599999999964-7988999797887613677


No 480
>PRK13645 cbiO cobalt transporter ATP-binding subunit; Provisional
Probab=66.10  E-value=1.1  Score=23.24  Aligned_cols=38  Identities=13%  Similarity=0.233  Sum_probs=25.0

Q ss_pred             HHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHH
Q ss_conf             8999999988887512455555411247761488678899999999
Q gi|254781187|r   53 RWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMM   98 (367)
Q Consensus        53 ~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~   98 (367)
                      +|..++|++|.=.+.++.        .++|.+..|+|||+++-.+.
T Consensus        21 ~~~~~AL~~vsl~i~~Ge--------~~aIiG~nGsGKSTL~~~l~   58 (289)
T PRK13645         21 PFEFKALNNTSLTFKKNK--------VTCVIGTTGSGKSTMIQLTN   58 (289)
T ss_pred             CCCCEEEECCEEEECCCC--------EEEEECCCCCHHHHHHHHHH
T ss_conf             883658653288988998--------99999999957999999996


No 481
>PRK13640 cbiO cobalt transporter ATP-binding subunit; Provisional
Probab=66.09  E-value=5.7  Score=18.79  Aligned_cols=34  Identities=18%  Similarity=0.180  Sum_probs=23.3

Q ss_pred             HHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHH
Q ss_conf             999888875124555554112477614886788999999999
Q gi|254781187|r   58 FMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMML   99 (367)
Q Consensus        58 ~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~l   99 (367)
                      +|+.|.=.+.++.        .++|.+..|+|||++...+.=
T Consensus        23 aL~~vsl~I~~Ge--------~vaiiG~nGsGKSTL~~~l~G   56 (283)
T PRK13640         23 ALKDVSFSIPRGS--------WTALIGHNGSGKSTISKLING   56 (283)
T ss_pred             EEECCEEEECCCC--------EEEEECCCCCHHHHHHHHHHC
T ss_conf             7877186998999--------999999999879999999964


No 482
>cd03114 ArgK-like The function of this protein family is unkown. The protein sequences are similar to the ArgK protein in E. coli. ArgK protein is a membrane ATPase which is required for transporting arginine, ornithine and lysine into the cells by the arginine and ornithine (AO system) and lysine, arginine and ornithine (LAO) transport systems.
Probab=66.00  E-value=9.1  Score=17.55  Aligned_cols=36  Identities=25%  Similarity=0.286  Sum_probs=27.1

Q ss_pred             EEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCH
Q ss_conf             77614886788999999999999708997799971537
Q gi|254781187|r   80 CAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSE  117 (367)
Q Consensus        80 ~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~  117 (367)
                      +-|...=|+|||+++..++..+.-.  +.++.++|.--
T Consensus         2 iGitG~pGaGKStLi~~l~~~~~~~--g~~VaVlavDP   37 (148)
T cd03114           2 IGITGVPGAGKSTLIDALITALRAR--GKRVAVLAIDP   37 (148)
T ss_pred             EEECCCCCCCHHHHHHHHHHHHHHC--CCEEEEEEECC
T ss_conf             7625899787899999999999978--98379999688


No 483
>COG1341 Predicted GTPase or GTP-binding protein [General function prediction only]
Probab=65.99  E-value=9.1  Score=17.55  Aligned_cols=56  Identities=18%  Similarity=0.168  Sum_probs=36.4

Q ss_pred             CCCCCHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHH
Q ss_conf             6668428999999988887512455555411247761488678899999999999970
Q gi|254781187|r   47 HFSQPHRWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLIST  104 (367)
Q Consensus        47 ~~~~p~~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~  104 (367)
                      ....|..| .+.++.|.+.-.+ .........++.|.++-.+|||+++++++.-++.-
T Consensus        45 ~ve~P~d~-~~~~e~i~~~~~~-~~~~~~~~~~vmvvG~vDSGKSTLt~~LaN~~l~r  100 (398)
T COG1341          45 LVEVPEDR-SEPLEEIADTWES-KSESAGKVGVVMVVGPVDSGKSTLTTYLANKLLAR  100 (398)
T ss_pred             CCCCCHHH-HHHHHHHHHCCCC-CCHHCCCCCEEEEECCCCCCHHHHHHHHHHHHHHC
T ss_conf             42281676-3178997632244-20120687389998986767889999999887644


No 484
>cd01862 Rab7 Rab7 subfamily.  Rab7 is a small Rab GTPase that regulates vesicular traffic from early to late endosomal stages of the endocytic pathway.  The yeast Ypt7 and mammalian Rab7 are both involved in transport to the vacuole/lysosome, whereas Ypt7 is also required for homotypic vacuole fusion.  Mammalian Rab7 is an essential participant in the autophagic pathway for sequestration and targeting of cytoplasmic components to the lytic compartment. Mammalian Rab7 is also proposed to function as a tumor suppressor. 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-
Probab=65.99  E-value=6.3  Score=18.54  Aligned_cols=21  Identities=33%  Similarity=0.483  Sum_probs=18.3

Q ss_pred             EEEEEECCCCCCHHHHHHHHH
Q ss_conf             247761488678899999999
Q gi|254781187|r   78 FKCAISAGRGIGKTTLNAWMM   98 (367)
Q Consensus        78 ~~~~v~sgrg~GKS~~~a~~~   98 (367)
                      +|+.+.+.-|+|||.++..++
T Consensus         1 ~KivlvGd~~VGKTsli~r~~   21 (172)
T cd01862           1 LKVIILGDSGVGKTSLMNQYV   21 (172)
T ss_pred             CEEEEECCCCCCHHHHHHHHH
T ss_conf             989999989978999999995


No 485
>COG1136 SalX ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]
Probab=65.94  E-value=5.7  Score=18.81  Aligned_cols=33  Identities=27%  Similarity=0.233  Sum_probs=22.8

Q ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEEC
Q ss_conf             477614886788999999999999708997799971
Q gi|254781187|r   79 KCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIA  114 (367)
Q Consensus        79 ~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A  114 (367)
                      -++|.+.-|+|||++...+.   .+-.|..-.+.+.
T Consensus        33 ~vaI~GpSGSGKSTLLniig---~ld~pt~G~v~i~   65 (226)
T COG1136          33 FVAIVGPSGSGKSTLLNLLG---GLDKPTSGEVLIN   65 (226)
T ss_pred             EEEEECCCCCCHHHHHHHHH---CCCCCCCCEEEEC
T ss_conf             99998999998999999996---4667888469999


No 486
>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=65.86  E-value=6.3  Score=18.54  Aligned_cols=21  Identities=24%  Similarity=0.398  Sum_probs=18.2

Q ss_pred             EEEEECCCCCCHHHHHHHHHH
Q ss_conf             477614886788999999999
Q gi|254781187|r   79 KCAISAGRGIGKTTLNAWMML   99 (367)
Q Consensus        79 ~~~v~sgrg~GKS~~~a~~~l   99 (367)
                      |+.|.+..|+|||.++..++-
T Consensus         2 Ki~vvG~~~vGKTsli~r~~~   22 (161)
T cd01861           2 KLVFLGDQSVGKTSIITRFMY   22 (161)
T ss_pred             EEEEECCCCCCHHHHHHHHHH
T ss_conf             799999799789999999931


No 487
>cd00615 Orn_deC_like Ornithine decarboxylase family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The major groups in this CD corresponds to ornithine decarboxylase (ODC), arginine decarboxylase (ADC) and lysine decarboxylase (LDC). ODC is a dodecamer composed of six homodimers and catalyzes the decarboxylation of tryptophan. ADC catalyzes the decarboxylation of arginine and LDC catalyzes the decarboxylation of lysine. Members of this family are widely found in all three forms of life.
Probab=65.86  E-value=9.2  Score=17.54  Aligned_cols=31  Identities=23%  Similarity=0.223  Sum_probs=23.9

Q ss_pred             HHHHHHHHHHHCCCCEEEEECCCHHHHHHHH
Q ss_conf             9999999997089977999715379999999
Q gi|254781187|r   94 NAWMMLWLISTRPGMSIICIANSETQLKNTL  124 (367)
Q Consensus        94 ~a~~~lw~~~~~~~~~v~~~A~t~~Q~~~~l  124 (367)
                      .+..+.-+.+++|+.+|++-.|..+.+-..+
T Consensus        86 ~g~~a~i~a~~~~gd~vlv~RN~HkSv~~gl  116 (294)
T cd00615          86 SSNKAVILAVCGPGDKILIDRNCHKSVINGL  116 (294)
T ss_pred             HHHHHHHHHHCCCCCEEEEECCCHHHHHHHH
T ss_conf             9999999983289998998265189999999


No 488
>PRK00080 ruvB Holliday junction DNA helicase RuvB; Reviewed
Probab=65.80  E-value=9.2  Score=17.53  Aligned_cols=94  Identities=16%  Similarity=0.175  Sum_probs=54.0

Q ss_pred             HHHHHHHHHHHH----HCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEE-ECCCHHHHHHHHHHHHH
Q ss_conf             999999888875----1245555541124776148867889999999999997089977999-71537999999999999
Q gi|254781187|r   55 QLEFMEAVDVHC----HSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIIC-IANSETQLKNTLWAEVS  129 (367)
Q Consensus        55 q~~~l~~~~~~~----~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~-~A~t~~Q~~~~lw~ei~  129 (367)
                      |.++.+.+.-.+    +|+..-+     -+...++-|.|||+++..++--+     +.++-+ .+|......|.. +.  
T Consensus        30 Q~~i~~~L~v~i~Aak~r~e~ld-----H~Ll~GPPGlGKTTLA~iiA~E~-----~~~~~~tsGP~lek~~DL~-~i--   96 (328)
T PRK00080         30 QEKVKENLKIFIEAAKKRGEALD-----HVLLYGPPGLGKTTLANIIANEM-----GVNIRITSGPALEKAGDLA-AL--   96 (328)
T ss_pred             HHHHHHHHHHHHHHHHHCCCCCC-----CEEEECCCCCCHHHHHHHHHHHH-----CCCCEECCCCCCCCHHHHH-HH--
T ss_conf             59999999999999996499988-----05765889988999999999986-----8881562450016747899-99--


Q ss_pred             HHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCEEEEECCCCCCHHHHH
Q ss_conf             99986231211233332100012333221111345776126621013544556521011358628999754559988999
Q gi|254781187|r  130 KWLSMLPHRHWFEMQSLSLHPSGWYAELLEQSMGIDSKHYTITCRTYSEERPDTFVGPHNTHGMAVFNDEASGTPDIINK  209 (367)
Q Consensus       130 k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~ea~~g~h~~~~~l~ivDEAsgI~d~i~e  209 (367)
                        +.                                                    .+. ++ ..+.+||..-++..+-|
T Consensus        97 --Lt----------------------------------------------------~l~-~~-dvLFIDEIHRl~~~vEE  120 (328)
T PRK00080         97 --LT----------------------------------------------------NLE-EG-DVLFIDEIHRLSPVVEE  120 (328)
T ss_pred             --HH----------------------------------------------------HCC-CC-CEEEEHHHHHCCHHHHH
T ss_conf             --96----------------------------------------------------088-78-76765065324888998


Q ss_pred             HHHHHHHC
Q ss_conf             98987406
Q gi|254781187|r  210 SILGFFTE  217 (367)
Q Consensus       210 ~i~g~Lt~  217 (367)
                      .+.++|-+
T Consensus       121 ~LY~AMED  128 (328)
T PRK00080        121 ILYPAMED  128 (328)
T ss_pred             HHHHHHHH
T ss_conf             85798775


No 489
>cd04112 Rab26 Rab26 subfamily.  First identified in rat pancreatic acinar cells, Rab26 is believed to play a role in recruiting mature granules to the plasma membrane upon beta-adrenergic stimulation.  Rab26 belongs to the Rab functional group III, which are considered key regulators of intracellular vesicle transport during exocytosis. 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=65.68  E-value=6.5  Score=18.45  Aligned_cols=21  Identities=33%  Similarity=0.506  Sum_probs=17.9

Q ss_pred             EEEEEECCCCCCHHHHHHHHH
Q ss_conf             247761488678899999999
Q gi|254781187|r   78 FKCAISAGRGIGKTTLNAWMM   98 (367)
Q Consensus        78 ~~~~v~sgrg~GKS~~~a~~~   98 (367)
                      ||+.|.+-.|+|||.++..++
T Consensus         1 ~KIv~vGd~~VGKTsli~r~~   21 (191)
T cd04112           1 FKVMLLGDSGVGKTCLLVRFK   21 (191)
T ss_pred             CEEEEECCCCCCHHHHHHHHH
T ss_conf             989999949987999999999


No 490
>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=65.56  E-value=5.9  Score=18.72  Aligned_cols=21  Identities=19%  Similarity=0.427  Sum_probs=17.7

Q ss_pred             EEEEECCCCCCHHHHHHHHHH
Q ss_conf             477614886788999999999
Q gi|254781187|r   79 KCAISAGRGIGKTTLNAWMML   99 (367)
Q Consensus        79 ~~~v~sgrg~GKS~~~a~~~l   99 (367)
                      |++|.+..|+|||.++..++-
T Consensus         1 Ki~ivG~~~vGKTsli~r~~~   21 (160)
T cd00876           1 KVVVLGAGGVGKSAITIQFVK   21 (160)
T ss_pred             CEEEECCCCCCHHHHHHHHHH
T ss_conf             999999699679999999961


No 491
>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=65.09  E-value=6.4  Score=18.49  Aligned_cols=22  Identities=27%  Similarity=0.335  Sum_probs=18.8

Q ss_pred             EEEEECCCCCCHHHHHHHHHHH
Q ss_conf             4776148867889999999999
Q gi|254781187|r   79 KCAISAGRGIGKTTLNAWMMLW  100 (367)
Q Consensus        79 ~~~v~sgrg~GKS~~~a~~~lw  100 (367)
                      +++|.+.-|+|||+++..+.=.
T Consensus        42 ~vaIvG~sGsGKSTL~~ll~gl   63 (226)
T cd03248          42 VTALVGPSGSGKSTVVALLENF   63 (226)
T ss_pred             EEEEECCCCCHHHHHHHHHHCC
T ss_conf             9999999998499999999645


No 492
>PRK07367 consensus
Probab=65.00  E-value=9.5  Score=17.43  Aligned_cols=64  Identities=14%  Similarity=0.114  Sum_probs=36.9

Q ss_pred             CHHHHHHHHHHHHHHHHCCC-CCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHH
Q ss_conf             42899999998888751245-5555411247761488678899999999999970899779997153799999
Q gi|254781187|r   51 PHRWQLEFMEAVDVHCHSNV-NNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLKN  122 (367)
Q Consensus        51 p~~wq~~~l~~~~~~~~~~~-~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~~  122 (367)
                      |..--.++.++|+++.++.. ....|+  .+.|..|=      ..|...+-.+++.||-+|++..|++..-..
T Consensus        63 ~~~G~~~lR~aia~~~~~~~g~~~~~d--~I~it~G~------~~al~~~~~~l~~pGD~Vlv~~P~y~~y~~  127 (385)
T PRK07367         63 PAAGEPALREAIAHKLRRENGLDYQAE--NILVTNGG------KQSLYNLMMALIDPGDEVIIPAPYWLSYPE  127 (385)
T ss_pred             CCCCCHHHHHHHHHHHHHHHCCCCCHH--EEEECCCH------HHHHHHHHHHHCCCCCEEEECCCCCCCCHH
T ss_conf             999989999999999999858999850--49990898------999999999974899989990698777199


No 493
>COG0542 clpA ATP-binding subunits of Clp protease and DnaK/DnaJ chaperones [Posttranslational modification, protein turnover, chaperones]
Probab=64.86  E-value=9.6  Score=17.42  Aligned_cols=134  Identities=23%  Similarity=0.191  Sum_probs=69.5

Q ss_pred             HHHHHHHHHHHHHHCC-CCCCCCCEE--EEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHHHH
Q ss_conf             9999999888875124-555554112--4776148867889999999999997089977999715379999999999999
Q gi|254781187|r   54 WQLEFMEAVDVHCHSN-VNNSNPTIF--KCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLKNTLWAEVSK  130 (367)
Q Consensus        54 wq~~~l~~~~~~~~~~-~~~~~~~~~--~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~~~lw~ei~k  130 (367)
                      .|.+++.+|++.+++. .+-..|.++  -..-+++-|+|||.++-.++-.+.  ......+-.=-++=|-+-.    +.+
T Consensus       495 GQd~AV~~v~~aIrraRaGL~dp~rPigsFlF~GPTGVGKTELAkaLA~~Lf--g~e~aliR~DMSEy~EkHs----VSr  568 (786)
T COG0542         495 GQDEAVEAVSDAIRRARAGLGDPNRPIGSFLFLGPTGVGKTELAKALAEALF--GDEQALIRIDMSEYMEKHS----VSR  568 (786)
T ss_pred             CHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHC--CCCCCCEEECHHHHHHHHH----HHH
T ss_conf             7399999999999998569999998735788667886569999999999965--9974445545687777877----998


Q ss_pred             HHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCEEEEECCCCCCHHHHHH
Q ss_conf             99862312112333321000123332211113457761266210135445565210113586289997545599889999
Q gi|254781187|r  131 WLSMLPHRHWFEMQSLSLHPSGWYAELLEQSMGIDSKHYTITCRTYSEERPDTFVGPHNTHGMAVFNDEASGTPDIINKS  210 (367)
Q Consensus       131 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~ea~~g~h~~~~~l~ivDEAsgI~d~i~e~  210 (367)
                      .+...|                +       +.+++.|..          -.|+..  +..+ ..+++||-..-.++|++.
T Consensus       569 LIGaPP----------------G-------YVGyeeGG~----------LTEaVR--r~Py-SViLlDEIEKAHpdV~ni  612 (786)
T COG0542         569 LIGAPP----------------G-------YVGYEEGGQ----------LTEAVR--RKPY-SVILLDEIEKAHPDVFNL  612 (786)
T ss_pred             HHCCCC----------------C-------CCEECCCCC----------HHHHHH--CCCC-EEEEECHHHHCCHHHHHH
T ss_conf             727999----------------8-------720065540----------037660--6998-688841264408899999


Q ss_pred             HH-----HHHHCCCCCE------EEEEEEC
Q ss_conf             89-----8740698825------8999807
Q gi|254781187|r  211 IL-----GFFTELNPNR------FWIMTSN  229 (367)
Q Consensus       211 i~-----g~Lt~~~~~~------~~i~igN  229 (367)
                      +.     |.||++.++.      +.+++||
T Consensus       613 lLQVlDdGrLTD~~Gr~VdFrNtiIImTSN  642 (786)
T COG0542         613 LLQVLDDGRLTDGQGRTVDFRNTIIIMTSN  642 (786)
T ss_pred             HHHHHCCCCEECCCCCEEECCEEEEEEECC
T ss_conf             999846780554899888430028998450


No 494
>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=64.85  E-value=6.5  Score=18.47  Aligned_cols=20  Identities=30%  Similarity=0.292  Sum_probs=16.7

Q ss_pred             EEEEECCCCCCHHHHHHHHH
Q ss_conf             47761488678899999999
Q gi|254781187|r   79 KCAISAGRGIGKTTLNAWMM   98 (367)
Q Consensus        79 ~~~v~sgrg~GKS~~~a~~~   98 (367)
                      -+++.+..|+|||++..++.
T Consensus        24 itaivG~NGaGKSTLl~~i~   43 (204)
T cd03240          24 LTLIVGQNGAGKTTIIEALK   43 (204)
T ss_pred             EEEEECCCCCCHHHHHHHHH
T ss_conf             89999899999999999986


No 495
>PTZ00132 GTP-binding nuclear protein; Provisional
Probab=64.84  E-value=7.5  Score=18.09  Aligned_cols=56  Identities=11%  Similarity=0.029  Sum_probs=33.2

Q ss_pred             CEEEEEEECCCCCCCH---HH-HHHHCCCCCEEEEEECCCCCCCCCHHHHHHHHHHCCCCC
Q ss_conf             2589998078999876---88-754112235046752333288889889999996216880
Q gi|254781187|r  221 NRFWIMTSNTRRLNGW---FY-DIFNIPLEDWKRYQIDTRTVEGIDSGFHEGIISRYGLDS  277 (367)
Q Consensus       221 ~~~~i~igNP~r~~g~---Fy-e~~~~~~~~w~~~~~~~~d~p~~~~~~i~~~~~~~gedS  277 (367)
                      ....+++||=......   -. ..|. ...+..-+..++.++-++..-|..-.++-+|...
T Consensus       110 ~ipivLVGNK~DL~~r~V~~~~~~~a-~~~~~~f~EtSAKtg~NV~e~F~~Lar~il~~~~  169 (209)
T PTZ00132        110 NIPIVLVGNKVDVKDRQVKAKQITFH-RKKNLQYYDISAKSNYNFEKPFLWLARRLANDPN  169 (209)
T ss_pred             CCCEEEEEECCCCCCCCCCHHHHHHH-HHCCCEEEEEECCCCCCHHHHHHHHHHHHHCCCC
T ss_conf             98789997623224135579999999-9879989997268993979999999999847999


No 496
>PRK10790 putative multidrug transporter membrane\ATP-binding components; Provisional
Probab=64.80  E-value=6.6  Score=18.39  Aligned_cols=18  Identities=33%  Similarity=0.530  Sum_probs=6.9

Q ss_pred             EEEECCCCCCHHHHHHHH
Q ss_conf             776148867889999999
Q gi|254781187|r   80 CAISAGRGIGKTTLNAWM   97 (367)
Q Consensus        80 ~~v~sgrg~GKS~~~a~~   97 (367)
                      +++.+.-|+|||+++..+
T Consensus       370 vaIVG~SGsGKSTL~~LL  387 (593)
T PRK10790        370 VALVGHTGSGKSTLASLL  387 (593)
T ss_pred             EEEECCCCCCHHHHHHHH
T ss_conf             998799988689999999


No 497
>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=64.78  E-value=5.9  Score=18.72  Aligned_cols=37  Identities=24%  Similarity=0.231  Sum_probs=23.6

Q ss_pred             CCCCEEEEECC-CCCCHHHHHHHHHHHHCCCCCEEEEEEE
Q ss_conf             58628999754-5599889999898740698825899980
Q gi|254781187|r  190 THGMAVFNDEA-SGTPDIINKSILGFFTELNPNRFWIMTS  228 (367)
Q Consensus       190 ~~~~l~ivDEA-sgI~d~i~e~i~g~Lt~~~~~~~~i~ig  228 (367)
                      .+..++++||+ +.++...-..+.-.+...+.-  +++++
T Consensus       108 ~~p~iliLDEpTs~LD~~~~~~l~~~l~~~~~T--vi~Vt  145 (166)
T cd03223         108 HKPKFVFLDEATSALDEESEDRLYQLLKELGIT--VISVG  145 (166)
T ss_pred             CCCCEEEECCCCCCCCHHHHHHHHHHHHHCCCE--EEEEE
T ss_conf             499999975853328999999999999977998--99994


No 498
>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=64.44  E-value=9.8  Score=17.37  Aligned_cols=52  Identities=17%  Similarity=0.160  Sum_probs=39.8

Q ss_pred             HHHHHHHHHHHHHCCCCCCCCCE-EEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHH
Q ss_conf             99999988887512455555411-247761488678899999999999970899779997153799
Q gi|254781187|r   55 QLEFMEAVDVHCHSNVNNSNPTI-FKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQ  119 (367)
Q Consensus        55 q~~~l~~~~~~~~~~~~~~~~~~-~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q  119 (367)
                      ..++|.++-..           . .-++|++-|  |||+.+|+++.-+--+..+.++++-....+-
T Consensus        96 R~~~Lael~~~-----------~k~~iaVaGtH--GKTTTTamia~~~~~aGLdPt~~~GG~~~~~  148 (491)
T TIGR01082        96 RAEMLAELMRK-----------RKESIAVAGTH--GKTTTTAMIAVILKEAGLDPTVIVGGEVKEA  148 (491)
T ss_pred             HHHHHHHHHHH-----------HCCEEEEECCC--CCHHHHHHHHHHHHHCCCCCCEEECCCCCCC
T ss_conf             78999999862-----------08707998368--7256899999999844999768986643665


No 499
>PRK13886 conjugal transfer protein TraL; Provisional
Probab=64.38  E-value=8.5  Score=17.75  Aligned_cols=30  Identities=17%  Similarity=0.155  Sum_probs=0.0

Q ss_pred             CCCHHHHHHHHHHHHHHHCCCCEEEEECCC
Q ss_conf             678899999999999970899779997153
Q gi|254781187|r   87 GIGKTTLNAWMMLWLISTRPGMSIICIANS  116 (367)
Q Consensus        87 g~GKS~~~a~~~lw~~~~~~~~~v~~~A~t  116 (367)
                      |+|||.+++.++=+++....+..++=|=|+
T Consensus        13 GVGKS~va~~LaQY~~~~~~~~~~iDTDpv   42 (241)
T PRK13886         13 GVGKSMIAATIAQYKAGKGQKPLCIDTDPV   42 (241)
T ss_pred             CCHHHHHHHHHHHHHHHCCCCCCEEECCCC
T ss_conf             630999999999999835999855608999


No 500
>cd01875 RhoG RhoG subfamily.  RhoG is a GTPase with high sequence similarity to members of the Rac subfamily, including the regions involved in effector recognition and binding.  However, RhoG does not bind to known Rac1 and Cdc42 effectors, including proteins containing a Cdc42/Rac interacting binding (CRIB) motif.  Instead, RhoG interacts directly with Elmo, an upstream regulator of Rac1, in a GTP-dependent manner and forms a ternary complex with Dock180 to induce activation of Rac1.  The RhoG-Elmo-Dock180 pathway is required for activation of Rac1 and cell spreading mediated by integrin, as well as for neurite outgrowth induced by nerve growth factor.  Thus RhoG activates Rac1 through Elmo and Dock180 to control cell morphology.  RhoG has also been shown to play a role in caveolar trafficking and has a novel role in signaling the neutrophil respiratory burst stimulated by G protein-coupled receptor (GPCR) agonists.  Most Rho proteins contain a lipid modification site at the C-termin
Probab=64.15  E-value=8  Score=17.91  Aligned_cols=21  Identities=29%  Similarity=0.498  Sum_probs=0.0

Q ss_pred             EEEEEECCCCCCHHHHHHHHH
Q ss_conf             247761488678899999999
Q gi|254781187|r   78 FKCAISAGRGIGKTTLNAWMM   98 (367)
Q Consensus        78 ~~~~v~sgrg~GKS~~~a~~~   98 (367)
                      +|+.+.+..|+|||.++..++
T Consensus         4 ~KivlvGd~~VGKTsli~r~~   24 (191)
T cd01875           4 IKCVVVGDGAVGKTCLLICYT   24 (191)
T ss_pred             EEEEEECCCCCCHHHHHHHHH
T ss_conf             899999999989999999997


Done!