Query         gi|254780916|ref|YP_003065329.1| putative sigma-54-dependent transcription regulator protein [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 482
No_of_seqs    221 out of 18694
Neff          7.7 
Searched_HMMs 39220
Date          Mon May 30 02:37:27 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254780916.hhm -d /home/congqian_1/database/cdd/Cdd.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 COG2204 AtoC Response regulato 100.0       0       0  955.1  29.6  452    7-481     1-460 (464)
  2 TIGR01818 ntrC nitrogen regula 100.0       0       0  954.3  20.1  458   13-475     1-471 (471)
  3 PRK11361 acetoacetate metaboli 100.0       0       0  921.1  31.0  447    7-478     1-457 (457)
  4 TIGR02915 PEP_resp_reg putativ 100.0       0       0  916.8  17.1  434   13-478     1-451 (451)
  5 PRK10923 glnG nitrogen regulat 100.0       0       0  888.0  30.3  461   10-478     3-469 (469)
  6 PRK10365 transcriptional regul 100.0       0       0  878.6  28.9  435    7-474     1-441 (441)
  7 TIGR01817 nifA Nif-specific re 100.0       0       0  782.7  11.9  464   13-482    42-574 (574)
  8 COG3829 RocR Transcriptional r 100.0       0       0  736.9  13.8  320  133-478   238-560 (560)
  9 PRK05022 anaerobic nitric oxid 100.0       0       0  704.8  19.1  319  139-479   185-510 (510)
 10 COG3604 FhlA Transcriptional r 100.0       0       0  705.6  15.6  330  136-481   219-549 (550)
 11 PRK10820 DNA-binding transcrip 100.0       0       0  662.5  16.8  312  134-480   198-509 (513)
 12 TIGR02974 phageshock_pspF psp  100.0       0       0  661.5  11.8  334  142-475     1-349 (349)
 13 PRK11388 DNA-binding transcrip 100.0       0       0  637.9  18.5  315  135-481   320-634 (639)
 14 PRK11608 pspF phage shock prot 100.0       0       0  637.0  18.3  319  139-477     5-325 (325)
 15 TIGR02329 propionate_PrpR prop 100.0       0       0  630.1  11.0  352  102-474   282-658 (658)
 16 COG3284 AcoR Transcriptional a 100.0       0       0  579.1  12.5  289  143-479   316-606 (606)
 17 COG3283 TyrR Transcriptional r 100.0       0       0  551.8  14.9  313  134-480   198-510 (511)
 18 COG1221 PspF Transcriptional r 100.0       0       0  545.4  13.7  328  134-480    72-401 (403)
 19 pfam00158 Sigma54_activat Sigm 100.0       0       0  374.4   6.8  167  142-308     1-168 (168)
 20 COG4650 RtcR Sigma54-dependent 100.0 9.8E-45       0  335.9   8.1  317  140-480   184-523 (531)
 21 TIGR02154 PhoB phosphate regul  99.9 1.2E-26 3.2E-31  207.8   8.6  169   10-194     2-174 (226)
 22 PRK10693 response regulator of  99.9 1.2E-24   3E-29  193.9  12.2  121    9-129     6-129 (337)
 23 PRK10046 dpiA two-component re  99.9 7.4E-24 1.9E-28  188.3  12.9  121    7-127     1-125 (225)
 24 PRK09468 ompR osmolarity respo  99.9 1.1E-23 2.7E-28  187.2  11.8  122    7-128     2-125 (239)
 25 PRK11083 DNA-binding response   99.9 3.7E-23 9.5E-28  183.3  12.4  121    7-128     1-123 (229)
 26 PRK09581 pleD response regulat  99.9 5.3E-23 1.4E-27  182.2  12.0  116   10-125     2-121 (457)
 27 PRK09836 DNA-binding transcrip  99.9 6.6E-23 1.7E-27  181.5  11.2  117   11-127     1-119 (226)
 28 PRK10161 transcriptional regul  99.9 1.1E-22 2.8E-27  180.0  12.0  118   10-127     2-123 (229)
 29 PRK10336 DNA-binding transcrip  99.9 6.1E-23 1.6E-27  181.7  10.5  117   11-127     1-119 (219)
 30 CHL00148 orf27 Ycf27; Reviewed  99.9 5.9E-23 1.5E-27  181.9   9.3  120    8-128     4-125 (240)
 31 PRK10430 DNA-binding transcrip  99.9 2.6E-22 6.6E-27  177.3  11.5  116   10-125     1-122 (239)
 32 pfam00072 Response_reg Respons  99.9 4.2E-22 1.1E-26  175.9  12.3  109   13-121     1-111 (111)
 33 PRK10610 chemotaxis regulatory  99.9 4.6E-22 1.2E-26  175.6  12.3  121    7-127     1-127 (129)
 34 PRK11517 transcriptional regul  99.9 5.7E-22 1.4E-26  174.9  12.0  116   11-127     1-118 (223)
 35 PRK10529 DNA-binding transcrip  99.9 2.3E-22 5.9E-27  177.7   9.0  118   10-128     1-120 (225)
 36 PRK09390 fixJ response regulat  99.9   1E-21 2.6E-26  173.1  11.4  118    9-126     2-121 (202)
 37 PRK10701 DNA-binding transcrip  99.9 2.2E-22 5.7E-27  177.8   7.9  119   10-129     1-121 (240)
 38 PRK11173 two-component respons  99.9 1.5E-21 3.8E-26  171.9  11.5  120    7-128     1-122 (237)
 39 PRK10643 DNA-binding transcrip  99.9 2.7E-21 6.9E-26  170.1  11.8  118   11-128     1-120 (222)
 40 cd00156 REC Signal receiver do  99.9 2.1E-21 5.4E-26  170.9  11.2  111   14-124     1-113 (113)
 41 PRK10955 DNA-binding transcrip  99.9 8.5E-22 2.2E-26  173.7   9.2  117   10-128     1-119 (232)
 42 PRK10710 DNA-binding transcrip  99.9 2.3E-21 5.8E-26  170.6  11.1  120    8-128     8-129 (240)
 43 PRK10766 DNA-binding transcrip  99.9 1.7E-21 4.2E-26  171.6  10.1  119   10-129     2-122 (224)
 44 PRK13557 histidine kinase; Pro  99.9 6.1E-21 1.6E-25  167.6  12.6  118    9-126   412-533 (538)
 45 PRK10816 DNA-binding transcrip  99.9 2.8E-21 7.1E-26  170.0  10.2  117   11-127     1-119 (223)
 46 COG0745 OmpR Response regulato  99.9 7.9E-21   2E-25  166.9  12.4  118   11-129     1-121 (229)
 47 COG4566 TtrR Response regulato  99.9 2.9E-21 7.4E-26  169.9   9.4  126    7-132     1-128 (202)
 48 TIGR01387 cztR_silR_copR heavy  99.9 3.5E-22 8.8E-27  176.4   4.2  129   13-142     1-131 (219)
 49 PRK13856 two-component respons  99.8 1.2E-20   3E-25  165.7  11.4  118   10-128     1-121 (241)
 50 COG4753 Response regulator con  99.8 6.4E-21 1.6E-25  167.5   9.5  117   10-126     1-122 (475)
 51 PRK10841 hybrid sensory kinase  99.8 2.2E-20 5.5E-25  163.7  12.1  116    9-124   823-940 (947)
 52 PRK11107 hybrid sensory histid  99.8 5.2E-20 1.3E-24  161.1  13.8  115   10-124   668-786 (920)
 53 PRK09959 hybrid sensory histid  99.8 5.8E-20 1.5E-24  160.7  12.9  116    7-122   955-1072(1197)
 54 PRK00742 chemotaxis-specific m  99.8 6.4E-19 1.6E-23  153.4  15.9  174   10-198     2-190 (345)
 55 PRK13435 response regulator; P  99.8 8.4E-20 2.1E-24  159.6  10.5  117   10-130     1-121 (141)
 56 PRK11466 hybrid sensory histid  99.8 3.1E-19 7.9E-24  155.6  12.6  117    9-125   680-799 (912)
 57 TIGR02902 spore_lonB ATP-depen  99.8   9E-20 2.3E-24  159.4   8.3  242  123-388    48-331 (532)
 58 PRK11091 aerobic respiration c  99.8 1.1E-18 2.9E-23  151.6  13.3  116    9-125   524-644 (779)
 59 PRK12555 chemotaxis-specific m  99.8 6.5E-18 1.7E-22  146.2  15.2  163   10-188     1-178 (340)
 60 TIGR02903 spore_lon_C ATP-depe  99.8 7.2E-19 1.8E-23  153.0   7.2  192  135-356   150-389 (616)
 61 COG3437 Response regulator con  99.8 3.9E-18   1E-22  147.8  10.5  124    1-124     5-133 (360)
 62 COG4565 CitB Response regulato  99.8 4.5E-18 1.1E-22  147.4   9.7  116   12-127     2-121 (224)
 63 TIGR02875 spore_0_A sporulatio  99.7 1.2E-17 3.2E-22  144.2   9.6  117   10-126     2-124 (270)
 64 PRK10403 transcriptional regul  99.7 1.9E-17 4.9E-22  142.9   9.8  120    7-126     3-126 (215)
 65 PRK10651 transcriptional regul  99.7 1.6E-17   4E-22  143.6   8.1  121    7-127     3-127 (216)
 66 PRK13837 two-component VirA-li  99.7 1.1E-16 2.7E-21  137.6  11.5  120    9-130   698-821 (831)
 67 PRK09958 DNA-binding transcrip  99.7 5.7E-17 1.5E-21  139.6   9.8  116   11-126     1-119 (204)
 68 COG3706 PleD Response regulato  99.7 7.6E-17 1.9E-21  138.7   9.9  122    9-130   131-256 (435)
 69 PRK09483 response regulator; P  99.7 1.5E-16 3.8E-21  136.6  10.4  118   10-127     1-122 (216)
 70 PRK09935 transcriptional regul  99.7 4.4E-16 1.1E-20  133.3  10.4  119    9-127     2-124 (210)
 71 COG3947 Response regulator con  99.7 2.7E-16 6.8E-21  134.8   8.4  123   11-135     1-125 (361)
 72 COG2197 CitB Response regulato  99.7 2.1E-15 5.3E-20  128.5  11.6  117   11-127     1-121 (211)
 73 KOG0519 consensus               99.6   2E-15 5.1E-20  128.6  10.5  117    8-124   664-784 (786)
 74 COG4567 Response regulator con  99.6 3.5E-15   9E-20  126.9  10.4  116    7-122     5-123 (182)
 75 PRK10840 transcriptional regul  99.6 5.2E-15 1.3E-19  125.7  10.9  116   10-125     3-125 (216)
 76 PRK10360 DNA-binding transcrip  99.6 2.2E-14 5.6E-19  121.3  10.4  115   10-127     1-119 (196)
 77 PRK11697 putative two-componen  99.6 4.3E-14 1.1E-18  119.2  10.7  115   10-127     1-119 (239)
 78 COG0784 CheY FOG: CheY-like re  99.6 1.1E-13 2.7E-18  116.4  12.4  113    9-121     4-121 (130)
 79 TIGR02956 TMAO_torS TMAO reduc  99.6 1.6E-14   4E-19  122.3   7.8  118    7-124   758-886 (1052)
 80 PRK09191 two-component respons  99.5 2.8E-14 7.1E-19  120.6   8.9  113   10-125   137-253 (261)
 81 COG2201 CheB Chemotaxis respon  99.5 8.6E-13 2.2E-17  110.0  14.5  175   10-197     1-190 (350)
 82 cd00009 AAA The AAA+ (ATPases   99.5 1.7E-14 4.2E-19  122.2   4.8  135  161-311    17-151 (151)
 83 PRK13765 ATP-dependent proteas  99.5 2.2E-13 5.6E-18  114.2  10.3  205  171-387   161-398 (637)
 84 pfam07724 AAA_2 AAA domain (Cd  99.5 6.9E-14 1.8E-18  117.8   6.7  127  164-290     4-132 (168)
 85 PRK13558 bacterio-opsin activa  99.5 1.6E-14 4.1E-19  122.2   2.9  112   12-125    19-132 (674)
 86 PRK13407 bchI magnesium chelat  99.4 5.2E-13 1.3E-17  111.6   8.1  161  136-312     4-202 (334)
 87 PRK10100 DNA-binding transcrip  99.4 3.2E-12 8.3E-17  106.0   9.0  119    9-128     9-129 (216)
 88 pfam07726 AAA_3 ATPase family   99.4 1.4E-12 3.5E-17  108.6   6.5  110  165-283     1-112 (131)
 89 PRK11034 clpA ATP-dependent Cl  99.4 3.3E-12 8.3E-17  105.9   8.4  342   11-370   279-713 (758)
 90 pfam07728 AAA_5 AAA domain (dy  99.4 2.7E-12 6.9E-17  106.5   7.6  115  165-284     1-124 (139)
 91 PRK13342 recombination factor   99.3 1.2E-11 3.2E-16  101.8  10.2  210  136-388     9-223 (417)
 92 PRK10865 protein disaggregatio  99.3 6.7E-12 1.7E-16  103.7   5.4  222  141-370   569-826 (857)
 93 CHL00095 clpC Clp protease ATP  99.3 1.5E-11 3.7E-16  101.3   6.8  223  140-370   509-781 (823)
 94 PRK13341 recombination factor   99.3 1.8E-11 4.6E-16  100.7   7.1  201  134-373    22-226 (726)
 95 TIGR03345 VI_ClpV1 type VI sec  99.2   7E-12 1.8E-16  103.6   4.8  221  140-370   566-828 (852)
 96 TIGR03346 chaperone_ClpB ATP-d  99.2 2.2E-11 5.6E-16  100.1   6.5  223  140-370   565-823 (852)
 97 CHL00081 chlI Mg-protoporyphyr  99.2 3.3E-11 8.5E-16   98.8   6.4  158  135-303     7-205 (347)
 98 PRK00440 rfc replication facto  99.2 7.5E-10 1.9E-14   89.3  11.8  208  137-387    13-223 (318)
 99 PRK01905 DNA-binding protein F  99.1 7.1E-11 1.8E-15   96.5   5.9   49  429-477    28-76  (77)
100 COG3707 AmiR Response regulato  99.1 2.1E-10 5.4E-15   93.1   8.3  120    9-129     4-126 (194)
101 PRK00430 fis DNA-binding prote  99.1 8.4E-11 2.2E-15   96.0   6.1   52  427-478    47-98  (98)
102 pfam00493 MCM MCM2/3/5 family.  99.1 6.6E-10 1.7E-14   89.6  10.6  114  161-283    55-173 (327)
103 COG0542 clpA ATP-binding subun  99.1   2E-10 5.1E-15   93.3   7.5  223  140-370   491-752 (786)
104 COG2256 MGS1 ATPase related to  99.1 3.8E-10 9.7E-15   91.3   8.5  204  136-388    26-237 (436)
105 COG0714 MoxR-like ATPases [Gen  99.1 1.2E-10 3.1E-15   94.9   5.7  144  152-303    32-181 (329)
106 pfam01078 Mg_chelatase Magnesi  99.1 1.4E-10 3.7E-15   94.3   5.6  142  139-284     2-159 (207)
107 CHL00195 ycf46 Ycf46; Provisio  99.1   4E-10   1E-14   91.2   7.1  184  162-387   258-461 (491)
108 COG1239 ChlI Mg-chelatase subu  99.0 1.3E-09 3.3E-14   87.5   8.8  158  135-303    12-210 (423)
109 pfam05496 RuvB_N Holliday junc  99.0 6.2E-10 1.6E-14   89.8   6.4  200  135-372    19-229 (234)
110 pfam02954 HTH_8 Bacterial regu  99.0 5.3E-10 1.4E-14   90.3   5.4   42  434-475     1-42  (42)
111 PRK11475 DNA-binding transcrip  99.0 2.2E-09 5.5E-14   86.0   8.4  103   23-125     3-114 (205)
112 COG3279 LytT Response regulato  99.0   1E-09 2.6E-14   88.3   6.3  115   10-126     1-119 (244)
113 PRK00080 ruvB Holliday junctio  99.0   1E-08 2.6E-13   81.2  11.3  253  135-475    20-300 (328)
114 PRK12402 replication factor C   99.0 6.3E-09 1.6E-13   82.7  10.0  209  137-385    12-246 (337)
115 smart00350 MCM minichromosome   98.9   9E-09 2.3E-13   81.6   9.8  114  161-283   234-352 (509)
116 PRK13406 bchD magnesium chelat  98.9 3.9E-08   1E-12   77.1  12.0  209  165-386    27-247 (584)
117 PRK08903 hypothetical protein;  98.8 2.4E-08 6.1E-13   78.6   9.2  209  131-386     9-223 (227)
118 PRK04195 replication factor C   98.8   2E-08 5.1E-13   79.2   8.6  203  137-384    11-221 (403)
119 TIGR03420 DnaA_homol_Hda DnaA   98.8 2.2E-08 5.7E-13   78.8   8.9  208  133-383     8-222 (226)
120 PRK03992 proteasome-activating  98.8   2E-08 5.2E-13   79.1   8.0  217  133-388   125-372 (390)
121 CHL00176 ftsH cell division pr  98.8 1.8E-08 4.6E-13   79.5   7.7  217  132-387   169-415 (631)
122 CHL00181 cbbX CbbX; Provisiona  98.8 1.8E-08 4.5E-13   79.6   7.6  166  161-371    57-253 (287)
123 COG2901 Fis Factor for inversi  98.8 8.9E-09 2.3E-13   81.7   5.7   50  428-477    48-97  (98)
124 PRK10787 DNA-binding ATP-depen  98.8 2.1E-08 5.2E-13   79.1   7.5  201  161-391   346-584 (784)
125 TIGR02442 Cob-chelat-sub cobal  98.8   1E-08 2.6E-13   81.2   5.5  239  139-386     3-306 (688)
126 TIGR00763 lon ATP-dependent pr  98.8 2.4E-09 6.1E-14   85.7   2.3  177  161-369   446-658 (941)
127 TIGR01241 FtsH_fam ATP-depende  98.8 4.6E-09 1.2E-13   83.7   3.4  219  126-388    45-299 (505)
128 COG1067 LonB Predicted ATP-dep  98.7 3.3E-08 8.4E-13   77.6   6.9  226  159-389   127-399 (647)
129 TIGR00635 ruvB Holliday juncti  98.7 4.5E-08 1.1E-12   76.7   6.8  241  138-472     2-276 (305)
130 TIGR02640 gas_vesic_GvpN gas v  98.7 3.2E-08 8.2E-13   77.7   5.7  158  145-310     3-185 (265)
131 PRK05642 DNA replication initi  98.7 1.1E-07 2.9E-12   73.9   8.3  210  131-383    10-229 (234)
132 KOG0730 consensus               98.7 2.6E-08 6.7E-13   78.3   5.0  175  161-376   466-656 (693)
133 PRK08084 DNA replication initi  98.7   6E-08 1.5E-12   75.8   6.7  208  130-382    12-229 (235)
134 pfam00308 Bac_DnaA Bacterial d  98.7 4.2E-08 1.1E-12   76.9   5.5  202  135-372     3-216 (219)
135 TIGR02040 PpsR-CrtJ transcript  98.6 4.7E-08 1.2E-12   76.5   5.3   45  433-477   409-453 (453)
136 COG1222 RPT1 ATP-dependent 26S  98.6 7.5E-08 1.9E-12   75.1   6.1  217  133-388   144-391 (406)
137 PRK09862 putative ATP-dependen  98.6   4E-08   1E-12   77.1   4.6  133  137-284   188-347 (506)
138 PRK08727 hypothetical protein;  98.6 1.8E-07 4.5E-12   72.5   7.8  208  133-383    12-225 (233)
139 COG0466 Lon ATP-dependent Lon   98.6 2.3E-08 5.8E-13   78.8   3.1  265  162-465   348-658 (782)
140 PRK10733 hflB ATP-dependent me  98.6 1.3E-07 3.3E-12   73.4   7.0  219  132-389   144-392 (644)
141 KOG0480 consensus               98.6 2.6E-07 6.7E-12   71.3   8.4  210  161-386   376-640 (764)
142 COG2255 RuvB Holliday junction  98.6 8.3E-07 2.1E-11   67.8  10.9  258  136-477    22-303 (332)
143 COG3706 PleD Response regulato  98.6   1E-07 2.6E-12   74.2   5.9  141   35-186    13-155 (435)
144 PRK05563 DNA polymerase III su  98.6   3E-07 7.6E-12   70.9   8.3  217  135-390    11-245 (541)
145 PRK06645 DNA polymerase III su  98.6 1.6E-06   4E-11   65.8  11.9  213  135-389    16-256 (507)
146 KOG1051 consensus               98.6 2.7E-07 6.8E-12   71.2   7.3  230  141-377   563-838 (898)
147 PRK00411 cdc6 cell division co  98.6 8.3E-07 2.1E-11   67.7   9.7  231  138-387    28-280 (394)
148 PRK05342 clpX ATP-dependent pr  98.5 1.2E-07 3.1E-12   73.6   5.3   91  162-262   108-217 (411)
149 PRK07270 DNA polymerase III su  98.5 5.6E-07 1.4E-11   68.9   8.1  215  135-389    10-244 (557)
150 PRK09581 pleD response regulat  98.5   5E-07 1.3E-11   69.3   7.9  117    9-126   154-274 (457)
151 smart00448 REC cheY-homologous  98.5 5.8E-07 1.5E-11   68.8   8.1   53   11-63      1-55  (55)
152 COG1241 MCM2 Predicted ATPase   98.5 4.8E-06 1.2E-10   62.4  12.6  215  161-387   317-590 (682)
153 pfam06490 FleQ Flagellar regul  98.5 1.1E-06 2.8E-11   66.9   8.7  106   12-124     1-108 (109)
154 PRK00149 dnaA chromosomal repl  98.5 3.3E-07 8.4E-12   70.6   5.9  221  133-387   112-344 (447)
155 COG0606 Predicted ATPase with   98.5   1E-07 2.6E-12   74.2   3.2  140  136-290   175-342 (490)
156 TIGR00382 clpX ATP-dependent C  98.4 4.9E-07 1.2E-11   69.4   6.2  200   52-280    35-288 (452)
157 PRK06893 DNA replication initi  98.4 9.6E-07 2.5E-11   67.3   7.5  207  133-383     9-224 (229)
158 PRK13531 regulatory ATPase Rav  98.4 7.8E-08   2E-12   75.0   1.9  151  152-316    28-184 (498)
159 TIGR01242 26Sp45 26S proteasom  98.4 3.7E-07 9.4E-12   70.2   5.3  213  132-384   114-358 (364)
160 TIGR02928 TIGR02928 orc1/cdc6   98.4 1.4E-07 3.5E-12   73.2   3.0  228  135-386    10-285 (383)
161 KOG0731 consensus               98.4 6.8E-07 1.7E-11   68.4   6.4  216  133-387   304-551 (774)
162 pfam00004 AAA ATPase family as  98.4   7E-08 1.8E-12   75.4   1.3   96  166-283     1-110 (131)
163 PRK07003 DNA polymerase III su  98.4 1.3E-05 3.3E-10   59.3  12.7  222  134-389    10-244 (816)
164 PRK12422 chromosomal replicati  98.4 6.6E-07 1.7E-11   68.4   5.9  220  133-386   104-340 (455)
165 PRK11107 hybrid sensory histid  98.4   9E-06 2.3E-10   60.4  11.5  112    9-122   535-648 (920)
166 TIGR02397 dnaX_nterm DNA polym  98.3 2.9E-06 7.3E-11   63.9   8.2  215  132-390     6-245 (363)
167 PRK06305 DNA polymerase III su  98.3 5.7E-06 1.5E-10   61.8   9.5  219  134-390    11-247 (462)
168 PRK07764 DNA polymerase III su  98.3 2.8E-06 7.2E-11   64.0   7.8  223  135-389    10-246 (775)
169 PRK08451 DNA polymerase III su  98.3 7.1E-06 1.8E-10   61.1   9.5  216  135-388     9-241 (523)
170 KOG0733 consensus               98.3 1.1E-06 2.7E-11   67.0   5.2  195  136-370   186-409 (802)
171 KOG2028 consensus               98.3 4.4E-07 1.1E-11   69.7   3.1  219  129-389   127-368 (554)
172 CHL00095 clpC Clp protease ATP  98.3 1.2E-06   3E-11   66.7   5.0  206  135-369   174-423 (823)
173 PRK08853 DNA polymerase III su  98.3 2.8E-05 7.1E-10   57.0  12.0  222  134-389    10-244 (717)
174 TIGR03015 pepcterm_ATPase puta  98.3 3.4E-06 8.8E-11   63.4   7.3  226  142-384    21-261 (269)
175 KOG0478 consensus               98.3 3.4E-06 8.8E-11   63.4   7.1  116  161-282   460-577 (804)
176 PRK10865 protein disaggregatio  98.3 1.3E-06 3.3E-11   66.4   4.9  200  135-368   173-422 (857)
177 PRK05201 hslU ATP-dependent pr  98.3 2.6E-06 6.6E-11   64.2   6.3  128  233-370   248-403 (442)
178 PRK06647 DNA polymerase III su  98.3   1E-05 2.6E-10   60.0   9.2  221  134-389    10-244 (560)
179 PRK06674 DNA polymerase III su  98.2 4.8E-06 1.2E-10   62.3   7.5  211  135-388    11-243 (563)
180 KOG0745 consensus               98.2 1.5E-06 3.7E-11   66.0   4.7   94  161-265   224-336 (564)
181 PRK07994 DNA polymerase III su  98.2 3.9E-05   1E-09   55.9  12.0  222  134-389    10-244 (643)
182 TIGR02881 spore_V_K stage V sp  98.2 2.6E-06 6.6E-11   64.3   5.9  165  161-370    40-236 (261)
183 KOG2004 consensus               98.2 1.2E-06 3.2E-11   66.5   4.1  176  162-369   436-642 (906)
184 TIGR02639 ClpA ATP-dependent C  98.2 9.4E-07 2.4E-11   67.4   3.4  217  140-369   497-751 (774)
185 TIGR00368 TIGR00368 Mg chelata  98.2 4.3E-07 1.1E-11   69.8   1.4  251   22-285    40-353 (505)
186 PRK09111 DNA polymerase III su  98.2 2.4E-05 6.2E-10   57.4  10.4  215  134-390    17-257 (600)
187 PRK08691 DNA polymerase III su  98.2 5.4E-05 1.4E-09   54.9  12.0  218  134-389    10-244 (704)
188 COG0593 DnaA ATPase involved i  98.2 2.9E-06 7.3E-11   63.9   5.4  221  131-388    78-312 (408)
189 TIGR02031 BchD-ChlD magnesium   98.2   1E-05 2.6E-10   60.1   8.2  216  166-386    20-306 (705)
190 TIGR03346 chaperone_ClpB ATP-d  98.2 1.6E-06 4.1E-11   65.7   3.9  200  135-368   168-417 (852)
191 COG1223 Predicted ATPase (AAA+  98.1 1.2E-06 3.1E-11   66.5   2.4  166  132-330   113-300 (368)
192 COG0464 SpoVK ATPases of the A  98.1 1.3E-06 3.3E-11   66.3   2.2  193  162-387   275-481 (494)
193 TIGR03345 VI_ClpV1 type VI sec  98.1 4.1E-06 1.1E-10   62.8   4.7  204  135-369   182-432 (852)
194 KOG0734 consensus               98.1 9.1E-06 2.3E-10   60.4   6.5  210  134-384   298-536 (752)
195 KOG0733 consensus               98.1 4.5E-06 1.1E-10   62.6   4.4  130  162-317   544-686 (802)
196 COG1219 ClpX ATP-dependent pro  98.1 7.2E-06 1.8E-10   61.1   5.4   96  159-268    93-213 (408)
197 COG4567 Response regulator con  98.1 2.8E-05 7.2E-10   56.9   8.4   42  434-475   138-179 (182)
198 PRK08770 DNA polymerase III su  98.1 0.00014 3.5E-09   52.0  11.9  222  134-389    10-244 (663)
199 PRK09087 hypothetical protein;  98.0 3.6E-05 9.1E-10   56.2   8.3  199  135-386    16-219 (226)
200 PHA02244 ATPase-like protein    98.0 1.1E-05 2.9E-10   59.7   5.6  130  143-283    99-230 (383)
201 PRK05896 DNA polymerase III su  98.0 5.9E-05 1.5E-09   54.7   9.1  209  135-388    11-243 (613)
202 PRK11034 clpA ATP-dependent Cl  98.0 2.6E-06 6.7E-11   64.2   2.0  154  135-317   181-356 (758)
203 KOG0727 consensus               98.0   1E-05 2.6E-10   60.1   4.7  136  152-319   180-332 (408)
204 PRK07133 DNA polymerase III su  98.0 5.5E-05 1.4E-09   54.9   8.1  209  135-387    13-241 (718)
205 smart00382 AAA ATPases associa  97.9 7.4E-06 1.9E-10   61.0   3.5  118  163-283     2-125 (148)
206 COG0465 HflB ATP-dependent Zn   97.9 8.5E-06 2.2E-10   60.6   2.9  214  134-387   144-388 (596)
207 PRK06872 DNA polymerase III su  97.9 0.00022 5.5E-09   50.7  10.1  223  134-390    10-245 (696)
208 PRK06620 hypothetical protein;  97.9 0.00025 6.4E-09   50.2  10.3  163  163-382    44-209 (214)
209 PRK05648 DNA polymerase III su  97.9 0.00016   4E-09   51.6   8.9  223  134-390    10-245 (705)
210 PRK08116 hypothetical protein;  97.8 1.9E-05 4.9E-10   58.1   3.6  139  147-304    89-233 (262)
211 KOG0989 consensus               97.8 0.00015 3.8E-09   51.8   8.1  208  135-380    31-244 (346)
212 KOG0737 consensus               97.8 2.5E-05 6.4E-10   57.3   3.9  177  162-372   126-311 (386)
213 PTZ00111 DNA replication licen  97.8 8.5E-05 2.2E-09   53.5   6.3  114  161-282   491-609 (916)
214 TIGR02880 cbbX_cfxQ CbbX prote  97.7   9E-05 2.3E-09   53.3   6.2  189  151-373    45-254 (284)
215 KOG0738 consensus               97.7   9E-05 2.3E-09   53.3   6.1  174  164-374   246-434 (491)
216 TIGR02030 BchI-ChlI magnesium   97.7 7.7E-05   2E-09   53.8   5.5  185  139-334     3-239 (340)
217 PRK12323 DNA polymerase III su  97.7 0.00024   6E-09   50.4   7.7  223  134-390    10-250 (721)
218 PRK07952 DNA replication prote  97.6 8.1E-05 2.1E-09   53.7   4.2  137  146-303    79-219 (242)
219 PRK08181 transposase; Validate  97.6 3.5E-05   9E-10   56.2   2.1  138  158-315   101-247 (269)
220 PRK06526 transposase; Provisio  97.6 6.3E-05 1.6E-09   54.5   3.2  111  157-287    92-204 (254)
221 KOG1969 consensus               97.5  0.0022 5.7E-08   43.5  11.1  179  165-373   328-519 (877)
222 KOG0736 consensus               97.5 7.9E-05   2E-09   53.7   3.3  120  162-299   704-839 (953)
223 PRK12377 putative replication   97.5 6.9E-05 1.8E-09   54.2   2.8  146  136-302    70-222 (248)
224 COG0470 HolB ATPase involved i  97.5 0.00025 6.5E-09   50.2   5.4  123  143-282     4-147 (325)
225 KOG0732 consensus               97.5 7.3E-05 1.9E-09   54.0   2.6  173  164-355   300-495 (1080)
226 PRK06835 DNA replication prote  97.5 0.00013 3.4E-09   52.1   3.9  143  143-304   157-307 (330)
227 COG1474 CDC6 Cdc6-related prot  97.4 0.00037 9.4E-09   49.0   5.9  202  165-385    44-261 (366)
228 TIGR02639 ClpA ATP-dependent C  97.4  0.0001 2.6E-09   52.9   3.0  122  134-284   202-349 (774)
229 KOG0739 consensus               97.4 0.00014 3.6E-09   52.0   3.2  123  164-316   167-305 (439)
230 KOG0729 consensus               97.4 0.00019 4.7E-09   51.1   3.6  213  132-384   169-413 (435)
231 pfam01695 IstB IstB-like ATP b  97.4 0.00025 6.5E-09   50.2   4.3  111  158-288    42-154 (178)
232 PRK09183 transposase/IS protei  97.3 0.00013 3.4E-09   52.2   2.7  109  157-287    95-208 (258)
233 pfam05673 DUF815 Protein of un  97.3 0.00019 4.8E-09   51.1   2.9  128  135-284    23-152 (248)
234 COG3267 ExeA Type II secretory  97.2 0.00079   2E-08   46.7   5.5  206  159-380    47-264 (269)
235 PRK05564 DNA polymerase III su  97.2 0.00043 1.1E-08   48.5   4.0  107  138-260     2-120 (313)
236 COG2812 DnaX DNA polymerase II  97.2  0.0015 3.8E-08   44.7   6.5  212  135-388    11-243 (515)
237 COG5271 MDN1 AAA ATPase contai  97.1  0.0012   3E-08   45.5   5.1   34  147-180  1157-1190(4600)
238 PRK09112 DNA polymerase III su  97.0  0.0019 4.8E-08   44.0   6.1  136  137-284    20-181 (352)
239 KOG0744 consensus               97.0  0.0011 2.8E-08   45.6   4.8   87  157-248   171-265 (423)
240 KOG0726 consensus               97.0  0.0019 4.8E-08   44.0   5.7  139  136-294   181-347 (440)
241 COG0542 clpA ATP-binding subun  97.0 0.00023 5.9E-09   50.5   0.7  125  135-284   165-309 (786)
242 KOG0742 consensus               96.9   0.006 1.5E-07   40.5   7.9  133  165-331   386-532 (630)
243 KOG0728 consensus               96.9   0.002 5.1E-08   43.9   5.5  168  162-370   180-366 (404)
244 KOG0740 consensus               96.9 0.00031 7.8E-09   49.6   1.0  132  165-330   188-336 (428)
245 KOG0477 consensus               96.9  0.0011 2.8E-08   45.7   3.8  113  162-283   481-598 (854)
246 PRK07471 DNA polymerase III su  96.8   0.003 7.7E-08   42.6   5.6  135  138-284    15-179 (363)
247 PRK06921 hypothetical protein;  96.8  0.0022 5.7E-08   43.5   4.9  118  161-302   114-239 (265)
248 KOG0730 consensus               96.8  0.0008   2E-08   46.7   2.5  125  162-316   217-357 (693)
249 TIGR01243 CDC48 AAA family ATP  96.8  0.0019   5E-08   43.9   4.4  126  162-317   239-381 (980)
250 TIGR01243 CDC48 AAA family ATP  96.8 0.00091 2.3E-08   46.2   2.6  129  150-296   564-704 (980)
251 pfam08298 AAA_PrkA PrkA AAA do  96.8  0.0012 3.1E-08   45.3   3.2   62  135-198    53-118 (358)
252 PTZ00112 origin recognition co  96.7  0.0021 5.3E-08   43.7   4.2  226  139-387   266-511 (650)
253 COG1484 DnaC DNA replication p  96.7  0.0022 5.5E-08   43.6   4.1  132  138-290    77-215 (254)
254 PRK05574 holA DNA polymerase I  96.6   0.074 1.9E-06   32.8  13.6  267  161-470    13-290 (336)
255 KOG0652 consensus               96.6  0.0051 1.3E-07   41.0   5.4  212  133-384   164-407 (424)
256 pfam05621 TniB Bacterial TniB   96.6    0.01 2.6E-07   38.8   6.7  220  140-384    34-284 (302)
257 KOG0741 consensus               96.5  0.0039   1E-07   41.8   4.5   23  164-186   257-279 (744)
258 COG2508 Regulator of polyketid  96.5  0.0098 2.5E-07   39.0   6.4   37  445-481   360-400 (421)
259 TIGR01815 TrpE-clade3 anthrani  96.5  0.0071 1.8E-07   40.0   5.7  104    8-116   522-629 (726)
260 PRK07940 DNA polymerase III su  96.5  0.0026 6.6E-08   43.0   3.4  120  137-260     2-147 (395)
261 PRK13566 anthranilate synthase  96.5   0.024 6.2E-07   36.2   8.3   34   53-86    260-295 (724)
262 PRK04132 replication factor C   96.4  0.0028 7.2E-08   42.8   3.2  109  137-258    22-135 (863)
263 PRK08939 primosomal protein Dn  96.3  0.0033 8.5E-08   42.3   3.2  124  147-290   139-268 (306)
264 TIGR02688 TIGR02688 conserved   96.3  0.0028 7.1E-08   42.8   2.8  168  161-361   215-404 (470)
265 KOG0482 consensus               96.2   0.015 3.7E-07   37.7   5.8  113  161-282   373-490 (721)
266 PRK07914 hypothetical protein;  96.2    0.13 3.3E-06   31.0  12.6  259  163-474     4-272 (320)
267 KOG0735 consensus               96.1  0.0054 1.4E-07   40.8   3.4  138  162-326   700-851 (952)
268 pfam03709 OKR_DC_1_N Orn/Lys/A  96.1   0.045 1.2E-06   34.3   7.9   66   23-91      6-74  (111)
269 smart00763 AAA_PrkA PrkA AAA d  96.1  0.0046 1.2E-07   41.3   2.7   61  140-200    51-119 (361)
270 cd03223 ABCD_peroxisomal_ALDP   96.1   0.029 7.5E-07   35.6   6.8   38  151-188    15-52  (166)
271 PRK05629 hypothetical protein;  96.0    0.15 3.8E-06   30.6  14.3  186  159-389    11-204 (331)
272 PRK07399 DNA polymerase III su  96.0  0.0076 1.9E-07   39.7   3.6  121  138-259     2-150 (314)
273 TIGR00764 lon_rel ATP-dependen  96.0    0.01 2.7E-07   38.7   4.2  142  225-373   227-390 (662)
274 PRK08058 DNA polymerase III su  95.9  0.0054 1.4E-07   40.8   2.7  118  139-260     4-137 (329)
275 KOG0651 consensus               95.9   0.016 4.1E-07   37.5   4.9  137  134-294   126-294 (388)
276 pfam06068 TIP49 TIP49 C-termin  95.8  0.0075 1.9E-07   39.8   2.9   98  233-353   275-377 (395)
277 COG5271 MDN1 AAA ATPase contai  95.8   0.021 5.3E-07   36.7   5.1   41  158-201  1538-1578(4600)
278 pfam05729 NACHT NACHT domain.   95.8   0.029 7.4E-07   35.6   5.8   83  165-247     2-93  (165)
279 TIGR00390 hslU heat shock prot  95.7  0.0071 1.8E-07   40.0   2.6   41  161-204    45-85  (463)
280 KOG1808 consensus               95.7  0.0099 2.5E-07   38.9   3.3  122  146-273   422-548 (1856)
281 PRK11131 ATP-dependent RNA hel  95.6  0.0087 2.2E-07   39.3   2.5   54   45-98    175-236 (1295)
282 PRK07132 DNA polymerase III su  95.5   0.025 6.3E-07   36.1   4.7  107  161-284    18-132 (303)
283 COG1224 TIP49 DNA helicase TIP  95.4   0.015 3.9E-07   37.6   3.2  286   45-359    55-399 (450)
284 COG2607 Predicted ATPase (AAA+  95.2   0.049 1.3E-06   34.0   5.3   98  163-284    85-184 (287)
285 pfam00437 GSPII_E Type II/IV s  95.1   0.012 3.1E-07   38.3   1.9   60  138-197   114-173 (283)
286 PRK13409 putative ATPase RIL;   95.0    0.23 5.8E-06   29.3   8.2   65   25-90    192-270 (590)
287 PRK11477 carbohydrate diacid t  94.9   0.036 9.2E-07   34.9   4.1   32  444-475   327-358 (385)
288 cd01380 MYSc_type_V Myosin mot  94.9   0.022 5.7E-07   36.4   3.0   24  161-184    84-107 (691)
289 PRK01172 ski2-like helicase; P  94.9   0.026 6.5E-07   36.0   3.2   51   52-104   135-192 (674)
290 COG1220 HslU ATP-dependent pro  94.8   0.023 5.9E-07   36.3   2.8  123  233-370   250-405 (444)
291 PRK05707 DNA polymerase III su  94.8    0.13 3.3E-06   31.1   6.6  110  149-260     8-133 (328)
292 TIGR01842 type_I_sec_PrtD type  94.7   0.037 9.4E-07   34.9   3.7   78  151-231   344-429 (556)
293 PRK11331 5-methylcytosine-spec  94.7    0.25 6.4E-06   29.0   7.9  121  161-284   192-335 (459)
294 PRK05917 DNA polymerase III su  94.7   0.055 1.4E-06   33.6   4.4  112  145-260     2-122 (290)
295 KOG0481 consensus               94.6   0.094 2.4E-06   32.0   5.5  216  161-387   362-637 (729)
296 COG1493 HprK Serine kinase of   94.6     0.1 2.6E-06   31.7   5.7  103   62-186    65-168 (308)
297 cd01384 MYSc_type_XI Myosin mo  94.5   0.044 1.1E-06   34.4   3.7   68  161-230    86-158 (674)
298 pfam03215 Rad17 Rad17 cell cyc  94.4    0.35 8.8E-06   28.0   8.0  119  236-370   131-260 (490)
299 COG5022 Myosin heavy chain [Cy  94.4   0.045 1.2E-06   34.3   3.4   78  161-245   150-240 (1463)
300 TIGR00634 recN DNA repair prot  94.3   0.031   8E-07   35.4   2.5   34  167-200    26-60  (605)
301 COG1224 TIP49 DNA helicase TIP  94.3    0.12 2.9E-06   31.4   5.3   68  134-202    33-103 (450)
302 TIGR02525 plasmid_TraJ plasmid  94.3   0.027 6.9E-07   35.8   2.1   32  166-197   152-185 (374)
303 TIGR02782 TrbB_P P-type conjug  94.3   0.018 4.5E-07   37.2   1.1   51  135-185   111-161 (315)
304 cd01130 VirB11-like_ATPase Typ  94.2    0.02 5.2E-07   36.7   1.4   47  150-197    12-58  (186)
305 pfam02310 B12-binding B12 bind  94.2    0.46 1.2E-05   27.2   8.3   75   17-91     11-92  (121)
306 cd03221 ABCF_EF-3 ABCF_EF-3  E  94.2    0.11 2.8E-06   31.5   5.1  100  151-260    14-116 (144)
307 COG1373 Predicted ATPase (AAA+  94.2   0.086 2.2E-06   32.3   4.6   78  165-258    39-118 (398)
308 pfam03969 AFG1_ATPase AFG1-lik  94.2    0.13 3.2E-06   31.1   5.4  118  162-298    60-181 (361)
309 PRK06585 holA DNA polymerase I  94.2    0.51 1.3E-05   26.8  11.0  188  163-390    20-211 (343)
310 PRK08769 DNA polymerase III su  94.1   0.095 2.4E-06   32.0   4.6  109  145-260     5-140 (319)
311 KOG0991 consensus               94.0   0.046 1.2E-06   34.2   2.8  187  138-369    25-219 (333)
312 KOG1051 consensus               94.0   0.021 5.2E-07   36.7   1.0  108  137-247   183-294 (898)
313 COG1204 Superfamily II helicas  93.9   0.033 8.5E-07   35.2   2.0  105   11-118    78-216 (766)
314 PRK13633 cobalt transporter AT  93.9     0.5 1.3E-05   26.9   8.1   24  161-184    35-58  (281)
315 cd01385 MYSc_type_IX Myosin mo  93.9   0.077   2E-06   32.6   3.9   23  161-183    92-114 (692)
316 KOG0735 consensus               93.9   0.058 1.5E-06   33.5   3.2   78  161-246   429-507 (952)
317 TIGR02418 acolac_catab acetola  93.9   0.025 6.3E-07   36.1   1.3  276   28-351    30-347 (553)
318 TIGR02173 cyt_kin_arch cytidyl  93.9    0.04   1E-06   34.6   2.3   21  166-186     3-23  (173)
319 PRK06871 DNA polymerase III su  93.8    0.46 1.2E-05   27.2   7.7   96  161-260    21-133 (324)
320 TIGR01193 bacteriocin_ABC ABC-  93.7    0.04   1E-06   34.7   2.1   96  151-253   488-607 (710)
321 COG3910 Predicted ATPase [Gene  93.7    0.18 4.5E-06   30.1   5.4   37  145-185    22-59  (233)
322 cd01386 MYSc_type_XVIII Myosin  93.7   0.048 1.2E-06   34.1   2.4   24  161-184    84-107 (767)
323 PRK06762 hypothetical protein;  93.6   0.055 1.4E-06   33.7   2.6   43  165-215     4-46  (166)
324 COG4615 PvdE ABC-type sideroph  93.5    0.23 5.9E-06   29.3   5.7   44  164-208   350-393 (546)
325 pfam05707 Zot Zonular occluden  93.5   0.093 2.4E-06   32.1   3.6   78  166-245     3-82  (183)
326 PRK05637 anthranilate synthase  93.4    0.39 9.8E-06   27.7   6.7   77   10-87      1-80  (208)
327 cd02068 radical_SAM_B12_BD B12  93.4    0.65 1.7E-05   26.1   7.9   88   21-109     3-96  (127)
328 PRK07261 topology modulation p  93.3   0.079   2E-06   32.5   3.0   33  164-199     1-33  (171)
329 cd02024 NRK1 Nicotinamide ribo  93.2    0.38 9.8E-06   27.7   6.4  159  166-360     2-179 (187)
330 PTZ00014 myosin A; Provisional  93.1   0.091 2.3E-06   32.1   3.1   25  161-185   182-206 (821)
331 cd04158 ARD1 ARD1 subfamily.    93.0    0.61 1.6E-05   26.3   7.3  119  166-294     2-121 (169)
332 PRK06090 DNA polymerase III su  93.0    0.13 3.3E-06   31.1   3.8  122  147-284     6-148 (319)
333 PRK05657 RNA polymerase sigma   93.0     0.2   5E-06   29.8   4.7   49  434-482   265-327 (328)
334 PRK13833 conjugal transfer pro  92.9   0.035 8.8E-07   35.1   0.8   50  137-186   118-167 (323)
335 smart00242 MYSc Myosin. Large   92.9    0.14 3.5E-06   30.9   3.8   23  161-183    90-112 (677)
336 cd00267 ABC_ATPase ABC (ATP-bi  92.9    0.28 7.2E-06   28.6   5.4  107  153-260    15-126 (157)
337 smart00177 ARF ARF-like small   92.9    0.66 1.7E-05   26.1   7.2  120  161-294    11-135 (175)
338 COG0512 PabA Anthranilate/para  92.9    0.66 1.7E-05   26.1   7.2   79   10-89      1-84  (191)
339 cd01378 MYSc_type_I Myosin mot  92.9    0.14 3.4E-06   30.9   3.7   24  161-184    84-107 (674)
340 PRK08118 topology modulation p  92.8   0.093 2.4E-06   32.1   2.8   32  165-199     3-34  (167)
341 PRK13900 type IV secretion sys  92.8   0.045 1.2E-06   34.3   1.2   46  151-197   148-193 (332)
342 PRK02362 ski2-like helicase; P  92.8   0.092 2.4E-06   32.1   2.8   53   51-105   136-195 (736)
343 PRK05428 HPr kinase/phosphoryl  92.8    0.18 4.5E-06   30.1   4.2  102   70-196    71-175 (308)
344 COG4172 ABC-type uncharacteriz  92.7    0.34 8.7E-06   28.1   5.6   43   46-89    169-217 (534)
345 TIGR02982 heterocyst_DevA ABC   92.7    0.12 2.9E-06   31.4   3.2   85  140-234     8-92  (220)
346 KOG1970 consensus               92.6    0.32 8.1E-06   28.3   5.3   20  166-185   113-132 (634)
347 TIGR01420 pilT_fam twitching m  92.6    0.11 2.8E-06   31.6   2.9  163  163-366   127-312 (350)
348 PRK13413 mpi multiple promoter  92.6    0.29 7.3E-06   28.6   5.1   28  449-476   170-197 (200)
349 cd01377 MYSc_type_II Myosin mo  92.6    0.13 3.3E-06   31.1   3.3   23  161-183    89-111 (693)
350 KOG0741 consensus               92.5   0.084 2.1E-06   32.4   2.2  190  138-366   505-717 (744)
351 cd00878 Arf_Arl Arf (ADP-ribos  92.5    0.91 2.3E-05   25.0   7.6  117  166-292     2-119 (158)
352 cd01124 KaiC KaiC is a circadi  92.5   0.071 1.8E-06   32.9   1.8   30  165-195     1-31  (187)
353 TIGR03608 L_ocin_972_ABC putat  92.3    0.37 9.5E-06   27.8   5.4   32  152-183    13-44  (206)
354 TIGR01846 type_I_sec_HlyB type  92.3    0.13 3.3E-06   31.0   3.1  138   65-205   372-535 (703)
355 cd04151 Arl1 Arl1 subfamily.    92.3    0.96 2.5E-05   24.9   7.5  116  166-294     2-121 (158)
356 PRK09302 circadian clock prote  92.2    0.52 1.3E-05   26.8   6.0   28  161-188   264-292 (501)
357 PRK13851 type IV secretion sys  92.2   0.056 1.4E-06   33.6   1.0   45  152-197   151-195 (343)
358 PRK13894 conjugal transfer ATP  92.1   0.054 1.4E-06   33.7   0.9   50  137-186   123-172 (320)
359 KOG2680 consensus               92.0    0.59 1.5E-05   26.4   6.1  130  232-384   287-424 (454)
360 cd04155 Arl3 Arl3 subfamily.    91.9       1 2.7E-05   24.6   7.4  126  161-296    12-138 (173)
361 cd04153 Arl5_Arl8 Arl5/Arl8 su  91.9     1.1 2.7E-05   24.6   7.7  123  161-296    13-139 (174)
362 COG1342 Predicted DNA-binding   91.9    0.37 9.4E-06   27.8   4.9   39  433-474    34-72  (99)
363 cd00569 HTH_Hin_like Helix-tur  91.9    0.26 6.7E-06   28.8   4.2   28  445-472    15-42  (42)
364 PRK11288 araG L-arabinose tran  91.9     1.1 2.7E-05   24.6   9.5  160   19-186   114-302 (501)
365 KOG2035 consensus               91.8    0.73 1.9E-05   25.7   6.4   38  235-283   129-166 (351)
366 TIGR02538 type_IV_pilB type IV  91.7   0.081 2.1E-06   32.5   1.4  102    9-114    92-218 (577)
367 pfam02001 DUF134 Protein of un  91.7    0.39   1E-05   27.6   4.9   39  433-474    37-75  (100)
368 COG3835 CdaR Sugar diacid util  91.7    0.25 6.5E-06   29.0   3.9   31  445-475   319-349 (376)
369 cd01387 MYSc_type_XV Myosin mo  91.6    0.13 3.3E-06   31.1   2.4   65  161-230    85-154 (677)
370 pfam06745 KaiC KaiC. This fami  91.6    0.13 3.4E-06   31.0   2.4   36  161-196    17-55  (231)
371 PRK10419 nikE nickel transport  91.5    0.15 3.8E-06   30.6   2.6   35  151-185    26-60  (266)
372 pfam09862 DUF2089 Protein of u  91.4    0.47 1.2E-05   27.1   5.0   37  441-477    39-79  (113)
373 TIGR02769 nickel_nikE nickel i  91.3    0.15 3.8E-06   30.6   2.4   57  136-192    11-67  (267)
374 PRK13768 GTPase; Provisional    91.3    0.14 3.5E-06   30.8   2.2   34  165-198     4-37  (253)
375 KOG1942 consensus               91.2    0.41   1E-05   27.5   4.6  109  232-366   295-409 (456)
376 PRK00254 ski2-like helicase; P  91.2    0.29 7.5E-06   28.5   3.9   52   51-104   137-192 (717)
377 COG1124 DppF ABC-type dipeptid  91.2    0.13 3.3E-06   31.1   2.0   26  162-187    32-57  (252)
378 cd04156 ARLTS1 ARLTS1 subfamil  91.2     1.3 3.2E-05   24.1   7.5  112  166-290     2-118 (160)
379 KOG0479 consensus               91.1    0.86 2.2E-05   25.2   6.1  112  161-283   332-450 (818)
380 cd04150 Arf1_5_like Arf1-Arf5-  91.1     1.3 3.3E-05   24.0   7.3  119  165-296     2-124 (159)
381 PRK03839 putative kinase; Prov  91.0    0.17 4.3E-06   30.2   2.5   22  165-186     2-23  (180)
382 pfam07693 KAP_NTPase KAP famil  91.0     1.2   3E-05   24.3   6.8   70  236-315   163-239 (301)
383 cd01379 MYSc_type_III Myosin m  91.0    0.12 3.2E-06   31.2   1.8   24  161-184    84-107 (653)
384 COG4178 ABC-type uncharacteriz  91.0    0.27 6.9E-06   28.8   3.5   53  140-192   396-448 (604)
385 KOG2543 consensus               91.0    0.23   6E-06   29.2   3.2   92  162-257    29-138 (438)
386 cd02067 B12-binding B12 bindin  90.9     1.3 3.4E-05   23.9  10.3   89   22-111    15-111 (119)
387 PRK04328 hypothetical protein;  90.9    0.16 4.2E-06   30.3   2.3   45  162-207    23-68  (250)
388 cd03227 ABC_Class2 ABC-type Cl  90.9     0.4   1E-05   27.6   4.3  108  165-284    23-141 (162)
389 pfam06068 TIP49 TIP49 C-termin  90.8    0.18 4.6E-06   30.0   2.5   68  134-202    18-88  (395)
390 cd04160 Arfrp1 Arfrp1 subfamil  90.8     1.2 3.1E-05   24.2   6.7   20  165-184     1-20  (167)
391 PRK09361 radB DNA repair and r  90.8    0.18 4.7E-06   30.0   2.4   46  162-207    22-67  (224)
392 KOG0924 consensus               90.8    0.11 2.7E-06   31.6   1.2   44  149-192   357-401 (1042)
393 COG1123 ATPase components of v  90.7    0.15 3.9E-06   30.5   2.0   25  162-186   316-340 (539)
394 PRK11308 dppF dipeptide transp  90.7    0.19 4.9E-06   29.8   2.5   25  161-185    39-63  (327)
395 smart00344 HTH_ASNC helix_turn  90.5    0.49 1.3E-05   26.9   4.5   37  438-475     4-41  (108)
396 TIGR01194 cyc_pep_trnsptr cycl  90.5    0.34 8.8E-06   28.0   3.6   43  162-205   367-409 (555)
397 COG0467 RAD55 RecA-superfamily  90.4    0.22 5.6E-06   29.4   2.6   52  161-213    21-74  (260)
398 pfam00063 Myosin_head Myosin h  90.4    0.27 6.8E-06   28.8   3.0   24  161-184    83-106 (679)
399 TIGR02203 MsbA_lipidA lipid A   90.3    0.36 9.3E-06   27.9   3.7   34  150-183   375-408 (603)
400 cd04152 Arl4_Arl7 Arl4/Arl7 su  90.3     1.5 3.8E-05   23.6   7.6  117  164-294     4-130 (183)
401 PRK10869 recombination and rep  90.3    0.33 8.4E-06   28.2   3.4   34  166-199    25-59  (553)
402 TIGR02788 VirB11 P-type DNA tr  90.3    0.14 3.6E-06   30.8   1.5   47  150-197   145-191 (328)
403 COG1654 BirA Biotin operon rep  90.3    0.73 1.9E-05   25.7   5.2   30  453-482    21-53  (79)
404 KOG2170 consensus               90.3    0.26 6.7E-06   28.9   2.9  195  139-369    81-300 (344)
405 PRK04841 transcriptional regul  90.3     1.4 3.5E-05   23.8   6.6   24  449-472   851-874 (903)
406 COG0444 DppD ABC-type dipeptid  90.2    0.22 5.6E-06   29.4   2.5   28  161-188    29-56  (316)
407 pfam06322 Phage_NinH Phage Nin  90.2    0.36 9.2E-06   27.9   3.5   34  442-475     7-40  (64)
408 COG0563 Adk Adenylate kinase a  90.0    0.28 7.2E-06   28.7   2.9   30  165-199     2-31  (178)
409 KOG0736 consensus               90.0    0.24 6.1E-06   29.1   2.5  193  161-387   429-651 (953)
410 PRK13698 plasmid-partitioning   89.9     1.3 3.3E-05   23.9   6.2   25  449-473   174-198 (323)
411 PRK05541 adenylylsulfate kinas  89.9    0.22 5.7E-06   29.4   2.3   47  162-214     6-52  (176)
412 PTZ00133 ADP-ribosylation fact  89.8     1.6 4.1E-05   23.3   7.5  119  161-293    15-138 (182)
413 cd01381 MYSc_type_VII Myosin m  89.7    0.28 7.1E-06   28.7   2.7   24  161-184    84-107 (671)
414 cd04149 Arf6 Arf6 subfamily.    89.7     1.6 4.2E-05   23.2   7.7  121  161-295     7-132 (168)
415 cd01383 MYSc_type_VIII Myosin   89.7    0.29 7.3E-06   28.6   2.7   64  161-231    90-158 (677)
416 KOG3347 consensus               89.7     0.2 5.1E-06   29.7   1.9   38  162-204     6-43  (176)
417 COG4608 AppF ABC-type oligopep  89.7    0.27 6.8E-06   28.8   2.5  100  161-261    37-156 (268)
418 PRK10938 putative molybdenum t  89.6     1.7 4.3E-05   23.2   8.5   25  161-185   284-308 (490)
419 cd01382 MYSc_type_VI Myosin mo  89.5    0.29 7.5E-06   28.5   2.7   25  161-185    89-113 (717)
420 TIGR01978 sufC FeS assembly AT  89.5     0.4   1E-05   27.6   3.3   29  163-197    26-54  (248)
421 pfam01057 Parvo_NS1 Parvovirus  89.5     1.7 4.4E-05   23.1   8.2  121  158-316   108-231 (271)
422 PRK09522 bifunctional anthrani  89.5     1.7 4.4E-05   23.1   7.7   77   10-87      1-84  (531)
423 PRK04217 hypothetical protein;  89.4    0.84 2.1E-05   25.3   4.9   39  433-474    43-81  (110)
424 pfam02796 HTH_7 Helix-turn-hel  89.4    0.48 1.2E-05   27.0   3.6   30  445-474    15-44  (45)
425 pfam00025 Arf ADP-ribosylation  89.3     1.8 4.5E-05   23.0   7.3  117  163-294    14-136 (174)
426 PRK03846 adenylylsulfate kinas  89.3    0.24 6.2E-06   29.1   2.1   42  157-198    18-59  (198)
427 PRK11022 dppD dipeptide transp  89.2    0.31 7.9E-06   28.4   2.6   26  161-186    31-56  (327)
428 PRK05703 flhF flagellar biosyn  89.1     0.4   1E-05   27.6   3.1   36  163-199   210-250 (412)
429 PRK07993 DNA polymerase III su  89.1     1.4 3.5E-05   23.8   5.9   98  161-260    22-135 (334)
430 PRK06761 hypothetical protein;  89.1     1.6 4.1E-05   23.3   6.2   83  276-368    88-173 (281)
431 TIGR01764 excise DNA binding d  89.1    0.35 8.8E-06   28.0   2.8   26  454-479     4-29  (49)
432 PRK06067 flagellar accessory p  89.1    0.28 7.1E-06   28.7   2.3   36  161-197    30-66  (241)
433 PRK10875 recD exonuclease V su  89.1     0.2 5.2E-06   29.6   1.6   53  233-299   260-312 (607)
434 pfam00931 NB-ARC NB-ARC domain  89.0    0.26 6.6E-06   28.9   2.1   39  149-187     5-43  (285)
435 cd03241 ABC_RecN RecN ATPase i  89.0    0.39   1E-05   27.6   3.0   34  166-199    24-58  (276)
436 cd00124 MYSc Myosin motor doma  89.0    0.36 9.2E-06   27.9   2.8   65  161-230    84-153 (679)
437 TIGR01967 DEAH_box_HrpA ATP-de  89.0    0.03 7.8E-07   35.5  -2.7  124  233-373   471-622 (1320)
438 TIGR02533 type_II_gspE general  89.0    0.19 4.7E-06   29.9   1.3  223   11-257    23-341 (495)
439 PRK06217 hypothetical protein;  89.0    0.38 9.7E-06   27.7   2.9   32  164-198     2-33  (185)
440 pfam01583 APS_kinase Adenylyls  88.9    0.29 7.3E-06   28.6   2.3   35  165-199     4-38  (157)
441 KOG0990 consensus               88.9     1.1 2.7E-05   24.6   5.1  122  138-282    39-169 (360)
442 cd01131 PilT Pilus retraction   88.9    0.43 1.1E-05   27.3   3.1   32  166-197     4-36  (198)
443 PRK13764 ATPase; Provisional    88.9    0.22 5.6E-06   29.4   1.6   36  155-190   251-286 (605)
444 COG4170 SapD ABC-type antimicr  88.8    0.26 6.6E-06   28.9   2.0   22  167-188    37-58  (330)
445 KOG0161 consensus               88.7    0.24 6.1E-06   29.1   1.7  215    5-245    25-259 (1930)
446 cd02023 UMPK Uridine monophosp  88.6    0.45 1.2E-05   27.2   3.1   22  166-187     2-23  (198)
447 COG1123 ATPase components of v  88.6    0.28 7.1E-06   28.7   2.0   43   46-89    166-214 (539)
448 cd03258 ABC_MetN_methionine_tr  88.6    0.35 8.8E-06   28.0   2.5   33  152-184    20-52  (233)
449 PRK10261 glutathione transport  88.6    0.36 9.3E-06   27.9   2.6   24  163-186   350-373 (623)
450 COG1136 SalX ABC-type antimicr  88.6     1.2   3E-05   24.3   5.2   32  152-183    20-51  (226)
451 cd02070 corrinoid_protein_B12-  88.5       2 5.1E-05   22.7  11.5   98   10-110    82-192 (201)
452 KOG2227 consensus               88.5    0.19 4.8E-06   29.9   1.1  205  140-371   150-378 (529)
453 cd01120 RecA-like_NTPases RecA  88.5    0.33 8.5E-06   28.1   2.4   33  166-198     2-34  (165)
454 cd03294 ABC_Pro_Gly_Bertaine T  88.4    0.38 9.6E-06   27.8   2.6   24  161-184    48-71  (269)
455 TIGR00455 apsK adenylylsulfate  88.4    0.31 7.8E-06   28.4   2.1   30  161-190    17-46  (187)
456 COG1466 HolA DNA polymerase II  88.4       2 5.2E-05   22.6   7.3  145  306-465   134-279 (334)
457 PRK00889 adenylylsulfate kinas  88.4    0.33 8.3E-06   28.2   2.2   36  163-198     4-39  (175)
458 cd04157 Arl6 Arl6 subfamily.    88.4       2 5.2E-05   22.6   7.4  119  165-294     1-125 (162)
459 PRK10982 galactose/methyl gala  88.3       2 5.2E-05   22.6  10.6  162   20-188   109-299 (491)
460 KOG1942 consensus               88.3    0.42 1.1E-05   27.4   2.8   63  136-199    34-99  (456)
461 KOG1802 consensus               88.3    0.23 5.9E-06   29.3   1.4   60  146-211   413-474 (935)
462 pfam05049 IIGP Interferon-indu  88.2    0.29 7.4E-06   28.6   1.9   43  148-190    20-62  (375)
463 cd02069 methionine_synthase_B1  88.2     2.1 5.3E-05   22.5   9.3   87   21-107   103-199 (213)
464 PRK09473 oppD oligopeptide tra  88.2    0.39   1E-05   27.6   2.6   26  161-186    40-65  (330)
465 TIGR03269 met_CoM_red_A2 methy  88.2     2.1 5.3E-05   22.5   8.7   27  162-188   309-335 (520)
466 PRK06696 uridine kinase; Valid  88.2    0.26 6.7E-06   28.9   1.7   57  145-201     7-64  (227)
467 PRK05480 uridine kinase; Provi  88.2    0.51 1.3E-05   26.8   3.1   23  165-187     8-30  (209)
468 pfam09848 DUF2075 Uncharacteri  88.1    0.38 9.7E-06   27.7   2.4   80  165-246     3-92  (348)
469 PRK11174 cysteine/glutathione   88.1     0.7 1.8E-05   25.8   3.8   43  146-188   359-401 (588)
470 pfam05225 HTH_psq helix-turn-h  88.1    0.74 1.9E-05   25.7   3.9   32  443-474     5-39  (45)
471 TIGR02142 modC_ABC molybdate A  88.1    0.64 1.6E-05   26.2   3.6  179  166-388    26-222 (361)
472 COG3311 AlpA Predicted transcr  88.0     0.4   1E-05   27.6   2.5   23  453-475    15-37  (70)
473 KOG3928 consensus               88.0    0.42 1.1E-05   27.4   2.6   34  163-199   179-213 (461)
474 COG0572 Udk Uridine kinase [Nu  88.0    0.44 1.1E-05   27.3   2.7   24  165-188    10-33  (218)
475 cd01844 SGNH_hydrolase_like_6   87.9     2.2 5.5E-05   22.4   6.7   58   32-89     29-102 (177)
476 cd01918 HprK_C HprK/P, the bif  87.9    0.49 1.3E-05   26.9   2.9   65  161-237    12-76  (149)
477 pfam00485 PRK Phosphoribulokin  87.9    0.49 1.2E-05   27.0   2.9   22  166-187     2-23  (196)
478 cd02027 APSK Adenosine 5'-phos  87.8    0.37 9.4E-06   27.8   2.2   41  166-211     2-42  (149)
479 cd02021 GntK Gluconate kinase   87.8    0.46 1.2E-05   27.2   2.7   28  166-196     2-29  (150)
480 PRK00131 aroK shikimate kinase  87.8    0.52 1.3E-05   26.8   3.0   33  163-198     4-36  (175)
481 PRK13642 cbiO cobalt transport  87.7    0.45 1.1E-05   27.2   2.6   27  161-187    31-57  (277)
482 pfam01527 Transposase_8 Transp  87.7     1.6 4.1E-05   23.3   5.4   38  437-475    10-47  (75)
483 PRK13650 cbiO cobalt transport  87.7    0.45 1.2E-05   27.2   2.6   26  161-186    28-53  (276)
484 PRK13635 cbiO cobalt transport  87.7    0.45 1.1E-05   27.2   2.6   33  154-186    24-56  (279)
485 TIGR02770 nickel_nikD nickel i  87.6    0.35 8.9E-06   28.0   2.0   20  165-184    14-33  (239)
486 COG2274 SunT ABC-type bacterio  87.5    0.53 1.3E-05   26.7   2.9   38  151-188   487-524 (709)
487 PRK10418 nikD nickel transport  87.5    0.58 1.5E-05   26.4   3.1   35  152-186    18-52  (254)
488 TIGR02653 Lon_rel_chp conserve  87.4    0.29 7.3E-06   28.6   1.5  141  153-313   205-364 (677)
489 PRK07649 para-aminobenzoate/an  87.4     2.2 5.5E-05   22.4   5.9   74   13-87      2-79  (195)
490 pfam00910 RNA_helicase RNA hel  87.3    0.38 9.6E-06   27.7   2.0   93  166-282     1-104 (105)
491 COG1936 Predicted nucleotide k  87.3    0.44 1.1E-05   27.3   2.4   20  165-184     2-21  (180)
492 COG1875 NYN ribonuclease and A  87.3     1.3 3.4E-05   23.9   4.8   44   68-111   107-150 (436)
493 cd03253 ABCC_ATM1_transporter   87.3    0.59 1.5E-05   26.4   3.0   33  152-184    16-48  (236)
494 pfam00126 HTH_1 Bacterial regu  87.2    0.69 1.7E-05   25.9   3.3   31  446-477     9-39  (60)
495 TIGR03499 FlhF flagellar biosy  87.2    0.66 1.7E-05   26.0   3.2   35  165-199   196-234 (282)
496 cd02028 UMPK_like Uridine mono  87.1    0.48 1.2E-05   27.0   2.5   21  166-186     2-22  (179)
497 TIGR02868 CydC ABC transporter  87.1    0.55 1.4E-05   26.6   2.8   39  150-188   374-412 (566)
498 COG1522 Lrp Transcriptional re  87.1     1.4 3.5E-05   23.8   4.8   11  356-366   115-125 (154)
499 TIGR00954 3a01203 Peroxysomal   87.1    0.54 1.4E-05   26.7   2.7   25  159-183   552-576 (788)
500 PRK13648 cbiO cobalt transport  87.1    0.49 1.3E-05   26.9   2.5   18  166-183    38-55  (269)

No 1  
>COG2204 AtoC Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]
Probab=100.00  E-value=0  Score=955.07  Aligned_cols=452  Identities=29%  Similarity=0.443  Sum_probs=410.9

Q ss_pred             CCCCCCEEEECCCHHHHHHHHHHHHHCCCEEEEECC--HHHHHHHCCCCCEEEEECCCCCCCHHHHHHHHHHHCCCCCEE
Q ss_conf             352883899869989999999999988988999893--799998608998999978546988899999999857898399
Q gi|254780916|r    7 LDRHKRVLIIDKDDEQIKIIKDHVESYGYDVFIVNV--SDLSTISKIQVNVIFLSLINCEDDKENILKNIVDKIPIVPII   84 (482)
Q Consensus         7 m~~~~rILIVDDd~~~~~~l~~~L~~~G~~v~~a~~--~al~~l~~~~~dlillD~~mP~~dGlell~~i~~~~p~ipvI   84 (482)
                      |....+|||||||+.+|..++..|+..||+|.++.+  ++++.+.+..+|+|++|++||++||+++++++++.+|++|||
T Consensus         1 ~~~~~~iLvVDDd~~ir~~l~~~L~~~G~~v~~a~~~~~al~~i~~~~~~lvl~Di~mp~~~Gl~ll~~i~~~~~~~pVI   80 (464)
T COG2204           1 MMMMARILVVDDDPDIRELLEQALELAGYEVVTAESAEEALEALSESPFDLVLLDIRMPGMDGLELLKEIKSRDPDLPVI   80 (464)
T ss_pred             CCCCCCEEEEECCHHHHHHHHHHHHHCCCEEEEECCHHHHHHHHHCCCCCEEEEECCCCCCCHHHHHHHHHHHCCCCCEE
T ss_conf             98768789992978999999999997697489858999999998628999899816789996699999999638999889


Q ss_pred             EEECCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC-----CCCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             9926899999998885057432222222222222222222222222222-----21111111122222222222222223
Q gi|254780916|r   85 VQTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALREGVVPSQE-----NEHCALDSLIAVSPAMIQVVDLARKA  159 (482)
Q Consensus        85 iiT~~~~~~~~~~a~~~g~~d~l~KP~~~~~L~~~i~~al~~~~~~~~~-----~~~~~~~~LiG~S~~m~~v~~~i~~~  159 (482)
                      +||||+++++++.|++.||+||+.|||++++|...+.++++......+.     ........++|+||+|+++++++.++
T Consensus        81 ~~Tg~g~i~~AV~A~k~GA~Dfl~KP~~~~~L~~~v~ral~~~~~~~e~~~~~~~~~~~~~~liG~S~am~~l~~~i~kv  160 (464)
T COG2204          81 VMTGHGDIDTAVEALRLGAFDFLEKPFDLDRLLAIVERALELRELQRENRRSLKRAKSLGGELVGESPAMQQLRRLIAKV  160 (464)
T ss_pred             EEECCCCHHHHHHHHHCCCCEEEECCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHHHHH
T ss_conf             98288999999999855703332189999999999999998765322210000013455677520699999999999998


Q ss_pred             CCCCEEEEEECCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCHHHHHCCCC-CCCCCCCCCCCCCCCCCCCEEE
Q ss_conf             443204887327774367999999842675433210123465542100243311255-5532211100123446671475
Q gi|254780916|r  160 GDCAIPIMIQGEFGVGKKRLSRFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFGDVD-LQTKNSAQFLGKFIEANGGTIV  238 (482)
Q Consensus       160 a~~~~~vli~Ge~GtGK~~~A~~iH~~s~r~~~~fi~v~c~~~~~~~~e~~lFG~~~-~~~~~~~~~~g~~~~a~~Gtl~  238 (482)
                      |.++.||||+||+|||||++||+||+.|.|+++|||.|||+++|++++|||||||++ +||||..++.|+||+|+|||||
T Consensus       161 A~s~a~VLI~GESGtGKElvAr~IH~~S~R~~~PFVavNcaAip~~l~ESELFGhekGAFTGA~~~r~G~fE~A~GGTLf  240 (464)
T COG2204         161 APSDASVLITGESGTGKELVARAIHQASPRAKGPFIAVNCAAIPENLLESELFGHEKGAFTGAITRRIGRFEQANGGTLF  240 (464)
T ss_pred             HCCCCCEEEECCCCCCHHHHHHHHHHHCCCCCCCCEEEECCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCEEECCCCEEE
T ss_conf             47799789977898758999999986074458992563346489888777761456567677643457615773796587


Q ss_pred             ECCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCEEEEECCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             16642001889998888776420011235532123431565214332111111233379998865433446778774422
Q gi|254780916|r  239 LEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYYRISVFLINISTLRSRSED  318 (482)
Q Consensus       239 l~ei~~L~~~~Q~~Ll~~l~~~~~~~~g~~~~~~~~~RiIa~t~~~L~~~~~~g~fr~dLy~rL~~~~i~iPpLReR~eD  318 (482)
                      ||||++||+++|.||||+||+++|+|+||++++++||||||+||+||++++++|+||+||||||||++|++||||||+||
T Consensus       241 LDEI~~mpl~~Q~kLLRvLqe~~~~rvG~~~~i~vdvRiIaaT~~dL~~~v~~G~FReDLyyRLnV~~i~iPpLRER~ED  320 (464)
T COG2204         241 LDEIGEMPLELQVKLLRVLQEREFERVGGNKPIKVDVRIIAATNRDLEEEVAAGRFREDLYYRLNVVPLRLPPLRERKED  320 (464)
T ss_pred             EECCCCCCHHHHHHHHHHHHCCEEEECCCCCEECEEEEEEEECCCCHHHHHHCCCCHHHHHHHHCCCEECCCCCCCCCHH
T ss_conf             32311099999999999987070673588860000169996057789999881973788886523311048762236200


Q ss_pred             HHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHCCCCCCCHHHHHHHHCCCCCCCCCCCC
Q ss_conf             22556677764101122333321111100012233898689999999999874389810688954542124454322343
Q gi|254780916|r  319 IPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQELKNILLRAVIGLKDSHLTEDRFVLLLSREGKKEREFHT  398 (482)
Q Consensus       319 I~~L~~~fl~~~~~~~~~~~~~ls~~a~~~L~~y~WPGNvREL~n~i~r~~i~~~~~~i~~~~~~~~l~~~~~~~~~~~~  398 (482)
                      ||+|++||++++|.++|+++++|+++|++.|+.|+||||||||+|+++|+++++.+..|..++++.....   ..     
T Consensus       321 Ip~L~~hfl~~~~~~~~~~~~~~s~~a~~~L~~y~WPGNVREL~N~ver~~il~~~~~i~~~~l~~~~~~---~~-----  392 (464)
T COG2204         321 IPLLAEHFLKRFAAELGRPPKGFSPEALAALLAYDWPGNVRELENVVERAVILSEGPEIEVEDLPLEILA---PA-----  392 (464)
T ss_pred             HHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHCCCCHHHHHHHHHHHHHHHCCCCCCCCHHHCCCCCCC---CC-----
T ss_conf             7999999999999980999888799999999738998189999999999985178654665441420035---42-----


Q ss_pred             CCCCCCCCCCCCCCCHHHCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHCCCHHHHHHHHHHHCCC
Q ss_conf             22222233444321000000001123444543258999999999999999828727899978489988999999981888
Q gi|254780916|r  399 ETACTCYTEGKSSDTILDNLSQESIPAIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKIREYNIE  478 (482)
Q Consensus       399 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~e~E~~~I~~aL~~~~Gn~~~aA~~LGIsR~tL~rKlk~~gi~  478 (482)
                          ....     ....   ...  +... ....+.++++|+++|.++|++|+||+++||+.|||+|+|||+|||+||++
T Consensus       393 ----~~~~-----~~~~---~~~--~~~~-~~l~~~~~~~Er~~I~~aL~~~~g~~~~aA~~LGi~R~tLy~Klk~~g~~  457 (464)
T COG2204         393 ----AEAL-----AGPA---GEA--ALPG-LPLGEALAEVERQLILQALERTGGNKSEAAERLGISRKTLYRKLKEYGID  457 (464)
T ss_pred             ----CCCC-----CCCC---CCC--CCCC-CCHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHCCCHHHHHHHHHHHCCC
T ss_conf             ----2233-----4445---655--4555-42788999999999999999968989999999799888999999994898


Q ss_pred             CCC
Q ss_conf             144
Q gi|254780916|r  479 VDS  481 (482)
Q Consensus       479 ~d~  481 (482)
                      ...
T Consensus       458 ~~~  460 (464)
T COG2204         458 RSD  460 (464)
T ss_pred             CCC
T ss_conf             344


No 2  
>TIGR01818 ntrC nitrogen regulation protein NR(I); InterPro: IPR010114   This entry represents Nitrogen regulatory protein C (NtrC), which is a bacterial enhancer-binding protein that activates the transcription of genes encoding enzymes required for nitrogen metabolism. It is phosphorylated by NtrB and interacts with sigma-54. One of the best studied examples is its activation of the gene glnA, which encodes the enzyme glutamine synthetase.. NtrC is composed of three domains , . The 124 residue N-terminal domain is homologous to receiver domains of other response regulator proteins in two-component signal transduction systems , . The 240 residue central domain of NtrC is homologous to a domain found in all activators of the sigma-54 RNA polymerase holoenzyme , . The C-terminal domain has been indicated to contain the determinants necessary for both DNA-binding and dimerization of full-length NtrC.; GO: 0000156 two-component response regulator activity, 0003677 DNA binding, 0005524 ATP binding, 0000160 two-component signal transduction system (phosphorelay), 0009399 nitrogen fixation, 0050906 detection of stimulus during sensory perception.
Probab=100.00  E-value=0  Score=954.32  Aligned_cols=458  Identities=25%  Similarity=0.390  Sum_probs=413.7

Q ss_pred             EEEECCCHHHHHHHHHHHHHCCCEEEEECCH--HHHHHHCC-CCCEEEEECCCCCCCHHHHHHHHHHHCCCCCEEEEECC
Q ss_conf             8998699899999999999889889998937--99998608-99899997854698889999999985789839999268
Q gi|254780916|r   13 VLIIDKDDEQIKIIKDHVESYGYDVFIVNVS--DLSTISKI-QVNVIFLSLINCEDDKENILKNIVDKIPIVPIIVQTTQ   89 (482)
Q Consensus        13 ILIVDDd~~~~~~l~~~L~~~G~~v~~a~~~--al~~l~~~-~~dlillD~~mP~~dGlell~~i~~~~p~ipvIiiT~~   89 (482)
                      |||||||.++|.+|...|...||.|.+.+++  .+..+.+. .||+|++|+.|||+||+++|.+|++.+|.+||||||||
T Consensus         1 vwvvDDD~siR~VL~~AL~~~g~~v~~f~~A~~~l~~l~~~p~pD~~~tD~rMPg~~Gl~LL~~ik~~~P~LPVIvM~A~   80 (471)
T TIGR01818         1 VWVVDDDRSIRWVLEKALSRAGIEVRTFDNAASVLRALAREPQPDLLITDVRMPGEDGLDLLKQIKKRHPKLPVIVMTAH   80 (471)
T ss_pred             CEEEECCCHHHHHHHHHHHHCCCEEEEHHHHHHHHHHHHCCCCCCEEEEECCCCCHHHHHHHHHHHHCCCCCCEEEECCC
T ss_conf             95776471899999999966695453113189999998447999879861226882489999999850899977987130


Q ss_pred             CCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC----CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEE
Q ss_conf             99999998885057432222222222222222222222222222----21111111122222222222222223443204
Q gi|254780916|r   90 DNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALREGVVPSQE----NEHCALDSLIAVSPAMIQVVDLARKAGDCAIP  165 (482)
Q Consensus        90 ~~~~~~~~a~~~g~~d~l~KP~~~~~L~~~i~~al~~~~~~~~~----~~~~~~~~LiG~S~~m~~v~~~i~~~a~~~~~  165 (482)
                      ++..+++.+...||++||+||||.++.+..+.+|+.....+...    ........|||+||+||+||+.|.|++.|+.+
T Consensus        81 ~dl~~Av~a~~~GAfEYLpKPFD~de~v~lv~RA~~~~~~~~~~~~~~~~~~~~~~liG~aPAMQevfR~igRL~~~~l~  160 (471)
T TIGR01818        81 SDLDSAVAAYQRGAFEYLPKPFDLDEAVTLVERALAHAQEQVALELDAGEAEDSAELIGEAPAMQEVFRAIGRLSRSDLS  160 (471)
T ss_pred             HHHHHHHHHHHCCCHHCCCCCCCHHHHHHHHHHHHCCCHHHHHHHCCCCCCCCCCCCCCCCCHHHHHHHHHHHHCCCCCE
T ss_conf             67899999973583021769876688999999861030012220001210125621236885168999999975169605


Q ss_pred             EEEECCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCHHHHHCCCC-CCCCCCCCCCCCCCCCCCCEEEECCCCH
Q ss_conf             887327774367999999842675433210123465542100243311255-5532211100123446671475166420
Q gi|254780916|r  166 IMIQGEFGVGKKRLSRFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFGDVD-LQTKNSAQFLGKFIEANGGTIVLEEPDA  244 (482)
Q Consensus       166 vli~Ge~GtGK~~~A~~iH~~s~r~~~~fi~v~c~~~~~~~~e~~lFG~~~-~~~~~~~~~~g~~~~a~~Gtl~l~ei~~  244 (482)
                      |||.||+|||||++|+++|.+|+|+++|||.+|+|+||.+|+|||||||++ +||||...+.|.||||+|||||||||+|
T Consensus       161 VlI~GESGTGKELVA~ALH~~s~R~~~PFiAlNmAAIP~~L~ESELFGHEkGAFTGA~~~~~GRFEQA~GGTLFLDEIGD  240 (471)
T TIGR01818       161 VLINGESGTGKELVARALHRHSPRARGPFIALNMAAIPKDLIESELFGHEKGAFTGANTRRQGRFEQADGGTLFLDEIGD  240 (471)
T ss_pred             EEEECCCCCCHHHHHHHHHCCCCCCCCCCEEECHHHCCHHHHHHHHCCCCCCCCCCCCCCCCCCEEECCCCCEECCCCCC
T ss_conf             88855757758999998401375557773273023222466554321456530001025567772534888210102167


Q ss_pred             HHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCEEEEECCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             01889998888776420011235532123431565214332111111233379998865433446778774422225566
Q gi|254780916|r  245 LPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYYRISVFLINISTLRSRSEDIPWLVH  324 (482)
Q Consensus       245 L~~~~Q~~Ll~~l~~~~~~~~g~~~~~~~~~RiIa~t~~~L~~~~~~g~fr~dLy~rL~~~~i~iPpLReR~eDI~~L~~  324 (482)
                      ||.+.|+||||+|++|+|++|||+.++++|||||||||+||+.+|.+|.||+||||||||++|+|||||||+||||.|++
T Consensus       241 MPl~~QTRLLRVL~~G~f~rVGG~~p~k~DVRi~AAThq~Le~lv~~G~FReDLfhRL~Vi~i~lPpLrER~eDi~~L~r  320 (471)
T TIGR01818       241 MPLDLQTRLLRVLADGEFYRVGGRTPIKVDVRIVAATHQDLEALVRQGKFREDLFHRLNVIRIHLPPLRERREDIPRLAR  320 (471)
T ss_pred             CCHHHHHHHHHHHCCCCEEEECCCEEEEEEEEEEECCCHHHHHHHHCCCCHHHHHHHHCEEEECCCCCCCHHHHHHHHHH
T ss_conf             87768777988640786577268202455046673366568999655881355555123346216872122668999999


Q ss_pred             HHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHCCCCCCCHHHHHHHHCCCCCCCCCCCCCCCCCC
Q ss_conf             77764101122333321111100012233898689999999999874389810688954542124454322343222222
Q gi|254780916|r  325 FFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQELKNILLRAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTC  404 (482)
Q Consensus       325 ~fl~~~~~~~~~~~~~ls~~a~~~L~~y~WPGNvREL~n~i~r~~i~~~~~~i~~~~~~~~l~~~~~~~~~~~~~~~~~~  404 (482)
                      |||...+++.+.+.+.+++++++.|.+|+||||||||+|+|+|+.+++++.+|...+++..+..............    
T Consensus       321 hFL~~a~~~l~~~~k~L~~~~~~~L~~~~WPGNVR~LEN~cR~l~~la~~~~v~~~d~~~eLA~~~~~~~~~~~~~----  396 (471)
T TIGR01818       321 HFLALAAKELDVEPKLLSPEALEALKRYDWPGNVRELENVCRRLTVLASGDEVLVSDLPAELALSERKASAPDSDA----  396 (471)
T ss_pred             HHHHHHHHHCCCCCCCCCHHHHHHHHHCCCCCCHHHHHHHHHHHHHHCCCCEEEEEECCHHHCCCCCCHHCCHHCC----
T ss_conf             9999988742865113488999999725889852457789999987346764677775765567763101000102----


Q ss_pred             CCCCCCCCCHHHCCCCCCC-----CCCCCCCHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHCCCHHHHHHHHHHH
Q ss_conf             3344432100000000112-----3444543258999999999999999828727899978489988999999981
Q gi|254780916|r  405 YTEGKSSDTILDNLSQESI-----PAIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKIREY  475 (482)
Q Consensus       405 ~~~~~~~~~~~~~~~~~~~-----~~~~~~~~~~~l~e~E~~~I~~aL~~~~Gn~~~aA~~LGIsR~tL~rKlk~~  475 (482)
                       .....+...+.......+     ..+....+...+.++||.+|+.||++|+|++.+||+.||++||||.||||++
T Consensus       397 -~~~~~w~~~l~~~~~~~~~~~~~G~P~~~L~~~~~~~~er~Ll~~AL~~T~G~~~~AA~~LG~gRNTLtrKl~~L  471 (471)
T TIGR01818       397 -VQQDDWEEALEAWAKQALSSGKDGVPEQGLLDEALPELERTLLEAALQHTRGRKQEAAKLLGLGRNTLTRKLKEL  471 (471)
T ss_pred             -CCHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHCCCCCHHHHHHCCCC
T ss_conf             -203469999999999986214567881668999999873999999997345506899986188410342220359


No 3  
>PRK11361 acetoacetate metabolism regulatory protein AtoC; Provisional
Probab=100.00  E-value=0  Score=921.06  Aligned_cols=447  Identities=26%  Similarity=0.414  Sum_probs=409.8

Q ss_pred             CCCCCCEEEECCCHHHHHHHHHHHHHCCCEEEEECCH--HHHHHHCCCCCEEEEECCCCCCCHHHHHHHHHHHCCCCCEE
Q ss_conf             3528838998699899999999999889889998937--99998608998999978546988899999999857898399
Q gi|254780916|r    7 LDRHKRVLIIDKDDEQIKIIKDHVESYGYDVFIVNVS--DLSTISKIQVNVIFLSLINCEDDKENILKNIVDKIPIVPII   84 (482)
Q Consensus         7 m~~~~rILIVDDd~~~~~~l~~~L~~~G~~v~~a~~~--al~~l~~~~~dlillD~~mP~~dGlell~~i~~~~p~ipvI   84 (482)
                      |+..+||||||||+.++..++.+|+..||+|.+|+++  |++.+.+.+||+|++|++||+|||+++++++++..|++|||
T Consensus         1 M~~~~rILIVDDd~~ir~~l~~~L~~~G~~V~~a~~~~~Al~~l~~~~~DlvllDi~mP~~~Glell~~ir~~~p~~pvI   80 (457)
T PRK11361          1 MTAINRILIVDDEDNVRRMLSTAFALQGFETHCANNGRTALHLFADIHPDVVLMDIRMPEMDGIKALKEMRSHETRTPVI   80 (457)
T ss_pred             CCCCCCEEEECCCHHHHHHHHHHHHHCCCEEEEECCHHHHHHHHHCCCCCEEEEECCCCCCCHHHHHHHHHHCCCCCCEE
T ss_conf             99999289983999999999999997799899989999999998668989999828799999999999998209899389


Q ss_pred             EEECCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC-------CCCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             99268999999988850574322222222222222222222222222-------22211111111222222222222222
Q gi|254780916|r   85 VQTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALREGVVPS-------QENEHCALDSLIAVSPAMIQVVDLAR  157 (482)
Q Consensus        85 iiT~~~~~~~~~~a~~~g~~d~l~KP~~~~~L~~~i~~al~~~~~~~-------~~~~~~~~~~LiG~S~~m~~v~~~i~  157 (482)
                      |+|||++++.+++|++.||+||+.|||+.++|..++.+|++......       +......+..++|+|++|+++++++.
T Consensus        81 vlTa~~~~~~av~A~k~GA~Dyl~KPf~~~~L~~~v~rAl~~~~l~~~~~~l~~~~~~~~~~~~lig~S~~m~~v~~~i~  160 (457)
T PRK11361         81 LMTAYAEVETAVEALRCGAFDYVIKPFDLDELNLIVQRALQLQSMKKEIRHLHQALSTSWQWGHILTNSPAMMDICKDTA  160 (457)
T ss_pred             EEECCCCHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCEECCHHHHHHHHHHH
T ss_conf             99689998999999975966325699999999999999999988777776665432012456774546999999999999


Q ss_pred             CCCCCCEEEEEECCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCHHHHHCCCC-CCCCCCCCCCCCCCCCCCCE
Q ss_conf             23443204887327774367999999842675433210123465542100243311255-55322111001234466714
Q gi|254780916|r  158 KAGDCAIPIMIQGEFGVGKKRLSRFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFGDVD-LQTKNSAQFLGKFIEANGGT  236 (482)
Q Consensus       158 ~~a~~~~~vli~Ge~GtGK~~~A~~iH~~s~r~~~~fi~v~c~~~~~~~~e~~lFG~~~-~~~~~~~~~~g~~~~a~~Gt  236 (482)
                      ++|.++.||||+||+||||+++||+||..|.|+++|||.|||+++|++++|++||||++ +|||+...+.|+|++|+|||
T Consensus       161 ~~A~s~~~VLI~GEsGTGKe~~Ar~IH~~S~r~~~pFv~vnc~ai~~~l~eseLFG~~kgaftga~~~~~G~~e~A~gGT  240 (457)
T PRK11361        161 KIALSQASVLISGESGTGKELIARAIHYNSRRAKGPFIKVNCAALPESLLESELFGHEKGAFTGAQTLRQGLFERANEGT  240 (457)
T ss_pred             HHHCCCCCEEEECCCCCCHHHHHHHHHHHCCCCCCCEEEEECCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCHHHCCCCC
T ss_conf             98488995899889985789999999983798899838764787985778999718766787885314698613359982


Q ss_pred             EEECCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCEEEEECCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             75166420018899988887764200112355321234315652143321111112333799988654334467787744
Q gi|254780916|r  237 IVLEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYYRISVFLINISTLRSRS  316 (482)
Q Consensus       237 l~l~ei~~L~~~~Q~~Ll~~l~~~~~~~~g~~~~~~~~~RiIa~t~~~L~~~~~~g~fr~dLy~rL~~~~i~iPpLReR~  316 (482)
                      ||||||++||+..|.|||++|++++|+|+|+++++++|+||||+|++||.+++++|.||+|||||||+++|++||||||+
T Consensus       241 LfLdeI~~l~~~~Q~kLLr~L~~~~~~~~g~~~~~~~dvRiIaaT~~~L~~~v~~g~Fr~DLyyrL~~~~i~lPpLReR~  320 (457)
T PRK11361        241 LLLDEIGEMPLVLQAKLLRILQEREFERIGGHQTIKVDIRIIAATNRDLQAMVKEGTFREDLFYRLNVIHLILPPLRDRR  320 (457)
T ss_pred             EECCCHHHHHHHHHHHHHHHHHCCCEEECCCCCEEEECCEEEECCCCCHHHHHHCCCCHHHHHHHHCEEEEECCCHHHCH
T ss_conf             63146645239999999999864927856997136653489965787859998758323889953022125173854587


Q ss_pred             HHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHCCCCCCCHHHHHHHHCCCCCCCCCC
Q ss_conf             22225566777641011223333211111000122338986899999999998743898106889545421244543223
Q gi|254780916|r  317 EDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQELKNILLRAVIGLKDSHLTEDRFVLLLSREGKKEREF  396 (482)
Q Consensus       317 eDI~~L~~~fl~~~~~~~~~~~~~ls~~a~~~L~~y~WPGNvREL~n~i~r~~i~~~~~~i~~~~~~~~l~~~~~~~~~~  396 (482)
                      ||||.|++||+.+++.+++++.++||++|++.|++|+||||||||+|+|+|+++++.+..|+.++++..+..........
T Consensus       321 eDI~~L~~~fl~~~~~~~~~~~~~~s~~a~~~L~~y~WPGNvREL~n~ierav~~~~~~~i~~~~l~~~~~~~~~~~~~~  400 (457)
T PRK11361        321 EDISLLANHFLQKFSSENQRDIIDIDPMAMSLLTAWSWPGNIRELSNVIERAVVMNSGPIIFSEDLPPQIRQPVCNAGEA  400 (457)
T ss_pred             HHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCCCCHHHHHHHHHHHHHHHCCCCCCCHHHCCHHHHCCCCCCCCC
T ss_conf             54999999999999997499989889999999956999979999999999999828998156676848661555677645


Q ss_pred             CCCCCCCCCCCCCCCCCHHHCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHCCCHHHHHHHHHHHC
Q ss_conf             43222222334443210000000011234445432589999999999999998287278999784899889999999818
Q gi|254780916|r  397 HTETACTCYTEGKSSDTILDNLSQESIPAIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKIREYN  476 (482)
Q Consensus       397 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~e~E~~~I~~aL~~~~Gn~~~aA~~LGIsR~tL~rKlk~~g  476 (482)
                      .               .          ...........++++|+.+|.++|++|+||+++||+.|||||+|||||||+||
T Consensus       401 ~---------------~----------~~~~~~~l~~~~~~~Er~~i~~aL~~~~gn~~~aA~~LGisR~tLyrKlkk~g  455 (457)
T PRK11361        401 K---------------T----------APVGERNLKEEIKRVEKRIIMEVLEQQEGNRTRTALMLGISRRALMYKLQEYG  455 (457)
T ss_pred             C---------------C----------CCCCCCCHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHC
T ss_conf             5---------------6----------77666789999999999999999998299899999998989999999999858


Q ss_pred             CC
Q ss_conf             88
Q gi|254780916|r  477 IE  478 (482)
Q Consensus       477 i~  478 (482)
                      |+
T Consensus       456 id  457 (457)
T PRK11361        456 ID  457 (457)
T ss_pred             CC
T ss_conf             29


No 4  
>TIGR02915 PEP_resp_reg putative PEP-CTERM system response regulator; InterPro: IPR014264   Members of this protein family share full-length homology with (but do not include) the acetoacetate metabolism regulatory protein AtoC (see Q06065 from SWISSPROT). These proteins have a Fis family DNA binding sequence, a response regulator receiver domain, and sigma-54 interaction domain. They are found strictly within a subset of Gram-negative bacterial species with the proposed PEP-CTERM/exosortase system, analogous to the LPXTG/sortase system  common in Gram-positive bacteria, where members of IPR014265 from INTERPRO and IPR014266 from INTERPRO also occur..
Probab=100.00  E-value=0  Score=916.84  Aligned_cols=434  Identities=28%  Similarity=0.388  Sum_probs=397.5

Q ss_pred             EEEECCCHHHHHHHHHHHHHCCCEEEEECC--HHHHHHHCCCCCEEEEECCCCCC-----CHHHHHHHHHHHCCCCCEEE
Q ss_conf             899869989999999999988988999893--79999860899899997854698-----88999999998578983999
Q gi|254780916|r   13 VLIIDKDDEQIKIIKDHVESYGYDVFIVNV--SDLSTISKIQVNVIFLSLINCED-----DKENILKNIVDKIPIVPIIV   85 (482)
Q Consensus        13 ILIVDDd~~~~~~l~~~L~~~G~~v~~a~~--~al~~l~~~~~dlillD~~mP~~-----dGlell~~i~~~~p~ipvIi   85 (482)
                      +||||||+.+...|+.-|... |++..|++  +|++.+++++|.||.||+-+|..     .|+..|++|-+..|++.|||
T Consensus         1 LLiVeDD~glQKQLkWs~G~~-Ye~~~A~DR~sAiA~vRRheP~VVTLDLGLPPd~d~a~EGl~~L~qIL~~~P~TKVIV   79 (451)
T TIGR02915         1 LLIVEDDLGLQKQLKWSFGAD-YEVAVAADRESAIALVRRHEPAVVTLDLGLPPDADGASEGLAALQQILAIAPDTKVIV   79 (451)
T ss_pred             CCEEECCHHHHHHHHHHCCCC-CEEEEECCHHHHHHHHHCCCCCEEECCCCCCCCCCCHHHHHHHHHHHHHHCCCCEEEE
T ss_conf             924536866567876415788-4035534757899986056996477367557898874589999999996389804899


Q ss_pred             EECCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC-----CCC---CCCCCCCCCCCCCCCCCCCCC
Q ss_conf             926899999998885057432222222222222222222222222222-----211---111111222222222222222
Q gi|254780916|r   86 QTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALREGVVPSQE-----NEH---CALDSLIAVSPAMIQVVDLAR  157 (482)
Q Consensus        86 iT~~~~~~~~~~a~~~g~~d~l~KP~~~~~L~~~i~~al~~~~~~~~~-----~~~---~~~~~LiG~S~~m~~v~~~i~  157 (482)
                      +||+++-+.+++|+.+|||||+.||++++.|.-.|.+|.+-..++.+.     ..+   ..+.++||+||.|++++..|+
T Consensus        80 iTGN~~r~NAlkAi~lGAYDFyqKP~d~d~L~liv~RAf~L~~Le~ENRrL~~~~~~Gst~~~Gli~~~~~m~kic~tIe  159 (451)
T TIGR02915        80 ITGNDDRENALKAIGLGAYDFYQKPIDPDVLKLIVDRAFRLYTLETENRRLQSALGGGSTALEGLITSSPGMQKICRTIE  159 (451)
T ss_pred             EECCCCCHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCEEECCCCHHHHHHHHH
T ss_conf             86689838899996437510135787578999999998888888887699874068874103652206850678988865


Q ss_pred             CCCCCCEEEEEECCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCHHHHHCCCC-CCCCCCCCCCCCCCCCCCCE
Q ss_conf             23443204887327774367999999842675433210123465542100243311255-55322111001234466714
Q gi|254780916|r  158 KAGDCAIPIMIQGEFGVGKKRLSRFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFGDVD-LQTKNSAQFLGKFIEANGGT  236 (482)
Q Consensus       158 ~~a~~~~~vli~Ge~GtGK~~~A~~iH~~s~r~~~~fi~v~c~~~~~~~~e~~lFG~~~-~~~~~~~~~~g~~~~a~~Gt  236 (482)
                      |+|.|+.+|||.||||||||.+||+||+.|.|+++|||.||||+||++|+|||||||+| +||||..+..|++|-|++||
T Consensus       160 kvA~sd~TvllLGESGTGKEV~ArA~H~~S~R~~~~FVAINCAAIPEnLLEsELFGyEKGAFTGA~k~T~GKIE~A~~GT  239 (451)
T TIGR02915       160 KVAPSDITVLLLGESGTGKEVLARALHELSDRKDKRFVAINCAAIPENLLESELFGYEKGAFTGAVKQTLGKIEYAHGGT  239 (451)
T ss_pred             HHCCCCCEEEEECCCCCHHHHHHHHHHHHCCCCCCCEEEEECCCCCCHHHHHHHHCCCCHHHHHHHCCCCCCEEEECCCC
T ss_conf             21200001301046671178999898420578977734441674575246677603410124220034776167506883


Q ss_pred             EEECCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCEEEEECCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             75166420018899988887764200112355321234315652143321111112333799988654334467787744
Q gi|254780916|r  237 IVLEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYYRISVFLINISTLRSRS  316 (482)
Q Consensus       237 l~l~ei~~L~~~~Q~~Ll~~l~~~~~~~~g~~~~~~~~~RiIa~t~~~L~~~~~~g~fr~dLy~rL~~~~i~iPpLReR~  316 (482)
                      ||||||++||+.+|+||||||||+-++|+||-+.+++|||||||||+||+.++++|.|||||||||+.++|+|||||||.
T Consensus       240 LFLDEIGDLP~~LQAKLLRFLQErVIER~GGR~eIPVDVRvvCATnqdL~~~i~eg~FREDLfYRl~Eisi~iPPLR~R~  319 (451)
T TIGR02915       240 LFLDEIGDLPLNLQAKLLRFLQERVIERLGGREEIPVDVRVVCATNQDLKKMIAEGTFREDLFYRLAEISITIPPLRDRD  319 (451)
T ss_pred             CCCCCHHCCCHHHHHHHHHHHHHHHHHCCCCCCCCCCCEEEEECCCHHHHHHHHCCCCCCCCEEEEEEEEEECCCCCCCH
T ss_conf             01111220676689999987546663105887245614267503224689998548972000134666786258899860


Q ss_pred             HHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHCCCCCCCHHHHHHHHCCCCCCCCCC
Q ss_conf             22225566777641011223333211111000122338986899999999998743898106889545421244543223
Q gi|254780916|r  317 EDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQELKNILLRAVIGLKDSHLTEDRFVLLLSREGKKEREF  396 (482)
Q Consensus       317 eDI~~L~~~fl~~~~~~~~~~~~~ls~~a~~~L~~y~WPGNvREL~n~i~r~~i~~~~~~i~~~~~~~~l~~~~~~~~~~  396 (482)
                      +|..+|+++|+++|+.++++..++||++|+..|..|.||||||||+|.|+|||+|+.++.|+.+|+-..-.+....    
T Consensus       320 gDa~lLA~~Fl~rf~~~~k~~~~~F~~DA~~ale~h~WPGNvRELEN~vKRAVIMa~g~qIt~~DLGl~~~Pi~~~----  395 (451)
T TIGR02915       320 GDAVLLANAFLERFARELKRKAKGFTDDALRALEAHKWPGNVRELENKVKRAVIMAEGNQITAEDLGLDAKPIERA----  395 (451)
T ss_pred             HHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHCCCCCCCHHHHHCHHHEEEEECCCCCCCHHHCCCCCCCCCCC----
T ss_conf             1899999999998878733021660699999976069988415440300213453378713565488886777754----


Q ss_pred             CCCCCCCCCCCCCCCCCHHHCCCCCCCCCCCCCCHHHHHH-HHHHHHHHHHHHHHCCCHHHHHHHHCCCHHHHHHHHHHH
Q ss_conf             4322222233444321000000001123444543258999-999999999999828727899978489988999999981
Q gi|254780916|r  397 HTETACTCYTEGKSSDTILDNLSQESIPAIGQDGEVRRLS-DIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKIREY  475 (482)
Q Consensus       397 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~-e~E~~~I~~aL~~~~Gn~~~aA~~LGIsR~tL~rKlk~~  475 (482)
                                     .+            ......++.++ +.|++.+.+|+.+++||+++||++|||+|-|||--|+||
T Consensus       396 ---------------~~------------~l~~~~LR~vRe~aEr~av~~A~a~~~GN~arAaElLGitRPTLYdLm~k~  448 (451)
T TIGR02915       396 ---------------ET------------PLEGLNLREVREKAEREAVRKAIARVDGNIARAAELLGITRPTLYDLMKKY  448 (451)
T ss_pred             ---------------CH------------HHCCCCHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHCCCHHHHHHHHHHH
T ss_conf             ---------------01------------111451889999999999999998726618889887258203599999972


Q ss_pred             CCC
Q ss_conf             888
Q gi|254780916|r  476 NIE  478 (482)
Q Consensus       476 gi~  478 (482)
                      ||+
T Consensus       449 g~~  451 (451)
T TIGR02915       449 GLK  451 (451)
T ss_pred             CCC
T ss_conf             589


No 5  
>PRK10923 glnG nitrogen regulation protein NR(I); Provisional
Probab=100.00  E-value=0  Score=888.04  Aligned_cols=461  Identities=23%  Similarity=0.345  Sum_probs=410.3

Q ss_pred             CCCEEEECCCHHHHHHHHHHHHHCCCEEEEECC--HHHHHHHCCCCCEEEEECCCCCCCHHHHHHHHHHHCCCCCEEEEE
Q ss_conf             883899869989999999999988988999893--799998608998999978546988899999999857898399992
Q gi|254780916|r   10 HKRVLIIDKDDEQIKIIKDHVESYGYDVFIVNV--SDLSTISKIQVNVIFLSLINCEDDKENILKNIVDKIPIVPIIVQT   87 (482)
Q Consensus        10 ~~rILIVDDd~~~~~~l~~~L~~~G~~v~~a~~--~al~~l~~~~~dlillD~~mP~~dGlell~~i~~~~p~ipvIiiT   87 (482)
                      +.||||||||+.++..++.+|+..||+|.++.+  ++++.+.+..||+|++|++||+|||+++++++++.+|++||||+|
T Consensus         3 k~kILiVDDd~~~r~~l~~~L~~~g~~v~~a~~~~~al~~l~~~~~dlvl~Di~mP~~~Gl~ll~~lr~~~~~~pvIviT   82 (469)
T PRK10923          3 RGIVWVVDDDSSIRWVLERALAGAGLTCTTFENGNEVLEALASKTPDVLLSDIRMPGMDGLALLKQIKQRHPMLPVIIMT   82 (469)
T ss_pred             CCEEEEEECCHHHHHHHHHHHHHCCCEEEEECCHHHHHHHHHCCCCCEEEECCCCCCCCHHHHHHHHHHCCCCCCEEEEE
T ss_conf             99799994989999999999987799899989999999998669999998789999989999999998429899789998


Q ss_pred             CCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC---CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCE
Q ss_conf             6899999998885057432222222222222222222222222---2222111111112222222222222222344320
Q gi|254780916|r   88 TQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALREGVVP---SQENEHCALDSLIAVSPAMIQVVDLARKAGDCAI  164 (482)
Q Consensus        88 ~~~~~~~~~~a~~~g~~d~l~KP~~~~~L~~~i~~al~~~~~~---~~~~~~~~~~~LiG~S~~m~~v~~~i~~~a~~~~  164 (482)
                      |+++++.+++|++.||+||+.|||++++|+..+.+|+......   ...........++|+|++|+++++++.++|.++.
T Consensus        83 ~~~~~~~av~A~~~GA~dyL~KP~~~~~L~~~v~ral~~~~~~~~~~~~~~~~~~~~liG~S~~m~~v~~~i~~~a~~~~  162 (469)
T PRK10923         83 AHSDLDAAVSAYQQGAFDYLPKPFDIDEAVALVERAISHYQEQQQPRNIQVNGPTTDIIGEAPAMQDVFRIIGRLSRSSI  162 (469)
T ss_pred             CCCCHHHHHHHHHCCHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCEECCHHHHHHHHHHHHHHCCCC
T ss_conf             99998999999855704430088999999999999999999986544312106755654689999999999999858899


Q ss_pred             EEEEECCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCHHHHHCCCCC-CCCCCCCCCCCCCCCCCCEEEECCCC
Q ss_conf             48873277743679999998426754332101234655421002433112555-53221110012344667147516642
Q gi|254780916|r  165 PIMIQGEFGVGKKRLSRFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFGDVDL-QTKNSAQFLGKFIEANGGTIVLEEPD  243 (482)
Q Consensus       165 ~vli~Ge~GtGK~~~A~~iH~~s~r~~~~fi~v~c~~~~~~~~e~~lFG~~~~-~~~~~~~~~g~~~~a~~Gtl~l~ei~  243 (482)
                      ||||+||+||||+++||+||..|.|+++||+.|||+++|++++|++||||.++ |||+...+.|+|++|+|||||||||+
T Consensus       163 pVLI~GE~GTGK~~~Ar~IH~~S~r~~~pfi~vnC~~~~~~~~e~eLFG~~~gaf~ga~~~~~g~~e~a~~GTLfLdeI~  242 (469)
T PRK10923        163 SVLINGESGTGKELVAHALHRHSPRAKAPFIALNMAAIPKDLIESELFGHEKGAFTGANTIRQGRFEQADGGTLFLDEIG  242 (469)
T ss_pred             CEEEECCCCCCHHHHHHHHHHCCCCCCCCCEEEECCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCHHHCCCCCEEHHHHH
T ss_conf             78998989826999999999748877999578767889977899997087667878864245873664389926566366


Q ss_pred             HHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCEEEEECCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             00188999888877642001123553212343156521433211111123337999886543344677877442222556
Q gi|254780916|r  244 ALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYYRISVFLINISTLRSRSEDIPWLV  323 (482)
Q Consensus       244 ~L~~~~Q~~Ll~~l~~~~~~~~g~~~~~~~~~RiIa~t~~~L~~~~~~g~fr~dLy~rL~~~~i~iPpLReR~eDI~~L~  323 (482)
                      .||+..|.+|+++|++++|+++|+.+++++|+||||+|++||.+++++|.||+|||||||+++|++||||||+|||+.|+
T Consensus       243 ~L~~~~Q~kLl~~L~~~~~~~~g~~~~~~~d~RiIaat~~~L~~~v~~g~Fr~dLyyrL~~~~I~lPpLReR~eDI~~L~  322 (469)
T PRK10923        243 DMPLDVQTRLLRVLADGQFYRVGGYAPVKVDVRIIAATHQNLEQRVQEGKFREDLFHRLNVIRVHLPPLRERREDIPRLA  322 (469)
T ss_pred             HCCHHHHHHHHHHHHCCCEEECCCCCEEEECCEEEEECCCCHHHHHHHCCHHHHHHHHHHHHCCCCCCHHHCHHHHHHHH
T ss_conf             48999999999998559378579985122143799707879999866081779999864424015846544653499999


Q ss_pred             HHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHCCCCCCCHHHHHHHHCCCCCCCCCCCCCCCCC
Q ss_conf             67776410112233332111110001223389868999999999987438981068895454212445432234322222
Q gi|254780916|r  324 HFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQELKNILLRAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACT  403 (482)
Q Consensus       324 ~~fl~~~~~~~~~~~~~ls~~a~~~L~~y~WPGNvREL~n~i~r~~i~~~~~~i~~~~~~~~l~~~~~~~~~~~~~~~~~  403 (482)
                      +||+.+++.++|..+++++++|++.|.+|+||||||||+|+++|+++++.+..|+..+++..+...........      
T Consensus       323 ~~fl~~~~~~~~~~~~~~s~~a~~~L~~y~WPGNvrEL~n~ier~~~~~~~~~i~~~dl~~~l~~~~~~~~~~~------  396 (469)
T PRK10923        323 RHFLQVAARELGVEAKLLHPETEAALTRLAWPGNVRQLENTCRWLTVMAAGQEVLIQDLPGELFESTVPDSTSQ------  396 (469)
T ss_pred             HHHHHHHHHHCCCCCCCCCHHHHHHHHCCCCCCHHHHHHHHHHHHHHHCCCCCCCHHHCCHHHHHCCCCCCCCC------
T ss_conf             99999999985999787899999999749999879999999999998579982547757298863337776545------


Q ss_pred             CCCCCCCCCCHHHCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHCCCHHHHHHHHHHHCCC
Q ss_conf             233444321000000001123444543258999999999999999828727899978489988999999981888
Q gi|254780916|r  404 CYTEGKSSDTILDNLSQESIPAIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKIREYNIE  478 (482)
Q Consensus       404 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~e~E~~~I~~aL~~~~Gn~~~aA~~LGIsR~tL~rKlk~~gi~  478 (482)
                        .................+.....+...+.++++||++|.++|++|+||+++||+.|||+|+|||||||||||+
T Consensus       397 --~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~Er~~I~~aL~~~~gn~~~aA~~LGisR~TLyrKlkk~gi~  469 (469)
T PRK10923        397 --MQPDSWATLLAQWADRALRSGHQNLLSEAQPELERTLLTTALRHTQGHKQEAARLLGWGRNTLTRKLKELGME  469 (469)
T ss_pred             --CCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHCCCHHHHHHHHHHHCCC
T ss_conf             --5774034442110011111342015899999999999999999909989999999898999999999986839


No 6  
>PRK10365 transcriptional regulatory protein ZraR; Provisional
Probab=100.00  E-value=0  Score=878.64  Aligned_cols=435  Identities=28%  Similarity=0.449  Sum_probs=398.5

Q ss_pred             CC-CCCCEEEECCCHHHHHHHHHHHHHCCCEEEEECCH--HHHHHHCCCCCEEEEECCCCCCCHHHHHHHHHHHCCCCCE
Q ss_conf             35-28838998699899999999999889889998937--9999860899899997854698889999999985789839
Q gi|254780916|r    7 LD-RHKRVLIIDKDDEQIKIIKDHVESYGYDVFIVNVS--DLSTISKIQVNVIFLSLINCEDDKENILKNIVDKIPIVPI   83 (482)
Q Consensus         7 m~-~~~rILIVDDd~~~~~~l~~~L~~~G~~v~~a~~~--al~~l~~~~~dlillD~~mP~~dGlell~~i~~~~p~ipv   83 (482)
                      |+ ++.+|||||||+.++..++.+|+..||+|.++.++  ++..+.+..||+|++|++||++||+++++++++..|++||
T Consensus         1 M~~~~~~ILIVDDd~~~~~~l~~~L~~~G~~v~~a~~~~~al~~l~~~~~DlvllD~~mp~~~Gl~lL~~l~~~~p~~pv   80 (441)
T PRK10365          1 MTHDNIDILVVDDDISHCTILQALLRGWGYNVALANSGRQALEQVREQVFDLVLCDVRMAEMDGIATLKEIKALNPAIPV   80 (441)
T ss_pred             CCCCCCEEEEECCCHHHHHHHHHHHHHCCCEEEEECCHHHHHHHHHCCCCCEEEECCCCCCCCHHHHHHHHHHHCCCCCE
T ss_conf             99899859998398999999999999779989998999999999864899999988999999899999999842989828


Q ss_pred             EEEECCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC--CCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             9992689999999888505743222222222222222222222222222--22111111112222222222222222344
Q gi|254780916|r   84 IVQTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALREGVVPSQ--ENEHCALDSLIAVSPAMIQVVDLARKAGD  161 (482)
Q Consensus        84 IiiT~~~~~~~~~~a~~~g~~d~l~KP~~~~~L~~~i~~al~~~~~~~~--~~~~~~~~~LiG~S~~m~~v~~~i~~~a~  161 (482)
                      ||+|||++++.+++|++.||+||+.|||+.++|...+.+++........  .........++|+|++|+++++++.++|.
T Consensus        81 IviT~~~~~~~av~A~k~GA~Dyl~KP~~~~~L~~~i~~al~~~~~~~~~~~~~~~~~~~liG~S~am~~v~~~i~~~A~  160 (441)
T PRK10365         81 LIMTAYSSVETAVEALKTGALDYLIKPLDFDNLQATLEKALAHTHSIDAETPAVSASQFGMVGKSPAMQHLLSEIALVAP  160 (441)
T ss_pred             EEEECCCCHHHHHHHHHHCCCEEEECCCCHHHHHHHHHHHHHHHHHHHHCCHHCCCCCCCCEECCHHHHHHHHHHHHHHC
T ss_conf             99969999899999998285123407888999999999999999876520000122257866689999999999999848


Q ss_pred             CCEEEEEECCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCHHHHHCCCC-CCCCCCCCCCCCCCCCCCCEEEEC
Q ss_conf             3204887327774367999999842675433210123465542100243311255-553221110012344667147516
Q gi|254780916|r  162 CAIPIMIQGEFGVGKKRLSRFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFGDVD-LQTKNSAQFLGKFIEANGGTIVLE  240 (482)
Q Consensus       162 ~~~~vli~Ge~GtGK~~~A~~iH~~s~r~~~~fi~v~c~~~~~~~~e~~lFG~~~-~~~~~~~~~~g~~~~a~~Gtl~l~  240 (482)
                      ++.||||+||+||||+++||+||..|.|+++|||.|||++++++++|++||||++ +|||+...+.|+|++|+|||||||
T Consensus       161 s~~pVLI~GE~GTGK~~~Ar~IH~~S~r~~~pfv~vnC~~l~~~l~eseLFG~~~gaftga~~~~~g~~~~A~gGTLfLd  240 (441)
T PRK10365        161 SEATVLIHGDSGTGKELVARAIHASSARSEKPLVTLNCAALNESLLESELFGHEKGAFTGADKRREGRFVEADGGTLFLD  240 (441)
T ss_pred             CCCCEEEECCCCHHHHHHHHHHHHCCCCCCCCCEEEECCCCCHHHHHHHHCCCCCCCCCCCCCCCCCCEEECCCCEECCC
T ss_conf             89948998999810999999999657877898079878989845558986177556878965346898778899825502


Q ss_pred             CCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCEEEEECCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             64200188999888877642001123553212343156521433211111123337999886543344677877442222
Q gi|254780916|r  241 EPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYYRISVFLINISTLRSRSEDIP  320 (482)
Q Consensus       241 ei~~L~~~~Q~~Ll~~l~~~~~~~~g~~~~~~~~~RiIa~t~~~L~~~~~~g~fr~dLy~rL~~~~i~iPpLReR~eDI~  320 (482)
                      ||++||+..|.|||++|++++|+|+|+++++++|+||||+|++||.++|.+|.||+|||||||+++|++||||||+||||
T Consensus       241 eI~~l~~~~Q~kLl~~l~~~~~~~~g~~~~~~~d~RiIaat~~~l~~~v~~g~Fr~dLy~rL~~~~i~lPpLReR~eDI~  320 (441)
T PRK10365        241 EIGDISPMMQVRLLRAIQEREVQRVGSNQTISVDVRLIAATHRDLAAEVNAGRFRQDLYYRLNVVAIEVPSLRQRREDIP  320 (441)
T ss_pred             CCCCCCHHHHHHHHHHHHHHHHCCCCCCCEEECCCEEEECCCCCHHHHHHCCCCHHHHHHHHCCHHCCCCCCCCCCCHHH
T ss_conf             31529999999999877752100058873441363799837889999988198258999886011137826000620099


Q ss_pred             HHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHCCCCCCCHHHHHHHHCCCCCCCCCCCCCC
Q ss_conf             55667776410112233332111110001223389868999999999987438981068895454212445432234322
Q gi|254780916|r  321 WLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQELKNILLRAVIGLKDSHLTEDRFVLLLSREGKKEREFHTET  400 (482)
Q Consensus       321 ~L~~~fl~~~~~~~~~~~~~ls~~a~~~L~~y~WPGNvREL~n~i~r~~i~~~~~~i~~~~~~~~l~~~~~~~~~~~~~~  400 (482)
                      .|++||+++++.++++..++||++|++.|++|+||||||||+|+++|+++++.+..|+..+++..+.......       
T Consensus       321 ~L~~~fl~~~~~~~~~~~~~~s~~a~~~L~~y~WPGNvREL~n~iera~~~~~~~~i~~~~l~~~~~~~~~~~-------  393 (441)
T PRK10365        321 LLAGHFLQRFAERNRKAVKGFTPQAMDLLIHYDWPGNIRELENAVERAVVLLTGEYISERELPLAIASTPIPL-------  393 (441)
T ss_pred             HHHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCCCCHHHHHHHHHHHHHHHCCCCCCCHHHCCHHHCCCCCCC-------
T ss_conf             9999999999998499988889999999970999989999999999999957898688465754330688887-------


Q ss_pred             CCCCCCCCCCCCCHHHCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHCCCHHHHHHHHHH
Q ss_conf             22223344432100000000112344454325899999999999999982872789997848998899999998
Q gi|254780916|r  401 ACTCYTEGKSSDTILDNLSQESIPAIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKIRE  474 (482)
Q Consensus       401 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~e~E~~~I~~aL~~~~Gn~~~aA~~LGIsR~tL~rKlk~  474 (482)
                                                ........+.++|+++|.++|++|+||+++||+.|||+|+||||||||
T Consensus       394 --------------------------~~~~~~~~l~e~Er~~I~~aL~~~~gn~~~aA~~LGisR~tLyrKl~k  441 (441)
T PRK10365        394 --------------------------GQSQDIQPLVEVEKEVILAALEKTGGNKTEAARQLGITRKTLLAKLSR  441 (441)
T ss_pred             --------------------------CCCCCCCCHHHHHHHHHHHHHHHHCCCHHHHHHHHCCCHHHHHHHHCC
T ss_conf             --------------------------766565669999999999999993998999999978899999999674


No 7  
>TIGR01817 nifA Nif-specific regulatory protein; InterPro: IPR010113   This entry represents NifA, a DNA-binding regulatory protein for nitrogen fixation. Not included in this group are: the homologue in Aquifex aeolicus (which lacks nitrogenase), transcriptional activators of alternative nitrogenases (VFe or FeFe instead of MoFe), and truncated forms.   In diazotrophic proteobacteria, the sigma54-dependent activator NifA activates transcription of the nif (nitrogen fixation) genes by a conserved mechanism common to members of the enhancer binding protein family. Although NifA proteins have similar domain structures, both transcriptional regulation of nifA expression and posttranslational regulation of NifA activity by oxygen and fixed nitrogen vary significantly from one organism to another. In Klebsiella pneumoniae and Azotobacter vinelandii, nifA is co-ordinately transcribed with a second gene, nifL, whose product inhibits NifA activity in response to oxygen and fixed nitrogen .; GO: 0003677 DNA binding, 0016563 transcription activator activity, 0009399 nitrogen fixation.
Probab=100.00  E-value=0  Score=782.72  Aligned_cols=464  Identities=24%  Similarity=0.314  Sum_probs=341.1

Q ss_pred             EEEECCCHHHHHHHHHHHHHCCCE------E-EEECCHHHHHHHCCCCCEEEEECCCCCCCHHHHHHHHH--HHCCC---
Q ss_conf             899869989999999999988988------9-99893799998608998999978546988899999999--85789---
Q gi|254780916|r   13 VLIIDKDDEQIKIIKDHVESYGYD------V-FIVNVSDLSTISKIQVNVIFLSLINCEDDKENILKNIV--DKIPI---   80 (482)
Q Consensus        13 ILIVDDd~~~~~~l~~~L~~~G~~------v-~~a~~~al~~l~~~~~dlillD~~mP~~dGlell~~i~--~~~p~---   80 (482)
                      |-|.|||-....+-........+.      + ..++.+++..+=+..-.+|+=|+---.    -|+.++.  -..++   
T Consensus        42 i~l~d~ege~~~~~a~~~~~e~~~~lg~~~~ry~vgeg~ig~i~~~G~~lVv~~va~~~----lF~d~~~~~l~~~~e~~  117 (574)
T TIGR01817        42 ISLSDSEGEPLLVAAIGWSEEEFAQLGSDDIRYRVGEGAIGQIVATGNSLVVPDVAAEP----LFLDRLSEVLSDPGEIP  117 (574)
T ss_pred             EEEECCCCCCEEEEEEECCCCCCCCCCCCCCEECCCCCHHHHHHHCCCEEEECCCCCCH----HHHHHHHHHHCCCCCEE
T ss_conf             89867888601101430386101123468850247340235663168706604667353----45776455405887431


Q ss_pred             CCEEEEECC-CCHHH----HHHHHHCCCCCC-CCCCCCCCCCCC-CCCCCCC------------------------CC--
Q ss_conf             839999268-99999----998885057432-222222222222-2222222------------------------22--
Q gi|254780916|r   81 VPIIVQTTQ-DNIKI----LNCFLYNRISKF-FLNLVSRKQLCD-SIICALR------------------------EG--  127 (482)
Q Consensus        81 ipvIiiT~~-~~~~~----~~~a~~~g~~d~-l~KP~~~~~L~~-~i~~al~------------------------~~--  127 (482)
                      +|+|-+-=. .|-++    ....+..|..++ +..-+..-..++ .+.+++|                        ..  
T Consensus       118 ~~FIgVPi~~~d~~~~GvL~~~r~~~g~~~~~~~~~vRFL~mVANL~gQtvRL~r~~~~~~~~~~~e~~~~~~~~~~~~s  197 (574)
T TIGR01817       118 VPFIGVPIKNADSETIGVLAIDRIKEGASRERLEEEVRFLEMVANLIGQTVRLHRLVAARRERLIAEAAQLSKQLRDKKS  197 (574)
T ss_pred             CCEEECCCCCCCCCCCEEEEEEECCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCC
T ss_conf             11340226677777112267720688884134614543799999999878887445654201105567778875214001


Q ss_pred             --CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCC
Q ss_conf             --222222211111111222222222222222234432048873277743679999998426754332101234655421
Q gi|254780916|r  128 --VVPSQENEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHESGKRAFFPFFIVNCGMIDQD  205 (482)
Q Consensus       128 --~~~~~~~~~~~~~~LiG~S~~m~~v~~~i~~~a~~~~~vli~Ge~GtGK~~~A~~iH~~s~r~~~~fi~v~c~~~~~~  205 (482)
                        .....+......+.+||.||+|++|+++|.++|.+|+.||+.||+|||||++|++||++|+|+.+|||.+|||+||++
T Consensus       198 Ga~~~~~~~~~~~~~~i~G~Spam~~v~~~~~~vA~~nSTVLlRGESGTGKEl~A~AIH~~SpR~~~PFVK~NCAALse~  277 (574)
T TIGR01817       198 GAEPEAARRRSGKEDGIVGKSPAMRQVVDQIKVVARSNSTVLLRGESGTGKELIAKAIHELSPRAKRPFVKLNCAALSET  277 (574)
T ss_pred             CCCCCHHHHHCCCCCCCCCCCHHHHHHHHHHHHHCCCCCEEEEECCCCCCHHHHHHHHCCCCCCCCCCCEEEECCCCCCC
T ss_conf             56554123312344740124789999998865201317667850565744334442340466455788545006447761


Q ss_pred             CCHHHHHCCCCC-CCCCCCCCCCCCCCCCCCEEEECCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCEEEEECCCC
Q ss_conf             002433112555-5322111001234466714751664200188999888877642001123553212343156521433
Q gi|254780916|r  206 KIEKFLFGDVDL-QTKNSAQFLGKFIEANGGTIVLEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKN  284 (482)
Q Consensus       206 ~~e~~lFG~~~~-~~~~~~~~~g~~~~a~~Gtl~l~ei~~L~~~~Q~~Ll~~l~~~~~~~~g~~~~~~~~~RiIa~t~~~  284 (482)
                      ++|||||||+|| ||||..+|+|+||.|||||||||||++.|+..|+||||+||||+|+||||++.+++|||||||||+|
T Consensus       278 lLESELFGHEKGAFTGA~~~RkGRFElAdGGTLFLDEIGEISPaFQAKLLRVLQEGEFERVGG~~TlKVdVRlvaATNrd  357 (574)
T TIGR01817       278 LLESELFGHEKGAFTGAVAQRKGRFELADGGTLFLDEIGEISPAFQAKLLRVLQEGEFERVGGNRTLKVDVRLVAATNRD  357 (574)
T ss_pred             HHHHHHHCCCCHHHHHHHHHCCCCEEECCCCCCCCCCCCCCCHHHHHHHHHHHHCCCEEEECCCEEEEEEEEEEECCCCC
T ss_conf             12454513430146888751777533027883200001467856888998875210025327872488736788613735


Q ss_pred             CCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHH
Q ss_conf             21111112333799988654334467787744222255667776410112233332111110001223389868999999
Q gi|254780916|r  285 LLPQVKSHVFRKDLYYRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQELKNI  364 (482)
Q Consensus       285 L~~~~~~g~fr~dLy~rL~~~~i~iPpLReR~eDI~~L~~~fl~~~~~~~~~~~~~ls~~a~~~L~~y~WPGNvREL~n~  364 (482)
                      |++.|+.|.||+||||||||++|.|||||||.+|||.|+++||++|+.+.+++...|++.|++.|++|.||||||||||+
T Consensus       358 LE~aV~~GeFRaDLYYRinVvPl~lPPLRER~~DIP~LA~~fL~kf~~en~R~mL~~~~~Ai~~Lm~c~wPGNVRELENC  437 (574)
T TIGR01817       358 LEEAVAKGEFRADLYYRINVVPLILPPLRERREDIPLLAEAFLEKFNRENGRPMLTLSPSAIRVLMSCKWPGNVRELENC  437 (574)
T ss_pred             HHHHHHCCCCCCHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHCCCEEEECHHHHHHHHCCCCCCCCEEHHHH
T ss_conf             58897278973023554422234078777873116899999999876651872032267899897517899974004437


Q ss_pred             HHHHHHHCCCCCCCHHHHHHHHCCCCCCCCCCC---------CCCCCCCCCCCCCCCCH-----HHCCCCCCCCCCCCCC
Q ss_conf             999987438981068895454212445432234---------32222223344432100-----0000001123444543
Q gi|254780916|r  365 LLRAVIGLKDSHLTEDRFVLLLSREGKKEREFH---------TETACTCYTEGKSSDTI-----LDNLSQESIPAIGQDG  430 (482)
Q Consensus       365 i~r~~i~~~~~~i~~~~~~~~l~~~~~~~~~~~---------~~~~~~~~~~~~~~~~~-----~~~~~~~~~~~~~~~~  430 (482)
                      |+|..+++.++.|+.+||.-.-.+.........         ............+....     .........|......
T Consensus       438 ~eRtAtLs~~~~It~~df~c~~~~c~s~~L~~~~~~~~~~P~~~~~p~~~~~~~pla~~~~~PA~~~pa~~~~p~~~~~~  517 (574)
T TIGR01817       438 VERTATLSRSGTITRSDFSCQSGQCLSKMLAKSSAYKKVDPAVPDAPLGAVSIVPLAETTALPAVESPASAALPAEVGLS  517 (574)
T ss_pred             HHHHHHHCCCCCCCCCEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEECCCCCCCCCCCHHHCCCCCCCCCCCCCC
T ss_conf             87787541688516423664278888888888887788778777888886532573014677522054334677667778


Q ss_pred             H-------HHHHHHHHHHHHHHHHHHHCCCHHHHHHHHCCCHHHHHHHHHHHCCCCCCC
Q ss_conf             2-------589999999999999998287278999784899889999999818881449
Q gi|254780916|r  431 E-------VRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKIREYNIEVDSL  482 (482)
Q Consensus       431 ~-------~~~l~e~E~~~I~~aL~~~~Gn~~~aA~~LGIsR~tL~rKlk~~gi~~d~~  482 (482)
                      .       ...+  -||+-+.+||++++|+|+|||++|||+.+-.=|.||+|||++..+
T Consensus       518 gteaCPavA~~l--~eRERli~AlE~aGWVQAKAARlLg~TPRQVgYalr~~~I~~kk~  574 (574)
T TIGR01817       518 GTEACPAVAPTL--SERERLIAALEKAGWVQAKAARLLGLTPRQVGYALRKLNIEVKKL  574 (574)
T ss_pred             CCCCCCCCCCCC--CCHHHHHHHHHHCCHHHHHHHHHHCCCHHHHHHHHHHCCCCCCCC
T ss_conf             755455678872--317899999975153799999973786558999998848765669


No 8  
>COG3829 RocR Transcriptional regulator containing PAS, AAA-type ATPase, and DNA-binding domains [Transcription / Signal transduction mechanisms]
Probab=100.00  E-value=0  Score=736.89  Aligned_cols=320  Identities=35%  Similarity=0.548  Sum_probs=289.8

Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCHHHHH
Q ss_conf             22111111112222222222222222344320488732777436799999984267543321012346554210024331
Q gi|254780916|r  133 ENEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHESGKRAFFPFFIVNCGMIDQDKIEKFLF  212 (482)
Q Consensus       133 ~~~~~~~~~LiG~S~~m~~v~~~i~~~a~~~~~vli~Ge~GtGK~~~A~~iH~~s~r~~~~fi~v~c~~~~~~~~e~~lF  212 (482)
                      ......++.|+|+|++|.++.+.+.++|.+++||||.||+|||||++||+||+.|+|+++|||.||||++|++++|||||
T Consensus       238 ~~a~y~f~~Iig~S~~m~~~~~~akr~A~tdstVLi~GESGTGKElfA~~IH~~S~R~~~PFIaiNCaAiPe~LlESELF  317 (560)
T COG3829         238 LKAKYTFDDIIGESPAMLRVLELAKRIAKTDSTVLILGESGTGKELFARAIHNLSPRANGPFIAINCAAIPETLLESELF  317 (560)
T ss_pred             CCCCCCHHHHCCCCHHHHHHHHHHHHHCCCCCCEEEECCCCCCHHHHHHHHHHCCCCCCCCEEEEECCCCCHHHHHHHHH
T ss_conf             44536610020589999999999986338998289953788668999999874484347980787643388888888872


Q ss_pred             CCC-CCCCCCCCC-CCCCCCCCCCCEEEECCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCEEEEECCCCCCCCCC
Q ss_conf             125-555322111-001234466714751664200188999888877642001123553212343156521433211111
Q gi|254780916|r  213 GDV-DLQTKNSAQ-FLGKFIEANGGTIVLEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVK  290 (482)
Q Consensus       213 G~~-~~~~~~~~~-~~g~~~~a~~Gtl~l~ei~~L~~~~Q~~Ll~~l~~~~~~~~g~~~~~~~~~RiIa~t~~~L~~~~~  290 (482)
                      |++ ++||||... ++|+||.|+|||||||||++||+++|+||||+||+++|+|+||++++++|+|||||||+||+++++
T Consensus       318 Gye~GAFTGA~~~GK~GlfE~A~gGTLFLDEIgempl~LQaKLLRVLQEkei~rvG~t~~~~vDVRIIAATN~nL~~~i~  397 (560)
T COG3829         318 GYEKGAFTGASKGGKPGLFELANGGTLFLDEIGEMPLPLQAKLLRVLQEKEIERVGGTKPIPVDVRIIAATNRNLEKMIA  397 (560)
T ss_pred             CCCCCCCCCCCCCCCCCCEEECCCCEEEEHHHCCCCHHHHHHHHHHHHHCEEEECCCCCCEEEEEEEEECCCCCHHHHHH
T ss_conf             76776424644579976054416983771232039989999999987535378537887535678999425758999986


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHH
Q ss_conf             12333799988654334467787744222255667776410112233332111110001223389868999999999987
Q gi|254780916|r  291 SHVFRKDLYYRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQELKNILLRAVI  370 (482)
Q Consensus       291 ~g~fr~dLy~rL~~~~i~iPpLReR~eDI~~L~~~fl~~~~~~~~~~~~~ls~~a~~~L~~y~WPGNvREL~n~i~r~~i  370 (482)
                      +|+||+||||||||++|++||||||+||||+|++||++++++.+++.++++++++++.|.+|+||||||||+|+|+|+++
T Consensus       398 ~G~FReDLYYRLNV~~i~iPPLReR~eDI~~L~~~Fl~k~s~~~~~~v~~ls~~a~~~L~~y~WPGNVRELeNviER~v~  477 (560)
T COG3829         398 EGTFREDLYYRLNVIPITIPPLRERKEDIPLLAEYFLDKFSRRYGRNVKGLSPDALALLLRYDWPGNVRELENVIERAVN  477 (560)
T ss_pred             CCCCHHHHEEEECEEEECCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHCCCCCHHHHHHHHHHHHHH
T ss_conf             39616553003040111477723382018999999999999872887666899999999868999609999999999981


Q ss_pred             -HCCCCCCCHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHH
Q ss_conf             -4389810688954542124454322343222222334443210000000011234445432589999999999999998
Q gi|254780916|r  371 -GLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILDNLSQESIPAIGQDGEVRRLSDIEKEIIGLAMKL  449 (482)
Q Consensus       371 -~~~~~~i~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~e~E~~~I~~aL~~  449 (482)
                       ..++..|+.++++............                ..          ...........++++|+.+|..||++
T Consensus       478 ~~~~~~~I~~~~lp~~~l~~k~~~~~----------------~~----------~~~~~~~l~~~~e~~Ek~~I~~aL~~  531 (560)
T COG3829         478 LVESDGLIDADDLPAFALEEKEPRPE----------------TT----------KQIEVGSLKEALEEYEKHLIREALER  531 (560)
T ss_pred             CCCCCCEEEHHHCCHHHHCCCCCCCC----------------CC----------CCCCCCCHHHHHHHHHHHHHHHHHHH
T ss_conf             06886622252262023113466767----------------66----------67666448889999999999999998


Q ss_pred             HCCCHHHHHHHHCCCHHHHHHHHHHHCCC
Q ss_conf             28727899978489988999999981888
Q gi|254780916|r  450 YRAQMSEVARRLGIGRSTLYRKIREYNIE  478 (482)
Q Consensus       450 ~~Gn~~~aA~~LGIsR~tL~rKlk~~gi~  478 (482)
                      ++||+++||+.|||||+|||||||+|+|+
T Consensus       532 ~~gn~~~aAk~LgIsrttL~rKlkk~~l~  560 (560)
T COG3829         532 HGGNKSKAAKELGISRTTLYRKLKKYGLR  560 (560)
T ss_pred             HCCCHHHHHHHHCCCHHHHHHHHHHHCCC
T ss_conf             27989899999699789999999985689


No 9  
>PRK05022 anaerobic nitric oxide reductase transcription regulator; Provisional
Probab=100.00  E-value=0  Score=704.82  Aligned_cols=319  Identities=28%  Similarity=0.452  Sum_probs=280.3

Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCHHHHHCCCC-C
Q ss_conf             111122222222222222223443204887327774367999999842675433210123465542100243311255-5
Q gi|254780916|r  139 LDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFGDVD-L  217 (482)
Q Consensus       139 ~~~LiG~S~~m~~v~~~i~~~a~~~~~vli~Ge~GtGK~~~A~~iH~~s~r~~~~fi~v~c~~~~~~~~e~~lFG~~~-~  217 (482)
                      ...|||+|++|+++++.|.++|.|+.||||+||+||||+++||+||+.|.|+++|||.|||+++|++++|||||||++ +
T Consensus       185 ~~elIG~S~~m~~l~~~i~~vA~sd~pVLI~GEtGTGKelvAr~IH~~S~R~~~Pfv~vNCaalpe~l~EseLFGh~kGa  264 (510)
T PRK05022        185 QGEMIGQSPAMQQLKKEIEVVAASDLNVLITGETGVGKELVARAIHQASPRAVKPLVYLNCAALPESLAESELFGHVKGA  264 (510)
T ss_pred             CCCEEECCHHHHHHHHHHHHHHCCCCCEEEECCCCCCHHHHHHHHHHCCCCCCCCCEEEECCCCCHHHHHHHHCCCCCCC
T ss_conf             89752089999999999999968999889889898139999999996688789985788899998567899865977788


Q ss_pred             CCCCCCCCCCCCCCCCCCEEEECCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCEEEEECCCCCCCCCCHHHHHHH
Q ss_conf             53221110012344667147516642001889998888776420011235532123431565214332111111233379
Q gi|254780916|r  218 QTKNSAQFLGKFIEANGGTIVLEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKD  297 (482)
Q Consensus       218 ~~~~~~~~~g~~~~a~~Gtl~l~ei~~L~~~~Q~~Ll~~l~~~~~~~~g~~~~~~~~~RiIa~t~~~L~~~~~~g~fr~d  297 (482)
                      |||+...+.|+||+|+|||||||||++||+.+|.||||+||+++|.|+|++++.++||||||+||+||.++|++|.||+|
T Consensus       265 FtGA~~~r~G~fe~A~gGTLfLDEI~~Lpl~~Q~KLLrvLq~g~iqrvG~~~~~~vdvRIIAATnrdL~~~V~~G~FR~D  344 (510)
T PRK05022        265 FTGAISNRSGKFELADGGTLFLDEIGELPLALQAKLLRVLQYGEIQRVGSDRSLRVDVRVIAATNRDLREEVLAGRFRAD  344 (510)
T ss_pred             CCCCCCCCCCCEEECCCCEEEEECHHHCCHHHHHHHHHHHHCCEEEECCCCCEEEEEEEEEEECCCCHHHHHHCCCHHHH
T ss_conf             68865567881017789879875745499999999999984795885589946666689996078359999883963899


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHCCCCC-
Q ss_conf             9988654334467787744222255667776410112233332111110001223389868999999999987438981-
Q gi|254780916|r  298 LYYRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQELKNILLRAVIGLKDSH-  376 (482)
Q Consensus       298 Ly~rL~~~~i~iPpLReR~eDI~~L~~~fl~~~~~~~~~~~~~ls~~a~~~L~~y~WPGNvREL~n~i~r~~i~~~~~~-  376 (482)
                      ||||||+++|+|||||||+|||+.|+.||+++++.++|...++|+++|++.|.+|+||||||||+|+|+|+++.+.+.. 
T Consensus       345 LYyRLsv~~I~vPPLRER~eDI~lLa~~FLe~~~~~~g~~~~~ls~eAl~~L~~Y~WPGNVRELenvIeRA~lla~~~~~  424 (510)
T PRK05022        345 LYHRLSVFPLPVPPLRERGDDVLLLAGYFLEQNRLRLGLSSLRLSPDAQAALLQYDWPGNVRELEHVISRAALLARARRA  424 (510)
T ss_pred             HHHHHHCCCCCCCCHHHCHHHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHCCCCC
T ss_conf             99876204034808655554099999999999999829898988899999997099997899999999999997156667


Q ss_pred             -----CCHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHC
Q ss_conf             -----068895454212445432234322222233444321000000001123444543258999999999999999828
Q gi|254780916|r  377 -----LTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILDNLSQESIPAIGQDGEVRRLSDIEKEIIGLAMKLYR  451 (482)
Q Consensus       377 -----i~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~e~E~~~I~~aL~~~~  451 (482)
                           |...++..........             .. ...        ...............++++||++|.++|++++
T Consensus       425 ~~~~~i~~~~l~~~~~~~~~~-------------~~-~~~--------~~~~~~~~~~~Lr~a~e~~Er~lI~~AL~~~~  482 (510)
T PRK05022        425 GDIVTLEAQHLDLPEASAASV-------------PL-PPP--------EAAAAPVASQNLREATEAFQRQLIRQALAQHN  482 (510)
T ss_pred             CCCCCCCHHHCCCCCCCCCCC-------------CC-CCC--------CCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHC
T ss_conf             764425676648754455555-------------67-775--------54456767899999999999999999999919


Q ss_pred             CCHHHHHHHHCCCHHHHHHHHHHHCCCC
Q ss_conf             7278999784899889999999818881
Q gi|254780916|r  452 AQMSEVARRLGIGRSTLYRKIREYNIEV  479 (482)
Q Consensus       452 Gn~~~aA~~LGIsR~tL~rKlk~~gi~~  479 (482)
                      ||+++||+.|||+|+|||||||+|||+.
T Consensus       483 GN~s~AAr~LGIsRstLyRk~KrLGIk~  510 (510)
T PRK05022        483 GNWAAAARALELDRANLHRLAKRLGLKD  510 (510)
T ss_pred             CCHHHHHHHHCCCHHHHHHHHHHHCCCC
T ss_conf             9899999997989999999999808999


No 10 
>COG3604 FhlA Transcriptional regulator containing GAF, AAA-type ATPase, and DNA binding domains [Transcription / Signal transduction mechanisms]
Probab=100.00  E-value=0  Score=705.65  Aligned_cols=330  Identities=31%  Similarity=0.475  Sum_probs=287.5

Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCHHHHHCCC
Q ss_conf             11111112222222222222222344320488732777436799999984267543321012346554210024331125
Q gi|254780916|r  136 HCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFGDV  215 (482)
Q Consensus       136 ~~~~~~LiG~S~~m~~v~~~i~~~a~~~~~vli~Ge~GtGK~~~A~~iH~~s~r~~~~fi~v~c~~~~~~~~e~~lFG~~  215 (482)
                      .....+|||+|++|..+.+.|..+|.|+++|||.||+|||||++||+||+.|.|+++|||.+||+++|++++|||||||+
T Consensus       219 ~~~~~~iIG~S~am~~ll~~i~~VA~Sd~tVLi~GETGtGKElvAraIH~~S~R~~kPfV~~NCAAlPesLlESELFGHe  298 (550)
T COG3604         219 VLEVGGIIGRSPAMRQLLKEIEVVAKSDSTVLIRGETGTGKELVARAIHQLSPRRDKPFVKLNCAALPESLLESELFGHE  298 (550)
T ss_pred             HCCCCCCCCCCHHHHHHHHHHHHHHCCCCEEEEECCCCCCHHHHHHHHHHHCCCCCCCCEEEECCCCCHHHHHHHHHCCC
T ss_conf             02445623069999999999998726898079845888538999999987375557986663122253788888874533


Q ss_pred             C-CCCCCCCCCCCCCCCCCCCEEEECCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCEEEEECCCCCCCCCCHHHH
Q ss_conf             5-553221110012344667147516642001889998888776420011235532123431565214332111111233
Q gi|254780916|r  216 D-LQTKNSAQFLGKFIEANGGTIVLEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVF  294 (482)
Q Consensus       216 ~-~~~~~~~~~~g~~~~a~~Gtl~l~ei~~L~~~~Q~~Ll~~l~~~~~~~~g~~~~~~~~~RiIa~t~~~L~~~~~~g~f  294 (482)
                      | +||||..++.|+||.|+|||||||||++||++.|.||||+||+|+|+|+|+++++++|||||||||+||+++|.+|+|
T Consensus       299 KGAFTGA~~~r~GrFElAdGGTLFLDEIGelPL~lQaKLLRvLQegEieRvG~~r~ikVDVRiIAATNRDL~~~V~~G~F  378 (550)
T COG3604         299 KGAFTGAINTRRGRFELADGGTLFLDEIGELPLALQAKLLRVLQEGEIERVGGDRTIKVDVRVIAATNRDLEEMVRDGEF  378 (550)
T ss_pred             CCCCCCCHHCCCCCEEECCCCEEECHHHCCCCHHHHHHHHHHHHHCCEEECCCCCEEEEEEEEEECCCHHHHHHHHCCCC
T ss_conf             22333510146763565579757602203678778899999986365253479963677789982135309999874951


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHCCC
Q ss_conf             37999886543344677877442222556677764101122333321111100012233898689999999999874389
Q gi|254780916|r  295 RKDLYYRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQELKNILLRAVIGLKD  374 (482)
Q Consensus       295 r~dLy~rL~~~~i~iPpLReR~eDI~~L~~~fl~~~~~~~~~~~~~ls~~a~~~L~~y~WPGNvREL~n~i~r~~i~~~~  374 (482)
                      |+||||||||++|.+||||||++|||+|+.||+++++.++|+....++++|++.|.+|+||||||||+|+|+|+++.+ +
T Consensus       379 RaDLYyRLsV~Pl~lPPLRER~~DIplLA~~Fle~~~~~~gr~~l~ls~~Al~~L~~y~wPGNVRELen~veRavlla-~  457 (550)
T COG3604         379 RADLYYRLSVFPLELPPLRERPEDIPLLAGYFLEKFRRRLGRAILSLSAEALELLSSYEWPGNVRELENVVERAVLLA-G  457 (550)
T ss_pred             HHHHHHCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCCCCCHHHHHHHHHHHHHHC-C
T ss_conf             554532102001378983458866799999999999886397640339899999973999971999998999999970-4


Q ss_pred             CCCCHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHCCCH
Q ss_conf             81068895454212445432234322222233444321000000001123444543258999999999999999828727
Q gi|254780916|r  375 SHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILDNLSQESIPAIGQDGEVRRLSDIEKEIIGLAMKLYRAQM  454 (482)
Q Consensus       375 ~~i~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~e~E~~~I~~aL~~~~Gn~  454 (482)
                      ..++..++ ..+............  ..+     .+.....     ...|.  .-......+++||+.|.+||++++||+
T Consensus       458 ~~~~~~d~-~~l~~~~~~~~~~~~--~~~-----~p~~~~~-----~~~p~--~~~l~~~~~~~eR~~I~~aL~~~~~~~  522 (550)
T COG3604         458 RLTRRGDL-CTLELSLSALLWKTL--PAP-----EPSALPE-----PALPG--EHTLREATEEFERQLIIAALEETNGNW  522 (550)
T ss_pred             CCCCCCCE-EEHHHHHHCCCCCCC--CCC-----CCCCCCC-----CCCCC--CCCHHHHHHHHHHHHHHHHHHHHCCHH
T ss_conf             76777651-016555301212467--899-----8655677-----55776--565155577899999999999819819


Q ss_pred             HHHHHHHCCCHHHHHHHHHHHCCCCCC
Q ss_conf             899978489988999999981888144
Q gi|254780916|r  455 SEVARRLGIGRSTLYRKIREYNIEVDS  481 (482)
Q Consensus       455 ~~aA~~LGIsR~tL~rKlk~~gi~~d~  481 (482)
                      ++||+.||+.|+||-++||+|||++..
T Consensus       523 a~AAr~LGl~~~~L~~~~kRlGI~~~~  549 (550)
T COG3604         523 AGAARRLGLTRRTLLYRMKRLGIKVKK  549 (550)
T ss_pred             HHHHHHHCCCHHHHHHHHHHCCCCCCC
T ss_conf             999999589988999999972888578


No 11 
>PRK10820 DNA-binding transcriptional regulator TyrR; Provisional
Probab=100.00  E-value=0  Score=662.48  Aligned_cols=312  Identities=29%  Similarity=0.521  Sum_probs=278.2

Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCHHHHHC
Q ss_conf             21111111122222222222222223443204887327774367999999842675433210123465542100243311
Q gi|254780916|r  134 NEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFG  213 (482)
Q Consensus       134 ~~~~~~~~LiG~S~~m~~v~~~i~~~a~~~~~vli~Ge~GtGK~~~A~~iH~~s~r~~~~fi~v~c~~~~~~~~e~~lFG  213 (482)
                      .....|+.++|+|++|+++++++.++|.+++||||+||+||||+++||+||+.|.|+++||+.|||+++|++++|++|||
T Consensus       198 ~~~~~F~~iig~S~~m~~v~~~a~r~A~~d~pVLI~GEsGTGKellAraIH~~S~R~~~pFv~vnC~alp~~l~eseLFG  277 (513)
T PRK10820        198 QDVSAFSQIVAVSPKMKHVVEQARKLAMLSAPLLITGDTGTGKDLFAYACHLASPRAKKPYLALNCASIPEDAVESELFG  277 (513)
T ss_pred             CCCCCHHHHEECCHHHHHHHHHHHHHHCCCCCEEEECCCCCCHHHHHHHHHHCCCCCCCCCEEEECCCCCHHHHHHHHCC
T ss_conf             54168777510899999999999998598998899898982499999999966887899826888998996789998638


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCEEEECCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCEEEEECCCCCCCCCCHHH
Q ss_conf             25555322111001234466714751664200188999888877642001123553212343156521433211111123
Q gi|254780916|r  214 DVDLQTKNSAQFLGKFIEANGGTIVLEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHV  293 (482)
Q Consensus       214 ~~~~~~~~~~~~~g~~~~a~~Gtl~l~ei~~L~~~~Q~~Ll~~l~~~~~~~~g~~~~~~~~~RiIa~t~~~L~~~~~~g~  293 (482)
                      |.      ...+.|+|++|+|||||||||++||+.+|.|||++|+++.|+|+|+.+++++||||||+|+.||.++|++|.
T Consensus       278 ~a------~~~~~G~fe~A~gGTLfLdEI~~l~~~~Q~kLLr~Lq~~~~~rvG~~~~~~~dvRiIaaT~~dL~~lv~~g~  351 (513)
T PRK10820        278 HA------PEGKKGFFEQANGGSVLLDEIGEMSPRMQAKLLRFLNDGTFRRVGEDHEVHVDVRVICATQKNLVELVQKGL  351 (513)
T ss_pred             CC------CCCCCCCEEECCCCEEEEECHHHCCHHHHHHHHHHHHCCEEEECCCCCEEEEEEEEEECCCHHHHHHHHCCC
T ss_conf             76------668897557858988999783659999999999998689799659985356778999626530999987298


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHCC
Q ss_conf             33799988654334467787744222255667776410112233332111110001223389868999999999987438
Q gi|254780916|r  294 FRKDLYYRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQELKNILLRAVIGLK  373 (482)
Q Consensus       294 fr~dLy~rL~~~~i~iPpLReR~eDI~~L~~~fl~~~~~~~~~~~~~ls~~a~~~L~~y~WPGNvREL~n~i~r~~i~~~  373 (482)
                      ||+|||||||+++|++||||||+||||+|++||+.+++.++|++.++|+++|++.|.+|+||||||||+|+|+|+++++.
T Consensus       352 FReDLyyRL~v~~I~lPpLReR~eDI~~L~~~fl~~~~~~~g~~~~~ls~~a~~~L~~y~WPGNVREL~n~iera~~~~~  431 (513)
T PRK10820        352 FREDLYYRLNVLTLNLPPLRDCPQDIMPLTELFVARFADEQGVPRPKLSADLSTVLTRYGWPGNVRQLKNAIYRALTQLE  431 (513)
T ss_pred             CCHHHHHHHHCCCCCCCCHHHCHHHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHCCCCCHHHHHHHHHHHHHHHCC
T ss_conf             50889998616725588834465569999999999999975999898479999999708999799999999999999579


Q ss_pred             CCCCCHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHCCC
Q ss_conf             98106889545421244543223432222223344432100000000112344454325899999999999999982872
Q gi|254780916|r  374 DSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILDNLSQESIPAIGQDGEVRRLSDIEKEIIGLAMKLYRAQ  453 (482)
Q Consensus       374 ~~~i~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~e~E~~~I~~aL~~~~Gn  453 (482)
                      +..|+.+|+.......         .  ....     .    +..    .    ........+++|+.+|.+++..+ ||
T Consensus       432 g~~i~~~di~lp~~~~---------~--~~~~-----~----~~~----~----~~sL~e~~~~~Er~~l~~l~~~~-~~  482 (513)
T PRK10820        432 GYELRPQDILLPDYDA---------A--TVAV-----G----EDA----M----EGSLDDITSRFERSVLTQLYRNY-PS  482 (513)
T ss_pred             CCCCCHHHCCCCCCCC---------C--CCCC-----C----CCC----C----CCCHHHHHHHHHHHHHHHHHHHC-CC
T ss_conf             9853499828854344---------4--4676-----6----444----4----79999999999999999999878-89


Q ss_pred             HHHHHHHHCCCHHHHHHHHHHHCCCCC
Q ss_conf             789997848998899999998188814
Q gi|254780916|r  454 MSEVARRLGIGRSTLYRKIREYNIEVD  480 (482)
Q Consensus       454 ~~~aA~~LGIsR~tL~rKlk~~gi~~d  480 (482)
                      .++||+.|||||+|||+|||+|||++.
T Consensus       483 ~~kaAk~LGISrttL~~KlkkyGI~~k  509 (513)
T PRK10820        483 TRKLAKRLGVSHTAIANKLREYGLSQK  509 (513)
T ss_pred             HHHHHHHHCCCHHHHHHHHHHCCCCCC
T ss_conf             999999979989999999998089987


No 12 
>TIGR02974 phageshock_pspF psp operon transcriptional activator PspF; InterPro: IPR014317   Members of this protein are PspF, the sigma-54-dependent transcriptional activator of the phage shock protein (psp) operon, found in Escherichia coli and numerous other species. The psp operon is induced by a number of stress conditions, including heat shock, ethanol and filamentous phage infection..
Probab=100.00  E-value=0  Score=661.49  Aligned_cols=334  Identities=25%  Similarity=0.355  Sum_probs=284.0

Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCEEEEEECCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCHHHHHCCC-CCCCC
Q ss_conf             12222222222222222344320488732777436799999984267543321012346554210024331125-55532
Q gi|254780916|r  142 LIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFGDV-DLQTK  220 (482)
Q Consensus       142 LiG~S~~m~~v~~~i~~~a~~~~~vli~Ge~GtGK~~~A~~iH~~s~r~~~~fi~v~c~~~~~~~~e~~lFG~~-~~~~~  220 (482)
                      +||+|++.-+|.+++.++|..+.||||.||.|||||+||.-+|..|+|.++|||++|||+|+++|+|||||||+ ++|||
T Consensus         1 liG~S~aFL~vLeqvS~lA~l~rPVLiiGERGTGKELiA~RLHyLS~RW~~Plv~LNCAALse~LldSELFGHEaGAFTG   80 (349)
T TIGR02974         1 LIGESNAFLEVLEQVSRLAPLDRPVLIIGERGTGKELIAARLHYLSKRWQQPLVKLNCAALSENLLDSELFGHEAGAFTG   80 (349)
T ss_pred             CCCCCHHHHHHHHHHHHCCCCCCCEEEEECCCCCHHHHHHHHHHHHHHHCCCCEEEECCCCCCHHHHHHHHHHCCCCHHH
T ss_conf             98872789999998751046788668861467468999988533246554886266101278255556653100100130


Q ss_pred             CCCCCCCCCCCCCCCEEEECCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCEEEEECCCCCCCCCCHHHHHHHHHH
Q ss_conf             21110012344667147516642001889998888776420011235532123431565214332111111233379998
Q gi|254780916|r  221 NSAQFLGKFIEANGGTIVLEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYY  300 (482)
Q Consensus       221 ~~~~~~g~~~~a~~Gtl~l~ei~~L~~~~Q~~Ll~~l~~~~~~~~g~~~~~~~~~RiIa~t~~~L~~~~~~g~fr~dLy~  300 (482)
                      |..++.|+||+|+|||||||||..+|..+|.|||||+|=|+|+||||.+...+|||||||||.||..|+++|.||.||.+
T Consensus        81 A~~rh~GRFERAdGGTLFLDElAtas~~VQEKLLRViEYG~fERVGG~~~l~vDVRlvaATN~DLP~lA~~G~FRaDLLD  160 (349)
T TIGR02974        81 AKKRHEGRFERADGGTLFLDELATASLAVQEKLLRVIEYGEFERVGGSQTLKVDVRLVAATNADLPALAAEGRFRADLLD  160 (349)
T ss_pred             HCCCCCCCCEECCCCCCHHHHHHCCCHHHHHHHHHHHCCCCEEECCCCCEEEECCEEEECCCCCHHHHHHCCCCCCHHHH
T ss_conf             30468898544368873888871421676786612010130330178604773513676214136989865898401455


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCC-CCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHCCCCCCCH
Q ss_conf             86543344677877442222556677764101122333-32111110001223389868999999999987438981068
Q gi|254780916|r  301 RISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQ-ISISDKALSLLTKYPWIDNVQELKNILLRAVIGLKDSHLTE  379 (482)
Q Consensus       301 rL~~~~i~iPpLReR~eDI~~L~~~fl~~~~~~~~~~~-~~ls~~a~~~L~~y~WPGNvREL~n~i~r~~i~~~~~~i~~  379 (482)
                      ||+=-.|++||||+|.+||++|++||--++|.+.+.+. .+||+.|.+.|++|+||||||||||||||+|.-........
T Consensus       161 RLAFDVi~LPPLR~R~~DI~lLAe~FA~~Ma~EL~~~~F~GFt~~A~~~L~~Y~WPGNvRELkNvvERsVyR~~~~~~~i  240 (349)
T TIGR02974       161 RLAFDVITLPPLRERQEDIMLLAEHFAIRMARELGLPLFPGFTPQAREQLLEYHWPGNVRELKNVVERSVYRHGREEAPI  240 (349)
T ss_pred             HHHHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHCCCCCCCH
T ss_conf             44565507978888723278999999999999707865511438999999706888852124446766653058766420


Q ss_pred             HHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCC------------HHHCCCCCCCCCCCCCC-HHHHHHHHHHHHHHHH
Q ss_conf             8954542124454322343222222334443210------------00000001123444543-2589999999999999
Q gi|254780916|r  380 DRFVLLLSREGKKEREFHTETACTCYTEGKSSDT------------ILDNLSQESIPAIGQDG-EVRRLSDIEKEIIGLA  446 (482)
Q Consensus       380 ~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~------------~~~~~~~~~~~~~~~~~-~~~~l~e~E~~~I~~a  446 (482)
                      +++...-...+.......................            ..........+....+. ......++|+++|.+|
T Consensus       241 ~~i~~dPF~Spw~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~P~dl~~~~~~~E~~ll~~A  320 (349)
T TIGR02974       241 EEIIIDPFASPWRRPQAAPAAAEVNSTPTDEPSPKESAPDVTTTQQVDTGTSSSSVPNASFPLDLKQAVQDYEIELLQQA  320 (349)
T ss_pred             HHEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHCCCCHHHHHHHHHHHHHHHH
T ss_conf             12010778888887766643334444444432233345655202433202553101232168768999999999999999


Q ss_pred             HHHHCCCHHHHHHHHCCCHHHHHHHHHHH
Q ss_conf             99828727899978489988999999981
Q gi|254780916|r  447 MKLYRAQMSEVARRLGIGRSTLYRKIREY  475 (482)
Q Consensus       447 L~~~~Gn~~~aA~~LGIsR~tL~rKlk~~  475 (482)
                      |+++++||.+||+.||++.--|+.-||||
T Consensus       321 L~~~~fNQr~AAe~LGLtYHQlRg~LkKy  349 (349)
T TIGR02974       321 LAEAQFNQRKAAELLGLTYHQLRGLLKKY  349 (349)
T ss_pred             HHHHCCCHHHHHHHHCCCHHHHHHHHCCC
T ss_conf             98730347899987257368999863149


No 13 
>PRK11388 DNA-binding transcriptional regulator DhaR; Provisional
Probab=100.00  E-value=0  Score=637.89  Aligned_cols=315  Identities=30%  Similarity=0.481  Sum_probs=285.3

Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCHHHHHCC
Q ss_conf             11111111222222222222222234432048873277743679999998426754332101234655421002433112
Q gi|254780916|r  135 EHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFGD  214 (482)
Q Consensus       135 ~~~~~~~LiG~S~~m~~v~~~i~~~a~~~~~vli~Ge~GtGK~~~A~~iH~~s~r~~~~fi~v~c~~~~~~~~e~~lFG~  214 (482)
                      ....++.++|.||.|+++.+++.++|.++.||||+||+||||+++||+||+.|.|+++|||.|||+++|++++|++|||+
T Consensus       320 ~~~~f~~l~g~s~~~~~~~~~a~~~a~~~~pVLI~GE~GtGKe~lAraIH~~S~r~~~pfv~vnC~ai~~~~~e~elfG~  399 (639)
T PRK11388        320 VSHTFDHMPQDSPQMRRLIHFGRQAAKSSFPILLCGEEGVGKALLAQAIHNESERAAGPYIAVNCQLLPDEALAEEFLGS  399 (639)
T ss_pred             CCCCHHHCCCCCHHHHHHHHHHHHHHCCCCCEEEECCCCCCHHHHHHHHHHCCCCCCCCEEEEECCCCCHHHHHHHHCCC
T ss_conf             88885544679999999999999996889968988989810999999999557778998189878989846789987387


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCEEEECCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCEEEEECCCCCCCCCCHHHH
Q ss_conf             55553221110012344667147516642001889998888776420011235532123431565214332111111233
Q gi|254780916|r  215 VDLQTKNSAQFLGKFIEANGGTIVLEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVF  294 (482)
Q Consensus       215 ~~~~~~~~~~~~g~~~~a~~Gtl~l~ei~~L~~~~Q~~Ll~~l~~~~~~~~g~~~~~~~~~RiIa~t~~~L~~~~~~g~f  294 (482)
                      ..+.  ....+.|+|++|+|||||||||++||+++|.+|+++|++++|.|+|+.+.+++|+|||++|+.||.++|++|.|
T Consensus       400 ~~~~--~~~g~~g~~e~A~gGTL~LdeI~~lp~~~Q~~LlrvL~~~~~~r~g~~~~~~vdvRiiaat~~~l~~~v~~g~f  477 (639)
T PRK11388        400 DRTD--SENGRLSKFELAHGGTLFLEKVEYLSVELQSALLQVLKTGVITRLDSRRLIPVDVRVIATTTADLAMLVEQNRF  477 (639)
T ss_pred             CCCC--CCCCCCCHHHCCCCCEEEECCHHHCCHHHHHHHHHHHHCCCEEECCCCCEEEEEEEEEEECCHHHHHHHHCCCC
T ss_conf             7676--43466862440369828846726499999999999986593785699946664279997364508999874985


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHCCC
Q ss_conf             37999886543344677877442222556677764101122333321111100012233898689999999999874389
Q gi|254780916|r  295 RKDLYYRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQELKNILLRAVIGLKD  374 (482)
Q Consensus       295 r~dLy~rL~~~~i~iPpLReR~eDI~~L~~~fl~~~~~~~~~~~~~ls~~a~~~L~~y~WPGNvREL~n~i~r~~i~~~~  374 (482)
                      |+||||||++++|+|||||||++|||.|++||+.+++.+++.. ..|+++|++.|.+|+||||||||+|+++++++.+.+
T Consensus       478 r~dLyyrl~~~~i~lPpLReR~~Di~~L~~~~l~~~~~~~~~~-~~ls~~a~~~L~~y~WPGNvrEL~nvl~~a~~~~~~  556 (639)
T PRK11388        478 SRQLYYALHAFEITIPPLRMRREDIPALVNNKLRSLEKRFSTR-LKIDDDALARLVSYRWPGNDFELRSVIENLALSSDN  556 (639)
T ss_pred             HHHHHHHHHHHHCCCCCHHHCHHHHHHHHHHHHHHHHHHCCCC-CCCCHHHHHHHHCCCCCCHHHHHHHHHHHHHHHCCC
T ss_conf             4999987674410573323253439999999999999971999-998999999997289997999999999999983899


Q ss_pred             CCCCHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHCCCH
Q ss_conf             81068895454212445432234322222233444321000000001123444543258999999999999999828727
Q gi|254780916|r  375 SHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILDNLSQESIPAIGQDGEVRRLSDIEKEIIGLAMKLYRAQM  454 (482)
Q Consensus       375 ~~i~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~e~E~~~I~~aL~~~~Gn~  454 (482)
                      +.|+.++++..+..........           ..            .      .....+++++||++|..+|++|+||+
T Consensus       557 ~~I~~~~Lp~~~~~~~~~~~~~-----------~~------------~------~~~~~~l~~~Er~~I~~aL~~~~gN~  607 (639)
T PRK11388        557 GRIRLSDLPEHLFTEQATDDVS-----------AP------------R------LSTSLSLAELEKQAIINAAQVCGGRI  607 (639)
T ss_pred             CCCCHHHCCHHHHHCCCCCCCC-----------CC------------C------CCCCCCHHHHHHHHHHHHHHHHCCCH
T ss_conf             8426797808775157777777-----------67------------7------77656799999999999999949979


Q ss_pred             HHHHHHHCCCHHHHHHHHHHHCCCCCC
Q ss_conf             899978489988999999981888144
Q gi|254780916|r  455 SEVARRLGIGRSTLYRKIREYNIEVDS  481 (482)
Q Consensus       455 ~~aA~~LGIsR~tL~rKlk~~gi~~d~  481 (482)
                      ++||+.|||||+|||||||+|||+.|.
T Consensus       608 s~aA~~LGIsR~TLYRKlk~~gI~~~~  634 (639)
T PRK11388        608 QEMAALLGIGRTTLWRKMKQHGIDANQ  634 (639)
T ss_pred             HHHHHHHCCCHHHHHHHHHHHCCCHHH
T ss_conf             999999898999999999994969788


No 14 
>PRK11608 pspF phage shock protein operon transcriptional activator; Provisional
Probab=100.00  E-value=0  Score=637.04  Aligned_cols=319  Identities=24%  Similarity=0.402  Sum_probs=281.9

Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCHHHHHCCC-CC
Q ss_conf             11112222222222222222344320488732777436799999984267543321012346554210024331125-55
Q gi|254780916|r  139 LDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFGDV-DL  217 (482)
Q Consensus       139 ~~~LiG~S~~m~~v~~~i~~~a~~~~~vli~Ge~GtGK~~~A~~iH~~s~r~~~~fi~v~c~~~~~~~~e~~lFG~~-~~  217 (482)
                      .+.|||+|++|+++++++.++|.++.||||+||+||||+++||+||+.|.|+++||+.|||+.++++++|++||||+ ++
T Consensus         5 ~~~liG~S~~m~~v~~~~~~~A~~~~pVLI~GE~GtGK~~~Ar~IH~~S~r~~~pfi~v~C~~l~~~~~e~~LFG~~~g~   84 (325)
T PRK11608          5 KDNLLGEANSFLEVLEQVSHLAPLDKPVLIIGERGTGKELIASRLHYLSSRWQGPFISLNCAALNENLLDSELFGHEAGA   84 (325)
T ss_pred             CCCCEECCHHHHHHHHHHHHHHCCCCCEEEECCCCCCHHHHHHHHHHCCCCCCCCCEEEECCCCCHHHHHHHHCCCCCCC
T ss_conf             89985899999999999999968899989889898379999999996588679997788779899778899872775567


Q ss_pred             CCCCCCCCCCCCCCCCCCEEEECCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCEEEEECCCCCCCCCCHHHHHHH
Q ss_conf             53221110012344667147516642001889998888776420011235532123431565214332111111233379
Q gi|254780916|r  218 QTKNSAQFLGKFIEANGGTIVLEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKD  297 (482)
Q Consensus       218 ~~~~~~~~~g~~~~a~~Gtl~l~ei~~L~~~~Q~~Ll~~l~~~~~~~~g~~~~~~~~~RiIa~t~~~L~~~~~~g~fr~d  297 (482)
                      |+|+.....|+|++|+|||||||||++||+..|.+|+++|+++.|.|+|+.++..+|+||||+|+.||.+++++|.||+|
T Consensus        85 ~~~~~~~~~g~le~a~gGTL~L~eI~~l~~~~Q~~Ll~~l~~~~~~r~g~~~~~~~~~RiIa~t~~~l~~lv~~g~fr~d  164 (325)
T PRK11608         85 FTGAQKRHPGRFERADGGTLFLDELATAPMLVQEKLLRVIEYGELERVGGSQPLQVNVRLVCATNADLPAMVNEGTFRAD  164 (325)
T ss_pred             CCCCCCCCCCHHHCCCCCEEEEECHHHCCHHHHHHHHHHHHCCCEEECCCCCCCCCCEEEEECCCHHHHHHHHHCCCHHH
T ss_conf             67753246873435689869973745479999999999986490885799876656468871332208999983956799


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCC-CCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHCCCCC
Q ss_conf             99886543344677877442222556677764101122333-32111110001223389868999999999987438981
Q gi|254780916|r  298 LYYRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQ-ISISDKALSLLTKYPWIDNVQELKNILLRAVIGLKDSH  376 (482)
Q Consensus       298 Ly~rL~~~~i~iPpLReR~eDI~~L~~~fl~~~~~~~~~~~-~~ls~~a~~~L~~y~WPGNvREL~n~i~r~~i~~~~~~  376 (482)
                      |||||++++|+|||||||+|||+.|++||+.+++++++.+. ++|+++|++.|.+|+||||||||+|+++|+++.+.+..
T Consensus       165 Ly~rL~~~~I~lPpLReR~eDI~~L~~~fl~~~~~~~~~~~~~~~s~~a~~~L~~y~WPGNvrEL~n~ierav~~~~~~~  244 (325)
T PRK11608        165 LLDRLAFDVVQLPPLRERQSDIMLMAEHFAIQMCRELGLPLFPGFTERARETLLNYRWPGNIRELKNVVERSVYRHGTSD  244 (325)
T ss_pred             HHHHHHHHHCCCCCHHHCCCCHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHCCCCCCHHHHHHHHHHHHHHHCCCCC
T ss_conf             98565301115868454710199999999999999829998888899999999619999659999999999998568876


Q ss_pred             CCHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHCCCHHH
Q ss_conf             06889545421244543223432222223344432100000000112344454325899999999999999982872789
Q gi|254780916|r  377 LTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILDNLSQESIPAIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSE  456 (482)
Q Consensus       377 i~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~e~E~~~I~~aL~~~~Gn~~~  456 (482)
                      +..+++...............         ..          .....|.. .......++++||++|..||++++||+++
T Consensus       245 ~~~~~~~~~~~~~~~~~~~~~---------~~----------~~~~~~~~-~~~l~~~~~~~Ek~~I~~aL~~~~gn~~~  304 (325)
T PRK11608        245 YPLDDIIIDPFKRRPPEEAIA---------VS----------EATSLPTL-PLDLREFQHQQEKELLQRSLQQAKFNQKR  304 (325)
T ss_pred             CCHHHHCCCHHHCCCCCCCCC---------CC----------CCCCCCCC-CCCHHHHHHHHHHHHHHHHHHHHCCCHHH
T ss_conf             555542137121056556778---------77----------75456677-86899999999999999999993998999


Q ss_pred             HHHHHCCCHHHHHHHHHHHCC
Q ss_conf             997848998899999998188
Q gi|254780916|r  457 VARRLGIGRSTLYRKIREYNI  477 (482)
Q Consensus       457 aA~~LGIsR~tL~rKlk~~gi  477 (482)
                      ||+.|||||+|||+|||||||
T Consensus       305 aA~~LGIsR~tL~~klkky~l  325 (325)
T PRK11608        305 AAELLGLTYHQFRALLKKHQI  325 (325)
T ss_pred             HHHHHCCCHHHHHHHHHHCCC
T ss_conf             999988899999999997589


No 15 
>TIGR02329 propionate_PrpR propionate catabolism operon regulatory protein PrpR; InterPro: IPR012704   At least five distinct pathways exist for the catabolism of propionate by way of propionyl-CoA. Members of this family represent the transcriptional regulatory protein PrpR which is, in most cases, divergently transcribed from the operon that encodes the genes involved in the methylcitric acid cycle of propionate catabolism. This protein is required for the expression of the proteins involved in this pathway . 2-methylcitric acid, an intermediate in this pathway, has been proposed to be a co-activator of PrpR .; GO: 0000156 two-component response regulator activity, 0003677 DNA binding, 0005524 ATP binding, 0000160 two-component signal transduction system (phosphorelay), 0019629 propionate catabolic process 2-methylcitrate cycle, 0005737 cytoplasm.
Probab=100.00  E-value=0  Score=630.15  Aligned_cols=352  Identities=28%  Similarity=0.423  Sum_probs=280.2

Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCCCHHHHHHH
Q ss_conf             57432222222222222222222222222222211111111222222222222222234432048873277743679999
Q gi|254780916|r  102 RISKFFLNLVSRKQLCDSIICALREGVVPSQENEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSR  181 (482)
Q Consensus       102 g~~d~l~KP~~~~~L~~~i~~al~~~~~~~~~~~~~~~~~LiG~S~~m~~v~~~i~~~a~~~~~vli~Ge~GtGK~~~A~  181 (482)
                      |+.|--+-.|...+-++.+.+.++..... +-.......+|+|+|+.|.+|+..|..+|.|++.|||.||+|||||++|+
T Consensus       282 GaadGtvftfqesraverldr~~~~~tr~-~lrtR~~~~dl~G~s~~Me~VR~~v~lYArs~atVLi~GE~GTGKElvAq  360 (658)
T TIGR02329       282 GAADGTVFTFQESRAVERLDRALRSATRN-QLRTRYRLDDLLGESAAMEQVRALVRLYARSAATVLIEGESGTGKELVAQ  360 (658)
T ss_pred             CCCCCCEEEEHHHHHHHHHHHHHCCHHHH-HHHCCCCHHHHCCCCCCHHHHHHHHHHHCCCCCEEEEECCCCCCHHHHHH
T ss_conf             53355045402247889998862130355-43203454765389821389999998526886506751477722899999


Q ss_pred             HHH--------HCCCCCCCCCCCCCCCCCCCCCCHHHHHCCC-CCCCCCCCC-CCCCCCCCCCCEEEECCCCHHHHHHHH
Q ss_conf             998--------4267543321012346554210024331125-555322111-001234466714751664200188999
Q gi|254780916|r  182 FIH--------ESGKRAFFPFFIVNCGMIDQDKIEKFLFGDV-DLQTKNSAQ-FLGKFIEANGGTIVLEEPDALPLAVQG  251 (482)
Q Consensus       182 ~iH--------~~s~r~~~~fi~v~c~~~~~~~~e~~lFG~~-~~~~~~~~~-~~g~~~~a~~Gtl~l~ei~~L~~~~Q~  251 (482)
                      .||        +.+.|+..|||.|||+++++.|+|+||||++ ++|||+-.. +.|+||-|++||||||||++||+++|+
T Consensus       361 ~~H~EY~~R~~~~~~r~~~pFVAiNCGAi~EsLLEaELFGYeeGAFTGaRrGG~~GL~E~Ah~GTLFLDEIGEmPLPLQt  440 (658)
T TIGR02329       361 AIHREYALRYDQLSGRRDRPFVAINCGAIAESLLEAELFGYEEGAFTGARRGGRTGLIEAAHRGTLFLDEIGEMPLPLQT  440 (658)
T ss_pred             HHHHHHHHHHHHHCCCCCCCCEEEECCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCHHHHHCCCCEEEHHHCCCCCHHHH
T ss_conf             97599987466650133788468747465688887764267666501677677612222005795100100357861467


Q ss_pred             HHHHHHHHHHCCCCCCCCCCCCCCEEEEECCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC
Q ss_conf             88887764200112355321234315652143321111112333799988654334467787744222255667776410
Q gi|254780916|r  252 RIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYYRISVFLINISTLRSRSEDIPWLVHFFLQSFC  331 (482)
Q Consensus       252 ~Ll~~l~~~~~~~~g~~~~~~~~~RiIa~t~~~L~~~~~~g~fr~dLy~rL~~~~i~iPpLReR~eDI~~L~~~fl~~~~  331 (482)
                      ||||+|||+++.|+|++.|+++||||||+|+.+|++.|++|+||.|||||||++.|.+||||||++||.+|+.+|+.+..
T Consensus       441 RLLRVLeEreV~RvG~~~P~~VDvRvvaAth~~L~~~v~~GrFR~DLfYRL~~Lri~lPpLR~R~~Di~~La~~~l~~~~  520 (658)
T TIGR02329       441 RLLRVLEEREVVRVGGTEPVPVDVRVVAATHCALETAVQQGRFRRDLFYRLSILRIDLPPLRERPDDILPLAAEYLKQAL  520 (658)
T ss_pred             HHHHHHHCCCEEECCCCCCCEEEEEEEECCCHHHHHHHHCCCCCHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHH
T ss_conf             77776512214761787540244434331222258798578824228999999851478766864459999999998753


Q ss_pred             CCCCCCC--CCCCCCC-------CCCCCCCCCCCCHHHHHHHHHHHHHHCC------CCCCCHHHHHHHHCCCCCCCCCC
Q ss_conf             1122333--3211111-------0001223389868999999999987438------98106889545421244543223
Q gi|254780916|r  332 TKNAIKQ--ISISDKA-------LSLLTKYPWIDNVQELKNILLRAVIGLK------DSHLTEDRFVLLLSREGKKEREF  396 (482)
Q Consensus       332 ~~~~~~~--~~ls~~a-------~~~L~~y~WPGNvREL~n~i~r~~i~~~------~~~i~~~~~~~~l~~~~~~~~~~  396 (482)
                      ++.-+..  ..+|+.+       -+.|++|+||||||||+|++||+++.-.      .+.|+.+-+....+ +.....+.
T Consensus       521 rrePr~~l~~P~s~~~~q~L~~~~~~L~~y~WpGNvRELrnl~ERl~~~l~dtda~~~~~~t~~~l~~~~P-er~s~le~  599 (658)
T TIGR02329       521 RREPRAALALPLSEAALQELAAVEDALQRYAWPGNVRELRNLVERLALYLSDTDAEPEGALTPDLLEALAP-ERQSILEL  599 (658)
T ss_pred             CCCCHHHHCCCCCHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHCC-CHHHHHHH
T ss_conf             22515765188638999887437889861689984378877999998886403556331100899998587-52479999


Q ss_pred             CCCCCCCCCCCCCCCCCHHHCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHCCCHHHHHHHHHH
Q ss_conf             432222223344432100000000112344454325899999999999999982872789997848998899999998
Q gi|254780916|r  397 HTETACTCYTEGKSSDTILDNLSQESIPAIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKIRE  474 (482)
Q Consensus       397 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~e~E~~~I~~aL~~~~Gn~~~aA~~LGIsR~tL~rKlk~  474 (482)
                      ........+.     ++....              ...-+.++-..|.+||++++||+..+|+.|||||+||||+||+
T Consensus       600 a~~s~~~Gyd-----~T~a~~--------------~~~rs~v~a~~~~~aL~~~~G~~~a~a~~LGiSrTTLWRrL~~  658 (658)
T TIGR02329       600 AEASTKAGYD-----KTSADS--------------LRERSRVEALAVRAALERFQGDRAAAAKALGISRTTLWRRLKA  658 (658)
T ss_pred             HHHHCCCCCC-----CCCHHH--------------HHHHHCCCHHHHHHHHHHHCCCHHHHHHHCCCCHHHHHHHHCC
T ss_conf             9752246776-----677477--------------7342043357689999872789689985427642457776139


No 16 
>COG3284 AcoR Transcriptional activator of acetoin/glycerol metabolism [Secondary metabolites biosynthesis, transport, and catabolism / Transcription]
Probab=100.00  E-value=0  Score=579.14  Aligned_cols=289  Identities=34%  Similarity=0.549  Sum_probs=267.0

Q ss_pred             CCCCCCCCCCCCCCCCCCCCCEEEEEECCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCHHHHHCCC-CCCCCC
Q ss_conf             2222222222222222344320488732777436799999984267543321012346554210024331125-555322
Q gi|254780916|r  143 IAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFGDV-DLQTKN  221 (482)
Q Consensus       143 iG~S~~m~~v~~~i~~~a~~~~~vli~Ge~GtGK~~~A~~iH~~s~r~~~~fi~v~c~~~~~~~~e~~lFG~~-~~~~~~  221 (482)
                      .+.++.....++++.+++.++.||++.||+||||+.+||+||+.|. ..+|||.|||+++|+++.||||||+. ++|||+
T Consensus       316 ~~~d~s~a~l~rk~~rv~~~~~pvll~GEtGtGKe~laraiH~~s~-~~gpfvAvNCaAip~~liesELFGy~~GafTga  394 (606)
T COG3284         316 PLLDPSRATLLRKAERVAATDLPVLLQGETGTGKEVLARAIHQNSE-AAGPFVAVNCAAIPEALIESELFGYVAGAFTGA  394 (606)
T ss_pred             CCCCHHHHHHHHHHHHHHHCCCCEEECCCCCHHHHHHHHHHHHCCC-CCCCEEEEEECCCHHHHHHHHHHCCCCCCCCCC
T ss_conf             4557889999999988762478768538765568999999985365-569837998503447764677744576564330


Q ss_pred             CCC-CCCCCCCCCCCEEEECCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCEEEEECCCCCCCCCCHHHHHHHHHH
Q ss_conf             111-0012344667147516642001889998888776420011235532123431565214332111111233379998
Q gi|254780916|r  222 SAQ-FLGKFIEANGGTIVLEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYY  300 (482)
Q Consensus       222 ~~~-~~g~~~~a~~Gtl~l~ei~~L~~~~Q~~Ll~~l~~~~~~~~g~~~~~~~~~RiIa~t~~~L~~~~~~g~fr~dLy~  300 (482)
                      ... ..|++++|+|||||||||++||..+|.+|||+|+++.+.|+|+.+ +++|+|||++|++||..+|++|.||+||||
T Consensus       395 ~~kG~~g~~~~A~gGtlFldeIgd~p~~~Qs~LLrVl~e~~v~p~g~~~-~~vdirvi~ath~dl~~lv~~g~fredLyy  473 (606)
T COG3284         395 RRKGYKGKLEQADGGTLFLDEIGDMPLALQSRLLRVLQEGVVTPLGGTR-IKVDIRVIAATHRDLAQLVEQGRFREDLYY  473 (606)
T ss_pred             HHCCCCCCCEECCCCCCHHHHHHHCHHHHHHHHHHHHHHCCEECCCCCC-EEEEEEEEECCCCCHHHHHHCCCCHHHHHH
T ss_conf             0106655410157876089876114189999999998618252358852-157799983467579999875971487888


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHCCCCCCCHH
Q ss_conf             86543344677877442222556677764101122333321111100012233898689999999999874389810688
Q gi|254780916|r  301 RISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQELKNILLRAVIGLKDSHLTED  380 (482)
Q Consensus       301 rL~~~~i~iPpLReR~eDI~~L~~~fl~~~~~~~~~~~~~ls~~a~~~L~~y~WPGNvREL~n~i~r~~i~~~~~~i~~~  380 (482)
                      |||+++|++||||||+|+||+|.+++.++ +.    ....+++++++.|..|.||||||||.|++++++++++++.+...
T Consensus       474 rL~~~~i~lP~lr~R~d~~~~l~~~~~~~-~~----~~~~l~~~~~~~l~~~~WPGNirel~~v~~~~~~l~~~g~~~~~  548 (606)
T COG3284         474 RLNAFVITLPPLRERSDRIPLLDRILKRE-ND----WRLQLDDDALARLLAYRWPGNIRELDNVIERLAALSDGGRIRVS  548 (606)
T ss_pred             HHCCEEECCCCHHCCCCCHHHHHHHHHHC-CC----CCCCCCHHHHHHHHHCCCCCCHHHHHHHHHHHHHCCCCCEEECC
T ss_conf             74471550686110466578999999872-68----77568999999998578998289999999999870799735714


Q ss_pred             HHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHCCCHHHHHHH
Q ss_conf             95454212445432234322222233444321000000001123444543258999999999999999828727899978
Q gi|254780916|r  381 RFVLLLSREGKKEREFHTETACTCYTEGKSSDTILDNLSQESIPAIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARR  460 (482)
Q Consensus       381 ~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~e~E~~~I~~aL~~~~Gn~~~aA~~  460 (482)
                      |++..+..+...                                         ...+.|+..+..||+.|+||+++||+.
T Consensus       549 dlp~~l~~~~~~-----------------------------------------~~~~~~~~~l~~al~~~~~~is~aa~~  587 (606)
T COG3284         549 DLPPELLEEQAT-----------------------------------------PREDIEKAALLAALQATNGNISEAARL  587 (606)
T ss_pred             CCCHHHHHHHCC-----------------------------------------CCCCHHHHHHHHHHHHCCCCHHHHHHH
T ss_conf             498888754325-----------------------------------------300157999999999808979999998


Q ss_pred             HCCCHHHHHHHHHHHCCCC
Q ss_conf             4899889999999818881
Q gi|254780916|r  461 LGIGRSTLYRKIREYNIEV  479 (482)
Q Consensus       461 LGIsR~tL~rKlk~~gi~~  479 (482)
                      |||+|+|||||||+|||.+
T Consensus       588 lgi~R~T~yrklk~~gi~~  606 (606)
T COG3284         588 LGISRSTLYRKLKRHGISK  606 (606)
T ss_pred             HCCCHHHHHHHHHHHCCCC
T ss_conf             5997888999999737789


No 17 
>COG3283 TyrR Transcriptional regulator of aromatic amino acids metabolism [Transcription / Amino acid transport and metabolism]
Probab=100.00  E-value=0  Score=551.78  Aligned_cols=313  Identities=29%  Similarity=0.506  Sum_probs=282.3

Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCHHHHHC
Q ss_conf             21111111122222222222222223443204887327774367999999842675433210123465542100243311
Q gi|254780916|r  134 NEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFG  213 (482)
Q Consensus       134 ~~~~~~~~LiG~S~~m~~v~~~i~~~a~~~~~vli~Ge~GtGK~~~A~~iH~~s~r~~~~fi~v~c~~~~~~~~e~~lFG  213 (482)
                      +....|+.+++.|..|+.+..++.++|..++|.||+||+||||+++|++-|..|+|.++||+.+||+++|++..||||||
T Consensus       198 ~~~~~F~~~v~~S~~mk~~v~qA~k~AmlDAPLLI~GeTGTGKdLlAkaCH~~S~R~~~pFlalNCA~lPe~~aEsElFG  277 (511)
T COG3283         198 QDVSGFEQIVAVSPKMKHVVEQAQKLAMLDAPLLITGETGTGKDLLAKACHLASPRHSKPFLALNCASLPEDAAESELFG  277 (511)
T ss_pred             CCCCCHHHHHHCCHHHHHHHHHHHHHHCCCCCEEEECCCCCHHHHHHHHHHHCCCCCCCCEEEEECCCCCHHHHHHHHHC
T ss_conf             75424477873039999999999865403787687448886188999987443845589736764477966676777735


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCEEEECCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCEEEEECCCCCCCCCCHHH
Q ss_conf             25555322111001234466714751664200188999888877642001123553212343156521433211111123
Q gi|254780916|r  214 DVDLQTKNSAQFLGKFIEANGGTIVLEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHV  293 (482)
Q Consensus       214 ~~~~~~~~~~~~~g~~~~a~~Gtl~l~ei~~L~~~~Q~~Ll~~l~~~~~~~~g~~~~~~~~~RiIa~t~~~L~~~~~~g~  293 (482)
                      |..|    ....+|.||+|+|||+|||||++||+.+|.||||+|++|.|+|||+.+++.+|||+||+|..||.++|++|.
T Consensus       278 ~apg----~~gk~GffE~AngGTVlLDeIgEmSp~lQaKLLRFL~DGtFRRVGee~Ev~vdVRVIcatq~nL~~lv~~g~  353 (511)
T COG3283         278 HAPG----DEGKKGFFEQANGGTVLLDEIGEMSPRLQAKLLRFLNDGTFRRVGEDHEVHVDVRVICATQVNLVELVQKGK  353 (511)
T ss_pred             CCCC----CCCCCCHHHHCCCCEEEEEHHHHCCHHHHHHHHHHHCCCCCCCCCCCCEEEEEEEEEECCCCCHHHHHHCCC
T ss_conf             6888----777634634026974885003324998999999986277600037754578778999616666999986372


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHCC
Q ss_conf             33799988654334467787744222255667776410112233332111110001223389868999999999987438
Q gi|254780916|r  294 FRKDLYYRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQELKNILLRAVIGLK  373 (482)
Q Consensus       294 fr~dLy~rL~~~~i~iPpLReR~eDI~~L~~~fl~~~~~~~~~~~~~ls~~a~~~L~~y~WPGNvREL~n~i~r~~i~~~  373 (482)
                      ||+||||||||.++++||||||.+||++|+++|++++|.+.|.+.+.|+++++..|+.|+||||||||+|++.||+..+.
T Consensus       354 fReDLfyRLNVLtl~~PpLRer~~di~pL~e~Fv~q~s~elg~p~pkl~~~~~~~L~~y~WpGNVRqL~N~iyRA~s~~E  433 (511)
T COG3283         354 FREDLFYRLNVLTLNLPPLRERPQDIMPLAELFVQQFSDELGVPRPKLAADLLTVLTRYAWPGNVRQLKNAIYRALTLLE  433 (511)
T ss_pred             HHHHHHHHHHEEEECCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHC
T ss_conf             58878877501342388500065210689999999999975899876687899999877999609999999999999851


Q ss_pred             CCCCCHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHCCC
Q ss_conf             98106889545421244543223432222223344432100000000112344454325899999999999999982872
Q gi|254780916|r  374 DSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILDNLSQESIPAIGQDGEVRRLSDIEKEIIGLAMKLYRAQ  453 (482)
Q Consensus       374 ~~~i~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~e~E~~~I~~aL~~~~Gn  453 (482)
                      +..++.+++.........                     ...+.....        ..-+.+..||+.++.+-+..+- .
T Consensus       434 g~~l~i~~i~Lp~~~~~~---------------------~~~~~~~~g--------sLdei~~~fE~~VL~rly~~yP-S  483 (511)
T COG3283         434 GYELRIEDILLPDYDAAT---------------------VVGEDALEG--------SLDEIVSRFERSVLTRLYRSYP-S  483 (511)
T ss_pred             CCCCCHHHCCCCCCCCCC---------------------CCCHHHCCC--------CHHHHHHHHHHHHHHHHHHHCC-C
T ss_conf             674443200467755343---------------------452133028--------7999999999999999998597-4


Q ss_pred             HHHHHHHHCCCHHHHHHHHHHHCCCCC
Q ss_conf             789997848998899999998188814
Q gi|254780916|r  454 MSEVARRLGIGRSTLYRKIREYNIEVD  480 (482)
Q Consensus       454 ~~~aA~~LGIsR~tL~rKlk~~gi~~d  480 (482)
                      ..+-|+.||+|-++.-.|+++|||.+.
T Consensus       484 tRkLAkRLgvSHTaIAnKLRqyGi~~~  510 (511)
T COG3283         484 TRKLAKRLGVSHTAIANKLRQYGIGQK  510 (511)
T ss_pred             HHHHHHHHCCCHHHHHHHHHHHCCCCC
T ss_conf             889999858737999989998277778


No 18 
>COG1221 PspF Transcriptional regulators containing an AAA-type ATPase domain and a DNA-binding domain [Transcription / Signal transduction mechanisms]
Probab=100.00  E-value=0  Score=545.41  Aligned_cols=328  Identities=29%  Similarity=0.414  Sum_probs=281.4

Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCCCHHHHHHHHHHHCCCC-CCCCCCCCCCCCCCCCCCHHHHH
Q ss_conf             21111111122222222222222223443204887327774367999999842675-43321012346554210024331
Q gi|254780916|r  134 NEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHESGKR-AFFPFFIVNCGMIDQDKIEKFLF  212 (482)
Q Consensus       134 ~~~~~~~~LiG~S~~m~~v~~~i~~~a~~~~~vli~Ge~GtGK~~~A~~iH~~s~r-~~~~fi~v~c~~~~~~~~e~~lF  212 (482)
                      .....+..+||.|++|+++++++..++.+..||||+||+||||+++|+.||..|.| +++|||.|||+++++++.+++||
T Consensus        72 ~~~~~~~~LIG~~~~~~~~~eqik~~ap~~~~vLi~GetGtGKel~A~~iH~~s~r~~~~PFI~~NCa~~~en~~~~eLF  151 (403)
T COG1221          72 LKSEALDDLIGESPSLQELREQIKAYAPSGLPVLIIGETGTGKELFARLIHALSARRAEAPFIAFNCAAYSENLQEAELF  151 (403)
T ss_pred             CCCHHHHHHHCCCHHHHHHHHHHHHHCCCCCCEEEECCCCCCHHHHHHHHHHHHHCCCCCCEEEEEHHHHCCCHHHHHHH
T ss_conf             02215666635688899999999861899984798668875388999999986121358987997777737677777773


Q ss_pred             CCCCC-CCCCCCCCCCCCCCCCCCEEEECCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCEEEEECCCCCCCCCCH
Q ss_conf             12555-53221110012344667147516642001889998888776420011235532123431565214332111111
Q gi|254780916|r  213 GDVDL-QTKNSAQFLGKFIEANGGTIVLEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKS  291 (482)
Q Consensus       213 G~~~~-~~~~~~~~~g~~~~a~~Gtl~l~ei~~L~~~~Q~~Ll~~l~~~~~~~~g~~~~~~~~~RiIa~t~~~L~~~~~~  291 (482)
                      ||++| |||+...+.|+||+|+|||||||||++||++.|.+||++|++++|+|+|++++.++|||+||||+.|+.+.+..
T Consensus       152 G~~kGaftGa~~~k~Glfe~A~GGtLfLDEI~~LP~~~Q~kLl~~le~g~~~rvG~~~~~~~dVRli~AT~~~l~~~~~~  231 (403)
T COG1221         152 GHEKGAFTGAQGGKAGLFEQANGGTLFLDEIHRLPPEGQEKLLRVLEEGEYRRVGGSQPRPVDVRLICATTEDLEEAVLA  231 (403)
T ss_pred             CCCCCEEECCCCCCCCHHEECCCCEEEHHHHHHCCHHHHHHHHHHHHCCCEEECCCCCCCCCCCEEEECCCCCHHHHHHH
T ss_conf             20000002566786764205279777656365379858999999987186576688888677740451356687999874


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHH
Q ss_conf             23337999886543344677877442222556677764101122333321111100012233898689999999999874
Q gi|254780916|r  292 HVFRKDLYYRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQELKNILLRAVIG  371 (482)
Q Consensus       292 g~fr~dLy~rL~~~~i~iPpLReR~eDI~~L~~~fl~~~~~~~~~~~~~ls~~a~~~L~~y~WPGNvREL~n~i~r~~i~  371 (482)
                      |   +|||||+++.+|++||||||++||++|++||+..+|++.+.+...++++|+..|.+|+||||||||+|+|+++++.
T Consensus       232 g---~dl~~rl~~~~I~LPpLrER~~Di~~L~e~Fl~~~~~~l~~~~~~~~~~a~~~L~~y~~pGNirELkN~Ve~~~~~  308 (403)
T COG1221         232 G---ADLTRRLNILTITLPPLRERKEDILLLAEHFLKSEARRLGLPLSVDSPEALRALLAYDWPGNIRELKNLVERAVAQ  308 (403)
T ss_pred             H---CCHHHHHCCCEECCCCHHHCHHHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHCCCCCCHHHHHHHHHHHHHH
T ss_conf             0---5255641675431897243555599999999999999739998888899999998488998399999999999997


Q ss_pred             CCCCCCCHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHC
Q ss_conf             38981068895454212445432234322222233444321000000001123444543258999999999999999828
Q gi|254780916|r  372 LKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILDNLSQESIPAIGQDGEVRRLSDIEKEIIGLAMKLYR  451 (482)
Q Consensus       372 ~~~~~i~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~e~E~~~I~~aL~~~~  451 (482)
                      +.+..+..++.............    .  ..  .....        ....++....+........+|...+..+|.++.
T Consensus       309 ~~~~~~~~~~~~~~~~~~~~~~~----~--~~--~~~~~--------~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~  372 (403)
T COG1221         309 ASGEGQDLEDLIISIRLDELPGL----N--DV--PAGIS--------LQLNLPELPLSLRETSLEQVEERLLQKALEQNK  372 (403)
T ss_pred             HCCCCCCCCCCCCHHHHCCCCCC----C--CC--HHHHH--------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             35456785102211221136543----3--31--01101--------233267776655533346789988899999852


Q ss_pred             CCHHHHHHHHCCCHHHHHHHHHHHCCCCC
Q ss_conf             72789997848998899999998188814
Q gi|254780916|r  452 AQMSEVARRLGIGRSTLYRKIREYNIEVD  480 (482)
Q Consensus       452 Gn~~~aA~~LGIsR~tL~rKlk~~gi~~d  480 (482)
                      ||+.++|+.|||+|.++++||++|++...
T Consensus       373 ~~~~~~~~~lg~s~~~l~~~l~~~~~~~~  401 (403)
T COG1221         373 GNKKKAARLLGISRKTLRYRLKKYGLTTF  401 (403)
T ss_pred             CCHHHHHHHCCCCHHHHHHHHHHHCCCCC
T ss_conf             02999998839989999999987033336


No 19 
>pfam00158 Sigma54_activat Sigma-54 interaction domain.
Probab=100.00  E-value=0  Score=374.40  Aligned_cols=167  Identities=37%  Similarity=0.589  Sum_probs=162.5

Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCEEEEEECCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCHHHHHCCCCC-CCC
Q ss_conf             1222222222222222234432048873277743679999998426754332101234655421002433112555-532
Q gi|254780916|r  142 LIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFGDVDL-QTK  220 (482)
Q Consensus       142 LiG~S~~m~~v~~~i~~~a~~~~~vli~Ge~GtGK~~~A~~iH~~s~r~~~~fi~v~c~~~~~~~~e~~lFG~~~~-~~~  220 (482)
                      |||+|++|+++++++.++|.++.||||+||+||||+++||+||+.|.|+++||+.|||++++++++|++|||++++ |+|
T Consensus         1 lIG~S~~m~~l~~~i~~~a~~~~pVLI~GE~GtGK~~lAr~IH~~S~r~~~pfi~vnc~~~~~~~le~~LFG~~~g~f~g   80 (168)
T pfam00158         1 LIGESPAMQEVLELAKRVAPTDATVLITGESGTGKELFARAIHQLSPRADGPFVAVNCAAIPEELLESELFGHEKGAFTG   80 (168)
T ss_pred             CEECCHHHHHHHHHHHHHHCCCCCEEEECCCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCHHHHHHHHCCCCCCCCCC
T ss_conf             97389999999999999958899889989998888999999998524356883125678998779999875876676689


Q ss_pred             CCCCCCCCCCCCCCCEEEECCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCEEEEECCCCCCCCCCHHHHHHHHHH
Q ss_conf             21110012344667147516642001889998888776420011235532123431565214332111111233379998
Q gi|254780916|r  221 NSAQFLGKFIEANGGTIVLEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYY  300 (482)
Q Consensus       221 ~~~~~~g~~~~a~~Gtl~l~ei~~L~~~~Q~~Ll~~l~~~~~~~~g~~~~~~~~~RiIa~t~~~L~~~~~~g~fr~dLy~  300 (482)
                      +...+.|+|++|+|||||||||++||++.|.+|+++|++++|.|+|+++++++|+||||+|+.||.++|++|.||+||||
T Consensus        81 a~~~~~G~le~A~gGTL~LdeI~~L~~~~Q~~Ll~~L~~~~~~~~g~~~~~~~~vRiIast~~~L~~~v~~G~Fr~DLyy  160 (168)
T pfam00158        81 AVSDRKGLFELADGGTLFLDEIGELPLELQAKLLRVLQEGEFERVGGTKPIKVDVRIIAATNRDLEEAVAEGRFREDLYY  160 (168)
T ss_pred             CCCCCCCCEEECCCCEEECCCHHHCCHHHHHHHHHHHHCCEEEECCCCCEEEEEEEEEEECCCCHHHHHHCCCCHHHHHH
T ss_conf             87578996422699878802441399999999999985796997799845888549999659889999883996399888


Q ss_pred             HHHHHHHH
Q ss_conf             86543344
Q gi|254780916|r  301 RISVFLIN  308 (482)
Q Consensus       301 rL~~~~i~  308 (482)
                      |||+++|+
T Consensus       161 rLnv~~ie  168 (168)
T pfam00158       161 RLNVVPIE  168 (168)
T ss_pred             HHCEEECC
T ss_conf             86523269


No 20 
>COG4650 RtcR Sigma54-dependent transcription regulator containing an AAA-type ATPase domain and a DNA-binding domain [Transcription / Signal transduction mechanisms]
Probab=100.00  E-value=9.8e-45  Score=335.93  Aligned_cols=317  Identities=22%  Similarity=0.310  Sum_probs=268.4

Q ss_pred             CCCCCCCCCCCCCCCCCCCCC-CCCEEEEEECCCCCHHHHHHHHHHHCC---CCCCCCCCCCCCCCCCCCCCHHHHHCCC
Q ss_conf             111222222222222222234-432048873277743679999998426---7543321012346554210024331125
Q gi|254780916|r  140 DSLIAVSPAMIQVVDLARKAG-DCAIPIMIQGEFGVGKKRLSRFIHESG---KRAFFPFFIVNCGMIDQDKIEKFLFGDV  215 (482)
Q Consensus       140 ~~LiG~S~~m~~v~~~i~~~a-~~~~~vli~Ge~GtGK~~~A~~iH~~s---~r~~~~fi~v~c~~~~~~~~e~~lFG~~  215 (482)
                      +++-+.+|+..+.+++|+++| .|.+|+|+.|++|.||..+||.|++.-   ..-.++||.|||+++-.+-.+|.||||.
T Consensus       184 sgiatrnp~fnrmieqierva~rsr~p~ll~gptgagksflarriyelk~arhq~sg~fvevncatlrgd~amsalfghv  263 (531)
T COG4650         184 SGIATRNPHFNRMIEQIERVAIRSRAPILLNGPTGAGKSFLARRIYELKQARHQFSGAFVEVNCATLRGDTAMSALFGHV  263 (531)
T ss_pred             HCCCCCCHHHHHHHHHHHHHHHHCCCCEEEECCCCCCHHHHHHHHHHHHHHHHHCCCCEEEEEEEEECCCHHHHHHHHHH
T ss_conf             33321585778899999999861469768646887436689999999998887537862788630004752889987640


Q ss_pred             C-CCCCCCCCCCCCCCCCCCCEEEECCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCEEEEECCCCCCCCCCHHHH
Q ss_conf             5-553221110012344667147516642001889998888776420011235532123431565214332111111233
Q gi|254780916|r  216 D-LQTKNSAQFLGKFIEANGGTIVLEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVF  294 (482)
Q Consensus       216 ~-~~~~~~~~~~g~~~~a~~Gtl~l~ei~~L~~~~Q~~Ll~~l~~~~~~~~g~~~~~~~~~RiIa~t~~~L~~~~~~g~f  294 (482)
                      + +|||+...+.|++..|+||.||||||++|..+.|+.||.++++++|+|.||+..+.+|+.+|+.|.+||.+.|++|.|
T Consensus       264 kgaftga~~~r~gllrsadggmlfldeigelgadeqamllkaieekrf~pfgsdr~v~sdfqliagtvrdlrq~vaeg~f  343 (531)
T COG4650         264 KGAFTGARESREGLLRSADGGMLFLDEIGELGADEQAMLLKAIEEKRFYPFGSDRQVSSDFQLIAGTVRDLRQLVAEGKF  343 (531)
T ss_pred             HCCCCCCHHHHHHHHCCCCCCEEEHHHHHHCCCCHHHHHHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCH
T ss_conf             01314633455442433778657567433247527889999988712677887400031067764118889999863613


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCC------CCCCCHHHHHHHHHHH
Q ss_conf             3799988654334467787744222255667776410112233332111110001223------3898689999999999
Q gi|254780916|r  295 RKDLYYRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKY------PWIDNVQELKNILLRA  368 (482)
Q Consensus       295 r~dLy~rL~~~~i~iPpLReR~eDI~~L~~~fl~~~~~~~~~~~~~ls~~a~~~L~~y------~WPGNvREL~n~i~r~  368 (482)
                      |+|||-|+|.+++.+|-|+.|+|||.+-++|-+++++...|.. ..|..+|......+      .|.||+|||..-|.|+
T Consensus       344 redl~arinlwtf~lpgl~qr~ediepnldyelerha~~~g~~-vrfntearra~l~fa~spqa~w~gnfrelsasvtrm  422 (531)
T COG4650         344 REDLYARINLWTFTLPGLRQRQEDIEPNLDYELERHASLTGDS-VRFNTEARRAWLAFATSPQATWRGNFRELSASVTRM  422 (531)
T ss_pred             HHHHHHHHHEEEEECCCCCCCCCCCCCCCCHHHHHHHHHHCCE-EEEEHHHHHHHHHHCCCCHHHHCCCHHHHHHHHHHH
T ss_conf             7878876311354066311570006988347899988861863-552079888899750583011126688876899999


Q ss_pred             HHHCCCCCCCHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf             87438981068895454212445432234322222233444321000000001123444543258999999999999999
Q gi|254780916|r  369 VIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILDNLSQESIPAIGQDGEVRRLSDIEKEIIGLAMK  448 (482)
Q Consensus       369 ~i~~~~~~i~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~e~E~~~I~~aL~  448 (482)
                      ..++.++.|+.+-+...+.+..........              ..+..+..         .....|+-+.+.-++.++.
T Consensus       423 atlad~grit~~~ve~ei~rlr~~w~~~~p--------------~~l~~llg---------~~a~aldlfdrmqle~v~~  479 (531)
T COG4650         423 ATLADSGRITLDVVEDEINRLRYNWQESRP--------------SALTALLG---------AEAEALDLFDRMQLEHVIA  479 (531)
T ss_pred             HHHHCCCCEEHHHHHHHHHHHHHHHHHCCC--------------CHHHHCCC---------CCHHHHHHHHHHHHHHHHH
T ss_conf             887127830088789999999987641386--------------02330346---------6527765788888999999


Q ss_pred             HHCCCHH--HHH-HHHCCCH---------HHHHHHHHHHCCCCC
Q ss_conf             8287278--999-7848998---------899999998188814
Q gi|254780916|r  449 LYRAQMS--EVA-RRLGIGR---------STLYRKIREYNIEVD  480 (482)
Q Consensus       449 ~~~Gn~~--~aA-~~LGIsR---------~tL~rKlk~~gi~~d  480 (482)
                      -|.+.++  .|- ++..+||         ..|++.+..+|++-+
T Consensus       480 vcr~aktls~agr~lf~vsrq~ka~vndadrlrkylarfgl~w~  523 (531)
T COG4650         480 ICRQAKSLSAAGRQLFDVSRQGKASVNDADRLRKYLARFGLTWE  523 (531)
T ss_pred             HHHCCCCHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHCCCHH
T ss_conf             98711516577677753333036898708999999998488799


No 21 
>TIGR02154 PhoB phosphate regulon transcriptional regulatory protein PhoB; InterPro: IPR011879    PhoB is a DNA-binding response regulator protein acting with PhoR in a 2-component system responding to phosphate ion. PhoB acts as a positive regulator of gene expression for phosphate-related genes such as phoA, phoS, phoE and ugpAB as well as itself . It is often found proximal to genes for the high-affinity phosphate ABC transporter (pstSCAB; GenProp0190) and presumably regulates these as well.; GO: 0000156 two-component response regulator activity, 0003677 DNA binding, 0000160 two-component signal transduction system (phosphorelay), 0006817 phosphate transport.
Probab=99.94  E-value=1.2e-26  Score=207.83  Aligned_cols=169  Identities=17%  Similarity=0.228  Sum_probs=134.3

Q ss_pred             CCCEEEECCCHHHHHHHHHHHHHCCCEEEEECC--HHHHHHHCCCCCEEEEECCCCCCCHHHHHHHHHHH--CCCCCEEE
Q ss_conf             883899869989999999999988988999893--79999860899899997854698889999999985--78983999
Q gi|254780916|r   10 HKRVLIIDKDDEQIKIIKDHVESYGYDVFIVNV--SDLSTISKIQVNVIFLSLINCEDDKENILKNIVDK--IPIVPIIV   85 (482)
Q Consensus        10 ~~rILIVDDd~~~~~~l~~~L~~~G~~v~~a~~--~al~~l~~~~~dlillD~~mP~~dGlell~~i~~~--~p~ipvIi   85 (482)
                      +++|||||||+.++++++-.|+..||+|..|++  +|+..+.+..||+||||||+||.+|+|+|+++|..  .-+|||||
T Consensus         2 ~~~iLvVEDE~AirEl~~~~L~~~gy~v~~A~d~~~A~~~~~E~~PDLILLDWMLPG~SGIel~R~Lr~~~~Tr~iPIIM   81 (226)
T TIGR02154         2 TRRILVVEDEPAIRELIAYNLEKAGYDVVEAGDGDEALTLINERLPDLILLDWMLPGTSGIELARRLRREPETRAIPIIM   81 (226)
T ss_pred             CCEEEEEECCHHHHHHHHHHHCCCCCEEEEECCHHHHHHHHHCCCCCEEEECCCCCCCCHHHHHHHHCCCCCCCCCCEEE
T ss_conf             87256770826899999998416894699807979999998607998899614789975699998734763314888177


Q ss_pred             EECCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEE
Q ss_conf             92689999999888505743222222222222222222222222222221111111122222222222222223443204
Q gi|254780916|r   86 QTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALREGVVPSQENEHCALDSLIAVSPAMIQVVDLARKAGDCAIP  165 (482)
Q Consensus        86 iT~~~~~~~~~~a~~~g~~d~l~KP~~~~~L~~~i~~al~~~~~~~~~~~~~~~~~LiG~S~~m~~v~~~i~~~a~~~~~  165 (482)
                      +||-++.+.-+.|+..||+||++|||++.+|+++|+..+|+..... ..+.....+|        .+=....|+..++.|
T Consensus        82 LTARGeE~Drv~GLetGADDYvtKPFSp~EL~ARikAVLRR~~P~~-~~~~i~~~~l--------~lD~~~HRV~~~~~~  152 (226)
T TIGR02154        82 LTARGEEEDRVRGLETGADDYVTKPFSPRELLARIKAVLRRIRPEL-SDEVIEVGDL--------ELDPVAHRVKRGGQP  152 (226)
T ss_pred             EECCCCCCCCCCCCCCCCCCEEECCCCHHHHHHHHHHHHHCCCHHH-HCCEEEECCE--------EECCCCCEEEECCEE
T ss_conf             4055560001131136887503678865889999999983167124-2020110347--------775102404313602


Q ss_pred             EEEECCCCCHHHHHHHHHHHCCCCCCCCC
Q ss_conf             88732777436799999984267543321
Q gi|254780916|r  166 IMIQGEFGVGKKRLSRFIHESGKRAFFPF  194 (482)
Q Consensus       166 vli~Ge~GtGK~~~A~~iH~~s~r~~~~f  194 (482)
                      |-| |+|     =+ |.+|.+-.....-|
T Consensus       153 ~~l-GPT-----Ef-RLL~FFM~HPeRV~  174 (226)
T TIGR02154       153 LEL-GPT-----EF-RLLHFFMTHPERVY  174 (226)
T ss_pred             CCC-CCH-----HH-HHHHHHHHCCCCEE
T ss_conf             146-870-----47-88999862377344


No 22 
>PRK10693 response regulator of RpoS; Provisional
Probab=99.92  E-value=1.2e-24  Score=193.90  Aligned_cols=121  Identities=12%  Similarity=0.218  Sum_probs=110.5

Q ss_pred             CCCCEEEECCCHHHHHHHHHHHHHCCCEEEEECCH--HHHHHHCCCCCEEEEECCCCCCCHHHHHHHHHHHCCCCCEEEE
Q ss_conf             28838998699899999999999889889998937--9999860899899997854698889999999985789839999
Q gi|254780916|r    9 RHKRVLIIDKDDEQIKIIKDHVESYGYDVFIVNVS--DLSTISKIQVNVIFLSLINCEDDKENILKNIVDKIPIVPIIVQ   86 (482)
Q Consensus         9 ~~~rILIVDDd~~~~~~l~~~L~~~G~~v~~a~~~--al~~l~~~~~dlillD~~mP~~dGlell~~i~~~~p~ipvIii   86 (482)
                      ..+||||||||+.+|..++.+|++.||+|..|.++  |++.+.+..||+||+|++||+|||+++|+++|+..+++|||++
T Consensus         6 ~gkkILIVDDd~~~r~~l~~~L~~~G~~V~~A~nG~eAl~~l~~~~pDLIi~Dl~MP~mdGlell~~lr~~~~~~PVIvl   85 (337)
T PRK10693          6 VGKQILIVEDEPVFRSLLDSWFSSLGATTVLAADGVDALELLGGFTPDLMICDIAMPRMNGLKFVEHLRNRGDQTPVLVI   85 (337)
T ss_pred             CCCEEEEECCCHHHHHHHHHHHHHCCCEEEEECCHHHHHHHHHCCCCCEEEEECCCCCCCHHHHHHHHHHHCCCCEEEEE
T ss_conf             89989999499999999999999789999998999999999865899999996899999989999999985899649999


Q ss_pred             ECCCCHHHHHHHHHCCCCCCCCCCC-CCCCCCCCCCCCCCCCCC
Q ss_conf             2689999999888505743222222-222222222222222222
Q gi|254780916|r   87 TTQDNIKILNCFLYNRISKFFLNLV-SRKQLCDSIICALREGVV  129 (482)
Q Consensus        87 T~~~~~~~~~~a~~~g~~d~l~KP~-~~~~L~~~i~~al~~~~~  129 (482)
                      |++++.+.+++|++.||.||+.||+ +..+|.+++...++....
T Consensus        86 Ta~~~~~d~v~al~~GA~DyL~KPI~d~~~Lr~~v~a~l~~~~~  129 (337)
T PRK10693         86 SATENMADIAKALRLGVEDVLLKPVKDLNRLREAVFACLYPSMF  129 (337)
T ss_pred             ECCCCHHHHHHHHHCCCCEEEECCCCCHHHHHHHHHHHHHHHHH
T ss_conf             86899999999997499589978969999999999987517778


No 23 
>PRK10046 dpiA two-component response regulator DpiA; Provisional
Probab=99.91  E-value=7.4e-24  Score=188.26  Aligned_cols=121  Identities=9%  Similarity=0.198  Sum_probs=111.0

Q ss_pred             CCCCCCEEEECCCHHHHHHHHHHHHH-CCCE-EEEECC--HHHHHHHCCCCCEEEEECCCCCCCHHHHHHHHHHHCCCCC
Q ss_conf             35288389986998999999999998-8988-999893--7999986089989999785469888999999998578983
Q gi|254780916|r    7 LDRHKRVLIIDKDDEQIKIIKDHVES-YGYD-VFIVNV--SDLSTISKIQVNVIFLSLINCEDDKENILKNIVDKIPIVP   82 (482)
Q Consensus         7 m~~~~rILIVDDd~~~~~~l~~~L~~-~G~~-v~~a~~--~al~~l~~~~~dlillD~~mP~~dGlell~~i~~~~p~ip   82 (482)
                      |+.+.||||||||+.++.+++.+|+. .||. |.+|++  +|++.+++.+||+||+|++||++||+++++++++..+.+|
T Consensus         1 M~~~i~VLIVEDd~~v~~~l~~~L~~~~gf~~V~~A~~~~eA~~~l~~~~pDLvLLDi~LPd~~Glell~~lr~~~~~~~   80 (225)
T PRK10046          1 MTAPLTLLIVEDETPLAEMHAEYIRHIPGFSQILLAGNLAQARMMIERFKPGLILLDNYLPDGRGINLLHELVQAHYPGD   80 (225)
T ss_pred             CCCCCEEEEEECCHHHHHHHHHHHHHCCCCEEEEEECCHHHHHHHHHHCCCCEEEEECCCCCCCHHHHHHHHHHHCCCCC
T ss_conf             99988699995989999999999972899549999899999999997359999998289899979999999996487998


Q ss_pred             EEEEECCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             999926899999998885057432222222222222222222222
Q gi|254780916|r   83 IIVQTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALREG  127 (482)
Q Consensus        83 vIiiT~~~~~~~~~~a~~~g~~d~l~KP~~~~~L~~~i~~al~~~  127 (482)
                      ||++||+++.+.+++|++.|+.||+.|||+.++|.+++.+-.+..
T Consensus        81 VI~iTA~~d~~~~~~Al~~Ga~DYLvKPf~~erl~~~L~~y~~~~  125 (225)
T PRK10046         81 VVFTTAASDMETVSEAVRCGVFDYLIKPIAYERLGQTLTRFRQRK  125 (225)
T ss_pred             EEEEECCCCHHHHHHHHHCCCCCCEECCCCHHHHHHHHHHHHHHH
T ss_conf             899968999999999997499831028999999999999999999


No 24 
>PRK09468 ompR osmolarity response regulator; Provisional
Probab=99.91  E-value=1.1e-23  Score=187.16  Aligned_cols=122  Identities=15%  Similarity=0.193  Sum_probs=114.9

Q ss_pred             CCCCCCEEEECCCHHHHHHHHHHHHHCCCEEEEECCH--HHHHHHCCCCCEEEEECCCCCCCHHHHHHHHHHHCCCCCEE
Q ss_conf             3528838998699899999999999889889998937--99998608998999978546988899999999857898399
Q gi|254780916|r    7 LDRHKRVLIIDKDDEQIKIIKDHVESYGYDVFIVNVS--DLSTISKIQVNVIFLSLINCEDDKENILKNIVDKIPIVPII   84 (482)
Q Consensus         7 m~~~~rILIVDDd~~~~~~l~~~L~~~G~~v~~a~~~--al~~l~~~~~dlillD~~mP~~dGlell~~i~~~~p~ipvI   84 (482)
                      |+++.||||||||+.++..++..|+..||+|..+.++  +++.+....||+|++|++||++||+++|+++|+..+.+|||
T Consensus         2 m~~~~kILiVEDd~~~~~~l~~~L~~~g~~v~~a~~~~~a~~~~~~~~~DlvilDi~lp~~dG~~l~~~iR~~~~~~pII   81 (239)
T PRK09468          2 MQENYKILVVDDDMRLRALLERYLTEQGFQVRSAANAEQMDRLLTRESFHLMVLDLMLPGEDGLSICRRLRSQNNPTPII   81 (239)
T ss_pred             CCCCCEEEEEECCHHHHHHHHHHHHHCCCEEEEECCHHHHHHHHHHCCCCEEEECCCCCCCCCCHHHHHHHHHCCCCCEE
T ss_conf             99897899990999999999999998899999989999999999758998999878998888734677787505787789


Q ss_pred             EEECCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             99268999999988850574322222222222222222222222
Q gi|254780916|r   85 VQTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALREGV  128 (482)
Q Consensus        85 iiT~~~~~~~~~~a~~~g~~d~l~KP~~~~~L~~~i~~al~~~~  128 (482)
                      ++|++++.+..+.|+..||.||+.|||++.+|+.++...+++..
T Consensus        82 ~LTa~~~~~d~i~~l~~GADDYi~KPf~~~EL~aRI~allrR~~  125 (239)
T PRK09468         82 MLTAKGEEVDRIVGLEMGADDYLPKPFNPRELLARIRAVLRRQA  125 (239)
T ss_pred             EEECCCCHHHHHHHHHCCCCEEEECCCCHHHHHHHHHHHHHHCC
T ss_conf             99466787899999976986885589998999999999986323


No 25 
>PRK11083 DNA-binding response regulator CreB; Provisional
Probab=99.90  E-value=3.7e-23  Score=183.27  Aligned_cols=121  Identities=12%  Similarity=0.156  Sum_probs=112.1

Q ss_pred             CCCCCCEEEECCCHHHHHHHHHHHHHCCCEEEEECCH--HHHHHHCCCCCEEEEECCCCCCCHHHHHHHHHHHCCCCCEE
Q ss_conf             3528838998699899999999999889889998937--99998608998999978546988899999999857898399
Q gi|254780916|r    7 LDRHKRVLIIDKDDEQIKIIKDHVESYGYDVFIVNVS--DLSTISKIQVNVIFLSLINCEDDKENILKNIVDKIPIVPII   84 (482)
Q Consensus         7 m~~~~rILIVDDd~~~~~~l~~~L~~~G~~v~~a~~~--al~~l~~~~~dlillD~~mP~~dGlell~~i~~~~p~ipvI   84 (482)
                      |.+ .||||||||+.++..+...|+..||+|..+.++  ++..+...+||+|++|++||++||+++|+++|+..+++|||
T Consensus         1 M~~-~kILiVEDd~~l~~~l~~~L~~~g~~v~~~~~~~~al~~~~~~~~DlvilDi~LP~~~G~~l~~~iR~~~~~~pII   79 (229)
T PRK11083          1 MQQ-PTILLVEDEQAIADTLVYALQSEGFTVEWFERGLPALDKLRQQPPDLVILDVGLPDISGFELCRQLRAFHPALPVI   79 (229)
T ss_pred             CCC-CEEEEEECCHHHHHHHHHHHHHCCCEEEEECCHHHHHHHHHHCCCCEEEECCCCCCCCHHHHHHHHHHHCCCCEEE
T ss_conf             999-9999996999999999999998899999989999999999718998999738899987688999999708997299


Q ss_pred             EEECCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             99268999999988850574322222222222222222222222
Q gi|254780916|r   85 VQTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALREGV  128 (482)
Q Consensus        85 iiT~~~~~~~~~~a~~~g~~d~l~KP~~~~~L~~~i~~al~~~~  128 (482)
                      ++|+.++.+....|...||.||+.|||++++|..++...+++..
T Consensus        80 ~lta~~~~~d~i~~l~~GADDYl~KPf~~~EL~aRi~a~lrR~~  123 (229)
T PRK11083         80 FLTARSDEVDRLVGLEIGADDYVAKPFSPREVAARVRTILRRVK  123 (229)
T ss_pred             EEECCCCHHHHHHHHHCCCCEEEECCCCHHHHHHHHHHHHHHHC
T ss_conf             98367898999999975998773087428999999999997643


No 26 
>PRK09581 pleD response regulator PleD; Reviewed
Probab=99.90  E-value=5.3e-23  Score=182.17  Aligned_cols=116  Identities=15%  Similarity=0.226  Sum_probs=106.5

Q ss_pred             CCCEEEECCCHHHHHHHHHHHHHCCCEEEEECCH--HHHHHHCCCCCEEEEECCCCCCCHHHHHHHHHHH--CCCCCEEE
Q ss_conf             8838998699899999999999889889998937--9999860899899997854698889999999985--78983999
Q gi|254780916|r   10 HKRVLIIDKDDEQIKIIKDHVESYGYDVFIVNVS--DLSTISKIQVNVIFLSLINCEDDKENILKNIVDK--IPIVPIIV   85 (482)
Q Consensus        10 ~~rILIVDDd~~~~~~l~~~L~~~G~~v~~a~~~--al~~l~~~~~dlillD~~mP~~dGlell~~i~~~--~p~ipvIi   85 (482)
                      +.|||||||++..+.+++..|+..||+|.+|.++  |++.+.+.+||+||+|++||+|||+++|+.+|+.  ..++|||+
T Consensus         2 ~~rILiVdD~~~~~~~l~~~L~~~~y~v~~a~~G~eAL~~~~~~~PDLILlDi~MP~mdG~ev~r~Lk~~~~~~~iPVIv   81 (457)
T PRK09581          2 TARILVVDDIPANVKLLEAKLLAEYYTVLTASSGAEAIEICEREQPDIILLDVMMPGMDGFEVCRRLKSDPATAHIPVVM   81 (457)
T ss_pred             CCCEEEECCCHHHHHHHHHHHHHCCCEEEEECCHHHHHHHHHHCCCCEEEEECCCCCCCHHHHHHHHHCCCCCCCCEEEE
T ss_conf             97199994989999999999987899999989999999999718999899928779999999999996598889984999


Q ss_pred             EECCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             9268999999988850574322222222222222222222
Q gi|254780916|r   86 QTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALR  125 (482)
Q Consensus        86 iT~~~~~~~~~~a~~~g~~d~l~KP~~~~~L~~~i~~al~  125 (482)
                      +||+++.+...+|+..||.||+.||++...|..++...++
T Consensus        82 lTa~~d~e~~~~al~~GA~DYL~KP~~~~~L~~ri~~l~r  121 (457)
T PRK09581         82 VTALDDPSDRVRGLEAGADDFLTKPINDVALFARVKSLTR  121 (457)
T ss_pred             EECCCCHHHHHHHHHCCCCEEEECCCCHHHHHHHHHHHHH
T ss_conf             9789999999999864887899899998999999999998


No 27 
>PRK09836 DNA-binding transcriptional activator CusR; Provisional
Probab=99.89  E-value=6.6e-23  Score=181.52  Aligned_cols=117  Identities=14%  Similarity=0.181  Sum_probs=110.8

Q ss_pred             CCEEEECCCHHHHHHHHHHHHHCCCEEEEECCH--HHHHHHCCCCCEEEEECCCCCCCHHHHHHHHHHHCCCCCEEEEEC
Q ss_conf             838998699899999999999889889998937--999986089989999785469888999999998578983999926
Q gi|254780916|r   11 KRVLIIDKDDEQIKIIKDHVESYGYDVFIVNVS--DLSTISKIQVNVIFLSLINCEDDKENILKNIVDKIPIVPIIVQTT   88 (482)
Q Consensus        11 ~rILIVDDd~~~~~~l~~~L~~~G~~v~~a~~~--al~~l~~~~~dlillD~~mP~~dGlell~~i~~~~p~ipvIiiT~   88 (482)
                      .||||||||+.++..++..|+..||+|..+.++  +++.+....||+|++|++||++||+++|+++|+..+++|||++|+
T Consensus         1 MkILiVEDd~~l~~~l~~~L~~~G~~v~~a~~g~~a~~~~~~~~~DlvilDi~lP~~~G~~l~~~iR~~~~~~PII~Lta   80 (226)
T PRK09836          1 MKLLIVEDEKKTGEYLTKGLTEAGFVVDLADNGLNGYHLAMTGDYDLIILDIMLPDVNGWDIVRMLRSANKGMPILLLTA   80 (226)
T ss_pred             CEEEEEECCHHHHHHHHHHHHHCCCEEEEECCHHHHHHHHHHCCCCEEEECCCCCCCCCCCHHHHHHHHCCCCEEEEEEC
T ss_conf             98999939999999999999878999999899999999985189999998899999987204356776167960999944


Q ss_pred             CCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             899999998885057432222222222222222222222
Q gi|254780916|r   89 QDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALREG  127 (482)
Q Consensus        89 ~~~~~~~~~a~~~g~~d~l~KP~~~~~L~~~i~~al~~~  127 (482)
                      .++.+....|+..||.||+.|||++++|..++...+++.
T Consensus        81 ~~~~~d~i~~l~~GADDYl~KPf~~~EL~aRi~allrr~  119 (226)
T PRK09836         81 LGTIEHRVKGLELGADDYLVKPFAFAELLARVRTLLRRG  119 (226)
T ss_pred             CCCHHHHHHHHHCCCCEEEECCCCHHHHHHHHHHHHCCC
T ss_conf             589889999997699688636876799999999996626


No 28 
>PRK10161 transcriptional regulator PhoB; Provisional
Probab=99.89  E-value=1.1e-22  Score=179.98  Aligned_cols=118  Identities=14%  Similarity=0.195  Sum_probs=110.3

Q ss_pred             CCCEEEECCCHHHHHHHHHHHHHCCCEEEEECC--HHHHHHHCCCCCEEEEECCCCCCCHHHHHHHHHHH--CCCCCEEE
Q ss_conf             883899869989999999999988988999893--79999860899899997854698889999999985--78983999
Q gi|254780916|r   10 HKRVLIIDKDDEQIKIIKDHVESYGYDVFIVNV--SDLSTISKIQVNVIFLSLINCEDDKENILKNIVDK--IPIVPIIV   85 (482)
Q Consensus        10 ~~rILIVDDd~~~~~~l~~~L~~~G~~v~~a~~--~al~~l~~~~~dlillD~~mP~~dGlell~~i~~~--~p~ipvIi   85 (482)
                      ++||||||||+.++..++..|+..||+|..|.+  ++++.+.+..||+|++|++||++||+++|+++|+.  .+++|||+
T Consensus         2 ~~kILiVEDd~~l~~~l~~~L~~~g~~v~~a~~g~~a~~~l~~~~~DliilDi~lP~~dG~~~~~~ir~~~~~~~~PII~   81 (229)
T PRK10161          2 ARRILVVEDEAPIREMVCFVLEQNGFQPVEAEDYDSAVNQLNEPWPDLILLDWMLPGGSGIQFIKHLKRESMTRDIPVVM   81 (229)
T ss_pred             CCCEEEEECCHHHHHHHHHHHHHCCCEEEEECCHHHHHHHHHCCCCCEEEEECCCCCCCCHHHHHHHHHCCCCCCCCEEE
T ss_conf             97199995999999999999997799999989999999998528998999978998876335878877502468975899


Q ss_pred             EECCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             926899999998885057432222222222222222222222
Q gi|254780916|r   86 QTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALREG  127 (482)
Q Consensus        86 iT~~~~~~~~~~a~~~g~~d~l~KP~~~~~L~~~i~~al~~~  127 (482)
                      +|+.++.+..+.|...||.||+.|||++.+|++++...+++.
T Consensus        82 lta~~~~~d~v~gl~~GADDYl~KPf~~~EL~aRi~a~lrR~  123 (229)
T PRK10161         82 LTARGEEEDRVRGLETGADDYITKPFSPKELVARIKAVMRRI  123 (229)
T ss_pred             EECCCCHHHHHHHHHCCCCEEEECCCCHHHHHHHHHHHHHHC
T ss_conf             955666577999987698765208999899999999997123


No 29 
>PRK10336 DNA-binding transcriptional regulator QseB; Provisional
Probab=99.89  E-value=6.1e-23  Score=181.74  Aligned_cols=117  Identities=16%  Similarity=0.169  Sum_probs=110.6

Q ss_pred             CCEEEECCCHHHHHHHHHHHHHCCCEEEEECCH--HHHHHHCCCCCEEEEECCCCCCCHHHHHHHHHHHCCCCCEEEEEC
Q ss_conf             838998699899999999999889889998937--999986089989999785469888999999998578983999926
Q gi|254780916|r   11 KRVLIIDKDDEQIKIIKDHVESYGYDVFIVNVS--DLSTISKIQVNVIFLSLINCEDDKENILKNIVDKIPIVPIIVQTT   88 (482)
Q Consensus        11 ~rILIVDDd~~~~~~l~~~L~~~G~~v~~a~~~--al~~l~~~~~dlillD~~mP~~dGlell~~i~~~~p~ipvIiiT~   88 (482)
                      .||||||||+.++..++..|+..||+|..+.++  |++.+.+.+||+|++|++||++||+++|+++|+..+.+|||++|+
T Consensus         1 mkILlVEDd~~l~~~l~~~L~~~g~~V~~a~~g~~a~~~~~~~~~DlvilDi~lP~~dG~~l~~~iR~~~~~~PII~lta   80 (219)
T PRK10336          1 MRILLIEDDMLIGDGIKTGLSKMGFSVDWFTQGRQGKEALYSAPYDAVILDLTLPGMDGRDILREWREKGQREPVLILTA   80 (219)
T ss_pred             CEEEEEECCHHHHHHHHHHHHHCCCEEEEECCHHHHHHHHHCCCCCEEEEECCCCCCCCCCCCCCHHHHCCCCCEEEEEC
T ss_conf             98999938999999999999987999999899999999986289699999799999985631010465278887899806


Q ss_pred             CCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             899999998885057432222222222222222222222
Q gi|254780916|r   89 QDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALREG  127 (482)
Q Consensus        89 ~~~~~~~~~a~~~g~~d~l~KP~~~~~L~~~i~~al~~~  127 (482)
                      +++.+....|+..||.||+.|||++.+|..++...+++.
T Consensus        81 ~~~~~d~i~~l~~GAdDYl~KPf~~~eL~ari~allrr~  119 (219)
T PRK10336         81 RDALAERVEGLRLGADDYLCKPFALIEVAARLEALMRRT  119 (219)
T ss_pred             CCCHHHHHHHHHCCCCEEEECCCCHHHHHHHHHHHHHHC
T ss_conf             899999999997699888688976799999999996115


No 30 
>CHL00148 orf27 Ycf27; Reviewed
Probab=99.89  E-value=5.9e-23  Score=181.88  Aligned_cols=120  Identities=19%  Similarity=0.268  Sum_probs=111.5

Q ss_pred             CCCCCEEEECCCHHHHHHHHHHHHHCCCEEEEECCH--HHHHHHCCCCCEEEEECCCCCCCHHHHHHHHHHHCCCCCEEE
Q ss_conf             528838998699899999999999889889998937--999986089989999785469888999999998578983999
Q gi|254780916|r    8 DRHKRVLIIDKDDEQIKIIKDHVESYGYDVFIVNVS--DLSTISKIQVNVIFLSLINCEDDKENILKNIVDKIPIVPIIV   85 (482)
Q Consensus         8 ~~~~rILIVDDd~~~~~~l~~~L~~~G~~v~~a~~~--al~~l~~~~~dlillD~~mP~~dGlell~~i~~~~p~ipvIi   85 (482)
                      ++++||||||||+.++..++..|+..||+|..+.++  |+..+....||+|++|++||++||+++|+++|+. .++|||+
T Consensus         4 ~~k~kILiVEDd~~l~~~l~~~L~~~G~~v~~a~~g~~a~~~~~~~~~DlviLDi~LP~~dG~~l~~~iR~~-~~~PII~   82 (240)
T CHL00148          4 SSKEKILVVDDEASIRRILETRLSIIGYEVITASDGEEALKLFHQEQPDLVILDVMMPKLDGYGVCQEIRKE-SDVPIIM   82 (240)
T ss_pred             CCCCEEEEEECCHHHHHHHHHHHHHCCCEEEEECCHHHHHHHHHHCCCCEEEEECCCCCCCCCEEEECCCCC-CCCCEEE
T ss_conf             999829999398999999999999789999998999999999974799999997999988866305414037-9954899


Q ss_pred             EECCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             9268999999988850574322222222222222222222222
Q gi|254780916|r   86 QTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALREGV  128 (482)
Q Consensus        86 iT~~~~~~~~~~a~~~g~~d~l~KP~~~~~L~~~i~~al~~~~  128 (482)
                      +|+.++.+..+.|+..||.||++|||++++|++++...+++..
T Consensus        83 LTa~~~~~d~v~gl~~GADDYi~KPf~~~EL~aRi~allrr~~  125 (240)
T CHL00148         83 LTALGDVSDRITGLELGADDYVVKPFSPKELEARIRSVLRRVN  125 (240)
T ss_pred             EECCCCHHHHHHHHHCCCCEEEECCCCHHHHHHHHHHHHHHHC
T ss_conf             8167898999999976997895278447999999999986630


No 31 
>PRK10430 DNA-binding transcriptional activator DcuR; Provisional
Probab=99.88  E-value=2.6e-22  Score=177.32  Aligned_cols=116  Identities=13%  Similarity=0.190  Sum_probs=104.3

Q ss_pred             CCCEEEECCCHHHHHHHHHHHHH-CCCEEEE-ECC--HHHHHH--HCCCCCEEEEECCCCCCCHHHHHHHHHHHCCCCCE
Q ss_conf             88389986998999999999998-8988999-893--799998--60899899997854698889999999985789839
Q gi|254780916|r   10 HKRVLIIDKDDEQIKIIKDHVES-YGYDVFI-VNV--SDLSTI--SKIQVNVIFLSLINCEDDKENILKNIVDKIPIVPI   83 (482)
Q Consensus        10 ~~rILIVDDd~~~~~~l~~~L~~-~G~~v~~-a~~--~al~~l--~~~~~dlillD~~mP~~dGlell~~i~~~~p~ipv   83 (482)
                      +.||||||||+.++++++.+|++ .||+|.. |++  +|++.+  .+.+||+||+|++||++||+++++++|+..|++||
T Consensus         1 MirVLIVEDD~~v~~~~~~~l~~~~gf~vv~~a~t~~eA~~~l~~~~~~~DLILLDi~mPd~~Glell~~lR~~~~~~~V   80 (239)
T PRK10430          1 MINVLIVDDDAMVAELNRRYVAQIPGFQCCGTASTLEKAKEIIFNSDTPIDLILLDIYMQQENGLDLLPVLHEAGCKSDV   80 (239)
T ss_pred             CCEEEEEECCHHHHHHHHHHHHHCCCCEEEEEECCHHHHHHHHHCCCCCCCEEEECCCCCCCCHHHHHHHHHHHCCCCEE
T ss_conf             98799992989999999999851899089999899999999996579998589978999999789999999985899819


Q ss_pred             EEEECCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             999268999999988850574322222222222222222222
Q gi|254780916|r   84 IVQTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALR  125 (482)
Q Consensus        84 IiiT~~~~~~~~~~a~~~g~~d~l~KP~~~~~L~~~i~~al~  125 (482)
                      |++||+++.+++.+|++.|+.||+.|||..++|.+++.+-.+
T Consensus        81 I~ITa~~d~~~v~~Al~~Ga~DYLiKPf~~~rl~~~L~~y~~  122 (239)
T PRK10430         81 IVISSAADAATIKDSLHYGVVDYLIKPFQASRFEEALTGWRQ  122 (239)
T ss_pred             EEEEECCCHHHHHHHHHCCCHHHEECCCCHHHHHHHHHHHHH
T ss_conf             999726889999999983950304899999999999999999


No 32 
>pfam00072 Response_reg Response regulator receiver domain. This domain receives the signal from the sensor partner in bacterial two-component systems. It is usually found N-terminal to a DNA binding effector domain.
Probab=99.88  E-value=4.2e-22  Score=175.87  Aligned_cols=109  Identities=21%  Similarity=0.281  Sum_probs=104.0

Q ss_pred             EEEECCCHHHHHHHHHHHHHCCCEEEEECCH--HHHHHHCCCCCEEEEECCCCCCCHHHHHHHHHHHCCCCCEEEEECCC
Q ss_conf             8998699899999999999889889998937--99998608998999978546988899999999857898399992689
Q gi|254780916|r   13 VLIIDKDDEQIKIIKDHVESYGYDVFIVNVS--DLSTISKIQVNVIFLSLINCEDDKENILKNIVDKIPIVPIIVQTTQD   90 (482)
Q Consensus        13 ILIVDDd~~~~~~l~~~L~~~G~~v~~a~~~--al~~l~~~~~dlillD~~mP~~dGlell~~i~~~~p~ipvIiiT~~~   90 (482)
                      |||||||+.++..++.+|+..||+|.++.++  +++.+++.+||+|++|++||++||+++++++|+..|++|||++||++
T Consensus         1 ILvVDD~~~~~~~l~~~L~~~g~~v~~a~~g~~al~~~~~~~~dlvi~Di~mP~~dG~el~~~ir~~~~~~piI~~T~~~   80 (111)
T pfam00072         1 VLIVDDDPLIRELLRQLLEKEGYVVAEADDGEEALELLKEKRPDLILLDIRMPGMDGLELLRRIRRRPPTTPVIVLTAHG   80 (111)
T ss_pred             EEEEECCHHHHHHHHHHHHHCCCEEEEECCHHHHHHHHHHCCCCEEEEECCCCCCCHHHHHHHHHHCCCCCEEEEEECCC
T ss_conf             09998989999999999998899999989999999999847998999953689950157999997359998099997508


Q ss_pred             CHHHHHHHHHCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             9999998885057432222222222222222
Q gi|254780916|r   91 NIKILNCFLYNRISKFFLNLVSRKQLCDSII  121 (482)
Q Consensus        91 ~~~~~~~a~~~g~~d~l~KP~~~~~L~~~i~  121 (482)
                      +.+...+++..|+.+|+.||+++++|+++++
T Consensus        81 ~~~~~~~a~~~Ga~~yl~KP~~~~~L~~~ir  111 (111)
T pfam00072        81 DEEDAVEALKAGANDFLSKPFDPEELVAALR  111 (111)
T ss_pred             CHHHHHHHHHCCCCEEEECCCCHHHHHHHCC
T ss_conf             9999999997798779949999899998529


No 33 
>PRK10610 chemotaxis regulatory protein CheY; Provisional
Probab=99.88  E-value=4.6e-22  Score=175.58  Aligned_cols=121  Identities=12%  Similarity=0.186  Sum_probs=110.1

Q ss_pred             CC-CCCCEEEECCCHHHHHHHHHHHHHCCC-EEEEECCH--HHHHHHCCCCCEEEEECCCCCCCHHHHHHHHHHH--CCC
Q ss_conf             35-288389986998999999999998898-89998937--9999860899899997854698889999999985--789
Q gi|254780916|r    7 LD-RHKRVLIIDKDDEQIKIIKDHVESYGY-DVFIVNVS--DLSTISKIQVNVIFLSLINCEDDKENILKNIVDK--IPI   80 (482)
Q Consensus         7 m~-~~~rILIVDDd~~~~~~l~~~L~~~G~-~v~~a~~~--al~~l~~~~~dlillD~~mP~~dGlell~~i~~~--~p~   80 (482)
                      |+ ++.||||||||+.++.+++.+|+..|| .|.++.++  +++.+.+..||+|++|+.||+|||+++++++|+.  .+.
T Consensus         1 m~~k~lrILivDD~~~~r~~l~~~L~~~g~~~v~~a~~g~~al~~~~~~~~Dlil~D~~MP~~dG~el~~~ir~~~~~~~   80 (129)
T PRK10610          1 MADKELKFLVVDDFSTMRRIVRNLLKELGFNNVEEAEDGVDALNKLQAGGFGFVISDWNMPNMDGLELLKTIRADGAMSA   80 (129)
T ss_pred             CCCCCCEEEEEECCHHHHHHHHHHHHHCCCCEEEEECCHHHHHHHHHHCCCCEEEEECCCCCCCHHHHHHHHHHCCCCCC
T ss_conf             98999899999798999999999999869978999899999999998589999998189999989999999985777789


Q ss_pred             CCEEEEECCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             83999926899999998885057432222222222222222222222
Q gi|254780916|r   81 VPIIVQTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALREG  127 (482)
Q Consensus        81 ipvIiiT~~~~~~~~~~a~~~g~~d~l~KP~~~~~L~~~i~~al~~~  127 (482)
                      +|||++|++++.+...++...|+.+|+.|||+...|.+++.+.+++.
T Consensus        81 ~Pii~~T~~~~~~~~~~a~~~Ga~~yl~KP~~~~~L~~~i~~vl~r~  127 (129)
T PRK10610         81 LPVLMVTAEAKKENIIAAAQAGASGYVVKPFTAATLEEKLNKIFEKL  127 (129)
T ss_pred             CCEEEEECCCCHHHHHHHHHCCCCEEEECCCCHHHHHHHHHHHHHHC
T ss_conf             96899988689999999998699889989899999999999999763


No 34 
>PRK11517 transcriptional regulatory protein YedW; Provisional
Probab=99.88  E-value=5.7e-22  Score=174.92  Aligned_cols=116  Identities=18%  Similarity=0.226  Sum_probs=108.3

Q ss_pred             CCEEEECCCHHHHHHHHHHHHHCCCEEEEECCH--HHHHHHCCCCCEEEEECCCCCCCHHHHHHHHHHHCCCCCEEEEEC
Q ss_conf             838998699899999999999889889998937--999986089989999785469888999999998578983999926
Q gi|254780916|r   11 KRVLIIDKDDEQIKIIKDHVESYGYDVFIVNVS--DLSTISKIQVNVIFLSLINCEDDKENILKNIVDKIPIVPIIVQTT   88 (482)
Q Consensus        11 ~rILIVDDd~~~~~~l~~~L~~~G~~v~~a~~~--al~~l~~~~~dlillD~~mP~~dGlell~~i~~~~p~ipvIiiT~   88 (482)
                      .||||||||+.++..++..|+..||+|.+|.++  ++..+.+..||+|++|++||++||+++|+++|+. +++|||++||
T Consensus         1 MkILiVEDd~~l~~~l~~~L~~~g~~V~~a~~g~~al~~~~~~~~DlvilDi~lP~~dG~~l~~~iR~~-~~~pII~lta   79 (223)
T PRK11517          1 MKILLIEDNQRTQEWVTQGLSEAGYVIDAVSDGRDGLYLALKDDYALIILDIMLPGMDGWQILQTLRTA-KQTPVICLTA   79 (223)
T ss_pred             CEEEEEECCHHHHHHHHHHHHHCCCEEEEECCHHHHHHHHHCCCCCEEEECCCCCCCCHHHHHHHHHHC-CCCCEEEEEC
T ss_conf             989999698999999999999889999998999999999852899999984999873689999999856-8864899956


Q ss_pred             CCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             899999998885057432222222222222222222222
Q gi|254780916|r   89 QDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALREG  127 (482)
Q Consensus        89 ~~~~~~~~~a~~~g~~d~l~KP~~~~~L~~~i~~al~~~  127 (482)
                      .++.+..+.|+..||.||+.|||++++|++++...+++.
T Consensus        80 ~~~~~d~i~~l~~GADDYl~KPf~~~EL~aRi~a~lrr~  118 (223)
T PRK11517         80 RDSVDDRVRGLDSGANDYLVKPFSFSELLARVRAQLRQH  118 (223)
T ss_pred             CCCHHHHHHHHHCCCCEEEECCCCHHHHHHHHHHHHCCC
T ss_conf             556578999998398776208977899999999996414


No 35 
>PRK10529 DNA-binding transcriptional activator KdpE; Provisional
Probab=99.88  E-value=2.3e-22  Score=177.67  Aligned_cols=118  Identities=17%  Similarity=0.228  Sum_probs=109.1

Q ss_pred             CCCEEEECCCHHHHHHHHHHHHHCCCEEEEECCH--HHHHHHCCCCCEEEEECCCCCCCHHHHHHHHHHHCCCCCEEEEE
Q ss_conf             8838998699899999999999889889998937--99998608998999978546988899999999857898399992
Q gi|254780916|r   10 HKRVLIIDKDDEQIKIIKDHVESYGYDVFIVNVS--DLSTISKIQVNVIFLSLINCEDDKENILKNIVDKIPIVPIIVQT   87 (482)
Q Consensus        10 ~~rILIVDDd~~~~~~l~~~L~~~G~~v~~a~~~--al~~l~~~~~dlillD~~mP~~dGlell~~i~~~~p~ipvIiiT   87 (482)
                      +.+|||||||+.++..++..|+..||+|..+.++  ++..+....||+|++|++||++||+++|+++|+.. .+|||++|
T Consensus         1 M~~ILivEDd~~l~~~l~~~L~~~g~~V~~a~~~~~al~~~~~~~~DlviLDi~lP~~dG~~l~~~iR~~~-~~pII~lt   79 (225)
T PRK10529          1 MTNVLIVEDEQAIRRFLRTALEGDGMRVFEAETLQRGLLEAATRKPDLIILDLGLPDGDGIEFIRDLRQWS-AIPVIVLS   79 (225)
T ss_pred             CCEEEEEECCHHHHHHHHHHHHHCCCEEEEECCHHHHHHHHHHCCCCEEEEECCCCCCCCCCCEEEEECCC-CCCEEEEE
T ss_conf             99899997989999999999998899999979999999986117998999807888888763310001279-98789995


Q ss_pred             CCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             68999999988850574322222222222222222222222
Q gi|254780916|r   88 TQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALREGV  128 (482)
Q Consensus        88 ~~~~~~~~~~a~~~g~~d~l~KP~~~~~L~~~i~~al~~~~  128 (482)
                      +.++.+....|+..||.||+.|||++.+|+.++...+++..
T Consensus        80 a~~~~~d~i~~l~~GADDYl~KPf~~~eL~aRi~a~lrr~~  120 (225)
T PRK10529         80 ARSEESDKIAALDAGADDYLSKPFGIGELQARLRVALRRHS  120 (225)
T ss_pred             CCCCHHHHHHHHHCCCCEEEECCCCHHHHHHHHHHHHHHCC
T ss_conf             46898999999976987654078545999999999971403


No 36 
>PRK09390 fixJ response regulator FixJ; Provisional
Probab=99.87  E-value=1e-21  Score=173.12  Aligned_cols=118  Identities=15%  Similarity=0.205  Sum_probs=109.4

Q ss_pred             CCCCEEEECCCHHHHHHHHHHHHHCCCEEEEECCH--HHHHHHCCCCCEEEEECCCCCCCHHHHHHHHHHHCCCCCEEEE
Q ss_conf             28838998699899999999999889889998937--9999860899899997854698889999999985789839999
Q gi|254780916|r    9 RHKRVLIIDKDDEQIKIIKDHVESYGYDVFIVNVS--DLSTISKIQVNVIFLSLINCEDDKENILKNIVDKIPIVPIIVQ   86 (482)
Q Consensus         9 ~~~rILIVDDd~~~~~~l~~~L~~~G~~v~~a~~~--al~~l~~~~~dlillD~~mP~~dGlell~~i~~~~p~ipvIii   86 (482)
                      .+.+||||||++.+|..++.+|+..||.|..+.++  +++.+...+||+|++|+.||++||+++++++++..|.+|||++
T Consensus         2 ~k~tIliVDDh~~vr~gl~~lL~~~~~~v~~~~~~~~~l~~~~~~~pdlvllDi~mP~~~G~e~l~~l~~~~p~~~vivl   81 (202)
T PRK09390          2 TKGVVHVVDDDEAMRDSLAFLLDSAGFEVRLFESAQAFLDALPGLRFGCVVTDVRMPGIDGIELLRRLKARGSPLPVIVM   81 (202)
T ss_pred             CCCEEEEECCCHHHHHHHHHHHHHCCCEEEEECCHHHHHHHHHCCCCCEEEECCCCCCCCCHHHHHHHHHCCCCCCEEEE
T ss_conf             99979998499999999999999889989998999999999765797999877999998960799998722899867999


Q ss_pred             ECCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             2689999999888505743222222222222222222222
Q gi|254780916|r   87 TTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALRE  126 (482)
Q Consensus        87 T~~~~~~~~~~a~~~g~~d~l~KP~~~~~L~~~i~~al~~  126 (482)
                      |++++.+.+.++++.||.+|+.||++.++|+..+..+++.
T Consensus        82 T~~~~~~~~~~al~~GA~gyl~K~~~~~~L~~aI~~~l~~  121 (202)
T PRK09390         82 TGHGDVPLAVEAMKLGAIDFIEKPFEDERLIGAIERALAQ  121 (202)
T ss_pred             EECCCHHHHHHHHHCCCHHHCCCCCCHHHHHHHHHHHHHH
T ss_conf             7457488889999829464455999999999999999971


No 37 
>PRK10701 DNA-binding transcriptional regulator RstA; Provisional
Probab=99.87  E-value=2.2e-22  Score=177.77  Aligned_cols=119  Identities=18%  Similarity=0.173  Sum_probs=108.6

Q ss_pred             CCCEEEECCCHHHHHHHHHHHHHCCCEEEEECCH--HHHHHHCCCCCEEEEECCCCCCCHHHHHHHHHHHCCCCCEEEEE
Q ss_conf             8838998699899999999999889889998937--99998608998999978546988899999999857898399992
Q gi|254780916|r   10 HKRVLIIDKDDEQIKIIKDHVESYGYDVFIVNVS--DLSTISKIQVNVIFLSLINCEDDKENILKNIVDKIPIVPIIVQT   87 (482)
Q Consensus        10 ~~rILIVDDd~~~~~~l~~~L~~~G~~v~~a~~~--al~~l~~~~~dlillD~~mP~~dGlell~~i~~~~p~ipvIiiT   87 (482)
                      +.||||||||+.++..++..|+..||+|..+.++  +++.+.+..||+|++|++||++||+++|++||+.. +.|||++|
T Consensus         1 M~kILlVEDd~~l~~~l~~~L~~~g~~v~~a~~g~~a~~~~~~~~~DlvilDi~LP~~dG~~l~~~iR~~~-~~PiI~lt   79 (240)
T PRK10701          1 MNTIVFVEDDAEVGSLIAAYLAKHDIDVTVEPRGDRAEETILREQPDLVLLDIMLPGKDGMTICRDLRPKW-SGPIVLLT   79 (240)
T ss_pred             CCEEEEEECCHHHHHHHHHHHHHCCCEEEEECCHHHHHHHHHHCCCCEEEEECCCCCCCCCEEEEECCCCC-CCCEEEEE
T ss_conf             99899997999999999999988799999989999999998617999999928997678878763110258-98789994


Q ss_pred             CCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             689999999888505743222222222222222222222222
Q gi|254780916|r   88 TQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALREGVV  129 (482)
Q Consensus        88 ~~~~~~~~~~a~~~g~~d~l~KP~~~~~L~~~i~~al~~~~~  129 (482)
                      +.++....+.|+..||.||+.|||++.+|++++...+++...
T Consensus        80 a~~~~~d~v~gl~~GADDYl~KPf~~~eL~aRi~a~lrr~~~  121 (240)
T PRK10701         80 SLDSDMNHILALEMGACDYILKTTPPAVLLARLRLHLRQNEQ  121 (240)
T ss_pred             ECCCHHHHHHHHHCCCCEEEECCCCHHHHHHHHHHHHHHHCC
T ss_conf             057578899999768877641799879999999999965325


No 38 
>PRK11173 two-component response regulator; Provisional
Probab=99.87  E-value=1.5e-21  Score=171.95  Aligned_cols=120  Identities=15%  Similarity=0.169  Sum_probs=109.2

Q ss_pred             CCCCCCEEEECCCHHHHHHHHHHHHHCCCEEEEECCH--HHHHHHCCCCCEEEEECCCCCCCHHHHHHHHHHHCCCCCEE
Q ss_conf             3528838998699899999999999889889998937--99998608998999978546988899999999857898399
Q gi|254780916|r    7 LDRHKRVLIIDKDDEQIKIIKDHVESYGYDVFIVNVS--DLSTISKIQVNVIFLSLINCEDDKENILKNIVDKIPIVPII   84 (482)
Q Consensus         7 m~~~~rILIVDDd~~~~~~l~~~L~~~G~~v~~a~~~--al~~l~~~~~dlillD~~mP~~dGlell~~i~~~~p~ipvI   84 (482)
                      |++ .||||||||+.++..++..|+..||+|..+.++  +++.+....||+|++|++||++||+++++++|+.. .+|+|
T Consensus         1 m~~-~~ILiVEDD~~~~~~l~~~L~~~G~~V~~a~~~~ea~~~l~~~~~DlvilDi~lp~~~G~~l~~~iR~~~-~~piI   78 (237)
T PRK11173          1 MQT-PHILIVEDELVTRNTLKSIFEAEGYDVFEATDGAEMHQILSENDINLVIMDINLPGKNGLLLARELREQA-NVALM   78 (237)
T ss_pred             CCC-CEEEEEECCHHHHHHHHHHHHHCCCEEEEECCHHHHHHHHHCCCCCEEEEECCCCCCCCHHHHHHHHHCC-CCCEE
T ss_conf             999-9899995989999999999998899999989999999998638998999938999887303555665168-84789


Q ss_pred             EEECCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             99268999999988850574322222222222222222222222
Q gi|254780916|r   85 VQTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALREGV  128 (482)
Q Consensus        85 iiT~~~~~~~~~~a~~~g~~d~l~KP~~~~~L~~~i~~al~~~~  128 (482)
                      ++|++++.+....|...||.||+.|||+.++|..++...+++..
T Consensus        79 ~lta~~~~~~~i~~l~~GaddYi~KPf~~~EL~arv~~~l~r~~  122 (237)
T PRK11173         79 FLTGRDNEVDKILGLEIGADDYITKPFNPRELTIRARNLLSRTM  122 (237)
T ss_pred             EEECCCCHHHHHHHHHCCCCEEEECCCCHHHHHHHHHHHHHHHC
T ss_conf             99432577889999976976788789887999999999986641


No 39 
>PRK10643 DNA-binding transcriptional regulator BasR; Provisional
Probab=99.87  E-value=2.7e-21  Score=170.11  Aligned_cols=118  Identities=17%  Similarity=0.207  Sum_probs=110.7

Q ss_pred             CCEEEECCCHHHHHHHHHHHHHCCCEEEEECCH--HHHHHHCCCCCEEEEECCCCCCCHHHHHHHHHHHCCCCCEEEEEC
Q ss_conf             838998699899999999999889889998937--999986089989999785469888999999998578983999926
Q gi|254780916|r   11 KRVLIIDKDDEQIKIIKDHVESYGYDVFIVNVS--DLSTISKIQVNVIFLSLINCEDDKENILKNIVDKIPIVPIIVQTT   88 (482)
Q Consensus        11 ~rILIVDDd~~~~~~l~~~L~~~G~~v~~a~~~--al~~l~~~~~dlillD~~mP~~dGlell~~i~~~~p~ipvIiiT~   88 (482)
                      .||||||||+.++..++..|+..||.|..+.++  +++.+....||+|++|++||++||+++|+++|+..+.+|||++|+
T Consensus         1 mkILlVEDd~~~~~~l~~~L~~~g~~V~~a~~~~ea~~~~~~~~~DlvilDi~lp~~~G~~l~~~ir~~~~~~pII~lt~   80 (222)
T PRK10643          1 MKILIVEDDTLLLQGLILAAQTEGYACDGVSTAREAEQSLESGHYSLVVLDLGLPDEDGLHFLARIRQKKYTLPVLILTA   80 (222)
T ss_pred             CEEEEEECCHHHHHHHHHHHHHCCCEEEEECCHHHHHHHHHHCCCCEEEEECCCCCCCCHHHHHHHHHCCCCCCEEEEEC
T ss_conf             97999928899999999999978999999899999999997489989999688899862268999983489988999821


Q ss_pred             CCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             8999999988850574322222222222222222222222
Q gi|254780916|r   89 QDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALREGV  128 (482)
Q Consensus        89 ~~~~~~~~~a~~~g~~d~l~KP~~~~~L~~~i~~al~~~~  128 (482)
                      +++.+....|+..||.||+.||++.++|..++...+++..
T Consensus        81 ~~~~~~~~~~l~~GAddyi~KP~~~~eL~ari~~~lrr~~  120 (222)
T PRK10643         81 RDTLEDRIAGLDVGADDYLVKPFALEELHARIRALLRRHN  120 (222)
T ss_pred             CCCHHHHHHHHHCCCCEEEECCCCHHHHHHHHHHHHHHCC
T ss_conf             0367889999975997764388768999999999970323


No 40 
>cd00156 REC Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; contains a phosphoacceptor site that is phosphorylated by histidine kinase homologs; usually found N-terminal to a DNA binding effector domain; forms homodimers
Probab=99.86  E-value=2.1e-21  Score=170.90  Aligned_cols=111  Identities=22%  Similarity=0.293  Sum_probs=104.8

Q ss_pred             EEECCCHHHHHHHHHHHHHCCCEEEEECCH--HHHHHHCCCCCEEEEECCCCCCCHHHHHHHHHHHCCCCCEEEEECCCC
Q ss_conf             998699899999999999889889998937--999986089989999785469888999999998578983999926899
Q gi|254780916|r   14 LIIDKDDEQIKIIKDHVESYGYDVFIVNVS--DLSTISKIQVNVIFLSLINCEDDKENILKNIVDKIPIVPIIVQTTQDN   91 (482)
Q Consensus        14 LIVDDd~~~~~~l~~~L~~~G~~v~~a~~~--al~~l~~~~~dlillD~~mP~~dGlell~~i~~~~p~ipvIiiT~~~~   91 (482)
                      |||||++.++..++..|+..||+|.++.++  +++.+.+.+||+|++|+.||+|||+++++++|+..|.+|||++||+++
T Consensus         1 LvVDD~~~~~~~l~~~L~~~g~~v~~a~~g~~al~~~~~~~~dlvi~D~~mP~~~G~el~~~ir~~~~~~pvI~lT~~~~   80 (113)
T cd00156           1 LIVDDDPLIRELLRRLLEKEGYEVVEAEDGEEALALLAEEKPDLILLDIMMPGMDGLELLRRIRKRGPDIPIIFLTAHGD   80 (113)
T ss_pred             CEECCCHHHHHHHHHHHHHCCCEEEEECCHHHHHHHHHHCCCCEEEECCCCCCCCCHHHHHHHHHHCCCCCEEEEECCCC
T ss_conf             98927299999999999988999999899999999987579999997799989872699999998589995999978789


Q ss_pred             HHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             999998885057432222222222222222222
Q gi|254780916|r   92 IKILNCFLYNRISKFFLNLVSRKQLCDSIICAL  124 (482)
Q Consensus        92 ~~~~~~a~~~g~~d~l~KP~~~~~L~~~i~~al  124 (482)
                      .+.+.+++..|+.+|+.||++.++|..++.+.+
T Consensus        81 ~~~~~~a~~~Ga~~yl~KP~~~~~L~~~v~~~l  113 (113)
T cd00156          81 DEDAVEALKAGADDYLTKPFSPEELLARIRALL  113 (113)
T ss_pred             HHHHHHHHHCCCCEEEECCCCHHHHHHHHHHHC
T ss_conf             999999997689789969899999999999869


No 41 
>PRK10955 DNA-binding transcriptional regulator CpxR; Provisional
Probab=99.86  E-value=8.5e-22  Score=173.67  Aligned_cols=117  Identities=17%  Similarity=0.291  Sum_probs=107.0

Q ss_pred             CCCEEEECCCHHHHHHHHHHHHHCCCEEEEECCH--HHHHHHCCCCCEEEEECCCCCCCHHHHHHHHHHHCCCCCEEEEE
Q ss_conf             8838998699899999999999889889998937--99998608998999978546988899999999857898399992
Q gi|254780916|r   10 HKRVLIIDKDDEQIKIIKDHVESYGYDVFIVNVS--DLSTISKIQVNVIFLSLINCEDDKENILKNIVDKIPIVPIIVQT   87 (482)
Q Consensus        10 ~~rILIVDDd~~~~~~l~~~L~~~G~~v~~a~~~--al~~l~~~~~dlillD~~mP~~dGlell~~i~~~~p~ipvIiiT   87 (482)
                      +.||||||||+.++..++..|+..||+|..|.++  +++.+. .+||+|++|++||++||+++|+++|+. +++|||++|
T Consensus         1 M~kILlVEDd~~l~~~l~~~L~~~G~~V~~a~~g~~al~~l~-~~~DlvilDi~LP~~dG~~l~~~iR~~-~~~PII~lt   78 (232)
T PRK10955          1 MNKILLVDDDRELTSLLKELLEMEGFNVIVAHDGEQALDLLD-DSIDLLLLDVMMPKKNGIDTLKALRQT-HQTPVIMLT   78 (232)
T ss_pred             CCEEEEEECCHHHHHHHHHHHHHCCCEEEEECCHHHHHHHHH-CCCCEEEEECCCCCCCCCCCCCEEECC-CCCCEEEEE
T ss_conf             988999969899999999999888999999899999999964-898999991899988867230124407-888789980


Q ss_pred             CCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             68999999988850574322222222222222222222222
Q gi|254780916|r   88 TQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALREGV  128 (482)
Q Consensus        88 ~~~~~~~~~~a~~~g~~d~l~KP~~~~~L~~~i~~al~~~~  128 (482)
                      +.++.+..+.|+..||.||+.|||++++|.+++...+++..
T Consensus        79 a~~~~~d~i~~l~~GADDYl~KPf~~~eL~ari~allrR~~  119 (232)
T PRK10955         79 ARGSELDRVLGLELGADDYLPKPFNDRELVARIRAILRRSH  119 (232)
T ss_pred             CCCCHHHHHHHHHCCCCEEECCCCCHHHHHHHHHHHHCCCC
T ss_conf             55676889999976975763389998999999999976154


No 42 
>PRK10710 DNA-binding transcriptional regulator BaeR; Provisional
Probab=99.86  E-value=2.3e-21  Score=170.65  Aligned_cols=120  Identities=15%  Similarity=0.186  Sum_probs=111.1

Q ss_pred             CCCCCEEEECCCHHHHHHHHHHHHHCCCEEEEECC--HHHHHHHCCCCCEEEEECCCCCCCHHHHHHHHHHHCCCCCEEE
Q ss_conf             52883899869989999999999988988999893--7999986089989999785469888999999998578983999
Q gi|254780916|r    8 DRHKRVLIIDKDDEQIKIIKDHVESYGYDVFIVNV--SDLSTISKIQVNVIFLSLINCEDDKENILKNIVDKIPIVPIIV   85 (482)
Q Consensus         8 ~~~~rILIVDDd~~~~~~l~~~L~~~G~~v~~a~~--~al~~l~~~~~dlillD~~mP~~dGlell~~i~~~~p~ipvIi   85 (482)
                      ++..||||||||+.++..++..|+..||+|.+|.+  ++++.+....||+|++|+.||++||+++++++|+. +.+|||+
T Consensus         8 ~~~~kILlVEDd~~l~~~l~~~L~~~g~~V~~a~~~~eal~~~~~~~~DliilDi~lp~~~Gl~l~~~lr~~-~~~piI~   86 (240)
T PRK10710          8 ENTPRILIVEDEPKLGQLLIDYLRAASYAPTLISHGDEVLPYVRQTPPDLILLDLMLPGTDGLTLCREIRRF-SDIPIVM   86 (240)
T ss_pred             CCCCEEEEEECCHHHHHHHHHHHHHCCCEEEEECCHHHHHHHHHHCCCCEEEECCCCCCCCCCCCHHHHHCC-CCCCEEE
T ss_conf             998879999298999999999999889999998999999999973799899987999888776321122115-7646899


Q ss_pred             EECCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             9268999999988850574322222222222222222222222
Q gi|254780916|r   86 QTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALREGV  128 (482)
Q Consensus        86 iT~~~~~~~~~~a~~~g~~d~l~KP~~~~~L~~~i~~al~~~~  128 (482)
                      +|++++.+....|...||.||+.|||+.++|+.++...+++..
T Consensus        87 lta~~~~~~~~~al~~GAddYl~KPf~~~eLlari~~~lrr~~  129 (240)
T PRK10710         87 VTAKIEEIDRLLGLEIGADDYICKPYSPREVVARVKTILRRCK  129 (240)
T ss_pred             ECCCCCHHHHHHHHHCCCCEEECCCCCHHHHHHHHHHHHHHHC
T ss_conf             8167888999999986998760077653899999999984523


No 43 
>PRK10766 DNA-binding transcriptional regulator TorR; Provisional
Probab=99.86  E-value=1.7e-21  Score=171.62  Aligned_cols=119  Identities=13%  Similarity=0.107  Sum_probs=109.6

Q ss_pred             CCCEEEECCCHHHHHHHHHHHHHCCCEEEEECCH--HHHHHHCCCCCEEEEECCCCCCCHHHHHHHHHHHCCCCCEEEEE
Q ss_conf             8838998699899999999999889889998937--99998608998999978546988899999999857898399992
Q gi|254780916|r   10 HKRVLIIDKDDEQIKIIKDHVESYGYDVFIVNVS--DLSTISKIQVNVIFLSLINCEDDKENILKNIVDKIPIVPIIVQT   87 (482)
Q Consensus        10 ~~rILIVDDd~~~~~~l~~~L~~~G~~v~~a~~~--al~~l~~~~~dlillD~~mP~~dGlell~~i~~~~p~ipvIiiT   87 (482)
                      ++||||||||+.++..++..|+..||+|..|.++  ++..+.+..||+|++|+.||++||+++|+++|+.. ++|||++|
T Consensus         2 ~~kILlVEDD~~l~~~l~~~L~~~g~~V~~~~~~~~a~~~l~~~~~DlvilDi~lp~~~G~el~~~iR~~~-~~piI~lt   80 (224)
T PRK10766          2 SYHILVVEDEPVTRARLQGYFEQEGYRVSEAASGAGMREIMQNQHVDLILLDINLPGEDGLMLTRELRSRS-TVGIILVT   80 (224)
T ss_pred             CCEEEEECCCHHHHHHHHHHHHHCCCEEEEECCHHHHHHHHHHCCCCEEEECCCCCCCCCCCHHHHHHHCC-CCCEEEEC
T ss_conf             97199991999999999999998799999989999999999608999999889999887661376763047-85568633


Q ss_pred             CCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             689999999888505743222222222222222222222222
Q gi|254780916|r   88 TQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALREGVV  129 (482)
Q Consensus        88 ~~~~~~~~~~a~~~g~~d~l~KP~~~~~L~~~i~~al~~~~~  129 (482)
                      ++++.+....|...||.||+.|||+..+|+.++...+++...
T Consensus        81 a~~~~~~~i~al~~GaddYl~KPf~~~eL~ari~allrR~~~  122 (224)
T PRK10766         81 GRTDSIDRIVGLEMGADDYVTKPFELRELLVRVKNLLWRISL  122 (224)
T ss_pred             CCCCHHHHHHHHHCCCHHHHCCCCCHHHHHHHHHHHHHHHHH
T ss_conf             558989999999849414513999889999999999725244


No 44 
>PRK13557 histidine kinase; Provisional
Probab=99.86  E-value=6.1e-21  Score=167.61  Aligned_cols=118  Identities=14%  Similarity=0.235  Sum_probs=107.5

Q ss_pred             CCCCEEEECCCHHHHHHHHHHHHHCCCEEEEECCH--HHHHHHCC-CCCEEEEECCCC-CCCHHHHHHHHHHHCCCCCEE
Q ss_conf             28838998699899999999999889889998937--99998608-998999978546-988899999999857898399
Q gi|254780916|r    9 RHKRVLIIDKDDEQIKIIKDHVESYGYDVFIVNVS--DLSTISKI-QVNVIFLSLINC-EDDKENILKNIVDKIPIVPII   84 (482)
Q Consensus         9 ~~~rILIVDDd~~~~~~l~~~L~~~G~~v~~a~~~--al~~l~~~-~~dlillD~~mP-~~dGlell~~i~~~~p~ipvI   84 (482)
                      ...+||||||++.++.+++.+|+..||+|.+|.++  |++.+.+. +||+||+|+.|| +|||+++++++|+..|.+|||
T Consensus       412 ~~~~ILvVDD~~~~r~~~~~~L~~~G~~v~~a~~G~eAl~~l~~~~~~Dlvl~D~~MPg~mdG~el~r~ir~~~p~i~ii  491 (538)
T PRK13557        412 GTETILIVDDRPDVAELARMILEDFGYRTLVASNGREALEILESHPEVDLLFTDLIMPGGMNGVMLAREARRRQPKIKVL  491 (538)
T ss_pred             CCCEEEEECCCHHHHHHHHHHHHHCCCEEEEECCHHHHHHHHHHCCCCCEEEECCCCCCCCCHHHHHHHHHHHCCCCEEE
T ss_conf             87258996798999999999999769999998999999999960999889988777999988999999998538998399


Q ss_pred             EEECCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             992689999999888505743222222222222222222222
Q gi|254780916|r   85 VQTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALRE  126 (482)
Q Consensus        85 iiT~~~~~~~~~~a~~~g~~d~l~KP~~~~~L~~~i~~al~~  126 (482)
                      ++|||.........+..|.++|+.|||+..+|...|..++..
T Consensus       492 ~~Tg~~~~~~~~~~~~~~~~~~l~KP~~~~~L~~~i~~~L~~  533 (538)
T PRK13557        492 LTTGYAEASIERTDVGGSEFDIVNKPYRRAELARRVRMVLDG  533 (538)
T ss_pred             EEECCCCHHHHHHHHHCCCCCEECCCCCHHHHHHHHHHHHCC
T ss_conf             997998778899775289988881989999999999998678


No 45 
>PRK10816 DNA-binding transcriptional regulator PhoP; Provisional
Probab=99.86  E-value=2.8e-21  Score=170.02  Aligned_cols=117  Identities=12%  Similarity=0.138  Sum_probs=110.9

Q ss_pred             CCEEEECCCHHHHHHHHHHHHHCCCEEEEECCH--HHHHHHCCCCCEEEEECCCCCCCHHHHHHHHHHHCCCCCEEEEEC
Q ss_conf             838998699899999999999889889998937--999986089989999785469888999999998578983999926
Q gi|254780916|r   11 KRVLIIDKDDEQIKIIKDHVESYGYDVFIVNVS--DLSTISKIQVNVIFLSLINCEDDKENILKNIVDKIPIVPIIVQTT   88 (482)
Q Consensus        11 ~rILIVDDd~~~~~~l~~~L~~~G~~v~~a~~~--al~~l~~~~~dlillD~~mP~~dGlell~~i~~~~p~ipvIiiT~   88 (482)
                      .||||||||+.++..+...|+..||+|..|.++  +++.+.+..||+|++|+.||++||+++++++|+..+.+|||++|+
T Consensus         1 mkILivEdd~~~~~~l~~~L~~~g~~V~~a~~~~~al~~~~~~~~dlvilD~~lp~~~G~~l~~~ir~~~~~~piI~lta   80 (223)
T PRK10816          1 MRVLVVEDNALLRHHLKVQLQDAGHQVDAAEDAKEADYYLNEHLPDIAIVDLGLPDEDGLSLIRRWRSNDVSLPILVLTA   80 (223)
T ss_pred             CEEEEEECCHHHHHHHHHHHHHCCCEEEEECCHHHHHHHHHHCCCCEEEEECCCCCCCCCCCCCCHHCCCCCCCEEEEEC
T ss_conf             98999959899999999999978999999899999999997579989999799989886400120110489876899944


Q ss_pred             CCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             899999998885057432222222222222222222222
Q gi|254780916|r   89 QDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALREG  127 (482)
Q Consensus        89 ~~~~~~~~~a~~~g~~d~l~KP~~~~~L~~~i~~al~~~  127 (482)
                      +++.+...+|+..|+.||+.||++.++|..++...+++.
T Consensus        81 ~~~~~~~~~al~~Gaddyl~KP~~~~eL~arv~~~lrr~  119 (223)
T PRK10816         81 RESWQDKVEVLSAGADDYVTKPFHIEEVMARMQALMRRN  119 (223)
T ss_pred             CCCHHHHHHHHHCCCCEEECCCCCHHHHHHHHHHHHCCC
T ss_conf             456778999998699886418977789999999996655


No 46 
>COG0745 OmpR Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]
Probab=99.86  E-value=7.9e-21  Score=166.85  Aligned_cols=118  Identities=21%  Similarity=0.279  Sum_probs=108.8

Q ss_pred             CCEEEECCCHHHHHHHHHHHHHCCCEEEEECCH--HHHHHHCCCCCEEEEECCCCCCCHHHHHHHHHHH-CCCCCEEEEE
Q ss_conf             838998699899999999999889889998937--9999860899899997854698889999999985-7898399992
Q gi|254780916|r   11 KRVLIIDKDDEQIKIIKDHVESYGYDVFIVNVS--DLSTISKIQVNVIFLSLINCEDDKENILKNIVDK-IPIVPIIVQT   87 (482)
Q Consensus        11 ~rILIVDDd~~~~~~l~~~L~~~G~~v~~a~~~--al~~l~~~~~dlillD~~mP~~dGlell~~i~~~-~p~ipvIiiT   87 (482)
                      .+|||||||+.++..++.+|+..||+|..+.++  +++.+... ||+|++|++||++||+++|+++|+. ...+|||++|
T Consensus         1 ~~ILiveDd~~i~~~l~~~L~~~G~~v~~~~~~~~a~~~~~~~-~dlviLD~~lP~~dG~~~~~~iR~~~~~~~PIi~Lt   79 (229)
T COG0745           1 MRILLVEDDPELAELLKEYLEEEGYEVDVAADGEEALEAAREQ-PDLVLLDLMLPDLDGLELCRRLRAKKGSGPPIIVLT   79 (229)
T ss_pred             CEEEEEECCHHHHHHHHHHHHHCCCEEEEECCHHHHHHHHHCC-CCEEEEECCCCCCCHHHHHHHHHHCCCCCCCEEEEE
T ss_conf             9899991888999999999987597899978989999997269-999999889998568999999985168999889996


Q ss_pred             CCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             689999999888505743222222222222222222222222
Q gi|254780916|r   88 TQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALREGVV  129 (482)
Q Consensus        88 ~~~~~~~~~~a~~~g~~d~l~KP~~~~~L~~~i~~al~~~~~  129 (482)
                      +.++.+..+.++..||.||+.|||++.+|++++...+|+...
T Consensus        80 a~~~~~d~v~gl~~GADDYl~KPf~~~EL~ARi~a~lRR~~~  121 (229)
T COG0745          80 ARDDEEDRVLGLEAGADDYLTKPFSPRELLARLRALLRRNAG  121 (229)
T ss_pred             CCCCHHHHHHHHHCCCHHHCCCCCCHHHHHHHHHHHHCCCCC
T ss_conf             687288899999756342334889989999999999673656


No 47 
>COG4566 TtrR Response regulator [Signal transduction mechanisms]
Probab=99.85  E-value=2.9e-21  Score=169.91  Aligned_cols=126  Identities=16%  Similarity=0.187  Sum_probs=113.4

Q ss_pred             CCCCCCEEEECCCHHHHHHHHHHHHHCCCEEEEECCHH--HHHHHCCCCCEEEEECCCCCCCHHHHHHHHHHHCCCCCEE
Q ss_conf             35288389986998999999999998898899989379--9998608998999978546988899999999857898399
Q gi|254780916|r    7 LDRHKRVLIIDKDDEQIKIIKDHVESYGYDVFIVNVSD--LSTISKIQVNVIFLSLINCEDDKENILKNIVDKIPIVPII   84 (482)
Q Consensus         7 m~~~~rILIVDDd~~~~~~l~~~L~~~G~~v~~a~~~a--l~~l~~~~~dlillD~~mP~~dGlell~~i~~~~p~ipvI   84 (482)
                      |....-|-|||||..+|..+..+|+..||+|.+..+++  ++......|.++++|++||+++|+++...+.+..+.+|||
T Consensus         1 ~~~~~~V~vVDDD~~vr~al~~Ll~s~G~~v~~~~s~~~fL~~~~~~~pGclllDvrMPg~sGlelq~~L~~~~~~~PVI   80 (202)
T COG4566           1 MPREPLVHVVDDDESVRDALAFLLESAGFQVKCFASAEEFLAAAPLDRPGCLLLDVRMPGMSGLELQDRLAERGIRLPVI   80 (202)
T ss_pred             CCCCCEEEEECCCHHHHHHHHHHHHHCCCEEEEECCHHHHHHHCCCCCCCEEEEECCCCCCCHHHHHHHHHHCCCCCCEE
T ss_conf             99887689976848899999999983895366504799998306678897699855788885089999999539998879


Q ss_pred             EEECCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             992689999999888505743222222222222222222222222222
Q gi|254780916|r   85 VQTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALREGVVPSQ  132 (482)
Q Consensus        85 iiT~~~~~~~~~~a~~~g~~d~l~KP~~~~~L~~~i~~al~~~~~~~~  132 (482)
                      ++|||+|+.+++++++.||.||+.|||+...|++++.+|++.......
T Consensus        81 fiTGhgDIpmaV~AmK~GAvDFLeKP~~~q~Lldav~~Al~~~~~~~~  128 (202)
T COG4566          81 FLTGHGDIPMAVQAMKAGAVDFLEKPFSEQDLLDAVERALARDASRRA  128 (202)
T ss_pred             EEECCCCHHHHHHHHHCCHHHHHHCCCCHHHHHHHHHHHHHHHHHHHH
T ss_conf             982788728999999742156774788548999999999998888887


No 48 
>TIGR01387 cztR_silR_copR heavy metal response regulator; InterPro: IPR006291   Members of this family contain a response regulator receiver domain and an associated transcriptional regulatory region. This group is separated phylogenetically from related proteins with similar architecture and contains a number of proteins associated with heavy metal resistance efflux systems for copper, silver, cadmium, and/or zinc. Most members are encoded by genes adjacent to genes which code for a member of the heavy metal sensor histidine kinase family (IPR006290 from INTERPRO), its partner in the two-component response regulator system. ; GO: 0000156 two-component response regulator activity, 0003677 DNA binding, 0000160 two-component signal transduction system (phosphorelay), 0007600 sensory perception.
Probab=99.85  E-value=3.5e-22  Score=176.44  Aligned_cols=129  Identities=16%  Similarity=0.196  Sum_probs=116.9

Q ss_pred             EEEECCCHHHHHHHHHHHHHCCCEEEEECCH--HHHHHHCCCCCEEEEECCCCCCCHHHHHHHHHHHCCCCCEEEEECCC
Q ss_conf             8998699899999999999889889998937--99998608998999978546988899999999857898399992689
Q gi|254780916|r   13 VLIIDKDDEQIKIIKDHVESYGYDVFIVNVS--DLSTISKIQVNVIFLSLINCEDDKENILKNIVDKIPIVPIIVQTTQD   90 (482)
Q Consensus        13 ILIVDDd~~~~~~l~~~L~~~G~~v~~a~~~--al~~l~~~~~dlillD~~mP~~dGlell~~i~~~~p~ipvIiiT~~~   90 (482)
                      |||||||+.-.+.+++-|...||.|-+++++  ++.+..+.+||+||||+|+|+|||.++++.+|+.....||+++||.+
T Consensus         1 iLvvEDeqkT~~YlqqGLsE~GYvvD~~~nG~DGL~lA~~~~Y~liILDvmLPG~DGW~vl~~LR~~~~~~PVl~LTA~D   80 (219)
T TIGR01387         1 ILVVEDEQKTAEYLQQGLSESGYVVDIASNGRDGLHLAEKDDYDLIILDVMLPGMDGWQVLKALRRSGKETPVLFLTARD   80 (219)
T ss_pred             CEEEECCCCHHHHHHCCCCCCCEEEEEEECCCCHHHHCCCCCCEEEEEECCCCCCCHHHHHHHHHCCCCCCCEEEEECCC
T ss_conf             96763086026765305201234798877686247543688830899632588950689999984078987348883378


Q ss_pred             CHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             9999998885057432222222222222222222222222222211111111
Q gi|254780916|r   91 NIKILNCFLYNRISKFFLNLVSRKQLCDSIICALREGVVPSQENEHCALDSL  142 (482)
Q Consensus        91 ~~~~~~~a~~~g~~d~l~KP~~~~~L~~~i~~al~~~~~~~~~~~~~~~~~L  142 (482)
                      ++..-++|+..||.|||+|||+..+|+++|...+|++....+. +.....+|
T Consensus        81 ~v~DkvkGLd~GAdDYLvKPF~F~ELlARvR~~LR~~~~~~~~-evl~i~DL  131 (219)
T TIGR01387        81 SVADKVKGLDLGADDYLVKPFEFAELLARVRTLLRRSESLEST-EVLEIADL  131 (219)
T ss_pred             CCCCEEEEECCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCC-CEEEECCC
T ss_conf             8454353011478654137877603799999876775203767-62686055


No 49 
>PRK13856 two-component response regulator VirG; Provisional
Probab=99.85  E-value=1.2e-20  Score=165.65  Aligned_cols=118  Identities=23%  Similarity=0.215  Sum_probs=106.2

Q ss_pred             CCCEEEECCCHHHHHHHHHHHHHCCCEEEEECCH--HHHHHHCCCCCEEEEECCCCCCCHHHHHHHHHHHCCCCCEEEEE
Q ss_conf             8838998699899999999999889889998937--99998608998999978546988899999999857898399992
Q gi|254780916|r   10 HKRVLIIDKDDEQIKIIKDHVESYGYDVFIVNVS--DLSTISKIQVNVIFLSLINCEDDKENILKNIVDKIPIVPIIVQT   87 (482)
Q Consensus        10 ~~rILIVDDd~~~~~~l~~~L~~~G~~v~~a~~~--al~~l~~~~~dlillD~~mP~~dGlell~~i~~~~p~ipvIiiT   87 (482)
                      ++||||||||+.++..+...|+..||+|..+.++  +++.+....||+|++|++||++||+++|+++++.. .+|+|++|
T Consensus         1 M~~ILlVEDD~~l~~~l~~~L~~~g~~v~~a~~~~~~~~~l~~~~~DlvIlDi~lp~~~Gl~~~~~ir~~~-~~piiilt   79 (241)
T PRK13856          1 MKHVLVIDDDVAMRHLIVEYLTIHAFKVTAVADSQQFNRVLSSETVDVVVVDLNLGREDGLEIVRSLATKS-DVPIIIIS   79 (241)
T ss_pred             CCEEEEEECCHHHHHHHHHHHHHCCCEEEEECCHHHHHHHHHCCCCCEEEEECCCCCCCCHHHHHHHCCCC-CCCEEEEE
T ss_conf             99899996989999999999987799999989999999998659999999969998766134555640369-97369997


Q ss_pred             C-CCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             6-8999999988850574322222222222222222222222
Q gi|254780916|r   88 T-QDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALREGV  128 (482)
Q Consensus        88 ~-~~~~~~~~~a~~~g~~d~l~KP~~~~~L~~~i~~al~~~~  128 (482)
                      + ..+......|...||.||+.|||++++|+.++...+++..
T Consensus        80 ~~~~~~~d~i~~l~~GADDYl~KPf~~~EL~aRi~~~lrr~~  121 (241)
T PRK13856         80 GDRLEEADKVVALELGATDFIAKPFGTREFLARIRVALRVRP  121 (241)
T ss_pred             CCCCCHHHHHHHHHCCCCEEEECCCCHHHHHHHHHHHHHHCC
T ss_conf             267878999999876998899777677799999999987454


No 50 
>COG4753 Response regulator containing CheY-like receiver domain and AraC-type DNA-binding domain [Signal transduction mechanisms]
Probab=99.85  E-value=6.4e-21  Score=167.46  Aligned_cols=117  Identities=16%  Similarity=0.253  Sum_probs=106.3

Q ss_pred             CCCEEEECCCHHHHHHHHHHHH--HCCCEEE-EECC--HHHHHHHCCCCCEEEEECCCCCCCHHHHHHHHHHHCCCCCEE
Q ss_conf             8838998699899999999999--8898899-9893--799998608998999978546988899999999857898399
Q gi|254780916|r   10 HKRVLIIDKDDEQIKIIKDHVE--SYGYDVF-IVNV--SDLSTISKIQVNVIFLSLINCEDDKENILKNIVDKIPIVPII   84 (482)
Q Consensus        10 ~~rILIVDDd~~~~~~l~~~L~--~~G~~v~-~a~~--~al~~l~~~~~dlillD~~mP~~dGlell~~i~~~~p~ipvI   84 (482)
                      +.+|||||||+.+|+-|..++.  ..|++|. +|.+  +|++.+.+.+||+|++|+.||+|||+++++.+++..|++-+|
T Consensus         1 MykVlIVDDE~lIr~GLk~lI~w~~~g~eiVgtA~NG~eAleli~e~~pDiviTDI~MP~mdGLdLI~~ike~~p~~~~I   80 (475)
T COG4753           1 MYKVLIVDDEPLIREGLKSLIDWEALGIEVVGTAANGKEALELIQETQPDIVITDINMPGMDGLDLIKAIKEQSPDTEFI   80 (475)
T ss_pred             CEEEEEECCHHHHHHHHHHHCCHHHCCCEEEEECCCHHHHHHHHHHCCCCEEEEECCCCCCCHHHHHHHHHHHCCCCEEE
T ss_conf             91399966729999999984885636975787514579999998734997899815788875799999999749985399


Q ss_pred             EEECCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             992689999999888505743222222222222222222222
Q gi|254780916|r   85 VQTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALRE  126 (482)
Q Consensus        85 iiT~~~~~~~~~~a~~~g~~d~l~KP~~~~~L~~~i~~al~~  126 (482)
                      |+||+++.+.+..|++.|+.||+.||++..+|...+.+....
T Consensus        81 ILSGy~eFeYak~Am~lGV~dYLLKP~~k~eL~~~L~ki~~k  122 (475)
T COG4753          81 ILSGYDEFEYAKKAMKLGVKDYLLKPVDKAELEEALKKIIGK  122 (475)
T ss_pred             EEECCCHHHHHHHHHHCCCHHHEECCCCHHHHHHHHHHHHHH
T ss_conf             984642058999998618521220769899999999999999


No 51 
>PRK10841 hybrid sensory kinase in two-component regulatory system with RcsB and YojN; Provisional
Probab=99.85  E-value=2.2e-20  Score=163.74  Aligned_cols=116  Identities=16%  Similarity=0.184  Sum_probs=107.5

Q ss_pred             CCCCEEEECCCHHHHHHHHHHHHHCCCEEEEECCH--HHHHHHCCCCCEEEEECCCCCCCHHHHHHHHHHHCCCCCEEEE
Q ss_conf             28838998699899999999999889889998937--9999860899899997854698889999999985789839999
Q gi|254780916|r    9 RHKRVLIIDKDDEQIKIIKDHVESYGYDVFIVNVS--DLSTISKIQVNVIFLSLINCEDDKENILKNIVDKIPIVPIIVQ   86 (482)
Q Consensus         9 ~~~rILIVDDd~~~~~~l~~~L~~~G~~v~~a~~~--al~~l~~~~~dlillD~~mP~~dGlell~~i~~~~p~ipvIii   86 (482)
                      ...+||||||++..+.+++..|+..||+|.+|.++  |++.+.+.+||+||+|++||.|||+++.++||+....+|||.+
T Consensus       823 ~~lrILVVEDNpINq~VL~~~L~~LG~~V~~A~NG~EALe~l~~~~fDLILMDIqMPvMDGyEaTr~IRe~~~~iPIIAL  902 (947)
T PRK10841        823 DDMMILVVDDHPINRRLLADQLGSLGYQCKTANDGVDALNVLSKNHIDIVLSDVNMPNMDGYRLTQRIRQLGLTLPVIGV  902 (947)
T ss_pred             CCCEEEEECCCHHHHHHHHHHHHHCCCEEEEECCHHHHHHHHHCCCCCEEEECCCCCCCCHHHHHHHHHCCCCCCEEEEE
T ss_conf             89889999078999999999999769999998999999999756998989970888998099999999808984949999


Q ss_pred             ECCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             26899999998885057432222222222222222222
Q gi|254780916|r   87 TTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICAL  124 (482)
Q Consensus        87 T~~~~~~~~~~a~~~g~~d~l~KP~~~~~L~~~i~~al  124 (482)
                      ||+...+...++...|..+|+.||++.+.|.+.+..-.
T Consensus       903 TAnA~~edkerCleAGMDdyLsKPV~l~~L~~vL~~Y~  940 (947)
T PRK10841        903 TANALAEEKQRCLEAGMDSCLSKPVTLDVLKQTLTVYA  940 (947)
T ss_pred             ECCCCHHHHHHHHHCCCCEEEECCCCHHHHHHHHHHHH
T ss_conf             38999899999998799999979897999999999998


No 52 
>PRK11107 hybrid sensory histidine kinase BarA; Provisional
Probab=99.84  E-value=5.2e-20  Score=161.05  Aligned_cols=115  Identities=14%  Similarity=0.141  Sum_probs=105.3

Q ss_pred             CCCEEEECCCHHHHHHHHHHHHHCCCEEEEECCH--HHHHHHCCCCCEEEEECCCCCCCHHHHHHHHHHH--CCCCCEEE
Q ss_conf             8838998699899999999999889889998937--9999860899899997854698889999999985--78983999
Q gi|254780916|r   10 HKRVLIIDKDDEQIKIIKDHVESYGYDVFIVNVS--DLSTISKIQVNVIFLSLINCEDDKENILKNIVDK--IPIVPIIV   85 (482)
Q Consensus        10 ~~rILIVDDd~~~~~~l~~~L~~~G~~v~~a~~~--al~~l~~~~~dlillD~~mP~~dGlell~~i~~~--~p~ipvIi   85 (482)
                      +.|||+|||++..+.++..+|++.|++|.+|.++  |++.+.+.+||+||+|++||+|||++.++.||+.  ..++|||.
T Consensus       668 ~lrVLvVEDN~iN~~vi~~lL~~lG~~v~~A~nG~eAle~~~~~~fDLILMDiqMP~MDG~eATr~IR~~~~~~~~PIIA  747 (920)
T PRK11107        668 PLTVMAVDDNPANLKLIGALLEEQVEHVVLCDSGHQAVELAKQRPFDLIFMDIQMPGMDGIRACELIRQLPHNQNTPIIA  747 (920)
T ss_pred             CCEEEEECCCHHHHHHHHHHHHHCCCEEEEECCHHHHHHHHHCCCCCEEEECCCCCCCCHHHHHHHHHHCCCCCCCEEEE
T ss_conf             77499984889999999999998498899989999999997479997899889999998999999998186789895999


Q ss_pred             EECCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             926899999998885057432222222222222222222
Q gi|254780916|r   86 QTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICAL  124 (482)
Q Consensus        86 iT~~~~~~~~~~a~~~g~~d~l~KP~~~~~L~~~i~~al  124 (482)
                      +||+...+...+++..|..||+.||++...|...+.+-.
T Consensus       748 lTA~a~~~dre~cl~aGMddyLtKPI~~~~L~~~L~~~~  786 (920)
T PRK11107        748 VTAHAMAGERERLLGAGMDDYLAKPIDEAALKQVLLRWK  786 (920)
T ss_pred             EECCCCHHHHHHHHHCCCCEEECCCCCHHHHHHHHHHHC
T ss_conf             979989899999997799938728799999999999867


No 53 
>PRK09959 hybrid sensory histidine kinase in two-component regulatory system with EvgA; Provisional
Probab=99.84  E-value=5.8e-20  Score=160.74  Aligned_cols=116  Identities=15%  Similarity=0.143  Sum_probs=106.5

Q ss_pred             CCCCCCEEEECCCHHHHHHHHHHHHHCCCEEEEECCH--HHHHHHCCCCCEEEEECCCCCCCHHHHHHHHHHHCCCCCEE
Q ss_conf             3528838998699899999999999889889998937--99998608998999978546988899999999857898399
Q gi|254780916|r    7 LDRHKRVLIIDKDDEQIKIIKDHVESYGYDVFIVNVS--DLSTISKIQVNVIFLSLINCEDDKENILKNIVDKIPIVPII   84 (482)
Q Consensus         7 m~~~~rILIVDDd~~~~~~l~~~L~~~G~~v~~a~~~--al~~l~~~~~dlillD~~mP~~dGlell~~i~~~~p~ipvI   84 (482)
                      .....+||||||++..+.+++..|+..||+|.+|.++  |++.+.+..||+||+|++||+|||+|+.+.||+....+|||
T Consensus       955 ~~~~l~ILvVeDn~~Nr~ll~~~L~~lG~~v~~a~nG~eAl~~~~~~~fDlILmDi~MP~MDG~e~tr~IR~~~~~~PIi 1034 (1197)
T PRK09959        955 LPEKLSILIADDHPTNRLLLKRQLNLLGYDVDEATDGVQALHKVSMQHYDLLITDVNMPNMDGFELTRKLREQNSSLPIW 1034 (1197)
T ss_pred             CCCCCEEEEECCCHHHHHHHHHHHHHCCCEEEEECCHHHHHHHHHCCCCCEEEECCCCCCCCHHHHHHHHHCCCCCCCEE
T ss_conf             77898799979989999999999998399999989999999997669999999879789998999999996469869489


Q ss_pred             EEECCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             99268999999988850574322222222222222222
Q gi|254780916|r   85 VQTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIIC  122 (482)
Q Consensus        85 iiT~~~~~~~~~~a~~~g~~d~l~KP~~~~~L~~~i~~  122 (482)
                      -+||+...+...++...|..||+.||+..+.|...+.+
T Consensus      1035 alTA~a~~~~~~~cl~aGMdd~L~KPi~l~~L~~~L~~ 1072 (1197)
T PRK09959       1035 GLTANAQANEREKGLNCGMNLCLFKPLTLDVLKTHLSQ 1072 (1197)
T ss_pred             EEECCCCHHHHHHHHHCCCCEEEECCCCHHHHHHHHHH
T ss_conf             99799999999999976998345188989999999985


No 54 
>PRK00742 chemotaxis-specific methylesterase; Provisional
Probab=99.83  E-value=6.4e-19  Score=153.36  Aligned_cols=174  Identities=17%  Similarity=0.202  Sum_probs=120.7

Q ss_pred             CCCEEEECCCHHHHHHHHHHHHHC-CCEEE-EECC--HHHHHHHCCCCCEEEEECCCCCCCHHHHHHHHHHHCCCCCEEE
Q ss_conf             883899869989999999999988-98899-9893--7999986089989999785469888999999998578983999
Q gi|254780916|r   10 HKRVLIIDKDDEQIKIIKDHVESY-GYDVF-IVNV--SDLSTISKIQVNVIFLSLINCEDDKENILKNIVDKIPIVPIIV   85 (482)
Q Consensus        10 ~~rILIVDDd~~~~~~l~~~L~~~-G~~v~-~a~~--~al~~l~~~~~dlillD~~mP~~dGlell~~i~~~~p~ipvIi   85 (482)
                      +.|||||||++.+|..++.+|+.. ||+|. +|.+  ++++.+.+.+||+|++|+.||+|||++++++|++.+| +||||
T Consensus         2 kirVLIVDDs~~~R~~l~~~L~~~~~~eVv~~A~nG~eAl~~~~~~~pDvVllDi~MP~mdGie~l~~I~~~~p-~pVim   80 (345)
T PRK00742          2 KIRVLVVDDSAFMRRLLSEILNSDPDIEVVGTARDGLEAVEKIKKLNPDVITLDVEMPVMDGIEALRKIMALRP-TPVVM   80 (345)
T ss_pred             CCEEEEEECCHHHHHHHHHHHHHCCCEEEEEEECCHHHHHHHHHHCCCCEEEEECCCCCCCHHHHHHHHHHHCC-CCEEE
T ss_conf             82699992988999999999972899089999899999999988609999998378899987999999997589-87799


Q ss_pred             EECC--CCHHHHHHHHHCCCCCCCCCCCCC-----CC----CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             9268--999999988850574322222222-----22----222222222222222222211111111222222222222
Q gi|254780916|r   86 QTTQ--DNIKILNCFLYNRISKFFLNLVSR-----KQ----LCDSIICALREGVVPSQENEHCALDSLIAVSPAMIQVVD  154 (482)
Q Consensus        86 iT~~--~~~~~~~~a~~~g~~d~l~KP~~~-----~~----L~~~i~~al~~~~~~~~~~~~~~~~~LiG~S~~m~~v~~  154 (482)
                      +|+.  .+.+.+.+|+..||.||+.||...     ++    |+..+..+-+....... ...         ++.    ..
T Consensus        81 vSs~~~~~~~~~~~Al~~GA~D~i~KP~~~~~~~~~~~~~~L~~ki~~~~~~~~~~~~-~~~---------~~~----~~  146 (345)
T PRK00742         81 VSSLTERGAEITLEALELGAVDFVPKPFLGISEGMDAAAELLAEKVRAAARAARLAAA-APA---------AAP----AA  146 (345)
T ss_pred             EEECCCCCHHHHHHHHHCCCCEEEECCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCC-CCC---------CCC----CC
T ss_conf             9722555659999999759224895788876532999999999999998518655678-888---------888----88


Q ss_pred             CCCCCCCCCEEEEEECCCCCHHHHHHHHHHHCCCCCCCCCCCCC
Q ss_conf             22223443204887327774367999999842675433210123
Q gi|254780916|r  155 LARKAGDCAIPIMIQGEFGVGKKRLSRFIHESGKRAFFPFFIVN  198 (482)
Q Consensus       155 ~i~~~a~~~~~vli~Ge~GtGK~~~A~~iH~~s~r~~~~fi~v~  198 (482)
                      ....-......|...|-+=-|=..+.+.+-........|++.+.
T Consensus       147 ~~~~~~~~~~~vV~IGaStGGp~aL~~il~~Lp~~~p~pivivQ  190 (345)
T PRK00742        147 LKAAPSGSSEKLVAIGASTGGPEALQKVLTQLPANFPAPIVIVQ  190 (345)
T ss_pred             CCCCCCCCCCCEEEEEECCCCHHHHHHHHHHCCCCCCCCEEEEE
T ss_conf             87777788871899983756899999999858988997489996


No 55 
>PRK13435 response regulator; Provisional
Probab=99.82  E-value=8.4e-20  Score=159.60  Aligned_cols=117  Identities=15%  Similarity=0.131  Sum_probs=101.1

Q ss_pred             CCCEEEECCCHHHHHHHHHHHHHCCCEEE-EECC--HHHHHHHCCCCCEEEEECCCCC-CCHHHHHHHHHHHCCCCCEEE
Q ss_conf             88389986998999999999998898899-9893--7999986089989999785469-888999999998578983999
Q gi|254780916|r   10 HKRVLIIDKDDEQIKIIKDHVESYGYDVF-IVNV--SDLSTISKIQVNVIFLSLINCE-DDKENILKNIVDKIPIVPIIV   85 (482)
Q Consensus        10 ~~rILIVDDd~~~~~~l~~~L~~~G~~v~-~a~~--~al~~l~~~~~dlillD~~mP~-~dGlell~~i~~~~p~ipvIi   85 (482)
                      +.||||||||+.++..++..|+..||+|. +|++  ++++.+++.+||+|++|++||+ ++|+++++++++. +++|||+
T Consensus         1 ~mRILIVEDe~~i~~~l~~~L~~~G~~vv~~A~~~~eAl~~~~~~~PDlvllDi~LpdG~~G~e~~r~l~~~-~~ipvI~   79 (141)
T PRK13435          1 QLRVLIVEDEALIALELEKLLEEAGHQVVGIASTSEQALALGRRAQPDVALVDIRLADGPTGVEVARRLSID-GGVEVIF   79 (141)
T ss_pred             CCEEEEECCCHHHHHHHHHHHHHCCCEEEEEECCHHHHHHHHHCCCCCEEEECCCCCCCCCHHHHHHHHHHC-CCCCEEE
T ss_conf             978999899899999999999987997999759999999997659998999788789999899999999875-9983899


Q ss_pred             EECCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             926899999998885057432222222222222222222222222
Q gi|254780916|r   86 QTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALREGVVP  130 (482)
Q Consensus        86 iT~~~~~~~~~~a~~~g~~d~l~KP~~~~~L~~~i~~al~~~~~~  130 (482)
                      +||+.+.   ..++..|+.||+.|||++++|.+++.++++++...
T Consensus        80 lTa~~d~---~~~~~aGA~dyl~KPf~~~eL~~ai~~~~~rr~~~  121 (141)
T PRK13435         80 MTANPER---VGHDFAGALGVIAKPYSLRQVARALSYVAARRVDD  121 (141)
T ss_pred             EECCHHH---HHHHHCCCCCEEECCCCHHHHHHHHHHHHHHCCCC
T ss_conf             9777998---60134599858989999899999999999715689


No 56 
>PRK11466 hybrid sensory histidine kinase TorS; Provisional
Probab=99.82  E-value=3.1e-19  Score=155.59  Aligned_cols=117  Identities=15%  Similarity=0.153  Sum_probs=106.4

Q ss_pred             CCCCEEEECCCHHHHHHHHHHHHHCCCEEEEECCH--HHHHHHCC-CCCEEEEECCCCCCCHHHHHHHHHHHCCCCCEEE
Q ss_conf             28838998699899999999999889889998937--99998608-9989999785469888999999998578983999
Q gi|254780916|r    9 RHKRVLIIDKDDEQIKIIKDHVESYGYDVFIVNVS--DLSTISKI-QVNVIFLSLINCEDDKENILKNIVDKIPIVPIIV   85 (482)
Q Consensus         9 ~~~rILIVDDd~~~~~~l~~~L~~~G~~v~~a~~~--al~~l~~~-~~dlillD~~mP~~dGlell~~i~~~~p~ipvIi   85 (482)
                      ...|||||||++..+.+++.+|+..||+|.+|.++  |++.+.+. +||+|++|+.||+|||+++.++||+..|.+|||.
T Consensus       680 ~~lrVLvVEDn~~N~~v~~~~L~~lG~~v~~A~nG~eAle~l~~~~~fDlVLmDi~MP~mDG~eatr~iR~~~~~~pIIA  759 (912)
T PRK11466        680 DGLRLLLIEDNPLTQRITVEMLNTSGAQVVAVGNAAQALETLQNSEPFAAALVDFDLPDYDGITLARQLAQQYPSLVLIG  759 (912)
T ss_pred             CCCEEEEEECCHHHHHHHHHHHHHCCCEEEEECCHHHHHHHHHHCCCCCEEEECCCCCCCCHHHHHHHHHHCCCCCCEEE
T ss_conf             88869999487889999999999869989998999999999971899858987699999989999999986199997899


Q ss_pred             EECCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             9268999999988850574322222222222222222222
Q gi|254780916|r   86 QTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALR  125 (482)
Q Consensus        86 iT~~~~~~~~~~a~~~g~~d~l~KP~~~~~L~~~i~~al~  125 (482)
                      +||+...+....+...|..+|+.||++++.|...+.+.+.
T Consensus       760 lTA~a~~ed~~~~l~aGmd~~L~KPv~~~~L~~~l~~~l~  799 (912)
T PRK11466        760 FSAHVIDETLRQRTSSLFRGIIPKPVPREVLGQLLAHYLQ  799 (912)
T ss_pred             ECCCCCHHHHHHHHHCCCCCEECCCCCHHHHHHHHHHHHC
T ss_conf             7798788999999976998775498999999999999846


No 57 
>TIGR02902 spore_lonB ATP-dependent protease LonB; InterPro: IPR014251   This entry represents LonB, a paralog of the ATP-dependent protease La (LonA, IPR004815 from INTERPRO). LonB proteins are unassigned peptidases belonging to the MEROPS peptidase family S16 (lon protease family, clan SJ) and are found strictly, and almost universally, in endospore-forming bacteria. This protease was shown, in Bacillus subtilis, to be expressed specifically in the forespore during sporulation, under control of sigmaF . The lonB gene, despite being located immediately upstream of lonA, was shown to be monocistronic. LonB appears to be involved in the post-translation control of sigmaH, but lonB mutation did not produce an obvious sporulation defect under the conditions tested . Note that additional paralogs of LonA and LonB occur in the Clostridium lineage and these are excluded from this entry. .
Probab=99.81  E-value=9e-20  Score=159.37  Aligned_cols=242  Identities=22%  Similarity=0.285  Sum_probs=177.2

Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCCCHHHHHHHHHHH------CCCCCC-CCCC
Q ss_conf             222222222222111111112222222222222222344320488732777436799999984------267543-3210
Q gi|254780916|r  123 ALREGVVPSQENEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHE------SGKRAF-FPFF  195 (482)
Q Consensus       123 al~~~~~~~~~~~~~~~~~LiG~S~~m~~v~~~i~~~a~~~~~vli~Ge~GtGK~~~A~~iH~------~s~r~~-~~fi  195 (482)
                      +++-....++...-.+|+.+||+..-++.+...+|  .-..++|.|+|++|+||+..||..=+      .|++++ ..||
T Consensus        48 ~I~Lt~PL~Ek~RP~SF~EIiGQe~GI~ALKAALC--GPNPQHVIiYGPPGVGKTAAARLVLeeAKk~~~SPFke~A~FV  125 (532)
T TIGR02902        48 AIRLTEPLSEKTRPKSFDEIIGQEEGIKALKAALC--GPNPQHVIIYGPPGVGKTAAARLVLEEAKKNPASPFKEEAAFV  125 (532)
T ss_pred             EEECCCCCCCCCCCCCCCCCCCCHHHHHHHHHHCC--CCCCCEEEEECCCCCCHHHHHHHHHHHHHCCCCCCCCCCCEEE
T ss_conf             34167887746677763325673556899998606--8689638987886961789999999986508753789886689


Q ss_pred             CCCCCCC--CCCCCHHHHHCCC-C-CCCCC--------CCCCCCCCCCCCCCEEEECCCCHHHHHHHHHHHHHHHHHHCC
Q ss_conf             1234655--4210024331125-5-55322--------111001234466714751664200188999888877642001
Q gi|254780916|r  196 IVNCGMI--DQDKIEKFLFGDV-D-LQTKN--------SAQFLGKFIEANGGTIVLEEPDALPLAVQGRIYNFIETGKIE  263 (482)
Q Consensus       196 ~v~c~~~--~~~~~e~~lFG~~-~-~~~~~--------~~~~~g~~~~a~~Gtl~l~ei~~L~~~~Q~~Ll~~l~~~~~~  263 (482)
                      .||..++  |+-=.-.=|.|.+ | -+.||        ..-+.|..-+||||.||||||++|.|-.=.|||.+|||+++.
T Consensus       126 EiDATT~RFDERGIADPLIGSVHDPIYQGAGplG~AGIPQPK~GAVT~AHGGvLFIDEIGELHP~~MNKLLKVLEDRKVF  205 (532)
T TIGR02902       126 EIDATTARFDERGIADPLIGSVHDPIYQGAGPLGVAGIPQPKPGAVTKAHGGVLFIDEIGELHPVQMNKLLKVLEDRKVF  205 (532)
T ss_pred             EEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEECCCCCCCHHHHHHHHHHHHCCCCH
T ss_conf             85051036021466665677615853337654578855758777632025865512124665824353141133022200


Q ss_pred             C-----CCCCCC------------CCCCCEEEEECCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--HHHHH
Q ss_conf             1-----235532------------1234315652143321111112333799988654334467787744222--25566
Q gi|254780916|r  264 F-----FDSRGA------------IRLDVRLIFLTEKNLLPQVKSHVFRKDLYYRISVFLINISTLRSRSEDI--PWLVH  324 (482)
Q Consensus       264 ~-----~g~~~~------------~~~~~RiIa~t~~~L~~~~~~g~fr~dLy~rL~~~~i~iPpLReR~eDI--~~L~~  324 (482)
                      -     .-++..            .+.|||+|-||++++++.-                    |.||-|.=.|  ..|-.
T Consensus       206 LdSAYY~s~~pniP~hI~dIFqnGlPADFRLiGATTR~PeEIp--------------------PAlRSRC~EIFFR~L~~  265 (532)
T TIGR02902       206 LDSAYYSSEDPNIPSHIRDIFQNGLPADFRLIGATTRNPEEIP--------------------PALRSRCVEIFFRPLLK  265 (532)
T ss_pred             HHCCCCCCCCCCCCHHHHHHHCCCCCCCEECCCCCCCCCCCCC--------------------HHHHCCCEEEEECCCCH
T ss_conf             0012358777865427899720678734012133369877678--------------------34650522677168887


Q ss_pred             HHHHHHCCCCCCC-CCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHH---HHCCCCCCCHHHHHHHHCC
Q ss_conf             7776410112233-33211111000122338986899999999998---7438981068895454212
Q gi|254780916|r  325 FFLQSFCTKNAIK-QISISDKALSLLTKYPWIDNVQELKNILLRAV---IGLKDSHLTEDRFVLLLSR  388 (482)
Q Consensus       325 ~fl~~~~~~~~~~-~~~ls~~a~~~L~~y~WPGNvREL~n~i~r~~---i~~~~~~i~~~~~~~~l~~  388 (482)
                      .-+++.|++.-.+ -..++++|++++..|.-  |=||=-|+|+-|+   +....+.|...|+.-....
T Consensus       266 EEi~~iAk~AaeKIg~~l~~~Al~~I~~Ya~--nGREAvN~~QLAaG~a~~E~Rk~I~~~DieWV~~~  331 (532)
T TIGR02902       266 EEIKEIAKNAAEKIGLNLEKEALDLIAKYAS--NGREAVNLVQLAAGIALGENRKRILAEDIEWVIES  331 (532)
T ss_pred             HHHHHHHHHHHHHCCCCCCHHHHHHHHHHHC--CCCHHHHHHHHHHHHEECCCCCEECHHHHHHHHHH
T ss_conf             8999998765653046547547999998740--54067789999731401288761205464455530


No 58 
>PRK11091 aerobic respiration control sensor protein ArcB; Provisional
Probab=99.80  E-value=1.1e-18  Score=151.55  Aligned_cols=116  Identities=11%  Similarity=0.154  Sum_probs=102.6

Q ss_pred             CCCCEEEECCCHHHHHHHHHHHHHCCCEEEEECCH--HHHHHHCCCCCEEEEECCCCCCCHHHHHHHHHHHCC---CCCE
Q ss_conf             28838998699899999999999889889998937--999986089989999785469888999999998578---9839
Q gi|254780916|r    9 RHKRVLIIDKDDEQIKIIKDHVESYGYDVFIVNVS--DLSTISKIQVNVIFLSLINCEDDKENILKNIVDKIP---IVPI   83 (482)
Q Consensus         9 ~~~rILIVDDd~~~~~~l~~~L~~~G~~v~~a~~~--al~~l~~~~~dlillD~~mP~~dGlell~~i~~~~p---~ipv   83 (482)
                      ...|||||||++..+.+++.+|+..||+|.+|.++  |++.+.+.+||+||+|++||+|||+++.+.||+..+   .+||
T Consensus       524 ~~lrILvVEDn~iN~~V~~~~L~~lG~~v~~A~nG~eALe~~~~~~fDLILMDiqMP~MDG~Eatr~IR~~~~~~~~~PI  603 (779)
T PRK11091        524 PALNILLVEDIELNVIVARSLLEKLGNSVDVAMTGKDALEMFKPGEYDLVLLDIQLPDMTGLDVARELRERYGREDLPPL  603 (779)
T ss_pred             CCCEEEEECCCHHHHHHHHHHHHHCCCEEEEECCHHHHHHHHCCCCCCEEEEECCCCCCCHHHHHHHHHHCCCCCCCCCE
T ss_conf             88818998688999999999999759999998999999998506999989982899999789999999842576899927


Q ss_pred             EEEECCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             999268999999988850574322222222222222222222
Q gi|254780916|r   84 IVQTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALR  125 (482)
Q Consensus        84 IiiT~~~~~~~~~~a~~~g~~d~l~KP~~~~~L~~~i~~al~  125 (482)
                      |.+||+.- +...++...|..||+.||++...|...+.+...
T Consensus       604 IALTAna~-~d~~~~l~aGMdd~L~KPi~~~~L~~~l~~~~~  644 (779)
T PRK11091        604 VALTANVL-KDKQEYLDAGMDDVLSKPLSVPALTAMIKKFWD  644 (779)
T ss_pred             EEEECCCC-HHHHHHHHCCCCCEEECCCCHHHHHHHHHHHHC
T ss_conf             98818741-769999976998475188989999999999846


No 59 
>PRK12555 chemotaxis-specific methylesterase; Provisional
Probab=99.79  E-value=6.5e-18  Score=146.22  Aligned_cols=163  Identities=15%  Similarity=0.105  Sum_probs=115.2

Q ss_pred             CCCEEEECCCHHHHHHHHHHHHHC-CCEEE-EECC--HHHHHHHCCCCCEEEEECCCCCCCHHHHHHHHHHHCCCCCEEE
Q ss_conf             883899869989999999999988-98899-9893--7999986089989999785469888999999998578983999
Q gi|254780916|r   10 HKRVLIIDKDDEQIKIIKDHVESY-GYDVF-IVNV--SDLSTISKIQVNVIFLSLINCEDDKENILKNIVDKIPIVPIIV   85 (482)
Q Consensus        10 ~~rILIVDDd~~~~~~l~~~L~~~-G~~v~-~a~~--~al~~l~~~~~dlillD~~mP~~dGlell~~i~~~~p~ipvIi   85 (482)
                      +.|||||||++.+|..++.+|+.. |++|. +|.+  ++++.+.+.+||+|++|+.||+|||++++++|++..| +||||
T Consensus         1 PirVLIVDDs~~~R~~l~~~L~~~~~~eVv~~A~~g~eAl~~~~~~~pDvVllDi~MP~mdGie~l~~I~~~~p-~PVim   79 (340)
T PRK12555          1 PMNVGIVDDSALAREALRRIIARRPDHRVLGVATDGLQARDLCKAQPPDVVLLDLEMPRMDGLTFLRRIMRRRP-CPVLI   79 (340)
T ss_pred             CCEEEEEECCHHHHHHHHHHHHHCCCCEEEEEECCHHHHHHHHHHHCCCEEEEECCCCCCCHHHHHHHHHHHCC-CCEEE
T ss_conf             98899990988999999999960999489999899999999988619999997278899987999999998789-98699


Q ss_pred             EECC--CCHHHHHHHHHCCCCCCCCCCCCC-----CC----CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             9268--999999988850574322222222-----22----222222222222222222211111111222222222222
Q gi|254780916|r   86 QTTQ--DNIKILNCFLYNRISKFFLNLVSR-----KQ----LCDSIICALREGVVPSQENEHCALDSLIAVSPAMIQVVD  154 (482)
Q Consensus        86 iT~~--~~~~~~~~a~~~g~~d~l~KP~~~-----~~----L~~~i~~al~~~~~~~~~~~~~~~~~LiG~S~~m~~v~~  154 (482)
                      +|+.  .+.+...+++..||.||+.||-..     +.    |+..+..+-+.. .........       ..+.      
T Consensus        80 vSs~~~~~~~~~~~AL~~GA~D~i~KP~~~~~~~~~~~~~~L~~ki~~~~~~~-~~~~~~~~~-------~~~~------  145 (340)
T PRK12555         80 VSSLTEAGASITYEALGAGALDAVDKPKLGIGRGLDAYAQELLAKIDQAARAL-VRRLARAAA-------PAPA------  145 (340)
T ss_pred             EEECCCCCHHHHHHHHHCCHHHEEECCCCCCCCHHHHHHHHHHHHHHHHHHCC-CCCCCCCCC-------CCCC------
T ss_conf             85035657699999997797766847887755319999999999999986442-456788888-------8899------


Q ss_pred             CCCCCCCCCEEEEEECCCCCHHHHHHHHHHHCCC
Q ss_conf             2222344320488732777436799999984267
Q gi|254780916|r  155 LARKAGDCAIPIMIQGEFGVGKKRLSRFIHESGK  188 (482)
Q Consensus       155 ~i~~~a~~~~~vli~Ge~GtGK~~~A~~iH~~s~  188 (482)
                       ..........|...|-+--|=..+.+.+-....
T Consensus       146 -~~~~~~~~~~vv~IGaSTGGp~aL~~il~~LP~  178 (340)
T PRK12555        146 -APAPFRTTEKLVAIGASAGGTEALAALLRGLPA  178 (340)
T ss_pred             -CCCCCCCCCCEEEEEECCCCHHHHHHHHHHCCC
T ss_conf             -876557888789999688999999999986786


No 60 
>TIGR02903 spore_lon_C ATP-dependent protease, Lon family; InterPro: IPR014252   This entry shows some relation to the widely distributed ATP-dependent protease La, also called Lon or LonA (IPR004815 from INTERPRO), but is more closely related to LonB (IPR014251 from INTERPRO), a LonA paralog found only in endospore-forming bacteria. Proteins in this entry are unassigned peptidases belonging to the MEROPS peptidase family S16 (lon protease family, clan SJ). They are restricted to a subset of endospore-forming species, and probably participate in the program of endospore formation. We propose the designation LonC..
Probab=99.77  E-value=7.2e-19  Score=152.97  Aligned_cols=192  Identities=26%  Similarity=0.366  Sum_probs=141.6

Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCC-CCCEEEEEECCCCCHHHHHHHHHHHCCCCC-------CCCCCCCCCCCCCCC-
Q ss_conf             11111111222222222222222234-432048873277743679999998426754-------332101234655421-
Q gi|254780916|r  135 EHCALDSLIAVSPAMIQVVDLARKAG-DCAIPIMIQGEFGVGKKRLSRFIHESGKRA-------FFPFFIVNCGMIDQD-  205 (482)
Q Consensus       135 ~~~~~~~LiG~S~~m~~v~~~i~~~a-~~~~~vli~Ge~GtGK~~~A~~iH~~s~r~-------~~~fi~v~c~~~~~~-  205 (482)
                      ....|+.+||+.-+++.+..   ++| ...++|++.|++|+||+++||..=+..++.       +.|||.||.++|-=| 
T Consensus       150 RP~~f~EiVGQerAI~aLla---K~aSPfPQHiiLYGPPGVGKTTaARl~LEe~K~~~~tPF~~DA~FvEVDGtTLRWDP  226 (616)
T TIGR02903       150 RPRAFSEIVGQERAIKALLA---KLASPFPQHIILYGPPGVGKTTAARLALEEAKKLKNTPFAEDAPFVEVDGTTLRWDP  226 (616)
T ss_pred             CCCCCCCCCCHHHHHHHHHH---HHCCCCCCCEEEECCCCCCHHHHHHHHHHHCCCCCCCCCCCCCCEEEECCCCCCCCC
T ss_conf             87667643334689999997---631888660785573388478999998762136874476113785751576266774


Q ss_pred             -CCHHHHHCCC-C----------CCCCCCCCCCCCCCCCCCCEEEECCCCHHHHHHHHHHHHHHHHHHCCCC-------C
Q ss_conf             -0024331125-5----------5532211100123446671475166420018899988887764200112-------3
Q gi|254780916|r  206 -KIEKFLFGDV-D----------LQTKNSAQFLGKFIEANGGTIVLEEPDALPLAVQGRIYNFIETGKIEFF-------D  266 (482)
Q Consensus       206 -~~e~~lFG~~-~----------~~~~~~~~~~g~~~~a~~Gtl~l~ei~~L~~~~Q~~Ll~~l~~~~~~~~-------g  266 (482)
                       -+-.=|.|.. +          +.+|-..-+.|+.-.||||.||+|||++|.+-+|.|||.+|++++++.-       +
T Consensus       227 REvTNPLLGSVHDPIYQGa~RDLAE~GvPEPk~GLVT~AHGGvLFIDEIGELD~lLQnKLLKVLEDKrV~F~SsYYDpdD  306 (616)
T TIGR02903       227 REVTNPLLGSVHDPIYQGARRDLAETGVPEPKLGLVTDAHGGVLFIDEIGELDPLLQNKLLKVLEDKRVEFSSSYYDPDD  306 (616)
T ss_pred             CCCCCCCCCCCCCCCCCCCCHHHCCCCCCCCCCCCCCCCCCCEEEEECHHHHHHHHHHHHHHHHCCCEEEEEECCCCCCC
T ss_conf             10147767762576556764011047879898987100477567650211222787632444322643665321248753


Q ss_pred             CCCC----------CCCCCEEEEECCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHH----------HHHHHHHHHHH
Q ss_conf             5532----------123431565214332111111233379998865433446778774----------42222556677
Q gi|254780916|r  267 SRGA----------IRLDVRLIFLTEKNLLPQVKSHVFRKDLYYRISVFLINISTLRSR----------SEDIPWLVHFF  326 (482)
Q Consensus       267 ~~~~----------~~~~~RiIa~t~~~L~~~~~~g~fr~dLy~rL~~~~i~iPpLReR----------~eDI~~L~~~f  326 (482)
                      .|-|          =+.||=+|-||++++++                   |+ |.||-|          ++||..+    
T Consensus       307 ~NvPkYIK~lFe~GAPADFvLIGATTr~P~e-------------------IN-pALRSRCaEvfFePL~p~dI~~I----  362 (616)
T TIGR02903       307 ENVPKYIKKLFEEGAPADFVLIGATTRDPEE-------------------IN-PALRSRCAEVFFEPLTPEDIKEI----  362 (616)
T ss_pred             CCCCHHHHHHHCCCCCCCEEEECCCCCCHHH-------------------CC-HHHHCCCCEEECCCCCHHHHHHH----
T ss_conf             7865588885226888256872661588244-------------------05-12330143132179887899999----


Q ss_pred             HHHHCCCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             764101122333321111100012233898
Q gi|254780916|r  327 LQSFCTKNAIKQISISDKALSLLTKYPWID  356 (482)
Q Consensus       327 l~~~~~~~~~~~~~ls~~a~~~L~~y~WPG  356 (482)
                      +.+++++.|.   .+.++.-++...|-=-|
T Consensus       363 v~~AA~klnv---~L~~gV~e~Ia~YTieG  389 (616)
T TIGR02903       363 VLNAAEKLNV---KLAEGVEELIARYTIEG  389 (616)
T ss_pred             HHHHHHHCCC---CCCCCHHHHHHHCCCCC
T ss_conf             9998886177---00036487872147131


No 61 
>COG3437 Response regulator containing a CheY-like receiver domain and an HD-GYP domain [Transcription / Signal transduction mechanisms]
Probab=99.77  E-value=3.9e-18  Score=147.76  Aligned_cols=124  Identities=19%  Similarity=0.306  Sum_probs=109.5

Q ss_pred             CCCCCCCCCCCCEEEECCCHHHHHHHHHHHHHCCCEEEEECCH--HHHHHHCCCCCEEEEECCCCCCCHHHHHHHHHHHC
Q ss_conf             9486643528838998699899999999999889889998937--99998608998999978546988899999999857
Q gi|254780916|r    1 MPRKKSLDRHKRVLIIDKDDEQIKIIKDHVESYGYDVFIVNVS--DLSTISKIQVNVIFLSLINCEDDKENILKNIVDKI   78 (482)
Q Consensus         1 ~p~~~~m~~~~rILIVDDd~~~~~~l~~~L~~~G~~v~~a~~~--al~~l~~~~~dlillD~~mP~~dGlell~~i~~~~   78 (482)
                      |+.+..-.++.+||+|||++..+..++..|+..||+|.++.++  +++.....++|+|++|++||+|||.++|.+++...
T Consensus         5 ~~~~~~~~~~~~vl~vDD~~~~~~~~~~lL~~~~y~v~~ae~g~~a~kl~~~~~~dlvllD~~mp~mdg~ev~~~lk~~~   84 (360)
T COG3437           5 MQGKNEPDEKLTVLLVDDEPDNLEALRQLLRMIGYRVIEAENGEEALKLLQEEPPDLVLLDVRMPEMDGAEVLNKLKAMS   84 (360)
T ss_pred             CCCCCCCCCCCEEEEECCCHHHHHHHHHHHHHCCCCEEEECCCHHHHHHHCCCCCCEEEEECCCCCCCHHHHHHHHHHCC
T ss_conf             68888874201488965866689999999974264146414750778875116885677642577765999999987249


Q ss_pred             C---CCCEEEEECCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             8---983999926899999998885057432222222222222222222
Q gi|254780916|r   79 P---IVPIIVQTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICAL  124 (482)
Q Consensus        79 p---~ipvIiiT~~~~~~~~~~a~~~g~~d~l~KP~~~~~L~~~i~~al  124 (482)
                      |   .+|||++|++++.+..+++...|+.+|+.||+++..|..++..-+
T Consensus        85 p~t~~ip~i~lT~~~d~~~~~~~~~~g~~dyl~KP~~~~~l~~rv~~~~  133 (360)
T COG3437          85 PSTRRIPVILLTAYADSEDRQRALEAGADDYLSKPISPKELVARVSSHL  133 (360)
T ss_pred             CCCCCCCEEEEEECCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHH
T ss_conf             7656532599860587699999997247777528898899999999999


No 62 
>COG4565 CitB Response regulator of citrate/malate metabolism [Transcription / Signal transduction mechanisms]
Probab=99.76  E-value=4.5e-18  Score=147.36  Aligned_cols=116  Identities=16%  Similarity=0.249  Sum_probs=105.1

Q ss_pred             CEEEECCCHHHHHHHHHHHHHC-CCEEEE-ECC--HHHHHHHCCCCCEEEEECCCCCCCHHHHHHHHHHHCCCCCEEEEE
Q ss_conf             3899869989999999999988-988999-893--799998608998999978546988899999999857898399992
Q gi|254780916|r   12 RVLIIDKDDEQIKIIKDHVESY-GYDVFI-VNV--SDLSTISKIQVNVIFLSLINCEDDKENILKNIVDKIPIVPIIVQT   87 (482)
Q Consensus        12 rILIVDDd~~~~~~l~~~L~~~-G~~v~~-a~~--~al~~l~~~~~dlillD~~mP~~dGlell~~i~~~~p~ipvIiiT   87 (482)
                      +|||||||+.+.++.+.+++.. ||++.. |++  +|+..+....||+||+|+.||+.+|++++.++++.+..+-||++|
T Consensus         2 ~VLIiEDD~mVaeih~~yv~~~~gF~~vg~A~~~~ea~~~i~~~~pDLILLDiYmPd~~Gi~lL~~ir~~~~~~DVI~iT   81 (224)
T COG4565           2 NVLIIEDDPMVAEIHRRYVKQIPGFSVVGTAGTLEEAKMIIEEFKPDLILLDIYMPDGNGIELLPELRSQHYPVDVIVIT   81 (224)
T ss_pred             CEEEECCCHHHHHHHHHHHHHCCCCEEEEEECCHHHHHHHHHHHCCCEEEEEECCCCCCCHHHHHHHHHCCCCCCEEEEE
T ss_conf             28997086589999999997389953898606499999999840899799960267985077999998468997889995


Q ss_pred             CCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             6899999998885057432222222222222222222222
Q gi|254780916|r   88 TQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALREG  127 (482)
Q Consensus        88 ~~~~~~~~~~a~~~g~~d~l~KP~~~~~L~~~i~~al~~~  127 (482)
                      |-++.++...+++.|+.||+.|||..+++.+++.+-.+..
T Consensus        82 AA~d~~tI~~alr~Gv~DYLiKPf~~eRl~~aL~~y~~~r  121 (224)
T COG4565          82 AASDMETIKEALRYGVVDYLIKPFTFERLQQALTRYRQKR  121 (224)
T ss_pred             CCCHHHHHHHHHHCCCHHHEECCEEHHHHHHHHHHHHHHH
T ss_conf             3443789999996582322056340999999999999999


No 63 
>TIGR02875 spore_0_A sporulation transcription factor Spo0A; InterPro: IPR012052   Members of this group are response regulators/transcription factors that contain CheY-like receiver (phosphoacceptor) domain and a unique DNA-binding domain. Spo0A controls the entry of Bacillus subtilis into the developmental process of sporulation . Activation of the Spo0A transcription factor by phosphorylation serves as a developmental checkpoint and to integrate several physiological signals that control entry into the sporulation pathway. The signals are generated by conditions of nutrient deprivation, high cell density, the Krebs cycle, DNA replication, DNA damage, and some aspect of the chromosome partitioning machinery .  Activated Spo0A has multiple functions . It represses promoters (such as the abrB promoter) by binding to sites (0A boxes) downstream from the transcription start site. Spo0A also activates transcription from promoters used by two forms of RNA polymerase that differ by containing either the major sigma factor, sigma A (e.g. the spoIIE and spoIIG promoters) or the alternate sigma factor, sigma H (e.g. the spoIIA promoter). At promoters activated by Spo0A, the 0A boxes lie upstream of the transcription-initiation site.; GO: 0003677 DNA binding, 0005509 calcium ion binding, 0000160 two-component signal transduction system (phosphorelay), 0042173 regulation of sporulation, 0045449 regulation of transcription, 0050906 detection of stimulus during sensory perception.
Probab=99.74  E-value=1.2e-17  Score=144.24  Aligned_cols=117  Identities=17%  Similarity=0.168  Sum_probs=101.8

Q ss_pred             CCCEEEECCCHHHHHHHHHHHHH-CCCEEEEE-CC--HHHHHHHCCCCCEEEEECCCCCCCHHHHHHHHHHHCCC--CCE
Q ss_conf             88389986998999999999998-89889998-93--79999860899899997854698889999999985789--839
Q gi|254780916|r   10 HKRVLIIDKDDEQIKIIKDHVES-YGYDVFIV-NV--SDLSTISKIQVNVIFLSLINCEDDKENILKNIVDKIPI--VPI   83 (482)
Q Consensus        10 ~~rILIVDDd~~~~~~l~~~L~~-~G~~v~~a-~~--~al~~l~~~~~dlillD~~mP~~dGlell~~i~~~~p~--ipv   83 (482)
                      +-||+|+||+..+|.+|+.+|.. ..++|.-. .+  ++++++++.+||+|+||+.||.+||+-+|+++.+..-.  .-|
T Consensus         2 KIri~i~DDNkEFc~lL~eY~~~Q~D~EVvG~A~nG~~a~~~I~~q~PD~vvLDIIMPhLDGiGVLEKl~~~~~~~~P~v   81 (270)
T TIGR02875         2 KIRIVIADDNKEFCNLLKEYLAAQEDMEVVGVAHNGVDALELIKEQKPDVVVLDIIMPHLDGIGVLEKLNEIELKARPRV   81 (270)
T ss_pred             CEEEEEEECCHHHHHHHHHHHHCCCCEEEEEECCCHHHHHHHHHHCCCCEEEECCCCCCCCHHHHHHHHHHHHHHCCCCE
T ss_conf             62899982888999999999852898389974147689999996089989995150430005799999889887448958


Q ss_pred             EEEECCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             9992689999999888505743222222222222222222222
Q gi|254780916|r   84 IVQTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALRE  126 (482)
Q Consensus        84 IiiT~~~~~~~~~~a~~~g~~d~l~KP~~~~~L~~~i~~al~~  126 (482)
                      |++||.|....+++|+..||+.|+.||||.+-|..+|......
T Consensus        82 i~LsAfGQE~ITqrA~~LGADYYvlKPfDle~L~~RIRQl~~~  124 (270)
T TIGR02875        82 IMLSAFGQEKITQRAVALGADYYVLKPFDLEILAARIRQLAEG  124 (270)
T ss_pred             EEEECCCHHHHHHHHHHCCCCCEEECHHHHHHHHHHHHHHHCC
T ss_conf             8852237558999999728981566504178899999986246


No 64 
>PRK10403 transcriptional regulator NarP; Provisional
Probab=99.73  E-value=1.9e-17  Score=142.88  Aligned_cols=120  Identities=17%  Similarity=0.191  Sum_probs=106.7

Q ss_pred             CCCCCCEEEECCCHHHHHHHHHHHHH-CCCEEE-EECC--HHHHHHHCCCCCEEEEECCCCCCCHHHHHHHHHHHCCCCC
Q ss_conf             35288389986998999999999998-898899-9893--7999986089989999785469888999999998578983
Q gi|254780916|r    7 LDRHKRVLIIDKDDEQIKIIKDHVES-YGYDVF-IVNV--SDLSTISKIQVNVIFLSLINCEDDKENILKNIVDKIPIVP   82 (482)
Q Consensus         7 m~~~~rILIVDDd~~~~~~l~~~L~~-~G~~v~-~a~~--~al~~l~~~~~dlillD~~mP~~dGlell~~i~~~~p~ip   82 (482)
                      +.++.|||||||++.++..++.+|+. .+|+|. ++++  ++++.+.+.+||+|++|+.||+++|+++++.+++..|.++
T Consensus         3 ~~~pirIlIvDD~~l~r~gl~~~L~~~~~~~vv~~a~~~~~~~~~~~~~~pDlvllD~~lp~~~G~~~~~~l~~~~p~~~   82 (215)
T PRK10403          3 EATPFQVLIVDDHPLMRRGVRQLLELDPGFEVVAEAGDGASAIDLANRLDIDVILLDLNMKGMSGLDTLNALRRDGVTAQ   82 (215)
T ss_pred             CCCCCEEEEECCCHHHHHHHHHHHHHCCCEEEEEEECCHHHHHHHHHHCCCCEEEECCCCCCCCCCCHHHHHHHCCCCCC
T ss_conf             89975799983989999999999975899289999899999999986449989998089989987412335654188773


Q ss_pred             EEEEECCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             99992689999999888505743222222222222222222222
Q gi|254780916|r   83 IIVQTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALRE  126 (482)
Q Consensus        83 vIiiT~~~~~~~~~~a~~~g~~d~l~KP~~~~~L~~~i~~al~~  126 (482)
                      ||++|++++.+....++..|+.+|+.|+.++++|+..+......
T Consensus        83 iivlt~~~~~~~~~~al~~Ga~gyl~K~~~~~~l~~ai~~v~~G  126 (215)
T PRK10403         83 IIILTVSDASSDIFALIDAGADGYLLKDSDPEVLLEAIRAGAKG  126 (215)
T ss_pred             EEEEECCCCHHHHHHHHHCCCCEEEECCCCHHHHHHHHHHHHCC
T ss_conf             68863243236789987468766884899999999999999849


No 65 
>PRK10651 transcriptional regulator NarL; Provisional
Probab=99.72  E-value=1.6e-17  Score=143.56  Aligned_cols=121  Identities=13%  Similarity=0.101  Sum_probs=107.9

Q ss_pred             CCCCCCEEEECCCHHHHHHHHHHHHHC-CCEEE-EECC--HHHHHHHCCCCCEEEEECCCCCCCHHHHHHHHHHHCCCCC
Q ss_conf             352883899869989999999999988-98899-9893--7999986089989999785469888999999998578983
Q gi|254780916|r    7 LDRHKRVLIIDKDDEQIKIIKDHVESY-GYDVF-IVNV--SDLSTISKIQVNVIFLSLINCEDDKENILKNIVDKIPIVP   82 (482)
Q Consensus         7 m~~~~rILIVDDd~~~~~~l~~~L~~~-G~~v~-~a~~--~al~~l~~~~~dlillD~~mP~~dGlell~~i~~~~p~ip   82 (482)
                      ..++.|||||||++.++..++.+|+.. +++|. .+.+  ++++.+.+.+||+|++|+.||+++|+++++++++..|.++
T Consensus         3 ~~~pirVlIvDDh~l~r~gl~~~L~~~~~~~vv~~a~~~~ea~~~~~~~~pDlvllDl~lp~~~G~~~~~~l~~~~~~~~   82 (216)
T PRK10651          3 NQEPATILLIDDHPMLRTGVKQLISMAPDITVVGEASNGEQGIELAESLDPDLILLDLNMPGMNGLETLDKLREKSLSGR   82 (216)
T ss_pred             CCCCCEEEEECCCHHHHHHHHHHHHHCCCEEEEEEECCHHHHHHHHHHCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCC
T ss_conf             99997899983999999999999975899389999899999999987079999999599999888764232334578874


Q ss_pred             EEEEECCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             999926899999998885057432222222222222222222222
Q gi|254780916|r   83 IIVQTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALREG  127 (482)
Q Consensus        83 vIiiT~~~~~~~~~~a~~~g~~d~l~KP~~~~~L~~~i~~al~~~  127 (482)
                      ||++|++++.+....++..|+.+|+.|+...++|...+..+.+..
T Consensus        83 iivlt~~~~~~~~~~al~~Ga~gyl~K~~~~~~L~~ai~~v~~g~  127 (216)
T PRK10651         83 IVVFSVSNHEEDVVTALKRGADGYLLKDMEPEDLLKALHQAAAGE  127 (216)
T ss_pred             EEEEECCCCHHHHHHHHHCCCCEEEECCCCHHHHHHHHHHHHCCC
T ss_conf             676305541889999996698789837899999999999998599


No 66 
>PRK13837 two-component VirA-like sensor kinase; Provisional
Probab=99.72  E-value=1.1e-16  Score=137.63  Aligned_cols=120  Identities=17%  Similarity=0.262  Sum_probs=106.6

Q ss_pred             CCCCEEEECCCHHHHHHHHHHHHHCCCEEEEECCH--HHHHHHCC--CCCEEEEECCCCCCCHHHHHHHHHHHCCCCCEE
Q ss_conf             28838998699899999999999889889998937--99998608--998999978546988899999999857898399
Q gi|254780916|r    9 RHKRVLIIDKDDEQIKIIKDHVESYGYDVFIVNVS--DLSTISKI--QVNVIFLSLINCEDDKENILKNIVDKIPIVPII   84 (482)
Q Consensus         9 ~~~rILIVDDd~~~~~~l~~~L~~~G~~v~~a~~~--al~~l~~~--~~dlillD~~mP~~dGlell~~i~~~~p~ipvI   84 (482)
                      ...+||+||||+.++.+...+|+..||+|..+.++  |++++++.  .+|+|++| +||+|+|.++.+.++...|++|||
T Consensus       698 ~ge~ILvVdDe~~vr~~~~~~L~~lGY~v~~a~~~~~Al~~~~~~~~~~DLvltD-~~p~~~g~~~~~~l~~~~p~lpVi  776 (831)
T PRK13837        698 NGETVLLVEPDDALLERYEEKLAALGYEPVGFSTLSAAIAWISKDGKRFDLVLVD-QPSLGDSQLAIAALHAAAPTLPII  776 (831)
T ss_pred             CCCEEEEECCCHHHHHHHHHHHHHCCCEEEEECCHHHHHHHHHHCCCCCEEEEEC-CCCCCCHHHHHHHHHHHCCCCEEE
T ss_conf             9977999859889999999999967996888689999999998389985399988-999998799999998618997499


Q ss_pred             EEECCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             9926899999998885057432222222222222222222222222
Q gi|254780916|r   85 VQTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALREGVVP  130 (482)
Q Consensus        85 iiT~~~~~~~~~~a~~~g~~d~l~KP~~~~~L~~~i~~al~~~~~~  130 (482)
                      + ||+........+...+...|+.|||+...|...+..++...+..
T Consensus       777 l-sg~~~~~~~~~~~~~~~~~fL~KPfs~~~LA~avR~aL~~~r~~  821 (831)
T PRK13837        777 L-AGSSLKMAAREALATAIAEILPKPISSRTLAYALRTALATARAA  821 (831)
T ss_pred             E-ECCCCHHHHHCHHHCCCCEEEECCCCHHHHHHHHHHHHHCCCCC
T ss_conf             9-76881443311022266706509999999999999998488887


No 67 
>PRK09958 DNA-binding transcriptional activator EvgA; Provisional
Probab=99.71  E-value=5.7e-17  Score=139.57  Aligned_cols=116  Identities=10%  Similarity=0.121  Sum_probs=104.8

Q ss_pred             CCEEEECCCHHHHHHHHHHHHHCCCEEEE-ECC--HHHHHHHCCCCCEEEEECCCCCCCHHHHHHHHHHHCCCCCEEEEE
Q ss_conf             83899869989999999999988988999-893--799998608998999978546988899999999857898399992
Q gi|254780916|r   11 KRVLIIDKDDEQIKIIKDHVESYGYDVFI-VNV--SDLSTISKIQVNVIFLSLINCEDDKENILKNIVDKIPIVPIIVQT   87 (482)
Q Consensus        11 ~rILIVDDd~~~~~~l~~~L~~~G~~v~~-a~~--~al~~l~~~~~dlillD~~mP~~dGlell~~i~~~~p~ipvIiiT   87 (482)
                      .+||||||++.+|..++.+|+..+++|.. +.+  ++++.+...+||++++|+.||+++|+++++++++..|..+||++|
T Consensus         1 m~vlivDDh~lvr~gl~~ll~~~~~~vv~~~~~~~~~l~~~~~~~pDvvllDl~lp~~~G~~~~~~ir~~~~~~~viv~s   80 (204)
T PRK09958          1 MNAIIIDDHPLAIAAIRNLLIKNDIEILAELTEGGSAVQRVETLKPDIVIIDVDIPGVNGIQVLETLRKRQYSGIIIIVS   80 (204)
T ss_pred             CEEEEECCCHHHHHHHHHHHHHCCCEEEEEECCHHHHHHHHHHCCCCEEEEECCCCCCCCHHHHHHHHHHCCCEEEEEEE
T ss_conf             98999869899999999999868998999979999999998743979999958999998416788898727980599997


Q ss_pred             CCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             689999999888505743222222222222222222222
Q gi|254780916|r   88 TQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALRE  126 (482)
Q Consensus        88 ~~~~~~~~~~a~~~g~~d~l~KP~~~~~L~~~i~~al~~  126 (482)
                      ++++......++..|+..|+.|....+++..++..+...
T Consensus        81 ~~~~~~~~~~a~~~Ga~g~l~K~~~~~~l~~aI~~v~~G  119 (204)
T PRK09958         81 AKNDHFYGKHCADAGANGFVSKKEGMNNIIAAIEAAKNG  119 (204)
T ss_pred             CCCCCHHHHHHHHCCCCEEEECCCCHHHHHHHHHHHHCC
T ss_conf             246521144335268637997899999999999999779


No 68 
>COG3706 PleD Response regulator containing a CheY-like receiver domain and a GGDEF domain [Signal transduction mechanisms]
Probab=99.71  E-value=7.6e-17  Score=138.70  Aligned_cols=122  Identities=14%  Similarity=0.229  Sum_probs=110.3

Q ss_pred             CCCCEEEECCCHHHHHHHHHHHHHCCCEEEEECCH--HHHHHHCCCCCEEEEECCCCCCCHHHHHHHHHHHC--CCCCEE
Q ss_conf             28838998699899999999999889889998937--99998608998999978546988899999999857--898399
Q gi|254780916|r    9 RHKRVLIIDKDDEQIKIIKDHVESYGYDVFIVNVS--DLSTISKIQVNVIFLSLINCEDDKENILKNIVDKI--PIVPII   84 (482)
Q Consensus         9 ~~~rILIVDDd~~~~~~l~~~L~~~G~~v~~a~~~--al~~l~~~~~dlillD~~mP~~dGlell~~i~~~~--p~ipvI   84 (482)
                      ...+||||||+...+..+..+|+..||.|..+.++  |+..+.+.+||+|++|+.||++||+++|+.+|+..  ..+|+|
T Consensus       131 ~~~kILvvdD~~~~~~~l~~~L~~~g~~v~~a~~~~~Al~~~~e~~~dlil~d~~mp~~dg~el~~~lr~~~~t~~ipii  210 (435)
T COG3706         131 APKKILVVDDDATQRERLRRILQVEGFRVVEATDGEEALLQLAELPPDLVLLDANMPDMDGLELCTRLRQLERTRDIPII  210 (435)
T ss_pred             CCCEEEEECCCHHHHHHHHHHHHHCCCEEEEECCHHHHHHHHHCCCCCEEEEECCCCCCCHHHHHHHHHCCCCCCCCCEE
T ss_conf             67508997480779999999987536336651598999999746898589995578766789999997244444566389


Q ss_pred             EEECCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             9926899999998885057432222222222222222222222222
Q gi|254780916|r   85 VQTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALREGVVP  130 (482)
Q Consensus        85 iiT~~~~~~~~~~a~~~g~~d~l~KP~~~~~L~~~i~~al~~~~~~  130 (482)
                      ++|+.++.+....|...|+.||+.||++...+.+++.+.+++.+..
T Consensus       211 ~~~~~~d~~~~~~Af~~G~~Dyi~kPi~~~~l~~Rl~~~l~~~~~~  256 (435)
T COG3706         211 LLSSKDDDELVVRAFELGVNDYITKPIEEGELRARLRRQLRRKRYE  256 (435)
T ss_pred             EEECCCCHHHHHHHHHCCCCCEEECCCCHHHHHHHHHHHHHHHHHH
T ss_conf             9952663478999997688516734778799999999999854188


No 69 
>PRK09483 response regulator; Provisional
Probab=99.70  E-value=1.5e-16  Score=136.64  Aligned_cols=118  Identities=14%  Similarity=0.134  Sum_probs=106.3

Q ss_pred             CCCEEEECCCHHHHHHHHHHHHHC-CCEEEE-ECC--HHHHHHHCCCCCEEEEECCCCCCCHHHHHHHHHHHCCCCCEEE
Q ss_conf             883899869989999999999988-988999-893--7999986089989999785469888999999998578983999
Q gi|254780916|r   10 HKRVLIIDKDDEQIKIIKDHVESY-GYDVFI-VNV--SDLSTISKIQVNVIFLSLINCEDDKENILKNIVDKIPIVPIIV   85 (482)
Q Consensus        10 ~~rILIVDDd~~~~~~l~~~L~~~-G~~v~~-a~~--~al~~l~~~~~dlillD~~mP~~dGlell~~i~~~~p~ipvIi   85 (482)
                      +.|||||||++.+|..++.+|+.. |++|.. +++  ++++.+.+.+||++++|+.||+++|+++++++++..|.++||+
T Consensus         1 Mi~VlIvDDh~l~r~gl~~~L~~~~~~~vv~~a~~~~~~l~~~~~~~pDvvllDl~lp~~~Gl~~~~~i~~~~p~~~viv   80 (216)
T PRK09483          1 MINVLLVDDHELVRAGIRRILEDIKGIKVVGEASCGEDAVKWCRTNAVDVVLMDMNMPGIGGLEATRKILRSTPDVKIIM   80 (216)
T ss_pred             CCEEEEECCCHHHHHHHHHHHHHCCCCEEEEEECCHHHHHHHHHHCCCCEEEECCCCCCCCCHHHHHHHHHHCCCCCEEE
T ss_conf             95899984999999999999974899589999899999999998559999998688989875237788874089985786


Q ss_pred             EECCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             926899999998885057432222222222222222222222
Q gi|254780916|r   86 QTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALREG  127 (482)
Q Consensus        86 iT~~~~~~~~~~a~~~g~~d~l~KP~~~~~L~~~i~~al~~~  127 (482)
                      +|++++.+....+++.|+.+|+.|+...++|...+..+....
T Consensus        81 ls~~~~~~~~~~al~~Ga~gyl~K~~~~~~l~~ai~~v~~G~  122 (216)
T PRK09483         81 LTVHTENPLPAKVMQAGAAGYLSKGAAPQEVVSAIRSVHSGQ  122 (216)
T ss_pred             ECCCCCHHHHHHHHHCCCCEEEECCCCHHHHHHHHHHHHCCC
T ss_conf             305663288999997488789947999999999999998599


No 70 
>PRK09935 transcriptional regulator FimZ; Provisional
Probab=99.68  E-value=4.4e-16  Score=133.30  Aligned_cols=119  Identities=12%  Similarity=0.114  Sum_probs=106.7

Q ss_pred             CCCCEEEECCCHHHHHHHHHHHHHC-CCEEE-EECC--HHHHHHHCCCCCEEEEECCCCCCCHHHHHHHHHHHCCCCCEE
Q ss_conf             2883899869989999999999988-98899-9893--799998608998999978546988899999999857898399
Q gi|254780916|r    9 RHKRVLIIDKDDEQIKIIKDHVESY-GYDVF-IVNV--SDLSTISKIQVNVIFLSLINCEDDKENILKNIVDKIPIVPII   84 (482)
Q Consensus         9 ~~~rILIVDDd~~~~~~l~~~L~~~-G~~v~-~a~~--~al~~l~~~~~dlillD~~mP~~dGlell~~i~~~~p~ipvI   84 (482)
                      ++.|||||||++.+|..++.+|+.. +++|. .+++  ++++.+...+||+|++|+.||+++|+++++++++.+|.++||
T Consensus         2 ~p~~VlIvDDh~l~r~gl~~~l~~~~~~~vv~~a~~~~~~~~~l~~~~~DvvllD~~lp~~~g~~~i~~i~~~~p~~~il   81 (210)
T PRK09935          2 KPASVIIMDEHPIVRMSIEVLLQKNSNIQVVLKTDDSRITIDYLRTYPVDLVILDIELPGTDGFTLLKRIKQIQETVKVL   81 (210)
T ss_pred             CCCEEEEECCCHHHHHHHHHHHHCCCCEEEEEEECCHHHHHHHHHHCCCCEEEECCCCCCCCCCCHHHHHHHHCCCCCEE
T ss_conf             97889998596999999999996298928999989999999999747999999889999988640567898738997089


Q ss_pred             EEECCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             9926899999998885057432222222222222222222222
Q gi|254780916|r   85 VQTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALREG  127 (482)
Q Consensus        85 iiT~~~~~~~~~~a~~~g~~d~l~KP~~~~~L~~~i~~al~~~  127 (482)
                      ++|++++...+..+++.|+.+|+.|..+.++|..++..+.+..
T Consensus        82 vls~~~~~~~~~~a~~~Ga~g~l~K~~~~~~l~~ai~~v~~G~  124 (210)
T PRK09935         82 FLSSKSECFYAGRAIRAGANGFVSKRKDLNDIYNAVQMILSGY  124 (210)
T ss_pred             EEECCCCHHHHHHHHHCCCCEEEECCCCHHHHHHHHHHHHCCC
T ss_conf             9717672999999996687768867899999999999998599


No 71 
>COG3947 Response regulator containing CheY-like receiver and SARP domains [Signal transduction mechanisms]
Probab=99.67  E-value=2.7e-16  Score=134.84  Aligned_cols=123  Identities=17%  Similarity=0.259  Sum_probs=107.6

Q ss_pred             CCEEEECCCHHHHHHHHHHHHHCCCEEEEECC--HHHHHHHCCCCCEEEEECCCCCCCHHHHHHHHHHHCCCCCEEEEEC
Q ss_conf             83899869989999999999988988999893--7999986089989999785469888999999998578983999926
Q gi|254780916|r   11 KRVLIIDKDDEQIKIIKDHVESYGYDVFIVNV--SDLSTISKIQVNVIFLSLINCEDDKENILKNIVDKIPIVPIIVQTT   88 (482)
Q Consensus        11 ~rILIVDDd~~~~~~l~~~L~~~G~~v~~a~~--~al~~l~~~~~dlillD~~mP~~dGlell~~i~~~~p~ipvIiiT~   88 (482)
                      .||+|||||..+...+..+|.+.|..+.+++.  +++..+....||+|++|+.||+|+|+|++++++...+.+|+|++|+
T Consensus         1 ~~~iiVDdd~a~~~~l~~iLs~~~~~~~~~~~~~eal~~Le~~kpDLifldI~mp~~ngiefaeQvr~i~~~v~iifIss   80 (361)
T COG3947           1 PRIIIVDDDAAIVKLLSVILSRAGHEVRSCSHPVEALDLLEVFKPDLIFLDIVMPYMNGIEFAEQVRDIESAVPIIFISS   80 (361)
T ss_pred             CCEEEECCHHHHHHHHHHHHHHCCCHHHCCCCHHHHHHHHHHCCCCEEEEEEECCCCCHHHHHHHHHHHHCCCCEEEEEC
T ss_conf             92799846389999999999861102100688788999998438877999852378608789999987531486899963


Q ss_pred             CCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             89999999888505743222222222222222222222222222221
Q gi|254780916|r   89 QDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALREGVVPSQENE  135 (482)
Q Consensus        89 ~~~~~~~~~a~~~g~~d~l~KP~~~~~L~~~i~~al~~~~~~~~~~~  135 (482)
                      |+  +.+..+....+.||++||+.++.|-.++.++.+.....+++..
T Consensus        81 h~--eya~dsf~~n~~dYl~KPvt~ekLnraIdr~~k~ve~~~eee~  125 (361)
T COG3947          81 HA--EYADDSFGMNLDDYLPKPVTPEKLNRAIDRRLKRVELTAEEES  125 (361)
T ss_pred             CH--HHHHHHCCCCHHHHCCCCCCHHHHHHHHHHHHCCCCCCCHHCC
T ss_conf             05--6523203556675416888888999999987402444410013


No 72 
>COG2197 CitB Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]
Probab=99.65  E-value=2.1e-15  Score=128.52  Aligned_cols=117  Identities=20%  Similarity=0.217  Sum_probs=105.4

Q ss_pred             CCEEEECCCHHHHHHHHHHHHHCC-CEEEEE-CC--HHHHHHHCCCCCEEEEECCCCCCCHHHHHHHHHHHCCCCCEEEE
Q ss_conf             838998699899999999999889-889998-93--79999860899899997854698889999999985789839999
Q gi|254780916|r   11 KRVLIIDKDDEQIKIIKDHVESYG-YDVFIV-NV--SDLSTISKIQVNVIFLSLINCEDDKENILKNIVDKIPIVPIIVQ   86 (482)
Q Consensus        11 ~rILIVDDd~~~~~~l~~~L~~~G-~~v~~a-~~--~al~~l~~~~~dlillD~~mP~~dGlell~~i~~~~p~ipvIii   86 (482)
                      .+||||||.+.++..++.+|+..+ ++|... .+  ++++.+...+||+|++|+.||+++|+++++.+++.+|+++|+++
T Consensus         1 ~~vlivDDh~l~r~gl~~~L~~~~~~~vv~~a~~~~~~l~~~~~~~pdvvl~Dl~mP~~~G~e~~~~l~~~~p~~~vvvl   80 (211)
T COG2197           1 IKVLIVDDHPLVREGLRQLLELEPDLEVVGEASNGEEALDLARELKPDVVLLDLSMPGMDGLEALKQLRARGPDIKVVVL   80 (211)
T ss_pred             CEEEEECCCHHHHHHHHHHHHHCCCCEEEEEECCHHHHHHHHHCCCCCEEEEECCCCCCCHHHHHHHHHHHCCCCEEEEE
T ss_conf             94999809777999999999868996699982788999998513799889983788998759999999986899729999


Q ss_pred             ECCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             26899999998885057432222222222222222222222
Q gi|254780916|r   87 TTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALREG  127 (482)
Q Consensus        87 T~~~~~~~~~~a~~~g~~d~l~KP~~~~~L~~~i~~al~~~  127 (482)
                      |++++.+....++..|+..|+.|..+++.+..++..+....
T Consensus        81 t~~~~~~~v~~~l~~Ga~gyl~K~~~~~~l~~ai~~v~~G~  121 (211)
T COG2197          81 TAHDDPAYVIRALRAGADGYLLKDASPEELVEAIRAVAAGG  121 (211)
T ss_pred             ECCCCHHHHHHHHHCCCCEEEECCCCHHHHHHHHHHHHCCC
T ss_conf             67789899999997799699867999999999999997588


No 73 
>KOG0519 consensus
Probab=99.64  E-value=2e-15  Score=128.64  Aligned_cols=117  Identities=19%  Similarity=0.206  Sum_probs=103.5

Q ss_pred             CCCCCEEEECCCHHHHHHHHHHHHHCCCEEEEECC--HHHHHHH-CCCCCEEEEECCCCCCCHHHHHHHHHHHC-CCCCE
Q ss_conf             52883899869989999999999988988999893--7999986-08998999978546988899999999857-89839
Q gi|254780916|r    8 DRHKRVLIIDKDDEQIKIIKDHVESYGYDVFIVNV--SDLSTIS-KIQVNVIFLSLINCEDDKENILKNIVDKI-PIVPI   83 (482)
Q Consensus         8 ~~~~rILIVDDd~~~~~~l~~~L~~~G~~v~~a~~--~al~~l~-~~~~dlillD~~mP~~dGlell~~i~~~~-p~ipv   83 (482)
                      .+..|||+|||+...+.+....|+..|.+|.++.+  +++..+. ...||+||+|+.||.|||+++.++||+.. ..+||
T Consensus       664 l~g~~iLlvddn~vn~~Va~~~l~~~g~~v~~~~sg~e~l~~~~~~~~y~~ifmD~qMP~mDG~e~~~~irk~~~~~~pI  743 (786)
T KOG0519         664 LTGPKILLVDDNPVNRKVATGMLKKLGAEVTEVNSGQEALDKLKPPHSYDVIFMDLQMPEMDGYEATREIRKKERWHLPI  743 (786)
T ss_pred             HCCCCEEEECCCCCCHHHHHHHHHHHCCEEEECCCHHHHHHHCCCCCCCCEEEEECCCCCCCHHHHHHHHHHHHCCCCCE
T ss_conf             03676578558710199999899973964574288699998638998632799975775555499999998751678877


Q ss_pred             EEEECCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             99926899999998885057432222222222222222222
Q gi|254780916|r   84 IVQTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICAL  124 (482)
Q Consensus        84 IiiT~~~~~~~~~~a~~~g~~d~l~KP~~~~~L~~~i~~al  124 (482)
                      |.+||+.+..+..+++..|.+.|+.||+..+.+...+...+
T Consensus       744 vAlTa~~~~~~~~~c~~~Gmd~yl~KP~~~~~l~~~l~~~~  784 (786)
T KOG0519         744 VALTADADPSTEEECLEVGMDGYLSKPFTLEKLVKILREFL  784 (786)
T ss_pred             EEEECCCCHHHHHHHHHHCCCEEECCCCCHHHHHHHHHHHH
T ss_conf             99746875788999998287646746331899999999973


No 74 
>COG4567 Response regulator consisting of a CheY-like receiver domain and a Fis-type HTH domain [Signal transduction mechanisms / Transcription]
Probab=99.63  E-value=3.5e-15  Score=126.92  Aligned_cols=116  Identities=10%  Similarity=0.170  Sum_probs=105.2

Q ss_pred             CCCCCC-EEEECCCHHHHHHHHHHHHHCCCEEEEECC--HHHHHHHCCCCCEEEEECCCCCCCHHHHHHHHHHHCCCCCE
Q ss_conf             352883-899869989999999999988988999893--79999860899899997854698889999999985789839
Q gi|254780916|r    7 LDRHKR-VLIIDKDDEQIKIIKDHVESYGYDVFIVNV--SDLSTISKIQVNVIFLSLINCEDDKENILKNIVDKIPIVPI   83 (482)
Q Consensus         7 m~~~~r-ILIVDDd~~~~~~l~~~L~~~G~~v~~a~~--~al~~l~~~~~dlillD~~mP~~dGlell~~i~~~~p~ipv   83 (482)
                      |..+.+ .||||||..+.+.|++.+++.||.|.++.+  +++...+...|.-.++|+.|.+++|+++++.+++..++.-+
T Consensus         5 ~~~pd~~lllvdDD~~f~~~LaRa~e~RGf~v~~a~~~~eal~~art~~PayAvvDlkL~~gsGL~~i~~lr~~~~d~ri   84 (182)
T COG4567           5 MIGPDKSLLLVDDDTPFLRTLARAMERRGFAVVTAESVEEALAAARTAPPAYAVVDLKLGDGSGLAVIEALRERRADMRI   84 (182)
T ss_pred             CCCCCCEEEEECCCHHHHHHHHHHHHCCCCEEEEECCHHHHHHHHHCCCCCEEEEEEEECCCCCHHHHHHHHHCCCCCEE
T ss_conf             14887605896187699999999986068625761449999999851798528898640688746899999824976438


Q ss_pred             EEEECCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             999268999999988850574322222222222222222
Q gi|254780916|r   84 IVQTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIIC  122 (482)
Q Consensus        84 IiiT~~~~~~~~~~a~~~g~~d~l~KP~~~~~L~~~i~~  122 (482)
                      |++|||+++-+++++++.|+.+|+.||-+.+.+...+..
T Consensus        85 vvLTGy~sIATAV~AvKlGA~~YLaKPAdaDdi~aAl~~  123 (182)
T COG4567          85 VVLTGYASIATAVEAVKLGACDYLAKPADADDILAALLR  123 (182)
T ss_pred             EEEECCHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHH
T ss_conf             988451179999999986245540797776899999860


No 75 
>PRK10840 transcriptional regulator RcsB; Provisional
Probab=99.62  E-value=5.2e-15  Score=125.73  Aligned_cols=116  Identities=22%  Similarity=0.235  Sum_probs=102.8

Q ss_pred             CCCEEEECCCHHHHHHHHHHHHHC-CCEEEE-ECCH--HHHHHHCCCCCEEEEECCCCC---CCHHHHHHHHHHHCCCCC
Q ss_conf             883899869989999999999988-988999-8937--999986089989999785469---888999999998578983
Q gi|254780916|r   10 HKRVLIIDKDDEQIKIIKDHVESY-GYDVFI-VNVS--DLSTISKIQVNVIFLSLINCE---DDKENILKNIVDKIPIVP   82 (482)
Q Consensus        10 ~~rILIVDDd~~~~~~l~~~L~~~-G~~v~~-a~~~--al~~l~~~~~dlillD~~mP~---~dGlell~~i~~~~p~ip   82 (482)
                      +.||+||||.+.+|..++.+|+.. +++|.. ++++  +++.+.+.+||+|++|+.||+   +||+++++.+++.+|.++
T Consensus         3 ~irIlIvDDh~lvr~Gl~~~L~~~~~~~vvg~a~~~~~~~~~~~~~~pDvvllDl~mpg~~~~dGl~~~~~i~~~~p~~~   82 (216)
T PRK10840          3 NMNVIIADDHPIVLFGIRKSLEQIEWVNVVGEFEDSTALINNLPKLDAHVLITDLSMPGDKYGDGITLIKYIKRHFPSLS   82 (216)
T ss_pred             CCEEEEECCHHHHHHHHHHHHCCCCCCEEEEEECCHHHHHHHHHHCCCCEEEEECCCCCCCCCCHHHHHHHHHHHCCCCE
T ss_conf             88899988979999999999815999689998799999999986239898998267799988789999999998589980


Q ss_pred             EEEEECCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             9999268999999988850574322222222222222222222
Q gi|254780916|r   83 IIVQTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALR  125 (482)
Q Consensus        83 vIiiT~~~~~~~~~~a~~~g~~d~l~KP~~~~~L~~~i~~al~  125 (482)
                      ||++|++++.....++++.|+..|+.|-..+.+|..++....+
T Consensus        83 vivls~~~~~~~v~~al~~Ga~Gyl~K~~~~~~L~~AI~~v~~  125 (216)
T PRK10840         83 IIVLTMNNNPAILSAVLDLDIEGIVLKQGAPTDLPKALAALQK  125 (216)
T ss_pred             EEEEECCCCHHHHHHHHHCCCCEEEECCCCHHHHHHHHHHHHC
T ss_conf             8998477878999999858974899878999999999999987


No 76 
>PRK10360 DNA-binding transcriptional activator UhpA; Provisional
Probab=99.57  E-value=2.2e-14  Score=121.28  Aligned_cols=115  Identities=13%  Similarity=0.080  Sum_probs=100.3

Q ss_pred             CCCEEEECCCHHHHHHHHHHHHH-CCCEEE-EECCH--HHHHHHCCCCCEEEEECCCCCCCHHHHHHHHHHHCCCCCEEE
Q ss_conf             88389986998999999999998-898899-98937--999986089989999785469888999999998578983999
Q gi|254780916|r   10 HKRVLIIDKDDEQIKIIKDHVES-YGYDVF-IVNVS--DLSTISKIQVNVIFLSLINCEDDKENILKNIVDKIPIVPIIV   85 (482)
Q Consensus        10 ~~rILIVDDd~~~~~~l~~~L~~-~G~~v~-~a~~~--al~~l~~~~~dlillD~~mP~~dGlell~~i~~~~p~ipvIi   85 (482)
                      +.||+||||++.+|..++.+|+. .+++|. .++++  +++.+.+.+||+|++|+.||+++|+++++++++   .++||+
T Consensus         1 Mi~I~IvDDh~l~r~gl~~~l~~~~~~~vv~~~~~~~~~l~~~~~~~~dvvllD~~mp~~~g~~~~~~l~~---~~~viv   77 (196)
T PRK10360          1 MITVALIDDHLIVRSGFAQLLGLEPDLQVVAEFGSGREALAGLPGRGVQVCICDISMPDISGLELLSQLPK---GMATIM   77 (196)
T ss_pred             CEEEEEECCCHHHHHHHHHHHHCCCCEEEEEEECCHHHHHHHHHHCCCCEEEECCCCCCCCCHHHHHHHHC---CCCEEE
T ss_conf             91999987979999999999812999599999899999999887449999998788788620779999843---874899


Q ss_pred             EECCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             926899999998885057432222222222222222222222
Q gi|254780916|r   86 QTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALREG  127 (482)
Q Consensus        86 iT~~~~~~~~~~a~~~g~~d~l~KP~~~~~L~~~i~~al~~~  127 (482)
                      +|++++.+.+..+++.|+..|+.|...+++|...+....+..
T Consensus        78 ls~~~~~~~~~~a~~~Ga~g~l~K~~~~~el~~aI~~v~~G~  119 (196)
T PRK10360         78 LSVHDSPALVEQALNAGARGFLSKRCSPDELIAAVHTVATGG  119 (196)
T ss_pred             EEECCCHHHHHHHHHCCCCEEEECCCCHHHHHHHHHHHHCCC
T ss_conf             973075999999997599889977899999999999998699


No 77 
>PRK11697 putative two-component response-regulatory protein YehT; Provisional
Probab=99.56  E-value=4.3e-14  Score=119.22  Aligned_cols=115  Identities=13%  Similarity=0.209  Sum_probs=94.7

Q ss_pred             CCCEEEECCCHHHHHHHHHHHHHCC-CEEE-EECCH--HHHHHHCCCCCEEEEECCCCCCCHHHHHHHHHHHCCCCCEEE
Q ss_conf             8838998699899999999999889-8899-98937--999986089989999785469888999999998578983999
Q gi|254780916|r   10 HKRVLIIDKDDEQIKIIKDHVESYG-YDVF-IVNVS--DLSTISKIQVNVIFLSLINCEDDKENILKNIVDKIPIVPIIV   85 (482)
Q Consensus        10 ~~rILIVDDd~~~~~~l~~~L~~~G-~~v~-~a~~~--al~~l~~~~~dlillD~~mP~~dGlell~~i~~~~p~ipvIi   85 (482)
                      +.||+|||||+..+..++..++..+ .++. .++++  ++..+.+.+||++++|+.||++||+++++.++.. ...++|+
T Consensus         1 M~ki~I~DDe~~~~~~l~~~l~~~~~i~~~~~~~~~~eal~~~~~~~~DllfLDI~m~~~~G~ela~~l~~~-~~~~iIF   79 (239)
T PRK11697          1 MIKVLIVDDEPLAREELRELLQEEGDIEIVGECSNAIEALGAIHRLKPDVVFLDIQMPRISGLELVGMLDPE-HMPYIVF   79 (239)
T ss_pred             CCEEEEECCCHHHHHHHHHHHHHCCCEEEEEEECCHHHHHHHHHHCCCCEEEECCCCCCCCHHHHHHHHCCC-CCCEEEE
T ss_conf             949999969999999999999758798999998999999999985399999983998695999999983733-4986999


Q ss_pred             EECCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             926899999998885057432222222222222222222222
Q gi|254780916|r   86 QTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALREG  127 (482)
Q Consensus        86 iT~~~~~~~~~~a~~~g~~d~l~KP~~~~~L~~~i~~al~~~  127 (482)
                      +|+|+  +.+..|....+.||+.||++.+++..++.++.+..
T Consensus        80 vT~~~--e~a~~af~~~a~dYllKP~~~e~l~~~l~r~~~~~  119 (239)
T PRK11697         80 VTAFD--EYAIKAFEEHAFDYLLKPIDPARLAKTLARLRQDR  119 (239)
T ss_pred             EECCH--HHHHHHHHCCCCEEEECCCCHHHHHHHHHHHHHHH
T ss_conf             95868--99999973097266538999999999999999975


No 78 
>COG0784 CheY FOG: CheY-like receiver [Signal transduction mechanisms]
Probab=99.55  E-value=1.1e-13  Score=116.45  Aligned_cols=113  Identities=19%  Similarity=0.289  Sum_probs=98.7

Q ss_pred             CCCCEEEECCCHHHHHHHHHHHHHCCCEEEEECC---HHHHHHHCC-CCCEEEEECCCCCCCHHHHHHHHHHHCCCCCEE
Q ss_conf             2883899869989999999999988988999893---799998608-998999978546988899999999857898399
Q gi|254780916|r    9 RHKRVLIIDKDDEQIKIIKDHVESYGYDVFIVNV---SDLSTISKI-QVNVIFLSLINCEDDKENILKNIVDKIPIVPII   84 (482)
Q Consensus         9 ~~~rILIVDDd~~~~~~l~~~L~~~G~~v~~a~~---~al~~l~~~-~~dlillD~~mP~~dGlell~~i~~~~p~ipvI   84 (482)
                      ...+||+|||++..+..++..|+..||.|..+.+   ++++.+... .||+|++|+.||++||+++++++++..+.+|+|
T Consensus         4 ~~~~vLivdD~~~~~~~~~~~l~~~g~~v~~a~~~~~~al~~~~~~~~~dlii~D~~mp~~~G~~~~~~l~~~~~~~pvv   83 (130)
T COG0784           4 SGLRVLVVDDEPVNRRLLKRLLEDLGYEVVEAADGEEEALELLRELPQPDLILLDINMPGMDGIELLRRLRARGPNIPVI   83 (130)
T ss_pred             CCCEEEEECCCHHHHHHHHHHHHHCCCEEEEECCCHHHHHHHHHCCCCCCEEEEECCCCCCCHHHHHHHHHHHCCCCCEE
T ss_conf             88889997899999999999998779789995783999999986278999999806887888899999999718999689


Q ss_pred             EEECCCCHHHHHHHHHCCCCCCCCCCCCCCC-CCCCCC
Q ss_conf             9926899999998885057432222222222-222222
Q gi|254780916|r   85 VQTTQDNIKILNCFLYNRISKFFLNLVSRKQ-LCDSII  121 (482)
Q Consensus        85 iiT~~~~~~~~~~a~~~g~~d~l~KP~~~~~-L~~~i~  121 (482)
                      ++|++........+...|+.+|+.||+.... +...+.
T Consensus        84 ~~t~~~~~~~~~~~~~~g~~~~l~kP~~~~~~l~~~i~  121 (130)
T COG0784          84 LLTAYADEADRERALAAGADDYLTKPIFLEEELLAALR  121 (130)
T ss_pred             EEECCCCHHHHHHHHHCCCCEEEECCCCCHHHHHHHHH
T ss_conf             99867867659999976876897589987999999999


No 79 
>TIGR02956 TMAO_torS TMAO reductase sytem sensor TorS; InterPro: IPR014302   This protein, TorS, is part of a regulatory system for the torCAD operon that encodes the pterin molybdenum cofactor-containing enzyme trimethylamine-N-oxide (TMAO) reductase (TorA), a cognate chaperone (TorD), and a penta-haem cytochrome (TorC). TorS works together with the inducer-binding protein TorT and the response regulator TorR. TorS contains histidine kinase ATPase (IPR003594 from INTERPRO), HAMP (IPR003660 from INTERPRO), phosphoacceptor (IPR003661 from INTERPRO), and phosphotransfer (IPR008207 from INTERPRO) domains and a response regulator receiver domain (IPR001789 from INTERPRO)..
Probab=99.55  E-value=1.6e-14  Score=122.32  Aligned_cols=118  Identities=16%  Similarity=0.227  Sum_probs=106.2

Q ss_pred             CCCCCCEEEECCCHHHHHHHHHHHHHCCCEEEEECC--HHHHHHHC-CCCCEEEEECCCCCCCHHHHHHHHHHHCC----
Q ss_conf             352883899869989999999999988988999893--79999860-89989999785469888999999998578----
Q gi|254780916|r    7 LDRHKRVLIIDKDDEQIKIIKDHVESYGYDVFIVNV--SDLSTISK-IQVNVIFLSLINCEDDKENILKNIVDKIP----   79 (482)
Q Consensus         7 m~~~~rILIVDDd~~~~~~l~~~L~~~G~~v~~a~~--~al~~l~~-~~~dlillD~~mP~~dGlell~~i~~~~p----   79 (482)
                      ++.-++||+|||++....+-+.+|++.|++|..|.+  .|+..+.+ +.||++++|+.+||.||.++++.+|+.++    
T Consensus       758 lsqyy~vLlVEDN~vN~~VA~gfL~~LGH~VtlA~s~~~A~~c~~~~~~FD~aLLDI~LPD~dGVtL~~~L~~~~~~k~~  837 (1052)
T TIGR02956       758 LSQYYRVLLVEDNEVNQMVAQGFLERLGHKVTLAESGQSALRCFHQDHRFDLALLDINLPDGDGVTLLQQLRAIYKAKND  837 (1052)
T ss_pred             HHHHCEEEEEECCHHHHHHHHHHHHCCCCEEEHHHHHHHHHHHHHCCCCCCEEEEECCCCCCCHHHHHHHHHHHHHHHCC
T ss_conf             53000132464474779999999842794472085499999998548876754551578898656789999999973204


Q ss_pred             ----CCCEEEEECCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             ----983999926899999998885057432222222222222222222
Q gi|254780916|r   80 ----IVPIIVQTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICAL  124 (482)
Q Consensus        80 ----~ipvIiiT~~~~~~~~~~a~~~g~~d~l~KP~~~~~L~~~i~~al  124 (482)
                          .+|+|-+|||=-.|........|=..|+.||+..++|..++...+
T Consensus       838 ~~~~p~k~iAvSAHVf~Edv~~y~~aGF~G~laKPl~~~~L~~~l~~~l  886 (1052)
T TIGR02956       838 SQDEPVKFIAVSAHVFNEDVAQYLAAGFDGFLAKPLVEEQLVAMLAKIL  886 (1052)
T ss_pred             CCCCCCCEEEEEHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHH
T ss_conf             4456777222113344776999975302663479987788999999987


No 80 
>PRK09191 two-component response regulator; Provisional
Probab=99.55  E-value=2.8e-14  Score=120.56  Aligned_cols=113  Identities=18%  Similarity=0.139  Sum_probs=93.2

Q ss_pred             CCCEEEECCCHHHHHHHHHHHHHCCCEEEE-ECC--HHHHHHHCCCCCEEEEECCCCC-CCHHHHHHHHHHHCCCCCEEE
Q ss_conf             883899869989999999999988988999-893--7999986089989999785469-888999999998578983999
Q gi|254780916|r   10 HKRVLIIDKDDEQIKIIKDHVESYGYDVFI-VNV--SDLSTISKIQVNVIFLSLINCE-DDKENILKNIVDKIPIVPIIV   85 (482)
Q Consensus        10 ~~rILIVDDd~~~~~~l~~~L~~~G~~v~~-a~~--~al~~l~~~~~dlillD~~mP~-~dGlell~~i~~~~p~ipvIi   85 (482)
                      ..||||||||+.+..-++.+|+..||+|.. +.+  +|++++.+.+||+|++|++++| +||++..++|++.. ++|||+
T Consensus       137 ~~rILIVEDE~lIAmdLe~~l~~lG~~V~GiA~t~~eAl~la~~~~PDlvL~DI~L~d~~sGIdaa~~I~~~~-~iPvIF  215 (261)
T PRK09191        137 ATSVLIIEDEPIIAMDLEQLVESLGHRVVGIARTRAEAVALAKKTRPGLILADIQLADGSSGIDAVNDILKTF-DVPVIF  215 (261)
T ss_pred             CCCEEEECCCHHHHHHHHHHHHHCCCEEEEEECCHHHHHHHHHCCCCCEEEEEEECCCCCCHHHHHHHHHHHC-CCCEEE
T ss_conf             7887998585999999999999879967876278999999974259898999534799987999999999828-999899


Q ss_pred             EECCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             9268999999988850574322222222222222222222
Q gi|254780916|r   86 QTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALR  125 (482)
Q Consensus        86 iT~~~~~~~~~~a~~~g~~d~l~KP~~~~~L~~~i~~al~  125 (482)
                      +|||.+.  ...+-+-...-++.|||.++.+...+..|+-
T Consensus       216 iTAyper--lltg~~~ep~~li~KPf~~~~v~aai~qAlf  253 (261)
T PRK09191        216 ITAFPER--LLTGERPEPAFLITKPFQPDTVKAAISQALF  253 (261)
T ss_pred             ECCCHHH--HCCCCCCCCCEEECCCCCHHHHHHHHHHHHH
T ss_conf             7778465--3027888874035698988999999999997


No 81 
>COG2201 CheB Chemotaxis response regulator containing a CheY-like receiver domain and a methylesterase domain [Cell motility and secretion / Signal transduction mechanisms]
Probab=99.52  E-value=8.6e-13  Score=110.03  Aligned_cols=175  Identities=21%  Similarity=0.187  Sum_probs=121.6

Q ss_pred             CCCEEEECCCHHHHHHHHHHHHHCC-CE-EEEECCH--HHHHHHCCCCCEEEEECCCCCCCHHHHHHHHHHHCCCCCEEE
Q ss_conf             8838998699899999999999889-88-9998937--999986089989999785469888999999998578983999
Q gi|254780916|r   10 HKRVLIIDKDDEQIKIIKDHVESYG-YD-VFIVNVS--DLSTISKIQVNVIFLSLINCEDDKENILKNIVDKIPIVPIIV   85 (482)
Q Consensus        10 ~~rILIVDDd~~~~~~l~~~L~~~G-~~-v~~a~~~--al~~l~~~~~dlillD~~mP~~dGlell~~i~~~~p~ipvIi   85 (482)
                      ..|||||||...+|..++++|+..| .+ |-++.++  +.+.+.+..||+|.+|+.||.|||++.++++.+. +.+|||+
T Consensus         1 ~irVlvVddsal~R~~i~~~l~~~~~i~vv~~a~ng~~a~~~~~~~~PDVi~ld~emp~mdgl~~l~~im~~-~p~pVim   79 (350)
T COG2201           1 KIRVLVVDDSALMRKVISDILNSDPDIEVVGTARNGREAIDKVKKLKPDVITLDVEMPVMDGLEALRKIMRL-RPLPVIM   79 (350)
T ss_pred             CCEEEEECCCHHHHHHHHHHHHCCCCEEEEEECCCHHHHHHHHHHCCCCEEEEECCCCCCCHHHHHHHHHCC-CCCCEEE
T ss_conf             947999858199999999998308973799733787999999972299789972566445479999998447-9986899


Q ss_pred             EECCC--CHHHHHHHHHCCCCCCCCCCCCCCC---------CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             92689--9999998885057432222222222---------222222222222222222211111111222222222222
Q gi|254780916|r   86 QTTQD--NIKILNCFLYNRISKFFLNLVSRKQ---------LCDSIICALREGVVPSQENEHCALDSLIAVSPAMIQVVD  154 (482)
Q Consensus        86 iT~~~--~~~~~~~a~~~g~~d~l~KP~~~~~---------L~~~i~~al~~~~~~~~~~~~~~~~~LiG~S~~m~~v~~  154 (482)
                      +|+..  ..+...++++.|+.||+.||...-.         +.+.+..+-+...........       -..+.......
T Consensus        80 vsslt~~g~~~t~~al~~gAvD~i~kp~~~i~~~~~~~~~~l~~kv~~~~~~~~~~l~~~~~-------~~~~~~~~~~~  152 (350)
T COG2201          80 VSSLTEEGAEATLEALELGAVDFIAKPSGGISLGLDEVAELLIEKVRAAARQNRKSLRTPEP-------PRAPAFRPVKP  152 (350)
T ss_pred             EECCCCCCHHHHHHHHHCCCCEEECCCCCCCCCCHHHHHHHHHHHHHHHHHCCCCCCCCCCC-------CCCCCCCCCCC
T ss_conf             95145213799999984574213217876544466788999999999875244201356677-------87543577777


Q ss_pred             CCCCCCCCCEEEEEECCCCCHHHHHHHHHHHCCCCCCCCCCCC
Q ss_conf             2222344320488732777436799999984267543321012
Q gi|254780916|r  155 LARKAGDCAIPIMIQGEFGVGKKRLSRFIHESGKRAFFPFFIV  197 (482)
Q Consensus       155 ~i~~~a~~~~~vli~Ge~GtGK~~~A~~iH~~s~r~~~~fi~v  197 (482)
                           .....++...|-+=-|=..+...+-....-...|++.+
T Consensus       153 -----~~~~~~iV~IGaStGGp~AL~~il~~lP~~~p~pvvIv  190 (350)
T COG2201         153 -----GPAARKIVAIGASTGGPAALRAVLPALPADFPAPVVIV  190 (350)
T ss_pred             -----CCCCCCEEEEEECCCCHHHHHHHHHHCCCCCCCCEEEE
T ss_conf             -----78876389999478999999999975898889987999


No 82 
>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=99.50  E-value=1.7e-14  Score=122.15  Aligned_cols=135  Identities=25%  Similarity=0.279  Sum_probs=102.9

Q ss_pred             CCCEEEEEECCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCHHHHHCCCCCCCCCCCCCCCCCCCCCCCEEEEC
Q ss_conf             43204887327774367999999842675433210123465542100243311255553221110012344667147516
Q gi|254780916|r  161 DCAIPIMIQGEFGVGKKRLSRFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFGDVDLQTKNSAQFLGKFIEANGGTIVLE  240 (482)
Q Consensus       161 ~~~~~vli~Ge~GtGK~~~A~~iH~~s~r~~~~fi~v~c~~~~~~~~e~~lFG~~~~~~~~~~~~~g~~~~a~~Gtl~l~  240 (482)
                      .+..+|||.|++||||+++|++|++.+.+...+|+.+||+.+......+..+++.     ......+..+.+.+++||+|
T Consensus        17 ~~~~~ill~GppGtGKT~la~~ia~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-----~~~~~~~~~~~~~~~vl~iD   91 (151)
T cd00009          17 PPPKNLLLYGPPGTGKTTLARAIANELFRPGAPFLYLNASDLLEGLVVAELFGHF-----LVRLLFELAEKAKPGVLFID   91 (151)
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHHHHHCCCCCCEEEEEHHHCCHHHHHHHHHHHH-----HHHHHHHHHHHCCCCEEEEE
T ss_conf             7998089989999886599999999712137982785477704677775760577-----88989999997699869820


Q ss_pred             CCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCEEEEECCCCCCCCCCHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             64200188999888877642001123553212343156521433211111123337999886543344677
Q gi|254780916|r  241 EPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYYRISVFLINIST  311 (482)
Q Consensus       241 ei~~L~~~~Q~~Ll~~l~~~~~~~~g~~~~~~~~~RiIa~t~~~L~~~~~~g~fr~dLy~rL~~~~i~iPp  311 (482)
                      ||+.|+...|..++++|+......     ....++++|++|+.+..     +.+..++|+|+. ..|.+|+
T Consensus        92 Ei~~l~~~~~~~~~~~l~~~~~~~-----~~~~~~~vI~~tn~~~~-----~~~~~~~~~R~~-~~i~~~~  151 (151)
T cd00009          92 EIDSLSRGAQNALLRVLETLNDLR-----IDRENVRVIGATNRPLL-----GDLDRALYDRLD-IRIVIPL  151 (151)
T ss_pred             CHHHCCHHHHHHHHHHHHHHCCCC-----CCCCCEEEEEEECCCCC-----CCHHHHHHCCCC-EEEECCC
T ss_conf             166559999999999998715754-----06788899995289988-----683776425598-6986389


No 83 
>PRK13765 ATP-dependent protease Lon; Provisional
Probab=99.50  E-value=2.2e-13  Score=114.20  Aligned_cols=205  Identities=12%  Similarity=0.134  Sum_probs=133.6

Q ss_pred             CCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCHHHHHCCC-------CC-CCCCCCC-CCCCCCCCCCCEEEECC
Q ss_conf             777436799999984267543321012346554210024331125-------55-5322111-00123446671475166
Q gi|254780916|r  171 EFGVGKKRLSRFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFGDV-------DL-QTKNSAQ-FLGKFIEANGGTIVLEE  241 (482)
Q Consensus       171 e~GtGK~~~A~~iH~~s~r~~~~fi~v~c~~~~~~~~e~~lFG~~-------~~-~~~~~~~-~~g~~~~a~~Gtl~l~e  241 (482)
                      ..+.+|..+.+.+-.+..++..|||--..      -.+..|+|..       +| .|-+..+ ..|.+.+||+|.||+||
T Consensus       161 ~~~~~~~~~pkllv~~~~~~~aPfvdAtg------a~a~aLlGdVrHdP~qsGGlgTPah~Rv~aGAiHkA~gGvL~IDe  234 (637)
T PRK13765        161 VMPKEDAMVPKLLVSNSDKKTAPFVDATG------AHAGALLGDVRHDPFQSGGLETPAHERVEAGAIHKAHKGVLFIDE  234 (637)
T ss_pred             HHCCCCCCCCCEEECCCCCCCCCEECCCC------CCHHHHCCCCCCCCCCCCCCCCCCEEEECCCHHHHCCCCEEEEEH
T ss_conf             62355355764012477777898330787------444665177424863348989996100026612113585699844


Q ss_pred             CCHHHHHHHHHHHHHHHHHHCCCCCC----------CCCCCCCCEEEEECCCCCCCCCCHHHHHHHHHHHH--HHHHHHH
Q ss_conf             42001889998888776420011235----------53212343156521433211111123337999886--5433446
Q gi|254780916|r  242 PDALPLAVQGRIYNFIETGKIEFFDS----------RGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYYRI--SVFLINI  309 (482)
Q Consensus       242 i~~L~~~~Q~~Ll~~l~~~~~~~~g~----------~~~~~~~~RiIa~t~~~L~~~~~~g~fr~dLy~rL--~~~~i~i  309 (482)
                      |..|.+..|..|+++||+++|.-.|.          ..++++|+++|+++|.|.-+.+     ...|.-|+  ..+.+.+
T Consensus       235 i~~L~~~~q~~Ll~alq~~k~~I~g~~e~SsgA~v~tepvP~Df~lV~aGn~d~~~~m-----~palrsri~g~gyev~~  309 (637)
T PRK13765        235 INTLRLESQQSLLTAMQEKKYPITGQSERSSGAMVRTEPVPCDFIMVAAGNLDAIENM-----HPALRSRIRGYGYEVYM  309 (637)
T ss_pred             HHHCCHHHHHHHHHHHHCCCEECCCCCCCCCCCCCCCCCCCEEEEEEEECCHHHHHHC-----CHHHHHHHHCCCEEEEE
T ss_conf             5647988999999999659153236886667762578986613699995372766643-----99888651047749982


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCC--CCC-------CHHHHHHHHHHHH---HHCCCCCC
Q ss_conf             77877442222556677764101122333321111100012233--898-------6899999999998---74389810
Q gi|254780916|r  310 STLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYP--WID-------NVQELKNILLRAV---IGLKDSHL  377 (482)
Q Consensus       310 PpLReR~eDI~~L~~~fl~~~~~~~~~~~~~ls~~a~~~L~~y~--WPG-------NvREL~n~i~r~~---i~~~~~~i  377 (482)
                      -+.-++..+...-.-.|+.+..++.|+ .+.|+.+|++.+..|.  |-|       .+|+|-++++-|-   .......+
T Consensus       310 ~~~m~dt~enr~k~arfiaqev~~dg~-iPhfdr~AVaeII~eA~R~AG~k~kLTLrLReL~~LIReAgdiA~~eg~~~V  388 (637)
T PRK13765        310 NDTMEDTPENRKKLVRFVAQEVKRDGK-IPHFDREAVEEIIREARRRAGRKGHLTLKLRDLGGLVRVAGDIARSEGADLV  388 (637)
T ss_pred             CCCCCCCHHHHHHHHHHHHHHHHHCCC-CCCCCHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCCC
T ss_conf             356778788999999999999974388-8999989999999999974054566305289887499998899997599966


Q ss_pred             CHHHHHHHHC
Q ss_conf             6889545421
Q gi|254780916|r  378 TEDRFVLLLS  387 (482)
Q Consensus       378 ~~~~~~~~l~  387 (482)
                      +.+|+.....
T Consensus       389 ta~hV~~A~~  398 (637)
T PRK13765        389 TAEHVLEAKK  398 (637)
T ss_pred             CHHHHHHHHH
T ss_conf             4999999999


No 84 
>pfam07724 AAA_2 AAA domain (Cdc48 subfamily). This Pfam entry includes some of the AAA proteins not detected by the pfam00004 model.
Probab=99.48  E-value=6.9e-14  Score=117.76  Aligned_cols=127  Identities=13%  Similarity=0.047  Sum_probs=99.4

Q ss_pred             EEEEEECCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCHHHHHCCCCCCCCCCCCC--CCCCCCCCCCEEEECC
Q ss_conf             04887327774367999999842675433210123465542100243311255553221110--0123446671475166
Q gi|254780916|r  164 IPIMIQGEFGVGKKRLSRFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFGDVDLQTKNSAQF--LGKFIEANGGTIVLEE  241 (482)
Q Consensus       164 ~~vli~Ge~GtGK~~~A~~iH~~s~r~~~~fi~v~c~~~~~~~~e~~lFG~~~~~~~~~~~~--~g~~~~a~~Gtl~l~e  241 (482)
                      ..+|+.|++||||+.+|++++..-.....+|+.+||+.+.+...-+.|+|+..++.|.....  ...+.+...+.+||||
T Consensus         4 ~~~l~~GPsGvGKT~lAk~la~~l~~~~~~~i~~dm~e~~~~~~v~~l~g~~~gyvg~~~~G~l~~~v~~~p~~VillDE   83 (168)
T pfam07724         4 GSFLFLGPTGVGKTELAKALAELLFGDERALIRIDMSEYMEEHSVSRLIGAPPGYVGYEEGGQLTEAVRRKPYSIVLIDE   83 (168)
T ss_pred             EEEEEECCCCCCHHHHHHHHHHHHCCCCCCEEEECCCCCCCHHHHHHHCCCCCCCCCCCCCCCHHHHHHHCCCCEEEEHH
T ss_conf             79998898998999999999999679853448855756542569998705899872624265078999838984898657


Q ss_pred             CCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCEEEEECCCCCCCCCC
Q ss_conf             4200188999888877642001123553212343156521433211111
Q gi|254780916|r  242 PDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVK  290 (482)
Q Consensus       242 i~~L~~~~Q~~Ll~~l~~~~~~~~g~~~~~~~~~RiIa~t~~~L~~~~~  290 (482)
                      |+...+.+|..||++|+++.+..-.+.+--..|+-||++||..-.+...
T Consensus        84 IeKa~~~V~~~LL~ild~g~~~d~~g~~v~~~n~i~i~Tsn~g~~~~~~  132 (168)
T pfam07724        84 IEKAHPGVQNDLLQILEGGTLTDKQGRKVDFRNTLFIMTGNFGSEKISD  132 (168)
T ss_pred             HHHHCHHHHHHHHHHCCCCCEECCCCCEEECCCEEEEECCCCCCHHHHH
T ss_conf             7665899999999870587063699967844647999768737299998


No 85 
>PRK13558 bacterio-opsin activator; Provisional
Probab=99.48  E-value=1.6e-14  Score=122.23  Aligned_cols=112  Identities=13%  Similarity=0.077  Sum_probs=94.1

Q ss_pred             CEEEECCCHHHHHHHHHHHHHCCCEEEEECC--HHHHHHHCCCCCEEEEECCCCCCCHHHHHHHHHHHCCCCCEEEEECC
Q ss_conf             3899869989999999999988988999893--79999860899899997854698889999999985789839999268
Q gi|254780916|r   12 RVLIIDKDDEQIKIIKDHVESYGYDVFIVNV--SDLSTISKIQVNVIFLSLINCEDDKENILKNIVDKIPIVPIIVQTTQ   89 (482)
Q Consensus        12 rILIVDDd~~~~~~l~~~L~~~G~~v~~a~~--~al~~l~~~~~dlillD~~mP~~dGlell~~i~~~~p~ipvIiiT~~   89 (482)
                      -||.|+|+|...-+-..+=+..-|+|.++.+  +|++.+....+|||++|+.||++||+++|+.+|+.+|++|||++|+.
T Consensus        19 ~~l~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~a~~r~~~~~~DCvv~dy~~~~~dGieLLe~vRe~~p~lP~Il~t~~   98 (674)
T PRK13558         19 GVLFAGSDPETGPAACDLDEDGRFDVTQIRDFVAARDRVDDPDIDCVVAVHEPDGFDGVAFLEAVRQTHAEFPVVVVPTA   98 (674)
T ss_pred             EEEEECCCCCCCCCCCCCCCCCCCCEEEECCHHHHHHHHCCCCCCEEEECCCCCCCCHHHHHHHHHHCCCCCCEEEEECC
T ss_conf             99994688877752345666774212763238889865315898769965657888679999998613899988999567


Q ss_pred             CCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             999999988850574322222222222222222222
Q gi|254780916|r   90 DNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALR  125 (482)
Q Consensus        90 ~~~~~~~~a~~~g~~d~l~KP~~~~~L~~~i~~al~  125 (482)
                      ++.+.+.+|+..|+.+|++|  ....+...+...+.
T Consensus        99 gsE~vas~AI~AGvt~Ylp~--~~~~~~~~~~~~i~  132 (674)
T PRK13558         99 VDEDVARRAVDADATGLVPA--VSEDATAAIADRIE  132 (674)
T ss_pred             CCHHHHHHHHHHCHHHHCCC--CCHHHHHHHHHHHH
T ss_conf             85899999875163643344--71768999999999


No 86 
>PRK13407 bchI magnesium chelatase subunit I; Provisional
Probab=99.43  E-value=5.2e-13  Score=111.60  Aligned_cols=161  Identities=14%  Similarity=0.122  Sum_probs=112.3

Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCC--CCCEEEEEECCCCCHHHHHHHHHHHCCCC------------------------
Q ss_conf             1111111222222222222222234--43204887327774367999999842675------------------------
Q gi|254780916|r  136 HCALDSLIAVSPAMIQVVDLARKAG--DCAIPIMIQGEFGVGKKRLSRFIHESGKR------------------------  189 (482)
Q Consensus       136 ~~~~~~LiG~S~~m~~v~~~i~~~a--~~~~~vli~Ge~GtGK~~~A~~iH~~s~r------------------------  189 (482)
                      ..-|..++|+..+    ...+.-+|  ..-..|||.|+.||||+++||.++..-+.                        
T Consensus         4 ~~Pfs~IvGQe~~----K~AL~laav~p~~ggvLi~G~~GtgKStlaR~l~~iLP~~~~~e~~~~~~~~~~~~~~~~~~~   79 (334)
T PRK13407          4 PFPFSAIVGQEEM----KQAMVLTAIDPGIGGVLVFGDRGTGKSTAVRALAALLPLIKAVEGCPVNSARPEDCPEWAEVS   79 (334)
T ss_pred             CCCHHHHCCCHHH----HHHHHHHHCCCCCCEEEEECCCCCCHHHHHHHHHHHCCCCCHHCCCCCCCCCCCCCHHHHHCC
T ss_conf             9992376493999----999999772789860899789986599999999972899511036755667742113343114


Q ss_pred             ------CCCCCCCCCCCCCCCCCCHHHHHCCCC---CC-CCCCCCCCCCCCCCCCCEEEECCCCHHHHHHHHHHHHHHHH
Q ss_conf             ------433210123465542100243311255---55-32211100123446671475166420018899988887764
Q gi|254780916|r  190 ------AFFPFFIVNCGMIDQDKIEKFLFGDVD---LQ-TKNSAQFLGKFIEANGGTIVLEEPDALPLAVQGRIYNFIET  259 (482)
Q Consensus       190 ------~~~~fi~v~c~~~~~~~~e~~lFG~~~---~~-~~~~~~~~g~~~~a~~Gtl~l~ei~~L~~~~Q~~Ll~~l~~  259 (482)
                            ...||+.+     |-.--|..++|.-+   +. .|...-.+|++.+||+|.||+|||..++..++.-|+..+++
T Consensus        80 ~~~~~~~~~p~v~l-----Pl~atedr~~G~ldie~al~~G~~~~~PGlLa~Ah~GVLylDEinll~~~vld~Ll~~~e~  154 (334)
T PRK13407         80 STTMVERPTPVIDL-----PLGATEDRVVGALDIERALTRGEKAFEPGLLARANRGYLYIDEVNLLEDHIVDLLLDVAQS  154 (334)
T ss_pred             CCCCCCCCCCCCCC-----CCCCCCCCCCCCCCHHHHHHCCCCCCCCCHHHHCCCCEEEEECHHHCCHHHHHHHHHHHHC
T ss_conf             55534489987678-----9999986644742188886269877886054340288678720533338899999988716


Q ss_pred             HH--CCCCCCCCCCCCCCEEEEECCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             20--011235532123431565214332111111233379998865433446778
Q gi|254780916|r  260 GK--IEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYYRISVFLINISTL  312 (482)
Q Consensus       260 ~~--~~~~g~~~~~~~~~RiIa~t~~~L~~~~~~g~fr~dLy~rL~~~~i~iPpL  312 (482)
                      |.  ++|-|-+-..+++|-+|++-|-      .+|.+|+-|..|.. +.+.+++.
T Consensus       155 G~~~IeReg~s~~~ParF~LVatmNP------eEg~Lrp~lLDRf~-l~v~v~~~  202 (334)
T PRK13407        155 GENVVEREGLSIRHPARFVLVGSGNP------EEGELRPQLLDRFG-LSVEVRSP  202 (334)
T ss_pred             CCEEEEECCEEEECCCCCEEEEEECC------CCCCCCHHHHHHHC-EEEEECCC
T ss_conf             95799977634603662658982088------87775989983610-06871487


No 87 
>PRK10100 DNA-binding transcriptional regulator CsgD; Provisional
Probab=99.37  E-value=3.2e-12  Score=105.96  Aligned_cols=119  Identities=13%  Similarity=0.191  Sum_probs=99.2

Q ss_pred             CCCCEEEECCCHHHHHHHHHHHHHCCCEEE-EECCHHHHHHHCCCCCEEEEECCCCCCCHHHHHHH-HHHHCCCCCEEEE
Q ss_conf             288389986998999999999998898899-98937999986089989999785469888999999-9985789839999
Q gi|254780916|r    9 RHKRVLIIDKDDEQIKIIKDHVESYGYDVF-IVNVSDLSTISKIQVNVIFLSLINCEDDKENILKN-IVDKIPIVPIIVQ   86 (482)
Q Consensus         9 ~~~rILIVDDd~~~~~~l~~~L~~~G~~v~-~a~~~al~~l~~~~~dlillD~~mP~~dGlell~~-i~~~~p~ipvIii   86 (482)
                      ...|||++||....+..++..|+.. ..+. .+.++....-.-.+||+|++|++||+|+|++.+++ +++..|+++||++
T Consensus         9 ~g~~vlL~~dp~l~~~~~a~~l~e~-l~v~~~l~~~~~al~~~~~pdViLmDi~mp~~~gi~~~~e~i~~~~p~~kVliL   87 (216)
T PRK10100          9 HGHTLLLITKPSLQATALLQHLKQS-LAITGKLHNIQRSLDDISSGSIILLDMMEADKKLIHYWQDTLSRKNNNIKILLL   87 (216)
T ss_pred             CCEEEEEECCCHHHHHHHHHHHHHH-HHHHHEECCHHHHHHHCCCCCEEEEECCCCCCHHHHHHHHHHHHCCCCCEEEEE
T ss_conf             6838999558429999999988987-647630247766776447999899848878830899999999725999779999


Q ss_pred             ECCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             268999999988850574322222222222222222222222
Q gi|254780916|r   87 TTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALREGV  128 (482)
Q Consensus        87 T~~~~~~~~~~a~~~g~~d~l~KP~~~~~L~~~i~~al~~~~  128 (482)
                      |.+++.+....+++.|+..|+.|-.++++|+..+....+...
T Consensus        88 Tt~dd~e~v~~al~aGa~GyllK~~~~~~Li~aIr~v~~G~~  129 (216)
T PRK10100         88 NTPEDYPYREIENWPHINGVFYAMEDQERVVNGLQGVLRGEC  129 (216)
T ss_pred             ECCCCHHHHHHHHHCCCCEEEECCCCHHHHHHHHHHHHCCCC
T ss_conf             688748999999765876676689999999999999987997


No 88 
>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=99.36  E-value=1.4e-12  Score=108.58  Aligned_cols=110  Identities=14%  Similarity=0.175  Sum_probs=83.1

Q ss_pred             EEEEECCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCHHHHHCCC--CCCCCCCCCCCCCCCCCCCCEEEECCC
Q ss_conf             488732777436799999984267543321012346554210024331125--555322111001234466714751664
Q gi|254780916|r  165 PIMIQGEFGVGKKRLSRFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFGDV--DLQTKNSAQFLGKFIEANGGTIVLEEP  242 (482)
Q Consensus       165 ~vli~Ge~GtGK~~~A~~iH~~s~r~~~~fi~v~c~~~~~~~~e~~lFG~~--~~~~~~~~~~~g~~~~a~~Gtl~l~ei  242 (482)
                      +|||.|++||||+.+|+++-...   +.+|+.|+|+   .++..+.|+|..  +...+...-..|.+.   +|.+|+|||
T Consensus         1 hVLL~GppG~GKT~l~~~lA~~~---~~~~~~i~~~---~~~~~~Dl~G~~~~~~~~~~~~~~~G~l~---~~vl~lDEi   71 (131)
T pfam07726         1 HVLLEGVPGLAKTLLARTLARSL---GLDFRRIQFT---PDLLPSDITGTEVYDQKTREFEFRPGPIF---ANVLLADEI   71 (131)
T ss_pred             CEEEECCCCCHHHHHHHHHHHHH---CCCCEEEEEC---CCCCCCCCCCCEEECCCCCEEEEECCCCC---CCCEEEEHH
T ss_conf             98789899876999999999995---9981688833---77670003684542378740898457310---370564012


Q ss_pred             CHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCEEEEECCC
Q ss_conf             20018899988887764200112355321234315652143
Q gi|254780916|r  243 DALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEK  283 (482)
Q Consensus       243 ~~L~~~~Q~~Ll~~l~~~~~~~~g~~~~~~~~~RiIa~t~~  283 (482)
                      ...|+++|..|+++|+++++...|..-..+.++|+||+.|.
T Consensus        72 n~a~~~v~~~Ll~~l~er~v~~~g~~~~~p~~f~viAt~NP  112 (131)
T pfam07726        72 NRAPPKTQSALLEAMQERQVTIGGETHPLPEPFFVLATQNP  112 (131)
T ss_pred             HCCCHHHHHHHHHHHHCEEEEECCEEEECCCCEEEEECCCC
T ss_conf             03998999999976326499779988527998499971698


No 89 
>PRK11034 clpA ATP-dependent Clp protease ATP-binding subunit; Provisional
Probab=99.36  E-value=3.3e-12  Score=105.95  Aligned_cols=342  Identities=13%  Similarity=0.153  Sum_probs=210.8

Q ss_pred             CCEEEECCCHH-------------HHHHHHHHHHHCCCEEEEECC-HHHHH-HH-----CCCCCEEEEECCCCC-CCHHH
Q ss_conf             83899869989-------------999999999988988999893-79999-86-----089989999785469-88899
Q gi|254780916|r   11 KRVLIIDKDDE-------------QIKIIKDHVESYGYDVFIVNV-SDLST-IS-----KIQVNVIFLSLINCE-DDKEN   69 (482)
Q Consensus        11 ~rILIVDDd~~-------------~~~~l~~~L~~~G~~v~~a~~-~al~~-l~-----~~~~dlillD~~mP~-~dGle   69 (482)
                      .-||.||+=..             ...+|+-+|.+-..+|..|.+ .+... +.     ..+|..|..+  -|. .+-+.
T Consensus       279 ~~ILFIDEiH~ivGaG~~~gg~~DaaNlLKP~LarG~l~~IgaTT~~EYrk~iekD~AL~RRFq~V~V~--EPs~e~t~~  356 (758)
T PRK11034        279 NSILFIDEIHTIIGAGAASGGQVDAANLIKPLLSSGKIRVIGSTTYQEFSNIFEKDRALARRFQKIDIT--EPSIEETVQ  356 (758)
T ss_pred             CEEEEEECHHHHCCCCCCCCCCCCHHHHHHHHHHCCCCEEEEECCHHHHHHCCCCCHHHHHCCCEEECC--CCCHHHHHH
T ss_conf             859998043442268876777646788745787469723999437799875032147888428265318--999899999


Q ss_pred             HHHHHHHHCCCCCEEEEECCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCC----------C---------
Q ss_conf             999999857898399992689999999888505743222222222222222222222222----------2---------
Q gi|254780916|r   70 ILKNIVDKIPIVPIIVQTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALREGVV----------P---------  130 (482)
Q Consensus        70 ll~~i~~~~p~ipvIiiT~~~~~~~~~~a~~~g~~d~l~KP~~~~~L~~~i~~al~~~~~----------~---------  130 (482)
                      +|+-++..+-.--=|-+| ...++.++.-...|+.+    -+-|+.-++.+-.|-.+.+.          .         
T Consensus       357 IL~gl~~~yE~~H~v~~~-d~al~~av~Ls~rYi~d----r~lPDKAIdllDea~a~~~l~~~~~~~~~v~~~di~~vv~  431 (758)
T PRK11034        357 IINGLKPKYEAHHDVRYT-AKAVRAAVELAVKYIND----RHLPDKAIDVIDEAGARARLMPVSKRKKTVNVADIESVVA  431 (758)
T ss_pred             HHHHHHHHHHHCCCCEEC-CHHHHHHHHHHHHHHCC----CCCCHHHHHHHHHHHHHHHCCHHHHHCCCCCHHHHHHHHH
T ss_conf             999899987323695774-38999999999765026----8896199999999988875134566316589999999998


Q ss_pred             -----------CCCC------CCCCCCCCCCCCCCCCCCCCCCCCCC----CCCEEE---EEECCCCCHHHHHHHHHHHC
Q ss_conf             -----------2222------11111111222222222222222234----432048---87327774367999999842
Q gi|254780916|r  131 -----------SQEN------EHCALDSLIAVSPAMIQVVDLARKAG----DCAIPI---MIQGEFGVGKKRLSRFIHES  186 (482)
Q Consensus       131 -----------~~~~------~~~~~~~LiG~S~~m~~v~~~i~~~a----~~~~~v---li~Ge~GtGK~~~A~~iH~~  186 (482)
                                 ..+.      +...-..++|+..++..|.+.+.+.-    ..+.|+   |+.|++|+||+-+|+.+-..
T Consensus       432 ~~t~ip~~~~~~~~~~~l~~le~~l~~~viGQ~~Ai~~v~~ai~~~raGL~~~~rPigsFlf~GPTGVGKTElak~LA~~  511 (758)
T PRK11034        432 RIARIPEKSVSQSDRDTLKNLGDRLKMLVFGQDKAIEALTEAIKMSRAGLGHEHKPVGSFLFAGPTGVGKTEVTVQLSKA  511 (758)
T ss_pred             HHHCCCHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCCCHHHHHHHHHHH
T ss_conf             75036076776779999998999987787454999999999999986388899997058999789987779999999999


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCHHHHHCCCCCCCCCCCCCCCCC----CCCCCCEEEECCCCHHHHHHHHHHHHHHHHHHC
Q ss_conf             6754332101234655421002433112555532211100123----446671475166420018899988887764200
Q gi|254780916|r  187 GKRAFFPFFIVNCGMIDQDKIEKFLFGDVDLQTKNSAQFLGKF----IEANGGTIVLEEPDALPLAVQGRIYNFIETGKI  262 (482)
Q Consensus       187 s~r~~~~fi~v~c~~~~~~~~e~~lFG~~~~~~~~~~~~~g~~----~~a~~Gtl~l~ei~~L~~~~Q~~Ll~~l~~~~~  262 (482)
                      -   ...++.+||+.+.+..--|.|.|..-|+-|-..  -|.|    ..--...++||||+...+++..-||++|++|+.
T Consensus       512 L---~~~lir~DMSEy~e~hsvsrLiGaPPGYVGy~e--GG~Lte~Vr~~PysVvL~DEIEKAhpdV~nilLQvlD~G~L  586 (758)
T PRK11034        512 L---GIELLRFDMSEYMERHTVSRLIGAPPGYVGFDQ--GGLLTDAVIKHPHAVLLLDEIEKAHPDVFNLLLQVMDNGTL  586 (758)
T ss_pred             H---HHHHHCCCHHHHCCHHHHHHHCCCCCCCCCCCC--CCCCCHHHHHCCCEEEEEHHHHHHCHHHHHHHHHHCCCCCC
T ss_conf             8---667721426653120147774489986667677--77012878739877997336756398999988732377830


Q ss_pred             CCCCCCCCCCCCCE---EEEECCCCCCCC----------------C--CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             11235532123431---565214332111----------------1--11233379998865433446778774422225
Q gi|254780916|r  263 EFFDSRGAIRLDVR---LIFLTEKNLLPQ----------------V--KSHVFRKDLYYRISVFLINISTLRSRSEDIPW  321 (482)
Q Consensus       263 ~~~g~~~~~~~~~R---iIa~t~~~L~~~----------------~--~~g~fr~dLy~rL~~~~i~iPpLReR~eDI~~  321 (482)
                      .   +...+++|||   ||.+||.--.+.                +  -...|+++++-|+..+. ..-||.+  +++..
T Consensus       587 t---D~~Gr~vdF~NtiIImTSN~Ga~~~~~~~~gf~~~~~~~~~~~~l~~~F~PEFlNRiD~ii-~F~~L~~--~~l~~  660 (758)
T PRK11034        587 T---DNNGRKADFRNVVLVMTTNAGVRETERKSIGLIHQDNSTDAMEEIKKIFTPEFRNRLDNII-WFDHLST--DVIHQ  660 (758)
T ss_pred             C---CCCCCEEECEEEEEEEECCCCHHHHHHHCCCCCCCCCHHHHHHHHHHHCCHHHHHHCCEEE-EECCCCH--HHHHH
T ss_conf             1---7999988440019998256174878642147554203599999999547986772367478-6388999--99999


Q ss_pred             HHHHHHHHHCCCCCCC--CCCCCCCCCCCCCCCCCC--CCHHHHHHHHHHHHH
Q ss_conf             5667776410112233--332111110001223389--868999999999987
Q gi|254780916|r  322 LVHFFLQSFCTKNAIK--QISISDKALSLLTKYPWI--DNVQELKNILLRAVI  370 (482)
Q Consensus       322 L~~~fl~~~~~~~~~~--~~~ls~~a~~~L~~y~WP--GNvREL~n~i~r~~i  370 (482)
                      +++-++.++.++....  ...+++++..+|....|-  =--|.|+.+|++-+.
T Consensus       661 Iv~~~l~~l~~rL~~~~i~l~~~~~a~~~l~~~gyd~~~GARpl~R~I~~~i~  713 (758)
T PRK11034        661 VVDKFIVELQAQLDQKGVSLEVSQEARDWLAEKGYDRAMGARPMARVIQDNLK  713 (758)
T ss_pred             HHHHHHHHHHHHHHHCCCEEEECHHHHHHHHHHCCCCCCCCCHHHHHHHHHHH
T ss_conf             99999999999999789859988999999998488945371128899999988


No 90 
>pfam07728 AAA_5 AAA domain (dynein-related subfamily). This Pfam entry includes some of the AAA proteins not detected by the pfam00004 model.
Probab=99.35  E-value=2.7e-12  Score=106.52  Aligned_cols=115  Identities=19%  Similarity=0.265  Sum_probs=86.4

Q ss_pred             EEEEECCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCHHHHHCCCCCCCCCCCCCCCCCCCC--CCCEEEECCC
Q ss_conf             48873277743679999998426754332101234655421002433112555532211100123446--6714751664
Q gi|254780916|r  165 PIMIQGEFGVGKKRLSRFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFGDVDLQTKNSAQFLGKFIEA--NGGTIVLEEP  242 (482)
Q Consensus       165 ~vli~Ge~GtGK~~~A~~iH~~s~r~~~~fi~v~c~~~~~~~~e~~lFG~~~~~~~~~~~~~g~~~~a--~~Gtl~l~ei  242 (482)
                      +||++|++||||+.+|+.+.+.-  .+.|++.++|+.   +.-.+.|+|......+...-..|.+-.|  ++|.||||||
T Consensus         1 ~vll~Gp~G~GKT~la~~la~~l--~~~~~~~i~~~~---~~~~~dl~G~~~~~~~~~~~~~g~l~~a~~~g~vl~lDEi   75 (139)
T pfam07728         1 GVLLVGPPGTGKSELAERLAAAL--SNRPVFYVQLTR---DTTEEDLKGRRNIANGTTSWVDGPLVRAAREGEIAVLDEI   75 (139)
T ss_pred             CEEEECCCCCHHHHHHHHHHHHC--CCCCCHHHCCCC---CCCHHHCCCCEECCCCCEEEECCHHHCCCCCCCEEEECCH
T ss_conf             98999899756999999999980--798311121465---5652220573423799357815514101012868996343


Q ss_pred             CHHHHHHHHHHHHHHHHHHCCCCCCCCCC-------CCCCEEEEECCCC
Q ss_conf             20018899988887764200112355321-------2343156521433
Q gi|254780916|r  243 DALPLAVQGRIYNFIETGKIEFFDSRGAI-------RLDVRLIFLTEKN  284 (482)
Q Consensus       243 ~~L~~~~Q~~Ll~~l~~~~~~~~g~~~~~-------~~~~RiIa~t~~~  284 (482)
                      ...++++|..|+.+|+++++....+.+..       ..++|+||+.|..
T Consensus        76 n~a~~~v~~~L~~~le~~~~~~~~~~~~~~~~~~~~~~~f~viaT~N~~  124 (139)
T pfam07728        76 NRANPDVLNSLLSLLDERRLLLPEGGELVKVAPDDFAKRFRLIATMNPL  124 (139)
T ss_pred             HHCCHHHHHHHHHHHCCCEEEECCCCEEECCCCCCCCCCEEEEEEECCC
T ss_conf             4489999999999974896983689727336666789996999975896


No 91 
>PRK13342 recombination factor protein RarA; Reviewed
Probab=99.34  E-value=1.2e-11  Score=101.85  Aligned_cols=210  Identities=19%  Similarity=0.217  Sum_probs=137.8

Q ss_pred             CCCCCCCCCCCCCCCC---CCCCCCCCCCCCEEEEEECCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCHHHHH
Q ss_conf             1111111222222222---2222222344320488732777436799999984267543321012346554210024331
Q gi|254780916|r  136 HCALDSLIAVSPAMIQ---VVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHESGKRAFFPFFIVNCGMIDQDKIEKFLF  212 (482)
Q Consensus       136 ~~~~~~LiG~S~~m~~---v~~~i~~~a~~~~~vli~Ge~GtGK~~~A~~iH~~s~r~~~~fi~v~c~~~~~~~~e~~lF  212 (482)
                      ...+++++|+...+-.   ++..+..  ..-.++++.|++||||+++|+.|-...   +.+|+.+|.+.-....+. +++
T Consensus         9 P~~lde~vGQ~hllg~~~~L~~~i~~--~~~~s~Il~GPPG~GKTTlA~iiA~~~---~~~f~~lnA~~~gv~dir-~ii   82 (417)
T PRK13342          9 PKTLDEVVGQEHLLGPGKPLRRMIEA--GRLSSMILWGPPGTGKTTLARIIAGAT---DAEFEALSAVTSGVKDLR-EVI   82 (417)
T ss_pred             CCCHHHHCCCHHHHCCCHHHHHHHHC--CCCCEEEEECCCCCCHHHHHHHHHHHH---CCCEEEEECCCCCHHHHH-HHH
T ss_conf             99888857987760897199999976--999759988969998999999999986---898899614103889999-999


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCC-EEEECCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCEEEEECCCCCCCCCCH
Q ss_conf             12555532211100123446671-47516642001889998888776420011235532123431565214332111111
Q gi|254780916|r  213 GDVDLQTKNSAQFLGKFIEANGG-TIVLEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKS  291 (482)
Q Consensus       213 G~~~~~~~~~~~~~g~~~~a~~G-tl~l~ei~~L~~~~Q~~Ll~~l~~~~~~~~g~~~~~~~~~RiIa~t~~~L~~~~~~  291 (482)
                      ..      +...      ...++ .||+||||.+....|.-||..+++|.             +-+|++|+.|+.-.+..
T Consensus        83 ~~------a~~~------~~~~~tilfiDEIHRfnK~QQD~LLp~vE~g~-------------iiLIgATTENP~f~in~  137 (417)
T PRK13342         83 EE------AKQS------RLGRRTILFIDEIHRFNKAQQDALLPHVEDGT-------------ITLIGATTENPSFEVNP  137 (417)
T ss_pred             HH------HHHH------HCCCCEEEEEECHHHCCHHHHHHHHHHHHCCC-------------EEEEEECCCCCHHHCCH
T ss_conf             99------8863------14896599997820058899999987511265-------------69997415792253489


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHH
Q ss_conf             23337999886543344677877442222556677764101122333321111100012233898689999999999874
Q gi|254780916|r  292 HVFRKDLYYRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQELKNILLRAVIG  371 (482)
Q Consensus       292 g~fr~dLy~rL~~~~i~iPpLReR~eDI~~L~~~fl~~~~~~~~~~~~~ls~~a~~~L~~y~WPGNvREL~n~i~r~~i~  371 (482)
                           -|..|..++  .+-||.  .+||..++..-++. .+..+. ...++++|++.|..+. -|..|-+=|.++.+...
T Consensus       138 -----aLlSRc~vf--~l~~L~--~~di~~iL~ral~~-e~~~~~-~i~i~~~al~~i~~~s-~GDaR~aLN~LE~a~~~  205 (417)
T PRK13342        138 -----ALLSRAQVF--ELKPLS--EEDLEQLLKRALED-ERGLGR-KLELDDEALDALARLA-DGDARRALNLLELAAAA  205 (417)
T ss_pred             -----HHHHHHHHE--ECCCCC--HHHHHHHHHHHHHH-HHCCCC-CCCCCHHHHHHHHHHC-CCCHHHHHHHHHHHHHC
T ss_conf             -----898565700--205899--99999999999987-743378-8776999999999814-98599999999999852


Q ss_pred             CC-CCCCCHHHHHHHHCC
Q ss_conf             38-981068895454212
Q gi|254780916|r  372 LK-DSHLTEDRFVLLLSR  388 (482)
Q Consensus       372 ~~-~~~i~~~~~~~~l~~  388 (482)
                      .. +..|+.+.+...+..
T Consensus       206 ~~~~~~i~~~~~~~~~~~  223 (417)
T PRK13342        206 AAGGEVITLELLEEALQR  223 (417)
T ss_pred             CCCCCCCCHHHHHHHHHH
T ss_conf             589973489999999844


No 92 
>PRK10865 protein disaggregation chaperone; Provisional
Probab=99.27  E-value=6.7e-12  Score=103.75  Aligned_cols=222  Identities=20%  Similarity=0.244  Sum_probs=156.4

Q ss_pred             CCCCCCCCCCCCCCCCCCCC----CCCEEE---EEECCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCHHHHHC
Q ss_conf             11222222222222222234----432048---87327774367999999842675433210123465542100243311
Q gi|254780916|r  141 SLIAVSPAMIQVVDLARKAG----DCAIPI---MIQGEFGVGKKRLSRFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFG  213 (482)
Q Consensus       141 ~LiG~S~~m~~v~~~i~~~a----~~~~~v---li~Ge~GtGK~~~A~~iH~~s~r~~~~fi~v~c~~~~~~~~e~~lFG  213 (482)
                      .++|+..++..|.+.|.+.-    .-+.||   |+.|++|+||+-+|+++-..-......+|.+||+.+.+..--|.|.|
T Consensus       569 rViGQd~AI~~v~~aI~~sraGL~dp~rPiGsFLFlGPTGVGKTElAK~LA~~LF~~e~~liriDMSEy~E~hsVSrLiG  648 (857)
T PRK10865        569 RVIGQNEAVEAVSNAIRRSRAGLSDPNRPIGSFLFLGPTGVGKTELCKALANFMFDSDDAMVRIDMSEFMEKHSVSRLVG  648 (857)
T ss_pred             HHCCHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHCCHHHEEEECCHHHCCCHHHHHHCC
T ss_conf             85280999999999999986389999997389998689878889999999999838933425625332113012767558


Q ss_pred             CCCCCCCCCCCCCCCC----CCCCCCEEEECCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCE---EEEECCCCC-
Q ss_conf             2555532211100123----44667147516642001889998888776420011235532123431---565214332-
Q gi|254780916|r  214 DVDLQTKNSAQFLGKF----IEANGGTIVLEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVR---LIFLTEKNL-  285 (482)
Q Consensus       214 ~~~~~~~~~~~~~g~~----~~a~~Gtl~l~ei~~L~~~~Q~~Ll~~l~~~~~~~~g~~~~~~~~~R---iIa~t~~~L-  285 (482)
                      ..-|+-|-..  -|.|    ..--...++||||+...++++.-||+++++|+..   +...+.+|||   ||.+||.-- 
T Consensus       649 aPPGYVGy~e--GG~LTeaVRr~PySVvLfDEIEKAHpdV~nilLQvlD~G~Lt---D~~Gr~vdF~NtIIImTSN~Gs~  723 (857)
T PRK10865        649 APPGYVGYEE--GGYLTEAVRRRPYSVILLDEVEKAHPDVFNILLQVLDDGRLT---DGQGRTVDFRNTVVIMTSNLGSD  723 (857)
T ss_pred             CCCCCCCCCC--CCCHHHHHHHCCCEEEEEHHHHHHCHHHHHHHHHHHCCCEEE---CCCCCEEEEEEEEEEECCCHHHH
T ss_conf             9987667577--881109998198778863257663858999999870368320---79998885133489964623369


Q ss_pred             --------------CC---CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCC--CCCCCCCCC
Q ss_conf             --------------11---11112333799988654334467787744222255667776410112233--332111110
Q gi|254780916|r  286 --------------LP---QVKSHVFRKDLYYRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIK--QISISDKAL  346 (482)
Q Consensus       286 --------------~~---~~~~g~fr~dLy~rL~~~~i~iPpLReR~eDI~~L~~~fl~~~~~~~~~~--~~~ls~~a~  346 (482)
                                    .+   .+-...|+++++-|+..+.+. -||-  .+++..++..++.+..+++...  ...+++++.
T Consensus       724 ~i~~~~~~~~~~~~~~~~~~~l~~~F~PEFlnRiD~iv~F-~pL~--~~~l~~Iv~~~l~~l~~rL~~~~i~l~~~~~a~  800 (857)
T PRK10865        724 LIQERFGELDYAHMKELVLGVVSHNFRPEFINRIDEVVVF-HPLG--EQHIASIAQIQLQRLYKRLEERGYEIHISDEAL  800 (857)
T ss_pred             HHHHHCCCCCHHHHHHHHHHHHHHHCCHHHHHCCCEEEEE-CCCC--HHHHHHHHHHHHHHHHHHHHHCCCEEEECHHHH
T ss_conf             9986506556688999999999864798888237848982-7899--999999999999999999997798499888999


Q ss_pred             CCCCCCCCC--CCHHHHHHHHHHHHH
Q ss_conf             001223389--868999999999987
Q gi|254780916|r  347 SLLTKYPWI--DNVQELKNILLRAVI  370 (482)
Q Consensus       347 ~~L~~y~WP--GNvREL~n~i~r~~i  370 (482)
                      ..|....+-  ---|.|+.+|++-+.
T Consensus       801 ~~l~~~gyd~~~GARpl~r~I~~~i~  826 (857)
T PRK10865        801 KLLSENGYDPVYGARPLKRAIQQQIE  826 (857)
T ss_pred             HHHHHHCCCCCCCHHHHHHHHHHHHH
T ss_conf             99998488977471378999999988


No 93 
>CHL00095 clpC Clp protease ATP binding subunit
Probab=99.26  E-value=1.5e-11  Score=101.32  Aligned_cols=223  Identities=14%  Similarity=0.220  Sum_probs=156.5

Q ss_pred             CCCCCCCCCCCCCCCCCCCC----CCCCEEE---EEECCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCHHHHH
Q ss_conf             11122222222222222223----4432048---8732777436799999984267543321012346554210024331
Q gi|254780916|r  140 DSLIAVSPAMIQVVDLARKA----GDCAIPI---MIQGEFGVGKKRLSRFIHESGKRAFFPFFIVNCGMIDQDKIEKFLF  212 (482)
Q Consensus       140 ~~LiG~S~~m~~v~~~i~~~----a~~~~~v---li~Ge~GtGK~~~A~~iH~~s~r~~~~fi~v~c~~~~~~~~e~~lF  212 (482)
                      ..++|+..++..|-+.+.+.    ...+.|+   |+.|++|+||+.+|+++-..-......+|.+||+.+.+..--|.|.
T Consensus       509 ~~ViGQd~AI~~vs~ai~rsraGl~~~~rPigsFlf~GPTGvGKTElAK~LA~~LFg~e~~liR~DMSEy~E~hsvsrLI  588 (823)
T CHL00095        509 KRIIGQDEAVVAVSKAIRRARVGLKNPNRPIASFIFCGPTGVGKTELTKALASYFFGSEEAMIRLDMSEYMEKHTVSKLI  588 (823)
T ss_pred             HHHCCCHHHHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHCCCCCCEEEECCCCCCCCCCHHHHC
T ss_conf             78407699999999999999708998999746899878998877999999999974782025885351015542076745


Q ss_pred             CCCCCCCCCCCCCCCCC----CCCCCCEEEECCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCE---EEEECCCCC
Q ss_conf             12555532211100123----44667147516642001889998888776420011235532123431---565214332
Q gi|254780916|r  213 GDVDLQTKNSAQFLGKF----IEANGGTIVLEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVR---LIFLTEKNL  285 (482)
Q Consensus       213 G~~~~~~~~~~~~~g~~----~~a~~Gtl~l~ei~~L~~~~Q~~Ll~~l~~~~~~~~g~~~~~~~~~R---iIa~t~~~L  285 (482)
                      |..-|+-|=..  -|.|    .+--...++||||+...+++..-||++|++|+..   +...+++|||   ||.+||.--
T Consensus       589 GaPPGYVGy~e--GG~LTeaVrr~PysVvLfDEIEKAHpdV~nilLQvlDdG~Lt---D~~Gr~vdF~NtIIImTSNlGs  663 (823)
T CHL00095        589 GSPPGYVGYNE--GGQLTEAVRKKPYTVVLFDEIEKAHPDIFNLLLQILDDGRLT---DSKGRTIDFKNTLIIMTSNLGS  663 (823)
T ss_pred             CCCCCCCCCCC--CCCHHHHHHCCCCEEEEECHHHHCCHHHHHHHHHHCCCCCCC---CCCCCEEECEEEEEEECCCCCH
T ss_conf             89987667787--882019887199869986213113889999887651688434---8999988431039997165055


Q ss_pred             CCC--------------------------------CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCC
Q ss_conf             111--------------------------------111233379998865433446778774422225566777641011
Q gi|254780916|r  286 LPQ--------------------------------VKSHVFRKDLYYRISVFLINISTLRSRSEDIPWLVHFFLQSFCTK  333 (482)
Q Consensus       286 ~~~--------------------------------~~~g~fr~dLy~rL~~~~i~iPpLReR~eDI~~L~~~fl~~~~~~  333 (482)
                      +..                                .-...|+++++-||..+.+. -||.  ++|+..+++.++....++
T Consensus       664 ~~i~~~~~~~gf~~~~~~~~~~~~~~~~~~~~v~~~l~~~F~PEFlnRiDeii~F-~~L~--~~~l~~Iv~~~l~~l~~r  740 (823)
T CHL00095        664 KVIEKGGGSLGFKLLEDGTKLDEKQYKRLSNLVNEELKQYFRPEFLNRLDEIIVF-RPLT--KDEVWEIAEIMLKELFKR  740 (823)
T ss_pred             HHHHHCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHCCHHHHHHCCEEEEE-CCCC--HHHHHHHHHHHHHHHHHH
T ss_conf             8887413443433344543220235899999999999843798787327827861-8999--999999999999999999


Q ss_pred             CCCC--CCCCCCCCCCCCCCCCC-C-CCHHHHHHHHHHHHH
Q ss_conf             2233--33211111000122338-9-868999999999987
Q gi|254780916|r  334 NAIK--QISISDKALSLLTKYPW-I-DNVQELKNILLRAVI  370 (482)
Q Consensus       334 ~~~~--~~~ls~~a~~~L~~y~W-P-GNvREL~n~i~r~~i  370 (482)
                      ....  ...+++++...|....+ | ---|.|+.+|++-+.
T Consensus       741 l~~~~i~l~~~~~a~~~l~~~gy~~~~GARpl~R~I~~~i~  781 (823)
T CHL00095        741 LNNQGIQLEVDERFKTLLAKEGYNPLYGARPLRRAIMRLLE  781 (823)
T ss_pred             HHHCCCEEEECHHHHHHHHHHCCCCCCCCHHHHHHHHHHHH
T ss_conf             99689859988899999999587977681368899999988


No 94 
>PRK13341 recombination factor protein RarA/unknown domain fusion protein; Reviewed
Probab=99.25  E-value=1.8e-11  Score=100.69  Aligned_cols=201  Identities=19%  Similarity=0.221  Sum_probs=131.5

Q ss_pred             CCCCCCCCCCCCCCCCCC---CCCCCCCCCCCCEEEEEECCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCHHH
Q ss_conf             211111111222222222---22222223443204887327774367999999842675433210123465542100243
Q gi|254780916|r  134 NEHCALDSLIAVSPAMIQ---VVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHESGKRAFFPFFIVNCGMIDQDKIEKF  210 (482)
Q Consensus       134 ~~~~~~~~LiG~S~~m~~---v~~~i~~~a~~~~~vli~Ge~GtGK~~~A~~iH~~s~r~~~~fi~v~c~~~~~~~~e~~  210 (482)
                      -....++.+||++..+-.   +++.|+  +..-.++.+.|++||||+++|+.|-+.+.   .+|+.+|...-...-+...
T Consensus        22 mRP~~Lde~vGQ~hllg~g~~Lrr~i~--~~~~~S~Il~GPPGtGKTTLA~iIA~~t~---~~F~~lsAv~sgvkdlr~i   96 (726)
T PRK13341         22 LRPRTLEEFVGQDHILGEGRLLRRAIK--ADRVGSLILYGPPGVGKTTLARIIANHTR---AHFSSLNAVLAGVKDLRAE   96 (726)
T ss_pred             HCCCCHHHHCCCHHHCCCCCHHHHHHH--CCCCCEEEEECCCCCCHHHHHHHHHHHHC---CCEEEEECCCCCHHHHHHH
T ss_conf             299987773595754289828999997--69998278889799999999999988748---8679985620377999999


Q ss_pred             HHCCCCCCCCCCCCCCCCCCCCC-CCEEEECCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCEEEEECCCCCCCCC
Q ss_conf             31125555322111001234466-71475166420018899988887764200112355321234315652143321111
Q gi|254780916|r  211 LFGDVDLQTKNSAQFLGKFIEAN-GGTIVLEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQV  289 (482)
Q Consensus       211 lFG~~~~~~~~~~~~~g~~~~a~-~Gtl~l~ei~~L~~~~Q~~Ll~~l~~~~~~~~g~~~~~~~~~RiIa~t~~~L~~~~  289 (482)
                       +      ..+ ..+   +..-+ .-.||+||||.+...-|.-||-++++|.+             -+|.+|+.|+--.|
T Consensus        97 -i------~~A-~~~---~~~~g~~tILFIDEIHRfNK~QQD~LLp~vE~G~i-------------~LIGATTENP~F~v  152 (726)
T PRK13341         97 -V------DAA-KER---LERHGKRTILFIDEVHRFNKAQQDALLPWVENGTV-------------TLIGATTENPYFEV  152 (726)
T ss_pred             -H------HHH-HHH---HHHCCCCEEEEEECHHHCCHHHHHHHHHHHCCCEE-------------EEEEECCCCCCEEE
T ss_conf             -9------999-999---87459965999862542588789987888606838-------------99970478974364


Q ss_pred             CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHH
Q ss_conf             11233379998865433446778774422225566777641011223333211111000122338986899999999998
Q gi|254780916|r  290 KSHVFRKDLYYRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQELKNILLRAV  369 (482)
Q Consensus       290 ~~g~fr~dLy~rL~~~~i~iPpLReR~eDI~~L~~~fl~~~~~~~~~~~~~ls~~a~~~L~~y~WPGNvREL~n~i~r~~  369 (482)
                      ..-     |.-|..++  .+-||.+  +||..++..-++...+.++.....++++|++.|..+. -|..|-+=|.++-++
T Consensus       153 n~A-----LlSR~~vf--~L~~L~~--~dl~~il~rAl~d~~~g~~~~~i~i~~~al~~l~~~s-~GDaR~aLN~LElav  222 (726)
T PRK13341        153 NKA-----LVSRSRLF--RLKSLED--EDLHQLLKRALQDKERGYGDRNIDLEPEAEKHLVDVA-NGDARSLLNALELAV  222 (726)
T ss_pred             CHH-----HHHHCEEE--EECCCCH--HHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHC-CCCHHHHHHHHHHHH
T ss_conf             298-----88323466--7438999--9999999999876743256678775989999999975-973999999999999


Q ss_pred             HHCC
Q ss_conf             7438
Q gi|254780916|r  370 IGLK  373 (482)
Q Consensus       370 i~~~  373 (482)
                      ..+.
T Consensus       223 ~~~~  226 (726)
T PRK13341        223 ESTP  226 (726)
T ss_pred             HHCC
T ss_conf             7074


No 95 
>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=99.25  E-value=7e-12  Score=103.58  Aligned_cols=221  Identities=15%  Similarity=0.212  Sum_probs=154.2

Q ss_pred             CCCCCCCCCCCCCCCCCCCCC----CCCEEE---EEECCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCHHHHH
Q ss_conf             111222222222222222234----432048---8732777436799999984267543321012346554210024331
Q gi|254780916|r  140 DSLIAVSPAMIQVVDLARKAG----DCAIPI---MIQGEFGVGKKRLSRFIHESGKRAFFPFFIVNCGMIDQDKIEKFLF  212 (482)
Q Consensus       140 ~~LiG~S~~m~~v~~~i~~~a----~~~~~v---li~Ge~GtGK~~~A~~iH~~s~r~~~~fi~v~c~~~~~~~~e~~lF  212 (482)
                      ..++|+..++..|-+.|.+.-    ..+.|+   |+.|++|+||+-+|+++-..-......+|.+||+.+.+..--|.|.
T Consensus       566 ~~ViGQ~~Av~~v~~ai~~sraGl~d~~rPigsFLFlGPTGVGKTElAK~LA~~LFg~e~~liR~DMSEy~E~hsvsrLi  645 (852)
T TIGR03345       566 ERVIGQDHALEAIAERIRTARAGLEDPRKPLGVFLLVGPSGVGKTETALALAELLYGGEQNLITINMSEFQEAHTVSRLK  645 (852)
T ss_pred             HHHCCHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHCCCCCCEEEECCHHHCCHHHHHHHC
T ss_conf             99728499999999999998717999999856899878998778999999999971986114784224321043687863


Q ss_pred             CCCCCCCCCCCCCCCCC----CCCCCCEEEECCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCE---EEEECCCCC
Q ss_conf             12555532211100123----44667147516642001889998888776420011235532123431---565214332
Q gi|254780916|r  213 GDVDLQTKNSAQFLGKF----IEANGGTIVLEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVR---LIFLTEKNL  285 (482)
Q Consensus       213 G~~~~~~~~~~~~~g~~----~~a~~Gtl~l~ei~~L~~~~Q~~Ll~~l~~~~~~~~g~~~~~~~~~R---iIa~t~~~L  285 (482)
                      |..-|+-|=..  -|.|    ..--...++||||+...+++..-||++|++|+..   +...+++|||   ||.+||.--
T Consensus       646 GaPPGYVGy~e--GG~LTe~Vrr~PysVvLfDEIEKAHpdV~nilLQvlD~G~Lt---D~~Gr~vdF~NtIIImTSN~Gs  720 (852)
T TIGR03345       646 GSPPGYVGYGE--GGVLTEAVRRKPYSVVLLDEVEKAHPDVLELFYQVFDKGVME---DGEGREIDFKNTVILLTSNAGS  720 (852)
T ss_pred             CCCCCCCCCCC--CCHHHHHHHHCCCEEEEECHHHHCCHHHHHHHHHHHCCCEEE---CCCCCEEECEEEEEEECCCHHH
T ss_conf             89997667487--772109888099868886113002889999999872467775---7999988452129997572447


Q ss_pred             -------------------CCCCC---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCC----CCCCC
Q ss_conf             -------------------11111---12333799988654334467787744222255667776410112----23333
Q gi|254780916|r  286 -------------------LPQVK---SHVFRKDLYYRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKN----AIKQI  339 (482)
Q Consensus       286 -------------------~~~~~---~g~fr~dLy~rL~~~~i~iPpLReR~eDI~~L~~~fl~~~~~~~----~~~~~  339 (482)
                                         .+.+.   ...||+++.-|+..+++.  ||-  .+++..++..++.+..++.    |. ..
T Consensus       721 ~~i~~~~~~~~~~~~~~~~~~~v~~~l~~~F~PEFlnRi~ii~F~--~L~--~~~l~~Iv~~~l~~l~~rL~~~~~i-~l  795 (852)
T TIGR03345       721 DLIMALCADPETAPDPEALLEALRPELLKVFKPAFLGRMTVIPYL--PLD--DDVLAAIVRLKLDRIARRLKENHGA-EL  795 (852)
T ss_pred             HHHHHHHCCCCCCCCHHHHHHHHHHHHHHHCCHHHHCCEEEEEEC--CCC--HHHHHHHHHHHHHHHHHHHHHCCCC-EE
T ss_conf             999864037655566899999999999834798886456689736--899--9999999999999999999862896-89


Q ss_pred             CCCCCCCCCCCCCCC--CCCHHHHHHHHHHHHH
Q ss_conf             211111000122338--9868999999999987
Q gi|254780916|r  340 SISDKALSLLTKYPW--IDNVQELKNILLRAVI  370 (482)
Q Consensus       340 ~ls~~a~~~L~~y~W--PGNvREL~n~i~r~~i  370 (482)
                      .+++++..+|....+  .=--|.|+.+|++-+.
T Consensus       796 ~~~~~~~~~l~~~g~~~~~GARpl~r~I~~~i~  828 (852)
T TIGR03345       796 VYSEALVEHIVARCTEVESGARNIDAILNQTLL  828 (852)
T ss_pred             EECHHHHHHHHHHCCCCCCCCCHHHHHHHHHHH
T ss_conf             988999999998289977686438999999988


No 96 
>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=99.23  E-value=2.2e-11  Score=100.08  Aligned_cols=223  Identities=19%  Similarity=0.240  Sum_probs=154.9

Q ss_pred             CCCCCCCCCCCCCCCCCCCCC----CCCEEE---EEECCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCHHHHH
Q ss_conf             111222222222222222234----432048---8732777436799999984267543321012346554210024331
Q gi|254780916|r  140 DSLIAVSPAMIQVVDLARKAG----DCAIPI---MIQGEFGVGKKRLSRFIHESGKRAFFPFFIVNCGMIDQDKIEKFLF  212 (482)
Q Consensus       140 ~~LiG~S~~m~~v~~~i~~~a----~~~~~v---li~Ge~GtGK~~~A~~iH~~s~r~~~~fi~v~c~~~~~~~~e~~lF  212 (482)
                      ..++|+..++..|.+.+.+.-    +-+.|+   |+.|++|+||+.+|+++-..-......++.+||+.+.+..--|.|.
T Consensus       565 ~rViGQd~AI~~I~~aI~~sraGL~dp~rP~GsFlf~GptGvGKTELAKaLAe~Lfg~~~~LIriDMSEy~E~hsvsrLi  644 (852)
T TIGR03346       565 ERVVGQDEAVEAVSDAIRRSRAGLSDPNRPIGSFLFLGPTGVGKTELAKALAEFLFDDEDAMVRIDMSEYMEKHSVARLI  644 (852)
T ss_pred             HHHCCHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHHCCCCCEEEECHHHHCCHHHHHHHC
T ss_conf             89717099999999999999718888999745899867887768999999999985585206984304430122477855


Q ss_pred             CCCCCCCCCCCCCCCCCC----CCCCCEEEECCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCE---EEEECCCCC
Q ss_conf             125555322111001234----4667147516642001889998888776420011235532123431---565214332
Q gi|254780916|r  213 GDVDLQTKNSAQFLGKFI----EANGGTIVLEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVR---LIFLTEKNL  285 (482)
Q Consensus       213 G~~~~~~~~~~~~~g~~~----~a~~Gtl~l~ei~~L~~~~Q~~Ll~~l~~~~~~~~g~~~~~~~~~R---iIa~t~~~L  285 (482)
                      |..-|+-|-..  -|.+-    .--...++||||+...++++.-||+++++|+..   +...+++|||   ||.+||..-
T Consensus       645 GaPPGYVGy~e--gG~Lte~vr~~PysVvL~DEIEKAh~~V~~~lLQilD~G~lt---D~~Gr~vdF~NtiiimTSN~Ga  719 (852)
T TIGR03346       645 GAPPGYVGYEE--GGQLTEAVRRKPYSVVLFDEVEKAHPDVFNVLLQVLDDGRLT---DGQGRTVDFRNTVIIMTSNLGS  719 (852)
T ss_pred             CCCCCCCCCCC--CCEECHHHHHCCCEEEEECCHHHHCHHHHHHHHHHHCCCEEE---CCCCCEEEEEEEEEEEECCCCH
T ss_conf             89997677687--874239898198879985305430768999999882367430---7999888535568986154065


Q ss_pred             CC------------------CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCC--CCCCCCCCC
Q ss_conf             11------------------1111233379998865433446778774422225566777641011223--333211111
Q gi|254780916|r  286 LP------------------QVKSHVFRKDLYYRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAI--KQISISDKA  345 (482)
Q Consensus       286 ~~------------------~~~~g~fr~dLy~rL~~~~i~iPpLReR~eDI~~L~~~fl~~~~~~~~~--~~~~ls~~a  345 (482)
                      ..                  ..-...|+++|+-|+..+.+ .-||.  .+++..++..++.+..++...  -...+++++
T Consensus       720 ~~i~~~~~~~~~~~~~~~~~~~~~~~F~PEflnRid~ii~-F~~L~--~~~l~~I~~~~l~~l~~~l~~~~i~l~~~~~~  796 (852)
T TIGR03346       720 QFIQELAGGDDYEEMREAVMEVLRAHFRPEFLNRIDEIVV-FHPLG--REQIARIVEIQLGRLRKRLAERKITLELSDAA  796 (852)
T ss_pred             HHHHHHCCCCCHHHHHHHHHHHHHHHCCHHHHHHCCEEEE-ECCCC--HHHHHHHHHHHHHHHHHHHHHCCCEEEECHHH
T ss_conf             9997411455579999999999996589989963786898-37899--99999999999999999999779849988899


Q ss_pred             CCCCCCCCCC--CCHHHHHHHHHHHHH
Q ss_conf             0001223389--868999999999987
Q gi|254780916|r  346 LSLLTKYPWI--DNVQELKNILLRAVI  370 (482)
Q Consensus       346 ~~~L~~y~WP--GNvREL~n~i~r~~i  370 (482)
                      ...|....+-  ---|.|+.+|++-+.
T Consensus       797 ~~~l~~~g~~~~~GAR~l~r~i~~~i~  823 (852)
T TIGR03346       797 LDFLAEAGYDPVYGARPLKRAIQREIE  823 (852)
T ss_pred             HHHHHHHCCCCCCCHHHHHHHHHHHHH
T ss_conf             999998488977471569999999988


No 97 
>CHL00081 chlI Mg-protoporyphyrin IX chelatase
Probab=99.20  E-value=3.3e-11  Score=98.81  Aligned_cols=158  Identities=18%  Similarity=0.130  Sum_probs=102.5

Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCCCHHHHHHHHHHHCCCC----CCCCCCCCCCCC---------
Q ss_conf             1111111122222222222222223443204887327774367999999842675----433210123465---------
Q gi|254780916|r  135 EHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHESGKR----AFFPFFIVNCGM---------  201 (482)
Q Consensus       135 ~~~~~~~LiG~S~~m~~v~~~i~~~a~~~~~vli~Ge~GtGK~~~A~~iH~~s~r----~~~~fi~v~c~~---------  201 (482)
                      ...-|..++|+...-..+.  +.-+...--.|||.|+.||||++++|++++.-+.    ++.||   ||--         
T Consensus         7 ~~fPf~aIvGQe~~k~aLl--l~av~p~iGgVLi~G~~GtgKStlvRala~lLP~i~~v~~~~f---~~~p~~p~~~~~~   81 (347)
T CHL00081          7 PVFPFTAIVGQEEMKLALL--LNVIDPKIGGVMIMGDRGTGKSTTIRALVDLLPEIEVVKNDPF---NSDPRDPDLMSDE   81 (347)
T ss_pred             CCCCHHHHCCHHHHHHHHH--HHHCCCCCCEEEEECCCCCCHHHHHHHHHHHCCCCEEECCCCC---CCCCCCCCCCCHH
T ss_conf             8898406538499999999--9825788786998789987499999999985787422068876---7898981002426


Q ss_pred             ----------------------CCCCCCHHHHHCCCC---CC-CCCCCCCCCCCCCCCCCEEEECCCCHHHHHHHHHHHH
Q ss_conf             ----------------------542100243311255---55-3221110012344667147516642001889998888
Q gi|254780916|r  202 ----------------------IDQDKIEKFLFGDVD---LQ-TKNSAQFLGKFIEANGGTIVLEEPDALPLAVQGRIYN  255 (482)
Q Consensus       202 ----------------------~~~~~~e~~lFG~~~---~~-~~~~~~~~g~~~~a~~Gtl~l~ei~~L~~~~Q~~Ll~  255 (482)
                                            +|-..-|..++|..+   +. .|...-..|++.+||+|.||+|||..|+..+|.-||.
T Consensus        82 ~~~~~~~~~~~~~~~~~~p~v~lPlgaTEDrv~GslDie~al~~G~~~f~pGlLa~A~rGiLyvDEINll~d~~v~~LLd  161 (347)
T CHL00081         82 VRERIRNGEKIPTKKIKIPMVDLPLGATEDRVCGTIDIEKALTEGVKAFEPGLLAKANRGILYVDEVNLLDDHLVDILLD  161 (347)
T ss_pred             HHHHHCCCCCCCCEECCCCEEECCCCCCCCEECCCHHHHHHHHCCCCCCCCCHHHHCCCCEEEEEHHHHHHHHHHHHHHH
T ss_conf             66543146667521146862536888852301140009989845871156531222038858861454323799999999


Q ss_pred             HHHHHH--CCCCCCCCCCCCCCEEEEECCCCCCCCCCHHHHHHHHHHHHH
Q ss_conf             776420--011235532123431565214332111111233379998865
Q gi|254780916|r  256 FIETGK--IEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYYRIS  303 (482)
Q Consensus       256 ~l~~~~--~~~~g~~~~~~~~~RiIa~t~~~L~~~~~~g~fr~dLy~rL~  303 (482)
                      ++++|.  +++-|=....++.|=+|++  .|++    +|.+|+-|..|..
T Consensus       162 a~a~G~~~VEReG~S~~~Pa~F~liaT--~NPe----EgeLrp~llDRF~  205 (347)
T CHL00081        162 SAASGWNTVEREGISIRHPARFVLIGS--GNPE----EGELRPQLLDRFG  205 (347)
T ss_pred             HHHCCEEEECCCCEEECCCCCEEEEEC--CCCC----CCCCCHHHHHHEE
T ss_conf             985580898046423305750068855--7865----5674888882632


No 98 
>PRK00440 rfc replication factor C small subunit; Reviewed
Probab=99.16  E-value=7.5e-10  Score=89.26  Aligned_cols=208  Identities=17%  Similarity=0.170  Sum_probs=124.1

Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCCCHHHHHHHHHHHC--CCCCCCCCCCCCCCCCC-CCCCHHHHHC
Q ss_conf             11111122222222222222223443204887327774367999999842--67543321012346554-2100243311
Q gi|254780916|r  137 CALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHES--GKRAFFPFFIVNCGMID-QDKIEKFLFG  213 (482)
Q Consensus       137 ~~~~~LiG~S~~m~~v~~~i~~~a~~~~~vli~Ge~GtGK~~~A~~iH~~--s~r~~~~fi~v~c~~~~-~~~~e~~lFG  213 (482)
                      ..+++++|+......+...+..  ..--++|+.|++||||+.+|+++-..  +.-....++.+|++.-. -+.+.+.+  
T Consensus        13 ~~l~di~g~~~~~~~L~~~i~~--~~~phlLf~GppG~GKTt~a~~la~~l~~~~~~~~~lelnasd~r~id~vr~~i--   88 (318)
T PRK00440         13 RSLDEVVGQEEIVERLKSFVKE--KNMPHLLFAGPPGTGKTTAALALARELYGEYWRENFLELNASDERGIDVIRNKI--   88 (318)
T ss_pred             CCHHHHCCCHHHHHHHHHHHHC--CCCCEEEEECCCCCCHHHHHHHHHHHHCCCCCCCCEEEECCCCCCCHHHHHHHH--
T ss_conf             9899941969999999999987--998669888959988999999999997698643476895164566717899999--


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCEEEECCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCEEEEECCCCCCCCCCHHH
Q ss_conf             25555322111001234466714751664200188999888877642001123553212343156521433211111123
Q gi|254780916|r  214 DVDLQTKNSAQFLGKFIEANGGTIVLEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHV  293 (482)
Q Consensus       214 ~~~~~~~~~~~~~g~~~~a~~Gtl~l~ei~~L~~~~Q~~Ll~~l~~~~~~~~g~~~~~~~~~RiIa~t~~~L~~~~~~g~  293 (482)
                        +.+.  ..   .-+.....-.++|||++.|+...|..|++.+++-           +.++|+|.+|+.. ......  
T Consensus        89 --~~~~--~~---~~~~~~~~kiiiiDE~d~l~~~aq~aL~~~mE~~-----------~~~~~fil~~n~~-~kii~~--  147 (318)
T PRK00440         89 --KEFA--RT---APVGGAPFKIIFLDEADNLTSDAQQALRRTMEMY-----------SQTTRFILSCNYS-SKIIDP--  147 (318)
T ss_pred             --HHHH--HH---CCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHCC-----------CCCCEEEEECCCC-CCCCCC--
T ss_conf             --9999--72---6778997389998685532255678887643105-----------6662588634883-337615--


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHCC
Q ss_conf             33799988654334467787744222255667776410112233332111110001223389868999999999987438
Q gi|254780916|r  294 FRKDLYYRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQELKNILLRAVIGLK  373 (482)
Q Consensus       294 fr~dLy~rL~~~~i~iPpLReR~eDI~~L~~~fl~~~~~~~~~~~~~ls~~a~~~L~~y~WPGNvREL~n~i~r~~i~~~  373 (482)
                          +--|  ...|+++|+.+  ++|.    ..|...|.+.|   ..++++++..+....= ||+|.--|.++.+..  .
T Consensus       148 ----i~SR--c~~i~f~~~~~--~~i~----~~L~~I~~~E~---i~~~~~~l~~i~~~s~-gdlR~ain~Lq~~~~--~  209 (318)
T PRK00440        148 ----IQSR--CAVFRFSPLPK--EAVI----ERLRYIAKNEG---LEITDDALEAIYYVSE-GDMRKAINALQAAAA--T  209 (318)
T ss_pred             ----HHHH--HEEEECCCCCH--HHHH----HHHHHHHHHCC---CCCCHHHHHHHHHHCC-CCHHHHHHHHHHHHH--C
T ss_conf             ----5655--10111578999--9999----99999999859---9989999999998649-989999999999997--4


Q ss_pred             CCCCCHHHHHHHHC
Q ss_conf             98106889545421
Q gi|254780916|r  374 DSHLTEDRFVLLLS  387 (482)
Q Consensus       374 ~~~i~~~~~~~~l~  387 (482)
                      +..++.+.+....+
T Consensus       210 ~~~it~~~v~~~~~  223 (318)
T PRK00440        210 GKEVTEEAVYKITG  223 (318)
T ss_pred             CCCCCHHHHHHHHC
T ss_conf             89878999999976


No 99 
>PRK01905 DNA-binding protein Fis; Provisional
Probab=99.15  E-value=7.1e-11  Score=96.47  Aligned_cols=49  Identities=31%  Similarity=0.347  Sum_probs=46.0

Q ss_pred             CCHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHCCCHHHHHHHHHHHCC
Q ss_conf             4325899999999999999982872789997848998899999998188
Q gi|254780916|r  429 DGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKIREYNI  477 (482)
Q Consensus       429 ~~~~~~l~e~E~~~I~~aL~~~~Gn~~~aA~~LGIsR~tL~rKlk~~gi  477 (482)
                      +.+...++++|+.+|..+|++|+||+++||++|||+|+||++||++|||
T Consensus        28 ~ly~~vl~evE~pLi~~vl~~~~gNQ~kAA~~LGinR~TLRkKlk~ygl   76 (77)
T PRK01905         28 DVYDMVLSCVEKPLLEVVMEQAGGNQSLAAEYLGINRNTLRKKLQQHGL   76 (77)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHCCCHHHHHHHHHHHCC
T ss_conf             6999999998999999999984594999999978658889999998089


No 100
>COG3707 AmiR Response regulator with putative antiterminator output domain [Signal transduction mechanisms]
Probab=99.15  E-value=2.1e-10  Score=93.13  Aligned_cols=120  Identities=14%  Similarity=0.151  Sum_probs=99.9

Q ss_pred             CCCCEEEECCCHHHHHHHHHHHHHCCCEEEEEC-C--HHHHHHHCCCCCEEEEECCCCCCCHHHHHHHHHHHCCCCCEEE
Q ss_conf             288389986998999999999998898899989-3--7999986089989999785469888999999998578983999
Q gi|254780916|r    9 RHKRVLIIDKDDEQIKIIKDHVESYGYDVFIVN-V--SDLSTISKIQVNVIFLSLINCEDDKENILKNIVDKIPIVPIIV   85 (482)
Q Consensus         9 ~~~rILIVDDd~~~~~~l~~~L~~~G~~v~~a~-~--~al~~l~~~~~dlillD~~mP~~dGlell~~i~~~~p~ipvIi   85 (482)
                      ...|||++||++..+..+...|...||++..+. +  .+.+.+...+||+|++|+.||..|-++-+ .+.+..+.-|+|+
T Consensus         4 ~~lrvlv~~d~~i~~~~i~~~l~eag~~~Vg~~~~~~~~~~~~~~~~pDvVildie~p~rd~~e~~-~~~~~~~~~piv~   82 (194)
T COG3707           4 MLLRVLVADDEALTRMDIREGLLEAGYQRVGEAADGLEAVEVCERLQPDVVILDIEMPRRDIIEAL-LLASENVARPIVA   82 (194)
T ss_pred             CCCCEEECCCCCCCHHHHHHHHHHCCCEEEEEECCCCCCCHHHHHCCCCEEEEECCCCCCCHHHHH-HHHHCCCCCCEEE
T ss_conf             665303424113555678989987597387654134475067785299879996678773289998-9860589987899


Q ss_pred             EECCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             92689999999888505743222222222222222222222222
Q gi|254780916|r   86 QTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALREGVV  129 (482)
Q Consensus        86 iT~~~~~~~~~~a~~~g~~d~l~KP~~~~~L~~~i~~al~~~~~  129 (482)
                      +|++++...+..+...|+..|++||++..++...+.-|..+...
T Consensus        83 lt~~s~p~~i~~a~~~Gv~ayivkpi~~~rl~p~L~vA~srf~~  126 (194)
T COG3707          83 LTAYSDPALIEAAIEAGVMAYIVKPLDESRLLPILDVAVSRFEE  126 (194)
T ss_pred             EECCCCHHHHHHHHHCCCEEEEECCCCHHHHHHHHHHHHHHHHH
T ss_conf             97167858999999738749883476542104799999998899


No 101
>PRK00430 fis DNA-binding protein Fis; Provisional
Probab=99.14  E-value=8.4e-11  Score=95.96  Aligned_cols=52  Identities=27%  Similarity=0.446  Sum_probs=47.7

Q ss_pred             CCCCHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHCCCHHHHHHHHHHHCCC
Q ss_conf             4543258999999999999999828727899978489988999999981888
Q gi|254780916|r  427 GQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKIREYNIE  478 (482)
Q Consensus       427 ~~~~~~~~l~e~E~~~I~~aL~~~~Gn~~~aA~~LGIsR~tL~rKlk~~gi~  478 (482)
                      ..+.+...++|+|+.+|..+|++|+||+++||++|||+|+||++||++|||.
T Consensus        47 ~~~ly~~vl~evE~pLl~~vL~~t~gNqskAA~~LGInR~TLRkKlk~ygl~   98 (98)
T PRK00430         47 VNDLYELVLAEVEAPLLDMVMQYTRGNQTRAALMLGINRGTLRKKLKKYGMN   98 (98)
T ss_pred             CHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHCCCHHHHHHHHHHHCCC
T ss_conf             2069999999989999999999966959999999787788999999984889


No 102
>pfam00493 MCM MCM2/3/5 family.
Probab=99.14  E-value=6.6e-10  Score=89.63  Aligned_cols=114  Identities=16%  Similarity=0.214  Sum_probs=84.7

Q ss_pred             CCCEEEEEECCCCCHHHHHHHHHHHCCCCCCCCCCCC-CCC--CCCCCCCHHHHHCCCCCCCCCCCCCCCCCCCCCCCEE
Q ss_conf             4320488732777436799999984267543321012-346--5542100243311255553221110012344667147
Q gi|254780916|r  161 DCAIPIMIQGEFGVGKKRLSRFIHESGKRAFFPFFIV-NCG--MIDQDKIEKFLFGDVDLQTKNSAQFLGKFIEANGGTI  237 (482)
Q Consensus       161 ~~~~~vli~Ge~GtGK~~~A~~iH~~s~r~~~~fi~v-~c~--~~~~~~~e~~lFG~~~~~~~~~~~~~g~~~~a~~Gtl  237 (482)
                      ..+.+||+.|.+||||+.+.++++..++|.  -|++- .++  +++....       ++..+|...-..|.+-.|++|++
T Consensus        55 Rg~ihiLLvGdPG~gKSqlLk~~~~~~pr~--~~tsg~~ss~~GLTa~~~-------~d~~~~~~~leaGalvlAd~Gv~  125 (327)
T pfam00493        55 RGDINVLLVGDPGTAKSQLLKYVAKLAPRA--VYTSGKGSSAAGLTAAVV-------RDPDTGEWTLEAGALVLADGGVC  125 (327)
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHHHHCCCC--EEECCCCCCCCCCEEEEE-------EECCCCCEEEECCCEEECCCCEE
T ss_conf             365118984699815609999999868870--883177665677615899-------80688836983684775589827


Q ss_pred             EECCCCHHHHHHHHHHHHHHHHHHCCCC--CCCCCCCCCCEEEEECCC
Q ss_conf             5166420018899988887764200112--355321234315652143
Q gi|254780916|r  238 VLEEPDALPLAVQGRIYNFIETGKIEFF--DSRGAIRLDVRLIFLTEK  283 (482)
Q Consensus       238 ~l~ei~~L~~~~Q~~Ll~~l~~~~~~~~--g~~~~~~~~~RiIa~t~~  283 (482)
                      ++||++.++...|..|+.+++++.+.--  |-....+..|-|||++|-
T Consensus       126 cIDEfdk~~~~d~saL~EAMEqqtVsIaKaGi~~tL~ar~sVlAaaNP  173 (327)
T pfam00493       126 CIDEFDKMNEEDRVAIHEAMEQQTISIAKAGIVATLNARCSVLAAANP  173 (327)
T ss_pred             EEECCCCCCHHHHHHHHHHHHHCEEEEECCCEEEEECCCCEEEEEECC
T ss_conf             850055588767999999998681776338538972587179985277


No 103
>COG0542 clpA ATP-binding subunits of Clp protease and DnaK/DnaJ chaperones [Posttranslational modification, protein turnover, chaperones]
Probab=99.13  E-value=2e-10  Score=93.34  Aligned_cols=223  Identities=20%  Similarity=0.260  Sum_probs=157.1

Q ss_pred             CCCCCCCCCCCCCCCCCCCCC----CCCEEE---EEECCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCHHHHH
Q ss_conf             111222222222222222234----432048---8732777436799999984267543321012346554210024331
Q gi|254780916|r  140 DSLIAVSPAMIQVVDLARKAG----DCAIPI---MIQGEFGVGKKRLSRFIHESGKRAFFPFFIVNCGMIDQDKIEKFLF  212 (482)
Q Consensus       140 ~~LiG~S~~m~~v~~~i~~~a----~~~~~v---li~Ge~GtGK~~~A~~iH~~s~r~~~~fi~v~c~~~~~~~~e~~lF  212 (482)
                      ..++|+..++..|-+.|+++-    ..+.|+   |+.|++|+||+-+|+++-..-......+|.+|++.+-+..--|.|.
T Consensus       491 ~rViGQd~AV~~v~~aIrraRaGL~dp~rPigsFlF~GPTGVGKTELAkaLA~~Lfg~e~aliR~DMSEy~EkHsVSrLI  570 (786)
T COG0542         491 KRVIGQDEAVEAVSDAIRRARAGLGDPNRPIGSFLFLGPTGVGKTELAKALAEALFGDEQALIRIDMSEYMEKHSVSRLI  570 (786)
T ss_pred             CCEECHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHCCCCCCCEEECHHHHHHHHHHHHHH
T ss_conf             65017399999999999998569999998735788667886569999999999965997444554568777787799872


Q ss_pred             CCCCCCCCCCCCCCCCCCCC----CCCEEEECCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCE---EEEECCCCC
Q ss_conf             12555532211100123446----67147516642001889998888776420011235532123431---565214332
Q gi|254780916|r  213 GDVDLQTKNSAQFLGKFIEA----NGGTIVLEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVR---LIFLTEKNL  285 (482)
Q Consensus       213 G~~~~~~~~~~~~~g~~~~a----~~Gtl~l~ei~~L~~~~Q~~Ll~~l~~~~~~~~g~~~~~~~~~R---iIa~t~~~L  285 (482)
                      |...|+-|-..  -|.+-+|    --..++||||+...++++.-||++|++|+.   .+.+.+++|||   ||.+||.--
T Consensus       571 GaPPGYVGyee--GG~LTEaVRr~PySViLlDEIEKAHpdV~nilLQVlDdGrL---TD~~Gr~VdFrNtiIImTSN~Gs  645 (786)
T COG0542         571 GAPPGYVGYEE--GGQLTEAVRRKPYSVILLDEIEKAHPDVFNLLLQVLDDGRL---TDGQGRTVDFRNTIIIMTSNAGS  645 (786)
T ss_pred             CCCCCCCEECC--CCCHHHHHHCCCCEEEEECHHHHCCHHHHHHHHHHHCCCCE---ECCCCCEEECCEEEEEEECCCCH
T ss_conf             79998720065--54003766069986888412644088999999998467805---54899888430028998450265


Q ss_pred             CCCC---------------------CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCC--CCCCC
Q ss_conf             1111---------------------112333799988654334467787744222255667776410112233--33211
Q gi|254780916|r  286 LPQV---------------------KSHVFRKDLYYRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIK--QISIS  342 (482)
Q Consensus       286 ~~~~---------------------~~g~fr~dLy~rL~~~~i~iPpLReR~eDI~~L~~~fl~~~~~~~~~~--~~~ls  342 (482)
                      ..+.                     -...|++++.-|+..+ |..-||.+  +++..+++.++++...++...  ...++
T Consensus       646 ~~i~~~~~~~~~~~~~~~~~~v~~~l~~~F~PEFLNRid~I-I~F~~L~~--~~l~~Iv~~~L~~l~~~L~~~~i~l~~s  722 (786)
T COG0542         646 EEILRDADGDDFADKEALKEAVMEELKKHFRPEFLNRIDEI-IPFNPLSK--EVLERIVDLQLNRLAKRLAERGITLELS  722 (786)
T ss_pred             HHHHHHCCCCCCCHHHHHHHHHHHHHHHHCCHHHHHHCCCE-EECCCCCH--HHHHHHHHHHHHHHHHHHHHCCCEEEEC
T ss_conf             98975313432100467889999999853899898512617-85067998--9999999999999999998689559988


Q ss_pred             CCCCCCCCCCCC--CCCHHHHHHHHHHHHH
Q ss_conf             111000122338--9868999999999987
Q gi|254780916|r  343 DKALSLLTKYPW--IDNVQELKNILLRAVI  370 (482)
Q Consensus       343 ~~a~~~L~~y~W--PGNvREL~n~i~r~~i  370 (482)
                      +++..+|...-+  ..--|-|+++|++-+.
T Consensus       723 ~~a~~~l~~~gyd~~~GARpL~R~Iq~~i~  752 (786)
T COG0542         723 DEAKDFLAEKGYDPEYGARPLRRAIQQEIE  752 (786)
T ss_pred             HHHHHHHHHHCCCCCCCCHHHHHHHHHHHH
T ss_conf             899999999646877673679999999998


No 104
>COG2256 MGS1 ATPase related to the helicase subunit of the Holliday junction resolvase [DNA replication, recombination, and repair]
Probab=99.12  E-value=3.8e-10  Score=91.34  Aligned_cols=204  Identities=20%  Similarity=0.212  Sum_probs=133.8

Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCHHHHHCCC
Q ss_conf             11111112222222222222222344320488732777436799999984267543321012346554210024331125
Q gi|254780916|r  136 HCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFGDV  215 (482)
Q Consensus       136 ~~~~~~LiG~S~~m~~v~~~i~~~a~~~~~vli~Ge~GtGK~~~A~~iH~~s~r~~~~fi~v~c~~~~~~~~e~~lFG~~  215 (482)
                      -.....|+|....++++.+.     .+-.+..+.|++||||+.+|+.|-...   +.+|..+|...-...-+        
T Consensus        26 ~vGQ~HLlg~~~~lrr~v~~-----~~l~SmIl~GPPG~GKTTlA~liA~~~---~~~f~~~sAv~~gvkdl--------   89 (436)
T COG2256          26 VVGQEHLLGEGKPLRRAVEA-----GHLHSMILWGPPGTGKTTLARLIAGTT---NAAFEALSAVTSGVKDL--------   89 (436)
T ss_pred             HCCHHHHHCCCCHHHHHHHC-----CCCCEEEEECCCCCCHHHHHHHHHHHH---CCCEEEECCCCCCHHHH--------
T ss_conf             55718661899438999964-----998605777899988889999998761---77669951523467999--------


Q ss_pred             CCCCCCCCCCCCCCCCC------C-CCEEEECCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCEEEEECCCCCCCC
Q ss_conf             55532211100123446------6-7147516642001889998888776420011235532123431565214332111
Q gi|254780916|r  216 DLQTKNSAQFLGKFIEA------N-GGTIVLEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQ  288 (482)
Q Consensus       216 ~~~~~~~~~~~g~~~~a------~-~Gtl~l~ei~~L~~~~Q~~Ll~~l~~~~~~~~g~~~~~~~~~RiIa~t~~~L~~~  288 (482)
                                ...+++|      + .-.||+||||++...-|.-||-++++|.+             -+|.+|+.|+.-.
T Consensus        90 ----------r~i~e~a~~~~~~gr~tiLflDEIHRfnK~QQD~lLp~vE~G~i-------------ilIGATTENPsF~  146 (436)
T COG2256          90 ----------REIIEEARKNRLLGRRTILFLDEIHRFNKAQQDALLPHVENGTI-------------ILIGATTENPSFE  146 (436)
T ss_pred             ----------HHHHHHHHHHHHCCCCEEEEEEHHHHCCHHHHHHHHHHHCCCEE-------------EEEECCCCCCCEE
T ss_conf             ----------99999999987258834998722533374456551033248868-------------9996267898714


Q ss_pred             CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHH
Q ss_conf             11123337999886543344677877442222556677764101122333321111100012233898689999999999
Q gi|254780916|r  289 VKSHVFRKDLYYRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQELKNILLRA  368 (482)
Q Consensus       289 ~~~g~fr~dLy~rL~~~~i~iPpLReR~eDI~~L~~~fl~~~~~~~~~~~~~ls~~a~~~L~~y~WPGNvREL~n~i~r~  368 (482)
                      +....     .-|--  .+.+-||-  .+||..++..-+..-.+.++.....++++|++.|..+. -|..|-+=|.+|-+
T Consensus       147 ln~AL-----lSR~~--vf~lk~L~--~~di~~~l~ra~~~~~rgl~~~~~~i~~~a~~~l~~~s-~GD~R~aLN~LE~~  216 (436)
T COG2256         147 LNPAL-----LSRAR--VFELKPLS--SEDIKKLLKRALLDEERGLGGQIIVLDEEALDYLVRLS-NGDARRALNLLELA  216 (436)
T ss_pred             ECHHH-----HHHHH--EEEEECCC--HHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHC-CCHHHHHHHHHHHH
T ss_conf             03888-----61104--15651699--89999999999865413777655668889999999862-86199998899999


Q ss_pred             HHHCCCC-CCCHHHHHHHHCC
Q ss_conf             8743898-1068895454212
Q gi|254780916|r  369 VIGLKDS-HLTEDRFVLLLSR  388 (482)
Q Consensus       369 ~i~~~~~-~i~~~~~~~~l~~  388 (482)
                      +.+.... .+..+.+...+..
T Consensus       217 ~~~~~~~~~~~~~~l~~~l~~  237 (436)
T COG2256         217 ALSAEPDEVLILELLEEILQR  237 (436)
T ss_pred             HHHCCCCCCCCHHHHHHHHHH
T ss_conf             986277752479999999865


No 105
>COG0714 MoxR-like ATPases [General function prediction only]
Probab=99.11  E-value=1.2e-10  Score=94.86  Aligned_cols=144  Identities=19%  Similarity=0.200  Sum_probs=101.3

Q ss_pred             CCCCCCCCCCCCEEEEEECCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCHHHHHCCCCCC-----CCCCCCCC
Q ss_conf             2222222344320488732777436799999984267543321012346554210024331125555-----32211100
Q gi|254780916|r  152 VVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFGDVDLQ-----TKNSAQFL  226 (482)
Q Consensus       152 v~~~i~~~a~~~~~vli~Ge~GtGK~~~A~~iH~~s~r~~~~fi~v~c~~~~~~~~e~~lFG~~~~~-----~~~~~~~~  226 (482)
                      +...+-.+..+..|||+.|++||||+++|+.+-..-   +.+|+.|+|   +.++..+.++|.....     ++...-..
T Consensus        32 ~~~~~l~a~~~~~~vll~G~PG~gKT~la~~lA~~l---~~~~~~i~~---t~~l~p~d~~G~~~~~~~~~~~~~~~~~~  105 (329)
T COG0714          32 VIELALLALLAGGHVLLEGPPGVGKTLLARALARAL---GLPFVRIQC---TPDLLPSDLLGTYAYAALLLEPGEFRFVP  105 (329)
T ss_pred             HHHHHHHHHHCCCCEEEECCCCCCHHHHHHHHHHHH---CCCCEEEEC---CCCCCHHHHCCHHHHHHHHCCCCEEEEEC
T ss_conf             999999999859977877989877799999999983---898189956---89988888205688876642577189846


Q ss_pred             CCCCCCCCCEEEECCCCHHHHHHHHHHHHHHHHHHCCCCCCC-CCCCCCCEEEEECCCCCCCCCCHHHHHHHHHHHHH
Q ss_conf             123446671475166420018899988887764200112355-32123431565214332111111233379998865
Q gi|254780916|r  227 GKFIEANGGTIVLEEPDALPLAVQGRIYNFIETGKIEFFDSR-GAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYYRIS  303 (482)
Q Consensus       227 g~~~~a~~Gtl~l~ei~~L~~~~Q~~Ll~~l~~~~~~~~g~~-~~~~~~~RiIa~t~~~L~~~~~~g~fr~dLy~rL~  303 (482)
                      |-+-.+.++.||+|||...++..|.-||.+|++++++--|.. ...+..+.+|+++|  ..+.-....+.+.++.|..
T Consensus       106 gpl~~~~~~ill~DEInra~p~~q~aLl~~l~e~~vt~~~~~~~~~~~~f~viaT~N--p~e~~g~~~l~eA~ldRf~  181 (329)
T COG0714         106 GPLFAAVRVILLLDEINRAPPEVQNALLEALEERQVTVPGLTTIRLPPPFIVIATQN--PGEYEGTYPLPEALLDRFL  181 (329)
T ss_pred             CCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHHCEEEECCCCCCCCCCCCEEEEECC--CCCCCCCCCCCHHHHCCCE
T ss_conf             873345133899870345898899999999972689707966533799878998268--6765788789988881038


No 106
>pfam01078 Mg_chelatase Magnesium chelatase, subunit ChlI. Magnesium-chelatase is a three-component enzyme that catalyses the insertion of Mg2+ into protoporphyrin IX. This is the first unique step in the synthesis of (bacterio)chlorophyll. Due to this, it is thought that Mg-chelatase has an important role in channelling inter- mediates into the (bacterio)chlorophyll branch in response to conditions suitable for photosynthetic growth. ChlI and BchD have molecular weight between 38-42 kDa.
Probab=99.09  E-value=1.4e-10  Score=94.32  Aligned_cols=142  Identities=15%  Similarity=0.115  Sum_probs=90.4

Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCCCHHHHHHHHHHHCCCCCC-CCCCCC----CCCCCCC--CCCHHHH
Q ss_conf             11112222222222222222344320488732777436799999984267543-321012----3465542--1002433
Q gi|254780916|r  139 LDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHESGKRAF-FPFFIV----NCGMIDQ--DKIEKFL  211 (482)
Q Consensus       139 ~~~LiG~S~~m~~v~~~i~~~a~~~~~vli~Ge~GtGK~~~A~~iH~~s~r~~-~~fi~v----~c~~~~~--~~~e~~l  211 (482)
                      |.+++|+..+-    +.++-+|.-..+||+.|++|+||+++|+.|...-+--. ...+.+    ..+++..  .++...=
T Consensus         2 f~di~GQ~~ak----rAl~iAaaG~H~lLl~GpPG~GKTmlA~rl~~iLP~l~~~e~le~~~i~S~~g~~~~~~l~~~rP   77 (207)
T pfam01078         2 LADVKGQEQAK----RALEIAAAGGHNLLMIGPPGSGKTMLAKRLPGILPPLTEQEALEVTAIHSVAGLGGDGGLIRRRP   77 (207)
T ss_pred             HHHHCCCHHHH----HHHHHHHCCCCCEEEECCCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCC
T ss_conf             76863859999----99999854787589788998029999976301489987899887776423036877777445798


Q ss_pred             HC--C----CCCCC-CCCCCCCCCCCCCCCCEEEECCCCHHHHHHHHHHHHHHHHHHC--CCCCCCCCCCCCCEEEEECC
Q ss_conf             11--2----55553-2211100123446671475166420018899988887764200--11235532123431565214
Q gi|254780916|r  212 FG--D----VDLQT-KNSAQFLGKFIEANGGTIVLEEPDALPLAVQGRIYNFIETGKI--EFFDSRGAIRLDVRLIFLTE  282 (482)
Q Consensus       212 FG--~----~~~~~-~~~~~~~g~~~~a~~Gtl~l~ei~~L~~~~Q~~Ll~~l~~~~~--~~~g~~~~~~~~~RiIa~t~  282 (482)
                      |-  |    ..+.. |...-+.|.+-.|++|.|||||+.+++..++..|...|+++++  .|.+..-..+.+|.+|+++|
T Consensus        78 fr~PHhs~s~~aliGGg~~~~PGeIslAH~GVLFLDE~~Ef~~~vle~LrqpLE~~~v~IsRa~~~~~~PA~f~LvaA~N  157 (207)
T pfam01078        78 FRAPHHSASAAALVGGGSIPRPGEISLAHNGVLFLDELPEFSRRVLESLRQPLEDGEITISRARAKVTFPARFQLVAAMN  157 (207)
T ss_pred             CCCCCCCCCHHHCCCCCCCCCCCCEEECCCCEEEECCHHHCCHHHHHHHHHHHCCCCEEEEECCCEEEECCCEEEEEECC
T ss_conf             65788764363322688889997066636878884764653988999998766049489995675898604348888505


Q ss_pred             CC
Q ss_conf             33
Q gi|254780916|r  283 KN  284 (482)
Q Consensus       283 ~~  284 (482)
                      -=
T Consensus       158 PC  159 (207)
T pfam01078       158 PC  159 (207)
T ss_pred             CC
T ss_conf             77


No 107
>CHL00195 ycf46 Ycf46; Provisional
Probab=99.07  E-value=4e-10  Score=91.15  Aligned_cols=184  Identities=14%  Similarity=0.207  Sum_probs=113.5

Q ss_pred             CCEEEEEECCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCHHHHHCCCCCCCCCCCCCCCCC---CCCCCCEEE
Q ss_conf             32048873277743679999998426754332101234655421002433112555532211100123---446671475
Q gi|254780916|r  162 CAIPIMIQGEFGVGKKRLSRFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFGDVDLQTKNSAQFLGKF---IEANGGTIV  238 (482)
Q Consensus       162 ~~~~vli~Ge~GtGK~~~A~~iH~~s~r~~~~fi~v~c~~~~~~~~e~~lFG~~~~~~~~~~~~~g~~---~~a~~Gtl~  238 (482)
                      ...-||+.|.+||||+++|+++-...   +-||+.++.+.+     -+.++|...      ..-...|   +...--.||
T Consensus       258 ~PkGvLL~GpPG~GKtl~AKAvA~e~---~~p~l~l~~~~l-----~~~~vGesE------~~~r~~f~~A~~~aP~ilf  323 (491)
T CHL00195        258 TPRGLLLVGIQGTGKSLTAKAIANEW---NLPLLRLDVGKL-----FGGIVGESE------SRMRQMIQLAETISPCILW  323 (491)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHHHH---CCCEEEEEHHHH-----HHHHCCHHH------HHHHHHHHHHHHHCCEEEE
T ss_conf             99879997999987899999998663---894699667997-----560067049------9999999999861985899


Q ss_pred             ECCCCHH-H-----------HHHHHHHHHHHHHHHCCCCCCCCCCCCCCEEEEECCCC---CCCCCCHHHHHHHHHHHHH
Q ss_conf             1664200-1-----------88999888877642001123553212343156521433---2111111233379998865
Q gi|254780916|r  239 LEEPDAL-P-----------LAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKN---LLPQVKSHVFRKDLYYRIS  303 (482)
Q Consensus       239 l~ei~~L-~-----------~~~Q~~Ll~~l~~~~~~~~g~~~~~~~~~RiIa~t~~~---L~~~~~~g~fr~dLy~rL~  303 (482)
                      +|||+.+ +           ..+...+|..+++           ....|=|||+||..   ..+++..|+|.+-+|    
T Consensus       324 iDEidk~~~~~~~~~d~g~s~rv~~~~Lt~m~e-----------~~~~VfViattN~~~~L~pellR~GRFD~~~~----  388 (491)
T CHL00195        324 IDEIDKAFSGLDSKGDSGTSNRVLATFITWLSE-----------KKSPVFVVATANNIDSLPLELLRKGRFDEIFF----  388 (491)
T ss_pred             EEHHHHHCCCCCCCCCCCHHHHHHHHHHHHHCC-----------CCCCEEEEEECCCCCCCCHHHCCCCCCCEEEE----
T ss_conf             746545425888888872328999999998646-----------89976999958997558987708987770476----


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHH--HCCCCCCCHHH
Q ss_conf             4334467787744222255667776410112233332111110001223389868999999999987--43898106889
Q gi|254780916|r  304 VFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQELKNILLRAVI--GLKDSHLTEDR  381 (482)
Q Consensus       304 ~~~i~iPpLReR~eDI~~L~~~fl~~~~~~~~~~~~~ls~~a~~~L~~y~WPGNvREL~n~i~r~~i--~~~~~~i~~~~  381 (482)
                         |.+|...+|.+    +++-++.++...   ....++-+.+.. ....|.|  .|++++|..++.  .+.+..++.+|
T Consensus       389 ---v~lP~~~~R~~----I~~ihl~~~~~~---~~~~~d~~~la~-~t~gfsG--AeIe~~v~~A~~~A~~~~r~~~~~d  455 (491)
T CHL00195        389 ---LDLPNLEEREL----IFKIHLKRFRPN---SWQNYDIEILSQ-LTNKFSG--AEIEQSIIEAMHHAFSEKREFTTED  455 (491)
T ss_pred             ---CCCCCHHHHHH----HHHHHHHCCCCC---CCCCCCHHHHHH-HCCCCCH--HHHHHHHHHHHHHHHHCCCCCCHHH
T ss_conf             ---48959899999----999998544788---755469999997-6859888--9999999999999987588665899


Q ss_pred             HHHHHC
Q ss_conf             545421
Q gi|254780916|r  382 FVLLLS  387 (482)
Q Consensus       382 ~~~~l~  387 (482)
                      +.....
T Consensus       456 l~~a~~  461 (491)
T CHL00195        456 ICLALK  461 (491)
T ss_pred             HHHHHH
T ss_conf             999998


No 108
>COG1239 ChlI Mg-chelatase subunit ChlI [Coenzyme metabolism]
Probab=99.05  E-value=1.3e-09  Score=87.53  Aligned_cols=158  Identities=18%  Similarity=0.180  Sum_probs=106.3

Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCCCHHHHHHHHHHHCCCCCCCCCCCCCC---------------
Q ss_conf             11111111222222222222222234432048873277743679999998426754332101234---------------
Q gi|254780916|r  135 EHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHESGKRAFFPFFIVNC---------------  199 (482)
Q Consensus       135 ~~~~~~~LiG~S~~m~~v~~~i~~~a~~~~~vli~Ge~GtGK~~~A~~iH~~s~r~~~~fi~v~c---------------  199 (482)
                      .+.-+..++|+.+.=..+.  +..+-..=..|||.|+.||||+++||+|+..-+-.  .-|. +|               
T Consensus        12 ~~~pf~aivGqd~lk~aL~--l~av~P~iggvLI~G~kGtaKSt~~Rala~LLp~~--~~V~-gc~f~cdP~~P~~~c~~   86 (423)
T COG1239          12 ENLPFTAIVGQDPLKLALG--LNAVDPQIGGALIAGEKGTAKSTLARALADLLPEI--EVVI-GCPFNCDPDDPEEMCDE   86 (423)
T ss_pred             HCCCHHHHCCCHHHHHHHH--HHHCCCCCCEEEEECCCCCCHHHHHHHHHHHCCCC--CEEC-CCCCCCCCCCHHHHHHH
T ss_conf             5166565437537778876--53026310426876688752779999999867963--3216-88788998870555199


Q ss_pred             --------------------CCCCCCCCHHHHHCCCC---CCC-CCCCCCCCCCCCCCCCEEEECCCCHHHHHHHHHHHH
Q ss_conf             --------------------65542100243311255---553-221110012344667147516642001889998888
Q gi|254780916|r  200 --------------------GMIDQDKIEKFLFGDVD---LQT-KNSAQFLGKFIEANGGTIVLEEPDALPLAVQGRIYN  255 (482)
Q Consensus       200 --------------------~~~~~~~~e~~lFG~~~---~~~-~~~~~~~g~~~~a~~Gtl~l~ei~~L~~~~Q~~Ll~  255 (482)
                                          -++|..--|..+-|..+   +.. |...-..|++.+||+|.||+|||..|+..+|.-||.
T Consensus        87 c~~k~~e~~~~~~~~r~v~~v~lPl~ateDrvvGslDi~ka~~~g~~af~PGlLa~AnRGIlYvDEvnlL~d~lvd~LLd  166 (423)
T COG1239          87 CRAKGDELEWLPREKRKVPFVALPLGATEDRLVGSLDIEKALEEGPKAFQPGLLARANRGILYVDEVNLLDDHLVDALLD  166 (423)
T ss_pred             HHHHCCCCCCCCCCCEECCEECCCCCCCHHHHCCCCCHHHHHHCCCCCCCCCCHHHCCCCEEEEECCCCCCHHHHHHHHH
T ss_conf             98620232445422100312238876304330045679999726830027751100358879872334351899999999


Q ss_pred             HHHHH--HCCCCCCCCCCCCCCEEEEECCCCCCCCCCHHHHHHHHHHHHH
Q ss_conf             77642--0011235532123431565214332111111233379998865
Q gi|254780916|r  256 FIETG--KIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYYRIS  303 (482)
Q Consensus       256 ~l~~~--~~~~~g~~~~~~~~~RiIa~t~~~L~~~~~~g~fr~dLy~rL~  303 (482)
                      ++++|  .+++-|-.-.-+++|=+|++.|  ++    +|.+|+-|..|..
T Consensus       167 ~aaeG~n~vereGisi~hpa~fvligTmN--PE----eGeLrpqLlDRfg  210 (423)
T COG1239         167 VAAEGVNDVEREGISIRHPARFLLIGTMN--PE----EGELRPQLLDRFG  210 (423)
T ss_pred             HHHHCCCEEEECCEEECCCCCEEEEEECC--CC----CCCCCHHHHHHHC
T ss_conf             99717740335750313676179996448--54----4663246675411


No 109
>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=99.02  E-value=6.2e-10  Score=89.82  Aligned_cols=200  Identities=14%  Similarity=0.162  Sum_probs=116.5

Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCC---CCCEEEEEECCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCHHHH
Q ss_conf             11111111222222222222222234---432048873277743679999998426754332101234655421002433
Q gi|254780916|r  135 EHCALDSLIAVSPAMIQVVDLARKAG---DCAIPIMIQGEFGVGKKRLSRFIHESGKRAFFPFFIVNCGMIDQDKIEKFL  211 (482)
Q Consensus       135 ~~~~~~~LiG~S~~m~~v~~~i~~~a---~~~~~vli~Ge~GtGK~~~A~~iH~~s~r~~~~fi~v~c~~~~~~~~e~~l  211 (482)
                      ....++.++|+......+...++..-   ..-.+++++|++||||+.+||.|-+..+   .+|..++...+...      
T Consensus        19 RP~~l~e~vGQehl~~~l~~~i~a~~~~~~~l~h~lf~GPPG~GKTTlAriiAk~~~---~~~~~~s~~~i~~~------   89 (234)
T pfam05496        19 RPRRLDEYIGQEKVKENLKIFIEAAKKRGEALDHVLLYGPPGLGKTTLANIIANEMG---VNIRITSGPALEKP------   89 (234)
T ss_pred             CCCCHHHCCCHHHHHHHHHHHHHHHHHCCCCCCEEEEECCCCCCHHHHHHHHHHHHC---CCEEEECCHHHHHH------
T ss_conf             989766606949999999999998874277766278878999988899999998408---75376142666438------


Q ss_pred             HCCCCCCCCCCCCCCCCCCCCCCC-EEEECCCCHHHHHHHHHHHHHHHHHHCCC-CCCCCC------CCCCCEEEEECCC
Q ss_conf             112555532211100123446671-47516642001889998888776420011-235532------1234315652143
Q gi|254780916|r  212 FGDVDLQTKNSAQFLGKFIEANGG-TIVLEEPDALPLAVQGRIYNFIETGKIEF-FDSRGA------IRLDVRLIFLTEK  283 (482)
Q Consensus       212 FG~~~~~~~~~~~~~g~~~~a~~G-tl~l~ei~~L~~~~Q~~Ll~~l~~~~~~~-~g~~~~------~~~~~RiIa~t~~  283 (482)
                                 .+-.+.+...+.+ .||+||||.+....|.-||-.++++.+.- +|....      ..-.|-+|.||+.
T Consensus        90 -----------~di~~~l~~~~~~~ILFIDEIHr~nK~qqd~Llp~vE~g~i~i~ig~~~~A~~~~~e~P~FtLIgATTe  158 (234)
T pfam05496        90 -----------GDLAAILTNLEPGDVLFIDEIHRLNRAVEEILYPAMEDFRLDIVIGKGPSARSIRLDLPPFTLVGATTR  158 (234)
T ss_pred             -----------HHHHHHHHHCCCCCEEEEECHHHCCHHHHHHCCCCCCCCEEEEEECCCCCCEEEECCCCCEEEEEECCC
T ss_conf             -----------999999984589988999665435876887445533461699996367663246526897599852156


Q ss_pred             CCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHH
Q ss_conf             32111111233379998865433446778774422225566777641011223333211111000122338986899999
Q gi|254780916|r  284 NLLPQVKSHVFRKDLYYRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQELKN  363 (482)
Q Consensus       284 ~L~~~~~~g~fr~dLy~rL~~~~i~iPpLReR~eDI~~L~~~fl~~~~~~~~~~~~~ls~~a~~~L~~y~WPGNvREL~n  363 (482)
                      +-       .+..-|.-|.+. ..++-||  ..+||..++    ++.++..|   ..++++|+..+..+. -|..|.--|
T Consensus       159 ~~-------~l~~pl~sR~~i-~~~l~~l--~~edl~~il----~r~~~~l~---i~i~~eal~~IA~~s-~Gd~R~ALn  220 (234)
T pfam05496       159 AG-------LLTSPLRDRFGI-VLRLEFY--SVEELEEIV----KRSARILG---VEIDEEGAAEIARRS-RGTPRIANR  220 (234)
T ss_pred             CC-------CCCHHHHHHHHH-EEECCCC--CHHHHHHHH----HHHHHHCC---CCCCHHHHHHHHHHC-CCCHHHHHH
T ss_conf             66-------477779976211-2442468--999999999----99999839---995999999999977-998999989


Q ss_pred             HHHHHHHHC
Q ss_conf             999998743
Q gi|254780916|r  364 ILLRAVIGL  372 (482)
Q Consensus       364 ~i~r~~i~~  372 (482)
                      .++|++-.+
T Consensus       221 lLe~v~d~a  229 (234)
T pfam05496       221 LLRRVRDFA  229 (234)
T ss_pred             HHHHHHHHH
T ss_conf             999999999


No 110
>pfam02954 HTH_8 Bacterial regulatory protein, Fis family.
Probab=99.00  E-value=5.3e-10  Score=90.31  Aligned_cols=42  Identities=45%  Similarity=0.720  Sum_probs=40.3

Q ss_pred             HHHHHHHHHHHHHHHHHCCCHHHHHHHHCCCHHHHHHHHHHH
Q ss_conf             999999999999999828727899978489988999999981
Q gi|254780916|r  434 RLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKIREY  475 (482)
Q Consensus       434 ~l~e~E~~~I~~aL~~~~Gn~~~aA~~LGIsR~tL~rKlk~~  475 (482)
                      +++++|+.+|..||++|+||+++||+.|||||+|||+||++|
T Consensus         1 tl~~~Er~~I~~aL~~~~gn~~~aA~~LGisr~tL~~kmkky   42 (42)
T pfam02954         1 SLEEVEKELIEAALERTGGNKSKAARLLGISRRTLYRKLKKY   42 (42)
T ss_pred             CHHHHHHHHHHHHHHHHCCCHHHHHHHHCCCHHHHHHHHHHC
T ss_conf             989999999999999949979999999796999999999739


No 111
>PRK11475 DNA-binding transcriptional activator BglJ; Provisional
Probab=99.00  E-value=2.2e-09  Score=86.01  Aligned_cols=103  Identities=17%  Similarity=0.161  Sum_probs=81.1

Q ss_pred             HHHHHHHHHHC-C--CEEEEEC---C--HHHHHHHCCCCCEEEEECCCCCCCHHHHHHHHHHHCCCCCEEEEECCCCHHH
Q ss_conf             99999999988-9--8899989---3--7999986089989999785469888999999998578983999926899999
Q gi|254780916|r   23 IKIIKDHVESY-G--YDVFIVN---V--SDLSTISKIQVNVIFLSLINCEDDKENILKNIVDKIPIVPIIVQTTQDNIKI   94 (482)
Q Consensus        23 ~~~l~~~L~~~-G--~~v~~a~---~--~al~~l~~~~~dlillD~~mP~~dGlell~~i~~~~p~ipvIiiT~~~~~~~   94 (482)
                      ..-++.+|+.. |  |.+..++   +  +|+..+....+|++++|+.||++||+++++++++++|++.+|++|.|++...
T Consensus         3 ~~gi~sl~~~~~~~~~~l~vv~e~~~g~EAl~~~~~~~v~~~LmDi~mP~~dGL~~~~~L~r~~P~vriLVLTm~d~e~~   82 (205)
T PRK11475          3 SIGIESLFDKFPGNPYKLHIFSSQSSFQDAMSRISFSAVIFSLSAMRSERREGLSCLTELAIKFPRMRRLVIADDDIEAR   82 (205)
T ss_pred             HHHHHHHHHHCCCCCEEEEEEECCCCHHHHHHCCCCCCCEEEEECCCCCCCCHHHHHHHHHHHCCCCEEEEEECCCCHHH
T ss_conf             78899998418998348999505456999986288666438985389999766999999999789971899974768799


Q ss_pred             HHHHHH-CCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             998885-0574322222222222222222222
Q gi|254780916|r   95 LNCFLY-NRISKFFLNLVSRKQLCDSIICALR  125 (482)
Q Consensus        95 ~~~a~~-~g~~d~l~KP~~~~~L~~~i~~al~  125 (482)
                      ...++. .|+..|+.|-...+.|...+..+..
T Consensus        83 v~~aL~~aga~Gyl~K~~~~~eL~~Ai~~~~~  114 (205)
T PRK11475         83 LIGSLSPSPLDGVLSKASTLEILQQELFLSLN  114 (205)
T ss_pred             HHHHHHHHHCCEEEECCCCHHHHHHHHHHHHC
T ss_conf             99999984166888567889999999999870


No 112
>COG3279 LytT Response regulator of the LytR/AlgR family [Transcription / Signal transduction mechanisms]
Probab=98.99  E-value=1e-09  Score=88.31  Aligned_cols=115  Identities=14%  Similarity=0.200  Sum_probs=94.8

Q ss_pred             CCCEEEECCCHHHHHHHHHHHHHC-CCEEEE-ECC--HHHHHHHCCCCCEEEEECCCCCCCHHHHHHHHHHHCCCCCEEE
Q ss_conf             883899869989999999999988-988999-893--7999986089989999785469888999999998578983999
Q gi|254780916|r   10 HKRVLIIDKDDEQIKIIKDHVESY-GYDVFI-VNV--SDLSTISKIQVNVIFLSLINCEDDKENILKNIVDKIPIVPIIV   85 (482)
Q Consensus        10 ~~rILIVDDd~~~~~~l~~~L~~~-G~~v~~-a~~--~al~~l~~~~~dlillD~~mP~~dGlell~~i~~~~p~ipvIi   85 (482)
                      +.+|+++||++..+..+..++... ++++.. +.+  .++..+....+|++++|+.||+++|+++...++...|..+|++
T Consensus         1 m~~i~i~dd~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~fldI~~~~~~G~ela~~i~~~~~~~~Ivf   80 (244)
T COG3279           1 MLKVLIVDDEPLAREELRRILNEIPDIEIVGEAENGEEALQLLQGLRPDLVFLDIAMPDINGIELAARIRKGDPRPAIVF   80 (244)
T ss_pred             CCCEEEECCCHHHHHHHHHHHHHHHHCCHHHHHCCHHHHHHHHHCCCCCEEEEEECCCCCCHHHHHHHHCCCCCCCEEEE
T ss_conf             98517714767679999999887442111133123031788876025776999723765244999998615698853999


Q ss_pred             EECCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             92689999999888505743222222222222222222222
Q gi|254780916|r   86 QTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALRE  126 (482)
Q Consensus        86 iT~~~~~~~~~~a~~~g~~d~l~KP~~~~~L~~~i~~al~~  126 (482)
                      +|+|+  +.+..+....+.||+.||+...++...+....+.
T Consensus        81 vt~~~--~~a~~afev~a~d~i~kp~~~~~l~~~l~~~~~~  119 (244)
T COG3279          81 VTAHD--EYAVAAFEVEALDYLLKPISEERLAKTLERLRRY  119 (244)
T ss_pred             EEEHH--HHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHH
T ss_conf             98615--4323331334667742854268999999998887


No 113
>PRK00080 ruvB Holliday junction DNA helicase RuvB; Reviewed
Probab=98.98  E-value=1e-08  Score=81.22  Aligned_cols=253  Identities=17%  Similarity=0.235  Sum_probs=153.2

Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCC---CCCEEEEEECCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCHHHH
Q ss_conf             11111111222222222222222234---432048873277743679999998426754332101234655421002433
Q gi|254780916|r  135 EHCALDSLIAVSPAMIQVVDLARKAG---DCAIPIMIQGEFGVGKKRLSRFIHESGKRAFFPFFIVNCGMIDQDKIEKFL  211 (482)
Q Consensus       135 ~~~~~~~LiG~S~~m~~v~~~i~~~a---~~~~~vli~Ge~GtGK~~~A~~iH~~s~r~~~~fi~v~c~~~~~~~~e~~l  211 (482)
                      ....++.++|+......+.-.+..+-   .+--+||+.|++|.||+++|+.|-+.-.   ..|...+..++...      
T Consensus        20 RP~~l~efiGQ~~i~~~L~v~i~Aak~r~e~ldH~Ll~GPPGlGKTTLA~iiA~E~~---~~~~~tsGP~lek~------   90 (328)
T PRK00080         20 RPKSLDEFIGQEKVKENLKIFIEAAKKRGEALDHVLLYGPPGLGKTTLANIIANEMG---VNIRITSGPALEKA------   90 (328)
T ss_pred             CCCCHHHCCCHHHHHHHHHHHHHHHHHCCCCCCCEEEECCCCCCHHHHHHHHHHHHC---CCCEECCCCCCCCH------
T ss_conf             988576635959999999999999996499988057658899889999999999868---88156245001674------


Q ss_pred             HCCCCCCCCCCCCCCCCCCCC-CCCEEEECCCCHHHHHHHHHHHHHHHHHHCCCCCCCC----CCC---CCCEEEEECCC
Q ss_conf             112555532211100123446-6714751664200188999888877642001123553----212---34315652143
Q gi|254780916|r  212 FGDVDLQTKNSAQFLGKFIEA-NGGTIVLEEPDALPLAVQGRIYNFIETGKIEFFDSRG----AIR---LDVRLIFLTEK  283 (482)
Q Consensus       212 FG~~~~~~~~~~~~~g~~~~a-~~Gtl~l~ei~~L~~~~Q~~Ll~~l~~~~~~~~g~~~----~~~---~~~RiIa~t~~  283 (482)
                                 .+-.+.+-.. .|-.||+||||.|+..++.-|.-++++-++.-+=+..    .+.   ..|-+|.||++
T Consensus        91 -----------~DL~~iLt~l~~~dvLFIDEIHRl~~~vEE~LY~AMEDf~iDi~iG~g~~Ar~~~i~L~pFTLIGATTr  159 (328)
T PRK00080         91 -----------GDLAALLTNLEEGDVLFIDEIHRLSPVVEEILYPAMEDFRLDIMIGKGPAARSIRLDLPPFTLIGATTR  159 (328)
T ss_pred             -----------HHHHHHHHHCCCCCEEEEHHHHHCCHHHHHHHHHHHHHCEEEEEECCCCCCEEEECCCCCEEEEECCCC
T ss_conf             -----------789999960887876765065324888998857987752345786478653245558998347401367


Q ss_pred             CCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH-----------HHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             321111112333799988654334467787744-----------222255667776410112233332111110001223
Q gi|254780916|r  284 NLLPQVKSHVFRKDLYYRISVFLINISTLRSRS-----------EDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKY  352 (482)
Q Consensus       284 ~L~~~~~~g~fr~dLy~rL~~~~i~iPpLReR~-----------eDI~~L~~~fl~~~~~~~~~~~~~ls~~a~~~L~~y  352 (482)
                      -       |..              -.|||+|-           +|+..+    +.+.|..++.   .+++++...+..+
T Consensus       160 ~-------g~L--------------s~PLrdRFGi~~~l~~Y~~eeL~~I----i~rsa~~l~i---~i~~~~~~eIA~r  211 (328)
T PRK00080        160 A-------GLL--------------TSPLRDRFGIVQRLEFYTVEELEKI----VKRSARILGI---EIDEEGALEIARR  211 (328)
T ss_pred             C-------CCC--------------CHHHHHHCCCEEEECCCCHHHHHHH----HHHHHHHHCC---CCCHHHHHHHHHH
T ss_conf             6-------657--------------7678975793366345899999999----9999998398---8789999999986


Q ss_pred             CCCCCHHHHHHHHHHHH---HHCCCCCCCHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHCCCCCCCCCCCCC
Q ss_conf             38986899999999998---743898106889545421244543223432222223344432100000000112344454
Q gi|254780916|r  353 PWIDNVQELKNILLRAV---IGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILDNLSQESIPAIGQD  429 (482)
Q Consensus       353 ~WPGNvREL~n~i~r~~---i~~~~~~i~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  429 (482)
                      .- |.=|---+.++|.-   .....+.|+.+.....+...+...                                    
T Consensus       212 SR-GTPRiAnrLLrRvrDfa~v~~~~~I~~~~~~~aL~~l~ID~------------------------------------  254 (328)
T PRK00080        212 SR-GTPRIANRLLRRVRDFAQVKGDGIITREIADKALDMLGVDE------------------------------------  254 (328)
T ss_pred             CC-CCCHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHCCCCC------------------------------------
T ss_conf             38-98399999999999999983799659999999999569863------------------------------------


Q ss_pred             CHHHHHHHHHHHHHHHHHHHHCCC---HHHHHHHHCCCHHHHHHHHHHH
Q ss_conf             325899999999999999982872---7899978489988999999981
Q gi|254780916|r  430 GEVRRLSDIEKEIIGLAMKLYRAQ---MSEVARRLGIGRSTLYRKIREY  475 (482)
Q Consensus       430 ~~~~~l~e~E~~~I~~aL~~~~Gn---~~~aA~~LGIsR~tL~rKlk~~  475 (482)
                         .-|++.++.|+....+.++|.   ..--|..+|..+.|+-..+.-|
T Consensus       255 ---~GLd~~Dr~~L~~l~~~f~GgPVGl~tLAa~lge~~~TIEdv~EPy  300 (328)
T PRK00080        255 ---LGLDEMDRKYLLTIIEKFGGGPVGLDTLAAALGEERDTIEDVYEPY  300 (328)
T ss_pred             ---CCCCHHHHHHHHHHHHHCCCCCCCHHHHHHHHCCCCCHHHHHHHHH
T ss_conf             ---4899889999999998529977009999999779821688875189


No 114
>PRK12402 replication factor C small subunit 2; Reviewed
Probab=98.98  E-value=6.3e-09  Score=82.71  Aligned_cols=209  Identities=19%  Similarity=0.204  Sum_probs=122.6

Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCCCHHHHHHHHHHHC--CCCCCCCCCCCCCCCCCCC----CCHHH
Q ss_conf             11111122222222222222223443204887327774367999999842--6754332101234655421----00243
Q gi|254780916|r  137 CALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHES--GKRAFFPFFIVNCGMIDQD----KIEKF  210 (482)
Q Consensus       137 ~~~~~LiG~S~~m~~v~~~i~~~a~~~~~vli~Ge~GtGK~~~A~~iH~~--s~r~~~~fi~v~c~~~~~~----~~e~~  210 (482)
                      ..+++++|+....+.+...+..  ..--.+|+.|++||||+.+|+++-..  +......+..+||+.+...    ..+..
T Consensus        12 ~~~~dvvGq~~i~~~L~~~~~~--~~~phlLf~GPpG~GKTt~A~~lA~~l~~~~~~~~~~~~nasd~~~~~~~~i~~~~   89 (337)
T PRK12402         12 SLFEDILGQESVVDHLSALAAS--GNLPHLVVYGPSGSGKTAAVRALARELYGDPWENNFTYFNVSDFFDQGKKYLVEDP   89 (337)
T ss_pred             CCHHHHCCCHHHHHHHHHHHHC--CCCCEEEEECCCCCCHHHHHHHHHHHHCCCCCCCCCCEECCCCCCCCCCCEEECCC
T ss_conf             9799803979999999999977--99876988892984899999999999679975678333116531135640010166


Q ss_pred             ----HHCCCCCCCCCCC-CC-CCCC--------CCCCCCEEEECCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCE
Q ss_conf             ----3112555532211-10-0123--------44667147516642001889998888776420011235532123431
Q gi|254780916|r  211 ----LFGDVDLQTKNSA-QF-LGKF--------IEANGGTIVLEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVR  276 (482)
Q Consensus       211 ----lFG~~~~~~~~~~-~~-~g~~--------~~a~~Gtl~l~ei~~L~~~~Q~~Ll~~l~~~~~~~~g~~~~~~~~~R  276 (482)
                          +++.. ...+... +. .-.+        ..+..-.++|||.+.|+...|..|++.|++-           +.++|
T Consensus        90 ~~~~~~~~~-~~~~~~~~d~i~~ii~~~a~~~p~~~~~KiiIlDEad~lt~~Aq~aLlk~lEe~-----------~~~~~  157 (337)
T PRK12402         90 RFAHFYDDP-KRKYKSVIDNFKHILKEYASMRPLSADYKLILFDNAEALREDAQQALRRIMERY-----------SETCR  157 (337)
T ss_pred             CHHHHHCCH-HHCCCCHHHHHHHHHHHHHCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHCC-----------CCCEE
T ss_conf             423442015-332773789999999998614887788049997071317999999999887408-----------87669


Q ss_pred             EEEECCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH------HHHHHHHHHHCCCCCCCCCCCCCCCCCCCC
Q ss_conf             56521433211111123337999886543344677877442222------556677764101122333321111100012
Q gi|254780916|r  277 LIFLTEKNLLPQVKSHVFRKDLYYRISVFLINISTLRSRSEDIP------WLVHFFLQSFCTKNAIKQISISDKALSLLT  350 (482)
Q Consensus       277 iIa~t~~~L~~~~~~g~fr~dLy~rL~~~~i~iPpLReR~eDI~------~L~~~fl~~~~~~~~~~~~~ls~~a~~~L~  350 (482)
                      +|.+|+.. ..+                    +||+|.|...+.      .-+...|...+++.|.   .+++++++.+.
T Consensus       158 fIl~t~~~-~~i--------------------i~tI~SRC~~i~F~~~s~~~i~~~L~~I~~~E~i---~~~~~~l~~ia  213 (337)
T PRK12402        158 FIFSTTQP-SKL--------------------IPPIRSRCLPLFFRPVPDDEIRSVLESIAAAEGV---EISDDGLDLIA  213 (337)
T ss_pred             EEEECCCC-CCC--------------------CHHHHHHCEEEECCCCCHHHHHHHHHHHHHHCCC---CCCHHHHHHHH
T ss_conf             98723864-447--------------------5247762445435898999999999999998499---98999999999


Q ss_pred             CCCCCCCHHHHHHHHHHHHHHCCCCCCCHHHHHHH
Q ss_conf             23389868999999999987438981068895454
Q gi|254780916|r  351 KYPWIDNVQELKNILLRAVIGLKDSHLTEDRFVLL  385 (482)
Q Consensus       351 ~y~WPGNvREL~n~i~r~~i~~~~~~i~~~~~~~~  385 (482)
                      ... -||+|.--|.++.+.. ..+..++...+...
T Consensus       214 ~~s-~GdlR~ain~Lq~~~~-~~~~~~~~~~~~~~  246 (337)
T PRK12402        214 YYA-EGDLRKAILTLQLAAE-AEGEVTTEAALEEL  246 (337)
T ss_pred             HHC-CCCHHHHHHHHHHHHH-HCCCCCCHHHHHHH
T ss_conf             986-9989999999999987-27997718899998


No 115
>smart00350 MCM minichromosome  maintenance proteins.
Probab=98.95  E-value=9e-09  Score=81.63  Aligned_cols=114  Identities=16%  Similarity=0.209  Sum_probs=83.0

Q ss_pred             CCCEEEEEECCCCCHHHHHHHHHHHCCCCCCCCCCCCC---CCCCCCCCCHHHHHCCCCCCCCCCCCCCCCCCCCCCCEE
Q ss_conf             43204887327774367999999842675433210123---465542100243311255553221110012344667147
Q gi|254780916|r  161 DCAIPIMIQGEFGVGKKRLSRFIHESGKRAFFPFFIVN---CGMIDQDKIEKFLFGDVDLQTKNSAQFLGKFIEANGGTI  237 (482)
Q Consensus       161 ~~~~~vli~Ge~GtGK~~~A~~iH~~s~r~~~~fi~v~---c~~~~~~~~e~~lFG~~~~~~~~~~~~~g~~~~a~~Gtl  237 (482)
                      ..+.+||+.|++||||+.+-++++..++|+  -|++-.   -++++....       ++..+|...-..|.+-.|++|.+
T Consensus       234 Rg~ihiLLvGDPGtgKSqlLk~~~~iaprs--vytsG~gsS~aGLTaav~-------rd~~~ge~~leaGALVlAD~Gic  304 (509)
T smart00350      234 RGDINILLLGDPGTAKSQLLKYVEKTAPRA--VYTTGKGSSAVGLTAAVT-------RDPETREFTLEGGALVLADNGVC  304 (509)
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHHHHCCCE--EEEECCCCCCCCCEEEEE-------ECCCCCCEEECCCCEECCCCCEE
T ss_conf             154149984699823629999999858860--687344455577068999-------81788837872564120567547


Q ss_pred             EECCCCHHHHHHHHHHHHHHHHHHCCCC--CCCCCCCCCCEEEEECCC
Q ss_conf             5166420018899988887764200112--355321234315652143
Q gi|254780916|r  238 VLEEPDALPLAVQGRIYNFIETGKIEFF--DSRGAIRLDVRLIFLTEK  283 (482)
Q Consensus       238 ~l~ei~~L~~~~Q~~Ll~~l~~~~~~~~--g~~~~~~~~~RiIa~t~~  283 (482)
                      ++||.+.|+...+..|+.+++.+.+.--  |=.......+-|+||+|-
T Consensus       305 cIDEfdKm~~~dr~alhEaMEQQtisiaKaGi~~tL~aR~sVlAAaNP  352 (509)
T smart00350      305 CIDEFDKMDDSDRTAIHEAMEQQTISIAKAGITTTLNARCSVLAAANP  352 (509)
T ss_pred             EEEEHHHCCHHHHHHHHHHHHHCEEEEECCCEEEEEECCCEEEEEECC
T ss_conf             852132078778999999997487787437517998557359986556


No 116
>PRK13406 bchD magnesium chelatase subunit D; Provisional
Probab=98.91  E-value=3.9e-08  Score=77.11  Aligned_cols=209  Identities=16%  Similarity=0.148  Sum_probs=129.3

Q ss_pred             EEEEECCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCHHHHHCCCCC----CCCCCCCCCCCCCCCCCCEEEEC
Q ss_conf             48873277743679999998426754332101234655421002433112555----53221110012344667147516
Q gi|254780916|r  165 PIMIQGEFGVGKKRLSRFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFGDVDL----QTKNSAQFLGKFIEANGGTIVLE  240 (482)
Q Consensus       165 ~vli~Ge~GtGK~~~A~~iH~~s~r~~~~fi~v~c~~~~~~~~e~~lFG~~~~----~~~~~~~~~g~~~~a~~Gtl~l~  240 (482)
                      =|+|.|+.||+|+++++.+...-+ ...||+.+     |...-|..|||--+-    .+|...-..|+|.+|++|.||+|
T Consensus        27 Gvlirg~~Gtakst~~r~l~~llp-~~~p~~~l-----Pl~~tedrl~G~lDi~~tL~~G~~v~~~GLLa~A~~gvLyvd  100 (584)
T PRK13406         27 GVVLRARAGPVRDRWLAALRALLP-AGTPLRRL-----PPGIADDRLLGGLDLAATLRAGRPVAERGLLAEADGGVLVLA  100 (584)
T ss_pred             CEEEECCCCCHHHHHHHHHHHHCC-CCCCEEEC-----CCCCCHHHHCCCCCHHHHHHCCCEECCCCHHHCCCCCEEEEE
T ss_conf             189977999579999999997568-99984656-----999974151471259999976898525753330369989985


Q ss_pred             CCCHHHHHHHHHHHHHHHHH--HCCCCCCCCCCCCCCEEEEECCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             64200188999888877642--0011235532123431565214332111111233379998865433446778774422
Q gi|254780916|r  241 EPDALPLAVQGRIYNFIETG--KIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYYRISVFLINISTLRSRSED  318 (482)
Q Consensus       241 ei~~L~~~~Q~~Ll~~l~~~--~~~~~g~~~~~~~~~RiIa~t~~~L~~~~~~g~fr~dLy~rL~~~~i~iPpLReR~eD  318 (482)
                      |++.|+..+...|+.++..|  .++|-|-....++.|-+|+..+...++.    ...+-|-.||. +.+.+-.++.+-.+
T Consensus       101 evnll~d~lv~~Ll~a~~~G~~~vEReGiS~~~parf~LIa~deg~e~de----~~~~~l~dRla-~~vd~~~~~~~~~~  175 (584)
T PRK13406        101 MAERLEPGTAARLAAALDAGEVAIERDGLALRMPARFGLVALDEGAEEDE----RAPAALADRLA-FHLDLDGLALRDTR  175 (584)
T ss_pred             CHHHCCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCEEEEEEECCCCCCCC----CHHHHHHHHHC-CCCCHHHHHHHHHH
T ss_conf             14737888999999998548740025876635665058999467887643----11078887650-70681676666401


Q ss_pred             HHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHH------HHHHHHHCCCCCCCHHHHHHHH
Q ss_conf             2255667776410112233332111110001223389868999999------9999874389810688954542
Q gi|254780916|r  319 IPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQELKNI------LLRAVIGLKDSHLTEDRFVLLL  386 (482)
Q Consensus       319 I~~L~~~fl~~~~~~~~~~~~~ls~~a~~~L~~y~WPGNvREL~n~------i~r~~i~~~~~~i~~~~~~~~l  386 (482)
                      -......=+.. + +...+...++++.++.+...-.-.+|.=++.-      .+-+..+.....++.+|+....
T Consensus       176 ~~~~~~~~i~~-A-r~~L~~V~i~d~~~~~l~~~a~~~gv~g~Ra~i~~~raArA~AAl~Gr~~V~~~Dl~~Aa  247 (584)
T PRK13406        176 EFPIDADDIAA-A-RARLAAVRVPPEAIEALCAAAAALGIASLRAPLLALRAARAAAALAGRTAVEEADIALAA  247 (584)
T ss_pred             HHHHHHHHHHH-H-HHHCCCCCCCHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHCCCCCCCHHHHHHHH
T ss_conf             11123689999-9-986786666999999999999983998620999999999999997499978899999999


No 117
>PRK08903 hypothetical protein; Validated
Probab=98.85  E-value=2.4e-08  Score=78.62  Aligned_cols=209  Identities=14%  Similarity=0.093  Sum_probs=124.5

Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC---CCEEEEEECCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             2222111111112222222222222222344---3204887327774367999999842675433210123465542100
Q gi|254780916|r  131 SQENEHCALDSLIAVSPAMIQVVDLARKAGD---CAIPIMIQGEFGVGKKRLSRFIHESGKRAFFPFFIVNCGMIDQDKI  207 (482)
Q Consensus       131 ~~~~~~~~~~~LiG~S~~m~~v~~~i~~~a~---~~~~vli~Ge~GtGK~~~A~~iH~~s~r~~~~fi~v~c~~~~~~~~  207 (482)
                      -......+++.++..+.  ..+...+.+.+.   ...+++|.|++|+||+++.+++.+.....+..-+.++|...+... 
T Consensus         9 ~~l~~~~tfdnFv~g~n--~~~~~~l~~~~~~~~~~~~l~i~G~~G~GKTHLl~a~~~~~~~~~~~~~yl~~~~~~~~~-   85 (227)
T PRK08903          9 LGPPPPPTFDNFIAGEN--AELVTRLRELAAGPVADRFFYLWGEAGSGRSHLLQALVAAASEGGKNARYLDPASPLLAF-   85 (227)
T ss_pred             CCCCCCCCHHCCCCCCH--HHHHHHHHHHHHCCCCCCEEEEECCCCCCHHHHHHHHHHHHHHCCCCEEEECCCCCHHHH-
T ss_conf             99999876431557775--999999998874388786699989999988899999999998069974996511045777-


Q ss_pred             HHHHHCCCCCCCCCCCCCCCCCCCCCCCEEEECCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCEEEEECCCCCCC
Q ss_conf             24331125555322111001234466714751664200188999888877642001123553212343156521433211
Q gi|254780916|r  208 EKFLFGDVDLQTKNSAQFLGKFIEANGGTIVLEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLP  287 (482)
Q Consensus       208 e~~lFG~~~~~~~~~~~~~g~~~~a~~Gtl~l~ei~~L~~~~Q~~Ll~~l~~~~~~~~g~~~~~~~~~RiIa~t~~~L~~  287 (482)
                      +   |                .+  +...+++|+|+.+....|..|+.++..-. .    +    -...++.+++.++..
T Consensus        86 ~---~----------------~~--~~d~l~iDDi~~i~~~~q~~lF~l~N~~~-~----~----~~~~ll~s~~~~p~~  135 (227)
T PRK08903         86 D---F----------------DP--RAELYAVDDVERLDDAQQIALFNLFNRVR-A----H----GKTALLVAGPAAPLA  135 (227)
T ss_pred             H---H----------------HH--CCCEEEEECCCCCCCHHHHHHHHHHHHHH-H----C----CCCEEEECCCCCHHH
T ss_conf             4---2----------------00--18989996411489569999999999999-7----2----994899718997120


Q ss_pred             CCCHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHH
Q ss_conf             1111233379998865-433446778774422225566777641011223333211111000122338986899999999
Q gi|254780916|r  288 QVKSHVFRKDLYYRIS-VFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQELKNILL  366 (482)
Q Consensus       288 ~~~~g~fr~dLy~rL~-~~~i~iPpLReR~eDI~~L~~~fl~~~~~~~~~~~~~ls~~a~~~L~~y~WPGNvREL~n~i~  366 (482)
                      +    .+++||--||+ +..+.++|+-+     . +....+.+.+...|   ..++++++++|..+ .++|+|+|..++.
T Consensus       136 l----~~~~DL~SRl~~gl~~~i~~pdd-----e-~~~~iL~~~a~~rg---l~l~~~v~~yl~~r-~~R~~~~L~~~l~  201 (227)
T PRK08903        136 L----DVREDLRTRLGWGLVYEVKPLSD-----E-DKIAALKAAAAERG---LQLADEVPDYLLTH-FRRDMPSLMALLD  201 (227)
T ss_pred             C----CCCHHHHHHHHCCCEEEEECCCH-----H-HHHHHHHHHHHHCC---CCCCHHHHHHHHHH-HCCCHHHHHHHHH
T ss_conf             1----20089999993897389979799-----9-99999999999629---99988999999998-3478999999999


Q ss_pred             HHHH--HCCCCCCCHHHHHHHH
Q ss_conf             9987--4389810688954542
Q gi|254780916|r  367 RAVI--GLKDSHLTEDRFVLLL  386 (482)
Q Consensus       367 r~~i--~~~~~~i~~~~~~~~l  386 (482)
                      ++-.  ...+..||..-+...+
T Consensus       202 ~Ld~~sl~~kr~iTi~lvkevL  223 (227)
T PRK08903        202 ALDRYSLEQKRAVTLPLLREML  223 (227)
T ss_pred             HHHHHHHHCCCCCCHHHHHHHH
T ss_conf             9999999829999999999985


No 118
>PRK04195 replication factor C large subunit; Provisional
Probab=98.84  E-value=2e-08  Score=79.16  Aligned_cols=203  Identities=19%  Similarity=0.247  Sum_probs=120.0

Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCC---CEEEEEECCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCC-CCCCHHHHH
Q ss_conf             11111122222222222222223443---20488732777436799999984267543321012346554-210024331
Q gi|254780916|r  137 CALDSLIAVSPAMIQVVDLARKAGDC---AIPIMIQGEFGVGKKRLSRFIHESGKRAFFPFFIVNCGMID-QDKIEKFLF  212 (482)
Q Consensus       137 ~~~~~LiG~S~~m~~v~~~i~~~a~~---~~~vli~Ge~GtGK~~~A~~iH~~s~r~~~~fi~v~c~~~~-~~~~e~~lF  212 (482)
                      ..+.+++|++...+.+..-+......   ..++|+.|++||||+++|++|-..-   +-.++.+|++.-- .+.++.. .
T Consensus        11 k~~~divg~~~~v~~l~~Wl~~w~~g~~~~k~lLL~GPpGvGKTT~a~~lAk~~---g~~viElNASD~R~~~~I~~~-i   86 (403)
T PRK04195         11 KSLSDVVGNEKAKKQLREWIESWLKGKPPKKALLLYGPPGVGKTSLAHALANDY---GWEVIELNASDQRTKDVIERV-A   86 (403)
T ss_pred             CCHHHHHCCHHHHHHHHHHHHHHHCCCCCCCEEEEECCCCCCHHHHHHHHHHHH---CCCEEEECCCCCCCHHHHHHH-H
T ss_conf             989998588999999999999987399657469988939987999999999984---998599771011478999999-9


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCEEEECCCCHHHHHHH----HHHHHHHHHHHCCCCCCCCCCCCCCEEEEECCCCCCCC
Q ss_conf             12555532211100123446671475166420018899----98888776420011235532123431565214332111
Q gi|254780916|r  213 GDVDLQTKNSAQFLGKFIEANGGTIVLEEPDALPLAVQ----GRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQ  288 (482)
Q Consensus       213 G~~~~~~~~~~~~~g~~~~a~~Gtl~l~ei~~L~~~~Q----~~Ll~~l~~~~~~~~g~~~~~~~~~RiIa~t~~~L~~~  288 (482)
                      +.  +.+     ...++ ....-.++|||++.|+...|    ..|++++++.             ...||+++|-.....
T Consensus        87 ~~--~~~-----~~sl~-~~~~KlIIlDEvD~l~~~~d~gg~~al~~~ik~s-------------~~PiIli~Nd~~~~~  145 (403)
T PRK04195         87 GE--AST-----SGSLF-GAKRKLILLDEVDGIHGNADRGGVRAILEIIKKA-------------KNPIILTANDPYDPS  145 (403)
T ss_pred             HH--HHH-----CCCCC-CCCCEEEEEECCCCCCCHHHHHHHHHHHHHHHCC-------------CCEEEEEECCCCCCC
T ss_conf             98--760-----68877-8873499963434457244479999999998548-------------870899826845567


Q ss_pred             CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHH
Q ss_conf             11123337999886543344677877442222556677764101122333321111100012233898689999999999
Q gi|254780916|r  289 VKSHVFRKDLYYRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQELKNILLRA  368 (482)
Q Consensus       289 ~~~g~fr~dLy~rL~~~~i~iPpLReR~eDI~~L~~~fl~~~~~~~~~~~~~ls~~a~~~L~~y~WPGNvREL~n~i~r~  368 (482)
                      ..  .++.      .+..|.++|+...  +    +...|.+.|.+.|.   .+++++++.+.... .|.+|..-|.++-+
T Consensus       146 ~~--~lrs------~c~~i~F~~~~~~--~----I~~~L~~I~~~Egi---~i~~~aL~~Ia~~s-~GDlR~aIN~LQ~~  207 (403)
T PRK04195        146 LR--PLRN------ACLMIEFKRLSKR--S----IVPVLKRICRKEGI---ECEEEALREIAERS-GGDLRSAINDLQAI  207 (403)
T ss_pred             HH--HHHH------HHHHCCCCCCCHH--H----HHHHHHHHHHHCCC---CCCHHHHHHHHHHC-CCHHHHHHHHHHHH
T ss_conf             17--7997------6612217994999--9----99999999997699---99999999999987-97399999999999


Q ss_pred             HHHCCCCCCCHHHHHH
Q ss_conf             8743898106889545
Q gi|254780916|r  369 VIGLKDSHLTEDRFVL  384 (482)
Q Consensus       369 ~i~~~~~~i~~~~~~~  384 (482)
                      .  ..+..++.+++..
T Consensus       208 ~--~~~~~~~~~~~~~  221 (403)
T PRK04195        208 A--EGGGRITLDDVKT  221 (403)
T ss_pred             H--CCCCCCCHHHHHH
T ss_conf             7--4899775666664


No 119
>TIGR03420 DnaA_homol_Hda DnaA regulatory inactivator Hda. Members of this protein family are Hda (Homologous to DnaA). These proteins are about half the length of DnaA and homologous over length of Hda. In the model species Escherichia coli, the initiation of DNA replication requires DnaA bound to ATP rather than ADP; Hda helps facilitate the conversion of DnaA-ATP to DnaA-ADP.
Probab=98.84  E-value=2.2e-08  Score=78.82  Aligned_cols=208  Identities=14%  Similarity=0.128  Sum_probs=122.3

Q ss_pred             CCCCCCCCCCC-CCCC-CCCCCCCCCCCCCCCCEEEEEECCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCHHH
Q ss_conf             22111111112-2222-222222222223443204887327774367999999842675433210123465542100243
Q gi|254780916|r  133 ENEHCALDSLI-AVSP-AMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHESGKRAFFPFFIVNCGMIDQDKIEKF  210 (482)
Q Consensus       133 ~~~~~~~~~Li-G~S~-~m~~v~~~i~~~a~~~~~vli~Ge~GtGK~~~A~~iH~~s~r~~~~fi~v~c~~~~~~~~e~~  210 (482)
                      .+...+++.++ |.+. +...+...+..  ....+++|.|++|+||+++++++-+.....+...+.++|..+.....+  
T Consensus         8 l~~~~tfdnFi~~~N~~~~~~l~~~~~~--~~~~~l~i~G~~GsGKTHLl~a~~~~~~~~~~~~~yl~~~~~~~~~~~--   83 (226)
T TIGR03420         8 LPDDPTFDNFYAGGNAELLAALRQLAAG--KGDRFLYLWGESGSGKSHLLQAACAAAEERGKSAIYLPLAELAQADPE--   83 (226)
T ss_pred             CCCCCCHHCCCCCCHHHHHHHHHHHHHC--CCCCEEEEECCCCCCHHHHHHHHHHHHHCCCCCEEEECHHHHHHHHHH--
T ss_conf             9998763123658679999999987646--688869998999998899999999998626995799529998775399--


Q ss_pred             HHCCCCCCCCCCCCCCCCCCCCCCCEEEECCCCHHH--HHHHHHHHHHHHHHHCCCCCCCCCCCCCCEEEEECCCCCCCC
Q ss_conf             311255553221110012344667147516642001--889998888776420011235532123431565214332111
Q gi|254780916|r  211 LFGDVDLQTKNSAQFLGKFIEANGGTIVLEEPDALP--LAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQ  288 (482)
Q Consensus       211 lFG~~~~~~~~~~~~~g~~~~a~~Gtl~l~ei~~L~--~~~Q~~Ll~~l~~~~~~~~g~~~~~~~~~RiIa~t~~~L~~~  288 (482)
                      .+              ..++  +...|++|+|+.+.  ...|..|+.++..-.          ....+||.+++..+.++
T Consensus        84 ~l--------------~~l~--~~d~l~iDDi~~i~~~~~~e~~lF~l~N~~~----------~~~~~ilits~~~p~~l  137 (226)
T TIGR03420        84 VL--------------EGLE--QADLVCLDDVEAIAGQPEWQEALFHLYNRVR----------EAGGRLLIAGRAAPAQL  137 (226)
T ss_pred             HH--------------HHCC--CCCEEEEECHHHHCCCHHHHHHHHHHHHHHH----------HHCCEEEEECCCCHHHC
T ss_conf             99--------------7274--4899999663334378378999999999998----------65282898678882320


Q ss_pred             CCHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHH
Q ss_conf             1112333799988654-334467787744222255667776410112233332111110001223389868999999999
Q gi|254780916|r  289 VKSHVFRKDLYYRISV-FLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQELKNILLR  367 (482)
Q Consensus       289 ~~~g~fr~dLy~rL~~-~~i~iPpLReR~eDI~~L~~~fl~~~~~~~~~~~~~ls~~a~~~L~~y~WPGNvREL~n~i~r  367 (482)
                      -   .+.+||--||+. ..++++++-+  +....+    +.+.+...|   ..+++++++.|..+ .+.|+|+|++++.+
T Consensus       138 ~---~~l~dL~SRl~~~~~~~I~~pdd--~~~~~i----L~k~~~~r~---i~i~~~vi~yl~~r-~~R~~~~l~~~l~~  204 (226)
T TIGR03420       138 P---LRLPDLRTRLAWGLVFQLPPLSD--EEKIAA----LQSRAARRG---LQLPDEVADYLLRH-GSRDMGSLMALLDA  204 (226)
T ss_pred             C---CCHHHHHHHHHCCCEEECCCCCH--HHHHHH----HHHHHHHCC---CCCCHHHHHHHHHH-CCCCHHHHHHHHHH
T ss_conf             3---20177999996885685279999--999999----999999859---98899999999986-37989999999999


Q ss_pred             HHH--HCCCCCCCHHHHH
Q ss_conf             987--4389810688954
Q gi|254780916|r  368 AVI--GLKDSHLTEDRFV  383 (482)
Q Consensus       368 ~~i--~~~~~~i~~~~~~  383 (482)
                      +-.  +..+..|+..-+.
T Consensus       205 Ld~~sl~~kr~ITi~l~k  222 (226)
T TIGR03420       205 LDRASLAAKRKITIPFVK  222 (226)
T ss_pred             HHHHHHHHCCCCCHHHHH
T ss_conf             999999808999999999


No 120
>PRK03992 proteasome-activating nucleotidase; Provisional
Probab=98.82  E-value=2e-08  Score=79.12  Aligned_cols=217  Identities=18%  Similarity=0.225  Sum_probs=127.7

Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCC----------CC-CCCEEEEEECCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCC
Q ss_conf             22111111112222222222222222----------34-43204887327774367999999842675433210123465
Q gi|254780916|r  133 ENEHCALDSLIAVSPAMIQVVDLARK----------AG-DCAIPIMIQGEFGVGKKRLSRFIHESGKRAFFPFFIVNCGM  201 (482)
Q Consensus       133 ~~~~~~~~~LiG~S~~m~~v~~~i~~----------~a-~~~~~vli~Ge~GtGK~~~A~~iH~~s~r~~~~fi~v~c~~  201 (482)
                      +.....++++-|-..+.+.+++.+.-          +. ....-||+.|++||||+++|+++-..+   +.+|+.|+++.
T Consensus       125 e~P~v~~~dIGGl~~~k~el~E~velPl~~pe~f~~~Gi~pPkGvLLyGPPGtGKTllAkAvA~e~---~~~fi~v~~s~  201 (390)
T PRK03992        125 ESPDVTYEDIGGLDEQIREVREAVELPLKNPELFEEVGIEPPKGVLLYGPPGTGKTLLAKAVAHET---NATFIRVVGSE  201 (390)
T ss_pred             CCCCCCHHHHCCHHHHHHHHHHHHHHHHHCHHHHHHCCCCCCCEEEEECCCCCCHHHHHHHHHHHH---CCCEEEEEHHH
T ss_conf             799998466149899999999999998659899997699999727868989997899999999874---88879966799


Q ss_pred             CCCCCCHHHHHCCCCCCCCCCCCCCCCCCCC---CCCEEEECCCCHHHH-----------HHHHHHHHHHHHHHCCCCCC
Q ss_conf             5421002433112555532211100123446---671475166420018-----------89998888776420011235
Q gi|254780916|r  202 IDQDKIEKFLFGDVDLQTKNSAQFLGKFIEA---NGGTIVLEEPDALPL-----------AVQGRIYNFIETGKIEFFDS  267 (482)
Q Consensus       202 ~~~~~~e~~lFG~~~~~~~~~~~~~g~~~~a---~~Gtl~l~ei~~L~~-----------~~Q~~Ll~~l~~~~~~~~g~  267 (482)
                      +-.     ...|+.      ...-.-+|+.|   ..-.+|+|||+.+..           .+|.-+..+|.+=     ++
T Consensus       202 l~s-----k~vGes------ek~vr~lF~~Ar~~aP~IiFiDEiDai~~~R~~~~~~g~~ev~r~l~qLL~em-----DG  265 (390)
T PRK03992        202 LVQ-----KFIGEG------ARLVRELFELAREKAPSIIFIDEIDAIAAKRTDSGTSGDREVQRTLMQLLAEM-----DG  265 (390)
T ss_pred             HHH-----CCCCHH------HHHHHHHHHHHHHHCCCEEEHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHC-----CC
T ss_conf             752-----454179------99999999999970990897143256633567788862088999999999974-----48


Q ss_pred             CCCCCCCCEEEEECCCC--CC-CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCC
Q ss_conf             53212343156521433--21-1111123337999886543344677877442222556677764101122333321111
Q gi|254780916|r  268 RGAIRLDVRLIFLTEKN--LL-PQVKSHVFRKDLYYRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDK  344 (482)
Q Consensus       268 ~~~~~~~~RiIa~t~~~--L~-~~~~~g~fr~dLy~rL~~~~i~iPpLReR~eDI~~L~~~fl~~~~~~~~~~~~~ls~~  344 (482)
                      -. ...++.||+|||..  |+ .+...|+|..       .+.|.+|.-.+|.+ |   +..++..    .... ..++-+
T Consensus       266 ~~-~~~~V~VIaATNrpd~LDpAllRpGRFDr-------~I~iplPd~~~R~~-I---lki~~~~----~~l~-~dvdl~  328 (390)
T PRK03992        266 FD-PRGNVKIIAATNRPDILDPALLRPGRFDR-------IIEVPLPDEEGRLE-I---LKIHTRK----MNLA-DDVDLE  328 (390)
T ss_pred             CC-CCCCEEEEEECCCCHHCCHHHHCCCCCCE-------EEEECCCCHHHHHH-H---HHHHHCC----CCCC-CCCCHH
T ss_conf             77-77882799606981005977754776523-------88708949999999-9---9998479----9999-888999


Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHHHC---CCCCCCHHHHHHHHCC
Q ss_conf             1000122338986899999999998743---8981068895454212
Q gi|254780916|r  345 ALSLLTKYPWIDNVQELKNILLRAVIGL---KDSHLTEDRFVLLLSR  388 (482)
Q Consensus       345 a~~~L~~y~WPGNvREL~n~i~r~~i~~---~~~~i~~~~~~~~l~~  388 (482)
                      .+..... .|  +-.+|+++|..|.+.+   ....|+.+||...+.+
T Consensus       329 ~lA~~T~-G~--SGADI~~lc~EA~m~Air~~r~~i~~~Df~~Ai~k  372 (390)
T PRK03992        329 ELAELTE-GA--SGADLKAICTEAGMFAIRDDRTEVTMEDFLKAIEK  372 (390)
T ss_pred             HHHHHCC-CC--CHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHH
T ss_conf             9997687-99--89999999999999999858986089999999999


No 121
>CHL00176 ftsH cell division protein; Validated
Probab=98.82  E-value=1.8e-08  Score=79.52  Aligned_cols=217  Identities=18%  Similarity=0.245  Sum_probs=126.8

Q ss_pred             CCCCCCCCCCCCCCCCCCCC---CCCCCCC-------CCCCCEEEEEECCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCC
Q ss_conf             22211111111222222222---2222222-------3443204887327774367999999842675433210123465
Q gi|254780916|r  132 QENEHCALDSLIAVSPAMIQ---VVDLARK-------AGDCAIPIMIQGEFGVGKKRLSRFIHESGKRAFFPFFIVNCGM  201 (482)
Q Consensus       132 ~~~~~~~~~~LiG~S~~m~~---v~~~i~~-------~a~~~~~vli~Ge~GtGK~~~A~~iH~~s~r~~~~fi~v~c~~  201 (482)
                      .......|.+..|...+-++   +.+.++.       =|....-||+.|++||||+++||++-..   ++-||+.+..+.
T Consensus       169 ~~~~~vtF~DVaG~~eaK~el~EivdfLk~P~k~~~~Gak~PkGvLL~GpPGTGKTlLAkAvAgE---a~vpF~~~sgs~  245 (631)
T CHL00176        169 EAKTGITFNDVAGVEEAKEELEEVVTFLKKPERFTAVGAKIPKGVLLVGPPGTGKTLLAKAIAGE---AEVPFFSISGSE  245 (631)
T ss_pred             CCCCCCCCCCCCCCHHHHHHHHHHHHHHCCHHHHHHCCCCCCCEEEEECCCCCCHHHHHHHHHCC---CCCCEEEEEHHH
T ss_conf             78999775322885899999999999835958876449968965898898998788999998565---588469988378


Q ss_pred             CCCCCCHHHHHCCCCCCCCCCCCCCCCCCCCCC---CEEEECCCCHHHHH----------H-HHHHHHHHHHHHCCCCCC
Q ss_conf             542100243311255553221110012344667---14751664200188----------9-998888776420011235
Q gi|254780916|r  202 IDQDKIEKFLFGDVDLQTKNSAQFLGKFIEANG---GTIVLEEPDALPLA----------V-QGRIYNFIETGKIEFFDS  267 (482)
Q Consensus       202 ~~~~~~e~~lFG~~~~~~~~~~~~~g~~~~a~~---Gtl~l~ei~~L~~~----------~-Q~~Ll~~l~~~~~~~~g~  267 (482)
                      +.     +...|.      ..++...+|++|..   -.+|+|||+.+...          . ..-|-++|-+     +++
T Consensus       246 F~-----e~~vGv------ga~rVR~LF~~Ar~~aP~IiFIDEiDaig~~Rg~~~~gg~~e~e~tlnqLL~e-----mDG  309 (631)
T CHL00176        246 FV-----EMFVGV------GAARVRDLFKKAKENSPCIVFIDEIDAVGRQRGAGVGGGNDEREQTLNQLLTE-----MDG  309 (631)
T ss_pred             HH-----HHHCCH------HHHHHHHHHHHHHHCCCEEEEEEEEEEEEECCCCCCCCCCCHHHHHHHHHHHH-----HCC
T ss_conf             55-----642155------58999999999986399699987101201147898889850899999999998-----428


Q ss_pred             CCCCCCCCEEEEECCCC--C-CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCC
Q ss_conf             53212343156521433--2-11111123337999886543344677877442222556677764101122333321111
Q gi|254780916|r  268 RGAIRLDVRLIFLTEKN--L-LPQVKSHVFRKDLYYRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDK  344 (482)
Q Consensus       268 ~~~~~~~~RiIa~t~~~--L-~~~~~~g~fr~dLy~rL~~~~i~iPpLReR~eDI~~L~~~fl~~~~~~~~~~~~~ls~~  344 (482)
                      -. ....+=+|+|||+.  | ..++..|+|..       .+.|.+|....|.+ |   +.+++...  .+.   ..++-+
T Consensus       310 f~-~~~gViViaATNrpd~LDpALlRPGRFDR-------~I~V~lPD~~gR~~-I---L~vh~k~~--~l~---~dvdl~  372 (631)
T CHL00176        310 FE-GNKGVIVIAATNRIDILDAALLRPGRFDR-------QVTVSLPDFEGRLD-I---LKVHARNK--KLA---EDVSLE  372 (631)
T ss_pred             CC-CCCCEEEEEECCCCCCCCHHHCCCCCCCE-------EEEECCCCHHHHHH-H---HHHHHHCC--CCC---CCHHHH
T ss_conf             88-78886999825885545686626887754-------99826989899999-9---99997078--666---530099


Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHHH---CCCCCCCHHHHHHHHC
Q ss_conf             100012233898689999999999874---3898106889545421
Q gi|254780916|r  345 ALSLLTKYPWIDNVQELKNILLRAVIG---LKDSHLTEDRFVLLLS  387 (482)
Q Consensus       345 a~~~L~~y~WPGNvREL~n~i~r~~i~---~~~~~i~~~~~~~~l~  387 (482)
                      .++... ..|  .--+|.|++..+.+.   .....|+..|+...+.
T Consensus       373 ~iA~~T-~Gf--SGAdLanlvNEAal~AaR~~~~~it~~d~~~Aid  415 (631)
T CHL00176        373 LIARRT-PGF--SGADLANLLNEAAILAARRRKNQITMSEIDEAID  415 (631)
T ss_pred             HHHHHC-CCC--CHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHH
T ss_conf             998626-998--6788876999999999984777647889999999


No 122
>CHL00181 cbbX CbbX; Provisional
Probab=98.82  E-value=1.8e-08  Score=79.55  Aligned_cols=166  Identities=18%  Similarity=0.223  Sum_probs=96.8

Q ss_pred             CCCEEEEEECCCCCHHHHHHHH----HHHCCCCCCCCCCCCCCCCCCCCCCHHHHHCCCCCCCCCCCCCCCCCCCCCCCE
Q ss_conf             4320488732777436799999----984267543321012346554210024331125555322111001234466714
Q gi|254780916|r  161 DCAIPIMIQGEFGVGKKRLSRF----IHESGKRAFFPFFIVNCGMIDQDKIEKFLFGDVDLQTKNSAQFLGKFIEANGGT  236 (482)
Q Consensus       161 ~~~~~vli~Ge~GtGK~~~A~~----iH~~s~r~~~~fi~v~c~~~~~~~~e~~lFG~~~~~~~~~~~~~g~~~~a~~Gt  236 (482)
                      ....++++.|.+||||+++||.    +|..+--+.+.|+.++.+.+-..-        . |.|.  ......+++|-||.
T Consensus        57 ~~s~h~vF~GnPGTGKTTVARl~a~il~~lG~L~~g~vve~~r~dLvg~y--------v-G~Ta--~kt~~~i~~a~GGV  125 (287)
T CHL00181         57 SPGLHMSFTGSPGTGKTTVALKMADILYRLGYIKKGHLITVTRDDLVGQY--------I-GHTA--PKTKEVLKKAMGGV  125 (287)
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHHHHHHHCCCCCCCEEEEECHHHHCCCC--------C-CCCH--HHHHHHHHHCCCCE
T ss_conf             87653888789986799999999999998699558958995358841635--------3-5216--99999999645987


Q ss_pred             EEECCCCHHH---------HHHHHHHHHHHHHHHCCCCCCCCCCCCCCEEEEECCCCCCCCCCHHHHHHHHHHHHHHHHH
Q ss_conf             7516642001---------8899988887764200112355321234315652143321111112333799988654334
Q gi|254780916|r  237 IVLEEPDALP---------LAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYYRISVFLI  307 (482)
Q Consensus       237 l~l~ei~~L~---------~~~Q~~Ll~~l~~~~~~~~g~~~~~~~~~RiIa~t~~~L~~~~~~g~fr~dLy~rL~~~~i  307 (482)
                      ||+||-..|.         .+.=.-|+..+++.+        .   ++=+|.+-..+  + ++  .|-       +    
T Consensus       126 LfIDEAY~L~~~~~~~dfg~eaidtLl~~me~~~--------~---~lvvI~AGY~~--e-M~--~fl-------~----  178 (287)
T CHL00181        126 LFIDEAYYLYKPDNERDYGAEAIEILLQVMENQR--------D---DLVVIFAGYKD--R-MD--KFY-------E----  178 (287)
T ss_pred             EEEECHHHHCCCCCCCCCHHHHHHHHHHHHHHCC--------C---CEEEEEECCHH--H-HH--HHH-------H----
T ss_conf             9982446535788999837999999999987079--------9---88999846789--9-99--999-------8----


Q ss_pred             HHHHHHHHH-----------HHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCC-------CCCCCCHHHHHHHHHHHH
Q ss_conf             467787744-----------22225566777641011223333211111000122-------338986899999999998
Q gi|254780916|r  308 NISTLRSRS-----------EDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTK-------YPWIDNVQELKNILLRAV  369 (482)
Q Consensus       308 ~iPpLReR~-----------eDI~~L~~~fl~~~~~~~~~~~~~ls~~a~~~L~~-------y~WPGNvREL~n~i~r~~  369 (482)
                      .=|-|+.|-           +++..++..++.+.    +   ..+++++...+..       .+--||-|+.+|+++++.
T Consensus       179 ~NpGL~sRf~~~i~F~dYt~~EL~~I~~~~~~~~----~---~~l~~~a~~~l~~~~~~~~~~~~FGNaR~vrnl~e~a~  251 (287)
T CHL00181        179 SNPGLSSRVANHVDFPDYTPEELLQIAKMMLEEQ----Q---YQLTPEAEKVLLDYIKRRMEQPLFANARSVRNAIDRAR  251 (287)
T ss_pred             HCCCHHHHCCCEEECCCCCHHHHHHHHHHHHHHC----C---CCCCHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHH
T ss_conf             5904787688723779859999999999999986----9---82587999999999998508999874899999999999


Q ss_pred             HH
Q ss_conf             74
Q gi|254780916|r  370 IG  371 (482)
Q Consensus       370 i~  371 (482)
                      ..
T Consensus       252 ~~  253 (287)
T CHL00181        252 MR  253 (287)
T ss_pred             HH
T ss_conf             99


No 123
>COG2901 Fis Factor for inversion stimulation Fis, transcriptional activator [Transcription / DNA replication, recombination, and repair]
Probab=98.80  E-value=8.9e-09  Score=81.67  Aligned_cols=50  Identities=28%  Similarity=0.498  Sum_probs=46.4

Q ss_pred             CCCHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHCCCHHHHHHHHHHHCC
Q ss_conf             54325899999999999999982872789997848998899999998188
Q gi|254780916|r  428 QDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKIREYNI  477 (482)
Q Consensus       428 ~~~~~~~l~e~E~~~I~~aL~~~~Gn~~~aA~~LGIsR~tL~rKlk~~gi  477 (482)
                      .+.+...|.|+|+.++..+++.|+||+++||.+|||+|.||++|+|+||+
T Consensus        48 ~~lY~mVL~evE~PLL~~VM~~~~gNQtrAa~mLGinR~TLRKKLkqygl   97 (98)
T COG2901          48 NDLYEMVLAEVEQPLLDMVMQYTRGNQTRAALMLGINRGTLRKKLKKYGL   97 (98)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHCCCHHHHHHHHHHHCC
T ss_conf             34999999999738999999993264889999974328899999998267


No 124
>PRK10787 DNA-binding ATP-dependent protease La; Provisional
Probab=98.80  E-value=2.1e-08  Score=79.09  Aligned_cols=201  Identities=19%  Similarity=0.219  Sum_probs=131.8

Q ss_pred             CCCEEE-EEECCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCHHHHHCCCCCCCCCCCCCC-CCCC--CCCCCE
Q ss_conf             432048-873277743679999998426754332101234655421002433112555532211100-1234--466714
Q gi|254780916|r  161 DCAIPI-MIQGEFGVGKKRLSRFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFGDVDLQTKNSAQFL-GKFI--EANGGT  236 (482)
Q Consensus       161 ~~~~~v-li~Ge~GtGK~~~A~~iH~~s~r~~~~fi~v~c~~~~~~~~e~~lFG~~~~~~~~~~~~~-g~~~--~a~~Gt  236 (482)
                      ....|| ++.|++|+||+.+|+.|-..-.   .+|+.+.++++.+   |+|+-||+.-+-||-..++ -.+.  ...|=.
T Consensus       346 ~~kg~IlclvGpPGvGKTSl~~sIA~al~---r~f~rislGGv~D---eaeirGHrrTYvgampGrii~~l~~a~~~nPv  419 (784)
T PRK10787        346 KIKGPILCLVGPPGVGKTSLGQSIAKATG---RKYVRMALGGVRD---EAEIRGHRRTYIGSMPGKLIQKMAKVGVKNPL  419 (784)
T ss_pred             CCCCCEEEEECCCCCCHHHHHHHHHHHHC---CCEEEEECCCCCC---HHHHCCCCCCCCCCCCHHHHHHHHHHCCCCCE
T ss_conf             67787799646998772469999999858---9869980688788---88825643343443683899999974898856


Q ss_pred             EEECCCCHHHHHHH----HHHHHHHH---HHHCCCCCCCCCCC---CCCEEEEECCCCCCCCCCHHHHHHHHHHHHHHHH
Q ss_conf             75166420018899----98888776---42001123553212---3431565214332111111233379998865433
Q gi|254780916|r  237 IVLEEPDALPLAVQ----GRIYNFIE---TGKIEFFDSRGAIR---LDVRLIFLTEKNLLPQVKSHVFRKDLYYRISVFL  306 (482)
Q Consensus       237 l~l~ei~~L~~~~Q----~~Ll~~l~---~~~~~~~g~~~~~~---~~~RiIa~t~~~L~~~~~~g~fr~dLy~rL~~~~  306 (482)
                      ++||||+.|+.+.+    ..||.+|+   +..|.  +-.-..+   ++|-+||+.| ++.  +                 
T Consensus       420 ~llDEiDK~~~~~~Gdp~salLEvLDpeQN~~F~--Dhyl~~~~DlS~v~Fi~TaN-~~~--i-----------------  477 (784)
T PRK10787        420 FLLDEIDKMSSDMRGDPASALLEVLDPEQNVAFS--DHYLEVDYDLSDVMFVATSN-SMN--I-----------------  477 (784)
T ss_pred             EEEHHHHHHCCCCCCCHHHHHHHHCCHHHCCCCC--CCEEECCCCHHHEEEEEECC-CCC--C-----------------
T ss_conf             6500355522455899889999845976556400--03220464522258997327-677--8-----------------


Q ss_pred             HHHHHHHHHHHHHH----------HH-HHHHHHHHCCCCCCC--CCCCCCCCCCCC-CCCCCCCCHHHHHHHHHH----H
Q ss_conf             44677877442222----------55-667776410112233--332111110001-223389868999999999----9
Q gi|254780916|r  307 INISTLRSRSEDIP----------WL-VHFFLQSFCTKNAIK--QISISDKALSLL-TKYPWIDNVQELKNILLR----A  368 (482)
Q Consensus       307 i~iPpLReR~eDI~----------~L-~~~fl~~~~~~~~~~--~~~ls~~a~~~L-~~y~WPGNvREL~n~i~r----~  368 (482)
                        -+||++|.|=|.          .+ -+|.+.+..+++|..  ...|+++|+..+ ..|.+-.-||+|+..+..    +
T Consensus       478 --p~pLlDRmE~i~~~gYt~~eK~~Ia~~~l~p~~~~~~gl~~~~~~~~~~~~~~ii~~ytrEaGvR~ler~i~~i~rk~  555 (784)
T PRK10787        478 --PAPLLDRMEVIRLSGYTEDEKLNIAKRHLLPKQIERNALKKGELTVDDSAIIGIIRYYTREAGVRSLEREISKLCRKA  555 (784)
T ss_pred             --CHHHHHHEEEEEECCCCHHHHHHHHHHHCHHHHHHHHCCCCCCCCCCHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHH
T ss_conf             --767763121554116767889999997453999998289965674399999998753365444251688999999999


Q ss_pred             HH--H-CCC---CCCCHHHHHHHHCCCCC
Q ss_conf             87--4-389---81068895454212445
Q gi|254780916|r  369 VI--G-LKD---SHLTEDRFVLLLSREGK  391 (482)
Q Consensus       369 ~i--~-~~~---~~i~~~~~~~~l~~~~~  391 (482)
                      +.  . ...   -.|+.+++...++....
T Consensus       556 ~~~~~~~~~~~~~~i~~~~l~~~lg~~~~  584 (784)
T PRK10787        556 VKQLLLDKSLKHIEINGDNLHDYLGVQRF  584 (784)
T ss_pred             HHHHHCCCCCCCEEECHHHHHHHHCCCCC
T ss_conf             99997078878558889999998299878


No 125
>TIGR02442 Cob-chelat-sub cobaltochelatase subunit; InterPro: IPR012804   Cobalamin (vitamin B12) can be complexed with metal via ATP-dependent reactions (aerobic pathway) (e.g., in Pseudomonas denitrificans) or via ATP-independent reactions (anaerobic pathway) (e.g., in Salmonella typhimurium) , . The corresponding cobalt chelatases are not homologous.   Cobaltochelatase is responsible for the insertion of cobalt into the corrin ring of coenzyme B12 during its biosynthesis. Two versions have been well described. CbiK/CbiX is a monomeric, anaerobic version which acts early in the biosynthesis (IPR010388 from INTERPRO). CobNST is a trimeric, ATP-dependent, aerobic version which acts late in the biosynthesis, (IPR011953 from INTERPRO, IPR006537 from INTERPRO, IPR006538 from INTERPRO) .    The two pathways differ in the point of cobalt insertion during corrin ring formation . There are apparently a number of variations on these two pathways, where the major differences seem to be concerned with the process of ring contraction .   Cobaltochelatase shows similarities with magnesium chelatase, which is also a complex ATP-dependent enzyme made up of two separable components. However, unlike the situation in cobaltochelatase, one of these two components is membrane bound in magnesium chelatase . .
Probab=98.78  E-value=1e-08  Score=81.21  Aligned_cols=239  Identities=15%  Similarity=0.155  Sum_probs=133.9

Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCCCHHHHHHHHHHHCCCC----CCCCCC---------CCCC------
Q ss_conf             111122222222222222223443204887327774367999999842675----433210---------1234------
Q gi|254780916|r  139 LDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHESGKR----AFFPFF---------IVNC------  199 (482)
Q Consensus       139 ~~~LiG~S~~m~~v~~~i~~~a~~~~~vli~Ge~GtGK~~~A~~iH~~s~r----~~~~fi---------~v~c------  199 (482)
                      |..+||+-.-=+.+  .++-+-..=--|||.||-||||+++||.||+..+-    ++.||-         =-.|      
T Consensus         3 F~AiVGQe~LK~AL--LL~Av~P~iGGVLirG~KGTAKSTaaR~L~~LLP~i~~v~gC~f~cdP~~P~~~C~~C~~~~~~   80 (688)
T TIGR02442         3 FTAIVGQEDLKLAL--LLNAVNPRIGGVLIRGEKGTAKSTAARGLAALLPDIDVVAGCPFSCDPDDPEEWCEECRRKLEE   80 (688)
T ss_pred             CCCCCCHHHHHHHH--HHEEECCCCCEEEEECCCCCHHHHHHHHHHHHCCHHHHHCCCCCCCCCCCCCCCCHHHHHHHHC
T ss_conf             74221427986532--1002526637078877888627898884876160236640478887778870400676755520


Q ss_pred             -------------CCCCCCCCHHHHHCCCC---CC-CCCCCCCCCCCCCCCCCEEEECCCCHHHHHHHHHHHHHHHHH--
Q ss_conf             -------------65542100243311255---55-322111001234466714751664200188999888877642--
Q gi|254780916|r  200 -------------GMIDQDKIEKFLFGDVD---LQ-TKNSAQFLGKFIEANGGTIVLEEPDALPLAVQGRIYNFIETG--  260 (482)
Q Consensus       200 -------------~~~~~~~~e~~lFG~~~---~~-~~~~~~~~g~~~~a~~Gtl~l~ei~~L~~~~Q~~Ll~~l~~~--  260 (482)
                                   =.||-.-=|..++|.-+   +. .|...=.+|+|.+||+|.||+|||.-|.-.+=.-||.+...|  
T Consensus        81 ~G~~~~~~~~~~~V~LPlgATEDRVvG~LDi~~al~~G~~~FqPGLLA~AhrGiLYiDEVNLLdDhlVD~lLDaaA~G~n  160 (688)
T TIGR02442        81 QGTLPSEQRPVPFVNLPLGATEDRVVGSLDIERALKEGEKAFQPGLLAEAHRGILYIDEVNLLDDHLVDVLLDAAAMGVN  160 (688)
T ss_pred             CCCCCCCCCCCEEEECCCCCCHHHHCCHHHHHHHHHHCHHHHCCCCHHHHCCCEEEEEEECCCCCHHHHHHHHHHHCCCE
T ss_conf             47753135873588658775233221305489998718566078861754687167852001441477899998764800


Q ss_pred             HCCCCCCCCCCCCCCEEEEECCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHH---HH------HHHHHHHHHHHHHHHC
Q ss_conf             00112355321234315652143321111112333799988654334467787---74------4222255667776410
Q gi|254780916|r  261 KIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYYRISVFLINISTLR---SR------SEDIPWLVHFFLQSFC  331 (482)
Q Consensus       261 ~~~~~g~~~~~~~~~RiIa~t~~~L~~~~~~g~fr~dLy~rL~~~~i~iPpLR---eR------~eDI~~L~~~fl~~~~  331 (482)
                      .++|=|=.-.-++  |+|-.-+-|+|    +|.+|+-|..|..-. |.+-.-+   +|      +.....==..|..+|.
T Consensus       161 ~VEREG~S~~Hpa--rf~L~GTMNPE----EG~LRPQLLDRFGL~-V~v~~~~d~~~R~Ev~~Rrl~~d~dP~~F~~~~~  233 (688)
T TIGR02442       161 RVEREGLSVSHPA--RFVLIGTMNPE----EGDLRPQLLDRFGLC-VDVAASRDPEERVEVIRRRLAFDADPEAFAARWA  233 (688)
T ss_pred             EEEECCCCHHCHH--HHHHHCCCCCC----HHHHCHHHHHHHHCE-EEECCCCCHHHHHHHHHHHHHHCCCCHHHHHHHH
T ss_conf             6763574300114--55322037852----211022324244011-5502435866899999999754026778899999


Q ss_pred             CCC------------CCCCCCCCCCCCCCCCCCCCCCCHHHHHHHH------HHHHHHCCCCCCCHHHHHHHH
Q ss_conf             112------------2333321111100012233898689999999------999874389810688954542
Q gi|254780916|r  332 TKN------------AIKQISISDKALSLLTKYPWIDNVQELKNIL------LRAVIGLKDSHLTEDRFVLLL  386 (482)
Q Consensus       332 ~~~------------~~~~~~ls~~a~~~L~~y~WPGNvREL~n~i------~r~~i~~~~~~i~~~~~~~~l  386 (482)
                      .+.            =.+-..++++.+.++..----+||.=.+.-|      +-++.+.....++.+||....
T Consensus       234 ~~~~~L~~~I~~AR~lLp~V~l~d~~~~~I~~lc~~~~V~GhRAdi~~~raArAlAAl~GR~~V~~eDv~~Aa  306 (688)
T TIGR02442       234 AEQEELRERIAAARSLLPSVRLSDSLLRFISELCIEFGVDGHRADIVMARAARALAALDGRRRVTAEDVREAA  306 (688)
T ss_pred             HHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHCCCCEECHHHHHHHH
T ss_conf             9999999999999975477658889999999999972888525999999999999877288535377899999


No 126
>TIGR00763 lon ATP-dependent protease La; InterPro: IPR004815   Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes . They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence . Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases .   Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base . The geometric orientations of the catalytic residues are similar between families, despite different protein folds . The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) , .   Peptidases are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry. Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins.   Families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule.    This signature defines the bacterial and eukaryotic lon proteases, which are ATP-dependent serine peptidases belonging to the MEROPS peptidase family S16 (lon protease family, clan SF). This family of sequences does not include the archaeal lon homologs, IPR004663 from INTERPRO. In the eukaryotes the majority of the proteins are located in the mitochondrial matrix , . In yeast, Pim1, is located in the mitochondrial matrix, is required for mitochondrial function, is constitutively expressed but is increased after thermal stress, suggesting that Pim1 may play a role in the heat shock response .; GO: 0004176 ATP-dependent peptidase activity, 0005524 ATP binding, 0006510 ATP-dependent proteolysis.
Probab=98.78  E-value=2.4e-09  Score=85.69  Aligned_cols=177  Identities=22%  Similarity=0.297  Sum_probs=122.3

Q ss_pred             CCCEE-E-EEECCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCHHHHHCCCCCCCCCCCCCCCCCCC------C
Q ss_conf             43204-8-87327774367999999842675433210123465542100243311255553221110012344------6
Q gi|254780916|r  161 DCAIP-I-MIQGEFGVGKKRLSRFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFGDVDLQTKNSAQFLGKFIE------A  232 (482)
Q Consensus       161 ~~~~~-v-li~Ge~GtGK~~~A~~iH~~s~r~~~~fi~v~c~~~~~~~~e~~lFG~~~~~~~~~~~~~g~~~~------a  232 (482)
                      ...-| | ++.|++|+||+.+|+.|=..=   +..||.+..+++.++   +|+=||+.-+=||-.   |++-+      .
T Consensus       446 ~~~GpqIlClvGPPGVGKTSlg~SIA~AL---nRkFvR~SlGG~~De---AEIrGHRRTYvGAMP---GriiQ~lk~~~t  516 (941)
T TIGR00763       446 KMKGPQILCLVGPPGVGKTSLGKSIAKAL---NRKFVRFSLGGVRDE---AEIRGHRRTYVGAMP---GRIIQGLKKAKT  516 (941)
T ss_pred             CCCCCEEEEEECCCCCCHHHHHHHHHHHH---CCEEEEEEECCCEEH---HHCCCCCCCCCCCCH---HHHHHHHHHCCC
T ss_conf             88887678720726954222789999996---880499952672203---112786432034672---578999876041


Q ss_pred             CCCEEEECCCCHHH--HHHHH----HHHHHH---HHHHCCCCCCCCCCCC---CCE--EEEECCCCCCCCCCHHHHHHHH
Q ss_conf             67147516642001--88999----888877---6420011235532123---431--5652143321111112333799
Q gi|254780916|r  233 NGGTIVLEEPDALP--LAVQG----RIYNFI---ETGKIEFFDSRGAIRL---DVR--LIFLTEKNLLPQVKSHVFRKDL  298 (482)
Q Consensus       233 ~~Gtl~l~ei~~L~--~~~Q~----~Ll~~l---~~~~~~~~g~~~~~~~---~~R--iIa~t~~~L~~~~~~g~fr~dL  298 (482)
                      .|=-+.||||+-++  -+.|.    -||.+|   |+..|.-  =+-.+++   +|=  +||+.|.               
T Consensus       517 ~NPl~LlDEIDK~~~~~~~~GDPaSALLEvLDPEQN~~F~D--HYldvp~DLS~V~CyFi~TAN~---------------  579 (941)
T TIGR00763       517 KNPLILLDEIDKIGLKSSFRGDPASALLEVLDPEQNNAFSD--HYLDVPFDLSKVLCYFIATANS---------------  579 (941)
T ss_pred             CCCEEEEEEEEEECCCCCCCCCHHHHHHHHCCHHHCCCCCC--CCCCCCCCHHHHHHHEEECCCC---------------
T ss_conf             58806862022001678865563788864128643604255--3002340042002100024475---------------


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHH----------HHHH-HHHHHHCCCCCCC--CCCCCCCCCCCCCCCCC-CCCHHHHHHH
Q ss_conf             9886543344677877442222----------5566-7776410112233--33211111000122338-9868999999
Q gi|254780916|r  299 YYRISVFLINISTLRSRSEDIP----------WLVH-FFLQSFCTKNAIK--QISISDKALSLLTKYPW-IDNVQELKNI  364 (482)
Q Consensus       299 y~rL~~~~i~iPpLReR~eDI~----------~L~~-~fl~~~~~~~~~~--~~~ls~~a~~~L~~y~W-PGNvREL~n~  364 (482)
                         +..  |- +|||||.|=|.          .+++ |++-+.-..+|..  ...|+++|+..|..|.- =--||.|+.-
T Consensus       580 ---~d~--IP-~PLLDRMEvI~lsGY~~~EK~~IA~~yLiP~~~~~~GL~~~~l~~~d~al~~lI~~YtREaGVRNL~r~  653 (941)
T TIGR00763       580 ---IDT--IP-RPLLDRMEVIELSGYTEEEKLEIAKKYLIPKALEDHGLKPDELKISDEALLLLIKYYTREAGVRNLERQ  653 (941)
T ss_pred             ---CCC--CC-CCCCCCEEEEECCCCCHHHHHHHHHHCCHHHHHHHHCCCCCCEEECHHHHHHHHHHHHHHHCCHHHHHH
T ss_conf             ---767--77-221374024523888767899999854713679870888132212689999999875132021338999


Q ss_pred             HHHHH
Q ss_conf             99998
Q gi|254780916|r  365 LLRAV  369 (482)
Q Consensus       365 i~r~~  369 (482)
                      |+.++
T Consensus       654 I~~i~  658 (941)
T TIGR00763       654 IEKIC  658 (941)
T ss_pred             HHHHH
T ss_conf             99999


No 127
>TIGR01241 FtsH_fam ATP-dependent metallopeptidase HflB; InterPro: IPR005936   Metalloproteases are the most diverse of the four main types of protease, with more than 50 families identified to date. In these enzymes, a divalent cation, usually zinc, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. The known metal ligands are His, Glu, Asp or Lys and at least one other residue is required for catalysis, which may play an electrophillic role. Of the known metalloproteases, around half contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site . The HEXXH motif is relatively common, but can be more stringently defined for metalloproteases as 'abXHEbbHbc', where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases .   Peptidases are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry. Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins.   Families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule.    This group of metallopeptidases belong to MEROPS peptidase family M41 (FtsH endopeptidase family, clan MA(E)). The predicted active site residues for members of this family and thermolysin, the type example for clan MA, occur in the motif HEXXH.    FtsH is a membrane-anchored ATP-dependent protease that degrades misfolded or misassembled membrane proteins as well as a subset of cytoplasmic regulatory proteins. FtsH is a 647-residue protein of 70 kDa, with two putative transmembrane segments towards its N terminus which anchor the protein to the membrane, giving rise to a periplasmic domain of 70 residues and a cytoplasmic segment of 520 residues containing the ATPase and protease domains . ; GO: 0004222 metalloendopeptidase activity, 0030163 protein catabolic process, 0016020 membrane.
Probab=98.77  E-value=4.6e-09  Score=83.72  Aligned_cols=219  Identities=17%  Similarity=0.244  Sum_probs=136.7

Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCC---CCCCCCCC-------CCCCEEEEEECCCCCHHHHHHHHHHHCCCCCCCCCC
Q ss_conf             22222222211111111222222222---22222223-------443204887327774367999999842675433210
Q gi|254780916|r  126 EGVVPSQENEHCALDSLIAVSPAMIQ---VVDLARKA-------GDCAIPIMIQGEFGVGKKRLSRFIHESGKRAFFPFF  195 (482)
Q Consensus       126 ~~~~~~~~~~~~~~~~LiG~S~~m~~---v~~~i~~~-------a~~~~~vli~Ge~GtGK~~~A~~iH~~s~r~~~~fi  195 (482)
                      +.+...++.....|.+.-|..++=++   |.+.++.=       |+...=||+.|++||||+|+|||+=-.   ++=||.
T Consensus        45 ~Ak~~~~~~~kv~F~DVAG~dEAKeEl~EiVdFLK~P~kf~~LGaKIPKGVLLvGPPGTGKTLLAKAvAGE---A~VPFF  121 (505)
T TIGR01241        45 KAKLLNEEKPKVTFKDVAGIDEAKEELVEIVDFLKNPSKFTKLGAKIPKGVLLVGPPGTGKTLLAKAVAGE---AGVPFF  121 (505)
T ss_pred             HHHHHCCCCCCEEECCCCCCHHHHHHHHHHHHHCCCCHHHHHCCCCCCCCEEEECCCCCCHHHHHHHHHCC---CCCCCE
T ss_conf             89873058981322344453233343331342226963798727889871473178784246788752025---889624


Q ss_pred             CCCCCCCCCCCCHHHHHCCCCCCCCCCCCCCCCCCCCCC---CEEEECCCCHHHHHHHHHHHHHHHHHHCCCCCCC--CC
Q ss_conf             123465542100243311255553221110012344667---1475166420018899988887764200112355--32
Q gi|254780916|r  196 IVNCGMIDQDKIEKFLFGDVDLQTKNSAQFLGKFIEANG---GTIVLEEPDALPLAVQGRIYNFIETGKIEFFDSR--GA  270 (482)
Q Consensus       196 ~v~c~~~~~~~~e~~lFG~~~~~~~~~~~~~g~~~~a~~---Gtl~l~ei~~L~~~~Q~~Ll~~l~~~~~~~~g~~--~~  270 (482)
                      +|.-|.+     -+.+-|-      ..++..-+|++|..   ..+|+|||+.-..+=+          .-.-.|+|  ++
T Consensus       122 ~iSGSdF-----VEMFVGV------GASRVRDLFeqAK~nAPCIIFIDEIDAVGr~RG----------aG~lGGGnDERE  180 (505)
T TIGR01241       122 SISGSDF-----VEMFVGV------GASRVRDLFEQAKKNAPCIIFIDEIDAVGRQRG----------AGELGGGNDERE  180 (505)
T ss_pred             EECCCCE-----EECCCCC------CCEEHHHHHHHHHHHCCCEEEEECHHHCCCCCC----------CCCCCCCCCHHH
T ss_conf             7407610-----1112056------400014457999971897056401000033356----------436676541355


Q ss_pred             CCC--------------CCEEEEECCCC--C-CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCC
Q ss_conf             123--------------43156521433--2-111111233379998865433446778774422225566777641011
Q gi|254780916|r  271 IRL--------------DVRLIFLTEKN--L-LPQVKSHVFRKDLYYRISVFLINISTLRSRSEDIPWLVHFFLQSFCTK  333 (482)
Q Consensus       271 ~~~--------------~~RiIa~t~~~--L-~~~~~~g~fr~dLy~rL~~~~i~iPpLReR~eDI~~L~~~fl~~~~~~  333 (482)
                      .+.              .|=||||||++  | ..|+.-|+|++       .+.|..|-++.|.+ |       |+=++++
T Consensus       181 QTLNQLLVEMDGF~~~~gvIv~AATNRPDvLD~ALLRPGRFDR-------Qv~V~~PD~~GR~~-I-------L~VH~~~  245 (505)
T TIGR01241       181 QTLNQLLVEMDGFGTNTGVIVIAATNRPDVLDPALLRPGRFDR-------QVVVDLPDIKGREE-I-------LKVHAKN  245 (505)
T ss_pred             HHHHHHHEECCCCCCCCCEEEEEECCCCCCCCCCCCCCCCCCC-------EEECCCCCHHHHHH-H-------HHHHHCC
T ss_conf             4332331331785898857998504884116510068787445-------13458887467899-9-------9998548


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCC-HHHHHHHHHHHHH-HC--CCCCCCHHHHHHHHCC
Q ss_conf             223333211111000122338986-8999999999987-43--8981068895454212
Q gi|254780916|r  334 NAIKQISISDKALSLLTKYPWIDN-VQELKNILLRAVI-GL--KDSHLTEDRFVLLLSR  388 (482)
Q Consensus       334 ~~~~~~~ls~~a~~~L~~y~WPGN-vREL~n~i~r~~i-~~--~~~~i~~~~~~~~l~~  388 (482)
                      ..     ++++.--.-.+--=||= =-+|.|+|=-|.+ .+  ....|+..|+..+..+
T Consensus       246 ~k-----La~~vdL~~~Ar~TPGfSGADLaNl~NEAALlAAR~n~~~i~~~~~eeA~Dr  299 (505)
T TIGR01241       246 KK-----LAPDVDLKAVARRTPGFSGADLANLLNEAALLAARKNKTEITMNDIEEAVDR  299 (505)
T ss_pred             CC-----CCCCCCHHHHHHHCCCCCHHHHHHHHHHHHHHHHHCCCCEECHHHHHHHHHH
T ss_conf             89-----9702477999701568767889999999999986179865628889878776


No 128
>COG1067 LonB Predicted ATP-dependent protease [Posttranslational modification, protein turnover, chaperones]
Probab=98.74  E-value=3.3e-08  Score=77.63  Aligned_cols=226  Identities=18%  Similarity=0.204  Sum_probs=138.1

Q ss_pred             CCCCCEEEEEEC----CCCCHHHHHHHHHHHC------CCC-CCCCCCCC---CCCCC--CCCCCHHHHHCCC--CCC--
Q ss_conf             344320488732----7774367999999842------675-43321012---34655--4210024331125--555--
Q gi|254780916|r  159 AGDCAIPIMIQG----EFGVGKKRLSRFIHES------GKR-AFFPFFIV---NCGMI--DQDKIEKFLFGDV--DLQ--  218 (482)
Q Consensus       159 ~a~~~~~vli~G----e~GtGK~~~A~~iH~~------s~r-~~~~fi~v---~c~~~--~~~~~e~~lFG~~--~~~--  218 (482)
                      +......+...+    ..|.++...++.+-..      +.. ...-|+..   +-+.+  ....-.+.|||..  +.+  
T Consensus       127 ~~~~~~~~~~~~~~~~~~gv~~~~~~~iv~~~~~~~~~~~~~~~~~~~~~~~~~~~p~v~a~~~~~~~LlG~Vr~~~~qG  206 (647)
T COG1067         127 LGPIEQQIILYGYNALLPGVLYAVAARIVLYEAKILKRSAVSVPKNFVELSPLDGAPVVFATGAIADQLLGSVRHDPYQG  206 (647)
T ss_pred             HHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCEEECCCCCHHHCCEEEEECCCCC
T ss_conf             22466666540455346216778998888765312531033304556540235589679668777465361277768887


Q ss_pred             ----CCCCCCCCCCCCCCCCCEEEECCCCHHHHHHHHHHHHHHHHHHCCCCCCC----------CCCCCCCEEEEECCCC
Q ss_conf             ----32211100123446671475166420018899988887764200112355----------3212343156521433
Q gi|254780916|r  219 ----TKNSAQFLGKFIEANGGTIVLEEPDALPLAVQGRIYNFIETGKIEFFDSR----------GAIRLDVRLIFLTEKN  284 (482)
Q Consensus       219 ----~~~~~~~~g~~~~a~~Gtl~l~ei~~L~~~~Q~~Ll~~l~~~~~~~~g~~----------~~~~~~~RiIa~t~~~  284 (482)
                          |+-..-+.|.+.+||||.||+|+|..|+...|-++|..++++++...|+.          .++++|+.+|.+-+.+
T Consensus       207 ~l~~~~~~~i~pGaVHkAngGVLiIdei~lL~~~~~w~~LKa~~~k~~~~~~~~~~s~~~~v~~e~vP~d~klI~~Gn~~  286 (647)
T COG1067         207 GLGTTGHIRVKPGAVHKANGGVLIIDEIGLLAQPLQWKLLKALLDKEQPIWGSSEPSSGAPVRPESVPLDLKLILAGNRE  286 (647)
T ss_pred             CCCCCCCCCCCCCCCCCCCCCEEEEEHHHHHCCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCHH
T ss_conf             66788864236761101258479997566328398999999998244566576740248615788855654899408899


Q ss_pred             -CCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCC---------C
Q ss_conf             -211111123337999886543344677877442222556677764101122333321111100012233---------8
Q gi|254780916|r  285 -LLPQVKSHVFRKDLYYRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYP---------W  354 (482)
Q Consensus       285 -L~~~~~~g~fr~dLy~rL~~~~i~iPpLReR~eDI~~L~~~fl~~~~~~~~~~~~~ls~~a~~~L~~y~---------W  354 (482)
                       +..+-..-.+|-++|---..+.=.+|   ...+.-..+++.|.+..++..+.+  .++.+|.+.|..|-         .
T Consensus       287 ~l~~l~~~~~~r~~g~~y~ae~~~~m~---~~~~nr~k~~~~~~q~v~~d~~ip--~~~~~Av~~li~~a~R~Ag~~~~L  361 (647)
T COG1067         287 DLEDLHEPDRSRIEGFGYEAEFEDTMP---ITDANRSKLVQFYVQELARDGNIP--HLDKDAVEELIREAARRAGDQNKL  361 (647)
T ss_pred             HHHHHCCCCHHHHHHCCEEEEECCCCC---CCHHHHHHHHHHHHHHHHHCCCCC--CCCHHHHHHHHHHHHHHCCCCCEE
T ss_conf             997655347778840556899768889---986899999999999998628999--888899999999999861656502


Q ss_pred             CCCHHHHHHHHHHHHHHCCC---CCCCHHHHHHHHCCC
Q ss_conf             98689999999999874389---810688954542124
Q gi|254780916|r  355 IDNVQELKNILLRAVIGLKD---SHLTEDRFVLLLSRE  389 (482)
Q Consensus       355 PGNvREL~n~i~r~~i~~~~---~~i~~~~~~~~l~~~  389 (482)
                      +=+.|+|.|+++-+...+..   ..|+.+|+...+.+.
T Consensus       362 tl~~rdl~~lv~~A~~ia~~~~~~~I~ae~Ve~a~~~~  399 (647)
T COG1067         362 TLRLRDLGNLVREAGDIAVSEGRKLITAEDVEEALQKR  399 (647)
T ss_pred             CCCHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHH
T ss_conf             14899999999986688853786647699999999874


No 129
>TIGR00635 ruvB Holliday junction DNA helicase RuvB; InterPro: IPR004605 All proteins in this family for which functions are known are 5'-3' DNA helicases that, as part of a complex with RuvA homologs serve as a 5'-3' Holliday junction helicase. RuvA specifically binds Holliday junctions as a sandwich of two tetramers and maintains the configuration of the junction. It forms a complex with two hexameric rings of RuvB, the subunit that contains helicase activity. The complex drives ATP-dependent branch migration of the Holliday junction recombination intermediate. The endonuclease RuvC resolves junctions.; GO: 0003677 DNA binding, 0005524 ATP binding, 0009378 Holliday junction helicase activity, 0006281 DNA repair, 0006310 DNA recombination.
Probab=98.70  E-value=4.5e-08  Score=76.69  Aligned_cols=241  Identities=18%  Similarity=0.242  Sum_probs=134.6

Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCC----CCEEEEEECCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCHHHHHC
Q ss_conf             111112222222222222222344----3204887327774367999999842675433210123465542100243311
Q gi|254780916|r  138 ALDSLIAVSPAMIQVVDLARKAGD----CAIPIMIQGEFGVGKKRLSRFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFG  213 (482)
Q Consensus       138 ~~~~LiG~S~~m~~v~~~i~~~a~----~~~~vli~Ge~GtGK~~~A~~iH~~s~r~~~~fi~v~c~~~~~~~~e~~lFG  213 (482)
                      .+.+++|+-..-+++.=.|+ +|+    +=-+||+.|++|-||+++|+-|=+      .  ..+||--.+.-.+|     
T Consensus         2 ~L~eFiGQ~~vk~~L~l~I~-AAk~R~e~LDH~LL~GPPGLGKTTLA~IiA~------E--mg~~l~iTsGP~L~-----   67 (305)
T TIGR00635         2 LLAEFIGQEKVKEQLQLFIE-AAKMRQEALDHLLLYGPPGLGKTTLAHIIAN------E--MGVNLKITSGPALE-----   67 (305)
T ss_pred             CCHHCCCCHHHHHHHHHHHH-HHHHCCCCCCCEEEECCCCCCHHHHHHHHHH------H--HCCCCEEEECCCCC-----
T ss_conf             80110582889999999999-9982489734166317568746789999999------8--38932674067554-----


Q ss_pred             CCCCCCCCCCCCCCCCC-CCCCCEEEECCCCHHHHHHHHHHHHHHHHHHCCCC-C---CCCCCCC---CCEEEEECCCCC
Q ss_conf             25555322111001234-46671475166420018899988887764200112-3---5532123---431565214332
Q gi|254780916|r  214 DVDLQTKNSAQFLGKFI-EANGGTIVLEEPDALPLAVQGRIYNFIETGKIEFF-D---SRGAIRL---DVRLIFLTEKNL  285 (482)
Q Consensus       214 ~~~~~~~~~~~~~g~~~-~a~~Gtl~l~ei~~L~~~~Q~~Ll~~l~~~~~~~~-g---~~~~~~~---~~RiIa~t~~~L  285 (482)
                             -..+-.|.+- .-.|-.||+||||.|++.+=.-|.=++|+=+..=+ |   +.+.++.   .|-+|-||++. 
T Consensus        68 -------kPgDlaaiLt~L~~gDVLFIDEIHRL~p~~EE~LYpAMEDF~lDi~IG~Gp~Ar~v~ldLpPFTLvGATTR~-  139 (305)
T TIGR00635        68 -------KPGDLAAILTNLEEGDVLFIDEIHRLSPAIEELLYPAMEDFRLDIVIGKGPSARSVRLDLPPFTLVGATTRA-  139 (305)
T ss_pred             -------CHHHHHHHHHHCCCCCEEECCHHHHCCHHHHHHCCCCCCCEEEEEEEECCCCCCEEEECCCCCCCCCCCCCC-
T ss_conf             -------757899999705689631012565048334531053001217877871289852576068694420000347-


Q ss_pred             CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-------HHHHHHHCCCCCCCCCCCCCCCCCCCCCCC-----
Q ss_conf             11111123337999886543344677877442222556-------677764101122333321111100012233-----
Q gi|254780916|r  286 LPQVKSHVFRKDLYYRISVFLINISTLRSRSEDIPWLV-------HFFLQSFCTKNAIKQISISDKALSLLTKYP-----  353 (482)
Q Consensus       286 ~~~~~~g~fr~dLy~rL~~~~i~iPpLReR~eDI~~L~-------~~fl~~~~~~~~~~~~~ls~~a~~~L~~y~-----  353 (482)
                            |..-              -|||+|-.=+..|=       ...+.+.+..++.   .+++++...+...+     
T Consensus       140 ------G~lt--------------~PLrdRFG~~~rl~fY~~~EL~~Iv~R~A~~L~~---ei~~~~a~~IArrSRGTPR  196 (305)
T TIGR00635       140 ------GMLT--------------SPLRDRFGIILRLEFYTPEELAEIVSRSAGLLNI---EIEQEAALEIARRSRGTPR  196 (305)
T ss_pred             ------CCCC--------------CCHHHHHHHHHHCCCCCHHHHHHHHHHHHHHCCC---CCCHHHHHHHHHHCCCCHH
T ss_conf             ------7410--------------3133454474540268987899998753344143---0077899999875478637


Q ss_pred             -------CCCCHHHHHHHHHHHHHHCCCCCCCHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHCCCCCCCCCC
Q ss_conf             -------8986899999999998743898106889545421244543223432222223344432100000000112344
Q gi|254780916|r  354 -------WIDNVQELKNILLRAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILDNLSQESIPAI  426 (482)
Q Consensus       354 -------WPGNvREL~n~i~r~~i~~~~~~i~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  426 (482)
                             |   ||..-.|       ..++.|+.+-....+..                                     .
T Consensus       197 IAnRLLRR---VRDfA~V-------~~~~~I~~~i~~~AL~~-------------------------------------L  229 (305)
T TIGR00635       197 IANRLLRR---VRDFAQV-------RGQGVITRDIALKALEM-------------------------------------L  229 (305)
T ss_pred             HHHHHHHH---HHHHHHH-------HCCCCCCHHHHHHHHHH-------------------------------------H
T ss_conf             88877676---6448887-------26787388999999886-------------------------------------2


Q ss_pred             CCCCHHHHHHHHHHHHHHHHHHHHCCC---HHHHHHHHCCCHHHHHHHH
Q ss_conf             454325899999999999999982872---7899978489988999999
Q gi|254780916|r  427 GQDGEVRRLSDIEKEIIGLAMKLYRAQ---MSEVARRLGIGRSTLYRKI  472 (482)
Q Consensus       427 ~~~~~~~~l~e~E~~~I~~aL~~~~Gn---~~~aA~~LGIsR~tL~rKl  472 (482)
                      .  -+..=|+++.++++....++|+|-   ..--|-.||+.+.|+-.+.
T Consensus       230 ~--iD~~GLd~~D~~~L~~li~~f~GGPVGl~tlA~a~GEd~~TiEdv~  276 (305)
T TIGR00635       230 D--IDELGLDEIDRKLLSVLIEKFQGGPVGLDTLAAALGEDADTIEDVY  276 (305)
T ss_pred             C--CCHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHCCCHHHHHCCC
T ss_conf             5--3330057998999999998628985238989988557511142034


No 130
>TIGR02640 gas_vesic_GvpN gas vesicle protein GvpN; InterPro: IPR013462    The GvpN protein is associated with the production of gas vesicles produced in some prokaryotes to give cells buoyancy , . It belongs to a larger family of ATPases .; GO: 0000166 nucleotide binding, 0005524 ATP binding, 0031412 gas vesicle organization and biogenesis, 0031411 gas vesicle.
Probab=98.69  E-value=3.2e-08  Score=77.73  Aligned_cols=158  Identities=19%  Similarity=0.243  Sum_probs=110.7

Q ss_pred             CCCCCCCCCCCCCCCCCCCEEEEEECCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCHHHHHCCCCCCCC--CC
Q ss_conf             2222222222222234432048873277743679999998426754332101234655421002433112555532--21
Q gi|254780916|r  145 VSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFGDVDLQTK--NS  222 (482)
Q Consensus       145 ~S~~m~~v~~~i~~~a~~~~~vli~Ge~GtGK~~~A~~iH~~s~r~~~~fi~v~c~~~~~~~~e~~lFG~~~~~~~--~~  222 (482)
                      +.+++++|.....+.-++.-||.+.|++||||+.+|..+=..   .+.|-+-++.   +.++-.+-|-|...+.+.  ..
T Consensus         3 ~t~~v~~v~~R~l~yL~~G~PvHl~GPaG~GKT~LA~hvA~~---r~RPV~l~~G---d~eL~~~DLvG~~~g~~~~kv~   76 (265)
T TIGR02640         3 ETDAVKRVTSRALRYLKSGYPVHLRGPAGTGKTTLAMHVARK---RDRPVVLING---DAELTTSDLVGSYAGYTRKKVV   76 (265)
T ss_pred             CCHHHHHHHHHHHHHHCCCCCEEEECCCCCCHHHHHHHHHHH---CCCCEEEEEC---CCCCCCCCCCCCCCCCEEEEEE
T ss_conf             772379999987663227886674478885568999999973---6896899865---8232654423154675222232


Q ss_pred             CC---CC--------------CCCCCCCCC-EEEECCCCHHHHHHHHHHHHHHHHHHCCCCCCC-----CCCCCCCEEEE
Q ss_conf             11---00--------------123446671-475166420018899988887764200112355-----32123431565
Q gi|254780916|r  223 AQ---FL--------------GKFIEANGG-TIVLEEPDALPLAVQGRIYNFIETGKIEFFDSR-----GAIRLDVRLIF  279 (482)
Q Consensus       223 ~~---~~--------------g~~~~a~~G-tl~l~ei~~L~~~~Q~~Ll~~l~~~~~~~~g~~-----~~~~~~~RiIa  279 (482)
                      .+   +.              .+...+.+| ||+-||=.+=-|..-.=||.++|||-..-.|..     -.++-+||+|.
T Consensus        77 DqfihnV~K~~d~~~~~W~D~rLt~Av~eG~TLVYdEF~RskP~~nNVLLSvlEE~vL~LPg~~~~~~Yv~VhP~FR~If  156 (265)
T TIGR02640        77 DQFIHNVVKLEDIVRQNWVDNRLTLAVREGFTLVYDEFTRSKPETNNVLLSVLEEGVLELPGKRGESRYVDVHPEFRVIF  156 (265)
T ss_pred             ECCEEEEECCCCCCCCCCCCCHHHHHHHCCCEEEECCCCCCCCHHHHHHHHHHHHHHHCCCCCCCCCCCEEECCCCCEEE
T ss_conf             01211134251220026678357899756972766475788620456567555523215888787787225788702463


Q ss_pred             ECCCCCCCCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf             2143321111112333799988654334467
Q gi|254780916|r  280 LTEKNLLPQVKSHVFRKDLYYRISVFLINIS  310 (482)
Q Consensus       280 ~t~~~L~~~~~~g~fr~dLy~rL~~~~i~iP  310 (482)
                      +||..  +-..=..=..-|..||-++.+.-|
T Consensus       157 TSNp~--EYAGVh~~QDALlDRL~ti~~D~~  185 (265)
T TIGR02640       157 TSNPV--EYAGVHETQDALLDRLVTISMDYP  185 (265)
T ss_pred             CCCCC--CCCCCCCHHHHHHHHHCCCCCCCC
T ss_conf             14870--105767716677664400457854


No 131
>PRK05642 DNA replication initiation factor; Validated
Probab=98.68  E-value=1.1e-07  Score=73.85  Aligned_cols=210  Identities=13%  Similarity=0.119  Sum_probs=124.6

Q ss_pred             CCCCCCCCCCCCCCC-C-CCCCCCCCCCCCCCC-CCEEEEEECCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             222211111111222-2-222222222222344-3204887327774367999999842675433210123465542100
Q gi|254780916|r  131 SQENEHCALDSLIAV-S-PAMIQVVDLARKAGD-CAIPIMIQGEFGVGKKRLSRFIHESGKRAFFPFFIVNCGMIDQDKI  207 (482)
Q Consensus       131 ~~~~~~~~~~~LiG~-S-~~m~~v~~~i~~~a~-~~~~vli~Ge~GtGK~~~A~~iH~~s~r~~~~fi~v~c~~~~~~~~  207 (482)
                      -..+...+|+.++.. + .+...+...+..... ...++.|.|++|+||+++.+++-..-...+.+.+.++|..+.... 
T Consensus        10 ~~l~~~~tfdnFi~g~N~~a~~~~~~l~~~~~~~~~~~l~i~G~~G~GKTHLL~A~~~~~~~~~~~~~yl~~~~~~~~~-   88 (234)
T PRK05642         10 VRLRDDATFANYYPGANAAALGYVERLCEADAGWTESLIYLWGKDGVGRSHLLQAACLRFEQRGEPAVYLPLAELLDRG-   88 (234)
T ss_pred             CCCCCCCCHHCCCCCCCHHHHHHHHHHHHCCCCCCCCEEEEECCCCCCHHHHHHHHHHHHHHCCCCEEEEEHHHHHHHH-
T ss_conf             9999977730357187599999999987606787788389988999988999999999998079967997899987544-


Q ss_pred             HHHHHCCCCCCCCCCCCCCCCCCCCCCCEEEECCCCHHH--HHHHHHHHHHHHHHHCCCCCCCCCCCCCCEEEEECCCCC
Q ss_conf             243311255553221110012344667147516642001--889998888776420011235532123431565214332
Q gi|254780916|r  208 EKFLFGDVDLQTKNSAQFLGKFIEANGGTIVLEEPDALP--LAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNL  285 (482)
Q Consensus       208 e~~lFG~~~~~~~~~~~~~g~~~~a~~Gtl~l~ei~~L~--~~~Q~~Ll~~l~~~~~~~~g~~~~~~~~~RiIa~t~~~L  285 (482)
                       .++|              -.++.+  ..+++|+|+.++  ...|..|+.++..-          .....++|.+++..+
T Consensus        89 -~~~~--------------~~l~~~--d~l~IDDi~~i~g~~~~e~~lF~l~N~~----------~~~~~~llits~~~P  141 (234)
T PRK05642         89 -PELL--------------DNLEQY--ELVCIDDLDVIAGKADWEEALFHLFNRL----------RDSGRRLLLAASKSP  141 (234)
T ss_pred             -HHHH--------------HHHHHC--CEEEEECHHHHCCCHHHHHHHHHHHHHH----------HHCCCEEEEECCCCH
T ss_conf             -9998--------------624227--9898936455468859999999999999----------983995999578795


Q ss_pred             CCCCCHHHHHHHHHHHHH-HHHHHHHHHH--HHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHH
Q ss_conf             111111233379998865-4334467787--7442222556677764101122333321111100012233898689999
Q gi|254780916|r  286 LPQVKSHVFRKDLYYRIS-VFLINISTLR--SRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQELK  362 (482)
Q Consensus       286 ~~~~~~g~fr~dLy~rL~-~~~i~iPpLR--eR~eDI~~L~~~fl~~~~~~~~~~~~~ls~~a~~~L~~y~WPGNvREL~  362 (482)
                      .++-   ...+||=-||+ +..++++|+-  +|..       - +.+.+...|   ..++++++++|.++ ++.|+++|.
T Consensus       142 ~~l~---~~l~DL~SRl~~~~~~~i~~l~d~~~~~-------i-L~~~a~~rg---i~l~~~v~~yl~~r-~~R~~~~L~  206 (234)
T PRK05642        142 RELP---VKLPDLKSRLTLALVFQMRGLSDEDKLR-------A-LQLRASRRG---LHLTDEVGHFILTR-GTRSMSALF  206 (234)
T ss_pred             HHHC---CCHHHHHHHHHCCCEEEECCCCHHHHHH-------H-HHHHHHHCC---CCCCHHHHHHHHHH-CCCCHHHHH
T ss_conf             5523---0016799999578127514899899999-------9-999977546---89998999999997-358899999


Q ss_pred             HHHHHHHH--HCCCCCCCHHHHH
Q ss_conf             99999987--4389810688954
Q gi|254780916|r  363 NILLRAVI--GLKDSHLTEDRFV  383 (482)
Q Consensus       363 n~i~r~~i--~~~~~~i~~~~~~  383 (482)
                      +++.++-.  +.....||..-+.
T Consensus       207 ~~l~~Ld~~sl~~kr~iTiplvk  229 (234)
T PRK05642        207 DLLERLDQASLQAQRKLTIPFLK  229 (234)
T ss_pred             HHHHHHHHHHHHHCCCCCHHHHH
T ss_conf             99999999999838999999999


No 132
>KOG0730 consensus
Probab=98.68  E-value=2.6e-08  Score=78.32  Aligned_cols=175  Identities=18%  Similarity=0.222  Sum_probs=108.5

Q ss_pred             CCCEEEEEECCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCHHHHHCCCCCCCCCCCCCCCCCCC---CCCCEE
Q ss_conf             43204887327774367999999842675433210123465542100243311255553221110012344---667147
Q gi|254780916|r  161 DCAIPIMIQGEFGVGKKRLSRFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFGDVDLQTKNSAQFLGKFIE---ANGGTI  237 (482)
Q Consensus       161 ~~~~~vli~Ge~GtGK~~~A~~iH~~s~r~~~~fi~v~c~~~~~~~~e~~lFG~~~~~~~~~~~~~g~~~~---a~~Gtl  237 (482)
                      +-..-||+.|++||||+++|++|-+.+   ..+|+.|.|.    + +-|..+|+....-.      -.|.+   +.--.+
T Consensus       466 ~ppkGVLlyGPPGC~KT~lAkalAne~---~~nFlsvkgp----E-L~sk~vGeSEr~ir------~iF~kAR~~aP~Ii  531 (693)
T KOG0730         466 SPPKGVLLYGPPGCGKTLLAKALANEA---GMNFLSVKGP----E-LFSKYVGESERAIR------EVFRKARQVAPCII  531 (693)
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHHHHH---CCCEEECCCH----H-HHHHHCCCHHHHHH------HHHHHHHHCCCEEE
T ss_conf             887547777899862478999986463---5872641578----9-98775182589999------99999862698377


Q ss_pred             EECCCCHHHHHH-------HHHHHHHHHHHHCCCCCCCCCCCCCCEEEEECCCCC---CCCCCHHHHHHHHHHHHHHHHH
Q ss_conf             516642001889-------998888776420011235532123431565214332---1111112333799988654334
Q gi|254780916|r  238 VLEEPDALPLAV-------QGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNL---LPQVKSHVFRKDLYYRISVFLI  307 (482)
Q Consensus       238 ~l~ei~~L~~~~-------Q~~Ll~~l~~~~~~~~g~~~~~~~~~RiIa~t~~~L---~~~~~~g~fr~dLy~rL~~~~i  307 (482)
                      |||||+.+..+=       +.++|..|-+-    +++- ...-+|=|||+||++.   ..++.-|+|.+=+|       |
T Consensus       532 FfDEiDsi~~~R~g~~~~v~~RVlsqLLtE----mDG~-e~~k~V~ViAATNRpd~ID~ALlRPGRlD~iiy-------V  599 (693)
T KOG0730         532 FFDEIDALAGSRGGSSSGVTDRVLSQLLTE----MDGL-EALKNVLVIAATNRPDMIDPALLRPGRLDRIIY-------V  599 (693)
T ss_pred             EHHHHHHHHHCCCCCCCCHHHHHHHHHHHH----CCCC-CCCCCEEEEECCCCHHHCCHHHCCCCCCCEEEE-------E
T ss_conf             446666666304787551489999999987----0041-014708999505881012697759865330575-------1


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCC-CCCCCCC--CCCCCCHHHHHHHHHHHHHHCCCCC
Q ss_conf             4677877442222556677764101122333321111-1000122--3389868999999999987438981
Q gi|254780916|r  308 NISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDK-ALSLLTK--YPWIDNVQELKNILLRAVIGLKDSH  376 (482)
Q Consensus       308 ~iPpLReR~eDI~~L~~~fl~~~~~~~~~~~~~ls~~-a~~~L~~--y~WPGNvREL~n~i~r~~i~~~~~~  376 (482)
                      -+|-+.-|.+ |       ++...++..     ++++ -++.|..  --+.  -+||.++|++|...+-...
T Consensus       600 plPD~~aR~~-I-------lk~~~kkmp-----~~~~vdl~~La~~T~g~S--GAel~~lCq~A~~~a~~e~  656 (693)
T KOG0730         600 PLPDLEARLE-I-------LKQCAKKMP-----FSEDVDLEELAQATEGYS--GAEIVAVCQEAALLALRES  656 (693)
T ss_pred             CCCCHHHHHH-H-------HHHHHHCCC-----CCCCCCHHHHHHHHCCCC--HHHHHHHHHHHHHHHHHHH
T ss_conf             5834788999-9-------999973399-----986556999999854677--3899999999999999875


No 133
>PRK08084 DNA replication initiation factor; Provisional
Probab=98.67  E-value=6e-08  Score=75.79  Aligned_cols=208  Identities=12%  Similarity=0.033  Sum_probs=120.7

Q ss_pred             CCCCCCCCCCCCCC-CCCCCCCCCCCCCCCC--CCCCEEEEEECCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             22222111111112-2222222222222223--44320488732777436799999984267543321012346554210
Q gi|254780916|r  130 PSQENEHCALDSLI-AVSPAMIQVVDLARKA--GDCAIPIMIQGEFGVGKKRLSRFIHESGKRAFFPFFIVNCGMIDQDK  206 (482)
Q Consensus       130 ~~~~~~~~~~~~Li-G~S~~m~~v~~~i~~~--a~~~~~vli~Ge~GtGK~~~A~~iH~~s~r~~~~fi~v~c~~~~~~~  206 (482)
                      .-......+|+.++ |.+....   ..+...  .....+++|.|++|+||+++.+++.+.....+..-+.+.|....  .
T Consensus        12 ~~~l~~~~tfdnFi~g~n~~~~---~al~~~~~~~~~~~l~l~G~~G~GKTHLLqA~~~~~~~~~~~~~yl~~~~~~--~   86 (235)
T PRK08084         12 PLYLPDDETFASFYPGDNDSLL---AALQNVLRQEHSGYIYLWGREGAGRSHLLHAACAELSQRGDAVGYVPLDKRA--W   86 (235)
T ss_pred             CCCCCCCCCHHCCCCCCCHHHH---HHHHHHHHCCCCCEEEEECCCCCCHHHHHHHHHHHHHCCCCCEEEEEHHHHH--H
T ss_conf             8999997663023448869999---9999998578987699989999888999999999997079857998779866--5


Q ss_pred             CHHHHHCCCCCCCCCCCCCCCCCCCCCCCEEEECCCCHHH--HHHHHHHHHHHHHHHCCCCCCCCCCCCCCEEEEECCCC
Q ss_conf             0243311255553221110012344667147516642001--88999888877642001123553212343156521433
Q gi|254780916|r  207 IEKFLFGDVDLQTKNSAQFLGKFIEANGGTIVLEEPDALP--LAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKN  284 (482)
Q Consensus       207 ~e~~lFG~~~~~~~~~~~~~g~~~~a~~Gtl~l~ei~~L~--~~~Q~~Ll~~l~~~~~~~~g~~~~~~~~~RiIa~t~~~  284 (482)
                      +..+++              .-++  +-..+++|+|+.+.  ...|..|+.++..-. .        .-+++||.+++..
T Consensus        87 ~~~~~l--------------~~l~--~~dll~iDDi~~i~g~~~~ee~lF~l~N~~~-~--------~g~~~ll~ts~~~  141 (235)
T PRK08084         87 FVPEVL--------------EGME--QLSLVCIDNIECIAGDELWEMAIFDLYNRIL-E--------SGKTRLLITGDRP  141 (235)
T ss_pred             HHHHHH--------------HHHH--HCCEEEEECHHHHCCCHHHHHHHHHHHHHHH-H--------HCCCEEEEECCCC
T ss_conf             179999--------------8764--1898998274554699789999999999999-8--------4896699967988


Q ss_pred             CCCCCCHHHHHHHHHHHHH-HHHHHHHHH--HHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHH
Q ss_conf             2111111233379998865-433446778--7744222255667776410112233332111110001223389868999
Q gi|254780916|r  285 LLPQVKSHVFRKDLYYRIS-VFLINISTL--RSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQEL  361 (482)
Q Consensus       285 L~~~~~~g~fr~dLy~rL~-~~~i~iPpL--ReR~eDI~~L~~~fl~~~~~~~~~~~~~ls~~a~~~L~~y~WPGNvREL  361 (482)
                      +.++-   .+-+||--||+ +..++++|+  -+|.+ |       +.+.+...|.   .++++..++|.. .++.|+|+|
T Consensus       142 P~~l~---~~l~DL~SRl~~g~~~~i~~~dde~~~~-i-------L~~~a~~rgl---~l~~~V~~yl~~-~~~R~~~~L  206 (235)
T PRK08084        142 PRQLN---LGLPDLASRLDWGQIYKLQPLSDEEKLQ-A-------LQLRARLRGF---ELPEDVGRFLLK-RLDREMRTL  206 (235)
T ss_pred             HHHCC---CCCHHHHHHHHCCCEEEECCCCHHHHHH-H-------HHHHHHHCCC---CCCHHHHHHHHH-HCCCCHHHH
T ss_conf             24302---3128899999569727855999899999-9-------9999997399---999899999998-615889999


Q ss_pred             HHHHHHHHH--HCCCCCCCHHHH
Q ss_conf             999999987--438981068895
Q gi|254780916|r  362 KNILLRAVI--GLKDSHLTEDRF  382 (482)
Q Consensus       362 ~n~i~r~~i--~~~~~~i~~~~~  382 (482)
                      .+++.++-.  +..+..||..-+
T Consensus       207 ~~~l~~Ld~~Sl~~kr~iTip~v  229 (235)
T PRK08084        207 FMTLDQLDKASITAQRKLTIPFV  229 (235)
T ss_pred             HHHHHHHHHHHHHCCCCCCHHHH
T ss_conf             99999999999981999999999


No 134
>pfam00308 Bac_DnaA Bacterial dnaA protein.
Probab=98.66  E-value=4.2e-08  Score=76.89  Aligned_cols=202  Identities=17%  Similarity=0.220  Sum_probs=116.5

Q ss_pred             CCCCCCCC-CCCCCCCCCCCCCCCCCC----CCCEEEEEECCCCCHHHHHHHHHHHCCC--CCCCCCCCCCCCCCCCCCC
Q ss_conf             11111111-222222222222222234----4320488732777436799999984267--5433210123465542100
Q gi|254780916|r  135 EHCALDSL-IAVSPAMIQVVDLARKAG----DCAIPIMIQGEFGVGKKRLSRFIHESGK--RAFFPFFIVNCGMIDQDKI  207 (482)
Q Consensus       135 ~~~~~~~L-iG~S~~m~~v~~~i~~~a----~~~~~vli~Ge~GtGK~~~A~~iH~~s~--r~~~~fi~v~c~~~~~~~~  207 (482)
                      ...+|+.+ +|.+-  +..+..+.+++    ..--|++|.|++|+||+++.+++-+...  ..+...+.+++..+....+
T Consensus         3 ~~~TFdnF~vg~~N--~~a~~~~~~i~~~~~~~~npl~i~G~~G~GKTHLLqA~~~~~~~~~~~~~v~yl~~~~~~~~~~   80 (219)
T pfam00308         3 KRYTFENFVIGSSN--RFAHAAALAVAEAPGKAYNPLFIYGGVGLGKTHLLHAIGNYALRNFPNLRVVYLTSEEFLNDFV   80 (219)
T ss_pred             CCCCCCCCCCCCCH--HHHHHHHHHHHHCCCCCCCCEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEEEHHHHHHHHH
T ss_conf             99871020236838--9999999999967587678269988999988899999999999849998288843999999889


Q ss_pred             HHHHHCCCCCCCCCCCCCCCCCCCCCCCEEEECCCCHHHH--HHHHHHHHHHHHHHCCCCCCCCCCCCCCEEEEECCCCC
Q ss_conf             2433112555532211100123446671475166420018--89998888776420011235532123431565214332
Q gi|254780916|r  208 EKFLFGDVDLQTKNSAQFLGKFIEANGGTIVLEEPDALPL--AVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNL  285 (482)
Q Consensus       208 e~~lFG~~~~~~~~~~~~~g~~~~a~~Gtl~l~ei~~L~~--~~Q~~Ll~~l~~~~~~~~g~~~~~~~~~RiIa~t~~~L  285 (482)
                      + .+.   .   +........++.+  ..|++|+|+.+..  ..|..|+.++..-.          ....++|.+++.++
T Consensus        81 ~-~l~---~---~~~~~f~~~l~~~--d~l~iDDi~~l~~~~~~ee~lf~l~N~~~----------~~~~~lllts~~~p  141 (219)
T pfam00308        81 D-ALR---D---NKIEAFKKSYRNV--DLLLIDDIQFLAGKEKTQEEFFHTFNALH----------ENNKQIVLTSDRPP  141 (219)
T ss_pred             H-HHH---C---CCHHHHHHHHHHC--CHHHHCCHHHHCCCHHHHHHHHHHHHHHH----------HCCCEEEEECCCCC
T ss_conf             9-998---1---8888999997632--33652236765686478999999999999----------72986999779981


Q ss_pred             CCCCCHHHHHHHHHHHHHH-H--HHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHH
Q ss_conf             1111112333799988654-3--344677877442222556677764101122333321111100012233898689999
Q gi|254780916|r  286 LPQVKSHVFRKDLYYRISV-F--LINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQELK  362 (482)
Q Consensus       286 ~~~~~~g~fr~dLy~rL~~-~--~i~iPpLReR~eDI~~L~~~fl~~~~~~~~~~~~~ls~~a~~~L~~y~WPGNvREL~  362 (482)
                      .++-   .+.+||--||+. .  .|..|.--+|.        .++.+.+.+.|.   .+++++.+.|.++ +++++|+|.
T Consensus       142 ~~l~---~~~~dL~SRL~~g~~~~i~~pdd~~~~--------~iL~~~a~~r~l---~l~~~v~~yl~~r-~~R~~r~L~  206 (219)
T pfam00308       142 KELE---GFEDRLRSRFEWGLIIAIEPPDLETRL--------AILRKKAEEENI---NIPNEVLNFIAQR-ITDNVRELE  206 (219)
T ss_pred             CCCC---CCCHHHHHHHHCCEEEECCCCCHHHHH--------HHHHHHHHHCCC---CCCHHHHHHHHHH-CCCCHHHHH
T ss_conf             0024---532779999868756611699999999--------999999998499---9999999999984-279899999


Q ss_pred             HHHHHHHHHC
Q ss_conf             9999998743
Q gi|254780916|r  363 NILLRAVIGL  372 (482)
Q Consensus       363 n~i~r~~i~~  372 (482)
                      .++.++...+
T Consensus       207 ~~L~~L~~~~  216 (219)
T pfam00308       207 GALNRLLAFA  216 (219)
T ss_pred             HHHHHHHHHH
T ss_conf             9999999855


No 135
>TIGR02040 PpsR-CrtJ transcriptional regulator PpsR; InterPro: IPR011785    This entry represents the transcriptional regulator PpsR which is strictly associated with photosynthetic proteobacteria and found in photosynthetic operons. PpsR has been reported to be a repressor . These proteins contain a Helix-Turn-Helix motif of the "fis" type..
Probab=98.64  E-value=4.7e-08  Score=76.53  Aligned_cols=45  Identities=31%  Similarity=0.509  Sum_probs=42.2

Q ss_pred             HHHHHHHHHHHHHHHHHHCCCHHHHHHHHCCCHHHHHHHHHHHCC
Q ss_conf             899999999999999982872789997848998899999998188
Q gi|254780916|r  433 RRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKIREYNI  477 (482)
Q Consensus       433 ~~l~e~E~~~I~~aL~~~~Gn~~~aA~~LGIsR~tL~rKlk~~gi  477 (482)
                      ++.+=+|+.+|+.||+-+++|++.||++||+||.+||-||++|||
T Consensus       409 ettdvvE~~cieAALeLtr~NR~sAAE~LgLSRQSLY~KLrrYgL  453 (453)
T TIGR02040       409 ETTDVVEQLCIEAALELTRDNRASAAEILGLSRQSLYVKLRRYGL  453 (453)
T ss_pred             HHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHCCC
T ss_conf             058999999999999860041789999974346888888774079


No 136
>COG1222 RPT1 ATP-dependent 26S proteasome regulatory subunit [Posttranslational modification, protein turnover, chaperones]
Probab=98.63  E-value=7.5e-08  Score=75.11  Aligned_cols=217  Identities=18%  Similarity=0.213  Sum_probs=134.1

Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCC-----------CCCEEEEEECCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCC
Q ss_conf             2211111111222222222222222234-----------43204887327774367999999842675433210123465
Q gi|254780916|r  133 ENEHCALDSLIAVSPAMIQVVDLARKAG-----------DCAIPIMIQGEFGVGKKRLSRFIHESGKRAFFPFFIVNCGM  201 (482)
Q Consensus       133 ~~~~~~~~~LiG~S~~m~~v~~~i~~~a-----------~~~~~vli~Ge~GtGK~~~A~~iH~~s~r~~~~fi~v~c~~  201 (482)
                      +....+++.+-|-...++++++.++-=-           .-..-||+.|++||||+++||++-+.   .+..||.|..+.
T Consensus       144 e~PdvtY~dIGGL~~Qi~EirE~VELPL~~PElF~~~GI~PPKGVLLYGPPGTGKTLLAkAVA~~---T~AtFIrvvgSE  220 (406)
T COG1222         144 EKPDVTYEDIGGLDEQIQEIREVVELPLKNPELFEELGIDPPKGVLLYGPPGTGKTLLAKAVANQ---TDATFIRVVGSE  220 (406)
T ss_pred             CCCCCCHHHCCCHHHHHHHHHHHHCCCCCCHHHHHHCCCCCCCCEEEECCCCCCHHHHHHHHHHC---CCCEEEEECCHH
T ss_conf             58987865335889999999998403366888999749999971276689997588999998720---586699942199


Q ss_pred             CCCCCCHHHHHCCCCCCCCCCCCCCCCCCCCC---CCEEEECCCCHH-----------HHHHHHHHHHHHHHHHCCCCCC
Q ss_conf             54210024331125555322111001234466---714751664200-----------1889998888776420011235
Q gi|254780916|r  202 IDQDKIEKFLFGDVDLQTKNSAQFLGKFIEAN---GGTIVLEEPDAL-----------PLAVQGRIYNFIETGKIEFFDS  267 (482)
Q Consensus       202 ~~~~~~e~~lFG~~~~~~~~~~~~~g~~~~a~---~Gtl~l~ei~~L-----------~~~~Q~~Ll~~l~~~~~~~~g~  267 (482)
                      +-     ....|+     |+.- ...+|+.|.   --.+|+|||+..           ..++|.-++.+|.+=     ++
T Consensus       221 lV-----qKYiGE-----GaRl-VRelF~lArekaPsIIFiDEIDAIg~kR~d~~t~gDrEVQRTmleLL~ql-----DG  284 (406)
T COG1222         221 LV-----QKYIGE-----GARL-VRELFELAREKAPSIIFIDEIDAIGAKRFDSGTSGDREVQRTMLELLNQL-----DG  284 (406)
T ss_pred             HH-----HHHHCC-----CHHH-HHHHHHHHHHCCCEEEEEECHHHHHCCCCCCCCCCHHHHHHHHHHHHHHC-----CC
T ss_conf             99-----998341-----1699-99999987414984999831122311113688885099999999999860-----58


Q ss_pred             CCCCCCCCEEEEECCCC--C-CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCC
Q ss_conf             53212343156521433--2-11111123337999886543344677877442222556677764101122333321111
Q gi|254780916|r  268 RGAIRLDVRLIFLTEKN--L-LPQVKSHVFRKDLYYRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDK  344 (482)
Q Consensus       268 ~~~~~~~~RiIa~t~~~--L-~~~~~~g~fr~dLy~rL~~~~i~iPpLReR~eDI~~L~~~fl~~~~~~~~~~~~~ls~~  344 (482)
                      -.+ .-|++||+|||+.  | ..+..-|+|..       -+.+-+|..+.|.+ |       ++-++++.+.. ..++=+
T Consensus       285 FD~-~~nvKVI~ATNR~D~LDPALLRPGR~DR-------kIEfplPd~~gR~~-I-------l~IHtrkM~l~-~dvd~e  347 (406)
T COG1222         285 FDP-RGNVKVIMATNRPDILDPALLRPGRFDR-------KIEFPLPDEEGRAE-I-------LKIHTRKMNLA-DDVDLE  347 (406)
T ss_pred             CCC-CCCEEEEEECCCCCCCCHHHCCCCCCCC-------EEECCCCCHHHHHH-H-------HHHHHHHCCCC-CCCCHH
T ss_conf             897-8876899855885555766508875453-------01168989789999-9-------99876214676-676999


Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHHH---CCCCCCCHHHHHHHHCC
Q ss_conf             100012233898689999999999874---38981068895454212
Q gi|254780916|r  345 ALSLLTKYPWIDNVQELKNILLRAVIG---LKDSHLTEDRFVLLLSR  388 (482)
Q Consensus       345 a~~~L~~y~WPGNvREL~n~i~r~~i~---~~~~~i~~~~~~~~l~~  388 (482)
                      .+..+..   -=|-.||+++|.-|-+.   ....+++.+||.....+
T Consensus       348 ~la~~~~---g~sGAdlkaictEAGm~AiR~~R~~Vt~~DF~~Av~K  391 (406)
T COG1222         348 LLARLTE---GFSGADLKAICTEAGMFAIRERRDEVTMEDFLKAVEK  391 (406)
T ss_pred             HHHHHCC---CCCHHHHHHHHHHHHHHHHHHCCCEECHHHHHHHHHH
T ss_conf             9987538---9956779999998759999860473339999999999


No 137
>PRK09862 putative ATP-dependent protease; Provisional
Probab=98.63  E-value=4e-08  Score=77.07  Aligned_cols=133  Identities=15%  Similarity=0.118  Sum_probs=93.9

Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCCCHHHHHHHHHHHCCCCC-------------------------C
Q ss_conf             111111222222222222222234432048873277743679999998426754-------------------------3
Q gi|254780916|r  137 CALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHESGKRA-------------------------F  191 (482)
Q Consensus       137 ~~~~~LiG~S~~m~~v~~~i~~~a~~~~~vli~Ge~GtGK~~~A~~iH~~s~r~-------------------------~  191 (482)
                      ..+.++.|+..    .++.+.-+|.-..++|+.|++|+||+++|+.+...-+--                         .
T Consensus       188 ~D~~dv~Gq~~----akraleIAAAGgHnlLl~GpPG~GKTMlA~rlp~ILPpLt~~e~lEv~~I~Svag~~~~~~~~~~  263 (506)
T PRK09862        188 HDLSDVVGQEQ----GKRGLEITAAGGHNLLLIGPPGTGKTMLASRINGLLPDLSNEEALESAAILSLVNAESVQKQWRQ  263 (506)
T ss_pred             CCHHHHCCCHH----HHHHHHHHHCCCCCEEEECCCCCCHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHCCCCCCCCCCC
T ss_conf             67565369799----99999997446886598769994598999775123899898999999999987189877775466


Q ss_pred             CCCCCCCCCCCCCCCCHHHHHCCCCCCCCCCCCCCCCCCCCCCCEEEECCCCHHHHHHHHHHHHHHHHHHC--CCCCCCC
Q ss_conf             32101234655421002433112555532211100123446671475166420018899988887764200--1123553
Q gi|254780916|r  192 FPFFIVNCGMIDQDKIEKFLFGDVDLQTKNSAQFLGKFIEANGGTIVLEEPDALPLAVQGRIYNFIETGKI--EFFDSRG  269 (482)
Q Consensus       192 ~~fi~v~c~~~~~~~~e~~lFG~~~~~~~~~~~~~g~~~~a~~Gtl~l~ei~~L~~~~Q~~Ll~~l~~~~~--~~~g~~~  269 (482)
                      .||-.-.-++     =..-|+|      |...-++|-+-.|++|.|||||..+.+..+..-|-+-|++|++  .|.++.-
T Consensus       264 rPfR~PHHs~-----S~~aliG------GG~~~~PGEISLAH~GVLFLDElpEF~r~vLe~LRqPLE~g~I~IsRa~~~~  332 (506)
T PRK09862        264 RPFRSPHHSA-----SLTAMVG------GGAIPGPGEISLAHNGVLFLDELPEFERRTLDALREPIESGQIHLSRTRAKI  332 (506)
T ss_pred             CCEECCCCCC-----CHHHHHC------CCCCCCCCCEEECCCCEEEECCHHCCCHHHHHHHHHHHCCCEEEEEECCCEE
T ss_conf             8503788765-----4766637------9999999722213575788455000688899987762247759999668679


Q ss_pred             CCCCCCEEEEECCCC
Q ss_conf             212343156521433
Q gi|254780916|r  270 AIRLDVRLIFLTEKN  284 (482)
Q Consensus       270 ~~~~~~RiIa~t~~~  284 (482)
                      ..+.+|.+|+++|-=
T Consensus       333 ~~PA~F~LVaAmNPC  347 (506)
T PRK09862        333 TYPARFQLVAAMNPS  347 (506)
T ss_pred             EECCHHHHEHHCCCC
T ss_conf             861533111103788


No 138
>PRK08727 hypothetical protein; Validated
Probab=98.62  E-value=1.8e-07  Score=72.50  Aligned_cols=208  Identities=16%  Similarity=0.154  Sum_probs=124.2

Q ss_pred             CCCCCCCCCCC-CCCCCCCCCCCCCCCCCCCCEEEEEECCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCHHHH
Q ss_conf             22111111112-22222222222222234432048873277743679999998426754332101234655421002433
Q gi|254780916|r  133 ENEHCALDSLI-AVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHESGKRAFFPFFIVNCGMIDQDKIEKFL  211 (482)
Q Consensus       133 ~~~~~~~~~Li-G~S~~m~~v~~~i~~~a~~~~~vli~Ge~GtGK~~~A~~iH~~s~r~~~~fi~v~c~~~~~~~~e~~l  211 (482)
                      .....+++.++ |.+..+..+...+  ...+..++.|.|++|+||+++++++.+.....+..-..+.|........    
T Consensus        12 ~~~~~tfdnFi~~~n~~~a~l~~~~--~~~~~~~lyl~G~~GsGKTHLl~a~~~~~~~~~~~~~yl~l~~~~~~~~----   85 (233)
T PRK08727         12 APSDQRFDSYIAAPDGLLAQLQALA--AGQSSDWLYLSGPAGTGKTHLALSLCAAAEQAGRSSAYLPLQAAAGRLR----   85 (233)
T ss_pred             CCCCCCHHHCCCCCHHHHHHHHHHH--CCCCCCEEEEECCCCCCHHHHHHHHHHHHHHCCCCEEEEEHHHHHHHHH----
T ss_conf             9972242120678559999999874--3888898999899999889999999999982799728844788532025----


Q ss_pred             HCCCCCCCCCCCCCCCCCCCCCCCEEEECCCCHHH--HHHHHHHHHHHHHHHCCCCCCCCCCCCCCEEEEECCCCCCCCC
Q ss_conf             11255553221110012344667147516642001--8899988887764200112355321234315652143321111
Q gi|254780916|r  212 FGDVDLQTKNSAQFLGKFIEANGGTIVLEEPDALP--LAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQV  289 (482)
Q Consensus       212 FG~~~~~~~~~~~~~g~~~~a~~Gtl~l~ei~~L~--~~~Q~~Ll~~l~~~~~~~~g~~~~~~~~~RiIa~t~~~L~~~~  289 (482)
                                  +...-++  ....+++|+|+.+.  ..-|..|+.++..-          ...+.+++.+++..+.++-
T Consensus        86 ------------~~l~~le--~~~ll~iDDid~i~g~~~~e~aLFhL~N~~----------~~~~~~ll~ts~~~P~~l~  141 (233)
T PRK08727         86 ------------DALEALE--GRSLVALDGVDSIAGQREDEVALFDFHNRA----------RAAGITLLYTARQMPDGLA  141 (233)
T ss_pred             ------------HHHHHHC--CCCEEEEECCHHCCCCHHHHHHHHHHHHHH----------HHCCCEEEEECCCCHHHHC
T ss_conf             ------------6775310--389789855011269827999999999999----------8619838997798956623


Q ss_pred             CHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHH
Q ss_conf             11233379998865-43344677877442222556677764101122333321111100012233898689999999999
Q gi|254780916|r  290 KSHVFRKDLYYRIS-VFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQELKNILLRA  368 (482)
Q Consensus       290 ~~g~fr~dLy~rL~-~~~i~iPpLReR~eDI~~L~~~fl~~~~~~~~~~~~~ls~~a~~~L~~y~WPGNvREL~n~i~r~  368 (482)
                         ...+||--||+ +..+.++|+-|-. -+.     .+.+.+...|   ..++++++++|.++ ++-|++.|.+++.++
T Consensus       142 ---~~l~DL~SRL~~~~~~~l~~~dD~~-~~~-----iL~~~a~~rg---l~l~~~V~~Yll~r-~~R~~~~l~~~l~~L  208 (233)
T PRK08727        142 ---LVLPDLRSRLSQCIRIGLPVLDDVA-RAA-----VLRDRAQRRG---LALDEAAIDWLLTH-GERELAGLVALLDRL  208 (233)
T ss_pred             ---CCHHHHHHHHHCCCEEEECCCCHHH-HHH-----HHHHHHHHCC---CCCCHHHHHHHHHH-CCCCHHHHHHHHHHH
T ss_conf             ---1002199999669228857889799-999-----9999999869---99998999999985-688999999999999


Q ss_pred             H--HHCCCCCCCHHHHH
Q ss_conf             8--74389810688954
Q gi|254780916|r  369 V--IGLKDSHLTEDRFV  383 (482)
Q Consensus       369 ~--i~~~~~~i~~~~~~  383 (482)
                      -  .+.....||..-+.
T Consensus       209 D~~SL~~kr~iTip~vk  225 (233)
T PRK08727        209 DRESLAAKRRITVPFLR  225 (233)
T ss_pred             HHHHHHCCCCCCHHHHH
T ss_conf             99999808988899999


No 139
>COG0466 Lon ATP-dependent Lon protease, bacterial type [Posttranslational modification, protein turnover, chaperones]
Probab=98.62  E-value=2.3e-08  Score=78.78  Aligned_cols=265  Identities=19%  Similarity=0.210  Sum_probs=151.8

Q ss_pred             CCEEE-EEECCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCHHHHHCCCCCCCCCCCCCC-CCCC--CCCCCEE
Q ss_conf             32048-873277743679999998426754332101234655421002433112555532211100-1234--4667147
Q gi|254780916|r  162 CAIPI-MIQGEFGVGKKRLSRFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFGDVDLQTKNSAQFL-GKFI--EANGGTI  237 (482)
Q Consensus       162 ~~~~v-li~Ge~GtGK~~~A~~iH~~s~r~~~~fi~v~c~~~~~~~~e~~lFG~~~~~~~~~~~~~-g~~~--~a~~Gtl  237 (482)
                      ...|| ++.|++|+||+.+++.|-..-.   .+|+.+..+++.+   |+|+-||+.-+-|+-..++ -.+.  ...|-..
T Consensus       348 ~kGpILcLVGPPGVGKTSLgkSIA~al~---RkfvR~sLGGvrD---EAEIRGHRRTYIGaMPGrIiQ~mkka~~~NPv~  421 (782)
T COG0466         348 LKGPILCLVGPPGVGKTSLGKSIAKALG---RKFVRISLGGVRD---EAEIRGHRRTYIGAMPGKIIQGMKKAGVKNPVF  421 (782)
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHHHC---CCEEEEECCCCCC---HHHHCCCCCCCCCCCCHHHHHHHHHHCCCCCEE
T ss_conf             7885799978998870118999999958---9779995476542---777535531233568728999999867768747


Q ss_pred             EECCCCHHHHHHH----HHHHHHHH---HHHCCCCCCCCCCC---CCCEEEEECCCCCCCCCCHHHHHHHHHHHHHHHHH
Q ss_conf             5166420018899----98888776---42001123553212---34315652143321111112333799988654334
Q gi|254780916|r  238 VLEEPDALPLAVQ----GRIYNFIE---TGKIEFFDSRGAIR---LDVRLIFLTEKNLLPQVKSHVFRKDLYYRISVFLI  307 (482)
Q Consensus       238 ~l~ei~~L~~~~Q----~~Ll~~l~---~~~~~~~g~~~~~~---~~~RiIa~t~~~L~~~~~~g~fr~dLy~rL~~~~i  307 (482)
                      .||||+.|+.+.|    ..||.+|+   +..|.-  -.-..+   ++|-+||+.|.=                  +.  |
T Consensus       422 LLDEIDKm~ss~rGDPaSALLEVLDPEQN~~F~D--hYLev~yDLS~VmFiaTANsl------------------~t--I  479 (782)
T COG0466         422 LLDEIDKMGSSFRGDPASALLEVLDPEQNNTFSD--HYLEVPYDLSKVMFIATANSL------------------DT--I  479 (782)
T ss_pred             EEECHHHCCCCCCCCHHHHHHHHCCHHHCCCHHH--CCCCCCCCHHHEEEEEECCCC------------------CC--C
T ss_conf             8640333167777886888886269765676122--201676644325888603751------------------32--9


Q ss_pred             HHHHHHHHHHHHHH----------H-HHHHHHHHCCCCCCC--CCCCCCCCCCCCCCCC-CCCCHHHHHHHH----HHHH
Q ss_conf             46778774422225----------5-667776410112233--3321111100012233-898689999999----9998
Q gi|254780916|r  308 NISTLRSRSEDIPW----------L-VHFFLQSFCTKNAIK--QISISDKALSLLTKYP-WIDNVQELKNIL----LRAV  369 (482)
Q Consensus       308 ~iPpLReR~eDI~~----------L-~~~fl~~~~~~~~~~--~~~ls~~a~~~L~~y~-WPGNvREL~n~i----~r~~  369 (482)
                       =.||.+|.|=|..          + -+|.+-+.-+++|.+  -..|+++|+..+.+|. ----||.|+..+    +.++
T Consensus       480 -P~PLlDRMEiI~lsgYt~~EKl~IAk~~LiPk~~~~~gL~~~el~i~d~ai~~iI~~YTREAGVR~LeR~i~ki~RK~~  558 (782)
T COG0466         480 -PAPLLDRMEVIRLSGYTEDEKLEIAKRHLIPKQLKEHGLKKGELTITDEAIKDIIRYYTREAGVRNLEREIAKICRKAA  558 (782)
T ss_pred             -CHHHHCCEEEEEECCCCHHHHHHHHHHHCCHHHHHHCCCCCCCEEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             -8678430305642688869999999984456899975998233556589999999987676210389999999999999


Q ss_pred             HH----CCCC--CCCHHHHHHHHCCCCCCCCCCC--------CCCCCCCCCCCCCCCCHHHCCCCCCCCCCCCCCHHHHH
Q ss_conf             74----3898--1068895454212445432234--------32222223344432100000000112344454325899
Q gi|254780916|r  370 IG----LKDS--HLTEDRFVLLLSREGKKEREFH--------TETACTCYTEGKSSDTILDNLSQESIPAIGQDGEVRRL  435 (482)
Q Consensus       370 i~----~~~~--~i~~~~~~~~l~~~~~~~~~~~--------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l  435 (482)
                      ..    ....  .++...+...++...-......        ...+++...-    ....  ......|..+.-...-.|
T Consensus       559 ~~i~~~~~k~~~~i~~~~l~~yLG~~~f~~~~~~~~~~vGvVtGLAWT~vGG----d~L~--IE~~~~~Gkg~l~lTG~L  632 (782)
T COG0466         559 KKILLKKEKSIVKIDEKNLKKYLGVPVFRYGKAEEEDQVGVVTGLAWTEVGG----DLLT--IEAVKMPGKGKLTLTGSL  632 (782)
T ss_pred             HHHHHCCCCCCEEECHHHHHHHHCCCCCCCCCCCCCCCCEEEEEEEEECCCC----EEEE--EEEEEECCCCCEEEECCH
T ss_conf             9997257566244278899997398634753112478870585444424786----4899--988871687507996057


Q ss_pred             HHHHHHHHHHHHHHHCCCHHHHHHHHCCCH
Q ss_conf             999999999999982872789997848998
Q gi|254780916|r  436 SDIEKEIIGLAMKLYRAQMSEVARRLGIGR  465 (482)
Q Consensus       436 ~e~E~~~I~~aL~~~~Gn~~~aA~~LGIsR  465 (482)
                      -++=|+=+..||...+-    -|..+||..
T Consensus       633 GdVMKESa~~A~s~vrs----~a~~~~i~~  658 (782)
T COG0466         633 GDVMKESAQAALSYVRS----RAEKLGIDP  658 (782)
T ss_pred             HHHHHHHHHHHHHHHHH----HHHHCCCCC
T ss_conf             99999999999999999----898719983


No 140
>PRK10733 hflB ATP-dependent metalloprotease; Reviewed
Probab=98.61  E-value=1.3e-07  Score=73.41  Aligned_cols=219  Identities=16%  Similarity=0.255  Sum_probs=125.5

Q ss_pred             CCCCCCCCCCCCCCCCCCC---CCCCCCCC-------CCCCCEEEEEECCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCC
Q ss_conf             2221111111122222222---22222222-------3443204887327774367999999842675433210123465
Q gi|254780916|r  132 QENEHCALDSLIAVSPAMI---QVVDLARK-------AGDCAIPIMIQGEFGVGKKRLSRFIHESGKRAFFPFFIVNCGM  201 (482)
Q Consensus       132 ~~~~~~~~~~LiG~S~~m~---~v~~~i~~-------~a~~~~~vli~Ge~GtGK~~~A~~iH~~s~r~~~~fi~v~c~~  201 (482)
                      .......|.+..|...+-+   ++.+.+..       =|....-||+.|++||||+++||++-..   ++-||+.+..+.
T Consensus       144 ~~~~~vtF~DVaG~~eaK~el~EiVdfLk~P~k~~~~Gak~PkGvLL~GPPGtGKTlLAkAvAgE---a~vpF~~~sgse  220 (644)
T PRK10733        144 EDQIKTTFADVAGCDEAKEEVAELVEYLREPSRFQKLGGKIPKGVLMVGPPGTGKTLLAKAIAGE---AKVPFFTISGSD  220 (644)
T ss_pred             CCCCCCCCCCCCCCHHHHHHHHHHHHHHHCHHHHHHCCCCCCCCEEEECCCCCCHHHHHHHHHCC---CCCEEEEEEHHH
T ss_conf             77898771040897899999999999812979999749979985177798998778999998645---598089978477


Q ss_pred             CCCCCCHHHHHCCCCCCCCCCCCCCCCCCCCCC---CEEEECCCCHHHH----------HHHHH-HHHHHHHHHCCCCCC
Q ss_conf             542100243311255553221110012344667---1475166420018----------89998-888776420011235
Q gi|254780916|r  202 IDQDKIEKFLFGDVDLQTKNSAQFLGKFIEANG---GTIVLEEPDALPL----------AVQGR-IYNFIETGKIEFFDS  267 (482)
Q Consensus       202 ~~~~~~e~~lFG~~~~~~~~~~~~~g~~~~a~~---Gtl~l~ei~~L~~----------~~Q~~-Ll~~l~~~~~~~~g~  267 (482)
                      +.+     ...|.      ..++..-+|++|..   -.+|+|||+.+..          +.... |-++|-+     +++
T Consensus       221 f~e-----~~vGv------ga~rVR~lF~~Ar~~aP~IIFIDEiDaig~~R~~~~~gg~~e~~~tlNqlL~E-----mDG  284 (644)
T PRK10733        221 FVE-----MFVGV------GASRVRDMFEQAKKAAPCIIFIDEIDAVGRQRGAGLGGGHDEREQTLNQMLVE-----MDG  284 (644)
T ss_pred             HHH-----EEEEC------CHHHHHHHHHHHHHCCCEEEEEECHHCCCCCCCCCCCCCCHHHHHHHHHHHHH-----HHC
T ss_conf             302-----22530------68999999999996699799995322036667898889832888789999999-----548


Q ss_pred             CCCCCCCCEEEEECCCC--C-CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCC
Q ss_conf             53212343156521433--2-11111123337999886543344677877442222556677764101122333321111
Q gi|254780916|r  268 RGAIRLDVRLIFLTEKN--L-LPQVKSHVFRKDLYYRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDK  344 (482)
Q Consensus       268 ~~~~~~~~RiIa~t~~~--L-~~~~~~g~fr~dLy~rL~~~~i~iPpLReR~eDI~~L~~~fl~~~~~~~~~~~~~ls~~  344 (482)
                      -.. ...+=+|++||+.  | ..+..-|+|..       .+.|.+|-..+|.+    ++..++++.    ... ..++-+
T Consensus       285 f~~-~~~ViviaATNrpd~LD~ALlRPGRFDr-------~I~V~lPd~~~R~~----ILkvh~~~~----~l~-~dvdl~  347 (644)
T PRK10733        285 FEG-NEGIIVIAATNRPDVLDPALLRPGRFDR-------QVVVGLPDVRGREQ----ILKVHMRRV----PLA-PDIDAA  347 (644)
T ss_pred             CCC-CCCEEEEEECCCCCCCCHHHHCCCCCCE-------EEEECCCCHHHHHH----HHHHHHCCC----CCC-CCCCHH
T ss_conf             888-7876999626997554777716888655-------99977989889999----999996488----777-311589


Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHHH---CCCCCCCHHHHHHHHCCC
Q ss_conf             100012233898689999999999874---389810688954542124
Q gi|254780916|r  345 ALSLLTKYPWIDNVQELKNILLRAVIG---LKDSHLTEDRFVLLLSRE  389 (482)
Q Consensus       345 a~~~L~~y~WPGNvREL~n~i~r~~i~---~~~~~i~~~~~~~~l~~~  389 (482)
                      .++.... -|.|  -+|+|++..|.+.   .....|+..|+.....+.
T Consensus       348 ~lA~~T~-GfSG--ADLaNlvNEAAl~AaR~~k~~It~~d~e~A~drV  392 (644)
T PRK10733        348 IIARGTP-GFSG--ADLANLVNEAALFAARGNKRVVSMVEFEKAKDKI  392 (644)
T ss_pred             HHHCCCC-CCCH--HHHCCHHHHHHHHHHHHCCCCCCHHHHHHHHHHH
T ss_conf             8844599-8670--3332599999999987087543076689988885


No 141
>KOG0480 consensus
Probab=98.61  E-value=2.6e-07  Score=71.26  Aligned_cols=210  Identities=14%  Similarity=0.220  Sum_probs=128.8

Q ss_pred             CCCEEEEEECCCCCHHHHHHHHHHHCCCCCCCCCCCC---CCCCCCCCCCHHHHHCCCCCCCCCCCCCCCCCCCCCCCEE
Q ss_conf             4320488732777436799999984267543321012---3465542100243311255553221110012344667147
Q gi|254780916|r  161 DCAIPIMIQGEFGVGKKRLSRFIHESGKRAFFPFFIV---NCGMIDQDKIEKFLFGDVDLQTKNSAQFLGKFIEANGGTI  237 (482)
Q Consensus       161 ~~~~~vli~Ge~GtGK~~~A~~iH~~s~r~~~~fi~v---~c~~~~~~~~e~~lFG~~~~~~~~~~~~~g~~~~a~~Gtl  237 (482)
                      ..+.+|+|.|.+||||.-+=++.-+.|+|+  -++.=   ..|+++..++       ++..+|...--.|.+-.|++|..
T Consensus       376 RGDinv~iVGDPgt~KSQfLk~v~~fsPR~--vYtsGkaSSaAGLTaaVv-------kD~esgdf~iEAGALmLADnGIC  446 (764)
T KOG0480         376 RGDINVCIVGDPGTGKSQFLKAVCAFSPRS--VYTSGKASSAAGLTAAVV-------KDEESGDFTIEAGALMLADNGIC  446 (764)
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHHCCCCCC--EEECCCCCCCCCCEEEEE-------ECCCCCCEEEECCCEEECCCCEE
T ss_conf             677318995799713889999986548731--585076344346468997-------63777733553473788169668


Q ss_pred             EECCCCHHHHHHHHHHHHHHHHHHCCCC--CCCCCCCCCCEEEEECCC-----CCCCCCCHH------HH-HHHHH----
Q ss_conf             5166420018899988887764200112--355321234315652143-----321111112------33-37999----
Q gi|254780916|r  238 VLEEPDALPLAVQGRIYNFIETGKIEFF--DSRGAIRLDVRLIFLTEK-----NLLPQVKSH------VF-RKDLY----  299 (482)
Q Consensus       238 ~l~ei~~L~~~~Q~~Ll~~l~~~~~~~~--g~~~~~~~~~RiIa~t~~-----~L~~~~~~g------~f-r~dLy----  299 (482)
                      ++||-+.|...-|..|+.+++.+.+.--  |-.-......-||||+|.     |=..-+.++      .+ |=|||    
T Consensus       447 CIDEFDKMd~~dqvAihEAMEQQtISIaKAGv~aTLnARtSIlAAANPv~GhYdR~ktl~eNi~msApimSRFDL~FiLl  526 (764)
T KOG0480         447 CIDEFDKMDVKDQVAIHEAMEQQTISIAKAGVVATLNARTSILAAANPVGGHYDRKKTLRENINMSAPIMSRFDLFFILL  526 (764)
T ss_pred             EECHHCCCCHHHHHHHHHHHHHHEEHHEECCEEEEECCHHHHHHHCCCCCCCCCCCCCHHHHCCCCCHHHHHHCEEEEEE
T ss_conf             83100035707689999998751000330206886222355555327767745533006652277804542222799993


Q ss_pred             --------HHHHHHHHHHHHHHHHHHHHHH--------HHHHHHHHHCCCCCCCCCCCCCCCCCCCCCC-----------
Q ss_conf             --------8865433446778774422225--------5667776410112233332111110001223-----------
Q gi|254780916|r  300 --------YRISVFLINISTLRSRSEDIPW--------LVHFFLQSFCTKNAIKQISISDKALSLLTKY-----------  352 (482)
Q Consensus       300 --------~rL~~~~i~iPpLReR~eDI~~--------L~~~fl~~~~~~~~~~~~~ls~~a~~~L~~y-----------  352 (482)
                              |.++...+.+   +-..+|-..        .++.|+. |++   .-.+.++.+|-+.|..+           
T Consensus       527 D~~nE~~D~~ia~hIld~---h~~i~~~~~~~~~~~~e~vrkYi~-yAR---~~~P~ls~ea~~~lve~Y~~lR~~~~~~  599 (764)
T KOG0480         527 DDCNEVVDYAIARHILDL---HRGIDDATERVCVYTLEQVRKYIR-YAR---NFKPKLSKEASEMLVEKYKGLRQRDAQG  599 (764)
T ss_pred             CCCCHHHHHHHHHHHHHH---HCCCCCCCCCCCCCCHHHHHHHHH-HHH---HCCCCCCHHHHHHHHHHHHHHHHHHCCC
T ss_conf             578667779999999987---436211023256664999999999-987---5375324899999999999987741025


Q ss_pred             ----CCCCCHHHHHHHHHHHHHH---CCCCCCCHHHHHHHH
Q ss_conf             ----3898689999999999874---389810688954542
Q gi|254780916|r  353 ----PWIDNVQELKNILLRAVIG---LKDSHLTEDRFVLLL  386 (482)
Q Consensus       353 ----~WPGNvREL~n~i~r~~i~---~~~~~i~~~~~~~~l  386 (482)
                          .||=-||||+++|+-.-..   .-...++.+++....
T Consensus       600 ~~~~s~~ITvRqLESlIRLsEA~Ar~~~~devt~~~v~ea~  640 (764)
T KOG0480         600 NNRSSYRITVRQLESLIRLSEARARVECRDEVTKEDVEEAV  640 (764)
T ss_pred             CCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHH
T ss_conf             67666650699989899999999863324232699999999


No 142
>COG2255 RuvB Holliday junction resolvasome, helicase subunit [DNA replication, recombination, and repair]
Probab=98.61  E-value=8.3e-07  Score=67.76  Aligned_cols=258  Identities=20%  Similarity=0.246  Sum_probs=140.9

Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCC---CCCCCEEEEEECCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCHHHHH
Q ss_conf             11111112222222222222222---344320488732777436799999984267543321012346554210024331
Q gi|254780916|r  136 HCALDSLIAVSPAMIQVVDLARK---AGDCAIPIMIQGEFGVGKKRLSRFIHESGKRAFFPFFIVNCGMIDQDKIEKFLF  212 (482)
Q Consensus       136 ~~~~~~LiG~S~~m~~v~~~i~~---~a~~~~~vli~Ge~GtGK~~~A~~iH~~s~r~~~~fi~v~c~~~~~~~~e~~lF  212 (482)
                      ...+..++|+...-..+.=.|+.   -...--.||+.|++|.||+++|+-|-+.        .-+||...+...+|.   
T Consensus        22 P~~l~efiGQ~~vk~~L~ifI~AAk~r~e~lDHvLl~GPPGlGKTTLA~IIA~E--------mgvn~k~tsGp~leK---   90 (332)
T COG2255          22 PKTLDEFIGQEKVKEQLQIFIKAAKKRGEALDHVLLFGPPGLGKTTLAHIIANE--------LGVNLKITSGPALEK---   90 (332)
T ss_pred             CCCHHHHCCHHHHHHHHHHHHHHHHHCCCCCCEEEEECCCCCCHHHHHHHHHHH--------HCCCEEECCCCCCCC---
T ss_conf             654888518399999999999999844987674786479987688899999998--------567737636620157---


Q ss_pred             CCCCCCCCCCCCCCCCCC-CCCCCEEEECCCCHHHHHHHHHHHHHHHHHHCCCC-C---CCCCCCC---CCEEEEECCCC
Q ss_conf             125555322111001234-46671475166420018899988887764200112-3---5532123---43156521433
Q gi|254780916|r  213 GDVDLQTKNSAQFLGKFI-EANGGTIVLEEPDALPLAVQGRIYNFIETGKIEFF-D---SRGAIRL---DVRLIFLTEKN  284 (482)
Q Consensus       213 G~~~~~~~~~~~~~g~~~-~a~~Gtl~l~ei~~L~~~~Q~~Ll~~l~~~~~~~~-g---~~~~~~~---~~RiIa~t~~~  284 (482)
                               ..+-.+++- .-.|-.||+||||.|++.+-.-|.-++++-+..-+ |   +.+.++.   .|-+|.||++-
T Consensus        91 ---------~gDlaaiLt~Le~~DVLFIDEIHrl~~~vEE~LYpaMEDf~lDI~IG~gp~Arsv~ldLppFTLIGATTr~  161 (332)
T COG2255          91 ---------PGDLAAILTNLEEGDVLFIDEIHRLSPAVEEVLYPAMEDFRLDIIIGKGPAARSIRLDLPPFTLIGATTRA  161 (332)
T ss_pred             ---------HHHHHHHHHCCCCCCEEEEEHHHHCCHHHHHHHHHHHHHEEEEEEECCCCCCCEEECCCCCEEEEEECCCC
T ss_conf             ---------26599998639867767772553147428989646753105778972487553476379981375101346


Q ss_pred             CCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-------HHHHHHHCCCCCCCCCCCCCCCCCCCCCCCC--C
Q ss_conf             211111123337999886543344677877442222556-------6777641011223333211111000122338--9
Q gi|254780916|r  285 LLPQVKSHVFRKDLYYRISVFLINISTLRSRSEDIPWLV-------HFFLQSFCTKNAIKQISISDKALSLLTKYPW--I  355 (482)
Q Consensus       285 L~~~~~~g~fr~dLy~rL~~~~i~iPpLReR~eDI~~L~-------~~fl~~~~~~~~~~~~~ls~~a~~~L~~y~W--P  355 (482)
                             |..              --|||+|-.=+..|-       ...+.+.+..++.   .+++++...+..+.-  |
T Consensus       162 -------G~l--------------t~PLrdRFGi~~rlefY~~~eL~~Iv~r~a~~l~i---~i~~~~a~eIA~rSRGTP  217 (332)
T COG2255         162 -------GML--------------TNPLRDRFGIIQRLEFYTVEELEEIVKRSAKILGI---EIDEEAALEIARRSRGTP  217 (332)
T ss_pred             -------CCC--------------CCHHHHHCCCEEEEECCCHHHHHHHHHHHHHHHCC---CCCHHHHHHHHHHCCCCC
T ss_conf             -------645--------------63368862860454058889999999988887387---768579999998636993


Q ss_pred             C-CHHHHHHHHHHHHHHCCCCCCCHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHCCCCCCCCCCCCCCHHHH
Q ss_conf             8-689999999999874389810688954542124454322343222222334443210000000011234445432589
Q gi|254780916|r  356 D-NVQELKNILLRAVIGLKDSHLTEDRFVLLLSREGKKEREFHTETACTCYTEGKSSDTILDNLSQESIPAIGQDGEVRR  434 (482)
Q Consensus       356 G-NvREL~n~i~r~~i~~~~~~i~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  434 (482)
                      - -.|=|+.|-..+-+ ..+..|+.+-....+....                                       -+..-
T Consensus       218 RIAnRLLrRVRDfa~V-~~~~~I~~~ia~~aL~~L~---------------------------------------Vd~~G  257 (332)
T COG2255         218 RIANRLLRRVRDFAQV-KGDGDIDRDIADKALKMLD---------------------------------------VDELG  257 (332)
T ss_pred             HHHHHHHHHHHHHHHH-HCCCCCCHHHHHHHHHHHC---------------------------------------CCCCC
T ss_conf             8999999999999998-1688204899999998729---------------------------------------64025


Q ss_pred             HHHHHHHHHHHHHHHHCCC---HHHHHHHHCCCHHHHHHHHHHHCC
Q ss_conf             9999999999999982872---789997848998899999998188
Q gi|254780916|r  435 LSDIEKEIIGLAMKLYRAQ---MSEVARRLGIGRSTLYRKIREYNI  477 (482)
Q Consensus       435 l~e~E~~~I~~aL~~~~Gn---~~~aA~~LGIsR~tL~rKlk~~gi  477 (482)
                      |+++.+.++....+.++|.   ..--|..+|..|.|+-.++.-|=|
T Consensus       258 Ld~~D~k~L~~li~~f~GgPVGl~tia~~lge~~~TiEdv~EPyLi  303 (332)
T COG2255         258 LDEIDRKYLRALIEQFGGGPVGLDTIAAALGEDRDTIEDVIEPYLI  303 (332)
T ss_pred             CCHHHHHHHHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHHHHHH
T ss_conf             5689999999999973799823999999965767778888748998


No 143
>COG3706 PleD Response regulator containing a CheY-like receiver domain and a GGDEF domain [Signal transduction mechanisms]
Probab=98.59  E-value=1e-07  Score=74.16  Aligned_cols=141  Identities=13%  Similarity=0.100  Sum_probs=102.2

Q ss_pred             CEEEEECC--HHHHHHHCCCCCEEEEECCCCCCCHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHHHCCCCCCCCCCCC
Q ss_conf             88999893--7999986089989999785469888999999998578983999926899999998885057432222222
Q gi|254780916|r   35 YDVFIVNV--SDLSTISKIQVNVIFLSLINCEDDKENILKNIVDKIPIVPIIVQTTQDNIKILNCFLYNRISKFFLNLVS  112 (482)
Q Consensus        35 ~~v~~a~~--~al~~l~~~~~dlillD~~mP~~dGlell~~i~~~~p~ipvIiiT~~~~~~~~~~a~~~g~~d~l~KP~~  112 (482)
                      |+|.++..  .+++.+...++|.+++|++||+++|+++|+.+++.- .. ++++|+.++...-..+...|+.+|+.||++
T Consensus        13 ~~v~~a~~g~~~l~~~~~~~~~~~lld~~m~~~~~~~~~~~lk~~~-~~-~v~~t~~~~~~~~~~~~~~~~~~~l~~~~~   90 (435)
T COG3706          13 KEVATAKKGLIALAILLDHKPDYKLLDVMMPGMDGFELCRRLKAEP-AT-VVMVTALDDSAPRVRGLKAGADDFLTKPVN   90 (435)
T ss_pred             HHHHHCCCHHHHHHHHHCCCCCEEEEECCCCCCCCHHHHHHHHCCC-CC-EEEEEECCCCCCCHHHHHHHHHHHCCCCCC
T ss_conf             5463425427799997448987487410068867301998763587-51-699860378777556776313441367777


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCCCHHHHHHHHHHHC
Q ss_conf             22222222222222222222221111111122222222222222223443204887327774367999999842
Q gi|254780916|r  113 RKQLCDSIICALREGVVPSQENEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHES  186 (482)
Q Consensus       113 ~~~L~~~i~~al~~~~~~~~~~~~~~~~~LiG~S~~m~~v~~~i~~~a~~~~~vli~Ge~GtGK~~~A~~iH~~  186 (482)
                      ...+..+.....+......+...........+.|+.+..-         ...-||+..+..+--..+.+.+-..
T Consensus        91 ~~~~~~r~~~l~~~k~~~de~~~~~~~~~~~~~~~~~~~~---------~~~kILvvdD~~~~~~~l~~~L~~~  155 (435)
T COG3706          91 DSQLFLRAKSLVRLKCSIDELRLREETGGELGVSPLLPED---------APKKILVVDDDATQRERLRRILQVE  155 (435)
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHHCCCCCCCCCCCCCCCCC---------CCCEEEEECCCHHHHHHHHHHHHHC
T ss_conf             1778875266314444578985145654212356455556---------6750899748077999999998753


No 144
>PRK05563 DNA polymerase III subunits gamma and tau; Validated
Probab=98.59  E-value=3e-07  Score=70.88  Aligned_cols=217  Identities=14%  Similarity=0.158  Sum_probs=123.7

Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCCCHHHHHHHHHHHCCC----CCCCCCCC-CCCCCCCCCCCHH
Q ss_conf             111111112222222222222222344320488732777436799999984267----54332101-2346554210024
Q gi|254780916|r  135 EHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHESGK----RAFFPFFI-VNCGMIDQDKIEK  209 (482)
Q Consensus       135 ~~~~~~~LiG~S~~m~~v~~~i~~~a~~~~~vli~Ge~GtGK~~~A~~iH~~s~----r~~~~fi~-v~c~~~~~~~~e~  209 (482)
                      ....|..++|+....+.+...+.. .......|+.|+.||||+.+||.+-..-.    ....|--. -+|.++.......
T Consensus        11 RP~~f~dvvgQ~~v~~~L~n~i~~-~~i~hayLf~GprG~GKTs~Ari~akalnc~~~~~~~pC~~C~~C~~i~~g~~~D   89 (541)
T PRK05563         11 RPRTFEDVVGQEHITTTLKNQIIN-NRIAHAYLFCGTRGTGKTSTAKIFAKAVNCLNPQDGEPCNECEICKKINEGLLMD   89 (541)
T ss_pred             CCCCHHHHCCCHHHHHHHHHHHHC-CCCCEEEEEECCCCCCHHHHHHHHHHHHCCCCCCCCCCCCCCHHHHHHHCCCCCC
T ss_conf             899776624849999999999984-9932045303879958999999999995799988898575148899985689887


Q ss_pred             HHHCCCCCCC--CCCCCCCCCCC-------CCCCCEEEECCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCEEEEE
Q ss_conf             3311255553--22111001234-------46671475166420018899988887764200112355321234315652
Q gi|254780916|r  210 FLFGDVDLQT--KNSAQFLGKFI-------EANGGTIVLEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFL  280 (482)
Q Consensus       210 ~lFG~~~~~~--~~~~~~~g~~~-------~a~~Gtl~l~ei~~L~~~~Q~~Ll~~l~~~~~~~~g~~~~~~~~~RiIa~  280 (482)
                      -+  +-+++.  |-..-| .+.+       .+.--...+||+|-|+...+..||+.|++.           +.++++|.+
T Consensus        90 v~--Eidaas~~gvd~iR-~~~~~~~~~p~~~~~Kv~IiDEvhmls~~a~nallKtlEeP-----------p~~~~Fila  155 (541)
T PRK05563         90 VI--EIDAASNNGVDDIR-EIIENVKYPPQEGKYKVYIMDEVHMLSQGAVNAFLKTLEEP-----------PSNVIFILA  155 (541)
T ss_pred             EE--EECCCCCCCHHHHH-HHHHHCEECCCCCCEEEEEEECCCCCCHHHHHHHHHHHHCC-----------CCCCEEEEE
T ss_conf             36--62444447889999-99976104876787059999772338999999999998548-----------777569997


Q ss_pred             CCCCCC---C-CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             143321---1-111123337999886543344677877442222556677764101122333321111100012233898
Q gi|254780916|r  281 TEKNLL---P-QVKSHVFRKDLYYRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWID  356 (482)
Q Consensus       281 t~~~L~---~-~~~~g~fr~dLy~rL~~~~i~iPpLReR~eDI~~L~~~fl~~~~~~~~~~~~~ls~~a~~~L~~y~WPG  356 (482)
                      |+..-.   . +....+|+        --.|..          ..++.+ |...+.+.|.   .++++|+.++.... -|
T Consensus       156 tte~~ki~~tI~SRcq~f~--------f~~i~~----------~~i~~~-L~~I~~~E~i---~~~~~al~lIa~~s-~G  212 (541)
T PRK05563        156 TTDPQKLPITILSRCQRFD--------FKRIKV----------KDIFKR-LRKIVEEQGI---FADDKSLNLIARMS-DG  212 (541)
T ss_pred             CCCCCCCCHHHHHHEEEEE--------EEECCH----------HHHHHH-HHHHHHHCCC---CCCHHHHHHHHHHC-CC
T ss_conf             6984427455674213577--------543899----------999999-9999998499---98789999999745-99


Q ss_pred             CHHHHHHHHHHHHHHCCCCCCCHHHHHHHHCCCC
Q ss_conf             6899999999998743898106889545421244
Q gi|254780916|r  357 NVQELKNILLRAVIGLKDSHLTEDRFVLLLSREG  390 (482)
Q Consensus       357 NvREL~n~i~r~~i~~~~~~i~~~~~~~~l~~~~  390 (482)
                      -+|.=-+++.+++..+ ++.|+.+++...++...
T Consensus       213 smRDAlslLdQ~is~~-~~~it~~~v~~~lG~~~  245 (541)
T PRK05563        213 AMRDALSILDQAISMG-DGKVDYDDVVSMLGLVT  245 (541)
T ss_pred             CHHHHHHHHHHHHHHC-CCCCCHHHHHHHHCCCC
T ss_conf             7788999999999835-99866999999968999


No 145
>PRK06645 DNA polymerase III subunits gamma and tau; Validated
Probab=98.59  E-value=1.6e-06  Score=65.80  Aligned_cols=213  Identities=15%  Similarity=0.126  Sum_probs=124.9

Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCCCHHHHHHHHHHHCC----CCCCCCCCC-----CCCCCCCC-
Q ss_conf             11111111222222222222222234432048873277743679999998426----754332101-----23465542-
Q gi|254780916|r  135 EHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHESG----KRAFFPFFI-----VNCGMIDQ-  204 (482)
Q Consensus       135 ~~~~~~~LiG~S~~m~~v~~~i~~~a~~~~~vli~Ge~GtGK~~~A~~iH~~s----~r~~~~fi~-----v~c~~~~~-  204 (482)
                      ....|+.++|+....+.+...+.. ......-|++|+.||||+.+||.+-..-    .-.++|-..     -+|.++.. 
T Consensus        16 RP~~f~~liGQ~~~~~~l~n~i~~-~~~~~aylf~G~rG~GKTt~Ari~ak~lnc~~~~~~~~~~~~c~~c~~c~~i~~~   94 (507)
T PRK06645         16 RPSNFAELQGQEVLVKVLSYTILN-DRLAGGYLLTGIRGVGKTTSARIIAKAVNCSALITENTTIKTCEKCTNCISFNNH   94 (507)
T ss_pred             CCCCHHHHCCCHHHHHHHHHHHHC-CCCCCEEEEECCCCCCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCHHHHHHHCC
T ss_conf             799765623939999999999973-9966347745879978899999999996799988889988888887678998658


Q ss_pred             ---CCCHHHHHCCCCCC--CCCCCCCCCCCCC-------CCCCEEEECCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCC
Q ss_conf             ---10024331125555--3221110012344-------66714751664200188999888877642001123553212
Q gi|254780916|r  205 ---DKIEKFLFGDVDLQ--TKNSAQFLGKFIE-------ANGGTIVLEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIR  272 (482)
Q Consensus       205 ---~~~e~~lFG~~~~~--~~~~~~~~g~~~~-------a~~Gtl~l~ei~~L~~~~Q~~Ll~~l~~~~~~~~g~~~~~~  272 (482)
                         +.+|      .+++  ||-..-| -+++.       +.--..++||+|-|+.+.+..||+.|++.           +
T Consensus        95 ~~~dv~E------iDaas~~gv~~ir-~l~~~~~~~p~~~~~kv~iidE~hmls~~a~nallktlEep-----------p  156 (507)
T PRK06645         95 NHPDIIE------IDAASKTSVDDIR-RIIESAEYKPLQGKHKIFIIDEVHMLSKGAFNALLKTLEEP-----------P  156 (507)
T ss_pred             CCCCEEE------EECCCCCCHHHHH-HHHHHCCCCCCCCCEEEEEECCHHHCCHHHHHHHHHHHHCC-----------C
T ss_conf             9998599------6378888889999-99863551787674358995214224899999999974278-----------6


Q ss_pred             CCCEEEEECCCCCC----CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCC
Q ss_conf             34315652143321----11111233379998865433446778774422225566777641011223333211111000
Q gi|254780916|r  273 LDVRLIFLTEKNLL----PQVKSHVFRKDLYYRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSL  348 (482)
Q Consensus       273 ~~~RiIa~t~~~L~----~~~~~g~fr~dLy~rL~~~~i~iPpLReR~eDI~~L~~~fl~~~~~~~~~~~~~ls~~a~~~  348 (482)
                      .++++|.+|+..=.    -+....+|+             +     |+=+...++.| |...+.+.+   ..++++|+.+
T Consensus       157 ~~~~Fi~atte~~kip~ti~srcq~f~-------------~-----~~i~~~~i~~~-l~~i~~~E~---~~~~~~al~~  214 (507)
T PRK06645        157 PHIIFIFATTEVQKIPATIISRCQRYD-------------L-----RRLSFEEIFKL-LEYITKQEN---LKADIEALRI  214 (507)
T ss_pred             CCEEEEEECCCHHHCCHHHHHHCEEEE-------------E-----ECCCHHHHHHH-HHHHHHHCC---CCCCHHHHHH
T ss_conf             443899974853648378885432787-------------5-----45997999999-999999768---7777899999


Q ss_pred             CCCCCCCCCHHHHHHHHHHHHHHC--CCCCCCHHHHHHHHCCC
Q ss_conf             122338986899999999998743--89810688954542124
Q gi|254780916|r  349 LTKYPWIDNVQELKNILLRAVIGL--KDSHLTEDRFVLLLSRE  389 (482)
Q Consensus       349 L~~y~WPGNvREL~n~i~r~~i~~--~~~~i~~~~~~~~l~~~  389 (482)
                      +.... -|-+|.=-+++.++...+  .++.|+.+++..-++-.
T Consensus       215 ia~~a-~Gs~RDalslldqai~~~~~~~~~I~~~~V~~MLGl~  256 (507)
T PRK06645        215 IAYKS-EGSARDAVSILDQAASMSAKSDNIISPQVINQMLGLV  256 (507)
T ss_pred             HHHHC-CCCHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHCCC
T ss_conf             99855-9986789999999999754898702699999983899


No 146
>KOG1051 consensus
Probab=98.56  E-value=2.7e-07  Score=71.23  Aligned_cols=230  Identities=14%  Similarity=0.145  Sum_probs=133.2

Q ss_pred             CCCCCCCCCCCCCCCCCCCC------CCCEEEEEECCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCHHHHHCC
Q ss_conf             11222222222222222234------432048873277743679999998426754332101234655421002433112
Q gi|254780916|r  141 SLIAVSPAMIQVVDLARKAG------DCAIPIMIQGEFGVGKKRLSRFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFGD  214 (482)
Q Consensus       141 ~LiG~S~~m~~v~~~i~~~a------~~~~~vli~Ge~GtGK~~~A~~iH~~s~r~~~~fi~v~c~~~~~~~~e~~lFG~  214 (482)
                      .++|+..++..|-+.|.+.-      +.+...|+.|++|+||+-+|+++-.+-......||.|||+.+.+   -+.+-|-
T Consensus       563 ~V~gQ~eAv~aIa~AI~~sr~gl~~~~~~awflflGpdgvGKt~lAkaLA~~~Fgse~~~IriDmse~~e---vskligs  639 (898)
T KOG1051         563 RVIGQDEAVAAIAAAIRRSRAGLKDPNPDAWFLFLGPDGVGKTELAKALAEYVFGSEENFIRLDMSEFQE---VSKLIGS  639 (898)
T ss_pred             HCCCHHHHHHHHHHHHHHCCCCCCCCCCCEEEEEECCCCHHHHHHHHHHHHHHCCCCCCEEEECHHHHHH---HHHCCCC
T ss_conf             4466377899999999843203578888858999788841389999999999728864268961455555---6530489


Q ss_pred             CCCCCC--CCCCCCCCCCCCCCCEEEECCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCE---EEEECCCCCCCCC
Q ss_conf             555532--21110012344667147516642001889998888776420011235532123431---5652143321111
Q gi|254780916|r  215 VDLQTK--NSAQFLGKFIEANGGTIVLEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVR---LIFLTEKNLLPQV  289 (482)
Q Consensus       215 ~~~~~~--~~~~~~g~~~~a~~Gtl~l~ei~~L~~~~Q~~Ll~~l~~~~~~~~g~~~~~~~~~R---iIa~t~~~L~~~~  289 (482)
                      ..++-|  +..+-...+..--.-.++||||+...+.+|..|++++++|++..   .+.+.++++   ||-++|..-....
T Consensus       640 p~gyvG~e~gg~LteavrrrP~sVvLfdeIEkAh~~v~n~llq~lD~GrltD---s~Gr~Vd~kN~I~IMTsn~~~~~i~  716 (898)
T KOG1051         640 PPGYVGKEEGGQLTEAVKRRPYSVVLFEEIEKAHPDVLNILLQLLDRGRLTD---SHGREVDFKNAIFIMTSNVGSSAIA  716 (898)
T ss_pred             CCCCCCCHHHHHHHHHHHCCCCEEEEEECHHHCCHHHHHHHHHHHHCCCCCC---CCCCEEECCCEEEEEECCCCHHHHH
T ss_conf             9555463057788899716996599983022228889999999986274005---8886750464599994263166664


Q ss_pred             -----------------------------CH----HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCC
Q ss_conf             -----------------------------11----233379998865433446778774422225566777641011223
Q gi|254780916|r  290 -----------------------------KS----HVFRKDLYYRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAI  336 (482)
Q Consensus       290 -----------------------------~~----g~fr~dLy~rL~~~~i~iPpLReR~eDI~~L~~~fl~~~~~~~~~  336 (482)
                                                   ..    ..||+++.-|++.+.+..|-=|+--..|...-...+.+-.++.+ 
T Consensus       717 ~~~~~~~~l~~~~~~~~~~~~~k~~v~~~~~~~~~~~~r~Ef~nrid~i~lf~~l~~~~~~~i~~~~~~e~~~r~~~~~-  795 (898)
T KOG1051         717 NDASLEEKLLDMDEKRGSYRLKKVQVSDAVRIYNKQFFRKEFLNRIDELDLNLPLDRDELIEIVNKQLTEIEKRLEERE-  795 (898)
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHCCCCEEEEECCCCHHHHHHHHHHHHHHHHHHHHHHH-
T ss_conf             0454100012310001233201333334320135655686785555405541425556666555667788887766667-


Q ss_pred             CCCCCCCCCCCCC--CCCCCCCCHHHHHHHHHHHHHHCCCCCC
Q ss_conf             3332111110001--2233898689999999999874389810
Q gi|254780916|r  337 KQISISDKALSLL--TKYPWIDNVQELKNILLRAVIGLKDSHL  377 (482)
Q Consensus       337 ~~~~ls~~a~~~L--~~y~WPGNvREL~n~i~r~~i~~~~~~i  377 (482)
                      -...+++.+...+  ..|+.-+-.|-++..|++.+..+-...+
T Consensus       796 ~~~~v~~~~~~~v~~~~~d~~ygAr~ikr~i~~~~~~~la~~~  838 (898)
T KOG1051         796 LLLLVTDRVDDKVLFKGYDFDYGARPIKRSIEERFENRLAEAL  838 (898)
T ss_pred             HHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             9999889997665305768477766899999999887776531


No 147
>PRK00411 cdc6 cell division control protein 6; Reviewed
Probab=98.55  E-value=8.3e-07  Score=67.74  Aligned_cols=231  Identities=15%  Similarity=0.127  Sum_probs=128.1

Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCC--CCEEEEEECCCCCHHHHHHHHHHHCCCCC--CCCCCCCCCCCCCCC-----CCH
Q ss_conf             111112222222222222222344--32048873277743679999998426754--332101234655421-----002
Q gi|254780916|r  138 ALDSLIAVSPAMIQVVDLARKAGD--CAIPIMIQGEFGVGKKRLSRFIHESGKRA--FFPFFIVNCGMIDQD-----KIE  208 (482)
Q Consensus       138 ~~~~LiG~S~~m~~v~~~i~~~a~--~~~~vli~Ge~GtGK~~~A~~iH~~s~r~--~~~fi~v~c~~~~~~-----~~e  208 (482)
                      ..+.|.+.-..++.+...+..+..  ...+++|.|.+||||+++++.+-..-...  +-.|+.|||..+...     .+-
T Consensus        28 vP~~l~~Re~Ei~~l~~~l~~~l~g~~~~n~~I~G~pGTGKT~~vk~v~~~l~~~~~~~~~vyINc~~~~t~~~i~~~i~  107 (394)
T PRK00411         28 VPENLPHREEQIEELAFALRPALRGSRPSNVLILGPPGTGKTTTVKKVFEELEEAALKVVYVYINCQIDRTRYAILSEIA  107 (394)
T ss_pred             CCCCCCCHHHHHHHHHHHHHHHHCCCCCCCEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEEECCCCCCHHHHHHHHH
T ss_conf             89989885999999999999997599998479988999989999999999999746896599996966898999999999


Q ss_pred             HHHHCCCCCCCCCCC----CC-CCCCCCCCCC-EEEECCCCHHHHHH-HHHHHHHHHHHHCCCCCCCCCCCCCCEEEEEC
Q ss_conf             433112555532211----10-0123446671-47516642001889-99888877642001123553212343156521
Q gi|254780916|r  209 KFLFGDVDLQTKNSA----QF-LGKFIEANGG-TIVLEEPDALPLAV-QGRIYNFIETGKIEFFDSRGAIRLDVRLIFLT  281 (482)
Q Consensus       209 ~~lFG~~~~~~~~~~----~~-~g~~~~a~~G-tl~l~ei~~L~~~~-Q~~Ll~~l~~~~~~~~g~~~~~~~~~RiIa~t  281 (482)
                      ..|+|+.-..+|-..    +. ...+..-++- .++||||+.|-... |.-|..++.-..      .. ..+.+-+|+.+
T Consensus       108 ~~L~~~~~p~~G~s~~~~~~~l~~~l~~~~~~~ivvLDEiD~L~~~~~~~vLY~L~r~~~------~~-~~~~~~vI~Is  180 (394)
T PRK00411        108 RSLFGHPPPSSGLSFDELFDKIAEYLDERDRVLIVALDDINYLVEKEGNDVLYSLLRAHE------EY-PGARIGVIGIS  180 (394)
T ss_pred             HHHCCCCCCCCCCCHHHHHHHHHHHHHCCCCEEEEEEECCCCCCCCCCCHHHHHHHHCCC------CC-CCCCEEEEEEE
T ss_conf             995699898778789999999999861669758999965540203665089999985402------26-88738999997


Q ss_pred             CC-CCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCC--CCCH
Q ss_conf             43-32111111233379998865433446778774422225566777641011223333211111000122338--9868
Q gi|254780916|r  282 EK-NLLPQVKSHVFRKDLYYRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPW--IDNV  358 (482)
Q Consensus       282 ~~-~L~~~~~~g~fr~dLy~rL~~~~i~iPpLReR~eDI~~L~~~fl~~~~~~~~~~~~~ls~~a~~~L~~y~W--PGNv  358 (482)
                      |. ++.+     .|.+-+--+|+.-.|..||-..-  .|-.++.+=++.     +...-.++++++.....+.=  .|+.
T Consensus       181 N~~~~~~-----~Ldprv~S~l~~~~i~F~PY~~~--qL~~IL~~R~~~-----af~~gv~~~~~i~~~A~~~a~~~GDa  248 (394)
T PRK00411        181 SDLTFLY-----ILDPRVKSVFGPEEIVFPPYTAD--EIFDILKDRVEE-----GFYPGVVSDEVLELIADLTGREHGDA  248 (394)
T ss_pred             CCCCHHH-----HHHHHHHCCCCCEEEEECCCCHH--HHHHHHHHHHHH-----CCCCCCCCHHHHHHHHHHHHHCCCCH
T ss_conf             6871776-----64077750278628985899989--999999999984-----14556789789999999985504758


Q ss_pred             HHHHHHHHHHHHHCC---CCCCCHHHHHHHHC
Q ss_conf             999999999987438---98106889545421
Q gi|254780916|r  359 QELKNILLRAVIGLK---DSHLTEDRFVLLLS  387 (482)
Q Consensus       359 REL~n~i~r~~i~~~---~~~i~~~~~~~~l~  387 (482)
                      |.=-.++++|.-.+.   .+.++.+|+.....
T Consensus       249 R~Aldllr~A~e~Ae~~g~~~Vt~~hV~~A~~  280 (394)
T PRK00411        249 RVAIDLLRRAGEIAEREGSRKVTEEDVRKAYE  280 (394)
T ss_pred             HHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHH
T ss_conf             99999999999999971899658999999999


No 148
>PRK05342 clpX ATP-dependent protease ATP-binding subunit ClpX; Provisional
Probab=98.54  E-value=1.2e-07  Score=73.59  Aligned_cols=91  Identities=20%  Similarity=0.280  Sum_probs=66.0

Q ss_pred             CCEEEEEECCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCC-----CCHHHHHCCCCCCCCCCCCCCCCCCCCCCCE
Q ss_conf             32048873277743679999998426754332101234655421-----0024331125555322111001234466714
Q gi|254780916|r  162 CAIPIMIQGEFGVGKKRLSRFIHESGKRAFFPFFIVNCGMIDQD-----KIEKFLFGDVDLQTKNSAQFLGKFIEANGGT  236 (482)
Q Consensus       162 ~~~~vli~Ge~GtGK~~~A~~iH~~s~r~~~~fi~v~c~~~~~~-----~~e~~lFG~~~~~~~~~~~~~g~~~~a~~Gt  236 (482)
                      ..++||+.|++||||+++|+.+-..   -+-||+.+||..+++.     -+|+-+.--..       ...+-++.|..|.
T Consensus       108 ~KsNILliGPTG~GKTlla~tLAk~---l~vPF~iaDAT~lTEaGYVGeDVE~ii~~Llq-------~Ad~dve~Ae~GI  177 (411)
T PRK05342        108 QKSNILLIGPTGSGKTLLAQTLARI---LNVPFAIADATTLTEAGYVGEDVENILLKLLQ-------AADYDVEKAQRGI  177 (411)
T ss_pred             CCCCEEEECCCCCCHHHHHHHHHHH---HCCCEEEEEECEECCCCCCCCCHHHHHHHHHH-------HCCCCHHHHHCCE
T ss_conf             3453899899997788999999998---69998998612001267456079999999999-------8288899883682


Q ss_pred             EEECCCCHHHH--------------HHHHHHHHHHHHHHC
Q ss_conf             75166420018--------------899988887764200
Q gi|254780916|r  237 IVLEEPDALPL--------------AVQGRIYNFIETGKI  262 (482)
Q Consensus       237 l~l~ei~~L~~--------------~~Q~~Ll~~l~~~~~  262 (482)
                      +|+|||+.+..              -+|.-||..++...+
T Consensus       178 V~IDEIDKIarks~~~s~trDVSgEGVQqaLLkiiEGt~v  217 (411)
T PRK05342        178 VYIDEIDKIARKSENPSITRDVSGEGVQQALLKILEGTVA  217 (411)
T ss_pred             EEEEEHHHHHHCCCCCCCCCCCCCHHHHHHHHHHHCCCEE
T ss_conf             8885023454247888887776512489999998758714


No 149
>PRK07270 DNA polymerase III subunits gamma and tau; Validated
Probab=98.52  E-value=5.6e-07  Score=68.92  Aligned_cols=215  Identities=16%  Similarity=0.185  Sum_probs=124.2

Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCCCHHHHHHHHHHHCCC---C-CCCCCC-CCCCCCCCCCCCHH
Q ss_conf             111111112222222222222222344320488732777436799999984267---5-433210-12346554210024
Q gi|254780916|r  135 EHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHESGK---R-AFFPFF-IVNCGMIDQDKIEK  209 (482)
Q Consensus       135 ~~~~~~~LiG~S~~m~~v~~~i~~~a~~~~~vli~Ge~GtGK~~~A~~iH~~s~---r-~~~~fi-~v~c~~~~~~~~e~  209 (482)
                      ....|+.++|+....+.+...+.+ .....-.|+.|+.||||+.+|+.+-..-.   . ...|-- --+|..+.......
T Consensus        10 RP~~F~dvvGQe~i~~~L~nal~~-~ri~HAyLF~GP~GtGKts~ArifAkaLnC~~~~~~~pC~~C~~C~~i~~g~~~D   88 (557)
T PRK07270         10 RSQTFDEMVGQEVVATTLKQAVES-GKISHAYLFSGPRGTGKTSAAKIFAKAMNCPNQVDGEPCNNCDICRDITNGSLED   88 (557)
T ss_pred             CCCCHHHHCCHHHHHHHHHHHHHC-CCCCEEEEEECCCCCCHHHHHHHHHHHHCCCCCCCCCCCCCCHHHHHHHCCCCCC
T ss_conf             899876714819999999999985-9954044210899868999999999995799989999888777999987589997


Q ss_pred             HHHCCCCCCCCC-CCCCCCC-----C--CCCCCCEEEECCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCEEEEEC
Q ss_conf             331125555322-1110012-----3--4466714751664200188999888877642001123553212343156521
Q gi|254780916|r  210 FLFGDVDLQTKN-SAQFLGK-----F--IEANGGTIVLEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLT  281 (482)
Q Consensus       210 ~lFG~~~~~~~~-~~~~~g~-----~--~~a~~Gtl~l~ei~~L~~~~Q~~Ll~~l~~~~~~~~g~~~~~~~~~RiIa~t  281 (482)
                       ++ +.++.... ..+-..+     +  .++..-..++||++.|+...|..||+.|++.           +.++.+|.+|
T Consensus        89 -vi-Eidaas~~gVd~IRei~~~~~~~P~~~~yKV~IIDEah~Ls~~A~NALLKtLEEP-----------P~~~vFIL~T  155 (557)
T PRK07270         89 -VI-EIDAASNNGVDEIRDIRDKSTYAPSRATYKVYIIDEVHMLSTGAFNALLKTLEEP-----------TENVVFILAT  155 (557)
T ss_pred             -EE-EECCCCCCCHHHHHHHHHHHCCCCCCCCEEEEEECCHHHCCHHHHHHHHHHHHCC-----------CCCEEEEEEE
T ss_conf             -48-7347776788999999998423877788389997144534999999899985289-----------9876999984


Q ss_pred             CCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH-------HHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             433211111123337999886543344677877442-------2225566777641011223333211111000122338
Q gi|254780916|r  282 EKNLLPQVKSHVFRKDLYYRISVFLINISTLRSRSE-------DIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPW  354 (482)
Q Consensus       282 ~~~L~~~~~~g~fr~dLy~rL~~~~i~iPpLReR~e-------DI~~L~~~fl~~~~~~~~~~~~~ls~~a~~~L~~y~W  354 (482)
                      +.. ..+                    +|+.+.|..       +...++.+ |...+.+.|.   .++++|+.++.... 
T Consensus       156 tep-~kI--------------------l~TI~SRCQrf~F~~i~~~~i~~~-L~~I~~~E~i---~~~~~aL~~Ia~~a-  209 (557)
T PRK07270        156 TEL-HKI--------------------PATILSRVQRFEFKSIKTKAIREH-LAWILDKEGI---SFEVEALNLIARRA-  209 (557)
T ss_pred             CCH-HHC--------------------CHHHHHHHHHCCCCCCCHHHHHHH-HHHHHHHCCC---CCCHHHHHHHHHHC-
T ss_conf             994-759--------------------288874300010888999999999-9999998399---86999999999977-


Q ss_pred             CCCHHHHHHHHHHHHHHCCCCCCCHHHHHHHHCCC
Q ss_conf             98689999999999874389810688954542124
Q gi|254780916|r  355 IDNVQELKNILLRAVIGLKDSHLTEDRFVLLLSRE  389 (482)
Q Consensus       355 PGNvREL~n~i~r~~i~~~~~~i~~~~~~~~l~~~  389 (482)
                      -|-.|.=-+++.+++..+.+..|+.+++...++..
T Consensus       210 ~G~mRdAlsiLdQ~~s~~~~~~it~~~v~~~~G~~  244 (557)
T PRK07270        210 EGGMRDALSILDQALSLSQDNQVTIAIAEEITGSI  244 (557)
T ss_pred             CCCHHHHHHHHHHHHHCCCCCCCCHHHHHHHHCCC
T ss_conf             99687899999999971799976799999996899


No 150
>PRK09581 pleD response regulator PleD; Reviewed
Probab=98.52  E-value=5e-07  Score=69.32  Aligned_cols=117  Identities=17%  Similarity=0.242  Sum_probs=95.6

Q ss_pred             CCCCEEEECCCHHHHHHHHHHHHHCCCEEEEECCH--HHHHHHCCCCCEEEEECCCCCCCHHHHHHHHHHHC--CCCCEE
Q ss_conf             28838998699899999999999889889998937--99998608998999978546988899999999857--898399
Q gi|254780916|r    9 RHKRVLIIDKDDEQIKIIKDHVESYGYDVFIVNVS--DLSTISKIQVNVIFLSLINCEDDKENILKNIVDKI--PIVPII   84 (482)
Q Consensus         9 ~~~rILIVDDd~~~~~~l~~~L~~~G~~v~~a~~~--al~~l~~~~~dlillD~~mP~~dGlell~~i~~~~--p~ipvI   84 (482)
                      ...+|++|||+......+...|... +.+....+.  ++.......+|++++|..|++.+|+.++..++...  ..+|++
T Consensus       154 ~~~~il~v~~~~~~~~~~~~~l~~~-~~~~~~~~~~~~l~~~~~~~~d~~i~~~~~~~~~~~~~~~~~r~~~~~~~~~i~  232 (457)
T PRK09581        154 EDGRILLVDDDVSQAERIANILKEE-FRVDVLSDPEEALIRAAEGNYDLIIVSASFENYDPLRLCSQLRSKERTRYVPIL  232 (457)
T ss_pred             CCCEEEEECCCHHHHHHHHHHHHHH-CCEEEECCHHHHHHHHCCCCCCEEEECCCCCCCCHHHHHHHHHCCCCCCCCEEE
T ss_conf             6761999879679999999997533-246885486999987435797689975656766468999999714343573299


Q ss_pred             EEECCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             992689999999888505743222222222222222222222
Q gi|254780916|r   85 VQTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALRE  126 (482)
Q Consensus        85 iiT~~~~~~~~~~a~~~g~~d~l~KP~~~~~L~~~i~~al~~  126 (482)
                      .++..++......+...|+.+|+.+|++..++...+...+++
T Consensus       233 ~~~~~~~~~~~~~~~~~g~~d~~~~~~~~~e~~~r~~~~~~~  274 (457)
T PRK09581        233 LLVDEDEDPRLVKALELGVNDYLMRPIDKNELLARVRTQIRR  274 (457)
T ss_pred             EEECCCCCHHHHHHHHCCCCEEEECCCCHHHHHHHHHHHHHH
T ss_conf             995688616676664146522884378627555879999998


No 151
>smart00448 REC cheY-homologous receiver domain. CheY regulates the clockwise rotation of E. coli flagellar motors. This domain contains a phosphoacceptor site that is phosphorylated by histidine kinase homologues.
Probab=98.52  E-value=5.8e-07  Score=68.82  Aligned_cols=53  Identities=23%  Similarity=0.372  Sum_probs=48.9

Q ss_pred             CCEEEECCCHHHHHHHHHHHHHCCCEEEEECCH--HHHHHHCCCCCEEEEECCCC
Q ss_conf             838998699899999999999889889998937--99998608998999978546
Q gi|254780916|r   11 KRVLIIDKDDEQIKIIKDHVESYGYDVFIVNVS--DLSTISKIQVNVIFLSLINC   63 (482)
Q Consensus        11 ~rILIVDDd~~~~~~l~~~L~~~G~~v~~a~~~--al~~l~~~~~dlillD~~mP   63 (482)
                      .|||||||++.++..++.+|+..||+|.+++++  +++.+.+.+||+|++|+.||
T Consensus         1 ~kVLivdD~~~~~~~l~~~l~~~g~~v~~~~~g~~~~~~~~~~~~dlil~D~~mP   55 (55)
T smart00448        1 MRILVVDDDPLLRELLKALLEREGYEVDEATDGEEALELLKEEKPDLILLDIMMP   55 (55)
T ss_pred             CEEEEEECCHHHHHHHHHHHHHCCCEEEEECCHHHHHHHHHCCCCCEEEEECCCC
T ss_conf             9899993799999999999997899999988999999999749999999967687


No 152
>COG1241 MCM2 Predicted ATPase involved in replication control, Cdc46/Mcm family [DNA replication, recombination, and repair]
Probab=98.51  E-value=4.8e-06  Score=62.38  Aligned_cols=215  Identities=15%  Similarity=0.156  Sum_probs=127.8

Q ss_pred             CCCEEEEEECCCCCHHHHHHHHHHHCCCCCCCCCCCCCCC---CCCCCCCHHHHHCCCCCCCCCCCCCCCCCCCCCCCEE
Q ss_conf             4320488732777436799999984267543321012346---5542100243311255553221110012344667147
Q gi|254780916|r  161 DCAIPIMIQGEFGVGKKRLSRFIHESGKRAFFPFFIVNCG---MIDQDKIEKFLFGDVDLQTKNSAQFLGKFIEANGGTI  237 (482)
Q Consensus       161 ~~~~~vli~Ge~GtGK~~~A~~iH~~s~r~~~~fi~v~c~---~~~~~~~e~~lFG~~~~~~~~~~~~~g~~~~a~~Gtl  237 (482)
                      ..+.+||+.|.+||||+.+=+++++.++|+  -|.+--++   +++....       ++..||...-..|.+-.|++|.+
T Consensus       317 RGDInILLvGDPgtaKSqlLk~v~~~aPr~--vytsgkgss~~GLTAav~-------rd~~tge~~LeaGALVlAD~Gv~  387 (682)
T COG1241         317 RGDIHILLVGDPGTAKSQLLKYVAKLAPRG--VYTSGKGSSAAGLTAAVV-------RDKVTGEWVLEAGALVLADGGVC  387 (682)
T ss_pred             CCCEEEEECCCCCHHHHHHHHHHHHHCCCE--EEECCCCCCCCCCEEEEE-------ECCCCCEEEEECCEEEEECCCEE
T ss_conf             242269981798251999999988648840--797264125457306999-------70677607886777999249779


Q ss_pred             EECCCCHHHHHHHHHHHHHHHHHHCCCCCCC--CCCCCCCEEEEECCCC-----CCCCCCHH-HHHHHHHHHHHHH----
Q ss_conf             5166420018899988887764200112355--3212343156521433-----21111112-3337999886543----
Q gi|254780916|r  238 VLEEPDALPLAVQGRIYNFIETGKIEFFDSR--GAIRLDVRLIFLTEKN-----LLPQVKSH-VFRKDLYYRISVF----  305 (482)
Q Consensus       238 ~l~ei~~L~~~~Q~~Ll~~l~~~~~~~~g~~--~~~~~~~RiIa~t~~~-----L~~~~~~g-~fr~dLy~rL~~~----  305 (482)
                      ++||.+.|+...+..|..+++.+.+.--.+.  ...++.|-++||+|--     ...-+.++ .|...|.-|--.+    
T Consensus       388 cIDEfdKm~~~dr~aihEaMEQQtIsIaKAGI~atLnARcsvLAAaNP~~Gryd~~~~~~enI~l~~~lLSRFDLifvl~  467 (682)
T COG1241         388 CIDEFDKMNEEDRVAIHEAMEQQTISIAKAGITATLNARCSVLAAANPKFGRYDPKKTVAENINLPAPLLSRFDLIFVLK  467 (682)
T ss_pred             EEEECCCCCHHHHHHHHHHHHHCEEEECCCCEEEECCHHHHHHHHHCCCCCCCCCCCCHHHHCCCCHHHHHHCCEEEEEC
T ss_conf             99705677767899999998752751205542541114444566518877767999997885589835775177547705


Q ss_pred             -----------HHHHHHHHHHH--HH-------------HHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCC------
Q ss_conf             -----------34467787744--22-------------22556677764101122333321111100012233------
Q gi|254780916|r  306 -----------LINISTLRSRS--ED-------------IPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYP------  353 (482)
Q Consensus       306 -----------~i~iPpLReR~--eD-------------I~~L~~~fl~~~~~~~~~~~~~ls~~a~~~L~~y~------  353 (482)
                                 --+|...+...  ++             =+.+++.|+.- +++.  ..+.++++|.+.|..|.      
T Consensus       468 D~~d~~~D~~ia~hil~~h~~~~~~~~~~~~~~~~~~~~~~~~lrkYI~Y-AR~~--v~P~lt~ea~e~l~~~Yv~~Rk~  544 (682)
T COG1241         468 DDPDEEKDEEIAEHILDKHRGEEPEETISLDGVDEVEERDFELLRKYISY-ARKN--VTPVLTEEAREELEDYYVEMRKK  544 (682)
T ss_pred             CCCCCCCHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHHHHHHH-HHCC--CCCCCCHHHHHHHHHHHHHHHHC
T ss_conf             78885335999999999863456532233332222234658999999998-7505--89612899999999999876520


Q ss_pred             ---------CCCCHHHHHHHHHHHHHHC---CCCCCCHHHHHHHHC
Q ss_conf             ---------8986899999999998743---898106889545421
Q gi|254780916|r  354 ---------WIDNVQELKNILLRAVIGL---KDSHLTEDRFVLLLS  387 (482)
Q Consensus       354 ---------WPGNvREL~n~i~r~~i~~---~~~~i~~~~~~~~l~  387 (482)
                               .|=-+|||+.+|+-+-..+   -...++.+|+..++.
T Consensus       545 ~~~~~~~~~~piT~RqLEsiiRLaeA~Ak~rLS~~V~~eD~~eAi~  590 (682)
T COG1241         545 SALVEEKRTIPITARQLESIIRLAEAHAKMRLSDVVEEEDVDEAIR  590 (682)
T ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHH
T ss_conf             1223456754561999999999999988654447778899999999


No 153
>pfam06490 FleQ Flagellar regulatory protein FleQ. This domain is found at the N terminus of a subset of sigma54-dependent transcriptional activators that are involved in regulation of flagellar motility e.g. FleQ in Pseudomonas aeruginosa. It is clearly related to pfam00072, but lacks the conserved aspartate residue that undergoes phosphorylation in the classic two-component system response regulator (pfam00072).
Probab=98.48  E-value=1.1e-06  Score=66.92  Aligned_cols=106  Identities=18%  Similarity=0.183  Sum_probs=81.5

Q ss_pred             CEEEECCCHHHHHHHHHHHHHCCCEEEEECCHHHHHH-HCC-CCCEEEEECCCCCCCHHHHHHHHHHHCCCCCEEEEECC
Q ss_conf             3899869989999999999988988999893799998-608-99899997854698889999999985789839999268
Q gi|254780916|r   12 RVLIIDKDDEQIKIIKDHVESYGYDVFIVNVSDLSTI-SKI-QVNVIFLSLINCEDDKENILKNIVDKIPIVPIIVQTTQ   89 (482)
Q Consensus        12 rILIVDDd~~~~~~l~~~L~~~G~~v~~a~~~al~~l-~~~-~~dlillD~~mP~~dGlell~~i~~~~p~ipvIiiT~~   89 (482)
                      ||||||||+..+.-++.+|+..|.++..++++++... .+. ...+++.+..++  +..+.++.+.+..|.+||++++.+
T Consensus         1 kILvIddd~~r~~~L~~ILeFlGE~~~~~~~~~~~~~~~~~~~~a~~v~~~~~~--~~~~~l~~l~~~~p~~Pvlllg~~   78 (109)
T pfam06490         1 KILVIDDDAERRHDLSTILEFLGEQCEAVSSEDLSAALLSSRWEALAVILGSVS--GLADLLKALAKWDPHLPVLLLGEH   78 (109)
T ss_pred             CEEEECCCHHHHHHHHHHHHHCCCCEEEECHHHHHHHHHHCCCCEEEEEECCCC--CHHHHHHHHHHHCCCCCEEEECCC
T ss_conf             989986888999979999986499649954889889886378852999967852--099999999964889999998788


Q ss_pred             CCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             99999998885057432222222222222222222
Q gi|254780916|r   90 DNIKILNCFLYNRISKFFLNLVSRKQLCDSIICAL  124 (482)
Q Consensus        90 ~~~~~~~~a~~~g~~d~l~KP~~~~~L~~~i~~al  124 (482)
                      ++...     ...+..-+.+|++-.+|.+.++++.
T Consensus        79 ~~~~~-----~~nvvg~Le~Pl~Y~qL~daLh~cQ  108 (109)
T pfam06490        79 DSAAE-----LANVIGELEEPLNYPQLTDLLHRCQ  108 (109)
T ss_pred             CCHHH-----CCCEEEEECCCCCHHHHHHHHHHHC
T ss_conf             75212-----0552587078898799999998752


No 154
>PRK00149 dnaA chromosomal replication initiation protein; Reviewed
Probab=98.47  E-value=3.3e-07  Score=70.57  Aligned_cols=221  Identities=17%  Similarity=0.232  Sum_probs=131.4

Q ss_pred             CCCCCCCCCC-CCCCCC--CCCCCCCCCCCCCCCEEEEEECCCCCHHHHHHHHHHHCCCC--CCCCCCCCCCCCCCCCCC
Q ss_conf             2211111111-222222--22222222223443204887327774367999999842675--433210123465542100
Q gi|254780916|r  133 ENEHCALDSL-IAVSPA--MIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHESGKR--AFFPFFIVNCGMIDQDKI  207 (482)
Q Consensus       133 ~~~~~~~~~L-iG~S~~--m~~v~~~i~~~a~~~~~vli~Ge~GtGK~~~A~~iH~~s~r--~~~~fi~v~c~~~~~~~~  207 (482)
                      .+...+|+.+ +|.|-.  .......+..-+..--|++|.|.+|.||+++-++|-+.-..  .+...+-+.+     +.+
T Consensus       112 Ln~~yTFdnFVvG~sN~lA~aAA~~Va~~pg~~yNPLfIyG~~GlGKTHLl~AIgn~~~~~~p~~~v~Y~ta-----e~F  186 (447)
T PRK00149        112 LNPKYTFDNFVVGKSNRLAHAAALAVAENPGKAYNPLFIYGGVGLGKTHLLHAIGNYILEKNPNAKVVYVSS-----EKF  186 (447)
T ss_pred             CCCCCCCCCCEECCCCHHHHHHHHHHHHCCCCCCCCEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEEEH-----HHH
T ss_conf             885560326222698599999999998376767785589779988788999999999998589972899549-----999


Q ss_pred             HHHHHCCCCCCCCCCCCCCCCCCCCCCCEEEECCCCHHH--HHHHHHHHHHHHHHHCCCCCCCCCCCCCCEEEEECCCCC
Q ss_conf             243311255553221110012344667147516642001--889998888776420011235532123431565214332
Q gi|254780916|r  208 EKFLFGDVDLQTKNSAQFLGKFIEANGGTIVLEEPDALP--LAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNL  285 (482)
Q Consensus       208 e~~lFG~~~~~~~~~~~~~g~~~~a~~Gtl~l~ei~~L~--~~~Q~~Ll~~l~~~~~~~~g~~~~~~~~~RiIa~t~~~L  285 (482)
                      ..++-..-+  .+......-.+..+  -.|++|+|+-+.  ..+|.-++..+..-.          ..+=+||.++.+.+
T Consensus       187 ~~~~v~al~--~~~~~~Fr~~yr~~--DvLliDDiqfl~gk~~tqeeff~~fn~l~----------~~~kqiv~tsd~~P  252 (447)
T PRK00149        187 TNDFVKALR--NNAMEEFKEKYRSV--DVLLIDDIQFLAGKEKTQEEFFHTFNALH----------ENNKQIVITSDRPP  252 (447)
T ss_pred             HHHHHHHHH--CCCHHHHHHHHHCC--CEEEECHHHHHHCCHHHHHHHHHHHHHHH----------HCCCEEEEECCCCH
T ss_conf             999999985--18699999999728--85432148886055779999999999999----------84996899578896


Q ss_pred             CCCCCHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHH
Q ss_conf             111111233379998865---43344677877442222556677764101122333321111100012233898689999
Q gi|254780916|r  286 LPQVKSHVFRKDLYYRIS---VFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQELK  362 (482)
Q Consensus       286 ~~~~~~g~fr~dLy~rL~---~~~i~iPpLReR~eDI~~L~~~fl~~~~~~~~~~~~~ls~~a~~~L~~y~WPGNvREL~  362 (482)
                      .++-   .|.+.|.-|++   +..|.-|-+--|..        ++++.++..+.   .+++++++.+.. ...+|||||+
T Consensus       253 ~~l~---~l~~rL~SRf~~Gl~~~i~~Pd~e~r~~--------Il~~k~~~~~~---~l~~~v~~~iA~-~~~~nvR~Le  317 (447)
T PRK00149        253 KELE---GLEDRLRSRFEWGLTVDIEPPDLETRVA--------ILQKKAEEEGI---NLPNEVLEFIAK-RIRSNIRELE  317 (447)
T ss_pred             HHCC---CCCHHHHHHHHCCEEEECCCCCHHHHHH--------HHHHHHHHCCC---CCCHHHHHHHHH-HCCCCHHHHH
T ss_conf             7656---5117788676376265105999999999--------99999997289---999899999997-1268899999


Q ss_pred             HHHHHHHHH--CCCCCCCHHHHHHHHC
Q ss_conf             999999874--3898106889545421
Q gi|254780916|r  363 NILLRAVIG--LKDSHLTEDRFVLLLS  387 (482)
Q Consensus       363 n~i~r~~i~--~~~~~i~~~~~~~~l~  387 (482)
                      .++-++...  ..+..|+.+.+...+.
T Consensus       318 Gal~~l~a~~~~~~~~i~~~~~~~~l~  344 (447)
T PRK00149        318 GALNRLVAYASLTGRPITLELAKEALK  344 (447)
T ss_pred             HHHHHHHHHHHHHCCCCCHHHHHHHHH
T ss_conf             999999999998689999999999999


No 155
>COG0606 Predicted ATPase with chaperone activity [Posttranslational modification, protein turnover, chaperones]
Probab=98.47  E-value=1e-07  Score=74.17  Aligned_cols=140  Identities=16%  Similarity=0.139  Sum_probs=94.0

Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCCCHHHHHHHHHHH------------------CCC--------C
Q ss_conf             11111112222222222222222344320488732777436799999984------------------267--------5
Q gi|254780916|r  136 HCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHE------------------SGK--------R  189 (482)
Q Consensus       136 ~~~~~~LiG~S~~m~~v~~~i~~~a~~~~~vli~Ge~GtGK~~~A~~iH~------------------~s~--------r  189 (482)
                      ...+.+++|++.+    .+.+.-+|....++|+.|++||||+++|.-+..                  .+.        -
T Consensus       175 ~~D~~DV~GQ~~A----KrAleiAAAGgHnLl~~GpPGtGKTmla~Rl~~lLPpls~~E~lE~s~I~s~~~~~~~~~~~~  250 (490)
T COG0606         175 APDFKDVKGQEQA----KRALEIAAAGGHNLLLVGPPGTGKTMLASRLPGLLPPLSIPEALEVSAIHSLAGDLHEGCPLK  250 (490)
T ss_pred             CCCHHHHCCCHHH----HHHHHHHHHCCCCEEEECCCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHHHCCCCCCCCCCC
T ss_conf             7666664384999----999999984388678756998865676423102599987088899988876354324678641


Q ss_pred             CCCCCCCCCCCCCCCCCCHHHHHCCCCCCCCCCCCCCCCCCCCCCCEEEECCCCHHHHHHHHHHHHHHHHHH--CCCCCC
Q ss_conf             433210123465542100243311255553221110012344667147516642001889998888776420--011235
Q gi|254780916|r  190 AFFPFFIVNCGMIDQDKIEKFLFGDVDLQTKNSAQFLGKFIEANGGTIVLEEPDALPLAVQGRIYNFIETGK--IEFFDS  267 (482)
Q Consensus       190 ~~~~fi~v~c~~~~~~~~e~~lFG~~~~~~~~~~~~~g~~~~a~~Gtl~l~ei~~L~~~~Q~~Ll~~l~~~~--~~~~g~  267 (482)
                      ...||..=.-+     .=...|.|      |...-++|-+-.|+||.|||||..+-...+=..|-.=|++|+  ++|.++
T Consensus       251 ~~rPFr~PHHs-----aS~~aLvG------GG~~p~PGeIsLAH~GVLFLDElpef~~~iLe~LR~PLE~g~i~IsRa~~  319 (490)
T COG0606         251 IHRPFRAPHHS-----ASLAALVG------GGGVPRPGEISLAHNGVLFLDELPEFKRSILEALREPLENGKIIISRAGS  319 (490)
T ss_pred             EECCCCCCCCC-----CHHHHHHC------CCCCCCCCCEEEECCCEEEEECCCHHHHHHHHHHHCCCCCCCEEEEECCC
T ss_conf             10787688740-----22889737------89988987354303877886144210599999973741258179997587


Q ss_pred             CCCCCCCCEEEEECCCCCCCCCC
Q ss_conf             53212343156521433211111
Q gi|254780916|r  268 RGAIRLDVRLIFLTEKNLLPQVK  290 (482)
Q Consensus       268 ~~~~~~~~RiIa~t~~~L~~~~~  290 (482)
                      .-..+.+|.+|+++|-.+--.-.
T Consensus       320 ~v~ypa~Fqlv~AmNpcpcG~~~  342 (490)
T COG0606         320 KVTYPARFQLVAAMNPCPCGNLG  342 (490)
T ss_pred             EEEEEEEEEEHHHCCCCCCCCCC
T ss_conf             16872126775223999764788


No 156
>TIGR00382 clpX ATP-dependent Clp protease, ATP-binding subunit ClpX; InterPro: IPR004487   ClpX is a member of the HSP (heat-shock protein) 100 family. Gel filtration and electron microscopy showed that ClpX subunits associate to form a six-membered ring that is stabilized by binding of ATP or nonhydrolyzable analogs of ATP . It functions as an ATP-depedent  molecular chaperone and is the regulatory subunit of the ClpXP protease .   ClpXP is involved in DNA damage repair, stationary-phase gene expression, and ssrA-mediated protein quality control. To date more than 50 proteins include transcription factors, metabolic enzymes, and proteins involved in the starvation and oxidative stress responses have been identified as substrates .    The N-terminal domain of ClpX is a C4-type zinc binding domain (ZBD) involved in substrate recognition. ZBD forms a very stable dimer that is essential for promoting the degradation of some typical ClpXP substrates such as lO and MuA .  ; GO: 0005515 protein binding, 0005524 ATP binding, 0016887 ATPase activity, 0015031 protein transport.
Probab=98.45  E-value=4.9e-07  Score=69.39  Aligned_cols=200  Identities=16%  Similarity=0.123  Sum_probs=113.5

Q ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHH-CCCCCEEEEECCCCH----HHHHHHHHCCCCCCCCCCCCCCCCCCC-------
Q ss_conf             99899997854698889999999985-789839999268999----999988850574322222222222222-------
Q gi|254780916|r   52 QVNVIFLSLINCEDDKENILKNIVDK-IPIVPIIVQTTQDNI----KILNCFLYNRISKFFLNLVSRKQLCDS-------  119 (482)
Q Consensus        52 ~~dlillD~~mP~~dGlell~~i~~~-~p~ipvIiiT~~~~~----~~~~~a~~~g~~d~l~KP~~~~~L~~~-------  119 (482)
                      .+||.++|.      =.++|..+-+. ..++|-.-....+..    .........--..++++|...+..++-       
T Consensus        35 g~~VyIC~e------C~~lc~~~l~e~~~~~~~~~~gerd~~~~~~~~~~~~~~~~~~~~lP~P~eik~~LD~YVIGQe~  108 (452)
T TIGR00382        35 GPGVYICDE------CIELCHDILEEELNSLLALKTGERDGTRLRRKESKEVEEELELSELPTPKEIKAHLDEYVIGQEQ  108 (452)
T ss_pred             CCCCEECHH------HHHHHHHHHHHHHHCCHHHCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHCCCCCCCCC
T ss_conf             898227512------89988887766542000000254310235654202456666652478827999972136123101


Q ss_pred             --------CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCCCHHHHHHHHHHHCCCCCC
Q ss_conf             --------222222222222222111111112222222222222222344320488732777436799999984267543
Q gi|254780916|r  120 --------IICALREGVVPSQENEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHESGKRAF  191 (482)
Q Consensus       120 --------i~~al~~~~~~~~~~~~~~~~~LiG~S~~m~~v~~~i~~~a~~~~~vli~Ge~GtGK~~~A~~iH~~s~r~~  191 (482)
                              |-+..+|-.......+....+     |.   --.+.++.+=-+.++||+.|+||+||+++|+.+=..   =+
T Consensus       109 AKKVLsVAVYNHYKRl~~~~~n~~~d~~D-----~n---velehleeVEL~KSNILLiGPTGSGKTLLAqTLA~~---L~  177 (452)
T TIGR00382       109 AKKVLSVAVYNHYKRLNLKEKNKKSDNGD-----SN---VELEHLEEVELSKSNILLIGPTGSGKTLLAQTLARI---LN  177 (452)
T ss_pred             CCEEEEEEEHHHHHHHHHHHHCCCCCCCC-----CH---HHHHHHHHHHHHCCCEEEECCCCCCHHHHHHHHHHH---CC
T ss_conf             05254324112466653243045558840-----00---235444443330066245468885268999999987---38


Q ss_pred             CCCCCCCCCCCCCCCCHHHHHCCCCCCCCCCCCC---------CCCCCCCCCCEEEECCCCHHHH--------------H
Q ss_conf             3210123465542100243311255553221110---------0123446671475166420018--------------8
Q gi|254780916|r  192 FPFFIVNCGMIDQDKIEKFLFGDVDLQTKNSAQF---------LGKFIEANGGTIVLEEPDALPL--------------A  248 (482)
Q Consensus       192 ~~fi~v~c~~~~~~~~e~~lFG~~~~~~~~~~~~---------~g~~~~a~~Gtl~l~ei~~L~~--------------~  248 (482)
                      =||..-|..+|++.       |+++    .+..+         .+=.++|..|.+|+|||+..+.              -
T Consensus       178 VPfAiADATtLTEA-------GYVG----EDVENIL~~Llq~ad~DV~kA~kGIiYIDEIDKIaRkSEN~SITRDVSGEG  246 (452)
T TIGR00382       178 VPFAIADATTLTEA-------GYVG----EDVENILLKLLQAADYDVEKAQKGIIYIDEIDKIARKSENPSITRDVSGEG  246 (452)
T ss_pred             CCEEECCHHHHHCC-------CCCC----CCHHHHHHHHHHHCCCCHHHHCCCEEEEECCCCHHHHCCCCEEEEEECCCH
T ss_conf             87421111102006-------6424----228899999987414552452785089842231012157780112217554


Q ss_pred             HHHHHHHHHHHHHCC---CCCCCCC--------CCCCCEEEEE
Q ss_conf             999888877642001---1235532--------1234315652
Q gi|254780916|r  249 VQGRIYNFIETGKIE---FFDSRGA--------IRLDVRLIFL  280 (482)
Q Consensus       249 ~Q~~Ll~~l~~~~~~---~~g~~~~--------~~~~~RiIa~  280 (482)
                      +|+.||..|+ |.+.   |-||-+.        -++|.=+||+
T Consensus       247 VQQALLKi~E-GTvA~vPPqGGRKHP~~~~iqiDTs~ILFICG  288 (452)
T TIGR00382       247 VQQALLKIIE-GTVANVPPQGGRKHPQQEFIQIDTSNILFICG  288 (452)
T ss_pred             HHHHHHHHHH-CCEEEECCCCCCCCCCCCEEEECCCCEEEEEC
T ss_conf             9999998760-32343175448868865768864764001105


No 157
>PRK06893 DNA replication initiation factor; Validated
Probab=98.44  E-value=9.6e-07  Score=67.28  Aligned_cols=207  Identities=15%  Similarity=0.086  Sum_probs=118.3

Q ss_pred             CCCCCCCCCCC-CCCC-CCCCCCCCCCCCCCCCEE-EEEECCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCHH
Q ss_conf             22111111112-2222-222222222223443204-88732777436799999984267543321012346554210024
Q gi|254780916|r  133 ENEHCALDSLI-AVSP-AMIQVVDLARKAGDCAIP-IMIQGEFGVGKKRLSRFIHESGKRAFFPFFIVNCGMIDQDKIEK  209 (482)
Q Consensus       133 ~~~~~~~~~Li-G~S~-~m~~v~~~i~~~a~~~~~-vli~Ge~GtGK~~~A~~iH~~s~r~~~~fi~v~c~~~~~~~~e~  209 (482)
                      ..+...++.++ |.+. .+..+.+   ..+....| +.|.|++|+||+++.+++-+.-...+.+-+.+.|..       .
T Consensus         9 ~~~~~tfdnF~~~~n~~~~~~l~~---~~~~~~~~~l~i~G~~gsGKTHLLqa~~~~~~~~~~~~~yi~~~~-------~   78 (229)
T PRK06893          9 QIDDETLDNFYSDNNLLLLDSLRK---NFIDLKQPFFYIWGGKSSGKSHLLKAVSNHYLLNQRTAIYIPLSK-------S   78 (229)
T ss_pred             CCCCCCHHCCCCCCHHHHHHHHHH---HCCCCCCCEEEEECCCCCCHHHHHHHHHHHHHHHCCCEEEEEHHH-------H
T ss_conf             998665431546874999999997---550246987999899999889999999999997189859997377-------5


Q ss_pred             HHHCCCCCCCCCCCCCCCCCCCCCCCEEEECCCCHHH--HHHHHHHHHHHHHHHCCCCCCCCCCCCCC-EEEEECCCCCC
Q ss_conf             3311255553221110012344667147516642001--88999888877642001123553212343-15652143321
Q gi|254780916|r  210 FLFGDVDLQTKNSAQFLGKFIEANGGTIVLEEPDALP--LAVQGRIYNFIETGKIEFFDSRGAIRLDV-RLIFLTEKNLL  286 (482)
Q Consensus       210 ~lFG~~~~~~~~~~~~~g~~~~a~~Gtl~l~ei~~L~--~~~Q~~Ll~~l~~~~~~~~g~~~~~~~~~-RiIa~t~~~L~  286 (482)
                      +-|..      ..-  . -++  +...+++|+|+.+.  .+.|..|+.++..-.          .... .++.+++.++.
T Consensus        79 ~~~~~------~~l--~-~l~--~~d~l~iDDi~~i~g~~~~e~~lF~l~N~l~----------~~~~~~ll~ss~~~p~  137 (229)
T PRK06893         79 QYFSP------AVL--E-NLE--QQDLVCLDDLQAVIGNEEWELAIFDLFNRIK----------ESGKTLLLISANQSPH  137 (229)
T ss_pred             HHCCH------HHH--H-HHH--HCCEEEEECHHHHCCCHHHHHHHHHHHHHHH----------HCCCCEEEEECCCCHH
T ss_conf             64069------999--8-765--4797999672342488389999999999999----------7599179985798833


Q ss_pred             CCCCHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHH
Q ss_conf             11111233379998865-43344677877442222556677764101122333321111100012233898689999999
Q gi|254780916|r  287 PQVKSHVFRKDLYYRIS-VFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQELKNIL  365 (482)
Q Consensus       287 ~~~~~g~fr~dLy~rL~-~~~i~iPpLReR~eDI~~L~~~fl~~~~~~~~~~~~~ls~~a~~~L~~y~WPGNvREL~n~i  365 (482)
                      ++-   ...+||--||+ +..++++|+-+-. -+     ..+.+.+...|.   .+++++++++.++ ++.|+++|..++
T Consensus       138 ~l~---~~l~DL~SRl~~~~~~~i~~~dd~~-~~-----~iL~~~a~~rgl---~l~~~v~~yl~~r-~~R~~~~l~~~l  204 (229)
T PRK06893        138 ALQ---IKLPDLASRLTWGEIYQLNDLTDEQ-KI-----EVLQRNAYQRGI---ELSDETANFLLKR-LDRDMHTLFDAL  204 (229)
T ss_pred             HHC---CHHHHHHHHHHCCEEEEECCCCHHH-HH-----HHHHHHHHHCCC---CCCHHHHHHHHHH-HCCCHHHHHHHH
T ss_conf             221---0026799999688369966777579-99-----999999996499---9998999999998-347899999999


Q ss_pred             HHHHH--HCCCCCCCHHHHH
Q ss_conf             99987--4389810688954
Q gi|254780916|r  366 LRAVI--GLKDSHLTEDRFV  383 (482)
Q Consensus       366 ~r~~i--~~~~~~i~~~~~~  383 (482)
                      .++-.  +...+.||..-+.
T Consensus       205 ~~Ld~~sl~~kr~iTiplvk  224 (229)
T PRK06893        205 DLLDKASLQAQRKLTIPFVK  224 (229)
T ss_pred             HHHHHHHHHHCCCCCHHHHH
T ss_conf             99999999808999999999


No 158
>PRK13531 regulatory ATPase RavA; Provisional
Probab=98.44  E-value=7.8e-08  Score=75.01  Aligned_cols=151  Identities=14%  Similarity=0.150  Sum_probs=97.0

Q ss_pred             CCCCCCCCCCCCEEEEEECCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCHHHHHCCCC--CCC--CCCCC-CC
Q ss_conf             22222223443204887327774367999999842675433210123465542100243311255--553--22111-00
Q gi|254780916|r  152 VVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFGDVD--LQT--KNSAQ-FL  226 (482)
Q Consensus       152 v~~~i~~~a~~~~~vli~Ge~GtGK~~~A~~iH~~s~r~~~~fi~v~c~~~~~~~~e~~lFG~~~--~~~--~~~~~-~~  226 (482)
                      +.+.+--++-+..+|++.|++||+|+.+||.+...=  .++.|...=..-++.   -+|+||..+  +..  |...+ ..
T Consensus        28 ~i~l~lLaalagehvlllGPPGtAKS~larrl~~~~--~~a~~FeyLltRFst---PeElFGP~si~~Lk~~g~y~R~t~  102 (498)
T PRK13531         28 AIRLCLLAALSGESVFLLGPPGIAKSLIARRLKFAF--QHARAFEYLMTRFST---PEEVFGPLSIQALKDEGRYERLTS  102 (498)
T ss_pred             HHHHHHHHHHCCCCEEEECCCCHHHHHHHHHHHHHH--CCCHHHHHHHHCCCC---HHHHCCCCCHHHHHHCCEEEEECC
T ss_conf             999999999728946988899513889999999985--574089999874698---888538332998711784897226


Q ss_pred             CCCCCCCCCEEEECCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCE-EEEECCCCCCCCCCHHHHHHHHHHHHHHH
Q ss_conf             12344667147516642001889998888776420011235532123431-56521433211111123337999886543
Q gi|254780916|r  227 GKFIEANGGTIVLEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVR-LIFLTEKNLLPQVKSHVFRKDLYYRISVF  305 (482)
Q Consensus       227 g~~~~a~~Gtl~l~ei~~L~~~~Q~~Ll~~l~~~~~~~~g~~~~~~~~~R-iIa~t~~~L~~~~~~g~fr~dLy~rL~~~  305 (482)
                      |.+-.|+  ..|||||-.-+.....-||.+|.++.|+.  +...+++..+ +|+|||.=+++    +.=-+-||.|+ .+
T Consensus       103 G~LP~A~--iaFLDEIfKansAILNtLLtilNEr~f~n--G~~~~~vPL~~li~ASNElP~~----~~~L~AlyDRf-L~  173 (498)
T PRK13531        103 GYLPEAE--IVFLDEIWKAGPAILNTLLTAINERRFRN--GAHEEKIPMRLLVAASNELPEA----DSSLEALYDRM-LI  173 (498)
T ss_pred             CCCCCCE--EEHHHHHHHCCHHHHHHHHHHHHHHEECC--CCCEECCCHHHHHHCCCCCCCC----CCCHHHHHHHH-HH
T ss_conf             7588661--31578786148899999999864640347--9831304468864304679999----84078888764-41


Q ss_pred             HHHHHHHHHHH
Q ss_conf             34467787744
Q gi|254780916|r  306 LINISTLRSRS  316 (482)
Q Consensus       306 ~i~iPpLReR~  316 (482)
                      .+.|.|+.++.
T Consensus       174 R~~v~~v~~~~  184 (498)
T PRK13531        174 RLWLDKVQDKA  184 (498)
T ss_pred             HEECCCCCCHH
T ss_conf             02231316766


No 159
>TIGR01242 26Sp45 26S proteasome subunit P45 family; InterPro: IPR005937    Intracellular proteins, including short-lived proteins such as cyclin, Mos, Myc, p53, NF-kappaB, and IkappaB, are degraded by the ubiquitin-proteasome system. The 26S proteasome (a 2 MDa complex) is made up of two subcomplexes: the 20S proteasome and the regulatory complex. The former is a 700 kDa cylindrical protease complex consisting of four stacks of heptameric rings with 28 subunits (i.e., 7777) with molecular masses of about 20-35 kDa, whereas the latter is a 700-1000 kDa complex consisting of at least 18 subunits with molecular masses of 28-110 kDa, including 6 putative ATPases (Rpt1-Rpt6) and 12 non-ATPase subunits (Rpn1-12).     Members of the 26S proteasome subunit P45 family: ATPase p45/Sug1/Rpt6 may be phosphorylated within the proteasome. This phosphorylation event may play a key role in ATP-dependent proteolysis because a good correlation exists between the inhibition pattern of protein kinase inhibitors against the phosphorylation of p45 and that against the ATP-dependent proteolytic activity , .   More information about these protein can be found at Protein of the Month: AAA ATPases .; GO: 0016787 hydrolase activity, 0030163 protein catabolic process, 0005634 nucleus, 0005737 cytoplasm.
Probab=98.43  E-value=3.7e-07  Score=70.22  Aligned_cols=213  Identities=17%  Similarity=0.214  Sum_probs=123.3

Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCC-----------CCEEEEEECCCCCHHHHHHHHHHHCCCCCCCCCCCCCCC
Q ss_conf             222111111112222222222222222344-----------320488732777436799999984267543321012346
Q gi|254780916|r  132 QENEHCALDSLIAVSPAMIQVVDLARKAGD-----------CAIPIMIQGEFGVGKKRLSRFIHESGKRAFFPFFIVNCG  200 (482)
Q Consensus       132 ~~~~~~~~~~LiG~S~~m~~v~~~i~~~a~-----------~~~~vli~Ge~GtGK~~~A~~iH~~s~r~~~~fi~v~c~  200 (482)
                      .++....+.++-|=...|+++++.+.-=-.           -..=||+.|++||||+++|+++-+.   .+.-||.|=.|
T Consensus       114 ~E~P~V~y~diGGL~~Q~~E~~E~v~LPlk~PeLF~~vGI~PPKGvLLyGPPGtGKTLlAKAvA~e---t~ATFIrvVgS  190 (364)
T TIGR01242       114 EERPNVSYEDIGGLEKQIREIREAVELPLKKPELFEEVGIEPPKGVLLYGPPGTGKTLLAKAVAHE---TNATFIRVVGS  190 (364)
T ss_pred             ECCCCEEEECCCCHHHHHHHHHHHHHCCCCCCHHHHHCCCCCCCCEEEECCCCCCHHHHHHHHHCC---CCCEEEEEEHH
T ss_conf             217823340267878999999888734688831677628898986570075797688999986314---55126886044


Q ss_pred             CCCCCCCHHHHHCCCCCCCCCCCCCCCCCCCC---CCCEEEECCCCHH-----------HHHHHHHHHHHHHH-HHCCCC
Q ss_conf             55421002433112555532211100123446---6714751664200-----------18899988887764-200112
Q gi|254780916|r  201 MIDQDKIEKFLFGDVDLQTKNSAQFLGKFIEA---NGGTIVLEEPDAL-----------PLAVQGRIYNFIET-GKIEFF  265 (482)
Q Consensus       201 ~~~~~~~e~~lFG~~~~~~~~~~~~~g~~~~a---~~Gtl~l~ei~~L-----------~~~~Q~~Ll~~l~~-~~~~~~  265 (482)
                      .+    + ....|+     ||. =..+.|+.|   .-..+|+|||+..           ..++|.-|+++|.+ .-|.+-
T Consensus       191 El----V-~KyIGE-----GAr-LV~~~F~LAkEKaPsIiFIDEiDAiaakR~~~~TsGdREV~RTlmQLLAElDGFd~r  259 (364)
T TIGR01242       191 EL----V-RKYIGE-----GAR-LVREVFELAKEKAPSIIFIDEIDAIAAKRVDSSTSGDREVQRTLMQLLAELDGFDPR  259 (364)
T ss_pred             HH----H-HHHHCC-----HHH-HHHHHHHHHHCCCCCEEEEECHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHCCCCCC
T ss_conf             44----4-444133-----168-999999985306981686101333543211467787315788999999752488876


Q ss_pred             CCCCCCCCCCEEEEECCCC-C--CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCC
Q ss_conf             3553212343156521433-2--111111233379998865433446778774422225566777641011223333211
Q gi|254780916|r  266 DSRGAIRLDVRLIFLTEKN-L--LPQVKSHVFRKDLYYRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISIS  342 (482)
Q Consensus       266 g~~~~~~~~~RiIa~t~~~-L--~~~~~~g~fr~dLy~rL~~~~i~iPpLReR~eDI~~L~~~fl~~~~~~~~~~~~~ls  342 (482)
                      |       ||.||+|||+. +  ..+..-|+|..       .+.+-+|.++=|.+ |       |+-+.++.... ..++
T Consensus       260 g-------~VkviaATNR~DilDPA~LRPGRFDR-------~IEVPlP~~~GR~e-I-------lkiHTr~~~la-~dVd  316 (364)
T TIGR01242       260 G-------NVKVIAATNRPDILDPAILRPGRFDR-------IIEVPLPDFEGRLE-I-------LKIHTRKMKLA-EDVD  316 (364)
T ss_pred             C-------CEEEEEECCCCHHCCCCCCCCCCCCC-------EEECCCCCCCCHHH-H-------HHHHHCCCCCC-CCCC
T ss_conf             7-------61688720762020432148886132-------57316978322056-6-------55521000012-3568


Q ss_pred             CCCCCCCCCCCCCCCHHHHHHHHHHHHHH---CCCCCCCHHHHHH
Q ss_conf             11100012233898689999999999874---3898106889545
Q gi|254780916|r  343 DKALSLLTKYPWIDNVQELKNILLRAVIG---LKDSHLTEDRFVL  384 (482)
Q Consensus       343 ~~a~~~L~~y~WPGNvREL~n~i~r~~i~---~~~~~i~~~~~~~  384 (482)
                      =++++.+..= ..  -.+|+.+|--|-..   .....+|.+|+..
T Consensus       317 l~~~A~~TeG-~s--GAdlKAi~tEAG~~AIR~~r~~vT~~Df~k  358 (364)
T TIGR01242       317 LEAIAKLTEG-AS--GADLKAICTEAGMFAIREERDYVTMDDFLK  358 (364)
T ss_pred             HHHHHHHHCC-CC--CCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             7999987478-86--630423434620477774456766999999


No 160
>TIGR02928 TIGR02928 orc1/cdc6 family replication initiation protein; InterPro: IPR014277   This set of DNA binding proteins shows homology to the origin recognition complex subunit 1/cell division control protein 6 family in eukaryotes. The proteins in this entry are found exclusively in the archaea. Several members may be found in a genome and interact with each other..
Probab=98.42  E-value=1.4e-07  Score=73.24  Aligned_cols=228  Identities=21%  Similarity=0.257  Sum_probs=131.0

Q ss_pred             CCCCCC--CCCCCCCCCCCCCCCCCCCCC---CCEEEEEECCCCCHHHHHHHHH----HHCCCCCCCC-C--CCCCCCCC
Q ss_conf             111111--112222222222222222344---3204887327774367999999----8426754332-1--01234655
Q gi|254780916|r  135 EHCALD--SLIAVSPAMIQVVDLARKAGD---CAIPIMIQGEFGVGKKRLSRFI----HESGKRAFFP-F--FIVNCGMI  202 (482)
Q Consensus       135 ~~~~~~--~LiG~S~~m~~v~~~i~~~a~---~~~~vli~Ge~GtGK~~~A~~i----H~~s~r~~~~-f--i~v~c~~~  202 (482)
                      .....+  .|+|....|..+...+.-+-.   ...+|||.|+|||||+++++++    +..+..++.. |  +.|||..+
T Consensus        10 ~dY~Pden~i~hRdeqI~~l~~~L~~~l~PG~~P~Ni~iYGkTGtGKT~vt~~v~~~l~~~~~~~d~~D~~~~~~NC~~~   89 (383)
T TIGR02928        10 PDYVPDENRIVHRDEQIEELAKALRPILRPGSRPSNIFIYGKTGTGKTAVTKYVMKELEEAAEDRDVRDVSTVYINCQIL   89 (383)
T ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCCCCCEEEECCCCCCHHHHHHHHHHHHHHHHHCCCCCCEEEEEECCCCC
T ss_conf             57702742466867899999999887506748987258878889878899999999999986226997158999778546


Q ss_pred             CCC-C----CHHHH----HCCCCCCCCCCCCC----CC-CCCCCCCCE--EEECCCCHH--HHHHHH-----HHHHHHHH
Q ss_conf             421-0----02433----11255553221110----01-234466714--751664200--188999-----88887764
Q gi|254780916|r  203 DQD-K----IEKFL----FGDVDLQTKNSAQF----LG-KFIEANGGT--IVLEEPDAL--PLAVQG-----RIYNFIET  259 (482)
Q Consensus       203 ~~~-~----~e~~l----FG~~~~~~~~~~~~----~g-~~~~a~~Gt--l~l~ei~~L--~~~~Q~-----~Ll~~l~~  259 (482)
                      +.. .    +-..|    +|..=..||=..++    .- .++...+|+  ++||||+.|  .. ...     -|-.+...
T Consensus        90 ~T~y~~~~~L~~~ln~~~~~~~vP~tG~s~~~~~~~l~~~l~~~~~~~~~ivLDEiD~Lv~~~-~d~PAyS~~LY~L~Ra  168 (383)
T TIGR02928        90 DTSYQVLVELANQLNRRGSGEEVPTTGLSTSEVFRELYKELNRERGDSLIIVLDEIDKLVRKD-DDDPAYSKLLYQLSRA  168 (383)
T ss_pred             CCHHHHHHHHHHHHCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCEEEEEECCCCHHHCCC-CCCHHHHHHHHHHHHH
T ss_conf             846999999999851577888898877878999999999983201887999862310221588-8880787885343310


Q ss_pred             HHCCCCCCCCCCC-CCCEEEEECCC-----CCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHC-
Q ss_conf             2001123553212-34315652143-----321111112333799988654334467787744-222255667776410-
Q gi|254780916|r  260 GKIEFFDSRGAIR-LDVRLIFLTEK-----NLLPQVKSHVFRKDLYYRISVFLINISTLRSRS-EDIPWLVHFFLQSFC-  331 (482)
Q Consensus       260 ~~~~~~g~~~~~~-~~~RiIa~t~~-----~L~~~~~~g~fr~dLy~rL~~~~i~iPpLReR~-eDI~~L~~~fl~~~~-  331 (482)
                            .++.... +.+=||+.||.     +|...|++-         |+--.|..||=-+.- .||       |+.=. 
T Consensus       169 ------~~~~~~~~~~vgvIgISND~~f~~~Ld~RVkSs---------L~~eei~FpPYdA~eL~~I-------L~~R~v  226 (383)
T TIGR02928       169 ------RENGDLENAKVGVIGISNDLKFRENLDPRVKSS---------LCEEEIVFPPYDAEELRDI-------LENRAV  226 (383)
T ss_pred             ------HHCCCCCCCCEEEEEEECCCHHHHHCCCCEECC---------CCCCCCEECCCCHHHHHHH-------HHHHHH
T ss_conf             ------003577885348999865714364457530132---------4874004079886999999-------972031


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCC--CCCHHHHHHHHHHHHH---HCCCCCCCHHHHHHHH
Q ss_conf             11223333211111000122338--9868999999999987---4389810688954542
Q gi|254780916|r  332 TKNAIKQISISDKALSLLTKYPW--IDNVQELKNILLRAVI---GLKDSHLTEDRFVLLL  386 (482)
Q Consensus       332 ~~~~~~~~~ls~~a~~~L~~y~W--PGNvREL~n~i~r~~i---~~~~~~i~~~~~~~~l  386 (482)
                      +. .-..=-++++++.+-.++.=  -|+-|.=--+++.|.-   ......++.+|+..+-
T Consensus       227 ~~-AF~dGvl~d~VI~lcAA~aAq~hGDAR~AiDLLR~AGe~A~~~g~~~Vt~~HV~~A~  285 (383)
T TIGR02928       227 EK-AFYDGVLDDGVIPLCAALAAQEHGDARKAIDLLRVAGEIAEREGAERVTEDHVEEAQ  285 (383)
T ss_pred             HH-CCCCCCCCHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHH
T ss_conf             20-336885462279999998620678789999999987687531576310088899999


No 161
>KOG0731 consensus
Probab=98.42  E-value=6.8e-07  Score=68.37  Aligned_cols=216  Identities=17%  Similarity=0.191  Sum_probs=123.7

Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCC----------CCCCCCEEEEEECCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCC
Q ss_conf             2211111111222222222222222----------234432048873277743679999998426754332101234655
Q gi|254780916|r  133 ENEHCALDSLIAVSPAMIQVVDLAR----------KAGDCAIPIMIQGEFGVGKKRLSRFIHESGKRAFFPFFIVNCGMI  202 (482)
Q Consensus       133 ~~~~~~~~~LiG~S~~m~~v~~~i~----------~~a~~~~~vli~Ge~GtGK~~~A~~iH~~s~r~~~~fi~v~c~~~  202 (482)
                      ......|.+.-|...+-+++.+.+.          .=|....=|||+|++||||+++|+++-..   ++=||+.++.+.+
T Consensus       304 ~~t~V~FkDVAG~deAK~El~E~V~fLKNP~~Y~~lGAKiPkGvLL~GPPGTGKTLLAKAiAGE---AgVPF~svSGSEF  380 (774)
T KOG0731         304 GNTGVKFKDVAGVDEAKEELMEFVKFLKNPEQYQELGAKIPKGVLLVGPPGTGKTLLAKAIAGE---AGVPFFSVSGSEF  380 (774)
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHHHHCCHHHHHHCCCCCCCCEEEECCCCCCHHHHHHHHHCC---CCCCEEEECHHHH
T ss_conf             8988760102670899999999999843989998747767675178789998678999988530---5896464133788


Q ss_pred             CCCCCHHHHHCCCCCCCCCCCCCCCCCCCCCC---CEEEECCCCHHHHHHHH-----------H-HHHHHHHHHCCCCCC
Q ss_conf             42100243311255553221110012344667---14751664200188999-----------8-888776420011235
Q gi|254780916|r  203 DQDKIEKFLFGDVDLQTKNSAQFLGKFIEANG---GTIVLEEPDALPLAVQG-----------R-IYNFIETGKIEFFDS  267 (482)
Q Consensus       203 ~~~~~e~~lFG~~~~~~~~~~~~~g~~~~a~~---Gtl~l~ei~~L~~~~Q~-----------~-Ll~~l~~~~~~~~g~  267 (482)
                      -      |+|+-.     ..++...+|..|..   -.+|+|||+.....-+.           . |-++|-+     +++
T Consensus       381 v------E~~~g~-----~asrvr~lf~~ar~~aP~iifideida~~~~r~G~~~~~~~~e~e~tlnQll~e-----mDg  444 (774)
T KOG0731         381 V------EMFVGV-----GASRVRDLFPLARKNAPSIIFIDEIDAVGRKRGGKGTGGGQDEREQTLNQLLVE-----MDG  444 (774)
T ss_pred             H------HHHCCC-----CHHHHHHHHHHHHCCCCEEEEECCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHH-----HCC
T ss_conf             8------876034-----348889999874326980797145420031255666678880788899988787-----527


Q ss_pred             CCCCCCCCEEEEECCCC---CCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCC
Q ss_conf             53212343156521433---211111123337999886543344677877442222556677764101122333321111
Q gi|254780916|r  268 RGAIRLDVRLIFLTEKN---LLPQVKSHVFRKDLYYRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDK  344 (482)
Q Consensus       268 ~~~~~~~~RiIa~t~~~---L~~~~~~g~fr~dLy~rL~~~~i~iPpLReR~eDI~~L~~~fl~~~~~~~~~~~~~ls~~  344 (482)
                      .... ..|=++|+||+.   -..++.-|+|..       .+.|.+|...+|. +|..       -+.+.....   .++.
T Consensus       445 f~~~-~~vi~~a~tnr~d~ld~allrpGRfdr-------~i~i~~p~~~~r~-~i~~-------~h~~~~~~~---~e~~  505 (774)
T KOG0731         445 FETS-KGVIVLAATNRPDILDPALLRPGRFDR-------QIQIDLPDVKGRA-SILK-------VHLRKKKLD---DEDV  505 (774)
T ss_pred             CCCC-CCEEEEECCCCCCCCCHHHCCCCCCCC-------CEECCCCCHHHHH-HHHH-------HHHHCCCCC---CCHH
T ss_conf             7677-847998116886642887649875555-------2324698514168-9999-------986215776---3156


Q ss_pred             CCCCCCCCCCCCCH-HHHHHHHHHHHHHC---CCCCCCHHHHHHHHC
Q ss_conf             10001223389868-99999999998743---898106889545421
Q gi|254780916|r  345 ALSLLTKYPWIDNV-QELKNILLRAVIGL---KDSHLTEDRFVLLLS  387 (482)
Q Consensus       345 a~~~L~~y~WPGNv-REL~n~i~r~~i~~---~~~~i~~~~~~~~l~  387 (482)
                      -+.. .+-.=||+. -+|.|++-.+.+.+   ....|+..++...+.
T Consensus       506 dl~~-~a~~t~gf~gadl~n~~neaa~~a~r~~~~~i~~~~~~~a~~  551 (774)
T KOG0731         506 DLSK-LASLTPGFSGADLANLCNEAALLAARKGLREIGTKDLEYAIE  551 (774)
T ss_pred             HHHH-HHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHH
T ss_conf             7999-986089996789986424999999873367301564999999


No 162
>pfam00004 AAA ATPase family associated with various cellular activities (AAA). AAA family proteins often perform chaperone-like functions that assist in the assembly, operation, or disassembly of protein complexes.
Probab=98.42  E-value=7e-08  Score=75.35  Aligned_cols=96  Identities=19%  Similarity=0.238  Sum_probs=61.6

Q ss_pred             EEEECCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCHHHHHCCCCCCCCCCCCCCCCCCC---CCCCEEEECCC
Q ss_conf             887327774367999999842675433210123465542100243311255553221110012344---66714751664
Q gi|254780916|r  166 IMIQGEFGVGKKRLSRFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFGDVDLQTKNSAQFLGKFIE---ANGGTIVLEEP  242 (482)
Q Consensus       166 vli~Ge~GtGK~~~A~~iH~~s~r~~~~fi~v~c~~~~~~~~e~~lFG~~~~~~~~~~~~~g~~~~---a~~Gtl~l~ei  242 (482)
                      ||+.|++||||+++|++|-+..   +.+|+.++|+.+.....     |..      ...-...|..   .+...||+||+
T Consensus         1 iLl~GppGtGKT~~a~~la~~~---~~~~~~v~~~~~~~~~~-----g~~------~~~i~~~f~~a~~~~p~Il~iDe~   66 (131)
T pfam00004         1 LLLYGPPGTGKTTLAKAVAKEL---GAPFIEISGSELVSKYV-----GES------EKRLRELFEAAKKLAPCVIFIDEI   66 (131)
T ss_pred             CEEECCCCCCHHHHHHHHHHHH---CCCCEECCCCCCCCCCC-----CHH------HHHHHHHHHHHHHCCCCEEEECHH
T ss_conf             9878999999999999999997---89853324201222334-----506------888999999999749918983116


Q ss_pred             CHHHHH-----------HHHHHHHHHHHHHCCCCCCCCCCCCCCEEEEECCC
Q ss_conf             200188-----------99988887764200112355321234315652143
Q gi|254780916|r  243 DALPLA-----------VQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEK  283 (482)
Q Consensus       243 ~~L~~~-----------~Q~~Ll~~l~~~~~~~~g~~~~~~~~~RiIa~t~~  283 (482)
                      +.+...           .+..|+..++.-        .....++.+|++||.
T Consensus        67 d~l~~~~~~~~~~~~~~~~~~ll~~ld~~--------~~~~~~v~~I~tTN~  110 (131)
T pfam00004        67 DALAGSRGSGGDSESRRVVNQLLTELDGF--------TSSLSKVIVIAATNR  110 (131)
T ss_pred             HHHHCCCCCCCCCCCHHHHHHHHHHHHHC--------CCCCCCEEEEEECCC
T ss_conf             77751678888875132687899998502--------246887699997599


No 163
>PRK07003 DNA polymerase III subunits gamma and tau; Validated
Probab=98.41  E-value=1.3e-05  Score=59.30  Aligned_cols=222  Identities=17%  Similarity=0.207  Sum_probs=123.9

Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCCCHHHHHHHHHHHCCCCCC----CCC-CCCCCCCCCCCCCH
Q ss_conf             2111111112222222222222222344320488732777436799999984267543----321-01234655421002
Q gi|254780916|r  134 NEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHESGKRAF----FPF-FIVNCGMIDQDKIE  208 (482)
Q Consensus       134 ~~~~~~~~LiG~S~~m~~v~~~i~~~a~~~~~vli~Ge~GtGK~~~A~~iH~~s~r~~----~~f-i~v~c~~~~~~~~e  208 (482)
                      .....|..++|+.-..+.+...+.. .....--|++|..|+||+.+||.+-+.-.-.+    .|- .--+|..+.+..+-
T Consensus        10 ~RP~~f~e~vGQ~~v~~~l~nal~~-~rl~haylf~G~rGvGKTt~aRi~Ak~lnC~~~~~~~pcg~C~~C~~i~~g~~~   88 (816)
T PRK07003         10 WRPKDFASLVGQEHVVRALTHALDG-GRLHHAYLFTGTRGVGKTTLSRIFAKALNCETGVTSQPCGVCRACREIDEGRFV   88 (816)
T ss_pred             HCCCCHHHHCCCHHHHHHHHHHHHC-CCCCCEEEEECCCCCCHHHHHHHHHHHHCCCCCCCCCCCCCCHHHHHHHCCCCC
T ss_conf             0898576623849999999999970-986314751178988888999999998678999998978775557877558877


Q ss_pred             HHHHCCCCCC-CCCCCCCCCCCCCC-------CCCEEEECCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCEEEEE
Q ss_conf             4331125555-32211100123446-------671475166420018899988887764200112355321234315652
Q gi|254780916|r  209 KFLFGDVDLQ-TKNSAQFLGKFIEA-------NGGTIVLEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFL  280 (482)
Q Consensus       209 ~~lFG~~~~~-~~~~~~~~g~~~~a-------~~Gtl~l~ei~~L~~~~Q~~Ll~~l~~~~~~~~g~~~~~~~~~RiIa~  280 (482)
                      ..  =+.++. .....+...+++.+       .--..+|||+|-|+.....-||..|++-           +-+|.+|.+
T Consensus        89 d~--iEiDaAS~~~vd~~r~l~~~~~y~p~~~r~KvyiiDEvHmls~~afnalLKtlEep-----------P~hv~Fila  155 (816)
T PRK07003         89 DY--VEMDAASNRGVDEMAALLERAVYAPVDARFKVYMIDEVHMLTNHAFNAMLKTLEEP-----------PPHVKFILA  155 (816)
T ss_pred             CE--EEEECCCCCCHHHHHHHHHHCCCCCCCCCEEEEEEECHHHCCHHHHHHHHHHHCCC-----------CCCEEEEEE
T ss_conf             54--78635543576899999986224786674479998415433999999999840379-----------866489995


Q ss_pred             CCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCHHH
Q ss_conf             14332111111233379998865433446778774422225566777641011223333211111000122338986899
Q gi|254780916|r  281 TEKNLLPQVKSHVFRKDLYYRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQE  360 (482)
Q Consensus       281 t~~~L~~~~~~g~fr~dLy~rL~~~~i~iPpLReR~eDI~~L~~~fl~~~~~~~~~~~~~ls~~a~~~L~~y~WPGNvRE  360 (482)
                      |+.. .++- .-....=|-|.|..++         .++|   ..| |...+.+.+   ..++++|+.+|.... -|-+|.
T Consensus       156 TTd~-~k~p-~tilSRc~~f~l~~~~---------~~~i---~~~-l~~i~~~E~---i~~e~~al~lia~~a-~GsmRD  216 (816)
T PRK07003        156 TTDP-QKIP-VTVLSRCLQFNLKQMP---------AGHI---VSH-LERILGEER---IAFEPQALRLLARAA-QGSMRD  216 (816)
T ss_pred             CCCH-HHCC-HHHHHHHHHCCCCCCC---------HHHH---HHH-HHHHHHHCC---CCCCHHHHHHHHHHC-CCCHHH
T ss_conf             5880-1152-8898777652236799---------9999---999-999999829---977999999999976-773788


Q ss_pred             HHHHHHHHHHHCCCCCCCHHHHHHHHCCC
Q ss_conf             99999999874389810688954542124
Q gi|254780916|r  361 LKNILLRAVIGLKDSHLTEDRFVLLLSRE  389 (482)
Q Consensus       361 L~n~i~r~~i~~~~~~i~~~~~~~~l~~~  389 (482)
                      =-++..+++..+ ++.|+.+++..-++..
T Consensus       217 alsl~dQaia~~-~g~~~~~~v~~mLG~~  244 (816)
T PRK07003        217 ALSLTDQAIAYS-ANEVTETAVSGMLGAL  244 (816)
T ss_pred             HHHHHHHHHHHC-CCCCCHHHHHHHHCCC
T ss_conf             885999999846-9973799999985888


No 164
>PRK12422 chromosomal replication initiation protein; Provisional
Probab=98.40  E-value=6.6e-07  Score=68.42  Aligned_cols=220  Identities=16%  Similarity=0.168  Sum_probs=125.8

Q ss_pred             CCCCCCCCCC-CCCCCCCCC--CCCCCCCCCC----CCEEEEEECCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCC
Q ss_conf             2211111111-222222222--2222222344----32048873277743679999998426754332101234655421
Q gi|254780916|r  133 ENEHCALDSL-IAVSPAMIQ--VVDLARKAGD----CAIPIMIQGEFGVGKKRLSRFIHESGKRAFFPFFIVNCGMIDQD  205 (482)
Q Consensus       133 ~~~~~~~~~L-iG~S~~m~~--v~~~i~~~a~----~~~~vli~Ge~GtGK~~~A~~iH~~s~r~~~~fi~v~c~~~~~~  205 (482)
                      .+....|+.+ +|.|-.+..  ....+...+.    .=-|++|.|.+|.||+++-++|-+.-...+...+-+     +.+
T Consensus       104 lNp~ytFd~FVvG~~N~lA~~aa~~va~~~~~~~g~~yNPLfIyG~~GlGKTHLL~AIgn~i~~~~~kV~Yv-----tae  178 (455)
T PRK12422        104 VDPEMTFANFLVTPENDLPFRILQEFAKVSEQGKGFPFNPIYLFGPEGSGKTHLMQAAVSALRESGGKILYV-----SSE  178 (455)
T ss_pred             CCCCCCCCCEEECCCCHHHHHHHHHHHHCCCCCCCCCCCCEEEECCCCCCHHHHHHHHHHHHHCCCCEEEEE-----CHH
T ss_conf             897783558331586099999999998375535887678758878999978999999999853799869997-----499


Q ss_pred             CCHHHHHCCCCCCCCCCCCCCCCCCCCCCCEEEECCCCHHHH--HHHHHHHHHHHHHHCCCCCCCCCCCCCCEEEEECCC
Q ss_conf             002433112555532211100123446671475166420018--899988887764200112355321234315652143
Q gi|254780916|r  206 KIEKFLFGDVDLQTKNSAQFLGKFIEANGGTIVLEEPDALPL--AVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEK  283 (482)
Q Consensus       206 ~~e~~lFG~~~~~~~~~~~~~g~~~~a~~Gtl~l~ei~~L~~--~~Q~~Ll~~l~~~~~~~~g~~~~~~~~~RiIa~t~~  283 (482)
                      .+..++...-+  .+......-.+..+  -.|++|+|+-+.-  .+|.-++..+..=.          ..+=+||.++.+
T Consensus       179 ~F~~~~v~ai~--~~~~~~Fr~~yr~~--DvLLIDDIQfl~gK~~tqeEff~tfN~L~----------~~~KQIVitsDr  244 (455)
T PRK12422        179 LFTEHLVSAIR--SGEMQRFRSFYRNV--DALFIEDIEVFSGKGATQEEFFHTFNSLH----------TEGKLIVISSSY  244 (455)
T ss_pred             HHHHHHHHHHH--CCCHHHHHHHHHCC--CEEEEEHHHHHHCCHHHHHHHHHHHHHHH----------HCCCEEEEECCC
T ss_conf             99999999997--58899999999638--87763147887284889999999999999----------859969996898


Q ss_pred             CCCCCCCHHHHHHHHHHHHH-HH--HHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCHHH
Q ss_conf             32111111233379998865-43--3446778774422225566777641011223333211111000122338986899
Q gi|254780916|r  284 NLLPQVKSHVFRKDLYYRIS-VF--LINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQE  360 (482)
Q Consensus       284 ~L~~~~~~g~fr~dLy~rL~-~~--~i~iPpLReR~eDI~~L~~~fl~~~~~~~~~~~~~ls~~a~~~L~~y~WPGNvRE  360 (482)
                      .+.++-   .|.+.|.-|+. ++  .|.-|-+-.|..        ++.+.++..+.   .+++++++.+ .-...+||||
T Consensus       245 ~P~el~---~l~~RL~SRf~~GL~v~I~~Pd~etr~~--------Il~~k~~~~~~---~l~~ev~~~i-A~~i~~niRe  309 (455)
T PRK12422        245 APGDLK---AMEERLISRFEWGIAIPIHPLTREGLRS--------FLMRQAEQLSI---RIEETALDFL-IQALSSNVKT  309 (455)
T ss_pred             CHHHHH---HHHHHHHHHHHCCEEECCCCCCHHHHHH--------HHHHHHHHCCC---CCCHHHHHHH-HHHHHHHHHH
T ss_conf             957651---2689999886376132168999899999--------99999987188---8844689999-9997551799


Q ss_pred             HHHHHHHHHHH-----CCCCCCCHHHHHHHH
Q ss_conf             99999999874-----389810688954542
Q gi|254780916|r  361 LKNILLRAVIG-----LKDSHLTEDRFVLLL  386 (482)
Q Consensus       361 L~n~i~r~~i~-----~~~~~i~~~~~~~~l  386 (482)
                      |+..+.++...     ..+..++.+.+...+
T Consensus       310 LeGal~~l~~~~~~~~~~~~~i~~~~~~~~l  340 (455)
T PRK12422        310 LLHALTLLAKRVAYKKLSHQLLYEDDIKALL  340 (455)
T ss_pred             HHHHHHHHHHHHHHHHCCCCCCCHHHHHHHH
T ss_conf             9999999999999871568836499999999


No 165
>PRK11107 hybrid sensory histidine kinase BarA; Provisional
Probab=98.39  E-value=9e-06  Score=60.42  Aligned_cols=112  Identities=11%  Similarity=0.091  Sum_probs=87.9

Q ss_pred             CCCCEEEECCCHHHHHHHHHHHHHCCCEEEEECCHHHHHHHCCCCCEEEEECCCCCCCHHHHHHHHHH-HCCC-CCEEEE
Q ss_conf             28838998699899999999999889889998937999986089989999785469888999999998-5789-839999
Q gi|254780916|r    9 RHKRVLIIDKDDEQIKIIKDHVESYGYDVFIVNVSDLSTISKIQVNVIFLSLINCEDDKENILKNIVD-KIPI-VPIIVQ   86 (482)
Q Consensus         9 ~~~rILIVDDd~~~~~~l~~~L~~~G~~v~~a~~~al~~l~~~~~dlillD~~mP~~dGlell~~i~~-~~p~-ipvIii   86 (482)
                      ..++||+||+++..+..+...|..+|++|..+.+  ++.+....+|++++|+.||.+++.+.+..... ..+. -++|++
T Consensus       535 ~g~~vlvve~~~~~~~~l~~~L~~~g~~v~~~~~--~~~l~~~~~D~~li~~~~~~~~~~~~~~~~l~~~~~~~~~~il~  612 (920)
T PRK11107        535 AGKRLLYVEPNSLAAQATLDLLSETPLEVTYSPT--LSQLPEAHYDYLLLGCPVTFREPLTMLHERLAKAKSMTDFLILA  612 (920)
T ss_pred             CCCEEEEECCCHHHHHHHHHHHHHCCCEEEECCC--HHHHHCCCCCEEEECCCCCCCCHHHHHHHHHHHHCCCCCCEEEE
T ss_conf             5876999769778999999999974964575178--87751368887996166666540667899986300357846997


Q ss_pred             ECCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             268999999988850574322222222222222222
Q gi|254780916|r   87 TTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIIC  122 (482)
Q Consensus        87 T~~~~~~~~~~a~~~g~~d~l~KP~~~~~L~~~i~~  122 (482)
                      +..............|...++.||+...+|...+..
T Consensus       613 ~~s~~~~~~~~~~~~~~~~~L~kPv~~~~L~~~L~~  648 (920)
T PRK11107        613 LPCHEQVNAEQLKQPGADACLSKPLSETRLLPALLT  648 (920)
T ss_pred             ECCCCHHHHHHHHHCCCCHHCCCCCCHHHHHHHHHC
T ss_conf             156434557887642530211277768899998722


No 166
>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=98.35  E-value=2.9e-06  Score=63.93  Aligned_cols=215  Identities=17%  Similarity=0.215  Sum_probs=133.8

Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCCCHHHHHHHHHHHC---CCCCCCCCCC-CCCCCCCC---
Q ss_conf             2221111111122222222222222223443204887327774367999999842---6754332101-23465542---
Q gi|254780916|r  132 QENEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHES---GKRAFFPFFI-VNCGMIDQ---  204 (482)
Q Consensus       132 ~~~~~~~~~~LiG~S~~m~~v~~~i~~~a~~~~~vli~Ge~GtGK~~~A~~iH~~---s~r~~~~fi~-v~c~~~~~---  204 (482)
                      +.-....|++++|++-..+.+...+.. ..-..-=|..|+.||||+.+||-+=..   ......|-=. =+|-++..   
T Consensus         6 RKyRP~~F~d~~GQ~~iv~tL~NAi~~-~ri~HAYLF~GpRGtGKTS~ARIfAKaLNC~~~~~~PCn~C~~C~~i~~g~~   84 (363)
T TIGR02397         6 RKYRPQTFEDVIGQEHIVKTLKNAIKN-GRIAHAYLFSGPRGTGKTSIARIFAKALNCQGPDGEPCNECESCKEINSGSS   84 (363)
T ss_pred             ECCCCCCCCCCCCCHHHHHHHHHHHHH-CCCCCEEEECCCCCCCHHHHHHHHHHHHCCCCCCCCCCCCCCHHHHHHCCCC
T ss_conf             223788611023517999999999971-8966234502859976355899999986588787787777502277652898


Q ss_pred             -CCCHHHHHCCCCCCC--CCCCCCCCCCCC----CCC---CEEEECCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCC
Q ss_conf             -100243311255553--221110012344----667---1475166420018899988887764200112355321234
Q gi|254780916|r  205 -DKIEKFLFGDVDLQT--KNSAQFLGKFIE----ANG---GTIVLEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLD  274 (482)
Q Consensus       205 -~~~e~~lFG~~~~~~--~~~~~~~g~~~~----a~~---Gtl~l~ei~~L~~~~Q~~Ll~~l~~~~~~~~g~~~~~~~~  274 (482)
                       |.+|      -+|+.  |-..-| -+.+.    -..   =.-.+||+|=||...=.-||..|||.           |.+
T Consensus        85 ~DviE------iDAASN~gVD~IR-~l~e~v~y~P~~~kYKvYIIDEVHMLS~~AFNALLKTLEEP-----------P~h  146 (363)
T TIGR02397        85 LDVIE------IDAASNNGVDDIR-ELRENVKYAPSKGKYKVYIIDEVHMLSKSAFNALLKTLEEP-----------PEH  146 (363)
T ss_pred             CCEEE------ECCCCCCCHHHHH-HHHHHHCCCCCCCCCCEEEEECCCCCCHHHHHHHHHHHCCC-----------CCC
T ss_conf             66688------6486568788999-99873036875544335887323028656899987652279-----------876


Q ss_pred             CEEEEECCCC----CCCCCCHHHH--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCC
Q ss_conf             3156521433----2111111233--379998865433446778774422225566777641011223333211111000
Q gi|254780916|r  275 VRLIFLTEKN----LLPQVKSHVF--RKDLYYRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSL  348 (482)
Q Consensus       275 ~RiIa~t~~~----L~~~~~~g~f--r~dLy~rL~~~~i~iPpLReR~eDI~~L~~~fl~~~~~~~~~~~~~ls~~a~~~  348 (482)
                      |-+|.||+..    ..=+....+|  ++          |...-          ++.| |+..+.+.|   ..++++|+++
T Consensus       147 V~FIlATTE~~KiP~TIlSRCQrF~Fk~----------i~~~~----------i~~~-L~~I~~~E~---I~~e~~AL~~  202 (363)
T TIGR02397       147 VVFILATTEPHKIPATILSRCQRFDFKR----------IPLED----------IVER-LKKILDKEG---IKIEDEALEL  202 (363)
T ss_pred             EEEEEECCCHHHCCCCCEEECEEECCCC----------CCHHH----------HHHH-HHHHHHHHC---CCCCHHHHHH
T ss_conf             2888734871120554021000312678----------99899----------9999-999998708---8317789999


Q ss_pred             CCCCCCCCCHHHHHHHHHHHHHHCCC--CCCCHHHHHHHHCCCC
Q ss_conf             12233898689999999999874389--8106889545421244
Q gi|254780916|r  349 LTKYPWIDNVQELKNILLRAVIGLKD--SHLTEDRFVLLLSREG  390 (482)
Q Consensus       349 L~~y~WPGNvREL~n~i~r~~i~~~~--~~i~~~~~~~~l~~~~  390 (482)
                      +..+. -|=+|.=.+++.+++....+  +.|+.+++...++-..
T Consensus       203 IA~~a-~GS~RDAlsllDQ~~~~~~~~DG~i~~~~v~~~lGl~~  245 (363)
T TIGR02397       203 IARAA-DGSMRDALSLLDQAISFGNGSDGKITYEDVNEMLGLVD  245 (363)
T ss_pred             HHHHC-CCCCCHHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCC
T ss_conf             99962-89610688999999982688788657899999835777


No 167
>PRK06305 DNA polymerase III subunits gamma and tau; Validated
Probab=98.33  E-value=5.7e-06  Score=61.83  Aligned_cols=219  Identities=15%  Similarity=0.150  Sum_probs=125.6

Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCCCHHHHHHHHHHHCCC----CCC-CCCC-CCCCCCCCC---
Q ss_conf             2111111112222222222222222344320488732777436799999984267----543-3210-123465542---
Q gi|254780916|r  134 NEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHESGK----RAF-FPFF-IVNCGMIDQ---  204 (482)
Q Consensus       134 ~~~~~~~~LiG~S~~m~~v~~~i~~~a~~~~~vli~Ge~GtGK~~~A~~iH~~s~----r~~-~~fi-~v~c~~~~~---  204 (482)
                      -....|++++|+....+.+...+.. .....-.|+.|+.||||+.+||.+-..=.    ..+ .|-- --+|..+..   
T Consensus        11 YRP~~F~dvVGQ~~vv~~L~nai~~-~ri~HAyLF~GprGtGKTT~ArilAkaLnC~~~~~~~~pCg~C~~C~~I~~g~~   89 (462)
T PRK06305         11 YRPQTFSEILGQDAVVTVLKNALRF-NRAAHAYLFSGIRGTGKTTLARIFAKALNCQNPTEDQEPCNQCAICKEISSGTS   89 (462)
T ss_pred             HCCCCHHHHCCCHHHHHHHHHHHHC-CCCCCEEEEECCCCCCHHHHHHHHHHHHCCCCCCCCCCCCCCCHHHHHHHCCCC
T ss_conf             3889876604909999999999984-997623430389985999999999999679999888898876688899863899


Q ss_pred             -CCCHHHHHCCCCCCC--CCCCCCC----CCCCCCC--CCEEEECCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCC
Q ss_conf             -100243311255553--2211100----1234466--714751664200188999888877642001123553212343
Q gi|254780916|r  205 -DKIEKFLFGDVDLQT--KNSAQFL----GKFIEAN--GGTIVLEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDV  275 (482)
Q Consensus       205 -~~~e~~lFG~~~~~~--~~~~~~~----g~~~~a~--~Gtl~l~ei~~L~~~~Q~~Ll~~l~~~~~~~~g~~~~~~~~~  275 (482)
                       +.+|      .+++.  |-..-|.    -.+.-+.  .-..+|||++.|+...+..||+.|++.           +.++
T Consensus        90 ~DViE------iDaAs~~gVddIRel~e~v~~~P~~~~yKVyIIDEvhmLs~~AfNALLKtLEEP-----------P~~v  152 (462)
T PRK06305         90 LDVIE------IDGASHRGIEDIRQINETVLFTPSKSQYKIYIIDEVHMLTKEAFNSLLKTLEEP-----------PQHV  152 (462)
T ss_pred             CCEEE------ECCCCCCCHHHHHHHHHHHCCCCCCCCEEEEEEECHHHCCHHHHHHHHHHHHCC-----------CCCE
T ss_conf             98686------435534466899999977100886775059998152117999999999986189-----------8774


Q ss_pred             EEEEECCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             15652143321111112333799988654334467787744222255667776410112233332111110001223389
Q gi|254780916|r  276 RLIFLTEKNLLPQVKSHVFRKDLYYRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWI  355 (482)
Q Consensus       276 RiIa~t~~~L~~~~~~g~fr~dLy~rL~~~~i~iPpLReR~eDI~~L~~~fl~~~~~~~~~~~~~ls~~a~~~L~~y~WP  355 (482)
                      ++|.+|+.. .++...      ..-|  +-.+.+.++.  .+||   +.| |...+.+.+   ..++++|+.++.... -
T Consensus       153 ~FILaTTe~-~KIp~T------IlSR--CQrf~F~~i~--~~~I---~~~-L~~I~~~E~---i~~e~~AL~lIA~~a-~  213 (462)
T PRK06305        153 KFFLATTEI-HKIPGT------ILSR--CQKMHLKRIP--EETI---IDK-LALIAQQDG---IETSREALLPIARAA-Q  213 (462)
T ss_pred             EEEEEECCH-HHCCHH------HHHH--HHEEECCCCC--HHHH---HHH-HHHHHHHCC---CCCCHHHHHHHHHHC-C
T ss_conf             999981881-428547------8765--4023325799--9999---999-999999839---985999999999985-8


Q ss_pred             CCHHHHHHHHHHHHHHCCCCCCCHHHHHHHHCCCC
Q ss_conf             86899999999998743898106889545421244
Q gi|254780916|r  356 DNVQELKNILLRAVIGLKDSHLTEDRFVLLLSREG  390 (482)
Q Consensus       356 GNvREL~n~i~r~~i~~~~~~i~~~~~~~~l~~~~  390 (482)
                      |-+|.=.+++.+++.. .++.|+.+++...++-..
T Consensus       214 GsmRDAlslLDQ~i~~-~~~~it~~~V~~~lG~v~  247 (462)
T PRK06305        214 GSLRDAESLYDYVVGL-FPKSLSPDTVAKALGLLS  247 (462)
T ss_pred             CCHHHHHHHHHHHHHH-CCCCCCHHHHHHHHCCCC
T ss_conf             9587899999999984-799868999999868998


No 168
>PRK07764 DNA polymerase III subunits gamma and tau; Validated
Probab=98.33  E-value=2.8e-06  Score=63.97  Aligned_cols=223  Identities=14%  Similarity=0.182  Sum_probs=128.3

Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCCCHHHHHHHHHHHCCCCCCCCCC-----CCCCCCCCCCCCHH
Q ss_conf             1111111122222222222222223443204887327774367999999842675433210-----12346554210024
Q gi|254780916|r  135 EHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHESGKRAFFPFF-----IVNCGMIDQDKIEK  209 (482)
Q Consensus       135 ~~~~~~~LiG~S~~m~~v~~~i~~~a~~~~~vli~Ge~GtGK~~~A~~iH~~s~r~~~~fi-----~v~c~~~~~~~~e~  209 (482)
                      .-..|+.+||+....+.+...+.. .....--|+.|+.||||+.+||.+-..-.-.++|-.     --+|..|....--+
T Consensus        10 RP~~F~eviGQe~v~~~L~~Ai~~-gri~HAYLFsGprG~GKTt~ARilAkaLNC~~~~~~~PCg~C~sC~~i~~g~~~~   88 (775)
T PRK07764         10 RPATFAEVVGQEHVTEPLSTALDS-GRINHAYLFSGPRGCGKTSSARILARSLNCAQGPTSTPCGVCDSCVALAPGGPGS   88 (775)
T ss_pred             CCCCHHHHCCCHHHHHHHHHHHHC-CCCCCEEEEECCCCCCHHHHHHHHHHHHCCCCCCCCCCCCCCHHHHHHHCCCCCC
T ss_conf             788766622859999999999981-9976337623788878889999999996689999989888876378886389888


Q ss_pred             HHHCCCCCC-CCCCCCCCCCCCC-------CCCCEEEECCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCEEEEEC
Q ss_conf             331125555-3221110012344-------66714751664200188999888877642001123553212343156521
Q gi|254780916|r  210 FLFGDVDLQ-TKNSAQFLGKFIE-------ANGGTIVLEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLT  281 (482)
Q Consensus       210 ~lFG~~~~~-~~~~~~~~g~~~~-------a~~Gtl~l~ei~~L~~~~Q~~Ll~~l~~~~~~~~g~~~~~~~~~RiIa~t  281 (482)
                      .-+=+.++. .+...+-..+.+.       ..--..+|||+|-|+......||+.|++-           +.++-+|.+|
T Consensus        89 ~DviEiDAAS~~gVddiReL~e~~~y~P~~~ryKVyIIDEaHmls~~afNALLKtLEEP-----------P~hvvFIlaT  157 (775)
T PRK07764         89 LDVVEIDAASHGGVDDARELRERAFFAPAQSRYRIFIIDEAHMVTTAGFNALLKIVEEP-----------PEHLIFIFAT  157 (775)
T ss_pred             CCEEEECCCCCCCHHHHHHHHHHCCCCCCCCCEEEEEEECHHHHCHHHHHHHHHHHCCC-----------CCCEEEEEEC
T ss_conf             86687315655688999999985476876786359998535440799999998862278-----------6462799954


Q ss_pred             CCCCCCCCCHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCHHH
Q ss_conf             433211111123337999886543344-6778774422225566777641011223333211111000122338986899
Q gi|254780916|r  282 EKNLLPQVKSHVFRKDLYYRISVFLIN-ISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQE  360 (482)
Q Consensus       282 ~~~L~~~~~~g~fr~dLy~rL~~~~i~-iPpLReR~eDI~~L~~~fl~~~~~~~~~~~~~ls~~a~~~L~~y~WPGNvRE  360 (482)
                      +.. +++...      ..-|-..+.++ ||     .++|    ..+|.+.|.+.|.   .++++++.++..... |-+|.
T Consensus       158 Tep-~kip~T------I~SRcq~f~Fr~i~-----~~~~----~~~l~~i~~~E~i---~~~~~al~li~r~~~-Gs~RD  217 (775)
T PRK07764        158 TEP-EKVIGT------IRSRTHHYPFRLVP-----PGTM----RPYLERICAQEGV---VVDDAVLPLVIRAGG-GSPRD  217 (775)
T ss_pred             CCH-HHCCHH------HHHHCCCCCCCCCC-----HHHH----HHHHHHHHHHCCC---CCCHHHHHHHHHHCC-CCHHH
T ss_conf             873-547167------76410234526699-----9999----9999999998399---879899999999828-96676


Q ss_pred             HHHHHHHHHHHCCCCCCCHHHHHHHHCCC
Q ss_conf             99999999874389810688954542124
Q gi|254780916|r  361 LKNILLRAVIGLKDSHLTEDRFVLLLSRE  389 (482)
Q Consensus       361 L~n~i~r~~i~~~~~~i~~~~~~~~l~~~  389 (482)
                      =-+++.+++..+.++.|+.++....++..
T Consensus       218 alS~ldQl~a~~~~~~v~~~~a~~llG~~  246 (775)
T PRK07764        218 TLSVLDQLLAGAGDDGVTYERAVALLGVT  246 (775)
T ss_pred             HHHHHHHHHHCCCCCCEEHHHHHHHHCCC
T ss_conf             89999999840488841099999985888


No 169
>PRK08451 DNA polymerase III subunits gamma and tau; Validated
Probab=98.31  E-value=7.1e-06  Score=61.15  Aligned_cols=216  Identities=17%  Similarity=0.201  Sum_probs=122.6

Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCCCHHHHHHHHHHHCC----CCCCCCC-CCCCCCCCCC----C
Q ss_conf             11111111222222222222222234432048873277743679999998426----7543321-0123465542----1
Q gi|254780916|r  135 EHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHESG----KRAFFPF-FIVNCGMIDQ----D  205 (482)
Q Consensus       135 ~~~~~~~LiG~S~~m~~v~~~i~~~a~~~~~vli~Ge~GtGK~~~A~~iH~~s----~r~~~~f-i~v~c~~~~~----~  205 (482)
                      ....|+.++|+....+.+...+.. .......|+.|+.||||+.+||.+-..=    .....|- .--+|..+..    +
T Consensus         9 RP~~F~evIGQe~iv~~L~nAi~~-~Rl~HAYLFsGPrGvGKTt~ArifAkaLnC~~~~~~~PCg~C~sC~~i~~g~hpD   87 (523)
T PRK08451          9 RPKHFDELIGQESVSKTLSLALDN-NRLAHAYLFSGLRGSGKTSSARIFSRALVCEQGPSSTPCGTCAQCQAALEGRHID   87 (523)
T ss_pred             CCCCHHHCCCCHHHHHHHHHHHHC-CCCCCEEEEECCCCCCHHHHHHHHHHHHCCCCCCCCCCCCCCHHHHHHHCCCCCC
T ss_conf             899654404949999999999985-9967158757899868899999999997599999989888788899986489998


Q ss_pred             CCHHHHHCCCCCCC-CCCCCCCCCCCC-------CCCCEEEECCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCEE
Q ss_conf             00243311255553-221110012344-------6671475166420018899988887764200112355321234315
Q gi|254780916|r  206 KIEKFLFGDVDLQT-KNSAQFLGKFIE-------ANGGTIVLEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRL  277 (482)
Q Consensus       206 ~~e~~lFG~~~~~~-~~~~~~~g~~~~-------a~~Gtl~l~ei~~L~~~~Q~~Ll~~l~~~~~~~~g~~~~~~~~~Ri  277 (482)
                      .+|      .++.. ....+-..+.+.       +..-..++||++.|+.+.+..||..|++.           +.++.+
T Consensus        88 ViE------iDaasn~gID~IReLie~~~~~P~~gryKV~IIDEah~Lt~~A~NALLKTLEEP-----------P~~vvF  150 (523)
T PRK08451         88 IIE------MDAASNRGIDDIRNLIEQTKYKPSMARFKIFIIDEVHMLTKEAFNALLKTLEEP-----------PSYVKF  150 (523)
T ss_pred             EEE------ECCCCCCCHHHHHHHHHHHCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHCCCC-----------CCCCEE
T ss_conf             551------055333689999999997235886797279998260304899999999970389-----------878379


Q ss_pred             EEECCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             65214332111111233379998865433446778774422225566777641011223333211111000122338986
Q gi|254780916|r  278 IFLTEKNLLPQVKSHVFRKDLYYRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDN  357 (482)
Q Consensus       278 Ia~t~~~L~~~~~~g~fr~dLy~rL~~~~i~iPpLReR~eDI~~L~~~fl~~~~~~~~~~~~~ls~~a~~~L~~y~WPGN  357 (482)
                      |.+|+.. ..+...      ..-|-.  .+.+.++     ....++.| |...+.+.+   ..++++|+.++.... -|-
T Consensus       151 ILaTTep-~KLp~T------IlSRCQ--~f~Fk~I-----~~~~I~~~-L~~I~~~E~---i~~e~~AL~~IA~~a-~Gs  211 (523)
T PRK08451        151 ILATTDP-LKLPAT------ILSRTQ--HFRFKQI-----PQNSIISH-LKTILNKEG---VSYEPEALEILARSG-SGS  211 (523)
T ss_pred             EEECCCH-HHCHHH------HHHHHH--CCCCCCC-----CHHHHHHH-HHHHHHHCC---CCCCHHHHHHHHHHC-CCC
T ss_conf             9975994-768488------874203--1103379-----99999999-999999839---987999999999977-894


Q ss_pred             HHHHHHHHHHHHHHCCCCCCCHHHHHHHHCC
Q ss_conf             8999999999987438981068895454212
Q gi|254780916|r  358 VQELKNILLRAVIGLKDSHLTEDRFVLLLSR  388 (482)
Q Consensus       358 vREL~n~i~r~~i~~~~~~i~~~~~~~~l~~  388 (482)
                      +|.=-+++.+++..+. +.|+.+++...++.
T Consensus       212 lRDalslLdQ~i~~~~-~~i~~~~v~~~lG~  241 (523)
T PRK08451        212 LRDTLTLLDQAIIFCK-NAITESKVADMLGL  241 (523)
T ss_pred             HHHHHHHHHHHHHHCC-CCCCHHHHHHHHCC
T ss_conf             8689879999998479-98779999998588


No 170
>KOG0733 consensus
Probab=98.31  E-value=1.1e-06  Score=66.98  Aligned_cols=195  Identities=16%  Similarity=0.216  Sum_probs=111.3

Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCC----------CCEEEEEECCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCC
Q ss_conf             11111112222222222222222344----------32048873277743679999998426754332101234655421
Q gi|254780916|r  136 HCALDSLIAVSPAMIQVVDLARKAGD----------CAIPIMIQGEFGVGKKRLSRFIHESGKRAFFPFFIVNCGMIDQD  205 (482)
Q Consensus       136 ~~~~~~LiG~S~~m~~v~~~i~~~a~----------~~~~vli~Ge~GtGK~~~A~~iH~~s~r~~~~fi~v~c~~~~~~  205 (482)
                      +..+..+-|-+.....+.+.+..+-.          -..-||+.|++||||+.+|++|-...   .-||+.|+...+   
T Consensus       186 nv~f~diGG~d~~~~el~~li~~i~~Pe~~~~lGv~PprGvLlHGPPGCGKT~lA~AiAgel---~vPf~~isApei---  259 (802)
T KOG0733         186 NVSFSDIGGLDKTLAELCELIIHIKHPEVFSSLGVRPPRGVLLHGPPGCGKTSLANAIAGEL---GVPFLSISAPEI---  259 (802)
T ss_pred             CCCHHHCCCHHHHHHHHHHHHHHHCCCHHHHHCCCCCCCCEEEECCCCCCHHHHHHHHHHHC---CCCEEEECCHHH---
T ss_conf             86365416738999999999988528116866287799751644899864789999975212---885485141465---


Q ss_pred             CCHHHHHCCCCCCCCCCCCCC-CCCCCCCCC---EEEECCCCHHHHH-------HHH----HHHHHHHHHHCCCCCCCCC
Q ss_conf             002433112555532211100-123446671---4751664200188-------999----8888776420011235532
Q gi|254780916|r  206 KIEKFLFGDVDLQTKNSAQFL-GKFIEANGG---TIVLEEPDALPLA-------VQG----RIYNFIETGKIEFFDSRGA  270 (482)
Q Consensus       206 ~~e~~lFG~~~~~~~~~~~~~-g~~~~a~~G---tl~l~ei~~L~~~-------~Q~----~Ll~~l~~~~~~~~g~~~~  270 (482)
                       +        .|..|....++ -+|++|.+-   .+|+|||+...+.       +-.    .||.-+++-.....     
T Consensus       260 -v--------SGvSGESEkkiRelF~~A~~~aPcivFiDeIDAI~pkRe~aqreMErRiVaQLlt~mD~l~~~~~-----  325 (802)
T KOG0733         260 -V--------SGVSGESEKKIRELFDQAKSNAPCIVFIDEIDAITPKREEAQREMERRIVAQLLTSMDELSNEKT-----  325 (802)
T ss_pred             -H--------CCCCCCCHHHHHHHHHHHHCCCCEEEEEECCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCC-----
T ss_conf             -3--------15575228999999998736697599851100136440457889999999999985100256666-----


Q ss_pred             CCCCCEEEEECCCC--C-CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCC
Q ss_conf             12343156521433--2-11111123337999886543344677877442222556677764101122333321111100
Q gi|254780916|r  271 IRLDVRLIFLTEKN--L-LPQVKSHVFRKDLYYRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALS  347 (482)
Q Consensus       271 ~~~~~RiIa~t~~~--L-~~~~~~g~fr~dLy~rL~~~~i~iPpLReR~eDI~~L~~~fl~~~~~~~~~~~~~ls~~a~~  347 (482)
                      ..-.|-+|++||++  | ..+-..|+|..+       +.|.+|.=-.|. +|       |...|+...... .|+-+-++
T Consensus       326 ~g~~VlVIgATnRPDslDpaLRRaGRFdrE-------I~l~vP~e~aR~-~I-------L~~~~~~lrl~g-~~d~~qlA  389 (802)
T KOG0733         326 KGDPVLVIGATNRPDSLDPALRRAGRFDRE-------ICLGVPSETARE-EI-------LRIICRGLRLSG-DFDFKQLA  389 (802)
T ss_pred             CCCCEEEEECCCCCCCCCHHHHCCCCCCCE-------EEECCCCHHHHH-HH-------HHHHHHHCCCCC-CCCHHHHH
T ss_conf             899769982478976558777325655323-------530689668899-99-------999986277787-76899997


Q ss_pred             CCCCCCCCCCHH-HHHHHHHHHHH
Q ss_conf             012233898689-99999999987
Q gi|254780916|r  348 LLTKYPWIDNVQ-ELKNILLRAVI  370 (482)
Q Consensus       348 ~L~~y~WPGNvR-EL~n~i~r~~i  370 (482)
                      .|    -||=|. .|+.++..|..
T Consensus       390 ~l----TPGfVGADL~AL~~~Aa~  409 (802)
T KOG0733         390 KL----TPGFVGADLMALCREAAF  409 (802)
T ss_pred             HC----CCCCCCHHHHHHHHHHHH
T ss_conf             51----887521419999999999


No 171
>KOG2028 consensus
Probab=98.30  E-value=4.4e-07  Score=69.67  Aligned_cols=219  Identities=20%  Similarity=0.237  Sum_probs=116.3

Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC-CCE-EEEEECCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             222222111111112222222222222222344-320-488732777436799999984267543321012346554210
Q gi|254780916|r  129 VPSQENEHCALDSLIAVSPAMIQVVDLARKAGD-CAI-PIMIQGEFGVGKKRLSRFIHESGKRAFFPFFIVNCGMIDQDK  206 (482)
Q Consensus       129 ~~~~~~~~~~~~~LiG~S~~m~~v~~~i~~~a~-~~~-~vli~Ge~GtGK~~~A~~iH~~s~r~~~~fi~v~c~~~~~~~  206 (482)
                      ..++......+++.+|++...-. .-.++.+.. ... ++.+.|++||||+.+||.|-..|....-.||.+....-..  
T Consensus       127 PLaermRPktL~dyvGQ~hlv~q-~gllrs~ieq~~ipSmIlWGppG~GKTtlArlia~tsk~~SyrfvelSAt~a~t--  203 (554)
T KOG2028         127 PLAERMRPKTLDDYVGQSHLVGQ-DGLLRSLIEQNRIPSMILWGPPGTGKTTLARLIASTSKKHSYRFVELSATNAKT--  203 (554)
T ss_pred             CHHHHCCCCHHHHHCCHHHHCCC-CHHHHHHHHCCCCCCEEEECCCCCCHHHHHHHHHHHCCCCCEEEEEEECCCCCH--
T ss_conf             74554184368775053441483-268999987088870588669987658899999860577742799974145661--


Q ss_pred             CHHHHHCCCCCCCCCCCCCCCCCCCC--------CCCEEEECCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCEEE
Q ss_conf             02433112555532211100123446--------6714751664200188999888877642001123553212343156
Q gi|254780916|r  207 IEKFLFGDVDLQTKNSAQFLGKFIEA--------NGGTIVLEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLI  278 (482)
Q Consensus       207 ~e~~lFG~~~~~~~~~~~~~g~~~~a--------~~Gtl~l~ei~~L~~~~Q~~Ll~~l~~~~~~~~g~~~~~~~~~RiI  278 (482)
                                      .+..+.||+|        ..-.||+|||+..-..-|.-+|-.+++|.+             -+|
T Consensus       204 ----------------~dvR~ife~aq~~~~l~krkTilFiDEiHRFNksQQD~fLP~VE~G~I-------------~lI  254 (554)
T KOG2028         204 ----------------NDVRDIFEQAQNEKSLTKRKTILFIDEIHRFNKSQQDTFLPHVENGDI-------------TLI  254 (554)
T ss_pred             ----------------HHHHHHHHHHHHHHHHHCCEEEEEEHHHHHHHHHHHHCCCCEECCCCE-------------EEE
T ss_conf             ----------------889999999887876524406987377655323211003421306706-------------998


Q ss_pred             EECCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--CCCC--CCCC--CCCCCCCCCCCCCC
Q ss_conf             5214332111111233379998865433446778774422225566777641--0112--2333--32111110001223
Q gi|254780916|r  279 FLTEKNLLPQVKSHVFRKDLYYRISVFLINISTLRSRSEDIPWLVHFFLQSF--CTKN--AIKQ--ISISDKALSLLTKY  352 (482)
Q Consensus       279 a~t~~~L~~~~~~g~fr~dLy~rL~~~~i~iPpLReR~eDI~~L~~~fl~~~--~~~~--~~~~--~~ls~~a~~~L~~y  352 (482)
                      .+|+.|+.=.+..     -|.-|--+++++  +|.  .+.+..+..+=+...  +++.  +.+.  ..++..+++.| .|
T Consensus       255 GATTENPSFqln~-----aLlSRC~VfvLe--kL~--~n~v~~iL~raia~l~dser~~~~l~n~s~~ve~siidyl-a~  324 (554)
T KOG2028         255 GATTENPSFQLNA-----ALLSRCRVFVLE--KLP--VNAVVTILMRAIASLGDSERPTDPLPNSSMFVEDSIIDYL-AY  324 (554)
T ss_pred             ECCCCCCCCCHHH-----HHHHCCCEEEEC--CCC--HHHHHHHHHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHHH-HH
T ss_conf             5366897601127-----787316066733--688--8999999999987632102568899983124568899999-87


Q ss_pred             CCCCCHHHHHHHHHHH--HHHCCCC-----CCCHHHHHHHHCCC
Q ss_conf             3898689999999999--8743898-----10688954542124
Q gi|254780916|r  353 PWIDNVQELKNILLRA--VIGLKDS-----HLTEDRFVLLLSRE  389 (482)
Q Consensus       353 ~WPGNvREL~n~i~r~--~i~~~~~-----~i~~~~~~~~l~~~  389 (482)
                      ---|.-|-=-|.++-.  ......+     .++.+|+...+...
T Consensus       325 lsdGDaR~aLN~Lems~~m~~tr~g~~~~~~lSidDvke~lq~s  368 (554)
T KOG2028         325 LSDGDARAALNALEMSLSMFCTRSGQSSRVLLSIDDVKEGLQRS  368 (554)
T ss_pred             HCCCHHHHHHHHHHHHHHHHHHHCCCCCCCEECHHHHHHHHHHC
T ss_conf             04731888877899999988752477656400288899998531


No 172
>CHL00095 clpC Clp protease ATP binding subunit
Probab=98.29  E-value=1.2e-06  Score=66.66  Aligned_cols=206  Identities=16%  Similarity=0.172  Sum_probs=105.4

Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCCCHHHHHHHHHHHCCCCCC-------CCCCCCCCCCCCCCCC
Q ss_conf             111111112222222222222222344320488732777436799999984267543-------3210123465542100
Q gi|254780916|r  135 EHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHESGKRAF-------FPFFIVNCGMIDQDKI  207 (482)
Q Consensus       135 ~~~~~~~LiG~S~~m~~v~~~i~~~a~~~~~vli~Ge~GtGK~~~A~~iH~~s~r~~-------~~fi~v~c~~~~~~~~  207 (482)
                      .....++++|+...++++.+-++|  .+..+.++.||+|+||+.+++.+-..=-..+       ..++.+|.+++     
T Consensus       174 ~~GklDpvIGRd~EI~r~i~IL~R--R~KNNpiLvGepGVGKTAIvEGLA~rI~~g~VP~~L~~~~i~sLDl~~L-----  246 (823)
T CHL00095        174 YEGNLDPVIGRDKEIERVIQILGR--RTKNNPILIGEPGVGKTAIAEGLAQRIANRDVPDILEDKLVLTLDIGLL-----  246 (823)
T ss_pred             HHCCCCCCCCCHHHHHHHHHHHHH--HCCCCCEEECCCCCCHHHHHHHHHHHHHCCCCCHHHCCCCEEEEEHHHH-----
T ss_conf             838999875956999999999977--3248850237999879999999999760889986875993688428877-----


Q ss_pred             HHHHHCCCCCCCCCCCCCC-C---CCCCCCCCEEEECCCCHH--------HHHHHHHHHHHHHHHHCCCCCCCCCCCCCC
Q ss_conf             2433112555532211100-1---234466714751664200--------188999888877642001123553212343
Q gi|254780916|r  208 EKFLFGDVDLQTKNSAQFL-G---KFIEANGGTIVLEEPDAL--------PLAVQGRIYNFIETGKIEFFDSRGAIRLDV  275 (482)
Q Consensus       208 e~~lFG~~~~~~~~~~~~~-g---~~~~a~~Gtl~l~ei~~L--------~~~~Q~~Ll~~l~~~~~~~~g~~~~~~~~~  275 (482)
                         +=|-+  +-|....|. +   -+.++.+-.||+||||.+        +.+.-.-|--+|..|             ++
T Consensus       247 ---~AGtk--yRGeFEeRlk~il~ei~~~~~iILFIDEiHtlvGaG~~~g~~DaaNlLKPaLarG-------------el  308 (823)
T CHL00095        247 ---LAGTK--YRGEFEERIKKIMDEIKKANNIILVIDEIHTLIGAGAAEGAIDAANILKPALARG-------------KL  308 (823)
T ss_pred             ---HHCCC--CCHHHHHHHHHHHHHHHHCCCEEEEECCHHHHCCCCCCCCCHHHHHHHHHHHHCC-------------CC
T ss_conf             ---53342--2267999999999999857986999735165328897666431788765786489-------------86


Q ss_pred             EEEEECCCCC-CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---------------HHHCCCCCCCCC
Q ss_conf             1565214332-111111233379998865433446778774422225566777---------------641011223333
Q gi|254780916|r  276 RLIFLTEKNL-LPQVKSHVFRKDLYYRISVFLINISTLRSRSEDIPWLVHFFL---------------QSFCTKNAIKQI  339 (482)
Q Consensus       276 RiIa~t~~~L-~~~~~~g~fr~dLy~rL~~~~i~iPpLReR~eDI~~L~~~fl---------------~~~~~~~~~~~~  339 (482)
                      |+|.+|+.+= .+-++.   ...|=-|...+.|.=|+.-+-..=+.-+...|=               -+++.+|=. -+
T Consensus       309 ~~IGATT~~EYrk~iEk---D~AL~RRFq~V~V~EPs~e~t~~IL~gl~~~yE~~H~V~i~d~Ai~aav~LS~RYi~-dr  384 (823)
T CHL00095        309 QCIGATTLEEYRKHIEK---DPALERRFQPVYVGEPSVEETIEILLGLRDRYEKHHNLSISDKALEAAAKLSDQYIK-DR  384 (823)
T ss_pred             EEEEECCHHHHHHHHHC---CHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHCC-CC
T ss_conf             69970788999998530---588996268410289987999999999999998750885047899999998776403-77


Q ss_pred             CCCCCCCCC---------CCCCCCCCCHHHHHHHHHHHH
Q ss_conf             211111000---------122338986899999999998
Q gi|254780916|r  340 SISDKALSL---------LTKYPWIDNVQELKNILLRAV  369 (482)
Q Consensus       340 ~ls~~a~~~---------L~~y~WPGNvREL~n~i~r~~  369 (482)
                      .+++.|+.+         +..+..|..+.+++.-+..+.
T Consensus       385 ~LPDKAIDllDeA~A~~~~~~~~~~~~~~~~~~~~~~~~  423 (823)
T CHL00095        385 FLPDKAIDLLDEAGSRVRLINKQLPPAARELDKELRHIL  423 (823)
T ss_pred             CCCHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHH
T ss_conf             782178888999989999873258678999999999999


No 173
>PRK08853 DNA polymerase III subunits gamma and tau; Validated
Probab=98.28  E-value=2.8e-05  Score=56.97  Aligned_cols=222  Identities=14%  Similarity=0.170  Sum_probs=123.3

Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCCCHHHHHHHHHHHCCCC----CCCCCC-CCCCCCCCCCCCH
Q ss_conf             21111111122222222222222223443204887327774367999999842675----433210-1234655421002
Q gi|254780916|r  134 NEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHESGKR----AFFPFF-IVNCGMIDQDKIE  208 (482)
Q Consensus       134 ~~~~~~~~LiG~S~~m~~v~~~i~~~a~~~~~vli~Ge~GtGK~~~A~~iH~~s~r----~~~~fi-~v~c~~~~~~~~e  208 (482)
                      -....|..+||+.-..+.+...+.. .....--|++|..||||+.+||.+-..-.-    ...|-- --+|..+....+-
T Consensus        10 ~RP~~f~e~vGQ~~v~~~L~nal~~-~rl~haylf~G~rGvGKTt~ARi~Ak~lNC~~~~~~~pcg~C~~C~~i~~g~~~   88 (717)
T PRK08853         10 WRPTQFKEVVGQSHVLTALENALAH-NRLHHAYLFSGTRGVGKTTIGRLFAKGLNCETGITSTPCGQCATCKEIDEGRFV   88 (717)
T ss_pred             HCCCCHHHHCCCHHHHHHHHHHHHC-CCCCCEEEEECCCCCCHHHHHHHHHHHHCCCCCCCCCCCCCCCCHHHHHCCCCC
T ss_conf             1798565513859999999999970-997405761088988898999999998678999999978887026767447877


Q ss_pred             HHHHCCCCCC-CCCCCCCCCCCCCC-------CCCEEEECCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCEEEEE
Q ss_conf             4331125555-32211100123446-------671475166420018899988887764200112355321234315652
Q gi|254780916|r  209 KFLFGDVDLQ-TKNSAQFLGKFIEA-------NGGTIVLEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFL  280 (482)
Q Consensus       209 ~~lFG~~~~~-~~~~~~~~g~~~~a-------~~Gtl~l~ei~~L~~~~Q~~Ll~~l~~~~~~~~g~~~~~~~~~RiIa~  280 (482)
                      ..+  +.++. .....+-.-+++.+       .--..+|||+|-|+......||..|++.           +-+|.+|.+
T Consensus        89 d~~--EiDaAs~~~vdd~rel~~~~~y~p~~~~yKvyiiDEvHmls~~afnAlLKtlEEP-----------P~hv~Fila  155 (717)
T PRK08853         89 DLL--EIDAASRTKVEDTRELLDNVQYKPARGRFKVYLIDEVHMLSRHSFNALLKTLEEP-----------PEYVKFLLA  155 (717)
T ss_pred             CEE--EECCCCCCCHHHHHHHHHHCCCCCCCCCEEEEEEECHHHCCHHHHHHHHHHHCCC-----------CCCEEEEEE
T ss_conf             524--5405656788999999985554887785479998305443899999998760378-----------756489984


Q ss_pred             CCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCHHH
Q ss_conf             14332111111233379998865433446778774422225566777641011223333211111000122338986899
Q gi|254780916|r  281 TEKNLLPQVKSHVFRKDLYYRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQE  360 (482)
Q Consensus       281 t~~~L~~~~~~g~fr~dLy~rL~~~~i~iPpLReR~eDI~~L~~~fl~~~~~~~~~~~~~ls~~a~~~L~~y~WPGNvRE  360 (482)
                      |+.. .++- .-.+.+=+-|.|..+.         .++|   +.| |.....+.+   ..++++|+.++.... -|-+|.
T Consensus       156 TT~~-~kip-~TilSRc~~f~l~~~~---------~~~i---~~~-l~~i~~~E~---i~~~~~al~~ia~~a-~Gs~Rd  216 (717)
T PRK08853        156 TTDP-QKLP-VTILSRCLQFHLKPIS---------VDQI---HQQ-LDFVLDKEQ---VSAEARALGLIAHAA-DGSMRD  216 (717)
T ss_pred             CCCH-HHCC-HHHHHHHHHCCCCCCC---------HHHH---HHH-HHHHHHHCC---CCCCHHHHHHHHHHC-CCCHHH
T ss_conf             3873-4373-8898765442326899---------9999---999-999999759---876999999999976-883778


Q ss_pred             HHHHHHHHHHHCCCCCCCHHHHHHHHCCC
Q ss_conf             99999999874389810688954542124
Q gi|254780916|r  361 LKNILLRAVIGLKDSHLTEDRFVLLLSRE  389 (482)
Q Consensus       361 L~n~i~r~~i~~~~~~i~~~~~~~~l~~~  389 (482)
                      =-+++.+++... ++.++.+++..-++..
T Consensus       217 alsl~dqaia~~-~g~~~~~~v~~mlg~~  244 (717)
T PRK08853        217 ALSLTDQAIALG-NGQVTTDIVSHMLGTL  244 (717)
T ss_pred             HHHHHHHHHHHC-CCCCCHHHHHHHHCCC
T ss_conf             888999999965-8971699999985888


No 174
>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=98.28  E-value=3.4e-06  Score=63.38  Aligned_cols=226  Identities=12%  Similarity=0.105  Sum_probs=116.4

Q ss_pred             CCCCCCCCCCCCCCCCCCCC-CCEEEEEECCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCC-CCHHH--HHCCCCC
Q ss_conf             12222222222222222344-32048873277743679999998426754332101234655421-00243--3112555
Q gi|254780916|r  142 LIAVSPAMIQVVDLARKAGD-CAIPIMIQGEFGVGKKRLSRFIHESGKRAFFPFFIVNCGMIDQD-KIEKF--LFGDVDL  217 (482)
Q Consensus       142 LiG~S~~m~~v~~~i~~~a~-~~~~vli~Ge~GtGK~~~A~~iH~~s~r~~~~fi~v~c~~~~~~-~~e~~--lFG~~~~  217 (482)
                      +.=.|+.-+++...+.-... ....++|+||.||||+++.|.+=..-....-.++.+....++.. ++..-  -||..-.
T Consensus        21 ~~y~s~~h~~al~~L~~~l~~~~g~~lltGe~GtGKTtllr~l~~~l~~~~~~~~~i~~~~l~~~~ll~~i~~~lg~~~~  100 (269)
T TIGR03015        21 FFYPSKGHKRAMAYLEYGLSQREGFILITGEVGAGKTTLIRNLLKRLDQERVVAAKLVNTRVDAEDLLRMVAADFGLETE  100 (269)
T ss_pred             HCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCCCCHHHHHHHHHHHCCCCCEEEEEECCCCCCHHHHHHHHHHHCCCCCC
T ss_conf             41478669999999999996489659997299898899999999845934548999769999999999999998598988


Q ss_pred             CCC--CCCCCC-C-CCCCC---CCCEEEECCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCEEEEECCCCCCCCCC
Q ss_conf             532--211100-1-23446---6714751664200188999888877642001123553212343156521433211111
Q gi|254780916|r  218 QTK--NSAQFL-G-KFIEA---NGGTIVLEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVK  290 (482)
Q Consensus       218 ~~~--~~~~~~-g-~~~~a---~~Gtl~l~ei~~L~~~~Q~~Ll~~l~~~~~~~~g~~~~~~~~~RiIa~t~~~L~~~~~  290 (482)
                      ..+  ...+.. . +.+..   ..-.|++||-+.||.+.=..| |.|-+-+.   ++.+    -+.+|-.-...|.+...
T Consensus       101 ~~~~~~~~~~l~~~L~~~~~~g~~~vliIDEAq~L~~~~Le~L-r~L~n~e~---~~~~----ll~iiL~GqpeL~~~L~  172 (269)
T TIGR03015       101 GRDKAALLRELEDFLIEQFAAGKRALLVVDEAQNLTPELLEEL-RMLSNFQT---DNAK----LLQIFLVGQPEFRETLQ  172 (269)
T ss_pred             CCCHHHHHHHHHHHHHHHHHCCCCEEEEEECHHHCCHHHHHHH-HHHHCCCC---CCCC----CEEEEEECCHHHHHHHC
T ss_conf             9899999999999999999669946999724221999999999-99970135---8887----04899957867999872


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCC-CCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHH
Q ss_conf             1233379998865433446778774422225566777641011223-333211111000122338986899999999998
Q gi|254780916|r  291 SHVFRKDLYYRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAI-KQISISDKALSLLTKYPWIDNVQELKNILLRAV  369 (482)
Q Consensus       291 ~g~fr~dLy~rL~~~~i~iPpLReR~eDI~~L~~~fl~~~~~~~~~-~~~~ls~~a~~~L~~y~WPGNvREL~n~i~r~~  369 (482)
                      ...++. |-.|++ ..++++||.  ++|...-++|=++..    |. ...-|+++|++.+..+. -|+-|..-++|.+++
T Consensus       173 ~~~~~~-l~qRI~-~~~~L~pl~--~eet~~YI~~RL~~A----G~~~~~~Ft~~A~~~I~~~S-~G~PR~IN~Lc~~aL  243 (269)
T TIGR03015       173 SPQLQQ-LRQRII-ASCHLGPLD--REETREYIEHRLERA----GNRDAPVFSEGAFDAIHRFS-RGIPRLINILCDRLL  243 (269)
T ss_pred             CCCHHH-HHHCEE-EEEEECCCC--HHHHHHHHHHHHHHC----CCCCCCCCCHHHHHHHHHHC-CCCHHHHHHHHHHHH
T ss_conf             740254-555076-799847999--899999999999866----99999985999999999986-990089999999999


Q ss_pred             H---HCCCCCCCHHHHHH
Q ss_conf             7---43898106889545
Q gi|254780916|r  370 I---GLKDSHLTEDRFVL  384 (482)
Q Consensus       370 i---~~~~~~i~~~~~~~  384 (482)
                      +   ......|+.+.+..
T Consensus       244 l~a~~~~~~~I~~~~v~~  261 (269)
T TIGR03015       244 LSAFLEEKREIGGEEVRE  261 (269)
T ss_pred             HHHHHHCCCCCCHHHHHH
T ss_conf             999994888679999999


No 175
>KOG0478 consensus
Probab=98.27  E-value=3.4e-06  Score=63.38  Aligned_cols=116  Identities=13%  Similarity=0.192  Sum_probs=76.9

Q ss_pred             CCCEEEEEECCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCHHHHHCCCCCCCCCCCCCCCCCCCCCCCEEEEC
Q ss_conf             43204887327774367999999842675433210123465542100243311255553221110012344667147516
Q gi|254780916|r  161 DCAIPIMIQGEFGVGKKRLSRFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFGDVDLQTKNSAQFLGKFIEANGGTIVLE  240 (482)
Q Consensus       161 ~~~~~vli~Ge~GtGK~~~A~~iH~~s~r~~~~fi~v~c~~~~~~~~e~~lFG~~~~~~~~~~~~~g~~~~a~~Gtl~l~  240 (482)
                      .++.+||+.|.+||||+.+=+++|..++|.  .+..=-.    ...+.-+..=-+++.|+-..-..|.+-.++||..+||
T Consensus       460 R~~INILL~GDPGtsKSqlLqyv~~l~pRg--~yTSGkG----sSavGLTayVtrd~dtkqlVLesGALVLSD~GiCCID  533 (804)
T KOG0478         460 RGDINILLVGDPGTSKSQLLQYCHRLLPRG--VYTSGKG----SSAVGLTAYVTKDPDTRQLVLESGALVLSDNGICCID  533 (804)
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHHHHCCCC--EEECCCC----CCHHCCEEEEEECCCCCEEEEECCCEEECCCCEEECH
T ss_conf             455228994699867899999999747754--0405876----3022003567765765546650484897289657711


Q ss_pred             CCCHHHHHHHHHHHHHHHHHHCCCC--CCCCCCCCCCEEEEECC
Q ss_conf             6420018899988887764200112--35532123431565214
Q gi|254780916|r  241 EPDALPLAVQGRIYNFIETGKIEFF--DSRGAIRLDVRLIFLTE  282 (482)
Q Consensus       241 ei~~L~~~~Q~~Ll~~l~~~~~~~~--g~~~~~~~~~RiIa~t~  282 (482)
                      |.+.|+-+.|.-|+.++|.+.+.--  |--......+-|+|+.|
T Consensus       534 EFDKM~dStrSvLhEvMEQQTvSIAKAGII~sLNAR~SVLAaAN  577 (804)
T KOG0478         534 EFDKMSDSTRSVLHEVMEQQTLSIAKAGIIASLNARCSVLAAAN  577 (804)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHCCEEEECCCCCEEEEEEC
T ss_conf             23333277889999999876311743022342166530344535


No 176
>PRK10865 protein disaggregation chaperone; Provisional
Probab=98.27  E-value=1.3e-06  Score=66.38  Aligned_cols=200  Identities=13%  Similarity=0.190  Sum_probs=105.5

Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCCCHHHHHHHHHHHCC---C----CCCCCCCCCCCCCCCCCCC
Q ss_conf             11111111222222222222222234432048873277743679999998426---7----5433210123465542100
Q gi|254780916|r  135 EHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHESG---K----RAFFPFFIVNCGMIDQDKI  207 (482)
Q Consensus       135 ~~~~~~~LiG~S~~m~~v~~~i~~~a~~~~~vli~Ge~GtGK~~~A~~iH~~s---~----r~~~~fi~v~c~~~~~~~~  207 (482)
                      .....+++||....++++.+-++|  .+.-+.++.||+|+||+.++..+-..=   .    -++...+.+|.+++-    
T Consensus       173 ~~gkldpvIGRd~EI~r~i~IL~R--R~KNNpiLvGepGVGKTAIvEGLA~rI~~g~VP~~L~~~~I~~LDlg~L~----  246 (857)
T PRK10865        173 EQGKLDPVIGRDEEIRRTIQVLQR--RTKNNPVLIGEPGVGKTAIVEGLAQRIINGEVPEGLKGRRVLALDMGALV----  246 (857)
T ss_pred             HCCCCCCCCCCHHHHHHHHHHHHC--CCCCCCEEECCCCCCHHHHHHHHHHHHHCCCCCHHHCCCCEEEEEHHHHH----
T ss_conf             829999885829999999999702--57899758789998899999999999983899978816902473388786----


Q ss_pred             HHHHHCCCCCCCCCCCCCC-CCCCC---C-CCCEEEECCCCHH--------HHHHHHHHHHHHHHHHCCCCCCCCCCCCC
Q ss_conf             2433112555532211100-12344---6-6714751664200--------18899988887764200112355321234
Q gi|254780916|r  208 EKFLFGDVDLQTKNSAQFL-GKFIE---A-NGGTIVLEEPDAL--------PLAVQGRIYNFIETGKIEFFDSRGAIRLD  274 (482)
Q Consensus       208 e~~lFG~~~~~~~~~~~~~-g~~~~---a-~~Gtl~l~ei~~L--------~~~~Q~~Ll~~l~~~~~~~~g~~~~~~~~  274 (482)
                          =|-+  +-|....|. ..+.+   . .+-.||+||||.+        +.+.-.-|--+|..|             +
T Consensus       247 ----AGak--yRGeFEeRLk~il~ev~~~~~~iILFIDEiHtlvGaG~~~G~~DaaNlLKPaLaRG-------------e  307 (857)
T PRK10865        247 ----AGAK--YRGEFEERLKGVLNDLAKQEGNVILFIDELHTMVGAGKADGAMDAGNMLKPALARG-------------E  307 (857)
T ss_pred             ----HCCC--CCHHHHHHHHHHHHHHHHCCCCEEEEECCHHHHCCCCCCCCCCCHHHHHHHHHHCC-------------C
T ss_conf             ----1476--52117999999999998478986999734354336887777534788867887379-------------8


Q ss_pred             CEEEEECCCCCCCCCCHHHHHH------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---------------HHHCCC
Q ss_conf             3156521433211111123337------9998865433446778774422225566777---------------641011
Q gi|254780916|r  275 VRLIFLTEKNLLPQVKSHVFRK------DLYYRISVFLINISTLRSRSEDIPWLVHFFL---------------QSFCTK  333 (482)
Q Consensus       275 ~RiIa~t~~~L~~~~~~g~fr~------dLy~rL~~~~i~iPpLReR~eDI~~L~~~fl---------------~~~~~~  333 (482)
                      +|+|++|+.+        .||+      -|=-|...+.|.=|+--+-.+=+.-+...|=               -+++.+
T Consensus       308 lr~IGATT~~--------EYrk~iEkD~AL~RRFq~V~V~EPs~e~ti~ILrgl~~~yE~hH~V~itdeAl~aAV~LS~R  379 (857)
T PRK10865        308 LHCVGATTLD--------EYRQYIEKDAALERRFQKVFVAEPSVEDTIAILRGLKERYELHHHVQITDPAIVAAATLSHR  379 (857)
T ss_pred             CEEEEECCHH--------HHHHHCCCCHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHCCCCEECHHHHHHHHHHHHC
T ss_conf             5499945899--------99987134588998537100689987999999998888998737915879999999998624


Q ss_pred             CCCCCCCCCCCCCCC---------CCCCCCCCCHHHHHHHHHHH
Q ss_conf             223333211111000---------12233898689999999999
Q gi|254780916|r  334 NAIKQISISDKALSL---------LTKYPWIDNVQELKNILLRA  368 (482)
Q Consensus       334 ~~~~~~~ls~~a~~~---------L~~y~WPGNvREL~n~i~r~  368 (482)
                      |= +-+.+++.|+.+         +.....|..+.+|++-+..+
T Consensus       380 YI-~dR~LPDKAIDLLDeA~A~vr~~~~~~p~~l~~l~~~i~~l  422 (857)
T PRK10865        380 YI-ADRQLPDKAIDLIDEAASSIRMQIDSKPEELDRLDRRIIQL  422 (857)
T ss_pred             CC-CCCCCCHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHH
T ss_conf             56-66678148988999998888763246844689999999999


No 177
>PRK05201 hslU ATP-dependent protease ATP-binding subunit; Provisional
Probab=98.26  E-value=2.6e-06  Score=64.24  Aligned_cols=128  Identities=14%  Similarity=0.258  Sum_probs=66.6

Q ss_pred             CCCEEEECCCCHHH------------HHHHHHHHHHHHHHHCC-CCCCCCCCCCCCEEEEECCCCCCCCCCHHHHHHHHH
Q ss_conf             67147516642001------------88999888877642001-123553212343156521433211111123337999
Q gi|254780916|r  233 NGGTIVLEEPDALP------------LAVQGRIYNFIETGKIE-FFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLY  299 (482)
Q Consensus       233 ~~Gtl~l~ei~~L~------------~~~Q~~Ll~~l~~~~~~-~~g~~~~~~~~~RiIa~t~~~L~~~~~~g~fr~dLy  299 (482)
                      +.|.+|||||+.+.            ..+|.-||..++-..+. +.|  .-.+-++-+||+---+   .+.-.-+-++|-
T Consensus       248 q~GIVFIDEIDKIa~~~~~~g~DVS~EGVQrdLLpivEGt~V~tK~G--~V~TdhILFIasGAFh---~sKPSDLIPEl~  322 (442)
T PRK05201        248 QNGIVFIDEIDKIAKRGEGSGPDVSREGVQRDLLPLVEGSTVSTKYG--MVKTDHILFIASGAFH---VAKPSDLIPELQ  322 (442)
T ss_pred             HCCCEEECHHHHHHCCCCCCCCCCCCHHHHHHHHHHHCCCCCCCCCC--CCCCCEEEEECCCCCC---CCCCCHHHHHHC
T ss_conf             61704511465653035788989773307888788753885556777--6025503455045001---478202249871


Q ss_pred             HHHHHHHHHHHHHHHHHHHHH--------HHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCC-------CHHHHHHH
Q ss_conf             886543344677877442222--------556677764101122333321111100012233898-------68999999
Q gi|254780916|r  300 YRISVFLINISTLRSRSEDIP--------WLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWID-------NVQELKNI  364 (482)
Q Consensus       300 ~rL~~~~i~iPpLReR~eDI~--------~L~~~fl~~~~~~~~~~~~~ls~~a~~~L~~y~WPG-------NvREL~n~  364 (482)
                      -||-+ .+.+-||-  .+|+-        .|+..|-.-|..+ |.. ..|+++|+..+....+--       --|-|+.+
T Consensus       323 GRlPv-~v~L~~L~--~~dl~~ILtepknsL~kQy~~Lf~~e-gv~-L~Ft~~Al~~IA~~A~~~n~~~~~iGAR~L~tI  397 (442)
T PRK05201        323 GRFPI-RVELDALT--EEDFVRILTEPKASLIKQYQALLATE-GVT-LEFTDDAIRRIAEIAYQVNEKTENIGARRLHTV  397 (442)
T ss_pred             CCCEE-EEECCCCC--HHHHHHHHCCCCHHHHHHHHHHHHHC-CCE-EEECHHHHHHHHHHHHHHCCCCCCCCHHHHHHH
T ss_conf             75505-88824499--99999996786157899999998624-967-998479999999999985144766773788999


Q ss_pred             HHHHHH
Q ss_conf             999987
Q gi|254780916|r  365 LLRAVI  370 (482)
Q Consensus       365 i~r~~i  370 (482)
                      +++++.
T Consensus       398 ~E~vl~  403 (442)
T PRK05201        398 MEKLLE  403 (442)
T ss_pred             HHHHHH
T ss_conf             999989


No 178
>PRK06647 DNA polymerase III subunits gamma and tau; Validated
Probab=98.25  E-value=1e-05  Score=60.02  Aligned_cols=221  Identities=18%  Similarity=0.166  Sum_probs=125.9

Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCCCHHHHHHHHHHHCCCCCC----CCC-CCCCCCCCCCCCCH
Q ss_conf             2111111112222222222222222344320488732777436799999984267543----321-01234655421002
Q gi|254780916|r  134 NEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHESGKRAF----FPF-FIVNCGMIDQDKIE  208 (482)
Q Consensus       134 ~~~~~~~~LiG~S~~m~~v~~~i~~~a~~~~~vli~Ge~GtGK~~~A~~iH~~s~r~~----~~f-i~v~c~~~~~~~~e  208 (482)
                      -....|+.++|+....+.+...+.. ......-|+.|+.||||+.+||.+-..=.-.+    .|- .--+|..+.....-
T Consensus        10 YRP~~F~dvvGQe~vv~~L~nai~~-~rl~HAyLFsGprG~GKTt~ArilAk~LnC~~~~~~~PCg~C~sC~~i~~g~~~   88 (560)
T PRK06647         10 RRPRDFNSLEGQDFVVETLKHSIEK-NKIANAYIFSGPRGVGKTSSARAFARCLNCVNGPTIMPCGECFSCKSIDNDSSL   88 (560)
T ss_pred             HCCCCHHHHCCCHHHHHHHHHHHHC-CCCCCEEEEECCCCCCHHHHHHHHHHHHCCCCCCCCCCCCCCHHHHHHHCCCCC
T ss_conf             2898654403949999999999974-997743663289987899999999999659999998888788788887459998


Q ss_pred             HHHHCCCCCC--CCCCCCCCCCCCC-------CCCCEEEECCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCEEEE
Q ss_conf             4331125555--3221110012344-------667147516642001889998888776420011235532123431565
Q gi|254780916|r  209 KFLFGDVDLQ--TKNSAQFLGKFIE-------ANGGTIVLEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIF  279 (482)
Q Consensus       209 ~~lFG~~~~~--~~~~~~~~g~~~~-------a~~Gtl~l~ei~~L~~~~Q~~Ll~~l~~~~~~~~g~~~~~~~~~RiIa  279 (482)
                      . ++ +.+++  ++-..-| .+.+.       +..-..+|||++.|+...|..||+.|++.           +.++++|.
T Consensus        89 D-vi-Eidaasn~~VddIR-~l~e~v~~~P~~~~yKV~IIDEahmLt~~A~NALLKtLEEP-----------P~~~~FIL  154 (560)
T PRK06647         89 D-VI-EIDGASNTSVQDVR-QIKEEIMFPPASSRYRVYIIDEVHMLSNSAFNALLKTIEEP-----------PPYIVFIF  154 (560)
T ss_pred             C-EE-EECCCCCCCHHHHH-HHHHHHCCCCCCCCEEEEEECCHHHCCHHHHHHHHHHHHCC-----------CCCEEEEE
T ss_conf             7-57-64364548889999-99998632876687069996465655999999999986348-----------87559999


Q ss_pred             ECCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCHH
Q ss_conf             21433211111123337999886543344677877442222556677764101122333321111100012233898689
Q gi|254780916|r  280 LTEKNLLPQVKSHVFRKDLYYRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQ  359 (482)
Q Consensus       280 ~t~~~L~~~~~~g~fr~dLy~rL~~~~i~iPpLReR~eDI~~L~~~fl~~~~~~~~~~~~~ls~~a~~~L~~y~WPGNvR  359 (482)
                      +|+.. ..+..      -..-|  +-.+...||.+  +||   +.| |+..+.+.+   ..++++|+.++.... -|-+|
T Consensus       155 aTte~-~KI~~------TI~SR--CQ~f~Fk~i~~--~~I---~~~-L~~I~~~E~---i~~e~~AL~lIa~~a-~Gs~R  215 (560)
T PRK06647        155 ATTEV-HKLPA------TIKSR--CQHFNFRLLSL--EKI---YEM-LKKVCLEDD---IKYEDEALKWIAYKS-GGSVR  215 (560)
T ss_pred             ECCCH-HHCHH------HHHHH--HEEEECCCCCH--HHH---HHH-HHHHHHHCC---CCCCHHHHHHHHHHC-CCCHH
T ss_conf             77994-76848------99965--10410555999--999---999-999998679---887999999999977-89588


Q ss_pred             HHHHHHHHHHHHCCCCCCCHHHHHHHHCCC
Q ss_conf             999999999874389810688954542124
Q gi|254780916|r  360 ELKNILLRAVIGLKDSHLTEDRFVLLLSRE  389 (482)
Q Consensus       360 EL~n~i~r~~i~~~~~~i~~~~~~~~l~~~  389 (482)
                      .=-+++.+++..+ ++.|+.+++...++-.
T Consensus       216 Dalslldq~i~~~-~~~i~~~~v~~~lG~~  244 (560)
T PRK06647        216 DAYTLFDQIVSFS-NSDITLEQIRSKMGLT  244 (560)
T ss_pred             HHHHHHHHHHHCC-CCCCCHHHHHHHHCCC
T ss_conf             8999999999607-9977899999986898


No 179
>PRK06674 DNA polymerase III subunits gamma and tau; Validated
Probab=98.25  E-value=4.8e-06  Score=62.34  Aligned_cols=211  Identities=15%  Similarity=0.235  Sum_probs=112.3

Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCCCHHHHHHHHHHHCCCC----CCCCCC-CCCCCCCC----CC
Q ss_conf             1111111122222222222222223443204887327774367999999842675----433210-12346554----21
Q gi|254780916|r  135 EHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHESGKR----AFFPFF-IVNCGMID----QD  205 (482)
Q Consensus       135 ~~~~~~~LiG~S~~m~~v~~~i~~~a~~~~~vli~Ge~GtGK~~~A~~iH~~s~r----~~~~fi-~v~c~~~~----~~  205 (482)
                      ....|++++|+....+.+...+. -.....--|+.|+.||||+.+||.+-..=.-    ...|-- --+|..+.    .+
T Consensus        11 RP~~F~dvvGQ~~v~~~L~nai~-~~ri~HAyLF~GprGtGKts~Ari~AkaLnC~~~~~~~pC~~C~~C~~i~~g~~~D   89 (563)
T PRK06674         11 RPQKFEDVVGQEHVTKTLQNALL-QEKVSHAYLFSGPRGTGKTSIAKVFAKAVNCEHAPVAEPCNECPSCLGITNGSISD   89 (563)
T ss_pred             CCCCHHHHCCHHHHHHHHHHHHH-CCCCCCEEEEECCCCCCHHHHHHHHHHHHCCCCCCCCCCCCCCHHHHHHHCCCCCC
T ss_conf             89976552480999999999998-49965034312899868999999999985799999988776687899985589987


Q ss_pred             CCHHHHHCCCCCCCCCCCCCCC------CCC--CCCCCEEEECCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCEE
Q ss_conf             0024331125555322111001------234--46671475166420018899988887764200112355321234315
Q gi|254780916|r  206 KIEKFLFGDVDLQTKNSAQFLG------KFI--EANGGTIVLEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRL  277 (482)
Q Consensus       206 ~~e~~lFG~~~~~~~~~~~~~g------~~~--~a~~Gtl~l~ei~~L~~~~Q~~Ll~~l~~~~~~~~g~~~~~~~~~Ri  277 (482)
                      .+|      .++......+.+-      .+.  .+..-..++||++.|+...+..||..|++.           +.++.+
T Consensus        90 viE------iDaasn~gVd~IR~i~~~v~~~P~~~~yKV~IIDeah~Lt~~A~NALLKtLEEP-----------P~~viF  152 (563)
T PRK06674         90 VLE------IDAASNNGVDEIRDIRDKVKFAPSAVEYKVYIIDEVHMLSIGAFNALLKTLEEP-----------PGHVIF  152 (563)
T ss_pred             EEE------ECCCCCCCHHHHHHHHHHHCCCCCCCCEEEEEEECHHHCCHHHHHHHHHHHHCC-----------CCCEEE
T ss_conf             798------525555787999999998264886787379998545637999999999986388-----------756499


Q ss_pred             EEECCCCCCCCC-----CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             652143321111-----112333799988654334467787744222255667776410112233332111110001223
Q gi|254780916|r  278 IFLTEKNLLPQV-----KSHVFRKDLYYRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKY  352 (482)
Q Consensus       278 Ia~t~~~L~~~~-----~~g~fr~dLy~rL~~~~i~iPpLReR~eDI~~L~~~fl~~~~~~~~~~~~~ls~~a~~~L~~y  352 (482)
                      |.+|+.. ..+.     ...+|+   |     -.|..       +|   ++.+ |...+.+.|.   .++++|+.++...
T Consensus       153 ILaTtep-~ki~~TI~SRCQrf~---F-----~ri~~-------~~---i~~r-L~~I~~~E~i---~~~~~aL~~Ia~~  209 (563)
T PRK06674        153 ILATTEP-HKIPPTIISRCQRFD---F-----RRISV-------ND---IVER-LSTVVTNEGT---QVEDEALQIIARA  209 (563)
T ss_pred             EEECCCH-HHCCHHHHHHHEEEE---C-----CCCCH-------HH---HHHH-HHHHHHHCCC---CCCHHHHHHHHHH
T ss_conf             9965994-758478873310312---7-----88999-------99---9999-9999998499---9878899999997


Q ss_pred             CCCCCHHHHHHHHHHHHHHCCCCCCCHHHHHHHHCC
Q ss_conf             389868999999999987438981068895454212
Q gi|254780916|r  353 PWIDNVQELKNILLRAVIGLKDSHLTEDRFVLLLSR  388 (482)
Q Consensus       353 ~WPGNvREL~n~i~r~~i~~~~~~i~~~~~~~~l~~  388 (482)
                      . -|-+|.=-+++.+++..+ ++.|+.+++...++.
T Consensus       210 a-~GsmRDAlsiLdQ~~s~~-~~~i~~~~v~~~lG~  243 (563)
T PRK06674        210 A-DGGMRDALSLLDQAISFS-DERVTTEDVLAVTGA  243 (563)
T ss_pred             C-CCCHHHHHHHHHHHHHHC-CCCCCHHHHHHHHCC
T ss_conf             6-997889999999999715-997689999998689


No 180
>KOG0745 consensus
Probab=98.24  E-value=1.5e-06  Score=66.01  Aligned_cols=94  Identities=21%  Similarity=0.297  Sum_probs=67.9

Q ss_pred             CCCEEEEEECCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCC-----CCHHHHHCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             432048873277743679999998426754332101234655421-----002433112555532211100123446671
Q gi|254780916|r  161 DCAIPIMIQGEFGVGKKRLSRFIHESGKRAFFPFFIVNCGMIDQD-----KIEKFLFGDVDLQTKNSAQFLGKFIEANGG  235 (482)
Q Consensus       161 ~~~~~vli~Ge~GtGK~~~A~~iH~~s~r~~~~fi~v~c~~~~~~-----~~e~~lFG~~~~~~~~~~~~~g~~~~a~~G  235 (482)
                      -..++||+.|++|+||+++|+.+-..-   +-||+..||.+++..     -+|+-+--   -    ...-.+-.|+|..|
T Consensus       224 LeKSNvLllGPtGsGKTllaqTLAr~l---dVPfaIcDcTtLTQAGYVGeDVEsvi~K---L----l~~A~~nVekAQqG  293 (564)
T KOG0745         224 LEKSNVLLLGPTGSGKTLLAQTLARVL---DVPFAICDCTTLTQAGYVGEDVESVIQK---L----LQEAEYNVEKAQQG  293 (564)
T ss_pred             EECCCEEEECCCCCCHHHHHHHHHHHH---CCCEEEECCCCHHHCCCCCCCHHHHHHH---H----HHHCCCCHHHHHCC
T ss_conf             403547997788876438999999970---8876873255220055345429999999---9----99725789988267


Q ss_pred             EEEECCCCHHH--------------HHHHHHHHHHHHHHHCCCC
Q ss_conf             47516642001--------------8899988887764200112
Q gi|254780916|r  236 TIVLEEPDALP--------------LAVQGRIYNFIETGKIEFF  265 (482)
Q Consensus       236 tl~l~ei~~L~--------------~~~Q~~Ll~~l~~~~~~~~  265 (482)
                      .+|||||+.+.              .-+|..||.+|+- .+--|
T Consensus       294 IVflDEvDKi~~~~~~i~~~RDVsGEGVQQaLLKllEG-tvVnV  336 (564)
T KOG0745         294 IVFLDEVDKITKKAESIHTSRDVSGEGVQQALLKLLEG-TVVNV  336 (564)
T ss_pred             EEEEEHHHHHCCCCCCCCCCCCCCCHHHHHHHHHHHCC-CEECC
T ss_conf             38876012441367654544456626699999998526-27702


No 181
>PRK07994 DNA polymerase III subunits gamma and tau; Validated
Probab=98.24  E-value=3.9e-05  Score=55.91  Aligned_cols=222  Identities=14%  Similarity=0.214  Sum_probs=118.1

Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCCCHHHHHHHHHHHCCCCCCC----CC-CCCCCCCCCCCCCH
Q ss_conf             21111111122222222222222223443204887327774367999999842675433----21-01234655421002
Q gi|254780916|r  134 NEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHESGKRAFF----PF-FIVNCGMIDQDKIE  208 (482)
Q Consensus       134 ~~~~~~~~LiG~S~~m~~v~~~i~~~a~~~~~vli~Ge~GtGK~~~A~~iH~~s~r~~~----~f-i~v~c~~~~~~~~e  208 (482)
                      .....|+.++|+.-..+.+...+.. ......-|++|..|+||+.+||.+-..-.-.++    |- .--+|..+....+-
T Consensus        10 ~Rp~~f~~~vGQ~~v~~~l~na~~~-~r~~haylf~G~rG~GKtt~ari~ak~lnc~~~~~~~pcg~c~~c~~i~~g~~~   88 (643)
T PRK07994         10 WRPQTFADVVGQEHVLTALANGLSL-GRIHHAYLFSGTRGVGKTSIARLLAKGLNCETGITATPCGVCDNCREIEQGRFV   88 (643)
T ss_pred             HCCCCHHHHCCCHHHHHHHHHHHHH-CCCCCEEEEECCCCCCHHHHHHHHHHHHCCCCCCCCCCCCCCHHHHHHHCCCCC
T ss_conf             2888666653879999999999982-986634874589988888999999999679999999978767768988658988


Q ss_pred             HHHHCCCCCC-CCCCCCCCCCCCCC-------CCCEEEECCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCEEEEE
Q ss_conf             4331125555-32211100123446-------671475166420018899988887764200112355321234315652
Q gi|254780916|r  209 KFLFGDVDLQ-TKNSAQFLGKFIEA-------NGGTIVLEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFL  280 (482)
Q Consensus       209 ~~lFG~~~~~-~~~~~~~~g~~~~a-------~~Gtl~l~ei~~L~~~~Q~~Ll~~l~~~~~~~~g~~~~~~~~~RiIa~  280 (482)
                      . ++ +.++. .....+-..+++.+       .--..++||+|-|+...+.-||..|++.           +.++.+|.+
T Consensus        89 d-~~-eidaas~~~vd~~rel~~~~~y~p~~~r~kvyiidEvhmls~~afnalLKtlEeP-----------p~hv~fila  155 (643)
T PRK07994         89 D-LI-EIDAASRTKVEDTRDLLDNVQYAPARGRFKVYLIDEVHMLSRHSFNALLKTLEEP-----------PAHVKFLLA  155 (643)
T ss_pred             C-EE-EEECCCCCCHHHHHHHHHHCCCCCCCCCEEEEEEECHHHCCHHHHHHHHHHHCCC-----------CHHCEEEEE
T ss_conf             7-58-8636777888999999984466887785369997221015899999999862378-----------610089986


Q ss_pred             CCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCHHH
Q ss_conf             14332111111233379998865433446778774422225566777641011223333211111000122338986899
Q gi|254780916|r  281 TEKNLLPQVKSHVFRKDLYYRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQE  360 (482)
Q Consensus       281 t~~~L~~~~~~g~fr~dLy~rL~~~~i~iPpLReR~eDI~~L~~~fl~~~~~~~~~~~~~ls~~a~~~L~~y~WPGNvRE  360 (482)
                      |+.. .++.. -.+.+=+=|-|.  .|          ....++.| |...+.+.+   ..++++|+.++.... -|-+|.
T Consensus       156 TT~~-~k~p~-TilSRC~~f~~~--~~----------~~~~i~~~-l~~i~~~e~---i~~~~~al~~ia~~a-~gs~rd  216 (643)
T PRK07994        156 TTDP-QKLPV-TILSRCLQFHLK--AL----------DVEQIRHQ-LEHILNEEH---IAHEPRALQLLARAA-DGSLRD  216 (643)
T ss_pred             CCCH-HHCCH-HHHHHHHHEECC--CC----------CHHHHHHH-HHHHHHHCC---CCCCHHHHHHHHHHC-CCCHHH
T ss_conf             0774-54847-899777650016--69----------99999999-999999759---987889999999974-786566


Q ss_pred             HHHHHHHHHHHCCCCCCCHHHHHHHHCCC
Q ss_conf             99999999874389810688954542124
Q gi|254780916|r  361 LKNILLRAVIGLKDSHLTEDRFVLLLSRE  389 (482)
Q Consensus       361 L~n~i~r~~i~~~~~~i~~~~~~~~l~~~  389 (482)
                      =-++..+++.. .++.|+.+++...++..
T Consensus       217 alsl~dq~i~~-~~~~~~~~~v~~mlg~~  244 (643)
T PRK07994        217 ALSLTDQAIAS-GDGQVSTQAVSAMLGTL  244 (643)
T ss_pred             HHHHHHHHHHH-CCCCCCHHHHHHHHCCC
T ss_conf             88899999986-58974799999985899


No 182
>TIGR02881 spore_V_K stage V sporulation protein K; InterPro: IPR014232   Proteins in this entry include the stage V sporulation protein K (SpoVK), a close homologue of the Rubisco expression protein CbbX (IPR000470 from INTERPRO), and are members of an ATPase family associated with various cellular activities. These proteins are strictly limited to bacterial endospore-forming species, but are not found universally among members of this group; they are missing from the Clostridium species..
Probab=98.24  E-value=2.6e-06  Score=64.27  Aligned_cols=165  Identities=18%  Similarity=0.252  Sum_probs=102.1

Q ss_pred             CCCEEEEEECCCCCHHHHHHHHHH----HCCCCCCCCCCCCCCCCCCCCCCHHHHHCCCCCCCCCCCCCCCCCCCCCCCE
Q ss_conf             432048873277743679999998----4267543321012346554210024331125555322111001234466714
Q gi|254780916|r  161 DCAIPIMIQGEFGVGKKRLSRFIH----ESGKRAFFPFFIVNCGMIDQDKIEKFLFGDVDLQTKNSAQFLGKFIEANGGT  236 (482)
Q Consensus       161 ~~~~~vli~Ge~GtGK~~~A~~iH----~~s~r~~~~fi~v~c~~~~~~~~e~~lFG~~~~~~~~~~~~~g~~~~a~~Gt  236 (482)
                      ....+.+..|-|||||++|||.|=    +..=-..|.+|.+-=|.         |-|+==|. +|.. ..-.+.+|-||.
T Consensus        40 ~~~LHMiFKGNPGTGKTTVAR~~gklf~emnvL~KGH~iE~ERAD---------LVGEYIGH-TAqk-TRe~~kkA~GGv  108 (261)
T TIGR02881        40 KQVLHMIFKGNPGTGKTTVARLLGKLFKEMNVLSKGHLIEVERAD---------LVGEYIGH-TAQK-TREVIKKALGGV  108 (261)
T ss_pred             CCEEEEEEECCCCCCHHHHHHHHHHHHHHCCCCCCCCEEEEEECC---------CCCCCCCC-HHHH-HHHHHHHHCCCC
T ss_conf             844787742786684389999999998533756788678876222---------12232030-0489-999999863880


Q ss_pred             EEECCCCHHH--------HHHHHHHHHHHHHHHCCCCCCCCCCCCCCEEEEECCCCCCCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf             7516642001--------88999888877642001123553212343156521433211111123337999886543344
Q gi|254780916|r  237 IVLEEPDALP--------LAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYYRISVFLIN  308 (482)
Q Consensus       237 l~l~ei~~L~--------~~~Q~~Ll~~l~~~~~~~~g~~~~~~~~~RiIa~t~~~L~~~~~~g~fr~dLy~rL~~~~i~  308 (482)
                      ||+||==.|+        .+.=.-|++.+++++-           ++=+|.|            -+..+-=|.|+..   
T Consensus       109 LFiDEAYSLaRGGEKDFGKEAIDtLVK~mEd~~~-----------~lvlILA------------GY~~EM~yFL~~N---  162 (261)
T TIGR02881       109 LFIDEAYSLARGGEKDFGKEAIDTLVKAMEDQRN-----------ELVLILA------------GYSDEMDYFLSLN---  162 (261)
T ss_pred             HHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHCCC-----------CEEEEEE------------CCHHHHHHHHHCC---
T ss_conf             0557777761488887662088899998761569-----------8689970------------8768999986207---


Q ss_pred             HHHHHHH-----------HHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCC----CC-----CCCHHHHHHHHHHH
Q ss_conf             6778774-----------4222255667776410112233332111110001223----38-----98689999999999
Q gi|254780916|r  309 ISTLRSR-----------SEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKY----PW-----IDNVQELKNILLRA  368 (482)
Q Consensus       309 iPpLReR-----------~eDI~~L~~~fl~~~~~~~~~~~~~ls~~a~~~L~~y----~W-----PGNvREL~n~i~r~  368 (482)
                       |-|+-|           .|.+..++..++++-       -..||++|...|..|    +|     -||-|=.+|+||+|
T Consensus       163 -PGL~SRFPi~i~FPdY~~eeL~~Ia~~m~~~R-------eY~Lt~~A~~~lr~~l~~~~~~~~~~~sNaR~vRN~iE~A  234 (261)
T TIGR02881       163 -PGLRSRFPISIDFPDYTVEELMEIAERMVKER-------EYKLTEEAKWKLREHLAKVDQLSSREFSNARYVRNIIEKA  234 (261)
T ss_pred             -CCCCCCCCCEEECCCCCHHHHHHHHHHHHHHH-------HHCCCHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHH
T ss_conf             -79777665054188998889999999998646-------4225788999999997412444210057620124288999


Q ss_pred             HH
Q ss_conf             87
Q gi|254780916|r  369 VI  370 (482)
Q Consensus       369 ~i  370 (482)
                      +=
T Consensus       235 IR  236 (261)
T TIGR02881       235 IR  236 (261)
T ss_pred             HH
T ss_conf             99


No 183
>KOG2004 consensus
Probab=98.23  E-value=1.2e-06  Score=66.51  Aligned_cols=176  Identities=22%  Similarity=0.282  Sum_probs=115.2

Q ss_pred             CCEEE-EEECCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCHHHHHCCCCCCCCCCCCCCCCCCC------CCC
Q ss_conf             32048-87327774367999999842675433210123465542100243311255553221110012344------667
Q gi|254780916|r  162 CAIPI-MIQGEFGVGKKRLSRFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFGDVDLQTKNSAQFLGKFIE------ANG  234 (482)
Q Consensus       162 ~~~~v-li~Ge~GtGK~~~A~~iH~~s~r~~~~fi~v~c~~~~~~~~e~~lFG~~~~~~~~~~~~~g~~~~------a~~  234 (482)
                      +.-+| .+.|++|+||+.+||.|-..-.|   .|..+..+++.+.   +++=||+.-+-||-.   |++.+      .+|
T Consensus       436 ~qGkIlCf~GPPGVGKTSI~kSIA~ALnR---kFfRfSvGG~tDv---AeIkGHRRTYVGAMP---GkiIq~LK~v~t~N  506 (906)
T KOG2004         436 VQGKILCFVGPPGVGKTSIAKSIARALNR---KFFRFSVGGMTDV---AEIKGHRRTYVGAMP---GKIIQCLKKVKTEN  506 (906)
T ss_pred             CCCCEEEEECCCCCCCCCHHHHHHHHHCC---CEEEEECCCCCCH---HHHCCCCEEEECCCC---HHHHHHHHHHCCCC
T ss_conf             78837998689987732189999998487---4699853663427---764254211001488---48999998617788


Q ss_pred             CEEEECCCCHHHHHHH----HHHHHHHH---HHHCCCCCCCCCCCCC---CEEEEECCCCCCCCCCHHHHHHHHHHHHHH
Q ss_conf             1475166420018899----98888776---4200112355321234---315652143321111112333799988654
Q gi|254780916|r  235 GTIVLEEPDALPLAVQ----GRIYNFIE---TGKIEFFDSRGAIRLD---VRLIFLTEKNLLPQVKSHVFRKDLYYRISV  304 (482)
Q Consensus       235 Gtl~l~ei~~L~~~~Q----~~Ll~~l~---~~~~~~~g~~~~~~~~---~RiIa~t~~~L~~~~~~g~fr~dLy~rL~~  304 (482)
                      --++||||+.+....|    ..||.+|+   +..|.  +-.-.+++|   |-+||+.|  -.+                 
T Consensus       507 PliLiDEvDKlG~g~qGDPasALLElLDPEQNanFl--DHYLdVp~DLSkVLFicTAN--~id-----------------  565 (906)
T KOG2004         507 PLILIDEVDKLGSGHQGDPASALLELLDPEQNANFL--DHYLDVPVDLSKVLFICTAN--VID-----------------  565 (906)
T ss_pred             CEEEEEHHHHHCCCCCCCHHHHHHHHCCHHHCCCHH--HHCCCCCCCHHHEEEEEECC--CCC-----------------
T ss_conf             658853223417887798689998743965355345--42026642111068898536--445-----------------


Q ss_pred             HHHHHHHHHHHHHHHH----------HHHH-HHHHHHCCCCCCCC--CCCCCCCCCCCCCCC-CCCCHHHHHHHHHHHH
Q ss_conf             3344677877442222----------5566-77764101122333--321111100012233-8986899999999998
Q gi|254780916|r  305 FLINISTLRSRSEDIP----------WLVH-FFLQSFCTKNAIKQ--ISISDKALSLLTKYP-WIDNVQELKNILLRAV  369 (482)
Q Consensus       305 ~~i~iPpLReR~eDI~----------~L~~-~fl~~~~~~~~~~~--~~ls~~a~~~L~~y~-WPGNvREL~n~i~r~~  369 (482)
                       +| =|||++|.|=|.          .+++ |++.+....+|..+  ..++++|+..|..|. ----||.|+.-|+.++
T Consensus       566 -tI-P~pLlDRMEvIelsGYv~eEKv~IA~~yLip~a~~~~gl~~e~v~is~~al~~lI~~YcrEaGVRnLqk~iekI~  642 (906)
T KOG2004         566 -TI-PPPLLDRMEVIELSGYVAEEKVKIAERYLIPQALKDCGLKPEQVKISDDALLALIERYCREAGVRNLQKQIEKIC  642 (906)
T ss_pred             -CC-CHHHHHHHHEEECCCCCHHHHHHHHHHHHHHHHHHHCCCCHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             -69-856641223220367227989999998412578987499878658629999999999988876778999999999


No 184
>TIGR02639 ClpA ATP-dependent Clp protease ATP-binding subunit ClpA; InterPro: IPR013461    Proteins in this entry are related to ClpA () from Escherichia coli. ClpA is an ATP-dependent chaperone and part of the ClpAP protease that participates in regulatory protein degradation and the dissolution and degradation of protein aggregates . ClpA recognises sequences in specific proteins, which it then unfolds in an ATP-dependent manner and transports into the degradation chamber of the associated ClpP protein , . A small adaptor-like protein, ClpS, modulates the activity of ClpA and is an important regulatory factor for this protein . It protects ClpA from autodegradation and appears to redirect its activity away from soluble proteins and toward aggregated proteins..
Probab=98.23  E-value=9.4e-07  Score=67.37  Aligned_cols=217  Identities=15%  Similarity=0.217  Sum_probs=151.7

Q ss_pred             CCCCCCCCCCCCCCCCCCCCC----CCCEEE---EEECCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCHHHHH
Q ss_conf             111222222222222222234----432048---8732777436799999984267543321012346554210024331
Q gi|254780916|r  140 DSLIAVSPAMIQVVDLARKAG----DCAIPI---MIQGEFGVGKKRLSRFIHESGKRAFFPFFIVNCGMIDQDKIEKFLF  212 (482)
Q Consensus       140 ~~LiG~S~~m~~v~~~i~~~a----~~~~~v---li~Ge~GtGK~~~A~~iH~~s~r~~~~fi~v~c~~~~~~~~e~~lF  212 (482)
                      ..+.||..++..|-..|.+.-    ..+.||   |..|+||+||+=+||.+=..=   +=+|+.+|+|-+-+-.-=|.|-
T Consensus       497 ~kIfGQD~AI~~lv~aiK~SrAGl~~~nkP~GSFLF~GPTGVGKTElak~LA~~L---Gv~l~RFDMSEYmEKHTVsRLI  573 (774)
T TIGR02639       497 AKIFGQDEAIEQLVSAIKRSRAGLGEPNKPVGSFLFVGPTGVGKTELAKQLAEEL---GVHLLRFDMSEYMEKHTVSRLI  573 (774)
T ss_pred             CCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHH---CCHHCCCCCHHHHHHHHHHHHH
T ss_conf             1315158999999999999874247788816888864798962578899999970---8200104650446899998741


Q ss_pred             CCCC--------CC-CCCCCCCCCCCCCCCCCEEEECCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCE---EEEE
Q ss_conf             1255--------55-3221110012344667147516642001889998888776420011235532123431---5652
Q gi|254780916|r  213 GDVD--------LQ-TKNSAQFLGKFIEANGGTIVLEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVR---LIFL  280 (482)
Q Consensus       213 G~~~--------~~-~~~~~~~~g~~~~a~~Gtl~l~ei~~L~~~~Q~~Ll~~l~~~~~~~~g~~~~~~~~~R---iIa~  280 (482)
                      |..-        |. |.|....       =+-.|.||||+..-++.=.=||++++..+   +-++..+++|||   +|=+
T Consensus       574 GsPPGYVGfEqGGLLT~AvrK~-------P~cVLLLDEIEKAHpDI~NILLQVMD~At---LTDN~GrKaDFRNVILIMT  643 (774)
T TIGR02639       574 GSPPGYVGFEQGGLLTDAVRKH-------PHCVLLLDEIEKAHPDIYNILLQVMDYAT---LTDNNGRKADFRNVILIMT  643 (774)
T ss_pred             CCCCCCCCCCCCCCCHHHHCCC-------CCEEEHHHHHHHHHHHHHHHHHHHHCCCE---EECCCCCEEEECCEEEEEC
T ss_conf             6888851316777212233128-------85354234666631336667876633543---4058885763113688840


Q ss_pred             CCCCCCCCCCHH-HHHHHHHH-HH--HHHHHHHHHHHHHHHH-----------HHHHHHHHHHHHCCCCCCCC--CCCCC
Q ss_conf             143321111112-33379998-86--5433446778774422-----------22556677764101122333--32111
Q gi|254780916|r  281 TEKNLLPQVKSH-VFRKDLYY-RI--SVFLINISTLRSRSED-----------IPWLVHFFLQSFCTKNAIKQ--ISISD  343 (482)
Q Consensus       281 t~~~L~~~~~~g-~fr~dLy~-rL--~~~~i~iPpLReR~eD-----------I~~L~~~fl~~~~~~~~~~~--~~ls~  343 (482)
                      ||.-..++-+.- -|-.+--- .-  .+-.+.=|=-|.|-++           +..++..+|.++..++..+.  ..|++
T Consensus       644 SNaGa~E~~~~~iGF~~~~~~~~~~~Aikk~F~PEFRNRLDaii~F~~L~~~~~~~i~~K~l~el~~~L~eK~v~l~l~~  723 (774)
T TIGR02639       644 SNAGAREMSKNPIGFGGERVEDKSEKAIKKLFSPEFRNRLDAIIAFNDLSEEVAEKIVKKFLDELQKQLNEKNVELELTD  723 (774)
T ss_pred             CCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHCCCCCCCCCCCEEECCCCCHHHHHHHHHHHHHHHHHHHHHCCEEEEECH
T ss_conf             37001023677644255541233488897315874201334644169988999999999999999975530653787647


Q ss_pred             CCCCCCCCCCCCCC--HHHHHHHHHHHH
Q ss_conf             11000122338986--899999999998
Q gi|254780916|r  344 KALSLLTKYPWIDN--VQELKNILLRAV  369 (482)
Q Consensus       344 ~a~~~L~~y~WPGN--vREL~n~i~r~~  369 (482)
                      +|..+|..--+--+  .|+|..+|+.-+
T Consensus       724 ~a~~~LA~KGY~~efGARpl~R~I~~~i  751 (774)
T TIGR02639       724 DAIKYLAEKGYDEEFGARPLARVIQEEI  751 (774)
T ss_pred             HHHHHHHHHCCCCCCCCCHHHHHHHHHH
T ss_conf             8999998636781105544899988741


No 185
>TIGR00368 TIGR00368 Mg chelatase homolog; InterPro: IPR004482   This family of bacterial proteins are variously described as 'hypothetical protein yifB', 'competence protein', 'hypothetical protein' or 'Mg chelatase-related protein'. These proteins are a subset of the magnesium chelatase, ChlI subunit family and either belong to or show significant homology to the non-peptidase homologs of the MEROPS peptidase family S16 (lon protease family, clan SF), IPR001984 from INTERPRO. .
Probab=98.21  E-value=4.3e-07  Score=69.78  Aligned_cols=251  Identities=12%  Similarity=0.088  Sum_probs=132.4

Q ss_pred             HHHHHHHHHHHCCCEE-----EE--ECC-----H-------HHHHHH-CCCCCEEEE-ECCC-CCC--CH----H-HHHH
Q ss_conf             9999999999889889-----99--893-----7-------999986-089989999-7854-698--88----9-9999
Q gi|254780916|r   22 QIKIIKDHVESYGYDV-----FI--VNV-----S-------DLSTIS-KIQVNVIFL-SLIN-CED--DK----E-NILK   72 (482)
Q Consensus        22 ~~~~l~~~L~~~G~~v-----~~--a~~-----~-------al~~l~-~~~~dlill-D~~m-P~~--dG----l-ell~   72 (482)
                      -|+-++..|.-.||+.     ..  |-.     +       |...+. +++.|.=.| |+.+ .+|  ||    + -++.
T Consensus        40 sreRVksAl~Ns~F~fP~~rI~iNLAPAdl~KeG~~FDLpIAI~ilaaseq~da~~L~~yl~lGEL~LdG~lR~i~gvlP  119 (505)
T TIGR00368        40 SRERVKSALKNSGFKFPAKRITINLAPADLPKEGGRFDLPIAIGILAASEQLDAKKLDEYLFLGELALDGKLRGIKGVLP  119 (505)
T ss_pred             HHHHHHHHHHHCCCCCCCCEEEEECCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHCCCCEEEHHHHHHCCCCCHHHHHHH
T ss_conf             67899999861576688540166538888766788863389999999863330431440110011332475110456899


Q ss_pred             HHH-HHCCCCCEEEEECCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCC----CCCCCC-------CCCCCCCCCCCCC
Q ss_conf             999-8578983999926899999998885057432222222222222222----222222-------2222222111111
Q gi|254780916|r   73 NIV-DKIPIVPIIVQTTQDNIKILNCFLYNRISKFFLNLVSRKQLCDSII----CALREG-------VVPSQENEHCALD  140 (482)
Q Consensus        73 ~i~-~~~p~ipvIiiT~~~~~~~~~~a~~~g~~d~l~KP~~~~~L~~~i~----~al~~~-------~~~~~~~~~~~~~  140 (482)
                      -+. +....+..||+...+..|+   ++-+|..-|+.+  +..+.++-+.    +.+...       ...........+.
T Consensus       120 ~~~~A~k~~~~~~iVp~~N~~Ea---Slv~G~~~y~~~--~L~~vv~fl~ql~~~~L~~~t~~~~~~~~~~s~~~~~DL~  194 (505)
T TIGR00368       120 AIALAQKSGRKFIIVPKENAEEA---SLVDGLNVYGAD--HLKEVVKFLEQLGSEKLPPRTNTKAKSIINVSLIIDLDLK  194 (505)
T ss_pred             HHHHHHHCCCCEEEECCCCCCCE---EEECCCCEEHHH--HHHHHHHHHHHHCCCCCCCCCCCCCCHHHHHCCHHHCCCC
T ss_conf             99999865876776216675520---266387402047--4899999997623101777545553103441320104432


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCCCHHHHHHHHHHHCCC-CCCCCCCCCC-CCCCCCC-----CCH-HHHH
Q ss_conf             112222222222222222344320488732777436799999984267-5433210123-4655421-----002-4331
Q gi|254780916|r  141 SLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHESGK-RAFFPFFIVN-CGMIDQD-----KIE-KFLF  212 (482)
Q Consensus       141 ~LiG~S~~m~~v~~~i~~~a~~~~~vli~Ge~GtGK~~~A~~iH~~s~-r~~~~fi~v~-c~~~~~~-----~~e-~~lF  212 (482)
                      +++|++.    -++-++-+|.-..++|+.|++||||+++|+.+...=+ -.+.-.+.++ .-++...     .+- ..=|
T Consensus       195 dv~GQ~~----akRAleIAaAGGHNlll~GPPGsGKTmla~r~~giLP~L~~~EalE~~~v~S~~~~l~~~~~~~rQRPF  270 (505)
T TIGR00368       195 DVKGQQH----AKRALEIAAAGGHNLLLLGPPGSGKTMLASRLQGILPPLTNEEALETARVLSLVGKLIDRKQWKRQRPF  270 (505)
T ss_pred             CCCCHHH----CCHHHHHHHHCCCCEEEECCCCCCHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHCCCHHCCCCC
T ss_conf             2545101----102677753135643767824962689998751057864512666678888888757652301106867


Q ss_pred             C--CCCC----C-CCCCCCCCCCCCCCCCCEEEECCCCHHHHHHHHHHHHHH----HHHH--CCCCCCCCC-CCCCCEEE
Q ss_conf             1--2555----5-322111001234466714751664200188999888877----6420--011235532-12343156
Q gi|254780916|r  213 G--DVDL----Q-TKNSAQFLGKFIEANGGTIVLEEPDALPLAVQGRIYNFI----ETGK--IEFFDSRGA-IRLDVRLI  278 (482)
Q Consensus       213 G--~~~~----~-~~~~~~~~g~~~~a~~Gtl~l~ei~~L~~~~Q~~Ll~~l----~~~~--~~~~g~~~~-~~~~~RiI  278 (482)
                      -  |=.+    . -|...-++|-+-.|++|.|||||.-+    ...+.|.+|    |+|+  +.|-.+.-. .+.+|.+|
T Consensus       271 R~PHHsAS~~~lvGGG~~P~PGEiSLAhnGvLFLDEl~E----F~r~vL~~LR~PlEdg~i~iSRa~~ki~kyPA~FqL~  346 (505)
T TIGR00368       271 RSPHHSASKPALVGGGSIPKPGEISLAHNGVLFLDELPE----FKRKVLDALREPLEDGSISISRAKAKIFKYPARFQLV  346 (505)
T ss_pred             CCCCCCCCCCCCCCCCCCCCCCCEEHHCCCCHHHHCCHH----HHHHHHHHHCCCCCCCCEEEEECCCHHHCCCHHHHHH
T ss_conf             786500256664058752228512020054104322204----4678998717874267068863220100087245567


Q ss_pred             EECCCCC
Q ss_conf             5214332
Q gi|254780916|r  279 FLTEKNL  285 (482)
Q Consensus       279 a~t~~~L  285 (482)
                      +|+|-.+
T Consensus       347 aAmNpcP  353 (505)
T TIGR00368       347 AAMNPCP  353 (505)
T ss_pred             HHHCCCC
T ss_conf             5617887


No 186
>PRK09111 DNA polymerase III subunits gamma and tau; Validated
Probab=98.21  E-value=2.4e-05  Score=57.36  Aligned_cols=215  Identities=18%  Similarity=0.212  Sum_probs=126.3

Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCCCHHHHHHHHHHHCCC-----CCCCCCCC-----CCCCCCC
Q ss_conf             2111111112222222222222222344320488732777436799999984267-----54332101-----2346554
Q gi|254780916|r  134 NEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHESGK-----RAFFPFFI-----VNCGMID  203 (482)
Q Consensus       134 ~~~~~~~~LiG~S~~m~~v~~~i~~~a~~~~~vli~Ge~GtGK~~~A~~iH~~s~-----r~~~~fi~-----v~c~~~~  203 (482)
                      -....|..++|+....+.+...+. ........|++|..||||+++||.+-..-.     ..++|-..     -+|.++.
T Consensus        17 ~rp~~f~~~~gq~~~~~~l~~~~~-~~~~~~a~l~~g~rg~gktt~ari~a~~lnc~~~~~~~~~~~~~c~~c~~c~~i~   95 (600)
T PRK09111         17 YRPQTFDDLIGQEAMVRTLRNAFE-TGRIAQAFMLTGVRGVGKTTTARILARALNYKGPDGVGGPTIDPCGVGEHCQAIM   95 (600)
T ss_pred             CCCCCHHHHCCCHHHHHHHHHHHH-CCCCCCEEEEECCCCCCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCHHHHHHH
T ss_conf             179877663385999999999997-2984204764578987899999999999669887666899889899886589886


Q ss_pred             CC----CCHHHHHCCCCCC-CCCCCCCCCCCCC-------CCCCEEEECCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCC
Q ss_conf             21----0024331125555-3221110012344-------6671475166420018899988887764200112355321
Q gi|254780916|r  204 QD----KIEKFLFGDVDLQ-TKNSAQFLGKFIE-------ANGGTIVLEEPDALPLAVQGRIYNFIETGKIEFFDSRGAI  271 (482)
Q Consensus       204 ~~----~~e~~lFG~~~~~-~~~~~~~~g~~~~-------a~~Gtl~l~ei~~L~~~~Q~~Ll~~l~~~~~~~~g~~~~~  271 (482)
                      ..    .+|      .+++ .....+-.-+++.       +.--...+||+|-|+.+.-..||..|++.           
T Consensus        96 ~~~~~d~~e------~daas~~~v~~~r~~~~~~~~~p~~~~~kv~iidevhmls~~afnallktleep-----------  158 (600)
T PRK09111         96 EGRHVDVIE------MDAASHTGVDDIREIIESVRYRPVSARYKVYIIDEVHMLSTAAFNALLKTLEEP-----------  158 (600)
T ss_pred             CCCCCCEEE------EECCCCCCHHHHHHHHHHHCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHCC-----------
T ss_conf             689987588------515545788899999986053887775469996001105799999999876259-----------


Q ss_pred             CCCCEEEEECCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHH----HHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCC
Q ss_conf             23431565214332111111233379998865433446778774----42222556677764101122333321111100
Q gi|254780916|r  272 RLDVRLIFLTEKNLLPQVKSHVFRKDLYYRISVFLINISTLRSR----SEDIPWLVHFFLQSFCTKNAIKQISISDKALS  347 (482)
Q Consensus       272 ~~~~RiIa~t~~~L~~~~~~g~fr~dLy~rL~~~~i~iPpLReR----~eDI~~L~~~fl~~~~~~~~~~~~~ls~~a~~  347 (482)
                      +.+|.+|.+|+..=.                  +++.|=+=..|    +=+...|+.| |...+.+.+   ..++++|+.
T Consensus       159 p~~~~fi~att~~~k------------------~p~ti~src~~f~~~~~~~~~~~~~-l~~i~~~e~---~~~~~~al~  216 (600)
T PRK09111        159 PPHVKFIFATTEIRK------------------VPVTVLSRCQRFDLRRIEAEVLAAH-LARIAEKEG---VEVEPDALA  216 (600)
T ss_pred             CCCEEEEEECCCHHH------------------CCHHHHHHHHEECCCCCCHHHHHHH-HHHHHHHCC---CCCCHHHHH
T ss_conf             865499996285343------------------7589985441201057999999999-999998607---686677999


Q ss_pred             CCCCCCCCCCHHHHHHHHHHHHHHCCCCCCCHHHHHHHHCCCC
Q ss_conf             0122338986899999999998743898106889545421244
Q gi|254780916|r  348 LLTKYPWIDNVQELKNILLRAVIGLKDSHLTEDRFVLLLSREG  390 (482)
Q Consensus       348 ~L~~y~WPGNvREL~n~i~r~~i~~~~~~i~~~~~~~~l~~~~  390 (482)
                      ++.... -|-+|.=-+++.+++.. .++.|+.+++...++-..
T Consensus       217 ~ia~~a-~GS~RDaLSlLDQai~~-~~~~i~~~~v~~mLGl~d  257 (600)
T PRK09111        217 LIARAA-EGSVRDGLSLLDQAIAH-GAGEVTAEQVRDMLGLAD  257 (600)
T ss_pred             HHHHHC-CCCCCHHHHHHHHHHHC-CCCCCCHHHHHHHHCCCC
T ss_conf             999974-89842189999999972-798756999999868876


No 187
>PRK08691 DNA polymerase III subunits gamma and tau; Validated
Probab=98.20  E-value=5.4e-05  Score=54.95  Aligned_cols=218  Identities=15%  Similarity=0.180  Sum_probs=122.9

Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCCCHHHHHHHHHHHCCCCCC----CCCC-CCCCCCCCCC---
Q ss_conf             2111111112222222222222222344320488732777436799999984267543----3210-1234655421---
Q gi|254780916|r  134 NEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHESGKRAF----FPFF-IVNCGMIDQD---  205 (482)
Q Consensus       134 ~~~~~~~~LiG~S~~m~~v~~~i~~~a~~~~~vli~Ge~GtGK~~~A~~iH~~s~r~~----~~fi-~v~c~~~~~~---  205 (482)
                      -....|..++|+.-..+.+...+.. .....--|+.|..|+||+.+||.+-..-.-.+    .|-= --+|-.+...   
T Consensus        10 ~RP~~F~e~vGQ~~v~~~L~nal~~-~rl~haylf~G~rGvGKTt~Ari~Ak~lNC~~~~~~~pCg~C~~C~~i~~g~~~   88 (704)
T PRK08691         10 WRPKTFADLVGQEHVVKALQNALDE-GRLHHAYLLTGTRGVGKTTIARILAKSLNCENAQHGEPCGVCQSCTQIDAGRYV   88 (704)
T ss_pred             HCCCCHHHHCCCHHHHHHHHHHHHH-CCCCCEEEEECCCCCCHHHHHHHHHHHHCCCCCCCCCCCCCCHHHHHHHCCCCC
T ss_conf             1887475641869999999999981-997523750278987888999999999679999999978777767878558998


Q ss_pred             -CCHHHHHCCCCCC-CCCCCCCCCCCCCC-------CCCEEEECCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCE
Q ss_conf             -0024331125555-32211100123446-------67147516642001889998888776420011235532123431
Q gi|254780916|r  206 -KIEKFLFGDVDLQ-TKNSAQFLGKFIEA-------NGGTIVLEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVR  276 (482)
Q Consensus       206 -~~e~~lFG~~~~~-~~~~~~~~g~~~~a-------~~Gtl~l~ei~~L~~~~Q~~Ll~~l~~~~~~~~g~~~~~~~~~R  276 (482)
                       ++|      .++. .....+-..+++.+       .--..+|||+|-|+.....-||..|++.           +..+.
T Consensus        89 D~~E------iDaAs~~~vdd~R~l~~~~~y~P~~~~yKVyiiDEvhmLs~~afNAlLKtLEEP-----------P~~v~  151 (704)
T PRK08691         89 DLLE------IDAASNTGIDNIREVLENAQYAPTAGKYKVYIIDEVHMLSKSAFNAMLKTLEEP-----------PEHVK  151 (704)
T ss_pred             CEEE------EECCCCCCHHHHHHHHHHCCCCCCCCCEEEEEEECHHHCCHHHHHHHHHHHCCC-----------CCCEE
T ss_conf             7477------424544588999999985346886785359998315443899999999861479-----------75608


Q ss_pred             EEEECCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             56521433211111123337999886543344677877442222556677764101122333321111100012233898
Q gi|254780916|r  277 LIFLTEKNLLPQVKSHVFRKDLYYRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWID  356 (482)
Q Consensus       277 iIa~t~~~L~~~~~~g~fr~dLy~rL~~~~i~iPpLReR~eDI~~L~~~fl~~~~~~~~~~~~~ls~~a~~~L~~y~WPG  356 (482)
                      +|.+|+.. .++.. -.+.+=+-|.|..            =+...++.| |...+.+.+   ..++++|+.++.... -|
T Consensus       152 FilaTTdp-~Klp~-TIlSRC~~f~l~~------------~~~~~i~~~-L~~i~~~E~---i~~e~~al~~ia~~a-~G  212 (704)
T PRK08691        152 FILATTDP-HKVPV-TVLSRCLQFVLRN------------MTAQQVADH-LAHVLDSEK---IAYEPPALQLLGRAA-AG  212 (704)
T ss_pred             EEEECCCH-HHCCH-HHHHHHHHHCCCC------------CCHHHHHHH-HHHHHHHCC---CCCCHHHHHHHHHHC-CC
T ss_conf             99854884-64758-9998887710268------------999999999-999999839---856899999999975-78


Q ss_pred             CHHHHHHHHHHHHHHCCCCCCCHHHHHHHHCCC
Q ss_conf             689999999999874389810688954542124
Q gi|254780916|r  357 NVQELKNILLRAVIGLKDSHLTEDRFVLLLSRE  389 (482)
Q Consensus       357 NvREL~n~i~r~~i~~~~~~i~~~~~~~~l~~~  389 (482)
                      -+|.=-+++.+++... ++.++.+++..-++..
T Consensus       213 s~RDalslldQaia~~-~g~~~~~~v~~mLG~~  244 (704)
T PRK08691        213 SMRDALSLLDQAIALG-SGKVAENDVRQMIGAV  244 (704)
T ss_pred             CHHHHHHHHHHHHHHC-CCCCCHHHHHHHHCCC
T ss_conf             5777988999999964-8962699999985888


No 188
>COG0593 DnaA ATPase involved in DNA replication initiation [DNA replication, recombination, and repair]
Probab=98.20  E-value=2.9e-06  Score=63.92  Aligned_cols=221  Identities=17%  Similarity=0.172  Sum_probs=128.0

Q ss_pred             CCCCCCCCCCCCC-CCCCCCCCCCCCCCCCC----CCCEEEEEECCCCCHHHHHHHHHHHCCCCCCC--CCCCCCCCCCC
Q ss_conf             2222111111112-22222222222222234----43204887327774367999999842675433--21012346554
Q gi|254780916|r  131 SQENEHCALDSLI-AVSPAMIQVVDLARKAG----DCAIPIMIQGEFGVGKKRLSRFIHESGKRAFF--PFFIVNCGMID  203 (482)
Q Consensus       131 ~~~~~~~~~~~Li-G~S~~m~~v~~~i~~~a----~~~~~vli~Ge~GtGK~~~A~~iH~~s~r~~~--~fi~v~c~~~~  203 (482)
                      ...+....|+.++ |.|-  +-.+..+..++    ...-|++|.|++|.||+++.++|-+.......  .++.+....+.
T Consensus        78 ~~l~~~ytFdnFv~g~~N--~~A~aa~~~va~~~g~~~nplfi~G~~GlGKTHLl~Aign~~~~~~~~a~v~y~~se~f~  155 (408)
T COG0593          78 SGLNPKYTFDNFVVGPSN--RLAYAAAKAVAENPGGAYNPLFIYGGVGLGKTHLLQAIGNEALANGPNARVVYLTSEDFT  155 (408)
T ss_pred             CCCCCCCCHHHEEECCCH--HHHHHHHHHHHHCCCCCCCCEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEECCHHHHH
T ss_conf             568988855422047744--999999999875668868957998799997899999999999862998648850489989


Q ss_pred             CCCCHHHHHCCCCCCCCCCCCCCCCCCCCCCCEEEECCCCHHHHH--HHHHHHHHHHHHHCCCCCCCCCCCCCCEEEEEC
Q ss_conf             210024331125555322111001234466714751664200188--999888877642001123553212343156521
Q gi|254780916|r  204 QDKIEKFLFGDVDLQTKNSAQFLGKFIEANGGTIVLEEPDALPLA--VQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLT  281 (482)
Q Consensus       204 ~~~~e~~lFG~~~~~~~~~~~~~g~~~~a~~Gtl~l~ei~~L~~~--~Q~~Ll~~l~~~~~~~~g~~~~~~~~~RiIa~t  281 (482)
                      .+.+.+-..       +......-..   +=..|++|+|+.+...  .|.-++..+..=.     ..     .-+||.++
T Consensus       156 ~~~v~a~~~-------~~~~~Fk~~y---~~dlllIDDiq~l~gk~~~qeefFh~FN~l~-----~~-----~kqIvlts  215 (408)
T COG0593         156 NDFVKALRD-------NEMEKFKEKY---SLDLLLIDDIQFLAGKERTQEEFFHTFNALL-----EN-----GKQIVLTS  215 (408)
T ss_pred             HHHHHHHHH-------HHHHHHHHHH---CCCEEEECHHHHHCCCHHHHHHHHHHHHHHH-----HC-----CCEEEEEC
T ss_conf             999999885-------0488888764---2673555138675677157999999999888-----50-----88799970


Q ss_pred             CCCCCCCCCHHHHHHHHHHHHH-HH--HHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCH
Q ss_conf             4332111111233379998865-43--34467787744222255667776410112233332111110001223389868
Q gi|254780916|r  282 EKNLLPQVKSHVFRKDLYYRIS-VF--LINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNV  358 (482)
Q Consensus       282 ~~~L~~~~~~g~fr~dLy~rL~-~~--~i~iPpLReR~eDI~~L~~~fl~~~~~~~~~~~~~ls~~a~~~L~~y~WPGNv  358 (482)
                      .+.+.++.   .+.+||.-|+. +.  .|+-|.+..|..=        |.+.+...+   ..++++++..+. ..++.|+
T Consensus       216 dr~P~~l~---~~~~rL~SR~~~Gl~~~I~~Pd~e~r~ai--------L~kka~~~~---~~i~~ev~~~la-~~~~~nv  280 (408)
T COG0593         216 DRPPKELN---GLEDRLRSRLEWGLVVEIEPPDDETRLAI--------LRKKAEDRG---IEIPDEVLEFLA-KRLDRNV  280 (408)
T ss_pred             CCCCHHHC---CCCHHHHHHHHCEEEEEECCCCHHHHHHH--------HHHHHHHCC---CCCCHHHHHHHH-HHHHCCH
T ss_conf             78832211---03588998986305775279888999999--------999998658---888879999999-9700309


Q ss_pred             HHHHHHHHHHHHH--CCCCCCCHHHHHHHHCC
Q ss_conf             9999999999874--38981068895454212
Q gi|254780916|r  359 QELKNILLRAVIG--LKDSHLTEDRFVLLLSR  388 (482)
Q Consensus       359 REL~n~i~r~~i~--~~~~~i~~~~~~~~l~~  388 (482)
                      |||+-.+.++...  ..+..|+.+.+...+..
T Consensus       281 ReLegaL~~l~~~a~~~~~~iTi~~v~e~L~~  312 (408)
T COG0593         281 RELEGALNRLDAFALFTKRAITIDLVKEILKD  312 (408)
T ss_pred             HHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHH
T ss_conf             99999999999999853875769999999998


No 189
>TIGR02031 BchD-ChlD magnesium chelatase ATPase subunit D; InterPro: IPR011776    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. Unlike subunit I (IPR011775 from INTERPRO), this subunit is not found in archaea.; GO: 0005524 ATP binding, 0016851 magnesium chelatase activity, 0015995 chlorophyll biosynthetic process.
Probab=98.20  E-value=1e-05  Score=60.10  Aligned_cols=216  Identities=18%  Similarity=0.179  Sum_probs=134.1

Q ss_pred             EEEECCCCCHHHHHHHHHHHCCCCCC--CCCCCCCC------------------------------------CCCCCCCC
Q ss_conf             88732777436799999984267543--32101234------------------------------------65542100
Q gi|254780916|r  166 IMIQGEFGVGKKRLSRFIHESGKRAF--FPFFIVNC------------------------------------GMIDQDKI  207 (482)
Q Consensus       166 vli~Ge~GtGK~~~A~~iH~~s~r~~--~~fi~v~c------------------------------------~~~~~~~~  207 (482)
                      |.|.|-.||||..++|++|+.=+...  .+-+..||                                    ..+|-+.=
T Consensus        20 v~I~~r~Gtgk~al~ral~~~Lp~~~~~~g~~i~~~~PA~P~~W~~~~~ER~~~~~GlsD~~~~~~~~~~p~~~lP~~vt   99 (705)
T TIGR02031        20 VAIRARAGTGKTALARALAEILPPIEELEGSIISNADPAEPDEWEDDLDERIEEEAGLSDSEVKVVIVKAPFVELPLGVT   99 (705)
T ss_pred             EEEECCCCHHHHHHHHHHHHHCCCCCEECCCCCCCCCCCCCCCHHHHHHHHHHHHCCCCCCCCCEEEECCCCEECCCCCC
T ss_conf             55416777388999999998588874326620147888887323445654233204776662204650564102589873


Q ss_pred             HHHHHCCCCC----CCCCCCCCCCCCCCCCCCEEEECCCCHHHHHHHHHHHHHHHHHH--CCCCCCCCCCCCCCEEEEEC
Q ss_conf             2433112555----53221110012344667147516642001889998888776420--01123553212343156521
Q gi|254780916|r  208 EKFLFGDVDL----QTKNSAQFLGKFIEANGGTIVLEEPDALPLAVQGRIYNFIETGK--IEFFDSRGAIRLDVRLIFLT  281 (482)
Q Consensus       208 e~~lFG~~~~----~~~~~~~~~g~~~~a~~Gtl~l~ei~~L~~~~Q~~Ll~~l~~~~--~~~~g~~~~~~~~~RiIa~t  281 (482)
                      |..|.|-.+-    ..|...-+.|+|.+|++|.||+|.++.|....-.+|+.+|.+|.  ++|=|=..-.++++=+|++=
T Consensus       100 edrL~G~iDve~sl~~G~~V~~~GlL~~A~~gvlyvd~~~lld~~~~n~l~~AL~~G~~~vEREGiS~~~Pa~f~Liaty  179 (705)
T TIGR02031       100 EDRLLGGIDVEESLASGQRVLQPGLLDEANRGVLYVDSLNLLDDSLVNRLLDALDEGVVIVEREGISVVHPAKFVLIATY  179 (705)
T ss_pred             CCCCCCCCCCCCCCCCCEEEEECCCHHHCCCCCEECCCHHHHHHHHHHHHHHHHHCCCEEEEECCCCCCCCCCCEEEEEC
T ss_conf             20302640020146878254407603116897043154541106899999988654976888656563047673036631


Q ss_pred             CCCCCCCCCHHHHHHHHHHHHHHH--HHHHHHHHHHHHHHHHHHHHHHHH---HCCCCCCCC----------------CC
Q ss_conf             433211111123337999886543--344677877442222556677764---101122333----------------32
Q gi|254780916|r  282 EKNLLPQVKSHVFRKDLYYRISVF--LINISTLRSRSEDIPWLVHFFLQS---FCTKNAIKQ----------------IS  340 (482)
Q Consensus       282 ~~~L~~~~~~g~fr~dLy~rL~~~--~i~iPpLReR~eDI~~L~~~fl~~---~~~~~~~~~----------------~~  340 (482)
                      +-.  +  -.+.+|+-|.+||.-+  ...+-++..|. .|.-+.+.|-+.   +...++-+.                ..
T Consensus       180 dp~--E--~~~~lr~~L~DRla~~v~~~~~~~~~~R~-~iv~~~~~F~~~~~~~~~~~~~e~~~~~~~ie~ARe~L~~V~  254 (705)
T TIGR02031       180 DPA--E--GDGALREHLLDRLALIVSLEEVASLEARV-EIVRRAELFSELQEEVFEEVNDELLLLRGQIEAARELLPQVT  254 (705)
T ss_pred             CCC--C--CCCCCCHHHHHHHHHEECCHHCCCHHHHH-HHHHHHHHHHHHCCCCHHHCCCCHHHHHHHHHHHHHHCCCCC
T ss_conf             777--7--87766204540344110511025788899-998899888750663201157624578999999998567873


Q ss_pred             CCCCCCCCCCCCCCCCCHHHHHH------HHHHHHHHCCCCCCCHHHHHHHH
Q ss_conf             11111000122338986899999------99999874389810688954542
Q gi|254780916|r  341 ISDKALSLLTKYPWIDNVQELKN------ILLRAVIGLKDSHLTEDRFVLLL  386 (482)
Q Consensus       341 ls~~a~~~L~~y~WPGNvREL~n------~i~r~~i~~~~~~i~~~~~~~~l  386 (482)
                      +|.+-++.|..-..-+=|.=++.      +.+-...+.....++.+|+....
T Consensus       255 is~eq~~~lv~~a~~lGv~g~RAdLfa~raA~a~AAl~gR~~V~~eDL~~AV  306 (705)
T TIGR02031       255 ISAEQVKELVLTALSLGVEGHRADLFAVRAAKALAALEGRTEVEEEDLKLAV  306 (705)
T ss_pred             CCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHH
T ss_conf             6489999999999973887301789999999999998707245888999887


No 190
>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=98.18  E-value=1.6e-06  Score=65.74  Aligned_cols=200  Identities=15%  Similarity=0.188  Sum_probs=106.6

Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCCCHHHHHHHHHHHCCCC-------CCCCCCCCCCCCCCCCCC
Q ss_conf             1111111122222222222222223443204887327774367999999842675-------433210123465542100
Q gi|254780916|r  135 EHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHESGKR-------AFFPFFIVNCGMIDQDKI  207 (482)
Q Consensus       135 ~~~~~~~LiG~S~~m~~v~~~i~~~a~~~~~vli~Ge~GtGK~~~A~~iH~~s~r-------~~~~fi~v~c~~~~~~~~  207 (482)
                      .....++++|....++++.+-++|  .+.-+.++.||+|+||+.++..+-..=-.       ++...+.+|.+++-    
T Consensus       168 ~~gklDpviGRd~Ei~r~i~IL~R--r~KNNpiLVGepGVGKTAIvEGLA~rI~~g~VP~~L~~~~i~~LDlg~Lv----  241 (852)
T TIGR03346       168 REGKLDPVIGRDEEIRRTIQVLSR--RTKNNPVLIGEPGVGKTAIVEGLAQRIVNGDVPESLKNKRLLALDMGALI----  241 (852)
T ss_pred             HCCCCCCCCCCHHHHHHHHHHHHH--HCCCCCCEECCCCCCHHHHHHHHHHHHHCCCCCHHHHHCCCEEEEHHHHH----
T ss_conf             828999773836999999999987--32489721279998799999999999866999978851851275288775----


Q ss_pred             HHHHHCCCCCCCCCCCCCC-CCCCC---CC-CCEEEECCCCHH--------HHHHHHHHHHHHHHHHCCCCCCCCCCCCC
Q ss_conf             2433112555532211100-12344---66-714751664200--------18899988887764200112355321234
Q gi|254780916|r  208 EKFLFGDVDLQTKNSAQFL-GKFIE---AN-GGTIVLEEPDAL--------PLAVQGRIYNFIETGKIEFFDSRGAIRLD  274 (482)
Q Consensus       208 e~~lFG~~~~~~~~~~~~~-g~~~~---a~-~Gtl~l~ei~~L--------~~~~Q~~Ll~~l~~~~~~~~g~~~~~~~~  274 (482)
                          =|-+  +-|....|. ..+++   ++ +-.||+||||.|        +.+.-.-|=-+|..|             .
T Consensus       242 ----AGtk--yRGeFEeRlk~ii~ev~~~~~~iILFIDEiHtliGaG~~~G~~DAaNlLKPaLarG-------------e  302 (852)
T TIGR03346       242 ----AGAK--YRGEFEERLKAVLNEVTKSEGQIILFIDELHTLVGAGKAEGAMDAGNMLKPALARG-------------E  302 (852)
T ss_pred             ----CCCC--CCHHHHHHHHHHHHHHHHCCCCEEEEEHHHHHHCCCCCCCCCCCHHHHHHHHHHCC-------------C
T ss_conf             ----2153--00789999999999998589987999612555326887666410677743787479-------------8


Q ss_pred             CEEEEECCCCCCCCCCHHHHHH------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---------------HHHCCC
Q ss_conf             3156521433211111123337------9998865433446778774422225566777---------------641011
Q gi|254780916|r  275 VRLIFLTEKNLLPQVKSHVFRK------DLYYRISVFLINISTLRSRSEDIPWLVHFFL---------------QSFCTK  333 (482)
Q Consensus       275 ~RiIa~t~~~L~~~~~~g~fr~------dLy~rL~~~~i~iPpLReR~eDI~~L~~~fl---------------~~~~~~  333 (482)
                      +|+|++|+.+        .||+      -|=-|...+.|.=|+.-+-..=+.-+...|=               -+++.+
T Consensus       303 lr~IgATT~~--------EYrk~iEkD~AL~RRFq~I~V~EPs~e~t~~IL~gl~~~yE~hH~V~i~d~Ai~aav~LS~R  374 (852)
T TIGR03346       303 LHCIGATTLD--------EYRKYIEKDAALERRFQPVFVDEPTVEDTISILRGLKERYEVHHGVRITDPAIVAAATLSHR  374 (852)
T ss_pred             CEEEEECCHH--------HHHHHHHCCHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHCCCCEECHHHHHHHHHHHCC
T ss_conf             5599827899--------99988322688997377120479986899999997699997627926739999999997134


Q ss_pred             CCCCCCCCCCCCCCCC---------CCCCCCCCHHHHHHHHHHH
Q ss_conf             2233332111110001---------2233898689999999999
Q gi|254780916|r  334 NAIKQISISDKALSLL---------TKYPWIDNVQELKNILLRA  368 (482)
Q Consensus       334 ~~~~~~~ls~~a~~~L---------~~y~WPGNvREL~n~i~r~  368 (482)
                      |= +-+.+++.|+.+|         ....+|-.+.+++.-+.++
T Consensus       375 Yi-~~R~LPDKAIDlLDeA~a~~~~~~~~~p~~l~~~~~~~~~l  417 (852)
T TIGR03346       375 YI-TDRFLPDKAIDLIDEAAARIRMEIDSKPEELDELDRRIIQL  417 (852)
T ss_pred             CC-CCCCCCHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHH
T ss_conf             66-77889618999999999988762378946799999999999


No 191
>COG1223 Predicted ATPase (AAA+ superfamily) [General function prediction only]
Probab=98.13  E-value=1.2e-06  Score=66.53  Aligned_cols=166  Identities=21%  Similarity=0.333  Sum_probs=95.2

Q ss_pred             CCCCCCCCCCCCCCCCCCCCCC------CCCCCCCC-CCEEEEEECCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCC
Q ss_conf             2221111111122222222222------22222344-3204887327774367999999842675433210123465542
Q gi|254780916|r  132 QENEHCALDSLIAVSPAMIQVV------DLARKAGD-CAIPIMIQGEFGVGKKRLSRFIHESGKRAFFPFFIVNCGMIDQ  204 (482)
Q Consensus       132 ~~~~~~~~~~LiG~S~~m~~v~------~~i~~~a~-~~~~vli~Ge~GtGK~~~A~~iH~~s~r~~~~fi~v~c~~~~~  204 (482)
                      .......+++.||+-.+-++++      +.=.+... ...+||..|++||||++.|+++-+.   .+-||+.|+..    
T Consensus       113 e~~~~it~ddViGqEeAK~kcrli~~yLenPe~Fg~WAPknVLFyGppGTGKTm~Akalane---~kvp~l~vkat----  185 (368)
T COG1223         113 EIISDITLDDVIGQEEAKRKCRLIMEYLENPERFGDWAPKNVLFYGPPGTGKTMMAKALANE---AKVPLLLVKAT----  185 (368)
T ss_pred             HHHCCCCHHHHHCHHHHHHHHHHHHHHHHCHHHHCCCCCCEEEEECCCCCCHHHHHHHHHCC---CCCCEEEECHH----
T ss_conf             66136617664163988888799999964968763457541687789996487999987254---57854871168----


Q ss_pred             CCCHHHHHC-CCCCCCCCCCCCC-CCCCC---CCCCEEEECCCCHHHHH--HHHH------HHHHHHHHHCCCCCCCCCC
Q ss_conf             100243311-2555532211100-12344---66714751664200188--9998------8887764200112355321
Q gi|254780916|r  205 DKIEKFLFG-DVDLQTKNSAQFL-GKFIE---ANGGTIVLEEPDALPLA--VQGR------IYNFIETGKIEFFDSRGAI  271 (482)
Q Consensus       205 ~~~e~~lFG-~~~~~~~~~~~~~-g~~~~---a~~Gtl~l~ei~~L~~~--~Q~~------Ll~~l~~~~~~~~g~~~~~  271 (482)
                           +|.| |.+    ..++++ -+++.   +.--.+||||++.+.++  .|.-      ..++|-+. ...+..+.  
T Consensus       186 -----~liGehVG----dgar~Ihely~rA~~~aPcivFiDE~DAiaLdRryQelRGDVsEiVNALLTe-lDgi~ene--  253 (368)
T COG1223         186 -----ELIGEHVG----DGARRIHELYERARKAAPCIVFIDELDAIALDRRYQELRGDVSEIVNALLTE-LDGIKENE--  253 (368)
T ss_pred             -----HHHHHHHH----HHHHHHHHHHHHHHHCCCEEEEEHHHHHHHHHHHHHHHCCCHHHHHHHHHHH-CCCCCCCC--
T ss_conf             -----88887743----5989999999988751984998400245553045788645499999999985-01744577--


Q ss_pred             CCCCEEEEECCCC--CCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             2343156521433--2111111233379998865433446778774422225566777641
Q gi|254780916|r  272 RLDVRLIFLTEKN--LLPQVKSHVFRKDLYYRISVFLINISTLRSRSEDIPWLVHFFLQSF  330 (482)
Q Consensus       272 ~~~~RiIa~t~~~--L~~~~~~g~fr~dLy~rL~~~~i~iPpLReR~eDI~~L~~~fl~~~  330 (482)
                        -+=.||+||+.  |+..+ ..+|-++       +.+.+|.=+||.+    +.+++++.+
T Consensus       254 --GVvtIaaTN~p~~LD~ai-RsRFEeE-------IEF~LP~~eEr~~----ile~y~k~~  300 (368)
T COG1223         254 --GVVTIAATNRPELLDPAI-RSRFEEE-------IEFKLPNDEERLE----ILEYYAKKF  300 (368)
T ss_pred             --CEEEEEECCCHHHCCHHH-HHHHHHE-------EEEECCCHHHHHH----HHHHHHHHC
T ss_conf             --569995059846507888-8655650-------6564888589999----999989858


No 192
>COG0464 SpoVK ATPases of the AAA+ class [Posttranslational modification, protein turnover, chaperones]
Probab=98.11  E-value=1.3e-06  Score=66.34  Aligned_cols=193  Identities=16%  Similarity=0.150  Sum_probs=100.2

Q ss_pred             CCEEEEEECCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCHHHHHCCCCCCCCCCCCCCCCCCCC---CCCEEE
Q ss_conf             32048873277743679999998426754332101234655421002433112555532211100123446---671475
Q gi|254780916|r  162 CAIPIMIQGEFGVGKKRLSRFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFGDVDLQTKNSAQFLGKFIEA---NGGTIV  238 (482)
Q Consensus       162 ~~~~vli~Ge~GtGK~~~A~~iH~~s~r~~~~fi~v~c~~~~~~~~e~~lFG~~~~~~~~~~~~~g~~~~a---~~Gtl~  238 (482)
                      ...-||+.|++||||+++|+++-..+   +.+|+.++++.+..     ..+|+..      ..-.-.|..|   ....+|
T Consensus       275 ~~~giLl~GpPGtGKT~lAkava~~~---~~~fi~v~~~~l~s-----k~vGese------k~ir~~F~~A~~~~p~iif  340 (494)
T COG0464         275 PPKGVLLYGPPGTGKTLLAKAVALES---RSRFISVKGSELLS-----KWVGESE------KNIRELFEKARKLAPSIIF  340 (494)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHHHC---CCCEEEECCHHHHH-----HHHHHHH------HHHHHHHHHHHHCCCCEEE
T ss_conf             88369998899975899999987544---98248843355540-----7765999------9999999999966998897


Q ss_pred             ECCCCHHHHHHHHH----HHHHHHHHHCCCCCCCCCCCCCCEEEEECCCC--C-CCCCCHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             16642001889998----88877642001123553212343156521433--2-11111123337999886543344677
Q gi|254780916|r  239 LEEPDALPLAVQGR----IYNFIETGKIEFFDSRGAIRLDVRLIFLTEKN--L-LPQVKSHVFRKDLYYRISVFLINIST  311 (482)
Q Consensus       239 l~ei~~L~~~~Q~~----Ll~~l~~~~~~~~g~~~~~~~~~RiIa~t~~~--L-~~~~~~g~fr~dLy~rL~~~~i~iPp  311 (482)
                      +|||+.+-..-...    -.|++.+--+..-  .-+...+|.+|++||..  + ..+...|+|++       .+.|..|.
T Consensus       341 iDEiDs~~~~r~~~~~~~~~rv~~~ll~~~d--~~e~~~~v~vi~aTN~p~~ld~a~lR~gRfd~-------~i~v~~pd  411 (494)
T COG0464         341 IDEIDSLASGRGPSEDGSGRRVVGQLLTELD--GIEKAEGVLVIAATNRPDDLDPALLRPGRFDR-------LIYVPLPD  411 (494)
T ss_pred             HHHHHHHHCCCCCCCCCHHHHHHHHHHHHHH--CCCCCCCEEEEECCCCCCCCCHHHHCCCCCEE-------EEEECCCC
T ss_conf             4886667412899876379999999999974--75443764899647983326875624366303-------78717989


Q ss_pred             HHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHCC----CCCCCHHHHHHHHC
Q ss_conf             87744222255667776410112233332111110001223389868999999999987438----98106889545421
Q gi|254780916|r  312 LRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQELKNILLRAVIGLK----DSHLTEDRFVLLLS  387 (482)
Q Consensus       312 LReR~eDI~~L~~~fl~~~~~~~~~~~~~ls~~a~~~L~~y~WPGNvREL~n~i~r~~i~~~----~~~i~~~~~~~~l~  387 (482)
                      ..+|.+=+    .+++.......   ...++-+.+...... |  .-.++.++++.+....-    ...++.+|+...+.
T Consensus       412 ~~~r~~i~----~~~~~~~~~~~---~~~~~~~~l~~~t~~-~--sgadi~~i~~ea~~~~~~~~~~~~~~~~~~~~a~~  481 (494)
T COG0464         412 LEERLEIF----KIHLRDKKPPL---AEDVDLEELAEITEG-Y--SGADIAALVREAALEALREARRREVTLDDFLDALK  481 (494)
T ss_pred             HHHHHHHH----HHHHCCCCCCH---HHHHHHHHHHHHHCC-C--CHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHH
T ss_conf             89999999----99854156511---556419999987527-7--89999999999999899854577634999999986


No 193
>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=98.11  E-value=4.1e-06  Score=62.81  Aligned_cols=204  Identities=16%  Similarity=0.181  Sum_probs=108.0

Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCCCHHHHHHHHHHHCCCC-------CCCCCCCCCCCCCCCCCC
Q ss_conf             1111111122222222222222223443204887327774367999999842675-------433210123465542100
Q gi|254780916|r  135 EHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHESGKR-------AFFPFFIVNCGMIDQDKI  207 (482)
Q Consensus       135 ~~~~~~~LiG~S~~m~~v~~~i~~~a~~~~~vli~Ge~GtGK~~~A~~iH~~s~r-------~~~~fi~v~c~~~~~~~~  207 (482)
                      .....+++||....++++.+-++|  .+..+.++.||+|+||+.++..+-..=-.       ++...+.+|.+++     
T Consensus       182 ~~gklDPvIGRd~EI~r~iqIL~R--r~KNNPiLVGepGVGKTAIvEGLA~rI~~g~VP~~L~~~~i~sLDlg~L-----  254 (852)
T TIGR03345       182 REGKIDPVLGRDDEIRQMIDILLR--RRQNNPILTGEAGVGKTAVVEGLALRIAAGDVPPALRNVRLLSLDLGLL-----  254 (852)
T ss_pred             HCCCCCCCCCCHHHHHHHHHHHHH--HCCCCCEEECCCCCCHHHHHHHHHHHHHCCCCCHHHHCCEEEEEEHHHH-----
T ss_conf             839999886949999999999986--2479974657999879999999999997699986774385678678888-----


Q ss_pred             HHHHHCCCCCCCCCCCCCC-CCCCC---CCC-CEEEECCCCHHH--------HHHHHHHHH-HHHHHHCCCCCCCCCCCC
Q ss_conf             2433112555532211100-12344---667-147516642001--------889998888-776420011235532123
Q gi|254780916|r  208 EKFLFGDVDLQTKNSAQFL-GKFIE---ANG-GTIVLEEPDALP--------LAVQGRIYN-FIETGKIEFFDSRGAIRL  273 (482)
Q Consensus       208 e~~lFG~~~~~~~~~~~~~-g~~~~---a~~-Gtl~l~ei~~L~--------~~~Q~~Ll~-~l~~~~~~~~g~~~~~~~  273 (482)
                         +=|-+  +-|....|. +.+.+   +.+ -.||+||||.+=        .+. ..+|. +|..|             
T Consensus       255 ---vAGtk--yRGeFEeRlk~ii~ei~~~~~~iILFIDEiHtlvGAG~~~G~~Da-aNiLKPaLarG-------------  315 (852)
T TIGR03345       255 ---QAGAS--VKGEFENRLKSVIDEVKASPQPIILFIDEAHTLIGAGGQAGQGDA-ANLLKPALARG-------------  315 (852)
T ss_pred             ---HHCCC--CCCHHHHHHHHHHHHHHHCCCCEEEEEEHHHHHCCCCCCCCCCCH-HHHHHHHHHCC-------------
T ss_conf             ---64035--763599999999999984899769996348775289988886227-88751787378-------------


Q ss_pred             CCEEEEECCCCCCCCCCHHHHHH--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---------------HHCCCCCC
Q ss_conf             43156521433211111123337--99988654334467787744222255667776---------------41011223
Q gi|254780916|r  274 DVRLIFLTEKNLLPQVKSHVFRK--DLYYRISVFLINISTLRSRSEDIPWLVHFFLQ---------------SFCTKNAI  336 (482)
Q Consensus       274 ~~RiIa~t~~~L~~~~~~g~fr~--dLy~rL~~~~i~iPpLReR~eDI~~L~~~fl~---------------~~~~~~~~  336 (482)
                      ++|+|.+|+.+=-    ...|-+  -|=-|...+.|.=|+--+-.+=+.-|...|=.               +.+.+|= 
T Consensus       316 elr~IGATT~~EY----rk~iEkD~AL~RRFq~V~V~EPs~eeti~IL~glk~~yE~hH~V~i~d~Ai~aAv~LS~RYI-  390 (852)
T TIGR03345       316 ELRTIAATTWAEY----KKYFEKDPALTRRFQVVKVEEPDEETAIRMLRGLAPVLEKHHGVLILDEAVVAAVELSHRYI-  390 (852)
T ss_pred             CCEEEEECCHHHH----HHHHHCCHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHCCCEEEEHHHHHHHHHHHHHHC-
T ss_conf             7349983578999----88864268899624755279998799999999879998554796870899999999987215-


Q ss_pred             CCCCCCCCCCCCC---------CCCCCCCCHHHHHHHHHHHH
Q ss_conf             3332111110001---------22338986899999999998
Q gi|254780916|r  337 KQISISDKALSLL---------TKYPWIDNVQELKNILLRAV  369 (482)
Q Consensus       337 ~~~~ls~~a~~~L---------~~y~WPGNvREL~n~i~r~~  369 (482)
                      +-+.+++.|+.+|         .....|-.+.+|++-+..+-
T Consensus       391 ~dR~LPDKAIDLlDeA~A~~~~~~~~~p~~l~~~~~~~~~~~  432 (852)
T TIGR03345       391 PGRQLPDKAVSLLDTACARVALSQNATPAALEDLRRRIAALE  432 (852)
T ss_pred             CCCCCCHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHH
T ss_conf             545584278999999999999860489568999999999999


No 194
>KOG0734 consensus
Probab=98.11  E-value=9.1e-06  Score=60.39  Aligned_cols=210  Identities=17%  Similarity=0.258  Sum_probs=116.6

Q ss_pred             CCCCCCCCCCCCCCCC---CCCCCCCC------CCC-CCCEEEEEECCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCC
Q ss_conf             2111111112222222---22222222------234-4320488732777436799999984267543321012346554
Q gi|254780916|r  134 NEHCALDSLIAVSPAM---IQVVDLAR------KAG-DCAIPIMIQGEFGVGKKRLSRFIHESGKRAFFPFFIVNCGMID  203 (482)
Q Consensus       134 ~~~~~~~~LiG~S~~m---~~v~~~i~------~~a-~~~~~vli~Ge~GtGK~~~A~~iH~~s~r~~~~fi~v~c~~~~  203 (482)
                      ..+..|++.-|...+=   ++|.+.++      ++. ....-||++|++||||+++||+|-..   ++-||.....+.  
T Consensus       298 ~~nv~F~dVkG~DEAK~ELeEiVefLkdP~kftrLGGKLPKGVLLvGPPGTGKTlLARAvAGE---A~VPFF~~sGSE--  372 (752)
T KOG0734         298 MKNVTFEDVKGVDEAKQELEEIVEFLKDPTKFTRLGGKLPKGVLLVGPPGTGKTLLARAVAGE---AGVPFFYASGSE--  372 (752)
T ss_pred             HCCCCCCCCCCHHHHHHHHHHHHHHHCCCHHHHHCCCCCCCCEEEECCCCCCHHHHHHHHHCC---CCCCEEECCCCC--
T ss_conf             416550021472789999999999860908764314758885387689997556999986055---689747416620--


Q ss_pred             CCCCHHHHHCCCCCCCCCCCCCCCCCCCCC---CCEEEECCCCHHH-----HHHH---HHHHHHHHH-HHCCCCCCCCCC
Q ss_conf             210024331125555322111001234466---7147516642001-----8899---988887764-200112355321
Q gi|254780916|r  204 QDKIEKFLFGDVDLQTKNSAQFLGKFIEAN---GGTIVLEEPDALP-----LAVQ---GRIYNFIET-GKIEFFDSRGAI  271 (482)
Q Consensus       204 ~~~~e~~lFG~~~~~~~~~~~~~g~~~~a~---~Gtl~l~ei~~L~-----~~~Q---~~Ll~~l~~-~~~~~~g~~~~~  271 (482)
                         +++.+-|.     | ..+...+|.+|.   --.+|+|||+...     .+.+   .-|-++|-+ .-|.+   +.  
T Consensus       373 ---FdEm~VGv-----G-ArRVRdLF~aAk~~APcIIFIDEiDavG~kR~~~~~~y~kqTlNQLLvEmDGF~q---Ne--  438 (752)
T KOG0734         373 ---FDEMFVGV-----G-ARRVRDLFAAAKARAPCIIFIDEIDAVGGKRNPSDQHYAKQTLNQLLVEMDGFKQ---NE--  438 (752)
T ss_pred             ---HHHHHHCC-----C-HHHHHHHHHHHHHCCCEEEEEECHHHHCCCCCCCHHHHHHHHHHHHHHHHCCCCC---CC--
T ss_conf             ---44542201-----4-8999999999873498599972002205667862778999899999998428676---88--


Q ss_pred             CCCCEEEEECCCC--C-CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCC
Q ss_conf             2343156521433--2-111111233379998865433446778774422225566777641011223333211111000
Q gi|254780916|r  272 RLDVRLIFLTEKN--L-LPQVKSHVFRKDLYYRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSL  348 (482)
Q Consensus       272 ~~~~RiIa~t~~~--L-~~~~~~g~fr~dLy~rL~~~~i~iPpLReR~eDI~~L~~~fl~~~~~~~~~~~~~ls~~a~~~  348 (482)
                        -+=||++||.+  | ..++.-|+|..       .+++..|-+|-|.| |   ..+++.+.-...     .++++.   
T Consensus       439 --GiIvigATNfpe~LD~AL~RPGRFD~-------~v~Vp~PDv~GR~e-I---L~~yl~ki~~~~-----~VD~~i---  497 (752)
T KOG0734         439 --GIIVIGATNFPEALDKALTRPGRFDR-------HVTVPLPDVRGRTE-I---LKLYLSKIPLDE-----DVDPKI---  497 (752)
T ss_pred             --CEEEEECCCCHHHHHHHHCCCCCCCE-------EEECCCCCCCCHHH-H---HHHHHHCCCCCC-----CCCHHH---
T ss_conf             --66999516874555687348875533-------67468977332899-9---999983487656-----778767---


Q ss_pred             CCCCCCCC-CHHHHHHHHHHHHHHC---CCCCCCHHHHHH
Q ss_conf             12233898-6899999999998743---898106889545
Q gi|254780916|r  349 LTKYPWID-NVQELKNILLRAVIGL---KDSHLTEDRFVL  384 (482)
Q Consensus       349 L~~y~WPG-NvREL~n~i~r~~i~~---~~~~i~~~~~~~  384 (482)
                       ....-|| +-.+|.|+|-+|.+-+   ....++..++.-
T Consensus       498 -iARGT~GFsGAdLaNlVNqAAlkAa~dga~~VtM~~LE~  536 (752)
T KOG0734         498 -IARGTPGFSGADLANLVNQAALKAAVDGAEMVTMKHLEF  536 (752)
T ss_pred             -HCCCCCCCCHHHHHHHHHHHHHHHHHCCCCCCCHHHHHH
T ss_conf             -226889876578998888999999863740110887765


No 195
>KOG0733 consensus
Probab=98.08  E-value=4.5e-06  Score=62.57  Aligned_cols=130  Identities=22%  Similarity=0.279  Sum_probs=81.9

Q ss_pred             CCEEEEEECCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCHHHHHCCCCCCCCCCCCCCCCCCCCCC---CEEE
Q ss_conf             3204887327774367999999842675433210123465542100243311255553221110012344667---1475
Q gi|254780916|r  162 CAIPIMIQGEFGVGKKRLSRFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFGDVDLQTKNSAQFLGKFIEANG---GTIV  238 (482)
Q Consensus       162 ~~~~vli~Ge~GtGK~~~A~~iH~~s~r~~~~fi~v~c~~~~~~~~e~~lFG~~~~~~~~~~~~~g~~~~a~~---Gtl~  238 (482)
                      ...-||+.|++|+||+++|+++-+.+.   ..||.|-.    .+++ +.--|+.   .-|   ..-.|..|..   -.+|
T Consensus       544 ~PsGvLL~GPPGCGKTLlAKAVANEag---~NFisVKG----PELl-NkYVGES---ErA---VR~vFqRAR~saPCVIF  609 (802)
T KOG0733         544 APSGVLLCGPPGCGKTLLAKAVANEAG---ANFISVKG----PELL-NKYVGES---ERA---VRQVFQRARASAPCVIF  609 (802)
T ss_pred             CCCCEEEECCCCCCHHHHHHHHHHHCC---CCEEEECC----HHHH-HHHHHHH---HHH---HHHHHHHHHCCCCEEEE
T ss_conf             987238757998618899999850304---75476238----8999-8774237---899---99999986238983898


Q ss_pred             ECCCCHHHH-------HHHHHHHHHHHHHHCCCCCCCCCCCCCCEEEEECCCCC---CCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf             166420018-------89998888776420011235532123431565214332---11111123337999886543344
Q gi|254780916|r  239 LEEPDALPL-------AVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNL---LPQVKSHVFRKDLYYRISVFLIN  308 (482)
Q Consensus       239 l~ei~~L~~-------~~Q~~Ll~~l~~~~~~~~g~~~~~~~~~RiIa~t~~~L---~~~~~~g~fr~dLy~rL~~~~i~  308 (482)
                      +|||+.|-+       +.-.+++..|-+-    +++-. ....|-||++||++-   ..+..-|+|..=||       +.
T Consensus       610 FDEiDaL~p~R~~~~s~~s~RvvNqLLtE----lDGl~-~R~gV~viaATNRPDiIDpAiLRPGRlDk~Ly-------V~  677 (802)
T KOG0733         610 FDEIDALVPRRSDEGSSVSSRVVNQLLTE----LDGLE-ERRGVYVIAATNRPDIIDPAILRPGRLDKLLY-------VG  677 (802)
T ss_pred             ECCHHHCCCCCCCCCCHHHHHHHHHHHHH----HCCCC-CCCCEEEEEECCCCCCCCHHHCCCCCCCCEEE-------EC
T ss_conf             51112027655777750589999999987----31621-11425999506897655565518775574245-------06


Q ss_pred             HHHHHHHHH
Q ss_conf             677877442
Q gi|254780916|r  309 ISTLRSRSE  317 (482)
Q Consensus       309 iPpLReR~e  317 (482)
                      +|+-.||.+
T Consensus       678 lPn~~eR~~  686 (802)
T KOG0733         678 LPNAEERVA  686 (802)
T ss_pred             CCCHHHHHH
T ss_conf             998788999


No 196
>COG1219 ClpX ATP-dependent protease Clp, ATPase subunit [Posttranslational modification, protein turnover, chaperones]
Probab=98.07  E-value=7.2e-06  Score=61.10  Aligned_cols=96  Identities=22%  Similarity=0.267  Sum_probs=68.2

Q ss_pred             CCCCCEEEEEECCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCHHHHHCCCCCCCCCCCCC---------CCCC
Q ss_conf             3443204887327774367999999842675433210123465542100243311255553221110---------0123
Q gi|254780916|r  159 AGDCAIPIMIQGEFGVGKKRLSRFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFGDVDLQTKNSAQF---------LGKF  229 (482)
Q Consensus       159 ~a~~~~~vli~Ge~GtGK~~~A~~iH~~s~r~~~~fi~v~c~~~~~~~~e~~lFG~~~~~~~~~~~~---------~g~~  229 (482)
                      +--+.++||+.|++|+||+++|+.+-..   -+-||..-||.++++.       |+.    |.+...         ..-.
T Consensus        93 vEL~KSNILLiGPTGsGKTlLAqTLAk~---LnVPFaiADATtLTEA-------GYV----GEDVENillkLlqaadydV  158 (408)
T COG1219          93 VELSKSNILLIGPTGSGKTLLAQTLAKI---LNVPFAIADATTLTEA-------GYV----GEDVENILLKLLQAADYDV  158 (408)
T ss_pred             EEEEECCEEEECCCCCCHHHHHHHHHHH---HCCCEEECCCCCHHHC-------CCC----CHHHHHHHHHHHHHCCCCH
T ss_conf             3532031799888997577999999998---4898475144412106-------635----5008999999998764588


Q ss_pred             CCCCCCEEEECCCCHHHH--------------HHHHHHHHHHHHH--HCCCCCCC
Q ss_conf             446671475166420018--------------8999888877642--00112355
Q gi|254780916|r  230 IEANGGTIVLEEPDALPL--------------AVQGRIYNFIETG--KIEFFDSR  268 (482)
Q Consensus       230 ~~a~~Gtl~l~ei~~L~~--------------~~Q~~Ll~~l~~~--~~~~~g~~  268 (482)
                      +.|..|.+|+|||+.++.              -+|..||..++-.  .+-|-|+.
T Consensus       159 ~rAerGIIyIDEIDKIarkSen~SITRDVSGEGVQQALLKiiEGTvasVPPqGGR  213 (408)
T COG1219         159 ERAERGIIYIDEIDKIARKSENPSITRDVSGEGVQQALLKIIEGTVASVPPQGGR  213 (408)
T ss_pred             HHHHCCEEEEECHHHHHCCCCCCCCCCCCCCHHHHHHHHHHHCCCEECCCCCCCC
T ss_conf             8882885998510254205789872343673589999999970751023999888


No 197
>COG4567 Response regulator consisting of a CheY-like receiver domain and a Fis-type HTH domain [Signal transduction mechanisms / Transcription]
Probab=98.07  E-value=2.8e-05  Score=56.90  Aligned_cols=42  Identities=31%  Similarity=0.378  Sum_probs=38.6

Q ss_pred             HHHHHHHHHHHHHHHHHCCCHHHHHHHHCCCHHHHHHHHHHH
Q ss_conf             999999999999999828727899978489988999999981
Q gi|254780916|r  434 RLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKIREY  475 (482)
Q Consensus       434 ~l~e~E~~~I~~aL~~~~Gn~~~aA~~LGIsR~tL~rKlk~~  475 (482)
                      +++.++.+.|.++|+.|+||++++|+.|||.|+||.||+.|-
T Consensus       138 S~~rl~WEhIqrvl~e~~~NiSeTARrL~MHRRTLqRkL~KR  179 (182)
T COG4567         138 SADRLRWEHIQRVLEECEGNISETARRLNMHRRTLQRKLAKR  179 (182)
T ss_pred             CHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHCC
T ss_conf             456766999999999937777899999621399999997414


No 198
>PRK08770 DNA polymerase III subunits gamma and tau; Validated
Probab=98.07  E-value=0.00014  Score=52.04  Aligned_cols=222  Identities=14%  Similarity=0.155  Sum_probs=120.1

Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCCCHHHHHHHHHHHCCCCCCCCC-----CCCCCCCCCCCCCH
Q ss_conf             2111111112222222222222222344320488732777436799999984267543321-----01234655421002
Q gi|254780916|r  134 NEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHESGKRAFFPF-----FIVNCGMIDQDKIE  208 (482)
Q Consensus       134 ~~~~~~~~LiG~S~~m~~v~~~i~~~a~~~~~vli~Ge~GtGK~~~A~~iH~~s~r~~~~f-----i~v~c~~~~~~~~e  208 (482)
                      .....|..++|+.-..+.+...+.. .....--|++|..|+||+.+||.+-+.-.-..++-     .--+|..+....+-
T Consensus        10 ~rp~~f~~~~gq~~~~~~l~~~~~~-~~~~~a~lf~g~rg~gkt~~ar~~a~~lnc~~~~~~~pc~~c~~c~~i~~~~~~   88 (663)
T PRK08770         10 WRPKRFAELVGQEHVVRALSNALDS-GRVHHAFLFTGTRGVGKTTIARIFAKSLNCETGTSADPCGQCPACLDIDAGRYI   88 (663)
T ss_pred             HCCCCHHHHCCCHHHHHHHHHHHHC-CCCCEEEEEECCCCCCHHHHHHHHHHHHCCCCCCCCCCCCCCHHHHHHHCCCCC
T ss_conf             0887464522859999999999970-997404762279988888999999998678999999978778778988548988


Q ss_pred             HHHHCCCCCC-CCCCCCCCCCCCC-------CCCCEEEECCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCEEEEE
Q ss_conf             4331125555-3221110012344-------6671475166420018899988887764200112355321234315652
Q gi|254780916|r  209 KFLFGDVDLQ-TKNSAQFLGKFIE-------ANGGTIVLEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFL  280 (482)
Q Consensus       209 ~~lFG~~~~~-~~~~~~~~g~~~~-------a~~Gtl~l~ei~~L~~~~Q~~Ll~~l~~~~~~~~g~~~~~~~~~RiIa~  280 (482)
                      ..+  +.++. .....+-.-+++.       ..--..++||+|-|+...=.-||..|++-           +-+|.+|.+
T Consensus        89 d~~--e~daas~~~v~~~r~~~~~~~~~p~~~~~kvy~idevhmls~~~fna~lktleep-----------p~~v~f~~a  155 (663)
T PRK08770         89 DLL--EIDAASNTGVDDVREVIENAQYMPSRGKFKVYLIDEVHMLSKAAFNALLKTLEEP-----------PEHVKFLLA  155 (663)
T ss_pred             CEE--EEECCCCCCHHHHHHHHHHCCCCCCCCCEEEEEEECHHHCCHHHHHHHHHHHCCC-----------CCCEEEEEE
T ss_conf             658--8646765888999999984435887774369997004332899999998740278-----------644289985


Q ss_pred             CCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCHHH
Q ss_conf             14332111111233379998865433446778774422225566777641011223333211111000122338986899
Q gi|254780916|r  281 TEKNLLPQVKSHVFRKDLYYRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQE  360 (482)
Q Consensus       281 t~~~L~~~~~~g~fr~dLy~rL~~~~i~iPpLReR~eDI~~L~~~fl~~~~~~~~~~~~~ls~~a~~~L~~y~WPGNvRE  360 (482)
                      |+.. .++- --.+.+=|-|-|.-  |..       ++   ++.| |.....+.+   ..++++|+..+.. .=-|-+|.
T Consensus       156 tt~~-~k~p-~t~~src~~f~~~~--~~~-------~~---~~~~-l~~~~~~e~---~~~~~~~~~~~~~-~~~gs~rd  216 (663)
T PRK08770        156 TTDP-QKLP-VTVLSRCLQFNLKR--LDE-------DQ---IQGQ-MTRILAAEQ---IESDPSAIVQLSK-AADGSLRD  216 (663)
T ss_pred             CCCH-HHCC-HHHHHHHHHCCCCC--CCH-------HH---HHHH-HHHHHHHCC---CCCCHHHHHHHHH-HCCCCHHH
T ss_conf             4873-3374-89998887634377--999-------99---9999-999999839---9769999999999-74785677


Q ss_pred             HHHHHHHHHHHCCCCCCCHHHHHHHHCCC
Q ss_conf             99999999874389810688954542124
Q gi|254780916|r  361 LKNILLRAVIGLKDSHLTEDRFVLLLSRE  389 (482)
Q Consensus       361 L~n~i~r~~i~~~~~~i~~~~~~~~l~~~  389 (482)
                      =-++..+++..+ ++.|+.+++..-++..
T Consensus       217 ~lsl~~q~~~~~-~~~~~~~~v~~mlg~~  244 (663)
T PRK08770        217 GLSLLDQAIAYA-GGALREDVVRTMLGTV  244 (663)
T ss_pred             HHHHHHHHHHHC-CCCCCHHHHHHHHCCC
T ss_conf             888999999866-8976899999984888


No 199
>PRK09087 hypothetical protein; Validated
Probab=98.03  E-value=3.6e-05  Score=56.19  Aligned_cols=199  Identities=17%  Similarity=0.186  Sum_probs=116.0

Q ss_pred             CCCCCCCC-CCCCCCCCCCCCCCCCCCCCCEE-EEEECCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCHHHHH
Q ss_conf             11111111-22222222222222223443204-88732777436799999984267543321012346554210024331
Q gi|254780916|r  135 EHCALDSL-IAVSPAMIQVVDLARKAGDCAIP-IMIQGEFGVGKKRLSRFIHESGKRAFFPFFIVNCGMIDQDKIEKFLF  212 (482)
Q Consensus       135 ~~~~~~~L-iG~S~~m~~v~~~i~~~a~~~~~-vli~Ge~GtGK~~~A~~iH~~s~r~~~~fi~v~c~~~~~~~~e~~lF  212 (482)
                      ....++.+ +|.+-  +..++.+.+......| +.|.|+.|+||+++++...+.+.   ..  .+++..++.+..     
T Consensus        16 ~~~~~dnF~vs~~N--~~a~~~l~~~~~w~~~~~~L~Gp~gsGKTHL~~~~~~~~~---a~--~~~~~~~~~~~~-----   83 (226)
T PRK09087         16 PGYGRDDLVVTESN--RAAVSLVDRWPNWPSPVVVLAGPVGSGKTHLASIWREKAD---AL--LVHPNEIGSDAA-----   83 (226)
T ss_pred             CCCCCCCEEECCCH--HHHHHHHHHCCCCCCCEEEEECCCCCCHHHHHHHHHHHHC---CE--EECHHHCCHHHH-----
T ss_conf             77873364775769--9999999847267777589989999988699999999809---96--836687474667-----


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCEEEECCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCEEEEECCCCCCCCCCHH
Q ss_conf             12555532211100123446671475166420018899988887764200112355321234315652143321111112
Q gi|254780916|r  213 GDVDLQTKNSAQFLGKFIEANGGTIVLEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSH  292 (482)
Q Consensus       213 G~~~~~~~~~~~~~g~~~~a~~Gtl~l~ei~~L~~~~Q~~Ll~~l~~~~~~~~g~~~~~~~~~RiIa~t~~~L~~~~~~g  292 (482)
                                       ....++.+++|+++..+.+ +..|+.++..=          +....+++.+++.++.++--. 
T Consensus        84 -----------------~~~~~~~~~idd~d~~~~d-Ee~LFhl~N~~----------~~~~~~LLlts~~~p~~l~~~-  134 (226)
T PRK09087         84 -----------------NAAAERPVLIEDIDAGGFD-ETGLFHLINSV----------RQAGTSLLMTSRLWPSAWNVK-  134 (226)
T ss_pred             -----------------HHHCCCCEEEECCCCCCCC-HHHHHHHHHHH----------HHCCCEEEEECCCCHHHCCCC-
T ss_conf             -----------------6532798899748777747-89999999999----------853987999889895666762-


Q ss_pred             HHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHH--
Q ss_conf             3337999886543-3446778774422225566777641011223333211111000122338986899999999998--
Q gi|254780916|r  293 VFRKDLYYRISVF-LINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQELKNILLRAV--  369 (482)
Q Consensus       293 ~fr~dLy~rL~~~-~i~iPpLReR~eDI~~L~~~fl~~~~~~~~~~~~~ls~~a~~~L~~y~WPGNvREL~n~i~r~~--  369 (482)
                        .+||=-||+.. .++++++-    |-  +....+.+.+..-|   ..++++.+.+|..+ ++-++..|.+++.++=  
T Consensus       135 --L~DL~SRL~~~~~~~I~~pd----D~--ll~~~L~k~~~~r~---l~l~~~v~~yll~r-~~Rs~~~l~~~l~~LD~~  202 (226)
T PRK09087        135 --LPDLKSRLKAATVVEIGEPD----DA--LLSGVIFKLFADRQ---LYVEPHVVYYLVSR-MERSLFAAQTIVERLDRL  202 (226)
T ss_pred             --CHHHHHHHHCCEEEEECCCC----HH--HHHHHHHHHHHHCC---CCCCHHHHHHHHHH-CCCCHHHHHHHHHHHHHH
T ss_conf             --46899998578579835999----89--99999999987576---57888899999984-588999999999999999


Q ss_pred             HHCCCCCCCHHHHHHHH
Q ss_conf             74389810688954542
Q gi|254780916|r  370 IGLKDSHLTEDRFVLLL  386 (482)
Q Consensus       370 i~~~~~~i~~~~~~~~l  386 (482)
                      .+..+..||..-+...+
T Consensus       203 SL~~kr~ITiplikevL  219 (226)
T PRK09087        203 ALERKSRITRALAAEVL  219 (226)
T ss_pred             HHHCCCCCCHHHHHHHH
T ss_conf             99818999899999999


No 200
>PHA02244 ATPase-like protein
Probab=98.02  E-value=1.1e-05  Score=59.72  Aligned_cols=130  Identities=26%  Similarity=0.305  Sum_probs=88.4

Q ss_pred             CCCCCCCCCCCCCCCCCCCCCEEEEEECCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCHHHHHCCCCCCCCCC
Q ss_conf             22222222222222223443204887327774367999999842675433210123465542100243311255553221
Q gi|254780916|r  143 IAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFGDVDLQTKNS  222 (482)
Q Consensus       143 iG~S~~m~~v~~~i~~~a~~~~~vli~Ge~GtGK~~~A~~iH~~s~r~~~~fi~v~c~~~~~~~~e~~lFG~~~~~~~~~  222 (482)
                      +...|...--...+.++.+.+.||.+.|..|+||+.+|+-|-..-   +-||--.+.  +   .-|-+|-|..++ .|..
T Consensus        99 iasnpt~hy~~~~i~~~v~~nipV~L~G~AGsGKt~~A~qIA~aL---dl~FYf~gA--I---~~ef~L~Gf~DA-nG~y  169 (383)
T PHA02244         99 IASNPTFHYETADIAKIVNANIPVFLKGGAGSGKNHIAEQIAEAL---DLDFYFMNA--I---MDEFELKGFIDA-NGKF  169 (383)
T ss_pred             CCCCCCHHHHHHHHHHHHHCCCCEEEECCCCCCHHHHHHHHHHHH---CCCCEECHH--H---HHHHHCCCEECC-CCCE
T ss_conf             147863234587899987359856997588886348999999985---888244132--3---013430125648-9967


Q ss_pred             CC--CCCCCCCCCCCEEEECCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCEEEEECCC
Q ss_conf             11--00123446671475166420018899988887764200112355321234315652143
Q gi|254780916|r  223 AQ--FLGKFIEANGGTIVLEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEK  283 (482)
Q Consensus       223 ~~--~~g~~~~a~~Gtl~l~ei~~L~~~~Q~~Ll~~l~~~~~~~~g~~~~~~~~~RiIa~t~~  283 (482)
                      ..  ..-.|+  +||.++||||+.--+..=..|-.+|.++.+....+.-..+-|||+|++.|-
T Consensus       170 h~T~f~kaFk--~GGLfLlDEiDASnP~aL~~lNaALAN~fm~FPdG~V~~HedFr~IAagNT  230 (383)
T PHA02244        170 HETPFYEAFK--KGGLFFIDEIDASIPEALIIINSAIANKFFDFADERVTAHEDFRVISAGNT  230 (383)
T ss_pred             ECCHHHHHHH--CCCEEEEEHHCCCCHHHHHHHHHHHHCCCCCCCCCHHHCCCCEEEEEECCC
T ss_conf             2638999986--188799732004487999999899864763476421100576389972465


No 201
>PRK05896 DNA polymerase III subunits gamma and tau; Validated
Probab=98.01  E-value=5.9e-05  Score=54.67  Aligned_cols=209  Identities=15%  Similarity=0.168  Sum_probs=117.4

Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCCCHHHHHHHHHHHC----CCCCCCCCC-CCCCCCCCC----C
Q ss_conf             1111111122222222222222223443204887327774367999999842----675433210-123465542----1
Q gi|254780916|r  135 EHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHES----GKRAFFPFF-IVNCGMIDQ----D  205 (482)
Q Consensus       135 ~~~~~~~LiG~S~~m~~v~~~i~~~a~~~~~vli~Ge~GtGK~~~A~~iH~~----s~r~~~~fi-~v~c~~~~~----~  205 (482)
                      ....|+.++|+....+.+...+.+= .....-|+.|+.|+||+.+||.+-..    +.....|-- --+|..+..    +
T Consensus        11 RPk~F~eIIGQe~iv~~L~nAI~~~-RiaHAYLFsGPrGvGKTTlArifAkaLnC~~~~~~dpCg~C~sC~~I~~g~h~D   89 (613)
T PRK05896         11 RPHNFKQIIGQELIKKILVNAILNN-KLTHAYIFSGPRGIGKTSIAKIFAKAINCLNPKDGDCCNSCSVCESINTNQSVD   89 (613)
T ss_pred             CCCCHHHHCCCHHHHHHHHHHHHCC-CCCCEEEEECCCCCCHHHHHHHHHHHHCCCCCCCCCCCCCCHHHHHHHCCCCCC
T ss_conf             7997655238299999999999849-976227755899848899999999996699999999888887899985699998


Q ss_pred             CCHHHHHCCCCCCCC-CCCCCCCCCCC-------CCCCEEEECCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCEE
Q ss_conf             002433112555532-21110012344-------6671475166420018899988887764200112355321234315
Q gi|254780916|r  206 KIEKFLFGDVDLQTK-NSAQFLGKFIE-------ANGGTIVLEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRL  277 (482)
Q Consensus       206 ~~e~~lFG~~~~~~~-~~~~~~g~~~~-------a~~Gtl~l~ei~~L~~~~Q~~Ll~~l~~~~~~~~g~~~~~~~~~Ri  277 (482)
                      .+|      .+++.. ...+-..+.+.       ...-..++||.+.|+.+.+..||..|++.           +.++.+
T Consensus        90 viE------Idaasn~gIDeIReLie~~~~~P~~gkyKV~IIDEah~Ln~~AaNALLKtLEEP-----------P~~viF  152 (613)
T PRK05896         90 IVE------LDAASNNGVDEIRNIIDNINYLPTTFKYKVYIIDEAHMLSTSAWNALLKTLEEP-----------PKHVVF  152 (613)
T ss_pred             EEE------EECCCCCCHHHHHHHHHHHCCCCCCCCCEEEEECCHHHCCHHHHHHHHHHCCCC-----------CCCCEE
T ss_conf             688------406555788999999997085875799459998162217999999999853489-----------878379


Q ss_pred             EEECCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH-------HHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCC
Q ss_conf             6521433211111123337999886543344677877442-------222556677764101122333321111100012
Q gi|254780916|r  278 IFLTEKNLLPQVKSHVFRKDLYYRISVFLINISTLRSRSE-------DIPWLVHFFLQSFCTKNAIKQISISDKALSLLT  350 (482)
Q Consensus       278 Ia~t~~~L~~~~~~g~fr~dLy~rL~~~~i~iPpLReR~e-------DI~~L~~~fl~~~~~~~~~~~~~ls~~a~~~L~  350 (482)
                      |.+|+.. ..                    -+|+.+-|..       +...++.+ |...+.+.+   ..++++|+..+.
T Consensus       153 IL~Ttep-~K--------------------LLpTIlSRCQrf~Fkri~~~~I~~~-L~~I~~kE~---i~ie~~AL~~Ia  207 (613)
T PRK05896        153 IFATTEF-QK--------------------IPLTIISRCQRYNFKKLNNSELQEL-LKSIAKKEK---IKIEDNAIDKIA  207 (613)
T ss_pred             EEEECCH-HH--------------------CCHHHHHCCCCEECCCCCHHHHHHH-HHHHHHHCC---CCCCHHHHHHHH
T ss_conf             9982881-54--------------------9376640355001788998999999-999999739---987899999999


Q ss_pred             CCCCCCCHHHHHHHHHHHHHHCCCCCCCHHHHHHHHCC
Q ss_conf             23389868999999999987438981068895454212
Q gi|254780916|r  351 KYPWIDNVQELKNILLRAVIGLKDSHLTEDRFVLLLSR  388 (482)
Q Consensus       351 ~y~WPGNvREL~n~i~r~~i~~~~~~i~~~~~~~~l~~  388 (482)
                      ... -|-+|.=-+++.+++.. .++.|+.+++...++-
T Consensus       208 ~~a-dGs~RDAlslLdQ~~~~-~~~~it~~~v~~~~g~  243 (613)
T PRK05896        208 DLA-DGSLRDGLSILDQLSTF-KNKKIDIEDINKTFGL  243 (613)
T ss_pred             HHC-CCCHHHHHHHHHHHHHH-CCCCCCHHHHHHHHCC
T ss_conf             976-88487898899999983-5688629999999677


No 202
>PRK11034 clpA ATP-dependent Clp protease ATP-binding subunit; Provisional
Probab=98.00  E-value=2.6e-06  Score=64.21  Aligned_cols=154  Identities=16%  Similarity=0.230  Sum_probs=84.2

Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCCCHHHHHHHHHHHCCC-------CCCCCCCCCCCCCCCCCCC
Q ss_conf             111111112222222222222222344320488732777436799999984267-------5433210123465542100
Q gi|254780916|r  135 EHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHESGK-------RAFFPFFIVNCGMIDQDKI  207 (482)
Q Consensus       135 ~~~~~~~LiG~S~~m~~v~~~i~~~a~~~~~vli~Ge~GtGK~~~A~~iH~~s~-------r~~~~fi~v~c~~~~~~~~  207 (482)
                      .....+++||....++++.+-++|  .+.-+.++.||+|+||+.++..+-..=-       -++...+.+|.+++     
T Consensus       181 r~gklDPviGR~~Ei~r~i~iL~R--r~KNNpiLvGepGVGKTAIvEGLA~rI~~g~VP~~L~~~~i~~Ldl~~L-----  253 (758)
T PRK11034        181 RVGGIDPLIGREKELERAIQVLCR--RRKNNPLLVGESGVGKTAIAEGLAWRIVQGDVPEVMADCTIYSLDIGSL-----  253 (758)
T ss_pred             HCCCCCCCCCCHHHHHHHHHHHHH--HCCCCCEEECCCCCCHHHHHHHHHHHHHCCCCCHHHCCCEEEEEEHHHH-----
T ss_conf             828999873848999999999976--3258960216999869999999999997389976558988998458778-----


Q ss_pred             HHHHHCCCCCCCCCCCCCC----CCCCCCCCCEEEECCCCHHH---------HHHHHHHHHHHHHHHCCCCCCCCCCCCC
Q ss_conf             2433112555532211100----12344667147516642001---------8899988887764200112355321234
Q gi|254780916|r  208 EKFLFGDVDLQTKNSAQFL----GKFIEANGGTIVLEEPDALP---------LAVQGRIYNFIETGKIEFFDSRGAIRLD  274 (482)
Q Consensus       208 e~~lFG~~~~~~~~~~~~~----g~~~~a~~Gtl~l~ei~~L~---------~~~Q~~Ll~~l~~~~~~~~g~~~~~~~~  274 (482)
                         +=|.+  +-|....|.    .-++...+-.||+||||.+=         .+.-.-|--+|..|             +
T Consensus       254 ---iAGtk--yRGefEeRlk~vi~e~~~~~~~ILFIDEiH~ivGaG~~~gg~~DaaNlLKP~LarG-------------~  315 (758)
T PRK11034        254 ---LAGTK--YRGDFEKRFKALLKQLEQDTNSILFIDEIHTIIGAGAASGGQVDAANLIKPLLSSG-------------K  315 (758)
T ss_pred             ---HCCCC--CCHHHHHHHHHHHHHHHHCCCEEEEEECHHHHCCCCCCCCCCCCHHHHHHHHHHCC-------------C
T ss_conf             ---61686--41549999999999998579859998043442268876777646788745787469-------------7


Q ss_pred             CEEEEECCCCCCCCCCHHHHHHH--HHHHHHHHHHHHHHHHHHHH
Q ss_conf             31565214332111111233379--99886543344677877442
Q gi|254780916|r  275 VRLIFLTEKNLLPQVKSHVFRKD--LYYRISVFLINISTLRSRSE  317 (482)
Q Consensus       275 ~RiIa~t~~~L~~~~~~g~fr~d--Ly~rL~~~~i~iPpLReR~e  317 (482)
                      +|+|.+|+.+=-.    ..|-+|  |=-|...+.|.=|+.-+-..
T Consensus       316 l~~IgaTT~~EYr----k~iekD~AL~RRFq~V~V~EPs~e~t~~  356 (758)
T PRK11034        316 IRVIGSTTYQEFS----NIFEKDRALARRFQKIDITEPSIEETVQ  356 (758)
T ss_pred             CEEEEECCHHHHH----HCCCCCHHHHHCCCEEECCCCCHHHHHH
T ss_conf             2399943779987----5032147888428265318999899999


No 203
>KOG0727 consensus
Probab=97.98  E-value=1e-05  Score=60.09  Aligned_cols=136  Identities=18%  Similarity=0.221  Sum_probs=84.3

Q ss_pred             CCCCCCCCCCCCEEEEEECCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCHHHHHCCCCCCCCCCCCCCCCC--
Q ss_conf             222222234432048873277743679999998426754332101234655421002433112555532211100123--
Q gi|254780916|r  152 VVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFGDVDLQTKNSAQFLGKF--  229 (482)
Q Consensus       152 v~~~i~~~a~~~~~vli~Ge~GtGK~~~A~~iH~~s~r~~~~fi~v~c~~~~~~~~e~~lFG~~~~~~~~~~~~~g~~--  229 (482)
                      ++++|+.  .-..-||+.|++||||+++|+++-++.   ...||.|+.+.+-     ..-.|+..     .- ....|  
T Consensus       180 ly~qigi--dpprgvllygppg~gktml~kava~~t---~a~firvvgsefv-----qkylgegp-----rm-vrdvfrl  243 (408)
T KOG0727         180 LYKQIGI--DPPRGVLLYGPPGTGKTMLAKAVANHT---TAAFIRVVGSEFV-----QKYLGEGP-----RM-VRDVFRL  243 (408)
T ss_pred             HHHHHCC--CCCCCEEEECCCCCCHHHHHHHHHHCC---CHHEEEECCHHHH-----HHHHCCCC-----HH-HHHHHHH
T ss_conf             9997088--998622775799975789999986126---1114463018999-----99855483-----89-9999998


Q ss_pred             -CCCCCCEEEECCCCHH-----------HHHHHHHHHHHHHHHHCCCCCCCCCCCCCCEEEEECCCC--C-CCCCCHHHH
Q ss_conf             -4466714751664200-----------188999888877642001123553212343156521433--2-111111233
Q gi|254780916|r  230 -IEANGGTIVLEEPDAL-----------PLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKN--L-LPQVKSHVF  294 (482)
Q Consensus       230 -~~a~~Gtl~l~ei~~L-----------~~~~Q~~Ll~~l~~~~~~~~g~~~~~~~~~RiIa~t~~~--L-~~~~~~g~f  294 (482)
                       .+-.-..+|+|||+..           ..++|.-|+.+|..-     ++ -....|+.+|-+||+-  | ..+..-|++
T Consensus       244 akenapsiifideidaiatkrfdaqtgadrevqril~ellnqm-----dg-fdq~~nvkvimatnradtldpallrpgrl  317 (408)
T KOG0727         244 AKENAPSIIFIDEIDAIATKRFDAQTGADREVQRILIELLNQM-----DG-FDQTTNVKVIMATNRADTLDPALLRPGRL  317 (408)
T ss_pred             HHCCCCCEEEEEHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHC-----CC-CCCCCCEEEEEECCCCCCCCHHHCCCCCC
T ss_conf             7616983798622456766412444463189999999999751-----47-67666558998327555668766287643


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             3799988654334467787744222
Q gi|254780916|r  295 RKDLYYRISVFLINISTLRSRSEDI  319 (482)
Q Consensus       295 r~dLy~rL~~~~i~iPpLReR~eDI  319 (482)
                      ..         .|+.| |++|+.--
T Consensus       318 dr---------kiefp-lpdrrqkr  332 (408)
T KOG0727         318 DR---------KIEFP-LPDRRQKR  332 (408)
T ss_pred             CC---------CCCCC-CCCHHHHH
T ss_conf             44---------43577-98546652


No 204
>PRK07133 DNA polymerase III subunits gamma and tau; Validated
Probab=97.96  E-value=5.5e-05  Score=54.89  Aligned_cols=209  Identities=16%  Similarity=0.196  Sum_probs=112.3

Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCCCHHHHHHHHHHHCC---CCCC--CCCCCCCCCC---CCCCC
Q ss_conf             11111111222222222222222234432048873277743679999998426---7543--3210123465---54210
Q gi|254780916|r  135 EHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHESG---KRAF--FPFFIVNCGM---IDQDK  206 (482)
Q Consensus       135 ~~~~~~~LiG~S~~m~~v~~~i~~~a~~~~~vli~Ge~GtGK~~~A~~iH~~s---~r~~--~~fi~v~c~~---~~~~~  206 (482)
                      ....|..++|+....+.+...+.. ......-|+.|+.||||+.+||.+-..-   ...+  +|  --.|..   -+.+.
T Consensus        13 RPk~F~EVIGQe~Vv~tL~nAI~~-gRIaHAYLF~GPRGvGKTT~ARIfAKaLNC~~~~d~~~p--C~~C~~~~~~s~DV   89 (718)
T PRK07133         13 RPKKFDEIKGQDHIIETLKNIIKS-GKISHAYLFSGPHGTGKTSVAKIFANALNCSHKTDLIEP--CQNCIENFNNNLDI   89 (718)
T ss_pred             CCCCHHHHCCCHHHHHHHHHHHHC-CCCCCEEEEECCCCCCHHHHHHHHHHHHCCCCCCCCCCC--CCCHHHCCCCCCCE
T ss_conf             899754422859999999999974-997505862389986889999999999679999999997--70214304789873


Q ss_pred             CHHHHHCCCCCCCC-CCCCCCCCCCC-----CCC--CEEEECCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCEEE
Q ss_conf             02433112555532-21110012344-----667--14751664200188999888877642001123553212343156
Q gi|254780916|r  207 IEKFLFGDVDLQTK-NSAQFLGKFIE-----ANG--GTIVLEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLI  278 (482)
Q Consensus       207 ~e~~lFG~~~~~~~-~~~~~~g~~~~-----a~~--Gtl~l~ei~~L~~~~Q~~Ll~~l~~~~~~~~g~~~~~~~~~RiI  278 (482)
                      +|      .+++.. ...+-..+.+.     ..|  -...+||+|-|+.+.+..||..|++.           +.++-+|
T Consensus        90 iE------IDAASn~gVDdIReLie~v~y~P~~gkYKVyIIDEvHMLS~~AfNALLKtLEEP-----------P~hvvFI  152 (718)
T PRK07133         90 IE------MDAASNNGVDEIRELRENVKNLPQISKYKIYIIDEVHMLSKSAFNALLKTLEEP-----------PKHVIFI  152 (718)
T ss_pred             EE------ECCCCCCCHHHHHHHHHHHCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHCCC-----------CCCCEEE
T ss_conf             77------545566888999999998255887787249999662007999999999850279-----------8782799


Q ss_pred             EECCCCC----CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             5214332----111111233379998865433446778774422225566777641011223333211111000122338
Q gi|254780916|r  279 FLTEKNL----LPQVKSHVFRKDLYYRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPW  354 (482)
Q Consensus       279 a~t~~~L----~~~~~~g~fr~dLy~rL~~~~i~iPpLReR~eDI~~L~~~fl~~~~~~~~~~~~~ls~~a~~~L~~y~W  354 (482)
                      .+|+..=    .-+....+|             .+     |+=+...++.| |...+.+.+   ..++++|+.++.... 
T Consensus       153 LaTTep~KIP~TIlSRCQrF-------------dF-----krI~~~~I~~~-L~~I~~kE~---I~~e~eAL~lIA~~a-  209 (718)
T PRK07133        153 LATTDVQKIPLTILSRVQRF-------------NF-----RRISEDVIVHQ-LENILEKEK---IKYEKNALKLIASLA-  209 (718)
T ss_pred             EEECCHHHCCHHHHHCCEEE-------------EC-----CCCCHHHHHHH-HHHHHHHCC---CCCCHHHHHHHHHHC-
T ss_conf             97088254848774122033-------------58-----88999999999-999999859---977899999999976-


Q ss_pred             CCCHHHHHHHHHHHHHHCCCCCCCHHHHHHHHC
Q ss_conf             986899999999998743898106889545421
Q gi|254780916|r  355 IDNVQELKNILLRAVIGLKDSHLTEDRFVLLLS  387 (482)
Q Consensus       355 PGNvREL~n~i~r~~i~~~~~~i~~~~~~~~l~  387 (482)
                      -|-+|.=-+++.++...+ ++.|+..++...++
T Consensus       210 ~GSmRDAlSlLDQv~~f~-ng~it~k~v~~~~G  241 (718)
T PRK07133        210 SGSLRDALSIADQVSIFG-NGNITLKNVNELFG  241 (718)
T ss_pred             CCCHHHHHHHHHHHHHHC-CCCCCHHHHHHHHC
T ss_conf             884888987999999854-89872999999967


No 205
>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=97.94  E-value=7.4e-06  Score=61.01  Aligned_cols=118  Identities=16%  Similarity=0.121  Sum_probs=69.4

Q ss_pred             CEEEEEECCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCHH---HHHCCCCCCCCCCCCCCCCCCCCCC---CE
Q ss_conf             20488732777436799999984267543321012346554210024---3311255553221110012344667---14
Q gi|254780916|r  163 AIPIMIQGEFGVGKKRLSRFIHESGKRAFFPFFIVNCGMIDQDKIEK---FLFGDVDLQTKNSAQFLGKFIEANG---GT  236 (482)
Q Consensus       163 ~~~vli~Ge~GtGK~~~A~~iH~~s~r~~~~fi~v~c~~~~~~~~e~---~lFG~~~~~~~~~~~~~g~~~~a~~---Gt  236 (482)
                      ...++|.|++||||+.+++.+-........+++.++|..........   ..+................++.|..   +.
T Consensus         2 ~~~ill~G~~GsGKTtl~~~la~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v   81 (148)
T smart00382        2 GEVILIVGPPGSGKTTLARALARELGPPGGGVIYIDGEDILEEVLDQLLLIIVGGKKASGSGELRLRLALALARKLKPDV   81 (148)
T ss_pred             CCEEEEECCCCHHHHHHHHHHHHHHCCCCCCEEEEEHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHCCCCE
T ss_conf             97899999997029999999998726689968998759989888987653000112210519999999999998449989


Q ss_pred             EEECCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCEEEEECCC
Q ss_conf             75166420018899988887764200112355321234315652143
Q gi|254780916|r  237 IVLEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEK  283 (482)
Q Consensus       237 l~l~ei~~L~~~~Q~~Ll~~l~~~~~~~~g~~~~~~~~~RiIa~t~~  283 (482)
                      +|+||++.+....+..+.......   ..........+..+|++++.
T Consensus        82 iiiDei~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~vi~~~n~  125 (148)
T smart00382       82 LILDEITSLLDAEQEALLLLLEEL---RLLLLLKSEKNLTVILTTND  125 (148)
T ss_pred             EEEECCHHHCCCCCHHHHHHHHHH---HHHCCCCCCCCEEEEEEECC
T ss_conf             998275021476207999999999---98517657899899995699


No 206
>COG0465 HflB ATP-dependent Zn proteases [Posttranslational modification, protein turnover, chaperones]
Probab=97.88  E-value=8.5e-06  Score=60.60  Aligned_cols=214  Identities=16%  Similarity=0.228  Sum_probs=122.0

Q ss_pred             CCCCCCCCCCCCCCCCC---CCCCCCCCCC-------CCCEEEEEECCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCC
Q ss_conf             21111111122222222---2222222234-------4320488732777436799999984267543321012346554
Q gi|254780916|r  134 NEHCALDSLIAVSPAMI---QVVDLARKAG-------DCAIPIMIQGEFGVGKKRLSRFIHESGKRAFFPFFIVNCGMID  203 (482)
Q Consensus       134 ~~~~~~~~LiG~S~~m~---~v~~~i~~~a-------~~~~~vli~Ge~GtGK~~~A~~iH~~s~r~~~~fi~v~c~~~~  203 (482)
                      .....|.+..|..++-+   ++.+.++.-.       ....-||+.|++||||+++|+++-..   ++=||..+..+.+-
T Consensus       144 ~~~v~F~DVAG~dEakeel~EiVdfLk~p~ky~~lGakiPkGvlLvGpPGTGKTLLAkAvAgE---A~VPFf~iSGS~FV  220 (596)
T COG0465         144 QVKVTFADVAGVDEAKEELSELVDFLKNPKKYQALGAKIPKGVLLVGPPGTGKTLLAKAVAGE---AGVPFFSISGSDFV  220 (596)
T ss_pred             CCCCCHHHHCCCHHHHHHHHHHHHHHHCCHHHHHCCCCCCCCEEEECCCCCCCHHHHHHHHCC---CCCCCEECCCHHHH
T ss_conf             667675664186799999999999863855667523534565268559998727899998454---68983530344464


Q ss_pred             CCCCHHHHHCCCCCCCCCCCCCCCCCCCCCC---CEEEECCCCHHHHHH----------H-HHHHHHHHHHHCCCCCCCC
Q ss_conf             2100243311255553221110012344667---147516642001889----------9-9888877642001123553
Q gi|254780916|r  204 QDKIEKFLFGDVDLQTKNSAQFLGKFIEANG---GTIVLEEPDALPLAV----------Q-GRIYNFIETGKIEFFDSRG  269 (482)
Q Consensus       204 ~~~~e~~lFG~~~~~~~~~~~~~g~~~~a~~---Gtl~l~ei~~L~~~~----------Q-~~Ll~~l~~~~~~~~g~~~  269 (482)
                      +     .+-| .     ..++..-+|++|..   -.+|+|||+.....-          . ..|-++|.+--  ..++++
T Consensus       221 e-----mfVG-v-----GAsRVRdLF~qAkk~aP~IIFIDEiDAvGr~Rg~g~GggnderEQTLNQlLvEmD--GF~~~~  287 (596)
T COG0465         221 E-----MFVG-V-----GASRVRDLFEQAKKNAPCIIFIDEIDAVGRQRGAGLGGGNDEREQTLNQLLVEMD--GFGGNE  287 (596)
T ss_pred             H-----HHCC-C-----CCHHHHHHHHHHHCCCCCEEEEEHHHHCCCCCCCCCCCCCHHHHHHHHHHHHHHC--CCCCCC
T ss_conf             4-----3147-8-----8388899999855159966987634331454577889980699999988885201--578887


Q ss_pred             CCCCCCEEEEECCCC--C-CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCC
Q ss_conf             212343156521433--2-1111112333799988654334467787744222255667776410112233332111110
Q gi|254780916|r  270 AIRLDVRLIFLTEKN--L-LPQVKSHVFRKDLYYRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKAL  346 (482)
Q Consensus       270 ~~~~~~RiIa~t~~~--L-~~~~~~g~fr~dLy~rL~~~~i~iPpLReR~eDI~~L~~~fl~~~~~~~~~~~~~ls~~a~  346 (482)
                      .    +=+|++||+.  | ..+...|+|..       .+.|..|-++.|.+=.        +-+++.     +.++++.-
T Consensus       288 g----viviaaTNRpdVlD~ALlRpgRFDR-------qI~V~~PDi~gRe~Il--------kvH~~~-----~~l~~~V~  343 (596)
T COG0465         288 G----VIVIAATNRPDVLDPALLRPGRFDR-------QILVELPDIKGREQIL--------KVHAKN-----KPLAEDVD  343 (596)
T ss_pred             C----EEEECCCCCCCCCHHHHCCCCCCCE-------EEECCCCCHHHHHHHH--------HHHHHC-----CCCCCCCC
T ss_conf             5----4885267874333176528877662-------5544785156578887--------886415-----77776678


Q ss_pred             CCCCCCCCCCCHH-HHHHHHHHHHH-H--CCCCCCCHHHHHHHHC
Q ss_conf             0012233898689-99999999987-4--3898106889545421
Q gi|254780916|r  347 SLLTKYPWIDNVQ-ELKNILLRAVI-G--LKDSHLTEDRFVLLLS  387 (482)
Q Consensus       347 ~~L~~y~WPGNvR-EL~n~i~r~~i-~--~~~~~i~~~~~~~~l~  387 (482)
                      -....+.-||..- .|.|++=.+.+ .  .....++..++.....
T Consensus       344 l~~iAr~tpGfsGAdL~nl~NEAal~aar~n~~~i~~~~i~ea~d  388 (596)
T COG0465         344 LKKIARGTPGFSGADLANLLNEAALLAARRNKKEITMRDIEEAID  388 (596)
T ss_pred             HHHHHHHCCCCCCCHHHHHHHHHHHHHHHHCCEEEECCCHHHHHH
T ss_conf             889864377856306765566889999883684675345388999


No 207
>PRK06872 DNA polymerase III subunits gamma and tau; Provisional
Probab=97.88  E-value=0.00022  Score=50.66  Aligned_cols=223  Identities=12%  Similarity=0.169  Sum_probs=126.2

Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCCCHHHHHHHHHHHCCCCCC----CCCC-CCCCCCCCCCCCH
Q ss_conf             2111111112222222222222222344320488732777436799999984267543----3210-1234655421002
Q gi|254780916|r  134 NEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHESGKRAF----FPFF-IVNCGMIDQDKIE  208 (482)
Q Consensus       134 ~~~~~~~~LiG~S~~m~~v~~~i~~~a~~~~~vli~Ge~GtGK~~~A~~iH~~s~r~~----~~fi-~v~c~~~~~~~~e  208 (482)
                      .....|..++|+.-..+.+...+.. .....--|++|..|+||+.+||.+-..-.-..    .|-= --+|..+....+-
T Consensus        10 ~rp~~f~~~vgq~~v~~~l~~a~~~-~r~~haylf~g~rg~gktt~ari~ak~lnc~~~~~~~pcg~c~~c~~i~~g~~~   88 (696)
T PRK06872         10 WRPKTFSEVVGQEHILTALSNGLKE-NRLHHAYLFSGTRGVGKTSIARLFAKGLNCVHGVTATPCGECENCKAIEEGNFI   88 (696)
T ss_pred             HCCCCHHHHCCCHHHHHHHHHHHHC-CCCCCEEEEECCCCCCHHHHHHHHHHHHCCCCCCCCCCCCCCHHHHHHHCCCCC
T ss_conf             1887564523859999999999971-986304751178988888999999998678999999978886225767447877


Q ss_pred             HHHHCCCCCC-CCCCCCCCCCCCCC-------CCCEEEECCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCEEEEE
Q ss_conf             4331125555-32211100123446-------671475166420018899988887764200112355321234315652
Q gi|254780916|r  209 KFLFGDVDLQ-TKNSAQFLGKFIEA-------NGGTIVLEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFL  280 (482)
Q Consensus       209 ~~lFG~~~~~-~~~~~~~~g~~~~a-------~~Gtl~l~ei~~L~~~~Q~~Ll~~l~~~~~~~~g~~~~~~~~~RiIa~  280 (482)
                      ..+  +.++. .+...+-.-+++.+       .--.-++||+|-|+......||..|++-           +..|.+|.+
T Consensus        89 d~~--eidaas~~~v~~~r~l~~~~~~~p~~~~~kvy~idevhmls~~~fnallktleep-----------p~~v~f~la  155 (696)
T PRK06872         89 DLI--EIDAASRTKVEDTRELLDNVQYKPVVGRFKVYLIDEVHMLSRHSFNALLKTLEEP-----------PEYVKFLLA  155 (696)
T ss_pred             CEE--EEECCCCCCHHHHHHHHHHCCCCCCCCCEEEEEEEHHHHCCHHHHHHHHHHHCCC-----------CCCEEEEEE
T ss_conf             546--7505655788999999984545776775479997005443899999998750279-----------754489984


Q ss_pred             CCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCHHH
Q ss_conf             14332111111233379998865433446778774422225566777641011223333211111000122338986899
Q gi|254780916|r  281 TEKNLLPQVKSHVFRKDLYYRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQE  360 (482)
Q Consensus       281 t~~~L~~~~~~g~fr~dLy~rL~~~~i~iPpLReR~eDI~~L~~~fl~~~~~~~~~~~~~ls~~a~~~L~~y~WPGNvRE  360 (482)
                      |+.. .+ +-.-.+..=|-|.|..+            +...++.|+ ...+.+.+   ..++++|+.+|... =-|-+|.
T Consensus       156 tt~~-~k-~p~tilsrc~~f~~~~~------------~~~~i~~~l-~~i~~~e~---~~~~~~al~~~a~~-a~gs~rd  216 (696)
T PRK06872        156 TTDP-QK-LPITILSRCMQFHLKAL------------DQTQIAQHL-EFILTQEN---IPFESPALEKLAKA-AQGSIRD  216 (696)
T ss_pred             CCCH-HH-CCHHHHHHHHHEECCCC------------CHHHHHHHH-HHHHHHCC---CCCCHHHHHHHHHH-CCCCHHH
T ss_conf             3863-22-74889876653002689------------999999999-99999849---97799999999997-5895677


Q ss_pred             HHHHHHHHHHHCCCCCCCHHHHHHHHCCCC
Q ss_conf             999999998743898106889545421244
Q gi|254780916|r  361 LKNILLRAVIGLKDSHLTEDRFVLLLSREG  390 (482)
Q Consensus       361 L~n~i~r~~i~~~~~~i~~~~~~~~l~~~~  390 (482)
                      =-++..+++... ++.|+.+++..-++...
T Consensus       217 alsl~dqai~~~-~g~~~~~~v~~mlg~~~  245 (696)
T PRK06872        217 SLSLTDQAIAMS-NANITLDVVSNMLGLLD  245 (696)
T ss_pred             HHHHHHHHHHHC-CCCCCHHHHHHHHCCCC
T ss_conf             888999999975-89616999999858887


No 208
>PRK06620 hypothetical protein; Validated
Probab=97.87  E-value=0.00025  Score=50.21  Aligned_cols=163  Identities=15%  Similarity=0.210  Sum_probs=92.5

Q ss_pred             CEEEEEECCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCHHHHHCCCCCCCCCCCCCCCCCCCCCCCEEEECCC
Q ss_conf             20488732777436799999984267543321012346554210024331125555322111001234466714751664
Q gi|254780916|r  163 AIPIMIQGEFGVGKKRLSRFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFGDVDLQTKNSAQFLGKFIEANGGTIVLEEP  242 (482)
Q Consensus       163 ~~~vli~Ge~GtGK~~~A~~iH~~s~r~~~~fi~v~c~~~~~~~~e~~lFG~~~~~~~~~~~~~g~~~~a~~Gtl~l~ei  242 (482)
                      ..+++|.|++|+||+++++..-+.+   +..+  +++..+++.                      .+  .+.+.+++|+|
T Consensus        44 ~~~l~I~Gp~gSGKTHL~~i~~~~~---~a~~--~~~~~~~~~----------------------~~--~~~~~~iiddi   94 (214)
T PRK06620         44 KFTLLIKGPSSSGKTYLTKIWQNLS---NAYI--IKDIFFNEE----------------------IL--EKYNAFIIEDI   94 (214)
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHHH---CCEE--ECHHHCCHH----------------------HH--HHCCCEEEECC
T ss_conf             5559998799998899999999982---8588--151214587----------------------88--43793798467


Q ss_pred             CHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCEEEEECCCCCCCCCCHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHH
Q ss_conf             2001889998888776420011235532123431565214332111111233379998865433-446778774422225
Q gi|254780916|r  243 DALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYYRISVFL-INISTLRSRSEDIPW  321 (482)
Q Consensus       243 ~~L~~~~Q~~Ll~~l~~~~~~~~g~~~~~~~~~RiIa~t~~~L~~~~~~g~fr~dLy~rL~~~~-i~iPpLReR~eDI~~  321 (482)
                      +..+.+..-.|+..+.+.             ...++.+++..+.+.    . -+||--||..+. +.+.+.    +| . 
T Consensus        95 d~~~e~~lfhlfN~~~~~-------------~~~llits~~~p~~~----~-L~DL~SRl~~~~~~~i~~P----dD-~-  150 (214)
T PRK06620         95 ENWQEPALLHIFNIINEK-------------QKYLLLTSSDKSRNF----T-LPDLSSRIKSVLSILLNSP----DD-E-  150 (214)
T ss_pred             CCCCHHHHHHHHHHHHHC-------------CCEEEEEECCCCCCC----C-CCCHHHHHHCCCEEECCCC----CH-H-
T ss_conf             757467999999999715-------------987999827985224----5-3578999854644332698----98-9-


Q ss_pred             HHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHH--HCCCCCCCHHHH
Q ss_conf             5667776410112233332111110001223389868999999999987--438981068895
Q gi|254780916|r  322 LVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQELKNILLRAVI--GLKDSHLTEDRF  382 (482)
Q Consensus       322 L~~~fl~~~~~~~~~~~~~ls~~a~~~L~~y~WPGNvREL~n~i~r~~i--~~~~~~i~~~~~  382 (482)
                      +....+.+++...+   ..++++.++.|..+ .+-|++.+..++..+--  +..+..|+..-+
T Consensus       151 l~~~ll~k~~~~r~---i~i~~~vi~yl~~r-i~Rs~~~l~~~v~~ld~~sl~~kr~Iti~li  209 (214)
T PRK06620        151 LIKILIFKHFSISS---VTISRQIIDFLLVN-LPREYSKIIEILENINYFALISKRKITISLV  209 (214)
T ss_pred             HHHHHHHHHHHHCC---CCCCHHHHHHHHHH-HCCCHHHHHHHHHHHHHHHHHCCCCCCHHHH
T ss_conf             99999999999869---98875599999998-5178999999999999999983999889999


No 209
>PRK05648 DNA polymerase III subunits gamma and tau; Reviewed
Probab=97.85  E-value=0.00016  Score=51.63  Aligned_cols=223  Identities=11%  Similarity=0.133  Sum_probs=125.4

Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCCCHHHHHHHHHHHCCCCCCCC----C-CCCCCCCCCCCCCH
Q ss_conf             211111111222222222222222234432048873277743679999998426754332----1-01234655421002
Q gi|254780916|r  134 NEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHESGKRAFFP----F-FIVNCGMIDQDKIE  208 (482)
Q Consensus       134 ~~~~~~~~LiG~S~~m~~v~~~i~~~a~~~~~vli~Ge~GtGK~~~A~~iH~~s~r~~~~----f-i~v~c~~~~~~~~e  208 (482)
                      .....|..++|+.-..+.+...+.. .....--|++|..|+||+.+||.+-+.-.-..++    - .--+|..+....+-
T Consensus        10 ~rp~~f~~~~gq~~~~~~l~~~~~~-~~~~~a~l~~g~rg~gkt~~ar~~ak~lnc~~~~~~~pc~~c~~c~~i~~~~~~   88 (705)
T PRK05648         10 WRPRSFREMVGQTHVLKALINALDN-QRLHHAYLFTGTRGVGKTTIARIIAKCLNCETGVSSTPCGECSVCREIDEGRFV   88 (705)
T ss_pred             HCCCCHHHHCCHHHHHHHHHHHHHC-CCCCCEEEEECCCCCCHHHHHHHHHHHHCCCCCCCCCCCCCCHHHHHHHCCCCC
T ss_conf             1787576632819999999999970-986304650078988898999999998677899988978776004666248977


Q ss_pred             HHHHCCCCCC-CCCCCCCCCCCCC-------CCCCEEEECCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCEEEEE
Q ss_conf             4331125555-3221110012344-------6671475166420018899988887764200112355321234315652
Q gi|254780916|r  209 KFLFGDVDLQ-TKNSAQFLGKFIE-------ANGGTIVLEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFL  280 (482)
Q Consensus       209 ~~lFG~~~~~-~~~~~~~~g~~~~-------a~~Gtl~l~ei~~L~~~~Q~~Ll~~l~~~~~~~~g~~~~~~~~~RiIa~  280 (482)
                      ..+  +.++. .....+-.-+++.       ..--..++||+|-|+...=.-||..|++-           +.+|.+|.+
T Consensus        89 d~~--e~d~as~~~v~~~r~~~~~~~~~p~~~~~kv~~idevhmls~~~fnallktleep-----------p~~v~f~~a  155 (705)
T PRK05648         89 DLI--EVDAASRTKVEDTRELLDNVQYAPTRGRYKVYLIDEVHMLSSHSFNALLKTLEEP-----------PPHVKFLLA  155 (705)
T ss_pred             CEE--EECCCCCCCHHHHHHHHHHCCCCCCCCCEEEEEEEHHHHCCHHHHHHHHHHCCCC-----------CCCEEEEEE
T ss_conf             634--4515544788999999985551776774579998426541799999998740479-----------754599984


Q ss_pred             CCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCHHH
Q ss_conf             14332111111233379998865433446778774422225566777641011223333211111000122338986899
Q gi|254780916|r  281 TEKNLLPQVKSHVFRKDLYYRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQE  360 (482)
Q Consensus       281 t~~~L~~~~~~g~fr~dLy~rL~~~~i~iPpLReR~eDI~~L~~~fl~~~~~~~~~~~~~ls~~a~~~L~~y~WPGNvRE  360 (482)
                      |+.. .++- --.+.+=|-|.|..+            ....++.|+ .....+.|   ..++++|+.++... --|-+|.
T Consensus       156 tt~~-~k~p-~t~~src~~~~~~~~------------~~~~~~~~l-~~~~~~e~---~~~~~~~~~~~~~~-~~g~~rd  216 (705)
T PRK05648        156 TTDP-QKLP-VTILSRCLQFSLKNM------------SPERVVEHL-SHVLGAEN---VPFEEDALWLLGRA-ADGSMRD  216 (705)
T ss_pred             CCCH-HHCC-HHHHHHHHHCCCCCC------------CHHHHHHHH-HHHHHHCC---CCCCHHHHHHHHHH-CCCCHHH
T ss_conf             2873-5375-899976643023689------------999999999-99999759---97789999999997-4896777


Q ss_pred             HHHHHHHHHHHCCCCCCCHHHHHHHHCCCC
Q ss_conf             999999998743898106889545421244
Q gi|254780916|r  361 LKNILLRAVIGLKDSHLTEDRFVLLLSREG  390 (482)
Q Consensus       361 L~n~i~r~~i~~~~~~i~~~~~~~~l~~~~  390 (482)
                      =-++..+++..+ ++.|+.+++..-++...
T Consensus       217 ~ls~~dq~~~~~-~~~~~~~~v~~mlg~~~  245 (705)
T PRK05648        217 AMSLTDQAIAFG-EGKVLAADVRAMLGTLD  245 (705)
T ss_pred             HHHHHHHHHHCC-CCCCCHHHHHHHHCCCC
T ss_conf             999999998606-88407999999858887


No 210
>PRK08116 hypothetical protein; Validated
Probab=97.80  E-value=1.9e-05  Score=58.07  Aligned_cols=139  Identities=19%  Similarity=0.207  Sum_probs=78.0

Q ss_pred             CCCCCCCCCCCCCC---CCCEEEEEECCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCHHHHHC-CCCCCCCCC
Q ss_conf             22222222222234---43204887327774367999999842675433210123465542100243311-255553221
Q gi|254780916|r  147 PAMIQVVDLARKAG---DCAIPIMIQGEFGVGKKRLSRFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFG-DVDLQTKNS  222 (482)
Q Consensus       147 ~~m~~v~~~i~~~a---~~~~~vli~Ge~GtGK~~~A~~iH~~s~r~~~~fi~v~c~~~~~~~~e~~lFG-~~~~~~~~~  222 (482)
                      +++....+.+....   ..+..+++.|.+||||+++|-+|-+.--..+.+-+-++..    +++ .+|.. ..++.....
T Consensus        89 ~a~~~a~~Y~~~f~~~~~~~~GLll~G~~GtGKThLa~aIa~~l~~~g~~V~~~~~~----~ll-~~lk~~~~~~~~~~~  163 (262)
T PRK08116         89 KAYKVAVKYVKKFEEMKKESVGLLLWGSPGNGKTYLAAAIANELIEKGVPVVFVNVP----ELL-NRIKSTYNSEGKEDE  163 (262)
T ss_pred             HHHHHHHHHHHHHHHHCCCCCEEEEECCCCCCHHHHHHHHHHHHHHCCCEEEEEEHH----HHH-HHHHHHHHCCCCHHH
T ss_conf             999999999998987364686189989899989999999999999879939998899----999-999999863561019


Q ss_pred             CCCCCCCCCCCCCEEEECCCCH--HHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCEEEEECCCCCCCCCCHHHHHHHHHH
Q ss_conf             1100123446671475166420--01889998888776420011235532123431565214332111111233379998
Q gi|254780916|r  223 AQFLGKFIEANGGTIVLEEPDA--LPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYY  300 (482)
Q Consensus       223 ~~~~g~~~~a~~Gtl~l~ei~~--L~~~~Q~~Ll~~l~~~~~~~~g~~~~~~~~~RiIa~t~~~L~~~~~~g~fr~dLy~  300 (482)
                      .+....+..  ---|+||+++.  .+...+..|+.+|+.+. .   ..++      +|.+||.+++++..  .|-+-.|.
T Consensus       164 ~e~l~~l~~--~dLLIiDDlG~e~~t~w~~e~lf~IIn~Ry-~---~~kp------tIiTTNl~~~eL~~--~~~~Ri~s  229 (262)
T PRK08116        164 NEIIRALDN--ADLLILDDLGAEKDTEWVREKLYNIIDSRY-R---KGLP------TIFTTNLSLEELKN--QYGKRTYS  229 (262)
T ss_pred             HHHHHHHHC--CCEEEEEHHCCCCCCHHHHHHHHHHHHHHH-H---CCCC------EEEECCCCHHHHHH--HHHHHHHH
T ss_conf             999998612--998998322145698789999999999999-7---6999------89987999999999--86379999


Q ss_pred             HHHH
Q ss_conf             8654
Q gi|254780916|r  301 RISV  304 (482)
Q Consensus       301 rL~~  304 (482)
                      ||..
T Consensus       230 Rl~e  233 (262)
T PRK08116        230 RILE  233 (262)
T ss_pred             HHHH
T ss_conf             9986


No 211
>KOG0989 consensus
Probab=97.80  E-value=0.00015  Score=51.85  Aligned_cols=208  Identities=17%  Similarity=0.157  Sum_probs=112.9

Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCEE-EEEECCCCCHHHHHHHHHHHCCCCCCCCC----CCCCCCCCCC-CCCH
Q ss_conf             1111111122222222222222223443204-88732777436799999984267543321----0123465542-1002
Q gi|254780916|r  135 EHCALDSLIAVSPAMIQVVDLARKAGDCAIP-IMIQGEFGVGKKRLSRFIHESGKRAFFPF----FIVNCGMIDQ-DKIE  208 (482)
Q Consensus       135 ~~~~~~~LiG~S~~m~~v~~~i~~~a~~~~~-vli~Ge~GtGK~~~A~~iH~~s~r~~~~f----i~v~c~~~~~-~~~e  208 (482)
                      ....++.++|+....+.+...+.+   -+.| .|+.|++||||+..|++.-..-.- ...|    ...|.+.... +..-
T Consensus        31 rPkt~de~~gQe~vV~~L~~a~~~---~~lp~~LFyGPpGTGKTStalafar~L~~-~~~~~~rvl~lnaSderGisvvr  106 (346)
T KOG0989          31 RPKTFDELAGQEHVVQVLKNALLR---RILPHYLFYGPPGTGKTSTALAFARALNC-EQLFPCRVLELNASDERGISVVR  106 (346)
T ss_pred             CCCCHHHHCCHHHHHHHHHHHHHH---CCCCEEEEECCCCCCHHHHHHHHHHHHCC-CCCCCCCHHHHCCCCCCCCCCHH
T ss_conf             787377650159999999999860---68860786689998676899999998557-42355542431366001431006


Q ss_pred             HHHHCCCCCCCCCCCCCCCCCCCCCCCEEEECCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCEEEEECCCCCCCC
Q ss_conf             43311255553221110012344667147516642001889998888776420011235532123431565214332111
Q gi|254780916|r  209 KFLFGDVDLQTKNSAQFLGKFIEANGGTIVLEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQ  288 (482)
Q Consensus       209 ~~lFG~~~~~~~~~~~~~g~~~~a~~Gtl~l~ei~~L~~~~Q~~Ll~~l~~~~~~~~g~~~~~~~~~RiIa~t~~~L~~~  288 (482)
                      ..+++..+- +.......|.- .----++.|||-+.|+-+.|.-|.|++++-           .-.+|+|..||.- ..+
T Consensus       107 ~Kik~fakl-~~~~~~~~~~~-~~~fKiiIlDEcdsmtsdaq~aLrr~mE~~-----------s~~trFiLIcnyl-sri  172 (346)
T KOG0989         107 EKIKNFAKL-TVLLKRSDGYP-CPPFKIIILDECDSMTSDAQAALRRTMEDF-----------SRTTRFILICNYL-SRI  172 (346)
T ss_pred             HHHCCHHHH-HHCCCCCCCCC-CCCCEEEEEECHHHHHHHHHHHHHHHHHCC-----------CCCEEEEEECCCH-HHC
T ss_conf             652379987-50255656788-986328997416453099999999998625-----------4665999973885-647


Q ss_pred             CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHH
Q ss_conf             11123337999886543344677877442222556677764101122333321111100012233898689999999999
Q gi|254780916|r  289 VKSHVFRKDLYYRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQELKNILLRA  368 (482)
Q Consensus       289 ~~~g~fr~dLy~rL~~~~i~iPpLReR~eDI~~L~~~fl~~~~~~~~~~~~~ls~~a~~~L~~y~WPGNvREL~n~i~r~  368 (482)
                      +      .-+--|.+  .++.|||-+  +||-.-    |+..|.+.|.   .++++|++.+..+. -|..|.=..+++.+
T Consensus       173 i------~pi~SRC~--KfrFk~L~d--~~iv~r----L~~Ia~~E~v---~~d~~al~~I~~~S-~GdLR~Ait~Lqsl  234 (346)
T KOG0989         173 I------RPLVSRCQ--KFRFKKLKD--EDIVDR----LEKIASKEGV---DIDDDALKLIAKIS-DGDLRRAITTLQSL  234 (346)
T ss_pred             C------HHHHHHHH--HHCCCCCCH--HHHHHH----HHHHHHHHCC---CCCHHHHHHHHHHC-CCCHHHHHHHHHHH
T ss_conf             7------28774677--712887644--789999----9999888589---97878999999973-87289999999986


Q ss_pred             HHHCCCCCCCHH
Q ss_conf             874389810688
Q gi|254780916|r  369 VIGLKDSHLTED  380 (482)
Q Consensus       369 ~i~~~~~~i~~~  380 (482)
                      ..  .|..|+..
T Consensus       235 s~--~gk~It~~  244 (346)
T KOG0989         235 SL--LGKRITTS  244 (346)
T ss_pred             HC--CCCCCCHH
T ss_conf             10--47636458


No 212
>KOG0737 consensus
Probab=97.78  E-value=2.5e-05  Score=57.28  Aligned_cols=177  Identities=17%  Similarity=0.189  Sum_probs=96.5

Q ss_pred             CCEEEEEECCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCHHHHHCCCCCCCCCCCCCCCCCCCCCCCEEEECC
Q ss_conf             32048873277743679999998426754332101234655421002433112555532211100123446671475166
Q gi|254780916|r  162 CAIPIMIQGEFGVGKKRLSRFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFGDVDLQTKNSAQFLGKFIEANGGTIVLEE  241 (482)
Q Consensus       162 ~~~~vli~Ge~GtGK~~~A~~iH~~s~r~~~~fi~v~c~~~~~~~~e~~lFG~~~~~~~~~~~~~g~~~~a~~Gtl~l~e  241 (482)
                      -..-||+.|++||||+++|+++-..   +..+||.|..+.+++     +-||+..-...+......++   ..-.+|+||
T Consensus       126 p~kGiLL~GPpG~GKTmlAKA~Ake---aga~fInv~~s~lt~-----KWfgE~eKlv~AvFslAsKl---~P~iIFIDE  194 (386)
T KOG0737         126 PPKGILLYGPPGTGKTMLAKAIAKE---AGANFINVSVSNLTS-----KWFGEAQKLVKAVFSLASKL---QPSIIFIDE  194 (386)
T ss_pred             CCCCCEECCCCCCHHHHHHHHHHHH---CCCCCCEEECCCCCH-----HHHHHHHHHHHHHHHHHHHC---CCCEEEHHH
T ss_conf             8643051189982188999999987---279710001365532-----66777888999998206534---861565665


Q ss_pred             CCHHHHHHH---HHHHHHHHHHHCCCC-CCC-CCCCCCCEEEEECCCC--CCCCCCHHHHHHHHHHHH-HHHHHHHHHHH
Q ss_conf             420018899---988887764200112-355-3212343156521433--211111123337999886-54334467787
Q gi|254780916|r  242 PDALPLAVQ---GRIYNFIETGKIEFF-DSR-GAIRLDVRLIFLTEKN--LLPQVKSHVFRKDLYYRI-SVFLINISTLR  313 (482)
Q Consensus       242 i~~L~~~~Q---~~Ll~~l~~~~~~~~-g~~-~~~~~~~RiIa~t~~~--L~~~~~~g~fr~dLy~rL-~~~~i~iPpLR  313 (482)
                      |+.+-..=|   ..-.+.+ ..+|.-. ++. ..-...+-|++|||++  |++.+         .-|+ ..++|.+|...
T Consensus       195 vds~L~~R~s~dHEa~a~m-K~eFM~~WDGl~s~~~~rVlVlgATNRP~DlDeAi---------iRR~p~rf~V~lP~~~  264 (386)
T KOG0737         195 VDSFLGQRRSTDHEATAMM-KNEFMALWDGLSSKDSERVLVLGATNRPFDLDEAI---------IRRLPRRFHVGLPDAE  264 (386)
T ss_pred             HHHHHHHCCCCHHHHHHHH-HHHHHHHHCCCCCCCCCEEEEEECCCCCCCHHHHH---------HHHCCCEEEECCCCHH
T ss_conf             8889864046427999999-99999986164678871599970799984378999---------9847643653798444


Q ss_pred             HHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCC-CCCCCCCCCHHHHHHHHHHHHHHC
Q ss_conf             74422225566777641011223333211111000-122338986899999999998743
Q gi|254780916|r  314 SRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSL-LTKYPWIDNVQELKNILLRAVIGL  372 (482)
Q Consensus       314 eR~eDI~~L~~~fl~~~~~~~~~~~~~ls~~a~~~-L~~y~WPGNvREL~n~i~r~~i~~  372 (482)
                      +|. .|.-+   +|+.-..+-     .|+-.-++. =..|.    -++|+|+|..|....
T Consensus       265 qR~-kILkv---iLk~e~~e~-----~vD~~~iA~~t~GyS----GSDLkelC~~Aa~~~  311 (386)
T KOG0737         265 QRR-KILKV---ILKKEKLED-----DVDLDEIAQMTEGYS----GSDLKELCRLAALRP  311 (386)
T ss_pred             HHH-HHHHH---HHCCCCCCC-----CCCHHHHHHHCCCCC----HHHHHHHHHHHHHHH
T ss_conf             499-99999---942434687-----769888887608986----778999999876768


No 213
>PTZ00111 DNA replication licensing factor MCM4; Provisional
Probab=97.76  E-value=8.5e-05  Score=53.53  Aligned_cols=114  Identities=14%  Similarity=0.189  Sum_probs=75.9

Q ss_pred             CCCEEEEEECCCCCHHHHHHHHHHHCCCCCCCCCCCC---CCCCCCCCCCHHHHHCCCCCCCCCCCCCCCCCCCCCCCEE
Q ss_conf             4320488732777436799999984267543321012---3465542100243311255553221110012344667147
Q gi|254780916|r  161 DCAIPIMIQGEFGVGKKRLSRFIHESGKRAFFPFFIV---NCGMIDQDKIEKFLFGDVDLQTKNSAQFLGKFIEANGGTI  237 (482)
Q Consensus       161 ~~~~~vli~Ge~GtGK~~~A~~iH~~s~r~~~~fi~v---~c~~~~~~~~e~~lFG~~~~~~~~~~~~~g~~~~a~~Gtl  237 (482)
                      ..+.+||+.|.+||+|.-+-+++|..++|.  -|..=   ..++++....      ..+..||...--.|.+-.|++|..
T Consensus       491 RgdIniLl~GDPgtaKSQlL~yv~~iaPRg--vytsGkgsSavGLTA~v~------~~d~~tg~~~LEaGALVLaD~Gvc  562 (916)
T PTZ00111        491 RGIINVLLCGDPGTAKSQLLHYTHLLSPRS--IYTSGKSSSSVGLTASIK------FNESDNGRAMIQPGAVVLANGGVC  562 (916)
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHHHHCCCE--EEECCCCCCCCCCEEEEE------ECCCCCCCEEEECCCEEECCCCEE
T ss_conf             454059995799601899999999728742--674598654226468998------326887868985480897279879


Q ss_pred             EECCCCHHHHHHHHHHHHHHHHHHCCCC--CCCCCCCCCCEEEEECC
Q ss_conf             5166420018899988887764200112--35532123431565214
Q gi|254780916|r  238 VLEEPDALPLAVQGRIYNFIETGKIEFF--DSRGAIRLDVRLIFLTE  282 (482)
Q Consensus       238 ~l~ei~~L~~~~Q~~Ll~~l~~~~~~~~--g~~~~~~~~~RiIa~t~  282 (482)
                      ++||.+.|+...+..|..+++.+.+.--  |-.-.....+-|+|+.|
T Consensus       563 cIDEFDKM~~~~rs~lhEaMEQQtvSIAKAGI~~tLnARtSvLAaAN  609 (916)
T PTZ00111        563 CIDELDKCHNESRLSLYEVMEQQTVTIAKAGIVATLKAETAILASCN  609 (916)
T ss_pred             EEEHHHCCCHHHHHHHHHHHHHHHHHHHHCCEEEEECHHHHHHHHCC
T ss_conf             96222036856788999988663123532350454120345655328


No 214
>TIGR02880 cbbX_cfxQ CbbX protein; InterPro: IPR000470 Proteins in this family are now designated CbbX. Some previously were CfxQ (carbon fixation Q). Its gene is often found immmediately downstream of the Rubisco large and small chain genes, and it is suggested to be necessary for Rubisco expression. CbbX has been shown to be necessary for photoautotrophic growth. The Cfx genes in Alcaligenes eutrophus encode a number of Calvin cycle enzymes . The observed sizes of two of the gene products, CfxX and CfxY, are 35 kDa and 27 kDa respectively . No functions could be assigned to CfxX and CfxY. These proteins show a high degree of similarity to the Bacillus subtilis stage V sporulation protein K . ; GO: 0005524 ATP binding.
Probab=97.74  E-value=9e-05  Score=53.35  Aligned_cols=189  Identities=16%  Similarity=0.231  Sum_probs=115.8

Q ss_pred             CCCCCCCCCC-CCCEEEEEECCCCCHHHHHH----HHHHHCCCCCCCCCCCCCCCCCCCCCCHHHHHCCCCCCCCCCCCC
Q ss_conf             2222222234-43204887327774367999----999842675433210123465542100243311255553221110
Q gi|254780916|r  151 QVVDLARKAG-DCAIPIMIQGEFGVGKKRLS----RFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFGDVDLQTKNSAQF  225 (482)
Q Consensus       151 ~v~~~i~~~a-~~~~~vli~Ge~GtGK~~~A----~~iH~~s~r~~~~fi~v~c~~~~~~~~e~~lFG~~~~~~~~~~~~  225 (482)
                      +++....-.+ .-...+-.+|.+||||+.+|    ..+|..+.-+.+.+|++.-    ++++ -...||.      ....
T Consensus        45 ~~r~~~~l~~~~P~lhm~ftG~PGtGkttva~~m~~~l~~lGy~r~G~~~~~tr----ddlv-Gqy~Ght------aPkt  113 (284)
T TIGR02880        45 RLRQKLGLASAAPSLHMSFTGNPGTGKTTVALRMAQILHRLGYVRKGHLVSVTR----DDLV-GQYIGHT------APKT  113 (284)
T ss_pred             HHHHHHHHHHCCCCEEEEECCCCCCCHHHHHHHHHHHHHHCCCCCCCCEEEEEH----HHHH-HHHHCCC------CCHH
T ss_conf             999874221048832677516898724899999999998715400362678530----0131-1221257------7226


Q ss_pred             CCCCCCCCCCEEEECCCCHHHH---------HHHHHHHHHHHHHHCCCCCCCCCCCCCCEEEEECCCCCCCCCCHHHHHH
Q ss_conf             0123446671475166420018---------8999888877642001123553212343156521433211111123337
Q gi|254780916|r  226 LGKFIEANGGTIVLEEPDALPL---------AVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRK  296 (482)
Q Consensus       226 ~g~~~~a~~Gtl~l~ei~~L~~---------~~Q~~Ll~~l~~~~~~~~g~~~~~~~~~RiIa~t~~~L~~~~~~g~fr~  296 (482)
                      ...+.+|.||.||+||--.|-.         +.-.-||+++++.+           -++=||.+--.|          |-
T Consensus       114 ke~lk~a~GGvlfideayyly~P~nerdyG~eaieillq~men~r-----------~~lvvi~aGy~~----------rm  172 (284)
T TIGR02880       114 KEVLKRAMGGVLFIDEAYYLYRPDNERDYGQEAIEILLQVMENQR-----------DDLVVILAGYKD----------RM  172 (284)
T ss_pred             HHHHHHHCCCEEEEECHHHHCCCCCCCHHHHHHHHHHHHHHHCCC-----------CCEEEEEECCHH----------HH
T ss_conf             899987428736642203321776410223799999999872365-----------537888717078----------88


Q ss_pred             HHHHHHH-------HHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHH
Q ss_conf             9998865-------433446778774422225566777641011223333211111000122338986899999999998
Q gi|254780916|r  297 DLYYRIS-------VFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQELKNILLRAV  369 (482)
Q Consensus       297 dLy~rL~-------~~~i~iPpLReR~eDI~~L~~~fl~~~~~~~~~~~~~ls~~a~~~L~~y~WPGNvREL~n~i~r~~  369 (482)
                      |-||.=|       ..+|..|--.  .+++..++..+++....++.......-.+.+..=...+|=.|-|-.+|.+.|+-
T Consensus       173 ~~f~~snPG~~sr~a~h~~fPdy~--~~~l~~ia~~~l~~~~y~~~~~~~~~~~~y~~~r~~~P~f~nars~rna~dr~r  250 (284)
T TIGR02880       173 DSFFESNPGLSSRVAHHVDFPDYS--EEELLAIAELMLEEQQYRLSAEAEEALADYIALRRKQPFFANARSIRNALDRAR  250 (284)
T ss_pred             HHHHHCCCCHHHHHHHHCCCCCCC--HHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHH
T ss_conf             887511786246776431588877--678999999988654121118899999999998631783146788999998898


Q ss_pred             HHCC
Q ss_conf             7438
Q gi|254780916|r  370 IGLK  373 (482)
Q Consensus       370 i~~~  373 (482)
                      +-..
T Consensus       251 lr~a  254 (284)
T TIGR02880       251 LRQA  254 (284)
T ss_pred             HHHH
T ss_conf             8889


No 215
>KOG0738 consensus
Probab=97.73  E-value=9e-05  Score=53.34  Aligned_cols=174  Identities=18%  Similarity=0.180  Sum_probs=97.6

Q ss_pred             EEEEEECCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCHHHHHCCCCCCCCCCCCCCCCCCCC---CCCEEEEC
Q ss_conf             048873277743679999998426754332101234655421002433112555532211100123446---67147516
Q gi|254780916|r  164 IPIMIQGEFGVGKKRLSRFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFGDVDLQTKNSAQFLGKFIEA---NGGTIVLE  240 (482)
Q Consensus       164 ~~vli~Ge~GtGK~~~A~~iH~~s~r~~~~fi~v~c~~~~~~~~e~~lFG~~~~~~~~~~~~~g~~~~a---~~Gtl~l~  240 (482)
                      .-||+.|++||||+++|+++.....   .-|..|..+.+..-     --|+.      ..-..=+|+.|   .--|+|||
T Consensus       246 kgvLm~GPPGTGKTlLAKAvATEc~---tTFFNVSsstltSK-----wRGeS------EKlvRlLFemARfyAPStIFiD  311 (491)
T KOG0738         246 KGVLMVGPPGTGKTLLAKAVATECG---TTFFNVSSSTLTSK-----WRGES------EKLVRLLFEMARFYAPSTIFID  311 (491)
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHHC---CEEEEECHHHHHHH-----HCCCH------HHHHHHHHHHHHHHCCCEEEHH
T ss_conf             0005567999747899999988616---72787402456555-----32526------9999999999987488535335


Q ss_pred             CCCHHH------------HHHHHHHHHHHHHHHCCCCCCCCCCCCCCEEEEECCCCCCCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf             642001------------88999888877642001123553212343156521433211111123337999886543344
Q gi|254780916|r  241 EPDALP------------LAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYYRISVFLIN  308 (482)
Q Consensus       241 ei~~L~------------~~~Q~~Ll~~l~~~~~~~~g~~~~~~~~~RiIa~t~~~L~~~~~~g~fr~dLy~rL~~~~i~  308 (482)
                      ||+.|.            ..+-..||-.++ |    ++......--|-+.|+||-+- +. ++ .||..|=-|   +-|.
T Consensus       312 EIDslcs~RG~s~EHEaSRRvKsELLvQmD-G----~~~t~e~~k~VmVLAATN~PW-di-DE-AlrRRlEKR---IyIP  380 (491)
T KOG0738         312 EIDSLCSQRGGSSEHEASRRVKSELLVQMD-G----VQGTLENSKVVMVLAATNFPW-DI-DE-ALRRRLEKR---IYIP  380 (491)
T ss_pred             HHHHHHHCCCCCCCHHHHHHHHHHHHHHHH-C----CCCCCCCCEEEEEEECCCCCC-CH-HH-HHHHHHHHH---EEEE
T ss_conf             677887257986503678888889999863-3----444445651699984368982-05-79-999987630---3312


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHCCC
Q ss_conf             677877442222556677764101122333321111100012233898689999999999874389
Q gi|254780916|r  309 ISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQELKNILLRAVIGLKD  374 (482)
Q Consensus       309 iPpLReR~eDI~~L~~~fl~~~~~~~~~~~~~ls~~a~~~L~~y~WPGNvREL~n~i~r~~i~~~~  374 (482)
                      +|.--.|..=|..+..    ...    .....-.++..+.+..|.    -.+..|+|+.+.++.-.
T Consensus       381 LP~~~~R~~Li~~~l~----~~~----~~~~~~~~~lae~~eGyS----GaDI~nvCreAsm~~mR  434 (491)
T KOG0738         381 LPDAEARSALIKILLR----SVE----LDDPVNLEDLAERSEGYS----GADITNVCREASMMAMR  434 (491)
T ss_pred             CCCHHHHHHHHHHHHC----CCC----CCCCCCHHHHHHHHCCCC----HHHHHHHHHHHHHHHHH
T ss_conf             8787899999997623----566----888756999999856887----37799999999999999


No 216
>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=97.71  E-value=7.7e-05  Score=53.83  Aligned_cols=185  Identities=18%  Similarity=0.197  Sum_probs=108.3

Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCCCHHHHHHHHHHHCCCC----CCCCCCCCCCCC-------------
Q ss_conf             111122222222222222223443204887327774367999999842675----433210123465-------------
Q gi|254780916|r  139 LDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHESGKR----AFFPFFIVNCGM-------------  201 (482)
Q Consensus       139 ~~~LiG~S~~m~~v~~~i~~~a~~~~~vli~Ge~GtGK~~~A~~iH~~s~r----~~~~fi~v~c~~-------------  201 (482)
                      |..|+|+.. | ++-=.++-+--.=-=|||.|..||||++.-|++=+.=+.    ++.|   +||+=             
T Consensus         3 F~AIVGQ~e-m-KlAllL~vidP~IGGVmvmGdRGTgKSTavRALAalLP~IkaVagcP---~n~~Ps~~~~~c~e~r~~   77 (340)
T TIGR02030         3 FSAIVGQEE-M-KLALLLTVIDPKIGGVMVMGDRGTGKSTAVRALAALLPEIKAVAGCP---FNSAPSDREELCEEVRIL   77 (340)
T ss_pred             CEEEECHHH-H-HHHHHHEEECCCCCEEEEECCCCCCHHHHHHHHHHHCCCEEEECCCC---CCCCCCCCCCCCHHHHHH
T ss_conf             315641688-8-77775200068856288867789835689999997499407861768---788888861357677775


Q ss_pred             ---------------------CCCCCCHHHHHCC---CCCCC-CCCCCCCCCCCCCCCCEEEECCCCHHHHHHHHHHHHH
Q ss_conf             ---------------------5421002433112---55553-2211100123446671475166420018899988887
Q gi|254780916|r  202 ---------------------IDQDKIEKFLFGD---VDLQT-KNSAQFLGKFIEANGGTIVLEEPDALPLAVQGRIYNF  256 (482)
Q Consensus       202 ---------------------~~~~~~e~~lFG~---~~~~~-~~~~~~~g~~~~a~~Gtl~l~ei~~L~~~~Q~~Ll~~  256 (482)
                                           +|--.-|...-|-   +++.| |...-.+|+|.+||.|-||+|||.-|.-.+=.-||-+
T Consensus        78 ~~~~Gkt~~~~~i~~pvpvVDLPLGaTEDRVcGtlDIerALt~GvkAFePGLLArANRG~LYiDEVNLLeDHlVDvLLDv  157 (340)
T TIGR02030        78 EDSSGKTKKLAVIEKPVPVVDLPLGATEDRVCGTLDIERALTEGVKAFEPGLLARANRGYLYIDEVNLLEDHLVDVLLDV  157 (340)
T ss_pred             HHCCCCCCCCEEEECCCCEEECCCCCCCCCEECHHHHHHHHHCCCCCCCCCCHHHHCCCCEEEEEEHHHHHHHHHHHHHH
T ss_conf             31268656751551576536479886213134402476775047210366304666178425521000124566566522


Q ss_pred             HHHH--HCCCCCCCCCCCCCCEEEEECCCCCCCCCCHHHHHHHHHHHHHHH----HHHHHHHH----HHHHHHHHHHHHH
Q ss_conf             7642--001123553212343156521433211111123337999886543----34467787----7442222556677
Q gi|254780916|r  257 IETG--KIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYYRISVF----LINISTLR----SRSEDIPWLVHFF  326 (482)
Q Consensus       257 l~~~--~~~~~g~~~~~~~~~RiIa~t~~~L~~~~~~g~fr~dLy~rL~~~----~i~iPpLR----eR~eDI~~L~~~f  326 (482)
                      =+.|  .++|=|=  ++.=..|++--=|.|++    +|.+|+-|+.|....    +|+=|.+|    +|+..--.==+-|
T Consensus       158 AasG~NvVEREG~--SiRHPARFVLVGSGNPE----EGeLRPQLLDRFGlhaeirt~rdve~RVeiv~rR~eyDadp~aF  231 (340)
T TIGR02030       158 AASGVNVVEREGV--SIRHPARFVLVGSGNPE----EGELRPQLLDRFGLHAEIRTVRDVEERVEIVKRRDEYDADPFAF  231 (340)
T ss_pred             CCCCCEEEEECCE--EEECCCCEEEECCCCCC----CCCCCCHHHHHCCCEEEEECCCCHHHHHHHEEEHHHHCCCCCHH
T ss_conf             0478305863560--23037635871578887----66667401524465278722677222012201003317788534


Q ss_pred             HHHHCCCC
Q ss_conf             76410112
Q gi|254780916|r  327 LQSFCTKN  334 (482)
Q Consensus       327 l~~~~~~~  334 (482)
                      +++|..+.
T Consensus       232 ~ekw~~E~  239 (340)
T TIGR02030       232 VEKWAKED  239 (340)
T ss_pred             HHHHHHHH
T ss_conf             55578889


No 217
>PRK12323 DNA polymerase III subunits gamma and tau; Provisional
Probab=97.68  E-value=0.00024  Score=50.41  Aligned_cols=223  Identities=14%  Similarity=0.151  Sum_probs=125.8

Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCCCHHHHHHHHHHHCCCC-----CCCCCC-----CCCCCCCC
Q ss_conf             21111111122222222222222223443204887327774367999999842675-----433210-----12346554
Q gi|254780916|r  134 NEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHESGKR-----AFFPFF-----IVNCGMID  203 (482)
Q Consensus       134 ~~~~~~~~LiG~S~~m~~v~~~i~~~a~~~~~vli~Ge~GtGK~~~A~~iH~~s~r-----~~~~fi-----~v~c~~~~  203 (482)
                      -....|..+||+.-..+.+...+.. .....--|++|..|+||+.+||.+-..-.-     ..++-.     --+|-.+.
T Consensus        10 ~RP~~F~~~vGQ~~v~~~l~na~~~-~r~~haylf~G~rGvGKTt~ari~Ak~lnc~~~~~~~g~~~~pcg~C~~C~~i~   88 (721)
T PRK12323         10 WRPRDFTTLVGQEHVVRALTHALEQ-QRLHHAYLFTGTRGVGKTTLSRILAKSLNCTGPDGEGGITAQPCGQCRACTEID   88 (721)
T ss_pred             HCCCCHHHHCCCHHHHHHHHHHHHC-CCCCCEEEEECCCCCCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCHHHHHHH
T ss_conf             0798665532859999999999971-997544750279988898999999999768998667898788787765468775


Q ss_pred             CCCCHHHHHCCCCCC-CCCCCCCCCCCCC-------CCCCEEEECCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCC
Q ss_conf             210024331125555-3221110012344-------66714751664200188999888877642001123553212343
Q gi|254780916|r  204 QDKIEKFLFGDVDLQ-TKNSAQFLGKFIE-------ANGGTIVLEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDV  275 (482)
Q Consensus       204 ~~~~e~~lFG~~~~~-~~~~~~~~g~~~~-------a~~Gtl~l~ei~~L~~~~Q~~Ll~~l~~~~~~~~g~~~~~~~~~  275 (482)
                      ...+-.. + +.++. .....+-.-+++.       ..--..++||+|-|+...-.-||..|++-           +-+|
T Consensus        89 ~g~~~d~-~-EiDaas~~~v~~~r~l~~~~~y~P~~~~~KvyiiDevhmls~~afnalLKtlEeP-----------P~hv  155 (721)
T PRK12323         89 AGRFVDY-I-EMDAASNRGVDEMAQLLDQAVYAPTAGRFKVYMIDEVHMLTNHAFNAMLKTLEEP-----------PPHV  155 (721)
T ss_pred             CCCCCCE-E-EEECCCCCCHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHCCC-----------CCCE
T ss_conf             6898764-7-7436767888999999985455887664469998540005899999999840179-----------7553


Q ss_pred             EEEEECCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             15652143321111112333799988654334467787744222255667776410112233332111110001223389
Q gi|254780916|r  276 RLIFLTEKNLLPQVKSHVFRKDLYYRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWI  355 (482)
Q Consensus       276 RiIa~t~~~L~~~~~~g~fr~dLy~rL~~~~i~iPpLReR~eDI~~L~~~fl~~~~~~~~~~~~~ls~~a~~~L~~y~WP  355 (482)
                      .+|.+|+.. .++- .-....=+-|.|.-            =+...++.| |...+.+.+   ..++++|+.++... =-
T Consensus       156 ~FilaTT~~-~Kip-~TilSRc~~f~~~~------------~~~~~i~~~-l~~i~~~E~---i~~~~~al~~ia~~-a~  216 (721)
T PRK12323        156 KFILATTDP-QKIP-VTVLSRCLQFNLKQ------------MPPGHIVSH-LDAILGQEG---IGHEGNALRLLAQA-AH  216 (721)
T ss_pred             EEEEECCCH-HHCC-HHHHHHHHHCCCCC------------CCHHHHHHH-HHHHHHHCC---CCCCHHHHHHHHHH-CC
T ss_conf             899943863-4485-88987765423478------------999999999-999999839---97799999999997-58


Q ss_pred             CCHHHHHHHHHHHHHHCCCCCCCHHHHHHHHCCCC
Q ss_conf             86899999999998743898106889545421244
Q gi|254780916|r  356 DNVQELKNILLRAVIGLKDSHLTEDRFVLLLSREG  390 (482)
Q Consensus       356 GNvREL~n~i~r~~i~~~~~~i~~~~~~~~l~~~~  390 (482)
                      |-+|.=-+++.+++..+. +.|+.+++...++...
T Consensus       217 Gs~RDalslldQaia~~~-g~~~~~~v~~mlg~~d  250 (721)
T PRK12323        217 GSMRDALSLTDQAIAYSA-GNVSEEAVRGMLGAID  250 (721)
T ss_pred             CCHHHHHHHHHHHHHHCC-CCCCHHHHHHHHCCCC
T ss_conf             964768889999998658-9626999999868887


No 218
>PRK07952 DNA replication protein DnaC; Validated
Probab=97.59  E-value=8.1e-05  Score=53.67  Aligned_cols=137  Identities=16%  Similarity=0.198  Sum_probs=83.0

Q ss_pred             CCCCCCCCCCCCCCCCCCEEEEEECCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCHHH--HHCCCCCCCCCCC
Q ss_conf             22222222222223443204887327774367999999842675433210123465542100243--3112555532211
Q gi|254780916|r  146 SPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHESGKRAFFPFFIVNCGMIDQDKIEKF--LFGDVDLQTKNSA  223 (482)
Q Consensus       146 S~~m~~v~~~i~~~a~~~~~vli~Ge~GtGK~~~A~~iH~~s~r~~~~fi~v~c~~~~~~~~e~~--lFG~~~~~~~~~~  223 (482)
                      -+++...+..+..........++.|.+||||+++|-+|-+.--.+..+.+-+..+    +++...  -|+..+ .  ...
T Consensus        79 ~~al~~a~~y~enf~~~~~gLlF~G~~GTGKThLA~aIan~Li~~G~sVlf~t~~----dLl~~lr~t~~~~~-~--~e~  151 (242)
T PRK07952         79 MNALSKARQYVEEFDGNIASFIFSGKPGTGKNHLAAAICNELLLRGKSVLIITVA----DIMSAMKDTFRNSE-T--SEE  151 (242)
T ss_pred             HHHHHHHHHHHHHHCCCCCEEEEECCCCCCHHHHHHHHHHHHHHCCCEEEEEEHH----HHHHHHHHHHHCCC-C--CHH
T ss_conf             9999999999986543887179978999978999999999999879949997799----99999999980687-5--699


Q ss_pred             CCCCCCCCCCCCEEEECCCCH--HHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCEEEEECCCCCCCCCCHHHHHHHHHHH
Q ss_conf             100123446671475166420--018899988887764200112355321234315652143321111112333799988
Q gi|254780916|r  224 QFLGKFIEANGGTIVLEEPDA--LPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYYR  301 (482)
Q Consensus       224 ~~~g~~~~a~~Gtl~l~ei~~--L~~~~Q~~Ll~~l~~~~~~~~g~~~~~~~~~RiIa~t~~~L~~~~~~g~fr~dLy~r  301 (482)
                      +..-.+.  +-.-|+|||++.  .+...+..|..++..+. .   ..+|      .|.+||.+++++-.  .+-+-.+.|
T Consensus       152 ~~l~~l~--~~dLLIiDdlG~e~~t~~~~~~lf~iId~Ry-~---~~kp------~IitTNl~~~eL~~--~lGeR~~dR  217 (242)
T PRK07952        152 QLLNDLS--NVDLLVIDEIGVQTESRYEKVIINQIVDRRS-S---SKRP------TGMLTNSNMEEMTK--LLGERVMDR  217 (242)
T ss_pred             HHHHHHH--CCCEEEEECCCCCCCCHHHHHHHHHHHHHHH-H---CCCC------EEEEECCCHHHHHH--HHHHHHHHH
T ss_conf             9999863--1898987301466588889999999999999-7---1698------89981799999999--970899999


Q ss_pred             HH
Q ss_conf             65
Q gi|254780916|r  302 IS  303 (482)
Q Consensus       302 L~  303 (482)
                      |.
T Consensus       218 l~  219 (242)
T PRK07952        218 MR  219 (242)
T ss_pred             HH
T ss_conf             97


No 219
>PRK08181 transposase; Validated
Probab=97.57  E-value=3.5e-05  Score=56.22  Aligned_cols=138  Identities=12%  Similarity=0.118  Sum_probs=73.2

Q ss_pred             CCCCCCEEEEEECCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCHHHHHCCCCCCCCCCCCCCCCCCCCCCCEE
Q ss_conf             23443204887327774367999999842675433210123465542100243311255553221110012344667147
Q gi|254780916|r  158 KAGDCAIPIMIQGEFGVGKKRLSRFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFGDVDLQTKNSAQFLGKFIEANGGTI  237 (482)
Q Consensus       158 ~~a~~~~~vli~Ge~GtGK~~~A~~iH~~s~r~~~~fi~v~c~~~~~~~~e~~lFG~~~~~~~~~~~~~g~~~~a~~Gtl  237 (482)
                      +......+|+|.|++||||+++|-+|-..--+.+..-.-+.|+.+=.++..+    +.+   +........+..+  --|
T Consensus       101 ~fi~~~~Nvil~Gp~GtGKThLA~Alg~~A~~~G~~V~f~~~~~L~~~L~~a----~~~---~~~~~~~~~l~~~--dLL  171 (269)
T PRK08181        101 SWLAKGANLLLFGPPGGGKSHLAAAIGLALIENGWRVLFTRTTDLVQKLQVA----RRE---LQLESAIAKLDKF--DLL  171 (269)
T ss_pred             HHHHCCCEEEEECCCCCCHHHHHHHHHHHHHHCCCEEEEEEHHHHHHHHHHH----HHC---CCHHHHHHHHHCC--CEE
T ss_conf             5886487089989999878899999999999879939997899999999997----755---8399999997444--601


Q ss_pred             EECCCCHHHHHHHH--HHHHHHHHHHCCCCCCCCCCCCCCEEEEECCCCCCC---CCCHHHHHHHHHHHH----HHHHHH
Q ss_conf             51664200188999--888877642001123553212343156521433211---111123337999886----543344
Q gi|254780916|r  238 VLEEPDALPLAVQG--RIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLP---QVKSHVFRKDLYYRI----SVFLIN  308 (482)
Q Consensus       238 ~l~ei~~L~~~~Q~--~Ll~~l~~~~~~~~g~~~~~~~~~RiIa~t~~~L~~---~~~~g~fr~dLy~rL----~~~~i~  308 (482)
                      +|||++.+|.+.+.  -|++++.++ +.+    +      -+|.+||.+..+   ...+...-.-+..||    .++.+.
T Consensus       172 IiDe~G~~~~~~~~~~~lf~lI~~R-ye~----~------S~IITSn~~~~~W~~~f~D~~la~AiLDRLvH~a~~i~l~  240 (269)
T PRK08181        172 ILDDLAYVTKDQAETSVLFELISAR-YER----R------SILITANQPFGEWNRVFPDPAMTLAAVDRLVHHATIFEMN  240 (269)
T ss_pred             EEHHCCCCCCCHHHHHHHHHHHHHH-HCC----C------CEEEECCCCHHHHHHHCCCHHHHHHHHHHHHCCEEEEEEC
T ss_conf             2201056679989999999999998-578----8------8899889997788775386889999999870152899755


Q ss_pred             HHHHHHH
Q ss_conf             6778774
Q gi|254780916|r  309 ISTLRSR  315 (482)
Q Consensus       309 iPpLReR  315 (482)
                      =++.|-|
T Consensus       241 GeSyR~k  247 (269)
T PRK08181        241 VESYRRR  247 (269)
T ss_pred             CCCCCCH
T ss_conf             8761205


No 220
>PRK06526 transposase; Provisional
Probab=97.55  E-value=6.3e-05  Score=54.46  Aligned_cols=111  Identities=13%  Similarity=0.094  Sum_probs=65.0

Q ss_pred             CCCCCCCEEEEEECCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCHHHHHCCCCCCCCCCCCCCCCCCCCCCCE
Q ss_conf             22344320488732777436799999984267543321012346554210024331125555322111001234466714
Q gi|254780916|r  157 RKAGDCAIPIMIQGEFGVGKKRLSRFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFGDVDLQTKNSAQFLGKFIEANGGT  236 (482)
Q Consensus       157 ~~~a~~~~~vli~Ge~GtGK~~~A~~iH~~s~r~~~~fi~v~c~~~~~~~~e~~lFG~~~~~~~~~~~~~g~~~~a~~Gt  236 (482)
                      +.......+|+|.|++||||+++|-+|-..--+++.+-.-+.|..+-.++..+    +.   .|........+..++  -
T Consensus        92 ~~fi~~~~Nvil~G~~GtGKThLA~Alg~~A~~~G~~v~f~~~~~L~~~L~~a----~~---~g~~~~~~~~l~~~d--L  162 (254)
T PRK06526         92 LDFVTGKENVVFLGPPGTGKTHLAIGLGIRACQAGHRVLFATAAQWVARLAAA----HH---AGRLQDELVKLGRIP--L  162 (254)
T ss_pred             CCHHHCCCCEEEECCCCCCHHHHHHHHHHHHHHCCCCEEEEEHHHHHHHHHHH----HH---CCCHHHHHHHHHCCC--E
T ss_conf             71776588789989999868999999999999869967998779999999998----85---580999999851368--7


Q ss_pred             EEECCCCHHHHHHH--HHHHHHHHHHHCCCCCCCCCCCCCCEEEEECCCCCCC
Q ss_conf             75166420018899--9888877642001123553212343156521433211
Q gi|254780916|r  237 IVLEEPDALPLAVQ--GRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLP  287 (482)
Q Consensus       237 l~l~ei~~L~~~~Q--~~Ll~~l~~~~~~~~g~~~~~~~~~RiIa~t~~~L~~  287 (482)
                      |+|||++..|.+..  .-|+.++.++ +.+       .   -+|-+||.+..+
T Consensus       163 LIiDe~g~~~~~~~~a~~lf~li~~R-ye~-------~---S~IiTSn~~~~~  204 (254)
T PRK06526        163 LIVDEVGYIPFEAEAANLFFQLVSSR-YER-------A---SLIVTSNKPFGR  204 (254)
T ss_pred             EEEECCCCCCCCHHHHHHHHHHHHHH-HCC-------C---CEEEECCCCHHH
T ss_conf             76502136447889999999999999-745-------8---867665898668


No 221
>KOG1969 consensus
Probab=97.55  E-value=0.0022  Score=43.50  Aligned_cols=179  Identities=17%  Similarity=0.256  Sum_probs=94.2

Q ss_pred             EEEEECCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCC-CCCCCHHHHHCCCC--CCCCCCCCCCCCCCCCCCCEEEECC
Q ss_conf             48873277743679999998426754332101234655-42100243311255--5532211100123446671475166
Q gi|254780916|r  165 PIMIQGEFGVGKKRLSRFIHESGKRAFFPFFIVNCGMI-DQDKIEKFLFGDVD--LQTKNSAQFLGKFIEANGGTIVLEE  241 (482)
Q Consensus       165 ~vli~Ge~GtGK~~~A~~iH~~s~r~~~~fi~v~c~~~-~~~~~e~~lFG~~~--~~~~~~~~~~g~~~~a~~Gtl~l~e  241 (482)
                      =.|++|++|-||+++|+.|-..+..   .-+.||.+.- +...++..+-+-..  .+.+|.+         +--+|++||
T Consensus       328 ilLL~GppGlGKTTLAHViAkqaGY---sVvEINASDeRt~~~v~~kI~~avq~~s~l~ads---------rP~CLViDE  395 (877)
T KOG1969         328 ILLLCGPPGLGKTTLAHVIAKQAGY---SVVEINASDERTAPMVKEKIENAVQNHSVLDADS---------RPVCLVIDE  395 (877)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHCCC---EEEEECCCCCCCHHHHHHHHHHHHHHCCCCCCCC---------CCCEEEEEC
T ss_conf             6875368878724799999986285---4887325554347889999999886411225688---------863599842


Q ss_pred             CCHHHHHHHHHHHHHHHHHHCCCCCCCCC---CC------CCCE-EEEECCCCCCCCCCHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             42001889998888776420011235532---12------3431-56521433211111123337999886543344677
Q gi|254780916|r  242 PDALPLAVQGRIYNFIETGKIEFFDSRGA---IR------LDVR-LIFLTEKNLLPQVKSHVFRKDLYYRISVFLINIST  311 (482)
Q Consensus       242 i~~L~~~~Q~~Ll~~l~~~~~~~~g~~~~---~~------~~~R-iIa~t~~~L~~~~~~g~fr~dLy~rL~~~~i~iPp  311 (482)
                      |+--|...=.-++..+....-.-.|....   .+      .=.| |||.+|-=.......  +|.     ..-+...+||
T Consensus       396 IDGa~~~~Vdvilslv~a~~k~~~Gkq~~~~~~rkkkr~~~L~RPIICICNdLYaPaLR~--Lr~-----~A~ii~f~~p  468 (877)
T KOG1969         396 IDGAPRAAVDVILSLVKATNKQATGKQAKKDKKRKKKRSKLLTRPIICICNDLYAPALRP--LRP-----FAEIIAFVPP  468 (877)
T ss_pred             CCCCCHHHHHHHHHHHHHHCCHHHCCCCCCHHHHHHHCCCCCCCCEEEEECCCCCHHHHH--CCC-----CEEEEEECCC
T ss_conf             468728999999999974161421686632034555304654587789864755533331--021-----0489995699


Q ss_pred             HHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHCC
Q ss_conf             87744222255667776410112233332111110001223389868999999999987438
Q gi|254780916|r  312 LRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQELKNILLRAVIGLK  373 (482)
Q Consensus       312 LReR~eDI~~L~~~fl~~~~~~~~~~~~~ls~~a~~~L~~y~WPGNvREL~n~i~r~~i~~~  373 (482)
                      .-.|--+-       |+..|...|+   ..+..++..|..|. -+.||-=-|.++.+.....
T Consensus       469 ~~s~Lv~R-------L~~IC~rE~m---r~d~~aL~~L~el~-~~DIRsCINtLQfLa~~~~  519 (877)
T KOG1969         469 SQSRLVER-------LNEICHRENM---RADSKALNALCELT-QNDIRSCINTLQFLASNVD  519 (877)
T ss_pred             CHHHHHHH-------HHHHHHHHCC---CCCHHHHHHHHHHH-CCHHHHHHHHHHHHHHHCC
T ss_conf             76689999-------9999764157---78878999999986-1309888889999997044


No 222
>KOG0736 consensus
Probab=97.52  E-value=7.9e-05  Score=53.74  Aligned_cols=120  Identities=21%  Similarity=0.249  Sum_probs=65.3

Q ss_pred             CCEEEEEECCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCHHHHHCCCCCCCCCCCCCCCCCCCC---CCCEEE
Q ss_conf             32048873277743679999998426754332101234655421002433112555532211100123446---671475
Q gi|254780916|r  162 CAIPIMIQGEFGVGKKRLSRFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFGDVDLQTKNSAQFLGKFIEA---NGGTIV  238 (482)
Q Consensus       162 ~~~~vli~Ge~GtGK~~~A~~iH~~s~r~~~~fi~v~c~~~~~~~~e~~lFG~~~~~~~~~~~~~g~~~~a---~~Gtl~  238 (482)
                      -.+-||+.|++||||+++|+++-..-   +-.|+.|-.    ++++. .--|+.      ..+..-.|++|   .--.+|
T Consensus       704 kRSGILLYGPPGTGKTLlAKAVATEc---sL~FlSVKG----PELLN-MYVGqS------E~NVR~VFerAR~A~PCVIF  769 (953)
T KOG0736         704 KRSGILLYGPPGTGKTLLAKAVATEC---SLNFLSVKG----PELLN-MYVGQS------EENVREVFERARSAAPCVIF  769 (953)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHHHC---EEEEEEECC----HHHHH-HHHCCH------HHHHHHHHHHHHCCCCEEEE
T ss_conf             13505887799985579999987543---036785058----89988-774301------88899999985446974998


Q ss_pred             ECCCCHHHHH---------HHHHHHH-HHHHHHCCCCCCCCCCCCCCEEEEECCCC-C--CCCCCHHHHHHHHH
Q ss_conf             1664200188---------9998888-77642001123553212343156521433-2--11111123337999
Q gi|254780916|r  239 LEEPDALPLA---------VQGRIYN-FIETGKIEFFDSRGAIRLDVRLIFLTEKN-L--LPQVKSHVFRKDLY  299 (482)
Q Consensus       239 l~ei~~L~~~---------~Q~~Ll~-~l~~~~~~~~g~~~~~~~~~RiIa~t~~~-L--~~~~~~g~fr~dLy  299 (482)
                      +|||+.|.+.         +-.|... +|.+=    -|-+..-.-++=||.|||++ |  ..+..-|+|.+=+|
T Consensus       770 FDELDSlAP~RG~sGDSGGVMDRVVSQLLAEL----Dgls~~~s~~VFViGATNRPDLLDpALLRPGRFDKLvy  839 (953)
T KOG0736         770 FDELDSLAPNRGRSGDSGGVMDRVVSQLLAEL----DGLSDSSSQDVFVIGATNRPDLLDPALLRPGRFDKLVY  839 (953)
T ss_pred             ECCCCCCCCCCCCCCCCCCCHHHHHHHHHHHH----HCCCCCCCCCEEEEECCCCCCCCCHHHCCCCCCCEEEE
T ss_conf             31212327567887886540899999999986----26667888865998258885545765538876552488


No 223
>PRK12377 putative replication protein; Provisional
Probab=97.49  E-value=6.9e-05  Score=54.18  Aligned_cols=146  Identities=15%  Similarity=0.156  Sum_probs=78.4

Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCC----CCCEEEEEECCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCHHHH
Q ss_conf             1111111222222222222222234----432048873277743679999998426754332101234655421002433
Q gi|254780916|r  136 HCALDSLIAVSPAMIQVVDLARKAG----DCAIPIMIQGEFGVGKKRLSRFIHESGKRAFFPFFIVNCGMIDQDKIEKFL  211 (482)
Q Consensus       136 ~~~~~~LiG~S~~m~~v~~~i~~~a----~~~~~vli~Ge~GtGK~~~A~~iH~~s~r~~~~fi~v~c~~~~~~~~e~~l  211 (482)
                      +..|+.+.-+++..+....++..++    ....++++.|.+||||+++|-+|-..--+....-.-+.++    +++ ..|
T Consensus        70 ~~~f~ny~~~~~~~~~a~~~a~~~~~~F~~~~~NlIf~G~pGtGKTHLA~AIg~~a~~~G~sVlF~t~~----dLv-~~L  144 (248)
T PRK12377         70 KCSFANYQVQNDGQRYALSQAKSIADELMTGCTNFVFSGKPGTGKNHLAAAIGNRLLAKGRSVIVVTVP----DVM-SRL  144 (248)
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCEEEEECCCCCCHHHHHHHHHHHHHHCCCEEEEEEHH----HHH-HHH
T ss_conf             386345645787899999999999998731886089989999878899999999999879969998899----999-999


Q ss_pred             HCC-CCCCCCCCCCCCCCCCCCCCCEEEECCCCHHHHHHH--HHHHHHHHHHHCCCCCCCCCCCCCCEEEEECCCCCCCC
Q ss_conf             112-555532211100123446671475166420018899--98888776420011235532123431565214332111
Q gi|254780916|r  212 FGD-VDLQTKNSAQFLGKFIEANGGTIVLEEPDALPLAVQ--GRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQ  288 (482)
Q Consensus       212 FG~-~~~~~~~~~~~~g~~~~a~~Gtl~l~ei~~L~~~~Q--~~Ll~~l~~~~~~~~g~~~~~~~~~RiIa~t~~~L~~~  288 (482)
                      ... .++.+.  ....-.+.  .-.-|+|||++..|.+.+  ..|..++..+ ++..   ++      +|.+||.+..+.
T Consensus       145 ~~a~~~g~~~--~k~l~~l~--~~dLLIIDElG~~~~s~~~~~llfqlI~~R-y~~~---ks------~IiTTNL~f~ew  210 (248)
T PRK12377        145 HESYDNGQSG--EKFLQELC--KVDLLVLDEIGIQRETKNEQVVLNQIIDRR-TASM---RS------VGMLTNLNHEAM  210 (248)
T ss_pred             HHHHHCCCCH--HHHHHHHH--CCCEEEEHHCCCCCCCHHHHHHHHHHHHHH-HHCC---CC------EEEECCCCHHHH
T ss_conf             9999848509--99999973--389898600057889867999999999999-8557---98------689758997799


Q ss_pred             CCHHHHHHHHHHHH
Q ss_conf             11123337999886
Q gi|254780916|r  289 VKSHVFRKDLYYRI  302 (482)
Q Consensus       289 ~~~g~fr~dLy~rL  302 (482)
                      -+  .|-+..+.||
T Consensus       211 ~~--ilgdailDRL  222 (248)
T PRK12377        211 ST--LLGERVMDRM  222 (248)
T ss_pred             HH--HHHHHHHHHH
T ss_conf             88--8759999999


No 224
>COG0470 HolB ATPase involved in DNA replication [DNA replication, recombination, and repair]
Probab=97.46  E-value=0.00025  Score=50.17  Aligned_cols=123  Identities=15%  Similarity=0.174  Sum_probs=63.8

Q ss_pred             CCCCCCCCCCCCCCCCCCCCCEEEEEECCCCCHHHHHHHHHHHCCC----CCC-----------------CCCCCCCCCC
Q ss_conf             2222222222222222344320488732777436799999984267----543-----------------3210123465
Q gi|254780916|r  143 IAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHESGK----RAF-----------------FPFFIVNCGM  201 (482)
Q Consensus       143 iG~S~~m~~v~~~i~~~a~~~~~vli~Ge~GtGK~~~A~~iH~~s~----r~~-----------------~~fi~v~c~~  201 (482)
                      ++..+....+...+..-......+|+.|++|+||+.+|.++=..-.    ...                 -.|+.+|-+.
T Consensus         4 ~~~~~~~~~l~~~~~~~~~~~halL~~Gp~G~Gktt~a~~lA~~l~~~~~~~~~~~~~~~~~~~~~~~~~~d~lel~~s~   83 (325)
T COG0470           4 VPWQEAVKRLLVQALESGRLPHALLFYGPPGVGKTTAALALAKELLCENPTGLLPCGHCRSCKLIPAGNHPDFLELNPSD   83 (325)
T ss_pred             CCCHHHHHHHHHHHHHCCCCCCCEEEECCCCCCHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHCCCCCCCEEEECCCC
T ss_conf             33235899999999865888761003799999789999999999658664334552002244432025688659977321


Q ss_pred             CCCCCCHHHHHCCCCCCCCCCCCCCCCCCCCCCCEEEECCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCEEEEEC
Q ss_conf             54210024331125555322111001234466714751664200188999888877642001123553212343156521
Q gi|254780916|r  202 IDQDKIEKFLFGDVDLQTKNSAQFLGKFIEANGGTIVLEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLT  281 (482)
Q Consensus       202 ~~~~~~e~~lFG~~~~~~~~~~~~~g~~~~a~~Gtl~l~ei~~L~~~~Q~~Ll~~l~~~~~~~~g~~~~~~~~~RiIa~t  281 (482)
                      .....+.-+.-.   .+....... +  .....-.+++||++.|....|..|++.+++.           +.+.++|..|
T Consensus        84 ~~~~~i~~~~vr---~~~~~~~~~-~--~~~~~kviiidead~mt~~A~nallk~lEep-----------~~~~~~il~~  146 (325)
T COG0470          84 LRKIDIIVEQVR---ELAEFLSES-P--LEGGYKVVIIDEADKLTEDAANALLKTLEEP-----------PKNTRFILIT  146 (325)
T ss_pred             CCCCCCHHHHHH---HHHHHCCCC-C--CCCCCEEEEEECCCCCCHHHHHHHHHHCCCC-----------CCCEEEEEEE
T ss_conf             333300699999---999860446-5--6677269997320326988887675433248-----------8871699974


Q ss_pred             C
Q ss_conf             4
Q gi|254780916|r  282 E  282 (482)
Q Consensus       282 ~  282 (482)
                      +
T Consensus       147 n  147 (325)
T COG0470         147 N  147 (325)
T ss_pred             C
T ss_conf             9


No 225
>KOG0732 consensus
Probab=97.46  E-value=7.3e-05  Score=54.00  Aligned_cols=173  Identities=16%  Similarity=0.156  Sum_probs=90.7

Q ss_pred             EEEEEECCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCHHHHHCCCCCCCCCCCCCCCCCCCCCC---CEEEEC
Q ss_conf             04887327774367999999842675433210123465542100243311255553221110012344667---147516
Q gi|254780916|r  164 IPIMIQGEFGVGKKRLSRFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFGDVDLQTKNSAQFLGKFIEANG---GTIVLE  240 (482)
Q Consensus       164 ~~vli~Ge~GtGK~~~A~~iH~~s~r~~~~fi~v~c~~~~~~~~e~~lFG~~~~~~~~~~~~~g~~~~a~~---Gtl~l~  240 (482)
                      .-||..|++||||+++||++-..-.+.+..+-.. ...-.  -.-+.-+|+.      ..+-.=+|++|..   -.+|+|
T Consensus       300 rgvL~~GppGTGkTl~araLa~~~s~~~~kisff-mrkga--D~lskwvgEa------ERqlrllFeeA~k~qPSIIffd  370 (1080)
T KOG0732         300 RGVLFHGPPGTGKTLMARALAAACSRGNRKISFF-MRKGA--DCLSKWVGEA------ERQLRLLFEEAQKTQPSIIFFD  370 (1080)
T ss_pred             CCEEECCCCCCCHHHHHHHHHHHHCCCCCCCCHH-HHCCC--HHHCCCCCCH------HHHHHHHHHHHHCCCCEEEECC
T ss_conf             6323028998725688886665405411020244-31484--4332544757------7889988988744485177305


Q ss_pred             CCCHHH-----HHHHHH------HHHHHHHHHCCCCCCCCCCCCCCEEEEECCCCC---CCCCCHHHHHHHHHHHHHHH-
Q ss_conf             642001-----889998------888776420011235532123431565214332---11111123337999886543-
Q gi|254780916|r  241 EPDALP-----LAVQGR------IYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNL---LPQVKSHVFRKDLYYRISVF-  305 (482)
Q Consensus       241 ei~~L~-----~~~Q~~------Ll~~l~~~~~~~~g~~~~~~~~~RiIa~t~~~L---~~~~~~g~fr~dLy~rL~~~-  305 (482)
                      ||+-|.     ...|.+      ||-++ +        .-+-.-.|.+|.+||+.-   ..+..-|+|..++|+-|... 
T Consensus       371 eIdGlapvrSskqEqih~SIvSTLLaLm-d--------GldsRgqVvvigATnRpda~dpaLRRPgrfdref~f~lp~~~  441 (1080)
T KOG0732         371 EIDGLAPVRSSKQEQIHASIVSTLLALM-D--------GLDSRGQVVVIGATNRPDAIDPALRRPGRFDREFYFPLPDVD  441 (1080)
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHHHHHC-C--------CCCCCCCEEEECCCCCCCCCCHHHCCCCCCCEEEEEECCCHH
T ss_conf             5566465653667774456777788760-4--------777778658971567833246544288666525750378667


Q ss_pred             -HHHHHHHHHHHHHHHHHHHHHHHHHCCCC----CCCCCCCCCCCCCCCCCCCCC
Q ss_conf             -34467787744222255667776410112----233332111110001223389
Q gi|254780916|r  306 -LINISTLRSRSEDIPWLVHFFLQSFCTKN----AIKQISISDKALSLLTKYPWI  355 (482)
Q Consensus       306 -~i~iPpLReR~eDI~~L~~~fl~~~~~~~----~~~~~~ls~~a~~~L~~y~WP  355 (482)
                       .-++=-++-|+-. +++..+++..++...    |.+.+.+..+|.=...+-.+|
T Consensus       442 ar~~Il~Ihtrkw~-~~i~~~l~~~la~~t~gy~gaDlkaLCTeAal~~~~r~~P  495 (1080)
T KOG0732         442 ARAKILDIHTRKWE-PPISRELLLWLAEETSGYGGADLKALCTEAALIALRRSFP  495 (1080)
T ss_pred             HHHHHHHHHCCCCC-CCCCHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHCCCCC
T ss_conf             88899987515777-8877789999988623400578998888875543045658


No 226
>PRK06835 DNA replication protein DnaC; Validated
Probab=97.46  E-value=0.00013  Score=52.12  Aligned_cols=143  Identities=13%  Similarity=0.243  Sum_probs=85.7

Q ss_pred             CCCCC--CCCCCC----CCCCCCCCCCEEEEEECCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCHHHHHCCCC
Q ss_conf             22222--222222----222223443204887327774367999999842675433210123465542100243311255
Q gi|254780916|r  143 IAVSP--AMIQVV----DLARKAGDCAIPIMIQGEFGVGKKRLSRFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFGDVD  216 (482)
Q Consensus       143 iG~S~--~m~~v~----~~i~~~a~~~~~vli~Ge~GtGK~~~A~~iH~~s~r~~~~fi~v~c~~~~~~~~e~~lFG~~~  216 (482)
                      .|.||  -|..++    +.+........++|+.|.+||||+++|.+|-+.--.++...+-+....+-+. +.+.-|... 
T Consensus       157 ~~~sprenm~~i~~~~~~fi~~F~~~~~nLlf~G~~G~GKTfLa~~IA~ell~~g~sViy~ta~~L~~~-l~~~~~~~~-  234 (330)
T PRK06835        157 EPISPRENMENILEKCLNFIKNFDKNNENLLFYGNTGTGKTFLSNCIAKELLDRGKTVIYRTSDELIEN-LREIRFNND-  234 (330)
T ss_pred             CCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEECCCCCCHHHHHHHHHHHHHHCCCEEEEEEHHHHHHH-HHHHHCCCC-
T ss_conf             898989999999999999987247888866988999998899999999999987994999629999999-999754576-


Q ss_pred             CCCCCCCCCCCCCCCCCCCEEEECCCCH--HHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCEEEEECCCCCCCCCCHHHH
Q ss_conf             5532211100123446671475166420--01889998888776420011235532123431565214332111111233
Q gi|254780916|r  217 LQTKNSAQFLGKFIEANGGTIVLEEPDA--LPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVF  294 (482)
Q Consensus       217 ~~~~~~~~~~g~~~~a~~Gtl~l~ei~~--L~~~~Q~~Ll~~l~~~~~~~~g~~~~~~~~~RiIa~t~~~L~~~~~~g~f  294 (482)
                         +........+..++  -|+||+++.  .+......|+.++.++.-.    .+      -.|.+||-+++++.+  .+
T Consensus       235 ---~~~~~~~~~l~~~D--LLIIDDLG~E~~t~~~~~~Lf~iIN~R~~~----~k------~tIITTNl~~~eL~~--~y  297 (330)
T PRK06835        235 ---NDAPELEDLLINCD--LLIIDDLGTESITEFSKTELFNLINKRLLM----NK------KMIISTNLSLEELLK--TY  297 (330)
T ss_pred             ---CCHHHHHHHHHHCC--EEEEECCCCCCCCHHHHHHHHHHHHHHHHC----CC------CEEEECCCCHHHHHH--HH
T ss_conf             ---44899999996189--899721034558868999999999999867----99------979988999899999--87


Q ss_pred             HHHHHHHHHH
Q ss_conf             3799988654
Q gi|254780916|r  295 RKDLYYRISV  304 (482)
Q Consensus       295 r~dLy~rL~~  304 (482)
                      .+-.|-||-.
T Consensus       298 ~eRi~SRi~~  307 (330)
T PRK06835        298 SERIASRLLG  307 (330)
T ss_pred             HHHHHHHHHH
T ss_conf             4899999981


No 227
>COG1474 CDC6 Cdc6-related protein, AAA superfamily ATPase [DNA replication, recombination, and repair / Posttranslational modification, protein turnover, chaperones]
Probab=97.44  E-value=0.00037  Score=49.02  Aligned_cols=202  Identities=18%  Similarity=0.211  Sum_probs=107.8

Q ss_pred             EEEEECCCCCHHHHHHHHHHHCCC-CCCCC-CCCCCCCCCCCC-CCHHHHHCCC-C-CCCCCCCCC----CCCCCCCCCC
Q ss_conf             488732777436799999984267-54332-101234655421-0024331125-5-553221110----0123446671
Q gi|254780916|r  165 PIMIQGEFGVGKKRLSRFIHESGK-RAFFP-FFIVNCGMIDQD-KIEKFLFGDV-D-LQTKNSAQF----LGKFIEANGG  235 (482)
Q Consensus       165 ~vli~Ge~GtGK~~~A~~iH~~s~-r~~~~-fi~v~c~~~~~~-~~e~~lFG~~-~-~~~~~~~~~----~g~~~~a~~G  235 (482)
                      +++|.|.+||||+.+++.+-..-. -+... ++.|||-.++.. .+-+.++-.. + ..+|.....    .-..-...++
T Consensus        44 n~~iyG~~GTGKT~~~~~v~~~l~~~~~~~~~~yINc~~~~t~~~i~~~i~~~~~~~p~~g~~~~~~~~~l~~~~~~~~~  123 (366)
T COG1474          44 NIIIYGPTGTGKTATVKFVMEELEESSANVEVVYINCLELRTPYQVLSKILNKLGKVPLTGDSSLEILKRLYDNLSKKGK  123 (366)
T ss_pred             CEEEECCCCCCHHHHHHHHHHHHHHHCCCCCEEEEEEEECCCHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHCCC
T ss_conf             07998899987328999999999733156757999513078787999999998268997676326899999997774187


Q ss_pred             E--EEECCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCEEEEECCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             4--75166420018899988887764200112355321234315652143321111112333799988654334467787
Q gi|254780916|r  236 T--IVLEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYYRISVFLINISTLR  313 (482)
Q Consensus       236 t--l~l~ei~~L~~~~Q~~Ll~~l~~~~~~~~g~~~~~~~~~RiIa~t~~~L~~~~~~g~fr~dLy~rL~~~~i~iPpLR  313 (482)
                      |  +.|||++.|-...|.-|..++...        ....+.+=+|+.+|..  ..  ...|.+.+--+|....|..||=-
T Consensus       124 ~~IvvLDEid~L~~~~~~~LY~L~r~~--------~~~~~~v~vi~i~n~~--~~--~~~ld~rv~s~l~~~~I~F~pY~  191 (366)
T COG1474         124 TVIVILDEVDALVDKDGEVLYSLLRAP--------GENKVKVSIIAVSNDD--KF--LDYLDPRVKSSLGPSEIVFPPYT  191 (366)
T ss_pred             EEEEEECCHHHHHCCCCCHHHHEECCC--------CCCCEEEEEEEEECCH--HH--HHHHHHHHHHCCCCCEEEECCCC
T ss_conf             599997647654154641455111247--------7675379999973548--89--99875667650687635528989


Q ss_pred             HHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCC--CCCCCCCHHHHHHHHHHHHHHCC---CCCCCHHHHHHH
Q ss_conf             7442222556677764101122333321111100012--23389868999999999987438---981068895454
Q gi|254780916|r  314 SRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLT--KYPWIDNVQELKNILLRAVIGLK---DSHLTEDRFVLL  385 (482)
Q Consensus       314 eR~eDI~~L~~~fl~~~~~~~~~~~~~ls~~a~~~L~--~y~WPGNvREL~n~i~r~~i~~~---~~~i~~~~~~~~  385 (482)
                      .-     .|.+-.-++.  +.+.....++++++++..  ...=-|..|---.+++++.-.+.   .+.++.+++...
T Consensus       192 a~-----el~~Il~~R~--~~~~~~~~~~~~vl~lia~~~a~~~GDAR~aidilr~A~eiAe~~~~~~v~~~~v~~a  261 (366)
T COG1474         192 AE-----ELYDILRERV--EEGFSAGVIDDDVLKLIAALVAAESGDARKAIDILRRAGEIAEREGSRKVSEDHVREA  261 (366)
T ss_pred             HH-----HHHHHHHHHH--HHHHCCCCCCHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHH
T ss_conf             89-----9999999999--8540468748039999999887618647760899999999865407885370047889


No 228
>TIGR02639 ClpA ATP-dependent Clp protease ATP-binding subunit ClpA; InterPro: IPR013461    Proteins in this entry are related to ClpA () from Escherichia coli. ClpA is an ATP-dependent chaperone and part of the ClpAP protease that participates in regulatory protein degradation and the dissolution and degradation of protein aggregates . ClpA recognises sequences in specific proteins, which it then unfolds in an ATP-dependent manner and transports into the degradation chamber of the associated ClpP protein , . A small adaptor-like protein, ClpS, modulates the activity of ClpA and is an important regulatory factor for this protein . It protects ClpA from autodegradation and appears to redirect its activity away from soluble proteins and toward aggregated proteins..
Probab=97.43  E-value=0.0001  Score=52.93  Aligned_cols=122  Identities=16%  Similarity=0.259  Sum_probs=75.1

Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCCCHHHHHHH----HHHHCCCCCCCCCCCCCCCCCCCCCCHH
Q ss_conf             211111111222222222222222234432048873277743679999----9984267543321012346554210024
Q gi|254780916|r  134 NEHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSR----FIHESGKRAFFPFFIVNCGMIDQDKIEK  209 (482)
Q Consensus       134 ~~~~~~~~LiG~S~~m~~v~~~i~~~a~~~~~vli~Ge~GtGK~~~A~----~iH~~s~r~~~~fi~v~c~~~~~~~~e~  209 (482)
                      ..+-..++|||+-..+++..+-+||=-+.| | |..||+|+||+.+|.    .|-+.+             .+|+.|-.+
T Consensus       202 A~~GkiDPLIGRE~EleRtiQvLCRR~KNN-P-l~VGEPGVGKTAI~EGLA~~I~~~~-------------kvPe~Lkn~  266 (774)
T TIGR02639       202 AKNGKIDPLIGREDELERTIQVLCRRKKNN-P-LLVGEPGVGKTAIVEGLAQRIAEGQ-------------KVPEVLKNA  266 (774)
T ss_pred             HHCCCCCCCCCCHHHHHHHHHHHCCCCCCC-C-CEECCCCCCHHHHHHHHHHHHHCCC-------------CCCHHHCCC
T ss_conf             860887873456688742333203456788-7-2044888644899999999864156-------------467002478


Q ss_pred             HHH---------C--CCCCCCCCCCCCCCCCCCCCCC-EEEECCCCHH---------HHHHHHHHHH-HHHHHHCCCCCC
Q ss_conf             331---------1--2555532211100123446671-4751664200---------1889998888-776420011235
Q gi|254780916|r  210 FLF---------G--DVDLQTKNSAQFLGKFIEANGG-TIVLEEPDAL---------PLAVQGRIYN-FIETGKIEFFDS  267 (482)
Q Consensus       210 ~lF---------G--~~~~~~~~~~~~~g~~~~a~~G-tl~l~ei~~L---------~~~~Q~~Ll~-~l~~~~~~~~g~  267 (482)
                      .+|         |  +++-|-.-..+.+--+++..+- .||+||||.+         +++. ..||. +|.+|.+     
T Consensus       267 ~IY~LDmG~LLAGTKYRGDFE~RLK~V~~Ei~~~~~anILFIDEIHTIVGAGATSGGsmDA-SNLLKPaL~~G~i-----  340 (774)
T TIGR02639       267 KIYSLDMGTLLAGTKYRGDFEERLKAVVSEIEKEPNANILFIDEIHTIVGAGATSGGSMDA-SNLLKPALASGKI-----  340 (774)
T ss_pred             CEEEECHHHHHHHCCCCCHHHHHHHHHHHHHHCCCCCCEEEEECCCCEEECCCCCCHHHHH-HHHHHHHHHCCCE-----
T ss_conf             3454043456410245424789999999998528999546641101033178787515524-4321125307877-----


Q ss_pred             CCCCCCCCEEEEECCCC
Q ss_conf             53212343156521433
Q gi|254780916|r  268 RGAIRLDVRLIFLTEKN  284 (482)
Q Consensus       268 ~~~~~~~~RiIa~t~~~  284 (482)
                              |.|-||+..
T Consensus       341 --------RCIGsTTy~  349 (774)
T TIGR02639       341 --------RCIGSTTYE  349 (774)
T ss_pred             --------EEECCCCHH
T ss_conf             --------862265248


No 229
>KOG0739 consensus
Probab=97.38  E-value=0.00014  Score=52.00  Aligned_cols=123  Identities=20%  Similarity=0.262  Sum_probs=71.7

Q ss_pred             EEEEEECCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCHHHHHCCCCCCCCCCCCCCCCCCCCC---CCEEEEC
Q ss_conf             0488732777436799999984267543321012346554210024331125555322111001234466---7147516
Q gi|254780916|r  164 IPIMIQGEFGVGKKRLSRFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFGDVDLQTKNSAQFLGKFIEAN---GGTIVLE  240 (482)
Q Consensus       164 ~~vli~Ge~GtGK~~~A~~iH~~s~r~~~~fi~v~c~~~~~~~~e~~lFG~~~~~~~~~~~~~g~~~~a~---~Gtl~l~  240 (482)
                      .-+|+.|++||||..+|+++-..   ++..|..|..+.+     .|.-.|+..      .-...+|+.|.   -..+|+|
T Consensus       167 rgiLLyGPPGTGKSYLAKAVATE---AnSTFFSvSSSDL-----vSKWmGESE------kLVknLFemARe~kPSIIFiD  232 (439)
T KOG0739         167 RGILLYGPPGTGKSYLAKAVATE---ANSTFFSVSSSDL-----VSKWMGESE------KLVKNLFEMARENKPSIIFID  232 (439)
T ss_pred             EEEEEECCCCCCHHHHHHHHHHH---CCCCEEEEEHHHH-----HHHHHCCHH------HHHHHHHHHHHHCCCCEEEEE
T ss_conf             25788679997577999998741---4770687301788-----998732179------999999999873499479863


Q ss_pred             CCCHHHH-----------HHHHHHHHHHHHHHCCCCCCCCCCCCCCEEEEECCCC--CCCCCCHHHHHHHHHHHHHHHHH
Q ss_conf             6420018-----------8999888877642001123553212343156521433--21111112333799988654334
Q gi|254780916|r  241 EPDALPL-----------AVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKN--LLPQVKSHVFRKDLYYRISVFLI  307 (482)
Q Consensus       241 ei~~L~~-----------~~Q~~Ll~~l~~~~~~~~g~~~~~~~~~RiIa~t~~~--L~~~~~~g~fr~dLy~rL~~~~i  307 (482)
                      ||+.|.-           .....+|-.+|     -||-+..   -+-+..+||.+  |+..+.. +|-+..|       |
T Consensus       233 EiDslcg~r~enEseasRRIKTEfLVQMq-----GVG~d~~---gvLVLgATNiPw~LDsAIRR-RFekRIY-------I  296 (439)
T KOG0739         233 EIDSLCGSRSENESEASRRIKTEFLVQMQ-----GVGNDND---GVLVLGATNIPWVLDSAIRR-RFEKRIY-------I  296 (439)
T ss_pred             HHHHHCCCCCCCCHHHHHHHHHHHHHHHH-----CCCCCCC---CEEEEECCCCCHHHHHHHHH-HHHCCEE-------C
T ss_conf             44443268877711777777778887640-----6665888---64897237884367799998-7650230-------1


Q ss_pred             HHHHHHHHH
Q ss_conf             467787744
Q gi|254780916|r  308 NISTLRSRS  316 (482)
Q Consensus       308 ~iPpLReR~  316 (482)
                      -+|-...|.
T Consensus       297 PLPe~~AR~  305 (439)
T KOG0739         297 PLPEAHARA  305 (439)
T ss_pred             CCCCHHHHH
T ss_conf             087378765


No 230
>KOG0729 consensus
Probab=97.36  E-value=0.00019  Score=51.12  Aligned_cols=213  Identities=15%  Similarity=0.199  Sum_probs=111.2

Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCC-----------CCCEEEEEECCCCCHHHHHHHHHHHCCCCCCCCCCCCCCC
Q ss_conf             22211111111222222222222222234-----------4320488732777436799999984267543321012346
Q gi|254780916|r  132 QENEHCALDSLIAVSPAMIQVVDLARKAG-----------DCAIPIMIQGEFGVGKKRLSRFIHESGKRAFFPFFIVNCG  200 (482)
Q Consensus       132 ~~~~~~~~~~LiG~S~~m~~v~~~i~~~a-----------~~~~~vli~Ge~GtGK~~~A~~iH~~s~r~~~~fi~v~c~  200 (482)
                      ++......+++-|.-..+.++++.++---           .-..-||+.|++||||+++||++-+   |.+.-||.|-.+
T Consensus       169 EekPDvTY~DvGGCKeqIEklREVVE~PlL~PErfv~LGIdPPKGvllyGPPGtGKTL~ARAVAN---RTdAcFIRViGS  245 (435)
T KOG0729         169 EEKPDVTYSDVGGCKEQIEKLREVVELPLLHPERFVNLGIDPPKGVLLYGPPGTGKTLCARAVAN---RTDACFIRVIGS  245 (435)
T ss_pred             ECCCCCCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHCCCCCCCCEEEECCCCCCHHHHHHHHHC---CCCCEEEEEHHH
T ss_conf             12798630345366999999999884325588888752789987337868999861089998745---667458763118


Q ss_pred             CCCCCCCHHHHHCCCCCCCCCCCCCCCCCCCCCCC---EEEECCCCHH-----------HHHHHHHHHHHHHH-HHCCCC
Q ss_conf             55421002433112555532211100123446671---4751664200-----------18899988887764-200112
Q gi|254780916|r  201 MIDQDKIEKFLFGDVDLQTKNSAQFLGKFIEANGG---TIVLEEPDAL-----------PLAVQGRIYNFIET-GKIEFF  265 (482)
Q Consensus       201 ~~~~~~~e~~lFG~~~~~~~~~~~~~g~~~~a~~G---tl~l~ei~~L-----------~~~~Q~~Ll~~l~~-~~~~~~  265 (482)
                      .+-..     ..|+     ||.- ..-+|+.|..-   .+|+|||+..           ..++|.-.|.++.. .-|.|-
T Consensus       246 ELVQK-----YvGE-----GARM-VRElFeMAr~KKACiiFFDEiDAiGGaRFDDg~ggDNEVQRTMLEli~QLDGFDpR  314 (435)
T KOG0729         246 ELVQK-----YVGE-----GARM-VRELFEMARTKKACIIFFDEIDAIGGARFDDGAGGDNEVQRTMLELINQLDGFDPR  314 (435)
T ss_pred             HHHHH-----HHHH-----HHHH-HHHHHHHHCCCCEEEEEEECCCCCCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCCC
T ss_conf             99999-----8624-----6899-99999985236527998410102267203578887279999999999860377888


Q ss_pred             CCCCCCCCCCEEEEECCCC--C-CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCC
Q ss_conf             3553212343156521433--2-111111233379998865433446778774422225566777641011223333211
Q gi|254780916|r  266 DSRGAIRLDVRLIFLTEKN--L-LPQVKSHVFRKDLYYRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISIS  342 (482)
Q Consensus       266 g~~~~~~~~~RiIa~t~~~--L-~~~~~~g~fr~dLy~rL~~~~i~iPpLReR~eDI~~L~~~fl~~~~~~~~~~~~~ls  342 (482)
                      |       |..+..+||++  | ..++.-|++..       -+.+-+|-|.-|.        |.+.-+++..+.. +.+-
T Consensus       315 G-------NIKVlmATNRPdtLDpALlRPGRlDR-------KVEF~LPDlegR~--------~I~kIHaksMsve-rdIR  371 (435)
T KOG0729         315 G-------NIKVLMATNRPDTLDPALLRPGRLDR-------KVEFGLPDLEGRT--------HIFKIHAKSMSVE-RDIR  371 (435)
T ss_pred             C-------CEEEEEECCCCCCCCHHHCCCCCCCC-------CEECCCCCCCCCC--------EEEEEECCCCCCC-CCHH
T ss_conf             8-------75898634898876876628764231-------1210587623551--------2577741114423-2216


Q ss_pred             CCCCCCCCCCCCCCCHHHHHHHHHHHHH---HCCCCCCCHHHHHH
Q ss_conf             1110001223389868999999999987---43898106889545
Q gi|254780916|r  343 DKALSLLTKYPWIDNVQELKNILLRAVI---GLKDSHLTEDRFVL  384 (482)
Q Consensus       343 ~~a~~~L~~y~WPGNvREL~n~i~r~~i---~~~~~~i~~~~~~~  384 (482)
                      -+.+..|..-.   --.|++++|-.+-+   .+...+.++.|+..
T Consensus       372 ~eLlarLCpns---TGAeiRSVCtEAGMfAIraRRkvaTEKDFL~  413 (435)
T KOG0729         372 FELLARLCPNS---TGAEIRSVCTEAGMFAIRARRKVATEKDFLD  413 (435)
T ss_pred             HHHHHHHCCCC---CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             99998658897---4257888887743788887762200888999


No 231
>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=97.36  E-value=0.00025  Score=50.17  Aligned_cols=111  Identities=20%  Similarity=0.240  Sum_probs=61.9

Q ss_pred             CCCCCCEEEEEECCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCHHHHHCCCCCCCCCCCCCCCCCCCCCCCEE
Q ss_conf             23443204887327774367999999842675433210123465542100243311255553221110012344667147
Q gi|254780916|r  158 KAGDCAIPIMIQGEFGVGKKRLSRFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFGDVDLQTKNSAQFLGKFIEANGGTI  237 (482)
Q Consensus       158 ~~a~~~~~vli~Ge~GtGK~~~A~~iH~~s~r~~~~fi~v~c~~~~~~~~e~~lFG~~~~~~~~~~~~~g~~~~a~~Gtl  237 (482)
                      ..-....+|+++|++||||+++|-+|=..--+.+....-+.+.    ++++..-....+   +...+....+..+  -.|
T Consensus        42 ~~i~~~~Nlll~G~~GtGKThLA~Ai~~~~~~~g~~v~f~~~~----~L~~~l~~~~~~---~~~~~~l~~~~~~--dlL  112 (178)
T pfam01695        42 DWIEQAENLLLLGPPGVGKTHLACALGHQACRAGYSVLFTRTP----DLVEQLKRARGD---GRLARTLQRLAKA--DLL  112 (178)
T ss_pred             CCHHCCCCEEEECCCCCCHHHHHHHHHHHHHHCCCEEEEEECH----HHHHHHHHHHHC---CCHHHHHHHHHCC--CEE
T ss_conf             7421587689989999878999999999999869859999616----799999987526---7499999996258--978


Q ss_pred             EECCCCHHHH--HHHHHHHHHHHHHHCCCCCCCCCCCCCCEEEEECCCCCCCC
Q ss_conf             5166420018--89998888776420011235532123431565214332111
Q gi|254780916|r  238 VLEEPDALPL--AVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQ  288 (482)
Q Consensus       238 ~l~ei~~L~~--~~Q~~Ll~~l~~~~~~~~g~~~~~~~~~RiIa~t~~~L~~~  288 (482)
                      +||+++..+.  .....|+.++..+ +.+    +      -+|.+||.++.+.
T Consensus       113 IiDDlG~~~~s~~~~~~lf~li~~R-ye~----~------stIiTSN~~~~~W  154 (178)
T pfam01695       113 ILDDIGYLPLSQEAAHLLFELISDR-YER----R------STILTSNLPFGEW  154 (178)
T ss_pred             EEEHHCCCCCCHHHHHHHHHHHHHH-HCC----C------CEEEECCCCHHHH
T ss_conf             8720016568989999999999999-756----8------8687768997899


No 232
>PRK09183 transposase/IS protein; Provisional
Probab=97.34  E-value=0.00013  Score=52.16  Aligned_cols=109  Identities=17%  Similarity=0.174  Sum_probs=61.8

Q ss_pred             CCCCCCCEEEEEECCCCCHHHHHHHHHHHCCCCCCC--CCCCCCCCCCCCCCCHHHHHCCCCCCCCCCCCCCC-CCCCCC
Q ss_conf             223443204887327774367999999842675433--21012346554210024331125555322111001-234466
Q gi|254780916|r  157 RKAGDCAIPIMIQGEFGVGKKRLSRFIHESGKRAFF--PFFIVNCGMIDQDKIEKFLFGDVDLQTKNSAQFLG-KFIEAN  233 (482)
Q Consensus       157 ~~~a~~~~~vli~Ge~GtGK~~~A~~iH~~s~r~~~--~fi~v~c~~~~~~~~e~~lFG~~~~~~~~~~~~~g-~~~~a~  233 (482)
                      +..-....+|+|.|++||||+++|-+|=..--+.+.  -|++  +    .++++..--.+.+   |....... .+..  
T Consensus        95 ~~fi~~~~Nvil~G~~GtGKThLA~Alg~~A~~~G~~v~f~~--~----~~L~~~L~~a~~~---~~~~~~l~r~l~~--  163 (258)
T PRK09183         95 LSFIERNENIVLLGPSGVGKTHLAIALGYEAVRAGIKVRFTT--A----ADLLLQLSTAQRQ---GRYKTTLQRGVMA--  163 (258)
T ss_pred             CCHHHCCCCEEEECCCCCCHHHHHHHHHHHHHHCCCEEEEEE--H----HHHHHHHHHHHHC---CCHHHHHHHHHCC--
T ss_conf             816655886799899998689999999999998799399978--9----9999999999876---8599999987434--


Q ss_pred             CCEEEECCCCHHHHHHHHH--HHHHHHHHHCCCCCCCCCCCCCCEEEEECCCCCCC
Q ss_conf             7147516642001889998--88877642001123553212343156521433211
Q gi|254780916|r  234 GGTIVLEEPDALPLAVQGR--IYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLP  287 (482)
Q Consensus       234 ~Gtl~l~ei~~L~~~~Q~~--Ll~~l~~~~~~~~g~~~~~~~~~RiIa~t~~~L~~  287 (482)
                      -.-|+|||++.+|.+.+..  |+.++.++ +.+       .   -+|.+||.+..+
T Consensus       164 ~dLLIiDdlG~~~~~~~~~~~lfeli~~R-ye~-------~---S~IiTSn~~~~~  208 (258)
T PRK09183        164 PRLLIIDEIGYLPFSQEEANLFFQVIAKR-YEK-------G---AMILTSNLPFGQ  208 (258)
T ss_pred             CCEEEEHHHHCCCCCHHHHHHHHHHHHHH-HCC-------C---CEEEECCCCHHH
T ss_conf             65144313315468888999999999998-576-------7---789988999789


No 233
>pfam05673 DUF815 Protein of unknown function (DUF815). This family consists of several bacterial proteins of unknown function.
Probab=97.28  E-value=0.00019  Score=51.12  Aligned_cols=128  Identities=11%  Similarity=0.045  Sum_probs=81.0

Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCC--CCEEEEEECCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCHHHHH
Q ss_conf             111111112222222222222222344--320488732777436799999984267543321012346554210024331
Q gi|254780916|r  135 EHCALDSLIAVSPAMIQVVDLARKAGD--CAIPIMIQGEFGVGKKRLSRFIHESGKRAFFPFFIVNCGMIDQDKIEKFLF  212 (482)
Q Consensus       135 ~~~~~~~LiG~S~~m~~v~~~i~~~a~--~~~~vli~Ge~GtGK~~~A~~iH~~s~r~~~~fi~v~c~~~~~~~~e~~lF  212 (482)
                      ....++.|+|-......+.+...+...  ...+||+.|..||||+.+.++++..-...+-.+|.|....+..=   ..|+
T Consensus        23 d~v~l~~L~Gie~Qk~~l~~NT~~F~~G~pAnnvLLwG~RGtGKSSlVKall~~~~~~gLrlIEv~k~~L~~L---p~i~   99 (248)
T pfam05673        23 DPVDLDDLVGIDRQKEALLRNTEQFLAGLPANNVLLWGARGTGKSSLVKALLNEYADQGLRLIEVDKDDLGDL---PDIV   99 (248)
T ss_pred             CCCCHHHHCCHHHHHHHHHHHHHHHHCCCCCCCEEEECCCCCCHHHHHHHHHHHHHHCCCEEEEECHHHHCCH---HHHH
T ss_conf             9899889349399999999999999808986136767689898889999999986314956999878887219---9999


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCEEEECCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCEEEEECCCC
Q ss_conf             125555322111001234466714751664200188999888877642001123553212343156521433
Q gi|254780916|r  213 GDVDLQTKNSAQFLGKFIEANGGTIVLEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKN  284 (482)
Q Consensus       213 G~~~~~~~~~~~~~g~~~~a~~Gtl~l~ei~~L~~~~Q~~Ll~~l~~~~~~~~g~~~~~~~~~RiIa~t~~~  284 (482)
                      ..       ...+.-+|      .||+|.+.==+.+..=|.|+.+-+|      |-...+.|++|-|+||+-
T Consensus       100 ~~-------l~~~~~kF------IiF~DDLSFe~~d~~yk~LKs~LeG------~l~~~p~NvliYaTSNRR  152 (248)
T pfam05673       100 DL-------LRGRPYRF------ILFCDDLSFEEGESSYKALKSVLEG------GLEARPDNVLIYATSNRR  152 (248)
T ss_pred             HH-------HHCCCCCE------EEEECCCCCCCCCHHHHHHHHHHCC------CCCCCCCEEEEEEECCCH
T ss_conf             99-------96499757------9996355767897369999999657------644688738999842700


No 234
>COG3267 ExeA Type II secretory pathway, component ExeA (predicted ATPase) [Intracellular trafficking and secretion]
Probab=97.21  E-value=0.00079  Score=46.70  Aligned_cols=206  Identities=16%  Similarity=0.195  Sum_probs=112.1

Q ss_pred             CCCCCEEEEEECCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCHHHHHCCCCC---CC---CCCCCCCCCCCCC
Q ss_conf             34432048873277743679999998426754332101234655421002433112555---53---2211100123446
Q gi|254780916|r  159 AGDCAIPIMIQGEFGVGKKRLSRFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFGDVDL---QT---KNSAQFLGKFIEA  232 (482)
Q Consensus       159 ~a~~~~~vli~Ge~GtGK~~~A~~iH~~s~r~~~~fi~v~c~~~~~~~~e~~lFG~~~~---~~---~~~~~~~g~~~~a  232 (482)
                      ++....-+.++||.||||+++.|++-+.-.....--+.++--.++...+-..+|-.-..   .+   -......++.+..
T Consensus        47 i~d~qg~~~vtGevGsGKTv~~Ral~~s~~~d~~~~v~i~~~~~s~~~~~~ai~~~l~~~p~~~~~~~~e~~~~~L~al~  126 (269)
T COG3267          47 IADGQGILAVTGEVGSGKTVLRRALLASLNEDQVAVVVIDKPTLSDATLLEAIVADLESQPKVNVNAVLEQIDRELAALV  126 (269)
T ss_pred             HHCCCCEEEEEECCCCCHHHHHHHHHHHCCCCCEEEEEECCCCHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHH
T ss_conf             75178559997447776369999999855788517998357630178899999998405832006889999999999999


Q ss_pred             CC----CEEEECCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCEEEEECCCCCCCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf             67----14751664200188999888877642001123553212343156521433211111123337999886543344
Q gi|254780916|r  233 NG----GTIVLEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYYRISVFLIN  308 (482)
Q Consensus       233 ~~----Gtl~l~ei~~L~~~~Q~~Ll~~l~~~~~~~~g~~~~~~~~~RiIa~t~~~L~~~~~~g~fr~dLy~rL~~~~i~  308 (482)
                      ..    -.++.||-++|..+. -.-||.+.+..-   ++.++    .+++-.-..-|........+++ +=||.- +.|+
T Consensus       127 ~~g~r~v~l~vdEah~L~~~~-le~Lrll~nl~~---~~~~~----l~ivL~Gqp~L~~~lr~~~l~e-~~~R~~-ir~~  196 (269)
T COG3267         127 KKGKRPVVLMVDEAHDLNDSA-LEALRLLTNLEE---DSSKL----LSIVLIGQPKLRPRLRLPVLRE-LEQRID-IRIE  196 (269)
T ss_pred             HHCCCCEEEEEHHHHHHCHHH-HHHHHHHHHHCC---CCCCC----EEEEECCCCCCCHHHCHHHHHH-HHHEEE-EEEE
T ss_conf             817887378501676617548-999999886203---46672----1145507801143544288985-431677-8995


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCC--CCCCCCCHHHHHHHHHHHHHHCCCCCCCHH
Q ss_conf             677877442222556677764101122333321111100012--233898689999999999874389810688
Q gi|254780916|r  309 ISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLT--KYPWIDNVQELKNILLRAVIGLKDSHLTED  380 (482)
Q Consensus       309 iPpLReR~eDI~~L~~~fl~~~~~~~~~~~~~ls~~a~~~L~--~y~WPGNvREL~n~i~r~~i~~~~~~i~~~  380 (482)
                      +||+-+=  .+...+.|-++..    +.+..-|+++|+..+.  ..-||+=|.++--..--++..+.++-++.+
T Consensus       197 l~P~~~~--~t~~yl~~~Le~a----~~~~~l~~~~a~~~i~~~sqg~P~lin~~~~~Al~~a~~a~~~~v~~a  264 (269)
T COG3267         197 LPPLTEA--ETGLYLRHRLEGA----GLPEPLFSDDALLLIHEASQGIPRLINNLATLALDAAYSAGEDGVSEA  264 (269)
T ss_pred             CCCCCHH--HHHHHHHHHHHCC----CCCCCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHCCCCCCCHH
T ss_conf             3886747--8999999998505----899666770578999998525548999988999999987399751256


No 235
>PRK05564 DNA polymerase III subunit delta'; Validated
Probab=97.19  E-value=0.00043  Score=48.54  Aligned_cols=107  Identities=15%  Similarity=0.149  Sum_probs=64.7

Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCCCHHHHHHHHHHHC----CCCCCCC-CCCCCCCCCCCCCCHHHHH
Q ss_conf             1111122222222222222223443204887327774367999999842----6754332-1012346554210024331
Q gi|254780916|r  138 ALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHES----GKRAFFP-FFIVNCGMIDQDKIEKFLF  212 (482)
Q Consensus       138 ~~~~LiG~S~~m~~v~~~i~~~a~~~~~vli~Ge~GtGK~~~A~~iH~~----s~r~~~~-fi~v~c~~~~~~~~e~~lF  212 (482)
                      .|+.++|+....+.+...+.+ .......|++|+.|+||+.+|+.+=..    ....+.| ++.++-             
T Consensus         2 ~f~~iiGq~~i~~~L~~~i~~-~rl~HAyLF~Gp~G~GK~~~A~~~A~~ll~~~~~~~~~D~~~~~~-------------   67 (313)
T PRK05564          2 SFRTIIGHENIKNRIDNSIIK-GKFSHASLIVGEDGIGKSILAKEIANKILGKSEQREYVDIIEYKP-------------   67 (313)
T ss_pred             CHHHCCCHHHHHHHHHHHHHC-CCCCCEEEEECCCCCCHHHHHHHHHHHHHCCCCCCCCCCEEEEEC-------------
T ss_conf             832326829999999999987-998750432799985099999999999828997788986588633-------------


Q ss_pred             CCCCCCCCCCCCCCCCCC-------CCCCCEEEECCCCHHHHHHHHHHHHHHHHH
Q ss_conf             125555322111001234-------466714751664200188999888877642
Q gi|254780916|r  213 GDVDLQTKNSAQFLGKFI-------EANGGTIVLEEPDALPLAVQGRIYNFIETG  260 (482)
Q Consensus       213 G~~~~~~~~~~~~~g~~~-------~a~~Gtl~l~ei~~L~~~~Q~~Ll~~l~~~  260 (482)
                       ..+..-+-..-| .+.+       ++..-..++|+.+.|+.+.+..||..|||.
T Consensus        68 -~~~~~I~vd~IR-~l~~~~~~~p~~g~~KV~II~~ae~m~~~AaNALLKtLEEP  120 (313)
T PRK05564         68 -INKKSIGVDDIR-NIIEEVNKKPYEGDKKVIIIYKSEKMTEQAQNAFLKTIEEP  120 (313)
T ss_pred             -CCCCCCCHHHHH-HHHHHHHHCCCCCCCEEEEECCHHHHCHHHHHHHHHCCCCC
T ss_conf             -225699989999-99999840862589569998077775899999984550368


No 236
>COG2812 DnaX DNA polymerase III, gamma/tau subunits [DNA replication, recombination, and repair]
Probab=97.16  E-value=0.0015  Score=44.75  Aligned_cols=212  Identities=17%  Similarity=0.226  Sum_probs=118.1

Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCCCHHHHHHHHHHHCCC----CCCCCCCC-CCCCCCCCC----
Q ss_conf             111111112222222222222222344320488732777436799999984267----54332101-234655421----
Q gi|254780916|r  135 EHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHESGK----RAFFPFFI-VNCGMIDQD----  205 (482)
Q Consensus       135 ~~~~~~~LiG~S~~m~~v~~~i~~~a~~~~~vli~Ge~GtGK~~~A~~iH~~s~----r~~~~fi~-v~c~~~~~~----  205 (482)
                      ....|+.++|+...-..+...+. ......--|+.|+.||||+.+||.+-..-.    -...|... .+|-++...    
T Consensus        11 RP~~F~evvGQe~v~~~L~nal~-~~ri~hAYlfsG~RGvGKTt~Ari~AkalNC~~~~~~ePC~~C~~Ck~I~~g~~~D   89 (515)
T COG2812          11 RPKTFDDVVGQEHVVKTLSNALE-NGRIAHAYLFSGPRGVGKTTIARILAKALNCENGPTAEPCGKCISCKEINEGSLID   89 (515)
T ss_pred             CCCCHHHHCCCHHHHHHHHHHHH-HCCCHHHHHHCCCCCCCCHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHCCCCCC
T ss_conf             83007776364899999999998-08423336513777767104999999995688987777225316668651488641


Q ss_pred             CCHHHHHCCCCC-CCCCCCCCCCCCC-------CCCCCEEEECCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCEE
Q ss_conf             002433112555-5322111001234-------46671475166420018899988887764200112355321234315
Q gi|254780916|r  206 KIEKFLFGDVDL-QTKNSAQFLGKFI-------EANGGTIVLEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRL  277 (482)
Q Consensus       206 ~~e~~lFG~~~~-~~~~~~~~~g~~~-------~a~~Gtl~l~ei~~L~~~~Q~~Ll~~l~~~~~~~~g~~~~~~~~~Ri  277 (482)
                      ++|      -++ +....++-.-+.+       +++--..++||+|-|+......||..||+.           +.+|-+
T Consensus        90 viE------iDaASn~gVddiR~i~e~v~y~P~~~ryKVyiIDEvHMLS~~afNALLKTLEEP-----------P~hV~F  152 (515)
T COG2812          90 VIE------IDAASNTGVDDIREIIEKVNYAPSEGRYKVYIIDEVHMLSKQAFNALLKTLEEP-----------PSHVKF  152 (515)
T ss_pred             CHH------HHHHHCCCHHHHHHHHHHHCCCCCCCCCEEEEEECHHHHHHHHHHHHHCCCCCC-----------CCCEEE
T ss_conf             011------364445486799999987246886666418998318764378888875111368-----------667489


Q ss_pred             EEECCCCC----CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             65214332----11111123337999886543344677877442222556677764101122333321111100012233
Q gi|254780916|r  278 IFLTEKNL----LPQVKSHVFRKDLYYRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYP  353 (482)
Q Consensus       278 Ia~t~~~L----~~~~~~g~fr~dLy~rL~~~~i~iPpLReR~eDI~~L~~~fl~~~~~~~~~~~~~ls~~a~~~L~~y~  353 (482)
                      |.+|+..-    .-+....+|      .+.-++         .++|...    ++.++.+.+   ..++++|+..+.. .
T Consensus       153 IlATTe~~Kip~TIlSRcq~f------~fkri~---------~~~I~~~----L~~i~~~E~---I~~e~~aL~~ia~-~  209 (515)
T COG2812         153 ILATTEPQKIPNTILSRCQRF------DFKRLD---------LEEIAKH----LAAILDKEG---INIEEDALSLIAR-A  209 (515)
T ss_pred             EEECCCCCCCCHHHHHCCCCC------CCCCCC---------HHHHHHH----HHHHHHHCC---CCCCHHHHHHHHH-H
T ss_conf             985388676840455212202------225799---------9999999----999987448---7547999999999-8


Q ss_pred             CCCCHHHHHHHHHHHHHHCCCCCCCHHHHHHHHCC
Q ss_conf             89868999999999987438981068895454212
Q gi|254780916|r  354 WIDNVQELKNILLRAVIGLKDSHLTEDRFVLLLSR  388 (482)
Q Consensus       354 WPGNvREL~n~i~r~~i~~~~~~i~~~~~~~~l~~  388 (482)
                      --|-.|+--+.+.++...+. +.|+.+.+...++.
T Consensus       210 a~Gs~RDalslLDq~i~~~~-~~It~~~v~~~lG~  243 (515)
T COG2812         210 AEGSLRDALSLLDQAIAFGE-GEITLESVRDMLGL  243 (515)
T ss_pred             CCCCHHHHHHHHHHHHHCCC-CCCCHHHHHHHHCC
T ss_conf             28974567778999997067-76569999999688


No 237
>COG5271 MDN1 AAA ATPase containing von Willebrand factor type A (vWA) domain [General function prediction only]
Probab=97.06  E-value=0.0012  Score=45.48  Aligned_cols=34  Identities=26%  Similarity=0.343  Sum_probs=18.7

Q ss_pred             CCCCCCCCCCCCCCCCCEEEEEECCCCCHHHHHH
Q ss_conf             2222222222223443204887327774367999
Q gi|254780916|r  147 PAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLS  180 (482)
Q Consensus       147 ~~m~~v~~~i~~~a~~~~~vli~Ge~GtGK~~~A  180 (482)
                      ..|.++...+.+.-.+..|||+.||+|+||+++.
T Consensus      1157 ~~m~rl~~lv~~Cl~~kepvlLVgetgcgktt~c 1190 (4600)
T COG5271        1157 EPMCRLERLVGKCLVTKEPVLLVGETGCGKTTGC 1190 (4600)
T ss_pred             CCHHHHHHHHHHHHCCCCCEEEEEECCCCHHHHH
T ss_conf             4302336687776523685489961475435789


No 238
>PRK09112 DNA polymerase III subunit delta'; Validated
Probab=97.05  E-value=0.0019  Score=44.03  Aligned_cols=136  Identities=13%  Similarity=0.156  Sum_probs=71.3

Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCCCHHHHHHHHHH----HCCCCCCCCCC--CCC--C---C----C
Q ss_conf             111111222222222222222234432048873277743679999998----42675433210--123--4---6----5
Q gi|254780916|r  137 CALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIH----ESGKRAFFPFF--IVN--C---G----M  201 (482)
Q Consensus       137 ~~~~~LiG~S~~m~~v~~~i~~~a~~~~~vli~Ge~GtGK~~~A~~iH----~~s~r~~~~fi--~v~--c---~----~  201 (482)
                      ..+..++|+..+.+.+.+.+. -.....-.|++|+.|+||.++|+.+=    ........|--  ..+  |   .    +
T Consensus        20 r~~~~liGq~~~~~~L~~a~~-~gRl~HA~Lf~GP~GiGKaTlA~~~A~~Ll~~~~~~~~~~~~~~pd~~~~~~r~i~~g   98 (352)
T PRK09112         20 SENNRLFGHEEARAFLAQAYR-EGRLHHALLFEGPEGIGKATLAFHLANHILSHPDPNEAPETLADPDPASPLWRQIAQG   98 (352)
T ss_pred             CCHHHHCCHHHHHHHHHHHHH-CCCCCCEEEEECCCCCCHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCHHHHHHHCC
T ss_conf             446462786999999999998-4996524653589980899999999999866998666865567888787789999748


Q ss_pred             CCCCCCH-HHHHCCCCC-C-CC---CCCCCC-CCCC--CCCCC--EEEECCCCHHHHHHHHHHHHHHHHHHCCCCCCCCC
Q ss_conf             5421002-433112555-5-32---211100-1234--46671--47516642001889998888776420011235532
Q gi|254780916|r  202 IDQDKIE-KFLFGDVDL-Q-TK---NSAQFL-GKFI--EANGG--TIVLEEPDALPLAVQGRIYNFIETGKIEFFDSRGA  270 (482)
Q Consensus       202 ~~~~~~e-~~lFG~~~~-~-~~---~~~~~~-g~~~--~a~~G--tl~l~ei~~L~~~~Q~~Ll~~l~~~~~~~~g~~~~  270 (482)
                      -..++++ ..-|-.+.+ + +.   ...+.. ..|.  ...||  .+++|+.+.|+...+..||+.||+.          
T Consensus        99 ~hpdl~~i~r~~d~k~~~~~~~I~vd~iR~l~~~~~~~~~~~~~kv~Iid~ad~m~~~aaNALLK~LEEP----------  168 (352)
T PRK09112         99 AHPNLLHLTRPFDEKTGKFKTAITVDEIRRVTHFLSQTSGDGNWRIVIIDPADDMNRNAANAILKTLEEP----------  168 (352)
T ss_pred             CCCCEEEEECCCCHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCEEEEEECCHHHHHHHHHHHHHHHHHCC----------
T ss_conf             9999565534322021454335777999999998454886688069998187874699999999985348----------


Q ss_pred             CCCCCEEEEECCCC
Q ss_conf             12343156521433
Q gi|254780916|r  271 IRLDVRLIFLTEKN  284 (482)
Q Consensus       271 ~~~~~RiIa~t~~~  284 (482)
                       +.++.+|..|+..
T Consensus       169 -p~~~~fiLit~~~  181 (352)
T PRK09112        169 -PARALFILISHSS  181 (352)
T ss_pred             -CCCEEEEEEECCH
T ss_conf             -9874899886997


No 239
>KOG0744 consensus
Probab=97.03  E-value=0.0011  Score=45.63  Aligned_cols=87  Identities=16%  Similarity=0.219  Sum_probs=52.1

Q ss_pred             CCCCCCCEEEEEECCCCCHHHHHHHHHHH------CCCCCCCCCCCCCCCCCCCCCCHHHHHCCCCCCCCCCCCCCCCCC
Q ss_conf             22344320488732777436799999984------267543321012346554210024331125555322111001234
Q gi|254780916|r  157 RKAGDCAIPIMIQGEFGVGKKRLSRFIHE------SGKRAFFPFFIVNCGMIDQDKIEKFLFGDVDLQTKNSAQFLGKFI  230 (482)
Q Consensus       157 ~~~a~~~~~vli~Ge~GtGK~~~A~~iH~------~s~r~~~~fi~v~c~~~~~~~~e~~lFG~~~~~~~~~~~~~g~~~  230 (482)
                      ..+...+.=||+.|++||||+.+.+++-+      .+....+.+|.+||.++     =|.-|++.+---.-..+.+--+.
T Consensus       171 tnlIt~NRliLlhGPPGTGKTSLCKaLaQkLSIR~~~~y~~~~liEinshsL-----FSKWFsESgKlV~kmF~kI~ELv  245 (423)
T KOG0744         171 TNLITWNRLILLHGPPGTGKTSLCKALAQKLSIRTNDRYYKGQLIEINSHSL-----FSKWFSESGKLVAKMFQKIQELV  245 (423)
T ss_pred             CCEEEEEEEEEEECCCCCCHHHHHHHHHHHHEEEECCCCCCCEEEEEEHHHH-----HHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             7446641489985799988227999998751465237644406999704678-----89887121138999999999997


Q ss_pred             CCCCC--EEEECCCCHHHHH
Q ss_conf             46671--4751664200188
Q gi|254780916|r  231 EANGG--TIVLEEPDALPLA  248 (482)
Q Consensus       231 ~a~~G--tl~l~ei~~L~~~  248 (482)
                      +-.|-  .+.+||++.|...
T Consensus       246 ~d~~~lVfvLIDEVESLa~a  265 (423)
T KOG0744         246 EDRGNLVFVLIDEVESLAAA  265 (423)
T ss_pred             HCCCCEEEEEEHHHHHHHHH
T ss_conf             17896899980787888999


No 240
>KOG0726 consensus
Probab=96.99  E-value=0.0019  Score=44.01  Aligned_cols=139  Identities=17%  Similarity=0.214  Sum_probs=77.9

Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCC-----------CCCEEEEEECCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCC
Q ss_conf             1111111222222222222222234-----------43204887327774367999999842675433210123465542
Q gi|254780916|r  136 HCALDSLIAVSPAMIQVVDLARKAG-----------DCAIPIMIQGEFGVGKKRLSRFIHESGKRAFFPFFIVNCGMIDQ  204 (482)
Q Consensus       136 ~~~~~~LiG~S~~m~~v~~~i~~~a-----------~~~~~vli~Ge~GtGK~~~A~~iH~~s~r~~~~fi~v~c~~~~~  204 (482)
                      ...+..+-|-...++++.+.++---           .-..-|.+.|++||||+++|+++-+..   ...|+.|-.+.   
T Consensus       181 ~Ety~diGGle~QiQEiKEsvELPLthPE~YeemGikpPKGVIlyG~PGTGKTLLAKAVANqT---SATFlRvvGse---  254 (440)
T KOG0726         181 QETYADIGGLESQIQEIKESVELPLTHPEYYEEMGIKPPKGVILYGEPGTGKTLLAKAVANQT---SATFLRVVGSE---  254 (440)
T ss_pred             HHHHCCCCCHHHHHHHHHHHHCCCCCCHHHHHHCCCCCCCEEEEECCCCCCHHHHHHHHHCCC---CHHHHHHHHHH---
T ss_conf             011134425789999999863388898789997288999705886799975368888772455---21245565089---


Q ss_pred             CCCHHHHHCCCCCCCCCCCCCCCCCCC---CCCCEEEECCCCHHH-----------HHHHHHHHHHHHHHHCCCCCCCCC
Q ss_conf             100243311255553221110012344---667147516642001-----------889998888776420011235532
Q gi|254780916|r  205 DKIEKFLFGDVDLQTKNSAQFLGKFIE---ANGGTIVLEEPDALP-----------LAVQGRIYNFIETGKIEFFDSRGA  270 (482)
Q Consensus       205 ~~~e~~lFG~~~~~~~~~~~~~g~~~~---a~~Gtl~l~ei~~L~-----------~~~Q~~Ll~~l~~~~~~~~g~~~~  270 (482)
                       ++. .-.|.-     + .-..-+|..   -.-..+|+|||+...           .+.|.-+|.+|..     +++...
T Consensus       255 -LiQ-kylGdG-----p-klvRqlF~vA~e~apSIvFiDEIdAiGtKRyds~SggerEiQrtmLELLNQ-----ldGFds  321 (440)
T KOG0726         255 -LIQ-KYLGDG-----P-KLVRELFRVAEEHAPSIVFIDEIDAIGTKRYDSNSGGEREIQRTMLELLNQ-----LDGFDS  321 (440)
T ss_pred             -HHH-HHHCCC-----H-HHHHHHHHHHHHCCCCEEEEEHHHHHCCCCCCCCCCHHHHHHHHHHHHHHH-----CCCCCC
T ss_conf             -999-873655-----1-999999988875298269864001104521347885078999999999874-----268665


Q ss_pred             CCCCCEEEEECCCC--C-CCCCCHHHH
Q ss_conf             12343156521433--2-111111233
Q gi|254780916|r  271 IRLDVRLIFLTEKN--L-LPQVKSHVF  294 (482)
Q Consensus       271 ~~~~~RiIa~t~~~--L-~~~~~~g~f  294 (482)
                       .-|+.+|-+||+=  | ..++.-|+.
T Consensus       322 -rgDvKvimATnrie~LDPaLiRPGrI  347 (440)
T KOG0726         322 -RGDVKVIMATNRIETLDPALIRPGRI  347 (440)
T ss_pred             -CCCEEEEEECCCCCCCCHHHCCCCCC
T ss_conf             -67758997416534467755278754


No 241
>COG0542 clpA ATP-binding subunits of Clp protease and DnaK/DnaJ chaperones [Posttranslational modification, protein turnover, chaperones]
Probab=96.95  E-value=0.00023  Score=50.46  Aligned_cols=125  Identities=14%  Similarity=0.202  Sum_probs=67.9

Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCCCHHHHHHHHHHHCCCCCCCC-------CCCCCCCCCCCCCC
Q ss_conf             11111111222222222222222234432048873277743679999998426754332-------10123465542100
Q gi|254780916|r  135 EHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHESGKRAFFP-------FFIVNCGMIDQDKI  207 (482)
Q Consensus       135 ~~~~~~~LiG~S~~m~~v~~~i~~~a~~~~~vli~Ge~GtGK~~~A~~iH~~s~r~~~~-------fi~v~c~~~~~~~~  207 (482)
                      .....++.||....++++.+-+.|=  +.-+-++.||+|+||+.++..+-..=-..+-|       .+.+|.+++     
T Consensus       165 r~gklDPvIGRd~EI~r~iqIL~RR--~KNNPvLiGEpGVGKTAIvEGLA~rIv~g~VP~~L~~~~i~sLD~g~L-----  237 (786)
T COG0542         165 REGKLDPVIGRDEEIRRTIQILSRR--TKNNPVLVGEPGVGKTAIVEGLAQRIVNGDVPESLKDKRIYSLDLGSL-----  237 (786)
T ss_pred             HCCCCCCCCCHHHHHHHHHHHHHCC--CCCCCEEECCCCCCHHHHHHHHHHHHHCCCCCHHHCCCEEEEECHHHH-----
T ss_conf             6589887737479999999998356--889984766898889999989999974699997875887997148767-----


Q ss_pred             HHHHHCCCCCCCCCCCCCC-C---CCCCCCCCEEEECCCCHHHH---------HHHHHHHHHHHHHHCCCCCCCCCCCCC
Q ss_conf             2433112555532211100-1---23446671475166420018---------899988887764200112355321234
Q gi|254780916|r  208 EKFLFGDVDLQTKNSAQFL-G---KFIEANGGTIVLEEPDALPL---------AVQGRIYNFIETGKIEFFDSRGAIRLD  274 (482)
Q Consensus       208 e~~lFG~~~~~~~~~~~~~-g---~~~~a~~Gtl~l~ei~~L~~---------~~Q~~Ll~~l~~~~~~~~g~~~~~~~~  274 (482)
                         .=|-+  +-|....|. +   -++++.+-.||+||||.+=-         +.-.-|--+|.-|             .
T Consensus       238 ---vAGak--yRGeFEeRlk~vl~ev~~~~~vILFIDEiHtiVGAG~~~g~a~DAaNiLKPaLARG-------------e  299 (786)
T COG0542         238 ---VAGAK--YRGEFEERLKAVLKEVEKSKNVILFIDEIHTIVGAGATEGGAMDAANLLKPALARG-------------E  299 (786)
T ss_pred             ---HCCCC--CCCCHHHHHHHHHHHHHCCCCEEEEEECHHHHCCCCCCCCCCCCHHHHHHHHHHCC-------------C
T ss_conf             ---46465--35738999999999985179849998235540577766666512566467787458-------------7


Q ss_pred             CEEEEECCCC
Q ss_conf             3156521433
Q gi|254780916|r  275 VRLIFLTEKN  284 (482)
Q Consensus       275 ~RiIa~t~~~  284 (482)
                      .|.|.+|+.+
T Consensus       300 L~~IGATT~~  309 (786)
T COG0542         300 LRCIGATTLD  309 (786)
T ss_pred             EEEEEECCHH
T ss_conf             3799735589


No 242
>KOG0742 consensus
Probab=96.95  E-value=0.006  Score=40.49  Aligned_cols=133  Identities=20%  Similarity=0.234  Sum_probs=69.7

Q ss_pred             EEEEECCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCC--HHHHHCCCCCCCCCCCCCCCCCCCCCCCEEEECCC
Q ss_conf             4887327774367999999842675433210123465542100--24331125555322111001234466714751664
Q gi|254780916|r  165 PIMIQGEFGVGKKRLSRFIHESGKRAFFPFFIVNCGMIDQDKI--EKFLFGDVDLQTKNSAQFLGKFIEANGGTIVLEEP  242 (482)
Q Consensus       165 ~vli~Ge~GtGK~~~A~~iH~~s~r~~~~fi~v~c~~~~~~~~--e~~lFG~~~~~~~~~~~~~g~~~~a~~Gtl~l~ei  242 (482)
                      +||+.|++||||+++||-|-..|.--..-..-=|.+-+-.+-+  .-+||.-      +...+.|+       -||+||-
T Consensus       386 NilfyGPPGTGKTm~ArelAr~SGlDYA~mTGGDVAPlG~qaVTkiH~lFDW------akkS~rGL-------llFIDEA  452 (630)
T KOG0742         386 NILFYGPPGTGKTMFARELARHSGLDYAIMTGGDVAPLGAQAVTKIHKLFDW------AKKSRRGL-------LLFIDEA  452 (630)
T ss_pred             HEEEECCCCCCHHHHHHHHHHHCCCCEEHHCCCCCCCCHHHHHHHHHHHHHH------HHHCCCCE-------EEEEHHH
T ss_conf             0032479998604999999885287410013787555217889999998788------75156644-------9986116


Q ss_pred             CH---------HHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCEEEEECCCC--CCCCCCHHHHHHHHHHHHH-HHHHHHH
Q ss_conf             20---------0188999888877642001123553212343156521433--2111111233379998865-4334467
Q gi|254780916|r  243 DA---------LPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKN--LLPQVKSHVFRKDLYYRIS-VFLINIS  310 (482)
Q Consensus       243 ~~---------L~~~~Q~~Ll~~l~~~~~~~~g~~~~~~~~~RiIa~t~~~--L~~~~~~g~fr~dLy~rL~-~~~i~iP  310 (482)
                      +.         ||.. |..-|++|-    +|.|.+   .-++-++.+||++  |+..|.         .|++ ++.+.+|
T Consensus       453 DAFLceRnktymSEa-qRsaLNAlL----fRTGdq---SrdivLvlAtNrpgdlDsAV~---------DRide~veFpLP  515 (630)
T KOG0742         453 DAFLCERNKTYMSEA-QRSALNALL----FRTGDQ---SRDIVLVLATNRPGDLDSAVN---------DRIDEVVEFPLP  515 (630)
T ss_pred             HHHHHHHCCCCCCHH-HHHHHHHHH----HHCCCC---CCCEEEEEECCCCCCHHHHHH---------HHHHHHEECCCC
T ss_conf             789987520102588-999998898----762565---542689960588321016787---------655541306899


Q ss_pred             HHHHHHHHHHHHHHHHHHHHC
Q ss_conf             787744222255667776410
Q gi|254780916|r  311 TLRSRSEDIPWLVHFFLQSFC  331 (482)
Q Consensus       311 pLReR~eDI~~L~~~fl~~~~  331 (482)
                      ---||--    |+..|++++-
T Consensus       516 GeEERfk----ll~lYlnkyi  532 (630)
T KOG0742         516 GEEERFK----LLNLYLNKYI  532 (630)
T ss_pred             CHHHHHH----HHHHHHHHHH
T ss_conf             7789999----9999999981


No 243
>KOG0728 consensus
Probab=96.95  E-value=0.002  Score=43.86  Aligned_cols=168  Identities=17%  Similarity=0.215  Sum_probs=91.4

Q ss_pred             CCEEEEEECCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCHHHHHCCCCCCCCCCCCCCCCCCCC---CCCEEE
Q ss_conf             32048873277743679999998426754332101234655421002433112555532211100123446---671475
Q gi|254780916|r  162 CAIPIMIQGEFGVGKKRLSRFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFGDVDLQTKNSAQFLGKFIEA---NGGTIV  238 (482)
Q Consensus       162 ~~~~vli~Ge~GtGK~~~A~~iH~~s~r~~~~fi~v~c~~~~~~~~e~~lFG~~~~~~~~~~~~~g~~~~a---~~Gtl~  238 (482)
                      ...-||+.|++||||+++||+..+++.   ..||.|..+.+-     ....|+.     +.- ...+|-.|   .-..+|
T Consensus       180 QPKGvlLygppgtGktLlaraVahht~---c~firvsgselv-----qk~igeg-----srm-vrelfvmarehapsiif  245 (404)
T KOG0728         180 QPKGVLLYGPPGTGKTLLARAVAHHTD---CTFIRVSGSELV-----QKYIGEG-----SRM-VRELFVMAREHAPSIIF  245 (404)
T ss_pred             CCCCEEEECCCCCCHHHHHHHHHHHCC---EEEEEECHHHHH-----HHHHHHH-----HHH-HHHHHHHHHHCCCCEEE
T ss_conf             876048846999756299999875414---079996449999-----9985013-----899-99999998750882675


Q ss_pred             ECCCCHH-----------HHHHHHHHHHHHHHHHCCCCCCCCCCCCCCEEEEECCCC-C--CCCCCHHHHHHHHHHHHHH
Q ss_conf             1664200-----------188999888877642001123553212343156521433-2--1111112333799988654
Q gi|254780916|r  239 LEEPDAL-----------PLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKN-L--LPQVKSHVFRKDLYYRISV  304 (482)
Q Consensus       239 l~ei~~L-----------~~~~Q~~Ll~~l~~~~~~~~g~~~~~~~~~RiIa~t~~~-L--~~~~~~g~fr~dLy~rL~~  304 (482)
                      .|||+..           .-++|.-.|.+|..-     ++.+ -+-|..+|-+||+= .  ..+..-|+...        
T Consensus       246 mdeidsigs~r~e~~~ggdsevqrtmlellnql-----dgfe-atknikvimatnridild~allrpgridr--------  311 (404)
T KOG0728         246 MDEIDSIGSSRVESGSGGDSEVQRTMLELLNQL-----DGFE-ATKNIKVIMATNRIDILDPALLRPGRIDR--------  311 (404)
T ss_pred             EHHCCCCCCCCCCCCCCCCHHHHHHHHHHHHHC-----CCCC-CCCCEEEEEECCCCCCCCHHHCCCCCCCC--------
T ss_conf             000012123434578986389999999999740-----2400-03662699841642224686638775455--------


Q ss_pred             HHHHHHHHHH-HHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCC-HHHHHHHHHHHHH
Q ss_conf             3344677877-4422225566777641011223333211111000122338986-8999999999987
Q gi|254780916|r  305 FLINISTLRS-RSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDN-VQELKNILLRAVI  370 (482)
Q Consensus       305 ~~i~iPpLRe-R~eDI~~L~~~fl~~~~~~~~~~~~~ls~~a~~~L~~y~WPGN-vREL~n~i~r~~i  370 (482)
                       .|+.||=.| -+-||       |.-++++.+.. +++.-.-++    -..||- -.|++.+|-.+-.
T Consensus       312 -kiefp~p~e~ar~~i-------lkihsrkmnl~-rgi~l~kia----ekm~gasgaevk~vcteagm  366 (404)
T KOG0728         312 -KIEFPPPNEEARLDI-------LKIHSRKMNLT-RGINLRKIA----EKMPGASGAEVKGVCTEAGM  366 (404)
T ss_pred             -CCCCCCCCHHHHHHH-------HHHHHHHHHHH-CCCCHHHHH----HHCCCCCCCHHHHHHHHHHH
T ss_conf             -564899877888789-------98855530133-066789999----86789863025434335457


No 244
>KOG0740 consensus
Probab=96.90  E-value=0.00031  Score=49.59  Aligned_cols=132  Identities=23%  Similarity=0.259  Sum_probs=71.0

Q ss_pred             EEEEECCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCC-HHHHHCCCCCCCCCCCCCCCCCCCC---CCCEEEEC
Q ss_conf             4887327774367999999842675433210123465542100-2433112555532211100123446---67147516
Q gi|254780916|r  165 PIMIQGEFGVGKKRLSRFIHESGKRAFFPFFIVNCGMIDQDKI-EKFLFGDVDLQTKNSAQFLGKFIEA---NGGTIVLE  240 (482)
Q Consensus       165 ~vli~Ge~GtGK~~~A~~iH~~s~r~~~~fi~v~c~~~~~~~~-e~~lFG~~~~~~~~~~~~~g~~~~a---~~Gtl~l~  240 (482)
                      .+|+.|++||||+++|++|-..|.   .-|..|..+++..--+ |+|-++|            .+|.-|   .-+.+|+|
T Consensus       188 glLLfGPpgtGKtmL~~aiAsE~~---atff~iSassLtsK~~Ge~eK~vr------------alf~vAr~~qPsvifid  252 (428)
T KOG0740         188 GLLLFGPPGTGKTMLAKAIATESG---ATFFNISASSLTSKYVGESEKLVR------------ALFKVARSLQPSVIFID  252 (428)
T ss_pred             HHHEECCCCCCHHHHHHHHHHHHC---CEEEECCHHHHHHHCCCHHHHHHH------------HHHHHHHHCCCEEEEEC
T ss_conf             112005898844799999986206---657630688865324670778999------------99999871397089840


Q ss_pred             CCCHH-----------HHHHHHHHHHHHHHHHCCCCCCCCCCCCCCEEEEECCCC--CCCCCCHHHHHHHHHHHHHHHHH
Q ss_conf             64200-----------188999888877642001123553212343156521433--21111112333799988654334
Q gi|254780916|r  241 EPDAL-----------PLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKN--LLPQVKSHVFRKDLYYRISVFLI  307 (482)
Q Consensus       241 ei~~L-----------~~~~Q~~Ll~~l~~~~~~~~g~~~~~~~~~RiIa~t~~~--L~~~~~~g~fr~dLy~rL~~~~i  307 (482)
                      ||+.+           +...+..   +|-+.    .|.+..-.-.+.+|++||.+  +++.+.. +|..-+|       |
T Consensus       253 Eidslls~Rs~~e~e~srr~kte---fLiq~----~~~~s~~~drvlvigaTN~P~e~Dea~~R-rf~kr~y-------i  317 (428)
T KOG0740         253 EIDSLLSKRSDNEHESSRRLKTE---FLLQF----DGKNSAPDDRVLVIGATNRPWELDEAARR-RFVKRLY-------I  317 (428)
T ss_pred             HHHHHHHHCCCCCCCCCHHHHHH---HHHHH----CCCCCCCCCEEEEEECCCCCHHHHHHHHH-HHCCEEE-------E
T ss_conf             25678863687545445556557---77654----04457888707998158883677888888-7103155-------3


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             46778774422225566777641
Q gi|254780916|r  308 NISTLRSRSEDIPWLVHFFLQSF  330 (482)
Q Consensus       308 ~iPpLReR~eDI~~L~~~fl~~~  330 (482)
                      .+|-=-.|..    ++.++|.+.
T Consensus       318 plPd~etr~~----~~~~ll~~~  336 (428)
T KOG0740         318 PLPDYETRSL----LWKQLLKEQ  336 (428)
T ss_pred             CCCCHHHHHH----HHHHHHHHC
T ss_conf             5988789999----999999768


No 245
>KOG0477 consensus
Probab=96.89  E-value=0.0011  Score=45.71  Aligned_cols=113  Identities=16%  Similarity=0.183  Sum_probs=72.9

Q ss_pred             CCEEEEEECCCCCHHHHHHHHHHHCCCCCCCCCCCCCC---CCCCCCCCHHHHHCCCCCCCCCCCCCCCCCCCCCCCEEE
Q ss_conf             32048873277743679999998426754332101234---655421002433112555532211100123446671475
Q gi|254780916|r  162 CAIPIMIQGEFGVGKKRLSRFIHESGKRAFFPFFIVNC---GMIDQDKIEKFLFGDVDLQTKNSAQFLGKFIEANGGTIV  238 (482)
Q Consensus       162 ~~~~vli~Ge~GtGK~~~A~~iH~~s~r~~~~fi~v~c---~~~~~~~~e~~lFG~~~~~~~~~~~~~g~~~~a~~Gtl~  238 (482)
                      -+.+||+.|.+||||.-+-+++-+.|+|+  -|.+=-.   .+++...       +++.-++...---|.+-.|++|..+
T Consensus       481 GDinvLL~GDPGTaKSQFLKY~eK~s~RA--V~tTGqGASavGLTa~v-------~KdPvtrEWTLEaGALVLADkGvCl  551 (854)
T KOG0477         481 GDINVLLLGDPGTAKSQFLKYAEKTSPRA--VFTTGQGASAVGLTAYV-------RKDPVTREWTLEAGALVLADKGVCL  551 (854)
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHHCCCCE--EEECCCCCCCCCEEEEE-------EECCCCCEEEECCCEEEECCCCEEE
T ss_conf             44028984699822899999998627531--68506775433326887-------5178653036516728972685377


Q ss_pred             ECCCCHHHHHHHHHHHHHHHHHHCCC--CCCCCCCCCCCEEEEECCC
Q ss_conf             16642001889998888776420011--2355321234315652143
Q gi|254780916|r  239 LEEPDALPLAVQGRIYNFIETGKIEF--FDSRGAIRLDVRLIFLTEK  283 (482)
Q Consensus       239 l~ei~~L~~~~Q~~Ll~~l~~~~~~~--~g~~~~~~~~~RiIa~t~~  283 (482)
                      +||-+.|.-.-.+.+..+++.+.+.-  -|--......|-+||++|-
T Consensus       552 IDEFDKMndqDRtSIHEAMEQQSISISKAGIVtsLqArctvIAAanP  598 (854)
T KOG0477         552 IDEFDKMNDQDRTSIHEAMEQQSISISKAGIVTSLQARCTVIAAANP  598 (854)
T ss_pred             EEHHHHHCCCCCCHHHHHHHHCCHHHHHHHHHHHHHHHHHHHEECCC
T ss_conf             41211204011015999987512014466689988755443000277


No 246
>PRK07471 DNA polymerase III subunit delta'; Validated
Probab=96.82  E-value=0.003  Score=42.57  Aligned_cols=135  Identities=16%  Similarity=0.185  Sum_probs=71.4

Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCCCHHHHHHHHHHH--CCCCCCCCCCCCCCC---CCCCC-----CC
Q ss_conf             111112222222222222222344320488732777436799999984--267543321012346---55421-----00
Q gi|254780916|r  138 ALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHE--SGKRAFFPFFIVNCG---MIDQD-----KI  207 (482)
Q Consensus       138 ~~~~LiG~S~~m~~v~~~i~~~a~~~~~vli~Ge~GtGK~~~A~~iH~--~s~r~~~~fi~v~c~---~~~~~-----~~  207 (482)
                      .+..++|+..+.+.+.+.+.. .......|++|+.|+||..+|+.+=.  .+......+-...|.   .++.+     .+
T Consensus        15 ~~~~liGqe~~~~~L~~a~~~-grl~HA~Lf~Gp~GiGK~tlA~~~A~~ll~~~~~~~~~~~~~~~~l~~~~~~p~~r~i   93 (363)
T PRK07471         15 ETTALFGHAAAEAALLDAYRS-GRLHHAWLIGGPQGIGKATLAYRMARFLLATPPPGGDAVFPPPASLAVDPDHPVARRI   93 (363)
T ss_pred             CCCCCCCHHHHHHHHHHHHHC-CCCCCEEEEECCCCCCHHHHHHHHHHHHHCCCCCCCCCCCCCHHHHCCCCCCCHHHHH
T ss_conf             827316819999999999985-9976458767999818899999999998579997777767870531258777289999


Q ss_pred             HHH----HHCCCCCCCC-----------CCCCCC-CCCC--CCCC--CEEEECCCCHHHHHHHHHHHHHHHHHHCCCCCC
Q ss_conf             243----3112555532-----------211100-1234--4667--147516642001889998888776420011235
Q gi|254780916|r  208 EKF----LFGDVDLQTK-----------NSAQFL-GKFI--EANG--GTIVLEEPDALPLAVQGRIYNFIETGKIEFFDS  267 (482)
Q Consensus       208 e~~----lFG~~~~~~~-----------~~~~~~-g~~~--~a~~--Gtl~l~ei~~L~~~~Q~~Ll~~l~~~~~~~~g~  267 (482)
                      .+.    ++.-......           +..+.. ..+.  -..|  -.+++|+.+.|....+..||..|||.       
T Consensus        94 ~~~~hpdl~~i~r~~d~k~~~~~~~I~Vd~iR~l~~~~~~~p~~g~~kV~IId~ad~mn~~aaNALLK~LEEP-------  166 (363)
T PRK07471         94 AAGAHGGLLTLERSWNEKGKRLRTVITVDEVRETIGFFGLTAAEGGWRVVIVDTADEMNANAANALLKVLEEP-------  166 (363)
T ss_pred             HCCCCCCEEEEECCCCCCCCCCCCCCCHHHHHHHHHHHCCCCCCCCCEEEEEECHHHHCHHHHHHHHHHHCCC-------
T ss_conf             5269998466762001133321244539999999999724852489669998687873889999999972158-------


Q ss_pred             CCCCCCCCEEEEECCCC
Q ss_conf             53212343156521433
Q gi|254780916|r  268 RGAIRLDVRLIFLTEKN  284 (482)
Q Consensus       268 ~~~~~~~~RiIa~t~~~  284 (482)
                          +.++-+|..|+..
T Consensus       167 ----P~~t~fiLit~~~  179 (363)
T PRK07471        167 ----PARSLLLLVSHAP  179 (363)
T ss_pred             ----CCCEEEEEEECCH
T ss_conf             ----9883899863997


No 247
>PRK06921 hypothetical protein; Provisional
Probab=96.82  E-value=0.0022  Score=43.49  Aligned_cols=118  Identities=14%  Similarity=0.141  Sum_probs=66.2

Q ss_pred             CCCEEEEEECCCCCHHHHHHHHHHHCCC-CCCCCCCCCCCCCCCCCCCHHHHHCCCCCCCCCCCCCCCCCCCCCCCEEEE
Q ss_conf             4320488732777436799999984267-543321012346554210024331125555322111001234466714751
Q gi|254780916|r  161 DCAIPIMIQGEFGVGKKRLSRFIHESGK-RAFFPFFIVNCGMIDQDKIEKFLFGDVDLQTKNSAQFLGKFIEANGGTIVL  239 (482)
Q Consensus       161 ~~~~~vli~Ge~GtGK~~~A~~iH~~s~-r~~~~fi~v~c~~~~~~~~e~~lFG~~~~~~~~~~~~~g~~~~a~~Gtl~l  239 (482)
                      ....++++.|++|+||+++|-+|-..-- +...+-+-++-    .+     +|..-+............+.+|  --|++
T Consensus       114 ~~~~~l~f~G~~G~GKThLa~aIa~~Ll~~~~~~Vly~~~----~~-----~~~~lk~~~~~~~~~l~~~~~~--dlLII  182 (265)
T PRK06921        114 CRKNSIALLGQPGSGKTHLLTAAANELMRKKGVPVLYFPF----VE-----GFGDLKDDFDLLEAKLNRMKKV--EVLFI  182 (265)
T ss_pred             CCCCCEEEECCCCCCHHHHHHHHHHHHHHHCCCEEEEEEH----HH-----HHHHHHHHHHHHHHHHHHHHCC--CEEEE
T ss_conf             7766279972898988999999999999962971999887----99-----9999998888899999986329--99998


Q ss_pred             CCC-------CHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCEEEEECCCCCCCCCCHHHHHHHHHHHH
Q ss_conf             664-------200188999888877642001123553212343156521433211111123337999886
Q gi|254780916|r  240 EEP-------DALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYYRI  302 (482)
Q Consensus       240 ~ei-------~~L~~~~Q~~Ll~~l~~~~~~~~g~~~~~~~~~RiIa~t~~~L~~~~~~g~fr~dLy~rL  302 (482)
                      |++       +..+.....++...|..+..    ..+|      +|.+|+.++++++.   +.+-+.-||
T Consensus       183 DDLfk~~~G~e~~te~~~~~lf~iIN~Ry~----~~kp------tIiSSNl~~~~L~~---i~e~i~SRi  239 (265)
T PRK06921        183 DDLFKPVNGKPRATEWQIEQTYSVVNYRYL----NHKP------ILISSELTIDELLD---IDEALGSRI  239 (265)
T ss_pred             ECCCCCCCCCCCCCHHHHHHHHHHHHHHHH----CCCC------EEEECCCCHHHHHH---HHHHHHHHH
T ss_conf             221223479878988999999999999997----6999------89986899899987---637988889


No 248
>KOG0730 consensus
Probab=96.81  E-value=0.0008  Score=46.66  Aligned_cols=125  Identities=21%  Similarity=0.255  Sum_probs=69.1

Q ss_pred             CCEEEEEECCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCHHHHHCCCCCCCCCCCCCCCCCCCCC----CCEE
Q ss_conf             320488732777436799999984267543321012346554210024331125555322111001234466----7147
Q gi|254780916|r  162 CAIPIMIQGEFGVGKKRLSRFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFGDVDLQTKNSAQFLGKFIEAN----GGTI  237 (482)
Q Consensus       162 ~~~~vli~Ge~GtGK~~~A~~iH~~s~r~~~~fi~v~c~~~~~~~~e~~lFG~~~~~~~~~~~~~g~~~~a~----~Gtl  237 (482)
                      -...+|..|++||||+.+++++-+...   ..|+.+||..+     .+.+-|+.+    ..-  .-.|++|.    .-++
T Consensus       217 ~prg~Ll~gppg~Gkt~l~~aVa~e~~---a~~~~i~~pel-----i~k~~gEte----~~L--R~~f~~a~k~~~psii  282 (693)
T KOG0730         217 PPRGLLLYGPPGTGKTFLVRAVANEYG---AFLFLINGPEL-----ISKFPGETE----SNL--RKAFAEALKFQVPSII  282 (693)
T ss_pred             CCCCCCCCCCCCCCHHHHHHHHHHHHC---CEEEECCCHHH-----HHHCCCCHH----HHH--HHHHHHHHCCCCCEEE
T ss_conf             998744438999981899999999737---22574062899-----985246317----789--9999998665998077


Q ss_pred             EECCCCHHHH----------HHHHHHHHHHHHHHCCCCCCCCCCCCCCEEEEECCCC--CCCCCCHHHHHHHHHHHHHHH
Q ss_conf             5166420018----------8999888877642001123553212343156521433--211111123337999886543
Q gi|254780916|r  238 VLEEPDALPL----------AVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKN--LLPQVKSHVFRKDLYYRISVF  305 (482)
Q Consensus       238 ~l~ei~~L~~----------~~Q~~Ll~~l~~~~~~~~g~~~~~~~~~RiIa~t~~~--L~~~~~~g~fr~dLy~rL~~~  305 (482)
                      |+|||+.+-+          ..-..|+.++..        .+ -..++=+|++|++.  |......|+|..++       
T Consensus       283 ~IdEld~l~p~r~~~~~~e~Rv~sqlltL~dg--------~~-~~~~vivl~atnrp~sld~alRRgRfd~ev-------  346 (693)
T KOG0730         283 FIDELDALCPKREGADDVESRVVSQLLTLLDG--------LK-PDAKVIVLAATNRPDSLDPALRRGRFDREV-------  346 (693)
T ss_pred             EHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHH--------CC-CCCCEEEEEECCCCCCCCHHHHCCCCCCEE-------
T ss_conf             58767623776433324888999999999852--------76-767469997158855568565247885315-------


Q ss_pred             HHHHHHHHHHH
Q ss_conf             34467787744
Q gi|254780916|r  306 LINISTLRSRS  316 (482)
Q Consensus       306 ~i~iPpLReR~  316 (482)
                      .|.+|.--+|.
T Consensus       347 ~IgiP~~~~Rl  357 (693)
T KOG0730         347 EIGIPGSDGRL  357 (693)
T ss_pred             EECCCCCHHHH
T ss_conf             74489833588


No 249
>TIGR01243 CDC48 AAA family ATPase, CDC48 subfamily; InterPro: IPR005938    The ATPase Cdc48 is required for membrane fusion and protein degradation. It possesses chaperone-like activities and can functionally interact with Hsc70. Yeast CDC48 plays a role in cell division control whereas eukaryotic homologues are involved in the budding and transfer of membrane from the transitional endoplasmic reticulum to the Golgi apparatus.; GO: 0016787 hydrolase activity.
Probab=96.80  E-value=0.0019  Score=43.92  Aligned_cols=126  Identities=21%  Similarity=0.291  Sum_probs=59.2

Q ss_pred             CCEEEEEECCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCHHHHHCCCCCCCCCCCCCCCCCCCC---CCCEEE
Q ss_conf             32048873277743679999998426754332101234655421002433112555532211100123446---671475
Q gi|254780916|r  162 CAIPIMIQGEFGVGKKRLSRFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFGDVDLQTKNSAQFLGKFIEA---NGGTIV  238 (482)
Q Consensus       162 ~~~~vli~Ge~GtGK~~~A~~iH~~s~r~~~~fi~v~c~~~~~~~~e~~lFG~~~~~~~~~~~~~g~~~~a---~~Gtl~  238 (482)
                      -..-||+.|++||||+++|+++-+.   .+..|+.+|...     +.|..+|+..      .+-...|++|   .-..+|
T Consensus       239 PPkG~ll~GPPGtGktllaka~ane---~~a~f~~inGPe-----imsky~Ge~e------~~lr~if~eaeenaP~iif  304 (980)
T TIGR01243       239 PPKGVLLYGPPGTGKTLLAKAVANE---AGAYFIAINGPE-----IMSKYYGESE------ERLREIFKEAEENAPSIIF  304 (980)
T ss_pred             CCCCEEEECCCCCCHHHHHHHHHHH---CCCEEEEECCCH-----HHHHHCCCCH------HHHHHHHHHHHHCCCCEEE
T ss_conf             9873587558986178999998753---055178850603-----4433136307------8999999865305870787


Q ss_pred             ECCCCHHHHH-------HHHH----HHHHHHHHHCCCCCCCCCCCCCCEEEEECCCC--C-CCCCCHHHHHHHHHHHHHH
Q ss_conf             1664200188-------9998----88877642001123553212343156521433--2-1111112333799988654
Q gi|254780916|r  239 LEEPDALPLA-------VQGR----IYNFIETGKIEFFDSRGAIRLDVRLIFLTEKN--L-LPQVKSHVFRKDLYYRISV  304 (482)
Q Consensus       239 l~ei~~L~~~-------~Q~~----Ll~~l~~~~~~~~g~~~~~~~~~RiIa~t~~~--L-~~~~~~g~fr~dLy~rL~~  304 (482)
                      +|||+.+.+.       +..+    ||.+++        +-+.+- .+=+|.+||++  + ..+-.-|+|..+       
T Consensus       305 ideidaiaPkr~e~~Geve~r~v~qlltlmd--------Glk~rG-~v~viGatnrP~a~dPalrrPGrfdre-------  368 (980)
T TIGR01243       305 IDEIDAIAPKREEVTGEVEKRVVAQLLTLMD--------GLKGRG-KVIVIGATNRPDALDPALRRPGRFDRE-------  368 (980)
T ss_pred             EECHHHCCCCCCCHHHHHHHHHHHHHHHHHH--------HHCCCC-EEEEEECCCCCCCCCHHHCCCCCCCCE-------
T ss_conf             4121100764100001688999999999974--------002487-289981468850026224278864433-------


Q ss_pred             HHHHHHHHHHHHH
Q ss_conf             3344677877442
Q gi|254780916|r  305 FLINISTLRSRSE  317 (482)
Q Consensus       305 ~~i~iPpLReR~e  317 (482)
                      +.|.+|-=+.|+|
T Consensus       369 i~~~~Pd~~~r~e  381 (980)
T TIGR01243       369 IEIGVPDKEGRKE  381 (980)
T ss_pred             EEECCCCHHHHHH
T ss_conf             5741885456788


No 250
>TIGR01243 CDC48 AAA family ATPase, CDC48 subfamily; InterPro: IPR005938    The ATPase Cdc48 is required for membrane fusion and protein degradation. It possesses chaperone-like activities and can functionally interact with Hsc70. Yeast CDC48 plays a role in cell division control whereas eukaryotic homologues are involved in the budding and transfer of membrane from the transitional endoplasmic reticulum to the Golgi apparatus.; GO: 0016787 hydrolase activity.
Probab=96.76  E-value=0.00091  Score=46.25  Aligned_cols=129  Identities=19%  Similarity=0.169  Sum_probs=75.2

Q ss_pred             CCCCCCCCCCCCCCEEEEEECCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCHHHHHCCCCCCCCCCCCCCCCC
Q ss_conf             22222222234432048873277743679999998426754332101234655421002433112555532211100123
Q gi|254780916|r  150 IQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFGDVDLQTKNSAQFLGKF  229 (482)
Q Consensus       150 ~~v~~~i~~~a~~~~~vli~Ge~GtGK~~~A~~iH~~s~r~~~~fi~v~c~~~~~~~~e~~lFG~~~~~~~~~~~~~g~~  229 (482)
                      .++++.++-  .-..-||+.|++||||+++|+++-..|.   ..||.|....+     -|.-.|+..-   +...---+-
T Consensus       564 ~~~f~k~G~--~PP~Gvll~GPPGtGktllakava~es~---anfi~v~GPe~-----lskWvGese~---~ir~if~~a  630 (980)
T TIGR01243       564 PEVFEKLGI--RPPKGVLLFGPPGTGKTLLAKAVATESG---ANFIAVRGPEI-----LSKWVGESEK---AIREIFRKA  630 (980)
T ss_pred             HHHHHHCCC--CCCCCEEEECCCCCCHHHHHHHHHHCCC---CCEEEECCCHH-----HHHHHCHHHH---HHHHHHHHH
T ss_conf             589986078--8997348746898616888887740145---64677407312-----2344032479---999999986


Q ss_pred             CCCCCCEEEECCCCHHHHHH---------HHHHHHHHHHHHCCCCCCCCCCCCCCEEEEECCCCC---CCCCCHHHHHH
Q ss_conf             44667147516642001889---------998888776420011235532123431565214332---11111123337
Q gi|254780916|r  230 IEANGGTIVLEEPDALPLAV---------QGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNL---LPQVKSHVFRK  296 (482)
Q Consensus       230 ~~a~~Gtl~l~ei~~L~~~~---------Q~~Ll~~l~~~~~~~~g~~~~~~~~~RiIa~t~~~L---~~~~~~g~fr~  296 (482)
                      .+|.-..+|+|||+.+.+.-         -.++...|-    .-+++- ....++=+|++||++-   ..++.-|+|..
T Consensus       631 rq~aP~~~f~deidaiaP~rG~~~~~~~vtd~~~nqll----~e~dG~-~~~~~vvvi~atnrPdi~dPallrPGr~dr  704 (980)
T TIGR01243       631 RQAAPAIIFFDEIDAIAPARGASLDEKGVTDRIVNQLL----TELDGL-EELSDVVVIAATNRPDILDPALLRPGRLDR  704 (980)
T ss_pred             HHCCCEEEEEECHHHHCCCCCCCCCCCCHHHHHHHHHH----HHHHCC-CCCCCEEEEEECCCCCCCCCCCCCCCCCCE
T ss_conf             41287378730211105412442100102689999999----864044-343665898615887423610048874121


No 251
>pfam08298 AAA_PrkA PrkA AAA domain. This is a family of PrkA bacterial and archaeal serine kinases approximately 630 residues long. This is the N-terminal AAA domain.
Probab=96.76  E-value=0.0012  Score=45.33  Aligned_cols=62  Identities=16%  Similarity=0.285  Sum_probs=43.9

Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCC----CCEEEEEECCCCCHHHHHHHHHHHCCCCCCCCCCCCC
Q ss_conf             111111112222222222222222344----3204887327774367999999842675433210123
Q gi|254780916|r  135 EHCALDSLIAVSPAMIQVVDLARKAGD----CAIPIMIQGEFGVGKKRLSRFIHESGKRAFFPFFIVN  198 (482)
Q Consensus       135 ~~~~~~~LiG~S~~m~~v~~~i~~~a~----~~~~vli~Ge~GtGK~~~A~~iH~~s~r~~~~fi~v~  198 (482)
                      ....|+.+.|....+.++......+|.    ...=+++.|+.|+||+.+|+.+-..-.+  .|+-++.
T Consensus        53 rY~~F~dffGme~~i~~iV~~~ksAA~g~e~~kqIllL~GPVGsGKSsl~e~LK~glE~--y~~Y~i~  118 (358)
T pfam08298        53 RYPAFADFFGMEETIERIVNYFRHAAQGLEERKQILYLLGPVGGGKSSLAERLKKLLEL--VPIYALK  118 (358)
T ss_pred             CCCCCCCCCCHHHHHHHHHHHHHHHHHCCCCCEEEEEEECCCCCCHHHHHHHHHHHHCC--CCEEEEC
T ss_conf             25542320015999999999999997236721058999778987758999999987205--8648844


No 252
>PTZ00112 origin recognition complex 1 protein; Provisional
Probab=96.74  E-value=0.0021  Score=43.74  Aligned_cols=226  Identities=13%  Similarity=0.139  Sum_probs=129.8

Q ss_pred             CCCCCCCCCCCCCCCCCCCCCC---CCCEEEEEECCCCCHHHHHHH----HHHHCCCCC---CCCCCCCCCCCCCCC---
Q ss_conf             1111222222222222222234---432048873277743679999----998426754---332101234655421---
Q gi|254780916|r  139 LDSLIAVSPAMIQVVDLARKAG---DCAIPIMIQGEFGVGKKRLSR----FIHESGKRA---FFPFFIVNCGMIDQD---  205 (482)
Q Consensus       139 ~~~LiG~S~~m~~v~~~i~~~a---~~~~~vli~Ge~GtGK~~~A~----~iH~~s~r~---~~~fi~v~c~~~~~~---  205 (482)
                      .+.+.++-...+.++..++.--   .+..-+.|.|-+||||+...+    .++......   .-.||.||+-.++.-   
T Consensus       266 pe~lpcRe~E~~~I~~Fie~~i~q~GtG~cLYISGVPGTGKTATV~eVIr~L~~~~~~~~lp~F~fVEINGMkLt~P~qa  345 (650)
T PTZ00112        266 PEYILGREKEAKEIRTFLETGIKQGGTGQILYISGVPGTGKTATVYMVIKELQNKKLKGQLPWFNLFEINGVNLVHPNAA  345 (650)
T ss_pred             CCCCCCCHHHHHHHHHHHHHHCCCCCCCCEEEEECCCCCCCHHHHHHHHHHHHHHHHCCCCCCCEEEEECCEECCCHHHH
T ss_conf             74477707899999999986411688665699978999980036999999999999708999815999736377987889


Q ss_pred             --CCHHHHHCCCCCCC-CCCCCCCCCCCCCCC-CEEEECCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCEEEEEC
Q ss_conf             --00243311255553-221110012344667-14751664200188999888877642001123553212343156521
Q gi|254780916|r  206 --KIEKFLFGDVDLQT-KNSAQFLGKFIEANG-GTIVLEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLT  281 (482)
Q Consensus       206 --~~e~~lFG~~~~~~-~~~~~~~g~~~~a~~-Gtl~l~ei~~L~~~~Q~~Ll~~l~~~~~~~~g~~~~~~~~~RiIa~t  281 (482)
                        .+=..|+|.+.... .+..--.-.|-.... -.|++||++.|--.-|.-|..+++=.        ....+.+=+|+..
T Consensus       346 Y~~L~e~Ltg~k~~~~~~A~~lL~k~F~~~r~p~VlLvDELD~LvTkkQ~VlYNLFdWP--------T~~~SkLIVIaIA  417 (650)
T PTZ00112        346 YRVFYKKLFNKKPPNALNSYKELDKLFNNNRTPSILIVDEADYIVTKTQKVLFTLFDWP--------TKKNSKLILIIIS  417 (650)
T ss_pred             HHHHHHHHHCCCCCCHHHHHHHHHHHHCCCCCCEEEEECHHHHHHHCCCCEEEECCCCC--------CCCCCEEEEEEEE
T ss_conf             99999998489888678999999998268997189997157777636774577736688--------9888707999985


Q ss_pred             -CCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCC--CCCCCCH
Q ss_conf             -4332111111233379998865433446778774422225566777641011223333211111000122--3389868
Q gi|254780916|r  282 -EKNLLPQVKSHVFRKDLYYRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTK--YPWIDNV  358 (482)
Q Consensus       282 -~~~L~~~~~~g~fr~dLy~rL~~~~i~iPpLReR~eDI~~L~~~fl~~~~~~~~~~~~~ls~~a~~~L~~--y~WPGNv  358 (482)
                       +-||.+.+. ++    .=-||.-..|..+|-.-.  .+..++.+=|+      +  ...|+++|+++...  ....|..
T Consensus       418 NTMDLPERL~-~R----VsSRLGltRltF~PYt~~--QL~eII~sRL~------~--~~~f~~dAIQl~ARKVAavSGDA  482 (650)
T PTZ00112        418 NTMDLPYKMK-PS----CRSRLAFGRLVFSPYKYQ--QIEKVIKERLE------N--CEIIDHTALQLCARRVTNYSGDM  482 (650)
T ss_pred             ECCCCCHHHH-HH----HHHHCCCCEECCCCCCHH--HHHHHHHHHHC------C--CCCCCHHHHHHHHHHHHHHCCHH
T ss_conf             0678606566-66----555228850043998999--99999999862------6--77788789999988887503148


Q ss_pred             HHHHHHHHHHHHHCCCCCCCHHHHHHHHC
Q ss_conf             99999999998743898106889545421
Q gi|254780916|r  359 QELKNILLRAVIGLKDSHLTEDRFVLLLS  387 (482)
Q Consensus       359 REL~n~i~r~~i~~~~~~i~~~~~~~~l~  387 (482)
                      |-==.+|+||+....+..|+..|+.....
T Consensus       483 RRALdICRRAvE~~~~~ki~~~~i~~a~n  511 (650)
T PTZ00112        483 RKALQICKLAFENKNGGKITPRDMTRASN  511 (650)
T ss_pred             HHHHHHHHHHHHHCCCCEEEHHHHHHHHH
T ss_conf             99999999999735687342489999988


No 253
>COG1484 DnaC DNA replication protein [DNA replication, recombination, and repair]
Probab=96.70  E-value=0.0022  Score=43.61  Aligned_cols=132  Identities=11%  Similarity=0.075  Sum_probs=67.4

Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCC---CCCEEEEEECCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCHHHHHCC
Q ss_conf             11111222222222222222234---432048873277743679999998426754332101234655421002433112
Q gi|254780916|r  138 ALDSLIAVSPAMIQVVDLARKAG---DCAIPIMIQGEFGVGKKRLSRFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFGD  214 (482)
Q Consensus       138 ~~~~LiG~S~~m~~v~~~i~~~a---~~~~~vli~Ge~GtGK~~~A~~iH~~s~r~~~~fi~v~c~~~~~~~~e~~lFG~  214 (482)
                      ....+-+.+...+..+..+...+   .....+++.|.+||||+++|-+|=..--+++.+..-+.++    +++. +|   
T Consensus        77 ~~~d~~~~~~~~~~~l~~~~~~~~~~~~~~nl~l~G~~G~GKthLa~Ai~~~l~~~g~sv~f~~~~----el~~-~L---  148 (254)
T COG1484          77 EEFDFEFQPGIDKKALEDLASLVEFFERGENLVLLGPPGVGKTHLAIAIGNELLKAGISVLFITAP----DLLS-KL---  148 (254)
T ss_pred             CCCCCCCCCHHHHHHHHHHHHHHHHHCCCCCEEEECCCCCCHHHHHHHHHHHHHHCCCEEEEEEHH----HHHH-HH---
T ss_conf             430235885566999999999998732588289989999879999999999999839849998859----9999-99---


Q ss_pred             CCCCCCCCCCCCCC-CC-CCCCCEEEECCCCHHHHH--HHHHHHHHHHHHHCCCCCCCCCCCCCCEEEEECCCCCCCCCC
Q ss_conf             55553221110012-34-466714751664200188--999888877642001123553212343156521433211111
Q gi|254780916|r  215 VDLQTKNSAQFLGK-FI-EANGGTIVLEEPDALPLA--VQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVK  290 (482)
Q Consensus       215 ~~~~~~~~~~~~g~-~~-~a~~Gtl~l~ei~~L~~~--~Q~~Ll~~l~~~~~~~~g~~~~~~~~~RiIa~t~~~L~~~~~  290 (482)
                       +.+... ...... .. ..+---|+||+|+..+..  ...-++.+|....-++           +.|.+||.+..++-.
T Consensus       149 -k~~~~~-~~~~~~l~~~l~~~dlLIiDDlG~~~~~~~~~~~~~q~I~~r~~~~-----------~~~~tsN~~~~~~~~  215 (254)
T COG1484         149 -KAAFDE-GRLEEKLLRELKKVDLLIIDDIGYEPFSQEEADLLFQLISRRYESR-----------SLIITSNLSFGEWDE  215 (254)
T ss_pred             -HHHHHC-CCHHHHHHHHHHHCCEEEEECCCCCCCCCHHHHHHHHHHHHHHHHC-----------CCCEEECCCHHHHHH
T ss_conf             -998745-5268999988752898998236776688155879999999999730-----------542020588278886


No 254
>PRK05574 holA DNA polymerase III subunit delta; Reviewed
Probab=96.60  E-value=0.074  Score=32.76  Aligned_cols=267  Identities=14%  Similarity=0.115  Sum_probs=127.3

Q ss_pred             CCCEEE-EEECCCCCHHHHHHHHHHH-CCC--CCCCCCCCCCCCCCCCCCCHHHHHCCCCCCCCCCCCCCCCCCCCCCCE
Q ss_conf             432048-8732777436799999984-267--543321012346554210024331125555322111001234466714
Q gi|254780916|r  161 DCAIPI-MIQGEFGVGKKRLSRFIHE-SGK--RAFFPFFIVNCGMIDQDKIEKFLFGDVDLQTKNSAQFLGKFIEANGGT  236 (482)
Q Consensus       161 ~~~~~v-li~Ge~GtGK~~~A~~iH~-~s~--r~~~~fi~v~c~~~~~~~~e~~lFG~~~~~~~~~~~~~g~~~~a~~Gt  236 (482)
                      ..=.|| ||.||---=+....+.|-+ ...  ..+-.++.++|...+.+.+.+++            +..++|.  +.-.
T Consensus        13 k~l~pvyli~G~e~~li~~~~~~i~~~~~~~~~~~~n~~~~d~~~~~~~~l~~~~------------~t~slf~--~krl   78 (336)
T PRK05574         13 KGLAPVYLLYGDEPLLLQEAKDAIRAAARAQGFDERNVFTVDGSETDWDDVLEAC------------QSLPLFS--DRKL   78 (336)
T ss_pred             CCCCCEEEEECCHHHHHHHHHHHHHHHHHCCCCCCEEEEEEECCCCCHHHHHHHH------------CCCCCCC--CCEE
T ss_conf             7898679998586999999999999986077865305899716869999999986------------4899778--9759


Q ss_pred             EEECCCCHHHHH----HHHHHHHHHHHHHCCCCCCCCCCCCCCEEEEECCCCCCCCCCHHHHHHHHHHHHH--HHHHHHH
Q ss_conf             751664200188----9998888776420011235532123431565214332111111233379998865--4334467
Q gi|254780916|r  237 IVLEEPDALPLA----VQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYYRIS--VFLINIS  310 (482)
Q Consensus       237 l~l~ei~~L~~~----~Q~~Ll~~l~~~~~~~~g~~~~~~~~~RiIa~t~~~L~~~~~~g~fr~dLy~rL~--~~~i~iP  310 (482)
                      +++++...++..    .-..|...+++.         +...++ ++..+...+.......    .+|--+.  +..|...
T Consensus        79 Viv~~~~~~~~k~~~~~l~~l~~~l~~~---------~~~~~l-vli~~~~~~d~~~k~~----k~~k~l~~~~~~i~~~  144 (336)
T PRK05574         79 VELRLPEGLTGKKGEEALKRLEAYLENP---------LPHTDL-LLLAPLPKLDKRKEKS----AWFKALKKKAVVVEAQ  144 (336)
T ss_pred             EEEECCCCCCCHHHHHHHHHHHHHHHCC---------CCCCEE-EEEEECCCCCHHHHHH----HHHHHHHHCEEEEEEC
T ss_conf             9998887665311379999999987079---------999769-9998778633688889----9999998480799806


Q ss_pred             HHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHCCCCCCCHHHHHHHHCCCC
Q ss_conf             78774422225566777641011223333211111000122338986899999999998743898106889545421244
Q gi|254780916|r  311 TLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQELKNILLRAVIGLKDSHLTEDRFVLLLSREG  390 (482)
Q Consensus       311 pLReR~eDI~~L~~~fl~~~~~~~~~~~~~ls~~a~~~L~~y~WPGNvREL~n~i~r~~i~~~~~~i~~~~~~~~l~~~~  390 (482)
                      ++.+  .+++..+..++.+    .|.   .++++|.+.|..+ -+||.+.+.|-++.++..+.++.|+.+++........
T Consensus       145 ~~~~--~~l~~~i~~~~~~----~g~---~i~~~a~~~L~~~-~g~dl~~l~~EleKL~ly~~~~~It~~dV~~~v~~~~  214 (336)
T PRK05574        145 TPKE--AELPQWIQQRLKQ----QGL---RIDAAALQLLAER-VEGNLLALAQEIEKLALLYPDGKITLEDVEEAVPDSA  214 (336)
T ss_pred             CCCH--HHHHHHHHHHHHH----CCC---CCCHHHHHHHHHH-HHCCHHHHHHHHHHHHHHCCCCCCCHHHHHHHHCCCC
T ss_conf             9998--9999999999998----499---9898999999997-2113999999999999837888878999999861643


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCHHHCCCCCCCCCCCCCCHHHHH-HHHHHHHHHHHHHHHCCCHHHHHHHHCCCHHHHH
Q ss_conf             543223432222223344432100000000112344454325899-9999999999999828727899978489988999
Q gi|254780916|r  391 KKEREFHTETACTCYTEGKSSDTILDNLSQESIPAIGQDGEVRRL-SDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLY  469 (482)
Q Consensus       391 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l-~e~E~~~I~~aL~~~~Gn~~~aA~~LGIsR~tL~  469 (482)
                      ........+....  ......-.....+.....+.   -.....+ ..+.+-+....+...+.+...+|+.|||...-.+
T Consensus       215 ~~~~f~L~dai~~--~~~~~al~~l~~l~~~~~~~---~~il~~l~~~~r~l~~ik~~~~~g~~~~~i~~~l~i~~~~~~  289 (336)
T PRK05574        215 RFDVFDLVDAILA--GKIARALRILDGLRLEGEEP---IKLLAALQREFRLLLQLKILLQQGYPLQQLFKELRVWPYRRK  289 (336)
T ss_pred             CCCHHHHHHHHHC--CCHHHHHHHHHHHHHCCCCH---HHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHCCCCHHHHH
T ss_conf             3567999999987--89999999999999779972---999999999999999999998769999999988399999999


Q ss_pred             H
Q ss_conf             9
Q gi|254780916|r  470 R  470 (482)
Q Consensus       470 r  470 (482)
                      .
T Consensus       290 ~  290 (336)
T PRK05574        290 L  290 (336)
T ss_pred             H
T ss_conf             9


No 255
>KOG0652 consensus
Probab=96.60  E-value=0.0051  Score=40.97  Aligned_cols=212  Identities=16%  Similarity=0.190  Sum_probs=103.7

Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCC----------CCC-CCCEEEEEECCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCC
Q ss_conf             2211111111222222222222222----------234-43204887327774367999999842675433210123465
Q gi|254780916|r  133 ENEHCALDSLIAVSPAMIQVVDLAR----------KAG-DCAIPIMIQGEFGVGKKRLSRFIHESGKRAFFPFFIVNCGM  201 (482)
Q Consensus       133 ~~~~~~~~~LiG~S~~m~~v~~~i~----------~~a-~~~~~vli~Ge~GtGK~~~A~~iH~~s~r~~~~fi~v~c~~  201 (482)
                      +......+.+-|-...++++.+.|-          .+. .-..-||..|++||||+++||+--..   -+..|..+..- 
T Consensus       164 ekPtE~YsDiGGldkQIqELvEAiVLpmth~ekF~~lgi~pPKGvLmYGPPGTGKTlmARAcAaq---T~aTFLKLAgP-  239 (424)
T KOG0652         164 EKPTEQYSDIGGLDKQIQELVEAIVLPMTHKEKFENLGIRPPKGVLMYGPPGTGKTLMARACAAQ---TNATFLKLAGP-  239 (424)
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHCCCCCCHHHHHHCCCCCCCCEEEECCCCCCHHHHHHHHHHH---CCCHHHHHCCH-
T ss_conf             68743200032578999999988614565687887468889972276579997577999999874---01068873264-


Q ss_pred             CCCCCCHHHHHCCCCCCCCCCCCCCCCCCC---CCCCEEEECCCCHHH-----------HHHHHHHHHHHHHHHCCCCCC
Q ss_conf             542100243311255553221110012344---667147516642001-----------889998888776420011235
Q gi|254780916|r  202 IDQDKIEKFLFGDVDLQTKNSAQFLGKFIE---ANGGTIVLEEPDALP-----------LAVQGRIYNFIETGKIEFFDS  267 (482)
Q Consensus       202 ~~~~~~e~~lFG~~~~~~~~~~~~~g~~~~---a~~Gtl~l~ei~~L~-----------~~~Q~~Ll~~l~~~~~~~~g~  267 (482)
                         . +-..+.|..     +.- ....|..   -.--.+|+||++...           .++|.-.|.+|..-     ++
T Consensus       240 ---Q-LVQMfIGdG-----AkL-VRDAFaLAKEkaP~IIFIDElDAIGtKRfDSek~GDREVQRTMLELLNQL-----DG  304 (424)
T KOG0652         240 ---Q-LVQMFIGDG-----AKL-VRDAFALAKEKAPTIIFIDELDAIGTKRFDSEKAGDREVQRTMLELLNQL-----DG  304 (424)
T ss_pred             ---H-HHHHHHCCH-----HHH-HHHHHHHHHCCCCEEEEEECHHHHCCCCCCCCCCCCHHHHHHHHHHHHHC-----CC
T ss_conf             ---7-776653341-----889-99999875334983899730023233436531234389999999999860-----48


Q ss_pred             CCCCCCCCEEEEECCCC-C--CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCC-CCCCC
Q ss_conf             53212343156521433-2--11111123337999886543344677877442222556677764101122333-32111
Q gi|254780916|r  268 RGAIRLDVRLIFLTEKN-L--LPQVKSHVFRKDLYYRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQ-ISISD  343 (482)
Q Consensus       268 ~~~~~~~~RiIa~t~~~-L--~~~~~~g~fr~dLy~rL~~~~i~iPpLReR~eDI~~L~~~fl~~~~~~~~~~~-~~ls~  343 (482)
                      ..+ .-++.+||+||+- .  ..+..+|++..       -+.+..|.=-.|. -|       ++-++++.+... ..|.+
T Consensus       305 Fss-~~~vKviAATNRvDiLDPALlRSGRLDR-------KIEfP~Pne~aRa-rI-------lQIHsRKMnv~~DvNfeE  368 (424)
T KOG0652         305 FSS-DDRVKVIAATNRVDILDPALLRSGRLDR-------KIEFPHPNEEARA-RI-------LQIHSRKMNVSDDVNFEE  368 (424)
T ss_pred             CCC-CCCEEEEEECCCCCCCCHHHHHCCCCCC-------CCCCCCCCHHHHH-HH-------HHHHHHCCCCCCCCCHHH
T ss_conf             997-5626788521643434888864466444-------4348899778988-99-------988640057788879899


Q ss_pred             CCCCCCCCCCCCCCHHHHHHHHHHHHHH---CCCCCCCHHHHHH
Q ss_conf             1100012233898689999999999874---3898106889545
Q gi|254780916|r  344 KALSLLTKYPWIDNVQELKNILLRAVIG---LKDSHLTEDRFVL  384 (482)
Q Consensus       344 ~a~~~L~~y~WPGNvREL~n~i~r~~i~---~~~~~i~~~~~~~  384 (482)
                           |..-.=-=|-.|++.+|-.+-+.   .....++.+|+..
T Consensus       369 -----LaRsTddFNGAQcKAVcVEAGMiALRr~atev~heDfme  407 (424)
T KOG0652         369 -----LARSTDDFNGAQCKAVCVEAGMIALRRGATEVTHEDFME  407 (424)
T ss_pred             -----HHHCCCCCCCHHHEEEHHHHHHHHHHCCCCCCCHHHHHH
T ss_conf             -----853335667232133005540899864653012788999


No 256
>pfam05621 TniB Bacterial TniB protein. This family consists of several bacterial TniB NTP-binding proteins. TniB is a probable ATP-binding protein which is involved in Tn5053 mercury resistance transposition.
Probab=96.55  E-value=0.01  Score=38.84  Aligned_cols=220  Identities=13%  Similarity=0.179  Sum_probs=104.0

Q ss_pred             CCCCCCCC---CCCCCCCCCCCCCCCCE-EEEEECCCCCHHHHHHHHH---HH---CCCCCCCCCCCCCCCCCCCC--CC
Q ss_conf             11122222---22222222222344320-4887327774367999999---84---26754332101234655421--00
Q gi|254780916|r  140 DSLIAVSP---AMIQVVDLARKAGDCAI-PIMIQGEFGVGKKRLSRFI---HE---SGKRAFFPFFIVNCGMIDQD--KI  207 (482)
Q Consensus       140 ~~LiG~S~---~m~~v~~~i~~~a~~~~-~vli~Ge~GtGK~~~A~~i---H~---~s~r~~~~fi~v~c~~~~~~--~~  207 (482)
                      +.-||...   ++.++-+.+..--.... .+||.|++|.||+++.+--   |.   ...+..-|-+.+.+..-|.+  +.
T Consensus        34 ~rWIgY~~A~~~L~~Le~Ll~~P~~~Rmp~lLlvGdsnnGKT~Iv~rF~~~hp~~~d~~~~~~PVl~vq~P~~p~~~~lY  113 (302)
T pfam05621        34 DRWIGYPRAVEALNRLEALYAWPNKQRMPNLLLVGPTNNGKSMIVEKFRRAHPAGSDADQEHIPVLVVQMPSEPSVIRFY  113 (302)
T ss_pred             CCCCCCHHHHHHHHHHHHHHHCCCCCCCCCEEEEECCCCCHHHHHHHHHHHCCCCCCCCCCCCEEEEEECCCCCCHHHHH
T ss_conf             85327789999999999998468646887558870798878999999999679987866670218999769998868999


Q ss_pred             HHHH--HCCCCCCCCCC----CCCCCCCCCCCCCEEEECCCCHH---HHHHHHHHHHHHHHHHCCCCCCCCCCCCCCEEE
Q ss_conf             2433--11255553221----11001234466714751664200---188999888877642001123553212343156
Q gi|254780916|r  208 EKFL--FGDVDLQTKNS----AQFLGKFIEANGGTIVLEEPDAL---PLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLI  278 (482)
Q Consensus       208 e~~l--FG~~~~~~~~~----~~~~g~~~~a~~Gtl~l~ei~~L---~~~~Q~~Ll~~l~~~~~~~~g~~~~~~~~~RiI  278 (482)
                      .+-|  +|..-..++..    .+...+|...+-..|.+||++++   +...|..++.+|..     +|..-.+    =||
T Consensus       114 ~~IL~~l~aP~~~~~~~~~~~~~~~~ll~~~~vrmLIIDEiHnlL~Gs~~~qr~~ln~LK~-----L~Nel~I----piV  184 (302)
T pfam05621       114 VALLAAMGAPLRPRPRLPEMEQLALALLRKVGVRMLVIDELHNVLAGNSVNRREFLNLLRF-----LGNELRI----PLV  184 (302)
T ss_pred             HHHHHHHCCCCCCCCCHHHHHHHHHHHHHHCCCCEEEEECHHHHCCCCHHHHHHHHHHHHH-----HHHCCCC----CEE
T ss_conf             9999983787788877899999999999974987899854365604868899999999999-----8636587----869


Q ss_pred             EECCCCCCCCCC-----HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCC-CCCCCCCCC-CCCCC
Q ss_conf             521433211111-----12333799988654334467787744222255667776410112233-332111110-00122
Q gi|254780916|r  279 FLTEKNLLPQVK-----SHVFRKDLYYRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIK-QISISDKAL-SLLTK  351 (482)
Q Consensus       279 a~t~~~L~~~~~-----~g~fr~dLy~rL~~~~i~iPpLReR~eDI~~L~~~fl~~~~~~~~~~-~~~ls~~a~-~~L~~  351 (482)
                      +.-..+--..+.     +++|.          ++.+|.-+. .+|...|...|-..    .-.. +-.++...+ +.+..
T Consensus       185 ~vGt~eA~~ai~tD~QlasRF~----------~~~Lp~W~~-d~ef~~LL~sfe~~----LPL~~~S~L~~~~~a~~I~~  249 (302)
T pfam05621       185 GVGTRDAYLAIRSDDQLENRFE----------PMLLPPWEA-NDDCCSLLASFAAS----LPLRRPSPIATLDMARYLLT  249 (302)
T ss_pred             EECCHHHHHHHHCCHHHHHHCC----------CCCCCCCCC-CCHHHHHHHHHHHH----CCCCCCCCCCCHHHHHHHHH
T ss_conf             9531999999706888885058----------611688889-80899999999986----88877768888999999999


Q ss_pred             CCCCCCHHHHHHHHHHHH---HHCCCCCCCHHHHHH
Q ss_conf             338986899999999998---743898106889545
Q gi|254780916|r  352 YPWIDNVQELKNILLRAV---IGLKDSHLTEDRFVL  384 (482)
Q Consensus       352 y~WPGNvREL~n~i~r~~---i~~~~~~i~~~~~~~  384 (482)
                      .. -||+.|+.+++..++   +.+....|+.+.+..
T Consensus       250 ~S-eG~iGei~~Ll~~aA~~AI~sG~E~It~~~l~~  284 (302)
T pfam05621       250 RS-EGTIGELAHLLMAAAIAAVESGEEAINHRTLSM  284 (302)
T ss_pred             HC-CCCHHHHHHHHHHHHHHHHHCCCCCCCHHHHHH
T ss_conf             85-992879999999999999847871008999966


No 257
>KOG0741 consensus
Probab=96.54  E-value=0.0039  Score=41.76  Aligned_cols=23  Identities=30%  Similarity=0.424  Sum_probs=10.9

Q ss_pred             EEEEEECCCCCHHHHHHHHHHHC
Q ss_conf             04887327774367999999842
Q gi|254780916|r  164 IPIMIQGEFGVGKKRLSRFIHES  186 (482)
Q Consensus       164 ~~vli~Ge~GtGK~~~A~~iH~~  186 (482)
                      .-+|+.|++||||+++||-|-..
T Consensus       257 KGiLLyGPPGTGKTLiARqIGkM  279 (744)
T KOG0741         257 KGILLYGPPGTGKTLIARQIGKM  279 (744)
T ss_pred             EEEEEECCCCCCHHHHHHHHHHH
T ss_conf             35788779998701899998787


No 258
>COG2508 Regulator of polyketide synthase expression [Signal transduction mechanisms / Secondary metabolites biosynthesis, transport, and catabolism]
Probab=96.52  E-value=0.0098  Score=38.97  Aligned_cols=37  Identities=24%  Similarity=0.344  Sum_probs=29.9

Q ss_pred             HHHHHHCCCHHHHHHHHCCCHHHHHHHHHHH----CCCCCC
Q ss_conf             9999828727899978489988999999981----888144
Q gi|254780916|r  445 LAMKLYRAQMSEVARRLGIGRSTLYRKIREY----NIEVDS  481 (482)
Q Consensus       445 ~aL~~~~Gn~~~aA~~LGIsR~tL~rKlk~~----gi~~d~  481 (482)
                      .++-.++||.++||+.|.|.||||.+||+|.    |++.++
T Consensus       360 ~~yl~~~~ni~~tAk~L~iHRNTL~YRi~kieEltg~dL~~  400 (421)
T COG2508         360 RAYLKNNGNISATAKRLFVHRNTLRYRLKKIEELTGIDLKD  400 (421)
T ss_pred             HHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCCC
T ss_conf             99998489799999983745423999999999994879877


No 259
>TIGR01815 TrpE-clade3 anthranilate synthase; InterPro: IPR010112   This entry represents a small clade of anthranilate synthases from alpha proteobacteria and Nostoc (a cyanobacterium). This enzyme is the first step in the pathway for the biosynthesis of tryprophan from chorismate.; GO: 0004049 anthranilate synthase activity, 0000162 tryptophan biosynthetic process.
Probab=96.51  E-value=0.0071  Score=39.96  Aligned_cols=104  Identities=14%  Similarity=0.153  Sum_probs=75.2

Q ss_pred             CCCCCEEEECCCHHHHHHHHHHHHHCCCEEEEECCH-HHHHHHCCCCCEEEEECCCCC-CCHHHHHHHHHHH-CCCCCEE
Q ss_conf             528838998699899999999999889889998937-999986089989999785469-8889999999985-7898399
Q gi|254780916|r    8 DRHKRVLIIDKDDEQIKIIKDHVESYGYDVFIVNVS-DLSTISKIQVNVIFLSLINCE-DDKENILKNIVDK-IPIVPII   84 (482)
Q Consensus         8 ~~~~rILIVDDd~~~~~~l~~~L~~~G~~v~~a~~~-al~~l~~~~~dlillD~~mP~-~dGlell~~i~~~-~p~ipvI   84 (482)
                      ..-++||+||.|.++...|+.+|++-|-.|+|...+ +-+++.+.+||+|+|.= =|| -.-+++-..|++. .-++||=
T Consensus       522 q~G~~iLLvDHeDSFVHTLAnY~RqTGAsVTTlRh~~ae~~fd~~rPDLVVLSP-GPGrP~dFdv~~Ti~aa~ar~lP~F  600 (726)
T TIGR01815       522 QEGKRILLVDHEDSFVHTLANYLRQTGASVTTLRHSFAEELFDEERPDLVVLSP-GPGRPKDFDVKETIKAALARDLPVF  600 (726)
T ss_pred             CCCCEEEEEECCCCHHHHHHHHHHHCCCEEEECCCHHHHHHHHCCCCCEEEECC-CCCCCCCCCHHHHHHHHHHCCCCEE
T ss_conf             258779998547543777788876348755304304789997327998898687-3123875447889999997289857


Q ss_pred             EE-ECCCCHHHHHHHHHCCCCCCCCCCCCCCCC
Q ss_conf             99-268999999988850574322222222222
Q gi|254780916|r   85 VQ-TTQDNIKILNCFLYNRISKFFLNLVSRKQL  116 (482)
Q Consensus        85 ii-T~~~~~~~~~~a~~~g~~d~l~KP~~~~~L  116 (482)
                      =+ -|   .+.++++ +-|.-+-|..|.+=+-=
T Consensus       601 GVCLG---LQg~vEa-fGG~L~vL~~P~HGK~s  629 (726)
T TIGR01815       601 GVCLG---LQGLVEA-FGGELDVLAIPVHGKAS  629 (726)
T ss_pred             EEHHH---HHHHHHH-HCCCCCCCCCCCCCCCC
T ss_conf             74134---6899987-46721357888788633


No 260
>PRK07940 DNA polymerase III subunit delta'; Validated
Probab=96.50  E-value=0.0026  Score=43.05  Aligned_cols=120  Identities=13%  Similarity=0.083  Sum_probs=66.0

Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCC-----------CCCCEEEEEECCCCCHHHHHHHHHHHCCCC--CC-CC-CCCCCCCC
Q ss_conf             11111122222222222222223-----------443204887327774367999999842675--43-32-10123465
Q gi|254780916|r  137 CALDSLIAVSPAMIQVVDLARKA-----------GDCAIPIMIQGEFGVGKKRLSRFIHESGKR--AF-FP-FFIVNCGM  201 (482)
Q Consensus       137 ~~~~~LiG~S~~m~~v~~~i~~~-----------a~~~~~vli~Ge~GtGK~~~A~~iH~~s~r--~~-~~-fi~v~c~~  201 (482)
                      ..|+.++|+-.+.+.++..++.-           ......-|+.|+.|+||+.+|+++-..-.=  .+ .| -.--+|..
T Consensus         2 ~~f~~ivGQe~v~~~L~~A~~~~R~~~~~~~~~~~~~~HAyLF~Gp~G~Gk~~~A~~~A~~l~C~~~~~~~cg~C~~C~~   81 (395)
T PRK07940          2 GVWDRLVGQDAVVAELRAAARAARADSAHSAAAGSGMTHAWLFTGPPGSGRSNAARAFAAALQCTDPGVPGCGECRACRT   81 (395)
T ss_pred             CCCHHHCCCHHHHHHHHHHHHHCCCCCCCCCCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHCCCCCCCCCCCCCHHHHH
T ss_conf             97013159299999999999836343443333468766037636899878899999999996699999999987878999


Q ss_pred             CCC----CCCHHHHHCCCCCCCCCCCCCCCCC-------CCCCCCEEEECCCCHHHHHHHHHHHHHHHHH
Q ss_conf             542----1002433112555532211100123-------4466714751664200188999888877642
Q gi|254780916|r  202 IDQ----DKIEKFLFGDVDLQTKNSAQFLGKF-------IEANGGTIVLEEPDALPLAVQGRIYNFIETG  260 (482)
Q Consensus       202 ~~~----~~~e~~lFG~~~~~~~~~~~~~g~~-------~~a~~Gtl~l~ei~~L~~~~Q~~Ll~~l~~~  260 (482)
                      +..    |..+   +-. .+.+-...+-..+.       .+++.-..++|+.+.|....+..||..|+|.
T Consensus        82 i~~g~hpDv~~---i~p-~~~~i~id~iR~l~~~~~~~p~~~~~kv~ii~~a~~m~~~a~NalLKtLEEP  147 (395)
T PRK07940         82 VLAGTHPDVRV---VVP-EGLSIGVDEVREIVQIAARRPTTGRWRIVVIEDADRLTERAANALLKAVEEP  147 (395)
T ss_pred             HHCCCCCCEEE---EEC-CCCCCCHHHHHHHHHHHHHCCCCCCCEEEEEECHHHHCHHHHHHHHHHHCCC
T ss_conf             87689987189---826-8776889999999999852730379559998077874899999999852178


No 261
>PRK13566 anthranilate synthase; Provisional
Probab=96.49  E-value=0.024  Score=36.19  Aligned_cols=34  Identities=12%  Similarity=0.145  Sum_probs=18.6

Q ss_pred             CCEEEEECCC--CCCCHHHHHHHHHHHCCCCCEEEE
Q ss_conf             9899997854--698889999999985789839999
Q gi|254780916|r   53 VNVIFLSLIN--CEDDKENILKNIVDKIPIVPIIVQ   86 (482)
Q Consensus        53 ~dlillD~~m--P~~dGlell~~i~~~~p~ipvIii   86 (482)
                      +.+|++--.-  ...+-+++.+.+|..+|..-+-++
T Consensus       260 FQvVlSqrf~~~~~~~p~~~Yr~LR~~NPSPYm~~~  295 (724)
T PRK13566        260 FEVVPGQTFYEPCERSPSELFRRLKRINPSPYGFLI  295 (724)
T ss_pred             EEECCCEEECCCCCCCHHHHHHHHHHCCCCCEEEEE
T ss_conf             998471577345899999999999706999738999


No 262
>PRK04132 replication factor C small subunit; Provisional
Probab=96.42  E-value=0.0028  Score=42.78  Aligned_cols=109  Identities=18%  Similarity=0.189  Sum_probs=58.8

Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCCCHHHHHHHHHHH--CCCCCCCCCCCCCCCCCCCCCCHHHH---
Q ss_conf             1111112222222222222222344320488732777436799999984--26754332101234655421002433---
Q gi|254780916|r  137 CALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHE--SGKRAFFPFFIVNCGMIDQDKIEKFL---  211 (482)
Q Consensus       137 ~~~~~LiG~S~~m~~v~~~i~~~a~~~~~vli~Ge~GtGK~~~A~~iH~--~s~r~~~~fi~v~c~~~~~~~~e~~l---  211 (482)
                      ..++.++|+.....++.+.+.+  .|--+.|.-|++||||++.|-++-.  ++......|+.+|.+.--......+.   
T Consensus        22 k~LddIVgQehIVkRLK~YVk~--~smPHLLFaGPPGvGKt~~al~lar~l~ge~wr~nflelnas~~~~~~~~~~~v~~   99 (863)
T PRK04132         22 QRLDEIVGQDHIVKRLKHYVKT--GSMPHLLFAGPPGVGKTTAALALARELFGENWRHNFLELNASDERGINVIREKVKE   99 (863)
T ss_pred             CCHHHHCCHHHHHHHHHHHHCC--CCCCCEEECCCCCCCCHHHHHHHHHHHHCCHHHHHHHHHCCCCCCCCHHHHHHHHH
T ss_conf             6165522749999999988623--88854430489987714478888887614314555664144212363488887775


Q ss_pred             HCCCCCCCCCCCCCCCCCCCCCCCEEEECCCCHHHHHHHHHHHHHHH
Q ss_conf             11255553221110012344667147516642001889998888776
Q gi|254780916|r  212 FGDVDLQTKNSAQFLGKFIEANGGTIVLEEPDALPLAVQGRIYNFIE  258 (482)
Q Consensus       212 FG~~~~~~~~~~~~~g~~~~a~~Gtl~l~ei~~L~~~~Q~~Ll~~l~  258 (482)
                      ||..+.           +--|.-+.||+||.+-|..+.|..+-+..+
T Consensus       100 ~~~~~p-----------~~~~~~k~~~~de~~~l~~d~~~~~r~~~e  135 (863)
T PRK04132        100 FARTKP-----------IGGASFKIIFLDEADALTQDAQQALRRTME  135 (863)
T ss_pred             CCCCCC-----------CCCCCCCEEEECCCCCCCCCCHHHHHHHHH
T ss_conf             068664-----------578654246443656401011577876677


No 263
>PRK08939 primosomal protein DnaI; Reviewed
Probab=96.34  E-value=0.0033  Score=42.25  Aligned_cols=124  Identities=16%  Similarity=0.176  Sum_probs=72.2

Q ss_pred             CCCCCCCCCCCCCC--CCCEEEEEECCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCHHHHHCCCCCCCC--CC
Q ss_conf             22222222222234--432048873277743679999998426754332101234655421002433112555532--21
Q gi|254780916|r  147 PAMIQVVDLARKAG--DCAIPIMIQGEFGVGKKRLSRFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFGDVDLQTK--NS  222 (482)
Q Consensus       147 ~~m~~v~~~i~~~a--~~~~~vli~Ge~GtGK~~~A~~iH~~s~r~~~~fi~v~c~~~~~~~~e~~lFG~~~~~~~--~~  222 (482)
                      .+...+.+.+..+.  ....-++|.|..||||+.++-+|.+.-.+++.+.+-+....    ++ .+|    +++++  ..
T Consensus       139 ~a~~~a~~F~~~y~~~~~~kGlyl~G~~G~GKTyL~~aian~La~~g~~v~~v~~p~----~~-~~l----K~s~~d~s~  209 (306)
T PRK08939        139 DALMAALDFLEAYKPGEKVKGLYLYGDFGVGKTYLLAAIANELAKKGVSSTLVHFPE----FI-REL----KNAISDGSV  209 (306)
T ss_pred             HHHHHHHHHHHHHCCCCCCCEEEEECCCCCCHHHHHHHHHHHHHHCCCEEEEEEHHH----HH-HHH----HHHHCCCCH
T ss_conf             999999999997376988877889899999899999999999998699299987599----99-999----998648988


Q ss_pred             CCCCCCCCCCCCCEEEECCCCH--HHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCEEEEECCCCCCCCCC
Q ss_conf             1100123446671475166420--0188999888877642001123553212343156521433211111
Q gi|254780916|r  223 AQFLGKFIEANGGTIVLEEPDA--LPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVK  290 (482)
Q Consensus       223 ~~~~g~~~~a~~Gtl~l~ei~~--L~~~~Q~~Ll~~l~~~~~~~~g~~~~~~~~~RiIa~t~~~L~~~~~  290 (482)
                      ....-.+..+  -.|+||+|+.  ++..+...+|.+|-+.++.   ...|      .+.+||-+++++-.
T Consensus       210 ~~~i~~~k~~--~vLiLDDiGaE~~t~W~rd~vl~~IL~~Rm~---~~lP------TffTSN~~~~eLe~  268 (306)
T PRK08939        210 KEKIDAVKEA--PVLMLDDIGAEQMSSWVRDEVLGVILQYRMQ---EELP------TFFTSNFDFDELEH  268 (306)
T ss_pred             HHHHHHHHCC--CEEEEECCCCCCCCHHHHHHHHHHHHHHHHH---CCCC------EEEECCCCHHHHHH
T ss_conf             9999998449--9899844465426777899899999999997---4999------79977999999999


No 264
>TIGR02688 TIGR02688 conserved hypothetical protein TIGR02688; InterPro: IPR014061   Members of this entry are uncharacterised proteins sporadically distributed in bacteria and archaea, about 470 amino acids in length. Several members of this family appear in public databases with annotation as ATP-dependent protease La, despite the lack of similarity to families IPR004815 from INTERPRO (ATP-dependent protease La) or IPR003111 from INTERPRO (ATP-dependent protease La (LON) domain). The proteins in this entry are encoded by genes repeatedly found downstream of another gene that encodes an uncharacterised protein of about 880 amino acids in length (see IPR014060 from INTERPRO)..
Probab=96.34  E-value=0.0028  Score=42.83  Aligned_cols=168  Identities=21%  Similarity=0.326  Sum_probs=105.3

Q ss_pred             CCCEEEEEECCCCCHHHHHHHHHHHCCCCCCCCCC-CCCCCCCCCCCCHHHHHCCCCCCCCCCCCCCCCCCCCCCCEEEE
Q ss_conf             43204887327774367999999842675433210-12346554210024331125555322111001234466714751
Q gi|254780916|r  161 DCAIPIMIQGEFGVGKKRLSRFIHESGKRAFFPFF-IVNCGMIDQDKIEKFLFGDVDLQTKNSAQFLGKFIEANGGTIVL  239 (482)
Q Consensus       161 ~~~~~vli~Ge~GtGK~~~A~~iH~~s~r~~~~fi-~v~c~~~~~~~~e~~lFG~~~~~~~~~~~~~g~~~~a~~Gtl~l  239 (482)
                      ..+.+..=.|+-||||+++=+-|        .|.+ -|..+.++...    |      |........|++..  .-.+.|
T Consensus       215 E~N~Nl~ELgPk~TGKSY~Y~n~--------Sp~~~liSGG~~T~A~----L------FyN~~t~~~Glv~~--~D~Vaf  274 (470)
T TIGR02688       215 EKNYNLVELGPKGTGKSYIYENL--------SPYVILISGGEITVAK----L------FYNISTRKIGLVGL--WDVVAF  274 (470)
T ss_pred             CCCCCEEEECCCCCCCCHHEECC--------CCCEEEEECCCCCCCC----C------EEECCCCCCCEEEE--EEEEEE
T ss_conf             28713487578887730010067--------8777998388205330----0------24756886433431--335655


Q ss_pred             CCCCHH----HHHHHHHHHHHHHHHHCCCCCCCCCCCCCCEEEEECCCCCCC----CCCHH--------HHHHH--HHHH
Q ss_conf             664200----188999888877642001123553212343156521433211----11112--------33379--9988
Q gi|254780916|r  240 EEPDAL----PLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLP----QVKSH--------VFRKD--LYYR  301 (482)
Q Consensus       240 ~ei~~L----~~~~Q~~Ll~~l~~~~~~~~g~~~~~~~~~RiIa~t~~~L~~----~~~~g--------~fr~d--Ly~r  301 (482)
                      |||..+    |.++=..|=..|++|+|.| |+.+...+++=++.--|.|.++    ++...        .||+|  +++|
T Consensus       275 DEv~~~~~~~~~e~~~~LK~Y~e~G~f~R-GG~~~~~s~AS~v~~GNVn~~~~~E~~~~~~~Lf~~LPe~~r~DsAFLDR  353 (470)
T TIGR02688       275 DEVATLKFEKPKELIGILKDYLESGSFTR-GGDETLSSDASFVFLGNVNVNLTSESMVKQSDLFSPLPEFMREDSAFLDR  353 (470)
T ss_pred             CCHHCCCCCCCHHHHHHHHHHHHCCCCCC-CCCEEECCCEEEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHH
T ss_conf             02101001680678877555642576301-56311011323776631468888787466666430387220000147867


Q ss_pred             HHHHH--HHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCC-CCCCCCHHHH
Q ss_conf             65433--446778774422225566777641011223333211111000122-3389868999
Q gi|254780916|r  302 ISVFL--INISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTK-YPWIDNVQEL  361 (482)
Q Consensus       302 L~~~~--i~iPpLReR~eDI~~L~~~fl~~~~~~~~~~~~~ls~~a~~~L~~-y~WPGNvREL  361 (482)
                      +..+-  =+||-+|+-+           +-+++.+|.. ..+=.||+.-|.+ +++.+++.++
T Consensus       354 iHgylPGWeipki~qs~-----------e~f~~~YG~~-vDyfaE~L~~lR~~~~~~~~~~r~  404 (470)
T TIGR02688       354 IHGYLPGWEIPKIRQSK-----------EMFSNGYGLV-VDYFAEALRELREDHEYADLVDRH  404 (470)
T ss_pred             HHHCCCCCCCCCCCCCH-----------HHHHCCCCEE-EHHHHHHHHHHCCCCCHHHHHHHH
T ss_conf             74038886335125631-----------2433554256-304789999841637866786676


No 265
>KOG0482 consensus
Probab=96.19  E-value=0.015  Score=37.72  Aligned_cols=113  Identities=18%  Similarity=0.221  Sum_probs=75.0

Q ss_pred             CCCEEEEEECCCCCHHHHHHHHHHHCCCCCCCCCCCCCCC---CCCCCCCHHHHHCCCCCCCCCCCCCCCCCCCCCCCEE
Q ss_conf             4320488732777436799999984267543321012346---5542100243311255553221110012344667147
Q gi|254780916|r  161 DCAIPIMIQGEFGVGKKRLSRFIHESGKRAFFPFFIVNCG---MIDQDKIEKFLFGDVDLQTKNSAQFLGKFIEANGGTI  237 (482)
Q Consensus       161 ~~~~~vli~Ge~GtGK~~~A~~iH~~s~r~~~~fi~v~c~---~~~~~~~e~~lFG~~~~~~~~~~~~~g~~~~a~~Gtl  237 (482)
                      .-+.+|++.|.+|+-|.-+-.+|-..++|.  .+-+=-.+   +++...+       ++.-||.-.---|.+-.|++|..
T Consensus       373 RGdINicLmGDPGVAKSQLLkyi~rlapRg--vYTTGrGSSGVGLTAAVm-------kDpvTgEM~LEGGALVLAD~GIC  443 (721)
T KOG0482         373 RGDINICLMGDPGVAKSQLLKYISRLAPRG--VYTTGRGSSGVGLTAAVM-------KDPVTGEMVLEGGALVLADGGIC  443 (721)
T ss_pred             ECCEEEEECCCCCHHHHHHHHHHHHCCCCC--CEECCCCCCCCCCCHHHH-------CCCCCCEEEECCCEEEECCCCEE
T ss_conf             253469963897133899999998507665--030388877655111211-------37777706860663897169657


Q ss_pred             EECCCCHHHHHHHHHHHHHHHHHHCCC--CCCCCCCCCCCEEEEECC
Q ss_conf             516642001889998888776420011--235532123431565214
Q gi|254780916|r  238 VLEEPDALPLAVQGRIYNFIETGKIEF--FDSRGAIRLDVRLIFLTE  282 (482)
Q Consensus       238 ~l~ei~~L~~~~Q~~Ll~~l~~~~~~~--~g~~~~~~~~~RiIa~t~  282 (482)
                      ++||.+.|...-...+..+++.+.+.-  -|-.......+-|+|+.|
T Consensus       444 CIDEfDKM~e~DRtAIHEVMEQQTISIaKAGI~TtLNAR~sILaAAN  490 (721)
T KOG0482         444 CIDEFDKMDESDRTAIHEVMEQQTISIAKAGINTTLNARTSILAAAN  490 (721)
T ss_pred             EEHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHCC
T ss_conf             61233323033357999998765445634201000505677665447


No 266
>PRK07914 hypothetical protein; Reviewed
Probab=96.15  E-value=0.13  Score=31.03  Aligned_cols=259  Identities=13%  Similarity=0.113  Sum_probs=126.0

Q ss_pred             CEEE-EEECCCCCHHH-HHHHHHHHCCCC---CCCCCCCCCCCCCCCCCCHHHHHCCCCCCCCCCCCCCCCCCCCCCCEE
Q ss_conf             2048-87327774367-999999842675---433210123465542100243311255553221110012344667147
Q gi|254780916|r  163 AIPI-MIQGEFGVGKK-RLSRFIHESGKR---AFFPFFIVNCGMIDQDKIEKFLFGDVDLQTKNSAQFLGKFIEANGGTI  237 (482)
Q Consensus       163 ~~~v-li~Ge~GtGK~-~~A~~iH~~s~r---~~~~fi~v~c~~~~~~~~e~~lFG~~~~~~~~~~~~~g~~~~a~~Gtl  237 (482)
                      ..|| ||.|+-.-=.+ .+.+.++....+   .+-++..++.+..+...+...             ..+.+|  ++.-.+
T Consensus         4 pAPvyLi~G~E~~L~erav~~~~~~ar~~~~~~d~~~~~l~a~~~~~~~l~~~-------------~spSLF--ae~RlV   68 (320)
T PRK07914          4 PSPLHLVLGDEELLVERAVAAVLRSARKRAGTADVPVDRLRAGDVSTYELAEL-------------LSPSLF--AEERVV   68 (320)
T ss_pred             CCCEEEEECCHHHHHHHHHHHHHHHHHHHCCCCCCEEEEECCCCCCHHHHHHH-------------HCCCCC--CCCEEE
T ss_conf             99879997081999999999999999850379984346621466888899987-------------186766--884499


Q ss_pred             EECCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCEEEEECCCCCCCCCCHHHHHHHHHHHHHHH---HHHHHHHHH
Q ss_conf             51664200188999888877642001123553212343156521433211111123337999886543---344677877
Q gi|254780916|r  238 VLEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYYRISVF---LINISTLRS  314 (482)
Q Consensus       238 ~l~ei~~L~~~~Q~~Ll~~l~~~~~~~~g~~~~~~~~~RiIa~t~~~L~~~~~~g~fr~dLy~rL~~~---~i~iPpLRe  314 (482)
                      ++.+.++++.+....|+..+.+.          -+..+=|+..+..+      .   ++-||..|.-.   .+..|+|..
T Consensus        69 vv~~~~~~~~~~~~~l~~yl~~p----------~~~t~LV~~h~gg~------k---~Kkl~~~lkk~ga~v~~~~~l~k  129 (320)
T PRK07914         69 VLEAAAEAGKDAVALIESAAADL----------PAGTVLVVVHSGGG------R---AKALANQLRKLGAQVHPCARITK  129 (320)
T ss_pred             EEECCCCCCHHHHHHHHHHHCCC----------CCCEEEEEEECCCC------H---HHHHHHHHHHCCCEEEECCCCCC
T ss_conf             98361102688999999985299----------99808999705874------0---46799999976998986556588


Q ss_pred             HHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHCCCCCCCHHHHHHHHCCCCCCCC
Q ss_conf             44222255667776410112233332111110001223389868999999999987438981068895454212445432
Q gi|254780916|r  315 RSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQELKNILLRAVIGLKDSHLTEDRFVLLLSREGKKER  394 (482)
Q Consensus       315 R~eDI~~L~~~fl~~~~~~~~~~~~~ls~~a~~~L~~y~WPGNvREL~n~i~r~~i~~~~~~i~~~~~~~~l~~~~~~~~  394 (482)
                      ..|=+     .|+.+-.+..|+   .++++|.+.|..- -=+|++||.+.|.+++... ++.|+.+++............
T Consensus       130 ~~e~~-----~~v~~e~~~~g~---~i~~~A~~~Lv~~-vG~dl~eLaae~~qL~~d~-~g~It~~~V~~~~~g~~e~~~  199 (320)
T PRK07914        130 ASERA-----DFVRKEFRSLRV---KVDDETVTALLDA-VGSDIRELASACSQLVADT-GGAVDAAAVRRYHSGKAEVKG  199 (320)
T ss_pred             HHHHH-----HHHHHHHHHCCC---CCCHHHHHHHHHH-HHHHHHHHHHHHHHHHHCC-CCCCCHHHHHHHHCCCCEEEH
T ss_conf             68999-----999999998599---9999999999999-8623999999999996057-997369999999289712209


Q ss_pred             CCCCCCCCCCCCCCCCCC--CHHHCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHCCCHHHHHHHH
Q ss_conf             234322222233444321--000000001123444543258999999999999999828727899978489988999999
Q gi|254780916|r  395 EFHTETACTCYTEGKSSD--TILDNLSQESIPAIGQDGEVRRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKI  472 (482)
Q Consensus       395 ~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~l~e~E~~~I~~aL~~~~Gn~~~aA~~LGIsR~tL~rKl  472 (482)
                      ....+.    ...+....  ..+.+......+...   ....|..-=| .|.++ ..-+|+..+.|+.|||..=.+.+-+
T Consensus       200 F~vaDa----a~~g~~~~AL~~lr~al~~G~~pv~---i~~alA~~~R-~la~v-~~~~~~~~~~A~~lg~~Pw~v~ka~  270 (320)
T PRK07914        200 FDIADK----AVAGDVAGAAEALRWAMMRGEPHVV---LADALAEAVH-TIGRV-GPLSGDPYRLAGQLGMPPWRVQKAQ  270 (320)
T ss_pred             HHHHHH----HHCCCHHHHHHHHHHHHHCCCCHHH---HHHHHHHHHH-HHHHH-HHHCCCHHHHHHHHCCCHHHHHHHH
T ss_conf             999999----9878999999999999974997499---9999999999-99998-8613998999988299959999999


Q ss_pred             HH
Q ss_conf             98
Q gi|254780916|r  473 RE  474 (482)
Q Consensus       473 k~  474 (482)
                      +.
T Consensus       271 ~q  272 (320)
T PRK07914        271 KQ  272 (320)
T ss_pred             HH
T ss_conf             99


No 267
>KOG0735 consensus
Probab=96.14  E-value=0.0054  Score=40.78  Aligned_cols=138  Identities=21%  Similarity=0.237  Sum_probs=60.3

Q ss_pred             CCEEEEEECCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCHHHHHCCCCCCCCCCCCC-CCCCCC---CCCCEE
Q ss_conf             3204887327774367999999842675433210123465542100243311255553221110-012344---667147
Q gi|254780916|r  162 CAIPIMIQGEFGVGKKRLSRFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFGDVDLQTKNSAQF-LGKFIE---ANGGTI  237 (482)
Q Consensus       162 ~~~~vli~Ge~GtGK~~~A~~iH~~s~r~~~~fi~v~c~~~~~~~~e~~lFG~~~~~~~~~~~~-~g~~~~---a~~Gtl  237 (482)
                      ...-||+.|++||||+++|-++-..+.   -.||.|-.    ++++ +...|       +..+. .-+|+.   |.--.|
T Consensus       700 ~~~giLLyGppGcGKT~la~a~a~~~~---~~fisvKG----PElL-~KyIG-------aSEq~vR~lF~rA~~a~PCiL  764 (952)
T KOG0735         700 LRTGILLYGPPGCGKTLLASAIASNSN---LRFISVKG----PELL-SKYIG-------ASEQNVRDLFERAQSAKPCIL  764 (952)
T ss_pred             CCCCEEEECCCCCCHHHHHHHHHHHCC---EEEEEECC----HHHH-HHHHC-------CCHHHHHHHHHHHHCCCCEEE
T ss_conf             655458877999857888888885378---05998258----8999-98745-------007889999998651497489


Q ss_pred             EECCCCHHHHH-------HHHHHHHHHHHHHCCCCCCCCCCCCCCEEEEECCCC-C--CCCCCHHHHHHHHHHHHHHHHH
Q ss_conf             51664200188-------999888877642001123553212343156521433-2--1111112333799988654334
Q gi|254780916|r  238 VLEEPDALPLA-------VQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKN-L--LPQVKSHVFRKDLYYRISVFLI  307 (482)
Q Consensus       238 ~l~ei~~L~~~-------~Q~~Ll~~l~~~~~~~~g~~~~~~~~~RiIa~t~~~-L--~~~~~~g~fr~dLy~rL~~~~i  307 (482)
                      |+||.+.+.+.       +-.|....|-+.    +++-+. ---|-|+|+|+++ |  ..+..-|+|.+-.|       -
T Consensus       765 FFDEfdSiAPkRGhDsTGVTDRVVNQlLTe----lDG~Eg-l~GV~i~aaTsRpdliDpALLRpGRlD~~v~-------C  832 (952)
T KOG0735         765 FFDEFDSIAPKRGHDSTGVTDRVVNQLLTE----LDGAEG-LDGVYILAATSRPDLIDPALLRPGRLDKLVY-------C  832 (952)
T ss_pred             EECCCCCCCCCCCCCCCCCHHHHHHHHHHH----HCCCCC-CCEEEEEEECCCCCCCCHHHCCCCCCCEEEE-------C
T ss_conf             712102437666877777429999999876----036334-4538999733783436776628876540156-------7


Q ss_pred             HHHHHHHHHHHHHHHHHHH
Q ss_conf             4677877442222556677
Q gi|254780916|r  308 NISTLRSRSEDIPWLVHFF  326 (482)
Q Consensus       308 ~iPpLReR~eDI~~L~~~f  326 (482)
                      .+|.=-||-|=+..|...+
T Consensus       833 ~~P~~~eRl~il~~ls~s~  851 (952)
T KOG0735         833 PLPDEPERLEILQVLSNSL  851 (952)
T ss_pred             CCCCCHHHHHHHHHHHHCC
T ss_conf             9989289999999985345


No 268
>pfam03709 OKR_DC_1_N Orn/Lys/Arg decarboxylase, N-terminal domain. This domain has a flavodoxin-like fold, and is termed the "wing" domain because of its position in the overall 3D structure.
Probab=96.10  E-value=0.045  Score=34.27  Aligned_cols=66  Identities=18%  Similarity=0.306  Sum_probs=51.4

Q ss_pred             HHHHHHHHHHCCCEEEEECC-H-HHHHHHCC-CCCEEEEECCCCCCCHHHHHHHHHHHCCCCCEEEEECCCC
Q ss_conf             99999999988988999893-7-99998608-9989999785469888999999998578983999926899
Q gi|254780916|r   23 IKIIKDHVESYGYDVFIVNV-S-DLSTISKI-QVNVIFLSLINCEDDKENILKNIVDKIPIVPIIVQTTQDN   91 (482)
Q Consensus        23 ~~~l~~~L~~~G~~v~~a~~-~-al~~l~~~-~~dlillD~~mP~~dGlell~~i~~~~p~ipvIiiT~~~~   91 (482)
                      .+.+...|+..||+|..+.+ + +...++.. +.++|++||   +....+++++++++.+++||-+++-+..
T Consensus         6 ~~~l~~~l~~~~~~vv~~~~~~d~~~~~~~~~~i~avil~~---~~~~~~ll~~ir~~n~~lPvFl~~~~~~   74 (111)
T pfam03709         6 SRELAEALEATGREVVDATSTDDLLSLIETFTDIAAVVLSW---DDEARGLLDEIRRRNFDLPVFLLAETRT   74 (111)
T ss_pred             HHHHHHHHHHCCCEEEEECCHHHHHHHHHHCCCCCEEEEEE---CHHHHHHHHHHHHHCCCCCEEEEECHHH
T ss_conf             89999999978988997487899999998387876899984---6068999999997478999898844125


No 269
>smart00763 AAA_PrkA PrkA AAA domain. This is a family of PrkA bacterial and archaeal serine kinases approximately 630 residues long. This is the N-terminal AAA domain.
Probab=96.07  E-value=0.0046  Score=41.29  Aligned_cols=61  Identities=16%  Similarity=0.211  Sum_probs=44.2

Q ss_pred             CCCCCCCCCCCCCCCCCCCCCC----CCEEEEEECCCCCHHHHHHHHHH----HCCCCCCCCCCCCCCC
Q ss_conf             1112222222222222222344----32048873277743679999998----4267543321012346
Q gi|254780916|r  140 DSLIAVSPAMIQVVDLARKAGD----CAIPIMIQGEFGVGKKRLSRFIH----ESGKRAFFPFFIVNCG  200 (482)
Q Consensus       140 ~~LiG~S~~m~~v~~~i~~~a~----~~~~vli~Ge~GtGK~~~A~~iH----~~s~r~~~~fi~v~c~  200 (482)
                      +.+.|....+.++.+.++.+|.    ...=+++.|+.|+||+.+++.|-    ++|....++.-++.-.
T Consensus        51 d~~fG~e~~i~~~V~~~k~AA~g~~~~k~IllL~GPvGsGKStl~~~Lk~~lE~ys~t~eG~~Y~~~w~  119 (361)
T smart00763       51 HDFFGMEEAIERFVNYFKSAAQGLEERKQILYLLGPVGGGKSSLVECLKRGLEEYSKTPEGRRYTFKWN  119 (361)
T ss_pred             HHHCCCHHHHHHHHHHHHHHHHCCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHHHCCCCCCEEEEEEC
T ss_conf             131164899999999999998446712569999889988779999999999998626776855999833


No 270
>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=96.06  E-value=0.029  Score=35.59  Aligned_cols=38  Identities=18%  Similarity=0.089  Sum_probs=28.1

Q ss_pred             CCCCCCCCCCCCCEEEEEECCCCCHHHHHHHHHHHCCC
Q ss_conf             22222222344320488732777436799999984267
Q gi|254780916|r  151 QVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHESGK  188 (482)
Q Consensus       151 ~v~~~i~~~a~~~~~vli~Ge~GtGK~~~A~~iH~~s~  188 (482)
                      .+++.+.--.....-|.|.|++|+||+++.+.|-..-+
T Consensus        15 ~il~~isl~i~~Ge~v~i~G~sGsGKSTLl~~l~Gl~~   52 (166)
T cd03223          15 VLLKDLSFEIKPGDRLLITGPSGTGKSSLFRALAGLWP   52 (166)
T ss_pred             EEEEEEEEEECCCCEEEEECCCCCCHHHHHHHHCCCCC
T ss_conf             88944588988999999995899988999999869876


No 271
>PRK05629 hypothetical protein; Validated
Probab=96.02  E-value=0.15  Score=30.59  Aligned_cols=186  Identities=12%  Similarity=0.099  Sum_probs=103.2

Q ss_pred             CCCCCEEE-EEECCCCCHHHHHHH-HHH---HCCCC-CCCCCCCCCCCCCCCCCCHHHHHCCCCCCCCCCCCCCCCCCCC
Q ss_conf             34432048-873277743679999-998---42675-4332101234655421002433112555532211100123446
Q gi|254780916|r  159 AGDCAIPI-MIQGEFGVGKKRLSR-FIH---ESGKR-AFFPFFIVNCGMIDQDKIEKFLFGDVDLQTKNSAQFLGKFIEA  232 (482)
Q Consensus       159 ~a~~~~~v-li~Ge~GtGK~~~A~-~iH---~~s~r-~~~~fi~v~c~~~~~~~~e~~lFG~~~~~~~~~~~~~g~~~~a  232 (482)
                      .|+-.-|| ||.||-.-=.+..-+ .++   ..... .+-.+..+++...+...+.+.           .  ....|  +
T Consensus        11 ~~~~~pPvYLl~G~E~yLid~a~~~l~~~i~~~~~~~~~~n~~~~~~~e~~~~~l~~a-----------~--~~~~F--~   75 (331)
T PRK05629         11 PISVQPAVHLVLGEDEFLAERARINIVHDIRSSMASPDSLQVTTLKASEITQGELLDA-----------L--SPSLF--A   75 (331)
T ss_pred             CCCCCCCEEEEECCHHHHHHHHHHHHHHHHHHHCCCCCCCEEEEEECCCCCHHHHHHH-----------C--CCCCC--C
T ss_conf             9999999799971719999999999999998628874462258850787999999987-----------3--75888--8


Q ss_pred             CCCEEEECCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCEEEEECCCCCCCCCCHHHHHHHHHHHHH--HHHHHHH
Q ss_conf             67147516642001889998888776420011235532123431565214332111111233379998865--4334467
Q gi|254780916|r  233 NGGTIVLEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYYRIS--VFLINIS  310 (482)
Q Consensus       233 ~~Gtl~l~ei~~L~~~~Q~~Ll~~l~~~~~~~~g~~~~~~~~~RiIa~t~~~L~~~~~~g~fr~dLy~rL~--~~~i~iP  310 (482)
                      +.-.+++.+.+.++...+..++..+.+          +.+.-+=|++....|      .   |+-||-.|.  +..++.+
T Consensus        76 ~~RlVvv~~~~~~~~~~~d~ll~y~~~----------p~p~t~LV~~~~~~d------k---rkkl~k~l~k~g~v~e~~  136 (331)
T PRK05629         76 EDRVVVLTNMDQAGQDAVDLALSAAVD----------PSPGTYLIVMHSGGG------R---SKSMVKKLEKVAVVHDAA  136 (331)
T ss_pred             CCEEEEEECHHHCCHHHHHHHHHHHHC----------CCCCEEEEEEECCCC------C---CHHHHHHHHCCEEEEECC
T ss_conf             825999957253064479999998419----------999649999845875------1---067999986074698668


Q ss_pred             HHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHCCCCCCCHHHHHHHHCCC
Q ss_conf             7877442222556677764101122333321111100012233898689999999999874389810688954542124
Q gi|254780916|r  311 TLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQELKNILLRAVIGLKDSHLTEDRFVLLLSRE  389 (482)
Q Consensus       311 pLReR~eDI~~L~~~fl~~~~~~~~~~~~~ls~~a~~~L~~y~WPGNvREL~n~i~r~~i~~~~~~i~~~~~~~~l~~~  389 (482)
                      +|.++  |++..+...    .++.|   +.++++|.+.|..+ .-.|.++|.|-|+.++. ..++.|+.+++.......
T Consensus       137 ~l~~~--~l~~wi~~~----~~~~g---~~i~~~A~~~L~~~-~G~DL~~l~~El~KL~~-~~~g~It~e~V~~~~~~~  204 (331)
T PRK05629        137 KLKDR--DRPGWVKQE----FKNHK---VQVTPDVIHALLEG-VGSDLRELASAVSQLVE-DTQGNVTVEKVRAYYVGV  204 (331)
T ss_pred             CCCHH--HHHHHHHHH----HHHCC---CCCCHHHHHHHHHH-HCCCHHHHHHHHHHHHC-CCCCCCCHHHHHHHHCCC
T ss_conf             89999--999999999----99869---99799999999999-68049999999999840-779985899999982697


No 272
>PRK07399 DNA polymerase III subunit delta'; Validated
Probab=96.01  E-value=0.0076  Score=39.73  Aligned_cols=121  Identities=16%  Similarity=0.102  Sum_probs=63.7

Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCCCHHHHHHHHHHHCCCCCCCCCCCCCCC----CCCCC-------C
Q ss_conf             111112222222222222222344320488732777436799999984267543321012346----55421-------0
Q gi|254780916|r  138 ALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHESGKRAFFPFFIVNCG----MIDQD-------K  206 (482)
Q Consensus       138 ~~~~LiG~S~~m~~v~~~i~~~a~~~~~vli~Ge~GtGK~~~A~~iH~~s~r~~~~fi~v~c~----~~~~~-------~  206 (482)
                      .|+.++|+..+...+...+.+ .......|+.|+.|+||..+|+.+-..=.-.+.+-....|.    .-|+=       .
T Consensus         2 ~F~~iiGq~~~~~~L~~ai~~-~rl~hAyLF~Gp~G~GK~~~A~~fa~~Ll~~~~~~~~~~~ri~~~nHPDl~~i~P~~~   80 (314)
T PRK07399          2 LFANLIGQPLAIELLTAAIEQ-NRIAPAYLFAGPEGVGRKLAALRFIEGLLSQGSPSKNIRRRLEEGNHPDLLWVEPTYQ   80 (314)
T ss_pred             CCCCCCCCHHHHHHHHHHHHC-CCCCCEEEEECCCCCCHHHHHHHHHHHHHCCCCCCCCHHHHHHCCCCCCEEEEECCCC
T ss_conf             833125949999999999985-9967448778999832999999999998578999976655875189997788605620


Q ss_pred             CHHHHHCCCCC-CCCC---------CCC--CC-CCC----CCCCCCEEEECCCCHHHHHHHHHHHHHHHH
Q ss_conf             02433112555-5322---------111--00-123----446671475166420018899988887764
Q gi|254780916|r  207 IEKFLFGDVDL-QTKN---------SAQ--FL-GKF----IEANGGTIVLEEPDALPLAVQGRIYNFIET  259 (482)
Q Consensus       207 ~e~~lFG~~~~-~~~~---------~~~--~~-g~~----~~a~~Gtl~l~ei~~L~~~~Q~~Ll~~l~~  259 (482)
                      .+..++....+ ..+.         ..+  .. ..+    -++..-.+++++.+.|..+.+..||..||+
T Consensus        81 ~~g~~~~~~~~~~~~~~~~~~~~I~idqIR~l~~~l~~~p~~~~~kVvII~~ae~m~~~AaNaLLKtLEE  150 (314)
T PRK07399         81 HQGKLITASEAEEAGLKRKSPPQIRLEQIREIKRFLSRPPLEAPRKVVVIEDAETMNEAAANALLKTLEE  150 (314)
T ss_pred             CCCCCCCHHHHHHHHHHCCCCCCCCHHHHHHHHHHHCCCCCCCCCEEEEECCHHHCCHHHHHHHHHHHCC
T ss_conf             0345455778987653026877787999999999973188568847999889787199999999986147


No 273
>TIGR00764 lon_rel ATP-dependent protease, putative; InterPro: IPR004663   Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes . They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence . Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases .   Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base . The geometric orientations of the catalytic residues are similar between families, despite different protein folds . The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) , .   Peptidases are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry. Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins.   Families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule.    This signature defines the archaeal lon protease homologs, which are ATP-dependent serine peptidases belonging to the MEROPS peptidase family S16 (lon protease family, clan SF). Members of this family from Pyrococcus horikoshii and Pyrococcus abyssi each contain a predicted intein conserved region.; GO: 0004176 ATP-dependent peptidase activity, 0005524 ATP binding, 0030163 protein catabolic process.
Probab=95.95  E-value=0.01  Score=38.75  Aligned_cols=142  Identities=18%  Similarity=0.193  Sum_probs=82.1

Q ss_pred             CCCCCCCCCCCEEEECCCCHHHHHHHHHHHHHHHHHHCCCCCCC----------CCCCCCCEEEEECCCCCCCCCCHHHH
Q ss_conf             00123446671475166420018899988887764200112355----------32123431565214332111111233
Q gi|254780916|r  225 FLGKFIEANGGTIVLEEPDALPLAVQGRIYNFIETGKIEFFDSR----------GAIRLDVRLIFLTEKNLLPQVKSHVF  294 (482)
Q Consensus       225 ~~g~~~~a~~Gtl~l~ei~~L~~~~Q~~Ll~~l~~~~~~~~g~~----------~~~~~~~RiIa~t~~~L~~~~~~g~f  294 (482)
                      ..|.+.+|+.|.||+|||..++...|..++..+++++|--.|.+          .++++|+-++++-+.+  .+.   .+
T Consensus       227 ~~g~~h~~~~g~l~~d~~~~~~~~~~~~~l~~~~~~~~p~~g~~~~~~g~~~~~~p~pcdf~l~~~g~~~--~~~---~~  301 (662)
T TIGR00764       227 EAGAIHRAHKGVLYIDEIGTLPLEVQQYLLTALQDKKFPITGQSENSSGAMVRTEPVPCDFILVASGNLD--DLE---GL  301 (662)
T ss_pred             HHHHHHHHCCCEEEEECCCCCCHHHHHHHHHHHHHCCCCCCCCCCCCCCCEEECCCCCCCEEEEECCCHH--HHH---HC
T ss_conf             3221233205505540113221135788887654113543567765556412115666214455146545--654---10


Q ss_pred             HHHHHHHHHHH--HHHH-HHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCC---------CCCCCHHHHH
Q ss_conf             37999886543--3446-7787744222255667776410112233332111110001223---------3898689999
Q gi|254780916|r  295 RKDLYYRISVF--LINI-STLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKY---------PWIDNVQELK  362 (482)
Q Consensus       295 r~dLy~rL~~~--~i~i-PpLReR~eDI~~L~~~fl~~~~~~~~~~~~~ls~~a~~~L~~y---------~WPGNvREL~  362 (482)
                      +.-|..|+.++  .+.+ -.+-+-++.-..|+++..++..+....  ..|+.++..-+...         ...=.+|+|-
T Consensus       302 ~~~l~~~~~g~gy~~~~~~~~~~~~~~~~~l~~f~~~~~~~~g~~--~~~~~~~~~~~~~~~~~~~g~~~~l~l~l~~l~  379 (662)
T TIGR00764       302 HPALRSRIRGYGYEVYLKDTMPDTPENRDKLVQFVAQEVKKDGRL--PHFTRDAVEEIVREAQRRAGRKDHLTLRLRELG  379 (662)
T ss_pred             CHHHHHHHCCCCEEEEECCCCCCCHHHHHHHHHHHHHHHHHCCCC--CCCCHHHHHHHHHHHHHHCCCCCCCEEHHHHHH
T ss_conf             045665430144168872667775024789999999987624788--864267899999998862276442010256663


Q ss_pred             HHHHHHHHHCC
Q ss_conf             99999987438
Q gi|254780916|r  363 NILLRAVIGLK  373 (482)
Q Consensus       363 n~i~r~~i~~~  373 (482)
                      ++++.+--.+.
T Consensus       380 ~~~~~~~d~~~  390 (662)
T TIGR00764       380 GLVRAAGDIAK  390 (662)
T ss_pred             HHHHHHCCHHC
T ss_conf             36653100111


No 274
>PRK08058 DNA polymerase III subunit delta'; Validated
Probab=95.94  E-value=0.0054  Score=40.76  Aligned_cols=118  Identities=20%  Similarity=0.332  Sum_probs=58.9

Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCCCHHHHHHHHHHH---C-CCCCCCCC-CCCCCCCCC----CCCCHH
Q ss_conf             11112222222222222222344320488732777436799999984---2-67543321-012346554----210024
Q gi|254780916|r  139 LDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHE---S-GKRAFFPF-FIVNCGMID----QDKIEK  209 (482)
Q Consensus       139 ~~~LiG~S~~m~~v~~~i~~~a~~~~~vli~Ge~GtGK~~~A~~iH~---~-s~r~~~~f-i~v~c~~~~----~~~~e~  209 (482)
                      .+.++|.=+.+.+.....-.-.......|+.|+.|+||..+|+++=.   + ++....|= .--+|..+.    +|... 
T Consensus         4 ~~~~~~~Q~~i~~~L~~~i~~~rl~HA~Lf~Gp~G~GK~~~A~~~A~~LlC~~~~~~~~Cg~C~~C~~~~~~~HPD~~~-   82 (329)
T PRK08058          4 WEQLTALQPIVVKMLQNSIAKNRLAHAYLFEGAKGTGKKATALWLAKSLFCLERNGVEPCGTCTNCKRIESGNHPDVHL-   82 (329)
T ss_pred             HHHHHHHHHHHHHHHHHHHHCCCCCCEEEEECCCCCCHHHHHHHHHHHHCCCCCCCCCCCCCCHHHHHHHCCCCCCEEE-
T ss_conf             7888831899999999999859966156557899988999999999997399999999887888999987699997677-


Q ss_pred             HHHCCCCCCCCCCCCCCCC---C----CCCCCCEEEECCCCHHHHHHHHHHHHHHHHH
Q ss_conf             3311255553221110012---3----4466714751664200188999888877642
Q gi|254780916|r  210 FLFGDVDLQTKNSAQFLGK---F----IEANGGTIVLEEPDALPLAVQGRIYNFIETG  260 (482)
Q Consensus       210 ~lFG~~~~~~~~~~~~~g~---~----~~a~~Gtl~l~ei~~L~~~~Q~~Ll~~l~~~  260 (482)
                       ++.  ++.+-...+-.-+   +    .+++.-..++++.+.|..+.+..||..|||.
T Consensus        83 -i~p--~~~~i~idqiR~L~~~~~~~p~~g~~KV~II~~Ae~m~~~AaNALLKtLEEP  137 (329)
T PRK08058         83 -VAP--DGQSIKKDQIRYLKEEFSKSGVESNKKVYIIEHADKMTASAANSLLKFLEEP  137 (329)
T ss_pred             -ECC--CCCCCCHHHHHHHHHHHCCCCCCCCCEEEEEECHHHHCHHHHHHHHHHHHCC
T ss_conf             -456--6140779999999999643875788679997347762999999999986468


No 275
>KOG0651 consensus
Probab=95.90  E-value=0.016  Score=37.46  Aligned_cols=137  Identities=13%  Similarity=0.157  Sum_probs=75.6

Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCC-----------CCCEEEEEECCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCC
Q ss_conf             211111111222222222222222234-----------432048873277743679999998426754332101234655
Q gi|254780916|r  134 NEHCALDSLIAVSPAMIQVVDLARKAG-----------DCAIPIMIQGEFGVGKKRLSRFIHESGKRAFFPFFIVNCGMI  202 (482)
Q Consensus       134 ~~~~~~~~LiG~S~~m~~v~~~i~~~a-----------~~~~~vli~Ge~GtGK~~~A~~iH~~s~r~~~~fi~v~c~~~  202 (482)
                      ..+..++.+-|-...+.++++.++---           .-..-++|.|++||||++.||++-..-.   -.|+.+-.+++
T Consensus       126 ~~~~s~~~~ggl~~qirelre~ielpl~np~lf~rvgIk~Pkg~ll~GppGtGKTlla~~Vaa~mg---~nfl~v~ss~l  202 (388)
T KOG0651         126 PRNISFENVGGLFYQIRELREVIELPLTNPELFLRVGIKPPKGLLLYGPPGTGKTLLARAVAATMG---VNFLKVVSSAL  202 (388)
T ss_pred             CCCCCHHHHCCHHHHHHHHHHHEEEECCCCHHCCCCCCCCCCEEEEECCCCCCHHHHHHHHHHHCC---CCEEEEEHHHH
T ss_conf             554678771783888899886557402481002345777882568767999864599999998659---85477447666


Q ss_pred             CCCCC------HHHHHCCCCCCCCCCCCCCCCCCCCCCCEEEECCCCHH-----------HHHHHHHHHHHHHHH-HCCC
Q ss_conf             42100------24331125555322111001234466714751664200-----------188999888877642-0011
Q gi|254780916|r  203 DQDKI------EKFLFGDVDLQTKNSAQFLGKFIEANGGTIVLEEPDAL-----------PLAVQGRIYNFIETG-KIEF  264 (482)
Q Consensus       203 ~~~~~------e~~lFG~~~~~~~~~~~~~g~~~~a~~Gtl~l~ei~~L-----------~~~~Q~~Ll~~l~~~-~~~~  264 (482)
                      -+..+      -.+.|.+.      .. .       .--.+|+|||+..           ...+|.-|..++..= .|. 
T Consensus       203 v~kyiGEsaRlIRemf~yA------~~-~-------~pciifmdeiDAigGRr~se~Ts~dreiqrTLMeLlnqmdgfd-  267 (388)
T KOG0651         203 VDKYIGESARLIRDMFRYA------RE-V-------IPCIIFMDEIDAIGGRRFSEGTSSDREIQRTLMELLNQMDGFD-  267 (388)
T ss_pred             HHHHCCCHHHHHHHHHHHH------HH-H-------CCEEEEEHHHHHHCCEEECCCCCHHHHHHHHHHHHHHHHCCCH-
T ss_conf             3300265788999999778------65-2-------7557751012311457733555205999999999987421401-


Q ss_pred             CCCCCCCCCCCEEEEECCCCC---CCCCCHHHH
Q ss_conf             235532123431565214332---111111233
Q gi|254780916|r  265 FDSRGAIRLDVRLIFLTEKNL---LPQVKSHVF  294 (482)
Q Consensus       265 ~g~~~~~~~~~RiIa~t~~~L---~~~~~~g~f  294 (482)
                            .--.|.+|++||..-   ..++..|++
T Consensus       268 ------~l~rVk~ImatNrpdtLdpaLlRpGRl  294 (388)
T KOG0651         268 ------TLHRVKTIMATNRPDTLDPALLRPGRL  294 (388)
T ss_pred             ------HCCCCCEEEECCCCCCCCHHHCCCCCC
T ss_conf             ------206631798538866566554287521


No 276
>pfam06068 TIP49 TIP49 C-terminus. This family consists of the C-terminal region of several eukaryotic and archaeal RuvB-like 1 (Pontin or TIP49a) and RuvB-like 2 (Reptin or TIP49b) proteins. The N-terminal domain contains the pfam00004 domain. In zebrafish, the liebeskummer (lik) mutation, causes development of hyperplastic embryonic hearts. lik encodes Reptin, a component of a DNA-stimulated ATPase complex. Beta-catenin and Pontin, a DNA-stimulated ATPase that is often part of complexes with Reptin, are in the same genetic pathways. The Reptin/Pontin ratio serves to regulate heart growth during development, at least in part via the beta-catenin pathway. TBP-interacting protein 49 (TIP49) was originally identified as a TBP-binding protein, and two related proteins are encoded by individual genes, tip49a and b. Although the function of this gene family has not been elucidated, they are supposed to play a critical role in nuclear events because they interact with various kinds of nuclear
Probab=95.81  E-value=0.0075  Score=39.77  Aligned_cols=98  Identities=21%  Similarity=0.303  Sum_probs=61.1

Q ss_pred             CCCEEEECCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCEEEEECCCCCC-----CCCCHHHHHHHHHHHHHHHHH
Q ss_conf             671475166420018899988887764200112355321234315652143321-----111112333799988654334
Q gi|254780916|r  233 NGGTIVLEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLL-----PQVKSHVFRKDLYYRISVFLI  307 (482)
Q Consensus       233 ~~Gtl~l~ei~~L~~~~Q~~Ll~~l~~~~~~~~g~~~~~~~~~RiIa~t~~~L~-----~~~~~g~fr~dLy~rL~~~~i  307 (482)
                      --|.||+||+|-|..+.=.-|-|+|++ .+.|           =||.+||+-..     +...-.-+--||+.||=.++ 
T Consensus       275 vpGVLFIDEvHMLDiEcFsfLnralEs-~laP-----------ivI~ATNRG~~~IRGTd~~sPHGiP~DlLDRllII~-  341 (395)
T pfam06068       275 VPGVLFIDEVHMLDIECFSFLNRALES-ELAP-----------IVILATNRGICTIRGTDIISPHGIPLDLLDRLLIIT-  341 (395)
T ss_pred             ECCCEEEECCHHCCHHHHHHHHHHHCC-CCCC-----------EEEEEECCCCEEECCCCCCCCCCCCHHHHHHEEEEE-
T ss_conf             427468850000005899888776505-6787-----------699984465203525677588899877773025885-


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             4677877442222556677764101122333321111100012233
Q gi|254780916|r  308 NISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYP  353 (482)
Q Consensus       308 ~iPpLReR~eDI~~L~~~fl~~~~~~~~~~~~~ls~~a~~~L~~y~  353 (482)
                         ..-=-.+||..+    +..-|++.+   ..++++|+..|....
T Consensus       342 ---T~py~~~ei~~I----i~iRa~~E~---v~l~~~al~~L~~ig  377 (395)
T pfam06068       342 ---TEPYTREEIKQI----LEIRAQEEG---VEISEEALDLLAKIG  377 (395)
T ss_pred             ---CCCCCHHHHHHH----HHHHHHHHC---CCCCHHHHHHHHHHH
T ss_conf             ---688998999999----998777607---877989999999865


No 277
>COG5271 MDN1 AAA ATPase containing von Willebrand factor type A (vWA) domain [General function prediction only]
Probab=95.79  E-value=0.021  Score=36.68  Aligned_cols=41  Identities=24%  Similarity=0.318  Sum_probs=17.3

Q ss_pred             CCCCCCEEEEEECCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCC
Q ss_conf             23443204887327774367999999842675433210123465
Q gi|254780916|r  158 KAGDCAIPIMIQGEFGVGKKRLSRFIHESGKRAFFPFFIVNCGM  201 (482)
Q Consensus       158 ~~a~~~~~vli~Ge~GtGK~~~A~~iH~~s~r~~~~fi~v~c~~  201 (482)
                      |+.+...|+|+.|-+|+||+.+-.++-...   ++.++.||.+.
T Consensus      1538 RAmqv~kpilLEGsPGVGKTSlItaLAr~t---G~kliRINLSe 1578 (4600)
T COG5271        1538 RAMQVGKPILLEGSPGVGKTSLITALARKT---GKKLIRINLSE 1578 (4600)
T ss_pred             HHHHCCCCEEECCCCCCCHHHHHHHHHHHH---CCCEEEEECCC
T ss_conf             998528854622799866789999999974---57247863201


No 278
>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=95.76  E-value=0.029  Score=35.62  Aligned_cols=83  Identities=19%  Similarity=0.326  Sum_probs=41.2

Q ss_pred             EEEEECCCCCHHHHHHHHHH-HCCCC---CCCCC-CCCCCCCCCCC---CCHHHHHCCCCCCCCCCCC-CCCCCCCCCCC
Q ss_conf             48873277743679999998-42675---43321-01234655421---0024331125555322111-00123446671
Q gi|254780916|r  165 PIMIQGEFGVGKKRLSRFIH-ESGKR---AFFPF-FIVNCGMIDQD---KIEKFLFGDVDLQTKNSAQ-FLGKFIEANGG  235 (482)
Q Consensus       165 ~vli~Ge~GtGK~~~A~~iH-~~s~r---~~~~f-i~v~c~~~~~~---~~e~~lFG~~~~~~~~~~~-~~g~~~~a~~G  235 (482)
                      .|+|.|++|+||+++++.+- ..+..   +...| +.+.|..++..   -+...|+-+-......... ..-.+...+.-
T Consensus         2 ~i~i~G~aG~GKTtll~kl~~~wa~g~~~~~~~~vf~~~~r~~~~~~~~sl~~ll~~~~~~~~~~~~~~~~~~~~~~~k~   81 (165)
T pfam05729         2 TVILQGEAGSGKTTLLQKLALLWAQGKLPQDFDFVFFLPCRELSRSGEASLADLLFSQWPEPAAPVSEVWAVILELPERV   81 (165)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHCCCCCCCCCEEEEEEHHHHCCCCCCCHHHHHHHHCCCCCCCHHHHHHHHHHCCCCE
T ss_conf             89998279898999999999999869843697289999956707776689999999876774576378999998397728


Q ss_pred             EEEECCCCHHHH
Q ss_conf             475166420018
Q gi|254780916|r  236 TIVLEEPDALPL  247 (482)
Q Consensus       236 tl~l~ei~~L~~  247 (482)
                      -++||.+++++.
T Consensus        82 L~ilDGlDE~~~   93 (165)
T pfam05729        82 LLILDGLDELAS   93 (165)
T ss_pred             EEEECCHHHHCC
T ss_conf             999648455144


No 279
>TIGR00390 hslU heat shock protein HslVU, ATPase subunit HslU; InterPro: IPR004491   This family of proteins represent HslU, a bacterial clpX homolog, which is an ATPase and chaperone belonging to the AAA Clp/Hsp100 family and a component of the eubacterial proteasome.    ATP-dependent protease complexes are present in all three kingdoms of life, where they rid the cell of misfolded or damaged proteins and control the level of certain regulatory proteins. They include the proteasome in Eukaryotes, Archaea, and Actinomycetales and the HslVU (ClpQY, ClpXP) complex in other eubacteria. Genes homologous to eubacterial HslV, IPR001353 from INTERPRO, (ClpQ,) and HslU (ClpY, ClpX) have also been demonstrated in to be present in the genome of trypanosomatid protozoa. They are expressed as precursors, with a propeptide that is removed to produce the active protease. The protease is probably located in the kinetoplast (mitochondrion). Phylogenetic analysis shows that HslV and HslU from trypanosomatids form a single clad with other eubacterial homologs . ; GO: 0005515 protein binding, 0005524 ATP binding, 0009377 HslUV protease activity, 0016887 ATPase activity, 0005737 cytoplasm, 0009376 HslUV protease complex.
Probab=95.75  E-value=0.0071  Score=39.95  Aligned_cols=41  Identities=24%  Similarity=0.372  Sum_probs=31.2

Q ss_pred             CCCEEEEEECCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCC
Q ss_conf             43204887327774367999999842675433210123465542
Q gi|254780916|r  161 DCAIPIMIQGEFGVGKKRLSRFIHESGKRAFFPFFIVNCGMIDQ  204 (482)
Q Consensus       161 ~~~~~vli~Ge~GtGK~~~A~~iH~~s~r~~~~fi~v~c~~~~~  204 (482)
                      .+..+||-.|+||+||+=+||-|=..+   +.|||.|-.+-+++
T Consensus        45 V~PKNILMiGpTGVGKTEIARRlAKL~---~aPFiKVEAtKfTE   85 (463)
T TIGR00390        45 VTPKNILMIGPTGVGKTEIARRLAKLA---NAPFIKVEATKFTE   85 (463)
T ss_pred             CCCCCEEEECCCCCCHHHHHHHHHHHH---CCCCEEEEEEEEEE
T ss_conf             587430432788985447999999984---48914666410011


No 280
>KOG1808 consensus
Probab=95.74  E-value=0.0099  Score=38.93  Aligned_cols=122  Identities=16%  Similarity=0.206  Sum_probs=76.6

Q ss_pred             CCCCCCCCCCCCCCCCC-CEEEEEECCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCHHHHHC-CCCCCCCCCC
Q ss_conf             22222222222223443-204887327774367999999842675433210123465542100243311-2555532211
Q gi|254780916|r  146 SPAMIQVVDLARKAGDC-AIPIMIQGEFGVGKKRLSRFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFG-DVDLQTKNSA  223 (482)
Q Consensus       146 S~~m~~v~~~i~~~a~~-~~~vli~Ge~GtGK~~~A~~iH~~s~r~~~~fi~v~c~~~~~~~~e~~lFG-~~~~~~~~~~  223 (482)
                      ++..++....+.++-.+ ..|+||+|++|+||+.+...+-..   ....++.+|--... +  -.++.| +....+|...
T Consensus       422 T~~vq~~la~~~~a~~~~~~pillqG~tssGKtsii~~la~~---~g~~~vrinnheht-d--~qeyig~y~~~~~g~l~  495 (1856)
T KOG1808         422 TPRVQKNLADLARAISSGKFPILLQGPTSSGKTSIIKELARA---TGKNIVRINNHEHT-D--LQEYIGTYVADDNGDLV  495 (1856)
T ss_pred             CHHHHHHHHHHHHHHHCCCCCEEEECCCCCCCHHHHHHHHHH---HCCCCEEHHCCCCC-H--HHHHHHHHEECCCCCEE
T ss_conf             689998899999999658998677547676811599999998---54673420024633-3--99998665007889725


Q ss_pred             CCCCCCCC-CCCC-EEEECCCCHHHHHHHHHHHHHHHH-HHCCCCCCCCCCCC
Q ss_conf             10012344-6671-475166420018899988887764-20011235532123
Q gi|254780916|r  224 QFLGKFIE-ANGG-TIVLEEPDALPLAVQGRIYNFIET-GKIEFFDSRGAIRL  273 (482)
Q Consensus       224 ~~~g~~~~-a~~G-tl~l~ei~~L~~~~Q~~Ll~~l~~-~~~~~~g~~~~~~~  273 (482)
                      -+.|.+-+ +.+| -+|||+|.--+-+.=.-|.|+|.+ ++++-...+..++.
T Consensus       496 freg~LV~Alr~G~~~vlD~lnla~~dvL~aLnrllddnRel~ipe~~rlv~~  548 (1856)
T KOG1808         496 FREGVLVQALRNGDWIVLDELNLAPHDVLEALNRLLDDNRELFIPETQRLVKA  548 (1856)
T ss_pred             EEHHHHHHHHHHCCEEEECCCCCCCHHHHHHHHHHHHHHCCCCCCCCCEEECC
T ss_conf             53468999987087798402012406789999840454041256344323224


No 281
>PRK11131 ATP-dependent RNA helicase HrpA; Provisional
Probab=95.57  E-value=0.0087  Score=39.31  Aligned_cols=54  Identities=15%  Similarity=0.239  Sum_probs=36.7

Q ss_pred             HHHHHC----CCCCEEEEECC-CCCCCH---HHHHHHHHHHCCCCCEEEEECCCCHHHHHHH
Q ss_conf             999860----89989999785-469888---9999999985789839999268999999988
Q gi|254780916|r   45 LSTISK----IQVNVIFLSLI-NCEDDK---ENILKNIVDKIPIVPIIVQTTQDNIKILNCF   98 (482)
Q Consensus        45 l~~l~~----~~~dlillD~~-mP~~dG---lell~~i~~~~p~ipvIiiT~~~~~~~~~~a   98 (482)
                      +..+..    ..+++|++|-- -=..+.   +-+++.+....|++.||+|||.-+.+.....
T Consensus       175 L~e~~~d~~L~~y~~iIiDEaHERsl~~D~LLg~Lk~ll~~R~dLKvIimSATid~e~fs~y  236 (1295)
T PRK11131        175 LAEIQQDRLLMQYDTIIIDEAHERSLNIDFILGYLKELLPRRPDLKVIITSATIDPERFSRH  236 (1295)
T ss_pred             HHHHHHCCCCCCCCEEEEECCCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCCCHHHHHHH
T ss_conf             99862099878877799868556880199999999999833999889995586897999965


No 282
>PRK07132 DNA polymerase III subunit delta'; Validated
Probab=95.53  E-value=0.025  Score=36.11  Aligned_cols=107  Identities=8%  Similarity=0.130  Sum_probs=54.6

Q ss_pred             CCCEEEEEECCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCHHHHHCCCCCCCCCCCCCC---CC-----CCCC
Q ss_conf             432048873277743679999998426754332101234655421002433112555532211100---12-----3446
Q gi|254780916|r  161 DCAIPIMIQGEFGVGKKRLSRFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFGDVDLQTKNSAQFL---GK-----FIEA  232 (482)
Q Consensus       161 ~~~~~vli~Ge~GtGK~~~A~~iH~~s~r~~~~fi~v~c~~~~~~~~e~~lFG~~~~~~~~~~~~~---g~-----~~~a  232 (482)
                      ....--|+.|+.|+||...|+.+-..-.-...  -..+|...+.+...-...+    ...+..+..   ..     ++..
T Consensus        18 klsHAYLF~G~~G~Gk~~~a~~~a~~l~~~~~--~~~~~~~~~~~~~~id~~~----~~i~~~~i~~~i~~~~~~~~~~~   91 (303)
T PRK07132         18 KISHSFLLKSNYNNDLDESILYFLNKFNNLQS--LNLNLEELPYNIFLFDIFD----EDLSKEEFLSAIEKFSFSSFVSN   91 (303)
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHHHHHCCCCC--CCCCCCCCCCCCEEECCCC----CCHHHHHHHHHHHHHHHCCCCCC
T ss_conf             97616886789986799999999999729987--8887545653230413322----20016889999999973665568


Q ss_pred             CCCEEEECCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCEEEEECCCC
Q ss_conf             6714751664200188999888877642001123553212343156521433
Q gi|254780916|r  233 NGGTIVLEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKN  284 (482)
Q Consensus       233 ~~Gtl~l~ei~~L~~~~Q~~Ll~~l~~~~~~~~g~~~~~~~~~RiIa~t~~~  284 (482)
                      ..-..++||++.|+.+.+..||..|++.           +.++.+|.+|+..
T Consensus        92 ~~Kv~IIdea~~lt~~A~NaLLKtLEEP-----------p~~~~fil~t~~~  132 (303)
T PRK07132         92 QKKILIIKNIEKTSNSSLNALLKTIEEP-----------SKNTYFLLTTKNI  132 (303)
T ss_pred             CEEEEEEECHHHCCHHHHHHHHHHCCCC-----------CCCEEEEEEECCH
T ss_conf             7069998165533999999999870389-----------8684899972882


No 283
>COG1224 TIP49 DNA helicase TIP49, TBP-interacting protein [Transcription]
Probab=95.36  E-value=0.015  Score=37.59  Aligned_cols=286  Identities=15%  Similarity=0.122  Sum_probs=136.1

Q ss_pred             HHHHHCCCCC--EEEEECCCCCCCHHHHHHHH--HHHCCCCCEEEEECCC-------CHHHHHHHHHCCCCCCCCCCCCC
Q ss_conf             9998608998--99997854698889999999--9857898399992689-------99999988850574322222222
Q gi|254780916|r   45 LSTISKIQVN--VIFLSLINCEDDKENILKNI--VDKIPIVPIIVQTTQD-------NIKILNCFLYNRISKFFLNLVSR  113 (482)
Q Consensus        45 l~~l~~~~~d--lillD~~mP~~dGlell~~i--~~~~p~ipvIiiT~~~-------~~~~~~~a~~~g~~d~l~KP~~~  113 (482)
                      ..++++.+..  .||  +.-|...|-..+.--  ++..+++|++-++|..       -.|+..++++.-+---+   -..
T Consensus        55 v~mik~gk~aGrgiL--i~GppgTGKTAlA~gIa~eLG~dvPF~~isgsEiYS~E~kKTE~L~qa~RraIGvri---kE~  129 (450)
T COG1224          55 VKMIKQGKMAGRGIL--IVGPPGTGKTALAMGIARELGEDVPFVAISGSEIYSLEVKKTEALTQALRRAIGVRI---KET  129 (450)
T ss_pred             HHHHHHCCCCCCEEE--EECCCCCCHHHHHHHHHHHHCCCCCCEEECCCEEEEECCCHHHHHHHHHHHHHCEEE---EEE
T ss_conf             999971766661799--978999768899999999858999821501332233100088999999998645486---466


Q ss_pred             CCCCCCCCCC--CCCCCCCCCCC-CCCCCCCCCCCCCCCCCCC-------CCCCCCCCCCE-EEEEECCCCCH----HHH
Q ss_conf             2222222222--22222222222-1111111122222222222-------22222344320-48873277743----679
Q gi|254780916|r  114 KQLCDSIICA--LREGVVPSQEN-EHCALDSLIAVSPAMIQVV-------DLARKAGDCAI-PIMIQGEFGVG----KKR  178 (482)
Q Consensus       114 ~~L~~~i~~a--l~~~~~~~~~~-~~~~~~~LiG~S~~m~~v~-------~~i~~~a~~~~-~vli~Ge~GtG----K~~  178 (482)
                      .....-....  .++...+-..- ......-+.-.+..|.+.+       +++.+.....- -|.|.-|+|.=    +..
T Consensus       130 reV~EGeV~~l~i~~~~~p~~~y~~~~~~~~i~LkT~d~~k~~~lg~~i~~ql~~~~V~~GDVI~Id~etG~V~klGrs~  209 (450)
T COG1224         130 REVYEGEVVELEIRRARNPLNPYGKVPSGAIITLKTKDEEKTLRLGPEIAEQLVKEGVEEGDVIYIDAETGRVKKLGRSK  209 (450)
T ss_pred             EEEEEEEEEEEEEEECCCCCCCCCCCCCCEEEEEEECCCCEEEECCHHHHHHHHHHCCCCCCEEEEECCCCEEEEEECCC
T ss_conf             68887789999876235799876655453289999636645762598999999983744587899982566799942242


Q ss_pred             HHHHHHHC-------CCCCCCCC------C-CCCCCCCCCC-----CCHHHHHCCCCCCCCCC----CC-CCCCCCC---
Q ss_conf             99999842-------67543321------0-1234655421-----00243311255553221----11-0012344---
Q gi|254780916|r  179 LSRFIHES-------GKRAFFPF------F-IVNCGMIDQD-----KIEKFLFGDVDLQTKNS----AQ-FLGKFIE---  231 (482)
Q Consensus       179 ~A~~iH~~-------s~r~~~~f------i-~v~c~~~~~~-----~~e~~lFG~~~~~~~~~----~~-~~g~~~~---  231 (482)
                      .+.. ..+       -+-..+|.      + .|..-.++..     -+-+.+||..+.-+...    +. ..+++++   
T Consensus       210 ~~~~-~~~dl~~~~~V~~P~Gev~K~KEi~~~vTLHDlDv~nar~~G~~sl~~~~~~eI~~evR~~vn~~V~~~ieeGkA  288 (450)
T COG1224         210 ARAR-EDFDLEDTRFVPLPEGEVQKRKEIVQTVTLHDLDVANARAQGILSLFSGGTGEITDEVREEVNEKVKKWIEEGKA  288 (450)
T ss_pred             CCCC-CCCCCCCEEEEECCCCCEEEEEEEEEEEEEHHHHHHHCCCCCHHHHHCCCCCCCCHHHHHHHHHHHHHHHHCCCE
T ss_conf             3354-223344217987798852566778999870031343204111375652776657889999999999999854957


Q ss_pred             -CCCCEEEECCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCEEEEECCCCCCC-----CCCHHHHHHHHHHHHHHH
Q ss_conf             -66714751664200188999888877642001123553212343156521433211-----111123337999886543
Q gi|254780916|r  232 -ANGGTIVLEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLP-----QVKSHVFRKDLYYRISVF  305 (482)
Q Consensus       232 -a~~Gtl~l~ei~~L~~~~Q~~Ll~~l~~~~~~~~g~~~~~~~~~RiIa~t~~~L~~-----~~~~g~fr~dLy~rL~~~  305 (482)
                       -=-|.||+||+|-|..+.=.-|-|+|++ .|.|           =||.|||+-...     ...-.-.-.||+.||-. 
T Consensus       289 ElVpGVLFIDEvHmLDIE~FsFlnrAlEs-e~aP-----------Iii~AtNRG~~kiRGTd~~sPhGIP~DlLDRllI-  355 (450)
T COG1224         289 ELVPGVLFIDEVHMLDIECFSFLNRALES-ELAP-----------IIILATNRGMTKIRGTDIESPHGIPLDLLDRLLI-  355 (450)
T ss_pred             EEECCEEEEECHHHHHHHHHHHHHHHHHC-CCCC-----------EEEEECCCCEEEECCCCCCCCCCCCHHHHHHEEE-
T ss_conf             86134289732134557899999987631-4675-----------7999717750012166776888898766622567-


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCHH
Q ss_conf             344677877442222556677764101122333321111100012233898689
Q gi|254780916|r  306 LINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQ  359 (482)
Q Consensus       306 ~i~iPpLReR~eDI~~L~~~fl~~~~~~~~~~~~~ls~~a~~~L~~y~WPGNvR  359 (482)
                         ++.+.--+++|..++..    -+++.+   ..++++|++.|..-.----+|
T Consensus       356 ---I~t~py~~~EireIi~i----Ra~ee~---i~l~~~Ale~L~~ig~etSLR  399 (450)
T COG1224         356 ---ISTRPYSREEIREIIRI----RAKEED---IELSDDALEYLTDIGEETSLR  399 (450)
T ss_pred             ---EECCCCCHHHHHHHHHH----HHHHHC---CCCCHHHHHHHHHHCHHHHHH
T ss_conf             ---74477988999999997----643540---304888999997515034489


No 284
>COG2607 Predicted ATPase (AAA+ superfamily) [General function prediction only]
Probab=95.18  E-value=0.049  Score=33.99  Aligned_cols=98  Identities=13%  Similarity=0.076  Sum_probs=60.3

Q ss_pred             CEEEEEECCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCC--CCCHHHHHCCCCCCCCCCCCCCCCCCCCCCCEEEEC
Q ss_conf             204887327774367999999842675433210123465542--100243311255553221110012344667147516
Q gi|254780916|r  163 AIPIMIQGEFGVGKKRLSRFIHESGKRAFFPFFIVNCGMIDQ--DKIEKFLFGDVDLQTKNSAQFLGKFIEANGGTIVLE  240 (482)
Q Consensus       163 ~~~vli~Ge~GtGK~~~A~~iH~~s~r~~~~fi~v~c~~~~~--~~~e~~lFG~~~~~~~~~~~~~g~~~~a~~Gtl~l~  240 (482)
                      .-+||+.|-.||||+.+-+++|+.-.-....+|.|+-..+..  .+++ +|=+           +.-+|      .||.|
T Consensus        85 ANnVLLwGaRGtGKSSLVKA~~~e~~~~glrLVEV~k~dl~~Lp~l~~-~Lr~-----------~~~kF------IlFcD  146 (287)
T COG2607          85 ANNVLLWGARGTGKSSLVKALLNEYADEGLRLVEVDKEDLATLPDLVE-LLRA-----------RPEKF------ILFCD  146 (287)
T ss_pred             CCCEEEECCCCCCHHHHHHHHHHHHHHCCCEEEEECHHHHHHHHHHHH-HHHC-----------CCCEE------EEEEC
T ss_conf             523677637777747999999999874177079976888865799999-9961-----------88608------99956


Q ss_pred             CCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCEEEEECCCC
Q ss_conf             64200188999888877642001123553212343156521433
Q gi|254780916|r  241 EPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKN  284 (482)
Q Consensus       241 ei~~L~~~~Q~~Ll~~l~~~~~~~~g~~~~~~~~~RiIa~t~~~  284 (482)
                      ...==.-+.--|.|...-+      |+-..++.||=+-|++|+.
T Consensus       147 DLSFe~gd~~yK~LKs~Le------G~ve~rP~NVl~YATSNRR  184 (287)
T COG2607         147 DLSFEEGDDAYKALKSALE------GGVEGRPANVLFYATSNRR  184 (287)
T ss_pred             CCCCCCCCHHHHHHHHHHC------CCCCCCCCEEEEEEECCCC
T ss_conf             7777778138999999853------8855688707999715875


No 285
>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=95.07  E-value=0.012  Score=38.32  Aligned_cols=60  Identities=18%  Similarity=0.171  Sum_probs=40.4

Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCCCHHHHHHHHHHHCCCCCCCCCCCC
Q ss_conf             111112222222222222222344320488732777436799999984267543321012
Q gi|254780916|r  138 ALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHESGKRAFFPFFIV  197 (482)
Q Consensus       138 ~~~~LiG~S~~m~~v~~~i~~~a~~~~~vli~Ge~GtGK~~~A~~iH~~s~r~~~~fi~v  197 (482)
                      ..+.++-....-..+.+.++.+.....++||.|++|+||+++.+++=..-+..+..+++|
T Consensus       114 tl~~L~~~g~~~~~~~~~L~~~v~~~~~ilIsG~TGSGKTT~l~all~~i~~~~~riiti  173 (283)
T pfam00437       114 TLDDLGMTGAFDADIAEFLRQAVQARGNILVSGGTGSGKTTLLYALLNEINTDDERIVTI  173 (283)
T ss_pred             CHHHHCCCCCCHHHHHHHHHHHHHCCCEEEEECCCCCCHHHHHHHHHHHCCCCCCCEEEE
T ss_conf             999973897785999999999998197599988999988999999998408777627873


No 286
>PRK13409 putative ATPase RIL; Provisional
Probab=94.98  E-value=0.23  Score=29.32  Aligned_cols=65  Identities=14%  Similarity=0.141  Sum_probs=35.6

Q ss_pred             HHHHHHHHCCCE------EEEECCHH-----HHHHHCCCCCEEEEECCCCCCCH---HHHHHHHHHHCCCCCEEEEECCC
Q ss_conf             999999988988------99989379-----99986089989999785469888---99999999857898399992689
Q gi|254780916|r   25 IIKDHVESYGYD------VFIVNVSD-----LSTISKIQVNVIFLSLINCEDDK---ENILKNIVDKIPIVPIIVQTTQD   90 (482)
Q Consensus        25 ~l~~~L~~~G~~------v~~a~~~a-----l~~l~~~~~dlillD~~mP~~dG---lell~~i~~~~p~ipvIiiT~~~   90 (482)
                      .+..+++..|.+      +..-+.+.     ++..--..||+.++|--....|=   +.+.+.+++....-.|||+| |+
T Consensus       192 ~~~el~~~lgL~~~~~r~~~~lSgG~~qrv~~a~~l~~~~~~~~lDEPtn~LDi~~r~~l~~~lr~L~~~~tvIVVe-HD  270 (590)
T PRK13409        192 KLDEVVEELGLENVLDRDISELSGGELQRVAIAAALLRDADFYFFDEPTSYLDIRQRLNVARLIRELAEGKYVLVVE-HD  270 (590)
T ss_pred             HHHHHHHHCCCCHHHCCCHHHCCHHHHHHHHHHHHHHCCCCEEEECCCCCCCCHHHHHHHHHHHHHHHCCCCEEEEE-EH
T ss_conf             89999997399535379300289989999999999843999899648755489999999999999985698689998-63


No 287
>PRK11477 carbohydrate diacid transcriptional activator CdaR; Provisional
Probab=94.94  E-value=0.036  Score=34.95  Aligned_cols=32  Identities=22%  Similarity=0.048  Sum_probs=28.8

Q ss_pred             HHHHHHHCCCHHHHHHHHCCCHHHHHHHHHHH
Q ss_conf             99999828727899978489988999999981
Q gi|254780916|r  444 GLAMKLYRAQMSEVARRLGIGRSTLYRKIREY  475 (482)
Q Consensus       444 ~~aL~~~~Gn~~~aA~~LGIsR~tL~rKlk~~  475 (482)
                      ..++-.+|||.++||+.|.|.|+||.+||+|.
T Consensus       327 L~~yfe~n~si~~tA~~L~IHRNTL~YRL~KI  358 (385)
T PRK11477        327 LAAWFRHNVQPLATSKALFIHRNTLEYRLNRI  358 (385)
T ss_pred             HHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHH
T ss_conf             99999809999999998486450699999999


No 288
>cd01380 MYSc_type_V Myosin motor domain, type V myosins. Myosins V transport a variety of intracellular cargo processively along actin filaments, such as membraneous organelles and mRNA. This catalytic (head) domain has ATPase activity and belongs to the larger group of P-loop NTPases. Myosins are actin-dependent molecular motors that play important roles in muscle contraction, cell motility, and organelle transport. The head domain is a molecular motor, which utilizes ATP hydrolysis to generate directed movement toward the plus end along actin filaments. A cyclical interaction between myosin and actin provides the driving force. Rates of ATP hydrolysis and consequently the speed of movement along actin filaments vary widely, from about 0.04 micrometer per second for myosin I to 4.5 micrometer per second for myosin II in skeletal muscle. Myosin II moves in discrete steps about 5-10 nm long and generates 1-5 piconewtons of force. Upon ATP binding, the myosin head dissociates from an act
Probab=94.93  E-value=0.022  Score=36.42  Aligned_cols=24  Identities=29%  Similarity=0.548  Sum_probs=20.2

Q ss_pred             CCCEEEEEECCCCCHHHHHHHHHH
Q ss_conf             432048873277743679999998
Q gi|254780916|r  161 DCAIPIMIQGEFGVGKKRLSRFIH  184 (482)
Q Consensus       161 ~~~~~vli~Ge~GtGK~~~A~~iH  184 (482)
                      ..+..|+|.||+|+||+..++.|=
T Consensus        84 ~~~QsIiiSGESGaGKTe~~K~il  107 (691)
T cd01380          84 EKNQSIIVSGESGAGKTVSAKYIM  107 (691)
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHH
T ss_conf             998069996279998779999999


No 289
>PRK01172 ski2-like helicase; Provisional
Probab=94.91  E-value=0.026  Score=36.01  Aligned_cols=51  Identities=18%  Similarity=0.139  Sum_probs=32.4

Q ss_pred             CCCEEEEE-CCCCCC--CH--H-HHHHHHHHHCCCCCEEEEECC-CCHHHHHHHHHCCCC
Q ss_conf             99899997-854698--88--9-999999985789839999268-999999988850574
Q gi|254780916|r   52 QVNVIFLS-LINCED--DK--E-NILKNIVDKIPIVPIIVQTTQ-DNIKILNCFLYNRIS  104 (482)
Q Consensus        52 ~~dlillD-~~mP~~--dG--l-ell~~i~~~~p~ipvIiiT~~-~~~~~~~~a~~~g~~  104 (482)
                      ..++|+.| +.|=+.  =|  + .++.+++...|++.+|.+||. ++.+....  +.++.
T Consensus       135 ~v~~vViDEiH~i~d~~RG~~lE~~l~kl~~l~~~~qiIgLSATi~N~~~la~--WL~a~  192 (674)
T PRK01172        135 DVGLIVADEIHIIGDEDRGPTLETVLSSARYVNPDARILALSATVSNANELAQ--WLNAS  192 (674)
T ss_pred             CCCEEEEECCEECCCCCCHHHHHHHHHHHHHCCCCEEEEEECCCCCCHHHHHH--HHCCC
T ss_conf             36989982652506877249999999999853866079971578689999998--83885


No 290
>COG1220 HslU ATP-dependent protease HslVU (ClpYQ), ATPase subunit [Posttranslational modification, protein turnover, chaperones]
Probab=94.83  E-value=0.023  Score=36.33  Aligned_cols=123  Identities=16%  Similarity=0.297  Sum_probs=61.1

Q ss_pred             CCCEEEECCCCHHHHH------------HHHHHHHHHHHHHCCCCCCCCCCCCC-CEEEEECCCC---CCCCCC--HHHH
Q ss_conf             6714751664200188------------99988887764200112355321234-3156521433---211111--1233
Q gi|254780916|r  233 NGGTIVLEEPDALPLA------------VQGRIYNFIETGKIEFFDSRGAIRLD-VRLIFLTEKN---LLPQVK--SHVF  294 (482)
Q Consensus       233 ~~Gtl~l~ei~~L~~~------------~Q~~Ll~~l~~~~~~~~g~~~~~~~~-~RiIa~t~~~---L~~~~~--~g~f  294 (482)
                      +.|.+|+|||+.....            +|.-||-+++-..+.-  -+.+++.| .-+||+---.   +.+++-  +|+|
T Consensus       250 ~~GIvFIDEIDKIa~~~~~g~~dvSREGVQRDlLPlvEGstV~T--KyG~VkTdHILFIasGAFh~sKPSDLiPELQGRf  327 (444)
T COG1220         250 QNGIVFIDEIDKIAKRGGSGGPDVSREGVQRDLLPLVEGSTVST--KYGPVKTDHILFIASGAFHVAKPSDLIPELQGRF  327 (444)
T ss_pred             HCCEEEEEHHHHHHHCCCCCCCCCCHHHHCCCCCCCCCCCEEEC--CCCCCCCCEEEEEECCCEECCCHHHCCHHHCCCC
T ss_conf             56908973466787437889988664320102103105754431--5444014437887148200378132176662777


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHH--------HHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCH-------H
Q ss_conf             37999886543344677877442222--------55667776410112233332111110001223389868-------9
Q gi|254780916|r  295 RKDLYYRISVFLINISTLRSRSEDIP--------WLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNV-------Q  359 (482)
Q Consensus       295 r~dLy~rL~~~~i~iPpLReR~eDI~--------~L~~~fl~~~~~~~~~~~~~ls~~a~~~L~~y~WPGNv-------R  359 (482)
                               .+.+++-+|-  .+|.-        .|+..|-+-+. ..|.. ..|+++|+..+....|-=|-       |
T Consensus       328 ---------PIRVEL~~Lt--~~Df~rILtep~~sLikQY~aLlk-TE~v~-l~FtddaI~~iAeiA~~vN~~~ENIGAR  394 (444)
T COG1220         328 ---------PIRVELDALT--KEDFERILTEPKASLIKQYKALLK-TEGVE-LEFTDDAIKRIAEIAYQVNEKTENIGAR  394 (444)
T ss_pred             ---------CEEEECCCCC--HHHHHHHHCCCHHHHHHHHHHHHH-HCCEE-EEECHHHHHHHHHHHHHHCCCCCCHHHH
T ss_conf             ---------3488704489--989999963760789999999973-15834-8853799999999999855430001178


Q ss_pred             HHHHHHHHHHH
Q ss_conf             99999999987
Q gi|254780916|r  360 ELKNILLRAVI  370 (482)
Q Consensus       360 EL~n~i~r~~i  370 (482)
                      -|..++++++-
T Consensus       395 RLhTvlErlLe  405 (444)
T COG1220         395 RLHTVLERLLE  405 (444)
T ss_pred             HHHHHHHHHHH
T ss_conf             89999999998


No 291
>PRK05707 DNA polymerase III subunit delta'; Validated
Probab=94.81  E-value=0.13  Score=31.07  Aligned_cols=110  Identities=13%  Similarity=0.136  Sum_probs=54.0

Q ss_pred             CCCCCCCCCCCCCCCEEEEEECCCCCHHHHHHHHHHHC----CCCCCCCC-CCCCCCCC----CCCCCHHHHHCCCCCCC
Q ss_conf             22222222223443204887327774367999999842----67543321-01234655----42100243311255553
Q gi|254780916|r  149 MIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHES----GKRAFFPF-FIVNCGMI----DQDKIEKFLFGDVDLQT  219 (482)
Q Consensus       149 m~~v~~~i~~~a~~~~~vli~Ge~GtGK~~~A~~iH~~----s~r~~~~f-i~v~c~~~----~~~~~e~~lFG~~~~~~  219 (482)
                      .+..++++-.-.....-.|+.|+.|+||..+|+.+=..    .+....|= .--+|..+    .+|...  ++-+.++-+
T Consensus         8 ~~~~w~~l~~~~rl~HA~Lf~G~~G~GK~~lA~~~A~~LlC~~~~~~~~Cg~C~sC~~~~~~~HPD~~~--i~pe~~~~~   85 (328)
T PRK05707          8 QQSLWQQLAGRGRHAHAYLLHGPAGIGKRALAERLAAFLLCEAPQGGGACGSCKGCQLLAAGSHPDNFV--LEPEEADKP   85 (328)
T ss_pred             CHHHHHHHHHCCCCCEEEEEECCCCCCHHHHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHCCCCCCEEE--EECCCCCCC
T ss_conf             489999999779822046447999867999999999998489999989998888999987589998799--842666776


Q ss_pred             CCCCCCCCCC-------CCCCCCEEEECCCCHHHHHHHHHHHHHHHHH
Q ss_conf             2211100123-------4466714751664200188999888877642
Q gi|254780916|r  220 KNSAQFLGKF-------IEANGGTIVLEEPDALPLAVQGRIYNFIETG  260 (482)
Q Consensus       220 ~~~~~~~g~~-------~~a~~Gtl~l~ei~~L~~~~Q~~Ll~~l~~~  260 (482)
                      -...+-..+.       .+.+.-..++++.+.|....+..||..|||.
T Consensus        86 I~IdqIR~l~~~~~~~~~~g~~KV~iI~~Ae~m~~~AaNALLKtLEEP  133 (328)
T PRK05707         86 IKVDQVRELVSFVVQTAQLGGRKVVLIEPAEAMNRNAANALLKSLEEP  133 (328)
T ss_pred             CCHHHHHHHHHHHHHCCCCCCCEEEEEEHHHHHCHHHHHHHHHHHHCC
T ss_conf             979999999999831766789579995028773899999999985078


No 292
>TIGR01842 type_I_sec_PrtD type I secretion system ATPase; InterPro: IPR010128   Type I protein secretion is a system in some Gram-negative bacteria to export proteins (often proteases) across both inner and outer membranes to the extracellular medium. This is one of three proteins of the type I secretion apparatus. Targeted proteins are not cleaved at the N terminus, but rather carry signals located toward the extreme C terminus to direct type I secretion.; GO: 0005524 ATP binding, 0015031 protein transport, 0016021 integral to membrane.
Probab=94.74  E-value=0.037  Score=34.90  Aligned_cols=78  Identities=17%  Similarity=0.134  Sum_probs=52.9

Q ss_pred             CCCCCCCCCCCCCEEEEEECCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCHHHHHC-CCCC-------CCCCC
Q ss_conf             222222223443204887327774367999999842675433210123465542100243311-2555-------53221
Q gi|254780916|r  151 QVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFG-DVDL-------QTKNS  222 (482)
Q Consensus       151 ~v~~~i~~~a~~~~~vli~Ge~GtGK~~~A~~iH~~s~r~~~~fi~v~c~~~~~~~~e~~lFG-~~~~-------~~~~~  222 (482)
                      .+.+.|.-.-+--.-|=|.|++||||+++||.|=--=.-..| =|.+|.+.+.  ..+.|-|| |.+.       |.|..
T Consensus       344 ~~l~gi~F~~~aGe~laIIGPSgSGKStLaR~~vG~W~~~~G-~VRLDGadl~--qWD~e~lG~~iGYLPQdvELF~GTv  420 (556)
T TIGR01842       344 PTLRGISFAIQAGEALAIIGPSGSGKSTLARILVGIWPPASG-SVRLDGADLK--QWDRETLGKHIGYLPQDVELFSGTV  420 (556)
T ss_pred             HHHCCCCEEECCCCEEEEECCCCCCHHHHHHHHHHCCCCCCC-CEEEEHHHHH--CCCHHHCCCCCCCCCCCCCCCCCCH
T ss_conf             422786215637745888747865258898788721013565-3364033440--2375365880154798505076767


Q ss_pred             CCCCCCCCC
Q ss_conf             110012344
Q gi|254780916|r  223 AQFLGKFIE  231 (482)
Q Consensus       223 ~~~~g~~~~  231 (482)
                      .+++-+|++
T Consensus       421 a~NIARF~e  429 (556)
T TIGR01842       421 AENIARFGE  429 (556)
T ss_pred             HHHCCCCCC
T ss_conf             640244688


No 293
>PRK11331 5-methylcytosine-specific restriction enzyme subunit McrB; Provisional
Probab=94.72  E-value=0.25  Score=28.99  Aligned_cols=121  Identities=22%  Similarity=0.220  Sum_probs=67.6

Q ss_pred             CCCEEEEEECCCCCHHHHHHHHHHHC--CCCCCCCCCCCCCCCCCCCCCHHHHHCCCCCCCCCCCCCCCCC----CCC--
Q ss_conf             43204887327774367999999842--6754332101234655421002433112555532211100123----446--
Q gi|254780916|r  161 DCAIPIMIQGEFGVGKKRLSRFIHES--GKRAFFPFFIVNCGMIDQDKIEKFLFGDVDLQTKNSAQFLGKF----IEA--  232 (482)
Q Consensus       161 ~~~~~vli~Ge~GtGK~~~A~~iH~~--s~r~~~~fi~v~c~~~~~~~~e~~lFG~~~~~~~~~~~~~g~~----~~a--  232 (482)
                      .+...|.++|.+||||+.+|+.+-..  +.+.++.+--|...  |.=..|..+.|.+... +....+.|.|    ++|  
T Consensus       192 ktKknvIL~G~pGtGKT~lAk~lA~~l~g~~~~~rv~~Vqfh--psysYEDfi~Gyrp~~-~gf~~~~G~f~~~~~~A~~  268 (459)
T PRK11331        192 TIKKNIILQGPPGVGKTFVARRLAYLLTGEKAPQRVNMVQFH--QSYSYEDFIQGYRPNG-VGFRRKDGIFYNFCQQAKE  268 (459)
T ss_pred             CCCCCEEEECCCCCCHHHHHHHHHHHHHCCCCCCCEEEEEEC--CCCCHHHHHCCCCCCC-CCCEECCCHHHHHHHHHHH
T ss_conf             458827965899988789999999997078877846899835--8866178764605688-8613268369999999984


Q ss_pred             ---CCCEEEECCCCHHHHH-HHHHHHHHHHHHHC------CC---C--CCCCCCCCCCEEEEECCCC
Q ss_conf             ---6714751664200188-99988887764200------11---2--3553212343156521433
Q gi|254780916|r  233 ---NGGTIVLEEPDALPLA-VQGRIYNFIETGKI------EF---F--DSRGAIRLDVRLIFLTEKN  284 (482)
Q Consensus       233 ---~~Gtl~l~ei~~L~~~-~Q~~Ll~~l~~~~~------~~---~--g~~~~~~~~~RiIa~t~~~  284 (482)
                         +.=.+++|||..--.+ .=.-|+.+|+..+-      .-   -  |..=.++.|+.||.+-|-.
T Consensus       269 ~p~~~y~~iideinr~~~~~~fgel~~liE~dkR~~~~~~~l~ys~~~~~~f~vP~Nl~iigtmNta  335 (459)
T PRK11331        269 QPEKKYVFIIDEINRANLSKVFGEVMMLMEHDKRGENWSVPLTYSENDEERFYVPENVYIIGLMNTA  335 (459)
T ss_pred             CCCCCEEEEEEHHHCCCHHHHHHHHHHHHHHCCCCCCCEEEEECCCCCCCEECCCCCEEEEEECCCC
T ss_conf             9898769998432033889999999999641256765225630036888533468865999850334


No 294
>PRK05917 DNA polymerase III subunit delta'; Validated
Probab=94.65  E-value=0.055  Score=33.65  Aligned_cols=112  Identities=14%  Similarity=0.089  Sum_probs=57.9

Q ss_pred             CCCCCCCCCCCCCCCCCCCEEEEEECCCCCHHHHHHHHHHHCCCCCCCCC--CCCCCCCCCCCCCHHHHHCCCCCCCCCC
Q ss_conf             22222222222222344320488732777436799999984267543321--0123465542100243311255553221
Q gi|254780916|r  145 VSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHESGKRAFFPF--FIVNCGMIDQDKIEKFLFGDVDLQTKNS  222 (482)
Q Consensus       145 ~S~~m~~v~~~i~~~a~~~~~vli~Ge~GtGK~~~A~~iH~~s~r~~~~f--i~v~c~~~~~~~~e~~lFG~~~~~~~~~  222 (482)
                      +|.+++.+...+.+ .......|+.|+.|+||..+|+.+-..=--.+.|-  ..+. ....+|..+  ++-..++.....
T Consensus         2 ~~~~We~L~~~i~~-~Rl~HAyLf~Gp~G~GK~~~A~~~A~~LLc~~~p~~~~~i~-~~~HPD~~~--i~pe~k~~~~~I   77 (290)
T PRK05917          2 ENAAWEALLQRVRD-QKVPSAILLHGQDLSNLSQYAYELASLILLESSPEAQYKIS-QKIHPDIHE--FFPEGKGRLHSI   77 (290)
T ss_pred             CCHHHHHHHHHHHC-CCCCEEEEEECCCCCCHHHHHHHHHHHHHCCCCCCHHHHHH-HCCCCCEEE--ECCCCCCCCCCH
T ss_conf             85499999999983-99660687689998659999999999985789961688987-468998599--615777887867


Q ss_pred             CCCCCCCC-------CCCCCEEEECCCCHHHHHHHHHHHHHHHHH
Q ss_conf             11001234-------466714751664200188999888877642
Q gi|254780916|r  223 AQFLGKFI-------EANGGTIVLEEPDALPLAVQGRIYNFIETG  260 (482)
Q Consensus       223 ~~~~g~~~-------~a~~Gtl~l~ei~~L~~~~Q~~Ll~~l~~~  260 (482)
                      .+...+.+       +...-..++++.+.|..+.+..||..|||.
T Consensus        78 d~iR~l~~~i~~~p~~g~~KV~IId~Ad~Mn~~AaNALLKtLEEP  122 (290)
T PRK05917         78 ETPRAIKKQIWIHPYEANYKIYIIHEADRMTLDAISAFLKVLEDP  122 (290)
T ss_pred             HHHHHHHHHHCCCCCCCCCEEEEECCHHHHCHHHHHHHHHHHCCC
T ss_conf             899999999641864688269997567763899999999973479


No 295
>KOG0481 consensus
Probab=94.62  E-value=0.094  Score=32.01  Aligned_cols=216  Identities=16%  Similarity=0.127  Sum_probs=113.3

Q ss_pred             CCCEEEEEECCCCCHHHHHHHHHHHCCCCCCCCCCC---CCCCCCCCCCCHHHHHCCCCCCCCCCCCCCCCCCCCCCCEE
Q ss_conf             432048873277743679999998426754332101---23465542100243311255553221110012344667147
Q gi|254780916|r  161 DCAIPIMIQGEFGVGKKRLSRFIHESGKRAFFPFFI---VNCGMIDQDKIEKFLFGDVDLQTKNSAQFLGKFIEANGGTI  237 (482)
Q Consensus       161 ~~~~~vli~Ge~GtGK~~~A~~iH~~s~r~~~~fi~---v~c~~~~~~~~e~~lFG~~~~~~~~~~~~~g~~~~a~~Gtl  237 (482)
                      .-+.+||+.|.+||-|.-+-+.+-..|+-+  -+-.   -..|+++...+-       +..|...----|.+-.|+||.+
T Consensus       362 RGDINVLLLGDPgtAKSQlLKFvEkvsPIa--VYTSGKGSSAAGLTASV~R-------D~~tReFylEGGAMVLADgGVv  432 (729)
T KOG0481         362 RGDINVLLLGDPGTAKSQLLKFVEKVSPIA--VYTSGKGSSAAGLTASVIR-------DPSTREFYLEGGAMVLADGGVV  432 (729)
T ss_pred             CCCEEEEEECCCCHHHHHHHHHHHHCCCEE--EEECCCCCCCCCCEEEEEE-------CCCCCEEEEECCEEEEECCCEE
T ss_conf             264028983698526899999998608637--9946887643346246786-------6876338982665998169789


Q ss_pred             EECCCCHHHHHHHHHHHHHHHHHHCC--CCCCCCCCCCCCEEEEECCCCC---CCCC---CHHHHHHHHHHH--------
Q ss_conf             51664200188999888877642001--1235532123431565214332---1111---112333799988--------
Q gi|254780916|r  238 VLEEPDALPLAVQGRIYNFIETGKIE--FFDSRGAIRLDVRLIFLTEKNL---LPQV---KSHVFRKDLYYR--------  301 (482)
Q Consensus       238 ~l~ei~~L~~~~Q~~Ll~~l~~~~~~--~~g~~~~~~~~~RiIa~t~~~L---~~~~---~~g~fr~dLy~r--------  301 (482)
                      ++||-+.|-.+-...+..+++.+.+.  .-|-.....+.+-+.|+.|.-.   +++-   +.=.|-.-.+-|        
T Consensus       433 CIDEFDKMre~DRVAIHEAMEQQTISIAKAGITT~LNSRtSVLAAANpvfGRyDd~Kt~~dNIDf~~TILSRFDmIFIVK  512 (729)
T KOG0481         433 CIDEFDKMREDDRVAIHEAMEQQTISIAKAGITTTLNSRTSVLAAANPVFGRYDDTKTGEDNIDFMPTILSRFDMIFIVK  512 (729)
T ss_pred             EEEHHHCCCCHHHHHHHHHHHHHHHHHHHHCCEEEECCHHHHHHHCCCCCCCCCCCCCCCCCCCHHHHHHHHCCEEEEEE
T ss_conf             83000025820156898998765577755052256424033445337866554346785556322346764513799983


Q ss_pred             ----------H--HHHHHHHH---HHHHH---HHHHHHHHHHHHHHHCCCC-CCCCCCCCCCCCCCCCCCC---------
Q ss_conf             ----------6--54334467---78774---4222255667776410112-2333321111100012233---------
Q gi|254780916|r  302 ----------I--SVFLINIS---TLRSR---SEDIPWLVHFFLQSFCTKN-AIKQISISDKALSLLTKYP---------  353 (482)
Q Consensus       302 ----------L--~~~~i~iP---pLReR---~eDI~~L~~~fl~~~~~~~-~~~~~~ls~~a~~~L~~y~---------  353 (482)
                                |  .++.+++-   ...+-   .+|.  +--+++++|-.-. -+-.+.+|++|-+.|.+|.         
T Consensus       513 D~h~~~~D~~lAkHVI~vH~~~~n~~~~~~~~~~~e--i~~~~~KryI~YcR~kc~PrLs~~AaekL~~~yV~~R~~~~q  590 (729)
T KOG0481         513 DEHDEERDITLAKHVINVHVSKANAQTDSQEENEGE--IPIEKLKRYIQYCRLKCGPRLSAEAAEKLSSRYVTMRKGVRQ  590 (729)
T ss_pred             CCCCCHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCC--CCHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHH
T ss_conf             367603536898775310004444556743347882--238999999999986038888999999998779678778877


Q ss_pred             ----------CCCCHHHHHHHHHHHHH---HCCCCCCCHHHHHHHHC
Q ss_conf             ----------89868999999999987---43898106889545421
Q gi|254780916|r  354 ----------WIDNVQELKNILLRAVI---GLKDSHLTEDRFVLLLS  387 (482)
Q Consensus       354 ----------WPGNvREL~n~i~r~~i---~~~~~~i~~~~~~~~l~  387 (482)
                                -|=-||||+.+|+-+-.   +.-.+.-++.|+...+.
T Consensus       591 ~e~~s~~rssIPITVRQLEAIiRI~ESLAKm~Ls~~ate~hV~EA~R  637 (729)
T KOG0481         591 HEQDSDKRSSIPITVRQLEAIIRIAESLAKMELSPFATEAHVEEALR  637 (729)
T ss_pred             HHHCCCCCCCCCEEHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHH
T ss_conf             54312546777635899999999998887610785466777999998


No 296
>COG1493 HprK Serine kinase of the HPr protein, regulates carbohydrate metabolism [Signal transduction mechanisms]
Probab=94.60  E-value=0.1  Score=31.73  Aligned_cols=103  Identities=14%  Similarity=0.136  Sum_probs=55.2

Q ss_pred             CCCCCHHHHHHHHHHHCCCCCEEEEE-CCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             46988899999999857898399992-68999999988850574322222222222222222222222222222111111
Q gi|254780916|r   62 NCEDDKENILKNIVDKIPIVPIIVQT-TQDNIKILNCFLYNRISKFFLNLVSRKQLCDSIICALREGVVPSQENEHCALD  140 (482)
Q Consensus        62 mP~~dGlell~~i~~~~p~ipvIiiT-~~~~~~~~~~a~~~g~~d~l~KP~~~~~L~~~i~~al~~~~~~~~~~~~~~~~  140 (482)
                      ||..+-...+.++.  ..+.|.|++| +....+.+..+++.+-.--+.-+....+|...+..-+.+...++ ..-|..+-
T Consensus        65 ~~~~~r~~~i~~~~--~~~~P~iI~sk~~~~p~~l~~~a~~~~~pil~s~~~ts~l~~~l~~yL~~~lA~~-~~vHGvl~  141 (308)
T COG1493          65 LSSEERKKRIGKLF--SLDTPALIVSKGLPIPEELLDAAKKYNIPILTSKLSTSELSFTLTNYLSRPLAER-VNVHGVLL  141 (308)
T ss_pred             CCHHHHHHHHHHHH--CCCCCEEEEECCCCCCHHHHHHHHHCCCCEEEECCHHHHHHHHHHHHHHHHCCCC-EEEEEEEE
T ss_conf             58455899999974--7699779997899997899999887099669853318999999999861310520-25546899


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCCCHHHHHHHHHHHC
Q ss_conf             1122222222222222223443204887327774367999999842
Q gi|254780916|r  141 SLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHES  186 (482)
Q Consensus       141 ~LiG~S~~m~~v~~~i~~~a~~~~~vli~Ge~GtGK~~~A~~iH~~  186 (482)
                      .+.|                   .-|||+|++|.||+-+|=.+=..
T Consensus       142 ~I~G-------------------vGVLItG~SG~GKSElALeLi~r  168 (308)
T COG1493         142 DIFG-------------------VGVLITGPSGAGKSELALELIKR  168 (308)
T ss_pred             EEEE-------------------EEEEEECCCCCCHHHHHHHHHHH
T ss_conf             9942-------------------58999878988776899999984


No 297
>cd01384 MYSc_type_XI Myosin motor domain, plant-specific type XI myosin, involved in organelle transport. This catalytic (head) domain has ATPase activity and belongs to the larger group of P-loop NTPases. Myosins are actin-dependent molecular motors that play important roles in muscle contraction, cell motility, and organelle transport. The head domain is a molecular motor, which utilizes ATP hydrolysis to generate directed movement toward the plus end along actin filaments. A cyclical interaction between myosin and actin provides the driving force. Rates of ATP hydrolysis and consequently the speed of movement along actin filaments vary widely, from about 0.04 micrometer per second for myosin I to 4.5 micrometer per second for myosin II in skeletal muscle. Myosin II moves in discrete steps about 5-10 nm long and generates 1-5 piconewtons of force. Upon ATP binding, the myosin head dissociates from an actin filament. ATP hydrolysis causes the head to pivot and associate with a new act
Probab=94.55  E-value=0.044  Score=34.37  Aligned_cols=68  Identities=25%  Similarity=0.402  Sum_probs=34.1

Q ss_pred             CCCEEEEEECCCCCHHHHHHHHHH-H---CCCCCCCCCCCCCCCCCC-CCCCHHHHHCCCCCCCCCCCCCCCCCC
Q ss_conf             432048873277743679999998-4---267543321012346554-210024331125555322111001234
Q gi|254780916|r  161 DCAIPIMIQGEFGVGKKRLSRFIH-E---SGKRAFFPFFIVNCGMID-QDKIEKFLFGDVDLQTKNSAQFLGKFI  230 (482)
Q Consensus       161 ~~~~~vli~Ge~GtGK~~~A~~iH-~---~s~r~~~~fi~v~c~~~~-~~~~e~~lFG~~~~~~~~~~~~~g~~~  230 (482)
                      ..+..|+|.||+|+||+..++.|= .   .|......--.+...-+. .-++|  =||..+-...+.+.|-|++-
T Consensus        86 ~~nQsIiiSGESGAGKTes~K~il~yL~~~~~~~~~~~~~i~~~il~~npiLE--AFGNAkT~~N~NSSRFGK~i  158 (674)
T cd01384          86 GKSQSILVSGESGAGKTETTKMLMRYLAYMGGRAGVEGRTVEQQVLESNPVLE--AFGNAKTVRNNNSSRFGKFV  158 (674)
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHH--HHHCCCCCCCCCCCCCCEEE
T ss_conf             89966999558988889999999999999718887654169999987514999--85155656898767510678


No 298
>pfam03215 Rad17 Rad17 cell cycle checkpoint protein.
Probab=94.40  E-value=0.35  Score=28.01  Aligned_cols=119  Identities=12%  Similarity=0.056  Sum_probs=57.5

Q ss_pred             EEEECCCCHH----HHHHHHHHHHHHHHHHCCCCCCCCCCCCCCEEEEECC-------CCCCCCCCHHHHHHHHHHHHHH
Q ss_conf             4751664200----1889998888776420011235532123431565214-------3321111112333799988654
Q gi|254780916|r  236 TIVLEEPDAL----PLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTE-------KNLLPQVKSHVFRKDLYYRISV  304 (482)
Q Consensus       236 tl~l~ei~~L----~~~~Q~~Ll~~l~~~~~~~~g~~~~~~~~~RiIa~t~-------~~L~~~~~~g~fr~dLy~rL~~  304 (482)
                      .++++|+-..    +...+.-|+++|+...      ..|.-   =||+-|+       .+....-....|-+|++.-..+
T Consensus       131 iILIEE~Pn~~~~d~~~fr~~L~~~L~s~~------~~PlV---~IiSEt~s~~g~~~~~~~~~ta~rLlg~eIl~hp~i  201 (490)
T pfam03215       131 LILVEELPNQFYSDAEKFREVIREVLQSIW------HLPLI---FCLTECNSLEGDNNQDRFGIDAETIMTKDILIMPRI  201 (490)
T ss_pred             EEEEECCCCCCCCCHHHHHHHHHHHHHHCC------CCCEE---EEEEECCCCCCCCCCCCCCCHHHHHCCHHHHHCCCC
T ss_conf             999965887442366999999999997089------99879---999704666677643323210786359888708896


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHH
Q ss_conf             334467787744222255667776410112233332111110001223389868999999999987
Q gi|254780916|r  305 FLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQELKNILLRAVI  370 (482)
Q Consensus       305 ~~i~iPpLReR~eDI~~L~~~fl~~~~~~~~~~~~~ls~~a~~~L~~y~WPGNvREL~n~i~r~~i  370 (482)
                      ..|..=|..      |......|.+.+.+.++....-....++.+..- --|.||-=-|.++-.+.
T Consensus       202 ~~I~FNpIA------pT~M~KaL~~I~~kE~~~~~~~~~~~le~Ia~~-S~GDIRsAInsLQF~~~  260 (490)
T pfam03215       202 DTITFNPIA------PTFMKKALVRISVQEGKLKSPKSDSKLEVICQE-AGGDLRSAINSLQFSSS  260 (490)
T ss_pred             CEEEECCCC------HHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHH-CCCCHHHHHHHHHHHCC
T ss_conf             369868887------889999999999985765567520389999986-48729999999998626


No 299
>COG5022 Myosin heavy chain [Cytoskeleton]
Probab=94.37  E-value=0.045  Score=34.26  Aligned_cols=78  Identities=23%  Similarity=0.359  Sum_probs=45.7

Q ss_pred             CCCEEEEEECCCCCHHHHHHHHHHHCCCCCCCCCCCCC-CCCCCCCCCH---------HHHHCCCCCCCCCCCCCCCCCC
Q ss_conf             43204887327774367999999842675433210123-4655421002---------4331125555322111001234
Q gi|254780916|r  161 DCAIPIMIQGEFGVGKKRLSRFIHESGKRAFFPFFIVN-CGMIDQDKIE---------KFLFGDVDLQTKNSAQFLGKFI  230 (482)
Q Consensus       161 ~~~~~vli~Ge~GtGK~~~A~~iH~~s~r~~~~fi~v~-c~~~~~~~~e---------~~lFG~~~~~~~~~~~~~g~~~  230 (482)
                      .-+..|+|+||+|.||+--|+.|-++       |..|. |.+.....+|         -|=||..+-.-.+-+.|-|++-
T Consensus       150 ~eNQtIiISGESGAGKTe~aK~ImqY-------lasv~~s~~~~~~~iE~~ILaTNPILEAFGNAkTvRNdNSSRFGKyi  222 (1463)
T COG5022         150 KENQTIIISGESGAGKTENAKRIMQY-------LASVTSSSTVEISSIEKQILATNPILEAFGNAKTVRNDNSSRFGKYI  222 (1463)
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHH-------HHHHCCCCCCHHHHHHHHHHHCCHHHHHHCCCCCCCCCCCCCCCCEE
T ss_conf             89853999647888830889999999-------99860678621899999998416288872364002367731234518


Q ss_pred             C---CCCCEEEECCCCHH
Q ss_conf             4---66714751664200
Q gi|254780916|r  231 E---ANGGTIVLEEPDAL  245 (482)
Q Consensus       231 ~---a~~Gtl~l~ei~~L  245 (482)
                      +   -++|++.=..|+.-
T Consensus       223 kI~Fd~~g~I~GA~I~~Y  240 (1463)
T COG5022         223 KIEFDENGEICGAKIETY  240 (1463)
T ss_pred             EEEECCCCCEECHHHHHH
T ss_conf             999779984510223555


No 300
>TIGR00634 recN DNA repair protein RecN; InterPro: IPR004604   DNA repair protein RecN is thought to be DNA damage inducible and involved in recombinational processes. The N-terminal region of most of the bacterial RecN proteins sequenced to date contains an ATP/GTP binding domain within an SMC-like motif. SMC-like domains are involved in chromosomal scaffolding and segregation. It is possible that the function of RecN in homologous recombination is either structural or enzymatic or both. RecN may be involved in the proper positioning of the recombining segments of DNA, ensuring normal recombination. The observation that inactivation of this gene leads to a decreased transformation efficiency, as well as increased sensitivity to DNA-damaging agents, may be due to some defect in chromosomal partitioning or positioning during these recombination-dependent processes . The protein may function presynaptically to process double-stranded breaks to produce 3 single-stranded DNA intermediates during recombination. ; GO: 0005524 ATP binding, 0006281 DNA repair, 0006310 DNA recombination.
Probab=94.35  E-value=0.031  Score=35.40  Aligned_cols=34  Identities=24%  Similarity=0.276  Sum_probs=26.9

Q ss_pred             EEECCCCCHHHHHHHHHHH-CCCCCCCCCCCCCCC
Q ss_conf             8732777436799999984-267543321012346
Q gi|254780916|r  167 MIQGEFGVGKKRLSRFIHE-SGKRAFFPFFIVNCG  200 (482)
Q Consensus       167 li~Ge~GtGK~~~A~~iH~-~s~r~~~~fi~v~c~  200 (482)
                      .|+|||||||+++--+||- .|.|.+..+|.-.|.
T Consensus        26 VLTGETGaGKSm~i~Al~LL~G~r~~~~~vR~G~~   60 (605)
T TIGR00634        26 VLTGETGAGKSMIIDALSLLLGQRAGASLVRSGEN   60 (605)
T ss_pred             EEECCCCCCHHHHHHHHHHCCCCCCCCCEEECCCC
T ss_conf             43046455078877669870588547631233787


No 301
>COG1224 TIP49 DNA helicase TIP49, TBP-interacting protein [Transcription]
Probab=94.29  E-value=0.12  Score=31.40  Aligned_cols=68  Identities=22%  Similarity=0.230  Sum_probs=48.2

Q ss_pred             CCCCCCCCCCCCCCC---CCCCCCCCCCCCCCCEEEEEECCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCC
Q ss_conf             211111111222222---222222222234432048873277743679999998426754332101234655
Q gi|254780916|r  134 NEHCALDSLIAVSPA---MIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHESGKRAFFPFFIVNCGMI  202 (482)
Q Consensus       134 ~~~~~~~~LiG~S~~---m~~v~~~i~~~a~~~~~vli~Ge~GtGK~~~A~~iH~~s~r~~~~fi~v~c~~~  202 (482)
                      ......++++|+-.+   +--+.+.++.=--.-.-|||.|++||||+.+|-+|-..- ..+-||++++.+.+
T Consensus        33 ~~k~~~dG~VGQ~~AReAaGvIv~mik~gk~aGrgiLi~GppgTGKTAlA~gIa~eL-G~dvPF~~isgsEi  103 (450)
T COG1224          33 KAKFIGDGLVGQEEAREAAGVIVKMIKQGKMAGRGILIVGPPGTGKTALAMGIAREL-GEDVPFVAISGSEI  103 (450)
T ss_pred             CEEECCCCCCCHHHHHHHHHHHHHHHHHCCCCCCEEEEECCCCCCHHHHHHHHHHHH-CCCCCCEEECCCEE
T ss_conf             874768861124988876259999997176666179997899976889999999985-89998215013322


No 302
>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=94.27  E-value=0.027  Score=35.83  Aligned_cols=32  Identities=25%  Similarity=0.159  Sum_probs=25.1

Q ss_pred             EEEECCCCCHHHHHHHHHHHCC--CCCCCCCCCC
Q ss_conf             8873277743679999998426--7543321012
Q gi|254780916|r  166 IMIQGEFGVGKKRLSRFIHESG--KRAFFPFFIV  197 (482)
Q Consensus       166 vli~Ge~GtGK~~~A~~iH~~s--~r~~~~fi~v  197 (482)
                      =||.||||+||+++|-+|+.+-  ...++..|++
T Consensus       152 GLiCG~TGSGKSTl~AaiY~~~l~t~pdRKivT~  185 (374)
T TIGR02525       152 GLICGETGSGKSTLAAAIYRHCLETYPDRKIVTY  185 (374)
T ss_pred             EEECCCCCCCHHHHHHHHHHHHCCCCCCCEEEEE
T ss_conf             0221778972899999999985074889707986


No 303
>TIGR02782 TrbB_P P-type conjugative transfer ATPase TrbB; InterPro: IPR014149   This entry represents TrbB, a protein, which is encoded in the trb locus of Agrobacterium Ti plasmids where it is involved in the type IV secretion system for plasmid conjugative transfer . TrbB is a homologue of the vir system VirB11 ATPase , and the Flp pilus system ATPase TadA ..
Probab=94.26  E-value=0.018  Score=37.16  Aligned_cols=51  Identities=22%  Similarity=0.268  Sum_probs=36.0

Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCCCHHHHHHHHHHH
Q ss_conf             111111112222222222222222344320488732777436799999984
Q gi|254780916|r  135 EHCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHE  185 (482)
Q Consensus       135 ~~~~~~~LiG~S~~m~~v~~~i~~~a~~~~~vli~Ge~GtGK~~~A~~iH~  185 (482)
                      .-+++++++-..---..-++.+..+-.+..+|||.|=|||||+++|.|+=+
T Consensus       111 ~vfTLDdYV~~gimtaaQ~d~l~~Av~ar~NIlv~GGTGSGKTTLaNAlla  161 (315)
T TIGR02782       111 RVFTLDDYVEAGIMTAAQRDVLREAVAARKNILVVGGTGSGKTTLANALLA  161 (315)
T ss_pred             CCCCCHHHHHHCCCCHHHHHHHHHHHHHCCCEEEECCCCCCHHHHHHHHHH
T ss_conf             104707776404455789999999997129889981458857999999999


No 304
>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=94.23  E-value=0.02  Score=36.73  Aligned_cols=47  Identities=17%  Similarity=0.068  Sum_probs=35.1

Q ss_pred             CCCCCCCCCCCCCCEEEEEECCCCCHHHHHHHHHHHCCCCCCCCCCCC
Q ss_conf             222222222344320488732777436799999984267543321012
Q gi|254780916|r  150 IQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHESGKRAFFPFFIV  197 (482)
Q Consensus       150 ~~v~~~i~~~a~~~~~vli~Ge~GtGK~~~A~~iH~~s~r~~~~fi~v  197 (482)
                      .++.+.+..+.....+|+|.|++|+||+.+.+++-..-+.. ..++++
T Consensus        12 ~~~~~~L~~~v~~~~nIlIsG~tGSGKTTll~al~~~i~~~-~rivti   58 (186)
T cd01130          12 PLQAAYLWLAVEARKNILISGGTGSGKTTLLNALLAFIPPD-ERIITI   58 (186)
T ss_pred             HHHHHHHHHHHHCCCCEEEECCCCCCHHHHHHHHHHHCCCC-CCEEEE
T ss_conf             99999999999859989998999998999999999613345-645984


No 305
>pfam02310 B12-binding B12 binding domain. This domain binds to B12 (adenosylcobamide), it is found in several enzymes, such as glutamate mutase, methionine synthase and methylmalonyl-CoA mutase.
Probab=94.22  E-value=0.46  Score=27.16  Aligned_cols=75  Identities=15%  Similarity=0.240  Sum_probs=55.0

Q ss_pred             CCCHHHHHHHHHHHHHCCCEEEEECC----HH-HHHHHCCCCCEEEEECCC-CCCCH-HHHHHHHHHHCCCCCEEEEECC
Q ss_conf             69989999999999988988999893----79-999860899899997854-69888-9999999985789839999268
Q gi|254780916|r   17 DKDDEQIKIIKDHVESYGYDVFIVNV----SD-LSTISKIQVNVIFLSLIN-CEDDK-ENILKNIVDKIPIVPIIVQTTQ   89 (482)
Q Consensus        17 DDd~~~~~~l~~~L~~~G~~v~~a~~----~a-l~~l~~~~~dlillD~~m-P~~dG-lell~~i~~~~p~ipvIiiT~~   89 (482)
                      |=-|.-...++..|+..||+|...+.    .+ .+.+.+.+||+|-+...| ...+. .++++.+|+..|++++|+--.+
T Consensus        11 ~~~plGl~~la~~l~~~G~~V~~~d~~~~~~~i~~~i~~~~pdiVgiS~~~~~~~~~~~~l~~~ik~~~p~~~iv~GG~~   90 (121)
T pfam02310        11 DLHPLGLNYVAAALRAAGFEVILLGADVPPEDIVEAIRAENPDVVGLSALMTTNLPAAKELARLLKRIRPGVKVVVGGPH   90 (121)
T ss_pred             CCCHHHHHHHHHHHHHCCCCCCCEECCCCHHHHHHHHHHCCCCEEEEECCCCCCCHHHHHHHHHHHHHCCCCEEEEECCC
T ss_conf             75848999999999985995001024799999999999809999999523211211368999999985989759983876


Q ss_pred             CC
Q ss_conf             99
Q gi|254780916|r   90 DN   91 (482)
Q Consensus        90 ~~   91 (482)
                      .+
T Consensus        91 ~t   92 (121)
T pfam02310        91 PT   92 (121)
T ss_pred             CC
T ss_conf             34


No 306
>cd03221 ABCF_EF-3 ABCF_EF-3  Elongation factor 3 (EF-3) is a cytosolic protein required by fungal ribosomes for in vitro protein synthesis and for in vivo growth.  EF-3 stimulates the binding of the EF-1: GTP: aa-tRNA ternary complex to the ribosomal A site by facilitated release of the deacylated tRNA from the E site.  The reaction requires ATP hydrolysis.  EF-3 contains two ATP nucleotide binding sequence (NBS) motifs.  NBSI is sufficient for the intrinsic ATPase activity. NBSII is essential for the ribosome-stimulated functions.
Probab=94.22  E-value=0.11  Score=31.51  Aligned_cols=100  Identities=15%  Similarity=0.090  Sum_probs=59.7

Q ss_pred             CCCCCCCCCCCCCEEEEEECCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCHHHHHCCCCCCCCCCCCCCCC--
Q ss_conf             222222223443204887327774367999999842675433210123465542100243311255553221110012--
Q gi|254780916|r  151 QVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFGDVDLQTKNSAQFLGK--  228 (482)
Q Consensus       151 ~v~~~i~~~a~~~~~vli~Ge~GtGK~~~A~~iH~~s~r~~~~fi~v~c~~~~~~~~e~~lFG~~~~~~~~~~~~~g~--  228 (482)
                      .+++.+.--.....-|-|.|++|+||+++.+.|...-....+.+ .++..         .-+++.....|...++..+  
T Consensus        14 ~vl~~is~~i~~ge~~~l~G~NGsGKTTl~~~l~G~~~~~~G~i-~~~~~---------~~i~y~~QLSgGqkqr~~la~   83 (144)
T cd03221          14 LLLKDISLTINPGDRIGLVGRNGAGKSTLLKLIAGELEPDEGIV-TWGST---------VKIGYFEQLSGGEKMRLALAK   83 (144)
T ss_pred             EEEEEEEEEECCCCEEEEECCCCCCHHHHHHHHHCCCCCCCEEE-EECCC---------CEEEEEHHCCHHHHHHHHHHH
T ss_conf             99963489987999999998999849999999848988985099-99996---------089987007999999999999


Q ss_pred             CCCCCCCEEEECCCCH-HHHHHHHHHHHHHHHH
Q ss_conf             3446671475166420-0188999888877642
Q gi|254780916|r  229 FIEANGGTIVLEEPDA-LPLAVQGRIYNFIETG  260 (482)
Q Consensus       229 ~~~a~~Gtl~l~ei~~-L~~~~Q~~Ll~~l~~~  260 (482)
                      .-..+.-.++|||... |.+..+..+.+.|.+.
T Consensus        84 al~~~p~iliLDEPt~~LD~~~~~~i~~~l~~~  116 (144)
T cd03221          84 LLLENPNLLLLDEPTNHLDLESIEALEEALKEY  116 (144)
T ss_pred             HHCCCCCEEEEECCCCCCCHHHHHHHHHHHHHC
T ss_conf             972599899995775558999999999999970


No 307
>COG1373 Predicted ATPase (AAA+ superfamily) [General function prediction only]
Probab=94.21  E-value=0.086  Score=32.28  Aligned_cols=78  Identities=21%  Similarity=0.236  Sum_probs=45.1

Q ss_pred             EEEEECCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCH--HHHHCCCCCCCCCCCCCCCCCCCCCCCEEEECCC
Q ss_conf             48873277743679999998426754332101234655421002--4331125555322111001234466714751664
Q gi|254780916|r  165 PIMIQGEFGVGKKRLSRFIHESGKRAFFPFFIVNCGMIDQDKIE--KFLFGDVDLQTKNSAQFLGKFIEANGGTIVLEEP  242 (482)
Q Consensus       165 ~vli~Ge~GtGK~~~A~~iH~~s~r~~~~fi~v~c~~~~~~~~e--~~lFG~~~~~~~~~~~~~g~~~~a~~Gtl~l~ei  242 (482)
                      .++|.|+.++||+++.+.++......   ++-+|--.+..+..+  ..+...        ..   .... ...-+|||||
T Consensus        39 i~~i~GpR~~GKTtllk~l~~~~~~~---~iy~~~~d~~~~~~~l~d~~~~~--------~~---~~~~-~~~yifLDEI  103 (398)
T COG1373          39 IILILGPRQVGKTTLLKLLIKGLLEE---IIYINFDDLRLDRIELLDLLRAY--------IE---LKER-EKSYIFLDEI  103 (398)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHCCCC---EEEEECCCCCCCHHHHHHHHHHH--------HH---HHCC-CCCEEEEEEE
T ss_conf             49998886477899999999747773---59997362000135677899999--------98---5222-5745999833


Q ss_pred             CHHHHHHHHHHHHHHH
Q ss_conf             2001889998888776
Q gi|254780916|r  243 DALPLAVQGRIYNFIE  258 (482)
Q Consensus       243 ~~L~~~~Q~~Ll~~l~  258 (482)
                      +..+.. +..|-.+.+
T Consensus       104 q~v~~W-~~~lk~l~d  118 (398)
T COG1373         104 QNVPDW-ERALKYLYD  118 (398)
T ss_pred             CCCHHH-HHHHHHHHC
T ss_conf             376108-999999975


No 308
>pfam03969 AFG1_ATPase AFG1-like ATPase. This family of proteins contains a P-loop motif and are predicted to be ATPases.
Probab=94.17  E-value=0.13  Score=31.09  Aligned_cols=118  Identities=15%  Similarity=0.057  Sum_probs=60.5

Q ss_pred             CCEEEEEECCCCCHHHHHHHHHHHCCCCCCC---CCCCCCCCCCCCCCCHHHHHCCCCCCCCCCCCCCCCCCCCCC-CEE
Q ss_conf             3204887327774367999999842675433---210123465542100243311255553221110012344667-147
Q gi|254780916|r  162 CAIPIMIQGEFGVGKKRLSRFIHESGKRAFF---PFFIVNCGMIDQDKIEKFLFGDVDLQTKNSAQFLGKFIEANG-GTI  237 (482)
Q Consensus       162 ~~~~vli~Ge~GtGK~~~A~~iH~~s~r~~~---~fi~v~c~~~~~~~~e~~lFG~~~~~~~~~~~~~g~~~~a~~-Gtl  237 (482)
                      ...-+.|.|..|+||+++--..++.-+-..+   +|... +..+-..+  ..+-|..+..    . ... =+.|++ -.|
T Consensus        60 ~~kGlYl~G~VGrGKTmLMDlFy~~lp~~~K~R~HFh~F-M~~vH~~l--~~~~~~~dpl----~-~va-~~l~~~~~lL  130 (361)
T pfam03969        60 PVRGLYLWGGVGRGKTHLMDSFFESLPGERKRRTHFHRF-MFRVHDEL--TTLQGGDDPL----P-IAA-DRFANEARLL  130 (361)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHHHCCCCCCCCCCHHHH-HHHHHHHH--HHHHCCCCCH----H-HHH-HHHHHCCCEE
T ss_conf             998689889988869999999998677534445667899-99999999--9976677638----9-999-9997258779


Q ss_pred             EECCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCEEEEECCCCCCCCCCHHHHHHHH
Q ss_conf             5166420018899988887764200112355321234315652143321111112333799
Q gi|254780916|r  238 VLEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDL  298 (482)
Q Consensus       238 ~l~ei~~L~~~~Q~~Ll~~l~~~~~~~~g~~~~~~~~~RiIa~t~~~L~~~~~~g~fr~dL  298 (482)
                      |+||.+--.. .-+.+|.-|-+.-|.         ..+.+|++||..+++|-..|.-|+.+
T Consensus       131 CfDEFqV~DI-aDAMIL~rLf~~Lf~---------~gvvlV~TSN~~P~~LY~~GLqR~~F  181 (361)
T pfam03969       131 CFDEFEVDDI-GDAMILGRLFEALFA---------RGVSLVATSNTAPEQLYRNGLNRQRF  181 (361)
T ss_pred             EEEEEEECCH-HHHHHHHHHHHHHHH---------CCCEEEEECCCCHHHHHCCCCCHHHH
T ss_conf             9763561678-889999999999997---------79789980899989983687417788


No 309
>PRK06585 holA DNA polymerase III subunit delta; Reviewed
Probab=94.16  E-value=0.51  Score=26.85  Aligned_cols=188  Identities=14%  Similarity=0.090  Sum_probs=96.7

Q ss_pred             CEEEEEECCCCCHHHHHHHHH-HHCCCCCCCCCCCCC--CCCCCCCCCHHHHHCCCCCCCCCCCCCCCCCCCCCCCEEEE
Q ss_conf             204887327774367999999-842675433210123--46554210024331125555322111001234466714751
Q gi|254780916|r  163 AIPIMIQGEFGVGKKRLSRFI-HESGKRAFFPFFIVN--CGMIDQDKIEKFLFGDVDLQTKNSAQFLGKFIEANGGTIVL  239 (482)
Q Consensus       163 ~~~vli~Ge~GtGK~~~A~~i-H~~s~r~~~~fi~v~--c~~~~~~~~e~~lFG~~~~~~~~~~~~~g~~~~a~~Gtl~l  239 (482)
                      -.-+|+.||----+...++.| .......+.||-.++  ...+..+  .+.||.+-.        ...+|.  +.-.+++
T Consensus        20 ~~~~LlyG~d~glv~e~~~~l~~~~~~~~~~~f~~~~l~~~el~~d--~~~l~de~~--------t~slF~--~~rlI~i   87 (343)
T PRK06585         20 IRAVLLYGPDRGLVRERARRLAKSVVDDPDDPFAVVRLDGDELDAD--PARLEDEAN--------TISLFG--GRRLIWV   87 (343)
T ss_pred             CEEEEEECCCHHHHHHHHHHHHHHHCCCCCCCCEEEEECHHHHHCC--HHHHHHHHH--------CCCCCC--CCEEEEE
T ss_conf             6589996387647999999999972556678741577479988339--999999984--------768768--9848997


Q ss_pred             CCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCEEEEECCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             66420018899988887764200112355321234315652143321111112333799988654334467787744222
Q gi|254780916|r  240 EEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYYRISVFLINISTLRSRSEDI  319 (482)
Q Consensus       240 ~ei~~L~~~~Q~~Ll~~l~~~~~~~~g~~~~~~~~~RiIa~t~~~L~~~~~~g~fr~dLy~rL~~~~i~iPpLReR~eDI  319 (482)
                      ++.++       ++...|++---.+.       -++.+|..+ .+|..   ...+|+ +|-. +...+.+|--.+=..++
T Consensus        88 ~~~~d-------~~~~~l~~~l~~~~-------~~~~lIi~a-~~L~k---~skLrk-~~e~-~~~~~~i~cY~d~~~~l  147 (343)
T PRK06585         88 RAGGK-------SLAAALKALLAEPP-------GDAFIVIEA-GDLKK---GSSLRK-LFET-AASAAAIPCYADDERDL  147 (343)
T ss_pred             ECCCH-------HHHHHHHHHHHCCC-------CCEEEEEEC-CCCCC---CCHHHH-HHHH-CCCEEEEEECCCCHHHH
T ss_conf             26872-------56999999981789-------982899973-89773---118999-9986-47869995006998899


Q ss_pred             HHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHH-CCCCCCCHHHHHHHHCCCC
Q ss_conf             2556677764101122333321111100012233898689999999999874-3898106889545421244
Q gi|254780916|r  320 PWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQELKNILLRAVIG-LKDSHLTEDRFVLLLSREG  390 (482)
Q Consensus       320 ~~L~~~fl~~~~~~~~~~~~~ls~~a~~~L~~y~WPGNvREL~n~i~r~~i~-~~~~~i~~~~~~~~l~~~~  390 (482)
                      +.++..++.++    |.   +++++|++.|..+- .||-..++|-++.+... ...+.|+.+++...+....
T Consensus       148 ~~~i~~~l~~~----g~---~i~~~a~~~L~~~~-g~d~~~~~~EleKL~ly~~~~~~It~edv~~~v~~~~  211 (343)
T PRK06585        148 ARLIDDELAKA----GL---RITPDARAYLVALL-GGDRLASRNEIEKLALYAHGKGEITLDDVRAVVGDAS  211 (343)
T ss_pred             HHHHHHHHHHC----CC---CCCHHHHHHHHHHC-CCHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHCCCC
T ss_conf             99999999982----99---97799999999873-4279999999999999848999789999999868641


No 310
>PRK08769 DNA polymerase III subunit delta'; Validated
Probab=94.08  E-value=0.095  Score=32.00  Aligned_cols=109  Identities=18%  Similarity=0.155  Sum_probs=57.0

Q ss_pred             CCCCCCCCCCCCCCCC---CCCEEEEEECCCCCHHHHHHHHHHHCCCC-CCCCCCCCCCCCCCCCCCHHHHHC-CCCC--
Q ss_conf             2222222222222234---43204887327774367999999842675-433210123465542100243311-2555--
Q gi|254780916|r  145 VSPAMIQVVDLARKAG---DCAIPIMIQGEFGVGKKRLSRFIHESGKR-AFFPFFIVNCGMIDQDKIEKFLFG-DVDL--  217 (482)
Q Consensus       145 ~S~~m~~v~~~i~~~a---~~~~~vli~Ge~GtGK~~~A~~iH~~s~r-~~~~fi~v~c~~~~~~~~e~~lFG-~~~~--  217 (482)
                      -+|.-+..++++.++-   ....-.|+.|+.|+||..+|+.+=..--- ...+-..-+|..    ++.   -| |.+-  
T Consensus         5 ~~PWq~~~~~~L~~~i~~~rl~HA~Lf~Gp~G~GK~~~A~~~A~~llc~~~~~~~~~~~~~----~i~---~g~HPD~~~   77 (319)
T PRK08769          5 FSPWQQRAFDQTVAALDAGRLGHGLLICGPEGLGKRAVALALAEHVLASGPDPALAQRTRQ----LIA---AGTHPDLQL   77 (319)
T ss_pred             CCCCCHHHHHHHHHHHHCCCCCCEEEEECCCCCCHHHHHHHHHHHHHCCCCCCCCCCHHHH----HHH---CCCCCCEEE
T ss_conf             5877689999999999769942068758999878999999999998379979765433889----996---689989687


Q ss_pred             ------CCCCC-------CCCCCCCC-------CCCCCEEEECCCCHHHHHHHHHHHHHHHHH
Q ss_conf             ------53221-------11001234-------466714751664200188999888877642
Q gi|254780916|r  218 ------QTKNS-------AQFLGKFI-------EANGGTIVLEEPDALPLAVQGRIYNFIETG  260 (482)
Q Consensus       218 ------~~~~~-------~~~~g~~~-------~a~~Gtl~l~ei~~L~~~~Q~~Ll~~l~~~  260 (482)
                            .++..       .+-..+.+       +...-.+++|+.+.|....+..||..|||-
T Consensus        78 i~~~~~~~~~k~k~~I~IdqiR~l~~~~~~~p~~g~~KV~IId~Ad~mn~~AaNalLK~LEEP  140 (319)
T PRK08769         78 VSFIPNRTGDKLRTEIVIEQVREISQKLALTPQYGIAQVVIVDPADAINRSACNALLKTLEEP  140 (319)
T ss_pred             EECCCCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCCCEEEEECCHHHCCHHHHHHHHHHHCCC
T ss_conf             753444454311234869999999999613720279569998066752899999999982279


No 311
>KOG0991 consensus
Probab=94.01  E-value=0.046  Score=34.23  Aligned_cols=187  Identities=17%  Similarity=0.223  Sum_probs=95.8

Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCE-EEEEECCCCCHHHHHHHHHH-H-CCCCCCCCCCCCCCCCCCC-CCCH--HHH
Q ss_conf             111112222222222222222344320-48873277743679999998-4-2675433210123465542-1002--433
Q gi|254780916|r  138 ALDSLIAVSPAMIQVVDLARKAGDCAI-PIMIQGEFGVGKKRLSRFIH-E-SGKRAFFPFFIVNCGMIDQ-DKIE--KFL  211 (482)
Q Consensus       138 ~~~~LiG~S~~m~~v~~~i~~~a~~~~-~vli~Ge~GtGK~~~A~~iH-~-~s~r~~~~fi~v~c~~~~~-~~~e--~~l  211 (482)
                      .+.+++|+-..|.++.-.+ +  .-+. +++|.|++||||++.+..+- . .++.-......+|.+.--. +.+-  -..
T Consensus        25 ~l~dIVGNe~tv~rl~via-~--~gnmP~liisGpPG~GKTTsi~~LAr~LLG~~~ke~vLELNASdeRGIDvVRn~IK~  101 (333)
T KOG0991          25 VLQDIVGNEDTVERLSVIA-K--EGNMPNLIISGPPGTGKTTSILCLARELLGDSYKEAVLELNASDERGIDVVRNKIKM  101 (333)
T ss_pred             HHHHHHCCHHHHHHHHHHH-H--CCCCCCEEEECCCCCCHHHHHHHHHHHHHCHHHHHHHHHCCCCCCCCCHHHHHHHHH
T ss_conf             9988217798999999999-7--289986675279998616489999999838066657632057655460899999999


Q ss_pred             HCCCCCCCCCCCCCCCCCCCCCCCEEEECCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCEEEEECCCCCCCCCCH
Q ss_conf             11255553221110012344667147516642001889998888776420011235532123431565214332111111
Q gi|254780916|r  212 FGDVDLQTKNSAQFLGKFIEANGGTIVLEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKS  291 (482)
Q Consensus       212 FG~~~~~~~~~~~~~g~~~~a~~Gtl~l~ei~~L~~~~Q~~Ll~~l~~~~~~~~g~~~~~~~~~RiIa~t~~~L~~~~~~  291 (482)
                      |..++          -.+-....-.+.|||-+.|.-..|..|-|.++=.           ...+|+..++|.. ++.++-
T Consensus       102 FAQ~k----------v~lp~grhKIiILDEADSMT~gAQQAlRRtMEiy-----------S~ttRFalaCN~s-~KIiEP  159 (333)
T KOG0991         102 FAQKK----------VTLPPGRHKIIILDEADSMTAGAQQALRRTMEIY-----------SNTTRFALACNQS-EKIIEP  159 (333)
T ss_pred             HHHHH----------CCCCCCCEEEEEEECCCHHHHHHHHHHHHHHHHH-----------CCCCHHHHHHCCH-HHHHHH
T ss_conf             98720----------3489985248996152202068999999999997-----------0632000001542-132226


Q ss_pred             HHHHHH-H-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHH
Q ss_conf             233379-9-98865433446778774422225566777641011223333211111000122338986899999999998
Q gi|254780916|r  292 HVFRKD-L-YYRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQELKNILLRAV  369 (482)
Q Consensus       292 g~fr~d-L-y~rL~~~~i~iPpLReR~eDI~~L~~~fl~~~~~~~~~~~~~ls~~a~~~L~~y~WPGNvREL~n~i~r~~  369 (482)
                      =.=|-- | |.||              +|--.|.+  +.+.++.   ....++++.++++. +---|..||=-|-++-.+
T Consensus       160 IQSRCAiLRyskl--------------sd~qiL~R--l~~v~k~---Ekv~yt~dgLeaii-fta~GDMRQalNnLQst~  219 (333)
T KOG0991         160 IQSRCAILRYSKL--------------SDQQILKR--LLEVAKA---EKVNYTDDGLEAII-FTAQGDMRQALNNLQSTV  219 (333)
T ss_pred             HHHHHHHHHHCCC--------------CHHHHHHH--HHHHHHH---HCCCCCCCHHHHHH-HHCCCHHHHHHHHHHHHH
T ss_conf             7734576532226--------------78999999--9999987---07887711477855-441661999999999874


No 312
>KOG1051 consensus
Probab=93.97  E-value=0.021  Score=36.68  Aligned_cols=108  Identities=19%  Similarity=0.245  Sum_probs=57.4

Q ss_pred             CCCCCCCCC-CCCCCCCCCCCCCCCCCCEEEEEECCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCHHHHHCCC
Q ss_conf             111111222-2222222222222344320488732777436799999984267543321012346554210024331125
Q gi|254780916|r  137 CALDSLIAV-SPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFGDV  215 (482)
Q Consensus       137 ~~~~~LiG~-S~~m~~v~~~i~~~a~~~~~vli~Ge~GtGK~~~A~~iH~~s~r~~~~fi~v~c~~~~~~~~e~~lFG~~  215 (482)
                      ...++.+|. ...++++.+-+.+--. +-| +|.|++|+||+.++..+-+.-.+.+-|-.--++..+.-+ +.+...|.+
T Consensus       183 gk~dPvigr~deeirRvi~iL~Rr~k-~NP-vLVG~~gvgktaiv~gla~ri~~G~vp~~l~~~~l~~l~-~g~l~aGa~  259 (898)
T KOG1051         183 GKLDPVIGRHDEEIRRVIEILSRKTK-NNP-VLVGEPGVGKTAIVEGLAQRIATGDVPETLKDKKLIALD-FGSLVAGAK  259 (898)
T ss_pred             CCCCCCCCCCHHHHHHHHHHHHCCCC-CCC-EEEECCCCCCHHHHHHHHHHHHCCCCCCCCCCCCEEEEE-HHHCCCCCC
T ss_conf             68788658852889999999814678-996-698368777216899999876617888533455248987-000035864


Q ss_pred             -CC-CCCCCCCCCCCCCCCCCC-EEEECCCCHHHH
Q ss_conf             -55-532211100123446671-475166420018
Q gi|254780916|r  216 -DL-QTKNSAQFLGKFIEANGG-TIVLEEPDALPL  247 (482)
Q Consensus       216 -~~-~~~~~~~~~g~~~~a~~G-tl~l~ei~~L~~  247 (482)
                       .+ +-+-.....-..+.+++| .||++|++.+-.
T Consensus       260 ~rge~E~rlk~l~k~v~~~~~gvILfigelh~lvg  294 (898)
T KOG1051         260 RRGEFEERLKELLKEVESGGGGVILFLGELHWLVG  294 (898)
T ss_pred             CCHHHHHHHHHHHHHHHCCCCCEEEEECCEEEEEC
T ss_conf             21278899999999985479868998321432204


No 313
>COG1204 Superfamily II helicase [General function prediction only]
Probab=93.94  E-value=0.033  Score=35.20  Aligned_cols=105  Identities=14%  Similarity=0.130  Sum_probs=55.8

Q ss_pred             CCEEEECCCHHHHHHHHHH--HHHCCCEEEEE-CC-----------------HH-HHHHHCC------CCCEEEEE-CCC
Q ss_conf             8389986998999999999--99889889998-93-----------------79-9998608------99899997-854
Q gi|254780916|r   11 KRVLIIDKDDEQIKIIKDH--VESYGYDVFIV-NV-----------------SD-LSTISKI------QVNVIFLS-LIN   62 (482)
Q Consensus        11 ~rILIVDDd~~~~~~l~~~--L~~~G~~v~~a-~~-----------------~a-l~~l~~~------~~dlillD-~~m   62 (482)
                      +-|.||=.-.-..+....+  ++..|++|... ++                 .+ +..+.++      ..++|++| +.|
T Consensus        78 k~vYivPlkALa~Ek~~~~~~~~~~GirV~~~TgD~~~~~~~l~~~~ViVtT~EK~Dsl~R~~~~~~~~V~lvViDEiH~  157 (766)
T COG1204          78 KVVYIVPLKALAEEKYEEFSRLEELGIRVGISTGDYDLDDERLARYDVIVTTPEKLDSLTRKRPSWIEEVDLVVIDEIHL  157 (766)
T ss_pred             CEEEEECHHHHHHHHHHHHHHHHHCCCEEEEECCCCCCCHHHHCCCCEEEECHHHHHHHHHCCCCHHHCCCEEEEEEEEE
T ss_conf             38999075999999999866688659779996488655533414588799746786676506753334016899942101


Q ss_pred             CCCC-----HHHHHHHHHHHCCCCCEEEEECC-CCHHHHHHHHHCCCCCCCCCCCCCCCCCC
Q ss_conf             6988-----89999999985789839999268-99999998885057432222222222222
Q gi|254780916|r   63 CEDD-----KENILKNIVDKIPIVPIIVQTTQ-DNIKILNCFLYNRISKFFLNLVSRKQLCD  118 (482)
Q Consensus        63 P~~d-----Glell~~i~~~~p~ipvIiiT~~-~~~~~~~~a~~~g~~d~l~KP~~~~~L~~  118 (482)
                      -+.+     ...++.+++...+.+-+|-+|+. ++.+.  -|-+.++..+ ..+|.+..+..
T Consensus       158 l~d~~RG~~lE~iv~r~~~~~~~~rivgLSATlpN~~e--vA~wL~a~~~-~~~~rp~~l~~  216 (766)
T COG1204         158 LGDRTRGPVLESIVARMRRLNELIRIVGLSATLPNAEE--VADWLNAKLV-ESDWRPVPLRR  216 (766)
T ss_pred             CCCCCCCCEEHHHHHHHHHHCCCEEEEEEEEECCCHHH--HHHHHCCCCC-CCCCCCCCCCC
T ss_conf             48756586402279888852755179887311688899--9998588355-56778862015


No 314
>PRK13633 cobalt transporter ATP-binding subunit; Provisional
Probab=93.94  E-value=0.5  Score=26.86  Aligned_cols=24  Identities=21%  Similarity=0.389  Sum_probs=19.9

Q ss_pred             CCCEEEEEECCCCCHHHHHHHHHH
Q ss_conf             432048873277743679999998
Q gi|254780916|r  161 DCAIPIMIQGEFGVGKKRLSRFIH  184 (482)
Q Consensus       161 ~~~~~vli~Ge~GtGK~~~A~~iH  184 (482)
                      .-..-|-|.|++|+||++++|.|-
T Consensus        35 ~~GE~v~iiG~nGsGKSTL~r~l~   58 (281)
T PRK13633         35 KKGEFLVILGHNGSGKSTIAKHMN   58 (281)
T ss_pred             CCCCEEEEECCCCCHHHHHHHHHH
T ss_conf             799899999999984999999997


No 315
>cd01385 MYSc_type_IX Myosin motor domain, type IX myosins. Myosin IX is a processive single-headed motor, which might play a role in signalling. This catalytic (head) domain has ATPase activity and belongs to the larger group of P-loop NTPases. Myosins are actin-dependent molecular motors that play important roles in muscle contraction, cell motility, and organelle transport. The head domain is a molecular motor, which utilizes ATP hydrolysis to generate directed movement toward the plus end along actin filaments. A cyclical interaction between myosin and actin provides the driving force. Rates of ATP hydrolysis and consequently the speed of movement along actin filaments vary widely, from about 0.04 micrometer per second for myosin I to 4.5 micrometer per second for myosin II in skeletal muscle. Myosin II moves in discrete steps about 5-10 nm long and generates 1-5 piconewtons of force. Upon ATP binding, the myosin head dissociates from an actin filament. ATP hydrolysis causes the hea
Probab=93.93  E-value=0.077  Score=32.63  Aligned_cols=23  Identities=35%  Similarity=0.548  Sum_probs=19.3

Q ss_pred             CCCEEEEEECCCCCHHHHHHHHH
Q ss_conf             43204887327774367999999
Q gi|254780916|r  161 DCAIPIMIQGEFGVGKKRLSRFI  183 (482)
Q Consensus       161 ~~~~~vli~Ge~GtGK~~~A~~i  183 (482)
                      ..+..|+|.||+|+||+..++.|
T Consensus        92 ~~~QsIiiSGESGaGKTe~~K~i  114 (692)
T cd01385          92 KVNQCIVISGESGSGKTESTNFL  114 (692)
T ss_pred             CCCEEEEEECCCCCCHHHHHHHH
T ss_conf             99828999648989878999999


No 316
>KOG0735 consensus
Probab=93.93  E-value=0.058  Score=33.52  Aligned_cols=78  Identities=23%  Similarity=0.266  Sum_probs=47.5

Q ss_pred             CCCEEEEEECCCCCHHHHHHHHHHHC-CCCCCCCCCCCCCCCCCCCCCHHHHHCCCCCCCCCCCCCCCCCCCCCCCEEEE
Q ss_conf             43204887327774367999999842-67543321012346554210024331125555322111001234466714751
Q gi|254780916|r  161 DCAIPIMIQGEFGVGKKRLSRFIHES-GKRAFFPFFIVNCGMIDQDKIEKFLFGDVDLQTKNSAQFLGKFIEANGGTIVL  239 (482)
Q Consensus       161 ~~~~~vli~Ge~GtGK~~~A~~iH~~-s~r~~~~fi~v~c~~~~~~~~e~~lFG~~~~~~~~~~~~~g~~~~a~~Gtl~l  239 (482)
                      -....|||.|..|+||+.++++|-+. +.--...+..++|+++...-+|+.==--...|+.+        .+-.-..++|
T Consensus       429 ~~~~~Ill~G~~GsGKT~L~kal~~~~~k~~~~hv~~v~Cs~l~~~~~e~iQk~l~~vfse~--------~~~~PSiIvL  500 (952)
T KOG0735         429 FRHGNILLNGPKGSGKTNLVKALFDYYSKDLIAHVEIVSCSTLDGSSLEKIQKFLNNVFSEA--------LWYAPSIIVL  500 (952)
T ss_pred             CCCCCEEEECCCCCCHHHHHHHHHHHHCCCCCEEEEEEECHHCCCHHHHHHHHHHHHHHHHH--------HHHCCCEEEE
T ss_conf             34661898679987776999999987515650699997522104204899999999999998--------8637808997


Q ss_pred             CCCCHHH
Q ss_conf             6642001
Q gi|254780916|r  240 EEPDALP  246 (482)
Q Consensus       240 ~ei~~L~  246 (482)
                      |+++.|-
T Consensus       501 Ddld~l~  507 (952)
T KOG0735         501 DDLDCLA  507 (952)
T ss_pred             CCHHHHH
T ss_conf             0503540


No 317
>TIGR02418 acolac_catab acetolactate synthase, catabolic; InterPro: IPR012782    Acetolactate synthase is a thiamin pyrophosphate-dependent enzyme that combines two molecules of pyruvate to yield 2-acetolactate with the release of CO2. It exists in two distinct forms that have different properties, though they are clearly related , . The biosynthetic form, found in plants, fungi and bacteria, is involved in the biosynthesis of branched-chain amino acids and contains non-catalytic FAD. The catabolic form is found only in some bacteria, participates in butanediol fermentation, and does not contain FAD.   This entry represents the catabolic form of acetolactate synthase, generally found in species that posses acetolactate decarboxylase, which is often encoded in the same operon. The enzyme is thought to be a homotetramer, though this has not conclusively been shown. Each monomer consists of three distinct domains, designated, starting from the N-terminus, as alpha, beta and gamma . The core of the alpha and gamma domains is a six-stranded parallel beta sheet surrounded by alpha helices, while the the beta domain forms a double Rossman fold. The thiamin pyrophosphate cofactor has an unusual conformation that has not been seen in other enzymes using this cofactor, including the biosynthetic form of acetolactate synthase. The active site is located in a funnel at the dimer interface, bordered by residues from all three domains.; GO: 0000287 magnesium ion binding, 0003984 acetolactate synthase activity, 0030976 thiamin pyrophosphate binding, 0050660 FAD binding.
Probab=93.89  E-value=0.025  Score=36.10  Aligned_cols=276  Identities=13%  Similarity=0.157  Sum_probs=151.8

Q ss_pred             HHHHHCCC-----EEEEEC---CHH-HH-HHH--CCCCCEEEEECCCCCCCHH-HHHHHHHHHCCCCCEEEEECCCC---
Q ss_conf             99998898-----899989---379-99-986--0899899997854698889-99999998578983999926899---
Q gi|254780916|r   28 DHVESYGY-----DVFIVN---VSD-LS-TIS--KIQVNVIFLSLINCEDDKE-NILKNIVDKIPIVPIIVQTTQDN---   91 (482)
Q Consensus        28 ~~L~~~G~-----~v~~a~---~~a-l~-~l~--~~~~dlillD~~mP~~dGl-ell~~i~~~~p~ipvIiiT~~~~---   91 (482)
                      ..|++.+-     +...+.   +++ |+ .+.  ..+|.|+|.= .=||.+=| +-|-.-.. ..| |||-|.|+=-   
T Consensus        30 daLeD~~iGqkvP~lIv~RHEqNAaFMAqavGRlTGkpGV~lvT-SGPG~sNL~TGl~TAn~-EGD-PVvAiGG~VkR~D  106 (553)
T TIGR02418        30 DALEDKGIGQKVPELIVVRHEQNAAFMAQAVGRLTGKPGVALVT-SGPGVSNLVTGLLTANS-EGD-PVVAIGGQVKRAD  106 (553)
T ss_pred             CHHCCCCCCCCCCEEEECCCHHHHHHHHHHHHHHCCCCCEEEEE-CCCCHHHHHHHHHEECC-CCC-HHHHCCCCCCHHH
T ss_conf             02207887754761541322145899999986305998659980-68881446743310156-776-3541167763244


Q ss_pred             ------HHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC----------C-CCCCCCC-------CCCC
Q ss_conf             ------99999888505743222222222222222222222222222221----------1-1111112-------2222
Q gi|254780916|r   92 ------IKILNCFLYNRISKFFLNLVSRKQLCDSIICALREGVVPSQENE----------H-CALDSLI-------AVSP  147 (482)
Q Consensus        92 ------~~~~~~a~~~g~~d~l~KP~~~~~L~~~i~~al~~~~~~~~~~~----------~-~~~~~Li-------G~S~  147 (482)
                            ..+=.-++..-+++|=.---+++.|-+.+.+|.|-...-+.-..          . ......|       -.++
T Consensus       107 ~~k~tHQS~d~valf~piTKYSaEvqd~~~lsE~vaNAfR~A~~Gk~GAaFvS~PQDV~~~kp~s~~~i~~~~~P~~Gaa  186 (553)
T TIGR02418       107 LLKLTHQSMDNVALFRPITKYSAEVQDPDALSEVVANAFRLAESGKPGAAFVSLPQDVVDSKPVSVKAIPAVAAPKLGAA  186 (553)
T ss_pred             HHHHHHCCHHHHHHHCCCCCCEEEEECCCCHHHHHHHHHHHHHHCCCCCCEEECCCCCCCCCCCCHHHHHHHHCCCCCCC
T ss_conf             22233011245777078020134566676547899999999971489662550573214887555345212214678887


Q ss_pred             CCCCCCCCCCCCCCCCEEEEEECCCCCHHHHHHHHHHHCCCCCCCCCCC-CCCCC-CCCCCCHHHHHCCCCCCCCCCCCC
Q ss_conf             2222222222234432048873277743679999998426754332101-23465-542100243311255553221110
Q gi|254780916|r  148 AMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHESGKRAFFPFFI-VNCGM-IDQDKIEKFLFGDVDLQTKNSAQF  225 (482)
Q Consensus       148 ~m~~v~~~i~~~a~~~~~vli~Ge~GtGK~~~A~~iH~~s~r~~~~fi~-v~c~~-~~~~~~e~~lFG~~~~~~~~~~~~  225 (482)
                      +-.++-..++++.+...|||+.|-.|+- .-.++|+|.+-+...-|+|. ...|+ ++.|+...++||..+-|..-.-+.
T Consensus       187 ~~~~i~~~~~~I~~Ak~PVlLlG~~aS~-~~~~~Av~rll~k~~LPvVeTfQgAG~vsrele~~TFfGRvGLFrNQ~GD~  265 (553)
T TIGR02418       187 ADADIDEVAEAIKNAKLPVLLLGLRASS-QETTEAVRRLLKKTQLPVVETFQGAGVVSRELEDETFFGRVGLFRNQPGDK  265 (553)
T ss_pred             HHHHHHHHHHHHHHCCCCEEEEECCCCC-HHHHHHHHHHHCCCCCCCEEEEECCEEECHHCCCCCCEECCCCCCCCCCHH
T ss_conf             3889999999998319966985047888-899999999864606882140200513110024565210011445870025


Q ss_pred             CCCCCCCCCCEEEECCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCEEEEECCCCCCCCCCHHHHHHHHHHHHHHH
Q ss_conf             01234466714751664200188999888877642001123553212343156521433211111123337999886543
Q gi|254780916|r  226 LGKFIEANGGTIVLEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRKDLYYRISVF  305 (482)
Q Consensus       226 ~g~~~~a~~Gtl~l~ei~~L~~~~Q~~Ll~~l~~~~~~~~g~~~~~~~~~RiIa~t~~~L~~~~~~g~fr~dLy~rL~~~  305 (482)
                        ||++|+   |+|- |+.=|.             +|+|-.=|+  ..+++||..=     ...++             +
T Consensus       266 --LLk~aD---LvIt-IGYdPI-------------EYep~~WN~--~~~~~Iv~iD-----~~~A~-------------i  306 (553)
T TIGR02418       266 --LLKQAD---LVIT-IGYDPI-------------EYEPRNWNS--ELDATIVHID-----VEPAE-------------I  306 (553)
T ss_pred             --HHHHCC---EEEE-ECCCCE-------------ECCHHHCCC--CCCCEEEEEE-----EEEEE-------------H
T ss_conf             --775669---7898-338850-------------307554477--8872068973-----14421-------------2


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             3446778774422225566777641011223333211111000122
Q gi|254780916|r  306 LINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTK  351 (482)
Q Consensus       306 ~i~iPpLReR~eDI~~L~~~fl~~~~~~~~~~~~~ls~~a~~~L~~  351 (482)
                      ..+.=|=||=-.||+.=++++.++....     ..|++++.+.|..
T Consensus       307 ~~~yqP~~eLvGdia~tl~~l~~~~~~~-----~~L~~~~~~~L~~  347 (553)
T TIGR02418       307 DNNYQPDLELVGDIASTLDLLAERVEGF-----YELPEDAQDILED  347 (553)
T ss_pred             HHCCCCCHHHHCCHHHHHHHHHHHHCCC-----CCCCHHHHHHHHH
T ss_conf             0036861443257277799995862466-----1058889999999


No 318
>TIGR02173 cyt_kin_arch cytidylate kinase, putative; InterPro: IPR011892    Proteins in this family are believed to be cytidylate kinase. Members of this family are found in the archaea and in spirochaetes, and differ considerably from the common bacterial form of cytidylate kinase described by IPR003136 from INTERPRO.; GO: 0004127 cytidylate kinase activity, 0005524 ATP binding, 0006139 nucleobase nucleoside nucleotide and nucleic acid metabolic process.
Probab=93.86  E-value=0.04  Score=34.64  Aligned_cols=21  Identities=33%  Similarity=0.596  Sum_probs=18.4

Q ss_pred             EEEECCCCCHHHHHHHHHHHC
Q ss_conf             887327774367999999842
Q gi|254780916|r  166 IMIQGEFGVGKKRLSRFIHES  186 (482)
Q Consensus       166 vli~Ge~GtGK~~~A~~iH~~  186 (482)
                      |.|.|++||||+++|+.|=..
T Consensus         3 I~ISGpPGSGktTvA~~lA~~   23 (173)
T TIGR02173         3 ITISGPPGSGKTTVAKILAEK   23 (173)
T ss_pred             EEEECCCCCCHHHHHHHHHHH
T ss_conf             887358968647899999986


No 319
>PRK06871 DNA polymerase III subunit delta'; Validated
Probab=93.85  E-value=0.46  Score=27.18  Aligned_cols=96  Identities=14%  Similarity=0.136  Sum_probs=49.3

Q ss_pred             CCCEEEEEECCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCC------C----CCCCCHHHHHCCCCCCC-CCCCCC--CC
Q ss_conf             43204887327774367999999842675433210123465------5----42100243311255553-221110--01
Q gi|254780916|r  161 DCAIPIMIQGEFGVGKKRLSRFIHESGKRAFFPFFIVNCGM------I----DQDKIEKFLFGDVDLQT-KNSAQF--LG  227 (482)
Q Consensus       161 ~~~~~vli~Ge~GtGK~~~A~~iH~~s~r~~~~fi~v~c~~------~----~~~~~e~~lFG~~~~~~-~~~~~~--~g  227 (482)
                      ....-.|+.|+.|+||+.+|+.+-..-- ...|--.-.|+.      +    .+|...   .-..++-+ +-..-|  ..
T Consensus        21 r~~HA~L~~G~~G~Gk~~la~~~a~~ll-C~~~~~~~~Cg~C~sC~l~~~g~HPD~~~---i~~~~~k~I~vd~IR~l~~   96 (324)
T PRK06871         21 RGHHALLFKADSGLGTEQLIRALAQWLM-CQAPGDEQPCGQCHSCHLFQAGNHPDFHI---LEPIDGKDIGVDQVREINE   96 (324)
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHHHHHH-CCCCCCCCCCCCCHHHHHHHCCCCCCEEE---EECCCCCCCCHHHHHHHHH
T ss_conf             9543787689999789999999999982-89999999888898999997389998799---8467888788999999999


Q ss_pred             CC----CCCCCCEEEECCCCHHHHHHHHHHHHHHHHH
Q ss_conf             23----4466714751664200188999888877642
Q gi|254780916|r  228 KF----IEANGGTIVLEEPDALPLAVQGRIYNFIETG  260 (482)
Q Consensus       228 ~~----~~a~~Gtl~l~ei~~L~~~~Q~~Ll~~l~~~  260 (482)
                      .+    .+.+.-.+++++.+.|....+..||..|||.
T Consensus        97 ~~~~~~~~g~~KV~iI~~ae~m~~~AaNALLKtLEEP  133 (324)
T PRK06871         97 KVSQFAQQGGNKVVYIQGAERLTEAAANALLKTLEEP  133 (324)
T ss_pred             HHHHCCCCCCCEEEEECCHHHHHHHHHHHHHHHHCCC
T ss_conf             9864622059669997588885799999999983389


No 320
>TIGR01193 bacteriocin_ABC ABC-type bacteriocin transporter; InterPro: IPR005897   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 contains ABC-type bacteriocin transporter. In general, bacteriocins are agents which are responsible for killing or inhibiting the closely related species or even different strains of the same species. Bacteriocins are encoded by bacterial plasmids. Bacteriocins are named after the species and hence in literature one encounters various names e.g., leucocin from Leuconostic geldium; pedicocin from Pedicoccus acidilactici; sakacin from Lactobacillus sake etc.    Peptide bacteriocins are exported across the cytoplasmic membrane by a dedicated ATP-binding cassette (ABC) transporter. These ABC-transporters have an N-terminal peptidase domain that belong to MEROPS peptidase family C39 (clan CA); a central multi-pass transmembrane region and a C-terminal ABC transporter domain. These transporters have dual function: (i) they remove the N-terminal leader peptide from its bacteriocin precursor by cleavage at a Gly-Gly bond and (ii) transport the mature bacteriocin across the cytoplasmic membrane. This represents a novel strategy for secretion of bacterial proteins . Many bacteria are known to regulate diverse physiological processes through this system, such as bioluminescence, regulation of sporulation, virulence factor expression, antibiotics production, competence for genetic transformation, and activation of biofilm formation .; GO: 0008234 cysteine-type peptidase activity, 0019534 toxin transporter activity, 0006810 transport, 0016020 membrane.
Probab=93.71  E-value=0.04  Score=34.68  Aligned_cols=96  Identities=17%  Similarity=0.164  Sum_probs=52.8

Q ss_pred             CCCCCCCCCCCCCEEEEEECCCCCHHHHHHHHHHHCC--CCCCCCCCCCCCCC----------------------CCCCC
Q ss_conf             2222222234432048873277743679999998426--75433210123465----------------------54210
Q gi|254780916|r  151 QVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHESG--KRAFFPFFIVNCGM----------------------IDQDK  206 (482)
Q Consensus       151 ~v~~~i~~~a~~~~~vli~Ge~GtGK~~~A~~iH~~s--~r~~~~fi~v~c~~----------------------~~~~~  206 (482)
                      .+.+.+.---..+.-+-|.|-+|+||+++|+.+=.+-  +-..| =|.+|.-.                      ++..-
T Consensus       488 ~~L~di~L~I~~n~k~tiVGmSGSGKsTLaKLLV~FfePQ~~sG-~I~Lng~~l~~iD~h~LRq~INYlPQeP~IF~GsI  566 (710)
T TIGR01193       488 NVLSDISLTIKKNEKITIVGMSGSGKSTLAKLLVGFFEPQAESG-EILLNGISLKDIDRHELRQFINYLPQEPYIFSGSI  566 (710)
T ss_pred             CCCCCCEEEEECCCEEEEECCCCCCHHHHHHHHHCCCCCCCCCC-EEEECCCCHHHCCHHHHCCCCCCCCCCCEEECCCH
T ss_conf             32026423650785489973679748999987520358998877-36527824453373444123355688784512317


Q ss_pred             CHHHHHCCCCCCCCCCCCCCCCCCCCCCCEEEECCCCHHHHHHHHHH
Q ss_conf             02433112555532211100123446671475166420018899988
Q gi|254780916|r  207 IEKFLFGDVDLQTKNSAQFLGKFIEANGGTIVLEEPDALPLAVQGRI  253 (482)
Q Consensus       207 ~e~~lFG~~~~~~~~~~~~~g~~~~a~~Gtl~l~ei~~L~~~~Q~~L  253 (482)
                      +|..|.|.+.+.+...-.+.=.+.|      .=++|+.||.-.|+.|
T Consensus       567 LeNLLlGak~~~~~~~i~~A~~iAE------Ik~DIe~mp~Gy~T~L  607 (710)
T TIGR01193       567 LENLLLGAKENVSQDEILKAVEIAE------IKDDIEKMPLGYQTEL  607 (710)
T ss_pred             HHHHHHCCCCCCCHHHHHHHHHHCC------CHHHHHHCCCCCCEEE
T ss_conf             8876503789989899998840201------1245831888766000


No 321
>COG3910 Predicted ATPase [General function prediction only]
Probab=93.69  E-value=0.18  Score=30.05  Aligned_cols=37  Identities=32%  Similarity=0.450  Sum_probs=25.5

Q ss_pred             CCCCCCCCCCCCCCCCCCCEEE-EEECCCCCHHHHHHHHHHH
Q ss_conf             2222222222222234432048-8732777436799999984
Q gi|254780916|r  145 VSPAMIQVVDLARKAGDCAIPI-MIQGEFGVGKKRLSRFIHE  185 (482)
Q Consensus       145 ~S~~m~~v~~~i~~~a~~~~~v-li~Ge~GtGK~~~A~~iH~  185 (482)
                      +=|+|+.+...+    ....|| .|+||.|+||.++-.+|-.
T Consensus        22 slPa~r~l~~~L----eF~apIT~i~GENGsGKSTLLEaiA~   59 (233)
T COG3910          22 SLPAFRHLEERL----EFRAPITFITGENGSGKSTLLEAIAA   59 (233)
T ss_pred             CCHHHHHHHHHC----CCCCCEEEEECCCCCCHHHHHHHHHH
T ss_conf             356777554422----34686489976898657889999996


No 322
>cd01386 MYSc_type_XVIII Myosin motor domain, type XVIII myosins. This catalytic (head) domain has ATPase activity and belongs to the larger group of P-loop NTPases. Myosins are actin-dependent molecular motors that play important roles in muscle contraction, cell motility, and organelle transport. The head domain is a molecular motor, which utilizes ATP hydrolysis to generate directed movement toward the plus end along actin filaments. A cyclical interaction between myosin and actin provides the driving force. Rates of ATP hydrolysis and consequently the speed of movement along actin filaments vary widely, from about 0.04 micrometer per second for myosin I to 4.5 micrometer per second for myosin II in skeletal muscle. Myosin II moves in discrete steps about 5-10 nm long and generates 1-5 piconewtons of force. Upon ATP binding, the myosin head dissociates from an actin filament. ATP hydrolysis causes the head to pivot and associate with a new actin subunit. The release of Pi causes the 
Probab=93.67  E-value=0.048  Score=34.08  Aligned_cols=24  Identities=21%  Similarity=0.281  Sum_probs=18.9

Q ss_pred             CCCEEEEEECCCCCHHHHHHHHHH
Q ss_conf             432048873277743679999998
Q gi|254780916|r  161 DCAIPIMIQGEFGVGKKRLSRFIH  184 (482)
Q Consensus       161 ~~~~~vli~Ge~GtGK~~~A~~iH  184 (482)
                      ..+..|+|.||+|+||+..++.|=
T Consensus        84 ~~nQsIIiSGESGAGKTEstK~im  107 (767)
T cd01386          84 RRDQSIIFLGRSGAGKTTSCKHAL  107 (767)
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHH
T ss_conf             899579995589888889999999


No 323
>PRK06762 hypothetical protein; Provisional
Probab=93.60  E-value=0.055  Score=33.66  Aligned_cols=43  Identities=23%  Similarity=0.380  Sum_probs=31.3

Q ss_pred             EEEEECCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCHHHHHCCC
Q ss_conf             488732777436799999984267543321012346554210024331125
Q gi|254780916|r  165 PIMIQGEFGVGKKRLSRFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFGDV  215 (482)
Q Consensus       165 ~vli~Ge~GtGK~~~A~~iH~~s~r~~~~fi~v~c~~~~~~~~e~~lFG~~  215 (482)
                      =|.|.|.+|+||+.+|+.+|..-.+        +|+-++.+.+-.++.-.+
T Consensus         4 LIiiRGNSgSGKtT~Ak~L~~~~G~--------g~lLvsQD~vRR~mLr~k   46 (166)
T PRK06762          4 LIIIRGNSGSGKTTIAKQLQERLGR--------GTLLVSQDVVRRDMLRVK   46 (166)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHCC--------CCEEEEHHHHHHHHHHCC
T ss_conf             8999788888878999999998688--------857853758999984055


No 324
>COG4615 PvdE ABC-type siderophore export system, fused ATPase and permease components [Secondary metabolites biosynthesis, transport, and catabolism / Inorganic ion transport and metabolism]
Probab=93.52  E-value=0.23  Score=29.26  Aligned_cols=44  Identities=14%  Similarity=0.187  Sum_probs=30.7

Q ss_pred             EEEEEECCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCH
Q ss_conf             048873277743679999998426754332101234655421002
Q gi|254780916|r  164 IPIMIQGEFGVGKKRLSRFIHESGKRAFFPFFIVNCGMIDQDKIE  208 (482)
Q Consensus       164 ~~vli~Ge~GtGK~~~A~~iH~~s~r~~~~fi~v~c~~~~~~~~e  208 (482)
                      .=|+|+|+.|+||++++..+-..-.-..| =|-+|..-++.+..|
T Consensus       350 elvFliG~NGsGKST~~~LLtGL~~PqsG-~I~ldg~pV~~e~le  393 (546)
T COG4615         350 ELVFLIGGNGSGKSTLAMLLTGLYQPQSG-EILLDGKPVSAEQLE  393 (546)
T ss_pred             CEEEEECCCCCCHHHHHHHHHHCCCCCCC-CEEECCCCCCCCCHH
T ss_conf             38999888996388999999706688888-266789348844789


No 325
>pfam05707 Zot Zonular occludens toxin (Zot). This family consists of bacterial and viral proteins which are very similar to the Zonular occludens toxin (Zot). Zot is elaborated by bacteriophages present in toxigenic strains of Vibrio cholerae. Zot is a single polypeptide chain of 44.8 kDa, with the ability to reversibly alter intestinal epithelial tight junctions, allowing the passage of macromolecules through mucosal barriers
Probab=93.48  E-value=0.093  Score=32.06  Aligned_cols=78  Identities=17%  Similarity=0.163  Sum_probs=41.1

Q ss_pred             EEEECCCCCHHHHHHHHHHHCC-CCCCCCCCCCCCCCCCCCCCHHHHHCCCCCCC-CCCCCCCCCCCCCCCCEEEECCCC
Q ss_conf             8873277743679999998426-75433210123465542100243311255553-221110012344667147516642
Q gi|254780916|r  166 IMIQGEFGVGKKRLSRFIHESG-KRAFFPFFIVNCGMIDQDKIEKFLFGDVDLQT-KNSAQFLGKFIEANGGTIVLEEPD  243 (482)
Q Consensus       166 vli~Ge~GtGK~~~A~~iH~~s-~r~~~~fi~v~c~~~~~~~~e~~lFG~~~~~~-~~~~~~~g~~~~a~~Gtl~l~ei~  243 (482)
                      .||+|-+|+||++.|=..|-.- -.++.| |..|..++..+.+ .+.||...... .......-+...-+|+-+++||.+
T Consensus         3 ~litG~pGsGKS~~aV~~~i~~al~~GR~-V~tNI~gL~~~~~-~~~~~~~~~~~~~~~~~~~~w~~~p~g~liViDE~~   80 (183)
T pfam05707         3 YLITGKPGSGKTLEAVSYHILPALKKGRK-VITNIDGLNLERF-PKVFGEDVRERLEDIGYMDPWRTYPKGALLVIDEAQ   80 (183)
T ss_pred             EEEECCCCCCCCHHHHHHHHHHHHHCCCE-EEECCCCCCCHHC-CCCCCCCCCCCCCCCCCCHHHCCCCCCCEEEEECCH
T ss_conf             99935999962299999999999878998-9987865352210-122344454320000122233149998799998976


Q ss_pred             HH
Q ss_conf             00
Q gi|254780916|r  244 AL  245 (482)
Q Consensus       244 ~L  245 (482)
                      ..
T Consensus        81 ~~   82 (183)
T pfam05707        81 TW   82 (183)
T ss_pred             HH
T ss_conf             55


No 326
>PRK05637 anthranilate synthase component II; Provisional
Probab=93.43  E-value=0.39  Score=27.69  Aligned_cols=77  Identities=19%  Similarity=0.245  Sum_probs=54.1

Q ss_pred             CCCEEEECCCHHHHHHHHHHHHHCCCEEEEECC-HHHHHHHCCCCCEEEEEC--CCCCCCHHHHHHHHHHHCCCCCEEEE
Q ss_conf             883899869989999999999988988999893-799998608998999978--54698889999999985789839999
Q gi|254780916|r   10 HKRVLIIDKDDEQIKIIKDHVESYGYDVFIVNV-SDLSTISKIQVNVIFLSL--INCEDDKENILKNIVDKIPIVPIIVQ   86 (482)
Q Consensus        10 ~~rILIVDDd~~~~~~l~~~L~~~G~~v~~a~~-~al~~l~~~~~dlillD~--~mP~~dGlell~~i~~~~p~ipvIii   86 (482)
                      ++|||+||...++-..+...|+..|++|.+..+ ..++.+....||.|++.=  -.|...|. .++-++.....+||+=+
T Consensus         1 M~~ILlIDnyDSFT~Nl~~~l~~~g~~v~V~rn~~~~~~~~~~~pd~ivlSPGPg~P~d~g~-~~~~~~~~~~~iPILGI   79 (208)
T PRK05637          1 MTHVVLIDNHDSFVYNLVDAFAVAGYKCTVFRNTVPVETILAANPDLICLSPGPGYPADAGN-MMALIERTLGQIPLLGI   79 (208)
T ss_pred             CCEEEEEECCCCHHHHHHHHHHHCCCEEEEEECCCCHHHHHHCCCCEEEECCCCCCHHHCCC-HHHHHHHHHCCCCEEEH
T ss_conf             97799994889759999999986799079996999999998519995999999999577757-49999997356982211


Q ss_pred             E
Q ss_conf             2
Q gi|254780916|r   87 T   87 (482)
Q Consensus        87 T   87 (482)
                      -
T Consensus        80 C   80 (208)
T PRK05637         80 C   80 (208)
T ss_pred             H
T ss_conf             4


No 327
>cd02068 radical_SAM_B12_BD B12 binding domain_like associated with radical SAM domain. This domain shows similarity with B12 (adenosylcobamide) binding domains found in several enzymes, such as glutamate mutase, methionine synthase and methylmalonyl-CoA mutase, but it lacks the signature motif Asp-X-His-X-X-Gly, which contains the histidine that acts as a cobalt ligand. The function of this domain remains unclear.
Probab=93.41  E-value=0.65  Score=26.08  Aligned_cols=88  Identities=15%  Similarity=0.114  Sum_probs=58.8

Q ss_pred             HHHHHHHHHHHHCCCEEEEECC----HHH-HHHHCCCCCEEEEECCCCCCC-HHHHHHHHHHHCCCCCEEEEECCCCHHH
Q ss_conf             9999999999988988999893----799-998608998999978546988-8999999998578983999926899999
Q gi|254780916|r   21 EQIKIIKDHVESYGYDVFIVNV----SDL-STISKIQVNVIFLSLINCEDD-KENILKNIVDKIPIVPIIVQTTQDNIKI   94 (482)
Q Consensus        21 ~~~~~l~~~L~~~G~~v~~a~~----~al-~~l~~~~~dlillD~~mP~~d-Glell~~i~~~~p~ipvIiiT~~~~~~~   94 (482)
                      .-...++..|++.||+|.....    ..+ +.++..+||+|-...+.+... ..++++.+|+..|++++|+--.|.+...
T Consensus         3 LGl~ylaa~L~~~G~~v~~~d~~~~~~~~e~~~~~~~pdvvg~s~~~~~~~~~~~~~~~~k~~~p~~~iv~GG~h~t~~p   82 (127)
T cd02068           3 LGLAYLAAVLEDAGFIVAEHDVLSADDIVEDIKELLKPDVVGISLMTSAIYEALELAKIAKEVLPNVIVVVGGPHATFFP   82 (127)
T ss_pred             HHHHHHHHHHHHCCCEEEEEECCCCCCHHHHHHHCCCCCEEEEEEEHHHHHHHHHHHHHHHHHCCCCEEEECCCCCCCCH
T ss_conf             79999999999789957998578762039999864996999999768899999999999999789978998598745499


Q ss_pred             HHHHHHCCCCCCCCC
Q ss_conf             998885057432222
Q gi|254780916|r   95 LNCFLYNRISKFFLN  109 (482)
Q Consensus        95 ~~~a~~~g~~d~l~K  109 (482)
                       ...+.....||+..
T Consensus        83 -~~~l~~~~~D~vv~   96 (127)
T cd02068          83 -EEILEEPGVDFVVI   96 (127)
T ss_pred             -HHHHHCCCCCEEEE
T ss_conf             -99970758778996


No 328
>PRK07261 topology modulation protein; Provisional
Probab=93.25  E-value=0.079  Score=32.55  Aligned_cols=33  Identities=30%  Similarity=0.470  Sum_probs=26.4

Q ss_pred             EEEEEECCCCCHHHHHHHHHHHCCCCCCCCCCCCCC
Q ss_conf             048873277743679999998426754332101234
Q gi|254780916|r  164 IPIMIQGEFGVGKKRLSRFIHESGKRAFFPFFIVNC  199 (482)
Q Consensus       164 ~~vli~Ge~GtGK~~~A~~iH~~s~r~~~~fi~v~c  199 (482)
                      +-|+|.|-+|+||+++||.|.+.   -+-|++.+|.
T Consensus         1 MrI~IiG~sGsGKSTlAr~L~~~---~~ip~~~LD~   33 (171)
T PRK07261          1 MKIAIIGYSGSGKSTLARFLGQH---YNCPVLHLDQ   33 (171)
T ss_pred             CEEEEECCCCCCHHHHHHHHHHH---HCCCEEEECC
T ss_conf             98999889998689999999998---7979797022


No 329
>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=93.21  E-value=0.38  Score=27.70  Aligned_cols=159  Identities=15%  Similarity=0.181  Sum_probs=72.1

Q ss_pred             EEEECCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCHHHHHCCCCCCCCCCCCCCCCCCCCCCCEEEECCCCHH
Q ss_conf             88732777436799999984267543321012346554210024331125555322111001234466714751664200
Q gi|254780916|r  166 IMIQGEFGVGKKRLSRFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFGDVDLQTKNSAQFLGKFIEANGGTIVLEEPDAL  245 (482)
Q Consensus       166 vli~Ge~GtGK~~~A~~iH~~s~r~~~~fi~v~c~~~~~~~~e~~lFG~~~~~~~~~~~~~g~~~~a~~Gtl~l~ei~~L  245 (482)
                      |=|.|-+|+||+++|+.|++.-+         +|.-+..+.+           .-..+    -+.....|..=.|..+.+
T Consensus         2 IgIaG~S~SGKTTla~~L~~~l~---------~~~iI~qDdy-----------Yk~~~----~~~~~~~~~~NfDhP~Ai   57 (187)
T cd02024           2 VGISGVTNSGKTTLAKLLQRILP---------NCCVIHQDDF-----------FKPED----EIPVDENGFKQWDVLEAL   57 (187)
T ss_pred             EEEECCCCCCHHHHHHHHHHHCC---------CCEEECCCCC-----------CCCCC----CCCHHHCCCCCCCCCCCC
T ss_conf             89968888759999999999879---------9889715446-----------78843----276213057687670120


Q ss_pred             HHHHHHHHHHHHHHHH-CC-CCCCC----CCCC-------CCCEEEEECC-CCCCCCCCHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             1889998888776420-01-12355----3212-------3431565214-33211111123337999886543344677
Q gi|254780916|r  246 PLAVQGRIYNFIETGK-IE-FFDSR----GAIR-------LDVRLIFLTE-KNLLPQVKSHVFRKDLYYRISVFLINIST  311 (482)
Q Consensus       246 ~~~~Q~~Ll~~l~~~~-~~-~~g~~----~~~~-------~~~RiIa~t~-~~L~~~~~~g~fr~dLy~rL~~~~i~iPp  311 (482)
                      ..+.-..-|+.|.++. +. ++-+.    .+..       ...|---... .+..-.+-+|.|           ..+-|.
T Consensus        58 D~~~l~~~L~~l~~~~~~~~~~~s~~~~~~~~~~~~~~~~~~~r~~~~~~~~p~~iiIvEG~l-----------l~~~~~  126 (187)
T cd02024          58 DMEAMMSTLDYWRETGHFPKFLRSHGNENDPEKEFIEDAQIEETKADLLGAEDLHILIVDGFL-----------LYNYKP  126 (187)
T ss_pred             CHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCHHHHHCCCCCCCCCCCCEEEEEECHH-----------HCCCHH
T ss_conf             589999999999948976431013343566775674102221120001146896499991778-----------719899


Q ss_pred             HHHHHHHHHHHHH-----HHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCHHH
Q ss_conf             8774422225566-----777641011223333211111000122338986899
Q gi|254780916|r  312 LRSRSEDIPWLVH-----FFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQE  360 (482)
Q Consensus       312 LReR~eDI~~L~~-----~fl~~~~~~~~~~~~~ls~~a~~~L~~y~WPGNvRE  360 (482)
                      ||+.- |+...++     .+..+..+..-....+++++-...+.++-||+=+.-
T Consensus       127 lr~l~-DlkiFvd~~~d~~l~RR~~Rd~~~~~~g~~~D~~~yf~~~V~P~y~k~  179 (187)
T cd02024         127 LVDLF-DIRYFLRVPYETCKRRREARTGYVTLEGFWPDPPGYFDGHVWPMYLKH  179 (187)
T ss_pred             HHHHC-CEEEEEECCHHHHHHHHHCCCCCCCCCCCCCCCCHHHHCEECHHHHHH
T ss_conf             99863-967999699999999975257854268478999526525041538988


No 330
>PTZ00014 myosin A; Provisional
Probab=93.10  E-value=0.091  Score=32.13  Aligned_cols=25  Identities=24%  Similarity=0.474  Sum_probs=21.0

Q ss_pred             CCCEEEEEECCCCCHHHHHHHHHHH
Q ss_conf             4320488732777436799999984
Q gi|254780916|r  161 DCAIPIMIQGEFGVGKKRLSRFIHE  185 (482)
Q Consensus       161 ~~~~~vli~Ge~GtGK~~~A~~iH~  185 (482)
                      ..+..|+|.||+|+||+-.++.|=+
T Consensus       182 ~~nQsIiISGESGAGKTEstK~im~  206 (821)
T PTZ00014        182 KYSQTIIVSGESGAGKTEATKQMMR  206 (821)
T ss_pred             CCCEEEEEEECCCCCHHHHHHHHHH
T ss_conf             9981699982798997899999999


No 331
>cd04158 ARD1 ARD1 subfamily.  ARD1 (ADP-ribosylation factor domain protein 1) is an unusual member of the Arf family.  In addition to the C-terminal Arf domain, ARD1 has an additional 46-kDa N-terminal domain that contains a RING finger domain, two predicted B-Boxes, and a coiled-coil protein interaction motif.  This domain belongs to the TRIM (tripartite motif) or RBCC (RING, B-Box, coiled-coil) family.  Like most Arfs, the ARD1 Arf domain lacks detectable GTPase activity.  However, unlike most Arfs, the full-length ARD1 protein has significant GTPase activity due to the GAP (GTPase-activating protein) activity exhibited by the 46-kDa N-terminal domain.  The GAP domain of ARD1 is specific for its own Arf domain and does not bind other Arfs.  The rate of GDP dissociation from the ARD1 Arf domain is slowed by the adjacent 15 amino acids, which act as a GDI (GDP-dissociation inhibitor) domain.  ARD1 is ubiquitously expressed in cells and localizes to the Golgi and to the lysosomal membra
Probab=93.04  E-value=0.61  Score=26.27  Aligned_cols=119  Identities=9%  Similarity=0.147  Sum_probs=57.9

Q ss_pred             EEEECCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCHHHHHCCCCCCCCCCCCCCCCCCCCCCCEEEECCCCHH
Q ss_conf             88732777436799999984267543321012346554210024331125555322111001234466714751664200
Q gi|254780916|r  166 IMIQGEFGVGKKRLSRFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFGDVDLQTKNSAQFLGKFIEANGGTIVLEEPDAL  245 (482)
Q Consensus       166 vli~Ge~GtGK~~~A~~iH~~s~r~~~~fi~v~c~~~~~~~~e~~lFG~~~~~~~~~~~~~g~~~~a~~Gtl~l~ei~~L  245 (482)
                      |++.|..|+||+.+.+.++........|-+-+|...+....+.-+++-- +|...-..--.-.+..|++-.+++|--+.-
T Consensus         2 IlilGl~~sGKTtil~~l~~~~~~~~~pT~G~~~~~i~~~~~~l~iwD~-gG~~~~r~~w~~Yy~~~~~iIfVvDssd~~   80 (169)
T cd04158           2 VVTLGLDGAGKTTILFKLKQDEFMQPIPTIGFNVETVEYKNLKFTIWDV-GGKHKLRPLWKHYYLNTQAVVFVVDSSHRD   80 (169)
T ss_pred             EEEECCCCCCHHHHHHHHHCCCCCCCCCCCCCCEEEEEECCEEEEEEEC-CCCCCCCHHHHHHCCCCCEEEEEEECCHHH
T ss_conf             9999989998899999995799689778688166999989889999989-997244636787555762799999863067


Q ss_pred             HH-HHHHHHHHHHHHHHCCCCCCCCCCCCCCEEEEECCCCCCCCCCHHHH
Q ss_conf             18-89998888776420011235532123431565214332111111233
Q gi|254780916|r  246 PL-AVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVF  294 (482)
Q Consensus       246 ~~-~~Q~~Ll~~l~~~~~~~~g~~~~~~~~~RiIa~t~~~L~~~~~~g~f  294 (482)
                      .. +.+..|-.++++...      ...+   =+|.+...|+...+.....
T Consensus        81 ~~~ea~~~l~~ll~~~~~------~~~p---iLIlaNK~Dl~~~~~~~ei  121 (169)
T cd04158          81 RVSEAHSELAKLLTEKEL------RDAL---LLIFANKQDVAGALSVEEM  121 (169)
T ss_pred             HHHHHHHHHHHHHHHHHH------CCCE---EEEEEECCCCCCCCCHHHH
T ss_conf             799999999999712753------7984---9999735567779899999


No 332
>PRK06090 DNA polymerase III subunit delta'; Validated
Probab=93.01  E-value=0.13  Score=31.05  Aligned_cols=122  Identities=13%  Similarity=0.182  Sum_probs=61.3

Q ss_pred             CCCCCCCCCCCC---CCCCCEEEEEECCCCCHHHHHHHHHHHC---CCCCCCCCCCCCCCCCC-CCCCHH-------HHH
Q ss_conf             222222222222---3443204887327774367999999842---67543321012346554-210024-------331
Q gi|254780916|r  147 PAMIQVVDLARK---AGDCAIPIMIQGEFGVGKKRLSRFIHES---GKRAFFPFFIVNCGMID-QDKIEK-------FLF  212 (482)
Q Consensus       147 ~~m~~v~~~i~~---~a~~~~~vli~Ge~GtGK~~~A~~iH~~---s~r~~~~fi~v~c~~~~-~~~~e~-------~lF  212 (482)
                      |..+..++++..   ......-.||.|+.|+||+.+|+.+-..   ......|     |+.-. ..++.+       .++
T Consensus         6 PWl~~~~~~l~~~~~~~rl~HA~L~~g~~G~Gk~~la~~la~~LlC~~~~~~~-----Cg~C~sC~l~~~g~HPD~~~i~   80 (319)
T PRK06090          6 PWLVPVWQNWKSGLDAERIPGALLLQSDEGLGVESLVELFSHALLCQNYQSEA-----CGFCHSCELMKSGNHPDLHVIK   80 (319)
T ss_pred             CCCHHHHHHHHHHHHCCCCCCEEEEECCCCCCHHHHHHHHHHHHHCCCCCCCC-----CCCCHHHHHHHCCCCCCCEEEE
T ss_conf             88379999999999869963067667999857999999999998089999998-----8778779998758999823661


Q ss_pred             CCCCCCCCCCCC-C-C-CCC-CCC---CCCEEEECCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCEEEEECCCC
Q ss_conf             125555322111-0-0-123-446---6714751664200188999888877642001123553212343156521433
Q gi|254780916|r  213 GDVDLQTKNSAQ-F-L-GKF-IEA---NGGTIVLEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKN  284 (482)
Q Consensus       213 G~~~~~~~~~~~-~-~-g~~-~~a---~~Gtl~l~ei~~L~~~~Q~~Ll~~l~~~~~~~~g~~~~~~~~~RiIa~t~~~  284 (482)
                      -++++-+-...+ | . -.+ ..+   ..-.+++++.+.|....+..||..|||.           +.++-+|..|+..
T Consensus        81 pe~~~k~I~vd~IR~l~~~~~~~~~~g~~KV~iI~~ae~m~~~AaNALLKtLEEP-----------p~~t~fiL~t~~~  148 (319)
T PRK06090         81 PEKEGKSITVEQIRQCNRLAQESSQLGGYRLFVIEPADAMNESASNALLKTLEEP-----------APNCLFLLVTHNQ  148 (319)
T ss_pred             CCCCCCCCCHHHHHHHHHHHHHCCCCCCCEEEEECCHHHCCHHHHHHHHHHHCCC-----------CCCEEEEEEECCH
T ss_conf             2335676879999999999754521069369998144434999999999984289-----------9883899876851


No 333
>PRK05657 RNA polymerase sigma factor RpoS; Validated
Probab=92.99  E-value=0.2  Score=29.76  Aligned_cols=49  Identities=29%  Similarity=0.455  Sum_probs=32.1

Q ss_pred             HHHHHHHHHHHHHHHHHCC---CHHHHHHHHCCCH-----------HHHHHHHHHHCCCCCCC
Q ss_conf             9999999999999998287---2789997848998-----------89999999818881449
Q gi|254780916|r  434 RLSDIEKEIIGLAMKLYRA---QMSEVARRLGIGR-----------STLYRKIREYNIEVDSL  482 (482)
Q Consensus       434 ~l~e~E~~~I~~aL~~~~G---n~~~aA~~LGIsR-----------~tL~rKlk~~gi~~d~~  482 (482)
                      .|.+-|+.+|..-+-..++   ...+.|+.+||||           ..|++.+++-||+.|++
T Consensus       265 ~L~~REr~II~~RfGL~~~e~~TL~EIg~~lgvSRERVRQIE~~AL~KLR~~l~~~~l~~~~~  327 (328)
T PRK05657        265 ELNDKQREVIERRFGLNGYEAATLEEVAREIGLTRERVRQIQVEALRRLREILQTQGLSKDAL  327 (328)
T ss_pred             CCCHHHHHHHHHHCCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHCCCCHHHC
T ss_conf             699999999999808899896059999989697999999999999999879999869973424


No 334
>PRK13833 conjugal transfer protein TrbB; Provisional
Probab=92.95  E-value=0.035  Score=35.09  Aligned_cols=50  Identities=22%  Similarity=0.258  Sum_probs=34.9

Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCCCHHHHHHHHHHHC
Q ss_conf             11111122222222222222223443204887327774367999999842
Q gi|254780916|r  137 CALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHES  186 (482)
Q Consensus       137 ~~~~~LiG~S~~m~~v~~~i~~~a~~~~~vli~Ge~GtGK~~~A~~iH~~  186 (482)
                      ...++++.....-....+.++.+.....+++|.|.+|+||+++.+++-..
T Consensus       118 ~tl~dlv~~g~~t~~~~~~L~~aV~~r~nilVsGgTGSGKTTllnaL~~~  167 (323)
T PRK13833        118 IPLDDYVRSKVMTEAQASTIRSAISSRLNIVISGGTGSGKTTLANAVIAE  167 (323)
T ss_pred             CCHHHHHHCCCCCHHHHHHHHHHHHCCCCEEEECCCCCCHHHHHHHHHHH
T ss_conf             99999987699999999999999981896899917777568999999986


No 335
>smart00242 MYSc Myosin. Large ATPases. ATPase; molecular motor. Muscle contraction consists of a cyclical interaction between myosin and actin. The core of the myosin structure is similar in fold to that of kinesin.
Probab=92.93  E-value=0.14  Score=30.90  Aligned_cols=23  Identities=35%  Similarity=0.475  Sum_probs=19.3

Q ss_pred             CCCEEEEEECCCCCHHHHHHHHH
Q ss_conf             43204887327774367999999
Q gi|254780916|r  161 DCAIPIMIQGEFGVGKKRLSRFI  183 (482)
Q Consensus       161 ~~~~~vli~Ge~GtGK~~~A~~i  183 (482)
                      ..+..|+|.||+|+||+..++.|
T Consensus        90 ~~~QsIiisGESGaGKTes~K~i  112 (677)
T smart00242       90 KENQSIIISGESGAGKTENTKKI  112 (677)
T ss_pred             CCCCEEEEECCCCCCHHHHHHHH
T ss_conf             99927999688988877999999


No 336
>cd00267 ABC_ATPase ABC (ATP-binding cassette) transporter nucleotide-binding domain; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules.  The nucleotide-binding domain shows the highest similarity between all members of the family.  ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.
Probab=92.90  E-value=0.28  Score=28.64  Aligned_cols=107  Identities=20%  Similarity=0.164  Sum_probs=58.3

Q ss_pred             CCCCCCCCCCCEEEEEECCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCH--HHHHCCCCCCCCCCCCCCCC--
Q ss_conf             22222234432048873277743679999998426754332101234655421002--43311255553221110012--
Q gi|254780916|r  153 VDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHESGKRAFFPFFIVNCGMIDQDKIE--KFLFGDVDLQTKNSAQFLGK--  228 (482)
Q Consensus       153 ~~~i~~~a~~~~~vli~Ge~GtGK~~~A~~iH~~s~r~~~~fi~v~c~~~~~~~~e--~~lFG~~~~~~~~~~~~~g~--  228 (482)
                      .+.+.--.....-+.|.|++|+||+++.+.|-..-....+ -|.++...+......  ..-.|......|...++..+  
T Consensus        15 l~~i~~~i~~Ge~~~i~G~nGaGKSTLl~~l~gl~~~~~G-~i~~~g~~~~~~~~~~~~~~i~~v~QLSgGqkqrv~iA~   93 (157)
T cd00267          15 LDNVSLTLKAGEIVALVGPNGSGKSTLLRAIAGLLKPTSG-EILIDGKDIAKLPLEELRRRIGYVPQLSGGQRQRVALAR   93 (157)
T ss_pred             EEEEEEEECCCCEEEEECCCCCCHHHHHHHHHCCCCCCCC-EEEECCEECCCCCHHHHHHCCCCCCCCCHHHHHHHHHHH
T ss_conf             8211789879979999878899989999999588479962-899999999979999999406087668869999999999


Q ss_pred             CCCCCCCEEEECCCCH-HHHHHHHHHHHHHHHH
Q ss_conf             3446671475166420-0188999888877642
Q gi|254780916|r  229 FIEANGGTIVLEEPDA-LPLAVQGRIYNFIETG  260 (482)
Q Consensus       229 ~~~a~~Gtl~l~ei~~-L~~~~Q~~Ll~~l~~~  260 (482)
                      --..+--.++|||... |.+..+..+...+.+-
T Consensus        94 al~~~p~ililDEPtsgLD~~~~~~l~~~i~~l  126 (157)
T cd00267          94 ALLLNPDLLLLDEPTSGLDPASRERLLELLREL  126 (157)
T ss_pred             HHHCCCCEEEEECCCCCCCHHHHHHHHHHHHHH
T ss_conf             997099999996987668999999999999999


No 337
>smart00177 ARF ARF-like small GTPases; ARF, ADP-ribosylation factor. Ras homologues involved in vesicular transport. Activator of phospholipase D isoforms. Unlike Ras proteins they lack cysteine residues at their C-termini and therefore are unlikely to be prenylated. ARFs are N-terminally myristoylated. Contains ATP/GTP-binding motif (P-loop).
Probab=92.89  E-value=0.66  Score=26.05  Aligned_cols=120  Identities=12%  Similarity=0.192  Sum_probs=58.8

Q ss_pred             CCCEEEEEECCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCHHHHHCCCCCCCCCCCC----CCCCCCCCCCCE
Q ss_conf             4320488732777436799999984267543321012346554210024331125555322111----001234466714
Q gi|254780916|r  161 DCAIPIMIQGEFGVGKKRLSRFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFGDVDLQTKNSAQ----FLGKFIEANGGT  236 (482)
Q Consensus       161 ~~~~~vli~Ge~GtGK~~~A~~iH~~s~r~~~~fi~v~c~~~~~~~~e~~lFG~~~~~~~~~~~----~~g~~~~a~~Gt  236 (482)
                      .-..-|++.|..|+||+.+-+.++.......-|-+-+|...+....++-.++-     ++...+    -.-.+..|++-.
T Consensus        11 kk~~kililG~~~~GKTsil~~l~~~~~~~~~pTvg~~~~~~~~~~~~l~iwD-----~~Gqe~~r~l~~~Yy~~a~~iI   85 (175)
T smart00177       11 NKEMRILMVGLDAAGKTTILYKLKLGESVTTIPTIGFNVETVTYKNISFTVWD-----VGGQDKIRPLWRHYYTNTQGLI   85 (175)
T ss_pred             CCEEEEEEECCCCCCHHHHHHHHHCCCCCCCCCCCCCEEEEEEECCEEEEEEE-----CCCCCCCCHHHHHHCCCCCEEE
T ss_conf             88899999988999989999999659977757978810799998989999998-----9998545536777557761899


Q ss_pred             EEECCCCHHHH-HHHHHHHHHHHHHHCCCCCCCCCCCCCCEEEEECCCCCCCCCCHHHH
Q ss_conf             75166420018-89998888776420011235532123431565214332111111233
Q gi|254780916|r  237 IVLEEPDALPL-AVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVF  294 (482)
Q Consensus       237 l~l~ei~~L~~-~~Q~~Ll~~l~~~~~~~~g~~~~~~~~~RiIa~t~~~L~~~~~~g~f  294 (482)
                      +++|--..-+. +.+..|..++++...      +..+   =+|.+...|+...+.....
T Consensus        86 fVvD~sd~~~~~~~~~~l~~~l~~~~~------~~~p---iLil~NK~Dl~~~~~~~ei  135 (175)
T smart00177       86 FVVDSNDRDRIDEAREELHRMLNEDEL------RDAV---ILVFANKQDLPDAMKAAEI  135 (175)
T ss_pred             EEEECCCHHHHHHHHHHHHHHHCCHHH------CCCE---EEEEEECCCCCCCCCHHHH
T ss_conf             998668778999999999999631531------6986---9999845667678899999


No 338
>COG0512 PabA Anthranilate/para-aminobenzoate synthases component II [Amino acid transport and metabolism / Coenzyme metabolism]
Probab=92.88  E-value=0.66  Score=26.05  Aligned_cols=79  Identities=20%  Similarity=0.189  Sum_probs=55.4

Q ss_pred             CCCEEEECCCHHHHHHHHHHHHHCCCEEEEECCH--HHHHHHCCCCCEEEEECC--CCCCCHHHHHHHHHHHCCCCCEEE
Q ss_conf             8838998699899999999999889889998937--999986089989999785--469888999999998578983999
Q gi|254780916|r   10 HKRVLIIDKDDEQIKIIKDHVESYGYDVFIVNVS--DLSTISKIQVNVIFLSLI--NCEDDKENILKNIVDKIPIVPIIV   85 (482)
Q Consensus        10 ~~rILIVDDd~~~~~~l~~~L~~~G~~v~~a~~~--al~~l~~~~~dlillD~~--mP~~dGlell~~i~~~~p~ipvIi   85 (482)
                      +++||+||...++-..|...|...|++|.+..+.  ....++...||.|++.=-  -|..-|. .++.|++....+|++-
T Consensus         1 ~~~IL~IDNyDSFtyNLv~yl~~lg~~v~V~rnd~~~~~~~~~~~pd~iviSPGPG~P~d~G~-~~~~i~~~~~~~PiLG   79 (191)
T COG0512           1 MMMILLIDNYDSFTYNLVQYLRELGAEVTVVRNDDISLELIEALKPDAIVISPGPGTPKDAGI-SLELIRRFAGRIPILG   79 (191)
T ss_pred             CCEEEEEECCCCHHHHHHHHHHHCCCCEEEEECCCCCHHHHHHCCCCEEEECCCCCCHHHCCH-HHHHHHHHCCCCCEEE
T ss_conf             956999977442499999999973993499988965877886049998998489979377361-8999998608998899


Q ss_pred             EE-CC
Q ss_conf             92-68
Q gi|254780916|r   86 QT-TQ   89 (482)
Q Consensus        86 iT-~~   89 (482)
                      +- ||
T Consensus        80 VCLGH   84 (191)
T COG0512          80 VCLGH   84 (191)
T ss_pred             ECCCH
T ss_conf             87437


No 339
>cd01378 MYSc_type_I Myosin motor domain, type I myosins. Myosin I generates movement at the leading edge in cell motility, and class I myosins have been implicated in phagocytosis and vesicle transport. Myosin I, an unconventional myosin, does not form dimers. This catalytic (head) domain has ATPase activity and belongs to the larger group of P-loop NTPases. Myosins are actin-dependent molecular motors that play important roles in muscle contraction, cell motility, and organelle transport. The head domain is a molecular motor, which utilizes ATP hydrolysis to generate directed movement toward the plus end along actin filaments. A cyclical interaction between myosin and actin provides the driving force. Rates of ATP hydrolysis and consequently the speed of movement along actin filaments vary widely, from about 0.04 micrometer per second for myosin I to 4.5 micrometer per second for myosin II in skeletal muscle. Myosin II moves in discrete steps about 5-10 nm long and generates 1-5 picon
Probab=92.86  E-value=0.14  Score=30.91  Aligned_cols=24  Identities=29%  Similarity=0.419  Sum_probs=19.3

Q ss_pred             CCCEEEEEECCCCCHHHHHHHHHH
Q ss_conf             432048873277743679999998
Q gi|254780916|r  161 DCAIPIMIQGEFGVGKKRLSRFIH  184 (482)
Q Consensus       161 ~~~~~vli~Ge~GtGK~~~A~~iH  184 (482)
                      ..+..|+|.||+|+||+..++.|=
T Consensus        84 ~~nQsIiisGESGaGKTe~~K~il  107 (674)
T cd01378          84 NENQCVIISGESGAGKTEAAKKIM  107 (674)
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHH
T ss_conf             999379996788788889999999


No 340
>PRK08118 topology modulation protein; Reviewed
Probab=92.81  E-value=0.093  Score=32.06  Aligned_cols=32  Identities=28%  Similarity=0.445  Sum_probs=25.3

Q ss_pred             EEEEECCCCCHHHHHHHHHHHCCCCCCCCCCCCCC
Q ss_conf             48873277743679999998426754332101234
Q gi|254780916|r  165 PIMIQGEFGVGKKRLSRFIHESGKRAFFPFFIVNC  199 (482)
Q Consensus       165 ~vli~Ge~GtGK~~~A~~iH~~s~r~~~~fi~v~c  199 (482)
                      -|+|.|.+|+||+++|+.|-+.   -+-|++.+|.
T Consensus         3 rI~IiG~~GsGKSTlAr~L~~~---~~ip~~~LD~   34 (167)
T PRK08118          3 KIILIGSGGSGKSTLARQLGEK---LNIPVHHLDA   34 (167)
T ss_pred             EEEEECCCCCCHHHHHHHHHHH---HCCCEEECCC
T ss_conf             7999889998799999999998---8969796443


No 341
>PRK13900 type IV secretion system ATPase VirB11; Provisional
Probab=92.79  E-value=0.045  Score=34.26  Aligned_cols=46  Identities=15%  Similarity=0.143  Sum_probs=35.5

Q ss_pred             CCCCCCCCCCCCCEEEEEECCCCCHHHHHHHHHHHCCCCCCCCCCCC
Q ss_conf             22222222344320488732777436799999984267543321012
Q gi|254780916|r  151 QVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHESGKRAFFPFFIV  197 (482)
Q Consensus       151 ~v~~~i~~~a~~~~~vli~Ge~GtGK~~~A~~iH~~s~r~~~~fi~v  197 (482)
                      ++.+.++.+.....+++|.|++|+||+++++++-..-+. +..+|+|
T Consensus       148 ~~~~fL~~aV~~r~NilI~G~TgSGKTTll~aL~~~ip~-~eRiitI  193 (332)
T PRK13900        148 KIKEFLEHAVISKKNIIISGGTSTGKTTFTNAALREIPA-IERLITV  193 (332)
T ss_pred             HHHHHHHHHHHCCCCEEEECCCCCCHHHHHHHHHHCCCC-CCCEEEE
T ss_conf             799999999864871999888898899999999835895-3535663


No 342
>PRK02362 ski2-like helicase; Provisional
Probab=92.78  E-value=0.092  Score=32.08  Aligned_cols=53  Identities=9%  Similarity=0.072  Sum_probs=32.8

Q ss_pred             CCCCEEEEE-CCCCC-CC-H--H-HHHHHHHHHCCCCCEEEEECC-CCHHHHHHHHHCCCCC
Q ss_conf             899899997-85469-88-8--9-999999985789839999268-9999999888505743
Q gi|254780916|r   51 IQVNVIFLS-LINCE-DD-K--E-NILKNIVDKIPIVPIIVQTTQ-DNIKILNCFLYNRISK  105 (482)
Q Consensus        51 ~~~dlillD-~~mP~-~d-G--l-ell~~i~~~~p~ipvIiiT~~-~~~~~~~~a~~~g~~d  105 (482)
                      ...++|+.| +.|=+ .+ |  + .++.+++...|++.+|.+||. ++.+...  -+.++.-
T Consensus       136 ~~v~lVViDEiHli~d~~RG~~lE~~lskl~~~~~~iqiIgLSATl~N~~~la--~WL~a~~  195 (736)
T PRK02362        136 DDISCVVADEVHLIDSPNRGPTLEVTLAKLRRLNPDMQVIALSATIGNADELA--AWLDAEL  195 (736)
T ss_pred             HCCCEEEEECCEEECCCCCHHHHHHHHHHHHHCCCCCEEEEEECCCCCHHHHH--HHHCCCC
T ss_conf             50898998176786688724999999999973387743898624558999999--9838862


No 343
>PRK05428 HPr kinase/phosphorylase; Provisional
Probab=92.76  E-value=0.18  Score=30.06  Aligned_cols=102  Identities=19%  Similarity=0.170  Sum_probs=53.2

Q ss_pred             HHHHHHHH-CCCCCEEEEECCC-CHHHHHHHHHC-CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             99999985-7898399992689-99999988850-574322222222222222222222222222222111111112222
Q gi|254780916|r   70 ILKNIVDK-IPIVPIIVQTTQD-NIKILNCFLYN-RISKFFLNLVSRKQLCDSIICALREGVVPSQENEHCALDSLIAVS  146 (482)
Q Consensus        70 ll~~i~~~-~p~ipvIiiT~~~-~~~~~~~a~~~-g~~d~l~KP~~~~~L~~~i~~al~~~~~~~~~~~~~~~~~LiG~S  146 (482)
                      ..+.+.+. ..++|.+++|..- -.+.+.+.++. +..- |.-|....++...+..-+....++.. ..|..+-++    
T Consensus        71 ~~~~~~~l~~~~~P~iIvt~~~~~~~~l~~~a~~~~ipl-l~t~~~ts~~i~~l~~~L~~~lAp~~-~~HGvlvdV----  144 (308)
T PRK05428         71 RKERLKKLFSFEPPCIIVTRGLEPPEELLEAAKEAGIPL-LRTKLSTTRLISKLTNYLDRKLAPRT-SVHGVLVDV----  144 (308)
T ss_pred             HHHHHHHHHCCCCCEEEEECCCCCCHHHHHHHHHHCCCE-EECCCCHHHHHHHHHHHHHHHCCCCE-EEEEEEEEE----
T ss_conf             999999985769978999799999999999999849958-98287599999999999998608747-886589999----


Q ss_pred             CCCCCCCCCCCCCCCCCEEEEEECCCCCHHHHHHHHHHHCCCCCCCCCCC
Q ss_conf             22222222222234432048873277743679999998426754332101
Q gi|254780916|r  147 PAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHESGKRAFFPFFI  196 (482)
Q Consensus       147 ~~m~~v~~~i~~~a~~~~~vli~Ge~GtGK~~~A~~iH~~s~r~~~~fi~  196 (482)
                                     ...=|||+|++|.||+-+|=.+=..+    +.||+
T Consensus       145 ---------------~G~GVLI~G~SGiGKSE~aLeLI~RG----HrLVA  175 (308)
T PRK05428        145 ---------------YGIGVLITGESGIGKSETALELIKRG----HRLVA  175 (308)
T ss_pred             ---------------EEEEEEEECCCCCCHHHHHHHHHHCC----CEEEE
T ss_conf             ---------------44489997588888128999999849----93670


No 344
>COG4172 ABC-type uncharacterized transport system, duplicated ATPase component [General function prediction only]
Probab=92.74  E-value=0.34  Score=28.05  Aligned_cols=43  Identities=12%  Similarity=0.122  Sum_probs=29.2

Q ss_pred             HHHHCCCCCEEEEECCCCCCC------HHHHHHHHHHHCCCCCEEEEECC
Q ss_conf             998608998999978546988------89999999985789839999268
Q gi|254780916|r   46 STISKIQVNVIFLSLINCEDD------KENILKNIVDKIPIVPIIVQTTQ   89 (482)
Q Consensus        46 ~~l~~~~~dlillD~~mP~~d------Glell~~i~~~~p~ipvIiiT~~   89 (482)
                      ++.-.++||+.+.|-----.|      =+++++.+++.. .+.+++||-.
T Consensus       169 AMALan~P~lLIADEPTTALDVtvQaQIL~Ll~~Lq~~~-gMa~lfITHD  217 (534)
T COG4172         169 AMALANEPDLLIADEPTTALDVTVQAQILDLLKELQAEL-GMAILFITHD  217 (534)
T ss_pred             HHHHCCCCCEEEECCCCCHHHHHHHHHHHHHHHHHHHHH-CCEEEEEECC
T ss_conf             999738998686169852200305999999999999974-9579999442


No 345
>TIGR02982 heterocyst_DevA ABC exporter ATP-binding subunit, DevA family; InterPro: IPR014324   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 DevA, found mostly in the Cyanobacteria, but also in the Planctomycetes. Cyanobacterial examples are involved in heterocyst formation, by which some fraction of members of the colony undergo a developmental change and become capable of nitrogen fixation. The ABC transporter encoded by the devBCA operon is induced by nitrogen deficiency and is necessary for the formation of the laminated layer which envelops heterocysts , . It is thought to be involved in the export of either the heterocyst-specific glycolipids found in the laminated layer, or an enzyme essential for their formation..
Probab=92.70  E-value=0.12  Score=31.40  Aligned_cols=85  Identities=14%  Similarity=0.054  Sum_probs=51.3

Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCHHHHHCCCCCCC
Q ss_conf             11122222222222222223443204887327774367999999842675433210123465542100243311255553
Q gi|254780916|r  140 DSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFGDVDLQT  219 (482)
Q Consensus       140 ~~LiG~S~~m~~v~~~i~~~a~~~~~vli~Ge~GtGK~~~A~~iH~~s~r~~~~fi~v~c~~~~~~~~e~~lFG~~~~~~  219 (482)
                      +-+.|+...=+.|...+.---..-.=|+++|++||||+++=-.|=..-.-.+|.+-          .+..+|.|-.+..-
T Consensus         8 nHyyG~G~~rkQvL~di~L~i~~GEiViltGPSGSGKTTLLtLiG~LR~~Q~G~L~----------vlg~~L~ga~~~~l   77 (220)
T TIGR02982         8 NHYYGEGSLRKQVLFDINLEINPGEIVILTGPSGSGKTTLLTLIGGLRSVQEGSLK----------VLGQELKGASKKEL   77 (220)
T ss_pred             CCEECCCCCCCEEECCCCEEECCCEEEEEECCCCCCHHHHHHHHHHHCCCCCCEEE----------EECCHHCCCCHHHH
T ss_conf             41114687421001276317717647984378898468899988762565556047----------82201026788899


Q ss_pred             CCCCCCCCCCCCCCC
Q ss_conf             221110012344667
Q gi|254780916|r  220 KNSAQFLGKFIEANG  234 (482)
Q Consensus       220 ~~~~~~~g~~~~a~~  234 (482)
                      ...-+++|.+=+++|
T Consensus        78 ~~~RR~iGyIFQ~HN   92 (220)
T TIGR02982        78 VQVRRNIGYIFQAHN   92 (220)
T ss_pred             HHHHHHCCCEECCCH
T ss_conf             999876391441200


No 346
>KOG1970 consensus
Probab=92.60  E-value=0.32  Score=28.28  Aligned_cols=20  Identities=20%  Similarity=0.539  Sum_probs=16.4

Q ss_pred             EEEECCCCCHHHHHHHHHHH
Q ss_conf             88732777436799999984
Q gi|254780916|r  166 IMIQGEFGVGKKRLSRFIHE  185 (482)
Q Consensus       166 vli~Ge~GtGK~~~A~~iH~  185 (482)
                      .||+|++|+||++.-+.+-.
T Consensus       113 LLltGPsGcGKSTtvkvLsk  132 (634)
T KOG1970         113 LLLTGPSGCGKSTTVKVLSK  132 (634)
T ss_pred             EEEECCCCCCCHHHHHHHHH
T ss_conf             99857988871319999998


No 347
>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=92.60  E-value=0.11  Score=31.60  Aligned_cols=163  Identities=18%  Similarity=0.241  Sum_probs=79.1

Q ss_pred             CEEEEEECCCCCHHH-HHHHHHHHCCCCCCCCCCCCCCCCCCCCCCHHHHHCCCCCC-----CC-CCCCCC----CCCCC
Q ss_conf             204887327774367-99999984267543321012346554210024331125555-----32-211100----12344
Q gi|254780916|r  163 AIPIMIQGEFGVGKK-RLSRFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFGDVDLQ-----TK-NSAQFL----GKFIE  231 (482)
Q Consensus       163 ~~~vli~Ge~GtGK~-~~A~~iH~~s~r~~~~fi~v~c~~~~~~~~e~~lFG~~~~~-----~~-~~~~~~----g~~~~  231 (482)
                      .-=||++|+||+||+ ++|--|=+-=..+....++|      +|-+| -+|-+++..     =| +..++.    -.|.+
T Consensus       127 ~GLiLVTGPTGSGKSTTlAsmIDyIN~~~~~HIiTI------EDPIE-yvh~~~~sli~QREvG~DT~sF~~ALraALRe  199 (350)
T TIGR01420       127 RGLILVTGPTGSGKSTTLASMIDYINKNKAGHIITI------EDPIE-YVHKNKRSLINQREVGLDTLSFANALRAALRE  199 (350)
T ss_pred             CCCEEEECCCCCCHHHHHHHHHHHHHCCCCCCCEEE------ECCEE-EEECCCEEEEECCCCCCCHHHHHHHHHHHHCC
T ss_conf             993898768898678999999978740388882563------17731-41047702454362467545799997684102


Q ss_pred             CCCCEEEECCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCEEEEEC-CCCCCCCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf             66714751664200188999888877642001123553212343156521-43321111112333799988654334467
Q gi|254780916|r  232 ANGGTIVLEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLT-EKNLLPQVKSHVFRKDLYYRISVFLINIS  310 (482)
Q Consensus       232 a~~Gtl~l~ei~~L~~~~Q~~Ll~~l~~~~~~~~g~~~~~~~~~RiIa~t-~~~L~~~~~~g~fr~dLy~rL~~~~i~iP  310 (482)
                       +--.+|+=|+=|+.-  =.-=|.+=|+|               .+|.+| |-|    -+.....     |    -|.+=
T Consensus       200 -DPDvILiGE~RD~ET--~~~AL~AAETG---------------HLV~gTLHTn----sA~~ti~-----R----Iid~F  248 (350)
T TIGR01420       200 -DPDVILIGEMRDLET--VELALTAAETG---------------HLVFGTLHTN----SAAKTIE-----R----IIDVF  248 (350)
T ss_pred             -CCCEEEEECCCCHHH--HHHHHHHHHHC---------------CHHHHHHHHH----HHHHHHH-----H----HHCCC
T ss_conf             -898899825562789--99999874213---------------1567666642----3888767-----7----74259


Q ss_pred             HHHHHHHHHHHHHHHHHHHHCCCCCCCCCC-----------CCCCCCCCCCCCCCCCCHHHHHHHHH
Q ss_conf             787744222255667776410112233332-----------11111000122338986899999999
Q gi|254780916|r  311 TLRSRSEDIPWLVHFFLQSFCTKNAIKQIS-----------ISDKALSLLTKYPWIDNVQELKNILL  366 (482)
Q Consensus       311 pLReR~eDI~~L~~~fl~~~~~~~~~~~~~-----------ls~~a~~~L~~y~WPGNvREL~n~i~  366 (482)
                      |..||..=--.|+..++.-+++++=.+.-+           -+|...++..+   ||++.|++.+++
T Consensus       249 P~~~~~qiR~~La~~L~Av~sQrL~p~~~G~GRv~~~Eil~~Tpav~~lIre---~gk~~qi~~~i~  312 (350)
T TIGR01420       249 PAEEQEQIRTQLAESLVAVISQRLLPKKNGGGRVLAVEILINTPAVRNLIRE---EGKTHQIKSVIQ  312 (350)
T ss_pred             CHHHHHHHHHHHHHHHHHHHCCCCEEECCCCCEEEEEEEECCCHHHHHHHCC---CCCHHHHHHHHH
T ss_conf             7756689999998767877000542233896258888752158789996028---788768999987


No 348
>PRK13413 mpi multiple promoter invertase; Provisional
Probab=92.59  E-value=0.29  Score=28.59  Aligned_cols=28  Identities=29%  Similarity=0.392  Sum_probs=24.1

Q ss_pred             HHCCCHHHHHHHHCCCHHHHHHHHHHHC
Q ss_conf             8287278999784899889999999818
Q gi|254780916|r  449 LYRAQMSEVARRLGIGRSTLYRKIREYN  476 (482)
Q Consensus       449 ~~~Gn~~~aA~~LGIsR~tL~rKlk~~g  476 (482)
                      ..+-+.++.|+.+||||+|+||-+|.|.
T Consensus       170 ~~g~s~~~iak~~gvsrsTvyR~lK~~~  197 (200)
T PRK13413        170 KKGTTKSEIAKKLKVSRTTLARFLKTMY  197 (200)
T ss_pred             HCCCCHHHHHHHHCCCHHHHHHHHHHHH
T ss_conf             8889999999998929999999997441


No 349
>cd01377 MYSc_type_II Myosin motor domain, type II myosins. Myosin II mediates cortical contraction in cell motility, and is the motor in smooth and skeletal muscle. This catalytic (head) domain has ATPase activity and belongs to the larger group of P-loop NTPases. Myosins are actin-dependent molecular motors that play important roles in muscle contraction, cell motility, and organelle transport. The head domain is a molecular motor, which utilizes ATP hydrolysis to generate directed movement toward the plus end along actin filaments. A cyclical interaction between myosin and actin provides the driving force. Rates of ATP hydrolysis and consequently the speed of movement along actin filaments vary widely, from about 0.04 micrometer per second for myosin I to 4.5 micrometer per second for myosin II in skeletal muscle. Myosin II moves in discrete steps about 5-10 nm long and generates 1-5 piconewtons of force. Upon ATP binding, the myosin head dissociates from an actin filament. ATP hydro
Probab=92.57  E-value=0.13  Score=31.06  Aligned_cols=23  Identities=30%  Similarity=0.452  Sum_probs=19.2

Q ss_pred             CCCEEEEEECCCCCHHHHHHHHH
Q ss_conf             43204887327774367999999
Q gi|254780916|r  161 DCAIPIMIQGEFGVGKKRLSRFI  183 (482)
Q Consensus       161 ~~~~~vli~Ge~GtGK~~~A~~i  183 (482)
                      ..+..|+|.||+|+||+..++.|
T Consensus        89 ~~~QsIiiSGESGAGKTes~K~i  111 (693)
T cd01377          89 RENQSILITGESGAGKTENTKKV  111 (693)
T ss_pred             CCCCEEEEECCCCCCHHHHHHHH
T ss_conf             99806999688988889999999


No 350
>KOG0741 consensus
Probab=92.50  E-value=0.084  Score=32.38  Aligned_cols=190  Identities=17%  Similarity=0.233  Sum_probs=90.8

Q ss_pred             CCCCCCCCCCCCCCCCCCCC----CCCC----CCEEEEEECCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCC--
Q ss_conf             11111222222222222222----2344----3204887327774367999999842675433210123465542100--
Q gi|254780916|r  138 ALDSLIAVSPAMIQVVDLAR----KAGD----CAIPIMIQGEFGVGKKRLSRFIHESGKRAFFPFFIVNCGMIDQDKI--  207 (482)
Q Consensus       138 ~~~~LiG~S~~m~~v~~~i~----~~a~----~~~~vli~Ge~GtGK~~~A~~iH~~s~r~~~~fi~v~c~~~~~~~~--  207 (482)
                      ...+++..++-..++.+...    ++-+    .-.+||+.|++|+||+.+|--|-..|.   -|||.+ |+  |++.+  
T Consensus       505 ~~~Gmi~~g~~v~~il~~G~llv~qvk~s~~s~lvSvLl~Gp~~sGKTaLAA~iA~~S~---FPFvKi-iS--pe~miG~  578 (744)
T KOG0741         505 VMNGMINWGPPVTRILDDGKLLVQQVKNSERSPLVSVLLEGPPGSGKTALAAKIALSSD---FPFVKI-IS--PEDMIGL  578 (744)
T ss_pred             HHCCCEEECCCHHHHHHHHHHHHHHHHCCCCCCCEEEEEECCCCCCHHHHHHHHHHHCC---CCEEEE-EC--HHHHCCC
T ss_conf             85785451630778876688999986334667635899866998876889999975279---984797-37--7870374


Q ss_pred             -HHHHHCCC-CCCCCCCCCCCCCCCCCCCCEEEECCCCHH------H-----HHHHHHHHHHHHHHHCCCCCCCCCCCCC
Q ss_conf             -24331125-555322111001234466714751664200------1-----8899988887764200112355321234
Q gi|254780916|r  208 -EKFLFGDV-DLQTKNSAQFLGKFIEANGGTIVLEEPDAL------P-----LAVQGRIYNFIETGKIEFFDSRGAIRLD  274 (482)
Q Consensus       208 -e~~lFG~~-~~~~~~~~~~~g~~~~a~~Gtl~l~ei~~L------~-----~~~Q~~Ll~~l~~~~~~~~g~~~~~~~~  274 (482)
                       |+.=--|. +.|-+|...        --..+++|+|+.|      .     .-.|+ |+-+|...   |.   +.++  
T Consensus       579 sEsaKc~~i~k~F~DAYkS--------~lsiivvDdiErLiD~vpIGPRfSN~vlQa-L~VllK~~---pp---kg~k--  641 (744)
T KOG0741         579 SESAKCAHIKKIFEDAYKS--------PLSIIVVDDIERLLDYVPIGPRFSNLVLQA-LLVLLKKQ---PP---KGRK--  641 (744)
T ss_pred             CHHHHHHHHHHHHHHHHCC--------CCEEEEECCHHHHHCCCCCCCCHHHHHHHH-HHHHHCCC---CC---CCCE--
T ss_conf             6678899999988876338--------650899815565620024684035799999-99995248---98---8845--


Q ss_pred             CEEEEECCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             31565214332111111233379998865433446778774422225566777641011223333211111000122338
Q gi|254780916|r  275 VRLIFLTEKNLLPQVKSHVFRKDLYYRISVFLINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPW  354 (482)
Q Consensus       275 ~RiIa~t~~~L~~~~~~g~fr~dLy~rL~~~~i~iPpLReR~eDI~~L~~~fl~~~~~~~~~~~~~ls~~a~~~L~~y~W  354 (482)
                      .-|+++|+ .-+-+-+-|     +|... ..+|+||.|-.-.++...|.+  +..|+.      -.....+.+.+....|
T Consensus       642 Lli~~TTS-~~~vL~~m~-----i~~~F-~~~i~Vpnl~~~~~~~~vl~~--~n~fsd------~~~~~~~~~~~~~~~~  706 (744)
T KOG0741         642 LLIFGTTS-RREVLQEMG-----ILDCF-SSTIHVPNLTTGEQLLEVLEE--LNIFSD------DEVRAIAEQLLSKKVN  706 (744)
T ss_pred             EEEEECCC-HHHHHHHCC-----HHHHH-HHEEECCCCCCHHHHHHHHHH--CCCCCC------CHHHHHHHHHHCCCCC
T ss_conf             99996240-799999727-----78751-110546756864789999997--166784------1467899987422321


Q ss_pred             CCCHHHHHHHHH
Q ss_conf             986899999999
Q gi|254780916|r  355 IDNVQELKNILL  366 (482)
Q Consensus       355 PGNvREL~n~i~  366 (482)
                      +| |..|--.|+
T Consensus       707 vg-IKklL~lie  717 (744)
T KOG0741         707 VG-IKKLLMLIE  717 (744)
T ss_pred             HH-HHHHHHHHH
T ss_conf             31-999999988


No 351
>cd00878 Arf_Arl Arf (ADP-ribosylation factor)/Arl (Arf-like) small GTPases.  Arf proteins are activators of phospholipase D isoforms.  Unlike Ras proteins they lack cysteine residues at their C-termini and therefore are unlikely to be prenylated.  Arfs are N-terminally myristoylated.  Members of the Arf family are regulators of vesicle formation in intracellular traffic that interact reversibly with membranes of the secretory and endocytic compartments in a GTP-dependent manner.  They depart from other small GTP-binding proteins by a unique structural device, interswitch toggle, that implements front-back communication from N-terminus to the nucleotide binding site.  Arf-like (Arl) proteins are close relatives of the Arf, but only Arl1 has been shown to function in membrane traffic like the Arf proteins.  Arl2 has an unrelated function in the folding of native tubulin, and Arl4 may function in the nucleus.  Most other Arf family proteins are so far relatively poorly characterized.  Thu
Probab=92.47  E-value=0.91  Score=25.04  Aligned_cols=117  Identities=15%  Similarity=0.200  Sum_probs=49.8

Q ss_pred             EEEECCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCHHHHHCCCCCCCCCCCCCCCCCCCCCCCEEEECCCCHH
Q ss_conf             88732777436799999984267543321012346554210024331125555322111001234466714751664200
Q gi|254780916|r  166 IMIQGEFGVGKKRLSRFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFGDVDLQTKNSAQFLGKFIEANGGTIVLEEPDAL  245 (482)
Q Consensus       166 vli~Ge~GtGK~~~A~~iH~~s~r~~~~fi~v~c~~~~~~~~e~~lFG~~~~~~~~~~~~~g~~~~a~~Gtl~l~ei~~L  245 (482)
                      |++.|.+|+||+.+-+.+.....-...|-+-++...+.-..+.-.++.- .|...-..-....+..|++-.+++|--..-
T Consensus         2 i~ilG~~~vGKTsll~~l~~~~~~~~~pTig~~~~~i~~~~~~l~iwDt-~G~~~~~~~~~~y~~~a~~~i~V~D~t~~~   80 (158)
T cd00878           2 ILILGLDGAGKTTILYKLKLGEVVTTIPTIGFNVETVEYKNVSFTVWDV-GGQDKIRPLWKHYYENTNGIIFVVDSSDRE   80 (158)
T ss_pred             EEEECCCCCCHHHHHHHHHCCCCCCCCCEECCCEEEEEECCEEEEEEEC-CCCCCCCHHHHHHHCCCCEEEEEEECCCHH
T ss_conf             9999999998899999995399887445607408999848899999988-997221448998727687768998379888


Q ss_pred             HHH-HHHHHHHHHHHHHCCCCCCCCCCCCCCEEEEECCCCCCCCCCHH
Q ss_conf             188-99988887764200112355321234315652143321111112
Q gi|254780916|r  246 PLA-VQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSH  292 (482)
Q Consensus       246 ~~~-~Q~~Ll~~l~~~~~~~~g~~~~~~~~~RiIa~t~~~L~~~~~~g  292 (482)
                      +.+ ....+-+++....      ....+   =+|+++..||...+...
T Consensus        81 s~~~~~~~~~~~~~~~~------~~~~p---iliv~NK~Dl~~~~~~~  119 (158)
T cd00878          81 RIEEAKEELHKLLNEEE------LKGVP---LLIFANKQDLPGALSVS  119 (158)
T ss_pred             HHHHHHHHHHHHHHHCC------CCCCE---EEEEEECCCCCCCCCHH
T ss_conf             99999999999986605------57653---89876054766578999


No 352
>cd01124 KaiC KaiC is a circadian clock protein primarily found in cyanobacteria KaiC is a RecA-like ATPase, having both Walker A and Walker B motifs. A related protein is found in archaea.
Probab=92.45  E-value=0.071  Score=32.90  Aligned_cols=30  Identities=17%  Similarity=0.171  Sum_probs=19.9

Q ss_pred             EEEEECCCCCHHHHHHHH-HHHCCCCCCCCCC
Q ss_conf             488732777436799999-9842675433210
Q gi|254780916|r  165 PIMIQGEFGVGKKRLSRF-IHESGKRAFFPFF  195 (482)
Q Consensus       165 ~vli~Ge~GtGK~~~A~~-iH~~s~r~~~~fi  195 (482)
                      ++||.|++||||+.+|-- +++. -+.+.+-+
T Consensus         1 stLi~G~pGsGKT~~a~qfl~~~-a~~ge~~l   31 (187)
T cd01124           1 STLLSGGPGTGKTTFALQFLYAG-LARGEPGL   31 (187)
T ss_pred             CEEEEECCCCCHHHHHHHHHHHH-HHCCCCEE
T ss_conf             91587689999999999999999-87699789


No 353
>TIGR03608 L_ocin_972_ABC putative bacteriocin export ABC transporter, lactococcin 972 group. A gene pair with a fairly wide distribution consists of a polypeptide related to the lactococcin 972 (see TIGR01653) and multiple-membrane-spanning putative immunity protein (see TIGR01654). This model represents a small clade within the ABC transporters that regularly are found adjacent to these bacteriocin system gene pairs and are likely serve as export proteins.
Probab=92.35  E-value=0.37  Score=27.79  Aligned_cols=32  Identities=28%  Similarity=0.308  Sum_probs=23.3

Q ss_pred             CCCCCCCCCCCCEEEEEECCCCCHHHHHHHHH
Q ss_conf             22222223443204887327774367999999
Q gi|254780916|r  152 VVDLARKAGDCAIPIMIQGEFGVGKKRLSRFI  183 (482)
Q Consensus       152 v~~~i~~~a~~~~~vli~Ge~GtGK~~~A~~i  183 (482)
                      +.+.+.--.....-|.|.|++|+||+++-+.|
T Consensus        13 vL~~vsl~i~~Ge~~~i~GpSGsGKSTLL~~i   44 (206)
T TIGR03608        13 ILDDLNLTIEKGKMVAIVGESGSGKSTLLNII   44 (206)
T ss_pred             EECCEEEEECCCCEEEEECCCCCCHHHHHHHH
T ss_conf             97580779869989999879997099999999


No 354
>TIGR01846 type_I_sec_HlyB type I secretion system ATPase; InterPro: IPR010132   Type I protein secretion is a system in some Gram-negative bacteria to export proteins (often proteases) across both inner and outer membranes to the extracellular medium. This entry contains one of three proteins of the type I secretion apparatus. Targeted proteins are not cleaved at the N terminus, but rather carry signals located toward the extreme C terminus to direct type I secretion.; GO: 0005524 ATP binding, 0008565 protein transporter activity, 0015031 protein transport, 0016021 integral to membrane.
Probab=92.32  E-value=0.13  Score=30.99  Aligned_cols=138  Identities=16%  Similarity=0.105  Sum_probs=64.9

Q ss_pred             CCHHHHHHHHHHH---CCCCCEEEEECCCCHHHHHHHHHCCCCCCCCCCCCCC-CCC---CCCCCCCCCCC-C---CCCC
Q ss_conf             8889999999985---7898399992689999999888505743222222222-222---22222222222-2---2222
Q gi|254780916|r   65 DDKENILKNIVDK---IPIVPIIVQTTQDNIKILNCFLYNRISKFFLNLVSRK-QLC---DSIICALREGV-V---PSQE  133 (482)
Q Consensus        65 ~dGlell~~i~~~---~p~ipvIiiT~~~~~~~~~~a~~~g~~d~l~KP~~~~-~L~---~~i~~al~~~~-~---~~~~  133 (482)
                      .-|++++.++...   +-.+ -.|+.|.=++-..++ .++ ...++..|+-+- ++-   +.+.-++++-- .   |.+.
T Consensus       372 ~Q~I~LI~K~t~a~~LWfGa-~lVi~G~ls~G~LVA-FNM-lAG~V~~PvlRLAQ~WQDFQq~~Ia~~RlGDiLn~P~E~  448 (703)
T TIGR01846       372 SQAIELINKLTAALLLWFGA-HLVIKGELSVGQLVA-FNM-LAGRVSQPVLRLAQLWQDFQQVGIAIERLGDILNSPTEP  448 (703)
T ss_pred             HHHHHHHHHHHHHHHHHCCC-EEEECCCCCHHHHHH-HHH-HCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCC
T ss_conf             88999999999999985051-477626677437998-733-136302358989987666887766653121005868488


Q ss_pred             ---CCCCCCCCCCC----------CCCCCCCCCCCCCCCCCCCEEEEEECCCCCHHHHHHHHHHHCCCCCCCCC-C-CCC
Q ss_conf             ---21111111122----------22222222222222344320488732777436799999984267543321-0-123
Q gi|254780916|r  134 ---NEHCALDSLIA----------VSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHESGKRAFFPF-F-IVN  198 (482)
Q Consensus       134 ---~~~~~~~~LiG----------~S~~m~~v~~~i~~~a~~~~~vli~Ge~GtGK~~~A~~iH~~s~r~~~~f-i-~v~  198 (482)
                         ....+...+-|          ..|.--+|.+.+.---.--.-+=|+|++|+||++++|.+-...--..|.- | -+|
T Consensus       449 ~~d~g~aalP~l~G~i~F~nirFRY~pD~PeVL~nl~L~I~~Ge~IGIvGpSGSGKSTLTKL~QRLYtP~~GqVLVDG~D  528 (703)
T TIGR01846       449 SSDAGLAALPELKGSITFENIRFRYKPDSPEVLSNLSLDIKPGEVIGIVGPSGSGKSTLTKLLQRLYTPEHGQVLVDGVD  528 (703)
T ss_pred             CCCCCCCCCCCCCCCEEEEEEEECCCCCCCHHHHCCCCCCCCCEEEEEECCCCCCHHHHHHHHHHHCCCCCCEEEECCCC
T ss_conf             99987303542257267875331468887178732687657865799872789867899999886148888747770300


Q ss_pred             CCCCCCC
Q ss_conf             4655421
Q gi|254780916|r  199 CGMIDQD  205 (482)
Q Consensus       199 c~~~~~~  205 (482)
                      .|-.|+.
T Consensus       529 LA~~DP~  535 (703)
T TIGR01846       529 LAIADPA  535 (703)
T ss_pred             CCCCCCC
T ss_conf             0101852


No 355
>cd04151 Arl1 Arl1 subfamily.  Arl1 (Arf-like 1) localizes to the Golgi complex, where it is believed to recruit effector proteins to the trans-Golgi network.  Like most members of the Arf family, Arl1 is myristoylated at its N-terminal helix and mutation of the myristoylation site disrupts Golgi targeting.  In humans, the Golgi-localized proteins golgin-97 and golgin-245 have been identified as Arl1 effectors.  Golgins are large coiled-coil proteins found in the Golgi, and these golgins contain a C-terminal GRIP domain, which is the site of Arl1 binding.  Additional Arl1 effectors include the GARP (Golgi-associated retrograde protein)/VFT (Vps53) vesicle-tethering complex and Arfaptin 2.  Arl1 is not required for exocytosis, but appears necessary for trafficking from the endosomes to the Golgi.  In Drosophila zygotes, mutation of Arl1 is lethal, and in the host-bloodstream form of Trypanosoma brucei, Arl1 is essential for viability.
Probab=92.28  E-value=0.96  Score=24.88  Aligned_cols=116  Identities=12%  Similarity=0.192  Sum_probs=54.6

Q ss_pred             EEEECCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCHHHHH---CCCCCCCCCCCCCCCCCCCCCCCEEEECCC
Q ss_conf             88732777436799999984267543321012346554210024331---125555322111001234466714751664
Q gi|254780916|r  166 IMIQGEFGVGKKRLSRFIHESGKRAFFPFFIVNCGMIDQDKIEKFLF---GDVDLQTKNSAQFLGKFIEANGGTIVLEEP  242 (482)
Q Consensus       166 vli~Ge~GtGK~~~A~~iH~~s~r~~~~fi~v~c~~~~~~~~e~~lF---G~~~~~~~~~~~~~g~~~~a~~Gtl~l~ei  242 (482)
                      |++.|..|+||+.+-+.++........|-+-+|...+..+.+.-.++   |+++.    ..-..-.+..|++-.+++|--
T Consensus         2 il~lG~~~~GKTsll~~~~~~~~~~~~pTig~~~~~i~~~~~~~~iwD~~G~e~~----r~~~~~y~~~~~~ii~VvD~s   77 (158)
T cd04151           2 ILILGLDNAGKTTILYRLQLGEVVTTIPTIGFNVETVTYKNLKFQVWDLGGQTSI----RPYWRCYYSNTDAIIYVVDST   77 (158)
T ss_pred             EEEECCCCCCHHHHHHHHHCCCCCCCCCCCCCCEEEEEECCEEEEEEECCCCCCC----CHHHHHHCCCCCEEEEEEECC
T ss_conf             9999999998999999997099677578488246999989889999967986244----627887466788999997457


Q ss_pred             CHHHHH-HHHHHHHHHHHHHCCCCCCCCCCCCCCEEEEECCCCCCCCCCHHHH
Q ss_conf             200188-9998888776420011235532123431565214332111111233
Q gi|254780916|r  243 DALPLA-VQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVF  294 (482)
Q Consensus       243 ~~L~~~-~Q~~Ll~~l~~~~~~~~g~~~~~~~~~RiIa~t~~~L~~~~~~g~f  294 (482)
                      ..-+.+ ....|..++++...      ...+   -+|.+...|+...+.....
T Consensus        78 d~~~~~~~~~~l~~~l~~~~~------~~~p---iliv~NK~Dl~~~~~~~~i  121 (158)
T cd04151          78 DRDRLGTAKEELHAMLEEEEL------KGAV---LLVFANKQDMPGALSEAEI  121 (158)
T ss_pred             CHHHHHHHHHHHHHHHHHHHH------CCCC---EEEEEECCCCCCCCCHHHH
T ss_conf             878999999999999834653------6981---9999976677657799999


No 356
>PRK09302 circadian clock protein KaiC; Reviewed
Probab=92.21  E-value=0.52  Score=26.80  Aligned_cols=28  Identities=25%  Similarity=0.351  Sum_probs=20.0

Q ss_pred             CCCEEEEEECCCCCHHHHHHH-HHHHCCC
Q ss_conf             432048873277743679999-9984267
Q gi|254780916|r  161 DCAIPIMIQGEFGVGKKRLSR-FIHESGK  188 (482)
Q Consensus       161 ~~~~~vli~Ge~GtGK~~~A~-~iH~~s~  188 (482)
                      .....+||.|++||||+++|- ++.+.-.
T Consensus       264 ~~GsstLi~Gp~GtGKTtla~qFl~~~a~  292 (501)
T PRK09302        264 FRGSIILVSGATGTGKTLLVSKFAEAACR  292 (501)
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHHHHHHH
T ss_conf             58946999889998889999999999986


No 357
>PRK13851 type IV secretion system protein VirB11; Provisional
Probab=92.18  E-value=0.056  Score=33.60  Aligned_cols=45  Identities=11%  Similarity=0.147  Sum_probs=34.1

Q ss_pred             CCCCCCCCCCCCEEEEEECCCCCHHHHHHHHHHHCCCCCCCCCCCC
Q ss_conf             2222222344320488732777436799999984267543321012
Q gi|254780916|r  152 VVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHESGKRAFFPFFIV  197 (482)
Q Consensus       152 v~~~i~~~a~~~~~vli~Ge~GtGK~~~A~~iH~~s~r~~~~fi~v  197 (482)
                      +...++.+.....+++|.|.+||||+++.+++=..-+. +...++|
T Consensus       151 ~~~fL~~aV~~r~NIlIsGgTGSGKTTllnALl~~IP~-~eRIvtI  195 (343)
T PRK13851        151 LEAFLHACVVGRLTMLLCGPTGSGKTTMSKTLISAIPP-QERLITI  195 (343)
T ss_pred             HHHHHHHHHHCCCCEEEECCCCCCHHHHHHHHHHCCCC-CCCEEEE
T ss_conf             99999999976988999888986199999999962896-5527996


No 358
>PRK13894 conjugal transfer ATPase TrbB; Provisional
Probab=92.07  E-value=0.054  Score=33.71  Aligned_cols=50  Identities=20%  Similarity=0.186  Sum_probs=34.1

Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCCCHHHHHHHHHHHC
Q ss_conf             11111122222222222222223443204887327774367999999842
Q gi|254780916|r  137 CALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHES  186 (482)
Q Consensus       137 ~~~~~LiG~S~~m~~v~~~i~~~a~~~~~vli~Ge~GtGK~~~A~~iH~~  186 (482)
                      ...++++.....-....+.+..+.....+++|.|.+|+||+++.+++-..
T Consensus       123 ~tL~dlv~~G~~~~~~a~~L~~~V~~r~nilI~G~TgsGKTTll~all~~  172 (320)
T PRK13894        123 FTLDQYVERGIMTAEQREAIIAAVRAHRNILVIGGTGSGKTTLVNAIINE  172 (320)
T ss_pred             CCHHHHHHCCCCCHHHHHHHHHHHHCCCCEEEECCCCCCHHHHHHHHHHH
T ss_conf             99999987699999999999999972875899858886568999999863


No 359
>KOG2680 consensus
Probab=91.97  E-value=0.59  Score=26.37  Aligned_cols=130  Identities=17%  Similarity=0.236  Sum_probs=77.6

Q ss_pred             CCCCEEEECCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCEEEEECCCCCCCCC-----CHHHHHHHHHHHHHHHH
Q ss_conf             6671475166420018899988887764200112355321234315652143321111-----11233379998865433
Q gi|254780916|r  232 ANGGTIVLEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQV-----KSHVFRKDLYYRISVFL  306 (482)
Q Consensus       232 a~~Gtl~l~ei~~L~~~~Q~~Ll~~l~~~~~~~~g~~~~~~~~~RiIa~t~~~L~~~~-----~~g~fr~dLy~rL~~~~  306 (482)
                      -..|.||+||++-|..+.=.-|-|+|++ .+.|+           +|.+||+-....-     ......-||+.|+-.+ 
T Consensus       287 ivpGVLFIDEvHMLDIEcFsFlNrAlE~-d~~Pi-----------iimaTNrgit~iRGTn~~SphGiP~D~lDR~lII-  353 (454)
T KOG2680         287 IVPGVLFIDEVHMLDIECFSFLNRALEN-DMAPI-----------IIMATNRGITRIRGTNYRSPHGIPIDLLDRMLII-  353 (454)
T ss_pred             ECCCEEEEEEEHHHHHHHHHHHHHHHHH-CCCCE-----------EEEECCCCEEEEECCCCCCCCCCCHHHHHHHHEE-
T ss_conf             2255178740021115799988887650-46857-----------9997277557760577789888867776441255-


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHH---HHHHHHCCCCCCCHHHHH
Q ss_conf             44677877442222556677764101122333321111100012233898689999999---999874389810688954
Q gi|254780916|r  307 INISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQELKNIL---LRAVIGLKDSHLTEDRFV  383 (482)
Q Consensus       307 i~iPpLReR~eDI~~L~~~fl~~~~~~~~~~~~~ls~~a~~~L~~y~WPGNvREL~n~i---~r~~i~~~~~~i~~~~~~  383 (482)
                       ..-|  -..+|+..+...    -|++.+   ..++++|+.+|..-.----+|=--|+|   ...+.-..+.++..+|+.
T Consensus       354 -~t~p--y~~~d~~~IL~i----Rc~EEd---v~m~~~A~d~Lt~i~~~tsLRYai~Lit~a~~~~~krk~~~v~~~di~  423 (454)
T KOG2680         354 -STQP--YTEEDIKKILRI----RCQEED---VEMNPDALDLLTKIGEATSLRYAIHLITAASLVCLKRKGKVVEVDDIE  423 (454)
T ss_pred             -ECCC--CCHHHHHHHHHH----HHHHHC---CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCEEEHHHHH
T ss_conf             -2565--768899999875----500521---335878999999861312378999998899999987548565446789


Q ss_pred             H
Q ss_conf             5
Q gi|254780916|r  384 L  384 (482)
Q Consensus       384 ~  384 (482)
                      .
T Consensus       424 r  424 (454)
T KOG2680         424 R  424 (454)
T ss_pred             H
T ss_conf             9


No 360
>cd04155 Arl3 Arl3 subfamily.  Arl3 (Arf-like 3) is an Arf family protein that differs from most Arf family members in the N-terminal extension.  In is inactive, GDP-bound form, the N-terminal extension forms an elongated loop that is hydrophobically anchored into the membrane surface; however, it has been proposed that this region might form a helix in the GTP-bound form.  The delta subunit of the rod-specific cyclic GMP phosphodiesterase type 6 (PDEdelta) is an Arl3 effector.  Arl3 binds microtubules in a regulated manner to alter specific aspects of cytokinesis via interactions with retinitis pigmentosa 2 (RP2).  It has been proposed that RP2 functions in concert with Arl3 to link the cell membrane and the cytoskeleton in photoreceptors as part of the cell signaling or vesicular transport machinery.  In mice, the absence of Arl3 is associated with abnormal epithelial cell proliferation and cyst formation.
Probab=91.94  E-value=1  Score=24.62  Aligned_cols=126  Identities=14%  Similarity=0.178  Sum_probs=57.4

Q ss_pred             CCCEEEEEECCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCHHHHHCCCCCCCCCCCCCCCCCCCCCCCEEEEC
Q ss_conf             43204887327774367999999842675433210123465542100243311255553221110012344667147516
Q gi|254780916|r  161 DCAIPIMIQGEFGVGKKRLSRFIHESGKRAFFPFFIVNCGMIDQDKIEKFLFGDVDLQTKNSAQFLGKFIEANGGTIVLE  240 (482)
Q Consensus       161 ~~~~~vli~Ge~GtGK~~~A~~iH~~s~r~~~~fi~v~c~~~~~~~~e~~lFG~~~~~~~~~~~~~g~~~~a~~Gtl~l~  240 (482)
                      .-..-|+|.|..|+||+.+-+.+.....-...|-+-+|...+..+...-.++- ..|.-.-..-..-.+..|++=.+++|
T Consensus        12 ~~~~Ki~ilG~~~sGKTsll~~l~~~~~~~~~pT~g~~~~~v~~~~~~~~lwD-~~G~~~~~~~~~~y~~~a~~iI~VvD   90 (173)
T cd04155          12 SEEPRILILGLDNAGKTTILKQLASEDISHITPTQGFNIKTVQSDGFKLNVWD-IGGQRAIRPYWRNYFENTDCLIYVID   90 (173)
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHHCCCCCCCCCCCCEEEEEEEECCEEEEEEE-CCCCHHHHHHHHHHCCCCCEEEEEEE
T ss_conf             87758999979999889999998569986606811323799998999999985-58751012689976555637999996


Q ss_pred             CCCHHHH-HHHHHHHHHHHHHHCCCCCCCCCCCCCCEEEEECCCCCCCCCCHHHHHH
Q ss_conf             6420018-8999888877642001123553212343156521433211111123337
Q gi|254780916|r  241 EPDALPL-AVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRK  296 (482)
Q Consensus       241 ei~~L~~-~~Q~~Ll~~l~~~~~~~~g~~~~~~~~~RiIa~t~~~L~~~~~~g~fr~  296 (482)
                      --+.-+. +....|..+|++..      ....+   =+|.+...|+...+....+.+
T Consensus        91 ~td~~~~~~~~~~l~~~l~~~~------~~~~P---iLiv~NK~Dl~~a~~~~eI~~  138 (173)
T cd04155          91 SADKKRLEEAGAELVELLEEEK------LAGVP---VLVFANKQDLATAAPAEEIAE  138 (173)
T ss_pred             CCCHHHHHHHHHHHHHHHHHHH------CCCCC---EEEEEECCCCCCCCCHHHHHH
T ss_conf             6756889999999999974130------06983---899997666777899999999


No 361
>cd04153 Arl5_Arl8 Arl5/Arl8 subfamily.  Arl5 (Arf-like 5) and Arl8, like Arl4 and Arl7, are localized to the nucleus and nucleolus.  Arl5 is developmentally regulated during embryogenesis in mice.  Human Arl5 interacts with the heterochromatin protein 1-alpha (HP1alpha), a nonhistone chromosomal protein that is associated with heterochromatin and telomeres, and prevents telomere fusion.  Arl5 may also play a role in embryonic nuclear dynamics and/or signaling cascades. Arl8 was identified from a fetal cartilage cDNA library.  It is found in brain, heart, lung, cartilage, and kidney.  No function has been assigned for Arl8 to date.
Probab=91.91  E-value=1.1  Score=24.59  Aligned_cols=123  Identities=13%  Similarity=0.176  Sum_probs=58.8

Q ss_pred             CCCEEEEEECCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCHHHHH---CCCCCCCCCCCCCCCCCCCCCCCEE
Q ss_conf             4320488732777436799999984267543321012346554210024331---1255553221110012344667147
Q gi|254780916|r  161 DCAIPIMIQGEFGVGKKRLSRFIHESGKRAFFPFFIVNCGMIDQDKIEKFLF---GDVDLQTKNSAQFLGKFIEANGGTI  237 (482)
Q Consensus       161 ~~~~~vli~Ge~GtGK~~~A~~iH~~s~r~~~~fi~v~c~~~~~~~~e~~lF---G~~~~~~~~~~~~~g~~~~a~~Gtl  237 (482)
                      +-..-|++.|..|+||+.+-+.+.........|=+-+|...+.....+-.++   |++..    ..-..-.+..|++-.+
T Consensus        13 ~k~~KililG~~~sGKTsil~~l~~~~~~~~~pT~G~~~~~i~~~~~~~~iwD~~G~e~~----~~~~~~y~~~a~~ii~   88 (174)
T cd04153          13 RKEYKVIIVGLDNAGKTTILYQFLLGEVVHTSPTIGSNVEEIVYKNIRFLMWDIGGQESL----RSSWNTYYTNTDAVIL   88 (174)
T ss_pred             CCEEEEEEECCCCCCHHHHHHHHHCCCCCCCCCCCCCCEEEEEECCEEEEEEECCCCCCC----CCHHHHHHCCCCEEEE
T ss_conf             977999999899998899999997399277167236046999978889999989998656----6226777057753799


Q ss_pred             EECCCCHHHH-HHHHHHHHHHHHHHCCCCCCCCCCCCCCEEEEECCCCCCCCCCHHHHHH
Q ss_conf             5166420018-8999888877642001123553212343156521433211111123337
Q gi|254780916|r  238 VLEEPDALPL-AVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVKSHVFRK  296 (482)
Q Consensus       238 ~l~ei~~L~~-~~Q~~Ll~~l~~~~~~~~g~~~~~~~~~RiIa~t~~~L~~~~~~g~fr~  296 (482)
                      ++|--..-+. .....|.+++++...      ...+   =+|.+...|+...+......+
T Consensus        89 VvD~sd~~~~~~~~~~l~~~l~~~~~------~~~p---ili~~NK~Dl~~~~~~~ei~~  139 (174)
T cd04153          89 VIDSTDRERLPLTKEELYKMLAHEDL------RKAV---LLVLANKQDLKGAMTPAEISE  139 (174)
T ss_pred             EEECCCHHHHHHHHHHHHHHHHCCCC------CCCC---EEEEEECCCCCCCCCHHHHHH
T ss_conf             99767888999999999999726101------6982---899995555655789999999


No 362
>COG1342 Predicted DNA-binding proteins [General function prediction only]
Probab=91.90  E-value=0.37  Score=27.83  Aligned_cols=39  Identities=23%  Similarity=0.348  Sum_probs=27.9

Q ss_pred             HHHHHHHHHHHHHHHHHHCCCHHHHHHHHCCCHHHHHHHHHH
Q ss_conf             899999999999999982872789997848998899999998
Q gi|254780916|r  433 RRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKIRE  474 (482)
Q Consensus       433 ~~l~e~E~~~I~~aL~~~~Gn~~~aA~~LGIsR~tL~rKlk~  474 (482)
                      .+++|+|.-=   .-...+-++.+||...||||.|+|+-+++
T Consensus        34 lt~eElEAlR---LvD~~~l~QeeAA~rMgISr~Tfwr~l~s   72 (99)
T COG1342          34 LTIEELEALR---LVDYEGLTQEEAALRMGISRQTFWRLLTS   72 (99)
T ss_pred             ECHHHHHHHH---HHHHHHCCHHHHHHHHCCCHHHHHHHHHH
T ss_conf             2299988999---88686105789999846429999999999


No 363
>cd00569 HTH_Hin_like Helix-turn-helix domain of Hin and related proteins, a family of DNA-binding domains unique to bacteria and represented by the Hin protein of Salmonella. The basic HTH domain is a simple fold comprised of three core helices that form a right-handed helical bundle. The principal DNA-protein interface is formed by the third helix, the recognition helix, inserting itself into the major groove of the DNA. A diverse array of HTH domains participate in a variety of functions that depend on their DNA-binding properties. HTH_Hin represents one of the simplest versions of the HTH domains; the characterization of homologous relationships between various sequence-diverse HTH domain families remains difficult. The Hin recombinase induces the site-specific inversion of a chromosomal DNA segment containing a promoter, which controls the alternate expression of two genes by reversibly switching orientation. The Hin recombinase consists of a single polypeptide chain containing a D
Probab=91.88  E-value=0.26  Score=28.85  Aligned_cols=28  Identities=43%  Similarity=0.662  Sum_probs=23.1

Q ss_pred             HHHHHHCCCHHHHHHHHCCCHHHHHHHH
Q ss_conf             9999828727899978489988999999
Q gi|254780916|r  445 LAMKLYRAQMSEVARRLGIGRSTLYRKI  472 (482)
Q Consensus       445 ~aL~~~~Gn~~~aA~~LGIsR~tL~rKl  472 (482)
                      ..|-..+..+++.|+.+||||+|+||.+
T Consensus        15 r~l~~~G~~~~~iA~~~GVsr~Tiyr~l   42 (42)
T cd00569          15 RRLLAAGESVAEIARRLGVSRSTLYRYL   42 (42)
T ss_pred             HHHHHCCCCHHHHHHHHCCCHHHHHHHC
T ss_conf             9999978989999999797999998659


No 364
>PRK11288 araG L-arabinose transporter ATP-binding protein; Provisional
Probab=91.86  E-value=1.1  Score=24.56  Aligned_cols=160  Identities=11%  Similarity=0.070  Sum_probs=69.6

Q ss_pred             CHHHHHHHHHHHHHCCCEEEEE------CCHH-----HHHHHCCCCCEEEEECCCCCCCH------HHHHHHHHHHCCCC
Q ss_conf             9899999999999889889998------9379-----99986089989999785469888------99999999857898
Q gi|254780916|r   19 DDEQIKIIKDHVESYGYDVFIV------NVSD-----LSTISKIQVNVIFLSLINCEDDK------ENILKNIVDKIPIV   81 (482)
Q Consensus        19 d~~~~~~l~~~L~~~G~~v~~a------~~~a-----l~~l~~~~~dlillD~~mP~~dG------lell~~i~~~~p~i   81 (482)
                      ....+......|+..|.+....      +-+.     ++..-...|+++++|--....|-      +++++++++.  ..
T Consensus       114 ~~~~~~~~~~~l~~~gl~~~~~~~~~~LSgG~kQrv~ia~aL~~~p~lliLDEPts~LD~~~~~~l~~~l~~l~~~--G~  191 (501)
T PRK11288        114 RRLLNYEAREQLEHLGVDIDPDTPLKYLSIGQRQMVEIAKALMRNARVIAFDEPTSSLSAREIEQLFRVIRELRAE--GR  191 (501)
T ss_pred             HHHHHHHHHHHHHHCCCCCCCCCCHHHCCHHHHHHHHHHHHHHCCCCEEEECCCCCCCCHHHHHHHHHHHHHHHHH--CC
T ss_conf             9999999999998769986657842669999999999999986099899965874568989999998899999872--76


Q ss_pred             CEEEEECCCCHHHHHH-----HHHCCC-CCCCCC--CCCCCCCCCCC-CCCCCCC---CCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             3999926899999998-----885057-432222--22222222222-2222222---2222222111111112222222
Q gi|254780916|r   82 PIIVQTTQDNIKILNC-----FLYNRI-SKFFLN--LVSRKQLCDSI-ICALREG---VVPSQENEHCALDSLIAVSPAM  149 (482)
Q Consensus        82 pvIiiT~~~~~~~~~~-----a~~~g~-~d~l~K--P~~~~~L~~~i-~~al~~~---~~~~~~~~~~~~~~LiG~S~~m  149 (482)
                      - |+++.|.-.+...-     .+++|- ..-+..  -...+.+.... .+.+...   ..............+-+     
T Consensus       192 t-il~isH~l~~~~~~~Drv~vl~~G~iv~~~~~~~~~~~~~l~~~~~~r~~~~~~~~~~~~~~~~~l~~~~l~~-----  265 (501)
T PRK11288        192 V-ILYVSHRMEEIFALCDAITVFRDGRYVATFDDMAQVDRDRLVQAMVGREIGDIYGYRPRPLGDVRLRLKGLKG-----  265 (501)
T ss_pred             C-EEEECCCHHHHHHHCCEEEEEECCEEEEECCCHHHCCHHHHHHHHHCCCHHHCCCCCCCCCCCEEEEEEECCC-----
T ss_conf             1-2651332899997588789711885997637213379999999862855354058788887743799985037-----


Q ss_pred             CCCCCCCCCCCCCCEEEEEECCCCCHHHHHHHHHHHC
Q ss_conf             2222222223443204887327774367999999842
Q gi|254780916|r  150 IQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHES  186 (482)
Q Consensus       150 ~~v~~~i~~~a~~~~~vli~Ge~GtGK~~~A~~iH~~  186 (482)
                      ..+.+-+.--.....-|-|.|++|+||+++++.|-..
T Consensus       266 ~~~~~~vsl~v~~GEivgivG~nGsGKSTL~k~L~Gl  302 (501)
T PRK11288        266 PGLREPISFAVRRGEIVGFFGLVGAGRSELMKLLYGA  302 (501)
T ss_pred             CCCCCCEEEEEECCEEEEEECCCCCCHHHHHHHHCCC
T ss_conf             8745663478708839997568886487999984387


No 365
>KOG2035 consensus
Probab=91.83  E-value=0.73  Score=25.73  Aligned_cols=38  Identities=24%  Similarity=0.366  Sum_probs=31.2

Q ss_pred             CEEEECCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCEEEEECCC
Q ss_conf             1475166420018899988887764200112355321234315652143
Q gi|254780916|r  235 GTIVLEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEK  283 (482)
Q Consensus       235 Gtl~l~ei~~L~~~~Q~~Ll~~l~~~~~~~~g~~~~~~~~~RiIa~t~~  283 (482)
                      -.++|.|.+.|..+.|..|-|.++.           ...++|+|-.+|.
T Consensus       129 Kvvvi~ead~LT~dAQ~aLRRTMEk-----------Ys~~~RlIl~cns  166 (351)
T KOG2035         129 KVVVINEADELTRDAQHALRRTMEK-----------YSSNCRLILVCNS  166 (351)
T ss_pred             EEEEEECHHHHHHHHHHHHHHHHHH-----------HHCCCEEEEEECC
T ss_conf             8999803576508899999999999-----------8607169999267


No 366
>TIGR02538 type_IV_pilB type IV-A pilus assembly ATPase PilB; InterPro: IPR013374    This model describes a protein involved in type IV pilus biogenesis designated PilB in Pseudomonas aeruginosa but PilF in Neisseria gonorrhoeae; the more common usage, reflected here, is PilB. This protein is an ATPase involved in protein export for pilin assembly, and is closely related to GspE (IPR013369 from INTERPRO) of type II secretion systems (also referred to as the main terminal branch of the general secretion pathway). Note that type IV pilus systems are often divided into type IV-A and IV-B, with the latter group including bundle-forming pilus, mannose-sensitive hemagglutinin, etc. Members of this family are found in type IV-A systems.; GO: 0005524 ATP binding, 0008565 protein transporter activity, 0009297 pilus biogenesis.
Probab=91.68  E-value=0.081  Score=32.46  Aligned_cols=102  Identities=18%  Similarity=0.134  Sum_probs=49.3

Q ss_pred             CCCCEEEECCCHHHHHHHHHHHHHCCCEEEEE--CCHHHH-HHHC-----CCCCEEEEECCCCCC---------------
Q ss_conf             28838998699899999999999889889998--937999-9860-----899899997854698---------------
Q gi|254780916|r    9 RHKRVLIIDKDDEQIKIIKDHVESYGYDVFIV--NVSDLS-TISK-----IQVNVIFLSLINCED---------------   65 (482)
Q Consensus         9 ~~~rILIVDDd~~~~~~l~~~L~~~G~~v~~a--~~~al~-~l~~-----~~~dlillD~~mP~~---------------   65 (482)
                      +..++.|.=.||.....+..+==.-|++|..+  ....+. ++.+     ..-..-+-|.-+..+               
T Consensus        92 ~G~~L~~A~~DPtn~~a~~~i~F~tg~~ve~v~v~ed~l~~~i~~~y~~s~~~~~~~~~~d~g~~e~~d~~~~~~~~~~~  171 (577)
T TIGR02538        92 RGNTLFVAVSDPTNISALDDIKFATGLNVEVVVVEEDKLSALIEKYYGESDSLAKELEDEDIGDLEELDVSAIDDEDPDS  171 (577)
T ss_pred             CCCEEEEEEECCCCHHHHHHHHHHCCCEEEEEECCHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCC
T ss_conf             58847999757545688999874149679999727289999999985344443321254202443321356432555556


Q ss_pred             --CHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHHHCCCCCCCCCCCCCC
Q ss_conf             --8899999999857898399992689999999888505743222222222
Q gi|254780916|r   66 --DKENILKNIVDKIPIVPIIVQTTQDNIKILNCFLYNRISKFFLNLVSRK  114 (482)
Q Consensus        66 --dGlell~~i~~~~p~ipvIiiT~~~~~~~~~~a~~~g~~d~l~KP~~~~  114 (482)
                        +..+--..+-+-..+-|||=.=    -.....|++.||.|-=.-|+...
T Consensus       172 ~~~~~d~~~dmDqfnaDAPvvKFv----N~iL~DAir~GASDIHFEPYE~~  218 (577)
T TIGR02538       172 EDEEEDAEDDMDQFNADAPVVKFV----NKILLDAIRKGASDIHFEPYEKK  218 (577)
T ss_pred             CCCCCCCHHHHHHHCCCCCCHHHH----HHHHHHHHHCCCCCCCCCCCCCC
T ss_conf             554200013455423688701338----78799998468861211367687


No 367
>pfam02001 DUF134 Protein of unknown function DUF134. This family of archaeal proteins has no known function.
Probab=91.67  E-value=0.39  Score=27.65  Aligned_cols=39  Identities=23%  Similarity=0.322  Sum_probs=28.1

Q ss_pred             HHHHHHHHHHHHHHHHHHCCCHHHHHHHHCCCHHHHHHHHHH
Q ss_conf             899999999999999982872789997848998899999998
Q gi|254780916|r  433 RRLSDIEKEIIGLAMKLYRAQMSEVARRLGIGRSTLYRKIRE  474 (482)
Q Consensus       433 ~~l~e~E~~~I~~aL~~~~Gn~~~aA~~LGIsR~tL~rKlk~  474 (482)
                      -+++|+|--   ......+-++.+||+..||||+|+||-+..
T Consensus        37 L~~dE~EAi---RL~D~egl~QeeaA~~MgVSR~Tf~ril~~   75 (100)
T pfam02001        37 ITLDEFEAI---RLVDYEDYTQEEAAKLMGISRRTVWRLLTS   75 (100)
T ss_pred             ECHHHHHHH---HHHHHCCCCHHHHHHHCCCCHHHHHHHHHH
T ss_conf             349999999---987360798999998849769999999999


No 368
>COG3835 CdaR Sugar diacid utilization regulator [Transcription / Signal transduction mechanisms]
Probab=91.66  E-value=0.25  Score=28.97  Aligned_cols=31  Identities=23%  Similarity=0.193  Sum_probs=27.2

Q ss_pred             HHHHHHCCCHHHHHHHHCCCHHHHHHHHHHH
Q ss_conf             9999828727899978489988999999981
Q gi|254780916|r  445 LAMKLYRAQMSEVARRLGIGRSTLYRKIREY  475 (482)
Q Consensus       445 ~aL~~~~Gn~~~aA~~LGIsR~tL~rKlk~~  475 (482)
                      +.+-.+||+-..||+.|+|.|+||++|++|-
T Consensus       319 ~~~f~~N~~l~~tA~~L~IHrNTLrYRL~kI  349 (376)
T COG3835         319 QTYFAHNGQLNATAEALFIHRNTLRYRLEKI  349 (376)
T ss_pred             HHHHHHCCCHHHHHHHHCCCHHHHHHHHHHH
T ss_conf             9999855999899998451051599999999


No 369
>cd01387 MYSc_type_XV Myosin motor domain, type XV myosins. In vertebrates, myosin XV appears to be expressed in sensory tissue and play a role in hearing. This catalytic (head) domain has ATPase activity and belongs to the larger group of P-loop NTPases. Myosins are actin-dependent molecular motors that play important roles in muscle contraction, cell motility, and organelle transport. The head domain is a molecular motor, which utilizes ATP hydrolysis to generate directed movement toward the plus end along actin filaments. A cyclical interaction between myosin and actin provides the driving force. Rates of ATP hydrolysis and consequently the speed of movement along actin filaments vary widely, from about 0.04 micrometer per second for myosin I to 4.5 micrometer per second for myosin II in skeletal muscle. Myosin II moves in discrete steps about 5-10 nm long and generates 1-5 piconewtons of force. Upon ATP binding, the myosin head dissociates from an actin filament. ATP hydrolysis caus
Probab=91.63  E-value=0.13  Score=31.07  Aligned_cols=65  Identities=22%  Similarity=0.295  Sum_probs=33.9

Q ss_pred             CCCEEEEEECCCCCHHHHHHHHHH-HCCCCCCCCCCCCCCCCCCCCCCH----HHHHCCCCCCCCCCCCCCCCCC
Q ss_conf             432048873277743679999998-426754332101234655421002----4331125555322111001234
Q gi|254780916|r  161 DCAIPIMIQGEFGVGKKRLSRFIH-ESGKRAFFPFFIVNCGMIDQDKIE----KFLFGDVDLQTKNSAQFLGKFI  230 (482)
Q Consensus       161 ~~~~~vli~Ge~GtGK~~~A~~iH-~~s~r~~~~fi~v~c~~~~~~~~e----~~lFG~~~~~~~~~~~~~g~~~  230 (482)
                      ..+..|+|.||+|+||+..++.|= .......+.-     ..+.+..++    -|=||..+-...+.+.|-|++-
T Consensus        85 ~~~QsIiisGESGAGKTes~K~il~yL~~~~~~~~-----~~~~~~il~~npiLEAFGNAkT~~N~NSSRFGK~~  154 (677)
T cd01387          85 KQNQCVIISGESGSGKTEATKLILRYLAAMNQGGS-----AVITEQILEATPLLEAFGNAKTVRNDNSSRFGKFV  154 (677)
T ss_pred             CCCCEEEEEECCCCCHHHHHHHHHHHHHHHCCCCC-----CHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCEEEE
T ss_conf             99925999827978898899999999876538998-----42999998651698875064147899757703459


No 370
>pfam06745 KaiC KaiC. This family represents a conserved region within bacterial and archaeal proteins, most of which are hypothetical. More than one copy is sometimes found in each protein. This family includes KaiC, which is one of the Kai proteins among which direct protein-protein association may be a critical process in the generation of circadian rhythms in cyanobacteria.
Probab=91.61  E-value=0.13  Score=30.95  Aligned_cols=36  Identities=17%  Similarity=0.204  Sum_probs=23.7

Q ss_pred             CCCEEEEEECCCCCHHHHHH-HHHHHCCCCC--CCCCCC
Q ss_conf             43204887327774367999-9998426754--332101
Q gi|254780916|r  161 DCAIPIMIQGEFGVGKKRLS-RFIHESGKRA--FFPFFI  196 (482)
Q Consensus       161 ~~~~~vli~Ge~GtGK~~~A-~~iH~~s~r~--~~~fi~  196 (482)
                      .-...+||.|++||||+.+| +.+++.-.+.  +.-|++
T Consensus        17 ~~gs~~LI~G~pGsGKT~la~qfl~~ga~~~ge~~lYis   55 (231)
T pfam06745        17 PEGRVVLITGGPGTGKTIFGLQFLYNGALEYGEPGVYVT   55 (231)
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEE
T ss_conf             299699998589725999999999999986589689998


No 371
>PRK10419 nikE nickel transporter ATP-binding protein; Provisional
Probab=91.55  E-value=0.15  Score=30.64  Aligned_cols=35  Identities=20%  Similarity=0.312  Sum_probs=24.9

Q ss_pred             CCCCCCCCCCCCCEEEEEECCCCCHHHHHHHHHHH
Q ss_conf             22222222344320488732777436799999984
Q gi|254780916|r  151 QVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHE  185 (482)
Q Consensus       151 ~v~~~i~~~a~~~~~vli~Ge~GtGK~~~A~~iH~  185 (482)
                      .+.+.+.--.....-+-|.||+|+||++++++|-.
T Consensus        26 ~~l~~vs~~i~~GE~l~ivGeSGsGKSTL~r~i~g   60 (266)
T PRK10419         26 AVLNNVSLTLKSGETVALLGRSGCGKSTLARLLVG   60 (266)
T ss_pred             EEEECCEEEECCCCEEEEECCCCCHHHHHHHHHHC
T ss_conf             88858175888998999999999779999999966


No 372
>pfam09862 DUF2089 Protein of unknown function(DUF2089). This domain, found in various hypothetical prokaryotic proteins, has no known function.
Probab=91.35  E-value=0.47  Score=27.09  Aligned_cols=37  Identities=19%  Similarity=0.224  Sum_probs=28.0

Q ss_pred             HHHHHHHHHHCCCHHHHHHHHCCCHHHHHHHH----HHHCC
Q ss_conf             99999999828727899978489988999999----98188
Q gi|254780916|r  441 EIIGLAMKLYRAQMSEVARRLGIGRSTLYRKI----REYNI  477 (482)
Q Consensus       441 ~~I~~aL~~~~Gn~~~aA~~LGIsR~tL~rKl----k~~gi  477 (482)
                      ......+-++.||..+.|+.||||..|.+.|+    +++|.
T Consensus        39 l~Fi~~fi~~~Gnlke~~~~lgiSYpTvR~rLd~ii~~lGy   79 (113)
T pfam09862        39 LEFVELFIKCRGNIKEVEKELGISYPTVRNRLDEIIAALGY   79 (113)
T ss_pred             HHHHHHHHHHCCCHHHHHHHHCCCCHHHHHHHHHHHHHCCC
T ss_conf             99999999916889999999788818899999999998089


No 373
>TIGR02769 nickel_nikE nickel import ATP-binding protein NikE; InterPro: IPR014137   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 represents the NikE subunit of a multisubunit nickel import ABC transporter complex. Nickel, once imported, may be used in urease and in certain classes of hydrogenase and superoxide dismutase..
Probab=91.26  E-value=0.15  Score=30.58  Aligned_cols=57  Identities=19%  Similarity=0.146  Sum_probs=45.1

Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCCCHHHHHHHHHHHCCCCCCC
Q ss_conf             111111122222222222222223443204887327774367999999842675433
Q gi|254780916|r  136 HCALDSLIAVSPAMIQVVDLARKAGDCAIPIMIQGEFGVGKKRLSRFIHESGKRAFF  192 (482)
Q Consensus       136 ~~~~~~LiG~S~~m~~v~~~i~~~a~~~~~vli~Ge~GtGK~~~A~~iH~~s~r~~~  192 (482)
                      ......|+|.......|.+.|.---..-..|=+.|-+|+||.++||.|=..-+-+.|
T Consensus        11 ~Y~~~~L~~r~~~~~~VL~~vsL~l~~Ge~~gLLG~SG~GKSTLArlLlGLe~P~~G   67 (267)
T TIGR02769        11 TYRTGGLLGRKKQRKAVLDNVSLSLEEGETVGLLGRSGCGKSTLARLLLGLEKPAQG   67 (267)
T ss_pred             EECCCHHHHHHHHHHHHCCCCCEEECCCCEEEECCCCCCCHHHHHHHHHHCCCCCCC
T ss_conf             100201345545443103674323137750552367887377899998750788874


No 374
>PRK13768 GTPase; Provisional
Probab=91.25  E-value=0.14  Score=30.82  Aligned_cols=34  Identities=24%  Similarity=0.275  Sum_probs=24.9

Q ss_pred             EEEEECCCCCHHHHHHHHHHHCCCCCCCCCCCCC
Q ss_conf             4887327774367999999842675433210123
Q gi|254780916|r  165 PIMIQGEFGVGKKRLSRFIHESGKRAFFPFFIVN  198 (482)
Q Consensus       165 ~vli~Ge~GtGK~~~A~~iH~~s~r~~~~fi~v~  198 (482)
                      -+++.|++|+||+++.+.++++-...+.+-..||
T Consensus         4 ~~~ViGpaGSGKsT~~~~l~~~l~~~~r~~~vvN   37 (253)
T PRK13768          4 IVFFLGTAGSGKTTLVGALSDWLEEQGYDVAIVN   37 (253)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHCCCCEEEEE
T ss_conf             8999899999889999999999997699759997


No 375
>KOG1942 consensus
Probab=91.23  E-value=0.41  Score=27.50  Aligned_cols=109  Identities=18%  Similarity=0.284  Sum_probs=73.3

Q ss_pred             CCCCEEEECCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCEEEEECCCCC------CCCCCHHHHHHHHHHHHHHH
Q ss_conf             667147516642001889998888776420011235532123431565214332------11111123337999886543
Q gi|254780916|r  232 ANGGTIVLEEPDALPLAVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNL------LPQVKSHVFRKDLYYRISVF  305 (482)
Q Consensus       232 a~~Gtl~l~ei~~L~~~~Q~~Ll~~l~~~~~~~~g~~~~~~~~~RiIa~t~~~L------~~~~~~g~fr~dLy~rL~~~  305 (482)
                      ---|.||+||++-|..+.=.-|-++|++.. .           --+|++||+..      ++...-...-.||+.||-. 
T Consensus       295 lvPGVLFIDEVhMLDiEcFTyL~kalES~i-a-----------PivifAsNrG~~~irGt~d~~sPhGip~dllDRl~I-  361 (456)
T KOG1942         295 LVPGVLFIDEVHMLDIECFTYLHKALESPI-A-----------PIVIFASNRGMCTIRGTEDILSPHGIPPDLLDRLLI-  361 (456)
T ss_pred             HCCCCEEEEEHHHHHHHHHHHHHHHHCCCC-C-----------CEEEEECCCCCEEECCCCCCCCCCCCCHHHHHHEEE-
T ss_conf             367626863013242699999999862778-7-----------569996277610221776787878899778612667-


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHH
Q ss_conf             3446778774422225566777641011223333211111000122338986899999999
Q gi|254780916|r  306 LINISTLRSRSEDIPWLVHFFLQSFCTKNAIKQISISDKALSLLTKYPWIDNVQELKNILL  366 (482)
Q Consensus       306 ~i~iPpLReR~eDI~~L~~~fl~~~~~~~~~~~~~ls~~a~~~L~~y~WPGNvREL~n~i~  366 (482)
                         ++.++--.+|+..++..    -++..|   ..++++|+.+|..-.   --+-|+..++
T Consensus       362 ---irt~~y~~~e~r~Ii~~----Ra~~E~---l~~~e~a~~~l~~~g---t~tsLRy~vq  409 (456)
T KOG1942         362 ---IRTLPYDEEEIRQIIKI----RAQVEG---LQVEEEALDLLAEIG---TSTSLRYAVQ  409 (456)
T ss_pred             ---EEECCCCHHHHHHHHHH----HHHHHC---CEECHHHHHHHHHHC---CCHHHHHHHH
T ss_conf             ---86036998999999999----876514---232288999987605---4145788988


No 376
>PRK00254 ski2-like helicase; Provisional
Probab=91.22  E-value=0.29  Score=28.52  Aligned_cols=52  Identities=10%  Similarity=0.023  Sum_probs=27.3

Q ss_pred             CCCCEEEEE-CCCCCC--CHHHHHHHHHHHCCCCCEEEEECC-CCHHHHHHHHHCCCC
Q ss_conf             899899997-854698--889999999985789839999268-999999988850574
Q gi|254780916|r   51 IQVNVIFLS-LINCED--DKENILKNIVDKIPIVPIIVQTTQ-DNIKILNCFLYNRIS  104 (482)
Q Consensus        51 ~~~dlillD-~~mP~~--dGlell~~i~~~~p~ipvIiiT~~-~~~~~~~~a~~~g~~  104 (482)
                      ...++|+.| +.|=+.  =|..+=.-+....+.+.+|.+||. ++.+....  +.++.
T Consensus       137 ~~i~lvViDEiH~igD~~RG~~lE~~l~~l~~~~qiIgLSATi~N~~~la~--WL~a~  192 (717)
T PRK00254        137 KDVKLLVADEIHLIGSRDRGATLEFILTHMLGRAQIIGLSATIGNPEELAE--WLNAE  192 (717)
T ss_pred             HCCCEEEEECEEECCCCCCHHHHHHHHHHHHCCCEEEEEEEECCCHHHHHH--HHCCC
T ss_conf             326989997607888987409999999951003669999633499899999--82885


No 377
>COG1124 DppF ABC-type dipeptide/oligopeptide/nickel transport system, ATPase component [Amino acid transport and metabolism / Inorganic ion transport and metabolism]
Probab=91.21  E-value=0.13  Score=31.06  Aligned_cols=26  Identities=31%  Similarity=0.390  Sum_probs=20.9

Q ss_pred             CCEEEEEECCCCCHHHHHHHHHHHCC
Q ss_conf             32048873277743679999998426
Q gi|254780916|r  162 CAIPIMIQGEFGVGKKRLSRFIHESG  187 (482)
Q Consensus       162 ~~~~vli~Ge~GtGK~~~A~~iH~~s  187 (482)
                      ....+=|.||+|+||+++||+|-..-
T Consensus        32 ~Ge~lgivGeSGsGKSTL~r~l~Gl~   57 (252)
T COG1124          32 RGETLGIVGESGSGKSTLARLLAGLE   57 (252)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHCCC
T ss_conf             89789998489898889999995656


No 378
>cd04156 ARLTS1 ARLTS1 subfamily.  ARLTS1 (Arf-like tumor suppressor gene 1), also known as Arl11, is a member of the Arf family of small GTPases that is believed to play a major role in apoptotic signaling.  ARLTS1 is widely expressed and functions as a tumor suppressor gene in several human cancers.  ARLTS1 is a low-penetrance suppressor that accounts for a small percentage of familial melanoma or familial chronic lymphocytic leukemia (CLL).  ARLTS1 inactivation seems to occur most frequently through biallelic down-regulation by hypermethylation of the promoter.  In breast cancer, ARLTS1 alterations were typically a combination of a hypomorphic polymorphism plus loss of heterozygosity.  In a case of thyroid adenoma, ARLTS1 alterations were polymorphism plus promoter hypermethylation.  The nonsense polymorphism Trp149Stop occurs with significantly greater frequency in familial cancer cases than in sporadic cancer cases, and the Cys148Arg polymorphism is associated with an increase in h
Probab=91.17  E-value=1.3  Score=24.07  Aligned_cols=112  Identities=13%  Similarity=0.221  Sum_probs=52.2

Q ss_pred             EEEECCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCC-CCHHHHH---CCCCCCCCCCCCCCCCCCCCCCCEEEECC
Q ss_conf             8873277743679999998426754332101234655421-0024331---12555532211100123446671475166
Q gi|254780916|r  166 IMIQGEFGVGKKRLSRFIHESGKRAFFPFFIVNCGMIDQD-KIEKFLF---GDVDLQTKNSAQFLGKFIEANGGTIVLEE  241 (482)
Q Consensus       166 vli~Ge~GtGK~~~A~~iH~~s~r~~~~fi~v~c~~~~~~-~~e~~lF---G~~~~~~~~~~~~~g~~~~a~~Gtl~l~e  241 (482)
                      |++.|..|+||+.+-+.+-........|-+-+|...+.-+ .+.-.++   |.+..    ..-....+..|++-.+++|-
T Consensus         2 ivilG~~~~GKTsil~r~~~~~~~~~~pTig~~~~~~~~~~~~~l~iwD~~G~e~~----~~~~~~y~~~a~~iI~V~D~   77 (160)
T cd04156           2 VLLLGLDSAGKSTLLYKLKHAELVTTIPTVGFNVEMLQLEKHLSLTVWDVGGQEKM----RTVWKCYLENTDGLVYVVDS   77 (160)
T ss_pred             EEEECCCCCCHHHHHHHHHCCCCCCCCCCCCEEEEEEEECCEEEEEEEECCCCCCC----CHHHHHHHCCCCEEEEEEEC
T ss_conf             99999999999999999956987775776150389999899899999978986247----41588774567789999856


Q ss_pred             CCHHHH-HHHHHHHHHHHHHHCCCCCCCCCCCCCCEEEEECCCCCCCCCC
Q ss_conf             420018-8999888877642001123553212343156521433211111
Q gi|254780916|r  242 PDALPL-AVQGRIYNFIETGKIEFFDSRGAIRLDVRLIFLTEKNLLPQVK  290 (482)
Q Consensus       242 i~~L~~-~~Q~~Ll~~l~~~~~~~~g~~~~~~~~~RiIa~t~~~L~~~~~  290 (482)
                      -..-+. ..+..+-.++++..      .+..+   =+|.+...|+...+.
T Consensus        78 td~~~~~~~~~~~~~~l~~~~------~~~~p---ili~~NK~Dl~~~~~  118 (160)
T cd04156          78 SDEARLDESQKELKHILKNEH------IKGVP---VVLLANKQDLPGALT  118 (160)
T ss_pred             CCHHHHHHHHHHHHHHHHHHC------CCCCE---EEEEEECCCCCCCCC
T ss_conf             867887879999999986635------37874---999998633656679


No 379
>KOG0479 consensus
Probab=91.09  E-value=0.86  Score=25.23  Aligned_cols=112  Identities=15%  Similarity=0.198  Sum_probs=74.0

Q ss_pred             CCCEEEEEECCCCCHHHHHHHHHHHCCCCCCCCCCCCCCC-----CCCCCCCHHHHHCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             4320488732777436799999984267543321012346-----55421002433112555532211100123446671
Q gi|254780916|r  161 DCAIPIMIQGEFGVGKKRLSRFIHESGKRAFFPFFIVNCG-----MIDQDKIEKFLFGDVDLQTKN