Query         gi|254780903|ref|YP_003065316.1| two-component sensor histidine kinase protein [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 766
No_of_seqs    271 out of 20348
Neff          8.4 
Searched_HMMs 39220
Date          Mon May 30 09:57:37 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254780903.hhm -d /home/congqian_1/database/cdd/Cdd.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 PRK11091 aerobic respiration c 100.0       0       0  615.5  44.8  362  238-765   138-504 (779)
  2 PRK10841 hybrid sensory kinase 100.0       0       0  586.8  38.4  337  372-765   347-689 (947)
  3 PRK09959 hybrid sensory histid 100.0       0       0  549.7  44.8  358  365-765   559-935 (1197)
  4 PRK13557 histidine kinase; Pro 100.0       0       0  548.0  44.7  345  252-766    25-392 (538)
  5 PRK11107 hybrid sensory histid 100.0       0       0  507.7  54.3  235  526-765   276-517 (920)
  6 PRK11360 sensory histidine kin 100.0       0       0  487.1  64.9  335  376-765   255-598 (607)
  7 TIGR02966 phoR_proteo phosphat 100.0       0       0  531.6  32.7  332  379-764     3-339 (339)
  8 TIGR02956 TMAO_torS TMAO reduc 100.0       0       0  540.5  24.5  250  510-765   465-734 (1052)
  9 PRK11006 phoR phosphate regulo 100.0       0       0  512.5  41.0  338  370-766    86-423 (431)
 10 PRK11466 hybrid sensory histid 100.0       0       0  513.2  32.5  245  512-765   413-661 (912)
 11 PRK13560 hypothetical protein; 100.0       0       0  449.3  52.4  574   98-765   181-802 (807)
 12 PRK09303 adaptive-response sen 100.0       0       0  476.0  33.1  242  521-765   127-374 (378)
 13 PRK11073 glnL nitrogen regulat 100.0       0       0  420.7  37.8  322  385-765    10-346 (348)
 14 PRK10490 sensor protein KdpD;  100.0       0       0  430.2  30.2  225  536-766   657-882 (895)
 15 PRK13837 two-component VirA-li 100.0       0       0  418.1  33.2  233  515-766   430-678 (831)
 16 PRK10549 signal transduction h 100.0       0       0  416.1  32.4  240  521-765   219-458 (467)
 17 PRK10364 sensor protein ZraS;  100.0       0       0  415.5  32.8  223  529-765   225-448 (455)
 18 PRK11100 sensory histidine kin 100.0       0       0  413.2  32.9  219  542-766   255-473 (475)
 19 PRK09835 sensor kinase CusS; P 100.0       0       0  411.2  32.9  241  521-766   240-480 (482)
 20 COG5002 VicK Signal transducti 100.0       0       0  409.3  28.0  347  364-765    92-447 (459)
 21 PRK11086 sensory histidine kin 100.0       0       0  351.4  57.3  192  543-766   338-534 (541)
 22 PRK09470 cpxA two-component se 100.0       0       0  380.5  31.6  235  521-765   221-456 (461)
 23 PRK10604 sensor protein RstB;  100.0       0       0  380.9  29.2  234  521-766   190-423 (433)
 24 PRK10755 sensor protein BasS/P 100.0       0       0  371.9  30.3  234  519-766   119-355 (355)
 25 PRK10337 sensor protein QseC;  100.0       0       0  369.9  30.7  234  521-764   212-446 (446)
 26 COG2205 KdpD Osmosensitive K+  100.0       0       0  368.9  29.5  223  539-766   656-879 (890)
 27 TIGR01386 cztS_silS_copS heavy 100.0       0       0  364.8  23.5  245  517-765   235-483 (483)
 28 TIGR02938 nifL_nitrog nitrogen 100.0       0       0  358.4  26.2  463  255-765     4-495 (496)
 29 PRK10815 sensor protein PhoQ;  100.0       0       0  352.4  30.3  234  521-766   244-477 (484)
 30 PRK09467 envZ osmolarity senso 100.0 1.4E-45       0  347.6  29.3  225  521-765   209-434 (437)
 31 PRK09776 putative sensor prote 100.0 4.1E-43       0  329.2  42.1  369  111-496   294-686 (1116)
 32 COG4191 Signal transduction hi 100.0 5.2E-43       0  328.5  30.5  249  508-766   347-601 (603)
 33 COG4251 Bacteriophytochrome (l 100.0 2.4E-43       0  330.9  25.0  231  527-765   508-740 (750)
 34 COG3852 NtrB Signal transducti 100.0 9.1E-41 2.8E-45  312.3  31.2  325  385-766    10-354 (363)
 35 COG5000 NtrY Signal transducti 100.0 5.2E-38 1.3E-42  292.4  32.5  332  372-766   360-708 (712)
 36 TIGR02916 PEP_his_kin putative 100.0 5.9E-36 1.5E-40  277.5  26.2  204  545-765   488-696 (696)
 37 COG3290 CitA Signal transducti 100.0 3.5E-31   9E-36  243.0  48.2  189  547-766   337-531 (537)
 38 COG0642 BaeS Signal transducti 100.0 8.4E-34 2.1E-38  262.0  31.4  214  542-766   114-329 (336)
 39 PRK09776 putative sensor prote 100.0 3.2E-32 8.1E-37  250.6  29.6  255  239-495   288-554 (1116)
 40 COG4192 Signal transduction hi 100.0 5.2E-28 1.3E-32  220.2  24.1  213  542-764   450-664 (673)
 41 PRK13560 hypothetical protein; 100.0 1.5E-27 3.8E-32  216.9  25.9  258  238-498   187-476 (807)
 42 smart00387 HATPase_c Histidine 100.0 8.2E-28 2.1E-32  218.7  14.5  110  656-766     1-110 (111)
 43 pfam02518 HATPase_c Histidine  100.0 3.7E-27 9.5E-32  214.0  14.8  110  656-766     1-110 (111)
 44 PRK11359 cAMP phosphodiesteras  99.9 7.2E-25 1.8E-29  197.5  24.9  227  126-376    20-257 (799)
 45 PRK13559 hypothetical protein;  99.9 5.8E-22 1.5E-26  176.5  33.1  307  253-765    43-360 (363)
 46 cd00075 HATPase_c Histidine ki  99.9 1.2E-25   3E-30  203.2  13.2  102  661-764     1-103 (103)
 47 PRK10618 phosphotransfer inter  99.9 1.6E-21 4.2E-26  173.2  33.4  327  374-765   335-667 (881)
 48 PRK11359 cAMP phosphodiesteras  99.9 3.5E-22 8.9E-27  178.1  23.5  236  248-490     5-254 (799)
 49 KOG0519 consensus               99.9 5.3E-26 1.4E-30  205.6   3.1  233  526-765   202-487 (786)
 50 PRK10547 chemotaxis protein Ch  99.9 5.5E-19 1.4E-23  155.0  21.6  142  619-765   334-514 (662)
 51 COG0643 CheA Chemotaxis protei  99.8 8.5E-18 2.2E-22  146.4  24.0  167  586-765   364-572 (716)
 52 PRK10935 nitrate/nitrite senso  99.8 3.9E-17   1E-21  141.6  27.1  190  548-766   366-562 (568)
 53 PRK10600 nitrate/nitrite senso  99.8 1.4E-14 3.5E-19  123.2  26.5  193  543-766   362-556 (569)
 54 PRK11644 sensory histidine kin  99.7 1.2E-13   3E-18  116.5  24.4  191  543-766   304-496 (497)
 55 pfam08447 PAS_3 PAS fold. The   99.7 1.3E-15 3.3E-20  130.7  11.7   88  277-364     1-90  (90)
 56 COG3920 Signal transduction hi  99.7 2.6E-13 6.6E-18  114.0  23.0  188  542-766    18-215 (221)
 57 COG2972 Predicted signal trans  99.7 5.1E-13 1.3E-17  111.9  23.8  179  547-766   263-452 (456)
 58 COG4585 Signal transduction hi  99.6 8.8E-13 2.3E-17  110.2  24.2  161  577-766   203-365 (365)
 59 pfam00989 PAS PAS fold. The PA  99.6 1.9E-14 4.9E-19  122.2  11.5  111  255-367     1-112 (112)
 60 COG3850 NarQ Signal transducti  99.6 4.9E-12 1.2E-16  104.8  23.7  188  548-765   374-567 (574)
 61 PRK13558 bacterio-opsin activa  99.6   2E-13 5.1E-18  114.8  15.2  138  255-395   158-300 (674)
 62 PRK03660 anti-sigma F factor;   99.5 3.6E-13 9.2E-18  113.0  11.6   96  658-764    37-136 (146)
 63 COG3275 LytS Putative regulato  99.5 5.5E-11 1.4E-15   97.2  22.3  168  550-766   372-551 (557)
 64 pfam08448 PAS_4 PAS fold. The   99.4 1.2E-12   3E-17  109.3  10.4  109  261-372     1-110 (110)
 65 TIGR00229 sensory_box PAS doma  99.4 2.7E-12 6.8E-17  106.7  11.3  125  251-377     1-130 (130)
 66 COG3851 UhpB Signal transducti  99.4 3.6E-10 9.2E-15   91.3  22.1  189  544-766   304-494 (497)
 67 PRK11091 aerobic respiration c  99.3 1.2E-11   3E-16  102.0  10.0  146   99-260   133-287 (779)
 68 PRK10060 RNase II stability mo  99.3 8.5E-10 2.2E-14   88.7  18.1  155  257-415   113-288 (663)
 69 pfam00512 HisKA His Kinase A (  99.3 8.8E-12 2.2E-16  103.0   7.4   66  542-611     1-66  (66)
 70 COG4564 Signal transduction hi  99.3 6.6E-08 1.7E-12   75.0  26.2  181  554-766   262-447 (459)
 71 KOG0787 consensus               99.2 4.3E-09 1.1E-13   83.6  18.3  200  561-764   154-378 (414)
 72 PRK13557 histidine kinase; Pro  99.1 1.4E-08 3.5E-13   79.9  16.8  114  126-255    36-157 (538)
 73 TIGR02938 nifL_nitrog nitrogen  99.1 4.3E-10 1.1E-14   90.8   9.0  256  126-398    12-287 (496)
 74 smart00388 HisKA His Kinase A   99.1 7.5E-10 1.9E-14   89.0   8.3   65  543-611     2-66  (66)
 75 cd00082 HisKA Histidine Kinase  99.0 1.4E-09 3.5E-14   87.2   6.7   64  541-607     2-65  (65)
 76 cd00130 PAS PAS domain; PAS mo  99.0 2.3E-08 5.9E-13   78.3  12.4  101  265-367     2-103 (103)
 77 PRK10060 RNase II stability mo  98.9 1.2E-07 3.1E-12   73.1  15.4  150  126-295   119-291 (663)
 78 pfam00989 PAS PAS fold. The PA  98.9 7.4E-09 1.9E-13   81.9   7.9   93  382-474     1-98  (112)
 79 COG1389 DNA topoisomerase VI,   98.9 2.5E-08 6.3E-13   78.1   9.5   29  579-607   498-528 (538)
 80 PRK11006 phoR phosphate regulo  98.8 7.8E-07   2E-11   67.2  15.2  125  237-378    80-205 (431)
 81 COG2202 AtoS FOG: PAS/PAC doma  98.8 1.1E-06 2.8E-11   66.2  15.9  135  238-374    95-232 (232)
 82 PRK04184 DNA topoisomerase VI   98.7 1.8E-07 4.5E-12   71.9   9.2   57  107-164    38-97  (533)
 83 PRK11360 sensory histidine kin  98.6   1E-06 2.6E-11   66.4  12.1  130  248-382   254-384 (607)
 84 PRK13559 hypothetical protein;  98.6 1.5E-05 3.8E-10   58.0  17.5  125  352-486    23-161 (363)
 85 pfam08448 PAS_4 PAS fold. The   98.6   2E-07   5E-12   71.6   7.8  102  388-489     1-110 (110)
 86 PRK04069 serine-protein kinase  98.6 1.4E-06 3.4E-11   65.5  11.7   97  659-763    41-140 (158)
 87 TIGR01052 top6b DNA topoisomer  98.6 2.4E-07 6.1E-12   71.0   7.2   35  381-415   196-231 (662)
 88 PRK11073 glnL nitrogen regulat  98.5 3.5E-06   9E-11   62.5  12.8  118  258-383    10-127 (348)
 89 COG3829 RocR Transcriptional r  98.5 1.8E-05 4.6E-10   57.4  15.8  136  238-385    99-237 (560)
 90 TIGR02040 PpsR-CrtJ transcript  98.5 7.4E-06 1.9E-10   60.2  13.6  275  127-432     5-312 (453)
 91 TIGR01925 spIIAB anti-sigma F   98.4   1E-06 2.6E-11   66.4   7.8   94  659-763    38-135 (137)
 92 KOG3558 consensus               98.4 2.2E-06 5.5E-11   64.1   9.2  218  127-370   128-379 (768)
 93 TIGR00229 sensory_box PAS doma  98.4   2E-06 5.1E-11   64.3   8.9  113  379-491     2-127 (130)
 94 PRK10841 hybrid sensory kinase  98.4 0.00028 7.2E-09   48.8  25.1  178  181-382   282-461 (947)
 95 COG2202 AtoS FOG: PAS/PAC doma  98.4  0.0001 2.6E-09   52.0  16.6  190  269-464     3-198 (232)
 96 KOG0519 consensus               98.3   1E-06 2.6E-11   66.4   5.7  225  524-751   367-619 (786)
 97 PRK00095 mutL DNA mismatch rep  98.3 2.4E-06 6.1E-11   63.8   6.1   25  658-682   571-595 (612)
 98 COG2172 RsbW Anti-sigma regula  98.2 2.2E-05 5.6E-10   56.8  10.9   96  657-763    37-140 (146)
 99 smart00086 PAC Motif C-termina  98.2 2.8E-06 7.3E-11   63.2   6.1   42  329-370     1-43  (43)
100 KOG3558 consensus               98.2 3.7E-05 9.4E-10   55.2  10.8  185  256-454   119-336 (768)
101 TIGR02040 PpsR-CrtJ transcript  98.1 1.5E-05 3.9E-10   57.9   8.1  163  300-462    39-222 (453)
102 PRK13558 bacterio-opsin activa  98.1 0.00017 4.4E-09   50.3  13.5  125  123-263   163-295 (674)
103 smart00091 PAS PAS domain. PAS  98.0 9.5E-06 2.4E-10   59.4   5.1   61  256-318     2-62  (67)
104 COG5002 VicK Signal transducti  98.0  0.0017 4.4E-08   43.1  16.4  134  238-380    93-228 (459)
105 COG3829 RocR Transcriptional r  98.0  0.0016 4.1E-08   43.3  16.0  161  258-431     4-166 (560)
106 COG3290 CitA Signal transducti  97.9  0.0025 6.3E-08   42.0  19.3  286   75-384    38-334 (537)
107 smart00091 PAS PAS domain. PAS  97.8 6.5E-05 1.7E-09   53.4   6.5   56  382-437     1-56  (67)
108 TIGR00585 mutl DNA mismatch re  97.8 7.8E-05   2E-09   52.8   6.8   56  660-718    22-77  (367)
109 TIGR02966 phoR_proteo phosphat  97.7  0.0005 1.3E-08   47.0  10.0  115  253-379     4-120 (339)
110 PRK10820 DNA-binding transcrip  97.7  0.0032   8E-08   41.2  13.3  109  252-370    77-188 (513)
111 PRK10820 DNA-binding transcrip  97.6   0.002 5.1E-08   42.7  11.7   39  128-166    90-128 (513)
112 pfam10090 DUF2328 Uncharacteri  97.6  0.0079   2E-07   38.3  18.8  177  559-760     2-179 (181)
113 KOG3559 consensus               97.6 0.00021 5.3E-09   49.8   6.1  216  128-375    89-337 (598)
114 cd00130 PAS PAS domain; PAS mo  97.5 0.00085 2.2E-08   45.3   8.7   84  391-474     1-88  (103)
115 KOG3560 consensus               97.5 0.00024 6.2E-09   49.3   5.9  222  128-369   121-385 (712)
116 PRK09959 hybrid sensory histid  97.5 0.00075 1.9E-08   45.7   7.9  147  235-384   556-705 (1197)
117 COG5385 Uncharacterized protei  97.5   0.011 2.8E-07   37.3  18.2  193  546-765    18-213 (214)
118 COG0323 MutL DNA mismatch repa  97.3 0.00042 1.1E-08   47.6   5.2   51  614-664   501-551 (638)
119 PTZ00272 heat shock protein 83  97.3  0.0018 4.7E-08   42.9   8.0   27  130-159    63-89  (701)
120 PRK11086 sensory histidine kin  97.0    0.03 7.6E-07   34.2  27.2  291   65-381    34-336 (541)
121 COG0326 HtpG Molecular chapero  97.0  0.0015 3.9E-08   43.5   5.1   95  618-715   452-552 (623)
122 TIGR01924 rsbW_low_gc anti-sig  97.0   0.002   5E-08   42.7   5.6   91  660-756    43-137 (161)
123 PRK05218 heat shock protein 90  96.9  0.0014 3.6E-08   43.7   4.6   28  129-159    62-89  (612)
124 KOG3559 consensus               96.8   0.013 3.3E-07   36.8   8.9  180  266-468    89-303 (598)
125 PTZ00130 heat shock protein 90  96.3  0.0073 1.9E-07   38.6   4.7   27  680-706   653-679 (824)
126 COG5000 NtrY Signal transducti  96.3   0.091 2.3E-06   30.7  17.4  129  245-381   360-488 (712)
127 KOG0501 consensus               96.2   0.012 2.9E-07   37.2   5.1  103  263-372    32-138 (971)
128 pfam08447 PAS_3 PAS fold. The   96.1    0.02 5.2E-07   35.4   6.2   75  404-478     1-84  (90)
129 COG5381 Uncharacterized protei  96.1   0.016   4E-07   36.2   5.5   90  655-748    54-158 (184)
130 PRK10364 sensor protein ZraS;   95.8    0.15 3.8E-06   29.1  16.6  102   45-154    12-114 (455)
131 KOG3560 consensus               94.3    0.39   1E-05   26.1  16.4   71  399-469   290-362 (712)
132 KOG3753 consensus               94.3   0.055 1.4E-06   32.3   3.7   41  400-440   339-379 (1114)
133 KOG0019 consensus               93.9   0.094 2.4E-06   30.6   4.3   21  681-701   535-555 (656)
134 KOG3561 consensus               93.8    0.11 2.9E-06   30.0   4.5  329  125-467   102-450 (803)
135 PTZ00108 DNA topoisomerase II;  93.7   0.082 2.1E-06   31.0   3.6   17  265-281   821-837 (1506)
136 PTZ00109 DNA gyrase subunit b;  93.7   0.019 4.8E-07   35.6   0.4   43  326-368   409-452 (941)
137 pfam07310 PAS_5 PAS domain. Th  93.4    0.55 1.4E-05   25.1   8.6   94  266-364    40-136 (137)
138 TIGR01058 parE_Gpos DNA topois  93.3    0.15 3.7E-06   29.2   4.5   44  320-363   248-291 (655)
139 KOG1979 consensus               93.3    0.13 3.4E-06   29.5   4.2   29  110-138    26-54  (694)
140 KOG0020 consensus               93.2    0.21 5.2E-06   28.1   5.0   12  265-276   324-335 (785)
141 COG3283 TyrR Transcriptional r  93.1    0.61 1.6E-05   24.7   9.5   39  128-166    90-128 (511)
142 KOG1977 consensus               92.4    0.39   1E-05   26.1   5.6   16  729-744  1067-1082(1142)
143 TIGR01059 gyrB DNA gyrase, B s  92.3    0.11 2.9E-06   30.0   2.7  124  546-674   609-746 (818)
144 TIGR01055 parE_Gneg DNA topois  92.3     0.1 2.6E-06   30.3   2.5   60  328-397   258-318 (647)
145 PRK05559 DNA topoisomerase IV   92.3   0.015 3.9E-07   36.3  -1.8   39  330-368   252-290 (633)
146 smart00433 TOP2c Topoisomerase  92.2    0.02   5E-07   35.5  -1.3   39  330-368   219-257 (594)
147 pfam08269 Cache_2 Cache domain  91.3    0.98 2.5E-05   23.2   7.8   79   78-159     8-86  (95)
148 PRK13374 purine nucleoside pho  91.2    0.63 1.6E-05   24.6   5.5   10  307-316    19-28  (233)
149 PRK05819 deoD purine nucleosid  90.2    0.87 2.2E-05   23.6   5.5   10  307-316    18-27  (235)
150 PRK05644 gyrB DNA gyrase subun  89.6   0.035   9E-07   33.6  -2.0   42  327-368   255-296 (725)
151 pfam08348 PAS_6 YheO-like PAS   89.4     1.4 3.6E-05   22.1   7.6   49  327-377    67-116 (118)
152 COG0187 GyrB Type IIA topoisom  88.1   0.086 2.2E-06   30.8  -0.8   37  327-363   252-288 (635)
153 COG2461 Uncharacterized conser  86.1    0.92 2.3E-05   23.4   3.5  107  381-490   289-401 (409)
154 pfam08670 MEKHLA MEKHLA domain  83.0     2.9 7.4E-05   19.8   7.9   50  384-434    34-85  (148)
155 TIGR01815 TrpE-clade3 anthrani  81.1    0.56 1.4E-05   25.0   0.7   88  665-765   536-636 (726)
156 KOG0355 consensus               80.6     2.4 6.2E-05   20.4   3.8   83  659-747   712-812 (842)
157 TIGR02373 photo_yellow photoac  80.4     1.8 4.5E-05   21.4   3.1   56  386-441    22-77  (126)
158 PRK11388 DNA-binding transcrip  80.1     3.6 9.2E-05   19.1  20.2   60  238-297   183-245 (639)
159 KOG0859 consensus               78.3     3.7 9.5E-05   19.0   4.2   12  594-605   140-151 (217)
160 PRK03124 S-adenosylmethionine   76.4     4.6 0.00012   18.4   6.4   83  643-725     7-108 (127)
161 KOG1229 consensus               74.4     1.5 3.9E-05   21.8   1.3   35  130-164   169-203 (775)
162 PRK09966 hypothetical protein;  69.4     6.6 0.00017   17.2  15.5   66   74-145    40-105 (407)
163 pfam05127 DUF699 Putative ATPa  69.2       4  0.0001   18.8   2.5   44  693-736    76-120 (160)
164 COG0093 RplN Ribosomal protein  66.7     6.7 0.00017   17.2   3.2   30  333-362    68-100 (122)
165 TIGR01622 SF-CC1 splicing fact  64.8       8 0.00021   16.6   3.7   26  136-161   126-151 (531)
166 PRK02770 S-adenosylmethionine   64.8       8 0.00021   16.6   5.6   81  641-721    18-117 (139)
167 TIGR02865 spore_II_E stage II   64.5     8.2 0.00021   16.6   4.3  122  595-734   435-584 (794)
168 PRK01706 S-adenosylmethionine   56.5      11 0.00028   15.6   6.2   75  643-717     9-103 (123)
169 TIGR02470 sucr_synth sucrose s  56.3      11 0.00028   15.7   2.8   88  654-757   601-694 (790)
170 PRK00529 elongation factor P;   56.1      11 0.00029   15.6   4.7   58  650-707    77-143 (186)
171 pfam07568 HisKA_2 Histidine ki  55.8      11 0.00029   15.6   8.6   73  550-635     2-74  (76)
172 PRK11178 uridine phosphorylase  54.0      12 0.00031   15.4   5.0   11  306-316    21-31  (251)
173 TIGR02035 D_Ser_am_lyase D-ser  53.1     4.8 0.00012   18.2   0.5   26  100-125    32-57  (431)
174 pfam11212 DUF2999 Protein of u  52.2      13 0.00033   15.2   3.9   54  555-615    27-81  (82)
175 TIGR01067 rplN_bact ribosomal   49.8      14 0.00035   14.9   3.0   31  333-363    74-107 (128)
176 COG0397 Uncharacterized conser  49.0      14 0.00036   14.8   4.8   23  136-158    31-53  (488)
177 TIGR00868 hCaCC calcium-activa  44.9      16 0.00042   14.4   2.7   30  689-718   646-675 (874)
178 PRK12299 obgE GTPase ObgE; Rev  44.9      16 0.00042   14.4   5.8   12  622-633   315-326 (334)
179 KOG1135 consensus               44.5     6.1 0.00016   17.5  -0.1   47  654-705   696-743 (764)
180 PRK13719 conjugal transfer tra  44.4      17 0.00043   14.3   8.7   41  380-420    17-57  (220)
181 COG1444 Predicted P-loop ATPas  44.3      17 0.00043   14.3   2.5   19  326-344   383-403 (758)
182 PTZ00054 60S ribosomal protein  43.6      17 0.00044   14.3   5.1   32  332-363    85-119 (139)
183 TIGR01634 tail_P2_I phage tail  43.5      13 0.00034   15.1   1.5   82  298-383    48-131 (139)
184 PRK12297 obgE GTPase ObgE; Rev  43.2      17 0.00044   14.2   5.8   12  265-276    90-101 (429)
185 TIGR03330 SAM_DCase_Bsu S-aden  43.0      17 0.00045   14.2   5.5   74  644-717     7-99  (112)
186 TIGR02789 nickel_nikB nickel A  42.5      15 0.00038   14.6   1.7   13  379-391   223-235 (315)
187 PRK13858 type IV secretion sys  42.4      18 0.00046   14.1   5.5   73  554-636    55-136 (148)
188 TIGR01818 ntrC nitrogen regula  41.6      18 0.00047   14.0   3.6   36  534-569   310-346 (471)
189 PRK00029 hypothetical protein;  40.8      19 0.00048   14.0   4.1   23  136-158    31-53  (487)
190 TIGR02749 prenyl_cyano solanes  40.3      19 0.00048   13.9   1.9   25  373-397   166-190 (325)
191 pfam02675 AdoMet_dc S-adenosyl  39.9      19  0.0005   13.9   5.5   66  652-717    11-94  (107)
192 PRK08383 putative monovalent c  39.6      20  0.0005   13.8   4.2   52  665-718   108-160 (167)
193 COG3284 AcoR Transcriptional a  38.6      20 0.00052   13.7   6.0   55  238-292   198-259 (606)
194 PRK07831 short chain dehydroge  38.6      18 0.00045   14.1   1.6   25  359-383    69-93  (261)
195 COG0536 Obg Predicted GTPase [  38.3      20 0.00052   13.7   4.6   16  621-636   320-335 (369)
196 PRK12298 obgE GTPase ObgE; Rev  36.1      22 0.00056   13.5   5.7   13  622-634   321-333 (380)
197 TIGR00107 deoD purine nucleosi  35.8      22 0.00057   13.4   2.4   61  257-327    79-146 (234)
198 TIGR03673 rpl14p_arch 50S ribo  35.4      23 0.00058   13.4   3.6   34  332-365    77-113 (131)
199 PRK03578 hscB co-chaperone Hsc  35.1      14 0.00036   14.8   0.6   30  280-309     4-39  (176)
200 COG2200 Rtn c-di-GMP phosphodi  34.8      23 0.00059   13.3   7.7   22  720-741   178-199 (256)
201 PRK06841 short chain dehydroge  34.0      24 0.00061   13.2   1.6   22  362-383    65-86  (255)
202 PRK11564 stationary phase indu  33.8      24 0.00061   13.2   6.5   20  620-639   254-273 (426)
203 TIGR01605 PYST-D Plasmodium yo  33.7      22 0.00056   13.5   1.4   11  731-741    13-23  (55)
204 PRK01356 hscB co-chaperone Hsc  33.7      22 0.00057   13.4   1.4   27  283-309     3-35  (166)
205 COG5388 Uncharacterized protei  33.2      24 0.00062   13.1   4.0   82  282-368    78-160 (209)
206 PRK12426 elongation factor P;   33.2      24 0.00062   13.1   3.5   52  653-704    80-140 (185)
207 PRK08571 rpl14p 50S ribosomal   33.1      24 0.00062   13.1   5.2   33  332-364    78-113 (132)
208 PRK06935 2-deoxy-D-gluconate 3  33.1      25 0.00063   13.1   1.6   22  360-381    65-86  (258)
209 pfam03281 Mab-21 Mab-21 protei  32.2      25 0.00065   13.0   3.8   14  621-634   335-348 (360)
210 TIGR01120 rpiB ribose 5-phosph  31.2      15 0.00038   14.7   0.2   40  634-675    18-59  (143)
211 KOG3938 consensus               30.9      27 0.00068   12.9   2.7   34  252-289    77-110 (334)
212 pfam07328 VirD1 T-DNA border e  30.3      27 0.00069   12.8   5.5   41  554-604    55-95  (147)
213 TIGR01108 oadA oxaloacetate de  29.7      28 0.00071   12.7   5.5  167  243-421     6-199 (616)
214 pfam08446 PAS_2 PAS fold. The   29.4      28 0.00072   12.7   8.3   24  400-423    24-47  (107)
215 PRK01773 hscB co-chaperone Hsc  29.3      25 0.00063   13.1   1.1   27  283-309     3-35  (173)
216 KOG4426 consensus               28.3      29 0.00074   12.6   1.4   69  560-633   512-589 (656)
217 pfam01899 MNHE Na+/H+ ion anti  28.1      29 0.00075   12.6   4.3   51  664-717    48-98  (106)
218 TIGR02386 rpoC_TIGR DNA-direct  28.1      29 0.00075   12.6   1.3   11  654-664   854-864 (1552)
219 KOG0242 consensus               28.1      30 0.00075   12.5   2.8   13  280-292   143-155 (675)
220 TIGR02451 anti_sig_ChrR anti-s  28.0      25 0.00063   13.1   0.9   25  692-717   208-232 (234)
221 KOG2036 consensus               27.8      30 0.00076   12.5   2.6   82  584-666   882-968 (1011)
222 PRK06114 short chain dehydroge  27.4      30 0.00077   12.5   1.6   19  362-380    70-88  (262)
223 TIGR00021 rpiA ribose 5-phosph  27.4      30 0.00077   12.5   3.7   55  652-711   137-195 (236)
224 MTH00204 ND4 NADH dehydrogenas  27.1      31 0.00078   12.4   1.6   17  663-679   469-485 (486)
225 PRK00294 hscB co-chaperone Hsc  26.9      28 0.00072   12.7   1.0   29  281-309     3-37  (173)
226 KOG3491 consensus               26.9      31 0.00079   12.4   2.6   23   51-73     37-59  (65)
227 TIGR02885 spore_sigF RNA polym  26.9      31 0.00079   12.4   4.9   59  245-317    94-158 (231)
228 TIGR02110 PQQ_syn_pqqF coenzym  26.1      15 0.00037   14.8  -0.6   30  107-136   170-199 (737)
229 TIGR02748 GerC3_HepT heptapren  25.9      32 0.00082   12.3   1.5   99  228-334    52-157 (325)
230 PRK00458 S-adenosylmethionine   25.5      33 0.00083   12.2   4.8   73  644-716    19-112 (127)
231 PRK04542 elongation factor P;   25.1      33 0.00085   12.2   4.2   25  396-420    74-98  (189)
232 pfam08066 PMC2NT PMC2NT (NUC01  25.0      33 0.00085   12.2   5.1   53  582-635    24-76  (91)
233 PRK04025 S-adenosylmethionine   25.0      33 0.00085   12.2   5.8   74  643-716     7-100 (139)
234 PRK06124 gluconate 5-dehydroge  24.9      33 0.00085   12.2   1.6   23  654-676   222-244 (259)
235 PRK05014 hscB co-chaperone Hsc  24.7      34 0.00086   12.1   1.1   26  284-309     3-34  (171)
236 KOG3822 consensus               24.5      34 0.00087   12.1   4.0   11  396-406   210-220 (516)
237 pfam03671 Ufm1 Ubiquitin fold   24.4      34 0.00087   12.1   1.0   19  695-713    47-66  (76)
238 PRK02991 D-serine dehydratase;  24.0      14 0.00036   14.8  -1.0   21  104-124    43-63  (443)
239 TIGR00459 aspS_bact aspartyl-t  23.9      33 0.00083   12.2   0.9   91  651-752   514-613 (653)
240 COG1666 Uncharacterized protei  23.9      35 0.00089   12.0   6.7   66  619-684    12-83  (165)
241 COG1134 TagH ABC-type polysacc  23.7      35 0.00089   12.0   2.8   16  552-567   122-137 (249)
242 PRK07985 oxidoreductase; Provi  23.6      35  0.0009   12.0   1.5   13  365-377   107-119 (294)
243 PRK09804 putative cryptic C4-d  23.5      14 0.00035   14.9  -1.1   21  543-563   302-322 (455)
244 pfam04701 Pox_D2 Pox virus D2   23.5      35  0.0009   12.0   2.6   50  628-678    81-133 (143)
245 COG1586 SpeD S-adenosylmethion  23.0      36 0.00092   11.9   5.1   62  653-714    28-108 (136)
246 cd06447 D-Ser-dehyd D-Serine d  22.7      16 0.00042   14.4  -0.9   18  107-124    21-38  (404)
247 TIGR00658 orni_carb_tr ornithi  22.6      37 0.00094   11.8   1.4   20  311-330   204-223 (341)
248 PRK02625 DNA-directed RNA poly  22.2      28 0.00072   12.7   0.3   51  337-390   238-293 (627)
249 PRK06701 short chain dehydroge  22.1      38 0.00096   11.8   1.5   24  361-384    98-121 (289)
250 TIGR02986 restrict_Alw26I type  22.0      38 0.00096   11.8   1.2   65  264-336    25-103 (461)
251 pfam07492 Trehalase_Ca-bi Neut  21.6      38 0.00098   11.7   1.7   15  689-703    10-24  (30)
252 PRK12820 bifunctional aspartyl  21.2      28 0.00072   12.7   0.1   15  129-143    37-51  (706)
253 TIGR01433 CyoA ubiquinol oxida  21.1      39   0.001   11.6   1.6   22  215-236    35-56  (228)
254 PRK06128 oxidoreductase; Provi  21.0      39   0.001   11.6   1.5   18  363-380   111-128 (300)
255 PRK11034 clpA ATP-dependent Cl  20.8      40   0.001   11.6   9.6   82  620-701   656-750 (758)
256 PRK05483 rplN 50S ribosomal pr  20.8      40   0.001   11.6   4.0   32  332-363    67-101 (122)
257 cd06257 DnaJ DnaJ domain or J-  20.6      40   0.001   11.6   1.3   26  284-309     2-31  (55)

No 1  
>PRK11091 aerobic respiration control sensor protein ArcB; Provisional
Probab=100.00  E-value=0  Score=615.49  Aligned_cols=362  Identities=25%  Similarity=0.381  Sum_probs=329.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEEEEECCCCEEEECHHHHHHCCCCHHHCCCCHHHHHHHHCCCCHHHHHHH
Q ss_conf             89999999999999999999999722597459897689789997889977299943305898899976081205899999
Q gi|254780903|r  238 RQAKKNKENDTILLEANICVETALSRGRCGLWNFNFDNKKFHLSRSMYEIMGIPYENKTLSFRAIARLIHYDNKKICEIA  317 (766)
Q Consensus       238 ~dit~~r~ae~~l~ese~rl~~al~~a~~GiWd~D~~~~~i~ws~~~~~llG~~~~e~~~s~~~~~~~vHPdDr~~~~~a  317 (766)
                      ..+.+|++++..|.+....+|.+++++|+.+|--|+++.++-+|++|++++|++.++..+.  +-.+++.|+-.+.+...
T Consensus       138 ~e~~~r~~~q~~l~~~~~llRs~~D~~Pdli~~rd~~g~f~gCNrafe~~~G~~e~eliG~--t~~d~~~~e~a~~~~~~  215 (779)
T PRK11091        138 NEIKEREETQIELEQQSSLLRSFLDASPDLVYYRNEDGEFSGCNRAMELLTGKSEKQLVGL--TPKDVYSPEAAEKVIET  215 (779)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEEEECCCCCCCCCCHHHHHHHCCCHHHHCCC--CHHHHCCHHHHHHHHHH
T ss_conf             9999989999999998899998850287515787798765341099998809998998499--83552799889999973


Q ss_pred             HHHHHCCCCEEEEEEEEECCCCCEEEEEEEEEEEEECCCEE-EEEEEEECCCHHHHHHHHHHHHHHHHHHHHHHHHHHEE
Q ss_conf             99972489848999998869898899889999998379606-99999844617999999999999999999985445515
Q gi|254780903|r  318 RSVTGKHVKQLDQIFHMRHASGADIWIQVRAQMMRTISGGM-NIIGIAMDLTEKYHLEKRYAEADQRLSKAIECTSEALV  396 (766)
Q Consensus       318 ~~~~~~~~~~~~~e~Ri~~~DG~~~Wi~~r~~~i~d~~G~~-~~iGi~~DITErK~ae~~l~ese~rlr~~ie~~~~~i~  396 (766)
                      .+.+.+.+.+...|-++..+||+..|+..+-.|++|..|++ +++|+.+||||||++|++|                   
T Consensus       216 D~~v~~~~~~~~~e~w~~~~dG~~~~~e~~k~P~~d~~g~~~G~~g~~rDITerk~aeeaL-------------------  276 (779)
T PRK11091        216 DEKVFRHNVSLTYEQWLDYPDGRKACFELRKVPFYDRVGKRHGLMGFGRDITERKRYQDAL-------------------  276 (779)
T ss_pred             HHHHHHCCCCCEEEEEEECCCCCEEEEEEEEEEEECCCCCEEEEEEEEECCHHHHHHHHHH-------------------
T ss_conf             8999864798211134664898667899864013538997887863001601778999999-------------------


Q ss_pred             EECCCCEEEEECHHHHHHHCCCHHHHCCCCCHHHHCCCHHHHHHHHHHHCCCCCCCEEEEEEECCCEEEEECCEECCCCC
Q ss_conf             88349969970178988839997894289717881652013789998521124564058999169628742232456997
Q gi|254780903|r  397 LWDKNDRLVMCNANYQKAYGLPDHVLVPGNARSIIQDAQTRPIIEYRTSDPERSQDMSKEIKLADSRWLQINEWCTHDGG  476 (766)
Q Consensus       397 ~~D~~g~i~~~N~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~dg~~~~i~~~~~~dg~  476 (766)
                                                                                                      
T Consensus       277 --------------------------------------------------------------------------------  276 (779)
T PRK11091        277 --------------------------------------------------------------------------------  276 (779)
T ss_pred             --------------------------------------------------------------------------------
T ss_conf             --------------------------------------------------------------------------------


Q ss_pred             EEEEEEEEEHHHCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             89998862010001122322222221100001788998644457999999999999999988789999999987675222
Q gi|254780903|r  477 TISVGTDITLLKHNQAQLRESKRRLKATINDLSTSRQILERQKTELSIANAKYQVEKERAETANKTKSEFLAKMSHELRT  556 (766)
Q Consensus       477 ~v~v~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~~~~~l~~~~~~ae~an~~k~efla~isHelrt  556 (766)
                                                                                  |+||++|++|+|+|||||||
T Consensus       277 ------------------------------------------------------------E~AsraKS~FLAnMSHEIRT  296 (779)
T PRK11091        277 ------------------------------------------------------------EKASRDKTTFISTISHELRT  296 (779)
T ss_pred             ------------------------------------------------------------HHHHHHHHHHHHHHHHHHCH
T ss_conf             ------------------------------------------------------------99999999999872687565


Q ss_pred             HHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCEEEECHHHHHHHHHHHHHHH
Q ss_conf             47899999999860346889938999999999999999999977767788874198301203316999999999999999
Q gi|254780903|r  557 PLNAILGFSEVIKKEIFGELGSVKYYEYAQDIHYSGQHLLNMINNILEMSKIETEKISIDKQNADLIPIINEGIRLIGSS  636 (766)
Q Consensus       557 PL~aI~g~~ell~~~~~~~~~~e~~~~~l~~I~~~~~~l~~lI~diLd~srieag~~~~~~~~~dl~~~i~~~~~~~~~~  636 (766)
                      |||+|+|++++|.+.   ++ ++++++|++.|..|+++|+.+|||||||||||+|+++++.++||+.++++++...+.+.
T Consensus       297 PLNgIlG~seLL~~t---~L-~~eQre~l~~I~~S~~~Ll~LINDILD~SKIEaGkl~l~~~~fdl~~ll~~v~~~~~~~  372 (779)
T PRK11091        297 PLNGIVGLSRMLLDT---EL-TAEQEKYLKTIHVSAITLGNIFNDIIDMDKMDRRKLQLDNQPVDFTDFLADLENLSGLQ  372 (779)
T ss_pred             HHHHHHHHHHHHHCC---CC-CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCEEEEEEECHHHHHHHHHHHHHHH
T ss_conf             399999999998079---99-99999999999999999999999999999996699678877675999999999999999


Q ss_pred             HHHCCCEEEEEECCCCE--EEECHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEEE-CCEEEEEEEECCCCCCHHHHHHHC
Q ss_conf             98479589998089978--998689999999998865653468988899999997-998999999788978977854304
Q gi|254780903|r  637 AQSKNIKIEKKIPSELF--FNADKRIIKKILFPILSNSIKFTNNNGKMMIRTSKI-GQCVIITIADTGIGIPKSALEKIG  713 (766)
Q Consensus       637 ~~~k~i~l~~~~~~~l~--v~~D~~~l~QVl~NLi~NAik~t~~~g~I~i~~~~~-~~~v~i~V~D~G~GI~~e~~~~iF  713 (766)
                      +.+|++.+.+++++++|  +.+|+.+|+|||.||++||+|||+. |.|++++... ++.++|+|+|||+|||++.+++||
T Consensus       373 A~~Kgl~l~~~~~~~lP~~v~gD~~RLrQIL~NLlsNAIKFT~~-G~V~l~v~~~~~~~l~f~V~DTGiGI~~e~l~~IF  451 (779)
T PRK11091        373 AEQKGLRFDLEPLLPLPHKVITDGTRLRQILWNLISNAVKFTQQ-GQVTVRVRYEDGDMLHFEVEDSGIGIPEDELDKIF  451 (779)
T ss_pred             HHHCCCEEEEEECCCCCCEEECCHHHHHHHHHHHHHHHHHCCCC-CCEEEEEEECCCCEEEEEEEECCCCCCHHHHHHHH
T ss_conf             99749889999789998628638999999999999999773899-97799999827988999999579999999999870


Q ss_pred             CCEEECCCCCCC-CCCCCCHHHHHHHHHHHHCCCEEEEEEECCCCEEEEEECC
Q ss_conf             650531467556-7788761689999999962986999979899529999735
Q gi|254780903|r  714 QPFEPLHNQYDQ-SIGGFGLGLAISDALTNLHGGRLKIISQEGKGTIVTICMP  765 (766)
Q Consensus       714 ~pF~q~~~~~t~-~~~GtGLGLaI~k~iVe~hgG~I~v~S~~g~Gttf~i~LP  765 (766)
                      +||+|++++.++ .++||||||+|||+||++|||+|+|+|++|+||||+|+||
T Consensus       452 ~~F~Q~~~s~~~r~~~GTGLGLaI~k~LvelMGG~I~V~S~~G~GStFt~~Lp  504 (779)
T PRK11091        452 AMYYQVKDSHGGKPATGTGIGLAVSRRLAQNMGGDITVTSEEGKGSTFTLTIH  504 (779)
T ss_pred             CCCEECCCCCCCCCCCCCCHHHHHHHHHHHHCCCEEEEEECCCCCCEEEEEEE
T ss_conf             57560667877767788760799999999984997999955998717999997


No 2  
>PRK10841 hybrid sensory kinase in two-component regulatory system with RcsB and YojN; Provisional
Probab=100.00  E-value=0  Score=586.81  Aligned_cols=337  Identities=24%  Similarity=0.346  Sum_probs=297.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHEEEEC-CCCEEEEECHHHHHHHCCCHHHHCCCCCHHHHCCCHHHHHHHHHHHCCCCC
Q ss_conf             9999999999999999985445515883-499699701789888399978942897178816520137899985211245
Q gi|254780903|r  372 HLEKRYAEADQRLSKAIECTSEALVLWD-KNDRLVMCNANYQKAYGLPDHVLVPGNARSIIQDAQTRPIIEYRTSDPERS  450 (766)
Q Consensus       372 ~ae~~l~ese~rlr~~ie~~~~~i~~~D-~~g~i~~~N~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  450 (766)
                      +...+|.|+|+.-|.+++++|.|+++.. .||..+..|..+...+..-.             +.++ .......+   ..
T Consensus       347 ~~a~~l~e~e~fnr~~i~~apvg~~~l~~~dg~~~~~n~~~~~~~~~~~-------------~~~~-~~~~~~~~---~~  409 (947)
T PRK10841        347 SNALRLEEHEQFNRKIVASAPVGICILRTSDGTNILSNELAHNYLNMLT-------------HEDR-QRLTQIIC---GQ  409 (947)
T ss_pred             HHHHHHHHHHHHHHHHHHHCCCEEEEEECCCCCEEECHHHHHHHHHHCC-------------CCHH-HHHHHHHH---CC
T ss_conf             7788998788877889861771379997068863310389999876237-------------5528-99999986---13


Q ss_pred             CCEEEEEEECCCEEEEECCEECCCCC---EEEEEEEEEHHHCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             64058999169628742232456997---899988620100011223222222211000017889986444579999999
Q gi|254780903|r  451 QDMSKEIKLADSRWLQINEWCTHDGG---TISVGTDITLLKHNQAQLRESKRRLKATINDLSTSRQILERQKTELSIANA  527 (766)
Q Consensus       451 ~~~~~e~~~~dg~~~~i~~~~~~dg~---~v~v~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~~~~  527 (766)
                      ..-..++...+++.++++-.+++..|   .+++..||+.+                                   +++++
T Consensus       410 ~~~~~~~~~~~~~~l~~~~~~~ry~~~~v~~c~~~Disar-----------------------------------~~~e~  454 (947)
T PRK10841        410 QVNFVDVLTSNNTNLQISFVHSRYRNENVAICVLVDVSAR-----------------------------------VKMEE  454 (947)
T ss_pred             CCCCEEEEECCCCEEEEEEEEEEECCCCEEEEEEEECHHH-----------------------------------HHHHH
T ss_conf             7883489935985799998653126860799999854078-----------------------------------99999


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             99999999988789999999987675222478999999998603468899389999999999999999999777677888
Q gi|254780903|r  528 KYQVEKERAETANKTKSEFLAKMSHELRTPLNAILGFSEVIKKEIFGELGSVKYYEYAQDIHYSGQHLLNMINNILEMSK  607 (766)
Q Consensus       528 ~l~~~~~~ae~an~~k~efla~isHelrtPL~aI~g~~ell~~~~~~~~~~e~~~~~l~~I~~~~~~l~~lI~diLd~sr  607 (766)
                      .|++.++.||+||++||+|||+||||||||||+|+|++|||++.   ++ ++++++|++.|+.|++.|+.+|||||||||
T Consensus       455 ~L~~a~~AAE~AN~AKS~FLAnMSHEIRTPLnGIlG~lELL~~t---~L-~~~Qr~~l~tI~~Ss~~LL~lINDILDfSK  530 (947)
T PRK10841        455 SLQEMAQAAEQASQSKSMFLATVSHELRTPLYGIIGNLDLLQTK---EL-PKGVDRLVTAMNNSSSLLLKIISDILDFSK  530 (947)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHCCHHHCHHHHHHHHHHHHHCCC---CC-CHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             99999999999999998998758564361289999999998079---99-989999999999999999999999999998


Q ss_pred             HHCCCCCCCEEEECHHHHHHHHHHHHHHHHHHCCCEEEEEECCCCE--EEECHHHHHHHHHHHHHHHHHCCCCCCEEEEE
Q ss_conf             7419830120331699999999999999998479589998089978--99868999999999886565346898889999
Q gi|254780903|r  608 IETEKISIDKQNADLIPIINEGIRLIGSSAQSKNIKIEKKIPSELF--FNADKRIIKKILFPILSNSIKFTNNNGKMMIR  685 (766)
Q Consensus       608 ieag~~~~~~~~~dl~~~i~~~~~~~~~~~~~k~i~l~~~~~~~l~--v~~D~~~l~QVl~NLi~NAik~t~~~g~I~i~  685 (766)
                      ||+|+++++.++||+.++++++...+.+.+.+|++.|...+++++|  +.+|+.+|+|||.||++||||||+. |.|.|+
T Consensus       531 IEAGkl~Le~~~F~l~~lv~~v~~~~~~~A~~K~L~L~~~idp~vP~~v~GDp~RLrQIL~NLLsNAIKFT~~-G~I~L~  609 (947)
T PRK10841        531 IESEQLKIEPREFSPREVMNHITANYLPLVVKKQLGLYCFIEPDVPVSLNGDPMRLQQVISNLLSNAIKFTDT-GCIILH  609 (947)
T ss_pred             HHCCCCEEEEECCCHHHHHHHHHHHHHHHHHHCCCEEEEEECCCCCCCEEECHHHHHHHHHHHHHHHEEECCC-CEEEEE
T ss_conf             8049847985256899999999999999999739879999799999658606889999999988777466799-589999


Q ss_pred             EEEECCEEEEEEEECCCCCCHHHHHHHCCCEEECCCCCCCCCCCCCHHHHHHHHHHHHCCCEEEEEEECCCCEEEEEECC
Q ss_conf             99979989999997889789778543046505314675567788761689999999962986999979899529999735
Q gi|254780903|r  686 TSKIGQCVIITIADTGIGIPKSALEKIGQPFEPLHNQYDQSIGGFGLGLAISDALTNLHGGRLKIISQEGKGTIVTICMP  765 (766)
Q Consensus       686 ~~~~~~~v~i~V~D~G~GI~~e~~~~iF~pF~q~~~~~t~~~~GtGLGLaI~k~iVe~hgG~I~v~S~~g~Gttf~i~LP  765 (766)
                      ++..+++++|+|+|||+|||++.+++||+||+|++++.++++|||||||+|||+||++|||+|+|+|++|+||+|+|+||
T Consensus       610 V~~~~~~L~fsV~DTGIGIsee~~~~LFepF~QaD~S~tR~yGGTGLGLAI~krLVeLMGG~I~VeSe~G~GStFtf~LP  689 (947)
T PRK10841        610 VRVDGDYLSFRVRDTGVGIPAKEVVRLFDPFFQVGTGVQRNFQGTGLGLAICEKLINMMDGDISVDSEPGMGSQFTVRIP  689 (947)
T ss_pred             EEECCCEEEEEEEECCCCCCHHHHHHHHCHHHCCCCCCCCCCCCCCCHHHHHHHHHHHCCCEEEEEECCCCEEEEEEEEE
T ss_conf             99849999999998289989999998847111578754345799874199999999975995899916998079999975


No 3  
>PRK09959 hybrid sensory histidine kinase in two-component regulatory system with EvgA; Provisional
Probab=100.00  E-value=0  Score=549.70  Aligned_cols=358  Identities=23%  Similarity=0.319  Sum_probs=276.2

Q ss_pred             ECCCHHHHHHHHHHHHHHHHHHHHHHHHHHEEEECCCCEEEEECHHHHHHHCCCHHH--HCCCCCHHHHCCC--HHHHHH
Q ss_conf             446179999999999999999999854455158834996997017898883999789--4289717881652--013789
Q gi|254780903|r  365 MDLTEKYHLEKRYAEADQRLSKAIECTSEALVLWDKNDRLVMCNANYQKAYGLPDHV--LVPGNARSIIQDA--QTRPII  440 (766)
Q Consensus       365 ~DITErK~ae~~l~ese~rlr~~ie~~~~~i~~~D~~g~i~~~N~~~~~~~g~~~~~--~~~~~~~~~~~~~--~~~~~~  440 (766)
                      +-|-.||++|.+|++.....+.++|++|.++++.|.+|+++.||.+|+..|+-+...  ..+....+.....  ......
T Consensus       559 r~ir~R~~ae~~L~~ql~f~~~L~d~iP~pi~v~d~~g~~i~~N~a~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~~~~~  638 (1197)
T PRK09959        559 RSVRRRKVIQGDLENQISFRKALSDSLPNPTYVVNWQGNVISHNSAFEHYFTADYYKNAMLPLENSESPFKDVFSNTHEV  638 (1197)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEEEECCCCCCHHHHHHHHHHHCCCHHHHCCCCCCCCCCHHHHHHHHHHHH
T ss_conf             99999999999999889999999836998769982556122411888987523144421356532222156777777899


Q ss_pred             HHHHHCCCCCCCEEEEEEECCC-------EEEEECCEECCCC-CEEEEEEEEEHHHCCCCCCCCCCCCCCCCCCHHHHHH
Q ss_conf             9985211245640589991696-------2874223245699-7899988620100011223222222211000017889
Q gi|254780903|r  441 EYRTSDPERSQDMSKEIKLADS-------RWLQINEWCTHDG-GTISVGTDITLLKHNQAQLRESKRRLKATINDLSTSR  512 (766)
Q Consensus       441 ~~~~~~~~~~~~~~~e~~~~dg-------~~~~i~~~~~~dg-~~v~v~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~  512 (766)
                      ..............++  ..+|       .|......+..++ ++++...||                            
T Consensus       639 ~~~~~~~~~~~~~~~~--~~~g~~~~~i~~w~~~~~~~~~~~~~~i~gw~DI----------------------------  688 (1197)
T PRK09959        639 TAETKENRTIYTQVFE--IDNGIEKRCINHWHTLCNLPASDHAVYICGWQDI----------------------------  688 (1197)
T ss_pred             HHHHHHCCCCCCEEEE--CCCCCCCEEEEEEEEEECCCCCCCEEEECCEEEH----------------------------
T ss_conf             8753101210001453--0577542367753100037644440101154641----------------------------


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHH
Q ss_conf             98644457999999999999999988789999999987675222478999999998603468899389999999999999
Q gi|254780903|r  513 QILERQKTELSIANAKYQVEKERAETANKTKSEFLAKMSHELRTPLNAILGFSEVIKKEIFGELGSVKYYEYAQDIHYSG  592 (766)
Q Consensus       513 ~~~~~~~~~L~~~~~~l~~~~~~ae~an~~k~efla~isHelrtPL~aI~g~~ell~~~~~~~~~~e~~~~~l~~I~~~~  592 (766)
                             ++.+++++.|+++|++||+||++||+|||+||||||||||+|+|++++|...   ++..++..++++.|+.|+
T Consensus       689 -------Terk~~e~~L~~Ak~~Ae~An~AKS~FLA~MSHEIRTPLn~IiG~~eLL~~~---~l~~~q~~~~l~~~~~Sa  758 (1197)
T PRK09959        689 -------TETRDLIHALEVERNKAINATVAKSQFLATMSHEIRTPISSIMGFLELLSGS---GLSKEQRVEAISLAYATG  758 (1197)
T ss_pred             -------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHCCHHHHHHHHHHHHHCC---CCCHHHHHHHHHHHHHHH
T ss_conf             -------2899999999999999999988888888747353165689999999998468---999899999999999999


Q ss_pred             HHHHHHHHHHHHHHHHHCCCCCCCEEEECHHHHHHHHHHHHHHHHHHCCCEEEEEECCC--CEEEECHHHHHHHHHHHHH
Q ss_conf             99999977767788874198301203316999999999999999984795899980899--7899868999999999886
Q gi|254780903|r  593 QHLLNMINNILEMSKIETEKISIDKQNADLIPIINEGIRLIGSSAQSKNIKIEKKIPSE--LFFNADKRIIKKILFPILS  670 (766)
Q Consensus       593 ~~l~~lI~diLd~srieag~~~~~~~~~dl~~~i~~~~~~~~~~~~~k~i~l~~~~~~~--l~v~~D~~~l~QVl~NLi~  670 (766)
                      +.|+.||||||||||||+|+++++++++|+.+++++++..+.+.+.+|++.|.++...+  ..+.+|+.+|+|||.||++
T Consensus       759 ~~LL~LInDILD~SKIEaG~l~l~~~~~~l~~li~~v~~~~~~~A~~K~l~l~~~~~~p~~~~v~~D~~Rl~QIL~NLls  838 (1197)
T PRK09959        759 QSLLGLIGEILDVDKIESGNYQLQPQWVDIPTLVQNTCHSFGAIAASKSIALSCSSTFPEHYLVKIDPQAFKQVLSNLLS  838 (1197)
T ss_pred             HHHHHHHHHHHHHHHHHCCCCEEEEEEECHHHHHHHHHHHHHHHHHHCCCEEEEECCCCCCCEECCCHHHHHHHHHHHHH
T ss_conf             99999888889998985388621452017999999999999999996796899955898751352678899999999987


Q ss_pred             HHHHCCCCCCEEEEEEEEE--C---CEEEEEEEECCCCCCHHHHHHHCCCEEECCCCCCCCCCCCCHHHHHHHHHHHHCC
Q ss_conf             5653468988899999997--9---9899999978897897785430465053146755677887616899999999629
Q gi|254780903|r  671 NSIKFTNNNGKMMIRTSKI--G---QCVIITIADTGIGIPKSALEKIGQPFEPLHNQYDQSIGGFGLGLAISDALTNLHG  745 (766)
Q Consensus       671 NAik~t~~~g~I~i~~~~~--~---~~v~i~V~D~G~GI~~e~~~~iF~pF~q~~~~~t~~~~GtGLGLaI~k~iVe~hg  745 (766)
                      ||+|||+. |.|.|++...  +   ..+.|+|+|||||||++.+++||+||+|++  .+++++||||||+|||++|++||
T Consensus       839 NAIKFT~~-G~V~i~~~~~~~~~~~~~l~~~V~DTGiGI~~~~~~~iF~pF~Q~s--~~r~~~GTGLGLaI~k~LvelMg  915 (1197)
T PRK09959        839 NALKFTTE-GAVKITTSLGHIDDNHAVIKMTIMDSGSGLSQEEQQQLFKRYSQTS--AGRQQTGSGLGLMICKELIKNMQ  915 (1197)
T ss_pred             HHCCCCCC-CEEEEEEEEEECCCCEEEEEEEEEECCCCCCHHHHHHHCCCCCCCC--CCCCCCCCCCHHHHHHHHHHHCC
T ss_conf             53746879-7899999986517980699999997787889889975367862477--88788984835999999999879


Q ss_pred             CEEEEEEECCCCEEEEEECC
Q ss_conf             86999979899529999735
Q gi|254780903|r  746 GRLKIISQEGKGTIVTICMP  765 (766)
Q Consensus       746 G~I~v~S~~g~Gttf~i~LP  765 (766)
                      |+|+|+|++|+||+|+|+||
T Consensus       916 G~I~v~S~~G~GS~F~~~lp  935 (1197)
T PRK09959        916 GDLSLESHPGIGTTFTITIP  935 (1197)
T ss_pred             CEEEEEECCCCCEEEEEEEE
T ss_conf             92899935999449999997


No 4  
>PRK13557 histidine kinase; Provisional
Probab=100.00  E-value=0  Score=548.00  Aligned_cols=345  Identities=18%  Similarity=0.319  Sum_probs=300.4

Q ss_pred             HHHHHHHHHHHCCCCCEEEEEC---CCCEEEECHHHHHHCCCCHHHCCCCHHHHHHHHCCC-CHHHHHHHHHHHHCCCCE
Q ss_conf             9999999997225974598976---897899978899772999433058988999760812-058999999997248984
Q gi|254780903|r  252 EANICVETALSRGRCGLWNFNF---DNKKFHLSRSMYEIMGIPYENKTLSFRAIARLIHYD-NKKICEIARSVTGKHVKQ  327 (766)
Q Consensus       252 ese~rl~~al~~a~~GiWd~D~---~~~~i~ws~~~~~llG~~~~e~~~s~~~~~~~vHPd-Dr~~~~~a~~~~~~~~~~  327 (766)
                      +..+.|.++++.+++.+|..|+   ++..+|||+++++|+||+++|..+..  +.-+.||+ |++.+...++.+. .+..
T Consensus        25 ~~~~~~~~~v~~~~~~~~~~d~~~~Dg~I~~vN~af~~~tGYs~eEviGk~--~~~L~~p~~~~~~~~~~~~~i~-~~~~  101 (538)
T PRK13557         25 HRSDIFFAAVETTRMPMIVTDPRQPDNPIVFANRAFLEMTGYAAEEIIGNN--CRFLQGPETDRATVADVRDAIA-ERRE  101 (538)
T ss_pred             HHHHHHHHHHHHCCCCEEEECCCCCCCEEEEECHHHHHHHCCCHHHHCCCC--HHHCCCCCCCHHHHHHHHHHHH-CCCC
T ss_conf             889999999960797389935899998799983999998795999986999--8770898899999999999997-5993


Q ss_pred             EEEEEEEECCCCCEEEEEEEEEEEEECCCEE-EEEEEEECCCHHHHHHHHHHHHHHHHHHHHHHHHHHEEEECCCCEEEE
Q ss_conf             8999998869898899889999998379606-999998446179999999999999999999854455158834996997
Q gi|254780903|r  328 LDQIFHMRHASGADIWIQVRAQMMRTISGGM-NIIGIAMDLTEKYHLEKRYAEADQRLSKAIECTSEALVLWDKNDRLVM  406 (766)
Q Consensus       328 ~~~e~Ri~~~DG~~~Wi~~r~~~i~d~~G~~-~~iGi~~DITErK~ae~~l~ese~rlr~~ie~~~~~i~~~D~~g~i~~  406 (766)
                      |..|.+.+++||+.+|+.....|++|++|++ +++|+.+||||||++|++|++++.                        
T Consensus       102 ~~~E~~n~rKDG~~~w~~~~i~pv~d~~G~~~~~~~i~~DITerk~~E~~L~qaqk------------------------  157 (538)
T PRK13557        102 IATEILNYRKDGSSFWNALFVSPVYNDAGDLVYFFGSQLDVSRRRDAEDALRQAQK------------------------  157 (538)
T ss_pred             EEEEEEEECCCCCEEEEEEEEEEEECCCCCEEEEEEEEECHHHHHHHHHHHHHHHH------------------------
T ss_conf             68799998799999999989999998999999999988344499999999999999------------------------


Q ss_pred             ECHHHHHHHCCCHHHHCCCCCHHHHCCCHHHHHHHHHHHCCCCCCCEEEEEEECCCEEEEECCEECCCCCEEEEEEEEEH
Q ss_conf             01789888399978942897178816520137899985211245640589991696287422324569978999886201
Q gi|254780903|r  407 CNANYQKAYGLPDHVLVPGNARSIIQDAQTRPIIEYRTSDPERSQDMSKEIKLADSRWLQINEWCTHDGGTISVGTDITL  486 (766)
Q Consensus       407 ~N~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~dg~~~~i~~~~~~dg~~v~v~~~i~~  486 (766)
                                                                                                      
T Consensus       158 --------------------------------------------------------------------------------  157 (538)
T PRK13557        158 --------------------------------------------------------------------------------  157 (538)
T ss_pred             --------------------------------------------------------------------------------
T ss_conf             --------------------------------------------------------------------------------


Q ss_pred             HHCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             00011223222222211000017889986444579999999999999999887899999999876752224789999999
Q gi|254780903|r  487 LKHNQAQLRESKRRLKATINDLSTSRQILERQKTELSIANAKYQVEKERAETANKTKSEFLAKMSHELRTPLNAILGFSE  566 (766)
Q Consensus       487 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~~~~~l~~~~~~ae~an~~k~efla~isHelrtPL~aI~g~~e  566 (766)
                                                                           .+++++|+++||||||||||+|+||++
T Consensus       158 -----------------------------------------------------lealg~~~a~isHEirnPL~~I~G~~~  184 (538)
T PRK13557        158 -----------------------------------------------------MEALGQLTGGIAHDFNNLLQVMSGYLD  184 (538)
T ss_pred             -----------------------------------------------------HHHHHHHHHHHHHHHHCHHHHHHHHHH
T ss_conf             -----------------------------------------------------999999998878876269999999999


Q ss_pred             HHHCCCCCC-CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCEEEECHHHHHHHHHHHHHHHHHHCCCEEE
Q ss_conf             986034688-9938999999999999999999977767788874198301203316999999999999999984795899
Q gi|254780903|r  567 VIKKEIFGE-LGSVKYYEYAQDIHYSGQHLLNMINNILEMSKIETEKISIDKQNADLIPIINEGIRLIGSSAQSKNIKIE  645 (766)
Q Consensus       567 ll~~~~~~~-~~~e~~~~~l~~I~~~~~~l~~lI~diLd~srieag~~~~~~~~~dl~~~i~~~~~~~~~~~~~k~i~l~  645 (766)
                      +|......+ ...++..++++.|..+++++..||+++|+|||    +..++.+++||+++++++..+++.. ..+++.+.
T Consensus       185 lL~~~~~~~~~~~~~~~~~l~~i~~~~~r~~~Li~~lL~fsr----~~~l~~~~~~l~~lv~~~~~l~~~~-~~~~i~l~  259 (538)
T PRK13557        185 VLQMALSKPDADRERIARSVEHIRAAAERAATLTQQLLAFAR----KQKLDGRVVNLNGLVSGMGEMAERT-LGDAVTIE  259 (538)
T ss_pred             HHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC----CCCCCCEEECHHHHHHHHHHHHHHH-HCCCEEEE
T ss_conf             998640168889999999999999999999999999999758----2768771772999999999999998-52991999


Q ss_pred             EEECCCCE-EEECHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEEE---------------CCEEEEEEEECCCCCCHHHH
Q ss_conf             98089978-998689999999998865653468988899999997---------------99899999978897897785
Q gi|254780903|r  646 KKIPSELF-FNADKRIIKKILFPILSNSIKFTNNNGKMMIRTSKI---------------GQCVIITIADTGIGIPKSAL  709 (766)
Q Consensus       646 ~~~~~~l~-v~~D~~~l~QVl~NLi~NAik~t~~~g~I~i~~~~~---------------~~~v~i~V~D~G~GI~~e~~  709 (766)
                      .++++++| +.+|+.+|+|||+||++||+||++++|.|+|+++..               +++++|+|+|||+|||++.+
T Consensus       260 ~~~~~~l~~~~~D~~~l~qvl~NLl~NA~~a~~~gg~i~i~~~~~~~~~~~~~~~~~~~~g~~v~i~V~DtG~GI~~e~~  339 (538)
T PRK13557        260 TDLAPDLWNCRIDPTQAEVALLNVLINARDAMPEGGRVTVRTENVEITEHDLAMYHQLPPGRYVSIAVTDTGSGMPPEIL  339 (538)
T ss_pred             EEECCCCCEEEECHHHHHHHHHHHHHHHHHHCCCCCEEEEEEEEEECCCCCCCCCCCCCCCCEEEEEEEECCCCCCHHHH
T ss_conf             98079887087558999999999898799865789759999987641542100124578887899999986898898999


Q ss_pred             HHHCCCEEECCCCCCCCCC-CCCHHHHHHHHHHHHCCCEEEEEEECCCCEEEEEECCC
Q ss_conf             4304650531467556778-87616899999999629869999798995299997359
Q gi|254780903|r  710 EKIGQPFEPLHNQYDQSIG-GFGLGLAISDALTNLHGGRLKIISQEGKGTIVTICMPQ  766 (766)
Q Consensus       710 ~~iF~pF~q~~~~~t~~~~-GtGLGLaI~k~iVe~hgG~I~v~S~~g~Gttf~i~LP~  766 (766)
                      +|||+|||     +||..+ ||||||+|||+||++|||+|+|+|++|+||||+|+||.
T Consensus       340 ~rIFepFf-----ttk~~~~GtGLGLaIv~~iV~~~gG~I~v~S~~G~GttF~v~lP~  392 (538)
T PRK13557        340 ARVMEPFF-----TTKEEGKGTGLGLSMVYGFAKQSGGAVRIYSEVGEGTTVRLYFPA  392 (538)
T ss_pred             HHHHCCCE-----EECCCCCCCCCCHHHHHHHHHHCCCEEEEEECCCCCEEEEEEEEC
T ss_conf             97725010-----422457877724999999999879959999328987799999867


No 5  
>PRK11107 hybrid sensory histidine kinase BarA; Provisional
Probab=100.00  E-value=0  Score=507.68  Aligned_cols=235  Identities=34%  Similarity=0.529  Sum_probs=218.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             99999999999887899999999876752224789999999986034688993899999999999999999997776778
Q gi|254780903|r  526 NAKYQVEKERAETANKTKSEFLAKMSHELRTPLNAILGFSEVIKKEIFGELGSVKYYEYAQDIHYSGQHLLNMINNILEM  605 (766)
Q Consensus       526 ~~~l~~~~~~ae~an~~k~efla~isHelrtPL~aI~g~~ell~~~~~~~~~~e~~~~~l~~I~~~~~~l~~lI~diLd~  605 (766)
                      +.++..+|++|++||++||+|+||||||||||||+|+||++++.+..   + ++.+++|++.|..++++|+.+|||||||
T Consensus       276 n~el~~ak~~A~~A~r~Ks~FLAnmSHEiRTPLn~IiG~~~ll~~~~---l-~~~q~~~l~~i~~s~~~Ll~lIndiLD~  351 (920)
T PRK11107        276 NVELDLAKKRAQEAARIKSEFLANMSHELRTPLNGVIGFTRQTLKTP---L-TPTQRDYLQTIERSANNLLAIINDILDF  351 (920)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHCHHHHCHHHHHHHHHHHHHHCCC---C-CHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             89999999999999999999999664865421999999999985699---9-9999999999999999999999999999


Q ss_pred             HHHHCCCCCCCEEEECHHHHHHHHHHHHHHHHHHCCCEEEEEECCCCE--EEECHHHHHHHHHHHHHHHHHCCCCCCEEE
Q ss_conf             887419830120331699999999999999998479589998089978--998689999999998865653468988899
Q gi|254780903|r  606 SKIETEKISIDKQNADLIPIINEGIRLIGSSAQSKNIKIEKKIPSELF--FNADKRIIKKILFPILSNSIKFTNNNGKMM  683 (766)
Q Consensus       606 srieag~~~~~~~~~dl~~~i~~~~~~~~~~~~~k~i~l~~~~~~~l~--v~~D~~~l~QVl~NLi~NAik~t~~~g~I~  683 (766)
                      ||||+|+++++..+||+.+++++++.++.+.+.+|+++|.+++++++|  |.+|+.+|+|||.||++||+|||+. |.|.
T Consensus       352 SkiEag~l~le~~~f~l~~~~~~v~~~~~~~a~~k~l~l~~~~~~~~p~~v~gD~~Rl~QIl~NLl~NAiKfT~~-G~I~  430 (920)
T PRK11107        352 SKLEAGKLILENIPFSLRETLDEVVTLLAHSAHEKGLELTLNIDPDVPDNVIGDPLRLQQIITNLVGNAIKFTES-GNID  430 (920)
T ss_pred             HHHHCCCCEEEECCCCHHHHHHHHHHHHHHHHHHCCCEEEEEECCCCCCCEEECHHHHHHHHHHHHHHHHHCCCC-CCEE
T ss_conf             998459836740167899999999999999999739879999789997306538999999999999999971889-9379


Q ss_pred             EEEEEEC---C--EEEEEEEECCCCCCHHHHHHHCCCEEECCCCCCCCCCCCCHHHHHHHHHHHHCCCEEEEEEECCCCE
Q ss_conf             9999979---9--8999999788978977854304650531467556778876168999999996298699997989952
Q gi|254780903|r  684 IRTSKIG---Q--CVIITIADTGIGIPKSALEKIGQPFEPLHNQYDQSIGGFGLGLAISDALTNLHGGRLKIISQEGKGT  758 (766)
Q Consensus       684 i~~~~~~---~--~v~i~V~D~G~GI~~e~~~~iF~pF~q~~~~~t~~~~GtGLGLaI~k~iVe~hgG~I~v~S~~g~Gt  758 (766)
                      |++....   +  .+.|+|+|||+|||++.+++||+||+|+++++++++|||||||+|||+||++|||+|+|+|++|+||
T Consensus       431 v~v~~~~~~~~~~~l~~~V~DTGiGI~~~~~~~iF~~F~q~d~s~~r~~gGtGLGLaI~k~Lv~~mgG~I~v~S~~g~GS  510 (920)
T PRK11107        431 ILVELRALSDEKVQLEVQIRDTGIGISERQQSQLFQAFRQADASISRRHGGTGLGLVITQKLVNEMGGDISFHSQPNRGS  510 (920)
T ss_pred             EEEEEEECCCCEEEEEEEEEEECCCCCHHHHHHHHCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHCCCCEEEEECCCCCE
T ss_conf             99999964798489999999970586999999785420156765445679877429999999998099179995489974


Q ss_pred             EEEEECC
Q ss_conf             9999735
Q gi|254780903|r  759 IVTICMP  765 (766)
Q Consensus       759 tf~i~LP  765 (766)
                      ||+|+||
T Consensus       511 ~F~Ftlp  517 (920)
T PRK11107        511 TFWFHLP  517 (920)
T ss_pred             EEEEEEE
T ss_conf             8999998


No 6  
>PRK11360 sensory histidine kinase AtoS; Provisional
Probab=100.00  E-value=0  Score=487.12  Aligned_cols=335  Identities=26%  Similarity=0.374  Sum_probs=255.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHEEEECCCCEEEEECHHHHHHHCCCHHHHCCCCCHHHHCCCHHHHH-HHHHHHCCCCCCCEE
Q ss_conf             9999999999999854455158834996997017898883999789428971788165201378-999852112456405
Q gi|254780903|r  376 RYAEADQRLSKAIECTSEALVLWDKNDRLVMCNANYQKAYGLPDHVLVPGNARSIIQDAQTRPI-IEYRTSDPERSQDMS  454 (766)
Q Consensus       376 ~l~ese~rlr~~ie~~~~~i~~~D~~g~i~~~N~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~  454 (766)
                      +|++.......+++++.+|++..|.+|+++.+|+++.+++|++.+++++. ++..+.+...... ....+..........
T Consensus       255 ~L~~~~~~~e~IL~sm~dGVIaiD~~G~I~~~N~~A~~llg~~~~e~ig~-~~~~l~~~~~~~~~~~~~l~~~~~~~~~~  333 (607)
T PRK11360        255 ALREARTLNELIIENAADGIIAIDRQGDITTMNPAAEVITGYQRHELVGQ-PYSMLFDNTQFYSPVLDTLEHGTEHVALE  333 (607)
T ss_pred             HHHHHHHHHHHHHHHHCCEEEEECCCCCEEEECHHHHHHHCCCHHHHCCC-CHHHHCCCHHHHHHHHHHHHCCCCCCCEE
T ss_conf             99999998999986104669999799949998389999858797898596-79995795767799999985377421248


Q ss_pred             EEEEECCCE-EEEECCEECCC--C---CEEEEEEEEEHHHCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             899916962-87422324569--9---78999886201000112232222222110000178899864445799999999
Q gi|254780903|r  455 KEIKLADSR-WLQINEWCTHD--G---GTISVGTDITLLKHNQAQLRESKRRLKATINDLSTSRQILERQKTELSIANAK  528 (766)
Q Consensus       455 ~e~~~~dg~-~~~i~~~~~~d--g---~~v~v~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~~~~~  528 (766)
                      .+....++. ++.++..+..+  |   |.+.+..|+|+.++.                                   +++
T Consensus       334 ~~~~~~~~~~~l~~~~s~~~~~~g~~~G~v~~~~DiTe~~~l-----------------------------------e~~  378 (607)
T PRK11360        334 ISFPGRDRTIELSVTTSRLHDTHGEMIGAVVIFSDLTARKRL-----------------------------------QRR  378 (607)
T ss_pred             EEECCCCCEEEEEEEEEEEECCCCCEEEEEEEEEECCHHHHH-----------------------------------HHH
T ss_conf             996058834999999853576898588999999957789999-----------------------------------999


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             99999999887899999999876752224789999999986034688993899999999999999999997776778887
Q gi|254780903|r  529 YQVEKERAETANKTKSEFLAKMSHELRTPLNAILGFSEVIKKEIFGELGSVKYYEYAQDIHYSGQHLLNMINNILEMSKI  608 (766)
Q Consensus       529 l~~~~~~ae~an~~k~efla~isHelrtPL~aI~g~~ell~~~~~~~~~~e~~~~~l~~I~~~~~~l~~lI~diLd~sri  608 (766)
                      +.    ++|. ..++++|+|++||||||||++|.||+++|.++..    ++..++|++.|.+.++||.++|+|+|+|||.
T Consensus       379 l~----~~er-laalGe~~A~vaHElRnPLt~I~g~~elL~~~~~----~~~~~~~l~~i~~e~~Rl~~li~~lL~~sr~  449 (607)
T PRK11360        379 MA----RAER-LAALGELMAGVAHEIRNPLTAIRGYVQILRQQTS----DPIHQEYLSVVLREVDSLNKVIQQLLEFSRP  449 (607)
T ss_pred             HH----HHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCC----CHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC
T ss_conf             99----9999-9999999999899871549999999999866899----8799999999999999999999999985277


Q ss_pred             HCCCCCCCEEEECHHHHHHHHHHHHHHHHHHCCCEEEEEECCCCE-EEECHHHHHHHHHHHHHHHHHCCCCCCEEEEEEE
Q ss_conf             419830120331699999999999999998479589998089978-9986899999999988656534689888999999
Q gi|254780903|r  609 ETEKISIDKQNADLIPIINEGIRLIGSSAQSKNIKIEKKIPSELF-FNADKRIIKKILFPILSNSIKFTNNNGKMMIRTS  687 (766)
Q Consensus       609 eag~~~~~~~~~dl~~~i~~~~~~~~~~~~~k~i~l~~~~~~~l~-v~~D~~~l~QVl~NLi~NAik~t~~~g~I~i~~~  687 (766)
                      +..    +.+++|+++++++++..+++.+.++++.+..++++++| +.+|+.+|+|||.||+.||+||+|++|+|+|++.
T Consensus       450 ~~~----~~~~v~l~~l~~~~~~~~~~~~~~~~i~l~~~~~~~~~~v~~D~~~l~qvl~NLi~NAi~a~~~~g~I~i~~~  525 (607)
T PRK11360        450 RHS----QWQQVSLNALVEEVLVLVQTAGVQARVDFITELDNELPPINADRELLKQVLLNILINAVQAISARGKIRIRTW  525 (607)
T ss_pred             CCC----CCCEECHHHHHHHHHHHHHHHHHHCCCEEEEECCCCCCEEEECHHHHHHHHHHHHHHHHHHCCCCCEEEEEEE
T ss_conf             888----8847869999999999999988867968999818988769988899999999999996286289967999999


Q ss_pred             EE-CCEEEEEEEECCCCCCHHHHHHHCCCEEECCCCCCCCCCCCCHHHHHHHHHHHHCCCEEEEEEECCCCEEEEEECC
Q ss_conf             97-9989999997889789778543046505314675567788761689999999962986999979899529999735
Q gi|254780903|r  688 KI-GQCVIITIADTGIGIPKSALEKIGQPFEPLHNQYDQSIGGFGLGLAISDALTNLHGGRLKIISQEGKGTIVTICMP  765 (766)
Q Consensus       688 ~~-~~~v~i~V~D~G~GI~~e~~~~iF~pF~q~~~~~t~~~~GtGLGLaI~k~iVe~hgG~I~v~S~~g~Gttf~i~LP  765 (766)
                      .. ++.+.|+|+|||+|||++.++|||+|||      |++.+||||||||||+||+.|||+|+|+|++|+||+|+|+||
T Consensus       526 ~~~~~~v~i~V~D~G~GI~~e~~~~IFepF~------ttk~~GtGLGLaI~k~Ive~hgG~I~v~S~~g~GT~F~i~LP  598 (607)
T PRK11360        526 QYSDSQQAISIEDNGCGIDLELLKKIFDPFF------TTKASGTGLGLALSQRIINAHQGDIRVASLPGYGTTFTLILP  598 (607)
T ss_pred             EECCCEEEEEEEECCCCCCHHHHHHHCCCCC------CCCCCCCCHHHHHHHHHHHHCCCEEEEEECCCCCEEEEEEEE
T ss_conf             9369879999998676869899964558975------489998133799999999988998999966999869999980


No 7  
>TIGR02966 phoR_proteo phosphate regulon sensor kinase PhoR; InterPro: IPR014310   Members of this protein are the regulatory histidine kinase PhoR associated with the phosphate ABC transporter found in most Proteobacteria, and related proteins from Gram-positive organisms are excluded. The phoR gene usually is adjacent to the response regulator phoB gene (IPR011879 from INTERPRO)..
Probab=100.00  E-value=0  Score=531.62  Aligned_cols=332  Identities=21%  Similarity=0.336  Sum_probs=298.4

Q ss_pred             HHHHHHHHHHHHHHHHEEEECCCCEEEEECHHHHHHHCCCHHHHCCCCCHHHHCCCHHHHHHHHHHHCCCC-CCC--EEE
Q ss_conf             99999999998544551588349969970178988839997894289717881652013789998521124-564--058
Q gi|254780903|r  379 EADQRLSKAIECTSEALVLWDKNDRLVMCNANYQKAYGLPDHVLVPGNARSIIQDAQTRPIIEYRTSDPER-SQD--MSK  455 (766)
Q Consensus       379 ese~rlr~~ie~~~~~i~~~D~~g~i~~~N~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~--~~~  455 (766)
                      ..-.+|+.+++++|+|++++|.++.|.+||++++++||+.-..-.+..    +...-++|.+..+++.... ...  ...
T Consensus         3 ~~~~rf~~a~~AlPDavv~ld~~~~I~W~N~~A~~~LGl~~p~D~Gq~----i~~l~R~P~F~~yl~~~~~t~~p~~L~~   78 (339)
T TIGR02966         3 ALLSRFRAAAQALPDAVVVLDEEGQIEWCNKAAERLLGLRWPDDLGQR----ITNLIRHPEFVEYLAAGRFTSEPEQLEL   78 (339)
T ss_pred             HHHHHHHHHHHHCCCEEEEECCCCCEEEEEHHHHHHCCCCCCHHHCCC----HHHHCCCHHHHHHHHCCCCCCCCCCEEE
T ss_conf             688999999975898299972898378621488986274273450770----2121057679999733555578853110


Q ss_pred             E-EEECCCEEEEECCEECCCCCEEEEEEEEEHHHCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             9-991696287422324569978999886201000112232222222110000178899864445799999999999999
Q gi|254780903|r  456 E-IKLADSRWLQINEWCTHDGGTISVGTDITLLKHNQAQLRESKRRLKATINDLSTSRQILERQKTELSIANAKYQVEKE  534 (766)
Q Consensus       456 e-~~~~dg~~~~i~~~~~~dg~~v~v~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~~~~~l~~~~~  534 (766)
                      . ......+.+.+.-.|..++.++-+..|||.+++                                             
T Consensus        79 ~~~p~~~~~~l~~r~~PY~~~~~Ll~~RDvT~l~r---------------------------------------------  113 (339)
T TIGR02966        79 PDSPINEERVLEIRIMPYGEEQKLLVARDVTRLRR---------------------------------------------  113 (339)
T ss_pred             CCCCCCCCCEEEEEEEEECCCCEEEEEECHHHHHH---------------------------------------------
T ss_conf             46888866479999997569837999876368999---------------------------------------------


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCC
Q ss_conf             99887899999999876752224789999999986034688993899999999999999999997776778887419830
Q gi|254780903|r  535 RAETANKTKSEFLAKMSHELRTPLNAILGFSEVIKKEIFGELGSVKYYEYAQDIHYSGQHLLNMINNILEMSKIETEKIS  614 (766)
Q Consensus       535 ~ae~an~~k~efla~isHelrtPL~aI~g~~ell~~~~~~~~~~e~~~~~l~~I~~~~~~l~~lI~diLd~srieag~~~  614 (766)
                          ..++..+|+||+|||||||||+|.||+|+|.+.... ..++...+|++.|...++||..||+|||.+||||+....
T Consensus       114 ----Le~mRrDFVANVSHELRTPLTVl~GyLEtl~~~~~~-~~~~~~~~~l~~M~~Q~~RM~~LV~dLL~LSrlE~~~~~  188 (339)
T TIGR02966       114 ----LEQMRRDFVANVSHELRTPLTVLRGYLETLEDGPVD-EDPEEWNRALELMQEQSQRMQSLVEDLLTLSRLESAANP  188 (339)
T ss_pred             ----HHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHCCCC-CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCC
T ss_conf             ----986534311445211145403556899975523677-880889999999999999999999999888764157888


Q ss_pred             CCEEEECHHHHHHHHHHHHHHHHHHCCCEEEEEE-CCCCEEEECHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEEECCEE
Q ss_conf             1203316999999999999999984795899980-899789986899999999988656534689888999999979989
Q gi|254780903|r  615 IDKQNADLIPIINEGIRLIGSSAQSKNIKIEKKI-PSELFFNADKRIIKKILFPILSNSIKFTNNNGKMMIRTSKIGQCV  693 (766)
Q Consensus       615 ~~~~~~dl~~~i~~~~~~~~~~~~~k~i~l~~~~-~~~l~v~~D~~~l~QVl~NLi~NAik~t~~~g~I~i~~~~~~~~v  693 (766)
                      ...++||+..+++.+.+.......+|+.+|.+++ ++++.|.||+.+|+++|.|||+|||||||+||+|+|+.+..++.+
T Consensus       189 ~~~~~V~~~~ll~~l~~~A~~ls~~~~h~I~~~~pd~~~~~~G~e~~L~SAf~NLv~NAikYTp~gg~I~v~W~~~~~ga  268 (339)
T TIGR02966       189 PEDEPVDVPALLDHLRDEAEALSQGKQHQITFEIPDAGLDLLGNEDELRSAFSNLVSNAIKYTPEGGTITVRWRRDEGGA  268 (339)
T ss_pred             CCCCCCCHHHHHHHHHHHHHHHHHCCCEEEEEEECCCCCCCCCCHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEEECCEE
T ss_conf             45565687999999999999997118838999823888530144777999999998875300899887999999857803


Q ss_pred             EEEEEECCCCCCHHHHHHHCCCEEECCCCCCCCCCCCCHHHHHHHHHHHHCCCEEEEEEECCCCEEEEEEC
Q ss_conf             99999788978977854304650531467556778876168999999996298699997989952999973
Q gi|254780903|r  694 IITIADTGIGIPKSALEKIGQPFEPLHNQYDQSIGGFGLGLAISDALTNLHGGRLKIISQEGKGTIVTICM  764 (766)
Q Consensus       694 ~i~V~D~G~GI~~e~~~~iF~pF~q~~~~~t~~~~GtGLGLaI~k~iVe~hgG~I~v~S~~g~Gttf~i~L  764 (766)
                      +|+|+|||+||||+.++||+|+|||||.+.++..|||||||||||.++++|++++.|+|++|+||||+|.+
T Consensus       269 ~fsV~DtG~GI~~eHipRLTERFYRVD~~RSR~tGGTGLGLAIVKH~L~rH~a~L~I~Se~G~GS~F~~~F  339 (339)
T TIGR02966       269 EFSVTDTGIGIAPEHIPRLTERFYRVDKSRSRDTGGTGLGLAIVKHVLSRHHARLEIESELGKGSTFSFIF  339 (339)
T ss_pred             EEEEEECCCCCCHHHCCCCCCEEEEECHHHCCCCCCCCCHHHHHHHHHHCCCCEEEEEEEECCCEEEEEEC
T ss_conf             99998779898731377542001230533415788984336899998741487899998853760688759


No 8  
>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=100.00  E-value=0  Score=540.48  Aligned_cols=250  Identities=35%  Similarity=0.552  Sum_probs=232.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHH-------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHH
Q ss_conf             889986444579999999999-------9999998878999999998767522247899999999860346889938999
Q gi|254780903|r  510 TSRQILERQKTELSIANAKYQ-------VEKERAETANKTKSEFLAKMSHELRTPLNAILGFSEVIKKEIFGELGSVKYY  582 (766)
Q Consensus       510 ~~~~~~~~~~~~L~~~~~~l~-------~~~~~ae~an~~k~efla~isHelrtPL~aI~g~~ell~~~~~~~~~~e~~~  582 (766)
                      ...+.+..++.||+..|.+|.       .++..||+||||||.|||.||||||||||+|+|-++||.+..   + +..++
T Consensus       465 ~LE~~v~~RT~EL~~~N~rLN~E~~~H~kAR~~AE~AnrAKS~FLAtMSHEIRTPlNG~LGT~~LL~d~~---L-~~~Q~  540 (1052)
T TIGR02956       465 SLEQLVAQRTQELKETNERLNAEVLNHAKARAEAEEANRAKSAFLATMSHEIRTPLNGILGTLELLGDTG---L-TSQQQ  540 (1052)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHCCCC---C-CHHHH
T ss_conf             9999999988999997467639998799999999997488768874135113201136899997505899---8-88899


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHCC--CCCCCEEEECHHHHHHHHHHHHHHHHHHCCCEEEEEECCCCE--EEECH
Q ss_conf             99999999999999997776778887419--830120331699999999999999998479589998089978--99868
Q gi|254780903|r  583 EYAQDIHYSGQHLLNMINNILEMSKIETE--KISIDKQNADLIPIINEGIRLIGSSAQSKNIKIEKKIPSELF--FNADK  658 (766)
Q Consensus       583 ~~l~~I~~~~~~l~~lI~diLd~srieag--~~~~~~~~~dl~~~i~~~~~~~~~~~~~k~i~l~~~~~~~l~--v~~D~  658 (766)
                      +|++.|++||+.|+.+.||||||||||+|  ++++.+++||+..++++++.+++.++..|+|+|.++.++++|  ..+|+
T Consensus       541 ~yl~~In~SGe~LL~iLNDILDYSkIEaGGthl~i~~~~fd~~~L~~dv~~Lm~sRA~~Kg~~L~~~~~~~~~~~~~gD~  620 (1052)
T TIGR02956       541 QYLQVINRSGESLLDILNDILDYSKIEAGGTHLSISPRPFDLNKLLEDVHHLMESRAQEKGIQLILNIDEQLPNWWQGDL  620 (1052)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHCCCCEEEECCCCCHHHHHHCCC
T ss_conf             99999986227899998467546776108746534556778888999999999987740372567427654278875366


Q ss_pred             HHHHHHHHHHHHHHHHCCCCCCEEEEEEEEECCE------EEEEEEECCCCCCHHHHHHHCCCEEECCCCCCCCCCCCCH
Q ss_conf             9999999998865653468988899999997998------9999997889789778543046505314675567788761
Q gi|254780903|r  659 RIIKKILFPILSNSIKFTNNNGKMMIRTSKIGQC------VIITIADTGIGIPKSALEKIGQPFEPLHNQYDQSIGGFGL  732 (766)
Q Consensus       659 ~~l~QVl~NLi~NAik~t~~~g~I~i~~~~~~~~------v~i~V~D~G~GI~~e~~~~iF~pF~q~~~~~t~~~~GtGL  732 (766)
                      .+|+|||.|||+||||||.. |.|+|++...++.      +.|.|.||||||||+.++.||+||.|++.. -|+.|||||
T Consensus       621 ~riRQvL~NLvgNaIKFT~~-Gsv~l~~~l~~~~~~gdsel~F~V~DtG~GIae~~~~~lF~aF~Qa~eg-~~~~gGTGL  698 (1052)
T TIGR02956       621 RRIRQVLINLVGNAIKFTDR-GSVVLRVSLNDDSSSGDSELLFEVEDTGVGIAEEEQATLFDAFTQADEG-RRKSGGTGL  698 (1052)
T ss_pred             CHHHHHHHHHHHCCCEECCC-CEEEEEEEECCCCCCCCCEEEEEEEECCCCCCHHHHHHHCCCCCCCCCC-CCCCCCCCC
T ss_conf             13447676544132004345-2699998855888986634788886247799879998543310121013-731377650


Q ss_pred             HHHHHHHHHHHCCCE---EEEEEECCCCEEEEEECC
Q ss_conf             689999999962986---999979899529999735
Q gi|254780903|r  733 GLAISDALTNLHGGR---LKIISQEGKGTIVTICMP  765 (766)
Q Consensus       733 GLaI~k~iVe~hgG~---I~v~S~~g~Gttf~i~LP  765 (766)
                      |||||++||+.|||+   |+|+|++|+||||+|+||
T Consensus       699 GLAIs~~Lv~AM~G~GrGl~v~S~~~~GScF~F~lp  734 (1052)
T TIGR02956       699 GLAISRRLVEAMDGEGRGLGVESELGQGSCFWFTLP  734 (1052)
T ss_pred             HHHHHHHHHHHHCCCCCCCEEEEECCCCCEEEEECC
T ss_conf             689999999970888765016664587502212423


No 9  
>PRK11006 phoR phosphate regulon sensor protein; Provisional
Probab=100.00  E-value=0  Score=512.54  Aligned_cols=338  Identities=21%  Similarity=0.320  Sum_probs=287.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHEEEECCCCEEEEECHHHHHHHCCCHHHHCCCCCHHHHCCCHHHHHHHHHHHCCCC
Q ss_conf             99999999999999999998544551588349969970178988839997894289717881652013789998521124
Q gi|254780903|r  370 KYHLEKRYAEADQRLSKAIECTSEALVLWDKNDRLVMCNANYQKAYGLPDHVLVPGNARSIIQDAQTRPIIEYRTSDPER  449 (766)
Q Consensus       370 rK~ae~~l~ese~rlr~~ie~~~~~i~~~D~~g~i~~~N~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  449 (766)
                      +++..++|.....||+.+.+++|+|+++.|.+|++..||++++++|||...+..+......+..+.    ....+...+ 
T Consensus        86 ~~~~~~~l~~~~~rfr~~~ealpDavvv~d~~g~I~~~N~aAe~l~G~~~~~~~G~~I~~Lir~p~----f~~~~~~~~-  160 (431)
T PRK11006         86 NKKRRRELGNLIKRFRSGAESLPDAVVLTTEEGNIFWCNGLAQQLLGLRWPEDNGQNILNLLRYPE----FTQYLKTRD-  160 (431)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHCCCEEEEECCCCCEEEEHHHHHHHHCCCCHHHCCCCHHHHHCCHH----HHHHHHCCC-
T ss_conf             799999999999999999964897699998999588356999998389983326997789808845----999986266-


Q ss_pred             CCCEEEEEEECCCEEEEECCEECCCCCEEEEEEEEEHHHCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             56405899916962874223245699789998862010001122322222221100001788998644457999999999
Q gi|254780903|r  450 SQDMSKEIKLADSRWLQINEWCTHDGGTISVGTDITLLKHNQAQLRESKRRLKATINDLSTSRQILERQKTELSIANAKY  529 (766)
Q Consensus       450 ~~~~~~e~~~~dg~~~~i~~~~~~dg~~v~v~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~~~~~l  529 (766)
                       .....+....+++.+++.-.+..+|..+.+..|||+.++                                        
T Consensus       161 -~~~p~~~~~~~~~~le~~~~p~~~~~~llv~rDiT~~~~----------------------------------------  199 (431)
T PRK11006        161 -FSRPLNLVLNNGRHLEIRVMPYTEGQLLMVARDVTQMHQ----------------------------------------  199 (431)
T ss_pred             -CCCCEEEECCCCCEEEEEEEECCCCCEEEEEEECCHHHH----------------------------------------
T ss_conf             -557625543887479999977379958999985659999----------------------------------------


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             99999998878999999998767522247899999999860346889938999999999999999999977767788874
Q gi|254780903|r  530 QVEKERAETANKTKSEFLAKMSHELRTPLNAILGFSEVIKKEIFGELGSVKYYEYAQDIHYSGQHLLNMINNILEMSKIE  609 (766)
Q Consensus       530 ~~~~~~ae~an~~k~efla~isHelrtPL~aI~g~~ell~~~~~~~~~~e~~~~~l~~I~~~~~~l~~lI~diLd~srie  609 (766)
                               +.+++.+|+||||||||||||+|.||+|+|.+..   ..++...++++.|.++++||..||+|+|++||+|
T Consensus       200 ---------lE~~R~dFvAnvSHELRTPLT~I~G~~ElL~~~~---~~~~~~~~~l~~i~~~~~Rm~~LI~dLL~lsrle  267 (431)
T PRK11006        200 ---------LEGARRNFFANVSHELRTPLTVLQGYLEMMEEQP---LEGPMREKALHTMREQTQRMEGLVKQLLTLSKIE  267 (431)
T ss_pred             ---------HHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHCCC---CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             ---------9999999998620866177999999999985799---9809999999999999999999999999997642


Q ss_pred             CCCCCCCEEEECHHHHHHHHHHHHHHHHHHCCCEEEEEECCCCEEEECHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEEE
Q ss_conf             19830120331699999999999999998479589998089978998689999999998865653468988899999997
Q gi|254780903|r  610 TEKISIDKQNADLIPIINEGIRLIGSSAQSKNIKIEKKIPSELFFNADKRIIKKILFPILSNSIKFTNNNGKMMIRTSKI  689 (766)
Q Consensus       610 ag~~~~~~~~~dl~~~i~~~~~~~~~~~~~k~i~l~~~~~~~l~v~~D~~~l~QVl~NLi~NAik~t~~~g~I~i~~~~~  689 (766)
                      ++......+++|+..+++.+...... +.+++..+..+++++++|.+|+.+|+|||.||++||+||||+||+|.|++...
T Consensus       268 ~~~~~~~~~~vd~~~ll~~l~~~~~~-l~~~~~~i~~~~~~~~~v~~D~~~L~qvl~NLi~NAikytp~g~~I~I~~~~~  346 (431)
T PRK11006        268 AAPTHLLNEKVDVPMMLRVLEREAQT-LSQKKHTITFEVDDSLKVLGNEDQLRSAISNLVYNAVNHTPEGTHITVRWQRV  346 (431)
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHHH-HHHHCCCCCCCCCCCCEEEECHHHHHHHHHHHHHHHHHHCCCCCEEEEEEEEE
T ss_conf             58752136531399999999999999-98625666556899827997899999999999998997479997799999994


Q ss_pred             CCEEEEEEEECCCCCCHHHHHHHCCCEEECCCCCCCCCCCCCHHHHHHHHHHHHCCCEEEEEEECCCCEEEEEECCC
Q ss_conf             99899999978897897785430465053146755677887616899999999629869999798995299997359
Q gi|254780903|r  690 GQCVIITIADTGIGIPKSALEKIGQPFEPLHNQYDQSIGGFGLGLAISDALTNLHGGRLKIISQEGKGTIVTICMPQ  766 (766)
Q Consensus       690 ~~~v~i~V~D~G~GI~~e~~~~iF~pF~q~~~~~t~~~~GtGLGLaI~k~iVe~hgG~I~v~S~~g~Gttf~i~LP~  766 (766)
                      ++.++|+|+|||+|||++.++|||+||||++++.+++.+||||||||||+||++|||+|+|+|++|+||||+|+||+
T Consensus       347 ~~~~~i~V~D~G~GI~~e~~~riFerFyR~d~~rs~~~gGtGLGLaIvK~Ive~HgG~I~v~S~~g~Gt~F~~~lP~  423 (431)
T PRK11006        347 PHGAEFSVEDNGPGIAPEHIPRLTERFYRVDKARSRQTGGSGLGLAIVKHALNHHDSRLEIESTVGKGTRFSFVLPE  423 (431)
T ss_pred             CCEEEEEEEECCCCCCHHHHHHHCCCCEECCCCCCCCCCCCCHHHHHHHHHHHHCCCEEEEEECCCCCEEEEEECCC
T ss_conf             99899999983878598999986268882888887999955489999999999859989999559985599998486


No 10 
>PRK11466 hybrid sensory histidine kinase TorS; Provisional
Probab=100.00  E-value=0  Score=513.22  Aligned_cols=245  Identities=29%  Similarity=0.512  Sum_probs=226.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHH
Q ss_conf             99864445799999999999999998878999999998767522247899999999860346889938999999999999
Q gi|254780903|r  512 RQILERQKTELSIANAKYQVEKERAETANKTKSEFLAKMSHELRTPLNAILGFSEVIKKEIFGELGSVKYYEYAQDIHYS  591 (766)
Q Consensus       512 ~~~~~~~~~~L~~~~~~l~~~~~~ae~an~~k~efla~isHelrtPL~aI~g~~ell~~~~~~~~~~e~~~~~l~~I~~~  591 (766)
                      +.....++.+|++++....++|++||+||++||+|+|+||||||||||+|+||+++|...   ++ ++++++|++.|..+
T Consensus       413 e~~V~~RT~eL~~~~~~~~~Ar~~AE~AnrAKS~FLA~MSHEIRTPLNgIlG~~eLL~~~---~l-~~~qr~~l~~I~~s  488 (912)
T PRK11466        413 AAQVKARTAELQELVIEHRQARAEAEKASQAKSAFLAAMSHEIRTPLYGILGTAQLLADN---PA-LNAQRDDLRAITDS  488 (912)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHCC---CC-CHHHHHHHHHHHHH
T ss_conf             999999999999998999999999999999999999871397677599999999998479---99-98999999999999


Q ss_pred             HHHHHHHHHHHHHHHHHHCC--CCCCCEEEECHHHHHHHHHHHHHHHHHHCCCEEEEEECCCCE--EEECHHHHHHHHHH
Q ss_conf             99999997776778887419--830120331699999999999999998479589998089978--99868999999999
Q gi|254780903|r  592 GQHLLNMINNILEMSKIETE--KISIDKQNADLIPIINEGIRLIGSSAQSKNIKIEKKIPSELF--FNADKRIIKKILFP  667 (766)
Q Consensus       592 ~~~l~~lI~diLd~srieag--~~~~~~~~~dl~~~i~~~~~~~~~~~~~k~i~l~~~~~~~l~--v~~D~~~l~QVl~N  667 (766)
                      +++|+.+|||||||||||+|  +++++.+||++.+++++++.++++.+.+|++.+..++++++|  +.+|+.+|+|||.|
T Consensus       489 ~~~LL~lInDILD~SkiEaG~~~l~l~~~pf~l~~ll~~v~~~~~~~a~~k~l~l~~~~~~~lp~~v~gD~~RLrQIL~N  568 (912)
T PRK11466        489 GESLLTILNDILDYSAIEAGGKNVSVSDEPFEPRPLLESTLQLMSGRVKGRPIRLATDIADDVPSALMGDPRRIRQVITN  568 (912)
T ss_pred             HHHHHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHHHHHHHHHHHHCCCEEEEEECCCCCCEEEECHHHHHHHHHH
T ss_conf             99999999999999998189981388611568999999999999999983797899972799986086358899999999


Q ss_pred             HHHHHHHCCCCCCEEEEEEEEECCEEEEEEEECCCCCCHHHHHHHCCCEEECCCCCCCCCCCCCHHHHHHHHHHHHCCCE
Q ss_conf             88656534689888999999979989999997889789778543046505314675567788761689999999962986
Q gi|254780903|r  668 ILSNSIKFTNNNGKMMIRTSKIGQCVIITIADTGIGIPKSALEKIGQPFEPLHNQYDQSIGGFGLGLAISDALTNLHGGR  747 (766)
Q Consensus       668 Li~NAik~t~~~g~I~i~~~~~~~~v~i~V~D~G~GI~~e~~~~iF~pF~q~~~~~t~~~~GtGLGLaI~k~iVe~hgG~  747 (766)
                      |++||+|||+. |.|.++++..++.++|+|+|||||||++.+++||+||+|++    ++++||||||+|||+||++|||+
T Consensus       569 LlsNAiKFT~~-G~V~l~~~~~~~~l~~~V~DTGiGI~~e~~~~IF~~F~Q~~----~~~gGtGLGLaI~k~LvelMGG~  643 (912)
T PRK11466        569 LLSNALRFTDE-GSIVLRSRTDGEQWLVEVEDSGCGIDPAKLAEIFQPFVQVS----GKRGGTGLGLTISSRLAQAMGGE  643 (912)
T ss_pred             HHHHHCCCCCC-CEEEEEEEECCCEEEEEEEECCCCCCHHHHHHHHCCCCCCC----CCCCCCCHHHHHHHHHHHHCCCE
T ss_conf             99987061899-67999999869789999850899999999998844761588----99899266899999999987997


Q ss_pred             EEEEEECCCCEEEEEECC
Q ss_conf             999979899529999735
Q gi|254780903|r  748 LKIISQEGKGTIVTICMP  765 (766)
Q Consensus       748 I~v~S~~g~Gttf~i~LP  765 (766)
                      |+|+|++|+||+|+|+||
T Consensus       644 I~V~S~~G~GS~F~~~LP  661 (912)
T PRK11466        644 LSATSTPEVGSCFCLRLP  661 (912)
T ss_pred             EEEECCCCCCEEEEEEEE
T ss_conf             999716998728999997


No 11 
>PRK13560 hypothetical protein; Provisional
Probab=100.00  E-value=0  Score=449.31  Aligned_cols=574  Identities=16%  Similarity=0.149  Sum_probs=405.9

Q ss_pred             CCCHHHHHHHHHHHHHHHHHHHHHHHH---CCCCCEEEEECCCCCEEEECCCHHHHCCCCHHHHCCCCHHHHCCCCCCCH
Q ss_conf             100112235548999999999885310---17897899996998089971420555199788960761043205443320
Q gi|254780903|r   98 QNNNIKFDLASQKKAESMLGQLLAKTR---FLSESFILLAQPNELVFASSTKNSHYIGKKIGEIIPELSRSRSRSKTVQM  174 (766)
Q Consensus        98 ~~~~~~~d~~~~~~ae~~L~~~~~~~~---~~~~~~i~i~d~~g~i~~~n~~~~~~~G~~~~~~~~~~~~~~~~~~~~~~  174 (766)
                      ..+....|+|+||++|.+|.+.+.--.   ...++.++..|.+|+++.+|.+++.++|++.++++|.+..+..+.+.+..
T Consensus       181 ~~~g~~~DITERKraE~rl~~ql~flq~LlDnipdpvF~kD~~G~ylgcN~afe~~~G~~re~i~G~ti~Dl~p~e~ad~  260 (807)
T PRK13560        181 QVDGFAEDITERKRAEERIDEALHFLQQLLDNIADPAFWKDEDAKVFGCNDAACLACGFRREEIIGMSIHDFAPAQPADD  260 (807)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEEEECCCCCEEEECHHHHHHCCCCHHHHCCCCCCCCCCHHHHHH
T ss_conf             55567787677778999999999999999854887469977995189620999988099999956861012781556899


Q ss_pred             H----HHHCCCCHHEEEEEECCCCCCEEE---EEEECCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             2----321153100001233157782599---997423210123455655456878878999999998888999999999
Q gi|254780903|r  175 S----EASLDQQPYHVLSVNLPHNSGSIL---IINSRVPLLRLWREEVTLEVVFFSIISALLLFILFSYYRQAKKNKEND  247 (766)
Q Consensus       175 ~----~~~l~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~a~~~dit~~r~ae  247 (766)
                      -    ...++.........+.....|...   +.....+..+.              .+.+.+.+  ....|||+||+||
T Consensus       261 y~~~d~~~l~~~~~~~~E~~v~~~DG~~~~~~v~~nka~~~d~--------------~g~~~Glv--Gv~~DITeRK~aE  324 (807)
T PRK13560        261 YQEADAAKFDADGSQIIEAEFQNKDGRTRPVDVIFNHAEFDDK--------------ENHCAGLV--GAITDISGRRAAE  324 (807)
T ss_pred             HHHHHHHHHCCCCCEEEEEEEECCCCCEEEEEEEEEEEEECCC--------------CCCEEEEE--EEEEEHHHHHHHH
T ss_conf             9875088641887557552037799857579999862233387--------------88665688--8876156778899


Q ss_pred             HHHHHHHHHHHHHHHCCCCCEEEEECCCCEEE-ECHHHHHHCCCCHHHCCCCH----------HH---HHHHHCCCCHHH
Q ss_conf             99999999999997225974598976897899-97889977299943305898----------89---997608120589
Q gi|254780903|r  248 TILLEANICVETALSRGRCGLWNFNFDNKKFH-LSRSMYEIMGIPYENKTLSF----------RA---IARLIHYDNKKI  313 (766)
Q Consensus       248 ~~l~ese~rl~~al~~a~~GiWd~D~~~~~i~-ws~~~~~llG~~~~e~~~s~----------~~---~~~~vHPdDr~~  313 (766)
                      ++|+|||+|||.++++++.|+|..|++++.++ ||++..+|+||+.++.....          +.   -...+|||.+..
T Consensus       325 e~LresEer~R~i~E~a~~gI~~~D~~g~i~~~~n~aae~m~G~s~eE~lg~~lw~~~pe~~~e~~~~~~~~~~pdgr~~  404 (807)
T PRK13560        325 RELLEKEDMLRAIIEAAPIAAIGLDADGNICFVNNNAAERMLGWSAAEVMGKPLPGMDPELNEEFWCGDFQEWYPDGRPM  404 (807)
T ss_pred             HHHHHHHHHHHHHHHHCCCCEEEECCCCCEEEECCHHHHHHHCCCHHHHCCCCCCCCCHHHHHHHCCCCHHHHCCCCCCC
T ss_conf             99999899999998736653478626761576126167876268768860774335683441333134065516665634


Q ss_pred             HHHH--HHHHHCCCCEEE-EEEEEECCCCCEEEEEEEEEEEEECCCEE-EEEEEEECCCHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             9999--999724898489-99998869898899889999998379606-9999984461799999999999999999998
Q gi|254780903|r  314 CEIA--RSVTGKHVKQLD-QIFHMRHASGADIWIQVRAQMMRTISGGM-NIIGIAMDLTEKYHLEKRYAEADQRLSKAIE  389 (766)
Q Consensus       314 ~~~a--~~~~~~~~~~~~-~e~Ri~~~DG~~~Wi~~r~~~i~d~~G~~-~~iGi~~DITErK~ae~~l~ese~rlr~~ie  389 (766)
                      ....  ...+..++..++ .|+++.++||+.+|+...+.|++|.+|++ +.+|+..||||||++|++|++++    .+++
T Consensus       405 ~~~~c~~a~~~r~g~~~~g~E~~~~RkDGt~~~~~~~~~pL~D~dG~~~gal~i~~DITERKqAEeaLr~sn----~iLE  480 (807)
T PRK13560        405 AFDACPMAKTIKGGKIFDGQEVLIEREDDGPADCSAYAEPLHDADGNIIGAIALLVDITERKQVEEQLLLAN----LIVE  480 (807)
T ss_pred             CCCHHHHHHHHHCCCCCCCCEEEEEECCCCEEEEEECCEEEECCCCCEEEEEEHHHCCHHHHHHHHHHHHHH----HHHH
T ss_conf             310123667761378778863799906996577886130225678885331100112427788999999988----8875


Q ss_pred             HHHHHEEEECCC-CEEEEECHHHHHHHCCCHHHHCCCC-CHHHHCCCHHHHHHHHHHHCCC----CCCCEEEEEEECCCE
Q ss_conf             544551588349-9699701789888399978942897-1788165201378999852112----456405899916962
Q gi|254780903|r  390 CTSEALVLWDKN-DRLVMCNANYQKAYGLPDHVLVPGN-ARSIIQDAQTRPIIEYRTSDPE----RSQDMSKEIKLADSR  463 (766)
Q Consensus       390 ~~~~~i~~~D~~-g~i~~~N~~~~~~~g~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~e~~~~dg~  463 (766)
                      ++|..++.|+.+ +-.+..|.....+|||+.++++.+. .+..+.++.....+...+....    ......+.+..++|.
T Consensus       481 nSp~il~~~~~~~gw~ve~vs~~v~~fGYt~eE~isg~~~~~~lvhPeDr~~v~~~l~~~~~~G~~~f~~eyRi~~kdGs  560 (807)
T PRK13560        481 NSPLVLFRWKAEEGWPVELVSKNITQFGYEPDEFISGKRMFAAIIHPADLEQVAAEVAEFAAQGVDRFEQEYRILGKGGA  560 (807)
T ss_pred             CCCCEEEEEECCCCCCEEEECCHHHHHCCCHHHHCCCCEEHHCCCCHHHHHHHHHHHHHHHCCCCCCCCEEEEEECCCCC
T ss_conf             29740478751578623752321455088878842423101205797888889999998741575522016888769996


Q ss_pred             EEEE--CCEECCC--CC---EEEEEEEEEHHHCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             8742--2324569--97---899988620100011223222222211000017889986444579999999999999999
Q gi|254780903|r  464 WLQI--NEWCTHD--GG---TISVGTDITLLKHNQAQLRESKRRLKATINDLSTSRQILERQKTELSIANAKYQVEKERA  536 (766)
Q Consensus       464 ~~~i--~~~~~~d--g~---~v~v~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~~~~~l~~~~~~a  536 (766)
                      |.++  ...+.+|  |.   +..+..|||+.|..+                                   +       ++
T Consensus       561 vrWI~~~~~~irDe~G~V~~~~giv~DIT~~k~ae-----------------------------------e-------~l  598 (807)
T PRK13560        561 VCWIDDQSAAERDEEGQISHFEGIVIDISERKHAE-----------------------------------E-------KI  598 (807)
T ss_pred             EEEEEEEEEEECCCCCCEEEEEEEEECCHHHHHHH-----------------------------------H-------HH
T ss_conf             89997013561178887544444674352888899-----------------------------------9-------99


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCC
Q ss_conf             88789999999987675222478999999998603468899389999999999999999999777677888741983012
Q gi|254780903|r  537 ETANKTKSEFLAKMSHELRTPLNAILGFSEVIKKEIFGELGSVKYYEYAQDIHYSGQHLLNMINNILEMSKIETEKISID  616 (766)
Q Consensus       537 e~an~~k~efla~isHelrtPL~aI~g~~ell~~~~~~~~~~e~~~~~l~~I~~~~~~l~~lI~diLd~srieag~~~~~  616 (766)
                      ..+...|.-+|.-|.|-.+|+|..|.+++.|-.+...    +++.++.+...++-..-|. +|.+.|.-        +-+
T Consensus       599 ~asL~EKE~LLkEIHHRVKNNLQiIsSLL~LQar~~~----d~ear~aL~esq~RI~SmA-lVHe~Ly~--------S~d  665 (807)
T PRK13560        599 KAALTEKEVLLKEIHHRVKNNLQIISSLLDLQAEKLH----DEEAKCAFAESQDRICAMA-LAHEKLYQ--------SED  665 (807)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC----CHHHHHHHHHHHHHHHHHH-HHHHHHHC--------CCC
T ss_conf             9999988999998776752039999999998876559----9999999999999999999-99999856--------999


Q ss_pred             EEEECHHHHHHHHHHHHHHHHHHC--CCEEEEEECCCCEEEECH-HHHHHHHHHHHHHHHHCCCC---CCEEEEEEEEEC
Q ss_conf             033169999999999999999847--958999808997899868-99999999988656534689---888999999979
Q gi|254780903|r  617 KQNADLIPIINEGIRLIGSSAQSK--NIKIEKKIPSELFFNADK-RIIKKILFPILSNSIKFTNN---NGKMMIRTSKIG  690 (766)
Q Consensus       617 ~~~~dl~~~i~~~~~~~~~~~~~k--~i~l~~~~~~~l~v~~D~-~~l~QVl~NLi~NAik~t~~---~g~I~i~~~~~~  690 (766)
                      ...+|+.+.+++.+..+.......  .|.+.++.+ ++.+..|. ..|..|+.+|++||+||..+   .|.|+|+.+..+
T Consensus       666 l~~Id~~~yi~~L~~~L~~s~~~~~~~I~l~vd~d-~~~L~~d~AiPLgLIlnELVtNAlKHAF~~~~~G~I~Isl~~~~  744 (807)
T PRK13560        666 LADIDFLDYIESLTAHLKNSFAIDFGRIDCKIDAD-DGCLDIDKAIPCGLIISELLSNALKHAFPDGAAGNIKVEIREQG  744 (807)
T ss_pred             CCEECHHHHHHHHHHHHHHHHCCCCCEEEEEEECC-CCEECHHHHHHHHHHHHHHHHHHHHHCCCCCCCCEEEEEEEECC
T ss_conf             76572999999999999997378986389999736-70565888767999999999998986089999827999999867


Q ss_pred             -CEEEEEEEECCCCCCHHHHHHHCCCEEECCCCCCCCCCCCCHHHHHHHHHHHHCCCEEEEEEECCCCEEEEEECC
Q ss_conf             -989999997889789778543046505314675567788761689999999962986999979899529999735
Q gi|254780903|r  691 -QCVIITIADTGIGIPKSALEKIGQPFEPLHNQYDQSIGGFGLGLAISDALTNLHGGRLKIISQEGKGTIVTICMP  765 (766)
Q Consensus       691 -~~v~i~V~D~G~GI~~e~~~~iF~pF~q~~~~~t~~~~GtGLGLaI~k~iVe~hgG~I~v~S~~g~Gttf~i~LP  765 (766)
                       +.+.++|+|||+|||+.     |++           ..+.+|||.||+.+|++.+|+|.++|.  .||+|+|++|
T Consensus       745 ~~~v~L~V~DnG~GlP~~-----fd~-----------~~s~sLGL~LV~~Lv~QL~G~l~i~s~--~Gt~f~I~FP  802 (807)
T PRK13560        745 DGMVNLCVADDGIGLPAG-----FDF-----------RAAETLGLQLVCALVKQLDGEIALDSR--GGARFNIRFP  802 (807)
T ss_pred             CCEEEEEEEECCCCCCCC-----CCC-----------CCCCCCHHHHHHHHHHHCCCEEEEECC--CCEEEEEEEE
T ss_conf             998999998798158999-----897-----------889997699999999974989999859--9869999971


No 12 
>PRK09303 adaptive-response sensory kinase; Validated
Probab=100.00  E-value=0  Score=476.00  Aligned_cols=242  Identities=27%  Similarity=0.399  Sum_probs=218.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHH----HHHHHH
Q ss_conf             9999999999999999887899999999876752224789999999986034688993899999999999----999999
Q gi|254780903|r  521 ELSIANAKYQVEKERAETANKTKSEFLAKMSHELRTPLNAILGFSEVIKKEIFGELGSVKYYEYAQDIHY----SGQHLL  596 (766)
Q Consensus       521 ~L~~~~~~l~~~~~~ae~an~~k~efla~isHelrtPL~aI~g~~ell~~~~~~~~~~e~~~~~l~~I~~----~~~~l~  596 (766)
                      .|++..-.++++++++.++.++|++|+|+||||||||||+|.||+++|+....++.. +...++++.+.+    ..++|.
T Consensus       127 ~l~d~~~~Lrqe~E~L~e~~r~K~~Fla~vSHELRTPLTaI~g~~e~L~~~~~~~~~-~~~~~~l~~l~~~~~~~~~~L~  205 (378)
T PRK09303        127 QLSDELFVLRQENETLLEQLKFKDRLLAMLAHDLRTPLTAASLAVETLELGQIDPSE-ELSPALIEQLQDQARRQLEEIE  205 (378)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHCCCCCCCC-HHHHHHHHHHHHHHHHHHHHHH
T ss_conf             878899999998999999999999999973676153199999999998642579741-6679999999999999999999


Q ss_pred             HHHHHHHHHHHHHCCCCCCCEEEECHHHHHHHHHHHHHHHHHHCCCEEEEEECCCCE-EEECHHHHHHHHHHHHHHHHHC
Q ss_conf             997776778887419830120331699999999999999998479589998089978-9986899999999988656534
Q gi|254780903|r  597 NMINNILEMSKIETEKISIDKQNADLIPIINEGIRLIGSSAQSKNIKIEKKIPSELF-FNADKRIIKKILFPILSNSIKF  675 (766)
Q Consensus       597 ~lI~diLd~srieag~~~~~~~~~dl~~~i~~~~~~~~~~~~~k~i~l~~~~~~~l~-v~~D~~~l~QVl~NLi~NAik~  675 (766)
                      .||+|+|++||+++|++.++++++||.+++.+++..+++.+.+|++++..++++++| |++|+.+|+|||.|||+||+||
T Consensus       206 ~LI~DLLd~sr~e~g~l~l~~~~~dL~~lv~evi~~~~~~a~~k~i~l~~dip~dlp~V~aD~~rL~QVl~NLL~NAiKy  285 (378)
T PRK09303        206 RLITDLLEVGRTRWEALQFNPQKLDLGSLCQEVILELEKRWLAKSLEIQTDIPSDLPSVYADQRRIRQVLLNLLDNAIKY  285 (378)
T ss_pred             HHHHHHHHHHHHHCCCCEEEEEEECHHHHHHHHHHHHHHHHHHCCCEEEEECCCCCCEEEECHHHHHHHHHHHHHHHHHH
T ss_conf             99999999988753886314688769999999999989899838978999768999728768999999999999999985


Q ss_pred             CCCCCEEEEEE-EEECCEEEEEEEECCCCCCHHHHHHHCCCEEECCCCCCCCCCCCCHHHHHHHHHHHHCCCEEEEEEEC
Q ss_conf             68988899999-99799899999978897897785430465053146755677887616899999999629869999798
Q gi|254780903|r  676 TNNNGKMMIRT-SKIGQCVIITIADTGIGIPKSALEKIGQPFEPLHNQYDQSIGGFGLGLAISDALTNLHGGRLKIISQE  754 (766)
Q Consensus       676 t~~~g~I~i~~-~~~~~~v~i~V~D~G~GI~~e~~~~iF~pF~q~~~~~t~~~~GtGLGLaI~k~iVe~hgG~I~v~S~~  754 (766)
                      ||+||.|+|++ ...++.|.|+|+|||+|||++.+++||+||+|++.  +++.+||||||||||+||++|||+|||+|++
T Consensus       286 T~~gG~I~I~~~~~~~~~V~isV~DtG~GIp~e~~~rIFe~F~R~~~--s~~~~GtGLGLaIvk~IVe~HgG~I~V~S~~  363 (378)
T PRK09303        286 TPEGGTITLTMLHRTTQKVQVSICDTGPGIPEEEQERIFEDRVRLPR--DEGTEGYGIGLSVCRRIVEVHYGQIWVDSEP  363 (378)
T ss_pred             CCCCCEEEEEEEEECCCEEEEEEEEECCCCCHHHHHHHCCCCEECCC--CCCCCCEEHHHHHHHHHHHHCCCEEEEEECC
T ss_conf             89998699999981399899999980788898999875636344568--9998831279999999999879979999439


Q ss_pred             CCCEEEEEECC
Q ss_conf             99529999735
Q gi|254780903|r  755 GKGTIVTICMP  765 (766)
Q Consensus       755 g~Gttf~i~LP  765 (766)
                      |+||||+|+||
T Consensus       364 g~GS~Ft~tLP  374 (378)
T PRK09303        364 GQGSCFHFTLP  374 (378)
T ss_pred             CCCEEEEEEEE
T ss_conf             98359999982


No 13 
>PRK11073 glnL nitrogen regulation protein NR(II); Provisional
Probab=100.00  E-value=0  Score=420.71  Aligned_cols=322  Identities=18%  Similarity=0.292  Sum_probs=245.3

Q ss_pred             HHHHHHHHHHEEEECCCCEEEEECHHHHHHHCCCHHHHCCCCCHHHHCCCHHHHH-HHHHHHCCCCCCCEEEEEEECCC-
Q ss_conf             9999854455158834996997017898883999789428971788165201378-99985211245640589991696-
Q gi|254780903|r  385 SKAIECTSEALVLWDKNDRLVMCNANYQKAYGLPDHVLVPGNARSIIQDAQTRPI-IEYRTSDPERSQDMSKEIKLADS-  462 (766)
Q Consensus       385 r~~ie~~~~~i~~~D~~g~i~~~N~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~e~~~~dg-  462 (766)
                      ..++++++++|+++|.+|++++||++++++||++.+++++....+.+........ ....+............. ..+| 
T Consensus        10 ~~Il~~~~d~Iiv~D~~g~I~~~N~aa~~l~g~~~~~~~G~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~   88 (348)
T PRK11073         10 GQILNSLINSILLLDDNLAIHYANPAAQQLLAQSSRKLFGTPLPELLSYFSLNIELMQESLQAGQGFTDNEVTL-VIDGR   88 (348)
T ss_pred             HHHHHHHHHHHEEECCCCCEEEECHHHHHHHCCCHHHHCCCCHHHHHCCCCCCHHHHHHHHHCCCCCCCCEEEE-EECCE
T ss_conf             99998660796499897970128399999978598998599689984665301899999997389741323999-98996


Q ss_pred             -EEEEECCEECCCCCEEEEEEEEEHHHCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             -2874223245699789998862010001122322222221100001788998644457999999999999999988789
Q gi|254780903|r  463 -RWLQINEWCTHDGGTISVGTDITLLKHNQAQLRESKRRLKATINDLSTSRQILERQKTELSIANAKYQVEKERAETANK  541 (766)
Q Consensus       463 -~~~~i~~~~~~dg~~v~v~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~~~~~l~~~~~~ae~an~  541 (766)
                       .|+.++..+..++..+....+++..+                                   ++++++.+   .++  ..
T Consensus        89 ~~~~~~~~~~~~~~~~l~~~~di~~~k-----------------------------------~l~~e~~~---~~~--~~  128 (348)
T PRK11073         89 SHILSLTAQRLPEGMILLEMAPMDNQR-----------------------------------RLSQEQLQ---HAQ--QV  128 (348)
T ss_pred             EEEEEEEEEECCCCEEEEEEEECHHHH-----------------------------------HHHHHHHH---HHH--HH
T ss_conf             999999999825868999999627999-----------------------------------99999999---999--99


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCEEEEC
Q ss_conf             99999998767522247899999999860346889938999999999999999999977767788874198301203316
Q gi|254780903|r  542 TKSEFLAKMSHELRTPLNAILGFSEVIKKEIFGELGSVKYYEYAQDIHYSGQHLLNMINNILEMSKIETEKISIDKQNAD  621 (766)
Q Consensus       542 ~k~efla~isHelrtPL~aI~g~~ell~~~~~~~~~~e~~~~~l~~I~~~~~~l~~lI~diLd~srieag~~~~~~~~~d  621 (766)
                      ++++|++++||||||||++|.|++++|.+..    .++...+|++.|..++++|.++|+++|+++|...      ..+.+
T Consensus       129 ~~~e~~~~iaHelrnPL~~I~g~~~ll~~~~----~d~~~~e~~~~i~~~~~rl~~li~~ll~~~~~~~------~~~~~  198 (348)
T PRK11073        129 AARDLVRGLAHEIKNPLGGLRGAAQLLSKAL----PDPALTEYTKVIIEQADRLRNLVDRLLGPQRPGT------HITES  198 (348)
T ss_pred             HHHHHHHHHHHHHCCHHHHHHHHHHHHHHHC----CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCC------CCCCC
T ss_conf             9999998401874785799999999997417----9989999999999999999999999864412688------77547


Q ss_pred             HHHHHHHHHHHHHHHHHHCCCEEEEEECCCCE-EEECHHHHHHHHHHHHHHHHHC-CCCCCEEEEEEEEECC--------
Q ss_conf             99999999999999998479589998089978-9986899999999988656534-6898889999999799--------
Q gi|254780903|r  622 LIPIINEGIRLIGSSAQSKNIKIEKKIPSELF-FNADKRIIKKILFPILSNSIKF-TNNNGKMMIRTSKIGQ--------  691 (766)
Q Consensus       622 l~~~i~~~~~~~~~~~~~k~i~l~~~~~~~l~-v~~D~~~l~QVl~NLi~NAik~-t~~~g~I~i~~~~~~~--------  691 (766)
                      +..+++++..++.... .+++.+..+.++.+| +.+|+.+|+|||.|||+||+|| ++.+|+|.|+++...+        
T Consensus       199 l~~~~~~~~~~~~~~~-~~~i~i~~~~~~~~~~i~~d~~~l~qVl~NLl~NAik~~~~~~g~i~i~~~~~~~~~i~~~~~  277 (348)
T PRK11073        199 IHKVAERVVQLVSLEL-PDNVRLIRDYDPSLPELAHDPDQIEQVLLNIVRNALQALGPEGGEITLRTRTAFQLTLHGERY  277 (348)
T ss_pred             HHHHHHHHHHHHHHHC-CCCCEEEEEECCCCCEEEECHHHHHHHHHHHHHHHHHHHCCCCCEEEEEEEECCCCCCCCCCC
T ss_conf             9999999999999856-578099996078887264468788999999999999983669977999996433322145323


Q ss_pred             --EEEEEEEECCCCCCHHHHHHHCCCEEECCCCCCCCCCCCCHHHHHHHHHHHHCCCEEEEEEECCCCEEEEEECC
Q ss_conf             --89999997889789778543046505314675567788761689999999962986999979899529999735
Q gi|254780903|r  692 --CVIITIADTGIGIPKSALEKIGQPFEPLHNQYDQSIGGFGLGLAISDALTNLHGGRLKIISQEGKGTIVTICMP  765 (766)
Q Consensus       692 --~v~i~V~D~G~GI~~e~~~~iF~pF~q~~~~~t~~~~GtGLGLaI~k~iVe~hgG~I~v~S~~g~Gttf~i~LP  765 (766)
                        .+.|+|+|||+|||++.++|||+||+     +| +.+||||||+|||+||+.|||+|+|+|+||+ |+|+|+||
T Consensus       278 ~~~~~i~V~D~G~GI~~e~~~~iF~pf~-----tt-k~~GtGLGL~ivk~ive~hgG~I~v~S~~g~-t~F~i~lP  346 (348)
T PRK11073        278 RLAARIDIEDNGPGIPPHLQDTLFYPMV-----SG-REGGTGLGLSIARNLIDQHSGKIEFTSWPGH-TEFSVYLP  346 (348)
T ss_pred             CEEEEEEEEECCCCCCHHHHHHHCCCCC-----CC-CCCCCCHHHHHHHHHHHHCCCEEEEEEECCE-EEEEEEEE
T ss_conf             3048999999088789899997377836-----79-9898177899999999986998999982891-99999996


No 14 
>PRK10490 sensor protein KdpD; Provisional
Probab=100.00  E-value=0  Score=430.24  Aligned_cols=225  Identities=23%  Similarity=0.465  Sum_probs=206.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCC
Q ss_conf             98878999999998767522247899999999860346889938999999999999999999977767788874198301
Q gi|254780903|r  536 AETANKTKSEFLAKMSHELRTPLNAILGFSEVIKKEIFGELGSVKYYEYAQDIHYSGQHLLNMINNILEMSKIETEKISI  615 (766)
Q Consensus       536 ae~an~~k~efla~isHelrtPL~aI~g~~ell~~~~~~~~~~e~~~~~l~~I~~~~~~l~~lI~diLd~srieag~~~~  615 (766)
                      +.+.++.|+.||+.+||||||||++|.|++++|......  ..++..+++..|.+.+.++.+||+|||||||||+|.+.+
T Consensus       657 ~aE~ErLRsalLssVSHDLRTPLtsI~G~a~~L~~~~~~--~~~~~~~~~~~I~~e~~rL~rLV~nLLdmsRle~G~l~l  734 (895)
T PRK10490        657 ASEREQLRNALLAALSHDLRTPLTVLFGQAEILTLDLAS--EGSPHARQASEIRQHVLNTTRLVNNLLDMARIQSGGFNL  734 (895)
T ss_pred             HHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHCCCCC--CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCC
T ss_conf             777778999999860343578699999999998547778--828899999999999999999999999998763699766


Q ss_pred             CEEEECHHHHHHHHHHHHHHHHHHCCCEEEEEECCCCE-EEECHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEEECCEEE
Q ss_conf             20331699999999999999998479589998089978-99868999999999886565346898889999999799899
Q gi|254780903|r  616 DKQNADLIPIINEGIRLIGSSAQSKNIKIEKKIPSELF-FNADKRIIKKILFPILSNSIKFTNNNGKMMIRTSKIGQCVI  694 (766)
Q Consensus       616 ~~~~~dl~~~i~~~~~~~~~~~~~k~i~l~~~~~~~l~-v~~D~~~l~QVl~NLi~NAik~t~~~g~I~i~~~~~~~~v~  694 (766)
                      +++++++.+++.+++..+++.+.+++|.+  ++++++| |.+|+.+|+|||.||+.||+||||++|.|.|+++..++.+.
T Consensus       735 ~~~~~~l~evv~~al~~~~~~~~~~~i~v--~~~~~~~~v~~D~~lleQVL~NLl~NAiKytp~~~~I~v~a~~~~~~v~  812 (895)
T PRK10490        735 KKEWLTLEEVVGSALQMLEPGLSQHPINL--SLPEPLTLIHVDGPLFERVLINLLENAVKYAGAQAEIGIDAHVEGENLQ  812 (895)
T ss_pred             CCCCCCHHHHHHHHHHHHHHHHCCCCEEE--EECCCCCEEEECHHHHHHHHHHHHHHHHHHCCCCCEEEEEEEEECCEEE
T ss_conf             46420699999999999986612696799--9569870698789999999999999999858999709999999799999


Q ss_pred             EEEEECCCCCCHHHHHHHCCCEEECCCCCCCCCCCCCHHHHHHHHHHHHCCCEEEEEEECCCCEEEEEECCC
Q ss_conf             999978897897785430465053146755677887616899999999629869999798995299997359
Q gi|254780903|r  695 ITIADTGIGIPKSALEKIGQPFEPLHNQYDQSIGGFGLGLAISDALTNLHGGRLKIISQEGKGTIVTICMPQ  766 (766)
Q Consensus       695 i~V~D~G~GI~~e~~~~iF~pF~q~~~~~t~~~~GtGLGLaI~k~iVe~hgG~I~v~S~~g~Gttf~i~LP~  766 (766)
                      |+|.|+|+|||++.+++||++|+|.+..  +..+||||||||||+||+.|||+|+++|.+|+||+|+|+||.
T Consensus       813 i~V~D~G~GIp~~~~~~IFe~F~R~~~~--~~~~GtGLGLaI~k~IveAhGG~I~~~s~~ggGa~F~~~LPl  882 (895)
T PRK10490        813 LDVWDNGPGIPPGQEQLIFDKFARGNKE--SAVPGVGLGLAICRAIVDVHGGTITAENRPEGGACFRVTLPQ  882 (895)
T ss_pred             EEEEEECCCCCHHHHHHHCCCCCCCCCC--CCCCCCCHHHHHHHHHHHHCCCEEEEEECCCCEEEEEEEECC
T ss_conf             9999808987979999755687128999--999974478999999999879989999569980699998329


No 15 
>PRK13837 two-component VirA-like sensor kinase; Provisional
Probab=100.00  E-value=0  Score=418.08  Aligned_cols=233  Identities=22%  Similarity=0.381  Sum_probs=203.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHH
Q ss_conf             64445799999999999999998878999999998767522247899999999860346889938999999999999999
Q gi|254780903|r  515 LERQKTELSIANAKYQVEKERAETANKTKSEFLAKMSHELRTPLNAILGFSEVIKKEIFGELGSVKYYEYAQDIHYSGQH  594 (766)
Q Consensus       515 ~~~~~~~L~~~~~~l~~~~~~ae~an~~k~efla~isHelrtPL~aI~g~~ell~~~~~~~~~~e~~~~~l~~I~~~~~~  594 (766)
                      ..+..+|-+.++++|++.     +.+.+.+++.++|+|||||||++|+||++++......   .++..++++.|.++++|
T Consensus       430 ~~r~etER~~LE~qL~qA-----QKmEAiG~LAgGIAHDFNNiLt~I~G~aeLa~~~l~~---~~~~~~~L~~I~~aa~R  501 (831)
T PRK13837        430 RRRLETERDALERRLEHA-----RRLEAVGTLASGIAHNFNNILGAILGYAEMALNKLRR---HSRARRHIDEIISSGDR  501 (831)
T ss_pred             HHHHHHHHHHHHHHHHHH-----HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCC---CCHHHHHHHHHHHHHHH
T ss_conf             988799999999999999-----9999999999899998700899999999998620699---84778999999999999


Q ss_pred             HHHHHHHHHHHHHHHCCCCCCCEEEECHHHHHHHHHHHHHHHHHHCCCEEEEEECCCC-EEEECHHHHHHHHHHHHHHHH
Q ss_conf             9999777677888741983012033169999999999999999847958999808997-899868999999999886565
Q gi|254780903|r  595 LLNMINNILEMSKIETEKISIDKQNADLIPIINEGIRLIGSSAQSKNIKIEKKIPSEL-FFNADKRIIKKILFPILSNSI  673 (766)
Q Consensus       595 l~~lI~diLd~srieag~~~~~~~~~dl~~~i~~~~~~~~~~~~~k~i~l~~~~~~~l-~v~~D~~~l~QVl~NLi~NAi  673 (766)
                      ..+||++||+|||    +...+++++||++++++++.+++...+ ++|++..++++++ +|.+|+.+|+|||+||+.||.
T Consensus       502 a~~Lv~qLL~FSR----~~~~~~~~vdl~~lv~e~~~llr~~l~-~~I~l~~~~~~~~~~V~aD~~QL~QVllNL~~NA~  576 (831)
T PRK13837        502 ARLIIDQILTFGR----KGERRTKPFSLSELVTEIAPLLRVSLP-PTVELDFDFDQEPAVVEGNPAQLQQVILNLCKNAA  576 (831)
T ss_pred             HHHHHHHHHHHHC----CCCCCCCEECHHHHHHHHHHHHHHHCC-CCEEEEEECCCCCCEEEECHHHHHHHHHHHHHHHH
T ss_conf             9999999999858----999977177499999999999998758-98699997189885388879999999999999999


Q ss_pred             HCCCCCCEEEEEEEEE---------------CCEEEEEEEECCCCCCHHHHHHHCCCEEECCCCCCCCCCCCCHHHHHHH
Q ss_conf             3468988899999997---------------9989999997889789778543046505314675567788761689999
Q gi|254780903|r  674 KFTNNNGKMMIRTSKI---------------GQCVIITIADTGIGIPKSALEKIGQPFEPLHNQYDQSIGGFGLGLAISD  738 (766)
Q Consensus       674 k~t~~~g~I~i~~~~~---------------~~~v~i~V~D~G~GI~~e~~~~iF~pF~q~~~~~t~~~~GtGLGLaI~k  738 (766)
                      ++++++|+|+|++...               +++|+|+|+|||+|||++.++|||||||     ||| .+|||||||+|+
T Consensus       577 dAM~~gG~l~I~~~~~~~~~~~~~~~~~~~~G~yv~L~VsDtG~GI~~e~l~RIFEPFF-----TTK-~~GTGLGLAvV~  650 (831)
T PRK13837        577 QAMDENGRVDIRLSRVDLRKPKVLAHGTAPPGRYVLLRVSDTGRGIDEAVLPHIFEPFF-----TTR-ARGTGLGLATVH  650 (831)
T ss_pred             HHCCCCCEEEEEEEEEECCCHHHHCCCCCCCCCEEEEEEEECCCCCCHHHHHHHCCCCC-----CCC-CCCCCCCHHHHH
T ss_conf             97679986999985553363232115778998989999986799989899966048986-----788-998874699999


Q ss_pred             HHHHHCCCEEEEEEECCCCEEEEEECCC
Q ss_conf             9999629869999798995299997359
Q gi|254780903|r  739 ALTNLHGGRLKIISQEGKGTIVTICMPQ  766 (766)
Q Consensus       739 ~iVe~hgG~I~v~S~~g~Gttf~i~LP~  766 (766)
                      +||+.|||.|.|+|+||+||+|+|+||.
T Consensus       651 gIV~~hgG~I~V~S~pG~GTtF~v~LP~  678 (831)
T PRK13837        651 GIVSAHAGYIDVQSTVGRGTRFDVYLPP  678 (831)
T ss_pred             HHHHHCCCEEEEECCCCCCEEEEEEEEC
T ss_conf             9999869869997269997189998317


No 16 
>PRK10549 signal transduction histidine-protein kinase BaeS; Provisional
Probab=100.00  E-value=0  Score=416.15  Aligned_cols=240  Identities=22%  Similarity=0.375  Sum_probs=219.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             99999999999999998878999999998767522247899999999860346889938999999999999999999977
Q gi|254780903|r  521 ELSIANAKYQVEKERAETANKTKSEFLAKMSHELRTPLNAILGFSEVIKKEIFGELGSVKYYEYAQDIHYSGQHLLNMIN  600 (766)
Q Consensus       521 ~L~~~~~~l~~~~~~ae~an~~k~efla~isHelrtPL~aI~g~~ell~~~~~~~~~~e~~~~~l~~I~~~~~~l~~lI~  600 (766)
                      |+.++.+......++++...+.+.+|++++||||||||++|.|++|+|+++...     ...+++..|...+.+|.++|+
T Consensus       219 Eig~La~~fN~Ma~~Le~~~~~rr~f~a~iSHELRTPLt~i~g~le~l~d~~~~-----~~~e~l~~i~~e~~rl~~Lv~  293 (467)
T PRK10549        219 ELGKLAQDFNQLASTLEKNQQMRRDFMADISHELRTPLAVLRGELEAIQDGVRK-----FTPESVASLQAEVGTLTKLVD  293 (467)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHCCCC-----CCHHHHHHHHHHHHHHHHHHH
T ss_conf             799999999999999999999999999988887515899999999998716554-----579999999999999999999


Q ss_pred             HHHHHHHHHCCCCCCCEEEECHHHHHHHHHHHHHHHHHHCCCEEEEEECCCCEEEECHHHHHHHHHHHHHHHHHCCCCCC
Q ss_conf             76778887419830120331699999999999999998479589998089978998689999999998865653468988
Q gi|254780903|r  601 NILEMSKIETEKISIDKQNADLIPIINEGIRLIGSSAQSKNIKIEKKIPSELFFNADKRIIKKILFPILSNSIKFTNNNG  680 (766)
Q Consensus       601 diLd~srieag~~~~~~~~~dl~~~i~~~~~~~~~~~~~k~i~l~~~~~~~l~v~~D~~~l~QVl~NLi~NAik~t~~~g  680 (766)
                      |+|++|+.+.|.+.++.+++|+.+++++++..+++.+.++++++..++++++++.+|+.+|+|||.||++||+||++++|
T Consensus       294 dLl~ls~~~~~~~~~~~~~vdl~~ll~~~~~~~~~~~~~~~i~l~~~~~~~~~v~~D~~~L~qvl~NLl~NAikyt~~~g  373 (467)
T PRK10549        294 DLHQLSLSDEGALAYQKTPVDLVPLLEVAGGAFRERFASRGLTLQFSLPDSATVFGDPDRLMQLFNNLLENSLRYTDSGG  373 (467)
T ss_pred             HHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCEEEEECCCCCEEEECHHHHHHHHHHHHHHHHHHCCCCC
T ss_conf             99999875456754467333389999999999999998459589997598846997799999999999999998489998


Q ss_pred             EEEEEEEEECCEEEEEEEECCCCCCHHHHHHHCCCEEECCCCCCCCCCCCCHHHHHHHHHHHHCCCEEEEEEECCCCEEE
Q ss_conf             89999999799899999978897897785430465053146755677887616899999999629869999798995299
Q gi|254780903|r  681 KMMIRTSKIGQCVIITIADTGIGIPKSALEKIGQPFEPLHNQYDQSIGGFGLGLAISDALTNLHGGRLKIISQEGKGTIV  760 (766)
Q Consensus       681 ~I~i~~~~~~~~v~i~V~D~G~GI~~e~~~~iF~pF~q~~~~~t~~~~GtGLGLaI~k~iVe~hgG~I~v~S~~g~Gttf  760 (766)
                      .|.|++...++.++|+|+|+|+|||++.+++||+||||++++.++..+||||||||||+||+.|||+|+++|.+|+||+|
T Consensus       374 ~I~I~~~~~~~~v~i~V~D~G~GI~~e~l~~IFe~Fyr~d~sr~r~~gGsGLGLaIvk~Iv~~HgG~I~v~s~~~~G~~f  453 (467)
T PRK10549        374 SLHISAEQHDKTLRLTFADSAPGVSDEQLQKLFERFYRTEGSRNRASGGSGLGLAICLNIVEAHNGRIIAAHSPFGGVSI  453 (467)
T ss_pred             EEEEEEEEECCEEEEEEEEECCCCCHHHHHHHCCCCEECCCCCCCCCCCCCHHHHHHHHHHHHCCCEEEEEECCCCEEEE
T ss_conf             79999999799999999981888798999986689873888888999961289999999999839989999679985799


Q ss_pred             EEECC
Q ss_conf             99735
Q gi|254780903|r  761 TICMP  765 (766)
Q Consensus       761 ~i~LP  765 (766)
                      +|+||
T Consensus       454 ~i~LP  458 (467)
T PRK10549        454 TVELP  458 (467)
T ss_pred             EEEEE
T ss_conf             99952


No 17 
>PRK10364 sensor protein ZraS; Provisional
Probab=100.00  E-value=0  Score=415.49  Aligned_cols=223  Identities=28%  Similarity=0.458  Sum_probs=202.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             99999999887899999999876752224789999999986034688993899999999999999999997776778887
Q gi|254780903|r  529 YQVEKERAETANKTKSEFLAKMSHELRTPLNAILGFSEVIKKEIFGELGSVKYYEYAQDIHYSGQHLLNMINNILEMSKI  608 (766)
Q Consensus       529 l~~~~~~ae~an~~k~efla~isHelrtPL~aI~g~~ell~~~~~~~~~~e~~~~~l~~I~~~~~~l~~lI~diLd~sri  608 (766)
                      ++++..+.|+. .+.+++.|++||||||||++|.||++++.++..   .+++.+++++.|.+.++|+.++|+++|+|+| 
T Consensus       225 Lq~el~r~EKL-AaLG~LAAgVAHEIRNPLtsI~G~AqlL~~~~~---~~~e~~e~~~iI~~E~~RL~~iI~~LL~faR-  299 (455)
T PRK10364        225 LQDEMKRKEKL-VALGHLAAGVAHEIRNPLSSIKGLAKYFAERAP---AGGEAHQLAQVMAKEADRLNRVVSELLELVK-  299 (455)
T ss_pred             HHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCC---CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHC-
T ss_conf             99999999899-999999999899885649999999999867699---9857999999999999999999999998728-


Q ss_pred             HCCCCCCCEEEECHHHHHHHHHHHHHHHHHHCCCEEEEEECCCCE-EEECHHHHHHHHHHHHHHHHHCCCCCCEEEEEEE
Q ss_conf             419830120331699999999999999998479589998089978-9986899999999988656534689888999999
Q gi|254780903|r  609 ETEKISIDKQNADLIPIINEGIRLIGSSAQSKNIKIEKKIPSELF-FNADKRIIKKILFPILSNSIKFTNNNGKMMIRTS  687 (766)
Q Consensus       609 eag~~~~~~~~~dl~~~i~~~~~~~~~~~~~k~i~l~~~~~~~l~-v~~D~~~l~QVl~NLi~NAik~t~~~g~I~i~~~  687 (766)
                         ...++.+++|+++++++++.++++.+..|+|++..+.++++| |.+|+.+|+|||+||+.||+++++++|+|+|++.
T Consensus       300 ---p~~~~~~~vdL~~li~~~l~l~~~~a~~k~I~l~~~~~~~lp~I~~D~~~L~QVl~NLl~NAi~A~~~gg~I~I~~~  376 (455)
T PRK10364        300 ---PTHLALQAVDLNTLINHSLQLVSQDANSREIQLRFTANDTLPEIQADPDRLTQVLLNLYLNAIQAIGQHGVISVTAS  376 (455)
T ss_pred             ---CCCCCCCEECHHHHHHHHHHHHHHHHHHCCEEEEEECCCCCCEEEECHHHHHHHHHHHHHHHHHHCCCCCEEEEEEE
T ss_conf             ---99898848849999999999998688648909999738888759888999999999999999997589977999999


Q ss_pred             EECCEEEEEEEECCCCCCHHHHHHHCCCEEECCCCCCCCCCCCCHHHHHHHHHHHHCCCEEEEEEECCCCEEEEEECC
Q ss_conf             979989999997889789778543046505314675567788761689999999962986999979899529999735
Q gi|254780903|r  688 KIGQCVIITIADTGIGIPKSALEKIGQPFEPLHNQYDQSIGGFGLGLAISDALTNLHGGRLKIISQEGKGTIVTICMP  765 (766)
Q Consensus       688 ~~~~~v~i~V~D~G~GI~~e~~~~iF~pF~q~~~~~t~~~~GtGLGLaI~k~iVe~hgG~I~v~S~~g~Gttf~i~LP  765 (766)
                      ..++.++|+|+|||+|||+|.++|||+|||     +| +.+||||||+|||+||+.|||+|+++|++|+||+|+|+||
T Consensus       377 ~~~~~V~I~V~DnG~GIp~E~l~rIFePFf-----TT-K~~GTGLGLaIv~~IVe~HgG~I~v~S~~G~GT~FtI~LP  448 (455)
T PRK10364        377 ESGAGVKISVTDSGKGIAADQLEAIFTPYF-----TT-KAEGTGLGLAVVHNIVEQHGGTIQVASQEGKGATFTLWLP  448 (455)
T ss_pred             ECCCEEEEEEEECCCCCCHHHHHHHCCCCC-----CC-CCCCCCHHHHHHHHHHHHCCCEEEEEECCCCCEEEEEEEE
T ss_conf             859989999997699979789878658976-----48-9897028899999999988997999955999879999982


No 18 
>PRK11100 sensory histidine kinase CreC; Provisional
Probab=100.00  E-value=0  Score=413.19  Aligned_cols=219  Identities=24%  Similarity=0.429  Sum_probs=203.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCEEEEC
Q ss_conf             99999998767522247899999999860346889938999999999999999999977767788874198301203316
Q gi|254780903|r  542 TKSEFLAKMSHELRTPLNAILGFSEVIKKEIFGELGSVKYYEYAQDIHYSGQHLLNMINNILEMSKIETEKISIDKQNAD  621 (766)
Q Consensus       542 ~k~efla~isHelrtPL~aI~g~~ell~~~~~~~~~~e~~~~~l~~I~~~~~~l~~lI~diLd~srieag~~~~~~~~~d  621 (766)
                      ...+|++++||||||||++|.|++|+|+..    ..+++.++|++.|.+.++||.+||+|+|++||+|++....+++++|
T Consensus       255 ~~e~fva~vSHELRTPLt~I~g~~ElL~~~----~~~e~~~~~l~~I~~e~~RL~~LV~~LL~larle~~~~~~~~~~vd  330 (475)
T PRK11100        255 YVEQYVQTLTHELKSPLAAIRGAAELLQED----PPPEDRQRFTGNILAQSARLQQLIDRLLELARLEQRQELEVLEPVA  330 (475)
T ss_pred             HHHHHHHHCHHHHHHHHHHHHHHHHHHHCC----CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCEEEC
T ss_conf             999999854086511799999999997389----9989999999999999999999999999998751588767554875


Q ss_pred             HHHHHHHHHHHHHHHHHHCCCEEEEEECCCCEEEECHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEEECCEEEEEEEECC
Q ss_conf             99999999999999998479589998089978998689999999998865653468988899999997998999999788
Q gi|254780903|r  622 LIPIINEGIRLIGSSAQSKNIKIEKKIPSELFFNADKRIIKKILFPILSNSIKFTNNNGKMMIRTSKIGQCVIITIADTG  701 (766)
Q Consensus       622 l~~~i~~~~~~~~~~~~~k~i~l~~~~~~~l~v~~D~~~l~QVl~NLi~NAik~t~~~g~I~i~~~~~~~~v~i~V~D~G  701 (766)
                      +.+++++++..+++.+.+|++++..+.+ ++.|.+|+.+|+||+.||+.||+||+|++|.|+|++...++.++|+|+|+|
T Consensus       331 l~~ll~~~~~~~~~~~~~~~i~l~~~~~-~~~v~~D~~~L~qvl~NLl~NAikys~~~g~I~I~~~~~~~~~~i~V~D~G  409 (475)
T PRK11100        331 LAALLEELVEAREAQAAAKGITLRLRPD-DAAVLGDPFLLRQALGNLLDNAIDFTPEGGTITLSAERDGEQVALSVEDSG  409 (475)
T ss_pred             HHHHHHHHHHHHHHHHHHCCEEEEEECC-CCEEEECHHHHHHHHHHHHHHHHHHCCCCCEEEEEEEEECCEEEEEEEECC
T ss_conf             9999999999999999868929999578-766970899999999999999997389997799999996999999999848


Q ss_pred             CCCCHHHHHHHCCCEEECCCCCCCCCCCCCHHHHHHHHHHHHCCCEEEEEEECCCCEEEEEECCC
Q ss_conf             97897785430465053146755677887616899999999629869999798995299997359
Q gi|254780903|r  702 IGIPKSALEKIGQPFEPLHNQYDQSIGGFGLGLAISDALTNLHGGRLKIISQEGKGTIVTICMPQ  766 (766)
Q Consensus       702 ~GI~~e~~~~iF~pF~q~~~~~t~~~~GtGLGLaI~k~iVe~hgG~I~v~S~~g~Gttf~i~LP~  766 (766)
                      +|||++.+++||+|||++.... .+.+||||||||||.||++|||+|+++|.+|+||+|+|+|||
T Consensus       410 ~GIp~e~l~~IFerFys~~r~~-~~~~GsGLGLsIvk~Iv~~HgG~I~v~s~~~~Gt~f~i~LP~  473 (475)
T PRK11100        410 PGIPDYALPRIFERFYSLPRPA-NGRKSTGLGLAFVREVARLHGGEVTLRNRPEGGVLATLTLPR  473 (475)
T ss_pred             CCCCHHHHHHHCCCCCCCCCCC-CCCCCCCHHHHHHHHHHHHCCCEEEEEECCCCEEEEEEECCC
T ss_conf             8878899988616780377799-998863079999999999859989999669980799999389


No 19 
>PRK09835 sensor kinase CusS; Provisional
Probab=100.00  E-value=0  Score=411.19  Aligned_cols=241  Identities=18%  Similarity=0.321  Sum_probs=221.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             99999999999999998878999999998767522247899999999860346889938999999999999999999977
Q gi|254780903|r  521 ELSIANAKYQVEKERAETANKTKSEFLAKMSHELRTPLNAILGFSEVIKKEIFGELGSVKYYEYAQDIHYSGQHLLNMIN  600 (766)
Q Consensus       521 ~L~~~~~~l~~~~~~ae~an~~k~efla~isHelrtPL~aI~g~~ell~~~~~~~~~~e~~~~~l~~I~~~~~~l~~lI~  600 (766)
                      |+.++...+....++++.+.....+|++++||||||||++|.|+++++...   +...+++++++..+.+..+||.++|+
T Consensus       240 El~~La~~fN~M~~rl~~~~~~~~~f~a~vSHELRTPLt~i~~~~e~~l~~---~~~~~~~~~~l~~~~~e~~rl~~lv~  316 (482)
T PRK09835        240 ELEQLVLSFNHMIERIEDVFTRQSNFSADIAHEIRTPITNLITQTEIALSQ---SRSQKELEDVLYSNLEELTRMAKMVS  316 (482)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC---CCCHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             799999999999999999999999999998898718999999999998538---99869999999999999999999999


Q ss_pred             HHHHHHHHHCCCCCCCEEEECHHHHHHHHHHHHHHHHHHCCCEEEEEECCCCEEEECHHHHHHHHHHHHHHHHHCCCCCC
Q ss_conf             76778887419830120331699999999999999998479589998089978998689999999998865653468988
Q gi|254780903|r  601 NILEMSKIETEKISIDKQNADLIPIINEGIRLIGSSAQSKNIKIEKKIPSELFFNADKRIIKKILFPILSNSIKFTNNNG  680 (766)
Q Consensus       601 diLd~srieag~~~~~~~~~dl~~~i~~~~~~~~~~~~~k~i~l~~~~~~~l~v~~D~~~l~QVl~NLi~NAik~t~~~g  680 (766)
                      ++|++||.|.+....+.+++|+.+++.+++..+.+.+++|++++..+. +++.|.+|+.+|+|+|.|||+||+||+|+||
T Consensus       317 ~lL~lar~e~~~~~~~~~~~dl~~~~~~~~~~~~~~~~~~~i~~~~~~-~~~~v~~d~~~l~~~l~NLl~NAikys~~g~  395 (482)
T PRK09835        317 DMLFLAQADNNQLIPEKKMLNLADEVGKVFDFFEALAEDRGVELRFVG-DPCQVAGDPLMLRRALSNLLSNALRYTPEGE  395 (482)
T ss_pred             HHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCEEEEEC-CCEEEEECHHHHHHHHHHHHHHHHHHCCCCC
T ss_conf             999987743588766673456999999999999999986892899827-8708998799999999999999998489998


Q ss_pred             EEEEEEEEECCEEEEEEEECCCCCCHHHHHHHCCCEEECCCCCCCCCCCCCHHHHHHHHHHHHCCCEEEEEEECCCCEEE
Q ss_conf             89999999799899999978897897785430465053146755677887616899999999629869999798995299
Q gi|254780903|r  681 KMMIRTSKIGQCVIITIADTGIGIPKSALEKIGQPFEPLHNQYDQSIGGFGLGLAISDALTNLHGGRLKIISQEGKGTIV  760 (766)
Q Consensus       681 ~I~i~~~~~~~~v~i~V~D~G~GI~~e~~~~iF~pF~q~~~~~t~~~~GtGLGLaI~k~iVe~hgG~I~v~S~~g~Gttf  760 (766)
                      .|+|++...++.+.|+|+|+|+|||++.+++||+||||++.+.+++.+||||||||||+||+.|||+|+++|+ ++||+|
T Consensus       396 ~i~i~~~~~~~~v~i~V~D~G~GI~~e~~~~iFerFyR~d~sr~~~~~G~GLGLaIvk~Iv~~hgG~i~v~s~-~~Gt~f  474 (482)
T PRK09835        396 AIVVRCQTVDHQVQVVVENPGTPIAPEHLPRLFDRFYRVDPSRQRKGEGSGIGLAIVKSIVVAHKGTVAVTSD-ARGTRF  474 (482)
T ss_pred             EEEEEEEEECCEEEEEEEECCCCCCHHHHHHHCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHCCCEEEEEEC-CCCEEE
T ss_conf             6999999829989999996587889899987667975189888899994648999999999982998999963-991899


Q ss_pred             EEECCC
Q ss_conf             997359
Q gi|254780903|r  761 TICMPQ  766 (766)
Q Consensus       761 ~i~LP~  766 (766)
                      +|+|||
T Consensus       475 ~i~lPr  480 (482)
T PRK09835        475 VISLPR  480 (482)
T ss_pred             EEEEEC
T ss_conf             999307


No 20 
>COG5002 VicK Signal transduction histidine kinase [Signal transduction mechanisms]
Probab=100.00  E-value=0  Score=409.32  Aligned_cols=347  Identities=23%  Similarity=0.428  Sum_probs=276.4

Q ss_pred             EECCCHHHHHHHHHHHHH-HHHHHHHHHHHHHEEEECCCCEEEEECHHHHHHHCCCHHHHCCCCCHHHHCCCHHHHHHHH
Q ss_conf             844617999999999999-9999999854455158834996997017898883999789428971788165201378999
Q gi|254780903|r  364 AMDLTEKYHLEKRYAEAD-QRLSKAIECTSEALVLWDKNDRLVMCNANYQKAYGLPDHVLVPGNARSIIQDAQTRPIIEY  442 (766)
Q Consensus       364 ~~DITErK~ae~~l~ese-~rlr~~ie~~~~~i~~~D~~g~i~~~N~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~  442 (766)
                      .-|.|++-+..++..++| .+|..++..+.+|++..|..|++++.|+.+.+++|.+.+++.+....+.+.-.+...... 
T Consensus        92 fn~Lt~~~~~aq~n~e~Er~kL~SvlayMtDGViATdRrG~iI~iN~~A~k~L~~~~E~~~~~~i~elL~i~d~y~~~d-  170 (459)
T COG5002          92 FNDLTKRVQEAQANTEQERRKLDSVLAYMTDGVIATDRRGKIILINKPALKMLGVSKEDALGRSILELLKIEDTYTFED-  170 (459)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCEEEECCCCCEEEECCHHHHHHCCCHHHHHCCCHHHHHCCCCCEEHHH-
T ss_conf             9789999999987678888889989998707657645778689935079998486778771653788857754302888-


Q ss_pred             HHHCCCCCCCEEEEEEE-CCCEEEEEC--CEECC---CCCEEEEEEEEEHHHCCCCCCCCCCCCCCCCCCHHHHHHHHHH
Q ss_conf             85211245640589991-696287422--32456---9978999886201000112232222222110000178899864
Q gi|254780903|r  443 RTSDPERSQDMSKEIKL-ADSRWLQIN--EWCTH---DGGTISVGTDITLLKHNQAQLRESKRRLKATINDLSTSRQILE  516 (766)
Q Consensus       443 ~~~~~~~~~~~~~e~~~-~dg~~~~i~--~~~~~---dg~~v~v~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  516 (766)
                      -+   +...+...+... ..+..++++  ..+..   -.|++.|..|+|+..                            
T Consensus       171 L~---e~~~s~lld~~~~~E~~~lrv~Fs~i~rEsGfisGlIaVlhDvTEqe----------------------------  219 (459)
T COG5002         171 LV---EKNDSLLLDSSDEEEGYVLRVNFSVIQRESGFISGLIAVLHDVTEQE----------------------------  219 (459)
T ss_pred             HH---HCCCCEEEEECCCCCCEEEEEEEEEEEECCCCCCEEEEEEECCCHHH----------------------------
T ss_conf             87---25982898604788637999988888511466440699873143878----------------------------


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHH
Q ss_conf             44579999999999999999887899999999876752224789999999986034688993899999999999999999
Q gi|254780903|r  517 RQKTELSIANAKYQVEKERAETANKTKSEFLAKMSHELRTPLNAILGFSEVIKKEIFGELGSVKYYEYAQDIHYSGQHLL  596 (766)
Q Consensus       517 ~~~~~L~~~~~~l~~~~~~ae~an~~k~efla~isHelrtPL~aI~g~~ell~~~~~~~~~~e~~~~~l~~I~~~~~~l~  596 (766)
                                           +..+...+|.||+||||||||++..+|+|.|..++..+  .+-...++..-.+..+||.
T Consensus       220 ---------------------k~e~ErRefvanvSHElRTPltsmksyLEALe~ga~~d--~eiAp~Fl~vt~~ETeRMi  276 (459)
T COG5002         220 ---------------------KVERERREFVANVSHELRTPLTSMKSYLEALEEGAWED--KEIAPRFLRVTLNETERMI  276 (459)
T ss_pred             ---------------------HHHHHHHHHHHHCCHHHCCCHHHHHHHHHHHHCCCCCC--HHHHHHHHHHHHHHHHHHH
T ss_conf             ---------------------88999999988614031473678999999974687447--1232689987478899999


Q ss_pred             HHHHHHHHHHHHHCCCCCCCEEEECHHHHHHHHHHHHHHHHHHCCCE-EEEEECC-CCEEEECHHHHHHHHHHHHHHHHH
Q ss_conf             99777677888741983012033169999999999999999847958-9998089-978998689999999998865653
Q gi|254780903|r  597 NMINNILEMSKIETEKISIDKQNADLIPIINEGIRLIGSSAQSKNIK-IEKKIPS-ELFFNADKRIIKKILFPILSNSIK  674 (766)
Q Consensus       597 ~lI~diLd~srieag~~~~~~~~~dl~~~i~~~~~~~~~~~~~k~i~-l~~~~~~-~l~v~~D~~~l~QVl~NLi~NAik  674 (766)
                      +||||+|.+||++..+..++++-+++...+...+.-+...+.+..+. +..++|. +.+|..|+..+.||+.|+|+||+|
T Consensus       277 RlV~DLl~lsr~d~~~~qln~e~inft~fl~~ii~R~e~~~~~e~~~~~vR~~p~~~~~veiD~DK~tQVldNii~NA~K  356 (459)
T COG5002         277 RLVNDLLQLSRMDNARYQLNKEWINFTAFLNEIINRFEMILKKETIARFVRDIPKQDIWVEIDPDKMTQVLDNIISNALK  356 (459)
T ss_pred             HHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCEEEEECHHHHHHHHHHHHHHHHH
T ss_conf             99999987725763256665788874889999999999987567788999608888648996706899999999877752


Q ss_pred             CCCCCCEEEEEEEEECCEEEEEEEECCCCCCHHHHHHHCCCEEECCCCCCCCCCCCCHHHHHHHHHHHHCCCEEEEEEEC
Q ss_conf             46898889999999799899999978897897785430465053146755677887616899999999629869999798
Q gi|254780903|r  675 FTNNNGKMMIRTSKIGQCVIITIADTGIGIPKSALEKIGQPFEPLHNQYDQSIGGFGLGLAISDALTNLHGGRLKIISQE  754 (766)
Q Consensus       675 ~t~~~g~I~i~~~~~~~~v~i~V~D~G~GI~~e~~~~iF~pF~q~~~~~t~~~~GtGLGLaI~k~iVe~hgG~I~v~S~~  754 (766)
                      |+|+||+|++++...++.+.++|+|.|.|||++.+++||++|+|++...+++.|||||||||+|.||+.|||+||++|+.
T Consensus       357 YsP~Gg~Itv~~~~~~~~v~iSI~D~G~gIPk~d~~~iFdrfyRvdkARsR~~gGTGLGLaIakeiV~~hgG~iWA~s~~  436 (459)
T COG5002         357 YSPDGGRITVSVKQRETWVEISISDQGLGIPKEDLEKIFDRFYRVDKARSRKMGGTGLGLAIAKEIVQAHGGRIWAESEE  436 (459)
T ss_pred             CCCCCCEEEEEEEEECCEEEEEECCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHCCEEEEECCC
T ss_conf             48999739999963075899997468889984068999998852236654037877612999999999709857776045


Q ss_pred             CCCEEEEEECC
Q ss_conf             99529999735
Q gi|254780903|r  755 GKGTIVTICMP  765 (766)
Q Consensus       755 g~Gttf~i~LP  765 (766)
                      |+||||+|+||
T Consensus       437 gkgtt~~ftLP  447 (459)
T COG5002         437 GKGTTFSFTLP  447 (459)
T ss_pred             CCCEEEEEEEC
T ss_conf             88617999954


No 21 
>PRK11086 sensory histidine kinase DcuS; Provisional
Probab=100.00  E-value=0  Score=351.42  Aligned_cols=192  Identities=21%  Similarity=0.237  Sum_probs=148.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCEEEECH
Q ss_conf             99999987675222478999999998603468899389999999999999999999777677888741983012033169
Q gi|254780903|r  543 KSEFLAKMSHELRTPLNAILGFSEVIKKEIFGELGSVKYYEYAQDIHYSGQHLLNMINNILEMSKIETEKISIDKQNADL  622 (766)
Q Consensus       543 k~efla~isHelrtPL~aI~g~~ell~~~~~~~~~~e~~~~~l~~I~~~~~~l~~lI~diLd~srieag~~~~~~~~~dl  622 (766)
                      ..+++...+||++|||+.|.|++++-+        .++..+|+..+   .......++.+++--+          .    
T Consensus       338 ~~e~Lra~sHE~~n~L~~I~Gll~l~~--------~d~~~~~i~~~---~~~~~~~~~~l~~~i~----------~----  392 (541)
T PRK11086        338 YADALRAQSHEFMNKLHVILGLLHLKS--------YDQLEDYILKT---ANNYQEEIGSLLGKIK----------S----  392 (541)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHCH--------HHHHHHHHHHH---HHHHHHHHHHHHHHCC----------C----
T ss_conf             999987611666405799988886430--------89999999999---9999999999998611----------6----


Q ss_pred             HHHHHHHHHHHHHHHHHCCCEEEEEECCCCEEEECHH---HHHHHHHHHHHHHHHCCC--CCCEEEEEEEEECCEEEEEE
Q ss_conf             9999999999999998479589998089978998689---999999998865653468--98889999999799899999
Q gi|254780903|r  623 IPIINEGIRLIGSSAQSKNIKIEKKIPSELFFNADKR---IIKKILFPILSNSIKFTN--NNGKMMIRTSKIGQCVIITI  697 (766)
Q Consensus       623 ~~~i~~~~~~~~~~~~~k~i~l~~~~~~~l~v~~D~~---~l~QVl~NLi~NAik~t~--~~g~I~i~~~~~~~~v~i~V  697 (766)
                       .++...+.--...+.++++.|.++.+..+|...|+.   +|.|||.||+.||+||++  ++|+|.|+....++.+.|+|
T Consensus       393 -p~la~~Llgk~~~a~E~gi~L~i~~~~~l~~~~~~~~~~~l~tVlgNLidNAi~A~~~~~~g~V~v~l~~~~~~l~i~V  471 (541)
T PRK11086        393 -PVIAGFLLGKISRARELGITLIISEDSQLPDSDDEDQVHELITILGNLIENALEAVSNEEGGEISVSLHYRHGWLHIEV  471 (541)
T ss_pred             -HHHHHHHHHHHHHHHHCCCEEEEECCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEECCCEEEEEE
T ss_conf             -8889999988999996698599706776778886466657999999999999997316899679999998899899999


Q ss_pred             EECCCCCCHHHHHHHCCCEEECCCCCCCCCCCCCHHHHHHHHHHHHCCCEEEEEEECCCCEEEEEECCC
Q ss_conf             978897897785430465053146755677887616899999999629869999798995299997359
Q gi|254780903|r  698 ADTGIGIPKSALEKIGQPFEPLHNQYDQSIGGFGLGLAISDALTNLHGGRLKIISQEGKGTIVTICMPQ  766 (766)
Q Consensus       698 ~D~G~GI~~e~~~~iF~pF~q~~~~~t~~~~GtGLGLaI~k~iVe~hgG~I~v~S~~g~Gttf~i~LP~  766 (766)
                      +|||+|||++.+++||+|||     +| +.+||||||||||++|+.|||+|+|+|++|+||+|+|+||+
T Consensus       472 ~D~G~GI~~e~~~~IFerg~-----St-K~~g~GLGLaIvk~iVe~~gG~I~veS~~g~GT~Fti~LP~  534 (541)
T PRK11086        472 SDDGPGIAPEEIEAIFDKGY-----ST-KGSNRGVGLYLVKQSVENLGGSIAVESEPGIGTQFFVQIPW  534 (541)
T ss_pred             EECCCCCCHHHHHHHCCCCC-----CC-CCCCCCCCHHHHHHHHHHCCCEEEEEECCCCCEEEEEEECC
T ss_conf             97798859779988717987-----41-89991103999999999859989999669993799999606


No 22 
>PRK09470 cpxA two-component sensor protein; Provisional
Probab=100.00  E-value=0  Score=380.53  Aligned_cols=235  Identities=25%  Similarity=0.371  Sum_probs=207.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             99999999999999998878999999998767522247899999999860346889938999999999999999999977
Q gi|254780903|r  521 ELSIANAKYQVEKERAETANKTKSEFLAKMSHELRTPLNAILGFSEVIKKEIFGELGSVKYYEYAQDIHYSGQHLLNMIN  600 (766)
Q Consensus       521 ~L~~~~~~l~~~~~~ae~an~~k~efla~isHelrtPL~aI~g~~ell~~~~~~~~~~e~~~~~l~~I~~~~~~l~~lI~  600 (766)
                      |+.++.+......++++++.....+|++++||||||||+.|.++.+++.+.. ++      .+.++.|.+.+++|.++|+
T Consensus       221 Ei~~La~~fN~M~~~L~~~~~~q~~f~advSHELRTPLt~i~~~~~ll~~~~-~~------~~~l~~i~~e~~rl~~li~  293 (461)
T PRK09470        221 EFRAAGASFNQMVTALERMMSSQQRLLSDISHELRTPLTRLQLATALLRRRQ-GE------SKELERIETEAQRLDSMIN  293 (461)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHCCC-CC------HHHHHHHHHHHHHHHHHHH
T ss_conf             9999999999999999999999999998645553278999999999864044-78------5999999999999999999


Q ss_pred             HHHHHHHHHCCCCCCCEEEECHHHHHHHHHHHHHHHHHHCCCEEEEEECC-CCEEEECHHHHHHHHHHHHHHHHHCCCCC
Q ss_conf             76778887419830120331699999999999999998479589998089-97899868999999999886565346898
Q gi|254780903|r  601 NILEMSKIETEKISIDKQNADLIPIINEGIRLIGSSAQSKNIKIEKKIPS-ELFFNADKRIIKKILFPILSNSIKFTNNN  679 (766)
Q Consensus       601 diLd~srieag~~~~~~~~~dl~~~i~~~~~~~~~~~~~k~i~l~~~~~~-~l~v~~D~~~l~QVl~NLi~NAik~t~~~  679 (766)
                      ++|++||.+.+. .+..+++|+.++++++++.+...+..+++.+.++.++ .++|.+|+.+|+||+.||+.||+||+++ 
T Consensus       294 ~lL~lsr~~~~~-~~~~e~~~l~~l~~~v~~~~~~~a~~~~~~l~~~~~~~~~~v~~d~~~l~~vl~NLl~NAikys~~-  371 (461)
T PRK09470        294 DLLVLSRNQVKN-HLVRETIKANSLWSEVLEDAAFEAEQMGKSLTVNQPPGPWPINGNPNALESALENIVRNALRYSHT-  371 (461)
T ss_pred             HHHHHHHHCCCC-CCCCCEECHHHHHHHHHHHHHHHHHHCCCEEEEEECCCCEEEEECHHHHHHHHHHHHHHHHHHCCC-
T ss_conf             999997620546-555651539999999999999999975976999727875489978999999999999999974899-


Q ss_pred             CEEEEEEEEECCEEEEEEEECCCCCCHHHHHHHCCCEEECCCCCCCCCCCCCHHHHHHHHHHHHCCCEEEEEEECCCCEE
Q ss_conf             88999999979989999997889789778543046505314675567788761689999999962986999979899529
Q gi|254780903|r  680 GKMMIRTSKIGQCVIITIADTGIGIPKSALEKIGQPFEPLHNQYDQSIGGFGLGLAISDALTNLHGGRLKIISQEGKGTI  759 (766)
Q Consensus       680 g~I~i~~~~~~~~v~i~V~D~G~GI~~e~~~~iF~pF~q~~~~~t~~~~GtGLGLaI~k~iVe~hgG~I~v~S~~g~Gtt  759 (766)
                       .|+|++...++.+.|+|+|+|+|||++.+++||+||||++.+.+++.+||||||||||+||+.|||+|+++|.++.||+
T Consensus       372 -~i~v~~~~~~~~~~i~V~D~G~GI~~e~l~~iFepFyR~d~sr~~~~gG~GLGLaIv~~iv~~hgG~i~~~~~~~~G~~  450 (461)
T PRK09470        372 -KIEVGFSVDKDGLTITVDDDGPGVPEEEREQIFRPFYRVDEARDRESGGTGLGLAIVENAIQQHRGWVKAEDSPLGGLR  450 (461)
T ss_pred             -CEEEEEEEECCEEEEEEEECCCCCCHHHHHHHCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHCCCEEEEEECCCCEEE
T ss_conf             -5899999999999999997799989999987627972289888899997138899999999982998999977998569


Q ss_pred             EEEECC
Q ss_conf             999735
Q gi|254780903|r  760 VTICMP  765 (766)
Q Consensus       760 f~i~LP  765 (766)
                      |+|+||
T Consensus       451 ~~i~LP  456 (461)
T PRK09470        451 LTIWLP  456 (461)
T ss_pred             EEEEEE
T ss_conf             999965


No 23 
>PRK10604 sensor protein RstB; Provisional
Probab=100.00  E-value=0  Score=380.91  Aligned_cols=234  Identities=20%  Similarity=0.328  Sum_probs=204.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             99999999999999998878999999998767522247899999999860346889938999999999999999999977
Q gi|254780903|r  521 ELSIANAKYQVEKERAETANKTKSEFLAKMSHELRTPLNAILGFSEVIKKEIFGELGSVKYYEYAQDIHYSGQHLLNMIN  600 (766)
Q Consensus       521 ~L~~~~~~l~~~~~~ae~an~~k~efla~isHelrtPL~aI~g~~ell~~~~~~~~~~e~~~~~l~~I~~~~~~l~~lI~  600 (766)
                      ++.++.+......++.+..-..+.+|++++||||||||+.|.+.++++..    +. .++    .+.+.+...+|.++|+
T Consensus       190 Ei~~La~~FN~Ma~~l~~~~~~~r~f~a~vSHELRTPLt~i~~~lell~~----~~-~~e----~~~l~~~i~~l~~lv~  260 (433)
T PRK10604        190 SFERLGVAFNQMADNINALIASKKQLIDGIAHELRTPLVRLRYRLEMSDN----LS-AAE----SQALNRDIGQLEALIE  260 (433)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHCCHHHHHHHHHHHHCC----CC-HHH----HHHHHHHHHHHHHHHH
T ss_conf             59999999999999999999999999874024431689999999997049----98-578----9999999999999999


Q ss_pred             HHHHHHHHHCCCCCCCEEEECHHHHHHHHHHHHHHHHHHCCCEEEEEECCCCEEEECHHHHHHHHHHHHHHHHHCCCCCC
Q ss_conf             76778887419830120331699999999999999998479589998089978998689999999998865653468988
Q gi|254780903|r  601 NILEMSKIETEKISIDKQNADLIPIINEGIRLIGSSAQSKNIKIEKKIPSELFFNADKRIIKKILFPILSNSIKFTNNNG  680 (766)
Q Consensus       601 diLd~srieag~~~~~~~~~dl~~~i~~~~~~~~~~~~~k~i~l~~~~~~~l~v~~D~~~l~QVl~NLi~NAik~t~~~g  680 (766)
                      ++|++||++.+...++++++|+.+++.+++..+++...++++.+... .++..+.+|+.+|+|++.||++||+||+  +|
T Consensus       261 ~lL~larl~~~~~~l~~~~~dl~~~i~~~~~~~~~~~~~~~i~l~~~-~~~~~~~~D~~~l~~~l~NLl~NA~kys--~~  337 (433)
T PRK10604        261 ELLTYARLDRPQNELHLSEPDLPAWLSTHLADIQAVTPEKTVRLKTP-HQGDYGALDMRLMERVLDNLLNNALRYS--HS  337 (433)
T ss_pred             HHHHHHHCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCCEEEECC-CCCCEEEECHHHHHHHHHHHHHHHHHCC--CC
T ss_conf             99999763689787877023699999999999997655996799717-9886698789999999999999998718--99


Q ss_pred             EEEEEEEEECCEEEEEEEECCCCCCHHHHHHHCCCEEECCCCCCCCCCCCCHHHHHHHHHHHHCCCEEEEEEECCCCEEE
Q ss_conf             89999999799899999978897897785430465053146755677887616899999999629869999798995299
Q gi|254780903|r  681 KMMIRTSKIGQCVIITIADTGIGIPKSALEKIGQPFEPLHNQYDQSIGGFGLGLAISDALTNLHGGRLKIISQEGKGTIV  760 (766)
Q Consensus       681 ~I~i~~~~~~~~v~i~V~D~G~GI~~e~~~~iF~pF~q~~~~~t~~~~GtGLGLaI~k~iVe~hgG~I~v~S~~g~Gttf  760 (766)
                      +|.|++...++.++|+|+|+|+|||++.+++||+||+|++.+.+++.+|+||||||||+||+.|||+|+++|.+|+||+|
T Consensus       338 ~v~v~~~~~~~~~~i~V~D~G~GI~~e~~~~IFepFyR~d~sr~~~~gG~GLGLaIvk~Iv~~hgG~i~v~s~~~gGa~f  417 (433)
T PRK10604        338 TVETSLLLDGDQATLIVEDDGPGIAPEERERIFEPFVRLDPSRDRATGGCGLGLAIVHSIALAMGGSVNCDTSELGGARF  417 (433)
T ss_pred             CEEEEEEEECCEEEEEEEECCCCCCHHHHHHHCCCCEECCCCCCCCCCCCCHHHHHHHHHHHHCCCEEEEEECCCCEEEE
T ss_conf             78999999999999999977878898999986579452888889999961388999999999819989999669984799


Q ss_pred             EEECCC
Q ss_conf             997359
Q gi|254780903|r  761 TICMPQ  766 (766)
Q Consensus       761 ~i~LP~  766 (766)
                      +|+||.
T Consensus       418 ~i~LP~  423 (433)
T PRK10604        418 SFSWPV  423 (433)
T ss_pred             EEEECC
T ss_conf             999779


No 24 
>PRK10755 sensor protein BasS/PmrB; Provisional
Probab=100.00  E-value=0  Score=371.90  Aligned_cols=234  Identities=18%  Similarity=0.328  Sum_probs=202.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             57999999999999999988789999999987675222478999999998603468899389999999999999999999
Q gi|254780903|r  519 KTELSIANAKYQVEKERAETANKTKSEFLAKMSHELRTPLNAILGFSEVIKKEIFGELGSVKYYEYAQDIHYSGQHLLNM  598 (766)
Q Consensus       519 ~~~L~~~~~~l~~~~~~ae~an~~k~efla~isHelrtPL~aI~g~~ell~~~~~~~~~~e~~~~~l~~I~~~~~~l~~l  598 (766)
                      ..|+.++.+.+.+..++++.+.....+|++++||||||||++|.|++|++++...     .    ..+.+.+..++|..+
T Consensus       119 ~dEl~~L~~~fN~M~~rL~~~~~~qr~Fia~~SHELRTPLt~I~~~lEll~~~~~-----~----~~~~~~~~i~rl~~l  189 (355)
T PRK10755        119 TLEIEAVTSALNQLVSRLTSTLDNERLFTADVAHELRTPLAGVRLHLELLAKTHH-----I----DVAPLIARLDQMMHS  189 (355)
T ss_pred             CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHCCCC-----C----CHHHHHHHHHHHHHH
T ss_conf             7189999999999999999999999999997577740389999999999737575-----3----199999999999999


Q ss_pred             HHHHHHHHHHHCCCCCCCEEEEC-HHHHHHHHHHHHHHHHHHCCCEEEEEEC-CCCEEEECHHHHHHHHHHHHHHHHHCC
Q ss_conf             77767788874198301203316-9999999999999999847958999808-997899868999999999886565346
Q gi|254780903|r  599 INNILEMSKIETEKISIDKQNAD-LIPIINEGIRLIGSSAQSKNIKIEKKIP-SELFFNADKRIIKKILFPILSNSIKFT  676 (766)
Q Consensus       599 I~diLd~srieag~~~~~~~~~d-l~~~i~~~~~~~~~~~~~k~i~l~~~~~-~~l~v~~D~~~l~QVl~NLi~NAik~t  676 (766)
                      |+++|+++|++.+....+.++++ +.+++......+.+.+..++..+.+..+ .+++|.+|+.+|+||+.||++||+||+
T Consensus       190 i~~LL~Lar~~~~~~~~~~~~~~ll~~li~~~~~~l~~~~~~~~~~l~~~~~~~~~~v~~D~~lL~~vl~NLi~NAikys  269 (355)
T PRK10755        190 VSQLLQLARAGQSFSSGNYQTVKLLEDVILPSYDELSTMLEQRQQTLLLPESAADITVQGDATLLRLLLRNLVENAHRYS  269 (355)
T ss_pred             HHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCEEEEECCCCCEEEEECHHHHHHHHHHHHHHHHHHC
T ss_conf             99999998588864345442132599999999999999999759959996588771899689999999999999899748


Q ss_pred             CCCCEEEEEEEEECCEEEEEEEECCCCCCHHHHHHHCCCEEECCCCCCCCCCCCCHHHHHHHHHHHHCCCEEEEEEEC-C
Q ss_conf             898889999999799899999978897897785430465053146755677887616899999999629869999798-9
Q gi|254780903|r  677 NNNGKMMIRTSKIGQCVIITIADTGIGIPKSALEKIGQPFEPLHNQYDQSIGGFGLGLAISDALTNLHGGRLKIISQE-G  755 (766)
Q Consensus       677 ~~~g~I~i~~~~~~~~v~i~V~D~G~GI~~e~~~~iF~pF~q~~~~~t~~~~GtGLGLaI~k~iVe~hgG~I~v~S~~-g  755 (766)
                      |+||.|.|+....+ .++++|+|+|+|||++.+++||+||+|+++    +.+|+||||||||+||+.|||+|+++|+| |
T Consensus       270 ~~g~~I~I~l~~~~-~~~i~V~D~G~GI~~e~~~~iFerFyR~d~----~~gGsGLGLaIvk~Iv~~HgG~I~l~s~~~g  344 (355)
T PRK10755        270 PEGSNITIKLQEDG-GAVMAVEDEGPGIDESKCGELSKAFVRMDS----RYGGIGLGLSIVSRITQLHHGQFFLQNRQER  344 (355)
T ss_pred             CCCCEEEEEEEECC-CEEEEEEECCCCCCHHHHHHHCCCCCCCCC----CCCCCCHHHHHHHHHHHHCCCEEEEEECCCC
T ss_conf             99976999999779-889999987999897999885588613899----9998758999999999991998999987989


Q ss_pred             CCEEEEEECCC
Q ss_conf             95299997359
Q gi|254780903|r  756 KGTIVTICMPQ  766 (766)
Q Consensus       756 ~Gttf~i~LP~  766 (766)
                      .||+|+|+|||
T Consensus       345 gGt~~~v~LPk  355 (355)
T PRK10755        345 SGTRAWVWLKK  355 (355)
T ss_pred             CEEEEEEEECC
T ss_conf             87899999479


No 25 
>PRK10337 sensor protein QseC; Provisional
Probab=100.00  E-value=0  Score=369.92  Aligned_cols=234  Identities=19%  Similarity=0.269  Sum_probs=205.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             99999999999999998878999999998767522247899999999860346889938999999999999999999977
Q gi|254780903|r  521 ELSIANAKYQVEKERAETANKTKSEFLAKMSHELRTPLNAILGFSEVIKKEIFGELGSVKYYEYAQDIHYSGQHLLNMIN  600 (766)
Q Consensus       521 ~L~~~~~~l~~~~~~ae~an~~k~efla~isHelrtPL~aI~g~~ell~~~~~~~~~~e~~~~~l~~I~~~~~~l~~lI~  600 (766)
                      |+..+...+....++.+++.....+|.+++||||||||++|.+.+|++....   ..++.+++++..|....+||.+||+
T Consensus       212 El~~L~~a~N~ml~rl~~~~~~~r~F~adaAHELRTPLt~i~~~~e~~~~~~---~~~~~~~~~l~~i~~~~~rl~~lv~  288 (446)
T PRK10337        212 EVRPLVEALNQLFARTHAMMVRERRFTSDAAHELRSPLTALKVQTEVAQLSD---DDPQARKKALLQLHSGIDRATRLVD  288 (446)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHCCC---CCHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             8999999999999999999999999999788875168999999999984279---9989999999999999999999999


Q ss_pred             HHHHHHHHHCCCCCCCEEEECHHHHHHHHHHHHHHHHHHCCCEEEEEECCC-CEEEECHHHHHHHHHHHHHHHHHCCCCC
Q ss_conf             767788874198301203316999999999999999984795899980899-7899868999999999886565346898
Q gi|254780903|r  601 NILEMSKIETEKISIDKQNADLIPIINEGIRLIGSSAQSKNIKIEKKIPSE-LFFNADKRIIKKILFPILSNSIKFTNNN  679 (766)
Q Consensus       601 diLd~srieag~~~~~~~~~dl~~~i~~~~~~~~~~~~~k~i~l~~~~~~~-l~v~~D~~~l~QVl~NLi~NAik~t~~~  679 (766)
                      ++|.+||++++.....++++||.+++++++..+.+.+..+++++.++.++. +++.+|+..|+|++.|||.||+||+|+|
T Consensus       289 ~LL~Lar~d~~~~~~~~~~v~l~~l~~~~v~~~~~~a~~~~i~l~~~~~~~~~~~~~d~~ll~~~l~NLl~NAikytp~g  368 (446)
T PRK10337        289 QLLTLSRLDSLDNLQDVAEIPLEDLLQSAVMDIYHTAQQAKIDVRLTLNAHGIKRTGQPLLLSLLVRNLLDNAVRYSPQG  368 (446)
T ss_pred             HHHHHHHHHCCCCCCCCCEECHHHHHHHHHHHHHHHHHHCCCEEEEECCCCCEEEECCHHHHHHHHHHHHHHHHHHCCCC
T ss_conf             99998775446565678175299999999999999999759779996288770671689999999999999999748999


Q ss_pred             CEEEEEEEEECCEEEEEEEECCCCCCHHHHHHHCCCEEECCCCCCCCCCCCCHHHHHHHHHHHHCCCEEEEEEECCCCEE
Q ss_conf             88999999979989999997889789778543046505314675567788761689999999962986999979899529
Q gi|254780903|r  680 GKMMIRTSKIGQCVIITIADTGIGIPKSALEKIGQPFEPLHNQYDQSIGGFGLGLAISDALTNLHGGRLKIISQEGKGTI  759 (766)
Q Consensus       680 g~I~i~~~~~~~~v~i~V~D~G~GI~~e~~~~iF~pF~q~~~~~t~~~~GtGLGLaI~k~iVe~hgG~I~v~S~~g~Gtt  759 (766)
                      |.|.|+....    .++|+|||+|||++.++||||||||.++   +..+|+|||||||++|+++|||+|+++|.|+.|++
T Consensus       369 ~~I~v~~~~~----~l~V~D~G~GIp~e~~~~iFeRFyR~~~---~~~~GsGLGLaIV~~I~~~hgG~i~l~~~~~GG~~  441 (446)
T PRK10337        369 SVVDVTLNAR----NFTVRDNGPGVTPEALARIGERFYRPPG---QTATGSGLGLSIVQRIAKLHGMNVSFGNAEEGGFE  441 (446)
T ss_pred             CEEEEEEECC----EEEEEECCCCCCHHHHHHHCCCCCCCCC---CCCCCCCHHHHHHHHHHHHHCCEEEEEECCCCEEE
T ss_conf             7699999807----7999976999999999874279706999---99998267499999999981998999978989279


Q ss_pred             EEEEC
Q ss_conf             99973
Q gi|254780903|r  760 VTICM  764 (766)
Q Consensus       760 f~i~L  764 (766)
                      |+|+.
T Consensus       442 ~~vt~  446 (446)
T PRK10337        442 AKVSW  446 (446)
T ss_pred             EEEEC
T ss_conf             99969


No 26 
>COG2205 KdpD Osmosensitive K+ channel histidine kinase [Signal transduction mechanisms]
Probab=100.00  E-value=0  Score=368.88  Aligned_cols=223  Identities=25%  Similarity=0.468  Sum_probs=205.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCEE
Q ss_conf             78999999998767522247899999999860346889938999999999999999999977767788874198301203
Q gi|254780903|r  539 ANKTKSEFLAKMSHELRTPLNAILGFSEVIKKEIFGELGSVKYYEYAQDIHYSGQHLLNMINNILEMSKIETEKISIDKQ  618 (766)
Q Consensus       539 an~~k~efla~isHelrtPL~aI~g~~ell~~~~~~~~~~e~~~~~l~~I~~~~~~l~~lI~diLd~srieag~~~~~~~  618 (766)
                      ..+..+-||+.+||||||||++|.|.++.|.... ..++++...+.+..|.+.+++|.++|++||||+||++|-++++++
T Consensus       656 ~E~lRsaLL~sISHDLRTPLt~i~Gaa~tL~~~~-~~l~~~~~aeLl~~I~ees~~L~rlV~NLLdmTRi~sG~~~l~~~  734 (890)
T COG2205         656 RERLRSALLASISHDLRTPLTAIMGAAETLLLDG-EALSPEDRAELLSSIREESERLTRLVTNLLDMTRLQSGGVNLKLD  734 (890)
T ss_pred             HHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHCC-CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCC
T ss_conf             9999999998741024672898861488864234-015937699999999999999999999877677771378641445


Q ss_pred             EECHHHHHHHHHHHHHHHHHHCCCEEEEEECCCCE-EEECHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEEECCEEEEEE
Q ss_conf             31699999999999999998479589998089978-99868999999999886565346898889999999799899999
Q gi|254780903|r  619 NADLIPIINEGIRLIGSSAQSKNIKIEKKIPSELF-FNADKRIIKKILFPILSNSIKFTNNNGKMMIRTSKIGQCVIITI  697 (766)
Q Consensus       619 ~~dl~~~i~~~~~~~~~~~~~k~i~l~~~~~~~l~-v~~D~~~l~QVl~NLi~NAik~t~~~g~I~i~~~~~~~~v~i~V  697 (766)
                      +..+.+++.+++.-++.....+.  +.++++++++ +.+|...+.|||.|||.||+||+|++.+|.|.+....+.++|+|
T Consensus       735 ~~~veEvVg~Al~r~~k~~~~~~--i~v~~~~dl~li~~D~~LieQVLiNLleNA~Kyap~~s~I~I~~~~~~~~v~~~V  812 (890)
T COG2205         735 WVLVEEVVGEALQRLRKRFTGHK--IVVSVPVDLPLIHVDSPLIEQVLINLLENALKYAPPGSEIRINAGVERENVVFSV  812 (890)
T ss_pred             HHHHHHHHHHHHHHHHHHCCCCE--EEEECCCCCCEEECCHHHHHHHHHHHHHHHHHHCCCCCEEEEEEEEECCEEEEEE
T ss_conf             20399999999998663047835--8995588871676478899999999998787428999769999998245699999


Q ss_pred             EECCCCCCHHHHHHHCCCEEECCCCCCCCCCCCCHHHHHHHHHHHHCCCEEEEEEECCCCEEEEEECCC
Q ss_conf             978897897785430465053146755677887616899999999629869999798995299997359
Q gi|254780903|r  698 ADTGIGIPKSALEKIGQPFEPLHNQYDQSIGGFGLGLAISDALTNLHGGRLKIISQEGKGTIVTICMPQ  766 (766)
Q Consensus       698 ~D~G~GI~~e~~~~iF~pF~q~~~~~t~~~~GtGLGLaI~k~iVe~hgG~I~v~S~~g~Gttf~i~LP~  766 (766)
                      .|+|+|||++.+++||+||++.++..  ...|+|||||||++||+.|||+|++++.++.|++|+|+||.
T Consensus       813 ~DeGpGIP~~~~~~IFD~F~r~~~~~--~~~G~GLGLsIc~~iv~ahgG~I~a~~~~~gGa~f~~~LP~  879 (890)
T COG2205         813 IDEGPGIPEGELERIFDKFYRGNKES--ATRGVGLGLAICRGIVEAHGGTISAENNPGGGAIFVFTLPV  879 (890)
T ss_pred             EECCCCCCHHHHHHHHHHHHCCCCCC--CCCCCCCCHHHHHHHHHHCCCEEEEEECCCCCEEEEEEEEC
T ss_conf             71899988567887646541488877--88876622999999999748868987769993589999406


No 27 
>TIGR01386 cztS_silS_copS heavy metal sensor kinase; InterPro: IPR006290   Members of this family contain a sensor histidine kinase domain (IPR003661 from INTERPRO) and a domain found in bacterial signal proteins (IPR003660 from INTERPRO). 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. ; GO: 0000155 two-component sensor activity, 0016775 phosphotransferase activity nitrogenous group as acceptor, 0000160 two-component signal transduction system (phosphorelay), 0007600 sensory perception.
Probab=100.00  E-value=0  Score=364.83  Aligned_cols=245  Identities=23%  Similarity=0.367  Sum_probs=228.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHH
Q ss_conf             44579999999999999999887899999999876752224789999999986034688993899999999999999999
Q gi|254780903|r  517 RQKTELSIANAKYQVEKERAETANKTKSEFLAKMSHELRTPLNAILGFSEVIKKEIFGELGSVKYYEYAQDIHYSGQHLL  596 (766)
Q Consensus       517 ~~~~~L~~~~~~l~~~~~~ae~an~~k~efla~isHelrtPL~aI~g~~ell~~~~~~~~~~e~~~~~l~~I~~~~~~l~  596 (766)
                      ..-.||+++........+|+|.+-+-.++|-|.++|||||||+..++-+|....+.   =..+.|++.+..=...-+||.
T Consensus       235 ~~P~EL~~l~~~FNaML~RLEd~f~rLs~FSaDlAHElRTPltNL~~~tQVaLS~~---R~~~eY~e~l~snlEEl~RL~  311 (483)
T TIGR01386       235 RLPAELRELAQSFNAMLDRLEDAFQRLSQFSADLAHELRTPLTNLLGQTQVALSRP---RSGEEYREVLESNLEELERLS  311 (483)
T ss_pred             CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHCCHHHHHHHHHEEECCC---CCHHHHHHHHHHHHHHHHHHH
T ss_conf             47866899999999998889999999973171456664012544566500200568---898899999986189999999


Q ss_pred             HHHHHHHHHHHHHCCCCCCCEEEECHHHHHH-HHHHHHHHHHHHCC--CEEEEEECCCCEEEECHHHHHHHHHHHHHHHH
Q ss_conf             9977767788874198301203316999999-99999999998479--58999808997899868999999999886565
Q gi|254780903|r  597 NMINNILEMSKIETEKISIDKQNADLIPIIN-EGIRLIGSSAQSKN--IKIEKKIPSELFFNADKRIIKKILFPILSNSI  673 (766)
Q Consensus       597 ~lI~diLd~srieag~~~~~~~~~dl~~~i~-~~~~~~~~~~~~k~--i~l~~~~~~~l~v~~D~~~l~QVl~NLi~NAi  673 (766)
                      ++|+|+|=++|-+.++..++.+.+||++=++ .+.+.+.+.+++++  +.|.++..| ..+.||+..++.+|.|||+||+
T Consensus       312 rMv~DMLFLAraD~~~~~~~~~~ldL~ae~~l~~~~~fE~lAee~~Piv~l~v~G~P-~~~~gD~~lfrRA~sNLLsNA~  390 (483)
T TIGR01386       312 RMVEDMLFLARADNGRLALEREELDLAAELALKVAEYFEPLAEERGPIVSLRVEGEP-AEVRGDALLFRRALSNLLSNAL  390 (483)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCEEEEEEECCC-CEEECCHHHHHHHHHHHHHHHH
T ss_conf             999899989985234567778751278888788887742027678866899983242-0560247888999999999998


Q ss_pred             HCCCCCCEEEEEEEEECCEEEEEEEECCCCCCHHHHHHHCCCEEECCCCCCC-CCCCCCHHHHHHHHHHHHCCCEEEEEE
Q ss_conf             3468988899999997998999999788978977854304650531467556-778876168999999996298699997
Q gi|254780903|r  674 KFTNNNGKMMIRTSKIGQCVIITIADTGIGIPKSALEKIGQPFEPLHNQYDQ-SIGGFGLGLAISDALTNLHGGRLKIIS  752 (766)
Q Consensus       674 k~t~~~g~I~i~~~~~~~~v~i~V~D~G~GI~~e~~~~iF~pF~q~~~~~t~-~~~GtGLGLaI~k~iVe~hgG~I~v~S  752 (766)
                      +|||+||.|+|++....|.+.|.|+|+|.||||+.++||||+|||+|.+.+. +..||||||||||+|++.|||++.|+|
T Consensus       391 rhtp~g~~I~v~~~~~~d~~~~~v~N~G~~Ip~e~L~rLFdRFYR~D~aR~~G~~~g~GLGLAIV~SI~~~HGG~~~aeS  470 (483)
T TIGR01386       391 RHTPAGSTIDVRVERRADEVRVSVENTGDGIPPEHLSRLFDRFYRVDPARSNGSQEGTGLGLAIVRSIMEAHGGRAEAES  470 (483)
T ss_pred             HHCCCCCEEEEEEEECCCEEEEEEECCCCCCCCCCCCCCCCCCCCCCHHHCCCCCCCCCHHHHHHHHHHHHCCCEEEEEE
T ss_conf             60899885899996147756899835879998523565553002676333276645676048999999982398689986


Q ss_pred             ECCCCEEEEEECC
Q ss_conf             9899529999735
Q gi|254780903|r  753 QEGKGTIVTICMP  765 (766)
Q Consensus       753 ~~g~Gttf~i~LP  765 (766)
                      .++.=|+|.+.+|
T Consensus       471 ~~~~~t~F~l~fp  483 (483)
T TIGR01386       471 EADGKTRFKLRFP  483 (483)
T ss_pred             CCCCEEEEEEECC
T ss_conf             4892489876339


No 28 
>TIGR02938 nifL_nitrog nitrogen fixation negative regulator NifL; InterPro: IPR014285   NifL modulates the activity of the nitrogen fixation positive regulator protein NifA, acting as a negative regulator by binding NifA. NifA and NifL are encoded by adjacent genes..
Probab=100.00  E-value=0  Score=358.40  Aligned_cols=463  Identities=17%  Similarity=0.228  Sum_probs=354.5

Q ss_pred             HHHHHHHHCCCCCEEEEECCCCEEEECHHHHHHCCCCHHHCCCCHHHHHH--HHCCCCHHHHHHHHHHHHCCCCEEEEEE
Q ss_conf             99999972259745989768978999788997729994330589889997--6081205899999999724898489999
Q gi|254780903|r  255 ICVETALSRGRCGLWNFNFDNKKFHLSRSMYEIMGIPYENKTLSFRAIAR--LIHYDNKKICEIARSVTGKHVKQLDQIF  332 (766)
Q Consensus       255 ~rl~~al~~a~~GiWd~D~~~~~i~ws~~~~~llG~~~~e~~~s~~~~~~--~vHPdDr~~~~~a~~~~~~~~~~~~~e~  332 (766)
                      +-+|.+++.|++.|=..|+.-+.+|.|++|.++.||.++|..+..+++++  ..+|   +.|...+..+.. .+||.=..
T Consensus         4 e~~RqtVdqAp~AISITDlKANILyaN~AF~~iTGY~~eE~iGkNES~LSn~tTPp---eVYQaLWg~la~-qkPW~G~L   79 (496)
T TIGR02938         4 ELYRQTVDQAPVAISITDLKANILYANDAFSEITGYAKEEVIGKNESVLSNRTTPP---EVYQALWGSLAE-QKPWAGKL   79 (496)
T ss_pred             HHHHHHHHHCCCEEEECCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCH---HHHHHHHHHHHH-CCCCCCCE
T ss_conf             56888662288036431014569999566321558656211125540126858871---799999988630-58986510


Q ss_pred             EEECCCCCEEEEEEEEEEEEECCCEE-EEEEEEECCCHHHHHHHHHHHHHHHHHHHHHHHHHHEEEECCCCEEEEECHHH
Q ss_conf             98869898899889999998379606-99999844617999999999999999999985445515883499699701789
Q gi|254780903|r  333 HMRHASGADIWIQVRAQMMRTISGGM-NIIGIAMDLTEKYHLEKRYAEADQRLSKAIECTSEALVLWDKNDRLVMCNANY  411 (766)
Q Consensus       333 Ri~~~DG~~~Wi~~r~~~i~d~~G~~-~~iGi~~DITErK~ae~~l~ese~rlr~~ie~~~~~i~~~D~~g~i~~~N~~~  411 (766)
                      =-||+||+..=-.....|+-|+.|.+ ||+|.++||||..++|++.+.+...+.++++++|.++++.|..||++.-|+.|
T Consensus        80 lNRrkDg~lYLAeLtvaPvlneaGeT~hflGMHRd~tElh~Leq~V~nQ~l~iE~VV~aaPva~vllD~~gRv~LdN~~y  159 (496)
T TIGR02938        80 LNRRKDGELYLAELTVAPVLNEAGETTHFLGMHRDVTELHRLEQRVANQKLLIEAVVDAAPVAAVLLDEQGRVVLDNLEY  159 (496)
T ss_pred             ECCCCCCCHHHHHHCCCCHHCCCCCCEEEECCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHEECCCCCEEECCHHH
T ss_conf             00011653002220202000146881587325454357889988897646789999878654100056998688167768


Q ss_pred             HHHHCCCHHHHCCCCCH----HHHCCCHHHHHHHHHHHCCCCCCCEEEEEEECCC---EEEEECCEEC------------
Q ss_conf             88839997894289717----8816520137899985211245640589991696---2874223245------------
Q gi|254780903|r  412 QKAYGLPDHVLVPGNAR----SIIQDAQTRPIIEYRTSDPERSQDMSKEIKLADS---RWLQINEWCT------------  472 (766)
Q Consensus       412 ~~~~g~~~~~~~~~~~~----~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~dg---~~~~i~~~~~------------  472 (766)
                      +++.-    ++.-.-|-    +.+.+....+. ...-.........+..+-.+.|   ||+.+..+-.            
T Consensus       160 k~La~----DL~v~epa~~~l~lLre~~~e~~-~~~~~q~~afsn~E~rfD~ggGR~~RWlSc~g~~i~~e~~~ad~fF~  234 (496)
T TIGR02938       160 KKLAS----DLKVEEPAELLLKLLREELAEDL-EELENQEKAFSNKELRFDRGGGRSARWLSCAGRVIRIEEDSADSFFA  234 (496)
T ss_pred             HHHHH----HCCCCCCHHHHHHHHHHHHHHHH-HHHCCCCCEECCCEEEEECCCCCCCCCEEECCCEEEEECCCCCEEEC
T ss_conf             87874----21414417999998508765278-65202110101540354168878850102023235311364011561


Q ss_pred             --CCCCEEEEEEEEEHHHCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             --699789998862010001122322222221100001788998644457999999999999999988789999999987
Q gi|254780903|r  473 --HDGGTISVGTDITLLKHNQAQLRESKRRLKATINDLSTSRQILERQKTELSIANAKYQVEKERAETANKTKSEFLAKM  550 (766)
Q Consensus       473 --~dg~~v~v~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~~~~~l~~~~~~ae~an~~k~efla~i  550 (766)
                        ..+++.-+-.||+.++..++...                          + .+-+.+-++.|+.|   ..|.-|.|. 
T Consensus       235 ~~e~~yLLLti~Dis~lr~~Qe~~R--------------------------l-~aLqAlmAEEE~le---~~rEtl~AA-  283 (496)
T TIGR02938       235 AAEKRYLLLTIDDISELRKKQERAR--------------------------L-SALQALMAEEEKLE---ALRETLSAA-  283 (496)
T ss_pred             CCCCCCEEEEEHHHHHHHHHHHHHH--------------------------H-HHHHHHHHHHHHHH---HHHHHHHHH-
T ss_conf             6899830566364788899999999--------------------------9-99899998998888---876668888-


Q ss_pred             HHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCEEEECHHHHHHHHH
Q ss_conf             67522247899999999860346889938999999999999999999977767788874198301203316999999999
Q gi|254780903|r  551 SHELRTPLNAILGFSEVIKKEIFGELGSVKYYEYAQDIHYSGQHLLNMINNILEMSKIETEKISIDKQNADLIPIINEGI  630 (766)
Q Consensus       551 sHelrtPL~aI~g~~ell~~~~~~~~~~e~~~~~l~~I~~~~~~l~~lI~diLd~srieag~~~~~~~~~dl~~~i~~~~  630 (766)
                      =|-|..|||.|.....+|++++-++.++......++.+..++...++-.....=-      +..-...||+||+++++++
T Consensus       284 Ihrl~gP~NlisaA~~~L~RRlGD~AGn~a~~~~lqqa~~ag~e~~e~L~~~IP~------s~~e~~~pVNlN~~lrdvi  357 (496)
T TIGR02938       284 IHRLQGPLNLISAAISVLERRLGDDAGNDAVAALLQQALAAGREALEALEKVIPQ------SDAEAVVPVNLNQVLRDVI  357 (496)
T ss_pred             HHHHCCCHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCC------CCCCCCCCCCHHHHHHHHH
T ss_conf             8885287107889999863205832379799999999988639999975057887------7244546642778999999


Q ss_pred             HHHHHHHHHCCCEEEEEECCCCE-EEECHHHHHHHHHHHHHHHHHCCCCCC----EEEEEEEEECCEEEEEEEECCCCCC
Q ss_conf             99999998479589998089978-998689999999998865653468988----8999999979989999997889789
Q gi|254780903|r  631 RLIGSSAQSKNIKIEKKIPSELF-FNADKRIIKKILFPILSNSIKFTNNNG----KMMIRTSKIGQCVIITIADTGIGIP  705 (766)
Q Consensus       631 ~~~~~~~~~k~i~l~~~~~~~l~-v~~D~~~l~QVl~NLi~NAik~t~~~g----~I~i~~~~~~~~v~i~V~D~G~GI~  705 (766)
                      .++.+++-..||.+++.....|| |.|-+.+++..|=.|+.|||+.|...+    ...|.++..++-|+++|.|+|||||
T Consensus       358 ~l~T~rLLA~GIvVdW~Pa~~LP~~~G~e~~lRslfK~LvdNAIeaM~~~~~~RREL~i~t~~~~~li~~~i~DsGPGIP  437 (496)
T TIGR02938       358 TLLTERLLAAGIVVDWQPAAVLPAVLGSESRLRSLFKALVDNAIEAMAQKGVKRRELSILTAVEDDLIRVEIEDSGPGIP  437 (496)
T ss_pred             HHHHHHHHHCCCEECCCCCCCCCHHHCCCHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHCCCEEEEEEEECCCCCC
T ss_conf             86105575575415165610162220785257899999999999985307841023101022308568999973587987


Q ss_pred             HHHHHHHCCCEEECCCCCCCCCCCCCHHHHHHHHHHHHCCCEEEEEEECCCCEEEEEECC
Q ss_conf             778543046505314675567788761689999999962986999979899529999735
Q gi|254780903|r  706 KSALEKIGQPFEPLHNQYDQSIGGFGLGLAISDALTNLHGGRLKIISQEGKGTIVTICMP  765 (766)
Q Consensus       706 ~e~~~~iF~pF~q~~~~~t~~~~GtGLGLaI~k~iVe~hgG~I~v~S~~g~Gttf~i~LP  765 (766)
                      ++-.-|+|||||..+++.  +-.|-|.||+.++.||..|+|=|.|+..+-.|+...+.+|
T Consensus       438 ~dlr~kvFEPFFttK~~~--Gr~h~G~GL~vaqeiVa~H~G~i~~D~dy~eGCri~vef~  495 (496)
T TIGR02938       438 ADLRLKVFEPFFTTKASS--GRKHVGMGLAVAQEIVAKHAGLIDVDDDYREGCRIVVEFE  495 (496)
T ss_pred             CCCCEEEECCCCCCCCCC--CCCCCCCCCHHHHHHHHHCCCEEEECCCCCCCCEEEEEEC
T ss_conf             244225236732268887--7842334626889997504987973688877735777623


No 29 
>PRK10815 sensor protein PhoQ; Provisional
Probab=100.00  E-value=0  Score=352.41  Aligned_cols=234  Identities=17%  Similarity=0.238  Sum_probs=205.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             99999999999999998878999999998767522247899999999860346889938999999999999999999977
Q gi|254780903|r  521 ELSIANAKYQVEKERAETANKTKSEFLAKMSHELRTPLNAILGFSEVIKKEIFGELGSVKYYEYAQDIHYSGQHLLNMIN  600 (766)
Q Consensus       521 ~L~~~~~~l~~~~~~ae~an~~k~efla~isHelrtPL~aI~g~~ell~~~~~~~~~~e~~~~~l~~I~~~~~~l~~lI~  600 (766)
                      |+..+...+....++.+.+.....+|++++||||||||++|.|+++.+..+.   ...+   +....+....+||.++|+
T Consensus       244 Ei~~La~~fN~ml~rl~~~~~rqr~F~adaSHELRTPLa~l~~~le~L~~~~---~~~~---~~~~~~le~i~Rl~~li~  317 (484)
T PRK10815        244 ELTSLVRNLNRLLKSERERYDKYRTTLTDLTHSLKTPLAVLQSTLRSLRTEK---MSVS---DAEPVMLEQISRISQQIG  317 (484)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHCCHHHHHHHHHHHHHCCC---CCHH---HHHHHHHHHHHHHHHHHH
T ss_conf             9999999999999999999999999985443643456999999999974699---8878---999999999999999999


Q ss_pred             HHHHHHHHHCCCCCCCEEEECHHHHHHHHHHHHHHHHHHCCCEEEEEECCCCEEEECHHHHHHHHHHHHHHHHHCCCCCC
Q ss_conf             76778887419830120331699999999999999998479589998089978998689999999998865653468988
Q gi|254780903|r  601 NILEMSKIETEKISIDKQNADLIPIINEGIRLIGSSAQSKNIKIEKKIPSELFFNADKRIIKKILFPILSNSIKFTNNNG  680 (766)
Q Consensus       601 diLd~srieag~~~~~~~~~dl~~~i~~~~~~~~~~~~~k~i~l~~~~~~~l~v~~D~~~l~QVl~NLi~NAik~t~~~g  680 (766)
                      ++|+.++++++...+..+.+++..++++++..+...+.+|++.+..++++++.+.+|+..|.|++.||+.||+||++++ 
T Consensus       318 ~lL~~a~~~~~~~~~~~e~~~l~~ll~~l~~~l~~~~~~k~i~l~~~~~~~~~~~gd~~~l~~~l~NLldNAikys~~~-  396 (484)
T PRK10815        318 YYLHRASMRGEGTLLSRELHPVAPLLDNLTSALNKVYQRKGVNISLDISPEISFVGEQNDFMEVMGNVLDNACKYCLEF-  396 (484)
T ss_pred             HHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCEEEEECCCCEEEECCHHHHHHHHHHHHHHHHHHCCCC-
T ss_conf             9999987038986302555669999999999999999964977999648760795578999999999999999728886-


Q ss_pred             EEEEEEEEECCEEEEEEEECCCCCCHHHHHHHCCCEEECCCCCCCCCCCCCHHHHHHHHHHHHCCCEEEEEEECCCCEEE
Q ss_conf             89999999799899999978897897785430465053146755677887616899999999629869999798995299
Q gi|254780903|r  681 KMMIRTSKIGQCVIITIADTGIGIPKSALEKIGQPFEPLHNQYDQSIGGFGLGLAISDALTNLHGGRLKIISQEGKGTIV  760 (766)
Q Consensus       681 ~I~i~~~~~~~~v~i~V~D~G~GI~~e~~~~iF~pF~q~~~~~t~~~~GtGLGLaI~k~iVe~hgG~I~v~S~~g~Gttf  760 (766)
                       |.|+++..++.++|.|+|+|+|||++.+++||+||+|++.+    ..|+||||||||.||+.|||+|+++|.|+.||+|
T Consensus       397 -v~I~~~~~~~~~~I~V~D~GpGIp~e~~~~IFeRF~R~d~~----r~GsGLGLaIvk~Iv~~hgG~I~l~~s~~gG~~f  471 (484)
T PRK10815        397 -VEISARQTDEHLHIVVEDDGPGIPESKRELIFDRGQRVDTL----RPGQGVGLAVAREITEQYEGKIVASESPLGGARM  471 (484)
T ss_pred             -EEEEEEEECCEEEEEEEECCCCCCHHHHHHHCCCCCCCCCC----CCCCCHHHHHHHHHHHHCCCEEEEEECCCCCEEE
T ss_conf             -79999996999999999739999989998624688779999----9985767999999999889989999569992489


Q ss_pred             EEECCC
Q ss_conf             997359
Q gi|254780903|r  761 TICMPQ  766 (766)
Q Consensus       761 ~i~LP~  766 (766)
                      +|++||
T Consensus       472 ~I~F~~  477 (484)
T PRK10815        472 EVIFGR  477 (484)
T ss_pred             EEEECC
T ss_conf             999738


No 30 
>PRK09467 envZ osmolarity sensor protein; Provisional
Probab=100.00  E-value=1.4e-45  Score=347.63  Aligned_cols=225  Identities=22%  Similarity=0.347  Sum_probs=186.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             99999999999999998878999999998767522247899999999860346889938999999999999999999977
Q gi|254780903|r  521 ELSIANAKYQVEKERAETANKTKSEFLAKMSHELRTPLNAILGFSEVIKKEIFGELGSVKYYEYAQDIHYSGQHLLNMIN  600 (766)
Q Consensus       521 ~L~~~~~~l~~~~~~ae~an~~k~efla~isHelrtPL~aI~g~~ell~~~~~~~~~~e~~~~~l~~I~~~~~~l~~lI~  600 (766)
                      |+.++.+...+..++.++....+.+|++++||||||||+.|.+++|+|..+      ++   ...+.|.+..++|.++|+
T Consensus       209 Ev~~l~~aFN~M~~~l~~~~~~r~~~la~vSHeLRTPLT~irl~~e~l~~~------~~---~~~~~i~~~i~~m~~li~  279 (437)
T PRK09467        209 EVRSVTRAFNQMSAGIKQLEDDRALLMAGVSHDLRTPLTRIRLATEMMSEE------DG---YLAESINKDIEECNAIIE  279 (437)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHCCCC------HH---HHHHHHHHHHHHHHHHHH
T ss_conf             999999999999999999999999999753444327899999998746753------18---999999999999999999


Q ss_pred             HHHHHHHHHCCCCCCCEEEECHHHHHHHHHHHHHHHHHHCCCEEEEEECCC-CEEEECHHHHHHHHHHHHHHHHHCCCCC
Q ss_conf             767788874198301203316999999999999999984795899980899-7899868999999999886565346898
Q gi|254780903|r  601 NILEMSKIETEKISIDKQNADLIPIINEGIRLIGSSAQSKNIKIEKKIPSE-LFFNADKRIIKKILFPILSNSIKFTNNN  679 (766)
Q Consensus       601 diLd~srieag~~~~~~~~~dl~~~i~~~~~~~~~~~~~k~i~l~~~~~~~-l~v~~D~~~l~QVl~NLi~NAik~t~~~  679 (766)
                      ++|+|+|.+.   ....+++|+++++++++....    ..+..+..+.++. ..+.+|+.+|+|+|.||+.||+||+  +
T Consensus       280 ~~L~~~r~~~---~~~~~~~dl~~l~~~~~~~~~----~~~~~i~~~~~~~~~~v~~d~~~l~r~l~NLi~NA~ky~--~  350 (437)
T PRK09467        280 QFIDYLRTDQ---EMPMEMADLNALLGEVIAAES----GYEREIETALYPGPIEVPMNPIAIKRALANLVVNAARYG--N  350 (437)
T ss_pred             HHHHHHHHCC---CCCCCCCCHHHHHHHHHHHHH----CCCCEEEEECCCCCEEEEECHHHHHHHHHHHHHHHHHCC--C
T ss_conf             9999986215---566751159999999999875----549838996288764898579999999999999887607--9


Q ss_pred             CEEEEEEEEECCEEEEEEEECCCCCCHHHHHHHCCCEEECCCCCCCCCCCCCHHHHHHHHHHHHCCCEEEEEEECCCCEE
Q ss_conf             88999999979989999997889789778543046505314675567788761689999999962986999979899529
Q gi|254780903|r  680 GKMMIRTSKIGQCVIITIADTGIGIPKSALEKIGQPFEPLHNQYDQSIGGFGLGLAISDALTNLHGGRLKIISQEGKGTI  759 (766)
Q Consensus       680 g~I~i~~~~~~~~v~i~V~D~G~GI~~e~~~~iF~pF~q~~~~~t~~~~GtGLGLaI~k~iVe~hgG~I~v~S~~g~Gtt  759 (766)
                      |.|.|++...++.+.|+|.|+|+|||++.+++||+||+|++++.  ..+||||||||||+||+.|||+|+++|.++.|++
T Consensus       351 ~~i~V~~~~~~~~~~i~V~D~GpGI~~e~l~~if~pF~R~d~sR--~~~GsGLGLaIv~~Iv~~HgG~i~l~~~~~gGl~  428 (437)
T PRK09467        351 GWIKVSSGTEGNRAWFQVEDNGPGIPEEQIKHLFQPFTRGDSAR--GSSGTGLGLAIVKRIVDQHQGKVELGNREEGGLS  428 (437)
T ss_pred             CEEEEEEEEECCEEEEEEEECCCCCCHHHHHHHCCCCCCCCCCC--CCCCEEHHHHHHHHHHHHCCCEEEEEECCCCCEE
T ss_conf             83999999868999999997599999899987616852188899--9997728899999999986998999977999459


Q ss_pred             EEEECC
Q ss_conf             999735
Q gi|254780903|r  760 VTICMP  765 (766)
Q Consensus       760 f~i~LP  765 (766)
                      |+|+||
T Consensus       429 ~~i~lP  434 (437)
T PRK09467        429 ARAWLP  434 (437)
T ss_pred             EEEEEC
T ss_conf             999971


No 31 
>PRK09776 putative sensor protein; Provisional
Probab=100.00  E-value=4.1e-43  Score=329.22  Aligned_cols=369  Identities=15%  Similarity=0.164  Sum_probs=273.8

Q ss_pred             HHHHHHHHHHHHHHCC---CCCEEEEECCCCCEEEECCCHHHHCCCCHHHHCCCCHHHHCCCCCCCHHHH----HCCCCH
Q ss_conf             9999999988531017---897899996998089971420555199788960761043205443320232----115310
Q gi|254780903|r  111 KAESMLGQLLAKTRFL---SESFILLAQPNELVFASSTKNSHYIGKKIGEIIPELSRSRSRSKTVQMSEA----SLDQQP  183 (766)
Q Consensus       111 ~ae~~L~~~~~~~~~~---~~~~i~i~d~~g~i~~~n~~~~~~~G~~~~~~~~~~~~~~~~~~~~~~~~~----~l~~~~  183 (766)
                      +..+.|.+++.++|..   +...+++++.+|+++.+|++.++++||+.+++.+.+..+..+|+.......    .+.|..
T Consensus       294 ~~~~~l~~SE~rfR~~~e~saiGmAlV~~dGr~l~VN~alc~mlGYs~~ELl~ltf~diThPdDl~~dl~~~~~LlaGei  373 (1116)
T PRK09776        294 AERKHISESETRFRNAMEYSAIGMALVGTEGQWLQVNKALCQFLGYSQEELRGLTFQQLTWPEDLNKDLQQVEKLLSGEI  373 (1116)
T ss_pred             HHHHHHHHHHHHHHHHHHHCCCCEEEECCCCCEEEECHHHHHHHCCCHHHHHHCCHHHHCCCCCHHHHHHHHHHHHCCCC
T ss_conf             88888776799999998746664699868981898169999884989999852989881696217778999999976996


Q ss_pred             -HEEEE-EECCCCCCEEEEEEECCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             -00012-3315778259999742321012345565545687887899999999888899999999999999999999997
Q gi|254780903|r  184 -YHVLS-VNLPHNSGSILIINSRVPLLRLWREEVTLEVVFFSIISALLLFILFSYYRQAKKNKENDTILLEANICVETAL  261 (766)
Q Consensus       184 -~~~~~-~~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~a~~~dit~~r~ae~~l~ese~rl~~al  261 (766)
                       .+... +-.+.++..+|+........+...    .+.            .+++...|||++|++|++++++++|++.+.
T Consensus       374 ~~y~lEKRyirkDG~~vW~~ltvSlvRd~~G----~p~------------~fI~~v~DIterK~aE~~lr~l~erl~la~  437 (1116)
T PRK09776        374 NSYSMEKRYYNRDGDVVWALLAVSLVRDTDG----TPL------------YFIAQIEDINELKRTEQVNERLMERITLAN  437 (1116)
T ss_pred             CCCCCEEEEECCCCCEEEEEEEEEEEECCCC----CEE------------EEEEEEEECHHHHHHHHHHHHHHHHHHHHH
T ss_conf             6454112467369979999989999976999----844------------899999733377999999999999999998


Q ss_pred             HCCCCCEEEEECCCCEEEECHHHHHHCCCCHHHCCCCHHHHHHHHCCCCHHHHHHHHHHHHCCCCEEEEEEEEECCCCCE
Q ss_conf             22597459897689789997889977299943305898899976081205899999999724898489999988698988
Q gi|254780903|r  262 SRGRCGLWNFNFDNKKFHLSRSMYEIMGIPYENKTLSFRAIARLIHYDNKKICEIARSVTGKHVKQLDQIFHMRHASGAD  341 (766)
Q Consensus       262 ~~a~~GiWd~D~~~~~i~ws~~~~~llG~~~~e~~~s~~~~~~~vHPdDr~~~~~a~~~~~~~~~~~~~e~Ri~~~DG~~  341 (766)
                      +++++|+|+||+.++.++||+++++|+|++++. ..+.+.|.+.+||||+..+....+.......+|+.|||++++||++
T Consensus       438 ea~~iGiwe~d~~~~~i~~~~r~~~l~g~~~~~-~~~~~~w~~~ihPdD~~~v~~~~~~~l~~~~~~d~E~Rl~~~dG~~  516 (1116)
T PRK09776        438 EAGGIGIWEWDLKPNIISWDKRMFELYEIPPHI-KPNWQVWYACLHPEDRQRVEKEIRDALQGRSPFKLEFRIVVPDGEI  516 (1116)
T ss_pred             HHCCCCEEEEECCCCCEECCHHHHHHHCCCCCC-CCCHHHHHHHCCHHHHHHHHHHHHHHHHCCCCCCCEEEEECCCCCE
T ss_conf             624766355205665021137899984888222-6688999872391568999999999971588756046788479978


Q ss_pred             EEEEEEEEEEEECCCEE-EEEEEEECCCHHHHHHHHHHHHHHHHHHHHHHHHHHEEEECCCCEEEEECHHHHHHHCCCHH
Q ss_conf             99889999998379606-99999844617999999999999999999985445515883499699701789888399978
Q gi|254780903|r  342 IWIQVRAQMMRTISGGM-NIIGIAMDLTEKYHLEKRYAEADQRLSKAIECTSEALVLWDKNDRLVMCNANYQKAYGLPDH  420 (766)
Q Consensus       342 ~Wi~~r~~~i~d~~G~~-~~iGi~~DITErK~ae~~l~ese~rlr~~ie~~~~~i~~~D~~g~i~~~N~~~~~~~g~~~~  420 (766)
                      +|++.++.+++|++|.+ +++|+..||||||++|++|.+++++++..+++++++++.+|.+++++++|+++++++||+.+
T Consensus       517 r~i~~~a~~~~d~~G~~~r~~G~~~DITe~K~~eeaL~e~~erl~~~l~si~d~vi~tD~~~ri~~~Npaae~~tG~~~~  596 (1116)
T PRK09776        517 RHIRALANRVLNKDGEVERLLGINMDMTEVRQLNEALFEEKERLHITLDSIGEAVVCTDAAMKVTFMNPVAEKMTGWTQE  596 (1116)
T ss_pred             EEEEEEEEEEECCCCCEEEEEEEEECCCHHHHHHHHHHHHHHHHHHHHHCCCCEEEEECCCCCEEEECHHHHHHHCCCHH
T ss_conf             99986214898689988988731323207789999999999999999834022489973788678886999998298879


Q ss_pred             HHCCCCCHHHHC--CCHHHHH----HHHHHHCCCCC-CCEEEEEEECCCEEE--E--ECCEECCCC---CEEEEEEEEEH
Q ss_conf             942897178816--5201378----99985211245-640589991696287--4--223245699---78999886201
Q gi|254780903|r  421 VLVPGNARSIIQ--DAQTRPI----IEYRTSDPERS-QDMSKEIKLADSRWL--Q--INEWCTHDG---GTISVGTDITL  486 (766)
Q Consensus       421 ~~~~~~~~~~~~--~~~~~~~----~~~~~~~~~~~-~~~~~e~~~~dg~~~--~--i~~~~~~dg---~~v~v~~~i~~  486 (766)
                      +..+......+.  .....+.    ........... .......+..+|...  +  +++.+..+|   |.|.+..|||+
T Consensus       597 e~~G~~~~~v~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~l~~~~G~~~~v~~s~~pi~~~~g~~~g~V~v~~Dit~  676 (1116)
T PRK09776        597 EALGVPLLTVLHITFGDNGPLMENPVEICLADTSRSYLEQDVVLHSRSGGSYDVQYSIAPLSTLDGENIGSVLVFQDVTE  676 (1116)
T ss_pred             HHCCCCHHHHHHCCCCCCCHHHHHHHHHHHHHCCCCCCCCCEEEEECCCCEEEEEEEECCCCCCCCCEEEEEEEECCHHH
T ss_conf             98499878970036644211112199999740787331235368826996899997304513477855447985201229


Q ss_pred             HHCCCCCCCC
Q ss_conf             0001122322
Q gi|254780903|r  487 LKHNQAQLRE  496 (766)
Q Consensus       487 ~~~~~~~~~~  496 (766)
                      .|..+.++..
T Consensus       677 ~k~~~~~l~~  686 (1116)
T PRK09776        677 SRAMLRQLSY  686 (1116)
T ss_pred             HHHHHHHHHH
T ss_conf             9999999987


No 32 
>COG4191 Signal transduction histidine kinase regulating C4-dicarboxylate transport system [Signal transduction mechanisms]
Probab=100.00  E-value=5.2e-43  Score=328.50  Aligned_cols=249  Identities=22%  Similarity=0.377  Sum_probs=213.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--HHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHH
Q ss_conf             1788998644457999999999999999988789--99999998767522247899999999860346889938999999
Q gi|254780903|r  508 LSTSRQILERQKTELSIANAKYQVEKERAETANK--TKSEFLAKMSHELRTPLNAILGFSEVIKKEIFGELGSVKYYEYA  585 (766)
Q Consensus       508 ~~~~~~~~~~~~~~L~~~~~~l~~~~~~ae~an~--~k~efla~isHelrtPL~aI~g~~ell~~~~~~~~~~e~~~~~l  585 (766)
                      +......+...+.+.++++..++...+.+-+|++  +.+++.+.+|||||+||.+|..|++-... +...--.+...+.+
T Consensus       347 L~~~n~~l~~EIaer~~ae~~LR~~QdeLvQA~kLA~LGQmSA~iaHElNQPLaaiRt~adna~~-lLergr~e~a~~Nl  425 (603)
T COG4191         347 LTRANARLQAEIAEREQAEAALRRAQDELVQAGKLAALGQMSAGIAHELNQPLAAIRTYADNARL-LLERGRTEEARENL  425 (603)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHH-HHHCCCHHHHHHHH
T ss_conf             88766888889998887899999878999987778998888888788743708999867778999-98758867777679


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCEEEECHHHHHHHHHHHHHHHHHHCCCEEEEEECC-CCEEEECHHHHHHH
Q ss_conf             99999999999997776778887419830120331699999999999999998479589998089-97899868999999
Q gi|254780903|r  586 QDIHYSGQHLLNMINNILEMSKIETEKISIDKQNADLIPIINEGIRLIGSSAQSKNIKIEKKIPS-ELFFNADKRIIKKI  664 (766)
Q Consensus       586 ~~I~~~~~~l~~lI~diLd~srieag~~~~~~~~~dl~~~i~~~~~~~~~~~~~k~i~l~~~~~~-~l~v~~D~~~l~QV  664 (766)
                      ..|..-.+||..++..+-.|+|    |-.-..+++.+.++|++++.+++++....+..+..+.++ +++|.+++.+|+||
T Consensus       426 ~~I~~LteRma~It~~Lk~FAr----k~~~a~~~v~l~~ai~~Al~ll~~R~~~~~~~l~~~~~~~~~~V~~~~iRLeQV  501 (603)
T COG4191         426 ERISALTERMAAITAHLKSFAR----KSRDAAGPVSLREAIEGALELLRGRLRAAGVELELDLPDAPLWVMANEIRLEQV  501 (603)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHC----CCCCCCCCCCHHHHHHHHHHHHHHHHHCCCCEEECCCCCCCCEEECCHHHHHHH
T ss_conf             9999999999889999999833----676666776579999999999887641367626504898775564132209999


Q ss_pred             HHHHHHHHHHCC--CCCCEEEEEEEEECCEEEEEEEECCCCCCHHHHHHHCCCEEECCCCCCCCCC-CCCHHHHHHHHHH
Q ss_conf             999886565346--8988899999997998999999788978977854304650531467556778-8761689999999
Q gi|254780903|r  665 LFPILSNSIKFT--NNNGKMMIRTSKIGQCVIITIADTGIGIPKSALEKIGQPFEPLHNQYDQSIG-GFGLGLAISDALT  741 (766)
Q Consensus       665 l~NLi~NAik~t--~~~g~I~i~~~~~~~~v~i~V~D~G~GI~~e~~~~iF~pF~q~~~~~t~~~~-GtGLGLaI~k~iV  741 (766)
                      |.|||+||++++  ++.++|.|++...++.|+|+|+|||+||||+.+.++|+|||     |||+.+ |.||||+||+.|+
T Consensus       502 LvNLl~NALDA~~~~~~~~i~i~~~~~~~~v~l~VrDnGpGi~~e~~~~lFePF~-----TtK~~~~GLGLGLaIS~~i~  576 (603)
T COG4191         502 LVNLLQNALDAMAGQEDRRLSIRAQREGGQVVLTVRDNGPGIAPEALPHLFEPFF-----TTKPVGKGLGLGLAISQNIA  576 (603)
T ss_pred             HHHHHHHHHHHHCCCCCCEEEEEEEECCCEEEEEECCCCCCCCHHHHHHHCCCCC-----CCCCCCCCCCHHHHHHHHHH
T ss_conf             9999998999845887871699987159869999826999989789986137750-----36766677560289899899


Q ss_pred             HHCCCEEEEEEECCCCEEEEEECCC
Q ss_conf             9629869999798995299997359
Q gi|254780903|r  742 NLHGGRLKIISQEGKGTIVTICMPQ  766 (766)
Q Consensus       742 e~hgG~I~v~S~~g~Gttf~i~LP~  766 (766)
                      .-+||+|.+.+.++.|+.|+|+||+
T Consensus       577 ~d~GGsL~v~n~~~~Ga~F~i~L~~  601 (603)
T COG4191         577 RDLGGSLEVANHPEGGASFTIELRR  601 (603)
T ss_pred             HHHCCEEEEECCCCCCEEEEEEEEC
T ss_conf             9818807940278884489999615


No 33 
>COG4251 Bacteriophytochrome (light-regulated signal transduction histidine kinase) [Signal transduction mechanisms]
Probab=100.00  E-value=2.4e-43  Score=330.91  Aligned_cols=231  Identities=23%  Similarity=0.353  Sum_probs=209.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             99999999998878999999998767522247899999999860346889938999999999999999999977767788
Q gi|254780903|r  527 AKYQVEKERAETANKTKSEFLAKMSHELRTPLNAILGFSEVIKKEIFGELGSVKYYEYAQDIHYSGQHLLNMINNILEMS  606 (766)
Q Consensus       527 ~~l~~~~~~ae~an~~k~efla~isHelrtPL~aI~g~~ell~~~~~~~~~~e~~~~~l~~I~~~~~~l~~lI~diLd~s  606 (766)
                      +.+......+|.+|.....|.+.+|||+++||+.|.+|++++.+.+.+.+ ++++++++..|.+....|..||+|+|.||
T Consensus       508 eela~l~r~lersn~el~~f~yv~sHdlqePl~~I~~~a~lL~~~~~~~~-d~~~~~~i~~~~~~~~~~~~lidd~l~~s  586 (750)
T COG4251         508 EELAQLRRELERSNAELRAFAYVASHDLQEPLRQISNYAQLLSERYSDAL-DEEAKEFITFISRLTSLMQQLIDDLLTYS  586 (750)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCC-CHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             99998998876515899999998610466799999999976663436665-75889999999999999999999774231


Q ss_pred             HHHCCCCCCCEEEECHHHHHHHHHHHHHHHHHHCCCEEEEEECCCCE-EEECHHHHHHHHHHHHHHHHHCC-CCCCEEEE
Q ss_conf             87419830120331699999999999999998479589998089978-99868999999999886565346-89888999
Q gi|254780903|r  607 KIETEKISIDKQNADLIPIINEGIRLIGSSAQSKNIKIEKKIPSELF-FNADKRIIKKILFPILSNSIKFT-NNNGKMMI  684 (766)
Q Consensus       607 rieag~~~~~~~~~dl~~~i~~~~~~~~~~~~~k~i~l~~~~~~~l~-v~~D~~~l~QVl~NLi~NAik~t-~~~g~I~i  684 (766)
                      ++  |......+++|+.+++++++..+.....+.++.+.+.  + +| |.+|+.++.||+.|||.||+||. |++..|.|
T Consensus       587 ~l--~~~~~~l~~td~~~vv~~vl~~l~~ri~dtgaei~i~--~-lp~v~~d~~~l~qv~~NLi~Naik~~~~e~~~i~I  661 (750)
T COG4251         587 KL--GLTEAPLQPTDVQKVVDKVLLELSQRIADTGAEIRIA--P-LPVVAADATQLGQVFQNLIANAIKFGGPENPDIEI  661 (750)
T ss_pred             HH--CCCCCCCCCCCHHHHHHHHHHHCCCCCCCCCCEEEEC--C-CCEEECCHHHHHHHHHHHHHHHEECCCCCCCCEEE
T ss_conf             20--5545777775267899999973453112565247862--5-64464088899999999876552107888981588


Q ss_pred             EEEEECCEEEEEEEECCCCCCHHHHHHHCCCEEECCCCCCCCCCCCCHHHHHHHHHHHHCCCEEEEEEECCCCEEEEEEC
Q ss_conf             99997998999999788978977854304650531467556778876168999999996298699997989952999973
Q gi|254780903|r  685 RTSKIGQCVIITIADTGIGIPKSALEKIGQPFEPLHNQYDQSIGGFGLGLAISDALTNLHGGRLKIISQEGKGTIVTICM  764 (766)
Q Consensus       685 ~~~~~~~~v~i~V~D~G~GI~~e~~~~iF~pF~q~~~~~t~~~~GtGLGLaI~k~iVe~hgG~I~v~S~~g~Gttf~i~L  764 (766)
                      ++...++.++|.|+|||+||.++..+|||.+|.|.++  +.++.|||+||+|||+|+|.|+|+|||||++|+|+||.|+|
T Consensus       662 ~~~r~ed~~t~sV~dng~Gi~~a~~~riF~iFqRl~s--~~~y~gtG~GL~I~kkI~e~H~G~i~vEs~~gEgsTF~f~l  739 (750)
T COG4251         662 SAERQEDEWTFSVRDNGIGIDPAYFERIFVIFQRLHS--RDEYLGTGLGLAICKKIAERHQGRIWVESTPGEGSTFYFTL  739 (750)
T ss_pred             EEECCCCCEEEEECCCCCCCCHHHHHHHHHHHHHCCC--HHHHCCCCCCHHHHHHHHHHHCCEEEEEECCCCCEEEEEEE
T ss_conf             5332587307985478777698999888998870375--65514777338999999998484588860478741689984


Q ss_pred             C
Q ss_conf             5
Q gi|254780903|r  765 P  765 (766)
Q Consensus       765 P  765 (766)
                      |
T Consensus       740 p  740 (750)
T COG4251         740 P  740 (750)
T ss_pred             E
T ss_conf             0


No 34 
>COG3852 NtrB Signal transduction histidine kinase, nitrogen specific [Signal transduction mechanisms]
Probab=100.00  E-value=9.1e-41  Score=312.27  Aligned_cols=325  Identities=15%  Similarity=0.242  Sum_probs=239.9

Q ss_pred             HHHHHHHHHHEEEECCCCEEEEECHHHHHHHCCCHHHHCCCCCHHHHCCCHHHHHHHHHHHCCCCCCCEEEEEEEC-CCE
Q ss_conf             9999854455158834996997017898883999789428971788165201378999852112456405899916-962
Q gi|254780903|r  385 SKAIECTSEALVLWDKNDRLVMCNANYQKAYGLPDHVLVPGNARSIIQDAQTRPIIEYRTSDPERSQDMSKEIKLA-DSR  463 (766)
Q Consensus       385 r~~ie~~~~~i~~~D~~g~i~~~N~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~-dg~  463 (766)
                      ..++++++..+.+.|.++.+.|+|++++.+|+.+..-+.+.+ ...+.+....-...-............++..+. +|.
T Consensus        10 ~~~Ln~~~~pVl~vd~~~~i~yaN~aAe~~~~~Sa~~L~~~~-l~~l~~~gs~ll~ll~q~~~~~~~~~~~~v~l~~~g~   88 (363)
T COG3852          10 GAILNNLINPVLLVDDELAIHYANPAAEQLLAVSARRLAGTR-LSELLPFGSLLLSLLDQVLERGQPVTEYEVTLVILGR   88 (363)
T ss_pred             HHHHHCCCCCEEEECCCCCEEECCHHHHHHHHHHHHHHHCCC-HHHHCCCCCHHHHHHHHHHHHCCCCCCCEEEEEECCC
T ss_conf             768745578569982778289608889999997788882487-7887177728899998999835885101024420786


Q ss_pred             --EEEECCE--ECCCCCEEEEEEEEEHHHCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             --8742232--456997899988620100011223222222211000017889986444579999999999999999887
Q gi|254780903|r  464 --WLQINEW--CTHDGGTISVGTDITLLKHNQAQLRESKRRLKATINDLSTSRQILERQKTELSIANAKYQVEKERAETA  539 (766)
Q Consensus       464 --~~~i~~~--~~~dg~~v~v~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~~~~~l~~~~~~ae~a  539 (766)
                        .+.....  ...+|..+-...-+                          .+         ...+.+   ++.+  -.+
T Consensus        89 ~~~v~~~v~~v~~~~G~vlle~~~~--------------------------~~---------~~ridr---e~~q--~a~  128 (363)
T COG3852          89 SHIVDLTVAPVPEEPGSVLLEFHPR--------------------------DM---------QRRLDR---EQTQ--HAQ  128 (363)
T ss_pred             CCEEEEEEEECCCCCCEEEEEECHH--------------------------HH---------HHHHHH---HHHH--HHH
T ss_conf             5237899862268997489995325--------------------------77---------767669---9998--888


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCEEE
Q ss_conf             89999999987675222478999999998603468899389999999999999999999777677888741983012033
Q gi|254780903|r  540 NKTKSEFLAKMSHELRTPLNAILGFSEVIKKEIFGELGSVKYYEYAQDIHYSGQHLLNMINNILEMSKIETEKISIDKQN  619 (766)
Q Consensus       540 n~~k~efla~isHelrtPL~aI~g~~ell~~~~~~~~~~e~~~~~l~~I~~~~~~l~~lI~diLd~srieag~~~~~~~~  619 (766)
                      +++...+..+.+||++|||..|.|.++||.....+    +..++|.+.|.+.++|+.+|++.+.-||-    ....+..+
T Consensus       129 ~~a~~~L~r~LAHEIKNPL~GiRGAAQLLe~~lpd----~~~~~lt~lIieE~DRl~~LVDRme~~~~----~rp~~r~~  200 (363)
T COG3852         129 QRAVKGLVRGLAHEIKNPLGGIRGAAQLLERALPD----EALRELTQLIIEEADRLRNLVDRLEVLGP----QRPGDRVP  200 (363)
T ss_pred             HHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHCCC----HHHHHHHHHHHHHHHHHHHHHHHHHHCCC----CCCCCCCC
T ss_conf             88999999877887228531014499999745898----67789999999999999999999875087----89855354


Q ss_pred             ECHHHHHHHHHHHHHHHHHHCCCEEEEEECCCCE-EEECHHHHHHHHHHHHHHHHHCCC----CCCEEEEEEEEEC----
Q ss_conf             1699999999999999998479589998089978-998689999999998865653468----9888999999979----
Q gi|254780903|r  620 ADLIPIINEGIRLIGSSAQSKNIKIEKKIPSELF-FNADKRIIKKILFPILSNSIKFTN----NNGKMMIRTSKIG----  690 (766)
Q Consensus       620 ~dl~~~i~~~~~~~~~~~~~k~i~l~~~~~~~l~-v~~D~~~l~QVl~NLi~NAik~t~----~~g~I~i~~~~~~----  690 (766)
                      ++++++++.+..++...+.. +|.|.-+++|++| +++|+.+|.|||+||+.||..+..    ++|+|+++++..-    
T Consensus       201 ~NIH~VLerV~~lv~~e~~~-~i~l~rdYDPSLP~v~~d~DqliQv~LNlVrNAaqA~~~~~~~~g~I~LrTR~~~q~~i  279 (363)
T COG3852         201 VNIHEVLERVRALVEAEFAD-NVRLIRDYDPSLPEVLGDRDQLIQVFLNLVRNAAQALGGRADEGGEIILRTRTGIQLTI  279 (363)
T ss_pred             CHHHHHHHHHHHHHHCCCCC-CEEEEECCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCCEEEEEECCCEEEEC
T ss_conf             31999999999998543677-55885027998853236989999999999999999716778778569997224258871


Q ss_pred             ------CEEEEEEEECCCCCCHHHHHHHCCCEEECCCCCCCCCCCCCHHHHHHHHHHHHCCCEEEEEEECCCCEEEEEEC
Q ss_conf             ------98999999788978977854304650531467556778876168999999996298699997989952999973
Q gi|254780903|r  691 ------QCVIITIADTGIGIPKSALEKIGQPFEPLHNQYDQSIGGFGLGLAISDALTNLHGGRLKIISQEGKGTIVTICM  764 (766)
Q Consensus       691 ------~~v~i~V~D~G~GI~~e~~~~iF~pF~q~~~~~t~~~~GtGLGLaI~k~iVe~hgG~I~v~S~~g~Gttf~i~L  764 (766)
                            -.+.++|.|||+|||++.++++|.||.      |.+.+||||||+|+++||..|||.|+++|.||. |+|+|.|
T Consensus       280 ~g~r~rl~l~leViDNGPGVP~~L~~~lF~P~V------s~r~~GsGLGLala~~li~qH~G~Ie~~S~Pg~-T~Frvll  352 (363)
T COG3852         280 AGTRYRLALPLEVIDNGPGVPPDLQDHLFYPMV------SGREGGTGLGLALAQNLIDQHGGKIEFDSWPGR-TVFRVLL  352 (363)
T ss_pred             CCCEEEEEEEEEEECCCCCCCHHHHHHCCCCCC------CCCCCCCCCCHHHHHHHHHHCCCEEEEECCCCC-EEEEEEE
T ss_conf             674246631169861899998678643002302------068898661489999989852978987426894-5899986


Q ss_pred             CC
Q ss_conf             59
Q gi|254780903|r  765 PQ  766 (766)
Q Consensus       765 P~  766 (766)
                      |-
T Consensus       353 P~  354 (363)
T COG3852         353 PI  354 (363)
T ss_pred             EC
T ss_conf             33


No 35 
>COG5000 NtrY Signal transduction histidine kinase involved in nitrogen fixation and metabolism regulation [Signal transduction mechanisms]
Probab=100.00  E-value=5.2e-38  Score=292.37  Aligned_cols=332  Identities=19%  Similarity=0.283  Sum_probs=253.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHEEEECCCCEEEEECHHHHHHHCCCHHHHCCCCCHHHHCCCHHHHHHHHHHHCCCCCC
Q ss_conf             99999999999999999854455158834996997017898883999789428971788165201378999852112456
Q gi|254780903|r  372 HLEKRYAEADQRLSKAIECTSEALVLWDKNDRLVMCNANYQKAYGLPDHVLVPGNARSIIQDAQTRPIIEYRTSDPERSQ  451 (766)
Q Consensus       372 ~ae~~l~ese~rlr~~ie~~~~~i~~~D~~g~i~~~N~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  451 (766)
                      ++..++.++.+.+..+++..+.|++.+|.+|++..+|+..++++|.|..++.+.. ...+.|.-.....+.  ... ...
T Consensus       360 ~ak~~~e~rr~f~E~VLsgvtaGVi~~d~~g~i~t~N~~ae~~l~~~~~~~~G~~-lsa~ap~~~~vf~~~--~a~-~~~  435 (712)
T COG5000         360 RAKDALEQRRRFLEAVLSGLTAGVIGFDNRGCITTVNPSAEQILGKPFDQLLGQS-LSAIAPELEEVFAEA--GAA-ART  435 (712)
T ss_pred             HHHHHHHHHHHHHHHHHHCCCEEEEEECCCCEEEEECCHHHHHHCCCHHHHHCHH-HHHHHHHHHHHHHHH--HHH-CCC
T ss_conf             8788899999889999815850389974787077626017888468706764402-664213789999976--540-387


Q ss_pred             CEEEEEEEC---CCEEEEECCEEC---CCCCEEEEEEEEEHHHCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHH
Q ss_conf             405899916---962874223245---69978999886201000112232222222110000178899864445799999
Q gi|254780903|r  452 DMSKEIKLA---DSRWLQINEWCT---HDGGTISVGTDITLLKHNQAQLRESKRRLKATINDLSTSRQILERQKTELSIA  525 (766)
Q Consensus       452 ~~~~e~~~~---dg~~~~i~~~~~---~dg~~v~v~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~~  525 (766)
                      ....++.+.   +.+-+.+...+.   .++|+|.+.-|||++-..+.                                 
T Consensus       436 ~~~~ev~~~r~g~~rtl~Vq~t~~~~d~~~gyVvt~DDITdLV~AQR---------------------------------  482 (712)
T COG5000         436 DKRVEVKLAREGEERTLNVQATREPEDNGNGYVVTFDDITDLVIAQR---------------------------------  482 (712)
T ss_pred             CCCEEEECCCCCCCEEEEEEEEECCCCCCCCEEEEECCHHHHHHHHH---------------------------------
T ss_conf             74201000147874156667532144468856999635089999999---------------------------------


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCH--HHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             99999999999887899999999876752224789999999986034688993--8999999999999999999977767
Q gi|254780903|r  526 NAKYQVEKERAETANKTKSEFLAKMSHELRTPLNAILGFSEVIKKEIFGELGS--VKYYEYAQDIHYSGQHLLNMINNIL  603 (766)
Q Consensus       526 ~~~l~~~~~~ae~an~~k~efla~isHelrtPL~aI~g~~ell~~~~~~~~~~--e~~~~~l~~I~~~~~~l~~lI~diL  603 (766)
                                    +.+.++-+--++||++|||++|.-.+|-+..++-..+..  +...++.+.|.+....+.+++++.-
T Consensus       483 --------------s~AW~dVArRIAHEIKNPLTPIQLSAERl~rk~gk~i~eDrevfd~~tdTIirQV~dI~rMVdeF~  548 (712)
T COG5000         483 --------------SAAWGDVARRIAHEIKNPLTPIQLSAERLLRKLGKEIDEDREVFDRCTDTIIRQVEDIKRMVDEFR  548 (712)
T ss_pred             --------------HHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             --------------878999999998872499862200289999883741234899999999999999999999999999


Q ss_pred             HHHHHHCCCCCCCEEEECHHHHHHHHHHHHHHHHHHCCCEEEEEECCC-CEEEECHHHHHHHHHHHHHHHHHCC------
Q ss_conf             788874198301203316999999999999999984795899980899-7899868999999999886565346------
Q gi|254780903|r  604 EMSKIETEKISIDKQNADLIPIINEGIRLIGSSAQSKNIKIEKKIPSE-LFFNADKRIIKKILFPILSNSIKFT------  676 (766)
Q Consensus       604 d~srieag~~~~~~~~~dl~~~i~~~~~~~~~~~~~k~i~l~~~~~~~-l~v~~D~~~l~QVl~NLi~NAik~t------  676 (766)
                      +|+|    ..++.++..||++++.++..+....  ..+|.+..+.+.. +...+|+++|.|||.||+.||..+.      
T Consensus       549 afAR----mP~p~~e~~dL~~ll~e~~~L~e~~--~~~i~f~~e~g~epl~~~~D~~~l~Qvf~NliKNA~EAi~~~~~~  622 (712)
T COG5000         549 AFAR----MPAPKLEKSDLRALLKEVSFLYEIG--NDHIVFAAEFGGEPLIGMADATLLGQVFGNLLKNAAEAIEAVEAE  622 (712)
T ss_pred             HHHC----CCCCCCCCCHHHHHHHHHHHHHHCC--CCCEEEEEECCCCCEEEECCHHHHHHHHHHHHHHHHHHHHHCCCC
T ss_conf             8714----8998777422999999999999626--877699753189862532489999999999987199875310134


Q ss_pred             -CCCCEEEEEEEEECCEEEEEEEECCCCCCHHHHHHHCCCEEECCCCCCCCCCCCCHHHHHHHHHHHHCCCEEEEEEE-C
Q ss_conf             -89888999999979989999997889789778543046505314675567788761689999999962986999979-8
Q gi|254780903|r  677 -NNNGKMMIRTSKIGQCVIITIADTGIGIPKSALEKIGQPFEPLHNQYDQSIGGFGLGLAISDALTNLHGGRLKIISQ-E  754 (766)
Q Consensus       677 -~~~g~I~i~~~~~~~~v~i~V~D~G~GI~~e~~~~iF~pF~q~~~~~t~~~~GtGLGLaI~k~iVe~hgG~I~v~S~-~  754 (766)
                       ++++.|+++....++.+++.|.|||.|.|.|.+.|+||||-      |.+.+||||||+|||+|||-|||++..... .
T Consensus       623 e~~~~~i~~~~~~~~g~i~v~V~DNGkG~p~e~r~r~~EPYv------Ttr~KGTGLGLAiVKkIvEeHGG~leL~da~d  696 (712)
T COG5000         623 ERRTALIRVSLDDADGRIVVDVIDNGKGFPRENRHRALEPYV------TTREKGTGLGLAIVKKIVEEHGGRLELHNAPD  696 (712)
T ss_pred             CCCCCEEEEEEECCCCEEEEEEECCCCCCCHHHHHHHCCCCE------ECCCCCCCCCHHHHHHHHHHCCCEEEECCCCC
T ss_conf             677643899984479849999810898799678643236714------21656666239999999996388277247899


Q ss_pred             CCCEEEEEECCC
Q ss_conf             995299997359
Q gi|254780903|r  755 GKGTIVTICMPQ  766 (766)
Q Consensus       755 g~Gttf~i~LP~  766 (766)
                      -.|+.+.+.+|.
T Consensus       697 ~~GA~i~i~fp~  708 (712)
T COG5000         697 FDGAMIRIKFPL  708 (712)
T ss_pred             CCCCEEEEECCC
T ss_conf             997679998365


No 36 
>TIGR02916 PEP_his_kin putative PEP-CTERM system histidine kinase; InterPro: IPR014265   Proteins in this entry are putative periplasmic sensor signal transduction histidine kinases. They all contain a GAF domain that is present in phytochromes and cGMP-specific phosphodiesterases, and which has been experimentally proven to be involved in protein:protein interactions. They also contain a C-terminal histidine kinase domain, which is composed of a dimerisation sub-domain and an ATP/ADP-binding phosphotransfer, or catalytic, sub-domain. The proteins in this entry 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 IPR014264 from INTERPRO and IPR014266 from INTERPRO also occur..
Probab=100.00  E-value=5.9e-36  Score=277.51  Aligned_cols=204  Identities=19%  Similarity=0.355  Sum_probs=174.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCC-CCCEEEECHH
Q ss_conf             999987675222478999999998603468899389999999999999999999777677888741983-0120331699
Q gi|254780903|r  545 EFLAKMSHELRTPLNAILGFSEVIKKEIFGELGSVKYYEYAQDIHYSGQHLLNMINNILEMSKIETEKI-SIDKQNADLI  623 (766)
Q Consensus       545 efla~isHelrtPL~aI~g~~ell~~~~~~~~~~e~~~~~l~~I~~~~~~l~~lI~diLd~srieag~~-~~~~~~~dl~  623 (766)
                      .+-+-+=|||+|-.....-...-.+++..   ++|=+.|.+++|..+.+||..|+.++..      ++. +-+.+.||+.
T Consensus       488 R~SaFvVHDLKNLvaQLSL~l~NA~~Hk~---NPeFq~DmL~Tv~~~v~RM~~ll~qLr~------~~~p~~~~~~~~l~  558 (696)
T TIGR02916       488 RMSAFVVHDLKNLVAQLSLLLRNAERHKD---NPEFQDDMLETVESAVNRMKKLLAQLRE------KGLPEEEKKTVDLV  558 (696)
T ss_pred             CCEEEEEEHHHHHHHHHHHHHHHHHHCCC---CHHHHHHHHHHHHHHHHHHHHHHHHHHC------CCCCCHHHHEEHHH
T ss_conf             80342110258999999999998874178---9668999999899999999999999730------68974056410389


Q ss_pred             HHHHHHHHHHHHHHHHCCCEEEEEECCC--CEEEECHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEEEC-CEEEEEEEEC
Q ss_conf             9999999999999984795899980899--789986899999999988656534689888999999979-9899999978
Q gi|254780903|r  624 PIINEGIRLIGSSAQSKNIKIEKKIPSE--LFFNADKRIIKKILFPILSNSIKFTNNNGKMMIRTSKIG-QCVIITIADT  700 (766)
Q Consensus       624 ~~i~~~~~~~~~~~~~k~i~l~~~~~~~--l~v~~D~~~l~QVl~NLi~NAik~t~~~g~I~i~~~~~~-~~v~i~V~D~  700 (766)
                      ++++++.+.-+.+  +..+++... +.+  +.|.+|+.+|+.|+.||+-||+++||+.|+|.|++.+.+ +.++|+|+||
T Consensus       559 ~L~~~~~~~k~~q--~p~~e~~~~-~~~~rl~~~a~~erl~rV~gHL~QNAlEAT~~~G~V~~~~~~~~~~~a~i~i~D~  635 (696)
T TIGR02916       559 DLLRRVIASKRAQ--QPRPEVSIE-DTDFRLSVRADRERLERVLGHLVQNALEATPEEGRVKIRVERECGGAAVIEIEDS  635 (696)
T ss_pred             HHHHHHHHHHHHC--CCCEEEEEC-CCCEEEEEEECHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEECCCCEEEEEEEEC
T ss_conf             9999999998631--894489971-7541788875288899999999998886049996289998741888227999865


Q ss_pred             CCCCCHHH-HHHHCCCEEECCCCCCCCCCCCCHHHHHHHHHHHHCCCEEEEEEECCCCEEEEEECC
Q ss_conf             89789778-543046505314675567788761689999999962986999979899529999735
Q gi|254780903|r  701 GIGIPKSA-LEKIGQPFEPLHNQYDQSIGGFGLGLAISDALTNLHGGRLKIISQEGKGTIVTICMP  765 (766)
Q Consensus       701 G~GI~~e~-~~~iF~pF~q~~~~~t~~~~GtGLGLaI~k~iVe~hgG~I~v~S~~g~Gttf~i~LP  765 (766)
                      |+||+++. ++|+|.||.     +||+..|.|+|.+=||++|+.|||+|+|+|+||+||+|++.||
T Consensus       636 G~GM~~~FiR~rLF~PF~-----tTK~~aGMGIG~YE~~~yv~e~GG~i~V~S~pG~Gt~ftl~LP  696 (696)
T TIGR02916       636 GCGMSEAFIRERLFKPFD-----TTKGNAGMGIGVYECRQYVEELGGRIEVESTPGKGTIFTLVLP  696 (696)
T ss_pred             CCCCCHHHHHHHCCCCCC-----CCCCCCCCCCCHHHHHHHHHHHCCCEEEEEECCCCEEEEEECC
T ss_conf             789985899840789975-----4456678720189999999983890588863588548887449


No 37 
>COG3290 CitA Signal transduction histidine kinase regulating citrate/malate metabolism [Signal transduction mechanisms]
Probab=100.00  E-value=3.5e-31  Score=243.04  Aligned_cols=189  Identities=26%  Similarity=0.355  Sum_probs=149.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCEEEECHHHHH
Q ss_conf             99876752224789999999986034688993899999999999999999997776778887419830120331699999
Q gi|254780903|r  547 LAKMSHELRTPLNAILGFSEVIKKEIFGELGSVKYYEYAQDIHYSGQHLLNMINNILEMSKIETEKISIDKQNADLIPII  626 (766)
Q Consensus       547 la~isHelrtPL~aI~g~~ell~~~~~~~~~~e~~~~~l~~I~~~~~~l~~lI~diLd~srieag~~~~~~~~~dl~~~i  626 (766)
                      |-..+||+.|-|++|.|+.++-.        -++..+|+..+.   +.-.++++.+..       +..        ++++
T Consensus       337 LRaq~HEfmNkLhtI~GLlql~~--------yd~a~~~I~~~~---~~qq~~~~~l~~-------~i~--------~~~l  390 (537)
T COG3290         337 LRAQSHEFMNKLHTILGLLQLGE--------YDDALDYIQQES---EEQQELIDSLSE-------KIK--------DPVL  390 (537)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHCC--------HHHHHHHHHHHH---HHHHHHHHHHHH-------HCC--------CHHH
T ss_conf             98852888888999987885053--------789999999987---640456899998-------512--------0888


Q ss_pred             HHHHHHHHHHHHHCCCEEEEEECCCC---EEEECHHHHHHHHHHHHHHHHHCCC---CCCEEEEEEEEECCEEEEEEEEC
Q ss_conf             99999999999847958999808997---8998689999999998865653468---98889999999799899999978
Q gi|254780903|r  627 NEGIRLIGSSAQSKNIKIEKKIPSEL---FFNADKRIIKKILFPILSNSIKFTN---NNGKMMIRTSKIGQCVIITIADT  700 (766)
Q Consensus       627 ~~~~~~~~~~~~~k~i~l~~~~~~~l---~v~~D~~~l~QVl~NLi~NAik~t~---~~g~I~i~~~~~~~~v~i~V~D~  700 (766)
                      ...+---..++.+++++|.++....+   |-.-++.-+--|+-|||.||+.++-   ++..|.+.....++.++|+|+||
T Consensus       391 Ag~LlgK~~rArElgv~l~Id~~S~l~~~p~~~~~~~litIlGNLidNA~eA~~~~~~~k~I~l~i~~~~~~lvieV~D~  470 (537)
T COG3290         391 AGFLLGKISRARELGVSLIIDPNSQLPQLPSELQPHDLVTILGNLIDNALEALLAPEENKEIELSLSDRGDELVIEVADT  470 (537)
T ss_pred             HHHHHHHHHHHHHCCCEEEECCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEECCCEEEEEEECC
T ss_conf             99988689999972965997579867889876676789999999887788885155789679999983698799999579


Q ss_pred             CCCCCHHHHHHHCCCEEECCCCCCCCCCCCCHHHHHHHHHHHHCCCEEEEEEECCCCEEEEEECCC
Q ss_conf             897897785430465053146755677887616899999999629869999798995299997359
Q gi|254780903|r  701 GIGIPKSALEKIGQPFEPLHNQYDQSIGGFGLGLAISDALTNLHGGRLKIISQEGKGTIVTICMPQ  766 (766)
Q Consensus       701 G~GI~~e~~~~iF~pF~q~~~~~t~~~~GtGLGLaI~k~iVe~hgG~I~v~S~~g~Gttf~i~LP~  766 (766)
                      ||||||+..++||+.=+     .||..+|.|.||++||++|+.+||.|+++|+.+.||+|+++||+
T Consensus       471 G~GI~~~~~~~iFe~G~-----Stk~~~~rGiGL~Lvkq~V~~~~G~I~~~s~~~~Gt~F~i~iP~  531 (537)
T COG3290         471 GPGIPPEVRDKIFEKGV-----STKNTGGRGIGLYLVKQLVERLGGSIEVESEKGQGTRFSIYIPK  531 (537)
T ss_pred             CCCCCHHHHHHHHHCCC-----CCCCCCCCCHHHHHHHHHHHHCCCEEEEEECCCCCEEEEEECCC
T ss_conf             99989688777873484-----14677887612889999998749669995078981499998888


No 38 
>COG0642 BaeS Signal transduction histidine kinase [Signal transduction mechanisms]
Probab=100.00  E-value=8.4e-34  Score=262.00  Aligned_cols=214  Identities=36%  Similarity=0.590  Sum_probs=189.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCC-CCCCEEEE
Q ss_conf             99999998767522247899999999860346889938999999999999999999977767788874198-30120331
Q gi|254780903|r  542 TKSEFLAKMSHELRTPLNAILGFSEVIKKEIFGELGSVKYYEYAQDIHYSGQHLLNMINNILEMSKIETEK-ISIDKQNA  620 (766)
Q Consensus       542 ~k~efla~isHelrtPL~aI~g~~ell~~~~~~~~~~e~~~~~l~~I~~~~~~l~~lI~diLd~srieag~-~~~~~~~~  620 (766)
                      .+..|++.++||+|||++++.++++++...   ..  ....+++..+....+++..++++++++++++.+. .....+.+
T Consensus       114 ~~~~~~~~~~hel~~pl~~~~~~~~~~~~~---~~--~~~~~~~~~i~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~  188 (336)
T COG0642         114 AKREFLANISHELRTPLTAIRGLLELLLEG---LL--DPQRELLEIIEEEAERLLRLVNDLLDLSRLEAGTKLKLLLELV  188 (336)
T ss_pred             HHHHHHHHHHHHHCCHHHHHHHHHHHHHCC---CC--CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCC
T ss_conf             999999999888589799999999997414---65--2599999999999999999999999999764457442234645


Q ss_pred             CHHHHHHHHHHHHHHHHHHCCCEEEEEECCCCEEEECHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEEECCEEEEEEEEC
Q ss_conf             69999999999999999847958999808997899868999999999886565346898889999999799899999978
Q gi|254780903|r  621 DLIPIINEGIRLIGSSAQSKNIKIEKKIPSELFFNADKRIIKKILFPILSNSIKFTNNNGKMMIRTSKIGQCVIITIADT  700 (766)
Q Consensus       621 dl~~~i~~~~~~~~~~~~~k~i~l~~~~~~~l~v~~D~~~l~QVl~NLi~NAik~t~~~g~I~i~~~~~~~~v~i~V~D~  700 (766)
                      ++..++.++...+......+.+.+....++...+.+|+..+.|||.||++||+||++ ++.|.|++...++.++++|+|+
T Consensus       189 ~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~~~~l~~vl~nLi~NAi~~~~-~~~i~i~~~~~~~~i~i~V~D~  267 (336)
T COG0642         189 DLAELLEEVVRLLAPLAQEKGIELAVDLPELPYVLGDPERLRQVLVNLLSNAIKYTP-GGEITISVRQDDEQVTISVEDT  267 (336)
T ss_pred             CHHHHHHHHHHHHHHHHHHCCEEEEEECCCCEEEEECHHHHHHHHHHHHHHHHHHCC-CCEEEEEEEECCCEEEEEEECC
T ss_conf             599999999999998766348489982376607860788999999999998998668-9859999996387799999807


Q ss_pred             CCCCCHHHHHHHCCCEEECCCCCCCCCC-CCCHHHHHHHHHHHHCCCEEEEEEECCCCEEEEEECCC
Q ss_conf             8978977854304650531467556778-87616899999999629869999798995299997359
Q gi|254780903|r  701 GIGIPKSALEKIGQPFEPLHNQYDQSIG-GFGLGLAISDALTNLHGGRLKIISQEGKGTIVTICMPQ  766 (766)
Q Consensus       701 G~GI~~e~~~~iF~pF~q~~~~~t~~~~-GtGLGLaI~k~iVe~hgG~I~v~S~~g~Gttf~i~LP~  766 (766)
                      |+|||++.++++|+||++.     +..+ ||||||+|||++++.|||+++++|.+|.||+|+|+||.
T Consensus       268 G~Gi~~~~~~~if~~~~~~-----~~~~~g~GlGL~i~~~~~~~~~g~i~~~~~~~~Gt~~~i~lP~  329 (336)
T COG0642         268 GPGIPEEELERIFEPFFRT-----DKSRSGTGLGLAIVKRIVELHGGTISVESEPGKGTTFTIRLPL  329 (336)
T ss_pred             CCCCCHHHHHHHHCCCCCC-----CCCCCCCCHHHHHHHHHHHHCCCEEEEECCCCCCEEEEEEEEC
T ss_conf             8997988999881886347-----9998988632999999999879989995079997799999847


No 39 
>PRK09776 putative sensor protein; Provisional
Probab=100.00  E-value=3.2e-32  Score=250.59  Aligned_cols=255  Identities=12%  Similarity=0.165  Sum_probs=207.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHCCCCCEEEEECCCCEEEECHHHHHHCCCCHHHCCCCHHHHHHHHCCCCHHHH-HHH
Q ss_conf             9999999999999999999999722597459897689789997889977299943305898899976081205899-999
Q gi|254780903|r  239 QAKKNKENDTILLEANICVETALSRGRCGLWNFNFDNKKFHLSRSMYEIMGIPYENKTLSFRAIARLIHYDNKKIC-EIA  317 (766)
Q Consensus       239 dit~~r~ae~~l~ese~rl~~al~~a~~GiWd~D~~~~~i~ws~~~~~llG~~~~e~~~s~~~~~~~vHPdDr~~~-~~a  317 (766)
                      -....|+....+++||+|||.+++.++.|++..+++++++++|+++|+|+||++++...  -.|.+++||||...- ...
T Consensus       288 ~~~~~r~~~~~l~~SE~rfR~~~e~saiGmAlV~~dGr~l~VN~alc~mlGYs~~ELl~--ltf~diThPdDl~~dl~~~  365 (1116)
T PRK09776        288 VMYAFRAERKHISESETRFRNAMEYSAIGMALVGTEGQWLQVNKALCQFLGYSQEELRG--LTFQQLTWPEDLNKDLQQV  365 (1116)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHCCCCEEEECCCCCEEEECHHHHHHHCCCHHHHHH--CCHHHHCCCCCHHHHHHHH
T ss_conf             99999988888776799999998746664699868981898169999884989999852--9898816962177789999


Q ss_pred             HHHHHCCCCEEEEEEEEECCCCCEEEEEEEEEEEEECCCEE-EEEEEEECCCHHHHHHHHHHHHHHHHHHHHHHHHHHEE
Q ss_conf             99972489848999998869898899889999998379606-99999844617999999999999999999985445515
Q gi|254780903|r  318 RSVTGKHVKQLDQIFHMRHASGADIWIQVRAQMMRTISGGM-NIIGIAMDLTEKYHLEKRYAEADQRLSKAIECTSEALV  396 (766)
Q Consensus       318 ~~~~~~~~~~~~~e~Ri~~~DG~~~Wi~~r~~~i~d~~G~~-~~iGi~~DITErK~ae~~l~ese~rlr~~ie~~~~~i~  396 (766)
                      .+...|+.+.|..|.|++++||+++|+....+++||++|+| +++|++.||||||++|+++++++++++.+.|+.+.++|
T Consensus       366 ~~LlaGei~~y~lEKRyirkDG~~vW~~ltvSlvRd~~G~p~~fI~~v~DIterK~aE~~lr~l~erl~la~ea~~iGiw  445 (1116)
T PRK09776        366 EKLLSGEINSYSMEKRYYNRDGDVVWALLAVSLVRDTDGTPLYFIAQIEDINELKRTEQVNERLMERITLANEAGGIGIW  445 (1116)
T ss_pred             HHHHCCCCCCCCCEEEEECCCCCEEEEEEEEEEEECCCCCEEEEEEEEEECHHHHHHHHHHHHHHHHHHHHHHHCCCCEE
T ss_conf             99976996645411246736997999998999997699984489999973337799999999999999999862476635


Q ss_pred             EECCCCEEEEECHHHHHHHCCCHHHHCCC-CCHHHHCCCHHHHHHHHH--HHCCCCCCCEEEEEEECCC--EEEEECCE-
Q ss_conf             88349969970178988839997894289-717881652013789998--5211245640589991696--28742232-
Q gi|254780903|r  397 LWDKNDRLVMCNANYQKAYGLPDHVLVPG-NARSIIQDAQTRPIIEYR--TSDPERSQDMSKEIKLADS--RWLQINEW-  470 (766)
Q Consensus       397 ~~D~~g~i~~~N~~~~~~~g~~~~~~~~~-~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~e~~~~dg--~~~~i~~~-  470 (766)
                      .||.....+.+|..+.+++|++.+..... .+.+.++|++........  ..........+|+....||  +|+..... 
T Consensus       446 e~d~~~~~i~~~~r~~~l~g~~~~~~~~~~~w~~~ihPdD~~~v~~~~~~~l~~~~~~d~E~Rl~~~dG~~r~i~~~a~~  525 (1116)
T PRK09776        446 EWDLKPNIISWDKRMFELYEIPPHIKPNWQVWYACLHPEDRQRVEKEIRDALQGRSPFKLEFRIVVPDGEIRHIRALANR  525 (1116)
T ss_pred             EEECCCCCEECCHHHHHHHCCCCCCCCCHHHHHHHCCHHHHHHHHHHHHHHHHCCCCCCCEEEEECCCCCEEEEEEEEEE
T ss_conf             52056650211378999848882226688999872391568999999999971588756046788479978999862148


Q ss_pred             -ECCCCC---EEEEEEEEEHHHCCCCCCC
Q ss_conf             -456997---8999886201000112232
Q gi|254780903|r  471 -CTHDGG---TISVGTDITLLKHNQAQLR  495 (766)
Q Consensus       471 -~~~dg~---~v~v~~~i~~~~~~~~~~~  495 (766)
                       +..+|.   .+.+..|||+.|+.++.+.
T Consensus       526 ~~d~~G~~~r~~G~~~DITe~K~~eeaL~  554 (1116)
T PRK09776        526 VLNKDGEVERLLGINMDMTEVRQLNEALF  554 (1116)
T ss_pred             EECCCCCEEEEEEEEECCCHHHHHHHHHH
T ss_conf             98689988988731323207789999999


No 40 
>COG4192 Signal transduction histidine kinase regulating phosphoglycerate transport system [Signal transduction mechanisms]
Probab=99.97  E-value=5.2e-28  Score=220.19  Aligned_cols=213  Identities=21%  Similarity=0.333  Sum_probs=180.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCEEEEC
Q ss_conf             99999998767522247899999999860346889938999999999999999999977767788874198301203316
Q gi|254780903|r  542 TKSEFLAKMSHELRTPLNAILGFSEVIKKEIFGELGSVKYYEYAQDIHYSGQHLLNMINNILEMSKIETEKISIDKQNAD  621 (766)
Q Consensus       542 ~k~efla~isHelrtPL~aI~g~~ell~~~~~~~~~~e~~~~~l~~I~~~~~~l~~lI~diLd~srieag~~~~~~~~~d  621 (766)
                      ..++-+..+|||++.||||...|.=-...- ..+..++....++++|..-.+|+..+|+.+..|+|-.++..+  .+||+
T Consensus       450 vVGqTmTslaHEinQPLnAmsaYLFsA~~A-~e~~~s~qa~~~L~kie~L~eR~~~Iv~sLRqF~Rk~s~~~~--lqpV~  526 (673)
T COG4192         450 VVGQTMTSLAHEINQPLNAMSAYLFSARLA-LEEAPSAQAATSLDKIENLTERMGKIVNSLRQFARKNSSDES--LQPVR  526 (673)
T ss_pred             HHHHHHHHHHHHHCCCHHHHHHHHHHHHHH-HHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCC--CCCCC
T ss_conf             987788888988557568899999987888-851745889989998877999999999999999752577787--64110


Q ss_pred             HHHHHHHHHHHHHHHHHHCCCEEEEEECCCCEEEECHHHHHHHHHHHHHHHHHCCC-CCCEEEEEEEE-ECCEEEEEEEE
Q ss_conf             99999999999999998479589998089978998689999999998865653468-98889999999-79989999997
Q gi|254780903|r  622 LIPIINEGIRLIGSSAQSKNIKIEKKIPSELFFNADKRIIKKILFPILSNSIKFTN-NNGKMMIRTSK-IGQCVIITIAD  699 (766)
Q Consensus       622 l~~~i~~~~~~~~~~~~~k~i~l~~~~~~~l~v~~D~~~l~QVl~NLi~NAik~t~-~~g~I~i~~~~-~~~~v~i~V~D  699 (766)
                      |+.+++.+.+++..+.+.+.+.+..-. ++++|.||...++|||+||+.||.+++. ..+.|.|.+-. .++..++.|.|
T Consensus       527 L~~~v~~AweLl~~khk~rQ~~Li~pt-D~~~V~gd~v~ieQVlvNl~~NaldA~~h~~p~i~~~~~~~~~e~l~i~i~D  605 (673)
T COG4192         527 LNSVVEQAWELLQTKHKRRQIKLINPT-DDLMVMGDAVSIEQVLVNLIVNALDASTHFAPWIKLIALGTEQEMLRIAIID  605 (673)
T ss_pred             HHHHHHHHHHHHHHHHHHCCCCCCCCC-CCCEECCHHHHHHHHHHHHHHHHHHHHCCCCCEEEEEEECCCCCCEEEEEEC
T ss_conf             999999999999854200024423776-5300000156499999999998886641578627998642764215899844


Q ss_pred             CCCCCCHHHHHHHCCCEEECCCCCCCCCCCCCHHHHHHHHHHHHCCCEEEEEEECCCCEEEEEEC
Q ss_conf             88978977854304650531467556778876168999999996298699997989952999973
Q gi|254780903|r  700 TGIGIPKSALEKIGQPFEPLHNQYDQSIGGFGLGLAISDALTNLHGGRLKIISQEGKGTIVTICM  764 (766)
Q Consensus       700 ~G~GI~~e~~~~iF~pF~q~~~~~t~~~~GtGLGLaI~k~iVe~hgG~I~v~S~~g~Gttf~i~L  764 (766)
                      ||.|-|-+..+|+|.||.      |.+.-|.|||||||.++++.|.|++.+-|..-+|+.+...+
T Consensus       606 nGqGwp~~l~dkLl~PFt------tsK~vgLGlGLSIsqSlmeqmqG~l~lAStLt~nA~ViL~f  664 (673)
T COG4192         606 NGQGWPHELVDKLLTPFT------TSKEVGLGLGLSISQSLMEQMQGRLALASTLTKNAMVILEF  664 (673)
T ss_pred             CCCCCCHHHHHHHCCCCC------CCCCCCCCCCHHHHHHHHHHHCCCCHHHHHCCCCCEEEEEE
T ss_conf             899984567788607766------43100555325678999998427444865513574899998


No 41 
>PRK13560 hypothetical protein; Provisional
Probab=99.97  E-value=1.5e-27  Score=216.89  Aligned_cols=258  Identities=14%  Similarity=0.042  Sum_probs=192.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEEEEECCCCEEEECHHHHHHCCCCHHHCCCCHHHHHHHHCCCC-HHHHHH
Q ss_conf             8999999999999999999999972259745989768978999788997729994330589889997608120-589999
Q gi|254780903|r  238 RQAKKNKENDTILLEANICVETALSRGRCGLWNFNFDNKKFHLSRSMYEIMGIPYENKTLSFRAIARLIHYDN-KKICEI  316 (766)
Q Consensus       238 ~dit~~r~ae~~l~ese~rl~~al~~a~~GiWd~D~~~~~i~ws~~~~~llG~~~~e~~~s~~~~~~~vHPdD-r~~~~~  316 (766)
                      -|||+||++|.+++++...++.++++.|+-++--|.++.+++||..++.++||++++..+. . ..++ -|+. .+.+..
T Consensus       187 ~DITERKraE~rl~~ql~flq~LlDnipdpvF~kD~~G~ylgcN~afe~~~G~~re~i~G~-t-i~Dl-~p~e~ad~y~~  263 (807)
T PRK13560        187 EDITERKRAEERIDEALHFLQQLLDNIADPAFWKDEDAKVFGCNDAACLACGFRREEIIGM-S-IHDF-APAQPADDYQE  263 (807)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEEEECCCCCEEEECHHHHHHCCCCHHHHCCC-C-CCCC-CCHHHHHHHHH
T ss_conf             8767777899999999999999985488746997799518962099998809999995686-1-0127-81556899987


Q ss_pred             HHHHHHCCCCEEEEEEEEECCCCCEE--EEEEEEEEEEECCCEE-EEEEEEECCCHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             99997248984899999886989889--9889999998379606-99999844617999999999999999999985445
Q gi|254780903|r  317 ARSVTGKHVKQLDQIFHMRHASGADI--WIQVRAQMMRTISGGM-NIIGIAMDLTEKYHLEKRYAEADQRLSKAIECTSE  393 (766)
Q Consensus       317 a~~~~~~~~~~~~~e~Ri~~~DG~~~--Wi~~r~~~i~d~~G~~-~~iGi~~DITErK~ae~~l~ese~rlr~~ie~~~~  393 (766)
                      .............+|-.++.+||..+  |+.....+++|..|.+ .++|+..||||||++|++|++++++||.++|+++.
T Consensus       264 ~d~~~l~~~~~~~~E~~v~~~DG~~~~~~v~~nka~~~d~~g~~~GlvGv~~DITeRK~aEe~LresEer~R~i~E~a~~  343 (807)
T PRK13560        264 ADAAKFDADGSQIIEAEFQNKDGRTRPVDVIFNHAEFDDKENHCAGLVGAITDISGRRAAERELLEKEDMLRAIIEAAPI  343 (807)
T ss_pred             HHHHHHCCCCCEEEEEEEECCCCCEEEEEEEEEEEEECCCCCCEEEEEEEEEEHHHHHHHHHHHHHHHHHHHHHHHHCCC
T ss_conf             50886418875575520377998575799998622333878866568888761567788999999989999999873665


Q ss_pred             HEEEECCCCEEEEE-CHHHHHHHCCCHHHHCCCCCH---------------HHHCCCHHHH-HHH----HHHHCCCCCCC
Q ss_conf             51588349969970-178988839997894289717---------------8816520137-899----98521124564
Q gi|254780903|r  394 ALVLWDKNDRLVMC-NANYQKAYGLPDHVLVPGNAR---------------SIIQDAQTRP-IIE----YRTSDPERSQD  452 (766)
Q Consensus       394 ~i~~~D~~g~i~~~-N~~~~~~~g~~~~~~~~~~~~---------------~~~~~~~~~~-~~~----~~~~~~~~~~~  452 (766)
                      +|+..|.+|+++++ |++..+++||+.+++.+.+.+               ....|+.+.. ...    ...........
T Consensus       344 gI~~~D~~g~i~~~~n~aae~m~G~s~eE~lg~~lw~~~pe~~~e~~~~~~~~~~pdgr~~~~~~c~~a~~~r~g~~~~g  423 (807)
T PRK13560        344 AAIGLDADGNICFVNNNAAERMLGWSAAEVMGKPLPGMDPELNEEFWCGDFQEWYPDGRPMAFDACPMAKTIKGGKIFDG  423 (807)
T ss_pred             CEEEECCCCCEEEECCHHHHHHHCCCHHHHCCCCCCCCCHHHHHHHCCCCHHHHCCCCCCCCCCHHHHHHHHHCCCCCCC
T ss_conf             34786267615761261678762687688607743356834413331340655166656343101236677613787788


Q ss_pred             EEEEEEECCC--EEEEECCEECC--CCC---EEEEEEEEEHHHCCCCCCCCCC
Q ss_conf             0589991696--28742232456--997---8999886201000112232222
Q gi|254780903|r  453 MSKEIKLADS--RWLQINEWCTH--DGG---TISVGTDITLLKHNQAQLRESK  498 (766)
Q Consensus       453 ~~~e~~~~dg--~~~~i~~~~~~--dg~---~v~v~~~i~~~~~~~~~~~~~~  498 (766)
                      .+.....+||  .|..++..+..  ||.   .+.+..|||++|..++.+....
T Consensus       424 ~E~~~~RkDGt~~~~~~~~~pL~D~dG~~~gal~i~~DITERKqAEeaLr~sn  476 (807)
T PRK13560        424 QEVLIEREDDGPADCSAYAEPLHDADGNIIGAIALLVDITERKQVEEQLLLAN  476 (807)
T ss_pred             CEEEEEECCCCEEEEEECCEEEECCCCCEEEEEEHHHCCHHHHHHHHHHHHHH
T ss_conf             63799906996577886130225678885331100112427788999999988


No 42 
>smart00387 HATPase_c Histidine kinase-like ATPases. Histidine kinase-, DNA gyrase B-, phytochrome-like ATPases.
Probab=99.96  E-value=8.2e-28  Score=218.74  Aligned_cols=110  Identities=38%  Similarity=0.673  Sum_probs=104.0

Q ss_pred             ECHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEEECCEEEEEEEECCCCCCHHHHHHHCCCEEECCCCCCCCCCCCCHHHH
Q ss_conf             86899999999988656534689888999999979989999997889789778543046505314675567788761689
Q gi|254780903|r  656 ADKRIIKKILFPILSNSIKFTNNNGKMMIRTSKIGQCVIITIADTGIGIPKSALEKIGQPFEPLHNQYDQSIGGFGLGLA  735 (766)
Q Consensus       656 ~D~~~l~QVl~NLi~NAik~t~~~g~I~i~~~~~~~~v~i~V~D~G~GI~~e~~~~iF~pF~q~~~~~t~~~~GtGLGLa  735 (766)
                      +|+.+|.||+.||++||+||+++++.|+|++...++.+.|.|+|||+|||++.++++|+||++.+.. ....+|+||||+
T Consensus         1 ~d~~~l~~il~Nli~NAik~~~~~~~I~i~~~~~~~~~~i~V~D~G~Gi~~~~~~~if~~f~~~~~~-~~~~~g~GlGL~   79 (111)
T smart00387        1 GDPDRLRQVLSNLLDNAIKYTPEGGRITVTLERDGDHLEITVEDNGPGIPPEDLEKIFEPFFRTDGR-SRKIGGTGLGLS   79 (111)
T ss_pred             CCHHHHHHHHHHHHHHHHHHCCCCCEEEEEEEECCCEEEEEEEECCCCCCHHHHHHCCCCCEECCCC-CCCCCCCCHHHH
T ss_conf             9889999999999999999677997899999983999999999889973989996426994777999-988797664899


Q ss_pred             HHHHHHHHCCCEEEEEEECCCCEEEEEECCC
Q ss_conf             9999999629869999798995299997359
Q gi|254780903|r  736 ISDALTNLHGGRLKIISQEGKGTIVTICMPQ  766 (766)
Q Consensus       736 I~k~iVe~hgG~I~v~S~~g~Gttf~i~LP~  766 (766)
                      |||.++++|||+|+++|++++||+|+|+||-
T Consensus        80 i~~~i~~~~~G~i~i~s~~~~Gt~~~i~lP~  110 (111)
T smart00387       80 IVKKLVELHGGEISVESEPGGGTTFTITLPL  110 (111)
T ss_pred             HHHHHHHHCCCEEEEEECCCCEEEEEEEEEC
T ss_conf             9999999879989999659981899999981


No 43 
>pfam02518 HATPase_c Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase. This family represents the structurally related ATPase domains of histidine kinase, DNA gyrase B and HSP90.
Probab=99.95  E-value=3.7e-27  Score=213.99  Aligned_cols=110  Identities=35%  Similarity=0.628  Sum_probs=104.2

Q ss_pred             ECHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEEECCEEEEEEEECCCCCCHHHHHHHCCCEEECCCCCCCCCCCCCHHHH
Q ss_conf             86899999999988656534689888999999979989999997889789778543046505314675567788761689
Q gi|254780903|r  656 ADKRIIKKILFPILSNSIKFTNNNGKMMIRTSKIGQCVIITIADTGIGIPKSALEKIGQPFEPLHNQYDQSIGGFGLGLA  735 (766)
Q Consensus       656 ~D~~~l~QVl~NLi~NAik~t~~~g~I~i~~~~~~~~v~i~V~D~G~GI~~e~~~~iF~pF~q~~~~~t~~~~GtGLGLa  735 (766)
                      +|+.+|.||+.||++||+||++++|.|.|++...++.++|+|+|||+|||++.++++|+||+|.+.. .+..+|+||||+
T Consensus         1 ~d~~~l~~i~~nll~NAik~~~~~~~I~i~~~~~~~~~~i~V~D~G~Gi~~~~~~~if~~f~~~~~~-~~~~~g~GlGL~   79 (111)
T pfam02518         1 GDEDRLRQVLSNLLDNAIKHAPAGGEIEVTLERDGGRLRITVEDNGIGIPPEDLPKIFEPFFRTDKD-SRKVGGTGLGLS   79 (111)
T ss_pred             CCHHHHHHHHHHHHHHHHHHCCCCCEEEEEEEEECCEEEEEEEECCCCCCHHHHHHHCCCCEECCCC-CCCCCCCCHHHH
T ss_conf             9889999999999999999779997599999995999999999899995989998874991777999-977797764799


Q ss_pred             HHHHHHHHCCCEEEEEEECCCCEEEEEECCC
Q ss_conf             9999999629869999798995299997359
Q gi|254780903|r  736 ISDALTNLHGGRLKIISQEGKGTIVTICMPQ  766 (766)
Q Consensus       736 I~k~iVe~hgG~I~v~S~~g~Gttf~i~LP~  766 (766)
                      +||.+++.|||+|+++|++++||+|+|+||.
T Consensus        80 i~~~~~~~~~g~i~~~s~~~~Gt~~~i~lp~  110 (111)
T pfam02518        80 IVRKLVELHGGTITVESEPGGGTTFTFTLPL  110 (111)
T ss_pred             HHHHHHHHCCCEEEEEECCCCEEEEEEEEEE
T ss_conf             9999999879989999659983899999970


No 44 
>PRK11359 cAMP phosphodiesterase; Provisional
Probab=99.95  E-value=7.2e-25  Score=197.46  Aligned_cols=227  Identities=11%  Similarity=0.026  Sum_probs=157.2

Q ss_pred             CCCCEEEEECCCCCEEEECCCHHHHCCCCHHHHCCCCHHHHCCCCCCCHHH----HHCCC-CHH----EEEEEECCCCCC
Q ss_conf             789789999699808997142055519978896076104320544332023----21153-100----001233157782
Q gi|254780903|r  126 LSESFILLAQPNELVFASSTKNSHYIGKKIGEIIPELSRSRSRSKTVQMSE----ASLDQ-QPY----HVLSVNLPHNSG  196 (766)
Q Consensus       126 ~~~~~i~i~d~~g~i~~~n~~~~~~~G~~~~~~~~~~~~~~~~~~~~~~~~----~~l~~-~~~----~~~~~~~~~~~~  196 (766)
                      .+...|+++|.+|+|+++||+++.++||+.++++|.......+........    ....+ ...    .......+.++.
T Consensus        20 ~s~~GIviiD~~GrIv~~N~aa~~l~GYs~eEllG~~~~~L~p~d~~~~~~~~l~~~~~~g~~~~~g~~~E~~~~RKDGs   99 (799)
T PRK11359         20 QNMMGAVLINENDEVMFFNPAAEKLWGYKREEVIGNNIDMLIPRDLRPAHPEYIRHNREGGKARVEGMSRELQLEKKDGS   99 (799)
T ss_pred             HCCCEEEEECCCCCEEEECHHHHHHHCCCHHHHCCCCHHHHCCCCCCHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCC
T ss_conf             18854999969990998718999987929999859988992785333123999998774265544564048999858888


Q ss_pred             EEEEEEECCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEEEEECCCC
Q ss_conf             59999742321012345565545687887899999999888899999999999999999999997225974598976897
Q gi|254780903|r  197 SILIINSRVPLLRLWREEVTLEVVFFSIISALLLFILFSYYRQAKKNKENDTILLEANICVETALSRGRCGLWNFNFDNK  276 (766)
Q Consensus       197 ~~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~a~~~dit~~r~ae~~l~ese~rl~~al~~a~~GiWd~D~~~~  276 (766)
                      .+++.....+.....+.                  ..++..+|||+++    +++++++++..++++++.++|.||.++.
T Consensus       100 ~~~velsvs~i~~~g~i------------------~~l~ivrDITee~----a~~e~~r~l~~~ld~~~~~I~i~D~~g~  157 (799)
T PRK11359        100 KIWTRFALSKVSAEGKV------------------YYLALVRDASVEM----AQKEQTRQLIIAVDHLDRPVIVLDPERH  157 (799)
T ss_pred             EEEEEEEEEEECCCCCE------------------EEEEEEEECCHHH----HHHHHHHHHHHHHHCCCCEEEEECCCCC
T ss_conf             99999999776479928------------------9999999768999----9999999999998626872999918987


Q ss_pred             EEEECHHHHHHCCCCHHHCCCCHHHHHHHH-CCCCHHHHHHHHHHHHCCCCEEEEEEEEECCCCCEEEEEEEEEEEEECC
Q ss_conf             899978899772999433058988999760-8120589999999972489848999998869898899889999998379
Q gi|254780903|r  277 KFHLSRSMYEIMGIPYENKTLSFRAIARLI-HYDNKKICEIARSVTGKHVKQLDQIFHMRHASGADIWIQVRAQMMRTIS  355 (766)
Q Consensus       277 ~i~ws~~~~~llG~~~~e~~~s~~~~~~~v-HPdDr~~~~~a~~~~~~~~~~~~~e~Ri~~~DG~~~Wi~~r~~~i~d~~  355 (766)
                      .++||+++.+|+||++++..+.  .+..++ +|++.............+...+..|++++++||+++|++..+.|++|..
T Consensus       158 i~~vN~a~~el~Gy~~eEl~G~--~~~~ll~~pe~~~~~~~~~~~~l~~~~~~~~E~~~~~kdG~~~wv~~s~~pi~d~~  235 (799)
T PRK11359        158 IVQCNRAFTEMFGYCISEASGM--QPDTLLNIPEFPADNRIRLQQLLWKTARDQDEFLLLTRTGEKIWIKASISPVYDVL  235 (799)
T ss_pred             EEEECHHHHHHHCCCHHHHCCC--CHHHHHCCCCCCHHHHHHHHHHHHCCCCCEEEEEEECCCCCEEEEEEEEEEEECCC
T ss_conf             8998778999859987897489--88998348788479999999998648973058999826997999998988998488


Q ss_pred             CEE-EEEEEEECCCHHHHHHHH
Q ss_conf             606-999998446179999999
Q gi|254780903|r  356 GGM-NIIGIAMDLTEKYHLEKR  376 (766)
Q Consensus       356 G~~-~~iGi~~DITErK~ae~~  376 (766)
                      |.+ +++++..||||+|++++.
T Consensus       236 g~~~~~v~i~~DITErr~~~~l  257 (799)
T PRK11359        236 AHLQNLVMTFSDITEERQIRQL  257 (799)
T ss_pred             CCEEEEEEEEEECCHHHHHHHH
T ss_conf             9888999999731588899999


No 45 
>PRK13559 hypothetical protein; Provisional
Probab=99.94  E-value=5.8e-22  Score=176.47  Aligned_cols=307  Identities=13%  Similarity=0.175  Sum_probs=216.7

Q ss_pred             HHHHHHHHHHCCCCCEEEEECCC---CEEEECHHHHHHCCCCHHHCCCCHHHHHHHHCCCCHHHHHHHHHHHHCCCCEEE
Q ss_conf             99999999722597459897689---789997889977299943305898899976081205899999999724898489
Q gi|254780903|r  253 ANICVETALSRGRCGLWNFNFDN---KKFHLSRSMYEIMGIPYENKTLSFRAIARLIHYDNKKICEIARSVTGKHVKQLD  329 (766)
Q Consensus       253 se~rl~~al~~a~~GiWd~D~~~---~~i~ws~~~~~llG~~~~e~~~s~~~~~~~vHPdDr~~~~~a~~~~~~~~~~~~  329 (766)
                      |...|..|+++.++-+...|+..   -.+|||+++++|.||+.++..+..  |.-+-+|+.-.........+...+.++.
T Consensus        43 ~~~~~~~a~~~~r~a~~itd~~~~d~PIiy~N~aF~~lTGYs~~EviGrn--crfLqGp~t~~~~v~~ir~ai~~~~~~~  120 (363)
T PRK13559         43 SGRLFEQAMEQTRMAMCITDPHQPDLPIVLANQAFLDLTGYAAEEVVGRN--CRFLQGAGTDPAAVAKIRAAIAAERVVV  120 (363)
T ss_pred             CCHHHHHHHHHCCCCEEEECCCCCCCCEEEECHHHHHHHCCCHHHHCCCC--CHHCCCCCCCHHHHHHHHHHHHCCCCEE
T ss_conf             31479999974774389968999999889988799976398979984999--2410899999899999999998399469


Q ss_pred             EEEEEECCCCCEEEEEEEEEEEEECCCEE-EEEEEEECCCHHHHHHHHHHHHHHHHHHHHHHHHHHEEEECCCCEEEEEC
Q ss_conf             99998869898899889999998379606-99999844617999999999999999999985445515883499699701
Q gi|254780903|r  330 QIFHMRHASGADIWIQVRAQMMRTISGGM-NIIGIAMDLTEKYHLEKRYAEADQRLSKAIECTSEALVLWDKNDRLVMCN  408 (766)
Q Consensus       330 ~e~Ri~~~DG~~~Wi~~r~~~i~d~~G~~-~~iGi~~DITErK~ae~~l~ese~rlr~~ie~~~~~i~~~D~~g~i~~~N  408 (766)
                      .+++..+|||+.+|......|++|++|++ +++|+..||||+|+.+.+-+.                             
T Consensus       121 ~el~nyrKDGs~fwn~l~isPV~D~~G~v~~fig~q~DvTd~~~~~a~e~~-----------------------------  171 (363)
T PRK13559        121 VELLNYRKDGSPFWNALHLGPIYDEDGKLLYFFGSQWDVTDIRAVRALEAH-----------------------------  171 (363)
T ss_pred             EEEEEECCCCCEEEEEEEEEEEECCCCCEEEEEEEEEEECCCCCHHHHHHH-----------------------------
T ss_conf             999998269982477689888798999799999999851554204558999-----------------------------


Q ss_pred             HHHHHHHCCCHHHHCCCCCHHHHCCCHHHHHHHHHHHCCCCCCCEEEEEEECCCEEEEECCEECCCCCEEEEEEEEEHHH
Q ss_conf             78988839997894289717881652013789998521124564058999169628742232456997899988620100
Q gi|254780903|r  409 ANYQKAYGLPDHVLVPGNARSIIQDAQTRPIIEYRTSDPERSQDMSKEIKLADSRWLQINEWCTHDGGTISVGTDITLLK  488 (766)
Q Consensus       409 ~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~dg~~~~i~~~~~~dg~~v~v~~~i~~~~  488 (766)
                                                                                                      
T Consensus       172 --------------------------------------------------------------------------------  171 (363)
T PRK13559        172 --------------------------------------------------------------------------------  171 (363)
T ss_pred             --------------------------------------------------------------------------------
T ss_conf             --------------------------------------------------------------------------------


Q ss_pred             CCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             01122322222221100001788998644457999999999999999988789999999987675222478999999998
Q gi|254780903|r  489 HNQAQLRESKRRLKATINDLSTSRQILERQKTELSIANAKYQVEKERAETANKTKSEFLAKMSHELRTPLNAILGFSEVI  568 (766)
Q Consensus       489 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~~~~~l~~~~~~ae~an~~k~efla~isHelrtPL~aI~g~~ell  568 (766)
                                                                            +..++.-|.|=.+|-|..|.+.+.+-
T Consensus       172 ------------------------------------------------------~~~LlrEl~HRVKN~LavV~Si~rlq  197 (363)
T PRK13559        172 ------------------------------------------------------ERRLAREVDHRSKNVFAVVDSIVRLT  197 (363)
T ss_pred             ------------------------------------------------------HHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             ------------------------------------------------------99999998887661999999999965


Q ss_pred             HCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCEEEECHHHHHHHHHHHHHHHHHHCCCEEEEEE
Q ss_conf             60346889938999999999999999999977767788874198301203316999999999999999984795899980
Q gi|254780903|r  569 KKEIFGELGSVKYYEYAQDIHYSGQHLLNMINNILEMSKIETEKISIDKQNADLIPIINEGIRLIGSSAQSKNIKIEKKI  648 (766)
Q Consensus       569 ~~~~~~~~~~e~~~~~l~~I~~~~~~l~~lI~diLd~srieag~~~~~~~~~dl~~~i~~~~~~~~~~~~~k~i~l~~~~  648 (766)
                      .+.   . +.   .++.+.+..-..-|..+=+.+|.         .-..+.++|.+++...+.-+.+    .+..+.++.
T Consensus       198 ~R~---~-~~---~~~~~~l~~RI~ALa~aH~~Ll~---------~~~~~~v~l~~ll~~~l~~~~~----~~~ri~~~g  257 (363)
T PRK13559        198 GRA---D-DA---SLYAAAIQERVQALARAHETLLD---------ERGWETVEVEELIRAQVAPYAP----RGTRVAFEG  257 (363)
T ss_pred             CCC---C-CH---HHHHHHHHHHHHHHHHHHHHHHC---------CCCCCCEEHHHHHHHHHHHCCC----CCCEEEEEC
T ss_conf             347---9-84---99999999999999999999865---------7776623299999999985078----886699988


Q ss_pred             CCCCEEEEC-HHHHHHHHHHHHHHHHHCC---CCCCEEEEEEE--EECCEEEEEEEECCCCCCHHHHHHHCCCEEECCCC
Q ss_conf             899789986-8999999999886565346---89888999999--97998999999788978977854304650531467
Q gi|254780903|r  649 PSELFFNAD-KRIIKKILFPILSNSIKFT---NNNGKMMIRTS--KIGQCVIITIADTGIGIPKSALEKIGQPFEPLHNQ  722 (766)
Q Consensus       649 ~~~l~v~~D-~~~l~QVl~NLi~NAik~t---~~~g~I~i~~~--~~~~~v~i~V~D~G~GI~~e~~~~iF~pF~q~~~~  722 (766)
                      + ++.+..+ ...|.-||--|+.||+||.   .++|+|.|+..  ..++.+.+.+.|+|.|.++.               
T Consensus       258 p-~v~l~~~~A~~L~LilhELaTNA~KyGals~~~G~V~V~w~~~~~~~~l~l~W~E~Ggp~v~~---------------  321 (363)
T PRK13559        258 P-GIRLGAASVQPLGLVLHELAVNAIKHGALSADAGRISISWRPSREGGGLVLDWQEQGGPTPPK---------------  321 (363)
T ss_pred             C-CEEECHHHHHHHHHHHHHHHHHHHHHCCCCCCCCEEEEEEEECCCCCEEEEEEECCCCCCCCC---------------
T ss_conf             9-756868887789999999987088735667899779999998178987999997789999989---------------


Q ss_pred             CCCCCCCCCHHHHHHHHHH-HHCCCEEEEEEECCCCEEEEEECC
Q ss_conf             5567788761689999999-962986999979899529999735
Q gi|254780903|r  723 YDQSIGGFGLGLAISDALT-NLHGGRLKIISQEGKGTIVTICMP  765 (766)
Q Consensus       723 ~t~~~~GtGLGLaI~k~iV-e~hgG~I~v~S~~g~Gttf~i~LP  765 (766)
                          ..++|+|.-++.+.+ ...||++..+=.+ .|..++|++|
T Consensus       322 ----p~~~GFGs~LI~~~v~~qL~G~v~~~~~~-~Gl~~~i~~P  360 (363)
T PRK13559        322 ----LQKRGFGTVIISAMVESQLKGQIEKDWAD-DGLLARIEIP  360 (363)
T ss_pred             ----CCCCCCHHHHHHHHHHHHCCCEEEEEECC-CEEEEEEEEE
T ss_conf             ----99998569999999898759879999879-9089999996


No 46 
>cd00075 HATPase_c Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins
Probab=99.94  E-value=1.2e-25  Score=203.20  Aligned_cols=102  Identities=38%  Similarity=0.661  Sum_probs=95.1

Q ss_pred             HHHHHHHHHHHHHHCCCC-CCEEEEEEEEECCEEEEEEEECCCCCCHHHHHHHCCCEEECCCCCCCCCCCCCHHHHHHHH
Q ss_conf             999999988656534689-8889999999799899999978897897785430465053146755677887616899999
Q gi|254780903|r  661 IKKILFPILSNSIKFTNN-NGKMMIRTSKIGQCVIITIADTGIGIPKSALEKIGQPFEPLHNQYDQSIGGFGLGLAISDA  739 (766)
Q Consensus       661 l~QVl~NLi~NAik~t~~-~g~I~i~~~~~~~~v~i~V~D~G~GI~~e~~~~iF~pF~q~~~~~t~~~~GtGLGLaI~k~  739 (766)
                      |+|||.||++||+||+++ .+.|+|++...++.+.|+|+|||+|||++.++++|+||++...  ++..+|+||||++||.
T Consensus         1 l~~vl~nLl~NAik~~~~~~~~I~i~~~~~~~~~~i~V~D~G~Gi~~~~~~~if~~f~~~~~--~~~~~g~GlGL~i~~~   78 (103)
T cd00075           1 LQQVLLNLLSNAIKHTPEGGGRITISVERDGDHLEIRVEDNGPGIPEEDLERIFERFSDGSR--SRKGGGTGLGLSIVKK   78 (103)
T ss_pred             CHHHHHHHHHHHHHHCCCCCCEEEEEEEECCCEEEEEEEECCCCCCHHHHHHCCCCCCCCCC--CCCCCCCCCHHHHHHH
T ss_conf             96999999999998678999489999998399999999977994088999760697501788--8778986505999999


Q ss_pred             HHHHCCCEEEEEEECCCCEEEEEEC
Q ss_conf             9996298699997989952999973
Q gi|254780903|r  740 LTNLHGGRLKIISQEGKGTIVTICM  764 (766)
Q Consensus       740 iVe~hgG~I~v~S~~g~Gttf~i~L  764 (766)
                      +++.|||+|+++|++|+||+|+|+|
T Consensus        79 i~~~~~G~i~i~s~~~~Gt~~~i~l  103 (103)
T cd00075          79 LVELHGGRIEVESEPGGGTTFTITL  103 (103)
T ss_pred             HHHHCCCEEEEEECCCCCEEEEEEC
T ss_conf             9998899899996599919999989


No 47 
>PRK10618 phosphotransfer intermediate protein in two-component regulatory system with RcsBC; Provisional
Probab=99.93  E-value=1.6e-21  Score=173.25  Aligned_cols=327  Identities=18%  Similarity=0.254  Sum_probs=236.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHEEEEC-CCCEEEEECHHHHHHHCCCHHHHCCCCCHHHHCCCHHHHHHHHHHHCCCCCCC
Q ss_conf             99999999999999985445515883-49969970178988839997894289717881652013789998521124564
Q gi|254780903|r  374 EKRYAEADQRLSKAIECTSEALVLWD-KNDRLVMCNANYQKAYGLPDHVLVPGNARSIIQDAQTRPIIEYRTSDPERSQD  452 (766)
Q Consensus       374 e~~l~ese~rlr~~ie~~~~~i~~~D-~~g~i~~~N~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  452 (766)
                      -.+|+-.+..-+.++.++|-|+.++| ...+.+.+|+-+..++-.=+        ..-+..   +.. ++.-.-......
T Consensus       335 ~~eL~~~~~l~~eIIs~lP~GlLVYdF~sN~~i~SNkIAdhLLPhl~--------LqkI~~---MA~-qH~GvIQ~tInN  402 (881)
T PRK10618        335 SGELRILRAINEEIVSLLPLGLLVYDFSSNRTVISNKIADHLLPHLN--------LQKITT---MAE-QHQGVIQATINN  402 (881)
T ss_pred             HHHHHHHHHHHHHHHHCCCCEEEEEECCCCCEEEHHHHHHHHCCCCC--------HHHHHH---HHH-HHCCEEEEEECC
T ss_conf             88999998868889854875069997468957730267886557667--------899999---999-737868998836


Q ss_pred             EEEEEEECCCEEEEECCEECCCCCEEEEEEEEEHHHCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             05899916962874223245699789998862010001122322222221100001788998644457999999999999
Q gi|254780903|r  453 MSKEIKLADSRWLQINEWCTHDGGTISVGTDITLLKHNQAQLRESKRRLKATINDLSTSRQILERQKTELSIANAKYQVE  532 (766)
Q Consensus       453 ~~~e~~~~dg~~~~i~~~~~~dg~~v~v~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~~~~~l~~~  532 (766)
                      ..||+++....        ..+..+...      +.+                .+    ++         .-.+++++.+
T Consensus       403 evYEIr~~rSq--------~~p~T~LFi------i~D----------------qD----kE---------vLvnKkLq~A  439 (881)
T PRK10618        403 ELYEIRMFRSQ--------VAPRTQLFI------IRD----------------QD----RE---------VLVNKKLQQA  439 (881)
T ss_pred             EEEEEEEEECC--------CCCCEEEEE------EEC----------------CC----HH---------HHHHHHHHHH
T ss_conf             06788854225--------787537999------975----------------75----89---------9988999999


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCC
Q ss_conf             99998878999999998767522247899999999860346889938999999999999999999977767788874198
Q gi|254780903|r  533 KERAETANKTKSEFLAKMSHELRTPLNAILGFSEVIKKEIFGELGSVKYYEYAQDIHYSGQHLLNMINNILEMSKIETEK  612 (766)
Q Consensus       533 ~~~ae~an~~k~efla~isHelrtPL~aI~g~~ell~~~~~~~~~~e~~~~~l~~I~~~~~~l~~lI~diLd~srieag~  612 (766)
                      ...-++--+++..|+.||++||+.|+..+.-.+.-+...    . +   .+.+..+...+.++.++|++|--.-++|++.
T Consensus       440 qreYeKN~qaRk~~l~Ni~~el~~Pl~~l~~~~~~l~~~----~-~---~~~l~~L~~qs~~i~~lidnI~Lln~LEsq~  511 (881)
T PRK10618        440 QREYEKNQQARRAFLQNIGDELKEPVQSLAELAAQLNAP----E-S---QQLLKQLAEQADVLVRLIDNIQLANMLENDE  511 (881)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC----C-H---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC
T ss_conf             999986699999999999999877899999999986252----4-4---6799999999999999998899998886056


Q ss_pred             CCCCEEEECHHHHHHHHHHHHHHHHHHCCCEEEEEECC--CCEEEECHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEEE-
Q ss_conf             30120331699999999999999998479589998089--978998689999999998865653468988899999997-
Q gi|254780903|r  613 ISIDKQNADLIPIINEGIRLIGSSAQSKNIKIEKKIPS--ELFFNADKRIIKKILFPILSNSIKFTNNNGKMMIRTSKI-  689 (766)
Q Consensus       613 ~~~~~~~~dl~~~i~~~~~~~~~~~~~k~i~l~~~~~~--~l~v~~D~~~l~QVl~NLi~NAik~t~~~g~I~i~~~~~-  689 (766)
                      -+...++|.+.++|++++...-|.+..||+.|....-.  +-...+|+..|+.|+.=|+.=||--| .-|+|++.+..+ 
T Consensus       512 W~~~~~~Fsl~~Lid~~l~e~Lp~i~~KGL~L~~hn~l~~~~~~~gD~~aLrkil~lLl~YaitTT-~~GKItl~v~~~~  590 (881)
T PRK10618        512 WKSEQTLFSLQDLIDEVVPEVLPAIKRKGLQLLIHNHLKANDMRRGDRDALRKILLLLLQYAVTTT-QYGKITLEVDQDE  590 (881)
T ss_pred             CCCCCCCCCHHHHHHHHHHHHHHHHHHCCCEEEEECCCCHHHHCCCCHHHHHHHHHHHHHHHHHCC-CCCEEEEEEECCC
T ss_conf             765677104999999999987689874270333234798899704789999999999998881114-4525999982587


Q ss_pred             --CCEEEEEEEECCCCCCHHHHHHHCCCEEECCCCCCCCCCCCCHHHHHHHHHHHHCCCEEEEEEECCCCEEEEEECC
Q ss_conf             --9989999997889789778543046505314675567788761689999999962986999979899529999735
Q gi|254780903|r  690 --GQCVIITIADTGIGIPKSALEKIGQPFEPLHNQYDQSIGGFGLGLAISDALTNLHGGRLKIISQEGKGTIVTICMP  765 (766)
Q Consensus       690 --~~~v~i~V~D~G~GI~~e~~~~iF~pF~q~~~~~t~~~~GtGLGLaI~k~iVe~hgG~I~v~S~~g~Gttf~i~LP  765 (766)
                        .+.+.|.|.|||.|++.+.++.+=-||- .+....+-..|+||-.++|+.+...|||...+.|.++-||.++|+||
T Consensus       591 ~~~~~l~i~i~DTG~Gls~~El~Nl~~PFl-~~t~~Dry~~~SGlTf~LC~qLc~KlgG~l~I~Sk~~iGT~Y~i~lp  667 (881)
T PRK10618        591 SSEERLTFRILDTGEGVSIHEIDNLHFPFL-NQTQGDRYGKASGLTFWLCNQLCRKLGGHLNIKSREDLGTRYSVHLK  667 (881)
T ss_pred             CCCCEEEEEEECCCCCCCHHHHHHCCCCCC-CCHHHHHCCCCCCCHHHHHHHHHHHHCCEEEEECCCCCCCCEEEEEC
T ss_conf             778638999954788878888855379776-83122111378872999999999984896788415677664799842


No 48 
>PRK11359 cAMP phosphodiesterase; Provisional
Probab=99.92  E-value=3.5e-22  Score=178.08  Aligned_cols=236  Identities=13%  Similarity=0.152  Sum_probs=175.5

Q ss_pred             HHHHHHHHHHHHHHHCCCCCEEEEECCCCEEEECHHHHHHCCCCHHHCCCCHHHHHHHHCCCCHHHHHH-HHHHHH---C
Q ss_conf             999999999999972259745989768978999788997729994330589889997608120589999-999972---4
Q gi|254780903|r  248 TILLEANICVETALSRGRCGLWNFNFDNKKFHLSRSMYEIMGIPYENKTLSFRAIARLIHYDNKKICEI-ARSVTG---K  323 (766)
Q Consensus       248 ~~l~ese~rl~~al~~a~~GiWd~D~~~~~i~ws~~~~~llG~~~~e~~~s~~~~~~~vHPdDr~~~~~-a~~~~~---~  323 (766)
                      ++..+++.+|+.+++.+++|++..|.+++.++||+++++||||++++..+.  .+..++|+++...... ......   .
T Consensus         5 ~~~~~~~~~fr~~lE~s~~GIviiD~~GrIv~~N~aa~~l~GYs~eEllG~--~~~~L~p~d~~~~~~~~l~~~~~~g~~   82 (799)
T PRK11359          5 DADNAADGIFFPALEQNMMGAVLINENDEVMFFNPAAEKLWGYKREEVIGN--NIDMLIPRDLRPAHPEYIRHNREGGKA   82 (799)
T ss_pred             CCCCCCHHHHHHHHHHCCCEEEEECCCCCEEEECHHHHHHHCCCHHHHCCC--CHHHHCCCCCCHHHHHHHHHHHHCCCC
T ss_conf             013454799999996188549999699909987189999879299998599--889927853331239999987742655


Q ss_pred             CCCEEEEEEEEECCCCCEEEEEEEEEEEEECCCEEEEEEEEECCCHHHHHHHHHHHHHHHHHHHHHHHHHHEEEECCCCE
Q ss_conf             89848999998869898899889999998379606999998446179999999999999999999854455158834996
Q gi|254780903|r  324 HVKQLDQIFHMRHASGADIWIQVRAQMMRTISGGMNIIGIAMDLTEKYHLEKRYAEADQRLSKAIECTSEALVLWDKNDR  403 (766)
Q Consensus       324 ~~~~~~~e~Ri~~~DG~~~Wi~~r~~~i~d~~G~~~~iGi~~DITErK~ae~~l~ese~rlr~~ie~~~~~i~~~D~~g~  403 (766)
                      ....+..|++++++||+.+|++....++ +.+|++.++++++|||+++.    +++++.++..++++++++++++|.+++
T Consensus        83 ~~~g~~~E~~~~RKDGs~~~velsvs~i-~~~g~i~~l~ivrDITee~a----~~e~~r~l~~~ld~~~~~I~i~D~~g~  157 (799)
T PRK11359         83 RVEGMSRELQLEKKDGSKIWTRFALSKV-SAEGKVYYLALVRDASVEMA----QKEQTRQLIIAVDHLDRPVIVLDPERH  157 (799)
T ss_pred             CCCCCEEEEEEECCCCCEEEEEEEEEEE-CCCCCEEEEEEEEECCHHHH----HHHHHHHHHHHHHCCCCEEEEECCCCC
T ss_conf             4456404899985888899999999776-47992899999997689999----999999999998626872999918987


Q ss_pred             EEEECHHHHHHHCCCHHHHCCCCCHHHHCCCHHHHHHHHHHHC---CCCCCCEEEEEEECCCE--EEEECCEEC--CCC-
Q ss_conf             9970178988839997894289717881652013789998521---12456405899916962--874223245--699-
Q gi|254780903|r  404 LVMCNANYQKAYGLPDHVLVPGNARSIIQDAQTRPIIEYRTSD---PERSQDMSKEIKLADSR--WLQINEWCT--HDG-  475 (766)
Q Consensus       404 i~~~N~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~e~~~~dg~--~~~i~~~~~--~dg-  475 (766)
                      ++++|++|++++||+.+++.+.++.+.+..+.........+..   .......++.....||+  |...+..+.  .+| 
T Consensus       158 i~~vN~a~~el~Gy~~eEl~G~~~~~ll~~pe~~~~~~~~~~~~l~~~~~~~~E~~~~~kdG~~~wv~~s~~pi~d~~g~  237 (799)
T PRK11359        158 IVQCNRAFTEMFGYCISEASGMQPDTLLNIPEFPADNRIRLQQLLWKTARDQDEFLLLTRTGEKIWIKASISPVYDVLAH  237 (799)
T ss_pred             EEEECHHHHHHHCCCHHHHCCCCHHHHHCCCCCCHHHHHHHHHHHHCCCCCEEEEEEECCCCCEEEEEEEEEEEECCCCC
T ss_conf             89987789998599878974898899834878847999999999864897305899982699799999898899848898


Q ss_pred             --CEEEEEEEEEHHHCC
Q ss_conf             --789998862010001
Q gi|254780903|r  476 --GTISVGTDITLLKHN  490 (766)
Q Consensus       476 --~~v~v~~~i~~~~~~  490 (766)
                        +++.+..|||+.+..
T Consensus       238 ~~~~v~i~~DITErr~~  254 (799)
T PRK11359        238 LQNLVMTFSDITEERQI  254 (799)
T ss_pred             EEEEEEEEEECCHHHHH
T ss_conf             88999999731588899


No 49 
>KOG0519 consensus
Probab=99.92  E-value=5.3e-26  Score=205.64  Aligned_cols=233  Identities=25%  Similarity=0.303  Sum_probs=202.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHH--HHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             99999999999887899999--9998767522247899999999860346889938999999999999999999977767
Q gi|254780903|r  526 NAKYQVEKERAETANKTKSE--FLAKMSHELRTPLNAILGFSEVIKKEIFGELGSVKYYEYAQDIHYSGQHLLNMINNIL  603 (766)
Q Consensus       526 ~~~l~~~~~~ae~an~~k~e--fla~isHelrtPL~aI~g~~ell~~~~~~~~~~e~~~~~l~~I~~~~~~l~~lI~diL  603 (766)
                      .-.+.+.....+.+...+++  |++++|||||+|++.  |....+    .++..+..++.+.+.++.++..++.++++++
T Consensus       202 ~~~~~~~~~~~e~~~~~~sq~~~~~~~sHeir~p~~~--~~~~~~----~~t~~~~~~~~~~~~~~~~~~~~~s~ln~i~  275 (786)
T KOG0519         202 LVELQKKLASDEAAVWSPSQKGFLATLSHEIRTPLNG--GMLGGL----SDTDLDSDQRLILNTDRVSAKSLLSLLNDIL  275 (786)
T ss_pred             HHHHHHHHCCCCCHHCCCCCHHCCCCCCCEEECCCCC--CCCCEE----ECCCCCHHHHHHHCCCHHHHHCHHHHHHHHH
T ss_conf             5212566512530002742011134456324434445--664122----0344215689874300122000013777764


Q ss_pred             HHHHHHCCCCCCCEEEECHHHHHHHHHHHHHHHHHHCCCEEEEEECCCCE--EEECHHHHHHHHHHHHHHHHHCCCCCCE
Q ss_conf             78887419830120331699999999999999998479589998089978--9986899999999988656534689888
Q gi|254780903|r  604 EMSKIETEKISIDKQNADLIPIINEGIRLIGSSAQSKNIKIEKKIPSELF--FNADKRIIKKILFPILSNSIKFTNNNGK  681 (766)
Q Consensus       604 d~srieag~~~~~~~~~dl~~~i~~~~~~~~~~~~~k~i~l~~~~~~~l~--v~~D~~~l~QVl~NLi~NAik~t~~~g~  681 (766)
                      |.+++++|.+.+.-.+||+..+++.++..+.+.+.+|++.+....+.+.|  +.+|+.++.||+.|+++||+||++. |.
T Consensus       276 d~~~v~~g~~~l~~~rf~l~~ll~~~~~~~~~~~~~~~~~~~~~~~~~~p~~v~~de~~~~qv~~n~v~naik~t~~-~~  354 (786)
T KOG0519         276 DLSKVESGKGELVAKRFDLRTLLNFVISLLSELSQAKYAILVLDLSSGVPRNVRGDEARLRQVIANLVSNAIKFTHA-GH  354 (786)
T ss_pred             HHCCCCCCCCCCEECCCCHHHHHHHHHHHHHHHHHCCCCEEEECCCCCCCCCCCCCCCCCCCCCHHHCCCCCCCCCC-CC
T ss_conf             01135323554032234526666777877666551367346520787776420356101100033320144354446-62


Q ss_pred             EEEEEEEEC------------------------------------------------CEEEEEEEECCCCCCHHHHHH-H
Q ss_conf             999999979------------------------------------------------989999997889789778543-0
Q gi|254780903|r  682 MMIRTSKIG------------------------------------------------QCVIITIADTGIGIPKSALEK-I  712 (766)
Q Consensus       682 I~i~~~~~~------------------------------------------------~~v~i~V~D~G~GI~~e~~~~-i  712 (766)
                      |.++....+                                                -.-.+.+.|+|+||+.+.... +
T Consensus       355 i~~~~~~~~~~~~~~~~l~~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~l~~~~~~~~~~~~~i~~~~~~~~~  434 (786)
T KOG0519         355 LEESVIAREELSESNDVLLRAKEEAHMAGKARIDFLQKMSHAMRAPRHNIISLLSLLLQDIVLSPDSGLEIQTVMRSSNV  434 (786)
T ss_pred             EEEEEEECHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHCCCCCCCCCCCCCCCHHHHHHEEECCCCCEEEEECCCCHHH
T ss_conf             24666512110046789975457765351556678887413312422042122357665202236664068502330465


Q ss_pred             CCCEEECCCCCCCCCCCCCHHHHHHHHHHHHCCCEEEEEEECCCCEEEEEECC
Q ss_conf             46505314675567788761689999999962986999979899529999735
Q gi|254780903|r  713 GQPFEPLHNQYDQSIGGFGLGLAISDALTNLHGGRLKIISQEGKGTIVTICMP  765 (766)
Q Consensus       713 F~pF~q~~~~~t~~~~GtGLGLaI~k~iVe~hgG~I~v~S~~g~Gttf~i~LP  765 (766)
                      |.+|-|+....++.++|||+|+.+|++++++++|.+.+.+.+..|++|+|++|
T Consensus       435 ~~~~~q~~~~~~~~~~gt~~~~~i~~~l~~l~~~~~~~~~~~~~~~t~~~~~~  487 (786)
T KOG0519         435 FTSLIQADPDITRLYGGTGLGESIVFSLVELMSGEISDISCISLGKTFSFTLD  487 (786)
T ss_pred             HHHHHCCCHHCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHCCCCCEEEEEEC
T ss_conf             55451466100345687645332223288998867432110034752223312


No 50 
>PRK10547 chemotaxis protein CheA; Provisional
Probab=99.86  E-value=5.5e-19  Score=154.98  Aligned_cols=142  Identities=24%  Similarity=0.415  Sum_probs=115.8

Q ss_pred             EECHHHHHHHHHHHHHHHHHH--CCCEEEEEECCCCEEEECHHHHHHH---HHHHHHHHHHCC------------CCCCE
Q ss_conf             316999999999999999984--7958999808997899868999999---999886565346------------89888
Q gi|254780903|r  619 NADLIPIINEGIRLIGSSAQS--KNIKIEKKIPSELFFNADKRIIKKI---LFPILSNSIKFT------------NNNGK  681 (766)
Q Consensus       619 ~~dl~~~i~~~~~~~~~~~~~--k~i~l~~~~~~~l~v~~D~~~l~QV---l~NLi~NAik~t------------~~~g~  681 (766)
                      .+.+..+....-++++..+.+  |.+.|.+...+   +..|+.-|.++   |+.||.||++|.            |+.|+
T Consensus       334 MvP~~~lf~r~~R~VRdlar~~gK~V~L~i~G~d---telDr~Ile~L~dPL~HLlRNAvDHGIE~peeR~a~GKp~~G~  410 (662)
T PRK10547        334 MMPMEYVFSRFPRLVRDLAGKLGKQVELTLVGSS---TELDKSLIERIIDPLTHLVRNSLDHGIELPEKRLAAGKNSVGN  410 (662)
T ss_pred             CEEHHHHHHHHHHHHHHHHHHHCCEEEEEEECCC---EEEHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHCCCCCEEE
T ss_conf             5218998888789999999986982599996686---7771999998887999998742430489988998759997279


Q ss_pred             EEEEEEEECCEEEEEEEECCCCCCHHHH---------------------HHHCCC-EEECCCCCCCCCCCCCHHHHHHHH
Q ss_conf             9999999799899999978897897785---------------------430465-053146755677887616899999
Q gi|254780903|r  682 MMIRTSKIGQCVIITIADTGIGIPKSAL---------------------EKIGQP-FEPLHNQYDQSIGGFGLGLAISDA  739 (766)
Q Consensus       682 I~i~~~~~~~~v~i~V~D~G~GI~~e~~---------------------~~iF~p-F~q~~~~~t~~~~GtGLGLaI~k~  739 (766)
                      |+++++..+++|+|+|+|+|-||+.+..                     .-||.| |.+.+.  .+...|-|.||-+||+
T Consensus       411 I~l~a~~~g~~v~I~v~DDGrGiD~e~Ir~kAv~kGL~~~e~lsd~e~~~LIF~PGFSTa~~--Vt~lSGRGVGmDVV~~  488 (662)
T PRK10547        411 LILSAEHQGGNICIEVTDDGAGLNRERILAKAASQGLAVSENMSDDEVGMLIFAPGFSTAEQ--VTDVSGRGVGMDVVKR  488 (662)
T ss_pred             EEEEEEECCCEEEEEEEECCCCCCHHHHHHHHHHCCCCCCCCCCHHHHHHHHHCCCCCCCCC--CCCCCCCCCCHHHHHH
T ss_conf             99999985999999998189998999999999984999853389999999971799862322--3568886646899999


Q ss_pred             HHHHCCCEEEEEEECCCCEEEEEECC
Q ss_conf             99962986999979899529999735
Q gi|254780903|r  740 LTNLHGGRLKIISQEGKGTIVTICMP  765 (766)
Q Consensus       740 iVe~hgG~I~v~S~~g~Gttf~i~LP  765 (766)
                      -|+.+||+|.|+|++|+||+|+++||
T Consensus       489 ~v~~l~G~v~v~S~~G~GT~F~l~lP  514 (662)
T PRK10547        489 NIQEMGGHVEIQSKQGTGTTIRILLP  514 (662)
T ss_pred             HHHHCCCEEEEEEECCCCEEEEEECC
T ss_conf             99982998999960898079999788


No 51 
>COG0643 CheA Chemotaxis protein histidine kinase and related kinases [Cell motility and secretion / Signal transduction mechanisms]
Probab=99.84  E-value=8.5e-18  Score=146.40  Aligned_cols=167  Identities=20%  Similarity=0.406  Sum_probs=127.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCEEEECHHHHHHHHHHHHHHHHH--HCCCEEEEEECCCCEEEECHHHHHH
Q ss_conf             99999999999997776778887419830120331699999999999999998--4795899980899789986899999
Q gi|254780903|r  586 QDIHYSGQHLLNMINNILEMSKIETEKISIDKQNADLIPIINEGIRLIGSSAQ--SKNIKIEKKIPSELFFNADKRIIKK  663 (766)
Q Consensus       586 ~~I~~~~~~l~~lI~diLd~srieag~~~~~~~~~dl~~~i~~~~~~~~~~~~--~k~i~l~~~~~~~l~v~~D~~~l~Q  663 (766)
                      +........+.+++.+|-+--      |..  ..+.+..++..--++++..+.  .|.|+|.++..+   ...|+.-|.+
T Consensus       364 ~el~~~~~~l~~~~~~LQd~v------m~~--RMvP~~~vf~RfpR~VRdla~~lgK~V~L~ieG~~---telDksIlE~  432 (716)
T COG0643         364 EELDEALRQLSRLTTDLQDEV------MKI--RMVPFEQVFSRFPRMVRDLARKLGKQVELVIEGED---TELDKSILER  432 (716)
T ss_pred             HHHHHHHHHHHHHHHHHHHHH------HHH--HCEEHHHHHHHCCHHHHHHHHHHCCEEEEEEECCC---EEEHHHHHHH
T ss_conf             999999999999999999999------997--00039998744409999999986991699996487---1342989988


Q ss_pred             H---HHHHHHHHHHC------------CCCCCEEEEEEEEECCEEEEEEEECCCCCCHHH--------------------
Q ss_conf             9---99988656534------------689888999999979989999997889789778--------------------
Q gi|254780903|r  664 I---LFPILSNSIKF------------TNNNGKMMIRTSKIGQCVIITIADTGIGIPKSA--------------------  708 (766)
Q Consensus       664 V---l~NLi~NAik~------------t~~~g~I~i~~~~~~~~v~i~V~D~G~GI~~e~--------------------  708 (766)
                      +   |+.||.||++|            -|+.|+|++++...++.++|+|+|+|-||+++.                    
T Consensus       433 l~dPL~HLvRNAvDHGIE~pE~R~a~GKp~~G~I~L~A~~~gn~ivIev~DDG~Gid~ekI~~KAiErGli~~~~a~~lS  512 (716)
T COG0643         433 LGDPLTHLVRNAVDHGIETPEERRAAGKPEEGTITLSAYHEGNNIVIEVSDDGAGIDREKIREKAIERGLITEEEAETLS  512 (716)
T ss_pred             HCCCHHHHHHCCHHCCCCCHHHHHHCCCCCCCEEEEEEECCCCEEEEEEEECCCCCCHHHHHHHHHHCCCCCHHHHCCCC
T ss_conf             64669988850011058988999875989863699999837986999995689987999999999982998867752079


Q ss_pred             ----HHHHCCC-EEECCCCCCCCCCCCCHHHHHHHHHHHHCCCEEEEEEECCCCEEEEEECC
Q ss_conf             ----5430465-05314675567788761689999999962986999979899529999735
Q gi|254780903|r  709 ----LEKIGQP-FEPLHNQYDQSIGGFGLGLAISDALTNLHGGRLKIISQEGKGTIVTICMP  765 (766)
Q Consensus       709 ----~~~iF~p-F~q~~~~~t~~~~GtGLGLaI~k~iVe~hgG~I~v~S~~g~Gttf~i~LP  765 (766)
                          ..-||.| |.+.+.  -+...|-|.||=+||+-|+.+||+|.|+|++|+||+|++.||
T Consensus       513 d~Ei~~LIF~PGFSTa~~--VtdvSGRGVGMDVVk~~I~~LgG~I~V~S~~G~GT~Fti~LP  572 (716)
T COG0643         513 DEEILNLIFAPGFSTAEQ--VTDVSGRGVGMDVVKTNIEQLGGSISVSSEPGKGTTFTIRLP  572 (716)
T ss_pred             HHHHHHHHHCCCCCCCHH--HHCCCCCCCCHHHHHHHHHHCCCEEEEEECCCCCEEEEEECC
T ss_conf             999998873699873411--101657765789999999973998999962789769999668


No 52 
>PRK10935 nitrate/nitrite sensor protein NarQ; Provisional
Probab=99.84  E-value=3.9e-17  Score=141.62  Aligned_cols=190  Identities=20%  Similarity=0.279  Sum_probs=133.8

Q ss_pred             HHHHHHHHHHHHHHHHHHH----HHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCEEEECHH
Q ss_conf             9876752224789999999----986034688993899999999999999999997776778887419830120331699
Q gi|254780903|r  548 AKMSHELRTPLNAILGFSE----VIKKEIFGELGSVKYYEYAQDIHYSGQHLLNMINNILEMSKIETEKISIDKQNADLI  623 (766)
Q Consensus       548 a~isHelrtPL~aI~g~~e----ll~~~~~~~~~~e~~~~~l~~I~~~~~~l~~lI~diLd~srieag~~~~~~~~~dl~  623 (766)
                      +.|+|||-.+|.-.+.|..    ++.+.+......++..+.+..+.+.......=+..+|.-.|     .  .....+|.
T Consensus       366 ~~IARELHDsLaQ~Ls~lkiq~~lL~~~l~~~~~~~~~~~~l~~i~~~l~~a~~qlReLl~~fR-----l--~l~~~~L~  438 (568)
T PRK10935        366 ATIARELHDSLAQVLSYLKIQLTLLKRSLPKSCDNAKAESIIADFDEGLSDAYRQLRELLTTFR-----L--TIQEANLG  438 (568)
T ss_pred             HHHHHHHCCHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC-----C--CCCCCCHH
T ss_conf             8999984412665789999999999987422565388999999999999999999999999832-----2--67756879


Q ss_pred             HHHHHHHHHHHHHHHHCCCEEEEEEC-CCCEEEECH-HHHHHHHHHHHHHHHHCCCCCCEEEEEEEEEC-CEEEEEEEEC
Q ss_conf             99999999999999847958999808-997899868-99999999988656534689888999999979-9899999978
Q gi|254780903|r  624 PIINEGIRLIGSSAQSKNIKIEKKIP-SELFFNADK-RIIKKILFPILSNSIKFTNNNGKMMIRTSKIG-QCVIITIADT  700 (766)
Q Consensus       624 ~~i~~~~~~~~~~~~~k~i~l~~~~~-~~l~v~~D~-~~l~QVl~NLi~NAik~t~~~g~I~i~~~~~~-~~v~i~V~D~  700 (766)
                      +.++..++.++.+   .++.+.+++. ++.++..+. ..+-||+.+.++|++||+ ..++|+|++...+ +.+.++|+||
T Consensus       439 ~AL~~~~~~~~~q---~~~~i~l~~~l~~~~l~~~~~i~llrIvqEALtN~~KHA-~A~~V~V~~~~~~~~~v~l~V~Dn  514 (568)
T PRK10935        439 SALEEMLDQLRNQ---TSAKITLDCRLPSQALDAQQQVHLLQIIREATLNAIKHA-NASEIAVSCVTNPDGEVTVSIRDD  514 (568)
T ss_pred             HHHHHHHHHHHHH---CCCEEEEECCCCCCCCCHHHHHHHHHHHHHHHHHHHHHC-CCCEEEEEEEECCCCEEEEEEEEC
T ss_conf             9999999999751---194699970688777888899999999999999999808-998799999974898799999779


Q ss_pred             CCCCCHHHHHHHCCCEEECCCCCCCCCCCCCHHHHHHHHHHHHCCCEEEEEEECCCCEEEEEECCC
Q ss_conf             897897785430465053146755677887616899999999629869999798995299997359
Q gi|254780903|r  701 GIGIPKSALEKIGQPFEPLHNQYDQSIGGFGLGLAISDALTNLHGGRLKIISQEGKGTIVTICMPQ  766 (766)
Q Consensus       701 G~GI~~e~~~~iF~pF~q~~~~~t~~~~GtGLGLaI~k~iVe~hgG~I~v~S~~g~Gttf~i~LP~  766 (766)
                      |+|||+..                 . .+.++||.|.+.-++.+||++.++|.||.||++++++|.
T Consensus       515 G~Gf~~~~-----------------~-~~~h~GL~iMrERa~~lgG~l~i~s~p~~GT~V~l~~P~  562 (568)
T PRK10935        515 GVGIGELK-----------------E-PEGHYGLNIMHERASRLGGTLTFSQNPGGGTTVSLTFPS  562 (568)
T ss_pred             CCCCCCCC-----------------C-CCCCCCHHHHHHHHHHCCCEEEEEECCCCCEEEEEEECC
T ss_conf             94789878-----------------8-899857599999999669989999779996699998589


No 53 
>PRK10600 nitrate/nitrite sensor protein NarX; Provisional
Probab=99.75  E-value=1.4e-14  Score=123.23  Aligned_cols=193  Identities=12%  Similarity=0.174  Sum_probs=137.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCEEEECH
Q ss_conf             99999987675222478999999998603468899389999999999999999999777677888741983012033169
Q gi|254780903|r  543 KSEFLAKMSHELRTPLNAILGFSEVIKKEIFGELGSVKYYEYAQDIHYSGQHLLNMINNILEMSKIETEKISIDKQNADL  622 (766)
Q Consensus       543 k~efla~isHelrtPL~aI~g~~ell~~~~~~~~~~e~~~~~l~~I~~~~~~l~~lI~diLd~srieag~~~~~~~~~dl  622 (766)
                      ++-.+--+-..+-+.|+.+.--+++++...  +..+++.++.+..|.........-+..+|.--|     .+  ...-+|
T Consensus       362 R~~IARELHDslaQ~Ls~Lkiq~~~l~~~~--~~~~~~~~~~l~~i~~~~~~a~~~lReLl~~fR-----~~--l~~~~l  432 (569)
T PRK10600        362 RATIARELHDSIAQSLSCMKMQVSCLQMQG--DALPESSRELLSQIRNELNASWAQLRELLTTFR-----LQ--LTEPGL  432 (569)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHC--CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHC-----CC--CCCCCH
T ss_conf             999999988887222789999999999730--579888999999999999999999999999835-----57--775667


Q ss_pred             HHHHHHHHHHHHHHHHHCCCEEEEEECCCC-EEEE-CHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEEECCEEEEEEEEC
Q ss_conf             999999999999999847958999808997-8998-68999999999886565346898889999999799899999978
Q gi|254780903|r  623 IPIINEGIRLIGSSAQSKNIKIEKKIPSEL-FFNA-DKRIIKKILFPILSNSIKFTNNNGKMMIRTSKIGQCVIITIADT  700 (766)
Q Consensus       623 ~~~i~~~~~~~~~~~~~k~i~l~~~~~~~l-~v~~-D~~~l~QVl~NLi~NAik~t~~~g~I~i~~~~~~~~v~i~V~D~  700 (766)
                      .+-++..++.++.+.   ++.+.+++..+. ++.. -...+-||+..-++|++||... .+|+|+....++.+.++|+||
T Consensus       433 ~~aL~~~i~~~~~~~---g~~i~l~~~~~~~~l~~~~~i~l~rIvqEALsNv~KHA~A-~~v~V~l~~~~~~~~l~I~Dd  508 (569)
T PRK10600        433 RPALEASCEEFSARF---GFPVKLDYQLPPRLVPSHQAIHLLQIAREALSNALKHAQA-SEVVVTVAQNDNQVKLSVQDN  508 (569)
T ss_pred             HHHHHHHHHHHHHHC---CCEEEEEECCCCCCCCHHHHHHHHHHHHHHHHHHHHCCCC-CEEEEEEEECCCEEEEEEEEC
T ss_conf             999999999999760---9779999558866798789999999999999999970899-879999997699899999889


Q ss_pred             CCCCCHHHHHHHCCCEEECCCCCCCCCCCCCHHHHHHHHHHHHCCCEEEEEEECCCCEEEEEECCC
Q ss_conf             897897785430465053146755677887616899999999629869999798995299997359
Q gi|254780903|r  701 GIGIPKSALEKIGQPFEPLHNQYDQSIGGFGLGLAISDALTNLHGGRLKIISQEGKGTIVTICMPQ  766 (766)
Q Consensus       701 G~GI~~e~~~~iF~pF~q~~~~~t~~~~GtGLGLaI~k~iVe~hgG~I~v~S~~g~Gttf~i~LP~  766 (766)
                      |+|+|++                  ...+.+.||.|-+.=++..||++.++|.||+||++++++|.
T Consensus       509 G~Gf~~~------------------~~~~~h~GL~iMrERa~~lgG~l~i~s~p~~GT~V~l~f~P  556 (569)
T PRK10600        509 GCGVPEN------------------AERSNHYGLIIMRDRAQSLRGDCSVRRRESGGTEVVVTFIP  556 (569)
T ss_pred             CCCCCCC------------------CCCCCCCCHHHHHHHHHHCCCEEEEEECCCCCEEEEEEECC
T ss_conf             9898988------------------88899978159999999769989998669995899999758


No 54 
>PRK11644 sensory histidine kinase UhpB; Provisional
Probab=99.69  E-value=1.2e-13  Score=116.48  Aligned_cols=191  Identities=17%  Similarity=0.251  Sum_probs=134.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCEEEECH
Q ss_conf             99999987675222478999999998603468899389999999999999999999777677888741983012033169
Q gi|254780903|r  543 KSEFLAKMSHELRTPLNAILGFSEVIKKEIFGELGSVKYYEYAQDIHYSGQHLLNMINNILEMSKIETEKISIDKQNADL  622 (766)
Q Consensus       543 k~efla~isHelrtPL~aI~g~~ell~~~~~~~~~~e~~~~~l~~I~~~~~~l~~lI~diLd~srieag~~~~~~~~~dl  622 (766)
                      +.+..--.--|+-+-|++|.-.+.++++...+   +...++..+.|...+.++.+-+.+++.-=|      ....+.+.|
T Consensus       304 Rr~IARELHDEiGQ~LTAIr~~a~~i~r~~~~---~~~~~~~a~~I~~l~~~i~~~vR~ll~~LR------P~~LDdLGL  374 (497)
T PRK11644        304 RRDVARELHDEIGQTITAIRTQASIVKRLAAD---NASVKQSGQLIEQLSLGVYDAVRRLLGRLR------PRQLDDLTL  374 (497)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCC---CHHHHHHHHHHHHHHHHHHHHHHHHHHHCC------CCCHHHCCH
T ss_conf             99999970003405999999999998632699---766899999999999999999999998609------031112489


Q ss_pred             HHHHHHHHHHHHHHHHHCCCEEEEEECCCCE-EE-ECHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEEECCEEEEEEEEC
Q ss_conf             9999999999999998479589998089978-99-868999999999886565346898889999999799899999978
Q gi|254780903|r  623 IPIINEGIRLIGSSAQSKNIKIEKKIPSELF-FN-ADKRIIKKILFPILSNSIKFTNNNGKMMIRTSKIGQCVIITIADT  700 (766)
Q Consensus       623 ~~~i~~~~~~~~~~~~~k~i~l~~~~~~~l~-v~-~D~~~l~QVl~NLi~NAik~t~~~g~I~i~~~~~~~~v~i~V~D~  700 (766)
                      .+.++..++.+...  ..++.+..+...+.. +. .-...+-.|...-++|++||... .+|.|+....++.+.++|+||
T Consensus       375 ~~AL~~Lv~e~~~~--~~gi~~~l~~~~~~~~L~~~~~itlYRIvQEaLTNi~KHA~A-~~V~I~L~~~~~~l~L~I~DD  451 (497)
T PRK11644        375 EQAIRSLMRELELE--DRGIVSHLDWQIDESALSETQRVTLFRVCQEGLNNIVKHADA-SAVTIQGWQQDERLMLVIEDN  451 (497)
T ss_pred             HHHHHHHHHHHHHH--CCCCEEEEEECCCCCCCCHHHHHHHHHHHHHHHHHHHHCCCC-CEEEEEEEECCCEEEEEEEEC
T ss_conf             99999999987652--579559998268766798246889999999999999973788-769999997699899999889


Q ss_pred             CCCCCHHHHHHHCCCEEECCCCCCCCCCCCCHHHHHHHHHHHHCCCEEEEEEECCCCEEEEEECCC
Q ss_conf             897897785430465053146755677887616899999999629869999798995299997359
Q gi|254780903|r  701 GIGIPKSALEKIGQPFEPLHNQYDQSIGGFGLGLAISDALTNLHGGRLKIISQEGKGTIVTICMPQ  766 (766)
Q Consensus       701 G~GI~~e~~~~iF~pF~q~~~~~t~~~~GtGLGLaI~k~iVe~hgG~I~v~S~~g~Gttf~i~LP~  766 (766)
                      |+|++++.               .+    .|+||.--|.=|+..||++.++|++  ||+..|+||+
T Consensus       452 G~Gf~~~~---------------~~----~G~GL~GMrERV~aLGG~l~I~S~~--GT~I~V~LP~  496 (497)
T PRK11644        452 GSGLPPGS---------------GQ----QGFGLRGMQERVSALGGTLTISCTH--GTRLSVTLPQ  496 (497)
T ss_pred             CCCCCCCC---------------CC----CCCCCHHHHHHHHHCCCEEEEEECC--CCEEEEECCC
T ss_conf             98989898---------------99----9989267999999749979998289--9779995899


No 55 
>pfam08447 PAS_3 PAS fold. The PAS fold corresponds to the structural domain that has previously been defined as PAS and PAC motifs. The PAS fold appears in archaea, eubacteria and eukarya.
Probab=99.67  E-value=1.3e-15  Score=130.66  Aligned_cols=88  Identities=22%  Similarity=0.344  Sum_probs=80.4

Q ss_pred             EEEECHHHHHHCCCCHHHCCCCHHHHHHHHCCCCHHHHHHHH-HHHHCCCCEEEEEEEEECCCCCEEEEEEEEEEEEECC
Q ss_conf             899978899772999433058988999760812058999999-9972489848999998869898899889999998379
Q gi|254780903|r  277 KFHLSRSMYEIMGIPYENKTLSFRAIARLIHYDNKKICEIAR-SVTGKHVKQLDQIFHMRHASGADIWIQVRAQMMRTIS  355 (766)
Q Consensus       277 ~i~ws~~~~~llG~~~~e~~~s~~~~~~~vHPdDr~~~~~a~-~~~~~~~~~~~~e~Ri~~~DG~~~Wi~~r~~~i~d~~  355 (766)
                      .+|||+++++||||+|++...++..|.+++||||++.+..+. +.+.+....++.|||++++||+++|+..++.+++|++
T Consensus         1 v~y~s~~~~~i~G~~~~e~~~~~~~~~~~ihpdD~~~~~~~~~~~~~~~~~~~~~e~R~~~~dG~~~wi~~~~~~~~d~~   80 (90)
T pfam08447         1 IIYWSPRFEEILGYTPEELKSSYEDWLDLVHPEDRERVRRALQEFSLKKGEPYSGEYRIRRKDGEYRWVEARGRPIRDEN   80 (90)
T ss_pred             CEEECHHHHHHHCCCCHHCCCCHHHHHHHCCCHHHHHHHHHHHHHHHHCCCCEEEEEEEECCCCCEEEEEEEEEEEECCC
T ss_conf             99999899998499901107998899987190568899988788886058740468999815993999999999999999


Q ss_pred             CEE-EEEEEE
Q ss_conf             606-999998
Q gi|254780903|r  356 GGM-NIIGIA  364 (766)
Q Consensus       356 G~~-~~iGi~  364 (766)
                      |++ +++||+
T Consensus        81 G~~~~~~Gi~   90 (90)
T pfam08447        81 GKPVRVIGVA   90 (90)
T ss_pred             CCEEEEEEEC
T ss_conf             9999999689


No 56 
>COG3920 Signal transduction histidine kinase [Signal transduction mechanisms]
Probab=99.66  E-value=2.6e-13  Score=114.04  Aligned_cols=188  Identities=21%  Similarity=0.297  Sum_probs=139.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCC---CEE
Q ss_conf             99999998767522247899999999860346889938999999999999999999977767788874198301---203
Q gi|254780903|r  542 TKSEFLAKMSHELRTPLNAILGFSEVIKKEIFGELGSVKYYEYAQDIHYSGQHLLNMINNILEMSKIETEKISI---DKQ  618 (766)
Q Consensus       542 ~k~efla~isHelrtPL~aI~g~~ell~~~~~~~~~~e~~~~~l~~I~~~~~~l~~lI~diLd~srieag~~~~---~~~  618 (766)
                      .|.-++.-+.|-++|-|..|.+.+.+-.+...++     ..+++..          ..+.+..||.+   +-.+   ...
T Consensus        18 ~~~~ll~Ei~HRVKNnLqiIsSll~lq~r~~~~~-----~~e~~~~----------~~~Ri~sla~~---He~L~~s~~~   79 (221)
T COG3920          18 EKELLLREIHHRVKNNLQIISSLLRLQARKFEDE-----VLEALRE----------SQNRIQSLALI---HELLYKSGDD   79 (221)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCH-----HHHHHHH----------HHHHHHHHHHH---HHHHCCCCCC
T ss_conf             8999999999998879999999999777523667-----8999999----------98899999999---9998068865


Q ss_pred             EECHHHHHHHHHHHHHHHHHHCCCEEEEEECCCCEEEECH-HHHHHHHHHHHHHHHHCCC---CCCEEEEEEEEECCE--
Q ss_conf             3169999999999999999847958999808997899868-9999999998865653468---988899999997998--
Q gi|254780903|r  619 NADLIPIINEGIRLIGSSAQSKNIKIEKKIPSELFFNADK-RIIKKILFPILSNSIKFTN---NNGKMMIRTSKIGQC--  692 (766)
Q Consensus       619 ~~dl~~~i~~~~~~~~~~~~~k~i~l~~~~~~~l~v~~D~-~~l~QVl~NLi~NAik~t~---~~g~I~i~~~~~~~~--  692 (766)
                      .++...+++.+...+.+....+.+.+.....+++.+..|. ..|.-|+--|++||+||..   ++|+|.|+....++.  
T Consensus        80 ~~~~~~y~~~L~~~l~~~~~~~~~~~~~~~~~~~~l~~d~A~~Lgliv~EL~tNa~Khaf~~~~~G~I~I~~~~~~~~~~  159 (221)
T COG3920          80 TWDFASYLELLASNLFPSYGGKDIRLILDSGPNVFLDPDTAVPLGLIVHELVTNALKHAFLSRPGGEIRITLSREGDGGR  159 (221)
T ss_pred             CCCHHHHHHHHHHHHHHHCCCCCCEEEEECCCCEEECHHHHHHHHHHHHHHHHHHHHHCCCCCCCCEEEEEEEECCCCCE
T ss_conf             17599999999999887627887527882288622673678899999999999889861788899779999998479971


Q ss_pred             EEEEEEECCCCCCHHHHHHHCCCEEECCCCCCCCCCCCCHHHHHHHHHH-HHCCCEEEEEEECCCCEEEEEECCC
Q ss_conf             9999997889789778543046505314675567788761689999999-9629869999798995299997359
Q gi|254780903|r  693 VIITIADTGIGIPKSALEKIGQPFEPLHNQYDQSIGGFGLGLAISDALT-NLHGGRLKIISQEGKGTIVTICMPQ  766 (766)
Q Consensus       693 v~i~V~D~G~GI~~e~~~~iF~pF~q~~~~~t~~~~GtGLGLaI~k~iV-e~hgG~I~v~S~~g~Gttf~i~LP~  766 (766)
                      ..+.|.|+|.|+|.+.               . . ...|+|+.+++.+| ++.||.+...+..  ||+|+|++|.
T Consensus       160 ~~l~v~deg~G~~~~~---------------~-~-~~~g~G~~Lv~~lv~~q~~g~~~~~~~~--Gt~~~i~~~~  215 (221)
T COG3920         160 FLLTVWDEGGGPPVEA---------------P-L-SRGGFGLQLVERLVPEQLGGELEDERPD--GTEFRLRFPL  215 (221)
T ss_pred             EEEEEEECCCCCCCCC---------------C-C-CCCCCHHHHHHHHHHHHCCCEEEEECCC--CEEEEEEEEC
T ss_conf             7999987898988888---------------8-7-8998379999999999679727997499--7799999886


No 57 
>COG2972 Predicted signal transduction protein with a C-terminal ATPase domain [Signal transduction mechanisms]
Probab=99.65  E-value=5.1e-13  Score=111.90  Aligned_cols=179  Identities=26%  Similarity=0.261  Sum_probs=120.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCEEEECHHHHH
Q ss_conf             99876752224789999999986034688993899999999999999999997776778887419830120331699999
Q gi|254780903|r  547 LAKMSHELRTPLNAILGFSEVIKKEIFGELGSVKYYEYAQDIHYSGQHLLNMINNILEMSKIETEKISIDKQNADLIPII  626 (766)
Q Consensus       547 la~isHelrtPL~aI~g~~ell~~~~~~~~~~e~~~~~l~~I~~~~~~l~~lI~diLd~srieag~~~~~~~~~dl~~~i  626 (766)
                      .-.-.|.|.|-|++|.++++.-.        .   +++.+.+...++.+.      .++++        ....+++.+=+
T Consensus       263 sqi~pHfL~NtL~~I~~~~~~~~--------~---~~~~~~v~~l~~llR------~~l~~--------~~~~~~l~~E~  317 (456)
T COG2972         263 SQINPHFLYNTLETIRMLAEEDD--------P---EEAAKVVKALSKLLR------YSLSN--------LDNIVTLEIEL  317 (456)
T ss_pred             HCCCCHHHHHHHHHHHHHHHHCC--------H---HHHHHHHHHHHHHHH------HHHHC--------CCCCCCHHHHH
T ss_conf             21261689999999999987357--------9---999999999999999------75006--------55534199999


Q ss_pred             HHHHHHHHHHHHHCCCEEEEEECCCCE---E-EECHHHHHHHHHHHHHHHHHCC----CCCCEEEEEEEEECCEEEEEEE
Q ss_conf             999999999998479589998089978---9-9868999999999886565346----8988899999997998999999
Q gi|254780903|r  627 NEGIRLIGSSAQSKNIKIEKKIPSELF---F-NADKRIIKKILFPILSNSIKFT----NNNGKMMIRTSKIGQCVIITIA  698 (766)
Q Consensus       627 ~~~~~~~~~~~~~k~i~l~~~~~~~l~---v-~~D~~~l~QVl~NLi~NAik~t----~~~g~I~i~~~~~~~~v~i~V~  698 (766)
                      .-+...+.  +++.++....+++.+..   . ..||   +-+|.+|+.||++|.    .++|.|.|.+...++.++++|+
T Consensus       318 ~~~~kyl~--iq~~r~~~~le~~~~i~~~~~~l~~p---~l~lqpLvENAi~hgi~~~~~~~~I~i~~~~~~~~i~i~i~  392 (456)
T COG2972         318 LLIEKYLE--IQKLRIGDRLEVPLPIDEELEPLIDP---KLVLQPLVENAIEHGIEPKRPGGSIAISAKKQDDVIQISIS  392 (456)
T ss_pred             HHHHHHHH--HHHCCCCEEEEEEECCCCCCCCCCCH---HHHHHHHHHHHHHHHHCCCCCCCEEEEEEECCCCEEEEEEC
T ss_conf             99999999--99819987999972037533202327---88988879999998620469995799999405879999977


Q ss_pred             ECCCCCCHHHHHHHCCCEEECCCCCCCCCCC-CCHHHHHHHHHHHHCCCE--EEEEEECCCCEEEEEECCC
Q ss_conf             7889789778543046505314675567788-761689999999962986--9999798995299997359
Q gi|254780903|r  699 DTGIGIPKSALEKIGQPFEPLHNQYDQSIGG-FGLGLAISDALTNLHGGR--LKIISQEGKGTIVTICMPQ  766 (766)
Q Consensus       699 D~G~GI~~e~~~~iF~pF~q~~~~~t~~~~G-tGLGLaI~k~iVe~hgG~--I~v~S~~g~Gttf~i~LP~  766 (766)
                      |||+||+++....+..           +.++ +|+||+=++...+.|-|.  +.++|++|+||+..+++|+
T Consensus       393 Dng~g~~~~~~~~~~~-----------~~~~r~giGL~Nv~~rl~~~~g~~~~~i~s~~~~gt~v~~~~~~  452 (456)
T COG2972         393 DNGPGIDEEKLEGLST-----------KGENRSGIGLSNVKERLKLYFGEPGLSIDSQPGKGTFVQIIIPK  452 (456)
T ss_pred             CCCCCCCHHHHHHHHH-----------CCCCCCCCCHHHHHHHHHHCCCCCCEEEEEECCCCEEEEEEEEH
T ss_conf             6999958788866764-----------15777773588799999871897621799964895899999863


No 58 
>COG4585 Signal transduction histidine kinase [Signal transduction mechanisms]
Probab=99.64  E-value=8.8e-13  Score=110.19  Aligned_cols=161  Identities=19%  Similarity=0.301  Sum_probs=105.0

Q ss_pred             CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCEEEECHHHHHHHHHHHHHHHHHHCCCEEEEEECCC-CEEE
Q ss_conf             938999999999999999999977767788874198301203316999999999999999984795899980899-7899
Q gi|254780903|r  577 GSVKYYEYAQDIHYSGQHLLNMINNILEMSKIETEKISIDKQNADLIPIINEGIRLIGSSAQSKNIKIEKKIPSE-LFFN  655 (766)
Q Consensus       577 ~~e~~~~~l~~I~~~~~~l~~lI~diLd~srieag~~~~~~~~~dl~~~i~~~~~~~~~~~~~k~i~l~~~~~~~-l~v~  655 (766)
                      +.++.++.++.+.+-   +.+-++++...-+      .+.+...+-..+.+.....+...-..-++++.....+. .++.
T Consensus       203 ~~e~~~~~l~~i~~~---~~e~l~evR~~v~------~Lrp~~l~~~~l~~~l~~~~~~~~~~~~~~~~~~~~~~~~~L~  273 (365)
T COG4585         203 DAEKAQEELKEIEKL---LREALQEVRALVR------DLRPVELEGLGLVEALRALLADFEERTGITVDLSLGSELERLP  273 (365)
T ss_pred             CHHHHHHHHHHHHHH---HHHHHHHHHHHHH------HCCCHHHHHHHHHHHHHHHHHHHHHHCCEEEEEECCCCCCCCC
T ss_conf             848899999999999---9999999999999------7197322121179999999999877508378861576446799


Q ss_pred             -ECHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEEECCEEEEEEEECCCCCCHHHHHHHCCCEEECCCCCCCCCCCCCHHH
Q ss_conf             -8689999999998865653468988899999997998999999788978977854304650531467556778876168
Q gi|254780903|r  656 -ADKRIIKKILFPILSNSIKFTNNNGKMMIRTSKIGQCVIITIADTGIGIPKSALEKIGQPFEPLHNQYDQSIGGFGLGL  734 (766)
Q Consensus       656 -~D~~~l~QVl~NLi~NAik~t~~~g~I~i~~~~~~~~v~i~V~D~G~GI~~e~~~~iF~pF~q~~~~~t~~~~GtGLGL  734 (766)
                       .-...+-.++.-.++||+||+.. .+|.|+....++.++++|.|||.|.+++.                .   |+|+||
T Consensus       274 ~~~e~~l~rivQEaltN~~rHa~A-~~v~V~l~~~~~~l~l~V~DnG~Gf~~~~----------------~---~~~~GL  333 (365)
T COG4585         274 PEAEDALFRIVQEALTNAIRHAQA-TEVRVTLERTDDELRLEVIDNGVGFDPDK----------------E---GGGFGL  333 (365)
T ss_pred             HHHHHHHHHHHHHHHHHHHHCCCC-CEEEEEEEECCCEEEEEEEECCCCCCCCC----------------C---CCCCCH
T ss_conf             689999999999999899875784-56999999829889999998997889764----------------5---777667


Q ss_pred             HHHHHHHHHCCCEEEEEEECCCCEEEEEECCC
Q ss_conf             99999999629869999798995299997359
Q gi|254780903|r  735 AISDALTNLHGGRLKIISQEGKGTIVTICMPQ  766 (766)
Q Consensus       735 aI~k~iVe~hgG~I~v~S~~g~Gttf~i~LP~  766 (766)
                      .--|.=|+..||++.++|.||+||++++++|-
T Consensus       334 ~~mreRv~~lgG~l~i~S~~g~Gt~i~i~lPl  365 (365)
T COG4585         334 LGMRERVEALGGTLTIDSAPGQGTTVTITLPL  365 (365)
T ss_pred             HHHHHHHHHCCCEEEEEECCCCCEEEEEEEEC
T ss_conf             66999999869989998559997799999509


No 59 
>pfam00989 PAS PAS fold. The PAS fold corresponds to the structural domain that has previously been defined as PAS and PAC motifs. The PAS fold appears in archaea, eubacteria and eukarya.
Probab=99.59  E-value=1.9e-14  Score=122.21  Aligned_cols=111  Identities=16%  Similarity=0.243  Sum_probs=97.9

Q ss_pred             HHHHHHHHCCCCCEEEEECCCCEEEECHHHHHHCCCCHHHCCCCHHHHHHHHCCCCHHHHH-HHHHHHHCCCCEEEEEEE
Q ss_conf             9999997225974598976897899978899772999433058988999760812058999-999997248984899999
Q gi|254780903|r  255 ICVETALSRGRCGLWNFNFDNKKFHLSRSMYEIMGIPYENKTLSFRAIARLIHYDNKKICE-IARSVTGKHVKQLDQIFH  333 (766)
Q Consensus       255 ~rl~~al~~a~~GiWd~D~~~~~i~ws~~~~~llG~~~~e~~~s~~~~~~~vHPdDr~~~~-~a~~~~~~~~~~~~~e~R  333 (766)
                      +||+.+++++++|+|.+|.++..++||+++++||||++++..+  ..+..++||+|..... ...+.+..+......|++
T Consensus         1 er~r~i~e~~~~~i~~~D~~g~i~~~N~a~~~l~G~~~~el~G--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~   78 (112)
T pfam00989         1 EDLRAILESLPDGIFVVDEDGRILYVNAAAEELLGLSREEVIG--KSLLDLIPEEDDAEVAELLRQALLQGEESRGGEVS   78 (112)
T ss_pred             CHHHHHHHHHHHHEEEECCCCCEEEECCCCCCCCCCCHHHHCC--CCCCCCCCCCCHHHHHHHHHHHHHCCCCEEEEEEE
T ss_conf             9799999834246199989999999916533225863667437--52012457534399999999999819976887765


Q ss_pred             EECCCCCEEEEEEEEEEEEECCCEEEEEEEEECC
Q ss_conf             8869898899889999998379606999998446
Q gi|254780903|r  334 MRHASGADIWIQVRAQMMRTISGGMNIIGIAMDL  367 (766)
Q Consensus       334 i~~~DG~~~Wi~~r~~~i~d~~G~~~~iGi~~DI  367 (766)
                      ++++||+.+|+..++.|++|++|.++++|+++||
T Consensus        79 ~~~~dG~~~~~~~~~~pi~d~~g~~g~v~i~rDI  112 (112)
T pfam00989        79 FRVPDGRPRHVEVRASPVRDAGGEIGFLGVLRDI  112 (112)
T ss_pred             EECCCCCEEEEEEEEEEEECCCCCEEEEEEEECC
T ss_conf             2879998999999999999199999999999849


No 60 
>COG3850 NarQ Signal transduction histidine kinase, nitrate/nitrite-specific [Signal transduction mechanisms]
Probab=99.59  E-value=4.9e-12  Score=104.82  Aligned_cols=188  Identities=24%  Similarity=0.359  Sum_probs=141.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHH----HHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCEEEECHH
Q ss_conf             98767522247899999999----86034688993899999999999999999997776778887419830120331699
Q gi|254780903|r  548 AKMSHELRTPLNAILGFSEV----IKKEIFGELGSVKYYEYAQDIHYSGQHLLNMINNILEMSKIETEKISIDKQNADLI  623 (766)
Q Consensus       548 a~isHelrtPL~aI~g~~el----l~~~~~~~~~~e~~~~~l~~I~~~~~~l~~lI~diLd~srieag~~~~~~~~~dl~  623 (766)
                      +.|+-||---+.-.+.|..+    |+... .+...++..+.+..|.++.+-.=.=+..+|.=.|     .+  .++=+|.
T Consensus       374 atIAReLHDSiAQsLS~LkiQvt~L~~~~-~~~~~e~s~~~i~~~r~~Ln~~Y~QLRELLtTFR-----lt--L~e~~L~  445 (574)
T COG3850         374 ATIARELHDSIAQSLSFLKIQVTLLKTAI-PEELPEKAREIIAQIRQGLNDAYRQLRELLTTFR-----LT--LQEAELP  445 (574)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHC-CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-----HH--CCCCCHH
T ss_conf             99999877899999999999999998427-8656687999999999999999999999999878-----76--0567638


Q ss_pred             HHHHHHHHHHHHHHHHCCCEEEEEEC-CCCEEEEC-HHHHHHHHHHHHHHHHHCCCCCCEEEEEEEEECCEEEEEEEECC
Q ss_conf             99999999999999847958999808-99789986-89999999998865653468988899999997998999999788
Q gi|254780903|r  624 PIINEGIRLIGSSAQSKNIKIEKKIP-SELFFNAD-KRIIKKILFPILSNSIKFTNNNGKMMIRTSKIGQCVIITIADTG  701 (766)
Q Consensus       624 ~~i~~~~~~~~~~~~~k~i~l~~~~~-~~l~v~~D-~~~l~QVl~NLi~NAik~t~~~g~I~i~~~~~~~~v~i~V~D~G  701 (766)
                      ..+++++..++.+.   +++++.++. ++..+.++ ...+-||+-.=++||+|++ .+.+|.|++...++.+.++|+|||
T Consensus       446 ~AL~~~~~~f~~qt---g~~~~l~~qlp~~~lpa~qqvHlLqIvREAlsNa~KHa-~As~i~V~~~~~~g~~~~~VeDnG  521 (574)
T COG3850         446 PALEQMLAEFSNQT---GITVTLDYQLPPRALPAHQQVHLLQIVREALSNAIKHA-QASEIKVTVSQNDGQVTLTVEDNG  521 (574)
T ss_pred             HHHHHHHHHHHHCC---CCEEEEECCCCCCCCCHHHHHHHHHHHHHHHHHHHHHC-CCCEEEEEEEECCCEEEEEEEECC
T ss_conf             99999999997346---97388725689889987899999999999999899852-667589999865964899994288


Q ss_pred             CCCCHHHHHHHCCCEEECCCCCCCCCCCCCHHHHHHHHHHHHCCCEEEEEEECCCCEEEEEECC
Q ss_conf             9789778543046505314675567788761689999999962986999979899529999735
Q gi|254780903|r  702 IGIPKSALEKIGQPFEPLHNQYDQSIGGFGLGLAISDALTNLHGGRLKIISQEGKGTIVTICMP  765 (766)
Q Consensus       702 ~GI~~e~~~~iF~pF~q~~~~~t~~~~GtGLGLaI~k~iVe~hgG~I~v~S~~g~Gttf~i~LP  765 (766)
                      +|||+..                 ...| --||.|-+.=.+..+|.+++++.+|+||.+.+++|
T Consensus       522 ~Gi~~~~-----------------e~~g-HyGL~IM~ERA~~L~~~L~i~~~~~gGT~V~ltf~  567 (574)
T COG3850         522 VGIDEAA-----------------EPSG-HYGLNIMRERAQRLGGQLRIRRREGGGTEVSLTFP  567 (574)
T ss_pred             CCCCCCC-----------------CCCC-CCCHHHHHHHHHHHCCEEEEEECCCCCEEEEEEEC
T ss_conf             3779756-----------------7788-72369999999972575777645999817999956


No 61 
>PRK13558 bacterio-opsin activator; Provisional
Probab=99.57  E-value=2e-13  Score=114.85  Aligned_cols=138  Identities=14%  Similarity=0.164  Sum_probs=111.0

Q ss_pred             HHHHHHHHCCCCCEEEE---ECCCCEEEECHHHHHHCCCCHHHCCCCHHHHHHHHCCC-CHHHHHHHHHHHHCCCCEEEE
Q ss_conf             99999972259745989---76897899978899772999433058988999760812-058999999997248984899
Q gi|254780903|r  255 ICVETALSRGRCGLWNF---NFDNKKFHLSRSMYEIMGIPYENKTLSFRAIARLIHYD-NKKICEIARSVTGKHVKQLDQ  330 (766)
Q Consensus       255 ~rl~~al~~a~~GiWd~---D~~~~~i~ws~~~~~llG~~~~e~~~s~~~~~~~vHPd-Dr~~~~~a~~~~~~~~~~~~~  330 (766)
                      ++.+.+++.+|+|+--.   +++++.+|+|+++.+|.||++++..+....|+..  |+ +.+.+...+. ....+..+..
T Consensus       158 ~~~~ra~d~a~v~i~~a~~~~p~~~i~~~n~a~~eitGy~~~e~~g~~~r~lq~--~~~~~e~~~~~~~-ai~~~~~~~v  234 (674)
T PRK13558        158 RLKEQALDEAPIGITISDATDPEEPIIYINDSFEDITGYSPDEVVGANHRFLQG--PKTNEDRVAEFWT-AITEDHDTQV  234 (674)
T ss_pred             HHHHHHHHCCCCEEEEECCCCCCCCEEEEEHHHHHHCCCCHHHHCCCCHHHHCC--CCCCHHHHHHHHH-HHHCCCCCEE
T ss_conf             988756640572599846888887438860123653189817864974012106--8888057999999-9755886334


Q ss_pred             EEEEECCCCCEEEEEEEEEEEEECCCEE-EEEEEEECCCHHHHHHHHHHHHHHHHHHHHHHHHHHE
Q ss_conf             9998869898899889999998379606-9999984461799999999999999999998544551
Q gi|254780903|r  331 IFHMRHASGADIWIQVRAQMMRTISGGM-NIIGIAMDLTEKYHLEKRYAEADQRLSKAIECTSEAL  395 (766)
Q Consensus       331 e~Ri~~~DG~~~Wi~~r~~~i~d~~G~~-~~iGi~~DITErK~ae~~l~ese~rlr~~ie~~~~~i  395 (766)
                      ++|..++||..+|....+.|++|++|.+ +|+|+.+||||||++|++|+.....|..+++.+..-|
T Consensus       235 e~r~~r~dG~~~w~~~~i~pi~Dedg~v~~~Vg~~~DiteRke~E~~L~~~~~~l~~~L~RiN~LI  300 (674)
T PRK13558        235 VLRNYRRDGSLFWNQVDISPIYDEDGTVSHYVGFQMDVSERMAAQQELQGERQSLDRLLDRVNGLM  300 (674)
T ss_pred             EEEEECCCCCEEEEECCCCCCCCCCCCEEEEEEECCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             533314688378741245521057885899986214477889999999986889999999999999


No 62 
>PRK03660 anti-sigma F factor; Provisional
Probab=99.50  E-value=3.6e-13  Score=113.00  Aligned_cols=96  Identities=24%  Similarity=0.382  Sum_probs=80.1

Q ss_pred             HHHHHHHHHHHHHHHHHCC---CCCCEEEEEEEEECCEEEEEEEECCCCCCHHHHHHHCCCEEECCCCCCCC-CCCCCHH
Q ss_conf             8999999999886565346---89888999999979989999997889789778543046505314675567-7887616
Q gi|254780903|r  658 KRIIKKILFPILSNSIKFT---NNNGKMMIRTSKIGQCVIITIADTGIGIPKSALEKIGQPFEPLHNQYDQS-IGGFGLG  733 (766)
Q Consensus       658 ~~~l~QVl~NLi~NAik~t---~~~g~I~i~~~~~~~~v~i~V~D~G~GI~~e~~~~iF~pF~q~~~~~t~~-~~GtGLG  733 (766)
                      -..++-++...+.|||+|.   .++|.|.|.+...++.+.|.|+|+|+||++  .++.|+||+.     ++. ..++|||
T Consensus        37 ~~di~lAV~EA~tNaI~H~y~~~~~g~I~I~~~~~~~~l~I~V~D~G~Gid~--~~~~~~P~~t-----~~~~~~~~GlG  109 (146)
T PRK03660         37 LTEIKTAVSEAVTNAIIHGYENNPDGIVYIEAEIEDEELEITVRDEGKGIED--VEEARQPLFT-----TKPELERSGMG  109 (146)
T ss_pred             HHHHHHHHHHHHHHHHHHHCCCCCCCEEEEEEEEECCEEEEEEEECCCCCCC--HHHCCCCCCC-----CCCCCCCCCHH
T ss_conf             9999999999999999860367999279999998099999999973789473--7664388776-----68766756405


Q ss_pred             HHHHHHHHHHCCCEEEEEEECCCCEEEEEEC
Q ss_conf             8999999996298699997989952999973
Q gi|254780903|r  734 LAISDALTNLHGGRLKIISQEGKGTIVTICM  764 (766)
Q Consensus       734 LaI~k~iVe~hgG~I~v~S~~g~Gttf~i~L  764 (766)
                      |+++++++    ++++++|.+|+|||++++-
T Consensus       110 l~li~~Lm----DeVei~s~~g~GTtV~m~k  136 (146)
T PRK03660        110 FTFMESFM----DEVEVESEPGKGTTIRMKK  136 (146)
T ss_pred             HHHHHHHC----CEEEEEECCCCCEEEEEEE
T ss_conf             89999838----8699995599978999999


No 63 
>COG3275 LytS Putative regulator of cell autolysis [Signal transduction mechanisms]
Probab=99.50  E-value=5.5e-11  Score=97.24  Aligned_cols=168  Identities=24%  Similarity=0.267  Sum_probs=118.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCC-EEEECHHHHHHH
Q ss_conf             7675222478999999998603468899389999999999999999999777677888741983012-033169999999
Q gi|254780903|r  550 MSHELRTPLNAILGFSEVIKKEIFGELGSVKYYEYAQDIHYSGQHLLNMINNILEMSKIETEKISID-KQNADLIPIINE  628 (766)
Q Consensus       550 isHelrtPL~aI~g~~ell~~~~~~~~~~e~~~~~l~~I~~~~~~l~~lI~diLd~srieag~~~~~-~~~~dl~~~i~~  628 (766)
                      =+|=|=|-||+|.   .++..      ++|+.++.+              -++=.|-|-.   ++-+ .+.++|.+=++.
T Consensus       372 nPHFLFNaLNTIs---a~IR~------npdkAreLi--------------l~LS~yfR~N---L~~~~~~~v~L~kEl~~  425 (557)
T COG3275         372 NPHFLFNALNTIS---AVIRR------NPDKARELI--------------LYLSTYFRYN---LENNTQEIVTLSKELEH  425 (557)
T ss_pred             CHHHHHHHHHHHH---HHHCC------CHHHHHHHH--------------HHHHHHHHHH---HCCCCCEEEEHHHHHHH
T ss_conf             7088888888778---88617------827999999--------------9999999987---34787158655999999


Q ss_pred             HHHHHHH---HHHHCCCEEEEEECCCCE-EEECHHHHHHHHHHHHHHHHHCC----CCCCEEEEEEEEECCEEEEEEEEC
Q ss_conf             9999999---998479589998089978-99868999999999886565346----898889999999799899999978
Q gi|254780903|r  629 GIRLIGS---SAQSKNIKIEKKIPSELF-FNADKRIIKKILFPILSNSIKFT----NNNGKMMIRTSKIGQCVIITIADT  700 (766)
Q Consensus       629 ~~~~~~~---~~~~k~i~l~~~~~~~l~-v~~D~~~l~QVl~NLi~NAik~t----~~~g~I~i~~~~~~~~v~i~V~D~  700 (766)
                      +-.-++.   +.++ .+++.+++++.+. +.. |.-   ++.-|+.||+|+.    .++|+|+|++...+..+.+.|+||
T Consensus       426 v~AYl~IEkARF~~-rL~v~i~id~~l~~~~i-P~f---ilQPLVENAIKHG~~~~~~~g~V~I~V~~~d~~l~i~VeDn  500 (557)
T COG3275         426 VNAYLSIEKARFGD-RLDVVIDIDEELRQVQI-PSF---ILQPLVENAIKHGISQLKDTGRVTISVEKEDADLRIEVEDN  500 (557)
T ss_pred             HHHHHHHHHHHCCC-CEEEEEECCHHHHHCCC-CHH---HHHHHHHHHHHHCCCCHHCCCCEEEEEEEECCEEEEEEECC
T ss_conf             99999899864488-44799946877753368-616---67788888887536444208817999998088389999418


Q ss_pred             CCCCCHHHHHHHCCCEEECCCCCCCCCCCCCHHHHHHHHHHHHCCC---EEEEEEECCCCEEEEEECCC
Q ss_conf             8978977854304650531467556778876168999999996298---69999798995299997359
Q gi|254780903|r  701 GIGIPKSALEKIGQPFEPLHNQYDQSIGGFGLGLAISDALTNLHGG---RLKIISQEGKGTIVTICMPQ  766 (766)
Q Consensus       701 G~GI~~e~~~~iF~pF~q~~~~~t~~~~GtGLGLaI~k~iVe~hgG---~I~v~S~~g~Gttf~i~LP~  766 (766)
                      |-||+|+                  +..|+|+||+.+++=++.|=|   -+.++|.+-+||+++|+||-
T Consensus       501 g~li~p~------------------~~~g~giGL~nv~~RLk~lyG~~~gl~i~~~~q~gTri~f~lp~  551 (557)
T COG3275         501 GGLIQPD------------------EEDGTGIGLANVHKRLKLLYGDDEGLHIESLEQAGTRIIFRLPL  551 (557)
T ss_pred             CCCCCCC------------------CCCCCCHHHHHHHHHHHHHCCCCCCCEEEECCCCCCEEEEEECC
T ss_conf             8776997------------------78898717889999999864821031378616778689999447


No 64 
>pfam08448 PAS_4 PAS fold. The PAS fold corresponds to the structural domain that has previously been defined as PAS and PAC motifs. The PAS fold appears in archaea, eubacteria and eukarya.
Probab=99.44  E-value=1.2e-12  Score=109.34  Aligned_cols=109  Identities=18%  Similarity=0.188  Sum_probs=91.9

Q ss_pred             HHCCCCCEEEEECCCCEEEECHHHHHHCCCCHHHCCCCHHHHHHHHCCCCHHHHHHHHHHHHCCCCEEEEEEEEECCCCC
Q ss_conf             72259745989768978999788997729994330589889997608120589999999972489848999998869898
Q gi|254780903|r  261 LSRGRCGLWNFNFDNKKFHLSRSMYEIMGIPYENKTLSFRAIARLIHYDNKKICEIARSVTGKHVKQLDQIFHMRHASGA  340 (766)
Q Consensus       261 l~~a~~GiWd~D~~~~~i~ws~~~~~llG~~~~e~~~s~~~~~~~vHPdDr~~~~~a~~~~~~~~~~~~~e~Ri~~~DG~  340 (766)
                      ++++++++|..|.+++.++||+++++++|+++++..+.  .+.++++|++.+.+....+.+..++.....+ ...+++|.
T Consensus         1 ~d~~p~~i~~~D~~g~i~~~N~a~~~~~g~~~~~~iG~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~g~   77 (110)
T pfam08448         1 LDSLPDALAVLDPDGRVRYANAAAAELFGLPPEELLGK--TLAELLPPEDAARLERALRRALEGEEPIDFL-EELLLNGE   77 (110)
T ss_pred             CCCCCHHHEEECCCCCEEEEEHHHHHHCCCCHHHHCCC--CCHHCCCCHHHHHHHHHHHHHHCCCCEEEEE-EEECCCCC
T ss_conf             99857353799499969999347466709898998095--1210068034566777899997389558866-43025885


Q ss_pred             EEEEEEEEEEEEECCCEE-EEEEEEECCCHHHH
Q ss_conf             899889999998379606-99999844617999
Q gi|254780903|r  341 DIWIQVRAQMMRTISGGM-NIIGIAMDLTEKYH  372 (766)
Q Consensus       341 ~~Wi~~r~~~i~d~~G~~-~~iGi~~DITErK~  372 (766)
                      .+|+..+..|++|++|++ +++++++||||||+
T Consensus        78 ~~~~~~~~~pi~d~~G~~~g~v~~~~DITerKq  110 (110)
T pfam08448        78 ERHYELRLTPLRDPDGEVIGVLVISRDITERRR  110 (110)
T ss_pred             CEEEEEEEEEEECCCCCEEEEEEEEEECCHHCC
T ss_conf             200043576689899999999999998833129


No 65 
>TIGR00229 sensory_box PAS domain S-box; InterPro: IPR000014   PAS domains are involved in many signalling proteins where they are used as a signal sensor domain. PAS domains appear in archaea, bacteria and eukaryotes. Several PAS-domain proteins are known to detect their signal by way of an associated cofactor. Haeme, flavin, and a 4-hydroxycinnamyl chromophore are used in different proteins. The PAS domain was named after three proteins that it occurs in:  Per- period circadian protein Arnt- Ah receptor nuclear translocator protein Sim- single-minded protein.   PAS domains are often associated with PAC domains IPR001610 from INTERPRO. It appears that these domains are directly linked, and that together they form the conserved 3D PAS fold. The division between the PAS and PAC domains is caused by major differences in sequences in the region connecting these two motifs . In human PAS kinase, this region has been shown to be very flexible, and adopts different conformations depending on the bound ligand . Probably the most surprising identification of a PAS domain was that in EAG-like K^+-channels . ; GO: 0004871 signal transducer activity, 0007165 signal transduction.
Probab=99.42  E-value=2.7e-12  Score=106.71  Aligned_cols=125  Identities=16%  Similarity=0.304  Sum_probs=107.1

Q ss_pred             HHHHHHHHHHHHCCCCCEEEEECCCCEEEECHHHHHHCCCCHHHCCCCHHHHHHHHCCCCHHHHHHH-HHHHH-CCCCEE
Q ss_conf             9999999999722597459897689789997889977299943305898899976081205899999-99972-489848
Q gi|254780903|r  251 LEANICVETALSRGRCGLWNFNFDNKKFHLSRSMYEIMGIPYENKTLSFRAIARLIHYDNKKICEIA-RSVTG-KHVKQL  328 (766)
Q Consensus       251 ~ese~rl~~al~~a~~GiWd~D~~~~~i~ws~~~~~llG~~~~e~~~s~~~~~~~vHPdDr~~~~~a-~~~~~-~~~~~~  328 (766)
                      ++++++++.+++.+++++|..|..+..++||+++++++||++++..+. . +..++||++.+..... ..... +....+
T Consensus         1 ~~~e~~~~~~~e~~~~~~~~~d~~g~~~~~n~~~~~~~Gy~~~e~~g~-~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   78 (130)
T TIGR00229         1 RESEERYRAIFESSPDAIIVVDLEGNILYVNPAFEELFGYSAEELLGR-N-VLELIPEEDREELRERIERLLETGEREPV   78 (130)
T ss_pred             CCHHHHHHHHHHCCCCCEEEEECCCCEEEECHHHHHHHCCCHHHHCCC-C-CCCCCCCCHHHHHHHHHHHHHCCCCCCCC
T ss_conf             915899999862245426887057615750325777617875895387-5-10002764146899999876326754320


Q ss_pred             EEEEEE--ECCCCCEEEEEEEEEEEEECCCE-EEEEEEEECCCHHHHHHHHH
Q ss_conf             999998--86989889988999999837960-69999984461799999999
Q gi|254780903|r  329 DQIFHM--RHASGADIWIQVRAQMMRTISGG-MNIIGIAMDLTEKYHLEKRY  377 (766)
Q Consensus       329 ~~e~Ri--~~~DG~~~Wi~~r~~~i~d~~G~-~~~iGi~~DITErK~ae~~l  377 (766)
                      ..++++  +++||..+|+.....++++..|. +.+++++.|||++|++++++
T Consensus        79 ~~~~~~~~~~~~G~~~~~~~~~~~~~~~~g~~~~~~~~~~d~t~~~~~~~~l  130 (130)
T TIGR00229        79 SEERRVLGRRKDGSEIWVEVSVSPIRDSNGGVLGVLGIVRDITERKEAEEAL  130 (130)
T ss_pred             EEEEEEEEECCCCCEEEEEEECCCCCCCCCCEEEEEEEEECHHHHHHHHHCC
T ss_conf             1234666443789688998730100001377036776652114789988509


No 66 
>COG3851 UhpB Signal transduction histidine kinase, glucose-6-phosphate specific [Signal transduction mechanisms]
Probab=99.42  E-value=3.6e-10  Score=91.34  Aligned_cols=189  Identities=18%  Similarity=0.282  Sum_probs=138.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCEEEECHH
Q ss_conf             99999876752224789999999986034688993899999999999999999997776778887419830120331699
Q gi|254780903|r  544 SEFLAKMSHELRTPLNAILGFSEVIKKEIFGELGSVKYYEYAQDIHYSGQHLLNMINNILEMSKIETEKISIDKQNADLI  623 (766)
Q Consensus       544 ~efla~isHelrtPL~aI~g~~ell~~~~~~~~~~e~~~~~l~~I~~~~~~l~~lI~diLd~srieag~~~~~~~~~dl~  623 (766)
                      .+.+--.-.|+-+..+||.--+.+.++-  .+  ..+.++..+.|+.-+.+.-.-+..+|.-=|      .-....+.+.
T Consensus       304 k~vARELHDeIGQnITAIr~Qa~ivkR~--~~--~~q~kqaas~Ie~LslrI~~svrqLL~rLR------P~~LDdL~l~  373 (497)
T COG3851         304 KDVARELHDEIGQNITAIRTQAGIVKRA--AD--NAQVKQAASLIEQLSLRIYDSVRQLLGRLR------PRQLDDLTLE  373 (497)
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHHHHHHC--CC--CHHHHHHHHHHHHHHHHHHHHHHHHHHHCC------CCCCCCCCHH
T ss_conf             9999998998646078999999999865--79--777887889999999899999999987159------7322225789


Q ss_pred             HHHHHHHHHHHHHHHHCCCEEEEEECCC-CEE-EECHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEEECCEEEEEEEECC
Q ss_conf             9999999999999984795899980899-789-98689999999998865653468988899999997998999999788
Q gi|254780903|r  624 PIINEGIRLIGSSAQSKNIKIEKKIPSE-LFF-NADKRIIKKILFPILSNSIKFTNNNGKMMIRTSKIGQCVIITIADTG  701 (766)
Q Consensus       624 ~~i~~~~~~~~~~~~~k~i~l~~~~~~~-l~v-~~D~~~l~QVl~NLi~NAik~t~~~g~I~i~~~~~~~~v~i~V~D~G  701 (766)
                      +.+...++.++  ..+++|....+...+ .+. ..-+.-|..+...+++|-+|+. +...|+|..+..+..++++|+|||
T Consensus       374 qai~~l~~Em~--~~ergihcq~~~~~n~~~ldet~rvTLyRl~QE~LNNI~KHA-~AS~V~i~l~~~~e~l~Lei~DdG  450 (497)
T COG3851         374 QAIRSLLREME--LEERGIHCQLDWRINETALDETQRVTLYRLCQELLNNICKHA-DASAVTIQLWQQDERLMLEIEDDG  450 (497)
T ss_pred             HHHHHHHHHHH--HHHCCEEEEEECCCCCCCCCCCEEEEHHHHHHHHHHHHHHCC-CCCEEEEEEEECCCEEEEEEECCC
T ss_conf             99999999852--544562798705667667885437728999999999997500-226279999517818999982588


Q ss_pred             CCCCHHHHHHHCCCEEECCCCCCCCCCCCCHHHHHHHHHHHHCCCEEEEEEECCCCEEEEEECCC
Q ss_conf             97897785430465053146755677887616899999999629869999798995299997359
Q gi|254780903|r  702 IGIPKSALEKIGQPFEPLHNQYDQSIGGFGLGLAISDALTNLHGGRLKIISQEGKGTIVTICMPQ  766 (766)
Q Consensus       702 ~GI~~e~~~~iF~pF~q~~~~~t~~~~GtGLGLaI~k~iVe~hgG~I~v~S~~g~Gttf~i~LP~  766 (766)
                      .|+|+.                   .+=+|+||-=-+.=|...||+...+|.  .||.+.|.||+
T Consensus       451 ~Gl~~~-------------------~~v~G~Gl~GmrERVsaLGG~l~lssq--~GTrviVnLPq  494 (497)
T COG3851         451 SGLPPG-------------------SGVQGFGLTGMRERVSALGGTLTLSSQ--HGTRVIVNLPQ  494 (497)
T ss_pred             CCCCCC-------------------CCCCCCCCCHHHHHHHHHCCCEEEEEC--CCCEEEEECCH
T ss_conf             678999-------------------985675720089999974782588743--68589994603


No 67 
>PRK11091 aerobic respiration control sensor protein ArcB; Provisional
Probab=99.34  E-value=1.2e-11  Score=102.03  Aligned_cols=146  Identities=9%  Similarity=0.026  Sum_probs=93.7

Q ss_pred             CCHHHHHHHHHHHHHHHHHHHHH---HHHCCCCCEEEEECCCCCEEEECCCHHHHCCCCHHHHCCCCHHHHCCCCCCCHH
Q ss_conf             00112235548999999999885---310178978999969980899714205551997889607610432054433202
Q gi|254780903|r   99 NNNIKFDLASQKKAESMLGQLLA---KTRFLSESFILLAQPNELVFASSTKNSHYIGKKIGEIIPELSRSRSRSKTVQMS  175 (766)
Q Consensus        99 ~~~~~~d~~~~~~ae~~L~~~~~---~~~~~~~~~i~i~d~~g~i~~~n~~~~~~~G~~~~~~~~~~~~~~~~~~~~~~~  175 (766)
                      ......++.+|+++|..|.+...   ..-...++.|+..|.+|+++-+|++++.++|++..+++|.++.+++.++.+...
T Consensus       133 ~~~l~~e~~~r~~~q~~l~~~~~llRs~~D~~Pdli~~rd~~g~f~gCNrafe~~~G~~e~eliG~t~~d~~~~e~a~~~  212 (779)
T PRK11091        133 FEDLKNEIKEREETQIELEQQSSLLRSFLDASPDLVYYRNEDGEFSGCNRAMELLTGKSEKQLVGLTPKDVYSPEAAEKV  212 (779)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEEEECCCCCCCCCCHHHHHHHCCCHHHHCCCCHHHHCCHHHHHHH
T ss_conf             99999999998999999999889999885028751578779876534109999880999899849983552799889999


Q ss_pred             HH----HCCCCHHEEEEEECCC-CCCEEEEEEECCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             32----1153100001233157-782599997423210123455655456878878999999998888999999999999
Q gi|254780903|r  176 EA----SLDQQPYHVLSVNLPH-NSGSILIINSRVPLLRLWREEVTLEVVFFSIISALLLFILFSYYRQAKKNKENDTIL  250 (766)
Q Consensus       176 ~~----~l~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~a~~~dit~~r~ae~~l  250 (766)
                      ..    .+..........++.- ++...++.....|.++.              .+..+++++  +.+|||+||++++++
T Consensus       213 ~~~D~~v~~~~~~~~~e~w~~~~dG~~~~~e~~k~P~~d~--------------~g~~~G~~g--~~rDITerk~aeeaL  276 (779)
T PRK11091        213 IETDEKVFRHNVSLTYEQWLDYPDGRKACFELRKVPFYDR--------------VGKRHGLMG--FGRDITERKRYQDAL  276 (779)
T ss_pred             HHHHHHHHHCCCCCEEEEEEECCCCCEEEEEEEEEEEECC--------------CCCEEEEEE--EEECCHHHHHHHHHH
T ss_conf             9738999864798211134664898667899864013538--------------997887863--001601778999999


Q ss_pred             HHH-HHHHHHH
Q ss_conf             999-9999999
Q gi|254780903|r  251 LEA-NICVETA  260 (766)
Q Consensus       251 ~es-e~rl~~a  260 (766)
                      ++. +..-+.+
T Consensus       277 E~AsraKS~FL  287 (779)
T PRK11091        277 EKASRDKTTFI  287 (779)
T ss_pred             HHHHHHHHHHH
T ss_conf             99999999999


No 68 
>PRK10060 RNase II stability modulator; Provisional
Probab=99.31  E-value=8.5e-10  Score=88.66  Aligned_cols=155  Identities=14%  Similarity=0.139  Sum_probs=107.4

Q ss_pred             HHHHHHCCCCCEEEEECCCCEEEECHHHHHHCCCCHHHCCCCHHHHHHHHCCCC-HHHHHHHHHHHHCCCCEEEEEEEEE
Q ss_conf             999972259745989768978999788997729994330589889997608120-5899999999724898489999988
Q gi|254780903|r  257 VETALSRGRCGLWNFNFDNKKFHLSRSMYEIMGIPYENKTLSFRAIARLIHYDN-KKICEIARSVTGKHVKQLDQIFHMR  335 (766)
Q Consensus       257 l~~al~~a~~GiWd~D~~~~~i~ws~~~~~llG~~~~e~~~s~~~~~~~vHPdD-r~~~~~a~~~~~~~~~~~~~e~Ri~  335 (766)
                      -...++.++.|+...|..++.+.+|+++.+|.||+.+|..+.. .+.-+..+.+ ...+...+ ....++..|.-|...+
T Consensus       113 Aa~Vfe~a~egI~ItD~~~~I~~vN~af~~iTGy~~~eviG~n-~~~l~~s~~~~~~~~~~~~-~~l~~~~~w~gE~w~r  190 (663)
T PRK10060        113 AEQVVSEANSVIVILDSRGNIQRFNRLCEEYTGLKEHDVIGQS-VFKLFMSRREAAASRRNIR-GFFRSGNAYEVERWIK  190 (663)
T ss_pred             HHHHHHCCCCEEEEECCCCCEEEEHHHHHHHHCCCHHHHCCCC-HHHHHCCCCCCHHHHHHHH-HHHHCCCCEEEEEEEE
T ss_conf             9999854586499997999988786797788689999918998-7998357554488999999-9997498189888874


Q ss_pred             CCCCCEEEEEEEEEEEEECCCEE--EEEEEEECCCHHHHHHHHHHHH---------------HHHHHHHHHHH---HHHE
Q ss_conf             69898899889999998379606--9999984461799999999999---------------99999999854---4551
Q gi|254780903|r  336 HASGADIWIQVRAQMMRTISGGM--NIIGIAMDLTEKYHLEKRYAEA---------------DQRLSKAIECT---SEAL  395 (766)
Q Consensus       336 ~~DG~~~Wi~~r~~~i~d~~G~~--~~iGi~~DITErK~ae~~l~es---------------e~rlr~~ie~~---~~~i  395 (766)
                      ++||...+ ..+...+.+..|+.  +++++..||||||++|++|+..               .+++..++...   ..++
T Consensus       191 ~k~G~~~~-~~~~~~v~~~~~~~~~~~i~~f~DITe~k~~ee~l~~lA~~D~LTgLPNR~~~~~rL~~ai~~~~~~~~Av  269 (663)
T PRK10060        191 TRKGQRLF-LFRNKFVHSGSGKNEIFLICSGTDITEERRAQERLRILANTDSITGLPNRNAIQELIDHAIAQADNNQVGI  269 (663)
T ss_pred             ECCCCEEE-EEEEEEEECCCCCEEEEEEEEEEECCHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHCCCCCEEE
T ss_conf             05896457-98878776078970699999888804899999999987367742386628999999999997176993899


Q ss_pred             EEECCCCEEEEECHHHHHHH
Q ss_conf             58834996997017898883
Q gi|254780903|r  396 VLWDKNDRLVMCNANYQKAY  415 (766)
Q Consensus       396 ~~~D~~g~i~~~N~~~~~~~  415 (766)
                      +..|.|+ +..+|..+-.-.
T Consensus       270 lfiDLD~-FK~INDt~GH~~  288 (663)
T PRK10060        270 VYLDLDN-FKKVNDAYGHMF  288 (663)
T ss_pred             EEEECCC-CCHHHHCCCCHH
T ss_conf             9997867-683446627088


No 69 
>pfam00512 HisKA His Kinase A (phosphoacceptor) domain. dimerization and phosphoacceptor domain of histidine kinases.
Probab=99.29  E-value=8.8e-12  Score=102.98  Aligned_cols=66  Identities=47%  Similarity=0.718  Sum_probs=59.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC
Q ss_conf             9999999876752224789999999986034688993899999999999999999997776778887419
Q gi|254780903|r  542 TKSEFLAKMSHELRTPLNAILGFSEVIKKEIFGELGSVKYYEYAQDIHYSGQHLLNMINNILEMSKIETE  611 (766)
Q Consensus       542 ~k~efla~isHelrtPL~aI~g~~ell~~~~~~~~~~e~~~~~l~~I~~~~~~l~~lI~diLd~srieag  611 (766)
                      +|++|++++||||||||++|.|++++++....    +++..++++.|.++++++.++|+++|+|||+++|
T Consensus         1 ~k~~f~~~isHelrtPL~~i~~~~~~l~~~~~----~~~~~~~l~~i~~~~~rl~~li~~ll~~sr~e~g   66 (66)
T pfam00512         1 AKSEFLANLSHELRTPLTAIRGYLELLLDTEL----SEEQREYLETILRSAERLLRLINDLLDLSRIEAG   66 (66)
T ss_pred             CHHHHHHHHHHHHCCHHHHHHHHHHHHHHHCC----HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCC
T ss_conf             98899998729871848888748899887232----7999999997689999999999999999865489


No 70 
>COG4564 Signal transduction histidine kinase [Signal transduction mechanisms]
Probab=99.27  E-value=6.6e-08  Score=74.99  Aligned_cols=181  Identities=17%  Similarity=0.240  Sum_probs=127.2

Q ss_pred             HHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCEEEEC---HHHHHHHHH
Q ss_conf             22247899999999860346889938999999999999999999977767788874198301203316---999999999
Q gi|254780903|r  554 LRTPLNAILGFSEVIKKEIFGELGSVKYYEYAQDIHYSGQHLLNMINNILEMSKIETEKISIDKQNAD---LIPIINEGI  630 (766)
Q Consensus       554 lrtPL~aI~g~~ell~~~~~~~~~~e~~~~~l~~I~~~~~~l~~lI~diLd~srieag~~~~~~~~~d---l~~~i~~~~  630 (766)
                      +.+.|-+..-..|+.......|.+-     .-..|.+++..|..-|+.+.-.|-      .+.+..+|   |...++..+
T Consensus       262 IsQ~LVs~k~~lela~~ql~~p~~~-----a~~aieKaa~aL~~Ai~EVRRiSH------~LRP~~LDDLGL~aALe~L~  330 (459)
T COG4564         262 ISQNLVSVKCALELAARQLNPPKGG-----AHPAIEKAADALNGAIKEVRRISH------DLRPRALDDLGLTAALEALL  330 (459)
T ss_pred             HHHHHHHHHHHHHHHHCCCCCCCCC-----CCHHHHHHHHHHHHHHHHHHHHCC------CCCHHHHHHHHHHHHHHHHH
T ss_conf             7777799999999996267799888-----750156678999989999998502------35745554430799999999


Q ss_pred             HHHHHHHHHCCCEEEEEECCCC-E-EEECHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEEECCEEEEEEEECCCCCCHHH
Q ss_conf             9999999847958999808997-8-9986899999999988656534689888999999979989999997889789778
Q gi|254780903|r  631 RLIGSSAQSKNIKIEKKIPSEL-F-FNADKRIIKKILFPILSNSIKFTNNNGKMMIRTSKIGQCVIITIADTGIGIPKSA  708 (766)
Q Consensus       631 ~~~~~~~~~k~i~l~~~~~~~l-~-v~~D~~~l~QVl~NLi~NAik~t~~~g~I~i~~~~~~~~v~i~V~D~G~GI~~e~  708 (766)
                      +.++   ...++.++.+.+... . .-.-...|..|...-++|--+++ ...+|+|.....++.|.+.|+|||.|.|-+.
T Consensus       331 ~~f~---~~tg~~itle~~~~p~~l~~e~~talyRv~QEaltNIErHa-~Atrv~ill~~~~d~vql~vrDnG~GF~~~~  406 (459)
T COG4564         331 EDFK---ERTGIEITLEFDTQPGKLKPEVATALYRVVQEALTNIERHA-GATRVTILLQQMGDMVQLMVRDNGVGFSVKE  406 (459)
T ss_pred             HHHH---HCCCEEEEEEECCCCCCCCCHHHHHHHHHHHHHHHHHHHHC-CCEEEEEEECCCCCCEEEEEECCCCCCCCHH
T ss_conf             9864---36683799970578644782788899999999987788606-8717999861577606999823899856165


Q ss_pred             HHHHCCCEEECCCCCCCCCCCCCHHHHHHHHHHHHCCCEEEEEEECCCCEEEEEECCC
Q ss_conf             5430465053146755677887616899999999629869999798995299997359
Q gi|254780903|r  709 LEKIGQPFEPLHNQYDQSIGGFGLGLAISDALTNLHGGRLKIISQEGKGTIVTICMPQ  766 (766)
Q Consensus       709 ~~~iF~pF~q~~~~~t~~~~GtGLGLaI~k~iVe~hgG~I~v~S~~g~Gttf~i~LP~  766 (766)
                      .                ...-.||||---+.-++..||+..|+|.|. ||..++.||.
T Consensus       407 ~----------------~~~~~GiGLRNMrERma~~GG~~~v~s~p~-GTel~v~Lp~  447 (459)
T COG4564         407 A----------------LQKRHGIGLRNMRERMAHFGGELEVESSPQ-GTELTVLLPL  447 (459)
T ss_pred             H----------------CCCCCCCCCCCHHHHHHHHCCEEEEEECCC-CCEEEEEECC
T ss_conf             3----------------167556451009999997486589975698-7279998140


No 71 
>KOG0787 consensus
Probab=99.23  E-value=4.3e-09  Score=83.56  Aligned_cols=200  Identities=21%  Similarity=0.290  Sum_probs=142.3

Q ss_pred             HHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHCCCCC------CCEEEECHHHHHHHHHHHH
Q ss_conf             9999999860346889938999999999999999999977767-78887419830------1203316999999999999
Q gi|254780903|r  561 ILGFSEVIKKEIFGELGSVKYYEYAQDIHYSGQHLLNMINNIL-EMSKIETEKIS------IDKQNADLIPIINEGIRLI  633 (766)
Q Consensus       561 I~g~~ell~~~~~~~~~~e~~~~~l~~I~~~~~~l~~lI~diL-d~srieag~~~------~~~~~~dl~~~i~~~~~~~  633 (766)
                      +.|..|.-.... +|...+..+.+++....+=--+.-|+|.-+ -|+   .|+-.      .-...+++.++|.++.+..
T Consensus       154 A~Gl~E~~~~~~-dp~~~~~iqyFLdr~y~sRIsiRMLv~qh~~l~~---~~kp~~~~~iG~I~~~c~v~~vi~~a~e~a  229 (414)
T KOG0787         154 AQGLIEYREKDG-DPVTEKNIQYFLDRFYMSRISIRMLVNQHLLLFA---SGKPDHPRHIGIIDPRCSVKKVIKDASENA  229 (414)
T ss_pred             HHHHHHHHHHCC-CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHEEC---CCCCCCCCEEEEECCCCCHHHHHHHHHHHH
T ss_conf             988999998528-8406778999999999988999999865552002---799987664433179999999999999999


Q ss_pred             HHHHHHCC---CEEEEEECCCCEEE-ECHHHHHHHHHHHHHHHHHCCC----CCC----EEEEEEEEECCEEEEEEEECC
Q ss_conf             99998479---58999808997899-8689999999998865653468----988----899999997998999999788
Q gi|254780903|r  634 GSSAQSKN---IKIEKKIPSELFFN-ADKRIIKKILFPILSNSIKFTN----NNG----KMMIRTSKIGQCVIITIADTG  701 (766)
Q Consensus       634 ~~~~~~k~---i~l~~~~~~~l~v~-~D~~~l~QVl~NLi~NAik~t~----~~g----~I~i~~~~~~~~v~i~V~D~G  701 (766)
                      +-....+-   =++..+....+.-. +=|..|..++..|+.||..+|-    ..+    .|.|.+-..++.+.|.|+|-|
T Consensus       230 r~lCd~yy~~sPel~i~~~~a~~~~vyvPshL~ymlfElfKNamrATve~h~~~~~~~ppI~V~V~~gdeDl~ikISDrG  309 (414)
T KOG0787         230 RFLCDQYYLNSPELIIEGHNALSFTVYVPSHLYYMLFELFKNAMRATVEHHGDDGDELPPIKVTVAKGDEDLLIKISDRG  309 (414)
T ss_pred             HHHHHHHCCCCCEEEECCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEECCCCCEEEEEECCC
T ss_conf             99999863379706753766676760456189999999999999999997444888899859998638863589971378


Q ss_pred             CCCCHHHHHHHCCCEEEC------CCCCCCCCCCCCHHHHHHHHHHHHCCCEEEEEEECCCCEEEEEEC
Q ss_conf             978977854304650531------467556778876168999999996298699997989952999973
Q gi|254780903|r  702 IGIPKSALEKIGQPFEPL------HNQYDQSIGGFGLGLAISDALTNLHGGRLKIISQEGKGTIVTICM  764 (766)
Q Consensus       702 ~GI~~e~~~~iF~pF~q~------~~~~t~~~~GtGLGLaI~k~iVe~hgG~I~v~S~~g~Gttf~i~L  764 (766)
                      -|||.+..+++|.--+-.      ++..+..-.|.|.||.|||-..+-.||.+.+.|=.|-||-..|+|
T Consensus       310 GGV~~~~~drlf~Y~ySTa~~~~~d~~~~~plaGfG~GLPisrlYa~yf~Gdl~L~SleG~GTD~yI~L  378 (414)
T KOG0787         310 GGVPHRDIDRLFSYMYSTAPAPSSDNNRTAPLAGFGFGLPISRLYARYFGGDLKLQSLEGIGTDVYIYL  378 (414)
T ss_pred             CCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHCCCEEEEEEECCCCCEEEEE
T ss_conf             996805789998661256889877887767666555687379999999488705785203544268995


No 72 
>PRK13557 histidine kinase; Provisional
Probab=99.13  E-value=1.4e-08  Score=79.90  Aligned_cols=114  Identities=13%  Similarity=0.132  Sum_probs=70.1

Q ss_pred             CCCCEEEEEC---CCCCEEEECCCHHHHCCCCHHHHCCCCHHHHCCCCCCCHH-----HHHCCCCHHEEEEEECCCCCCE
Q ss_conf             7897899996---9980899714205551997889607610432054433202-----3211531000012331577825
Q gi|254780903|r  126 LSESFILLAQ---PNELVFASSTKNSHYIGKKIGEIIPELSRSRSRSKTVQMS-----EASLDQQPYHVLSVNLPHNSGS  197 (766)
Q Consensus       126 ~~~~~i~i~d---~~g~i~~~n~~~~~~~G~~~~~~~~~~~~~~~~~~~~~~~-----~~~l~~~~~~~~~~~~~~~~~~  197 (766)
                      .+.+.++++|   +||+|+++|++++.++||+.+|++|+.......++.....     .....+..........+.++..
T Consensus        36 ~~~~~~~~~d~~~~Dg~I~~vN~af~~~tGYs~eEviGk~~~~L~~p~~~~~~~~~~~~~i~~~~~~~~E~~n~rKDG~~  115 (538)
T PRK13557         36 TTRMPMIVTDPRQPDNPIVFANRAFLEMTGYAAEEIIGNNCRFLQGPETDRATVADVRDAIAERREIATEILNYRKDGSS  115 (538)
T ss_pred             HCCCCEEEECCCCCCCEEEEECHHHHHHHCCCHHHHCCCCHHHCCCCCCCHHHHHHHHHHHHCCCCEEEEEEEECCCCCE
T ss_conf             07973899358999987999839999987959999869998770898899999999999997599368799998799999


Q ss_pred             EEEEEECCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             9999742321012345565545687887899999999888899999999999999999
Q gi|254780903|r  198 ILIINSRVPLLRLWREEVTLEVVFFSIISALLLFILFSYYRQAKKNKENDTILLEANI  255 (766)
Q Consensus       198 ~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~a~~~dit~~r~ae~~l~ese~  255 (766)
                      .|+.....+..+.-...+                ..++..+|||++|++|++|+++++
T Consensus       116 ~w~~~~i~pv~d~~G~~~----------------~~~~i~~DITerk~~E~~L~qaqk  157 (538)
T PRK13557        116 FWNALFVSPVYNDAGDLV----------------YFFGSQLDVSRRRDAEDALRQAQK  157 (538)
T ss_pred             EEEEEEEEEEECCCCCEE----------------EEEEEEECHHHHHHHHHHHHHHHH
T ss_conf             999989999998999999----------------999988344499999999999999


No 73 
>TIGR02938 nifL_nitrog nitrogen fixation negative regulator NifL; InterPro: IPR014285   NifL modulates the activity of the nitrogen fixation positive regulator protein NifA, acting as a negative regulator by binding NifA. NifA and NifL are encoded by adjacent genes..
Probab=99.12  E-value=4.3e-10  Score=90.78  Aligned_cols=256  Identities=10%  Similarity=0.062  Sum_probs=174.8

Q ss_pred             CCCCEEEEECCCCCEEEECCCHHHHCCCCHHHHCCCCHHHHCCCCCCCHHHHHCCCCHHEEEEEECCCCCCEEEEEEECC
Q ss_conf             78978999969980899714205551997889607610432054433202321153100001233157782599997423
Q gi|254780903|r  126 LSESFILLAQPNELVFASSTKNSHYIGKKIGEIIPELSRSRSRSKTVQMSEASLDQQPYHVLSVNLPHNSGSILIINSRV  205 (766)
Q Consensus       126 ~~~~~i~i~d~~g~i~~~n~~~~~~~G~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~  205 (766)
                      .++-+|-|+|-..+|+|+|.++..++||..+|++|+......-...+....-.|-+.       -....+|......+.+
T Consensus        12 qAp~AISITDlKANILyaN~AF~~iTGY~~eE~iGkNES~LSn~tTPpeVYQaLWg~-------la~qkPW~G~LlNRrk   84 (496)
T TIGR02938        12 QAPVAISITDLKANILYANDAFSEITGYAKEEVIGKNESVLSNRTTPPEVYQALWGS-------LAEQKPWAGKLLNRRK   84 (496)
T ss_pred             HCCCEEEECCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHH-------HHHCCCCCCCEECCCC
T ss_conf             288036431014569999566321558656211125540126858871799999988-------6305898651000011


Q ss_pred             CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEEEEECCCCEEEECHHHH
Q ss_conf             21012345565545687887899999999888899999999999999999999997225974598976897899978899
Q gi|254780903|r  206 PLLRLWREEVTLEVVFFSIISALLLFILFSYYRQAKKNKENDTILLEANICVETALSRGRCGLWNFNFDNKKFHLSRSMY  285 (766)
Q Consensus       206 ~~~~~~r~~~~~~~~~~~~~~~~~~~~~~a~~~dit~~r~ae~~l~ese~rl~~al~~a~~GiWd~D~~~~~i~ws~~~~  285 (766)
                      ....+.=..+..  ++.+.+|...-  .++.|||+|+..+=++..+.-..-+++.++++|...--.|..++.+-=|..++
T Consensus        85 Dg~lYLAeLtva--PvlneaGeT~h--flGMHRd~tElh~Leq~V~nQ~l~iE~VV~aaPva~vllD~~gRv~LdN~~yk  160 (496)
T TIGR02938        85 DGELYLAELTVA--PVLNEAGETTH--FLGMHRDVTELHRLEQRVANQKLLIEAVVDAAPVAAVLLDEQGRVVLDNLEYK  160 (496)
T ss_pred             CCCHHHHHHCCC--CHHCCCCCCEE--EECCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHEECCCCCEEECCHHHH
T ss_conf             653002220202--00014688158--73254543578899888976467899998786541000569986881677688


Q ss_pred             HHCCCCHHHCCCCHHHHHHHHCCCCHHHHHHHHHHHHCCCCE-EEEEEEEECCCCC-EEEEEEEEEEEEECCCEE-----
Q ss_conf             772999433058988999760812058999999997248984-8999998869898-899889999998379606-----
Q gi|254780903|r  286 EIMGIPYENKTLSFRAIARLIHYDNKKICEIARSVTGKHVKQ-LDQIFHMRHASGA-DIWIQVRAQMMRTISGGM-----  358 (766)
Q Consensus       286 ~llG~~~~e~~~s~~~~~~~vHPdDr~~~~~a~~~~~~~~~~-~~~e~Ri~~~DG~-~~Wi~~r~~~i~d~~G~~-----  358 (766)
                      .+-- +-.... +-..+.+++-|+-++.+...+    ..+.. -..|.|+-...|. -||+.+.|..++-+++..     
T Consensus       161 ~La~-DL~v~e-pa~~~l~lLre~~~e~~~~~~----~q~~afsn~E~rfD~ggGR~~RWlSc~g~~i~~e~~~ad~fF~  234 (496)
T TIGR02938       161 KLAS-DLKVEE-PAELLLKLLREELAEDLEELE----NQEKAFSNKELRFDRGGGRSARWLSCAGRVIRIEEDSADSFFA  234 (496)
T ss_pred             HHHH-HCCCCC-CHHHHHHHHHHHHHHHHHHHC----CCCCEECCCEEEEECCCCCCCCCEEECCCEEEEECCCCCEEEC
T ss_conf             7874-214144-179999985087652786520----2110101540354168878850102023235311364011561


Q ss_pred             -----EEEEEEECCCHHHHHHHHHH--------HHHHHHHHHHHHHHHHEEEE
Q ss_conf             -----99999844617999999999--------99999999998544551588
Q gi|254780903|r  359 -----NIIGIAMDLTEKYHLEKRYA--------EADQRLSKAIECTSEALVLW  398 (766)
Q Consensus       359 -----~~iGi~~DITErK~ae~~l~--------ese~rlr~~ie~~~~~i~~~  398 (766)
                           ++.=|+-|||++|+-+++.|        ..|+++..+=|+...+|+-.
T Consensus       235 ~~e~~yLLLti~Dis~lr~~Qe~~Rl~aLqAlmAEEE~le~~rEtl~AAIhrl  287 (496)
T TIGR02938       235 AAEKRYLLLTIDDISELRKKQERARLSALQALMAEEEKLEALRETLSAAIHRL  287 (496)
T ss_pred             CCCCCCEEEEEHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             68998305663647888999999999998999989988888766688888885


No 74 
>smart00388 HisKA His Kinase A (phosphoacceptor) domain. Dimerisation and phosphoacceptor domain of histidine kinases.
Probab=99.07  E-value=7.5e-10  Score=89.05  Aligned_cols=65  Identities=48%  Similarity=0.764  Sum_probs=57.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC
Q ss_conf             999999876752224789999999986034688993899999999999999999997776778887419
Q gi|254780903|r  543 KSEFLAKMSHELRTPLNAILGFSEVIKKEIFGELGSVKYYEYAQDIHYSGQHLLNMINNILEMSKIETE  611 (766)
Q Consensus       543 k~efla~isHelrtPL~aI~g~~ell~~~~~~~~~~e~~~~~l~~I~~~~~~l~~lI~diLd~srieag  611 (766)
                      +++|++++|||+||||++|.+++++++..   +.. ++..++++.|..+++++..+|+++|+|||++.|
T Consensus         2 ~~~~~~~isHelrtPL~~i~~~~~~l~~~---~~~-~~~~~~~~~i~~~~~~~~~li~~il~~sr~~~~   66 (66)
T smart00388        2 KREFLANLSHELRTPLTAIRGYLELLEDT---ELS-EEQREYLETILRSAERLLRLINDLLDLSRIEAG   66 (66)
T ss_pred             HHHHHHHHHHHHHCHHHHHHHHHHHHHCC---CCC-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCC
T ss_conf             88999997698708188899998865302---799-999999998899999999999999999873699


No 75 
>cd00082 HisKA Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via trans-autophosphorylation by the catalytic domain of the histidine kinase. They subsequently transfer the phosphoryl group to the Asp acceptor residue of a response regulator protein. Two-component signalling systems, consisting of a histidine protein kinase that senses a signal input and a response regulator that mediates the output, are ancient and evolutionarily conserved signaling mechanisms in prokaryotes and eukaryotes.
Probab=98.98  E-value=1.4e-09  Score=87.18  Aligned_cols=64  Identities=42%  Similarity=0.713  Sum_probs=57.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             9999999987675222478999999998603468899389999999999999999999777677888
Q gi|254780903|r  541 KTKSEFLAKMSHELRTPLNAILGFSEVIKKEIFGELGSVKYYEYAQDIHYSGQHLLNMINNILEMSK  607 (766)
Q Consensus       541 ~~k~efla~isHelrtPL~aI~g~~ell~~~~~~~~~~e~~~~~l~~I~~~~~~l~~lI~diLd~sr  607 (766)
                      .++++|++++||||||||++|.|+++++......   ++...++++.|.++++++..+|+++|+++|
T Consensus         2 ~~~~~~~a~iaHelrtPL~~i~~~~~~l~~~~~~---~~~~~~~~~~i~~~~~~l~~lv~~~l~~~~   65 (65)
T cd00082           2 QAKGEFLANVSHELRTPLTAIRGALELLEEELLD---DEEQREYLERIREEAERLLRLINDLLDLSR   65 (65)
T ss_pred             CHHHHHHHHHHHHHCCHHHHHHCCHHHHHHCCCC---CHHHHHHHHHHHHHHHHHHHHHHHHHHHCC
T ss_conf             3599999987298704888886014898856688---699999999999999999999999998609


No 76 
>cd00130 PAS PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in signal transduction.
Probab=98.96  E-value=2.3e-08  Score=78.29  Aligned_cols=101  Identities=16%  Similarity=0.274  Sum_probs=87.6

Q ss_pred             CCCEEEEECCCCEEEECHHHHHHCCCCHHHCCCCHHHHHHHHCCCCHHHHHHHHHHHHCCCCEEEEEEEEECCCCCEEEE
Q ss_conf             97459897689789997889977299943305898899976081205899999999724898489999988698988998
Q gi|254780903|r  265 RCGLWNFNFDNKKFHLSRSMYEIMGIPYENKTLSFRAIARLIHYDNKKICEIARSVTGKHVKQLDQIFHMRHASGADIWI  344 (766)
Q Consensus       265 ~~GiWd~D~~~~~i~ws~~~~~llG~~~~e~~~s~~~~~~~vHPdDr~~~~~a~~~~~~~~~~~~~e~Ri~~~DG~~~Wi  344 (766)
                      +.|+|.+|.++..++||+++++++|+++++....  .+.+++||+|...+.............+..++++.+++|+++|+
T Consensus         2 ~~~i~~~d~~g~i~~~N~~~~~~~g~~~~e~~g~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~   79 (103)
T cd00130           2 PDGVIVLDLDGRILYANPAAEQLLGYSPEELIGK--SLLDLIHPEDREELRERLENLLSGGEPVTLEVRLRRKDGSVIWV   79 (103)
T ss_pred             CEEEEEECCCCCEEEECHHHHHHHCCCHHHHCCC--CHHHEECCHHHHHHHHHHHHHHHCCCCCEEEEEEECCCCCEEEE
T ss_conf             6289999798989999889999879887891699--65424552116999999999997499852489999999999999


Q ss_pred             EEEEEEEEECCCEE-EEEEEEECC
Q ss_conf             89999998379606-999998446
Q gi|254780903|r  345 QVRAQMMRTISGGM-NIIGIAMDL  367 (766)
Q Consensus       345 ~~r~~~i~d~~G~~-~~iGi~~DI  367 (766)
                      .....+..+.+|.. .++++..||
T Consensus        80 ~~~~~~~~~~~~~~~~~~~~~~di  103 (103)
T cd00130          80 LVSLTPIRDEGGEVIGLLGVVRDI  103 (103)
T ss_pred             EEEEEEEECCCCCEEEEEEEEECC
T ss_conf             999999999998999999999829


No 77 
>PRK10060 RNase II stability modulator; Provisional
Probab=98.94  E-value=1.2e-07  Score=73.09  Aligned_cols=150  Identities=13%  Similarity=0.152  Sum_probs=81.3

Q ss_pred             CCCCEEEEECCCCCEEEECCCHHHHCCCCHHHHCCCCH-HHHCCCCCCCH----HHHHCCCCHHEEEEEECCCCCCEEEE
Q ss_conf             78978999969980899714205551997889607610-43205443320----23211531000012331577825999
Q gi|254780903|r  126 LSESFILLAQPNELVFASSTKNSHYIGKKIGEIIPELS-RSRSRSKTVQM----SEASLDQQPYHVLSVNLPHNSGSILI  200 (766)
Q Consensus       126 ~~~~~i~i~d~~g~i~~~n~~~~~~~G~~~~~~~~~~~-~~~~~~~~~~~----~~~~l~~~~~~~~~~~~~~~~~~~~~  200 (766)
                      .+...|+|+|++|+|+.+||+++.+.||+.+|++|+.+ ..+..+.....    +...+.......-..+.+...|....
T Consensus       119 ~a~egI~ItD~~~~I~~vN~af~~iTGy~~~eviG~n~~~l~~s~~~~~~~~~~~~~~l~~~~~w~gE~w~r~k~G~~~~  198 (663)
T PRK10060        119 EANSVIVILDSRGNIQRFNRLCEEYTGLKEHDVIGQSVFKLFMSRREAAASRRNIRGFFRSGNAYEVERWIKTRKGQRLF  198 (663)
T ss_pred             CCCCEEEEECCCCCEEEEHHHHHHHHCCCHHHHCCCCHHHHHCCCCCCHHHHHHHHHHHHCCCCEEEEEEEEECCCCEEE
T ss_conf             45864999979999887867977886899999189987998357554488999999999749818988887405896457


Q ss_pred             EEECCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---------------HHHHHHHHHHCC-
Q ss_conf             9742321012345565545687887899999999888899999999999999---------------999999997225-
Q gi|254780903|r  201 INSRVPLLRLWREEVTLEVVFFSIISALLLFILFSYYRQAKKNKENDTILLE---------------ANICVETALSRG-  264 (766)
Q Consensus       201 ~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~a~~~dit~~r~ae~~l~e---------------se~rl~~al~~a-  264 (766)
                               .|+...     +..+.+... ...++.+.|||++|++|+.++.               -.+|++.++... 
T Consensus       199 ---------~~~~~~-----v~~~~~~~~-~~~i~~f~DITe~k~~ee~l~~lA~~D~LTgLPNR~~~~~rL~~ai~~~~  263 (663)
T PRK10060        199 ---------LFRNKF-----VHSGSGKNE-IFLICSGTDITEERRAQERLRILANTDSITGLPNRNAIQELIDHAIAQAD  263 (663)
T ss_pred             ---------EEEEEE-----EECCCCCEE-EEEEEEEEECCHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHCC
T ss_conf             ---------988787-----760789706-99999888804899999999987367742386628999999999997176


Q ss_pred             --CCCEEEEECCCCEEEECHHHHHHCCCCHHHC
Q ss_conf             --9745989768978999788997729994330
Q gi|254780903|r  265 --RCGLWNFNFDNKKFHLSRSMYEIMGIPYENK  295 (766)
Q Consensus       265 --~~GiWd~D~~~~~i~ws~~~~~llG~~~~e~  295 (766)
                        ..++.-.|+++-+ .+|+.    +|..-.+.
T Consensus       264 ~~~~AvlfiDLD~FK-~INDt----~GH~~GD~  291 (663)
T PRK10060        264 NNQVGIVYLDLDNFK-KVNDA----YGHMFGDQ  291 (663)
T ss_pred             CCCEEEEEEECCCCC-HHHHC----CCCHHHHH
T ss_conf             993899999786768-34466----27088999


No 78 
>pfam00989 PAS PAS fold. The PAS fold corresponds to the structural domain that has previously been defined as PAS and PAC motifs. The PAS fold appears in archaea, eubacteria and eukarya.
Probab=98.90  E-value=7.4e-09  Score=81.86  Aligned_cols=93  Identities=16%  Similarity=0.286  Sum_probs=66.9

Q ss_pred             HHHHHHHHHHHHHEEEECCCCEEEEECHHHHHHHCCCHHHHCCCCCHHHHCCCHHHHHHHHH---HHCCCCCCCEEEEEE
Q ss_conf             99999998544551588349969970178988839997894289717881652013789998---521124564058999
Q gi|254780903|r  382 QRLSKAIECTSEALVLWDKNDRLVMCNANYQKAYGLPDHVLVPGNARSIIQDAQTRPIIEYR---TSDPERSQDMSKEIK  458 (766)
Q Consensus       382 ~rlr~~ie~~~~~i~~~D~~g~i~~~N~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~e~~  458 (766)
                      +||+.++|++|++++.+|.+|+++++|+++++++||+.+++++....+.+++..........   +.........+....
T Consensus         1 er~r~i~e~~~~~i~~~D~~g~i~~~N~a~~~l~G~~~~el~G~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~   80 (112)
T pfam00989         1 EDLRAILESLPDGIFVVDEDGRILYVNAAAEELLGLSREEVIGKSLLDLIPEEDDAEVAELLRQALLQGEESRGGEVSFR   80 (112)
T ss_pred             CHHHHHHHHHHHHEEEECCCCCEEEECCCCCCCCCCCHHHHCCCCCCCCCCCCCHHHHHHHHHHHHHCCCCEEEEEEEEE
T ss_conf             97999998342461999899999999165332258636674375201245753439999999999981997688776528


Q ss_pred             ECCC--EEEEECCEECCC
Q ss_conf             1696--287422324569
Q gi|254780903|r  459 LADS--RWLQINEWCTHD  474 (766)
Q Consensus       459 ~~dg--~~~~i~~~~~~d  474 (766)
                      .+||  .|+.++..+..|
T Consensus        81 ~~dG~~~~~~~~~~pi~d   98 (112)
T pfam00989        81 VPDGRPRHVEVRASPVRD   98 (112)
T ss_pred             CCCCCEEEEEEEEEEEEC
T ss_conf             799989999999999991


No 79 
>COG1389 DNA topoisomerase VI, subunit B [DNA replication, recombination, and repair]
Probab=98.86  E-value=2.5e-08  Score=78.08  Aligned_cols=29  Identities=14%  Similarity=0.155  Sum_probs=13.3

Q ss_pred             HHHHHHHHHH--HHHHHHHHHHHHHHHHHHH
Q ss_conf             8999999999--9999999999777677888
Q gi|254780903|r  579 VKYYEYAQDI--HYSGQHLLNMINNILEMSK  607 (766)
Q Consensus       579 e~~~~~l~~I--~~~~~~l~~lI~diLd~sr  607 (766)
                      +.+.+.+..+  ..-..++.+++.+-+++.-
T Consensus       498 ~~i~~~~~~~~~~~~ve~~~~~~~~~~~~v~  528 (538)
T COG1389         498 EDIREKLAKLMEKKIVERLVKLVAEGLELVT  528 (538)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHCCCCCCC
T ss_conf             1355899999878899999876412443341


No 80 
>PRK11006 phoR phosphate regulon sensor protein; Provisional
Probab=98.79  E-value=7.8e-07  Score=67.25  Aligned_cols=125  Identities=12%  Similarity=0.108  Sum_probs=84.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEEEEECCCCEEEECHHHHHHCCCCHHHCCCCHHHHHHHH-CCCCHHHHH
Q ss_conf             8899999999999999999999997225974598976897899978899772999433058988999760-812058999
Q gi|254780903|r  237 YRQAKKNKENDTILLEANICVETALSRGRCGLWNFNFDNKKFHLSRSMYEIMGIPYENKTLSFRAIARLI-HYDNKKICE  315 (766)
Q Consensus       237 ~~dit~~r~ae~~l~ese~rl~~al~~a~~GiWd~D~~~~~i~ws~~~~~llG~~~~e~~~s~~~~~~~v-HPdDr~~~~  315 (766)
                      ++...+.++....|...-+||+.++++.|+|+.-.|.++...+||++..+||||..++..+.  ....++ +|+ ...+.
T Consensus        80 ~~~~~~~~~~~~~l~~~~~rfr~~~ealpDavvv~d~~g~I~~~N~aAe~l~G~~~~~~~G~--~I~~Lir~p~-f~~~~  156 (431)
T PRK11006         80 HQMQLRNKKRRRELGNLIKRFRSGAESLPDAVVLTTEEGNIFWCNGLAQQLLGLRWPEDNGQ--NILNLLRYPE-FTQYL  156 (431)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHCCCEEEEECCCCCEEEEHHHHHHHHCCCCHHHCCC--CHHHHHCCHH-HHHHH
T ss_conf             99999879999999999999999996489769999899958835699999838998332699--7789808845-99998


Q ss_pred             HHHHHHHCCCCEEEEEEEEECCCCCEEEEEEEEEEEEECCCEEEEEEEEECCCHHHHHHHHHH
Q ss_conf             999997248984899999886989889988999999837960699999844617999999999
Q gi|254780903|r  316 IARSVTGKHVKQLDQIFHMRHASGADIWIQVRAQMMRTISGGMNIIGIAMDLTEKYHLEKRYA  378 (766)
Q Consensus       316 ~a~~~~~~~~~~~~~e~Ri~~~DG~~~Wi~~r~~~i~d~~G~~~~iGi~~DITErK~ae~~l~  378 (766)
                            ...  .++....+...+|.  .+..+..|+.  +|.  .+.+++|||++|++|+..+
T Consensus       157 ------~~~--~~~~p~~~~~~~~~--~le~~~~p~~--~~~--~llv~rDiT~~~~lE~~R~  205 (431)
T PRK11006        157 ------KTR--DFSRPLNLVLNNGR--HLEIRVMPYT--EGQ--LLMVARDVTQMHQLEGARR  205 (431)
T ss_pred             ------HCC--CCCCCEEEECCCCC--EEEEEEEECC--CCC--EEEEEEECCHHHHHHHHHH
T ss_conf             ------626--65576255438874--7999997737--995--8999985659999999999


No 81 
>COG2202 AtoS FOG: PAS/PAC domain [Signal transduction mechanisms]
Probab=98.78  E-value=1.1e-06  Score=66.21  Aligned_cols=135  Identities=21%  Similarity=0.343  Sum_probs=104.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEEEEECCCCEEEECHHHHHHCCCCHHHCCCCHH-HHHHHHCCCCHHHHHH
Q ss_conf             899999999999999999999997225974598976897899978899772999433058988-9997608120589999
Q gi|254780903|r  238 RQAKKNKENDTILLEANICVETALSRGRCGLWNFNFDNKKFHLSRSMYEIMGIPYENKTLSFR-AIARLIHYDNKKICEI  316 (766)
Q Consensus       238 ~dit~~r~ae~~l~ese~rl~~al~~a~~GiWd~D~~~~~i~ws~~~~~llG~~~~e~~~s~~-~~~~~vHPdDr~~~~~  316 (766)
                      .+++..+..+..++..+.+++.+++..++++|.+|.++..++||+.+.+++|+++.+...... .+....+++.. ....
T Consensus        95 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~n~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~-~~~~  173 (232)
T COG2202          95 RDITERKRAEEALRESEERLRALLEASPDGIWVLDEDGRILYANPAAEELLGYSPEEELGRGLSDLIHPEDEERR-ELEL  173 (232)
T ss_pred             CHHHHHHHHHHHHHHHHHHHHHHHHCCCCEEEEEECCCCEEEECHHHHHHHCCCHHHHHCCCHHHHCCCCCHHHH-HHHH
T ss_conf             115778889999875799999999568967999909998999758999986979899827760654034630466-7899


Q ss_pred             HHHHHHCCCCEEEEEEEEECCCCCE-EEEEEEEEEEEECCCEE-EEEEEEECCCHHHHHH
Q ss_conf             9999724898489999988698988-99889999998379606-9999984461799999
Q gi|254780903|r  317 ARSVTGKHVKQLDQIFHMRHASGAD-IWIQVRAQMMRTISGGM-NIIGIAMDLTEKYHLE  374 (766)
Q Consensus       317 a~~~~~~~~~~~~~e~Ri~~~DG~~-~Wi~~r~~~i~d~~G~~-~~iGi~~DITErK~ae  374 (766)
                      ...........+..++++..++|.. .|......+... .|.+ .+.+...|+|++++++
T Consensus       174 ~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~-~~~~~~~~~~~~d~~~~~~~~  232 (232)
T COG2202         174 ARALAEGRGGPLEIEYRVRRKDGERVRWILSRISPVRD-DGEIVGVVGIARDITERKQAE  232 (232)
T ss_pred             HHHHHCCCCCCEEEEEEEEECCCCEEEEEEEEECCCCC-CCCEEEEEEEEECHHHHHHHC
T ss_conf             99975245764058999994389799999987313246-885778999987346899749


No 82 
>PRK04184 DNA topoisomerase VI subunit B; Validated
Probab=98.68  E-value=1.8e-07  Score=71.90  Aligned_cols=57  Identities=11%  Similarity=0.092  Sum_probs=23.9

Q ss_pred             HHHHHH-HHHHHHHHHHHHCCCCCEEEEECCCC--CEEEECCCHHHHCCCCHHHHCCCCHH
Q ss_conf             548999-99999988531017897899996998--08997142055519978896076104
Q gi|254780903|r  107 ASQKKA-ESMLGQLLAKTRFLSESFILLAQPNE--LVFASSTKNSHYIGKKIGEIIPELSR  164 (766)
Q Consensus       107 ~~~~~a-e~~L~~~~~~~~~~~~~~i~i~d~~g--~i~~~n~~~~~~~G~~~~~~~~~~~~  164 (766)
                      +..+++ ++.|..-+.. +++++..|-+..-+.  -.+.+-..++.+....+..++|+...
T Consensus        38 ttvkE~VdNsLDAcEe~-gILPdI~v~I~~~~~~~y~v~VeDNGpGI~~~~ip~vFGk~L~   97 (533)
T PRK04184         38 TTVKELVDNSLDACEEA-GILPDIKVEIRRVGEDYYRVIVEDNGPGIPPEQIPKVFGKLLY   97 (533)
T ss_pred             HHHHHHHHCCHHHHHHH-CCCCCEEEEEEECCCCEEEEEEECCCCCCCHHHHHHHHHHHHC
T ss_conf             99999973317668860-8898659999983785699999448899886788899988850


No 83 
>PRK11360 sensory histidine kinase AtoS; Provisional
Probab=98.64  E-value=1e-06  Score=66.41  Aligned_cols=130  Identities=15%  Similarity=0.151  Sum_probs=99.4

Q ss_pred             HHHHHHHHHHHHHHHCCCCCEEEEECCCCEEEECHHHHHHCCCCHHHCCCCHHHHHHHHCCCCHHHHHHHHHHHHCCCCE
Q ss_conf             99999999999997225974598976897899978899772999433058988999760812058999999997248984
Q gi|254780903|r  248 TILLEANICVETALSRGRCGLWNFNFDNKKFHLSRSMYEIMGIPYENKTLSFRAIARLIHYDNKKICEIARSVTGKHVKQ  327 (766)
Q Consensus       248 ~~l~ese~rl~~al~~a~~GiWd~D~~~~~i~ws~~~~~llG~~~~e~~~s~~~~~~~vHPdDr~~~~~a~~~~~~~~~~  327 (766)
                      ..|++.+...+.++++..+|+.-.|.++..+.||+++.+||||++++..+.  .+..++++.+  ...........+...
T Consensus       254 ~~L~~~~~~~e~IL~sm~dGVIaiD~~G~I~~~N~~A~~llg~~~~e~ig~--~~~~l~~~~~--~~~~~~~~l~~~~~~  329 (607)
T PRK11360        254 QALREARTLNELIIENAADGIIAIDRQGDITTMNPAAEVITGYQRHELVGQ--PYSMLFDNTQ--FYSPVLDTLEHGTEH  329 (607)
T ss_pred             HHHHHHHHHHHHHHHHHCCEEEEECCCCCEEEECHHHHHHHCCCHHHHCCC--CHHHHCCCHH--HHHHHHHHHHCCCCC
T ss_conf             999999998999986104669999799949998389999858797898596--7999579576--779999998537742


Q ss_pred             EEEEEEEECCCCCEEEEEEEEEEEEECCCEE-EEEEEEECCCHHHHHHHHHHHHHH
Q ss_conf             8999998869898899889999998379606-999998446179999999999999
Q gi|254780903|r  328 LDQIFHMRHASGADIWIQVRAQMMRTISGGM-NIIGIAMDLTEKYHLEKRYAEADQ  382 (766)
Q Consensus       328 ~~~e~Ri~~~DG~~~Wi~~r~~~i~d~~G~~-~~iGi~~DITErK~ae~~l~ese~  382 (766)
                      .+.+..+.++|| ..++.....++.+.+|.. +.+.+.+||||+|++|+++++++.
T Consensus       330 ~~~~~~~~~~~~-~~~l~~~~s~~~~~~g~~~G~v~~~~DiTe~~~le~~l~~~er  384 (607)
T PRK11360        330 VALEISFPGRDR-TIELSVTTSRLHDTHGEMIGAVVIFSDLTARKRLQRRMARAER  384 (607)
T ss_pred             CCEEEEECCCCC-EEEEEEEEEEEECCCCCEEEEEEEEEECCHHHHHHHHHHHHHH
T ss_conf             124899605883-4999999853576898588999999957789999999999999


No 84 
>PRK13559 hypothetical protein; Provisional
Probab=98.62  E-value=1.5e-05  Score=58.00  Aligned_cols=125  Identities=19%  Similarity=0.231  Sum_probs=77.1

Q ss_pred             EECCCE-EEEEEEEECCCHHHHHHHHHHHHHHHHHHHHHHHHHHEEEECCC---CEEEEECHHHHHHHCCCHHHHCCCCC
Q ss_conf             837960-69999984461799999999999999999998544551588349---96997017898883999789428971
Q gi|254780903|r  352 RTISGG-MNIIGIAMDLTEKYHLEKRYAEADQRLSKAIECTSEALVLWDKN---DRLVMCNANYQKAYGLPDHVLVPGNA  427 (766)
Q Consensus       352 ~d~~G~-~~~iGi~~DITErK~ae~~l~ese~rlr~~ie~~~~~i~~~D~~---g~i~~~N~~~~~~~g~~~~~~~~~~~  427 (766)
                      ++.+++ .+.++.-.|.+         ..+...|..+++....++++.|+.   +-|+|+|++|++++||+.+++++..+
T Consensus        23 ~~~~~~~~~~~~~~~~~~---------~~~~~~~~~a~~~~r~a~~itd~~~~d~PIiy~N~aF~~lTGYs~~EviGrnc   93 (363)
T PRK13559         23 FDADRKELAAIHDPRDFR---------GASGRLFEQAMEQTRMAMCITDPHQPDLPIVLANQAFLDLTGYAAEEVVGRNC   93 (363)
T ss_pred             CCCCCCCEEEECCCCCCC---------CCCCHHHHHHHHHCCCCEEEECCCCCCCCEEEECHHHHHHHCCCHHHHCCCCC
T ss_conf             054446012343631124---------54314799999747743899689999998899887999763989799849992


Q ss_pred             HHHHCCCHHHHHHHHHHHCC-CCCCCEEEEEE--ECCC--EEEE--ECCEECCCCCEE---EEEEEEEH
Q ss_conf             78816520137899985211-24564058999--1696--2874--223245699789---99886201
Q gi|254780903|r  428 RSIIQDAQTRPIIEYRTSDP-ERSQDMSKEIK--LADS--RWLQ--INEWCTHDGGTI---SVGTDITL  486 (766)
Q Consensus       428 ~~~~~~~~~~~~~~~~~~~~-~~~~~~~~e~~--~~dg--~~~~--i~~~~~~dg~~v---~v~~~i~~  486 (766)
                      . .+..++..+.....+... ........+..  .+||  .|..  +++.+..+|..+   .+-.|+|+
T Consensus        94 r-fLqGp~t~~~~v~~ir~ai~~~~~~~~el~nyrKDGs~fwn~l~isPV~D~~G~v~~fig~q~DvTd  161 (363)
T PRK13559         94 R-FLQGAGTDPAAVAKIRAAIAAERVVVVELLNYRKDGSPFWNALHLGPIYDEDGKLLYFFGSQWDVTD  161 (363)
T ss_pred             H-HCCCCCCCHHHHHHHHHHHHCCCCEEEEEEEECCCCCEEEEEEEEEEEECCCCCEEEEEEEEEEECC
T ss_conf             4-1089999989999999999839946999999826998247768988879899979999999985155


No 85 
>pfam08448 PAS_4 PAS fold. The PAS fold corresponds to the structural domain that has previously been defined as PAS and PAC motifs. The PAS fold appears in archaea, eubacteria and eukarya.
Probab=98.61  E-value=2e-07  Score=71.56  Aligned_cols=102  Identities=20%  Similarity=0.298  Sum_probs=70.7

Q ss_pred             HHHHHHHEEEECCCCEEEEECHHHHHHHCCCHHHHCCCCCHHHHCCCHHHHHHHHHHHCCCCCCCEE-EEEEECCC--EE
Q ss_conf             9854455158834996997017898883999789428971788165201378999852112456405-89991696--28
Q gi|254780903|r  388 IECTSEALVLWDKNDRLVMCNANYQKAYGLPDHVLVPGNARSIIQDAQTRPIIEYRTSDPERSQDMS-KEIKLADS--RW  464 (766)
Q Consensus       388 ie~~~~~i~~~D~~g~i~~~N~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~e~~~~dg--~~  464 (766)
                      +|++|++|++.|.+|++++||+++++++|++.+++++.++++.+.+...............+..... ......+|  +|
T Consensus         1 ~d~~p~~i~~~D~~g~i~~~N~a~~~~~g~~~~~~iG~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~   80 (110)
T pfam08448         1 LDSLPDALAVLDPDGRVRYANAAAAELFGLPPEELLGKTLAELLPPEDAARLERALRRALEGEEPIDFLEELLLNGEERH   80 (110)
T ss_pred             CCCCCHHHEEECCCCCEEEEEHHHHHHCCCCHHHHCCCCCHHCCCCHHHHHHHHHHHHHHCCCCEEEEEEEECCCCCCEE
T ss_conf             99857353799499969999347466709898998095121006803456677789999738955886643025885200


Q ss_pred             EEECCEECCC--C---CEEEEEEEEEHHHC
Q ss_conf             7422324569--9---78999886201000
Q gi|254780903|r  465 LQINEWCTHD--G---GTISVGTDITLLKH  489 (766)
Q Consensus       465 ~~i~~~~~~d--g---~~v~v~~~i~~~~~  489 (766)
                      +.++..|..|  |   +++.+..|||+.|+
T Consensus        81 ~~~~~~pi~d~~G~~~g~v~~~~DITerKq  110 (110)
T pfam08448        81 YELRLTPLRDPDGEVIGVLVISRDITERRR  110 (110)
T ss_pred             EEEEEEEEECCCCCEEEEEEEEEECCHHCC
T ss_conf             043576689899999999999998833129


No 86 
>PRK04069 serine-protein kinase RsbW; Provisional
Probab=98.59  E-value=1.4e-06  Score=65.54  Aligned_cols=97  Identities=19%  Similarity=0.294  Sum_probs=74.7

Q ss_pred             HHHHHHHHHHHHHHHHCC---CCCCEEEEEEEEECCEEEEEEEECCCCCCHHHHHHHCCCEEECCCCCCCCCCCCCHHHH
Q ss_conf             999999999886565346---89888999999979989999997889789778543046505314675567788761689
Q gi|254780903|r  659 RIIKKILFPILSNSIKFT---NNNGKMMIRTSKIGQCVIITIADTGIGIPKSALEKIGQPFEPLHNQYDQSIGGFGLGLA  735 (766)
Q Consensus       659 ~~l~QVl~NLi~NAik~t---~~~g~I~i~~~~~~~~v~i~V~D~G~GI~~e~~~~iF~pF~q~~~~~t~~~~GtGLGLa  735 (766)
                      ..++-++.--+.|||+|.   .+.+.|.|.....++.+.|.|+|+|.|++++....-..|+...+.  -......|+||+
T Consensus        41 ~di~LAV~EA~tNaI~Hay~~~~~~~i~i~~~~~~~~l~i~V~D~G~gfD~~~~~~~~~P~~~~~~--l~~~~~gGlGl~  118 (158)
T PRK04069         41 EDLKIAVSEACTNAVQHAYKEEEVGEINIRFEIYEDRLEIVVADNGDSFDYETTKSKIGPYDPSEP--IDDLREGGLGLF  118 (158)
T ss_pred             HHHHHHHHHHHHHHHHHHCCCCCCCEEEEEEEEECCEEEEEEEECCCCCCHHHCCCCCCCCCCCCC--HHHCCCCCCHHH
T ss_conf             889999999999999975156999479999999599999999991748795674324588888886--111367874099


Q ss_pred             HHHHHHHHCCCEEEEEEECCCCEEEEEE
Q ss_conf             9999999629869999798995299997
Q gi|254780903|r  736 ISDALTNLHGGRLKIISQEGKGTIVTIC  763 (766)
Q Consensus       736 I~k~iVe~hgG~I~v~S~~g~Gttf~i~  763 (766)
                      +.+++++    .+.++|  +.||+++.+
T Consensus       119 lI~~lmD----eV~~~~--~~Gt~v~m~  140 (158)
T PRK04069        119 LIETLMD----DVTVYK--DSGVTVSMT  140 (158)
T ss_pred             HHHHHCC----EEEEEE--CCCEEEEEE
T ss_conf             9997525----589990--898299999


No 87 
>TIGR01052 top6b DNA topoisomerase VI, B subunit; InterPro: IPR005734   DNA topoisomerases regulate the number of topological links between two DNA strands (i.e. change the number of superhelical turns) by catalysing transient single- or double-strand breaks, crossing the strands through one another, then resealing the breaks. These enzymes have several functions: to remove DNA supercoils during transcription and DNA replication; for strand breakage during recombination; for chromosome condensation; and to disentangle intertwined DNA during mitosis , . DNA topoisomerases are divided into two classes: type I enzymes (5.99.1.2 from EC; topoisomerases I, III and V) break single-strand DNA, and type II enzymes (5.99.1.3 from EC; topoisomerases II, IV and VI) break double-strand DNA .   Type II topoisomerases are ATP-dependent enzymes, and can be subdivided according to their structure and reaction mechanisms: type IIA (topoisomerase II or gyrase, and topoisomerase IV) and type IIB (topoisomerase VI). These enzymes are responsible for relaxing supercoiled DNA as well as for introducing both negative and positive supercoils .   This entry represents subunit B of topoisomerase VI, a type IIB topoisomerase found predominantly in archaea, but also in a few eukayotes, such as the plant  Arabidopsis thaliana . This enzyme assembles as a heterotetramer, consisting of two A subunits required for DNA cleavage and two B subunits required for ATP hydrolysis. The B subunit is structurally similar to the ATPase domain of type IIA topoisomerases, but the A subunit is distinct, and instead shares homology with the Spo11 protein that mediates double-strand DNA breaks during meiotic recombination in eukaryotes . Therefore, though related to type IIA topoisomerases, topoisomerase VI may have a distinctive mechanism of action.   More information about this protein can be found at Protein of the Month: DNA Topoisomerase .; GO: 0003677 DNA binding, 0003918 DNA topoisomerase (ATP-hydrolyzing) activity, 0006265 DNA topological change, 0006268 DNA unwinding during replication, 0005694 chromosome.
Probab=98.57  E-value=2.4e-07  Score=70.99  Aligned_cols=35  Identities=9%  Similarity=0.127  Sum_probs=22.7

Q ss_pred             HHHHHHHHHHHH-HHEEEECCCCEEEEECHHHHHHH
Q ss_conf             999999998544-55158834996997017898883
Q gi|254780903|r  381 DQRLSKAIECTS-EALVLWDKNDRLVMCNANYQKAY  415 (766)
Q Consensus       381 e~rlr~~ie~~~-~~i~~~D~~g~i~~~N~~~~~~~  415 (766)
                      -+.||..-=..| .-|++.|++|.+..++....++=
T Consensus       196 yEYlrrt~~anPHA~I~l~~PdG~~~~F~R~~~~iP  231 (662)
T TIGR01052       196 YEYLRRTAVANPHAKIVLVEPDGEIYVFPRSTDEIP  231 (662)
T ss_pred             HHHHHHHHHHCCCCEEEEECCCCCEEECCCCCCCCC
T ss_conf             589899875186408998869863775366312376


No 88 
>PRK11073 glnL nitrogen regulation protein NR(II); Provisional
Probab=98.55  E-value=3.5e-06  Score=62.52  Aligned_cols=118  Identities=11%  Similarity=0.077  Sum_probs=80.8

Q ss_pred             HHHHHCCCCCEEEEECCCCEEEECHHHHHHCCCCHHHCCCCHHHHHHHHCCCCHHHHHHHHHHHHCCCCEEEEEEEEECC
Q ss_conf             99972259745989768978999788997729994330589889997608120589999999972489848999998869
Q gi|254780903|r  258 ETALSRGRCGLWNFNFDNKKFHLSRSMYEIMGIPYENKTLSFRAIARLIHYDNKKICEIARSVTGKHVKQLDQIFHMRHA  337 (766)
Q Consensus       258 ~~al~~a~~GiWd~D~~~~~i~ws~~~~~llG~~~~e~~~s~~~~~~~vHPdDr~~~~~a~~~~~~~~~~~~~e~Ri~~~  337 (766)
                      ..++++.+.|+.-.|.++..++||+++.++|||++++..+.  .+..+.++.+.+. ....+.........+.+..+. .
T Consensus        10 ~~Il~~~~d~Iiv~D~~g~I~~~N~aa~~l~g~~~~~~~G~--~~~~l~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~-~   85 (348)
T PRK11073         10 GQILNSLINSILLLDDNLAIHYANPAAQQLLAQSSRKLFGT--PLPELLSYFSLNI-ELMQESLQAGQGFTDNEVTLV-I   85 (348)
T ss_pred             HHHHHHHHHHHEEECCCCCEEEECHHHHHHHCCCHHHHCCC--CHHHHHCCCCCCH-HHHHHHHHCCCCCCCCEEEEE-E
T ss_conf             99998660796499897970128399999978598998599--6899846653018-999999973897413239999-8


Q ss_pred             CCCEEEEEEEEEEEEECCCEEEEEEEEECCCHHHHHHHHHHHHHHH
Q ss_conf             8988998899999983796069999984461799999999999999
Q gi|254780903|r  338 SGADIWIQVRAQMMRTISGGMNIIGIAMDLTEKYHLEKRYAEADQR  383 (766)
Q Consensus       338 DG~~~Wi~~r~~~i~d~~G~~~~iGi~~DITErK~ae~~l~ese~r  383 (766)
                      ||..+|+..+..|+.+  +  .++....|||++|++++++.+....
T Consensus        86 ~~~~~~~~~~~~~~~~--~--~~l~~~~di~~~k~l~~e~~~~~~~  127 (348)
T PRK11073         86 DGRSHILSLTAQRLPE--G--MILLEMAPMDNQRRLSQEQLQHAQQ  127 (348)
T ss_pred             CCEEEEEEEEEEECCC--C--EEEEEEEECHHHHHHHHHHHHHHHH
T ss_conf             9969999999998258--6--8999999627999999999999999


No 89 
>COG3829 RocR Transcriptional regulator containing PAS, AAA-type ATPase, and DNA-binding domains [Transcription / Signal transduction mechanisms]
Probab=98.52  E-value=1.8e-05  Score=57.39  Aligned_cols=136  Identities=15%  Similarity=0.182  Sum_probs=88.5

Q ss_pred             HHHHHHHHHHHH-HHHHHHHHHHHHHCCCCCEEEEECCCCEEEECHHHHHHCCCCHHHCCCCHHHHHHHH-CCCCHHHHH
Q ss_conf             899999999999-999999999997225974598976897899978899772999433058988999760-812058999
Q gi|254780903|r  238 RQAKKNKENDTI-LLEANICVETALSRGRCGLWNFNFDNKKFHLSRSMYEIMGIPYENKTLSFRAIARLI-HYDNKKICE  315 (766)
Q Consensus       238 ~dit~~r~ae~~-l~ese~rl~~al~~a~~GiWd~D~~~~~i~ws~~~~~llG~~~~e~~~s~~~~~~~v-HPdDr~~~~  315 (766)
                      .++++....-+. ++...++|+.+++....|+...|-.+..++||.++..++|+++++....  ...+++ -++|-..  
T Consensus        99 ~~~~e~~~~~~~~l~~~~~~l~~il~~~~~~l~vvD~~G~~i~~N~~~~~~~gl~~e~~~gk--~~~~v~~~~~~s~~--  174 (560)
T COG3829          99 LDISEALELIEENLRQLRQRLEAILDSIDDGLLVVDEDGIIIYYNKAYAKLLGLSPEEVLGK--HLLDVVSAGEDSTL--  174 (560)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCEEEECCCCCEEEECHHHHHHHCCCHHHHCCC--CHHHHHHCCCCCEE--
T ss_conf             51498999999999999999999986256745998699968998477898839998998197--18988723677410--


Q ss_pred             HHHHHHHCCCCEEEEEEEEECCCCCEEEEEEEEEEEEECCCE-EEEEEEEECCCHHHHHHHHHHHHHHHHH
Q ss_conf             999997248984899999886989889988999999837960-6999998446179999999999999999
Q gi|254780903|r  316 IARSVTGKHVKQLDQIFHMRHASGADIWIQVRAQMMRTISGG-MNIIGIAMDLTEKYHLEKRYAEADQRLS  385 (766)
Q Consensus       316 ~a~~~~~~~~~~~~~e~Ri~~~DG~~~Wi~~r~~~i~d~~G~-~~~iGi~~DITErK~ae~~l~ese~rlr  385 (766)
                        .+ ....+++....+-..  .|... +..+ .|++ .+|. .+.+++..|+++-+.+..++.+++..++
T Consensus       175 --l~-vl~~~kp~~~~~~~~--~~~~~-i~~~-~pv~-~~g~l~G~v~~~~~~~~l~~l~~~~~~~~~~~~  237 (560)
T COG3829         175 --LE-VLRTGKPIRDVVQTY--NGNKI-IVNV-APVY-ADGQLIGVVGISKDVSELERLTRELEESEGLLR  237 (560)
T ss_pred             --HH-HHHCCCCCEEEEEEE--CCCCE-EEEE-CCEE-CCCCEEEEEEEECCHHHHHHHHHHHHHHHHHHC
T ss_conf             --11-341588512035530--48734-6764-4473-178278899752024888999999998753220


No 90 
>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=98.51  E-value=7.4e-06  Score=60.20  Aligned_cols=275  Identities=14%  Similarity=0.161  Sum_probs=162.1

Q ss_pred             CCCEEEEECCCCCEEEE--CC------CHHHHCCCCHHHHCCCCHHHHCC-----CCCCC-------HHHHHCC---CCH
Q ss_conf             89789999699808997--14------20555199788960761043205-----44332-------0232115---310
Q gi|254780903|r  127 SESFILLAQPNELVFAS--ST------KNSHYIGKKIGEIIPELSRSRSR-----SKTVQ-------MSEASLD---QQP  183 (766)
Q Consensus       127 ~~~~i~i~d~~g~i~~~--n~------~~~~~~G~~~~~~~~~~~~~~~~-----~~~~~-------~~~~~l~---~~~  183 (766)
                      +.|+-++.|.+|.|..+  ++      ...+..|++..|++-+-..++..     +...+       ......+   ..|
T Consensus         5 ~~Dv~L~~d~~Gvvre~~~~~~~~s~~~~~~W~G~~w~ei~~~es~~k~~~~l~~a~~~g~~a~r~~~~~~~~P~~~ElP   84 (453)
T TIGR02040         5 AADVTLLLDAEGVVREVALSNDELSAEALSEWLGRRWEEIVTEESKEKVEALLSEAKRTGVGAVRVELNRFVLPSDLELP   84 (453)
T ss_pred             CCCCEEEECCCCCEEEEECCCCCCCHHHHCCCCCCCHHHHCCHHHHHHHHHHHHHCCCCCCCHHHHHHHHHCCCCCCCCC
T ss_conf             47703555178707764428855241413024588444413577899999999714688885777766541179997244


Q ss_pred             HEEEEEECCC---CCCEEEEEEECCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----HHHHHHHHHH
Q ss_conf             0001233157---78259999742321012345565545687887899999999888899999999----9999999999
Q gi|254780903|r  184 YHVLSVNLPH---NSGSILIINSRVPLLRLWREEVTLEVVFFSIISALLLFILFSYYRQAKKNKEN----DTILLEANIC  256 (766)
Q Consensus       184 ~~~~~~~~~~---~~~~~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~a~~~dit~~r~a----e~~l~ese~r  256 (766)
                      -.+....++.   ....+..+-+.      -|....+                   -.+.-.+++|    --.+|+.|.|
T Consensus        85 ~~F~~~~L~~sdGk~~~vLa~Grd------Lr~vA~l-------------------qq~lv~AQ~AmErDYW~lR~~EtR  139 (453)
T TIGR02040        85 MEFVLVRLGASDGKDEGVLALGRD------LRAVAEL-------------------QQRLVEAQQAMERDYWKLREMETR  139 (453)
T ss_pred             EEEEEECCCCCCCCCCCEEEECCC------CHHHHHH-------------------HHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             034676167878888735888465------2478999-------------------999999987888879998667544


Q ss_pred             HHHHHHCCCCCEEEEECCCCEEE-ECHHHHHHCCCCHH--HCCCCHHHHHHHHCCCCHHHHHHHHHHHHCCCCEEEEEEE
Q ss_conf             99997225974598976897899-97889977299943--3058988999760812058999999997248984899999
Q gi|254780903|r  257 VETALSRGRCGLWNFNFDNKKFH-LSRSMYEIMGIPYE--NKTLSFRAIARLIHYDNKKICEIARSVTGKHVKQLDQIFH  333 (766)
Q Consensus       257 l~~al~~a~~GiWd~D~~~~~i~-ws~~~~~llG~~~~--e~~~s~~~~~~~vHPdDr~~~~~a~~~~~~~~~~~~~e~R  333 (766)
                      ||..++.+++++--.|..++++. .|+..-.|||-...  +.+.+ ..+..-+..-+++.+..........+..  .+.+
T Consensus       140 YR~ll~~s~davllv~~st~rileaN~~A~~lLg~~~~~rd~LvG-~~~~~e~~~~~~~~l~~~l~~~~atg~A--~~~~  216 (453)
T TIGR02040       140 YRLLLEVSSDAVLLVDVSTGRILEANSAAAALLGAEGQRRDSLVG-REFPQELEEREREELELLLREVRATGKA--AEVR  216 (453)
T ss_pred             HHHHHHCCCCCEEEEECCCCHHHHHHHHHHHHHCCCCCCCHHHHC-CHHHCCCCCCCHHHHHHHHHHHHHCCCC--CCCE
T ss_conf             433541148867998536534778679999985026775012311-1343146645436899999864301577--8717


Q ss_pred             EECCCCCEEEEEEEEEEEEECCCEEEEEEEEECCCHHHHHHHHHHHHHHHHHHHHHHHHHHEEEECCCCEEEEECHHHHH
Q ss_conf             88698988998899999983796069999984461799999999999999999998544551588349969970178988
Q gi|254780903|r  334 MRHASGADIWIQVRAQMMRTISGGMNIIGIAMDLTEKYHLEKRYAEADQRLSKAIECTSEALVLWDKNDRLVMCNANYQK  413 (766)
Q Consensus       334 i~~~DG~~~Wi~~r~~~i~d~~G~~~~iGi~~DITErK~ae~~l~ese~rlr~~ie~~~~~i~~~D~~g~i~~~N~~~~~  413 (766)
                      +.-+++.-.|. ..++..+ .++.++|.-=.--|-+....+....+ ...|..++++.|++|+..|.+|++..+|.+|.+
T Consensus       217 i~l~~~~~~~~-v~~s~~r-~~~~~~fL~~l~~~~~~~~~~~~~s~-~sml~~l~~~~pDaiv~~D~~G~i~~aN~aFl~  293 (453)
T TIGR02040       217 ILLAESRKELL-VVVSLFR-QDSESLFLVRLSPAGASAAVGDVLSE-NSMLAKLVEEAPDAIVVVDADGRIKRANEAFLE  293 (453)
T ss_pred             EEECCCCCCEE-EEEEEEE-CCCCCHHHEEECCCCCCCCCCCCCCC-HHHHHHHHHHCCCEEEEECCCCCHHHHHHHHHH
T ss_conf             87457887317-8877640-23664101130311244677776674-278999997429879997788732888899998


Q ss_pred             HHCCCHHHHCCCCCHHHHC
Q ss_conf             8399978942897178816
Q gi|254780903|r  414 AYGLPDHVLVPGNARSIIQ  432 (766)
Q Consensus       414 ~~g~~~~~~~~~~~~~~~~  432 (766)
                      +...+..+-+.|...+...
T Consensus       294 l~~~ss~~~v~G~~L~~wL  312 (453)
T TIGR02040       294 LVEVSSKEAVRGRTLDRWL  312 (453)
T ss_pred             HHHHCCHHHHCCCCHHHHH
T ss_conf             9871775453133235541


No 91 
>TIGR01925 spIIAB anti-sigma F factor; InterPro: IPR010194   This entry describes the SpoIIAB anti-sigma F factor. Sigma F regulates spore development in B subtilis. SpoIIAB binds to sigma F, preventing formation of the transcription complex at the promoter . SpoIIAA (anti-anti-sigma F factor) binds to SpoIIAB to inhibit association with sigma F, however SpoIIAB can phosphorylate SpoIIAA, causing disassociation of the SpoIIAA/B complex . The SpoIIE phosphatase dephosphorylates SpoIIAA.; GO: 0004674 protein serine/threonine kinase activity, 0005524 ATP binding, 0016989 sigma factor antagonist activity, 0006468 protein amino acid phosphorylation, 0030435 sporulation, 0045892 negative regulation of transcription DNA-dependent.
Probab=98.44  E-value=1e-06  Score=66.38  Aligned_cols=94  Identities=24%  Similarity=0.333  Sum_probs=79.7

Q ss_pred             HHHHHHHHHHHHHHHHCCC---CCCEEEEEEEEECCEEEEEEEECCCCCCHHHHHHHCCCEEECCCCCCCCCC-CCCHHH
Q ss_conf             9999999998865653468---988899999997998999999788978977854304650531467556778-876168
Q gi|254780903|r  659 RIIKKILFPILSNSIKFTN---NNGKMMIRTSKIGQCVIITIADTGIGIPKSALEKIGQPFEPLHNQYDQSIG-GFGLGL  734 (766)
Q Consensus       659 ~~l~QVl~NLi~NAik~t~---~~g~I~i~~~~~~~~v~i~V~D~G~GI~~e~~~~iF~pF~q~~~~~t~~~~-GtGLGL  734 (766)
                      .-++-++..=+.|||=|.-   .+|.|.|++...++.+.++|.|+|+||  +.+++--+|.|     |+|+.- -+|+|-
T Consensus        38 ~diK~~VSEAVTNAIIHGYE~~~~~~V~I~~~~~d~~~~~~v~D~G~GI--~~lE~A~~PLy-----TskPeLERSGMGF  110 (137)
T TIGR01925        38 TDIKTAVSEAVTNAIIHGYEENKEGVVIISATIEDDEVSITVRDEGIGI--ENLEEAREPLY-----TSKPELERSGMGF  110 (137)
T ss_pred             HHHHHHHHHHHHCCEEECEEECCCCEEEEEEEEECCEEEEEEEECCCCH--HHHHHHCCCCC-----CCCCCCCCCCCCE
T ss_conf             5554333223212053145637997789999960548999986467572--33785326645-----7998722067860


Q ss_pred             HHHHHHHHHCCCEEEEEEECCCCEEEEEE
Q ss_conf             99999999629869999798995299997
Q gi|254780903|r  735 AISDALTNLHGGRLKIISQEGKGTIVTIC  763 (766)
Q Consensus       735 aI~k~iVe~hgG~I~v~S~~g~Gttf~i~  763 (766)
                      .|-    |..=-.|.|+|++++||+..+.
T Consensus       111 TvM----E~FMD~~~v~S~~~~GT~I~~~  135 (137)
T TIGR01925       111 TVM----ESFMDDVEVDSEKEKGTKIILK  135 (137)
T ss_pred             EEE----CCCCCCEEEEECCCCCCEEEEE
T ss_conf             121----1124512686238998468875


No 92 
>KOG3558 consensus
Probab=98.43  E-value=2.2e-06  Score=64.08  Aligned_cols=218  Identities=13%  Similarity=0.144  Sum_probs=135.3

Q ss_pred             CCCEEEEECCCCCEEEECCCHHHHCCCCHHHHCCCCHHHHCCCCCCCHHHHHCCCC---------------HHEEEEE--
Q ss_conf             89789999699808997142055519978896076104320544332023211531---------------0000123--
Q gi|254780903|r  127 SESFILLAQPNELVFASSTKNSHYIGKKIGEIIPELSRSRSRSKTVQMSEASLDQQ---------------PYHVLSV--  189 (766)
Q Consensus       127 ~~~~i~i~d~~g~i~~~n~~~~~~~G~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~---------------~~~~~~~--  189 (766)
                      -+.+|++++.+|.++|.+-....++|.+..|++|.+..++.++-....+...+...               +.+....  
T Consensus       128 LDGFVm~l~~dG~~lYiSEtVS~yLGLSQvELTG~SvFDfiHP~DheE~~eqL~l~~~~p~~~es~~~~teRsFflRMKs  207 (768)
T KOG3558         128 LDGFVMALTQDGDFLYISETVSIYLGLSQVELTGSSVFDFIHPCDHEEIAEQLGLRLTTPEVKESTDTSTERSFFLRMKS  207 (768)
T ss_pred             CCCEEEEECCCCCEEEEECHHHHHHCCCCEEEECCHHHHCCCCCCHHHHHHHHCCCCCCCCCCCCCCCCCCEEEEEEEEE
T ss_conf             24438998167877998203576617110243054132125766789999874335688762324567543257998531


Q ss_pred             ---------ECCCCCCEEEEEEECCCCHHHHHHHHHHHHHHHH----HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             ---------3157782599997423210123455655456878----878999999998888999999999999999999
Q gi|254780903|r  190 ---------NLPHNSGSILIINSRVPLLRLWREEVTLEVVFFS----IISALLLFILFSYYRQAKKNKENDTILLEANIC  256 (766)
Q Consensus       190 ---------~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~~~~----~~~~~~~~~~~a~~~dit~~r~ae~~l~ese~r  256 (766)
                               .+...++.+.-..-.-   ..+.. ..-+.++..    ..+.|++...+. +--.            .|-+
T Consensus       208 TLT~RGRtlnlKSa~yKvlh~tgh~---rv~~~-~sh~s~~~g~~~Pl~~lV~~a~alp-~ps~------------~Eip  270 (768)
T KOG3558         208 TLTKRGRTLNLKSAGYKVLHCTGHL---RVYNN-PSHNSPLCGYKEPLLGLVALAEALP-PPSY------------TEIP  270 (768)
T ss_pred             EECCCCCEEEEECCCEEEEEEEEEE---EECCC-CCCCCCCCCCCCCCHHEEEEECCCC-CCCC------------CCCC
T ss_conf             5516773566501422689886345---40467-7777755576655210045411379-9865------------6666


Q ss_pred             HHHHHHCCCCC--EEEEECCCCEEEECHHHHHHCCCCHHHCCCCHHHHHHHHCCCCHHHHHHHHHHHHCCCCEEEEEEEE
Q ss_conf             99997225974--5989768978999788997729994330589889997608120589999999972489848999998
Q gi|254780903|r  257 VETALSRGRCG--LWNFNFDNKKFHLSRSMYEIMGIPYENKTLSFRAIARLIHYDNKKICEIARSVTGKHVKQLDQIFHM  334 (766)
Q Consensus       257 l~~al~~a~~G--iWd~D~~~~~i~ws~~~~~llG~~~~e~~~s~~~~~~~vHPdDr~~~~~a~~~~~~~~~~~~~e~Ri  334 (766)
                      +       .|+  +-..+++-+..|++++.-+++||.|++.++  ..+.+++|+.|.+.+......+..++....--||+
T Consensus       271 L-------~~~~FvtRhs~DmkityCedRisdlm~y~PeeLvG--rS~Ye~~Ha~Ds~~v~KSh~dL~~KGQv~TgyYR~  341 (768)
T KOG3558         271 L-------DCHMFVTRHSLDMKITYCEDRISDLMDYEPEELVG--RSCYEFVHALDSDRVRKSHHDLLTKGQVVTGYYRL  341 (768)
T ss_pred             C-------CCCEEEEEEECCEEEEEECHHHHHHHCCCHHHHHC--HHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHH
T ss_conf             5-------77516776414516888735678876479788626--04887633765667788899997547451067788


Q ss_pred             ECCCCCEEEEEEEEEEEEECC-CEE-EEEEEEECCCHH
Q ss_conf             869898899889999998379-606-999998446179
Q gi|254780903|r  335 RHASGADIWIQVRAQMMRTIS-GGM-NIIGIAMDLTEK  370 (766)
Q Consensus       335 ~~~DG~~~Wi~~r~~~i~d~~-G~~-~~iGi~~DITEr  370 (766)
                      ..++|.|+|+...+.++.+.. ++. .+|.+.-=|+.+
T Consensus       342 lak~GGyvWlQTqATVi~~tkn~q~q~IicVnYVlS~~  379 (768)
T KOG3558         342 LAKNGGYVWLQTQATVIYNTKNPQEQNIICVNYVLSNI  379 (768)
T ss_pred             HHHCCCEEEEEEEEEEEECCCCCCCCEEEEEEEEECCC
T ss_conf             77449769998654798558889851589998661343


No 93 
>TIGR00229 sensory_box PAS domain S-box; InterPro: IPR000014   PAS domains are involved in many signalling proteins where they are used as a signal sensor domain. PAS domains appear in archaea, bacteria and eukaryotes. Several PAS-domain proteins are known to detect their signal by way of an associated cofactor. Haeme, flavin, and a 4-hydroxycinnamyl chromophore are used in different proteins. The PAS domain was named after three proteins that it occurs in:  Per- period circadian protein Arnt- Ah receptor nuclear translocator protein Sim- single-minded protein.   PAS domains are often associated with PAC domains IPR001610 from INTERPRO. It appears that these domains are directly linked, and that together they form the conserved 3D PAS fold. The division between the PAS and PAC domains is caused by major differences in sequences in the region connecting these two motifs . In human PAS kinase, this region has been shown to be very flexible, and adopts different conformations depending on the bound ligand . Probably the most surprising identification of a PAS domain was that in EAG-like K^+-channels . ; GO: 0004871 signal transducer activity, 0007165 signal transduction.
Probab=98.42  E-value=2e-06  Score=64.30  Aligned_cols=113  Identities=18%  Similarity=0.355  Sum_probs=80.1

Q ss_pred             HHHHHHHHHHHHHHHHEEEECCCCEEEEECHHHHHHHCCCHHHHCCCCCHHHHCCCHHHHHHHHHHHCCC----CCCCEE
Q ss_conf             9999999999854455158834996997017898883999789428971788165201378999852112----456405
Q gi|254780903|r  379 EADQRLSKAIECTSEALVLWDKNDRLVMCNANYQKAYGLPDHVLVPGNARSIIQDAQTRPIIEYRTSDPE----RSQDMS  454 (766)
Q Consensus       379 ese~rlr~~ie~~~~~i~~~D~~g~i~~~N~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~  454 (766)
                      +++.+++.+++++++++++.|.+|.++++|+++++++||+.+++.+......+.+...............    ......
T Consensus         2 ~~e~~~~~~~e~~~~~~~~~d~~g~~~~~n~~~~~~~Gy~~~e~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   81 (130)
T TIGR00229         2 ESEERYRAIFESSPDAIIVVDLEGNILYVNPAFEELFGYSAEELLGRNVLELIPEEDREELRERIERLLETGEREPVSEE   81 (130)
T ss_pred             CHHHHHHHHHHCCCCCEEEEECCCCEEEECHHHHHHHCCCHHHHCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCCCCEEE
T ss_conf             15899999862245426887057615750325777617875895387510002764146899999876326754320123


Q ss_pred             EEE--EECCC--EEEEECCEECC--CCC---EEEEEEEEEHHHCCC
Q ss_conf             899--91696--28742232456--997---899988620100011
Q gi|254780903|r  455 KEI--KLADS--RWLQINEWCTH--DGG---TISVGTDITLLKHNQ  491 (766)
Q Consensus       455 ~e~--~~~dg--~~~~i~~~~~~--dg~---~v~v~~~i~~~~~~~  491 (766)
                      +..  ...||  .|..++..+..  .|+   ++.+..|||+.+..+
T Consensus        82 ~~~~~~~~~G~~~~~~~~~~~~~~~~g~~~~~~~~~~d~t~~~~~~  127 (130)
T TIGR00229        82 RRVLGRRKDGSEIWVEVSVSPIRDSNGGVLGVLGIVRDITERKEAE  127 (130)
T ss_pred             EEEEEECCCCCEEEEEEECCCCCCCCCCEEEEEEEEECHHHHHHHH
T ss_conf             4666443789688998730100001377036776652114789988


No 94 
>PRK10841 hybrid sensory kinase in two-component regulatory system with RcsB and YojN; Provisional
Probab=98.40  E-value=0.00028  Score=48.79  Aligned_cols=178  Identities=15%  Similarity=0.132  Sum_probs=102.7

Q ss_pred             CCHHEEEEEECCCCCCEEEEEEECCCCHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHH-HHHHHHHHHHHHHHHHHHH
Q ss_conf             3100001233157782599997423210123455655456878878999999-9988889-9999999999999999999
Q gi|254780903|r  181 QQPYHVLSVNLPHNSGSILIINSRVPLLRLWREEVTLEVVFFSIISALLLFI-LFSYYRQ-AKKNKENDTILLEANICVE  258 (766)
Q Consensus       181 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~-~~a~~~d-it~~r~ae~~l~ese~rl~  258 (766)
                      |-..+.....++..++.++..-|....+...+-.....+.+ .....+++.. ..-|.+- ..-+.+.-..|.|+|+-=+
T Consensus       282 ~~~~l~~~k~l~~~~~~~vy~~~~~~~~~~~~~~~~~~~~l-~~~~~~~~~~~~~~~~rr~~~pa~~~a~~l~e~e~fnr  360 (947)
T PRK10841        282 GFRELVLKKNLPPSSLSIVYSVPVDTVLERIRMLILNAILL-NVLSGAVLFTLARMFERRIFIPAESNALRLEEHEQFNR  360 (947)
T ss_pred             CHHHHHHHCCCCCCCEEEEEEEEHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHH
T ss_conf             81778752448966338999948899887617999999999-99999999999999886642735677889987888778


Q ss_pred             HHHHCCCCCEEEEECCCCEEEECHHHHHHCCCCHHHCCCCHHHHHHHHCCCCHHHHHHHHHHHHCCCCEEEEEEEEECCC
Q ss_conf             99722597459897689789997889977299943305898899976081205899999999724898489999988698
Q gi|254780903|r  259 TALSRGRCGLWNFNFDNKKFHLSRSMYEIMGIPYENKTLSFRAIARLIHYDNKKICEIARSVTGKHVKQLDQIFHMRHAS  338 (766)
Q Consensus       259 ~al~~a~~GiWd~D~~~~~i~ws~~~~~llG~~~~e~~~s~~~~~~~vHPdDr~~~~~a~~~~~~~~~~~~~e~Ri~~~D  338 (766)
                      ++++.||+|+-......|....|....              ..|..+..++|+.+...   ...++...|. +  +...+
T Consensus       361 ~~i~~apvg~~~l~~~dg~~~~~n~~~--------------~~~~~~~~~~~~~~~~~---~~~~~~~~~~-~--~~~~~  420 (947)
T PRK10841        361 KIVASAPVGICILRTSDGTNILSNELA--------------HNYLNMLTHEDRQRLTQ---IICGQQVNFV-D--VLTSN  420 (947)
T ss_pred             HHHHHCCCEEEEEECCCCCEEECHHHH--------------HHHHHHCCCCHHHHHHH---HHHCCCCCCE-E--EEECC
T ss_conf             898617713799970688633103899--------------99876237552899999---9861378834-8--99359


Q ss_pred             CCEEEEEEEEEEEEECCCEEEEEEEEECCCHHHHHHHHHHHHHH
Q ss_conf             98899889999998379606999998446179999999999999
Q gi|254780903|r  339 GADIWIQVRAQMMRTISGGMNIIGIAMDLTEKYHLEKRYAEADQ  382 (766)
Q Consensus       339 G~~~Wi~~r~~~i~d~~G~~~~iGi~~DITErK~ae~~l~ese~  382 (766)
                      |+...  ....+.|-. |+--++++..|||+||+.|+.|+++..
T Consensus       421 ~~~l~--~~~~~~ry~-~~~v~~c~~~Disar~~~e~~L~~a~~  461 (947)
T PRK10841        421 NTNLQ--ISFVHSRYR-NENVAICVLVDVSARVKMEESLQEMAQ  461 (947)
T ss_pred             CCEEE--EEEEEEEEC-CCCEEEEEEEECHHHHHHHHHHHHHHH
T ss_conf             85799--998653126-860799999854078999999999999


No 95 
>COG2202 AtoS FOG: PAS/PAC domain [Signal transduction mechanisms]
Probab=98.37  E-value=0.0001  Score=52.02  Aligned_cols=190  Identities=13%  Similarity=0.244  Sum_probs=115.7

Q ss_pred             EEEECCCCEEEECHHHHHHCCCCHHHCCCCHHHHHHHHCCCCHHHHHHHHHHHHCCCCEEEEEEEEECCCCCEEEEEEEE
Q ss_conf             98976897899978899772999433058988999760812058999999997248984899999886989889988999
Q gi|254780903|r  269 WNFNFDNKKFHLSRSMYEIMGIPYENKTLSFRAIARLIHYDNKKICEIARSVTGKHVKQLDQIFHMRHASGADIWIQVRA  348 (766)
Q Consensus       269 Wd~D~~~~~i~ws~~~~~llG~~~~e~~~s~~~~~~~vHPdDr~~~~~a~~~~~~~~~~~~~e~Ri~~~DG~~~Wi~~r~  348 (766)
                      +.++......+.+.....++++.+.....    +.....+.+...........................++...|+....
T Consensus         3 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   78 (232)
T COG2202           3 LVLDRDGRIIYANEAAEELLGYSAEELLG----LLLALHPEDRDRLRELLRRLLAGEELLSEELRLVRKDGEERWVELSA   78 (232)
T ss_pred             EEECCCCCEEEECHHHHHHHCCCHHHHHC----CHHCCCHHHHHHHHHHHHHHHHCCCCHHHEEEEEECCCCEEEEEEEE
T ss_conf             47716664244415568875334465531----02101045677888999997630000001023541367447887410


Q ss_pred             EEEEECC-CEE-EEEEEEECCCHHHHHHHHHHHHHHHHHHHHHHHHHHEEEECCCCEEEEECHHHHHHHCCCHHHHCCCC
Q ss_conf             9998379-606-99999844617999999999999999999985445515883499699701789888399978942897
Q gi|254780903|r  349 QMMRTIS-GGM-NIIGIAMDLTEKYHLEKRYAEADQRLSKAIECTSEALVLWDKNDRLVMCNANYQKAYGLPDHVLVPGN  426 (766)
Q Consensus       349 ~~i~d~~-G~~-~~iGi~~DITErK~ae~~l~ese~rlr~~ie~~~~~i~~~D~~g~i~~~N~~~~~~~g~~~~~~~~~~  426 (766)
                      ... ... +.. ...+. .|+++.+..++.++..+.+++.++++.+++++.+|.++.++++|+.+.+++|++..+.....
T Consensus        79 ~~~-~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~n~~~~~~~g~~~~~~~~~~  156 (232)
T COG2202          79 APL-RDGEGRVLGLLGL-RDITERKRAEEALRESEERLRALLEASPDGIWVLDEDGRILYANPAAEELLGYSPEEELGRG  156 (232)
T ss_pred             EEE-ECCCCHHHHHHHH-CHHHHHHHHHHHHHHHHHHHHHHHHCCCCEEEEEECCCCEEEECHHHHHHHCCCHHHHHCCC
T ss_conf             011-1233035555301-11577888999987579999999956896799990999899975899998697989982776


Q ss_pred             CHHHHCCCHHH----HHHHHHHHCCCCCCCEEEEEEECCCEE
Q ss_conf             17881652013----789998521124564058999169628
Q gi|254780903|r  427 ARSIIQDAQTR----PIIEYRTSDPERSQDMSKEIKLADSRW  464 (766)
Q Consensus       427 ~~~~~~~~~~~----~~~~~~~~~~~~~~~~~~e~~~~dg~~  464 (766)
                      ...........    .................+.....+|.+
T Consensus       157 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~  198 (232)
T COG2202         157 LSDLIHPEDEERRELELARALAEGRGGPLEIEYRVRRKDGER  198 (232)
T ss_pred             HHHHCCCCCHHHHHHHHHHHHHCCCCCCEEEEEEEEECCCCE
T ss_conf             065403463046678999997524576405899999438979


No 96 
>KOG0519 consensus
Probab=98.34  E-value=1e-06  Score=66.39  Aligned_cols=225  Identities=17%  Similarity=0.198  Sum_probs=173.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             99999999999998878999999998767522247899999999860346889938999999999999999999977767
Q gi|254780903|r  524 IANAKYQVEKERAETANKTKSEFLAKMSHELRTPLNAILGFSEVIKKEIFGELGSVKYYEYAQDIHYSGQHLLNMINNIL  603 (766)
Q Consensus       524 ~~~~~l~~~~~~ae~an~~k~efla~isHelrtPL~aI~g~~ell~~~~~~~~~~e~~~~~l~~I~~~~~~l~~lI~diL  603 (766)
                      ..+..++..++++..++.+...++..++|..++|.+.+++...++.+...-...   ..-.++...++...+..+++.-.
T Consensus       367 ~~~~~l~~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~l~~~~~~~~~---~~~~i~~~~~~~~~~~~~~q~~~  443 (786)
T KOG0519         367 ESNDVLLRAKEEAHMAGKARIDFLQKMSHAMRAPRHNIISLLSLLLQDIVLSPD---SGLEIQTVMRSSNVFTSLIQADP  443 (786)
T ss_pred             HHHHHHHHHHHHHHHCCHHHHHHHHHHCCCCCCCCCCCCCCCHHHHHHEEECCC---CCEEEEECCCCHHHHHHHHCCCH
T ss_conf             467899754577653515566788874133124220421223576652022366---64068502330465554514661


Q ss_pred             HHHHHHCCCCCCCEEEECHHHHHHHHHHHHHHHHHHCCCEEEEEECCCCE--EEECHHHHHHHHHHHHHHHHH--CCCCC
Q ss_conf             78887419830120331699999999999999998479589998089978--998689999999998865653--46898
Q gi|254780903|r  604 EMSKIETEKISIDKQNADLIPIINEGIRLIGSSAQSKNIKIEKKIPSELF--FNADKRIIKKILFPILSNSIK--FTNNN  679 (766)
Q Consensus       604 d~srieag~~~~~~~~~dl~~~i~~~~~~~~~~~~~k~i~l~~~~~~~l~--v~~D~~~l~QVl~NLi~NAik--~t~~~  679 (766)
                      +.++-..|..........|..++...+.........+...+...+..+.+  +..|..++.|++.+..+|+.+  ++..+
T Consensus       444 ~~~~~~~gt~~~~~i~~~l~~l~~~~~~~~~~~~~~~t~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~~~~~~~~~~  523 (786)
T KOG0519         444 DITRLYGGTGLGESIVFSLVELMSGEISDISCISLGKTFSFTLDLLTNLPKSVVGDEKRLFQIILDFNGMLALLIDTKLG  523 (786)
T ss_pred             HCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHCCCCCEEEEEECCCCCCCCCHHHHHHHHHHHHHHHCCHHHHHHCCCCC
T ss_conf             00345687645332223288998867432110034752223312356887310110344544555430122232003357


Q ss_pred             CE--EEEEEEE---------------------ECC-EEEEEEEECCCCCCHHHHHHHCCCEEECCCCCCCCCCCCCHHHH
Q ss_conf             88--9999999---------------------799-89999997889789778543046505314675567788761689
Q gi|254780903|r  680 GK--MMIRTSK---------------------IGQ-CVIITIADTGIGIPKSALEKIGQPFEPLHNQYDQSIGGFGLGLA  735 (766)
Q Consensus       680 g~--I~i~~~~---------------------~~~-~v~i~V~D~G~GI~~e~~~~iF~pF~q~~~~~t~~~~GtGLGLa  735 (766)
                      ..  +.+....                     ..+ .+++.++++..|+........|.-|.+....+++...+.++.++
T Consensus       524 ~~~~~~~~~~~~~~~vd~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~  603 (786)
T KOG0519         524 REQIFQVLAELLGISVDVSLSLSLAFWFLDLSLSDLEVCKQIEDNEEGSNNGDISSSNPLHKSLRDLTSKLSSGSGLSLA  603 (786)
T ss_pred             CCEEEEEEECCCCCCCCCCCCHHHHHHHCCCCCCCHHHHEEEECCCCCCCCCCCCHHHHHHHCCCCCCCCCCCCCCCCCC
T ss_conf             62069998012665411144310566643666100244223310303467777204565540034542002455542012


Q ss_pred             HHHHHHHHCCCEEEEE
Q ss_conf             9999999629869999
Q gi|254780903|r  736 ISDALTNLHGGRLKII  751 (766)
Q Consensus       736 I~k~iVe~hgG~I~v~  751 (766)
                      .|...++.+.|.+++.
T Consensus       604 ~~~~~~~~~~~~~~~~  619 (786)
T KOG0519         604 LCPENSQLMEGNIGLV  619 (786)
T ss_pred             CCHHHHHHHHCCCCCC
T ss_conf             3656777753143355


No 97 
>PRK00095 mutL DNA mismatch repair protein; Reviewed
Probab=98.26  E-value=2.4e-06  Score=63.76  Aligned_cols=25  Identities=12%  Similarity=0.042  Sum_probs=10.2

Q ss_pred             HHHHHHHHHHHHHHHHHCCCCCCEE
Q ss_conf             8999999999886565346898889
Q gi|254780903|r  658 KRIIKKILFPILSNSIKFTNNNGKM  682 (766)
Q Consensus       658 ~~~l~QVl~NLi~NAik~t~~~g~I  682 (766)
                      ...++.++-+|-.=---|+-++|+-
T Consensus       571 ~~Em~~Ll~~L~~~~~P~~CPHGRP  595 (612)
T PRK00095        571 LEEMNALLRQLEATENPGTCPHGRP  595 (612)
T ss_pred             HHHHHHHHHHHHCCCCCCCCCCCCC
T ss_conf             9999999999972899695989992


No 98 
>COG2172 RsbW Anti-sigma regulatory factor (Ser/Thr protein kinase) [Signal transduction mechanisms]
Probab=98.25  E-value=2.2e-05  Score=56.78  Aligned_cols=96  Identities=25%  Similarity=0.221  Sum_probs=69.0

Q ss_pred             CHHHHHHHHHHHHHHHHHCCCC----CCEEEEEEEEECCEEEEEEEECCCCCCHHHHHHHCCCEEECCCCCCCCCC-CCC
Q ss_conf             6899999999988656534689----88899999997998999999788978977854304650531467556778-876
Q gi|254780903|r  657 DKRIIKKILFPILSNSIKFTNN----NGKMMIRTSKIGQCVIITIADTGIGIPKSALEKIGQPFEPLHNQYDQSIG-GFG  731 (766)
Q Consensus       657 D~~~l~QVl~NLi~NAik~t~~----~g~I~i~~~~~~~~v~i~V~D~G~GI~~e~~~~iF~pF~q~~~~~t~~~~-GtG  731 (766)
                      |-.+++-++.-++.||++|...    .|.|.|.....++.+.+.|.|.|.||  +..+..++|-+     ++.... .-|
T Consensus        37 ~~~~l~~av~E~~~N~v~Ha~~~~~~~g~I~i~~~~~~~~~~i~i~D~G~~~--~~~~~~~~~~~-----~~~~~~~~~G  109 (146)
T COG2172          37 DIADLAIAVSEALTNAVKHAYKLDPSEGEIRIEVSLDDGKLEIRIWDQGPGI--EDLEESLGPGD-----TTAEGLQEGG  109 (146)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHCCCCCCCEEEEEEEECCCEEEEEEEECCCCC--CCHHHHCCCCC-----CCCCCCCCCC
T ss_conf             9999999999999899997630389986599999970993999999579898--78888538888-----8887532473


Q ss_pred             HHHHHHHHHHHHCCCEEEEEEECCC---CEEEEEE
Q ss_conf             1689999999962986999979899---5299997
Q gi|254780903|r  732 LGLAISDALTNLHGGRLKIISQEGK---GTIVTIC  763 (766)
Q Consensus       732 LGLaI~k~iVe~hgG~I~v~S~~g~---Gttf~i~  763 (766)
                      +||.+.++++.    ++.++++++.   +++++.+
T Consensus       110 ~Gl~l~~~~~D----~~~~~~~~~~~~~~~~~~~~  140 (146)
T COG2172         110 LGLFLAKRLMD----EFSYERSEDGRNRLTKITLR  140 (146)
T ss_pred             CCHHHHHHHHE----EEEEEEECCCCEEEEEEEEC
T ss_conf             13788862110----79999606985589999962


No 99 
>smart00086 PAC Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain). PAC motif occurs C-terminal to a subset of all known PAS motifs. It is proposed to contribute to the PAS domain fold.
Probab=98.23  E-value=2.8e-06  Score=63.20  Aligned_cols=42  Identities=31%  Similarity=0.649  Sum_probs=38.9

Q ss_pred             EEEEEEECCCCCEEEEEEEEEEEEECCCEE-EEEEEEECCCHH
Q ss_conf             999998869898899889999998379606-999998446179
Q gi|254780903|r  329 DQIFHMRHASGADIWIQVRAQMMRTISGGM-NIIGIAMDLTEK  370 (766)
Q Consensus       329 ~~e~Ri~~~DG~~~Wi~~r~~~i~d~~G~~-~~iGi~~DITEr  370 (766)
                      ..|||++++||+++|+..++.|++|.+|++ +++|+.+||||+
T Consensus         1 ~~e~r~~~~dG~~~w~~~~~~~~~~~~g~~~~~i~~~~DIte~   43 (43)
T smart00086        1 TVEYRLRRKDGSYIWVLVSASPIRDEDGEVEGILGVVRDITER   43 (43)
T ss_pred             CEEEEEECCCCCEEEEEEEEEEEECCCCCEEEEEEEEEECCCC
T ss_conf             9699999889999999999999999898999999999717798


No 100
>KOG3558 consensus
Probab=98.18  E-value=3.7e-05  Score=55.17  Aligned_cols=185  Identities=9%  Similarity=0.096  Sum_probs=107.4

Q ss_pred             HHHHHHHCCCCC-EEEEECCCCEEEECHHHHHHCCCCHHHCCCCHHHHHHHHCCCCHHHHHHHHHHHHC-------CCC-
Q ss_conf             999997225974-59897689789997889977299943305898899976081205899999999724-------898-
Q gi|254780903|r  256 CVETALSRGRCG-LWNFNFDNKKFHLSRSMYEIMGIPYENKTLSFRAIARLIHYDNKKICEIARSVTGK-------HVK-  326 (766)
Q Consensus       256 rl~~al~~a~~G-iWd~D~~~~~i~ws~~~~~llG~~~~e~~~s~~~~~~~vHPdDr~~~~~a~~~~~~-------~~~-  326 (766)
                      .+..-.-.+=+| +.-.+-+++.+|.|+..--.+|++.-|.  +...+.+++||-|-+.+.........       ... 
T Consensus       119 ~l~~~iLqsLDGFVm~l~~dG~~lYiSEtVS~yLGLSQvEL--TG~SvFDfiHP~DheE~~eqL~l~~~~p~~~es~~~~  196 (768)
T KOG3558         119 HLGDHILQSLDGFVMALTQDGDFLYISETVSIYLGLSQVEL--TGSSVFDFIHPCDHEEIAEQLGLRLTTPEVKESTDTS  196 (768)
T ss_pred             HHHHHHHHHCCCEEEEECCCCCEEEEECHHHHHHCCCCEEE--ECCHHHHCCCCCCHHHHHHHHCCCCCCCCCCCCCCCC
T ss_conf             52014876324438998167877998203576617110243--0541321257667899998743356887623245675


Q ss_pred             -EEEEEEEEE---CCCCC--------EEEEEEEEEEE-EECCCE--E---------EEEEEEECCCHHHHHHHHHHHHHH
Q ss_conf             -489999988---69898--------89988999999-837960--6---------999998446179999999999999
Q gi|254780903|r  327 -QLDQIFHMR---HASGA--------DIWIQVRAQMM-RTISGG--M---------NIIGIAMDLTEKYHLEKRYAEADQ  382 (766)
Q Consensus       327 -~~~~e~Ri~---~~DG~--------~~Wi~~r~~~i-~d~~G~--~---------~~iGi~~DITErK~ae~~l~ese~  382 (766)
                       ..++-.||+   .+-|.        |+-+++.|..- ++..+.  +         .++-++.-|---+-.|-.|     
T Consensus       197 teRsFflRMKsTLT~RGRtlnlKSa~yKvlh~tgh~rv~~~~sh~s~~~g~~~Pl~~lV~~a~alp~ps~~EipL-----  271 (768)
T KOG3558         197 TERSFFLRMKSTLTKRGRTLNLKSAGYKVLHCTGHLRVYNNPSHNSPLCGYKEPLLGLVALAEALPPPSYTEIPL-----  271 (768)
T ss_pred             CCEEEEEEEEEEECCCCCEEEEECCCEEEEEEEEEEEECCCCCCCCCCCCCCCCCHHEEEEECCCCCCCCCCCCC-----
T ss_conf             432579985315516773566501422689886345404677777755576655210045411379986566665-----


Q ss_pred             HHHHHHHHHHHHEEEECCCCEEEEECHHHHHHHCCCHHHHCCCCCHHHHCCCHHHHHHHHHHHCCCCCCCEE
Q ss_conf             999999854455158834996997017898883999789428971788165201378999852112456405
Q gi|254780903|r  383 RLSKAIECTSEALVLWDKNDRLVMCNANYQKAYGLPDHVLVPGNARSIIQDAQTRPIIEYRTSDPERSQDMS  454 (766)
Q Consensus       383 rlr~~ie~~~~~i~~~D~~g~i~~~N~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  454 (766)
                            ++ ...+.-...|-++++|.+.+.++.||..+++++...|+.+++.+..........-..++...+
T Consensus       272 ------~~-~~FvtRhs~DmkityCedRisdlm~y~PeeLvGrS~Ye~~Ha~Ds~~v~KSh~dL~~KGQv~T  336 (768)
T KOG3558         272 ------DC-HMFVTRHSLDMKITYCEDRISDLMDYEPEELVGRSCYEFVHALDSDRVRKSHHDLLTKGQVVT  336 (768)
T ss_pred             ------CC-CEEEEEEECCEEEEEECHHHHHHHCCCHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCH
T ss_conf             ------77-516776414516888735678876479788626048876337656677888999975474510


No 101
>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=98.14  E-value=1.5e-05  Score=57.94  Aligned_cols=163  Identities=17%  Similarity=0.198  Sum_probs=120.7

Q ss_pred             HHHHHHHCCCCHHHHHHHHHHH-HCCCCEEEEEEE-EECCCCCEEEEEEEEEEEEECCCEE-EEEEEEECCC---H----
Q ss_conf             8999760812058999999997-248984899999-8869898899889999998379606-9999984461---7----
Q gi|254780903|r  300 RAIARLIHYDNKKICEIARSVT-GKHVKQLDQIFH-MRHASGADIWIQVRAQMMRTISGGM-NIIGIAMDLT---E----  369 (766)
Q Consensus       300 ~~~~~~vHPdDr~~~~~a~~~~-~~~~~~~~~e~R-i~~~DG~~~Wi~~r~~~i~d~~G~~-~~iGi~~DIT---E----  369 (766)
                      ..|.+++.|+.+++++...+.+ .....++..+.- +..|.+..+++.....-.-+.+|++ +++.+.+|.=   |    
T Consensus        39 ~~w~ei~~~es~~k~~~~l~~a~~~g~~a~r~~~~~~~~P~~~ElP~~F~~~~L~~sdGk~~~vLa~GrdLr~vA~lqq~  118 (453)
T TIGR02040        39 RRWEEIVTEESKEKVEALLSEAKRTGVGAVRVELNRFVLPSDLELPMEFVLVRLGASDGKDEGVLALGRDLRAVAELQQR  118 (453)
T ss_pred             CCHHHHCCHHHHHHHHHHHHHCCCCCCCHHHHHHHHHCCCCCCCCCEEEEEECCCCCCCCCCCEEEECCCCHHHHHHHHH
T ss_conf             84444135778999999997146888857777665411799972440346761678788887358884652478999999


Q ss_pred             ----HHHHH---HHHHHHHHHHHHHHHHHHHHEEEEC-CCCEEEEECHHHHHHHCCCHH---HHCCCCCHHHHCCCHHHH
Q ss_conf             ----99999---9999999999999985445515883-499699701789888399978---942897178816520137
Q gi|254780903|r  370 ----KYHLE---KRYAEADQRLSKAIECTSEALVLWD-KNDRLVMCNANYQKAYGLPDH---VLVPGNARSIIQDAQTRP  438 (766)
Q Consensus       370 ----rK~ae---~~l~ese~rlr~~ie~~~~~i~~~D-~~g~i~~~N~~~~~~~g~~~~---~~~~~~~~~~~~~~~~~~  438 (766)
                          |+-.|   .++|+.|.|||.++|-+.++++++| +++|++.+|+++..++|-...   .++|......+......+
T Consensus       119 lv~AQ~AmErDYW~lR~~EtRYR~ll~~s~davllv~~st~rileaN~~A~~lLg~~~~~rd~LvG~~~~~e~~~~~~~~  198 (453)
T TIGR02040       119 LVEAQQAMERDYWKLREMETRYRLLLEVSSDAVLLVDVSTGRILEANSAAAALLGAEGQRRDSLVGREFPQELEEREREE  198 (453)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHHHHHHHCCCCCCCHHHHCCHHHCCCCCCCHHH
T ss_conf             99998788887999866754443354114886799853653477867999998502677501231113431466454368


Q ss_pred             HHHHHHHCCCCCCCEEEEEEECCC
Q ss_conf             899985211245640589991696
Q gi|254780903|r  439 IIEYRTSDPERSQDMSKEIKLADS  462 (766)
Q Consensus       439 ~~~~~~~~~~~~~~~~~e~~~~dg  462 (766)
                      .....-.....+.....++.++++
T Consensus       199 l~~~l~~~~atg~A~~~~i~l~~~  222 (453)
T TIGR02040       199 LELLLREVRATGKAAEVRILLAES  222 (453)
T ss_pred             HHHHHHHHHHCCCCCCCEEEECCC
T ss_conf             999998643015778717874578


No 102
>PRK13558 bacterio-opsin activator; Provisional
Probab=98.14  E-value=0.00017  Score=50.31  Aligned_cols=125  Identities=11%  Similarity=0.076  Sum_probs=70.2

Q ss_pred             HHCCCCCEEEEEC---CCCCEEEECCCHHHHCCCCHHHHCCCCHHHHCCCC----CCCHHHHHC-CCCHHEEEEEECCCC
Q ss_conf             1017897899996---99808997142055519978896076104320544----332023211-531000012331577
Q gi|254780903|r  123 TRFLSESFILLAQ---PNELVFASSTKNSHYIGKKIGEIIPELSRSRSRSK----TVQMSEASL-DQQPYHVLSVNLPHN  194 (766)
Q Consensus       123 ~~~~~~~~i~i~d---~~g~i~~~n~~~~~~~G~~~~~~~~~~~~~~~~~~----~~~~~~~~l-~~~~~~~~~~~~~~~  194 (766)
                      +...++..|.+.|   ++.+++++|+++.++.||...+++|+.........    ....+...+ .+.......+..+..
T Consensus       163 a~d~a~v~i~~a~~~~p~~~i~~~n~a~~eitGy~~~e~~g~~~r~lq~~~~~~e~~~~~~~ai~~~~~~~ve~r~~r~d  242 (674)
T PRK13558        163 ALDEAPIGITISDATDPEEPIIYINDSFEDITGYSPDEVVGANHRFLQGPKTNEDRVAEFWTAITEDHDTQVVLRNYRRD  242 (674)
T ss_pred             HHHCCCCEEEEECCCCCCCCEEEEEHHHHHHCCCCHHHHCCCCHHHHCCCCCCHHHHHHHHHHHHCCCCCEEEEEEECCC
T ss_conf             66405725998468888874388601236531898178649740121068888057999999975588633453331468


Q ss_pred             CCEEEEEEECCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC
Q ss_conf             825999974232101234556554568788789999999988889999999999999999999999722
Q gi|254780903|r  195 SGSILIINSRVPLLRLWREEVTLEVVFFSIISALLLFILFSYYRQAKKNKENDTILLEANICVETALSR  263 (766)
Q Consensus       195 ~~~~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~a~~~dit~~r~ae~~l~ese~rl~~al~~  263 (766)
                      +..+|......++.+.              .+.+.-.  .++.+|||+||++|++|+.-++-|...|++
T Consensus       243 G~~~w~~~~i~pi~De--------------dg~v~~~--Vg~~~DiteRke~E~~L~~~~~~l~~~L~R  295 (674)
T PRK13558        243 GSLFWNQVDISPIYDE--------------DGTVSHY--VGFQMDVSERMAAQQELQGERQSLDRLLDR  295 (674)
T ss_pred             CCEEEEECCCCCCCCC--------------CCCEEEE--EEECCCHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             8378741245521057--------------8858999--862144778899999999868899999999


No 103
>smart00091 PAS PAS domain. PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels ([1]; Ponting & Aravind, in press).
Probab=98.01  E-value=9.5e-06  Score=59.43  Aligned_cols=61  Identities=16%  Similarity=0.239  Sum_probs=40.7

Q ss_pred             HHHHHHHCCCCCEEEEECCCCEEEECHHHHHHCCCCHHHCCCCHHHHHHHHCCCCHHHHHHHH
Q ss_conf             999997225974598976897899978899772999433058988999760812058999999
Q gi|254780903|r  256 CVETALSRGRCGLWNFNFDNKKFHLSRSMYEIMGIPYENKTLSFRAIARLIHYDNKKICEIAR  318 (766)
Q Consensus       256 rl~~al~~a~~GiWd~D~~~~~i~ws~~~~~llG~~~~e~~~s~~~~~~~vHPdDr~~~~~a~  318 (766)
                      +++.+++..+.|+|.+|.++..++||+++.++|||++++..+.  .+..++||+|++.+....
T Consensus         2 ~~~~~~~~~~~~i~~~d~~g~i~~~N~~~~~~~g~~~~e~~g~--~~~~~~~~~~~~~~~~~~   62 (67)
T smart00091        2 RLRAILESLPDGIFVLDLDGRILYANPAAEELLGYSPEELIGK--SLLELIHPEDREEVQEAL   62 (67)
T ss_pred             HHHHHHHHHHHHHEEECCCCCEEEECHHHHHHHCCCHHHHCCC--CHHHHCCHHHHHHHHHHH
T ss_conf             7999999655798588699948998859999889099999599--899946998999999999


No 104
>COG5002 VicK Signal transduction histidine kinase [Signal transduction mechanisms]
Probab=98.00  E-value=0.0017  Score=43.12  Aligned_cols=134  Identities=14%  Similarity=0.148  Sum_probs=97.6

Q ss_pred             HHHHH-HHHHHHHHHHHHHHHHHHHHCCCCCEEEEECCCCEEEECHHHHHHCCCCHHHCCCCHHHHHHHHCCCCHHHHHH
Q ss_conf             89999-99999999999999999972259745989768978999788997729994330589889997608120589999
Q gi|254780903|r  238 RQAKK-NKENDTILLEANICVETALSRGRCGLWNFNFDNKKFHLSRSMYEIMGIPYENKTLSFRAIARLIHYDNKKICEI  316 (766)
Q Consensus       238 ~dit~-~r~ae~~l~ese~rl~~al~~a~~GiWd~D~~~~~i~ws~~~~~llG~~~~e~~~s~~~~~~~vHPdDr~~~~~  316 (766)
                      .+.++ -+.|+..+..-+.|++..+.-..+|+.-.|-.+..+..|.....|+|.+.++....  ...++..-+|-=.+  
T Consensus        93 n~Lt~~~~~aq~n~e~Er~kL~SvlayMtDGViATdRrG~iI~iN~~A~k~L~~~~E~~~~~--~i~elL~i~d~y~~--  168 (459)
T COG5002          93 NDLTKRVQEAQANTEQERRKLDSVLAYMTDGVIATDRRGKIILINKPALKMLGVSKEDALGR--SILELLKIEDTYTF--  168 (459)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCEEEECCCCCEEEECCHHHHHHCCCHHHHHCC--CHHHHHCCCCCEEH--
T ss_conf             78999999998767888888998999870765764577868993507999848677877165--37888577543028--


Q ss_pred             HHHHHHCCCCEEEEEEEEECCCCCEEEEEEEEEEEEECCCEE-EEEEEEECCCHHHHHHHHHHHH
Q ss_conf             999972489848999998869898899889999998379606-9999984461799999999999
Q gi|254780903|r  317 ARSVTGKHVKQLDQIFHMRHASGADIWIQVRAQMMRTISGGM-NIIGIAMDLTEKYHLEKRYAEA  380 (766)
Q Consensus       317 a~~~~~~~~~~~~~e~Ri~~~DG~~~Wi~~r~~~i~d~~G~~-~~iGi~~DITErK~ae~~l~es  380 (766)
                        +.+....+.+-.+.+   .+++..-++++..+++.+.|.. +++.+..|+|||.+.|++.++.
T Consensus       169 --~dL~e~~~s~lld~~---~~~E~~~lrv~Fs~i~rEsGfisGlIaVlhDvTEqek~e~ErRef  228 (459)
T COG5002         169 --EDLVEKNDSLLLDSS---DEEEGYVLRVNFSVIQRESGFISGLIAVLHDVTEQEKVERERREF  228 (459)
T ss_pred             --HHHHHCCCCEEEEEC---CCCCCEEEEEEEEEEEECCCCCCEEEEEEECCCHHHHHHHHHHHH
T ss_conf             --888725982898604---788637999988888511466440699873143878889999999


No 105
>COG3829 RocR Transcriptional regulator containing PAS, AAA-type ATPase, and DNA-binding domains [Transcription / Signal transduction mechanisms]
Probab=97.98  E-value=0.0016  Score=43.32  Aligned_cols=161  Identities=12%  Similarity=0.131  Sum_probs=113.9

Q ss_pred             HHHHHCCCCCEEEEECCCCEEEECHHHHHHCCCCHHHCCCCHHHHHHHHCCCCHHHHHHHHHHHHCCCCEEEEEEEEECC
Q ss_conf             99972259745989768978999788997729994330589889997608120589999999972489848999998869
Q gi|254780903|r  258 ETALSRGRCGLWNFNFDNKKFHLSRSMYEIMGIPYENKTLSFRAIARLIHYDNKKICEIARSVTGKHVKQLDQIFHMRHA  337 (766)
Q Consensus       258 ~~al~~a~~GiWd~D~~~~~i~ws~~~~~llG~~~~e~~~s~~~~~~~vHPdDr~~~~~a~~~~~~~~~~~~~e~Ri~~~  337 (766)
                      +..++...+|.-..|..++..+.|.-...+++-...... ++ .....+.+-..+.+.        .........+...+
T Consensus         4 ~~~l~~~~~~~~vi~~~~~~~~~~~~a~~~~~~~~~~~i-~~-~~~~i~~~~~~~~v~--------~~~~~~~~~~~~~~   73 (560)
T COG3829           4 EGILKSILDGPVVIDKNTGIDVANALALAKRQKNAEAVI-GR-PLREILETLGMERVE--------QSRDKELTERLKLK   73 (560)
T ss_pred             HHHHHHCCCCEEEEECCCCEEEECHHHHHHHHCCEEEEE-CC-CHHHHHCCCCCCEEE--------CCCCCCEEEEEECC
T ss_conf             445665046408997177547603377765105447874-23-411111125862341--------06765201355406


Q ss_pred             CCCEEEEEEEEEEEEECCCEE-EEEEEEECCCHHHHHHHHH-HHHHHHHHHHHHHHHHHEEEECCCCEEEEECHHHHHHH
Q ss_conf             898899889999998379606-9999984461799999999-99999999999854455158834996997017898883
Q gi|254780903|r  338 SGADIWIQVRAQMMRTISGGM-NIIGIAMDLTEKYHLEKRY-AEADQRLSKAIECTSEALVLWDKNDRLVMCNANYQKAY  415 (766)
Q Consensus       338 DG~~~Wi~~r~~~i~d~~G~~-~~iGi~~DITErK~ae~~l-~ese~rlr~~ie~~~~~i~~~D~~g~i~~~N~~~~~~~  415 (766)
                       + .+-+-.. .+..++.+++ .++.+..|++|....-+.. +...++|+.+++.+.+++++.|.+|+++++|+++..++
T Consensus        74 -~-~~~~~~~-~~~~~~~~~~~g~~~~~~~~~e~~~~~~~~l~~~~~~l~~il~~~~~~l~vvD~~G~~i~~N~~~~~~~  150 (560)
T COG3829          74 -V-KRIVVVG-KTPVDEQGRVVGVLEVFLDISEALELIEENLRQLRQRLEAILDSIDDGLLVVDEDGIIIYYNKAYAKLL  150 (560)
T ss_pred             -C-EEEEECC-CCEEECCCCEEEEEHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCEEEECCCCCEEEECHHHHHHH
T ss_conf             -4-0489817-852412774445512545149899999999999999999998625674599869996899847789883


Q ss_pred             CCCHHHHCCCCCHHHH
Q ss_conf             9997894289717881
Q gi|254780903|r  416 GLPDHVLVPGNARSII  431 (766)
Q Consensus       416 g~~~~~~~~~~~~~~~  431 (766)
                      |++.+++++....+.+
T Consensus       151 gl~~e~~~gk~~~~v~  166 (560)
T COG3829         151 GLSPEEVLGKHLLDVV  166 (560)
T ss_pred             CCCHHHHCCCCHHHHH
T ss_conf             9998998197189887


No 106
>COG3290 CitA Signal transduction histidine kinase regulating citrate/malate metabolism [Signal transduction mechanisms]
Probab=97.92  E-value=0.0025  Score=42.00  Aligned_cols=286  Identities=13%  Similarity=0.079  Sum_probs=144.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHCC-CCCEEEEECCCCCEEEECCCHHHHCCC
Q ss_conf             6888999899999999999985010011223554899999999988531017-897899996998089971420555199
Q gi|254780903|r   75 YAQQEKMTNQTSLMLTEAIEIIFQNNNIKFDLASQKKAESMLGQLLAKTRFL-SESFILLAQPNELVFASSTKNSHYIGK  153 (766)
Q Consensus        75 ~~~~~~~~~~~~~lla~~~~~~~~~~~~~~d~~~~~~ae~~L~~~~~~~~~~-~~~~i~i~d~~g~i~~~n~~~~~~~G~  153 (766)
                      +...+....+.+...|..++.    .....+.-..++.+..++....+.+.. ..++|++.|.+| |-...|..+. .|+
T Consensus        38 ~~~~~~q~~~~Al~~Ar~vA~----~p~v~e~l~~~~~~~~iq~~~~~i~~~t~a~fIVV~d~~g-IR~~HP~per-IGk  111 (537)
T COG3290          38 SDTLRDQLEHKALSTARTVAS----NPEVIEALENKDQEARIQAIAEAIRSITDADFIVVGDMKG-IRLTHPNPER-IGK  111 (537)
T ss_pred             HHHHHHHHHHHHHHHHHHHHC----CHHHHHHHHCCCCCHHHHHHHHHHHHHCCCEEEEEECCCC-CEECCCCHHH-HCC
T ss_conf             999999999899999999853----9899999865992045899999998651961899956886-2404899588-389


Q ss_pred             CHH-----H-HCCCCHHHHCCCCCCCHHHHHCCCCHHEEEEEECCCCCCEEEEEEECCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf             788-----9-6076104320544332023211531000012331577825999974232101234556554568788789
Q gi|254780903|r  154 KIG-----E-IIPELSRSRSRSKTVQMSEASLDQQPYHVLSVNLPHNSGSILIINSRVPLLRLWREEVTLEVVFFSIISA  227 (766)
Q Consensus       154 ~~~-----~-~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~  227 (766)
                      +..     . +-|+.-...    ..+.....+.+........  ...-|.|.+-... +....|......+..+..-...
T Consensus       112 p~~ggde~a~~~G~~yvS~----~kGslg~s~R~~~PI~d~~--g~~IGvVsVG~~l-~~i~~~i~~~~~~l~~~~vl~l  184 (537)
T COG3290         112 PFQGGDEEAALAGESYVST----AKGSLGKSLRAKVPIFDED--GKQIGVVSVGYLL-SEIDDVILEFLRPLALIVVLGL  184 (537)
T ss_pred             CCCCCCHHHHHCCCEEEEE----EECCCHHHHEEECCEECCC--CCEEEEEEEEEEH-HHHHHHHHHHHHHHHHHHHHHH
T ss_conf             7668888898578606998----5213024013404458799--9788899986672-6589999998998999999999


Q ss_pred             HHHHHHHHHHHHHHHHH----HHHHHHHHHHHHHHHHHHCCCCCEEEEECCCCEEEECHHHHHHCCCCHHHCCCCHHHHH
Q ss_conf             99999998888999999----99999999999999997225974598976897899978899772999433058988999
Q gi|254780903|r  228 LLLFILFSYYRQAKKNK----ENDTILLEANICVETALSRGRCGLWNFNFDNKKFHLSRSMYEIMGIPYENKTLSFRAIA  303 (766)
Q Consensus       228 ~~~~~~~a~~~dit~~r----~ae~~l~ese~rl~~al~~a~~GiWd~D~~~~~i~ws~~~~~llG~~~~e~~~s~~~~~  303 (766)
                      .++.++..+..-..++.    +.++..+-.++| ...+++...|+.-||..+....+|.+.++|+|+.......-...+.
T Consensus       185 ligl~ga~~la~~ikr~~~glEP~EIa~l~~er-~A~l~si~EGviAvd~~G~It~~N~~A~~ll~~~~~~~~~ig~~i~  263 (537)
T COG3290         185 LIGLLGAWILARHIKRQMLGLEPEEIATLLEER-QAMLQSIKEGVIAVDKKGVITLINQAAQKLLGLRQPSGDPIGRSIV  263 (537)
T ss_pred             HHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHH-HHHHHHHHCEEEEECCCCEEEEHHHHHHHHHCCCCCCCCCCCCCCE
T ss_conf             999999999999999998289979999999999-9999876362899878985761128899984656767564466103


Q ss_pred             HHHCCCCHHHHHHHHHHHHCCCCEEEEEEEEECCCCCEEEEEEEEEEEEECCCEEEEEEEEECCCHHHHHHHHHHHHHHH
Q ss_conf             76081205899999999724898489999988698988998899999983796069999984461799999999999999
Q gi|254780903|r  304 RLIHYDNKKICEIARSVTGKHVKQLDQIFHMRHASGADIWIQVRAQMMRTISGGMNIIGIAMDLTEKYHLEKRYAEADQR  383 (766)
Q Consensus       304 ~~vHPdDr~~~~~a~~~~~~~~~~~~~e~Ri~~~DG~~~Wi~~r~~~i~d~~G~~~~iGi~~DITErK~ae~~l~ese~r  383 (766)
                      ..+.|| -....    ........++.++|+   +|.  |+...-.|++-.+...+++.+++|=||-+.+-++|..-...
T Consensus       264 ~v~~p~-~~l~~----vl~~~~~~~~~e~~~---ng~--~~i~nr~pI~~~~~~~GaI~tFRdktei~~L~eqLt~vr~y  333 (537)
T COG3290         264 EVLPPD-SDLPE----VLETGKPQHDEEIRI---NGR--LLVANRVPIRSGGQIVGAIITFRDKTEIKKLTEQLTGVRQY  333 (537)
T ss_pred             EEECCC-CCCHH----HHHCCCCCCCHHHHC---CCE--EEEEEECCEEECCEEEEEEEEEECHHHHHHHHHHHHHHHHH
T ss_conf             761563-67577----875077631134414---775--99998523788897768999876377899999999989999


Q ss_pred             H
Q ss_conf             9
Q gi|254780903|r  384 L  384 (766)
Q Consensus       384 l  384 (766)
                      .
T Consensus       334 a  334 (537)
T COG3290         334 A  334 (537)
T ss_pred             H
T ss_conf             9


No 107
>smart00091 PAS PAS domain. PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels ([1]; Ponting & Aravind, in press).
Probab=97.82  E-value=6.5e-05  Score=53.39  Aligned_cols=56  Identities=16%  Similarity=0.328  Sum_probs=49.1

Q ss_pred             HHHHHHHHHHHHHEEEECCCCEEEEECHHHHHHHCCCHHHHCCCCCHHHHCCCHHH
Q ss_conf             99999998544551588349969970178988839997894289717881652013
Q gi|254780903|r  382 QRLSKAIECTSEALVLWDKNDRLVMCNANYQKAYGLPDHVLVPGNARSIIQDAQTR  437 (766)
Q Consensus       382 ~rlr~~ie~~~~~i~~~D~~g~i~~~N~~~~~~~g~~~~~~~~~~~~~~~~~~~~~  437 (766)
                      .+++.++++++++++++|.+|++++||+++.+++|++.+++.+...++.+++.+..
T Consensus         1 ~~~~~~~~~~~~~i~~~d~~g~i~~~N~~~~~~~g~~~~e~~g~~~~~~~~~~~~~   56 (67)
T smart00091        1 ERLRAILESLPDGIFVLDLDGRILYANPAAEELLGYSPEELIGKSLLELIHPEDRE   56 (67)
T ss_pred             CHHHHHHHHHHHHHEEECCCCCEEEECHHHHHHHCCCHHHHCCCCHHHHCCHHHHH
T ss_conf             97999999655798588699948998859999889099999599899946998999


No 108
>TIGR00585 mutl DNA mismatch repair protein MutL; InterPro: IPR014763   This entry represents DNA mismatch repair proteins, such as MutL. The dimeric MutL protein has a key function in communicating mismatch recognition by MutS to downstream repair processes. Mismatch repair contributes to the overall fidelity of DNA replication by targeting mispaired bases that arise through replication errors during homologous recombination and as a result of DNA damage. It involves the correction of mismatched base pairs that have been missed by the proofreading element of the DNA polymerase complex ..
Probab=97.81  E-value=7.8e-05  Score=52.83  Aligned_cols=56  Identities=21%  Similarity=0.295  Sum_probs=42.8

Q ss_pred             HHHHHHHHHHHHHHHCCCCCCEEEEEEEEECCEEEEEEEECCCCCCHHHHHHHCCCEEE
Q ss_conf             99999999886565346898889999999799899999978897897785430465053
Q gi|254780903|r  660 IIKKILFPILSNSIKFTNNNGKMMIRTSKIGQCVIITIADTGIGIPKSALEKIGQPFEP  718 (766)
Q Consensus       660 ~l~QVl~NLi~NAik~t~~~g~I~i~~~~~~~~v~i~V~D~G~GI~~e~~~~iF~pF~q  718 (766)
                      ..-.|+=-|+-||+++.  .-+|.|.....|= =.|.|+|||.||++++++.+.+||.+
T Consensus        22 ~p~~vVKELvENSLDAG--At~I~v~~~~gG~-~~I~V~DNG~Gi~~~d~~~~~~~haT   77 (367)
T TIGR00585        22 RPASVVKELVENSLDAG--ATKIEVEIEEGGL-KLIEVSDNGSGIDKEDLELACERHAT   77 (367)
T ss_pred             HHHHHHHHHHHHHHCCC--CCEEEEEEEECCE-EEEEEEECCCCCCHHHHHHHHCCCCC
T ss_conf             27999999887312148--8589999962653-58999977856777779986123577


No 109
>TIGR02966 phoR_proteo phosphate regulon sensor kinase PhoR; InterPro: IPR014310   Members of this protein are the regulatory histidine kinase PhoR associated with the phosphate ABC transporter found in most Proteobacteria, and related proteins from Gram-positive organisms are excluded. The phoR gene usually is adjacent to the response regulator phoB gene (IPR011879 from INTERPRO)..
Probab=97.74  E-value=0.0005  Score=46.99  Aligned_cols=115  Identities=10%  Similarity=0.020  Sum_probs=76.5

Q ss_pred             HHHHHHHHHHCCCCCEEEEECCCCEEEECHHHHHHCCCCHHHCCCCHHHHHHHH-CCCCHHHHHHHHHHHHCCCCEEEEE
Q ss_conf             999999997225974598976897899978899772999433058988999760-8120589999999972489848999
Q gi|254780903|r  253 ANICVETALSRGRCGLWNFNFDNKKFHLSRSMYEIMGIPYENKTLSFRAIARLI-HYDNKKICEIARSVTGKHVKQLDQI  331 (766)
Q Consensus       253 se~rl~~al~~a~~GiWd~D~~~~~i~ws~~~~~llG~~~~e~~~s~~~~~~~v-HPdDr~~~~~a~~~~~~~~~~~~~e  331 (766)
                      --.||+.++++-|+|+.-.|-.+...|||+...++||+.-..+.+  ..+..++ ||+ ...|..  +.-. ...+=..+
T Consensus         4 ~~~rf~~a~~AlPDavv~ld~~~~I~W~N~~A~~~LGl~~p~D~G--q~i~~l~R~P~-F~~yl~--~~~~-t~~p~~L~   77 (339)
T TIGR02966         4 LLSRFRAAAQALPDAVVVLDEEGQIEWCNKAAERLLGLRWPDDLG--QRITNLIRHPE-FVEYLA--AGRF-TSEPEQLE   77 (339)
T ss_pred             HHHHHHHHHHHCCCEEEEECCCCCEEEEEHHHHHHCCCCCCHHHC--CCHHHHCCCHH-HHHHHH--CCCC-CCCCCCEE
T ss_conf             889999999758982999728983786214889862742734507--70212105767-999973--3555-57885311


Q ss_pred             EEEE-CCCCCEEEEEEEEEEEEECCCEEEEEEEEECCCHHHHHHHHHHH
Q ss_conf             9988-69898899889999998379606999998446179999999999
Q gi|254780903|r  332 FHMR-HASGADIWIQVRAQMMRTISGGMNIIGIAMDLTEKYHLEKRYAE  379 (766)
Q Consensus       332 ~Ri~-~~DG~~~Wi~~r~~~i~d~~G~~~~iGi~~DITErK~ae~~l~e  379 (766)
                        +. .+-++-+-+..+..|.-++    +.+-+++|||+-+|+|+--++
T Consensus        78 --~~~~p~~~~~~l~~r~~PY~~~----~~Ll~~RDvT~l~rLe~mRrD  120 (339)
T TIGR02966        78 --LPDSPINEERVLEIRIMPYGEE----QKLLVARDVTRLRRLEQMRRD  120 (339)
T ss_pred             --ECCCCCCCCCEEEEEEEEECCC----CEEEEEECHHHHHHHHHHHHH
T ss_conf             --0468888664799999975698----379998763689999865343


No 110
>PRK10820 DNA-binding transcriptional regulator TyrR; Provisional
Probab=97.68  E-value=0.0032  Score=41.22  Aligned_cols=109  Identities=10%  Similarity=0.079  Sum_probs=67.4

Q ss_pred             HHHHHHHHHHHCCCCCEEEEECCCCEEEECHHHHHHCCCCHHHCCCCHHHHHHHHCCCCHHHHHHHHHHHHCCCCEEEEE
Q ss_conf             99999999972259745989768978999788997729994330589889997608120589999999972489848999
Q gi|254780903|r  252 EANICVETALSRGRCGLWNFNFDNKKFHLSRSMYEIMGIPYENKTLSFRAIARLIHYDNKKICEIARSVTGKHVKQLDQI  331 (766)
Q Consensus       252 ese~rl~~al~~a~~GiWd~D~~~~~i~ws~~~~~llG~~~~e~~~s~~~~~~~vHPdDr~~~~~a~~~~~~~~~~~~~e  331 (766)
                      +.+..+++++++.++|++.+|..+....+|+++.++||++.++..+.  ....+++.-+...+     ...+....  ..
T Consensus        77 r~~~~L~alLdsl~dgV~svD~~G~I~~~N~aa~~i~~~~~~~~~G~--~i~~~~~~~~~~~~-----l~~~~~~~--~~  147 (513)
T PRK10820         77 REHLALSALLEALPEPVLSIDMKSKVELANPASCQLFGQSEERLRNH--TAAQLINGFNFLRW-----LESEPQDS--HN  147 (513)
T ss_pred             HHHHHHHHHHHHCCCCEEEECCCCCEEEEHHHHHHHHCCCHHHHCCC--CHHHHCCCCCHHHH-----HHCCCCCC--CC
T ss_conf             68889999997389978998599819976399999849896887797--99997187569999-----86289876--63


Q ss_pred             EEEECCCCCEEEEEEEEEEEEECCCEEEEEEE---EECCCHH
Q ss_conf             99886989889988999999837960699999---8446179
Q gi|254780903|r  332 FHMRHASGADIWIQVRAQMMRTISGGMNIIGI---AMDLTEK  370 (766)
Q Consensus       332 ~Ri~~~DG~~~Wi~~r~~~i~d~~G~~~~iGi---~~DITEr  370 (766)
                      .++. -+|.-..+...-..+.|++|...++|.   ..|.++.
T Consensus       148 ~~~~-~~~~~~~~~~~pi~~~~~~~~~~~~GaV~~lk~~~~~  188 (513)
T PRK10820        148 EHVV-INGQNFLMEITPVYLQDENDQHVLTGAVVMLRSTIRM  188 (513)
T ss_pred             EEEE-ECCCEEEEEEEEEEECCCCCCCEEEEEEEEECCHHHH
T ss_conf             5998-7696789997678752778860366689882468999


No 111
>PRK10820 DNA-binding transcriptional regulator TyrR; Provisional
Probab=97.63  E-value=0.002  Score=42.67  Aligned_cols=39  Identities=8%  Similarity=0.027  Sum_probs=19.9

Q ss_pred             CCEEEEECCCCCEEEECCCHHHHCCCCHHHHCCCCHHHH
Q ss_conf             978999969980899714205551997889607610432
Q gi|254780903|r  128 ESFILLAQPNELVFASSTKNSHYIGKKIGEIIPELSRSR  166 (766)
Q Consensus       128 ~~~i~i~d~~g~i~~~n~~~~~~~G~~~~~~~~~~~~~~  166 (766)
                      ++.|+.+|.+|+|+.+|++++.++|.+..+++|+.....
T Consensus        90 ~dgV~svD~~G~I~~~N~aa~~i~~~~~~~~~G~~i~~~  128 (513)
T PRK10820         90 PEPVLSIDMKSKVELANPASCQLFGQSEERLRNHTAAQL  128 (513)
T ss_pred             CCCEEEECCCCCEEEEHHHHHHHHCCCHHHHCCCCHHHH
T ss_conf             997899859981997639999984989688779799997


No 112
>pfam10090 DUF2328 Uncharacterized protein conserved in bacteria (DUF2328). Members of this family of hypothetical bacterial proteins have no known function.
Probab=97.57  E-value=0.0079  Score=38.34  Aligned_cols=177  Identities=14%  Similarity=0.110  Sum_probs=115.4

Q ss_pred             HHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCEEEECHHHHHHHHHHHHHHHHH
Q ss_conf             89999999986034688993899999999999999999997776778887419830120331699999999999999998
Q gi|254780903|r  559 NAILGFSEVIKKEIFGELGSVKYYEYAQDIHYSGQHLLNMINNILEMSKIETEKISIDKQNADLIPIINEGIRLIGSSAQ  638 (766)
Q Consensus       559 ~aI~g~~ell~~~~~~~~~~e~~~~~l~~I~~~~~~l~~lI~diLd~srieag~~~~~~~~~dl~~~i~~~~~~~~~~~~  638 (766)
                      .+|....|+|...-  .   ....+.++-|.+|+.....-    |.|.|+--|... .-+.+|..++-+-+-..++    
T Consensus         2 GAI~NGLELL~~~~--~---~~~~~~m~LI~~Sa~~A~aR----l~F~RlAfGaag-~~~~i~~~e~~~~~~~~~~----   67 (181)
T pfam10090         2 GAIVNGLELLDDEG--D---PEMGPEMALIRESARNASAR----LRFFRLAFGAAG-AGQQIDLAEAKSVLEGYLA----   67 (181)
T ss_pred             CCHHHHHHHHCCCC--C---CCCHHHHHHHHHHHHHHHHH----HHHHHHHHCCCC-CCCCCCHHHHHHHHHHHHH----
T ss_conf             31255588870789--8---64168999999999999999----999999808468-8885699999999999983----


Q ss_pred             HCCCEEEEEECCCCEEEECHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEEE-CCEEEEEEEECCCCCCHHHHHHHCCCEE
Q ss_conf             479589998089978998689999999998865653468988899999997-9989999997889789778543046505
Q gi|254780903|r  639 SKNIKIEKKIPSELFFNADKRIIKKILFPILSNSIKFTNNNGKMMIRTSKI-GQCVIITIADTGIGIPKSALEKIGQPFE  717 (766)
Q Consensus       639 ~k~i~l~~~~~~~l~v~~D~~~l~QVl~NLi~NAik~t~~~g~I~i~~~~~-~~~v~i~V~D~G~GI~~e~~~~iF~pF~  717 (766)
                      ...+++.++.+.+.   . +...-+.++||+-=+..++|-||.|+|..... +..+.++-+=.-+.++++..+-+=..= 
T Consensus        68 ~~r~~l~W~~~~~~---~-~k~~vklllnl~l~~~~AlprGG~i~V~~~~~~~~~~~v~a~g~r~~~~~~~~~~L~g~~-  142 (181)
T pfam10090        68 GGRITLDWQLERDL---L-PKPEVKLLLNLLLIAEDALPRGGEIDVGEGSDGAGGWRVTAEGERLRIDPDLWAALAGGA-  142 (181)
T ss_pred             CCCEEEEECCCCCC---C-CHHHHHHHHHHHHHHHHHCCCCCEEEEEEECCCCCEEEEEEEECCCCCCHHHHHHHCCCC-
T ss_conf             88538983587454---8-879999999999999975477877899984178975999997046789978999856999-


Q ss_pred             ECCCCCCCCCCCCCHHHHHHHHHHHHCCCEEEEEEECCCCEEE
Q ss_conf             3146755677887616899999999629869999798995299
Q gi|254780903|r  718 PLHNQYDQSIGGFGLGLAISDALTNLHGGRLKIISQEGKGTIV  760 (766)
Q Consensus       718 q~~~~~t~~~~GtGLGLaI~k~iVe~hgG~I~v~S~~g~Gttf  760 (766)
                           ........-.=-+....+.+..|++|.++.+.. +.+|
T Consensus       143 -----~~~~l~~~~VQ~~~l~~la~~~G~~l~~~~~~~-~i~l  179 (181)
T pfam10090       143 -----PEEELDARNVQFYLLPLLAREAGGTLSYEITED-GIVL  179 (181)
T ss_pred             -----CCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCC-EEEE
T ss_conf             -----877899876499999999998699117886497-7998


No 113
>KOG3559 consensus
Probab=97.57  E-value=0.00021  Score=49.75  Aligned_cols=216  Identities=12%  Similarity=0.095  Sum_probs=132.2

Q ss_pred             CCEEEEECCCCCEEEECCCHHHHCCCCHHHHCCCCHHHHCCCCCCCHHHHHCCCCHHEEEEE-------------E----
Q ss_conf             97899996998089971420555199788960761043205443320232115310000123-------------3----
Q gi|254780903|r  128 ESFILLAQPNELVFASSTKNSHYIGKKIGEIIPELSRSRSRSKTVQMSEASLDQQPYHVLSV-------------N----  190 (766)
Q Consensus       128 ~~~i~i~d~~g~i~~~n~~~~~~~G~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~-------------~----  190 (766)
                      +.+|+|++++|.|++.+....-.+|.+.-|+.|.+..+...+.....+...+.....+....             .    
T Consensus        89 DGF~fvva~dGkimYISETaSvhLGLSQVElTGNsi~eYIH~~D~demna~L~~h~H~qeyeIErsfflrmkCvlakrna  168 (598)
T KOG3559          89 DGFIFVVAPDGKIMYISETASVHLGLSQVELTGNSIYEYIHPQDHDEMNAVLTAHQHLQEYEIERSFFLRMKCVLAKRNA  168 (598)
T ss_pred             CCEEEEEECCCCEEEEECCEEEEECCEEEEEECCHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC
T ss_conf             54599992799889985011345230004650623766406012578988876432444300334311234331000024


Q ss_pred             -CCCCCCEEEEE-------E---ECCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             -15778259999-------7---4232101234556554568788789999999988-8899999999999999999999
Q gi|254780903|r  191 -LPHNSGSILII-------N---SRVPLLRLWREEVTLEVVFFSIISALLLFILFSY-YRQAKKNKENDTILLEANICVE  258 (766)
Q Consensus       191 -~~~~~~~~~~~-------~---~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~a~-~~dit~~r~ae~~l~ese~rl~  258 (766)
                       +...+..++-.       +   ...+-...+.+.           +.|  +++... ..-+|+                
T Consensus       169 glt~sg~kvihcSgylKir~y~~~m~p~dscyqn~-----------glv--AvG~slP~saite----------------  219 (598)
T KOG3559         169 GLTCSGYKVIHCSGYLKIRQYELDMSPNDSCYQNV-----------GLV--AVGHSLPPSAITE----------------  219 (598)
T ss_pred             CCCCCCCCEEEECCCCEEEEEEECCCCCCCCCCCC-----------EEE--EECCCCCCCCCEE----------------
T ss_conf             65336863486057606899653258774510001-----------069--9557789541147----------------


Q ss_pred             HHHHCCCCCEEEEECCCCEEEECHHHHHHCCCCHHHCCCCHHHHHHHHCCCCHHHHHHHHHHHHCCCCEEEEEEEEECCC
Q ss_conf             99722597459897689789997889977299943305898899976081205899999999724898489999988698
Q gi|254780903|r  259 TALSRGRCGLWNFNFDNKKFHLSRSMYEIMGIPYENKTLSFRAIARLIHYDNKKICEIARSVTGKHVKQLDQIFHMRHAS  338 (766)
Q Consensus       259 ~al~~a~~GiWd~D~~~~~i~ws~~~~~llG~~~~e~~~s~~~~~~~vHPdDr~~~~~a~~~~~~~~~~~~~e~Ri~~~D  338 (766)
                       +--..++-++...++-..+|.+.+..+++||+|.+...  .....+||--|......+-..+...+..-.--||+..+.
T Consensus       220 -ikl~sNmFmfraslDlkliF~D~rv~qltgYepqdlie--ktLY~~ih~~D~~~lr~~H~~ll~kGqvtTkYYR~l~k~  296 (598)
T KOG3559         220 -IKLHSNMFMFRASLDLKLIFLDSRVHQLTGYEPQDLIE--KTLYHHIHGCDSFHLRCAHHLLLVKGQVTTKYYRFLLKQ  296 (598)
T ss_pred             -EEECCCEEEEEEECCEEEEEHHHHHHHHHCCCCHHHHH--HHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCC
T ss_conf             -88546507998621157885044678860899422566--778887511128899888899986143140788987707


Q ss_pred             CCEEEEEEEEEEEEECCC-EEEEE-EE--EECCCHHHHHHH
Q ss_conf             988998899999983796-06999-99--844617999999
Q gi|254780903|r  339 GADIWIQVRAQMMRTISG-GMNII-GI--AMDLTEKYHLEK  375 (766)
Q Consensus       339 G~~~Wi~~r~~~i~d~~G-~~~~i-Gi--~~DITErK~ae~  375 (766)
                      |.|+|+...+..+.+.-. +++++ .+  +.-++|-|.+.-
T Consensus       297 ggwvwvqsyat~vHnSrSSR~~fivSvnyVls~~EyK~LqL  337 (598)
T KOG3559         297 GGWVWVQSYATFVHNSRSSRPHFIVSVNYVLSELEYKELQL  337 (598)
T ss_pred             CCEEEEEEEEEEEECCCCCCCEEEEEEEEEEEHHHHHHHEE
T ss_conf             85399997446884254577405776656520010334240


No 114
>cd00130 PAS PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in signal transduction.
Probab=97.52  E-value=0.00085  Score=45.33  Aligned_cols=84  Identities=12%  Similarity=0.231  Sum_probs=55.4

Q ss_pred             HHHHEEEECCCCEEEEECHHHHHHHCCCHHHHCCCCCHHHHCCCHHHHHHHHHHHCC--CCCCCEEEEEEECCCE--EEE
Q ss_conf             445515883499699701789888399978942897178816520137899985211--2456405899916962--874
Q gi|254780903|r  391 TSEALVLWDKNDRLVMCNANYQKAYGLPDHVLVPGNARSIIQDAQTRPIIEYRTSDP--ERSQDMSKEIKLADSR--WLQ  466 (766)
Q Consensus       391 ~~~~i~~~D~~g~i~~~N~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~e~~~~dg~--~~~  466 (766)
                      ++++++++|.+|+++++|+++++++|++.+++.+...++.+++..............  .......++....+|.  |+.
T Consensus         1 ~~~~i~~~d~~g~i~~~N~~~~~~~g~~~~e~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~   80 (103)
T cd00130           1 LPDGVIVLDLDGRILYANPAAEQLLGYSPEELIGKSLLDLIHPEDREELRERLENLLSGGEPVTLEVRLRRKDGSVIWVL   80 (103)
T ss_pred             CCEEEEEECCCCCEEEECHHHHHHHCCCHHHHCCCCHHHEECCHHHHHHHHHHHHHHHCCCCCEEEEEEECCCCCEEEEE
T ss_conf             96289999798989999889999879887891699654245521169999999999974998524899999999999999


Q ss_pred             ECCEECCC
Q ss_conf             22324569
Q gi|254780903|r  467 INEWCTHD  474 (766)
Q Consensus       467 i~~~~~~d  474 (766)
                      ....+..+
T Consensus        81 ~~~~~~~~   88 (103)
T cd00130          81 VSLTPIRD   88 (103)
T ss_pred             EEEEEEEC
T ss_conf             99999999


No 115
>KOG3560 consensus
Probab=97.52  E-value=0.00024  Score=49.27  Aligned_cols=222  Identities=16%  Similarity=0.140  Sum_probs=122.3

Q ss_pred             CCEEEEECCCCCEEEECCCHHHHCCCCHHHHCCCCHHHHCCCCCCCHHHHHCC----CCHHEE-EEEECCCCCCEEEEEE
Q ss_conf             97899996998089971420555199788960761043205443320232115----310000-1233157782599997
Q gi|254780903|r  128 ESFILLAQPNELVFASSTKNSHYIGKKIGEIIPELSRSRSRSKTVQMSEASLD----QQPYHV-LSVNLPHNSGSILIIN  202 (766)
Q Consensus       128 ~~~i~i~d~~g~i~~~n~~~~~~~G~~~~~~~~~~~~~~~~~~~~~~~~~~l~----~~~~~~-~~~~~~~~~~~~~~~~  202 (766)
                      ..+++|+..+|.|.+++..-+.++|....|++.++.++....+.-....-.|.    -..... ....+...+......+
T Consensus       121 nGF~lVvt~eg~ifyAS~tIedYLGFhQSDV~HQsVYdlIHseDR~dfqrQLhwa~~ppq~~~s~q~~~e~~~~~~~~~~  200 (712)
T KOG3560         121 NGFALVVTAEGEIFYASATIEDYLGFHQSDVMHQSVYDLIHSEDRQDFQRQLHWAMDPPQVVFSQQPPLETGDDAILRAQ  200 (712)
T ss_pred             CCEEEEEECCCEEEEEHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHCCCCCCCCCCCCCCEEEE
T ss_conf             77599995383699740017765352300101045887742220999999876425874332057873113664100110


Q ss_pred             ECC----CCHHH--HHHHHHHHHHHHHHHHHHHHH--------------------------HHHHHH-----HHHHHHHH
Q ss_conf             423----21012--345565545687887899999--------------------------999888-----89999999
Q gi|254780903|r  203 SRV----PLLRL--WREEVTLEVVFFSIISALLLF--------------------------ILFSYY-----RQAKKNKE  245 (766)
Q Consensus       203 ~~~----~~~~~--~r~~~~~~~~~~~~~~~~~~~--------------------------~~~a~~-----~dit~~r~  245 (766)
                      ...    +..+.  -|....+..-+++.+++.+..                          ..|++.     -.+.+.+ 
T Consensus       201 ~~~d~~ppens~yleRcficR~RCLLDnTsGFLamdfqGklk~LhGqkkk~~~g~~lpP~LaLf~iatP~~pPS~lEi~-  279 (712)
T KOG3560         201 EWGDGTPPENSAYLERCFICRFRCLLDNTSGFLAMDFQGKLKFLHGQKKKAPSGAMLPPRLALFCIATPFLPPSALEIK-  279 (712)
T ss_pred             CCCCCCCCCCCHHHHHHHEEEEEEEECCCCCEEEEECCCCEEEECCCCCCCCCCCCCCCCEEEEEEECCCCCCHHHHHH-
T ss_conf             1676678651057764220267776538755056621232100027744488876478850478985377893165410-


Q ss_pred             HHHHHHHHHHHHHHHHHCCCCCEEEEECCCCEEEECHHHHHHCCCCHHHCCCCHHHHHHHHCCCCHHHHHHHHHHHHCCC
Q ss_conf             99999999999999972259745989768978999788997729994330589889997608120589999999972489
Q gi|254780903|r  246 NDTILLEANICVETALSRGRCGLWNFNFDNKKFHLSRSMYEIMGIPYENKTLSFRAIARLIHYDNKKICEIARSVTGKHV  325 (766)
Q Consensus       246 ae~~l~ese~rl~~al~~a~~GiWd~D~~~~~i~ws~~~~~llG~~~~e~~~s~~~~~~~vHPdDr~~~~~a~~~~~~~~  325 (766)
                      ...++..+.-++                ++-.+-.+...+.++||...|...  ..-.++||-||...+..+-......+
T Consensus       280 ~k~~i~rtKhkl----------------Dfa~vs~Dak~k~~lgy~eaEL~~--m~gY~lvH~~D~~y~Aeah~e~iktg  341 (712)
T KOG3560         280 MKSAILRTKHKL----------------DFALVSMDAKVKATLGYCEAELHG--MPGYNLVHVEDKVYMAEAHSEGIKTG  341 (712)
T ss_pred             HHHHHHHCCCCC----------------CCCEECCCHHHHHHHCCCHHHCCC--CCCCCEEEHHHHHHHHHHHHHHHHCC
T ss_conf             366665200225----------------654003213355543201544057--87633123223455358899986358


Q ss_pred             CEEEEEEEEECCCCCEEEEEEEEEEEEECCCEEE-EEEEEECCCH
Q ss_conf             8489999988698988998899999983796069-9999844617
Q gi|254780903|r  326 KQLDQIFHMRHASGADIWIQVRAQMMRTISGGMN-IIGIAMDLTE  369 (766)
Q Consensus       326 ~~~~~e~Ri~~~DG~~~Wi~~r~~~i~d~~G~~~-~iGi~~DITE  369 (766)
                      ..=-+.||...++|.|-|+..++..++ .+|+|- ++-+.+-.++
T Consensus       342 eSGmlvyR~qtk~grw~wvqssarlly-kngkPD~vi~thr~l~D  385 (712)
T KOG3560         342 ESGMLVYREQTKAGRWAWVQSSARLLY-KNGKPDLVIDTHRGLGD  385 (712)
T ss_pred             CCCEEEEEEEECCCCEEEEECCCEEEE-ECCCCCEEEECCCCCCC
T ss_conf             764489998604783798534662434-16888888845877651


No 116
>PRK09959 hybrid sensory histidine kinase in two-component regulatory system with EvgA; Provisional
Probab=97.48  E-value=0.00075  Score=45.72  Aligned_cols=147  Identities=11%  Similarity=0.041  Sum_probs=88.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEEEEECCCCEEEECHHHHHHCCCCHHHCCC-CHHHHHHHHCCCCHHH
Q ss_conf             888899999999999999999999997225974598976897899978899772999433058-9889997608120589
Q gi|254780903|r  235 SYYRQAKKNKENDTILLEANICVETALSRGRCGLWNFNFDNKKFHLSRSMYEIMGIPYENKTL-SFRAIARLIHYDNKKI  313 (766)
Q Consensus       235 a~~~dit~~r~ae~~l~ese~rl~~al~~a~~GiWd~D~~~~~i~ws~~~~~llG~~~~e~~~-s~~~~~~~vHPdDr~~  313 (766)
                      -..+++.+|++++.+|.+...-.+.++++.|..++-.|.+++.+.+|.++...||-+...... .... ....+++....
T Consensus       556 ~L~r~ir~R~~ae~~L~~ql~f~~~L~d~iP~pi~v~d~~g~~i~~N~a~~~~~~~d~~~~~~~~~~~-~~~~~~~~~~~  634 (1197)
T PRK09959        556 YLLRSVRRRKVIQGDLENQISFRKALSDSLPNPTYVVNWQGNVISHNSAFEHYFTADYYKNAMLPLEN-SESPFKDVFSN  634 (1197)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEEEECCCCCCHHHHHHHHHHHCCCHHHHCCCCCCC-CCCHHHHHHHH
T ss_conf             99999999999999999889999999836998769982556122411888987523144421356532-22215677777


Q ss_pred             HHHHHHHHHCCCCEEEEEEEEECCCC-CEEEEEEEEEEEEECCCEE-EEEEEEECCCHHHHHHHHHHHHHHHH
Q ss_conf             99999997248984899999886989-8899889999998379606-99999844617999999999999999
Q gi|254780903|r  314 CEIARSVTGKHVKQLDQIFHMRHASG-ADIWIQVRAQMMRTISGGM-NIIGIAMDLTEKYHLEKRYAEADQRL  384 (766)
Q Consensus       314 ~~~a~~~~~~~~~~~~~e~Ri~~~DG-~~~Wi~~r~~~i~d~~G~~-~~iGi~~DITErK~ae~~l~ese~rl  384 (766)
                      ..............+...|.+  .+| .-+++.-...+...+.+.. .++|..+||||||++|++|+++.+.=
T Consensus       635 ~~~~~~~~~~~~~~~~~~~~~--~~g~~~~~i~~w~~~~~~~~~~~~~~i~gw~DITerk~~e~~L~~Ak~~A  705 (1197)
T PRK09959        635 THEVTAETKENRTIYTQVFEI--DNGIEKRCINHWHTLCNLPASDHAVYICGWQDITETRDLIHALEVERNKA  705 (1197)
T ss_pred             HHHHHHHHHHCCCCCCEEEEC--CCCCCCEEEEEEEEEECCCCCCCEEEECCEEEHHHHHHHHHHHHHHHHHH
T ss_conf             789987531012100014530--57754236775310003764444010115464128999999999999999


No 117
>COG5385 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=97.46  E-value=0.011  Score=37.33  Aligned_cols=193  Identities=13%  Similarity=0.152  Sum_probs=127.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCEEEECHHHH
Q ss_conf             99987675222478999999998603468899389999999999999999999777677888741983012033169999
Q gi|254780903|r  546 FLAKMSHELRTPLNAILGFSEVIKKEIFGELGSVKYYEYAQDIHYSGQHLLNMINNILEMSKIETEKISIDKQNADLIPI  625 (766)
Q Consensus       546 fla~isHelrtPL~aI~g~~ell~~~~~~~~~~e~~~~~l~~I~~~~~~l~~lI~diLd~srieag~~~~~~~~~dl~~~  625 (766)
                      +.+-+.||+-.|..+|..-+|||.++..       ..+.++.|..|+..+.    +.|.|+|+--|-.-..-..+|-.+.
T Consensus        18 LcsRvCHDiISPvgAInnGLeLLdeg~a-------ddDAm~LIrsSArnas----~rLqFaR~AFGAsgSag~~iDtgea   86 (214)
T COG5385          18 LCSRVCHDIISPVGAINNGLELLDEGGA-------DDDAMDLIRSSARNAS----VRLQFARLAFGASGSAGASIDTGEA   86 (214)
T ss_pred             HHHHHHHHCCCCHHHHHCHHHHHCCCCC-------CHHHHHHHHHHHHHHH----HHHHHHHHHHCCCCCCCCCCCCHHH
T ss_conf             9998875404817776032566426896-------4789999999765178----8877889872555543335660669


Q ss_pred             HHHHHHHHHHHHHHCCCEEEEEECCCCEEEECHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEEECCEEEEEEEECCC--C
Q ss_conf             99999999999984795899980899789986899999999988656534689888999999979989999997889--7
Q gi|254780903|r  626 INEGIRLIGSSAQSKNIKIEKKIPSELFFNADKRIIKKILFPILSNSIKFTNNNGKMMIRTSKIGQCVIITIADTGI--G  703 (766)
Q Consensus       626 i~~~~~~~~~~~~~k~i~l~~~~~~~l~v~~D~~~l~QVl~NLi~NAik~t~~~g~I~i~~~~~~~~v~i~V~D~G~--G  703 (766)
                      =.-+...+.   .+| -++.++.+..+   ...++. ..++||+-=|--..|.||.+.++.+..+..-+|+|.-.|.  -
T Consensus        87 ek~A~~~~a---~ek-pe~~W~g~r~~---~~Kn~v-kllLNl~lia~~aiPrGG~~~vtle~~e~d~rfsi~akG~m~R  158 (214)
T COG5385          87 EKAAQDFFA---NEK-PELTWNGPRAI---LPKNRV-KLLLNLFLIAYGAIPRGGSLVVTLENPETDARFSIIAKGRMMR  158 (214)
T ss_pred             HHHHHHHHH---CCC-CCCCCCCCHHH---CCCCHH-HHHHHHHHHHCCCCCCCCEEEEEEECCCCCCEEEEEECCCCCC
T ss_conf             999999986---238-71235587422---475058-9999999997055788982689953677674389983275344


Q ss_pred             CCHHHHHHH-CCCEEECCCCCCCCCCCCCHHHHHHHHHHHHCCCEEEEEEECCCCEEEEEECC
Q ss_conf             897785430-46505314675567788761689999999962986999979899529999735
Q gi|254780903|r  704 IPKSALEKI-GQPFEPLHNQYDQSIGGFGLGLAISDALTNLHGGRLKIISQEGKGTIVTICMP  765 (766)
Q Consensus       704 I~~e~~~~i-F~pF~q~~~~~t~~~~GtGLGLaI~k~iVe~hgG~I~v~S~~g~Gttf~i~LP  765 (766)
                      .||+.++-+ .+|-       ....++.-.-=+-.--+++.-|++|.|++... -..|+-..|
T Consensus       159 vppk~lel~~G~~~-------eE~vdahsVQpyYt~lLa~eAgm~I~v~~~~e-~iv~~A~v~  213 (214)
T COG5385         159 VPPKFLELHSGEPP-------EEAVDAHSVQPYYTLLLAEEAGMTISVHATAE-RIVFTAWVV  213 (214)
T ss_pred             CCHHHHHHHCCCCC-------CCCCCCCCCCHHHHHHHHHHCCCEEEEEECCC-EEEEEEECC
T ss_conf             79899865059984-------22478753039999999997098689996364-379997514


No 118
>COG0323 MutL DNA mismatch repair enzyme (predicted ATPase) [DNA replication, recombination, and repair]
Probab=97.33  E-value=0.00042  Score=47.56  Aligned_cols=51  Identities=10%  Similarity=0.018  Sum_probs=25.1

Q ss_pred             CCCEEEECHHHHHHHHHHHHHHHHHHCCCEEEEEECCCCEEEECHHHHHHH
Q ss_conf             012033169999999999999999847958999808997899868999999
Q gi|254780903|r  614 SIDKQNADLIPIINEGIRLIGSSAQSKNIKIEKKIPSELFFNADKRIIKKI  664 (766)
Q Consensus       614 ~~~~~~~dl~~~i~~~~~~~~~~~~~k~i~l~~~~~~~l~v~~D~~~l~QV  664 (766)
                      -+-+..++|.+--...+..-...+...++.+....+..+.|..=|..++|.
T Consensus       501 LliP~~~~l~~~e~~~~~~~~~~l~~~G~~i~~~g~~~~~v~~vP~~l~~~  551 (638)
T COG0323         501 LLIPIRLELSPEEADVLEEHKEELEKLGFEIESFGENSVAVRSVPAMLGKA  551 (638)
T ss_pred             CCCCEEEECCHHHHHHHHHHHHHHHHCCEEEEECCCCEEEEEECCHHHCCC
T ss_conf             444825414989999999989999867889997389469998168243542


No 119
>PTZ00272 heat shock protein 83 kDa (Hsp83); Provisional
Probab=97.28  E-value=0.0018  Score=42.91  Aligned_cols=27  Identities=4%  Similarity=0.199  Sum_probs=17.2

Q ss_pred             EEEEECCCCCEEEECCCHHHHCCCCHHHHC
Q ss_conf             899996998089971420555199788960
Q gi|254780903|r  130 FILLAQPNELVFASSTKNSHYIGKKIGEII  159 (766)
Q Consensus       130 ~i~i~d~~g~i~~~n~~~~~~~G~~~~~~~  159 (766)
                      +-+..|.+.+.+.....+.   |.+-++++
T Consensus        63 I~I~~D~~~~tltI~D~GI---GMt~~el~   89 (701)
T PTZ00272         63 IRVVPDKENKTLTVEDNGI---GMTKADLV   89 (701)
T ss_pred             EEEEECCCCCEEEEEECCC---CCCHHHHH
T ss_conf             9999758789799994388---88999999


No 120
>PRK11086 sensory histidine kinase DcuS; Provisional
Probab=97.03  E-value=0.03  Score=34.16  Aligned_cols=291  Identities=13%  Similarity=0.060  Sum_probs=135.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCC-CEEEEECCCCCEEEE
Q ss_conf             9999999967688899989999999999998501001122355489999999998853101789-789999699808997
Q gi|254780903|r   65 TSSIIKVTTRYAQQEKMTNQTSLMLTEAIEIIFQNNNIKFDLASQKKAESMLGQLLAKTRFLSE-SFILLAQPNELVFAS  143 (766)
Q Consensus        65 ~~~~~~i~~~~~~~~~~~~~~~~lla~~~~~~~~~~~~~~d~~~~~~ae~~L~~~~~~~~~~~~-~~i~i~d~~g~i~~~  143 (766)
                      +..++.......+.+......+...|..++..   ..+...... +.....++.+....+..++ ++|++.|.+|. .++
T Consensus        34 ~~~~~~~~~~~~~~~~~~~~~a~~~A~~vA~~---p~v~~~~~~-~~~~~~lq~~~~~ir~~~~~~fIvv~d~~gi-r~s  108 (541)
T PRK11086         34 VVHLLYFSQISDMTRDGLAEKALAVARTVADS---PIVIQGLQK-KPQESGIQTYAEAVRKRNDLLFIVVTDMQGI-RYS  108 (541)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC---HHHHHHHHC-CCCCHHHHHHHHHHHHHCCCEEEEEECCCCE-EEE
T ss_conf             99999999999999999999999999999769---689998618-9960889999999999729829999869971-853


Q ss_pred             CCCHHHHCCCCHHHHCCCCHHHHCCCCCCCHHHHHCCCCHHEEEEEECCCCC----CEEEEEEECCCCHHHHHHHHHHHH
Q ss_conf             1420555199788960761043205443320232115310000123315778----259999742321012345565545
Q gi|254780903|r  144 STKNSHYIGKKIGEIIPELSRSRSRSKTVQMSEASLDQQPYHVLSVNLPHNS----GSILIINSRVPLLRLWREEVTLEV  219 (766)
Q Consensus       144 n~~~~~~~G~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~----~~~~~~~~~~~~~~~~r~~~~~~~  219 (766)
                      .|. +...|.+...  +...+......+.......+  .++.-...++.+..    |.+.+........... .....  
T Consensus       109 Hp~-~~~iG~~~~g--~d~~~aL~g~~~~s~~~Gtl--G~s~r~~~Pv~~~~g~~iG~V~VG~~~~~i~~~~-~~~~~--  180 (541)
T PRK11086        109 HPN-PQKIGKPFIG--GDELPALQGKENVSINRGTL--GQSLRVFTPVYDENGKQIGVVAVGISLSEVTQQI-NESRW--  180 (541)
T ss_pred             CCC-HHHCCCCCCC--CCHHHHHCCCCEEEEEECCC--CCEEEEEECCCCCCCCEEEEEEEEECHHHHHHHH-HHHHH--
T ss_conf             899-7886997768--87678857763599961455--6457998551838997899999981188899999-99999--


Q ss_pred             HHHHHHHHHHHH-HHHHHH--HHHHHH---HHHHHHHHHHHHHHHHHHHCCCCCEEEEECCCCEEEECHHHHHHCCCCHH
Q ss_conf             687887899999-999888--899999---99999999999999999722597459897689789997889977299943
Q gi|254780903|r  220 VFFSIISALLLF-ILFSYY--RQAKKN---KENDTILLEANICVETALSRGRCGLWNFNFDNKKFHLSRSMYEIMGIPYE  293 (766)
Q Consensus       220 ~~~~~~~~~~~~-~~~a~~--~dit~~---r~ae~~l~ese~rl~~al~~a~~GiWd~D~~~~~i~ws~~~~~llG~~~~  293 (766)
                      .++......+++ ++.+++  +-+++.   -+.++..+-.++| +.++++.+.|+.-.|.++..+.+|+++.+||+..+.
T Consensus       181 ~i~~~~~~~lllg~~~a~~lar~ikr~l~glEP~eIa~l~~er-~aiL~s~~eGVIavD~~g~I~l~N~~A~~ll~~~~~  259 (541)
T PRK11086        181 SIYWSILFGALVGLIGAVILVRVLKKILFGLEPYEISTLFEQR-QAMLQSIKEGVIAVDDRGEVTLINDEAQRLFYKKGQ  259 (541)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHH-HHHHHHHHCEEEEECCCCEEEEECHHHHHHHCCCCC
T ss_conf             9999999999999999999999999986379999999999999-999853001699975898799984999987433588


Q ss_pred             H-CCCCHHHHHHHHCCCCHHHHHHHHHHHHCCCCEEEEEEEEECCCCCEEEEEEEEEEEEECCCEEEEEEEEECCCHHHH
Q ss_conf             3-058988999760812058999999997248984899999886989889988999999837960699999844617999
Q gi|254780903|r  294 N-KTLSFRAIARLIHYDNKKICEIARSVTGKHVKQLDQIFHMRHASGADIWIQVRAQMMRTISGGMNIIGIAMDLTEKYH  372 (766)
Q Consensus       294 e-~~~s~~~~~~~vHPdDr~~~~~a~~~~~~~~~~~~~e~Ri~~~DG~~~Wi~~r~~~i~d~~G~~~~iGi~~DITErK~  372 (766)
                      + ...+ ....+ +.|++.     ..+.........+.+.++   +|..  +.....|+...+...+.+.+.+|+||.++
T Consensus       260 ~~~~~g-~~~~~-~~~~~~-----l~~vl~~~~~~~d~e~~~---~~~~--l~~~~~pi~~~g~~~G~V~~~rD~TE~~~  327 (541)
T PRK11086        260 EDDPLS-TDVHS-WSPVSR-----LKEVLRTGTPRRDEEINI---NGRL--LLTNTVPVRVNGEIIGAISTFRDKTEVRQ  327 (541)
T ss_pred             CCCCCC-CCHHH-HCCCHH-----HHHHHHCCCCCCEEEEEE---CCEE--EEEEEEEEEECCEEEEEEEEEECHHHHHH
T ss_conf             743125-51777-275455-----999984488531079998---9989--99997776548906899999844278999


Q ss_pred             HHHHHHHHH
Q ss_conf             999999999
Q gi|254780903|r  373 LEKRYAEAD  381 (766)
Q Consensus       373 ae~~l~ese  381 (766)
                      ++++|....
T Consensus       328 L~~~L~~v~  336 (541)
T PRK11086        328 LAQRLDGVV  336 (541)
T ss_pred             HHHHHHHHH
T ss_conf             999999999


No 121
>COG0326 HtpG Molecular chaperone, HSP90 family [Posttranslational modification, protein turnover, chaperones]
Probab=96.98  E-value=0.0015  Score=43.51  Aligned_cols=95  Identities=16%  Similarity=0.102  Sum_probs=45.7

Q ss_pred             EEECHHHHHHHHHHHHHHHHHHCCCEEEEEECCCCEEE-----ECHHHHHHHHHHHHHHHHHCC-CCCCEEEEEEEEECC
Q ss_conf             33169999999999999999847958999808997899-----868999999999886565346-898889999999799
Q gi|254780903|r  618 QNADLIPIINEGIRLIGSSAQSKNIKIEKKIPSELFFN-----ADKRIIKKILFPILSNSIKFT-NNNGKMMIRTSKIGQ  691 (766)
Q Consensus       618 ~~~dl~~~i~~~~~~~~~~~~~k~i~l~~~~~~~l~v~-----~D~~~l~QVl~NLi~NAik~t-~~~g~I~i~~~~~~~  691 (766)
                      +.+-+.+-|++..-..-+..+.|.+.-....+..+.-.     .+....++.+--|+.=.-+.. .....|+++.+..+.
T Consensus       452 eVL~l~d~iDe~~l~~~~e~egk~~~~i~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~~~k~~L~~~vk~Vr~s~rl~ds  531 (623)
T COG0326         452 EVLLLTDRIDEFMLTMLPEFEGKPFKSITKGDLDLELLEEEDEADSEEEKKEFKPLLERVKEILGDKVKDVRLSHRLTDS  531 (623)
T ss_pred             EEEECCCCCHHHHHHHHHHCCCCCCEEECCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEEEEECCCCCC
T ss_conf             79954765217876410320576334512354433335011220057777778999999999846732115730346789


Q ss_pred             EEEEEEEECCCCCCHHHHHHHCCC
Q ss_conf             899999978897897785430465
Q gi|254780903|r  692 CVIITIADTGIGIPKSALEKIGQP  715 (766)
Q Consensus       692 ~v~i~V~D~G~GI~~e~~~~iF~p  715 (766)
                      -.++.+...++.   .+++|++..
T Consensus       532 pa~l~~~~~~~~---~~m~r~l~~  552 (623)
T COG0326         532 PACLTTDGADLS---TQMERLLKA  552 (623)
T ss_pred             CCEEECCCCCHH---HHHHHHHHH
T ss_conf             634554766635---999999985


No 122
>TIGR01924 rsbW_low_gc anti-sigma B factor; InterPro: IPR010193   This entry describes the anti-sigma B factor also known as serine-protein kinase RsbW. Sigma B controls the general stress regulon in B subtilis and is activated by cell stresses such as stationary phase and heat shock. RsbW binds to sigma B and prevents formation of the transcription complex at the promoter . RsbV (anti-anti-sigma factor) binds to RsbW to inhibit association with sigma B, however RsbW can phosphorylate RsbV, causing disassociation of the RsbV/RsbW complex . Low ATP level or environmental stress causes the dephosphorylation of RsbV .; GO: 0004674 protein serine/threonine kinase activity, 0005524 ATP binding, 0016989 sigma factor antagonist activity, 0006468 protein amino acid phosphorylation, 0045892 negative regulation of transcription DNA-dependent.
Probab=96.96  E-value=0.002  Score=42.68  Aligned_cols=91  Identities=18%  Similarity=0.240  Sum_probs=67.0

Q ss_pred             HHHHHHHHHHHHHHHCCC---CC-CEEEEEEEEECCEEEEEEEECCCCCCHHHHHHHCCCEEECCCCCCCCCCCCCHHHH
Q ss_conf             999999998865653468---98-88999999979989999997889789778543046505314675567788761689
Q gi|254780903|r  660 IIKKILFPILSNSIKFTN---NN-GKMMIRTSKIGQCVIITIADTGIGIPKSALEKIGQPFEPLHNQYDQSIGGFGLGLA  735 (766)
Q Consensus       660 ~l~QVl~NLi~NAik~t~---~~-g~I~i~~~~~~~~v~i~V~D~G~GI~~e~~~~iF~pF~q~~~~~t~~~~GtGLGLa  735 (766)
                      =||=.+.-=|.|||||.-   ++ |.|+|+...-+|.+.|.|+|+|-=.+-+....=-.||-.-+.--.=+.|  ||||.
T Consensus        43 D~KIAVSEA~TN~V~HAYke~~nvG~~~i~F~iyEDklev~vsD~G~SFD~d~~k~~lGPyd~~~~i~~L~eG--GLGLF  120 (161)
T TIGR01924        43 DLKIAVSEACTNAVKHAYKEEENVGEISIEFEIYEDKLEVIVSDEGDSFDLDTKKQELGPYDKSEDIDQLREG--GLGLF  120 (161)
T ss_pred             HHHHHHHHHHCCCEEEEECCCCCEEEEEEEEEEEEEEEEEEEECCCCCCCHHHHHHHCCCCCCCCCHHHHHCC--CCHHH
T ss_conf             0677665553033112230898367899888788757899982078641110025325897957875432017--71366


Q ss_pred             HHHHHHHHCCCEEEEEEECCC
Q ss_conf             999999962986999979899
Q gi|254780903|r  736 ISDALTNLHGGRLKIISQEGK  756 (766)
Q Consensus       736 I~k~iVe~hgG~I~v~S~~g~  756 (766)
                      +.    |-.==.+++....|.
T Consensus       121 Li----etLMD~V~~~~~sGV  137 (161)
T TIGR01924       121 LI----ETLMDEVKVYEDSGV  137 (161)
T ss_pred             HH----HCCCCEEEEEECCCE
T ss_conf             45----103761699832860


No 123
>PRK05218 heat shock protein 90; Provisional
Probab=96.93  E-value=0.0014  Score=43.72  Aligned_cols=28  Identities=14%  Similarity=0.133  Sum_probs=16.5

Q ss_pred             CEEEEECCCCCEEEECCCHHHHCCCCHHHHC
Q ss_conf             7899996998089971420555199788960
Q gi|254780903|r  129 SFILLAQPNELVFASSTKNSHYIGKKIGEII  159 (766)
Q Consensus       129 ~~i~i~d~~g~i~~~n~~~~~~~G~~~~~~~  159 (766)
                      .+-+..|.+.+.+.....+.   |.+.+|+.
T Consensus        62 ~I~I~~d~~~~tl~I~D~GI---GMt~~El~   89 (612)
T PRK05218         62 RIRISFDKEARTLTISDNGI---GMTREEVI   89 (612)
T ss_pred             EEEEEECCCCCEEEEEECCC---CCCHHHHH
T ss_conf             69999759899899995388---88999999


No 124
>KOG3559 consensus
Probab=96.85  E-value=0.013  Score=36.81  Aligned_cols=180  Identities=12%  Similarity=0.163  Sum_probs=103.7

Q ss_pred             CC-EEEEECCCCEEEECHHHHHHCCCCHHHCCCCHHHHHHHHCCCCHHHHHHHHHHHHCCCCEEEEE-------------
Q ss_conf             74-5989768978999788997729994330589889997608120589999999972489848999-------------
Q gi|254780903|r  266 CG-LWNFNFDNKKFHLSRSMYEIMGIPYENKTLSFRAIARLIHYDNKKICEIARSVTGKHVKQLDQI-------------  331 (766)
Q Consensus       266 ~G-iWd~D~~~~~i~ws~~~~~llG~~~~e~~~s~~~~~~~vHPdDr~~~~~a~~~~~~~~~~~~~e-------------  331 (766)
                      +| ++..+.+++.+|.|+..---+|++.-|  ++...+.+.|||.|.+.+......-. ....+++|             
T Consensus        89 DGF~fvva~dGkimYISETaSvhLGLSQVE--lTGNsi~eYIH~~D~demna~L~~h~-H~qeyeIErsfflrmkCvlak  165 (598)
T KOG3559          89 DGFIFVVAPDGKIMYISETASVHLGLSQVE--LTGNSIYEYIHPQDHDEMNAVLTAHQ-HLQEYEIERSFFLRMKCVLAK  165 (598)
T ss_pred             CCEEEEEECCCCEEEEECCEEEEECCEEEE--EECCHHHHHHCCCCHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHH
T ss_conf             545999927998899850113452300046--50623766406012578988876432-444300334311234331000


Q ss_pred             ---------EEEECCCCCEEEEEEEEEEEE-ECCC----EEEEEEEEE-----CCCHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             ---------998869898899889999998-3796----069999984-----461799999999999999999998544
Q gi|254780903|r  332 ---------FHMRHASGADIWIQVRAQMMR-TISG----GMNIIGIAM-----DLTEKYHLEKRYAEADQRLSKAIECTS  392 (766)
Q Consensus       332 ---------~Ri~~~DG~~~Wi~~r~~~i~-d~~G----~~~~iGi~~-----DITErK~ae~~l~ese~rlr~~ie~~~  392 (766)
                               |..+|..|-+   ..+-..+. +..+    +++++.+..     -|||-|--                 ..
T Consensus       166 rnaglt~sg~kvihcSgyl---Kir~y~~~m~p~dscyqn~glvAvG~slP~saiteikl~-----------------sN  225 (598)
T KOG3559         166 RNAGLTCSGYKVIHCSGYL---KIRQYELDMSPNDSCYQNVGLVAVGHSLPPSAITEIKLH-----------------SN  225 (598)
T ss_pred             HCCCCCCCCCCEEEECCCC---EEEEEEECCCCCCCCCCCCEEEEECCCCCCCCCEEEEEC-----------------CC
T ss_conf             0246533686348605760---689965325877451000106995577895411478854-----------------65


Q ss_pred             HHEEEECCCCEEEEECHHHHHHHCCCHHHHCCCCCHHHHCCCHHHHHHHHHHHCCCCC--CCEEEEEEECCCEEEEEC
Q ss_conf             5515883499699701789888399978942897178816520137899985211245--640589991696287422
Q gi|254780903|r  393 EALVLWDKNDRLVMCNANYQKAYGLPDHVLVPGNARSIIQDAQTRPIIEYRTSDPERS--QDMSKEIKLADSRWLQIN  468 (766)
Q Consensus       393 ~~i~~~D~~g~i~~~N~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~e~~~~dg~~~~i~  468 (766)
                      ..++....|-.+++...+..+++||++.+++.++.|..++..+..........-..++  ...-|+..+..|-|.++-
T Consensus       226 mFmfraslDlkliF~D~rv~qltgYepqdliektLY~~ih~~D~~~lr~~H~~ll~kGqvtTkYYR~l~k~ggwvwvq  303 (598)
T KOG3559         226 MFMFRASLDLKLIFLDSRVHQLTGYEPQDLIEKTLYHHIHGCDSFHLRCAHHLLLVKGQVTTKYYRFLLKQGGWVWVQ  303 (598)
T ss_pred             EEEEEEECCEEEEEHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCEEEEE
T ss_conf             079986211578850446788608994225667788875111288998888999861431407889877078539999


No 125
>PTZ00130 heat shock protein 90; Provisional
Probab=96.30  E-value=0.0073  Score=38.61  Aligned_cols=27  Identities=11%  Similarity=0.037  Sum_probs=16.1

Q ss_pred             CEEEEEEEEECCEEEEEEEECCCCCCH
Q ss_conf             889999999799899999978897897
Q gi|254780903|r  680 GKMMIRTSKIGQCVIITIADTGIGIPK  706 (766)
Q Consensus       680 g~I~i~~~~~~~~v~i~V~D~G~GI~~  706 (766)
                      ..|.|+-|..+.-+|+.-.+.|..-..
T Consensus       653 ~~V~vS~RL~dSP~~LVa~e~G~SanM  679 (824)
T PTZ00130        653 FKVEISRRLVDAPCAVVSTEWGLSGQM  679 (824)
T ss_pred             EEEEECCCCCCCCEEEECCCCCCCHHH
T ss_conf             089832775788828981787888889


No 126
>COG5000 NtrY Signal transduction histidine kinase involved in nitrogen fixation and metabolism regulation [Signal transduction mechanisms]
Probab=96.30  E-value=0.091  Score=30.68  Aligned_cols=129  Identities=16%  Similarity=0.132  Sum_probs=83.7

Q ss_pred             HHHHHHHHHHHHHHHHHHCCCCCEEEEECCCCEEEECHHHHHHCCCCHHHCCCCHHHHHHHHCCCCHHHHHHHHHHHHCC
Q ss_conf             99999999999999997225974598976897899978899772999433058988999760812058999999997248
Q gi|254780903|r  245 ENDTILLEANICVETALSRGRCGLWNFNFDNKKFHLSRSMYEIMGIPYENKTLSFRAIARLIHYDNKKICEIARSVTGKH  324 (766)
Q Consensus       245 ~ae~~l~ese~rl~~al~~a~~GiWd~D~~~~~i~ws~~~~~llG~~~~e~~~s~~~~~~~vHPdDr~~~~~a~~~~~~~  324 (766)
                      ++-+++++++.-++..++....|+.-.|-.+....+|++..+|||.+..+..+.  + ++-+-|+=-..+..+ ....  
T Consensus       360 ~ak~~~e~rr~f~E~VLsgvtaGVi~~d~~g~i~t~N~~ae~~l~~~~~~~~G~--~-lsa~ap~~~~vf~~~-~a~~--  433 (712)
T COG5000         360 RAKDALEQRRRFLEAVLSGLTAGVIGFDNRGCITTVNPSAEQILGKPFDQLLGQ--S-LSAIAPELEEVFAEA-GAAA--  433 (712)
T ss_pred             HHHHHHHHHHHHHHHHHHCCCEEEEEECCCCEEEEECCHHHHHHCCCHHHHHCH--H-HHHHHHHHHHHHHHH-HHHC--
T ss_conf             878889999988999981585038997478707762601788846870676440--2-664213789999976-5403--


Q ss_pred             CCEEEEEEEEECCCCCEEEEEEEEEEEEECCCEEEEEEEEECCCHHHHHHHHHHHHH
Q ss_conf             984899999886989889988999999837960699999844617999999999999
Q gi|254780903|r  325 VKQLDQIFHMRHASGADIWIQVRAQMMRTISGGMNIIGIAMDLTEKYHLEKRYAEAD  381 (766)
Q Consensus       325 ~~~~~~e~Ri~~~DG~~~Wi~~r~~~i~d~~G~~~~iGi~~DITErK~ae~~l~ese  381 (766)
                      ...+..+.-+-+ -|+.+-++.++.....+ +.-.++-++-|||+--.|+....-++
T Consensus       434 ~~~~~~ev~~~r-~g~~rtl~Vq~t~~~~d-~~~gyVvt~DDITdLV~AQRs~AW~d  488 (712)
T COG5000         434 RTDKRVEVKLAR-EGEERTLNVQATREPED-NGNGYVVTFDDITDLVIAQRSAAWGD  488 (712)
T ss_pred             CCCCCEEEECCC-CCCCEEEEEEEEECCCC-CCCCEEEEECCHHHHHHHHHHHHHHH
T ss_conf             877420100014-78741566675321444-68856999635089999999878999


No 127
>KOG0501 consensus
Probab=96.15  E-value=0.012  Score=37.16  Aligned_cols=103  Identities=10%  Similarity=0.113  Sum_probs=66.7

Q ss_pred             CCCCCEEEEECCCCEEEECHHHHHHCCCCHHHCCCCHHHHHHHHCCC--CHHHHHHHHHHHH-CCCCEEEEEEEEECCCC
Q ss_conf             25974598976897899978899772999433058988999760812--0589999999972-48984899999886989
Q gi|254780903|r  263 RGRCGLWNFNFDNKKFHLSRSMYEIMGIPYENKTLSFRAIARLIHYD--NKKICEIARSVTG-KHVKQLDQIFHMRHASG  339 (766)
Q Consensus       263 ~a~~GiWd~D~~~~~i~ws~~~~~llG~~~~e~~~s~~~~~~~vHPd--Dr~~~~~a~~~~~-~~~~~~~~e~Ri~~~DG  339 (766)
                      -++.-+-||-    .+|.|+.+|.+-||...+.... ...-+++|-|  |.+.++..++.+. .+...  .|.-+..++-
T Consensus        32 L~NAQiVD~P----iVY~NdgFcKlsGY~RAevMQK-s~tc~FMyGEltdk~ti~k~~~t~eN~~~~q--fEillyKKN~  104 (971)
T KOG0501          32 LANAQIVDWP----IVYCNDGFCKLSGYHRAEVMQK-SCTCSFMYGELTDKGTIEKVRQTLENYETNQ--FEILLYKKNR  104 (971)
T ss_pred             ECCCEEECCC----EEEECCCCHHCCCCCHHHHHCC-CCEEEEEECCCCCHHHHHHHHHHHHHHHHCC--EEEEEEECCC
T ss_conf             4355253140----5883476211247459988625-6423332013345116999999997543121--2367661589


Q ss_pred             CEEEEEEEEEEEEECCCEE-EEEEEEECCCHHHH
Q ss_conf             8899889999998379606-99999844617999
Q gi|254780903|r  340 ADIWIQVRAQMMRTISGGM-NIIGIAMDLTEKYH  372 (766)
Q Consensus       340 ~~~Wi~~r~~~i~d~~G~~-~~iGi~~DITErK~  372 (766)
                      ..+|+.....|++++...+ -+..+..|||.-|+
T Consensus       105 TPvW~~vqiAPIrNe~d~VVLfLctFkDIT~~KQ  138 (971)
T KOG0501         105 TPVWLLVQIAPIRNEKDKVVLFLCTFKDITALKQ  138 (971)
T ss_pred             CCEEEEEEEECCCCCCCEEEEEEEECCCCHHHCC
T ss_conf             8559999840235777518999951146443238


No 128
>pfam08447 PAS_3 PAS fold. The PAS fold corresponds to the structural domain that has previously been defined as PAS and PAC motifs. The PAS fold appears in archaea, eubacteria and eukarya.
Probab=96.11  E-value=0.02  Score=35.38  Aligned_cols=75  Identities=9%  Similarity=0.204  Sum_probs=46.0

Q ss_pred             EEEECHHHHHHHCCCHHHHCCCC--CHHHHCCCHHHHHHHHHH---HCCCCCCCEEEEEEECCC--EEEEECCEEC--CC
Q ss_conf             99701789888399978942897--178816520137899985---211245640589991696--2874223245--69
Q gi|254780903|r  404 LVMCNANYQKAYGLPDHVLVPGN--ARSIIQDAQTRPIIEYRT---SDPERSQDMSKEIKLADS--RWLQINEWCT--HD  474 (766)
Q Consensus       404 i~~~N~~~~~~~g~~~~~~~~~~--~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~e~~~~dg--~~~~i~~~~~--~d  474 (766)
                      ++++|+++.+++||+++++.+..  ..+.++|++.........   .........++++..+||  +|+.....+.  .+
T Consensus         1 v~y~s~~~~~i~G~~~~e~~~~~~~~~~~ihpdD~~~~~~~~~~~~~~~~~~~~~e~R~~~~dG~~~wi~~~~~~~~d~~   80 (90)
T pfam08447         1 IIYWSPRFEEILGYTPEELKSSYEDWLDLVHPEDRERVRRALQEFSLKKGEPYSGEYRIRRKDGEYRWVEARGRPIRDEN   80 (90)
T ss_pred             CEEECHHHHHHHCCCCHHCCCCHHHHHHHCCCHHHHHHHHHHHHHHHHCCCCEEEEEEEECCCCCEEEEEEEEEEEECCC
T ss_conf             99999899998499901107998899987190568899988788886058740468999815993999999999999999


Q ss_pred             CCEE
Q ss_conf             9789
Q gi|254780903|r  475 GGTI  478 (766)
Q Consensus       475 g~~v  478 (766)
                      |..+
T Consensus        81 G~~~   84 (90)
T pfam08447        81 GKPV   84 (90)
T ss_pred             CCEE
T ss_conf             9999


No 129
>COG5381 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=96.07  E-value=0.016  Score=36.18  Aligned_cols=90  Identities=22%  Similarity=0.355  Sum_probs=53.3

Q ss_pred             EECHHHHHH---HHHH-HHHHHHHCCCCCCEEEEEEEEECCEEEEEEEECCCCCCHHHHHHH------CCCE----EECC
Q ss_conf             986899999---9999-886565346898889999999799899999978897897785430------4650----5314
Q gi|254780903|r  655 NADKRIIKK---ILFP-ILSNSIKFTNNNGKMMIRTSKIGQCVIITIADTGIGIPKSALEKI------GQPF----EPLH  720 (766)
Q Consensus       655 ~~D~~~l~Q---Vl~N-Li~NAik~t~~~g~I~i~~~~~~~~v~i~V~D~G~GI~~e~~~~i------F~pF----~q~~  720 (766)
                      .+|...++.   -+.| ||.||+||.. +|.|.|.+........+.|+.--.+=......++      .+|-    +|.+
T Consensus        54 r~dy~evrhsvgYl~NELiENAVKfra-~geIvieasl~s~~f~~kvsN~vd~~t~~~f~~ll~~it~gDP~dLlieRiE  132 (184)
T COG5381          54 RADYDEVRHSVGYLANELIENAVKFRA-TGEIVIEASLYSHKFIFKVSNIVDLPTTIDFENLLKVITEGDPLDLLIERIE  132 (184)
T ss_pred             CCCHHHHHHHHHHHHHHHHHHHHCCCC-CCCEEEEEEECCCEEEEEECCCCCCCCHHHHHHHHHHHHCCCHHHHHHHHHH
T ss_conf             441888734588989999986660157-9858999983140688873035788518889999999860792999999998


Q ss_pred             CCCCC-CCCCCCHHHHHHHHHHHHCCCEE
Q ss_conf             67556-77887616899999999629869
Q gi|254780903|r  721 NQYDQ-SIGGFGLGLAISDALTNLHGGRL  748 (766)
Q Consensus       721 ~~~t~-~~~GtGLGLaI~k~iVe~hgG~I  748 (766)
                      .+-+. ...|+||||-.-   +.-+|-+.
T Consensus       133 anA~~~d~~gSglGLLTl---msDYgA~f  158 (184)
T COG5381         133 ANALESDCEGSGLGLLTL---MSDYGAQF  158 (184)
T ss_pred             HHCCCCCCCCCCCCCEEH---HHHHCCEE
T ss_conf             603588876566410001---23423326


No 130
>PRK10364 sensor protein ZraS; Provisional
Probab=95.80  E-value=0.15  Score=29.10  Aligned_cols=102  Identities=8%  Similarity=0.093  Sum_probs=45.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             25788765899999999999999999996768889998999999999999850100112235548999999999885310
Q gi|254780903|r   45 FSSFNQTIPMISMVFLVFIATSSIIKVTTRYAQQEKMTNQTSLMLTEAIEIIFQNNNIKFDLASQKKAESMLGQLLAKTR  124 (766)
Q Consensus        45 ~~~~rr~ip~~i~~fli~~~~~~~~~i~~~~~~~~~~~~~~~~lla~~~~~~~~~~~~~~d~~~~~~ae~~L~~~~~~~~  124 (766)
                      -.|+-..+|.   +.++.+....++.+.+..|+.+...+..+.--+..+-+..+-...-  ..-+.. ...++..+....
T Consensus        12 ~~~~~~~~~~---~~~~~~~~~~~~~~~~~~r~~~~~~~~l~~~g~~li~a~eag~r~g--m~~~~~-~~~~q~ll~e~a   85 (455)
T PRK10364         12 AKWLSAILPV---VIVGLVGLFAVTVIRDYGRETAAARQTLLEKGSVLIRALESGSRVG--MGMRMH-HAQQQALLEEMA   85 (455)
T ss_pred             HHHHHHHHHH---HHHHHHHHHHEEEECCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHH--CCCCCH-HHHHHHHHHHHH
T ss_conf             9999999999---9999998871357510125899999999998899999987032021--552420-479999999971


Q ss_pred             CCCC-CEEEEECCCCCEEEECCCHHHHCCCC
Q ss_conf             1789-78999969980899714205551997
Q gi|254780903|r  125 FLSE-SFILLAQPNELVFASSTKNSHYIGKK  154 (766)
Q Consensus       125 ~~~~-~~i~i~d~~g~i~~~n~~~~~~~G~~  154 (766)
                      ..++ .++.++|.+|+|++-+..  ...|.+
T Consensus        86 ~q~~v~~~~v~d~~g~i~~hs~~--~~~g~~  114 (455)
T PRK10364         86 GQPGVLWFAVTDEQGTIIMHSNS--GMVGKQ  114 (455)
T ss_pred             CCCCEEEEEEECCCCCEEEECCH--HHCCCC
T ss_conf             59986999998899638984785--644885


No 131
>KOG3560 consensus
Probab=94.27  E-value=0.39  Score=26.08  Aligned_cols=71  Identities=11%  Similarity=0.088  Sum_probs=53.1

Q ss_pred             CCCCEEEEECHHHHHHHCCCHHHHCCCCCHHHHCCCHHHHHH--HHHHHCCCCCCCEEEEEEECCCEEEEECC
Q ss_conf             349969970178988839997894289717881652013789--99852112456405899916962874223
Q gi|254780903|r  399 DKNDRLVMCNANYQKAYGLPDHVLVPGNARSIIQDAQTRPII--EYRTSDPERSQDMSKEIKLADSRWLQINE  469 (766)
Q Consensus       399 D~~g~i~~~N~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~e~~~~dg~~~~i~~  469 (766)
                      -.|+.++-|..+...++||.+.++.++.-|+.++-++.....  ..........+-..|+.+.++|+|.++-.
T Consensus       290 klDfa~vs~Dak~k~~lgy~eaEL~~m~gY~lvH~~D~~y~Aeah~e~iktgeSGmlvyR~qtk~grw~wvqs  362 (712)
T KOG3560         290 KLDFALVSMDAKVKATLGYCEAELHGMPGYNLVHVEDKVYMAEAHSEGIKTGESGMLVYREQTKAGRWAWVQS  362 (712)
T ss_pred             CCCCCEECCCHHHHHHHCCCHHHCCCCCCCCEEEHHHHHHHHHHHHHHHHCCCCCEEEEEEEECCCCEEEEEC
T ss_conf             2565400321335554320154405787633123223455358899986358764489998604783798534


No 132
>KOG3753 consensus
Probab=94.27  E-value=0.055  Score=32.27  Aligned_cols=41  Identities=5%  Similarity=0.044  Sum_probs=22.7

Q ss_pred             CCCEEEEECHHHHHHHCCCHHHHCCCCCHHHHCCCHHHHHH
Q ss_conf             49969970178988839997894289717881652013789
Q gi|254780903|r  400 KNDRLVMCNANYQKAYGLPDHVLVPGNARSIIQDAQTRPII  440 (766)
Q Consensus       400 ~~g~i~~~N~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~  440 (766)
                      ...-+..+..+..-++||-..++++......+++.++....
T Consensus       339 ptClf~hVDeaAVp~LGyLPqDLIG~sil~f~H~eDr~vm~  379 (1114)
T KOG3753         339 PTCLFQHVDEAAVPLLGYLPQDLIGTSILAFVHPEDRHVMV  379 (1114)
T ss_pred             CCCEEEECCHHHHHHHCCCCHHHHCCCHHHHHCCCCHHHHH
T ss_conf             86003413254422320472655264165531677428999


No 133
>KOG0019 consensus
Probab=93.93  E-value=0.094  Score=30.58  Aligned_cols=21  Identities=19%  Similarity=0.352  Sum_probs=11.9

Q ss_pred             EEEEEEEEECCEEEEEEEECC
Q ss_conf             899999997998999999788
Q gi|254780903|r  681 KMMIRTSKIGQCVIITIADTG  701 (766)
Q Consensus       681 ~I~i~~~~~~~~v~i~V~D~G  701 (766)
                      .|+|+-+....-++|.+..-|
T Consensus       535 kV~vs~RlvssPc~I~t~~~g  555 (656)
T KOG0019         535 KVTVNNRLVSHPAMITTLEYG  555 (656)
T ss_pred             EEEECCCCCCCCEEEEECCCC
T ss_conf             999537546885289850001


No 134
>KOG3561 consensus
Probab=93.80  E-value=0.11  Score=30.01  Aligned_cols=329  Identities=8%  Similarity=0.013  Sum_probs=148.8

Q ss_pred             CCCCCEEEEECCCCCEEEECCCHHHHCCCCHHHHCCCCHHHHCCCCCCCHHHHHCC--CCHHEEEEEECCCCCCEEEEEE
Q ss_conf             17897899996998089971420555199788960761043205443320232115--3100001233157782599997
Q gi|254780903|r  125 FLSESFILLAQPNELVFASSTKNSHYIGKKIGEIIPELSRSRSRSKTVQMSEASLD--QQPYHVLSVNLPHNSGSILIIN  202 (766)
Q Consensus       125 ~~~~~~i~i~d~~g~i~~~n~~~~~~~G~~~~~~~~~~~~~~~~~~~~~~~~~~l~--~~~~~~~~~~~~~~~~~~~~~~  202 (766)
                      .+.+.+++++..+|+|++++.....++||...|+++.+.+.+..+...+.....+-  ........+.+....+.. . .
T Consensus       102 eAlDGF~fvV~cdG~IvyVSeSVT~~L~y~QsDL~~qSly~ilhp~d~~~~~~ql~~r~~e~~f~~r~l~~~~~~~-~-~  179 (803)
T KOG3561         102 EALDGFLFVVNCDGRIVYVSESVTSVLGYLQSDLMGQSLYDILHPLDNDKPREQLSPRSNEHTFNCRLLDGKTGPP-P-E  179 (803)
T ss_pred             HHHCCEEEEEECCCEEEEEECCHHHHHCCCHHHHHCCHHHHHCCCCCCCCCCCCCCCCCCCCCCCHHHHCCCCCCC-H-H
T ss_conf             9746748999657459999554477658687887334198760843247636012664222350032213678986-5-7


Q ss_pred             ECCCCHHHHHHHHHHHHHH---HHHHHHHH-------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEEEEE
Q ss_conf             4232101234556554568---78878999-------9999988889999999999999999999999722597459897
Q gi|254780903|r  203 SRVPLLRLWREEVTLEVVF---FSIISALL-------LFILFSYYRQAKKNKENDTILLEANICVETALSRGRCGLWNFN  272 (766)
Q Consensus       203 ~~~~~~~~~r~~~~~~~~~---~~~~~~~~-------~~~~~a~~~dit~~r~ae~~l~ese~rl~~al~~a~~GiWd~D  272 (766)
                      +........+..+...-.-   |.+...+.       -.+.++ .+-.+.....+  +--...|+....   +- -|+|-
T Consensus       180 E~~~~~~~~~~~~~~~~~s~e~~~~~i~~~~~~~~~~~~~~~~-~r~~~p~~~~~--~~~id~~~~~~a---Rr-sfe~r  252 (803)
T KOG3561         180 EAVKFYGNFQCFTNSQPKSIEGFQSTICRQRRKAEGDRVCFGV-SRLTTPQLIGE--MCIIDTRLCEGA---RR-SFECR  252 (803)
T ss_pred             HHHHHHHHCCCCCCCCCCCCCCCCCCCEEECCCCCCCCCCCCC-CCCCCHHHCCC--EECCCCCCCCCC---CC-CHHHH
T ss_conf             7654331012234467532234213300103456667554432-22354112032--000355101134---43-53355


Q ss_pred             CCCCEEEECHHHHHHCCCCHHHCCCCHHHHHHHHCCCCHHHHHHHHHHHHCCCCEEEEEEEEECCCCCEEEEEEEEEEE-
Q ss_conf             6897899978899772999433058988999760812058999999997248984899999886989889988999999-
Q gi|254780903|r  273 FDNKKFHLSRSMYEIMGIPYENKTLSFRAIARLIHYDNKKICEIARSVTGKHVKQLDQIFHMRHASGADIWIQVRAQMM-  351 (766)
Q Consensus       273 ~~~~~i~ws~~~~~llG~~~~e~~~s~~~~~~~vHPdDr~~~~~a~~~~~~~~~~~~~e~Ri~~~DG~~~Wi~~r~~~i-  351 (766)
                      +.    +.+.++.-+-||.+-+....+... ...|-+|...+........-....-..-||...++-+|+|+......- 
T Consensus       253 ~r----~~~~r~~p~~gy~~~~~~g~~~~~-~~~~~~~~~~y~~~h~~g~~~s~~~~c~~~~~t~~~q~~~~~~d~~i~~  327 (803)
T KOG3561         253 MR----FCDHRAPPIIGYEPFEVLGTSRNY-DYYHKDDLPNYRVIHCTGYIKSAGPSCKYRFLTKGQQWIWLPQDDYISY  327 (803)
T ss_pred             HH----HCCCCCCCCCCCCCEEECCCCCCC-CCCCCCCCCCEEEEEEEEEEECCCCCCEECCCCCCCCCCCCCCCCCCCC
T ss_conf             24----315567764444530004523464-3445576421578740046721687530021245545323674445465


Q ss_pred             EECCCEEEEE-EEEECCCHHH-HHHHHHHHH-HHHHHHHHHHH-HHHEEEECCCCEEEEECHHHHHHHCCCHHHHCCCCC
Q ss_conf             8379606999-9984461799-999999999-99999999854-455158834996997017898883999789428971
Q gi|254780903|r  352 RTISGGMNII-GIAMDLTEKY-HLEKRYAEA-DQRLSKAIECT-SEALVLWDKNDRLVMCNANYQKAYGLPDHVLVPGNA  427 (766)
Q Consensus       352 ~d~~G~~~~i-Gi~~DITErK-~ae~~l~es-e~rlr~~ie~~-~~~i~~~D~~g~i~~~N~~~~~~~g~~~~~~~~~~~  427 (766)
                      ..-++++.++ -....+|-+- +......-. +.-.+..-... .+-+.-...+|.++++-.....+.||...++.+..+
T Consensus       328 ~~~~s~p~~v~~~~~~vs~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~sr~~~~g~~~~~dqr~~~i~~~~~~~~~g~ss  407 (803)
T KOG3561         328 HQWNSKPCLVAIGRLVVSYAEVRVPSRADMSIEGPRQQPSSPQSSEFISRSSSDGSFTFVDQRASAILGYQPQELLGRSS  407 (803)
T ss_pred             CCCCCCCCEEEECCCCCCHHHCCCCCCCCCCCCCCCCCCCCCCCCHHHCCCCCCCCEECCCCCCCCCCCCCCHHHCCCCC
T ss_conf             45578743367435101033125862346765665445567653111104676786201455644223668543327663


Q ss_pred             HHHHCCCHHHHHHHH---HHHCCCCCCCEEEEEEECCCEEEEE
Q ss_conf             788165201378999---8521124564058999169628742
Q gi|254780903|r  428 RSIIQDAQTRPIIEY---RTSDPERSQDMSKEIKLADSRWLQI  467 (766)
Q Consensus       428 ~~~~~~~~~~~~~~~---~~~~~~~~~~~~~e~~~~dg~~~~i  467 (766)
                      +...+..+..+....   ............+.....+|.|...
T Consensus       408 ~~s~h~~d~~~~~~s~~~~~~~s~~~~~~~yr~~~~n~~~~~~  450 (803)
T KOG3561         408 YESSHPADSSPLSESLKQVQALSEQRSTLLYRFRSKNGSSIPN  450 (803)
T ss_pred             CCCCCCCCCCHHHCHHHHHHHHCCCCCCCCCCCCCCCCCCCCC
T ss_conf             0025755543012469999870466543222454678875434


No 135
>PTZ00108 DNA topoisomerase II; Provisional
Probab=93.67  E-value=0.082  Score=31.01  Aligned_cols=17  Identities=18%  Similarity=0.251  Sum_probs=7.1

Q ss_pred             CCCEEEEECCCCEEEEC
Q ss_conf             97459897689789997
Q gi|254780903|r  265 RCGLWNFNFDNKKFHLS  281 (766)
Q Consensus       265 ~~GiWd~D~~~~~i~ws  281 (766)
                      |+|-|-.-+.+|.-..|
T Consensus       821 P~GqFGtR~~GGkDaas  837 (1506)
T PTZ00108        821 PCGQFGSRKEGGKDASA  837 (1506)
T ss_pred             CCCCCCCCCCCCCCCCC
T ss_conf             57875254558875556


No 136
>PTZ00109 DNA gyrase subunit b; Provisional
Probab=93.66  E-value=0.019  Score=35.60  Aligned_cols=43  Identities=14%  Similarity=0.224  Sum_probs=26.6

Q ss_pred             CEEEEEEEEECCCCCE-EEEEEEEEEEEECCCEEEEEEEEECCC
Q ss_conf             8489999988698988-998899999983796069999984461
Q gi|254780903|r  326 KQLDQIFHMRHASGAD-IWIQVRAQMMRTISGGMNIIGIAMDLT  368 (766)
Q Consensus       326 ~~~~~e~Ri~~~DG~~-~Wi~~r~~~i~d~~G~~~~iGi~~DIT  368 (766)
                      ....+|+.+.+-+|.| -.+.+.+.-+.+.+|++|.-|.-.=+|
T Consensus       409 ~~i~ve~al~w~~~~y~e~i~SFvNnI~T~dGGTH~~GFrsALt  452 (941)
T PTZ00109        409 KNIHIDLRLKWLQGEYHEHIISFVNNVNTTDGGTHVDALKYAIS  452 (941)
T ss_pred             CCEEEEEEEEECCCCCCCEEEEEECCCCCCCCCCHHHHHHHHHH
T ss_conf             67579999996578875058877436668999737999999999


No 137
>pfam07310 PAS_5 PAS domain. This family contains a number of hypothetical bacterial proteins of unknown function approximately 200 residues long. This region is is distantly similar to other PAS domains.
Probab=93.45  E-value=0.55  Score=25.06  Aligned_cols=94  Identities=9%  Similarity=0.035  Sum_probs=71.0

Q ss_pred             CCEEEEECCCCEE--EECHHHHHHCCCCHHHCCCCHHHHHHHHCCCCHHHHHHHHHHHHCCCCEEEEEEEEECCCCCEEE
Q ss_conf             7459897689789--99788997729994330589889997608120589999999972489848999998869898899
Q gi|254780903|r  266 CGLWNFNFDNKKF--HLSRSMYEIMGIPYENKTLSFRAIARLIHYDNKKICEIARSVTGKHVKQLDQIFHMRHASGADIW  343 (766)
Q Consensus       266 ~GiWd~D~~~~~i--~ws~~~~~llG~~~~e~~~s~~~~~~~vHPdDr~~~~~a~~~~~~~~~~~~~e~Ri~~~DG~~~W  343 (766)
                      +-+-+.+..+...  ..-...+++||++...     ..+.++..|++++.+............+..........+|....
T Consensus        40 ~file~~~~~~~r~RlaGt~l~~~~G~d~~G-----~~~~~l~~~~~r~~~~~~l~~v~~~~~p~~~~~~~~~~~g~~~~  114 (137)
T pfam07310        40 VFILERDAPGGAPFRLAGTRLCALFGRELRG-----IPFSALWTEASRREIARVLDVVFDRTLPVLAGVDAEARNGRSLH  114 (137)
T ss_pred             CEEEEEECCCCEEEEEECHHHHHHHCCCCCC-----CCHHHHHCHHHHHHHHHHHHHHHCCCCEEEEEEEEECCCCCCEE
T ss_conf             3899984799679998178899982998889-----78899619677999999999997589439999778638987015


Q ss_pred             EEEEEEEEEECCCEE-EEEEEE
Q ss_conf             889999998379606-999998
Q gi|254780903|r  344 IQVRAQMMRTISGGM-NIIGIA  364 (766)
Q Consensus       344 i~~r~~~i~d~~G~~-~~iGi~  364 (766)
                      .+.---|+.+++|.+ +++|+.
T Consensus       115 ~e~LlLPL~~d~g~vdriLG~l  136 (137)
T pfam07310       115 FELLLLPLATRSGTPDRFLGLL  136 (137)
T ss_pred             EEEEECCCCCCCCCHHHHHHCC
T ss_conf             4355525789999722333104


No 138
>TIGR01058 parE_Gpos DNA topoisomerase IV, B subunit; InterPro: IPR005740   DNA topoisomerases regulate the number of topological links between two DNA strands (i.e. change the number of superhelical turns) by catalysing transient single- or double-strand breaks, crossing the strands through one another, then resealing the breaks. These enzymes have several functions: to remove DNA supercoils during transcription and DNA replication; for strand breakage during recombination; for chromosome condensation; and to disentangle intertwined DNA during mitosis , . DNA topoisomerases are divided into two classes: type I enzymes (5.99.1.2 from EC; topoisomerases I, III and V) break single-strand DNA, and type II enzymes (5.99.1.3 from EC; topoisomerases II, IV and VI) break double-strand DNA .   Type II topoisomerases are ATP-dependent enzymes, and can be subdivided according to their structure and reaction mechanisms: type IIA (topoisomerase II or gyrase, and topoisomerase IV) and type IIB (topoisomerase VI). These enzymes are responsible for relaxing supercoiled DNA as well as for introducing both negative and positive supercoils .   This entry represents subunit B (parE) of topoisomerase IV from Gram positive bacteria. Topoisomerase IV primarily decatenates DNA and relaxes positive supercoils, which is important in bacteria, where the circular chromosome becomes catenated, or linked, during replication . Topoisomerase IV consists of two polypeptide subunits, parC (subunit A), which is homologous to gyrA of topoisomerase II, and parE (subunit B), which is homologous to gyrB of topoisomerase II.   More information about this protein can be found at Protein of the Month: DNA Topoisomerase .; GO: 0003677 DNA binding, 0003918 DNA topoisomerase (ATP-hydrolyzing) activity, 0005524 ATP binding, 0006265 DNA topological change, 0005694 chromosome.
Probab=93.34  E-value=0.15  Score=29.18  Aligned_cols=44  Identities=16%  Similarity=0.141  Sum_probs=29.9

Q ss_pred             HHHCCCCEEEEEEEEECCCCCEEEEEEEEEEEEECCCEEEEEEE
Q ss_conf             97248984899999886989889988999999837960699999
Q gi|254780903|r  320 VTGKHVKQLDQIFHMRHASGADIWIQVRAQMMRTISGGMNIIGI  363 (766)
Q Consensus       320 ~~~~~~~~~~~e~Ri~~~DG~~~Wi~~r~~~i~d~~G~~~~iGi  363 (766)
                      .+.++...+++|+-+.-.||.-=-+.+.+--++..+|++|=-|.
T Consensus       248 ~f~ge~~~i~Ve~afQfnd~~~e~ilSF~N~vkT~eGG~HE~g~  291 (655)
T TIGR01058       248 YFEGEKNGIEVEVAFQFNDGDSENILSFANSVKTKEGGTHENGF  291 (655)
T ss_pred             EEEECCCCEEEEEEEEECCCCCCEEEEEEEEEEECCCCCCHHHH
T ss_conf             88764762589999974278875379864003406887207889


No 139
>KOG1979 consensus
Probab=93.34  E-value=0.13  Score=29.49  Aligned_cols=29  Identities=10%  Similarity=0.098  Sum_probs=15.5

Q ss_pred             HHHHHHHHHHHHHHHCCCCCEEEEECCCC
Q ss_conf             99999999988531017897899996998
Q gi|254780903|r  110 KKAESMLGQLLAKTRFLSESFILLAQPNE  138 (766)
Q Consensus       110 ~~ae~~L~~~~~~~~~~~~~~i~i~d~~g  138 (766)
                      .+..+++.+.+.....+....|-|.-.+|
T Consensus        26 ~RP~NAlKEliENSLDA~ST~I~V~vk~G   54 (694)
T KOG1979          26 QRPVNALKELIENSLDANSTSIDVLVKDG   54 (694)
T ss_pred             HCHHHHHHHHHHCCCCCCCCEEEEEEECC
T ss_conf             35578999998614157985699998159


No 140
>KOG0020 consensus
Probab=93.19  E-value=0.21  Score=28.13  Aligned_cols=12  Identities=17%  Similarity=0.598  Sum_probs=7.8

Q ss_pred             CCCEEEEECCCC
Q ss_conf             974598976897
Q gi|254780903|r  265 RCGLWNFNFDNK  276 (766)
Q Consensus       265 ~~GiWd~D~~~~  276 (766)
                      .--+|||.+-++
T Consensus       324 ~kT~wdWel~Nd  335 (785)
T KOG0020         324 EKTVWDWELLND  335 (785)
T ss_pred             HHCCHHHHHHCC
T ss_conf             030011545425


No 141
>COG3283 TyrR Transcriptional regulator of aromatic amino acids metabolism [Transcription / Amino acid transport and metabolism]
Probab=93.10  E-value=0.61  Score=24.69  Aligned_cols=39  Identities=10%  Similarity=0.054  Sum_probs=25.3

Q ss_pred             CCEEEEECCCCCEEEECCCHHHHCCCCHHHHCCCCHHHH
Q ss_conf             978999969980899714205551997889607610432
Q gi|254780903|r  128 ESFILLAQPNELVFASSTKNSHYIGKKIGEIIPELSRSR  166 (766)
Q Consensus       128 ~~~i~i~d~~g~i~~~n~~~~~~~G~~~~~~~~~~~~~~  166 (766)
                      ++.|+-+|..|.+..+||++++++|.+.+++.|......
T Consensus        90 ~~pVlsvd~kg~v~~aNpAa~~l~~~~~~~~~g~~~~~l  128 (511)
T COG3283          90 PEPVLSVDMKGKVDMANPAACQLFGRKEDRLRGHTAAQL  128 (511)
T ss_pred             CCCEEEECCCCCEEECCHHHHHHHCCCHHHHCCCCHHHH
T ss_conf             875687527774332588999984888354057569986


No 142
>KOG1977 consensus
Probab=92.39  E-value=0.39  Score=26.09  Aligned_cols=16  Identities=31%  Similarity=0.245  Sum_probs=10.1

Q ss_pred             CCCHHHHHHHHHHHHC
Q ss_conf             8761689999999962
Q gi|254780903|r  729 GFGLGLAISDALTNLH  744 (766)
Q Consensus       729 GtGLGLaI~k~iVe~h  744 (766)
                      |-||-+.=|-.|++..
T Consensus      1067 gD~L~~qEc~~lI~~L 1082 (1142)
T KOG1977        1067 GDGLSLQECCRLIEAL 1082 (1142)
T ss_pred             CCCCCHHHHHHHHHHH
T ss_conf             7765789999999988


No 143
>TIGR01059 gyrB DNA gyrase, B subunit; InterPro: IPR011557   DNA topoisomerases regulate the number of topological links between two DNA strands (i.e. change the number of superhelical turns) by catalysing transient single- or double-strand breaks, crossing the strands through one another, then resealing the breaks. These enzymes have several functions: to remove DNA supercoils during transcription and DNA replication; for strand breakage during recombination; for chromosome condensation; and to disentangle intertwined DNA during mitosis , . DNA topoisomerases are divided into two classes: type I enzymes (5.99.1.2 from EC; topoisomerases I, III and V) break single-strand DNA, and type II enzymes (5.99.1.3 from EC; topoisomerases II, IV and VI) break double-strand DNA .   Type II topoisomerases are ATP-dependent enzymes, and can be subdivided according to their structure and reaction mechanisms: type IIA (topoisomerase II or gyrase, and topoisomerase IV) and type IIB (topoisomerase VI). These enzymes are responsible for relaxing supercoiled DNA as well as for introducing both negative and positive supercoils .    Topoisomerase II (called gyrase in bacteria) primarily introduces negative supercoils into DNA. In bacteria, topoisomerase II consists of two polypeptide subunits, gyrA and gyrB, which form a heterotetramer: (BA)2. In most eukaryotes, topoisomerase II consists of a single polypeptide, where the N- and C-terminal regions correspond to gyrB and gyrA, respectively.   This entry represents the B subunit (gyrB) as found predominantly in bacteria, but does not include the topoisomerase II enzymes composed of a single polypeptide, as are found in most eukaryotes. GyrB has two functional domains: an N-terminal ATPase and a C-terminal responsible for subunit interactions, the latter differing between subunit B and single polypeptide topoisomerase II .   More information about this protein can be found at Protein of the Month: DNA Topoisomerase .; GO: 0003677 DNA binding, 0003918 DNA topoisomerase (ATP-hydrolyzing) activity, 0005524 ATP binding, 0006265 DNA topological change, 0005694 chromosome.
Probab=92.31  E-value=0.11  Score=29.98  Aligned_cols=124  Identities=13%  Similarity=0.085  Sum_probs=54.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHH-HHHHHHHHHHHHHHHHHHH------HH----HHHH--H-HHCC
Q ss_conf             999876752224789999999986034688993899-9999999999999999977------76----7788--8-7419
Q gi|254780903|r  546 FLAKMSHELRTPLNAILGFSEVIKKEIFGELGSVKY-YEYAQDIHYSGQHLLNMIN------NI----LEMS--K-IETE  611 (766)
Q Consensus       546 fla~isHelrtPL~aI~g~~ell~~~~~~~~~~e~~-~~~l~~I~~~~~~l~~lI~------di----Ld~s--r-ieag  611 (766)
                      |+..|.-.+..+...+..+.+++...++.+...-+. .+..-.+...-+....+-.      ..    ..++  + ++. 
T Consensus       609 l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~y~~~~~E~~~~~~~~~~~~~~~~~~f~~~vvR~G~~~-  687 (818)
T TIGR01059       609 LINRLERKAIRFSEELLIYQDLLEKELLEYESAVKYWLQGALYIYSDKEKEEAKTQLPVHKNAEKELFESSVVRHGLDT-  687 (818)
T ss_pred             HHHHHHHHHCCCHHHHHHHHHHHCHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHEEECCCCC-
T ss_conf             7999987404355788875553022220014688889999998875565788887422356778875412114437763-


Q ss_pred             CCCCCEEEECHHHHHHHHHHHHHHHHHHCCCEEEEEECCCCEEEECHHHHHHHHHHHHHHHHH
Q ss_conf             830120331699999999999999998479589998089978998689999999998865653
Q gi|254780903|r  612 KISIDKQNADLIPIINEGIRLIGSSAQSKNIKIEKKIPSELFFNADKRIIKKILFPILSNSIK  674 (766)
Q Consensus       612 ~~~~~~~~~dl~~~i~~~~~~~~~~~~~k~i~l~~~~~~~l~v~~D~~~l~QVl~NLi~NAik  674 (766)
                      ...|..+-+.+.++.+.+-..+.+.--.  .+............  -..+.||+..|+.++-|
T Consensus       688 ~~~L~~~q~~~~e~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~--~~~~~~~~~~l~~~~~~  746 (818)
T TIGR01059       688 DYILEKEQLELFEYGEIISLELSLQGLF--ETRAKLIRKNKKFE--INSLEEALDKLVELGRK  746 (818)
T ss_pred             CHHHHHHHHHHHHHHHHHHHHCCHHHHH--HHHHHHCCCCCCCC--CCCHHHHHHHHHHCCCC
T ss_conf             2001666643323454344211034554--43432100122310--02589999999840789


No 144
>TIGR01055 parE_Gneg DNA topoisomerase IV, B subunit; InterPro: IPR005737   DNA topoisomerases regulate the number of topological links between two DNA strands (i.e. change the number of superhelical turns) by catalysing transient single- or double-strand breaks, crossing the strands through one another, then resealing the breaks. These enzymes have several functions: to remove DNA supercoils during transcription and DNA replication; for strand breakage during recombination; for chromosome condensation; and to disentangle intertwined DNA during mitosis , . DNA topoisomerases are divided into two classes: type I enzymes (5.99.1.2 from EC; topoisomerases I, III and V) break single-strand DNA, and type II enzymes (5.99.1.3 from EC; topoisomerases II, IV and VI) break double-strand DNA .   Type II topoisomerases are ATP-dependent enzymes, and can be subdivided according to their structure and reaction mechanisms: type IIA (topoisomerase II or gyrase, and topoisomerase IV) and type IIB (topoisomerase VI). These enzymes are responsible for relaxing supercoiled DNA as well as for introducing both negative and positive supercoils .   This entry represents subunit B (parE) of topoisomerase IV from Gram negative bacteria. Topoisomerase IV primarily decatenates DNA and relaxes positive supercoils, which is important in bacteria, where the circular chromosome becomes catenated, or linked, during replication . Topoisomerase IV consists of two polypeptide subunits, parC (subunit A), which is homologous to gyrA of topoisomerase II, and parE (subunit B), which is homologous to gyrB of topoisomerase II.   More information about this protein can be found at Protein of the Month: DNA Topoisomerase .; GO: 0003677 DNA binding, 0003918 DNA topoisomerase (ATP-hydrolyzing) activity, 0005524 ATP binding, 0006265 DNA topological change, 0005694 chromosome.
Probab=92.30  E-value=0.1  Score=30.35  Aligned_cols=60  Identities=15%  Similarity=0.291  Sum_probs=33.7

Q ss_pred             EEEEEEEEC-CCCCEEEEEEEEEEEEECCCEEEEEEEEECCCHHHHHHHHHHHHHHHHHHHHHHHHHHEEE
Q ss_conf             899999886-9898899889999998379606999998446179999999999999999999854455158
Q gi|254780903|r  328 LDQIFHMRH-ASGADIWIQVRAQMMRTISGGMNIIGIAMDLTEKYHLEKRYAEADQRLSKAIECTSEALVL  397 (766)
Q Consensus       328 ~~~e~Ri~~-~DG~~~Wi~~r~~~i~d~~G~~~~iGi~~DITErK~ae~~l~ese~rlr~~ie~~~~~i~~  397 (766)
                      ...++-+.+ ++|...-..+.+..+....|++|.-|          +.+.+-.+-..|....+..|-++-+
T Consensus       258 ~~~~WAl~W~~~~~~~~~~SY~N~iPT~QGGTH~~G----------L~~~lL~a~~~f~E~~~~~P~~~~L  318 (647)
T TIGR01055       258 EAVEWALLWLPEGGELLMESYVNLIPTIQGGTHVNG----------LRQGLLDALREFCEMRNLLPRGVKL  318 (647)
T ss_pred             HHCCEEEEECCCCCHHHHHCCCCCCCCCCCCCHHHH----------HHHHHHHHHHHHHHHHCCCCCEEEC
T ss_conf             100244663278840032041101578988710457----------8999999999988875188640221


No 145
>PRK05559 DNA topoisomerase IV subunit B; Reviewed
Probab=92.28  E-value=0.015  Score=36.29  Aligned_cols=39  Identities=18%  Similarity=0.215  Sum_probs=17.3

Q ss_pred             EEEEEECCCCCEEEEEEEEEEEEECCCEEEEEEEEECCC
Q ss_conf             999988698988998899999983796069999984461
Q gi|254780903|r  330 QIFHMRHASGADIWIQVRAQMMRTISGGMNIIGIAMDLT  368 (766)
Q Consensus       330 ~e~Ri~~~DG~~~Wi~~r~~~i~d~~G~~~~iGi~~DIT  368 (766)
                      .|+-+.+.++.-.-+.+.+.-+...+|+.|+-|+..=||
T Consensus       252 veval~~~~~~~~~~~SFVN~I~T~~GGTHv~g~~~al~  290 (633)
T PRK05559        252 VEWALAWLEGGSENIESYVNLIPTPDGGTHENGFREGLL  290 (633)
T ss_pred             EEEEEEECCCCCCEEEEEECCCCCCCCCCHHHHHHHHHH
T ss_conf             999999447888447656887057999876788998999


No 146
>smart00433 TOP2c TopoisomeraseII. Eukaryotic DNA topoisomerase II, GyrB, ParE
Probab=92.22  E-value=0.02  Score=35.48  Aligned_cols=39  Identities=21%  Similarity=0.133  Sum_probs=20.4

Q ss_pred             EEEEEECCCCCEEEEEEEEEEEEECCCEEEEEEEEECCC
Q ss_conf             999988698988998899999983796069999984461
Q gi|254780903|r  330 QIFHMRHASGADIWIQVRAQMMRTISGGMNIIGIAMDLT  368 (766)
Q Consensus       330 ~e~Ri~~~DG~~~Wi~~r~~~i~d~~G~~~~iGi~~DIT  368 (766)
                      .|+-+.+.++.-.-+.+.+.-+...+|+.|+-|+..-||
T Consensus       219 ~eva~~~s~~~~~~~~SFvN~I~T~~GGTHv~gf~~al~  257 (594)
T smart00433      219 VEVAFQYTDGYSENIVSFVNNIATTEGGTHENGFKDALT  257 (594)
T ss_pred             EEEEEEECCCCCCCCCEEEEEEECCCCCCHHHHHHHHHH
T ss_conf             999999659887210002314788999848899999999


No 147
>pfam08269 Cache_2 Cache domain.
Probab=91.31  E-value=0.98  Score=23.22  Aligned_cols=79  Identities=11%  Similarity=0.171  Sum_probs=49.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEEEEECCCCCEEEECCCHHHHCCCCHHH
Q ss_conf             89998999999999999850100112235548999999999885310178978999969980899714205551997889
Q gi|254780903|r   78 QEKMTNQTSLMLTEAIEIIFQNNNIKFDLASQKKAESMLGQLLAKTRFLSESFILLAQPNELVFASSTKNSHYIGKKIGE  157 (766)
Q Consensus        78 ~~~~~~~~~~lla~~~~~~~~~~~~~~d~~~~~~ae~~L~~~~~~~~~~~~~~i~i~d~~g~i~~~n~~~~~~~G~~~~~  157 (766)
                      .....++.+......+......  ......++.+|++...+.+...+...+..+|+.|.+|+.+ ++|.-+.+.|..+.+
T Consensus         8 rk~~lk~~v~~a~s~i~~~~~~--~~~G~ls~~eA~~~a~~~l~~~ryg~~gY~fi~d~~g~~l-~hP~~p~l~G~n~~~   84 (95)
T pfam08269         8 RKAELKAVVESALSIIKEYYQQ--AQKGKLTREEAQAQAKALLRALRYDGDGYFFAYDSNGTNV-MHPIKPELVGKNLSN   84 (95)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHH--HHCCCCCHHHHHHHHHHHHHHCCCCCCCEEEEEECCCCEE-ECCCCCCCCCCCCCC
T ss_conf             9999999999999999999999--8779999999999999999853478985699980999889-878991106977663


Q ss_pred             HC
Q ss_conf             60
Q gi|254780903|r  158 II  159 (766)
Q Consensus       158 ~~  159 (766)
                      +.
T Consensus        85 ~~   86 (95)
T pfam08269        85 LK   86 (95)
T ss_pred             CC
T ss_conf             89


No 148
>PRK13374 purine nucleoside phosphorylase; Provisional
Probab=91.15  E-value=0.63  Score=24.60  Aligned_cols=10  Identities=0%  Similarity=-0.204  Sum_probs=4.4

Q ss_pred             CCCCHHHHHH
Q ss_conf             8120589999
Q gi|254780903|r  307 HYDNKKICEI  316 (766)
Q Consensus       307 HPdDr~~~~~  316 (766)
                      -|-|-.+++.
T Consensus        19 ~~GDP~Ra~~   28 (233)
T PRK13374         19 MPGDPLRAKY   28 (233)
T ss_pred             ECCCHHHHHH
T ss_conf             4689899999


No 149
>PRK05819 deoD purine nucleoside phosphorylase; Reviewed
Probab=90.15  E-value=0.87  Score=23.58  Aligned_cols=10  Identities=0%  Similarity=-0.204  Sum_probs=4.5

Q ss_pred             CCCCHHHHHH
Q ss_conf             8120589999
Q gi|254780903|r  307 HYDNKKICEI  316 (766)
Q Consensus       307 HPdDr~~~~~  316 (766)
                      -|-|-.+++.
T Consensus        18 ~~GDP~Ra~~   27 (235)
T PRK05819         18 MPGDPLRAKY   27 (235)
T ss_pred             ECCCHHHHHH
T ss_conf             3789799999


No 150
>PRK05644 gyrB DNA gyrase subunit B; Validated
Probab=89.62  E-value=0.035  Score=33.64  Aligned_cols=42  Identities=17%  Similarity=0.181  Sum_probs=23.4

Q ss_pred             EEEEEEEEECCCCCEEEEEEEEEEEEECCCEEEEEEEEECCC
Q ss_conf             489999988698988998899999983796069999984461
Q gi|254780903|r  327 QLDQIFHMRHASGADIWIQVRAQMMRTISGGMNIIGIAMDLT  368 (766)
Q Consensus       327 ~~~~e~Ri~~~DG~~~Wi~~r~~~i~d~~G~~~~iGi~~DIT  368 (766)
                      ....|.-+.+.||----+.+.+.-+...+|+.|.-|.-.=+|
T Consensus       255 ~i~vEvAlqw~d~~~e~i~SFvN~I~T~eGGTHv~Gfr~aLt  296 (725)
T PRK05644        255 GIGVEVAMQWNDSYSENVLCFTNNIPTRDGGTHLAGFRAALT  296 (725)
T ss_pred             CEEEEEEEEECCCCCCEEEEEECCEECCCCCCHHHHHHHHHH
T ss_conf             806999998547766314554214355889818899999999


No 151
>pfam08348 PAS_6 YheO-like PAS domain. This family contains various hypothetical bacterial proteins that are similar to the E. coli protein YheO. Their function is unknown, but are likely to be involved in signalling based on the presence of this PAS domain.
Probab=89.37  E-value=1.4  Score=22.09  Aligned_cols=49  Identities=14%  Similarity=0.222  Sum_probs=39.5

Q ss_pred             EEEEEEEEECCCCCEEEEEEEEEEEEECCCEE-EEEEEEECCCHHHHHHHHH
Q ss_conf             48999998869898899889999998379606-9999984461799999999
Q gi|254780903|r  327 QLDQIFHMRHASGADIWIQVRAQMMRTISGGM-NIIGIAMDLTEKYHLEKRY  377 (766)
Q Consensus       327 ~~~~e~Ri~~~DG~~~Wi~~r~~~i~d~~G~~-~~iGi~~DITErK~ae~~l  377 (766)
                      .+-.-|..+.+||+  -+++...+++|++|++ +++++..|||.-..+.+-|
T Consensus        67 ~~~~~Y~~~~~dGr--~lkSsT~~ird~~g~~iG~LCIN~Dis~~~~~~~~L  116 (118)
T pfam08348        67 DVLGNYETRTADGR--LLKSSTIVIRDSDGKPIGMLCINLDVSVFDGAQQFL  116 (118)
T ss_pred             CCCCCCEEECCCCC--EEEEEEEEEECCCCCEEEEEEEEECCHHHHHHHHHH
T ss_conf             72526402779998--999999999999999999999865508999999986


No 152
>COG0187 GyrB Type IIA topoisomerase (DNA gyrase/topo II, topoisomerase IV), B subunit [DNA replication, recombination, and repair]
Probab=88.15  E-value=0.086  Score=30.84  Aligned_cols=37  Identities=16%  Similarity=0.142  Sum_probs=22.4

Q ss_pred             EEEEEEEEECCCCCEEEEEEEEEEEEECCCEEEEEEE
Q ss_conf             4899999886989889988999999837960699999
Q gi|254780903|r  327 QLDQIFHMRHASGADIWIQVRAQMMRTISGGMNIIGI  363 (766)
Q Consensus       327 ~~~~e~Ri~~~DG~~~Wi~~r~~~i~d~~G~~~~iGi  363 (766)
                      ....|+-+.+-||.---+.+.+.-+...+|++|..|.
T Consensus       252 ~~~vEvA~q~~d~~~e~~~SFvNnI~T~eGGTH~~Gf  288 (635)
T COG0187         252 GIAVEVALQWNDGYSENILSFVNNIPTREGGTHEAGF  288 (635)
T ss_pred             CEEEEEEEEEECCCCEEEEEEECCCCCCCCCHHHHHH
T ss_conf             6379999998068844799864585589986089999


No 153
>COG2461 Uncharacterized conserved protein [Function unknown]
Probab=86.05  E-value=0.92  Score=23.44  Aligned_cols=107  Identities=17%  Similarity=0.246  Sum_probs=70.6

Q ss_pred             HHHHHHHHHHHHHHEEEECCCCEEEEECHHHHHHHCCCHHHHCCCCCHHHHCCCHHHHHHHHHHHCCCCCCCEEEEEEEC
Q ss_conf             99999999854455158834996997017898883999789428971788165201378999852112456405899916
Q gi|254780903|r  381 DQRLSKAIECTSEALVLWDKNDRLVMCNANYQKAYGLPDHVLVPGNARSIIQDAQTRPIIEYRTSDPERSQDMSKEIKLA  460 (766)
Q Consensus       381 e~rlr~~ie~~~~~i~~~D~~g~i~~~N~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~  460 (766)
                      -+.+.+++.+.|.-|-.+|.++++.+.++. .++|-.+...+  |.....++|+.....+..-++....+.....+.-..
T Consensus       289 ~~e~naif~~lP~Ditfvdk~diV~ffs~~-~rif~rt~svi--Gr~v~~chpPksv~iv~ki~~~fksG~kd~~efw~~  365 (409)
T COG2461         289 LEELNAIFKHLPVDITFVDKNDIVRFFSGG-ERIFPRTPSVI--GRRVQLCHPPKSVHIVEKILKDFKSGEKDFAEFWIN  365 (409)
T ss_pred             HHHHHHHHHHCCCCEEEECCCCEEEECCCC-CEECCCCHHHH--CCCCCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHCC
T ss_conf             999999995388732785456627844896-32013376761--871557899842789999999865377456777455


Q ss_pred             C-CEEEEECCEECC--CCCEE---EEEEEEEHHHCC
Q ss_conf             9-628742232456--99789---998862010001
Q gi|254780903|r  461 D-SRWLQINEWCTH--DGGTI---SVGTDITLLKHN  490 (766)
Q Consensus       461 d-g~~~~i~~~~~~--dg~~v---~v~~~i~~~~~~  490 (766)
                      . +....++....+  +|.+.   -|..|||+++.-
T Consensus       366 ~~~~~i~i~Y~av~de~ge~~g~le~~qdi~~i~~l  401 (409)
T COG2461         366 MGDKFIHIRYFAVKDEEGEYLGTLEVVQDITRIKEL  401 (409)
T ss_pred             CCCCEEEEEEEEEECCCCCEEEEEHHHHHHHHHHHC
T ss_conf             787358999999875888366542232203777742


No 154
>pfam08670 MEKHLA MEKHLA domain. The MEKHLA domain shares similarity with the PAS domain and is found in the 3' end of plant HD-ZIP III homeobox genes, and bacterial proteins.
Probab=82.98  E-value=2.9  Score=19.81  Aligned_cols=50  Identities=10%  Similarity=0.001  Sum_probs=26.5

Q ss_pred             HHHHHHHHHHHEEEEC--CCCEEEEECHHHHHHHCCCHHHHCCCCCHHHHCCC
Q ss_conf             9999985445515883--49969970178988839997894289717881652
Q gi|254780903|r  384 LSKAIECTSEALVLWD--KNDRLVMCNANYQKAYGLPDHVLVPGNARSIIQDA  434 (766)
Q Consensus       384 lr~~ie~~~~~i~~~D--~~g~i~~~N~~~~~~~g~~~~~~~~~~~~~~~~~~  434 (766)
                      ++.++ +.|.+|+-++  .+-.++|.|.+..++++++-+++....+.....+.
T Consensus        34 ~k~L~-~ap~ail~h~~~~dP~f~yaN~aaL~l~e~~w~el~~lpsr~tae~~   85 (148)
T pfam08670        34 LKALW-HHPDAVLCHSLKADPVFNYANQAALDLLETTWVELQDLPSRKTAEES   85 (148)
T ss_pred             HHHHH-CCCCEEEECCCCCCCEEEEHHHHHHHHHCCCHHHHHCCCHHHHCCHH
T ss_conf             99996-39978997679989746541499999966889998459666516835


No 155
>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=81.14  E-value=0.56  Score=24.99  Aligned_cols=88  Identities=25%  Similarity=0.447  Sum_probs=58.3

Q ss_pred             HHHHHHHHHHCCCCCCEEE-EEEE--------EECCEEEEEEEECCCCCCHHHHHHHCCCEEECCCCCCCCCC--CCCHH
Q ss_conf             9998865653468988899-9999--------97998999999788978977854304650531467556778--87616
Q gi|254780903|r  665 LFPILSNSIKFTNNNGKMM-IRTS--------KIGQCVIITIADTGIGIPKSALEKIGQPFEPLHNQYDQSIG--GFGLG  733 (766)
Q Consensus       665 l~NLi~NAik~t~~~g~I~-i~~~--------~~~~~v~i~V~D~G~GI~~e~~~~iF~pF~q~~~~~t~~~~--GtGLG  733 (766)
                      |+.=|.|=+.-|  |-.|| ++..        ...|-|+++   =|+|=|.+     |+-=.+++....+...  |-=||
T Consensus       536 FVHTLAnY~RqT--GAsVTTlRh~~ae~~fd~~rPDLVVLS---PGPGrP~d-----Fdv~~Ti~aa~ar~lP~FGVCLG  605 (726)
T TIGR01815       536 FVHTLANYLRQT--GASVTTLRHSFAEELFDEERPDLVVLS---PGPGRPKD-----FDVKETIKAALARDLPVFGVCLG  605 (726)
T ss_pred             HHHHHHHHHHHC--CCEEEECCCHHHHHHHHCCCCCEEEEC---CCCCCCCC-----CCHHHHHHHHHHCCCCEEEEHHH
T ss_conf             377778887634--875530430478999732799889868---73123875-----44788999999728985774134


Q ss_pred             HHHHHHHHHHCCCEEEEEEEC--CCCEEEEEECC
Q ss_conf             899999999629869999798--99529999735
Q gi|254780903|r  734 LAISDALTNLHGGRLKIISQE--GKGTIVTICMP  765 (766)
Q Consensus       734 LaI~k~iVe~hgG~I~v~S~~--g~Gttf~i~LP  765 (766)
                      |   +.|||..||.+.+=..|  ||-|.+.|.=|
T Consensus       606 L---Qg~vEafGG~L~vL~~P~HGK~srirVl~p  636 (726)
T TIGR01815       606 L---QGLVEAFGGELDVLAIPVHGKASRIRVLEP  636 (726)
T ss_pred             H---HHHHHHHCCCCCCCCCCCCCCCCEEEEECC
T ss_conf             6---899987467213578887886336888368


No 156
>KOG0355 consensus
Probab=80.64  E-value=2.4  Score=20.36  Aligned_cols=83  Identities=11%  Similarity=0.223  Sum_probs=41.3

Q ss_pred             HHHHHHHHHHHHHHH-------HCCCCC-CEEE-EEEEEECCEEEEEEEECCCCCCHHHHHHHCCCEEECCCCCCCCCC-
Q ss_conf             999999999886565-------346898-8899-999997998999999788978977854304650531467556778-
Q gi|254780903|r  659 RIIKKILFPILSNSI-------KFTNNN-GKMM-IRTSKIGQCVIITIADTGIGIPKSALEKIGQPFEPLHNQYDQSIG-  728 (766)
Q Consensus       659 ~~l~QVl~NLi~NAi-------k~t~~~-g~I~-i~~~~~~~~v~i~V~D~G~GI~~e~~~~iF~pF~q~~~~~t~~~~-  728 (766)
                      .-|.+-+.||-.|-+       +|+... ..++ +--...++.+....-|.|--|+|+..+-|  |-.=+.    ..+| 
T Consensus       712 ~sl~~ti~~l~q~~~gkdaa~~ryi~t~l~~~tr~~f~~~dd~ll~~~~~~~~~vep~y~pi~--p~vlvn----gaegi  785 (842)
T KOG0355         712 QSLMSTIVNLAQDFVGKDAASARYIFTKLSPLTRLLFPPADDLLLKYLNEDGQRVEPEYCPII--PMVLVN----GAEGI  785 (842)
T ss_pred             HHHHHHHHHHHHHHCCCCCHHHHHHHHHCCHHHHHCCCCCCHHHHHHHCCCCCCCCCCCCCCE--EEEEEE----CCCCC
T ss_conf             769999998887505884023678988527365402788832676652257867175224414--688850----56545


Q ss_pred             CCCHHHH--------HHHHHHHHCCCE
Q ss_conf             8761689--------999999962986
Q gi|254780903|r  729 GFGLGLA--------ISDALTNLHGGR  747 (766)
Q Consensus       729 GtGLGLa--------I~k~iVe~hgG~  747 (766)
                      |||---.        |++.+=.+..|.
T Consensus       786 GtGws~~i~n~n~~~iv~~~r~~~~~~  812 (842)
T KOG0355         786 GTGWSTFIPNYNPREIVKNIRRLINGE  812 (842)
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHCCC
T ss_conf             567656688889899999998863699


No 157
>TIGR02373 photo_yellow photoactive yellow protein; InterPro: IPR012130   Members of this family are photoactive yellow protein, a cytosolic, 14-kDa light-sensing protein which has a 4-hydroxycinnamyl (p-coumaric acid) chromophore covalently linked to a Cys residue. The enzyme 4-coumarate--CoA ligase as described by IPR012743 from INTERPRO is required for its biosynthesis. The modified Cys is in a PAS domain, frequently found in signal transducing proteins. Members are known in alpha and gamma Proteobacteria that include Rhodobacter capsulatus, Halorhodospira halophila, Rhodospirillum centenum, etc.; GO: 0009881 photoreceptor activity, 0007602 phototransduction, 0018298 protein-chromophore linkage.
Probab=80.45  E-value=1.8  Score=21.36  Aligned_cols=56  Identities=13%  Similarity=0.112  Sum_probs=48.1

Q ss_pred             HHHHHHHHHEEEECCCCEEEEECHHHHHHHCCCHHHHCCCCCHHHHCCCHHHHHHH
Q ss_conf             99985445515883499699701789888399978942897178816520137899
Q gi|254780903|r  386 KAIECTSEALVLWDKNDRLVMCNANYQKAYGLPDHVLVPGNARSIIQDAQTRPIIE  441 (766)
Q Consensus       386 ~~ie~~~~~i~~~D~~g~i~~~N~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~  441 (766)
                      +-+|++|-|-+.+|..|+|...|.+-.++.|-.++.++++..+..+.|.-..+...
T Consensus        22 A~~d~LpfGAiqlD~~G~I~~YN~aEg~l~GR~P~~VIGrnFF~evAPCt~~~~F~   77 (126)
T TIGR02373        22 AQLDSLPFGAIQLDGSGRILKYNAAEGELTGRDPERVIGRNFFKEVAPCTDIPEFS   77 (126)
T ss_pred             CCCCCCCCCEEEECCCCCHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
T ss_conf             64225541048866988302110110001387977322743423327888884432


No 158
>PRK11388 DNA-binding transcriptional regulator DhaR; Provisional
Probab=80.13  E-value=3.6  Score=19.12  Aligned_cols=60  Identities=13%  Similarity=0.117  Sum_probs=40.9

Q ss_pred             HHHHHHHHHHHHHHHHHH---HHHHHHHCCCCCEEEEECCCCEEEECHHHHHHCCCCHHHCCC
Q ss_conf             899999999999999999---999997225974598976897899978899772999433058
Q gi|254780903|r  238 RQAKKNKENDTILLEANI---CVETALSRGRCGLWNFNFDNKKFHLSRSMYEIMGIPYENKTL  297 (766)
Q Consensus       238 ~dit~~r~ae~~l~ese~---rl~~al~~a~~GiWd~D~~~~~i~ws~~~~~llG~~~~e~~~  297 (766)
                      ++|..+-..+....+...   .+...++....|+.-||.++..+..|+...++||.++.....
T Consensus       183 ~~Ie~~L~~~~~~~~~~~~l~~~~~~l~~~~~gvla~d~~G~i~~~N~~A~~~L~~~~~~~~g  245 (639)
T PRK11388        183 REVGNLLLTDSLLAESNRHLNQLNALLESMDDGVIAWDEQGNLQFLNAQAARLLRLDATASQG  245 (639)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCEEEECCCCCEEHHHHHHHHHHCCCHHHHCC
T ss_conf             999999999999999999987768886488762899889991740048999885988456447


No 159
>KOG0859 consensus
Probab=78.26  E-value=3.7  Score=19.03  Aligned_cols=12  Identities=17%  Similarity=0.448  Sum_probs=5.6

Q ss_pred             HHHHHHHHHHHH
Q ss_conf             999997776778
Q gi|254780903|r  594 HLLNMINNILEM  605 (766)
Q Consensus       594 ~l~~lI~diLd~  605 (766)
                      -|.+-|+.+||=
T Consensus       140 vM~eNIekvldR  151 (217)
T KOG0859         140 VMMENIEKVLDR  151 (217)
T ss_pred             HHHHHHHHHHHC
T ss_conf             999979999824


No 160
>PRK03124 S-adenosylmethionine decarboxylase proenzyme; Provisional
Probab=76.39  E-value=4.6  Score=18.37  Aligned_cols=83  Identities=10%  Similarity=0.015  Sum_probs=56.1

Q ss_pred             EEEEEEC-CCCEEEECHHHHHHHHHHHHHHH---------HHCCCCC---------CEEEEEEEEECCEEEEEEEECCCC
Q ss_conf             8999808-99789986899999999988656---------5346898---------889999999799899999978897
Q gi|254780903|r  643 KIEKKIP-SELFFNADKRIIKKILFPILSNS---------IKFTNNN---------GKMMIRTSKIGQCVIITIADTGIG  703 (766)
Q Consensus       643 ~l~~~~~-~~l~v~~D~~~l~QVl~NLi~NA---------ik~t~~~---------g~I~i~~~~~~~~v~i~V~D~G~G  703 (766)
                      .+..++- .+..+..|...+++++...+..+         -||.|.|         ++|+|.+..+.+++.+-|==-|..
T Consensus         7 Hli~Dl~gc~~~~L~d~~~l~~~l~~a~~~~gatil~~~~h~F~P~GvT~v~lLaESHisiHTwPE~g~aavDiftCg~~   86 (127)
T PRK03124          7 HVIAELYGCDFDKLNDMEFIEDIMVDAALKAGAEVREVAFHKFAPQGVSGVVVISESHLTIHTWPEHGYAAVDVFTCGDR   86 (127)
T ss_pred             EEEEEEECCCHHHCCCHHHHHHHHHHHHHHCCCEEEEEEEEECCCCCEEEEEEEECCEEEEEECCCCCEEEEEEEECCCC
T ss_conf             99999988783668799999999999999849979878838659996899999402168999667688599999945999


Q ss_pred             CCHHHHHHHCCCEEECCCCCCC
Q ss_conf             8977854304650531467556
Q gi|254780903|r  704 IPKSALEKIGQPFEPLHNQYDQ  725 (766)
Q Consensus       704 I~~e~~~~iF~pF~q~~~~~t~  725 (766)
                      +.|+..-+....+++.+...++
T Consensus        87 ~~P~~a~~~L~~~lk~~~~~~~  108 (127)
T PRK03124         87 VDPWDAANYIAEGLNAKTREAI  108 (127)
T ss_pred             CCHHHHHHHHHHHHCCCCEEEE
T ss_conf             9999999999998598927999


No 161
>KOG1229 consensus
Probab=74.40  E-value=1.5  Score=21.79  Aligned_cols=35  Identities=14%  Similarity=0.202  Sum_probs=16.3

Q ss_pred             EEEEECCCCCEEEECCCHHHHCCCCHHHHCCCCHH
Q ss_conf             89999699808997142055519978896076104
Q gi|254780903|r  130 FILLAQPNELVFASSTKNSHYIGKKIGEIIPELSR  164 (766)
Q Consensus       130 ~i~i~d~~g~i~~~n~~~~~~~G~~~~~~~~~~~~  164 (766)
                      +|-+.|.+..|.|+||+++.+.|+.-.+++|+...
T Consensus       169 AiEI~~ddhViQYVNpAfE~mmG~hkgEliGke~a  203 (775)
T KOG1229         169 AIEICDDDHVIQYVNPAFENMMGCHKGELIGKEEA  203 (775)
T ss_pred             HHEECCCHHHHHHHCHHHHHHHCCHHHHHCCCCHH
T ss_conf             32004634689873578886331010212377222


No 162
>PRK09966 hypothetical protein; Provisional
Probab=69.40  E-value=6.6  Score=17.24  Aligned_cols=66  Identities=11%  Similarity=0.037  Sum_probs=40.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEEEEECCCCCEEEECC
Q ss_conf             768889998999999999999850100112235548999999999885310178978999969980899714
Q gi|254780903|r   74 RYAQQEKMTNQTSLMLTEAIEIIFQNNNIKFDLASQKKAESMLGQLLAKTRFLSESFILLAQPNELVFASST  145 (766)
Q Consensus        74 ~~~~~~~~~~~~~~lla~~~~~~~~~~~~~~d~~~~~~ae~~L~~~~~~~~~~~~~~i~i~d~~g~i~~~n~  145 (766)
                      ..-..+.-+++.+.++|..++.-.....+-.|...   ++..|...-...   .-..+.|.|++|++++.-+
T Consensus        40 ~~~~l~~ya~~nl~l~A~tls~~~eaAlvF~D~~a---A~e~L~~l~~~~---~v~~a~V~d~~g~~~A~w~  105 (407)
T PRK09966         40 SVLTLKQYAQKNLALTAATMTYSLEAAVVFADGPA---ATETLAALGQQG---QFSTAEVRDKQQNILASWH  105 (407)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHCCCHHHCCCCHHH---HHHHHHHHHCCC---CEEEEEEECCCCCEEEECC
T ss_conf             99999999997899999987630202501288999---999999854677---7679999989999888712


No 163
>pfam05127 DUF699 Putative ATPase (DUF699). This putative domain is about 350 amino acid residues long and appears to have a P-loop motif, suggesting this is an ATPase. This domain is often associated with pfam00583. This domain is found in isolation in the uncharacterized protein HI1254 from Haemophilus influenzae.
Probab=69.22  E-value=4  Score=18.82  Aligned_cols=44  Identities=18%  Similarity=0.329  Sum_probs=35.6

Q ss_pred             EEEEEEECCCCCCHHHHHHHCCCEEE-CCCCCCCCCCCCCHHHHH
Q ss_conf             99999978897897785430465053-146755677887616899
Q gi|254780903|r  693 VIITIADTGIGIPKSALEKIGQPFEP-LHNQYDQSIGGFGLGLAI  736 (766)
Q Consensus       693 v~i~V~D~G~GI~~e~~~~iF~pF~q-~~~~~t~~~~GtGLGLaI  736 (766)
                      .-+-|-|--.+||...+.++.+.|.+ +=++|..+|+|||=|+++
T Consensus        76 ~DllvVDEAAaIP~p~L~~ll~~~~rvvfaTTihGYEGtGRgF~l  120 (160)
T pfam05127        76 ADLLVVDEAAAIPLPLLKQLLEGFPRVVFATTVHGYEGTGRGFSL  120 (160)
T ss_pred             CCEEEEEHHHCCCHHHHHHHHHHCCEEEEEEECCCCCCCCHHHHH
T ss_conf             768997324218889999998508869999633651145812456


No 164
>COG0093 RplN Ribosomal protein L14 [Translation, ribosomal structure and biogenesis]
Probab=66.66  E-value=6.7  Score=17.18  Aligned_cols=30  Identities=23%  Similarity=0.339  Sum_probs=25.3

Q ss_pred             EEECCCCCEEEEEEEEEEEEECCCEE---EEEE
Q ss_conf             98869898899889999998379606---9999
Q gi|254780903|r  333 HMRHASGADIWIQVRAQMMRTISGGM---NIIG  362 (766)
Q Consensus       333 Ri~~~DG~~~Wi~~r~~~i~d~~G~~---~~iG  362 (766)
                      .++++||+++-+...+-++-+++|.|   +..|
T Consensus        68 ~~rR~DGs~i~FddNA~Viin~~g~PrGtrI~G  100 (122)
T COG0093          68 EVRRPDGSYIKFDDNAAVIINPDGEPRGTRIFG  100 (122)
T ss_pred             CEECCCCCEEEECCCEEEEECCCCCCCCCEEEC
T ss_conf             508699888986785599989999855335856


No 165
>TIGR01622 SF-CC1 splicing factor, CC1-like family; InterPro: IPR006509   These sequences represent a subfamily of RNA splicing factors including the Pad-1 protein (Neurospora crassa), CAPER (mouse) and CC1.3 (human). All are characterised by an N-terminal arginine-rich, low complexity domain followed by three (or in the case of 4 human paralogs, two) RNA recognition domains. These splicing factors are closely related to the U2AF splicing factor family (IPR006529 from INTERPRO). ; GO: 0003723 RNA binding, 0006397 mRNA processing, 0005634 nucleus.
Probab=64.79  E-value=8  Score=16.62  Aligned_cols=26  Identities=4%  Similarity=-0.078  Sum_probs=12.9

Q ss_pred             CCCCEEEECCCHHHHCCCCHHHHCCC
Q ss_conf             99808997142055519978896076
Q gi|254780903|r  136 PNELVFASSTKNSHYIGKKIGEIIPE  161 (766)
Q Consensus       136 ~~g~i~~~n~~~~~~~G~~~~~~~~~  161 (766)
                      +|.+-+++.+-...+--+.+.|++.+
T Consensus       126 RD~rTVf~~qL~~k~~~Rd~~EFFs~  151 (531)
T TIGR01622       126 RDARTVFVLQLALKARERDLYEFFSK  151 (531)
T ss_pred             HCCHHHHHHHHHHCCCCCCHHHHHHH
T ss_conf             01133444503112773311232442


No 166
>PRK02770 S-adenosylmethionine decarboxylase proenzyme; Provisional
Probab=64.79  E-value=8  Score=16.62  Aligned_cols=81  Identities=7%  Similarity=-0.051  Sum_probs=54.4

Q ss_pred             CCEEEEEEC-CCCEEEECHHHHHHHHHHHHHHH---------HHCCCCC---------CEEEEEEEEECCEEEEEEEECC
Q ss_conf             958999808-99789986899999999988656---------5346898---------8899999997998999999788
Q gi|254780903|r  641 NIKIEKKIP-SELFFNADKRIIKKILFPILSNS---------IKFTNNN---------GKMMIRTSKIGQCVIITIADTG  701 (766)
Q Consensus       641 ~i~l~~~~~-~~l~v~~D~~~l~QVl~NLi~NA---------ik~t~~~---------g~I~i~~~~~~~~v~i~V~D~G  701 (766)
                      |-.+..++- .+..+..|...|++++...+.-+         -||.|.|         ++|.|.++.+.+++.+-|==-|
T Consensus        18 G~Hli~Dlygc~~~~L~d~~~l~~~l~~a~~~~g~til~~~~hkF~P~GvT~v~lLaESHiSiHTWPE~gyaavDiftCG   97 (139)
T PRK02770         18 GKHCILELYDCDAEKLNDEAFLRTTLTEAAKRAGATLLNLITHRFEPQGVTALALLAESHISIHTWPESGYAAVDVFTCG   97 (139)
T ss_pred             CCEEEEEEECCCHHHCCCHHHHHHHHHHHHHHCCCEEEEEEEEEECCCCEEEEEEECCCEEEEEECCCCCEEEEEEEECC
T ss_conf             67999999877924477999999999999998799798889998079968999993042789996676884999998059


Q ss_pred             CCCCHHHHHHHCCCEEECCC
Q ss_conf             97897785430465053146
Q gi|254780903|r  702 IGIPKSALEKIGQPFEPLHN  721 (766)
Q Consensus       702 ~GI~~e~~~~iF~pF~q~~~  721 (766)
                      -+..|+..-+.....+..+.
T Consensus        98 ~~~~P~~a~~~L~~~l~~~~  117 (139)
T PRK02770         98 DHTMPEKACQYLIEELMAKR  117 (139)
T ss_pred             CCCCHHHHHHHHHHHHCCCE
T ss_conf             99999999999999859882


No 167
>TIGR02865 spore_II_E stage II sporulation protein E; InterPro: IPR014221   This entry contains the stage II sporulation protein E (SpoIIE), which is a multiple membrane spanning protein with two separable functions. It plays a role in the switch to polar cell division during sporulation and it has phosphatase activity, located in the C-terminal region, which is required to activate sigma-F. All members of this entry are found in endospore-forming Gram-positive bacteria. A homologous protein, not a member of this entry, is found in the Cyanobacterium-like (and presumably non-spore-forming) photosynthesizer Heliobacillus mobilis..
Probab=64.47  E-value=8.2  Score=16.58  Aligned_cols=122  Identities=17%  Similarity=0.253  Sum_probs=65.0

Q ss_pred             HHHHHHHHHHHHHHHCCCCCCCEEEECHHHHHHHHHHHHHHHHHH--CCCEEEEEECCCCEEEECHHHHHHHHHHHHHHH
Q ss_conf             999977767788874198301203316999999999999999984--795899980899789986899999999988656
Q gi|254780903|r  595 LLNMINNILEMSKIETEKISIDKQNADLIPIINEGIRLIGSSAQS--KNIKIEKKIPSELFFNADKRIIKKILFPILSNS  672 (766)
Q Consensus       595 l~~lI~diLd~srieag~~~~~~~~~dl~~~i~~~~~~~~~~~~~--k~i~l~~~~~~~l~v~~D~~~l~QVl~NLi~NA  672 (766)
                      +.+.+++++++-++   ...+.++--+-++++.+-+..+....++  |.|.-+        +.=+...=+||+.-|=-|-
T Consensus       435 l~~~~~~~~~~y~~---~~~w~~rl~e~r~l~a~Ql~gv~~~~~~~~~ei~~~--------~~f~~~~E~~I~~~L~k~g  503 (794)
T TIGR02865       435 LVKTTEEILNNYKI---NEMWRKRLEEGRELVAEQLKGVAESVEDIAKEINKE--------ISFNQLLEEKIIRALNKNG  503 (794)
T ss_pred             HHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--------HHCCHHHHHHHHHHHHHCC
T ss_conf             99999999876888---899999988989999999751999999999986301--------2201667999999984438


Q ss_pred             HHCC------CCCCEEEEEEEEECC------------------EEEEEEEECCCCCCHH-HHHHHCCCEEECCCCCCCCC
Q ss_conf             5346------898889999999799------------------8999999788978977-85430465053146755677
Q gi|254780903|r  673 IKFT------NNNGKMMIRTSKIGQ------------------CVIITIADTGIGIPKS-ALEKIGQPFEPLHNQYDQSI  727 (766)
Q Consensus       673 ik~t------~~~g~I~i~~~~~~~------------------~v~i~V~D~G~GI~~e-~~~~iF~pF~q~~~~~t~~~  727 (766)
                      |++.      .++|++.|+......                  .=.+.|+|..|||.++ ...++  -|.     .|+++
T Consensus       504 I~~~~v~~y~~~~g~~~v~~~~~~c~g~~~~~k~I~p~i~~~~g~~~~v~~~~c~~~~~ng~C~~--~F~-----~~~~y  576 (794)
T TIGR02865       504 IEVEDVLIYNTEGGRIIVELTIAACGGKGECEKKIAPIISEVTGELMVVKDERCSIDPKNGRCHL--TFE-----ETPKY  576 (794)
T ss_pred             CCEEEEEEEECCCCCEEEEEEECCCCCCCCCCCCCCCHHHHHCCCEEEEECCCCCCCCCCCEEEE--ECC-----CCCCH
T ss_conf             90557988875998258998733788987651025413245114345652233586899871367--505-----78023


Q ss_pred             C-CCCHHH
Q ss_conf             8-876168
Q gi|254780903|r  728 G-GFGLGL  734 (766)
Q Consensus       728 ~-GtGLGL  734 (766)
                      . -||.|-
T Consensus       577 ~v~t~~~~  584 (794)
T TIGR02865       577 HVSTGVAK  584 (794)
T ss_pred             HHHHHHHH
T ss_conf             65556553


No 168
>PRK01706 S-adenosylmethionine decarboxylase proenzyme; Validated
Probab=56.46  E-value=11  Score=15.63  Aligned_cols=75  Identities=13%  Similarity=0.099  Sum_probs=50.5

Q ss_pred             EEEEEECC-CCEEEECHHHHHHHHHHHHHHH---------HHCCCCC---------CEEEEEEEEECCEEEEEEEECCCC
Q ss_conf             89998089-9789986899999999988656---------5346898---------889999999799899999978897
Q gi|254780903|r  643 KIEKKIPS-ELFFNADKRIIKKILFPILSNS---------IKFTNNN---------GKMMIRTSKIGQCVIITIADTGIG  703 (766)
Q Consensus       643 ~l~~~~~~-~l~v~~D~~~l~QVl~NLi~NA---------ik~t~~~---------g~I~i~~~~~~~~v~i~V~D~G~G  703 (766)
                      .+..++-. +.....|...|++++.+.+.-+         -||.|.|         ++|.|.+..+.+++.+-|==-|-.
T Consensus         9 Hli~Dl~gc~~~~L~d~~~l~~~l~~a~~~~~~tvl~~~~h~F~p~GvT~v~lLaESHiSiHTwPE~g~aaiDiFTCG~~   88 (123)
T PRK01706          9 HIIVDLWGVDFSLLDDMYFLEHHLVHAADLSGAHVLNVSTKEFDPHGVTVLVLLSESHLSIHTYPEKNFAAIDCYTCGTT   88 (123)
T ss_pred             EEEEEEECCCHHHCCCHHHHHHHHHHHHHHCCCEEEEEEEEECCCCCEEEEEEEECCEEEEEECCCCCEEEEEEECCCCC
T ss_conf             99999988783467699999999999999869989977738779998899999750268999756588799999857998


Q ss_pred             CCHHHH-HHHCCCEE
Q ss_conf             897785-43046505
Q gi|254780903|r  704 IPKSAL-EKIGQPFE  717 (766)
Q Consensus       704 I~~e~~-~~iF~pF~  717 (766)
                      ++|+.. +.|-+.|.
T Consensus        89 ~~p~~a~~~L~~~l~  103 (123)
T PRK01706         89 VEPQIAIDYIVSILK  103 (123)
T ss_pred             CCHHHHHHHHHHHHC
T ss_conf             999999999999749


No 169
>TIGR02470 sucr_synth sucrose synthase; InterPro: IPR012820    This entry represents sucrose synthase an enzyme that despite its name, generally uses rather produces sucrose. Sucrose plus UDP (or ADP) becomes D-fructose plus UDP-glucose (or ADP-glucose), which is then available for cell wall (or starch) biosynthesis. The enzyme is homologous to sucrose phosphate synthase, which catalyses the penultimate step in sucrose synthesis. Sucrose synthase is found, so far, exclusively in plants and cyanobacteria.; GO: 0016157 sucrose synthase activity.
Probab=56.30  E-value=11  Score=15.66  Aligned_cols=88  Identities=22%  Similarity=0.319  Sum_probs=53.5

Q ss_pred             EEECHHHHHHH--HHHHHHHHHHCCCCCCEEE-EEEEE---ECCEEEEEEEECCCCCCHHHHHHHCCCEEECCCCCCCCC
Q ss_conf             99868999999--9998865653468988899-99999---799899999978897897785430465053146755677
Q gi|254780903|r  654 FNADKRIIKKI--LFPILSNSIKFTNNNGKMM-IRTSK---IGQCVIITIADTGIGIPKSALEKIGQPFEPLHNQYDQSI  727 (766)
Q Consensus       654 v~~D~~~l~QV--l~NLi~NAik~t~~~g~I~-i~~~~---~~~~v~i~V~D~G~GI~~e~~~~iF~pF~q~~~~~t~~~  727 (766)
                      =--|+....+|  +-|||.   +|.= +|+|+ |+++.   ..+.+.=.|+|+ -||  =.++-+||.|=     .| =.
T Consensus       601 ~S~DrEE~~Ei~kmh~lid---~Y~L-~G~iRWi~~q~~~~~~GElYR~IAD~-~Gi--FVQPA~yEAFG-----LT-v~  667 (790)
T TIGR02470       601 ESKDREEQAEIEKMHNLID---QYQL-HGQIRWIGAQLNRVRNGELYRYIADT-KGI--FVQPALYEAFG-----LT-VV  667 (790)
T ss_pred             CCCCHHHHHHHHHHHHHHH---HHCC-CCCEEEEEECCCCCCCCEEEEEEECC-CCC--EECCCHHHHHH-----HH-HH
T ss_conf             4678789999999999888---6466-97167700006853146467644257-750--33330444532-----57-99


Q ss_pred             CCCCHHHHHHHHHHHHCCCEEEEEEECCCC
Q ss_conf             887616899999999629869999798995
Q gi|254780903|r  728 GGFGLGLAISDALTNLHGGRLKIISQEGKG  757 (766)
Q Consensus       728 ~GtGLGLaI~k~iVe~hgG~I~v~S~~g~G  757 (766)
                      +-.==||   =.+...|||-.+|--.--.|
T Consensus       668 EAM~cGL---PTFAT~~GGP~EII~dgvsG  694 (790)
T TIGR02470       668 EAMTCGL---PTFATRFGGPLEIIQDGVSG  694 (790)
T ss_pred             HHHHCCC---HHHHHHCCCCEEEEEECCCC
T ss_conf             9863011---24676268963687728835


No 170
>PRK00529 elongation factor P; Validated
Probab=56.11  E-value=11  Score=15.59  Aligned_cols=58  Identities=16%  Similarity=0.315  Sum_probs=33.8

Q ss_pred             CCCEEEECHHHHHHHHHH--HHHHHHHCCCCCCEEEEEEEE-------ECCEEEEEEEECCCCCCHH
Q ss_conf             997899868999999999--886565346898889999999-------7998999999788978977
Q gi|254780903|r  650 SELFFNADKRIIKKILFP--ILSNSIKFTNNNGKMMIRTSK-------IGQCVIITIADTGIGIPKS  707 (766)
Q Consensus       650 ~~l~v~~D~~~l~QVl~N--Li~NAik~t~~~g~I~i~~~~-------~~~~v~i~V~D~G~GI~~e  707 (766)
                      .+..+..|..-..|+-++  +++++.+|.-+|-.+.|....       .+..|.+.|.++-+|+--+
T Consensus        77 g~~~~FMd~etyEQi~l~~~~ig~~~~~L~e~~~v~v~~~~~~~i~v~lP~~V~l~V~et~p~vKGd  143 (186)
T PRK00529         77 GEMYVFMDTETYEQIEVPAEQVGDAAKFLKEGMEVTVTFYNGEPISVELPNTVELEVTETEPGVKGD  143 (186)
T ss_pred             CCCEEEECCCCCCCEECCHHHHHHHHHHHCCCCEEEEEEECCEEEEEECCCEEEEEEEECCCCCCCC
T ss_conf             9953997699741143478897778874237978999998999985558985999999889964444


No 171
>pfam07568 HisKA_2 Histidine kinase. This is the dimerization and phosphoacceptor domain of a sub-family of histidine kinases. It shares sequence similarity with pfam00512 and pfam07536. It is usually found adjacent to a C-terminal ATPase domain (pfam02518). This domain is found in a wide range of Bacteria and also several Archaea.
Probab=55.82  E-value=11  Score=15.56  Aligned_cols=73  Identities=12%  Similarity=0.062  Sum_probs=49.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCEEEECHHHHHHHH
Q ss_conf             76752224789999999986034688993899999999999999999997776778887419830120331699999999
Q gi|254780903|r  550 MSHELRTPLNAILGFSEVIKKEIFGELGSVKYYEYAQDIHYSGQHLLNMINNILEMSKIETEKISIDKQNADLIPIINEG  629 (766)
Q Consensus       550 isHelrtPL~aI~g~~ell~~~~~~~~~~e~~~~~l~~I~~~~~~l~~lI~diLd~srieag~~~~~~~~~dl~~~i~~~  629 (766)
                      +.|=.+|-|..|.++..+-.....    ++..++.+..+..-..-+..+=+ .|.        ..-+...+|+.+.+++.
T Consensus         2 v~HRVKNnLq~i~sll~lq~~~~~----~~~~~~~l~~~~~RI~a~a~vH~-~Ly--------~~~~~~~v~~~~yl~~L   68 (76)
T pfam07568         2 IHHRVKNNLQVISSLLRLQARRAK----DEEVKEALRESQNRVLSMALIHE-ELY--------KSEDLDTVDFSEYLEKL   68 (76)
T ss_pred             CHHHHHHHHHHHHHHHHHHHHHCC----CHHHHHHHHHHHHHHHHHHHHHH-HHH--------CCCCCCEECHHHHHHHH
T ss_conf             038898579999999998734259----99999999999999999999999-997--------69997846399999999


Q ss_pred             HHHHHH
Q ss_conf             999999
Q gi|254780903|r  630 IRLIGS  635 (766)
Q Consensus       630 ~~~~~~  635 (766)
                      +..+..
T Consensus        69 ~~~l~~   74 (76)
T pfam07568        69 TENLFS   74 (76)
T ss_pred             HHHHHH
T ss_conf             999997


No 172
>PRK11178 uridine phosphorylase; Provisional
Probab=53.99  E-value=12  Score=15.35  Aligned_cols=11  Identities=18%  Similarity=0.030  Sum_probs=4.5

Q ss_pred             HCCCCHHHHHH
Q ss_conf             08120589999
Q gi|254780903|r  306 IHYDNKKICEI  316 (766)
Q Consensus       306 vHPdDr~~~~~  316 (766)
                      +-|-|-.++..
T Consensus        21 il~GDP~Rv~~   31 (251)
T PRK11178         21 IVPGDPERVEK   31 (251)
T ss_pred             EECCCHHHHHH
T ss_conf             96799899999


No 173
>TIGR02035 D_Ser_am_lyase D-serine ammonia-lyase; InterPro: IPR011780    This family consists of D-serine ammonia-lyases, pyridoxal-phosphate enzymes that convert D-serine to pyruvate and NH3. These enzyme are also called D-serine dehydratase and D-serine deaminase and was previously designated 4.2.1.14 from EC. It is homologous to an enzyme that acts on threonine and may itself act weakly on threonine.; GO: 0008721 D-serine ammonia-lyase activity, 0030170 pyridoxal phosphate binding, 0046416 D-amino acid metabolic process.
Probab=53.15  E-value=4.8  Score=18.25  Aligned_cols=26  Identities=12%  Similarity=0.091  Sum_probs=14.2

Q ss_pred             CHHHHHHHHHHHHHHHHHHHHHHHHC
Q ss_conf             01122355489999999998853101
Q gi|254780903|r  100 NNIKFDLASQKKAESMLGQLLAKTRF  125 (766)
Q Consensus       100 ~~~~~d~~~~~~ae~~L~~~~~~~~~  125 (766)
                      ..+....++.+.|+++|.++-|-...
T Consensus        32 ~~~~l~~~~~~~A~~RL~RFAP~ia~   57 (431)
T TIGR02035        32 PKVGLKAQEVAEAEARLQRFAPYIAK   57 (431)
T ss_pred             CCCCCHHHHHHHHHHHHHHCCHHHHH
T ss_conf             34783055699999886411005775


No 174
>pfam11212 DUF2999 Protein of unknown function (DUF2999). This family of proteins with unknown function appears to be restricted to Gammaproteobacteria.
Probab=52.19  E-value=13  Score=15.16  Aligned_cols=54  Identities=19%  Similarity=0.332  Sum_probs=30.8

Q ss_pred             HHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHCCCCCC
Q ss_conf             224789999999986034688993899999999999999999997776-7788874198301
Q gi|254780903|r  555 RTPLNAILGFSEVIKKEIFGELGSVKYYEYAQDIHYSGQHLLNMINNI-LEMSKIETEKISI  615 (766)
Q Consensus       555 rtPL~aI~g~~ell~~~~~~~~~~e~~~~~l~~I~~~~~~l~~lI~di-Ld~srieag~~~~  615 (766)
                      .|||.+.--..++      | +..|+.+..+.....+-.-+.+-++.+ |||||+|+.+-++
T Consensus        27 eNP~~AM~~i~qL------G-ip~eKLQ~lm~~VM~nP~LIkeAv~elgLdfskve~Akakl   81 (82)
T pfam11212        27 ENPLMAMATIQQL------G-IPPEKLQQLMMLVMQNPALIKEAVEELGLDFSKVEAAKAKL   81 (82)
T ss_pred             HCHHHHHHHHHHC------C-CCHHHHHHHHHHHHCCHHHHHHHHHHHCCCHHHHHHHHHHC
T ss_conf             2979999999980------8-99999999999997192889999999678789999998753


No 175
>TIGR01067 rplN_bact ribosomal protein L14; InterPro: IPR005745   Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites , . About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits.    Many of ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome , .    Ribosomal protein L14 is one of the proteins from the large ribosomal subunit. In bacteria, L14 is known to bind directly to the 23S rRNA. It belongs to a family of ribosomal proteins which have been grouped on the basis of sequence similarities . L14 is a protein of 119 to 137 amino-acid residues. This family distinguishes bacterial and most organellar examples of ribosomal protein L14 from all archaeal and eukaryotic forms. ; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0015934 large ribosomal subunit.
Probab=49.84  E-value=14  Score=14.91  Aligned_cols=31  Identities=19%  Similarity=0.222  Sum_probs=25.9

Q ss_pred             EEECCCCCEEEEEEEEEEEEECCCEE---EEEEE
Q ss_conf             98869898899889999998379606---99999
Q gi|254780903|r  333 HMRHASGADIWIQVRAQMMRTISGGM---NIIGI  363 (766)
Q Consensus       333 Ri~~~DG~~~Wi~~r~~~i~d~~G~~---~~iGi  363 (766)
                      -++|+||+++-+...+-++-+.++.|   |++|-
T Consensus        74 ~~~R~dG~~i~Fd~NAcVll~~~~~P~GTRifGP  107 (128)
T TIGR01067        74 EVRRKDGSYIRFDDNACVLLNKNKEPRGTRIFGP  107 (128)
T ss_pred             CCCCCCCCEEEECCCEEEEEECCCCCCEEEEEEC
T ss_conf             8388999788818927999816988830178601


No 176
>COG0397 Uncharacterized conserved protein [Function unknown]
Probab=49.03  E-value=14  Score=14.82  Aligned_cols=23  Identities=13%  Similarity=0.120  Sum_probs=15.3

Q ss_pred             CCCCEEEECCCHHHHCCCCHHHH
Q ss_conf             99808997142055519978896
Q gi|254780903|r  136 PNELVFASSTKNSHYIGKKIGEI  158 (766)
Q Consensus       136 ~~g~i~~~n~~~~~~~G~~~~~~  158 (766)
                      ++-+.+..|+.....+|.+...+
T Consensus        31 ~~~~L~~~n~~la~~LgLd~~~~   53 (488)
T COG0397          31 PNPRLRWRNDRLAATLGLDPSLL   53 (488)
T ss_pred             CCCEEEEECHHHHHHCCCCHHHC
T ss_conf             88555432786787629986762


No 177
>TIGR00868 hCaCC calcium-activated chloride channel protein 1; InterPro: IPR004727   This entry represents a family of Ca(2+)-regulated chloride channels (CLCA) which includes bovine, murine and human proteins , . Each CLCA exhibits a distinct, often overlapping, tissue expression pattern. With the exception of the truncated, secreted protein hCLCA3 , they are synthesized as an approximately 125 kDa precursor transmembrane glycoprotein that is rapidly cleaved into 90 and 35 kDa subunits. The human proteins have been shown to affect a large number of cell functions including chloride conductance, epithelial secretion, cell-cell adhesion, apoptosis, cell cycle control, mucus production in asthma, and blood pressure. The CLCA proteins expressed on the luminal surface of lung vascular endothelia (bCLCA2; mCLCA1; hCLCA2) serve as adhesion molecules for lung metastatic cancer cells, mediating vascular arrest and lung colonization. Expression of hCLCA2 in normal mammary epithelium is consistently lost in human breast cancer and in all tumorigenic breast cancer cell lines. Re-expression of hCLCA2 in human breast cancer cells abrogates tumorigenicity in nude mice, implying that hCLCA2 acts as a tumour suppressor in breast cancer..
Probab=44.93  E-value=16  Score=14.39  Aligned_cols=30  Identities=20%  Similarity=0.286  Sum_probs=27.1

Q ss_pred             ECCEEEEEEEECCCCCCHHHHHHHCCCEEE
Q ss_conf             799899999978897897785430465053
Q gi|254780903|r  689 IGQCVIITIADTGIGIPKSALEKIGQPFEP  718 (766)
Q Consensus       689 ~~~~v~i~V~D~G~GI~~e~~~~iF~pF~q  718 (766)
                      .|..+.++.-|||.|=+.-.-|=|+-+||+
T Consensus       646 ~Gh~vtLELlDNGAGAD~~KNDGiYsRYFT  675 (874)
T TIGR00868       646 NGHTVTLELLDNGAGADTVKNDGIYSRYFT  675 (874)
T ss_pred             CCCEEEEEEEECCCCCCCCCCCCCEEEEEE
T ss_conf             997899886417766566005831220120


No 178
>PRK12299 obgE GTPase ObgE; Reviewed
Probab=44.90  E-value=16  Score=14.39  Aligned_cols=12  Identities=8%  Similarity=0.130  Sum_probs=4.5

Q ss_pred             HHHHHHHHHHHH
Q ss_conf             999999999999
Q gi|254780903|r  622 LIPIINEGIRLI  633 (766)
Q Consensus       622 l~~~i~~~~~~~  633 (766)
                      +.+++..+.+.+
T Consensus       315 l~eL~~~i~~~L  326 (334)
T PRK12299        315 LDELLRALWEFL  326 (334)
T ss_pred             HHHHHHHHHHHH
T ss_conf             999999999999


No 179
>KOG1135 consensus
Probab=44.53  E-value=6.1  Score=17.50  Aligned_cols=47  Identities=21%  Similarity=0.312  Sum_probs=25.4

Q ss_pred             EEECHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEEECCEEEEEEEECC-CCCC
Q ss_conf             998689999999998865653468988899999997998999999788-9789
Q gi|254780903|r  654 FNADKRIIKKILFPILSNSIKFTNNNGKMMIRTSKIGQCVIITIADTG-IGIP  705 (766)
Q Consensus       654 v~~D~~~l~QVl~NLi~NAik~t~~~g~I~i~~~~~~~~v~i~V~D~G-~GI~  705 (766)
                      +.+|+ +|.+.=.=|..+.+++-..||-..    ..++.|-++..|+| ++|.
T Consensus       696 ~igd~-rLadfKq~L~~kgi~aEf~ggglL----~~~g~VavRk~d~G~i~ie  743 (764)
T KOG1135         696 LIGDL-RLADFKQLLTEKGIQAEFKGGGLL----VCNGCVAVRKVDTGKITIE  743 (764)
T ss_pred             EECCH-HHHHHHHHHHHCCEEEEEECCCEE----EECCEEEEEECCCCEEEEE
T ss_conf             63670-299999998737837898258489----9788899998079617882


No 180
>PRK13719 conjugal transfer transcriptional regulator TraJ; Provisional
Probab=44.42  E-value=17  Score=14.34  Aligned_cols=41  Identities=12%  Similarity=0.130  Sum_probs=34.5

Q ss_pred             HHHHHHHHHHHHHHHEEEECCCCEEEEECHHHHHHHCCCHH
Q ss_conf             99999999985445515883499699701789888399978
Q gi|254780903|r  380 ADQRLSKAIECTSEALVLWDKNDRLVMCNANYQKAYGLPDH  420 (766)
Q Consensus       380 se~rlr~~ie~~~~~i~~~D~~g~i~~~N~~~~~~~g~~~~  420 (766)
                      -.+.+.+++...|-+.++-+.+|.++.+|.+|.+.|.-...
T Consensus        17 l~~sl~~~i~~~~~PvCIRn~sG~Fi~~N~~F~~~F~~~~~   57 (220)
T PRK13719         17 LLESLTAFIDDYSIPACIRNEDGSFIFFNTLFSKEFLGSLQ   57 (220)
T ss_pred             HHHHHHHHHHCCCCCEEEECCCCCCCCCCHHHHHHHHHCCC
T ss_conf             79999999971899648977899830152789999874113


No 181
>COG1444 Predicted P-loop ATPase fused to an acetyltransferase [General function prediction only]
Probab=44.30  E-value=17  Score=14.32  Aligned_cols=19  Identities=26%  Similarity=0.552  Sum_probs=9.1

Q ss_pred             CEEEEEEEEECCCCC--EEEE
Q ss_conf             848999998869898--8998
Q gi|254780903|r  326 KQLDQIFHMRHASGA--DIWI  344 (766)
Q Consensus       326 ~~~~~e~Ri~~~DG~--~~Wi  344 (766)
                      ..++.+..+|.+-|.  ..|+
T Consensus       383 ~~~~l~ePIRya~gDPiE~wl  403 (758)
T COG1444         383 HELELEEPIRYAPGDPIEKWL  403 (758)
T ss_pred             EEEECCCCCCCCCCCCHHHHH
T ss_conf             998546873168999679999


No 182
>PTZ00054 60S ribosomal protein L23; Provisional
Probab=43.62  E-value=17  Score=14.25  Aligned_cols=32  Identities=25%  Similarity=0.279  Sum_probs=25.4

Q ss_pred             EEEECCCCCEEEEEEEEEEEEECCCEE---EEEEE
Q ss_conf             998869898899889999998379606---99999
Q gi|254780903|r  332 FHMRHASGADIWIQVRAQMMRTISGGM---NIIGI  363 (766)
Q Consensus       332 ~Ri~~~DG~~~Wi~~r~~~i~d~~G~~---~~iGi  363 (766)
                      .-++++||+++-+...+.++-|++|+|   ++.|-
T Consensus        85 k~~rR~DGs~I~FddNA~Viin~~g~pkGTrIfGP  119 (139)
T PTZ00054         85 KAWRRREGYFIYFEDNAGVIVNPKGEMKGSAITGP  119 (139)
T ss_pred             CCEECCCCCEEEECCCEEEEECCCCCEEEEEEECC
T ss_conf             34271899999977876999999998814168371


No 183
>TIGR01634 tail_P2_I phage tail protein I; InterPro: IPR006521   These sequences represent the family of phage P2 protein I and related tail proteins from a number of temperate phage of Gram-negative bacteria..
Probab=43.51  E-value=13  Score=15.06  Aligned_cols=82  Identities=11%  Similarity=0.048  Sum_probs=33.3

Q ss_pred             CHHHHHHHHCCCC--HHHHHHHHHHHHCCCCEEEEEEEEECCCCCEEEEEEEEEEEEECCCEEEEEEEEECCCHHHHHHH
Q ss_conf             9889997608120--58999999997248984899999886989889988999999837960699999844617999999
Q gi|254780903|r  298 SFRAIARLIHYDN--KKICEIARSVTGKHVKQLDQIFHMRHASGADIWIQVRAQMMRTISGGMNIIGIAMDLTEKYHLEK  375 (766)
Q Consensus       298 s~~~~~~~vHPdD--r~~~~~a~~~~~~~~~~~~~e~Ri~~~DG~~~Wi~~r~~~i~d~~G~~~~iGi~~DITErK~ae~  375 (766)
                      |...|.+ --||-  |+....|...-..+|.. ...=|++.+=|..+-|..-=+  .++.|.||-+-+..|+|+.=-.|+
T Consensus        48 SVD~W~~-~Wp~~vKR~~ir~A~~~~~~KGt~-~avR~Vves~G~~v~i~EWWq--~~P~~~pgTF~L~~~l~~~G~~~~  123 (139)
T TIGR01634        48 SVDRWDS-TWPEKVKRDVIRSAYLIQRHKGTV-KAVRRVVESFGGLVDITEWWQ--TEPAGAPGTFELTLTLSGSGGDEE  123 (139)
T ss_pred             CCCCCCC-CCCHHHHHHHHHHHHHHHCCCCCH-HHHHHHHCCCCCEEEEECCCC--CCCCCCCCCEEEEEEECCCCCCHH
T ss_conf             3566456-785324589999999985357861-323333203465011010224--774336964378875227885478


Q ss_pred             HHHHHHHH
Q ss_conf             99999999
Q gi|254780903|r  376 RYAEADQR  383 (766)
Q Consensus       376 ~l~ese~r  383 (766)
                      -..+-+..
T Consensus       124 t~~~~~~l  131 (139)
T TIGR01634       124 TVLEVERL  131 (139)
T ss_pred             HHHHHHHH
T ss_conf             89999998


No 184
>PRK12297 obgE GTPase ObgE; Reviewed
Probab=43.17  E-value=17  Score=14.20  Aligned_cols=12  Identities=8%  Similarity=-0.069  Sum_probs=4.3

Q ss_pred             CCCEEEEECCCC
Q ss_conf             974598976897
Q gi|254780903|r  265 RCGLWNFNFDNK  276 (766)
Q Consensus       265 ~~GiWd~D~~~~  276 (766)
                      |+|.-.+|.+++
T Consensus        90 P~GT~v~d~~~~  101 (429)
T PRK12297         90 PVGTTVKDAETG  101 (429)
T ss_pred             CCCCEEEECCCC
T ss_conf             897678866899


No 185
>TIGR03330 SAM_DCase_Bsu S-adenosylmethionine decarboxylase proenzyme, Bacillus form. Members of this protein family are the single chain precursor of the two chains of the mature S-adenosylmethionine decarboxylase as found in Methanocaldococcus jannaschii, Bacillus subtilis, and a wide range of other species. It differs substantially in architecture from the form as found in Escherichia coli, and lacks any extended homology to the eukaryotic form (TIGR00535).
Probab=42.99  E-value=17  Score=14.19  Aligned_cols=74  Identities=12%  Similarity=-0.009  Sum_probs=49.2

Q ss_pred             EEEEECC-CCEEEECHHHHHHHHHHHHHHH---------HHCCCCC---------CEEEEEEEEECCEEEEEEEECCCCC
Q ss_conf             9998089-9789986899999999988656---------5346898---------8899999997998999999788978
Q gi|254780903|r  644 IEKKIPS-ELFFNADKRIIKKILFPILSNS---------IKFTNNN---------GKMMIRTSKIGQCVIITIADTGIGI  704 (766)
Q Consensus       644 l~~~~~~-~l~v~~D~~~l~QVl~NLi~NA---------ik~t~~~---------g~I~i~~~~~~~~v~i~V~D~G~GI  704 (766)
                      +..++-. +..+..|...+++++.+.+..+         -+|.|.|         ++|.|.+..+.+++.+-|==-|...
T Consensus         7 li~Dl~gc~~~~L~d~~~l~~~l~~a~~~~~~~il~~~~~~f~p~GvT~v~ll~ESHisiHTwPE~g~aaiDiftCg~~~   86 (112)
T TIGR03330         7 LIVDLYGCDPEKLDDVEFIEEILLEAAKVAGATLVASHFHKFSPGGVSGVVLLAESHISIHTWPEYGYAAVDVFTCGDHS   86 (112)
T ss_pred             EEEEEECCCHHHCCCHHHHHHHHHHHHHHCCCEEEEEEEEECCCCCEEEEEEECCCEEEEEECCCCCEEEEEEEECCCCC
T ss_conf             99999777957877999999999999998699799888697499979999993243699998678884999998638999


Q ss_pred             CHHHHHHHCCCEE
Q ss_conf             9778543046505
Q gi|254780903|r  705 PKSALEKIGQPFE  717 (766)
Q Consensus       705 ~~e~~~~iF~pF~  717 (766)
                      .|+..-+....++
T Consensus        87 ~p~~a~~~l~~~f   99 (112)
T TIGR03330        87 DPEKAFEYLVEAL   99 (112)
T ss_pred             CHHHHHHHHHHHH
T ss_conf             9999999999972


No 186
>TIGR02789 nickel_nikB nickel ABC transporter, permease subunit NikB; InterPro: IPR014156   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 consists of the NikB family of nickel ABC transporter permeases. Operons that contain this protein also contain a homologous permease subunit NikC. Nickel is used in cells as part of urease or certain hydrogenases or superoxide dismutases..
Probab=42.53  E-value=15  Score=14.65  Aligned_cols=13  Identities=23%  Similarity=-0.005  Sum_probs=5.6

Q ss_pred             HHHHHHHHHHHHH
Q ss_conf             9999999999854
Q gi|254780903|r  379 EADQRLSKAIECT  391 (766)
Q Consensus       379 ese~rlr~~ie~~  391 (766)
                      ..++-||.++...
T Consensus       223 ~~~H~Lrna~~p~  235 (315)
T TIGR02789       223 IRRHILRNAILPM  235 (315)
T ss_pred             HHHHHCCCCHHHH
T ss_conf             8863241110256


No 187
>PRK13858 type IV secretion system T-DNA border endonuclease VirD1; Provisional
Probab=42.37  E-value=18  Score=14.12  Aligned_cols=73  Identities=26%  Similarity=0.270  Sum_probs=35.8

Q ss_pred             HHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---------HHHCCCCCCCEEEECHHH
Q ss_conf             22247899999999860346889938999999999999999999977767788---------874198301203316999
Q gi|254780903|r  554 LRTPLNAILGFSEVIKKEIFGELGSVKYYEYAQDIHYSGQHLLNMINNILEMS---------KIETEKISIDKQNADLIP  624 (766)
Q Consensus       554 lrtPL~aI~g~~ell~~~~~~~~~~e~~~~~l~~I~~~~~~l~~lI~diLd~s---------rieag~~~~~~~~~dl~~  624 (766)
                      +|--..-|-||.|+=          .+.++.++.|..+.-.+..-||++|.-.         ..++.|..+-++--||..
T Consensus        55 iRvAvRRIgGFlEiD----------A~Tr~~me~i~~sIg~ls~ni~~l~~a~a~~~~~dlea~~aeR~afG~~fa~Ld~  124 (148)
T PRK13858         55 IRVAVRRIGGFLEID----------AKTREKMEAILQSIGTLSSNINALLSAYAENPRPDLEAFRAERIAFGKEFADLDG  124 (148)
T ss_pred             HHHHHHHHHHHHHCC----------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHH
T ss_conf             999999970055412----------9899999999999999988999999998449986389999999999899998899


Q ss_pred             HHHHHHHHHHHH
Q ss_conf             999999999999
Q gi|254780903|r  625 IINEGIRLIGSS  636 (766)
Q Consensus       625 ~i~~~~~~~~~~  636 (766)
                      ++...+..-+.+
T Consensus       125 lLrsilsVSRRR  136 (148)
T PRK13858        125 LLRSILSVSRRR  136 (148)
T ss_pred             HHHHHHHHHHHH
T ss_conf             999999998862


No 188
>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=41.56  E-value=18  Score=14.04  Aligned_cols=36  Identities=28%  Similarity=0.279  Sum_probs=21.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHH
Q ss_conf             9998878999999998767522247899999-99986
Q gi|254780903|r  534 ERAETANKTKSEFLAKMSHELRTPLNAILGF-SEVIK  569 (766)
Q Consensus       534 ~~ae~an~~k~efla~isHelrtPL~aI~g~-~ell~  569 (766)
                      +|-|...+....||+..+.++-=+...+..- .+.|.
T Consensus       310 ER~eDi~~L~rhFL~~a~~~l~~~~k~L~~~~~~~L~  346 (471)
T TIGR01818       310 ERREDIPRLARHFLALAAKELDVEPKLLSPEALEALK  346 (471)
T ss_pred             CHHHHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHH
T ss_conf             2266899999999999887428651134889999997


No 189
>PRK00029 hypothetical protein; Validated
Probab=40.81  E-value=19  Score=13.96  Aligned_cols=23  Identities=13%  Similarity=0.160  Sum_probs=15.5

Q ss_pred             CCCCEEEECCCHHHHCCCCHHHH
Q ss_conf             99808997142055519978896
Q gi|254780903|r  136 PNELVFASSTKNSHYIGKKIGEI  158 (766)
Q Consensus       136 ~~g~i~~~n~~~~~~~G~~~~~~  158 (766)
                      ++-+++..|+.....+|.....+
T Consensus        31 ~~p~l~~~n~~la~~lgl~~~~~   53 (487)
T PRK00029         31 PAPRLRFRNDELAALLGLDPEEL   53 (487)
T ss_pred             CCCEEEEECHHHHHHCCCCHHHC
T ss_conf             99878985899998769880325


No 190
>TIGR02749 prenyl_cyano solanesyl diphosphate synthase; InterPro: IPR014120   This entry contains solanesyl diphosphate synthases from cyanobacteria or plastid-containing eukaryotes. A member from Arabidopsis (where both plastoquinone and ubiquinone contain the C(45) prenyl moiety) was characterised by heterologous expression as a solanesyl diphosphate synthase..
Probab=40.27  E-value=19  Score=13.95  Aligned_cols=25  Identities=16%  Similarity=0.230  Sum_probs=10.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHEEE
Q ss_conf             9999999999999999854455158
Q gi|254780903|r  373 LEKRYAEADQRLSKAIECTSEALVL  397 (766)
Q Consensus       373 ae~~l~ese~rlr~~ie~~~~~i~~  397 (766)
                      .|+=+..|=-+-..++-+++-|..+
T Consensus       166 le~YleKSyYKTASL~AaSskaAAv  190 (325)
T TIGR02749       166 LEDYLEKSYYKTASLVAASSKAAAV  190 (325)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             8876656446789999999899888


No 191
>pfam02675 AdoMet_dc S-adenosylmethionine decarboxylase. This family contains several S-adenosylmethionine decarboxylase proteins from bacterial and archaebacterial species. S-adenosylmethionine decarboxylase (AdoMetDC), a key enzyme in the biosynthesis of spermidine and spermine, is first synthesized as a proenzyme, which is cleaved post translationally to form alpha and beta subunits. The alpha subunit contains a covalently bound pyruvoyl group derived from serine that is essential for activity.
Probab=39.87  E-value=19  Score=13.86  Aligned_cols=66  Identities=12%  Similarity=-0.009  Sum_probs=47.7

Q ss_pred             CEEEECHHHHHHHHHHHHHHH---------HHCCCCC---------CEEEEEEEEECCEEEEEEEECCCCCCHHHHHHHC
Q ss_conf             789986899999999988656---------5346898---------8899999997998999999788978977854304
Q gi|254780903|r  652 LFFNADKRIIKKILFPILSNS---------IKFTNNN---------GKMMIRTSKIGQCVIITIADTGIGIPKSALEKIG  713 (766)
Q Consensus       652 l~v~~D~~~l~QVl~NLi~NA---------ik~t~~~---------g~I~i~~~~~~~~v~i~V~D~G~GI~~e~~~~iF  713 (766)
                      ..+..|...+++++.+++.-+         -+|.|.|         +.|.|.+..+.+++.+-|==-|.++.|+..-+..
T Consensus        11 ~~~L~d~~~i~~~l~~a~~~~~~tvl~~~~~~f~p~Gvt~v~ll~ESHisiHTwPE~g~aaiDiftCg~~~~p~~a~~~l   90 (107)
T pfam02675        11 ADLLNDAERLERILREAAKAAGATLLGIAFHKFEPQGVSGVALLAESHISIHTWPEYGYAAVDVFTCGEHADPWKALEYL   90 (107)
T ss_pred             HHHCCCHHHHHHHHHHHHHHCCCEEEEEEEEECCCCCEEEEEEECCCEEEEEECCCCCCEEEEEECCCCCCCHHHHHHHH
T ss_conf             46787999999999999998799899999897599988999992266389998268893899997178989999999999


Q ss_pred             CCEE
Q ss_conf             6505
Q gi|254780903|r  714 QPFE  717 (766)
Q Consensus       714 ~pF~  717 (766)
                      ..+|
T Consensus        91 ~~~f   94 (107)
T pfam02675        91 KEAL   94 (107)
T ss_pred             HHHH
T ss_conf             9972


No 192
>PRK08383 putative monovalent cation/H+ antiporter subunit E; Reviewed
Probab=39.55  E-value=20  Score=13.82  Aligned_cols=52  Identities=27%  Similarity=0.441  Sum_probs=40.7

Q ss_pred             HHHHHHHHHHCCCCCCEEEEEEEEECCEEEEEEEECCCCCC-HHHHHHHCCCEEE
Q ss_conf             99988656534689888999999979989999997889789-7785430465053
Q gi|254780903|r  665 LFPILSNSIKFTNNNGKMMIRTSKIGQCVIITIADTGIGIP-KSALEKIGQPFEP  718 (766)
Q Consensus       665 l~NLi~NAik~t~~~g~I~i~~~~~~~~v~i~V~D~G~GI~-~e~~~~iF~pF~q  718 (766)
                      -.-++.|.+--||  |++++.+..+++.+.+..-|-..|.. +|..+.|.++|+.
T Consensus       108 ~~t~lansITLTP--GTltvdv~~d~~~lyVH~idv~~~~~~~e~~~~I~~~FEk  160 (167)
T PRK08383        108 QYTILSNSITLTP--GTLTIEACPEEKALYVHWINIPEGLEWPESSEPVSGPFEK  160 (167)
T ss_pred             HHHHHHHHHCCCC--CEEEEEECCCCCEEEEEEEECCCCCCCHHHHHHHHHHHHH
T ss_conf             8999986331689--7799997499987999998789877704568898677999


No 193
>COG3284 AcoR Transcriptional activator of acetoin/glycerol metabolism [Secondary metabolites biosynthesis, transport, and catabolism / Transcription]
Probab=38.64  E-value=20  Score=13.73  Aligned_cols=55  Identities=11%  Similarity=0.102  Sum_probs=33.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHC-------CCCCEEEEECCCCEEEECHHHHHHCCCCH
Q ss_conf             89999999999999999999999722-------59745989768978999788997729994
Q gi|254780903|r  238 RQAKKNKENDTILLEANICVETALSR-------GRCGLWNFNFDNKKFHLSRSMYEIMGIPY  292 (766)
Q Consensus       238 ~dit~~r~ae~~l~ese~rl~~al~~-------a~~GiWd~D~~~~~i~ws~~~~~llG~~~  292 (766)
                      .++.++-+++.-++..+..+..-+..       ...+..-+|.++..+-.|.+.+.+++.+.
T Consensus       198 ~~~ar~IE~~~~~~~~~~~~~lr~~~~p~~~d~~~~~~lavd~~grvl~at~aA~~~La~~~  259 (606)
T COG3284         198 TDAARRIEAELFLAAFEGHWLLRIALAPDYLDSQSEALLAVDQDGRVLGATRAARQLLALTD  259 (606)
T ss_pred             HHHHHHHHHHHHHHHCCCCHHHHHHCCCCCCCCCCCEEEEECCCCHHHHCCHHHHHHHCCCH
T ss_conf             99999999999987537526777761855457665400012576655532288997623446


No 194
>PRK07831 short chain dehydrogenase; Provisional
Probab=38.62  E-value=18  Score=14.14  Aligned_cols=25  Identities=20%  Similarity=0.345  Sum_probs=13.8

Q ss_pred             EEEEEEECCCHHHHHHHHHHHHHHH
Q ss_conf             9999984461799999999999999
Q gi|254780903|r  359 NIIGIAMDLTEKYHLEKRYAEADQR  383 (766)
Q Consensus       359 ~~iGi~~DITErK~ae~~l~ese~r  383 (766)
                      ++.++..|||+....+....+....
T Consensus        69 ~v~~~~~Dvt~~~~v~~~v~~~~~~   93 (261)
T PRK07831         69 RVEGVVCDVTSEAQVDALIDAAVER   93 (261)
T ss_pred             EEEEEECCCCCHHHHHHHHHHHHHH
T ss_conf             2899975689999999999999998


No 195
>COG0536 Obg Predicted GTPase [General function prediction only]
Probab=38.29  E-value=20  Score=13.69  Aligned_cols=16  Identities=13%  Similarity=0.181  Sum_probs=7.3

Q ss_pred             CHHHHHHHHHHHHHHH
Q ss_conf             6999999999999999
Q gi|254780903|r  621 DLIPIINEGIRLIGSS  636 (766)
Q Consensus       621 dl~~~i~~~~~~~~~~  636 (766)
                      .+.+++..+.+++...
T Consensus       320 g~~~L~~~~~~~l~~~  335 (369)
T COG0536         320 GLDELLRALAELLEET  335 (369)
T ss_pred             CHHHHHHHHHHHHHHH
T ss_conf             8799999999999975


No 196
>PRK12298 obgE GTPase ObgE; Reviewed
Probab=36.10  E-value=22  Score=13.45  Aligned_cols=13  Identities=8%  Similarity=0.003  Sum_probs=5.4

Q ss_pred             HHHHHHHHHHHHH
Q ss_conf             9999999999999
Q gi|254780903|r  622 LIPIINEGIRLIG  634 (766)
Q Consensus       622 l~~~i~~~~~~~~  634 (766)
                      +.+++..+.+++.
T Consensus       321 ~~~L~~~i~~~l~  333 (380)
T PRK12298        321 TKELCWDLMTFIE  333 (380)
T ss_pred             HHHHHHHHHHHHH
T ss_conf             9999999999998


No 197
>TIGR00107 deoD purine nucleoside phosphorylase; InterPro: IPR004402 Purine nucleoside phosphorylase 2.4.2.1 from EC also called inosine phosphorylase (pnp) cleave guanosine or inosine to respective bases and sugar-1-phosphate molecules. These enzymes are involved in the salvage of nucleotides and nucleosides.; GO: 0004731 purine-nucleoside phosphorylase activity, 0006139 nucleobase nucleoside nucleotide and nucleic acid metabolic process.
Probab=35.84  E-value=22  Score=13.43  Aligned_cols=61  Identities=15%  Similarity=0.129  Sum_probs=26.3

Q ss_pred             HHHHHHCCCCCEEEEECCCC-EE----EECHHHH-HHCCCC-HHHCCCCHHHHHHHHCCCCHHHHHHHHHHHHCCCCE
Q ss_conf             99997225974598976897-89----9978899-772999-433058988999760812058999999997248984
Q gi|254780903|r  257 VETALSRGRCGLWNFNFDNK-KF----HLSRSMY-EIMGIP-YENKTLSFRAIARLIHYDNKKICEIARSVTGKHVKQ  327 (766)
Q Consensus       257 l~~al~~a~~GiWd~D~~~~-~i----~ws~~~~-~llG~~-~~e~~~s~~~~~~~vHPdDr~~~~~a~~~~~~~~~~  327 (766)
                      .+.+++.|.||-..-++.=+ .+    -|+++-+ ++.|.+ |++....          -|-+.++.|.+.+...+-.
T Consensus        79 V~~iiRiGSCGA~~~~vkl~D~iiA~~A~tdS~~nr~~f~~~P~D~~~~----------Adf~L~~~A~~tAk~~g~~  146 (234)
T TIGR00107        79 VKTIIRIGSCGAIRPDVKLRDVIIAMGASTDSKVNRVRFVEVPEDFAAI----------ADFELVELAYDTAKALGID  146 (234)
T ss_pred             CCEEEEEECCCCCCCCCCEEEEEEECCCCCHHHHHHHHCCCCCCCCCCC----------CCHHHHHHHHHHHHHCCCC
T ss_conf             4457886213011356760688971142322335555056876443347----------8989999999999867972


No 198
>TIGR03673 rpl14p_arch 50S ribosomal protein L14P. Part of the 50S ribosomal subunit. Forms a cluster with proteins L3 and L24e, part of which may contact the 16S rRNA in 2 intersubunit bridges.
Probab=35.41  E-value=23  Score=13.38  Aligned_cols=34  Identities=21%  Similarity=0.223  Sum_probs=26.6

Q ss_pred             EEEECCCCCEEEEEEEEEEEEECCCEE---EEEEEEE
Q ss_conf             998869898899889999998379606---9999984
Q gi|254780903|r  332 FHMRHASGADIWIQVRAQMMRTISGGM---NIIGIAM  365 (766)
Q Consensus       332 ~Ri~~~DG~~~Wi~~r~~~i~d~~G~~---~~iGi~~  365 (766)
                      +.++++||.++-+...+.++-+++|.|   ++.|.+-
T Consensus        77 k~~rR~DGs~i~FddNa~VLin~~g~P~GTRI~GPV~  113 (131)
T TIGR03673        77 KEYRRPDGTRVKFEDNAVVIVTPDGEPKGTEIKGPVA  113 (131)
T ss_pred             CCEECCCCCEEEECCCEEEEECCCCCEEEEEEECCCH
T ss_conf             7669089999981897699998999990617826404


No 199
>PRK03578 hscB co-chaperone HscB; Provisional
Probab=35.12  E-value=14  Score=14.83  Aligned_cols=30  Identities=20%  Similarity=0.494  Sum_probs=17.7

Q ss_pred             ECHHHHHHCCCCHHH------CCCCHHHHHHHHCCC
Q ss_conf             978899772999433------058988999760812
Q gi|254780903|r  280 LSRSMYEIMGIPYEN------KTLSFRAIARLIHYD  309 (766)
Q Consensus       280 ws~~~~~llG~~~~e------~~~s~~~~~~~vHPd  309 (766)
                      .+..++++||+++.=      ....|..+...+|||
T Consensus         4 ~~~nyF~lf~lp~~f~iD~~~L~~~y~~LQ~~~HPD   39 (176)
T PRK03578          4 LKDDHFSLFGLPARFALDEAALDAAYRTVQAQVHPD   39 (176)
T ss_pred             CCCCHHHHCCCCCCCCCCHHHHHHHHHHHHHHHCCC
T ss_conf             665678882999767779999999999999987967


No 200
>COG2200 Rtn c-di-GMP phosphodiesterase class I (EAL domain) [Signal    transduction mechanisms]
Probab=34.80  E-value=23  Score=13.31  Aligned_cols=22  Identities=14%  Similarity=0.132  Sum_probs=7.4

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHH
Q ss_conf             4675567788761689999999
Q gi|254780903|r  720 HNQYDQSIGGFGLGLAISDALT  741 (766)
Q Consensus       720 ~~~~t~~~~GtGLGLaI~k~iV  741 (766)
                      |.++.+......-+..++++||
T Consensus       178 D~~fv~~i~~~~~~~~iv~~iv  199 (256)
T COG2200         178 DRSFVRDLETDARDQAIVRAIV  199 (256)
T ss_pred             CHHHHHHHCCCCHHHHHHHHHH
T ss_conf             6999986303831179999999


No 201
>PRK06841 short chain dehydrogenase; Provisional
Probab=33.98  E-value=24  Score=13.22  Aligned_cols=22  Identities=23%  Similarity=0.326  Sum_probs=11.9

Q ss_pred             EEEECCCHHHHHHHHHHHHHHH
Q ss_conf             9984461799999999999999
Q gi|254780903|r  362 GIAMDLTEKYHLEKRYAEADQR  383 (766)
Q Consensus       362 Gi~~DITErK~ae~~l~ese~r  383 (766)
                      .+..|||+....++...+..++
T Consensus        65 ~~~~Dvt~~~~v~~~v~~~~~~   86 (255)
T PRK06841         65 GLVCDVSDSQSVEAAVAAAISA   86 (255)
T ss_pred             EEEEECCCHHHHHHHHHHHHHH
T ss_conf             9998469999999999999998


No 202
>PRK11564 stationary phase inducible protein CsiE; Provisional
Probab=33.79  E-value=24  Score=13.20  Aligned_cols=20  Identities=5%  Similarity=0.026  Sum_probs=13.5

Q ss_pred             ECHHHHHHHHHHHHHHHHHH
Q ss_conf             16999999999999999984
Q gi|254780903|r  620 ADLIPIINEGIRLIGSSAQS  639 (766)
Q Consensus       620 ~dl~~~i~~~~~~~~~~~~~  639 (766)
                      -|=.++++.....+.|..-.
T Consensus       254 ~~d~~L~~~L~~HL~PAl~R  273 (426)
T PRK11564        254 SDEQGLCDQLYAHLAQALNR  273 (426)
T ss_pred             CCHHHHHHHHHHHHHHHHHH
T ss_conf             88699999999999999999


No 203
>TIGR01605 PYST-D Plasmodium yoelii subtelomeric family PYST-D; InterPro: IPR006492    The proteins in this set represent a paralogous family of Plasmodium yoelii genes preferentially located in the subtelomeric regions of the chromosomes. These genes are generally very short (ca. 50 residues). There are no obvious homologs to these genes in any other organism. .
Probab=33.75  E-value=22  Score=13.48  Aligned_cols=11  Identities=55%  Similarity=0.800  Sum_probs=7.2

Q ss_pred             CHHHHHHHHHH
Q ss_conf             61689999999
Q gi|254780903|r  731 GLGLAISDALT  741 (766)
Q Consensus       731 GLGLaI~k~iV  741 (766)
                      ||||||.=.|+
T Consensus        13 GLGlSi~LhLI   23 (55)
T TIGR01605        13 GLGLSITLHLI   23 (55)
T ss_pred             CCHHHHHHHHH
T ss_conf             00488999999


No 204
>PRK01356 hscB co-chaperone HscB; Provisional
Probab=33.67  E-value=22  Score=13.40  Aligned_cols=27  Identities=19%  Similarity=0.381  Sum_probs=13.4

Q ss_pred             HHHHHCCCCHH------HCCCCHHHHHHHHCCC
Q ss_conf             89977299943------3058988999760812
Q gi|254780903|r  283 SMYEIMGIPYE------NKTLSFRAIARLIHYD  309 (766)
Q Consensus       283 ~~~~llG~~~~------e~~~s~~~~~~~vHPd  309 (766)
                      .++++||+++.      .....|..+...+|||
T Consensus         3 NyFelf~l~~~f~iD~~~L~~~y~~LQ~~~HPD   35 (166)
T PRK01356          3 NYFQLLGLPQTYNIDLKILEKQYFAMQVKYHPD   35 (166)
T ss_pred             CHHHHCCCCCCCCCCHHHHHHHHHHHHHHHCCC
T ss_conf             789883999646779999999999999987978


No 205
>COG5388 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=33.21  E-value=24  Score=13.14  Aligned_cols=82  Identities=12%  Similarity=0.095  Sum_probs=59.6

Q ss_pred             HHHHHHCCCCHHHCCCCHHHHHHHHCCCCHHHHHHHHHHHHCCCCEEEEEEEEECCCCCEEEEEEEEEEEEECCCE-EEE
Q ss_conf             8899772999433058988999760812058999999997248984899999886989889988999999837960-699
Q gi|254780903|r  282 RSMYEIMGIPYENKTLSFRAIARLIHYDNKKICEIARSVTGKHVKQLDQIFHMRHASGADIWIQVRAQMMRTISGG-MNI  360 (766)
Q Consensus       282 ~~~~~llG~~~~e~~~s~~~~~~~vHPdDr~~~~~a~~~~~~~~~~~~~e~Ri~~~DG~~~Wi~~r~~~i~d~~G~-~~~  360 (766)
                      -..|.+||.+-.     .-.|.++..+-|+.........+.....+.-+.+-.+...|.-.-++.-..|+..++|+ +++
T Consensus        78 TriC~LfGRELr-----~~~F~sLW~~~~~~~~~r~~~~v~~~~tPvl~~~dg~s~~G~sl~fEmLl~PL~~~~g~~~R~  152 (209)
T COG5388          78 TRICDLFGRELR-----GRDFLSLWAEADRLELKRAADGVRKRRTPVLVTADGRSHGGRSLGFEMLLAPLQGASGETDRF  152 (209)
T ss_pred             CCHHHHHCHHHC-----CCCHHHHCCCCCHHHHHHHHHHHHHCCCCEEEECCHHHCCCCCCCEEEEEECCCCCCCCCCCH
T ss_conf             420333365542-----995567536103389999998876425746994120222586533056640134777876301


Q ss_pred             EEEEECCC
Q ss_conf             99984461
Q gi|254780903|r  361 IGIAMDLT  368 (766)
Q Consensus       361 iGi~~DIT  368 (766)
                      .|...-+.
T Consensus       153 LGais~~~  160 (209)
T COG5388         153 LGAISPIA  160 (209)
T ss_pred             HHHCCCCC
T ss_conf             21136665


No 206
>PRK12426 elongation factor P; Provisional
Probab=33.17  E-value=24  Score=13.13  Aligned_cols=52  Identities=13%  Similarity=0.201  Sum_probs=20.7

Q ss_pred             EEEECHHHHHHHHHH--HHHHHHHCCCCCCEEEEEEEE-------ECCEEEEEEEECCCCC
Q ss_conf             899868999999999--886565346898889999999-------7998999999788978
Q gi|254780903|r  653 FFNADKRIIKKILFP--ILSNSIKFTNNNGKMMIRTSK-------IGQCVIITIADTGIGI  704 (766)
Q Consensus       653 ~v~~D~~~l~QVl~N--Li~NAik~t~~~g~I~i~~~~-------~~~~v~i~V~D~G~GI  704 (766)
                      .+..|..-..|+-+.  +++++.+|.-+|-.|.|....       .+..|.+.|.++-+++
T Consensus        80 ~~FMd~etyEQ~~v~~~~lg~~~~~L~e~~~v~v~~~~~~~i~v~lP~~V~l~V~et~p~~  140 (185)
T PRK12426         80 YLFLDLGNYEKIYIPKEIMKDNFLFLKAGVTVSALVYDNTVFSVELPHFLELMVSKTDFPG  140 (185)
T ss_pred             EEEECCCCCCCEECCHHHCCHHHHHHCCCCEEEEEEECCEEEEEECCCEEEEEEEECCCCC
T ss_conf             8995799833178145560035653037866999991883899888997999999899996


No 207
>PRK08571 rpl14p 50S ribosomal protein L14P; Reviewed
Probab=33.15  E-value=24  Score=13.13  Aligned_cols=33  Identities=21%  Similarity=0.244  Sum_probs=26.1

Q ss_pred             EEEECCCCCEEEEEEEEEEEEECCCEE---EEEEEE
Q ss_conf             998869898899889999998379606---999998
Q gi|254780903|r  332 FHMRHASGADIWIQVRAQMMRTISGGM---NIIGIA  364 (766)
Q Consensus       332 ~Ri~~~DG~~~Wi~~r~~~i~d~~G~~---~~iGi~  364 (766)
                      ..++++||.++-+...+.++-+.+|+|   ++.|.+
T Consensus        78 k~~rR~dGs~i~FddNA~VLin~~~~P~GTRI~GPV  113 (132)
T PRK08571         78 KEYRRPDGTRVKFEDNAAVIVTPEGTPKGTEIKGPV  113 (132)
T ss_pred             CCEECCCCCEEEECCCEEEEECCCCCEEEEEEECCH
T ss_conf             631848999998189679999899999152794531


No 208
>PRK06935 2-deoxy-D-gluconate 3-dehydrogenase; Provisional
Probab=33.07  E-value=25  Score=13.12  Aligned_cols=22  Identities=36%  Similarity=0.289  Sum_probs=11.3

Q ss_pred             EEEEEECCCHHHHHHHHHHHHH
Q ss_conf             9999844617999999999999
Q gi|254780903|r  360 IIGIAMDLTEKYHLEKRYAEAD  381 (766)
Q Consensus       360 ~iGi~~DITErK~ae~~l~ese  381 (766)
                      ...+..|+|+....++...+..
T Consensus        65 ~~~~~~Dvs~~~~v~~~v~~~~   86 (258)
T PRK06935         65 VTFVQLDLTKKESAEAVVAEAL   86 (258)
T ss_pred             EEEEEECCCCHHHHHHHHHHHH
T ss_conf             7999904899999999999999


No 209
>pfam03281 Mab-21 Mab-21 protein.
Probab=32.23  E-value=25  Score=13.03  Aligned_cols=14  Identities=21%  Similarity=0.074  Sum_probs=4.8

Q ss_pred             CHHHHHHHHHHHHH
Q ss_conf             69999999999999
Q gi|254780903|r  621 DLIPIINEGIRLIG  634 (766)
Q Consensus       621 dl~~~i~~~~~~~~  634 (766)
                      +|..+...+..+.+
T Consensus       335 ~ld~~Ak~~wrl~r  348 (360)
T pfam03281       335 ALENAAKQVWRLTR  348 (360)
T ss_pred             HHHHHHHHHHHHHH
T ss_conf             78999999999999


No 210
>TIGR01120 rpiB ribose 5-phosphate isomerase B; InterPro: IPR004785   Ribose 5-phosphate isomerase (5.3.1.6 from EC) forms a homodimer and catalyses the interconversion of D-ribose 5-phosphate and D-ribulose 5-phosphate in the non-oxidative branch of the pentose phosphate pathway. This reaction permits the synthesis of ribose from other sugars, as well as the recycling of sugars from nucleotide breakdown. Two unrelated enzymes can catalyse this reaction: RpiA (found in most organisms) and RpiB (found in some bacteria and eukaryotes). RpiB is also involved in metabolism of the rare sugar, allose, in addition to ribose sugars. The structures of RpiA and RpiB are distinct, RpiB having a Rossmann-type alpha/beta/alpha sandwich topology . This entry represents the RpiB enzyme.; GO: 0004751 ribose-5-phosphate isomerase activity, 0006098 pentose-phosphate shunt.
Probab=31.20  E-value=15  Score=14.69  Aligned_cols=40  Identities=13%  Similarity=0.081  Sum_probs=23.5

Q ss_pred             HHHHHHCCCEEEEEECCCCE--EEECHHHHHHHHHHHHHHHHHC
Q ss_conf             99998479589998089978--9986899999999988656534
Q gi|254780903|r  634 GSSAQSKNIKIEKKIPSELF--FNADKRIIKKILFPILSNSIKF  675 (766)
Q Consensus       634 ~~~~~~k~i~l~~~~~~~l~--v~~D~~~l~QVl~NLi~NAik~  675 (766)
                      ..-+.+++.++.-.  ...|  =.=+|..=+||..-..+|+.++
T Consensus        18 k~fL~~~g~kvid~--GT~~~ertdYP~YAk~V~~av~~g~~~~   59 (143)
T TIGR01120        18 KEFLEDKGFKVIDV--GTLASERTDYPDYAKEVVRAVLEGKAER   59 (143)
T ss_pred             HHHHCCCCEEEEEE--CCCCCCCCCCCHHHHHHHHHHHCCCCCC
T ss_conf             99861398579875--3788676366068999999974487667


No 211
>KOG3938 consensus
Probab=30.93  E-value=27  Score=12.88  Aligned_cols=34  Identities=15%  Similarity=0.189  Sum_probs=14.8

Q ss_pred             HHHHHHHHHHHCCCCCEEEEECCCCEEEECHHHHHHCC
Q ss_conf             99999999972259745989768978999788997729
Q gi|254780903|r  252 EANICVETALSRGRCGLWNFNFDNKKFHLSRSMYEIMG  289 (766)
Q Consensus       252 ese~rl~~al~~a~~GiWd~D~~~~~i~ws~~~~~llG  289 (766)
                      |-.+.+..+++.++.-+.-..+.+-.    .-|.+|||
T Consensus        77 ELY~kIAe~F~Is~~dIlfcTlNshK----vDM~~llg  110 (334)
T KOG3938          77 ELYQKIAEAFDISPDDILFCTLNSHK----VDMKRLLG  110 (334)
T ss_pred             HHHHHHHHHHCCCCCCEEEEECCCCC----CCHHHHHC
T ss_conf             99999999856882016999657876----36888736


No 212
>pfam07328 VirD1 T-DNA border endonuclease VirD1. This family consists of several T-DNA border endonuclease VirD1 proteins which appear to be found exclusively in Agrobacterium species. Agrobacterium, a plant pathogen, is capable to stably transform the plant cell with a segment of its own DNA called T-DNA (transferred DNA). This process depends, among others, on the specialized bacterial virulence proteins VirD1 and VirD2 that excise the T-DNA from its adjacent sequences. VirD1 is thought to interact with VirD2 in this process.
Probab=30.31  E-value=27  Score=12.81  Aligned_cols=41  Identities=27%  Similarity=0.238  Sum_probs=21.6

Q ss_pred             HHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             222478999999998603468899389999999999999999999777677
Q gi|254780903|r  554 LRTPLNAILGFSEVIKKEIFGELGSVKYYEYAQDIHYSGQHLLNMINNILE  604 (766)
Q Consensus       554 lrtPL~aI~g~~ell~~~~~~~~~~e~~~~~l~~I~~~~~~l~~lI~diLd  604 (766)
                      +|--..-|-||.|+=          .+.++.++.|..+.-.+..-|++++.
T Consensus        55 iRiAvRRIgGFlEiD----------A~Tr~~me~i~~sIg~ls~ni~~l~~   95 (147)
T pfam07328        55 IRVAVRRIGGFLEID----------AETREKMEAILQSIGILSSNIAALLS   95 (147)
T ss_pred             HHHHHHHHHHHHHCC----------HHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             999999970055412----------99999999999999999899999999


No 213
>TIGR01108 oadA oxaloacetate decarboxylase alpha subunit; InterPro: IPR005776    This family describes the bacterial oxaloacetate decarboxylase alpha subunit and its equivalents in archaea . The oxaloacetate decarboxylase Na+ pump is the paradigm of the family of Na+ transport decarboxylases that present in bacteria and archaea. It a multi subunit enzyme consisting of a peripheral alpha-subunit and integral membrane subunits beta and gamma. The energy released by the decarboxylation reaction of oxaloacetate is coupled to Na+ ion pumping across the membrane.; GO: 0008948 oxaloacetate decarboxylase activity, 0006814 sodium ion transport.
Probab=29.67  E-value=28  Score=12.73  Aligned_cols=167  Identities=14%  Similarity=0.146  Sum_probs=91.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHCC----CCCEEEEECCCCEEEECHHHHHHCCCCHHHCCC---------------CHHHHH
Q ss_conf             9999999999999999997225----974598976897899978899772999433058---------------988999
Q gi|254780903|r  243 NKENDTILLEANICVETALSRG----RCGLWNFNFDNKKFHLSRSMYEIMGIPYENKTL---------------SFRAIA  303 (766)
Q Consensus       243 ~r~ae~~l~ese~rl~~al~~a----~~GiWd~D~~~~~i~ws~~~~~llG~~~~e~~~---------------s~~~~~  303 (766)
                      .|-|.+.|-..+-|.+.-|-..    ++|+|....=+|-+|  |+|.++|+-+|.+-+-               ..+-..
T Consensus         6 LRDaHQSL~ATRmRteDMLPi~~~LD~vGfwSLEvWGGATF--DaC~RFL~EDPW~RLR~lk~~~pnT~L~MLLRGQNLl   83 (616)
T TIGR01108         6 LRDAHQSLIATRMRTEDMLPILEKLDDVGFWSLEVWGGATF--DACIRFLNEDPWERLRELKKALPNTKLQMLLRGQNLL   83 (616)
T ss_pred             ECCHHHHHHHHHCCHHHHHHHHHHHHHCCCEEEEECCCHHH--HHHHHHCCCCHHHHHHHHHHHCCCCCHHHHHCCCCCC
T ss_conf             52067766753057313689998750249556520244105--5784424888558999999735787512342045423


Q ss_pred             HHH-CCCCHHHHHHHHHHHHCCCCEEEEEEEEECCCCCEEEEEEEEEEEEECCCEEEEEEE-EECCCHHHHHHHHHHHHH
Q ss_conf             760-812058999999997248984899999886989889988999999837960699999-844617999999999999
Q gi|254780903|r  304 RLI-HYDNKKICEIARSVTGKHVKQLDQIFHMRHASGADIWIQVRAQMMRTISGGMNIIGI-AMDLTEKYHLEKRYAEAD  381 (766)
Q Consensus       304 ~~v-HPdDr~~~~~a~~~~~~~~~~~~~e~Ri~~~DG~~~Wi~~r~~~i~d~~G~~~~iGi-~~DITErK~ae~~l~ese  381 (766)
                      .+= .|||  .|+...+.+..+|-   ..||+.-+=...|-+......++-.+. -|.-|+ +==||=-+-+|.=|.-+ 
T Consensus        84 GYRHYADD--VVe~FV~~a~~NG~---DVFRiFDALND~RNl~~ai~a~Kk~g~-dHvQg~iSYTtSPvHTl~~yl~la-  156 (616)
T TIGR01108        84 GYRHYADD--VVEAFVKKAVENGL---DVFRIFDALNDPRNLQKAIEAAKKHGA-DHVQGAISYTTSPVHTLEKYLELA-  156 (616)
T ss_pred             CCCCCCHH--HHHHHHHHHHHCCC---EEEEEECCCCCHHHHHHHHHHHHHHCC-CEEEEEEECCCCCHHHHHHHHHHH-
T ss_conf             44158436--89999999997598---089951245887789999999997389-789999712468436788899999-


Q ss_pred             HHHHHHHHHHHHHEEEECCCCEEEE-----ECHHHHHHHC-CCHHH
Q ss_conf             9999999854455158834996997-----0178988839-99789
Q gi|254780903|r  382 QRLSKAIECTSEALVLWDKNDRLVM-----CNANYQKAYG-LPDHV  421 (766)
Q Consensus       382 ~rlr~~ie~~~~~i~~~D~~g~i~~-----~N~~~~~~~g-~~~~~  421 (766)
                         +.+++---|.|++.|..|-+.=     .-++.-+-+| +|.+-
T Consensus       157 ---~~L~~~G~DSI~IKDMaGlLTP~~AYELV~alK~~~~n~pvhL  199 (616)
T TIGR01108       157 ---KELLEMGVDSICIKDMAGLLTPKVAYELVSALKKEFGNLPVHL  199 (616)
T ss_pred             ---HHHHHHCCCEEEEECCCCCCCHHHHHHHHHHHHHHCCCEEEEE
T ss_conf             ---9999818860552020046441589999999974239746886


No 214
>pfam08446 PAS_2 PAS fold. The PAS fold corresponds to the structural domain that has previously been defined as PAS and PAC motifs. The PAS fold appears in archaea, eubacteria and eukarya.
Probab=29.37  E-value=28  Score=12.70  Aligned_cols=24  Identities=21%  Similarity=0.303  Sum_probs=10.6

Q ss_pred             CCCEEEEECHHHHHHHCCCHHHHC
Q ss_conf             499699701789888399978942
Q gi|254780903|r  400 KNDRLVMCNANYQKAYGLPDHVLV  423 (766)
Q Consensus       400 ~~g~i~~~N~~~~~~~g~~~~~~~  423 (766)
                      .+++++.++....+++|.+.+++.
T Consensus        24 ~~~~I~qaS~N~~~~lG~~~~~ll   47 (107)
T pfam08446        24 PDFRVLQASENAAEMLGLVAQQLL   47 (107)
T ss_pred             CCCEEEEECCCHHHHHCCCHHHHC
T ss_conf             998799985588888585958985


No 215
>PRK01773 hscB co-chaperone HscB; Provisional
Probab=29.29  E-value=25  Score=13.09  Aligned_cols=27  Identities=15%  Similarity=0.401  Sum_probs=13.6

Q ss_pred             HHHHHCCCCHH------HCCCCHHHHHHHHCCC
Q ss_conf             89977299943------3058988999760812
Q gi|254780903|r  283 SMYEIMGIPYE------NKTLSFRAIARLIHYD  309 (766)
Q Consensus       283 ~~~~llG~~~~------e~~~s~~~~~~~vHPd  309 (766)
                      .++++||+++.      .....|..+...+|||
T Consensus         3 NyFelf~L~~~f~ID~~~L~~~y~~LQ~~~HPD   35 (173)
T PRK01773          3 NPFALFDLPVDFQLDQALLSERYLALQKSLHPD   35 (173)
T ss_pred             CHHHHCCCCCCCCCCHHHHHHHHHHHHHHHCCC
T ss_conf             837762999777679999999999999986968


No 216
>KOG4426 consensus
Probab=28.35  E-value=29  Score=12.58  Aligned_cols=69  Identities=16%  Similarity=0.270  Sum_probs=29.2

Q ss_pred             HHHHHHHHHHCCCCCCC-CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCC--------EEEECHHHHHHHHH
Q ss_conf             99999999860346889-9389999999999999999999777677888741983012--------03316999999999
Q gi|254780903|r  560 AILGFSEVIKKEIFGEL-GSVKYYEYAQDIHYSGQHLLNMINNILEMSKIETEKISID--------KQNADLIPIINEGI  630 (766)
Q Consensus       560 aI~g~~ell~~~~~~~~-~~e~~~~~l~~I~~~~~~l~~lI~diLd~srieag~~~~~--------~~~~dl~~~i~~~~  630 (766)
                      -|-+|-.+|.++..... .--.+...+..+..++..-..|++-+-.-     |++.++        +.-+.+.+.+..++
T Consensus       512 Y~FSFDkML~DrGnTAvYLLYa~tRIcSI~rksg~d~~~l~~~lkkT-----~ki~LDH~~E~kLg~~lLkf~e~v~~~~  586 (656)
T KOG4426         512 YIFSFDKMLEDRGNTAVYLLYAYTRICSIARKSGKDNVDLIKELKKT-----GKIALDHEKEWKLGKHLLKFAEIVEKAL  586 (656)
T ss_pred             EEEEHHHHHHCCCCCEEHHHHHHHHHHHHHHHCCCCHHHHHHHHHHC-----CCCCCCCHHHHHHHHHHHHHHHHHHHHH
T ss_conf             16568888654686100358999999999987177425689999856-----8623677778899999985899999999


Q ss_pred             HHH
Q ss_conf             999
Q gi|254780903|r  631 RLI  633 (766)
Q Consensus       631 ~~~  633 (766)
                      +.+
T Consensus       587 ~~L  589 (656)
T KOG4426         587 DSL  589 (656)
T ss_pred             HHH
T ss_conf             988


No 217
>pfam01899 MNHE Na+/H+ ion antiporter subunit. Subunit of a Na+/H+ Prokaryotic antiporter complex.
Probab=28.12  E-value=29  Score=12.55  Aligned_cols=51  Identities=27%  Similarity=0.316  Sum_probs=34.5

Q ss_pred             HHHHHHHHHHHCCCCCCEEEEEEEEECCEEEEEEEECCCCCCHHHHHHHCCCEE
Q ss_conf             999988656534689888999999979989999997889789778543046505
Q gi|254780903|r  664 ILFPILSNSIKFTNNNGKMMIRTSKIGQCVIITIADTGIGIPKSALEKIGQPFE  717 (766)
Q Consensus       664 Vl~NLi~NAik~t~~~g~I~i~~~~~~~~v~i~V~D~G~GI~~e~~~~iF~pF~  717 (766)
                      .-.-++.|++--||  |++++....+.+.+.+.+-|-- .-+++..+.|-++|+
T Consensus        48 ~~~~llansITLTP--GTltvdv~~d~~~L~VH~ld~~-~~~~~~~~~i~~~~E   98 (106)
T pfam01899        48 TGLTILANSITLTP--GTLTIDLDPEERKLYVHWIDVE-TNSPRSSEDIVGPFE   98 (106)
T ss_pred             HHHHHHHHHHHCCC--CEEEEEEECCCCEEEEEEEECC-CCCHHHHHHHHHHHH
T ss_conf             89999998771699--7799998189998999996679-951789988518889


No 218
>TIGR02386 rpoC_TIGR DNA-directed RNA polymerase, beta' subunit; InterPro: IPR012754   DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme . The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length . The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel.   RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise:  RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors.  RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs.  Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kD, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits.   This entry represents the beta-prime subunit, RpoC, found in most bacteria. It excludes some, mainly cyanobacterial, species where RpoC is replaced by two homologous proteins that include an additional domain. One arm of the "claw" is predominantly formed by this subunit, the other being predominantly formed by the beta subunit. The active site of the enzyme is defined by three invariant aspartate residues within the beta-prime subunit .; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006350 transcription.
Probab=28.11  E-value=29  Score=12.57  Aligned_cols=11  Identities=0%  Similarity=0.138  Sum_probs=6.2

Q ss_pred             EEECHHHHHHH
Q ss_conf             99868999999
Q gi|254780903|r  654 FNADKRIIKKI  664 (766)
Q Consensus       654 v~~D~~~l~QV  664 (766)
                      ..|...+++|.
T Consensus       854 ARGN~sq~rQL  864 (1552)
T TIGR02386       854 ARGNISQFRQL  864 (1552)
T ss_pred             CCCCHHHHHHH
T ss_conf             64357888887


No 219
>KOG0242 consensus
Probab=28.08  E-value=30  Score=12.55  Aligned_cols=13  Identities=0%  Similarity=0.084  Sum_probs=8.8

Q ss_pred             ECHHHHHHCCCCH
Q ss_conf             9788997729994
Q gi|254780903|r  280 LSRSMYEIMGIPY  292 (766)
Q Consensus       280 ws~~~~~llG~~~  292 (766)
                      +|+..+++|..+.
T Consensus       143 YNE~I~DLL~~~~  155 (675)
T KOG0242         143 YNERIRDLLNPDG  155 (675)
T ss_pred             ECCCCCCCCCCCC
T ss_conf             5120103458999


No 220
>TIGR02451 anti_sig_ChrR anti-sigma factor, putative, ChrR family; InterPro: IPR012807    The member of this family from Rhodobacter sphaeroides has been shown both to form a complex with sigma(E) and to negatively regulate tetrapyrrole biosynthesis. This protein likely contains (at least) two distinct functional domains as several smaller homologues (excluded in this entry) show homology only to the C-terminal region including a motif: PxHxHxGxE..
Probab=28.00  E-value=25  Score=13.09  Aligned_cols=25  Identities=24%  Similarity=0.575  Sum_probs=9.8

Q ss_pred             EEEEEEEECCCCCCHHHHHHHCCCEE
Q ss_conf             89999997889789778543046505
Q gi|254780903|r  692 CVIITIADTGIGIPKSALEKIGQPFE  717 (766)
Q Consensus       692 ~v~i~V~D~G~GI~~e~~~~iF~pF~  717 (766)
                      -+|++|-|.=+=+ ..-..|||+||+
T Consensus       208 ClClavLd~Pl~f-~~~~~rLl~Pf~  232 (234)
T TIGR02451       208 CLCLAVLDAPLRF-TSGVARLLQPFF  232 (234)
T ss_pred             CEEEEECCCCHHH-CCCHHHHHHHHC
T ss_conf             1477511540111-254124442201


No 221
>KOG2036 consensus
Probab=27.75  E-value=30  Score=12.51  Aligned_cols=82  Identities=11%  Similarity=0.062  Sum_probs=43.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHCC-----CCCCCEEEECHHHHHHHHHHHHHHHHHHCCCEEEEEECCCCEEEECH
Q ss_conf             9999999999999997776778887419-----83012033169999999999999999847958999808997899868
Q gi|254780903|r  584 YAQDIHYSGQHLLNMINNILEMSKIETE-----KISIDKQNADLIPIINEGIRLIGSSAQSKNIKIEKKIPSELFFNADK  658 (766)
Q Consensus       584 ~l~~I~~~~~~l~~lI~diLd~srieag-----~~~~~~~~~dl~~~i~~~~~~~~~~~~~k~i~l~~~~~~~l~v~~D~  658 (766)
                      .+....+..+++....+++..-+ ||.+     ....++.++.+.+-+++....+..+..++.-.|...--....+.+|.
T Consensus       882 ~~all~k~~kk~~~~~~~v~~~~-ie~~l~~~~~~~~e~~~~sl~~dl~e~ake~~~~~r~~~~~L~~~~L~~y~i~gd~  960 (1011)
T KOG2036         882 LLALLTKAMKKLSKYFDEVEEKA-IEETLPREKDRVNEPTPVSLEDDLEEAAKEAEEQMREKQKELKAEELDKYAIIGDE  960 (1011)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHH-HHHHCHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCH
T ss_conf             99999999999999999999999-98643234653078675647789999999999999999999875556666642987


Q ss_pred             HHHHHHHH
Q ss_conf             99999999
Q gi|254780903|r  659 RIIKKILF  666 (766)
Q Consensus       659 ~~l~QVl~  666 (766)
                      ........
T Consensus       961 e~~a~~~~  968 (1011)
T KOG2036         961 EEWAEALE  968 (1011)
T ss_pred             HHHHHHHH
T ss_conf             99999986


No 222
>PRK06114 short chain dehydrogenase; Provisional
Probab=27.37  E-value=30  Score=12.46  Aligned_cols=19  Identities=37%  Similarity=0.368  Sum_probs=8.7

Q ss_pred             EEEECCCHHHHHHHHHHHH
Q ss_conf             9984461799999999999
Q gi|254780903|r  362 GIAMDLTEKYHLEKRYAEA  380 (766)
Q Consensus       362 Gi~~DITErK~ae~~l~es  380 (766)
                      .+..|+|+....++...+.
T Consensus        70 ~~~~Dvt~~~~v~~~v~~~   88 (262)
T PRK06114         70 QIAADVTSKSDLAAAVART   88 (262)
T ss_pred             EEECCCCCHHHHHHHHHHH
T ss_conf             9981689999999999999


No 223
>TIGR00021 rpiA ribose 5-phosphate isomerase A; InterPro: IPR004788 Ribose 5-phosphate isomerase (5.3.1.6 from EC), also known as phosphoriboisomerase, catalyses the conversion of D-ribose 5-phosphate to D-ribulose 5-phosphate in the non-oxidative branch of the pentose phosphate pathway.; GO: 0004751 ribose-5-phosphate isomerase activity, 0009052 pentose-phosphate shunt non-oxidative branch.
Probab=27.36  E-value=30  Score=12.46  Aligned_cols=55  Identities=15%  Similarity=-0.005  Sum_probs=27.0

Q ss_pred             CEEEECHHHHHHHHH--HHHHHHHHCCCCC-CEEEEEEE-EECCEEEEEEEECCCCCCHHHHHH
Q ss_conf             789986899999999--9886565346898-88999999-979989999997889789778543
Q gi|254780903|r  652 LFFNADKRIIKKILF--PILSNSIKFTNNN-GKMMIRTS-KIGQCVIITIADTGIGIPKSALEK  711 (766)
Q Consensus       652 l~v~~D~~~l~QVl~--NLi~NAik~t~~~-g~I~i~~~-~~~~~v~i~V~D~G~GI~~e~~~~  711 (766)
                      |||..-|-.-++++.  .|-. | -+ -.| +..++|.. ..++  ...|+|||-=|=.-...+
T Consensus       137 LPvEV~Pf~~~~~~~~l~~~~-A-~l-l~Gl~~~~LR~~~v~~~--~~~~TDNGN~IlD~~~~~  195 (236)
T TIGR00021       137 LPVEVVPFAWKATARRLKLEK-A-VL-LLGLGEPTLRKGKVNKG--GPVVTDNGNYILDCHFGK  195 (236)
T ss_pred             CCEEEECCCCHHHHHHHHHHH-H-HH-HCCCCEEEEEECCCCCC--CEEEEECCCEEEEEECCC
T ss_conf             047880368078999899888-7-65-23771278953322798--017960797899977698


No 224
>MTH00204 ND4 NADH dehydrogenase subunit 4; Provisional
Probab=27.13  E-value=31  Score=12.43  Aligned_cols=17  Identities=18%  Similarity=0.343  Sum_probs=14.9

Q ss_pred             HHHHHHHHHHHHCCCCC
Q ss_conf             99999886565346898
Q gi|254780903|r  663 KILFPILSNSIKFTNNN  679 (766)
Q Consensus       663 QVl~NLi~NAik~t~~~  679 (766)
                      +.++|++.||++|+|.|
T Consensus       469 ~~il~~i~~sv~~~~~~  485 (486)
T MTH00204        469 FPIIDLVKNSLVFSPGG  485 (486)
T ss_pred             HHHHHHHHHHEECCCCC
T ss_conf             98998887742418899


No 225
>PRK00294 hscB co-chaperone HscB; Provisional
Probab=26.92  E-value=28  Score=12.69  Aligned_cols=29  Identities=17%  Similarity=0.348  Sum_probs=14.4

Q ss_pred             CHHHHHHCCCCHHH------CCCCHHHHHHHHCCC
Q ss_conf             78899772999433------058988999760812
Q gi|254780903|r  281 SRSMYEIMGIPYEN------KTLSFRAIARLIHYD  309 (766)
Q Consensus       281 s~~~~~llG~~~~e------~~~s~~~~~~~vHPd  309 (766)
                      ++..+++||+++.=      ....|..+...+|||
T Consensus         3 ~~~hF~lf~l~~~f~iD~~~L~~~y~~LQ~~~HPD   37 (173)
T PRK00294          3 TPCHFALFDLQPSFRLDLDQLATRYRELAREVHPD   37 (173)
T ss_pred             CCCHHHHCCCCCCCCCCHHHHHHHHHHHHHHHCCC
T ss_conf             97664644999767679999999999999986957


No 226
>KOG3491 consensus
Probab=26.89  E-value=31  Score=12.40  Aligned_cols=23  Identities=13%  Similarity=0.342  Sum_probs=17.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             65899999999999999999996
Q gi|254780903|r   51 TIPMISMVFLVFIATSSIIKVTT   73 (766)
Q Consensus        51 ~ip~~i~~fli~~~~~~~~~i~~   73 (766)
                      +=|+|+-.|..++|+.++++|.-
T Consensus        37 vgPwLlglFvFVVcGSa~FqIIr   59 (65)
T KOG3491          37 VGPWLLGLFVFVVCGSALFQIIR   59 (65)
T ss_pred             CCHHHHHHHHHHHHCHHHHHHHH
T ss_conf             52289888999861599999999


No 227
>TIGR02885 spore_sigF RNA polymerase sigma-F factor; InterPro: IPR014236   The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme . RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes.   With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognized by the major sigma factors , .    Members of this entry represent RNA polymerase sigma factor F. Within the Firmicutes, Sigma-F is specifically, and universally, a component of the endospore formation program, and is expressed in the forespore to turn on the expression of dozens of genes. It is closely related to sigma-G, which is also expressed in the forespore.; GO: 0003677 DNA binding, 0003700 transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, 0006355 regulation of transcription DNA-dependent.
Probab=26.85  E-value=31  Score=12.40  Aligned_cols=59  Identities=15%  Similarity=0.156  Sum_probs=27.9

Q ss_pred             HHHHHHHHHHHHHHHHHHCCCCCEEEEECCCCEEEECHHHHHHCCCCHHHCCC------CHHHHHHHHCCCCHHHHHHH
Q ss_conf             99999999999999997225974598976897899978899772999433058------98899976081205899999
Q gi|254780903|r  245 ENDTILLEANICVETALSRGRCGLWNFNFDNKKFHLSRSMYEIMGIPYENKTL------SFRAIARLIHYDNKKICEIA  317 (766)
Q Consensus       245 ~ae~~l~ese~rl~~al~~a~~GiWd~D~~~~~i~ws~~~~~llG~~~~e~~~------s~~~~~~~vHPdDr~~~~~a  317 (766)
                      +.-..++..++.|-.-+++.|.-              +...+.+|++||+...      +.....+.||.||.+.+...
T Consensus        94 ~la~k~~~~kE~L~~~l~R~PTi--------------~Elae~lg~~~EEiv~A~Es~~~~~sly~tvh~dDGdPi~Ll  158 (231)
T TIGR02885        94 ELARKIRYEKEELTKKLGREPTI--------------NELAEALGVSPEEIVMALESARSLQSLYDTVHEDDGDPILLL  158 (231)
T ss_pred             HHHHHHHHHHHHHHHHHCCCCCH--------------HHHHHHHCCCHHHHHHHHHCCCCCCHHCCEEECCCCCHHHHH
T ss_conf             99999987799999983899888--------------999887587887866442025761011001141794644676


No 228
>TIGR02110 PQQ_syn_pqqF coenzyme PQQ biosynthesis protein PqqF; InterPro: IPR011844   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 family of metallopeptidases belong to MEROPS peptidase family M16, subfamily M16A (clan ME). In the subset of species that make coenzyme PQQ (pyrrolo-quinoline-quinone), this peptidase is found in the PQQ biosynthesis region and is thought to act as a protease on PqqA (IPR011725 from INTERPRO), a probable peptide precursor of the coenzyme. PQQ is required for some glucose dehydrogenases and alcohol dehydrogenases .; GO: 0008234 cysteine-type peptidase activity, 0008270 zinc ion binding, 0018189 pyrroloquinoline quinone biosynthetic process.
Probab=26.10  E-value=15  Score=14.76  Aligned_cols=30  Identities=10%  Similarity=0.101  Sum_probs=20.6

Q ss_pred             HHHHHHHHHHHHHHHHHHCCCCCEEEEECC
Q ss_conf             548999999999885310178978999969
Q gi|254780903|r  107 ASQKKAESMLGQLLAKTRFLSESFILLAQP  136 (766)
Q Consensus       107 ~~~~~ae~~L~~~~~~~~~~~~~~i~i~d~  136 (766)
                      ......|.+|+++...+....-+..++..+
T Consensus       170 ~~~~AfQ~AL~~FH~~~Y~A~~M~LwLqGP  199 (737)
T TIGR02110       170 LPNDAFQQALRDFHRRHYQAGNMQLWLQGP  199 (737)
T ss_pred             CCHHHHHHHHHHHHHHHHHHHCCEEECCCC
T ss_conf             984899999999999840443040304879


No 229
>TIGR02748 GerC3_HepT heptaprenyl diphosphate synthase component II; InterPro: IPR014119    The proteins in this entry are component II of the heterodimeric heptaprenyl diphosphate synthase. They are found proximate to the gene for component I (IPR009920 from INTERPRO). This enzyme acts in menaquinone-7 isoprenoid side chain biosynthesis..
Probab=25.94  E-value=32  Score=12.28  Aligned_cols=99  Identities=12%  Similarity=0.059  Sum_probs=42.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEEEEECCCCEE----EECHHHHHHCCCCHHHCC--CCHHH
Q ss_conf             999999988889999999999999999999999722597459897689789----997889977299943305--89889
Q gi|254780903|r  228 LLLFILFSYYRQAKKNKENDTILLEANICVETALSRGRCGLWNFNFDNKKF----HLSRSMYEIMGIPYENKT--LSFRA  301 (766)
Q Consensus       228 ~~~~~~~a~~~dit~~r~ae~~l~ese~rl~~al~~a~~GiWd~D~~~~~i----~ws~~~~~llG~~~~e~~--~s~~~  301 (766)
                      |+++.-++-..|..+-|..--+|+    .+.+|-=.--+-|=+-|+.+|+-    .|+++..-..|    +..  .+.+.
T Consensus        52 VLLag~fGP~Ydl~~~K~vAV~LE----LIHMASLVHDDVID~A~LRRG~~Ti~skW~NRiAMYTG----DYlfA~slE~  123 (325)
T TIGR02748        52 VLLAGKFGPDYDLDKIKHVAVALE----LIHMASLVHDDVIDDADLRRGKPTIKSKWDNRIAMYTG----DYLFAKSLET  123 (325)
T ss_pred             HHHHHHCCCCCCHHHHHHHHHHHH----HHHCCCCCCCCCCCCCCCCCCCHHHCCCCCCEEEEHHH----HHHHHHHHHH
T ss_conf             986763077533554656765576----77353202565205876778842012102773220033----5899999999


Q ss_pred             HHHHHCCCCHH-HHHHHHHHHHCCCCEEEEEEEE
Q ss_conf             99760812058-9999999972489848999998
Q gi|254780903|r  302 IARLIHYDNKK-ICEIARSVTGKHVKQLDQIFHM  334 (766)
Q Consensus       302 ~~~~vHPdDr~-~~~~a~~~~~~~~~~~~~e~Ri  334 (766)
                      ...+-.|.=-. ......+.+.|+.++....|++
T Consensus       124 ~t~i~dp~~H~~LS~tivEvc~GEIEQIkDkYN~  157 (325)
T TIGR02748       124 MTEIKDPRAHQILSKTIVEVCLGEIEQIKDKYNF  157 (325)
T ss_pred             HHCCCCHHHHHHHHHHHHHHHHCCCHHHHCCCCC
T ss_conf             8516982788999999998862210100101378


No 230
>PRK00458 S-adenosylmethionine decarboxylase proenzyme; Provisional
Probab=25.48  E-value=33  Score=12.23  Aligned_cols=73  Identities=15%  Similarity=0.126  Sum_probs=47.3

Q ss_pred             EEEEEC-CCCEEEECHHHHHHHHHHHHHHH---------HHCCCCCC----------EEEEEEEEECCEEEEEEEECCCC
Q ss_conf             999808-99789986899999999988656---------53468988----------89999999799899999978897
Q gi|254780903|r  644 IEKKIP-SELFFNADKRIIKKILFPILSNS---------IKFTNNNG----------KMMIRTSKIGQCVIITIADTGIG  703 (766)
Q Consensus       644 l~~~~~-~~l~v~~D~~~l~QVl~NLi~NA---------ik~t~~~g----------~I~i~~~~~~~~v~i~V~D~G~G  703 (766)
                      +..++- .+..+..|...+++++...+..+         -||.|.+|          +|+|.++.+.+++.+-|==-|.-
T Consensus        19 li~dlygc~~~~L~d~~~i~~~l~~a~~~~~atil~~~~h~F~P~gGvtgv~llaESHiSIHTWPE~gyaaiDiFTCG~~   98 (127)
T PRK00458         19 VYGNLYGCDEELLKDEERLETIVKEAAKIANMTLLDVKSWKFGPKGGVSVIALVLESHIAIHTWPEYNFATVDVYTCGEH   98 (127)
T ss_pred             EEEEEECCCHHHCCCHHHHHHHHHHHHHHCCCEEEEEEEEECCCCCCEEEEEEEECCEEEEEECCCCCEEEEEEEECCCC
T ss_conf             99999888958978999999999999998699899788486489883799999750368998667687699999863898


Q ss_pred             CCH-HHHHHHCCCE
Q ss_conf             897-7854304650
Q gi|254780903|r  704 IPK-SALEKIGQPF  716 (766)
Q Consensus       704 I~~-e~~~~iF~pF  716 (766)
                      ..| ...+.|=+.|
T Consensus        99 ~~P~~a~~~i~~~l  112 (127)
T PRK00458         99 TDPMAAFEYIVSQL  112 (127)
T ss_pred             CCHHHHHHHHHHHH
T ss_conf             89999999999872


No 231
>PRK04542 elongation factor P; Provisional
Probab=25.09  E-value=33  Score=12.18  Aligned_cols=25  Identities=12%  Similarity=0.238  Sum_probs=10.9

Q ss_pred             EEECCCCEEEEECHHHHHHHCCCHH
Q ss_conf             5883499699701789888399978
Q gi|254780903|r  396 VLWDKNDRLVMCNANYQKAYGLPDH  420 (766)
Q Consensus       396 ~~~D~~g~i~~~N~~~~~~~g~~~~  420 (766)
                      +++.....+.++|+.-.+-+.++.+
T Consensus        74 yLY~dg~~~~FMd~etyEQi~l~~~   98 (189)
T PRK04542         74 FSYVDGDEYVFMDNEDYTPYTFTKD   98 (189)
T ss_pred             EEEECCCEEEEEECCCHHHEEECHH
T ss_conf             9995899179996998332652789


No 232
>pfam08066 PMC2NT PMC2NT (NUC016) domain. This domain is found at the N-terminus of 3'-5' exonucleases with HRDC domains, and also in putative exosome components.
Probab=25.05  E-value=33  Score=12.17  Aligned_cols=53  Identities=21%  Similarity=0.295  Sum_probs=30.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCEEEECHHHHHHHHHHHHHH
Q ss_conf             999999999999999997776778887419830120331699999999999999
Q gi|254780903|r  582 YEYAQDIHYSGQHLLNMINNILEMSKIETEKISIDKQNADLIPIINEGIRLIGS  635 (766)
Q Consensus       582 ~~~l~~I~~~~~~l~~lI~diLd~srieag~~~~~~~~~dl~~~i~~~~~~~~~  635 (766)
                      .++-+.+...++||+.++|++|...-... +.....+..++.+-.+.+.+.+-.
T Consensus        24 p~~~~~ld~~s~rLl~l~n~ll~~~~~~~-~~~~~~~~~~~e~~w~~vvdv~D~   76 (91)
T pfam08066        24 PEFSQSLDEQSQRLLSLINDLLQSAGSKS-DIPDRSDEDDVEDQWEGVVDVNDS   76 (91)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHCCCCC-CCCCCCCCCCHHHHHHHHHHHHHH
T ss_conf             88999999999999999999998447667-887875423188999999999999


No 233
>PRK04025 S-adenosylmethionine decarboxylase proenzyme; Validated
Probab=24.96  E-value=33  Score=12.16  Aligned_cols=74  Identities=12%  Similarity=0.122  Sum_probs=47.7

Q ss_pred             EEEEEEC-CCCEEEECHHHHHHHHHHHHHHH---------HHCCCCC---------CEEEEEEEEECCEEEEEEEECCCC
Q ss_conf             8999808-99789986899999999988656---------5346898---------889999999799899999978897
Q gi|254780903|r  643 KIEKKIP-SELFFNADKRIIKKILFPILSNS---------IKFTNNN---------GKMMIRTSKIGQCVIITIADTGIG  703 (766)
Q Consensus       643 ~l~~~~~-~~l~v~~D~~~l~QVl~NLi~NA---------ik~t~~~---------g~I~i~~~~~~~~v~i~V~D~G~G  703 (766)
                      .+..++- .+..+..|...|++++.+.+..+         -||.|.|         ++|+|.+.++.+++.+-|==-|-=
T Consensus         7 Hii~Dl~gc~~~~L~d~~~i~~~~~~Aa~~~gatil~~~~h~F~P~GvTgv~lLaESHiSIHTWPE~g~aavDiFTCGd~   86 (139)
T PRK04025          7 HYIVEAAGCDPEVLGDADKIREIFLEAAKVGNMEVKASYFFKFSPMGVSGVVIVAESHISVHTWPEKGYAALDVYTCGET   86 (139)
T ss_pred             EEEEEEECCCHHHCCCHHHHHHHHHHHHHHCCCEEEEEEEEECCCCCEEEEEEEEEEEEEEEECCCCCEEEEEEECCCCC
T ss_conf             99999967796887899999999999999869989977869859997899999751168999656478699999868998


Q ss_pred             CCHHH-HHHHCCCE
Q ss_conf             89778-54304650
Q gi|254780903|r  704 IPKSA-LEKIGQPF  716 (766)
Q Consensus       704 I~~e~-~~~iF~pF  716 (766)
                      +.|+. .+.|=+.|
T Consensus        87 ~~P~~A~~~l~~~l  100 (139)
T PRK04025         87 ADPEKAVDYILEQF  100 (139)
T ss_pred             CCHHHHHHHHHHHH
T ss_conf             99999999999984


No 234
>PRK06124 gluconate 5-dehydrogenase; Provisional
Probab=24.91  E-value=33  Score=12.15  Aligned_cols=23  Identities=9%  Similarity=-0.060  Sum_probs=11.1

Q ss_pred             EEECHHHHHHHHHHHHHHHHHCC
Q ss_conf             99868999999999886565346
Q gi|254780903|r  654 FNADKRIIKKILFPILSNSIKFT  676 (766)
Q Consensus       654 v~~D~~~l~QVl~NLi~NAik~t  676 (766)
                      =.+.|..+-.++.-|++++-.|.
T Consensus       222 R~g~pedia~~v~fL~Sd~ssyi  244 (259)
T PRK06124        222 RWGRPEEIAGAAVFLASPAASYV  244 (259)
T ss_pred             CCCCHHHHHHHHHHHHCCHHCCC
T ss_conf             98599999999999958443586


No 235
>PRK05014 hscB co-chaperone HscB; Provisional
Probab=24.73  E-value=34  Score=12.13  Aligned_cols=26  Identities=23%  Similarity=0.611  Sum_probs=14.4

Q ss_pred             HHHHCCCCHH------HCCCCHHHHHHHHCCC
Q ss_conf             9977299943------3058988999760812
Q gi|254780903|r  284 MYEIMGIPYE------NKTLSFRAIARLIHYD  309 (766)
Q Consensus       284 ~~~llG~~~~------e~~~s~~~~~~~vHPd  309 (766)
                      ++++||+++.      .....|..+...+|||
T Consensus         3 yF~lf~l~~~f~iD~~~L~~~y~~Lq~~~HPD   34 (171)
T PRK05014          3 YFTLFGLPARYDIDTQLLSLRYQELQRQVHPD   34 (171)
T ss_pred             HHHHCCCCCCCCCCHHHHHHHHHHHHHHHCHH
T ss_conf             77666999878879999999999999986977


No 236
>KOG3822 consensus
Probab=24.54  E-value=34  Score=12.11  Aligned_cols=11  Identities=18%  Similarity=0.184  Sum_probs=6.3

Q ss_pred             EEECCCCEEEE
Q ss_conf             58834996997
Q gi|254780903|r  396 VLWDKNDRLVM  406 (766)
Q Consensus       396 ~~~D~~g~i~~  406 (766)
                      |-.|.-|.+++
T Consensus       210 wkAD~~GNvvF  220 (516)
T KOG3822         210 WKADRAGNVVF  220 (516)
T ss_pred             HHCCCCCCEEE
T ss_conf             30475566666


No 237
>pfam03671 Ufm1 Ubiquitin fold modifier 1 protein. This is a family of short ubiquitin-like proteins, that is like neither type-1 or type-2. It is a ubiquitin-fold modifier 1 (Ufm1) that is synthesized in a precursor form of 85 amino-acid residues. In humans the enzyme for Ufm1 is Uba5 and the conjugating enzyme is Ufc1. Prior to activation by Uba5 the extra two amino acids at the C-terminal region of the human pro-Ufm1 protein are removed to expose Gly whose residue is necessary for conjugation to target molecule(s). The mature Ufm1 is conjugated to yet unidentified endogenous proteins,. While Ubiquitin and many Ubls possess the conserved C-terminal di-glycine that is adenylated by each specific E1 or E1-like enzyme, respectively, in an ATP-dependent manner, Ufm1(1-83) possesses a single glycine at its C-terminus, which is followed by a Ser-Cys dipeptide in the precursor form of Ufm1. The C-terminally processed Ufm1(1-83) is specifically activated by Uba5, an E1-like enzyme, and then t
Probab=24.40  E-value=34  Score=12.09  Aligned_cols=19  Identities=26%  Similarity=0.384  Sum_probs=13.1

Q ss_pred             EEEEECCCCCCHHHH-HHHC
Q ss_conf             999978897897785-4304
Q gi|254780903|r  695 ITIADTGIGIPKSAL-EKIG  713 (766)
Q Consensus       695 i~V~D~G~GI~~e~~-~~iF  713 (766)
                      -.|.++|+||.|.+- ..+|
T Consensus        47 AiiTndGvGINP~qtAGnvf   66 (76)
T pfam03671        47 AIITNDGIGINPAQSAGNVF   66 (76)
T ss_pred             EEEECCCCCCCHHHCCCCCH
T ss_conf             68945861208454343111


No 238
>PRK02991 D-serine dehydratase; Provisional
Probab=23.98  E-value=14  Score=14.84  Aligned_cols=21  Identities=19%  Similarity=0.154  Sum_probs=10.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHH
Q ss_conf             235548999999999885310
Q gi|254780903|r  104 FDLASQKKAESMLGQLLAKTR  124 (766)
Q Consensus       104 ~d~~~~~~ae~~L~~~~~~~~  124 (766)
                      ....+...|+++|.++-|-..
T Consensus        43 l~~~dv~dA~~Rl~RFAPyla   63 (443)
T PRK02991         43 LTEADVQDAEARLQRFAPYLA   63 (443)
T ss_pred             CCHHHHHHHHHHHHHHHHHHH
T ss_conf             998899999999998789999


No 239
>TIGR00459 aspS_bact aspartyl-tRNA synthetase; InterPro: IPR004524   The aminoacyl-tRNA synthetases (6.1.1. from EC) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state, and have limited sequence homology . The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric . Class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet fold flanked by alpha-helices , and are mostly dimeric or multimeric, containing at least three conserved regions , , . However, tRNA binding involves an alpha-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan and valine belong to class I synthetases; these synthetases are further divided into three subclasses, a, b and c, according to sequence homology. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine belong to class-II synthetases .   Aspartyl tRNA synthetase 6.1.1.12 from EC is an alpha2 dimer that belongs to class IIb. Structural analysis combined with mutagenesis and enzymology data on the yeast enzyme point to a tRNA binding process that starts by a recognition event between the tRNA anticodon loop and the synthetase anticodon binding module .     This family represents aspartyl-tRNA synthetases from the bacteria and from mitochondria. In some species, this enzyme aminoacylates tRNA for both Asp and Asn; Asp-tRNA(asn) is subsequently transamidated to Asn-tRNA(asn). ; GO: 0000166 nucleotide binding, 0004815 aspartate-tRNA ligase activity, 0005524 ATP binding, 0006412 translation, 0006422 aspartyl-tRNA aminoacylation, 0005737 cytoplasm.
Probab=23.95  E-value=33  Score=12.23  Aligned_cols=91  Identities=19%  Similarity=0.233  Sum_probs=50.5

Q ss_pred             CCEEEECHHHHHHHHHHHHHHHHHCCC-----CCCEEEEEEEEECCEEEEEEEECCCCCCHHHH----HHHCCCEEECCC
Q ss_conf             978998689999999998865653468-----98889999999799899999978897897785----430465053146
Q gi|254780903|r  651 ELFFNADKRIIKKILFPILSNSIKFTN-----NNGKMMIRTSKIGQCVIITIADTGIGIPKSAL----EKIGQPFEPLHN  721 (766)
Q Consensus       651 ~l~v~~D~~~l~QVl~NLi~NAik~t~-----~~g~I~i~~~~~~~~v~i~V~D~G~GI~~e~~----~~iF~pF~q~~~  721 (766)
                      +.|..-|...|+..=.+-++||-+--=     .||.|.|--...-+    .|=.+=+||+|+..    ..|-|.|.    
T Consensus       514 T~Pk~~~~~~lE~~p~~a~a~aYDlVlNG~ElGGGSiRIh~~~~Q~----~~F~d~Lgid~eea~EkFGFLLeA~~----  585 (653)
T TIGR00459       514 TMPKPEDLEDLETAPEEALAEAYDLVLNGVELGGGSIRIHDPEVQE----KVFEDILGIDPEEAREKFGFLLEAFK----  585 (653)
T ss_pred             CCCCCCCHHHHHCCHHHHHHHCCCEEEEEEEECCCEEEECCHHHHH----HHHHHHHCCCHHHHHHHHHHHHHHHH----
T ss_conf             9875122787740745541202876883069887104642878999----99987628898998776356875873----


Q ss_pred             CCCCCCCCCCHHHHHHHHHHHHCCCEEEEEE
Q ss_conf             7556778876168999999996298699997
Q gi|254780903|r  722 QYDQSIGGFGLGLAISDALTNLHGGRLKIIS  752 (766)
Q Consensus       722 ~~t~~~~GtGLGLaI~k~iVe~hgG~I~v~S  752 (766)
                      --|-.|+|-||||   =+|+=++.++=.|+.
T Consensus       586 yGaPPHgG~A~Gl---DRL~Mll~~~~nIRD  613 (653)
T TIGR00459       586 YGAPPHGGLALGL---DRLVMLLTGTDNIRD  613 (653)
T ss_pred             CCCCCCHHHHHHH---HHHHHHHCCCCCCCE
T ss_conf             5768510155558---999999808997220


No 240
>COG1666 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=23.91  E-value=35  Score=12.03  Aligned_cols=66  Identities=14%  Similarity=0.143  Sum_probs=45.5

Q ss_pred             EECHHHH---HHHHHHHHHHHHHHCCCEEEEEECC--CCEEEE-CHHHHHHHHHHHHHHHHHCCCCCCEEEE
Q ss_conf             3169999---9999999999998479589998089--978998-6899999999988656534689888999
Q gi|254780903|r  619 NADLIPI---INEGIRLIGSSAQSKNIKIEKKIPS--ELFFNA-DKRIIKKILFPILSNSIKFTNNNGKMMI  684 (766)
Q Consensus       619 ~~dl~~~---i~~~~~~~~~~~~~k~i~l~~~~~~--~l~v~~-D~~~l~QVl~NLi~NAik~t~~~g~I~i  684 (766)
                      .+|+.++   ++++...+..++.=|++.-.++..+  .+.+.+ +.-+|.|++-=|.++.+|-.-++..+.+
T Consensus        12 evd~qEv~NAve~A~kel~sR~Dfkg~~~~iel~e~e~i~l~s~sdf~l~ql~DIl~~kliKRgi~~k~~d~   83 (165)
T COG1666          12 EVDLQEVRNAVENANKELASRFDFKGVKASIELKENETIKLTSESDFQLEQLKDILRSKLIKRGISGKALDI   83 (165)
T ss_pred             HCCHHHHHHHHHHHHHHHHHHHCCCCCCCEEECCCCCEEEEECCCHHHHHHHHHHHHHHHHHCCCCHHHCCC
T ss_conf             413999999999999987655055788421750787159985063666999999999999873997554145


No 241
>COG1134 TagH ABC-type polysaccharide/polyol phosphate transport system, ATPase component [Carbohydrate transport and metabolism / Cell envelope biogenesis, outer membrane]
Probab=23.75  E-value=35  Score=12.00  Aligned_cols=16  Identities=25%  Similarity=0.615  Sum_probs=6.2

Q ss_pred             HHHHHHHHHHHHHHHH
Q ss_conf             7522247899999999
Q gi|254780903|r  552 HELRTPLNAILGFSEV  567 (766)
Q Consensus       552 HelrtPL~aI~g~~el  567 (766)
                      -|+..-..-|+-|+||
T Consensus       122 ~ei~~~~~eIieFaEL  137 (249)
T COG1134         122 KEIDEKVDEIIEFAEL  137 (249)
T ss_pred             HHHHHHHHHHHHHHHH
T ss_conf             9999888999999877


No 242
>PRK07985 oxidoreductase; Provisional
Probab=23.59  E-value=35  Score=11.98  Aligned_cols=13  Identities=15%  Similarity=0.115  Sum_probs=5.6

Q ss_pred             ECCCHHHHHHHHH
Q ss_conf             4461799999999
Q gi|254780903|r  365 MDLTEKYHLEKRY  377 (766)
Q Consensus       365 ~DITErK~ae~~l  377 (766)
                      -|||+....+...
T Consensus       107 ~Dvs~~~~v~~lv  119 (294)
T PRK07985        107 GDLSDEKFARSLV  119 (294)
T ss_pred             CCCCCHHHHHHHH
T ss_conf             6789999999999


No 243
>PRK09804 putative cryptic C4-dicarboxylate transporter DcuD; Provisional
Probab=23.54  E-value=14  Score=14.95  Aligned_cols=21  Identities=10%  Similarity=0.300  Sum_probs=14.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHH
Q ss_conf             999999876752224789999
Q gi|254780903|r  543 KSEFLAKMSHELRTPLNAILG  563 (766)
Q Consensus       543 k~efla~isHelrtPL~aI~g  563 (766)
                      ...|..+|.+-+-+-..-|.+
T Consensus       302 ~~~Ff~GMG~~f~~VV~LIIA  322 (455)
T PRK09804        302 VQAFFDGMGTQFANVVTLVVA  322 (455)
T ss_pred             HHHHHHHHHHHHHHHHHHHHH
T ss_conf             999999888999889999986


No 244
>pfam04701 Pox_D2 Pox virus D2 protein.
Probab=23.52  E-value=35  Score=11.97  Aligned_cols=50  Identities=18%  Similarity=0.198  Sum_probs=28.5

Q ss_pred             HHHHHHHHHHHHCCCEEEEEECCCCE---EEECHHHHHHHHHHHHHHHHHCCCC
Q ss_conf             99999999998479589998089978---9986899999999988656534689
Q gi|254780903|r  628 EGIRLIGSSAQSKNIKIEKKIPSELF---FNADKRIIKKILFPILSNSIKFTNN  678 (766)
Q Consensus       628 ~~~~~~~~~~~~k~i~l~~~~~~~l~---v~~D~~~l~QVl~NLi~NAik~t~~  678 (766)
                      .+.+.+.+..+.+.+.|........+   ..-|+...+-||++|- ||.||...
T Consensus        81 ~i~es~epl~P~~Tv~l~~~~~~~~~~~~~p~~~~~~k~iLLeLF-NsFr~gk~  133 (143)
T pfam04701        81 SVLESIEPLLPDYTVNLSRKNSETPDLQSAPDDPEGTKMILLELF-NSFRFGKG  133 (143)
T ss_pred             HHHHHHCCCCCCCEEEEEECCCCCCCCCCCCCCCHHHHHHHHHHH-HHHHCCCC
T ss_conf             789872445874113421047789865568788411899999998-77631788


No 245
>COG1586 SpeD S-adenosylmethionine decarboxylase [Amino acid transport and metabolism]
Probab=23.02  E-value=36  Score=11.91  Aligned_cols=62  Identities=16%  Similarity=0.119  Sum_probs=42.5

Q ss_pred             EEEECHHHHHHHHHHHH--HHH-------HHCCCCC---------CEEEEEEEEECCEEEEEEEECCCCCCHHHH-HHHC
Q ss_conf             89986899999999988--656-------5346898---------889999999799899999978897897785-4304
Q gi|254780903|r  653 FFNADKRIIKKILFPIL--SNS-------IKFTNNN---------GKMMIRTSKIGQCVIITIADTGIGIPKSAL-EKIG  713 (766)
Q Consensus       653 ~v~~D~~~l~QVl~NLi--~NA-------ik~t~~~---------g~I~i~~~~~~~~v~i~V~D~G~GI~~e~~-~~iF  713 (766)
                      ....|..+|++++.+-.  .||       -||.|.|         .+|+|.+.++-+++-|.|--.|.-++|..- +-|-
T Consensus        28 ~~l~d~e~l~~i~~eAa~~~gati~~~~~~~f~p~GvSgvvliaESHitiHTwPEyg~A~iDVyTCG~~~~p~~A~~yi~  107 (136)
T COG1586          28 DLLYDAERLEEILLEAAKIAGATILNIAFHKFSPQGVSGVVLIAESHITIHTWPEYGYATIDVYTCGDHIDPLKAFNYLV  107 (136)
T ss_pred             HHHCCHHHHHHHHHHHHHHHCCEEEEEEEEEECCCCEEEEEEEEEEEEEEECCCCCCCEEEEEECCCCCCCHHHHHHHHH
T ss_conf             89436999999999999970978998775884599748999998412368607766856788881589899999999999


Q ss_pred             C
Q ss_conf             6
Q gi|254780903|r  714 Q  714 (766)
Q Consensus       714 ~  714 (766)
                      +
T Consensus       108 ~  108 (136)
T COG1586         108 E  108 (136)
T ss_pred             H
T ss_conf             9


No 246
>cd06447 D-Ser-dehyd D-Serine dehydratase is a pyridoxal phosphate (PLP)-dependent enzyme which catalyzes the conversion of L- or D-serine  to pyruvate and ammonia.  D-serine dehydratase serves as a detoxifying enzyme in most E. coli strains where D-serine is a competitive antagonist of beta-alanine in the biosynthetic pathway to pentothenate and coenzyme A.  D-serine dehydratase is different from other pyridoxal-5'-phosphate-dependent enzymes in that it catalyzes alpha, beta-elimination reactions on amino acids.
Probab=22.67  E-value=16  Score=14.41  Aligned_cols=18  Identities=17%  Similarity=0.065  Sum_probs=9.2

Q ss_pred             HHHHHHHHHHHHHHHHHH
Q ss_conf             548999999999885310
Q gi|254780903|r  107 ASQKKAESMLGQLLAKTR  124 (766)
Q Consensus       107 ~~~~~ae~~L~~~~~~~~  124 (766)
                      .+...|+++|.++-|-..
T Consensus        21 ~di~dA~~Rl~RFAP~la   38 (404)
T cd06447          21 EDIFDAEARLKRFAPYIA   38 (404)
T ss_pred             HHHHHHHHHHHHHHHHHH
T ss_conf             899999999998789999


No 247
>TIGR00658 orni_carb_tr ornithine carbamoyltransferase; InterPro: IPR002292 The ornithine carbamoyltransferases are a family of enzymes that catalyse the production of citrulline from carbamoyl-phosphate and ornithine . This reaction is part of the arginine biosynthetic pathway, and in some organisms the reaction is also part of the arginine deaminase pathway . In most prokaryotes, and some lower eukaryotes, the enzyme is found in the cytoplasm, but in higher eukaryotes, such as mammals, the enzyme is found in the mitochondrial matrix and functions as part of the urea cycle. In most organisms analysed to date, the enzyme has been shown to consist of a trimer of identical or nonidentical subunits . Extensive similarity has been found within the ornithine carbamoyltransferase family, some of the conserved areas being important in catalysis .   The C-terminal region of these enzymes shows a degree of similarity to the aspartate carbamoyltransferases, which are also known to bind carbamoyl- phosphate . This region contains a highly conserved Cys residue (in a His-Cys-Lys-Pro motif) implicated in ornithine binding . ; GO: 0004585 ornithine carbamoyltransferase activity, 0006520 amino acid metabolic process, 0009348 ornithine carbamoyltransferase complex.
Probab=22.59  E-value=37  Score=11.85  Aligned_cols=20  Identities=10%  Similarity=0.215  Sum_probs=10.1

Q ss_pred             HHHHHHHHHHHHCCCCEEEE
Q ss_conf             58999999997248984899
Q gi|254780903|r  311 KKICEIARSVTGKHVKQLDQ  330 (766)
Q Consensus       311 r~~~~~a~~~~~~~~~~~~~  330 (766)
                      .+.+..+.+.+...+..++.
T Consensus       204 ~~~v~~A~~~a~e~Gg~~~l  223 (341)
T TIGR00658       204 AEIVKKAKKIAKENGGSVEL  223 (341)
T ss_pred             HHHHHHHHHHHHHCCCEEEE
T ss_conf             78999999999717985999


No 248
>PRK02625 DNA-directed RNA polymerase subunit gamma; Provisional
Probab=22.22  E-value=28  Score=12.70  Aligned_cols=51  Identities=16%  Similarity=0.210  Sum_probs=28.1

Q ss_pred             CCCCEEEEEEEEEEEEECCCEE--EEEE---EEECCCHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             9898899889999998379606--9999---9844617999999999999999999985
Q gi|254780903|r  337 ASGADIWIQVRAQMMRTISGGM--NIIG---IAMDLTEKYHLEKRYAEADQRLSKAIEC  390 (766)
Q Consensus       337 ~DG~~~Wi~~r~~~i~d~~G~~--~~iG---i~~DITErK~ae~~l~ese~rlr~~ie~  390 (766)
                      .+-..-|+-...-|+--++=+|  .+-|   +.-|+++-   =.+....+.+|..+.+.
T Consensus       238 S~~rPEWMIL~vLPVlPP~LRP~v~Ldggr~a~sDlN~l---YrriI~rNnrLk~~~~~  293 (627)
T PRK02625        238 TGARPEWMVLDVIPVIPPDLRPMVQLDGGRFATSDLNDL---YRRVINRNNRLARLQEI  293 (627)
T ss_pred             CCCCCHHEEEECCCCCCCCCCCCEEECCCCCCCCCHHHH---HHHHHHHHHHHHHHHHC
T ss_conf             698835078732355898777427866886566665899---99999999999998865


No 249
>PRK06701 short chain dehydrogenase; Provisional
Probab=22.14  E-value=38  Score=11.79  Aligned_cols=24  Identities=17%  Similarity=0.210  Sum_probs=12.6

Q ss_pred             EEEEECCCHHHHHHHHHHHHHHHH
Q ss_conf             999844617999999999999999
Q gi|254780903|r  361 IGIAMDLTEKYHLEKRYAEADQRL  384 (766)
Q Consensus       361 iGi~~DITErK~ae~~l~ese~rl  384 (766)
                      +.+.-|||+....++...+..+.|
T Consensus        98 ~~~~~Dv~d~~~v~~~v~~~~~~f  121 (289)
T PRK06701         98 LLIPGDVSDEQFCKDAVEETVREL  121 (289)
T ss_pred             EEEECCCCCHHHHHHHHHHHHHHH
T ss_conf             999847899999999999999985


No 250
>TIGR02986 restrict_Alw26I type II restriction endonuclease, Alw26I/Eco31I/Esp3I family; InterPro: IPR014328   Type II restriction endonucleases (3.1.21.4 from EC) are components of prokaryotic DNA restriction-modification mechanisms that protect the organism against invading foreign DNA. These site-specific deoxyribonucleases catalyse the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. Of the 3000 restriction endonucleases that have been characterised, most are homodimeric or tetrameric enzymes that cleave target DNA at sequence-specific sites close to the recognition site. For homodimeric enzymes, the recognition site is usually a palindromic sequence 4-8 bp in length. Most enzymes require magnesium ions as a cofactor for catalysis. Although they can vary in their mode of recognition, many restriction endonucleases share a similar structural core comprising four beta-strands and one alpha-helix, as well as a similar mechanism of cleavage, suggesting a common ancestral origin . However, there is still considerable diversity amongst restriction endonucleases , . The target site recognition process triggers large conformational changes of the enzyme and the target DNA, leading to the activation of the catalytic centres. Like other DNA binding proteins, restriction enzymes are capable of non-specific DNA binding as well, which is the prerequisite for efficient target site location by facilitated diffusion. Non-specific binding usually does not involve interactions with the bases but only with the DNA backbone .    There are four classes of restriction endonucleases: types I, II,III and IV. All types of enzymes recognise specific short DNA sequences and carry out the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. They differ in their recognition sequence, subunit composition, cleavage position, and cofactor requirements , , as summarised below:    Type I enzymes (3.1.21.3 from EC) cleave at sites remote from recognition site; require both ATP and S-adenosyl-L-methionine to function; multifunctional protein with both restriction and methylase (2.1.1.72 from EC) activities. Type II enzymes (3.1.21.4 from EC) cleave within or at short specific distances from recognition site; most require magnesium; single function (restriction) enzymes independent of methylase. Type III enzymes (3.1.21.5 from EC) cleave at sites a short distance from recognition site; require ATP (but doesn't hydrolyse it); S-adenosyl-L-methionine stimulates reaction but is not required; exists as part of a complex with a modification methylase methylase (2.1.1.72 from EC). Type IV enzymes target methylated DNA.    This entry represents type II restriction endonucleases of the Alw26I/Eco31I/Esp3I family , whose recognition sequences are 5'-GTCTC-3' (Alw26I), 5'-GGTCTC-3' (Eco31I) and 5'-CGTCTC-3' (Esp3I)..
Probab=21.99  E-value=38  Score=11.77  Aligned_cols=65  Identities=26%  Similarity=0.372  Sum_probs=33.6

Q ss_pred             CCCCEEEEECCCCEE-------------EECHHHHHHCCCC-HHHCCCCHHHHHHHHCCCCHHHHHHHHHHHHCCCCEEE
Q ss_conf             597459897689789-------------9978899772999-43305898899976081205899999999724898489
Q gi|254780903|r  264 GRCGLWNFNFDNKKF-------------HLSRSMYEIMGIP-YENKTLSFRAIARLIHYDNKKICEIARSVTGKHVKQLD  329 (766)
Q Consensus       264 a~~GiWd~D~~~~~i-------------~ws~~~~~llG~~-~~e~~~s~~~~~~~vHPdDr~~~~~a~~~~~~~~~~~~  329 (766)
                      ..+|-|.|-...+..             ||..-.-+ +|++ +.....-|...+.+|||=-.-.+       ..-|...+
T Consensus        25 ~~DG~I~W~~~s~~~~g~F~~~~~~R~~Ww~~KA~e-LGi~G~~~e~~~~s~~ar~IHPt~~kpC-------~~CG~~m~   96 (461)
T TIGR02986        25 GEDGRISWEASSKKTTGKFKEYYQARRKWWEQKADE-LGIPGKDSENGRYSKAARLIHPTGVKPC-------KKCGKEMS   96 (461)
T ss_pred             CCCCCEEEECCCCCCCCCHHHHHHHHHHHHHHHHHH-CCCCCCCCCHHHHHHHHHHHCCCCCCCH-------HHCCCEEE
T ss_conf             898516656268963131077668999999998987-2877688706899999888547885621-------02684466


Q ss_pred             EEEEEEC
Q ss_conf             9999886
Q gi|254780903|r  330 QIFHMRH  336 (766)
Q Consensus       330 ~e~Ri~~  336 (766)
                      +.|-+..
T Consensus        97 l~Y~Ypn  103 (461)
T TIGR02986        97 LGYSYPN  103 (461)
T ss_pred             EEEECCC
T ss_conf             7654113


No 251
>pfam07492 Trehalase_Ca-bi Neutral trehalase Ca2+ binding domain. Neutral trehalases mobilize trehalose accumulated by fungal cells as a protective and storage carbohydrate. This family represents a calcium-binding domain similar to EF hand. Residues 97 and 108 in neutral trehalase from Schizosaccharomyces pombe have been implicated in this interaction. It is thought that this domain may provide a general mechanism for regulating neutral trehalase activity in yeasts and filamentous fungi.
Probab=21.62  E-value=38  Score=11.72  Aligned_cols=15  Identities=40%  Similarity=0.306  Sum_probs=10.3

Q ss_pred             ECCEEEEEEEECCCC
Q ss_conf             799899999978897
Q gi|254780903|r  689 IGQCVIITIADTGIG  703 (766)
Q Consensus       689 ~~~~v~i~V~D~G~G  703 (766)
                      .++...|+|.|+|+-
T Consensus        10 TD~n~QITIeD~GPK   24 (30)
T pfam07492        10 TDGNKQITIEDTGPK   24 (30)
T ss_pred             CCCCEEEEEECCCCE
T ss_conf             688707888638983


No 252
>PRK12820 bifunctional aspartyl-tRNA synthetase/aspartyl/glutamyl-tRNA amidotransferase subunit C; Provisional
Probab=21.16  E-value=28  Score=12.67  Aligned_cols=15  Identities=33%  Similarity=0.386  Sum_probs=8.7

Q ss_pred             CEEEEECCCCCEEEE
Q ss_conf             789999699808997
Q gi|254780903|r  129 SFILLAQPNELVFAS  143 (766)
Q Consensus       129 ~~i~i~d~~g~i~~~  143 (766)
                      .++-+.|..|.+..+
T Consensus        37 ~FidLRD~~G~vQvv   51 (706)
T PRK12820         37 LFIHLRDRNGFIQAV   51 (706)
T ss_pred             EEEEEEECCCCEEEE
T ss_conf             999997289458999


No 253
>TIGR01433 CyoA ubiquinol oxidase, subunit II; InterPro: IPR006333   Members of this domain catalyze the oxidation of ubiquinol with the concomitant reduction of molecular oxygen to water. This acts as the terminal electron acceptor in the respiratory chain. Subunit II is responsible for binding and oxidation of the ubiquinone substrate. This sequence is closely related to QoxA, which oxidizes quinol in Gram-positive bacteria but which is in complex with subunits which utilise cytochrome a in the reduction of molecular oxygen. Slightly more distantly related is subunit II of cytochrome c oxidase which uses cytochrome c as the oxidant . ; GO: 0016682 oxidoreductase activity acting on diphenols and related substances as donors oxygen as acceptor, 0006118 electron transport, 0016020 membrane.
Probab=21.08  E-value=39  Score=11.64  Aligned_cols=22  Identities=18%  Similarity=0.627  Sum_probs=14.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             6554568788789999999988
Q gi|254780903|r  215 VTLEVVFFSIISALLLFILFSY  236 (766)
Q Consensus       215 ~~~~~~~~~~~~~~~~~~~~a~  236 (766)
                      ++..+-|+.-...+++.+.+|.
T Consensus        35 ~a~~~MLlvviPVI~~Tl~FAW   56 (228)
T TIGR01433        35 TAFGLMLLVVIPVILLTLFFAW   56 (228)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHH
T ss_conf             9999999999999999998778


No 254
>PRK06128 oxidoreductase; Provisional
Probab=21.02  E-value=39  Score=11.63  Aligned_cols=18  Identities=17%  Similarity=0.191  Sum_probs=8.6

Q ss_pred             EEECCCHHHHHHHHHHHH
Q ss_conf             984461799999999999
Q gi|254780903|r  363 IAMDLTEKYHLEKRYAEA  380 (766)
Q Consensus       363 i~~DITErK~ae~~l~es  380 (766)
                      +.-|||+....++...+.
T Consensus       111 v~~Dvsd~~~~~~~v~~~  128 (300)
T PRK06128        111 VPGDLKDEAFCRQLVERA  128 (300)
T ss_pred             EECCCCCHHHHHHHHHHH
T ss_conf             974789999999999999


No 255
>PRK11034 clpA ATP-dependent Clp protease ATP-binding subunit; Provisional
Probab=20.82  E-value=40  Score=11.60  Aligned_cols=82  Identities=13%  Similarity=0.157  Sum_probs=48.3

Q ss_pred             ECHHHHHHHHHHHHHHHHHHCCCEEEEEECC-------CC-EEEEC---HHHHHHHHHHHHHHHHHCC--CCCCEEEEEE
Q ss_conf             1699999999999999998479589998089-------97-89986---8999999999886565346--8988899999
Q gi|254780903|r  620 ADLIPIINEGIRLIGSSAQSKNIKIEKKIPS-------EL-FFNAD---KRIIKKILFPILSNSIKFT--NNNGKMMIRT  686 (766)
Q Consensus       620 ~dl~~~i~~~~~~~~~~~~~k~i~l~~~~~~-------~l-~v~~D---~~~l~QVl~NLi~NAik~t--~~~g~I~i~~  686 (766)
                      -++..+++-.+..+..++.+++|.|.++-..       +. |.+|-   ++.+++-+.+.|+..+=+.  .+|+.|.|..
T Consensus       656 ~~l~~Iv~~~l~~l~~rL~~~~i~l~~~~~a~~~l~~~gyd~~~GARpl~R~I~~~i~~~La~~il~g~~~~g~~v~v~~  735 (758)
T PRK11034        656 DVIHQVVDKFIVELQAQLDQKGVSLEVSQEARDWLAEKGYDRAMGARPMARVIQDNLKKPLANELLFGSLVDGGQVTVAL  735 (758)
T ss_pred             HHHHHHHHHHHHHHHHHHHHCCCEEEECHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCCEEEEEE
T ss_conf             99999999999999999997898599889999999984889453711288999999889999999729888989899999


Q ss_pred             EEECCEEEEEEEECC
Q ss_conf             997998999999788
Q gi|254780903|r  687 SKIGQCVIITIADTG  701 (766)
Q Consensus       687 ~~~~~~v~i~V~D~G  701 (766)
                      ....+.+.|.++-..
T Consensus       736 ~~~~~~l~f~~~~~~  750 (758)
T PRK11034        736 DKEKNELTYGFQSAQ  750 (758)
T ss_pred             ECCCCEEEEEEECCC
T ss_conf             789987999960577


No 256
>PRK05483 rplN 50S ribosomal protein L14; Validated
Probab=20.82  E-value=40  Score=11.60  Aligned_cols=32  Identities=22%  Similarity=0.261  Sum_probs=23.5

Q ss_pred             EEEECCCCCEEEEEEEEEEEEECCCEE---EEEEE
Q ss_conf             998869898899889999998379606---99999
Q gi|254780903|r  332 FHMRHASGADIWIQVRAQMMRTISGGM---NIIGI  363 (766)
Q Consensus       332 ~Ri~~~DG~~~Wi~~r~~~i~d~~G~~---~~iGi  363 (766)
                      +.++++||.+.-+...+.++-++.|.|   ++.|.
T Consensus        67 k~~~R~dG~~i~Fd~Na~Vli~~~~~P~GTrI~Gp  101 (122)
T PRK05483         67 KGVRRPDGSYIRFDDNAAVLLNNDGEPRGTRIFGP  101 (122)
T ss_pred             CCEECCCCCEEEECCCEEEEECCCCCEEEEEEECC
T ss_conf             53066998888837837999989998836379736


No 257
>cd06257 DnaJ DnaJ domain or J-domain.  DnaJ/Hsp40 (heat shock protein 40) proteins are highly conserved and play crucial roles in protein translation, folding, unfolding, translocation, and degradation. They act primarily by stimulating the ATPase activity of Hsp70s, an important chaperonine family. Hsp40 proteins are characterized by the presence of a J domain, which mediates the interaction with Hsp70. They may contain other domains as well, and the architectures provide a means of classification.
Probab=20.57  E-value=40  Score=11.57  Aligned_cols=26  Identities=31%  Similarity=0.614  Sum_probs=15.4

Q ss_pred             HHHHCCCCHHH----CCCCHHHHHHHHCCC
Q ss_conf             99772999433----058988999760812
Q gi|254780903|r  284 MYEIMGIPYEN----KTLSFRAIARLIHYD  309 (766)
Q Consensus       284 ~~~llG~~~~e----~~~s~~~~~~~vHPd  309 (766)
                      +|++||+++..    ....+.......|||
T Consensus         2 ~Y~vLgl~~~at~~~Ik~ayr~l~~~~HPD   31 (55)
T cd06257           2 YYDILGVPPDASDEEIKKAYRKLALKYHPD   31 (55)
T ss_pred             HHHHCCCCCCCCHHHHHHHHHHHHHHHCCC
T ss_conf             287779999939999999999999881998


Done!